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a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/dependency_links.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/dependency_links.txt new file mode 100644 index 0000000000000000000000000000000000000000..8b137891791fe96927ad78e64b0aad7bded08bdc --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/dependency_links.txt @@ -0,0 +1 @@ + diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/entry_points.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/entry_points.txt new file mode 100644 index 0000000000000000000000000000000000000000..0db0a6c8f1b8d9c0ad4a25db6892e29f8988fcf2 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/entry_points.txt @@ -0,0 +1,51 @@ +[distutils.commands] +alias = setuptools.command.alias:alias +bdist_egg = setuptools.command.bdist_egg:bdist_egg +bdist_rpm = setuptools.command.bdist_rpm:bdist_rpm +bdist_wheel = setuptools.command.bdist_wheel:bdist_wheel +build = setuptools.command.build:build +build_clib = setuptools.command.build_clib:build_clib +build_ext = setuptools.command.build_ext:build_ext +build_py = setuptools.command.build_py:build_py +develop = setuptools.command.develop:develop +dist_info = setuptools.command.dist_info:dist_info +easy_install = setuptools.command.easy_install:easy_install +editable_wheel = setuptools.command.editable_wheel:editable_wheel +egg_info = setuptools.command.egg_info:egg_info +install = setuptools.command.install:install +install_egg_info = setuptools.command.install_egg_info:install_egg_info +install_lib = setuptools.command.install_lib:install_lib +install_scripts = setuptools.command.install_scripts:install_scripts +rotate = setuptools.command.rotate:rotate +saveopts = setuptools.command.saveopts:saveopts +sdist = setuptools.command.sdist:sdist +setopt = setuptools.command.setopt:setopt + +[distutils.setup_keywords] +dependency_links = setuptools.dist:assert_string_list +eager_resources = setuptools.dist:assert_string_list +entry_points = setuptools.dist:check_entry_points +exclude_package_data = setuptools.dist:check_package_data +extras_require = setuptools.dist:check_extras +include_package_data = setuptools.dist:assert_bool +install_requires = setuptools.dist:check_requirements +namespace_packages = setuptools.dist:check_nsp +package_data = setuptools.dist:check_package_data +packages = setuptools.dist:check_packages +python_requires = setuptools.dist:check_specifier +setup_requires = setuptools.dist:check_requirements +use_2to3 = setuptools.dist:invalid_unless_false +zip_safe = setuptools.dist:assert_bool + +[egg_info.writers] +PKG-INFO = setuptools.command.egg_info:write_pkg_info +dependency_links.txt = setuptools.command.egg_info:overwrite_arg +eager_resources.txt = setuptools.command.egg_info:overwrite_arg +entry_points.txt = setuptools.command.egg_info:write_entries +namespace_packages.txt = setuptools.command.egg_info:overwrite_arg +requires.txt = setuptools.command.egg_info:write_requirements +top_level.txt = setuptools.command.egg_info:write_toplevel_names + +[setuptools.finalize_distribution_options] +keywords = setuptools.dist:Distribution._finalize_setup_keywords +parent_finalize = setuptools.dist:_Distribution.finalize_options diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/requires.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/requires.txt new file mode 100644 index 0000000000000000000000000000000000000000..fc4015ad09eda715d3bafd8dda0968f2d1c8f1ab --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/requires.txt @@ -0,0 +1,83 @@ + +[certs] + +[check] +pytest-checkdocs>=2.4 + +[check:sys_platform != "cygwin"] +pytest-ruff>=0.2.1 +ruff>=0.8.0 + +[core] +packaging>=24.2 +more_itertools>=8.8 +jaraco.text>=3.7 +wheel>=0.43.0 +platformdirs>=4.2.2 +jaraco.functools>=4 +more_itertools + +[core:python_version < "3.10"] +importlib_metadata>=6 + +[core:python_version < "3.11"] +tomli>=2.0.1 + +[cover] +pytest-cov + +[doc] +sphinx>=3.5 +jaraco.packaging>=9.3 +rst.linker>=1.9 +furo +sphinx-lint +jaraco.tidelift>=1.4 +pygments-github-lexers==0.0.5 +sphinx-favicon +sphinx-inline-tabs +sphinx-reredirects +sphinxcontrib-towncrier +sphinx-notfound-page<2,>=1 +pyproject-hooks!=1.1 +towncrier<24.7 + +[enabler] +pytest-enabler>=2.2 + +[ssl] + +[test] +pytest!=8.1.*,>=6 +virtualenv>=13.0.0 +wheel>=0.44.0 +pip>=19.1 +packaging>=24.2 +jaraco.envs>=2.2 +pytest-xdist>=3 +jaraco.path>=3.7.2 +build[virtualenv]>=1.0.3 +filelock>=3.4.0 +ini2toml[lite]>=0.14 +tomli-w>=1.0.0 +pytest-timeout +pytest-home>=0.5 +pytest-subprocess +pyproject-hooks!=1.1 +jaraco.test>=5.5 + +[test:python_version >= "3.9" and sys_platform != "cygwin"] +jaraco.develop>=7.21 + +[test:sys_platform != "cygwin"] +pytest-perf + +[type] +pytest-mypy +mypy==1.14.* + +[type:python_version < "3.10"] +importlib_metadata>=7.0.2 + +[type:sys_platform != "cygwin"] +jaraco.develop>=7.21 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/top_level.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/top_level.txt new file mode 100644 index 0000000000000000000000000000000000000000..b5ac1070294b478b7cc2ce677207ee08813bfa37 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools-80.10.2-py3.10.egg-info/top_level.txt @@ -0,0 +1,3 @@ +_distutils_hack +pkg_resources +setuptools diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/INSTALLER new file mode 100644 index 0000000000000000000000000000000000000000..f79e4cb9aaf0b2d9e8ba78861e2071317b2384b3 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/INSTALLER @@ -0,0 +1 @@ +conda \ No newline at end of file diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..1bb5a44356f00884a71ceeefd24ded6caaba2418 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/LICENSE @@ -0,0 +1,17 @@ +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to +deal in the Software without restriction, including without limitation the +rights to use, copy, modify, merge, publish, distribute, sublicense, and/or +sell copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS +IN THE SOFTWARE. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/METADATA new file mode 100644 index 0000000000000000000000000000000000000000..db0a2dcdbe5f55f5815b2eaa243c507d0bdad002 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/METADATA @@ -0,0 +1,46 @@ +Metadata-Version: 2.1 +Name: backports.tarfile +Version: 1.2.0 +Summary: Backport of CPython tarfile module +Author-email: "Jason R. Coombs" +Project-URL: Homepage, https://github.com/jaraco/backports.tarfile +Classifier: Development Status :: 5 - Production/Stable +Classifier: Intended Audience :: Developers +Classifier: License :: OSI Approved :: MIT License +Classifier: Programming Language :: Python :: 3 +Classifier: Programming Language :: Python :: 3 :: Only +Requires-Python: >=3.8 +Description-Content-Type: text/x-rst +License-File: LICENSE +Provides-Extra: docs +Requires-Dist: sphinx >=3.5 ; extra == 'docs' +Requires-Dist: jaraco.packaging >=9.3 ; extra == 'docs' +Requires-Dist: rst.linker >=1.9 ; extra == 'docs' +Requires-Dist: furo ; extra == 'docs' +Requires-Dist: sphinx-lint ; extra == 'docs' +Provides-Extra: testing +Requires-Dist: pytest !=8.1.*,>=6 ; extra == 'testing' +Requires-Dist: pytest-checkdocs >=2.4 ; extra == 'testing' +Requires-Dist: pytest-cov ; extra == 'testing' +Requires-Dist: pytest-enabler >=2.2 ; extra == 'testing' +Requires-Dist: jaraco.test ; extra == 'testing' +Requires-Dist: pytest !=8.0.* ; extra == 'testing' + +.. image:: https://img.shields.io/pypi/v/backports.tarfile.svg + :target: https://pypi.org/project/backports.tarfile + +.. image:: https://img.shields.io/pypi/pyversions/backports.tarfile.svg + +.. image:: https://github.com/jaraco/backports.tarfile/actions/workflows/main.yml/badge.svg + :target: https://github.com/jaraco/backports.tarfile/actions?query=workflow%3A%22tests%22 + :alt: tests + +.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json + :target: https://github.com/astral-sh/ruff + :alt: Ruff + +.. .. image:: https://readthedocs.org/projects/backportstarfile/badge/?version=latest +.. :target: https://backportstarfile.readthedocs.io/en/latest/?badge=latest + +.. image:: https://img.shields.io/badge/skeleton-2024-informational + :target: https://blog.jaraco.com/skeleton diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/RECORD new file mode 100644 index 0000000000000000000000000000000000000000..c7d2c25bc103c6b3b1f60b23337276d81f24b5c4 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/RECORD @@ -0,0 +1,12 @@ +backports.tarfile-1.2.0.dist-info/INSTALLER,sha256=5hhM4Q4mYTT9z6QB6PGpUAW81PGNFrYrdXMj4oM_6ak,2 +backports.tarfile-1.2.0.dist-info/LICENSE,sha256=htoPAa6uRjSKPD1GUZXcHOzN55956HdppkuNoEsqR0E,1023 +backports.tarfile-1.2.0.dist-info/METADATA,sha256=ghXFTq132dxaEIolxr3HK1mZqm9iyUmaRANZQSr6WlE,2020 +backports.tarfile-1.2.0.dist-info/RECORD,, +backports.tarfile-1.2.0.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 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a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/WHEEL new file mode 100644 index 0000000000000000000000000000000000000000..bab98d675883cc7567a79df485cd7b4f015e376f --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/WHEEL @@ -0,0 +1,5 @@ +Wheel-Version: 1.0 +Generator: bdist_wheel (0.43.0) +Root-Is-Purelib: true +Tag: py3-none-any + diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/top_level.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/top_level.txt new file mode 100644 index 0000000000000000000000000000000000000000..99d2be5b64d7dc414f8ab9c002de06456b4bada2 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports.tarfile-1.2.0.dist-info/top_level.txt @@ -0,0 +1 @@ +backports diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports/tarfile/compat/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports/tarfile/compat/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports/tarfile/compat/py38.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports/tarfile/compat/py38.py new file mode 100644 index 0000000000000000000000000000000000000000..20fbbfc1c095baf9f8c72902b24296b50ad3ab9d --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/backports/tarfile/compat/py38.py @@ -0,0 +1,24 @@ +import sys + + +if sys.version_info < (3, 9): + + def removesuffix(self, suffix): + # suffix='' should not call self[:-0]. + if suffix and self.endswith(suffix): + return self[: -len(suffix)] + else: + return self[:] + + def removeprefix(self, prefix): + if self.startswith(prefix): + return self[len(prefix) :] + else: + return self[:] +else: + + def removesuffix(self, suffix): + return self.removesuffix(suffix) + + def removeprefix(self, prefix): + return self.removeprefix(prefix) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/INSTALLER new file mode 100644 index 0000000000000000000000000000000000000000..f79e4cb9aaf0b2d9e8ba78861e2071317b2384b3 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/INSTALLER @@ -0,0 +1 @@ +conda \ No newline at end of file diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/METADATA new file mode 100644 index 0000000000000000000000000000000000000000..9d894b433dc0e27e53d3be160edb861358db99fd --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/METADATA @@ -0,0 +1,133 @@ +Metadata-Version: 2.4 +Name: importlib_metadata +Version: 8.7.1 +Summary: Read metadata from Python packages +Author-email: "Jason R. Coombs" +License-Expression: Apache-2.0 +Project-URL: Source, https://github.com/python/importlib_metadata +Classifier: Development Status :: 5 - Production/Stable +Classifier: Intended Audience :: Developers +Classifier: Programming Language :: Python :: 3 +Classifier: Programming Language :: Python :: 3 :: Only +Requires-Python: >=3.9 +Description-Content-Type: text/x-rst +License-File: LICENSE +Requires-Dist: zipp>=3.20 +Provides-Extra: test +Requires-Dist: pytest!=8.1.*,>=6; extra == "test" +Requires-Dist: packaging; extra == "test" +Requires-Dist: pyfakefs; extra == "test" +Requires-Dist: flufl.flake8; extra == "test" +Requires-Dist: pytest-perf>=0.9.2; extra == "test" +Requires-Dist: jaraco.test>=5.4; extra == "test" +Provides-Extra: doc +Requires-Dist: sphinx>=3.5; extra == "doc" +Requires-Dist: jaraco.packaging>=9.3; extra == "doc" +Requires-Dist: rst.linker>=1.9; extra == "doc" +Requires-Dist: furo; extra == "doc" +Requires-Dist: sphinx-lint; extra == "doc" +Requires-Dist: jaraco.tidelift>=1.4; extra == "doc" +Provides-Extra: perf +Requires-Dist: ipython; extra == "perf" +Provides-Extra: check +Requires-Dist: pytest-checkdocs>=2.4; extra == "check" +Requires-Dist: pytest-ruff>=0.2.1; sys_platform != "cygwin" and extra == "check" +Provides-Extra: cover +Requires-Dist: pytest-cov; extra == "cover" +Provides-Extra: enabler +Requires-Dist: pytest-enabler>=3.4; extra == "enabler" +Provides-Extra: type +Requires-Dist: pytest-mypy>=1.0.1; extra == "type" +Requires-Dist: mypy<1.19; platform_python_implementation == "PyPy" and extra == "type" +Dynamic: license-file + +.. image:: https://img.shields.io/pypi/v/importlib_metadata.svg + :target: https://pypi.org/project/importlib_metadata + +.. image:: https://img.shields.io/pypi/pyversions/importlib_metadata.svg + +.. image:: https://github.com/python/importlib_metadata/actions/workflows/main.yml/badge.svg + :target: https://github.com/python/importlib_metadata/actions?query=workflow%3A%22tests%22 + :alt: tests + +.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json + :target: https://github.com/astral-sh/ruff + :alt: Ruff + +.. image:: https://readthedocs.org/projects/importlib-metadata/badge/?version=latest + :target: https://importlib-metadata.readthedocs.io/en/latest/?badge=latest + +.. image:: https://img.shields.io/badge/skeleton-2025-informational + :target: https://blog.jaraco.com/skeleton + +.. image:: https://tidelift.com/badges/package/pypi/importlib-metadata + :target: https://tidelift.com/subscription/pkg/pypi-importlib-metadata?utm_source=pypi-importlib-metadata&utm_medium=readme + +Library to access the metadata for a Python package. + +This package supplies third-party access to the functionality of +`importlib.metadata `_ +including improvements added to subsequent Python versions. + + +Compatibility +============= + +New features are introduced in this third-party library and later merged +into CPython. The following table indicates which versions of this library +were contributed to different versions in the standard library: + +.. list-table:: + :header-rows: 1 + + * - importlib_metadata + - stdlib + * - 7.0 + - 3.13 + * - 6.5 + - 3.12 + * - 4.13 + - 3.11 + * - 4.6 + - 3.10 + * - 1.4 + - 3.8 + + +Usage +===== + +See the `online documentation `_ +for usage details. + +`Finder authors +`_ can +also add support for custom package installers. See the above documentation +for details. + + +Caveats +======= + +This project primarily supports third-party packages installed by PyPA +tools (or other conforming packages). It does not support: + +- Packages in the stdlib. +- Packages installed without metadata. + +Project details +=============== + + * Project home: https://github.com/python/importlib_metadata + * Report bugs at: https://github.com/python/importlib_metadata/issues + * Code hosting: https://github.com/python/importlib_metadata + * Documentation: https://importlib-metadata.readthedocs.io/ + +For Enterprise +============== + +Available as part of the Tidelift Subscription. + +This project and the maintainers of thousands of other packages are working with Tidelift to deliver one enterprise subscription that covers all of the open source you use. + +`Learn more `_. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/RECORD new file mode 100644 index 0000000000000000000000000000000000000000..78aa761cab1c52d856213f18e2785001bdb02904 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/RECORD @@ -0,0 +1,21 @@ +importlib_metadata-8.7.1.dist-info/INSTALLER,sha256=5hhM4Q4mYTT9z6QB6PGpUAW81PGNFrYrdXMj4oM_6ak,2 +importlib_metadata-8.7.1.dist-info/METADATA,sha256=o-OLnuQyYonUhkcE8w4pnudp4jCc6fSnXw3hpQrQo1Y,4670 +importlib_metadata-8.7.1.dist-info/RECORD,, +importlib_metadata-8.7.1.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 +importlib_metadata-8.7.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91 +importlib_metadata-8.7.1.dist-info/licenses/LICENSE,sha256=RYUC4S2Xu_ZEOGBqIARKqF6wX7CoqAe7NdvsJT_R_AQ,10278 +importlib_metadata-8.7.1.dist-info/top_level.txt,sha256=CO3fD9yylANiXkrMo4qHLV_mqXL2sC5JFKgt1yWAT-A,19 +importlib_metadata/__init__.py,sha256=u7Ew4-UkpzNY-ka6k-WRkDhQZS1akkLMfWs2eEnUmGo,37734 +importlib_metadata/_adapters.py,sha256=r5i8XLrKT6xmrpoREZhZrfczOYDmrVZeJBW5u0HzIGU,3797 +importlib_metadata/_collections.py,sha256=CxAhzlF3g1rwu_fMiB53JtRQiUFh0RgiMpoOvmK_ocg,760 +importlib_metadata/_compat.py,sha256=VC5ZDLlT-BcshauCShdFJvMNLntJJfZzNK1meGa-enw,1313 +importlib_metadata/_functools.py,sha256=0pA2OoiVK6wnsGq8HvVIzgdkvLiZ0nfnfw7IsndjoHk,3510 +importlib_metadata/_itertools.py,sha256=nMvp9SfHAQ_JYwK4L2i64lr3GRXGlYlikGTVzWbys_E,5351 +importlib_metadata/_meta.py,sha256=EtHyiJ5kGzWFDfKyQ2XQp6Vu113CeadKW1Vf6aGc1B4,1765 +importlib_metadata/_text.py,sha256=HCsFksZpJLeTP3NEk_ngrAeXVRRtTrtyh9eOABoRP4A,2166 +importlib_metadata/_typing.py,sha256=EQKhhsEgz_Sa-FnePI-faC72rNOOQwopjA1i5pG8FDU,367 +importlib_metadata/compat/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 +importlib_metadata/compat/py311.py,sha256=uqm-K-uohyj1042TH4a9Er_I5o7667DvulcD-gC_fSA,608 +importlib_metadata/compat/py39.py,sha256=J3W7PUVRPNYMmcvT12RF8ndBU9e8_T0Ac4U87Bsrq70,1187 +importlib_metadata/diagnose.py,sha256=nkSRMiowlmkhLYhKhvCg9glmt_11Cox-EmLzEbqYTa8,379 +importlib_metadata/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/REQUESTED b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/REQUESTED new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/WHEEL new file mode 100644 index 0000000000000000000000000000000000000000..e7fa31b6f3f78deb1022c1f7927f07d4d16da822 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/WHEEL @@ -0,0 +1,5 @@ +Wheel-Version: 1.0 +Generator: setuptools (80.9.0) +Root-Is-Purelib: true +Tag: py3-none-any + diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/licenses/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/licenses/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..5c1d8bbc02a6624cf8e957c40e6f761c1575d180 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/licenses/LICENSE @@ -0,0 +1,73 @@ +Apache License +Version 2.0, January 2004 +http://www.apache.org/licenses/ + +TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + +1. 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We also recommend that a file or class name and description of purpose be included on the same "printed page" as the copyright notice for easier identification within third-party archives. + +Copyright 2025 [name of copyright owner] + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + +http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/top_level.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/top_level.txt new file mode 100644 index 0000000000000000000000000000000000000000..bbb07547a19c30031d13c45cf01cba61dc434e47 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata-8.7.1.dist-info/top_level.txt @@ -0,0 +1 @@ +importlib_metadata diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..508b02e4fce3fa9463b7466138cca7414db0e9b9 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/__init__.py @@ -0,0 +1,1191 @@ +""" +APIs exposing metadata from third-party Python packages. + +This codebase is shared between importlib.metadata in the stdlib +and importlib_metadata in PyPI. See +https://github.com/python/importlib_metadata/wiki/Development-Methodology +for more detail. +""" + +from __future__ import annotations + +import abc +import collections +import email +import functools +import itertools +import operator +import os +import pathlib +import posixpath +import re +import sys +import textwrap +import types +from collections.abc import Iterable, Mapping +from contextlib import suppress +from importlib import import_module +from importlib.abc import MetaPathFinder +from itertools import starmap +from typing import Any + +from . import _meta +from ._collections import FreezableDefaultDict, Pair +from ._compat import ( + NullFinder, + install, +) +from ._functools import method_cache, noop, pass_none, passthrough +from ._itertools import always_iterable, bucket, unique_everseen +from ._meta import PackageMetadata, SimplePath +from ._typing import md_none +from .compat import py39, py311 + +__all__ = [ + 'Distribution', + 'DistributionFinder', + 'PackageMetadata', + 'PackageNotFoundError', + 'SimplePath', + 'distribution', + 'distributions', + 'entry_points', + 'files', + 'metadata', + 'packages_distributions', + 'requires', + 'version', +] + + +class PackageNotFoundError(ModuleNotFoundError): + """The package was not found.""" + + def __str__(self) -> str: + return f"No package metadata was found for {self.name}" + + @property + def name(self) -> str: # type: ignore[override] # make readonly + (name,) = self.args + return name + + +class Sectioned: + """ + A simple entry point config parser for performance + + >>> for item in Sectioned.read(Sectioned._sample): + ... print(item) + Pair(name='sec1', value='# comments ignored') + Pair(name='sec1', value='a = 1') + Pair(name='sec1', value='b = 2') + Pair(name='sec2', value='a = 2') + + >>> res = Sectioned.section_pairs(Sectioned._sample) + >>> item = next(res) + >>> item.name + 'sec1' + >>> item.value + Pair(name='a', value='1') + >>> item = next(res) + >>> item.value + Pair(name='b', value='2') + >>> item = next(res) + >>> item.name + 'sec2' + >>> item.value + Pair(name='a', value='2') + >>> list(res) + [] + """ + + _sample = textwrap.dedent( + """ + [sec1] + # comments ignored + a = 1 + b = 2 + + [sec2] + a = 2 + """ + ).lstrip() + + @classmethod + def section_pairs(cls, text): + return ( + section._replace(value=Pair.parse(section.value)) + for section in cls.read(text, filter_=cls.valid) + if section.name is not None + ) + + @staticmethod + def read(text, filter_=None): + lines = filter(filter_, map(str.strip, text.splitlines())) + name = None + for value in lines: + section_match = value.startswith('[') and value.endswith(']') + if section_match: + name = value.strip('[]') + continue + yield Pair(name, value) + + @staticmethod + def valid(line: str): + return line and not line.startswith('#') + + +class _EntryPointMatch(types.SimpleNamespace): + module: str + attr: str + extras: str + + +class EntryPoint: + """An entry point as defined by Python packaging conventions. + + See `the packaging docs on entry points + `_ + for more information. + + >>> ep = EntryPoint( + ... name=None, group=None, value='package.module:attr [extra1, extra2]') + >>> ep.module + 'package.module' + >>> ep.attr + 'attr' + >>> ep.extras + ['extra1', 'extra2'] + + If the value package or module are not valid identifiers, a + ValueError is raised on access. + + >>> EntryPoint(name=None, group=None, value='invalid-name').module + Traceback (most recent call last): + ... + ValueError: ('Invalid object reference...invalid-name... + >>> EntryPoint(name=None, group=None, value='invalid-name').attr + Traceback (most recent call last): + ... + ValueError: ('Invalid object reference...invalid-name... + >>> EntryPoint(name=None, group=None, value='invalid-name').extras + Traceback (most recent call last): + ... + ValueError: ('Invalid object reference...invalid-name... + + The same thing happens on construction. + + >>> EntryPoint(name=None, group=None, value='invalid-name') + Traceback (most recent call last): + ... + ValueError: ('Invalid object reference...invalid-name... + + """ + + pattern = re.compile( + r'(?P[\w.]+)\s*' + r'(:\s*(?P[\w.]+)\s*)?' + r'((?P\[.*\])\s*)?$' + ) + """ + A regular expression describing the syntax for an entry point, + which might look like: + + - module + - package.module + - package.module:attribute + - package.module:object.attribute + - package.module:attr [extra1, extra2] + + Other combinations are possible as well. + + The expression is lenient about whitespace around the ':', + following the attr, and following any extras. + """ + + name: str + value: str + group: str + + dist: Distribution | None = None + + def __init__(self, name: str, value: str, group: str) -> None: + vars(self).update(name=name, value=value, group=group) + self.module + + def load(self) -> Any: + """Load the entry point from its definition. If only a module + is indicated by the value, return that module. Otherwise, + return the named object. + """ + module = import_module(self.module) + attrs = filter(None, (self.attr or '').split('.')) + return functools.reduce(getattr, attrs, module) + + @property + def module(self) -> str: + return self._match.module + + @property + def attr(self) -> str: + return self._match.attr + + @property + def extras(self) -> list[str]: + return re.findall(r'\w+', self._match.extras or '') + + @functools.cached_property + def _match(self) -> _EntryPointMatch: + match = self.pattern.match(self.value) + if not match: + raise ValueError( + 'Invalid object reference. ' + 'See https://packaging.python.org' + '/en/latest/specifications/entry-points/#data-model', + self.value, + ) + return _EntryPointMatch(**match.groupdict()) + + def _for(self, dist): + vars(self).update(dist=dist) + return self + + def matches(self, **params): + """ + EntryPoint matches the given parameters. + + >>> ep = EntryPoint(group='foo', name='bar', value='bing:bong [extra1, extra2]') + >>> ep.matches(group='foo') + True + >>> ep.matches(name='bar', value='bing:bong [extra1, extra2]') + True + >>> ep.matches(group='foo', name='other') + False + >>> ep.matches() + True + >>> ep.matches(extras=['extra1', 'extra2']) + True + >>> ep.matches(module='bing') + True + >>> ep.matches(attr='bong') + True + """ + self._disallow_dist(params) + attrs = (getattr(self, param) for param in params) + return all(map(operator.eq, params.values(), attrs)) + + @staticmethod + def _disallow_dist(params): + """ + Querying by dist is not allowed (dist objects are not comparable). + >>> EntryPoint(name='fan', value='fav', group='fag').matches(dist='foo') + Traceback (most recent call last): + ... + ValueError: "dist" is not suitable for matching... + """ + if "dist" in params: + raise ValueError( + '"dist" is not suitable for matching. ' + "Instead, use Distribution.entry_points.select() on a " + "located distribution." + ) + + def _key(self): + return self.name, self.value, self.group + + def __lt__(self, other): + return self._key() < other._key() + + def __eq__(self, other): + return self._key() == other._key() + + def __setattr__(self, name, value): + raise AttributeError("EntryPoint objects are immutable.") + + def __repr__(self): + return ( + f'EntryPoint(name={self.name!r}, value={self.value!r}, ' + f'group={self.group!r})' + ) + + def __hash__(self) -> int: + return hash(self._key()) + + +class EntryPoints(tuple): + """ + An immutable collection of selectable EntryPoint objects. + """ + + __slots__ = () + + def __getitem__(self, name: str) -> EntryPoint: # type: ignore[override] # Work with str instead of int + """ + Get the EntryPoint in self matching name. + """ + try: + return next(iter(self.select(name=name))) + except StopIteration: + raise KeyError(name) + + def __repr__(self): + """ + Repr with classname and tuple constructor to + signal that we deviate from regular tuple behavior. + """ + return '%s(%r)' % (self.__class__.__name__, tuple(self)) + + def select(self, **params) -> EntryPoints: + """ + Select entry points from self that match the + given parameters (typically group and/or name). + """ + return EntryPoints(ep for ep in self if py39.ep_matches(ep, **params)) + + @property + def names(self) -> set[str]: + """ + Return the set of all names of all entry points. + """ + return {ep.name for ep in self} + + @property + def groups(self) -> set[str]: + """ + Return the set of all groups of all entry points. + """ + return {ep.group for ep in self} + + @classmethod + def _from_text_for(cls, text, dist): + return cls(ep._for(dist) for ep in cls._from_text(text)) + + @staticmethod + def _from_text(text): + return ( + EntryPoint(name=item.value.name, value=item.value.value, group=item.name) + for item in Sectioned.section_pairs(text or '') + ) + + +class PackagePath(pathlib.PurePosixPath): + """A reference to a path in a package""" + + hash: FileHash | None + size: int + dist: Distribution + + def read_text(self, encoding: str = 'utf-8') -> str: + return self.locate().read_text(encoding=encoding) + + def read_binary(self) -> bytes: + return self.locate().read_bytes() + + def locate(self) -> SimplePath: + """Return a path-like object for this path""" + return self.dist.locate_file(self) + + +class FileHash: + def __init__(self, spec: str) -> None: + self.mode, _, self.value = spec.partition('=') + + def __repr__(self) -> str: + return f'' + + +class Distribution(metaclass=abc.ABCMeta): + """ + An abstract Python distribution package. + + Custom providers may derive from this class and define + the abstract methods to provide a concrete implementation + for their environment. Some providers may opt to override + the default implementation of some properties to bypass + the file-reading mechanism. + """ + + @abc.abstractmethod + def read_text(self, filename) -> str | None: + """Attempt to load metadata file given by the name. + + Python distribution metadata is organized by blobs of text + typically represented as "files" in the metadata directory + (e.g. package-1.0.dist-info). These files include things + like: + + - METADATA: The distribution metadata including fields + like Name and Version and Description. + - entry_points.txt: A series of entry points as defined in + `the entry points spec `_. + - RECORD: A record of files according to + `this recording spec `_. + + A package may provide any set of files, including those + not listed here or none at all. + + :param filename: The name of the file in the distribution info. + :return: The text if found, otherwise None. + """ + + @abc.abstractmethod + def locate_file(self, path: str | os.PathLike[str]) -> SimplePath: + """ + Given a path to a file in this distribution, return a SimplePath + to it. + + This method is used by callers of ``Distribution.files()`` to + locate files within the distribution. If it's possible for a + Distribution to represent files in the distribution as + ``SimplePath`` objects, it should implement this method + to resolve such objects. + + Some Distribution providers may elect not to resolve SimplePath + objects within the distribution by raising a + NotImplementedError, but consumers of such a Distribution would + be unable to invoke ``Distribution.files()``. + """ + + @classmethod + def from_name(cls, name: str) -> Distribution: + """Return the Distribution for the given package name. + + :param name: The name of the distribution package to search for. + :return: The Distribution instance (or subclass thereof) for the named + package, if found. + :raises PackageNotFoundError: When the named package's distribution + metadata cannot be found. + :raises ValueError: When an invalid value is supplied for name. + """ + if not name: + raise ValueError("A distribution name is required.") + try: + return next(iter(cls._prefer_valid(cls.discover(name=name)))) + except StopIteration: + raise PackageNotFoundError(name) + + @classmethod + def discover( + cls, *, context: DistributionFinder.Context | None = None, **kwargs + ) -> Iterable[Distribution]: + """Return an iterable of Distribution objects for all packages. + + Pass a ``context`` or pass keyword arguments for constructing + a context. + + :context: A ``DistributionFinder.Context`` object. + :return: Iterable of Distribution objects for packages matching + the context. + """ + if context and kwargs: + raise ValueError("cannot accept context and kwargs") + context = context or DistributionFinder.Context(**kwargs) + return itertools.chain.from_iterable( + resolver(context) for resolver in cls._discover_resolvers() + ) + + @staticmethod + def _prefer_valid(dists: Iterable[Distribution]) -> Iterable[Distribution]: + """ + Prefer (move to the front) distributions that have metadata. + + Ref python/importlib_resources#489. + """ + buckets = bucket(dists, lambda dist: bool(dist.metadata)) + return itertools.chain(buckets[True], buckets[False]) + + @staticmethod + def at(path: str | os.PathLike[str]) -> Distribution: + """Return a Distribution for the indicated metadata path. + + :param path: a string or path-like object + :return: a concrete Distribution instance for the path + """ + return PathDistribution(pathlib.Path(path)) + + @staticmethod + def _discover_resolvers(): + """Search the meta_path for resolvers (MetadataPathFinders).""" + declared = ( + getattr(finder, 'find_distributions', None) for finder in sys.meta_path + ) + return filter(None, declared) + + @property + def metadata(self) -> _meta.PackageMetadata | None: + """Return the parsed metadata for this Distribution. + + The returned object will have keys that name the various bits of + metadata per the + `Core metadata specifications `_. + + Custom providers may provide the METADATA file or override this + property. + """ + + text = ( + self.read_text('METADATA') + or self.read_text('PKG-INFO') + # This last clause is here to support old egg-info files. Its + # effect is to just end up using the PathDistribution's self._path + # (which points to the egg-info file) attribute unchanged. + or self.read_text('') + ) + return self._assemble_message(text) + + @staticmethod + @pass_none + def _assemble_message(text: str) -> _meta.PackageMetadata: + # deferred for performance (python/cpython#109829) + from . import _adapters + + return _adapters.Message(email.message_from_string(text)) + + @property + def name(self) -> str: + """Return the 'Name' metadata for the distribution package.""" + return md_none(self.metadata)['Name'] + + @property + def _normalized_name(self): + """Return a normalized version of the name.""" + return Prepared.normalize(self.name) + + @property + def version(self) -> str: + """Return the 'Version' metadata for the distribution package.""" + return md_none(self.metadata)['Version'] + + @property + def entry_points(self) -> EntryPoints: + """ + Return EntryPoints for this distribution. + + Custom providers may provide the ``entry_points.txt`` file + or override this property. + """ + return EntryPoints._from_text_for(self.read_text('entry_points.txt'), self) + + @property + def files(self) -> list[PackagePath] | None: + """Files in this distribution. + + :return: List of PackagePath for this distribution or None + + Result is `None` if the metadata file that enumerates files + (i.e. RECORD for dist-info, or installed-files.txt or + SOURCES.txt for egg-info) is missing. + Result may be empty if the metadata exists but is empty. + + Custom providers are recommended to provide a "RECORD" file (in + ``read_text``) or override this property to allow for callers to be + able to resolve filenames provided by the package. + """ + + def make_file(name, hash=None, size_str=None): + result = PackagePath(name) + result.hash = FileHash(hash) if hash else None + result.size = int(size_str) if size_str else None + result.dist = self + return result + + @pass_none + def make_files(lines): + # Delay csv import, since Distribution.files is not as widely used + # as other parts of importlib.metadata + import csv + + return starmap(make_file, csv.reader(lines)) + + @pass_none + def skip_missing_files(package_paths): + return list(filter(lambda path: path.locate().exists(), package_paths)) + + return skip_missing_files( + make_files( + self._read_files_distinfo() + or self._read_files_egginfo_installed() + or self._read_files_egginfo_sources() + ) + ) + + def _read_files_distinfo(self): + """ + Read the lines of RECORD. + """ + text = self.read_text('RECORD') + return text and text.splitlines() + + def _read_files_egginfo_installed(self): + """ + Read installed-files.txt and return lines in a similar + CSV-parsable format as RECORD: each file must be placed + relative to the site-packages directory and must also be + quoted (since file names can contain literal commas). + + This file is written when the package is installed by pip, + but it might not be written for other installation methods. + Assume the file is accurate if it exists. + """ + text = self.read_text('installed-files.txt') + # Prepend the .egg-info/ subdir to the lines in this file. + # But this subdir is only available from PathDistribution's + # self._path. + subdir = getattr(self, '_path', None) + if not text or not subdir: + return + + paths = ( + py311 + .relative_fix((subdir / name).resolve()) + .relative_to(self.locate_file('').resolve(), walk_up=True) + .as_posix() + for name in text.splitlines() + ) + return map('"{}"'.format, paths) + + def _read_files_egginfo_sources(self): + """ + Read SOURCES.txt and return lines in a similar CSV-parsable + format as RECORD: each file name must be quoted (since it + might contain literal commas). + + Note that SOURCES.txt is not a reliable source for what + files are installed by a package. This file is generated + for a source archive, and the files that are present + there (e.g. setup.py) may not correctly reflect the files + that are present after the package has been installed. + """ + text = self.read_text('SOURCES.txt') + return text and map('"{}"'.format, text.splitlines()) + + @property + def requires(self) -> list[str] | None: + """Generated requirements specified for this Distribution""" + reqs = self._read_dist_info_reqs() or self._read_egg_info_reqs() + return reqs and list(reqs) + + def _read_dist_info_reqs(self): + return self.metadata.get_all('Requires-Dist') + + def _read_egg_info_reqs(self): + source = self.read_text('requires.txt') + return pass_none(self._deps_from_requires_text)(source) + + @classmethod + def _deps_from_requires_text(cls, source): + return cls._convert_egg_info_reqs_to_simple_reqs(Sectioned.read(source)) + + @staticmethod + def _convert_egg_info_reqs_to_simple_reqs(sections): + """ + Historically, setuptools would solicit and store 'extra' + requirements, including those with environment markers, + in separate sections. More modern tools expect each + dependency to be defined separately, with any relevant + extras and environment markers attached directly to that + requirement. This method converts the former to the + latter. See _test_deps_from_requires_text for an example. + """ + + def make_condition(name): + return name and f'extra == "{name}"' + + def quoted_marker(section): + section = section or '' + extra, sep, markers = section.partition(':') + if extra and markers: + markers = f'({markers})' + conditions = list(filter(None, [markers, make_condition(extra)])) + return '; ' + ' and '.join(conditions) if conditions else '' + + def url_req_space(req): + """ + PEP 508 requires a space between the url_spec and the quoted_marker. + Ref python/importlib_metadata#357. + """ + # '@' is uniquely indicative of a url_req. + return ' ' * ('@' in req) + + for section in sections: + space = url_req_space(section.value) + yield section.value + space + quoted_marker(section.name) + + @property + def origin(self): + return self._load_json('direct_url.json') + + def _load_json(self, filename): + # Deferred for performance (python/importlib_metadata#503) + import json + + return pass_none(json.loads)( + self.read_text(filename), + object_hook=lambda data: types.SimpleNamespace(**data), + ) + + +class DistributionFinder(MetaPathFinder): + """ + A MetaPathFinder capable of discovering installed distributions. + + Custom providers should implement this interface in order to + supply metadata. + """ + + class Context: + """ + Keyword arguments presented by the caller to + ``distributions()`` or ``Distribution.discover()`` + to narrow the scope of a search for distributions + in all DistributionFinders. + + Each DistributionFinder may expect any parameters + and should attempt to honor the canonical + parameters defined below when appropriate. + + This mechanism gives a custom provider a means to + solicit additional details from the caller beyond + "name" and "path" when searching distributions. + For example, imagine a provider that exposes suites + of packages in either a "public" or "private" ``realm``. + A caller may wish to query only for distributions in + a particular realm and could call + ``distributions(realm="private")`` to signal to the + custom provider to only include distributions from that + realm. + """ + + name = None + """ + Specific name for which a distribution finder should match. + A name of ``None`` matches all distributions. + """ + + def __init__(self, **kwargs): + vars(self).update(kwargs) + + @property + def path(self) -> list[str]: + """ + The sequence of directory path that a distribution finder + should search. + + Typically refers to Python installed package paths such as + "site-packages" directories and defaults to ``sys.path``. + """ + return vars(self).get('path', sys.path) + + @abc.abstractmethod + def find_distributions(self, context=Context()) -> Iterable[Distribution]: + """ + Find distributions. + + Return an iterable of all Distribution instances capable of + loading the metadata for packages matching the ``context``, + a DistributionFinder.Context instance. + """ + + +@passthrough +def _clear_after_fork(cached): + """Ensure ``func`` clears cached state after ``fork`` when supported. + + ``FastPath`` caches zip-backed ``pathlib.Path`` objects that retain a + reference to the parent's open ``ZipFile`` handle. Re-using a cached + instance in a forked child can therefore resurrect invalid file pointers + and trigger ``BadZipFile``/``OSError`` failures (python/importlib_metadata#520). + Registering ``cache_clear`` with ``os.register_at_fork`` keeps each process + on its own cache. + """ + getattr(os, 'register_at_fork', noop)(after_in_child=cached.cache_clear) + + +class FastPath: + """ + Micro-optimized class for searching a root for children. + + Root is a path on the file system that may contain metadata + directories either as natural directories or within a zip file. + + >>> FastPath('').children() + ['...'] + + FastPath objects are cached and recycled for any given root. + + >>> FastPath('foobar') is FastPath('foobar') + True + """ + + @_clear_after_fork # type: ignore[misc] + @functools.lru_cache() + def __new__(cls, root): + return super().__new__(cls) + + def __init__(self, root): + self.root = root + + def joinpath(self, child): + return pathlib.Path(self.root, child) + + def children(self): + with suppress(Exception): + return os.listdir(self.root or '.') + with suppress(Exception): + return self.zip_children() + return [] + + def zip_children(self): + # deferred for performance (python/importlib_metadata#502) + from zipp.compat.overlay import zipfile + + zip_path = zipfile.Path(self.root) + names = zip_path.root.namelist() + self.joinpath = zip_path.joinpath + + return dict.fromkeys(child.split(posixpath.sep, 1)[0] for child in names) + + def search(self, name): + return self.lookup(self.mtime).search(name) + + @property + def mtime(self): + with suppress(OSError): + return os.stat(self.root).st_mtime + self.lookup.cache_clear() + + @method_cache + def lookup(self, mtime): + return Lookup(self) + + +class Lookup: + """ + A micro-optimized class for searching a (fast) path for metadata. + """ + + def __init__(self, path: FastPath): + """ + Calculate all of the children representing metadata. + + From the children in the path, calculate early all of the + children that appear to represent metadata (infos) or legacy + metadata (eggs). + """ + + base = os.path.basename(path.root).lower() + base_is_egg = base.endswith(".egg") + self.infos = FreezableDefaultDict(list) + self.eggs = FreezableDefaultDict(list) + + for child in path.children(): + low = child.lower() + if low.endswith((".dist-info", ".egg-info")): + # rpartition is faster than splitext and suitable for this purpose. + name = low.rpartition(".")[0].partition("-")[0] + normalized = Prepared.normalize(name) + self.infos[normalized].append(path.joinpath(child)) + elif base_is_egg and low == "egg-info": + name = base.rpartition(".")[0].partition("-")[0] + legacy_normalized = Prepared.legacy_normalize(name) + self.eggs[legacy_normalized].append(path.joinpath(child)) + + self.infos.freeze() + self.eggs.freeze() + + def search(self, prepared: Prepared): + """ + Yield all infos and eggs matching the Prepared query. + """ + infos = ( + self.infos[prepared.normalized] + if prepared + else itertools.chain.from_iterable(self.infos.values()) + ) + eggs = ( + self.eggs[prepared.legacy_normalized] + if prepared + else itertools.chain.from_iterable(self.eggs.values()) + ) + return itertools.chain(infos, eggs) + + +class Prepared: + """ + A prepared search query for metadata on a possibly-named package. + + Pre-calculates the normalization to prevent repeated operations. + + >>> none = Prepared(None) + >>> none.normalized + >>> none.legacy_normalized + >>> bool(none) + False + >>> sample = Prepared('Sample__Pkg-name.foo') + >>> sample.normalized + 'sample_pkg_name_foo' + >>> sample.legacy_normalized + 'sample__pkg_name.foo' + >>> bool(sample) + True + """ + + normalized = None + legacy_normalized = None + + def __init__(self, name: str | None): + self.name = name + if name is None: + return + self.normalized = self.normalize(name) + self.legacy_normalized = self.legacy_normalize(name) + + @staticmethod + def normalize(name): + """ + PEP 503 normalization plus dashes as underscores. + """ + return re.sub(r"[-_.]+", "-", name).lower().replace('-', '_') + + @staticmethod + def legacy_normalize(name): + """ + Normalize the package name as found in the convention in + older packaging tools versions and specs. + """ + return name.lower().replace('-', '_') + + def __bool__(self): + return bool(self.name) + + +@install +class MetadataPathFinder(NullFinder, DistributionFinder): + """A degenerate finder for distribution packages on the file system. + + This finder supplies only a find_distributions() method for versions + of Python that do not have a PathFinder find_distributions(). + """ + + @classmethod + def find_distributions( + cls, context=DistributionFinder.Context() + ) -> Iterable[PathDistribution]: + """ + Find distributions. + + Return an iterable of all Distribution instances capable of + loading the metadata for packages matching ``context.name`` + (or all names if ``None`` indicated) along the paths in the list + of directories ``context.path``. + """ + found = cls._search_paths(context.name, context.path) + return map(PathDistribution, found) + + @classmethod + def _search_paths(cls, name, paths): + """Find metadata directories in paths heuristically.""" + prepared = Prepared(name) + return itertools.chain.from_iterable( + path.search(prepared) for path in map(FastPath, paths) + ) + + @classmethod + def invalidate_caches(cls) -> None: + FastPath.__new__.cache_clear() + + +class PathDistribution(Distribution): + def __init__(self, path: SimplePath) -> None: + """Construct a distribution. + + :param path: SimplePath indicating the metadata directory. + """ + self._path = path + + def read_text(self, filename: str | os.PathLike[str]) -> str | None: + with suppress( + FileNotFoundError, + IsADirectoryError, + KeyError, + NotADirectoryError, + PermissionError, + ): + return self._path.joinpath(filename).read_text(encoding='utf-8') + + return None + + read_text.__doc__ = Distribution.read_text.__doc__ + + def locate_file(self, path: str | os.PathLike[str]) -> SimplePath: + return self._path.parent / path + + @property + def _normalized_name(self): + """ + Performance optimization: where possible, resolve the + normalized name from the file system path. + """ + stem = os.path.basename(str(self._path)) + return ( + pass_none(Prepared.normalize)(self._name_from_stem(stem)) + or super()._normalized_name + ) + + @staticmethod + def _name_from_stem(stem): + """ + >>> PathDistribution._name_from_stem('foo-3.0.egg-info') + 'foo' + >>> PathDistribution._name_from_stem('CherryPy-3.0.dist-info') + 'CherryPy' + >>> PathDistribution._name_from_stem('face.egg-info') + 'face' + >>> PathDistribution._name_from_stem('foo.bar') + """ + filename, ext = os.path.splitext(stem) + if ext not in ('.dist-info', '.egg-info'): + return + name, sep, rest = filename.partition('-') + return name + + +def distribution(distribution_name: str) -> Distribution: + """Get the ``Distribution`` instance for the named package. + + :param distribution_name: The name of the distribution package as a string. + :return: A ``Distribution`` instance (or subclass thereof). + """ + return Distribution.from_name(distribution_name) + + +def distributions(**kwargs) -> Iterable[Distribution]: + """Get all ``Distribution`` instances in the current environment. + + :return: An iterable of ``Distribution`` instances. + """ + return Distribution.discover(**kwargs) + + +def metadata(distribution_name: str) -> _meta.PackageMetadata | None: + """Get the metadata for the named package. + + :param distribution_name: The name of the distribution package to query. + :return: A PackageMetadata containing the parsed metadata. + """ + return Distribution.from_name(distribution_name).metadata + + +def version(distribution_name: str) -> str: + """Get the version string for the named package. + + :param distribution_name: The name of the distribution package to query. + :return: The version string for the package as defined in the package's + "Version" metadata key. + """ + return distribution(distribution_name).version + + +_unique = functools.partial( + unique_everseen, + key=py39.normalized_name, +) +""" +Wrapper for ``distributions`` to return unique distributions by name. +""" + + +def entry_points(**params) -> EntryPoints: + """Return EntryPoint objects for all installed packages. + + Pass selection parameters (group or name) to filter the + result to entry points matching those properties (see + EntryPoints.select()). + + :return: EntryPoints for all installed packages. + """ + eps = itertools.chain.from_iterable( + dist.entry_points for dist in _unique(distributions()) + ) + return EntryPoints(eps).select(**params) + + +def files(distribution_name: str) -> list[PackagePath] | None: + """Return a list of files for the named package. + + :param distribution_name: The name of the distribution package to query. + :return: List of files composing the distribution. + """ + return distribution(distribution_name).files + + +def requires(distribution_name: str) -> list[str] | None: + """ + Return a list of requirements for the named package. + + :return: An iterable of requirements, suitable for + packaging.requirement.Requirement. + """ + return distribution(distribution_name).requires + + +def packages_distributions() -> Mapping[str, list[str]]: + """ + Return a mapping of top-level packages to their + distributions. + + >>> import collections.abc + >>> pkgs = packages_distributions() + >>> all(isinstance(dist, collections.abc.Sequence) for dist in pkgs.values()) + True + """ + pkg_to_dist = collections.defaultdict(list) + for dist in distributions(): + for pkg in _top_level_declared(dist) or _top_level_inferred(dist): + pkg_to_dist[pkg].append(md_none(dist.metadata)['Name']) + return dict(pkg_to_dist) + + +def _top_level_declared(dist): + return (dist.read_text('top_level.txt') or '').split() + + +def _topmost(name: PackagePath) -> str | None: + """ + Return the top-most parent as long as there is a parent. + """ + top, *rest = name.parts + return top if rest else None + + +def _get_toplevel_name(name: PackagePath) -> str: + """ + Infer a possibly importable module name from a name presumed on + sys.path. + + >>> _get_toplevel_name(PackagePath('foo.py')) + 'foo' + >>> _get_toplevel_name(PackagePath('foo')) + 'foo' + >>> _get_toplevel_name(PackagePath('foo.pyc')) + 'foo' + >>> _get_toplevel_name(PackagePath('foo/__init__.py')) + 'foo' + >>> _get_toplevel_name(PackagePath('foo.pth')) + 'foo.pth' + >>> _get_toplevel_name(PackagePath('foo.dist-info')) + 'foo.dist-info' + """ + # Defer import of inspect for performance (python/cpython#118761) + import inspect + + return _topmost(name) or inspect.getmodulename(name) or str(name) + + +def _top_level_inferred(dist): + opt_names = set(map(_get_toplevel_name, always_iterable(dist.files))) + + def importable_name(name): + return '.' not in name + + return filter(importable_name, opt_names) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_adapters.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_adapters.py new file mode 100644 index 0000000000000000000000000000000000000000..dede395d79a38bab322d56a66d916703af84f77b --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_adapters.py @@ -0,0 +1,136 @@ +import email.message +import email.policy +import re +import textwrap + +from ._text import FoldedCase + + +class RawPolicy(email.policy.EmailPolicy): + def fold(self, name, value): + folded = self.linesep.join( + textwrap + .indent(value, prefix=' ' * 8, predicate=lambda line: True) + .lstrip() + .splitlines() + ) + return f'{name}: {folded}{self.linesep}' + + +class Message(email.message.Message): + r""" + Specialized Message subclass to handle metadata naturally. + + Reads values that may have newlines in them and converts the + payload to the Description. + + >>> msg_text = textwrap.dedent(''' + ... Name: Foo + ... Version: 3.0 + ... License: blah + ... de-blah + ... + ... First line of description. + ... Second line of description. + ... + ... Fourth line! + ... ''').lstrip().replace('', '') + >>> msg = Message(email.message_from_string(msg_text)) + >>> msg['Description'] + 'First line of description.\nSecond line of description.\n\nFourth line!\n' + + Message should render even if values contain newlines. + + >>> print(msg) + Name: Foo + Version: 3.0 + License: blah + de-blah + Description: First line of description. + Second line of description. + + Fourth line! + + + """ + + multiple_use_keys = set( + map( + FoldedCase, + [ + 'Classifier', + 'Obsoletes-Dist', + 'Platform', + 'Project-URL', + 'Provides-Dist', + 'Provides-Extra', + 'Requires-Dist', + 'Requires-External', + 'Supported-Platform', + 'Dynamic', + ], + ) + ) + """ + Keys that may be indicated multiple times per PEP 566. + """ + + def __new__(cls, orig: email.message.Message): + res = super().__new__(cls) + vars(res).update(vars(orig)) + return res + + def __init__(self, *args, **kwargs): + self._headers = self._repair_headers() + + # suppress spurious error from mypy + def __iter__(self): + return super().__iter__() + + def __getitem__(self, item): + """ + Override parent behavior to typical dict behavior. + + ``email.message.Message`` will emit None values for missing + keys. Typical mappings, including this ``Message``, will raise + a key error for missing keys. + + Ref python/importlib_metadata#371. + """ + res = super().__getitem__(item) + if res is None: + raise KeyError(item) + return res + + def _repair_headers(self): + def redent(value): + "Correct for RFC822 indentation" + indent = ' ' * 8 + if not value or '\n' + indent not in value: + return value + return textwrap.dedent(indent + value) + + headers = [(key, redent(value)) for key, value in vars(self)['_headers']] + if self._payload: + headers.append(('Description', self.get_payload())) + self.set_payload('') + return headers + + def as_string(self): + return super().as_string(policy=RawPolicy()) + + @property + def json(self): + """ + Convert PackageMetadata to a JSON-compatible format + per PEP 0566. + """ + + def transform(key): + value = self.get_all(key) if key in self.multiple_use_keys else self[key] + if key == 'Keywords': + value = re.split(r'\s+', value) + tk = key.lower().replace('-', '_') + return tk, value + + return dict(map(transform, map(FoldedCase, self))) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_collections.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_collections.py new file mode 100644 index 0000000000000000000000000000000000000000..fc5045d36be57251000393b32baba7baa9cd8c4f --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_collections.py @@ -0,0 +1,34 @@ +import collections +import typing + + +# from jaraco.collections 3.3 +class FreezableDefaultDict(collections.defaultdict): + """ + Often it is desirable to prevent the mutation of + a default dict after its initial construction, such + as to prevent mutation during iteration. + + >>> dd = FreezableDefaultDict(list) + >>> dd[0].append('1') + >>> dd.freeze() + >>> dd[1] + [] + >>> len(dd) + 1 + """ + + def __missing__(self, key): + return getattr(self, '_frozen', super().__missing__)(key) + + def freeze(self): + self._frozen = lambda key: self.default_factory() + + +class Pair(typing.NamedTuple): + name: str + value: str + + @classmethod + def parse(cls, text): + return cls(*map(str.strip, text.split("=", 1))) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_compat.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_compat.py new file mode 100644 index 0000000000000000000000000000000000000000..01356d69b97c95a6d41818e5c2c50a299146bef4 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_compat.py @@ -0,0 +1,56 @@ +import platform +import sys + +__all__ = ['install', 'NullFinder'] + + +def install(cls): + """ + Class decorator for installation on sys.meta_path. + + Adds the backport DistributionFinder to sys.meta_path and + attempts to disable the finder functionality of the stdlib + DistributionFinder. + """ + sys.meta_path.append(cls()) + disable_stdlib_finder() + return cls + + +def disable_stdlib_finder(): + """ + Give the backport primacy for discovering path-based distributions + by monkey-patching the stdlib O_O. + + See #91 for more background for rationale on this sketchy + behavior. + """ + + def matches(finder): + return getattr( + finder, '__module__', None + ) == '_frozen_importlib_external' and hasattr(finder, 'find_distributions') + + for finder in filter(matches, sys.meta_path): # pragma: nocover + del finder.find_distributions + + +class NullFinder: + """ + A "Finder" (aka "MetaPathFinder") that never finds any modules, + but may find distributions. + """ + + @staticmethod + def find_spec(*args, **kwargs): + return None + + +def pypy_partial(val): + """ + Adjust for variable stacklevel on partial under PyPy. + + Workaround for #327. + """ + is_pypy = platform.python_implementation() == 'PyPy' + return val + is_pypy diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_functools.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_functools.py new file mode 100644 index 0000000000000000000000000000000000000000..b1fd04a84ab4c129b19f71a13f7489c37d1a9e9e --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_functools.py @@ -0,0 +1,135 @@ +import functools +import types +from typing import Callable, TypeVar + + +# from jaraco.functools 3.3 +def method_cache(method, cache_wrapper=None): + """ + Wrap lru_cache to support storing the cache data in the object instances. + + Abstracts the common paradigm where the method explicitly saves an + underscore-prefixed protected property on first call and returns that + subsequently. + + >>> class MyClass: + ... calls = 0 + ... + ... @method_cache + ... def method(self, value): + ... self.calls += 1 + ... return value + + >>> a = MyClass() + >>> a.method(3) + 3 + >>> for x in range(75): + ... res = a.method(x) + >>> a.calls + 75 + + Note that the apparent behavior will be exactly like that of lru_cache + except that the cache is stored on each instance, so values in one + instance will not flush values from another, and when an instance is + deleted, so are the cached values for that instance. + + >>> b = MyClass() + >>> for x in range(35): + ... res = b.method(x) + >>> b.calls + 35 + >>> a.method(0) + 0 + >>> a.calls + 75 + + Note that if method had been decorated with ``functools.lru_cache()``, + a.calls would have been 76 (due to the cached value of 0 having been + flushed by the 'b' instance). + + Clear the cache with ``.cache_clear()`` + + >>> a.method.cache_clear() + + Same for a method that hasn't yet been called. + + >>> c = MyClass() + >>> c.method.cache_clear() + + Another cache wrapper may be supplied: + + >>> cache = functools.lru_cache(maxsize=2) + >>> MyClass.method2 = method_cache(lambda self: 3, cache_wrapper=cache) + >>> a = MyClass() + >>> a.method2() + 3 + + Caution - do not subsequently wrap the method with another decorator, such + as ``@property``, which changes the semantics of the function. + + See also + http://code.activestate.com/recipes/577452-a-memoize-decorator-for-instance-methods/ + for another implementation and additional justification. + """ + cache_wrapper = cache_wrapper or functools.lru_cache() + + def wrapper(self, *args, **kwargs): + # it's the first call, replace the method with a cached, bound method + bound_method = types.MethodType(method, self) + cached_method = cache_wrapper(bound_method) + setattr(self, method.__name__, cached_method) + return cached_method(*args, **kwargs) + + # Support cache clear even before cache has been created. + wrapper.cache_clear = lambda: None + + return wrapper + + +# From jaraco.functools 3.3 +def pass_none(func): + """ + Wrap func so it's not called if its first param is None + + >>> print_text = pass_none(print) + >>> print_text('text') + text + >>> print_text(None) + """ + + @functools.wraps(func) + def wrapper(param, *args, **kwargs): + if param is not None: + return func(param, *args, **kwargs) + + return wrapper + + +# From jaraco.functools 4.4 +def noop(*args, **kwargs): + """ + A no-operation function that does nothing. + + >>> noop(1, 2, three=3) + """ + + +_T = TypeVar('_T') + + +# From jaraco.functools 4.4 +def passthrough(func: Callable[..., object]) -> Callable[[_T], _T]: + """ + Wrap the function to always return the first parameter. + + >>> passthrough(print)('3') + 3 + '3' + """ + + @functools.wraps(func) + def wrapper(first: _T, *args, **kwargs) -> _T: + func(first, *args, **kwargs) + return first + + return wrapper # type: ignore[return-value] diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_itertools.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_itertools.py new file mode 100644 index 0000000000000000000000000000000000000000..79d37198ce7aff317873f6e4e84cd904a46a69de --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_itertools.py @@ -0,0 +1,171 @@ +from collections import defaultdict, deque +from itertools import filterfalse + + +def unique_everseen(iterable, key=None): + "List unique elements, preserving order. Remember all elements ever seen." + # unique_everseen('AAAABBBCCDAABBB') --> A B C D + # unique_everseen('ABBCcAD', str.lower) --> A B C D + seen = set() + seen_add = seen.add + if key is None: + for element in filterfalse(seen.__contains__, iterable): + seen_add(element) + yield element + else: + for element in iterable: + k = key(element) + if k not in seen: + seen_add(k) + yield element + + +# copied from more_itertools 8.8 +def always_iterable(obj, base_type=(str, bytes)): + """If *obj* is iterable, return an iterator over its items:: + + >>> obj = (1, 2, 3) + >>> list(always_iterable(obj)) + [1, 2, 3] + + If *obj* is not iterable, return a one-item iterable containing *obj*:: + + >>> obj = 1 + >>> list(always_iterable(obj)) + [1] + + If *obj* is ``None``, return an empty iterable: + + >>> obj = None + >>> list(always_iterable(None)) + [] + + By default, binary and text strings are not considered iterable:: + + >>> obj = 'foo' + >>> list(always_iterable(obj)) + ['foo'] + + If *base_type* is set, objects for which ``isinstance(obj, base_type)`` + returns ``True`` won't be considered iterable. + + >>> obj = {'a': 1} + >>> list(always_iterable(obj)) # Iterate over the dict's keys + ['a'] + >>> list(always_iterable(obj, base_type=dict)) # Treat dicts as a unit + [{'a': 1}] + + Set *base_type* to ``None`` to avoid any special handling and treat objects + Python considers iterable as iterable: + + >>> obj = 'foo' + >>> list(always_iterable(obj, base_type=None)) + ['f', 'o', 'o'] + """ + if obj is None: + return iter(()) + + if (base_type is not None) and isinstance(obj, base_type): + return iter((obj,)) + + try: + return iter(obj) + except TypeError: + return iter((obj,)) + + +# Copied from more_itertools 10.3 +class bucket: + """Wrap *iterable* and return an object that buckets the iterable into + child iterables based on a *key* function. + + >>> iterable = ['a1', 'b1', 'c1', 'a2', 'b2', 'c2', 'b3'] + >>> s = bucket(iterable, key=lambda x: x[0]) # Bucket by 1st character + >>> sorted(list(s)) # Get the keys + ['a', 'b', 'c'] + >>> a_iterable = s['a'] + >>> next(a_iterable) + 'a1' + >>> next(a_iterable) + 'a2' + >>> list(s['b']) + ['b1', 'b2', 'b3'] + + The original iterable will be advanced and its items will be cached until + they are used by the child iterables. This may require significant storage. + + By default, attempting to select a bucket to which no items belong will + exhaust the iterable and cache all values. + If you specify a *validator* function, selected buckets will instead be + checked against it. + + >>> from itertools import count + >>> it = count(1, 2) # Infinite sequence of odd numbers + >>> key = lambda x: x % 10 # Bucket by last digit + >>> validator = lambda x: x in {1, 3, 5, 7, 9} # Odd digits only + >>> s = bucket(it, key=key, validator=validator) + >>> 2 in s + False + >>> list(s[2]) + [] + + """ + + def __init__(self, iterable, key, validator=None): + self._it = iter(iterable) + self._key = key + self._cache = defaultdict(deque) + self._validator = validator or (lambda x: True) + + def __contains__(self, value): + if not self._validator(value): + return False + + try: + item = next(self[value]) + except StopIteration: + return False + else: + self._cache[value].appendleft(item) + + return True + + def _get_values(self, value): + """ + Helper to yield items from the parent iterator that match *value*. + Items that don't match are stored in the local cache as they + are encountered. + """ + while True: + # If we've cached some items that match the target value, emit + # the first one and evict it from the cache. + if self._cache[value]: + yield self._cache[value].popleft() + # Otherwise we need to advance the parent iterator to search for + # a matching item, caching the rest. + else: + while True: + try: + item = next(self._it) + except StopIteration: + return + item_value = self._key(item) + if item_value == value: + yield item + break + elif self._validator(item_value): + self._cache[item_value].append(item) + + def __iter__(self): + for item in self._it: + item_value = self._key(item) + if self._validator(item_value): + self._cache[item_value].append(item) + + yield from self._cache.keys() + + def __getitem__(self, value): + if not self._validator(value): + return iter(()) + + return self._get_values(value) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_meta.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_meta.py new file mode 100644 index 0000000000000000000000000000000000000000..0c20eff3da75223a5ca76a1743b7c5b8fa1dc1f6 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_meta.py @@ -0,0 +1,71 @@ +from __future__ import annotations + +import os +from collections.abc import Iterator +from typing import ( + Any, + Protocol, + TypeVar, + overload, +) + +_T = TypeVar("_T") + + +class PackageMetadata(Protocol): + def __len__(self) -> int: ... # pragma: no cover + + def __contains__(self, item: str) -> bool: ... # pragma: no cover + + def __getitem__(self, key: str) -> str: ... # pragma: no cover + + def __iter__(self) -> Iterator[str]: ... # pragma: no cover + + @overload + def get( + self, name: str, failobj: None = None + ) -> str | None: ... # pragma: no cover + + @overload + def get(self, name: str, failobj: _T) -> str | _T: ... # pragma: no cover + + # overload per python/importlib_metadata#435 + @overload + def get_all( + self, name: str, failobj: None = None + ) -> list[Any] | None: ... # pragma: no cover + + @overload + def get_all(self, name: str, failobj: _T) -> list[Any] | _T: + """ + Return all values associated with a possibly multi-valued key. + """ + + @property + def json(self) -> dict[str, str | list[str]]: + """ + A JSON-compatible form of the metadata. + """ + + +class SimplePath(Protocol): + """ + A minimal subset of pathlib.Path required by Distribution. + """ + + def joinpath( + self, other: str | os.PathLike[str] + ) -> SimplePath: ... # pragma: no cover + + def __truediv__( + self, other: str | os.PathLike[str] + ) -> SimplePath: ... # pragma: no cover + + @property + def parent(self) -> SimplePath: ... # pragma: no cover + + def read_text(self, encoding=None) -> str: ... # pragma: no cover + + def read_bytes(self) -> bytes: ... # pragma: no cover + + def exists(self) -> bool: ... # pragma: no cover diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_text.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_text.py new file mode 100644 index 0000000000000000000000000000000000000000..c88cfbb2349c6401336bc5ba6623f51afd1eb59d --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_text.py @@ -0,0 +1,99 @@ +import re + +from ._functools import method_cache + + +# from jaraco.text 3.5 +class FoldedCase(str): + """ + A case insensitive string class; behaves just like str + except compares equal when the only variation is case. + + >>> s = FoldedCase('hello world') + + >>> s == 'Hello World' + True + + >>> 'Hello World' == s + True + + >>> s != 'Hello World' + False + + >>> s.index('O') + 4 + + >>> s.split('O') + ['hell', ' w', 'rld'] + + >>> sorted(map(FoldedCase, ['GAMMA', 'alpha', 'Beta'])) + ['alpha', 'Beta', 'GAMMA'] + + Sequence membership is straightforward. + + >>> "Hello World" in [s] + True + >>> s in ["Hello World"] + True + + You may test for set inclusion, but candidate and elements + must both be folded. + + >>> FoldedCase("Hello World") in {s} + True + >>> s in {FoldedCase("Hello World")} + True + + String inclusion works as long as the FoldedCase object + is on the right. + + >>> "hello" in FoldedCase("Hello World") + True + + But not if the FoldedCase object is on the left: + + >>> FoldedCase('hello') in 'Hello World' + False + + In that case, use in_: + + >>> FoldedCase('hello').in_('Hello World') + True + + >>> FoldedCase('hello') > FoldedCase('Hello') + False + """ + + def __lt__(self, other): + return self.lower() < other.lower() + + def __gt__(self, other): + return self.lower() > other.lower() + + def __eq__(self, other): + return self.lower() == other.lower() + + def __ne__(self, other): + return self.lower() != other.lower() + + def __hash__(self): + return hash(self.lower()) + + def __contains__(self, other): + return super().lower().__contains__(other.lower()) + + def in_(self, other): + "Does self appear in other?" + return self in FoldedCase(other) + + # cache lower since it's likely to be called frequently. + @method_cache + def lower(self): + return super().lower() + + def index(self, sub): + return self.lower().index(sub.lower()) + + def split(self, splitter=' ', maxsplit=0): + pattern = re.compile(re.escape(splitter), re.I) + return pattern.split(self, maxsplit) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_typing.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_typing.py new file mode 100644 index 0000000000000000000000000000000000000000..32b1d2b98ac987e8361f60362b8bdabcdc6fb1c8 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/_typing.py @@ -0,0 +1,15 @@ +import functools +import typing + +from ._meta import PackageMetadata + +md_none = functools.partial(typing.cast, PackageMetadata) +""" +Suppress type errors for optional metadata. + +Although Distribution.metadata can return None when metadata is corrupt +and thus None, allow callers to assume it's not None and crash if +that's the case. + +# python/importlib_metadata#493 +""" diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/compat/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/compat/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/compat/py311.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/compat/py311.py new file mode 100644 index 0000000000000000000000000000000000000000..3a5327436f9b1d9eae371e321c491a270634b3cf --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/compat/py311.py @@ -0,0 +1,22 @@ +import os +import pathlib +import sys +import types + + +def wrap(path): # pragma: no cover + """ + Workaround for https://github.com/python/cpython/issues/84538 + to add backward compatibility for walk_up=True. + An example affected package is dask-labextension, which uses + jupyter-packaging to install JupyterLab javascript files outside + of site-packages. + """ + + def relative_to(root, *, walk_up=False): + return pathlib.Path(os.path.relpath(path, root)) + + return types.SimpleNamespace(relative_to=relative_to) + + +relative_fix = wrap if sys.version_info < (3, 12) else lambda x: x diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/compat/py39.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/compat/py39.py new file mode 100644 index 0000000000000000000000000000000000000000..3eb9c01ecbbdcdf7b79d8840ee91c2fe7a734a1c --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/compat/py39.py @@ -0,0 +1,42 @@ +""" +Compatibility layer with Python 3.8/3.9 +""" + +from __future__ import annotations + +from typing import TYPE_CHECKING, Any + +if TYPE_CHECKING: # pragma: no cover + # Prevent circular imports on runtime. + from .. import Distribution, EntryPoint +else: + Distribution = EntryPoint = Any + +from .._typing import md_none + + +def normalized_name(dist: Distribution) -> str | None: + """ + Honor name normalization for distributions that don't provide ``_normalized_name``. + """ + try: + return dist._normalized_name + except AttributeError: + from .. import Prepared # -> delay to prevent circular imports. + + return Prepared.normalize( + getattr(dist, "name", None) or md_none(dist.metadata)['Name'] + ) + + +def ep_matches(ep: EntryPoint, **params) -> bool: + """ + Workaround for ``EntryPoint`` objects without the ``matches`` method. + """ + try: + return ep.matches(**params) + except AttributeError: + from .. import EntryPoint # -> delay to prevent circular imports. + + # Reconstruct the EntryPoint object to make sure it is compatible. + return EntryPoint(ep.name, ep.value, ep.group).matches(**params) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/diagnose.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/diagnose.py new file mode 100644 index 0000000000000000000000000000000000000000..e405471ac4d94371b1ee9b1622227ff76b337180 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/diagnose.py @@ -0,0 +1,21 @@ +import sys + +from . import Distribution + + +def inspect(path): + print("Inspecting", path) + dists = list(Distribution.discover(path=[path])) + if not dists: + return + print("Found", len(dists), "packages:", end=' ') + print(', '.join(dist.name for dist in dists)) + + +def run(): + for path in sys.path: + inspect(path) + + +if __name__ == '__main__': + run() diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/py.typed b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/importlib_metadata/py.typed new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/INSTALLER new file mode 100644 index 0000000000000000000000000000000000000000..f79e4cb9aaf0b2d9e8ba78861e2071317b2384b3 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/INSTALLER @@ -0,0 +1 @@ +conda \ No newline at end of file diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..1bb5a44356f00884a71ceeefd24ded6caaba2418 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/LICENSE @@ -0,0 +1,17 @@ +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to +deal in the Software without restriction, including without limitation the +rights to use, copy, modify, merge, publish, distribute, sublicense, and/or +sell copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS +IN THE SOFTWARE. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/METADATA new file mode 100644 index 0000000000000000000000000000000000000000..797b9da7334a85347e0439d48c11ee0d1b101f49 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/METADATA @@ -0,0 +1,96 @@ +Metadata-Version: 2.1 +Name: jaraco.text +Version: 4.0.0 +Summary: Module for text manipulation +Author-email: "Jason R. Coombs" +Project-URL: Source, https://github.com/jaraco/jaraco.text +Classifier: Development Status :: 5 - Production/Stable +Classifier: Intended Audience :: Developers +Classifier: License :: OSI Approved :: MIT License +Classifier: Programming Language :: Python :: 3 +Classifier: Programming Language :: Python :: 3 :: Only +Requires-Python: >=3.8 +Description-Content-Type: text/x-rst +License-File: LICENSE +Requires-Dist: jaraco.functools +Requires-Dist: jaraco.context >=4.1 +Requires-Dist: autocommand +Requires-Dist: more-itertools +Requires-Dist: importlib-resources ; python_version < "3.9" +Provides-Extra: doc +Requires-Dist: sphinx >=3.5 ; extra == 'doc' +Requires-Dist: jaraco.packaging >=9.3 ; extra == 'doc' +Requires-Dist: rst.linker >=1.9 ; extra == 'doc' +Requires-Dist: furo ; extra == 'doc' +Requires-Dist: sphinx-lint ; extra == 'doc' +Requires-Dist: jaraco.tidelift >=1.4 ; extra == 'doc' +Provides-Extra: inflect +Requires-Dist: inflect ; extra == 'inflect' +Provides-Extra: test +Requires-Dist: pytest !=8.1.*,>=6 ; extra == 'test' +Requires-Dist: pytest-checkdocs >=2.4 ; extra == 'test' +Requires-Dist: pytest-cov ; extra == 'test' +Requires-Dist: pytest-mypy ; extra == 'test' +Requires-Dist: pytest-enabler >=2.2 ; extra == 'test' +Requires-Dist: pathlib2 ; (python_version < "3.10") and extra == 'test' +Requires-Dist: pytest-ruff >=0.2.1 ; (sys_platform != "cygwin") and extra == 'test' + +.. image:: https://img.shields.io/pypi/v/jaraco.text.svg + :target: https://pypi.org/project/jaraco.text + +.. image:: https://img.shields.io/pypi/pyversions/jaraco.text.svg + +.. image:: https://github.com/jaraco/jaraco.text/actions/workflows/main.yml/badge.svg + :target: https://github.com/jaraco/jaraco.text/actions?query=workflow%3A%22tests%22 + :alt: tests + +.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json + :target: https://github.com/astral-sh/ruff + :alt: Ruff + +.. image:: https://readthedocs.org/projects/jaracotext/badge/?version=latest + :target: https://jaracotext.readthedocs.io/en/latest/?badge=latest + +.. image:: https://img.shields.io/badge/skeleton-2024-informational + :target: https://blog.jaraco.com/skeleton + +.. image:: https://tidelift.com/badges/package/pypi/jaraco.text + :target: https://tidelift.com/subscription/pkg/pypi-jaraco.text?utm_source=pypi-jaraco.text&utm_medium=readme + + +This package provides handy routines for dealing with text, such as +wrapping, substitution, trimming, stripping, prefix and suffix removal, +line continuation, indentation, comment processing, identifier processing, +values parsing, case insensitive comparison, and more. See the docs +(linked in the badge above) for the detailed documentation and examples. + +Layouts +======= + +One of the features of this package is the layouts module, which +provides a simple example of translating keystrokes from one keyboard +layout to another:: + + echo qwerty | python -m jaraco.text.to-dvorak + ',.pyf + echo "',.pyf" | python -m jaraco.text.to-qwerty + qwerty + +Newline Reporting +================= + +Need to know what newlines appear in a file? + +:: + + $ python -m jaraco.text.show-newlines README.rst + newline is '\n' + +For Enterprise +============== + +Available as part of the Tidelift Subscription. + +This project and the maintainers of thousands of other packages are working with Tidelift to deliver one enterprise subscription that covers all of the open source you use. + +`Learn more `_. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/RECORD 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a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/WHEEL new file mode 100644 index 0000000000000000000000000000000000000000..ecaf39f3c3df8b0075a2951da9b1a27fcb08a173 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/WHEEL @@ -0,0 +1,5 @@ +Wheel-Version: 1.0 +Generator: setuptools (71.1.0) +Root-Is-Purelib: true +Tag: py3-none-any + diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/top_level.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/top_level.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6205a5f19a533fd30f90a433e610325ff02f989 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco.text-4.0.0.dist-info/top_level.txt @@ -0,0 +1 @@ +jaraco diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/context/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/context/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..41ad609edd407ac93f87731d07435a25a3d6435d --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/context/__init__.py @@ -0,0 +1,367 @@ +from __future__ import annotations + +import contextlib +import errno +import functools +import operator +import os +import platform +import shutil +import stat +import subprocess +import sys +import tempfile +import urllib.request +from collections.abc import Iterator + +if sys.version_info < (3, 12): + from backports import tarfile +else: + import tarfile + + +@contextlib.contextmanager +def pushd(dir: str | os.PathLike) -> Iterator[str | os.PathLike]: + """ + >>> tmp_path = getfixture('tmp_path') + >>> with pushd(tmp_path): + ... assert os.getcwd() == os.fspath(tmp_path) + >>> assert os.getcwd() != os.fspath(tmp_path) + """ + + orig = os.getcwd() + os.chdir(dir) + try: + yield dir + finally: + os.chdir(orig) + + +@contextlib.contextmanager +def tarball( + url, target_dir: str | os.PathLike | None = None +) -> Iterator[str | os.PathLike]: + """ + Get a URL to a tarball, download, extract, yield, then clean up. + + Assumes everything in the tarball is prefixed with a common + directory. That common path is stripped and the contents + are extracted to ``target_dir``, similar to passing + ``-C {target} --strip-components 1`` to the ``tar`` command. + + Uses the streaming protocol to extract the contents from a + stream in a single pass without loading the whole file into + memory. + + >>> import urllib.request + >>> url = getfixture('tarfile_served') + >>> target = getfixture('tmp_path') / 'out' + >>> tb = tarball(url, target_dir=target) + >>> import pathlib + >>> with tb as extracted: + ... contents = pathlib.Path(extracted, 'contents.txt').read_text(encoding='utf-8') + >>> assert not os.path.exists(extracted) + + If the target is not specified, contents are extracted to a + directory relative to the current working directory named after + the name of the file as extracted from the URL. + + >>> target = getfixture('tmp_path') + >>> with pushd(target), tarball(url): + ... target.joinpath('served').is_dir() + True + """ + if target_dir is None: + target_dir = os.path.basename(url).replace('.tar.gz', '').replace('.tgz', '') + os.mkdir(target_dir) + try: + req = urllib.request.urlopen(url) + with tarfile.open(fileobj=req, mode='r|*') as tf: + tf.extractall(path=target_dir, filter=_default_filter) + yield target_dir + finally: + shutil.rmtree(target_dir) + + +def _compose_tarfile_filters(*filters): + def compose_two(f1, f2): + return lambda member, path: f1(f2(member, path), path) + + return functools.reduce(compose_two, filters, lambda member, path: member) + + +def strip_first_component( + member: tarfile.TarInfo, + path, +) -> tarfile.TarInfo: + _, member.name = member.name.split('/', 1) + return member + + +_default_filter = _compose_tarfile_filters(tarfile.data_filter, strip_first_component) + + +def _compose(*cmgrs): + """ + Compose any number of dependent context managers into a single one. + + The last, innermost context manager may take arbitrary arguments, but + each successive context manager should accept the result from the + previous as a single parameter. + + Like :func:`jaraco.functools.compose`, behavior works from right to + left, so the context manager should be indicated from outermost to + innermost. + + Example, to create a context manager to change to a temporary + directory: + + >>> temp_dir_as_cwd = _compose(pushd, temp_dir) + >>> with temp_dir_as_cwd() as dir: + ... assert os.path.samefile(os.getcwd(), dir) + """ + + def compose_two(inner, outer): + def composed(*args, **kwargs): + with inner(*args, **kwargs) as saved, outer(saved) as res: + yield res + + return contextlib.contextmanager(composed) + + return functools.reduce(compose_two, reversed(cmgrs)) + + +tarball_cwd = _compose(pushd, tarball) +""" +A tarball context with the current working directory pointing to the contents. +""" + + +def remove_readonly(func, path, exc_info): + """ + Add support for removing read-only files on Windows. + """ + _, exc, _ = exc_info + if func in (os.rmdir, os.remove, os.unlink) and exc.errno == errno.EACCES: + # change the file to be readable,writable,executable: 0777 + os.chmod(path, stat.S_IRWXU | stat.S_IRWXG | stat.S_IRWXO) + # retry + func(path) + else: + raise + + +def robust_remover(): + return ( + functools.partial(shutil.rmtree, onerror=remove_readonly) + if platform.system() == 'Windows' + else shutil.rmtree + ) + + +@contextlib.contextmanager +def temp_dir(remover=shutil.rmtree): + """ + Create a temporary directory context. Pass a custom remover + to override the removal behavior. + + >>> import pathlib + >>> with temp_dir() as the_dir: + ... assert os.path.isdir(the_dir) + >>> assert not os.path.exists(the_dir) + """ + temp_dir = tempfile.mkdtemp() + try: + yield temp_dir + finally: + remover(temp_dir) + + +robust_temp_dir = functools.partial(temp_dir, remover=robust_remover()) + + +@contextlib.contextmanager +def repo_context( + url, branch: str | None = None, quiet: bool = True, dest_ctx=robust_temp_dir +): + """ + Check out the repo indicated by url. + + If dest_ctx is supplied, it should be a context manager + to yield the target directory for the check out. + + >>> getfixture('ensure_git') + >>> getfixture('needs_internet') + >>> repo = repo_context('https://github.com/jaraco/jaraco.context') + >>> with repo as dest: + ... listing = os.listdir(dest) + >>> 'README.rst' in listing + True + """ + exe = 'git' if 'git' in url else 'hg' + with dest_ctx() as repo_dir: + cmd = [exe, 'clone', url, repo_dir] + cmd.extend(['--branch', branch] * bool(branch)) + stream = subprocess.DEVNULL if quiet else None + subprocess.check_call(cmd, stdout=stream, stderr=stream) + yield repo_dir + + +class ExceptionTrap: + """ + A context manager that will catch certain exceptions and provide an + indication they occurred. + + >>> with ExceptionTrap() as trap: + ... raise Exception() + >>> bool(trap) + True + + >>> with ExceptionTrap() as trap: + ... pass + >>> bool(trap) + False + + >>> with ExceptionTrap(ValueError) as trap: + ... raise ValueError("1 + 1 is not 3") + >>> bool(trap) + True + >>> trap.value + ValueError('1 + 1 is not 3') + >>> trap.tb + + + >>> with ExceptionTrap(ValueError) as trap: + ... raise Exception() + Traceback (most recent call last): + ... + Exception + + >>> bool(trap) + False + """ + + exc_info = None, None, None + + def __init__(self, exceptions=(Exception,)): + self.exceptions = exceptions + + def __enter__(self): + return self + + @property + def type(self): + return self.exc_info[0] + + @property + def value(self): + return self.exc_info[1] + + @property + def tb(self): + return self.exc_info[2] + + def __exit__(self, *exc_info): + type = exc_info[0] + matches = type and issubclass(type, self.exceptions) + if matches: + self.exc_info = exc_info + return matches + + def __bool__(self): + return bool(self.type) + + def raises(self, func, *, _test=bool): + """ + Wrap func and replace the result with the truth + value of the trap (True if an exception occurred). + + First, give the decorator an alias to support Python 3.8 + Syntax. + + >>> raises = ExceptionTrap(ValueError).raises + + Now decorate a function that always fails. + + >>> @raises + ... def fail(): + ... raise ValueError('failed') + >>> fail() + True + """ + + @functools.wraps(func) + def wrapper(*args, **kwargs): + with ExceptionTrap(self.exceptions) as trap: + func(*args, **kwargs) + return _test(trap) + + return wrapper + + def passes(self, func): + """ + Wrap func and replace the result with the truth + value of the trap (True if no exception). + + First, give the decorator an alias to support Python 3.8 + Syntax. + + >>> passes = ExceptionTrap(ValueError).passes + + Now decorate a function that always fails. + + >>> @passes + ... def fail(): + ... raise ValueError('failed') + + >>> fail() + False + """ + return self.raises(func, _test=operator.not_) + + +class suppress(contextlib.suppress, contextlib.ContextDecorator): + """ + A version of contextlib.suppress with decorator support. + + >>> @suppress(KeyError) + ... def key_error(): + ... {}[''] + >>> key_error() + """ + + +class on_interrupt(contextlib.ContextDecorator): + """ + Replace a KeyboardInterrupt with SystemExit(1). + + Useful in conjunction with console entry point functions. + + >>> def do_interrupt(): + ... raise KeyboardInterrupt() + >>> on_interrupt('error')(do_interrupt)() + Traceback (most recent call last): + ... + SystemExit: 1 + >>> on_interrupt('error', code=255)(do_interrupt)() + Traceback (most recent call last): + ... + SystemExit: 255 + >>> on_interrupt('suppress')(do_interrupt)() + >>> with __import__('pytest').raises(KeyboardInterrupt): + ... on_interrupt('ignore')(do_interrupt)() + """ + + def __init__(self, action='error', /, code=1): + self.action = action + self.code = code + + def __enter__(self): + return self + + def __exit__(self, exctype, excinst, exctb): + if exctype is not KeyboardInterrupt or self.action == 'ignore': + return + elif self.action == 'error': + raise SystemExit(self.code) from excinst + return self.action == 'suppress' diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/context/py.typed b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/context/py.typed new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/functools/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/functools/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..df32e2e924bdfb14aa7dfcfc503d22081c1f0d74 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/functools/__init__.py @@ -0,0 +1,722 @@ +from __future__ import annotations + +import collections.abc +import functools +import inspect +import itertools +import operator +import time +import types +import warnings +from typing import Callable, TypeVar + +import more_itertools + + +def compose(*funcs): + """ + Compose any number of unary functions into a single unary function. + + Comparable to + `function composition `_ + in mathematics: + + ``h = g ∘ f`` implies ``h(x) = g(f(x))``. + + In Python, ``h = compose(g, f)``. + + >>> import textwrap + >>> expected = str.strip(textwrap.dedent(compose.__doc__)) + >>> strip_and_dedent = compose(str.strip, textwrap.dedent) + >>> strip_and_dedent(compose.__doc__) == expected + True + + Compose also allows the innermost function to take arbitrary arguments. + + >>> round_three = lambda x: round(x, ndigits=3) + >>> f = compose(round_three, int.__truediv__) + >>> [f(3*x, x+1) for x in range(1,10)] + [1.5, 2.0, 2.25, 2.4, 2.5, 2.571, 2.625, 2.667, 2.7] + """ + + def compose_two(f1, f2): + return lambda *args, **kwargs: f1(f2(*args, **kwargs)) + + return functools.reduce(compose_two, funcs) + + +def once(func): + """ + Decorate func so it's only ever called the first time. + + This decorator can ensure that an expensive or non-idempotent function + will not be expensive on subsequent calls and is idempotent. + + >>> add_three = once(lambda a: a+3) + >>> add_three(3) + 6 + >>> add_three(9) + 6 + >>> add_three('12') + 6 + + To reset the stored value, simply clear the property ``saved_result``. + + >>> del add_three.saved_result + >>> add_three(9) + 12 + >>> add_three(8) + 12 + + Or invoke 'reset()' on it. + + >>> add_three.reset() + >>> add_three(-3) + 0 + >>> add_three(0) + 0 + """ + + @functools.wraps(func) + def wrapper(*args, **kwargs): + if not hasattr(wrapper, 'saved_result'): + wrapper.saved_result = func(*args, **kwargs) + return wrapper.saved_result + + wrapper.reset = lambda: vars(wrapper).__delitem__('saved_result') + return wrapper + + +def method_cache(method, cache_wrapper=functools.lru_cache()): + """ + Wrap lru_cache to support storing the cache data in the object instances. + + Abstracts the common paradigm where the method explicitly saves an + underscore-prefixed protected property on first call and returns that + subsequently. + + >>> class MyClass: + ... calls = 0 + ... + ... @method_cache + ... def method(self, value): + ... self.calls += 1 + ... return value + + >>> a = MyClass() + >>> a.method(3) + 3 + >>> for x in range(75): + ... res = a.method(x) + >>> a.calls + 75 + + Note that the apparent behavior will be exactly like that of lru_cache + except that the cache is stored on each instance, so values in one + instance will not flush values from another, and when an instance is + deleted, so are the cached values for that instance. + + >>> b = MyClass() + >>> for x in range(35): + ... res = b.method(x) + >>> b.calls + 35 + >>> a.method(0) + 0 + >>> a.calls + 75 + + Note that if method had been decorated with ``functools.lru_cache()``, + a.calls would have been 76 (due to the cached value of 0 having been + flushed by the 'b' instance). + + Clear the cache with ``.cache_clear()`` + + >>> a.method.cache_clear() + + Same for a method that hasn't yet been called. + + >>> c = MyClass() + >>> c.method.cache_clear() + + Another cache wrapper may be supplied: + + >>> cache = functools.lru_cache(maxsize=2) + >>> MyClass.method2 = method_cache(lambda self: 3, cache_wrapper=cache) + >>> a = MyClass() + >>> a.method2() + 3 + + Caution - do not subsequently wrap the method with another decorator, such + as ``@property``, which changes the semantics of the function. + + See also + http://code.activestate.com/recipes/577452-a-memoize-decorator-for-instance-methods/ + for another implementation and additional justification. + """ + + def wrapper(self, *args, **kwargs): + # it's the first call, replace the method with a cached, bound method + bound_method = types.MethodType(method, self) + cached_method = cache_wrapper(bound_method) + setattr(self, method.__name__, cached_method) + return cached_method(*args, **kwargs) + + # Support cache clear even before cache has been created. + wrapper.cache_clear = lambda: None + + return _special_method_cache(method, cache_wrapper) or wrapper + + +def _special_method_cache(method, cache_wrapper): + """ + Because Python treats special methods differently, it's not + possible to use instance attributes to implement the cached + methods. + + Instead, install the wrapper method under a different name + and return a simple proxy to that wrapper. + + https://github.com/jaraco/jaraco.functools/issues/5 + """ + name = method.__name__ + special_names = '__getattr__', '__getitem__' + + if name not in special_names: + return None + + wrapper_name = '__cached' + name + + def proxy(self, /, *args, **kwargs): + if wrapper_name not in vars(self): + bound = types.MethodType(method, self) + cache = cache_wrapper(bound) + setattr(self, wrapper_name, cache) + else: + cache = getattr(self, wrapper_name) + return cache(*args, **kwargs) + + return proxy + + +def apply(transform): + """ + Decorate a function with a transform function that is + invoked on results returned from the decorated function. + + >>> @apply(reversed) + ... def get_numbers(start): + ... "doc for get_numbers" + ... return range(start, start+3) + >>> list(get_numbers(4)) + [6, 5, 4] + >>> get_numbers.__doc__ + 'doc for get_numbers' + """ + + def wrap(func): + return functools.wraps(func)(compose(transform, func)) + + return wrap + + +def result_invoke(action): + r""" + Decorate a function with an action function that is + invoked on the results returned from the decorated + function (for its side effect), then return the original + result. + + >>> @result_invoke(print) + ... def add_two(a, b): + ... return a + b + >>> x = add_two(2, 3) + 5 + >>> x + 5 + """ + + def wrap(func): + @functools.wraps(func) + def wrapper(*args, **kwargs): + result = func(*args, **kwargs) + action(result) + return result + + return wrapper + + return wrap + + +def invoke(f, /, *args, **kwargs): + """ + Call a function for its side effect after initialization. + + The benefit of using the decorator instead of simply invoking a function + after defining it is that it makes explicit the author's intent for the + function to be called immediately. Whereas if one simply calls the + function immediately, it's less obvious if that was intentional or + incidental. It also avoids repeating the name - the two actions, defining + the function and calling it immediately are modeled separately, but linked + by the decorator construct. + + The benefit of having a function construct (opposed to just invoking some + behavior inline) is to serve as a scope in which the behavior occurs. It + avoids polluting the global namespace with local variables, provides an + anchor on which to attach documentation (docstring), keeps the behavior + logically separated (instead of conceptually separated or not separated at + all), and provides potential to re-use the behavior for testing or other + purposes. + + This function is named as a pithy way to communicate, "call this function + primarily for its side effect", or "while defining this function, also + take it aside and call it". It exists because there's no Python construct + for "define and call" (nor should there be, as decorators serve this need + just fine). The behavior happens immediately and synchronously. + + >>> @invoke + ... def func(): print("called") + called + >>> func() + called + + Use functools.partial to pass parameters to the initial call + + >>> @functools.partial(invoke, name='bingo') + ... def func(name): print('called with', name) + called with bingo + """ + f(*args, **kwargs) + return f + + +_T = TypeVar('_T') + + +def passthrough(func: Callable[..., object]) -> Callable[[_T], _T]: + """ + Wrap the function to always return the first parameter. + + >>> passthrough(print)('3') + 3 + '3' + """ + + @functools.wraps(func) + def wrapper(first: _T, *args, **kwargs) -> _T: + func(first, *args, **kwargs) + return first + + return wrapper + + +class Throttler: + """Rate-limit a function (or other callable).""" + + def __init__(self, func, max_rate=float('Inf')): + if isinstance(func, Throttler): + func = func.func + self.func = func + self.max_rate = max_rate + self.reset() + + def reset(self): + self.last_called = 0 + + def __call__(self, *args, **kwargs): + self._wait() + return self.func(*args, **kwargs) + + def _wait(self): + """Ensure at least 1/max_rate seconds from last call.""" + elapsed = time.time() - self.last_called + must_wait = 1 / self.max_rate - elapsed + time.sleep(max(0, must_wait)) + self.last_called = time.time() + + def __get__(self, obj, owner=None): + return first_invoke(self._wait, functools.partial(self.func, obj)) + + +def first_invoke(func1, func2): + """ + Return a function that when invoked will invoke func1 without + any parameters (for its side effect) and then invoke func2 + with whatever parameters were passed, returning its result. + """ + + def wrapper(*args, **kwargs): + func1() + return func2(*args, **kwargs) + + return wrapper + + +method_caller = first_invoke( + lambda: warnings.warn( + '`jaraco.functools.method_caller` is deprecated, ' + 'use `operator.methodcaller` instead', + DeprecationWarning, + stacklevel=3, + ), + operator.methodcaller, +) + + +def retry_call(func, cleanup=lambda: None, retries=0, trap=()): + """ + Given a callable func, trap the indicated exceptions + for up to 'retries' times, invoking cleanup on the + exception. On the final attempt, allow any exceptions + to propagate. + """ + attempts = itertools.count() if retries == float('inf') else range(retries) + for _ in attempts: + try: + return func() + except trap: + cleanup() + + return func() + + +def retry(*r_args, **r_kwargs): + """ + Decorator wrapper for retry_call. Accepts arguments to retry_call + except func and then returns a decorator for the decorated function. + + Ex: + + >>> @retry(retries=3) + ... def my_func(a, b): + ... "this is my funk" + ... print(a, b) + >>> my_func.__doc__ + 'this is my funk' + """ + + def decorate(func): + @functools.wraps(func) + def wrapper(*f_args, **f_kwargs): + bound = functools.partial(func, *f_args, **f_kwargs) + return retry_call(bound, *r_args, **r_kwargs) + + return wrapper + + return decorate + + +def print_yielded(func): + """ + Convert a generator into a function that prints all yielded elements. + + >>> @print_yielded + ... def x(): + ... yield 3; yield None + >>> x() + 3 + None + """ + print_all = functools.partial(map, print) + print_results = compose(more_itertools.consume, print_all, func) + return functools.wraps(func)(print_results) + + +def pass_none(func): + """ + Wrap func so it's not called if its first param is None. + + >>> print_text = pass_none(print) + >>> print_text('text') + text + >>> print_text(None) + """ + + @functools.wraps(func) + def wrapper(param, /, *args, **kwargs): + if param is not None: + return func(param, *args, **kwargs) + return None + + return wrapper + + +def none_as(value, replacement=None): + """ + >>> none_as(None, 'foo') + 'foo' + >>> none_as('bar', 'foo') + 'bar' + """ + return replacement if value is None else value + + +def assign_params(func, namespace): + """ + Assign parameters from namespace where func solicits. + + >>> def func(x, y=3): + ... print(x, y) + >>> assigned = assign_params(func, dict(x=2, z=4)) + >>> assigned() + 2 3 + + The usual errors are raised if a function doesn't receive + its required parameters: + + >>> assigned = assign_params(func, dict(y=3, z=4)) + >>> assigned() + Traceback (most recent call last): + TypeError: func() ...argument... + + It even works on methods: + + >>> class Handler: + ... def meth(self, arg): + ... print(arg) + >>> assign_params(Handler().meth, dict(arg='crystal', foo='clear'))() + crystal + """ + sig = inspect.signature(func) + params = sig.parameters.keys() + call_ns = {k: namespace[k] for k in params if k in namespace} + return functools.partial(func, **call_ns) + + +def save_method_args(method): + """ + Wrap a method such that when it is called, the args and kwargs are + saved on the method. + + >>> class MyClass: + ... @save_method_args + ... def method(self, a, b): + ... print(a, b) + >>> my_ob = MyClass() + >>> my_ob.method(1, 2) + 1 2 + >>> my_ob._saved_method.args + (1, 2) + >>> my_ob._saved_method.kwargs + {} + >>> my_ob.method(a=3, b='foo') + 3 foo + >>> my_ob._saved_method.args + () + >>> my_ob._saved_method.kwargs == dict(a=3, b='foo') + True + + The arguments are stored on the instance, allowing for + different instance to save different args. + + >>> your_ob = MyClass() + >>> your_ob.method({str('x'): 3}, b=[4]) + {'x': 3} [4] + >>> your_ob._saved_method.args + ({'x': 3},) + >>> my_ob._saved_method.args + () + """ + args_and_kwargs = collections.namedtuple('args_and_kwargs', 'args kwargs') # noqa: PYI024 # Internal; stubs used for typing + + @functools.wraps(method) + def wrapper(self, /, *args, **kwargs): + attr_name = '_saved_' + method.__name__ + attr = args_and_kwargs(args, kwargs) + setattr(self, attr_name, attr) + return method(self, *args, **kwargs) + + return wrapper + + +def except_(*exceptions, replace=None, use=None): + """ + Replace the indicated exceptions, if raised, with the indicated + literal replacement or evaluated expression (if present). + + >>> safe_int = except_(ValueError)(int) + >>> safe_int('five') + >>> safe_int('5') + 5 + + Specify a literal replacement with ``replace``. + + >>> safe_int_r = except_(ValueError, replace=0)(int) + >>> safe_int_r('five') + 0 + + Provide an expression to ``use`` to pass through particular parameters. + + >>> safe_int_pt = except_(ValueError, use='args[0]')(int) + >>> safe_int_pt('five') + 'five' + + """ + + def decorate(func): + @functools.wraps(func) + def wrapper(*args, **kwargs): + try: + return func(*args, **kwargs) + except exceptions: + try: + return eval(use) + except TypeError: + return replace + + return wrapper + + return decorate + + +def identity(x): + """ + Return the argument. + + >>> o = object() + >>> identity(o) is o + True + """ + return x + + +def bypass_when(check, *, _op=identity): + """ + Decorate a function to return its parameter when ``check``. + + >>> bypassed = [] # False + + >>> @bypass_when(bypassed) + ... def double(x): + ... return x * 2 + >>> double(2) + 4 + >>> bypassed[:] = [object()] # True + >>> double(2) + 2 + """ + + def decorate(func): + @functools.wraps(func) + def wrapper(param, /): + return param if _op(check) else func(param) + + return wrapper + + return decorate + + +def bypass_unless(check): + """ + Decorate a function to return its parameter unless ``check``. + + >>> enabled = [object()] # True + + >>> @bypass_unless(enabled) + ... def double(x): + ... return x * 2 + >>> double(2) + 4 + >>> del enabled[:] # False + >>> double(2) + 2 + """ + return bypass_when(check, _op=operator.not_) + + +@functools.singledispatch +def _splat_inner(args, func): + """Splat args to func.""" + return func(*args) + + +@_splat_inner.register +def _(args: collections.abc.Mapping, func): + """Splat kargs to func as kwargs.""" + return func(**args) + + +def splat(func): + """ + Wrap func to expect its parameters to be passed positionally in a tuple. + + Has a similar effect to that of ``itertools.starmap`` over + simple ``map``. + + >>> pairs = [(-1, 1), (0, 2)] + >>> more_itertools.consume(itertools.starmap(print, pairs)) + -1 1 + 0 2 + >>> more_itertools.consume(map(splat(print), pairs)) + -1 1 + 0 2 + + The approach generalizes to other iterators that don't have a "star" + equivalent, such as a "starfilter". + + >>> list(filter(splat(operator.add), pairs)) + [(0, 2)] + + Splat also accepts a mapping argument. + + >>> def is_nice(msg, code): + ... return "smile" in msg or code == 0 + >>> msgs = [ + ... dict(msg='smile!', code=20), + ... dict(msg='error :(', code=1), + ... dict(msg='unknown', code=0), + ... ] + >>> for msg in filter(splat(is_nice), msgs): + ... print(msg) + {'msg': 'smile!', 'code': 20} + {'msg': 'unknown', 'code': 0} + """ + return functools.wraps(func)(functools.partial(_splat_inner, func=func)) + + +_T = TypeVar('_T') + + +def chainable(method: Callable[[_T, ...], None]) -> Callable[[_T, ...], _T]: + """ + Wrap an instance method to always return self. + + + >>> class Dingus: + ... @chainable + ... def set_attr(self, name, val): + ... setattr(self, name, val) + >>> d = Dingus().set_attr('a', 'eh!') + >>> d.a + 'eh!' + >>> d2 = Dingus().set_attr('a', 'eh!').set_attr('b', 'bee!') + >>> d2.a + d2.b + 'eh!bee!' + + Enforces that the return value is null. + + >>> class BorkedDingus: + ... @chainable + ... def set_attr(self, name, val): + ... setattr(self, name, val) + ... return len(name) + >>> BorkedDingus().set_attr('a', 'eh!') + Traceback (most recent call last): + ... + AssertionError + """ + + @functools.wraps(method) + def wrapper(self, *args, **kwargs): + assert method(self, *args, **kwargs) is None + return self + + return wrapper + + +def noop(*args, **kwargs): + """ + A no-operation function that does nothing. + + >>> noop(1, 2, three=3) + """ diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/functools/__init__.pyi b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/functools/__init__.pyi new file mode 100644 index 0000000000000000000000000000000000000000..6f834bf06d962463dd198c40931ad86546b1a359 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/functools/__init__.pyi @@ -0,0 +1,123 @@ +from collections.abc import Callable, Hashable, Iterator +from functools import partial +from operator import methodcaller +from typing import ( + Any, + Generic, + Protocol, + TypeVar, + overload, +) + +from typing_extensions import Concatenate, ParamSpec, TypeVarTuple, Unpack + +_P = ParamSpec('_P') +_R = TypeVar('_R') +_T = TypeVar('_T') +_Ts = TypeVarTuple('_Ts') +_R1 = TypeVar('_R1') +_R2 = TypeVar('_R2') +_V = TypeVar('_V') +_S = TypeVar('_S') +_R_co = TypeVar('_R_co', covariant=True) + +class _OnceCallable(Protocol[_P, _R]): + saved_result: _R + reset: Callable[[], None] + def __call__(self, *args: _P.args, **kwargs: _P.kwargs) -> _R: ... + +class _ProxyMethodCacheWrapper(Protocol[_R_co]): + cache_clear: Callable[[], None] + def __call__(self, *args: Hashable, **kwargs: Hashable) -> _R_co: ... + +class _MethodCacheWrapper(Protocol[_R_co]): + def cache_clear(self) -> None: ... + def __call__(self, *args: Hashable, **kwargs: Hashable) -> _R_co: ... + +# `compose()` overloads below will cover most use cases. + +@overload +def compose( + __func1: Callable[[_R], _T], + __func2: Callable[_P, _R], + /, +) -> Callable[_P, _T]: ... +@overload +def compose( + __func1: Callable[[_R], _T], + __func2: Callable[[_R1], _R], + __func3: Callable[_P, _R1], + /, +) -> Callable[_P, _T]: ... +@overload +def compose( + __func1: Callable[[_R], _T], + __func2: Callable[[_R2], _R], + __func3: Callable[[_R1], _R2], + __func4: Callable[_P, _R1], + /, +) -> Callable[_P, _T]: ... +def once(func: Callable[_P, _R]) -> _OnceCallable[_P, _R]: ... +def method_cache( + method: Callable[..., _R], + cache_wrapper: Callable[[Callable[..., _R]], _MethodCacheWrapper[_R]] = ..., +) -> _MethodCacheWrapper[_R] | _ProxyMethodCacheWrapper[_R]: ... +def apply( + transform: Callable[[_R], _T], +) -> Callable[[Callable[_P, _R]], Callable[_P, _T]]: ... +def result_invoke( + action: Callable[[_R], Any], +) -> Callable[[Callable[_P, _R]], Callable[_P, _R]]: ... +def invoke( + f: Callable[_P, _R], /, *args: _P.args, **kwargs: _P.kwargs +) -> Callable[_P, _R]: ... + +class Throttler(Generic[_R]): + last_called: float + func: Callable[..., _R] + max_rate: float + def __init__( + self, func: Callable[..., _R] | Throttler[_R], max_rate: float = ... + ) -> None: ... + def reset(self) -> None: ... + def __call__(self, *args: Any, **kwargs: Any) -> _R: ... + def __get__(self, obj: Any, owner: type[Any] | None = ...) -> Callable[..., _R]: ... + +def first_invoke( + func1: Callable[..., Any], func2: Callable[_P, _R] +) -> Callable[_P, _R]: ... + +method_caller: Callable[..., methodcaller] + +def retry_call( + func: Callable[..., _R], + cleanup: Callable[..., None] = ..., + retries: float = ..., + trap: type[BaseException] | tuple[type[BaseException], ...] = ..., +) -> _R: ... +def retry( + cleanup: Callable[..., None] = ..., + retries: float = ..., + trap: type[BaseException] | tuple[type[BaseException], ...] = ..., +) -> Callable[[Callable[..., _R]], Callable[..., _R]]: ... +def print_yielded(func: Callable[_P, Iterator[Any]]) -> Callable[_P, None]: ... +def pass_none( + func: Callable[Concatenate[_T, _P], _R], +) -> Callable[Concatenate[_T, _P], _R]: ... +def assign_params( + func: Callable[..., _R], namespace: dict[str, Any] +) -> partial[_R]: ... +def save_method_args( + method: Callable[Concatenate[_S, _P], _R], +) -> Callable[Concatenate[_S, _P], _R]: ... +def except_( + *exceptions: type[BaseException], replace: Any = ..., use: Any = ... +) -> Callable[[Callable[_P, Any]], Callable[_P, Any]]: ... +def identity(x: _T) -> _T: ... +def bypass_when( + check: _V, *, _op: Callable[[_V], Any] = ... +) -> Callable[[Callable[[_T], _R]], Callable[[_T], _T | _R]]: ... +def bypass_unless( + check: Any, +) -> Callable[[Callable[[_T], _R]], Callable[[_T], _T | _R]]: ... +def splat(func: Callable[[Unpack[_Ts]], _R]) -> Callable[[tuple[Unpack[_Ts]]], _R]: ... diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/functools/py.typed b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/functools/py.typed new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/Lorem ipsum.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/Lorem ipsum.txt new file mode 100644 index 0000000000000000000000000000000000000000..986f944b60b9900c22464a0c027d713854cc204e --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/Lorem ipsum.txt @@ -0,0 +1,2 @@ +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. +Curabitur pretium tincidunt lacus. Nulla gravida orci a odio. Nullam varius, turpis et commodo pharetra, est eros bibendum elit, nec luctus magna felis sollicitudin mauris. Integer in mauris eu nibh euismod gravida. Duis ac tellus et risus vulputate vehicula. Donec lobortis risus a elit. Etiam tempor. Ut ullamcorper, ligula eu tempor congue, eros est euismod turpis, id tincidunt sapien risus a quam. Maecenas fermentum consequat mi. Donec fermentum. Pellentesque malesuada nulla a mi. Duis sapien sem, aliquet nec, commodo eget, consequat quis, neque. Aliquam faucibus, elit ut dictum aliquet, felis nisl adipiscing sapien, sed malesuada diam lacus eget erat. Cras mollis scelerisque nunc. Nullam arcu. Aliquam consequat. Curabitur augue lorem, dapibus quis, laoreet et, pretium ac, nisi. Aenean magna nisl, mollis quis, molestie eu, feugiat in, orci. In hac habitasse platea dictumst. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..8567200ad7fad1ea127ff5f81c5509d96d37cbd7 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/__init__.py @@ -0,0 +1,647 @@ +import functools +import itertools +import re +import textwrap + +from typing import Iterable + +try: + from importlib.resources import files # type: ignore +except ImportError: # pragma: nocover + from importlib_resources import files # type: ignore + +from jaraco.context import ExceptionTrap +from jaraco.functools import compose, method_cache + + +def substitution(old, new): + """ + Return a function that will perform a substitution on a string + """ + return lambda s: s.replace(old, new) + + +def multi_substitution(*substitutions): + """ + Take a sequence of pairs specifying substitutions, and create + a function that performs those substitutions. + + >>> multi_substitution(('foo', 'bar'), ('bar', 'baz'))('foo') + 'baz' + """ + substitutions = itertools.starmap(substitution, substitutions) + # compose function applies last function first, so reverse the + # substitutions to get the expected order. + substitutions = reversed(tuple(substitutions)) + return compose(*substitutions) + + +class FoldedCase(str): + """ + A case insensitive string class; behaves just like str + except compares equal when the only variation is case. + + >>> s = FoldedCase('hello world') + + >>> s == 'Hello World' + True + + >>> 'Hello World' == s + True + + >>> s != 'Hello World' + False + + >>> s.index('O') + 4 + + >>> s.split('O') + ['hell', ' w', 'rld'] + + >>> sorted(map(FoldedCase, ['GAMMA', 'alpha', 'Beta'])) + ['alpha', 'Beta', 'GAMMA'] + + Sequence membership is straightforward. + + >>> "Hello World" in [s] + True + >>> s in ["Hello World"] + True + + Allows testing for set inclusion, but candidate and elements + must both be folded. + + >>> FoldedCase("Hello World") in {s} + True + >>> s in {FoldedCase("Hello World")} + True + + String inclusion works as long as the FoldedCase object + is on the right. + + >>> "hello" in FoldedCase("Hello World") + True + + But not if the FoldedCase object is on the left: + + >>> FoldedCase('hello') in 'Hello World' + False + + In that case, use ``in_``: + + >>> FoldedCase('hello').in_('Hello World') + True + + >>> FoldedCase('hello') > FoldedCase('Hello') + False + + >>> FoldedCase('ß') == FoldedCase('ss') + True + """ + + def __lt__(self, other): + return self.casefold() < other.casefold() + + def __gt__(self, other): + return self.casefold() > other.casefold() + + def __eq__(self, other): + return self.casefold() == other.casefold() + + def __ne__(self, other): + return self.casefold() != other.casefold() + + def __hash__(self): + return hash(self.casefold()) + + def __contains__(self, other): + return super().casefold().__contains__(other.casefold()) + + def in_(self, other): + "Does self appear in other?" + return self in FoldedCase(other) + + # cache casefold since it's likely to be called frequently. + @method_cache + def casefold(self): + return super().casefold() + + def index(self, sub): + return self.casefold().index(sub.casefold()) + + def split(self, splitter=' ', maxsplit=0): + pattern = re.compile(re.escape(splitter), re.I) + return pattern.split(self, maxsplit) + + +# Python 3.8 compatibility +_unicode_trap = ExceptionTrap(UnicodeDecodeError) + + +@_unicode_trap.passes +def is_decodable(value): + r""" + Return True if the supplied value is decodable (using the default + encoding). + + >>> is_decodable(b'\xff') + False + >>> is_decodable(b'\x32') + True + """ + value.decode() + + +def is_binary(value): + r""" + Return True if the value appears to be binary (that is, it's a byte + string and isn't decodable). + + >>> is_binary(b'\xff') + True + >>> is_binary('\xff') + False + """ + return isinstance(value, bytes) and not is_decodable(value) + + +def trim(s): + r""" + Trim something like a docstring to remove the whitespace that + is common due to indentation and formatting. + + >>> trim("\n\tfoo = bar\n\t\tbar = baz\n") + 'foo = bar\n\tbar = baz' + """ + return textwrap.dedent(s).strip() + + +def wrap(s): + """ + Wrap lines of text, retaining existing newlines as + paragraph markers. + + >>> print(wrap(lorem_ipsum)) + Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do + eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad + minim veniam, quis nostrud exercitation ullamco laboris nisi ut + aliquip ex ea commodo consequat. Duis aute irure dolor in + reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla + pariatur. Excepteur sint occaecat cupidatat non proident, sunt in + culpa qui officia deserunt mollit anim id est laborum. + + Curabitur pretium tincidunt lacus. Nulla gravida orci a odio. Nullam + varius, turpis et commodo pharetra, est eros bibendum elit, nec luctus + magna felis sollicitudin mauris. Integer in mauris eu nibh euismod + gravida. Duis ac tellus et risus vulputate vehicula. Donec lobortis + risus a elit. Etiam tempor. Ut ullamcorper, ligula eu tempor congue, + eros est euismod turpis, id tincidunt sapien risus a quam. Maecenas + fermentum consequat mi. Donec fermentum. Pellentesque malesuada nulla + a mi. Duis sapien sem, aliquet nec, commodo eget, consequat quis, + neque. Aliquam faucibus, elit ut dictum aliquet, felis nisl adipiscing + sapien, sed malesuada diam lacus eget erat. Cras mollis scelerisque + nunc. Nullam arcu. Aliquam consequat. Curabitur augue lorem, dapibus + quis, laoreet et, pretium ac, nisi. Aenean magna nisl, mollis quis, + molestie eu, feugiat in, orci. In hac habitasse platea dictumst. + """ + paragraphs = s.splitlines() + wrapped = ('\n'.join(textwrap.wrap(para)) for para in paragraphs) + return '\n\n'.join(wrapped) + + +def unwrap(s): + r""" + Given a multi-line string, return an unwrapped version. + + >>> wrapped = wrap(lorem_ipsum) + >>> wrapped.count('\n') + 20 + >>> unwrapped = unwrap(wrapped) + >>> unwrapped.count('\n') + 1 + >>> print(unwrapped) + Lorem ipsum dolor sit amet, consectetur adipiscing ... + Curabitur pretium tincidunt lacus. Nulla gravida orci ... + + """ + paragraphs = re.split(r'\n\n+', s) + cleaned = (para.replace('\n', ' ') for para in paragraphs) + return '\n'.join(cleaned) + + +lorem_ipsum: str = ( + files(__name__).joinpath('Lorem ipsum.txt').read_text(encoding='utf-8') +) + + +class Splitter: + """object that will split a string with the given arguments for each call + + >>> s = Splitter(',') + >>> s('hello, world, this is your, master calling') + ['hello', ' world', ' this is your', ' master calling'] + """ + + def __init__(self, *args): + self.args = args + + def __call__(self, s): + return s.split(*self.args) + + +def indent(string, prefix=' ' * 4): + """ + >>> indent('foo') + ' foo' + """ + return prefix + string + + +class WordSet(tuple): + """ + Given an identifier, return the words that identifier represents, + whether in camel case, underscore-separated, etc. + + >>> WordSet.parse("camelCase") + ('camel', 'Case') + + >>> WordSet.parse("under_sep") + ('under', 'sep') + + Acronyms should be retained + + >>> WordSet.parse("firstSNL") + ('first', 'SNL') + + >>> WordSet.parse("you_and_I") + ('you', 'and', 'I') + + >>> WordSet.parse("A simple test") + ('A', 'simple', 'test') + + Multiple caps should not interfere with the first cap of another word. + + >>> WordSet.parse("myABCClass") + ('my', 'ABC', 'Class') + + The result is a WordSet, providing access to other forms. + + >>> WordSet.parse("myABCClass").underscore_separated() + 'my_ABC_Class' + + >>> WordSet.parse('a-command').camel_case() + 'ACommand' + + >>> WordSet.parse('someIdentifier').lowered().space_separated() + 'some identifier' + + Slices of the result should return another WordSet. + + >>> WordSet.parse('taken-out-of-context')[1:].underscore_separated() + 'out_of_context' + + >>> WordSet.from_class_name(WordSet()).lowered().space_separated() + 'word set' + + >>> example = WordSet.parse('figured it out') + >>> example.headless_camel_case() + 'figuredItOut' + >>> example.dash_separated() + 'figured-it-out' + + """ + + _pattern = re.compile('([A-Z]?[a-z]+)|([A-Z]+(?![a-z]))') + + def capitalized(self): + return WordSet(word.capitalize() for word in self) + + def lowered(self): + return WordSet(word.lower() for word in self) + + def camel_case(self): + return ''.join(self.capitalized()) + + def headless_camel_case(self): + words = iter(self) + first = next(words).lower() + new_words = itertools.chain((first,), WordSet(words).camel_case()) + return ''.join(new_words) + + def underscore_separated(self): + return '_'.join(self) + + def dash_separated(self): + return '-'.join(self) + + def space_separated(self): + return ' '.join(self) + + def trim_right(self, item): + """ + Remove the item from the end of the set. + + >>> WordSet.parse('foo bar').trim_right('foo') + ('foo', 'bar') + >>> WordSet.parse('foo bar').trim_right('bar') + ('foo',) + >>> WordSet.parse('').trim_right('bar') + () + """ + return self[:-1] if self and self[-1] == item else self + + def trim_left(self, item): + """ + Remove the item from the beginning of the set. + + >>> WordSet.parse('foo bar').trim_left('foo') + ('bar',) + >>> WordSet.parse('foo bar').trim_left('bar') + ('foo', 'bar') + >>> WordSet.parse('').trim_left('bar') + () + """ + return self[1:] if self and self[0] == item else self + + def trim(self, item): + """ + >>> WordSet.parse('foo bar').trim('foo') + ('bar',) + """ + return self.trim_left(item).trim_right(item) + + def __getitem__(self, item): + result = super().__getitem__(item) + if isinstance(item, slice): + result = WordSet(result) + return result + + @classmethod + def parse(cls, identifier): + matches = cls._pattern.finditer(identifier) + return WordSet(match.group(0) for match in matches) + + @classmethod + def from_class_name(cls, subject): + return cls.parse(subject.__class__.__name__) + + +# for backward compatibility +words = WordSet.parse + + +def simple_html_strip(s): + r""" + Remove HTML from the string `s`. + + >>> str(simple_html_strip('')) + '' + + >>> print(simple_html_strip('A stormy day in paradise')) + A stormy day in paradise + + >>> print(simple_html_strip('Somebody tell the truth.')) + Somebody tell the truth. + + >>> print(simple_html_strip('What about
\nmultiple lines?')) + What about + multiple lines? + """ + html_stripper = re.compile('()|(<[^>]*>)|([^<]+)', re.DOTALL) + texts = (match.group(3) or '' for match in html_stripper.finditer(s)) + return ''.join(texts) + + +class SeparatedValues(str): + """ + A string separated by a separator. Overrides __iter__ for getting + the values. + + >>> list(SeparatedValues('a,b,c')) + ['a', 'b', 'c'] + + Whitespace is stripped and empty values are discarded. + + >>> list(SeparatedValues(' a, b , c, ')) + ['a', 'b', 'c'] + """ + + separator = ',' + + def __iter__(self): + parts = self.split(self.separator) + return filter(None, (part.strip() for part in parts)) + + +class Stripper: + r""" + Given a series of lines, find the common prefix and strip it from them. + + >>> lines = [ + ... 'abcdefg\n', + ... 'abc\n', + ... 'abcde\n', + ... ] + >>> res = Stripper.strip_prefix(lines) + >>> res.prefix + 'abc' + >>> list(res.lines) + ['defg\n', '\n', 'de\n'] + + If no prefix is common, nothing should be stripped. + + >>> lines = [ + ... 'abcd\n', + ... '1234\n', + ... ] + >>> res = Stripper.strip_prefix(lines) + >>> res.prefix = '' + >>> list(res.lines) + ['abcd\n', '1234\n'] + """ + + def __init__(self, prefix, lines): + self.prefix = prefix + self.lines = map(self, lines) + + @classmethod + def strip_prefix(cls, lines): + prefix_lines, lines = itertools.tee(lines) + prefix = functools.reduce(cls.common_prefix, prefix_lines) + return cls(prefix, lines) + + def __call__(self, line): + if not self.prefix: + return line + null, prefix, rest = line.partition(self.prefix) + return rest + + @staticmethod + def common_prefix(s1, s2): + """ + Return the common prefix of two lines. + """ + index = min(len(s1), len(s2)) + while s1[:index] != s2[:index]: + index -= 1 + return s1[:index] + + +def remove_prefix(text, prefix): + """ + Remove the prefix from the text if it exists. + + >>> remove_prefix('underwhelming performance', 'underwhelming ') + 'performance' + + >>> remove_prefix('something special', 'sample') + 'something special' + """ + null, prefix, rest = text.rpartition(prefix) + return rest + + +def remove_suffix(text, suffix): + """ + Remove the suffix from the text if it exists. + + >>> remove_suffix('name.git', '.git') + 'name' + + >>> remove_suffix('something special', 'sample') + 'something special' + """ + rest, suffix, null = text.partition(suffix) + return rest + + +def normalize_newlines(text): + r""" + Replace alternate newlines with the canonical newline. + + >>> normalize_newlines('Lorem Ipsum\u2029') + 'Lorem Ipsum\n' + >>> normalize_newlines('Lorem Ipsum\r\n') + 'Lorem Ipsum\n' + >>> normalize_newlines('Lorem Ipsum\x85') + 'Lorem Ipsum\n' + """ + newlines = ['\r\n', '\r', '\n', '\u0085', '\u2028', '\u2029'] + pattern = '|'.join(newlines) + return re.sub(pattern, '\n', text) + + +def _nonblank(str): + return str and not str.startswith('#') + + +@functools.singledispatch +def yield_lines(iterable): + r""" + Yield valid lines of a string or iterable. + + >>> list(yield_lines('')) + [] + >>> list(yield_lines(['foo', 'bar'])) + ['foo', 'bar'] + >>> list(yield_lines('foo\nbar')) + ['foo', 'bar'] + >>> list(yield_lines('\nfoo\n#bar\nbaz #comment')) + ['foo', 'baz #comment'] + >>> list(yield_lines(['foo\nbar', 'baz', 'bing\n\n\n'])) + ['foo', 'bar', 'baz', 'bing'] + """ + return itertools.chain.from_iterable(map(yield_lines, iterable)) + + +@yield_lines.register(str) +def _(text): + return clean(text.splitlines()) + + +def clean(lines: Iterable[str]): + """ + Yield non-blank, non-comment elements from lines. + """ + return filter(_nonblank, map(str.strip, lines)) + + +def drop_comment(line): + """ + Drop comments. + + >>> drop_comment('foo # bar') + 'foo' + + A hash without a space may be in a URL. + + >>> drop_comment('http://example.com/foo#bar') + 'http://example.com/foo#bar' + """ + return line.partition(' #')[0] + + +def join_continuation(lines): + r""" + Join lines continued by a trailing backslash. + + >>> list(join_continuation(['foo \\', 'bar', 'baz'])) + ['foobar', 'baz'] + >>> list(join_continuation(['foo \\', 'bar', 'baz'])) + ['foobar', 'baz'] + >>> list(join_continuation(['foo \\', 'bar \\', 'baz'])) + ['foobarbaz'] + + Not sure why, but... + The character preceding the backslash is also elided. + + >>> list(join_continuation(['goo\\', 'dly'])) + ['godly'] + + A terrible idea, but... + If no line is available to continue, suppress the lines. + + >>> list(join_continuation(['foo', 'bar\\', 'baz\\'])) + ['foo'] + """ + lines = iter(lines) + for item in lines: + while item.endswith('\\'): + try: + item = item[:-2].strip() + next(lines) + except StopIteration: + return + yield item + + +def read_newlines(filename, limit=1024): + r""" + >>> tmp_path = getfixture('tmp_path') + >>> filename = tmp_path / 'out.txt' + >>> _ = filename.write_text('foo\n', newline='', encoding='utf-8') + >>> read_newlines(filename) + '\n' + >>> _ = filename.write_text('foo\r\n', newline='', encoding='utf-8') + >>> read_newlines(filename) + '\r\n' + >>> _ = filename.write_text('foo\r\nbar\nbing\r', newline='', encoding='utf-8') + >>> read_newlines(filename) + ('\r', '\n', '\r\n') + """ + with open(filename, encoding='utf-8') as fp: + fp.read(limit) + return fp.newlines + + +def lines_from(input): + """ + Generate lines from a :class:`importlib.resources.abc.Traversable` path. + + >>> lines = lines_from(files(__name__).joinpath('Lorem ipsum.txt')) + >>> next(lines) + 'Lorem ipsum...' + >>> next(lines) + 'Curabitur pretium...' + """ + with input.open(encoding='utf-8') as stream: + yield from stream diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/layouts.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/layouts.py new file mode 100644 index 0000000000000000000000000000000000000000..9636f0f7b53cb4d1ea5842e1eb62c998ddb91070 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/layouts.py @@ -0,0 +1,25 @@ +qwerty = "-=qwertyuiop[]asdfghjkl;'zxcvbnm,./_+QWERTYUIOP{}ASDFGHJKL:\"ZXCVBNM<>?" +dvorak = "[]',.pyfgcrl/=aoeuidhtns-;qjkxbmwvz{}\"<>PYFGCRL?+AOEUIDHTNS_:QJKXBMWVZ" + + +to_dvorak = str.maketrans(qwerty, dvorak) +to_qwerty = str.maketrans(dvorak, qwerty) + + +def translate(input, translation): + """ + >>> translate('dvorak', to_dvorak) + 'ekrpat' + >>> translate('qwerty', to_qwerty) + 'x,dokt' + """ + return input.translate(translation) + + +def _translate_stream(stream, translation): + """ + >>> import io + >>> _translate_stream(io.StringIO('foo'), to_dvorak) + urr + """ + print(translate(stream.read(), translation)) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/show-newlines.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/show-newlines.py new file mode 100644 index 0000000000000000000000000000000000000000..ef4cc54c9e457728d63e9fb6033950fed074016c --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/show-newlines.py @@ -0,0 +1,32 @@ +import autocommand +import inflect +from more_itertools import always_iterable + +import jaraco.text + + +def report_newlines(filename): + r""" + Report the newlines in the indicated file. + + >>> tmp_path = getfixture('tmp_path') + >>> filename = tmp_path / 'out.txt' + >>> _ = filename.write_text('foo\nbar\n', newline='', encoding='utf-8') + >>> report_newlines(filename) + newline is '\n' + >>> filename = tmp_path / 'out.txt' + >>> _ = filename.write_text('foo\nbar\r\n', newline='', encoding='utf-8') + >>> report_newlines(filename) + newlines are ('\n', '\r\n') + """ + newlines = jaraco.text.read_newlines(filename) + count = len(tuple(always_iterable(newlines))) + engine = inflect.engine() + print( + engine.plural_noun("newline", count), + engine.plural_verb("is", count), + repr(newlines), + ) + + +autocommand.autocommand(__name__)(report_newlines) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/strip-prefix.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/strip-prefix.py new file mode 100644 index 0000000000000000000000000000000000000000..761717a9b9e1f837eeacf0e888822f6fad881361 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/strip-prefix.py @@ -0,0 +1,21 @@ +import sys + +import autocommand + +from jaraco.text import Stripper + + +def strip_prefix(): + r""" + Strip any common prefix from stdin. + + >>> import io, pytest + >>> getfixture('monkeypatch').setattr('sys.stdin', io.StringIO('abcdef\nabc123')) + >>> strip_prefix() + def + 123 + """ + sys.stdout.writelines(Stripper.strip_prefix(sys.stdin).lines) + + +autocommand.autocommand(__name__)(strip_prefix) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/to-dvorak.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/to-dvorak.py new file mode 100644 index 0000000000000000000000000000000000000000..14c8981e441dee59afa715853c87a84796b931fc --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/to-dvorak.py @@ -0,0 +1,5 @@ +import sys + +from . import layouts + +__name__ == '__main__' and layouts._translate_stream(sys.stdin, layouts.to_dvorak) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/to-qwerty.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/to-qwerty.py new file mode 100644 index 0000000000000000000000000000000000000000..23596fda930cde864e643152ec706b6149f130f2 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco/text/to-qwerty.py @@ -0,0 +1,5 @@ +import sys + +from . import layouts + +__name__ == '__main__' and layouts._translate_stream(sys.stdin, layouts.to_qwerty) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/INSTALLER new file mode 100644 index 0000000000000000000000000000000000000000..f79e4cb9aaf0b2d9e8ba78861e2071317b2384b3 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/INSTALLER @@ -0,0 +1 @@ +conda \ No newline at end of file diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/METADATA new file mode 100644 index 0000000000000000000000000000000000000000..8fb5e53da3f958a6566c3c379b50f3e59c04320e --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/METADATA @@ -0,0 +1,82 @@ +Metadata-Version: 2.4 +Name: jaraco.context +Version: 6.1.0 +Summary: Useful decorators and context managers +Author-email: "Jason R. Coombs" +License-Expression: MIT +Project-URL: Source, https://github.com/jaraco/jaraco.context +Classifier: Development Status :: 5 - Production/Stable +Classifier: Intended Audience :: Developers +Classifier: Programming Language :: Python :: 3 +Classifier: Programming Language :: Python :: 3 :: Only +Requires-Python: >=3.9 +Description-Content-Type: text/x-rst +License-File: LICENSE +Requires-Dist: backports.tarfile; python_version < "3.12" +Provides-Extra: test +Requires-Dist: pytest!=8.1.*,>=6; extra == "test" +Requires-Dist: jaraco.test>=5.6.0; extra == "test" +Requires-Dist: portend; extra == "test" +Provides-Extra: doc +Requires-Dist: sphinx>=3.5; extra == "doc" +Requires-Dist: jaraco.packaging>=9.3; extra == "doc" +Requires-Dist: rst.linker>=1.9; extra == "doc" +Requires-Dist: furo; extra == "doc" +Requires-Dist: sphinx-lint; extra == "doc" +Requires-Dist: jaraco.tidelift>=1.4; extra == "doc" +Provides-Extra: check +Requires-Dist: pytest-checkdocs>=2.4; extra == "check" +Requires-Dist: pytest-ruff>=0.2.1; sys_platform != "cygwin" and extra == "check" +Provides-Extra: cover +Requires-Dist: pytest-cov; extra == "cover" +Provides-Extra: enabler +Requires-Dist: pytest-enabler>=3.4; extra == "enabler" +Provides-Extra: type +Requires-Dist: pytest-mypy>=1.0.1; extra == "type" +Requires-Dist: mypy<1.19; platform_python_implementation == "PyPy" and extra == "type" +Dynamic: license-file + +.. image:: https://img.shields.io/pypi/v/jaraco.context.svg + :target: https://pypi.org/project/jaraco.context + +.. image:: https://img.shields.io/pypi/pyversions/jaraco.context.svg + +.. image:: https://github.com/jaraco/jaraco.context/actions/workflows/main.yml/badge.svg + :target: https://github.com/jaraco/jaraco.context/actions?query=workflow%3A%22tests%22 + :alt: tests + +.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json + :target: https://github.com/astral-sh/ruff + :alt: Ruff + +.. image:: https://readthedocs.org/projects/jaracocontext/badge/?version=latest + :target: https://jaracocontext.readthedocs.io/en/latest/?badge=latest + +.. image:: https://img.shields.io/badge/skeleton-2025-informational + :target: https://blog.jaraco.com/skeleton + +.. image:: https://tidelift.com/badges/package/pypi/jaraco.context + :target: https://tidelift.com/subscription/pkg/pypi-jaraco.context?utm_source=pypi-jaraco.context&utm_medium=readme + + +Highlights +========== + +See the docs linked from the badge above for the full details, but here are some features that may be of interest. + +- ``ExceptionTrap`` provides a general-purpose wrapper for trapping exceptions and then acting on the outcome. Includes ``passes`` and ``raises`` decorators to replace the result of a wrapped function by a boolean indicating the outcome of the exception trap. See `this keyring commit `_ for an example of it in production. +- ``suppress`` simply enables ``contextlib.suppress`` as a decorator. +- ``on_interrupt`` is a decorator used by CLI entry points to affect the handling of a ``KeyboardInterrupt``. Inspired by `Lucretiel/autocommand#18 `_. +- ``pushd`` is similar to pytest's ``monkeypatch.chdir`` or path's `default context `_, changes the current working directory for the duration of the context. +- ``tarball`` will download a tarball, extract it, change directory, yield, then clean up after. Convenient when working with web assets. +- ``null`` is there for those times when one code branch needs a context and the other doesn't; this null context provides symmetry across those branches. + + +For Enterprise +============== + +Available as part of the Tidelift Subscription. + +This project and the maintainers of thousands of other packages are working with Tidelift to deliver one enterprise subscription that covers all of the open source you use. + +`Learn more `_. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/RECORD new file mode 100644 index 0000000000000000000000000000000000000000..e5169f66596795d5883da25a272970be0e8acd50 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/RECORD @@ -0,0 +1,9 @@ +jaraco/context/__init__.py,sha256=br1ydYGo1Xr_Pu1anuEdd-QrjUiz_EY5L_5E4C03L4w,9809 +jaraco/context/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 +jaraco_context-6.1.0.dist-info/INSTALLER,sha256=5hhM4Q4mYTT9z6QB6PGpUAW81PGNFrYrdXMj4oM_6ak,2 +jaraco_context-6.1.0.dist-info/METADATA,sha256=BDXr_FIFXFqZdO0gwXG2RUOD6vnbsVCIFLp62XxZ1xI,4270 +jaraco_context-6.1.0.dist-info/RECORD,, +jaraco_context-6.1.0.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 +jaraco_context-6.1.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91 +jaraco_context-6.1.0.dist-info/licenses/LICENSE,sha256=l1WhhRlmbl8PTK49qtPXASvK5IpgCzEjfXXp_hNOZoM,1076 +jaraco_context-6.1.0.dist-info/top_level.txt,sha256=0JnN3LfXH4LIRfXL-QFOGCJzQWZO3ELx4R1d_louoQM,7 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/REQUESTED b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/REQUESTED new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/WHEEL new file mode 100644 index 0000000000000000000000000000000000000000..e7fa31b6f3f78deb1022c1f7927f07d4d16da822 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/WHEEL @@ -0,0 +1,5 @@ +Wheel-Version: 1.0 +Generator: setuptools (80.9.0) +Root-Is-Purelib: true +Tag: py3-none-any + diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/licenses/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/licenses/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..c891f411dc44c70ff121531af2ee189d3da4c871 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/licenses/LICENSE @@ -0,0 +1,18 @@ +MIT License + +Copyright (c) 2026 + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and +associated documentation files (the "Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the +following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial +portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT +LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO +EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER +IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE +USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/top_level.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/top_level.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6205a5f19a533fd30f90a433e610325ff02f989 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_context-6.1.0.dist-info/top_level.txt @@ -0,0 +1 @@ +jaraco diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/INSTALLER new file mode 100644 index 0000000000000000000000000000000000000000..f79e4cb9aaf0b2d9e8ba78861e2071317b2384b3 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/INSTALLER @@ -0,0 +1 @@ +conda \ No newline at end of file diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/METADATA new file mode 100644 index 0000000000000000000000000000000000000000..f2150dd88bea2b8701c2b6199bfc53b1fdb8f9a7 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/METADATA @@ -0,0 +1,69 @@ +Metadata-Version: 2.4 +Name: jaraco.functools +Version: 4.4.0 +Summary: Functools like those found in stdlib +Author-email: "Jason R. Coombs" +License-Expression: MIT +Project-URL: Source, https://github.com/jaraco/jaraco.functools +Classifier: Development Status :: 5 - Production/Stable +Classifier: Intended Audience :: Developers +Classifier: Programming Language :: Python :: 3 +Classifier: Programming Language :: Python :: 3 :: Only +Requires-Python: >=3.9 +Description-Content-Type: text/x-rst +License-File: LICENSE +Requires-Dist: more_itertools +Provides-Extra: test +Requires-Dist: pytest!=8.1.*,>=6; extra == "test" +Requires-Dist: jaraco.classes; extra == "test" +Provides-Extra: doc +Requires-Dist: sphinx>=3.5; extra == "doc" +Requires-Dist: jaraco.packaging>=9.3; extra == "doc" +Requires-Dist: rst.linker>=1.9; extra == "doc" +Requires-Dist: furo; extra == "doc" +Requires-Dist: sphinx-lint; extra == "doc" +Requires-Dist: jaraco.tidelift>=1.4; extra == "doc" +Provides-Extra: check +Requires-Dist: pytest-checkdocs>=2.4; extra == "check" +Requires-Dist: pytest-ruff>=0.2.1; sys_platform != "cygwin" and extra == "check" +Provides-Extra: cover +Requires-Dist: pytest-cov; extra == "cover" +Provides-Extra: enabler +Requires-Dist: pytest-enabler>=3.4; extra == "enabler" +Provides-Extra: type +Requires-Dist: pytest-mypy>=1.0.1; extra == "type" +Requires-Dist: mypy<1.19; platform_python_implementation == "PyPy" and extra == "type" +Dynamic: license-file + +.. image:: https://img.shields.io/pypi/v/jaraco.functools.svg + :target: https://pypi.org/project/jaraco.functools + +.. image:: https://img.shields.io/pypi/pyversions/jaraco.functools.svg + +.. image:: https://github.com/jaraco/jaraco.functools/actions/workflows/main.yml/badge.svg + :target: https://github.com/jaraco/jaraco.functools/actions?query=workflow%3A%22tests%22 + :alt: tests + +.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json + :target: https://github.com/astral-sh/ruff + :alt: Ruff + +.. image:: https://readthedocs.org/projects/jaracofunctools/badge/?version=latest + :target: https://jaracofunctools.readthedocs.io/en/latest/?badge=latest + +.. image:: https://img.shields.io/badge/skeleton-2025-informational + :target: https://blog.jaraco.com/skeleton + +.. image:: https://tidelift.com/badges/package/pypi/jaraco.functools + :target: https://tidelift.com/subscription/pkg/pypi-jaraco.functools?utm_source=pypi-jaraco.functools&utm_medium=readme + +Additional functools in the spirit of stdlib's functools. + +For Enterprise +============== + +Available as part of the Tidelift Subscription. + +This project and the maintainers of thousands of other packages are working with Tidelift to deliver one enterprise subscription that covers all of the open source you use. + +`Learn more `_. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/RECORD new file mode 100644 index 0000000000000000000000000000000000000000..3516c9f0396cc14d4ee246160a425447aad03abe --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/RECORD @@ -0,0 +1,10 @@ +jaraco/functools/__init__.py,sha256=ZJx9cMs2Nvk2xGUl8OjVGkpjdOaNlSzJrN4dGglgX2g,18599 +jaraco/functools/__init__.pyi,sha256=K4DcbnYIHE5QlMxqf9-cVp-WhycrhuTao4J7O7TMq4Y,3907 +jaraco/functools/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 +jaraco_functools-4.4.0.dist-info/INSTALLER,sha256=5hhM4Q4mYTT9z6QB6PGpUAW81PGNFrYrdXMj4oM_6ak,2 +jaraco_functools-4.4.0.dist-info/METADATA,sha256=LnnajcNGmSSr46yLIqP-tWkqeb-fR7vIa2U11hhkGEk,2960 +jaraco_functools-4.4.0.dist-info/RECORD,, +jaraco_functools-4.4.0.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 +jaraco_functools-4.4.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91 +jaraco_functools-4.4.0.dist-info/licenses/LICENSE,sha256=WlfLTbheKi3YjCkGKJCK3VfjRRRJ4KmnH9-zh3b9dZ0,1076 +jaraco_functools-4.4.0.dist-info/top_level.txt,sha256=0JnN3LfXH4LIRfXL-QFOGCJzQWZO3ELx4R1d_louoQM,7 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/REQUESTED b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/REQUESTED new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/WHEEL new file mode 100644 index 0000000000000000000000000000000000000000..e7fa31b6f3f78deb1022c1f7927f07d4d16da822 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/WHEEL @@ -0,0 +1,5 @@ +Wheel-Version: 1.0 +Generator: setuptools (80.9.0) +Root-Is-Purelib: true +Tag: py3-none-any + diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/licenses/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/licenses/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..f60bd572013c6abcb3a82ba9b50d84935de6394f --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/licenses/LICENSE @@ -0,0 +1,18 @@ +MIT License + +Copyright (c) 2025 + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and +associated documentation files (the "Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the +following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial +portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT +LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO +EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER +IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE +USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/top_level.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/top_level.txt new file mode 100644 index 0000000000000000000000000000000000000000..f6205a5f19a533fd30f90a433e610325ff02f989 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/jaraco_functools-4.4.0.dist-info/top_level.txt @@ -0,0 +1 @@ +jaraco diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/INSTALLER new file mode 100644 index 0000000000000000000000000000000000000000..f79e4cb9aaf0b2d9e8ba78861e2071317b2384b3 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/INSTALLER @@ -0,0 +1 @@ +conda \ No newline at end of file diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/METADATA new file mode 100644 index 0000000000000000000000000000000000000000..bb7a3db109905db8cc7f1f2f5047e0b609aaf4ce --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/METADATA @@ -0,0 +1,283 @@ +Metadata-Version: 2.4 +Name: more-itertools +Version: 10.8.0 +Summary: More routines for operating on iterables, beyond itertools +Keywords: itertools,iterator,iteration,filter,peek,peekable,chunk,chunked +Author-email: Erik Rose +Requires-Python: >=3.9 +Description-Content-Type: text/x-rst +License-Expression: MIT +Classifier: Development Status :: 5 - Production/Stable +Classifier: Intended Audience :: Developers +Classifier: Natural Language :: English +Classifier: Programming Language :: Python :: 3 +Classifier: Programming Language :: Python :: 3.9 +Classifier: Programming Language :: Python :: 3.10 +Classifier: Programming Language :: Python :: 3.11 +Classifier: Programming Language :: Python :: 3.12 +Classifier: Programming Language :: Python :: 3.13 +Classifier: Programming Language :: Python :: 3 :: Only +Classifier: Programming Language :: Python :: Implementation :: CPython +Classifier: Programming Language :: Python :: Implementation :: PyPy +Classifier: Topic :: Software Development :: Libraries +License-File: LICENSE +Project-URL: Documentation, https://more-itertools.readthedocs.io/en/stable/ +Project-URL: Homepage, https://github.com/more-itertools/more-itertools + +============== +More Itertools +============== + +.. image:: https://readthedocs.org/projects/more-itertools/badge/?version=latest + :target: https://more-itertools.readthedocs.io/en/stable/ + +Python's ``itertools`` library is a gem - you can compose elegant solutions +for a variety of problems with the functions it provides. In ``more-itertools`` +we collect additional building blocks, recipes, and routines for working with +Python iterables. + ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Grouping | `chunked `_, | +| | `ichunked `_, | +| | `chunked_even `_, | +| | `sliced `_, | +| | `constrained_batches `_, | +| | `distribute `_, | +| | `divide `_, | +| | `split_at `_, | +| | `split_before `_, | +| | `split_after `_, | +| | `split_into `_, | +| | `split_when `_, | +| | `bucket `_, | +| | `unzip `_, | +| | `batched `_, | +| | `grouper `_, | +| | `partition `_, | +| | `transpose `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Lookahead and lookback | `spy `_, | +| | `peekable `_, | +| | `seekable `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Windowing | `windowed `_, | +| | `substrings `_, | +| | `substrings_indexes `_, | +| | `stagger `_, | +| | `windowed_complete `_, | +| | `pairwise `_, | +| | `triplewise `_, | +| | `sliding_window `_, | +| | `subslices `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Augmenting | `count_cycle `_, | +| | `intersperse `_, | +| | `padded `_, | +| | `repeat_each `_, | +| | `mark_ends `_, | +| | `repeat_last `_, | +| | `adjacent `_, | +| | `groupby_transform `_, | +| | `pad_none `_, | +| | `ncycles `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Combining | `collapse `_, | +| | `sort_together `_, | +| | `interleave `_, | +| | `interleave_longest `_, | +| | `interleave_evenly `_, | +| | `interleave_randomly `_, | +| | `zip_offset `_, | +| | `zip_equal `_, | +| | `zip_broadcast `_, | +| | `flatten `_, | +| | `roundrobin `_, | +| | `prepend `_, | +| | `value_chain `_, | +| | `partial_product `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Summarizing | `ilen `_, | +| | `unique_to_each `_, | +| | `sample `_, | +| | `consecutive_groups `_, | +| | `run_length `_, | +| | `map_reduce `_, | +| | `join_mappings `_, | +| | `exactly_n `_, | +| | `is_sorted `_, | +| | `all_equal `_, | +| | `all_unique `_, | +| | `argmin `_, | +| | `argmax `_, | +| | `minmax `_, | +| | `first_true `_, | +| | `quantify `_, | +| | `iequals `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Selecting | `islice_extended `_, | +| | `first `_, | +| | `last `_, | +| | `one `_, | +| | `only `_, | +| | `strictly_n `_, | +| | `strip `_, | +| | `lstrip `_, | +| | `rstrip `_, | +| | `filter_except `_, | +| | `map_except `_, | +| | `filter_map `_, | +| | `iter_suppress `_, | +| | `nth_or_last `_, | +| | `extract `_, | +| | `unique_in_window `_, | +| | `before_and_after `_, | +| | `nth `_, | +| | `take `_, | +| | `tail `_, | +| | `unique_everseen `_, | +| | `unique_justseen `_, | +| | `unique `_, | +| | `duplicates_everseen `_, | +| | `duplicates_justseen `_, | +| | `classify_unique `_, | +| | `longest_common_prefix `_, | +| | `takewhile_inclusive `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Math | `dft `_, | +| | `idft `_, | +| | `convolve `_, | +| | `dotproduct `_, | +| | `matmul `_, | +| | `polynomial_from_roots `_, | +| | `polynomial_derivative `_, | +| | `polynomial_eval `_, | +| | `sum_of_squares `_, | +| | `running_median `_, | +| | `totient `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Integer math | `factor `_, | +| | `is_prime `_, | +| | `multinomial `_, | +| | `nth_prime `_, | +| | `sieve `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Combinatorics | `circular_shifts `_, | +| | `derangements `_, | +| | `gray_product `_, | +| | `outer_product `_, | +| | `partitions `_, | +| | `set_partitions `_, | +| | `powerset `_, | +| | `powerset_of_sets `_ | +| +-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| | `distinct_combinations `_, | +| | `distinct_permutations `_ | +| +-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| | `combination_index `_, | +| | `combination_with_replacement_index `_, | +| | `permutation_index `_, | +| | `product_index `_ | +| +-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| | `nth_combination `_, | +| | `nth_combination_with_replacement `_, | +| | `nth_permutation `_, | +| | `nth_product `_ | +| +-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| | `random_combination `_, | +| | `random_combination_with_replacement `_, | +| | `random_permutation `_, | +| | `random_product `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Wrapping | `always_iterable `_, | +| | `always_reversible `_, | +| | `countable `_, | +| | `consumer `_, | +| | `with_iter `_, | +| | `iter_except `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +| Others | `locate `_, | +| | `rlocate `_, | +| | `replace `_, | +| | `numeric_range `_, | +| | `side_effect `_, | +| | `iterate `_, | +| | `loops `_, | +| | `difference `_, | +| | `make_decorator `_, | +| | `SequenceView `_, | +| | `time_limited `_, | +| | `map_if `_, | +| | `iter_index `_, | +| | `consume `_, | +| | `tabulate `_, | +| | `repeatfunc `_, | +| | `reshape `_, | +| | `doublestarmap `_ | ++------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ + + +Getting started +=============== + +To get started, install the library with `pip `_: + +.. code-block:: shell + + pip install more-itertools + +The recipes from the `itertools docs `_ +are included in the top-level package: + +.. code-block:: python + + >>> from more_itertools import flatten + >>> iterable = [(0, 1), (2, 3)] + >>> list(flatten(iterable)) + [0, 1, 2, 3] + +Several new recipes are available as well: + +.. code-block:: python + + >>> from more_itertools import chunked + >>> iterable = [0, 1, 2, 3, 4, 5, 6, 7, 8] + >>> list(chunked(iterable, 3)) + [[0, 1, 2], [3, 4, 5], [6, 7, 8]] + + >>> from more_itertools import spy + >>> iterable = (x * x for x in range(1, 6)) + >>> head, iterable = spy(iterable, n=3) + >>> list(head) + [1, 4, 9] + >>> list(iterable) + [1, 4, 9, 16, 25] + + + +For the full listing of functions, see the `API documentation `_. + + +Links elsewhere +=============== + +Blog posts about ``more-itertools``: + +* `Yo, I heard you like decorators `__ +* `Tour of Python Itertools `__ (`Alternate `__) +* `Real-World Python More Itertools `_ + + +Development +=========== + +``more-itertools`` is maintained by `@erikrose `_ +and `@bbayles `_, with help from `many others `_. +If you have a problem or suggestion, please file a bug or pull request in this +repository. Thanks for contributing! + + +Version History +=============== + +The version history can be found in `documentation `_. + diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/RECORD new file mode 100644 index 0000000000000000000000000000000000000000..61ef7d6dd02d0a26d3373299cd2efa792fb23165 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/RECORD @@ -0,0 +1,13 @@ +more_itertools-10.8.0.dist-info/INSTALLER,sha256=5hhM4Q4mYTT9z6QB6PGpUAW81PGNFrYrdXMj4oM_6ak,2 +more_itertools-10.8.0.dist-info/METADATA,sha256=arNRUUWr5YsGfwh8hnYxz0z11lP-2BuWQu4SCGw5BLg,39413 +more_itertools-10.8.0.dist-info/RECORD,, +more_itertools-10.8.0.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 +more_itertools-10.8.0.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82 +more_itertools-10.8.0.dist-info/licenses/LICENSE,sha256=CfHIyelBrz5YTVlkHqm4fYPAyw_QB-te85Gn4mQ8GkY,1053 +more_itertools/__init__.py,sha256=5F7E_zpoGcEBW_T_3WE0WYYt8j-gJodIuiBcOJxrOv8,149 +more_itertools/__init__.pyi,sha256=5B3eTzON1BBuOLob1vCflyEb2lSd6usXQQ-Cv-hXkeA,43 +more_itertools/more.py,sha256=mNPKKu5UI7lRL460vgm0QTCWFiGMVCMosSPxVSdibos,163690 +more_itertools/more.pyi,sha256=fpEgNX3O66wY5cnT-s5VYDKNUpAcaCyU3iP84It3OOM,27119 +more_itertools/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 +more_itertools/recipes.py,sha256=Ma-kuBNZDFhaQDbIJgRmnrG86WzaupbOyUV3v8je3xw,41811 +more_itertools/recipes.pyi,sha256=LNRwN-OL3nkMfQAqx-PPc1fBaetUObb_Z6mdePyzh1c,6226 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/REQUESTED b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/REQUESTED new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/WHEEL new file mode 100644 index 0000000000000000000000000000000000000000..d8b9936dad9ab2513fa6979f411560d3b6b57e37 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/WHEEL @@ -0,0 +1,4 @@ +Wheel-Version: 1.0 +Generator: flit 3.12.0 +Root-Is-Purelib: true +Tag: py3-none-any diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/licenses/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/licenses/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..0a523bece3e50519653c4d7a38399baa487fefa1 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools-10.8.0.dist-info/licenses/LICENSE @@ -0,0 +1,19 @@ +Copyright (c) 2012 Erik Rose + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies +of the Software, and to permit persons to whom the Software is furnished to do +so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..24216c5c1feb8b6017f71d096124e5db0aac5bd2 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/__init__.py @@ -0,0 +1,6 @@ +"""More routines for operating on iterables, beyond itertools""" + +from .more import * # noqa +from .recipes import * # noqa + +__version__ = '10.8.0' diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/__init__.pyi b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/__init__.pyi new file mode 100644 index 0000000000000000000000000000000000000000..96f6e36c7f4ac9ea0aebdcd9e11b8d1ff092d2ef --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/__init__.pyi @@ -0,0 +1,2 @@ +from .more import * +from .recipes import * diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/more.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/more.py new file mode 100644 index 0000000000000000000000000000000000000000..bf501956ae6c77e7597948abdaede960ca259444 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/more.py @@ -0,0 +1,5303 @@ +import math +import warnings + +from collections import Counter, defaultdict, deque, abc +from collections.abc import Sequence +from contextlib import suppress +from functools import cached_property, partial, reduce, wraps +from heapq import heapify, heapreplace +from itertools import ( + chain, + combinations, + compress, + count, + cycle, + dropwhile, + groupby, + islice, + permutations, + repeat, + starmap, + takewhile, + tee, + zip_longest, + product, +) +from math import comb, e, exp, factorial, floor, fsum, log, log1p, perm, tau +from math import ceil +from queue import Empty, Queue +from random import random, randrange, shuffle, uniform +from operator import ( + attrgetter, + is_not, + itemgetter, + lt, + mul, + neg, + sub, + gt, +) +from sys import hexversion, maxsize +from time import monotonic + +from .recipes import ( + _marker, + _zip_equal, + UnequalIterablesError, + consume, + first_true, + flatten, + is_prime, + nth, + powerset, + sieve, + take, + unique_everseen, + all_equal, + batched, +) + +__all__ = [ + 'AbortThread', + 'SequenceView', + 'UnequalIterablesError', + 'adjacent', + 'all_unique', + 'always_iterable', + 'always_reversible', + 'argmax', + 'argmin', + 'bucket', + 'callback_iter', + 'chunked', + 'chunked_even', + 'circular_shifts', + 'collapse', + 'combination_index', + 'combination_with_replacement_index', + 'consecutive_groups', + 'constrained_batches', + 'consumer', + 'count_cycle', + 'countable', + 'derangements', + 'dft', + 'difference', + 'distinct_combinations', + 'distinct_permutations', + 'distribute', + 'divide', + 'doublestarmap', + 'duplicates_everseen', + 'duplicates_justseen', + 'classify_unique', + 'exactly_n', + 'extract', + 'filter_except', + 'filter_map', + 'first', + 'gray_product', + 'groupby_transform', + 'ichunked', + 'iequals', + 'idft', + 'ilen', + 'interleave', + 'interleave_evenly', + 'interleave_longest', + 'interleave_randomly', + 'intersperse', + 'is_sorted', + 'islice_extended', + 'iterate', + 'iter_suppress', + 'join_mappings', + 'last', + 'locate', + 'longest_common_prefix', + 'lstrip', + 'make_decorator', + 'map_except', + 'map_if', + 'map_reduce', + 'mark_ends', + 'minmax', + 'nth_or_last', + 'nth_permutation', + 'nth_prime', + 'nth_product', + 'nth_combination_with_replacement', + 'numeric_range', + 'one', + 'only', + 'outer_product', + 'padded', + 'partial_product', + 'partitions', + 'peekable', + 'permutation_index', + 'powerset_of_sets', + 'product_index', + 'raise_', + 'repeat_each', + 'repeat_last', + 'replace', + 'rlocate', + 'rstrip', + 'run_length', + 'sample', + 'seekable', + 'set_partitions', + 'side_effect', + 'sliced', + 'sort_together', + 'split_after', + 'split_at', + 'split_before', + 'split_into', + 'split_when', + 'spy', + 'stagger', + 'strip', + 'strictly_n', + 'substrings', + 'substrings_indexes', + 'takewhile_inclusive', + 'time_limited', + 'unique_in_window', + 'unique_to_each', + 'unzip', + 'value_chain', + 'windowed', + 'windowed_complete', + 'with_iter', + 'zip_broadcast', + 'zip_equal', + 'zip_offset', +] + +# math.sumprod is available for Python 3.12+ +try: + from math import sumprod as _fsumprod + +except ImportError: # pragma: no cover + # Extended precision algorithms from T. J. Dekker, + # "A Floating-Point Technique for Extending the Available Precision" + # https://csclub.uwaterloo.ca/~pbarfuss/dekker1971.pdf + # Formulas: (5.5) (5.6) and (5.8). Code: mul12() + + def dl_split(x: float): + "Split a float into two half-precision components." + t = x * 134217729.0 # Veltkamp constant = 2.0 ** 27 + 1 + hi = t - (t - x) + lo = x - hi + return hi, lo + + def dl_mul(x, y): + "Lossless multiplication." + xx_hi, xx_lo = dl_split(x) + yy_hi, yy_lo = dl_split(y) + p = xx_hi * yy_hi + q = xx_hi * yy_lo + xx_lo * yy_hi + z = p + q + zz = p - z + q + xx_lo * yy_lo + return z, zz + + def _fsumprod(p, q): + return fsum(chain.from_iterable(map(dl_mul, p, q))) + + +def chunked(iterable, n, strict=False): + """Break *iterable* into lists of length *n*: + + >>> list(chunked([1, 2, 3, 4, 5, 6], 3)) + [[1, 2, 3], [4, 5, 6]] + + By the default, the last yielded list will have fewer than *n* elements + if the length of *iterable* is not divisible by *n*: + + >>> list(chunked([1, 2, 3, 4, 5, 6, 7, 8], 3)) + [[1, 2, 3], [4, 5, 6], [7, 8]] + + To use a fill-in value instead, see the :func:`grouper` recipe. + + If the length of *iterable* is not divisible by *n* and *strict* is + ``True``, then ``ValueError`` will be raised before the last + list is yielded. + + """ + iterator = iter(partial(take, n, iter(iterable)), []) + if strict: + if n is None: + raise ValueError('n must not be None when using strict mode.') + + def ret(): + for chunk in iterator: + if len(chunk) != n: + raise ValueError('iterable is not divisible by n.') + yield chunk + + return ret() + else: + return iterator + + +def first(iterable, default=_marker): + """Return the first item of *iterable*, or *default* if *iterable* is + empty. + + >>> first([0, 1, 2, 3]) + 0 + >>> first([], 'some default') + 'some default' + + If *default* is not provided and there are no items in the iterable, + raise ``ValueError``. + + :func:`first` is useful when you have a generator of expensive-to-retrieve + values and want any arbitrary one. It is marginally shorter than + ``next(iter(iterable), default)``. + + """ + for item in iterable: + return item + if default is _marker: + raise ValueError( + 'first() was called on an empty iterable, ' + 'and no default value was provided.' + ) + return default + + +def last(iterable, default=_marker): + """Return the last item of *iterable*, or *default* if *iterable* is + empty. + + >>> last([0, 1, 2, 3]) + 3 + >>> last([], 'some default') + 'some default' + + If *default* is not provided and there are no items in the iterable, + raise ``ValueError``. + """ + try: + if isinstance(iterable, Sequence): + return iterable[-1] + # Work around https://bugs.python.org/issue38525 + if getattr(iterable, '__reversed__', None): + return next(reversed(iterable)) + return deque(iterable, maxlen=1)[-1] + except (IndexError, TypeError, StopIteration): + if default is _marker: + raise ValueError( + 'last() was called on an empty iterable, ' + 'and no default value was provided.' + ) + return default + + +def nth_or_last(iterable, n, default=_marker): + """Return the nth or the last item of *iterable*, + or *default* if *iterable* is empty. + + >>> nth_or_last([0, 1, 2, 3], 2) + 2 + >>> nth_or_last([0, 1], 2) + 1 + >>> nth_or_last([], 0, 'some default') + 'some default' + + If *default* is not provided and there are no items in the iterable, + raise ``ValueError``. + """ + return last(islice(iterable, n + 1), default=default) + + +class peekable: + """Wrap an iterator to allow lookahead and prepending elements. + + Call :meth:`peek` on the result to get the value that will be returned + by :func:`next`. This won't advance the iterator: + + >>> p = peekable(['a', 'b']) + >>> p.peek() + 'a' + >>> next(p) + 'a' + + Pass :meth:`peek` a default value to return that instead of raising + ``StopIteration`` when the iterator is exhausted. + + >>> p = peekable([]) + >>> p.peek('hi') + 'hi' + + peekables also offer a :meth:`prepend` method, which "inserts" items + at the head of the iterable: + + >>> p = peekable([1, 2, 3]) + >>> p.prepend(10, 11, 12) + >>> next(p) + 10 + >>> p.peek() + 11 + >>> list(p) + [11, 12, 1, 2, 3] + + peekables can be indexed. Index 0 is the item that will be returned by + :func:`next`, index 1 is the item after that, and so on: + The values up to the given index will be cached. + + >>> p = peekable(['a', 'b', 'c', 'd']) + >>> p[0] + 'a' + >>> p[1] + 'b' + >>> next(p) + 'a' + + Negative indexes are supported, but be aware that they will cache the + remaining items in the source iterator, which may require significant + storage. + + To check whether a peekable is exhausted, check its truth value: + + >>> p = peekable(['a', 'b']) + >>> if p: # peekable has items + ... list(p) + ['a', 'b'] + >>> if not p: # peekable is exhausted + ... list(p) + [] + + """ + + def __init__(self, iterable): + self._it = iter(iterable) + self._cache = deque() + + def __iter__(self): + return self + + def __bool__(self): + try: + self.peek() + except StopIteration: + return False + return True + + def peek(self, default=_marker): + """Return the item that will be next returned from ``next()``. + + Return ``default`` if there are no items left. If ``default`` is not + provided, raise ``StopIteration``. + + """ + if not self._cache: + try: + self._cache.append(next(self._it)) + except StopIteration: + if default is _marker: + raise + return default + return self._cache[0] + + def prepend(self, *items): + """Stack up items to be the next ones returned from ``next()`` or + ``self.peek()``. The items will be returned in + first in, first out order:: + + >>> p = peekable([1, 2, 3]) + >>> p.prepend(10, 11, 12) + >>> next(p) + 10 + >>> list(p) + [11, 12, 1, 2, 3] + + It is possible, by prepending items, to "resurrect" a peekable that + previously raised ``StopIteration``. + + >>> p = peekable([]) + >>> next(p) + Traceback (most recent call last): + ... + StopIteration + >>> p.prepend(1) + >>> next(p) + 1 + >>> next(p) + Traceback (most recent call last): + ... + StopIteration + + """ + self._cache.extendleft(reversed(items)) + + def __next__(self): + if self._cache: + return self._cache.popleft() + + return next(self._it) + + def _get_slice(self, index): + # Normalize the slice's arguments + step = 1 if (index.step is None) else index.step + if step > 0: + start = 0 if (index.start is None) else index.start + stop = maxsize if (index.stop is None) else index.stop + elif step < 0: + start = -1 if (index.start is None) else index.start + stop = (-maxsize - 1) if (index.stop is None) else index.stop + else: + raise ValueError('slice step cannot be zero') + + # If either the start or stop index is negative, we'll need to cache + # the rest of the iterable in order to slice from the right side. + if (start < 0) or (stop < 0): + self._cache.extend(self._it) + # Otherwise we'll need to find the rightmost index and cache to that + # point. + else: + n = min(max(start, stop) + 1, maxsize) + cache_len = len(self._cache) + if n >= cache_len: + self._cache.extend(islice(self._it, n - cache_len)) + + return list(self._cache)[index] + + def __getitem__(self, index): + if isinstance(index, slice): + return self._get_slice(index) + + cache_len = len(self._cache) + if index < 0: + self._cache.extend(self._it) + elif index >= cache_len: + self._cache.extend(islice(self._it, index + 1 - cache_len)) + + return self._cache[index] + + +def consumer(func): + """Decorator that automatically advances a PEP-342-style "reverse iterator" + to its first yield point so you don't have to call ``next()`` on it + manually. + + >>> @consumer + ... def tally(): + ... i = 0 + ... while True: + ... print('Thing number %s is %s.' % (i, (yield))) + ... i += 1 + ... + >>> t = tally() + >>> t.send('red') + Thing number 0 is red. + >>> t.send('fish') + Thing number 1 is fish. + + Without the decorator, you would have to call ``next(t)`` before + ``t.send()`` could be used. + + """ + + @wraps(func) + def wrapper(*args, **kwargs): + gen = func(*args, **kwargs) + next(gen) + return gen + + return wrapper + + +def ilen(iterable): + """Return the number of items in *iterable*. + + For example, there are 168 prime numbers below 1,000: + + >>> ilen(sieve(1000)) + 168 + + Equivalent to, but faster than:: + + def ilen(iterable): + count = 0 + for _ in iterable: + count += 1 + return count + + This fully consumes the iterable, so handle with care. + + """ + # This is the "most beautiful of the fast variants" of this function. + # If you think you can improve on it, please ensure that your version + # is both 10x faster and 10x more beautiful. + return sum(compress(repeat(1), zip(iterable))) + + +def iterate(func, start): + """Return ``start``, ``func(start)``, ``func(func(start))``, ... + + Produces an infinite iterator. To add a stopping condition, + use :func:`take`, ``takewhile``, or :func:`takewhile_inclusive`:. + + >>> take(10, iterate(lambda x: 2*x, 1)) + [1, 2, 4, 8, 16, 32, 64, 128, 256, 512] + + >>> collatz = lambda x: 3*x + 1 if x%2==1 else x // 2 + >>> list(takewhile_inclusive(lambda x: x!=1, iterate(collatz, 10))) + [10, 5, 16, 8, 4, 2, 1] + + """ + with suppress(StopIteration): + while True: + yield start + start = func(start) + + +def with_iter(context_manager): + """Wrap an iterable in a ``with`` statement, so it closes once exhausted. + + For example, this will close the file when the iterator is exhausted:: + + upper_lines = (line.upper() for line in with_iter(open('foo'))) + + Any context manager which returns an iterable is a candidate for + ``with_iter``. + + """ + with context_manager as iterable: + yield from iterable + + +def one(iterable, too_short=None, too_long=None): + """Return the first item from *iterable*, which is expected to contain only + that item. Raise an exception if *iterable* is empty or has more than one + item. + + :func:`one` is useful for ensuring that an iterable contains only one item. + For example, it can be used to retrieve the result of a database query + that is expected to return a single row. + + If *iterable* is empty, ``ValueError`` will be raised. You may specify a + different exception with the *too_short* keyword: + + >>> it = [] + >>> one(it) # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + ... + ValueError: too few items in iterable (expected 1)' + >>> too_short = IndexError('too few items') + >>> one(it, too_short=too_short) # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + ... + IndexError: too few items + + Similarly, if *iterable* contains more than one item, ``ValueError`` will + be raised. You may specify a different exception with the *too_long* + keyword: + + >>> it = ['too', 'many'] + >>> one(it) # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + ... + ValueError: Expected exactly one item in iterable, but got 'too', + 'many', and perhaps more. + >>> too_long = RuntimeError + >>> one(it, too_long=too_long) # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + ... + RuntimeError + + Note that :func:`one` attempts to advance *iterable* twice to ensure there + is only one item. See :func:`spy` or :func:`peekable` to check iterable + contents less destructively. + + """ + iterator = iter(iterable) + for first in iterator: + for second in iterator: + msg = ( + f'Expected exactly one item in iterable, but got {first!r}, ' + f'{second!r}, and perhaps more.' + ) + raise too_long or ValueError(msg) + return first + raise too_short or ValueError('too few items in iterable (expected 1)') + + +def raise_(exception, *args): + raise exception(*args) + + +def strictly_n(iterable, n, too_short=None, too_long=None): + """Validate that *iterable* has exactly *n* items and return them if + it does. If it has fewer than *n* items, call function *too_short* + with the actual number of items. If it has more than *n* items, call function + *too_long* with the number ``n + 1``. + + >>> iterable = ['a', 'b', 'c', 'd'] + >>> n = 4 + >>> list(strictly_n(iterable, n)) + ['a', 'b', 'c', 'd'] + + Note that the returned iterable must be consumed in order for the check to + be made. + + By default, *too_short* and *too_long* are functions that raise + ``ValueError``. + + >>> list(strictly_n('ab', 3)) # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + ... + ValueError: too few items in iterable (got 2) + + >>> list(strictly_n('abc', 2)) # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + ... + ValueError: too many items in iterable (got at least 3) + + You can instead supply functions that do something else. + *too_short* will be called with the number of items in *iterable*. + *too_long* will be called with `n + 1`. + + >>> def too_short(item_count): + ... raise RuntimeError + >>> it = strictly_n('abcd', 6, too_short=too_short) + >>> list(it) # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + ... + RuntimeError + + >>> def too_long(item_count): + ... print('The boss is going to hear about this') + >>> it = strictly_n('abcdef', 4, too_long=too_long) + >>> list(it) + The boss is going to hear about this + ['a', 'b', 'c', 'd'] + + """ + if too_short is None: + too_short = lambda item_count: raise_( + ValueError, + f'Too few items in iterable (got {item_count})', + ) + + if too_long is None: + too_long = lambda item_count: raise_( + ValueError, + f'Too many items in iterable (got at least {item_count})', + ) + + it = iter(iterable) + + sent = 0 + for item in islice(it, n): + yield item + sent += 1 + + if sent < n: + too_short(sent) + return + + for item in it: + too_long(n + 1) + return + + +def distinct_permutations(iterable, r=None): + """Yield successive distinct permutations of the elements in *iterable*. + + >>> sorted(distinct_permutations([1, 0, 1])) + [(0, 1, 1), (1, 0, 1), (1, 1, 0)] + + Equivalent to yielding from ``set(permutations(iterable))``, except + duplicates are not generated and thrown away. For larger input sequences + this is much more efficient. + + Duplicate permutations arise when there are duplicated elements in the + input iterable. The number of items returned is + `n! / (x_1! * x_2! * ... * x_n!)`, where `n` is the total number of + items input, and each `x_i` is the count of a distinct item in the input + sequence. The function :func:`multinomial` computes this directly. + + If *r* is given, only the *r*-length permutations are yielded. + + >>> sorted(distinct_permutations([1, 0, 1], r=2)) + [(0, 1), (1, 0), (1, 1)] + >>> sorted(distinct_permutations(range(3), r=2)) + [(0, 1), (0, 2), (1, 0), (1, 2), (2, 0), (2, 1)] + + *iterable* need not be sortable, but note that using equal (``x == y``) + but non-identical (``id(x) != id(y)``) elements may produce surprising + behavior. For example, ``1`` and ``True`` are equal but non-identical: + + >>> list(distinct_permutations([1, True, '3'])) # doctest: +SKIP + [ + (1, True, '3'), + (1, '3', True), + ('3', 1, True) + ] + >>> list(distinct_permutations([1, 2, '3'])) # doctest: +SKIP + [ + (1, 2, '3'), + (1, '3', 2), + (2, 1, '3'), + (2, '3', 1), + ('3', 1, 2), + ('3', 2, 1) + ] + """ + + # Algorithm: https://w.wiki/Qai + def _full(A): + while True: + # Yield the permutation we have + yield tuple(A) + + # Find the largest index i such that A[i] < A[i + 1] + for i in range(size - 2, -1, -1): + if A[i] < A[i + 1]: + break + # If no such index exists, this permutation is the last one + else: + return + + # Find the largest index j greater than j such that A[i] < A[j] + for j in range(size - 1, i, -1): + if A[i] < A[j]: + break + + # Swap the value of A[i] with that of A[j], then reverse the + # sequence from A[i + 1] to form the new permutation + A[i], A[j] = A[j], A[i] + A[i + 1 :] = A[: i - size : -1] # A[i + 1:][::-1] + + # Algorithm: modified from the above + def _partial(A, r): + # Split A into the first r items and the last r items + head, tail = A[:r], A[r:] + right_head_indexes = range(r - 1, -1, -1) + left_tail_indexes = range(len(tail)) + + while True: + # Yield the permutation we have + yield tuple(head) + + # Starting from the right, find the first index of the head with + # value smaller than the maximum value of the tail - call it i. + pivot = tail[-1] + for i in right_head_indexes: + if head[i] < pivot: + break + pivot = head[i] + else: + return + + # Starting from the left, find the first value of the tail + # with a value greater than head[i] and swap. + for j in left_tail_indexes: + if tail[j] > head[i]: + head[i], tail[j] = tail[j], head[i] + break + # If we didn't find one, start from the right and find the first + # index of the head with a value greater than head[i] and swap. + else: + for j in right_head_indexes: + if head[j] > head[i]: + head[i], head[j] = head[j], head[i] + break + + # Reverse head[i + 1:] and swap it with tail[:r - (i + 1)] + tail += head[: i - r : -1] # head[i + 1:][::-1] + i += 1 + head[i:], tail[:] = tail[: r - i], tail[r - i :] + + items = list(iterable) + + try: + items.sort() + sortable = True + except TypeError: + sortable = False + + indices_dict = defaultdict(list) + + for item in items: + indices_dict[items.index(item)].append(item) + + indices = [items.index(item) for item in items] + indices.sort() + + equivalent_items = {k: cycle(v) for k, v in indices_dict.items()} + + def permuted_items(permuted_indices): + return tuple( + next(equivalent_items[index]) for index in permuted_indices + ) + + size = len(items) + if r is None: + r = size + + # functools.partial(_partial, ... ) + algorithm = _full if (r == size) else partial(_partial, r=r) + + if 0 < r <= size: + if sortable: + return algorithm(items) + else: + return ( + permuted_items(permuted_indices) + for permuted_indices in algorithm(indices) + ) + + return iter(() if r else ((),)) + + +def derangements(iterable, r=None): + """Yield successive derangements of the elements in *iterable*. + + A derangement is a permutation in which no element appears at its original + index. In other words, a derangement is a permutation that has no fixed points. + + Suppose Alice, Bob, Carol, and Dave are playing Secret Santa. + The code below outputs all of the different ways to assign gift recipients + such that nobody is assigned to himself or herself: + + >>> for d in derangements(['Alice', 'Bob', 'Carol', 'Dave']): + ... print(', '.join(d)) + Bob, Alice, Dave, Carol + Bob, Carol, Dave, Alice + Bob, Dave, Alice, Carol + Carol, Alice, Dave, Bob + Carol, Dave, Alice, Bob + Carol, Dave, Bob, Alice + Dave, Alice, Bob, Carol + Dave, Carol, Alice, Bob + Dave, Carol, Bob, Alice + + If *r* is given, only the *r*-length derangements are yielded. + + >>> sorted(derangements(range(3), 2)) + [(1, 0), (1, 2), (2, 0)] + >>> sorted(derangements([0, 2, 3], 2)) + [(2, 0), (2, 3), (3, 0)] + + Elements are treated as unique based on their position, not on their value. + + Consider the Secret Santa example with two *different* people who have + the *same* name. Then there are two valid gift assignments even though + it might appear that a person is assigned to themselves: + + >>> names = ['Alice', 'Bob', 'Bob'] + >>> list(derangements(names)) + [('Bob', 'Bob', 'Alice'), ('Bob', 'Alice', 'Bob')] + + To avoid confusion, make the inputs distinct: + + >>> deduped = [f'{name}{index}' for index, name in enumerate(names)] + >>> list(derangements(deduped)) + [('Bob1', 'Bob2', 'Alice0'), ('Bob2', 'Alice0', 'Bob1')] + + The number of derangements of a set of size *n* is known as the + "subfactorial of n". For n > 0, the subfactorial is: + ``round(math.factorial(n) / math.e)``. + + References: + + * Article: https://www.numberanalytics.com/blog/ultimate-guide-to-derangements-in-combinatorics + * Sizes: https://oeis.org/A000166 + """ + xs = tuple(iterable) + ys = tuple(range(len(xs))) + return compress( + permutations(xs, r=r), + map(all, map(map, repeat(is_not), repeat(ys), permutations(ys, r=r))), + ) + + +def intersperse(e, iterable, n=1): + """Intersperse filler element *e* among the items in *iterable*, leaving + *n* items between each filler element. + + >>> list(intersperse('!', [1, 2, 3, 4, 5])) + [1, '!', 2, '!', 3, '!', 4, '!', 5] + + >>> list(intersperse(None, [1, 2, 3, 4, 5], n=2)) + [1, 2, None, 3, 4, None, 5] + + """ + if n == 0: + raise ValueError('n must be > 0') + elif n == 1: + # interleave(repeat(e), iterable) -> e, x_0, e, x_1, e, x_2... + # islice(..., 1, None) -> x_0, e, x_1, e, x_2... + return islice(interleave(repeat(e), iterable), 1, None) + else: + # interleave(filler, chunks) -> [e], [x_0, x_1], [e], [x_2, x_3]... + # islice(..., 1, None) -> [x_0, x_1], [e], [x_2, x_3]... + # flatten(...) -> x_0, x_1, e, x_2, x_3... + filler = repeat([e]) + chunks = chunked(iterable, n) + return flatten(islice(interleave(filler, chunks), 1, None)) + + +def unique_to_each(*iterables): + """Return the elements from each of the input iterables that aren't in the + other input iterables. + + For example, suppose you have a set of packages, each with a set of + dependencies:: + + {'pkg_1': {'A', 'B'}, 'pkg_2': {'B', 'C'}, 'pkg_3': {'B', 'D'}} + + If you remove one package, which dependencies can also be removed? + + If ``pkg_1`` is removed, then ``A`` is no longer necessary - it is not + associated with ``pkg_2`` or ``pkg_3``. Similarly, ``C`` is only needed for + ``pkg_2``, and ``D`` is only needed for ``pkg_3``:: + + >>> unique_to_each({'A', 'B'}, {'B', 'C'}, {'B', 'D'}) + [['A'], ['C'], ['D']] + + If there are duplicates in one input iterable that aren't in the others + they will be duplicated in the output. Input order is preserved:: + + >>> unique_to_each("mississippi", "missouri") + [['p', 'p'], ['o', 'u', 'r']] + + It is assumed that the elements of each iterable are hashable. + + """ + pool = [list(it) for it in iterables] + counts = Counter(chain.from_iterable(map(set, pool))) + uniques = {element for element in counts if counts[element] == 1} + return [list(filter(uniques.__contains__, it)) for it in pool] + + +def windowed(seq, n, fillvalue=None, step=1): + """Return a sliding window of width *n* over the given iterable. + + >>> all_windows = windowed([1, 2, 3, 4, 5], 3) + >>> list(all_windows) + [(1, 2, 3), (2, 3, 4), (3, 4, 5)] + + When the window is larger than the iterable, *fillvalue* is used in place + of missing values: + + >>> list(windowed([1, 2, 3], 4)) + [(1, 2, 3, None)] + + Each window will advance in increments of *step*: + + >>> list(windowed([1, 2, 3, 4, 5, 6], 3, fillvalue='!', step=2)) + [(1, 2, 3), (3, 4, 5), (5, 6, '!')] + + To slide into the iterable's items, use :func:`chain` to add filler items + to the left: + + >>> iterable = [1, 2, 3, 4] + >>> n = 3 + >>> padding = [None] * (n - 1) + >>> list(windowed(chain(padding, iterable), 3)) + [(None, None, 1), (None, 1, 2), (1, 2, 3), (2, 3, 4)] + """ + if n < 0: + raise ValueError('n must be >= 0') + if n == 0: + yield () + return + if step < 1: + raise ValueError('step must be >= 1') + + iterator = iter(seq) + + # Generate first window + window = deque(islice(iterator, n), maxlen=n) + + # Deal with the first window not being full + if not window: + return + if len(window) < n: + yield tuple(window) + ((fillvalue,) * (n - len(window))) + return + yield tuple(window) + + # Create the filler for the next windows. The padding ensures + # we have just enough elements to fill the last window. + padding = (fillvalue,) * (n - 1 if step >= n else step - 1) + filler = map(window.append, chain(iterator, padding)) + + # Generate the rest of the windows + for _ in islice(filler, step - 1, None, step): + yield tuple(window) + + +def substrings(iterable): + """Yield all of the substrings of *iterable*. + + >>> [''.join(s) for s in substrings('more')] + ['m', 'o', 'r', 'e', 'mo', 'or', 're', 'mor', 'ore', 'more'] + + Note that non-string iterables can also be subdivided. + + >>> list(substrings([0, 1, 2])) + [(0,), (1,), (2,), (0, 1), (1, 2), (0, 1, 2)] + + """ + # The length-1 substrings + seq = [] + for item in iterable: + seq.append(item) + yield (item,) + seq = tuple(seq) + item_count = len(seq) + + # And the rest + for n in range(2, item_count + 1): + for i in range(item_count - n + 1): + yield seq[i : i + n] + + +def substrings_indexes(seq, reverse=False): + """Yield all substrings and their positions in *seq* + + The items yielded will be a tuple of the form ``(substr, i, j)``, where + ``substr == seq[i:j]``. + + This function only works for iterables that support slicing, such as + ``str`` objects. + + >>> for item in substrings_indexes('more'): + ... print(item) + ('m', 0, 1) + ('o', 1, 2) + ('r', 2, 3) + ('e', 3, 4) + ('mo', 0, 2) + ('or', 1, 3) + ('re', 2, 4) + ('mor', 0, 3) + ('ore', 1, 4) + ('more', 0, 4) + + Set *reverse* to ``True`` to yield the same items in the opposite order. + + + """ + r = range(1, len(seq) + 1) + if reverse: + r = reversed(r) + return ( + (seq[i : i + L], i, i + L) for L in r for i in range(len(seq) - L + 1) + ) + + +class bucket: + """Wrap *iterable* and return an object that buckets the iterable into + child iterables based on a *key* function. + + >>> iterable = ['a1', 'b1', 'c1', 'a2', 'b2', 'c2', 'b3'] + >>> s = bucket(iterable, key=lambda x: x[0]) # Bucket by 1st character + >>> sorted(list(s)) # Get the keys + ['a', 'b', 'c'] + >>> a_iterable = s['a'] + >>> next(a_iterable) + 'a1' + >>> next(a_iterable) + 'a2' + >>> list(s['b']) + ['b1', 'b2', 'b3'] + + The original iterable will be advanced and its items will be cached until + they are used by the child iterables. This may require significant storage. + + By default, attempting to select a bucket to which no items belong will + exhaust the iterable and cache all values. + If you specify a *validator* function, selected buckets will instead be + checked against it. + + >>> from itertools import count + >>> it = count(1, 2) # Infinite sequence of odd numbers + >>> key = lambda x: x % 10 # Bucket by last digit + >>> validator = lambda x: x in {1, 3, 5, 7, 9} # Odd digits only + >>> s = bucket(it, key=key, validator=validator) + >>> 2 in s + False + >>> list(s[2]) + [] + + """ + + def __init__(self, iterable, key, validator=None): + self._it = iter(iterable) + self._key = key + self._cache = defaultdict(deque) + self._validator = validator or (lambda x: True) + + def __contains__(self, value): + if not self._validator(value): + return False + + try: + item = next(self[value]) + except StopIteration: + return False + else: + self._cache[value].appendleft(item) + + return True + + def _get_values(self, value): + """ + Helper to yield items from the parent iterator that match *value*. + Items that don't match are stored in the local cache as they + are encountered. + """ + while True: + # If we've cached some items that match the target value, emit + # the first one and evict it from the cache. + if self._cache[value]: + yield self._cache[value].popleft() + # Otherwise we need to advance the parent iterator to search for + # a matching item, caching the rest. + else: + while True: + try: + item = next(self._it) + except StopIteration: + return + item_value = self._key(item) + if item_value == value: + yield item + break + elif self._validator(item_value): + self._cache[item_value].append(item) + + def __iter__(self): + for item in self._it: + item_value = self._key(item) + if self._validator(item_value): + self._cache[item_value].append(item) + + return iter(self._cache) + + def __getitem__(self, value): + if not self._validator(value): + return iter(()) + + return self._get_values(value) + + +def spy(iterable, n=1): + """Return a 2-tuple with a list containing the first *n* elements of + *iterable*, and an iterator with the same items as *iterable*. + This allows you to "look ahead" at the items in the iterable without + advancing it. + + There is one item in the list by default: + + >>> iterable = 'abcdefg' + >>> head, iterable = spy(iterable) + >>> head + ['a'] + >>> list(iterable) + ['a', 'b', 'c', 'd', 'e', 'f', 'g'] + + You may use unpacking to retrieve items instead of lists: + + >>> (head,), iterable = spy('abcdefg') + >>> head + 'a' + >>> (first, second), iterable = spy('abcdefg', 2) + >>> first + 'a' + >>> second + 'b' + + The number of items requested can be larger than the number of items in + the iterable: + + >>> iterable = [1, 2, 3, 4, 5] + >>> head, iterable = spy(iterable, 10) + >>> head + [1, 2, 3, 4, 5] + >>> list(iterable) + [1, 2, 3, 4, 5] + + """ + p, q = tee(iterable) + return take(n, q), p + + +def interleave(*iterables): + """Return a new iterable yielding from each iterable in turn, + until the shortest is exhausted. + + >>> list(interleave([1, 2, 3], [4, 5], [6, 7, 8])) + [1, 4, 6, 2, 5, 7] + + For a version that doesn't terminate after the shortest iterable is + exhausted, see :func:`interleave_longest`. + + """ + return chain.from_iterable(zip(*iterables)) + + +def interleave_longest(*iterables): + """Return a new iterable yielding from each iterable in turn, + skipping any that are exhausted. + + >>> list(interleave_longest([1, 2, 3], [4, 5], [6, 7, 8])) + [1, 4, 6, 2, 5, 7, 3, 8] + + This function produces the same output as :func:`roundrobin`, but may + perform better for some inputs (in particular when the number of iterables + is large). + + """ + for xs in zip_longest(*iterables, fillvalue=_marker): + for x in xs: + if x is not _marker: + yield x + + +def interleave_evenly(iterables, lengths=None): + """ + Interleave multiple iterables so that their elements are evenly distributed + throughout the output sequence. + + >>> iterables = [1, 2, 3, 4, 5], ['a', 'b'] + >>> list(interleave_evenly(iterables)) + [1, 2, 'a', 3, 4, 'b', 5] + + >>> iterables = [[1, 2, 3], [4, 5], [6, 7, 8]] + >>> list(interleave_evenly(iterables)) + [1, 6, 4, 2, 7, 3, 8, 5] + + This function requires iterables of known length. Iterables without + ``__len__()`` can be used by manually specifying lengths with *lengths*: + + >>> from itertools import combinations, repeat + >>> iterables = [combinations(range(4), 2), ['a', 'b', 'c']] + >>> lengths = [4 * (4 - 1) // 2, 3] + >>> list(interleave_evenly(iterables, lengths=lengths)) + [(0, 1), (0, 2), 'a', (0, 3), (1, 2), 'b', (1, 3), (2, 3), 'c'] + + Based on Bresenham's algorithm. + """ + if lengths is None: + try: + lengths = [len(it) for it in iterables] + except TypeError: + raise ValueError( + 'Iterable lengths could not be determined automatically. ' + 'Specify them with the lengths keyword.' + ) + elif len(iterables) != len(lengths): + raise ValueError('Mismatching number of iterables and lengths.') + + dims = len(lengths) + + # sort iterables by length, descending + lengths_permute = sorted( + range(dims), key=lambda i: lengths[i], reverse=True + ) + lengths_desc = [lengths[i] for i in lengths_permute] + iters_desc = [iter(iterables[i]) for i in lengths_permute] + + # the longest iterable is the primary one (Bresenham: the longest + # distance along an axis) + delta_primary, deltas_secondary = lengths_desc[0], lengths_desc[1:] + iter_primary, iters_secondary = iters_desc[0], iters_desc[1:] + errors = [delta_primary // dims] * len(deltas_secondary) + + to_yield = sum(lengths) + while to_yield: + yield next(iter_primary) + to_yield -= 1 + # update errors for each secondary iterable + errors = [e - delta for e, delta in zip(errors, deltas_secondary)] + + # those iterables for which the error is negative are yielded + # ("diagonal step" in Bresenham) + for i, e_ in enumerate(errors): + if e_ < 0: + yield next(iters_secondary[i]) + to_yield -= 1 + errors[i] += delta_primary + + +def interleave_randomly(*iterables): + """Repeatedly select one of the input *iterables* at random and yield the next + item from it. + + >>> iterables = [1, 2, 3], 'abc', (True, False, None) + >>> list(interleave_randomly(*iterables)) # doctest: +SKIP + ['a', 'b', 1, 'c', True, False, None, 2, 3] + + The relative order of the items in each input iterable will preserved. Note the + sequences of items with this property are not equally likely to be generated. + + """ + iterators = [iter(e) for e in iterables] + while iterators: + idx = randrange(len(iterators)) + try: + yield next(iterators[idx]) + except StopIteration: + # equivalent to `list.pop` but slightly faster + iterators[idx] = iterators[-1] + del iterators[-1] + + +def collapse(iterable, base_type=None, levels=None): + """Flatten an iterable with multiple levels of nesting (e.g., a list of + lists of tuples) into non-iterable types. + + >>> iterable = [(1, 2), ([3, 4], [[5], [6]])] + >>> list(collapse(iterable)) + [1, 2, 3, 4, 5, 6] + + Binary and text strings are not considered iterable and + will not be collapsed. + + To avoid collapsing other types, specify *base_type*: + + >>> iterable = ['ab', ('cd', 'ef'), ['gh', 'ij']] + >>> list(collapse(iterable, base_type=tuple)) + ['ab', ('cd', 'ef'), 'gh', 'ij'] + + Specify *levels* to stop flattening after a certain level: + + >>> iterable = [('a', ['b']), ('c', ['d'])] + >>> list(collapse(iterable)) # Fully flattened + ['a', 'b', 'c', 'd'] + >>> list(collapse(iterable, levels=1)) # Only one level flattened + ['a', ['b'], 'c', ['d']] + + """ + stack = deque() + # Add our first node group, treat the iterable as a single node + stack.appendleft((0, repeat(iterable, 1))) + + while stack: + node_group = stack.popleft() + level, nodes = node_group + + # Check if beyond max level + if levels is not None and level > levels: + yield from nodes + continue + + for node in nodes: + # Check if done iterating + if isinstance(node, (str, bytes)) or ( + (base_type is not None) and isinstance(node, base_type) + ): + yield node + # Otherwise try to create child nodes + else: + try: + tree = iter(node) + except TypeError: + yield node + else: + # Save our current location + stack.appendleft(node_group) + # Append the new child node + stack.appendleft((level + 1, tree)) + # Break to process child node + break + + +def side_effect(func, iterable, chunk_size=None, before=None, after=None): + """Invoke *func* on each item in *iterable* (or on each *chunk_size* group + of items) before yielding the item. + + `func` must be a function that takes a single argument. Its return value + will be discarded. + + *before* and *after* are optional functions that take no arguments. They + will be executed before iteration starts and after it ends, respectively. + + `side_effect` can be used for logging, updating progress bars, or anything + that is not functionally "pure." + + Emitting a status message: + + >>> from more_itertools import consume + >>> func = lambda item: print('Received {}'.format(item)) + >>> consume(side_effect(func, range(2))) + Received 0 + Received 1 + + Operating on chunks of items: + + >>> pair_sums = [] + >>> func = lambda chunk: pair_sums.append(sum(chunk)) + >>> list(side_effect(func, [0, 1, 2, 3, 4, 5], 2)) + [0, 1, 2, 3, 4, 5] + >>> list(pair_sums) + [1, 5, 9] + + Writing to a file-like object: + + >>> from io import StringIO + >>> from more_itertools import consume + >>> f = StringIO() + >>> func = lambda x: print(x, file=f) + >>> before = lambda: print(u'HEADER', file=f) + >>> after = f.close + >>> it = [u'a', u'b', u'c'] + >>> consume(side_effect(func, it, before=before, after=after)) + >>> f.closed + True + + """ + try: + if before is not None: + before() + + if chunk_size is None: + for item in iterable: + func(item) + yield item + else: + for chunk in chunked(iterable, chunk_size): + func(chunk) + yield from chunk + finally: + if after is not None: + after() + + +def sliced(seq, n, strict=False): + """Yield slices of length *n* from the sequence *seq*. + + >>> list(sliced((1, 2, 3, 4, 5, 6), 3)) + [(1, 2, 3), (4, 5, 6)] + + By the default, the last yielded slice will have fewer than *n* elements + if the length of *seq* is not divisible by *n*: + + >>> list(sliced((1, 2, 3, 4, 5, 6, 7, 8), 3)) + [(1, 2, 3), (4, 5, 6), (7, 8)] + + If the length of *seq* is not divisible by *n* and *strict* is + ``True``, then ``ValueError`` will be raised before the last + slice is yielded. + + This function will only work for iterables that support slicing. + For non-sliceable iterables, see :func:`chunked`. + + """ + iterator = takewhile(len, (seq[i : i + n] for i in count(0, n))) + if strict: + + def ret(): + for _slice in iterator: + if len(_slice) != n: + raise ValueError("seq is not divisible by n.") + yield _slice + + return ret() + else: + return iterator + + +def split_at(iterable, pred, maxsplit=-1, keep_separator=False): + """Yield lists of items from *iterable*, where each list is delimited by + an item where callable *pred* returns ``True``. + + >>> list(split_at('abcdcba', lambda x: x == 'b')) + [['a'], ['c', 'd', 'c'], ['a']] + + >>> list(split_at(range(10), lambda n: n % 2 == 1)) + [[0], [2], [4], [6], [8], []] + + At most *maxsplit* splits are done. If *maxsplit* is not specified or -1, + then there is no limit on the number of splits: + + >>> list(split_at(range(10), lambda n: n % 2 == 1, maxsplit=2)) + [[0], [2], [4, 5, 6, 7, 8, 9]] + + By default, the delimiting items are not included in the output. + To include them, set *keep_separator* to ``True``. + + >>> list(split_at('abcdcba', lambda x: x == 'b', keep_separator=True)) + [['a'], ['b'], ['c', 'd', 'c'], ['b'], ['a']] + + """ + if maxsplit == 0: + yield list(iterable) + return + + buf = [] + it = iter(iterable) + for item in it: + if pred(item): + yield buf + if keep_separator: + yield [item] + if maxsplit == 1: + yield list(it) + return + buf = [] + maxsplit -= 1 + else: + buf.append(item) + yield buf + + +def split_before(iterable, pred, maxsplit=-1): + """Yield lists of items from *iterable*, where each list ends just before + an item for which callable *pred* returns ``True``: + + >>> list(split_before('OneTwo', lambda s: s.isupper())) + [['O', 'n', 'e'], ['T', 'w', 'o']] + + >>> list(split_before(range(10), lambda n: n % 3 == 0)) + [[0, 1, 2], [3, 4, 5], [6, 7, 8], [9]] + + At most *maxsplit* splits are done. If *maxsplit* is not specified or -1, + then there is no limit on the number of splits: + + >>> list(split_before(range(10), lambda n: n % 3 == 0, maxsplit=2)) + [[0, 1, 2], [3, 4, 5], [6, 7, 8, 9]] + """ + if maxsplit == 0: + yield list(iterable) + return + + buf = [] + it = iter(iterable) + for item in it: + if pred(item) and buf: + yield buf + if maxsplit == 1: + yield [item, *it] + return + buf = [] + maxsplit -= 1 + buf.append(item) + if buf: + yield buf + + +def split_after(iterable, pred, maxsplit=-1): + """Yield lists of items from *iterable*, where each list ends with an + item where callable *pred* returns ``True``: + + >>> list(split_after('one1two2', lambda s: s.isdigit())) + [['o', 'n', 'e', '1'], ['t', 'w', 'o', '2']] + + >>> list(split_after(range(10), lambda n: n % 3 == 0)) + [[0], [1, 2, 3], [4, 5, 6], [7, 8, 9]] + + At most *maxsplit* splits are done. If *maxsplit* is not specified or -1, + then there is no limit on the number of splits: + + >>> list(split_after(range(10), lambda n: n % 3 == 0, maxsplit=2)) + [[0], [1, 2, 3], [4, 5, 6, 7, 8, 9]] + + """ + if maxsplit == 0: + yield list(iterable) + return + + buf = [] + it = iter(iterable) + for item in it: + buf.append(item) + if pred(item) and buf: + yield buf + if maxsplit == 1: + buf = list(it) + if buf: + yield buf + return + buf = [] + maxsplit -= 1 + if buf: + yield buf + + +def split_when(iterable, pred, maxsplit=-1): + """Split *iterable* into pieces based on the output of *pred*. + *pred* should be a function that takes successive pairs of items and + returns ``True`` if the iterable should be split in between them. + + For example, to find runs of increasing numbers, split the iterable when + element ``i`` is larger than element ``i + 1``: + + >>> list(split_when([1, 2, 3, 3, 2, 5, 2, 4, 2], lambda x, y: x > y)) + [[1, 2, 3, 3], [2, 5], [2, 4], [2]] + + At most *maxsplit* splits are done. If *maxsplit* is not specified or -1, + then there is no limit on the number of splits: + + >>> list(split_when([1, 2, 3, 3, 2, 5, 2, 4, 2], + ... lambda x, y: x > y, maxsplit=2)) + [[1, 2, 3, 3], [2, 5], [2, 4, 2]] + + """ + if maxsplit == 0: + yield list(iterable) + return + + it = iter(iterable) + try: + cur_item = next(it) + except StopIteration: + return + + buf = [cur_item] + for next_item in it: + if pred(cur_item, next_item): + yield buf + if maxsplit == 1: + yield [next_item, *it] + return + buf = [] + maxsplit -= 1 + + buf.append(next_item) + cur_item = next_item + + yield buf + + +def split_into(iterable, sizes): + """Yield a list of sequential items from *iterable* of length 'n' for each + integer 'n' in *sizes*. + + >>> list(split_into([1,2,3,4,5,6], [1,2,3])) + [[1], [2, 3], [4, 5, 6]] + + If the sum of *sizes* is smaller than the length of *iterable*, then the + remaining items of *iterable* will not be returned. + + >>> list(split_into([1,2,3,4,5,6], [2,3])) + [[1, 2], [3, 4, 5]] + + If the sum of *sizes* is larger than the length of *iterable*, fewer items + will be returned in the iteration that overruns the *iterable* and further + lists will be empty: + + >>> list(split_into([1,2,3,4], [1,2,3,4])) + [[1], [2, 3], [4], []] + + When a ``None`` object is encountered in *sizes*, the returned list will + contain items up to the end of *iterable* the same way that + :func:`itertools.slice` does: + + >>> list(split_into([1,2,3,4,5,6,7,8,9,0], [2,3,None])) + [[1, 2], [3, 4, 5], [6, 7, 8, 9, 0]] + + :func:`split_into` can be useful for grouping a series of items where the + sizes of the groups are not uniform. An example would be where in a row + from a table, multiple columns represent elements of the same feature + (e.g. a point represented by x,y,z) but, the format is not the same for + all columns. + """ + # convert the iterable argument into an iterator so its contents can + # be consumed by islice in case it is a generator + it = iter(iterable) + + for size in sizes: + if size is None: + yield list(it) + return + else: + yield list(islice(it, size)) + + +def padded(iterable, fillvalue=None, n=None, next_multiple=False): + """Yield the elements from *iterable*, followed by *fillvalue*, such that + at least *n* items are emitted. + + >>> list(padded([1, 2, 3], '?', 5)) + [1, 2, 3, '?', '?'] + + If *next_multiple* is ``True``, *fillvalue* will be emitted until the + number of items emitted is a multiple of *n*: + + >>> list(padded([1, 2, 3, 4], n=3, next_multiple=True)) + [1, 2, 3, 4, None, None] + + If *n* is ``None``, *fillvalue* will be emitted indefinitely. + + To create an *iterable* of exactly size *n*, you can truncate with + :func:`islice`. + + >>> list(islice(padded([1, 2, 3], '?'), 5)) + [1, 2, 3, '?', '?'] + >>> list(islice(padded([1, 2, 3, 4, 5, 6, 7, 8], '?'), 5)) + [1, 2, 3, 4, 5] + + """ + iterator = iter(iterable) + iterator_with_repeat = chain(iterator, repeat(fillvalue)) + + if n is None: + return iterator_with_repeat + elif n < 1: + raise ValueError('n must be at least 1') + elif next_multiple: + + def slice_generator(): + for first in iterator: + yield (first,) + yield islice(iterator_with_repeat, n - 1) + + # While elements exist produce slices of size n + return chain.from_iterable(slice_generator()) + else: + # Ensure the first batch is at least size n then iterate + return chain(islice(iterator_with_repeat, n), iterator) + + +def repeat_each(iterable, n=2): + """Repeat each element in *iterable* *n* times. + + >>> list(repeat_each('ABC', 3)) + ['A', 'A', 'A', 'B', 'B', 'B', 'C', 'C', 'C'] + """ + return chain.from_iterable(map(repeat, iterable, repeat(n))) + + +def repeat_last(iterable, default=None): + """After the *iterable* is exhausted, keep yielding its last element. + + >>> list(islice(repeat_last(range(3)), 5)) + [0, 1, 2, 2, 2] + + If the iterable is empty, yield *default* forever:: + + >>> list(islice(repeat_last(range(0), 42), 5)) + [42, 42, 42, 42, 42] + + """ + item = _marker + for item in iterable: + yield item + final = default if item is _marker else item + yield from repeat(final) + + +def distribute(n, iterable): + """Distribute the items from *iterable* among *n* smaller iterables. + + >>> group_1, group_2 = distribute(2, [1, 2, 3, 4, 5, 6]) + >>> list(group_1) + [1, 3, 5] + >>> list(group_2) + [2, 4, 6] + + If the length of *iterable* is not evenly divisible by *n*, then the + length of the returned iterables will not be identical: + + >>> children = distribute(3, [1, 2, 3, 4, 5, 6, 7]) + >>> [list(c) for c in children] + [[1, 4, 7], [2, 5], [3, 6]] + + If the length of *iterable* is smaller than *n*, then the last returned + iterables will be empty: + + >>> children = distribute(5, [1, 2, 3]) + >>> [list(c) for c in children] + [[1], [2], [3], [], []] + + This function uses :func:`itertools.tee` and may require significant + storage. + + If you need the order items in the smaller iterables to match the + original iterable, see :func:`divide`. + + """ + if n < 1: + raise ValueError('n must be at least 1') + + children = tee(iterable, n) + return [islice(it, index, None, n) for index, it in enumerate(children)] + + +def stagger(iterable, offsets=(-1, 0, 1), longest=False, fillvalue=None): + """Yield tuples whose elements are offset from *iterable*. + The amount by which the `i`-th item in each tuple is offset is given by + the `i`-th item in *offsets*. + + >>> list(stagger([0, 1, 2, 3])) + [(None, 0, 1), (0, 1, 2), (1, 2, 3)] + >>> list(stagger(range(8), offsets=(0, 2, 4))) + [(0, 2, 4), (1, 3, 5), (2, 4, 6), (3, 5, 7)] + + By default, the sequence will end when the final element of a tuple is the + last item in the iterable. To continue until the first element of a tuple + is the last item in the iterable, set *longest* to ``True``:: + + >>> list(stagger([0, 1, 2, 3], longest=True)) + [(None, 0, 1), (0, 1, 2), (1, 2, 3), (2, 3, None), (3, None, None)] + + By default, ``None`` will be used to replace offsets beyond the end of the + sequence. Specify *fillvalue* to use some other value. + + """ + children = tee(iterable, len(offsets)) + + return zip_offset( + *children, offsets=offsets, longest=longest, fillvalue=fillvalue + ) + + +def zip_equal(*iterables): + """``zip`` the input *iterables* together but raise + ``UnequalIterablesError`` if they aren't all the same length. + + >>> it_1 = range(3) + >>> it_2 = iter('abc') + >>> list(zip_equal(it_1, it_2)) + [(0, 'a'), (1, 'b'), (2, 'c')] + + >>> it_1 = range(3) + >>> it_2 = iter('abcd') + >>> list(zip_equal(it_1, it_2)) # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + ... + more_itertools.more.UnequalIterablesError: Iterables have different + lengths + + """ + if hexversion >= 0x30A00A6: + warnings.warn( + ( + 'zip_equal will be removed in a future version of ' + 'more-itertools. Use the builtin zip function with ' + 'strict=True instead.' + ), + DeprecationWarning, + ) + + return _zip_equal(*iterables) + + +def zip_offset(*iterables, offsets, longest=False, fillvalue=None): + """``zip`` the input *iterables* together, but offset the `i`-th iterable + by the `i`-th item in *offsets*. + + >>> list(zip_offset('0123', 'abcdef', offsets=(0, 1))) + [('0', 'b'), ('1', 'c'), ('2', 'd'), ('3', 'e')] + + This can be used as a lightweight alternative to SciPy or pandas to analyze + data sets in which some series have a lead or lag relationship. + + By default, the sequence will end when the shortest iterable is exhausted. + To continue until the longest iterable is exhausted, set *longest* to + ``True``. + + >>> list(zip_offset('0123', 'abcdef', offsets=(0, 1), longest=True)) + [('0', 'b'), ('1', 'c'), ('2', 'd'), ('3', 'e'), (None, 'f')] + + By default, ``None`` will be used to replace offsets beyond the end of the + sequence. Specify *fillvalue* to use some other value. + + """ + if len(iterables) != len(offsets): + raise ValueError("Number of iterables and offsets didn't match") + + staggered = [] + for it, n in zip(iterables, offsets): + if n < 0: + staggered.append(chain(repeat(fillvalue, -n), it)) + elif n > 0: + staggered.append(islice(it, n, None)) + else: + staggered.append(it) + + if longest: + return zip_longest(*staggered, fillvalue=fillvalue) + + return zip(*staggered) + + +def sort_together( + iterables, key_list=(0,), key=None, reverse=False, strict=False +): + """Return the input iterables sorted together, with *key_list* as the + priority for sorting. All iterables are trimmed to the length of the + shortest one. + + This can be used like the sorting function in a spreadsheet. If each + iterable represents a column of data, the key list determines which + columns are used for sorting. + + By default, all iterables are sorted using the ``0``-th iterable:: + + >>> iterables = [(4, 3, 2, 1), ('a', 'b', 'c', 'd')] + >>> sort_together(iterables) + [(1, 2, 3, 4), ('d', 'c', 'b', 'a')] + + Set a different key list to sort according to another iterable. + Specifying multiple keys dictates how ties are broken:: + + >>> iterables = [(3, 1, 2), (0, 1, 0), ('c', 'b', 'a')] + >>> sort_together(iterables, key_list=(1, 2)) + [(2, 3, 1), (0, 0, 1), ('a', 'c', 'b')] + + To sort by a function of the elements of the iterable, pass a *key* + function. Its arguments are the elements of the iterables corresponding to + the key list:: + + >>> names = ('a', 'b', 'c') + >>> lengths = (1, 2, 3) + >>> widths = (5, 2, 1) + >>> def area(length, width): + ... return length * width + >>> sort_together([names, lengths, widths], key_list=(1, 2), key=area) + [('c', 'b', 'a'), (3, 2, 1), (1, 2, 5)] + + Set *reverse* to ``True`` to sort in descending order. + + >>> sort_together([(1, 2, 3), ('c', 'b', 'a')], reverse=True) + [(3, 2, 1), ('a', 'b', 'c')] + + If the *strict* keyword argument is ``True``, then + ``UnequalIterablesError`` will be raised if any of the iterables have + different lengths. + + """ + if key is None: + # if there is no key function, the key argument to sorted is an + # itemgetter + key_argument = itemgetter(*key_list) + else: + # if there is a key function, call it with the items at the offsets + # specified by the key function as arguments + key_list = list(key_list) + if len(key_list) == 1: + # if key_list contains a single item, pass the item at that offset + # as the only argument to the key function + key_offset = key_list[0] + key_argument = lambda zipped_items: key(zipped_items[key_offset]) + else: + # if key_list contains multiple items, use itemgetter to return a + # tuple of items, which we pass as *args to the key function + get_key_items = itemgetter(*key_list) + key_argument = lambda zipped_items: key( + *get_key_items(zipped_items) + ) + + zipper = zip_equal if strict else zip + return list( + zipper(*sorted(zipper(*iterables), key=key_argument, reverse=reverse)) + ) + + +def unzip(iterable): + """The inverse of :func:`zip`, this function disaggregates the elements + of the zipped *iterable*. + + The ``i``-th iterable contains the ``i``-th element from each element + of the zipped iterable. The first element is used to determine the + length of the remaining elements. + + >>> iterable = [('a', 1), ('b', 2), ('c', 3), ('d', 4)] + >>> letters, numbers = unzip(iterable) + >>> list(letters) + ['a', 'b', 'c', 'd'] + >>> list(numbers) + [1, 2, 3, 4] + + This is similar to using ``zip(*iterable)``, but it avoids reading + *iterable* into memory. Note, however, that this function uses + :func:`itertools.tee` and thus may require significant storage. + + """ + head, iterable = spy(iterable) + if not head: + # empty iterable, e.g. zip([], [], []) + return () + # spy returns a one-length iterable as head + head = head[0] + iterables = tee(iterable, len(head)) + + # If we have an iterable like iter([(1, 2, 3), (4, 5), (6,)]), + # the second unzipped iterable fails at the third tuple since + # it tries to access (6,)[1]. + # Same with the third unzipped iterable and the second tuple. + # To support these "improperly zipped" iterables, we suppress + # the IndexError, which just stops the unzipped iterables at + # first length mismatch. + return tuple( + iter_suppress(map(itemgetter(i), it), IndexError) + for i, it in enumerate(iterables) + ) + + +def divide(n, iterable): + """Divide the elements from *iterable* into *n* parts, maintaining + order. + + >>> group_1, group_2 = divide(2, [1, 2, 3, 4, 5, 6]) + >>> list(group_1) + [1, 2, 3] + >>> list(group_2) + [4, 5, 6] + + If the length of *iterable* is not evenly divisible by *n*, then the + length of the returned iterables will not be identical: + + >>> children = divide(3, [1, 2, 3, 4, 5, 6, 7]) + >>> [list(c) for c in children] + [[1, 2, 3], [4, 5], [6, 7]] + + If the length of the iterable is smaller than n, then the last returned + iterables will be empty: + + >>> children = divide(5, [1, 2, 3]) + >>> [list(c) for c in children] + [[1], [2], [3], [], []] + + This function will exhaust the iterable before returning. + If order is not important, see :func:`distribute`, which does not first + pull the iterable into memory. + + """ + if n < 1: + raise ValueError('n must be at least 1') + + try: + iterable[:0] + except TypeError: + seq = tuple(iterable) + else: + seq = iterable + + q, r = divmod(len(seq), n) + + ret = [] + stop = 0 + for i in range(1, n + 1): + start = stop + stop += q + 1 if i <= r else q + ret.append(iter(seq[start:stop])) + + return ret + + +def always_iterable(obj, base_type=(str, bytes)): + """If *obj* is iterable, return an iterator over its items:: + + >>> obj = (1, 2, 3) + >>> list(always_iterable(obj)) + [1, 2, 3] + + If *obj* is not iterable, return a one-item iterable containing *obj*:: + + >>> obj = 1 + >>> list(always_iterable(obj)) + [1] + + If *obj* is ``None``, return an empty iterable: + + >>> obj = None + >>> list(always_iterable(None)) + [] + + By default, binary and text strings are not considered iterable:: + + >>> obj = 'foo' + >>> list(always_iterable(obj)) + ['foo'] + + If *base_type* is set, objects for which ``isinstance(obj, base_type)`` + returns ``True`` won't be considered iterable. + + >>> obj = {'a': 1} + >>> list(always_iterable(obj)) # Iterate over the dict's keys + ['a'] + >>> list(always_iterable(obj, base_type=dict)) # Treat dicts as a unit + [{'a': 1}] + + Set *base_type* to ``None`` to avoid any special handling and treat objects + Python considers iterable as iterable: + + >>> obj = 'foo' + >>> list(always_iterable(obj, base_type=None)) + ['f', 'o', 'o'] + """ + if obj is None: + return iter(()) + + if (base_type is not None) and isinstance(obj, base_type): + return iter((obj,)) + + try: + return iter(obj) + except TypeError: + return iter((obj,)) + + +def adjacent(predicate, iterable, distance=1): + """Return an iterable over `(bool, item)` tuples where the `item` is + drawn from *iterable* and the `bool` indicates whether + that item satisfies the *predicate* or is adjacent to an item that does. + + For example, to find whether items are adjacent to a ``3``:: + + >>> list(adjacent(lambda x: x == 3, range(6))) + [(False, 0), (False, 1), (True, 2), (True, 3), (True, 4), (False, 5)] + + Set *distance* to change what counts as adjacent. For example, to find + whether items are two places away from a ``3``: + + >>> list(adjacent(lambda x: x == 3, range(6), distance=2)) + [(False, 0), (True, 1), (True, 2), (True, 3), (True, 4), (True, 5)] + + This is useful for contextualizing the results of a search function. + For example, a code comparison tool might want to identify lines that + have changed, but also surrounding lines to give the viewer of the diff + context. + + The predicate function will only be called once for each item in the + iterable. + + See also :func:`groupby_transform`, which can be used with this function + to group ranges of items with the same `bool` value. + + """ + # Allow distance=0 mainly for testing that it reproduces results with map() + if distance < 0: + raise ValueError('distance must be at least 0') + + i1, i2 = tee(iterable) + padding = [False] * distance + selected = chain(padding, map(predicate, i1), padding) + adjacent_to_selected = map(any, windowed(selected, 2 * distance + 1)) + return zip(adjacent_to_selected, i2) + + +def groupby_transform(iterable, keyfunc=None, valuefunc=None, reducefunc=None): + """An extension of :func:`itertools.groupby` that can apply transformations + to the grouped data. + + * *keyfunc* is a function computing a key value for each item in *iterable* + * *valuefunc* is a function that transforms the individual items from + *iterable* after grouping + * *reducefunc* is a function that transforms each group of items + + >>> iterable = 'aAAbBBcCC' + >>> keyfunc = lambda k: k.upper() + >>> valuefunc = lambda v: v.lower() + >>> reducefunc = lambda g: ''.join(g) + >>> list(groupby_transform(iterable, keyfunc, valuefunc, reducefunc)) + [('A', 'aaa'), ('B', 'bbb'), ('C', 'ccc')] + + Each optional argument defaults to an identity function if not specified. + + :func:`groupby_transform` is useful when grouping elements of an iterable + using a separate iterable as the key. To do this, :func:`zip` the iterables + and pass a *keyfunc* that extracts the first element and a *valuefunc* + that extracts the second element:: + + >>> from operator import itemgetter + >>> keys = [0, 0, 1, 1, 1, 2, 2, 2, 3] + >>> values = 'abcdefghi' + >>> iterable = zip(keys, values) + >>> grouper = groupby_transform(iterable, itemgetter(0), itemgetter(1)) + >>> [(k, ''.join(g)) for k, g in grouper] + [(0, 'ab'), (1, 'cde'), (2, 'fgh'), (3, 'i')] + + Note that the order of items in the iterable is significant. + Only adjacent items are grouped together, so if you don't want any + duplicate groups, you should sort the iterable by the key function. + + """ + ret = groupby(iterable, keyfunc) + if valuefunc: + ret = ((k, map(valuefunc, g)) for k, g in ret) + if reducefunc: + ret = ((k, reducefunc(g)) for k, g in ret) + + return ret + + +class numeric_range(abc.Sequence, abc.Hashable): + """An extension of the built-in ``range()`` function whose arguments can + be any orderable numeric type. + + With only *stop* specified, *start* defaults to ``0`` and *step* + defaults to ``1``. The output items will match the type of *stop*: + + >>> list(numeric_range(3.5)) + [0.0, 1.0, 2.0, 3.0] + + With only *start* and *stop* specified, *step* defaults to ``1``. The + output items will match the type of *start*: + + >>> from decimal import Decimal + >>> start = Decimal('2.1') + >>> stop = Decimal('5.1') + >>> list(numeric_range(start, stop)) + [Decimal('2.1'), Decimal('3.1'), Decimal('4.1')] + + With *start*, *stop*, and *step* specified the output items will match + the type of ``start + step``: + + >>> from fractions import Fraction + >>> start = Fraction(1, 2) # Start at 1/2 + >>> stop = Fraction(5, 2) # End at 5/2 + >>> step = Fraction(1, 2) # Count by 1/2 + >>> list(numeric_range(start, stop, step)) + [Fraction(1, 2), Fraction(1, 1), Fraction(3, 2), Fraction(2, 1)] + + If *step* is zero, ``ValueError`` is raised. Negative steps are supported: + + >>> list(numeric_range(3, -1, -1.0)) + [3.0, 2.0, 1.0, 0.0] + + Be aware of the limitations of floating-point numbers; the representation + of the yielded numbers may be surprising. + + ``datetime.datetime`` objects can be used for *start* and *stop*, if *step* + is a ``datetime.timedelta`` object: + + >>> import datetime + >>> start = datetime.datetime(2019, 1, 1) + >>> stop = datetime.datetime(2019, 1, 3) + >>> step = datetime.timedelta(days=1) + >>> items = iter(numeric_range(start, stop, step)) + >>> next(items) + datetime.datetime(2019, 1, 1, 0, 0) + >>> next(items) + datetime.datetime(2019, 1, 2, 0, 0) + + """ + + _EMPTY_HASH = hash(range(0, 0)) + + def __init__(self, *args): + argc = len(args) + if argc == 1: + (self._stop,) = args + self._start = type(self._stop)(0) + self._step = type(self._stop - self._start)(1) + elif argc == 2: + self._start, self._stop = args + self._step = type(self._stop - self._start)(1) + elif argc == 3: + self._start, self._stop, self._step = args + elif argc == 0: + raise TypeError( + f'numeric_range expected at least 1 argument, got {argc}' + ) + else: + raise TypeError( + f'numeric_range expected at most 3 arguments, got {argc}' + ) + + self._zero = type(self._step)(0) + if self._step == self._zero: + raise ValueError('numeric_range() arg 3 must not be zero') + self._growing = self._step > self._zero + + def __bool__(self): + if self._growing: + return self._start < self._stop + else: + return self._start > self._stop + + def __contains__(self, elem): + if self._growing: + if self._start <= elem < self._stop: + return (elem - self._start) % self._step == self._zero + else: + if self._start >= elem > self._stop: + return (self._start - elem) % (-self._step) == self._zero + + return False + + def __eq__(self, other): + if isinstance(other, numeric_range): + empty_self = not bool(self) + empty_other = not bool(other) + if empty_self or empty_other: + return empty_self and empty_other # True if both empty + else: + return ( + self._start == other._start + and self._step == other._step + and self._get_by_index(-1) == other._get_by_index(-1) + ) + else: + return False + + def __getitem__(self, key): + if isinstance(key, int): + return self._get_by_index(key) + elif isinstance(key, slice): + step = self._step if key.step is None else key.step * self._step + + if key.start is None or key.start <= -self._len: + start = self._start + elif key.start >= self._len: + start = self._stop + else: # -self._len < key.start < self._len + start = self._get_by_index(key.start) + + if key.stop is None or key.stop >= self._len: + stop = self._stop + elif key.stop <= -self._len: + stop = self._start + else: # -self._len < key.stop < self._len + stop = self._get_by_index(key.stop) + + return numeric_range(start, stop, step) + else: + raise TypeError( + 'numeric range indices must be ' + f'integers or slices, not {type(key).__name__}' + ) + + def __hash__(self): + if self: + return hash((self._start, self._get_by_index(-1), self._step)) + else: + return self._EMPTY_HASH + + def __iter__(self): + values = (self._start + (n * self._step) for n in count()) + if self._growing: + return takewhile(partial(gt, self._stop), values) + else: + return takewhile(partial(lt, self._stop), values) + + def __len__(self): + return self._len + + @cached_property + def _len(self): + if self._growing: + start = self._start + stop = self._stop + step = self._step + else: + start = self._stop + stop = self._start + step = -self._step + distance = stop - start + if distance <= self._zero: + return 0 + else: # distance > 0 and step > 0: regular euclidean division + q, r = divmod(distance, step) + return int(q) + int(r != self._zero) + + def __reduce__(self): + return numeric_range, (self._start, self._stop, self._step) + + def __repr__(self): + if self._step == 1: + return f"numeric_range({self._start!r}, {self._stop!r})" + return ( + f"numeric_range({self._start!r}, {self._stop!r}, {self._step!r})" + ) + + def __reversed__(self): + return iter( + numeric_range( + self._get_by_index(-1), self._start - self._step, -self._step + ) + ) + + def count(self, value): + return int(value in self) + + def index(self, value): + if self._growing: + if self._start <= value < self._stop: + q, r = divmod(value - self._start, self._step) + if r == self._zero: + return int(q) + else: + if self._start >= value > self._stop: + q, r = divmod(self._start - value, -self._step) + if r == self._zero: + return int(q) + + raise ValueError(f"{value} is not in numeric range") + + def _get_by_index(self, i): + if i < 0: + i += self._len + if i < 0 or i >= self._len: + raise IndexError("numeric range object index out of range") + return self._start + i * self._step + + +def count_cycle(iterable, n=None): + """Cycle through the items from *iterable* up to *n* times, yielding + the number of completed cycles along with each item. If *n* is omitted the + process repeats indefinitely. + + >>> list(count_cycle('AB', 3)) + [(0, 'A'), (0, 'B'), (1, 'A'), (1, 'B'), (2, 'A'), (2, 'B')] + + """ + seq = tuple(iterable) + if not seq: + return iter(()) + counter = count() if n is None else range(n) + return zip(repeat_each(counter, len(seq)), cycle(seq)) + + +def mark_ends(iterable): + """Yield 3-tuples of the form ``(is_first, is_last, item)``. + + >>> list(mark_ends('ABC')) + [(True, False, 'A'), (False, False, 'B'), (False, True, 'C')] + + Use this when looping over an iterable to take special action on its first + and/or last items: + + >>> iterable = ['Header', 100, 200, 'Footer'] + >>> total = 0 + >>> for is_first, is_last, item in mark_ends(iterable): + ... if is_first: + ... continue # Skip the header + ... if is_last: + ... continue # Skip the footer + ... total += item + >>> print(total) + 300 + """ + it = iter(iterable) + for a in it: + first = True + for b in it: + yield first, False, a + a = b + first = False + yield first, True, a + + +def locate(iterable, pred=bool, window_size=None): + """Yield the index of each item in *iterable* for which *pred* returns + ``True``. + + *pred* defaults to :func:`bool`, which will select truthy items: + + >>> list(locate([0, 1, 1, 0, 1, 0, 0])) + [1, 2, 4] + + Set *pred* to a custom function to, e.g., find the indexes for a particular + item. + + >>> list(locate(['a', 'b', 'c', 'b'], lambda x: x == 'b')) + [1, 3] + + If *window_size* is given, then the *pred* function will be called with + that many items. This enables searching for sub-sequences: + + >>> iterable = [0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3] + >>> pred = lambda *args: args == (1, 2, 3) + >>> list(locate(iterable, pred=pred, window_size=3)) + [1, 5, 9] + + Use with :func:`seekable` to find indexes and then retrieve the associated + items: + + >>> from itertools import count + >>> from more_itertools import seekable + >>> source = (3 * n + 1 if (n % 2) else n // 2 for n in count()) + >>> it = seekable(source) + >>> pred = lambda x: x > 100 + >>> indexes = locate(it, pred=pred) + >>> i = next(indexes) + >>> it.seek(i) + >>> next(it) + 106 + + """ + if window_size is None: + return compress(count(), map(pred, iterable)) + + if window_size < 1: + raise ValueError('window size must be at least 1') + + it = windowed(iterable, window_size, fillvalue=_marker) + return compress(count(), starmap(pred, it)) + + +def longest_common_prefix(iterables): + """Yield elements of the longest common prefix among given *iterables*. + + >>> ''.join(longest_common_prefix(['abcd', 'abc', 'abf'])) + 'ab' + + """ + return (c[0] for c in takewhile(all_equal, zip(*iterables))) + + +def lstrip(iterable, pred): + """Yield the items from *iterable*, but strip any from the beginning + for which *pred* returns ``True``. + + For example, to remove a set of items from the start of an iterable: + + >>> iterable = (None, False, None, 1, 2, None, 3, False, None) + >>> pred = lambda x: x in {None, False, ''} + >>> list(lstrip(iterable, pred)) + [1, 2, None, 3, False, None] + + This function is analogous to to :func:`str.lstrip`, and is essentially + an wrapper for :func:`itertools.dropwhile`. + + """ + return dropwhile(pred, iterable) + + +def rstrip(iterable, pred): + """Yield the items from *iterable*, but strip any from the end + for which *pred* returns ``True``. + + For example, to remove a set of items from the end of an iterable: + + >>> iterable = (None, False, None, 1, 2, None, 3, False, None) + >>> pred = lambda x: x in {None, False, ''} + >>> list(rstrip(iterable, pred)) + [None, False, None, 1, 2, None, 3] + + This function is analogous to :func:`str.rstrip`. + + """ + cache = [] + cache_append = cache.append + cache_clear = cache.clear + for x in iterable: + if pred(x): + cache_append(x) + else: + yield from cache + cache_clear() + yield x + + +def strip(iterable, pred): + """Yield the items from *iterable*, but strip any from the + beginning and end for which *pred* returns ``True``. + + For example, to remove a set of items from both ends of an iterable: + + >>> iterable = (None, False, None, 1, 2, None, 3, False, None) + >>> pred = lambda x: x in {None, False, ''} + >>> list(strip(iterable, pred)) + [1, 2, None, 3] + + This function is analogous to :func:`str.strip`. + + """ + return rstrip(lstrip(iterable, pred), pred) + + +class islice_extended: + """An extension of :func:`itertools.islice` that supports negative values + for *stop*, *start*, and *step*. + + >>> iterator = iter('abcdefgh') + >>> list(islice_extended(iterator, -4, -1)) + ['e', 'f', 'g'] + + Slices with negative values require some caching of *iterable*, but this + function takes care to minimize the amount of memory required. + + For example, you can use a negative step with an infinite iterator: + + >>> from itertools import count + >>> list(islice_extended(count(), 110, 99, -2)) + [110, 108, 106, 104, 102, 100] + + You can also use slice notation directly: + + >>> iterator = map(str, count()) + >>> it = islice_extended(iterator)[10:20:2] + >>> list(it) + ['10', '12', '14', '16', '18'] + + """ + + def __init__(self, iterable, *args): + it = iter(iterable) + if args: + self._iterator = _islice_helper(it, slice(*args)) + else: + self._iterator = it + + def __iter__(self): + return self + + def __next__(self): + return next(self._iterator) + + def __getitem__(self, key): + if isinstance(key, slice): + return islice_extended(_islice_helper(self._iterator, key)) + + raise TypeError('islice_extended.__getitem__ argument must be a slice') + + +def _islice_helper(it, s): + start = s.start + stop = s.stop + if s.step == 0: + raise ValueError('step argument must be a non-zero integer or None.') + step = s.step or 1 + + if step > 0: + start = 0 if (start is None) else start + + if start < 0: + # Consume all but the last -start items + cache = deque(enumerate(it, 1), maxlen=-start) + len_iter = cache[-1][0] if cache else 0 + + # Adjust start to be positive + i = max(len_iter + start, 0) + + # Adjust stop to be positive + if stop is None: + j = len_iter + elif stop >= 0: + j = min(stop, len_iter) + else: + j = max(len_iter + stop, 0) + + # Slice the cache + n = j - i + if n <= 0: + return + + for index in range(n): + if index % step == 0: + # pop and yield the item. + # We don't want to use an intermediate variable + # it would extend the lifetime of the current item + yield cache.popleft()[1] + else: + # just pop and discard the item + cache.popleft() + elif (stop is not None) and (stop < 0): + # Advance to the start position + next(islice(it, start, start), None) + + # When stop is negative, we have to carry -stop items while + # iterating + cache = deque(islice(it, -stop), maxlen=-stop) + + for index, item in enumerate(it): + if index % step == 0: + # pop and yield the item. + # We don't want to use an intermediate variable + # it would extend the lifetime of the current item + yield cache.popleft() + else: + # just pop and discard the item + cache.popleft() + cache.append(item) + else: + # When both start and stop are positive we have the normal case + yield from islice(it, start, stop, step) + else: + start = -1 if (start is None) else start + + if (stop is not None) and (stop < 0): + # Consume all but the last items + n = -stop - 1 + cache = deque(enumerate(it, 1), maxlen=n) + len_iter = cache[-1][0] if cache else 0 + + # If start and stop are both negative they are comparable and + # we can just slice. Otherwise we can adjust start to be negative + # and then slice. + if start < 0: + i, j = start, stop + else: + i, j = min(start - len_iter, -1), None + + for index, item in list(cache)[i:j:step]: + yield item + else: + # Advance to the stop position + if stop is not None: + m = stop + 1 + next(islice(it, m, m), None) + + # stop is positive, so if start is negative they are not comparable + # and we need the rest of the items. + if start < 0: + i = start + n = None + # stop is None and start is positive, so we just need items up to + # the start index. + elif stop is None: + i = None + n = start + 1 + # Both stop and start are positive, so they are comparable. + else: + i = None + n = start - stop + if n <= 0: + return + + cache = list(islice(it, n)) + + yield from cache[i::step] + + +def always_reversible(iterable): + """An extension of :func:`reversed` that supports all iterables, not + just those which implement the ``Reversible`` or ``Sequence`` protocols. + + >>> print(*always_reversible(x for x in range(3))) + 2 1 0 + + If the iterable is already reversible, this function returns the + result of :func:`reversed()`. If the iterable is not reversible, + this function will cache the remaining items in the iterable and + yield them in reverse order, which may require significant storage. + """ + try: + return reversed(iterable) + except TypeError: + return reversed(list(iterable)) + + +def consecutive_groups(iterable, ordering=None): + """Yield groups of consecutive items using :func:`itertools.groupby`. + The *ordering* function determines whether two items are adjacent by + returning their position. + + By default, the ordering function is the identity function. This is + suitable for finding runs of numbers: + + >>> iterable = [1, 10, 11, 12, 20, 30, 31, 32, 33, 40] + >>> for group in consecutive_groups(iterable): + ... print(list(group)) + [1] + [10, 11, 12] + [20] + [30, 31, 32, 33] + [40] + + To find runs of adjacent letters, apply :func:`ord` function + to convert letters to ordinals. + + >>> iterable = 'abcdfgilmnop' + >>> ordering = ord + >>> for group in consecutive_groups(iterable, ordering): + ... print(list(group)) + ['a', 'b', 'c', 'd'] + ['f', 'g'] + ['i'] + ['l', 'm', 'n', 'o', 'p'] + + Each group of consecutive items is an iterator that shares it source with + *iterable*. When an an output group is advanced, the previous group is + no longer available unless its elements are copied (e.g., into a ``list``). + + >>> iterable = [1, 2, 11, 12, 21, 22] + >>> saved_groups = [] + >>> for group in consecutive_groups(iterable): + ... saved_groups.append(list(group)) # Copy group elements + >>> saved_groups + [[1, 2], [11, 12], [21, 22]] + + """ + if ordering is None: + key = lambda x: x[0] - x[1] + else: + key = lambda x: x[0] - ordering(x[1]) + + for k, g in groupby(enumerate(iterable), key=key): + yield map(itemgetter(1), g) + + +def difference(iterable, func=sub, *, initial=None): + """This function is the inverse of :func:`itertools.accumulate`. By default + it will compute the first difference of *iterable* using + :func:`operator.sub`: + + >>> from itertools import accumulate + >>> iterable = accumulate([0, 1, 2, 3, 4]) # produces 0, 1, 3, 6, 10 + >>> list(difference(iterable)) + [0, 1, 2, 3, 4] + + *func* defaults to :func:`operator.sub`, but other functions can be + specified. They will be applied as follows:: + + A, B, C, D, ... --> A, func(B, A), func(C, B), func(D, C), ... + + For example, to do progressive division: + + >>> iterable = [1, 2, 6, 24, 120] + >>> func = lambda x, y: x // y + >>> list(difference(iterable, func)) + [1, 2, 3, 4, 5] + + If the *initial* keyword is set, the first element will be skipped when + computing successive differences. + + >>> it = [10, 11, 13, 16] # from accumulate([1, 2, 3], initial=10) + >>> list(difference(it, initial=10)) + [1, 2, 3] + + """ + a, b = tee(iterable) + try: + first = [next(b)] + except StopIteration: + return iter([]) + + if initial is not None: + first = [] + + return chain(first, map(func, b, a)) + + +class SequenceView(Sequence): + """Return a read-only view of the sequence object *target*. + + :class:`SequenceView` objects are analogous to Python's built-in + "dictionary view" types. They provide a dynamic view of a sequence's items, + meaning that when the sequence updates, so does the view. + + >>> seq = ['0', '1', '2'] + >>> view = SequenceView(seq) + >>> view + SequenceView(['0', '1', '2']) + >>> seq.append('3') + >>> view + SequenceView(['0', '1', '2', '3']) + + Sequence views support indexing, slicing, and length queries. They act + like the underlying sequence, except they don't allow assignment: + + >>> view[1] + '1' + >>> view[1:-1] + ['1', '2'] + >>> len(view) + 4 + + Sequence views are useful as an alternative to copying, as they don't + require (much) extra storage. + + """ + + def __init__(self, target): + if not isinstance(target, Sequence): + raise TypeError + self._target = target + + def __getitem__(self, index): + return self._target[index] + + def __len__(self): + return len(self._target) + + def __repr__(self): + return f'{self.__class__.__name__}({self._target!r})' + + +class seekable: + """Wrap an iterator to allow for seeking backward and forward. This + progressively caches the items in the source iterable so they can be + re-visited. + + Call :meth:`seek` with an index to seek to that position in the source + iterable. + + To "reset" an iterator, seek to ``0``: + + >>> from itertools import count + >>> it = seekable((str(n) for n in count())) + >>> next(it), next(it), next(it) + ('0', '1', '2') + >>> it.seek(0) + >>> next(it), next(it), next(it) + ('0', '1', '2') + + You can also seek forward: + + >>> it = seekable((str(n) for n in range(20))) + >>> it.seek(10) + >>> next(it) + '10' + >>> it.seek(20) # Seeking past the end of the source isn't a problem + >>> list(it) + [] + >>> it.seek(0) # Resetting works even after hitting the end + >>> next(it) + '0' + + Call :meth:`relative_seek` to seek relative to the source iterator's + current position. + + >>> it = seekable((str(n) for n in range(20))) + >>> next(it), next(it), next(it) + ('0', '1', '2') + >>> it.relative_seek(2) + >>> next(it) + '5' + >>> it.relative_seek(-3) # Source is at '6', we move back to '3' + >>> next(it) + '3' + >>> it.relative_seek(-3) # Source is at '4', we move back to '1' + >>> next(it) + '1' + + + Call :meth:`peek` to look ahead one item without advancing the iterator: + + >>> it = seekable('1234') + >>> it.peek() + '1' + >>> list(it) + ['1', '2', '3', '4'] + >>> it.peek(default='empty') + 'empty' + + Before the iterator is at its end, calling :func:`bool` on it will return + ``True``. After it will return ``False``: + + >>> it = seekable('5678') + >>> bool(it) + True + >>> list(it) + ['5', '6', '7', '8'] + >>> bool(it) + False + + You may view the contents of the cache with the :meth:`elements` method. + That returns a :class:`SequenceView`, a view that updates automatically: + + >>> it = seekable((str(n) for n in range(10))) + >>> next(it), next(it), next(it) + ('0', '1', '2') + >>> elements = it.elements() + >>> elements + SequenceView(['0', '1', '2']) + >>> next(it) + '3' + >>> elements + SequenceView(['0', '1', '2', '3']) + + By default, the cache grows as the source iterable progresses, so beware of + wrapping very large or infinite iterables. Supply *maxlen* to limit the + size of the cache (this of course limits how far back you can seek). + + >>> from itertools import count + >>> it = seekable((str(n) for n in count()), maxlen=2) + >>> next(it), next(it), next(it), next(it) + ('0', '1', '2', '3') + >>> list(it.elements()) + ['2', '3'] + >>> it.seek(0) + >>> next(it), next(it), next(it), next(it) + ('2', '3', '4', '5') + >>> next(it) + '6' + + """ + + def __init__(self, iterable, maxlen=None): + self._source = iter(iterable) + if maxlen is None: + self._cache = [] + else: + self._cache = deque([], maxlen) + self._index = None + + def __iter__(self): + return self + + def __next__(self): + if self._index is not None: + try: + item = self._cache[self._index] + except IndexError: + self._index = None + else: + self._index += 1 + return item + + item = next(self._source) + self._cache.append(item) + return item + + def __bool__(self): + try: + self.peek() + except StopIteration: + return False + return True + + def peek(self, default=_marker): + try: + peeked = next(self) + except StopIteration: + if default is _marker: + raise + return default + if self._index is None: + self._index = len(self._cache) + self._index -= 1 + return peeked + + def elements(self): + return SequenceView(self._cache) + + def seek(self, index): + self._index = index + remainder = index - len(self._cache) + if remainder > 0: + consume(self, remainder) + + def relative_seek(self, count): + if self._index is None: + self._index = len(self._cache) + + self.seek(max(self._index + count, 0)) + + +class run_length: + """ + :func:`run_length.encode` compresses an iterable with run-length encoding. + It yields groups of repeated items with the count of how many times they + were repeated: + + >>> uncompressed = 'abbcccdddd' + >>> list(run_length.encode(uncompressed)) + [('a', 1), ('b', 2), ('c', 3), ('d', 4)] + + :func:`run_length.decode` decompresses an iterable that was previously + compressed with run-length encoding. It yields the items of the + decompressed iterable: + + >>> compressed = [('a', 1), ('b', 2), ('c', 3), ('d', 4)] + >>> list(run_length.decode(compressed)) + ['a', 'b', 'b', 'c', 'c', 'c', 'd', 'd', 'd', 'd'] + + """ + + @staticmethod + def encode(iterable): + return ((k, ilen(g)) for k, g in groupby(iterable)) + + @staticmethod + def decode(iterable): + return chain.from_iterable(starmap(repeat, iterable)) + + +def exactly_n(iterable, n, predicate=bool): + """Return ``True`` if exactly ``n`` items in the iterable are ``True`` + according to the *predicate* function. + + >>> exactly_n([True, True, False], 2) + True + >>> exactly_n([True, True, False], 1) + False + >>> exactly_n([0, 1, 2, 3, 4, 5], 3, lambda x: x < 3) + True + + The iterable will be advanced until ``n + 1`` truthy items are encountered, + so avoid calling it on infinite iterables. + + """ + return ilen(islice(filter(predicate, iterable), n + 1)) == n + + +def circular_shifts(iterable, steps=1): + """Yield the circular shifts of *iterable*. + + >>> list(circular_shifts(range(4))) + [(0, 1, 2, 3), (1, 2, 3, 0), (2, 3, 0, 1), (3, 0, 1, 2)] + + Set *steps* to the number of places to rotate to the left + (or to the right if negative). Defaults to 1. + + >>> list(circular_shifts(range(4), 2)) + [(0, 1, 2, 3), (2, 3, 0, 1)] + + >>> list(circular_shifts(range(4), -1)) + [(0, 1, 2, 3), (3, 0, 1, 2), (2, 3, 0, 1), (1, 2, 3, 0)] + + """ + buffer = deque(iterable) + if steps == 0: + raise ValueError('Steps should be a non-zero integer') + + buffer.rotate(steps) + steps = -steps + n = len(buffer) + n //= math.gcd(n, steps) + + for _ in repeat(None, n): + buffer.rotate(steps) + yield tuple(buffer) + + +def make_decorator(wrapping_func, result_index=0): + """Return a decorator version of *wrapping_func*, which is a function that + modifies an iterable. *result_index* is the position in that function's + signature where the iterable goes. + + This lets you use itertools on the "production end," i.e. at function + definition. This can augment what the function returns without changing the + function's code. + + For example, to produce a decorator version of :func:`chunked`: + + >>> from more_itertools import chunked + >>> chunker = make_decorator(chunked, result_index=0) + >>> @chunker(3) + ... def iter_range(n): + ... return iter(range(n)) + ... + >>> list(iter_range(9)) + [[0, 1, 2], [3, 4, 5], [6, 7, 8]] + + To only allow truthy items to be returned: + + >>> truth_serum = make_decorator(filter, result_index=1) + >>> @truth_serum(bool) + ... def boolean_test(): + ... return [0, 1, '', ' ', False, True] + ... + >>> list(boolean_test()) + [1, ' ', True] + + The :func:`peekable` and :func:`seekable` wrappers make for practical + decorators: + + >>> from more_itertools import peekable + >>> peekable_function = make_decorator(peekable) + >>> @peekable_function() + ... def str_range(*args): + ... return (str(x) for x in range(*args)) + ... + >>> it = str_range(1, 20, 2) + >>> next(it), next(it), next(it) + ('1', '3', '5') + >>> it.peek() + '7' + >>> next(it) + '7' + + """ + + # See https://sites.google.com/site/bbayles/index/decorator_factory for + # notes on how this works. + def decorator(*wrapping_args, **wrapping_kwargs): + def outer_wrapper(f): + def inner_wrapper(*args, **kwargs): + result = f(*args, **kwargs) + wrapping_args_ = list(wrapping_args) + wrapping_args_.insert(result_index, result) + return wrapping_func(*wrapping_args_, **wrapping_kwargs) + + return inner_wrapper + + return outer_wrapper + + return decorator + + +def map_reduce(iterable, keyfunc, valuefunc=None, reducefunc=None): + """Return a dictionary that maps the items in *iterable* to categories + defined by *keyfunc*, transforms them with *valuefunc*, and + then summarizes them by category with *reducefunc*. + + *valuefunc* defaults to the identity function if it is unspecified. + If *reducefunc* is unspecified, no summarization takes place: + + >>> keyfunc = lambda x: x.upper() + >>> result = map_reduce('abbccc', keyfunc) + >>> sorted(result.items()) + [('A', ['a']), ('B', ['b', 'b']), ('C', ['c', 'c', 'c'])] + + Specifying *valuefunc* transforms the categorized items: + + >>> keyfunc = lambda x: x.upper() + >>> valuefunc = lambda x: 1 + >>> result = map_reduce('abbccc', keyfunc, valuefunc) + >>> sorted(result.items()) + [('A', [1]), ('B', [1, 1]), ('C', [1, 1, 1])] + + Specifying *reducefunc* summarizes the categorized items: + + >>> keyfunc = lambda x: x.upper() + >>> valuefunc = lambda x: 1 + >>> reducefunc = sum + >>> result = map_reduce('abbccc', keyfunc, valuefunc, reducefunc) + >>> sorted(result.items()) + [('A', 1), ('B', 2), ('C', 3)] + + You may want to filter the input iterable before applying the map/reduce + procedure: + + >>> all_items = range(30) + >>> items = [x for x in all_items if 10 <= x <= 20] # Filter + >>> keyfunc = lambda x: x % 2 # Evens map to 0; odds to 1 + >>> categories = map_reduce(items, keyfunc=keyfunc) + >>> sorted(categories.items()) + [(0, [10, 12, 14, 16, 18, 20]), (1, [11, 13, 15, 17, 19])] + >>> summaries = map_reduce(items, keyfunc=keyfunc, reducefunc=sum) + >>> sorted(summaries.items()) + [(0, 90), (1, 75)] + + Note that all items in the iterable are gathered into a list before the + summarization step, which may require significant storage. + + The returned object is a :obj:`collections.defaultdict` with the + ``default_factory`` set to ``None``, such that it behaves like a normal + dictionary. + + """ + + ret = defaultdict(list) + + if valuefunc is None: + for item in iterable: + key = keyfunc(item) + ret[key].append(item) + + else: + for item in iterable: + key = keyfunc(item) + value = valuefunc(item) + ret[key].append(value) + + if reducefunc is not None: + for key, value_list in ret.items(): + ret[key] = reducefunc(value_list) + + ret.default_factory = None + return ret + + +def rlocate(iterable, pred=bool, window_size=None): + """Yield the index of each item in *iterable* for which *pred* returns + ``True``, starting from the right and moving left. + + *pred* defaults to :func:`bool`, which will select truthy items: + + >>> list(rlocate([0, 1, 1, 0, 1, 0, 0])) # Truthy at 1, 2, and 4 + [4, 2, 1] + + Set *pred* to a custom function to, e.g., find the indexes for a particular + item: + + >>> iterator = iter('abcb') + >>> pred = lambda x: x == 'b' + >>> list(rlocate(iterator, pred)) + [3, 1] + + If *window_size* is given, then the *pred* function will be called with + that many items. This enables searching for sub-sequences: + + >>> iterable = [0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3] + >>> pred = lambda *args: args == (1, 2, 3) + >>> list(rlocate(iterable, pred=pred, window_size=3)) + [9, 5, 1] + + Beware, this function won't return anything for infinite iterables. + If *iterable* is reversible, ``rlocate`` will reverse it and search from + the right. Otherwise, it will search from the left and return the results + in reverse order. + + See :func:`locate` to for other example applications. + + """ + if window_size is None: + try: + len_iter = len(iterable) + return (len_iter - i - 1 for i in locate(reversed(iterable), pred)) + except TypeError: + pass + + return reversed(list(locate(iterable, pred, window_size))) + + +def replace(iterable, pred, substitutes, count=None, window_size=1): + """Yield the items from *iterable*, replacing the items for which *pred* + returns ``True`` with the items from the iterable *substitutes*. + + >>> iterable = [1, 1, 0, 1, 1, 0, 1, 1] + >>> pred = lambda x: x == 0 + >>> substitutes = (2, 3) + >>> list(replace(iterable, pred, substitutes)) + [1, 1, 2, 3, 1, 1, 2, 3, 1, 1] + + If *count* is given, the number of replacements will be limited: + + >>> iterable = [1, 1, 0, 1, 1, 0, 1, 1, 0] + >>> pred = lambda x: x == 0 + >>> substitutes = [None] + >>> list(replace(iterable, pred, substitutes, count=2)) + [1, 1, None, 1, 1, None, 1, 1, 0] + + Use *window_size* to control the number of items passed as arguments to + *pred*. This allows for locating and replacing subsequences. + + >>> iterable = [0, 1, 2, 5, 0, 1, 2, 5] + >>> window_size = 3 + >>> pred = lambda *args: args == (0, 1, 2) # 3 items passed to pred + >>> substitutes = [3, 4] # Splice in these items + >>> list(replace(iterable, pred, substitutes, window_size=window_size)) + [3, 4, 5, 3, 4, 5] + + """ + if window_size < 1: + raise ValueError('window_size must be at least 1') + + # Save the substitutes iterable, since it's used more than once + substitutes = tuple(substitutes) + + # Add padding such that the number of windows matches the length of the + # iterable + it = chain(iterable, repeat(_marker, window_size - 1)) + windows = windowed(it, window_size) + + n = 0 + for w in windows: + # If the current window matches our predicate (and we haven't hit + # our maximum number of replacements), splice in the substitutes + # and then consume the following windows that overlap with this one. + # For example, if the iterable is (0, 1, 2, 3, 4...) + # and the window size is 2, we have (0, 1), (1, 2), (2, 3)... + # If the predicate matches on (0, 1), we need to zap (0, 1) and (1, 2) + if pred(*w): + if (count is None) or (n < count): + n += 1 + yield from substitutes + consume(windows, window_size - 1) + continue + + # If there was no match (or we've reached the replacement limit), + # yield the first item from the window. + if w and (w[0] is not _marker): + yield w[0] + + +def partitions(iterable): + """Yield all possible order-preserving partitions of *iterable*. + + >>> iterable = 'abc' + >>> for part in partitions(iterable): + ... print([''.join(p) for p in part]) + ['abc'] + ['a', 'bc'] + ['ab', 'c'] + ['a', 'b', 'c'] + + This is unrelated to :func:`partition`. + + """ + sequence = list(iterable) + n = len(sequence) + for i in powerset(range(1, n)): + yield [sequence[i:j] for i, j in zip((0,) + i, i + (n,))] + + +def set_partitions(iterable, k=None, min_size=None, max_size=None): + """ + Yield the set partitions of *iterable* into *k* parts. Set partitions are + not order-preserving. + + >>> iterable = 'abc' + >>> for part in set_partitions(iterable, 2): + ... print([''.join(p) for p in part]) + ['a', 'bc'] + ['ab', 'c'] + ['b', 'ac'] + + + If *k* is not given, every set partition is generated. + + >>> iterable = 'abc' + >>> for part in set_partitions(iterable): + ... print([''.join(p) for p in part]) + ['abc'] + ['a', 'bc'] + ['ab', 'c'] + ['b', 'ac'] + ['a', 'b', 'c'] + + if *min_size* and/or *max_size* are given, the minimum and/or maximum size + per block in partition is set. + + >>> iterable = 'abc' + >>> for part in set_partitions(iterable, min_size=2): + ... print([''.join(p) for p in part]) + ['abc'] + >>> for part in set_partitions(iterable, max_size=2): + ... print([''.join(p) for p in part]) + ['a', 'bc'] + ['ab', 'c'] + ['b', 'ac'] + ['a', 'b', 'c'] + + """ + L = list(iterable) + n = len(L) + if k is not None: + if k < 1: + raise ValueError( + "Can't partition in a negative or zero number of groups" + ) + elif k > n: + return + + min_size = min_size if min_size is not None else 0 + max_size = max_size if max_size is not None else n + if min_size > max_size: + return + + def set_partitions_helper(L, k): + n = len(L) + if k == 1: + yield [L] + elif n == k: + yield [[s] for s in L] + else: + e, *M = L + for p in set_partitions_helper(M, k - 1): + yield [[e], *p] + for p in set_partitions_helper(M, k): + for i in range(len(p)): + yield p[:i] + [[e] + p[i]] + p[i + 1 :] + + if k is None: + for k in range(1, n + 1): + yield from filter( + lambda z: all(min_size <= len(bk) <= max_size for bk in z), + set_partitions_helper(L, k), + ) + else: + yield from filter( + lambda z: all(min_size <= len(bk) <= max_size for bk in z), + set_partitions_helper(L, k), + ) + + +class time_limited: + """ + Yield items from *iterable* until *limit_seconds* have passed. + If the time limit expires before all items have been yielded, the + ``timed_out`` parameter will be set to ``True``. + + >>> from time import sleep + >>> def generator(): + ... yield 1 + ... yield 2 + ... sleep(0.2) + ... yield 3 + >>> iterable = time_limited(0.1, generator()) + >>> list(iterable) + [1, 2] + >>> iterable.timed_out + True + + Note that the time is checked before each item is yielded, and iteration + stops if the time elapsed is greater than *limit_seconds*. If your time + limit is 1 second, but it takes 2 seconds to generate the first item from + the iterable, the function will run for 2 seconds and not yield anything. + As a special case, when *limit_seconds* is zero, the iterator never + returns anything. + + """ + + def __init__(self, limit_seconds, iterable): + if limit_seconds < 0: + raise ValueError('limit_seconds must be positive') + self.limit_seconds = limit_seconds + self._iterator = iter(iterable) + self._start_time = monotonic() + self.timed_out = False + + def __iter__(self): + return self + + def __next__(self): + if self.limit_seconds == 0: + self.timed_out = True + raise StopIteration + item = next(self._iterator) + if monotonic() - self._start_time > self.limit_seconds: + self.timed_out = True + raise StopIteration + + return item + + +def only(iterable, default=None, too_long=None): + """If *iterable* has only one item, return it. + If it has zero items, return *default*. + If it has more than one item, raise the exception given by *too_long*, + which is ``ValueError`` by default. + + >>> only([], default='missing') + 'missing' + >>> only([1]) + 1 + >>> only([1, 2]) # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + ... + ValueError: Expected exactly one item in iterable, but got 1, 2, + and perhaps more.' + >>> only([1, 2], too_long=TypeError) # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + ... + TypeError + + Note that :func:`only` attempts to advance *iterable* twice to ensure there + is only one item. See :func:`spy` or :func:`peekable` to check + iterable contents less destructively. + + """ + iterator = iter(iterable) + for first in iterator: + for second in iterator: + msg = ( + f'Expected exactly one item in iterable, but got {first!r}, ' + f'{second!r}, and perhaps more.' + ) + raise too_long or ValueError(msg) + return first + return default + + +def _ichunk(iterator, n): + cache = deque() + chunk = islice(iterator, n) + + def generator(): + with suppress(StopIteration): + while True: + if cache: + yield cache.popleft() + else: + yield next(chunk) + + def materialize_next(n=1): + # if n not specified materialize everything + if n is None: + cache.extend(chunk) + return len(cache) + + to_cache = n - len(cache) + + # materialize up to n + if to_cache > 0: + cache.extend(islice(chunk, to_cache)) + + # return number materialized up to n + return min(n, len(cache)) + + return (generator(), materialize_next) + + +def ichunked(iterable, n): + """Break *iterable* into sub-iterables with *n* elements each. + :func:`ichunked` is like :func:`chunked`, but it yields iterables + instead of lists. + + If the sub-iterables are read in order, the elements of *iterable* + won't be stored in memory. + If they are read out of order, :func:`itertools.tee` is used to cache + elements as necessary. + + >>> from itertools import count + >>> all_chunks = ichunked(count(), 4) + >>> c_1, c_2, c_3 = next(all_chunks), next(all_chunks), next(all_chunks) + >>> list(c_2) # c_1's elements have been cached; c_3's haven't been + [4, 5, 6, 7] + >>> list(c_1) + [0, 1, 2, 3] + >>> list(c_3) + [8, 9, 10, 11] + + """ + iterator = iter(iterable) + while True: + # Create new chunk + chunk, materialize_next = _ichunk(iterator, n) + + # Check to see whether we're at the end of the source iterable + if not materialize_next(): + return + + yield chunk + + # Fill previous chunk's cache + materialize_next(None) + + +def iequals(*iterables): + """Return ``True`` if all given *iterables* are equal to each other, + which means that they contain the same elements in the same order. + + The function is useful for comparing iterables of different data types + or iterables that do not support equality checks. + + >>> iequals("abc", ['a', 'b', 'c'], ('a', 'b', 'c'), iter("abc")) + True + + >>> iequals("abc", "acb") + False + + Not to be confused with :func:`all_equal`, which checks whether all + elements of iterable are equal to each other. + + """ + return all(map(all_equal, zip_longest(*iterables, fillvalue=object()))) + + +def distinct_combinations(iterable, r): + """Yield the distinct combinations of *r* items taken from *iterable*. + + >>> list(distinct_combinations([0, 0, 1], 2)) + [(0, 0), (0, 1)] + + Equivalent to ``set(combinations(iterable))``, except duplicates are not + generated and thrown away. For larger input sequences this is much more + efficient. + + """ + if r < 0: + raise ValueError('r must be non-negative') + elif r == 0: + yield () + return + pool = tuple(iterable) + generators = [unique_everseen(enumerate(pool), key=itemgetter(1))] + current_combo = [None] * r + level = 0 + while generators: + try: + cur_idx, p = next(generators[-1]) + except StopIteration: + generators.pop() + level -= 1 + continue + current_combo[level] = p + if level + 1 == r: + yield tuple(current_combo) + else: + generators.append( + unique_everseen( + enumerate(pool[cur_idx + 1 :], cur_idx + 1), + key=itemgetter(1), + ) + ) + level += 1 + + +def filter_except(validator, iterable, *exceptions): + """Yield the items from *iterable* for which the *validator* function does + not raise one of the specified *exceptions*. + + *validator* is called for each item in *iterable*. + It should be a function that accepts one argument and raises an exception + if that item is not valid. + + >>> iterable = ['1', '2', 'three', '4', None] + >>> list(filter_except(int, iterable, ValueError, TypeError)) + ['1', '2', '4'] + + If an exception other than one given by *exceptions* is raised by + *validator*, it is raised like normal. + """ + for item in iterable: + try: + validator(item) + except exceptions: + pass + else: + yield item + + +def map_except(function, iterable, *exceptions): + """Transform each item from *iterable* with *function* and yield the + result, unless *function* raises one of the specified *exceptions*. + + *function* is called to transform each item in *iterable*. + It should accept one argument. + + >>> iterable = ['1', '2', 'three', '4', None] + >>> list(map_except(int, iterable, ValueError, TypeError)) + [1, 2, 4] + + If an exception other than one given by *exceptions* is raised by + *function*, it is raised like normal. + """ + for item in iterable: + try: + yield function(item) + except exceptions: + pass + + +def map_if(iterable, pred, func, func_else=None): + """Evaluate each item from *iterable* using *pred*. If the result is + equivalent to ``True``, transform the item with *func* and yield it. + Otherwise, transform the item with *func_else* and yield it. + + *pred*, *func*, and *func_else* should each be functions that accept + one argument. By default, *func_else* is the identity function. + + >>> from math import sqrt + >>> iterable = list(range(-5, 5)) + >>> iterable + [-5, -4, -3, -2, -1, 0, 1, 2, 3, 4] + >>> list(map_if(iterable, lambda x: x > 3, lambda x: 'toobig')) + [-5, -4, -3, -2, -1, 0, 1, 2, 3, 'toobig'] + >>> list(map_if(iterable, lambda x: x >= 0, + ... lambda x: f'{sqrt(x):.2f}', lambda x: None)) + [None, None, None, None, None, '0.00', '1.00', '1.41', '1.73', '2.00'] + """ + + if func_else is None: + for item in iterable: + yield func(item) if pred(item) else item + + else: + for item in iterable: + yield func(item) if pred(item) else func_else(item) + + +def _sample_unweighted(iterator, k, strict): + # Algorithm L in the 1994 paper by Kim-Hung Li: + # "Reservoir-Sampling Algorithms of Time Complexity O(n(1+log(N/n)))". + + reservoir = list(islice(iterator, k)) + if strict and len(reservoir) < k: + raise ValueError('Sample larger than population') + W = 1.0 + + with suppress(StopIteration): + while True: + W *= random() ** (1 / k) + skip = floor(log(random()) / log1p(-W)) + element = next(islice(iterator, skip, None)) + reservoir[randrange(k)] = element + + shuffle(reservoir) + return reservoir + + +def _sample_weighted(iterator, k, weights, strict): + # Implementation of "A-ExpJ" from the 2006 paper by Efraimidis et al. : + # "Weighted random sampling with a reservoir". + + # Log-transform for numerical stability for weights that are small/large + weight_keys = (log(random()) / weight for weight in weights) + + # Fill up the reservoir (collection of samples) with the first `k` + # weight-keys and elements, then heapify the list. + reservoir = take(k, zip(weight_keys, iterator)) + if strict and len(reservoir) < k: + raise ValueError('Sample larger than population') + + heapify(reservoir) + + # The number of jumps before changing the reservoir is a random variable + # with an exponential distribution. Sample it using random() and logs. + smallest_weight_key, _ = reservoir[0] + weights_to_skip = log(random()) / smallest_weight_key + + for weight, element in zip(weights, iterator): + if weight >= weights_to_skip: + # The notation here is consistent with the paper, but we store + # the weight-keys in log-space for better numerical stability. + smallest_weight_key, _ = reservoir[0] + t_w = exp(weight * smallest_weight_key) + r_2 = uniform(t_w, 1) # generate U(t_w, 1) + weight_key = log(r_2) / weight + heapreplace(reservoir, (weight_key, element)) + smallest_weight_key, _ = reservoir[0] + weights_to_skip = log(random()) / smallest_weight_key + else: + weights_to_skip -= weight + + ret = [element for weight_key, element in reservoir] + shuffle(ret) + return ret + + +def _sample_counted(population, k, counts, strict): + element = None + remaining = 0 + + def feed(i): + # Advance *i* steps ahead and consume an element + nonlocal element, remaining + + while i + 1 > remaining: + i = i - remaining + element = next(population) + remaining = next(counts) + remaining -= i + 1 + return element + + with suppress(StopIteration): + reservoir = [] + for _ in range(k): + reservoir.append(feed(0)) + + if strict and len(reservoir) < k: + raise ValueError('Sample larger than population') + + with suppress(StopIteration): + W = 1.0 + while True: + W *= random() ** (1 / k) + skip = floor(log(random()) / log1p(-W)) + element = feed(skip) + reservoir[randrange(k)] = element + + shuffle(reservoir) + return reservoir + + +def sample(iterable, k, weights=None, *, counts=None, strict=False): + """Return a *k*-length list of elements chosen (without replacement) + from the *iterable*. + + Similar to :func:`random.sample`, but works on inputs that aren't + indexable (such as sets and dictionaries) and on inputs where the + size isn't known in advance (such as generators). + + >>> iterable = range(100) + >>> sample(iterable, 5) # doctest: +SKIP + [81, 60, 96, 16, 4] + + For iterables with repeated elements, you may supply *counts* to + indicate the repeats. + + >>> iterable = ['a', 'b'] + >>> counts = [3, 4] # Equivalent to 'a', 'a', 'a', 'b', 'b', 'b', 'b' + >>> sample(iterable, k=3, counts=counts) # doctest: +SKIP + ['a', 'a', 'b'] + + An iterable with *weights* may be given: + + >>> iterable = range(100) + >>> weights = (i * i + 1 for i in range(100)) + >>> sampled = sample(iterable, 5, weights=weights) # doctest: +SKIP + [79, 67, 74, 66, 78] + + Weighted selections are made without replacement. + After an element is selected, it is removed from the pool and the + relative weights of the other elements increase (this + does not match the behavior of :func:`random.sample`'s *counts* + parameter). Note that *weights* may not be used with *counts*. + + If the length of *iterable* is less than *k*, + ``ValueError`` is raised if *strict* is ``True`` and + all elements are returned (in shuffled order) if *strict* is ``False``. + + By default, the `Algorithm L `__ reservoir sampling + technique is used. When *weights* are provided, + `Algorithm A-ExpJ `__ is used instead. + + Notes on reproducibility: + + * The algorithms rely on inexact floating-point functions provided + by the underlying math library (e.g. ``log``, ``log1p``, and ``pow``). + Those functions can `produce slightly different results + `_ on + different builds. Accordingly, selections can vary across builds + even for the same seed. + + * The algorithms loop over the input and make selections based on + ordinal position, so selections from unordered collections (such as + sets) won't reproduce across sessions on the same platform using the + same seed. For example, this won't reproduce:: + + >> seed(8675309) + >> sample(set('abcdefghijklmnopqrstuvwxyz'), 10) + ['c', 'p', 'e', 'w', 's', 'a', 'j', 'd', 'n', 't'] + + """ + iterator = iter(iterable) + + if k < 0: + raise ValueError('k must be non-negative') + + if k == 0: + return [] + + if weights is not None and counts is not None: + raise TypeError('weights and counts are mutually exclusive') + + elif weights is not None: + weights = iter(weights) + return _sample_weighted(iterator, k, weights, strict) + + elif counts is not None: + counts = iter(counts) + return _sample_counted(iterator, k, counts, strict) + + else: + return _sample_unweighted(iterator, k, strict) + + +def is_sorted(iterable, key=None, reverse=False, strict=False): + """Returns ``True`` if the items of iterable are in sorted order, and + ``False`` otherwise. *key* and *reverse* have the same meaning that they do + in the built-in :func:`sorted` function. + + >>> is_sorted(['1', '2', '3', '4', '5'], key=int) + True + >>> is_sorted([5, 4, 3, 1, 2], reverse=True) + False + + If *strict*, tests for strict sorting, that is, returns ``False`` if equal + elements are found: + + >>> is_sorted([1, 2, 2]) + True + >>> is_sorted([1, 2, 2], strict=True) + False + + The function returns ``False`` after encountering the first out-of-order + item, which means it may produce results that differ from the built-in + :func:`sorted` function for objects with unusual comparison dynamics + (like ``math.nan``). If there are no out-of-order items, the iterable is + exhausted. + """ + it = iterable if (key is None) else map(key, iterable) + a, b = tee(it) + next(b, None) + if reverse: + b, a = a, b + return all(map(lt, a, b)) if strict else not any(map(lt, b, a)) + + +class AbortThread(BaseException): + pass + + +class callback_iter: + """Convert a function that uses callbacks to an iterator. + + Let *func* be a function that takes a `callback` keyword argument. + For example: + + >>> def func(callback=None): + ... for i, c in [(1, 'a'), (2, 'b'), (3, 'c')]: + ... if callback: + ... callback(i, c) + ... return 4 + + + Use ``with callback_iter(func)`` to get an iterator over the parameters + that are delivered to the callback. + + >>> with callback_iter(func) as it: + ... for args, kwargs in it: + ... print(args) + (1, 'a') + (2, 'b') + (3, 'c') + + The function will be called in a background thread. The ``done`` property + indicates whether it has completed execution. + + >>> it.done + True + + If it completes successfully, its return value will be available + in the ``result`` property. + + >>> it.result + 4 + + Notes: + + * If the function uses some keyword argument besides ``callback``, supply + *callback_kwd*. + * If it finished executing, but raised an exception, accessing the + ``result`` property will raise the same exception. + * If it hasn't finished executing, accessing the ``result`` + property from within the ``with`` block will raise ``RuntimeError``. + * If it hasn't finished executing, accessing the ``result`` property from + outside the ``with`` block will raise a + ``more_itertools.AbortThread`` exception. + * Provide *wait_seconds* to adjust how frequently the it is polled for + output. + + """ + + def __init__(self, func, callback_kwd='callback', wait_seconds=0.1): + self._func = func + self._callback_kwd = callback_kwd + self._aborted = False + self._future = None + self._wait_seconds = wait_seconds + # Lazily import concurrent.future + self._executor = __import__( + 'concurrent.futures' + ).futures.ThreadPoolExecutor(max_workers=1) + self._iterator = self._reader() + + def __enter__(self): + return self + + def __exit__(self, exc_type, exc_value, traceback): + self._aborted = True + self._executor.shutdown() + + def __iter__(self): + return self + + def __next__(self): + return next(self._iterator) + + @property + def done(self): + if self._future is None: + return False + return self._future.done() + + @property + def result(self): + if not self.done: + raise RuntimeError('Function has not yet completed') + + return self._future.result() + + def _reader(self): + q = Queue() + + def callback(*args, **kwargs): + if self._aborted: + raise AbortThread('canceled by user') + + q.put((args, kwargs)) + + self._future = self._executor.submit( + self._func, **{self._callback_kwd: callback} + ) + + while True: + try: + item = q.get(timeout=self._wait_seconds) + except Empty: + pass + else: + q.task_done() + yield item + + if self._future.done(): + break + + remaining = [] + while True: + try: + item = q.get_nowait() + except Empty: + break + else: + q.task_done() + remaining.append(item) + q.join() + yield from remaining + + +def windowed_complete(iterable, n): + """ + Yield ``(beginning, middle, end)`` tuples, where: + + * Each ``middle`` has *n* items from *iterable* + * Each ``beginning`` has the items before the ones in ``middle`` + * Each ``end`` has the items after the ones in ``middle`` + + >>> iterable = range(7) + >>> n = 3 + >>> for beginning, middle, end in windowed_complete(iterable, n): + ... print(beginning, middle, end) + () (0, 1, 2) (3, 4, 5, 6) + (0,) (1, 2, 3) (4, 5, 6) + (0, 1) (2, 3, 4) (5, 6) + (0, 1, 2) (3, 4, 5) (6,) + (0, 1, 2, 3) (4, 5, 6) () + + Note that *n* must be at least 0 and most equal to the length of + *iterable*. + + This function will exhaust the iterable and may require significant + storage. + """ + if n < 0: + raise ValueError('n must be >= 0') + + seq = tuple(iterable) + size = len(seq) + + if n > size: + raise ValueError('n must be <= len(seq)') + + for i in range(size - n + 1): + beginning = seq[:i] + middle = seq[i : i + n] + end = seq[i + n :] + yield beginning, middle, end + + +def all_unique(iterable, key=None): + """ + Returns ``True`` if all the elements of *iterable* are unique (no two + elements are equal). + + >>> all_unique('ABCB') + False + + If a *key* function is specified, it will be used to make comparisons. + + >>> all_unique('ABCb') + True + >>> all_unique('ABCb', str.lower) + False + + The function returns as soon as the first non-unique element is + encountered. Iterables with a mix of hashable and unhashable items can + be used, but the function will be slower for unhashable items. + """ + seenset = set() + seenset_add = seenset.add + seenlist = [] + seenlist_add = seenlist.append + for element in map(key, iterable) if key else iterable: + try: + if element in seenset: + return False + seenset_add(element) + except TypeError: + if element in seenlist: + return False + seenlist_add(element) + return True + + +def nth_product(index, *args): + """Equivalent to ``list(product(*args))[index]``. + + The products of *args* can be ordered lexicographically. + :func:`nth_product` computes the product at sort position *index* without + computing the previous products. + + >>> nth_product(8, range(2), range(2), range(2), range(2)) + (1, 0, 0, 0) + + ``IndexError`` will be raised if the given *index* is invalid. + """ + pools = list(map(tuple, reversed(args))) + ns = list(map(len, pools)) + + c = reduce(mul, ns) + + if index < 0: + index += c + + if not 0 <= index < c: + raise IndexError + + result = [] + for pool, n in zip(pools, ns): + result.append(pool[index % n]) + index //= n + + return tuple(reversed(result)) + + +def nth_permutation(iterable, r, index): + """Equivalent to ``list(permutations(iterable, r))[index]``` + + The subsequences of *iterable* that are of length *r* where order is + important can be ordered lexicographically. :func:`nth_permutation` + computes the subsequence at sort position *index* directly, without + computing the previous subsequences. + + >>> nth_permutation('ghijk', 2, 5) + ('h', 'i') + + ``ValueError`` will be raised If *r* is negative or greater than the length + of *iterable*. + ``IndexError`` will be raised if the given *index* is invalid. + """ + pool = list(iterable) + n = len(pool) + + if r is None or r == n: + r, c = n, factorial(n) + elif not 0 <= r < n: + raise ValueError + else: + c = perm(n, r) + assert c > 0 # factorial(n)>0, and r>> nth_combination_with_replacement(range(5), 3, 5) + (0, 1, 1) + + ``ValueError`` will be raised If *r* is negative or greater than the length + of *iterable*. + ``IndexError`` will be raised if the given *index* is invalid. + """ + pool = tuple(iterable) + n = len(pool) + if (r < 0) or (r > n): + raise ValueError + + c = comb(n + r - 1, r) + + if index < 0: + index += c + + if (index < 0) or (index >= c): + raise IndexError + + result = [] + i = 0 + while r: + r -= 1 + while n >= 0: + num_combs = comb(n + r - 1, r) + if index < num_combs: + break + n -= 1 + i += 1 + index -= num_combs + result.append(pool[i]) + + return tuple(result) + + +def value_chain(*args): + """Yield all arguments passed to the function in the same order in which + they were passed. If an argument itself is iterable then iterate over its + values. + + >>> list(value_chain(1, 2, 3, [4, 5, 6])) + [1, 2, 3, 4, 5, 6] + + Binary and text strings are not considered iterable and are emitted + as-is: + + >>> list(value_chain('12', '34', ['56', '78'])) + ['12', '34', '56', '78'] + + Pre- or postpend a single element to an iterable: + + >>> list(value_chain(1, [2, 3, 4, 5, 6])) + [1, 2, 3, 4, 5, 6] + >>> list(value_chain([1, 2, 3, 4, 5], 6)) + [1, 2, 3, 4, 5, 6] + + Multiple levels of nesting are not flattened. + + """ + for value in args: + if isinstance(value, (str, bytes)): + yield value + continue + try: + yield from value + except TypeError: + yield value + + +def product_index(element, *args): + """Equivalent to ``list(product(*args)).index(element)`` + + The products of *args* can be ordered lexicographically. + :func:`product_index` computes the first index of *element* without + computing the previous products. + + >>> product_index([8, 2], range(10), range(5)) + 42 + + ``ValueError`` will be raised if the given *element* isn't in the product + of *args*. + """ + index = 0 + + for x, pool in zip_longest(element, args, fillvalue=_marker): + if x is _marker or pool is _marker: + raise ValueError('element is not a product of args') + + pool = tuple(pool) + index = index * len(pool) + pool.index(x) + + return index + + +def combination_index(element, iterable): + """Equivalent to ``list(combinations(iterable, r)).index(element)`` + + The subsequences of *iterable* that are of length *r* can be ordered + lexicographically. :func:`combination_index` computes the index of the + first *element*, without computing the previous combinations. + + >>> combination_index('adf', 'abcdefg') + 10 + + ``ValueError`` will be raised if the given *element* isn't one of the + combinations of *iterable*. + """ + element = enumerate(element) + k, y = next(element, (None, None)) + if k is None: + return 0 + + indexes = [] + pool = enumerate(iterable) + for n, x in pool: + if x == y: + indexes.append(n) + tmp, y = next(element, (None, None)) + if tmp is None: + break + else: + k = tmp + else: + raise ValueError('element is not a combination of iterable') + + n, _ = last(pool, default=(n, None)) + + # Python versions below 3.8 don't have math.comb + index = 1 + for i, j in enumerate(reversed(indexes), start=1): + j = n - j + if i <= j: + index += comb(j, i) + + return comb(n + 1, k + 1) - index + + +def combination_with_replacement_index(element, iterable): + """Equivalent to + ``list(combinations_with_replacement(iterable, r)).index(element)`` + + The subsequences with repetition of *iterable* that are of length *r* can + be ordered lexicographically. :func:`combination_with_replacement_index` + computes the index of the first *element*, without computing the previous + combinations with replacement. + + >>> combination_with_replacement_index('adf', 'abcdefg') + 20 + + ``ValueError`` will be raised if the given *element* isn't one of the + combinations with replacement of *iterable*. + """ + element = tuple(element) + l = len(element) + element = enumerate(element) + + k, y = next(element, (None, None)) + if k is None: + return 0 + + indexes = [] + pool = tuple(iterable) + for n, x in enumerate(pool): + while x == y: + indexes.append(n) + tmp, y = next(element, (None, None)) + if tmp is None: + break + else: + k = tmp + if y is None: + break + else: + raise ValueError( + 'element is not a combination with replacement of iterable' + ) + + n = len(pool) + occupations = [0] * n + for p in indexes: + occupations[p] += 1 + + index = 0 + cumulative_sum = 0 + for k in range(1, n): + cumulative_sum += occupations[k - 1] + j = l + n - 1 - k - cumulative_sum + i = n - k + if i <= j: + index += comb(j, i) + + return index + + +def permutation_index(element, iterable): + """Equivalent to ``list(permutations(iterable, r)).index(element)``` + + The subsequences of *iterable* that are of length *r* where order is + important can be ordered lexicographically. :func:`permutation_index` + computes the index of the first *element* directly, without computing + the previous permutations. + + >>> permutation_index([1, 3, 2], range(5)) + 19 + + ``ValueError`` will be raised if the given *element* isn't one of the + permutations of *iterable*. + """ + index = 0 + pool = list(iterable) + for i, x in zip(range(len(pool), -1, -1), element): + r = pool.index(x) + index = index * i + r + del pool[r] + + return index + + +class countable: + """Wrap *iterable* and keep a count of how many items have been consumed. + + The ``items_seen`` attribute starts at ``0`` and increments as the iterable + is consumed: + + >>> iterable = map(str, range(10)) + >>> it = countable(iterable) + >>> it.items_seen + 0 + >>> next(it), next(it) + ('0', '1') + >>> list(it) + ['2', '3', '4', '5', '6', '7', '8', '9'] + >>> it.items_seen + 10 + """ + + def __init__(self, iterable): + self._iterator = iter(iterable) + self.items_seen = 0 + + def __iter__(self): + return self + + def __next__(self): + item = next(self._iterator) + self.items_seen += 1 + + return item + + +def chunked_even(iterable, n): + """Break *iterable* into lists of approximately length *n*. + Items are distributed such the lengths of the lists differ by at most + 1 item. + + >>> iterable = [1, 2, 3, 4, 5, 6, 7] + >>> n = 3 + >>> list(chunked_even(iterable, n)) # List lengths: 3, 2, 2 + [[1, 2, 3], [4, 5], [6, 7]] + >>> list(chunked(iterable, n)) # List lengths: 3, 3, 1 + [[1, 2, 3], [4, 5, 6], [7]] + + """ + iterator = iter(iterable) + + # Initialize a buffer to process the chunks while keeping + # some back to fill any underfilled chunks + min_buffer = (n - 1) * (n - 2) + buffer = list(islice(iterator, min_buffer)) + + # Append items until we have a completed chunk + for _ in islice(map(buffer.append, iterator), n, None, n): + yield buffer[:n] + del buffer[:n] + + # Check if any chunks need addition processing + if not buffer: + return + length = len(buffer) + + # Chunks are either size `full_size <= n` or `partial_size = full_size - 1` + q, r = divmod(length, n) + num_lists = q + (1 if r > 0 else 0) + q, r = divmod(length, num_lists) + full_size = q + (1 if r > 0 else 0) + partial_size = full_size - 1 + num_full = length - partial_size * num_lists + + # Yield chunks of full size + partial_start_idx = num_full * full_size + if full_size > 0: + for i in range(0, partial_start_idx, full_size): + yield buffer[i : i + full_size] + + # Yield chunks of partial size + if partial_size > 0: + for i in range(partial_start_idx, length, partial_size): + yield buffer[i : i + partial_size] + + +def zip_broadcast(*objects, scalar_types=(str, bytes), strict=False): + """A version of :func:`zip` that "broadcasts" any scalar + (i.e., non-iterable) items into output tuples. + + >>> iterable_1 = [1, 2, 3] + >>> iterable_2 = ['a', 'b', 'c'] + >>> scalar = '_' + >>> list(zip_broadcast(iterable_1, iterable_2, scalar)) + [(1, 'a', '_'), (2, 'b', '_'), (3, 'c', '_')] + + The *scalar_types* keyword argument determines what types are considered + scalar. It is set to ``(str, bytes)`` by default. Set it to ``None`` to + treat strings and byte strings as iterable: + + >>> list(zip_broadcast('abc', 0, 'xyz', scalar_types=None)) + [('a', 0, 'x'), ('b', 0, 'y'), ('c', 0, 'z')] + + If the *strict* keyword argument is ``True``, then + ``UnequalIterablesError`` will be raised if any of the iterables have + different lengths. + """ + + def is_scalar(obj): + if scalar_types and isinstance(obj, scalar_types): + return True + try: + iter(obj) + except TypeError: + return True + else: + return False + + size = len(objects) + if not size: + return + + new_item = [None] * size + iterables, iterable_positions = [], [] + for i, obj in enumerate(objects): + if is_scalar(obj): + new_item[i] = obj + else: + iterables.append(iter(obj)) + iterable_positions.append(i) + + if not iterables: + yield tuple(objects) + return + + zipper = _zip_equal if strict else zip + for item in zipper(*iterables): + for i, new_item[i] in zip(iterable_positions, item): + pass + yield tuple(new_item) + + +def unique_in_window(iterable, n, key=None): + """Yield the items from *iterable* that haven't been seen recently. + *n* is the size of the lookback window. + + >>> iterable = [0, 1, 0, 2, 3, 0] + >>> n = 3 + >>> list(unique_in_window(iterable, n)) + [0, 1, 2, 3, 0] + + The *key* function, if provided, will be used to determine uniqueness: + + >>> list(unique_in_window('abAcda', 3, key=lambda x: x.lower())) + ['a', 'b', 'c', 'd', 'a'] + + The items in *iterable* must be hashable. + + """ + if n <= 0: + raise ValueError('n must be greater than 0') + + window = deque(maxlen=n) + counts = defaultdict(int) + use_key = key is not None + + for item in iterable: + if len(window) == n: + to_discard = window[0] + if counts[to_discard] == 1: + del counts[to_discard] + else: + counts[to_discard] -= 1 + + k = key(item) if use_key else item + if k not in counts: + yield item + counts[k] += 1 + window.append(k) + + +def duplicates_everseen(iterable, key=None): + """Yield duplicate elements after their first appearance. + + >>> list(duplicates_everseen('mississippi')) + ['s', 'i', 's', 's', 'i', 'p', 'i'] + >>> list(duplicates_everseen('AaaBbbCccAaa', str.lower)) + ['a', 'a', 'b', 'b', 'c', 'c', 'A', 'a', 'a'] + + This function is analogous to :func:`unique_everseen` and is subject to + the same performance considerations. + + """ + seen_set = set() + seen_list = [] + use_key = key is not None + + for element in iterable: + k = key(element) if use_key else element + try: + if k not in seen_set: + seen_set.add(k) + else: + yield element + except TypeError: + if k not in seen_list: + seen_list.append(k) + else: + yield element + + +def duplicates_justseen(iterable, key=None): + """Yields serially-duplicate elements after their first appearance. + + >>> list(duplicates_justseen('mississippi')) + ['s', 's', 'p'] + >>> list(duplicates_justseen('AaaBbbCccAaa', str.lower)) + ['a', 'a', 'b', 'b', 'c', 'c', 'a', 'a'] + + This function is analogous to :func:`unique_justseen`. + + """ + return flatten(g for _, g in groupby(iterable, key) for _ in g) + + +def classify_unique(iterable, key=None): + """Classify each element in terms of its uniqueness. + + For each element in the input iterable, return a 3-tuple consisting of: + + 1. The element itself + 2. ``False`` if the element is equal to the one preceding it in the input, + ``True`` otherwise (i.e. the equivalent of :func:`unique_justseen`) + 3. ``False`` if this element has been seen anywhere in the input before, + ``True`` otherwise (i.e. the equivalent of :func:`unique_everseen`) + + >>> list(classify_unique('otto')) # doctest: +NORMALIZE_WHITESPACE + [('o', True, True), + ('t', True, True), + ('t', False, False), + ('o', True, False)] + + This function is analogous to :func:`unique_everseen` and is subject to + the same performance considerations. + + """ + seen_set = set() + seen_list = [] + use_key = key is not None + previous = None + + for i, element in enumerate(iterable): + k = key(element) if use_key else element + is_unique_justseen = not i or previous != k + previous = k + is_unique_everseen = False + try: + if k not in seen_set: + seen_set.add(k) + is_unique_everseen = True + except TypeError: + if k not in seen_list: + seen_list.append(k) + is_unique_everseen = True + yield element, is_unique_justseen, is_unique_everseen + + +def minmax(iterable_or_value, *others, key=None, default=_marker): + """Returns both the smallest and largest items from an iterable + or from two or more arguments. + + >>> minmax([3, 1, 5]) + (1, 5) + + >>> minmax(4, 2, 6) + (2, 6) + + If a *key* function is provided, it will be used to transform the input + items for comparison. + + >>> minmax([5, 30], key=str) # '30' sorts before '5' + (30, 5) + + If a *default* value is provided, it will be returned if there are no + input items. + + >>> minmax([], default=(0, 0)) + (0, 0) + + Otherwise ``ValueError`` is raised. + + This function makes a single pass over the input elements and takes care to + minimize the number of comparisons made during processing. + + Note that unlike the builtin ``max`` function, which always returns the first + item with the maximum value, this function may return another item when there are + ties. + + This function is based on the + `recipe `__ by + Raymond Hettinger. + """ + iterable = (iterable_or_value, *others) if others else iterable_or_value + + it = iter(iterable) + + try: + lo = hi = next(it) + except StopIteration as exc: + if default is _marker: + raise ValueError( + '`minmax()` argument is an empty iterable. ' + 'Provide a `default` value to suppress this error.' + ) from exc + return default + + # Different branches depending on the presence of key. This saves a lot + # of unimportant copies which would slow the "key=None" branch + # significantly down. + if key is None: + for x, y in zip_longest(it, it, fillvalue=lo): + if y < x: + x, y = y, x + if x < lo: + lo = x + if hi < y: + hi = y + + else: + lo_key = hi_key = key(lo) + + for x, y in zip_longest(it, it, fillvalue=lo): + x_key, y_key = key(x), key(y) + + if y_key < x_key: + x, y, x_key, y_key = y, x, y_key, x_key + if x_key < lo_key: + lo, lo_key = x, x_key + if hi_key < y_key: + hi, hi_key = y, y_key + + return lo, hi + + +def constrained_batches( + iterable, max_size, max_count=None, get_len=len, strict=True +): + """Yield batches of items from *iterable* with a combined size limited by + *max_size*. + + >>> iterable = [b'12345', b'123', b'12345678', b'1', b'1', b'12', b'1'] + >>> list(constrained_batches(iterable, 10)) + [(b'12345', b'123'), (b'12345678', b'1', b'1'), (b'12', b'1')] + + If a *max_count* is supplied, the number of items per batch is also + limited: + + >>> iterable = [b'12345', b'123', b'12345678', b'1', b'1', b'12', b'1'] + >>> list(constrained_batches(iterable, 10, max_count = 2)) + [(b'12345', b'123'), (b'12345678', b'1'), (b'1', b'12'), (b'1',)] + + If a *get_len* function is supplied, use that instead of :func:`len` to + determine item size. + + If *strict* is ``True``, raise ``ValueError`` if any single item is bigger + than *max_size*. Otherwise, allow single items to exceed *max_size*. + """ + if max_size <= 0: + raise ValueError('maximum size must be greater than zero') + + batch = [] + batch_size = 0 + batch_count = 0 + for item in iterable: + item_len = get_len(item) + if strict and item_len > max_size: + raise ValueError('item size exceeds maximum size') + + reached_count = batch_count == max_count + reached_size = item_len + batch_size > max_size + if batch_count and (reached_size or reached_count): + yield tuple(batch) + batch.clear() + batch_size = 0 + batch_count = 0 + + batch.append(item) + batch_size += item_len + batch_count += 1 + + if batch: + yield tuple(batch) + + +def gray_product(*iterables): + """Like :func:`itertools.product`, but return tuples in an order such + that only one element in the generated tuple changes from one iteration + to the next. + + >>> list(gray_product('AB','CD')) + [('A', 'C'), ('B', 'C'), ('B', 'D'), ('A', 'D')] + + This function consumes all of the input iterables before producing output. + If any of the input iterables have fewer than two items, ``ValueError`` + is raised. + + For information on the algorithm, see + `this section `__ + of Donald Knuth's *The Art of Computer Programming*. + """ + all_iterables = tuple(tuple(x) for x in iterables) + iterable_count = len(all_iterables) + for iterable in all_iterables: + if len(iterable) < 2: + raise ValueError("each iterable must have two or more items") + + # This is based on "Algorithm H" from section 7.2.1.1, page 20. + # a holds the indexes of the source iterables for the n-tuple to be yielded + # f is the array of "focus pointers" + # o is the array of "directions" + a = [0] * iterable_count + f = list(range(iterable_count + 1)) + o = [1] * iterable_count + while True: + yield tuple(all_iterables[i][a[i]] for i in range(iterable_count)) + j = f[0] + f[0] = 0 + if j == iterable_count: + break + a[j] = a[j] + o[j] + if a[j] == 0 or a[j] == len(all_iterables[j]) - 1: + o[j] = -o[j] + f[j] = f[j + 1] + f[j + 1] = j + 1 + + +def partial_product(*iterables): + """Yields tuples containing one item from each iterator, with subsequent + tuples changing a single item at a time by advancing each iterator until it + is exhausted. This sequence guarantees every value in each iterable is + output at least once without generating all possible combinations. + + This may be useful, for example, when testing an expensive function. + + >>> list(partial_product('AB', 'C', 'DEF')) + [('A', 'C', 'D'), ('B', 'C', 'D'), ('B', 'C', 'E'), ('B', 'C', 'F')] + """ + + iterators = list(map(iter, iterables)) + + try: + prod = [next(it) for it in iterators] + except StopIteration: + return + yield tuple(prod) + + for i, it in enumerate(iterators): + for prod[i] in it: + yield tuple(prod) + + +def takewhile_inclusive(predicate, iterable): + """A variant of :func:`takewhile` that yields one additional element. + + >>> list(takewhile_inclusive(lambda x: x < 5, [1, 4, 6, 4, 1])) + [1, 4, 6] + + :func:`takewhile` would return ``[1, 4]``. + """ + for x in iterable: + yield x + if not predicate(x): + break + + +def outer_product(func, xs, ys, *args, **kwargs): + """A generalized outer product that applies a binary function to all + pairs of items. Returns a 2D matrix with ``len(xs)`` rows and ``len(ys)`` + columns. + Also accepts ``*args`` and ``**kwargs`` that are passed to ``func``. + + Multiplication table: + + >>> list(outer_product(mul, range(1, 4), range(1, 6))) + [(1, 2, 3, 4, 5), (2, 4, 6, 8, 10), (3, 6, 9, 12, 15)] + + Cross tabulation: + + >>> xs = ['A', 'B', 'A', 'A', 'B', 'B', 'A', 'A', 'B', 'B'] + >>> ys = ['X', 'X', 'X', 'Y', 'Z', 'Z', 'Y', 'Y', 'Z', 'Z'] + >>> pair_counts = Counter(zip(xs, ys)) + >>> count_rows = lambda x, y: pair_counts[x, y] + >>> list(outer_product(count_rows, sorted(set(xs)), sorted(set(ys)))) + [(2, 3, 0), (1, 0, 4)] + + Usage with ``*args`` and ``**kwargs``: + + >>> animals = ['cat', 'wolf', 'mouse'] + >>> list(outer_product(min, animals, animals, key=len)) + [('cat', 'cat', 'cat'), ('cat', 'wolf', 'wolf'), ('cat', 'wolf', 'mouse')] + """ + ys = tuple(ys) + return batched( + starmap(lambda x, y: func(x, y, *args, **kwargs), product(xs, ys)), + n=len(ys), + ) + + +def iter_suppress(iterable, *exceptions): + """Yield each of the items from *iterable*. If the iteration raises one of + the specified *exceptions*, that exception will be suppressed and iteration + will stop. + + >>> from itertools import chain + >>> def breaks_at_five(x): + ... while True: + ... if x >= 5: + ... raise RuntimeError + ... yield x + ... x += 1 + >>> it_1 = iter_suppress(breaks_at_five(1), RuntimeError) + >>> it_2 = iter_suppress(breaks_at_five(2), RuntimeError) + >>> list(chain(it_1, it_2)) + [1, 2, 3, 4, 2, 3, 4] + """ + try: + yield from iterable + except exceptions: + return + + +def filter_map(func, iterable): + """Apply *func* to every element of *iterable*, yielding only those which + are not ``None``. + + >>> elems = ['1', 'a', '2', 'b', '3'] + >>> list(filter_map(lambda s: int(s) if s.isnumeric() else None, elems)) + [1, 2, 3] + """ + for x in iterable: + y = func(x) + if y is not None: + yield y + + +def powerset_of_sets(iterable): + """Yields all possible subsets of the iterable. + + >>> list(powerset_of_sets([1, 2, 3])) # doctest: +SKIP + [set(), {1}, {2}, {3}, {1, 2}, {1, 3}, {2, 3}, {1, 2, 3}] + >>> list(powerset_of_sets([1, 1, 0])) # doctest: +SKIP + [set(), {1}, {0}, {0, 1}] + + :func:`powerset_of_sets` takes care to minimize the number + of hash operations performed. + """ + sets = tuple(dict.fromkeys(map(frozenset, zip(iterable)))) + return chain.from_iterable( + starmap(set().union, combinations(sets, r)) + for r in range(len(sets) + 1) + ) + + +def join_mappings(**field_to_map): + """ + Joins multiple mappings together using their common keys. + + >>> user_scores = {'elliot': 50, 'claris': 60} + >>> user_times = {'elliot': 30, 'claris': 40} + >>> join_mappings(score=user_scores, time=user_times) + {'elliot': {'score': 50, 'time': 30}, 'claris': {'score': 60, 'time': 40}} + """ + ret = defaultdict(dict) + + for field_name, mapping in field_to_map.items(): + for key, value in mapping.items(): + ret[key][field_name] = value + + return dict(ret) + + +def _complex_sumprod(v1, v2): + """High precision sumprod() for complex numbers. + Used by :func:`dft` and :func:`idft`. + """ + + real = attrgetter('real') + imag = attrgetter('imag') + r1 = chain(map(real, v1), map(neg, map(imag, v1))) + r2 = chain(map(real, v2), map(imag, v2)) + i1 = chain(map(real, v1), map(imag, v1)) + i2 = chain(map(imag, v2), map(real, v2)) + return complex(_fsumprod(r1, r2), _fsumprod(i1, i2)) + + +def dft(xarr): + """Discrete Fourier Transform. *xarr* is a sequence of complex numbers. + Yields the components of the corresponding transformed output vector. + + >>> import cmath + >>> xarr = [1, 2-1j, -1j, -1+2j] # time domain + >>> Xarr = [2, -2-2j, -2j, 4+4j] # frequency domain + >>> magnitudes, phases = zip(*map(cmath.polar, Xarr)) + >>> all(map(cmath.isclose, dft(xarr), Xarr)) + True + + Inputs are restricted to numeric types that can add and multiply + with a complex number. This includes int, float, complex, and + Fraction, but excludes Decimal. + + See :func:`idft` for the inverse Discrete Fourier Transform. + """ + N = len(xarr) + roots_of_unity = [e ** (n / N * tau * -1j) for n in range(N)] + for k in range(N): + coeffs = [roots_of_unity[k * n % N] for n in range(N)] + yield _complex_sumprod(xarr, coeffs) + + +def idft(Xarr): + """Inverse Discrete Fourier Transform. *Xarr* is a sequence of + complex numbers. Yields the components of the corresponding + inverse-transformed output vector. + + >>> import cmath + >>> xarr = [1, 2-1j, -1j, -1+2j] # time domain + >>> Xarr = [2, -2-2j, -2j, 4+4j] # frequency domain + >>> all(map(cmath.isclose, idft(Xarr), xarr)) + True + + Inputs are restricted to numeric types that can add and multiply + with a complex number. This includes int, float, complex, and + Fraction, but excludes Decimal. + + See :func:`dft` for the Discrete Fourier Transform. + """ + N = len(Xarr) + roots_of_unity = [e ** (n / N * tau * 1j) for n in range(N)] + for k in range(N): + coeffs = [roots_of_unity[k * n % N] for n in range(N)] + yield _complex_sumprod(Xarr, coeffs) / N + + +def doublestarmap(func, iterable): + """Apply *func* to every item of *iterable* by dictionary unpacking + the item into *func*. + + The difference between :func:`itertools.starmap` and :func:`doublestarmap` + parallels the distinction between ``func(*a)`` and ``func(**a)``. + + >>> iterable = [{'a': 1, 'b': 2}, {'a': 40, 'b': 60}] + >>> list(doublestarmap(lambda a, b: a + b, iterable)) + [3, 100] + + ``TypeError`` will be raised if *func*'s signature doesn't match the + mapping contained in *iterable* or if *iterable* does not contain mappings. + """ + for item in iterable: + yield func(**item) + + +def _nth_prime_bounds(n): + """Bounds for the nth prime (counting from 1): lb < p_n < ub.""" + # At and above 688,383, the lb/ub spread is under 0.003 * p_n. + + if n < 1: + raise ValueError + + if n < 6: + return (n, 2.25 * n) + + # https://en.wikipedia.org/wiki/Prime-counting_function#Inequalities + upper_bound = n * log(n * log(n)) + lower_bound = upper_bound - n + if n >= 688_383: + upper_bound -= n * (1.0 - (log(log(n)) - 2.0) / log(n)) + + return lower_bound, upper_bound + + +def nth_prime(n, *, approximate=False): + """Return the nth prime (counting from 0). + + >>> nth_prime(0) + 2 + >>> nth_prime(100) + 547 + + If *approximate* is set to True, will return a prime close + to the nth prime. The estimation is much faster than computing + an exact result. + + >>> nth_prime(200_000_000, approximate=True) # Exact result is 4222234763 + 4217820427 + + """ + lb, ub = _nth_prime_bounds(n + 1) + + if not approximate or n <= 1_000_000: + return nth(sieve(ceil(ub)), n) + + # Search from the midpoint and return the first odd prime + odd = floor((lb + ub) / 2) | 1 + return first_true(count(odd, step=2), pred=is_prime) + + +def argmin(iterable, *, key=None): + """ + Index of the first occurrence of a minimum value in an iterable. + + >>> argmin('efghabcdijkl') + 4 + >>> argmin([3, 2, 1, 0, 4, 2, 1, 0]) + 3 + + For example, look up a label corresponding to the position + of a value that minimizes a cost function:: + + >>> def cost(x): + ... "Days for a wound to heal given a subject's age." + ... return x**2 - 20*x + 150 + ... + >>> labels = ['homer', 'marge', 'bart', 'lisa', 'maggie'] + >>> ages = [ 35, 30, 10, 9, 1 ] + + # Fastest healing family member + >>> labels[argmin(ages, key=cost)] + 'bart' + + # Age with fastest healing + >>> min(ages, key=cost) + 10 + + """ + if key is not None: + iterable = map(key, iterable) + return min(enumerate(iterable), key=itemgetter(1))[0] + + +def argmax(iterable, *, key=None): + """ + Index of the first occurrence of a maximum value in an iterable. + + >>> argmax('abcdefghabcd') + 7 + >>> argmax([0, 1, 2, 3, 3, 2, 1, 0]) + 3 + + For example, identify the best machine learning model:: + + >>> models = ['svm', 'random forest', 'knn', 'naïve bayes'] + >>> accuracy = [ 68, 61, 84, 72 ] + + # Most accurate model + >>> models[argmax(accuracy)] + 'knn' + + # Best accuracy + >>> max(accuracy) + 84 + + """ + if key is not None: + iterable = map(key, iterable) + return max(enumerate(iterable), key=itemgetter(1))[0] + + +def extract(iterable, indices): + """Yield values at the specified indices. + + Example: + + >>> data = 'abcdefghijklmnopqrstuvwxyz' + >>> list(extract(data, [7, 4, 11, 11, 14])) + ['h', 'e', 'l', 'l', 'o'] + + The *iterable* is consumed lazily and can be infinite. + The *indices* are consumed immediately and must be finite. + + Raises ``IndexError`` if an index lies beyond the iterable. + Raises ``ValueError`` for negative indices. + """ + + iterator = iter(iterable) + index_and_position = sorted(zip(indices, count())) + + if index_and_position and index_and_position[0][0] < 0: + raise ValueError('Indices must be non-negative') + + buffer = {} + iterator_position = -1 + next_to_emit = 0 + + for index, order in index_and_position: + advance = index - iterator_position + if advance: + try: + value = next(islice(iterator, advance - 1, None)) + except StopIteration: + raise IndexError(index) + iterator_position = index + + buffer[order] = value + + while next_to_emit in buffer: + yield buffer.pop(next_to_emit) + next_to_emit += 1 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/more.pyi b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/more.pyi new file mode 100644 index 0000000000000000000000000000000000000000..b5e33f8b747f70ae8c842c07dca5005449241a62 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/more.pyi @@ -0,0 +1,949 @@ +"""Stubs for more_itertools.more""" + +from __future__ import annotations + +import sys +import types + +from collections.abc import ( + Container, + Hashable, + Iterable, + Iterator, + Mapping, + Reversible, + Sequence, + Sized, +) +from contextlib import AbstractContextManager +from typing import ( + Any, + Callable, + Generic, + TypeVar, + overload, + type_check_only, +) +from typing_extensions import Protocol + +__all__ = [ + 'AbortThread', + 'SequenceView', + 'UnequalIterablesError', + 'adjacent', + 'all_unique', + 'always_iterable', + 'always_reversible', + 'argmax', + 'argmin', + 'bucket', + 'callback_iter', + 'chunked', + 'chunked_even', + 'circular_shifts', + 'collapse', + 'combination_index', + 'combination_with_replacement_index', + 'consecutive_groups', + 'constrained_batches', + 'consumer', + 'count_cycle', + 'countable', + 'derangements', + 'dft', + 'difference', + 'distinct_combinations', + 'distinct_permutations', + 'distribute', + 'divide', + 'doublestarmap', + 'duplicates_everseen', + 'duplicates_justseen', + 'classify_unique', + 'exactly_n', + 'extract', + 'filter_except', + 'filter_map', + 'first', + 'gray_product', + 'groupby_transform', + 'ichunked', + 'iequals', + 'idft', + 'ilen', + 'interleave', + 'interleave_evenly', + 'interleave_longest', + 'interleave_randomly', + 'intersperse', + 'is_sorted', + 'islice_extended', + 'iterate', + 'iter_suppress', + 'join_mappings', + 'last', + 'locate', + 'longest_common_prefix', + 'lstrip', + 'make_decorator', + 'map_except', + 'map_if', + 'map_reduce', + 'mark_ends', + 'minmax', + 'nth_or_last', + 'nth_permutation', + 'nth_prime', + 'nth_product', + 'nth_combination_with_replacement', + 'numeric_range', + 'one', + 'only', + 'outer_product', + 'padded', + 'partial_product', + 'partitions', + 'peekable', + 'permutation_index', + 'powerset_of_sets', + 'product_index', + 'raise_', + 'repeat_each', + 'repeat_last', + 'replace', + 'rlocate', + 'rstrip', + 'run_length', + 'sample', + 'seekable', + 'set_partitions', + 'side_effect', + 'sliced', + 'sort_together', + 'split_after', + 'split_at', + 'split_before', + 'split_into', + 'split_when', + 'spy', + 'stagger', + 'strip', + 'strictly_n', + 'substrings', + 'substrings_indexes', + 'takewhile_inclusive', + 'time_limited', + 'unique_in_window', + 'unique_to_each', + 'unzip', + 'value_chain', + 'windowed', + 'windowed_complete', + 'with_iter', + 'zip_broadcast', + 'zip_equal', + 'zip_offset', +] + +# Type and type variable definitions +_T = TypeVar('_T') +_T1 = TypeVar('_T1') +_T2 = TypeVar('_T2') +_T3 = TypeVar('_T3') +_T4 = TypeVar('_T4') +_T5 = TypeVar('_T5') +_U = TypeVar('_U') +_V = TypeVar('_V') +_W = TypeVar('_W') +_T_co = TypeVar('_T_co', covariant=True) +_GenFn = TypeVar('_GenFn', bound=Callable[..., Iterator[Any]]) +_Raisable = BaseException | type[BaseException] + +# The type of isinstance's second argument (from typeshed builtins) +if sys.version_info >= (3, 10): + _ClassInfo = type | types.UnionType | tuple[_ClassInfo, ...] +else: + _ClassInfo = type | tuple[_ClassInfo, ...] + +@type_check_only +class _SizedIterable(Protocol[_T_co], Sized, Iterable[_T_co]): ... + +@type_check_only +class _SizedReversible(Protocol[_T_co], Sized, Reversible[_T_co]): ... + +@type_check_only +class _SupportsSlicing(Protocol[_T_co]): + def __getitem__(self, __k: slice) -> _T_co: ... + +def chunked( + iterable: Iterable[_T], n: int | None, strict: bool = ... +) -> Iterator[list[_T]]: ... +@overload +def first(iterable: Iterable[_T]) -> _T: ... +@overload +def first(iterable: Iterable[_T], default: _U) -> _T | _U: ... +@overload +def last(iterable: Iterable[_T]) -> _T: ... +@overload +def last(iterable: Iterable[_T], default: _U) -> _T | _U: ... +@overload +def nth_or_last(iterable: Iterable[_T], n: int) -> _T: ... +@overload +def nth_or_last(iterable: Iterable[_T], n: int, default: _U) -> _T | _U: ... + +class peekable(Generic[_T], Iterator[_T]): + def __init__(self, iterable: Iterable[_T]) -> None: ... + def __iter__(self) -> peekable[_T]: ... + def __bool__(self) -> bool: ... + @overload + def peek(self) -> _T: ... + @overload + def peek(self, default: _U) -> _T | _U: ... + def prepend(self, *items: _T) -> None: ... + def __next__(self) -> _T: ... + @overload + def __getitem__(self, index: int) -> _T: ... + @overload + def __getitem__(self, index: slice) -> list[_T]: ... + +def consumer(func: _GenFn) -> _GenFn: ... +def ilen(iterable: Iterable[_T]) -> int: ... +def iterate(func: Callable[[_T], _T], start: _T) -> Iterator[_T]: ... +def with_iter( + context_manager: AbstractContextManager[Iterable[_T]], +) -> Iterator[_T]: ... +def one( + iterable: Iterable[_T], + too_short: _Raisable | None = ..., + too_long: _Raisable | None = ..., +) -> _T: ... +def raise_(exception: _Raisable, *args: Any) -> None: ... +def strictly_n( + iterable: Iterable[_T], + n: int, + too_short: _GenFn | None = ..., + too_long: _GenFn | None = ..., +) -> list[_T]: ... +def distinct_permutations( + iterable: Iterable[_T], r: int | None = ... +) -> Iterator[tuple[_T, ...]]: ... +def derangements( + iterable: Iterable[_T], r: int | None = None +) -> Iterator[tuple[_T, ...]]: ... +def intersperse( + e: _U, iterable: Iterable[_T], n: int = ... +) -> Iterator[_T | _U]: ... +def unique_to_each(*iterables: Iterable[_T]) -> list[list[_T]]: ... +@overload +def windowed( + seq: Iterable[_T], n: int, *, step: int = ... +) -> Iterator[tuple[_T | None, ...]]: ... +@overload +def windowed( + seq: Iterable[_T], n: int, fillvalue: _U, step: int = ... +) -> Iterator[tuple[_T | _U, ...]]: ... +def substrings(iterable: Iterable[_T]) -> Iterator[tuple[_T, ...]]: ... +def substrings_indexes( + seq: Sequence[_T], reverse: bool = ... +) -> Iterator[tuple[Sequence[_T], int, int]]: ... + +class bucket(Generic[_T, _U], Container[_U]): + def __init__( + self, + iterable: Iterable[_T], + key: Callable[[_T], _U], + validator: Callable[[_U], object] | None = ..., + ) -> None: ... + def __contains__(self, value: object) -> bool: ... + def __iter__(self) -> Iterator[_U]: ... + def __getitem__(self, value: object) -> Iterator[_T]: ... + +def spy( + iterable: Iterable[_T], n: int = ... +) -> tuple[list[_T], Iterator[_T]]: ... +def interleave(*iterables: Iterable[_T]) -> Iterator[_T]: ... +def interleave_longest(*iterables: Iterable[_T]) -> Iterator[_T]: ... +def interleave_evenly( + iterables: list[Iterable[_T]], lengths: list[int] | None = ... +) -> Iterator[_T]: ... +def interleave_randomly(*iterables: Iterable[_T]) -> Iterable[_T]: ... +def collapse( + iterable: Iterable[Any], + base_type: _ClassInfo | None = ..., + levels: int | None = ..., +) -> Iterator[Any]: ... +@overload +def side_effect( + func: Callable[[_T], object], + iterable: Iterable[_T], + chunk_size: None = ..., + before: Callable[[], object] | None = ..., + after: Callable[[], object] | None = ..., +) -> Iterator[_T]: ... +@overload +def side_effect( + func: Callable[[list[_T]], object], + iterable: Iterable[_T], + chunk_size: int, + before: Callable[[], object] | None = ..., + after: Callable[[], object] | None = ..., +) -> Iterator[_T]: ... +def sliced( + seq: _SupportsSlicing[_T], n: int, strict: bool = ... +) -> Iterator[_T]: ... +def split_at( + iterable: Iterable[_T], + pred: Callable[[_T], object], + maxsplit: int = ..., + keep_separator: bool = ..., +) -> Iterator[list[_T]]: ... +def split_before( + iterable: Iterable[_T], pred: Callable[[_T], object], maxsplit: int = ... +) -> Iterator[list[_T]]: ... +def split_after( + iterable: Iterable[_T], pred: Callable[[_T], object], maxsplit: int = ... +) -> Iterator[list[_T]]: ... +def split_when( + iterable: Iterable[_T], + pred: Callable[[_T, _T], object], + maxsplit: int = ..., +) -> Iterator[list[_T]]: ... +def split_into( + iterable: Iterable[_T], sizes: Iterable[int | None] +) -> Iterator[list[_T]]: ... +@overload +def padded( + iterable: Iterable[_T], + *, + n: int | None = ..., + next_multiple: bool = ..., +) -> Iterator[_T | None]: ... +@overload +def padded( + iterable: Iterable[_T], + fillvalue: _U, + n: int | None = ..., + next_multiple: bool = ..., +) -> Iterator[_T | _U]: ... +@overload +def repeat_last(iterable: Iterable[_T]) -> Iterator[_T]: ... +@overload +def repeat_last(iterable: Iterable[_T], default: _U) -> Iterator[_T | _U]: ... +def distribute(n: int, iterable: Iterable[_T]) -> list[Iterator[_T]]: ... +@overload +def stagger( + iterable: Iterable[_T], + offsets: _SizedIterable[int] = ..., + longest: bool = ..., +) -> Iterator[tuple[_T | None, ...]]: ... +@overload +def stagger( + iterable: Iterable[_T], + offsets: _SizedIterable[int] = ..., + longest: bool = ..., + fillvalue: _U = ..., +) -> Iterator[tuple[_T | _U, ...]]: ... + +class UnequalIterablesError(ValueError): + def __init__(self, details: tuple[int, int, int] | None = ...) -> None: ... + +# zip_equal +@overload +def zip_equal(__iter1: Iterable[_T1]) -> Iterator[tuple[_T1]]: ... +@overload +def zip_equal( + __iter1: Iterable[_T1], __iter2: Iterable[_T2] +) -> Iterator[tuple[_T1, _T2]]: ... +@overload +def zip_equal( + __iter1: Iterable[_T1], __iter2: Iterable[_T2], __iter3: Iterable[_T3] +) -> Iterator[tuple[_T1, _T2, _T3]]: ... +@overload +def zip_equal( + __iter1: Iterable[_T1], + __iter2: Iterable[_T2], + __iter3: Iterable[_T3], + __iter4: Iterable[_T4], +) -> Iterator[tuple[_T1, _T2, _T3, _T4]]: ... +@overload +def zip_equal( + __iter1: Iterable[_T1], + __iter2: Iterable[_T2], + __iter3: Iterable[_T3], + __iter4: Iterable[_T4], + __iter5: Iterable[_T5], +) -> Iterator[tuple[_T1, _T2, _T3, _T4, _T5]]: ... +@overload +def zip_equal( + __iter1: Iterable[Any], + __iter2: Iterable[Any], + __iter3: Iterable[Any], + __iter4: Iterable[Any], + __iter5: Iterable[Any], + __iter6: Iterable[Any], + *iterables: Iterable[Any], +) -> Iterator[tuple[Any, ...]]: ... + +# zip_offset +@overload +def zip_offset( + __iter1: Iterable[_T1], + *, + offsets: _SizedIterable[int], + longest: bool = ..., + fillvalue: None = None, +) -> Iterator[tuple[_T1 | None]]: ... +@overload +def zip_offset( + __iter1: Iterable[_T1], + __iter2: Iterable[_T2], + *, + offsets: _SizedIterable[int], + longest: bool = ..., + fillvalue: None = None, +) -> Iterator[tuple[_T1 | None, _T2 | None]]: ... +@overload +def zip_offset( + __iter1: Iterable[_T], + __iter2: Iterable[_T], + __iter3: Iterable[_T], + *iterables: Iterable[_T], + offsets: _SizedIterable[int], + longest: bool = ..., + fillvalue: None = None, +) -> Iterator[tuple[_T | None, ...]]: ... +@overload +def zip_offset( + __iter1: Iterable[_T1], + *, + offsets: _SizedIterable[int], + longest: bool = ..., + fillvalue: _U, +) -> Iterator[tuple[_T1 | _U]]: ... +@overload +def zip_offset( + __iter1: Iterable[_T1], + __iter2: Iterable[_T2], + *, + offsets: _SizedIterable[int], + longest: bool = ..., + fillvalue: _U, +) -> Iterator[tuple[_T1 | _U, _T2 | _U]]: ... +@overload +def zip_offset( + __iter1: Iterable[_T], + __iter2: Iterable[_T], + __iter3: Iterable[_T], + *iterables: Iterable[_T], + offsets: _SizedIterable[int], + longest: bool = ..., + fillvalue: _U, +) -> Iterator[tuple[_T | _U, ...]]: ... +def sort_together( + iterables: Iterable[Iterable[_T]], + key_list: Iterable[int] = ..., + key: Callable[..., Any] | None = ..., + reverse: bool = ..., + strict: bool = ..., +) -> list[tuple[_T, ...]]: ... +def unzip(iterable: Iterable[Sequence[_T]]) -> tuple[Iterator[_T], ...]: ... +def divide(n: int, iterable: Iterable[_T]) -> list[Iterator[_T]]: ... +def always_iterable( + obj: object, + base_type: _ClassInfo | None = ..., +) -> Iterator[Any]: ... +def adjacent( + predicate: Callable[[_T], bool], + iterable: Iterable[_T], + distance: int = ..., +) -> Iterator[tuple[bool, _T]]: ... +@overload +def groupby_transform( + iterable: Iterable[_T], + keyfunc: None = None, + valuefunc: None = None, + reducefunc: None = None, +) -> Iterator[tuple[_T, Iterator[_T]]]: ... +@overload +def groupby_transform( + iterable: Iterable[_T], + keyfunc: Callable[[_T], _U], + valuefunc: None, + reducefunc: None, +) -> Iterator[tuple[_U, Iterator[_T]]]: ... +@overload +def groupby_transform( + iterable: Iterable[_T], + keyfunc: None, + valuefunc: Callable[[_T], _V], + reducefunc: None, +) -> Iterator[tuple[_T, Iterator[_V]]]: ... +@overload +def groupby_transform( + iterable: Iterable[_T], + keyfunc: Callable[[_T], _U], + valuefunc: Callable[[_T], _V], + reducefunc: None, +) -> Iterator[tuple[_U, Iterator[_V]]]: ... +@overload +def groupby_transform( + iterable: Iterable[_T], + keyfunc: None, + valuefunc: None, + reducefunc: Callable[[Iterator[_T]], _W], +) -> Iterator[tuple[_T, _W]]: ... +@overload +def groupby_transform( + iterable: Iterable[_T], + keyfunc: Callable[[_T], _U], + valuefunc: None, + reducefunc: Callable[[Iterator[_T]], _W], +) -> Iterator[tuple[_U, _W]]: ... +@overload +def groupby_transform( + iterable: Iterable[_T], + keyfunc: None, + valuefunc: Callable[[_T], _V], + reducefunc: Callable[[Iterator[_V]], _W], +) -> Iterator[tuple[_T, _W]]: ... +@overload +def groupby_transform( + iterable: Iterable[_T], + keyfunc: Callable[[_T], _U], + valuefunc: Callable[[_T], _V], + reducefunc: Callable[[Iterator[_V]], _W], +) -> Iterator[tuple[_U, _W]]: ... + +class numeric_range(Generic[_T, _U], Sequence[_T], Hashable, Reversible[_T]): + @overload + def __init__(self, __stop: _T) -> None: ... + @overload + def __init__(self, __start: _T, __stop: _T) -> None: ... + @overload + def __init__(self, __start: _T, __stop: _T, __step: _U) -> None: ... + def __bool__(self) -> bool: ... + def __contains__(self, elem: object) -> bool: ... + def __eq__(self, other: object) -> bool: ... + @overload + def __getitem__(self, key: int) -> _T: ... + @overload + def __getitem__(self, key: slice) -> numeric_range[_T, _U]: ... + def __hash__(self) -> int: ... + def __iter__(self) -> Iterator[_T]: ... + def __len__(self) -> int: ... + def __reduce__( + self, + ) -> tuple[type[numeric_range[_T, _U]], tuple[_T, _T, _U]]: ... + def __repr__(self) -> str: ... + def __reversed__(self) -> Iterator[_T]: ... + def count(self, value: _T) -> int: ... + def index(self, value: _T) -> int: ... # type: ignore + +def count_cycle( + iterable: Iterable[_T], n: int | None = ... +) -> Iterable[tuple[int, _T]]: ... +def mark_ends( + iterable: Iterable[_T], +) -> Iterable[tuple[bool, bool, _T]]: ... +def locate( + iterable: Iterable[_T], + pred: Callable[..., Any] = ..., + window_size: int | None = ..., +) -> Iterator[int]: ... +def lstrip( + iterable: Iterable[_T], pred: Callable[[_T], object] +) -> Iterator[_T]: ... +def rstrip( + iterable: Iterable[_T], pred: Callable[[_T], object] +) -> Iterator[_T]: ... +def strip( + iterable: Iterable[_T], pred: Callable[[_T], object] +) -> Iterator[_T]: ... + +class islice_extended(Generic[_T], Iterator[_T]): + def __init__(self, iterable: Iterable[_T], *args: int | None) -> None: ... + def __iter__(self) -> islice_extended[_T]: ... + def __next__(self) -> _T: ... + def __getitem__(self, index: slice) -> islice_extended[_T]: ... + +def always_reversible(iterable: Iterable[_T]) -> Iterator[_T]: ... +def consecutive_groups( + iterable: Iterable[_T], ordering: None | Callable[[_T], int] = ... +) -> Iterator[Iterator[_T]]: ... +@overload +def difference( + iterable: Iterable[_T], + func: Callable[[_T, _T], _U] = ..., + *, + initial: None = ..., +) -> Iterator[_T | _U]: ... +@overload +def difference( + iterable: Iterable[_T], func: Callable[[_T, _T], _U] = ..., *, initial: _U +) -> Iterator[_U]: ... + +class SequenceView(Generic[_T], Sequence[_T]): + def __init__(self, target: Sequence[_T]) -> None: ... + @overload + def __getitem__(self, index: int) -> _T: ... + @overload + def __getitem__(self, index: slice) -> Sequence[_T]: ... + def __len__(self) -> int: ... + +class seekable(Generic[_T], Iterator[_T]): + def __init__( + self, iterable: Iterable[_T], maxlen: int | None = ... + ) -> None: ... + def __iter__(self) -> seekable[_T]: ... + def __next__(self) -> _T: ... + def __bool__(self) -> bool: ... + @overload + def peek(self) -> _T: ... + @overload + def peek(self, default: _U) -> _T | _U: ... + def elements(self) -> SequenceView[_T]: ... + def seek(self, index: int) -> None: ... + def relative_seek(self, count: int) -> None: ... + +class run_length: + @staticmethod + def encode(iterable: Iterable[_T]) -> Iterator[tuple[_T, int]]: ... + @staticmethod + def decode(iterable: Iterable[tuple[_T, int]]) -> Iterator[_T]: ... + +def exactly_n( + iterable: Iterable[_T], n: int, predicate: Callable[[_T], object] = ... +) -> bool: ... +def circular_shifts( + iterable: Iterable[_T], steps: int = 1 +) -> list[tuple[_T, ...]]: ... +def make_decorator( + wrapping_func: Callable[..., _U], result_index: int = ... +) -> Callable[..., Callable[[Callable[..., Any]], Callable[..., _U]]]: ... +@overload +def map_reduce( + iterable: Iterable[_T], + keyfunc: Callable[[_T], _U], + valuefunc: None = ..., + reducefunc: None = ..., +) -> dict[_U, list[_T]]: ... +@overload +def map_reduce( + iterable: Iterable[_T], + keyfunc: Callable[[_T], _U], + valuefunc: Callable[[_T], _V], + reducefunc: None = ..., +) -> dict[_U, list[_V]]: ... +@overload +def map_reduce( + iterable: Iterable[_T], + keyfunc: Callable[[_T], _U], + valuefunc: None = ..., + reducefunc: Callable[[list[_T]], _W] = ..., +) -> dict[_U, _W]: ... +@overload +def map_reduce( + iterable: Iterable[_T], + keyfunc: Callable[[_T], _U], + valuefunc: Callable[[_T], _V], + reducefunc: Callable[[list[_V]], _W], +) -> dict[_U, _W]: ... +def rlocate( + iterable: Iterable[_T], + pred: Callable[..., object] = ..., + window_size: int | None = ..., +) -> Iterator[int]: ... +def replace( + iterable: Iterable[_T], + pred: Callable[..., object], + substitutes: Iterable[_U], + count: int | None = ..., + window_size: int = ..., +) -> Iterator[_T | _U]: ... +def partitions(iterable: Iterable[_T]) -> Iterator[list[list[_T]]]: ... +def set_partitions( + iterable: Iterable[_T], + k: int | None = ..., + min_size: int | None = ..., + max_size: int | None = ..., +) -> Iterator[list[list[_T]]]: ... + +class time_limited(Generic[_T], Iterator[_T]): + def __init__( + self, limit_seconds: float, iterable: Iterable[_T] + ) -> None: ... + def __iter__(self) -> islice_extended[_T]: ... + def __next__(self) -> _T: ... + +@overload +def only( + iterable: Iterable[_T], *, too_long: _Raisable | None = ... +) -> _T | None: ... +@overload +def only( + iterable: Iterable[_T], default: _U, too_long: _Raisable | None = ... +) -> _T | _U: ... +def ichunked(iterable: Iterable[_T], n: int) -> Iterator[Iterator[_T]]: ... +def distinct_combinations( + iterable: Iterable[_T], r: int +) -> Iterator[tuple[_T, ...]]: ... +def filter_except( + validator: Callable[[Any], object], + iterable: Iterable[_T], + *exceptions: type[BaseException], +) -> Iterator[_T]: ... +def map_except( + function: Callable[[Any], _U], + iterable: Iterable[_T], + *exceptions: type[BaseException], +) -> Iterator[_U]: ... +def map_if( + iterable: Iterable[Any], + pred: Callable[[Any], bool], + func: Callable[[Any], Any], + func_else: Callable[[Any], Any] | None = ..., +) -> Iterator[Any]: ... +def _sample_unweighted( + iterator: Iterator[_T], k: int, strict: bool +) -> list[_T]: ... +def _sample_counted( + population: Iterator[_T], k: int, counts: Iterable[int], strict: bool +) -> list[_T]: ... +def _sample_weighted( + iterator: Iterator[_T], k: int, weights: Iterator[float], strict: bool +) -> list[_T]: ... +def sample( + iterable: Iterable[_T], + k: int, + weights: Iterable[float] | None = ..., + *, + counts: Iterable[int] | None = ..., + strict: bool = False, +) -> list[_T]: ... +def is_sorted( + iterable: Iterable[_T], + key: Callable[[_T], _U] | None = ..., + reverse: bool = False, + strict: bool = False, +) -> bool: ... + +class AbortThread(BaseException): + pass + +class callback_iter(Generic[_T], Iterator[_T]): + def __init__( + self, + func: Callable[..., Any], + callback_kwd: str = ..., + wait_seconds: float = ..., + ) -> None: ... + def __enter__(self) -> callback_iter[_T]: ... + def __exit__( + self, + exc_type: type[BaseException] | None, + exc_value: BaseException | None, + traceback: types.TracebackType | None, + ) -> bool | None: ... + def __iter__(self) -> callback_iter[_T]: ... + def __next__(self) -> _T: ... + def _reader(self) -> Iterator[_T]: ... + @property + def done(self) -> bool: ... + @property + def result(self) -> Any: ... + +def windowed_complete( + iterable: Iterable[_T], n: int +) -> Iterator[tuple[tuple[_T, ...], tuple[_T, ...], tuple[_T, ...]]]: ... +def all_unique( + iterable: Iterable[_T], key: Callable[[_T], _U] | None = ... +) -> bool: ... +def nth_product(index: int, *args: Iterable[_T]) -> tuple[_T, ...]: ... +def nth_combination_with_replacement( + iterable: Iterable[_T], r: int, index: int +) -> tuple[_T, ...]: ... +def nth_permutation( + iterable: Iterable[_T], r: int, index: int +) -> tuple[_T, ...]: ... +def value_chain(*args: _T | Iterable[_T]) -> Iterable[_T]: ... +def product_index(element: Iterable[_T], *args: Iterable[_T]) -> int: ... +def combination_index( + element: Iterable[_T], iterable: Iterable[_T] +) -> int: ... +def combination_with_replacement_index( + element: Iterable[_T], iterable: Iterable[_T] +) -> int: ... +def permutation_index( + element: Iterable[_T], iterable: Iterable[_T] +) -> int: ... +def repeat_each(iterable: Iterable[_T], n: int = ...) -> Iterator[_T]: ... + +class countable(Generic[_T], Iterator[_T]): + def __init__(self, iterable: Iterable[_T]) -> None: ... + def __iter__(self) -> countable[_T]: ... + def __next__(self) -> _T: ... + items_seen: int + +def chunked_even(iterable: Iterable[_T], n: int) -> Iterator[list[_T]]: ... +@overload +def zip_broadcast( + __obj1: _T | Iterable[_T], + *, + scalar_types: _ClassInfo | None = ..., + strict: bool = ..., +) -> Iterable[tuple[_T, ...]]: ... +@overload +def zip_broadcast( + __obj1: _T | Iterable[_T], + __obj2: _T | Iterable[_T], + *, + scalar_types: _ClassInfo | None = ..., + strict: bool = ..., +) -> Iterable[tuple[_T, ...]]: ... +@overload +def zip_broadcast( + __obj1: _T | Iterable[_T], + __obj2: _T | Iterable[_T], + __obj3: _T | Iterable[_T], + *, + scalar_types: _ClassInfo | None = ..., + strict: bool = ..., +) -> Iterable[tuple[_T, ...]]: ... +@overload +def zip_broadcast( + __obj1: _T | Iterable[_T], + __obj2: _T | Iterable[_T], + __obj3: _T | Iterable[_T], + __obj4: _T | Iterable[_T], + *, + scalar_types: _ClassInfo | None = ..., + strict: bool = ..., +) -> Iterable[tuple[_T, ...]]: ... +@overload +def zip_broadcast( + __obj1: _T | Iterable[_T], + __obj2: _T | Iterable[_T], + __obj3: _T | Iterable[_T], + __obj4: _T | Iterable[_T], + __obj5: _T | Iterable[_T], + *, + scalar_types: _ClassInfo | None = ..., + strict: bool = ..., +) -> Iterable[tuple[_T, ...]]: ... +@overload +def zip_broadcast( + __obj1: _T | Iterable[_T], + __obj2: _T | Iterable[_T], + __obj3: _T | Iterable[_T], + __obj4: _T | Iterable[_T], + __obj5: _T | Iterable[_T], + __obj6: _T | Iterable[_T], + *objects: _T | Iterable[_T], + scalar_types: _ClassInfo | None = ..., + strict: bool = ..., +) -> Iterable[tuple[_T, ...]]: ... +def unique_in_window( + iterable: Iterable[_T], n: int, key: Callable[[_T], _U] | None = ... +) -> Iterator[_T]: ... +def duplicates_everseen( + iterable: Iterable[_T], key: Callable[[_T], _U] | None = ... +) -> Iterator[_T]: ... +def duplicates_justseen( + iterable: Iterable[_T], key: Callable[[_T], _U] | None = ... +) -> Iterator[_T]: ... +def classify_unique( + iterable: Iterable[_T], key: Callable[[_T], _U] | None = ... +) -> Iterator[tuple[_T, bool, bool]]: ... + +class _SupportsLessThan(Protocol): + def __lt__(self, __other: Any) -> bool: ... + +_SupportsLessThanT = TypeVar("_SupportsLessThanT", bound=_SupportsLessThan) + +@overload +def minmax( + iterable_or_value: Iterable[_SupportsLessThanT], *, key: None = None +) -> tuple[_SupportsLessThanT, _SupportsLessThanT]: ... +@overload +def minmax( + iterable_or_value: Iterable[_T], *, key: Callable[[_T], _SupportsLessThan] +) -> tuple[_T, _T]: ... +@overload +def minmax( + iterable_or_value: Iterable[_SupportsLessThanT], + *, + key: None = None, + default: _U, +) -> _U | tuple[_SupportsLessThanT, _SupportsLessThanT]: ... +@overload +def minmax( + iterable_or_value: Iterable[_T], + *, + key: Callable[[_T], _SupportsLessThan], + default: _U, +) -> _U | tuple[_T, _T]: ... +@overload +def minmax( + iterable_or_value: _SupportsLessThanT, + __other: _SupportsLessThanT, + *others: _SupportsLessThanT, +) -> tuple[_SupportsLessThanT, _SupportsLessThanT]: ... +@overload +def minmax( + iterable_or_value: _T, + __other: _T, + *others: _T, + key: Callable[[_T], _SupportsLessThan], +) -> tuple[_T, _T]: ... +def longest_common_prefix( + iterables: Iterable[Iterable[_T]], +) -> Iterator[_T]: ... +def iequals(*iterables: Iterable[Any]) -> bool: ... +def constrained_batches( + iterable: Iterable[_T], + max_size: int, + max_count: int | None = ..., + get_len: Callable[[_T], object] = ..., + strict: bool = ..., +) -> Iterator[tuple[_T]]: ... +def gray_product(*iterables: Iterable[_T]) -> Iterator[tuple[_T, ...]]: ... +def partial_product(*iterables: Iterable[_T]) -> Iterator[tuple[_T, ...]]: ... +def takewhile_inclusive( + predicate: Callable[[_T], bool], iterable: Iterable[_T] +) -> Iterator[_T]: ... +def outer_product( + func: Callable[[_T, _U], _V], + xs: Iterable[_T], + ys: Iterable[_U], + *args: Any, + **kwargs: Any, +) -> Iterator[tuple[_V, ...]]: ... +def iter_suppress( + iterable: Iterable[_T], + *exceptions: type[BaseException], +) -> Iterator[_T]: ... +def filter_map( + func: Callable[[_T], _V | None], + iterable: Iterable[_T], +) -> Iterator[_V]: ... +def powerset_of_sets(iterable: Iterable[_T]) -> Iterator[set[_T]]: ... +def join_mappings( + **field_to_map: Mapping[_T, _V], +) -> dict[_T, dict[str, _V]]: ... +def doublestarmap( + func: Callable[..., _T], + iterable: Iterable[Mapping[str, Any]], +) -> Iterator[_T]: ... +def dft(xarr: Sequence[complex]) -> Iterator[complex]: ... +def idft(Xarr: Sequence[complex]) -> Iterator[complex]: ... +def _nth_prime_ub(n: int) -> float: ... +def nth_prime(n: int, *, approximate: bool = ...) -> int: ... +def argmin( + iterable: Iterable[_T], *, key: Callable[[_T], _U] | None = ... +) -> int: ... +def argmax( + iterable: Iterable[_T], *, key: Callable[[_T], _U] | None = ... +) -> int: ... +def extract( + iterable: Iterable[_T], indices: Iterable[int] +) -> Iterator[_T]: ... diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/py.typed b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/py.typed new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/recipes.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/recipes.py new file mode 100644 index 0000000000000000000000000000000000000000..dacf61407d454907d661edde2d774bee11cec92a --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/recipes.py @@ -0,0 +1,1471 @@ +"""Imported from the recipes section of the itertools documentation. + +All functions taken from the recipes section of the itertools library docs +[1]_. +Some backward-compatible usability improvements have been made. + +.. [1] http://docs.python.org/library/itertools.html#recipes + +""" + +import random + +from bisect import bisect_left, insort +from collections import deque +from contextlib import suppress +from functools import lru_cache, partial, reduce +from heapq import heappush, heappushpop +from itertools import ( + accumulate, + chain, + combinations, + compress, + count, + cycle, + groupby, + islice, + product, + repeat, + starmap, + takewhile, + tee, + zip_longest, +) +from math import prod, comb, isqrt, gcd +from operator import mul, not_, itemgetter, getitem, index +from random import randrange, sample, choice +from sys import hexversion + +__all__ = [ + 'all_equal', + 'batched', + 'before_and_after', + 'consume', + 'convolve', + 'dotproduct', + 'first_true', + 'factor', + 'flatten', + 'grouper', + 'is_prime', + 'iter_except', + 'iter_index', + 'loops', + 'matmul', + 'multinomial', + 'ncycles', + 'nth', + 'nth_combination', + 'padnone', + 'pad_none', + 'pairwise', + 'partition', + 'polynomial_eval', + 'polynomial_from_roots', + 'polynomial_derivative', + 'powerset', + 'prepend', + 'quantify', + 'reshape', + 'random_combination_with_replacement', + 'random_combination', + 'random_permutation', + 'random_product', + 'repeatfunc', + 'roundrobin', + 'running_median', + 'sieve', + 'sliding_window', + 'subslices', + 'sum_of_squares', + 'tabulate', + 'tail', + 'take', + 'totient', + 'transpose', + 'triplewise', + 'unique', + 'unique_everseen', + 'unique_justseen', +] + +_marker = object() + + +# zip with strict is available for Python 3.10+ +try: + zip(strict=True) +except TypeError: # pragma: no cover + _zip_strict = zip +else: # pragma: no cover + _zip_strict = partial(zip, strict=True) + + +# math.sumprod is available for Python 3.12+ +try: + from math import sumprod as _sumprod +except ImportError: # pragma: no cover + _sumprod = lambda x, y: dotproduct(x, y) + + +# heapq max-heap functions are available for Python 3.14+ +try: + from heapq import heappush_max, heappushpop_max +except ImportError: # pragma: no cover + _max_heap_available = False +else: # pragma: no cover + _max_heap_available = True + + +def take(n, iterable): + """Return first *n* items of the *iterable* as a list. + + >>> take(3, range(10)) + [0, 1, 2] + + If there are fewer than *n* items in the iterable, all of them are + returned. + + >>> take(10, range(3)) + [0, 1, 2] + + """ + return list(islice(iterable, n)) + + +def tabulate(function, start=0): + """Return an iterator over the results of ``func(start)``, + ``func(start + 1)``, ``func(start + 2)``... + + *func* should be a function that accepts one integer argument. + + If *start* is not specified it defaults to 0. It will be incremented each + time the iterator is advanced. + + >>> square = lambda x: x ** 2 + >>> iterator = tabulate(square, -3) + >>> take(4, iterator) + [9, 4, 1, 0] + + """ + return map(function, count(start)) + + +def tail(n, iterable): + """Return an iterator over the last *n* items of *iterable*. + + >>> t = tail(3, 'ABCDEFG') + >>> list(t) + ['E', 'F', 'G'] + + """ + try: + size = len(iterable) + except TypeError: + return iter(deque(iterable, maxlen=n)) + else: + return islice(iterable, max(0, size - n), None) + + +def consume(iterator, n=None): + """Advance *iterable* by *n* steps. If *n* is ``None``, consume it + entirely. + + Efficiently exhausts an iterator without returning values. Defaults to + consuming the whole iterator, but an optional second argument may be + provided to limit consumption. + + >>> i = (x for x in range(10)) + >>> next(i) + 0 + >>> consume(i, 3) + >>> next(i) + 4 + >>> consume(i) + >>> next(i) + Traceback (most recent call last): + File "", line 1, in + StopIteration + + If the iterator has fewer items remaining than the provided limit, the + whole iterator will be consumed. + + >>> i = (x for x in range(3)) + >>> consume(i, 5) + >>> next(i) + Traceback (most recent call last): + File "", line 1, in + StopIteration + + """ + # Use functions that consume iterators at C speed. + if n is None: + # feed the entire iterator into a zero-length deque + deque(iterator, maxlen=0) + else: + # advance to the empty slice starting at position n + next(islice(iterator, n, n), None) + + +def nth(iterable, n, default=None): + """Returns the nth item or a default value. + + >>> l = range(10) + >>> nth(l, 3) + 3 + >>> nth(l, 20, "zebra") + 'zebra' + + """ + return next(islice(iterable, n, None), default) + + +def all_equal(iterable, key=None): + """ + Returns ``True`` if all the elements are equal to each other. + + >>> all_equal('aaaa') + True + >>> all_equal('aaab') + False + + A function that accepts a single argument and returns a transformed version + of each input item can be specified with *key*: + + >>> all_equal('AaaA', key=str.casefold) + True + >>> all_equal([1, 2, 3], key=lambda x: x < 10) + True + + """ + iterator = groupby(iterable, key) + for first in iterator: + for second in iterator: + return False + return True + return True + + +def quantify(iterable, pred=bool): + """Return the how many times the predicate is true. + + >>> quantify([True, False, True]) + 2 + + """ + return sum(map(pred, iterable)) + + +def pad_none(iterable): + """Returns the sequence of elements and then returns ``None`` indefinitely. + + >>> take(5, pad_none(range(3))) + [0, 1, 2, None, None] + + Useful for emulating the behavior of the built-in :func:`map` function. + + See also :func:`padded`. + + """ + return chain(iterable, repeat(None)) + + +padnone = pad_none + + +def ncycles(iterable, n): + """Returns the sequence elements *n* times + + >>> list(ncycles(["a", "b"], 3)) + ['a', 'b', 'a', 'b', 'a', 'b'] + + """ + return chain.from_iterable(repeat(tuple(iterable), n)) + + +def dotproduct(vec1, vec2): + """Returns the dot product of the two iterables. + + >>> dotproduct([10, 15, 12], [0.65, 0.80, 1.25]) + 33.5 + >>> 10 * 0.65 + 15 * 0.80 + 12 * 1.25 + 33.5 + + In Python 3.12 and later, use ``math.sumprod()`` instead. + """ + return sum(map(mul, vec1, vec2)) + + +def flatten(listOfLists): + """Return an iterator flattening one level of nesting in a list of lists. + + >>> list(flatten([[0, 1], [2, 3]])) + [0, 1, 2, 3] + + See also :func:`collapse`, which can flatten multiple levels of nesting. + + """ + return chain.from_iterable(listOfLists) + + +def repeatfunc(func, times=None, *args): + """Call *func* with *args* repeatedly, returning an iterable over the + results. + + If *times* is specified, the iterable will terminate after that many + repetitions: + + >>> from operator import add + >>> times = 4 + >>> args = 3, 5 + >>> list(repeatfunc(add, times, *args)) + [8, 8, 8, 8] + + If *times* is ``None`` the iterable will not terminate: + + >>> from random import randrange + >>> times = None + >>> args = 1, 11 + >>> take(6, repeatfunc(randrange, times, *args)) # doctest:+SKIP + [2, 4, 8, 1, 8, 4] + + """ + if times is None: + return starmap(func, repeat(args)) + return starmap(func, repeat(args, times)) + + +def _pairwise(iterable): + """Returns an iterator of paired items, overlapping, from the original + + >>> take(4, pairwise(count())) + [(0, 1), (1, 2), (2, 3), (3, 4)] + + On Python 3.10 and above, this is an alias for :func:`itertools.pairwise`. + + """ + a, b = tee(iterable) + next(b, None) + return zip(a, b) + + +try: + from itertools import pairwise as itertools_pairwise +except ImportError: # pragma: no cover + pairwise = _pairwise +else: # pragma: no cover + + def pairwise(iterable): + return itertools_pairwise(iterable) + + pairwise.__doc__ = _pairwise.__doc__ + + +class UnequalIterablesError(ValueError): + def __init__(self, details=None): + msg = 'Iterables have different lengths' + if details is not None: + msg += (': index 0 has length {}; index {} has length {}').format( + *details + ) + + super().__init__(msg) + + +def _zip_equal_generator(iterables): + for combo in zip_longest(*iterables, fillvalue=_marker): + for val in combo: + if val is _marker: + raise UnequalIterablesError() + yield combo + + +def _zip_equal(*iterables): + # Check whether the iterables are all the same size. + try: + first_size = len(iterables[0]) + for i, it in enumerate(iterables[1:], 1): + size = len(it) + if size != first_size: + raise UnequalIterablesError(details=(first_size, i, size)) + # All sizes are equal, we can use the built-in zip. + return zip(*iterables) + # If any one of the iterables didn't have a length, start reading + # them until one runs out. + except TypeError: + return _zip_equal_generator(iterables) + + +def grouper(iterable, n, incomplete='fill', fillvalue=None): + """Group elements from *iterable* into fixed-length groups of length *n*. + + >>> list(grouper('ABCDEF', 3)) + [('A', 'B', 'C'), ('D', 'E', 'F')] + + The keyword arguments *incomplete* and *fillvalue* control what happens for + iterables whose length is not a multiple of *n*. + + When *incomplete* is `'fill'`, the last group will contain instances of + *fillvalue*. + + >>> list(grouper('ABCDEFG', 3, incomplete='fill', fillvalue='x')) + [('A', 'B', 'C'), ('D', 'E', 'F'), ('G', 'x', 'x')] + + When *incomplete* is `'ignore'`, the last group will not be emitted. + + >>> list(grouper('ABCDEFG', 3, incomplete='ignore', fillvalue='x')) + [('A', 'B', 'C'), ('D', 'E', 'F')] + + When *incomplete* is `'strict'`, a subclass of `ValueError` will be raised. + + >>> iterator = grouper('ABCDEFG', 3, incomplete='strict') + >>> list(iterator) # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + ... + UnequalIterablesError + + """ + iterators = [iter(iterable)] * n + if incomplete == 'fill': + return zip_longest(*iterators, fillvalue=fillvalue) + if incomplete == 'strict': + return _zip_equal(*iterators) + if incomplete == 'ignore': + return zip(*iterators) + else: + raise ValueError('Expected fill, strict, or ignore') + + +def roundrobin(*iterables): + """Visit input iterables in a cycle until each is exhausted. + + >>> list(roundrobin('ABC', 'D', 'EF')) + ['A', 'D', 'E', 'B', 'F', 'C'] + + This function produces the same output as :func:`interleave_longest`, but + may perform better for some inputs (in particular when the number of + iterables is small). + + """ + # Algorithm credited to George Sakkis + iterators = map(iter, iterables) + for num_active in range(len(iterables), 0, -1): + iterators = cycle(islice(iterators, num_active)) + yield from map(next, iterators) + + +def partition(pred, iterable): + """ + Returns a 2-tuple of iterables derived from the input iterable. + The first yields the items that have ``pred(item) == False``. + The second yields the items that have ``pred(item) == True``. + + >>> is_odd = lambda x: x % 2 != 0 + >>> iterable = range(10) + >>> even_items, odd_items = partition(is_odd, iterable) + >>> list(even_items), list(odd_items) + ([0, 2, 4, 6, 8], [1, 3, 5, 7, 9]) + + If *pred* is None, :func:`bool` is used. + + >>> iterable = [0, 1, False, True, '', ' '] + >>> false_items, true_items = partition(None, iterable) + >>> list(false_items), list(true_items) + ([0, False, ''], [1, True, ' ']) + + """ + if pred is None: + pred = bool + + t1, t2, p = tee(iterable, 3) + p1, p2 = tee(map(pred, p)) + return (compress(t1, map(not_, p1)), compress(t2, p2)) + + +def powerset(iterable): + """Yields all possible subsets of the iterable. + + >>> list(powerset([1, 2, 3])) + [(), (1,), (2,), (3,), (1, 2), (1, 3), (2, 3), (1, 2, 3)] + + :func:`powerset` will operate on iterables that aren't :class:`set` + instances, so repeated elements in the input will produce repeated elements + in the output. + + >>> seq = [1, 1, 0] + >>> list(powerset(seq)) + [(), (1,), (1,), (0,), (1, 1), (1, 0), (1, 0), (1, 1, 0)] + + For a variant that efficiently yields actual :class:`set` instances, see + :func:`powerset_of_sets`. + """ + s = list(iterable) + return chain.from_iterable(combinations(s, r) for r in range(len(s) + 1)) + + +def unique_everseen(iterable, key=None): + """ + Yield unique elements, preserving order. + + >>> list(unique_everseen('AAAABBBCCDAABBB')) + ['A', 'B', 'C', 'D'] + >>> list(unique_everseen('ABBCcAD', str.lower)) + ['A', 'B', 'C', 'D'] + + Sequences with a mix of hashable and unhashable items can be used. + The function will be slower (i.e., `O(n^2)`) for unhashable items. + + Remember that ``list`` objects are unhashable - you can use the *key* + parameter to transform the list to a tuple (which is hashable) to + avoid a slowdown. + + >>> iterable = ([1, 2], [2, 3], [1, 2]) + >>> list(unique_everseen(iterable)) # Slow + [[1, 2], [2, 3]] + >>> list(unique_everseen(iterable, key=tuple)) # Faster + [[1, 2], [2, 3]] + + Similarly, you may want to convert unhashable ``set`` objects with + ``key=frozenset``. For ``dict`` objects, + ``key=lambda x: frozenset(x.items())`` can be used. + + """ + seenset = set() + seenset_add = seenset.add + seenlist = [] + seenlist_add = seenlist.append + use_key = key is not None + + for element in iterable: + k = key(element) if use_key else element + try: + if k not in seenset: + seenset_add(k) + yield element + except TypeError: + if k not in seenlist: + seenlist_add(k) + yield element + + +def unique_justseen(iterable, key=None): + """Yields elements in order, ignoring serial duplicates + + >>> list(unique_justseen('AAAABBBCCDAABBB')) + ['A', 'B', 'C', 'D', 'A', 'B'] + >>> list(unique_justseen('ABBCcAD', str.lower)) + ['A', 'B', 'C', 'A', 'D'] + + """ + if key is None: + return map(itemgetter(0), groupby(iterable)) + + return map(next, map(itemgetter(1), groupby(iterable, key))) + + +def unique(iterable, key=None, reverse=False): + """Yields unique elements in sorted order. + + >>> list(unique([[1, 2], [3, 4], [1, 2]])) + [[1, 2], [3, 4]] + + *key* and *reverse* are passed to :func:`sorted`. + + >>> list(unique('ABBcCAD', str.casefold)) + ['A', 'B', 'c', 'D'] + >>> list(unique('ABBcCAD', str.casefold, reverse=True)) + ['D', 'c', 'B', 'A'] + + The elements in *iterable* need not be hashable, but they must be + comparable for sorting to work. + """ + sequenced = sorted(iterable, key=key, reverse=reverse) + return unique_justseen(sequenced, key=key) + + +def iter_except(func, exception, first=None): + """Yields results from a function repeatedly until an exception is raised. + + Converts a call-until-exception interface to an iterator interface. + Like ``iter(func, sentinel)``, but uses an exception instead of a sentinel + to end the loop. + + >>> l = [0, 1, 2] + >>> list(iter_except(l.pop, IndexError)) + [2, 1, 0] + + Multiple exceptions can be specified as a stopping condition: + + >>> l = [1, 2, 3, '...', 4, 5, 6] + >>> list(iter_except(lambda: 1 + l.pop(), (IndexError, TypeError))) + [7, 6, 5] + >>> list(iter_except(lambda: 1 + l.pop(), (IndexError, TypeError))) + [4, 3, 2] + >>> list(iter_except(lambda: 1 + l.pop(), (IndexError, TypeError))) + [] + + """ + with suppress(exception): + if first is not None: + yield first() + while True: + yield func() + + +def first_true(iterable, default=None, pred=None): + """ + Returns the first true value in the iterable. + + If no true value is found, returns *default* + + If *pred* is not None, returns the first item for which + ``pred(item) == True`` . + + >>> first_true(range(10)) + 1 + >>> first_true(range(10), pred=lambda x: x > 5) + 6 + >>> first_true(range(10), default='missing', pred=lambda x: x > 9) + 'missing' + + """ + return next(filter(pred, iterable), default) + + +def random_product(*args, repeat=1): + """Draw an item at random from each of the input iterables. + + >>> random_product('abc', range(4), 'XYZ') # doctest:+SKIP + ('c', 3, 'Z') + + If *repeat* is provided as a keyword argument, that many items will be + drawn from each iterable. + + >>> random_product('abcd', range(4), repeat=2) # doctest:+SKIP + ('a', 2, 'd', 3) + + This equivalent to taking a random selection from + ``itertools.product(*args, repeat=repeat)``. + + """ + pools = [tuple(pool) for pool in args] * repeat + return tuple(choice(pool) for pool in pools) + + +def random_permutation(iterable, r=None): + """Return a random *r* length permutation of the elements in *iterable*. + + If *r* is not specified or is ``None``, then *r* defaults to the length of + *iterable*. + + >>> random_permutation(range(5)) # doctest:+SKIP + (3, 4, 0, 1, 2) + + This equivalent to taking a random selection from + ``itertools.permutations(iterable, r)``. + + """ + pool = tuple(iterable) + r = len(pool) if r is None else r + return tuple(sample(pool, r)) + + +def random_combination(iterable, r): + """Return a random *r* length subsequence of the elements in *iterable*. + + >>> random_combination(range(5), 3) # doctest:+SKIP + (2, 3, 4) + + This equivalent to taking a random selection from + ``itertools.combinations(iterable, r)``. + + """ + pool = tuple(iterable) + n = len(pool) + indices = sorted(sample(range(n), r)) + return tuple(pool[i] for i in indices) + + +def random_combination_with_replacement(iterable, r): + """Return a random *r* length subsequence of elements in *iterable*, + allowing individual elements to be repeated. + + >>> random_combination_with_replacement(range(3), 5) # doctest:+SKIP + (0, 0, 1, 2, 2) + + This equivalent to taking a random selection from + ``itertools.combinations_with_replacement(iterable, r)``. + + """ + pool = tuple(iterable) + n = len(pool) + indices = sorted(randrange(n) for i in range(r)) + return tuple(pool[i] for i in indices) + + +def nth_combination(iterable, r, index): + """Equivalent to ``list(combinations(iterable, r))[index]``. + + The subsequences of *iterable* that are of length *r* can be ordered + lexicographically. :func:`nth_combination` computes the subsequence at + sort position *index* directly, without computing the previous + subsequences. + + >>> nth_combination(range(5), 3, 5) + (0, 3, 4) + + ``ValueError`` will be raised If *r* is negative or greater than the length + of *iterable*. + ``IndexError`` will be raised if the given *index* is invalid. + """ + pool = tuple(iterable) + n = len(pool) + if (r < 0) or (r > n): + raise ValueError + + c = 1 + k = min(r, n - r) + for i in range(1, k + 1): + c = c * (n - k + i) // i + + if index < 0: + index += c + + if (index < 0) or (index >= c): + raise IndexError + + result = [] + while r: + c, n, r = c * r // n, n - 1, r - 1 + while index >= c: + index -= c + c, n = c * (n - r) // n, n - 1 + result.append(pool[-1 - n]) + + return tuple(result) + + +def prepend(value, iterator): + """Yield *value*, followed by the elements in *iterator*. + + >>> value = '0' + >>> iterator = ['1', '2', '3'] + >>> list(prepend(value, iterator)) + ['0', '1', '2', '3'] + + To prepend multiple values, see :func:`itertools.chain` + or :func:`value_chain`. + + """ + return chain([value], iterator) + + +def convolve(signal, kernel): + """Discrete linear convolution of two iterables. + Equivalent to polynomial multiplication. + + For example, multiplying ``(x² -x - 20)`` by ``(x - 3)`` + gives ``(x³ -4x² -17x + 60)``. + + >>> list(convolve([1, -1, -20], [1, -3])) + [1, -4, -17, 60] + + Examples of popular kinds of kernels: + + * The kernel ``[0.25, 0.25, 0.25, 0.25]`` computes a moving average. + For image data, this blurs the image and reduces noise. + * The kernel ``[1/2, 0, -1/2]`` estimates the first derivative of + a function evaluated at evenly spaced inputs. + * The kernel ``[1, -2, 1]`` estimates the second derivative of a + function evaluated at evenly spaced inputs. + + Convolutions are mathematically commutative; however, the inputs are + evaluated differently. The signal is consumed lazily and can be + infinite. The kernel is fully consumed before the calculations begin. + + Supports all numeric types: int, float, complex, Decimal, Fraction. + + References: + + * Article: https://betterexplained.com/articles/intuitive-convolution/ + * Video by 3Blue1Brown: https://www.youtube.com/watch?v=KuXjwB4LzSA + + """ + # This implementation comes from an older version of the itertools + # documentation. While the newer implementation is a bit clearer, + # this one was kept because the inlined window logic is faster + # and it avoids an unnecessary deque-to-tuple conversion. + kernel = tuple(kernel)[::-1] + n = len(kernel) + window = deque([0], maxlen=n) * n + for x in chain(signal, repeat(0, n - 1)): + window.append(x) + yield _sumprod(kernel, window) + + +def before_and_after(predicate, it): + """A variant of :func:`takewhile` that allows complete access to the + remainder of the iterator. + + >>> it = iter('ABCdEfGhI') + >>> all_upper, remainder = before_and_after(str.isupper, it) + >>> ''.join(all_upper) + 'ABC' + >>> ''.join(remainder) # takewhile() would lose the 'd' + 'dEfGhI' + + Note that the first iterator must be fully consumed before the second + iterator can generate valid results. + """ + trues, after = tee(it) + trues = compress(takewhile(predicate, trues), zip(after)) + return trues, after + + +def triplewise(iterable): + """Return overlapping triplets from *iterable*. + + >>> list(triplewise('ABCDE')) + [('A', 'B', 'C'), ('B', 'C', 'D'), ('C', 'D', 'E')] + + """ + # This deviates from the itertools documentation recipe - see + # https://github.com/more-itertools/more-itertools/issues/889 + t1, t2, t3 = tee(iterable, 3) + next(t3, None) + next(t3, None) + next(t2, None) + return zip(t1, t2, t3) + + +def _sliding_window_islice(iterable, n): + # Fast path for small, non-zero values of n. + iterators = tee(iterable, n) + for i, iterator in enumerate(iterators): + next(islice(iterator, i, i), None) + return zip(*iterators) + + +def _sliding_window_deque(iterable, n): + # Normal path for other values of n. + iterator = iter(iterable) + window = deque(islice(iterator, n - 1), maxlen=n) + for x in iterator: + window.append(x) + yield tuple(window) + + +def sliding_window(iterable, n): + """Return a sliding window of width *n* over *iterable*. + + >>> list(sliding_window(range(6), 4)) + [(0, 1, 2, 3), (1, 2, 3, 4), (2, 3, 4, 5)] + + If *iterable* has fewer than *n* items, then nothing is yielded: + + >>> list(sliding_window(range(3), 4)) + [] + + For a variant with more features, see :func:`windowed`. + """ + if n > 20: + return _sliding_window_deque(iterable, n) + elif n > 2: + return _sliding_window_islice(iterable, n) + elif n == 2: + return pairwise(iterable) + elif n == 1: + return zip(iterable) + else: + raise ValueError(f'n should be at least one, not {n}') + + +def subslices(iterable): + """Return all contiguous non-empty subslices of *iterable*. + + >>> list(subslices('ABC')) + [['A'], ['A', 'B'], ['A', 'B', 'C'], ['B'], ['B', 'C'], ['C']] + + This is similar to :func:`substrings`, but emits items in a different + order. + """ + seq = list(iterable) + slices = starmap(slice, combinations(range(len(seq) + 1), 2)) + return map(getitem, repeat(seq), slices) + + +def polynomial_from_roots(roots): + """Compute a polynomial's coefficients from its roots. + + >>> roots = [5, -4, 3] # (x - 5) * (x + 4) * (x - 3) + >>> polynomial_from_roots(roots) # x³ - 4 x² - 17 x + 60 + [1, -4, -17, 60] + + Note that polynomial coefficients are specified in descending power order. + + Supports all numeric types: int, float, complex, Decimal, Fraction. + """ + + # This recipe differs from the one in itertools docs in that it + # applies list() after each call to convolve(). This avoids + # hitting stack limits with nested generators. + + poly = [1] + for root in roots: + poly = list(convolve(poly, (1, -root))) + return poly + + +def iter_index(iterable, value, start=0, stop=None): + """Yield the index of each place in *iterable* that *value* occurs, + beginning with index *start* and ending before index *stop*. + + + >>> list(iter_index('AABCADEAF', 'A')) + [0, 1, 4, 7] + >>> list(iter_index('AABCADEAF', 'A', 1)) # start index is inclusive + [1, 4, 7] + >>> list(iter_index('AABCADEAF', 'A', 1, 7)) # stop index is not inclusive + [1, 4] + + The behavior for non-scalar *values* matches the built-in Python types. + + >>> list(iter_index('ABCDABCD', 'AB')) + [0, 4] + >>> list(iter_index([0, 1, 2, 3, 0, 1, 2, 3], [0, 1])) + [] + >>> list(iter_index([[0, 1], [2, 3], [0, 1], [2, 3]], [0, 1])) + [0, 2] + + See :func:`locate` for a more general means of finding the indexes + associated with particular values. + + """ + seq_index = getattr(iterable, 'index', None) + if seq_index is None: + # Slow path for general iterables + iterator = islice(iterable, start, stop) + for i, element in enumerate(iterator, start): + if element is value or element == value: + yield i + else: + # Fast path for sequences + stop = len(iterable) if stop is None else stop + i = start - 1 + with suppress(ValueError): + while True: + yield (i := seq_index(value, i + 1, stop)) + + +def sieve(n): + """Yield the primes less than n. + + >>> list(sieve(30)) + [2, 3, 5, 7, 11, 13, 17, 19, 23, 29] + + """ + # This implementation comes from an older version of the itertools + # documentation. The newer implementation is easier to read but is + # less lazy. + if n > 2: + yield 2 + start = 3 + data = bytearray((0, 1)) * (n // 2) + for p in iter_index(data, 1, start, stop=isqrt(n) + 1): + yield from iter_index(data, 1, start, p * p) + data[p * p : n : p + p] = bytes(len(range(p * p, n, p + p))) + start = p * p + yield from iter_index(data, 1, start) + + +def _batched(iterable, n, *, strict=False): # pragma: no cover + """Batch data into tuples of length *n*. If the number of items in + *iterable* is not divisible by *n*: + * The last batch will be shorter if *strict* is ``False``. + * :exc:`ValueError` will be raised if *strict* is ``True``. + + >>> list(batched('ABCDEFG', 3)) + [('A', 'B', 'C'), ('D', 'E', 'F'), ('G',)] + + On Python 3.13 and above, this is an alias for :func:`itertools.batched`. + """ + if n < 1: + raise ValueError('n must be at least one') + iterator = iter(iterable) + while batch := tuple(islice(iterator, n)): + if strict and len(batch) != n: + raise ValueError('batched(): incomplete batch') + yield batch + + +if hexversion >= 0x30D00A2: # pragma: no cover + from itertools import batched as itertools_batched + + def batched(iterable, n, *, strict=False): + return itertools_batched(iterable, n, strict=strict) + + batched.__doc__ = _batched.__doc__ +else: # pragma: no cover + batched = _batched + + +def transpose(it): + """Swap the rows and columns of the input matrix. + + >>> list(transpose([(1, 2, 3), (11, 22, 33)])) + [(1, 11), (2, 22), (3, 33)] + + The caller should ensure that the dimensions of the input are compatible. + If the input is empty, no output will be produced. + """ + return _zip_strict(*it) + + +def _is_scalar(value, stringlike=(str, bytes)): + "Scalars are bytes, strings, and non-iterables." + try: + iter(value) + except TypeError: + return True + return isinstance(value, stringlike) + + +def _flatten_tensor(tensor): + "Depth-first iterator over scalars in a tensor." + iterator = iter(tensor) + while True: + try: + value = next(iterator) + except StopIteration: + return iterator + iterator = chain((value,), iterator) + if _is_scalar(value): + return iterator + iterator = chain.from_iterable(iterator) + + +def reshape(matrix, shape): + """Change the shape of a *matrix*. + + If *shape* is an integer, the matrix must be two dimensional + and the shape is interpreted as the desired number of columns: + + >>> matrix = [(0, 1), (2, 3), (4, 5)] + >>> cols = 3 + >>> list(reshape(matrix, cols)) + [(0, 1, 2), (3, 4, 5)] + + If *shape* is a tuple (or other iterable), the input matrix can have + any number of dimensions. It will first be flattened and then rebuilt + to the desired shape which can also be multidimensional: + + >>> matrix = [(0, 1), (2, 3), (4, 5)] # Start with a 3 x 2 matrix + + >>> list(reshape(matrix, (2, 3))) # Make a 2 x 3 matrix + [(0, 1, 2), (3, 4, 5)] + + >>> list(reshape(matrix, (6,))) # Make a vector of length six + [0, 1, 2, 3, 4, 5] + + >>> list(reshape(matrix, (2, 1, 3, 1))) # Make 2 x 1 x 3 x 1 tensor + [(((0,), (1,), (2,)),), (((3,), (4,), (5,)),)] + + Each dimension is assumed to be uniform, either all arrays or all scalars. + Flattening stops when the first value in a dimension is a scalar. + Scalars are bytes, strings, and non-iterables. + The reshape iterator stops when the requested shape is complete + or when the input is exhausted, whichever comes first. + + """ + if isinstance(shape, int): + return batched(chain.from_iterable(matrix), shape) + first_dim, *dims = shape + scalar_stream = _flatten_tensor(matrix) + reshaped = reduce(batched, reversed(dims), scalar_stream) + return islice(reshaped, first_dim) + + +def matmul(m1, m2): + """Multiply two matrices. + + >>> list(matmul([(7, 5), (3, 5)], [(2, 5), (7, 9)])) + [(49, 80), (41, 60)] + + The caller should ensure that the dimensions of the input matrices are + compatible with each other. + + Supports all numeric types: int, float, complex, Decimal, Fraction. + """ + n = len(m2[0]) + return batched(starmap(_sumprod, product(m1, transpose(m2))), n) + + +def _factor_pollard(n): + # Return a factor of n using Pollard's rho algorithm. + # Efficient when n is odd and composite. + for b in range(1, n): + x = y = 2 + d = 1 + while d == 1: + x = (x * x + b) % n + y = (y * y + b) % n + y = (y * y + b) % n + d = gcd(x - y, n) + if d != n: + return d + raise ValueError('prime or under 5') # pragma: no cover + + +_primes_below_211 = tuple(sieve(211)) + + +def factor(n): + """Yield the prime factors of n. + + >>> list(factor(360)) + [2, 2, 2, 3, 3, 5] + + Finds small factors with trial division. Larger factors are + either verified as prime with ``is_prime`` or split into + smaller factors with Pollard's rho algorithm. + """ + + # Corner case reduction + if n < 2: + return + + # Trial division reduction + for prime in _primes_below_211: + while not n % prime: + yield prime + n //= prime + + # Pollard's rho reduction + primes = [] + todo = [n] if n > 1 else [] + for n in todo: + if n < 211**2 or is_prime(n): + primes.append(n) + else: + fact = _factor_pollard(n) + todo += (fact, n // fact) + yield from sorted(primes) + + +def polynomial_eval(coefficients, x): + """Evaluate a polynomial at a specific value. + + Computes with better numeric stability than Horner's method. + + Evaluate ``x^3 - 4 * x^2 - 17 * x + 60`` at ``x = 2.5``: + + >>> coefficients = [1, -4, -17, 60] + >>> x = 2.5 + >>> polynomial_eval(coefficients, x) + 8.125 + + Note that polynomial coefficients are specified in descending power order. + + Supports all numeric types: int, float, complex, Decimal, Fraction. + """ + n = len(coefficients) + if n == 0: + return type(x)(0) + powers = map(pow, repeat(x), reversed(range(n))) + return _sumprod(coefficients, powers) + + +def sum_of_squares(it): + """Return the sum of the squares of the input values. + + >>> sum_of_squares([10, 20, 30]) + 1400 + + Supports all numeric types: int, float, complex, Decimal, Fraction. + """ + return _sumprod(*tee(it)) + + +def polynomial_derivative(coefficients): + """Compute the first derivative of a polynomial. + + Evaluate the derivative of ``x³ - 4 x² - 17 x + 60``: + + >>> coefficients = [1, -4, -17, 60] + >>> derivative_coefficients = polynomial_derivative(coefficients) + >>> derivative_coefficients + [3, -8, -17] + + Note that polynomial coefficients are specified in descending power order. + + Supports all numeric types: int, float, complex, Decimal, Fraction. + """ + n = len(coefficients) + powers = reversed(range(1, n)) + return list(map(mul, coefficients, powers)) + + +def totient(n): + """Return the count of natural numbers up to *n* that are coprime with *n*. + + Euler's totient function φ(n) gives the number of totatives. + Totative are integers k in the range 1 ≤ k ≤ n such that gcd(n, k) = 1. + + >>> n = 9 + >>> totient(n) + 6 + + >>> totatives = [x for x in range(1, n) if gcd(n, x) == 1] + >>> totatives + [1, 2, 4, 5, 7, 8] + >>> len(totatives) + 6 + + Reference: https://en.wikipedia.org/wiki/Euler%27s_totient_function + + """ + for prime in set(factor(n)): + n -= n // prime + return n + + +# Miller–Rabin primality test: https://oeis.org/A014233 +_perfect_tests = [ + (2047, (2,)), + (9080191, (31, 73)), + (4759123141, (2, 7, 61)), + (1122004669633, (2, 13, 23, 1662803)), + (2152302898747, (2, 3, 5, 7, 11)), + (3474749660383, (2, 3, 5, 7, 11, 13)), + (18446744073709551616, (2, 325, 9375, 28178, 450775, 9780504, 1795265022)), + ( + 3317044064679887385961981, + (2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41), + ), +] + + +@lru_cache +def _shift_to_odd(n): + 'Return s, d such that 2**s * d == n' + s = ((n - 1) ^ n).bit_length() - 1 + d = n >> s + assert (1 << s) * d == n and d & 1 and s >= 0 + return s, d + + +def _strong_probable_prime(n, base): + assert (n > 2) and (n & 1) and (2 <= base < n) + + s, d = _shift_to_odd(n - 1) + + x = pow(base, d, n) + if x == 1 or x == n - 1: + return True + + for _ in range(s - 1): + x = x * x % n + if x == n - 1: + return True + + return False + + +# Separate instance of Random() that doesn't share state +# with the default user instance of Random(). +_private_randrange = random.Random().randrange + + +def is_prime(n): + """Return ``True`` if *n* is prime and ``False`` otherwise. + + Basic examples: + + >>> is_prime(37) + True + >>> is_prime(3 * 13) + False + >>> is_prime(18_446_744_073_709_551_557) + True + + Find the next prime over one billion: + + >>> next(filter(is_prime, count(10**9))) + 1000000007 + + Generate random primes up to 200 bits and up to 60 decimal digits: + + >>> from random import seed, randrange, getrandbits + >>> seed(18675309) + + >>> next(filter(is_prime, map(getrandbits, repeat(200)))) + 893303929355758292373272075469392561129886005037663238028407 + + >>> next(filter(is_prime, map(randrange, repeat(10**60)))) + 269638077304026462407872868003560484232362454342414618963649 + + This function is exact for values of *n* below 10**24. For larger inputs, + the probabilistic Miller-Rabin primality test has a less than 1 in 2**128 + chance of a false positive. + """ + + if n < 17: + return n in {2, 3, 5, 7, 11, 13} + + if not (n & 1 and n % 3 and n % 5 and n % 7 and n % 11 and n % 13): + return False + + for limit, bases in _perfect_tests: + if n < limit: + break + else: + bases = (_private_randrange(2, n - 1) for i in range(64)) + + return all(_strong_probable_prime(n, base) for base in bases) + + +def loops(n): + """Returns an iterable with *n* elements for efficient looping. + Like ``range(n)`` but doesn't create integers. + + >>> i = 0 + >>> for _ in loops(5): + ... i += 1 + >>> i + 5 + + """ + return repeat(None, n) + + +def multinomial(*counts): + """Number of distinct arrangements of a multiset. + + The expression ``multinomial(3, 4, 2)`` has several equivalent + interpretations: + + * In the expansion of ``(a + b + c)⁹``, the coefficient of the + ``a³b⁴c²`` term is 1260. + + * There are 1260 distinct ways to arrange 9 balls consisting of 3 reds, 4 + greens, and 2 blues. + + * There are 1260 unique ways to place 9 distinct objects into three bins + with sizes 3, 4, and 2. + + The :func:`multinomial` function computes the length of + :func:`distinct_permutations`. For example, there are 83,160 distinct + anagrams of the word "abracadabra": + + >>> from more_itertools import distinct_permutations, ilen + >>> ilen(distinct_permutations('abracadabra')) + 83160 + + This can be computed directly from the letter counts, 5a 2b 2r 1c 1d: + + >>> from collections import Counter + >>> list(Counter('abracadabra').values()) + [5, 2, 2, 1, 1] + >>> multinomial(5, 2, 2, 1, 1) + 83160 + + A binomial coefficient is a special case of multinomial where there are + only two categories. For example, the number of ways to arrange 12 balls + with 5 reds and 7 blues is ``multinomial(5, 7)`` or ``math.comb(12, 5)``. + + Likewise, factorial is a special case of multinomial where + the multiplicities are all just 1 so that + ``multinomial(1, 1, 1, 1, 1, 1, 1) == math.factorial(7)``. + + Reference: https://en.wikipedia.org/wiki/Multinomial_theorem + + """ + return prod(map(comb, accumulate(counts), counts)) + + +def _running_median_minheap_and_maxheap(iterator): # pragma: no cover + "Non-windowed running_median() for Python 3.14+" + + read = iterator.__next__ + lo = [] # max-heap + hi = [] # min-heap (same size as or one smaller than lo) + + with suppress(StopIteration): + while True: + heappush_max(lo, heappushpop(hi, read())) + yield lo[0] + + heappush(hi, heappushpop_max(lo, read())) + yield (lo[0] + hi[0]) / 2 + + +def _running_median_minheap_only(iterator): # pragma: no cover + "Backport of non-windowed running_median() for Python 3.13 and prior." + + read = iterator.__next__ + lo = [] # max-heap (actually a minheap with negated values) + hi = [] # min-heap (same size as or one smaller than lo) + + with suppress(StopIteration): + while True: + heappush(lo, -heappushpop(hi, read())) + yield -lo[0] + + heappush(hi, -heappushpop(lo, -read())) + yield (hi[0] - lo[0]) / 2 + + +def _running_median_windowed(iterator, maxlen): + "Yield median of values in a sliding window." + + window = deque() + ordered = [] + + for x in iterator: + window.append(x) + insort(ordered, x) + + if len(ordered) > maxlen: + i = bisect_left(ordered, window.popleft()) + del ordered[i] + + n = len(ordered) + m = n // 2 + yield ordered[m] if n & 1 else (ordered[m - 1] + ordered[m]) / 2 + + +def running_median(iterable, *, maxlen=None): + """Cumulative median of values seen so far or values in a sliding window. + + Set *maxlen* to a positive integer to specify the maximum size + of the sliding window. The default of *None* is equivalent to + an unbounded window. + + For example: + + >>> list(running_median([5.0, 9.0, 4.0, 12.0, 8.0, 9.0])) + [5.0, 7.0, 5.0, 7.0, 8.0, 8.5] + >>> list(running_median([5.0, 9.0, 4.0, 12.0, 8.0, 9.0], maxlen=3)) + [5.0, 7.0, 5.0, 9.0, 8.0, 9.0] + + Supports numeric types such as int, float, Decimal, and Fraction, + but not complex numbers which are unorderable. + + On version Python 3.13 and prior, max-heaps are simulated with + negative values. The negation causes Decimal inputs to apply context + rounding, making the results slightly different than that obtained + by statistics.median(). + """ + + iterator = iter(iterable) + + if maxlen is not None: + maxlen = index(maxlen) + if maxlen <= 0: + raise ValueError('Window size should be positive') + return _running_median_windowed(iterator, maxlen) + + if not _max_heap_available: + return _running_median_minheap_only(iterator) # pragma: no cover + + return _running_median_minheap_and_maxheap(iterator) # pragma: no cover diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/recipes.pyi b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/recipes.pyi new file mode 100644 index 0000000000000000000000000000000000000000..de3d0a1777a547e986cba595de72f92b8e3cedbd --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/more_itertools/recipes.pyi @@ -0,0 +1,205 @@ +"""Stubs for more_itertools.recipes""" + +from __future__ import annotations + +from collections.abc import Iterable, Iterator, Sequence +from decimal import Decimal +from fractions import Fraction +from typing import ( + Any, + Callable, + TypeVar, + overload, +) + +__all__ = [ + 'all_equal', + 'batched', + 'before_and_after', + 'consume', + 'convolve', + 'dotproduct', + 'first_true', + 'factor', + 'flatten', + 'grouper', + 'is_prime', + 'iter_except', + 'iter_index', + 'loops', + 'matmul', + 'multinomial', + 'ncycles', + 'nth', + 'nth_combination', + 'padnone', + 'pad_none', + 'pairwise', + 'partition', + 'polynomial_eval', + 'polynomial_from_roots', + 'polynomial_derivative', + 'powerset', + 'prepend', + 'quantify', + 'reshape', + 'random_combination_with_replacement', + 'random_combination', + 'random_permutation', + 'random_product', + 'repeatfunc', + 'roundrobin', + 'running_median', + 'sieve', + 'sliding_window', + 'subslices', + 'sum_of_squares', + 'tabulate', + 'tail', + 'take', + 'totient', + 'transpose', + 'triplewise', + 'unique', + 'unique_everseen', + 'unique_justseen', +] + +# Type and type variable definitions +_T = TypeVar('_T') +_T1 = TypeVar('_T1') +_T2 = TypeVar('_T2') +_U = TypeVar('_U') +_NumberT = TypeVar("_NumberT", float, Decimal, Fraction) + +def take(n: int, iterable: Iterable[_T]) -> list[_T]: ... +def tabulate( + function: Callable[[int], _T], start: int = ... +) -> Iterator[_T]: ... +def tail(n: int, iterable: Iterable[_T]) -> Iterator[_T]: ... +def consume(iterator: Iterable[_T], n: int | None = ...) -> None: ... +@overload +def nth(iterable: Iterable[_T], n: int) -> _T | None: ... +@overload +def nth(iterable: Iterable[_T], n: int, default: _U) -> _T | _U: ... +def all_equal( + iterable: Iterable[_T], key: Callable[[_T], _U] | None = ... +) -> bool: ... +def quantify( + iterable: Iterable[_T], pred: Callable[[_T], bool] = ... +) -> int: ... +def pad_none(iterable: Iterable[_T]) -> Iterator[_T | None]: ... +def padnone(iterable: Iterable[_T]) -> Iterator[_T | None]: ... +def ncycles(iterable: Iterable[_T], n: int) -> Iterator[_T]: ... +def dotproduct(vec1: Iterable[_T1], vec2: Iterable[_T2]) -> Any: ... +def flatten(listOfLists: Iterable[Iterable[_T]]) -> Iterator[_T]: ... +def repeatfunc( + func: Callable[..., _U], times: int | None = ..., *args: Any +) -> Iterator[_U]: ... +def pairwise(iterable: Iterable[_T]) -> Iterator[tuple[_T, _T]]: ... +def grouper( + iterable: Iterable[_T], + n: int, + incomplete: str = ..., + fillvalue: _U = ..., +) -> Iterator[tuple[_T | _U, ...]]: ... +def roundrobin(*iterables: Iterable[_T]) -> Iterator[_T]: ... +def partition( + pred: Callable[[_T], object] | None, iterable: Iterable[_T] +) -> tuple[Iterator[_T], Iterator[_T]]: ... +def powerset(iterable: Iterable[_T]) -> Iterator[tuple[_T, ...]]: ... +def unique_everseen( + iterable: Iterable[_T], key: Callable[[_T], _U] | None = ... +) -> Iterator[_T]: ... +def unique_justseen( + iterable: Iterable[_T], key: Callable[[_T], object] | None = ... +) -> Iterator[_T]: ... +def unique( + iterable: Iterable[_T], + key: Callable[[_T], object] | None = ..., + reverse: bool = False, +) -> Iterator[_T]: ... +@overload +def iter_except( + func: Callable[[], _T], + exception: type[BaseException] | tuple[type[BaseException], ...], + first: None = ..., +) -> Iterator[_T]: ... +@overload +def iter_except( + func: Callable[[], _T], + exception: type[BaseException] | tuple[type[BaseException], ...], + first: Callable[[], _U], +) -> Iterator[_T | _U]: ... +@overload +def first_true( + iterable: Iterable[_T], *, pred: Callable[[_T], object] | None = ... +) -> _T | None: ... +@overload +def first_true( + iterable: Iterable[_T], + default: _U, + pred: Callable[[_T], object] | None = ..., +) -> _T | _U: ... +def random_product( + *args: Iterable[_T], repeat: int = ... +) -> tuple[_T, ...]: ... +def random_permutation( + iterable: Iterable[_T], r: int | None = ... +) -> tuple[_T, ...]: ... +def random_combination(iterable: Iterable[_T], r: int) -> tuple[_T, ...]: ... +def random_combination_with_replacement( + iterable: Iterable[_T], r: int +) -> tuple[_T, ...]: ... +def nth_combination( + iterable: Iterable[_T], r: int, index: int +) -> tuple[_T, ...]: ... +def prepend(value: _T, iterator: Iterable[_U]) -> Iterator[_T | _U]: ... +def convolve(signal: Iterable[_T], kernel: Iterable[_T]) -> Iterator[_T]: ... +def before_and_after( + predicate: Callable[[_T], bool], it: Iterable[_T] +) -> tuple[Iterator[_T], Iterator[_T]]: ... +def triplewise(iterable: Iterable[_T]) -> Iterator[tuple[_T, _T, _T]]: ... +def sliding_window( + iterable: Iterable[_T], n: int +) -> Iterator[tuple[_T, ...]]: ... +def subslices(iterable: Iterable[_T]) -> Iterator[list[_T]]: ... +def polynomial_from_roots(roots: Sequence[_T]) -> list[_T]: ... +def iter_index( + iterable: Iterable[_T], + value: Any, + start: int | None = ..., + stop: int | None = ..., +) -> Iterator[int]: ... +def sieve(n: int) -> Iterator[int]: ... +def _batched( + iterable: Iterable[_T], n: int, *, strict: bool = False +) -> Iterator[tuple[_T, ...]]: ... + +batched = _batched + +def transpose( + it: Iterable[Iterable[_T]], +) -> Iterator[tuple[_T, ...]]: ... +@overload +def reshape( + matrix: Iterable[Iterable[_T]], shape: int +) -> Iterator[tuple[_T, ...]]: ... +@overload +def reshape(matrix: Iterable[Any], shape: Iterable[int]) -> Iterator[Any]: ... +def matmul(m1: Sequence[_T], m2: Sequence[_T]) -> Iterator[tuple[_T]]: ... +def _factor_trial(n: int) -> Iterator[int]: ... +def _factor_pollard(n: int) -> int: ... +def factor(n: int) -> Iterator[int]: ... +def polynomial_eval(coefficients: Sequence[_T], x: _U) -> _U: ... +def sum_of_squares(it: Iterable[_T]) -> _T: ... +def polynomial_derivative(coefficients: Sequence[_T]) -> list[_T]: ... +def totient(n: int) -> int: ... +def _shift_to_odd(n: int) -> tuple[int, int]: ... +def _strong_probable_prime(n: int, base: int) -> bool: ... +def is_prime(n: int) -> bool: ... +def loops(n: int) -> Iterator[None]: ... +def multinomial(*counts: int) -> int: ... +def running_median( + iterable: Iterable[_NumberT], *, maxlen: int | None = ... +) -> Iterator[_NumberT]: ... diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/INSTALLER new file mode 100644 index 0000000000000000000000000000000000000000..f79e4cb9aaf0b2d9e8ba78861e2071317b2384b3 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/INSTALLER @@ -0,0 +1 @@ +conda \ No newline at end of file diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/METADATA new file mode 100644 index 0000000000000000000000000000000000000000..3200e601f970271fdde3fcc74f9af4423655a79d --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/METADATA @@ -0,0 +1,107 @@ +Metadata-Version: 2.4 +Name: packaging +Version: 26.0 +Summary: Core utilities for Python packages +Author-email: Donald Stufft +Requires-Python: >=3.8 +Description-Content-Type: text/x-rst +License-Expression: Apache-2.0 OR BSD-2-Clause +Classifier: Development Status :: 5 - Production/Stable +Classifier: Intended Audience :: Developers +Classifier: Programming Language :: Python +Classifier: Programming Language :: Python :: 3 +Classifier: Programming Language :: Python :: 3 :: Only +Classifier: Programming Language :: Python :: 3.8 +Classifier: Programming Language :: Python :: 3.9 +Classifier: Programming Language :: Python :: 3.10 +Classifier: Programming Language :: Python :: 3.11 +Classifier: Programming Language :: Python :: 3.12 +Classifier: Programming Language :: Python :: 3.13 +Classifier: Programming Language :: Python :: 3.14 +Classifier: Programming Language :: Python :: Implementation :: CPython +Classifier: Programming Language :: Python :: Implementation :: PyPy +Classifier: Typing :: Typed +License-File: LICENSE +License-File: LICENSE.APACHE +License-File: LICENSE.BSD +Project-URL: Documentation, https://packaging.pypa.io/ +Project-URL: Source, https://github.com/pypa/packaging + +packaging +========= + +.. start-intro + +Reusable core utilities for various Python Packaging +`interoperability specifications `_. + +This library provides utilities that implement the interoperability +specifications which have clearly one correct behaviour (eg: :pep:`440`) +or benefit greatly from having a single shared implementation (eg: :pep:`425`). + +.. end-intro + +The ``packaging`` project includes the following: version handling, specifiers, +markers, requirements, tags, metadata, lockfiles, utilities. + +Documentation +------------- + +The `documentation`_ provides information and the API for the following: + +- Version Handling +- Specifiers +- Markers +- Requirements +- Tags +- Metadata +- Lockfiles +- Utilities + +Installation +------------ + +Use ``pip`` to install these utilities:: + + pip install packaging + +The ``packaging`` library uses calendar-based versioning (``YY.N``). + +Discussion +---------- + +If you run into bugs, you can file them in our `issue tracker`_. + +You can also join ``#pypa`` on Freenode to ask questions or get involved. + + +.. _`documentation`: https://packaging.pypa.io/ +.. _`issue tracker`: https://github.com/pypa/packaging/issues + + +Code of Conduct +--------------- + +Everyone interacting in the packaging project's codebases, issue trackers, chat +rooms, and mailing lists is expected to follow the `PSF Code of Conduct`_. + +.. _PSF Code of Conduct: https://github.com/pypa/.github/blob/main/CODE_OF_CONDUCT.md + +Contributing +------------ + +The ``CONTRIBUTING.rst`` file outlines how to contribute to this project as +well as how to report a potential security issue. The documentation for this +project also covers information about `project development`_ and `security`_. + +.. _`project development`: https://packaging.pypa.io/en/latest/development/ +.. _`security`: https://packaging.pypa.io/en/latest/security/ + +Project History +--------------- + +Please review the ``CHANGELOG.rst`` file or the `Changelog documentation`_ for +recent changes and project history. + +.. _`Changelog documentation`: https://packaging.pypa.io/en/latest/changelog/ + diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/RECORD new file mode 100644 index 0000000000000000000000000000000000000000..38cdeafd21f1eab74d3f49f069bac093d7694f84 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/RECORD @@ -0,0 +1,26 @@ +packaging-26.0.dist-info/INSTALLER,sha256=5hhM4Q4mYTT9z6QB6PGpUAW81PGNFrYrdXMj4oM_6ak,2 +packaging-26.0.dist-info/METADATA,sha256=M2K7fWom2iliuo2qpHhc0LrKwhq6kIoRlcyPWVgKJlo,3309 +packaging-26.0.dist-info/RECORD,, +packaging-26.0.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 +packaging-26.0.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82 +packaging-26.0.dist-info/licenses/LICENSE,sha256=ytHvW9NA1z4HS6YU0m996spceUDD2MNIUuZcSQlobEg,197 +packaging-26.0.dist-info/licenses/LICENSE.APACHE,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174 +packaging-26.0.dist-info/licenses/LICENSE.BSD,sha256=tw5-m3QvHMb5SLNMFqo5_-zpQZY2S8iP8NIYDwAo-sU,1344 +packaging/__init__.py,sha256=y4lVbpeBzCGk-IPDw5BGBZ_b0P3ukEEJZAbGYc6Ey8c,494 +packaging/_elffile.py,sha256=-sKkptYqzYw2-x3QByJa5mB4rfPWu1pxkZHRx1WAFCY,3211 +packaging/_manylinux.py,sha256=Hf6nB0cOrayEs96-p3oIXAgGnFquv20DO5l-o2_Xnv0,9559 +packaging/_musllinux.py,sha256=Z6swjH3MA7XS3qXnmMN7QPhqP3fnoYI0eQ18e9-HgAE,2707 +packaging/_parser.py,sha256=U_DajsEx2VoC_F46fSVV3hDKNCWoQYkPkasO3dld0ig,10518 +packaging/_structures.py,sha256=Hn49Ta8zV9Wo8GiCL8Nl2ARZY983Un3pruZGVNldPwE,1514 +packaging/_tokenizer.py,sha256=M8EwNIdXeL9NMFuFrQtiOKwjka_xFx8KjRQnfE8O_z8,5421 +packaging/licenses/__init__.py,sha256=TwXLHZCXwSgdFwRLPxW602T6mSieunSFHM6fp8pgW78,5819 +packaging/licenses/_spdx.py,sha256=WW7DXiyg68up_YND_wpRYlr1SHhiV4FfJLQffghhMxQ,51122 +packaging/markers.py,sha256=ZX-cLvW1S3cZcEc0fHI4z7zSx5U2T19yMpDP_mE-CYw,12771 +packaging/metadata.py,sha256=CWVZpN_HfoYMSSDuCP7igOvGgqA9AOmpW8f3qTisfnc,39360 +packaging/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0 +packaging/pylock.py,sha256=-R1uNfJ4PaLto7Mg62YsGOHgvskuiIEqPwxOywl42Jk,22537 +packaging/requirements.py,sha256=PMCAWD8aNMnVD-6uZMedhBuAVX2573eZ4yPBLXmz04I,2870 +packaging/specifiers.py,sha256=EPNPimY_zFivthv1vdjZYz5IqkKGsnKR2yKh-EVyvZw,40797 +packaging/tags.py,sha256=cXLV1pJD3UtJlDg7Wz3zrfdQhRZqr8jumSAKKAAd2xE,22856 +packaging/utils.py,sha256=N4c6oZzFJy6klTZ3AnkNz7sSkJesuFWPp68LA3B5dAo,5040 +packaging/version.py,sha256=7XWlL2IDYLwDYC0ht6cFEhapLwLWbmyo4rb7sEFj0x8,23272 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/REQUESTED b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/REQUESTED new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/WHEEL new file mode 100644 index 0000000000000000000000000000000000000000..d8b9936dad9ab2513fa6979f411560d3b6b57e37 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/WHEEL @@ -0,0 +1,4 @@ +Wheel-Version: 1.0 +Generator: flit 3.12.0 +Root-Is-Purelib: true +Tag: py3-none-any diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/licenses/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/licenses/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..6f62d44e4ef733c0e713afcd2371fed7f2b3de67 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/licenses/LICENSE @@ -0,0 +1,3 @@ +This software is made available under the terms of *either* of the licenses +found in LICENSE.APACHE or LICENSE.BSD. Contributions to this software is made +under the terms of *both* these licenses. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/licenses/LICENSE.APACHE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/licenses/LICENSE.APACHE new file mode 100644 index 0000000000000000000000000000000000000000..f433b1a53f5b830a205fd2df78e2b34974656c7b --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging-26.0.dist-info/licenses/LICENSE.APACHE @@ -0,0 +1,177 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..21695a74b5107c96ba4bb2cbca6b7f259dacd330 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/__init__.py @@ -0,0 +1,15 @@ +# This file is dual licensed under the terms of the Apache License, Version +# 2.0, and the BSD License. See the LICENSE file in the root of this repository +# for complete details. + +__title__ = "packaging" +__summary__ = "Core utilities for Python packages" +__uri__ = "https://github.com/pypa/packaging" + +__version__ = "26.0" + +__author__ = "Donald Stufft and individual contributors" +__email__ = "donald@stufft.io" + +__license__ = "BSD-2-Clause or Apache-2.0" +__copyright__ = f"2014 {__author__}" diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_elffile.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_elffile.py new file mode 100644 index 0000000000000000000000000000000000000000..497b0645217512ae2ba8ff61341fd2bbfa3648cd --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_elffile.py @@ -0,0 +1,108 @@ +""" +ELF file parser. + +This provides a class ``ELFFile`` that parses an ELF executable in a similar +interface to ``ZipFile``. Only the read interface is implemented. + +ELF header: https://refspecs.linuxfoundation.org/elf/gabi4+/ch4.eheader.html +""" + +from __future__ import annotations + +import enum +import os +import struct +from typing import IO + + +class ELFInvalid(ValueError): + pass + + +class EIClass(enum.IntEnum): + C32 = 1 + C64 = 2 + + +class EIData(enum.IntEnum): + Lsb = 1 + Msb = 2 + + +class EMachine(enum.IntEnum): + I386 = 3 + S390 = 22 + Arm = 40 + X8664 = 62 + AArc64 = 183 + + +class ELFFile: + """ + Representation of an ELF executable. + """ + + def __init__(self, f: IO[bytes]) -> None: + self._f = f + + try: + ident = self._read("16B") + except struct.error as e: + raise ELFInvalid("unable to parse identification") from e + magic = bytes(ident[:4]) + if magic != b"\x7fELF": + raise ELFInvalid(f"invalid magic: {magic!r}") + + self.capacity = ident[4] # Format for program header (bitness). + self.encoding = ident[5] # Data structure encoding (endianness). + + try: + # e_fmt: Format for program header. + # p_fmt: Format for section header. + # p_idx: Indexes to find p_type, p_offset, and p_filesz. + e_fmt, self._p_fmt, self._p_idx = { + (1, 1): ("HHIIIIIHHH", ">IIIIIIII", (0, 1, 4)), # 32-bit MSB. + (2, 1): ("HHIQQQIHHH", ">IIQQQQQQ", (0, 2, 5)), # 64-bit MSB. + }[(self.capacity, self.encoding)] + except KeyError as e: + raise ELFInvalid( + f"unrecognized capacity ({self.capacity}) or encoding ({self.encoding})" + ) from e + + try: + ( + _, + self.machine, # Architecture type. + _, + _, + self._e_phoff, # Offset of program header. + _, + self.flags, # Processor-specific flags. + _, + self._e_phentsize, # Size of section. + self._e_phnum, # Number of sections. + ) = self._read(e_fmt) + except struct.error as e: + raise ELFInvalid("unable to parse machine and section information") from e + + def _read(self, fmt: str) -> tuple[int, ...]: + return struct.unpack(fmt, self._f.read(struct.calcsize(fmt))) + + @property + def interpreter(self) -> str | None: + """ + The path recorded in the ``PT_INTERP`` section header. + """ + for index in range(self._e_phnum): + self._f.seek(self._e_phoff + self._e_phentsize * index) + try: + data = self._read(self._p_fmt) + except struct.error: + continue + if data[self._p_idx[0]] != 3: # Not PT_INTERP. + continue + self._f.seek(data[self._p_idx[1]]) + return os.fsdecode(self._f.read(data[self._p_idx[2]])).strip("\0") + return None diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_manylinux.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_manylinux.py new file mode 100644 index 0000000000000000000000000000000000000000..0e79e8a882be74fe76c80ccf49a9cd68fb636fd4 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_manylinux.py @@ -0,0 +1,262 @@ +from __future__ import annotations + +import collections +import contextlib +import functools +import os +import re +import sys +import warnings +from typing import Generator, Iterator, NamedTuple, Sequence + +from ._elffile import EIClass, EIData, ELFFile, EMachine + +EF_ARM_ABIMASK = 0xFF000000 +EF_ARM_ABI_VER5 = 0x05000000 +EF_ARM_ABI_FLOAT_HARD = 0x00000400 + +_ALLOWED_ARCHS = { + "x86_64", + "aarch64", + "ppc64", + "ppc64le", + "s390x", + "loongarch64", + "riscv64", +} + + +# `os.PathLike` not a generic type until Python 3.9, so sticking with `str` +# as the type for `path` until then. +@contextlib.contextmanager +def _parse_elf(path: str) -> Generator[ELFFile | None, None, None]: + try: + with open(path, "rb") as f: + yield ELFFile(f) + except (OSError, TypeError, ValueError): + yield None + + +def _is_linux_armhf(executable: str) -> bool: + # hard-float ABI can be detected from the ELF header of the running + # process + # https://static.docs.arm.com/ihi0044/g/aaelf32.pdf + with _parse_elf(executable) as f: + return ( + f is not None + and f.capacity == EIClass.C32 + and f.encoding == EIData.Lsb + and f.machine == EMachine.Arm + and f.flags & EF_ARM_ABIMASK == EF_ARM_ABI_VER5 + and f.flags & EF_ARM_ABI_FLOAT_HARD == EF_ARM_ABI_FLOAT_HARD + ) + + +def _is_linux_i686(executable: str) -> bool: + with _parse_elf(executable) as f: + return ( + f is not None + and f.capacity == EIClass.C32 + and f.encoding == EIData.Lsb + and f.machine == EMachine.I386 + ) + + +def _have_compatible_abi(executable: str, archs: Sequence[str]) -> bool: + if "armv7l" in archs: + return _is_linux_armhf(executable) + if "i686" in archs: + return _is_linux_i686(executable) + return any(arch in _ALLOWED_ARCHS for arch in archs) + + +# If glibc ever changes its major version, we need to know what the last +# minor version was, so we can build the complete list of all versions. +# For now, guess what the highest minor version might be, assume it will +# be 50 for testing. Once this actually happens, update the dictionary +# with the actual value. +_LAST_GLIBC_MINOR: dict[int, int] = collections.defaultdict(lambda: 50) + + +class _GLibCVersion(NamedTuple): + major: int + minor: int + + +def _glibc_version_string_confstr() -> str | None: + """ + Primary implementation of glibc_version_string using os.confstr. + """ + # os.confstr is quite a bit faster than ctypes.DLL. It's also less likely + # to be broken or missing. This strategy is used in the standard library + # platform module. + # https://github.com/python/cpython/blob/fcf1d003bf4f0100c/Lib/platform.py#L175-L183 + try: + # Should be a string like "glibc 2.17". + version_string: str | None = os.confstr("CS_GNU_LIBC_VERSION") + assert version_string is not None + _, version = version_string.rsplit() + except (AssertionError, AttributeError, OSError, ValueError): + # os.confstr() or CS_GNU_LIBC_VERSION not available (or a bad value)... + return None + return version + + +def _glibc_version_string_ctypes() -> str | None: + """ + Fallback implementation of glibc_version_string using ctypes. + """ + try: + import ctypes # noqa: PLC0415 + except ImportError: + return None + + # ctypes.CDLL(None) internally calls dlopen(NULL), and as the dlopen + # manpage says, "If filename is NULL, then the returned handle is for the + # main program". This way we can let the linker do the work to figure out + # which libc our process is actually using. + # + # We must also handle the special case where the executable is not a + # dynamically linked executable. This can occur when using musl libc, + # for example. In this situation, dlopen() will error, leading to an + # OSError. Interestingly, at least in the case of musl, there is no + # errno set on the OSError. The single string argument used to construct + # OSError comes from libc itself and is therefore not portable to + # hard code here. In any case, failure to call dlopen() means we + # can proceed, so we bail on our attempt. + try: + process_namespace = ctypes.CDLL(None) + except OSError: + return None + + try: + gnu_get_libc_version = process_namespace.gnu_get_libc_version + except AttributeError: + # Symbol doesn't exist -> therefore, we are not linked to + # glibc. + return None + + # Call gnu_get_libc_version, which returns a string like "2.5" + gnu_get_libc_version.restype = ctypes.c_char_p + version_str: str = gnu_get_libc_version() + # py2 / py3 compatibility: + if not isinstance(version_str, str): + version_str = version_str.decode("ascii") + + return version_str + + +def _glibc_version_string() -> str | None: + """Returns glibc version string, or None if not using glibc.""" + return _glibc_version_string_confstr() or _glibc_version_string_ctypes() + + +def _parse_glibc_version(version_str: str) -> _GLibCVersion: + """Parse glibc version. + + We use a regexp instead of str.split because we want to discard any + random junk that might come after the minor version -- this might happen + in patched/forked versions of glibc (e.g. Linaro's version of glibc + uses version strings like "2.20-2014.11"). See gh-3588. + """ + m = re.match(r"(?P[0-9]+)\.(?P[0-9]+)", version_str) + if not m: + warnings.warn( + f"Expected glibc version with 2 components major.minor, got: {version_str}", + RuntimeWarning, + stacklevel=2, + ) + return _GLibCVersion(-1, -1) + return _GLibCVersion(int(m.group("major")), int(m.group("minor"))) + + +@functools.lru_cache +def _get_glibc_version() -> _GLibCVersion: + version_str = _glibc_version_string() + if version_str is None: + return _GLibCVersion(-1, -1) + return _parse_glibc_version(version_str) + + +# From PEP 513, PEP 600 +def _is_compatible(arch: str, version: _GLibCVersion) -> bool: + sys_glibc = _get_glibc_version() + if sys_glibc < version: + return False + # Check for presence of _manylinux module. + try: + import _manylinux # noqa: PLC0415 + except ImportError: + return True + if hasattr(_manylinux, "manylinux_compatible"): + result = _manylinux.manylinux_compatible(version[0], version[1], arch) + if result is not None: + return bool(result) + return True + if version == _GLibCVersion(2, 5) and hasattr(_manylinux, "manylinux1_compatible"): + return bool(_manylinux.manylinux1_compatible) + if version == _GLibCVersion(2, 12) and hasattr( + _manylinux, "manylinux2010_compatible" + ): + return bool(_manylinux.manylinux2010_compatible) + if version == _GLibCVersion(2, 17) and hasattr( + _manylinux, "manylinux2014_compatible" + ): + return bool(_manylinux.manylinux2014_compatible) + return True + + +_LEGACY_MANYLINUX_MAP: dict[_GLibCVersion, str] = { + # CentOS 7 w/ glibc 2.17 (PEP 599) + _GLibCVersion(2, 17): "manylinux2014", + # CentOS 6 w/ glibc 2.12 (PEP 571) + _GLibCVersion(2, 12): "manylinux2010", + # CentOS 5 w/ glibc 2.5 (PEP 513) + _GLibCVersion(2, 5): "manylinux1", +} + + +def platform_tags(archs: Sequence[str]) -> Iterator[str]: + """Generate manylinux tags compatible to the current platform. + + :param archs: Sequence of compatible architectures. + The first one shall be the closest to the actual architecture and be the part of + platform tag after the ``linux_`` prefix, e.g. ``x86_64``. + The ``linux_`` prefix is assumed as a prerequisite for the current platform to + be manylinux-compatible. + + :returns: An iterator of compatible manylinux tags. + """ + if not _have_compatible_abi(sys.executable, archs): + return + # Oldest glibc to be supported regardless of architecture is (2, 17). + too_old_glibc2 = _GLibCVersion(2, 16) + if set(archs) & {"x86_64", "i686"}: + # On x86/i686 also oldest glibc to be supported is (2, 5). + too_old_glibc2 = _GLibCVersion(2, 4) + current_glibc = _GLibCVersion(*_get_glibc_version()) + glibc_max_list = [current_glibc] + # We can assume compatibility across glibc major versions. + # https://sourceware.org/bugzilla/show_bug.cgi?id=24636 + # + # Build a list of maximum glibc versions so that we can + # output the canonical list of all glibc from current_glibc + # down to too_old_glibc2, including all intermediary versions. + for glibc_major in range(current_glibc.major - 1, 1, -1): + glibc_minor = _LAST_GLIBC_MINOR[glibc_major] + glibc_max_list.append(_GLibCVersion(glibc_major, glibc_minor)) + for arch in archs: + for glibc_max in glibc_max_list: + if glibc_max.major == too_old_glibc2.major: + min_minor = too_old_glibc2.minor + else: + # For other glibc major versions oldest supported is (x, 0). + min_minor = -1 + for glibc_minor in range(glibc_max.minor, min_minor, -1): + glibc_version = _GLibCVersion(glibc_max.major, glibc_minor) + if _is_compatible(arch, glibc_version): + yield "manylinux_{}_{}_{}".format(*glibc_version, arch) + + # Handle the legacy manylinux1, manylinux2010, manylinux2014 tags. + if legacy_tag := _LEGACY_MANYLINUX_MAP.get(glibc_version): + yield f"{legacy_tag}_{arch}" diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_musllinux.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_musllinux.py new file mode 100644 index 0000000000000000000000000000000000000000..4e8116a79ca80d60657542a23b4bbcbc3c518eaf --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_musllinux.py @@ -0,0 +1,85 @@ +"""PEP 656 support. + +This module implements logic to detect if the currently running Python is +linked against musl, and what musl version is used. +""" + +from __future__ import annotations + +import functools +import re +import subprocess +import sys +from typing import Iterator, NamedTuple, Sequence + +from ._elffile import ELFFile + + +class _MuslVersion(NamedTuple): + major: int + minor: int + + +def _parse_musl_version(output: str) -> _MuslVersion | None: + lines = [n for n in (n.strip() for n in output.splitlines()) if n] + if len(lines) < 2 or lines[0][:4] != "musl": + return None + m = re.match(r"Version (\d+)\.(\d+)", lines[1]) + if not m: + return None + return _MuslVersion(major=int(m.group(1)), minor=int(m.group(2))) + + +@functools.lru_cache +def _get_musl_version(executable: str) -> _MuslVersion | None: + """Detect currently-running musl runtime version. + + This is done by checking the specified executable's dynamic linking + information, and invoking the loader to parse its output for a version + string. If the loader is musl, the output would be something like:: + + musl libc (x86_64) + Version 1.2.2 + Dynamic Program Loader + """ + try: + with open(executable, "rb") as f: + ld = ELFFile(f).interpreter + except (OSError, TypeError, ValueError): + return None + if ld is None or "musl" not in ld: + return None + proc = subprocess.run([ld], check=False, stderr=subprocess.PIPE, text=True) + return _parse_musl_version(proc.stderr) + + +def platform_tags(archs: Sequence[str]) -> Iterator[str]: + """Generate musllinux tags compatible to the current platform. + + :param archs: Sequence of compatible architectures. + The first one shall be the closest to the actual architecture and be the part of + platform tag after the ``linux_`` prefix, e.g. ``x86_64``. + The ``linux_`` prefix is assumed as a prerequisite for the current platform to + be musllinux-compatible. + + :returns: An iterator of compatible musllinux tags. + """ + sys_musl = _get_musl_version(sys.executable) + if sys_musl is None: # Python not dynamically linked against musl. + return + for arch in archs: + for minor in range(sys_musl.minor, -1, -1): + yield f"musllinux_{sys_musl.major}_{minor}_{arch}" + + +if __name__ == "__main__": # pragma: no cover + import sysconfig + + plat = sysconfig.get_platform() + assert plat.startswith("linux-"), "not linux" + + print("plat:", plat) + print("musl:", _get_musl_version(sys.executable)) + print("tags:", end=" ") + for t in platform_tags(re.sub(r"[.-]", "_", plat.split("-", 1)[-1])): + print(t, end="\n ") diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_parser.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_parser.py new file mode 100644 index 0000000000000000000000000000000000000000..f6c1f5cd226b926f96a3bb1e9fb0f18d1bd021c9 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_parser.py @@ -0,0 +1,365 @@ +"""Handwritten parser of dependency specifiers. + +The docstring for each __parse_* function contains EBNF-inspired grammar representing +the implementation. +""" + +from __future__ import annotations + +import ast +from typing import List, Literal, NamedTuple, Sequence, Tuple, Union + +from ._tokenizer import DEFAULT_RULES, Tokenizer + + +class Node: + __slots__ = ("value",) + + def __init__(self, value: str) -> None: + self.value = value + + def __str__(self) -> str: + return self.value + + def __repr__(self) -> str: + return f"<{self.__class__.__name__}({self.value!r})>" + + def serialize(self) -> str: + raise NotImplementedError + + +class Variable(Node): + __slots__ = () + + def serialize(self) -> str: + return str(self) + + +class Value(Node): + __slots__ = () + + def serialize(self) -> str: + return f'"{self}"' + + +class Op(Node): + __slots__ = () + + def serialize(self) -> str: + return str(self) + + +MarkerLogical = Literal["and", "or"] +MarkerVar = Union[Variable, Value] +MarkerItem = Tuple[MarkerVar, Op, MarkerVar] +MarkerAtom = Union[MarkerItem, Sequence["MarkerAtom"]] +MarkerList = List[Union["MarkerList", MarkerAtom, MarkerLogical]] + + +class ParsedRequirement(NamedTuple): + name: str + url: str + extras: list[str] + specifier: str + marker: MarkerList | None + + +# -------------------------------------------------------------------------------------- +# Recursive descent parser for dependency specifier +# -------------------------------------------------------------------------------------- +def parse_requirement(source: str) -> ParsedRequirement: + return _parse_requirement(Tokenizer(source, rules=DEFAULT_RULES)) + + +def _parse_requirement(tokenizer: Tokenizer) -> ParsedRequirement: + """ + requirement = WS? IDENTIFIER WS? extras WS? requirement_details + """ + tokenizer.consume("WS") + + name_token = tokenizer.expect( + "IDENTIFIER", expected="package name at the start of dependency specifier" + ) + name = name_token.text + tokenizer.consume("WS") + + extras = _parse_extras(tokenizer) + tokenizer.consume("WS") + + url, specifier, marker = _parse_requirement_details(tokenizer) + tokenizer.expect("END", expected="end of dependency specifier") + + return ParsedRequirement(name, url, extras, specifier, marker) + + +def _parse_requirement_details( + tokenizer: Tokenizer, +) -> tuple[str, str, MarkerList | None]: + """ + requirement_details = AT URL (WS requirement_marker?)? + | specifier WS? (requirement_marker)? + """ + + specifier = "" + url = "" + marker = None + + if tokenizer.check("AT"): + tokenizer.read() + tokenizer.consume("WS") + + url_start = tokenizer.position + url = tokenizer.expect("URL", expected="URL after @").text + if tokenizer.check("END", peek=True): + return (url, specifier, marker) + + tokenizer.expect("WS", expected="whitespace after URL") + + # The input might end after whitespace. + if tokenizer.check("END", peek=True): + return (url, specifier, marker) + + marker = _parse_requirement_marker( + tokenizer, + span_start=url_start, + expected="semicolon (after URL and whitespace)", + ) + else: + specifier_start = tokenizer.position + specifier = _parse_specifier(tokenizer) + tokenizer.consume("WS") + + if tokenizer.check("END", peek=True): + return (url, specifier, marker) + + marker = _parse_requirement_marker( + tokenizer, + span_start=specifier_start, + expected=( + "comma (within version specifier), semicolon (after version specifier)" + if specifier + else "semicolon (after name with no version specifier)" + ), + ) + + return (url, specifier, marker) + + +def _parse_requirement_marker( + tokenizer: Tokenizer, *, span_start: int, expected: str +) -> MarkerList: + """ + requirement_marker = SEMICOLON marker WS? + """ + + if not tokenizer.check("SEMICOLON"): + tokenizer.raise_syntax_error( + f"Expected {expected} or end", + span_start=span_start, + span_end=None, + ) + tokenizer.read() + + marker = _parse_marker(tokenizer) + tokenizer.consume("WS") + + return marker + + +def _parse_extras(tokenizer: Tokenizer) -> list[str]: + """ + extras = (LEFT_BRACKET wsp* extras_list? wsp* RIGHT_BRACKET)? + """ + if not tokenizer.check("LEFT_BRACKET", peek=True): + return [] + + with tokenizer.enclosing_tokens( + "LEFT_BRACKET", + "RIGHT_BRACKET", + around="extras", + ): + tokenizer.consume("WS") + extras = _parse_extras_list(tokenizer) + tokenizer.consume("WS") + + return extras + + +def _parse_extras_list(tokenizer: Tokenizer) -> list[str]: + """ + extras_list = identifier (wsp* ',' wsp* identifier)* + """ + extras: list[str] = [] + + if not tokenizer.check("IDENTIFIER"): + return extras + + extras.append(tokenizer.read().text) + + while True: + tokenizer.consume("WS") + if tokenizer.check("IDENTIFIER", peek=True): + tokenizer.raise_syntax_error("Expected comma between extra names") + elif not tokenizer.check("COMMA"): + break + + tokenizer.read() + tokenizer.consume("WS") + + extra_token = tokenizer.expect("IDENTIFIER", expected="extra name after comma") + extras.append(extra_token.text) + + return extras + + +def _parse_specifier(tokenizer: Tokenizer) -> str: + """ + specifier = LEFT_PARENTHESIS WS? version_many WS? RIGHT_PARENTHESIS + | WS? version_many WS? + """ + with tokenizer.enclosing_tokens( + "LEFT_PARENTHESIS", + "RIGHT_PARENTHESIS", + around="version specifier", + ): + tokenizer.consume("WS") + parsed_specifiers = _parse_version_many(tokenizer) + tokenizer.consume("WS") + + return parsed_specifiers + + +def _parse_version_many(tokenizer: Tokenizer) -> str: + """ + version_many = (SPECIFIER (WS? COMMA WS? SPECIFIER)*)? + """ + parsed_specifiers = "" + while tokenizer.check("SPECIFIER"): + span_start = tokenizer.position + parsed_specifiers += tokenizer.read().text + if tokenizer.check("VERSION_PREFIX_TRAIL", peek=True): + tokenizer.raise_syntax_error( + ".* suffix can only be used with `==` or `!=` operators", + span_start=span_start, + span_end=tokenizer.position + 1, + ) + if tokenizer.check("VERSION_LOCAL_LABEL_TRAIL", peek=True): + tokenizer.raise_syntax_error( + "Local version label can only be used with `==` or `!=` operators", + span_start=span_start, + span_end=tokenizer.position, + ) + tokenizer.consume("WS") + if not tokenizer.check("COMMA"): + break + parsed_specifiers += tokenizer.read().text + tokenizer.consume("WS") + + return parsed_specifiers + + +# -------------------------------------------------------------------------------------- +# Recursive descent parser for marker expression +# -------------------------------------------------------------------------------------- +def parse_marker(source: str) -> MarkerList: + return _parse_full_marker(Tokenizer(source, rules=DEFAULT_RULES)) + + +def _parse_full_marker(tokenizer: Tokenizer) -> MarkerList: + retval = _parse_marker(tokenizer) + tokenizer.expect("END", expected="end of marker expression") + return retval + + +def _parse_marker(tokenizer: Tokenizer) -> MarkerList: + """ + marker = marker_atom (BOOLOP marker_atom)+ + """ + expression = [_parse_marker_atom(tokenizer)] + while tokenizer.check("BOOLOP"): + token = tokenizer.read() + expr_right = _parse_marker_atom(tokenizer) + expression.extend((token.text, expr_right)) + return expression + + +def _parse_marker_atom(tokenizer: Tokenizer) -> MarkerAtom: + """ + marker_atom = WS? LEFT_PARENTHESIS WS? marker WS? RIGHT_PARENTHESIS WS? + | WS? marker_item WS? + """ + + tokenizer.consume("WS") + if tokenizer.check("LEFT_PARENTHESIS", peek=True): + with tokenizer.enclosing_tokens( + "LEFT_PARENTHESIS", + "RIGHT_PARENTHESIS", + around="marker expression", + ): + tokenizer.consume("WS") + marker: MarkerAtom = _parse_marker(tokenizer) + tokenizer.consume("WS") + else: + marker = _parse_marker_item(tokenizer) + tokenizer.consume("WS") + return marker + + +def _parse_marker_item(tokenizer: Tokenizer) -> MarkerItem: + """ + marker_item = WS? marker_var WS? marker_op WS? marker_var WS? + """ + tokenizer.consume("WS") + marker_var_left = _parse_marker_var(tokenizer) + tokenizer.consume("WS") + marker_op = _parse_marker_op(tokenizer) + tokenizer.consume("WS") + marker_var_right = _parse_marker_var(tokenizer) + tokenizer.consume("WS") + return (marker_var_left, marker_op, marker_var_right) + + +def _parse_marker_var(tokenizer: Tokenizer) -> MarkerVar: # noqa: RET503 + """ + marker_var = VARIABLE | QUOTED_STRING + """ + if tokenizer.check("VARIABLE"): + return process_env_var(tokenizer.read().text.replace(".", "_")) + elif tokenizer.check("QUOTED_STRING"): + return process_python_str(tokenizer.read().text) + else: + tokenizer.raise_syntax_error( + message="Expected a marker variable or quoted string" + ) + + +def process_env_var(env_var: str) -> Variable: + if env_var in ("platform_python_implementation", "python_implementation"): + return Variable("platform_python_implementation") + else: + return Variable(env_var) + + +def process_python_str(python_str: str) -> Value: + value = ast.literal_eval(python_str) + return Value(str(value)) + + +def _parse_marker_op(tokenizer: Tokenizer) -> Op: + """ + marker_op = IN | NOT IN | OP + """ + if tokenizer.check("IN"): + tokenizer.read() + return Op("in") + elif tokenizer.check("NOT"): + tokenizer.read() + tokenizer.expect("WS", expected="whitespace after 'not'") + tokenizer.expect("IN", expected="'in' after 'not'") + return Op("not in") + elif tokenizer.check("OP"): + return Op(tokenizer.read().text) + else: + return tokenizer.raise_syntax_error( + "Expected marker operator, one of <=, <, !=, ==, >=, >, ~=, ===, in, not in" + ) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_structures.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_structures.py new file mode 100644 index 0000000000000000000000000000000000000000..225e2eee01238571c50595eb104e0b70d5f503c4 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_structures.py @@ -0,0 +1,69 @@ +# This file is dual licensed under the terms of the Apache License, Version +# 2.0, and the BSD License. See the LICENSE file in the root of this repository +# for complete details. + +import typing + + +@typing.final +class InfinityType: + __slots__ = () + + def __repr__(self) -> str: + return "Infinity" + + def __hash__(self) -> int: + return hash(repr(self)) + + def __lt__(self, other: object) -> bool: + return False + + def __le__(self, other: object) -> bool: + return False + + def __eq__(self, other: object) -> bool: + return isinstance(other, self.__class__) + + def __gt__(self, other: object) -> bool: + return True + + def __ge__(self, other: object) -> bool: + return True + + def __neg__(self: object) -> "NegativeInfinityType": + return NegativeInfinity + + +Infinity = InfinityType() + + +@typing.final +class NegativeInfinityType: + __slots__ = () + + def __repr__(self) -> str: + return "-Infinity" + + def __hash__(self) -> int: + return hash(repr(self)) + + def __lt__(self, other: object) -> bool: + return True + + def __le__(self, other: object) -> bool: + return True + + def __eq__(self, other: object) -> bool: + return isinstance(other, self.__class__) + + def __gt__(self, other: object) -> bool: + return False + + def __ge__(self, other: object) -> bool: + return False + + def __neg__(self: object) -> InfinityType: + return Infinity + + +NegativeInfinity = NegativeInfinityType() diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_tokenizer.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_tokenizer.py new file mode 100644 index 0000000000000000000000000000000000000000..e6d20dd3f56f880a92db7409a3e1335cb282a8f2 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/_tokenizer.py @@ -0,0 +1,193 @@ +from __future__ import annotations + +import contextlib +import re +from dataclasses import dataclass +from typing import Generator, Mapping, NoReturn + +from .specifiers import Specifier + + +@dataclass +class Token: + name: str + text: str + position: int + + +class ParserSyntaxError(Exception): + """The provided source text could not be parsed correctly.""" + + def __init__( + self, + message: str, + *, + source: str, + span: tuple[int, int], + ) -> None: + self.span = span + self.message = message + self.source = source + + super().__init__() + + def __str__(self) -> str: + marker = " " * self.span[0] + "~" * (self.span[1] - self.span[0]) + "^" + return f"{self.message}\n {self.source}\n {marker}" + + +DEFAULT_RULES: dict[str, re.Pattern[str]] = { + "LEFT_PARENTHESIS": re.compile(r"\("), + "RIGHT_PARENTHESIS": re.compile(r"\)"), + "LEFT_BRACKET": re.compile(r"\["), + "RIGHT_BRACKET": re.compile(r"\]"), + "SEMICOLON": re.compile(r";"), + "COMMA": re.compile(r","), + "QUOTED_STRING": re.compile( + r""" + ( + ('[^']*') + | + ("[^"]*") + ) + """, + re.VERBOSE, + ), + "OP": re.compile(r"(===|==|~=|!=|<=|>=|<|>)"), + "BOOLOP": re.compile(r"\b(or|and)\b"), + "IN": re.compile(r"\bin\b"), + "NOT": re.compile(r"\bnot\b"), + "VARIABLE": re.compile( + r""" + \b( + python_version + |python_full_version + |os[._]name + |sys[._]platform + |platform_(release|system) + |platform[._](version|machine|python_implementation) + |python_implementation + |implementation_(name|version) + |extras? + |dependency_groups + )\b + """, + re.VERBOSE, + ), + "SPECIFIER": re.compile( + Specifier._operator_regex_str + Specifier._version_regex_str, + re.VERBOSE | re.IGNORECASE, + ), + "AT": re.compile(r"\@"), + "URL": re.compile(r"[^ \t]+"), + "IDENTIFIER": re.compile(r"\b[a-zA-Z0-9][a-zA-Z0-9._-]*\b"), + "VERSION_PREFIX_TRAIL": re.compile(r"\.\*"), + "VERSION_LOCAL_LABEL_TRAIL": re.compile(r"\+[a-z0-9]+(?:[-_\.][a-z0-9]+)*"), + "WS": re.compile(r"[ \t]+"), + "END": re.compile(r"$"), +} + + +class Tokenizer: + """Context-sensitive token parsing. + + Provides methods to examine the input stream to check whether the next token + matches. + """ + + def __init__( + self, + source: str, + *, + rules: Mapping[str, re.Pattern[str]], + ) -> None: + self.source = source + self.rules = rules + self.next_token: Token | None = None + self.position = 0 + + def consume(self, name: str) -> None: + """Move beyond provided token name, if at current position.""" + if self.check(name): + self.read() + + def check(self, name: str, *, peek: bool = False) -> bool: + """Check whether the next token has the provided name. + + By default, if the check succeeds, the token *must* be read before + another check. If `peek` is set to `True`, the token is not loaded and + would need to be checked again. + """ + assert self.next_token is None, ( + f"Cannot check for {name!r}, already have {self.next_token!r}" + ) + assert name in self.rules, f"Unknown token name: {name!r}" + + expression = self.rules[name] + + match = expression.match(self.source, self.position) + if match is None: + return False + if not peek: + self.next_token = Token(name, match[0], self.position) + return True + + def expect(self, name: str, *, expected: str) -> Token: + """Expect a certain token name next, failing with a syntax error otherwise. + + The token is *not* read. + """ + if not self.check(name): + raise self.raise_syntax_error(f"Expected {expected}") + return self.read() + + def read(self) -> Token: + """Consume the next token and return it.""" + token = self.next_token + assert token is not None + + self.position += len(token.text) + self.next_token = None + + return token + + def raise_syntax_error( + self, + message: str, + *, + span_start: int | None = None, + span_end: int | None = None, + ) -> NoReturn: + """Raise ParserSyntaxError at the given position.""" + span = ( + self.position if span_start is None else span_start, + self.position if span_end is None else span_end, + ) + raise ParserSyntaxError( + message, + source=self.source, + span=span, + ) + + @contextlib.contextmanager + def enclosing_tokens( + self, open_token: str, close_token: str, *, around: str + ) -> Generator[None, None, None]: + if self.check(open_token): + open_position = self.position + self.read() + else: + open_position = None + + yield + + if open_position is None: + return + + if not self.check(close_token): + self.raise_syntax_error( + f"Expected matching {close_token} for {open_token}, after {around}", + span_start=open_position, + ) + + self.read() diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/licenses/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/licenses/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..335b275fa7575b0a7c525a713fbe0252ad2d956f --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/licenses/__init__.py @@ -0,0 +1,147 @@ +####################################################################################### +# +# Adapted from: +# https://github.com/pypa/hatch/blob/5352e44/backend/src/hatchling/licenses/parse.py +# +# MIT License +# +# Copyright (c) 2017-present Ofek Lev +# +# Permission is hereby granted, free of charge, to any person obtaining a copy of this +# software and associated documentation files (the "Software"), to deal in the Software +# without restriction, including without limitation the rights to use, copy, modify, +# merge, publish, distribute, sublicense, and/or sell copies of the Software, and to +# permit persons to whom the Software is furnished to do so, subject to the following +# conditions: +# +# The above copyright notice and this permission notice shall be included in all copies +# or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, +# INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A +# PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +# HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF +# CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE +# OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +# +# +# With additional allowance of arbitrary `LicenseRef-` identifiers, not just +# `LicenseRef-Public-Domain` and `LicenseRef-Proprietary`. +# +####################################################################################### +from __future__ import annotations + +import re +from typing import NewType, cast + +from ._spdx import EXCEPTIONS, LICENSES + +__all__ = [ + "InvalidLicenseExpression", + "NormalizedLicenseExpression", + "canonicalize_license_expression", +] + +license_ref_allowed = re.compile("^[A-Za-z0-9.-]*$") + +NormalizedLicenseExpression = NewType("NormalizedLicenseExpression", str) + + +class InvalidLicenseExpression(ValueError): + """Raised when a license-expression string is invalid + + >>> canonicalize_license_expression("invalid") + Traceback (most recent call last): + ... + packaging.licenses.InvalidLicenseExpression: Invalid license expression: 'invalid' + """ + + +def canonicalize_license_expression( + raw_license_expression: str, +) -> NormalizedLicenseExpression: + if not raw_license_expression: + message = f"Invalid license expression: {raw_license_expression!r}" + raise InvalidLicenseExpression(message) + + # Pad any parentheses so tokenization can be achieved by merely splitting on + # whitespace. + license_expression = raw_license_expression.replace("(", " ( ").replace(")", " ) ") + licenseref_prefix = "LicenseRef-" + license_refs = { + ref.lower(): "LicenseRef-" + ref[len(licenseref_prefix) :] + for ref in license_expression.split() + if ref.lower().startswith(licenseref_prefix.lower()) + } + + # Normalize to lower case so we can look up licenses/exceptions + # and so boolean operators are Python-compatible. + license_expression = license_expression.lower() + + tokens = license_expression.split() + + # Rather than implementing a parenthesis/boolean logic parser, create an + # expression that Python can parse. Everything that is not involved with the + # grammar itself is replaced with the placeholder `False` and the resultant + # expression should become a valid Python expression. + python_tokens = [] + for token in tokens: + if token not in {"or", "and", "with", "(", ")"}: + python_tokens.append("False") + elif token == "with": + python_tokens.append("or") + elif ( + token == "(" + and python_tokens + and python_tokens[-1] not in {"or", "and", "("} + ) or (token == ")" and python_tokens and python_tokens[-1] == "("): + message = f"Invalid license expression: {raw_license_expression!r}" + raise InvalidLicenseExpression(message) + else: + python_tokens.append(token) + + python_expression = " ".join(python_tokens) + try: + compile(python_expression, "", "eval") + except SyntaxError: + message = f"Invalid license expression: {raw_license_expression!r}" + raise InvalidLicenseExpression(message) from None + + # Take a final pass to check for unknown licenses/exceptions. + normalized_tokens = [] + for token in tokens: + if token in {"or", "and", "with", "(", ")"}: + normalized_tokens.append(token.upper()) + continue + + if normalized_tokens and normalized_tokens[-1] == "WITH": + if token not in EXCEPTIONS: + message = f"Unknown license exception: {token!r}" + raise InvalidLicenseExpression(message) + + normalized_tokens.append(EXCEPTIONS[token]["id"]) + else: + if token.endswith("+"): + final_token = token[:-1] + suffix = "+" + else: + final_token = token + suffix = "" + + if final_token.startswith("licenseref-"): + if not license_ref_allowed.match(final_token): + message = f"Invalid licenseref: {final_token!r}" + raise InvalidLicenseExpression(message) + normalized_tokens.append(license_refs[final_token] + suffix) + else: + if final_token not in LICENSES: + message = f"Unknown license: {final_token!r}" + raise InvalidLicenseExpression(message) + normalized_tokens.append(LICENSES[final_token]["id"] + suffix) + + normalized_expression = " ".join(normalized_tokens) + + return cast( + "NormalizedLicenseExpression", + normalized_expression.replace("( ", "(").replace(" )", ")"), + ) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/licenses/_spdx.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/licenses/_spdx.py new file mode 100644 index 0000000000000000000000000000000000000000..a277af28220b6dbe4599471104d1c7a2bd1e1288 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/licenses/_spdx.py @@ -0,0 +1,799 @@ + +from __future__ import annotations + +from typing import TypedDict + +class SPDXLicense(TypedDict): + id: str + deprecated: bool + +class SPDXException(TypedDict): + id: str + deprecated: bool + + +VERSION = '3.27.0' + +LICENSES: dict[str, SPDXLicense] = { + '0bsd': {'id': '0BSD', 'deprecated': False}, + '3d-slicer-1.0': {'id': '3D-Slicer-1.0', 'deprecated': False}, + 'aal': {'id': 'AAL', 'deprecated': False}, + 'abstyles': {'id': 'Abstyles', 'deprecated': False}, + 'adacore-doc': {'id': 'AdaCore-doc', 'deprecated': False}, + 'adobe-2006': {'id': 'Adobe-2006', 'deprecated': False}, + 'adobe-display-postscript': {'id': 'Adobe-Display-PostScript', 'deprecated': False}, + 'adobe-glyph': {'id': 'Adobe-Glyph', 'deprecated': False}, + 'adobe-utopia': {'id': 'Adobe-Utopia', 'deprecated': False}, + 'adsl': {'id': 'ADSL', 'deprecated': False}, + 'afl-1.1': {'id': 'AFL-1.1', 'deprecated': False}, + 'afl-1.2': {'id': 'AFL-1.2', 'deprecated': False}, + 'afl-2.0': {'id': 'AFL-2.0', 'deprecated': False}, + 'afl-2.1': {'id': 'AFL-2.1', 'deprecated': False}, + 'afl-3.0': {'id': 'AFL-3.0', 'deprecated': False}, + 'afmparse': {'id': 'Afmparse', 'deprecated': False}, + 'agpl-1.0': {'id': 'AGPL-1.0', 'deprecated': True}, + 'agpl-1.0-only': {'id': 'AGPL-1.0-only', 'deprecated': False}, + 'agpl-1.0-or-later': {'id': 'AGPL-1.0-or-later', 'deprecated': False}, + 'agpl-3.0': {'id': 'AGPL-3.0', 'deprecated': True}, + 'agpl-3.0-only': {'id': 'AGPL-3.0-only', 'deprecated': False}, + 'agpl-3.0-or-later': {'id': 'AGPL-3.0-or-later', 'deprecated': False}, + 'aladdin': {'id': 'Aladdin', 'deprecated': False}, + 'amd-newlib': {'id': 'AMD-newlib', 'deprecated': False}, + 'amdplpa': {'id': 'AMDPLPA', 'deprecated': False}, + 'aml': {'id': 'AML', 'deprecated': False}, + 'aml-glslang': {'id': 'AML-glslang', 'deprecated': False}, + 'ampas': {'id': 'AMPAS', 'deprecated': False}, + 'antlr-pd': {'id': 'ANTLR-PD', 'deprecated': False}, + 'antlr-pd-fallback': {'id': 'ANTLR-PD-fallback', 'deprecated': False}, + 'any-osi': {'id': 'any-OSI', 'deprecated': False}, + 'any-osi-perl-modules': {'id': 'any-OSI-perl-modules', 'deprecated': False}, + 'apache-1.0': {'id': 'Apache-1.0', 'deprecated': False}, + 'apache-1.1': {'id': 'Apache-1.1', 'deprecated': False}, + 'apache-2.0': {'id': 'Apache-2.0', 'deprecated': False}, + 'apafml': {'id': 'APAFML', 'deprecated': False}, + 'apl-1.0': {'id': 'APL-1.0', 'deprecated': False}, + 'app-s2p': {'id': 'App-s2p', 'deprecated': False}, + 'apsl-1.0': {'id': 'APSL-1.0', 'deprecated': False}, + 'apsl-1.1': {'id': 'APSL-1.1', 'deprecated': False}, + 'apsl-1.2': {'id': 'APSL-1.2', 'deprecated': False}, + 'apsl-2.0': {'id': 'APSL-2.0', 'deprecated': False}, + 'arphic-1999': {'id': 'Arphic-1999', 'deprecated': False}, + 'artistic-1.0': {'id': 'Artistic-1.0', 'deprecated': False}, + 'artistic-1.0-cl8': {'id': 'Artistic-1.0-cl8', 'deprecated': False}, + 'artistic-1.0-perl': {'id': 'Artistic-1.0-Perl', 'deprecated': False}, + 'artistic-2.0': {'id': 'Artistic-2.0', 'deprecated': False}, + 'artistic-dist': {'id': 'Artistic-dist', 'deprecated': False}, + 'aspell-ru': {'id': 'Aspell-RU', 'deprecated': False}, + 'aswf-digital-assets-1.0': {'id': 'ASWF-Digital-Assets-1.0', 'deprecated': False}, + 'aswf-digital-assets-1.1': {'id': 'ASWF-Digital-Assets-1.1', 'deprecated': False}, + 'baekmuk': {'id': 'Baekmuk', 'deprecated': False}, + 'bahyph': {'id': 'Bahyph', 'deprecated': False}, + 'barr': {'id': 'Barr', 'deprecated': False}, + 'bcrypt-solar-designer': {'id': 'bcrypt-Solar-Designer', 'deprecated': False}, + 'beerware': {'id': 'Beerware', 'deprecated': False}, + 'bitstream-charter': {'id': 'Bitstream-Charter', 'deprecated': False}, + 'bitstream-vera': {'id': 'Bitstream-Vera', 'deprecated': False}, + 'bittorrent-1.0': {'id': 'BitTorrent-1.0', 'deprecated': False}, + 'bittorrent-1.1': {'id': 'BitTorrent-1.1', 'deprecated': False}, + 'blessing': {'id': 'blessing', 'deprecated': False}, + 'blueoak-1.0.0': {'id': 'BlueOak-1.0.0', 'deprecated': False}, + 'boehm-gc': {'id': 'Boehm-GC', 'deprecated': False}, + 'boehm-gc-without-fee': {'id': 'Boehm-GC-without-fee', 'deprecated': False}, + 'borceux': {'id': 'Borceux', 'deprecated': False}, + 'brian-gladman-2-clause': {'id': 'Brian-Gladman-2-Clause', 'deprecated': False}, + 'brian-gladman-3-clause': {'id': 'Brian-Gladman-3-Clause', 'deprecated': False}, + 'bsd-1-clause': {'id': 'BSD-1-Clause', 'deprecated': False}, + 'bsd-2-clause': {'id': 'BSD-2-Clause', 'deprecated': False}, + 'bsd-2-clause-darwin': {'id': 'BSD-2-Clause-Darwin', 'deprecated': False}, + 'bsd-2-clause-first-lines': {'id': 'BSD-2-Clause-first-lines', 'deprecated': False}, + 'bsd-2-clause-freebsd': {'id': 'BSD-2-Clause-FreeBSD', 'deprecated': True}, + 'bsd-2-clause-netbsd': {'id': 'BSD-2-Clause-NetBSD', 'deprecated': True}, + 'bsd-2-clause-patent': {'id': 'BSD-2-Clause-Patent', 'deprecated': False}, + 'bsd-2-clause-pkgconf-disclaimer': {'id': 'BSD-2-Clause-pkgconf-disclaimer', 'deprecated': False}, + 'bsd-2-clause-views': {'id': 'BSD-2-Clause-Views', 'deprecated': False}, + 'bsd-3-clause': {'id': 'BSD-3-Clause', 'deprecated': False}, + 'bsd-3-clause-acpica': {'id': 'BSD-3-Clause-acpica', 'deprecated': False}, + 'bsd-3-clause-attribution': {'id': 'BSD-3-Clause-Attribution', 'deprecated': False}, + 'bsd-3-clause-clear': {'id': 'BSD-3-Clause-Clear', 'deprecated': False}, + 'bsd-3-clause-flex': {'id': 'BSD-3-Clause-flex', 'deprecated': False}, + 'bsd-3-clause-hp': {'id': 'BSD-3-Clause-HP', 'deprecated': False}, + 'bsd-3-clause-lbnl': {'id': 'BSD-3-Clause-LBNL', 'deprecated': False}, + 'bsd-3-clause-modification': {'id': 'BSD-3-Clause-Modification', 'deprecated': False}, + 'bsd-3-clause-no-military-license': {'id': 'BSD-3-Clause-No-Military-License', 'deprecated': False}, + 'bsd-3-clause-no-nuclear-license': {'id': 'BSD-3-Clause-No-Nuclear-License', 'deprecated': False}, + 'bsd-3-clause-no-nuclear-license-2014': {'id': 'BSD-3-Clause-No-Nuclear-License-2014', 'deprecated': False}, + 'bsd-3-clause-no-nuclear-warranty': {'id': 'BSD-3-Clause-No-Nuclear-Warranty', 'deprecated': False}, + 'bsd-3-clause-open-mpi': {'id': 'BSD-3-Clause-Open-MPI', 'deprecated': False}, + 'bsd-3-clause-sun': {'id': 'BSD-3-Clause-Sun', 'deprecated': False}, + 'bsd-4-clause': {'id': 'BSD-4-Clause', 'deprecated': False}, + 'bsd-4-clause-shortened': {'id': 'BSD-4-Clause-Shortened', 'deprecated': False}, + 'bsd-4-clause-uc': {'id': 'BSD-4-Clause-UC', 'deprecated': False}, + 'bsd-4.3reno': {'id': 'BSD-4.3RENO', 'deprecated': False}, + 'bsd-4.3tahoe': {'id': 'BSD-4.3TAHOE', 'deprecated': False}, + 'bsd-advertising-acknowledgement': {'id': 'BSD-Advertising-Acknowledgement', 'deprecated': False}, + 'bsd-attribution-hpnd-disclaimer': {'id': 'BSD-Attribution-HPND-disclaimer', 'deprecated': False}, + 'bsd-inferno-nettverk': {'id': 'BSD-Inferno-Nettverk', 'deprecated': False}, + 'bsd-protection': {'id': 'BSD-Protection', 'deprecated': False}, + 'bsd-source-beginning-file': {'id': 'BSD-Source-beginning-file', 'deprecated': False}, + 'bsd-source-code': {'id': 'BSD-Source-Code', 'deprecated': False}, + 'bsd-systemics': {'id': 'BSD-Systemics', 'deprecated': False}, + 'bsd-systemics-w3works': {'id': 'BSD-Systemics-W3Works', 'deprecated': False}, + 'bsl-1.0': {'id': 'BSL-1.0', 'deprecated': False}, + 'busl-1.1': {'id': 'BUSL-1.1', 'deprecated': False}, + 'bzip2-1.0.5': {'id': 'bzip2-1.0.5', 'deprecated': True}, + 'bzip2-1.0.6': {'id': 'bzip2-1.0.6', 'deprecated': False}, + 'c-uda-1.0': {'id': 'C-UDA-1.0', 'deprecated': False}, + 'cal-1.0': {'id': 'CAL-1.0', 'deprecated': False}, + 'cal-1.0-combined-work-exception': {'id': 'CAL-1.0-Combined-Work-Exception', 'deprecated': False}, + 'caldera': {'id': 'Caldera', 'deprecated': False}, + 'caldera-no-preamble': {'id': 'Caldera-no-preamble', 'deprecated': False}, + 'catharon': {'id': 'Catharon', 'deprecated': False}, + 'catosl-1.1': {'id': 'CATOSL-1.1', 'deprecated': False}, + 'cc-by-1.0': {'id': 'CC-BY-1.0', 'deprecated': False}, + 'cc-by-2.0': {'id': 'CC-BY-2.0', 'deprecated': False}, + 'cc-by-2.5': {'id': 'CC-BY-2.5', 'deprecated': False}, + 'cc-by-2.5-au': {'id': 'CC-BY-2.5-AU', 'deprecated': False}, + 'cc-by-3.0': {'id': 'CC-BY-3.0', 'deprecated': False}, + 'cc-by-3.0-at': {'id': 'CC-BY-3.0-AT', 'deprecated': False}, + 'cc-by-3.0-au': {'id': 'CC-BY-3.0-AU', 'deprecated': False}, + 'cc-by-3.0-de': {'id': 'CC-BY-3.0-DE', 'deprecated': False}, + 'cc-by-3.0-igo': {'id': 'CC-BY-3.0-IGO', 'deprecated': False}, + 'cc-by-3.0-nl': {'id': 'CC-BY-3.0-NL', 'deprecated': False}, + 'cc-by-3.0-us': {'id': 'CC-BY-3.0-US', 'deprecated': False}, + 'cc-by-4.0': {'id': 'CC-BY-4.0', 'deprecated': False}, + 'cc-by-nc-1.0': {'id': 'CC-BY-NC-1.0', 'deprecated': False}, + 'cc-by-nc-2.0': {'id': 'CC-BY-NC-2.0', 'deprecated': False}, + 'cc-by-nc-2.5': {'id': 'CC-BY-NC-2.5', 'deprecated': False}, + 'cc-by-nc-3.0': {'id': 'CC-BY-NC-3.0', 'deprecated': False}, + 'cc-by-nc-3.0-de': {'id': 'CC-BY-NC-3.0-DE', 'deprecated': False}, + 'cc-by-nc-4.0': {'id': 'CC-BY-NC-4.0', 'deprecated': False}, + 'cc-by-nc-nd-1.0': {'id': 'CC-BY-NC-ND-1.0', 'deprecated': False}, + 'cc-by-nc-nd-2.0': {'id': 'CC-BY-NC-ND-2.0', 'deprecated': False}, + 'cc-by-nc-nd-2.5': {'id': 'CC-BY-NC-ND-2.5', 'deprecated': False}, + 'cc-by-nc-nd-3.0': {'id': 'CC-BY-NC-ND-3.0', 'deprecated': False}, + 'cc-by-nc-nd-3.0-de': {'id': 'CC-BY-NC-ND-3.0-DE', 'deprecated': False}, + 'cc-by-nc-nd-3.0-igo': {'id': 'CC-BY-NC-ND-3.0-IGO', 'deprecated': False}, + 'cc-by-nc-nd-4.0': {'id': 'CC-BY-NC-ND-4.0', 'deprecated': False}, + 'cc-by-nc-sa-1.0': {'id': 'CC-BY-NC-SA-1.0', 'deprecated': False}, + 'cc-by-nc-sa-2.0': {'id': 'CC-BY-NC-SA-2.0', 'deprecated': False}, + 'cc-by-nc-sa-2.0-de': {'id': 'CC-BY-NC-SA-2.0-DE', 'deprecated': False}, + 'cc-by-nc-sa-2.0-fr': {'id': 'CC-BY-NC-SA-2.0-FR', 'deprecated': False}, + 'cc-by-nc-sa-2.0-uk': {'id': 'CC-BY-NC-SA-2.0-UK', 'deprecated': False}, + 'cc-by-nc-sa-2.5': {'id': 'CC-BY-NC-SA-2.5', 'deprecated': False}, + 'cc-by-nc-sa-3.0': {'id': 'CC-BY-NC-SA-3.0', 'deprecated': False}, + 'cc-by-nc-sa-3.0-de': {'id': 'CC-BY-NC-SA-3.0-DE', 'deprecated': False}, + 'cc-by-nc-sa-3.0-igo': {'id': 'CC-BY-NC-SA-3.0-IGO', 'deprecated': False}, + 'cc-by-nc-sa-4.0': {'id': 'CC-BY-NC-SA-4.0', 'deprecated': False}, + 'cc-by-nd-1.0': {'id': 'CC-BY-ND-1.0', 'deprecated': False}, + 'cc-by-nd-2.0': {'id': 'CC-BY-ND-2.0', 'deprecated': False}, + 'cc-by-nd-2.5': {'id': 'CC-BY-ND-2.5', 'deprecated': False}, + 'cc-by-nd-3.0': {'id': 'CC-BY-ND-3.0', 'deprecated': False}, + 'cc-by-nd-3.0-de': {'id': 'CC-BY-ND-3.0-DE', 'deprecated': False}, + 'cc-by-nd-4.0': {'id': 'CC-BY-ND-4.0', 'deprecated': False}, + 'cc-by-sa-1.0': {'id': 'CC-BY-SA-1.0', 'deprecated': False}, + 'cc-by-sa-2.0': {'id': 'CC-BY-SA-2.0', 'deprecated': False}, + 'cc-by-sa-2.0-uk': {'id': 'CC-BY-SA-2.0-UK', 'deprecated': False}, + 'cc-by-sa-2.1-jp': {'id': 'CC-BY-SA-2.1-JP', 'deprecated': False}, + 'cc-by-sa-2.5': {'id': 'CC-BY-SA-2.5', 'deprecated': False}, + 'cc-by-sa-3.0': {'id': 'CC-BY-SA-3.0', 'deprecated': False}, + 'cc-by-sa-3.0-at': {'id': 'CC-BY-SA-3.0-AT', 'deprecated': False}, + 'cc-by-sa-3.0-de': {'id': 'CC-BY-SA-3.0-DE', 'deprecated': False}, + 'cc-by-sa-3.0-igo': {'id': 'CC-BY-SA-3.0-IGO', 'deprecated': False}, + 'cc-by-sa-4.0': {'id': 'CC-BY-SA-4.0', 'deprecated': False}, + 'cc-pddc': {'id': 'CC-PDDC', 'deprecated': False}, + 'cc-pdm-1.0': {'id': 'CC-PDM-1.0', 'deprecated': False}, + 'cc-sa-1.0': {'id': 'CC-SA-1.0', 'deprecated': False}, + 'cc0-1.0': {'id': 'CC0-1.0', 'deprecated': False}, + 'cddl-1.0': {'id': 'CDDL-1.0', 'deprecated': False}, + 'cddl-1.1': {'id': 'CDDL-1.1', 'deprecated': False}, + 'cdl-1.0': {'id': 'CDL-1.0', 'deprecated': False}, + 'cdla-permissive-1.0': {'id': 'CDLA-Permissive-1.0', 'deprecated': False}, + 'cdla-permissive-2.0': {'id': 'CDLA-Permissive-2.0', 'deprecated': False}, + 'cdla-sharing-1.0': {'id': 'CDLA-Sharing-1.0', 'deprecated': False}, + 'cecill-1.0': {'id': 'CECILL-1.0', 'deprecated': False}, + 'cecill-1.1': {'id': 'CECILL-1.1', 'deprecated': False}, + 'cecill-2.0': {'id': 'CECILL-2.0', 'deprecated': False}, + 'cecill-2.1': {'id': 'CECILL-2.1', 'deprecated': False}, + 'cecill-b': {'id': 'CECILL-B', 'deprecated': False}, + 'cecill-c': {'id': 'CECILL-C', 'deprecated': False}, + 'cern-ohl-1.1': {'id': 'CERN-OHL-1.1', 'deprecated': False}, + 'cern-ohl-1.2': {'id': 'CERN-OHL-1.2', 'deprecated': False}, + 'cern-ohl-p-2.0': {'id': 'CERN-OHL-P-2.0', 'deprecated': False}, + 'cern-ohl-s-2.0': {'id': 'CERN-OHL-S-2.0', 'deprecated': False}, + 'cern-ohl-w-2.0': {'id': 'CERN-OHL-W-2.0', 'deprecated': False}, + 'cfitsio': {'id': 'CFITSIO', 'deprecated': False}, + 'check-cvs': {'id': 'check-cvs', 'deprecated': False}, + 'checkmk': {'id': 'checkmk', 'deprecated': False}, + 'clartistic': {'id': 'ClArtistic', 'deprecated': False}, + 'clips': {'id': 'Clips', 'deprecated': False}, + 'cmu-mach': {'id': 'CMU-Mach', 'deprecated': False}, + 'cmu-mach-nodoc': {'id': 'CMU-Mach-nodoc', 'deprecated': False}, + 'cnri-jython': {'id': 'CNRI-Jython', 'deprecated': False}, + 'cnri-python': {'id': 'CNRI-Python', 'deprecated': False}, + 'cnri-python-gpl-compatible': {'id': 'CNRI-Python-GPL-Compatible', 'deprecated': False}, + 'coil-1.0': {'id': 'COIL-1.0', 'deprecated': False}, + 'community-spec-1.0': {'id': 'Community-Spec-1.0', 'deprecated': False}, + 'condor-1.1': {'id': 'Condor-1.1', 'deprecated': False}, + 'copyleft-next-0.3.0': {'id': 'copyleft-next-0.3.0', 'deprecated': False}, + 'copyleft-next-0.3.1': {'id': 'copyleft-next-0.3.1', 'deprecated': False}, + 'cornell-lossless-jpeg': {'id': 'Cornell-Lossless-JPEG', 'deprecated': False}, + 'cpal-1.0': {'id': 'CPAL-1.0', 'deprecated': False}, + 'cpl-1.0': {'id': 'CPL-1.0', 'deprecated': False}, + 'cpol-1.02': {'id': 'CPOL-1.02', 'deprecated': False}, + 'cronyx': {'id': 'Cronyx', 'deprecated': False}, + 'crossword': {'id': 'Crossword', 'deprecated': False}, + 'cryptoswift': {'id': 'CryptoSwift', 'deprecated': False}, + 'crystalstacker': {'id': 'CrystalStacker', 'deprecated': False}, + 'cua-opl-1.0': {'id': 'CUA-OPL-1.0', 'deprecated': False}, + 'cube': {'id': 'Cube', 'deprecated': False}, + 'curl': {'id': 'curl', 'deprecated': False}, + 'cve-tou': {'id': 'cve-tou', 'deprecated': False}, + 'd-fsl-1.0': {'id': 'D-FSL-1.0', 'deprecated': False}, + 'dec-3-clause': {'id': 'DEC-3-Clause', 'deprecated': False}, + 'diffmark': {'id': 'diffmark', 'deprecated': False}, + 'dl-de-by-2.0': {'id': 'DL-DE-BY-2.0', 'deprecated': False}, + 'dl-de-zero-2.0': {'id': 'DL-DE-ZERO-2.0', 'deprecated': False}, + 'doc': {'id': 'DOC', 'deprecated': False}, + 'docbook-dtd': {'id': 'DocBook-DTD', 'deprecated': False}, + 'docbook-schema': {'id': 'DocBook-Schema', 'deprecated': False}, + 'docbook-stylesheet': {'id': 'DocBook-Stylesheet', 'deprecated': False}, + 'docbook-xml': {'id': 'DocBook-XML', 'deprecated': False}, + 'dotseqn': {'id': 'Dotseqn', 'deprecated': False}, + 'drl-1.0': {'id': 'DRL-1.0', 'deprecated': False}, + 'drl-1.1': {'id': 'DRL-1.1', 'deprecated': False}, + 'dsdp': {'id': 'DSDP', 'deprecated': False}, + 'dtoa': {'id': 'dtoa', 'deprecated': False}, + 'dvipdfm': {'id': 'dvipdfm', 'deprecated': False}, + 'ecl-1.0': {'id': 'ECL-1.0', 'deprecated': False}, + 'ecl-2.0': {'id': 'ECL-2.0', 'deprecated': False}, + 'ecos-2.0': {'id': 'eCos-2.0', 'deprecated': True}, + 'efl-1.0': {'id': 'EFL-1.0', 'deprecated': False}, + 'efl-2.0': {'id': 'EFL-2.0', 'deprecated': False}, + 'egenix': {'id': 'eGenix', 'deprecated': False}, + 'elastic-2.0': {'id': 'Elastic-2.0', 'deprecated': False}, + 'entessa': {'id': 'Entessa', 'deprecated': False}, + 'epics': {'id': 'EPICS', 'deprecated': False}, + 'epl-1.0': {'id': 'EPL-1.0', 'deprecated': False}, + 'epl-2.0': {'id': 'EPL-2.0', 'deprecated': False}, + 'erlpl-1.1': {'id': 'ErlPL-1.1', 'deprecated': False}, + 'etalab-2.0': {'id': 'etalab-2.0', 'deprecated': False}, + 'eudatagrid': {'id': 'EUDatagrid', 'deprecated': False}, + 'eupl-1.0': {'id': 'EUPL-1.0', 'deprecated': False}, + 'eupl-1.1': {'id': 'EUPL-1.1', 'deprecated': False}, + 'eupl-1.2': {'id': 'EUPL-1.2', 'deprecated': False}, + 'eurosym': {'id': 'Eurosym', 'deprecated': False}, + 'fair': {'id': 'Fair', 'deprecated': False}, + 'fbm': {'id': 'FBM', 'deprecated': False}, + 'fdk-aac': {'id': 'FDK-AAC', 'deprecated': False}, + 'ferguson-twofish': {'id': 'Ferguson-Twofish', 'deprecated': False}, + 'frameworx-1.0': {'id': 'Frameworx-1.0', 'deprecated': False}, + 'freebsd-doc': {'id': 'FreeBSD-DOC', 'deprecated': False}, + 'freeimage': {'id': 'FreeImage', 'deprecated': False}, + 'fsfap': {'id': 'FSFAP', 'deprecated': False}, + 'fsfap-no-warranty-disclaimer': {'id': 'FSFAP-no-warranty-disclaimer', 'deprecated': False}, + 'fsful': {'id': 'FSFUL', 'deprecated': False}, + 'fsfullr': {'id': 'FSFULLR', 'deprecated': False}, + 'fsfullrsd': {'id': 'FSFULLRSD', 'deprecated': False}, + 'fsfullrwd': {'id': 'FSFULLRWD', 'deprecated': False}, + 'fsl-1.1-alv2': {'id': 'FSL-1.1-ALv2', 'deprecated': False}, + 'fsl-1.1-mit': {'id': 'FSL-1.1-MIT', 'deprecated': False}, + 'ftl': {'id': 'FTL', 'deprecated': False}, + 'furuseth': {'id': 'Furuseth', 'deprecated': False}, + 'fwlw': {'id': 'fwlw', 'deprecated': False}, + 'game-programming-gems': {'id': 'Game-Programming-Gems', 'deprecated': False}, + 'gcr-docs': {'id': 'GCR-docs', 'deprecated': False}, + 'gd': {'id': 'GD', 'deprecated': False}, + 'generic-xts': {'id': 'generic-xts', 'deprecated': False}, + 'gfdl-1.1': {'id': 'GFDL-1.1', 'deprecated': True}, + 'gfdl-1.1-invariants-only': {'id': 'GFDL-1.1-invariants-only', 'deprecated': False}, + 'gfdl-1.1-invariants-or-later': {'id': 'GFDL-1.1-invariants-or-later', 'deprecated': False}, + 'gfdl-1.1-no-invariants-only': {'id': 'GFDL-1.1-no-invariants-only', 'deprecated': False}, + 'gfdl-1.1-no-invariants-or-later': {'id': 'GFDL-1.1-no-invariants-or-later', 'deprecated': False}, + 'gfdl-1.1-only': {'id': 'GFDL-1.1-only', 'deprecated': False}, + 'gfdl-1.1-or-later': {'id': 'GFDL-1.1-or-later', 'deprecated': False}, + 'gfdl-1.2': {'id': 'GFDL-1.2', 'deprecated': True}, + 'gfdl-1.2-invariants-only': {'id': 'GFDL-1.2-invariants-only', 'deprecated': False}, + 'gfdl-1.2-invariants-or-later': {'id': 'GFDL-1.2-invariants-or-later', 'deprecated': False}, + 'gfdl-1.2-no-invariants-only': {'id': 'GFDL-1.2-no-invariants-only', 'deprecated': False}, + 'gfdl-1.2-no-invariants-or-later': {'id': 'GFDL-1.2-no-invariants-or-later', 'deprecated': False}, + 'gfdl-1.2-only': {'id': 'GFDL-1.2-only', 'deprecated': False}, + 'gfdl-1.2-or-later': {'id': 'GFDL-1.2-or-later', 'deprecated': False}, + 'gfdl-1.3': {'id': 'GFDL-1.3', 'deprecated': True}, + 'gfdl-1.3-invariants-only': {'id': 'GFDL-1.3-invariants-only', 'deprecated': False}, + 'gfdl-1.3-invariants-or-later': {'id': 'GFDL-1.3-invariants-or-later', 'deprecated': False}, + 'gfdl-1.3-no-invariants-only': {'id': 'GFDL-1.3-no-invariants-only', 'deprecated': False}, + 'gfdl-1.3-no-invariants-or-later': {'id': 'GFDL-1.3-no-invariants-or-later', 'deprecated': False}, + 'gfdl-1.3-only': {'id': 'GFDL-1.3-only', 'deprecated': False}, + 'gfdl-1.3-or-later': {'id': 'GFDL-1.3-or-later', 'deprecated': False}, + 'giftware': {'id': 'Giftware', 'deprecated': False}, + 'gl2ps': {'id': 'GL2PS', 'deprecated': False}, + 'glide': {'id': 'Glide', 'deprecated': False}, + 'glulxe': {'id': 'Glulxe', 'deprecated': False}, + 'glwtpl': {'id': 'GLWTPL', 'deprecated': False}, + 'gnuplot': {'id': 'gnuplot', 'deprecated': False}, + 'gpl-1.0': {'id': 'GPL-1.0', 'deprecated': True}, + 'gpl-1.0+': {'id': 'GPL-1.0+', 'deprecated': True}, + 'gpl-1.0-only': {'id': 'GPL-1.0-only', 'deprecated': False}, + 'gpl-1.0-or-later': {'id': 'GPL-1.0-or-later', 'deprecated': False}, + 'gpl-2.0': {'id': 'GPL-2.0', 'deprecated': True}, + 'gpl-2.0+': {'id': 'GPL-2.0+', 'deprecated': True}, + 'gpl-2.0-only': {'id': 'GPL-2.0-only', 'deprecated': False}, + 'gpl-2.0-or-later': {'id': 'GPL-2.0-or-later', 'deprecated': False}, + 'gpl-2.0-with-autoconf-exception': {'id': 'GPL-2.0-with-autoconf-exception', 'deprecated': True}, + 'gpl-2.0-with-bison-exception': {'id': 'GPL-2.0-with-bison-exception', 'deprecated': True}, + 'gpl-2.0-with-classpath-exception': {'id': 'GPL-2.0-with-classpath-exception', 'deprecated': True}, + 'gpl-2.0-with-font-exception': {'id': 'GPL-2.0-with-font-exception', 'deprecated': True}, + 'gpl-2.0-with-gcc-exception': {'id': 'GPL-2.0-with-GCC-exception', 'deprecated': True}, + 'gpl-3.0': {'id': 'GPL-3.0', 'deprecated': True}, + 'gpl-3.0+': {'id': 'GPL-3.0+', 'deprecated': True}, + 'gpl-3.0-only': {'id': 'GPL-3.0-only', 'deprecated': False}, + 'gpl-3.0-or-later': {'id': 'GPL-3.0-or-later', 'deprecated': False}, + 'gpl-3.0-with-autoconf-exception': {'id': 'GPL-3.0-with-autoconf-exception', 'deprecated': True}, + 'gpl-3.0-with-gcc-exception': {'id': 'GPL-3.0-with-GCC-exception', 'deprecated': True}, + 'graphics-gems': {'id': 'Graphics-Gems', 'deprecated': False}, + 'gsoap-1.3b': {'id': 'gSOAP-1.3b', 'deprecated': False}, + 'gtkbook': {'id': 'gtkbook', 'deprecated': False}, + 'gutmann': {'id': 'Gutmann', 'deprecated': False}, + 'haskellreport': {'id': 'HaskellReport', 'deprecated': False}, + 'hdf5': {'id': 'HDF5', 'deprecated': False}, + 'hdparm': {'id': 'hdparm', 'deprecated': False}, + 'hidapi': {'id': 'HIDAPI', 'deprecated': False}, + 'hippocratic-2.1': {'id': 'Hippocratic-2.1', 'deprecated': False}, + 'hp-1986': {'id': 'HP-1986', 'deprecated': False}, + 'hp-1989': {'id': 'HP-1989', 'deprecated': False}, + 'hpnd': {'id': 'HPND', 'deprecated': False}, + 'hpnd-dec': {'id': 'HPND-DEC', 'deprecated': False}, + 'hpnd-doc': {'id': 'HPND-doc', 'deprecated': False}, + 'hpnd-doc-sell': {'id': 'HPND-doc-sell', 'deprecated': False}, + 'hpnd-export-us': {'id': 'HPND-export-US', 'deprecated': False}, + 'hpnd-export-us-acknowledgement': {'id': 'HPND-export-US-acknowledgement', 'deprecated': False}, + 'hpnd-export-us-modify': {'id': 'HPND-export-US-modify', 'deprecated': False}, + 'hpnd-export2-us': {'id': 'HPND-export2-US', 'deprecated': False}, + 'hpnd-fenneberg-livingston': {'id': 'HPND-Fenneberg-Livingston', 'deprecated': False}, + 'hpnd-inria-imag': {'id': 'HPND-INRIA-IMAG', 'deprecated': False}, + 'hpnd-intel': {'id': 'HPND-Intel', 'deprecated': False}, + 'hpnd-kevlin-henney': {'id': 'HPND-Kevlin-Henney', 'deprecated': False}, + 'hpnd-markus-kuhn': {'id': 'HPND-Markus-Kuhn', 'deprecated': False}, + 'hpnd-merchantability-variant': {'id': 'HPND-merchantability-variant', 'deprecated': False}, + 'hpnd-mit-disclaimer': {'id': 'HPND-MIT-disclaimer', 'deprecated': False}, + 'hpnd-netrek': {'id': 'HPND-Netrek', 'deprecated': False}, + 'hpnd-pbmplus': {'id': 'HPND-Pbmplus', 'deprecated': False}, + 'hpnd-sell-mit-disclaimer-xserver': {'id': 'HPND-sell-MIT-disclaimer-xserver', 'deprecated': False}, + 'hpnd-sell-regexpr': {'id': 'HPND-sell-regexpr', 'deprecated': False}, + 'hpnd-sell-variant': {'id': 'HPND-sell-variant', 'deprecated': False}, + 'hpnd-sell-variant-mit-disclaimer': {'id': 'HPND-sell-variant-MIT-disclaimer', 'deprecated': False}, + 'hpnd-sell-variant-mit-disclaimer-rev': {'id': 'HPND-sell-variant-MIT-disclaimer-rev', 'deprecated': False}, + 'hpnd-uc': {'id': 'HPND-UC', 'deprecated': False}, + 'hpnd-uc-export-us': {'id': 'HPND-UC-export-US', 'deprecated': False}, + 'htmltidy': {'id': 'HTMLTIDY', 'deprecated': False}, + 'ibm-pibs': {'id': 'IBM-pibs', 'deprecated': False}, + 'icu': {'id': 'ICU', 'deprecated': False}, + 'iec-code-components-eula': {'id': 'IEC-Code-Components-EULA', 'deprecated': False}, + 'ijg': {'id': 'IJG', 'deprecated': False}, + 'ijg-short': {'id': 'IJG-short', 'deprecated': False}, + 'imagemagick': {'id': 'ImageMagick', 'deprecated': False}, + 'imatix': {'id': 'iMatix', 'deprecated': False}, + 'imlib2': {'id': 'Imlib2', 'deprecated': False}, + 'info-zip': {'id': 'Info-ZIP', 'deprecated': False}, + 'inner-net-2.0': {'id': 'Inner-Net-2.0', 'deprecated': False}, + 'innosetup': {'id': 'InnoSetup', 'deprecated': False}, + 'intel': {'id': 'Intel', 'deprecated': False}, + 'intel-acpi': {'id': 'Intel-ACPI', 'deprecated': False}, + 'interbase-1.0': {'id': 'Interbase-1.0', 'deprecated': False}, + 'ipa': {'id': 'IPA', 'deprecated': False}, + 'ipl-1.0': {'id': 'IPL-1.0', 'deprecated': False}, + 'isc': {'id': 'ISC', 'deprecated': False}, + 'isc-veillard': {'id': 'ISC-Veillard', 'deprecated': False}, + 'jam': {'id': 'Jam', 'deprecated': False}, + 'jasper-2.0': {'id': 'JasPer-2.0', 'deprecated': False}, + 'jove': {'id': 'jove', 'deprecated': False}, + 'jpl-image': {'id': 'JPL-image', 'deprecated': False}, + 'jpnic': {'id': 'JPNIC', 'deprecated': False}, + 'json': {'id': 'JSON', 'deprecated': False}, + 'kastrup': {'id': 'Kastrup', 'deprecated': False}, + 'kazlib': {'id': 'Kazlib', 'deprecated': False}, + 'knuth-ctan': {'id': 'Knuth-CTAN', 'deprecated': False}, + 'lal-1.2': {'id': 'LAL-1.2', 'deprecated': False}, + 'lal-1.3': {'id': 'LAL-1.3', 'deprecated': False}, + 'latex2e': {'id': 'Latex2e', 'deprecated': False}, + 'latex2e-translated-notice': {'id': 'Latex2e-translated-notice', 'deprecated': False}, + 'leptonica': {'id': 'Leptonica', 'deprecated': False}, + 'lgpl-2.0': {'id': 'LGPL-2.0', 'deprecated': True}, + 'lgpl-2.0+': {'id': 'LGPL-2.0+', 'deprecated': True}, + 'lgpl-2.0-only': {'id': 'LGPL-2.0-only', 'deprecated': False}, + 'lgpl-2.0-or-later': {'id': 'LGPL-2.0-or-later', 'deprecated': False}, + 'lgpl-2.1': {'id': 'LGPL-2.1', 'deprecated': True}, + 'lgpl-2.1+': {'id': 'LGPL-2.1+', 'deprecated': True}, + 'lgpl-2.1-only': {'id': 'LGPL-2.1-only', 'deprecated': False}, + 'lgpl-2.1-or-later': {'id': 'LGPL-2.1-or-later', 'deprecated': False}, + 'lgpl-3.0': {'id': 'LGPL-3.0', 'deprecated': True}, + 'lgpl-3.0+': {'id': 'LGPL-3.0+', 'deprecated': True}, + 'lgpl-3.0-only': {'id': 'LGPL-3.0-only', 'deprecated': False}, + 'lgpl-3.0-or-later': {'id': 'LGPL-3.0-or-later', 'deprecated': False}, + 'lgpllr': {'id': 'LGPLLR', 'deprecated': False}, + 'libpng': {'id': 'Libpng', 'deprecated': False}, + 'libpng-1.6.35': {'id': 'libpng-1.6.35', 'deprecated': False}, + 'libpng-2.0': {'id': 'libpng-2.0', 'deprecated': False}, + 'libselinux-1.0': {'id': 'libselinux-1.0', 'deprecated': False}, + 'libtiff': {'id': 'libtiff', 'deprecated': False}, + 'libutil-david-nugent': {'id': 'libutil-David-Nugent', 'deprecated': False}, + 'liliq-p-1.1': {'id': 'LiLiQ-P-1.1', 'deprecated': False}, + 'liliq-r-1.1': {'id': 'LiLiQ-R-1.1', 'deprecated': False}, + 'liliq-rplus-1.1': {'id': 'LiLiQ-Rplus-1.1', 'deprecated': False}, + 'linux-man-pages-1-para': {'id': 'Linux-man-pages-1-para', 'deprecated': False}, + 'linux-man-pages-copyleft': {'id': 'Linux-man-pages-copyleft', 'deprecated': False}, + 'linux-man-pages-copyleft-2-para': {'id': 'Linux-man-pages-copyleft-2-para', 'deprecated': False}, + 'linux-man-pages-copyleft-var': {'id': 'Linux-man-pages-copyleft-var', 'deprecated': False}, + 'linux-openib': {'id': 'Linux-OpenIB', 'deprecated': False}, + 'loop': {'id': 'LOOP', 'deprecated': False}, + 'lpd-document': {'id': 'LPD-document', 'deprecated': False}, + 'lpl-1.0': {'id': 'LPL-1.0', 'deprecated': False}, + 'lpl-1.02': {'id': 'LPL-1.02', 'deprecated': False}, + 'lppl-1.0': {'id': 'LPPL-1.0', 'deprecated': False}, + 'lppl-1.1': {'id': 'LPPL-1.1', 'deprecated': False}, + 'lppl-1.2': {'id': 'LPPL-1.2', 'deprecated': False}, + 'lppl-1.3a': {'id': 'LPPL-1.3a', 'deprecated': False}, + 'lppl-1.3c': {'id': 'LPPL-1.3c', 'deprecated': False}, + 'lsof': {'id': 'lsof', 'deprecated': False}, + 'lucida-bitmap-fonts': {'id': 'Lucida-Bitmap-Fonts', 'deprecated': False}, + 'lzma-sdk-9.11-to-9.20': {'id': 'LZMA-SDK-9.11-to-9.20', 'deprecated': False}, + 'lzma-sdk-9.22': {'id': 'LZMA-SDK-9.22', 'deprecated': False}, + 'mackerras-3-clause': {'id': 'Mackerras-3-Clause', 'deprecated': False}, + 'mackerras-3-clause-acknowledgment': {'id': 'Mackerras-3-Clause-acknowledgment', 'deprecated': False}, + 'magaz': {'id': 'magaz', 'deprecated': False}, + 'mailprio': {'id': 'mailprio', 'deprecated': False}, + 'makeindex': {'id': 'MakeIndex', 'deprecated': False}, + 'man2html': {'id': 'man2html', 'deprecated': False}, + 'martin-birgmeier': {'id': 'Martin-Birgmeier', 'deprecated': False}, + 'mcphee-slideshow': {'id': 'McPhee-slideshow', 'deprecated': False}, + 'metamail': {'id': 'metamail', 'deprecated': False}, + 'minpack': {'id': 'Minpack', 'deprecated': False}, + 'mips': {'id': 'MIPS', 'deprecated': False}, + 'miros': {'id': 'MirOS', 'deprecated': False}, + 'mit': {'id': 'MIT', 'deprecated': False}, + 'mit-0': {'id': 'MIT-0', 'deprecated': False}, + 'mit-advertising': {'id': 'MIT-advertising', 'deprecated': False}, + 'mit-click': {'id': 'MIT-Click', 'deprecated': False}, + 'mit-cmu': {'id': 'MIT-CMU', 'deprecated': False}, + 'mit-enna': {'id': 'MIT-enna', 'deprecated': False}, + 'mit-feh': {'id': 'MIT-feh', 'deprecated': False}, + 'mit-festival': {'id': 'MIT-Festival', 'deprecated': False}, + 'mit-khronos-old': {'id': 'MIT-Khronos-old', 'deprecated': False}, + 'mit-modern-variant': {'id': 'MIT-Modern-Variant', 'deprecated': False}, + 'mit-open-group': {'id': 'MIT-open-group', 'deprecated': False}, + 'mit-testregex': {'id': 'MIT-testregex', 'deprecated': False}, + 'mit-wu': {'id': 'MIT-Wu', 'deprecated': False}, + 'mitnfa': {'id': 'MITNFA', 'deprecated': False}, + 'mmixware': {'id': 'MMIXware', 'deprecated': False}, + 'motosoto': {'id': 'Motosoto', 'deprecated': False}, + 'mpeg-ssg': {'id': 'MPEG-SSG', 'deprecated': False}, + 'mpi-permissive': {'id': 'mpi-permissive', 'deprecated': False}, + 'mpich2': {'id': 'mpich2', 'deprecated': False}, + 'mpl-1.0': {'id': 'MPL-1.0', 'deprecated': False}, + 'mpl-1.1': {'id': 'MPL-1.1', 'deprecated': False}, + 'mpl-2.0': {'id': 'MPL-2.0', 'deprecated': False}, + 'mpl-2.0-no-copyleft-exception': {'id': 'MPL-2.0-no-copyleft-exception', 'deprecated': False}, + 'mplus': {'id': 'mplus', 'deprecated': False}, + 'ms-lpl': {'id': 'MS-LPL', 'deprecated': False}, + 'ms-pl': {'id': 'MS-PL', 'deprecated': False}, + 'ms-rl': {'id': 'MS-RL', 'deprecated': False}, + 'mtll': {'id': 'MTLL', 'deprecated': False}, + 'mulanpsl-1.0': {'id': 'MulanPSL-1.0', 'deprecated': False}, + 'mulanpsl-2.0': {'id': 'MulanPSL-2.0', 'deprecated': False}, + 'multics': {'id': 'Multics', 'deprecated': False}, + 'mup': {'id': 'Mup', 'deprecated': False}, + 'naist-2003': {'id': 'NAIST-2003', 'deprecated': False}, + 'nasa-1.3': {'id': 'NASA-1.3', 'deprecated': False}, + 'naumen': {'id': 'Naumen', 'deprecated': False}, + 'nbpl-1.0': {'id': 'NBPL-1.0', 'deprecated': False}, + 'ncbi-pd': {'id': 'NCBI-PD', 'deprecated': False}, + 'ncgl-uk-2.0': {'id': 'NCGL-UK-2.0', 'deprecated': False}, + 'ncl': {'id': 'NCL', 'deprecated': False}, + 'ncsa': {'id': 'NCSA', 'deprecated': False}, + 'net-snmp': {'id': 'Net-SNMP', 'deprecated': True}, + 'netcdf': {'id': 'NetCDF', 'deprecated': False}, + 'newsletr': {'id': 'Newsletr', 'deprecated': False}, + 'ngpl': {'id': 'NGPL', 'deprecated': False}, + 'ngrep': {'id': 'ngrep', 'deprecated': False}, + 'nicta-1.0': {'id': 'NICTA-1.0', 'deprecated': False}, + 'nist-pd': {'id': 'NIST-PD', 'deprecated': False}, + 'nist-pd-fallback': {'id': 'NIST-PD-fallback', 'deprecated': False}, + 'nist-software': {'id': 'NIST-Software', 'deprecated': False}, + 'nlod-1.0': {'id': 'NLOD-1.0', 'deprecated': False}, + 'nlod-2.0': {'id': 'NLOD-2.0', 'deprecated': False}, + 'nlpl': {'id': 'NLPL', 'deprecated': False}, + 'nokia': {'id': 'Nokia', 'deprecated': False}, + 'nosl': {'id': 'NOSL', 'deprecated': False}, + 'noweb': {'id': 'Noweb', 'deprecated': False}, + 'npl-1.0': {'id': 'NPL-1.0', 'deprecated': False}, + 'npl-1.1': {'id': 'NPL-1.1', 'deprecated': False}, + 'nposl-3.0': {'id': 'NPOSL-3.0', 'deprecated': False}, + 'nrl': {'id': 'NRL', 'deprecated': False}, + 'ntia-pd': {'id': 'NTIA-PD', 'deprecated': False}, + 'ntp': {'id': 'NTP', 'deprecated': False}, + 'ntp-0': {'id': 'NTP-0', 'deprecated': False}, + 'nunit': {'id': 'Nunit', 'deprecated': True}, + 'o-uda-1.0': {'id': 'O-UDA-1.0', 'deprecated': False}, + 'oar': {'id': 'OAR', 'deprecated': False}, + 'occt-pl': {'id': 'OCCT-PL', 'deprecated': False}, + 'oclc-2.0': {'id': 'OCLC-2.0', 'deprecated': False}, + 'odbl-1.0': {'id': 'ODbL-1.0', 'deprecated': False}, + 'odc-by-1.0': {'id': 'ODC-By-1.0', 'deprecated': False}, + 'offis': {'id': 'OFFIS', 'deprecated': False}, + 'ofl-1.0': {'id': 'OFL-1.0', 'deprecated': False}, + 'ofl-1.0-no-rfn': {'id': 'OFL-1.0-no-RFN', 'deprecated': False}, + 'ofl-1.0-rfn': {'id': 'OFL-1.0-RFN', 'deprecated': False}, + 'ofl-1.1': {'id': 'OFL-1.1', 'deprecated': False}, + 'ofl-1.1-no-rfn': {'id': 'OFL-1.1-no-RFN', 'deprecated': False}, + 'ofl-1.1-rfn': {'id': 'OFL-1.1-RFN', 'deprecated': False}, + 'ogc-1.0': {'id': 'OGC-1.0', 'deprecated': False}, + 'ogdl-taiwan-1.0': {'id': 'OGDL-Taiwan-1.0', 'deprecated': False}, + 'ogl-canada-2.0': {'id': 'OGL-Canada-2.0', 'deprecated': False}, + 'ogl-uk-1.0': {'id': 'OGL-UK-1.0', 'deprecated': False}, + 'ogl-uk-2.0': {'id': 'OGL-UK-2.0', 'deprecated': False}, + 'ogl-uk-3.0': {'id': 'OGL-UK-3.0', 'deprecated': False}, + 'ogtsl': {'id': 'OGTSL', 'deprecated': False}, + 'oldap-1.1': {'id': 'OLDAP-1.1', 'deprecated': False}, + 'oldap-1.2': {'id': 'OLDAP-1.2', 'deprecated': False}, + 'oldap-1.3': {'id': 'OLDAP-1.3', 'deprecated': False}, + 'oldap-1.4': {'id': 'OLDAP-1.4', 'deprecated': False}, + 'oldap-2.0': {'id': 'OLDAP-2.0', 'deprecated': False}, + 'oldap-2.0.1': {'id': 'OLDAP-2.0.1', 'deprecated': False}, + 'oldap-2.1': {'id': 'OLDAP-2.1', 'deprecated': False}, + 'oldap-2.2': {'id': 'OLDAP-2.2', 'deprecated': False}, + 'oldap-2.2.1': {'id': 'OLDAP-2.2.1', 'deprecated': False}, + 'oldap-2.2.2': {'id': 'OLDAP-2.2.2', 'deprecated': False}, + 'oldap-2.3': {'id': 'OLDAP-2.3', 'deprecated': False}, + 'oldap-2.4': {'id': 'OLDAP-2.4', 'deprecated': False}, + 'oldap-2.5': {'id': 'OLDAP-2.5', 'deprecated': False}, + 'oldap-2.6': {'id': 'OLDAP-2.6', 'deprecated': False}, + 'oldap-2.7': {'id': 'OLDAP-2.7', 'deprecated': False}, + 'oldap-2.8': {'id': 'OLDAP-2.8', 'deprecated': False}, + 'olfl-1.3': {'id': 'OLFL-1.3', 'deprecated': False}, + 'oml': {'id': 'OML', 'deprecated': False}, + 'openpbs-2.3': {'id': 'OpenPBS-2.3', 'deprecated': False}, + 'openssl': {'id': 'OpenSSL', 'deprecated': False}, + 'openssl-standalone': {'id': 'OpenSSL-standalone', 'deprecated': False}, + 'openvision': {'id': 'OpenVision', 'deprecated': False}, + 'opl-1.0': {'id': 'OPL-1.0', 'deprecated': False}, + 'opl-uk-3.0': {'id': 'OPL-UK-3.0', 'deprecated': False}, + 'opubl-1.0': {'id': 'OPUBL-1.0', 'deprecated': False}, + 'oset-pl-2.1': {'id': 'OSET-PL-2.1', 'deprecated': False}, + 'osl-1.0': {'id': 'OSL-1.0', 'deprecated': False}, + 'osl-1.1': {'id': 'OSL-1.1', 'deprecated': False}, + 'osl-2.0': {'id': 'OSL-2.0', 'deprecated': False}, + 'osl-2.1': {'id': 'OSL-2.1', 'deprecated': False}, + 'osl-3.0': {'id': 'OSL-3.0', 'deprecated': False}, + 'padl': {'id': 'PADL', 'deprecated': False}, + 'parity-6.0.0': {'id': 'Parity-6.0.0', 'deprecated': False}, + 'parity-7.0.0': {'id': 'Parity-7.0.0', 'deprecated': False}, + 'pddl-1.0': {'id': 'PDDL-1.0', 'deprecated': False}, + 'php-3.0': {'id': 'PHP-3.0', 'deprecated': False}, + 'php-3.01': {'id': 'PHP-3.01', 'deprecated': False}, + 'pixar': {'id': 'Pixar', 'deprecated': False}, + 'pkgconf': {'id': 'pkgconf', 'deprecated': False}, + 'plexus': {'id': 'Plexus', 'deprecated': False}, + 'pnmstitch': {'id': 'pnmstitch', 'deprecated': False}, + 'polyform-noncommercial-1.0.0': {'id': 'PolyForm-Noncommercial-1.0.0', 'deprecated': False}, + 'polyform-small-business-1.0.0': {'id': 'PolyForm-Small-Business-1.0.0', 'deprecated': False}, + 'postgresql': {'id': 'PostgreSQL', 'deprecated': False}, + 'ppl': {'id': 'PPL', 'deprecated': False}, + 'psf-2.0': {'id': 'PSF-2.0', 'deprecated': False}, + 'psfrag': {'id': 'psfrag', 'deprecated': False}, + 'psutils': {'id': 'psutils', 'deprecated': False}, + 'python-2.0': {'id': 'Python-2.0', 'deprecated': False}, + 'python-2.0.1': {'id': 'Python-2.0.1', 'deprecated': False}, + 'python-ldap': {'id': 'python-ldap', 'deprecated': False}, + 'qhull': {'id': 'Qhull', 'deprecated': False}, + 'qpl-1.0': {'id': 'QPL-1.0', 'deprecated': False}, + 'qpl-1.0-inria-2004': {'id': 'QPL-1.0-INRIA-2004', 'deprecated': False}, + 'radvd': {'id': 'radvd', 'deprecated': False}, + 'rdisc': {'id': 'Rdisc', 'deprecated': False}, + 'rhecos-1.1': {'id': 'RHeCos-1.1', 'deprecated': False}, + 'rpl-1.1': {'id': 'RPL-1.1', 'deprecated': False}, + 'rpl-1.5': {'id': 'RPL-1.5', 'deprecated': False}, + 'rpsl-1.0': {'id': 'RPSL-1.0', 'deprecated': False}, + 'rsa-md': {'id': 'RSA-MD', 'deprecated': False}, + 'rscpl': {'id': 'RSCPL', 'deprecated': False}, + 'ruby': {'id': 'Ruby', 'deprecated': False}, + 'ruby-pty': {'id': 'Ruby-pty', 'deprecated': False}, + 'sax-pd': {'id': 'SAX-PD', 'deprecated': False}, + 'sax-pd-2.0': {'id': 'SAX-PD-2.0', 'deprecated': False}, + 'saxpath': {'id': 'Saxpath', 'deprecated': False}, + 'scea': {'id': 'SCEA', 'deprecated': False}, + 'schemereport': {'id': 'SchemeReport', 'deprecated': False}, + 'sendmail': {'id': 'Sendmail', 'deprecated': False}, + 'sendmail-8.23': {'id': 'Sendmail-8.23', 'deprecated': False}, + 'sendmail-open-source-1.1': {'id': 'Sendmail-Open-Source-1.1', 'deprecated': False}, + 'sgi-b-1.0': {'id': 'SGI-B-1.0', 'deprecated': False}, + 'sgi-b-1.1': {'id': 'SGI-B-1.1', 'deprecated': False}, + 'sgi-b-2.0': {'id': 'SGI-B-2.0', 'deprecated': False}, + 'sgi-opengl': {'id': 'SGI-OpenGL', 'deprecated': False}, + 'sgp4': {'id': 'SGP4', 'deprecated': False}, + 'shl-0.5': {'id': 'SHL-0.5', 'deprecated': False}, + 'shl-0.51': {'id': 'SHL-0.51', 'deprecated': False}, + 'simpl-2.0': {'id': 'SimPL-2.0', 'deprecated': False}, + 'sissl': {'id': 'SISSL', 'deprecated': False}, + 'sissl-1.2': {'id': 'SISSL-1.2', 'deprecated': False}, + 'sl': {'id': 'SL', 'deprecated': False}, + 'sleepycat': {'id': 'Sleepycat', 'deprecated': False}, + 'smail-gpl': {'id': 'SMAIL-GPL', 'deprecated': False}, + 'smlnj': {'id': 'SMLNJ', 'deprecated': False}, + 'smppl': {'id': 'SMPPL', 'deprecated': False}, + 'snia': {'id': 'SNIA', 'deprecated': False}, + 'snprintf': {'id': 'snprintf', 'deprecated': False}, + 'sofa': {'id': 'SOFA', 'deprecated': False}, + 'softsurfer': {'id': 'softSurfer', 'deprecated': False}, + 'soundex': {'id': 'Soundex', 'deprecated': False}, + 'spencer-86': {'id': 'Spencer-86', 'deprecated': False}, + 'spencer-94': {'id': 'Spencer-94', 'deprecated': False}, + 'spencer-99': {'id': 'Spencer-99', 'deprecated': False}, + 'spl-1.0': {'id': 'SPL-1.0', 'deprecated': False}, + 'ssh-keyscan': {'id': 'ssh-keyscan', 'deprecated': False}, + 'ssh-openssh': {'id': 'SSH-OpenSSH', 'deprecated': False}, + 'ssh-short': {'id': 'SSH-short', 'deprecated': False}, + 'ssleay-standalone': {'id': 'SSLeay-standalone', 'deprecated': False}, + 'sspl-1.0': {'id': 'SSPL-1.0', 'deprecated': False}, + 'standardml-nj': {'id': 'StandardML-NJ', 'deprecated': True}, + 'sugarcrm-1.1.3': {'id': 'SugarCRM-1.1.3', 'deprecated': False}, + 'sul-1.0': {'id': 'SUL-1.0', 'deprecated': False}, + 'sun-ppp': {'id': 'Sun-PPP', 'deprecated': False}, + 'sun-ppp-2000': {'id': 'Sun-PPP-2000', 'deprecated': False}, + 'sunpro': {'id': 'SunPro', 'deprecated': False}, + 'swl': {'id': 'SWL', 'deprecated': False}, + 'swrule': {'id': 'swrule', 'deprecated': False}, + 'symlinks': {'id': 'Symlinks', 'deprecated': False}, + 'tapr-ohl-1.0': {'id': 'TAPR-OHL-1.0', 'deprecated': False}, + 'tcl': {'id': 'TCL', 'deprecated': False}, + 'tcp-wrappers': {'id': 'TCP-wrappers', 'deprecated': False}, + 'termreadkey': {'id': 'TermReadKey', 'deprecated': False}, + 'tgppl-1.0': {'id': 'TGPPL-1.0', 'deprecated': False}, + 'thirdeye': {'id': 'ThirdEye', 'deprecated': False}, + 'threeparttable': {'id': 'threeparttable', 'deprecated': False}, + 'tmate': {'id': 'TMate', 'deprecated': False}, + 'torque-1.1': {'id': 'TORQUE-1.1', 'deprecated': False}, + 'tosl': {'id': 'TOSL', 'deprecated': False}, + 'tpdl': {'id': 'TPDL', 'deprecated': False}, + 'tpl-1.0': {'id': 'TPL-1.0', 'deprecated': False}, + 'trustedqsl': {'id': 'TrustedQSL', 'deprecated': False}, + 'ttwl': {'id': 'TTWL', 'deprecated': False}, + 'ttyp0': {'id': 'TTYP0', 'deprecated': False}, + 'tu-berlin-1.0': {'id': 'TU-Berlin-1.0', 'deprecated': False}, + 'tu-berlin-2.0': {'id': 'TU-Berlin-2.0', 'deprecated': False}, + 'ubuntu-font-1.0': {'id': 'Ubuntu-font-1.0', 'deprecated': False}, + 'ucar': {'id': 'UCAR', 'deprecated': False}, + 'ucl-1.0': {'id': 'UCL-1.0', 'deprecated': False}, + 'ulem': {'id': 'ulem', 'deprecated': False}, + 'umich-merit': {'id': 'UMich-Merit', 'deprecated': False}, + 'unicode-3.0': {'id': 'Unicode-3.0', 'deprecated': False}, + 'unicode-dfs-2015': {'id': 'Unicode-DFS-2015', 'deprecated': False}, + 'unicode-dfs-2016': {'id': 'Unicode-DFS-2016', 'deprecated': False}, + 'unicode-tou': {'id': 'Unicode-TOU', 'deprecated': False}, + 'unixcrypt': {'id': 'UnixCrypt', 'deprecated': False}, + 'unlicense': {'id': 'Unlicense', 'deprecated': False}, + 'unlicense-libtelnet': {'id': 'Unlicense-libtelnet', 'deprecated': False}, + 'unlicense-libwhirlpool': {'id': 'Unlicense-libwhirlpool', 'deprecated': False}, + 'upl-1.0': {'id': 'UPL-1.0', 'deprecated': False}, + 'urt-rle': {'id': 'URT-RLE', 'deprecated': False}, + 'vim': {'id': 'Vim', 'deprecated': False}, + 'vostrom': {'id': 'VOSTROM', 'deprecated': False}, + 'vsl-1.0': {'id': 'VSL-1.0', 'deprecated': False}, + 'w3c': {'id': 'W3C', 'deprecated': False}, + 'w3c-19980720': {'id': 'W3C-19980720', 'deprecated': False}, + 'w3c-20150513': {'id': 'W3C-20150513', 'deprecated': False}, + 'w3m': {'id': 'w3m', 'deprecated': False}, + 'watcom-1.0': {'id': 'Watcom-1.0', 'deprecated': False}, + 'widget-workshop': {'id': 'Widget-Workshop', 'deprecated': False}, + 'wsuipa': {'id': 'Wsuipa', 'deprecated': False}, + 'wtfpl': {'id': 'WTFPL', 'deprecated': False}, + 'wwl': {'id': 'wwl', 'deprecated': False}, + 'wxwindows': {'id': 'wxWindows', 'deprecated': True}, + 'x11': {'id': 'X11', 'deprecated': False}, + 'x11-distribute-modifications-variant': {'id': 'X11-distribute-modifications-variant', 'deprecated': False}, + 'x11-swapped': {'id': 'X11-swapped', 'deprecated': False}, + 'xdebug-1.03': {'id': 'Xdebug-1.03', 'deprecated': False}, + 'xerox': {'id': 'Xerox', 'deprecated': False}, + 'xfig': {'id': 'Xfig', 'deprecated': False}, + 'xfree86-1.1': {'id': 'XFree86-1.1', 'deprecated': False}, + 'xinetd': {'id': 'xinetd', 'deprecated': False}, + 'xkeyboard-config-zinoviev': {'id': 'xkeyboard-config-Zinoviev', 'deprecated': False}, + 'xlock': {'id': 'xlock', 'deprecated': False}, + 'xnet': {'id': 'Xnet', 'deprecated': False}, + 'xpp': {'id': 'xpp', 'deprecated': False}, + 'xskat': {'id': 'XSkat', 'deprecated': False}, + 'xzoom': {'id': 'xzoom', 'deprecated': False}, + 'ypl-1.0': {'id': 'YPL-1.0', 'deprecated': False}, + 'ypl-1.1': {'id': 'YPL-1.1', 'deprecated': False}, + 'zed': {'id': 'Zed', 'deprecated': False}, + 'zeeff': {'id': 'Zeeff', 'deprecated': False}, + 'zend-2.0': {'id': 'Zend-2.0', 'deprecated': False}, + 'zimbra-1.3': {'id': 'Zimbra-1.3', 'deprecated': False}, + 'zimbra-1.4': {'id': 'Zimbra-1.4', 'deprecated': False}, + 'zlib': {'id': 'Zlib', 'deprecated': False}, + 'zlib-acknowledgement': {'id': 'zlib-acknowledgement', 'deprecated': False}, + 'zpl-1.1': {'id': 'ZPL-1.1', 'deprecated': False}, + 'zpl-2.0': {'id': 'ZPL-2.0', 'deprecated': False}, + 'zpl-2.1': {'id': 'ZPL-2.1', 'deprecated': False}, +} + +EXCEPTIONS: dict[str, SPDXException] = { + '389-exception': {'id': '389-exception', 'deprecated': False}, + 'asterisk-exception': {'id': 'Asterisk-exception', 'deprecated': False}, + 'asterisk-linking-protocols-exception': {'id': 'Asterisk-linking-protocols-exception', 'deprecated': False}, + 'autoconf-exception-2.0': {'id': 'Autoconf-exception-2.0', 'deprecated': False}, + 'autoconf-exception-3.0': {'id': 'Autoconf-exception-3.0', 'deprecated': False}, + 'autoconf-exception-generic': {'id': 'Autoconf-exception-generic', 'deprecated': False}, + 'autoconf-exception-generic-3.0': {'id': 'Autoconf-exception-generic-3.0', 'deprecated': False}, + 'autoconf-exception-macro': {'id': 'Autoconf-exception-macro', 'deprecated': False}, + 'bison-exception-1.24': {'id': 'Bison-exception-1.24', 'deprecated': False}, + 'bison-exception-2.2': {'id': 'Bison-exception-2.2', 'deprecated': False}, + 'bootloader-exception': {'id': 'Bootloader-exception', 'deprecated': False}, + 'cgal-linking-exception': {'id': 'CGAL-linking-exception', 'deprecated': False}, + 'classpath-exception-2.0': {'id': 'Classpath-exception-2.0', 'deprecated': False}, + 'clisp-exception-2.0': {'id': 'CLISP-exception-2.0', 'deprecated': False}, + 'cryptsetup-openssl-exception': {'id': 'cryptsetup-OpenSSL-exception', 'deprecated': False}, + 'digia-qt-lgpl-exception-1.1': {'id': 'Digia-Qt-LGPL-exception-1.1', 'deprecated': False}, + 'digirule-foss-exception': {'id': 'DigiRule-FOSS-exception', 'deprecated': False}, + 'ecos-exception-2.0': {'id': 'eCos-exception-2.0', 'deprecated': False}, + 'erlang-otp-linking-exception': {'id': 'erlang-otp-linking-exception', 'deprecated': False}, + 'fawkes-runtime-exception': {'id': 'Fawkes-Runtime-exception', 'deprecated': False}, + 'fltk-exception': {'id': 'FLTK-exception', 'deprecated': False}, + 'fmt-exception': {'id': 'fmt-exception', 'deprecated': False}, + 'font-exception-2.0': {'id': 'Font-exception-2.0', 'deprecated': False}, + 'freertos-exception-2.0': {'id': 'freertos-exception-2.0', 'deprecated': False}, + 'gcc-exception-2.0': {'id': 'GCC-exception-2.0', 'deprecated': False}, + 'gcc-exception-2.0-note': {'id': 'GCC-exception-2.0-note', 'deprecated': False}, + 'gcc-exception-3.1': {'id': 'GCC-exception-3.1', 'deprecated': False}, + 'gmsh-exception': {'id': 'Gmsh-exception', 'deprecated': False}, + 'gnat-exception': {'id': 'GNAT-exception', 'deprecated': False}, + 'gnome-examples-exception': {'id': 'GNOME-examples-exception', 'deprecated': False}, + 'gnu-compiler-exception': {'id': 'GNU-compiler-exception', 'deprecated': False}, + 'gnu-javamail-exception': {'id': 'gnu-javamail-exception', 'deprecated': False}, + 'gpl-3.0-389-ds-base-exception': {'id': 'GPL-3.0-389-ds-base-exception', 'deprecated': False}, + 'gpl-3.0-interface-exception': {'id': 'GPL-3.0-interface-exception', 'deprecated': False}, + 'gpl-3.0-linking-exception': {'id': 'GPL-3.0-linking-exception', 'deprecated': False}, + 'gpl-3.0-linking-source-exception': {'id': 'GPL-3.0-linking-source-exception', 'deprecated': False}, + 'gpl-cc-1.0': {'id': 'GPL-CC-1.0', 'deprecated': False}, + 'gstreamer-exception-2005': {'id': 'GStreamer-exception-2005', 'deprecated': False}, + 'gstreamer-exception-2008': {'id': 'GStreamer-exception-2008', 'deprecated': False}, + 'harbour-exception': {'id': 'harbour-exception', 'deprecated': False}, + 'i2p-gpl-java-exception': {'id': 'i2p-gpl-java-exception', 'deprecated': False}, + 'independent-modules-exception': {'id': 'Independent-modules-exception', 'deprecated': False}, + 'kicad-libraries-exception': {'id': 'KiCad-libraries-exception', 'deprecated': False}, + 'lgpl-3.0-linking-exception': {'id': 'LGPL-3.0-linking-exception', 'deprecated': False}, + 'libpri-openh323-exception': {'id': 'libpri-OpenH323-exception', 'deprecated': False}, + 'libtool-exception': {'id': 'Libtool-exception', 'deprecated': False}, + 'linux-syscall-note': {'id': 'Linux-syscall-note', 'deprecated': False}, + 'llgpl': {'id': 'LLGPL', 'deprecated': False}, + 'llvm-exception': {'id': 'LLVM-exception', 'deprecated': False}, + 'lzma-exception': {'id': 'LZMA-exception', 'deprecated': False}, + 'mif-exception': {'id': 'mif-exception', 'deprecated': False}, + 'mxml-exception': {'id': 'mxml-exception', 'deprecated': False}, + 'nokia-qt-exception-1.1': {'id': 'Nokia-Qt-exception-1.1', 'deprecated': True}, + 'ocaml-lgpl-linking-exception': {'id': 'OCaml-LGPL-linking-exception', 'deprecated': False}, + 'occt-exception-1.0': {'id': 'OCCT-exception-1.0', 'deprecated': False}, + 'openjdk-assembly-exception-1.0': {'id': 'OpenJDK-assembly-exception-1.0', 'deprecated': False}, + 'openvpn-openssl-exception': {'id': 'openvpn-openssl-exception', 'deprecated': False}, + 'pcre2-exception': {'id': 'PCRE2-exception', 'deprecated': False}, + 'polyparse-exception': {'id': 'polyparse-exception', 'deprecated': False}, + 'ps-or-pdf-font-exception-20170817': {'id': 'PS-or-PDF-font-exception-20170817', 'deprecated': False}, + 'qpl-1.0-inria-2004-exception': {'id': 'QPL-1.0-INRIA-2004-exception', 'deprecated': False}, + 'qt-gpl-exception-1.0': {'id': 'Qt-GPL-exception-1.0', 'deprecated': False}, + 'qt-lgpl-exception-1.1': {'id': 'Qt-LGPL-exception-1.1', 'deprecated': False}, + 'qwt-exception-1.0': {'id': 'Qwt-exception-1.0', 'deprecated': False}, + 'romic-exception': {'id': 'romic-exception', 'deprecated': False}, + 'rrdtool-floss-exception-2.0': {'id': 'RRDtool-FLOSS-exception-2.0', 'deprecated': False}, + 'sane-exception': {'id': 'SANE-exception', 'deprecated': False}, + 'shl-2.0': {'id': 'SHL-2.0', 'deprecated': False}, + 'shl-2.1': {'id': 'SHL-2.1', 'deprecated': False}, + 'stunnel-exception': {'id': 'stunnel-exception', 'deprecated': False}, + 'swi-exception': {'id': 'SWI-exception', 'deprecated': False}, + 'swift-exception': {'id': 'Swift-exception', 'deprecated': False}, + 'texinfo-exception': {'id': 'Texinfo-exception', 'deprecated': False}, + 'u-boot-exception-2.0': {'id': 'u-boot-exception-2.0', 'deprecated': False}, + 'ubdl-exception': {'id': 'UBDL-exception', 'deprecated': False}, + 'universal-foss-exception-1.0': {'id': 'Universal-FOSS-exception-1.0', 'deprecated': False}, + 'vsftpd-openssl-exception': {'id': 'vsftpd-openssl-exception', 'deprecated': False}, + 'wxwindows-exception-3.1': {'id': 'WxWindows-exception-3.1', 'deprecated': False}, + 'x11vnc-openssl-exception': {'id': 'x11vnc-openssl-exception', 'deprecated': False}, +} diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/markers.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/markers.py new file mode 100644 index 0000000000000000000000000000000000000000..ca3706fe492f4cf0762f7734d84c2d269f88bbc5 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/markers.py @@ -0,0 +1,388 @@ +# This file is dual licensed under the terms of the Apache License, Version +# 2.0, and the BSD License. See the LICENSE file in the root of this repository +# for complete details. + +from __future__ import annotations + +import operator +import os +import platform +import sys +from typing import AbstractSet, Callable, Literal, Mapping, TypedDict, Union, cast + +from ._parser import MarkerAtom, MarkerList, Op, Value, Variable +from ._parser import parse_marker as _parse_marker +from ._tokenizer import ParserSyntaxError +from .specifiers import InvalidSpecifier, Specifier +from .utils import canonicalize_name + +__all__ = [ + "Environment", + "EvaluateContext", + "InvalidMarker", + "Marker", + "UndefinedComparison", + "UndefinedEnvironmentName", + "default_environment", +] + +Operator = Callable[[str, Union[str, AbstractSet[str]]], bool] +EvaluateContext = Literal["metadata", "lock_file", "requirement"] +MARKERS_ALLOWING_SET = {"extras", "dependency_groups"} +MARKERS_REQUIRING_VERSION = { + "implementation_version", + "platform_release", + "python_full_version", + "python_version", +} + + +class InvalidMarker(ValueError): + """ + An invalid marker was found, users should refer to PEP 508. + """ + + +class UndefinedComparison(ValueError): + """ + An invalid operation was attempted on a value that doesn't support it. + """ + + +class UndefinedEnvironmentName(ValueError): + """ + A name was attempted to be used that does not exist inside of the + environment. + """ + + +class Environment(TypedDict): + implementation_name: str + """The implementation's identifier, e.g. ``'cpython'``.""" + + implementation_version: str + """ + The implementation's version, e.g. ``'3.13.0a2'`` for CPython 3.13.0a2, or + ``'7.3.13'`` for PyPy3.10 v7.3.13. + """ + + os_name: str + """ + The value of :py:data:`os.name`. The name of the operating system dependent module + imported, e.g. ``'posix'``. + """ + + platform_machine: str + """ + Returns the machine type, e.g. ``'i386'``. + + An empty string if the value cannot be determined. + """ + + platform_release: str + """ + The system's release, e.g. ``'2.2.0'`` or ``'NT'``. + + An empty string if the value cannot be determined. + """ + + platform_system: str + """ + The system/OS name, e.g. ``'Linux'``, ``'Windows'`` or ``'Java'``. + + An empty string if the value cannot be determined. + """ + + platform_version: str + """ + The system's release version, e.g. ``'#3 on degas'``. + + An empty string if the value cannot be determined. + """ + + python_full_version: str + """ + The Python version as string ``'major.minor.patchlevel'``. + + Note that unlike the Python :py:data:`sys.version`, this value will always include + the patchlevel (it defaults to 0). + """ + + platform_python_implementation: str + """ + A string identifying the Python implementation, e.g. ``'CPython'``. + """ + + python_version: str + """The Python version as string ``'major.minor'``.""" + + sys_platform: str + """ + This string contains a platform identifier that can be used to append + platform-specific components to :py:data:`sys.path`, for instance. + + For Unix systems, except on Linux and AIX, this is the lowercased OS name as + returned by ``uname -s`` with the first part of the version as returned by + ``uname -r`` appended, e.g. ``'sunos5'`` or ``'freebsd8'``, at the time when Python + was built. + """ + + +def _normalize_extras( + result: MarkerList | MarkerAtom | str, +) -> MarkerList | MarkerAtom | str: + if not isinstance(result, tuple): + return result + + lhs, op, rhs = result + if isinstance(lhs, Variable) and lhs.value == "extra": + normalized_extra = canonicalize_name(rhs.value) + rhs = Value(normalized_extra) + elif isinstance(rhs, Variable) and rhs.value == "extra": + normalized_extra = canonicalize_name(lhs.value) + lhs = Value(normalized_extra) + return lhs, op, rhs + + +def _normalize_extra_values(results: MarkerList) -> MarkerList: + """ + Normalize extra values. + """ + + return [_normalize_extras(r) for r in results] + + +def _format_marker( + marker: list[str] | MarkerAtom | str, first: bool | None = True +) -> str: + assert isinstance(marker, (list, tuple, str)) + + # Sometimes we have a structure like [[...]] which is a single item list + # where the single item is itself it's own list. In that case we want skip + # the rest of this function so that we don't get extraneous () on the + # outside. + if ( + isinstance(marker, list) + and len(marker) == 1 + and isinstance(marker[0], (list, tuple)) + ): + return _format_marker(marker[0]) + + if isinstance(marker, list): + inner = (_format_marker(m, first=False) for m in marker) + if first: + return " ".join(inner) + else: + return "(" + " ".join(inner) + ")" + elif isinstance(marker, tuple): + return " ".join([m.serialize() for m in marker]) + else: + return marker + + +_operators: dict[str, Operator] = { + "in": lambda lhs, rhs: lhs in rhs, + "not in": lambda lhs, rhs: lhs not in rhs, + "<": lambda _lhs, _rhs: False, + "<=": operator.eq, + "==": operator.eq, + "!=": operator.ne, + ">=": operator.eq, + ">": lambda _lhs, _rhs: False, +} + + +def _eval_op(lhs: str, op: Op, rhs: str | AbstractSet[str], *, key: str) -> bool: + op_str = op.serialize() + if key in MARKERS_REQUIRING_VERSION: + try: + spec = Specifier(f"{op_str}{rhs}") + except InvalidSpecifier: + pass + else: + return spec.contains(lhs, prereleases=True) + + oper: Operator | None = _operators.get(op_str) + if oper is None: + raise UndefinedComparison(f"Undefined {op!r} on {lhs!r} and {rhs!r}.") + + return oper(lhs, rhs) + + +def _normalize( + lhs: str, rhs: str | AbstractSet[str], key: str +) -> tuple[str, str | AbstractSet[str]]: + # PEP 685 - Comparison of extra names for optional distribution dependencies + # https://peps.python.org/pep-0685/ + # > When comparing extra names, tools MUST normalize the names being + # > compared using the semantics outlined in PEP 503 for names + if key == "extra": + assert isinstance(rhs, str), "extra value must be a string" + # Both sides are normalized at this point already + return (lhs, rhs) + if key in MARKERS_ALLOWING_SET: + if isinstance(rhs, str): # pragma: no cover + return (canonicalize_name(lhs), canonicalize_name(rhs)) + else: + return (canonicalize_name(lhs), {canonicalize_name(v) for v in rhs}) + + # other environment markers don't have such standards + return lhs, rhs + + +def _evaluate_markers( + markers: MarkerList, environment: dict[str, str | AbstractSet[str]] +) -> bool: + groups: list[list[bool]] = [[]] + + for marker in markers: + if isinstance(marker, list): + groups[-1].append(_evaluate_markers(marker, environment)) + elif isinstance(marker, tuple): + lhs, op, rhs = marker + + if isinstance(lhs, Variable): + environment_key = lhs.value + lhs_value = environment[environment_key] + rhs_value = rhs.value + else: + lhs_value = lhs.value + environment_key = rhs.value + rhs_value = environment[environment_key] + + assert isinstance(lhs_value, str), "lhs must be a string" + lhs_value, rhs_value = _normalize(lhs_value, rhs_value, key=environment_key) + groups[-1].append(_eval_op(lhs_value, op, rhs_value, key=environment_key)) + elif marker == "or": + groups.append([]) + elif marker == "and": + pass + else: # pragma: nocover + raise TypeError(f"Unexpected marker {marker!r}") + + return any(all(item) for item in groups) + + +def format_full_version(info: sys._version_info) -> str: + version = f"{info.major}.{info.minor}.{info.micro}" + kind = info.releaselevel + if kind != "final": + version += kind[0] + str(info.serial) + return version + + +def default_environment() -> Environment: + iver = format_full_version(sys.implementation.version) + implementation_name = sys.implementation.name + return { + "implementation_name": implementation_name, + "implementation_version": iver, + "os_name": os.name, + "platform_machine": platform.machine(), + "platform_release": platform.release(), + "platform_system": platform.system(), + "platform_version": platform.version(), + "python_full_version": platform.python_version(), + "platform_python_implementation": platform.python_implementation(), + "python_version": ".".join(platform.python_version_tuple()[:2]), + "sys_platform": sys.platform, + } + + +class Marker: + def __init__(self, marker: str) -> None: + # Note: We create a Marker object without calling this constructor in + # packaging.requirements.Requirement. If any additional logic is + # added here, make sure to mirror/adapt Requirement. + + # If this fails and throws an error, the repr still expects _markers to + # be defined. + self._markers: MarkerList = [] + + try: + self._markers = _normalize_extra_values(_parse_marker(marker)) + # The attribute `_markers` can be described in terms of a recursive type: + # MarkerList = List[Union[Tuple[Node, ...], str, MarkerList]] + # + # For example, the following expression: + # python_version > "3.6" or (python_version == "3.6" and os_name == "unix") + # + # is parsed into: + # [ + # (, ')>, ), + # 'and', + # [ + # (, , ), + # 'or', + # (, , ) + # ] + # ] + except ParserSyntaxError as e: + raise InvalidMarker(str(e)) from e + + def __str__(self) -> str: + return _format_marker(self._markers) + + def __repr__(self) -> str: + return f"<{self.__class__.__name__}('{self}')>" + + def __hash__(self) -> int: + return hash(str(self)) + + def __eq__(self, other: object) -> bool: + if not isinstance(other, Marker): + return NotImplemented + + return str(self) == str(other) + + def evaluate( + self, + environment: Mapping[str, str | AbstractSet[str]] | None = None, + context: EvaluateContext = "metadata", + ) -> bool: + """Evaluate a marker. + + Return the boolean from evaluating the given marker against the + environment. environment is an optional argument to override all or + part of the determined environment. The *context* parameter specifies what + context the markers are being evaluated for, which influences what markers + are considered valid. Acceptable values are "metadata" (for core metadata; + default), "lock_file", and "requirement" (i.e. all other situations). + + The environment is determined from the current Python process. + """ + current_environment = cast( + "dict[str, str | AbstractSet[str]]", default_environment() + ) + if context == "lock_file": + current_environment.update( + extras=frozenset(), dependency_groups=frozenset() + ) + elif context == "metadata": + current_environment["extra"] = "" + + if environment is not None: + current_environment.update(environment) + if "extra" in current_environment: + # The API used to allow setting extra to None. We need to handle + # this case for backwards compatibility. Also skip running + # normalize name if extra is empty. + extra = cast("str | None", current_environment["extra"]) + current_environment["extra"] = canonicalize_name(extra) if extra else "" + + return _evaluate_markers( + self._markers, _repair_python_full_version(current_environment) + ) + + +def _repair_python_full_version( + env: dict[str, str | AbstractSet[str]], +) -> dict[str, str | AbstractSet[str]]: + """ + Work around platform.python_version() returning something that is not PEP 440 + compliant for non-tagged Python builds. + """ + python_full_version = cast("str", env["python_full_version"]) + if python_full_version.endswith("+"): + env["python_full_version"] = f"{python_full_version}local" + return env diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/metadata.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/metadata.py new file mode 100644 index 0000000000000000000000000000000000000000..253f6b1b7ebd711fdc6bbbab3b56897061bab515 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/metadata.py @@ -0,0 +1,978 @@ +from __future__ import annotations + +import email.feedparser +import email.header +import email.message +import email.parser +import email.policy +import keyword +import pathlib +import sys +import typing +from typing import ( + Any, + Callable, + Generic, + Literal, + TypedDict, + cast, +) + +from . import licenses, requirements, specifiers, utils +from . import version as version_module + +if typing.TYPE_CHECKING: + from .licenses import NormalizedLicenseExpression + +T = typing.TypeVar("T") + + +if sys.version_info >= (3, 11): # pragma: no cover + ExceptionGroup = ExceptionGroup # noqa: F821 +else: # pragma: no cover + + class ExceptionGroup(Exception): + """A minimal implementation of :external:exc:`ExceptionGroup` from Python 3.11. + + If :external:exc:`ExceptionGroup` is already defined by Python itself, + that version is used instead. + """ + + message: str + exceptions: list[Exception] + + def __init__(self, message: str, exceptions: list[Exception]) -> None: + self.message = message + self.exceptions = exceptions + + def __repr__(self) -> str: + return f"{self.__class__.__name__}({self.message!r}, {self.exceptions!r})" + + +class InvalidMetadata(ValueError): + """A metadata field contains invalid data.""" + + field: str + """The name of the field that contains invalid data.""" + + def __init__(self, field: str, message: str) -> None: + self.field = field + super().__init__(message) + + +# The RawMetadata class attempts to make as few assumptions about the underlying +# serialization formats as possible. The idea is that as long as a serialization +# formats offer some very basic primitives in *some* way then we can support +# serializing to and from that format. +class RawMetadata(TypedDict, total=False): + """A dictionary of raw core metadata. + + Each field in core metadata maps to a key of this dictionary (when data is + provided). The key is lower-case and underscores are used instead of dashes + compared to the equivalent core metadata field. Any core metadata field that + can be specified multiple times or can hold multiple values in a single + field have a key with a plural name. See :class:`Metadata` whose attributes + match the keys of this dictionary. + + Core metadata fields that can be specified multiple times are stored as a + list or dict depending on which is appropriate for the field. Any fields + which hold multiple values in a single field are stored as a list. + + """ + + # Metadata 1.0 - PEP 241 + metadata_version: str + name: str + version: str + platforms: list[str] + summary: str + description: str + keywords: list[str] + home_page: str + author: str + author_email: str + license: str + + # Metadata 1.1 - PEP 314 + supported_platforms: list[str] + download_url: str + classifiers: list[str] + requires: list[str] + provides: list[str] + obsoletes: list[str] + + # Metadata 1.2 - PEP 345 + maintainer: str + maintainer_email: str + requires_dist: list[str] + provides_dist: list[str] + obsoletes_dist: list[str] + requires_python: str + requires_external: list[str] + project_urls: dict[str, str] + + # Metadata 2.0 + # PEP 426 attempted to completely revamp the metadata format + # but got stuck without ever being able to build consensus on + # it and ultimately ended up withdrawn. + # + # However, a number of tools had started emitting METADATA with + # `2.0` Metadata-Version, so for historical reasons, this version + # was skipped. + + # Metadata 2.1 - PEP 566 + description_content_type: str + provides_extra: list[str] + + # Metadata 2.2 - PEP 643 + dynamic: list[str] + + # Metadata 2.3 - PEP 685 + # No new fields were added in PEP 685, just some edge case were + # tightened up to provide better interoperability. + + # Metadata 2.4 - PEP 639 + license_expression: str + license_files: list[str] + + # Metadata 2.5 - PEP 794 + import_names: list[str] + import_namespaces: list[str] + + +# 'keywords' is special as it's a string in the core metadata spec, but we +# represent it as a list. +_STRING_FIELDS = { + "author", + "author_email", + "description", + "description_content_type", + "download_url", + "home_page", + "license", + "license_expression", + "maintainer", + "maintainer_email", + "metadata_version", + "name", + "requires_python", + "summary", + "version", +} + +_LIST_FIELDS = { + "classifiers", + "dynamic", + "license_files", + "obsoletes", + "obsoletes_dist", + "platforms", + "provides", + "provides_dist", + "provides_extra", + "requires", + "requires_dist", + "requires_external", + "supported_platforms", + "import_names", + "import_namespaces", +} + +_DICT_FIELDS = { + "project_urls", +} + + +def _parse_keywords(data: str) -> list[str]: + """Split a string of comma-separated keywords into a list of keywords.""" + return [k.strip() for k in data.split(",")] + + +def _parse_project_urls(data: list[str]) -> dict[str, str]: + """Parse a list of label/URL string pairings separated by a comma.""" + urls = {} + for pair in data: + # Our logic is slightly tricky here as we want to try and do + # *something* reasonable with malformed data. + # + # The main thing that we have to worry about, is data that does + # not have a ',' at all to split the label from the Value. There + # isn't a singular right answer here, and we will fail validation + # later on (if the caller is validating) so it doesn't *really* + # matter, but since the missing value has to be an empty str + # and our return value is dict[str, str], if we let the key + # be the missing value, then they'd have multiple '' values that + # overwrite each other in a accumulating dict. + # + # The other potential issue is that it's possible to have the + # same label multiple times in the metadata, with no solid "right" + # answer with what to do in that case. As such, we'll do the only + # thing we can, which is treat the field as unparsable and add it + # to our list of unparsed fields. + # + # TODO: The spec doesn't say anything about if the keys should be + # considered case sensitive or not... logically they should + # be case-preserving and case-insensitive, but doing that + # would open up more cases where we might have duplicate + # entries. + label, _, url = (s.strip() for s in pair.partition(",")) + + if label in urls: + # The label already exists in our set of urls, so this field + # is unparsable, and we can just add the whole thing to our + # unparsable data and stop processing it. + raise KeyError("duplicate labels in project urls") + urls[label] = url + + return urls + + +def _get_payload(msg: email.message.Message, source: bytes | str) -> str: + """Get the body of the message.""" + # If our source is a str, then our caller has managed encodings for us, + # and we don't need to deal with it. + if isinstance(source, str): + payload = msg.get_payload() + assert isinstance(payload, str) + return payload + # If our source is a bytes, then we're managing the encoding and we need + # to deal with it. + else: + bpayload = msg.get_payload(decode=True) + assert isinstance(bpayload, bytes) + try: + return bpayload.decode("utf8", "strict") + except UnicodeDecodeError as exc: + raise ValueError("payload in an invalid encoding") from exc + + +# The various parse_FORMAT functions here are intended to be as lenient as +# possible in their parsing, while still returning a correctly typed +# RawMetadata. +# +# To aid in this, we also generally want to do as little touching of the +# data as possible, except where there are possibly some historic holdovers +# that make valid data awkward to work with. +# +# While this is a lower level, intermediate format than our ``Metadata`` +# class, some light touch ups can make a massive difference in usability. + +# Map METADATA fields to RawMetadata. +_EMAIL_TO_RAW_MAPPING = { + "author": "author", + "author-email": "author_email", + "classifier": "classifiers", + "description": "description", + "description-content-type": "description_content_type", + "download-url": "download_url", + "dynamic": "dynamic", + "home-page": "home_page", + "import-name": "import_names", + "import-namespace": "import_namespaces", + "keywords": "keywords", + "license": "license", + "license-expression": "license_expression", + "license-file": "license_files", + "maintainer": "maintainer", + "maintainer-email": "maintainer_email", + "metadata-version": "metadata_version", + "name": "name", + "obsoletes": "obsoletes", + "obsoletes-dist": "obsoletes_dist", + "platform": "platforms", + "project-url": "project_urls", + "provides": "provides", + "provides-dist": "provides_dist", + "provides-extra": "provides_extra", + "requires": "requires", + "requires-dist": "requires_dist", + "requires-external": "requires_external", + "requires-python": "requires_python", + "summary": "summary", + "supported-platform": "supported_platforms", + "version": "version", +} +_RAW_TO_EMAIL_MAPPING = {raw: email for email, raw in _EMAIL_TO_RAW_MAPPING.items()} + + +# This class is for writing RFC822 messages +class RFC822Policy(email.policy.EmailPolicy): + """ + This is :class:`email.policy.EmailPolicy`, but with a simple ``header_store_parse`` + implementation that handles multi-line values, and some nice defaults. + """ + + utf8 = True + mangle_from_ = False + max_line_length = 0 + + def header_store_parse(self, name: str, value: str) -> tuple[str, str]: + size = len(name) + 2 + value = value.replace("\n", "\n" + " " * size) + return (name, value) + + +# This class is for writing RFC822 messages +class RFC822Message(email.message.EmailMessage): + """ + This is :class:`email.message.EmailMessage` with two small changes: it defaults to + our `RFC822Policy`, and it correctly writes unicode when being called + with `bytes()`. + """ + + def __init__(self) -> None: + super().__init__(policy=RFC822Policy()) + + def as_bytes( + self, unixfrom: bool = False, policy: email.policy.Policy | None = None + ) -> bytes: + """ + Return the bytes representation of the message. + + This handles unicode encoding. + """ + return self.as_string(unixfrom, policy=policy).encode("utf-8") + + +def parse_email(data: bytes | str) -> tuple[RawMetadata, dict[str, list[str]]]: + """Parse a distribution's metadata stored as email headers (e.g. from ``METADATA``). + + This function returns a two-item tuple of dicts. The first dict is of + recognized fields from the core metadata specification. Fields that can be + parsed and translated into Python's built-in types are converted + appropriately. All other fields are left as-is. Fields that are allowed to + appear multiple times are stored as lists. + + The second dict contains all other fields from the metadata. This includes + any unrecognized fields. It also includes any fields which are expected to + be parsed into a built-in type but were not formatted appropriately. Finally, + any fields that are expected to appear only once but are repeated are + included in this dict. + + """ + raw: dict[str, str | list[str] | dict[str, str]] = {} + unparsed: dict[str, list[str]] = {} + + if isinstance(data, str): + parsed = email.parser.Parser(policy=email.policy.compat32).parsestr(data) + else: + parsed = email.parser.BytesParser(policy=email.policy.compat32).parsebytes(data) + + # We have to wrap parsed.keys() in a set, because in the case of multiple + # values for a key (a list), the key will appear multiple times in the + # list of keys, but we're avoiding that by using get_all(). + for name_with_case in frozenset(parsed.keys()): + # Header names in RFC are case insensitive, so we'll normalize to all + # lower case to make comparisons easier. + name = name_with_case.lower() + + # We use get_all() here, even for fields that aren't multiple use, + # because otherwise someone could have e.g. two Name fields, and we + # would just silently ignore it rather than doing something about it. + headers = parsed.get_all(name) or [] + + # The way the email module works when parsing bytes is that it + # unconditionally decodes the bytes as ascii using the surrogateescape + # handler. When you pull that data back out (such as with get_all() ), + # it looks to see if the str has any surrogate escapes, and if it does + # it wraps it in a Header object instead of returning the string. + # + # As such, we'll look for those Header objects, and fix up the encoding. + value = [] + # Flag if we have run into any issues processing the headers, thus + # signalling that the data belongs in 'unparsed'. + valid_encoding = True + for h in headers: + # It's unclear if this can return more types than just a Header or + # a str, so we'll just assert here to make sure. + assert isinstance(h, (email.header.Header, str)) + + # If it's a header object, we need to do our little dance to get + # the real data out of it. In cases where there is invalid data + # we're going to end up with mojibake, but there's no obvious, good + # way around that without reimplementing parts of the Header object + # ourselves. + # + # That should be fine since, if mojibacked happens, this key is + # going into the unparsed dict anyways. + if isinstance(h, email.header.Header): + # The Header object stores it's data as chunks, and each chunk + # can be independently encoded, so we'll need to check each + # of them. + chunks: list[tuple[bytes, str | None]] = [] + for binary, _encoding in email.header.decode_header(h): + try: + binary.decode("utf8", "strict") + except UnicodeDecodeError: + # Enable mojibake. + encoding = "latin1" + valid_encoding = False + else: + encoding = "utf8" + chunks.append((binary, encoding)) + + # Turn our chunks back into a Header object, then let that + # Header object do the right thing to turn them into a + # string for us. + value.append(str(email.header.make_header(chunks))) + # This is already a string, so just add it. + else: + value.append(h) + + # We've processed all of our values to get them into a list of str, + # but we may have mojibake data, in which case this is an unparsed + # field. + if not valid_encoding: + unparsed[name] = value + continue + + raw_name = _EMAIL_TO_RAW_MAPPING.get(name) + if raw_name is None: + # This is a bit of a weird situation, we've encountered a key that + # we don't know what it means, so we don't know whether it's meant + # to be a list or not. + # + # Since we can't really tell one way or another, we'll just leave it + # as a list, even though it may be a single item list, because that's + # what makes the most sense for email headers. + unparsed[name] = value + continue + + # If this is one of our string fields, then we'll check to see if our + # value is a list of a single item. If it is then we'll assume that + # it was emitted as a single string, and unwrap the str from inside + # the list. + # + # If it's any other kind of data, then we haven't the faintest clue + # what we should parse it as, and we have to just add it to our list + # of unparsed stuff. + if raw_name in _STRING_FIELDS and len(value) == 1: + raw[raw_name] = value[0] + # If this is import_names, we need to special case the empty field + # case, which converts to an empty list instead of None. We can't let + # the empty case slip through, as it will fail validation. + elif raw_name == "import_names" and value == [""]: + raw[raw_name] = [] + # If this is one of our list of string fields, then we can just assign + # the value, since email *only* has strings, and our get_all() call + # above ensures that this is a list. + elif raw_name in _LIST_FIELDS: + raw[raw_name] = value + # Special Case: Keywords + # The keywords field is implemented in the metadata spec as a str, + # but it conceptually is a list of strings, and is serialized using + # ", ".join(keywords), so we'll do some light data massaging to turn + # this into what it logically is. + elif raw_name == "keywords" and len(value) == 1: + raw[raw_name] = _parse_keywords(value[0]) + # Special Case: Project-URL + # The project urls is implemented in the metadata spec as a list of + # specially-formatted strings that represent a key and a value, which + # is fundamentally a mapping, however the email format doesn't support + # mappings in a sane way, so it was crammed into a list of strings + # instead. + # + # We will do a little light data massaging to turn this into a map as + # it logically should be. + elif raw_name == "project_urls": + try: + raw[raw_name] = _parse_project_urls(value) + except KeyError: + unparsed[name] = value + # Nothing that we've done has managed to parse this, so it'll just + # throw it in our unparsable data and move on. + else: + unparsed[name] = value + + # We need to support getting the Description from the message payload in + # addition to getting it from the the headers. This does mean, though, there + # is the possibility of it being set both ways, in which case we put both + # in 'unparsed' since we don't know which is right. + try: + payload = _get_payload(parsed, data) + except ValueError: + unparsed.setdefault("description", []).append( + parsed.get_payload(decode=isinstance(data, bytes)) # type: ignore[call-overload] + ) + else: + if payload: + # Check to see if we've already got a description, if so then both + # it, and this body move to unparsable. + if "description" in raw: + description_header = cast("str", raw.pop("description")) + unparsed.setdefault("description", []).extend( + [description_header, payload] + ) + elif "description" in unparsed: + unparsed["description"].append(payload) + else: + raw["description"] = payload + + # We need to cast our `raw` to a metadata, because a TypedDict only support + # literal key names, but we're computing our key names on purpose, but the + # way this function is implemented, our `TypedDict` can only have valid key + # names. + return cast("RawMetadata", raw), unparsed + + +_NOT_FOUND = object() + + +# Keep the two values in sync. +_VALID_METADATA_VERSIONS = ["1.0", "1.1", "1.2", "2.1", "2.2", "2.3", "2.4", "2.5"] +_MetadataVersion = Literal["1.0", "1.1", "1.2", "2.1", "2.2", "2.3", "2.4", "2.5"] + +_REQUIRED_ATTRS = frozenset(["metadata_version", "name", "version"]) + + +class _Validator(Generic[T]): + """Validate a metadata field. + + All _process_*() methods correspond to a core metadata field. The method is + called with the field's raw value. If the raw value is valid it is returned + in its "enriched" form (e.g. ``version.Version`` for the ``Version`` field). + If the raw value is invalid, :exc:`InvalidMetadata` is raised (with a cause + as appropriate). + """ + + name: str + raw_name: str + added: _MetadataVersion + + def __init__( + self, + *, + added: _MetadataVersion = "1.0", + ) -> None: + self.added = added + + def __set_name__(self, _owner: Metadata, name: str) -> None: + self.name = name + self.raw_name = _RAW_TO_EMAIL_MAPPING[name] + + def __get__(self, instance: Metadata, _owner: type[Metadata]) -> T: + # With Python 3.8, the caching can be replaced with functools.cached_property(). + # No need to check the cache as attribute lookup will resolve into the + # instance's __dict__ before __get__ is called. + cache = instance.__dict__ + value = instance._raw.get(self.name) + + # To make the _process_* methods easier, we'll check if the value is None + # and if this field is NOT a required attribute, and if both of those + # things are true, we'll skip the the converter. This will mean that the + # converters never have to deal with the None union. + if self.name in _REQUIRED_ATTRS or value is not None: + try: + converter: Callable[[Any], T] = getattr(self, f"_process_{self.name}") + except AttributeError: + pass + else: + value = converter(value) + + cache[self.name] = value + try: + del instance._raw[self.name] # type: ignore[misc] + except KeyError: + pass + + return cast("T", value) + + def _invalid_metadata( + self, msg: str, cause: Exception | None = None + ) -> InvalidMetadata: + exc = InvalidMetadata( + self.raw_name, msg.format_map({"field": repr(self.raw_name)}) + ) + exc.__cause__ = cause + return exc + + def _process_metadata_version(self, value: str) -> _MetadataVersion: + # Implicitly makes Metadata-Version required. + if value not in _VALID_METADATA_VERSIONS: + raise self._invalid_metadata(f"{value!r} is not a valid metadata version") + return cast("_MetadataVersion", value) + + def _process_name(self, value: str) -> str: + if not value: + raise self._invalid_metadata("{field} is a required field") + # Validate the name as a side-effect. + try: + utils.canonicalize_name(value, validate=True) + except utils.InvalidName as exc: + raise self._invalid_metadata( + f"{value!r} is invalid for {{field}}", cause=exc + ) from exc + else: + return value + + def _process_version(self, value: str) -> version_module.Version: + if not value: + raise self._invalid_metadata("{field} is a required field") + try: + return version_module.parse(value) + except version_module.InvalidVersion as exc: + raise self._invalid_metadata( + f"{value!r} is invalid for {{field}}", cause=exc + ) from exc + + def _process_summary(self, value: str) -> str: + """Check the field contains no newlines.""" + if "\n" in value: + raise self._invalid_metadata("{field} must be a single line") + return value + + def _process_description_content_type(self, value: str) -> str: + content_types = {"text/plain", "text/x-rst", "text/markdown"} + message = email.message.EmailMessage() + message["content-type"] = value + + content_type, parameters = ( + # Defaults to `text/plain` if parsing failed. + message.get_content_type().lower(), + message["content-type"].params, + ) + # Check if content-type is valid or defaulted to `text/plain` and thus was + # not parseable. + if content_type not in content_types or content_type not in value.lower(): + raise self._invalid_metadata( + f"{{field}} must be one of {list(content_types)}, not {value!r}" + ) + + charset = parameters.get("charset", "UTF-8") + if charset != "UTF-8": + raise self._invalid_metadata( + f"{{field}} can only specify the UTF-8 charset, not {list(charset)}" + ) + + markdown_variants = {"GFM", "CommonMark"} + variant = parameters.get("variant", "GFM") # Use an acceptable default. + if content_type == "text/markdown" and variant not in markdown_variants: + raise self._invalid_metadata( + f"valid Markdown variants for {{field}} are {list(markdown_variants)}, " + f"not {variant!r}", + ) + return value + + def _process_dynamic(self, value: list[str]) -> list[str]: + for dynamic_field in map(str.lower, value): + if dynamic_field in {"name", "version", "metadata-version"}: + raise self._invalid_metadata( + f"{dynamic_field!r} is not allowed as a dynamic field" + ) + elif dynamic_field not in _EMAIL_TO_RAW_MAPPING: + raise self._invalid_metadata( + f"{dynamic_field!r} is not a valid dynamic field" + ) + return list(map(str.lower, value)) + + def _process_provides_extra( + self, + value: list[str], + ) -> list[utils.NormalizedName]: + normalized_names = [] + try: + for name in value: + normalized_names.append(utils.canonicalize_name(name, validate=True)) + except utils.InvalidName as exc: + raise self._invalid_metadata( + f"{name!r} is invalid for {{field}}", cause=exc + ) from exc + else: + return normalized_names + + def _process_requires_python(self, value: str) -> specifiers.SpecifierSet: + try: + return specifiers.SpecifierSet(value) + except specifiers.InvalidSpecifier as exc: + raise self._invalid_metadata( + f"{value!r} is invalid for {{field}}", cause=exc + ) from exc + + def _process_requires_dist( + self, + value: list[str], + ) -> list[requirements.Requirement]: + reqs = [] + try: + for req in value: + reqs.append(requirements.Requirement(req)) + except requirements.InvalidRequirement as exc: + raise self._invalid_metadata( + f"{req!r} is invalid for {{field}}", cause=exc + ) from exc + else: + return reqs + + def _process_license_expression(self, value: str) -> NormalizedLicenseExpression: + try: + return licenses.canonicalize_license_expression(value) + except ValueError as exc: + raise self._invalid_metadata( + f"{value!r} is invalid for {{field}}", cause=exc + ) from exc + + def _process_license_files(self, value: list[str]) -> list[str]: + paths = [] + for path in value: + if ".." in path: + raise self._invalid_metadata( + f"{path!r} is invalid for {{field}}, " + "parent directory indicators are not allowed" + ) + if "*" in path: + raise self._invalid_metadata( + f"{path!r} is invalid for {{field}}, paths must be resolved" + ) + if ( + pathlib.PurePosixPath(path).is_absolute() + or pathlib.PureWindowsPath(path).is_absolute() + ): + raise self._invalid_metadata( + f"{path!r} is invalid for {{field}}, paths must be relative" + ) + if pathlib.PureWindowsPath(path).as_posix() != path: + raise self._invalid_metadata( + f"{path!r} is invalid for {{field}}, paths must use '/' delimiter" + ) + paths.append(path) + return paths + + def _process_import_names(self, value: list[str]) -> list[str]: + for import_name in value: + name, semicolon, private = import_name.partition(";") + name = name.rstrip() + for identifier in name.split("."): + if not identifier.isidentifier(): + raise self._invalid_metadata( + f"{name!r} is invalid for {{field}}; " + f"{identifier!r} is not a valid identifier" + ) + elif keyword.iskeyword(identifier): + raise self._invalid_metadata( + f"{name!r} is invalid for {{field}}; " + f"{identifier!r} is a keyword" + ) + if semicolon and private.lstrip() != "private": + raise self._invalid_metadata( + f"{import_name!r} is invalid for {{field}}; " + "the only valid option is 'private'" + ) + return value + + _process_import_namespaces = _process_import_names + + +class Metadata: + """Representation of distribution metadata. + + Compared to :class:`RawMetadata`, this class provides objects representing + metadata fields instead of only using built-in types. Any invalid metadata + will cause :exc:`InvalidMetadata` to be raised (with a + :py:attr:`~BaseException.__cause__` attribute as appropriate). + """ + + _raw: RawMetadata + + @classmethod + def from_raw(cls, data: RawMetadata, *, validate: bool = True) -> Metadata: + """Create an instance from :class:`RawMetadata`. + + If *validate* is true, all metadata will be validated. All exceptions + related to validation will be gathered and raised as an :class:`ExceptionGroup`. + """ + ins = cls() + ins._raw = data.copy() # Mutations occur due to caching enriched values. + + if validate: + exceptions: list[Exception] = [] + try: + metadata_version = ins.metadata_version + metadata_age = _VALID_METADATA_VERSIONS.index(metadata_version) + except InvalidMetadata as metadata_version_exc: + exceptions.append(metadata_version_exc) + metadata_version = None + + # Make sure to check for the fields that are present, the required + # fields (so their absence can be reported). + fields_to_check = frozenset(ins._raw) | _REQUIRED_ATTRS + # Remove fields that have already been checked. + fields_to_check -= {"metadata_version"} + + for key in fields_to_check: + try: + if metadata_version: + # Can't use getattr() as that triggers descriptor protocol which + # will fail due to no value for the instance argument. + try: + field_metadata_version = cls.__dict__[key].added + except KeyError: + exc = InvalidMetadata(key, f"unrecognized field: {key!r}") + exceptions.append(exc) + continue + field_age = _VALID_METADATA_VERSIONS.index( + field_metadata_version + ) + if field_age > metadata_age: + field = _RAW_TO_EMAIL_MAPPING[key] + exc = InvalidMetadata( + field, + f"{field} introduced in metadata version " + f"{field_metadata_version}, not {metadata_version}", + ) + exceptions.append(exc) + continue + getattr(ins, key) + except InvalidMetadata as exc: + exceptions.append(exc) + + if exceptions: + raise ExceptionGroup("invalid metadata", exceptions) + + return ins + + @classmethod + def from_email(cls, data: bytes | str, *, validate: bool = True) -> Metadata: + """Parse metadata from email headers. + + If *validate* is true, the metadata will be validated. All exceptions + related to validation will be gathered and raised as an :class:`ExceptionGroup`. + """ + raw, unparsed = parse_email(data) + + if validate: + exceptions: list[Exception] = [] + for unparsed_key in unparsed: + if unparsed_key in _EMAIL_TO_RAW_MAPPING: + message = f"{unparsed_key!r} has invalid data" + else: + message = f"unrecognized field: {unparsed_key!r}" + exceptions.append(InvalidMetadata(unparsed_key, message)) + + if exceptions: + raise ExceptionGroup("unparsed", exceptions) + + try: + return cls.from_raw(raw, validate=validate) + except ExceptionGroup as exc_group: + raise ExceptionGroup( + "invalid or unparsed metadata", exc_group.exceptions + ) from None + + metadata_version: _Validator[_MetadataVersion] = _Validator() + """:external:ref:`core-metadata-metadata-version` + (required; validated to be a valid metadata version)""" + # `name` is not normalized/typed to NormalizedName so as to provide access to + # the original/raw name. + name: _Validator[str] = _Validator() + """:external:ref:`core-metadata-name` + (required; validated using :func:`~packaging.utils.canonicalize_name` and its + *validate* parameter)""" + version: _Validator[version_module.Version] = _Validator() + """:external:ref:`core-metadata-version` (required)""" + dynamic: _Validator[list[str] | None] = _Validator( + added="2.2", + ) + """:external:ref:`core-metadata-dynamic` + (validated against core metadata field names and lowercased)""" + platforms: _Validator[list[str] | None] = _Validator() + """:external:ref:`core-metadata-platform`""" + supported_platforms: _Validator[list[str] | None] = _Validator(added="1.1") + """:external:ref:`core-metadata-supported-platform`""" + summary: _Validator[str | None] = _Validator() + """:external:ref:`core-metadata-summary` (validated to contain no newlines)""" + description: _Validator[str | None] = _Validator() # TODO 2.1: can be in body + """:external:ref:`core-metadata-description`""" + description_content_type: _Validator[str | None] = _Validator(added="2.1") + """:external:ref:`core-metadata-description-content-type` (validated)""" + keywords: _Validator[list[str] | None] = _Validator() + """:external:ref:`core-metadata-keywords`""" + home_page: _Validator[str | None] = _Validator() + """:external:ref:`core-metadata-home-page`""" + download_url: _Validator[str | None] = _Validator(added="1.1") + """:external:ref:`core-metadata-download-url`""" + author: _Validator[str | None] = _Validator() + """:external:ref:`core-metadata-author`""" + author_email: _Validator[str | None] = _Validator() + """:external:ref:`core-metadata-author-email`""" + maintainer: _Validator[str | None] = _Validator(added="1.2") + """:external:ref:`core-metadata-maintainer`""" + maintainer_email: _Validator[str | None] = _Validator(added="1.2") + """:external:ref:`core-metadata-maintainer-email`""" + license: _Validator[str | None] = _Validator() + """:external:ref:`core-metadata-license`""" + license_expression: _Validator[NormalizedLicenseExpression | None] = _Validator( + added="2.4" + ) + """:external:ref:`core-metadata-license-expression`""" + license_files: _Validator[list[str] | None] = _Validator(added="2.4") + """:external:ref:`core-metadata-license-file`""" + classifiers: _Validator[list[str] | None] = _Validator(added="1.1") + """:external:ref:`core-metadata-classifier`""" + requires_dist: _Validator[list[requirements.Requirement] | None] = _Validator( + added="1.2" + ) + """:external:ref:`core-metadata-requires-dist`""" + requires_python: _Validator[specifiers.SpecifierSet | None] = _Validator( + added="1.2" + ) + """:external:ref:`core-metadata-requires-python`""" + # Because `Requires-External` allows for non-PEP 440 version specifiers, we + # don't do any processing on the values. + requires_external: _Validator[list[str] | None] = _Validator(added="1.2") + """:external:ref:`core-metadata-requires-external`""" + project_urls: _Validator[dict[str, str] | None] = _Validator(added="1.2") + """:external:ref:`core-metadata-project-url`""" + # PEP 685 lets us raise an error if an extra doesn't pass `Name` validation + # regardless of metadata version. + provides_extra: _Validator[list[utils.NormalizedName] | None] = _Validator( + added="2.1", + ) + """:external:ref:`core-metadata-provides-extra`""" + provides_dist: _Validator[list[str] | None] = _Validator(added="1.2") + """:external:ref:`core-metadata-provides-dist`""" + obsoletes_dist: _Validator[list[str] | None] = _Validator(added="1.2") + """:external:ref:`core-metadata-obsoletes-dist`""" + import_names: _Validator[list[str] | None] = _Validator(added="2.5") + """:external:ref:`core-metadata-import-name`""" + import_namespaces: _Validator[list[str] | None] = _Validator(added="2.5") + """:external:ref:`core-metadata-import-namespace`""" + requires: _Validator[list[str] | None] = _Validator(added="1.1") + """``Requires`` (deprecated)""" + provides: _Validator[list[str] | None] = _Validator(added="1.1") + """``Provides`` (deprecated)""" + obsoletes: _Validator[list[str] | None] = _Validator(added="1.1") + """``Obsoletes`` (deprecated)""" + + def as_rfc822(self) -> RFC822Message: + """ + Return an RFC822 message with the metadata. + """ + message = RFC822Message() + self._write_metadata(message) + return message + + def _write_metadata(self, message: RFC822Message) -> None: + """ + Return an RFC822 message with the metadata. + """ + for name, validator in self.__class__.__dict__.items(): + if isinstance(validator, _Validator) and name != "description": + value = getattr(self, name) + email_name = _RAW_TO_EMAIL_MAPPING[name] + if value is not None: + if email_name == "project-url": + for label, url in value.items(): + message[email_name] = f"{label}, {url}" + elif email_name == "keywords": + message[email_name] = ",".join(value) + elif email_name == "import-name" and value == []: + message[email_name] = "" + elif isinstance(value, list): + for item in value: + message[email_name] = str(item) + else: + message[email_name] = str(value) + + # The description is a special case because it is in the body of the message. + if self.description is not None: + message.set_payload(self.description) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/py.typed b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/py.typed new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/pylock.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/pylock.py new file mode 100644 index 0000000000000000000000000000000000000000..a564f15246ad65038029f8fefb48621fa64a3abd --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/pylock.py @@ -0,0 +1,635 @@ +from __future__ import annotations + +import dataclasses +import logging +import re +from collections.abc import Mapping, Sequence +from dataclasses import dataclass +from datetime import datetime +from typing import ( + TYPE_CHECKING, + Any, + Callable, + Protocol, + TypeVar, +) + +from .markers import Marker +from .specifiers import SpecifierSet +from .utils import NormalizedName, is_normalized_name +from .version import Version + +if TYPE_CHECKING: # pragma: no cover + from pathlib import Path + + from typing_extensions import Self + +_logger = logging.getLogger(__name__) + +__all__ = [ + "Package", + "PackageArchive", + "PackageDirectory", + "PackageSdist", + "PackageVcs", + "PackageWheel", + "Pylock", + "PylockUnsupportedVersionError", + "PylockValidationError", + "is_valid_pylock_path", +] + +_T = TypeVar("_T") +_T2 = TypeVar("_T2") + + +class _FromMappingProtocol(Protocol): # pragma: no cover + @classmethod + def _from_dict(cls, d: Mapping[str, Any]) -> Self: ... + + +_FromMappingProtocolT = TypeVar("_FromMappingProtocolT", bound=_FromMappingProtocol) + + +_PYLOCK_FILE_NAME_RE = re.compile(r"^pylock\.([^.]+)\.toml$") + + +def is_valid_pylock_path(path: Path) -> bool: + """Check if the given path is a valid pylock file path.""" + return path.name == "pylock.toml" or bool(_PYLOCK_FILE_NAME_RE.match(path.name)) + + +def _toml_key(key: str) -> str: + return key.replace("_", "-") + + +def _toml_value(key: str, value: Any) -> Any: # noqa: ANN401 + if isinstance(value, (Version, Marker, SpecifierSet)): + return str(value) + if isinstance(value, Sequence) and key == "environments": + return [str(v) for v in value] + return value + + +def _toml_dict_factory(data: list[tuple[str, Any]]) -> dict[str, Any]: + return { + _toml_key(key): _toml_value(key, value) + for key, value in data + if value is not None + } + + +def _get(d: Mapping[str, Any], expected_type: type[_T], key: str) -> _T | None: + """Get a value from the dictionary and verify it's the expected type.""" + if (value := d.get(key)) is None: + return None + if not isinstance(value, expected_type): + raise PylockValidationError( + f"Unexpected type {type(value).__name__} " + f"(expected {expected_type.__name__})", + context=key, + ) + return value + + +def _get_required(d: Mapping[str, Any], expected_type: type[_T], key: str) -> _T: + """Get a required value from the dictionary and verify it's the expected type.""" + if (value := _get(d, expected_type, key)) is None: + raise _PylockRequiredKeyError(key) + return value + + +def _get_sequence( + d: Mapping[str, Any], expected_item_type: type[_T], key: str +) -> Sequence[_T] | None: + """Get a list value from the dictionary and verify it's the expected items type.""" + if (value := _get(d, Sequence, key)) is None: # type: ignore[type-abstract] + return None + if isinstance(value, (str, bytes)): + # special case: str and bytes are Sequences, but we want to reject it + raise PylockValidationError( + f"Unexpected type {type(value).__name__} (expected Sequence)", + context=key, + ) + for i, item in enumerate(value): + if not isinstance(item, expected_item_type): + raise PylockValidationError( + f"Unexpected type {type(item).__name__} " + f"(expected {expected_item_type.__name__})", + context=f"{key}[{i}]", + ) + return value + + +def _get_as( + d: Mapping[str, Any], + expected_type: type[_T], + target_type: Callable[[_T], _T2], + key: str, +) -> _T2 | None: + """Get a value from the dictionary, verify it's the expected type, + and convert to the target type. + + This assumes the target_type constructor accepts the value. + """ + if (value := _get(d, expected_type, key)) is None: + return None + try: + return target_type(value) + except Exception as e: + raise PylockValidationError(e, context=key) from e + + +def _get_required_as( + d: Mapping[str, Any], + expected_type: type[_T], + target_type: Callable[[_T], _T2], + key: str, +) -> _T2: + """Get a required value from the dict, verify it's the expected type, + and convert to the target type.""" + if (value := _get_as(d, expected_type, target_type, key)) is None: + raise _PylockRequiredKeyError(key) + return value + + +def _get_sequence_as( + d: Mapping[str, Any], + expected_item_type: type[_T], + target_item_type: Callable[[_T], _T2], + key: str, +) -> list[_T2] | None: + """Get list value from dictionary and verify expected items type.""" + if (value := _get_sequence(d, expected_item_type, key)) is None: + return None + result = [] + try: + for item in value: + typed_item = target_item_type(item) + result.append(typed_item) + except Exception as e: + raise PylockValidationError(e, context=f"{key}[{len(result)}]") from e + return result + + +def _get_object( + d: Mapping[str, Any], target_type: type[_FromMappingProtocolT], key: str +) -> _FromMappingProtocolT | None: + """Get a dictionary value from the dictionary and convert it to a dataclass.""" + if (value := _get(d, Mapping, key)) is None: # type: ignore[type-abstract] + return None + try: + return target_type._from_dict(value) + except Exception as e: + raise PylockValidationError(e, context=key) from e + + +def _get_sequence_of_objects( + d: Mapping[str, Any], target_item_type: type[_FromMappingProtocolT], key: str +) -> list[_FromMappingProtocolT] | None: + """Get a list value from the dictionary and convert its items to a dataclass.""" + if (value := _get_sequence(d, Mapping, key)) is None: # type: ignore[type-abstract] + return None + result: list[_FromMappingProtocolT] = [] + try: + for item in value: + typed_item = target_item_type._from_dict(item) + result.append(typed_item) + except Exception as e: + raise PylockValidationError(e, context=f"{key}[{len(result)}]") from e + return result + + +def _get_required_sequence_of_objects( + d: Mapping[str, Any], target_item_type: type[_FromMappingProtocolT], key: str +) -> Sequence[_FromMappingProtocolT]: + """Get a required list value from the dictionary and convert its items to a + dataclass.""" + if (result := _get_sequence_of_objects(d, target_item_type, key)) is None: + raise _PylockRequiredKeyError(key) + return result + + +def _validate_normalized_name(name: str) -> NormalizedName: + """Validate that a string is a NormalizedName.""" + if not is_normalized_name(name): + raise PylockValidationError(f"Name {name!r} is not normalized") + return NormalizedName(name) + + +def _validate_path_url(path: str | None, url: str | None) -> None: + if not path and not url: + raise PylockValidationError("path or url must be provided") + + +def _validate_hashes(hashes: Mapping[str, Any]) -> Mapping[str, Any]: + if not hashes: + raise PylockValidationError("At least one hash must be provided") + if not all(isinstance(hash_val, str) for hash_val in hashes.values()): + raise PylockValidationError("Hash values must be strings") + return hashes + + +class PylockValidationError(Exception): + """Raised when when input data is not spec-compliant.""" + + context: str | None = None + message: str + + def __init__( + self, + cause: str | Exception, + *, + context: str | None = None, + ) -> None: + if isinstance(cause, PylockValidationError): + if cause.context: + self.context = ( + f"{context}.{cause.context}" if context else cause.context + ) + else: + self.context = context + self.message = cause.message + else: + self.context = context + self.message = str(cause) + + def __str__(self) -> str: + if self.context: + return f"{self.message} in {self.context!r}" + return self.message + + +class _PylockRequiredKeyError(PylockValidationError): + def __init__(self, key: str) -> None: + super().__init__("Missing required value", context=key) + + +class PylockUnsupportedVersionError(PylockValidationError): + """Raised when encountering an unsupported `lock_version`.""" + + +@dataclass(frozen=True, init=False) +class PackageVcs: + type: str + url: str | None = None + path: str | None = None + requested_revision: str | None = None + commit_id: str # type: ignore[misc] + subdirectory: str | None = None + + def __init__( + self, + *, + type: str, + url: str | None = None, + path: str | None = None, + requested_revision: str | None = None, + commit_id: str, + subdirectory: str | None = None, + ) -> None: + # In Python 3.10+ make dataclass kw_only=True and remove __init__ + object.__setattr__(self, "type", type) + object.__setattr__(self, "url", url) + object.__setattr__(self, "path", path) + object.__setattr__(self, "requested_revision", requested_revision) + object.__setattr__(self, "commit_id", commit_id) + object.__setattr__(self, "subdirectory", subdirectory) + + @classmethod + def _from_dict(cls, d: Mapping[str, Any]) -> Self: + package_vcs = cls( + type=_get_required(d, str, "type"), + url=_get(d, str, "url"), + path=_get(d, str, "path"), + requested_revision=_get(d, str, "requested-revision"), + commit_id=_get_required(d, str, "commit-id"), + subdirectory=_get(d, str, "subdirectory"), + ) + _validate_path_url(package_vcs.path, package_vcs.url) + return package_vcs + + +@dataclass(frozen=True, init=False) +class PackageDirectory: + path: str + editable: bool | None = None + subdirectory: str | None = None + + def __init__( + self, + *, + path: str, + editable: bool | None = None, + subdirectory: str | None = None, + ) -> None: + # In Python 3.10+ make dataclass kw_only=True and remove __init__ + object.__setattr__(self, "path", path) + object.__setattr__(self, "editable", editable) + object.__setattr__(self, "subdirectory", subdirectory) + + @classmethod + def _from_dict(cls, d: Mapping[str, Any]) -> Self: + return cls( + path=_get_required(d, str, "path"), + editable=_get(d, bool, "editable"), + subdirectory=_get(d, str, "subdirectory"), + ) + + +@dataclass(frozen=True, init=False) +class PackageArchive: + url: str | None = None + path: str | None = None + size: int | None = None + upload_time: datetime | None = None + hashes: Mapping[str, str] # type: ignore[misc] + subdirectory: str | None = None + + def __init__( + self, + *, + url: str | None = None, + path: str | None = None, + size: int | None = None, + upload_time: datetime | None = None, + hashes: Mapping[str, str], + subdirectory: str | None = None, + ) -> None: + # In Python 3.10+ make dataclass kw_only=True and remove __init__ + object.__setattr__(self, "url", url) + object.__setattr__(self, "path", path) + object.__setattr__(self, "size", size) + object.__setattr__(self, "upload_time", upload_time) + object.__setattr__(self, "hashes", hashes) + object.__setattr__(self, "subdirectory", subdirectory) + + @classmethod + def _from_dict(cls, d: Mapping[str, Any]) -> Self: + package_archive = cls( + url=_get(d, str, "url"), + path=_get(d, str, "path"), + size=_get(d, int, "size"), + upload_time=_get(d, datetime, "upload-time"), + hashes=_get_required_as(d, Mapping, _validate_hashes, "hashes"), # type: ignore[type-abstract] + subdirectory=_get(d, str, "subdirectory"), + ) + _validate_path_url(package_archive.path, package_archive.url) + return package_archive + + +@dataclass(frozen=True, init=False) +class PackageSdist: + name: str | None = None + upload_time: datetime | None = None + url: str | None = None + path: str | None = None + size: int | None = None + hashes: Mapping[str, str] # type: ignore[misc] + + def __init__( + self, + *, + name: str | None = None, + upload_time: datetime | None = None, + url: str | None = None, + path: str | None = None, + size: int | None = None, + hashes: Mapping[str, str], + ) -> None: + # In Python 3.10+ make dataclass kw_only=True and remove __init__ + object.__setattr__(self, "name", name) + object.__setattr__(self, "upload_time", upload_time) + object.__setattr__(self, "url", url) + object.__setattr__(self, "path", path) + object.__setattr__(self, "size", size) + object.__setattr__(self, "hashes", hashes) + + @classmethod + def _from_dict(cls, d: Mapping[str, Any]) -> Self: + package_sdist = cls( + name=_get(d, str, "name"), + upload_time=_get(d, datetime, "upload-time"), + url=_get(d, str, "url"), + path=_get(d, str, "path"), + size=_get(d, int, "size"), + hashes=_get_required_as(d, Mapping, _validate_hashes, "hashes"), # type: ignore[type-abstract] + ) + _validate_path_url(package_sdist.path, package_sdist.url) + return package_sdist + + +@dataclass(frozen=True, init=False) +class PackageWheel: + name: str | None = None + upload_time: datetime | None = None + url: str | None = None + path: str | None = None + size: int | None = None + hashes: Mapping[str, str] # type: ignore[misc] + + def __init__( + self, + *, + name: str | None = None, + upload_time: datetime | None = None, + url: str | None = None, + path: str | None = None, + size: int | None = None, + hashes: Mapping[str, str], + ) -> None: + # In Python 3.10+ make dataclass kw_only=True and remove __init__ + object.__setattr__(self, "name", name) + object.__setattr__(self, "upload_time", upload_time) + object.__setattr__(self, "url", url) + object.__setattr__(self, "path", path) + object.__setattr__(self, "size", size) + object.__setattr__(self, "hashes", hashes) + + @classmethod + def _from_dict(cls, d: Mapping[str, Any]) -> Self: + package_wheel = cls( + name=_get(d, str, "name"), + upload_time=_get(d, datetime, "upload-time"), + url=_get(d, str, "url"), + path=_get(d, str, "path"), + size=_get(d, int, "size"), + hashes=_get_required_as(d, Mapping, _validate_hashes, "hashes"), # type: ignore[type-abstract] + ) + _validate_path_url(package_wheel.path, package_wheel.url) + return package_wheel + + +@dataclass(frozen=True, init=False) +class Package: + name: NormalizedName + version: Version | None = None + marker: Marker | None = None + requires_python: SpecifierSet | None = None + dependencies: Sequence[Mapping[str, Any]] | None = None + vcs: PackageVcs | None = None + directory: PackageDirectory | None = None + archive: PackageArchive | None = None + index: str | None = None + sdist: PackageSdist | None = None + wheels: Sequence[PackageWheel] | None = None + attestation_identities: Sequence[Mapping[str, Any]] | None = None + tool: Mapping[str, Any] | None = None + + def __init__( + self, + *, + name: NormalizedName, + version: Version | None = None, + marker: Marker | None = None, + requires_python: SpecifierSet | None = None, + dependencies: Sequence[Mapping[str, Any]] | None = None, + vcs: PackageVcs | None = None, + directory: PackageDirectory | None = None, + archive: PackageArchive | None = None, + index: str | None = None, + sdist: PackageSdist | None = None, + wheels: Sequence[PackageWheel] | None = None, + attestation_identities: Sequence[Mapping[str, Any]] | None = None, + tool: Mapping[str, Any] | None = None, + ) -> None: + # In Python 3.10+ make dataclass kw_only=True and remove __init__ + object.__setattr__(self, "name", name) + object.__setattr__(self, "version", version) + object.__setattr__(self, "marker", marker) + object.__setattr__(self, "requires_python", requires_python) + object.__setattr__(self, "dependencies", dependencies) + object.__setattr__(self, "vcs", vcs) + object.__setattr__(self, "directory", directory) + object.__setattr__(self, "archive", archive) + object.__setattr__(self, "index", index) + object.__setattr__(self, "sdist", sdist) + object.__setattr__(self, "wheels", wheels) + object.__setattr__(self, "attestation_identities", attestation_identities) + object.__setattr__(self, "tool", tool) + + @classmethod + def _from_dict(cls, d: Mapping[str, Any]) -> Self: + package = cls( + name=_get_required_as(d, str, _validate_normalized_name, "name"), + version=_get_as(d, str, Version, "version"), + requires_python=_get_as(d, str, SpecifierSet, "requires-python"), + dependencies=_get_sequence(d, Mapping, "dependencies"), # type: ignore[type-abstract] + marker=_get_as(d, str, Marker, "marker"), + vcs=_get_object(d, PackageVcs, "vcs"), + directory=_get_object(d, PackageDirectory, "directory"), + archive=_get_object(d, PackageArchive, "archive"), + index=_get(d, str, "index"), + sdist=_get_object(d, PackageSdist, "sdist"), + wheels=_get_sequence_of_objects(d, PackageWheel, "wheels"), + attestation_identities=_get_sequence(d, Mapping, "attestation-identities"), # type: ignore[type-abstract] + tool=_get(d, Mapping, "tool"), # type: ignore[type-abstract] + ) + distributions = bool(package.sdist) + len(package.wheels or []) + direct_urls = ( + bool(package.vcs) + bool(package.directory) + bool(package.archive) + ) + if distributions > 0 and direct_urls > 0: + raise PylockValidationError( + "None of vcs, directory, archive must be set if sdist or wheels are set" + ) + if distributions == 0 and direct_urls != 1: + raise PylockValidationError( + "Exactly one of vcs, directory, archive must be set " + "if sdist and wheels are not set" + ) + try: + for i, attestation_identity in enumerate( # noqa: B007 + package.attestation_identities or [] + ): + _get_required(attestation_identity, str, "kind") + except Exception as e: + raise PylockValidationError( + e, context=f"attestation-identities[{i}]" + ) from e + return package + + @property + def is_direct(self) -> bool: + return not (self.sdist or self.wheels) + + +@dataclass(frozen=True, init=False) +class Pylock: + """A class representing a pylock file.""" + + lock_version: Version + environments: Sequence[Marker] | None = None + requires_python: SpecifierSet | None = None + extras: Sequence[NormalizedName] | None = None + dependency_groups: Sequence[str] | None = None + default_groups: Sequence[str] | None = None + created_by: str # type: ignore[misc] + packages: Sequence[Package] # type: ignore[misc] + tool: Mapping[str, Any] | None = None + + def __init__( + self, + *, + lock_version: Version, + environments: Sequence[Marker] | None = None, + requires_python: SpecifierSet | None = None, + extras: Sequence[NormalizedName] | None = None, + dependency_groups: Sequence[str] | None = None, + default_groups: Sequence[str] | None = None, + created_by: str, + packages: Sequence[Package], + tool: Mapping[str, Any] | None = None, + ) -> None: + # In Python 3.10+ make dataclass kw_only=True and remove __init__ + object.__setattr__(self, "lock_version", lock_version) + object.__setattr__(self, "environments", environments) + object.__setattr__(self, "requires_python", requires_python) + object.__setattr__(self, "extras", extras) + object.__setattr__(self, "dependency_groups", dependency_groups) + object.__setattr__(self, "default_groups", default_groups) + object.__setattr__(self, "created_by", created_by) + object.__setattr__(self, "packages", packages) + object.__setattr__(self, "tool", tool) + + @classmethod + def _from_dict(cls, d: Mapping[str, Any]) -> Self: + pylock = cls( + lock_version=_get_required_as(d, str, Version, "lock-version"), + environments=_get_sequence_as(d, str, Marker, "environments"), + extras=_get_sequence_as(d, str, _validate_normalized_name, "extras"), + dependency_groups=_get_sequence(d, str, "dependency-groups"), + default_groups=_get_sequence(d, str, "default-groups"), + created_by=_get_required(d, str, "created-by"), + requires_python=_get_as(d, str, SpecifierSet, "requires-python"), + packages=_get_required_sequence_of_objects(d, Package, "packages"), + tool=_get(d, Mapping, "tool"), # type: ignore[type-abstract] + ) + if not Version("1") <= pylock.lock_version < Version("2"): + raise PylockUnsupportedVersionError( + f"pylock version {pylock.lock_version} is not supported" + ) + if pylock.lock_version > Version("1.0"): + _logger.warning( + "pylock minor version %s is not supported", pylock.lock_version + ) + return pylock + + @classmethod + def from_dict(cls, d: Mapping[str, Any], /) -> Self: + """Create and validate a Pylock instance from a TOML dictionary. + + Raises :class:`PylockValidationError` if the input data is not + spec-compliant. + """ + return cls._from_dict(d) + + def to_dict(self) -> Mapping[str, Any]: + """Convert the Pylock instance to a TOML dictionary.""" + return dataclasses.asdict(self, dict_factory=_toml_dict_factory) + + def validate(self) -> None: + """Validate the Pylock instance against the specification. + + Raises :class:`PylockValidationError` otherwise.""" + self.from_dict(self.to_dict()) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/requirements.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/requirements.py new file mode 100644 index 0000000000000000000000000000000000000000..3079be69bf880f47e64dbf62993f0e54754b7315 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/requirements.py @@ -0,0 +1,86 @@ +# This file is dual licensed under the terms of the Apache License, Version +# 2.0, and the BSD License. See the LICENSE file in the root of this repository +# for complete details. +from __future__ import annotations + +from typing import Iterator + +from ._parser import parse_requirement as _parse_requirement +from ._tokenizer import ParserSyntaxError +from .markers import Marker, _normalize_extra_values +from .specifiers import SpecifierSet +from .utils import canonicalize_name + + +class InvalidRequirement(ValueError): + """ + An invalid requirement was found, users should refer to PEP 508. + """ + + +class Requirement: + """Parse a requirement. + + Parse a given requirement string into its parts, such as name, specifier, + URL, and extras. Raises InvalidRequirement on a badly-formed requirement + string. + """ + + # TODO: Can we test whether something is contained within a requirement? + # If so how do we do that? Do we need to test against the _name_ of + # the thing as well as the version? What about the markers? + # TODO: Can we normalize the name and extra name? + + def __init__(self, requirement_string: str) -> None: + try: + parsed = _parse_requirement(requirement_string) + except ParserSyntaxError as e: + raise InvalidRequirement(str(e)) from e + + self.name: str = parsed.name + self.url: str | None = parsed.url or None + self.extras: set[str] = set(parsed.extras or []) + self.specifier: SpecifierSet = SpecifierSet(parsed.specifier) + self.marker: Marker | None = None + if parsed.marker is not None: + self.marker = Marker.__new__(Marker) + self.marker._markers = _normalize_extra_values(parsed.marker) + + def _iter_parts(self, name: str) -> Iterator[str]: + yield name + + if self.extras: + formatted_extras = ",".join(sorted(self.extras)) + yield f"[{formatted_extras}]" + + if self.specifier: + yield str(self.specifier) + + if self.url: + yield f" @ {self.url}" + if self.marker: + yield " " + + if self.marker: + yield f"; {self.marker}" + + def __str__(self) -> str: + return "".join(self._iter_parts(self.name)) + + def __repr__(self) -> str: + return f"<{self.__class__.__name__}('{self}')>" + + def __hash__(self) -> int: + return hash(tuple(self._iter_parts(canonicalize_name(self.name)))) + + def __eq__(self, other: object) -> bool: + if not isinstance(other, Requirement): + return NotImplemented + + return ( + canonicalize_name(self.name) == canonicalize_name(other.name) + and self.extras == other.extras + and self.specifier == other.specifier + and self.url == other.url + and self.marker == other.marker + ) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/specifiers.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/specifiers.py new file mode 100644 index 0000000000000000000000000000000000000000..5d26b0d1ae2d21b77e24b692d5a7e1fd01296edc --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/specifiers.py @@ -0,0 +1,1068 @@ +# This file is dual licensed under the terms of the Apache License, Version +# 2.0, and the BSD License. See the LICENSE file in the root of this repository +# for complete details. +""" +.. testsetup:: + + from packaging.specifiers import Specifier, SpecifierSet, InvalidSpecifier + from packaging.version import Version +""" + +from __future__ import annotations + +import abc +import itertools +import re +from typing import Callable, Final, Iterable, Iterator, TypeVar, Union + +from .utils import canonicalize_version +from .version import InvalidVersion, Version + +UnparsedVersion = Union[Version, str] +UnparsedVersionVar = TypeVar("UnparsedVersionVar", bound=UnparsedVersion) +CallableOperator = Callable[[Version, str], bool] + + +def _coerce_version(version: UnparsedVersion) -> Version | None: + if not isinstance(version, Version): + try: + version = Version(version) + except InvalidVersion: + return None + return version + + +def _public_version(version: Version) -> Version: + return version.__replace__(local=None) + + +def _base_version(version: Version) -> Version: + return version.__replace__(pre=None, post=None, dev=None, local=None) + + +class InvalidSpecifier(ValueError): + """ + Raised when attempting to create a :class:`Specifier` with a specifier + string that is invalid. + + >>> Specifier("lolwat") + Traceback (most recent call last): + ... + packaging.specifiers.InvalidSpecifier: Invalid specifier: 'lolwat' + """ + + +class BaseSpecifier(metaclass=abc.ABCMeta): + __slots__ = () + __match_args__ = ("_str",) + + @property + def _str(self) -> str: + """Internal property for match_args""" + return str(self) + + @abc.abstractmethod + def __str__(self) -> str: + """ + Returns the str representation of this Specifier-like object. This + should be representative of the Specifier itself. + """ + + @abc.abstractmethod + def __hash__(self) -> int: + """ + Returns a hash value for this Specifier-like object. + """ + + @abc.abstractmethod + def __eq__(self, other: object) -> bool: + """ + Returns a boolean representing whether or not the two Specifier-like + objects are equal. + + :param other: The other object to check against. + """ + + @property + @abc.abstractmethod + def prereleases(self) -> bool | None: + """Whether or not pre-releases as a whole are allowed. + + This can be set to either ``True`` or ``False`` to explicitly enable or disable + prereleases or it can be set to ``None`` (the default) to use default semantics. + """ + + @prereleases.setter # noqa: B027 + def prereleases(self, value: bool) -> None: + """Setter for :attr:`prereleases`. + + :param value: The value to set. + """ + + @abc.abstractmethod + def contains(self, item: str, prereleases: bool | None = None) -> bool: + """ + Determines if the given item is contained within this specifier. + """ + + @abc.abstractmethod + def filter( + self, iterable: Iterable[UnparsedVersionVar], prereleases: bool | None = None + ) -> Iterator[UnparsedVersionVar]: + """ + Takes an iterable of items and filters them so that only items which + are contained within this specifier are allowed in it. + """ + + +class Specifier(BaseSpecifier): + """This class abstracts handling of version specifiers. + + .. tip:: + + It is generally not required to instantiate this manually. You should instead + prefer to work with :class:`SpecifierSet` instead, which can parse + comma-separated version specifiers (which is what package metadata contains). + """ + + __slots__ = ("_prereleases", "_spec", "_spec_version") + + _operator_regex_str = r""" + (?P(~=|==|!=|<=|>=|<|>|===)) + """ + _version_regex_str = r""" + (?P + (?: + # The identity operators allow for an escape hatch that will + # do an exact string match of the version you wish to install. + # This will not be parsed by PEP 440 and we cannot determine + # any semantic meaning from it. This operator is discouraged + # but included entirely as an escape hatch. + (?<====) # Only match for the identity operator + \s* + [^\s;)]* # The arbitrary version can be just about anything, + # we match everything except for whitespace, a + # semi-colon for marker support, and a closing paren + # since versions can be enclosed in them. + ) + | + (?: + # The (non)equality operators allow for wild card and local + # versions to be specified so we have to define these two + # operators separately to enable that. + (?<===|!=) # Only match for equals and not equals + + \s* + v? + (?:[0-9]+!)? # epoch + [0-9]+(?:\.[0-9]+)* # release + + # You cannot use a wild card and a pre-release, post-release, a dev or + # local version together so group them with a | and make them optional. + (?: + \.\* # Wild card syntax of .* + | + (?: # pre release + [-_\.]? + (alpha|beta|preview|pre|a|b|c|rc) + [-_\.]? + [0-9]* + )? + (?: # post release + (?:-[0-9]+)|(?:[-_\.]?(post|rev|r)[-_\.]?[0-9]*) + )? + (?:[-_\.]?dev[-_\.]?[0-9]*)? # dev release + (?:\+[a-z0-9]+(?:[-_\.][a-z0-9]+)*)? # local + )? + ) + | + (?: + # The compatible operator requires at least two digits in the + # release segment. + (?<=~=) # Only match for the compatible operator + + \s* + v? + (?:[0-9]+!)? # epoch + [0-9]+(?:\.[0-9]+)+ # release (We have a + instead of a *) + (?: # pre release + [-_\.]? + (alpha|beta|preview|pre|a|b|c|rc) + [-_\.]? + [0-9]* + )? + (?: # post release + (?:-[0-9]+)|(?:[-_\.]?(post|rev|r)[-_\.]?[0-9]*) + )? + (?:[-_\.]?dev[-_\.]?[0-9]*)? # dev release + ) + | + (?: + # All other operators only allow a sub set of what the + # (non)equality operators do. Specifically they do not allow + # local versions to be specified nor do they allow the prefix + # matching wild cards. + (?=": "greater_than_equal", + "<": "less_than", + ">": "greater_than", + "===": "arbitrary", + } + + def __init__(self, spec: str = "", prereleases: bool | None = None) -> None: + """Initialize a Specifier instance. + + :param spec: + The string representation of a specifier which will be parsed and + normalized before use. + :param prereleases: + This tells the specifier if it should accept prerelease versions if + applicable or not. The default of ``None`` will autodetect it from the + given specifiers. + :raises InvalidSpecifier: + If the given specifier is invalid (i.e. bad syntax). + """ + match = self._regex.fullmatch(spec) + if not match: + raise InvalidSpecifier(f"Invalid specifier: {spec!r}") + + self._spec: tuple[str, str] = ( + match.group("operator").strip(), + match.group("version").strip(), + ) + + # Store whether or not this Specifier should accept prereleases + self._prereleases = prereleases + + # Specifier version cache + self._spec_version: tuple[str, Version] | None = None + + def _get_spec_version(self, version: str) -> Version | None: + """One element cache, as only one spec Version is needed per Specifier.""" + if self._spec_version is not None and self._spec_version[0] == version: + return self._spec_version[1] + + version_specifier = _coerce_version(version) + if version_specifier is None: + return None + + self._spec_version = (version, version_specifier) + return version_specifier + + def _require_spec_version(self, version: str) -> Version: + """Get spec version, asserting it's valid (not for === operator). + + This method should only be called for operators where version + strings are guaranteed to be valid PEP 440 versions (not ===). + """ + spec_version = self._get_spec_version(version) + assert spec_version is not None + return spec_version + + @property + def prereleases(self) -> bool | None: + # If there is an explicit prereleases set for this, then we'll just + # blindly use that. + if self._prereleases is not None: + return self._prereleases + + # Only the "!=" operator does not imply prereleases when + # the version in the specifier is a prerelease. + operator, version_str = self._spec + if operator != "!=": + # The == specifier with trailing .* cannot include prereleases + # e.g. "==1.0a1.*" is not valid. + if operator == "==" and version_str.endswith(".*"): + return False + + # "===" can have arbitrary string versions, so we cannot parse + # those, we take prereleases as unknown (None) for those. + version = self._get_spec_version(version_str) + if version is None: + return None + + # For all other operators, use the check if spec Version + # object implies pre-releases. + if version.is_prerelease: + return True + + return False + + @prereleases.setter + def prereleases(self, value: bool | None) -> None: + self._prereleases = value + + @property + def operator(self) -> str: + """The operator of this specifier. + + >>> Specifier("==1.2.3").operator + '==' + """ + return self._spec[0] + + @property + def version(self) -> str: + """The version of this specifier. + + >>> Specifier("==1.2.3").version + '1.2.3' + """ + return self._spec[1] + + def __repr__(self) -> str: + """A representation of the Specifier that shows all internal state. + + >>> Specifier('>=1.0.0') + =1.0.0')> + >>> Specifier('>=1.0.0', prereleases=False) + =1.0.0', prereleases=False)> + >>> Specifier('>=1.0.0', prereleases=True) + =1.0.0', prereleases=True)> + """ + pre = ( + f", prereleases={self.prereleases!r}" + if self._prereleases is not None + else "" + ) + + return f"<{self.__class__.__name__}({str(self)!r}{pre})>" + + def __str__(self) -> str: + """A string representation of the Specifier that can be round-tripped. + + >>> str(Specifier('>=1.0.0')) + '>=1.0.0' + >>> str(Specifier('>=1.0.0', prereleases=False)) + '>=1.0.0' + """ + return "{}{}".format(*self._spec) + + @property + def _canonical_spec(self) -> tuple[str, str]: + operator, version = self._spec + if operator == "===" or version.endswith(".*"): + return operator, version + + spec_version = self._require_spec_version(version) + + canonical_version = canonicalize_version( + spec_version, strip_trailing_zero=(operator != "~=") + ) + + return operator, canonical_version + + def __hash__(self) -> int: + return hash(self._canonical_spec) + + def __eq__(self, other: object) -> bool: + """Whether or not the two Specifier-like objects are equal. + + :param other: The other object to check against. + + The value of :attr:`prereleases` is ignored. + + >>> Specifier("==1.2.3") == Specifier("== 1.2.3.0") + True + >>> (Specifier("==1.2.3", prereleases=False) == + ... Specifier("==1.2.3", prereleases=True)) + True + >>> Specifier("==1.2.3") == "==1.2.3" + True + >>> Specifier("==1.2.3") == Specifier("==1.2.4") + False + >>> Specifier("==1.2.3") == Specifier("~=1.2.3") + False + """ + if isinstance(other, str): + try: + other = self.__class__(str(other)) + except InvalidSpecifier: + return NotImplemented + elif not isinstance(other, self.__class__): + return NotImplemented + + return self._canonical_spec == other._canonical_spec + + def _get_operator(self, op: str) -> CallableOperator: + operator_callable: CallableOperator = getattr( + self, f"_compare_{self._operators[op]}" + ) + return operator_callable + + def _compare_compatible(self, prospective: Version, spec: str) -> bool: + # Compatible releases have an equivalent combination of >= and ==. That + # is that ~=2.2 is equivalent to >=2.2,==2.*. This allows us to + # implement this in terms of the other specifiers instead of + # implementing it ourselves. The only thing we need to do is construct + # the other specifiers. + + # We want everything but the last item in the version, but we want to + # ignore suffix segments. + prefix = _version_join( + list(itertools.takewhile(_is_not_suffix, _version_split(spec)))[:-1] + ) + + # Add the prefix notation to the end of our string + prefix += ".*" + + return self._get_operator(">=")(prospective, spec) and self._get_operator("==")( + prospective, prefix + ) + + def _compare_equal(self, prospective: Version, spec: str) -> bool: + # We need special logic to handle prefix matching + if spec.endswith(".*"): + # In the case of prefix matching we want to ignore local segment. + normalized_prospective = canonicalize_version( + _public_version(prospective), strip_trailing_zero=False + ) + # Get the normalized version string ignoring the trailing .* + normalized_spec = canonicalize_version(spec[:-2], strip_trailing_zero=False) + # Split the spec out by bangs and dots, and pretend that there is + # an implicit dot in between a release segment and a pre-release segment. + split_spec = _version_split(normalized_spec) + + # Split the prospective version out by bangs and dots, and pretend + # that there is an implicit dot in between a release segment and + # a pre-release segment. + split_prospective = _version_split(normalized_prospective) + + # 0-pad the prospective version before shortening it to get the correct + # shortened version. + padded_prospective, _ = _pad_version(split_prospective, split_spec) + + # Shorten the prospective version to be the same length as the spec + # so that we can determine if the specifier is a prefix of the + # prospective version or not. + shortened_prospective = padded_prospective[: len(split_spec)] + + return shortened_prospective == split_spec + else: + # Convert our spec string into a Version + spec_version = self._require_spec_version(spec) + + # If the specifier does not have a local segment, then we want to + # act as if the prospective version also does not have a local + # segment. + if not spec_version.local: + prospective = _public_version(prospective) + + return prospective == spec_version + + def _compare_not_equal(self, prospective: Version, spec: str) -> bool: + return not self._compare_equal(prospective, spec) + + def _compare_less_than_equal(self, prospective: Version, spec: str) -> bool: + # NB: Local version identifiers are NOT permitted in the version + # specifier, so local version labels can be universally removed from + # the prospective version. + return _public_version(prospective) <= self._require_spec_version(spec) + + def _compare_greater_than_equal(self, prospective: Version, spec: str) -> bool: + # NB: Local version identifiers are NOT permitted in the version + # specifier, so local version labels can be universally removed from + # the prospective version. + return _public_version(prospective) >= self._require_spec_version(spec) + + def _compare_less_than(self, prospective: Version, spec_str: str) -> bool: + # Convert our spec to a Version instance, since we'll want to work with + # it as a version. + spec = self._require_spec_version(spec_str) + + # Check to see if the prospective version is less than the spec + # version. If it's not we can short circuit and just return False now + # instead of doing extra unneeded work. + if not prospective < spec: + return False + + # This special case is here so that, unless the specifier itself + # includes is a pre-release version, that we do not accept pre-release + # versions for the version mentioned in the specifier (e.g. <3.1 should + # not match 3.1.dev0, but should match 3.0.dev0). + if ( + not spec.is_prerelease + and prospective.is_prerelease + and _base_version(prospective) == _base_version(spec) + ): + return False + + # If we've gotten to here, it means that prospective version is both + # less than the spec version *and* it's not a pre-release of the same + # version in the spec. + return True + + def _compare_greater_than(self, prospective: Version, spec_str: str) -> bool: + # Convert our spec to a Version instance, since we'll want to work with + # it as a version. + spec = self._require_spec_version(spec_str) + + # Check to see if the prospective version is greater than the spec + # version. If it's not we can short circuit and just return False now + # instead of doing extra unneeded work. + if not prospective > spec: + return False + + # This special case is here so that, unless the specifier itself + # includes is a post-release version, that we do not accept + # post-release versions for the version mentioned in the specifier + # (e.g. >3.1 should not match 3.0.post0, but should match 3.2.post0). + if ( + not spec.is_postrelease + and prospective.is_postrelease + and _base_version(prospective) == _base_version(spec) + ): + return False + + # Ensure that we do not allow a local version of the version mentioned + # in the specifier, which is technically greater than, to match. + if prospective.local is not None and _base_version( + prospective + ) == _base_version(spec): + return False + + # If we've gotten to here, it means that prospective version is both + # greater than the spec version *and* it's not a pre-release of the + # same version in the spec. + return True + + def _compare_arbitrary(self, prospective: Version | str, spec: str) -> bool: + return str(prospective).lower() == str(spec).lower() + + def __contains__(self, item: str | Version) -> bool: + """Return whether or not the item is contained in this specifier. + + :param item: The item to check for. + + This is used for the ``in`` operator and behaves the same as + :meth:`contains` with no ``prereleases`` argument passed. + + >>> "1.2.3" in Specifier(">=1.2.3") + True + >>> Version("1.2.3") in Specifier(">=1.2.3") + True + >>> "1.0.0" in Specifier(">=1.2.3") + False + >>> "1.3.0a1" in Specifier(">=1.2.3") + True + >>> "1.3.0a1" in Specifier(">=1.2.3", prereleases=True) + True + """ + return self.contains(item) + + def contains(self, item: UnparsedVersion, prereleases: bool | None = None) -> bool: + """Return whether or not the item is contained in this specifier. + + :param item: + The item to check for, which can be a version string or a + :class:`Version` instance. + :param prereleases: + Whether or not to match prereleases with this Specifier. If set to + ``None`` (the default), it will follow the recommendation from + :pep:`440` and match prereleases, as there are no other versions. + + >>> Specifier(">=1.2.3").contains("1.2.3") + True + >>> Specifier(">=1.2.3").contains(Version("1.2.3")) + True + >>> Specifier(">=1.2.3").contains("1.0.0") + False + >>> Specifier(">=1.2.3").contains("1.3.0a1") + True + >>> Specifier(">=1.2.3", prereleases=False).contains("1.3.0a1") + False + >>> Specifier(">=1.2.3").contains("1.3.0a1") + True + """ + + return bool(list(self.filter([item], prereleases=prereleases))) + + def filter( + self, iterable: Iterable[UnparsedVersionVar], prereleases: bool | None = None + ) -> Iterator[UnparsedVersionVar]: + """Filter items in the given iterable, that match the specifier. + + :param iterable: + An iterable that can contain version strings and :class:`Version` instances. + The items in the iterable will be filtered according to the specifier. + :param prereleases: + Whether or not to allow prereleases in the returned iterator. If set to + ``None`` (the default), it will follow the recommendation from :pep:`440` + and match prereleases if there are no other versions. + + >>> list(Specifier(">=1.2.3").filter(["1.2", "1.3", "1.5a1"])) + ['1.3'] + >>> list(Specifier(">=1.2.3").filter(["1.2", "1.2.3", "1.3", Version("1.4")])) + ['1.2.3', '1.3', ] + >>> list(Specifier(">=1.2.3").filter(["1.2", "1.5a1"])) + ['1.5a1'] + >>> list(Specifier(">=1.2.3").filter(["1.3", "1.5a1"], prereleases=True)) + ['1.3', '1.5a1'] + >>> list(Specifier(">=1.2.3", prereleases=True).filter(["1.3", "1.5a1"])) + ['1.3', '1.5a1'] + """ + prereleases_versions = [] + found_non_prereleases = False + + # Determine if to include prereleases by default + include_prereleases = ( + prereleases if prereleases is not None else self.prereleases + ) + + # Get the matching operator + operator_callable = self._get_operator(self.operator) + + # Filter versions + for version in iterable: + parsed_version = _coerce_version(version) + if parsed_version is None: + # === operator can match arbitrary (non-version) strings + if self.operator == "===" and self._compare_arbitrary( + version, self.version + ): + yield version + elif operator_callable(parsed_version, self.version): + # If it's not a prerelease or prereleases are allowed, yield it directly + if not parsed_version.is_prerelease or include_prereleases: + found_non_prereleases = True + yield version + # Otherwise collect prereleases for potential later use + elif prereleases is None and self._prereleases is not False: + prereleases_versions.append(version) + + # If no non-prereleases were found and prereleases weren't + # explicitly forbidden, yield the collected prereleases + if ( + not found_non_prereleases + and prereleases is None + and self._prereleases is not False + ): + yield from prereleases_versions + + +_prefix_regex = re.compile(r"([0-9]+)((?:a|b|c|rc)[0-9]+)") + + +def _version_split(version: str) -> list[str]: + """Split version into components. + + The split components are intended for version comparison. The logic does + not attempt to retain the original version string, so joining the + components back with :func:`_version_join` may not produce the original + version string. + """ + result: list[str] = [] + + epoch, _, rest = version.rpartition("!") + result.append(epoch or "0") + + for item in rest.split("."): + match = _prefix_regex.fullmatch(item) + if match: + result.extend(match.groups()) + else: + result.append(item) + return result + + +def _version_join(components: list[str]) -> str: + """Join split version components into a version string. + + This function assumes the input came from :func:`_version_split`, where the + first component must be the epoch (either empty or numeric), and all other + components numeric. + """ + epoch, *rest = components + return f"{epoch}!{'.'.join(rest)}" + + +def _is_not_suffix(segment: str) -> bool: + return not any( + segment.startswith(prefix) for prefix in ("dev", "a", "b", "rc", "post") + ) + + +def _pad_version(left: list[str], right: list[str]) -> tuple[list[str], list[str]]: + left_split, right_split = [], [] + + # Get the release segment of our versions + left_split.append(list(itertools.takewhile(lambda x: x.isdigit(), left))) + right_split.append(list(itertools.takewhile(lambda x: x.isdigit(), right))) + + # Get the rest of our versions + left_split.append(left[len(left_split[0]) :]) + right_split.append(right[len(right_split[0]) :]) + + # Insert our padding + left_split.insert(1, ["0"] * max(0, len(right_split[0]) - len(left_split[0]))) + right_split.insert(1, ["0"] * max(0, len(left_split[0]) - len(right_split[0]))) + + return ( + list(itertools.chain.from_iterable(left_split)), + list(itertools.chain.from_iterable(right_split)), + ) + + +class SpecifierSet(BaseSpecifier): + """This class abstracts handling of a set of version specifiers. + + It can be passed a single specifier (``>=3.0``), a comma-separated list of + specifiers (``>=3.0,!=3.1``), or no specifier at all. + """ + + __slots__ = ("_prereleases", "_specs") + + def __init__( + self, + specifiers: str | Iterable[Specifier] = "", + prereleases: bool | None = None, + ) -> None: + """Initialize a SpecifierSet instance. + + :param specifiers: + The string representation of a specifier or a comma-separated list of + specifiers which will be parsed and normalized before use. + May also be an iterable of ``Specifier`` instances, which will be used + as is. + :param prereleases: + This tells the SpecifierSet if it should accept prerelease versions if + applicable or not. The default of ``None`` will autodetect it from the + given specifiers. + + :raises InvalidSpecifier: + If the given ``specifiers`` are not parseable than this exception will be + raised. + """ + + if isinstance(specifiers, str): + # Split on `,` to break each individual specifier into its own item, and + # strip each item to remove leading/trailing whitespace. + split_specifiers = [s.strip() for s in specifiers.split(",") if s.strip()] + + # Make each individual specifier a Specifier and save in a frozen set + # for later. + self._specs = frozenset(map(Specifier, split_specifiers)) + else: + # Save the supplied specifiers in a frozen set. + self._specs = frozenset(specifiers) + + # Store our prereleases value so we can use it later to determine if + # we accept prereleases or not. + self._prereleases = prereleases + + @property + def prereleases(self) -> bool | None: + # If we have been given an explicit prerelease modifier, then we'll + # pass that through here. + if self._prereleases is not None: + return self._prereleases + + # If we don't have any specifiers, and we don't have a forced value, + # then we'll just return None since we don't know if this should have + # pre-releases or not. + if not self._specs: + return None + + # Otherwise we'll see if any of the given specifiers accept + # prereleases, if any of them do we'll return True, otherwise False. + if any(s.prereleases for s in self._specs): + return True + + return None + + @prereleases.setter + def prereleases(self, value: bool | None) -> None: + self._prereleases = value + + def __repr__(self) -> str: + """A representation of the specifier set that shows all internal state. + + Note that the ordering of the individual specifiers within the set may not + match the input string. + + >>> SpecifierSet('>=1.0.0,!=2.0.0') + =1.0.0')> + >>> SpecifierSet('>=1.0.0,!=2.0.0', prereleases=False) + =1.0.0', prereleases=False)> + >>> SpecifierSet('>=1.0.0,!=2.0.0', prereleases=True) + =1.0.0', prereleases=True)> + """ + pre = ( + f", prereleases={self.prereleases!r}" + if self._prereleases is not None + else "" + ) + + return f"" + + def __str__(self) -> str: + """A string representation of the specifier set that can be round-tripped. + + Note that the ordering of the individual specifiers within the set may not + match the input string. + + >>> str(SpecifierSet(">=1.0.0,!=1.0.1")) + '!=1.0.1,>=1.0.0' + >>> str(SpecifierSet(">=1.0.0,!=1.0.1", prereleases=False)) + '!=1.0.1,>=1.0.0' + """ + return ",".join(sorted(str(s) for s in self._specs)) + + def __hash__(self) -> int: + return hash(self._specs) + + def __and__(self, other: SpecifierSet | str) -> SpecifierSet: + """Return a SpecifierSet which is a combination of the two sets. + + :param other: The other object to combine with. + + >>> SpecifierSet(">=1.0.0,!=1.0.1") & '<=2.0.0,!=2.0.1' + =1.0.0')> + >>> SpecifierSet(">=1.0.0,!=1.0.1") & SpecifierSet('<=2.0.0,!=2.0.1') + =1.0.0')> + """ + if isinstance(other, str): + other = SpecifierSet(other) + elif not isinstance(other, SpecifierSet): + return NotImplemented + + specifier = SpecifierSet() + specifier._specs = frozenset(self._specs | other._specs) + + if self._prereleases is None and other._prereleases is not None: + specifier._prereleases = other._prereleases + elif ( + self._prereleases is not None and other._prereleases is None + ) or self._prereleases == other._prereleases: + specifier._prereleases = self._prereleases + else: + raise ValueError( + "Cannot combine SpecifierSets with True and False prerelease overrides." + ) + + return specifier + + def __eq__(self, other: object) -> bool: + """Whether or not the two SpecifierSet-like objects are equal. + + :param other: The other object to check against. + + The value of :attr:`prereleases` is ignored. + + >>> SpecifierSet(">=1.0.0,!=1.0.1") == SpecifierSet(">=1.0.0,!=1.0.1") + True + >>> (SpecifierSet(">=1.0.0,!=1.0.1", prereleases=False) == + ... SpecifierSet(">=1.0.0,!=1.0.1", prereleases=True)) + True + >>> SpecifierSet(">=1.0.0,!=1.0.1") == ">=1.0.0,!=1.0.1" + True + >>> SpecifierSet(">=1.0.0,!=1.0.1") == SpecifierSet(">=1.0.0") + False + >>> SpecifierSet(">=1.0.0,!=1.0.1") == SpecifierSet(">=1.0.0,!=1.0.2") + False + """ + if isinstance(other, (str, Specifier)): + other = SpecifierSet(str(other)) + elif not isinstance(other, SpecifierSet): + return NotImplemented + + return self._specs == other._specs + + def __len__(self) -> int: + """Returns the number of specifiers in this specifier set.""" + return len(self._specs) + + def __iter__(self) -> Iterator[Specifier]: + """ + Returns an iterator over all the underlying :class:`Specifier` instances + in this specifier set. + + >>> sorted(SpecifierSet(">=1.0.0,!=1.0.1"), key=str) + [, =1.0.0')>] + """ + return iter(self._specs) + + def __contains__(self, item: UnparsedVersion) -> bool: + """Return whether or not the item is contained in this specifier. + + :param item: The item to check for. + + This is used for the ``in`` operator and behaves the same as + :meth:`contains` with no ``prereleases`` argument passed. + + >>> "1.2.3" in SpecifierSet(">=1.0.0,!=1.0.1") + True + >>> Version("1.2.3") in SpecifierSet(">=1.0.0,!=1.0.1") + True + >>> "1.0.1" in SpecifierSet(">=1.0.0,!=1.0.1") + False + >>> "1.3.0a1" in SpecifierSet(">=1.0.0,!=1.0.1") + True + >>> "1.3.0a1" in SpecifierSet(">=1.0.0,!=1.0.1", prereleases=True) + True + """ + return self.contains(item) + + def contains( + self, + item: UnparsedVersion, + prereleases: bool | None = None, + installed: bool | None = None, + ) -> bool: + """Return whether or not the item is contained in this SpecifierSet. + + :param item: + The item to check for, which can be a version string or a + :class:`Version` instance. + :param prereleases: + Whether or not to match prereleases with this SpecifierSet. If set to + ``None`` (the default), it will follow the recommendation from :pep:`440` + and match prereleases, as there are no other versions. + :param installed: + Whether or not the item is installed. If set to ``True``, it will + accept prerelease versions even if the specifier does not allow them. + + >>> SpecifierSet(">=1.0.0,!=1.0.1").contains("1.2.3") + True + >>> SpecifierSet(">=1.0.0,!=1.0.1").contains(Version("1.2.3")) + True + >>> SpecifierSet(">=1.0.0,!=1.0.1").contains("1.0.1") + False + >>> SpecifierSet(">=1.0.0,!=1.0.1").contains("1.3.0a1") + True + >>> SpecifierSet(">=1.0.0,!=1.0.1", prereleases=False).contains("1.3.0a1") + False + >>> SpecifierSet(">=1.0.0,!=1.0.1").contains("1.3.0a1", prereleases=True) + True + """ + version = _coerce_version(item) + + if version is not None and installed and version.is_prerelease: + prereleases = True + + check_item = item if version is None else version + return bool(list(self.filter([check_item], prereleases=prereleases))) + + def filter( + self, iterable: Iterable[UnparsedVersionVar], prereleases: bool | None = None + ) -> Iterator[UnparsedVersionVar]: + """Filter items in the given iterable, that match the specifiers in this set. + + :param iterable: + An iterable that can contain version strings and :class:`Version` instances. + The items in the iterable will be filtered according to the specifier. + :param prereleases: + Whether or not to allow prereleases in the returned iterator. If set to + ``None`` (the default), it will follow the recommendation from :pep:`440` + and match prereleases if there are no other versions. + + >>> list(SpecifierSet(">=1.2.3").filter(["1.2", "1.3", "1.5a1"])) + ['1.3'] + >>> list(SpecifierSet(">=1.2.3").filter(["1.2", "1.3", Version("1.4")])) + ['1.3', ] + >>> list(SpecifierSet(">=1.2.3").filter(["1.2", "1.5a1"])) + ['1.5a1'] + >>> list(SpecifierSet(">=1.2.3").filter(["1.3", "1.5a1"], prereleases=True)) + ['1.3', '1.5a1'] + >>> list(SpecifierSet(">=1.2.3", prereleases=True).filter(["1.3", "1.5a1"])) + ['1.3', '1.5a1'] + + An "empty" SpecifierSet will filter items based on the presence of prerelease + versions in the set. + + >>> list(SpecifierSet("").filter(["1.3", "1.5a1"])) + ['1.3'] + >>> list(SpecifierSet("").filter(["1.5a1"])) + ['1.5a1'] + >>> list(SpecifierSet("", prereleases=True).filter(["1.3", "1.5a1"])) + ['1.3', '1.5a1'] + >>> list(SpecifierSet("").filter(["1.3", "1.5a1"], prereleases=True)) + ['1.3', '1.5a1'] + """ + # Determine if we're forcing a prerelease or not, if we're not forcing + # one for this particular filter call, then we'll use whatever the + # SpecifierSet thinks for whether or not we should support prereleases. + if prereleases is None and self.prereleases is not None: + prereleases = self.prereleases + + # If we have any specifiers, then we want to wrap our iterable in the + # filter method for each one, this will act as a logical AND amongst + # each specifier. + if self._specs: + # When prereleases is None, we need to let all versions through + # the individual filters, then decide about prereleases at the end + # based on whether any non-prereleases matched ALL specs. + for spec in self._specs: + iterable = spec.filter( + iterable, prereleases=True if prereleases is None else prereleases + ) + + if prereleases is not None: + # If we have a forced prereleases value, + # we can immediately return the iterator. + return iter(iterable) + else: + # Handle empty SpecifierSet cases where prereleases is not None. + if prereleases is True: + return iter(iterable) + + if prereleases is False: + return ( + item + for item in iterable + if (version := _coerce_version(item)) is None + or not version.is_prerelease + ) + + # Finally if prereleases is None, apply PEP 440 logic: + # exclude prereleases unless there are no final releases that matched. + filtered_items: list[UnparsedVersionVar] = [] + found_prereleases: list[UnparsedVersionVar] = [] + found_final_release = False + + for item in iterable: + parsed_version = _coerce_version(item) + # Arbitrary strings are always included as it is not + # possible to determine if they are prereleases, + # and they have already passed all specifiers. + if parsed_version is None: + filtered_items.append(item) + found_prereleases.append(item) + elif parsed_version.is_prerelease: + found_prereleases.append(item) + else: + filtered_items.append(item) + found_final_release = True + + return iter(filtered_items if found_final_release else found_prereleases) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/tags.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/tags.py new file mode 100644 index 0000000000000000000000000000000000000000..5ef27c897a4df35a2a6923b608a5e04a0a38b9ee --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/tags.py @@ -0,0 +1,651 @@ +# This file is dual licensed under the terms of the Apache License, Version +# 2.0, and the BSD License. See the LICENSE file in the root of this repository +# for complete details. + +from __future__ import annotations + +import logging +import platform +import re +import struct +import subprocess +import sys +import sysconfig +from importlib.machinery import EXTENSION_SUFFIXES +from typing import ( + Any, + Iterable, + Iterator, + Sequence, + Tuple, + cast, +) + +from . import _manylinux, _musllinux + +logger = logging.getLogger(__name__) + +PythonVersion = Sequence[int] +AppleVersion = Tuple[int, int] + +INTERPRETER_SHORT_NAMES: dict[str, str] = { + "python": "py", # Generic. + "cpython": "cp", + "pypy": "pp", + "ironpython": "ip", + "jython": "jy", +} + + +_32_BIT_INTERPRETER = struct.calcsize("P") == 4 + + +class Tag: + """ + A representation of the tag triple for a wheel. + + Instances are considered immutable and thus are hashable. Equality checking + is also supported. + """ + + __slots__ = ["_abi", "_hash", "_interpreter", "_platform"] + + def __init__(self, interpreter: str, abi: str, platform: str) -> None: + self._interpreter = interpreter.lower() + self._abi = abi.lower() + self._platform = platform.lower() + # The __hash__ of every single element in a Set[Tag] will be evaluated each time + # that a set calls its `.disjoint()` method, which may be called hundreds of + # times when scanning a page of links for packages with tags matching that + # Set[Tag]. Pre-computing the value here produces significant speedups for + # downstream consumers. + self._hash = hash((self._interpreter, self._abi, self._platform)) + + @property + def interpreter(self) -> str: + return self._interpreter + + @property + def abi(self) -> str: + return self._abi + + @property + def platform(self) -> str: + return self._platform + + def __eq__(self, other: object) -> bool: + if not isinstance(other, Tag): + return NotImplemented + + return ( + (self._hash == other._hash) # Short-circuit ASAP for perf reasons. + and (self._platform == other._platform) + and (self._abi == other._abi) + and (self._interpreter == other._interpreter) + ) + + def __hash__(self) -> int: + return self._hash + + def __str__(self) -> str: + return f"{self._interpreter}-{self._abi}-{self._platform}" + + def __repr__(self) -> str: + return f"<{self} @ {id(self)}>" + + def __setstate__(self, state: tuple[None, dict[str, Any]]) -> None: + # The cached _hash is wrong when unpickling. + _, slots = state + for k, v in slots.items(): + setattr(self, k, v) + self._hash = hash((self._interpreter, self._abi, self._platform)) + + +def parse_tag(tag: str) -> frozenset[Tag]: + """ + Parses the provided tag (e.g. `py3-none-any`) into a frozenset of Tag instances. + + Returning a set is required due to the possibility that the tag is a + compressed tag set. + """ + tags = set() + interpreters, abis, platforms = tag.split("-") + for interpreter in interpreters.split("."): + for abi in abis.split("."): + for platform_ in platforms.split("."): + tags.add(Tag(interpreter, abi, platform_)) + return frozenset(tags) + + +def _get_config_var(name: str, warn: bool = False) -> int | str | None: + value: int | str | None = sysconfig.get_config_var(name) + if value is None and warn: + logger.debug( + "Config variable '%s' is unset, Python ABI tag may be incorrect", name + ) + return value + + +def _normalize_string(string: str) -> str: + return string.replace(".", "_").replace("-", "_").replace(" ", "_") + + +def _is_threaded_cpython(abis: list[str]) -> bool: + """ + Determine if the ABI corresponds to a threaded (`--disable-gil`) build. + + The threaded builds are indicated by a "t" in the abiflags. + """ + if len(abis) == 0: + return False + # expect e.g., cp313 + m = re.match(r"cp\d+(.*)", abis[0]) + if not m: + return False + abiflags = m.group(1) + return "t" in abiflags + + +def _abi3_applies(python_version: PythonVersion, threading: bool) -> bool: + """ + Determine if the Python version supports abi3. + + PEP 384 was first implemented in Python 3.2. The threaded (`--disable-gil`) + builds do not support abi3. + """ + return len(python_version) > 1 and tuple(python_version) >= (3, 2) and not threading + + +def _cpython_abis(py_version: PythonVersion, warn: bool = False) -> list[str]: + py_version = tuple(py_version) # To allow for version comparison. + abis = [] + version = _version_nodot(py_version[:2]) + threading = debug = pymalloc = ucs4 = "" + with_debug = _get_config_var("Py_DEBUG", warn) + has_refcount = hasattr(sys, "gettotalrefcount") + # Windows doesn't set Py_DEBUG, so checking for support of debug-compiled + # extension modules is the best option. + # https://github.com/pypa/pip/issues/3383#issuecomment-173267692 + has_ext = "_d.pyd" in EXTENSION_SUFFIXES + if with_debug or (with_debug is None and (has_refcount or has_ext)): + debug = "d" + if py_version >= (3, 13) and _get_config_var("Py_GIL_DISABLED", warn): + threading = "t" + if py_version < (3, 8): + with_pymalloc = _get_config_var("WITH_PYMALLOC", warn) + if with_pymalloc or with_pymalloc is None: + pymalloc = "m" + if py_version < (3, 3): + unicode_size = _get_config_var("Py_UNICODE_SIZE", warn) + if unicode_size == 4 or ( + unicode_size is None and sys.maxunicode == 0x10FFFF + ): + ucs4 = "u" + elif debug: + # Debug builds can also load "normal" extension modules. + # We can also assume no UCS-4 or pymalloc requirement. + abis.append(f"cp{version}{threading}") + abis.insert(0, f"cp{version}{threading}{debug}{pymalloc}{ucs4}") + return abis + + +def cpython_tags( + python_version: PythonVersion | None = None, + abis: Iterable[str] | None = None, + platforms: Iterable[str] | None = None, + *, + warn: bool = False, +) -> Iterator[Tag]: + """ + Yields the tags for a CPython interpreter. + + The tags consist of: + - cp-- + - cp-abi3- + - cp-none- + - cp-abi3- # Older Python versions down to 3.2. + + If python_version only specifies a major version then user-provided ABIs and + the 'none' ABItag will be used. + + If 'abi3' or 'none' are specified in 'abis' then they will be yielded at + their normal position and not at the beginning. + """ + if not python_version: + python_version = sys.version_info[:2] + + interpreter = f"cp{_version_nodot(python_version[:2])}" + + if abis is None: + abis = _cpython_abis(python_version, warn) if len(python_version) > 1 else [] + abis = list(abis) + # 'abi3' and 'none' are explicitly handled later. + for explicit_abi in ("abi3", "none"): + try: + abis.remove(explicit_abi) + except ValueError: # noqa: PERF203 + pass + + platforms = list(platforms or platform_tags()) + for abi in abis: + for platform_ in platforms: + yield Tag(interpreter, abi, platform_) + + threading = _is_threaded_cpython(abis) + use_abi3 = _abi3_applies(python_version, threading) + if use_abi3: + yield from (Tag(interpreter, "abi3", platform_) for platform_ in platforms) + yield from (Tag(interpreter, "none", platform_) for platform_ in platforms) + + if use_abi3: + for minor_version in range(python_version[1] - 1, 1, -1): + for platform_ in platforms: + version = _version_nodot((python_version[0], minor_version)) + interpreter = f"cp{version}" + yield Tag(interpreter, "abi3", platform_) + + +def _generic_abi() -> list[str]: + """ + Return the ABI tag based on EXT_SUFFIX. + """ + # The following are examples of `EXT_SUFFIX`. + # We want to keep the parts which are related to the ABI and remove the + # parts which are related to the platform: + # - linux: '.cpython-310-x86_64-linux-gnu.so' => cp310 + # - mac: '.cpython-310-darwin.so' => cp310 + # - win: '.cp310-win_amd64.pyd' => cp310 + # - win: '.pyd' => cp37 (uses _cpython_abis()) + # - pypy: '.pypy38-pp73-x86_64-linux-gnu.so' => pypy38_pp73 + # - graalpy: '.graalpy-38-native-x86_64-darwin.dylib' + # => graalpy_38_native + + ext_suffix = _get_config_var("EXT_SUFFIX", warn=True) + if not isinstance(ext_suffix, str) or ext_suffix[0] != ".": + raise SystemError("invalid sysconfig.get_config_var('EXT_SUFFIX')") + parts = ext_suffix.split(".") + if len(parts) < 3: + # CPython3.7 and earlier uses ".pyd" on Windows. + return _cpython_abis(sys.version_info[:2]) + soabi = parts[1] + if soabi.startswith("cpython"): + # non-windows + abi = "cp" + soabi.split("-")[1] + elif soabi.startswith("cp"): + # windows + abi = soabi.split("-")[0] + elif soabi.startswith("pypy"): + abi = "-".join(soabi.split("-")[:2]) + elif soabi.startswith("graalpy"): + abi = "-".join(soabi.split("-")[:3]) + elif soabi: + # pyston, ironpython, others? + abi = soabi + else: + return [] + return [_normalize_string(abi)] + + +def generic_tags( + interpreter: str | None = None, + abis: Iterable[str] | None = None, + platforms: Iterable[str] | None = None, + *, + warn: bool = False, +) -> Iterator[Tag]: + """ + Yields the tags for a generic interpreter. + + The tags consist of: + - -- + + The "none" ABI will be added if it was not explicitly provided. + """ + if not interpreter: + interp_name = interpreter_name() + interp_version = interpreter_version(warn=warn) + interpreter = f"{interp_name}{interp_version}" + abis = _generic_abi() if abis is None else list(abis) + platforms = list(platforms or platform_tags()) + if "none" not in abis: + abis.append("none") + for abi in abis: + for platform_ in platforms: + yield Tag(interpreter, abi, platform_) + + +def _py_interpreter_range(py_version: PythonVersion) -> Iterator[str]: + """ + Yields Python versions in descending order. + + After the latest version, the major-only version will be yielded, and then + all previous versions of that major version. + """ + if len(py_version) > 1: + yield f"py{_version_nodot(py_version[:2])}" + yield f"py{py_version[0]}" + if len(py_version) > 1: + for minor in range(py_version[1] - 1, -1, -1): + yield f"py{_version_nodot((py_version[0], minor))}" + + +def compatible_tags( + python_version: PythonVersion | None = None, + interpreter: str | None = None, + platforms: Iterable[str] | None = None, +) -> Iterator[Tag]: + """ + Yields the sequence of tags that are compatible with a specific version of Python. + + The tags consist of: + - py*-none- + - -none-any # ... if `interpreter` is provided. + - py*-none-any + """ + if not python_version: + python_version = sys.version_info[:2] + platforms = list(platforms or platform_tags()) + for version in _py_interpreter_range(python_version): + for platform_ in platforms: + yield Tag(version, "none", platform_) + if interpreter: + yield Tag(interpreter, "none", "any") + for version in _py_interpreter_range(python_version): + yield Tag(version, "none", "any") + + +def _mac_arch(arch: str, is_32bit: bool = _32_BIT_INTERPRETER) -> str: + if not is_32bit: + return arch + + if arch.startswith("ppc"): + return "ppc" + + return "i386" + + +def _mac_binary_formats(version: AppleVersion, cpu_arch: str) -> list[str]: + formats = [cpu_arch] + if cpu_arch == "x86_64": + if version < (10, 4): + return [] + formats.extend(["intel", "fat64", "fat32"]) + + elif cpu_arch == "i386": + if version < (10, 4): + return [] + formats.extend(["intel", "fat32", "fat"]) + + elif cpu_arch == "ppc64": + # TODO: Need to care about 32-bit PPC for ppc64 through 10.2? + if version > (10, 5) or version < (10, 4): + return [] + formats.append("fat64") + + elif cpu_arch == "ppc": + if version > (10, 6): + return [] + formats.extend(["fat32", "fat"]) + + if cpu_arch in {"arm64", "x86_64"}: + formats.append("universal2") + + if cpu_arch in {"x86_64", "i386", "ppc64", "ppc", "intel"}: + formats.append("universal") + + return formats + + +def mac_platforms( + version: AppleVersion | None = None, arch: str | None = None +) -> Iterator[str]: + """ + Yields the platform tags for a macOS system. + + The `version` parameter is a two-item tuple specifying the macOS version to + generate platform tags for. The `arch` parameter is the CPU architecture to + generate platform tags for. Both parameters default to the appropriate value + for the current system. + """ + version_str, _, cpu_arch = platform.mac_ver() + if version is None: + version = cast("AppleVersion", tuple(map(int, version_str.split(".")[:2]))) + if version == (10, 16): + # When built against an older macOS SDK, Python will report macOS 10.16 + # instead of the real version. + version_str = subprocess.run( + [ + sys.executable, + "-sS", + "-c", + "import platform; print(platform.mac_ver()[0])", + ], + check=True, + env={"SYSTEM_VERSION_COMPAT": "0"}, + stdout=subprocess.PIPE, + text=True, + ).stdout + version = cast("AppleVersion", tuple(map(int, version_str.split(".")[:2]))) + + if arch is None: + arch = _mac_arch(cpu_arch) + + if (10, 0) <= version < (11, 0): + # Prior to Mac OS 11, each yearly release of Mac OS bumped the + # "minor" version number. The major version was always 10. + major_version = 10 + for minor_version in range(version[1], -1, -1): + compat_version = major_version, minor_version + binary_formats = _mac_binary_formats(compat_version, arch) + for binary_format in binary_formats: + yield f"macosx_{major_version}_{minor_version}_{binary_format}" + + if version >= (11, 0): + # Starting with Mac OS 11, each yearly release bumps the major version + # number. The minor versions are now the midyear updates. + minor_version = 0 + for major_version in range(version[0], 10, -1): + compat_version = major_version, minor_version + binary_formats = _mac_binary_formats(compat_version, arch) + for binary_format in binary_formats: + yield f"macosx_{major_version}_{minor_version}_{binary_format}" + + if version >= (11, 0): + # Mac OS 11 on x86_64 is compatible with binaries from previous releases. + # Arm64 support was introduced in 11.0, so no Arm binaries from previous + # releases exist. + # + # However, the "universal2" binary format can have a + # macOS version earlier than 11.0 when the x86_64 part of the binary supports + # that version of macOS. + major_version = 10 + if arch == "x86_64": + for minor_version in range(16, 3, -1): + compat_version = major_version, minor_version + binary_formats = _mac_binary_formats(compat_version, arch) + for binary_format in binary_formats: + yield f"macosx_{major_version}_{minor_version}_{binary_format}" + else: + for minor_version in range(16, 3, -1): + compat_version = major_version, minor_version + binary_format = "universal2" + yield f"macosx_{major_version}_{minor_version}_{binary_format}" + + +def ios_platforms( + version: AppleVersion | None = None, multiarch: str | None = None +) -> Iterator[str]: + """ + Yields the platform tags for an iOS system. + + :param version: A two-item tuple specifying the iOS version to generate + platform tags for. Defaults to the current iOS version. + :param multiarch: The CPU architecture+ABI to generate platform tags for - + (the value used by `sys.implementation._multiarch` e.g., + `arm64_iphoneos` or `x84_64_iphonesimulator`). Defaults to the current + multiarch value. + """ + if version is None: + # if iOS is the current platform, ios_ver *must* be defined. However, + # it won't exist for CPython versions before 3.13, which causes a mypy + # error. + _, release, _, _ = platform.ios_ver() # type: ignore[attr-defined, unused-ignore] + version = cast("AppleVersion", tuple(map(int, release.split(".")[:2]))) + + if multiarch is None: + multiarch = sys.implementation._multiarch + multiarch = multiarch.replace("-", "_") + + ios_platform_template = "ios_{major}_{minor}_{multiarch}" + + # Consider any iOS major.minor version from the version requested, down to + # 12.0. 12.0 is the first iOS version that is known to have enough features + # to support CPython. Consider every possible minor release up to X.9. There + # highest the minor has ever gone is 8 (14.8 and 15.8) but having some extra + # candidates that won't ever match doesn't really hurt, and it saves us from + # having to keep an explicit list of known iOS versions in the code. Return + # the results descending order of version number. + + # If the requested major version is less than 12, there won't be any matches. + if version[0] < 12: + return + + # Consider the actual X.Y version that was requested. + yield ios_platform_template.format( + major=version[0], minor=version[1], multiarch=multiarch + ) + + # Consider every minor version from X.0 to the minor version prior to the + # version requested by the platform. + for minor in range(version[1] - 1, -1, -1): + yield ios_platform_template.format( + major=version[0], minor=minor, multiarch=multiarch + ) + + for major in range(version[0] - 1, 11, -1): + for minor in range(9, -1, -1): + yield ios_platform_template.format( + major=major, minor=minor, multiarch=multiarch + ) + + +def android_platforms( + api_level: int | None = None, abi: str | None = None +) -> Iterator[str]: + """ + Yields the :attr:`~Tag.platform` tags for Android. If this function is invoked on + non-Android platforms, the ``api_level`` and ``abi`` arguments are required. + + :param int api_level: The maximum `API level + `__ to return. Defaults + to the current system's version, as returned by ``platform.android_ver``. + :param str abi: The `Android ABI `__, + e.g. ``arm64_v8a``. Defaults to the current system's ABI , as returned by + ``sysconfig.get_platform``. Hyphens and periods will be replaced with + underscores. + """ + if platform.system() != "Android" and (api_level is None or abi is None): + raise TypeError( + "on non-Android platforms, the api_level and abi arguments are required" + ) + + if api_level is None: + # Python 3.13 was the first version to return platform.system() == "Android", + # and also the first version to define platform.android_ver(). + api_level = platform.android_ver().api_level # type: ignore[attr-defined] + + if abi is None: + abi = sysconfig.get_platform().split("-")[-1] + abi = _normalize_string(abi) + + # 16 is the minimum API level known to have enough features to support CPython + # without major patching. Yield every API level from the maximum down to the + # minimum, inclusive. + min_api_level = 16 + for ver in range(api_level, min_api_level - 1, -1): + yield f"android_{ver}_{abi}" + + +def _linux_platforms(is_32bit: bool = _32_BIT_INTERPRETER) -> Iterator[str]: + linux = _normalize_string(sysconfig.get_platform()) + if not linux.startswith("linux_"): + # we should never be here, just yield the sysconfig one and return + yield linux + return + if is_32bit: + if linux == "linux_x86_64": + linux = "linux_i686" + elif linux == "linux_aarch64": + linux = "linux_armv8l" + _, arch = linux.split("_", 1) + archs = {"armv8l": ["armv8l", "armv7l"]}.get(arch, [arch]) + yield from _manylinux.platform_tags(archs) + yield from _musllinux.platform_tags(archs) + for arch in archs: + yield f"linux_{arch}" + + +def _generic_platforms() -> Iterator[str]: + yield _normalize_string(sysconfig.get_platform()) + + +def platform_tags() -> Iterator[str]: + """ + Provides the platform tags for this installation. + """ + if platform.system() == "Darwin": + return mac_platforms() + elif platform.system() == "iOS": + return ios_platforms() + elif platform.system() == "Android": + return android_platforms() + elif platform.system() == "Linux": + return _linux_platforms() + else: + return _generic_platforms() + + +def interpreter_name() -> str: + """ + Returns the name of the running interpreter. + + Some implementations have a reserved, two-letter abbreviation which will + be returned when appropriate. + """ + name = sys.implementation.name + return INTERPRETER_SHORT_NAMES.get(name) or name + + +def interpreter_version(*, warn: bool = False) -> str: + """ + Returns the version of the running interpreter. + """ + version = _get_config_var("py_version_nodot", warn=warn) + return str(version) if version else _version_nodot(sys.version_info[:2]) + + +def _version_nodot(version: PythonVersion) -> str: + return "".join(map(str, version)) + + +def sys_tags(*, warn: bool = False) -> Iterator[Tag]: + """ + Returns the sequence of tag triples for the running interpreter. + + The order of the sequence corresponds to priority order for the + interpreter, from most to least important. + """ + + interp_name = interpreter_name() + if interp_name == "cp": + yield from cpython_tags(warn=warn) + else: + yield from generic_tags() + + if interp_name == "pp": + interp = "pp3" + elif interp_name == "cp": + interp = "cp" + interpreter_version(warn=warn) + else: + interp = None + yield from compatible_tags(interpreter=interp) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/utils.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/utils.py new file mode 100644 index 0000000000000000000000000000000000000000..c41c8137f2679a0fac21bb845596e231ae88dbd8 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/utils.py @@ -0,0 +1,158 @@ +# This file is dual licensed under the terms of the Apache License, Version +# 2.0, and the BSD License. See the LICENSE file in the root of this repository +# for complete details. + +from __future__ import annotations + +import re +from typing import NewType, Tuple, Union, cast + +from .tags import Tag, parse_tag +from .version import InvalidVersion, Version, _TrimmedRelease + +BuildTag = Union[Tuple[()], Tuple[int, str]] +NormalizedName = NewType("NormalizedName", str) + + +class InvalidName(ValueError): + """ + An invalid distribution name; users should refer to the packaging user guide. + """ + + +class InvalidWheelFilename(ValueError): + """ + An invalid wheel filename was found, users should refer to PEP 427. + """ + + +class InvalidSdistFilename(ValueError): + """ + An invalid sdist filename was found, users should refer to the packaging user guide. + """ + + +# Core metadata spec for `Name` +_validate_regex = re.compile(r"[A-Z0-9]|[A-Z0-9][A-Z0-9._-]*[A-Z0-9]", re.IGNORECASE) +_normalized_regex = re.compile(r"[a-z0-9]|[a-z0-9]([a-z0-9-](?!--))*[a-z0-9]") +# PEP 427: The build number must start with a digit. +_build_tag_regex = re.compile(r"(\d+)(.*)") + + +def canonicalize_name(name: str, *, validate: bool = False) -> NormalizedName: + if validate and not _validate_regex.fullmatch(name): + raise InvalidName(f"name is invalid: {name!r}") + # Ensure all ``.`` and ``_`` are ``-`` + # Emulates ``re.sub(r"[-_.]+", "-", name).lower()`` from PEP 503 + # Much faster than re, and even faster than str.translate + value = name.lower().replace("_", "-").replace(".", "-") + # Condense repeats (faster than regex) + while "--" in value: + value = value.replace("--", "-") + return cast("NormalizedName", value) + + +def is_normalized_name(name: str) -> bool: + return _normalized_regex.fullmatch(name) is not None + + +def canonicalize_version( + version: Version | str, *, strip_trailing_zero: bool = True +) -> str: + """ + Return a canonical form of a version as a string. + + >>> canonicalize_version('1.0.1') + '1.0.1' + + Per PEP 625, versions may have multiple canonical forms, differing + only by trailing zeros. + + >>> canonicalize_version('1.0.0') + '1' + >>> canonicalize_version('1.0.0', strip_trailing_zero=False) + '1.0.0' + + Invalid versions are returned unaltered. + + >>> canonicalize_version('foo bar baz') + 'foo bar baz' + """ + if isinstance(version, str): + try: + version = Version(version) + except InvalidVersion: + return str(version) + return str(_TrimmedRelease(version) if strip_trailing_zero else version) + + +def parse_wheel_filename( + filename: str, +) -> tuple[NormalizedName, Version, BuildTag, frozenset[Tag]]: + if not filename.endswith(".whl"): + raise InvalidWheelFilename( + f"Invalid wheel filename (extension must be '.whl'): {filename!r}" + ) + + filename = filename[:-4] + dashes = filename.count("-") + if dashes not in (4, 5): + raise InvalidWheelFilename( + f"Invalid wheel filename (wrong number of parts): {filename!r}" + ) + + parts = filename.split("-", dashes - 2) + name_part = parts[0] + # See PEP 427 for the rules on escaping the project name. + if "__" in name_part or re.match(r"^[\w\d._]*$", name_part, re.UNICODE) is None: + raise InvalidWheelFilename(f"Invalid project name: {filename!r}") + name = canonicalize_name(name_part) + + try: + version = Version(parts[1]) + except InvalidVersion as e: + raise InvalidWheelFilename( + f"Invalid wheel filename (invalid version): {filename!r}" + ) from e + + if dashes == 5: + build_part = parts[2] + build_match = _build_tag_regex.match(build_part) + if build_match is None: + raise InvalidWheelFilename( + f"Invalid build number: {build_part} in {filename!r}" + ) + build = cast("BuildTag", (int(build_match.group(1)), build_match.group(2))) + else: + build = () + tags = parse_tag(parts[-1]) + return (name, version, build, tags) + + +def parse_sdist_filename(filename: str) -> tuple[NormalizedName, Version]: + if filename.endswith(".tar.gz"): + file_stem = filename[: -len(".tar.gz")] + elif filename.endswith(".zip"): + file_stem = filename[: -len(".zip")] + else: + raise InvalidSdistFilename( + f"Invalid sdist filename (extension must be '.tar.gz' or '.zip'):" + f" {filename!r}" + ) + + # We are requiring a PEP 440 version, which cannot contain dashes, + # so we split on the last dash. + name_part, sep, version_part = file_stem.rpartition("-") + if not sep: + raise InvalidSdistFilename(f"Invalid sdist filename: {filename!r}") + + name = canonicalize_name(name_part) + + try: + version = Version(version_part) + except InvalidVersion as e: + raise InvalidSdistFilename( + f"Invalid sdist filename (invalid version): {filename!r}" + ) from e + + return (name, version) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/version.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/version.py new file mode 100644 index 0000000000000000000000000000000000000000..1206c462d4fcaa670a816e201bb88b27dfc9cf88 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/packaging/version.py @@ -0,0 +1,792 @@ +# This file is dual licensed under the terms of the Apache License, Version +# 2.0, and the BSD License. See the LICENSE file in the root of this repository +# for complete details. +""" +.. testsetup:: + + from packaging.version import parse, Version +""" + +from __future__ import annotations + +import re +import sys +import typing +from typing import ( + Any, + Callable, + Literal, + NamedTuple, + SupportsInt, + Tuple, + TypedDict, + Union, +) + +from ._structures import Infinity, InfinityType, NegativeInfinity, NegativeInfinityType + +if typing.TYPE_CHECKING: + from typing_extensions import Self, Unpack + +if sys.version_info >= (3, 13): # pragma: no cover + from warnings import deprecated as _deprecated +elif typing.TYPE_CHECKING: + from typing_extensions import deprecated as _deprecated +else: # pragma: no cover + import functools + import warnings + + def _deprecated(message: str) -> object: + def decorator(func: object) -> object: + @functools.wraps(func) + def wrapper(*args: object, **kwargs: object) -> object: + warnings.warn( + message, + category=DeprecationWarning, + stacklevel=2, + ) + return func(*args, **kwargs) + + return wrapper + + return decorator + + +_LETTER_NORMALIZATION = { + "alpha": "a", + "beta": "b", + "c": "rc", + "pre": "rc", + "preview": "rc", + "rev": "post", + "r": "post", +} + +__all__ = ["VERSION_PATTERN", "InvalidVersion", "Version", "parse"] + +LocalType = Tuple[Union[int, str], ...] + +CmpPrePostDevType = Union[InfinityType, NegativeInfinityType, Tuple[str, int]] +CmpLocalType = Union[ + NegativeInfinityType, + Tuple[Union[Tuple[int, str], Tuple[NegativeInfinityType, Union[int, str]]], ...], +] +CmpKey = Tuple[ + int, + Tuple[int, ...], + CmpPrePostDevType, + CmpPrePostDevType, + CmpPrePostDevType, + CmpLocalType, +] +VersionComparisonMethod = Callable[[CmpKey, CmpKey], bool] + + +class _VersionReplace(TypedDict, total=False): + epoch: int | None + release: tuple[int, ...] | None + pre: tuple[Literal["a", "b", "rc"], int] | None + post: int | None + dev: int | None + local: str | None + + +def parse(version: str) -> Version: + """Parse the given version string. + + >>> parse('1.0.dev1') + + + :param version: The version string to parse. + :raises InvalidVersion: When the version string is not a valid version. + """ + return Version(version) + + +class InvalidVersion(ValueError): + """Raised when a version string is not a valid version. + + >>> Version("invalid") + Traceback (most recent call last): + ... + packaging.version.InvalidVersion: Invalid version: 'invalid' + """ + + +class _BaseVersion: + __slots__ = () + + # This can also be a normal member (see the packaging_legacy package); + # we are just requiring it to be readable. Actually defining a property + # has runtime effect on subclasses, so it's typing only. + if typing.TYPE_CHECKING: + + @property + def _key(self) -> tuple[Any, ...]: ... + + def __hash__(self) -> int: + return hash(self._key) + + # Please keep the duplicated `isinstance` check + # in the six comparisons hereunder + # unless you find a way to avoid adding overhead function calls. + def __lt__(self, other: _BaseVersion) -> bool: + if not isinstance(other, _BaseVersion): + return NotImplemented + + return self._key < other._key + + def __le__(self, other: _BaseVersion) -> bool: + if not isinstance(other, _BaseVersion): + return NotImplemented + + return self._key <= other._key + + def __eq__(self, other: object) -> bool: + if not isinstance(other, _BaseVersion): + return NotImplemented + + return self._key == other._key + + def __ge__(self, other: _BaseVersion) -> bool: + if not isinstance(other, _BaseVersion): + return NotImplemented + + return self._key >= other._key + + def __gt__(self, other: _BaseVersion) -> bool: + if not isinstance(other, _BaseVersion): + return NotImplemented + + return self._key > other._key + + def __ne__(self, other: object) -> bool: + if not isinstance(other, _BaseVersion): + return NotImplemented + + return self._key != other._key + + +# Deliberately not anchored to the start and end of the string, to make it +# easier for 3rd party code to reuse + +# Note that ++ doesn't behave identically on CPython and PyPy, so not using it here +_VERSION_PATTERN = r""" + v?+ # optional leading v + (?: + (?:(?P[0-9]+)!)?+ # epoch + (?P[0-9]+(?:\.[0-9]+)*+) # release segment + (?P
                                          # pre-release
+            [._-]?+
+            (?Palpha|a|beta|b|preview|pre|c|rc)
+            [._-]?+
+            (?P[0-9]+)?
+        )?+
+        (?P                                         # post release
+            (?:-(?P[0-9]+))
+            |
+            (?:
+                [._-]?
+                (?Ppost|rev|r)
+                [._-]?
+                (?P[0-9]+)?
+            )
+        )?+
+        (?P                                          # dev release
+            [._-]?+
+            (?Pdev)
+            [._-]?+
+            (?P[0-9]+)?
+        )?+
+    )
+    (?:\+
+        (?P                                        # local version
+            [a-z0-9]+
+            (?:[._-][a-z0-9]+)*+
+        )
+    )?+
+"""
+
+_VERSION_PATTERN_OLD = _VERSION_PATTERN.replace("*+", "*").replace("?+", "?")
+
+# Possessive qualifiers were added in Python 3.11.
+# CPython 3.11.0-3.11.4 had a bug: https://github.com/python/cpython/pull/107795
+# Older PyPy also had a bug.
+VERSION_PATTERN = (
+    _VERSION_PATTERN_OLD
+    if (sys.implementation.name == "cpython" and sys.version_info < (3, 11, 5))
+    or (sys.implementation.name == "pypy" and sys.version_info < (3, 11, 13))
+    or sys.version_info < (3, 11)
+    else _VERSION_PATTERN
+)
+"""
+A string containing the regular expression used to match a valid version.
+
+The pattern is not anchored at either end, and is intended for embedding in larger
+expressions (for example, matching a version number as part of a file name). The
+regular expression should be compiled with the ``re.VERBOSE`` and ``re.IGNORECASE``
+flags set.
+
+:meta hide-value:
+"""
+
+
+# Validation pattern for local version in replace()
+_LOCAL_PATTERN = re.compile(r"[a-z0-9]+(?:[._-][a-z0-9]+)*", re.IGNORECASE)
+
+
+def _validate_epoch(value: object, /) -> int:
+    epoch = value or 0
+    if isinstance(epoch, int) and epoch >= 0:
+        return epoch
+    msg = f"epoch must be non-negative integer, got {epoch}"
+    raise InvalidVersion(msg)
+
+
+def _validate_release(value: object, /) -> tuple[int, ...]:
+    release = (0,) if value is None else value
+    if (
+        isinstance(release, tuple)
+        and len(release) > 0
+        and all(isinstance(i, int) and i >= 0 for i in release)
+    ):
+        return release
+    msg = f"release must be a non-empty tuple of non-negative integers, got {release}"
+    raise InvalidVersion(msg)
+
+
+def _validate_pre(value: object, /) -> tuple[Literal["a", "b", "rc"], int] | None:
+    if value is None:
+        return value
+    if (
+        isinstance(value, tuple)
+        and len(value) == 2
+        and value[0] in ("a", "b", "rc")
+        and isinstance(value[1], int)
+        and value[1] >= 0
+    ):
+        return value
+    msg = f"pre must be a tuple of ('a'|'b'|'rc', non-negative int), got {value}"
+    raise InvalidVersion(msg)
+
+
+def _validate_post(value: object, /) -> tuple[Literal["post"], int] | None:
+    if value is None:
+        return value
+    if isinstance(value, int) and value >= 0:
+        return ("post", value)
+    msg = f"post must be non-negative integer, got {value}"
+    raise InvalidVersion(msg)
+
+
+def _validate_dev(value: object, /) -> tuple[Literal["dev"], int] | None:
+    if value is None:
+        return value
+    if isinstance(value, int) and value >= 0:
+        return ("dev", value)
+    msg = f"dev must be non-negative integer, got {value}"
+    raise InvalidVersion(msg)
+
+
+def _validate_local(value: object, /) -> LocalType | None:
+    if value is None:
+        return value
+    if isinstance(value, str) and _LOCAL_PATTERN.fullmatch(value):
+        return _parse_local_version(value)
+    msg = f"local must be a valid version string, got {value!r}"
+    raise InvalidVersion(msg)
+
+
+# Backward compatibility for internals before 26.0. Do not use.
+class _Version(NamedTuple):
+    epoch: int
+    release: tuple[int, ...]
+    dev: tuple[str, int] | None
+    pre: tuple[str, int] | None
+    post: tuple[str, int] | None
+    local: LocalType | None
+
+
+class Version(_BaseVersion):
+    """This class abstracts handling of a project's versions.
+
+    A :class:`Version` instance is comparison aware and can be compared and
+    sorted using the standard Python interfaces.
+
+    >>> v1 = Version("1.0a5")
+    >>> v2 = Version("1.0")
+    >>> v1
+    
+    >>> v2
+    
+    >>> v1 < v2
+    True
+    >>> v1 == v2
+    False
+    >>> v1 > v2
+    False
+    >>> v1 >= v2
+    False
+    >>> v1 <= v2
+    True
+    """
+
+    __slots__ = ("_dev", "_epoch", "_key_cache", "_local", "_post", "_pre", "_release")
+    __match_args__ = ("_str",)
+
+    _regex = re.compile(r"\s*" + VERSION_PATTERN + r"\s*", re.VERBOSE | re.IGNORECASE)
+
+    _epoch: int
+    _release: tuple[int, ...]
+    _dev: tuple[str, int] | None
+    _pre: tuple[str, int] | None
+    _post: tuple[str, int] | None
+    _local: LocalType | None
+
+    _key_cache: CmpKey | None
+
+    def __init__(self, version: str) -> None:
+        """Initialize a Version object.
+
+        :param version:
+            The string representation of a version which will be parsed and normalized
+            before use.
+        :raises InvalidVersion:
+            If the ``version`` does not conform to PEP 440 in any way then this
+            exception will be raised.
+        """
+        # Validate the version and parse it into pieces
+        match = self._regex.fullmatch(version)
+        if not match:
+            raise InvalidVersion(f"Invalid version: {version!r}")
+        self._epoch = int(match.group("epoch")) if match.group("epoch") else 0
+        self._release = tuple(map(int, match.group("release").split(".")))
+        self._pre = _parse_letter_version(match.group("pre_l"), match.group("pre_n"))
+        self._post = _parse_letter_version(
+            match.group("post_l"), match.group("post_n1") or match.group("post_n2")
+        )
+        self._dev = _parse_letter_version(match.group("dev_l"), match.group("dev_n"))
+        self._local = _parse_local_version(match.group("local"))
+
+        # Key which will be used for sorting
+        self._key_cache = None
+
+    def __replace__(self, **kwargs: Unpack[_VersionReplace]) -> Self:
+        epoch = _validate_epoch(kwargs["epoch"]) if "epoch" in kwargs else self._epoch
+        release = (
+            _validate_release(kwargs["release"])
+            if "release" in kwargs
+            else self._release
+        )
+        pre = _validate_pre(kwargs["pre"]) if "pre" in kwargs else self._pre
+        post = _validate_post(kwargs["post"]) if "post" in kwargs else self._post
+        dev = _validate_dev(kwargs["dev"]) if "dev" in kwargs else self._dev
+        local = _validate_local(kwargs["local"]) if "local" in kwargs else self._local
+
+        if (
+            epoch == self._epoch
+            and release == self._release
+            and pre == self._pre
+            and post == self._post
+            and dev == self._dev
+            and local == self._local
+        ):
+            return self
+
+        new_version = self.__class__.__new__(self.__class__)
+        new_version._key_cache = None
+        new_version._epoch = epoch
+        new_version._release = release
+        new_version._pre = pre
+        new_version._post = post
+        new_version._dev = dev
+        new_version._local = local
+
+        return new_version
+
+    @property
+    def _key(self) -> CmpKey:
+        if self._key_cache is None:
+            self._key_cache = _cmpkey(
+                self._epoch,
+                self._release,
+                self._pre,
+                self._post,
+                self._dev,
+                self._local,
+            )
+        return self._key_cache
+
+    @property
+    @_deprecated("Version._version is private and will be removed soon")
+    def _version(self) -> _Version:
+        return _Version(
+            self._epoch, self._release, self._dev, self._pre, self._post, self._local
+        )
+
+    @_version.setter
+    @_deprecated("Version._version is private and will be removed soon")
+    def _version(self, value: _Version) -> None:
+        self._epoch = value.epoch
+        self._release = value.release
+        self._dev = value.dev
+        self._pre = value.pre
+        self._post = value.post
+        self._local = value.local
+        self._key_cache = None
+
+    def __repr__(self) -> str:
+        """A representation of the Version that shows all internal state.
+
+        >>> Version('1.0.0')
+        
+        """
+        return f""
+
+    def __str__(self) -> str:
+        """A string representation of the version that can be round-tripped.
+
+        >>> str(Version("1.0a5"))
+        '1.0a5'
+        """
+        # This is a hot function, so not calling self.base_version
+        version = ".".join(map(str, self.release))
+
+        # Epoch
+        if self.epoch:
+            version = f"{self.epoch}!{version}"
+
+        # Pre-release
+        if self.pre is not None:
+            version += "".join(map(str, self.pre))
+
+        # Post-release
+        if self.post is not None:
+            version += f".post{self.post}"
+
+        # Development release
+        if self.dev is not None:
+            version += f".dev{self.dev}"
+
+        # Local version segment
+        if self.local is not None:
+            version += f"+{self.local}"
+
+        return version
+
+    @property
+    def _str(self) -> str:
+        """Internal property for match_args"""
+        return str(self)
+
+    @property
+    def epoch(self) -> int:
+        """The epoch of the version.
+
+        >>> Version("2.0.0").epoch
+        0
+        >>> Version("1!2.0.0").epoch
+        1
+        """
+        return self._epoch
+
+    @property
+    def release(self) -> tuple[int, ...]:
+        """The components of the "release" segment of the version.
+
+        >>> Version("1.2.3").release
+        (1, 2, 3)
+        >>> Version("2.0.0").release
+        (2, 0, 0)
+        >>> Version("1!2.0.0.post0").release
+        (2, 0, 0)
+
+        Includes trailing zeroes but not the epoch or any pre-release / development /
+        post-release suffixes.
+        """
+        return self._release
+
+    @property
+    def pre(self) -> tuple[str, int] | None:
+        """The pre-release segment of the version.
+
+        >>> print(Version("1.2.3").pre)
+        None
+        >>> Version("1.2.3a1").pre
+        ('a', 1)
+        >>> Version("1.2.3b1").pre
+        ('b', 1)
+        >>> Version("1.2.3rc1").pre
+        ('rc', 1)
+        """
+        return self._pre
+
+    @property
+    def post(self) -> int | None:
+        """The post-release number of the version.
+
+        >>> print(Version("1.2.3").post)
+        None
+        >>> Version("1.2.3.post1").post
+        1
+        """
+        return self._post[1] if self._post else None
+
+    @property
+    def dev(self) -> int | None:
+        """The development number of the version.
+
+        >>> print(Version("1.2.3").dev)
+        None
+        >>> Version("1.2.3.dev1").dev
+        1
+        """
+        return self._dev[1] if self._dev else None
+
+    @property
+    def local(self) -> str | None:
+        """The local version segment of the version.
+
+        >>> print(Version("1.2.3").local)
+        None
+        >>> Version("1.2.3+abc").local
+        'abc'
+        """
+        if self._local:
+            return ".".join(str(x) for x in self._local)
+        else:
+            return None
+
+    @property
+    def public(self) -> str:
+        """The public portion of the version.
+
+        >>> Version("1.2.3").public
+        '1.2.3'
+        >>> Version("1.2.3+abc").public
+        '1.2.3'
+        >>> Version("1!1.2.3dev1+abc").public
+        '1!1.2.3.dev1'
+        """
+        return str(self).split("+", 1)[0]
+
+    @property
+    def base_version(self) -> str:
+        """The "base version" of the version.
+
+        >>> Version("1.2.3").base_version
+        '1.2.3'
+        >>> Version("1.2.3+abc").base_version
+        '1.2.3'
+        >>> Version("1!1.2.3dev1+abc").base_version
+        '1!1.2.3'
+
+        The "base version" is the public version of the project without any pre or post
+        release markers.
+        """
+        release_segment = ".".join(map(str, self.release))
+        return f"{self.epoch}!{release_segment}" if self.epoch else release_segment
+
+    @property
+    def is_prerelease(self) -> bool:
+        """Whether this version is a pre-release.
+
+        >>> Version("1.2.3").is_prerelease
+        False
+        >>> Version("1.2.3a1").is_prerelease
+        True
+        >>> Version("1.2.3b1").is_prerelease
+        True
+        >>> Version("1.2.3rc1").is_prerelease
+        True
+        >>> Version("1.2.3dev1").is_prerelease
+        True
+        """
+        return self.dev is not None or self.pre is not None
+
+    @property
+    def is_postrelease(self) -> bool:
+        """Whether this version is a post-release.
+
+        >>> Version("1.2.3").is_postrelease
+        False
+        >>> Version("1.2.3.post1").is_postrelease
+        True
+        """
+        return self.post is not None
+
+    @property
+    def is_devrelease(self) -> bool:
+        """Whether this version is a development release.
+
+        >>> Version("1.2.3").is_devrelease
+        False
+        >>> Version("1.2.3.dev1").is_devrelease
+        True
+        """
+        return self.dev is not None
+
+    @property
+    def major(self) -> int:
+        """The first item of :attr:`release` or ``0`` if unavailable.
+
+        >>> Version("1.2.3").major
+        1
+        """
+        return self.release[0] if len(self.release) >= 1 else 0
+
+    @property
+    def minor(self) -> int:
+        """The second item of :attr:`release` or ``0`` if unavailable.
+
+        >>> Version("1.2.3").minor
+        2
+        >>> Version("1").minor
+        0
+        """
+        return self.release[1] if len(self.release) >= 2 else 0
+
+    @property
+    def micro(self) -> int:
+        """The third item of :attr:`release` or ``0`` if unavailable.
+
+        >>> Version("1.2.3").micro
+        3
+        >>> Version("1").micro
+        0
+        """
+        return self.release[2] if len(self.release) >= 3 else 0
+
+
+class _TrimmedRelease(Version):
+    __slots__ = ()
+
+    def __init__(self, version: str | Version) -> None:
+        if isinstance(version, Version):
+            self._epoch = version._epoch
+            self._release = version._release
+            self._dev = version._dev
+            self._pre = version._pre
+            self._post = version._post
+            self._local = version._local
+            self._key_cache = version._key_cache
+            return
+        super().__init__(version)  # pragma: no cover
+
+    @property
+    def release(self) -> tuple[int, ...]:
+        """
+        Release segment without any trailing zeros.
+
+        >>> _TrimmedRelease('1.0.0').release
+        (1,)
+        >>> _TrimmedRelease('0.0').release
+        (0,)
+        """
+        # This leaves one 0.
+        rel = super().release
+        len_release = len(rel)
+        i = len_release
+        while i > 1 and rel[i - 1] == 0:
+            i -= 1
+        return rel if i == len_release else rel[:i]
+
+
+def _parse_letter_version(
+    letter: str | None, number: str | bytes | SupportsInt | None
+) -> tuple[str, int] | None:
+    if letter:
+        # We normalize any letters to their lower case form
+        letter = letter.lower()
+
+        # We consider some words to be alternate spellings of other words and
+        # in those cases we want to normalize the spellings to our preferred
+        # spelling.
+        letter = _LETTER_NORMALIZATION.get(letter, letter)
+
+        # We consider there to be an implicit 0 in a pre-release if there is
+        # not a numeral associated with it.
+        return letter, int(number or 0)
+
+    if number:
+        # We assume if we are given a number, but we are not given a letter
+        # then this is using the implicit post release syntax (e.g. 1.0-1)
+        return "post", int(number)
+
+    return None
+
+
+_local_version_separators = re.compile(r"[\._-]")
+
+
+def _parse_local_version(local: str | None) -> LocalType | None:
+    """
+    Takes a string like abc.1.twelve and turns it into ("abc", 1, "twelve").
+    """
+    if local is not None:
+        return tuple(
+            part.lower() if not part.isdigit() else int(part)
+            for part in _local_version_separators.split(local)
+        )
+    return None
+
+
+def _cmpkey(
+    epoch: int,
+    release: tuple[int, ...],
+    pre: tuple[str, int] | None,
+    post: tuple[str, int] | None,
+    dev: tuple[str, int] | None,
+    local: LocalType | None,
+) -> CmpKey:
+    # When we compare a release version, we want to compare it with all of the
+    # trailing zeros removed. We will use this for our sorting key.
+    len_release = len(release)
+    i = len_release
+    while i and release[i - 1] == 0:
+        i -= 1
+    _release = release if i == len_release else release[:i]
+
+    # We need to "trick" the sorting algorithm to put 1.0.dev0 before 1.0a0.
+    # We'll do this by abusing the pre segment, but we _only_ want to do this
+    # if there is not a pre or a post segment. If we have one of those then
+    # the normal sorting rules will handle this case correctly.
+    if pre is None and post is None and dev is not None:
+        _pre: CmpPrePostDevType = NegativeInfinity
+    # Versions without a pre-release (except as noted above) should sort after
+    # those with one.
+    elif pre is None:
+        _pre = Infinity
+    else:
+        _pre = pre
+
+    # Versions without a post segment should sort before those with one.
+    if post is None:
+        _post: CmpPrePostDevType = NegativeInfinity
+
+    else:
+        _post = post
+
+    # Versions without a development segment should sort after those with one.
+    if dev is None:
+        _dev: CmpPrePostDevType = Infinity
+
+    else:
+        _dev = dev
+
+    if local is None:
+        # Versions without a local segment should sort before those with one.
+        _local: CmpLocalType = NegativeInfinity
+    else:
+        # Versions with a local segment need that segment parsed to implement
+        # the sorting rules in PEP440.
+        # - Alpha numeric segments sort before numeric segments
+        # - Alpha numeric segments sort lexicographically
+        # - Numeric segments sort numerically
+        # - Shorter versions sort before longer versions when the prefixes
+        #   match exactly
+        _local = tuple(
+            (i, "") if isinstance(i, int) else (NegativeInfinity, i) for i in local
+        )
+
+    return epoch, _release, _pre, _post, _dev, _local
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/INSTALLER
new file mode 100644
index 0000000000000000000000000000000000000000..f79e4cb9aaf0b2d9e8ba78861e2071317b2384b3
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/INSTALLER
@@ -0,0 +1 @@
+conda
\ No newline at end of file
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/METADATA
new file mode 100644
index 0000000000000000000000000000000000000000..6b0908fb707440b3828bfe2edb1799382693199e
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/METADATA
@@ -0,0 +1,350 @@
+Metadata-Version: 2.4
+Name: platformdirs
+Version: 4.4.0
+Summary: A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`.
+Project-URL: Changelog, https://github.com/tox-dev/platformdirs/releases
+Project-URL: Documentation, https://platformdirs.readthedocs.io
+Project-URL: Homepage, https://github.com/tox-dev/platformdirs
+Project-URL: Source, https://github.com/tox-dev/platformdirs
+Project-URL: Tracker, https://github.com/tox-dev/platformdirs/issues
+Maintainer-email: Bernát Gábor , Julian Berman , Ofek Lev , Ronny Pfannschmidt 
+License-Expression: MIT
+License-File: LICENSE
+Keywords: appdirs,application,cache,directory,log,user
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.9
+Provides-Extra: docs
+Requires-Dist: furo>=2024.8.6; extra == 'docs'
+Requires-Dist: proselint>=0.14; extra == 'docs'
+Requires-Dist: sphinx-autodoc-typehints>=3; extra == 'docs'
+Requires-Dist: sphinx>=8.1.3; extra == 'docs'
+Provides-Extra: test
+Requires-Dist: appdirs==1.4.4; extra == 'test'
+Requires-Dist: covdefaults>=2.3; extra == 'test'
+Requires-Dist: pytest-cov>=6; extra == 'test'
+Requires-Dist: pytest-mock>=3.14; extra == 'test'
+Requires-Dist: pytest>=8.3.4; extra == 'test'
+Provides-Extra: type
+Requires-Dist: mypy>=1.14.1; extra == 'type'
+Description-Content-Type: text/x-rst
+
+The problem
+===========
+
+.. image:: https://badge.fury.io/py/platformdirs.svg
+   :target: https://badge.fury.io/py/platformdirs
+.. image:: https://img.shields.io/pypi/pyversions/platformdirs.svg
+   :target: https://pypi.python.org/pypi/platformdirs/
+.. image:: https://github.com/tox-dev/platformdirs/actions/workflows/check.yaml/badge.svg
+   :target: https://github.com/platformdirs/platformdirs/actions
+.. image:: https://static.pepy.tech/badge/platformdirs/month
+   :target: https://pepy.tech/project/platformdirs
+
+When writing desktop application, finding the right location to store user data
+and configuration varies per platform. Even for single-platform apps, there
+may by plenty of nuances in figuring out the right location.
+
+For example, if running on macOS, you should use::
+
+    ~/Library/Application Support/
+
+If on Windows (at least English Win) that should be::
+
+    C:\Documents and Settings\\Application Data\Local Settings\\
+
+or possibly::
+
+    C:\Documents and Settings\\Application Data\\
+
+for `roaming profiles `_ but that is another story.
+
+On Linux (and other Unices), according to the `XDG Basedir Spec`_, it should be::
+
+    ~/.local/share/
+
+.. _XDG Basedir Spec: https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html
+
+``platformdirs`` to the rescue
+==============================
+
+This kind of thing is what the ``platformdirs`` package is for.
+``platformdirs`` will help you choose an appropriate:
+
+- user data dir (``user_data_dir``)
+- user config dir (``user_config_dir``)
+- user cache dir (``user_cache_dir``)
+- site data dir (``site_data_dir``)
+- site config dir (``site_config_dir``)
+- user log dir (``user_log_dir``)
+- user documents dir (``user_documents_dir``)
+- user downloads dir (``user_downloads_dir``)
+- user pictures dir (``user_pictures_dir``)
+- user videos dir (``user_videos_dir``)
+- user music dir (``user_music_dir``)
+- user desktop dir (``user_desktop_dir``)
+- user runtime dir (``user_runtime_dir``)
+
+And also:
+
+- Is slightly opinionated on the directory names used. Look for "OPINION" in
+  documentation and code for when an opinion is being applied.
+
+Example output
+==============
+
+On macOS:
+
+.. code-block:: pycon
+
+    >>> from platformdirs import *
+    >>> appname = "SuperApp"
+    >>> appauthor = "Acme"
+    >>> user_data_dir(appname, appauthor)
+    '/Users/trentm/Library/Application Support/SuperApp'
+    >>> user_config_dir(appname, appauthor)
+    '/Users/trentm/Library/Application Support/SuperApp'
+    >>> user_cache_dir(appname, appauthor)
+    '/Users/trentm/Library/Caches/SuperApp'
+    >>> site_data_dir(appname, appauthor)
+    '/Library/Application Support/SuperApp'
+    >>> site_config_dir(appname, appauthor)
+    '/Library/Application Support/SuperApp'
+    >>> user_log_dir(appname, appauthor)
+    '/Users/trentm/Library/Logs/SuperApp'
+    >>> user_documents_dir()
+    '/Users/trentm/Documents'
+    >>> user_downloads_dir()
+    '/Users/trentm/Downloads'
+    >>> user_pictures_dir()
+    '/Users/trentm/Pictures'
+    >>> user_videos_dir()
+    '/Users/trentm/Movies'
+    >>> user_music_dir()
+    '/Users/trentm/Music'
+    >>> user_desktop_dir()
+    '/Users/trentm/Desktop'
+    >>> user_runtime_dir(appname, appauthor)
+    '/Users/trentm/Library/Caches/TemporaryItems/SuperApp'
+
+On Windows:
+
+.. code-block:: pycon
+
+    >>> from platformdirs import *
+    >>> appname = "SuperApp"
+    >>> appauthor = "Acme"
+    >>> user_data_dir(appname, appauthor)
+    'C:\\Users\\trentm\\AppData\\Local\\Acme\\SuperApp'
+    >>> user_data_dir(appname, appauthor, roaming=True)
+    'C:\\Users\\trentm\\AppData\\Roaming\\Acme\\SuperApp'
+    >>> user_config_dir(appname, appauthor)
+    'C:\\Users\\trentm\\AppData\\Local\\Acme\\SuperApp'
+    >>> user_cache_dir(appname, appauthor)
+    'C:\\Users\\trentm\\AppData\\Local\\Acme\\SuperApp\\Cache'
+    >>> site_data_dir(appname, appauthor)
+    'C:\\ProgramData\\Acme\\SuperApp'
+    >>> site_config_dir(appname, appauthor)
+    'C:\\ProgramData\\Acme\\SuperApp'
+    >>> user_log_dir(appname, appauthor)
+    'C:\\Users\\trentm\\AppData\\Local\\Acme\\SuperApp\\Logs'
+    >>> user_documents_dir()
+    'C:\\Users\\trentm\\Documents'
+    >>> user_downloads_dir()
+    'C:\\Users\\trentm\\Downloads'
+    >>> user_pictures_dir()
+    'C:\\Users\\trentm\\Pictures'
+    >>> user_videos_dir()
+    'C:\\Users\\trentm\\Videos'
+    >>> user_music_dir()
+    'C:\\Users\\trentm\\Music'
+    >>> user_desktop_dir()
+    'C:\\Users\\trentm\\Desktop'
+    >>> user_runtime_dir(appname, appauthor)
+    'C:\\Users\\trentm\\AppData\\Local\\Temp\\Acme\\SuperApp'
+
+On Linux:
+
+.. code-block:: pycon
+
+    >>> from platformdirs import *
+    >>> appname = "SuperApp"
+    >>> appauthor = "Acme"
+    >>> user_data_dir(appname, appauthor)
+    '/home/trentm/.local/share/SuperApp'
+    >>> user_config_dir(appname)
+    '/home/trentm/.config/SuperApp'
+    >>> user_cache_dir(appname, appauthor)
+    '/home/trentm/.cache/SuperApp'
+    >>> site_data_dir(appname, appauthor)
+    '/usr/local/share/SuperApp'
+    >>> site_data_dir(appname, appauthor, multipath=True)
+    '/usr/local/share/SuperApp:/usr/share/SuperApp'
+    >>> site_config_dir(appname)
+    '/etc/xdg/SuperApp'
+    >>> os.environ["XDG_CONFIG_DIRS"] = "/etc:/usr/local/etc"
+    >>> site_config_dir(appname, multipath=True)
+    '/etc/SuperApp:/usr/local/etc/SuperApp'
+    >>> user_log_dir(appname, appauthor)
+    '/home/trentm/.local/state/SuperApp/log'
+    >>> user_documents_dir()
+    '/home/trentm/Documents'
+    >>> user_downloads_dir()
+    '/home/trentm/Downloads'
+    >>> user_pictures_dir()
+    '/home/trentm/Pictures'
+    >>> user_videos_dir()
+    '/home/trentm/Videos'
+    >>> user_music_dir()
+    '/home/trentm/Music'
+    >>> user_desktop_dir()
+    '/home/trentm/Desktop'
+    >>> user_runtime_dir(appname, appauthor)
+    '/run/user/{os.getuid()}/SuperApp'
+
+On Android::
+
+    >>> from platformdirs import *
+    >>> appname = "SuperApp"
+    >>> appauthor = "Acme"
+    >>> user_data_dir(appname, appauthor)
+    '/data/data/com.myApp/files/SuperApp'
+    >>> user_config_dir(appname)
+    '/data/data/com.myApp/shared_prefs/SuperApp'
+    >>> user_cache_dir(appname, appauthor)
+    '/data/data/com.myApp/cache/SuperApp'
+    >>> site_data_dir(appname, appauthor)
+    '/data/data/com.myApp/files/SuperApp'
+    >>> site_config_dir(appname)
+    '/data/data/com.myApp/shared_prefs/SuperApp'
+    >>> user_log_dir(appname, appauthor)
+    '/data/data/com.myApp/cache/SuperApp/log'
+    >>> user_documents_dir()
+    '/storage/emulated/0/Documents'
+    >>> user_downloads_dir()
+    '/storage/emulated/0/Downloads'
+    >>> user_pictures_dir()
+    '/storage/emulated/0/Pictures'
+    >>> user_videos_dir()
+    '/storage/emulated/0/DCIM/Camera'
+    >>> user_music_dir()
+    '/storage/emulated/0/Music'
+    >>> user_desktop_dir()
+    '/storage/emulated/0/Desktop'
+    >>> user_runtime_dir(appname, appauthor)
+    '/data/data/com.myApp/cache/SuperApp/tmp'
+
+Note: Some android apps like Termux and Pydroid are used as shells. These
+apps are used by the end user to emulate Linux environment. Presence of
+``SHELL`` environment variable is used by Platformdirs to differentiate
+between general android apps and android apps used as shells. Shell android
+apps also support ``XDG_*`` environment variables.
+
+
+``PlatformDirs`` for convenience
+================================
+
+.. code-block:: pycon
+
+    >>> from platformdirs import PlatformDirs
+    >>> dirs = PlatformDirs("SuperApp", "Acme")
+    >>> dirs.user_data_dir
+    '/Users/trentm/Library/Application Support/SuperApp'
+    >>> dirs.user_config_dir
+    '/Users/trentm/Library/Application Support/SuperApp'
+    >>> dirs.user_cache_dir
+    '/Users/trentm/Library/Caches/SuperApp'
+    >>> dirs.site_data_dir
+    '/Library/Application Support/SuperApp'
+    >>> dirs.site_config_dir
+    '/Library/Application Support/SuperApp'
+    >>> dirs.user_cache_dir
+    '/Users/trentm/Library/Caches/SuperApp'
+    >>> dirs.user_log_dir
+    '/Users/trentm/Library/Logs/SuperApp'
+    >>> dirs.user_documents_dir
+    '/Users/trentm/Documents'
+    >>> dirs.user_downloads_dir
+    '/Users/trentm/Downloads'
+    >>> dirs.user_pictures_dir
+    '/Users/trentm/Pictures'
+    >>> dirs.user_videos_dir
+    '/Users/trentm/Movies'
+    >>> dirs.user_music_dir
+    '/Users/trentm/Music'
+    >>> dirs.user_desktop_dir
+    '/Users/trentm/Desktop'
+    >>> dirs.user_runtime_dir
+    '/Users/trentm/Library/Caches/TemporaryItems/SuperApp'
+
+Per-version isolation
+=====================
+
+If you have multiple versions of your app in use that you want to be
+able to run side-by-side, then you may want version-isolation for these
+dirs::
+
+    >>> from platformdirs import PlatformDirs
+    >>> dirs = PlatformDirs("SuperApp", "Acme", version="1.0")
+    >>> dirs.user_data_dir
+    '/Users/trentm/Library/Application Support/SuperApp/1.0'
+    >>> dirs.user_config_dir
+    '/Users/trentm/Library/Application Support/SuperApp/1.0'
+    >>> dirs.user_cache_dir
+    '/Users/trentm/Library/Caches/SuperApp/1.0'
+    >>> dirs.site_data_dir
+    '/Library/Application Support/SuperApp/1.0'
+    >>> dirs.site_config_dir
+    '/Library/Application Support/SuperApp/1.0'
+    >>> dirs.user_log_dir
+    '/Users/trentm/Library/Logs/SuperApp/1.0'
+    >>> dirs.user_documents_dir
+    '/Users/trentm/Documents'
+    >>> dirs.user_downloads_dir
+    '/Users/trentm/Downloads'
+    >>> dirs.user_pictures_dir
+    '/Users/trentm/Pictures'
+    >>> dirs.user_videos_dir
+    '/Users/trentm/Movies'
+    >>> dirs.user_music_dir
+    '/Users/trentm/Music'
+    >>> dirs.user_desktop_dir
+    '/Users/trentm/Desktop'
+    >>> dirs.user_runtime_dir
+    '/Users/trentm/Library/Caches/TemporaryItems/SuperApp/1.0'
+
+Be wary of using this for configuration files though; you'll need to handle
+migrating configuration files manually.
+
+Why this Fork?
+==============
+
+This repository is a friendly fork of the wonderful work started by
+`ActiveState `_ who created
+``appdirs``, this package's ancestor.
+
+Maintaining an open source project is no easy task, particularly
+from within an organization, and the Python community is indebted
+to ``appdirs`` (and to Trent Mick and Jeff Rouse in particular) for
+creating an incredibly useful simple module, as evidenced by the wide
+number of users it has attracted over the years.
+
+Nonetheless, given the number of long-standing open issues
+and pull requests, and no clear path towards `ensuring
+that maintenance of the package would continue or grow
+`_, this fork was
+created.
+
+Contributions are most welcome.
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/RECORD
new file mode 100644
index 0000000000000000000000000000000000000000..09572f1780ad3554e93d8309547e9bc802a60371
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/RECORD
@@ -0,0 +1,15 @@
+platformdirs-4.4.0.dist-info/INSTALLER,sha256=5hhM4Q4mYTT9z6QB6PGpUAW81PGNFrYrdXMj4oM_6ak,2
+platformdirs-4.4.0.dist-info/METADATA,sha256=u8UhbV9Md7-8VyJyZNUuZrzN5xzPeedeGmBG0CnTAiM,12831
+platformdirs-4.4.0.dist-info/RECORD,,
+platformdirs-4.4.0.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+platformdirs-4.4.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+platformdirs-4.4.0.dist-info/licenses/LICENSE,sha256=KeD9YukphQ6G6yjD_czwzv30-pSHkBHP-z0NS-1tTbY,1089
+platformdirs/__init__.py,sha256=iORRy6_lZ9tXLvO0W6fJPn8QV7F532ivl-f2WGmabBc,22284
+platformdirs/__main__.py,sha256=HnsUQHpiBaiTxwcmwVw-nFaPdVNZtQIdi1eWDtI-MzI,1493
+platformdirs/android.py,sha256=r0DshVBf-RO1jXJGX8C4Til7F1XWt-bkdWMgmvEiaYg,9013
+platformdirs/api.py,sha256=wPHOlwOsfz2oqQZ6A2FcCu5kEAj-JondzoNOHYFQ0h8,9281
+platformdirs/macos.py,sha256=0XoOgin1NK7Qki7iskD-oS8xKxw6bXgoKEgdqpCRAFQ,6322
+platformdirs/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+platformdirs/unix.py,sha256=WZmkUA--L3JNRGmz32s35YfoD3ica6xKIPdCV_HhLcs,10458
+platformdirs/version.py,sha256=i31fi3nNO19D2FdSx8aldD7IFLSqm2YrAo6SmkV0FLM,704
+platformdirs/windows.py,sha256=IFpiohUBwxPtCzlyKwNtxyW4Jk8haa6W8o59mfrDXVo,10125
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/REQUESTED b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/REQUESTED
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/WHEEL
new file mode 100644
index 0000000000000000000000000000000000000000..12228d414b6cfed7c39d3781c85c63256a1d7fb5
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/WHEEL
@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.27.0
+Root-Is-Purelib: true
+Tag: py3-none-any
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/licenses/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/licenses/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..f35fed9191b1142ddaada8a96de4a9461c5d796c
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs-4.4.0.dist-info/licenses/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2010-202x The platformdirs developers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..02daa5914a82da08293dc1675e75c11ed3fb2bd8
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/__init__.py
@@ -0,0 +1,631 @@
+"""
+Utilities for determining application-specific dirs.
+
+See  for details and usage.
+
+"""
+
+from __future__ import annotations
+
+import os
+import sys
+from typing import TYPE_CHECKING
+
+from .api import PlatformDirsABC
+from .version import __version__
+from .version import __version_tuple__ as __version_info__
+
+if TYPE_CHECKING:
+    from pathlib import Path
+    from typing import Literal
+
+if sys.platform == "win32":
+    from platformdirs.windows import Windows as _Result
+elif sys.platform == "darwin":
+    from platformdirs.macos import MacOS as _Result
+else:
+    from platformdirs.unix import Unix as _Result
+
+
+def _set_platform_dir_class() -> type[PlatformDirsABC]:
+    if os.getenv("ANDROID_DATA") == "/data" and os.getenv("ANDROID_ROOT") == "/system":
+        if os.getenv("SHELL") or os.getenv("PREFIX"):
+            return _Result
+
+        from platformdirs.android import _android_folder  # noqa: PLC0415
+
+        if _android_folder() is not None:
+            from platformdirs.android import Android  # noqa: PLC0415
+
+            return Android  # return to avoid redefinition of a result
+
+    return _Result
+
+
+if TYPE_CHECKING:
+    # Work around mypy issue: https://github.com/python/mypy/issues/10962
+    PlatformDirs = _Result
+else:
+    PlatformDirs = _set_platform_dir_class()  #: Currently active platform
+AppDirs = PlatformDirs  #: Backwards compatibility with appdirs
+
+
+def user_data_dir(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    roaming: bool = False,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> str:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param roaming: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: data directory tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        roaming=roaming,
+        ensure_exists=ensure_exists,
+    ).user_data_dir
+
+
+def site_data_dir(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    multipath: bool = False,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> str:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param multipath: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: data directory shared by users
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        multipath=multipath,
+        ensure_exists=ensure_exists,
+    ).site_data_dir
+
+
+def user_config_dir(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    roaming: bool = False,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> str:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param roaming: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: config directory tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        roaming=roaming,
+        ensure_exists=ensure_exists,
+    ).user_config_dir
+
+
+def site_config_dir(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    multipath: bool = False,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> str:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param multipath: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: config directory shared by the users
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        multipath=multipath,
+        ensure_exists=ensure_exists,
+    ).site_config_dir
+
+
+def user_cache_dir(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    opinion: bool = True,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> str:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param opinion: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: cache directory tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        opinion=opinion,
+        ensure_exists=ensure_exists,
+    ).user_cache_dir
+
+
+def site_cache_dir(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    opinion: bool = True,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> str:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param opinion: See `opinion `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: cache directory tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        opinion=opinion,
+        ensure_exists=ensure_exists,
+    ).site_cache_dir
+
+
+def user_state_dir(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    roaming: bool = False,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> str:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param roaming: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: state directory tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        roaming=roaming,
+        ensure_exists=ensure_exists,
+    ).user_state_dir
+
+
+def user_log_dir(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    opinion: bool = True,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> str:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param opinion: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: log directory tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        opinion=opinion,
+        ensure_exists=ensure_exists,
+    ).user_log_dir
+
+
+def user_documents_dir() -> str:
+    """:returns: documents directory tied to the user"""
+    return PlatformDirs().user_documents_dir
+
+
+def user_downloads_dir() -> str:
+    """:returns: downloads directory tied to the user"""
+    return PlatformDirs().user_downloads_dir
+
+
+def user_pictures_dir() -> str:
+    """:returns: pictures directory tied to the user"""
+    return PlatformDirs().user_pictures_dir
+
+
+def user_videos_dir() -> str:
+    """:returns: videos directory tied to the user"""
+    return PlatformDirs().user_videos_dir
+
+
+def user_music_dir() -> str:
+    """:returns: music directory tied to the user"""
+    return PlatformDirs().user_music_dir
+
+
+def user_desktop_dir() -> str:
+    """:returns: desktop directory tied to the user"""
+    return PlatformDirs().user_desktop_dir
+
+
+def user_runtime_dir(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    opinion: bool = True,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> str:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param opinion: See `opinion `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: runtime directory tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        opinion=opinion,
+        ensure_exists=ensure_exists,
+    ).user_runtime_dir
+
+
+def site_runtime_dir(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    opinion: bool = True,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> str:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param opinion: See `opinion `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: runtime directory shared by users
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        opinion=opinion,
+        ensure_exists=ensure_exists,
+    ).site_runtime_dir
+
+
+def user_data_path(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    roaming: bool = False,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> Path:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param roaming: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: data path tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        roaming=roaming,
+        ensure_exists=ensure_exists,
+    ).user_data_path
+
+
+def site_data_path(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    multipath: bool = False,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> Path:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param multipath: See `multipath `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: data path shared by users
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        multipath=multipath,
+        ensure_exists=ensure_exists,
+    ).site_data_path
+
+
+def user_config_path(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    roaming: bool = False,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> Path:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param roaming: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: config path tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        roaming=roaming,
+        ensure_exists=ensure_exists,
+    ).user_config_path
+
+
+def site_config_path(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    multipath: bool = False,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> Path:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param multipath: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: config path shared by the users
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        multipath=multipath,
+        ensure_exists=ensure_exists,
+    ).site_config_path
+
+
+def site_cache_path(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    opinion: bool = True,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> Path:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param opinion: See `opinion `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: cache directory tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        opinion=opinion,
+        ensure_exists=ensure_exists,
+    ).site_cache_path
+
+
+def user_cache_path(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    opinion: bool = True,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> Path:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param opinion: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: cache path tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        opinion=opinion,
+        ensure_exists=ensure_exists,
+    ).user_cache_path
+
+
+def user_state_path(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    roaming: bool = False,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> Path:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param roaming: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: state path tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        roaming=roaming,
+        ensure_exists=ensure_exists,
+    ).user_state_path
+
+
+def user_log_path(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    opinion: bool = True,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> Path:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param opinion: See `roaming `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: log path tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        opinion=opinion,
+        ensure_exists=ensure_exists,
+    ).user_log_path
+
+
+def user_documents_path() -> Path:
+    """:returns: documents a path tied to the user"""
+    return PlatformDirs().user_documents_path
+
+
+def user_downloads_path() -> Path:
+    """:returns: downloads path tied to the user"""
+    return PlatformDirs().user_downloads_path
+
+
+def user_pictures_path() -> Path:
+    """:returns: pictures path tied to the user"""
+    return PlatformDirs().user_pictures_path
+
+
+def user_videos_path() -> Path:
+    """:returns: videos path tied to the user"""
+    return PlatformDirs().user_videos_path
+
+
+def user_music_path() -> Path:
+    """:returns: music path tied to the user"""
+    return PlatformDirs().user_music_path
+
+
+def user_desktop_path() -> Path:
+    """:returns: desktop path tied to the user"""
+    return PlatformDirs().user_desktop_path
+
+
+def user_runtime_path(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    opinion: bool = True,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> Path:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param opinion: See `opinion `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: runtime path tied to the user
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        opinion=opinion,
+        ensure_exists=ensure_exists,
+    ).user_runtime_path
+
+
+def site_runtime_path(
+    appname: str | None = None,
+    appauthor: str | Literal[False] | None = None,
+    version: str | None = None,
+    opinion: bool = True,  # noqa: FBT001, FBT002
+    ensure_exists: bool = False,  # noqa: FBT001, FBT002
+) -> Path:
+    """
+    :param appname: See `appname `.
+    :param appauthor: See `appauthor `.
+    :param version: See `version `.
+    :param opinion: See `opinion `.
+    :param ensure_exists: See `ensure_exists `.
+    :returns: runtime path shared by users
+    """
+    return PlatformDirs(
+        appname=appname,
+        appauthor=appauthor,
+        version=version,
+        opinion=opinion,
+        ensure_exists=ensure_exists,
+    ).site_runtime_path
+
+
+__all__ = [
+    "AppDirs",
+    "PlatformDirs",
+    "PlatformDirsABC",
+    "__version__",
+    "__version_info__",
+    "site_cache_dir",
+    "site_cache_path",
+    "site_config_dir",
+    "site_config_path",
+    "site_data_dir",
+    "site_data_path",
+    "site_runtime_dir",
+    "site_runtime_path",
+    "user_cache_dir",
+    "user_cache_path",
+    "user_config_dir",
+    "user_config_path",
+    "user_data_dir",
+    "user_data_path",
+    "user_desktop_dir",
+    "user_desktop_path",
+    "user_documents_dir",
+    "user_documents_path",
+    "user_downloads_dir",
+    "user_downloads_path",
+    "user_log_dir",
+    "user_log_path",
+    "user_music_dir",
+    "user_music_path",
+    "user_pictures_dir",
+    "user_pictures_path",
+    "user_runtime_dir",
+    "user_runtime_path",
+    "user_state_dir",
+    "user_state_path",
+    "user_videos_dir",
+    "user_videos_path",
+]
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/__main__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/__main__.py
new file mode 100644
index 0000000000000000000000000000000000000000..922c521358e349470ec48d6372b8f8ee8641128a
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/__main__.py
@@ -0,0 +1,55 @@
+"""Main entry point."""
+
+from __future__ import annotations
+
+from platformdirs import PlatformDirs, __version__
+
+PROPS = (
+    "user_data_dir",
+    "user_config_dir",
+    "user_cache_dir",
+    "user_state_dir",
+    "user_log_dir",
+    "user_documents_dir",
+    "user_downloads_dir",
+    "user_pictures_dir",
+    "user_videos_dir",
+    "user_music_dir",
+    "user_runtime_dir",
+    "site_data_dir",
+    "site_config_dir",
+    "site_cache_dir",
+    "site_runtime_dir",
+)
+
+
+def main() -> None:
+    """Run the main entry point."""
+    app_name = "MyApp"
+    app_author = "MyCompany"
+
+    print(f"-- platformdirs {__version__} --")  # noqa: T201
+
+    print("-- app dirs (with optional 'version')")  # noqa: T201
+    dirs = PlatformDirs(app_name, app_author, version="1.0")
+    for prop in PROPS:
+        print(f"{prop}: {getattr(dirs, prop)}")  # noqa: T201
+
+    print("\n-- app dirs (without optional 'version')")  # noqa: T201
+    dirs = PlatformDirs(app_name, app_author)
+    for prop in PROPS:
+        print(f"{prop}: {getattr(dirs, prop)}")  # noqa: T201
+
+    print("\n-- app dirs (without optional 'appauthor')")  # noqa: T201
+    dirs = PlatformDirs(app_name)
+    for prop in PROPS:
+        print(f"{prop}: {getattr(dirs, prop)}")  # noqa: T201
+
+    print("\n-- app dirs (with disabled 'appauthor')")  # noqa: T201
+    dirs = PlatformDirs(app_name, appauthor=False)
+    for prop in PROPS:
+        print(f"{prop}: {getattr(dirs, prop)}")  # noqa: T201
+
+
+if __name__ == "__main__":
+    main()
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/android.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/android.py
new file mode 100644
index 0000000000000000000000000000000000000000..92efc852d3818b70a708ab61ba2b291eb5a6ee67
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/android.py
@@ -0,0 +1,249 @@
+"""Android."""
+
+from __future__ import annotations
+
+import os
+import re
+import sys
+from functools import lru_cache
+from typing import TYPE_CHECKING, cast
+
+from .api import PlatformDirsABC
+
+
+class Android(PlatformDirsABC):
+    """
+    Follows the guidance `from here `_.
+
+    Makes use of the `appname `, `version
+    `, `ensure_exists `.
+
+    """
+
+    @property
+    def user_data_dir(self) -> str:
+        """:return: data directory tied to the user, e.g. ``/data/user///files/``"""
+        return self._append_app_name_and_version(cast("str", _android_folder()), "files")
+
+    @property
+    def site_data_dir(self) -> str:
+        """:return: data directory shared by users, same as `user_data_dir`"""
+        return self.user_data_dir
+
+    @property
+    def user_config_dir(self) -> str:
+        """
+        :return: config directory tied to the user, e.g. \
+        ``/data/user///shared_prefs/``
+        """
+        return self._append_app_name_and_version(cast("str", _android_folder()), "shared_prefs")
+
+    @property
+    def site_config_dir(self) -> str:
+        """:return: config directory shared by the users, same as `user_config_dir`"""
+        return self.user_config_dir
+
+    @property
+    def user_cache_dir(self) -> str:
+        """:return: cache directory tied to the user, e.g.,``/data/user///cache/``"""
+        return self._append_app_name_and_version(cast("str", _android_folder()), "cache")
+
+    @property
+    def site_cache_dir(self) -> str:
+        """:return: cache directory shared by users, same as `user_cache_dir`"""
+        return self.user_cache_dir
+
+    @property
+    def user_state_dir(self) -> str:
+        """:return: state directory tied to the user, same as `user_data_dir`"""
+        return self.user_data_dir
+
+    @property
+    def user_log_dir(self) -> str:
+        """
+        :return: log directory tied to the user, same as `user_cache_dir` if not opinionated else ``log`` in it,
+          e.g. ``/data/user///cache//log``
+        """
+        path = self.user_cache_dir
+        if self.opinion:
+            path = os.path.join(path, "log")  # noqa: PTH118
+        return path
+
+    @property
+    def user_documents_dir(self) -> str:
+        """:return: documents directory tied to the user e.g. ``/storage/emulated/0/Documents``"""
+        return _android_documents_folder()
+
+    @property
+    def user_downloads_dir(self) -> str:
+        """:return: downloads directory tied to the user e.g. ``/storage/emulated/0/Downloads``"""
+        return _android_downloads_folder()
+
+    @property
+    def user_pictures_dir(self) -> str:
+        """:return: pictures directory tied to the user e.g. ``/storage/emulated/0/Pictures``"""
+        return _android_pictures_folder()
+
+    @property
+    def user_videos_dir(self) -> str:
+        """:return: videos directory tied to the user e.g. ``/storage/emulated/0/DCIM/Camera``"""
+        return _android_videos_folder()
+
+    @property
+    def user_music_dir(self) -> str:
+        """:return: music directory tied to the user e.g. ``/storage/emulated/0/Music``"""
+        return _android_music_folder()
+
+    @property
+    def user_desktop_dir(self) -> str:
+        """:return: desktop directory tied to the user e.g. ``/storage/emulated/0/Desktop``"""
+        return "/storage/emulated/0/Desktop"
+
+    @property
+    def user_runtime_dir(self) -> str:
+        """
+        :return: runtime directory tied to the user, same as `user_cache_dir` if not opinionated else ``tmp`` in it,
+          e.g. ``/data/user///cache//tmp``
+        """
+        path = self.user_cache_dir
+        if self.opinion:
+            path = os.path.join(path, "tmp")  # noqa: PTH118
+        return path
+
+    @property
+    def site_runtime_dir(self) -> str:
+        """:return: runtime directory shared by users, same as `user_runtime_dir`"""
+        return self.user_runtime_dir
+
+
+@lru_cache(maxsize=1)
+def _android_folder() -> str | None:  # noqa: C901
+    """:return: base folder for the Android OS or None if it cannot be found"""
+    result: str | None = None
+    # type checker isn't happy with our "import android", just don't do this when type checking see
+    # https://stackoverflow.com/a/61394121
+    if not TYPE_CHECKING:
+        try:
+            # First try to get a path to android app using python4android (if available)...
+            from android import mActivity  # noqa: PLC0415
+
+            context = cast("android.content.Context", mActivity.getApplicationContext())  # noqa: F821
+            result = context.getFilesDir().getParentFile().getAbsolutePath()
+        except Exception:  # noqa: BLE001
+            result = None
+    if result is None:
+        try:
+            # ...and fall back to using plain pyjnius, if python4android isn't available or doesn't deliver any useful
+            # result...
+            from jnius import autoclass  # noqa: PLC0415
+
+            context = autoclass("android.content.Context")
+            result = context.getFilesDir().getParentFile().getAbsolutePath()
+        except Exception:  # noqa: BLE001
+            result = None
+    if result is None:
+        # and if that fails, too, find an android folder looking at path on the sys.path
+        # warning: only works for apps installed under /data, not adopted storage etc.
+        pattern = re.compile(r"/data/(data|user/\d+)/(.+)/files")
+        for path in sys.path:
+            if pattern.match(path):
+                result = path.split("/files")[0]
+                break
+        else:
+            result = None
+    if result is None:
+        # one last try: find an android folder looking at path on the sys.path taking adopted storage paths into
+        # account
+        pattern = re.compile(r"/mnt/expand/[a-fA-F0-9-]{36}/(data|user/\d+)/(.+)/files")
+        for path in sys.path:
+            if pattern.match(path):
+                result = path.split("/files")[0]
+                break
+        else:
+            result = None
+    return result
+
+
+@lru_cache(maxsize=1)
+def _android_documents_folder() -> str:
+    """:return: documents folder for the Android OS"""
+    # Get directories with pyjnius
+    try:
+        from jnius import autoclass  # noqa: PLC0415
+
+        context = autoclass("android.content.Context")
+        environment = autoclass("android.os.Environment")
+        documents_dir: str = context.getExternalFilesDir(environment.DIRECTORY_DOCUMENTS).getAbsolutePath()
+    except Exception:  # noqa: BLE001
+        documents_dir = "/storage/emulated/0/Documents"
+
+    return documents_dir
+
+
+@lru_cache(maxsize=1)
+def _android_downloads_folder() -> str:
+    """:return: downloads folder for the Android OS"""
+    # Get directories with pyjnius
+    try:
+        from jnius import autoclass  # noqa: PLC0415
+
+        context = autoclass("android.content.Context")
+        environment = autoclass("android.os.Environment")
+        downloads_dir: str = context.getExternalFilesDir(environment.DIRECTORY_DOWNLOADS).getAbsolutePath()
+    except Exception:  # noqa: BLE001
+        downloads_dir = "/storage/emulated/0/Downloads"
+
+    return downloads_dir
+
+
+@lru_cache(maxsize=1)
+def _android_pictures_folder() -> str:
+    """:return: pictures folder for the Android OS"""
+    # Get directories with pyjnius
+    try:
+        from jnius import autoclass  # noqa: PLC0415
+
+        context = autoclass("android.content.Context")
+        environment = autoclass("android.os.Environment")
+        pictures_dir: str = context.getExternalFilesDir(environment.DIRECTORY_PICTURES).getAbsolutePath()
+    except Exception:  # noqa: BLE001
+        pictures_dir = "/storage/emulated/0/Pictures"
+
+    return pictures_dir
+
+
+@lru_cache(maxsize=1)
+def _android_videos_folder() -> str:
+    """:return: videos folder for the Android OS"""
+    # Get directories with pyjnius
+    try:
+        from jnius import autoclass  # noqa: PLC0415
+
+        context = autoclass("android.content.Context")
+        environment = autoclass("android.os.Environment")
+        videos_dir: str = context.getExternalFilesDir(environment.DIRECTORY_DCIM).getAbsolutePath()
+    except Exception:  # noqa: BLE001
+        videos_dir = "/storage/emulated/0/DCIM/Camera"
+
+    return videos_dir
+
+
+@lru_cache(maxsize=1)
+def _android_music_folder() -> str:
+    """:return: music folder for the Android OS"""
+    # Get directories with pyjnius
+    try:
+        from jnius import autoclass  # noqa: PLC0415
+
+        context = autoclass("android.content.Context")
+        environment = autoclass("android.os.Environment")
+        music_dir: str = context.getExternalFilesDir(environment.DIRECTORY_MUSIC).getAbsolutePath()
+    except Exception:  # noqa: BLE001
+        music_dir = "/storage/emulated/0/Music"
+
+    return music_dir
+
+
+__all__ = [
+    "Android",
+]
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/api.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/api.py
new file mode 100644
index 0000000000000000000000000000000000000000..251600e6d1b6f7d38f6fee0b91de34d31b2124d0
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/api.py
@@ -0,0 +1,299 @@
+"""Base API."""
+
+from __future__ import annotations
+
+import os
+from abc import ABC, abstractmethod
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from collections.abc import Iterator
+    from typing import Literal
+
+
+class PlatformDirsABC(ABC):  # noqa: PLR0904
+    """Abstract base class for platform directories."""
+
+    def __init__(  # noqa: PLR0913, PLR0917
+        self,
+        appname: str | None = None,
+        appauthor: str | Literal[False] | None = None,
+        version: str | None = None,
+        roaming: bool = False,  # noqa: FBT001, FBT002
+        multipath: bool = False,  # noqa: FBT001, FBT002
+        opinion: bool = True,  # noqa: FBT001, FBT002
+        ensure_exists: bool = False,  # noqa: FBT001, FBT002
+    ) -> None:
+        """
+        Create a new platform directory.
+
+        :param appname: See `appname`.
+        :param appauthor: See `appauthor`.
+        :param version: See `version`.
+        :param roaming: See `roaming`.
+        :param multipath: See `multipath`.
+        :param opinion: See `opinion`.
+        :param ensure_exists: See `ensure_exists`.
+
+        """
+        self.appname = appname  #: The name of application.
+        self.appauthor = appauthor
+        """
+        The name of the app author or distributing body for this application.
+
+        Typically, it is the owning company name. Defaults to `appname`. You may pass ``False`` to disable it.
+
+        """
+        self.version = version
+        """
+        An optional version path element to append to the path.
+
+        You might want to use this if you want multiple versions of your app to be able to run independently. If used,
+        this would typically be ``.``.
+
+        """
+        self.roaming = roaming
+        """
+        Whether to use the roaming appdata directory on Windows.
+
+        That means that for users on a Windows network setup for roaming profiles, this user data will be synced on
+        login (see
+        `here `_).
+
+        """
+        self.multipath = multipath
+        """
+        An optional parameter which indicates that the entire list of data dirs should be returned.
+
+        By default, the first item would only be returned.
+
+        """
+        self.opinion = opinion  #: A flag to indicating to use opinionated values.
+        self.ensure_exists = ensure_exists
+        """
+        Optionally create the directory (and any missing parents) upon access if it does not exist.
+
+        By default, no directories are created.
+
+        """
+
+    def _append_app_name_and_version(self, *base: str) -> str:
+        params = list(base[1:])
+        if self.appname:
+            params.append(self.appname)
+            if self.version:
+                params.append(self.version)
+        path = os.path.join(base[0], *params)  # noqa: PTH118
+        self._optionally_create_directory(path)
+        return path
+
+    def _optionally_create_directory(self, path: str) -> None:
+        if self.ensure_exists:
+            Path(path).mkdir(parents=True, exist_ok=True)
+
+    def _first_item_as_path_if_multipath(self, directory: str) -> Path:
+        if self.multipath:
+            # If multipath is True, the first path is returned.
+            directory = directory.partition(os.pathsep)[0]
+        return Path(directory)
+
+    @property
+    @abstractmethod
+    def user_data_dir(self) -> str:
+        """:return: data directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def site_data_dir(self) -> str:
+        """:return: data directory shared by users"""
+
+    @property
+    @abstractmethod
+    def user_config_dir(self) -> str:
+        """:return: config directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def site_config_dir(self) -> str:
+        """:return: config directory shared by the users"""
+
+    @property
+    @abstractmethod
+    def user_cache_dir(self) -> str:
+        """:return: cache directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def site_cache_dir(self) -> str:
+        """:return: cache directory shared by users"""
+
+    @property
+    @abstractmethod
+    def user_state_dir(self) -> str:
+        """:return: state directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def user_log_dir(self) -> str:
+        """:return: log directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def user_documents_dir(self) -> str:
+        """:return: documents directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def user_downloads_dir(self) -> str:
+        """:return: downloads directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def user_pictures_dir(self) -> str:
+        """:return: pictures directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def user_videos_dir(self) -> str:
+        """:return: videos directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def user_music_dir(self) -> str:
+        """:return: music directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def user_desktop_dir(self) -> str:
+        """:return: desktop directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def user_runtime_dir(self) -> str:
+        """:return: runtime directory tied to the user"""
+
+    @property
+    @abstractmethod
+    def site_runtime_dir(self) -> str:
+        """:return: runtime directory shared by users"""
+
+    @property
+    def user_data_path(self) -> Path:
+        """:return: data path tied to the user"""
+        return Path(self.user_data_dir)
+
+    @property
+    def site_data_path(self) -> Path:
+        """:return: data path shared by users"""
+        return Path(self.site_data_dir)
+
+    @property
+    def user_config_path(self) -> Path:
+        """:return: config path tied to the user"""
+        return Path(self.user_config_dir)
+
+    @property
+    def site_config_path(self) -> Path:
+        """:return: config path shared by the users"""
+        return Path(self.site_config_dir)
+
+    @property
+    def user_cache_path(self) -> Path:
+        """:return: cache path tied to the user"""
+        return Path(self.user_cache_dir)
+
+    @property
+    def site_cache_path(self) -> Path:
+        """:return: cache path shared by users"""
+        return Path(self.site_cache_dir)
+
+    @property
+    def user_state_path(self) -> Path:
+        """:return: state path tied to the user"""
+        return Path(self.user_state_dir)
+
+    @property
+    def user_log_path(self) -> Path:
+        """:return: log path tied to the user"""
+        return Path(self.user_log_dir)
+
+    @property
+    def user_documents_path(self) -> Path:
+        """:return: documents a path tied to the user"""
+        return Path(self.user_documents_dir)
+
+    @property
+    def user_downloads_path(self) -> Path:
+        """:return: downloads path tied to the user"""
+        return Path(self.user_downloads_dir)
+
+    @property
+    def user_pictures_path(self) -> Path:
+        """:return: pictures path tied to the user"""
+        return Path(self.user_pictures_dir)
+
+    @property
+    def user_videos_path(self) -> Path:
+        """:return: videos path tied to the user"""
+        return Path(self.user_videos_dir)
+
+    @property
+    def user_music_path(self) -> Path:
+        """:return: music path tied to the user"""
+        return Path(self.user_music_dir)
+
+    @property
+    def user_desktop_path(self) -> Path:
+        """:return: desktop path tied to the user"""
+        return Path(self.user_desktop_dir)
+
+    @property
+    def user_runtime_path(self) -> Path:
+        """:return: runtime path tied to the user"""
+        return Path(self.user_runtime_dir)
+
+    @property
+    def site_runtime_path(self) -> Path:
+        """:return: runtime path shared by users"""
+        return Path(self.site_runtime_dir)
+
+    def iter_config_dirs(self) -> Iterator[str]:
+        """:yield: all user and site configuration directories."""
+        yield self.user_config_dir
+        yield self.site_config_dir
+
+    def iter_data_dirs(self) -> Iterator[str]:
+        """:yield: all user and site data directories."""
+        yield self.user_data_dir
+        yield self.site_data_dir
+
+    def iter_cache_dirs(self) -> Iterator[str]:
+        """:yield: all user and site cache directories."""
+        yield self.user_cache_dir
+        yield self.site_cache_dir
+
+    def iter_runtime_dirs(self) -> Iterator[str]:
+        """:yield: all user and site runtime directories."""
+        yield self.user_runtime_dir
+        yield self.site_runtime_dir
+
+    def iter_config_paths(self) -> Iterator[Path]:
+        """:yield: all user and site configuration paths."""
+        for path in self.iter_config_dirs():
+            yield Path(path)
+
+    def iter_data_paths(self) -> Iterator[Path]:
+        """:yield: all user and site data paths."""
+        for path in self.iter_data_dirs():
+            yield Path(path)
+
+    def iter_cache_paths(self) -> Iterator[Path]:
+        """:yield: all user and site cache paths."""
+        for path in self.iter_cache_dirs():
+            yield Path(path)
+
+    def iter_runtime_paths(self) -> Iterator[Path]:
+        """:yield: all user and site runtime paths."""
+        for path in self.iter_runtime_dirs():
+            yield Path(path)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/macos.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/macos.py
new file mode 100644
index 0000000000000000000000000000000000000000..30ab368913061aa4b7935e65f5696f7d8cffcf4f
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/macos.py
@@ -0,0 +1,146 @@
+"""macOS."""
+
+from __future__ import annotations
+
+import os.path
+import sys
+from typing import TYPE_CHECKING
+
+from .api import PlatformDirsABC
+
+if TYPE_CHECKING:
+    from pathlib import Path
+
+
+class MacOS(PlatformDirsABC):
+    """
+    Platform directories for the macOS operating system.
+
+    Follows the guidance from
+    `Apple documentation `_.
+    Makes use of the `appname `,
+    `version `,
+    `ensure_exists `.
+
+    """
+
+    @property
+    def user_data_dir(self) -> str:
+        """:return: data directory tied to the user, e.g. ``~/Library/Application Support/$appname/$version``"""
+        return self._append_app_name_and_version(os.path.expanduser("~/Library/Application Support"))  # noqa: PTH111
+
+    @property
+    def site_data_dir(self) -> str:
+        """
+        :return: data directory shared by users, e.g. ``/Library/Application Support/$appname/$version``.
+          If we're using a Python binary managed by `Homebrew `_, the directory
+          will be under the Homebrew prefix, e.g. ``$homebrew_prefix/share/$appname/$version``.
+          If `multipath ` is enabled, and we're in Homebrew,
+          the response is a multi-path string separated by ":", e.g.
+          ``$homebrew_prefix/share/$appname/$version:/Library/Application Support/$appname/$version``
+        """
+        is_homebrew = "/opt/python" in sys.prefix
+        homebrew_prefix = sys.prefix.split("/opt/python")[0] if is_homebrew else ""
+        path_list = [self._append_app_name_and_version(f"{homebrew_prefix}/share")] if is_homebrew else []
+        path_list.append(self._append_app_name_and_version("/Library/Application Support"))
+        if self.multipath:
+            return os.pathsep.join(path_list)
+        return path_list[0]
+
+    @property
+    def site_data_path(self) -> Path:
+        """:return: data path shared by users. Only return the first item, even if ``multipath`` is set to ``True``"""
+        return self._first_item_as_path_if_multipath(self.site_data_dir)
+
+    @property
+    def user_config_dir(self) -> str:
+        """:return: config directory tied to the user, same as `user_data_dir`"""
+        return self.user_data_dir
+
+    @property
+    def site_config_dir(self) -> str:
+        """:return: config directory shared by the users, same as `site_data_dir`"""
+        return self.site_data_dir
+
+    @property
+    def user_cache_dir(self) -> str:
+        """:return: cache directory tied to the user, e.g. ``~/Library/Caches/$appname/$version``"""
+        return self._append_app_name_and_version(os.path.expanduser("~/Library/Caches"))  # noqa: PTH111
+
+    @property
+    def site_cache_dir(self) -> str:
+        """
+        :return: cache directory shared by users, e.g. ``/Library/Caches/$appname/$version``.
+          If we're using a Python binary managed by `Homebrew `_, the directory
+          will be under the Homebrew prefix, e.g. ``$homebrew_prefix/var/cache/$appname/$version``.
+          If `multipath ` is enabled, and we're in Homebrew,
+          the response is a multi-path string separated by ":", e.g.
+          ``$homebrew_prefix/var/cache/$appname/$version:/Library/Caches/$appname/$version``
+        """
+        is_homebrew = "/opt/python" in sys.prefix
+        homebrew_prefix = sys.prefix.split("/opt/python")[0] if is_homebrew else ""
+        path_list = [self._append_app_name_and_version(f"{homebrew_prefix}/var/cache")] if is_homebrew else []
+        path_list.append(self._append_app_name_and_version("/Library/Caches"))
+        if self.multipath:
+            return os.pathsep.join(path_list)
+        return path_list[0]
+
+    @property
+    def site_cache_path(self) -> Path:
+        """:return: cache path shared by users. Only return the first item, even if ``multipath`` is set to ``True``"""
+        return self._first_item_as_path_if_multipath(self.site_cache_dir)
+
+    @property
+    def user_state_dir(self) -> str:
+        """:return: state directory tied to the user, same as `user_data_dir`"""
+        return self.user_data_dir
+
+    @property
+    def user_log_dir(self) -> str:
+        """:return: log directory tied to the user, e.g. ``~/Library/Logs/$appname/$version``"""
+        return self._append_app_name_and_version(os.path.expanduser("~/Library/Logs"))  # noqa: PTH111
+
+    @property
+    def user_documents_dir(self) -> str:
+        """:return: documents directory tied to the user, e.g. ``~/Documents``"""
+        return os.path.expanduser("~/Documents")  # noqa: PTH111
+
+    @property
+    def user_downloads_dir(self) -> str:
+        """:return: downloads directory tied to the user, e.g. ``~/Downloads``"""
+        return os.path.expanduser("~/Downloads")  # noqa: PTH111
+
+    @property
+    def user_pictures_dir(self) -> str:
+        """:return: pictures directory tied to the user, e.g. ``~/Pictures``"""
+        return os.path.expanduser("~/Pictures")  # noqa: PTH111
+
+    @property
+    def user_videos_dir(self) -> str:
+        """:return: videos directory tied to the user, e.g. ``~/Movies``"""
+        return os.path.expanduser("~/Movies")  # noqa: PTH111
+
+    @property
+    def user_music_dir(self) -> str:
+        """:return: music directory tied to the user, e.g. ``~/Music``"""
+        return os.path.expanduser("~/Music")  # noqa: PTH111
+
+    @property
+    def user_desktop_dir(self) -> str:
+        """:return: desktop directory tied to the user, e.g. ``~/Desktop``"""
+        return os.path.expanduser("~/Desktop")  # noqa: PTH111
+
+    @property
+    def user_runtime_dir(self) -> str:
+        """:return: runtime directory tied to the user, e.g. ``~/Library/Caches/TemporaryItems/$appname/$version``"""
+        return self._append_app_name_and_version(os.path.expanduser("~/Library/Caches/TemporaryItems"))  # noqa: PTH111
+
+    @property
+    def site_runtime_dir(self) -> str:
+        """:return: runtime directory shared by users, same as `user_runtime_dir`"""
+        return self.user_runtime_dir
+
+
+__all__ = [
+    "MacOS",
+]
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/py.typed b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/py.typed
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/unix.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/unix.py
new file mode 100644
index 0000000000000000000000000000000000000000..fc75d8d0747b0d5ce84b96cfc37877a126d1a9b6
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/unix.py
@@ -0,0 +1,272 @@
+"""Unix."""
+
+from __future__ import annotations
+
+import os
+import sys
+from configparser import ConfigParser
+from pathlib import Path
+from typing import TYPE_CHECKING, NoReturn
+
+from .api import PlatformDirsABC
+
+if TYPE_CHECKING:
+    from collections.abc import Iterator
+
+if sys.platform == "win32":
+
+    def getuid() -> NoReturn:
+        msg = "should only be used on Unix"
+        raise RuntimeError(msg)
+
+else:
+    from os import getuid
+
+
+class Unix(PlatformDirsABC):  # noqa: PLR0904
+    """
+    On Unix/Linux, we follow the `XDG Basedir Spec `_.
+
+    The spec allows overriding directories with environment variables. The examples shown are the default values,
+    alongside the name of the environment variable that overrides them. Makes use of the `appname
+    `, `version `, `multipath
+    `, `opinion `, `ensure_exists
+    `.
+
+    """
+
+    @property
+    def user_data_dir(self) -> str:
+        """
+        :return: data directory tied to the user, e.g. ``~/.local/share/$appname/$version`` or
+         ``$XDG_DATA_HOME/$appname/$version``
+        """
+        path = os.environ.get("XDG_DATA_HOME", "")
+        if not path.strip():
+            path = os.path.expanduser("~/.local/share")  # noqa: PTH111
+        return self._append_app_name_and_version(path)
+
+    @property
+    def _site_data_dirs(self) -> list[str]:
+        path = os.environ.get("XDG_DATA_DIRS", "")
+        if not path.strip():
+            path = f"/usr/local/share{os.pathsep}/usr/share"
+        return [self._append_app_name_and_version(p) for p in path.split(os.pathsep)]
+
+    @property
+    def site_data_dir(self) -> str:
+        """
+        :return: data directories shared by users (if `multipath ` is
+         enabled and ``XDG_DATA_DIRS`` is set and a multi path the response is also a multi path separated by the
+         OS path separator), e.g. ``/usr/local/share/$appname/$version`` or ``/usr/share/$appname/$version``
+        """
+        # XDG default for $XDG_DATA_DIRS; only first, if multipath is False
+        dirs = self._site_data_dirs
+        if not self.multipath:
+            return dirs[0]
+        return os.pathsep.join(dirs)
+
+    @property
+    def user_config_dir(self) -> str:
+        """
+        :return: config directory tied to the user, e.g. ``~/.config/$appname/$version`` or
+         ``$XDG_CONFIG_HOME/$appname/$version``
+        """
+        path = os.environ.get("XDG_CONFIG_HOME", "")
+        if not path.strip():
+            path = os.path.expanduser("~/.config")  # noqa: PTH111
+        return self._append_app_name_and_version(path)
+
+    @property
+    def _site_config_dirs(self) -> list[str]:
+        path = os.environ.get("XDG_CONFIG_DIRS", "")
+        if not path.strip():
+            path = "/etc/xdg"
+        return [self._append_app_name_and_version(p) for p in path.split(os.pathsep)]
+
+    @property
+    def site_config_dir(self) -> str:
+        """
+        :return: config directories shared by users (if `multipath `
+         is enabled and ``XDG_CONFIG_DIRS`` is set and a multi path the response is also a multi path separated by
+         the OS path separator), e.g. ``/etc/xdg/$appname/$version``
+        """
+        # XDG default for $XDG_CONFIG_DIRS only first, if multipath is False
+        dirs = self._site_config_dirs
+        if not self.multipath:
+            return dirs[0]
+        return os.pathsep.join(dirs)
+
+    @property
+    def user_cache_dir(self) -> str:
+        """
+        :return: cache directory tied to the user, e.g. ``~/.cache/$appname/$version`` or
+         ``~/$XDG_CACHE_HOME/$appname/$version``
+        """
+        path = os.environ.get("XDG_CACHE_HOME", "")
+        if not path.strip():
+            path = os.path.expanduser("~/.cache")  # noqa: PTH111
+        return self._append_app_name_and_version(path)
+
+    @property
+    def site_cache_dir(self) -> str:
+        """:return: cache directory shared by users, e.g. ``/var/cache/$appname/$version``"""
+        return self._append_app_name_and_version("/var/cache")
+
+    @property
+    def user_state_dir(self) -> str:
+        """
+        :return: state directory tied to the user, e.g. ``~/.local/state/$appname/$version`` or
+         ``$XDG_STATE_HOME/$appname/$version``
+        """
+        path = os.environ.get("XDG_STATE_HOME", "")
+        if not path.strip():
+            path = os.path.expanduser("~/.local/state")  # noqa: PTH111
+        return self._append_app_name_and_version(path)
+
+    @property
+    def user_log_dir(self) -> str:
+        """:return: log directory tied to the user, same as `user_state_dir` if not opinionated else ``log`` in it"""
+        path = self.user_state_dir
+        if self.opinion:
+            path = os.path.join(path, "log")  # noqa: PTH118
+            self._optionally_create_directory(path)
+        return path
+
+    @property
+    def user_documents_dir(self) -> str:
+        """:return: documents directory tied to the user, e.g. ``~/Documents``"""
+        return _get_user_media_dir("XDG_DOCUMENTS_DIR", "~/Documents")
+
+    @property
+    def user_downloads_dir(self) -> str:
+        """:return: downloads directory tied to the user, e.g. ``~/Downloads``"""
+        return _get_user_media_dir("XDG_DOWNLOAD_DIR", "~/Downloads")
+
+    @property
+    def user_pictures_dir(self) -> str:
+        """:return: pictures directory tied to the user, e.g. ``~/Pictures``"""
+        return _get_user_media_dir("XDG_PICTURES_DIR", "~/Pictures")
+
+    @property
+    def user_videos_dir(self) -> str:
+        """:return: videos directory tied to the user, e.g. ``~/Videos``"""
+        return _get_user_media_dir("XDG_VIDEOS_DIR", "~/Videos")
+
+    @property
+    def user_music_dir(self) -> str:
+        """:return: music directory tied to the user, e.g. ``~/Music``"""
+        return _get_user_media_dir("XDG_MUSIC_DIR", "~/Music")
+
+    @property
+    def user_desktop_dir(self) -> str:
+        """:return: desktop directory tied to the user, e.g. ``~/Desktop``"""
+        return _get_user_media_dir("XDG_DESKTOP_DIR", "~/Desktop")
+
+    @property
+    def user_runtime_dir(self) -> str:
+        """
+        :return: runtime directory tied to the user, e.g. ``/run/user/$(id -u)/$appname/$version`` or
+         ``$XDG_RUNTIME_DIR/$appname/$version``.
+
+         For FreeBSD/OpenBSD/NetBSD, it would return ``/var/run/user/$(id -u)/$appname/$version`` if
+         exists, otherwise ``/tmp/runtime-$(id -u)/$appname/$version``, if``$XDG_RUNTIME_DIR``
+         is not set.
+        """
+        path = os.environ.get("XDG_RUNTIME_DIR", "")
+        if not path.strip():
+            if sys.platform.startswith(("freebsd", "openbsd", "netbsd")):
+                path = f"/var/run/user/{getuid()}"
+                if not Path(path).exists():
+                    path = f"/tmp/runtime-{getuid()}"  # noqa: S108
+            else:
+                path = f"/run/user/{getuid()}"
+        return self._append_app_name_and_version(path)
+
+    @property
+    def site_runtime_dir(self) -> str:
+        """
+        :return: runtime directory shared by users, e.g. ``/run/$appname/$version`` or \
+        ``$XDG_RUNTIME_DIR/$appname/$version``.
+
+        Note that this behaves almost exactly like `user_runtime_dir` if ``$XDG_RUNTIME_DIR`` is set, but will
+        fall back to paths associated to the root user instead of a regular logged-in user if it's not set.
+
+        If you wish to ensure that a logged-in root user path is returned e.g. ``/run/user/0``, use `user_runtime_dir`
+        instead.
+
+        For FreeBSD/OpenBSD/NetBSD, it would return ``/var/run/$appname/$version`` if ``$XDG_RUNTIME_DIR`` is not set.
+        """
+        path = os.environ.get("XDG_RUNTIME_DIR", "")
+        if not path.strip():
+            if sys.platform.startswith(("freebsd", "openbsd", "netbsd")):
+                path = "/var/run"
+            else:
+                path = "/run"
+        return self._append_app_name_and_version(path)
+
+    @property
+    def site_data_path(self) -> Path:
+        """:return: data path shared by users. Only return the first item, even if ``multipath`` is set to ``True``"""
+        return self._first_item_as_path_if_multipath(self.site_data_dir)
+
+    @property
+    def site_config_path(self) -> Path:
+        """:return: config path shared by the users, returns the first item, even if ``multipath`` is set to ``True``"""
+        return self._first_item_as_path_if_multipath(self.site_config_dir)
+
+    @property
+    def site_cache_path(self) -> Path:
+        """:return: cache path shared by users. Only return the first item, even if ``multipath`` is set to ``True``"""
+        return self._first_item_as_path_if_multipath(self.site_cache_dir)
+
+    def iter_config_dirs(self) -> Iterator[str]:
+        """:yield: all user and site configuration directories."""
+        yield self.user_config_dir
+        yield from self._site_config_dirs
+
+    def iter_data_dirs(self) -> Iterator[str]:
+        """:yield: all user and site data directories."""
+        yield self.user_data_dir
+        yield from self._site_data_dirs
+
+
+def _get_user_media_dir(env_var: str, fallback_tilde_path: str) -> str:
+    media_dir = _get_user_dirs_folder(env_var)
+    if media_dir is None:
+        media_dir = os.environ.get(env_var, "").strip()
+        if not media_dir:
+            media_dir = os.path.expanduser(fallback_tilde_path)  # noqa: PTH111
+
+    return media_dir
+
+
+def _get_user_dirs_folder(key: str) -> str | None:
+    """
+    Return directory from user-dirs.dirs config file.
+
+    See https://freedesktop.org/wiki/Software/xdg-user-dirs/.
+
+    """
+    user_dirs_config_path = Path(Unix().user_config_dir) / "user-dirs.dirs"
+    if user_dirs_config_path.exists():
+        parser = ConfigParser()
+
+        with user_dirs_config_path.open() as stream:
+            # Add fake section header, so ConfigParser doesn't complain
+            parser.read_string(f"[top]\n{stream.read()}")
+
+        if key not in parser["top"]:
+            return None
+
+        path = parser["top"][key].strip('"')
+        # Handle relative home paths
+        return path.replace("$HOME", os.path.expanduser("~"))  # noqa: PTH111
+
+    return None
+
+
+__all__ = [
+    "Unix",
+]
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/version.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/version.py
new file mode 100644
index 0000000000000000000000000000000000000000..b9451472c3c68e0d775e32c8b193bf93bf217107
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/version.py
@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '4.4.0'
+__version_tuple__ = version_tuple = (4, 4, 0)
+
+__commit_id__ = commit_id = None
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/windows.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/windows.py
new file mode 100644
index 0000000000000000000000000000000000000000..d7bc96091a2b1cd078a0847519cb5dd50a5d8898
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/platformdirs/windows.py
@@ -0,0 +1,272 @@
+"""Windows."""
+
+from __future__ import annotations
+
+import os
+import sys
+from functools import lru_cache
+from typing import TYPE_CHECKING
+
+from .api import PlatformDirsABC
+
+if TYPE_CHECKING:
+    from collections.abc import Callable
+
+
+class Windows(PlatformDirsABC):
+    """
+    `MSDN on where to store app data files `_.
+
+    Makes use of the `appname `, `appauthor
+    `, `version `, `roaming
+    `, `opinion `, `ensure_exists
+    `.
+
+    """
+
+    @property
+    def user_data_dir(self) -> str:
+        """
+        :return: data directory tied to the user, e.g.
+         ``%USERPROFILE%\\AppData\\Local\\$appauthor\\$appname`` (not roaming) or
+         ``%USERPROFILE%\\AppData\\Roaming\\$appauthor\\$appname`` (roaming)
+        """
+        const = "CSIDL_APPDATA" if self.roaming else "CSIDL_LOCAL_APPDATA"
+        path = os.path.normpath(get_win_folder(const))
+        return self._append_parts(path)
+
+    def _append_parts(self, path: str, *, opinion_value: str | None = None) -> str:
+        params = []
+        if self.appname:
+            if self.appauthor is not False:
+                author = self.appauthor or self.appname
+                params.append(author)
+            params.append(self.appname)
+            if opinion_value is not None and self.opinion:
+                params.append(opinion_value)
+            if self.version:
+                params.append(self.version)
+        path = os.path.join(path, *params)  # noqa: PTH118
+        self._optionally_create_directory(path)
+        return path
+
+    @property
+    def site_data_dir(self) -> str:
+        """:return: data directory shared by users, e.g. ``C:\\ProgramData\\$appauthor\\$appname``"""
+        path = os.path.normpath(get_win_folder("CSIDL_COMMON_APPDATA"))
+        return self._append_parts(path)
+
+    @property
+    def user_config_dir(self) -> str:
+        """:return: config directory tied to the user, same as `user_data_dir`"""
+        return self.user_data_dir
+
+    @property
+    def site_config_dir(self) -> str:
+        """:return: config directory shared by the users, same as `site_data_dir`"""
+        return self.site_data_dir
+
+    @property
+    def user_cache_dir(self) -> str:
+        """
+        :return: cache directory tied to the user (if opinionated with ``Cache`` folder within ``$appname``) e.g.
+         ``%USERPROFILE%\\AppData\\Local\\$appauthor\\$appname\\Cache\\$version``
+        """
+        path = os.path.normpath(get_win_folder("CSIDL_LOCAL_APPDATA"))
+        return self._append_parts(path, opinion_value="Cache")
+
+    @property
+    def site_cache_dir(self) -> str:
+        """:return: cache directory shared by users, e.g. ``C:\\ProgramData\\$appauthor\\$appname\\Cache\\$version``"""
+        path = os.path.normpath(get_win_folder("CSIDL_COMMON_APPDATA"))
+        return self._append_parts(path, opinion_value="Cache")
+
+    @property
+    def user_state_dir(self) -> str:
+        """:return: state directory tied to the user, same as `user_data_dir`"""
+        return self.user_data_dir
+
+    @property
+    def user_log_dir(self) -> str:
+        """:return: log directory tied to the user, same as `user_data_dir` if not opinionated else ``Logs`` in it"""
+        path = self.user_data_dir
+        if self.opinion:
+            path = os.path.join(path, "Logs")  # noqa: PTH118
+            self._optionally_create_directory(path)
+        return path
+
+    @property
+    def user_documents_dir(self) -> str:
+        """:return: documents directory tied to the user e.g. ``%USERPROFILE%\\Documents``"""
+        return os.path.normpath(get_win_folder("CSIDL_PERSONAL"))
+
+    @property
+    def user_downloads_dir(self) -> str:
+        """:return: downloads directory tied to the user e.g. ``%USERPROFILE%\\Downloads``"""
+        return os.path.normpath(get_win_folder("CSIDL_DOWNLOADS"))
+
+    @property
+    def user_pictures_dir(self) -> str:
+        """:return: pictures directory tied to the user e.g. ``%USERPROFILE%\\Pictures``"""
+        return os.path.normpath(get_win_folder("CSIDL_MYPICTURES"))
+
+    @property
+    def user_videos_dir(self) -> str:
+        """:return: videos directory tied to the user e.g. ``%USERPROFILE%\\Videos``"""
+        return os.path.normpath(get_win_folder("CSIDL_MYVIDEO"))
+
+    @property
+    def user_music_dir(self) -> str:
+        """:return: music directory tied to the user e.g. ``%USERPROFILE%\\Music``"""
+        return os.path.normpath(get_win_folder("CSIDL_MYMUSIC"))
+
+    @property
+    def user_desktop_dir(self) -> str:
+        """:return: desktop directory tied to the user, e.g. ``%USERPROFILE%\\Desktop``"""
+        return os.path.normpath(get_win_folder("CSIDL_DESKTOPDIRECTORY"))
+
+    @property
+    def user_runtime_dir(self) -> str:
+        """
+        :return: runtime directory tied to the user, e.g.
+         ``%USERPROFILE%\\AppData\\Local\\Temp\\$appauthor\\$appname``
+        """
+        path = os.path.normpath(os.path.join(get_win_folder("CSIDL_LOCAL_APPDATA"), "Temp"))  # noqa: PTH118
+        return self._append_parts(path)
+
+    @property
+    def site_runtime_dir(self) -> str:
+        """:return: runtime directory shared by users, same as `user_runtime_dir`"""
+        return self.user_runtime_dir
+
+
+def get_win_folder_from_env_vars(csidl_name: str) -> str:
+    """Get folder from environment variables."""
+    result = get_win_folder_if_csidl_name_not_env_var(csidl_name)
+    if result is not None:
+        return result
+
+    env_var_name = {
+        "CSIDL_APPDATA": "APPDATA",
+        "CSIDL_COMMON_APPDATA": "ALLUSERSPROFILE",
+        "CSIDL_LOCAL_APPDATA": "LOCALAPPDATA",
+    }.get(csidl_name)
+    if env_var_name is None:
+        msg = f"Unknown CSIDL name: {csidl_name}"
+        raise ValueError(msg)
+    result = os.environ.get(env_var_name)
+    if result is None:
+        msg = f"Unset environment variable: {env_var_name}"
+        raise ValueError(msg)
+    return result
+
+
+def get_win_folder_if_csidl_name_not_env_var(csidl_name: str) -> str | None:
+    """Get a folder for a CSIDL name that does not exist as an environment variable."""
+    if csidl_name == "CSIDL_PERSONAL":
+        return os.path.join(os.path.normpath(os.environ["USERPROFILE"]), "Documents")  # noqa: PTH118
+
+    if csidl_name == "CSIDL_DOWNLOADS":
+        return os.path.join(os.path.normpath(os.environ["USERPROFILE"]), "Downloads")  # noqa: PTH118
+
+    if csidl_name == "CSIDL_MYPICTURES":
+        return os.path.join(os.path.normpath(os.environ["USERPROFILE"]), "Pictures")  # noqa: PTH118
+
+    if csidl_name == "CSIDL_MYVIDEO":
+        return os.path.join(os.path.normpath(os.environ["USERPROFILE"]), "Videos")  # noqa: PTH118
+
+    if csidl_name == "CSIDL_MYMUSIC":
+        return os.path.join(os.path.normpath(os.environ["USERPROFILE"]), "Music")  # noqa: PTH118
+    return None
+
+
+def get_win_folder_from_registry(csidl_name: str) -> str:
+    """
+    Get folder from the registry.
+
+    This is a fallback technique at best. I'm not sure if using the registry for these guarantees us the correct answer
+    for all CSIDL_* names.
+
+    """
+    shell_folder_name = {
+        "CSIDL_APPDATA": "AppData",
+        "CSIDL_COMMON_APPDATA": "Common AppData",
+        "CSIDL_LOCAL_APPDATA": "Local AppData",
+        "CSIDL_PERSONAL": "Personal",
+        "CSIDL_DOWNLOADS": "{374DE290-123F-4565-9164-39C4925E467B}",
+        "CSIDL_MYPICTURES": "My Pictures",
+        "CSIDL_MYVIDEO": "My Video",
+        "CSIDL_MYMUSIC": "My Music",
+    }.get(csidl_name)
+    if shell_folder_name is None:
+        msg = f"Unknown CSIDL name: {csidl_name}"
+        raise ValueError(msg)
+    if sys.platform != "win32":  # only needed for mypy type checker to know that this code runs only on Windows
+        raise NotImplementedError
+    import winreg  # noqa: PLC0415
+
+    key = winreg.OpenKey(winreg.HKEY_CURRENT_USER, r"Software\Microsoft\Windows\CurrentVersion\Explorer\Shell Folders")
+    directory, _ = winreg.QueryValueEx(key, shell_folder_name)
+    return str(directory)
+
+
+def get_win_folder_via_ctypes(csidl_name: str) -> str:
+    """Get folder with ctypes."""
+    # There is no 'CSIDL_DOWNLOADS'.
+    # Use 'CSIDL_PROFILE' (40) and append the default folder 'Downloads' instead.
+    # https://learn.microsoft.com/en-us/windows/win32/shell/knownfolderid
+
+    import ctypes  # noqa: PLC0415
+
+    csidl_const = {
+        "CSIDL_APPDATA": 26,
+        "CSIDL_COMMON_APPDATA": 35,
+        "CSIDL_LOCAL_APPDATA": 28,
+        "CSIDL_PERSONAL": 5,
+        "CSIDL_MYPICTURES": 39,
+        "CSIDL_MYVIDEO": 14,
+        "CSIDL_MYMUSIC": 13,
+        "CSIDL_DOWNLOADS": 40,
+        "CSIDL_DESKTOPDIRECTORY": 16,
+    }.get(csidl_name)
+    if csidl_const is None:
+        msg = f"Unknown CSIDL name: {csidl_name}"
+        raise ValueError(msg)
+
+    buf = ctypes.create_unicode_buffer(1024)
+    windll = getattr(ctypes, "windll")  # noqa: B009 # using getattr to avoid false positive with mypy type checker
+    windll.shell32.SHGetFolderPathW(None, csidl_const, None, 0, buf)
+
+    # Downgrade to short path name if it has high-bit chars.
+    if any(ord(c) > 255 for c in buf):  # noqa: PLR2004
+        buf2 = ctypes.create_unicode_buffer(1024)
+        if windll.kernel32.GetShortPathNameW(buf.value, buf2, 1024):
+            buf = buf2
+
+    if csidl_name == "CSIDL_DOWNLOADS":
+        return os.path.join(buf.value, "Downloads")  # noqa: PTH118
+
+    return buf.value
+
+
+def _pick_get_win_folder() -> Callable[[str], str]:
+    try:
+        import ctypes  # noqa: PLC0415
+    except ImportError:
+        pass
+    else:
+        if hasattr(ctypes, "windll"):
+            return get_win_folder_via_ctypes
+    try:
+        import winreg  # noqa: PLC0415, F401
+    except ImportError:
+        return get_win_folder_from_env_vars
+    else:
+        return get_win_folder_from_registry
+
+
+get_win_folder = lru_cache(maxsize=None)(_pick_get_win_folder())
+
+__all__ = [
+    "Windows",
+]
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/INSTALLER
new file mode 100644
index 0000000000000000000000000000000000000000..f79e4cb9aaf0b2d9e8ba78861e2071317b2384b3
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/INSTALLER
@@ -0,0 +1 @@
+conda
\ No newline at end of file
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/METADATA
new file mode 100644
index 0000000000000000000000000000000000000000..ffe8e40d77f07e829e420f056b7ecd9c81ec38a5
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/METADATA
@@ -0,0 +1,270 @@
+Metadata-Version: 2.4
+Name: tomli
+Version: 2.4.0
+Summary: A lil' TOML parser
+Keywords: toml
+Author-email: Taneli Hukkinen 
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-Expression: MIT
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Typing :: Typed
+License-File: LICENSE
+Project-URL: Changelog, https://github.com/hukkin/tomli/blob/master/CHANGELOG.md
+Project-URL: Homepage, https://github.com/hukkin/tomli
+
+[![Build Status](https://github.com/hukkin/tomli/actions/workflows/tests.yaml/badge.svg?branch=master)](https://github.com/hukkin/tomli/actions?query=workflow%3ATests+branch%3Amaster+event%3Apush)
+[![codecov.io](https://codecov.io/gh/hukkin/tomli/branch/master/graph/badge.svg)](https://codecov.io/gh/hukkin/tomli)
+[![PyPI version](https://img.shields.io/pypi/v/tomli)](https://pypi.org/project/tomli)
+
+# Tomli
+
+> A lil' TOML parser
+
+**Table of Contents** *generated with [mdformat-toc](https://github.com/hukkin/mdformat-toc)*
+
+
+
+- [Intro](#intro)
+- [Installation](#installation)
+- [Usage](#usage)
+  - [Parse a TOML string](#parse-a-toml-string)
+  - [Parse a TOML file](#parse-a-toml-file)
+  - [Handle invalid TOML](#handle-invalid-toml)
+  - [Construct `decimal.Decimal`s from TOML floats](#construct-decimaldecimals-from-toml-floats)
+  - [Building a `tomli`/`tomllib` compatibility layer](#building-a-tomlitomllib-compatibility-layer)
+- [FAQ](#faq)
+  - [Why this parser?](#why-this-parser)
+  - [Is comment preserving round-trip parsing supported?](#is-comment-preserving-round-trip-parsing-supported)
+  - [Is there a `dumps`, `write` or `encode` function?](#is-there-a-dumps-write-or-encode-function)
+  - [How do TOML types map into Python types?](#how-do-toml-types-map-into-python-types)
+- [Performance](#performance)
+  - [Pure Python](#pure-python)
+  - [Mypyc generated wheel](#mypyc-generated-wheel)
+
+
+
+## Intro
+
+Tomli is a Python library for parsing [TOML](https://toml.io).
+Version 2.4.0 and later are compatible with [TOML v1.1.0](https://toml.io/en/v1.1.0).
+Older versions are [TOML v1.0.0](https://toml.io/en/v1.0.0) compatible.
+
+A version of Tomli, the `tomllib` module,
+was added to the standard library in Python 3.11
+via [PEP 680](https://www.python.org/dev/peps/pep-0680/).
+Tomli continues to provide a backport on PyPI for Python versions
+where the standard library module is not available
+and that have not yet reached their end-of-life.
+
+Tomli uses [mypyc](https://github.com/mypyc/mypyc)
+to generate binary wheels for most of the widely used platforms,
+so Python 3.11+ users may prefer it over `tomllib` for improved performance.
+Pure Python wheels are available on any platform and should perform the same as `tomllib`.
+
+## Installation
+
+```bash
+pip install tomli
+```
+
+## Usage
+
+### Parse a TOML string
+
+```python
+import tomli
+
+toml_str = """
+[[players]]
+name = "Lehtinen"
+number = 26
+
+[[players]]
+name = "Numminen"
+number = 27
+"""
+
+toml_dict = tomli.loads(toml_str)
+assert toml_dict == {
+    "players": [{"name": "Lehtinen", "number": 26}, {"name": "Numminen", "number": 27}]
+}
+```
+
+### Parse a TOML file
+
+```python
+import tomli
+
+with open("path_to_file/conf.toml", "rb") as f:
+    toml_dict = tomli.load(f)
+```
+
+The file must be opened in binary mode (with the `"rb"` flag).
+Binary mode will enforce decoding the file as UTF-8 with universal newlines disabled,
+both of which are required to correctly parse TOML.
+
+### Handle invalid TOML
+
+```python
+import tomli
+
+try:
+    toml_dict = tomli.loads("]] this is invalid TOML [[")
+except tomli.TOMLDecodeError:
+    print("Yep, definitely not valid.")
+```
+
+Note that error messages are considered informational only.
+They should not be assumed to stay constant across Tomli versions.
+
+### Construct `decimal.Decimal`s from TOML floats
+
+```python
+from decimal import Decimal
+import tomli
+
+toml_dict = tomli.loads("precision-matters = 0.982492", parse_float=Decimal)
+assert isinstance(toml_dict["precision-matters"], Decimal)
+assert toml_dict["precision-matters"] == Decimal("0.982492")
+```
+
+Note that `decimal.Decimal` can be replaced with another callable that converts a TOML float from string to a Python type.
+The `decimal.Decimal` is, however, a practical choice for use cases where float inaccuracies can not be tolerated.
+
+Illegal types are `dict` and `list`, and their subtypes.
+A `ValueError` will be raised if `parse_float` produces illegal types.
+
+### Building a `tomli`/`tomllib` compatibility layer
+
+Python versions 3.11+ ship with a version of Tomli:
+the `tomllib` standard library module.
+To build code that uses the standard library if available,
+but still works seamlessly with Python 3.6+,
+do the following.
+
+Instead of a hard Tomli dependency, use the following
+[dependency specifier](https://packaging.python.org/en/latest/specifications/dependency-specifiers/)
+to only require Tomli when the standard library module is not available:
+
+```
+tomli >= 1.1.0 ; python_version < "3.11"
+```
+
+Then, in your code, import a TOML parser using the following fallback mechanism:
+
+```python
+import sys
+
+if sys.version_info >= (3, 11):
+    import tomllib
+else:
+    import tomli as tomllib
+
+tomllib.loads("['This parses fine with Python 3.6+']")
+```
+
+## FAQ
+
+### Why this parser?
+
+- it's lil'
+- pure Python with zero dependencies
+- the fastest pure Python parser [\*](#pure-python):
+  18x as fast as [tomlkit](https://pypi.org/project/tomlkit/),
+  2.1x as fast as [toml](https://pypi.org/project/toml/)
+- outputs [basic data types](#how-do-toml-types-map-into-python-types) only
+- 100% spec compliant: passes all tests in
+  [toml-lang/toml-test](https://github.com/toml-lang/toml-test)
+  test suite
+- thoroughly tested: 100% branch coverage
+
+### Is comment preserving round-trip parsing supported?
+
+No.
+
+The `tomli.loads` function returns a plain `dict` that is populated with builtin types and types from the standard library only.
+Preserving comments requires a custom type to be returned so will not be supported,
+at least not by the `tomli.loads` and `tomli.load` functions.
+
+Look into [TOML Kit](https://github.com/sdispater/tomlkit) if preservation of style is what you need.
+
+### Is there a `dumps`, `write` or `encode` function?
+
+[Tomli-W](https://github.com/hukkin/tomli-w) is the write-only counterpart of Tomli, providing `dump` and `dumps` functions.
+
+The core library does not include write capability, as most TOML use cases are read-only, and Tomli intends to be minimal.
+
+### How do TOML types map into Python types?
+
+| TOML type        | Python type         | Details                                                      |
+| ---------------- | ------------------- | ------------------------------------------------------------ |
+| Document Root    | `dict`              |                                                              |
+| Key              | `str`               |                                                              |
+| String           | `str`               |                                                              |
+| Integer          | `int`               |                                                              |
+| Float            | `float`             |                                                              |
+| Boolean          | `bool`              |                                                              |
+| Offset Date-Time | `datetime.datetime` | `tzinfo` attribute set to an instance of `datetime.timezone` |
+| Local Date-Time  | `datetime.datetime` | `tzinfo` attribute set to `None`                             |
+| Local Date       | `datetime.date`     |                                                              |
+| Local Time       | `datetime.time`     |                                                              |
+| Array            | `list`              |                                                              |
+| Table            | `dict`              |                                                              |
+| Inline Table     | `dict`              |                                                              |
+
+## Performance
+
+The `benchmark/` folder in this repository contains a performance benchmark for comparing the various Python TOML parsers.
+
+Below are the results for commit [0724e2a](https://github.com/hukkin/tomli/tree/0724e2ab1858da7f5e05a9bffdb24c33589d951c).
+
+### Pure Python
+
+```console
+foo@bar:~/dev/tomli$ python --version
+Python 3.12.7
+foo@bar:~/dev/tomli$ pip freeze
+attrs==21.4.0
+click==8.1.7
+pytomlpp==1.0.13
+qtoml==0.3.1
+rtoml==0.11.0
+toml==0.10.2
+tomli @ file:///home/foo/dev/tomli
+tomlkit==0.13.2
+foo@bar:~/dev/tomli$ python benchmark/run.py
+Parsing data.toml 5000 times:
+------------------------------------------------------
+    parser |  exec time | performance (more is better)
+-----------+------------+-----------------------------
+     rtoml |    0.647 s | baseline (100%)
+  pytomlpp |    0.891 s | 72.62%
+     tomli |     3.14 s | 20.56%
+      toml |     6.69 s | 9.67%
+     qtoml |     8.27 s | 7.82%
+   tomlkit |     56.1 s | 1.15%
+```
+
+### Mypyc generated wheel
+
+```console
+foo@bar:~/dev/tomli$ python benchmark/run.py
+Parsing data.toml 5000 times:
+------------------------------------------------------
+    parser |  exec time | performance (more is better)
+-----------+------------+-----------------------------
+     rtoml |    0.668 s | baseline (100%)
+  pytomlpp |    0.893 s | 74.81%
+     tomli |     1.96 s | 34.18%
+      toml |     6.64 s | 10.07%
+     qtoml |     8.26 s | 8.09%
+   tomlkit |     52.9 s | 1.26%
+```
+
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/RECORD
new file mode 100644
index 0000000000000000000000000000000000000000..d2415a38de6198f1dad22ba1de542d15cd7065b3
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/RECORD
@@ -0,0 +1,11 @@
+tomli-2.4.0.dist-info/INSTALLER,sha256=5hhM4Q4mYTT9z6QB6PGpUAW81PGNFrYrdXMj4oM_6ak,2
+tomli-2.4.0.dist-info/METADATA,sha256=9awKH4-6kItGRs1lUwnpGq2Wm2eHYWrFccpGKjgy_84,10567
+tomli-2.4.0.dist-info/RECORD,,
+tomli-2.4.0.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+tomli-2.4.0.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+tomli-2.4.0.dist-info/licenses/LICENSE,sha256=uAgWsNUwuKzLTCIReDeQmEpuO2GSLCte6S8zcqsnQv4,1072
+tomli/__init__.py,sha256=ahtDjGJA2M_wWVvGpzx4YJtWxrWBx6qE-GH5-UYoECA,314
+tomli/_parser.py,sha256=txeATLE3zHyZ-ushXtYfrZ3LoIs7JzQF2W2KL1gwJPg,25958
+tomli/_re.py,sha256=oSNZ_ilFI6chEuQ01YRSoUydBQr_okF_mSdHTkFmv90,3396
+tomli/_types.py,sha256=-GTG2VUqkpxwMqzmVO4F7ybKddIbAnuAHXfmWQcTi3Q,254
+tomli/py.typed,sha256=8PjyZ1aVoQpRVvt71muvuq5qE-jTFZkK-GLHkhdebmc,26
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/REQUESTED b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/REQUESTED
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/WHEEL
new file mode 100644
index 0000000000000000000000000000000000000000..d8b9936dad9ab2513fa6979f411560d3b6b57e37
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/WHEEL
@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: flit 3.12.0
+Root-Is-Purelib: true
+Tag: py3-none-any
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/licenses/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/licenses/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..e859590f886cd78344206af1a8ccb3080d4385e0
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli-2.4.0.dist-info/licenses/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Taneli Hukkinen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..55699b1ea68247f72a382dc11cd2b5c4b07d24fd
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/__init__.py
@@ -0,0 +1,8 @@
+# SPDX-License-Identifier: MIT
+# SPDX-FileCopyrightText: 2021 Taneli Hukkinen
+# Licensed to PSF under a Contributor Agreement.
+
+__all__ = ("loads", "load", "TOMLDecodeError")
+__version__ = "2.4.0"  # DO NOT EDIT THIS LINE MANUALLY. LET bump2version UTILITY DO IT
+
+from ._parser import TOMLDecodeError, load, loads
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/_parser.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/_parser.py
new file mode 100644
index 0000000000000000000000000000000000000000..3038891afec8d4e6608ae4209365cf31f94b7f41
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/_parser.py
@@ -0,0 +1,782 @@
+# SPDX-License-Identifier: MIT
+# SPDX-FileCopyrightText: 2021 Taneli Hukkinen
+# Licensed to PSF under a Contributor Agreement.
+
+from __future__ import annotations
+
+import sys
+from types import MappingProxyType
+
+from ._re import (
+    RE_DATETIME,
+    RE_LOCALTIME,
+    RE_NUMBER,
+    match_to_datetime,
+    match_to_localtime,
+    match_to_number,
+)
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from collections.abc import Iterable
+    from typing import IO, Any, Final
+
+    from ._types import Key, ParseFloat, Pos
+
+# Inline tables/arrays are implemented using recursion. Pathologically
+# nested documents cause pure Python to raise RecursionError (which is OK),
+# but mypyc binary wheels will crash unrecoverably (not OK). According to
+# mypyc docs this will be fixed in the future:
+# https://mypyc.readthedocs.io/en/latest/differences_from_python.html#stack-overflows
+# Before mypyc's fix is in, recursion needs to be limited by this library.
+# Choosing `sys.getrecursionlimit()` as maximum inline table/array nesting
+# level, as it allows more nesting than pure Python, but still seems a far
+# lower number than where mypyc binaries crash.
+MAX_INLINE_NESTING: Final = sys.getrecursionlimit()
+
+ASCII_CTRL: Final = frozenset(chr(i) for i in range(32)) | frozenset(chr(127))
+
+# Neither of these sets include quotation mark or backslash. They are
+# currently handled as separate cases in the parser functions.
+ILLEGAL_BASIC_STR_CHARS: Final = ASCII_CTRL - frozenset("\t")
+ILLEGAL_MULTILINE_BASIC_STR_CHARS: Final = ASCII_CTRL - frozenset("\t\n")
+
+ILLEGAL_LITERAL_STR_CHARS: Final = ILLEGAL_BASIC_STR_CHARS
+ILLEGAL_MULTILINE_LITERAL_STR_CHARS: Final = ILLEGAL_MULTILINE_BASIC_STR_CHARS
+
+ILLEGAL_COMMENT_CHARS: Final = ILLEGAL_BASIC_STR_CHARS
+
+TOML_WS: Final = frozenset(" \t")
+TOML_WS_AND_NEWLINE: Final = TOML_WS | frozenset("\n")
+BARE_KEY_CHARS: Final = frozenset(
+    "abcdefghijklmnopqrstuvwxyz" "ABCDEFGHIJKLMNOPQRSTUVWXYZ" "0123456789" "-_"
+)
+KEY_INITIAL_CHARS: Final = BARE_KEY_CHARS | frozenset("\"'")
+HEXDIGIT_CHARS: Final = frozenset("abcdef" "ABCDEF" "0123456789")
+
+BASIC_STR_ESCAPE_REPLACEMENTS: Final = MappingProxyType(
+    {
+        "\\b": "\u0008",  # backspace
+        "\\t": "\u0009",  # tab
+        "\\n": "\u000a",  # linefeed
+        "\\f": "\u000c",  # form feed
+        "\\r": "\u000d",  # carriage return
+        "\\e": "\u001b",  # escape
+        '\\"': "\u0022",  # quote
+        "\\\\": "\u005c",  # backslash
+    }
+)
+
+
+class DEPRECATED_DEFAULT:
+    """Sentinel to be used as default arg during deprecation
+    period of TOMLDecodeError's free-form arguments."""
+
+
+class TOMLDecodeError(ValueError):
+    """An error raised if a document is not valid TOML.
+
+    Adds the following attributes to ValueError:
+    msg: The unformatted error message
+    doc: The TOML document being parsed
+    pos: The index of doc where parsing failed
+    lineno: The line corresponding to pos
+    colno: The column corresponding to pos
+    """
+
+    def __init__(
+        self,
+        msg: str | type[DEPRECATED_DEFAULT] = DEPRECATED_DEFAULT,
+        doc: str | type[DEPRECATED_DEFAULT] = DEPRECATED_DEFAULT,
+        pos: Pos | type[DEPRECATED_DEFAULT] = DEPRECATED_DEFAULT,
+        *args: Any,
+    ):
+        if (
+            args
+            or not isinstance(msg, str)
+            or not isinstance(doc, str)
+            or not isinstance(pos, int)
+        ):
+            import warnings
+
+            warnings.warn(
+                "Free-form arguments for TOMLDecodeError are deprecated. "
+                "Please set 'msg' (str), 'doc' (str) and 'pos' (int) arguments only.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+            if pos is not DEPRECATED_DEFAULT:
+                args = pos, *args
+            if doc is not DEPRECATED_DEFAULT:
+                args = doc, *args
+            if msg is not DEPRECATED_DEFAULT:
+                args = msg, *args
+            ValueError.__init__(self, *args)
+            return
+
+        lineno = doc.count("\n", 0, pos) + 1
+        if lineno == 1:
+            colno = pos + 1
+        else:
+            colno = pos - doc.rindex("\n", 0, pos)
+
+        if pos >= len(doc):
+            coord_repr = "end of document"
+        else:
+            coord_repr = f"line {lineno}, column {colno}"
+        errmsg = f"{msg} (at {coord_repr})"
+        ValueError.__init__(self, errmsg)
+
+        self.msg = msg
+        self.doc = doc
+        self.pos = pos
+        self.lineno = lineno
+        self.colno = colno
+
+
+def load(__fp: IO[bytes], *, parse_float: ParseFloat = float) -> dict[str, Any]:
+    """Parse TOML from a binary file object."""
+    b = __fp.read()
+    try:
+        s = b.decode()
+    except AttributeError:
+        raise TypeError(
+            "File must be opened in binary mode, e.g. use `open('foo.toml', 'rb')`"
+        ) from None
+    return loads(s, parse_float=parse_float)
+
+
+def loads(__s: str, *, parse_float: ParseFloat = float) -> dict[str, Any]:
+    """Parse TOML from a string."""
+
+    # The spec allows converting "\r\n" to "\n", even in string
+    # literals. Let's do so to simplify parsing.
+    try:
+        src = __s.replace("\r\n", "\n")
+    except (AttributeError, TypeError):
+        raise TypeError(
+            f"Expected str object, not '{type(__s).__qualname__}'"
+        ) from None
+    pos = 0
+    out = Output()
+    header: Key = ()
+    parse_float = make_safe_parse_float(parse_float)
+
+    # Parse one statement at a time
+    # (typically means one line in TOML source)
+    while True:
+        # 1. Skip line leading whitespace
+        pos = skip_chars(src, pos, TOML_WS)
+
+        # 2. Parse rules. Expect one of the following:
+        #    - end of file
+        #    - end of line
+        #    - comment
+        #    - key/value pair
+        #    - append dict to list (and move to its namespace)
+        #    - create dict (and move to its namespace)
+        # Skip trailing whitespace when applicable.
+        try:
+            char = src[pos]
+        except IndexError:
+            break
+        if char == "\n":
+            pos += 1
+            continue
+        if char in KEY_INITIAL_CHARS:
+            pos = key_value_rule(src, pos, out, header, parse_float)
+            pos = skip_chars(src, pos, TOML_WS)
+        elif char == "[":
+            try:
+                second_char: str | None = src[pos + 1]
+            except IndexError:
+                second_char = None
+            out.flags.finalize_pending()
+            if second_char == "[":
+                pos, header = create_list_rule(src, pos, out)
+            else:
+                pos, header = create_dict_rule(src, pos, out)
+            pos = skip_chars(src, pos, TOML_WS)
+        elif char != "#":
+            raise TOMLDecodeError("Invalid statement", src, pos)
+
+        # 3. Skip comment
+        pos = skip_comment(src, pos)
+
+        # 4. Expect end of line or end of file
+        try:
+            char = src[pos]
+        except IndexError:
+            break
+        if char != "\n":
+            raise TOMLDecodeError(
+                "Expected newline or end of document after a statement", src, pos
+            )
+        pos += 1
+
+    return out.data.dict
+
+
+class Flags:
+    """Flags that map to parsed keys/namespaces."""
+
+    # Marks an immutable namespace (inline array or inline table).
+    FROZEN: Final = 0
+    # Marks a nest that has been explicitly created and can no longer
+    # be opened using the "[table]" syntax.
+    EXPLICIT_NEST: Final = 1
+
+    def __init__(self) -> None:
+        self._flags: dict[str, dict[Any, Any]] = {}
+        self._pending_flags: set[tuple[Key, int]] = set()
+
+    def add_pending(self, key: Key, flag: int) -> None:
+        self._pending_flags.add((key, flag))
+
+    def finalize_pending(self) -> None:
+        for key, flag in self._pending_flags:
+            self.set(key, flag, recursive=False)
+        self._pending_flags.clear()
+
+    def unset_all(self, key: Key) -> None:
+        cont = self._flags
+        for k in key[:-1]:
+            if k not in cont:
+                return
+            cont = cont[k]["nested"]
+        cont.pop(key[-1], None)
+
+    def set(self, key: Key, flag: int, *, recursive: bool) -> None:  # noqa: A003
+        cont = self._flags
+        key_parent, key_stem = key[:-1], key[-1]
+        for k in key_parent:
+            if k not in cont:
+                cont[k] = {"flags": set(), "recursive_flags": set(), "nested": {}}
+            cont = cont[k]["nested"]
+        if key_stem not in cont:
+            cont[key_stem] = {"flags": set(), "recursive_flags": set(), "nested": {}}
+        cont[key_stem]["recursive_flags" if recursive else "flags"].add(flag)
+
+    def is_(self, key: Key, flag: int) -> bool:
+        if not key:
+            return False  # document root has no flags
+        cont = self._flags
+        for k in key[:-1]:
+            if k not in cont:
+                return False
+            inner_cont = cont[k]
+            if flag in inner_cont["recursive_flags"]:
+                return True
+            cont = inner_cont["nested"]
+        key_stem = key[-1]
+        if key_stem in cont:
+            inner_cont = cont[key_stem]
+            return flag in inner_cont["flags"] or flag in inner_cont["recursive_flags"]
+        return False
+
+
+class NestedDict:
+    def __init__(self) -> None:
+        # The parsed content of the TOML document
+        self.dict: dict[str, Any] = {}
+
+    def get_or_create_nest(
+        self,
+        key: Key,
+        *,
+        access_lists: bool = True,
+    ) -> dict[str, Any]:
+        cont: Any = self.dict
+        for k in key:
+            if k not in cont:
+                cont[k] = {}
+            cont = cont[k]
+            if access_lists and isinstance(cont, list):
+                cont = cont[-1]
+            if not isinstance(cont, dict):
+                raise KeyError("There is no nest behind this key")
+        return cont  # type: ignore[no-any-return]
+
+    def append_nest_to_list(self, key: Key) -> None:
+        cont = self.get_or_create_nest(key[:-1])
+        last_key = key[-1]
+        if last_key in cont:
+            list_ = cont[last_key]
+            if not isinstance(list_, list):
+                raise KeyError("An object other than list found behind this key")
+            list_.append({})
+        else:
+            cont[last_key] = [{}]
+
+
+class Output:
+    def __init__(self) -> None:
+        self.data = NestedDict()
+        self.flags = Flags()
+
+
+def skip_chars(src: str, pos: Pos, chars: Iterable[str]) -> Pos:
+    try:
+        while src[pos] in chars:
+            pos += 1
+    except IndexError:
+        pass
+    return pos
+
+
+def skip_until(
+    src: str,
+    pos: Pos,
+    expect: str,
+    *,
+    error_on: frozenset[str],
+    error_on_eof: bool,
+) -> Pos:
+    try:
+        new_pos = src.index(expect, pos)
+    except ValueError:
+        new_pos = len(src)
+        if error_on_eof:
+            raise TOMLDecodeError(f"Expected {expect!r}", src, new_pos) from None
+
+    if not error_on.isdisjoint(src[pos:new_pos]):
+        while src[pos] not in error_on:
+            pos += 1
+        raise TOMLDecodeError(f"Found invalid character {src[pos]!r}", src, pos)
+    return new_pos
+
+
+def skip_comment(src: str, pos: Pos) -> Pos:
+    try:
+        char: str | None = src[pos]
+    except IndexError:
+        char = None
+    if char == "#":
+        return skip_until(
+            src, pos + 1, "\n", error_on=ILLEGAL_COMMENT_CHARS, error_on_eof=False
+        )
+    return pos
+
+
+def skip_comments_and_array_ws(src: str, pos: Pos) -> Pos:
+    while True:
+        pos_before_skip = pos
+        pos = skip_chars(src, pos, TOML_WS_AND_NEWLINE)
+        pos = skip_comment(src, pos)
+        if pos == pos_before_skip:
+            return pos
+
+
+def create_dict_rule(src: str, pos: Pos, out: Output) -> tuple[Pos, Key]:
+    pos += 1  # Skip "["
+    pos = skip_chars(src, pos, TOML_WS)
+    pos, key = parse_key(src, pos)
+
+    if out.flags.is_(key, Flags.EXPLICIT_NEST) or out.flags.is_(key, Flags.FROZEN):
+        raise TOMLDecodeError(f"Cannot declare {key} twice", src, pos)
+    out.flags.set(key, Flags.EXPLICIT_NEST, recursive=False)
+    try:
+        out.data.get_or_create_nest(key)
+    except KeyError:
+        raise TOMLDecodeError("Cannot overwrite a value", src, pos) from None
+
+    if not src.startswith("]", pos):
+        raise TOMLDecodeError(
+            "Expected ']' at the end of a table declaration", src, pos
+        )
+    return pos + 1, key
+
+
+def create_list_rule(src: str, pos: Pos, out: Output) -> tuple[Pos, Key]:
+    pos += 2  # Skip "[["
+    pos = skip_chars(src, pos, TOML_WS)
+    pos, key = parse_key(src, pos)
+
+    if out.flags.is_(key, Flags.FROZEN):
+        raise TOMLDecodeError(f"Cannot mutate immutable namespace {key}", src, pos)
+    # Free the namespace now that it points to another empty list item...
+    out.flags.unset_all(key)
+    # ...but this key precisely is still prohibited from table declaration
+    out.flags.set(key, Flags.EXPLICIT_NEST, recursive=False)
+    try:
+        out.data.append_nest_to_list(key)
+    except KeyError:
+        raise TOMLDecodeError("Cannot overwrite a value", src, pos) from None
+
+    if not src.startswith("]]", pos):
+        raise TOMLDecodeError(
+            "Expected ']]' at the end of an array declaration", src, pos
+        )
+    return pos + 2, key
+
+
+def key_value_rule(
+    src: str, pos: Pos, out: Output, header: Key, parse_float: ParseFloat
+) -> Pos:
+    pos, key, value = parse_key_value_pair(src, pos, parse_float, nest_lvl=0)
+    key_parent, key_stem = key[:-1], key[-1]
+    abs_key_parent = header + key_parent
+
+    relative_path_cont_keys = (header + key[:i] for i in range(1, len(key)))
+    for cont_key in relative_path_cont_keys:
+        # Check that dotted key syntax does not redefine an existing table
+        if out.flags.is_(cont_key, Flags.EXPLICIT_NEST):
+            raise TOMLDecodeError(f"Cannot redefine namespace {cont_key}", src, pos)
+        # Containers in the relative path can't be opened with the table syntax or
+        # dotted key/value syntax in following table sections.
+        out.flags.add_pending(cont_key, Flags.EXPLICIT_NEST)
+
+    if out.flags.is_(abs_key_parent, Flags.FROZEN):
+        raise TOMLDecodeError(
+            f"Cannot mutate immutable namespace {abs_key_parent}", src, pos
+        )
+
+    try:
+        nest = out.data.get_or_create_nest(abs_key_parent)
+    except KeyError:
+        raise TOMLDecodeError("Cannot overwrite a value", src, pos) from None
+    if key_stem in nest:
+        raise TOMLDecodeError("Cannot overwrite a value", src, pos)
+    # Mark inline table and array namespaces recursively immutable
+    if isinstance(value, (dict, list)):
+        out.flags.set(header + key, Flags.FROZEN, recursive=True)
+    nest[key_stem] = value
+    return pos
+
+
+def parse_key_value_pair(
+    src: str, pos: Pos, parse_float: ParseFloat, nest_lvl: int
+) -> tuple[Pos, Key, Any]:
+    pos, key = parse_key(src, pos)
+    try:
+        char: str | None = src[pos]
+    except IndexError:
+        char = None
+    if char != "=":
+        raise TOMLDecodeError("Expected '=' after a key in a key/value pair", src, pos)
+    pos += 1
+    pos = skip_chars(src, pos, TOML_WS)
+    pos, value = parse_value(src, pos, parse_float, nest_lvl)
+    return pos, key, value
+
+
+def parse_key(src: str, pos: Pos) -> tuple[Pos, Key]:
+    pos, key_part = parse_key_part(src, pos)
+    key: Key = (key_part,)
+    pos = skip_chars(src, pos, TOML_WS)
+    while True:
+        try:
+            char: str | None = src[pos]
+        except IndexError:
+            char = None
+        if char != ".":
+            return pos, key
+        pos += 1
+        pos = skip_chars(src, pos, TOML_WS)
+        pos, key_part = parse_key_part(src, pos)
+        key += (key_part,)
+        pos = skip_chars(src, pos, TOML_WS)
+
+
+def parse_key_part(src: str, pos: Pos) -> tuple[Pos, str]:
+    try:
+        char: str | None = src[pos]
+    except IndexError:
+        char = None
+    if char in BARE_KEY_CHARS:
+        start_pos = pos
+        pos = skip_chars(src, pos, BARE_KEY_CHARS)
+        return pos, src[start_pos:pos]
+    if char == "'":
+        return parse_literal_str(src, pos)
+    if char == '"':
+        return parse_one_line_basic_str(src, pos)
+    raise TOMLDecodeError("Invalid initial character for a key part", src, pos)
+
+
+def parse_one_line_basic_str(src: str, pos: Pos) -> tuple[Pos, str]:
+    pos += 1
+    return parse_basic_str(src, pos, multiline=False)
+
+
+def parse_array(
+    src: str, pos: Pos, parse_float: ParseFloat, nest_lvl: int
+) -> tuple[Pos, list[Any]]:
+    pos += 1
+    array: list[Any] = []
+
+    pos = skip_comments_and_array_ws(src, pos)
+    if src.startswith("]", pos):
+        return pos + 1, array
+    while True:
+        pos, val = parse_value(src, pos, parse_float, nest_lvl)
+        array.append(val)
+        pos = skip_comments_and_array_ws(src, pos)
+
+        c = src[pos : pos + 1]
+        if c == "]":
+            return pos + 1, array
+        if c != ",":
+            raise TOMLDecodeError("Unclosed array", src, pos)
+        pos += 1
+
+        pos = skip_comments_and_array_ws(src, pos)
+        if src.startswith("]", pos):
+            return pos + 1, array
+
+
+def parse_inline_table(
+    src: str, pos: Pos, parse_float: ParseFloat, nest_lvl: int
+) -> tuple[Pos, dict[str, Any]]:
+    pos += 1
+    nested_dict = NestedDict()
+    flags = Flags()
+
+    pos = skip_comments_and_array_ws(src, pos)
+    if src.startswith("}", pos):
+        return pos + 1, nested_dict.dict
+    while True:
+        pos, key, value = parse_key_value_pair(src, pos, parse_float, nest_lvl)
+        key_parent, key_stem = key[:-1], key[-1]
+        if flags.is_(key, Flags.FROZEN):
+            raise TOMLDecodeError(f"Cannot mutate immutable namespace {key}", src, pos)
+        try:
+            nest = nested_dict.get_or_create_nest(key_parent, access_lists=False)
+        except KeyError:
+            raise TOMLDecodeError("Cannot overwrite a value", src, pos) from None
+        if key_stem in nest:
+            raise TOMLDecodeError(f"Duplicate inline table key {key_stem!r}", src, pos)
+        nest[key_stem] = value
+        pos = skip_comments_and_array_ws(src, pos)
+        c = src[pos : pos + 1]
+        if c == "}":
+            return pos + 1, nested_dict.dict
+        if c != ",":
+            raise TOMLDecodeError("Unclosed inline table", src, pos)
+        pos += 1
+        pos = skip_comments_and_array_ws(src, pos)
+        if src.startswith("}", pos):
+            return pos + 1, nested_dict.dict
+        if isinstance(value, (dict, list)):
+            flags.set(key, Flags.FROZEN, recursive=True)
+
+
+def parse_basic_str_escape(
+    src: str, pos: Pos, *, multiline: bool = False
+) -> tuple[Pos, str]:
+    escape_id = src[pos : pos + 2]
+    pos += 2
+    if multiline and escape_id in {"\\ ", "\\\t", "\\\n"}:
+        # Skip whitespace until next non-whitespace character or end of
+        # the doc. Error if non-whitespace is found before newline.
+        if escape_id != "\\\n":
+            pos = skip_chars(src, pos, TOML_WS)
+            try:
+                char = src[pos]
+            except IndexError:
+                return pos, ""
+            if char != "\n":
+                raise TOMLDecodeError("Unescaped '\\' in a string", src, pos)
+            pos += 1
+        pos = skip_chars(src, pos, TOML_WS_AND_NEWLINE)
+        return pos, ""
+    if escape_id == "\\x":
+        return parse_hex_char(src, pos, 2)
+    if escape_id == "\\u":
+        return parse_hex_char(src, pos, 4)
+    if escape_id == "\\U":
+        return parse_hex_char(src, pos, 8)
+    try:
+        return pos, BASIC_STR_ESCAPE_REPLACEMENTS[escape_id]
+    except KeyError:
+        raise TOMLDecodeError("Unescaped '\\' in a string", src, pos) from None
+
+
+def parse_basic_str_escape_multiline(src: str, pos: Pos) -> tuple[Pos, str]:
+    return parse_basic_str_escape(src, pos, multiline=True)
+
+
+def parse_hex_char(src: str, pos: Pos, hex_len: int) -> tuple[Pos, str]:
+    hex_str = src[pos : pos + hex_len]
+    if len(hex_str) != hex_len or not HEXDIGIT_CHARS.issuperset(hex_str):
+        raise TOMLDecodeError("Invalid hex value", src, pos)
+    pos += hex_len
+    hex_int = int(hex_str, 16)
+    if not is_unicode_scalar_value(hex_int):
+        raise TOMLDecodeError(
+            "Escaped character is not a Unicode scalar value", src, pos
+        )
+    return pos, chr(hex_int)
+
+
+def parse_literal_str(src: str, pos: Pos) -> tuple[Pos, str]:
+    pos += 1  # Skip starting apostrophe
+    start_pos = pos
+    pos = skip_until(
+        src, pos, "'", error_on=ILLEGAL_LITERAL_STR_CHARS, error_on_eof=True
+    )
+    return pos + 1, src[start_pos:pos]  # Skip ending apostrophe
+
+
+def parse_multiline_str(src: str, pos: Pos, *, literal: bool) -> tuple[Pos, str]:
+    pos += 3
+    if src.startswith("\n", pos):
+        pos += 1
+
+    if literal:
+        delim = "'"
+        end_pos = skip_until(
+            src,
+            pos,
+            "'''",
+            error_on=ILLEGAL_MULTILINE_LITERAL_STR_CHARS,
+            error_on_eof=True,
+        )
+        result = src[pos:end_pos]
+        pos = end_pos + 3
+    else:
+        delim = '"'
+        pos, result = parse_basic_str(src, pos, multiline=True)
+
+    # Add at maximum two extra apostrophes/quotes if the end sequence
+    # is 4 or 5 chars long instead of just 3.
+    if not src.startswith(delim, pos):
+        return pos, result
+    pos += 1
+    if not src.startswith(delim, pos):
+        return pos, result + delim
+    pos += 1
+    return pos, result + (delim * 2)
+
+
+def parse_basic_str(src: str, pos: Pos, *, multiline: bool) -> tuple[Pos, str]:
+    if multiline:
+        error_on = ILLEGAL_MULTILINE_BASIC_STR_CHARS
+        parse_escapes = parse_basic_str_escape_multiline
+    else:
+        error_on = ILLEGAL_BASIC_STR_CHARS
+        parse_escapes = parse_basic_str_escape
+    result = ""
+    start_pos = pos
+    while True:
+        try:
+            char = src[pos]
+        except IndexError:
+            raise TOMLDecodeError("Unterminated string", src, pos) from None
+        if char == '"':
+            if not multiline:
+                return pos + 1, result + src[start_pos:pos]
+            if src.startswith('"""', pos):
+                return pos + 3, result + src[start_pos:pos]
+            pos += 1
+            continue
+        if char == "\\":
+            result += src[start_pos:pos]
+            pos, parsed_escape = parse_escapes(src, pos)
+            result += parsed_escape
+            start_pos = pos
+            continue
+        if char in error_on:
+            raise TOMLDecodeError(f"Illegal character {char!r}", src, pos)
+        pos += 1
+
+
+def parse_value(
+    src: str, pos: Pos, parse_float: ParseFloat, nest_lvl: int
+) -> tuple[Pos, Any]:
+    if nest_lvl > MAX_INLINE_NESTING:
+        # Pure Python should have raised RecursionError already.
+        # This ensures mypyc binaries eventually do the same.
+        raise RecursionError(  # pragma: no cover
+            "TOML inline arrays/tables are nested more than the allowed"
+            f" {MAX_INLINE_NESTING} levels"
+        )
+
+    try:
+        char: str | None = src[pos]
+    except IndexError:
+        char = None
+
+    # IMPORTANT: order conditions based on speed of checking and likelihood
+
+    # Basic strings
+    if char == '"':
+        if src.startswith('"""', pos):
+            return parse_multiline_str(src, pos, literal=False)
+        return parse_one_line_basic_str(src, pos)
+
+    # Literal strings
+    if char == "'":
+        if src.startswith("'''", pos):
+            return parse_multiline_str(src, pos, literal=True)
+        return parse_literal_str(src, pos)
+
+    # Booleans
+    if char == "t":
+        if src.startswith("true", pos):
+            return pos + 4, True
+    if char == "f":
+        if src.startswith("false", pos):
+            return pos + 5, False
+
+    # Arrays
+    if char == "[":
+        return parse_array(src, pos, parse_float, nest_lvl + 1)
+
+    # Inline tables
+    if char == "{":
+        return parse_inline_table(src, pos, parse_float, nest_lvl + 1)
+
+    # Dates and times
+    datetime_match = RE_DATETIME.match(src, pos)
+    if datetime_match:
+        try:
+            datetime_obj = match_to_datetime(datetime_match)
+        except ValueError as e:
+            raise TOMLDecodeError("Invalid date or datetime", src, pos) from e
+        return datetime_match.end(), datetime_obj
+    localtime_match = RE_LOCALTIME.match(src, pos)
+    if localtime_match:
+        return localtime_match.end(), match_to_localtime(localtime_match)
+
+    # Integers and "normal" floats.
+    # The regex will greedily match any type starting with a decimal
+    # char, so needs to be located after handling of dates and times.
+    number_match = RE_NUMBER.match(src, pos)
+    if number_match:
+        return number_match.end(), match_to_number(number_match, parse_float)
+
+    # Special floats
+    first_three = src[pos : pos + 3]
+    if first_three in {"inf", "nan"}:
+        return pos + 3, parse_float(first_three)
+    first_four = src[pos : pos + 4]
+    if first_four in {"-inf", "+inf", "-nan", "+nan"}:
+        return pos + 4, parse_float(first_four)
+
+    raise TOMLDecodeError("Invalid value", src, pos)
+
+
+def is_unicode_scalar_value(codepoint: int) -> bool:
+    return (0 <= codepoint <= 55295) or (57344 <= codepoint <= 1114111)
+
+
+def make_safe_parse_float(parse_float: ParseFloat) -> ParseFloat:
+    """A decorator to make `parse_float` safe.
+
+    `parse_float` must not return dicts or lists, because these types
+    would be mixed with parsed TOML tables and arrays, thus confusing
+    the parser. The returned decorated callable raises `ValueError`
+    instead of returning illegal types.
+    """
+    # The default `float` callable never returns illegal types. Optimize it.
+    if parse_float is float:
+        return float
+
+    def safe_parse_float(float_str: str) -> Any:
+        float_value = parse_float(float_str)
+        if isinstance(float_value, (dict, list)):
+            raise ValueError("parse_float must not return dicts or lists")
+        return float_value
+
+    return safe_parse_float
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/_re.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/_re.py
new file mode 100644
index 0000000000000000000000000000000000000000..fc374ed63d3e3742a97134349fc25b14223ab57b
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/_re.py
@@ -0,0 +1,119 @@
+# SPDX-License-Identifier: MIT
+# SPDX-FileCopyrightText: 2021 Taneli Hukkinen
+# Licensed to PSF under a Contributor Agreement.
+
+from __future__ import annotations
+
+from datetime import date, datetime, time, timedelta, timezone, tzinfo
+from functools import lru_cache
+import re
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Any, Final
+
+    from ._types import ParseFloat
+
+_TIME_RE_STR: Final = r"""
+([01][0-9]|2[0-3])             # hours
+:([0-5][0-9])                  # minutes
+(?:
+    :([0-5][0-9])              # optional seconds
+    (?:\.([0-9]{1,6})[0-9]*)?  # optional fractions of a second
+)?
+"""
+
+RE_NUMBER: Final = re.compile(
+    r"""
+0
+(?:
+    x[0-9A-Fa-f](?:_?[0-9A-Fa-f])*   # hex
+    |
+    b[01](?:_?[01])*                 # bin
+    |
+    o[0-7](?:_?[0-7])*               # oct
+)
+|
+[+-]?(?:0|[1-9](?:_?[0-9])*)         # dec, integer part
+(?P
+    (?:\.[0-9](?:_?[0-9])*)?         # optional fractional part
+    (?:[eE][+-]?[0-9](?:_?[0-9])*)?  # optional exponent part
+)
+""",
+    flags=re.VERBOSE,
+)
+RE_LOCALTIME: Final = re.compile(_TIME_RE_STR, flags=re.VERBOSE)
+RE_DATETIME: Final = re.compile(
+    rf"""
+([0-9]{{4}})-(0[1-9]|1[0-2])-(0[1-9]|[12][0-9]|3[01])  # date, e.g. 1988-10-27
+(?:
+    [Tt ]
+    {_TIME_RE_STR}
+    (?:([Zz])|([+-])([01][0-9]|2[0-3]):([0-5][0-9]))?  # optional time offset
+)?
+""",
+    flags=re.VERBOSE,
+)
+
+
+def match_to_datetime(match: re.Match[str]) -> datetime | date:
+    """Convert a `RE_DATETIME` match to `datetime.datetime` or `datetime.date`.
+
+    Raises ValueError if the match does not correspond to a valid date
+    or datetime.
+    """
+    (
+        year_str,
+        month_str,
+        day_str,
+        hour_str,
+        minute_str,
+        sec_str,
+        micros_str,
+        zulu_time,
+        offset_sign_str,
+        offset_hour_str,
+        offset_minute_str,
+    ) = match.groups()
+    year, month, day = int(year_str), int(month_str), int(day_str)
+    if hour_str is None:
+        return date(year, month, day)
+    hour, minute = int(hour_str), int(minute_str)
+    sec = int(sec_str) if sec_str else 0
+    micros = int(micros_str.ljust(6, "0")) if micros_str else 0
+    if offset_sign_str:
+        tz: tzinfo | None = cached_tz(
+            offset_hour_str, offset_minute_str, offset_sign_str
+        )
+    elif zulu_time:
+        tz = timezone.utc
+    else:  # local date-time
+        tz = None
+    return datetime(year, month, day, hour, minute, sec, micros, tzinfo=tz)
+
+
+# No need to limit cache size. This is only ever called on input
+# that matched RE_DATETIME, so there is an implicit bound of
+# 24 (hours) * 60 (minutes) * 2 (offset direction) = 2880.
+@lru_cache(maxsize=None)
+def cached_tz(hour_str: str, minute_str: str, sign_str: str) -> timezone:
+    sign = 1 if sign_str == "+" else -1
+    return timezone(
+        timedelta(
+            hours=sign * int(hour_str),
+            minutes=sign * int(minute_str),
+        )
+    )
+
+
+def match_to_localtime(match: re.Match[str]) -> time:
+    hour_str, minute_str, sec_str, micros_str = match.groups()
+    sec = int(sec_str) if sec_str else 0
+    micros = int(micros_str.ljust(6, "0")) if micros_str else 0
+    return time(int(hour_str), int(minute_str), sec, micros)
+
+
+def match_to_number(match: re.Match[str], parse_float: ParseFloat) -> Any:
+    if match.group("floatpart"):
+        return parse_float(match.group())
+    return int(match.group(), 0)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/_types.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/_types.py
new file mode 100644
index 0000000000000000000000000000000000000000..d949412e03b29d70592c7721fe747e5085c2e280
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/_types.py
@@ -0,0 +1,10 @@
+# SPDX-License-Identifier: MIT
+# SPDX-FileCopyrightText: 2021 Taneli Hukkinen
+# Licensed to PSF under a Contributor Agreement.
+
+from typing import Any, Callable, Tuple
+
+# Type annotations
+ParseFloat = Callable[[str], Any]
+Key = Tuple[str, ...]
+Pos = int
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/py.typed b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/py.typed
new file mode 100644
index 0000000000000000000000000000000000000000..7632ecf77545c5e5501cb3fc5719df0761104ca2
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/tomli/py.typed
@@ -0,0 +1 @@
+# Marker file for PEP 561
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/INSTALLER
new file mode 100644
index 0000000000000000000000000000000000000000..f79e4cb9aaf0b2d9e8ba78861e2071317b2384b3
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/INSTALLER
@@ -0,0 +1 @@
+conda
\ No newline at end of file
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/METADATA
new file mode 100644
index 0000000000000000000000000000000000000000..77936a9eb631d1aad5a9a9d12ce825c97392943e
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/METADATA
@@ -0,0 +1,69 @@
+Metadata-Version: 2.4
+Name: wheel
+Version: 0.46.3
+Summary: Command line tool for manipulating wheel files
+Keywords: wheel,packaging
+Author-email: Daniel Holth 
+Maintainer-email: Alex Grönholm 
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
+License-Expression: MIT
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: System :: Archiving :: Packaging
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+License-File: LICENSE.txt
+Requires-Dist: packaging >= 24.0
+Requires-Dist: pytest >= 6.0.0 ; extra == "test"
+Requires-Dist: setuptools >= 77 ; extra == "test"
+Project-URL: Changelog, https://wheel.readthedocs.io/en/stable/news.html
+Project-URL: Documentation, https://wheel.readthedocs.io/
+Project-URL: Issue Tracker, https://github.com/pypa/wheel/issues
+Project-URL: Source, https://github.com/pypa/wheel
+Provides-Extra: test
+
+wheel
+=====
+
+This is a command line tool for manipulating Python wheel files, as defined in
+`PEP 427`_. It contains the following functionality:
+
+* Convert ``.egg`` archives into ``.whl``
+* Unpack wheel archives
+* Repack wheel archives
+* Add or remove tags in existing wheel archives
+
+.. _PEP 427: https://www.python.org/dev/peps/pep-0427/
+
+Historical note
+---------------
+
+This project used to contain the implementation of the setuptools_ ``bdist_wheel``
+command, but as of setuptools v70.1, it no longer needs ``wheel`` installed for that to
+work. Thus, you should install this **only** if you intend to use the ``wheel`` command
+line tool!
+
+.. _setuptools: https://pypi.org/project/setuptools/
+
+Documentation
+-------------
+
+The documentation_ can be found on Read The Docs.
+
+.. _documentation: https://wheel.readthedocs.io/
+
+Code of Conduct
+---------------
+
+Everyone interacting in the wheel project's codebases, issue trackers, chat
+rooms, and mailing lists is expected to follow the `PSF Code of Conduct`_.
+
+.. _PSF Code of Conduct: https://github.com/pypa/.github/blob/main/CODE_OF_CONDUCT.md
+
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/RECORD
new file mode 100644
index 0000000000000000000000000000000000000000..5890933bcb85e7a1f5bca660d3aa311b71884e5d
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/RECORD
@@ -0,0 +1,22 @@
+bin/wheel,sha256=OLjFs9G7MQ-f_mhuW2aLGpngsyphW_v5FIoyN88Hfk0,339
+wheel-0.46.3.dist-info/INSTALLER,sha256=5hhM4Q4mYTT9z6QB6PGpUAW81PGNFrYrdXMj4oM_6ak,2
+wheel-0.46.3.dist-info/METADATA,sha256=IpEKqXyonLzCCgGeJ_4xNgt5KaS9ZsoNMQ-ZpE9szTU,2410
+wheel-0.46.3.dist-info/RECORD,,
+wheel-0.46.3.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+wheel-0.46.3.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
+wheel-0.46.3.dist-info/entry_points.txt,sha256=JJdtSAGTvMLbIkTVZUAMvGKO39FtWfCVF8mp_NH6e4g,110
+wheel-0.46.3.dist-info/licenses/LICENSE.txt,sha256=MMI2GGeRCPPo6h0qZYx8pBe9_IkcmO8aifpP8MmChlQ,1107
+wheel/__init__.py,sha256=UweKvhe4SyP7zFyDoYo8BOuwTA6q3-_WpMmY2NNO54c,59
+wheel/__main__.py,sha256=_83wl9tyGU2cHiqfudpubGHdRL5uonPXnzeznznkxzs,512
+wheel/_bdist_wheel.py,sha256=bpmNa7_s-CYFkVgXf9ENAYTiJ01XBhRW4pxH1T8XYsI,21729
+wheel/_commands/__init__.py,sha256=fCRAQZNDyj2JLrufdgPsBlaRS_t_j_aBUMpXj09KZ4E,4432
+wheel/_commands/convert.py,sha256=0wSJMU0m-6LY16Om8Wmmloy-hJWFZeOmI8hT-2Z7Qms,12743
+wheel/_commands/pack.py,sha256=o3iwjfRHl7N9ul-M2kHbewLJZnqBLAWf0tzUCwoiTMw,3078
+wheel/_commands/tags.py,sha256=Rv2ySVb8-qX3osKp3uJgxcIMXkjt43XUD0-zvC6KvnY,4775
+wheel/_commands/unpack.py,sha256=AjDSS23XYyCSFfifnMutinrpPv-DK_2wbNHkKAUFwgM,1016
+wheel/_metadata.py,sha256=BP5jC9uC1hyicp7nL4FJ2LYixNFpEJIV_uMDY1KBZBg,6188
+wheel/_setuptools_logging.py,sha256=-5KC-lne0ilOUWIDfOkqapUWGMFZhuKYDIavIZiB5kM,781
+wheel/bdist_wheel.py,sha256=HrzYiSzMkh5ohAAhlQnYBS1p8qbr85X6F59xqxd9kBg,1102
+wheel/macosx_libfile.py,sha256=pL0wm88jRMl_4ASgGlNg_mz69Zmv5xm8JSkjLdwyvIQ,16712
+wheel/metadata.py,sha256=GknOO7JJiZMlcEe_fiD7nqnDTTLd0sX_-IgipM4L3-4,757
+wheel/wheelfile.py,sha256=m_g_7TNsEp-j-xnvSr5yDLEFb1nhyObueq9Q5_1_lBA,8720
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/REQUESTED b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/REQUESTED
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/WHEEL
new file mode 100644
index 0000000000000000000000000000000000000000..d8b9936dad9ab2513fa6979f411560d3b6b57e37
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/WHEEL
@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: flit 3.12.0
+Root-Is-Purelib: true
+Tag: py3-none-any
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/entry_points.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/entry_points.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dcebd58811da1ee2758dd0f45c575704afdd61bd
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/entry_points.txt
@@ -0,0 +1,6 @@
+[console_scripts]
+wheel=wheel._commands:main
+
+[distutils.commands]
+bdist_wheel=wheel.bdist_wheel:bdist_wheel
+
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/licenses/LICENSE.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/licenses/LICENSE.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a31470f14c5978d5fcc3bc173b8399b6c9a6443f
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel-0.46.3.dist-info/licenses/LICENSE.txt
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2012 Daniel Holth  and contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..b5b076f05a69ac941356361db47159d6cc06c296
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/__init__.py
@@ -0,0 +1,3 @@
+from __future__ import annotations
+
+__version__ = "0.46.3"
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/__main__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/__main__.py
new file mode 100644
index 0000000000000000000000000000000000000000..3c7de5fb7fd2fcc1bbb60b5c3977e82c3aa2f898
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/__main__.py
@@ -0,0 +1,25 @@
+"""
+Wheel command line tool (enables the ``python -m wheel`` syntax)
+"""
+
+from __future__ import annotations
+
+import sys
+from typing import NoReturn
+
+
+def main() -> NoReturn:  # needed for console script
+    if __package__ == "":
+        # To be able to run 'python wheel-0.9.whl/wheel':
+        import os.path
+
+        path = os.path.dirname(os.path.dirname(__file__))
+        sys.path[0:0] = [path]
+
+    from ._commands import main as cli_main
+
+    sys.exit(cli_main())
+
+
+if __name__ == "__main__":
+    main()
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_bdist_wheel.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_bdist_wheel.py
new file mode 100644
index 0000000000000000000000000000000000000000..575fbfb35105eb82faee5a368781ecf818379354
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_bdist_wheel.py
@@ -0,0 +1,616 @@
+"""
+Create a wheel (.whl) distribution.
+
+A wheel is a built archive format.
+"""
+
+from __future__ import annotations
+
+import logging
+import os
+import re
+import shutil
+import stat
+import struct
+import sys
+import sysconfig
+import warnings
+from collections.abc import Iterable, Sequence
+from email.generator import BytesGenerator, Generator
+from email.policy import EmailPolicy
+from glob import iglob
+from shutil import rmtree
+from typing import TYPE_CHECKING, Callable, Literal, cast
+from zipfile import ZIP_DEFLATED, ZIP_STORED
+
+import setuptools
+from packaging import tags
+from packaging import version as _packaging_version
+from setuptools import Command
+
+from . import __version__ as wheel_version
+from ._metadata import pkginfo_to_metadata
+from .wheelfile import WheelFile
+
+if TYPE_CHECKING:
+    import types
+
+# ensure Python logging is configured
+try:
+    __import__("setuptools.logging")
+except ImportError:
+    # setuptools < ??
+    from . import _setuptools_logging
+
+    _setuptools_logging.configure()
+
+log = logging.getLogger("wheel")
+
+
+def safe_name(name: str) -> str:
+    """Convert an arbitrary string to a standard distribution name
+    Any runs of non-alphanumeric/. characters are replaced with a single '-'.
+    """
+    return re.sub("[^A-Za-z0-9.]+", "-", name)
+
+
+def safe_version(version: str) -> str:
+    """
+    Convert an arbitrary string to a standard version string
+    """
+    try:
+        # normalize the version
+        return str(_packaging_version.Version(version))
+    except _packaging_version.InvalidVersion:
+        version = version.replace(" ", ".")
+        return re.sub("[^A-Za-z0-9.]+", "-", version)
+
+
+setuptools_major_version = int(setuptools.__version__.split(".")[0])
+
+PY_LIMITED_API_PATTERN = r"cp3\d"
+
+
+def _is_32bit_interpreter() -> bool:
+    return struct.calcsize("P") == 4
+
+
+def python_tag() -> str:
+    return f"py{sys.version_info[0]}"
+
+
+def get_platform(archive_root: str | None) -> str:
+    """Return our platform name 'win32', 'linux_x86_64'"""
+    result = sysconfig.get_platform()
+    if result.startswith("macosx") and archive_root is not None:
+        from .macosx_libfile import calculate_macosx_platform_tag
+
+        result = calculate_macosx_platform_tag(archive_root, result)
+    elif _is_32bit_interpreter():
+        if result == "linux-x86_64":
+            # pip pull request #3497
+            result = "linux-i686"
+        elif result == "linux-aarch64":
+            # packaging pull request #234
+            # TODO armv8l, packaging pull request #690 => this did not land
+            # in pip/packaging yet
+            result = "linux-armv7l"
+
+    return result.replace("-", "_")
+
+
+def get_flag(
+    var: str, fallback: bool, expected: bool = True, warn: bool = True
+) -> bool:
+    """Use a fallback value for determining SOABI flags if the needed config
+    var is unset or unavailable."""
+    val = sysconfig.get_config_var(var)
+    if val is None:
+        if warn:
+            warnings.warn(
+                f"Config variable '{var}' is unset, Python ABI tag may be incorrect",
+                RuntimeWarning,
+                stacklevel=2,
+            )
+        return fallback
+    return val == expected
+
+
+def get_abi_tag() -> str | None:
+    """Return the ABI tag based on SOABI (if available) or emulate SOABI (PyPy2)."""
+    soabi: str = sysconfig.get_config_var("SOABI")
+    impl = tags.interpreter_name()
+    if not soabi and impl in ("cp", "pp") and hasattr(sys, "maxunicode"):
+        d = ""
+        m = ""
+        u = ""
+        if get_flag("Py_DEBUG", hasattr(sys, "gettotalrefcount"), warn=(impl == "cp")):
+            d = "d"
+
+        if get_flag(
+            "WITH_PYMALLOC",
+            impl == "cp",
+            warn=(impl == "cp" and sys.version_info < (3, 8)),
+        ) and sys.version_info < (3, 8):
+            m = "m"
+
+        abi = f"{impl}{tags.interpreter_version()}{d}{m}{u}"
+    elif soabi and impl == "cp" and soabi.startswith("cpython"):
+        # non-Windows
+        abi = "cp" + soabi.split("-")[1]
+    elif soabi and impl == "cp" and soabi.startswith("cp"):
+        # Windows
+        abi = soabi.split("-")[0]
+    elif soabi and impl == "pp":
+        # we want something like pypy36-pp73
+        abi = "-".join(soabi.split("-")[:2])
+        abi = abi.replace(".", "_").replace("-", "_")
+    elif soabi and impl == "graalpy":
+        abi = "-".join(soabi.split("-")[:3])
+        abi = abi.replace(".", "_").replace("-", "_")
+    elif soabi:
+        abi = soabi.replace(".", "_").replace("-", "_")
+    else:
+        abi = None
+
+    return abi
+
+
+def safer_name(name: str) -> str:
+    return safe_name(name).replace("-", "_")
+
+
+def safer_version(version: str) -> str:
+    return safe_version(version).replace("-", "_")
+
+
+def remove_readonly(
+    func: Callable[..., object],
+    path: str,
+    excinfo: tuple[type[Exception], Exception, types.TracebackType],
+) -> None:
+    remove_readonly_exc(func, path, excinfo[1])
+
+
+def remove_readonly_exc(func: Callable[..., object], path: str, exc: Exception) -> None:
+    os.chmod(path, stat.S_IWRITE)
+    func(path)
+
+
+class bdist_wheel(Command):
+    description = "create a wheel distribution"
+
+    supported_compressions = {
+        "stored": ZIP_STORED,
+        "deflated": ZIP_DEFLATED,
+    }
+
+    user_options = [
+        ("bdist-dir=", "b", "temporary directory for creating the distribution"),
+        (
+            "plat-name=",
+            "p",
+            "platform name to embed in generated filenames "
+            f"(default: {get_platform(None)})",
+        ),
+        (
+            "keep-temp",
+            "k",
+            "keep the pseudo-installation tree around after "
+            "creating the distribution archive",
+        ),
+        ("dist-dir=", "d", "directory to put final built distributions in"),
+        ("skip-build", None, "skip rebuilding everything (for testing/debugging)"),
+        (
+            "relative",
+            None,
+            "build the archive using relative paths (default: false)",
+        ),
+        (
+            "owner=",
+            "u",
+            "Owner name used when creating a tar file [default: current user]",
+        ),
+        (
+            "group=",
+            "g",
+            "Group name used when creating a tar file [default: current group]",
+        ),
+        ("universal", None, "make a universal wheel (default: false)"),
+        (
+            "compression=",
+            None,
+            "zipfile compression (one of: {}) (default: 'deflated')".format(
+                ", ".join(supported_compressions)
+            ),
+        ),
+        (
+            "python-tag=",
+            None,
+            f"Python implementation compatibility tag (default: '{python_tag()}')",
+        ),
+        (
+            "build-number=",
+            None,
+            "Build number for this particular version. "
+            "As specified in PEP-0427, this must start with a digit. "
+            "[default: None]",
+        ),
+        (
+            "py-limited-api=",
+            None,
+            "Python tag (cp32|cp33|cpNN) for abi3 wheel tag (default: false)",
+        ),
+    ]
+
+    boolean_options = ["keep-temp", "skip-build", "relative", "universal"]
+
+    def initialize_options(self):
+        self.bdist_dir: str = None
+        self.data_dir = None
+        self.plat_name: str | None = None
+        self.plat_tag = None
+        self.format = "zip"
+        self.keep_temp = False
+        self.dist_dir: str | None = None
+        self.egginfo_dir = None
+        self.root_is_pure: bool | None = None
+        self.skip_build = None
+        self.relative = False
+        self.owner = None
+        self.group = None
+        self.universal: bool = False
+        self.compression: str | int = "deflated"
+        self.python_tag: str = python_tag()
+        self.build_number: str | None = None
+        self.py_limited_api: str | Literal[False] = False
+        self.plat_name_supplied = False
+
+    def finalize_options(self):
+        if self.bdist_dir is None:
+            bdist_base = self.get_finalized_command("bdist").bdist_base
+            self.bdist_dir = os.path.join(bdist_base, "wheel")
+
+        egg_info = self.distribution.get_command_obj("egg_info")
+        egg_info.ensure_finalized()  # needed for correct `wheel_dist_name`
+
+        self.data_dir = self.wheel_dist_name + ".data"
+        self.plat_name_supplied = self.plat_name is not None
+
+        try:
+            self.compression = self.supported_compressions[self.compression]
+        except KeyError:
+            raise ValueError(f"Unsupported compression: {self.compression}") from None
+
+        need_options = ("dist_dir", "plat_name", "skip_build")
+
+        self.set_undefined_options("bdist", *zip(need_options, need_options))
+
+        self.root_is_pure = not (
+            self.distribution.has_ext_modules() or self.distribution.has_c_libraries()
+        )
+
+        if self.py_limited_api and not re.match(
+            PY_LIMITED_API_PATTERN, self.py_limited_api
+        ):
+            raise ValueError(f"py-limited-api must match '{PY_LIMITED_API_PATTERN}'")
+
+        # Support legacy [wheel] section for setting universal
+        wheel = self.distribution.get_option_dict("wheel")
+        if "universal" in wheel:
+            # please don't define this in your global configs
+            log.warning(
+                "The [wheel] section is deprecated. Use [bdist_wheel] instead.",
+            )
+            val = wheel["universal"][1].strip()
+            if val.lower() in ("1", "true", "yes"):
+                self.universal = True
+
+        if self.build_number is not None and not self.build_number[:1].isdigit():
+            raise ValueError("Build tag (build-number) must start with a digit.")
+
+    @property
+    def wheel_dist_name(self):
+        """Return distribution full name with - replaced with _"""
+        components = (
+            safer_name(self.distribution.get_name()),
+            safer_version(self.distribution.get_version()),
+        )
+        if self.build_number:
+            components += (self.build_number,)
+        return "-".join(components)
+
+    def get_tag(self) -> tuple[str, str, str]:
+        # bdist sets self.plat_name if unset, we should only use it for purepy
+        # wheels if the user supplied it.
+        if self.plat_name_supplied:
+            plat_name = cast(str, self.plat_name)
+        elif self.root_is_pure:
+            plat_name = "any"
+        else:
+            # macosx contains system version in platform name so need special handle
+            if self.plat_name and not self.plat_name.startswith("macosx"):
+                plat_name = self.plat_name
+            else:
+                # on macosx always limit the platform name to comply with any
+                # c-extension modules in bdist_dir, since the user can specify
+                # a higher MACOSX_DEPLOYMENT_TARGET via tools like CMake
+
+                # on other platforms, and on macosx if there are no c-extension
+                # modules, use the default platform name.
+                plat_name = get_platform(self.bdist_dir)
+
+            if _is_32bit_interpreter():
+                if plat_name in ("linux-x86_64", "linux_x86_64"):
+                    plat_name = "linux_i686"
+                if plat_name in ("linux-aarch64", "linux_aarch64"):
+                    # TODO armv8l, packaging pull request #690 => this did not land
+                    # in pip/packaging yet
+                    plat_name = "linux_armv7l"
+
+        plat_name = (
+            plat_name.lower().replace("-", "_").replace(".", "_").replace(" ", "_")
+        )
+
+        if self.root_is_pure:
+            if self.universal:
+                impl = "py2.py3"
+            else:
+                impl = self.python_tag
+            tag = (impl, "none", plat_name)
+        else:
+            impl_name = tags.interpreter_name()
+            impl_ver = tags.interpreter_version()
+            impl = impl_name + impl_ver
+            # We don't work on CPython 3.1, 3.0.
+            if self.py_limited_api and (impl_name + impl_ver).startswith("cp3"):
+                impl = self.py_limited_api
+                abi_tag = "abi3"
+            else:
+                abi_tag = str(get_abi_tag()).lower()
+            tag = (impl, abi_tag, plat_name)
+            # issue gh-374: allow overriding plat_name
+            supported_tags = [
+                (t.interpreter, t.abi, plat_name) for t in tags.sys_tags()
+            ]
+            assert tag in supported_tags, (
+                f"would build wheel with unsupported tag {tag}"
+            )
+        return tag
+
+    def run(self):
+        build_scripts = self.reinitialize_command("build_scripts")
+        build_scripts.executable = "python"
+        build_scripts.force = True
+
+        build_ext = self.reinitialize_command("build_ext")
+        build_ext.inplace = False
+
+        if not self.skip_build:
+            self.run_command("build")
+
+        install = self.reinitialize_command("install", reinit_subcommands=True)
+        install.root = self.bdist_dir
+        install.compile = False
+        install.skip_build = self.skip_build
+        install.warn_dir = False
+
+        # A wheel without setuptools scripts is more cross-platform.
+        # Use the (undocumented) `no_ep` option to setuptools'
+        # install_scripts command to avoid creating entry point scripts.
+        install_scripts = self.reinitialize_command("install_scripts")
+        install_scripts.no_ep = True
+
+        # Use a custom scheme for the archive, because we have to decide
+        # at installation time which scheme to use.
+        for key in ("headers", "scripts", "data", "purelib", "platlib"):
+            setattr(install, "install_" + key, os.path.join(self.data_dir, key))
+
+        basedir_observed = ""
+
+        if os.name == "nt":
+            # win32 barfs if any of these are ''; could be '.'?
+            # (distutils.command.install:change_roots bug)
+            basedir_observed = os.path.normpath(os.path.join(self.data_dir, ".."))
+            self.install_libbase = self.install_lib = basedir_observed
+
+        setattr(
+            install,
+            "install_purelib" if self.root_is_pure else "install_platlib",
+            basedir_observed,
+        )
+
+        log.info(f"installing to {self.bdist_dir}")
+
+        self.run_command("install")
+
+        impl_tag, abi_tag, plat_tag = self.get_tag()
+        archive_basename = f"{self.wheel_dist_name}-{impl_tag}-{abi_tag}-{plat_tag}"
+        if not self.relative:
+            archive_root = self.bdist_dir
+        else:
+            archive_root = os.path.join(
+                self.bdist_dir, self._ensure_relative(install.install_base)
+            )
+
+        self.set_undefined_options("install_egg_info", ("target", "egginfo_dir"))
+        distinfo_dirname = (
+            f"{safer_name(self.distribution.get_name())}-"
+            f"{safer_version(self.distribution.get_version())}.dist-info"
+        )
+        distinfo_dir = os.path.join(self.bdist_dir, distinfo_dirname)
+        self.egg2dist(self.egginfo_dir, distinfo_dir)
+
+        self.write_wheelfile(distinfo_dir)
+
+        # Make the archive
+        if not os.path.exists(self.dist_dir):
+            os.makedirs(self.dist_dir)
+
+        wheel_path = os.path.join(self.dist_dir, archive_basename + ".whl")
+        with WheelFile(wheel_path, "w", self.compression) as wf:
+            wf.write_files(archive_root)
+
+        # Add to 'Distribution.dist_files' so that the "upload" command works
+        getattr(self.distribution, "dist_files", []).append(
+            (
+                "bdist_wheel",
+                "{}.{}".format(*sys.version_info[:2]),  # like 3.7
+                wheel_path,
+            )
+        )
+
+        if not self.keep_temp:
+            log.info(f"removing {self.bdist_dir}")
+            if not self.dry_run:
+                if sys.version_info < (3, 12):
+                    rmtree(self.bdist_dir, onerror=remove_readonly)
+                else:
+                    rmtree(self.bdist_dir, onexc=remove_readonly_exc)
+
+    def write_wheelfile(
+        self, wheelfile_base: str, generator: str = f"bdist_wheel ({wheel_version})"
+    ):
+        from email.message import Message
+
+        msg = Message()
+        msg["Wheel-Version"] = "1.0"  # of the spec
+        msg["Generator"] = generator
+        msg["Root-Is-Purelib"] = str(self.root_is_pure).lower()
+        if self.build_number is not None:
+            msg["Build"] = self.build_number
+
+        # Doesn't work for bdist_wininst
+        impl_tag, abi_tag, plat_tag = self.get_tag()
+        for impl in impl_tag.split("."):
+            for abi in abi_tag.split("."):
+                for plat in plat_tag.split("."):
+                    msg["Tag"] = "-".join((impl, abi, plat))
+
+        wheelfile_path = os.path.join(wheelfile_base, "WHEEL")
+        log.info(f"creating {wheelfile_path}")
+        with open(wheelfile_path, "wb") as f:
+            BytesGenerator(f, maxheaderlen=0).flatten(msg)
+
+    def _ensure_relative(self, path: str) -> str:
+        # copied from dir_util, deleted
+        drive, path = os.path.splitdrive(path)
+        if path[0:1] == os.sep:
+            path = drive + path[1:]
+        return path
+
+    @property
+    def license_paths(self) -> Iterable[str]:
+        if setuptools_major_version >= 57:
+            # Setuptools has resolved any patterns to actual file names
+            return self.distribution.metadata.license_files or ()
+
+        files: set[str] = set()
+        metadata = self.distribution.get_option_dict("metadata")
+        if setuptools_major_version >= 42:
+            # Setuptools recognizes the license_files option but does not do globbing
+            patterns = cast(Sequence[str], self.distribution.metadata.license_files)
+        else:
+            # Prior to those, wheel is entirely responsible for handling license files
+            if "license_files" in metadata:
+                patterns = metadata["license_files"][1].split()
+            else:
+                patterns = ()
+
+        if "license_file" in metadata:
+            warnings.warn(
+                'The "license_file" option is deprecated. Use "license_files" instead.',
+                DeprecationWarning,
+                stacklevel=2,
+            )
+            files.add(metadata["license_file"][1])
+
+        if not files and not patterns and not isinstance(patterns, list):
+            patterns = ("LICEN[CS]E*", "COPYING*", "NOTICE*", "AUTHORS*")
+
+        for pattern in patterns:
+            for path in iglob(pattern):
+                if path.endswith("~"):
+                    log.debug(
+                        f'ignoring license file "{path}" as it looks like a backup'
+                    )
+                    continue
+
+                if path not in files and os.path.isfile(path):
+                    log.info(
+                        f'adding license file "{path}" (matched pattern "{pattern}")'
+                    )
+                    files.add(path)
+
+        return files
+
+    def egg2dist(self, egginfo_path: str, distinfo_path: str):
+        """Convert an .egg-info directory into a .dist-info directory"""
+
+        def adios(p: str) -> None:
+            """Appropriately delete directory, file or link."""
+            if os.path.exists(p) and not os.path.islink(p) and os.path.isdir(p):
+                shutil.rmtree(p)
+            elif os.path.exists(p):
+                os.unlink(p)
+
+        adios(distinfo_path)
+
+        if not os.path.exists(egginfo_path):
+            # There is no egg-info. This is probably because the egg-info
+            # file/directory is not named matching the distribution name used
+            # to name the archive file. Check for this case and report
+            # accordingly.
+            import glob
+
+            pat = os.path.join(os.path.dirname(egginfo_path), "*.egg-info")
+            possible = glob.glob(pat)
+            err = f"Egg metadata expected at {egginfo_path} but not found"
+            if possible:
+                alt = os.path.basename(possible[0])
+                err += f" ({alt} found - possible misnamed archive file?)"
+
+            raise ValueError(err)
+
+        if os.path.isfile(egginfo_path):
+            # .egg-info is a single file
+            pkg_info = pkginfo_to_metadata(egginfo_path, egginfo_path)
+            os.mkdir(distinfo_path)
+        else:
+            # .egg-info is a directory
+            pkginfo_path = os.path.join(egginfo_path, "PKG-INFO")
+            pkg_info = pkginfo_to_metadata(egginfo_path, pkginfo_path)
+
+            # ignore common egg metadata that is useless to wheel
+            shutil.copytree(
+                egginfo_path,
+                distinfo_path,
+                ignore=lambda x, y: {
+                    "PKG-INFO",
+                    "requires.txt",
+                    "SOURCES.txt",
+                    "not-zip-safe",
+                },
+            )
+
+            # delete dependency_links if it is only whitespace
+            dependency_links_path = os.path.join(distinfo_path, "dependency_links.txt")
+            with open(dependency_links_path, encoding="utf-8") as dependency_links_file:
+                dependency_links = dependency_links_file.read().strip()
+            if not dependency_links:
+                adios(dependency_links_path)
+
+        pkg_info_path = os.path.join(distinfo_path, "METADATA")
+        serialization_policy = EmailPolicy(
+            utf8=True,
+            mangle_from_=False,
+            max_line_length=0,
+        )
+        with open(pkg_info_path, "w", encoding="utf-8") as out:
+            Generator(out, policy=serialization_policy).flatten(pkg_info)
+
+        for license_path in self.license_paths:
+            filename = os.path.basename(license_path)
+            shutil.copy(license_path, os.path.join(distinfo_path, filename))
+
+        adios(egginfo_path)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..42f1d7ef309663498fd2b4d691aa71e14be34e63
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/__init__.py
@@ -0,0 +1,153 @@
+"""
+Wheel command-line utility.
+"""
+
+from __future__ import annotations
+
+import argparse
+import os
+import sys
+from argparse import ArgumentTypeError
+
+from ..wheelfile import WheelError
+
+
+def unpack_f(args: argparse.Namespace) -> None:
+    from .unpack import unpack
+
+    unpack(args.wheelfile, args.dest)
+
+
+def pack_f(args: argparse.Namespace) -> None:
+    from .pack import pack
+
+    pack(args.directory, args.dest_dir, args.build_number)
+
+
+def convert_f(args: argparse.Namespace) -> None:
+    from .convert import convert
+
+    convert(args.files, args.dest_dir, args.verbose)
+
+
+def tags_f(args: argparse.Namespace) -> None:
+    from .tags import tags
+
+    names = (
+        tags(
+            wheel,
+            args.python_tag,
+            args.abi_tag,
+            args.platform_tag,
+            args.build,
+            args.remove,
+        )
+        for wheel in args.wheel
+    )
+
+    for name in names:
+        print(name)
+
+
+def version_f(args: argparse.Namespace) -> None:
+    from .. import __version__
+
+    print(f"wheel {__version__}")
+
+
+def parse_build_tag(build_tag: str) -> str:
+    if build_tag and not build_tag[0].isdigit():
+        raise ArgumentTypeError("build tag must begin with a digit")
+    elif "-" in build_tag:
+        raise ArgumentTypeError("invalid character ('-') in build tag")
+
+    return build_tag
+
+
+TAGS_HELP = """\
+Make a new wheel with given tags. Any tags unspecified will remain the same.
+Starting the tags with a "+" will append to the existing tags. Starting with a
+"-" will remove a tag (use --option=-TAG syntax). Multiple tags can be
+separated by ".". The original file will remain unless --remove is given.  The
+output filename(s) will be displayed on stdout for further processing.
+"""
+
+
+def parser() -> argparse.ArgumentParser:
+    p = argparse.ArgumentParser()
+    s = p.add_subparsers(help="commands")
+
+    unpack_parser = s.add_parser("unpack", help="Unpack wheel")
+    unpack_parser.add_argument(
+        "--dest", "-d", help="Destination directory", default="."
+    )
+    unpack_parser.add_argument("wheelfile", help="Wheel file")
+    unpack_parser.set_defaults(func=unpack_f)
+
+    repack_parser = s.add_parser("pack", help="Repack wheel")
+    repack_parser.add_argument("directory", help="Root directory of the unpacked wheel")
+    repack_parser.add_argument(
+        "--dest-dir",
+        "-d",
+        default=os.path.curdir,
+        help="Directory to store the wheel (default %(default)s)",
+    )
+    repack_parser.add_argument(
+        "--build-number", help="Build tag to use in the wheel name"
+    )
+    repack_parser.set_defaults(func=pack_f)
+
+    convert_parser = s.add_parser("convert", help="Convert egg or wininst to wheel")
+    convert_parser.add_argument("files", nargs="*", help="Files to convert")
+    convert_parser.add_argument(
+        "--dest-dir",
+        "-d",
+        default=os.path.curdir,
+        help="Directory to store wheels (default %(default)s)",
+    )
+    convert_parser.add_argument("--verbose", "-v", action="store_true")
+    convert_parser.set_defaults(func=convert_f)
+
+    tags_parser = s.add_parser(
+        "tags", help="Add or replace the tags on a wheel", description=TAGS_HELP
+    )
+    tags_parser.add_argument("wheel", nargs="*", help="Existing wheel(s) to retag")
+    tags_parser.add_argument(
+        "--remove",
+        action="store_true",
+        help="Remove the original files, keeping only the renamed ones",
+    )
+    tags_parser.add_argument(
+        "--python-tag", metavar="TAG", help="Specify an interpreter tag(s)"
+    )
+    tags_parser.add_argument("--abi-tag", metavar="TAG", help="Specify an ABI tag(s)")
+    tags_parser.add_argument(
+        "--platform-tag", metavar="TAG", help="Specify a platform tag(s)"
+    )
+    tags_parser.add_argument(
+        "--build", type=parse_build_tag, metavar="BUILD", help="Specify a build tag"
+    )
+    tags_parser.set_defaults(func=tags_f)
+
+    version_parser = s.add_parser("version", help="Print version and exit")
+    version_parser.set_defaults(func=version_f)
+
+    help_parser = s.add_parser("help", help="Show this help")
+    help_parser.set_defaults(func=lambda args: p.print_help())
+
+    return p
+
+
+def main() -> int:
+    p = parser()
+    args = p.parse_args()
+    if not hasattr(args, "func"):
+        p.print_help()
+    else:
+        try:
+            args.func(args)
+            return 0
+        except WheelError as e:
+            print(e, file=sys.stderr)
+
+    return 1
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/convert.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/convert.py
new file mode 100644
index 0000000000000000000000000000000000000000..cafd12c86cbc0a661e69b9243ec5525a95274c9e
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/convert.py
@@ -0,0 +1,337 @@
+from __future__ import annotations
+
+import os.path
+import re
+from abc import ABCMeta, abstractmethod
+from collections import defaultdict
+from collections.abc import Iterator
+from email.message import Message
+from email.parser import Parser
+from email.policy import EmailPolicy
+from glob import iglob
+from pathlib import Path
+from textwrap import dedent
+from zipfile import ZipFile
+
+from packaging.tags import parse_tag
+
+from .. import __version__
+from .._metadata import generate_requirements
+from ..wheelfile import WheelFile
+
+egg_filename_re = re.compile(
+    r"""
+    (?P.+?)-(?P.+?)
+    (-(?Ppy\d\.\d+)
+     (-(?P.+?))?
+    )?.egg$""",
+    re.VERBOSE,
+)
+egg_info_re = re.compile(
+    r"""
+    ^(?P.+?)-(?P.+?)
+    (-(?Ppy\d\.\d+)
+    )?.egg-info/""",
+    re.VERBOSE,
+)
+wininst_re = re.compile(
+    r"\.(?Pwin32|win-amd64)(?:-(?Ppy\d\.\d))?\.exe$"
+)
+pyd_re = re.compile(r"\.(?P[a-z0-9]+)-(?Pwin32|win_amd64)\.pyd$")
+serialization_policy = EmailPolicy(
+    utf8=True,
+    mangle_from_=False,
+    max_line_length=0,
+)
+GENERATOR = f"wheel {__version__}"
+
+
+def convert_requires(requires: str, metadata: Message) -> None:
+    extra: str | None = None
+    requirements: dict[str | None, list[str]] = defaultdict(list)
+    for line in requires.splitlines():
+        line = line.strip()
+        if not line:
+            continue
+
+        if line.startswith("[") and line.endswith("]"):
+            extra = line[1:-1]
+            continue
+
+        requirements[extra].append(line)
+
+    for key, value in generate_requirements(requirements):
+        metadata.add_header(key, value)
+
+
+def convert_pkg_info(pkginfo: str, metadata: Message) -> None:
+    parsed_message = Parser().parsestr(pkginfo)
+    for key, value in parsed_message.items():
+        key_lower = key.lower()
+        if value == "UNKNOWN":
+            continue
+
+        if key_lower == "description":
+            description_lines = value.splitlines()
+            if description_lines:
+                value = "\n".join(
+                    (
+                        description_lines[0].lstrip(),
+                        dedent("\n".join(description_lines[1:])),
+                        "\n",
+                    )
+                )
+            else:
+                value = "\n"
+
+            metadata.set_payload(value)
+        elif key_lower == "home-page":
+            metadata.add_header("Project-URL", f"Homepage, {value}")
+        elif key_lower == "download-url":
+            metadata.add_header("Project-URL", f"Download, {value}")
+        else:
+            metadata.add_header(key, value)
+
+    metadata.replace_header("Metadata-Version", "2.4")
+
+
+def normalize(name: str) -> str:
+    return re.sub(r"[-_.]+", "-", name).lower().replace("-", "_")
+
+
+class ConvertSource(metaclass=ABCMeta):
+    name: str
+    version: str
+    pyver: str = "py2.py3"
+    abi: str = "none"
+    platform: str = "any"
+    metadata: Message
+
+    @property
+    def dist_info_dir(self) -> str:
+        return f"{self.name}-{self.version}.dist-info"
+
+    @abstractmethod
+    def generate_contents(self) -> Iterator[tuple[str, bytes]]:
+        pass
+
+
+class EggFileSource(ConvertSource):
+    def __init__(self, path: Path):
+        if not (match := egg_filename_re.match(path.name)):
+            raise ValueError(f"Invalid egg file name: {path.name}")
+
+        # Binary wheels are assumed to be for CPython
+        self.path = path
+        self.name = normalize(match.group("name"))
+        self.version = match.group("ver")
+        if pyver := match.group("pyver"):
+            self.pyver = pyver.replace(".", "")
+            if arch := match.group("arch"):
+                self.abi = self.pyver.replace("py", "cp")
+                self.platform = normalize(arch)
+
+        self.metadata = Message()
+
+    def generate_contents(self) -> Iterator[tuple[str, bytes]]:
+        with ZipFile(self.path, "r") as zip_file:
+            for filename in sorted(zip_file.namelist()):
+                # Skip pure directory entries
+                if filename.endswith("/"):
+                    continue
+
+                # Handle files in the egg-info directory specially, selectively moving
+                # them to the dist-info directory while converting as needed
+                if filename.startswith("EGG-INFO/"):
+                    if filename == "EGG-INFO/requires.txt":
+                        requires = zip_file.read(filename).decode("utf-8")
+                        convert_requires(requires, self.metadata)
+                    elif filename == "EGG-INFO/PKG-INFO":
+                        pkginfo = zip_file.read(filename).decode("utf-8")
+                        convert_pkg_info(pkginfo, self.metadata)
+                    elif filename == "EGG-INFO/entry_points.txt":
+                        yield (
+                            f"{self.dist_info_dir}/entry_points.txt",
+                            zip_file.read(filename),
+                        )
+
+                    continue
+
+                # For any other file, just pass it through
+                yield filename, zip_file.read(filename)
+
+
+class EggDirectorySource(EggFileSource):
+    def generate_contents(self) -> Iterator[tuple[str, bytes]]:
+        for dirpath, _, filenames in os.walk(self.path):
+            for filename in sorted(filenames):
+                path = Path(dirpath, filename)
+                if path.parent.name == "EGG-INFO":
+                    if path.name == "requires.txt":
+                        requires = path.read_text("utf-8")
+                        convert_requires(requires, self.metadata)
+                    elif path.name == "PKG-INFO":
+                        pkginfo = path.read_text("utf-8")
+                        convert_pkg_info(pkginfo, self.metadata)
+                        if name := self.metadata.get("Name"):
+                            self.name = normalize(name)
+
+                        if version := self.metadata.get("Version"):
+                            self.version = version
+                    elif path.name == "entry_points.txt":
+                        yield (
+                            f"{self.dist_info_dir}/entry_points.txt",
+                            path.read_bytes(),
+                        )
+
+                    continue
+
+                # For any other file, just pass it through
+                yield str(path.relative_to(self.path)), path.read_bytes()
+
+
+class WininstFileSource(ConvertSource):
+    """
+    Handles distributions created with ``bdist_wininst``.
+
+    The egginfo filename has the format::
+
+        name-ver(-pyver)(-arch).egg-info
+
+    The installer filename has the format::
+
+        name-ver.arch(-pyver).exe
+
+    Some things to note:
+
+    1. The installer filename is not definitive. An installer can be renamed
+       and work perfectly well as an installer. So more reliable data should
+       be used whenever possible.
+    2. The egg-info data should be preferred for the name and version, because
+       these come straight from the distutils metadata, and are mandatory.
+    3. The pyver from the egg-info data should be ignored, as it is
+       constructed from the version of Python used to build the installer,
+       which is irrelevant - the installer filename is correct here (even to
+       the point that when it's not there, any version is implied).
+    4. The architecture must be taken from the installer filename, as it is
+       not included in the egg-info data.
+    5. Architecture-neutral installers still have an architecture because the
+       installer format itself (being executable) is architecture-specific. We
+       should therefore ignore the architecture if the content is pure-python.
+    """
+
+    def __init__(self, path: Path):
+        self.path = path
+        self.metadata = Message()
+
+        # Determine the initial architecture and Python version from the file name
+        # (if possible)
+        if match := wininst_re.search(path.name):
+            self.platform = normalize(match.group("platform"))
+            if pyver := match.group("pyver"):
+                self.pyver = pyver.replace(".", "")
+
+        # Look for an .egg-info directory and any .pyd files for more precise info
+        egg_info_found = pyd_found = False
+        with ZipFile(self.path) as zip_file:
+            for filename in zip_file.namelist():
+                prefix, filename = filename.split("/", 1)
+                if not egg_info_found and (match := egg_info_re.match(filename)):
+                    egg_info_found = True
+                    self.name = normalize(match.group("name"))
+                    self.version = match.group("ver")
+                    if pyver := match.group("pyver"):
+                        self.pyver = pyver.replace(".", "")
+                elif not pyd_found and (match := pyd_re.search(filename)):
+                    pyd_found = True
+                    self.abi = match.group("abi")
+                    self.platform = match.group("platform")
+
+                if egg_info_found and pyd_found:
+                    break
+
+    def generate_contents(self) -> Iterator[tuple[str, bytes]]:
+        dist_info_dir = f"{self.name}-{self.version}.dist-info"
+        data_dir = f"{self.name}-{self.version}.data"
+        with ZipFile(self.path, "r") as zip_file:
+            for filename in sorted(zip_file.namelist()):
+                # Skip pure directory entries
+                if filename.endswith("/"):
+                    continue
+
+                # Handle files in the egg-info directory specially, selectively moving
+                # them to the dist-info directory while converting as needed
+                prefix, target_filename = filename.split("/", 1)
+                if egg_info_re.search(target_filename):
+                    basename = target_filename.rsplit("/", 1)[-1]
+                    if basename == "requires.txt":
+                        requires = zip_file.read(filename).decode("utf-8")
+                        convert_requires(requires, self.metadata)
+                    elif basename == "PKG-INFO":
+                        pkginfo = zip_file.read(filename).decode("utf-8")
+                        convert_pkg_info(pkginfo, self.metadata)
+                    elif basename == "entry_points.txt":
+                        yield (
+                            f"{dist_info_dir}/entry_points.txt",
+                            zip_file.read(filename),
+                        )
+
+                    continue
+                elif prefix == "SCRIPTS":
+                    target_filename = f"{data_dir}/scripts/{target_filename}"
+
+                # For any other file, just pass it through
+                yield target_filename, zip_file.read(filename)
+
+
+def convert(files: list[str], dest_dir: str, verbose: bool) -> None:
+    for pat in files:
+        for archive in iglob(pat):
+            path = Path(archive)
+            if path.suffix == ".egg":
+                if path.is_dir():
+                    source: ConvertSource = EggDirectorySource(path)
+                else:
+                    source = EggFileSource(path)
+            else:
+                source = WininstFileSource(path)
+
+            if verbose:
+                print(f"{archive}...", flush=True, end="")
+
+            dest_path = Path(dest_dir) / (
+                f"{source.name}-{source.version}-{source.pyver}-{source.abi}"
+                f"-{source.platform}.whl"
+            )
+            with WheelFile(dest_path, "w") as wheelfile:
+                for name_or_zinfo, contents in source.generate_contents():
+                    wheelfile.writestr(name_or_zinfo, contents)
+
+                # Write the METADATA file
+                wheelfile.writestr(
+                    f"{source.dist_info_dir}/METADATA",
+                    source.metadata.as_string(policy=serialization_policy).encode(
+                        "utf-8"
+                    ),
+                )
+
+                # Write the WHEEL file
+                wheel_message = Message()
+                wheel_message.add_header("Wheel-Version", "1.0")
+                wheel_message.add_header("Generator", GENERATOR)
+                wheel_message.add_header(
+                    "Root-Is-Purelib", str(source.platform == "any").lower()
+                )
+                tags = parse_tag(f"{source.pyver}-{source.abi}-{source.platform}")
+                for tag in sorted(tags, key=lambda tag: tag.interpreter):
+                    wheel_message.add_header("Tag", str(tag))
+
+                wheelfile.writestr(
+                    f"{source.dist_info_dir}/WHEEL",
+                    wheel_message.as_string(policy=serialization_policy).encode(
+                        "utf-8"
+                    ),
+                )
+
+            if verbose:
+                print("OK")
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/pack.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/pack.py
new file mode 100644
index 0000000000000000000000000000000000000000..1321ce9308a68f00cf2f839d4ba02869c16ec26f
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/pack.py
@@ -0,0 +1,84 @@
+from __future__ import annotations
+
+import email.policy
+import os.path
+import re
+from email.generator import BytesGenerator
+from email.parser import BytesParser
+
+from ..wheelfile import WheelError, WheelFile
+
+DIST_INFO_RE = re.compile(r"^(?P(?P.+?)-(?P\d.*?))\.dist-info$")
+
+
+def pack(directory: str, dest_dir: str, build_number: str | None) -> None:
+    """Repack a previously unpacked wheel directory into a new wheel file.
+
+    The .dist-info/WHEEL file must contain one or more tags so that the target
+    wheel file name can be determined.
+
+    :param directory: The unpacked wheel directory
+    :param dest_dir: Destination directory (defaults to the current directory)
+    """
+    # Find the .dist-info directory
+    dist_info_dirs = [
+        fn
+        for fn in os.listdir(directory)
+        if os.path.isdir(os.path.join(directory, fn)) and DIST_INFO_RE.match(fn)
+    ]
+    if len(dist_info_dirs) > 1:
+        raise WheelError(f"Multiple .dist-info directories found in {directory}")
+    elif not dist_info_dirs:
+        raise WheelError(f"No .dist-info directories found in {directory}")
+
+    # Determine the target wheel filename
+    dist_info_dir = dist_info_dirs[0]
+    name_version = DIST_INFO_RE.match(dist_info_dir).group("namever")
+
+    # Read the tags and the existing build number from .dist-info/WHEEL
+    wheel_file_path = os.path.join(directory, dist_info_dir, "WHEEL")
+    with open(wheel_file_path, "rb") as f:
+        info = BytesParser(policy=email.policy.compat32).parse(f)
+        tags: list[str] = info.get_all("Tag", [])
+        existing_build_number = info.get("Build")
+
+        if not tags:
+            raise WheelError(
+                f"No tags present in {dist_info_dir}/WHEEL; cannot determine target "
+                f"wheel filename"
+            )
+
+    # Set the wheel file name and add/replace/remove the Build tag in .dist-info/WHEEL
+    build_number = build_number if build_number is not None else existing_build_number
+    if build_number is not None:
+        del info["Build"]
+        if build_number:
+            info["Build"] = build_number
+            name_version += "-" + build_number
+
+        if build_number != existing_build_number:
+            with open(wheel_file_path, "wb") as f:
+                BytesGenerator(f, maxheaderlen=0).flatten(info)
+
+    # Reassemble the tags for the wheel file
+    tagline = compute_tagline(tags)
+
+    # Repack the wheel
+    wheel_path = os.path.join(dest_dir, f"{name_version}-{tagline}.whl")
+    with WheelFile(wheel_path, "w") as wf:
+        print(f"Repacking wheel as {wheel_path}...", end="", flush=True)
+        wf.write_files(directory)
+
+    print("OK")
+
+
+def compute_tagline(tags: list[str]) -> str:
+    """Compute a tagline from a list of tags.
+
+    :param tags: A list of tags
+    :return: A tagline
+    """
+    impls = sorted({tag.split("-")[0] for tag in tags})
+    abivers = sorted({tag.split("-")[1] for tag in tags})
+    platforms = sorted({tag.split("-")[2] for tag in tags})
+    return "-".join([".".join(impls), ".".join(abivers), ".".join(platforms)])
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/tags.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/tags.py
new file mode 100644
index 0000000000000000000000000000000000000000..cec896b55b726d29a53f10e06d06b79e645b2e94
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/tags.py
@@ -0,0 +1,140 @@
+from __future__ import annotations
+
+import email.policy
+import itertools
+import os
+from collections.abc import Iterable
+from email.parser import BytesParser
+
+from ..wheelfile import WheelFile
+
+
+def _compute_tags(original_tags: Iterable[str], new_tags: str | None) -> set[str]:
+    """Add or replace tags. Supports dot-separated tags"""
+    if new_tags is None:
+        return set(original_tags)
+
+    if new_tags.startswith("+"):
+        return {*original_tags, *new_tags[1:].split(".")}
+
+    if new_tags.startswith("-"):
+        return set(original_tags) - set(new_tags[1:].split("."))
+
+    return set(new_tags.split("."))
+
+
+def tags(
+    wheel: str,
+    python_tags: str | None = None,
+    abi_tags: str | None = None,
+    platform_tags: str | None = None,
+    build_tag: str | None = None,
+    remove: bool = False,
+) -> str:
+    """Change the tags on a wheel file.
+
+    The tags are left unchanged if they are not specified. To specify "none",
+    use ["none"]. To append to the previous tags, a tag should start with a
+    "+".  If a tag starts with "-", it will be removed from existing tags.
+    Processing is done left to right.
+
+    :param wheel: The paths to the wheels
+    :param python_tags: The Python tags to set
+    :param abi_tags: The ABI tags to set
+    :param platform_tags: The platform tags to set
+    :param build_tag: The build tag to set
+    :param remove: Remove the original wheel
+    """
+    with WheelFile(wheel, "r") as f:
+        assert f.filename, f"{f.filename} must be available"
+
+        wheel_info = f.read(f.dist_info_path + "/WHEEL")
+        info = BytesParser(policy=email.policy.compat32).parsebytes(wheel_info)
+
+        original_wheel_name = os.path.basename(f.filename)
+        namever = f.parsed_filename.group("namever")
+        build = f.parsed_filename.group("build")
+        original_python_tags = f.parsed_filename.group("pyver").split(".")
+        original_abi_tags = f.parsed_filename.group("abi").split(".")
+        original_plat_tags = f.parsed_filename.group("plat").split(".")
+
+    tags: list[str] = info.get_all("Tag", [])
+    existing_build_tag = info.get("Build")
+
+    impls = {tag.split("-")[0] for tag in tags}
+    abivers = {tag.split("-")[1] for tag in tags}
+    platforms = {tag.split("-")[2] for tag in tags}
+
+    if impls != set(original_python_tags):
+        msg = f"Wheel internal tags {impls!r} != filename tags {original_python_tags!r}"
+        raise AssertionError(msg)
+
+    if abivers != set(original_abi_tags):
+        msg = f"Wheel internal tags {abivers!r} != filename tags {original_abi_tags!r}"
+        raise AssertionError(msg)
+
+    if platforms != set(original_plat_tags):
+        msg = (
+            f"Wheel internal tags {platforms!r} != filename tags {original_plat_tags!r}"
+        )
+        raise AssertionError(msg)
+
+    if existing_build_tag != build:
+        msg = (
+            f"Incorrect filename '{build}' "
+            f"& *.dist-info/WHEEL '{existing_build_tag}' build numbers"
+        )
+        raise AssertionError(msg)
+
+    # Start changing as needed
+    if build_tag is not None:
+        build = build_tag
+
+    final_python_tags = sorted(_compute_tags(original_python_tags, python_tags))
+    final_abi_tags = sorted(_compute_tags(original_abi_tags, abi_tags))
+    final_plat_tags = sorted(_compute_tags(original_plat_tags, platform_tags))
+
+    final_tags = [
+        namever,
+        ".".join(final_python_tags),
+        ".".join(final_abi_tags),
+        ".".join(final_plat_tags),
+    ]
+    if build:
+        final_tags.insert(1, build)
+
+    final_wheel_name = "-".join(final_tags) + ".whl"
+
+    if original_wheel_name != final_wheel_name:
+        del info["Tag"], info["Build"]
+        for a, b, c in itertools.product(
+            final_python_tags, final_abi_tags, final_plat_tags
+        ):
+            info["Tag"] = f"{a}-{b}-{c}"
+        if build:
+            info["Build"] = build
+
+        original_wheel_path = os.path.join(
+            os.path.dirname(f.filename), original_wheel_name
+        )
+        final_wheel_path = os.path.join(os.path.dirname(f.filename), final_wheel_name)
+
+        with (
+            WheelFile(original_wheel_path, "r") as fin,
+            WheelFile(final_wheel_path, "w") as fout,
+        ):
+            fout.comment = fin.comment  # preserve the comment
+            for item in fin.infolist():
+                if item.is_dir():
+                    continue
+                if item.filename == f.dist_info_path + "/RECORD":
+                    continue
+                if item.filename == f.dist_info_path + "/WHEEL":
+                    fout.writestr(item, info.as_bytes())
+                else:
+                    fout.writestr(item, fin.read(item))
+
+        if remove:
+            os.remove(original_wheel_path)
+
+    return final_wheel_name
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/unpack.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/unpack.py
new file mode 100644
index 0000000000000000000000000000000000000000..83dc7423f8171a3b6ffd6641475af037b7c59495
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_commands/unpack.py
@@ -0,0 +1,30 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+from ..wheelfile import WheelFile
+
+
+def unpack(path: str, dest: str = ".") -> None:
+    """Unpack a wheel.
+
+    Wheel content will be unpacked to {dest}/{name}-{ver}, where {name}
+    is the package name and {ver} its version.
+
+    :param path: The path to the wheel.
+    :param dest: Destination directory (default to current directory).
+    """
+    with WheelFile(path) as wf:
+        namever = wf.parsed_filename.group("namever")
+        destination = Path(dest) / namever
+        print(f"Unpacking to: {destination}...", end="", flush=True)
+        for zinfo in wf.filelist:
+            target_path = Path(wf.extract(zinfo, destination))
+
+            # Set permissions to the same values as they were set in the archive
+            # We have to do this manually due to
+            # https://github.com/python/cpython/issues/59999
+            permissions = zinfo.external_attr >> 16 & 0o777
+            target_path.chmod(permissions)
+
+    print("OK")
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_metadata.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_metadata.py
new file mode 100644
index 0000000000000000000000000000000000000000..e17a7b924526b9fcad83fc44996f17695dea0161
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_metadata.py
@@ -0,0 +1,184 @@
+"""
+Tools for converting old- to new-style metadata.
+"""
+
+from __future__ import annotations
+
+import functools
+import itertools
+import os.path
+import re
+import textwrap
+from collections.abc import Generator, Iterable, Iterator
+from email.message import Message
+from email.parser import Parser
+from typing import Literal
+
+from packaging.requirements import Requirement
+
+
+def _nonblank(str: str) -> bool | Literal[""]:
+    return str and not str.startswith("#")
+
+
+@functools.singledispatch
+def yield_lines(iterable: Iterable[str]) -> Iterator[str]:
+    r"""
+    Yield valid lines of a string or iterable.
+    >>> list(yield_lines(''))
+    []
+    >>> list(yield_lines(['foo', 'bar']))
+    ['foo', 'bar']
+    >>> list(yield_lines('foo\nbar'))
+    ['foo', 'bar']
+    >>> list(yield_lines('\nfoo\n#bar\nbaz #comment'))
+    ['foo', 'baz #comment']
+    >>> list(yield_lines(['foo\nbar', 'baz', 'bing\n\n\n']))
+    ['foo', 'bar', 'baz', 'bing']
+    """
+    return itertools.chain.from_iterable(map(yield_lines, iterable))
+
+
+@yield_lines.register(str)
+def _(text: str) -> Iterator[str]:
+    return filter(_nonblank, map(str.strip, text.splitlines()))
+
+
+def split_sections(
+    s: str | Iterator[str],
+) -> Generator[tuple[str | None, list[str]], None, None]:
+    """Split a string or iterable thereof into (section, content) pairs
+    Each ``section`` is a stripped version of the section header ("[section]")
+    and each ``content`` is a list of stripped lines excluding blank lines and
+    comment-only lines.  If there are any such lines before the first section
+    header, they're returned in a first ``section`` of ``None``.
+    """
+    section = None
+    content: list[str] = []
+    for line in yield_lines(s):
+        if line.startswith("["):
+            if line.endswith("]"):
+                if section or content:
+                    yield section, content
+                section = line[1:-1].strip()
+                content = []
+            else:
+                raise ValueError("Invalid section heading", line)
+        else:
+            content.append(line)
+
+    # wrap up last segment
+    yield section, content
+
+
+def safe_extra(extra: str) -> str:
+    """Convert an arbitrary string to a standard 'extra' name
+    Any runs of non-alphanumeric characters are replaced with a single '_',
+    and the result is always lowercased.
+    """
+    return re.sub("[^A-Za-z0-9.-]+", "_", extra).lower()
+
+
+def safe_name(name: str) -> str:
+    """Convert an arbitrary string to a standard distribution name
+    Any runs of non-alphanumeric/. characters are replaced with a single '-'.
+    """
+    return re.sub("[^A-Za-z0-9.]+", "-", name)
+
+
+def requires_to_requires_dist(requirement: Requirement) -> str:
+    """Return the version specifier for a requirement in PEP 345/566 fashion."""
+    if requirement.url:
+        return " @ " + requirement.url
+
+    requires_dist: list[str] = []
+    for spec in requirement.specifier:
+        requires_dist.append(spec.operator + spec.version)
+
+    if requires_dist:
+        return " " + ",".join(sorted(requires_dist))
+    else:
+        return ""
+
+
+def convert_requirements(requirements: list[str]) -> Iterator[str]:
+    """Yield Requires-Dist: strings for parsed requirements strings."""
+    for req in requirements:
+        parsed_requirement = Requirement(req)
+        spec = requires_to_requires_dist(parsed_requirement)
+        extras = ",".join(sorted(safe_extra(e) for e in parsed_requirement.extras))
+        if extras:
+            extras = f"[{extras}]"
+
+        yield safe_name(parsed_requirement.name) + extras + spec
+
+
+def generate_requirements(
+    extras_require: dict[str | None, list[str]],
+) -> Iterator[tuple[str, str]]:
+    """
+    Convert requirements from a setup()-style dictionary to
+    ('Requires-Dist', 'requirement') and ('Provides-Extra', 'extra') tuples.
+
+    extras_require is a dictionary of {extra: [requirements]} as passed to setup(),
+    using the empty extra {'': [requirements]} to hold install_requires.
+    """
+    for extra, depends in extras_require.items():
+        condition = ""
+        extra = extra or ""
+        if ":" in extra:  # setuptools extra:condition syntax
+            extra, condition = extra.split(":", 1)
+
+        extra = safe_extra(extra)
+        if extra:
+            yield "Provides-Extra", extra
+            if condition:
+                condition = "(" + condition + ") and "
+            condition += f"extra == '{extra}'"
+
+        if condition:
+            condition = " ; " + condition
+
+        for new_req in convert_requirements(depends):
+            canonical_req = str(Requirement(new_req + condition))
+            yield "Requires-Dist", canonical_req
+
+
+def pkginfo_to_metadata(egg_info_path: str, pkginfo_path: str) -> Message:
+    """
+    Convert .egg-info directory with PKG-INFO to the Metadata 2.1 format
+    """
+    with open(pkginfo_path, encoding="utf-8") as headers:
+        pkg_info = Parser().parse(headers)
+
+    pkg_info.replace_header("Metadata-Version", "2.1")
+    # Those will be regenerated from `requires.txt`.
+    del pkg_info["Provides-Extra"]
+    del pkg_info["Requires-Dist"]
+    requires_path = os.path.join(egg_info_path, "requires.txt")
+    if os.path.exists(requires_path):
+        with open(requires_path, encoding="utf-8") as requires_file:
+            requires = requires_file.read()
+
+        parsed_requirements = sorted(split_sections(requires), key=lambda x: x[0] or "")
+        for extra, reqs in parsed_requirements:
+            for key, value in generate_requirements({extra: reqs}):
+                if (key, value) not in pkg_info.items():
+                    pkg_info[key] = value
+
+    description = pkg_info["Description"]
+    if description:
+        description_lines = pkg_info["Description"].splitlines()
+        dedented_description = "\n".join(
+            # if the first line of long_description is blank,
+            # the first line here will be indented.
+            (
+                description_lines[0].lstrip(),
+                textwrap.dedent("\n".join(description_lines[1:])),
+                "\n",
+            )
+        )
+        pkg_info.set_payload(dedented_description)
+        del pkg_info["Description"]
+
+    return pkg_info
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_setuptools_logging.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_setuptools_logging.py
new file mode 100644
index 0000000000000000000000000000000000000000..a1a2482ba29ac5290c8f7d7688452ec3faf59332
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/_setuptools_logging.py
@@ -0,0 +1,26 @@
+# copied from setuptools.logging, omitting monkeypatching
+from __future__ import annotations
+
+import logging
+import sys
+
+
+def _not_warning(record: logging.LogRecord) -> bool:
+    return record.levelno < logging.WARNING
+
+
+def configure() -> None:
+    """
+    Configure logging to emit warning and above to stderr
+    and everything else to stdout. This behavior is provided
+    for compatibility with distutils.log but may change in
+    the future.
+    """
+    err_handler = logging.StreamHandler()
+    err_handler.setLevel(logging.WARNING)
+    out_handler = logging.StreamHandler(sys.stdout)
+    out_handler.addFilter(_not_warning)
+    handlers = err_handler, out_handler
+    logging.basicConfig(
+        format="{message}", style="{", handlers=handlers, level=logging.DEBUG
+    )
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/bdist_wheel.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/bdist_wheel.py
new file mode 100644
index 0000000000000000000000000000000000000000..24199c246d44a6874ad991c2f3492ca30fc10f27
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/bdist_wheel.py
@@ -0,0 +1,26 @@
+from typing import TYPE_CHECKING
+from warnings import warn
+
+warn(
+    "The 'wheel' package is no longer the canonical location of the 'bdist_wheel' "
+    "command, and will be removed in a future release. Please update to setuptools "
+    "v70.1 or later which contains an integrated version of this command.",
+    FutureWarning,
+    stacklevel=1,
+)
+
+if TYPE_CHECKING:
+    from ._bdist_wheel import bdist_wheel as bdist_wheel
+else:
+    try:
+        # Better integration/compatibility with setuptools:
+        # in the case new fixes or PEPs are implemented in setuptools
+        # there is no need to backport them to the deprecated code base.
+        # This is useful in the case of old packages in the ecosystem
+        # that are still used but have low maintenance.
+        from setuptools.command.bdist_wheel import bdist_wheel
+    except ImportError:
+        # Only used in the case of old setuptools versions.
+        # If the user wants to get the latest fixes/PEPs,
+        # they are encouraged to address the deprecation warning.
+        from ._bdist_wheel import bdist_wheel as bdist_wheel
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/macosx_libfile.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/macosx_libfile.py
new file mode 100644
index 0000000000000000000000000000000000000000..06e51af299d0fe15f7618f803cfb8ff52d199cf7
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/macosx_libfile.py
@@ -0,0 +1,486 @@
+"""
+IMPORTANT: DO NOT IMPORT THIS MODULE DIRECTLY.
+THIS IS ONLY KEPT IN PLACE FOR BACKWARDS COMPATIBILITY WITH
+setuptools.command.bdist_wheel.
+
+This module contains function to analyse dynamic library
+headers to extract system information
+
+Currently only for MacOSX
+
+Library file on macosx system starts with Mach-O or Fat field.
+This can be distinguish by first 32 bites and it is called magic number.
+Proper value of magic number is with suffix _MAGIC. Suffix _CIGAM means
+reversed bytes order.
+Both fields can occur in two types: 32 and 64 bytes.
+
+FAT field inform that this library contains few version of library
+(typically for different types version). It contains
+information where Mach-O headers starts.
+
+Each section started with Mach-O header contains one library
+(So if file starts with this field it contains only one version).
+
+After filed Mach-O there are section fields.
+Each of them starts with two fields:
+cmd - magic number for this command
+cmdsize - total size occupied by this section information.
+
+In this case only sections LC_VERSION_MIN_MACOSX (for macosx 10.13 and earlier)
+and LC_BUILD_VERSION (for macosx 10.14 and newer) are interesting,
+because them contains information about minimal system version.
+
+Important remarks:
+- For fat files this implementation looks for maximum number version.
+  It not check if it is 32 or 64 and do not compare it with currently built package.
+  So it is possible to false report higher version that needed.
+- All structures signatures are taken form macosx header files.
+- I think that binary format will be more stable than `otool` output.
+  and if apple introduce some changes both implementation will need to be updated.
+- The system compile will set the deployment target no lower than
+  11.0 for arm64 builds. For "Universal 2" builds use the x86_64 deployment
+  target when the arm64 target is 11.0.
+"""
+
+from __future__ import annotations
+
+import ctypes
+import os
+import sys
+from io import BufferedIOBase
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from typing import Union
+
+    StrPath = Union[str, os.PathLike[str]]
+
+"""here the needed const and struct from mach-o header files"""
+
+FAT_MAGIC = 0xCAFEBABE
+FAT_CIGAM = 0xBEBAFECA
+FAT_MAGIC_64 = 0xCAFEBABF
+FAT_CIGAM_64 = 0xBFBAFECA
+MH_MAGIC = 0xFEEDFACE
+MH_CIGAM = 0xCEFAEDFE
+MH_MAGIC_64 = 0xFEEDFACF
+MH_CIGAM_64 = 0xCFFAEDFE
+
+LC_VERSION_MIN_MACOSX = 0x24
+LC_BUILD_VERSION = 0x32
+
+CPU_TYPE_ARM64 = 0x0100000C
+
+mach_header_fields = [
+    ("magic", ctypes.c_uint32),
+    ("cputype", ctypes.c_int),
+    ("cpusubtype", ctypes.c_int),
+    ("filetype", ctypes.c_uint32),
+    ("ncmds", ctypes.c_uint32),
+    ("sizeofcmds", ctypes.c_uint32),
+    ("flags", ctypes.c_uint32),
+]
+"""
+struct mach_header {
+    uint32_t	magic;		/* mach magic number identifier */
+    cpu_type_t	cputype;	/* cpu specifier */
+    cpu_subtype_t	cpusubtype;	/* machine specifier */
+    uint32_t	filetype;	/* type of file */
+    uint32_t	ncmds;		/* number of load commands */
+    uint32_t	sizeofcmds;	/* the size of all the load commands */
+    uint32_t	flags;		/* flags */
+};
+typedef integer_t cpu_type_t;
+typedef integer_t cpu_subtype_t;
+"""
+
+mach_header_fields_64 = mach_header_fields + [("reserved", ctypes.c_uint32)]
+"""
+struct mach_header_64 {
+    uint32_t	magic;		/* mach magic number identifier */
+    cpu_type_t	cputype;	/* cpu specifier */
+    cpu_subtype_t	cpusubtype;	/* machine specifier */
+    uint32_t	filetype;	/* type of file */
+    uint32_t	ncmds;		/* number of load commands */
+    uint32_t	sizeofcmds;	/* the size of all the load commands */
+    uint32_t	flags;		/* flags */
+    uint32_t	reserved;	/* reserved */
+};
+"""
+
+fat_header_fields = [("magic", ctypes.c_uint32), ("nfat_arch", ctypes.c_uint32)]
+"""
+struct fat_header {
+    uint32_t	magic;		/* FAT_MAGIC or FAT_MAGIC_64 */
+    uint32_t	nfat_arch;	/* number of structs that follow */
+};
+"""
+
+fat_arch_fields = [
+    ("cputype", ctypes.c_int),
+    ("cpusubtype", ctypes.c_int),
+    ("offset", ctypes.c_uint32),
+    ("size", ctypes.c_uint32),
+    ("align", ctypes.c_uint32),
+]
+"""
+struct fat_arch {
+    cpu_type_t	cputype;	/* cpu specifier (int) */
+    cpu_subtype_t	cpusubtype;	/* machine specifier (int) */
+    uint32_t	offset;		/* file offset to this object file */
+    uint32_t	size;		/* size of this object file */
+    uint32_t	align;		/* alignment as a power of 2 */
+};
+"""
+
+fat_arch_64_fields = [
+    ("cputype", ctypes.c_int),
+    ("cpusubtype", ctypes.c_int),
+    ("offset", ctypes.c_uint64),
+    ("size", ctypes.c_uint64),
+    ("align", ctypes.c_uint32),
+    ("reserved", ctypes.c_uint32),
+]
+"""
+struct fat_arch_64 {
+    cpu_type_t	cputype;	/* cpu specifier (int) */
+    cpu_subtype_t	cpusubtype;	/* machine specifier (int) */
+    uint64_t	offset;		/* file offset to this object file */
+    uint64_t	size;		/* size of this object file */
+    uint32_t	align;		/* alignment as a power of 2 */
+    uint32_t	reserved;	/* reserved */
+};
+"""
+
+segment_base_fields = [("cmd", ctypes.c_uint32), ("cmdsize", ctypes.c_uint32)]
+"""base for reading segment info"""
+
+segment_command_fields = [
+    ("cmd", ctypes.c_uint32),
+    ("cmdsize", ctypes.c_uint32),
+    ("segname", ctypes.c_char * 16),
+    ("vmaddr", ctypes.c_uint32),
+    ("vmsize", ctypes.c_uint32),
+    ("fileoff", ctypes.c_uint32),
+    ("filesize", ctypes.c_uint32),
+    ("maxprot", ctypes.c_int),
+    ("initprot", ctypes.c_int),
+    ("nsects", ctypes.c_uint32),
+    ("flags", ctypes.c_uint32),
+]
+"""
+struct segment_command { /* for 32-bit architectures */
+    uint32_t	cmd;		/* LC_SEGMENT */
+    uint32_t	cmdsize;	/* includes sizeof section structs */
+    char		segname[16];	/* segment name */
+    uint32_t	vmaddr;		/* memory address of this segment */
+    uint32_t	vmsize;		/* memory size of this segment */
+    uint32_t	fileoff;	/* file offset of this segment */
+    uint32_t	filesize;	/* amount to map from the file */
+    vm_prot_t	maxprot;	/* maximum VM protection */
+    vm_prot_t	initprot;	/* initial VM protection */
+    uint32_t	nsects;		/* number of sections in segment */
+    uint32_t	flags;		/* flags */
+};
+typedef int vm_prot_t;
+"""
+
+segment_command_fields_64 = [
+    ("cmd", ctypes.c_uint32),
+    ("cmdsize", ctypes.c_uint32),
+    ("segname", ctypes.c_char * 16),
+    ("vmaddr", ctypes.c_uint64),
+    ("vmsize", ctypes.c_uint64),
+    ("fileoff", ctypes.c_uint64),
+    ("filesize", ctypes.c_uint64),
+    ("maxprot", ctypes.c_int),
+    ("initprot", ctypes.c_int),
+    ("nsects", ctypes.c_uint32),
+    ("flags", ctypes.c_uint32),
+]
+"""
+struct segment_command_64 { /* for 64-bit architectures */
+    uint32_t	cmd;		/* LC_SEGMENT_64 */
+    uint32_t	cmdsize;	/* includes sizeof section_64 structs */
+    char		segname[16];	/* segment name */
+    uint64_t	vmaddr;		/* memory address of this segment */
+    uint64_t	vmsize;		/* memory size of this segment */
+    uint64_t	fileoff;	/* file offset of this segment */
+    uint64_t	filesize;	/* amount to map from the file */
+    vm_prot_t	maxprot;	/* maximum VM protection */
+    vm_prot_t	initprot;	/* initial VM protection */
+    uint32_t	nsects;		/* number of sections in segment */
+    uint32_t	flags;		/* flags */
+};
+"""
+
+version_min_command_fields = segment_base_fields + [
+    ("version", ctypes.c_uint32),
+    ("sdk", ctypes.c_uint32),
+]
+"""
+struct version_min_command {
+    uint32_t	cmd;		/* LC_VERSION_MIN_MACOSX or
+                               LC_VERSION_MIN_IPHONEOS or
+                               LC_VERSION_MIN_WATCHOS or
+                               LC_VERSION_MIN_TVOS */
+    uint32_t	cmdsize;	/* sizeof(struct min_version_command) */
+    uint32_t	version;	/* X.Y.Z is encoded in nibbles xxxx.yy.zz */
+    uint32_t	sdk;		/* X.Y.Z is encoded in nibbles xxxx.yy.zz */
+};
+"""
+
+build_version_command_fields = segment_base_fields + [
+    ("platform", ctypes.c_uint32),
+    ("minos", ctypes.c_uint32),
+    ("sdk", ctypes.c_uint32),
+    ("ntools", ctypes.c_uint32),
+]
+"""
+struct build_version_command {
+    uint32_t	cmd;		/* LC_BUILD_VERSION */
+    uint32_t	cmdsize;	/* sizeof(struct build_version_command) plus */
+                                /* ntools * sizeof(struct build_tool_version) */
+    uint32_t	platform;	/* platform */
+    uint32_t	minos;		/* X.Y.Z is encoded in nibbles xxxx.yy.zz */
+    uint32_t	sdk;		/* X.Y.Z is encoded in nibbles xxxx.yy.zz */
+    uint32_t	ntools;		/* number of tool entries following this */
+};
+"""
+
+
+def swap32(x: int) -> int:
+    return (
+        ((x << 24) & 0xFF000000)
+        | ((x << 8) & 0x00FF0000)
+        | ((x >> 8) & 0x0000FF00)
+        | ((x >> 24) & 0x000000FF)
+    )
+
+
+def get_base_class_and_magic_number(
+    lib_file: BufferedIOBase,
+    seek: int | None = None,
+) -> tuple[type[ctypes.Structure], int]:
+    if seek is None:
+        seek = lib_file.tell()
+    else:
+        lib_file.seek(seek)
+    magic_number = ctypes.c_uint32.from_buffer_copy(
+        lib_file.read(ctypes.sizeof(ctypes.c_uint32))
+    ).value
+
+    # Handle wrong byte order
+    if magic_number in [FAT_CIGAM, FAT_CIGAM_64, MH_CIGAM, MH_CIGAM_64]:
+        if sys.byteorder == "little":
+            BaseClass = ctypes.BigEndianStructure
+        else:
+            BaseClass = ctypes.LittleEndianStructure
+
+        magic_number = swap32(magic_number)
+    else:
+        BaseClass = ctypes.Structure
+
+    lib_file.seek(seek)
+    return BaseClass, magic_number
+
+
+def read_data(struct_class: type[ctypes.Structure], lib_file: BufferedIOBase):
+    return struct_class.from_buffer_copy(lib_file.read(ctypes.sizeof(struct_class)))
+
+
+def extract_macosx_min_system_version(path_to_lib: str):
+    with open(path_to_lib, "rb") as lib_file:
+        BaseClass, magic_number = get_base_class_and_magic_number(lib_file, 0)
+        if magic_number not in [FAT_MAGIC, FAT_MAGIC_64, MH_MAGIC, MH_MAGIC_64]:
+            return
+
+        if magic_number in [FAT_MAGIC, FAT_CIGAM_64]:
+
+            class FatHeader(BaseClass):
+                _fields_ = fat_header_fields
+
+            fat_header = read_data(FatHeader, lib_file)
+            if magic_number == FAT_MAGIC:
+
+                class FatArch(BaseClass):
+                    _fields_ = fat_arch_fields
+
+            else:
+
+                class FatArch(BaseClass):
+                    _fields_ = fat_arch_64_fields
+
+            fat_arch_list = [
+                read_data(FatArch, lib_file) for _ in range(fat_header.nfat_arch)
+            ]
+
+            versions_list: list[tuple[int, int, int]] = []
+            for el in fat_arch_list:
+                try:
+                    version = read_mach_header(lib_file, el.offset)
+                    if version is not None:
+                        if el.cputype == CPU_TYPE_ARM64 and len(fat_arch_list) != 1:
+                            # Xcode will not set the deployment target below 11.0.0
+                            # for the arm64 architecture. Ignore the arm64 deployment
+                            # in fat binaries when the target is 11.0.0, that way
+                            # the other architectures can select a lower deployment
+                            # target.
+                            # This is safe because there is no arm64 variant for
+                            # macOS 10.15 or earlier.
+                            if version == (11, 0, 0):
+                                continue
+                        versions_list.append(version)
+                except ValueError:
+                    pass
+
+            if len(versions_list) > 0:
+                return max(versions_list)
+            else:
+                return None
+
+        else:
+            try:
+                return read_mach_header(lib_file, 0)
+            except ValueError:
+                """when some error during read library files"""
+                return None
+
+
+def read_mach_header(
+    lib_file: BufferedIOBase,
+    seek: int | None = None,
+) -> tuple[int, int, int] | None:
+    """
+    This function parses a Mach-O header and extracts
+    information about the minimal macOS version.
+
+    :param lib_file: reference to opened library file with pointer
+    """
+    base_class, magic_number = get_base_class_and_magic_number(lib_file, seek)
+    arch = "32" if magic_number == MH_MAGIC else "64"
+
+    class SegmentBase(base_class):
+        _fields_ = segment_base_fields
+
+    if arch == "32":
+
+        class MachHeader(base_class):
+            _fields_ = mach_header_fields
+
+    else:
+
+        class MachHeader(base_class):
+            _fields_ = mach_header_fields_64
+
+    mach_header = read_data(MachHeader, lib_file)
+    for _i in range(mach_header.ncmds):
+        pos = lib_file.tell()
+        segment_base = read_data(SegmentBase, lib_file)
+        lib_file.seek(pos)
+        if segment_base.cmd == LC_VERSION_MIN_MACOSX:
+
+            class VersionMinCommand(base_class):
+                _fields_ = version_min_command_fields
+
+            version_info = read_data(VersionMinCommand, lib_file)
+            return parse_version(version_info.version)
+        elif segment_base.cmd == LC_BUILD_VERSION:
+
+            class VersionBuild(base_class):
+                _fields_ = build_version_command_fields
+
+            version_info = read_data(VersionBuild, lib_file)
+            return parse_version(version_info.minos)
+        else:
+            lib_file.seek(pos + segment_base.cmdsize)
+            continue
+
+
+def parse_version(version: int) -> tuple[int, int, int]:
+    x = (version & 0xFFFF0000) >> 16
+    y = (version & 0x0000FF00) >> 8
+    z = version & 0x000000FF
+    return x, y, z
+
+
+def calculate_macosx_platform_tag(archive_root: StrPath, platform_tag: str) -> str:
+    """
+    Calculate proper macosx platform tag basing on files which are included to wheel
+
+    Example platform tag `macosx-10.14-x86_64`
+    """
+    prefix, base_version, suffix = platform_tag.split("-")
+    base_version = tuple(int(x) for x in base_version.split("."))
+    base_version = base_version[:2]
+    if base_version[0] > 10:
+        base_version = (base_version[0], 0)
+    assert len(base_version) == 2
+    if "MACOSX_DEPLOYMENT_TARGET" in os.environ:
+        deploy_target = tuple(
+            int(x) for x in os.environ["MACOSX_DEPLOYMENT_TARGET"].split(".")
+        )
+        deploy_target = deploy_target[:2]
+        if deploy_target[0] > 10:
+            deploy_target = (deploy_target[0], 0)
+        if deploy_target < base_version:
+            sys.stderr.write(
+                "[WARNING] MACOSX_DEPLOYMENT_TARGET is set to a lower value ({}) than "
+                "the version on which the Python interpreter was compiled ({}), and "
+                "will be ignored.\n".format(
+                    ".".join(str(x) for x in deploy_target),
+                    ".".join(str(x) for x in base_version),
+                )
+            )
+        else:
+            base_version = deploy_target
+
+    assert len(base_version) == 2
+    start_version = base_version
+    versions_dict: dict[str, tuple[int, int]] = {}
+    for dirpath, _dirnames, filenames in os.walk(archive_root):
+        for filename in filenames:
+            if filename.endswith(".dylib") or filename.endswith(".so"):
+                lib_path = os.path.join(dirpath, filename)
+                min_ver = extract_macosx_min_system_version(lib_path)
+                if min_ver is not None:
+                    min_ver = min_ver[0:2]
+                    if min_ver[0] > 10:
+                        min_ver = (min_ver[0], 0)
+                    versions_dict[lib_path] = min_ver
+
+    if len(versions_dict) > 0:
+        base_version = max(base_version, max(versions_dict.values()))
+
+    # macosx platform tag do not support minor bugfix release
+    fin_base_version = "_".join([str(x) for x in base_version])
+    if start_version < base_version:
+        problematic_files = [k for k, v in versions_dict.items() if v > start_version]
+        problematic_files = "\n".join(problematic_files)
+        if len(problematic_files) == 1:
+            files_form = "this file"
+        else:
+            files_form = "these files"
+        error_message = (
+            "[WARNING] This wheel needs a higher macOS version than {}  "
+            "To silence this warning, set MACOSX_DEPLOYMENT_TARGET to at least "
+            + fin_base_version
+            + " or recreate "
+            + files_form
+            + " with lower "
+            "MACOSX_DEPLOYMENT_TARGET:  \n" + problematic_files
+        )
+
+        if "MACOSX_DEPLOYMENT_TARGET" in os.environ:
+            error_message = error_message.format(
+                "is set in MACOSX_DEPLOYMENT_TARGET variable."
+            )
+        else:
+            error_message = error_message.format(
+                "the version your Python interpreter is compiled against."
+            )
+
+        sys.stderr.write(error_message)
+
+    platform_tag = prefix + "_" + fin_base_version + "_" + suffix
+    return platform_tag
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/metadata.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/metadata.py
new file mode 100644
index 0000000000000000000000000000000000000000..e27900a2565c859ff32b0e4bf497c2548e4912de
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/metadata.py
@@ -0,0 +1,17 @@
+from warnings import warn
+
+from ._metadata import convert_requirements as convert_requirements
+from ._metadata import generate_requirements as generate_requirements
+from ._metadata import pkginfo_to_metadata as pkginfo_to_metadata
+from ._metadata import requires_to_requires_dist as requires_to_requires_dist
+from ._metadata import safe_extra as safe_extra
+from ._metadata import safe_name as safe_name
+from ._metadata import split_sections as split_sections
+
+warn(
+    f"The {__name__!r} package has been made private and should no longer be imported. "
+    f"Please either copy the code or find an alternative library to import it from, as "
+    f"this warning will be removed in a future version of 'wheel'.",
+    DeprecationWarning,
+    stacklevel=2,
+)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/wheelfile.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/wheelfile.py
new file mode 100644
index 0000000000000000000000000000000000000000..7b6fd71621b9a14274a17086edeb287db58d7fe0
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/wheel/wheelfile.py
@@ -0,0 +1,241 @@
+from __future__ import annotations
+
+__all__ = ["WHEEL_INFO_RE", "WheelFile", "WheelError"]
+
+import base64
+import csv
+import hashlib
+import logging
+import os.path
+import re
+import stat
+import time
+from io import StringIO, TextIOWrapper
+from typing import IO, TYPE_CHECKING, Literal
+from zipfile import ZIP_DEFLATED, ZipFile, ZipInfo
+
+if TYPE_CHECKING:
+    from _typeshed import SizedBuffer, StrPath
+
+
+# Non-greedy matching of an optional build number may be too clever (more
+# invalid wheel filenames will match). Separate regex for .dist-info?
+WHEEL_INFO_RE = re.compile(
+    r"""^(?P(?P[^\s-]+?)-(?P[^\s-]+?))(-(?P\d[^\s-]*))?
+     -(?P[^\s-]+?)-(?P[^\s-]+?)-(?P\S+)\.whl$""",
+    re.VERBOSE,
+)
+MINIMUM_TIMESTAMP = 315532800  # 1980-01-01 00:00:00 UTC
+
+log = logging.getLogger("wheel")
+
+
+class WheelError(Exception):
+    pass
+
+
+def urlsafe_b64encode(data: bytes) -> bytes:
+    """urlsafe_b64encode without padding"""
+    return base64.urlsafe_b64encode(data).rstrip(b"=")
+
+
+def urlsafe_b64decode(data: bytes) -> bytes:
+    """urlsafe_b64decode without padding"""
+    pad = b"=" * (4 - (len(data) & 3))
+    return base64.urlsafe_b64decode(data + pad)
+
+
+def get_zipinfo_datetime(
+    timestamp: float | None = None,
+) -> tuple[int, int, int, int, int]:
+    # Some applications need reproducible .whl files, but they can't do this without
+    # forcing the timestamp of the individual ZipInfo objects. See issue #143.
+    timestamp = int(os.environ.get("SOURCE_DATE_EPOCH", timestamp or time.time()))
+    timestamp = max(timestamp, MINIMUM_TIMESTAMP)
+    return time.gmtime(timestamp)[0:6]
+
+
+class WheelFile(ZipFile):
+    """A ZipFile derivative class that also reads SHA-256 hashes from
+    .dist-info/RECORD and checks any read files against those.
+    """
+
+    _default_algorithm = hashlib.sha256
+
+    def __init__(
+        self,
+        file: StrPath,
+        mode: Literal["r", "w", "x", "a"] = "r",
+        compression: int = ZIP_DEFLATED,
+    ):
+        basename = os.path.basename(file)
+        self.parsed_filename = WHEEL_INFO_RE.match(basename)
+        if not basename.endswith(".whl") or self.parsed_filename is None:
+            raise WheelError(f"Bad wheel filename {basename!r}")
+
+        ZipFile.__init__(self, file, mode, compression=compression, allowZip64=True)
+
+        self.dist_info_path = "{}.dist-info".format(
+            self.parsed_filename.group("namever")
+        )
+        self.record_path = self.dist_info_path + "/RECORD"
+        self._file_hashes: dict[str, tuple[None, None] | tuple[int, bytes]] = {}
+        self._file_sizes = {}
+        if mode == "r":
+            # Ignore RECORD and any embedded wheel signatures
+            self._file_hashes[self.record_path] = None, None
+            self._file_hashes[self.record_path + ".jws"] = None, None
+            self._file_hashes[self.record_path + ".p7s"] = None, None
+
+            # Fill in the expected hashes by reading them from RECORD
+            try:
+                record = self.open(self.record_path)
+            except KeyError:
+                raise WheelError(f"Missing {self.record_path} file") from None
+
+            with record:
+                for line in csv.reader(
+                    TextIOWrapper(record, newline="", encoding="utf-8")
+                ):
+                    path, hash_sum, size = line
+                    if not hash_sum:
+                        continue
+
+                    algorithm, hash_sum = hash_sum.split("=")
+                    try:
+                        hashlib.new(algorithm)
+                    except ValueError:
+                        raise WheelError(
+                            f"Unsupported hash algorithm: {algorithm}"
+                        ) from None
+
+                    if algorithm.lower() in {"md5", "sha1"}:
+                        raise WheelError(
+                            f"Weak hash algorithm ({algorithm}) is not permitted by "
+                            f"PEP 427"
+                        )
+
+                    self._file_hashes[path] = (
+                        algorithm,
+                        urlsafe_b64decode(hash_sum.encode("ascii")),
+                    )
+
+    def open(
+        self,
+        name_or_info: str | ZipInfo,
+        mode: Literal["r", "w"] = "r",
+        pwd: bytes | None = None,
+    ) -> IO[bytes]:
+        def _update_crc(newdata: bytes) -> None:
+            eof = ef._eof
+            update_crc_orig(newdata)
+            running_hash.update(newdata)
+            if eof and running_hash.digest() != expected_hash:
+                raise WheelError(f"Hash mismatch for file '{ef_name}'")
+
+        ef_name = (
+            name_or_info.filename if isinstance(name_or_info, ZipInfo) else name_or_info
+        )
+        if (
+            mode == "r"
+            and not ef_name.endswith("/")
+            and ef_name not in self._file_hashes
+        ):
+            raise WheelError(f"No hash found for file '{ef_name}'")
+
+        ef = ZipFile.open(self, name_or_info, mode, pwd)
+        if mode == "r" and not ef_name.endswith("/"):
+            algorithm, expected_hash = self._file_hashes[ef_name]
+            if expected_hash is not None:
+                # Monkey patch the _update_crc method to also check for the hash from
+                # RECORD
+                running_hash = hashlib.new(algorithm)
+                update_crc_orig, ef._update_crc = ef._update_crc, _update_crc
+
+        return ef
+
+    def write_files(self, base_dir: str) -> None:
+        log.info("creating %r and adding %r to it", self.filename, base_dir)
+        deferred: list[tuple[str, str]] = []
+        for root, dirnames, filenames in os.walk(base_dir):
+            # Sort the directory names so that `os.walk` will walk them in a
+            # defined order on the next iteration.
+            dirnames.sort()
+            for name in sorted(filenames):
+                path = os.path.normpath(os.path.join(root, name))
+                if os.path.isfile(path):
+                    arcname = os.path.relpath(path, base_dir).replace(os.path.sep, "/")
+                    if arcname == self.record_path:
+                        pass
+                    elif root.endswith(".dist-info"):
+                        deferred.append((path, arcname))
+                    else:
+                        self.write(path, arcname)
+
+        deferred.sort()
+        for path, arcname in deferred:
+            self.write(path, arcname)
+
+    def write(
+        self,
+        filename: str,
+        arcname: str | None = None,
+        compress_type: int | None = None,
+    ) -> None:
+        with open(filename, "rb") as f:
+            st = os.fstat(f.fileno())
+            data = f.read()
+
+        zinfo = ZipInfo(
+            arcname or filename, date_time=get_zipinfo_datetime(st.st_mtime)
+        )
+        zinfo.external_attr = (stat.S_IMODE(st.st_mode) | stat.S_IFMT(st.st_mode)) << 16
+        zinfo.compress_type = compress_type or self.compression
+        self.writestr(zinfo, data, compress_type)
+
+    def writestr(
+        self,
+        zinfo_or_arcname: str | ZipInfo,
+        data: SizedBuffer | str,
+        compress_type: int | None = None,
+    ) -> None:
+        if isinstance(zinfo_or_arcname, str):
+            zinfo_or_arcname = ZipInfo(
+                zinfo_or_arcname, date_time=get_zipinfo_datetime()
+            )
+            zinfo_or_arcname.compress_type = self.compression
+            zinfo_or_arcname.external_attr = (0o664 | stat.S_IFREG) << 16
+
+        if isinstance(data, str):
+            data = data.encode("utf-8")
+
+        ZipFile.writestr(self, zinfo_or_arcname, data, compress_type)
+        fname = (
+            zinfo_or_arcname.filename
+            if isinstance(zinfo_or_arcname, ZipInfo)
+            else zinfo_or_arcname
+        )
+        log.info("adding %r", fname)
+        if fname != self.record_path:
+            hash_ = self._default_algorithm(data)
+            self._file_hashes[fname] = (
+                hash_.name,
+                urlsafe_b64encode(hash_.digest()).decode("ascii"),
+            )
+            self._file_sizes[fname] = len(data)
+
+    def close(self) -> None:
+        # Write RECORD
+        if self.fp is not None and self.mode == "w" and self._file_hashes:
+            data = StringIO()
+            writer = csv.writer(data, delimiter=",", quotechar='"', lineterminator="\n")
+            writer.writerows(
+                (
+                    (fname, algorithm + "=" + hash_, self._file_sizes[fname])
+                    for fname, (algorithm, hash_) in self._file_hashes.items()
+                )
+            )
+            writer.writerow((format(self.record_path), "", ""))
+            self.writestr(self.record_path, data.getvalue())
+
+        ZipFile.close(self)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/INSTALLER
new file mode 100644
index 0000000000000000000000000000000000000000..f79e4cb9aaf0b2d9e8ba78861e2071317b2384b3
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/INSTALLER
@@ -0,0 +1 @@
+conda
\ No newline at end of file
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/METADATA
new file mode 100644
index 0000000000000000000000000000000000000000..6420117987041c052142deea6b16884cdb435c2f
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/METADATA
@@ -0,0 +1,106 @@
+Metadata-Version: 2.4
+Name: zipp
+Version: 3.23.0
+Summary: Backport of pathlib-compatible object wrapper for zip files
+Author-email: "Jason R. Coombs" 
+License-Expression: MIT
+Project-URL: Source, https://github.com/jaraco/zipp
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Provides-Extra: test
+Requires-Dist: pytest!=8.1.*,>=6; extra == "test"
+Requires-Dist: jaraco.itertools; extra == "test"
+Requires-Dist: jaraco.functools; extra == "test"
+Requires-Dist: more_itertools; extra == "test"
+Requires-Dist: big-O; extra == "test"
+Requires-Dist: pytest-ignore-flaky; extra == "test"
+Requires-Dist: jaraco.test; extra == "test"
+Provides-Extra: doc
+Requires-Dist: sphinx>=3.5; extra == "doc"
+Requires-Dist: jaraco.packaging>=9.3; extra == "doc"
+Requires-Dist: rst.linker>=1.9; extra == "doc"
+Requires-Dist: furo; extra == "doc"
+Requires-Dist: sphinx-lint; extra == "doc"
+Requires-Dist: jaraco.tidelift>=1.4; extra == "doc"
+Provides-Extra: check
+Requires-Dist: pytest-checkdocs>=2.4; extra == "check"
+Requires-Dist: pytest-ruff>=0.2.1; sys_platform != "cygwin" and extra == "check"
+Provides-Extra: cover
+Requires-Dist: pytest-cov; extra == "cover"
+Provides-Extra: enabler
+Requires-Dist: pytest-enabler>=2.2; extra == "enabler"
+Provides-Extra: type
+Requires-Dist: pytest-mypy; extra == "type"
+Dynamic: license-file
+
+.. image:: https://img.shields.io/pypi/v/zipp.svg
+   :target: https://pypi.org/project/zipp
+
+.. image:: https://img.shields.io/pypi/pyversions/zipp.svg
+
+.. image:: https://github.com/jaraco/zipp/actions/workflows/main.yml/badge.svg
+   :target: https://github.com/jaraco/zipp/actions?query=workflow%3A%22tests%22
+   :alt: tests
+
+.. image:: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
+    :target: https://github.com/astral-sh/ruff
+    :alt: Ruff
+
+.. image:: https://readthedocs.org/projects/zipp/badge/?version=latest
+..    :target: https://zipp.readthedocs.io/en/latest/?badge=latest
+
+.. image:: https://img.shields.io/badge/skeleton-2025-informational
+   :target: https://blog.jaraco.com/skeleton
+
+.. image:: https://tidelift.com/badges/package/pypi/zipp
+   :target: https://tidelift.com/subscription/pkg/pypi-zipp?utm_source=pypi-zipp&utm_medium=readme
+
+
+A pathlib-compatible Zipfile object wrapper. Official backport of the standard library
+`Path object `_.
+
+
+Compatibility
+=============
+
+New features are introduced in this third-party library and later merged
+into CPython. The following table indicates which versions of this library
+were contributed to different versions in the standard library:
+
+.. list-table::
+   :header-rows: 1
+
+   * - zipp
+     - stdlib
+   * - 3.18
+     - 3.13
+   * - 3.16
+     - 3.12
+   * - 3.5
+     - 3.11
+   * - 3.2
+     - 3.10
+   * - 3.3 ??
+     - 3.9
+   * - 1.0
+     - 3.8
+
+
+Usage
+=====
+
+Use ``zipp.Path`` in place of ``zipfile.Path`` on any Python.
+
+For Enterprise
+==============
+
+Available as part of the Tidelift Subscription.
+
+This project and the maintainers of thousands of other packages are working with Tidelift to deliver one enterprise subscription that covers all of the open source you use.
+
+`Learn more `_.
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/RECORD
new file mode 100644
index 0000000000000000000000000000000000000000..167e234a530053b60d4bf6d51b12598723433a8c
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/RECORD
@@ -0,0 +1,14 @@
+zipp-3.23.0.dist-info/INSTALLER,sha256=5hhM4Q4mYTT9z6QB6PGpUAW81PGNFrYrdXMj4oM_6ak,2
+zipp-3.23.0.dist-info/METADATA,sha256=vdZ9TRbPC_O4k-fRjNPS13StuC837Zhbx3cMYHIms1s,3563
+zipp-3.23.0.dist-info/RECORD,,
+zipp-3.23.0.dist-info/REQUESTED,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+zipp-3.23.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+zipp-3.23.0.dist-info/licenses/LICENSE,sha256=WlfLTbheKi3YjCkGKJCK3VfjRRRJ4KmnH9-zh3b9dZ0,1076
+zipp-3.23.0.dist-info/top_level.txt,sha256=iAbdoSHfaGqBfVb2XuR9JqSQHCoOsOtG6y9C_LSpqFw,5
+zipp/__init__.py,sha256=ieXh9GIMdABjKRX_JUJtP9k5wdBLK4Mt5X4nszSkmYE,11976
+zipp/_functools.py,sha256=f6Kt9LxZ4TE-cY1lJVdXSId3memSXmH9IdgMbU-_x2k,575
+zipp/compat/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+zipp/compat/overlay.py,sha256=oEIGAnbr8yGjuKTrVSO2ByewPui71uppbX18BLnYTKE,783
+zipp/compat/py310.py,sha256=S7i6N9mToEn3asNb2ILyjnzvITOXrATD_J4emjyBbDU,256
+zipp/compat/py313.py,sha256=RndvDNtuY7H2D9ecnnzcPBMZ8mZc42gmXD_IwQAXXAE,654
+zipp/glob.py,sha256=DLV9LBsDxA6YVW82e3-tkoNrus1h4R-j3BR6VqS0AzE,3382
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/REQUESTED b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/REQUESTED
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/WHEEL
new file mode 100644
index 0000000000000000000000000000000000000000..e7fa31b6f3f78deb1022c1f7927f07d4d16da822
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/WHEEL
@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/licenses/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/licenses/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..f60bd572013c6abcb3a82ba9b50d84935de6394f
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/licenses/LICENSE
@@ -0,0 +1,18 @@
+MIT License
+
+Copyright (c) 2025 
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and
+associated documentation files (the "Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the
+following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial
+portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT
+LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO
+EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/top_level.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/top_level.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e82f676f82a3381fa909d1e6578c7a22044fafca
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp-3.23.0.dist-info/top_level.txt
@@ -0,0 +1 @@
+zipp
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..ed5b21463295b8cee93d855316fb5e9000f9b8ec
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/__init__.py
@@ -0,0 +1,456 @@
+"""
+A Path-like interface for zipfiles.
+
+This codebase is shared between zipfile.Path in the stdlib
+and zipp in PyPI. See
+https://github.com/python/importlib_metadata/wiki/Development-Methodology
+for more detail.
+"""
+
+import functools
+import io
+import itertools
+import pathlib
+import posixpath
+import re
+import stat
+import sys
+import zipfile
+
+from ._functools import save_method_args
+from .compat.py310 import text_encoding
+from .glob import Translator
+
+__all__ = ['Path']
+
+
+def _parents(path):
+    """
+    Given a path with elements separated by
+    posixpath.sep, generate all parents of that path.
+
+    >>> list(_parents('b/d'))
+    ['b']
+    >>> list(_parents('/b/d/'))
+    ['/b']
+    >>> list(_parents('b/d/f/'))
+    ['b/d', 'b']
+    >>> list(_parents('b'))
+    []
+    >>> list(_parents(''))
+    []
+    """
+    return itertools.islice(_ancestry(path), 1, None)
+
+
+def _ancestry(path):
+    """
+    Given a path with elements separated by
+    posixpath.sep, generate all elements of that path.
+
+    >>> list(_ancestry('b/d'))
+    ['b/d', 'b']
+    >>> list(_ancestry('/b/d/'))
+    ['/b/d', '/b']
+    >>> list(_ancestry('b/d/f/'))
+    ['b/d/f', 'b/d', 'b']
+    >>> list(_ancestry('b'))
+    ['b']
+    >>> list(_ancestry(''))
+    []
+
+    Multiple separators are treated like a single.
+
+    >>> list(_ancestry('//b//d///f//'))
+    ['//b//d///f', '//b//d', '//b']
+    """
+    path = path.rstrip(posixpath.sep)
+    while path.rstrip(posixpath.sep):
+        yield path
+        path, tail = posixpath.split(path)
+
+
+_dedupe = dict.fromkeys
+"""Deduplicate an iterable in original order"""
+
+
+def _difference(minuend, subtrahend):
+    """
+    Return items in minuend not in subtrahend, retaining order
+    with O(1) lookup.
+    """
+    return itertools.filterfalse(set(subtrahend).__contains__, minuend)
+
+
+class InitializedState:
+    """
+    Mix-in to save the initialization state for pickling.
+    """
+
+    @save_method_args
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+    def __getstate__(self):
+        return self._saved___init__.args, self._saved___init__.kwargs
+
+    def __setstate__(self, state):
+        args, kwargs = state
+        super().__init__(*args, **kwargs)
+
+
+class CompleteDirs(InitializedState, zipfile.ZipFile):
+    """
+    A ZipFile subclass that ensures that implied directories
+    are always included in the namelist.
+
+    >>> list(CompleteDirs._implied_dirs(['foo/bar.txt', 'foo/bar/baz.txt']))
+    ['foo/', 'foo/bar/']
+    >>> list(CompleteDirs._implied_dirs(['foo/bar.txt', 'foo/bar/baz.txt', 'foo/bar/']))
+    ['foo/']
+    """
+
+    @staticmethod
+    def _implied_dirs(names):
+        parents = itertools.chain.from_iterable(map(_parents, names))
+        as_dirs = (p + posixpath.sep for p in parents)
+        return _dedupe(_difference(as_dirs, names))
+
+    def namelist(self):
+        names = super().namelist()
+        return names + list(self._implied_dirs(names))
+
+    def _name_set(self):
+        return set(self.namelist())
+
+    def resolve_dir(self, name):
+        """
+        If the name represents a directory, return that name
+        as a directory (with the trailing slash).
+        """
+        names = self._name_set()
+        dirname = name + '/'
+        dir_match = name not in names and dirname in names
+        return dirname if dir_match else name
+
+    def getinfo(self, name):
+        """
+        Supplement getinfo for implied dirs.
+        """
+        try:
+            return super().getinfo(name)
+        except KeyError:
+            if not name.endswith('/') or name not in self._name_set():
+                raise
+            return zipfile.ZipInfo(filename=name)
+
+    @classmethod
+    def make(cls, source):
+        """
+        Given a source (filename or zipfile), return an
+        appropriate CompleteDirs subclass.
+        """
+        if isinstance(source, CompleteDirs):
+            return source
+
+        if not isinstance(source, zipfile.ZipFile):
+            return cls(source)
+
+        # Only allow for FastLookup when supplied zipfile is read-only
+        if 'r' not in source.mode:
+            cls = CompleteDirs
+
+        source.__class__ = cls
+        return source
+
+    @classmethod
+    def inject(cls, zf: zipfile.ZipFile) -> zipfile.ZipFile:
+        """
+        Given a writable zip file zf, inject directory entries for
+        any directories implied by the presence of children.
+        """
+        for name in cls._implied_dirs(zf.namelist()):
+            zf.writestr(name, b"")
+        return zf
+
+
+class FastLookup(CompleteDirs):
+    """
+    ZipFile subclass to ensure implicit
+    dirs exist and are resolved rapidly.
+    """
+
+    def namelist(self):
+        return self._namelist
+
+    @functools.cached_property
+    def _namelist(self):
+        return super().namelist()
+
+    def _name_set(self):
+        return self._name_set_prop
+
+    @functools.cached_property
+    def _name_set_prop(self):
+        return super()._name_set()
+
+
+def _extract_text_encoding(encoding=None, *args, **kwargs):
+    # compute stack level so that the caller of the caller sees any warning.
+    is_pypy = sys.implementation.name == 'pypy'
+    # PyPy no longer special cased after 7.3.19 (or maybe 7.3.18)
+    # See jaraco/zipp#143
+    is_old_pypi = is_pypy and sys.pypy_version_info < (7, 3, 19)
+    stack_level = 3 + is_old_pypi
+    return text_encoding(encoding, stack_level), args, kwargs
+
+
+class Path:
+    """
+    A :class:`importlib.resources.abc.Traversable` interface for zip files.
+
+    Implements many of the features users enjoy from
+    :class:`pathlib.Path`.
+
+    Consider a zip file with this structure::
+
+        .
+        ├── a.txt
+        └── b
+            ├── c.txt
+            └── d
+                └── e.txt
+
+    >>> data = io.BytesIO()
+    >>> zf = zipfile.ZipFile(data, 'w')
+    >>> zf.writestr('a.txt', 'content of a')
+    >>> zf.writestr('b/c.txt', 'content of c')
+    >>> zf.writestr('b/d/e.txt', 'content of e')
+    >>> zf.filename = 'mem/abcde.zip'
+
+    Path accepts the zipfile object itself or a filename
+
+    >>> path = Path(zf)
+
+    From there, several path operations are available.
+
+    Directory iteration (including the zip file itself):
+
+    >>> a, b = path.iterdir()
+    >>> a
+    Path('mem/abcde.zip', 'a.txt')
+    >>> b
+    Path('mem/abcde.zip', 'b/')
+
+    name property:
+
+    >>> b.name
+    'b'
+
+    join with divide operator:
+
+    >>> c = b / 'c.txt'
+    >>> c
+    Path('mem/abcde.zip', 'b/c.txt')
+    >>> c.name
+    'c.txt'
+
+    Read text:
+
+    >>> c.read_text(encoding='utf-8')
+    'content of c'
+
+    existence:
+
+    >>> c.exists()
+    True
+    >>> (b / 'missing.txt').exists()
+    False
+
+    Coercion to string:
+
+    >>> import os
+    >>> str(c).replace(os.sep, posixpath.sep)
+    'mem/abcde.zip/b/c.txt'
+
+    At the root, ``name``, ``filename``, and ``parent``
+    resolve to the zipfile.
+
+    >>> str(path)
+    'mem/abcde.zip/'
+    >>> path.name
+    'abcde.zip'
+    >>> path.filename == pathlib.Path('mem/abcde.zip')
+    True
+    >>> str(path.parent)
+    'mem'
+
+    If the zipfile has no filename, such attributes are not
+    valid and accessing them will raise an Exception.
+
+    >>> zf.filename = None
+    >>> path.name
+    Traceback (most recent call last):
+    ...
+    TypeError: ...
+
+    >>> path.filename
+    Traceback (most recent call last):
+    ...
+    TypeError: ...
+
+    >>> path.parent
+    Traceback (most recent call last):
+    ...
+    TypeError: ...
+
+    # workaround python/cpython#106763
+    >>> pass
+    """
+
+    __repr = "{self.__class__.__name__}({self.root.filename!r}, {self.at!r})"
+
+    def __init__(self, root, at=""):
+        """
+        Construct a Path from a ZipFile or filename.
+
+        Note: When the source is an existing ZipFile object,
+        its type (__class__) will be mutated to a
+        specialized type. If the caller wishes to retain the
+        original type, the caller should either create a
+        separate ZipFile object or pass a filename.
+        """
+        self.root = FastLookup.make(root)
+        self.at = at
+
+    def __eq__(self, other):
+        """
+        >>> Path(zipfile.ZipFile(io.BytesIO(), 'w')) == 'foo'
+        False
+        """
+        if self.__class__ is not other.__class__:
+            return NotImplemented
+        return (self.root, self.at) == (other.root, other.at)
+
+    def __hash__(self):
+        return hash((self.root, self.at))
+
+    def open(self, mode='r', *args, pwd=None, **kwargs):
+        """
+        Open this entry as text or binary following the semantics
+        of ``pathlib.Path.open()`` by passing arguments through
+        to io.TextIOWrapper().
+        """
+        if self.is_dir():
+            raise IsADirectoryError(self)
+        zip_mode = mode[0]
+        if zip_mode == 'r' and not self.exists():
+            raise FileNotFoundError(self)
+        stream = self.root.open(self.at, zip_mode, pwd=pwd)
+        if 'b' in mode:
+            if args or kwargs:
+                raise ValueError("encoding args invalid for binary operation")
+            return stream
+        # Text mode:
+        encoding, args, kwargs = _extract_text_encoding(*args, **kwargs)
+        return io.TextIOWrapper(stream, encoding, *args, **kwargs)
+
+    def _base(self):
+        return pathlib.PurePosixPath(self.at) if self.at else self.filename
+
+    @property
+    def name(self):
+        return self._base().name
+
+    @property
+    def suffix(self):
+        return self._base().suffix
+
+    @property
+    def suffixes(self):
+        return self._base().suffixes
+
+    @property
+    def stem(self):
+        return self._base().stem
+
+    @property
+    def filename(self):
+        return pathlib.Path(self.root.filename).joinpath(self.at)
+
+    def read_text(self, *args, **kwargs):
+        encoding, args, kwargs = _extract_text_encoding(*args, **kwargs)
+        with self.open('r', encoding, *args, **kwargs) as strm:
+            return strm.read()
+
+    def read_bytes(self):
+        with self.open('rb') as strm:
+            return strm.read()
+
+    def _is_child(self, path):
+        return posixpath.dirname(path.at.rstrip("/")) == self.at.rstrip("/")
+
+    def _next(self, at):
+        return self.__class__(self.root, at)
+
+    def is_dir(self):
+        return not self.at or self.at.endswith("/")
+
+    def is_file(self):
+        return self.exists() and not self.is_dir()
+
+    def exists(self):
+        return self.at in self.root._name_set()
+
+    def iterdir(self):
+        if not self.is_dir():
+            raise ValueError("Can't listdir a file")
+        subs = map(self._next, self.root.namelist())
+        return filter(self._is_child, subs)
+
+    def match(self, path_pattern):
+        return pathlib.PurePosixPath(self.at).match(path_pattern)
+
+    def is_symlink(self):
+        """
+        Return whether this path is a symlink.
+        """
+        info = self.root.getinfo(self.at)
+        mode = info.external_attr >> 16
+        return stat.S_ISLNK(mode)
+
+    def glob(self, pattern):
+        if not pattern:
+            raise ValueError(f"Unacceptable pattern: {pattern!r}")
+
+        prefix = re.escape(self.at)
+        tr = Translator(seps='/')
+        matches = re.compile(prefix + tr.translate(pattern)).fullmatch
+        return map(self._next, filter(matches, self.root.namelist()))
+
+    def rglob(self, pattern):
+        return self.glob(f'**/{pattern}')
+
+    def relative_to(self, other, *extra):
+        return posixpath.relpath(str(self), str(other.joinpath(*extra)))
+
+    def __str__(self):
+        return posixpath.join(self.root.filename, self.at)
+
+    def __repr__(self):
+        return self.__repr.format(self=self)
+
+    def joinpath(self, *other):
+        next = posixpath.join(self.at, *other)
+        return self._next(self.root.resolve_dir(next))
+
+    __truediv__ = joinpath
+
+    @property
+    def parent(self):
+        if not self.at:
+            return self.filename.parent
+        parent_at = posixpath.dirname(self.at.rstrip('/'))
+        if parent_at:
+            parent_at += '/'
+        return self._next(parent_at)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/_functools.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/_functools.py
new file mode 100644
index 0000000000000000000000000000000000000000..7390be21873e4ba439bde0553e4c0dcde8eb7d74
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/_functools.py
@@ -0,0 +1,20 @@
+import collections
+import functools
+
+
+# from jaraco.functools 4.0.2
+def save_method_args(method):
+    """
+    Wrap a method such that when it is called, the args and kwargs are
+    saved on the method.
+    """
+    args_and_kwargs = collections.namedtuple('args_and_kwargs', 'args kwargs')  # noqa: PYI024
+
+    @functools.wraps(method)
+    def wrapper(self, /, *args, **kwargs):
+        attr_name = '_saved_' + method.__name__
+        attr = args_and_kwargs(args, kwargs)
+        setattr(self, attr_name, attr)
+        return method(self, *args, **kwargs)
+
+    return wrapper
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/compat/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/compat/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/compat/overlay.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/compat/overlay.py
new file mode 100644
index 0000000000000000000000000000000000000000..5a97ee7cd8b98f3a5487c0a0b0a80ffde5ff4dfd
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/compat/overlay.py
@@ -0,0 +1,37 @@
+"""
+Expose zipp.Path as .zipfile.Path.
+
+Includes everything else in ``zipfile`` to match future usage. Just
+use:
+
+>>> from zipp.compat.overlay import zipfile
+
+in place of ``import zipfile``.
+
+Relative imports are supported too.
+
+>>> from zipp.compat.overlay.zipfile import ZipInfo
+
+The ``zipfile`` object added to ``sys.modules`` needs to be
+hashable (#126).
+
+>>> _ = hash(sys.modules['zipp.compat.overlay.zipfile'])
+"""
+
+import importlib
+import sys
+import types
+
+import zipp
+
+
+class HashableNamespace(types.SimpleNamespace):
+    def __hash__(self):
+        return hash(tuple(vars(self)))
+
+
+zipfile = HashableNamespace(**vars(importlib.import_module('zipfile')))
+zipfile.Path = zipp.Path
+zipfile._path = zipp
+
+sys.modules[__name__ + '.zipfile'] = zipfile  # type: ignore[assignment]
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/compat/py310.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/compat/py310.py
new file mode 100644
index 0000000000000000000000000000000000000000..e1e7ec229062b8556cdd85f530d1ff301b2e6845
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/compat/py310.py
@@ -0,0 +1,13 @@
+import io
+import sys
+
+
+def _text_encoding(encoding, stacklevel=2, /):  # pragma: no cover
+    return encoding
+
+
+text_encoding = (
+    io.text_encoding  # type: ignore[unused-ignore, attr-defined]
+    if sys.version_info > (3, 10)
+    else _text_encoding
+)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/compat/py313.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/compat/py313.py
new file mode 100644
index 0000000000000000000000000000000000000000..ae458690553f92107ce296adf4bb49add8e78250
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/compat/py313.py
@@ -0,0 +1,34 @@
+import functools
+import sys
+
+
+# from jaraco.functools 4.1
+def identity(x):
+    return x
+
+
+# from jaraco.functools 4.1
+def apply(transform):
+    def wrap(func):
+        return functools.wraps(func)(compose(transform, func))
+
+    return wrap
+
+
+# from jaraco.functools 4.1
+def compose(*funcs):
+    def compose_two(f1, f2):
+        return lambda *args, **kwargs: f1(f2(*args, **kwargs))
+
+    return functools.reduce(compose_two, funcs)
+
+
+def replace(pattern):
+    r"""
+    >>> replace(r'foo\z')
+    'foo\\Z'
+    """
+    return pattern[:-2] + pattern[-2:].replace(r'\z', r'\Z')
+
+
+legacy_end_marker = apply(replace) if sys.version_info < (3, 14) else identity
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/glob.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/glob.py
new file mode 100644
index 0000000000000000000000000000000000000000..1b4ffb33187b65b4378925c472071c845bcecc26
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/_vendor/zipp/glob.py
@@ -0,0 +1,116 @@
+import os
+import re
+
+from .compat.py313 import legacy_end_marker
+
+_default_seps = os.sep + str(os.altsep) * bool(os.altsep)
+
+
+class Translator:
+    """
+    >>> Translator('xyz')
+    Traceback (most recent call last):
+    ...
+    AssertionError: Invalid separators
+
+    >>> Translator('')
+    Traceback (most recent call last):
+    ...
+    AssertionError: Invalid separators
+    """
+
+    seps: str
+
+    def __init__(self, seps: str = _default_seps):
+        assert seps and set(seps) <= set(_default_seps), "Invalid separators"
+        self.seps = seps
+
+    def translate(self, pattern):
+        """
+        Given a glob pattern, produce a regex that matches it.
+        """
+        return self.extend(self.match_dirs(self.translate_core(pattern)))
+
+    @legacy_end_marker
+    def extend(self, pattern):
+        r"""
+        Extend regex for pattern-wide concerns.
+
+        Apply '(?s:)' to create a non-matching group that
+        matches newlines (valid on Unix).
+
+        Append '\z' to imply fullmatch even when match is used.
+        """
+        return rf'(?s:{pattern})\z'
+
+    def match_dirs(self, pattern):
+        """
+        Ensure that zipfile.Path directory names are matched.
+
+        zipfile.Path directory names always end in a slash.
+        """
+        return rf'{pattern}[/]?'
+
+    def translate_core(self, pattern):
+        r"""
+        Given a glob pattern, produce a regex that matches it.
+
+        >>> t = Translator()
+        >>> t.translate_core('*.txt').replace('\\\\', '')
+        '[^/]*\\.txt'
+        >>> t.translate_core('a?txt')
+        'a[^/]txt'
+        >>> t.translate_core('**/*').replace('\\\\', '')
+        '.*/[^/][^/]*'
+        """
+        self.restrict_rglob(pattern)
+        return ''.join(map(self.replace, separate(self.star_not_empty(pattern))))
+
+    def replace(self, match):
+        """
+        Perform the replacements for a match from :func:`separate`.
+        """
+        return match.group('set') or (
+            re.escape(match.group(0))
+            .replace('\\*\\*', r'.*')
+            .replace('\\*', rf'[^{re.escape(self.seps)}]*')
+            .replace('\\?', r'[^/]')
+        )
+
+    def restrict_rglob(self, pattern):
+        """
+        Raise ValueError if ** appears in anything but a full path segment.
+
+        >>> Translator().translate('**foo')
+        Traceback (most recent call last):
+        ...
+        ValueError: ** must appear alone in a path segment
+        """
+        seps_pattern = rf'[{re.escape(self.seps)}]+'
+        segments = re.split(seps_pattern, pattern)
+        if any('**' in segment and segment != '**' for segment in segments):
+            raise ValueError("** must appear alone in a path segment")
+
+    def star_not_empty(self, pattern):
+        """
+        Ensure that * will not match an empty segment.
+        """
+
+        def handle_segment(match):
+            segment = match.group(0)
+            return '?*' if segment == '*' else segment
+
+        not_seps_pattern = rf'[^{re.escape(self.seps)}]+'
+        return re.sub(not_seps_pattern, handle_segment, pattern)
+
+
+def separate(pattern):
+    """
+    Separate out character sets to avoid translating their contents.
+
+    >>> [m.group(0) for m in separate('*.txt')]
+    ['*.txt']
+    >>> [m.group(0) for m in separate('a[?]txt')]
+    ['a', '[?]', 'txt']
+    """
+    return re.finditer(r'([^\[]+)|(?P[\[].*?[\]])|([\[][^\]]*$)', pattern)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..50e6c2f54f38db5bf5175a7a4db219815785f1bc
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/__init__.py
@@ -0,0 +1,21 @@
+# mypy: disable_error_code=call-overload
+# pyright: reportCallIssue=false, reportArgumentType=false
+# Can't disable on the exact line because distutils doesn't exists on Python 3.12
+# and type-checkers aren't aware of distutils_hack,
+# causing distutils.command.bdist.bdist.format_commands to be Any.
+
+import sys
+
+from distutils.command.bdist import bdist
+
+if 'egg' not in bdist.format_commands:
+    try:
+        # format_commands is a dict in vendored distutils
+        # It used to be a list in older (stdlib) distutils
+        # We support both for backwards compatibility
+        bdist.format_commands['egg'] = ('bdist_egg', "Python .egg file")
+    except TypeError:
+        bdist.format_command['egg'] = ('bdist_egg', "Python .egg file")
+        bdist.format_commands.append('egg')
+
+del bdist, sys
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/_requirestxt.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/_requirestxt.py
new file mode 100644
index 0000000000000000000000000000000000000000..9029b125141158d4b12de1db8215819ce6ccf437
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/_requirestxt.py
@@ -0,0 +1,131 @@
+"""Helper code used to generate ``requires.txt`` files in the egg-info directory.
+
+The ``requires.txt`` file has an specific format:
+    - Environment markers need to be part of the section headers and
+      should not be part of the requirement spec itself.
+
+See https://setuptools.pypa.io/en/latest/deprecated/python_eggs.html#requires-txt
+"""
+
+from __future__ import annotations
+
+import io
+from collections import defaultdict
+from collections.abc import Mapping
+from itertools import filterfalse
+from typing import TypeVar
+
+from jaraco.text import yield_lines
+from packaging.requirements import Requirement
+
+from .. import _reqs
+from .._reqs import _StrOrIter
+
+# dict can work as an ordered set
+_T = TypeVar("_T")
+_Ordered = dict[_T, None]
+
+
+def _prepare(
+    install_requires: _StrOrIter, extras_require: Mapping[str, _StrOrIter]
+) -> tuple[list[str], dict[str, list[str]]]:
+    """Given values for ``install_requires`` and ``extras_require``
+    create modified versions in a way that can be written in ``requires.txt``
+    """
+    extras = _convert_extras_requirements(extras_require)
+    return _move_install_requirements_markers(install_requires, extras)
+
+
+def _convert_extras_requirements(
+    extras_require: Mapping[str, _StrOrIter],
+) -> defaultdict[str, _Ordered[Requirement]]:
+    """
+    Convert requirements in `extras_require` of the form
+    `"extra": ["barbazquux; {marker}"]` to
+    `"extra:{marker}": ["barbazquux"]`.
+    """
+    output = defaultdict[str, _Ordered[Requirement]](dict)
+    for section, v in extras_require.items():
+        # Do not strip empty sections.
+        output[section]
+        for r in _reqs.parse(v):
+            output[section + _suffix_for(r)].setdefault(r)
+
+    return output
+
+
+def _move_install_requirements_markers(
+    install_requires: _StrOrIter, extras_require: Mapping[str, _Ordered[Requirement]]
+) -> tuple[list[str], dict[str, list[str]]]:
+    """
+    The ``requires.txt`` file has an specific format:
+        - Environment markers need to be part of the section headers and
+          should not be part of the requirement spec itself.
+
+    Move requirements in ``install_requires`` that are using environment
+    markers ``extras_require``.
+    """
+
+    # divide the install_requires into two sets, simple ones still
+    # handled by install_requires and more complex ones handled by extras_require.
+
+    inst_reqs = list(_reqs.parse(install_requires))
+    simple_reqs = filter(_no_marker, inst_reqs)
+    complex_reqs = filterfalse(_no_marker, inst_reqs)
+    simple_install_requires = list(map(str, simple_reqs))
+
+    for r in complex_reqs:
+        extras_require[':' + str(r.marker)].setdefault(r)
+
+    expanded_extras = dict(
+        # list(dict.fromkeys(...))  ensures a list of unique strings
+        (k, list(dict.fromkeys(str(r) for r in map(_clean_req, v))))
+        for k, v in extras_require.items()
+    )
+
+    return simple_install_requires, expanded_extras
+
+
+def _suffix_for(req):
+    """Return the 'extras_require' suffix for a given requirement."""
+    return ':' + str(req.marker) if req.marker else ''
+
+
+def _clean_req(req):
+    """Given a Requirement, remove environment markers and return it"""
+    r = Requirement(str(req))  # create a copy before modifying
+    r.marker = None
+    return r
+
+
+def _no_marker(req):
+    return not req.marker
+
+
+def _write_requirements(stream, reqs):
+    lines = yield_lines(reqs or ())
+
+    def append_cr(line):
+        return line + '\n'
+
+    lines = map(append_cr, lines)
+    stream.writelines(lines)
+
+
+def write_requirements(cmd, basename, filename):
+    dist = cmd.distribution
+    data = io.StringIO()
+    install_requires, extras_require = _prepare(
+        dist.install_requires or (), dist.extras_require or {}
+    )
+    _write_requirements(data, install_requires)
+    for extra in sorted(extras_require):
+        data.write('\n[{extra}]\n'.format(**vars()))
+        _write_requirements(data, extras_require[extra])
+    cmd.write_or_delete_file("requirements", filename, data.getvalue())
+
+
+def write_setup_requirements(cmd, basename, filename):
+    data = io.StringIO()
+    _write_requirements(data, cmd.distribution.setup_requires)
+    cmd.write_or_delete_file("setup-requirements", filename, data.getvalue())
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/alias.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/alias.py
new file mode 100644
index 0000000000000000000000000000000000000000..b8d74af71d4464abf899b9f872b5741f23167165
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/alias.py
@@ -0,0 +1,77 @@
+from setuptools.command.setopt import config_file, edit_config, option_base
+
+from distutils.errors import DistutilsOptionError
+
+
+def shquote(arg):
+    """Quote an argument for later parsing by shlex.split()"""
+    for c in '"', "'", "\\", "#":
+        if c in arg:
+            return repr(arg)
+    if arg.split() != [arg]:
+        return repr(arg)
+    return arg
+
+
+class alias(option_base):
+    """Define a shortcut that invokes one or more commands"""
+
+    description = "define a shortcut to invoke one or more commands"
+    command_consumes_arguments = True
+
+    user_options = [
+        ('remove', 'r', 'remove (unset) the alias'),
+    ] + option_base.user_options
+
+    boolean_options = option_base.boolean_options + ['remove']
+
+    def initialize_options(self):
+        option_base.initialize_options(self)
+        self.args = None
+        self.remove = None
+
+    def finalize_options(self) -> None:
+        option_base.finalize_options(self)
+        if self.remove and len(self.args) != 1:
+            raise DistutilsOptionError(
+                "Must specify exactly one argument (the alias name) when using --remove"
+            )
+
+    def run(self) -> None:
+        aliases = self.distribution.get_option_dict('aliases')
+
+        if not self.args:
+            print("Command Aliases")
+            print("---------------")
+            for alias in aliases:
+                print("setup.py alias", format_alias(alias, aliases))
+            return
+
+        elif len(self.args) == 1:
+            (alias,) = self.args
+            if self.remove:
+                command = None
+            elif alias in aliases:
+                print("setup.py alias", format_alias(alias, aliases))
+                return
+            else:
+                print(f"No alias definition found for {alias!r}")
+                return
+        else:
+            alias = self.args[0]
+            command = ' '.join(map(shquote, self.args[1:]))
+
+        edit_config(self.filename, {'aliases': {alias: command}}, self.dry_run)
+
+
+def format_alias(name, aliases):
+    source, command = aliases[name]
+    if source == config_file('global'):
+        source = '--global-config '
+    elif source == config_file('user'):
+        source = '--user-config '
+    elif source == config_file('local'):
+        source = ''
+    else:
+        source = f'--filename={source!r}'
+    return source + name + ' ' + command
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/bdist_egg.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/bdist_egg.py
new file mode 100644
index 0000000000000000000000000000000000000000..ab452680f1a573a94507129433c6bc0788dfb5d8
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/bdist_egg.py
@@ -0,0 +1,482 @@
+"""setuptools.command.bdist_egg
+
+Build .egg distributions"""
+
+from __future__ import annotations
+
+import marshal
+import os
+import re
+import sys
+import textwrap
+from collections.abc import Iterator
+from sysconfig import get_path, get_platform, get_python_version
+from types import CodeType
+from typing import TYPE_CHECKING, AnyStr, Literal
+
+from setuptools import Command
+from setuptools.extension import Library
+
+from .._path import StrPath, StrPathT, ensure_directory
+
+from distutils import log
+from distutils.dir_util import mkpath, remove_tree
+
+if TYPE_CHECKING:
+    from _typeshed import GenericPath
+    from typing_extensions import TypeAlias
+
+# Same as zipfile._ZipFileMode from typeshed
+_ZipFileMode: TypeAlias = Literal["r", "w", "x", "a"]
+
+
+def _get_purelib():
+    return get_path("purelib")
+
+
+def strip_module(filename):
+    if '.' in filename:
+        filename = os.path.splitext(filename)[0]
+    filename = filename.removesuffix('module')
+    return filename
+
+
+def sorted_walk(
+    dir: GenericPath[AnyStr],
+) -> Iterator[tuple[AnyStr, list[AnyStr], list[AnyStr]]]:
+    """Do os.walk in a reproducible way,
+    independent of indeterministic filesystem readdir order
+    """
+    for base, dirs, files in os.walk(dir):
+        dirs.sort()
+        files.sort()
+        yield base, dirs, files
+
+
+def write_stub(resource, pyfile) -> None:
+    _stub_template = textwrap.dedent(
+        """
+        def __bootstrap__():
+            global __bootstrap__, __loader__, __file__
+            import sys, importlib.resources as irs, importlib.util
+            with irs.as_file(irs.files(__name__).joinpath(%r)) as __file__:
+                __loader__ = None; del __bootstrap__, __loader__
+                spec = importlib.util.spec_from_file_location(__name__,__file__)
+                mod = importlib.util.module_from_spec(spec)
+                spec.loader.exec_module(mod)
+        __bootstrap__()
+        """
+    ).lstrip()
+    with open(pyfile, 'w', encoding="utf-8") as f:
+        f.write(_stub_template % resource)
+
+
+class bdist_egg(Command):
+    description = 'create an "egg" distribution'
+
+    user_options = [
+        ('bdist-dir=', 'b', "temporary directory for creating the distribution"),
+        (
+            'plat-name=',
+            'p',
+            "platform name to embed in generated filenames "
+            "(by default uses `sysconfig.get_platform()`)",
+        ),
+        ('exclude-source-files', None, "remove all .py files from the generated egg"),
+        (
+            'keep-temp',
+            'k',
+            "keep the pseudo-installation tree around after "
+            "creating the distribution archive",
+        ),
+        ('dist-dir=', 'd', "directory to put final built distributions in"),
+        ('skip-build', None, "skip rebuilding everything (for testing/debugging)"),
+    ]
+
+    boolean_options = ['keep-temp', 'skip-build', 'exclude-source-files']
+
+    def initialize_options(self):
+        self.bdist_dir = None
+        self.plat_name = None
+        self.keep_temp = False
+        self.dist_dir = None
+        self.skip_build = False
+        self.egg_output = None
+        self.exclude_source_files = None
+
+    def finalize_options(self) -> None:
+        ei_cmd = self.ei_cmd = self.get_finalized_command("egg_info")
+        self.egg_info = ei_cmd.egg_info
+
+        if self.bdist_dir is None:
+            bdist_base = self.get_finalized_command('bdist').bdist_base
+            self.bdist_dir = os.path.join(bdist_base, 'egg')
+
+        if self.plat_name is None:
+            self.plat_name = get_platform()
+
+        self.set_undefined_options('bdist', ('dist_dir', 'dist_dir'))
+
+        if self.egg_output is None:
+            # Compute filename of the output egg
+            basename = ei_cmd._get_egg_basename(
+                py_version=get_python_version(),
+                platform=self.distribution.has_ext_modules() and self.plat_name,
+            )
+
+            self.egg_output = os.path.join(self.dist_dir, basename + '.egg')
+
+    def do_install_data(self) -> None:
+        # Hack for packages that install data to install's --install-lib
+        self.get_finalized_command('install').install_lib = self.bdist_dir
+
+        site_packages = os.path.normcase(os.path.realpath(_get_purelib()))
+        old, self.distribution.data_files = self.distribution.data_files, []
+
+        for item in old:
+            if isinstance(item, tuple) and len(item) == 2:
+                if os.path.isabs(item[0]):
+                    realpath = os.path.realpath(item[0])
+                    normalized = os.path.normcase(realpath)
+                    if normalized == site_packages or normalized.startswith(
+                        site_packages + os.sep
+                    ):
+                        item = realpath[len(site_packages) + 1 :], item[1]
+                        # XXX else: raise ???
+            self.distribution.data_files.append(item)
+
+        try:
+            log.info("installing package data to %s", self.bdist_dir)
+            self.call_command('install_data', force=False, root=None)
+        finally:
+            self.distribution.data_files = old
+
+    def get_outputs(self):
+        return [self.egg_output]
+
+    def call_command(self, cmdname, **kw):
+        """Invoke reinitialized command `cmdname` with keyword args"""
+        for dirname in INSTALL_DIRECTORY_ATTRS:
+            kw.setdefault(dirname, self.bdist_dir)
+        kw.setdefault('skip_build', self.skip_build)
+        kw.setdefault('dry_run', self.dry_run)
+        cmd = self.reinitialize_command(cmdname, **kw)
+        self.run_command(cmdname)
+        return cmd
+
+    def run(self) -> None:  # noqa: C901  # is too complex (14)  # FIXME
+        # Generate metadata first
+        self.run_command("egg_info")
+        # We run install_lib before install_data, because some data hacks
+        # pull their data path from the install_lib command.
+        log.info("installing library code to %s", self.bdist_dir)
+        instcmd = self.get_finalized_command('install')
+        old_root = instcmd.root
+        instcmd.root = None
+        if self.distribution.has_c_libraries() and not self.skip_build:
+            self.run_command('build_clib')
+        cmd = self.call_command('install_lib', warn_dir=False)
+        instcmd.root = old_root
+
+        all_outputs, ext_outputs = self.get_ext_outputs()
+        self.stubs = []
+        to_compile = []
+        for p, ext_name in enumerate(ext_outputs):
+            filename, _ext = os.path.splitext(ext_name)
+            pyfile = os.path.join(self.bdist_dir, strip_module(filename) + '.py')
+            self.stubs.append(pyfile)
+            log.info("creating stub loader for %s", ext_name)
+            if not self.dry_run:
+                write_stub(os.path.basename(ext_name), pyfile)
+            to_compile.append(pyfile)
+            ext_outputs[p] = ext_name.replace(os.sep, '/')
+
+        if to_compile:
+            cmd.byte_compile(to_compile)
+        if self.distribution.data_files:
+            self.do_install_data()
+
+        # Make the EGG-INFO directory
+        archive_root = self.bdist_dir
+        egg_info = os.path.join(archive_root, 'EGG-INFO')
+        self.mkpath(egg_info)
+        if self.distribution.scripts:
+            script_dir = os.path.join(egg_info, 'scripts')
+            log.info("installing scripts to %s", script_dir)
+            self.call_command('install_scripts', install_dir=script_dir, no_ep=True)
+
+        self.copy_metadata_to(egg_info)
+        native_libs = os.path.join(egg_info, "native_libs.txt")
+        if all_outputs:
+            log.info("writing %s", native_libs)
+            if not self.dry_run:
+                ensure_directory(native_libs)
+                with open(native_libs, 'wt', encoding="utf-8") as libs_file:
+                    libs_file.write('\n'.join(all_outputs))
+                    libs_file.write('\n')
+        elif os.path.isfile(native_libs):
+            log.info("removing %s", native_libs)
+            if not self.dry_run:
+                os.unlink(native_libs)
+
+        write_safety_flag(os.path.join(archive_root, 'EGG-INFO'), self.zip_safe())
+
+        if os.path.exists(os.path.join(self.egg_info, 'depends.txt')):
+            log.warn(
+                "WARNING: 'depends.txt' will not be used by setuptools 0.6!\n"
+                "Use the install_requires/extras_require setup() args instead."
+            )
+
+        if self.exclude_source_files:
+            self.zap_pyfiles()
+
+        # Make the archive
+        make_zipfile(
+            self.egg_output,
+            archive_root,
+            verbose=self.verbose,
+            dry_run=self.dry_run,  # type: ignore[arg-type] # Is an actual boolean in vendored _distutils
+            mode=self.gen_header(),
+        )
+        if not self.keep_temp:
+            remove_tree(self.bdist_dir, dry_run=self.dry_run)
+
+        # Add to 'Distribution.dist_files' so that the "upload" command works
+        getattr(self.distribution, 'dist_files', []).append((
+            'bdist_egg',
+            get_python_version(),
+            self.egg_output,
+        ))
+
+    def zap_pyfiles(self) -> None:
+        log.info("Removing .py files from temporary directory")
+        for base, dirs, files in walk_egg(self.bdist_dir):
+            for name in files:
+                path = os.path.join(base, name)
+
+                if name.endswith('.py'):
+                    log.debug("Deleting %s", path)
+                    os.unlink(path)
+
+                if base.endswith('__pycache__'):
+                    path_old = path
+
+                    pattern = r'(?P.+)\.(?P[^.]+)\.pyc'
+                    m = re.match(pattern, name)
+                    # We shouldn't find any non-pyc files in __pycache__
+                    assert m is not None
+                    path_new = os.path.join(base, os.pardir, m.group('name') + '.pyc')
+                    log.info(f"Renaming file from [{path_old}] to [{path_new}]")
+                    try:
+                        os.remove(path_new)
+                    except OSError:
+                        pass
+                    os.rename(path_old, path_new)
+
+    def zip_safe(self):
+        safe = getattr(self.distribution, 'zip_safe', None)
+        if safe is not None:
+            return safe
+        log.warn("zip_safe flag not set; analyzing archive contents...")
+        return analyze_egg(self.bdist_dir, self.stubs)
+
+    def gen_header(self) -> Literal["w"]:
+        return 'w'
+
+    def copy_metadata_to(self, target_dir) -> None:
+        "Copy metadata (egg info) to the target_dir"
+        # normalize the path (so that a forward-slash in egg_info will
+        # match using startswith below)
+        norm_egg_info = os.path.normpath(self.egg_info)
+        prefix = os.path.join(norm_egg_info, '')
+        for path in self.ei_cmd.filelist.files:
+            if path.startswith(prefix):
+                target = os.path.join(target_dir, path[len(prefix) :])
+                ensure_directory(target)
+                self.copy_file(path, target)
+
+    def get_ext_outputs(self):
+        """Get a list of relative paths to C extensions in the output distro"""
+
+        all_outputs = []
+        ext_outputs = []
+
+        paths = {self.bdist_dir: ''}
+        for base, dirs, files in sorted_walk(self.bdist_dir):
+            all_outputs.extend(
+                paths[base] + filename
+                for filename in files
+                if os.path.splitext(filename)[1].lower() in NATIVE_EXTENSIONS
+            )
+            for filename in dirs:
+                paths[os.path.join(base, filename)] = paths[base] + filename + '/'
+
+        if self.distribution.has_ext_modules():
+            build_cmd = self.get_finalized_command('build_ext')
+            for ext in build_cmd.extensions:
+                if isinstance(ext, Library):
+                    continue
+                fullname = build_cmd.get_ext_fullname(ext.name)
+                filename = build_cmd.get_ext_filename(fullname)
+                if not os.path.basename(filename).startswith('dl-'):
+                    if os.path.exists(os.path.join(self.bdist_dir, filename)):
+                        ext_outputs.append(filename)
+
+        return all_outputs, ext_outputs
+
+
+NATIVE_EXTENSIONS: dict[str, None] = dict.fromkeys('.dll .so .dylib .pyd'.split())
+
+
+def walk_egg(egg_dir: StrPath) -> Iterator[tuple[str, list[str], list[str]]]:
+    """Walk an unpacked egg's contents, skipping the metadata directory"""
+    walker = sorted_walk(egg_dir)
+    base, dirs, files = next(walker)
+    if 'EGG-INFO' in dirs:
+        dirs.remove('EGG-INFO')
+    yield base, dirs, files
+    yield from walker
+
+
+def analyze_egg(egg_dir, stubs):
+    # check for existing flag in EGG-INFO
+    for flag, fn in safety_flags.items():
+        if os.path.exists(os.path.join(egg_dir, 'EGG-INFO', fn)):
+            return flag
+    if not can_scan():
+        return False
+    safe = True
+    for base, dirs, files in walk_egg(egg_dir):
+        for name in files:
+            if name.endswith(('.py', '.pyw')):
+                continue
+            elif name.endswith(('.pyc', '.pyo')):
+                # always scan, even if we already know we're not safe
+                safe = scan_module(egg_dir, base, name, stubs) and safe
+    return safe
+
+
+def write_safety_flag(egg_dir, safe) -> None:
+    # Write or remove zip safety flag file(s)
+    for flag, fn in safety_flags.items():
+        fn = os.path.join(egg_dir, fn)
+        if os.path.exists(fn):
+            if safe is None or bool(safe) != flag:
+                os.unlink(fn)
+        elif safe is not None and bool(safe) == flag:
+            with open(fn, 'wt', encoding="utf-8") as f:
+                f.write('\n')
+
+
+safety_flags = {
+    True: 'zip-safe',
+    False: 'not-zip-safe',
+}
+
+
+def scan_module(egg_dir, base, name, stubs):
+    """Check whether module possibly uses unsafe-for-zipfile stuff"""
+
+    filename = os.path.join(base, name)
+    if filename[:-1] in stubs:
+        return True  # Extension module
+    pkg = base[len(egg_dir) + 1 :].replace(os.sep, '.')
+    module = pkg + (pkg and '.' or '') + os.path.splitext(name)[0]
+    skip = 16  # skip magic & reserved? & date & file size
+    f = open(filename, 'rb')
+    f.read(skip)
+    code = marshal.load(f)
+    f.close()
+    safe = True
+    symbols = dict.fromkeys(iter_symbols(code))
+    for bad in ['__file__', '__path__']:
+        if bad in symbols:
+            log.warn("%s: module references %s", module, bad)
+            safe = False
+    if 'inspect' in symbols:
+        for bad in [
+            'getsource',
+            'getabsfile',
+            'getfile',
+            'getsourcefile',
+            'getsourcelines',
+            'findsource',
+            'getcomments',
+            'getframeinfo',
+            'getinnerframes',
+            'getouterframes',
+            'stack',
+            'trace',
+        ]:
+            if bad in symbols:
+                log.warn("%s: module MAY be using inspect.%s", module, bad)
+                safe = False
+    return safe
+
+
+def iter_symbols(code: CodeType) -> Iterator[str]:
+    """Yield names and strings used by `code` and its nested code objects"""
+    yield from code.co_names
+    for const in code.co_consts:
+        if isinstance(const, str):
+            yield const
+        elif isinstance(const, CodeType):
+            yield from iter_symbols(const)
+
+
+def can_scan() -> bool:
+    if not sys.platform.startswith('java') and sys.platform != 'cli':
+        # CPython, PyPy, etc.
+        return True
+    log.warn("Unable to analyze compiled code on this platform.")
+    log.warn(
+        "Please ask the author to include a 'zip_safe'"
+        " setting (either True or False) in the package's setup.py"
+    )
+    return False
+
+
+# Attribute names of options for commands that might need to be convinced to
+# install to the egg build directory
+
+INSTALL_DIRECTORY_ATTRS = ['install_lib', 'install_dir', 'install_data', 'install_base']
+
+
+def make_zipfile(
+    zip_filename: StrPathT,
+    base_dir,
+    verbose: bool = False,
+    dry_run: bool = False,
+    compress=True,
+    mode: _ZipFileMode = 'w',
+) -> StrPathT:
+    """Create a zip file from all the files under 'base_dir'.  The output
+    zip file will be named 'base_dir' + ".zip".  Uses either the "zipfile"
+    Python module (if available) or the InfoZIP "zip" utility (if installed
+    and found on the default search path).  If neither tool is available,
+    raises DistutilsExecError.  Returns the name of the output zip file.
+    """
+    import zipfile
+
+    mkpath(os.path.dirname(zip_filename), dry_run=dry_run)  # type: ignore[arg-type] # python/mypy#18075
+    log.info("creating '%s' and adding '%s' to it", zip_filename, base_dir)
+
+    def visit(z, dirname, names):
+        for name in names:
+            path = os.path.normpath(os.path.join(dirname, name))
+            if os.path.isfile(path):
+                p = path[len(base_dir) + 1 :]
+                if not dry_run:
+                    z.write(path, p)
+                log.debug("adding '%s'", p)
+
+    compression = zipfile.ZIP_DEFLATED if compress else zipfile.ZIP_STORED
+    if not dry_run:
+        z = zipfile.ZipFile(zip_filename, mode, compression=compression)
+        for dirname, dirs, files in sorted_walk(base_dir):
+            visit(z, dirname, files)
+        z.close()
+    else:
+        for dirname, dirs, files in sorted_walk(base_dir):
+            visit(None, dirname, files)
+    return zip_filename
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/bdist_rpm.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/bdist_rpm.py
new file mode 100644
index 0000000000000000000000000000000000000000..6dbb27002a8cc7f1cafd4f5cbb75ba39aa7430e2
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/bdist_rpm.py
@@ -0,0 +1,42 @@
+from ..dist import Distribution
+from ..warnings import SetuptoolsDeprecationWarning
+
+import distutils.command.bdist_rpm as orig
+
+
+class bdist_rpm(orig.bdist_rpm):
+    """
+    Override the default bdist_rpm behavior to do the following:
+
+    1. Run egg_info to ensure the name and version are properly calculated.
+    2. Always run 'install' using --single-version-externally-managed to
+       disable eggs in RPM distributions.
+    """
+
+    distribution: Distribution  # override distutils.dist.Distribution with setuptools.dist.Distribution
+
+    def run(self) -> None:
+        SetuptoolsDeprecationWarning.emit(
+            "Deprecated command",
+            """
+            bdist_rpm is deprecated and will be removed in a future version.
+            Use bdist_wheel (wheel packages) instead.
+            """,
+            see_url="https://github.com/pypa/setuptools/issues/1988",
+            due_date=(2023, 10, 30),  # Deprecation introduced in 22 Oct 2021.
+        )
+
+        # ensure distro name is up-to-date
+        self.run_command('egg_info')
+
+        orig.bdist_rpm.run(self)
+
+    def _make_spec_file(self):
+        spec = orig.bdist_rpm._make_spec_file(self)
+        return [
+            line.replace(
+                "setup.py install ",
+                "setup.py install --single-version-externally-managed ",
+            ).replace("%setup", "%setup -n %{name}-%{unmangled_version}")
+            for line in spec
+        ]
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/bdist_wheel.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/bdist_wheel.py
new file mode 100644
index 0000000000000000000000000000000000000000..91ed00170e985250390e5dfa819a602be33f93a1
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/bdist_wheel.py
@@ -0,0 +1,604 @@
+"""
+Create a wheel (.whl) distribution.
+
+A wheel is a built archive format.
+"""
+
+from __future__ import annotations
+
+import os
+import re
+import shutil
+import struct
+import sys
+import sysconfig
+import warnings
+from collections.abc import Iterable, Sequence
+from email.generator import BytesGenerator
+from glob import iglob
+from typing import Literal, cast
+from zipfile import ZIP_DEFLATED, ZIP_STORED
+
+from packaging import tags, version as _packaging_version
+from wheel.wheelfile import WheelFile
+
+from .. import Command, __version__, _shutil
+from .._core_metadata import _safe_license_file
+from .._normalization import safer_name
+from ..warnings import SetuptoolsDeprecationWarning
+from .egg_info import egg_info as egg_info_cls
+
+from distutils import log
+
+
+def safe_version(version: str) -> str:
+    """
+    Convert an arbitrary string to a standard version string
+    """
+    try:
+        # normalize the version
+        return str(_packaging_version.Version(version))
+    except _packaging_version.InvalidVersion:
+        version = version.replace(" ", ".")
+        return re.sub("[^A-Za-z0-9.]+", "-", version)
+
+
+setuptools_major_version = int(__version__.split(".")[0])
+
+PY_LIMITED_API_PATTERN = r"cp3\d"
+
+
+def _is_32bit_interpreter() -> bool:
+    return struct.calcsize("P") == 4
+
+
+def python_tag() -> str:
+    return f"py{sys.version_info.major}"
+
+
+def get_platform(archive_root: str | None) -> str:
+    """Return our platform name 'win32', 'linux_x86_64'"""
+    result = sysconfig.get_platform()
+    if result.startswith("macosx") and archive_root is not None:  # pragma: no cover
+        from wheel.macosx_libfile import calculate_macosx_platform_tag
+
+        result = calculate_macosx_platform_tag(archive_root, result)
+    elif _is_32bit_interpreter():
+        if result == "linux-x86_64":
+            # pip pull request #3497
+            result = "linux-i686"
+        elif result == "linux-aarch64":
+            # packaging pull request #234
+            # TODO armv8l, packaging pull request #690 => this did not land
+            # in pip/packaging yet
+            result = "linux-armv7l"
+
+    return result.replace("-", "_")
+
+
+def get_flag(
+    var: str, fallback: bool, expected: bool = True, warn: bool = True
+) -> bool:
+    """Use a fallback value for determining SOABI flags if the needed config
+    var is unset or unavailable."""
+    val = sysconfig.get_config_var(var)
+    if val is None:
+        if warn:
+            warnings.warn(
+                f"Config variable '{var}' is unset, Python ABI tag may be incorrect",
+                RuntimeWarning,
+                stacklevel=2,
+            )
+        return fallback
+    return val == expected
+
+
+def get_abi_tag() -> str | None:
+    """Return the ABI tag based on SOABI (if available) or emulate SOABI (PyPy2)."""
+    soabi: str = sysconfig.get_config_var("SOABI")
+    impl = tags.interpreter_name()
+    if not soabi and impl in ("cp", "pp") and hasattr(sys, "maxunicode"):
+        d = ""
+        u = ""
+        if get_flag("Py_DEBUG", hasattr(sys, "gettotalrefcount"), warn=(impl == "cp")):
+            d = "d"
+
+        abi = f"{impl}{tags.interpreter_version()}{d}{u}"
+    elif soabi and impl == "cp" and soabi.startswith("cpython"):
+        # non-Windows
+        abi = "cp" + soabi.split("-")[1]
+    elif soabi and impl == "cp" and soabi.startswith("cp"):
+        # Windows
+        abi = soabi.split("-")[0]
+        if hasattr(sys, "gettotalrefcount"):
+            # using debug build; append "d" flag
+            abi += "d"
+    elif soabi and impl == "pp":
+        # we want something like pypy36-pp73
+        abi = "-".join(soabi.split("-")[:2])
+        abi = abi.replace(".", "_").replace("-", "_")
+    elif soabi and impl == "graalpy":
+        abi = "-".join(soabi.split("-")[:3])
+        abi = abi.replace(".", "_").replace("-", "_")
+    elif soabi:
+        abi = soabi.replace(".", "_").replace("-", "_")
+    else:
+        abi = None
+
+    return abi
+
+
+def safer_version(version: str) -> str:
+    return safe_version(version).replace("-", "_")
+
+
+class bdist_wheel(Command):
+    description = "create a wheel distribution"
+
+    supported_compressions = {
+        "stored": ZIP_STORED,
+        "deflated": ZIP_DEFLATED,
+    }
+
+    user_options = [
+        ("bdist-dir=", "b", "temporary directory for creating the distribution"),
+        (
+            "plat-name=",
+            "p",
+            "platform name to embed in generated filenames "
+            f"[default: {get_platform(None)}]",
+        ),
+        (
+            "keep-temp",
+            "k",
+            "keep the pseudo-installation tree around after "
+            "creating the distribution archive",
+        ),
+        ("dist-dir=", "d", "directory to put final built distributions in"),
+        ("skip-build", None, "skip rebuilding everything (for testing/debugging)"),
+        (
+            "relative",
+            None,
+            "build the archive using relative paths [default: false]",
+        ),
+        (
+            "owner=",
+            "u",
+            "Owner name used when creating a tar file [default: current user]",
+        ),
+        (
+            "group=",
+            "g",
+            "Group name used when creating a tar file [default: current group]",
+        ),
+        ("universal", None, "*DEPRECATED* make a universal wheel [default: false]"),
+        (
+            "compression=",
+            None,
+            f"zipfile compression (one of: {', '.join(supported_compressions)}) [default: 'deflated']",
+        ),
+        (
+            "python-tag=",
+            None,
+            f"Python implementation compatibility tag [default: '{python_tag()}']",
+        ),
+        (
+            "build-number=",
+            None,
+            "Build number for this particular version. "
+            "As specified in PEP-0427, this must start with a digit. "
+            "[default: None]",
+        ),
+        (
+            "py-limited-api=",
+            None,
+            "Python tag (cp32|cp33|cpNN) for abi3 wheel tag [default: false]",
+        ),
+        (
+            "dist-info-dir=",
+            None,
+            "directory where a pre-generated dist-info can be found (e.g. as a "
+            "result of calling the PEP517 'prepare_metadata_for_build_wheel' "
+            "method)",
+        ),
+    ]
+
+    boolean_options = ["keep-temp", "skip-build", "relative", "universal"]
+
+    def initialize_options(self) -> None:
+        self.bdist_dir: str | None = None
+        self.data_dir = ""
+        self.plat_name: str | None = None
+        self.plat_tag: str | None = None
+        self.format = "zip"
+        self.keep_temp = False
+        self.dist_dir: str | None = None
+        self.dist_info_dir = None
+        self.egginfo_dir: str | None = None
+        self.root_is_pure: bool | None = None
+        self.skip_build = False
+        self.relative = False
+        self.owner = None
+        self.group = None
+        self.universal = False
+        self.compression: str | int = "deflated"
+        self.python_tag = python_tag()
+        self.build_number: str | None = None
+        self.py_limited_api: str | Literal[False] = False
+        self.plat_name_supplied = False
+
+    def finalize_options(self) -> None:
+        if not self.bdist_dir:
+            bdist_base = self.get_finalized_command("bdist").bdist_base
+            self.bdist_dir = os.path.join(bdist_base, "wheel")
+
+        if self.dist_info_dir is None:
+            egg_info = cast(egg_info_cls, self.distribution.get_command_obj("egg_info"))
+            egg_info.ensure_finalized()  # needed for correct `wheel_dist_name`
+
+        self.data_dir = self.wheel_dist_name + ".data"
+        self.plat_name_supplied = bool(self.plat_name)
+
+        need_options = ("dist_dir", "plat_name", "skip_build")
+
+        self.set_undefined_options("bdist", *zip(need_options, need_options))
+
+        self.root_is_pure = not (
+            self.distribution.has_ext_modules() or self.distribution.has_c_libraries()
+        )
+
+        self._validate_py_limited_api()
+
+        # Support legacy [wheel] section for setting universal
+        wheel = self.distribution.get_option_dict("wheel")
+        if "universal" in wheel:  # pragma: no cover
+            # please don't define this in your global configs
+            log.warn("The [wheel] section is deprecated. Use [bdist_wheel] instead.")
+            val = wheel["universal"][1].strip()
+            if val.lower() in ("1", "true", "yes"):
+                self.universal = True
+
+        if self.universal:
+            SetuptoolsDeprecationWarning.emit(
+                "bdist_wheel.universal is deprecated",
+                """
+                With Python 2.7 end-of-life, support for building universal wheels
+                (i.e., wheels that support both Python 2 and Python 3)
+                is being obviated.
+                Please discontinue using this option, or if you still need it,
+                file an issue with pypa/setuptools describing your use case.
+                """,
+                due_date=(2025, 8, 30),  # Introduced in 2024-08-30
+            )
+
+        if self.build_number is not None and not self.build_number[:1].isdigit():
+            raise ValueError("Build tag (build-number) must start with a digit.")
+
+    def _validate_py_limited_api(self) -> None:
+        if not self.py_limited_api:
+            return
+
+        if not re.match(PY_LIMITED_API_PATTERN, self.py_limited_api):
+            raise ValueError(f"py-limited-api must match '{PY_LIMITED_API_PATTERN}'")
+
+        if sysconfig.get_config_var("Py_GIL_DISABLED"):
+            raise ValueError(
+                f"`py_limited_api={self.py_limited_api!r}` not supported. "
+                "`Py_LIMITED_API` is currently incompatible with "
+                "`Py_GIL_DISABLED`. "
+                "See https://github.com/python/cpython/issues/111506."
+            )
+
+    @property
+    def wheel_dist_name(self) -> str:
+        """Return distribution full name with - replaced with _"""
+        components = [
+            safer_name(self.distribution.get_name()),
+            safer_version(self.distribution.get_version()),
+        ]
+        if self.build_number:
+            components.append(self.build_number)
+        return "-".join(components)
+
+    def get_tag(self) -> tuple[str, str, str]:
+        # bdist sets self.plat_name if unset, we should only use it for purepy
+        # wheels if the user supplied it.
+        if self.plat_name_supplied and self.plat_name:
+            plat_name = self.plat_name
+        elif self.root_is_pure:
+            plat_name = "any"
+        else:
+            # macosx contains system version in platform name so need special handle
+            if self.plat_name and not self.plat_name.startswith("macosx"):
+                plat_name = self.plat_name
+            else:
+                # on macosx always limit the platform name to comply with any
+                # c-extension modules in bdist_dir, since the user can specify
+                # a higher MACOSX_DEPLOYMENT_TARGET via tools like CMake
+
+                # on other platforms, and on macosx if there are no c-extension
+                # modules, use the default platform name.
+                plat_name = get_platform(self.bdist_dir)
+
+            if _is_32bit_interpreter():
+                if plat_name in ("linux-x86_64", "linux_x86_64"):
+                    plat_name = "linux_i686"
+                if plat_name in ("linux-aarch64", "linux_aarch64"):
+                    # TODO armv8l, packaging pull request #690 => this did not land
+                    # in pip/packaging yet
+                    plat_name = "linux_armv7l"
+
+        plat_name = (
+            plat_name.lower().replace("-", "_").replace(".", "_").replace(" ", "_")
+        )
+
+        if self.root_is_pure:
+            if self.universal:
+                impl = "py2.py3"
+            else:
+                impl = self.python_tag
+            tag = (impl, "none", plat_name)
+        else:
+            impl_name = tags.interpreter_name()
+            impl_ver = tags.interpreter_version()
+            impl = impl_name + impl_ver
+            # We don't work on CPython 3.1, 3.0.
+            if self.py_limited_api and (impl_name + impl_ver).startswith("cp3"):
+                impl = self.py_limited_api
+                abi_tag = "abi3"
+            else:
+                abi_tag = str(get_abi_tag()).lower()
+            tag = (impl, abi_tag, plat_name)
+            # issue gh-374: allow overriding plat_name
+            supported_tags = [
+                (t.interpreter, t.abi, plat_name) for t in tags.sys_tags()
+            ]
+            assert tag in supported_tags, (
+                f"would build wheel with unsupported tag {tag}"
+            )
+        return tag
+
+    def run(self):
+        build_scripts = self.reinitialize_command("build_scripts")
+        build_scripts.executable = "python"
+        build_scripts.force = True
+
+        build_ext = self.reinitialize_command("build_ext")
+        build_ext.inplace = False
+
+        if not self.skip_build:
+            self.run_command("build")
+
+        install = self.reinitialize_command("install", reinit_subcommands=True)
+        install.root = self.bdist_dir
+        install.compile = False
+        install.skip_build = self.skip_build
+        install.warn_dir = False
+
+        # A wheel without setuptools scripts is more cross-platform.
+        # Use the (undocumented) `no_ep` option to setuptools'
+        # install_scripts command to avoid creating entry point scripts.
+        install_scripts = self.reinitialize_command("install_scripts")
+        install_scripts.no_ep = True
+
+        # Use a custom scheme for the archive, because we have to decide
+        # at installation time which scheme to use.
+        for key in ("headers", "scripts", "data", "purelib", "platlib"):
+            setattr(install, "install_" + key, os.path.join(self.data_dir, key))
+
+        basedir_observed = ""
+
+        if os.name == "nt":
+            # win32 barfs if any of these are ''; could be '.'?
+            # (distutils.command.install:change_roots bug)
+            basedir_observed = os.path.normpath(os.path.join(self.data_dir, ".."))
+            self.install_libbase = self.install_lib = basedir_observed
+
+        setattr(
+            install,
+            "install_purelib" if self.root_is_pure else "install_platlib",
+            basedir_observed,
+        )
+
+        log.info(f"installing to {self.bdist_dir}")
+
+        self.run_command("install")
+
+        impl_tag, abi_tag, plat_tag = self.get_tag()
+        archive_basename = f"{self.wheel_dist_name}-{impl_tag}-{abi_tag}-{plat_tag}"
+        if not self.relative:
+            archive_root = self.bdist_dir
+        else:
+            archive_root = os.path.join(
+                self.bdist_dir, self._ensure_relative(install.install_base)
+            )
+
+        self.set_undefined_options("install_egg_info", ("target", "egginfo_dir"))
+        distinfo_dirname = (
+            f"{safer_name(self.distribution.get_name())}-"
+            f"{safer_version(self.distribution.get_version())}.dist-info"
+        )
+        distinfo_dir = os.path.join(self.bdist_dir, distinfo_dirname)
+        if self.dist_info_dir:
+            # Use the given dist-info directly.
+            log.debug(f"reusing {self.dist_info_dir}")
+            shutil.copytree(self.dist_info_dir, distinfo_dir)
+            # Egg info is still generated, so remove it now to avoid it getting
+            # copied into the wheel.
+            _shutil.rmtree(self.egginfo_dir)
+        else:
+            # Convert the generated egg-info into dist-info.
+            self.egg2dist(self.egginfo_dir, distinfo_dir)
+
+        self.write_wheelfile(distinfo_dir)
+
+        # Make the archive
+        if not os.path.exists(self.dist_dir):
+            os.makedirs(self.dist_dir)
+
+        wheel_path = os.path.join(self.dist_dir, archive_basename + ".whl")
+        with WheelFile(wheel_path, "w", self._zip_compression()) as wf:
+            wf.write_files(archive_root)
+
+        # Add to 'Distribution.dist_files' so that the "upload" command works
+        getattr(self.distribution, "dist_files", []).append((
+            "bdist_wheel",
+            f"{sys.version_info.major}.{sys.version_info.minor}",
+            wheel_path,
+        ))
+
+        if not self.keep_temp:
+            log.info(f"removing {self.bdist_dir}")
+            if not self.dry_run:
+                _shutil.rmtree(self.bdist_dir)
+
+    def write_wheelfile(
+        self, wheelfile_base: str, generator: str = f"setuptools ({__version__})"
+    ) -> None:
+        from email.message import Message
+
+        msg = Message()
+        msg["Wheel-Version"] = "1.0"  # of the spec
+        msg["Generator"] = generator
+        msg["Root-Is-Purelib"] = str(self.root_is_pure).lower()
+        if self.build_number is not None:
+            msg["Build"] = self.build_number
+
+        # Doesn't work for bdist_wininst
+        impl_tag, abi_tag, plat_tag = self.get_tag()
+        for impl in impl_tag.split("."):
+            for abi in abi_tag.split("."):
+                for plat in plat_tag.split("."):
+                    msg["Tag"] = "-".join((impl, abi, plat))
+
+        wheelfile_path = os.path.join(wheelfile_base, "WHEEL")
+        log.info(f"creating {wheelfile_path}")
+        with open(wheelfile_path, "wb") as f:
+            BytesGenerator(f, maxheaderlen=0).flatten(msg)
+
+    def _ensure_relative(self, path: str) -> str:
+        # copied from dir_util, deleted
+        drive, path = os.path.splitdrive(path)
+        if path[0:1] == os.sep:
+            path = drive + path[1:]
+        return path
+
+    @property
+    def license_paths(self) -> Iterable[str]:
+        if setuptools_major_version >= 57:
+            # Setuptools has resolved any patterns to actual file names
+            return self.distribution.metadata.license_files or ()
+
+        files = set[str]()
+        metadata = self.distribution.get_option_dict("metadata")
+        if setuptools_major_version >= 42:
+            # Setuptools recognizes the license_files option but does not do globbing
+            patterns = cast(Sequence[str], self.distribution.metadata.license_files)
+        else:
+            # Prior to those, wheel is entirely responsible for handling license files
+            if "license_files" in metadata:
+                patterns = metadata["license_files"][1].split()
+            else:
+                patterns = ()
+
+        if "license_file" in metadata:
+            warnings.warn(
+                'The "license_file" option is deprecated. Use "license_files" instead.',
+                DeprecationWarning,
+                stacklevel=2,
+            )
+            files.add(metadata["license_file"][1])
+
+        if not files and not patterns and not isinstance(patterns, list):
+            patterns = ("LICEN[CS]E*", "COPYING*", "NOTICE*", "AUTHORS*")
+
+        for pattern in patterns:
+            for path in iglob(pattern):
+                if path.endswith("~"):
+                    log.debug(
+                        f'ignoring license file "{path}" as it looks like a backup'
+                    )
+                    continue
+
+                if path not in files and os.path.isfile(path):
+                    log.info(
+                        f'adding license file "{path}" (matched pattern "{pattern}")'
+                    )
+                    files.add(path)
+
+        return files
+
+    def egg2dist(self, egginfo_path: str, distinfo_path: str) -> None:
+        """Convert an .egg-info directory into a .dist-info directory"""
+
+        def adios(p: str) -> None:
+            """Appropriately delete directory, file or link."""
+            if os.path.exists(p) and not os.path.islink(p) and os.path.isdir(p):
+                _shutil.rmtree(p)
+            elif os.path.exists(p):
+                os.unlink(p)
+
+        adios(distinfo_path)
+
+        if not os.path.exists(egginfo_path):
+            # There is no egg-info. This is probably because the egg-info
+            # file/directory is not named matching the distribution name used
+            # to name the archive file. Check for this case and report
+            # accordingly.
+            import glob
+
+            pat = os.path.join(os.path.dirname(egginfo_path), "*.egg-info")
+            possible = glob.glob(pat)
+            err = f"Egg metadata expected at {egginfo_path} but not found"
+            if possible:
+                alt = os.path.basename(possible[0])
+                err += f" ({alt} found - possible misnamed archive file?)"
+
+            raise ValueError(err)
+
+        # .egg-info is a directory
+        pkginfo_path = os.path.join(egginfo_path, "PKG-INFO")
+
+        # ignore common egg metadata that is useless to wheel
+        shutil.copytree(
+            egginfo_path,
+            distinfo_path,
+            ignore=lambda x, y: {
+                "PKG-INFO",
+                "requires.txt",
+                "SOURCES.txt",
+                "not-zip-safe",
+            },
+        )
+
+        # delete dependency_links if it is only whitespace
+        dependency_links_path = os.path.join(distinfo_path, "dependency_links.txt")
+        with open(dependency_links_path, encoding="utf-8") as dependency_links_file:
+            dependency_links = dependency_links_file.read().strip()
+        if not dependency_links:
+            adios(dependency_links_path)
+
+        metadata_path = os.path.join(distinfo_path, "METADATA")
+        shutil.copy(pkginfo_path, metadata_path)
+
+        licenses_folder_path = os.path.join(distinfo_path, "licenses")
+        for license_path in self.license_paths:
+            safe_path = _safe_license_file(license_path)
+            dist_info_license_path = os.path.join(licenses_folder_path, safe_path)
+            os.makedirs(os.path.dirname(dist_info_license_path), exist_ok=True)
+            shutil.copy(license_path, dist_info_license_path)
+
+        adios(egginfo_path)
+
+    def _zip_compression(self) -> int:
+        if (
+            isinstance(self.compression, int)
+            and self.compression in self.supported_compressions.values()
+        ):
+            return self.compression
+
+        compression = self.supported_compressions.get(str(self.compression))
+        if compression is not None:
+            return compression
+
+        raise ValueError(f"Unsupported compression: {self.compression!r}")
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build.py
new file mode 100644
index 0000000000000000000000000000000000000000..54cbb8d2e7bf41de4e187613718879f2a4c3d8d3
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build.py
@@ -0,0 +1,135 @@
+from __future__ import annotations
+
+from typing import Protocol
+
+from ..dist import Distribution
+
+from distutils.command.build import build as _build
+
+_ORIGINAL_SUBCOMMANDS = {"build_py", "build_clib", "build_ext", "build_scripts"}
+
+
+class build(_build):
+    distribution: Distribution  # override distutils.dist.Distribution with setuptools.dist.Distribution
+
+    # copy to avoid sharing the object with parent class
+    sub_commands = _build.sub_commands[:]
+
+
+class SubCommand(Protocol):
+    """In order to support editable installations (see :pep:`660`) all
+    build subcommands **SHOULD** implement this protocol. They also **MUST** inherit
+    from ``setuptools.Command``.
+
+    When creating an :pep:`editable wheel <660>`, ``setuptools`` will try to evaluate
+    custom ``build`` subcommands using the following procedure:
+
+    1. ``setuptools`` will set the ``editable_mode`` attribute to ``True``
+    2. ``setuptools`` will execute the ``run()`` command.
+
+       .. important::
+          Subcommands **SHOULD** take advantage of ``editable_mode=True`` to adequate
+          its behaviour or perform optimisations.
+
+          For example, if a subcommand doesn't need to generate an extra file and
+          all it does is to copy a source file into the build directory,
+          ``run()`` **SHOULD** simply "early return".
+
+          Similarly, if the subcommand creates files that would be placed alongside
+          Python files in the final distribution, during an editable install
+          the command **SHOULD** generate these files "in place" (i.e. write them to
+          the original source directory, instead of using the build directory).
+          Note that ``get_output_mapping()`` should reflect that and include mappings
+          for "in place" builds accordingly.
+
+    3. ``setuptools`` use any knowledge it can derive from the return values of
+       ``get_outputs()`` and ``get_output_mapping()`` to create an editable wheel.
+       When relevant ``setuptools`` **MAY** attempt to use file links based on the value
+       of ``get_output_mapping()``. Alternatively, ``setuptools`` **MAY** attempt to use
+       :doc:`import hooks ` to redirect any attempt to import
+       to the directory with the original source code and other files built in place.
+
+    Please note that custom sub-commands **SHOULD NOT** rely on ``run()`` being
+    executed (or not) to provide correct return values for ``get_outputs()``,
+    ``get_output_mapping()`` or ``get_source_files()``. The ``get_*`` methods should
+    work independently of ``run()``.
+    """
+
+    editable_mode: bool = False
+    """Boolean flag that will be set to ``True`` when setuptools is used for an
+    editable installation (see :pep:`660`).
+    Implementations **SHOULD** explicitly set the default value of this attribute to
+    ``False``.
+    When subcommands run, they can use this flag to perform optimizations or change
+    their behaviour accordingly.
+    """
+
+    build_lib: str
+    """String representing the directory where the build artifacts should be stored,
+    e.g. ``build/lib``.
+    For example, if a distribution wants to provide a Python module named ``pkg.mod``,
+    then a corresponding file should be written to ``{build_lib}/package/module.py``.
+    A way of thinking about this is that the files saved under ``build_lib``
+    would be eventually copied to one of the directories in :obj:`site.PREFIXES`
+    upon installation.
+
+    A command that produces platform-independent files (e.g. compiling text templates
+    into Python functions), **CAN** initialize ``build_lib`` by copying its value from
+    the ``build_py`` command. On the other hand, a command that produces
+    platform-specific files **CAN** initialize ``build_lib`` by copying its value from
+    the ``build_ext`` command. In general this is done inside the ``finalize_options``
+    method with the help of the ``set_undefined_options`` command::
+
+        def finalize_options(self):
+            self.set_undefined_options("build_py", ("build_lib", "build_lib"))
+            ...
+    """
+
+    def initialize_options(self) -> None:
+        """(Required by the original :class:`setuptools.Command` interface)"""
+        ...
+
+    def finalize_options(self) -> None:
+        """(Required by the original :class:`setuptools.Command` interface)"""
+        ...
+
+    def run(self) -> None:
+        """(Required by the original :class:`setuptools.Command` interface)"""
+        ...
+
+    def get_source_files(self) -> list[str]:
+        """
+        Return a list of all files that are used by the command to create the expected
+        outputs.
+        For example, if your build command transpiles Java files into Python, you should
+        list here all the Java files.
+        The primary purpose of this function is to help populating the ``sdist``
+        with all the files necessary to build the distribution.
+        All files should be strings relative to the project root directory.
+        """
+        ...
+
+    def get_outputs(self) -> list[str]:
+        """
+        Return a list of files intended for distribution as they would have been
+        produced by the build.
+        These files should be strings in the form of
+        ``"{build_lib}/destination/file/path"``.
+
+        .. note::
+           The return value of ``get_output()`` should include all files used as keys
+           in ``get_output_mapping()`` plus files that are generated during the build
+           and don't correspond to any source file already present in the project.
+        """
+        ...
+
+    def get_output_mapping(self) -> dict[str, str]:
+        """
+        Return a mapping between destination files as they would be produced by the
+        build (dict keys) into the respective existing (source) files (dict values).
+        Existing (source) files should be represented as strings relative to the project
+        root directory.
+        Destination files should be strings in the form of
+        ``"{build_lib}/destination/file/path"``.
+        """
+        ...
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build_clib.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build_clib.py
new file mode 100644
index 0000000000000000000000000000000000000000..f376f4ce4d2afc4a58f1fa0e85624136edc93835
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build_clib.py
@@ -0,0 +1,103 @@
+from ..dist import Distribution
+from ..modified import newer_pairwise_group
+
+import distutils.command.build_clib as orig
+from distutils import log
+from distutils.errors import DistutilsSetupError
+
+
+class build_clib(orig.build_clib):
+    """
+    Override the default build_clib behaviour to do the following:
+
+    1. Implement a rudimentary timestamp-based dependency system
+       so 'compile()' doesn't run every time.
+    2. Add more keys to the 'build_info' dictionary:
+        * obj_deps - specify dependencies for each object compiled.
+                     this should be a dictionary mapping a key
+                     with the source filename to a list of
+                     dependencies. Use an empty string for global
+                     dependencies.
+        * cflags   - specify a list of additional flags to pass to
+                     the compiler.
+    """
+
+    distribution: Distribution  # override distutils.dist.Distribution with setuptools.dist.Distribution
+
+    def build_libraries(self, libraries) -> None:
+        for lib_name, build_info in libraries:
+            sources = build_info.get('sources')
+            if sources is None or not isinstance(sources, (list, tuple)):
+                raise DistutilsSetupError(
+                    f"in 'libraries' option (library '{lib_name}'), "
+                    "'sources' must be present and must be "
+                    "a list of source filenames"
+                )
+            sources = sorted(list(sources))
+
+            log.info("building '%s' library", lib_name)
+
+            # Make sure everything is the correct type.
+            # obj_deps should be a dictionary of keys as sources
+            # and a list/tuple of files that are its dependencies.
+            obj_deps = build_info.get('obj_deps', dict())
+            if not isinstance(obj_deps, dict):
+                raise DistutilsSetupError(
+                    f"in 'libraries' option (library '{lib_name}'), "
+                    "'obj_deps' must be a dictionary of "
+                    "type 'source: list'"
+                )
+            dependencies = []
+
+            # Get the global dependencies that are specified by the '' key.
+            # These will go into every source's dependency list.
+            global_deps = obj_deps.get('', list())
+            if not isinstance(global_deps, (list, tuple)):
+                raise DistutilsSetupError(
+                    f"in 'libraries' option (library '{lib_name}'), "
+                    "'obj_deps' must be a dictionary of "
+                    "type 'source: list'"
+                )
+
+            # Build the list to be used by newer_pairwise_group
+            # each source will be auto-added to its dependencies.
+            for source in sources:
+                src_deps = [source]
+                src_deps.extend(global_deps)
+                extra_deps = obj_deps.get(source, list())
+                if not isinstance(extra_deps, (list, tuple)):
+                    raise DistutilsSetupError(
+                        f"in 'libraries' option (library '{lib_name}'), "
+                        "'obj_deps' must be a dictionary of "
+                        "type 'source: list'"
+                    )
+                src_deps.extend(extra_deps)
+                dependencies.append(src_deps)
+
+            expected_objects = self.compiler.object_filenames(
+                sources,
+                output_dir=self.build_temp,
+            )
+
+            if newer_pairwise_group(dependencies, expected_objects) != ([], []):
+                # First, compile the source code to object files in the library
+                # directory.  (This should probably change to putting object
+                # files in a temporary build directory.)
+                macros = build_info.get('macros')
+                include_dirs = build_info.get('include_dirs')
+                cflags = build_info.get('cflags')
+                self.compiler.compile(
+                    sources,
+                    output_dir=self.build_temp,
+                    macros=macros,
+                    include_dirs=include_dirs,
+                    extra_postargs=cflags,
+                    debug=self.debug,
+                )
+
+            # Now "link" the object files together into a static library.
+            # (On Unix at least, this isn't really linking -- it just
+            # builds an archive.  Whatever.)
+            self.compiler.create_static_lib(
+                expected_objects, lib_name, output_dir=self.build_clib, debug=self.debug
+            )
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build_ext.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build_ext.py
new file mode 100644
index 0000000000000000000000000000000000000000..334fda62b8adc1da1928a6fd96adccbd98f8d96e
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build_ext.py
@@ -0,0 +1,472 @@
+from __future__ import annotations
+
+import itertools
+import operator
+import os
+import sys
+import textwrap
+from collections.abc import Iterator
+from importlib.machinery import EXTENSION_SUFFIXES
+from importlib.util import cache_from_source as _compiled_file_name
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+from setuptools.dist import Distribution
+from setuptools.errors import BaseError
+from setuptools.extension import Extension, Library
+
+from distutils import log
+from distutils.ccompiler import new_compiler
+from distutils.sysconfig import customize_compiler, get_config_var
+
+if TYPE_CHECKING:
+    # Cython not installed on CI tests, causing _build_ext to be `Any`
+    from distutils.command.build_ext import build_ext as _build_ext
+else:
+    try:
+        # Attempt to use Cython for building extensions, if available
+        from Cython.Distutils.build_ext import build_ext as _build_ext
+
+        # Additionally, assert that the compiler module will load
+        # also. Ref #1229.
+        __import__('Cython.Compiler.Main')
+    except ImportError:
+        from distutils.command.build_ext import build_ext as _build_ext
+
+# make sure _config_vars is initialized
+get_config_var("LDSHARED")
+# Not publicly exposed in typeshed distutils stubs, but this is done on purpose
+# See https://github.com/pypa/setuptools/pull/4228#issuecomment-1959856400
+from distutils.sysconfig import _config_vars as _CONFIG_VARS  # noqa: E402
+
+
+def _customize_compiler_for_shlib(compiler):
+    if sys.platform == "darwin":
+        # building .dylib requires additional compiler flags on OSX; here we
+        # temporarily substitute the pyconfig.h variables so that distutils'
+        # 'customize_compiler' uses them before we build the shared libraries.
+        tmp = _CONFIG_VARS.copy()
+        try:
+            # XXX Help!  I don't have any idea whether these are right...
+            _CONFIG_VARS['LDSHARED'] = (
+                "gcc -Wl,-x -dynamiclib -undefined dynamic_lookup"
+            )
+            _CONFIG_VARS['CCSHARED'] = " -dynamiclib"
+            _CONFIG_VARS['SO'] = ".dylib"
+            customize_compiler(compiler)
+        finally:
+            _CONFIG_VARS.clear()
+            _CONFIG_VARS.update(tmp)
+    else:
+        customize_compiler(compiler)
+
+
+have_rtld = False
+use_stubs = False
+libtype = 'shared'
+
+if sys.platform == "darwin":
+    use_stubs = True
+elif os.name != 'nt':
+    try:
+        import dl  # type: ignore[import-not-found] # https://github.com/python/mypy/issues/13002
+
+        use_stubs = have_rtld = hasattr(dl, 'RTLD_NOW')
+    except ImportError:
+        pass
+
+
+def get_abi3_suffix():
+    """Return the file extension for an abi3-compliant Extension()"""
+    for suffix in EXTENSION_SUFFIXES:
+        if '.abi3' in suffix:  # Unix
+            return suffix
+        elif suffix == '.pyd':  # Windows
+            return suffix
+    return None
+
+
+class build_ext(_build_ext):
+    distribution: Distribution  # override distutils.dist.Distribution with setuptools.dist.Distribution
+    editable_mode = False
+    inplace = False
+
+    def run(self) -> None:
+        """Build extensions in build directory, then copy if --inplace"""
+        old_inplace, self.inplace = self.inplace, False
+        _build_ext.run(self)
+        self.inplace = old_inplace
+        if old_inplace:
+            self.copy_extensions_to_source()
+
+    def _get_inplace_equivalent(self, build_py, ext: Extension) -> tuple[str, str]:
+        fullname = self.get_ext_fullname(ext.name)
+        filename = self.get_ext_filename(fullname)
+        modpath = fullname.split('.')
+        package = '.'.join(modpath[:-1])
+        package_dir = build_py.get_package_dir(package)
+        inplace_file = os.path.join(package_dir, os.path.basename(filename))
+        regular_file = os.path.join(self.build_lib, filename)
+        return (inplace_file, regular_file)
+
+    def copy_extensions_to_source(self) -> None:
+        build_py = self.get_finalized_command('build_py')
+        for ext in self.extensions:
+            inplace_file, regular_file = self._get_inplace_equivalent(build_py, ext)
+
+            # Always copy, even if source is older than destination, to ensure
+            # that the right extensions for the current Python/platform are
+            # used.
+            if os.path.exists(regular_file) or not ext.optional:
+                self.copy_file(regular_file, inplace_file, level=self.verbose)
+
+            if ext._needs_stub:
+                inplace_stub = self._get_equivalent_stub(ext, inplace_file)
+                self._write_stub_file(inplace_stub, ext, compile=True)
+                # Always compile stub and remove the original (leave the cache behind)
+                # (this behaviour was observed in previous iterations of the code)
+
+    def _get_equivalent_stub(self, ext: Extension, output_file: str) -> str:
+        dir_ = os.path.dirname(output_file)
+        _, _, name = ext.name.rpartition(".")
+        return f"{os.path.join(dir_, name)}.py"
+
+    def _get_output_mapping(self) -> Iterator[tuple[str, str]]:
+        if not self.inplace:
+            return
+
+        build_py = self.get_finalized_command('build_py')
+        opt = self.get_finalized_command('install_lib').optimize or ""
+
+        for ext in self.extensions:
+            inplace_file, regular_file = self._get_inplace_equivalent(build_py, ext)
+            yield (regular_file, inplace_file)
+
+            if ext._needs_stub:
+                # This version of `build_ext` always builds artifacts in another dir,
+                # when "inplace=True" is given it just copies them back.
+                # This is done in the `copy_extensions_to_source` function, which
+                # always compile stub files via `_compile_and_remove_stub`.
+                # At the end of the process, a `.pyc` stub file is created without the
+                # corresponding `.py`.
+
+                inplace_stub = self._get_equivalent_stub(ext, inplace_file)
+                regular_stub = self._get_equivalent_stub(ext, regular_file)
+                inplace_cache = _compiled_file_name(inplace_stub, optimization=opt)
+                output_cache = _compiled_file_name(regular_stub, optimization=opt)
+                yield (output_cache, inplace_cache)
+
+    def get_ext_filename(self, fullname: str) -> str:
+        so_ext = os.getenv('SETUPTOOLS_EXT_SUFFIX')
+        if so_ext:
+            filename = os.path.join(*fullname.split('.')) + so_ext
+        else:
+            filename = _build_ext.get_ext_filename(self, fullname)
+            ext_suffix = get_config_var('EXT_SUFFIX')
+            if not isinstance(ext_suffix, str):
+                raise OSError(
+                    "Configuration variable EXT_SUFFIX not found for this platform "
+                    "and environment variable SETUPTOOLS_EXT_SUFFIX is missing"
+                )
+            so_ext = ext_suffix
+
+        if fullname in self.ext_map:
+            ext = self.ext_map[fullname]
+            abi3_suffix = get_abi3_suffix()
+            if ext.py_limited_api and abi3_suffix:  # Use abi3
+                filename = filename[: -len(so_ext)] + abi3_suffix
+            if isinstance(ext, Library):
+                fn, ext = os.path.splitext(filename)
+                return self.shlib_compiler.library_filename(fn, libtype)
+            elif use_stubs and ext._links_to_dynamic:
+                d, fn = os.path.split(filename)
+                return os.path.join(d, 'dl-' + fn)
+        return filename
+
+    def initialize_options(self):
+        _build_ext.initialize_options(self)
+        self.shlib_compiler = None
+        self.shlibs = []
+        self.ext_map = {}
+        self.editable_mode = False
+
+    def finalize_options(self) -> None:
+        _build_ext.finalize_options(self)
+        self.extensions = self.extensions or []
+        self.check_extensions_list(self.extensions)
+        self.shlibs = [ext for ext in self.extensions if isinstance(ext, Library)]
+        if self.shlibs:
+            self.setup_shlib_compiler()
+        for ext in self.extensions:
+            ext._full_name = self.get_ext_fullname(ext.name)
+        for ext in self.extensions:
+            fullname = ext._full_name
+            self.ext_map[fullname] = ext
+
+            # distutils 3.1 will also ask for module names
+            # XXX what to do with conflicts?
+            self.ext_map[fullname.split('.')[-1]] = ext
+
+            ltd = self.shlibs and self.links_to_dynamic(ext) or False
+            ns = ltd and use_stubs and not isinstance(ext, Library)
+            ext._links_to_dynamic = ltd
+            ext._needs_stub = ns
+            filename = ext._file_name = self.get_ext_filename(fullname)
+            libdir = os.path.dirname(os.path.join(self.build_lib, filename))
+            if ltd and libdir not in ext.library_dirs:
+                ext.library_dirs.append(libdir)
+            if ltd and use_stubs and os.curdir not in ext.runtime_library_dirs:
+                ext.runtime_library_dirs.append(os.curdir)
+
+        if self.editable_mode:
+            self.inplace = True
+
+    def setup_shlib_compiler(self) -> None:
+        compiler = self.shlib_compiler = new_compiler(
+            compiler=self.compiler, dry_run=self.dry_run, force=self.force
+        )
+        _customize_compiler_for_shlib(compiler)
+
+        if self.include_dirs is not None:
+            compiler.set_include_dirs(self.include_dirs)
+        if self.define is not None:
+            # 'define' option is a list of (name,value) tuples
+            for name, value in self.define:
+                compiler.define_macro(name, value)
+        if self.undef is not None:
+            for macro in self.undef:
+                compiler.undefine_macro(macro)
+        if self.libraries is not None:
+            compiler.set_libraries(self.libraries)
+        if self.library_dirs is not None:
+            compiler.set_library_dirs(self.library_dirs)
+        if self.rpath is not None:
+            compiler.set_runtime_library_dirs(self.rpath)
+        if self.link_objects is not None:
+            compiler.set_link_objects(self.link_objects)
+
+        # hack so distutils' build_extension() builds a library instead
+        compiler.link_shared_object = link_shared_object.__get__(compiler)  # type: ignore[method-assign]
+
+    def get_export_symbols(self, ext):
+        if isinstance(ext, Library):
+            return ext.export_symbols
+        return _build_ext.get_export_symbols(self, ext)
+
+    def build_extension(self, ext) -> None:
+        ext._convert_pyx_sources_to_lang()
+        _compiler = self.compiler
+        try:
+            if isinstance(ext, Library):
+                self.compiler = self.shlib_compiler
+            _build_ext.build_extension(self, ext)
+            if ext._needs_stub:
+                build_lib = self.get_finalized_command('build_py').build_lib
+                self.write_stub(build_lib, ext)
+        finally:
+            self.compiler = _compiler
+
+    def links_to_dynamic(self, ext):
+        """Return true if 'ext' links to a dynamic lib in the same package"""
+        # XXX this should check to ensure the lib is actually being built
+        # XXX as dynamic, and not just using a locally-found version or a
+        # XXX static-compiled version
+        libnames = dict.fromkeys([lib._full_name for lib in self.shlibs])
+        pkg = '.'.join(ext._full_name.split('.')[:-1] + [''])
+        return any(pkg + libname in libnames for libname in ext.libraries)
+
+    def get_source_files(self) -> list[str]:
+        return [*_build_ext.get_source_files(self), *self._get_internal_depends()]
+
+    def _get_internal_depends(self) -> Iterator[str]:
+        """Yield ``ext.depends`` that are contained by the project directory"""
+        project_root = Path(self.distribution.src_root or os.curdir).resolve()
+        depends = (dep for ext in self.extensions for dep in ext.depends)
+
+        def skip(orig_path: str, reason: str) -> None:
+            log.info(
+                "dependency %s won't be automatically "
+                "included in the manifest: the path %s",
+                orig_path,
+                reason,
+            )
+
+        for dep in depends:
+            path = Path(dep)
+
+            if path.is_absolute():
+                skip(dep, "must be relative")
+                continue
+
+            if ".." in path.parts:
+                skip(dep, "can't have `..` segments")
+                continue
+
+            try:
+                resolved = (project_root / path).resolve(strict=True)
+            except OSError:
+                skip(dep, "doesn't exist")
+                continue
+
+            try:
+                resolved.relative_to(project_root)
+            except ValueError:
+                skip(dep, "must be inside the project root")
+                continue
+
+            yield path.as_posix()
+
+    def get_outputs(self) -> list[str]:
+        if self.inplace:
+            return list(self.get_output_mapping().keys())
+        return sorted(_build_ext.get_outputs(self) + self.__get_stubs_outputs())
+
+    def get_output_mapping(self) -> dict[str, str]:
+        """See :class:`setuptools.commands.build.SubCommand`"""
+        mapping = self._get_output_mapping()
+        return dict(sorted(mapping, key=operator.itemgetter(0)))
+
+    def __get_stubs_outputs(self):
+        # assemble the base name for each extension that needs a stub
+        ns_ext_bases = (
+            os.path.join(self.build_lib, *ext._full_name.split('.'))
+            for ext in self.extensions
+            if ext._needs_stub
+        )
+        # pair each base with the extension
+        pairs = itertools.product(ns_ext_bases, self.__get_output_extensions())
+        return list(base + fnext for base, fnext in pairs)
+
+    def __get_output_extensions(self):
+        yield '.py'
+        yield '.pyc'
+        if self.get_finalized_command('build_py').optimize:
+            yield '.pyo'
+
+    def write_stub(self, output_dir, ext, compile=False) -> None:
+        stub_file = os.path.join(output_dir, *ext._full_name.split('.')) + '.py'
+        self._write_stub_file(stub_file, ext, compile)
+
+    def _write_stub_file(self, stub_file: str, ext: Extension, compile=False):
+        log.info("writing stub loader for %s to %s", ext._full_name, stub_file)
+        if compile and os.path.exists(stub_file):
+            raise BaseError(stub_file + " already exists! Please delete.")
+        if not self.dry_run:
+            with open(stub_file, 'w', encoding="utf-8") as f:
+                content = (
+                    textwrap
+                    .dedent(f"""
+                    def __bootstrap__():
+                       global __bootstrap__, __file__, __loader__
+                       import sys, os, importlib.resources as irs, importlib.util
+                    #rtld   import dl
+                       with irs.files(__name__).joinpath(
+                         {os.path.basename(ext._file_name)!r}) as __file__:
+                          del __bootstrap__
+                          if '__loader__' in globals():
+                              del __loader__
+                    #rtld      old_flags = sys.getdlopenflags()
+                          old_dir = os.getcwd()
+                          try:
+                            os.chdir(os.path.dirname(__file__))
+                    #rtld        sys.setdlopenflags(dl.RTLD_NOW)
+                            spec = importlib.util.spec_from_file_location(
+                                       __name__, __file__)
+                            mod = importlib.util.module_from_spec(spec)
+                            spec.loader.exec_module(mod)
+                          finally:
+                    #rtld        sys.setdlopenflags(old_flags)
+                            os.chdir(old_dir)
+                    __bootstrap__()
+                    """)
+                    .lstrip()
+                    .replace('#rtld', '#rtld' * (not have_rtld))
+                )
+                f.write(content)
+        if compile:
+            self._compile_and_remove_stub(stub_file)
+
+    def _compile_and_remove_stub(self, stub_file: str):
+        from distutils.util import byte_compile
+
+        byte_compile([stub_file], optimize=0, force=True, dry_run=self.dry_run)
+        optimize = self.get_finalized_command('install_lib').optimize
+        if optimize > 0:
+            byte_compile(
+                [stub_file],
+                optimize=optimize,
+                force=True,
+                dry_run=self.dry_run,
+            )
+        if os.path.exists(stub_file) and not self.dry_run:
+            os.unlink(stub_file)
+
+
+if use_stubs or os.name == 'nt':
+    # Build shared libraries
+    #
+    def link_shared_object(
+        self,
+        objects,
+        output_libname,
+        output_dir=None,
+        libraries=None,
+        library_dirs=None,
+        runtime_library_dirs=None,
+        export_symbols=None,
+        debug: bool = False,
+        extra_preargs=None,
+        extra_postargs=None,
+        build_temp=None,
+        target_lang=None,
+    ) -> None:
+        self.link(
+            self.SHARED_LIBRARY,
+            objects,
+            output_libname,
+            output_dir,
+            libraries,
+            library_dirs,
+            runtime_library_dirs,
+            export_symbols,
+            debug,
+            extra_preargs,
+            extra_postargs,
+            build_temp,
+            target_lang,
+        )
+
+else:
+    # Build static libraries everywhere else
+    libtype = 'static'
+
+    def link_shared_object(
+        self,
+        objects,
+        output_libname,
+        output_dir=None,
+        libraries=None,
+        library_dirs=None,
+        runtime_library_dirs=None,
+        export_symbols=None,
+        debug: bool = False,
+        extra_preargs=None,
+        extra_postargs=None,
+        build_temp=None,
+        target_lang=None,
+    ) -> None:
+        # XXX we need to either disallow these attrs on Library instances,
+        # or warn/abort here if set, or something...
+        # libraries=None, library_dirs=None, runtime_library_dirs=None,
+        # export_symbols=None, extra_preargs=None, extra_postargs=None,
+        # build_temp=None
+
+        assert output_dir is None  # distutils build_ext doesn't pass this
+        output_dir, filename = os.path.split(output_libname)
+        basename, _ext = os.path.splitext(filename)
+        if self.library_filename("x").startswith('lib'):
+            # strip 'lib' prefix; this is kludgy if some platform uses
+            # a different prefix
+            basename = basename[3:]
+
+        self.create_static_lib(objects, basename, output_dir, debug, target_lang)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build_py.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build_py.py
new file mode 100644
index 0000000000000000000000000000000000000000..3c7c2d1bd6ac84dfaf82a0906d34cb30f69b9dc3
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/build_py.py
@@ -0,0 +1,403 @@
+from __future__ import annotations
+
+import fnmatch
+import itertools
+import operator
+import os
+import stat
+import textwrap
+from collections.abc import Iterable, Iterator
+from functools import partial
+from glob import glob
+from pathlib import Path
+from typing import Any
+
+from more_itertools import unique_everseen
+
+from .._path import StrPath, StrPathT
+from ..dist import Distribution
+from ..warnings import SetuptoolsDeprecationWarning
+
+import distutils.command.build_py as orig
+import distutils.errors
+from distutils.util import convert_path
+
+_IMPLICIT_DATA_FILES = ('*.pyi', 'py.typed')
+
+
+def make_writable(target) -> None:
+    os.chmod(target, os.stat(target).st_mode | stat.S_IWRITE)
+
+
+class build_py(orig.build_py):
+    """Enhanced 'build_py' command that includes data files with packages
+
+    The data files are specified via a 'package_data' argument to 'setup()'.
+    See 'setuptools.dist.Distribution' for more details.
+
+    Also, this version of the 'build_py' command allows you to specify both
+    'py_modules' and 'packages' in the same setup operation.
+    """
+
+    distribution: Distribution  # override distutils.dist.Distribution with setuptools.dist.Distribution
+    editable_mode: bool = False
+    existing_egg_info_dir: StrPath | None = None  #: Private API, internal use only.
+
+    def finalize_options(self) -> None:
+        orig.build_py.finalize_options(self)
+        self.package_data = self.distribution.package_data
+        self.exclude_package_data = self.distribution.exclude_package_data or {}
+        if 'data_files' in self.__dict__:
+            del self.__dict__['data_files']
+
+    def copy_file(  # type: ignore[override] # No overload, no bytes support
+        self,
+        infile: StrPath,
+        outfile: StrPathT,
+        preserve_mode: bool = True,
+        preserve_times: bool = True,
+        link: str | None = None,
+        level: object = 1,
+    ) -> tuple[StrPathT | str, bool]:
+        # Overwrite base class to allow using links
+        if link:
+            infile = str(Path(infile).resolve())
+            outfile = str(Path(outfile).resolve())  # type: ignore[assignment] # Re-assigning a str when outfile is StrPath is ok
+        return super().copy_file(  # pyright: ignore[reportReturnType] # pypa/distutils#309
+            infile, outfile, preserve_mode, preserve_times, link, level
+        )
+
+    def run(self) -> None:
+        """Build modules, packages, and copy data files to build directory"""
+        if not (self.py_modules or self.packages) or self.editable_mode:
+            return
+
+        if self.py_modules:
+            self.build_modules()
+
+        if self.packages:
+            self.build_packages()
+            self.build_package_data()
+
+        # Only compile actual .py files, using our base class' idea of what our
+        # output files are.
+        self.byte_compile(orig.build_py.get_outputs(self, include_bytecode=False))
+
+    # Should return "list[tuple[str, str, str, list[str]]] | Any" but can't do without typed distutils on Python 3.12+
+    def __getattr__(self, attr: str) -> Any:
+        "lazily compute data files"
+        if attr == 'data_files':
+            self.data_files = self._get_data_files()
+            return self.data_files
+        return orig.build_py.__getattr__(self, attr)
+
+    def _get_data_files(self):
+        """Generate list of '(package,src_dir,build_dir,filenames)' tuples"""
+        self.analyze_manifest()
+        return list(map(self._get_pkg_data_files, self.packages or ()))
+
+    def get_data_files_without_manifest(self) -> list[tuple[str, str, str, list[str]]]:
+        """
+        Generate list of ``(package,src_dir,build_dir,filenames)`` tuples,
+        but without triggering any attempt to analyze or build the manifest.
+        """
+        # Prevent eventual errors from unset `manifest_files`
+        # (that would otherwise be set by `analyze_manifest`)
+        self.__dict__.setdefault('manifest_files', {})
+        return list(map(self._get_pkg_data_files, self.packages or ()))
+
+    def _get_pkg_data_files(self, package: str) -> tuple[str, str, str, list[str]]:
+        # Locate package source directory
+        src_dir = self.get_package_dir(package)
+
+        # Compute package build directory
+        build_dir = os.path.join(*([self.build_lib] + package.split('.')))
+
+        # Strip directory from globbed filenames
+        filenames = [
+            os.path.relpath(file, src_dir)
+            for file in self.find_data_files(package, src_dir)
+        ]
+        return package, src_dir, build_dir, filenames
+
+    def find_data_files(self, package, src_dir):
+        """Return filenames for package's data files in 'src_dir'"""
+        patterns = self._get_platform_patterns(
+            self.package_data,
+            package,
+            src_dir,
+            extra_patterns=_IMPLICIT_DATA_FILES,
+        )
+        globs_expanded = map(partial(glob, recursive=True), patterns)
+        # flatten the expanded globs into an iterable of matches
+        globs_matches = itertools.chain.from_iterable(globs_expanded)
+        glob_files = filter(os.path.isfile, globs_matches)
+        files = itertools.chain(
+            self.manifest_files.get(package, []),
+            glob_files,
+        )
+        return self.exclude_data_files(package, src_dir, files)
+
+    def get_outputs(self, include_bytecode: bool = True) -> list[str]:  # type: ignore[override] # Using a real boolean instead of 0|1
+        """See :class:`setuptools.commands.build.SubCommand`"""
+        if self.editable_mode:
+            return list(self.get_output_mapping().keys())
+        return super().get_outputs(include_bytecode)
+
+    def get_output_mapping(self) -> dict[str, str]:
+        """See :class:`setuptools.commands.build.SubCommand`"""
+        mapping = itertools.chain(
+            self._get_package_data_output_mapping(),
+            self._get_module_mapping(),
+        )
+        return dict(sorted(mapping, key=operator.itemgetter(0)))
+
+    def _get_module_mapping(self) -> Iterator[tuple[str, str]]:
+        """Iterate over all modules producing (dest, src) pairs."""
+        for package, module, module_file in self.find_all_modules():
+            package = package.split('.')
+            filename = self.get_module_outfile(self.build_lib, package, module)
+            yield (filename, module_file)
+
+    def _get_package_data_output_mapping(self) -> Iterator[tuple[str, str]]:
+        """Iterate over package data producing (dest, src) pairs."""
+        for package, src_dir, build_dir, filenames in self.data_files:
+            for filename in filenames:
+                target = os.path.join(build_dir, filename)
+                srcfile = os.path.join(src_dir, filename)
+                yield (target, srcfile)
+
+    def build_package_data(self) -> None:
+        """Copy data files into build directory"""
+        for target, srcfile in self._get_package_data_output_mapping():
+            self.mkpath(os.path.dirname(target))
+            _outf, _copied = self.copy_file(srcfile, target)
+            make_writable(target)
+
+    def analyze_manifest(self) -> None:
+        self.manifest_files: dict[str, list[str]] = {}
+        if not self.distribution.include_package_data:
+            return
+        src_dirs: dict[str, str] = {}
+        for package in self.packages or ():
+            # Locate package source directory
+            src_dirs[assert_relative(self.get_package_dir(package))] = package
+
+        if (
+            self.existing_egg_info_dir
+            and Path(self.existing_egg_info_dir, "SOURCES.txt").exists()
+        ):
+            egg_info_dir = self.existing_egg_info_dir
+            manifest = Path(egg_info_dir, "SOURCES.txt")
+            files = manifest.read_text(encoding="utf-8").splitlines()
+        else:
+            self.run_command('egg_info')
+            ei_cmd = self.get_finalized_command('egg_info')
+            egg_info_dir = ei_cmd.egg_info
+            files = ei_cmd.filelist.files
+
+        check = _IncludePackageDataAbuse()
+        for path in self._filter_build_files(files, egg_info_dir):
+            d, f = os.path.split(assert_relative(path))
+            prev = None
+            oldf = f
+            while d and d != prev and d not in src_dirs:
+                prev = d
+                d, df = os.path.split(d)
+                f = os.path.join(df, f)
+            if d in src_dirs:
+                if f == oldf:
+                    if check.is_module(f):
+                        continue  # it's a module, not data
+                else:
+                    importable = check.importable_subpackage(src_dirs[d], f)
+                    if importable:
+                        check.warn(importable)
+                self.manifest_files.setdefault(src_dirs[d], []).append(path)
+
+    def _filter_build_files(
+        self, files: Iterable[str], egg_info: StrPath
+    ) -> Iterator[str]:
+        """
+        ``build_meta`` may try to create egg_info outside of the project directory,
+        and this can be problematic for certain plugins (reported in issue #3500).
+
+        Extensions might also include between their sources files created on the
+        ``build_lib`` and ``build_temp`` directories.
+
+        This function should filter this case of invalid files out.
+        """
+        build = self.get_finalized_command("build")
+        build_dirs = (egg_info, self.build_lib, build.build_temp, build.build_base)
+        norm_dirs = [os.path.normpath(p) for p in build_dirs if p]
+
+        for file in files:
+            norm_path = os.path.normpath(file)
+            if not os.path.isabs(file) or all(d not in norm_path for d in norm_dirs):
+                yield file
+
+    def get_data_files(self) -> None:
+        pass  # Lazily compute data files in _get_data_files() function.
+
+    def check_package(self, package, package_dir):
+        """Check namespace packages' __init__ for declare_namespace"""
+        try:
+            return self.packages_checked[package]
+        except KeyError:
+            pass
+
+        init_py = orig.build_py.check_package(self, package, package_dir)
+        self.packages_checked[package] = init_py
+
+        if not init_py or not self.distribution.namespace_packages:
+            return init_py
+
+        for pkg in self.distribution.namespace_packages:
+            if pkg == package or pkg.startswith(package + '.'):
+                break
+        else:
+            return init_py
+
+        with open(init_py, 'rb') as f:
+            contents = f.read()
+        if b'declare_namespace' not in contents:
+            raise distutils.errors.DistutilsError(
+                f"Namespace package problem: {package} is a namespace package, but "
+                "its\n__init__.py does not call declare_namespace()! Please "
+                'fix it.\n(See the setuptools manual under '
+                '"Namespace Packages" for details.)\n"'
+            )
+        return init_py
+
+    def initialize_options(self):
+        self.packages_checked = {}
+        orig.build_py.initialize_options(self)
+        self.editable_mode = False
+        self.existing_egg_info_dir = None
+
+    def get_package_dir(self, package: str) -> str:
+        res = orig.build_py.get_package_dir(self, package)
+        if self.distribution.src_root is not None:
+            return os.path.join(self.distribution.src_root, res)
+        return res
+
+    def exclude_data_files(self, package, src_dir, files):
+        """Filter filenames for package's data files in 'src_dir'"""
+        files = list(files)
+        patterns = self._get_platform_patterns(
+            self.exclude_package_data,
+            package,
+            src_dir,
+        )
+        match_groups = (fnmatch.filter(files, pattern) for pattern in patterns)
+        # flatten the groups of matches into an iterable of matches
+        matches = itertools.chain.from_iterable(match_groups)
+        bad = set(matches)
+        keepers = (fn for fn in files if fn not in bad)
+        # ditch dupes
+        return list(unique_everseen(keepers))
+
+    @staticmethod
+    def _get_platform_patterns(spec, package, src_dir, extra_patterns=()):
+        """
+        yield platform-specific path patterns (suitable for glob
+        or fn_match) from a glob-based spec (such as
+        self.package_data or self.exclude_package_data)
+        matching package in src_dir.
+        """
+        raw_patterns = itertools.chain(
+            extra_patterns,
+            spec.get('', []),
+            spec.get(package, []),
+        )
+        return (
+            # Each pattern has to be converted to a platform-specific path
+            os.path.join(src_dir, convert_path(pattern))
+            for pattern in raw_patterns
+        )
+
+
+def assert_relative(path):
+    if not os.path.isabs(path):
+        return path
+    from distutils.errors import DistutilsSetupError
+
+    msg = (
+        textwrap.dedent(
+            """
+        Error: setup script specifies an absolute path:
+
+            %s
+
+        setup() arguments must *always* be /-separated paths relative to the
+        setup.py directory, *never* absolute paths.
+        """
+        ).lstrip()
+        % path
+    )
+    raise DistutilsSetupError(msg)
+
+
+class _IncludePackageDataAbuse:
+    """Inform users that package or module is included as 'data file'"""
+
+    class _Warning(SetuptoolsDeprecationWarning):
+        _SUMMARY = """
+        Package {importable!r} is absent from the `packages` configuration.
+        """
+
+        _DETAILS = """
+        ############################
+        # Package would be ignored #
+        ############################
+        Python recognizes {importable!r} as an importable package[^1],
+        but it is absent from setuptools' `packages` configuration.
+
+        This leads to an ambiguous overall configuration. If you want to distribute this
+        package, please make sure that {importable!r} is explicitly added
+        to the `packages` configuration field.
+
+        Alternatively, you can also rely on setuptools' discovery methods
+        (for example by using `find_namespace_packages(...)`/`find_namespace:`
+        instead of `find_packages(...)`/`find:`).
+
+        You can read more about "package discovery" on setuptools documentation page:
+
+        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
+
+        If you don't want {importable!r} to be distributed and are
+        already explicitly excluding {importable!r} via
+        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
+        you can try to use `exclude_package_data`, or `include-package-data=False` in
+        combination with a more fine grained `package-data` configuration.
+
+        You can read more about "package data files" on setuptools documentation page:
+
+        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html
+
+
+        [^1]: For Python, any directory (with suitable naming) can be imported,
+              even if it does not contain any `.py` files.
+              On the other hand, currently there is no concept of package data
+              directory, all directories are treated like packages.
+        """
+        # _DUE_DATE: still not defined as this is particularly controversial.
+        # Warning initially introduced in May 2022. See issue #3340 for discussion.
+
+    def __init__(self) -> None:
+        self._already_warned = set[str]()
+
+    def is_module(self, file):
+        return file.endswith(".py") and file[: -len(".py")].isidentifier()
+
+    def importable_subpackage(self, parent, file):
+        pkg = Path(file).parent
+        parts = list(itertools.takewhile(str.isidentifier, pkg.parts))
+        if parts:
+            return ".".join([parent, *parts])
+        return None
+
+    def warn(self, importable):
+        if importable not in self._already_warned:
+            self._Warning.emit(importable=importable)
+            self._already_warned.add(importable)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/develop.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/develop.py
new file mode 100644
index 0000000000000000000000000000000000000000..2d468845e5d802a1c2891f6ed31d43c0fed26ec2
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/develop.py
@@ -0,0 +1,58 @@
+import site
+import subprocess
+import sys
+from typing import cast
+
+from setuptools import Command
+from setuptools.warnings import SetuptoolsDeprecationWarning
+
+
+class develop(Command):
+    """Set up package for development"""
+
+    user_options = [
+        ("install-dir=", "d", "install package to DIR"),
+        ('no-deps', 'N', "don't install dependencies"),
+        ('user', None, f"install in user site-package '{site.USER_SITE}'"),
+        ('prefix=', None, "installation prefix"),
+        ("index-url=", "i", "base URL of Python Package Index"),
+    ]
+    boolean_options = [
+        'no-deps',
+        'user',
+    ]
+
+    install_dir = None
+    no_deps = False
+    user = False
+    prefix = None
+    index_url = None
+
+    def run(self) -> None:
+        # Casting because mypy doesn't understand bool mult conditionals
+        cmd = cast(
+            list[str],
+            [sys.executable, '-m', 'pip', 'install', '-e', '.', '--use-pep517']
+            + ['--target', self.install_dir] * bool(self.install_dir)
+            + ['--no-deps'] * self.no_deps
+            + ['--user'] * self.user
+            + ['--prefix', self.prefix] * bool(self.prefix)
+            + ['--index-url', self.index_url] * bool(self.index_url),
+        )
+        subprocess.check_call(cmd)
+
+    def initialize_options(self) -> None:
+        DevelopDeprecationWarning.emit()
+
+    def finalize_options(self) -> None:
+        pass
+
+
+class DevelopDeprecationWarning(SetuptoolsDeprecationWarning):
+    _SUMMARY = "develop command is deprecated."
+    _DETAILS = """
+    Please avoid running ``setup.py`` and ``develop``.
+    Instead, use standards-based tools like pip or uv.
+    """
+    _SEE_URL = "https://github.com/pypa/setuptools/issues/917"
+    _DUE_DATE = 2025, 10, 31
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/dist_info.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/dist_info.py
new file mode 100644
index 0000000000000000000000000000000000000000..dca01ff0ce355dfd375512e4a06b05b909ee41b6
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/dist_info.py
@@ -0,0 +1,103 @@
+"""
+Create a dist_info directory
+As defined in the wheel specification
+"""
+
+import os
+import shutil
+from contextlib import contextmanager
+from pathlib import Path
+from typing import cast
+
+from .. import _normalization
+from .._shutil import rmdir as _rm
+from .egg_info import egg_info as egg_info_cls
+
+from distutils import log
+from distutils.core import Command
+
+
+class dist_info(Command):
+    """
+    This command is private and reserved for internal use of setuptools,
+    users should rely on ``setuptools.build_meta`` APIs.
+    """
+
+    description = "DO NOT CALL DIRECTLY, INTERNAL ONLY: create .dist-info directory"
+
+    user_options = [
+        (
+            'output-dir=',
+            'o',
+            "directory inside of which the .dist-info will be"
+            "created [default: top of the source tree]",
+        ),
+        ('tag-date', 'd', "Add date stamp (e.g. 20050528) to version number"),
+        ('tag-build=', 'b', "Specify explicit tag to add to version number"),
+        ('no-date', 'D', "Don't include date stamp [default]"),
+        ('keep-egg-info', None, "*TRANSITIONAL* will be removed in the future"),
+    ]
+
+    boolean_options = ['tag-date', 'keep-egg-info']
+    negative_opt = {'no-date': 'tag-date'}
+
+    def initialize_options(self):
+        self.output_dir = None
+        self.name = None
+        self.dist_info_dir = None
+        self.tag_date = None
+        self.tag_build = None
+        self.keep_egg_info = False
+
+    def finalize_options(self) -> None:
+        dist = self.distribution
+        project_dir = dist.src_root or os.curdir
+        self.output_dir = Path(self.output_dir or project_dir)
+
+        egg_info = cast(egg_info_cls, self.reinitialize_command("egg_info"))
+        egg_info.egg_base = str(self.output_dir)
+
+        if self.tag_date:
+            egg_info.tag_date = self.tag_date
+        else:
+            self.tag_date = egg_info.tag_date
+
+        if self.tag_build:
+            egg_info.tag_build = self.tag_build
+        else:
+            self.tag_build = egg_info.tag_build
+
+        egg_info.finalize_options()
+        self.egg_info = egg_info
+
+        name = _normalization.safer_name(dist.get_name())
+        version = _normalization.safer_best_effort_version(dist.get_version())
+        self.name = f"{name}-{version}"
+        self.dist_info_dir = os.path.join(self.output_dir, f"{self.name}.dist-info")
+
+    @contextmanager
+    def _maybe_bkp_dir(self, dir_path: str, requires_bkp: bool):
+        if requires_bkp:
+            bkp_name = f"{dir_path}.__bkp__"
+            _rm(bkp_name, ignore_errors=True)
+            shutil.copytree(dir_path, bkp_name, dirs_exist_ok=True, symlinks=True)
+            try:
+                yield
+            finally:
+                _rm(dir_path, ignore_errors=True)
+                shutil.move(bkp_name, dir_path)
+        else:
+            yield
+
+    def run(self) -> None:
+        self.output_dir.mkdir(parents=True, exist_ok=True)
+        self.egg_info.run()
+        egg_info_dir = self.egg_info.egg_info
+        assert os.path.isdir(egg_info_dir), ".egg-info dir should have been created"
+
+        log.info(f"creating '{os.path.abspath(self.dist_info_dir)}'")
+        bdist_wheel = self.get_finalized_command('bdist_wheel')
+
+        # TODO: if bdist_wheel if merged into setuptools, just add "keep_egg_info" there
+        with self._maybe_bkp_dir(egg_info_dir, self.keep_egg_info):
+            bdist_wheel.egg2dist(egg_info_dir, self.dist_info_dir)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/easy_install.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/easy_install.py
new file mode 100644
index 0000000000000000000000000000000000000000..8765793d4cdec9e47982f4817e56cb32323c21b9
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/easy_install.py
@@ -0,0 +1,30 @@
+import os
+import sys
+import types
+
+from setuptools import Command
+
+from .. import _scripts, warnings
+
+
+class easy_install(Command):
+    """Stubbed command for temporary pbr compatibility."""
+
+
+def __getattr__(name):
+    attr = getattr(
+        types.SimpleNamespace(
+            ScriptWriter=_scripts.ScriptWriter,
+            sys_executable=os.environ.get(
+                "__PYVENV_LAUNCHER__", os.path.normpath(sys.executable)
+            ),
+        ),
+        name,
+    )
+    warnings.SetuptoolsDeprecationWarning.emit(
+        summary="easy_install module is deprecated",
+        details="Avoid accessing attributes of setuptools.command.easy_install.",
+        due_date=(2025, 10, 31),
+        see_url="https://github.com/pypa/setuptools/issues/4976",
+    )
+    return attr
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/editable_wheel.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/editable_wheel.py
new file mode 100644
index 0000000000000000000000000000000000000000..d1d9e79b39c055e95a5231caa57b273f3a582c37
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/editable_wheel.py
@@ -0,0 +1,915 @@
+"""
+Create a wheel that, when installed, will make the source package 'editable'
+(add it to the interpreter's path, including metadata) per PEP 660. Replaces
+'setup.py develop'.
+
+.. note::
+   One of the mechanisms briefly mentioned in PEP 660 to implement editable installs is
+   to create a separated directory inside ``build`` and use a .pth file to point to that
+   directory. In the context of this file such directory is referred as
+   *auxiliary build directory* or ``auxiliary_dir``.
+"""
+
+from __future__ import annotations
+
+import io
+import logging
+import operator
+import os
+import shutil
+import traceback
+from collections.abc import Iterable, Iterator, Mapping
+from contextlib import suppress
+from enum import Enum
+from inspect import cleandoc
+from itertools import chain, starmap
+from pathlib import Path
+from tempfile import TemporaryDirectory
+from types import TracebackType
+from typing import TYPE_CHECKING, Protocol, TypeVar, cast
+
+from .. import Command, _normalization, _path, _shutil, errors, namespaces
+from .._path import StrPath
+from ..compat import py310, py312
+from ..discovery import find_package_path
+from ..dist import Distribution
+from ..warnings import InformationOnly, SetuptoolsDeprecationWarning
+from .build import build as build_cls
+from .build_py import build_py as build_py_cls
+from .dist_info import dist_info as dist_info_cls
+from .egg_info import egg_info as egg_info_cls
+from .install import install as install_cls
+from .install_scripts import install_scripts as install_scripts_cls
+
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
+    from .._vendor.wheel.wheelfile import WheelFile
+
+_P = TypeVar("_P", bound=StrPath)
+_logger = logging.getLogger(__name__)
+
+
+class _EditableMode(Enum):
+    """
+    Possible editable installation modes:
+    `lenient` (new files automatically added to the package - DEFAULT);
+    `strict` (requires a new installation when files are added/removed); or
+    `compat` (attempts to emulate `python setup.py develop` - DEPRECATED).
+    """
+
+    STRICT = "strict"
+    LENIENT = "lenient"
+    COMPAT = "compat"  # TODO: Remove `compat` after Dec/2022.
+
+    @classmethod
+    def convert(cls, mode: str | None) -> _EditableMode:
+        if not mode:
+            return _EditableMode.LENIENT  # default
+
+        _mode = mode.upper()
+        if _mode not in _EditableMode.__members__:
+            raise errors.OptionError(f"Invalid editable mode: {mode!r}. Try: 'strict'.")
+
+        if _mode == "COMPAT":
+            SetuptoolsDeprecationWarning.emit(
+                "Compat editable installs",
+                """
+                The 'compat' editable mode is transitional and will be removed
+                in future versions of `setuptools`.
+                Please adapt your code accordingly to use either the 'strict' or the
+                'lenient' modes.
+                """,
+                see_docs="userguide/development_mode.html",
+                # TODO: define due_date
+                # There is a series of shortcomings with the available editable install
+                # methods, and they are very controversial. This is something that still
+                # needs work.
+                # Moreover, `pip` is still hiding this warning, so users are not aware.
+            )
+
+        return _EditableMode[_mode]
+
+
+_STRICT_WARNING = """
+New or renamed files may not be automatically picked up without a new installation.
+"""
+
+_LENIENT_WARNING = """
+Options like `package-data`, `include/exclude-package-data` or
+`packages.find.exclude/include` may have no effect.
+"""
+
+
+class editable_wheel(Command):
+    """Build 'editable' wheel for development.
+    This command is private and reserved for internal use of setuptools,
+    users should rely on ``setuptools.build_meta`` APIs.
+    """
+
+    description = "DO NOT CALL DIRECTLY, INTERNAL ONLY: create PEP 660 editable wheel"
+
+    user_options = [
+        ("dist-dir=", "d", "directory to put final built distributions in"),
+        ("dist-info-dir=", "I", "path to a pre-build .dist-info directory"),
+        ("mode=", None, cleandoc(_EditableMode.__doc__ or "")),
+    ]
+
+    def initialize_options(self):
+        self.dist_dir = None
+        self.dist_info_dir = None
+        self.project_dir = None
+        self.mode = None
+
+    def finalize_options(self) -> None:
+        dist = self.distribution
+        self.project_dir = dist.src_root or os.curdir
+        self.package_dir = dist.package_dir or {}
+        self.dist_dir = Path(self.dist_dir or os.path.join(self.project_dir, "dist"))
+
+    def run(self) -> None:
+        try:
+            self.dist_dir.mkdir(exist_ok=True)
+            self._ensure_dist_info()
+
+            # Add missing dist_info files
+            self.reinitialize_command("bdist_wheel")
+            bdist_wheel = self.get_finalized_command("bdist_wheel")
+            bdist_wheel.write_wheelfile(self.dist_info_dir)
+
+            self._create_wheel_file(bdist_wheel)
+        except Exception as ex:
+            project = self.distribution.name or self.distribution.get_name()
+            py310.add_note(
+                ex,
+                f"An error occurred when building editable wheel for {project}.\n"
+                "See debugging tips in: "
+                "https://setuptools.pypa.io/en/latest/userguide/development_mode.html#debugging-tips",
+            )
+            raise
+
+    def _ensure_dist_info(self):
+        if self.dist_info_dir is None:
+            dist_info = cast(dist_info_cls, self.reinitialize_command("dist_info"))
+            dist_info.output_dir = self.dist_dir
+            dist_info.ensure_finalized()
+            dist_info.run()
+            self.dist_info_dir = dist_info.dist_info_dir
+        else:
+            assert str(self.dist_info_dir).endswith(".dist-info")
+            assert Path(self.dist_info_dir, "METADATA").exists()
+
+    def _install_namespaces(self, installation_dir, pth_prefix):
+        # XXX: Only required to support the deprecated namespace practice
+        dist = self.distribution
+        if not dist.namespace_packages:
+            return
+
+        src_root = Path(self.project_dir, self.package_dir.get("", ".")).resolve()
+        installer = _NamespaceInstaller(dist, installation_dir, pth_prefix, src_root)
+        installer.install_namespaces()
+
+    def _find_egg_info_dir(self) -> str | None:
+        parent_dir = Path(self.dist_info_dir).parent if self.dist_info_dir else Path()
+        candidates = map(str, parent_dir.glob("*.egg-info"))
+        return next(candidates, None)
+
+    def _configure_build(
+        self, name: str, unpacked_wheel: StrPath, build_lib: StrPath, tmp_dir: StrPath
+    ):
+        """Configure commands to behave in the following ways:
+
+        - Build commands can write to ``build_lib`` if they really want to...
+          (but this folder is expected to be ignored and modules are expected to live
+          in the project directory...)
+        - Binary extensions should be built in-place (editable_mode = True)
+        - Data/header/script files are not part of the "editable" specification
+          so they are written directly to the unpacked_wheel directory.
+        """
+        # Non-editable files (data, headers, scripts) are written directly to the
+        # unpacked_wheel
+
+        dist = self.distribution
+        wheel = str(unpacked_wheel)
+        build_lib = str(build_lib)
+        data = str(Path(unpacked_wheel, f"{name}.data", "data"))
+        headers = str(Path(unpacked_wheel, f"{name}.data", "headers"))
+        scripts = str(Path(unpacked_wheel, f"{name}.data", "scripts"))
+
+        # egg-info may be generated again to create a manifest (used for package data)
+        egg_info = cast(
+            egg_info_cls, dist.reinitialize_command("egg_info", reinit_subcommands=True)
+        )
+        egg_info.egg_base = str(tmp_dir)
+        egg_info.ignore_egg_info_in_manifest = True
+
+        build = cast(
+            build_cls, dist.reinitialize_command("build", reinit_subcommands=True)
+        )
+        install = cast(
+            install_cls, dist.reinitialize_command("install", reinit_subcommands=True)
+        )
+
+        build.build_platlib = build.build_purelib = build.build_lib = build_lib
+        install.install_purelib = install.install_platlib = install.install_lib = wheel
+        install.install_scripts = build.build_scripts = scripts
+        install.install_headers = headers
+        install.install_data = data
+
+        # For portability, ensure scripts are built with #!python shebang
+        # pypa/setuptools#4863
+        build_scripts = dist.get_command_obj("build_scripts")
+        build_scripts.executable = 'python'
+
+        install_scripts = cast(
+            install_scripts_cls, dist.get_command_obj("install_scripts")
+        )
+        install_scripts.no_ep = True
+
+        build.build_temp = str(tmp_dir)
+
+        build_py = cast(build_py_cls, dist.get_command_obj("build_py"))
+        build_py.compile = False
+        build_py.existing_egg_info_dir = self._find_egg_info_dir()
+
+        self._set_editable_mode()
+
+        build.ensure_finalized()
+        install.ensure_finalized()
+
+    def _set_editable_mode(self):
+        """Set the ``editable_mode`` flag in the build sub-commands"""
+        dist = self.distribution
+        build = dist.get_command_obj("build")
+        for cmd_name in build.get_sub_commands():
+            cmd = dist.get_command_obj(cmd_name)
+            if hasattr(cmd, "editable_mode"):
+                cmd.editable_mode = True
+            elif hasattr(cmd, "inplace"):
+                cmd.inplace = True  # backward compatibility with distutils
+
+    def _collect_build_outputs(self) -> tuple[list[str], dict[str, str]]:
+        files: list[str] = []
+        mapping: dict[str, str] = {}
+        build = self.get_finalized_command("build")
+
+        for cmd_name in build.get_sub_commands():
+            cmd = self.get_finalized_command(cmd_name)
+            if hasattr(cmd, "get_outputs"):
+                files.extend(cmd.get_outputs() or [])
+            if hasattr(cmd, "get_output_mapping"):
+                mapping.update(cmd.get_output_mapping() or {})
+
+        return files, mapping
+
+    def _run_build_commands(
+        self,
+        dist_name: str,
+        unpacked_wheel: StrPath,
+        build_lib: StrPath,
+        tmp_dir: StrPath,
+    ) -> tuple[list[str], dict[str, str]]:
+        self._configure_build(dist_name, unpacked_wheel, build_lib, tmp_dir)
+        self._run_build_subcommands()
+        files, mapping = self._collect_build_outputs()
+        self._run_install("headers")
+        self._run_install("scripts")
+        self._run_install("data")
+        return files, mapping
+
+    def _run_build_subcommands(self) -> None:
+        """
+        Issue #3501 indicates that some plugins/customizations might rely on:
+
+        1. ``build_py`` not running
+        2. ``build_py`` always copying files to ``build_lib``
+
+        However both these assumptions may be false in editable_wheel.
+        This method implements a temporary workaround to support the ecosystem
+        while the implementations catch up.
+        """
+        # TODO: Once plugins/customizations had the chance to catch up, replace
+        #       `self._run_build_subcommands()` with `self.run_command("build")`.
+        #       Also remove _safely_run, TestCustomBuildPy. Suggested date: Aug/2023.
+        build = self.get_finalized_command("build")
+        for name in build.get_sub_commands():
+            cmd = self.get_finalized_command(name)
+            if name == "build_py" and type(cmd) is not build_py_cls:
+                self._safely_run(name)
+            else:
+                self.run_command(name)
+
+    def _safely_run(self, cmd_name: str):
+        try:
+            return self.run_command(cmd_name)
+        except Exception:
+            SetuptoolsDeprecationWarning.emit(
+                "Customization incompatible with editable install",
+                f"""
+                {traceback.format_exc()}
+
+                If you are seeing this warning it is very likely that a setuptools
+                plugin or customization overrides the `{cmd_name}` command, without
+                taking into consideration how editable installs run build steps
+                starting from setuptools v64.0.0.
+
+                Plugin authors and developers relying on custom build steps are
+                encouraged to update their `{cmd_name}` implementation considering the
+                information about editable installs in
+                https://setuptools.pypa.io/en/latest/userguide/extension.html.
+
+                For the time being `setuptools` will silence this error and ignore
+                the faulty command, but this behavior will change in future versions.
+                """,
+                # TODO: define due_date
+                # There is a series of shortcomings with the available editable install
+                # methods, and they are very controversial. This is something that still
+                # needs work.
+            )
+
+    def _create_wheel_file(self, bdist_wheel):
+        from wheel.wheelfile import WheelFile
+
+        dist_info = self.get_finalized_command("dist_info")
+        dist_name = dist_info.name
+        tag = "-".join(bdist_wheel.get_tag())
+        build_tag = "0.editable"  # According to PEP 427 needs to start with digit
+        archive_name = f"{dist_name}-{build_tag}-{tag}.whl"
+        wheel_path = Path(self.dist_dir, archive_name)
+        if wheel_path.exists():
+            wheel_path.unlink()
+
+        unpacked_wheel = TemporaryDirectory(suffix=archive_name)
+        build_lib = TemporaryDirectory(suffix=".build-lib")
+        build_tmp = TemporaryDirectory(suffix=".build-temp")
+
+        with unpacked_wheel as unpacked, build_lib as lib, build_tmp as tmp:
+            unpacked_dist_info = Path(unpacked, Path(self.dist_info_dir).name)
+            shutil.copytree(self.dist_info_dir, unpacked_dist_info)
+            self._install_namespaces(unpacked, dist_name)
+            files, mapping = self._run_build_commands(dist_name, unpacked, lib, tmp)
+            strategy = self._select_strategy(dist_name, tag, lib)
+            with strategy, WheelFile(wheel_path, "w") as wheel_obj:
+                strategy(wheel_obj, files, mapping)
+                wheel_obj.write_files(unpacked)
+
+        return wheel_path
+
+    def _run_install(self, category: str):
+        has_category = getattr(self.distribution, f"has_{category}", None)
+        if has_category and has_category():
+            _logger.info(f"Installing {category} as non editable")
+            self.run_command(f"install_{category}")
+
+    def _select_strategy(
+        self,
+        name: str,
+        tag: str,
+        build_lib: StrPath,
+    ) -> EditableStrategy:
+        """Decides which strategy to use to implement an editable installation."""
+        build_name = f"__editable__.{name}-{tag}"
+        project_dir = Path(self.project_dir)
+        mode = _EditableMode.convert(self.mode)
+
+        if mode is _EditableMode.STRICT:
+            auxiliary_dir = _empty_dir(Path(self.project_dir, "build", build_name))
+            return _LinkTree(self.distribution, name, auxiliary_dir, build_lib)
+
+        packages = _find_packages(self.distribution)
+        has_simple_layout = _simple_layout(packages, self.package_dir, project_dir)
+        is_compat_mode = mode is _EditableMode.COMPAT
+        if set(self.package_dir) == {""} and has_simple_layout or is_compat_mode:
+            # src-layout(ish) is relatively safe for a simple pth file
+            src_dir = self.package_dir.get("", ".")
+            return _StaticPth(self.distribution, name, [Path(project_dir, src_dir)])
+
+        # Use a MetaPathFinder to avoid adding accidental top-level packages/modules
+        return _TopLevelFinder(self.distribution, name)
+
+
+class EditableStrategy(Protocol):
+    def __call__(
+        self, wheel: WheelFile, files: list[str], mapping: Mapping[str, str]
+    ) -> object: ...
+    def __enter__(self) -> Self: ...
+    def __exit__(
+        self,
+        _exc_type: type[BaseException] | None,
+        _exc_value: BaseException | None,
+        _traceback: TracebackType | None,
+    ) -> object: ...
+
+
+class _StaticPth:
+    def __init__(self, dist: Distribution, name: str, path_entries: list[Path]) -> None:
+        self.dist = dist
+        self.name = name
+        self.path_entries = path_entries
+
+    def __call__(
+        self, wheel: WheelFile, files: list[str], mapping: Mapping[str, str]
+    ) -> None:
+        entries = "\n".join(str(p.resolve()) for p in self.path_entries)
+        contents = _encode_pth(f"{entries}\n")
+        wheel.writestr(f"__editable__.{self.name}.pth", contents)
+
+    def __enter__(self) -> Self:
+        msg = f"""
+        Editable install will be performed using .pth file to extend `sys.path` with:
+        {list(map(os.fspath, self.path_entries))!r}
+        """
+        _logger.warning(msg + _LENIENT_WARNING)
+        return self
+
+    def __exit__(
+        self,
+        _exc_type: object,
+        _exc_value: object,
+        _traceback: object,
+    ) -> None:
+        pass
+
+
+class _LinkTree(_StaticPth):
+    """
+    Creates a ``.pth`` file that points to a link tree in the ``auxiliary_dir``.
+
+    This strategy will only link files (not dirs), so it can be implemented in
+    any OS, even if that means using hardlinks instead of symlinks.
+
+    By collocating ``auxiliary_dir`` and the original source code, limitations
+    with hardlinks should be avoided.
+    """
+
+    def __init__(
+        self,
+        dist: Distribution,
+        name: str,
+        auxiliary_dir: StrPath,
+        build_lib: StrPath,
+    ) -> None:
+        self.auxiliary_dir = Path(auxiliary_dir)
+        self.build_lib = Path(build_lib).resolve()
+        self._file = dist.get_command_obj("build_py").copy_file
+        super().__init__(dist, name, [self.auxiliary_dir])
+
+    def __call__(
+        self, wheel: WheelFile, files: list[str], mapping: Mapping[str, str]
+    ) -> None:
+        self._create_links(files, mapping)
+        super().__call__(wheel, files, mapping)
+
+    def _normalize_output(self, file: str) -> str | None:
+        # Files relative to build_lib will be normalized to None
+        with suppress(ValueError):
+            path = Path(file).resolve().relative_to(self.build_lib)
+            return str(path).replace(os.sep, '/')
+        return None
+
+    def _create_file(self, relative_output: str, src_file: str, link=None):
+        dest = self.auxiliary_dir / relative_output
+        if not dest.parent.is_dir():
+            dest.parent.mkdir(parents=True)
+        self._file(src_file, dest, link=link)
+
+    def _create_links(self, outputs, output_mapping: Mapping[str, str]):
+        self.auxiliary_dir.mkdir(parents=True, exist_ok=True)
+        link_type = "sym" if _can_symlink_files(self.auxiliary_dir) else "hard"
+        normalised = ((self._normalize_output(k), v) for k, v in output_mapping.items())
+        # remove files that are not relative to build_lib
+        mappings = {k: v for k, v in normalised if k is not None}
+
+        for output in outputs:
+            relative = self._normalize_output(output)
+            if relative and relative not in mappings:
+                self._create_file(relative, output)
+
+        for relative, src in mappings.items():
+            self._create_file(relative, src, link=link_type)
+
+    def __enter__(self) -> Self:
+        msg = "Strict editable install will be performed using a link tree.\n"
+        _logger.warning(msg + _STRICT_WARNING)
+        return self
+
+    def __exit__(
+        self,
+        _exc_type: object,
+        _exc_value: object,
+        _traceback: object,
+    ) -> None:
+        msg = f"""\n
+        Strict editable installation performed using the auxiliary directory:
+            {self.auxiliary_dir}
+
+        Please be careful to not remove this directory, otherwise you might not be able
+        to import/use your package.
+        """
+        InformationOnly.emit("Editable installation.", msg)
+
+
+class _TopLevelFinder:
+    def __init__(self, dist: Distribution, name: str) -> None:
+        self.dist = dist
+        self.name = name
+
+    def template_vars(self) -> tuple[str, str, dict[str, str], dict[str, list[str]]]:
+        src_root = self.dist.src_root or os.curdir
+        top_level = chain(_find_packages(self.dist), _find_top_level_modules(self.dist))
+        package_dir = self.dist.package_dir or {}
+        roots = _find_package_roots(top_level, package_dir, src_root)
+
+        namespaces_ = dict(
+            chain(
+                _find_namespaces(self.dist.packages or [], roots),
+                ((ns, []) for ns in _find_virtual_namespaces(roots)),
+            )
+        )
+
+        legacy_namespaces = {
+            pkg: find_package_path(pkg, roots, self.dist.src_root or "")
+            for pkg in self.dist.namespace_packages or []
+        }
+
+        mapping = {**roots, **legacy_namespaces}
+        # ^-- We need to explicitly add the legacy_namespaces to the mapping to be
+        #     able to import their modules even if another package sharing the same
+        #     namespace is installed in a conventional (non-editable) way.
+
+        name = f"__editable__.{self.name}.finder"
+        finder = _normalization.safe_identifier(name)
+        return finder, name, mapping, namespaces_
+
+    def get_implementation(self) -> Iterator[tuple[str, bytes]]:
+        finder, name, mapping, namespaces_ = self.template_vars()
+
+        content = bytes(_finder_template(name, mapping, namespaces_), "utf-8")
+        yield (f"{finder}.py", content)
+
+        content = _encode_pth(f"import {finder}; {finder}.install()")
+        yield (f"__editable__.{self.name}.pth", content)
+
+    def __call__(
+        self, wheel: WheelFile, files: list[str], mapping: Mapping[str, str]
+    ) -> None:
+        for file, content in self.get_implementation():
+            wheel.writestr(file, content)
+
+    def __enter__(self) -> Self:
+        msg = "Editable install will be performed using a meta path finder.\n"
+        _logger.warning(msg + _LENIENT_WARNING)
+        return self
+
+    def __exit__(
+        self,
+        _exc_type: object,
+        _exc_value: object,
+        _traceback: object,
+    ) -> None:
+        msg = """\n
+        Please be careful with folders in your working directory with the same
+        name as your package as they may take precedence during imports.
+        """
+        InformationOnly.emit("Editable installation.", msg)
+
+
+def _encode_pth(content: str) -> bytes:
+    """
+    Prior to Python 3.13 (see https://github.com/python/cpython/issues/77102),
+    .pth files are always read with 'locale' encoding, the recommendation
+    from the cpython core developers is to write them as ``open(path, "w")``
+    and ignore warnings (see python/cpython#77102, pypa/setuptools#3937).
+    This function tries to simulate this behavior without having to create an
+    actual file, in a way that supports a range of active Python versions.
+    (There seems to be some variety in the way different version of Python handle
+    ``encoding=None``, not all of them use ``locale.getpreferredencoding(False)``
+    or ``locale.getencoding()``).
+    """
+    with io.BytesIO() as buffer:
+        wrapper = io.TextIOWrapper(buffer, encoding=py312.PTH_ENCODING)
+        # TODO: Python 3.13 replace the whole function with `bytes(content, "utf-8")`
+        wrapper.write(content)
+        wrapper.flush()
+        buffer.seek(0)
+        return buffer.read()
+
+
+def _can_symlink_files(base_dir: Path) -> bool:
+    with TemporaryDirectory(dir=str(base_dir.resolve())) as tmp:
+        path1, path2 = Path(tmp, "file1.txt"), Path(tmp, "file2.txt")
+        path1.write_text("file1", encoding="utf-8")
+        with suppress(AttributeError, NotImplementedError, OSError):
+            os.symlink(path1, path2)
+            if path2.is_symlink() and path2.read_text(encoding="utf-8") == "file1":
+                return True
+
+        try:
+            os.link(path1, path2)  # Ensure hard links can be created
+        except Exception as ex:
+            msg = (
+                "File system does not seem to support either symlinks or hard links. "
+                "Strict editable installs require one of them to be supported."
+            )
+            raise LinksNotSupported(msg) from ex
+        return False
+
+
+def _simple_layout(
+    packages: Iterable[str], package_dir: dict[str, str], project_dir: StrPath
+) -> bool:
+    """Return ``True`` if:
+    - all packages are contained by the same parent directory, **and**
+    - all packages become importable if the parent directory is added to ``sys.path``.
+
+    >>> _simple_layout(['a'], {"": "src"}, "/tmp/myproj")
+    True
+    >>> _simple_layout(['a', 'a.b'], {"": "src"}, "/tmp/myproj")
+    True
+    >>> _simple_layout(['a', 'a.b'], {}, "/tmp/myproj")
+    True
+    >>> _simple_layout(['a', 'a.a1', 'a.a1.a2', 'b'], {"": "src"}, "/tmp/myproj")
+    True
+    >>> _simple_layout(['a', 'a.a1', 'a.a1.a2', 'b'], {"a": "a", "b": "b"}, ".")
+    True
+    >>> _simple_layout(['a', 'a.a1', 'a.a1.a2', 'b'], {"a": "_a", "b": "_b"}, ".")
+    False
+    >>> _simple_layout(['a', 'a.a1', 'a.a1.a2', 'b'], {"a": "_a"}, "/tmp/myproj")
+    False
+    >>> _simple_layout(['a', 'a.a1', 'a.a1.a2', 'b'], {"a.a1.a2": "_a2"}, ".")
+    False
+    >>> _simple_layout(['a', 'a.b'], {"": "src", "a.b": "_ab"}, "/tmp/myproj")
+    False
+    >>> # Special cases, no packages yet:
+    >>> _simple_layout([], {"": "src"}, "/tmp/myproj")
+    True
+    >>> _simple_layout([], {"a": "_a", "": "src"}, "/tmp/myproj")
+    False
+    """
+    layout = {pkg: find_package_path(pkg, package_dir, project_dir) for pkg in packages}
+    if not layout:
+        return set(package_dir) in ({}, {""})
+    parent = os.path.commonpath(starmap(_parent_path, layout.items()))
+    return all(
+        _path.same_path(Path(parent, *key.split('.')), value)
+        for key, value in layout.items()
+    )
+
+
+def _parent_path(pkg, pkg_path):
+    """Infer the parent path containing a package, that if added to ``sys.path`` would
+    allow importing that package.
+    When ``pkg`` is directly mapped into a directory with a different name, return its
+    own path.
+    >>> _parent_path("a", "src/a")
+    'src'
+    >>> _parent_path("b", "src/c")
+    'src/c'
+    """
+    parent = pkg_path.removesuffix(pkg)
+    return parent.rstrip("/" + os.sep)
+
+
+def _find_packages(dist: Distribution) -> Iterator[str]:
+    yield from iter(dist.packages or [])
+
+    py_modules = dist.py_modules or []
+    nested_modules = [mod for mod in py_modules if "." in mod]
+    if dist.ext_package:
+        yield dist.ext_package
+    else:
+        ext_modules = dist.ext_modules or []
+        nested_modules += [x.name for x in ext_modules if "." in x.name]
+
+    for module in nested_modules:
+        package, _, _ = module.rpartition(".")
+        yield package
+
+
+def _find_top_level_modules(dist: Distribution) -> Iterator[str]:
+    py_modules = dist.py_modules or []
+    yield from (mod for mod in py_modules if "." not in mod)
+
+    if not dist.ext_package:
+        ext_modules = dist.ext_modules or []
+        yield from (x.name for x in ext_modules if "." not in x.name)
+
+
+def _find_package_roots(
+    packages: Iterable[str],
+    package_dir: Mapping[str, str],
+    src_root: StrPath,
+) -> dict[str, str]:
+    pkg_roots: dict[str, str] = {
+        pkg: _absolute_root(find_package_path(pkg, package_dir, src_root))
+        for pkg in sorted(packages)
+    }
+
+    return _remove_nested(pkg_roots)
+
+
+def _absolute_root(path: StrPath) -> str:
+    """Works for packages and top-level modules"""
+    path_ = Path(path)
+    parent = path_.parent
+
+    if path_.exists():
+        return str(path_.resolve())
+    else:
+        return str(parent.resolve() / path_.name)
+
+
+def _find_virtual_namespaces(pkg_roots: dict[str, str]) -> Iterator[str]:
+    """By carefully designing ``package_dir``, it is possible to implement the logical
+    structure of PEP 420 in a package without the corresponding directories.
+
+    Moreover a parent package can be purposefully/accidentally skipped in the discovery
+    phase (e.g. ``find_packages(include=["mypkg.*"])``, when ``mypkg.foo`` is included
+    by ``mypkg`` itself is not).
+    We consider this case to also be a virtual namespace (ignoring the original
+    directory) to emulate a non-editable installation.
+
+    This function will try to find these kinds of namespaces.
+    """
+    for pkg in pkg_roots:
+        if "." not in pkg:
+            continue
+        parts = pkg.split(".")
+        for i in range(len(parts) - 1, 0, -1):
+            partial_name = ".".join(parts[:i])
+            path = Path(find_package_path(partial_name, pkg_roots, ""))
+            if not path.exists() or partial_name not in pkg_roots:
+                # partial_name not in pkg_roots ==> purposefully/accidentally skipped
+                yield partial_name
+
+
+def _find_namespaces(
+    packages: list[str], pkg_roots: dict[str, str]
+) -> Iterator[tuple[str, list[str]]]:
+    for pkg in packages:
+        path = find_package_path(pkg, pkg_roots, "")
+        if Path(path).exists() and not Path(path, "__init__.py").exists():
+            yield (pkg, [path])
+
+
+def _remove_nested(pkg_roots: dict[str, str]) -> dict[str, str]:
+    output = dict(pkg_roots.copy())
+
+    for pkg, path in reversed(list(pkg_roots.items())):
+        if any(
+            pkg != other and _is_nested(pkg, path, other, other_path)
+            for other, other_path in pkg_roots.items()
+        ):
+            output.pop(pkg)
+
+    return output
+
+
+def _is_nested(pkg: str, pkg_path: str, parent: str, parent_path: str) -> bool:
+    """
+    Return ``True`` if ``pkg`` is nested inside ``parent`` both logically and in the
+    file system.
+    >>> _is_nested("a.b", "path/a/b", "a", "path/a")
+    True
+    >>> _is_nested("a.b", "path/a/b", "a", "otherpath/a")
+    False
+    >>> _is_nested("a.b", "path/a/b", "c", "path/c")
+    False
+    >>> _is_nested("a.a", "path/a/a", "a", "path/a")
+    True
+    >>> _is_nested("b.a", "path/b/a", "a", "path/a")
+    False
+    """
+    norm_pkg_path = _path.normpath(pkg_path)
+    rest = pkg.replace(parent, "", 1).strip(".").split(".")
+    return pkg.startswith(parent) and norm_pkg_path == _path.normpath(
+        Path(parent_path, *rest)
+    )
+
+
+def _empty_dir(dir_: _P) -> _P:
+    """Create a directory ensured to be empty. Existing files may be removed."""
+    _shutil.rmtree(dir_, ignore_errors=True)
+    os.makedirs(dir_)
+    return dir_
+
+
+class _NamespaceInstaller(namespaces.Installer):
+    def __init__(self, distribution, installation_dir, editable_name, src_root) -> None:
+        self.distribution = distribution
+        self.src_root = src_root
+        self.installation_dir = installation_dir
+        self.editable_name = editable_name
+        self.outputs: list[str] = []
+        self.dry_run = False
+
+    def _get_nspkg_file(self):
+        """Installation target."""
+        return os.path.join(self.installation_dir, self.editable_name + self.nspkg_ext)
+
+    def _get_root(self):
+        """Where the modules/packages should be loaded from."""
+        return repr(str(self.src_root))
+
+
+_FINDER_TEMPLATE = """\
+from __future__ import annotations
+import sys
+from importlib.machinery import ModuleSpec, PathFinder
+from importlib.machinery import all_suffixes as module_suffixes
+from importlib.util import spec_from_file_location
+from itertools import chain
+from pathlib import Path
+
+MAPPING: dict[str, str] = {mapping!r}
+NAMESPACES: dict[str, list[str]] = {namespaces!r}
+PATH_PLACEHOLDER = {name!r} + ".__path_hook__"
+
+
+class _EditableFinder:  # MetaPathFinder
+    @classmethod
+    def find_spec(cls, fullname: str, path=None, target=None) -> ModuleSpec | None:  # type: ignore
+        # Top-level packages and modules (we know these exist in the FS)
+        if fullname in MAPPING:
+            pkg_path = MAPPING[fullname]
+            return cls._find_spec(fullname, Path(pkg_path))
+
+        # Handle immediate children modules (required for namespaces to work)
+        # To avoid problems with case sensitivity in the file system we delegate
+        # to the importlib.machinery implementation.
+        parent, _, child = fullname.rpartition(".")
+        if parent and parent in MAPPING:
+            return PathFinder.find_spec(fullname, path=[MAPPING[parent]])
+
+        # Other levels of nesting should be handled automatically by importlib
+        # using the parent path.
+        return None
+
+    @classmethod
+    def _find_spec(cls, fullname: str, candidate_path: Path) -> ModuleSpec | None:
+        init = candidate_path / "__init__.py"
+        candidates = (candidate_path.with_suffix(x) for x in module_suffixes())
+        for candidate in chain([init], candidates):
+            if candidate.exists():
+                return spec_from_file_location(fullname, candidate)
+        return None
+
+
+class _EditableNamespaceFinder:  # PathEntryFinder
+    @classmethod
+    def _path_hook(cls, path) -> type[_EditableNamespaceFinder]:
+        if path == PATH_PLACEHOLDER:
+            return cls
+        raise ImportError
+
+    @classmethod
+    def _paths(cls, fullname: str) -> list[str]:
+        paths = NAMESPACES[fullname]
+        if not paths and fullname in MAPPING:
+            paths = [MAPPING[fullname]]
+        # Always add placeholder, for 2 reasons:
+        # 1. __path__ cannot be empty for the spec to be considered namespace.
+        # 2. In the case of nested namespaces, we need to force
+        #    import machinery to query _EditableNamespaceFinder again.
+        return [*paths, PATH_PLACEHOLDER]
+
+    @classmethod
+    def find_spec(cls, fullname: str, target=None) -> ModuleSpec | None:  # type: ignore
+        if fullname in NAMESPACES:
+            spec = ModuleSpec(fullname, None, is_package=True)
+            spec.submodule_search_locations = cls._paths(fullname)
+            return spec
+        return None
+
+    @classmethod
+    def find_module(cls, _fullname) -> None:
+        return None
+
+
+def install():
+    if not any(finder == _EditableFinder for finder in sys.meta_path):
+        sys.meta_path.append(_EditableFinder)
+
+    if not NAMESPACES:
+        return
+
+    if not any(hook == _EditableNamespaceFinder._path_hook for hook in sys.path_hooks):
+        # PathEntryFinder is needed to create NamespaceSpec without private APIS
+        sys.path_hooks.append(_EditableNamespaceFinder._path_hook)
+    if PATH_PLACEHOLDER not in sys.path:
+        sys.path.append(PATH_PLACEHOLDER)  # Used just to trigger the path hook
+"""
+
+
+def _finder_template(
+    name: str, mapping: Mapping[str, str], namespaces: dict[str, list[str]]
+) -> str:
+    """Create a string containing the code for the``MetaPathFinder`` and
+    ``PathEntryFinder``.
+    """
+    mapping = dict(sorted(mapping.items(), key=operator.itemgetter(0)))
+    return _FINDER_TEMPLATE.format(name=name, mapping=mapping, namespaces=namespaces)
+
+
+class LinksNotSupported(errors.FileError):
+    """File system does not seem to support either symlinks or hard links."""
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/egg_info.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/egg_info.py
new file mode 100644
index 0000000000000000000000000000000000000000..d9de297ecfa99cb3e9de1b6ca61f906b69bcdfa4
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/egg_info.py
@@ -0,0 +1,719 @@
+"""setuptools.command.egg_info
+
+Create a distribution's .egg-info directory and contents"""
+
+from __future__ import annotations
+
+import functools
+import os
+import re
+import sys
+import time
+from collections.abc import Callable
+
+import packaging
+import packaging.requirements
+import packaging.version
+
+import setuptools.unicode_utils as unicode_utils
+from setuptools import Command
+from setuptools.command import bdist_egg
+from setuptools.command.sdist import sdist, walk_revctrl
+from setuptools.command.setopt import edit_config
+from setuptools.glob import glob
+
+from .. import _entry_points, _normalization
+from .._importlib import metadata
+from ..warnings import SetuptoolsDeprecationWarning
+from . import _requirestxt
+
+import distutils.errors
+import distutils.filelist
+from distutils import log
+from distutils.errors import DistutilsInternalError
+from distutils.filelist import FileList as _FileList
+from distutils.util import convert_path
+
+PY_MAJOR = f'{sys.version_info.major}.{sys.version_info.minor}'
+
+
+def translate_pattern(glob):  # noqa: C901  # is too complex (14)  # FIXME
+    """
+    Translate a file path glob like '*.txt' in to a regular expression.
+    This differs from fnmatch.translate which allows wildcards to match
+    directory separators. It also knows about '**/' which matches any number of
+    directories.
+    """
+    pat = ''
+
+    # This will split on '/' within [character classes]. This is deliberate.
+    chunks = glob.split(os.path.sep)
+
+    sep = re.escape(os.sep)
+    valid_char = f'[^{sep}]'
+
+    for c, chunk in enumerate(chunks):
+        last_chunk = c == len(chunks) - 1
+
+        # Chunks that are a literal ** are globstars. They match anything.
+        if chunk == '**':
+            if last_chunk:
+                # Match anything if this is the last component
+                pat += '.*'
+            else:
+                # Match '(name/)*'
+                pat += f'(?:{valid_char}+{sep})*'
+            continue  # Break here as the whole path component has been handled
+
+        # Find any special characters in the remainder
+        i = 0
+        chunk_len = len(chunk)
+        while i < chunk_len:
+            char = chunk[i]
+            if char == '*':
+                # Match any number of name characters
+                pat += valid_char + '*'
+            elif char == '?':
+                # Match a name character
+                pat += valid_char
+            elif char == '[':
+                # Character class
+                inner_i = i + 1
+                # Skip initial !/] chars
+                if inner_i < chunk_len and chunk[inner_i] == '!':
+                    inner_i = inner_i + 1
+                if inner_i < chunk_len and chunk[inner_i] == ']':
+                    inner_i = inner_i + 1
+
+                # Loop till the closing ] is found
+                while inner_i < chunk_len and chunk[inner_i] != ']':
+                    inner_i = inner_i + 1
+
+                if inner_i >= chunk_len:
+                    # Got to the end of the string without finding a closing ]
+                    # Do not treat this as a matching group, but as a literal [
+                    pat += re.escape(char)
+                else:
+                    # Grab the insides of the [brackets]
+                    inner = chunk[i + 1 : inner_i]
+                    char_class = ''
+
+                    # Class negation
+                    if inner[0] == '!':
+                        char_class = '^'
+                        inner = inner[1:]
+
+                    char_class += re.escape(inner)
+                    pat += f'[{char_class}]'
+
+                    # Skip to the end ]
+                    i = inner_i
+            else:
+                pat += re.escape(char)
+            i += 1
+
+        # Join each chunk with the dir separator
+        if not last_chunk:
+            pat += sep
+
+    pat += r'\Z'
+    return re.compile(pat, flags=re.MULTILINE | re.DOTALL)
+
+
+class InfoCommon:
+    tag_build = None
+    tag_date = None
+
+    @property
+    def name(self):
+        return _normalization.safe_name(self.distribution.get_name())
+
+    def tagged_version(self):
+        tagged = self._maybe_tag(self.distribution.get_version())
+        return _normalization.safe_version(tagged)
+
+    def _maybe_tag(self, version):
+        """
+        egg_info may be called more than once for a distribution,
+        in which case the version string already contains all tags.
+        """
+        return (
+            version
+            if self.vtags and self._already_tagged(version)
+            else version + self.vtags
+        )
+
+    def _already_tagged(self, version: str) -> bool:
+        # Depending on their format, tags may change with version normalization.
+        # So in addition the regular tags, we have to search for the normalized ones.
+        return version.endswith((self.vtags, self._safe_tags()))
+
+    def _safe_tags(self) -> str:
+        # To implement this we can rely on `safe_version` pretending to be version 0
+        # followed by tags. Then we simply discard the starting 0 (fake version number)
+        try:
+            return _normalization.safe_version(f"0{self.vtags}")[1:]
+        except packaging.version.InvalidVersion:
+            return _normalization.safe_name(self.vtags.replace(' ', '.'))
+
+    def tags(self) -> str:
+        version = ''
+        if self.tag_build:
+            version += self.tag_build
+        if self.tag_date:
+            version += time.strftime("%Y%m%d")
+        return version
+
+    vtags = property(tags)
+
+
+class egg_info(InfoCommon, Command):
+    description = "create a distribution's .egg-info directory"
+
+    user_options = [
+        (
+            'egg-base=',
+            'e',
+            "directory containing .egg-info directories"
+            " [default: top of the source tree]",
+        ),
+        ('tag-date', 'd', "Add date stamp (e.g. 20050528) to version number"),
+        ('tag-build=', 'b', "Specify explicit tag to add to version number"),
+        ('no-date', 'D', "Don't include date stamp [default]"),
+    ]
+
+    boolean_options = ['tag-date']
+    negative_opt = {
+        'no-date': 'tag-date',
+    }
+
+    def initialize_options(self):
+        self.egg_base = None
+        self.egg_name = None
+        self.egg_info = None
+        self.egg_version = None
+        self.ignore_egg_info_in_manifest = False
+
+    ####################################
+    # allow the 'tag_svn_revision' to be detected and
+    # set, supporting sdists built on older Setuptools.
+    @property
+    def tag_svn_revision(self) -> int | None:
+        pass
+
+    @tag_svn_revision.setter
+    def tag_svn_revision(self, value) -> None:
+        pass
+
+    ####################################
+
+    def save_version_info(self, filename) -> None:
+        """
+        Materialize the value of date into the
+        build tag. Install build keys in a deterministic order
+        to avoid arbitrary reordering on subsequent builds.
+        """
+        # follow the order these keys would have been added
+        # when PYTHONHASHSEED=0
+        egg_info = dict(tag_build=self.tags(), tag_date=0)
+        edit_config(filename, dict(egg_info=egg_info))
+
+    def finalize_options(self) -> None:
+        # Note: we need to capture the current value returned
+        # by `self.tagged_version()`, so we can later update
+        # `self.distribution.metadata.version` without
+        # repercussions.
+        self.egg_name = self.name
+        self.egg_version = self.tagged_version()
+        parsed_version = packaging.version.Version(self.egg_version)
+
+        try:
+            is_version = isinstance(parsed_version, packaging.version.Version)
+            spec = "%s==%s" if is_version else "%s===%s"
+            packaging.requirements.Requirement(spec % (self.egg_name, self.egg_version))
+        except ValueError as e:
+            raise distutils.errors.DistutilsOptionError(
+                f"Invalid distribution name or version syntax: {self.egg_name}-{self.egg_version}"
+            ) from e
+
+        if self.egg_base is None:
+            dirs = self.distribution.package_dir
+            self.egg_base = (dirs or {}).get('', os.curdir)
+
+        self.ensure_dirname('egg_base')
+        self.egg_info = _normalization.filename_component(self.egg_name) + '.egg-info'
+        if self.egg_base != os.curdir:
+            self.egg_info = os.path.join(self.egg_base, self.egg_info)
+
+        # Set package version for the benefit of dumber commands
+        # (e.g. sdist, bdist_wininst, etc.)
+        #
+        self.distribution.metadata.version = self.egg_version
+
+    def _get_egg_basename(self, py_version=PY_MAJOR, platform=None):
+        """Compute filename of the output egg. Private API."""
+        return _egg_basename(self.egg_name, self.egg_version, py_version, platform)
+
+    def write_or_delete_file(self, what, filename, data, force: bool = False) -> None:
+        """Write `data` to `filename` or delete if empty
+
+        If `data` is non-empty, this routine is the same as ``write_file()``.
+        If `data` is empty but not ``None``, this is the same as calling
+        ``delete_file(filename)`.  If `data` is ``None``, then this is a no-op
+        unless `filename` exists, in which case a warning is issued about the
+        orphaned file (if `force` is false), or deleted (if `force` is true).
+        """
+        if data:
+            self.write_file(what, filename, data)
+        elif os.path.exists(filename):
+            if data is None and not force:
+                log.warn("%s not set in setup(), but %s exists", what, filename)
+                return
+            else:
+                self.delete_file(filename)
+
+    def write_file(self, what, filename, data) -> None:
+        """Write `data` to `filename` (if not a dry run) after announcing it
+
+        `what` is used in a log message to identify what is being written
+        to the file.
+        """
+        log.info("writing %s to %s", what, filename)
+        data = data.encode("utf-8")
+        if not self.dry_run:
+            f = open(filename, 'wb')
+            f.write(data)
+            f.close()
+
+    def delete_file(self, filename) -> None:
+        """Delete `filename` (if not a dry run) after announcing it"""
+        log.info("deleting %s", filename)
+        if not self.dry_run:
+            os.unlink(filename)
+
+    def run(self) -> None:
+        # Pre-load to avoid iterating over entry-points while an empty .egg-info
+        # exists in sys.path. See pypa/pyproject-hooks#206
+        writers = list(metadata.entry_points(group='egg_info.writers'))
+
+        self.mkpath(self.egg_info)
+        try:
+            os.utime(self.egg_info, None)
+        except OSError as e:
+            msg = f"Cannot update time stamp of directory '{self.egg_info}'"
+            raise distutils.errors.DistutilsFileError(msg) from e
+        for ep in writers:
+            writer = ep.load()
+            writer(self, ep.name, os.path.join(self.egg_info, ep.name))
+
+        # Get rid of native_libs.txt if it was put there by older bdist_egg
+        nl = os.path.join(self.egg_info, "native_libs.txt")
+        if os.path.exists(nl):
+            self.delete_file(nl)
+
+        self.find_sources()
+
+    def find_sources(self) -> None:
+        """Generate SOURCES.txt manifest file"""
+        manifest_filename = os.path.join(self.egg_info, "SOURCES.txt")
+        mm = manifest_maker(self.distribution)
+        mm.ignore_egg_info_dir = self.ignore_egg_info_in_manifest
+        mm.manifest = manifest_filename
+        mm.run()
+        self.filelist = mm.filelist
+
+
+class FileList(_FileList):
+    # Implementations of the various MANIFEST.in commands
+
+    def __init__(
+        self, warn=None, debug_print=None, ignore_egg_info_dir: bool = False
+    ) -> None:
+        super().__init__(warn, debug_print)
+        self.ignore_egg_info_dir = ignore_egg_info_dir
+
+    def process_template_line(self, line) -> None:
+        # Parse the line: split it up, make sure the right number of words
+        # is there, and return the relevant words.  'action' is always
+        # defined: it's the first word of the line.  Which of the other
+        # three are defined depends on the action; it'll be either
+        # patterns, (dir and patterns), or (dir_pattern).
+        (action, patterns, dir, dir_pattern) = self._parse_template_line(line)
+
+        action_map: dict[str, Callable] = {
+            'include': self.include,
+            'exclude': self.exclude,
+            'global-include': self.global_include,
+            'global-exclude': self.global_exclude,
+            'recursive-include': functools.partial(
+                self.recursive_include,
+                dir,
+            ),
+            'recursive-exclude': functools.partial(
+                self.recursive_exclude,
+                dir,
+            ),
+            'graft': self.graft,
+            'prune': self.prune,
+        }
+        log_map = {
+            'include': "warning: no files found matching '%s'",
+            'exclude': ("warning: no previously-included files found matching '%s'"),
+            'global-include': (
+                "warning: no files found matching '%s' anywhere in distribution"
+            ),
+            'global-exclude': (
+                "warning: no previously-included files matching "
+                "'%s' found anywhere in distribution"
+            ),
+            'recursive-include': (
+                "warning: no files found matching '%s' under directory '%s'"
+            ),
+            'recursive-exclude': (
+                "warning: no previously-included files matching "
+                "'%s' found under directory '%s'"
+            ),
+            'graft': "warning: no directories found matching '%s'",
+            'prune': "no previously-included directories found matching '%s'",
+        }
+
+        try:
+            process_action = action_map[action]
+        except KeyError:
+            msg = f"Invalid MANIFEST.in: unknown action {action!r} in {line!r}"
+            raise DistutilsInternalError(msg) from None
+
+        # OK, now we know that the action is valid and we have the
+        # right number of words on the line for that action -- so we
+        # can proceed with minimal error-checking.
+
+        action_is_recursive = action.startswith('recursive-')
+        if action in {'graft', 'prune'}:
+            patterns = [dir_pattern]
+        extra_log_args = (dir,) if action_is_recursive else ()
+        log_tmpl = log_map[action]
+
+        self.debug_print(
+            ' '.join(
+                [action] + ([dir] if action_is_recursive else []) + patterns,
+            )
+        )
+        for pattern in patterns:
+            if not process_action(pattern):
+                log.warn(log_tmpl, pattern, *extra_log_args)
+
+    def _remove_files(self, predicate):
+        """
+        Remove all files from the file list that match the predicate.
+        Return True if any matching files were removed
+        """
+        found = False
+        for i in range(len(self.files) - 1, -1, -1):
+            if predicate(self.files[i]):
+                self.debug_print(" removing " + self.files[i])
+                del self.files[i]
+                found = True
+        return found
+
+    def include(self, pattern):
+        """Include files that match 'pattern'."""
+        found = [f for f in glob(pattern) if not os.path.isdir(f)]
+        self.extend(found)
+        return bool(found)
+
+    def exclude(self, pattern):
+        """Exclude files that match 'pattern'."""
+        match = translate_pattern(pattern)
+        return self._remove_files(match.match)
+
+    def recursive_include(self, dir, pattern):
+        """
+        Include all files anywhere in 'dir/' that match the pattern.
+        """
+        full_pattern = os.path.join(dir, '**', pattern)
+        found = [f for f in glob(full_pattern, recursive=True) if not os.path.isdir(f)]
+        self.extend(found)
+        return bool(found)
+
+    def recursive_exclude(self, dir, pattern):
+        """
+        Exclude any file anywhere in 'dir/' that match the pattern.
+        """
+        match = translate_pattern(os.path.join(dir, '**', pattern))
+        return self._remove_files(match.match)
+
+    def graft(self, dir):
+        """Include all files from 'dir/'."""
+        found = [
+            item
+            for match_dir in glob(dir)
+            for item in distutils.filelist.findall(match_dir)
+        ]
+        self.extend(found)
+        return bool(found)
+
+    def prune(self, dir):
+        """Filter out files from 'dir/'."""
+        match = translate_pattern(os.path.join(dir, '**'))
+        return self._remove_files(match.match)
+
+    def global_include(self, pattern):
+        """
+        Include all files anywhere in the current directory that match the
+        pattern. This is very inefficient on large file trees.
+        """
+        if self.allfiles is None:
+            self.findall()
+        match = translate_pattern(os.path.join('**', pattern))
+        found = [f for f in self.allfiles if match.match(f)]
+        self.extend(found)
+        return bool(found)
+
+    def global_exclude(self, pattern):
+        """
+        Exclude all files anywhere that match the pattern.
+        """
+        match = translate_pattern(os.path.join('**', pattern))
+        return self._remove_files(match.match)
+
+    def append(self, item) -> None:
+        item = item.removesuffix('\r')  # Fix older sdists built on Windows
+        path = convert_path(item)
+
+        if self._safe_path(path):
+            self.files.append(path)
+
+    def extend(self, paths) -> None:
+        self.files.extend(filter(self._safe_path, paths))
+
+    def _repair(self):
+        """
+        Replace self.files with only safe paths
+
+        Because some owners of FileList manipulate the underlying
+        ``files`` attribute directly, this method must be called to
+        repair those paths.
+        """
+        self.files = list(filter(self._safe_path, self.files))
+
+    def _safe_path(self, path):
+        enc_warn = "'%s' not %s encodable -- skipping"
+
+        # To avoid accidental trans-codings errors, first to unicode
+        u_path = unicode_utils.filesys_decode(path)
+        if u_path is None:
+            log.warn(f"'{path}' in unexpected encoding -- skipping")
+            return False
+
+        # Must ensure utf-8 encodability
+        utf8_path = unicode_utils.try_encode(u_path, "utf-8")
+        if utf8_path is None:
+            log.warn(enc_warn, path, 'utf-8')
+            return False
+
+        try:
+            # ignore egg-info paths
+            is_egg_info = ".egg-info" in u_path or b".egg-info" in utf8_path
+            if self.ignore_egg_info_dir and is_egg_info:
+                return False
+            # accept is either way checks out
+            if os.path.exists(u_path) or os.path.exists(utf8_path):
+                return True
+        # this will catch any encode errors decoding u_path
+        except UnicodeEncodeError:
+            log.warn(enc_warn, path, sys.getfilesystemencoding())
+
+
+class manifest_maker(sdist):
+    template = "MANIFEST.in"
+
+    def initialize_options(self) -> None:
+        self.use_defaults = True
+        self.prune = True
+        self.manifest_only = True
+        self.force_manifest = True
+        self.ignore_egg_info_dir = False
+
+    def finalize_options(self) -> None:
+        pass
+
+    def run(self) -> None:
+        self.filelist = FileList(ignore_egg_info_dir=self.ignore_egg_info_dir)
+        if not os.path.exists(self.manifest):
+            self.write_manifest()  # it must exist so it'll get in the list
+        self.add_defaults()
+        if os.path.exists(self.template):
+            self.read_template()
+        self.add_license_files()
+        self._add_referenced_files()
+        self.prune_file_list()
+        self.filelist.sort()
+        self.filelist.remove_duplicates()
+        self.write_manifest()
+
+    def _manifest_normalize(self, path):
+        path = unicode_utils.filesys_decode(path)
+        return path.replace(os.sep, '/')
+
+    def write_manifest(self) -> None:
+        """
+        Write the file list in 'self.filelist' to the manifest file
+        named by 'self.manifest'.
+        """
+        self.filelist._repair()
+
+        # Now _repairs should encodability, but not unicode
+        files = [self._manifest_normalize(f) for f in self.filelist.files]
+        msg = f"writing manifest file '{self.manifest}'"
+        self.execute(write_file, (self.manifest, files), msg)
+
+    def warn(self, msg) -> None:
+        if not self._should_suppress_warning(msg):
+            sdist.warn(self, msg)
+
+    @staticmethod
+    def _should_suppress_warning(msg):
+        """
+        suppress missing-file warnings from sdist
+        """
+        return re.match(r"standard file .*not found", msg)
+
+    def add_defaults(self) -> None:
+        sdist.add_defaults(self)
+        self.filelist.append(self.template)
+        self.filelist.append(self.manifest)
+        rcfiles = list(walk_revctrl())
+        if rcfiles:
+            self.filelist.extend(rcfiles)
+        elif os.path.exists(self.manifest):
+            self.read_manifest()
+
+        if os.path.exists("setup.py"):
+            # setup.py should be included by default, even if it's not
+            # the script called to create the sdist
+            self.filelist.append("setup.py")
+
+        ei_cmd = self.get_finalized_command('egg_info')
+        self.filelist.graft(ei_cmd.egg_info)
+
+    def add_license_files(self) -> None:
+        license_files = self.distribution.metadata.license_files or []
+        for lf in license_files:
+            log.info("adding license file '%s'", lf)
+        self.filelist.extend(license_files)
+
+    def _add_referenced_files(self):
+        """Add files referenced by the config (e.g. `file:` directive) to filelist"""
+        referenced = getattr(self.distribution, '_referenced_files', [])
+        # ^-- fallback if dist comes from distutils or is a custom class
+        for rf in referenced:
+            log.debug("adding file referenced by config '%s'", rf)
+        self.filelist.extend(referenced)
+
+    def _safe_data_files(self, build_py):
+        """
+        The parent class implementation of this method
+        (``sdist``) will try to include data files, which
+        might cause recursion problems when
+        ``include_package_data=True``.
+
+        Therefore, avoid triggering any attempt of
+        analyzing/building the manifest again.
+        """
+        if hasattr(build_py, 'get_data_files_without_manifest'):
+            return build_py.get_data_files_without_manifest()
+
+        SetuptoolsDeprecationWarning.emit(
+            "`build_py` command does not inherit from setuptools' `build_py`.",
+            """
+            Custom 'build_py' does not implement 'get_data_files_without_manifest'.
+            Please extend command classes from setuptools instead of distutils.
+            """,
+            see_url="https://peps.python.org/pep-0632/",
+            # due_date not defined yet, old projects might still do it?
+        )
+        return build_py.get_data_files()
+
+
+def write_file(filename, contents) -> None:
+    """Create a file with the specified name and write 'contents' (a
+    sequence of strings without line terminators) to it.
+    """
+    contents = "\n".join(contents)
+
+    # assuming the contents has been vetted for utf-8 encoding
+    contents = contents.encode("utf-8")
+
+    with open(filename, "wb") as f:  # always write POSIX-style manifest
+        f.write(contents)
+
+
+def write_pkg_info(cmd, basename, filename) -> None:
+    log.info("writing %s", filename)
+    if not cmd.dry_run:
+        metadata = cmd.distribution.metadata
+        metadata.version, oldver = cmd.egg_version, metadata.version
+        metadata.name, oldname = cmd.egg_name, metadata.name
+
+        try:
+            metadata.write_pkg_info(cmd.egg_info)
+        finally:
+            metadata.name, metadata.version = oldname, oldver
+
+        safe = getattr(cmd.distribution, 'zip_safe', None)
+
+        bdist_egg.write_safety_flag(cmd.egg_info, safe)
+
+
+def warn_depends_obsolete(cmd, basename, filename) -> None:
+    """
+    Unused: left to avoid errors when updating (from source) from <= 67.8.
+    Old installations have a .dist-info directory with the entry-point
+    ``depends.txt = setuptools.command.egg_info:warn_depends_obsolete``.
+    This may trigger errors when running the first egg_info in build_meta.
+    TODO: Remove this function in a version sufficiently > 68.
+    """
+
+
+# Export API used in entry_points
+write_requirements = _requirestxt.write_requirements
+write_setup_requirements = _requirestxt.write_setup_requirements
+
+
+def write_toplevel_names(cmd, basename, filename) -> None:
+    pkgs = dict.fromkeys([
+        k.split('.', 1)[0] for k in cmd.distribution.iter_distribution_names()
+    ])
+    cmd.write_file("top-level names", filename, '\n'.join(sorted(pkgs)) + '\n')
+
+
+def overwrite_arg(cmd, basename, filename) -> None:
+    write_arg(cmd, basename, filename, True)
+
+
+def write_arg(cmd, basename, filename, force: bool = False) -> None:
+    argname = os.path.splitext(basename)[0]
+    value = getattr(cmd.distribution, argname, None)
+    if value is not None:
+        value = '\n'.join(value) + '\n'
+    cmd.write_or_delete_file(argname, filename, value, force)
+
+
+def write_entries(cmd, basename, filename) -> None:
+    eps = _entry_points.load(cmd.distribution.entry_points)
+    defn = _entry_points.render(eps)
+    cmd.write_or_delete_file('entry points', filename, defn, True)
+
+
+def _egg_basename(egg_name, egg_version, py_version=None, platform=None):
+    """Compute filename of the output egg. Private API."""
+    name = _normalization.filename_component(egg_name)
+    version = _normalization.filename_component(egg_version)
+    egg = f"{name}-{version}-py{py_version or PY_MAJOR}"
+    if platform:
+        egg += f"-{platform}"
+    return egg
+
+
+class EggInfoDeprecationWarning(SetuptoolsDeprecationWarning):
+    """Deprecated behavior warning for EggInfo, bypassing suppression."""
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install.py
new file mode 100644
index 0000000000000000000000000000000000000000..19ca601458f99c50a6cceec1e70ce70ebd39e9cb
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install.py
@@ -0,0 +1,131 @@
+from __future__ import annotations
+
+import inspect
+import platform
+from collections.abc import Callable
+from typing import TYPE_CHECKING, Any, ClassVar
+
+from ..dist import Distribution
+from ..warnings import SetuptoolsDeprecationWarning, SetuptoolsWarning
+
+import distutils.command.install as orig
+from distutils.errors import DistutilsArgError
+
+if TYPE_CHECKING:
+    # This is only used for a type-cast, don't import at runtime or it'll cause deprecation warnings
+    from .easy_install import easy_install as easy_install_cls
+else:
+    easy_install_cls = None
+
+
+def __getattr__(name: str):  # pragma: no cover
+    if name == "_install":
+        SetuptoolsDeprecationWarning.emit(
+            "`setuptools.command._install` was an internal implementation detail "
+            "that was left in for numpy<1.9 support.",
+            due_date=(2025, 5, 2),  # Originally added on 2024-11-01
+        )
+        return orig.install
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+class install(orig.install):
+    """Use easy_install to install the package, w/dependencies"""
+
+    distribution: Distribution  # override distutils.dist.Distribution with setuptools.dist.Distribution
+
+    user_options = orig.install.user_options + [
+        ('old-and-unmanageable', None, "Try not to use this!"),
+        (
+            'single-version-externally-managed',
+            None,
+            "used by system package builders to create 'flat' eggs",
+        ),
+    ]
+    boolean_options = orig.install.boolean_options + [
+        'old-and-unmanageable',
+        'single-version-externally-managed',
+    ]
+    # Type the same as distutils.command.install.install.sub_commands
+    # Must keep the second tuple item potentially None due to invariance
+    new_commands: ClassVar[list[tuple[str, Callable[[Any], bool] | None]]] = [
+        ('install_egg_info', lambda self: True),
+        ('install_scripts', lambda self: True),
+    ]
+    _nc = dict(new_commands)
+
+    def initialize_options(self):
+        SetuptoolsDeprecationWarning.emit(
+            "setup.py install is deprecated.",
+            """
+            Please avoid running ``setup.py`` directly.
+            Instead, use pypa/build, pypa/installer or other
+            standards-based tools.
+            """,
+            see_url="https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html",
+            due_date=(2025, 10, 31),
+        )
+
+        super().initialize_options()
+        self.old_and_unmanageable = None
+        self.single_version_externally_managed = None
+
+    def finalize_options(self) -> None:
+        super().finalize_options()
+        if self.root:
+            self.single_version_externally_managed = True
+        elif self.single_version_externally_managed:
+            if not self.root and not self.record:
+                raise DistutilsArgError(
+                    "You must specify --record or --root when building system packages"
+                )
+
+    def handle_extra_path(self):
+        if self.root or self.single_version_externally_managed:
+            # explicit backward-compatibility mode, allow extra_path to work
+            return orig.install.handle_extra_path(self)
+
+        # Ignore extra_path when installing an egg (or being run by another
+        # command without --root or --single-version-externally-managed
+        self.path_file = None
+        self.extra_dirs = ''
+        return None
+
+    @staticmethod
+    def _called_from_setup(run_frame):
+        """
+        Attempt to detect whether run() was called from setup() or by another
+        command.  If called by setup(), the parent caller will be the
+        'run_command' method in 'distutils.dist', and *its* caller will be
+        the 'run_commands' method.  If called any other way, the
+        immediate caller *might* be 'run_command', but it won't have been
+        called by 'run_commands'. Return True in that case or if a call stack
+        is unavailable. Return False otherwise.
+        """
+        if run_frame is None:
+            msg = "Call stack not available. bdist_* commands may fail."
+            SetuptoolsWarning.emit(msg)
+            if platform.python_implementation() == 'IronPython':
+                msg = "For best results, pass -X:Frames to enable call stack."
+                SetuptoolsWarning.emit(msg)
+            return True
+
+        frames = inspect.getouterframes(run_frame)
+        for frame in frames[2:4]:
+            (caller,) = frame[:1]
+            info = inspect.getframeinfo(caller)
+            caller_module = caller.f_globals.get('__name__', '')
+
+            if caller_module == "setuptools.dist" and info.function == "run_command":
+                # Starting from v61.0.0 setuptools overwrites dist.run_command
+                continue
+
+            return caller_module == 'distutils.dist' and info.function == 'run_commands'
+
+        return False
+
+
+# XXX Python 3.1 doesn't see _nc if this is inside the class
+install.sub_commands = [
+    cmd for cmd in orig.install.sub_commands if cmd[0] not in install._nc
+] + install.new_commands
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install_egg_info.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install_egg_info.py
new file mode 100644
index 0000000000000000000000000000000000000000..44f22ccf51cc3fb1662b326c3150845356d77fc3
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install_egg_info.py
@@ -0,0 +1,58 @@
+import os
+
+from setuptools import Command, namespaces
+from setuptools.archive_util import unpack_archive
+
+from .._path import ensure_directory
+
+from distutils import dir_util, log
+
+
+class install_egg_info(namespaces.Installer, Command):
+    """Install an .egg-info directory for the package"""
+
+    description = "Install an .egg-info directory for the package"
+
+    user_options = [
+        ('install-dir=', 'd', "directory to install to"),
+    ]
+
+    def initialize_options(self):
+        self.install_dir = None
+
+    def finalize_options(self) -> None:
+        self.set_undefined_options('install_lib', ('install_dir', 'install_dir'))
+        ei_cmd = self.get_finalized_command("egg_info")
+        basename = f"{ei_cmd._get_egg_basename()}.egg-info"
+        self.source = ei_cmd.egg_info
+        self.target = os.path.join(self.install_dir, basename)
+        self.outputs: list[str] = []
+
+    def run(self) -> None:
+        self.run_command('egg_info')
+        if os.path.isdir(self.target) and not os.path.islink(self.target):
+            dir_util.remove_tree(self.target, dry_run=self.dry_run)
+        elif os.path.exists(self.target):
+            self.execute(os.unlink, (self.target,), "Removing " + self.target)
+        if not self.dry_run:
+            ensure_directory(self.target)
+        self.execute(self.copytree, (), f"Copying {self.source} to {self.target}")
+        self.install_namespaces()
+
+    def get_outputs(self):
+        return self.outputs
+
+    def copytree(self) -> None:
+        # Copy the .egg-info tree to site-packages
+        def skimmer(src, dst):
+            # filter out source-control directories; note that 'src' is always
+            # a '/'-separated path, regardless of platform.  'dst' is a
+            # platform-specific path.
+            for skip in '.svn/', 'CVS/':
+                if src.startswith(skip) or '/' + skip in src:
+                    return None
+            self.outputs.append(dst)
+            log.debug("Copying %s to %s", src, dst)
+            return dst
+
+        unpack_archive(self.source, self.target, skimmer)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install_lib.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install_lib.py
new file mode 100644
index 0000000000000000000000000000000000000000..8e1e07271028386e138585cac7619ab0338017cc
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install_lib.py
@@ -0,0 +1,137 @@
+from __future__ import annotations
+
+import os
+import sys
+from itertools import product, starmap
+
+from .._path import StrPath
+from ..dist import Distribution
+
+import distutils.command.install_lib as orig
+
+
+class install_lib(orig.install_lib):
+    """Don't add compiled flags to filenames of non-Python files"""
+
+    distribution: Distribution  # override distutils.dist.Distribution with setuptools.dist.Distribution
+
+    def run(self) -> None:
+        self.build()
+        outfiles = self.install()
+        if outfiles is not None:
+            # always compile, in case we have any extension stubs to deal with
+            self.byte_compile(outfiles)
+
+    def get_exclusions(self):
+        """
+        Return a collections.Sized collections.Container of paths to be
+        excluded for single_version_externally_managed installations.
+        """
+        all_packages = (
+            pkg
+            for ns_pkg in self._get_SVEM_NSPs()
+            for pkg in self._all_packages(ns_pkg)
+        )
+
+        excl_specs = product(all_packages, self._gen_exclusion_paths())
+        return set(starmap(self._exclude_pkg_path, excl_specs))
+
+    def _exclude_pkg_path(self, pkg, exclusion_path):
+        """
+        Given a package name and exclusion path within that package,
+        compute the full exclusion path.
+        """
+        parts = pkg.split('.') + [exclusion_path]
+        return os.path.join(self.install_dir, *parts)
+
+    @staticmethod
+    def _all_packages(pkg_name):
+        """
+        >>> list(install_lib._all_packages('foo.bar.baz'))
+        ['foo.bar.baz', 'foo.bar', 'foo']
+        """
+        while pkg_name:
+            yield pkg_name
+            pkg_name, _sep, _child = pkg_name.rpartition('.')
+
+    def _get_SVEM_NSPs(self):
+        """
+        Get namespace packages (list) but only for
+        single_version_externally_managed installations and empty otherwise.
+        """
+        # TODO: is it necessary to short-circuit here? i.e. what's the cost
+        # if get_finalized_command is called even when namespace_packages is
+        # False?
+        if not self.distribution.namespace_packages:
+            return []
+
+        install_cmd = self.get_finalized_command('install')
+        svem = install_cmd.single_version_externally_managed
+
+        return self.distribution.namespace_packages if svem else []
+
+    @staticmethod
+    def _gen_exclusion_paths():
+        """
+        Generate file paths to be excluded for namespace packages (bytecode
+        cache files).
+        """
+        # always exclude the package module itself
+        yield '__init__.py'
+
+        yield '__init__.pyc'
+        yield '__init__.pyo'
+
+        if not hasattr(sys, 'implementation'):
+            return
+
+        base = os.path.join('__pycache__', '__init__.' + sys.implementation.cache_tag)
+        yield base + '.pyc'
+        yield base + '.pyo'
+        yield base + '.opt-1.pyc'
+        yield base + '.opt-2.pyc'
+
+    def copy_tree(
+        self,
+        infile: StrPath,
+        outfile: str,
+        # override: Using actual booleans
+        preserve_mode: bool = True,  # type: ignore[override]
+        preserve_times: bool = True,  # type: ignore[override]
+        preserve_symlinks: bool = False,  # type: ignore[override]
+        level: object = 1,
+    ) -> list[str]:
+        assert preserve_mode
+        assert preserve_times
+        assert not preserve_symlinks
+        exclude = self.get_exclusions()
+
+        if not exclude:
+            return orig.install_lib.copy_tree(self, infile, outfile)
+
+        # Exclude namespace package __init__.py* files from the output
+
+        from setuptools.archive_util import unpack_directory
+
+        from distutils import log
+
+        outfiles: list[str] = []
+
+        def pf(src: str, dst: str):
+            if dst in exclude:
+                log.warn("Skipping installation of %s (namespace package)", dst)
+                return False
+
+            log.info("copying %s -> %s", src, os.path.dirname(dst))
+            outfiles.append(dst)
+            return dst
+
+        unpack_directory(infile, outfile, pf)
+        return outfiles
+
+    def get_outputs(self):
+        outputs = orig.install_lib.get_outputs(self)
+        exclude = self.get_exclusions()
+        if exclude:
+            return [f for f in outputs if f not in exclude]
+        return outputs
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install_scripts.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install_scripts.py
new file mode 100644
index 0000000000000000000000000000000000000000..537181e321520094c02d3ad15b88d895bde682c0
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/install_scripts.py
@@ -0,0 +1,67 @@
+from __future__ import annotations
+
+import os
+import sys
+
+from .._path import ensure_directory
+from ..dist import Distribution
+
+import distutils.command.install_scripts as orig
+from distutils import log
+
+
+class install_scripts(orig.install_scripts):
+    """Do normal script install, plus any egg_info wrapper scripts"""
+
+    distribution: Distribution  # override distutils.dist.Distribution with setuptools.dist.Distribution
+
+    def initialize_options(self) -> None:
+        orig.install_scripts.initialize_options(self)
+        self.no_ep = False
+
+    def run(self) -> None:
+        self.run_command("egg_info")
+        if self.distribution.scripts:
+            orig.install_scripts.run(self)  # run first to set up self.outfiles
+        else:
+            self.outfiles: list[str] = []
+        if self.no_ep:
+            # don't install entry point scripts into .egg file!
+            return
+        self._install_ep_scripts()
+
+    def _install_ep_scripts(self):
+        # Delay import side-effects
+        from .. import _scripts
+        from .._importlib import metadata
+
+        ei_cmd = self.get_finalized_command("egg_info")
+        dist = metadata.Distribution.at(path=ei_cmd.egg_info)
+        bs_cmd = self.get_finalized_command('build_scripts')
+        exec_param = getattr(bs_cmd, 'executable', None)
+        writer = _scripts.ScriptWriter
+        if exec_param == sys.executable:
+            # In case the path to the Python executable contains a space, wrap
+            # it so it's not split up.
+            exec_param = [exec_param]
+        # resolve the writer to the environment
+        writer = writer.best()
+        cmd = writer.command_spec_class.best().from_param(exec_param)
+        for args in writer.get_args(dist, cmd.as_header()):
+            self.write_script(*args)
+
+    def write_script(self, script_name, contents, mode: str = "t", *ignored) -> None:
+        """Write an executable file to the scripts directory"""
+        from .._shutil import attempt_chmod_verbose as chmod, current_umask
+
+        log.info("Installing %s script to %s", script_name, self.install_dir)
+        target = os.path.join(self.install_dir, script_name)
+        self.outfiles.append(target)
+
+        encoding = None if "b" in mode else "utf-8"
+        mask = current_umask()
+        if not self.dry_run:
+            ensure_directory(target)
+            with open(target, "w" + mode, encoding=encoding) as f:
+                f.write(contents)
+            chmod(target, 0o777 - mask)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/launcher manifest.xml b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/launcher manifest.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5972a96d8ded85cc14147ffc1400ec67c3b5a578
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/launcher manifest.xml	
@@ -0,0 +1,15 @@
+
+
+    
+    
+    
+        
+            
+                
+            
+        
+    
+
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/rotate.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/rotate.py
new file mode 100644
index 0000000000000000000000000000000000000000..acdce07baaf3e4fc87552c39d7ee6e0271fe2a72
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/rotate.py
@@ -0,0 +1,65 @@
+from __future__ import annotations
+
+import os
+from typing import ClassVar
+
+from .. import Command, _shutil
+
+from distutils import log
+from distutils.errors import DistutilsOptionError
+from distutils.util import convert_path
+
+
+class rotate(Command):
+    """Delete older distributions"""
+
+    description = "delete older distributions, keeping N newest files"
+    user_options = [
+        ('match=', 'm', "patterns to match (required)"),
+        ('dist-dir=', 'd', "directory where the distributions are"),
+        ('keep=', 'k', "number of matching distributions to keep"),
+    ]
+
+    boolean_options: ClassVar[list[str]] = []
+
+    def initialize_options(self):
+        self.match = None
+        self.dist_dir = None
+        self.keep = None
+
+    def finalize_options(self) -> None:
+        if self.match is None:
+            raise DistutilsOptionError(
+                "Must specify one or more (comma-separated) match patterns "
+                "(e.g. '.zip' or '.egg')"
+            )
+        if self.keep is None:
+            raise DistutilsOptionError("Must specify number of files to keep")
+        try:
+            self.keep = int(self.keep)
+        except ValueError as e:
+            raise DistutilsOptionError("--keep must be an integer") from e
+        if isinstance(self.match, str):
+            self.match = [convert_path(p.strip()) for p in self.match.split(',')]
+        self.set_undefined_options('bdist', ('dist_dir', 'dist_dir'))
+
+    def run(self) -> None:
+        self.run_command("egg_info")
+        from glob import glob
+
+        for pattern in self.match:
+            pattern = self.distribution.get_name() + '*' + pattern
+            files = glob(os.path.join(self.dist_dir, pattern))
+            files = [(os.path.getmtime(f), f) for f in files]
+            files.sort()
+            files.reverse()
+
+            log.info("%d file(s) matching %s", len(files), pattern)
+            files = files[self.keep :]
+            for t, f in files:
+                log.info("Deleting %s", f)
+                if not self.dry_run:
+                    if os.path.isdir(f):
+                        _shutil.rmtree(f)
+                    else:
+                        os.unlink(f)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/saveopts.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/saveopts.py
new file mode 100644
index 0000000000000000000000000000000000000000..2a2cbce6e2aad396f4a5ee9788d53387237df96d
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/saveopts.py
@@ -0,0 +1,21 @@
+from setuptools.command.setopt import edit_config, option_base
+
+
+class saveopts(option_base):
+    """Save command-line options to a file"""
+
+    description = "save supplied options to setup.cfg or other config file"
+
+    def run(self) -> None:
+        dist = self.distribution
+        settings: dict[str, dict[str, str]] = {}
+
+        for cmd in dist.command_options:
+            if cmd == 'saveopts':
+                continue  # don't save our own options!
+
+            for opt, (src, val) in dist.get_option_dict(cmd).items():
+                if src == "command line":
+                    settings.setdefault(cmd, {})[opt] = val
+
+        edit_config(self.filename, settings, self.dry_run)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/sdist.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/sdist.py
new file mode 100644
index 0000000000000000000000000000000000000000..17279ac421fce8cb8e062048549615e7f36aea9d
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/sdist.py
@@ -0,0 +1,218 @@
+from __future__ import annotations
+
+import contextlib
+import os
+import re
+from collections.abc import Iterator
+from itertools import chain
+from typing import ClassVar
+
+from .._importlib import metadata
+from ..dist import Distribution
+from .build import _ORIGINAL_SUBCOMMANDS
+
+import distutils.command.sdist as orig
+from distutils import log
+
+_default_revctrl = list
+
+
+def walk_revctrl(dirname='') -> Iterator:
+    """Find all files under revision control"""
+    for ep in metadata.entry_points(group='setuptools.file_finders'):
+        yield from ep.load()(dirname)
+
+
+class sdist(orig.sdist):
+    """Smart sdist that finds anything supported by revision control"""
+
+    user_options = [
+        ('formats=', None, "formats for source distribution (comma-separated list)"),
+        (
+            'keep-temp',
+            'k',
+            "keep the distribution tree around after creating archive file(s)",
+        ),
+        (
+            'dist-dir=',
+            'd',
+            "directory to put the source distribution archive(s) in [default: dist]",
+        ),
+        (
+            'owner=',
+            'u',
+            "Owner name used when creating a tar file [default: current user]",
+        ),
+        (
+            'group=',
+            'g',
+            "Group name used when creating a tar file [default: current group]",
+        ),
+    ]
+
+    distribution: Distribution  # override distutils.dist.Distribution with setuptools.dist.Distribution
+    negative_opt: ClassVar[dict[str, str]] = {}
+
+    README_EXTENSIONS = ['', '.rst', '.txt', '.md']
+    READMES = tuple(f'README{ext}' for ext in README_EXTENSIONS)
+
+    def run(self) -> None:
+        self.run_command('egg_info')
+        ei_cmd = self.get_finalized_command('egg_info')
+        self.filelist = ei_cmd.filelist
+        self.filelist.append(os.path.join(ei_cmd.egg_info, 'SOURCES.txt'))
+        self.check_readme()
+
+        # Run sub commands
+        for cmd_name in self.get_sub_commands():
+            self.run_command(cmd_name)
+
+        self.make_distribution()
+
+        dist_files = getattr(self.distribution, 'dist_files', [])
+        for file in self.archive_files:
+            data = ('sdist', '', file)
+            if data not in dist_files:
+                dist_files.append(data)
+
+    def initialize_options(self) -> None:
+        orig.sdist.initialize_options(self)
+
+    def make_distribution(self) -> None:
+        """
+        Workaround for #516
+        """
+        with self._remove_os_link():
+            orig.sdist.make_distribution(self)
+
+    @staticmethod
+    @contextlib.contextmanager
+    def _remove_os_link():
+        """
+        In a context, remove and restore os.link if it exists
+        """
+
+        class NoValue:
+            pass
+
+        orig_val = getattr(os, 'link', NoValue)
+        try:
+            del os.link
+        except Exception:
+            pass
+        try:
+            yield
+        finally:
+            if orig_val is not NoValue:
+                os.link = orig_val
+
+    def add_defaults(self) -> None:
+        super().add_defaults()
+        self._add_defaults_build_sub_commands()
+
+    def _add_defaults_optional(self):
+        super()._add_defaults_optional()
+        if os.path.isfile('pyproject.toml'):
+            self.filelist.append('pyproject.toml')
+
+    def _add_defaults_python(self):
+        """getting python files"""
+        if self.distribution.has_pure_modules():
+            build_py = self.get_finalized_command('build_py')
+            self.filelist.extend(build_py.get_source_files())
+            self._add_data_files(self._safe_data_files(build_py))
+
+    def _add_defaults_build_sub_commands(self):
+        build = self.get_finalized_command("build")
+        missing_cmds = set(build.get_sub_commands()) - _ORIGINAL_SUBCOMMANDS
+        # ^-- the original built-in sub-commands are already handled by default.
+        cmds = (self.get_finalized_command(c) for c in missing_cmds)
+        files = (c.get_source_files() for c in cmds if hasattr(c, "get_source_files"))
+        self.filelist.extend(chain.from_iterable(files))
+
+    def _safe_data_files(self, build_py):
+        """
+        Since the ``sdist`` class is also used to compute the MANIFEST
+        (via :obj:`setuptools.command.egg_info.manifest_maker`),
+        there might be recursion problems when trying to obtain the list of
+        data_files and ``include_package_data=True`` (which in turn depends on
+        the files included in the MANIFEST).
+
+        To avoid that, ``manifest_maker`` should be able to overwrite this
+        method and avoid recursive attempts to build/analyze the MANIFEST.
+        """
+        return build_py.data_files
+
+    def _add_data_files(self, data_files):
+        """
+        Add data files as found in build_py.data_files.
+        """
+        self.filelist.extend(
+            os.path.join(src_dir, name)
+            for _, src_dir, _, filenames in data_files
+            for name in filenames
+        )
+
+    def _add_defaults_data_files(self):
+        try:
+            super()._add_defaults_data_files()
+        except TypeError:
+            log.warn("data_files contains unexpected objects")
+
+    def prune_file_list(self) -> None:
+        super().prune_file_list()
+        # Prevent accidental inclusion of test-related cache dirs at the project root
+        sep = re.escape(os.sep)
+        self.filelist.exclude_pattern(r"^(\.tox|\.nox|\.venv)" + sep, is_regex=True)
+
+    def check_readme(self) -> None:
+        for f in self.READMES:
+            if os.path.exists(f):
+                return
+        else:
+            self.warn(
+                "standard file not found: should have one of " + ', '.join(self.READMES)
+            )
+
+    def make_release_tree(self, base_dir, files) -> None:
+        orig.sdist.make_release_tree(self, base_dir, files)
+
+        # Save any egg_info command line options used to create this sdist
+        dest = os.path.join(base_dir, 'setup.cfg')
+        if hasattr(os, 'link') and os.path.exists(dest):
+            # unlink and re-copy, since it might be hard-linked, and
+            # we don't want to change the source version
+            os.unlink(dest)
+            self.copy_file('setup.cfg', dest)
+
+        self.get_finalized_command('egg_info').save_version_info(dest)
+
+    def _manifest_is_not_generated(self):
+        # check for special comment used in 2.7.1 and higher
+        if not os.path.isfile(self.manifest):
+            return False
+
+        with open(self.manifest, 'rb') as fp:
+            first_line = fp.readline()
+        return first_line != b'# file GENERATED by distutils, do NOT edit\n'
+
+    def read_manifest(self) -> None:
+        """Read the manifest file (named by 'self.manifest') and use it to
+        fill in 'self.filelist', the list of files to include in the source
+        distribution.
+        """
+        log.info("reading manifest file '%s'", self.manifest)
+        manifest = open(self.manifest, 'rb')
+        for bytes_line in manifest:
+            # The manifest must contain UTF-8. See #303.
+            try:
+                line = bytes_line.decode('UTF-8')
+            except UnicodeDecodeError:
+                log.warn(f"{line!r} not UTF-8 decodable -- skipping")
+                continue
+            # ignore comments and blank lines
+            line = line.strip()
+            if line.startswith('#') or not line:
+                continue
+            self.filelist.append(line)
+        manifest.close()
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/setopt.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/setopt.py
new file mode 100644
index 0000000000000000000000000000000000000000..43cb5939993e9c39e91242c047872a15756e6959
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/setopt.py
@@ -0,0 +1,141 @@
+import configparser
+import os
+
+from .. import Command
+from ..unicode_utils import _cfg_read_utf8_with_fallback
+
+import distutils
+from distutils import log
+from distutils.errors import DistutilsOptionError
+from distutils.util import convert_path
+
+__all__ = ['config_file', 'edit_config', 'option_base', 'setopt']
+
+
+def config_file(kind="local"):
+    """Get the filename of the distutils, local, global, or per-user config
+
+    `kind` must be one of "local", "global", or "user"
+    """
+    if kind == 'local':
+        return 'setup.cfg'
+    if kind == 'global':
+        return os.path.join(os.path.dirname(distutils.__file__), 'distutils.cfg')
+    if kind == 'user':
+        dot = os.name == 'posix' and '.' or ''
+        return os.path.expanduser(convert_path(f"~/{dot}pydistutils.cfg"))
+    raise ValueError("config_file() type must be 'local', 'global', or 'user'", kind)
+
+
+def edit_config(filename, settings, dry_run=False) -> None:
+    """Edit a configuration file to include `settings`
+
+    `settings` is a dictionary of dictionaries or ``None`` values, keyed by
+    command/section name.  A ``None`` value means to delete the entire section,
+    while a dictionary lists settings to be changed or deleted in that section.
+    A setting of ``None`` means to delete that setting.
+    """
+    log.debug("Reading configuration from %s", filename)
+    opts = configparser.RawConfigParser()
+    opts.optionxform = lambda optionstr: optionstr  # type: ignore[method-assign] # overriding method
+    _cfg_read_utf8_with_fallback(opts, filename)
+
+    for section, options in settings.items():
+        if options is None:
+            log.info("Deleting section [%s] from %s", section, filename)
+            opts.remove_section(section)
+        else:
+            if not opts.has_section(section):
+                log.debug("Adding new section [%s] to %s", section, filename)
+                opts.add_section(section)
+            for option, value in options.items():
+                if value is None:
+                    log.debug("Deleting %s.%s from %s", section, option, filename)
+                    opts.remove_option(section, option)
+                    if not opts.options(section):
+                        log.info(
+                            "Deleting empty [%s] section from %s", section, filename
+                        )
+                        opts.remove_section(section)
+                else:
+                    log.debug(
+                        "Setting %s.%s to %r in %s", section, option, value, filename
+                    )
+                    opts.set(section, option, value)
+
+    log.info("Writing %s", filename)
+    if not dry_run:
+        with open(filename, 'w', encoding="utf-8") as f:
+            opts.write(f)
+
+
+class option_base(Command):
+    """Abstract base class for commands that mess with config files"""
+
+    user_options = [
+        ('global-config', 'g', "save options to the site-wide distutils.cfg file"),
+        ('user-config', 'u', "save options to the current user's pydistutils.cfg file"),
+        ('filename=', 'f', "configuration file to use (default=setup.cfg)"),
+    ]
+
+    boolean_options = [
+        'global-config',
+        'user-config',
+    ]
+
+    def initialize_options(self):
+        self.global_config = None
+        self.user_config = None
+        self.filename = None
+
+    def finalize_options(self) -> None:
+        filenames = []
+        if self.global_config:
+            filenames.append(config_file('global'))
+        if self.user_config:
+            filenames.append(config_file('user'))
+        if self.filename is not None:
+            filenames.append(self.filename)
+        if not filenames:
+            filenames.append(config_file('local'))
+        if len(filenames) > 1:
+            raise DistutilsOptionError(
+                "Must specify only one configuration file option", filenames
+            )
+        (self.filename,) = filenames
+
+
+class setopt(option_base):
+    """Save command-line options to a file"""
+
+    description = "set an option in setup.cfg or another config file"
+
+    user_options = [
+        ('command=', 'c', 'command to set an option for'),
+        ('option=', 'o', 'option to set'),
+        ('set-value=', 's', 'value of the option'),
+        ('remove', 'r', 'remove (unset) the value'),
+    ] + option_base.user_options
+
+    boolean_options = option_base.boolean_options + ['remove']
+
+    def initialize_options(self):
+        option_base.initialize_options(self)
+        self.command = None
+        self.option = None
+        self.set_value = None
+        self.remove = None
+
+    def finalize_options(self) -> None:
+        option_base.finalize_options(self)
+        if self.command is None or self.option is None:
+            raise DistutilsOptionError("Must specify --command *and* --option")
+        if self.set_value is None and not self.remove:
+            raise DistutilsOptionError("Must specify --set-value or --remove")
+
+    def run(self) -> None:
+        edit_config(
+            self.filename,
+            {self.command: {self.option.replace('-', '_'): self.set_value}},
+            self.dry_run,
+        )
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/test.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/test.py
new file mode 100644
index 0000000000000000000000000000000000000000..5d03c91102fa62d252adcbd858053e2e3d7ca7ef
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/command/test.py
@@ -0,0 +1,47 @@
+from __future__ import annotations
+
+from typing import NoReturn
+
+from setuptools import Command
+from setuptools.warnings import SetuptoolsDeprecationWarning
+
+
+# Would restrict to Literal["test"], but mypy doesn't support it: https://github.com/python/mypy/issues/8203
+def __getattr__(name: str) -> type[_test]:
+    if name == 'test':
+        SetuptoolsDeprecationWarning.emit(
+            "The test command is disabled and references to it are deprecated.",
+            "Please remove any references to `setuptools.command.test` in all "
+            "supported versions of the affected package.",
+            due_date=(2024, 11, 15),
+            stacklevel=2,
+        )
+        return _test
+    raise AttributeError(name)
+
+
+class _test(Command):
+    """
+    Stub to warn when test command is referenced or used.
+    """
+
+    description = "stub for old test command (do not use)"
+
+    user_options = [
+        ('test-module=', 'm', "Run 'test_suite' in specified module"),
+        (
+            'test-suite=',
+            's',
+            "Run single test, case or suite (e.g. 'module.test_suite')",
+        ),
+        ('test-runner=', 'r', "Test runner to use"),
+    ]
+
+    def initialize_options(self) -> None:
+        pass
+
+    def finalize_options(self) -> None:
+        pass
+
+    def run(self) -> NoReturn:
+        raise RuntimeError("Support for the test command was removed in Setuptools 72")
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py310.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py310.py
new file mode 100644
index 0000000000000000000000000000000000000000..58a4d9f36606d3be8c288418568b0f2e1ef8bcf2
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py310.py
@@ -0,0 +1,20 @@
+import sys
+
+__all__ = ['tomllib']
+
+
+if sys.version_info >= (3, 11):
+    import tomllib
+else:  # pragma: no cover
+    import tomli as tomllib
+
+
+if sys.version_info >= (3, 11):
+
+    def add_note(ex, note):
+        ex.add_note(note)
+
+else:  # pragma: no cover
+
+    def add_note(ex, note):
+        vars(ex).setdefault('__notes__', []).append(note)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py311.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py311.py
new file mode 100644
index 0000000000000000000000000000000000000000..52b58af32a28817deeaf592cc795f311434e39e7
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py311.py
@@ -0,0 +1,27 @@
+from __future__ import annotations
+
+import shutil
+import sys
+from typing import TYPE_CHECKING, Any, Callable
+
+if TYPE_CHECKING:
+    from _typeshed import ExcInfo, StrOrBytesPath
+    from typing_extensions import TypeAlias
+
+# Same as shutil._OnExcCallback from typeshed
+_OnExcCallback: TypeAlias = Callable[[Callable[..., Any], str, BaseException], object]
+
+
+def shutil_rmtree(
+    path: StrOrBytesPath,
+    ignore_errors: bool = False,
+    onexc: _OnExcCallback | None = None,
+) -> None:
+    if sys.version_info >= (3, 12):
+        return shutil.rmtree(path, ignore_errors, onexc=onexc)
+
+    def _handler(fn: Callable[..., Any], path: str, excinfo: ExcInfo) -> None:
+        if onexc:
+            onexc(fn, path, excinfo[1])
+
+    return shutil.rmtree(path, ignore_errors, onerror=_handler)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py312.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py312.py
new file mode 100644
index 0000000000000000000000000000000000000000..b20c5f697a861a680c4a747baf9ca9c901e72978
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py312.py
@@ -0,0 +1,13 @@
+from __future__ import annotations
+
+import sys
+
+if sys.version_info >= (3, 12, 4):
+    # Python 3.13 should support `.pth` files encoded in UTF-8
+    # See discussion in https://github.com/python/cpython/issues/77102
+    PTH_ENCODING: str | None = "utf-8"
+else:
+    from .py39 import LOCALE_ENCODING
+
+    # PTH_ENCODING = "locale"
+    PTH_ENCODING = LOCALE_ENCODING
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py39.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py39.py
new file mode 100644
index 0000000000000000000000000000000000000000..04a4abe5a9e61596f97dc3d1b0b3da93a558158f
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/compat/py39.py
@@ -0,0 +1,9 @@
+import sys
+
+# Explicitly use the ``"locale"`` encoding in versions that support it,
+# otherwise just rely on the implicit handling of ``encoding=None``.
+# Since all platforms that support ``EncodingWarning`` also support
+# ``encoding="locale"``, this can be used to suppress the warning.
+# However, please try to use UTF-8 when possible
+# (.pth files are the notorious exception: python/cpython#77102, pypa/setuptools#3937).
+LOCALE_ENCODING = "locale" if sys.version_info >= (3, 10) else None
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/NOTICE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/NOTICE
new file mode 100644
index 0000000000000000000000000000000000000000..01864511b0f52a6bf944f70b5e15b75364791935
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/NOTICE
@@ -0,0 +1,10 @@
+The following files include code from opensource projects
+(either as direct copies or modified versions):
+
+- `setuptools.schema.json`, `distutils.schema.json`:
+    - project: `validate-pyproject` - licensed under MPL-2.0
+      (https://github.com/abravalheri/validate-pyproject):
+
+      This Source Code Form is subject to the terms of the Mozilla Public
+      License, v. 2.0. If a copy of the MPL was not distributed with this file,
+      You can obtain one at https://mozilla.org/MPL/2.0/.
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..fcc7d008d6c9b3ab2610f2a1b05c4c1eeb5e1416
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/__init__.py
@@ -0,0 +1,43 @@
+"""For backward compatibility, expose main functions from
+``setuptools.config.setupcfg``
+"""
+
+from functools import wraps
+from typing import Callable, TypeVar, cast
+
+from ..warnings import SetuptoolsDeprecationWarning
+from . import setupcfg
+
+Fn = TypeVar("Fn", bound=Callable)
+
+__all__ = ('parse_configuration', 'read_configuration')
+
+
+def _deprecation_notice(fn: Fn) -> Fn:
+    @wraps(fn)
+    def _wrapper(*args, **kwargs):
+        SetuptoolsDeprecationWarning.emit(
+            "Deprecated API usage.",
+            f"""
+            As setuptools moves its configuration towards `pyproject.toml`,
+            `{__name__}.{fn.__name__}` became deprecated.
+
+            For the time being, you can use the `{setupcfg.__name__}` module
+            to access a backward compatible API, but this module is provisional
+            and might be removed in the future.
+
+            To read project metadata, consider using
+            ``build.util.project_wheel_metadata`` (https://pypi.org/project/build/).
+            For simple scenarios, you can also try parsing the file directly
+            with the help of ``configparser``.
+            """,
+            # due_date not defined yet, because the community still heavily relies on it
+            # Warning introduced in 24 Mar 2022
+        )
+        return fn(*args, **kwargs)
+
+    return cast(Fn, _wrapper)
+
+
+read_configuration = _deprecation_notice(setupcfg.read_configuration)
+parse_configuration = _deprecation_notice(setupcfg.parse_configuration)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_apply_pyprojecttoml.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_apply_pyprojecttoml.py
new file mode 100644
index 0000000000000000000000000000000000000000..2a59446042dc03078efed7bba0eb980ac346d924
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_apply_pyprojecttoml.py
@@ -0,0 +1,526 @@
+"""Translation layer between pyproject config and setuptools distribution and
+metadata objects.
+
+The distribution and metadata objects are modeled after (an old version of)
+core metadata, therefore configs in the format specified for ``pyproject.toml``
+need to be processed before being applied.
+
+**PRIVATE MODULE**: API reserved for setuptools internal usage only.
+"""
+
+from __future__ import annotations
+
+import logging
+import os
+from collections.abc import Mapping
+from email.headerregistry import Address
+from functools import partial, reduce
+from inspect import cleandoc
+from itertools import chain
+from types import MappingProxyType
+from typing import TYPE_CHECKING, Any, Callable, TypeVar, Union
+
+from .. import _static
+from .._path import StrPath
+from ..errors import InvalidConfigError, RemovedConfigError
+from ..extension import Extension
+from ..warnings import SetuptoolsDeprecationWarning, SetuptoolsWarning
+
+if TYPE_CHECKING:
+    from typing_extensions import TypeAlias
+
+    from setuptools._importlib import metadata
+    from setuptools.dist import Distribution
+
+    from distutils.dist import _OptionsList  # Comes from typeshed
+
+
+EMPTY: Mapping = MappingProxyType({})  # Immutable dict-like
+_ProjectReadmeValue: TypeAlias = Union[str, dict[str, str]]
+_Correspondence: TypeAlias = Callable[["Distribution", Any, Union[StrPath, None]], None]
+_T = TypeVar("_T")
+
+_logger = logging.getLogger(__name__)
+
+
+def apply(dist: Distribution, config: dict, filename: StrPath) -> Distribution:
+    """Apply configuration dict read with :func:`read_configuration`"""
+
+    if not config:
+        return dist  # short-circuit unrelated pyproject.toml file
+
+    root_dir = os.path.dirname(filename) or "."
+
+    _apply_project_table(dist, config, root_dir)
+    _apply_tool_table(dist, config, filename)
+
+    current_directory = os.getcwd()
+    os.chdir(root_dir)
+    try:
+        dist._finalize_requires()
+        dist._finalize_license_expression()
+        dist._finalize_license_files()
+    finally:
+        os.chdir(current_directory)
+
+    return dist
+
+
+def _apply_project_table(dist: Distribution, config: dict, root_dir: StrPath):
+    orig_config = config.get("project", {})
+    if not orig_config:
+        return  # short-circuit
+
+    project_table = {k: _static.attempt_conversion(v) for k, v in orig_config.items()}
+    _handle_missing_dynamic(dist, project_table)
+    _unify_entry_points(project_table)
+
+    for field, value in project_table.items():
+        norm_key = json_compatible_key(field)
+        corresp = PYPROJECT_CORRESPONDENCE.get(norm_key, norm_key)
+        if callable(corresp):
+            corresp(dist, value, root_dir)
+        else:
+            _set_config(dist, corresp, value)
+
+
+def _apply_tool_table(dist: Distribution, config: dict, filename: StrPath):
+    tool_table = config.get("tool", {}).get("setuptools", {})
+    if not tool_table:
+        return  # short-circuit
+
+    if "license-files" in tool_table:
+        if "license-files" in config.get("project", {}):
+            # https://github.com/pypa/setuptools/pull/4837#discussion_r2004983349
+            raise InvalidConfigError(
+                "'project.license-files' is defined already. "
+                "Remove 'tool.setuptools.license-files'."
+            )
+
+        pypa_guides = "guides/writing-pyproject-toml/#license-files"
+        SetuptoolsDeprecationWarning.emit(
+            "'tool.setuptools.license-files' is deprecated in favor of "
+            "'project.license-files' (available on setuptools>=77.0.0).",
+            see_url=f"https://packaging.python.org/en/latest/{pypa_guides}",
+            due_date=(2027, 2, 18),  # Warning introduced on 2025-02-18
+        )
+
+    for field, value in tool_table.items():
+        norm_key = json_compatible_key(field)
+
+        if norm_key in TOOL_TABLE_REMOVALS:
+            suggestion = cleandoc(TOOL_TABLE_REMOVALS[norm_key])
+            msg = f"""
+            The parameter `tool.setuptools.{field}` was long deprecated
+            and has been removed from `pyproject.toml`.
+            """
+            raise RemovedConfigError("\n".join([cleandoc(msg), suggestion]))
+
+        norm_key = TOOL_TABLE_RENAMES.get(norm_key, norm_key)
+        corresp = TOOL_TABLE_CORRESPONDENCE.get(norm_key, norm_key)
+        if callable(corresp):
+            corresp(dist, value)
+        else:
+            _set_config(dist, corresp, value)
+
+    _copy_command_options(config, dist, filename)
+
+
+def _handle_missing_dynamic(dist: Distribution, project_table: dict):
+    """Be temporarily forgiving with ``dynamic`` fields not listed in ``dynamic``"""
+    dynamic = set(project_table.get("dynamic", []))
+    for field, getter in _PREVIOUSLY_DEFINED.items():
+        if not (field in project_table or field in dynamic):
+            value = getter(dist)
+            if value:
+                _MissingDynamic.emit(field=field, value=value)
+                project_table[field] = _RESET_PREVIOUSLY_DEFINED.get(field)
+
+
+def json_compatible_key(key: str) -> str:
+    """As defined in :pep:`566#json-compatible-metadata`"""
+    return key.lower().replace("-", "_")
+
+
+def _set_config(dist: Distribution, field: str, value: Any):
+    val = _PREPROCESS.get(field, _noop)(dist, value)
+    setter = getattr(dist.metadata, f"set_{field}", None)
+    if setter:
+        setter(val)
+    elif hasattr(dist.metadata, field) or field in SETUPTOOLS_PATCHES:
+        setattr(dist.metadata, field, val)
+    else:
+        setattr(dist, field, val)
+
+
+_CONTENT_TYPES = {
+    ".md": "text/markdown",
+    ".rst": "text/x-rst",
+    ".txt": "text/plain",
+}
+
+
+def _guess_content_type(file: str) -> str | None:
+    _, ext = os.path.splitext(file.lower())
+    if not ext:
+        return None
+
+    if ext in _CONTENT_TYPES:
+        return _static.Str(_CONTENT_TYPES[ext])
+
+    valid = ", ".join(f"{k} ({v})" for k, v in _CONTENT_TYPES.items())
+    msg = f"only the following file extensions are recognized: {valid}."
+    raise ValueError(f"Undefined content type for {file}, {msg}")
+
+
+def _long_description(
+    dist: Distribution, val: _ProjectReadmeValue, root_dir: StrPath | None
+):
+    from setuptools.config import expand
+
+    file: str | tuple[()]
+    if isinstance(val, str):
+        file = val
+        text = expand.read_files(file, root_dir)
+        ctype = _guess_content_type(file)
+    else:
+        file = val.get("file") or ()
+        text = val.get("text") or expand.read_files(file, root_dir)
+        ctype = val["content-type"]
+
+    # XXX: Is it completely safe to assume static?
+    _set_config(dist, "long_description", _static.Str(text))
+
+    if ctype:
+        _set_config(dist, "long_description_content_type", _static.Str(ctype))
+
+    if file:
+        dist._referenced_files.add(file)
+
+
+def _license(dist: Distribution, val: str | dict, root_dir: StrPath | None):
+    from setuptools.config import expand
+
+    if isinstance(val, str):
+        if getattr(dist.metadata, "license", None):
+            SetuptoolsWarning.emit("`license` overwritten by `pyproject.toml`")
+            dist.metadata.license = None
+        _set_config(dist, "license_expression", _static.Str(val))
+    else:
+        pypa_guides = "guides/writing-pyproject-toml/#license"
+        SetuptoolsDeprecationWarning.emit(
+            "`project.license` as a TOML table is deprecated",
+            "Please use a simple string containing a SPDX expression for "
+            "`project.license`. You can also use `project.license-files`. "
+            "(Both options available on setuptools>=77.0.0).",
+            see_url=f"https://packaging.python.org/en/latest/{pypa_guides}",
+            due_date=(2027, 2, 18),  # Introduced on 2025-02-18
+        )
+        if "file" in val:
+            # XXX: Is it completely safe to assume static?
+            value = expand.read_files([val["file"]], root_dir)
+            _set_config(dist, "license", _static.Str(value))
+            dist._referenced_files.add(val["file"])
+        else:
+            _set_config(dist, "license", _static.Str(val["text"]))
+
+
+def _people(dist: Distribution, val: list[dict], _root_dir: StrPath | None, kind: str):
+    field = []
+    email_field = []
+    for person in val:
+        if "name" not in person:
+            email_field.append(person["email"])
+        elif "email" not in person:
+            field.append(person["name"])
+        else:
+            addr = Address(display_name=person["name"], addr_spec=person["email"])
+            email_field.append(str(addr))
+
+    if field:
+        _set_config(dist, kind, _static.Str(", ".join(field)))
+    if email_field:
+        _set_config(dist, f"{kind}_email", _static.Str(", ".join(email_field)))
+
+
+def _project_urls(dist: Distribution, val: dict, _root_dir: StrPath | None):
+    _set_config(dist, "project_urls", val)
+
+
+def _python_requires(dist: Distribution, val: str, _root_dir: StrPath | None):
+    _set_config(dist, "python_requires", _static.SpecifierSet(val))
+
+
+def _dependencies(dist: Distribution, val: list, _root_dir: StrPath | None):
+    if getattr(dist, "install_requires", []):
+        msg = "`install_requires` overwritten in `pyproject.toml` (dependencies)"
+        SetuptoolsWarning.emit(msg)
+    dist.install_requires = val
+
+
+def _optional_dependencies(dist: Distribution, val: dict, _root_dir: StrPath | None):
+    if getattr(dist, "extras_require", None):
+        msg = "`extras_require` overwritten in `pyproject.toml` (optional-dependencies)"
+        SetuptoolsWarning.emit(msg)
+    dist.extras_require = val
+
+
+def _ext_modules(dist: Distribution, val: list[dict]) -> list[Extension]:
+    existing = dist.ext_modules or []
+    args = ({k.replace("-", "_"): v for k, v in x.items()} for x in val)
+    new = [Extension(**kw) for kw in args]
+    return [*existing, *new]
+
+
+def _noop(_dist: Distribution, val: _T) -> _T:
+    return val
+
+
+def _identity(val: _T) -> _T:
+    return val
+
+
+def _unify_entry_points(project_table: dict):
+    project = project_table
+    given = project.pop("entry-points", project.pop("entry_points", {}))
+    entry_points = dict(given)  # Avoid problems with static
+    renaming = {"scripts": "console_scripts", "gui_scripts": "gui_scripts"}
+    for key, value in list(project.items()):  # eager to allow modifications
+        norm_key = json_compatible_key(key)
+        if norm_key in renaming:
+            # Don't skip even if value is empty (reason: reset missing `dynamic`)
+            entry_points[renaming[norm_key]] = project.pop(key)
+
+    if entry_points:
+        project["entry-points"] = {
+            name: [f"{k} = {v}" for k, v in group.items()]
+            for name, group in entry_points.items()
+            if group  # now we can skip empty groups
+        }
+        # Sometimes this will set `project["entry-points"] = {}`, and that is
+        # intentional (for resetting configurations that are missing `dynamic`).
+
+
+def _copy_command_options(pyproject: dict, dist: Distribution, filename: StrPath):
+    tool_table = pyproject.get("tool", {})
+    cmdclass = tool_table.get("setuptools", {}).get("cmdclass", {})
+    valid_options = _valid_command_options(cmdclass)
+
+    cmd_opts = dist.command_options
+    for cmd, config in pyproject.get("tool", {}).get("distutils", {}).items():
+        cmd = json_compatible_key(cmd)
+        valid = valid_options.get(cmd, set())
+        cmd_opts.setdefault(cmd, {})
+        for key, value in config.items():
+            key = json_compatible_key(key)
+            cmd_opts[cmd][key] = (str(filename), value)
+            if key not in valid:
+                # To avoid removing options that are specified dynamically we
+                # just log a warn...
+                _logger.warning(f"Command option {cmd}.{key} is not defined")
+
+
+def _valid_command_options(cmdclass: Mapping = EMPTY) -> dict[str, set[str]]:
+    from setuptools.dist import Distribution
+
+    from .._importlib import metadata
+
+    valid_options = {"global": _normalise_cmd_options(Distribution.global_options)}
+
+    unloaded_entry_points = metadata.entry_points(group='distutils.commands')
+    loaded_entry_points = (_load_ep(ep) for ep in unloaded_entry_points)
+    entry_points = (ep for ep in loaded_entry_points if ep)
+    for cmd, cmd_class in chain(entry_points, cmdclass.items()):
+        opts = valid_options.get(cmd, set())
+        opts = opts | _normalise_cmd_options(getattr(cmd_class, "user_options", []))
+        valid_options[cmd] = opts
+
+    return valid_options
+
+
+def _load_ep(ep: metadata.EntryPoint) -> tuple[str, type] | None:
+    if ep.value.startswith("wheel.bdist_wheel"):
+        # Ignore deprecated entrypoint from wheel and avoid warning pypa/wheel#631
+        # TODO: remove check when `bdist_wheel` has been fully removed from pypa/wheel
+        return None
+
+    # Ignore all the errors
+    try:
+        return (ep.name, ep.load())
+    except Exception as ex:
+        msg = f"{ex.__class__.__name__} while trying to load entry-point {ep.name}"
+        _logger.warning(f"{msg}: {ex}")
+        return None
+
+
+def _normalise_cmd_option_key(name: str) -> str:
+    return json_compatible_key(name).strip("_=")
+
+
+def _normalise_cmd_options(desc: _OptionsList) -> set[str]:
+    return {_normalise_cmd_option_key(fancy_option[0]) for fancy_option in desc}
+
+
+def _get_previous_entrypoints(dist: Distribution) -> dict[str, list]:
+    ignore = ("console_scripts", "gui_scripts")
+    value = getattr(dist, "entry_points", None) or {}
+    return {k: v for k, v in value.items() if k not in ignore}
+
+
+def _get_previous_scripts(dist: Distribution) -> list | None:
+    value = getattr(dist, "entry_points", None) or {}
+    return value.get("console_scripts")
+
+
+def _get_previous_gui_scripts(dist: Distribution) -> list | None:
+    value = getattr(dist, "entry_points", None) or {}
+    return value.get("gui_scripts")
+
+
+def _set_static_list_metadata(attr: str, dist: Distribution, val: list) -> None:
+    """Apply distutils metadata validation but preserve "static" behaviour"""
+    meta = dist.metadata
+    setter, getter = getattr(meta, f"set_{attr}"), getattr(meta, f"get_{attr}")
+    setter(val)
+    setattr(meta, attr, _static.List(getter()))
+
+
+def _attrgetter(attr):
+    """
+    Similar to ``operator.attrgetter`` but returns None if ``attr`` is not found
+    >>> from types import SimpleNamespace
+    >>> obj = SimpleNamespace(a=42, b=SimpleNamespace(c=13))
+    >>> _attrgetter("a")(obj)
+    42
+    >>> _attrgetter("b.c")(obj)
+    13
+    >>> _attrgetter("d")(obj) is None
+    True
+    """
+    return partial(reduce, lambda acc, x: getattr(acc, x, None), attr.split("."))
+
+
+def _some_attrgetter(*items):
+    """
+    Return the first "truth-y" attribute or None
+    >>> from types import SimpleNamespace
+    >>> obj = SimpleNamespace(a=42, b=SimpleNamespace(c=13))
+    >>> _some_attrgetter("d", "a", "b.c")(obj)
+    42
+    >>> _some_attrgetter("d", "e", "b.c", "a")(obj)
+    13
+    >>> _some_attrgetter("d", "e", "f")(obj) is None
+    True
+    """
+
+    def _acessor(obj):
+        values = (_attrgetter(i)(obj) for i in items)
+        return next((i for i in values if i is not None), None)
+
+    return _acessor
+
+
+PYPROJECT_CORRESPONDENCE: dict[str, _Correspondence] = {
+    "readme": _long_description,
+    "license": _license,
+    "authors": partial(_people, kind="author"),
+    "maintainers": partial(_people, kind="maintainer"),
+    "urls": _project_urls,
+    "dependencies": _dependencies,
+    "optional_dependencies": _optional_dependencies,
+    "requires_python": _python_requires,
+}
+
+TOOL_TABLE_RENAMES = {"script_files": "scripts"}
+TOOL_TABLE_REMOVALS = {
+    "namespace_packages": """
+        Please migrate to implicit native namespaces instead.
+        See https://packaging.python.org/en/latest/guides/packaging-namespace-packages/.
+        """,
+}
+TOOL_TABLE_CORRESPONDENCE = {
+    # Fields with corresponding core metadata need to be marked as static:
+    "obsoletes": partial(_set_static_list_metadata, "obsoletes"),
+    "provides": partial(_set_static_list_metadata, "provides"),
+    "platforms": partial(_set_static_list_metadata, "platforms"),
+}
+
+SETUPTOOLS_PATCHES = {
+    "long_description_content_type",
+    "project_urls",
+    "provides_extras",
+    "license_file",
+    "license_files",
+    "license_expression",
+}
+
+_PREPROCESS = {
+    "ext_modules": _ext_modules,
+}
+
+_PREVIOUSLY_DEFINED = {
+    "name": _attrgetter("metadata.name"),
+    "version": _attrgetter("metadata.version"),
+    "description": _attrgetter("metadata.description"),
+    "readme": _attrgetter("metadata.long_description"),
+    "requires-python": _some_attrgetter("python_requires", "metadata.python_requires"),
+    "license": _some_attrgetter("metadata.license_expression", "metadata.license"),
+    # XXX: `license-file` is currently not considered in the context of `dynamic`.
+    #      See TestPresetField.test_license_files_exempt_from_dynamic
+    "authors": _some_attrgetter("metadata.author", "metadata.author_email"),
+    "maintainers": _some_attrgetter("metadata.maintainer", "metadata.maintainer_email"),
+    "keywords": _attrgetter("metadata.keywords"),
+    "classifiers": _attrgetter("metadata.classifiers"),
+    "urls": _attrgetter("metadata.project_urls"),
+    "entry-points": _get_previous_entrypoints,
+    "scripts": _get_previous_scripts,
+    "gui-scripts": _get_previous_gui_scripts,
+    "dependencies": _attrgetter("install_requires"),
+    "optional-dependencies": _attrgetter("extras_require"),
+}
+
+
+_RESET_PREVIOUSLY_DEFINED: dict = {
+    # Fix improper setting: given in `setup.py`, but not listed in `dynamic`
+    # Use "immutable" data structures to avoid in-place modification.
+    # dict: pyproject name => value to which reset
+    "license": "",
+    # XXX: `license-file` is currently not considered in the context of `dynamic`.
+    #      See TestPresetField.test_license_files_exempt_from_dynamic
+    "authors": _static.EMPTY_LIST,
+    "maintainers": _static.EMPTY_LIST,
+    "keywords": _static.EMPTY_LIST,
+    "classifiers": _static.EMPTY_LIST,
+    "urls": _static.EMPTY_DICT,
+    "entry-points": _static.EMPTY_DICT,
+    "scripts": _static.EMPTY_DICT,
+    "gui-scripts": _static.EMPTY_DICT,
+    "dependencies": _static.EMPTY_LIST,
+    "optional-dependencies": _static.EMPTY_DICT,
+}
+
+
+class _MissingDynamic(SetuptoolsWarning):
+    _SUMMARY = "`{field}` defined outside of `pyproject.toml` is ignored."
+
+    _DETAILS = """
+    The following seems to be defined outside of `pyproject.toml`:
+
+    `{field} = {value!r}`
+
+    According to the spec (see the link below), however, setuptools CANNOT
+    consider this value unless `{field}` is listed as `dynamic`.
+
+    https://packaging.python.org/en/latest/specifications/pyproject-toml/#declaring-project-metadata-the-project-table
+
+    To prevent this problem, you can list `{field}` under `dynamic` or alternatively
+    remove the `[project]` table from your file and rely entirely on other means of
+    configuration.
+    """
+    # TODO: Consider removing this check in the future?
+    #       There is a trade-off here between improving "debug-ability" and the cost
+    #       of running/testing/maintaining these unnecessary checks...
+
+    @classmethod
+    def details(cls, field: str, value: Any) -> str:
+        return cls._DETAILS.format(field=field, value=value)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/NOTICE b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/NOTICE
new file mode 100644
index 0000000000000000000000000000000000000000..ac5464d88c6f071c18d8eceb1e81d2550573599b
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/NOTICE
@@ -0,0 +1,438 @@
+The code contained in this directory was automatically generated using the
+following command:
+
+    python -m validate_pyproject.pre_compile --output-dir=setuptools/config/_validate_pyproject --enable-plugins setuptools distutils --very-verbose -t setuptools=setuptools/config/setuptools.schema.json -t distutils=setuptools/config/distutils.schema.json
+
+Please avoid changing it manually.
+
+
+You can report issues or suggest changes directly to `validate-pyproject`
+(or to the relevant plugin repository)
+
+- https://github.com/abravalheri/validate-pyproject/issues
+
+
+***
+
+The following files include code from opensource projects
+(either as direct copies or modified versions):
+
+- `fastjsonschema_exceptions.py`:
+    - project: `fastjsonschema` - licensed under BSD-3-Clause
+      (https://github.com/horejsek/python-fastjsonschema)
+- `extra_validations.py` and `format.py`, `error_reporting.py`:
+    - project: `validate-pyproject` - licensed under MPL-2.0
+      (https://github.com/abravalheri/validate-pyproject)
+
+
+Additionally the following files are automatically generated by tools provided
+by the same projects:
+
+- `__init__.py`
+- `fastjsonschema_validations.py`
+
+The relevant copyright notes and licenses are included below.
+
+
+***
+
+`fastjsonschema`
+================
+
+Copyright (c) 2018, Michal Horejsek
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+  Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+  Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+  Neither the name of the {organization} nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+
+***
+
+`validate-pyproject`
+====================
+
+Mozilla Public License, version 2.0
+
+1. Definitions
+
+1.1. "Contributor"
+
+     means each individual or legal entity that creates, contributes to the
+     creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+
+     means the combination of the Contributions of others (if any) used by a
+     Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+
+     means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+
+     means Source Code Form to which the initial Contributor has attached the
+     notice in Exhibit A, the Executable Form of such Source Code Form, and
+     Modifications of such Source Code Form, in each case including portions
+     thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+     means
+
+     a. that the initial Contributor has attached the notice described in
+        Exhibit B to the Covered Software; or
+
+     b. that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the terms of
+        a Secondary License.
+
+1.6. "Executable Form"
+
+     means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+
+     means a work that combines Covered Software with other material, in a
+     separate file or files, that is not Covered Software.
+
+1.8. "License"
+
+     means this document.
+
+1.9. "Licensable"
+
+     means having the right to grant, to the maximum extent possible, whether
+     at the time of the initial grant or subsequently, any and all of the
+     rights conveyed by this License.
+
+1.10. "Modifications"
+
+     means any of the following:
+
+     a. any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered Software; or
+
+     b. any new file in Source Code Form that contains any Covered Software.
+
+1.11. "Patent Claims" of a Contributor
+
+      means any patent claim(s), including without limitation, method,
+      process, and apparatus claims, in any patent Licensable by such
+      Contributor that would be infringed, but for the grant of the License,
+      by the making, using, selling, offering for sale, having made, import,
+      or transfer of either its Contributions or its Contributor Version.
+
+1.12. "Secondary License"
+
+      means either the GNU General Public License, Version 2.0, the GNU Lesser
+      General Public License, Version 2.1, the GNU Affero General Public
+      License, Version 3.0, or any later versions of those licenses.
+
+1.13. "Source Code Form"
+
+      means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+
+      means an individual or a legal entity exercising rights under this
+      License. For legal entities, "You" includes any entity that controls, is
+      controlled by, or is under common control with You. For purposes of this
+      definition, "control" means (a) the power, direct or indirect, to cause
+      the direction or management of such entity, whether by contract or
+      otherwise, or (b) ownership of more than fifty percent (50%) of the
+      outstanding shares or beneficial ownership of such entity.
+
+
+2. License Grants and Conditions
+
+2.1. Grants
+
+     Each Contributor hereby grants You a world-wide, royalty-free,
+     non-exclusive license:
+
+     a. under intellectual property rights (other than patent or trademark)
+        Licensable by such Contributor to use, reproduce, make available,
+        modify, display, perform, distribute, and otherwise exploit its
+        Contributions, either on an unmodified basis, with Modifications, or
+        as part of a Larger Work; and
+
+     b. under Patent Claims of such Contributor to make, use, sell, offer for
+        sale, have made, import, and otherwise transfer either its
+        Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+     The licenses granted in Section 2.1 with respect to any Contribution
+     become effective for each Contribution on the date the Contributor first
+     distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+     The licenses granted in this Section 2 are the only rights granted under
+     this License. No additional rights or licenses will be implied from the
+     distribution or licensing of Covered Software under this License.
+     Notwithstanding Section 2.1(b) above, no patent license is granted by a
+     Contributor:
+
+     a. for any code that a Contributor has removed from Covered Software; or
+
+     b. for infringements caused by: (i) Your and any other third party's
+        modifications of Covered Software, or (ii) the combination of its
+        Contributions with other software (except as part of its Contributor
+        Version); or
+
+     c. under Patent Claims infringed by Covered Software in the absence of
+        its Contributions.
+
+     This License does not grant any rights in the trademarks, service marks,
+     or logos of any Contributor (except as may be necessary to comply with
+     the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+     No Contributor makes additional grants as a result of Your choice to
+     distribute the Covered Software under a subsequent version of this
+     License (see Section 10.2) or under the terms of a Secondary License (if
+     permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+     Each Contributor represents that the Contributor believes its
+     Contributions are its original creation(s) or it has sufficient rights to
+     grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+     This License is not intended to limit any rights You have under
+     applicable copyright doctrines of fair use, fair dealing, or other
+     equivalents.
+
+2.7. Conditions
+
+     Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted in
+     Section 2.1.
+
+
+3. Responsibilities
+
+3.1. Distribution of Source Form
+
+     All distribution of Covered Software in Source Code Form, including any
+     Modifications that You create or to which You contribute, must be under
+     the terms of this License. You must inform recipients that the Source
+     Code Form of the Covered Software is governed by the terms of this
+     License, and how they can obtain a copy of this License. You may not
+     attempt to alter or restrict the recipients' rights in the Source Code
+     Form.
+
+3.2. Distribution of Executable Form
+
+     If You distribute Covered Software in Executable Form then:
+
+     a. such Covered Software must also be made available in Source Code Form,
+        as described in Section 3.1, and You must inform recipients of the
+        Executable Form how they can obtain a copy of such Source Code Form by
+        reasonable means in a timely manner, at a charge no more than the cost
+        of distribution to the recipient; and
+
+     b. You may distribute such Executable Form under the terms of this
+        License, or sublicense it under different terms, provided that the
+        license for the Executable Form does not attempt to limit or alter the
+        recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+     You may create and distribute a Larger Work under terms of Your choice,
+     provided that You also comply with the requirements of this License for
+     the Covered Software. If the Larger Work is a combination of Covered
+     Software with a work governed by one or more Secondary Licenses, and the
+     Covered Software is not Incompatible With Secondary Licenses, this
+     License permits You to additionally distribute such Covered Software
+     under the terms of such Secondary License(s), so that the recipient of
+     the Larger Work may, at their option, further distribute the Covered
+     Software under the terms of either this License or such Secondary
+     License(s).
+
+3.4. Notices
+
+     You may not remove or alter the substance of any license notices
+     (including copyright notices, patent notices, disclaimers of warranty, or
+     limitations of liability) contained within the Source Code Form of the
+     Covered Software, except that You may alter any license notices to the
+     extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+     You may choose to offer, and to charge a fee for, warranty, support,
+     indemnity or liability obligations to one or more recipients of Covered
+     Software. However, You may do so only on Your own behalf, and not on
+     behalf of any Contributor. You must make it absolutely clear that any
+     such warranty, support, indemnity, or liability obligation is offered by
+     You alone, and You hereby agree to indemnify every Contributor for any
+     liability incurred by such Contributor as a result of warranty, support,
+     indemnity or liability terms You offer. You may include additional
+     disclaimers of warranty and limitations of liability specific to any
+     jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+
+   If it is impossible for You to comply with any of the terms of this License
+   with respect to some or all of the Covered Software due to statute,
+   judicial order, or regulation then You must: (a) comply with the terms of
+   this License to the maximum extent possible; and (b) describe the
+   limitations and the code they affect. Such description must be placed in a
+   text file included with all distributions of the Covered Software under
+   this License. Except to the extent prohibited by statute or regulation,
+   such description must be sufficiently detailed for a recipient of ordinary
+   skill to be able to understand it.
+
+5. Termination
+
+5.1. The rights granted under this License will terminate automatically if You
+     fail to comply with any of its terms. However, if You become compliant,
+     then the rights granted under this License from a particular Contributor
+     are reinstated (a) provisionally, unless and until such Contributor
+     explicitly and finally terminates Your grants, and (b) on an ongoing
+     basis, if such Contributor fails to notify You of the non-compliance by
+     some reasonable means prior to 60 days after You have come back into
+     compliance. Moreover, Your grants from a particular Contributor are
+     reinstated on an ongoing basis if such Contributor notifies You of the
+     non-compliance by some reasonable means, this is the first time You have
+     received notice of non-compliance with this License from such
+     Contributor, and You become compliant prior to 30 days after Your receipt
+     of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+     infringement claim (excluding declaratory judgment actions,
+     counter-claims, and cross-claims) alleging that a Contributor Version
+     directly or indirectly infringes any patent, then the rights granted to
+     You by any and all Contributors for the Covered Software under Section
+     2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all end user
+     license agreements (excluding distributors and resellers) which have been
+     validly granted by You or Your distributors under this License prior to
+     termination shall survive termination.
+
+6. Disclaimer of Warranty
+
+   Covered Software is provided under this License on an "as is" basis,
+   without warranty of any kind, either expressed, implied, or statutory,
+   including, without limitation, warranties that the Covered Software is free
+   of defects, merchantable, fit for a particular purpose or non-infringing.
+   The entire risk as to the quality and performance of the Covered Software
+   is with You. Should any Covered Software prove defective in any respect,
+   You (not any Contributor) assume the cost of any necessary servicing,
+   repair, or correction. This disclaimer of warranty constitutes an essential
+   part of this License. No use of  any Covered Software is authorized under
+   this License except under this disclaimer.
+
+7. Limitation of Liability
+
+   Under no circumstances and under no legal theory, whether tort (including
+   negligence), contract, or otherwise, shall any Contributor, or anyone who
+   distributes Covered Software as permitted above, be liable to You for any
+   direct, indirect, special, incidental, or consequential damages of any
+   character including, without limitation, damages for lost profits, loss of
+   goodwill, work stoppage, computer failure or malfunction, or any and all
+   other commercial damages or losses, even if such party shall have been
+   informed of the possibility of such damages. This limitation of liability
+   shall not apply to liability for death or personal injury resulting from
+   such party's negligence to the extent applicable law prohibits such
+   limitation. Some jurisdictions do not allow the exclusion or limitation of
+   incidental or consequential damages, so this exclusion and limitation may
+   not apply to You.
+
+8. Litigation
+
+   Any litigation relating to this License may be brought only in the courts
+   of a jurisdiction where the defendant maintains its principal place of
+   business and such litigation shall be governed by laws of that
+   jurisdiction, without reference to its conflict-of-law provisions. Nothing
+   in this Section shall prevent a party's ability to bring cross-claims or
+   counter-claims.
+
+9. Miscellaneous
+
+   This License represents the complete agreement concerning the subject
+   matter hereof. If any provision of this License is held to be
+   unenforceable, such provision shall be reformed only to the extent
+   necessary to make it enforceable. Any law or regulation which provides that
+   the language of a contract shall be construed against the drafter shall not
+   be used to construe this License against a Contributor.
+
+
+10. Versions of the License
+
+10.1. New Versions
+
+      Mozilla Foundation is the license steward. Except as provided in Section
+      10.3, no one other than the license steward has the right to modify or
+      publish new versions of this License. Each version will be given a
+      distinguishing version number.
+
+10.2. Effect of New Versions
+
+      You may distribute the Covered Software under the terms of the version
+      of the License under which You originally received the Covered Software,
+      or under the terms of any subsequent version published by the license
+      steward.
+
+10.3. Modified Versions
+
+      If you create software not governed by this License, and you want to
+      create a new license for such software, you may create and use a
+      modified version of this License if you rename the license and remove
+      any references to the name of the license steward (except to note that
+      such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+      Licenses If You choose to distribute Source Code Form that is
+      Incompatible With Secondary Licenses under the terms of this version of
+      the License, the notice described in Exhibit B of this License must be
+      attached.
+
+Exhibit A - Source Code Form License Notice
+
+      This Source Code Form is subject to the
+      terms of the Mozilla Public License, v.
+      2.0. If a copy of the MPL was not
+      distributed with this file, You can
+      obtain one at
+      https://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular file,
+then You may include the notice in a location (such as a LICENSE file in a
+relevant directory) where a recipient would be likely to look for such a
+notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+
+      This Source Code Form is "Incompatible
+      With Secondary Licenses", as defined by
+      the Mozilla Public License, v. 2.0.
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..4f612bd51c4ac1d272318ed6fb96e4aeb57e3e27
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/__init__.py
@@ -0,0 +1,34 @@
+from functools import reduce
+from typing import Any, Callable, Dict
+
+from . import formats
+from .error_reporting import detailed_errors, ValidationError
+from .extra_validations import EXTRA_VALIDATIONS
+from .fastjsonschema_exceptions import JsonSchemaException, JsonSchemaValueException
+from .fastjsonschema_validations import validate as _validate
+
+__all__ = [
+    "validate",
+    "FORMAT_FUNCTIONS",
+    "EXTRA_VALIDATIONS",
+    "ValidationError",
+    "JsonSchemaException",
+    "JsonSchemaValueException",
+]
+
+
+FORMAT_FUNCTIONS: Dict[str, Callable[[str], bool]] = {
+    fn.__name__.replace("_", "-"): fn
+    for fn in formats.__dict__.values()
+    if callable(fn) and not fn.__name__.startswith("_")
+}
+
+
+def validate(data: Any) -> bool:
+    """Validate the given ``data`` object using JSON Schema
+    This function raises ``ValidationError`` if ``data`` is invalid.
+    """
+    with detailed_errors():
+        _validate(data, custom_formats=FORMAT_FUNCTIONS)
+        reduce(lambda acc, fn: fn(acc), EXTRA_VALIDATIONS, data)
+    return True
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/error_reporting.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/error_reporting.py
new file mode 100644
index 0000000000000000000000000000000000000000..3591231c09f56494eb46119f9794053439b3fe8c
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/error_reporting.py
@@ -0,0 +1,336 @@
+import io
+import json
+import logging
+import os
+import re
+import typing
+from contextlib import contextmanager
+from textwrap import indent, wrap
+from typing import Any, Dict, Generator, Iterator, List, Optional, Sequence, Union
+
+from .fastjsonschema_exceptions import JsonSchemaValueException
+
+if typing.TYPE_CHECKING:
+    import sys
+
+    if sys.version_info < (3, 11):
+        from typing_extensions import Self
+    else:
+        from typing import Self
+
+_logger = logging.getLogger(__name__)
+
+_MESSAGE_REPLACEMENTS = {
+    "must be named by propertyName definition": "keys must be named by",
+    "one of contains definition": "at least one item that matches",
+    " same as const definition:": "",
+    "only specified items": "only items matching the definition",
+}
+
+_SKIP_DETAILS = (
+    "must not be empty",
+    "is always invalid",
+    "must not be there",
+)
+
+_NEED_DETAILS = {"anyOf", "oneOf", "allOf", "contains", "propertyNames", "not", "items"}
+
+_CAMEL_CASE_SPLITTER = re.compile(r"\W+|([A-Z][^A-Z\W]*)")
+_IDENTIFIER = re.compile(r"^[\w_]+$", re.I)
+
+_TOML_JARGON = {
+    "object": "table",
+    "property": "key",
+    "properties": "keys",
+    "property names": "keys",
+}
+
+_FORMATS_HELP = """
+For more details about `format` see
+https://validate-pyproject.readthedocs.io/en/latest/api/validate_pyproject.formats.html
+"""
+
+
+class ValidationError(JsonSchemaValueException):
+    """Report violations of a given JSON schema.
+
+    This class extends :exc:`~fastjsonschema.JsonSchemaValueException`
+    by adding the following properties:
+
+    - ``summary``: an improved version of the ``JsonSchemaValueException`` error message
+      with only the necessary information)
+
+    - ``details``: more contextual information about the error like the failing schema
+      itself and the value that violates the schema.
+
+    Depending on the level of the verbosity of the ``logging`` configuration
+    the exception message will be only ``summary`` (default) or a combination of
+    ``summary`` and ``details`` (when the logging level is set to :obj:`logging.DEBUG`).
+    """
+
+    summary = ""
+    details = ""
+    _original_message = ""
+
+    @classmethod
+    def _from_jsonschema(cls, ex: JsonSchemaValueException) -> "Self":
+        formatter = _ErrorFormatting(ex)
+        obj = cls(str(formatter), ex.value, formatter.name, ex.definition, ex.rule)
+        debug_code = os.getenv("JSONSCHEMA_DEBUG_CODE_GENERATION", "false").lower()
+        if debug_code != "false":  # pragma: no cover
+            obj.__cause__, obj.__traceback__ = ex.__cause__, ex.__traceback__
+        obj._original_message = ex.message
+        obj.summary = formatter.summary
+        obj.details = formatter.details
+        return obj
+
+
+@contextmanager
+def detailed_errors() -> Generator[None, None, None]:
+    try:
+        yield
+    except JsonSchemaValueException as ex:
+        raise ValidationError._from_jsonschema(ex) from None
+
+
+class _ErrorFormatting:
+    def __init__(self, ex: JsonSchemaValueException):
+        self.ex = ex
+        self.name = f"`{self._simplify_name(ex.name)}`"
+        self._original_message: str = self.ex.message.replace(ex.name, self.name)
+        self._summary = ""
+        self._details = ""
+
+    def __str__(self) -> str:
+        if _logger.getEffectiveLevel() <= logging.DEBUG and self.details:
+            return f"{self.summary}\n\n{self.details}"
+
+        return self.summary
+
+    @property
+    def summary(self) -> str:
+        if not self._summary:
+            self._summary = self._expand_summary()
+
+        return self._summary
+
+    @property
+    def details(self) -> str:
+        if not self._details:
+            self._details = self._expand_details()
+
+        return self._details
+
+    @staticmethod
+    def _simplify_name(name: str) -> str:
+        x = len("data.")
+        return name[x:] if name.startswith("data.") else name
+
+    def _expand_summary(self) -> str:
+        msg = self._original_message
+
+        for bad, repl in _MESSAGE_REPLACEMENTS.items():
+            msg = msg.replace(bad, repl)
+
+        if any(substring in msg for substring in _SKIP_DETAILS):
+            return msg
+
+        schema = self.ex.rule_definition
+        if self.ex.rule in _NEED_DETAILS and schema:
+            summary = _SummaryWriter(_TOML_JARGON)
+            return f"{msg}:\n\n{indent(summary(schema), '    ')}"
+
+        return msg
+
+    def _expand_details(self) -> str:
+        optional = []
+        definition = self.ex.definition or {}
+        desc_lines = definition.pop("$$description", [])
+        desc = definition.pop("description", None) or " ".join(desc_lines)
+        if desc:
+            description = "\n".join(
+                wrap(
+                    desc,
+                    width=80,
+                    initial_indent="    ",
+                    subsequent_indent="    ",
+                    break_long_words=False,
+                )
+            )
+            optional.append(f"DESCRIPTION:\n{description}")
+        schema = json.dumps(definition, indent=4)
+        value = json.dumps(self.ex.value, indent=4)
+        defaults = [
+            f"GIVEN VALUE:\n{indent(value, '    ')}",
+            f"OFFENDING RULE: {self.ex.rule!r}",
+            f"DEFINITION:\n{indent(schema, '    ')}",
+        ]
+        msg = "\n\n".join(optional + defaults)
+        epilog = f"\n{_FORMATS_HELP}" if "format" in msg.lower() else ""
+        return msg + epilog
+
+
+class _SummaryWriter:
+    _IGNORE = frozenset(("description", "default", "title", "examples"))
+
+    def __init__(self, jargon: Optional[Dict[str, str]] = None):
+        self.jargon: Dict[str, str] = jargon or {}
+        # Clarify confusing terms
+        self._terms = {
+            "anyOf": "at least one of the following",
+            "oneOf": "exactly one of the following",
+            "allOf": "all of the following",
+            "not": "(*NOT* the following)",
+            "prefixItems": f"{self._jargon('items')} (in order)",
+            "items": "items",
+            "contains": "contains at least one of",
+            "propertyNames": (
+                f"non-predefined acceptable {self._jargon('property names')}"
+            ),
+            "patternProperties": f"{self._jargon('properties')} named via pattern",
+            "const": "predefined value",
+            "enum": "one of",
+        }
+        # Attributes that indicate that the definition is easy and can be done
+        # inline (e.g. string and number)
+        self._guess_inline_defs = [
+            "enum",
+            "const",
+            "maxLength",
+            "minLength",
+            "pattern",
+            "format",
+            "minimum",
+            "maximum",
+            "exclusiveMinimum",
+            "exclusiveMaximum",
+            "multipleOf",
+        ]
+
+    def _jargon(self, term: Union[str, List[str]]) -> Union[str, List[str]]:
+        if isinstance(term, list):
+            return [self.jargon.get(t, t) for t in term]
+        return self.jargon.get(term, term)
+
+    def __call__(
+        self,
+        schema: Union[dict, List[dict]],
+        prefix: str = "",
+        *,
+        _path: Sequence[str] = (),
+    ) -> str:
+        if isinstance(schema, list):
+            return self._handle_list(schema, prefix, _path)
+
+        filtered = self._filter_unecessary(schema, _path)
+        simple = self._handle_simple_dict(filtered, _path)
+        if simple:
+            return f"{prefix}{simple}"
+
+        child_prefix = self._child_prefix(prefix, "  ")
+        item_prefix = self._child_prefix(prefix, "- ")
+        indent = len(prefix) * " "
+        with io.StringIO() as buffer:
+            for i, (key, value) in enumerate(filtered.items()):
+                child_path = [*_path, key]
+                line_prefix = prefix if i == 0 else indent
+                buffer.write(f"{line_prefix}{self._label(child_path)}:")
+                # ^  just the first item should receive the complete prefix
+                if isinstance(value, dict):
+                    filtered = self._filter_unecessary(value, child_path)
+                    simple = self._handle_simple_dict(filtered, child_path)
+                    buffer.write(
+                        f" {simple}"
+                        if simple
+                        else f"\n{self(value, child_prefix, _path=child_path)}"
+                    )
+                elif isinstance(value, list) and (
+                    key != "type" or self._is_property(child_path)
+                ):
+                    children = self._handle_list(value, item_prefix, child_path)
+                    sep = " " if children.startswith("[") else "\n"
+                    buffer.write(f"{sep}{children}")
+                else:
+                    buffer.write(f" {self._value(value, child_path)}\n")
+            return buffer.getvalue()
+
+    def _is_unecessary(self, path: Sequence[str]) -> bool:
+        if self._is_property(path) or not path:  # empty path => instruction @ root
+            return False
+        key = path[-1]
+        return any(key.startswith(k) for k in "$_") or key in self._IGNORE
+
+    def _filter_unecessary(
+        self, schema: Dict[str, Any], path: Sequence[str]
+    ) -> Dict[str, Any]:
+        return {
+            key: value
+            for key, value in schema.items()
+            if not self._is_unecessary([*path, key])
+        }
+
+    def _handle_simple_dict(self, value: dict, path: Sequence[str]) -> Optional[str]:
+        inline = any(p in value for p in self._guess_inline_defs)
+        simple = not any(isinstance(v, (list, dict)) for v in value.values())
+        if inline or simple:
+            return f"{{{', '.join(self._inline_attrs(value, path))}}}\n"
+        return None
+
+    def _handle_list(
+        self, schemas: list, prefix: str = "", path: Sequence[str] = ()
+    ) -> str:
+        if self._is_unecessary(path):
+            return ""
+
+        repr_ = repr(schemas)
+        if all(not isinstance(e, (dict, list)) for e in schemas) and len(repr_) < 60:
+            return f"{repr_}\n"
+
+        item_prefix = self._child_prefix(prefix, "- ")
+        return "".join(
+            self(v, item_prefix, _path=[*path, f"[{i}]"]) for i, v in enumerate(schemas)
+        )
+
+    def _is_property(self, path: Sequence[str]) -> bool:
+        """Check if the given path can correspond to an arbitrarily named property"""
+        counter = 0
+        for key in path[-2::-1]:
+            if key not in {"properties", "patternProperties"}:
+                break
+            counter += 1
+
+        # If the counter if even, the path correspond to a JSON Schema keyword
+        # otherwise it can be any arbitrary string naming a property
+        return counter % 2 == 1
+
+    def _label(self, path: Sequence[str]) -> str:
+        *parents, key = path
+        if not self._is_property(path):
+            norm_key = _separate_terms(key)
+            return self._terms.get(key) or " ".join(self._jargon(norm_key))
+
+        if parents[-1] == "patternProperties":
+            return f"(regex {key!r})"
+        return repr(key)  # property name
+
+    def _value(self, value: Any, path: Sequence[str]) -> str:
+        if path[-1] == "type" and not self._is_property(path):
+            type_ = self._jargon(value)
+            return f"[{', '.join(type_)}]" if isinstance(type_, list) else type_
+        return repr(value)
+
+    def _inline_attrs(self, schema: dict, path: Sequence[str]) -> Iterator[str]:
+        for key, value in schema.items():
+            child_path = [*path, key]
+            yield f"{self._label(child_path)}: {self._value(value, child_path)}"
+
+    def _child_prefix(self, parent_prefix: str, child_prefix: str) -> str:
+        return len(parent_prefix) * " " + child_prefix
+
+
+def _separate_terms(word: str) -> List[str]:
+    """
+    >>> _separate_terms("FooBar-foo")
+    ['foo', 'bar', 'foo']
+    """
+    return [w.lower() for w in _CAMEL_CASE_SPLITTER.split(word) if w]
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/extra_validations.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/extra_validations.py
new file mode 100644
index 0000000000000000000000000000000000000000..789411d0ff397041f87a834e634bac8488024326
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/extra_validations.py
@@ -0,0 +1,82 @@
+"""The purpose of this module is implement PEP 621 validations that are
+difficult to express as a JSON Schema (or that are not supported by the current
+JSON Schema library).
+"""
+
+from inspect import cleandoc
+from typing import Mapping, TypeVar
+
+from .error_reporting import ValidationError
+
+T = TypeVar("T", bound=Mapping)
+
+
+class RedefiningStaticFieldAsDynamic(ValidationError):
+    _DESC = """According to PEP 621:
+
+    Build back-ends MUST raise an error if the metadata specifies a field
+    statically as well as being listed in dynamic.
+    """
+    __doc__ = _DESC
+    _URL = (
+        "https://packaging.python.org/en/latest/specifications/"
+        "pyproject-toml/#dynamic"
+    )
+
+
+class IncludedDependencyGroupMustExist(ValidationError):
+    _DESC = """An included dependency group must exist and must not be cyclic.
+    """
+    __doc__ = _DESC
+    _URL = "https://peps.python.org/pep-0735/"
+
+
+def validate_project_dynamic(pyproject: T) -> T:
+    project_table = pyproject.get("project", {})
+    dynamic = project_table.get("dynamic", [])
+
+    for field in dynamic:
+        if field in project_table:
+            raise RedefiningStaticFieldAsDynamic(
+                message=f"You cannot provide a value for `project.{field}` and "
+                "list it under `project.dynamic` at the same time",
+                value={
+                    field: project_table[field],
+                    "...": " # ...",
+                    "dynamic": dynamic,
+                },
+                name=f"data.project.{field}",
+                definition={
+                    "description": cleandoc(RedefiningStaticFieldAsDynamic._DESC),
+                    "see": RedefiningStaticFieldAsDynamic._URL,
+                },
+                rule="PEP 621",
+            )
+
+    return pyproject
+
+
+def validate_include_depenency(pyproject: T) -> T:
+    dependency_groups = pyproject.get("dependency-groups", {})
+    for key, value in dependency_groups.items():
+        for each in value:
+            if (
+                isinstance(each, dict)
+                and (include_group := each.get("include-group"))
+                and include_group not in dependency_groups
+            ):
+                raise IncludedDependencyGroupMustExist(
+                    message=f"The included dependency group {include_group} doesn't exist",
+                    value=each,
+                    name=f"data.dependency_groups.{key}",
+                    definition={
+                        "description": cleandoc(IncludedDependencyGroupMustExist._DESC),
+                        "see": IncludedDependencyGroupMustExist._URL,
+                    },
+                    rule="PEP 735",
+                )
+    # TODO: check for `include-group` cycles (can be conditional to graphlib)
+    return pyproject
+
+
+EXTRA_VALIDATIONS = (validate_project_dynamic, validate_include_depenency)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_exceptions.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_exceptions.py
new file mode 100644
index 0000000000000000000000000000000000000000..d2dddd6a106f021a4723c1e8f5953ccc09e55e1f
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_exceptions.py
@@ -0,0 +1,51 @@
+import re
+
+
+SPLIT_RE = re.compile(r'[\.\[\]]+')
+
+
+class JsonSchemaException(ValueError):
+    """
+    Base exception of ``fastjsonschema`` library.
+    """
+
+
+class JsonSchemaValueException(JsonSchemaException):
+    """
+    Exception raised by validation function. Available properties:
+
+     * ``message`` containing human-readable information what is wrong (e.g. ``data.property[index] must be smaller than or equal to 42``),
+     * invalid ``value`` (e.g. ``60``),
+     * ``name`` of a path in the data structure (e.g. ``data.property[index]``),
+     * ``path`` as an array in the data structure (e.g. ``['data', 'property', 'index']``),
+     * the whole ``definition`` which the ``value`` has to fulfil (e.g. ``{'type': 'number', 'maximum': 42}``),
+     * ``rule`` which the ``value`` is breaking (e.g. ``maximum``)
+     * and ``rule_definition`` (e.g. ``42``).
+
+    .. versionchanged:: 2.14.0
+        Added all extra properties.
+    """
+
+    def __init__(self, message, value=None, name=None, definition=None, rule=None):
+        super().__init__(message)
+        self.message = message
+        self.value = value
+        self.name = name
+        self.definition = definition
+        self.rule = rule
+
+    @property
+    def path(self):
+        return [item for item in SPLIT_RE.split(self.name) if item != '']
+
+    @property
+    def rule_definition(self):
+        if not self.rule or not self.definition:
+            return None
+        return self.definition.get(self.rule)
+
+
+class JsonSchemaDefinitionException(JsonSchemaException):
+    """
+    Exception raised by generator of validation function.
+    """
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_validations.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_validations.py
new file mode 100644
index 0000000000000000000000000000000000000000..c69368a83ff1bdb89cf4853e00429f0125ca3dce
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/fastjsonschema_validations.py
@@ -0,0 +1,1412 @@
+# noqa
+# ruff: noqa
+# flake8: noqa
+# pylint: skip-file
+# mypy: ignore-errors
+# yapf: disable
+# pylama:skip=1
+
+
+# *** PLEASE DO NOT MODIFY DIRECTLY: Automatically generated code *** 
+
+
+VERSION = "2.20.0"
+from decimal import Decimal
+import re
+from .fastjsonschema_exceptions import JsonSchemaValueException
+
+
+REGEX_PATTERNS = {
+    '^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$': re.compile('^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])\\Z'),
+    '^.*$': re.compile('^.*$'),
+    '.+': re.compile('.+'),
+    '^.+$': re.compile('^.+$'),
+    'idn-email_re_pattern': re.compile('^[^@]+@[^@]+\\.[^@]+\\Z')
+}
+
+NoneType = type(None)
+
+def validate(data, custom_formats={}, name_prefix=None):
+    validate_https___packaging_python_org_en_latest_specifications_declaring_build_dependencies(data, custom_formats, (name_prefix or "data") + "")
+    return data
+
+def validate_https___packaging_python_org_en_latest_specifications_declaring_build_dependencies(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (dict)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be object", value=data, name="" + (name_prefix or "data") + "", definition={'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://packaging.python.org/en/latest/specifications/declaring-build-dependencies/', 'title': 'Data structure for ``pyproject.toml`` files', '$$description': ['File format containing build-time configurations for the Python ecosystem. ', ':pep:`517` initially defined a build-system independent format for source trees', 'which was complemented by :pep:`518` to provide a way of specifying dependencies ', 'for building Python projects.', 'Please notice the ``project`` table (as initially defined in  :pep:`621`) is not included', 'in this schema and should be considered separately.'], 'type': 'object', 'additionalProperties': False, 'properties': {'build-system': {'type': 'object', 'description': 'Table used to store build-related data', 'additionalProperties': False, 'properties': {'requires': {'type': 'array', '$$description': ['List of dependencies in the :pep:`508` format required to execute the build', 'system. Please notice that the resulting dependency graph', '**MUST NOT contain cycles**'], 'items': {'type': 'string'}}, 'build-backend': {'type': 'string', 'description': 'Python object that will be used to perform the build according to :pep:`517`', 'format': 'pep517-backend-reference'}, 'backend-path': {'type': 'array', '$$description': ['List of directories to be prepended to ``sys.path`` when loading the', 'back-end, and running its hooks'], 'items': {'type': 'string', '$comment': 'Should be a path (TODO: enforce it with format?)'}}}, 'required': ['requires']}, 'project': {'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://packaging.python.org/en/latest/specifications/pyproject-toml/', 'title': 'Package metadata stored in the ``project`` table', '$$description': ['Data structure for the **project** table inside ``pyproject.toml``', '(as initially defined in :pep:`621`)'], 'type': 'object', 'properties': {'name': {'type': 'string', 'description': 'The name (primary identifier) of the project. MUST be statically defined.', 'format': 'pep508-identifier'}, 'version': {'type': 'string', 'description': 'The version of the project as supported by :pep:`440`.', 'format': 'pep440'}, 'description': {'type': 'string', '$$description': ['The `summary description of the project', '`_']}, 'readme': {'$$description': ['`Full/detailed description of the project in the form of a README', '`_', "with meaning similar to the one defined in `core metadata's Description", '`_'], 'oneOf': [{'type': 'string', '$$description': ['Relative path to a text file (UTF-8) containing the full description', 'of the project. If the file path ends in case-insensitive ``.md`` or', '``.rst`` suffixes, then the content-type is respectively', '``text/markdown`` or ``text/x-rst``']}, {'type': 'object', 'allOf': [{'anyOf': [{'properties': {'file': {'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}}, 'required': ['file']}, {'properties': {'text': {'type': 'string', 'description': 'Full text describing the project.'}}, 'required': ['text']}]}, {'properties': {'content-type': {'type': 'string', '$$description': ['Content-type (:rfc:`1341`) of the full description', '(e.g. ``text/markdown``). The ``charset`` parameter is assumed', 'UTF-8 when not present.'], '$comment': 'TODO: add regex pattern or format?'}}, 'required': ['content-type']}]}]}, 'requires-python': {'type': 'string', 'format': 'pep508-versionspec', '$$description': ['`The Python version requirements of the project', '`_.']}, 'license': {'description': '`Project license `_.', 'oneOf': [{'type': 'string', 'description': 'An SPDX license identifier', 'format': 'SPDX'}, {'type': 'object', 'properties': {'file': {'type': 'string', '$$description': ['Relative path to the file (UTF-8) which contains the license for the', 'project.']}}, 'required': ['file']}, {'type': 'object', 'properties': {'text': {'type': 'string', '$$description': ['The license of the project whose meaning is that of the', '`License field from the core metadata', '`_.']}}, 'required': ['text']}]}, 'license-files': {'description': 'Paths or globs to paths of license files', 'type': 'array', 'items': {'type': 'string'}}, 'authors': {'type': 'array', 'items': {'$ref': '#/definitions/author'}, '$$description': ["The people or organizations considered to be the 'authors' of the project.", 'The exact meaning is open to interpretation (e.g. original or primary authors,', 'current maintainers, or owners of the package).']}, 'maintainers': {'type': 'array', 'items': {'$ref': '#/definitions/author'}, '$$description': ["The people or organizations considered to be the 'maintainers' of the project.", 'Similarly to ``authors``, the exact meaning is open to interpretation.']}, 'keywords': {'type': 'array', 'items': {'type': 'string'}, 'description': 'List of keywords to assist searching for the distribution in a larger catalog.'}, 'classifiers': {'type': 'array', 'items': {'type': 'string', 'format': 'trove-classifier', 'description': '`PyPI classifier `_.'}, '$$description': ['`Trove classifiers `_', 'which apply to the project.']}, 'urls': {'type': 'object', 'description': 'URLs associated with the project in the form ``label => value``.', 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', 'format': 'url'}}}, 'scripts': {'$ref': '#/definitions/entry-point-group', '$$description': ['Instruct the installer to create command-line wrappers for the given', '`entry points `_.']}, 'gui-scripts': {'$ref': '#/definitions/entry-point-group', '$$description': ['Instruct the installer to create GUI wrappers for the given', '`entry points `_.', 'The difference between ``scripts`` and ``gui-scripts`` is only relevant in', 'Windows.']}, 'entry-points': {'$$description': ['Instruct the installer to expose the given modules/functions via', '``entry-point`` discovery mechanism (useful for plugins).', 'More information available in the `Python packaging guide', '`_.'], 'propertyNames': {'format': 'python-entrypoint-group'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'$ref': '#/definitions/entry-point-group'}}}, 'dependencies': {'type': 'array', 'description': 'Project (mandatory) dependencies.', 'items': {'$ref': '#/definitions/dependency'}}, 'optional-dependencies': {'type': 'object', 'description': 'Optional dependency for the project', 'propertyNames': {'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'array', 'items': {'$ref': '#/definitions/dependency'}}}}, 'dynamic': {'type': 'array', '$$description': ['Specifies which fields are intentionally unspecified and expected to be', 'dynamically provided by build tools'], 'items': {'enum': ['version', 'description', 'readme', 'requires-python', 'license', 'license-files', 'authors', 'maintainers', 'keywords', 'classifiers', 'urls', 'scripts', 'gui-scripts', 'entry-points', 'dependencies', 'optional-dependencies']}}}, 'required': ['name'], 'additionalProperties': False, 'allOf': [{'if': {'not': {'required': ['dynamic'], 'properties': {'dynamic': {'contains': {'const': 'version'}, '$$description': ['version is listed in ``dynamic``']}}}, '$$comment': ['According to :pep:`621`:', '    If the core metadata specification lists a field as "Required", then', '    the metadata MUST specify the field statically or list it in dynamic', 'In turn, `core metadata`_ defines:', '    The required fields are: Metadata-Version, Name, Version.', '    All the other fields are optional.', 'Since ``Metadata-Version`` is defined by the build back-end, ``name`` and', '``version`` are the only mandatory information in ``pyproject.toml``.', '.. _core metadata: https://packaging.python.org/specifications/core-metadata/']}, 'then': {'required': ['version'], '$$description': ['version should be statically defined in the ``version`` field']}}, {'if': {'required': ['license-files']}, 'then': {'properties': {'license': {'type': 'string'}}}}], 'definitions': {'author': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, 'entry-point-group': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'dependency': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}, 'tool': {'type': 'object', 'properties': {'distutils': {'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://setuptools.pypa.io/en/latest/deprecated/distutils/configfile.html', 'title': '``tool.distutils`` table', '$$description': ['**EXPERIMENTAL** (NOT OFFICIALLY SUPPORTED): Use ``tool.distutils``', 'subtables to configure arguments for ``distutils`` commands.', 'Originally, ``distutils`` allowed developers to configure arguments for', '``setup.py`` commands via `distutils configuration files', '`_.', 'See also `the old Python docs _`.'], 'type': 'object', 'properties': {'global': {'type': 'object', 'description': 'Global options applied to all ``distutils`` commands'}}, 'patternProperties': {'.+': {'type': 'object'}}, '$comment': 'TODO: Is there a practical way of making this schema more specific?'}, 'setuptools': {'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html', 'title': '``tool.setuptools`` table', '$$description': ['``setuptools``-specific configurations that can be set by users that require', 'customization.', 'These configurations are completely optional and probably can be skipped when', 'creating simple packages. They are equivalent to some of the `Keywords', '`_', 'used by the ``setup.py`` file, and can be set via the ``tool.setuptools`` table.', 'It considers only ``setuptools`` `parameters', '`_', 'that are not covered by :pep:`621`; and intentionally excludes ``dependency_links``', 'and ``setup_requires`` (incompatible with modern workflows/standards).'], 'type': 'object', 'additionalProperties': False, 'properties': {'platforms': {'type': 'array', 'items': {'type': 'string'}}, 'provides': {'$$description': ['Package and virtual package names contained within this package', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, 'obsoletes': {'$$description': ['Packages which this package renders obsolete', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, 'zip-safe': {'$$description': ['Whether the project can be safely installed and run from a zip file.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'boolean'}, 'script-files': {'$$description': ['Legacy way of defining scripts (entry-points are preferred).', 'Equivalent to the ``script`` keyword in ``setup.py``', '(it was renamed to avoid confusion with entry-point based ``project.scripts``', 'defined in :pep:`621`).', '**DISCOURAGED**: generic script wrappers are tricky and may not work properly.', 'Whenever possible, please use ``project.scripts`` instead.'], 'type': 'array', 'items': {'type': 'string'}, '$comment': 'TODO: is this field deprecated/should be removed?'}, 'eager-resources': {'$$description': ['Resources that should be extracted together, if any of them is needed,', 'or if any C extensions included in the project are imported.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'array', 'items': {'type': 'string'}}, 'packages': {'$$description': ['Packages that should be included in the distribution.', 'It can be given either as a list of package identifiers', 'or as a ``dict``-like structure with a single key ``find``', 'which corresponds to a dynamic call to', '``setuptools.config.expand.find_packages`` function.', 'The ``find`` key is associated with a nested ``dict``-like structure that can', 'contain ``where``, ``include``, ``exclude`` and ``namespaces`` keys,', 'mimicking the keyword arguments of the associated function.'], 'oneOf': [{'title': 'Array of Python package identifiers', 'type': 'array', 'items': {'$ref': '#/definitions/package-name'}}, {'$ref': '#/definitions/find-directive'}]}, 'package-dir': {'$$description': [':class:`dict`-like structure mapping from package names to directories where their', 'code can be found.', 'The empty string (as key) means that all packages are contained inside', 'the given directory will be included in the distribution.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'const': ''}, {'$ref': '#/definitions/package-name'}]}, 'patternProperties': {'^.*$': {'type': 'string'}}}, 'package-data': {'$$description': ['Mapping from package names to lists of glob patterns.', 'Usually this option is not needed when using ``include-package-data = true``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'include-package-data': {'$$description': ['Automatically include any data files inside the package directories', 'that are specified by ``MANIFEST.in``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'boolean'}, 'exclude-package-data': {'$$description': ['Mapping from package names to lists of glob patterns that should be excluded', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'namespace-packages': {'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'https://setuptools.pypa.io/en/latest/userguide/package_discovery.html', 'description': '**DEPRECATED**: use implicit namespaces instead (:pep:`420`).'}, 'py-modules': {'description': 'Modules that setuptools will manipulate', 'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'TODO: clarify the relationship with ``packages``'}, 'ext-modules': {'description': 'Extension modules to be compiled by setuptools', 'type': 'array', 'items': {'$ref': '#/definitions/ext-module'}}, 'data-files': {'$$description': ['``dict``-like structure where each key represents a directory and', 'the value is a list of glob patterns that should be installed in them.', '**DISCOURAGED**: please notice this might not work as expected with wheels.', 'Whenever possible, consider using data files inside the package directories', '(or create a new namespace package that only contains data files).', 'See `data files support', '`_.'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'cmdclass': {'$$description': ['Mapping of distutils-style command names to ``setuptools.Command`` subclasses', 'which in turn should be represented by strings with a qualified class name', '(i.e., "dotted" form with module), e.g.::\n\n', '    cmdclass = {mycmd = "pkg.subpkg.module.CommandClass"}\n\n', 'The command class should be a directly defined at the top-level of the', 'containing module (no class nesting).'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'string', 'format': 'python-qualified-identifier'}}}, 'license-files': {'type': 'array', 'items': {'type': 'string'}, '$$description': ['**PROVISIONAL**: list of glob patterns for all license files being distributed.', '(likely to become standard with :pep:`639`).', "By default: ``['LICEN[CS]E*', 'COPYING*', 'NOTICE*', 'AUTHORS*']``"], '$comment': 'TODO: revise if PEP 639 is accepted. Probably ``project.license-files``?'}, 'dynamic': {'type': 'object', 'description': 'Instructions for loading :pep:`621`-related metadata dynamically', 'additionalProperties': False, 'properties': {'version': {'$$description': ['A version dynamically loaded via either the ``attr:`` or ``file:``', 'directives. Please make sure the given file or attribute respects :pep:`440`.', 'Also ensure to set ``project.dynamic`` accordingly.'], 'oneOf': [{'$ref': '#/definitions/attr-directive'}, {'$ref': '#/definitions/file-directive'}]}, 'classifiers': {'$ref': '#/definitions/file-directive'}, 'description': {'$ref': '#/definitions/file-directive'}, 'entry-points': {'$ref': '#/definitions/file-directive'}, 'dependencies': {'$ref': '#/definitions/file-directive-for-dependencies'}, 'optional-dependencies': {'type': 'object', 'propertyNames': {'type': 'string', 'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'.+': {'$ref': '#/definitions/file-directive-for-dependencies'}}}, 'readme': {'type': 'object', 'anyOf': [{'$ref': '#/definitions/file-directive'}, {'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'$ref': '#/definitions/file-directive/properties/file'}}, 'additionalProperties': False}], 'required': ['file']}}}}, 'definitions': {'package-name': {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}, 'ext-module': {'$id': '#/definitions/ext-module', 'title': 'Extension module', 'description': 'Parameters to construct a :class:`setuptools.Extension` object', 'type': 'object', 'required': ['name', 'sources'], 'additionalProperties': False, 'properties': {'name': {'type': 'string', 'format': 'python-module-name-relaxed'}, 'sources': {'type': 'array', 'items': {'type': 'string'}}, 'include-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'define-macros': {'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, 'undef-macros': {'type': 'array', 'items': {'type': 'string'}}, 'library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'libraries': {'type': 'array', 'items': {'type': 'string'}}, 'runtime-library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'extra-objects': {'type': 'array', 'items': {'type': 'string'}}, 'extra-compile-args': {'type': 'array', 'items': {'type': 'string'}}, 'extra-link-args': {'type': 'array', 'items': {'type': 'string'}}, 'export-symbols': {'type': 'array', 'items': {'type': 'string'}}, 'swig-opts': {'type': 'array', 'items': {'type': 'string'}}, 'depends': {'type': 'array', 'items': {'type': 'string'}}, 'language': {'type': 'string'}, 'optional': {'type': 'boolean'}, 'py-limited-api': {'type': 'boolean'}}}, 'file-directive': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'file-directive-for-dependencies': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}, 'attr-directive': {'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, 'find-directive': {'$id': '#/definitions/find-directive', 'title': "'find:' directive", 'type': 'object', 'additionalProperties': False, 'properties': {'find': {'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}}}}}}}, 'dependency-groups': {'type': 'object', 'description': 'Dependency groups following PEP 735', 'additionalProperties': False, 'patternProperties': {'^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$': {'type': 'array', 'items': {'oneOf': [{'type': 'string', 'description': 'Python package specifiers following PEP 508', 'format': 'pep508'}, {'type': 'object', 'additionalProperties': False, 'properties': {'include-group': {'description': 'Another dependency group to include in this one', 'type': 'string', 'pattern': '^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'}}}]}}}}}, 'project': {'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://packaging.python.org/en/latest/specifications/pyproject-toml/', 'title': 'Package metadata stored in the ``project`` table', '$$description': ['Data structure for the **project** table inside ``pyproject.toml``', '(as initially defined in :pep:`621`)'], 'type': 'object', 'properties': {'name': {'type': 'string', 'description': 'The name (primary identifier) of the project. MUST be statically defined.', 'format': 'pep508-identifier'}, 'version': {'type': 'string', 'description': 'The version of the project as supported by :pep:`440`.', 'format': 'pep440'}, 'description': {'type': 'string', '$$description': ['The `summary description of the project', '`_']}, 'readme': {'$$description': ['`Full/detailed description of the project in the form of a README', '`_', "with meaning similar to the one defined in `core metadata's Description", '`_'], 'oneOf': [{'type': 'string', '$$description': ['Relative path to a text file (UTF-8) containing the full description', 'of the project. If the file path ends in case-insensitive ``.md`` or', '``.rst`` suffixes, then the content-type is respectively', '``text/markdown`` or ``text/x-rst``']}, {'type': 'object', 'allOf': [{'anyOf': [{'properties': {'file': {'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}}, 'required': ['file']}, {'properties': {'text': {'type': 'string', 'description': 'Full text describing the project.'}}, 'required': ['text']}]}, {'properties': {'content-type': {'type': 'string', '$$description': ['Content-type (:rfc:`1341`) of the full description', '(e.g. ``text/markdown``). The ``charset`` parameter is assumed', 'UTF-8 when not present.'], '$comment': 'TODO: add regex pattern or format?'}}, 'required': ['content-type']}]}]}, 'requires-python': {'type': 'string', 'format': 'pep508-versionspec', '$$description': ['`The Python version requirements of the project', '`_.']}, 'license': {'description': '`Project license `_.', 'oneOf': [{'type': 'string', 'description': 'An SPDX license identifier', 'format': 'SPDX'}, {'type': 'object', 'properties': {'file': {'type': 'string', '$$description': ['Relative path to the file (UTF-8) which contains the license for the', 'project.']}}, 'required': ['file']}, {'type': 'object', 'properties': {'text': {'type': 'string', '$$description': ['The license of the project whose meaning is that of the', '`License field from the core metadata', '`_.']}}, 'required': ['text']}]}, 'license-files': {'description': 'Paths or globs to paths of license files', 'type': 'array', 'items': {'type': 'string'}}, 'authors': {'type': 'array', 'items': {'$ref': '#/definitions/author'}, '$$description': ["The people or organizations considered to be the 'authors' of the project.", 'The exact meaning is open to interpretation (e.g. original or primary authors,', 'current maintainers, or owners of the package).']}, 'maintainers': {'type': 'array', 'items': {'$ref': '#/definitions/author'}, '$$description': ["The people or organizations considered to be the 'maintainers' of the project.", 'Similarly to ``authors``, the exact meaning is open to interpretation.']}, 'keywords': {'type': 'array', 'items': {'type': 'string'}, 'description': 'List of keywords to assist searching for the distribution in a larger catalog.'}, 'classifiers': {'type': 'array', 'items': {'type': 'string', 'format': 'trove-classifier', 'description': '`PyPI classifier `_.'}, '$$description': ['`Trove classifiers `_', 'which apply to the project.']}, 'urls': {'type': 'object', 'description': 'URLs associated with the project in the form ``label => value``.', 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', 'format': 'url'}}}, 'scripts': {'$ref': '#/definitions/entry-point-group', '$$description': ['Instruct the installer to create command-line wrappers for the given', '`entry points `_.']}, 'gui-scripts': {'$ref': '#/definitions/entry-point-group', '$$description': ['Instruct the installer to create GUI wrappers for the given', '`entry points `_.', 'The difference between ``scripts`` and ``gui-scripts`` is only relevant in', 'Windows.']}, 'entry-points': {'$$description': ['Instruct the installer to expose the given modules/functions via', '``entry-point`` discovery mechanism (useful for plugins).', 'More information available in the `Python packaging guide', '`_.'], 'propertyNames': {'format': 'python-entrypoint-group'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'$ref': '#/definitions/entry-point-group'}}}, 'dependencies': {'type': 'array', 'description': 'Project (mandatory) dependencies.', 'items': {'$ref': '#/definitions/dependency'}}, 'optional-dependencies': {'type': 'object', 'description': 'Optional dependency for the project', 'propertyNames': {'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'array', 'items': {'$ref': '#/definitions/dependency'}}}}, 'dynamic': {'type': 'array', '$$description': ['Specifies which fields are intentionally unspecified and expected to be', 'dynamically provided by build tools'], 'items': {'enum': ['version', 'description', 'readme', 'requires-python', 'license', 'license-files', 'authors', 'maintainers', 'keywords', 'classifiers', 'urls', 'scripts', 'gui-scripts', 'entry-points', 'dependencies', 'optional-dependencies']}}}, 'required': ['name'], 'additionalProperties': False, 'allOf': [{'if': {'not': {'required': ['dynamic'], 'properties': {'dynamic': {'contains': {'const': 'version'}, '$$description': ['version is listed in ``dynamic``']}}}, '$$comment': ['According to :pep:`621`:', '    If the core metadata specification lists a field as "Required", then', '    the metadata MUST specify the field statically or list it in dynamic', 'In turn, `core metadata`_ defines:', '    The required fields are: Metadata-Version, Name, Version.', '    All the other fields are optional.', 'Since ``Metadata-Version`` is defined by the build back-end, ``name`` and', '``version`` are the only mandatory information in ``pyproject.toml``.', '.. _core metadata: https://packaging.python.org/specifications/core-metadata/']}, 'then': {'required': ['version'], '$$description': ['version should be statically defined in the ``version`` field']}}, {'if': {'required': ['license-files']}, 'then': {'properties': {'license': {'type': 'string'}}}}], 'definitions': {'author': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, 'entry-point-group': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'dependency': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}}, rule='type')
+    data_is_dict = isinstance(data, dict)
+    if data_is_dict:
+        data_keys = set(data.keys())
+        if "build-system" in data_keys:
+            data_keys.remove("build-system")
+            data__buildsystem = data["build-system"]
+            if not isinstance(data__buildsystem, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".build-system must be object", value=data__buildsystem, name="" + (name_prefix or "data") + ".build-system", definition={'type': 'object', 'description': 'Table used to store build-related data', 'additionalProperties': False, 'properties': {'requires': {'type': 'array', '$$description': ['List of dependencies in the :pep:`508` format required to execute the build', 'system. Please notice that the resulting dependency graph', '**MUST NOT contain cycles**'], 'items': {'type': 'string'}}, 'build-backend': {'type': 'string', 'description': 'Python object that will be used to perform the build according to :pep:`517`', 'format': 'pep517-backend-reference'}, 'backend-path': {'type': 'array', '$$description': ['List of directories to be prepended to ``sys.path`` when loading the', 'back-end, and running its hooks'], 'items': {'type': 'string', '$comment': 'Should be a path (TODO: enforce it with format?)'}}}, 'required': ['requires']}, rule='type')
+            data__buildsystem_is_dict = isinstance(data__buildsystem, dict)
+            if data__buildsystem_is_dict:
+                data__buildsystem__missing_keys = set(['requires']) - data__buildsystem.keys()
+                if data__buildsystem__missing_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".build-system must contain " + (str(sorted(data__buildsystem__missing_keys)) + " properties"), value=data__buildsystem, name="" + (name_prefix or "data") + ".build-system", definition={'type': 'object', 'description': 'Table used to store build-related data', 'additionalProperties': False, 'properties': {'requires': {'type': 'array', '$$description': ['List of dependencies in the :pep:`508` format required to execute the build', 'system. Please notice that the resulting dependency graph', '**MUST NOT contain cycles**'], 'items': {'type': 'string'}}, 'build-backend': {'type': 'string', 'description': 'Python object that will be used to perform the build according to :pep:`517`', 'format': 'pep517-backend-reference'}, 'backend-path': {'type': 'array', '$$description': ['List of directories to be prepended to ``sys.path`` when loading the', 'back-end, and running its hooks'], 'items': {'type': 'string', '$comment': 'Should be a path (TODO: enforce it with format?)'}}}, 'required': ['requires']}, rule='required')
+                data__buildsystem_keys = set(data__buildsystem.keys())
+                if "requires" in data__buildsystem_keys:
+                    data__buildsystem_keys.remove("requires")
+                    data__buildsystem__requires = data__buildsystem["requires"]
+                    if not isinstance(data__buildsystem__requires, (list, tuple)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".build-system.requires must be array", value=data__buildsystem__requires, name="" + (name_prefix or "data") + ".build-system.requires", definition={'type': 'array', '$$description': ['List of dependencies in the :pep:`508` format required to execute the build', 'system. Please notice that the resulting dependency graph', '**MUST NOT contain cycles**'], 'items': {'type': 'string'}}, rule='type')
+                    data__buildsystem__requires_is_list = isinstance(data__buildsystem__requires, (list, tuple))
+                    if data__buildsystem__requires_is_list:
+                        data__buildsystem__requires_len = len(data__buildsystem__requires)
+                        for data__buildsystem__requires_x, data__buildsystem__requires_item in enumerate(data__buildsystem__requires):
+                            if not isinstance(data__buildsystem__requires_item, (str)):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".build-system.requires[{data__buildsystem__requires_x}]".format(**locals()) + " must be string", value=data__buildsystem__requires_item, name="" + (name_prefix or "data") + ".build-system.requires[{data__buildsystem__requires_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+                if "build-backend" in data__buildsystem_keys:
+                    data__buildsystem_keys.remove("build-backend")
+                    data__buildsystem__buildbackend = data__buildsystem["build-backend"]
+                    if not isinstance(data__buildsystem__buildbackend, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".build-system.build-backend must be string", value=data__buildsystem__buildbackend, name="" + (name_prefix or "data") + ".build-system.build-backend", definition={'type': 'string', 'description': 'Python object that will be used to perform the build according to :pep:`517`', 'format': 'pep517-backend-reference'}, rule='type')
+                    if isinstance(data__buildsystem__buildbackend, str):
+                        if not custom_formats["pep517-backend-reference"](data__buildsystem__buildbackend):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".build-system.build-backend must be pep517-backend-reference", value=data__buildsystem__buildbackend, name="" + (name_prefix or "data") + ".build-system.build-backend", definition={'type': 'string', 'description': 'Python object that will be used to perform the build according to :pep:`517`', 'format': 'pep517-backend-reference'}, rule='format')
+                if "backend-path" in data__buildsystem_keys:
+                    data__buildsystem_keys.remove("backend-path")
+                    data__buildsystem__backendpath = data__buildsystem["backend-path"]
+                    if not isinstance(data__buildsystem__backendpath, (list, tuple)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".build-system.backend-path must be array", value=data__buildsystem__backendpath, name="" + (name_prefix or "data") + ".build-system.backend-path", definition={'type': 'array', '$$description': ['List of directories to be prepended to ``sys.path`` when loading the', 'back-end, and running its hooks'], 'items': {'type': 'string', '$comment': 'Should be a path (TODO: enforce it with format?)'}}, rule='type')
+                    data__buildsystem__backendpath_is_list = isinstance(data__buildsystem__backendpath, (list, tuple))
+                    if data__buildsystem__backendpath_is_list:
+                        data__buildsystem__backendpath_len = len(data__buildsystem__backendpath)
+                        for data__buildsystem__backendpath_x, data__buildsystem__backendpath_item in enumerate(data__buildsystem__backendpath):
+                            if not isinstance(data__buildsystem__backendpath_item, (str)):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".build-system.backend-path[{data__buildsystem__backendpath_x}]".format(**locals()) + " must be string", value=data__buildsystem__backendpath_item, name="" + (name_prefix or "data") + ".build-system.backend-path[{data__buildsystem__backendpath_x}]".format(**locals()) + "", definition={'type': 'string', '$comment': 'Should be a path (TODO: enforce it with format?)'}, rule='type')
+                if data__buildsystem_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".build-system must not contain "+str(data__buildsystem_keys)+" properties", value=data__buildsystem, name="" + (name_prefix or "data") + ".build-system", definition={'type': 'object', 'description': 'Table used to store build-related data', 'additionalProperties': False, 'properties': {'requires': {'type': 'array', '$$description': ['List of dependencies in the :pep:`508` format required to execute the build', 'system. Please notice that the resulting dependency graph', '**MUST NOT contain cycles**'], 'items': {'type': 'string'}}, 'build-backend': {'type': 'string', 'description': 'Python object that will be used to perform the build according to :pep:`517`', 'format': 'pep517-backend-reference'}, 'backend-path': {'type': 'array', '$$description': ['List of directories to be prepended to ``sys.path`` when loading the', 'back-end, and running its hooks'], 'items': {'type': 'string', '$comment': 'Should be a path (TODO: enforce it with format?)'}}}, 'required': ['requires']}, rule='additionalProperties')
+        if "project" in data_keys:
+            data_keys.remove("project")
+            data__project = data["project"]
+            validate_https___packaging_python_org_en_latest_specifications_pyproject_toml(data__project, custom_formats, (name_prefix or "data") + ".project")
+        if "tool" in data_keys:
+            data_keys.remove("tool")
+            data__tool = data["tool"]
+            if not isinstance(data__tool, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".tool must be object", value=data__tool, name="" + (name_prefix or "data") + ".tool", definition={'type': 'object', 'properties': {'distutils': {'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://setuptools.pypa.io/en/latest/deprecated/distutils/configfile.html', 'title': '``tool.distutils`` table', '$$description': ['**EXPERIMENTAL** (NOT OFFICIALLY SUPPORTED): Use ``tool.distutils``', 'subtables to configure arguments for ``distutils`` commands.', 'Originally, ``distutils`` allowed developers to configure arguments for', '``setup.py`` commands via `distutils configuration files', '`_.', 'See also `the old Python docs _`.'], 'type': 'object', 'properties': {'global': {'type': 'object', 'description': 'Global options applied to all ``distutils`` commands'}}, 'patternProperties': {'.+': {'type': 'object'}}, '$comment': 'TODO: Is there a practical way of making this schema more specific?'}, 'setuptools': {'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html', 'title': '``tool.setuptools`` table', '$$description': ['``setuptools``-specific configurations that can be set by users that require', 'customization.', 'These configurations are completely optional and probably can be skipped when', 'creating simple packages. They are equivalent to some of the `Keywords', '`_', 'used by the ``setup.py`` file, and can be set via the ``tool.setuptools`` table.', 'It considers only ``setuptools`` `parameters', '`_', 'that are not covered by :pep:`621`; and intentionally excludes ``dependency_links``', 'and ``setup_requires`` (incompatible with modern workflows/standards).'], 'type': 'object', 'additionalProperties': False, 'properties': {'platforms': {'type': 'array', 'items': {'type': 'string'}}, 'provides': {'$$description': ['Package and virtual package names contained within this package', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, 'obsoletes': {'$$description': ['Packages which this package renders obsolete', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, 'zip-safe': {'$$description': ['Whether the project can be safely installed and run from a zip file.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'boolean'}, 'script-files': {'$$description': ['Legacy way of defining scripts (entry-points are preferred).', 'Equivalent to the ``script`` keyword in ``setup.py``', '(it was renamed to avoid confusion with entry-point based ``project.scripts``', 'defined in :pep:`621`).', '**DISCOURAGED**: generic script wrappers are tricky and may not work properly.', 'Whenever possible, please use ``project.scripts`` instead.'], 'type': 'array', 'items': {'type': 'string'}, '$comment': 'TODO: is this field deprecated/should be removed?'}, 'eager-resources': {'$$description': ['Resources that should be extracted together, if any of them is needed,', 'or if any C extensions included in the project are imported.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'array', 'items': {'type': 'string'}}, 'packages': {'$$description': ['Packages that should be included in the distribution.', 'It can be given either as a list of package identifiers', 'or as a ``dict``-like structure with a single key ``find``', 'which corresponds to a dynamic call to', '``setuptools.config.expand.find_packages`` function.', 'The ``find`` key is associated with a nested ``dict``-like structure that can', 'contain ``where``, ``include``, ``exclude`` and ``namespaces`` keys,', 'mimicking the keyword arguments of the associated function.'], 'oneOf': [{'title': 'Array of Python package identifiers', 'type': 'array', 'items': {'$ref': '#/definitions/package-name'}}, {'$ref': '#/definitions/find-directive'}]}, 'package-dir': {'$$description': [':class:`dict`-like structure mapping from package names to directories where their', 'code can be found.', 'The empty string (as key) means that all packages are contained inside', 'the given directory will be included in the distribution.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'const': ''}, {'$ref': '#/definitions/package-name'}]}, 'patternProperties': {'^.*$': {'type': 'string'}}}, 'package-data': {'$$description': ['Mapping from package names to lists of glob patterns.', 'Usually this option is not needed when using ``include-package-data = true``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'include-package-data': {'$$description': ['Automatically include any data files inside the package directories', 'that are specified by ``MANIFEST.in``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'boolean'}, 'exclude-package-data': {'$$description': ['Mapping from package names to lists of glob patterns that should be excluded', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'namespace-packages': {'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'https://setuptools.pypa.io/en/latest/userguide/package_discovery.html', 'description': '**DEPRECATED**: use implicit namespaces instead (:pep:`420`).'}, 'py-modules': {'description': 'Modules that setuptools will manipulate', 'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'TODO: clarify the relationship with ``packages``'}, 'ext-modules': {'description': 'Extension modules to be compiled by setuptools', 'type': 'array', 'items': {'$ref': '#/definitions/ext-module'}}, 'data-files': {'$$description': ['``dict``-like structure where each key represents a directory and', 'the value is a list of glob patterns that should be installed in them.', '**DISCOURAGED**: please notice this might not work as expected with wheels.', 'Whenever possible, consider using data files inside the package directories', '(or create a new namespace package that only contains data files).', 'See `data files support', '`_.'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'cmdclass': {'$$description': ['Mapping of distutils-style command names to ``setuptools.Command`` subclasses', 'which in turn should be represented by strings with a qualified class name', '(i.e., "dotted" form with module), e.g.::\n\n', '    cmdclass = {mycmd = "pkg.subpkg.module.CommandClass"}\n\n', 'The command class should be a directly defined at the top-level of the', 'containing module (no class nesting).'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'string', 'format': 'python-qualified-identifier'}}}, 'license-files': {'type': 'array', 'items': {'type': 'string'}, '$$description': ['**PROVISIONAL**: list of glob patterns for all license files being distributed.', '(likely to become standard with :pep:`639`).', "By default: ``['LICEN[CS]E*', 'COPYING*', 'NOTICE*', 'AUTHORS*']``"], '$comment': 'TODO: revise if PEP 639 is accepted. Probably ``project.license-files``?'}, 'dynamic': {'type': 'object', 'description': 'Instructions for loading :pep:`621`-related metadata dynamically', 'additionalProperties': False, 'properties': {'version': {'$$description': ['A version dynamically loaded via either the ``attr:`` or ``file:``', 'directives. Please make sure the given file or attribute respects :pep:`440`.', 'Also ensure to set ``project.dynamic`` accordingly.'], 'oneOf': [{'$ref': '#/definitions/attr-directive'}, {'$ref': '#/definitions/file-directive'}]}, 'classifiers': {'$ref': '#/definitions/file-directive'}, 'description': {'$ref': '#/definitions/file-directive'}, 'entry-points': {'$ref': '#/definitions/file-directive'}, 'dependencies': {'$ref': '#/definitions/file-directive-for-dependencies'}, 'optional-dependencies': {'type': 'object', 'propertyNames': {'type': 'string', 'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'.+': {'$ref': '#/definitions/file-directive-for-dependencies'}}}, 'readme': {'type': 'object', 'anyOf': [{'$ref': '#/definitions/file-directive'}, {'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'$ref': '#/definitions/file-directive/properties/file'}}, 'additionalProperties': False}], 'required': ['file']}}}}, 'definitions': {'package-name': {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}, 'ext-module': {'$id': '#/definitions/ext-module', 'title': 'Extension module', 'description': 'Parameters to construct a :class:`setuptools.Extension` object', 'type': 'object', 'required': ['name', 'sources'], 'additionalProperties': False, 'properties': {'name': {'type': 'string', 'format': 'python-module-name-relaxed'}, 'sources': {'type': 'array', 'items': {'type': 'string'}}, 'include-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'define-macros': {'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, 'undef-macros': {'type': 'array', 'items': {'type': 'string'}}, 'library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'libraries': {'type': 'array', 'items': {'type': 'string'}}, 'runtime-library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'extra-objects': {'type': 'array', 'items': {'type': 'string'}}, 'extra-compile-args': {'type': 'array', 'items': {'type': 'string'}}, 'extra-link-args': {'type': 'array', 'items': {'type': 'string'}}, 'export-symbols': {'type': 'array', 'items': {'type': 'string'}}, 'swig-opts': {'type': 'array', 'items': {'type': 'string'}}, 'depends': {'type': 'array', 'items': {'type': 'string'}}, 'language': {'type': 'string'}, 'optional': {'type': 'boolean'}, 'py-limited-api': {'type': 'boolean'}}}, 'file-directive': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'file-directive-for-dependencies': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}, 'attr-directive': {'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, 'find-directive': {'$id': '#/definitions/find-directive', 'title': "'find:' directive", 'type': 'object', 'additionalProperties': False, 'properties': {'find': {'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}}}}}}}, rule='type')
+            data__tool_is_dict = isinstance(data__tool, dict)
+            if data__tool_is_dict:
+                data__tool_keys = set(data__tool.keys())
+                if "distutils" in data__tool_keys:
+                    data__tool_keys.remove("distutils")
+                    data__tool__distutils = data__tool["distutils"]
+                    validate_https___setuptools_pypa_io_en_latest_deprecated_distutils_configfile_html(data__tool__distutils, custom_formats, (name_prefix or "data") + ".tool.distutils")
+                if "setuptools" in data__tool_keys:
+                    data__tool_keys.remove("setuptools")
+                    data__tool__setuptools = data__tool["setuptools"]
+                    validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html(data__tool__setuptools, custom_formats, (name_prefix or "data") + ".tool.setuptools")
+        if "dependency-groups" in data_keys:
+            data_keys.remove("dependency-groups")
+            data__dependencygroups = data["dependency-groups"]
+            if not isinstance(data__dependencygroups, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".dependency-groups must be object", value=data__dependencygroups, name="" + (name_prefix or "data") + ".dependency-groups", definition={'type': 'object', 'description': 'Dependency groups following PEP 735', 'additionalProperties': False, 'patternProperties': {'^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$': {'type': 'array', 'items': {'oneOf': [{'type': 'string', 'description': 'Python package specifiers following PEP 508', 'format': 'pep508'}, {'type': 'object', 'additionalProperties': False, 'properties': {'include-group': {'description': 'Another dependency group to include in this one', 'type': 'string', 'pattern': '^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'}}}]}}}}, rule='type')
+            data__dependencygroups_is_dict = isinstance(data__dependencygroups, dict)
+            if data__dependencygroups_is_dict:
+                data__dependencygroups_keys = set(data__dependencygroups.keys())
+                for data__dependencygroups_key, data__dependencygroups_val in data__dependencygroups.items():
+                    if REGEX_PATTERNS['^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'].search(data__dependencygroups_key):
+                        if data__dependencygroups_key in data__dependencygroups_keys:
+                            data__dependencygroups_keys.remove(data__dependencygroups_key)
+                        if not isinstance(data__dependencygroups_val, (list, tuple)):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}".format(**locals()) + " must be array", value=data__dependencygroups_val, name="" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}".format(**locals()) + "", definition={'type': 'array', 'items': {'oneOf': [{'type': 'string', 'description': 'Python package specifiers following PEP 508', 'format': 'pep508'}, {'type': 'object', 'additionalProperties': False, 'properties': {'include-group': {'description': 'Another dependency group to include in this one', 'type': 'string', 'pattern': '^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'}}}]}}, rule='type')
+                        data__dependencygroups_val_is_list = isinstance(data__dependencygroups_val, (list, tuple))
+                        if data__dependencygroups_val_is_list:
+                            data__dependencygroups_val_len = len(data__dependencygroups_val)
+                            for data__dependencygroups_val_x, data__dependencygroups_val_item in enumerate(data__dependencygroups_val):
+                                data__dependencygroups_val_item_one_of_count1 = 0
+                                if data__dependencygroups_val_item_one_of_count1 < 2:
+                                    try:
+                                        if not isinstance(data__dependencygroups_val_item, (str)):
+                                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}]".format(**locals()) + " must be string", value=data__dependencygroups_val_item, name="" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}]".format(**locals()) + "", definition={'type': 'string', 'description': 'Python package specifiers following PEP 508', 'format': 'pep508'}, rule='type')
+                                        if isinstance(data__dependencygroups_val_item, str):
+                                            if not custom_formats["pep508"](data__dependencygroups_val_item):
+                                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}]".format(**locals()) + " must be pep508", value=data__dependencygroups_val_item, name="" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}]".format(**locals()) + "", definition={'type': 'string', 'description': 'Python package specifiers following PEP 508', 'format': 'pep508'}, rule='format')
+                                        data__dependencygroups_val_item_one_of_count1 += 1
+                                    except JsonSchemaValueException: pass
+                                if data__dependencygroups_val_item_one_of_count1 < 2:
+                                    try:
+                                        if not isinstance(data__dependencygroups_val_item, (dict)):
+                                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}]".format(**locals()) + " must be object", value=data__dependencygroups_val_item, name="" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}]".format(**locals()) + "", definition={'type': 'object', 'additionalProperties': False, 'properties': {'include-group': {'description': 'Another dependency group to include in this one', 'type': 'string', 'pattern': '^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'}}}, rule='type')
+                                        data__dependencygroups_val_item_is_dict = isinstance(data__dependencygroups_val_item, dict)
+                                        if data__dependencygroups_val_item_is_dict:
+                                            data__dependencygroups_val_item_keys = set(data__dependencygroups_val_item.keys())
+                                            if "include-group" in data__dependencygroups_val_item_keys:
+                                                data__dependencygroups_val_item_keys.remove("include-group")
+                                                data__dependencygroups_val_item__includegroup = data__dependencygroups_val_item["include-group"]
+                                                if not isinstance(data__dependencygroups_val_item__includegroup, (str)):
+                                                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}].include-group".format(**locals()) + " must be string", value=data__dependencygroups_val_item__includegroup, name="" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}].include-group".format(**locals()) + "", definition={'description': 'Another dependency group to include in this one', 'type': 'string', 'pattern': '^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'}, rule='type')
+                                                if isinstance(data__dependencygroups_val_item__includegroup, str):
+                                                    if not REGEX_PATTERNS['^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'].search(data__dependencygroups_val_item__includegroup):
+                                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}].include-group".format(**locals()) + " must match pattern ^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$", value=data__dependencygroups_val_item__includegroup, name="" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}].include-group".format(**locals()) + "", definition={'description': 'Another dependency group to include in this one', 'type': 'string', 'pattern': '^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'}, rule='pattern')
+                                            if data__dependencygroups_val_item_keys:
+                                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}]".format(**locals()) + " must not contain "+str(data__dependencygroups_val_item_keys)+" properties", value=data__dependencygroups_val_item, name="" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}]".format(**locals()) + "", definition={'type': 'object', 'additionalProperties': False, 'properties': {'include-group': {'description': 'Another dependency group to include in this one', 'type': 'string', 'pattern': '^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'}}}, rule='additionalProperties')
+                                        data__dependencygroups_val_item_one_of_count1 += 1
+                                    except JsonSchemaValueException: pass
+                                if data__dependencygroups_val_item_one_of_count1 != 1:
+                                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}]".format(**locals()) + " must be valid exactly by one definition" + (" (" + str(data__dependencygroups_val_item_one_of_count1) + " matches found)"), value=data__dependencygroups_val_item, name="" + (name_prefix or "data") + ".dependency-groups.{data__dependencygroups_key}[{data__dependencygroups_val_x}]".format(**locals()) + "", definition={'oneOf': [{'type': 'string', 'description': 'Python package specifiers following PEP 508', 'format': 'pep508'}, {'type': 'object', 'additionalProperties': False, 'properties': {'include-group': {'description': 'Another dependency group to include in this one', 'type': 'string', 'pattern': '^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'}}}]}, rule='oneOf')
+                if data__dependencygroups_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".dependency-groups must not contain "+str(data__dependencygroups_keys)+" properties", value=data__dependencygroups, name="" + (name_prefix or "data") + ".dependency-groups", definition={'type': 'object', 'description': 'Dependency groups following PEP 735', 'additionalProperties': False, 'patternProperties': {'^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$': {'type': 'array', 'items': {'oneOf': [{'type': 'string', 'description': 'Python package specifiers following PEP 508', 'format': 'pep508'}, {'type': 'object', 'additionalProperties': False, 'properties': {'include-group': {'description': 'Another dependency group to include in this one', 'type': 'string', 'pattern': '^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'}}}]}}}}, rule='additionalProperties')
+        if data_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must not contain "+str(data_keys)+" properties", value=data, name="" + (name_prefix or "data") + "", definition={'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://packaging.python.org/en/latest/specifications/declaring-build-dependencies/', 'title': 'Data structure for ``pyproject.toml`` files', '$$description': ['File format containing build-time configurations for the Python ecosystem. ', ':pep:`517` initially defined a build-system independent format for source trees', 'which was complemented by :pep:`518` to provide a way of specifying dependencies ', 'for building Python projects.', 'Please notice the ``project`` table (as initially defined in  :pep:`621`) is not included', 'in this schema and should be considered separately.'], 'type': 'object', 'additionalProperties': False, 'properties': {'build-system': {'type': 'object', 'description': 'Table used to store build-related data', 'additionalProperties': False, 'properties': {'requires': {'type': 'array', '$$description': ['List of dependencies in the :pep:`508` format required to execute the build', 'system. Please notice that the resulting dependency graph', '**MUST NOT contain cycles**'], 'items': {'type': 'string'}}, 'build-backend': {'type': 'string', 'description': 'Python object that will be used to perform the build according to :pep:`517`', 'format': 'pep517-backend-reference'}, 'backend-path': {'type': 'array', '$$description': ['List of directories to be prepended to ``sys.path`` when loading the', 'back-end, and running its hooks'], 'items': {'type': 'string', '$comment': 'Should be a path (TODO: enforce it with format?)'}}}, 'required': ['requires']}, 'project': {'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://packaging.python.org/en/latest/specifications/pyproject-toml/', 'title': 'Package metadata stored in the ``project`` table', '$$description': ['Data structure for the **project** table inside ``pyproject.toml``', '(as initially defined in :pep:`621`)'], 'type': 'object', 'properties': {'name': {'type': 'string', 'description': 'The name (primary identifier) of the project. MUST be statically defined.', 'format': 'pep508-identifier'}, 'version': {'type': 'string', 'description': 'The version of the project as supported by :pep:`440`.', 'format': 'pep440'}, 'description': {'type': 'string', '$$description': ['The `summary description of the project', '`_']}, 'readme': {'$$description': ['`Full/detailed description of the project in the form of a README', '`_', "with meaning similar to the one defined in `core metadata's Description", '`_'], 'oneOf': [{'type': 'string', '$$description': ['Relative path to a text file (UTF-8) containing the full description', 'of the project. If the file path ends in case-insensitive ``.md`` or', '``.rst`` suffixes, then the content-type is respectively', '``text/markdown`` or ``text/x-rst``']}, {'type': 'object', 'allOf': [{'anyOf': [{'properties': {'file': {'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}}, 'required': ['file']}, {'properties': {'text': {'type': 'string', 'description': 'Full text describing the project.'}}, 'required': ['text']}]}, {'properties': {'content-type': {'type': 'string', '$$description': ['Content-type (:rfc:`1341`) of the full description', '(e.g. ``text/markdown``). The ``charset`` parameter is assumed', 'UTF-8 when not present.'], '$comment': 'TODO: add regex pattern or format?'}}, 'required': ['content-type']}]}]}, 'requires-python': {'type': 'string', 'format': 'pep508-versionspec', '$$description': ['`The Python version requirements of the project', '`_.']}, 'license': {'description': '`Project license `_.', 'oneOf': [{'type': 'string', 'description': 'An SPDX license identifier', 'format': 'SPDX'}, {'type': 'object', 'properties': {'file': {'type': 'string', '$$description': ['Relative path to the file (UTF-8) which contains the license for the', 'project.']}}, 'required': ['file']}, {'type': 'object', 'properties': {'text': {'type': 'string', '$$description': ['The license of the project whose meaning is that of the', '`License field from the core metadata', '`_.']}}, 'required': ['text']}]}, 'license-files': {'description': 'Paths or globs to paths of license files', 'type': 'array', 'items': {'type': 'string'}}, 'authors': {'type': 'array', 'items': {'$ref': '#/definitions/author'}, '$$description': ["The people or organizations considered to be the 'authors' of the project.", 'The exact meaning is open to interpretation (e.g. original or primary authors,', 'current maintainers, or owners of the package).']}, 'maintainers': {'type': 'array', 'items': {'$ref': '#/definitions/author'}, '$$description': ["The people or organizations considered to be the 'maintainers' of the project.", 'Similarly to ``authors``, the exact meaning is open to interpretation.']}, 'keywords': {'type': 'array', 'items': {'type': 'string'}, 'description': 'List of keywords to assist searching for the distribution in a larger catalog.'}, 'classifiers': {'type': 'array', 'items': {'type': 'string', 'format': 'trove-classifier', 'description': '`PyPI classifier `_.'}, '$$description': ['`Trove classifiers `_', 'which apply to the project.']}, 'urls': {'type': 'object', 'description': 'URLs associated with the project in the form ``label => value``.', 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', 'format': 'url'}}}, 'scripts': {'$ref': '#/definitions/entry-point-group', '$$description': ['Instruct the installer to create command-line wrappers for the given', '`entry points `_.']}, 'gui-scripts': {'$ref': '#/definitions/entry-point-group', '$$description': ['Instruct the installer to create GUI wrappers for the given', '`entry points `_.', 'The difference between ``scripts`` and ``gui-scripts`` is only relevant in', 'Windows.']}, 'entry-points': {'$$description': ['Instruct the installer to expose the given modules/functions via', '``entry-point`` discovery mechanism (useful for plugins).', 'More information available in the `Python packaging guide', '`_.'], 'propertyNames': {'format': 'python-entrypoint-group'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'$ref': '#/definitions/entry-point-group'}}}, 'dependencies': {'type': 'array', 'description': 'Project (mandatory) dependencies.', 'items': {'$ref': '#/definitions/dependency'}}, 'optional-dependencies': {'type': 'object', 'description': 'Optional dependency for the project', 'propertyNames': {'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'array', 'items': {'$ref': '#/definitions/dependency'}}}}, 'dynamic': {'type': 'array', '$$description': ['Specifies which fields are intentionally unspecified and expected to be', 'dynamically provided by build tools'], 'items': {'enum': ['version', 'description', 'readme', 'requires-python', 'license', 'license-files', 'authors', 'maintainers', 'keywords', 'classifiers', 'urls', 'scripts', 'gui-scripts', 'entry-points', 'dependencies', 'optional-dependencies']}}}, 'required': ['name'], 'additionalProperties': False, 'allOf': [{'if': {'not': {'required': ['dynamic'], 'properties': {'dynamic': {'contains': {'const': 'version'}, '$$description': ['version is listed in ``dynamic``']}}}, '$$comment': ['According to :pep:`621`:', '    If the core metadata specification lists a field as "Required", then', '    the metadata MUST specify the field statically or list it in dynamic', 'In turn, `core metadata`_ defines:', '    The required fields are: Metadata-Version, Name, Version.', '    All the other fields are optional.', 'Since ``Metadata-Version`` is defined by the build back-end, ``name`` and', '``version`` are the only mandatory information in ``pyproject.toml``.', '.. _core metadata: https://packaging.python.org/specifications/core-metadata/']}, 'then': {'required': ['version'], '$$description': ['version should be statically defined in the ``version`` field']}}, {'if': {'required': ['license-files']}, 'then': {'properties': {'license': {'type': 'string'}}}}], 'definitions': {'author': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, 'entry-point-group': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'dependency': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}, 'tool': {'type': 'object', 'properties': {'distutils': {'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://setuptools.pypa.io/en/latest/deprecated/distutils/configfile.html', 'title': '``tool.distutils`` table', '$$description': ['**EXPERIMENTAL** (NOT OFFICIALLY SUPPORTED): Use ``tool.distutils``', 'subtables to configure arguments for ``distutils`` commands.', 'Originally, ``distutils`` allowed developers to configure arguments for', '``setup.py`` commands via `distutils configuration files', '`_.', 'See also `the old Python docs _`.'], 'type': 'object', 'properties': {'global': {'type': 'object', 'description': 'Global options applied to all ``distutils`` commands'}}, 'patternProperties': {'.+': {'type': 'object'}}, '$comment': 'TODO: Is there a practical way of making this schema more specific?'}, 'setuptools': {'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html', 'title': '``tool.setuptools`` table', '$$description': ['``setuptools``-specific configurations that can be set by users that require', 'customization.', 'These configurations are completely optional and probably can be skipped when', 'creating simple packages. They are equivalent to some of the `Keywords', '`_', 'used by the ``setup.py`` file, and can be set via the ``tool.setuptools`` table.', 'It considers only ``setuptools`` `parameters', '`_', 'that are not covered by :pep:`621`; and intentionally excludes ``dependency_links``', 'and ``setup_requires`` (incompatible with modern workflows/standards).'], 'type': 'object', 'additionalProperties': False, 'properties': {'platforms': {'type': 'array', 'items': {'type': 'string'}}, 'provides': {'$$description': ['Package and virtual package names contained within this package', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, 'obsoletes': {'$$description': ['Packages which this package renders obsolete', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, 'zip-safe': {'$$description': ['Whether the project can be safely installed and run from a zip file.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'boolean'}, 'script-files': {'$$description': ['Legacy way of defining scripts (entry-points are preferred).', 'Equivalent to the ``script`` keyword in ``setup.py``', '(it was renamed to avoid confusion with entry-point based ``project.scripts``', 'defined in :pep:`621`).', '**DISCOURAGED**: generic script wrappers are tricky and may not work properly.', 'Whenever possible, please use ``project.scripts`` instead.'], 'type': 'array', 'items': {'type': 'string'}, '$comment': 'TODO: is this field deprecated/should be removed?'}, 'eager-resources': {'$$description': ['Resources that should be extracted together, if any of them is needed,', 'or if any C extensions included in the project are imported.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'array', 'items': {'type': 'string'}}, 'packages': {'$$description': ['Packages that should be included in the distribution.', 'It can be given either as a list of package identifiers', 'or as a ``dict``-like structure with a single key ``find``', 'which corresponds to a dynamic call to', '``setuptools.config.expand.find_packages`` function.', 'The ``find`` key is associated with a nested ``dict``-like structure that can', 'contain ``where``, ``include``, ``exclude`` and ``namespaces`` keys,', 'mimicking the keyword arguments of the associated function.'], 'oneOf': [{'title': 'Array of Python package identifiers', 'type': 'array', 'items': {'$ref': '#/definitions/package-name'}}, {'$ref': '#/definitions/find-directive'}]}, 'package-dir': {'$$description': [':class:`dict`-like structure mapping from package names to directories where their', 'code can be found.', 'The empty string (as key) means that all packages are contained inside', 'the given directory will be included in the distribution.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'const': ''}, {'$ref': '#/definitions/package-name'}]}, 'patternProperties': {'^.*$': {'type': 'string'}}}, 'package-data': {'$$description': ['Mapping from package names to lists of glob patterns.', 'Usually this option is not needed when using ``include-package-data = true``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'include-package-data': {'$$description': ['Automatically include any data files inside the package directories', 'that are specified by ``MANIFEST.in``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'boolean'}, 'exclude-package-data': {'$$description': ['Mapping from package names to lists of glob patterns that should be excluded', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'namespace-packages': {'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'https://setuptools.pypa.io/en/latest/userguide/package_discovery.html', 'description': '**DEPRECATED**: use implicit namespaces instead (:pep:`420`).'}, 'py-modules': {'description': 'Modules that setuptools will manipulate', 'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'TODO: clarify the relationship with ``packages``'}, 'ext-modules': {'description': 'Extension modules to be compiled by setuptools', 'type': 'array', 'items': {'$ref': '#/definitions/ext-module'}}, 'data-files': {'$$description': ['``dict``-like structure where each key represents a directory and', 'the value is a list of glob patterns that should be installed in them.', '**DISCOURAGED**: please notice this might not work as expected with wheels.', 'Whenever possible, consider using data files inside the package directories', '(or create a new namespace package that only contains data files).', 'See `data files support', '`_.'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'cmdclass': {'$$description': ['Mapping of distutils-style command names to ``setuptools.Command`` subclasses', 'which in turn should be represented by strings with a qualified class name', '(i.e., "dotted" form with module), e.g.::\n\n', '    cmdclass = {mycmd = "pkg.subpkg.module.CommandClass"}\n\n', 'The command class should be a directly defined at the top-level of the', 'containing module (no class nesting).'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'string', 'format': 'python-qualified-identifier'}}}, 'license-files': {'type': 'array', 'items': {'type': 'string'}, '$$description': ['**PROVISIONAL**: list of glob patterns for all license files being distributed.', '(likely to become standard with :pep:`639`).', "By default: ``['LICEN[CS]E*', 'COPYING*', 'NOTICE*', 'AUTHORS*']``"], '$comment': 'TODO: revise if PEP 639 is accepted. Probably ``project.license-files``?'}, 'dynamic': {'type': 'object', 'description': 'Instructions for loading :pep:`621`-related metadata dynamically', 'additionalProperties': False, 'properties': {'version': {'$$description': ['A version dynamically loaded via either the ``attr:`` or ``file:``', 'directives. Please make sure the given file or attribute respects :pep:`440`.', 'Also ensure to set ``project.dynamic`` accordingly.'], 'oneOf': [{'$ref': '#/definitions/attr-directive'}, {'$ref': '#/definitions/file-directive'}]}, 'classifiers': {'$ref': '#/definitions/file-directive'}, 'description': {'$ref': '#/definitions/file-directive'}, 'entry-points': {'$ref': '#/definitions/file-directive'}, 'dependencies': {'$ref': '#/definitions/file-directive-for-dependencies'}, 'optional-dependencies': {'type': 'object', 'propertyNames': {'type': 'string', 'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'.+': {'$ref': '#/definitions/file-directive-for-dependencies'}}}, 'readme': {'type': 'object', 'anyOf': [{'$ref': '#/definitions/file-directive'}, {'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'$ref': '#/definitions/file-directive/properties/file'}}, 'additionalProperties': False}], 'required': ['file']}}}}, 'definitions': {'package-name': {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}, 'ext-module': {'$id': '#/definitions/ext-module', 'title': 'Extension module', 'description': 'Parameters to construct a :class:`setuptools.Extension` object', 'type': 'object', 'required': ['name', 'sources'], 'additionalProperties': False, 'properties': {'name': {'type': 'string', 'format': 'python-module-name-relaxed'}, 'sources': {'type': 'array', 'items': {'type': 'string'}}, 'include-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'define-macros': {'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, 'undef-macros': {'type': 'array', 'items': {'type': 'string'}}, 'library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'libraries': {'type': 'array', 'items': {'type': 'string'}}, 'runtime-library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'extra-objects': {'type': 'array', 'items': {'type': 'string'}}, 'extra-compile-args': {'type': 'array', 'items': {'type': 'string'}}, 'extra-link-args': {'type': 'array', 'items': {'type': 'string'}}, 'export-symbols': {'type': 'array', 'items': {'type': 'string'}}, 'swig-opts': {'type': 'array', 'items': {'type': 'string'}}, 'depends': {'type': 'array', 'items': {'type': 'string'}}, 'language': {'type': 'string'}, 'optional': {'type': 'boolean'}, 'py-limited-api': {'type': 'boolean'}}}, 'file-directive': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'file-directive-for-dependencies': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}, 'attr-directive': {'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, 'find-directive': {'$id': '#/definitions/find-directive', 'title': "'find:' directive", 'type': 'object', 'additionalProperties': False, 'properties': {'find': {'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}}}}}}}, 'dependency-groups': {'type': 'object', 'description': 'Dependency groups following PEP 735', 'additionalProperties': False, 'patternProperties': {'^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$': {'type': 'array', 'items': {'oneOf': [{'type': 'string', 'description': 'Python package specifiers following PEP 508', 'format': 'pep508'}, {'type': 'object', 'additionalProperties': False, 'properties': {'include-group': {'description': 'Another dependency group to include in this one', 'type': 'string', 'pattern': '^([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9._-]*[a-zA-Z0-9])$'}}}]}}}}}, 'project': {'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://packaging.python.org/en/latest/specifications/pyproject-toml/', 'title': 'Package metadata stored in the ``project`` table', '$$description': ['Data structure for the **project** table inside ``pyproject.toml``', '(as initially defined in :pep:`621`)'], 'type': 'object', 'properties': {'name': {'type': 'string', 'description': 'The name (primary identifier) of the project. MUST be statically defined.', 'format': 'pep508-identifier'}, 'version': {'type': 'string', 'description': 'The version of the project as supported by :pep:`440`.', 'format': 'pep440'}, 'description': {'type': 'string', '$$description': ['The `summary description of the project', '`_']}, 'readme': {'$$description': ['`Full/detailed description of the project in the form of a README', '`_', "with meaning similar to the one defined in `core metadata's Description", '`_'], 'oneOf': [{'type': 'string', '$$description': ['Relative path to a text file (UTF-8) containing the full description', 'of the project. If the file path ends in case-insensitive ``.md`` or', '``.rst`` suffixes, then the content-type is respectively', '``text/markdown`` or ``text/x-rst``']}, {'type': 'object', 'allOf': [{'anyOf': [{'properties': {'file': {'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}}, 'required': ['file']}, {'properties': {'text': {'type': 'string', 'description': 'Full text describing the project.'}}, 'required': ['text']}]}, {'properties': {'content-type': {'type': 'string', '$$description': ['Content-type (:rfc:`1341`) of the full description', '(e.g. ``text/markdown``). The ``charset`` parameter is assumed', 'UTF-8 when not present.'], '$comment': 'TODO: add regex pattern or format?'}}, 'required': ['content-type']}]}]}, 'requires-python': {'type': 'string', 'format': 'pep508-versionspec', '$$description': ['`The Python version requirements of the project', '`_.']}, 'license': {'description': '`Project license `_.', 'oneOf': [{'type': 'string', 'description': 'An SPDX license identifier', 'format': 'SPDX'}, {'type': 'object', 'properties': {'file': {'type': 'string', '$$description': ['Relative path to the file (UTF-8) which contains the license for the', 'project.']}}, 'required': ['file']}, {'type': 'object', 'properties': {'text': {'type': 'string', '$$description': ['The license of the project whose meaning is that of the', '`License field from the core metadata', '`_.']}}, 'required': ['text']}]}, 'license-files': {'description': 'Paths or globs to paths of license files', 'type': 'array', 'items': {'type': 'string'}}, 'authors': {'type': 'array', 'items': {'$ref': '#/definitions/author'}, '$$description': ["The people or organizations considered to be the 'authors' of the project.", 'The exact meaning is open to interpretation (e.g. original or primary authors,', 'current maintainers, or owners of the package).']}, 'maintainers': {'type': 'array', 'items': {'$ref': '#/definitions/author'}, '$$description': ["The people or organizations considered to be the 'maintainers' of the project.", 'Similarly to ``authors``, the exact meaning is open to interpretation.']}, 'keywords': {'type': 'array', 'items': {'type': 'string'}, 'description': 'List of keywords to assist searching for the distribution in a larger catalog.'}, 'classifiers': {'type': 'array', 'items': {'type': 'string', 'format': 'trove-classifier', 'description': '`PyPI classifier `_.'}, '$$description': ['`Trove classifiers `_', 'which apply to the project.']}, 'urls': {'type': 'object', 'description': 'URLs associated with the project in the form ``label => value``.', 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', 'format': 'url'}}}, 'scripts': {'$ref': '#/definitions/entry-point-group', '$$description': ['Instruct the installer to create command-line wrappers for the given', '`entry points `_.']}, 'gui-scripts': {'$ref': '#/definitions/entry-point-group', '$$description': ['Instruct the installer to create GUI wrappers for the given', '`entry points `_.', 'The difference between ``scripts`` and ``gui-scripts`` is only relevant in', 'Windows.']}, 'entry-points': {'$$description': ['Instruct the installer to expose the given modules/functions via', '``entry-point`` discovery mechanism (useful for plugins).', 'More information available in the `Python packaging guide', '`_.'], 'propertyNames': {'format': 'python-entrypoint-group'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'$ref': '#/definitions/entry-point-group'}}}, 'dependencies': {'type': 'array', 'description': 'Project (mandatory) dependencies.', 'items': {'$ref': '#/definitions/dependency'}}, 'optional-dependencies': {'type': 'object', 'description': 'Optional dependency for the project', 'propertyNames': {'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'array', 'items': {'$ref': '#/definitions/dependency'}}}}, 'dynamic': {'type': 'array', '$$description': ['Specifies which fields are intentionally unspecified and expected to be', 'dynamically provided by build tools'], 'items': {'enum': ['version', 'description', 'readme', 'requires-python', 'license', 'license-files', 'authors', 'maintainers', 'keywords', 'classifiers', 'urls', 'scripts', 'gui-scripts', 'entry-points', 'dependencies', 'optional-dependencies']}}}, 'required': ['name'], 'additionalProperties': False, 'allOf': [{'if': {'not': {'required': ['dynamic'], 'properties': {'dynamic': {'contains': {'const': 'version'}, '$$description': ['version is listed in ``dynamic``']}}}, '$$comment': ['According to :pep:`621`:', '    If the core metadata specification lists a field as "Required", then', '    the metadata MUST specify the field statically or list it in dynamic', 'In turn, `core metadata`_ defines:', '    The required fields are: Metadata-Version, Name, Version.', '    All the other fields are optional.', 'Since ``Metadata-Version`` is defined by the build back-end, ``name`` and', '``version`` are the only mandatory information in ``pyproject.toml``.', '.. _core metadata: https://packaging.python.org/specifications/core-metadata/']}, 'then': {'required': ['version'], '$$description': ['version should be statically defined in the ``version`` field']}}, {'if': {'required': ['license-files']}, 'then': {'properties': {'license': {'type': 'string'}}}}], 'definitions': {'author': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, 'entry-point-group': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'dependency': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}}, rule='additionalProperties')
+    return data
+
+def validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (dict)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be object", value=data, name="" + (name_prefix or "data") + "", definition={'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html', 'title': '``tool.setuptools`` table', '$$description': ['``setuptools``-specific configurations that can be set by users that require', 'customization.', 'These configurations are completely optional and probably can be skipped when', 'creating simple packages. They are equivalent to some of the `Keywords', '`_', 'used by the ``setup.py`` file, and can be set via the ``tool.setuptools`` table.', 'It considers only ``setuptools`` `parameters', '`_', 'that are not covered by :pep:`621`; and intentionally excludes ``dependency_links``', 'and ``setup_requires`` (incompatible with modern workflows/standards).'], 'type': 'object', 'additionalProperties': False, 'properties': {'platforms': {'type': 'array', 'items': {'type': 'string'}}, 'provides': {'$$description': ['Package and virtual package names contained within this package', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, 'obsoletes': {'$$description': ['Packages which this package renders obsolete', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, 'zip-safe': {'$$description': ['Whether the project can be safely installed and run from a zip file.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'boolean'}, 'script-files': {'$$description': ['Legacy way of defining scripts (entry-points are preferred).', 'Equivalent to the ``script`` keyword in ``setup.py``', '(it was renamed to avoid confusion with entry-point based ``project.scripts``', 'defined in :pep:`621`).', '**DISCOURAGED**: generic script wrappers are tricky and may not work properly.', 'Whenever possible, please use ``project.scripts`` instead.'], 'type': 'array', 'items': {'type': 'string'}, '$comment': 'TODO: is this field deprecated/should be removed?'}, 'eager-resources': {'$$description': ['Resources that should be extracted together, if any of them is needed,', 'or if any C extensions included in the project are imported.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'array', 'items': {'type': 'string'}}, 'packages': {'$$description': ['Packages that should be included in the distribution.', 'It can be given either as a list of package identifiers', 'or as a ``dict``-like structure with a single key ``find``', 'which corresponds to a dynamic call to', '``setuptools.config.expand.find_packages`` function.', 'The ``find`` key is associated with a nested ``dict``-like structure that can', 'contain ``where``, ``include``, ``exclude`` and ``namespaces`` keys,', 'mimicking the keyword arguments of the associated function.'], 'oneOf': [{'title': 'Array of Python package identifiers', 'type': 'array', 'items': {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}}, {'$id': '#/definitions/find-directive', 'title': "'find:' directive", 'type': 'object', 'additionalProperties': False, 'properties': {'find': {'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}}}]}, 'package-dir': {'$$description': [':class:`dict`-like structure mapping from package names to directories where their', 'code can be found.', 'The empty string (as key) means that all packages are contained inside', 'the given directory will be included in the distribution.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'const': ''}, {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}]}, 'patternProperties': {'^.*$': {'type': 'string'}}}, 'package-data': {'$$description': ['Mapping from package names to lists of glob patterns.', 'Usually this option is not needed when using ``include-package-data = true``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'include-package-data': {'$$description': ['Automatically include any data files inside the package directories', 'that are specified by ``MANIFEST.in``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'boolean'}, 'exclude-package-data': {'$$description': ['Mapping from package names to lists of glob patterns that should be excluded', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'namespace-packages': {'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'https://setuptools.pypa.io/en/latest/userguide/package_discovery.html', 'description': '**DEPRECATED**: use implicit namespaces instead (:pep:`420`).'}, 'py-modules': {'description': 'Modules that setuptools will manipulate', 'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'TODO: clarify the relationship with ``packages``'}, 'ext-modules': {'description': 'Extension modules to be compiled by setuptools', 'type': 'array', 'items': {'$id': '#/definitions/ext-module', 'title': 'Extension module', 'description': 'Parameters to construct a :class:`setuptools.Extension` object', 'type': 'object', 'required': ['name', 'sources'], 'additionalProperties': False, 'properties': {'name': {'type': 'string', 'format': 'python-module-name-relaxed'}, 'sources': {'type': 'array', 'items': {'type': 'string'}}, 'include-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'define-macros': {'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, 'undef-macros': {'type': 'array', 'items': {'type': 'string'}}, 'library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'libraries': {'type': 'array', 'items': {'type': 'string'}}, 'runtime-library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'extra-objects': {'type': 'array', 'items': {'type': 'string'}}, 'extra-compile-args': {'type': 'array', 'items': {'type': 'string'}}, 'extra-link-args': {'type': 'array', 'items': {'type': 'string'}}, 'export-symbols': {'type': 'array', 'items': {'type': 'string'}}, 'swig-opts': {'type': 'array', 'items': {'type': 'string'}}, 'depends': {'type': 'array', 'items': {'type': 'string'}}, 'language': {'type': 'string'}, 'optional': {'type': 'boolean'}, 'py-limited-api': {'type': 'boolean'}}}}, 'data-files': {'$$description': ['``dict``-like structure where each key represents a directory and', 'the value is a list of glob patterns that should be installed in them.', '**DISCOURAGED**: please notice this might not work as expected with wheels.', 'Whenever possible, consider using data files inside the package directories', '(or create a new namespace package that only contains data files).', 'See `data files support', '`_.'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'cmdclass': {'$$description': ['Mapping of distutils-style command names to ``setuptools.Command`` subclasses', 'which in turn should be represented by strings with a qualified class name', '(i.e., "dotted" form with module), e.g.::\n\n', '    cmdclass = {mycmd = "pkg.subpkg.module.CommandClass"}\n\n', 'The command class should be a directly defined at the top-level of the', 'containing module (no class nesting).'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'string', 'format': 'python-qualified-identifier'}}}, 'license-files': {'type': 'array', 'items': {'type': 'string'}, '$$description': ['**PROVISIONAL**: list of glob patterns for all license files being distributed.', '(likely to become standard with :pep:`639`).', "By default: ``['LICEN[CS]E*', 'COPYING*', 'NOTICE*', 'AUTHORS*']``"], '$comment': 'TODO: revise if PEP 639 is accepted. Probably ``project.license-files``?'}, 'dynamic': {'type': 'object', 'description': 'Instructions for loading :pep:`621`-related metadata dynamically', 'additionalProperties': False, 'properties': {'version': {'$$description': ['A version dynamically loaded via either the ``attr:`` or ``file:``', 'directives. Please make sure the given file or attribute respects :pep:`440`.', 'Also ensure to set ``project.dynamic`` accordingly.'], 'oneOf': [{'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}]}, 'classifiers': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'description': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'entry-points': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'dependencies': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}, 'optional-dependencies': {'type': 'object', 'propertyNames': {'type': 'string', 'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'.+': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}}}, 'readme': {'type': 'object', 'anyOf': [{'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, {'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'additionalProperties': False}], 'required': ['file']}}}}, 'definitions': {'package-name': {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}, 'ext-module': {'$id': '#/definitions/ext-module', 'title': 'Extension module', 'description': 'Parameters to construct a :class:`setuptools.Extension` object', 'type': 'object', 'required': ['name', 'sources'], 'additionalProperties': False, 'properties': {'name': {'type': 'string', 'format': 'python-module-name-relaxed'}, 'sources': {'type': 'array', 'items': {'type': 'string'}}, 'include-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'define-macros': {'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, 'undef-macros': {'type': 'array', 'items': {'type': 'string'}}, 'library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'libraries': {'type': 'array', 'items': {'type': 'string'}}, 'runtime-library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'extra-objects': {'type': 'array', 'items': {'type': 'string'}}, 'extra-compile-args': {'type': 'array', 'items': {'type': 'string'}}, 'extra-link-args': {'type': 'array', 'items': {'type': 'string'}}, 'export-symbols': {'type': 'array', 'items': {'type': 'string'}}, 'swig-opts': {'type': 'array', 'items': {'type': 'string'}}, 'depends': {'type': 'array', 'items': {'type': 'string'}}, 'language': {'type': 'string'}, 'optional': {'type': 'boolean'}, 'py-limited-api': {'type': 'boolean'}}}, 'file-directive': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'file-directive-for-dependencies': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}]}, 'attr-directive': {'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, 'find-directive': {'$id': '#/definitions/find-directive', 'title': "'find:' directive", 'type': 'object', 'additionalProperties': False, 'properties': {'find': {'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}}}}}, rule='type')
+    data_is_dict = isinstance(data, dict)
+    if data_is_dict:
+        data_keys = set(data.keys())
+        if "platforms" in data_keys:
+            data_keys.remove("platforms")
+            data__platforms = data["platforms"]
+            if not isinstance(data__platforms, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".platforms must be array", value=data__platforms, name="" + (name_prefix or "data") + ".platforms", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__platforms_is_list = isinstance(data__platforms, (list, tuple))
+            if data__platforms_is_list:
+                data__platforms_len = len(data__platforms)
+                for data__platforms_x, data__platforms_item in enumerate(data__platforms):
+                    if not isinstance(data__platforms_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".platforms[{data__platforms_x}]".format(**locals()) + " must be string", value=data__platforms_item, name="" + (name_prefix or "data") + ".platforms[{data__platforms_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "provides" in data_keys:
+            data_keys.remove("provides")
+            data__provides = data["provides"]
+            if not isinstance(data__provides, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".provides must be array", value=data__provides, name="" + (name_prefix or "data") + ".provides", definition={'$$description': ['Package and virtual package names contained within this package', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, rule='type')
+            data__provides_is_list = isinstance(data__provides, (list, tuple))
+            if data__provides_is_list:
+                data__provides_len = len(data__provides)
+                for data__provides_x, data__provides_item in enumerate(data__provides):
+                    if not isinstance(data__provides_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".provides[{data__provides_x}]".format(**locals()) + " must be string", value=data__provides_item, name="" + (name_prefix or "data") + ".provides[{data__provides_x}]".format(**locals()) + "", definition={'type': 'string', 'format': 'pep508-identifier'}, rule='type')
+                    if isinstance(data__provides_item, str):
+                        if not custom_formats["pep508-identifier"](data__provides_item):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".provides[{data__provides_x}]".format(**locals()) + " must be pep508-identifier", value=data__provides_item, name="" + (name_prefix or "data") + ".provides[{data__provides_x}]".format(**locals()) + "", definition={'type': 'string', 'format': 'pep508-identifier'}, rule='format')
+        if "obsoletes" in data_keys:
+            data_keys.remove("obsoletes")
+            data__obsoletes = data["obsoletes"]
+            if not isinstance(data__obsoletes, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".obsoletes must be array", value=data__obsoletes, name="" + (name_prefix or "data") + ".obsoletes", definition={'$$description': ['Packages which this package renders obsolete', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, rule='type')
+            data__obsoletes_is_list = isinstance(data__obsoletes, (list, tuple))
+            if data__obsoletes_is_list:
+                data__obsoletes_len = len(data__obsoletes)
+                for data__obsoletes_x, data__obsoletes_item in enumerate(data__obsoletes):
+                    if not isinstance(data__obsoletes_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".obsoletes[{data__obsoletes_x}]".format(**locals()) + " must be string", value=data__obsoletes_item, name="" + (name_prefix or "data") + ".obsoletes[{data__obsoletes_x}]".format(**locals()) + "", definition={'type': 'string', 'format': 'pep508-identifier'}, rule='type')
+                    if isinstance(data__obsoletes_item, str):
+                        if not custom_formats["pep508-identifier"](data__obsoletes_item):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".obsoletes[{data__obsoletes_x}]".format(**locals()) + " must be pep508-identifier", value=data__obsoletes_item, name="" + (name_prefix or "data") + ".obsoletes[{data__obsoletes_x}]".format(**locals()) + "", definition={'type': 'string', 'format': 'pep508-identifier'}, rule='format')
+        if "zip-safe" in data_keys:
+            data_keys.remove("zip-safe")
+            data__zipsafe = data["zip-safe"]
+            if not isinstance(data__zipsafe, (bool)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".zip-safe must be boolean", value=data__zipsafe, name="" + (name_prefix or "data") + ".zip-safe", definition={'$$description': ['Whether the project can be safely installed and run from a zip file.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'boolean'}, rule='type')
+        if "script-files" in data_keys:
+            data_keys.remove("script-files")
+            data__scriptfiles = data["script-files"]
+            if not isinstance(data__scriptfiles, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".script-files must be array", value=data__scriptfiles, name="" + (name_prefix or "data") + ".script-files", definition={'$$description': ['Legacy way of defining scripts (entry-points are preferred).', 'Equivalent to the ``script`` keyword in ``setup.py``', '(it was renamed to avoid confusion with entry-point based ``project.scripts``', 'defined in :pep:`621`).', '**DISCOURAGED**: generic script wrappers are tricky and may not work properly.', 'Whenever possible, please use ``project.scripts`` instead.'], 'type': 'array', 'items': {'type': 'string'}, '$comment': 'TODO: is this field deprecated/should be removed?'}, rule='type')
+            data__scriptfiles_is_list = isinstance(data__scriptfiles, (list, tuple))
+            if data__scriptfiles_is_list:
+                data__scriptfiles_len = len(data__scriptfiles)
+                for data__scriptfiles_x, data__scriptfiles_item in enumerate(data__scriptfiles):
+                    if not isinstance(data__scriptfiles_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".script-files[{data__scriptfiles_x}]".format(**locals()) + " must be string", value=data__scriptfiles_item, name="" + (name_prefix or "data") + ".script-files[{data__scriptfiles_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "eager-resources" in data_keys:
+            data_keys.remove("eager-resources")
+            data__eagerresources = data["eager-resources"]
+            if not isinstance(data__eagerresources, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".eager-resources must be array", value=data__eagerresources, name="" + (name_prefix or "data") + ".eager-resources", definition={'$$description': ['Resources that should be extracted together, if any of them is needed,', 'or if any C extensions included in the project are imported.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__eagerresources_is_list = isinstance(data__eagerresources, (list, tuple))
+            if data__eagerresources_is_list:
+                data__eagerresources_len = len(data__eagerresources)
+                for data__eagerresources_x, data__eagerresources_item in enumerate(data__eagerresources):
+                    if not isinstance(data__eagerresources_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".eager-resources[{data__eagerresources_x}]".format(**locals()) + " must be string", value=data__eagerresources_item, name="" + (name_prefix or "data") + ".eager-resources[{data__eagerresources_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "packages" in data_keys:
+            data_keys.remove("packages")
+            data__packages = data["packages"]
+            data__packages_one_of_count2 = 0
+            if data__packages_one_of_count2 < 2:
+                try:
+                    if not isinstance(data__packages, (list, tuple)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".packages must be array", value=data__packages, name="" + (name_prefix or "data") + ".packages", definition={'title': 'Array of Python package identifiers', 'type': 'array', 'items': {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}}, rule='type')
+                    data__packages_is_list = isinstance(data__packages, (list, tuple))
+                    if data__packages_is_list:
+                        data__packages_len = len(data__packages)
+                        for data__packages_x, data__packages_item in enumerate(data__packages):
+                            validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_package_name(data__packages_item, custom_formats, (name_prefix or "data") + ".packages[{data__packages_x}]".format(**locals()))
+                    data__packages_one_of_count2 += 1
+                except JsonSchemaValueException: pass
+            if data__packages_one_of_count2 < 2:
+                try:
+                    validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_find_directive(data__packages, custom_formats, (name_prefix or "data") + ".packages")
+                    data__packages_one_of_count2 += 1
+                except JsonSchemaValueException: pass
+            if data__packages_one_of_count2 != 1:
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".packages must be valid exactly by one definition" + (" (" + str(data__packages_one_of_count2) + " matches found)"), value=data__packages, name="" + (name_prefix or "data") + ".packages", definition={'$$description': ['Packages that should be included in the distribution.', 'It can be given either as a list of package identifiers', 'or as a ``dict``-like structure with a single key ``find``', 'which corresponds to a dynamic call to', '``setuptools.config.expand.find_packages`` function.', 'The ``find`` key is associated with a nested ``dict``-like structure that can', 'contain ``where``, ``include``, ``exclude`` and ``namespaces`` keys,', 'mimicking the keyword arguments of the associated function.'], 'oneOf': [{'title': 'Array of Python package identifiers', 'type': 'array', 'items': {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}}, {'$id': '#/definitions/find-directive', 'title': "'find:' directive", 'type': 'object', 'additionalProperties': False, 'properties': {'find': {'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}}}]}, rule='oneOf')
+        if "package-dir" in data_keys:
+            data_keys.remove("package-dir")
+            data__packagedir = data["package-dir"]
+            if not isinstance(data__packagedir, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-dir must be object", value=data__packagedir, name="" + (name_prefix or "data") + ".package-dir", definition={'$$description': [':class:`dict`-like structure mapping from package names to directories where their', 'code can be found.', 'The empty string (as key) means that all packages are contained inside', 'the given directory will be included in the distribution.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'const': ''}, {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}]}, 'patternProperties': {'^.*$': {'type': 'string'}}}, rule='type')
+            data__packagedir_is_dict = isinstance(data__packagedir, dict)
+            if data__packagedir_is_dict:
+                data__packagedir_keys = set(data__packagedir.keys())
+                for data__packagedir_key, data__packagedir_val in data__packagedir.items():
+                    if REGEX_PATTERNS['^.*$'].search(data__packagedir_key):
+                        if data__packagedir_key in data__packagedir_keys:
+                            data__packagedir_keys.remove(data__packagedir_key)
+                        if not isinstance(data__packagedir_val, (str)):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-dir.{data__packagedir_key}".format(**locals()) + " must be string", value=data__packagedir_val, name="" + (name_prefix or "data") + ".package-dir.{data__packagedir_key}".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+                if data__packagedir_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-dir must not contain "+str(data__packagedir_keys)+" properties", value=data__packagedir, name="" + (name_prefix or "data") + ".package-dir", definition={'$$description': [':class:`dict`-like structure mapping from package names to directories where their', 'code can be found.', 'The empty string (as key) means that all packages are contained inside', 'the given directory will be included in the distribution.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'const': ''}, {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}]}, 'patternProperties': {'^.*$': {'type': 'string'}}}, rule='additionalProperties')
+                data__packagedir_len = len(data__packagedir)
+                if data__packagedir_len != 0:
+                    data__packagedir_property_names = True
+                    for data__packagedir_key in data__packagedir:
+                        try:
+                            data__packagedir_key_any_of_count3 = 0
+                            if not data__packagedir_key_any_of_count3:
+                                try:
+                                    if data__packagedir_key != "":
+                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-dir must be same as const definition: ", value=data__packagedir_key, name="" + (name_prefix or "data") + ".package-dir", definition={'const': ''}, rule='const')
+                                    data__packagedir_key_any_of_count3 += 1
+                                except JsonSchemaValueException: pass
+                            if not data__packagedir_key_any_of_count3:
+                                try:
+                                    validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_package_name(data__packagedir_key, custom_formats, (name_prefix or "data") + ".package-dir")
+                                    data__packagedir_key_any_of_count3 += 1
+                                except JsonSchemaValueException: pass
+                            if not data__packagedir_key_any_of_count3:
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-dir cannot be validated by any definition", value=data__packagedir_key, name="" + (name_prefix or "data") + ".package-dir", definition={'anyOf': [{'const': ''}, {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}]}, rule='anyOf')
+                        except JsonSchemaValueException:
+                            data__packagedir_property_names = False
+                    if not data__packagedir_property_names:
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-dir must be named by propertyName definition", value=data__packagedir, name="" + (name_prefix or "data") + ".package-dir", definition={'$$description': [':class:`dict`-like structure mapping from package names to directories where their', 'code can be found.', 'The empty string (as key) means that all packages are contained inside', 'the given directory will be included in the distribution.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'const': ''}, {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}]}, 'patternProperties': {'^.*$': {'type': 'string'}}}, rule='propertyNames')
+        if "package-data" in data_keys:
+            data_keys.remove("package-data")
+            data__packagedata = data["package-data"]
+            if not isinstance(data__packagedata, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-data must be object", value=data__packagedata, name="" + (name_prefix or "data") + ".package-data", definition={'$$description': ['Mapping from package names to lists of glob patterns.', 'Usually this option is not needed when using ``include-package-data = true``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, rule='type')
+            data__packagedata_is_dict = isinstance(data__packagedata, dict)
+            if data__packagedata_is_dict:
+                data__packagedata_keys = set(data__packagedata.keys())
+                for data__packagedata_key, data__packagedata_val in data__packagedata.items():
+                    if REGEX_PATTERNS['^.*$'].search(data__packagedata_key):
+                        if data__packagedata_key in data__packagedata_keys:
+                            data__packagedata_keys.remove(data__packagedata_key)
+                        if not isinstance(data__packagedata_val, (list, tuple)):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-data.{data__packagedata_key}".format(**locals()) + " must be array", value=data__packagedata_val, name="" + (name_prefix or "data") + ".package-data.{data__packagedata_key}".format(**locals()) + "", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+                        data__packagedata_val_is_list = isinstance(data__packagedata_val, (list, tuple))
+                        if data__packagedata_val_is_list:
+                            data__packagedata_val_len = len(data__packagedata_val)
+                            for data__packagedata_val_x, data__packagedata_val_item in enumerate(data__packagedata_val):
+                                if not isinstance(data__packagedata_val_item, (str)):
+                                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-data.{data__packagedata_key}[{data__packagedata_val_x}]".format(**locals()) + " must be string", value=data__packagedata_val_item, name="" + (name_prefix or "data") + ".package-data.{data__packagedata_key}[{data__packagedata_val_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+                if data__packagedata_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-data must not contain "+str(data__packagedata_keys)+" properties", value=data__packagedata, name="" + (name_prefix or "data") + ".package-data", definition={'$$description': ['Mapping from package names to lists of glob patterns.', 'Usually this option is not needed when using ``include-package-data = true``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, rule='additionalProperties')
+                data__packagedata_len = len(data__packagedata)
+                if data__packagedata_len != 0:
+                    data__packagedata_property_names = True
+                    for data__packagedata_key in data__packagedata:
+                        try:
+                            data__packagedata_key_any_of_count4 = 0
+                            if not data__packagedata_key_any_of_count4:
+                                try:
+                                    if not isinstance(data__packagedata_key, (str)):
+                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-data must be string", value=data__packagedata_key, name="" + (name_prefix or "data") + ".package-data", definition={'type': 'string', 'format': 'python-module-name'}, rule='type')
+                                    if isinstance(data__packagedata_key, str):
+                                        if not custom_formats["python-module-name"](data__packagedata_key):
+                                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-data must be python-module-name", value=data__packagedata_key, name="" + (name_prefix or "data") + ".package-data", definition={'type': 'string', 'format': 'python-module-name'}, rule='format')
+                                    data__packagedata_key_any_of_count4 += 1
+                                except JsonSchemaValueException: pass
+                            if not data__packagedata_key_any_of_count4:
+                                try:
+                                    if data__packagedata_key != "*":
+                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-data must be same as const definition: *", value=data__packagedata_key, name="" + (name_prefix or "data") + ".package-data", definition={'const': '*'}, rule='const')
+                                    data__packagedata_key_any_of_count4 += 1
+                                except JsonSchemaValueException: pass
+                            if not data__packagedata_key_any_of_count4:
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-data cannot be validated by any definition", value=data__packagedata_key, name="" + (name_prefix or "data") + ".package-data", definition={'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, rule='anyOf')
+                        except JsonSchemaValueException:
+                            data__packagedata_property_names = False
+                    if not data__packagedata_property_names:
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".package-data must be named by propertyName definition", value=data__packagedata, name="" + (name_prefix or "data") + ".package-data", definition={'$$description': ['Mapping from package names to lists of glob patterns.', 'Usually this option is not needed when using ``include-package-data = true``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, rule='propertyNames')
+        if "include-package-data" in data_keys:
+            data_keys.remove("include-package-data")
+            data__includepackagedata = data["include-package-data"]
+            if not isinstance(data__includepackagedata, (bool)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".include-package-data must be boolean", value=data__includepackagedata, name="" + (name_prefix or "data") + ".include-package-data", definition={'$$description': ['Automatically include any data files inside the package directories', 'that are specified by ``MANIFEST.in``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'boolean'}, rule='type')
+        if "exclude-package-data" in data_keys:
+            data_keys.remove("exclude-package-data")
+            data__excludepackagedata = data["exclude-package-data"]
+            if not isinstance(data__excludepackagedata, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".exclude-package-data must be object", value=data__excludepackagedata, name="" + (name_prefix or "data") + ".exclude-package-data", definition={'$$description': ['Mapping from package names to lists of glob patterns that should be excluded', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, rule='type')
+            data__excludepackagedata_is_dict = isinstance(data__excludepackagedata, dict)
+            if data__excludepackagedata_is_dict:
+                data__excludepackagedata_keys = set(data__excludepackagedata.keys())
+                for data__excludepackagedata_key, data__excludepackagedata_val in data__excludepackagedata.items():
+                    if REGEX_PATTERNS['^.*$'].search(data__excludepackagedata_key):
+                        if data__excludepackagedata_key in data__excludepackagedata_keys:
+                            data__excludepackagedata_keys.remove(data__excludepackagedata_key)
+                        if not isinstance(data__excludepackagedata_val, (list, tuple)):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".exclude-package-data.{data__excludepackagedata_key}".format(**locals()) + " must be array", value=data__excludepackagedata_val, name="" + (name_prefix or "data") + ".exclude-package-data.{data__excludepackagedata_key}".format(**locals()) + "", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+                        data__excludepackagedata_val_is_list = isinstance(data__excludepackagedata_val, (list, tuple))
+                        if data__excludepackagedata_val_is_list:
+                            data__excludepackagedata_val_len = len(data__excludepackagedata_val)
+                            for data__excludepackagedata_val_x, data__excludepackagedata_val_item in enumerate(data__excludepackagedata_val):
+                                if not isinstance(data__excludepackagedata_val_item, (str)):
+                                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".exclude-package-data.{data__excludepackagedata_key}[{data__excludepackagedata_val_x}]".format(**locals()) + " must be string", value=data__excludepackagedata_val_item, name="" + (name_prefix or "data") + ".exclude-package-data.{data__excludepackagedata_key}[{data__excludepackagedata_val_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+                if data__excludepackagedata_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".exclude-package-data must not contain "+str(data__excludepackagedata_keys)+" properties", value=data__excludepackagedata, name="" + (name_prefix or "data") + ".exclude-package-data", definition={'$$description': ['Mapping from package names to lists of glob patterns that should be excluded', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, rule='additionalProperties')
+                data__excludepackagedata_len = len(data__excludepackagedata)
+                if data__excludepackagedata_len != 0:
+                    data__excludepackagedata_property_names = True
+                    for data__excludepackagedata_key in data__excludepackagedata:
+                        try:
+                            data__excludepackagedata_key_any_of_count5 = 0
+                            if not data__excludepackagedata_key_any_of_count5:
+                                try:
+                                    if not isinstance(data__excludepackagedata_key, (str)):
+                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".exclude-package-data must be string", value=data__excludepackagedata_key, name="" + (name_prefix or "data") + ".exclude-package-data", definition={'type': 'string', 'format': 'python-module-name'}, rule='type')
+                                    if isinstance(data__excludepackagedata_key, str):
+                                        if not custom_formats["python-module-name"](data__excludepackagedata_key):
+                                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".exclude-package-data must be python-module-name", value=data__excludepackagedata_key, name="" + (name_prefix or "data") + ".exclude-package-data", definition={'type': 'string', 'format': 'python-module-name'}, rule='format')
+                                    data__excludepackagedata_key_any_of_count5 += 1
+                                except JsonSchemaValueException: pass
+                            if not data__excludepackagedata_key_any_of_count5:
+                                try:
+                                    if data__excludepackagedata_key != "*":
+                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".exclude-package-data must be same as const definition: *", value=data__excludepackagedata_key, name="" + (name_prefix or "data") + ".exclude-package-data", definition={'const': '*'}, rule='const')
+                                    data__excludepackagedata_key_any_of_count5 += 1
+                                except JsonSchemaValueException: pass
+                            if not data__excludepackagedata_key_any_of_count5:
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".exclude-package-data cannot be validated by any definition", value=data__excludepackagedata_key, name="" + (name_prefix or "data") + ".exclude-package-data", definition={'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, rule='anyOf')
+                        except JsonSchemaValueException:
+                            data__excludepackagedata_property_names = False
+                    if not data__excludepackagedata_property_names:
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".exclude-package-data must be named by propertyName definition", value=data__excludepackagedata, name="" + (name_prefix or "data") + ".exclude-package-data", definition={'$$description': ['Mapping from package names to lists of glob patterns that should be excluded', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, rule='propertyNames')
+        if "namespace-packages" in data_keys:
+            data_keys.remove("namespace-packages")
+            data__namespacepackages = data["namespace-packages"]
+            if not isinstance(data__namespacepackages, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".namespace-packages must be array", value=data__namespacepackages, name="" + (name_prefix or "data") + ".namespace-packages", definition={'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'https://setuptools.pypa.io/en/latest/userguide/package_discovery.html', 'description': '**DEPRECATED**: use implicit namespaces instead (:pep:`420`).'}, rule='type')
+            data__namespacepackages_is_list = isinstance(data__namespacepackages, (list, tuple))
+            if data__namespacepackages_is_list:
+                data__namespacepackages_len = len(data__namespacepackages)
+                for data__namespacepackages_x, data__namespacepackages_item in enumerate(data__namespacepackages):
+                    if not isinstance(data__namespacepackages_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".namespace-packages[{data__namespacepackages_x}]".format(**locals()) + " must be string", value=data__namespacepackages_item, name="" + (name_prefix or "data") + ".namespace-packages[{data__namespacepackages_x}]".format(**locals()) + "", definition={'type': 'string', 'format': 'python-module-name-relaxed'}, rule='type')
+                    if isinstance(data__namespacepackages_item, str):
+                        if not custom_formats["python-module-name-relaxed"](data__namespacepackages_item):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".namespace-packages[{data__namespacepackages_x}]".format(**locals()) + " must be python-module-name-relaxed", value=data__namespacepackages_item, name="" + (name_prefix or "data") + ".namespace-packages[{data__namespacepackages_x}]".format(**locals()) + "", definition={'type': 'string', 'format': 'python-module-name-relaxed'}, rule='format')
+        if "py-modules" in data_keys:
+            data_keys.remove("py-modules")
+            data__pymodules = data["py-modules"]
+            if not isinstance(data__pymodules, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".py-modules must be array", value=data__pymodules, name="" + (name_prefix or "data") + ".py-modules", definition={'description': 'Modules that setuptools will manipulate', 'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'TODO: clarify the relationship with ``packages``'}, rule='type')
+            data__pymodules_is_list = isinstance(data__pymodules, (list, tuple))
+            if data__pymodules_is_list:
+                data__pymodules_len = len(data__pymodules)
+                for data__pymodules_x, data__pymodules_item in enumerate(data__pymodules):
+                    if not isinstance(data__pymodules_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".py-modules[{data__pymodules_x}]".format(**locals()) + " must be string", value=data__pymodules_item, name="" + (name_prefix or "data") + ".py-modules[{data__pymodules_x}]".format(**locals()) + "", definition={'type': 'string', 'format': 'python-module-name-relaxed'}, rule='type')
+                    if isinstance(data__pymodules_item, str):
+                        if not custom_formats["python-module-name-relaxed"](data__pymodules_item):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".py-modules[{data__pymodules_x}]".format(**locals()) + " must be python-module-name-relaxed", value=data__pymodules_item, name="" + (name_prefix or "data") + ".py-modules[{data__pymodules_x}]".format(**locals()) + "", definition={'type': 'string', 'format': 'python-module-name-relaxed'}, rule='format')
+        if "ext-modules" in data_keys:
+            data_keys.remove("ext-modules")
+            data__extmodules = data["ext-modules"]
+            if not isinstance(data__extmodules, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".ext-modules must be array", value=data__extmodules, name="" + (name_prefix or "data") + ".ext-modules", definition={'description': 'Extension modules to be compiled by setuptools', 'type': 'array', 'items': {'$id': '#/definitions/ext-module', 'title': 'Extension module', 'description': 'Parameters to construct a :class:`setuptools.Extension` object', 'type': 'object', 'required': ['name', 'sources'], 'additionalProperties': False, 'properties': {'name': {'type': 'string', 'format': 'python-module-name-relaxed'}, 'sources': {'type': 'array', 'items': {'type': 'string'}}, 'include-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'define-macros': {'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, 'undef-macros': {'type': 'array', 'items': {'type': 'string'}}, 'library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'libraries': {'type': 'array', 'items': {'type': 'string'}}, 'runtime-library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'extra-objects': {'type': 'array', 'items': {'type': 'string'}}, 'extra-compile-args': {'type': 'array', 'items': {'type': 'string'}}, 'extra-link-args': {'type': 'array', 'items': {'type': 'string'}}, 'export-symbols': {'type': 'array', 'items': {'type': 'string'}}, 'swig-opts': {'type': 'array', 'items': {'type': 'string'}}, 'depends': {'type': 'array', 'items': {'type': 'string'}}, 'language': {'type': 'string'}, 'optional': {'type': 'boolean'}, 'py-limited-api': {'type': 'boolean'}}}}, rule='type')
+            data__extmodules_is_list = isinstance(data__extmodules, (list, tuple))
+            if data__extmodules_is_list:
+                data__extmodules_len = len(data__extmodules)
+                for data__extmodules_x, data__extmodules_item in enumerate(data__extmodules):
+                    validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_ext_module(data__extmodules_item, custom_formats, (name_prefix or "data") + ".ext-modules[{data__extmodules_x}]".format(**locals()))
+        if "data-files" in data_keys:
+            data_keys.remove("data-files")
+            data__datafiles = data["data-files"]
+            if not isinstance(data__datafiles, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".data-files must be object", value=data__datafiles, name="" + (name_prefix or "data") + ".data-files", definition={'$$description': ['``dict``-like structure where each key represents a directory and', 'the value is a list of glob patterns that should be installed in them.', '**DISCOURAGED**: please notice this might not work as expected with wheels.', 'Whenever possible, consider using data files inside the package directories', '(or create a new namespace package that only contains data files).', 'See `data files support', '`_.'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, rule='type')
+            data__datafiles_is_dict = isinstance(data__datafiles, dict)
+            if data__datafiles_is_dict:
+                data__datafiles_keys = set(data__datafiles.keys())
+                for data__datafiles_key, data__datafiles_val in data__datafiles.items():
+                    if REGEX_PATTERNS['^.*$'].search(data__datafiles_key):
+                        if data__datafiles_key in data__datafiles_keys:
+                            data__datafiles_keys.remove(data__datafiles_key)
+                        if not isinstance(data__datafiles_val, (list, tuple)):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".data-files.{data__datafiles_key}".format(**locals()) + " must be array", value=data__datafiles_val, name="" + (name_prefix or "data") + ".data-files.{data__datafiles_key}".format(**locals()) + "", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+                        data__datafiles_val_is_list = isinstance(data__datafiles_val, (list, tuple))
+                        if data__datafiles_val_is_list:
+                            data__datafiles_val_len = len(data__datafiles_val)
+                            for data__datafiles_val_x, data__datafiles_val_item in enumerate(data__datafiles_val):
+                                if not isinstance(data__datafiles_val_item, (str)):
+                                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".data-files.{data__datafiles_key}[{data__datafiles_val_x}]".format(**locals()) + " must be string", value=data__datafiles_val_item, name="" + (name_prefix or "data") + ".data-files.{data__datafiles_key}[{data__datafiles_val_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "cmdclass" in data_keys:
+            data_keys.remove("cmdclass")
+            data__cmdclass = data["cmdclass"]
+            if not isinstance(data__cmdclass, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".cmdclass must be object", value=data__cmdclass, name="" + (name_prefix or "data") + ".cmdclass", definition={'$$description': ['Mapping of distutils-style command names to ``setuptools.Command`` subclasses', 'which in turn should be represented by strings with a qualified class name', '(i.e., "dotted" form with module), e.g.::\n\n', '    cmdclass = {mycmd = "pkg.subpkg.module.CommandClass"}\n\n', 'The command class should be a directly defined at the top-level of the', 'containing module (no class nesting).'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'string', 'format': 'python-qualified-identifier'}}}, rule='type')
+            data__cmdclass_is_dict = isinstance(data__cmdclass, dict)
+            if data__cmdclass_is_dict:
+                data__cmdclass_keys = set(data__cmdclass.keys())
+                for data__cmdclass_key, data__cmdclass_val in data__cmdclass.items():
+                    if REGEX_PATTERNS['^.*$'].search(data__cmdclass_key):
+                        if data__cmdclass_key in data__cmdclass_keys:
+                            data__cmdclass_keys.remove(data__cmdclass_key)
+                        if not isinstance(data__cmdclass_val, (str)):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".cmdclass.{data__cmdclass_key}".format(**locals()) + " must be string", value=data__cmdclass_val, name="" + (name_prefix or "data") + ".cmdclass.{data__cmdclass_key}".format(**locals()) + "", definition={'type': 'string', 'format': 'python-qualified-identifier'}, rule='type')
+                        if isinstance(data__cmdclass_val, str):
+                            if not custom_formats["python-qualified-identifier"](data__cmdclass_val):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".cmdclass.{data__cmdclass_key}".format(**locals()) + " must be python-qualified-identifier", value=data__cmdclass_val, name="" + (name_prefix or "data") + ".cmdclass.{data__cmdclass_key}".format(**locals()) + "", definition={'type': 'string', 'format': 'python-qualified-identifier'}, rule='format')
+        if "license-files" in data_keys:
+            data_keys.remove("license-files")
+            data__licensefiles = data["license-files"]
+            if not isinstance(data__licensefiles, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".license-files must be array", value=data__licensefiles, name="" + (name_prefix or "data") + ".license-files", definition={'type': 'array', 'items': {'type': 'string'}, '$$description': ['**PROVISIONAL**: list of glob patterns for all license files being distributed.', '(likely to become standard with :pep:`639`).', "By default: ``['LICEN[CS]E*', 'COPYING*', 'NOTICE*', 'AUTHORS*']``"], '$comment': 'TODO: revise if PEP 639 is accepted. Probably ``project.license-files``?'}, rule='type')
+            data__licensefiles_is_list = isinstance(data__licensefiles, (list, tuple))
+            if data__licensefiles_is_list:
+                data__licensefiles_len = len(data__licensefiles)
+                for data__licensefiles_x, data__licensefiles_item in enumerate(data__licensefiles):
+                    if not isinstance(data__licensefiles_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".license-files[{data__licensefiles_x}]".format(**locals()) + " must be string", value=data__licensefiles_item, name="" + (name_prefix or "data") + ".license-files[{data__licensefiles_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "dynamic" in data_keys:
+            data_keys.remove("dynamic")
+            data__dynamic = data["dynamic"]
+            if not isinstance(data__dynamic, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic must be object", value=data__dynamic, name="" + (name_prefix or "data") + ".dynamic", definition={'type': 'object', 'description': 'Instructions for loading :pep:`621`-related metadata dynamically', 'additionalProperties': False, 'properties': {'version': {'$$description': ['A version dynamically loaded via either the ``attr:`` or ``file:``', 'directives. Please make sure the given file or attribute respects :pep:`440`.', 'Also ensure to set ``project.dynamic`` accordingly.'], 'oneOf': [{'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}]}, 'classifiers': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'description': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'entry-points': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'dependencies': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}, 'optional-dependencies': {'type': 'object', 'propertyNames': {'type': 'string', 'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'.+': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}}}, 'readme': {'type': 'object', 'anyOf': [{'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, {'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'additionalProperties': False}], 'required': ['file']}}}, rule='type')
+            data__dynamic_is_dict = isinstance(data__dynamic, dict)
+            if data__dynamic_is_dict:
+                data__dynamic_keys = set(data__dynamic.keys())
+                if "version" in data__dynamic_keys:
+                    data__dynamic_keys.remove("version")
+                    data__dynamic__version = data__dynamic["version"]
+                    data__dynamic__version_one_of_count6 = 0
+                    if data__dynamic__version_one_of_count6 < 2:
+                        try:
+                            validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_attr_directive(data__dynamic__version, custom_formats, (name_prefix or "data") + ".dynamic.version")
+                            data__dynamic__version_one_of_count6 += 1
+                        except JsonSchemaValueException: pass
+                    if data__dynamic__version_one_of_count6 < 2:
+                        try:
+                            validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive(data__dynamic__version, custom_formats, (name_prefix or "data") + ".dynamic.version")
+                            data__dynamic__version_one_of_count6 += 1
+                        except JsonSchemaValueException: pass
+                    if data__dynamic__version_one_of_count6 != 1:
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.version must be valid exactly by one definition" + (" (" + str(data__dynamic__version_one_of_count6) + " matches found)"), value=data__dynamic__version, name="" + (name_prefix or "data") + ".dynamic.version", definition={'$$description': ['A version dynamically loaded via either the ``attr:`` or ``file:``', 'directives. Please make sure the given file or attribute respects :pep:`440`.', 'Also ensure to set ``project.dynamic`` accordingly.'], 'oneOf': [{'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}]}, rule='oneOf')
+                if "classifiers" in data__dynamic_keys:
+                    data__dynamic_keys.remove("classifiers")
+                    data__dynamic__classifiers = data__dynamic["classifiers"]
+                    validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive(data__dynamic__classifiers, custom_formats, (name_prefix or "data") + ".dynamic.classifiers")
+                if "description" in data__dynamic_keys:
+                    data__dynamic_keys.remove("description")
+                    data__dynamic__description = data__dynamic["description"]
+                    validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive(data__dynamic__description, custom_formats, (name_prefix or "data") + ".dynamic.description")
+                if "entry-points" in data__dynamic_keys:
+                    data__dynamic_keys.remove("entry-points")
+                    data__dynamic__entrypoints = data__dynamic["entry-points"]
+                    validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive(data__dynamic__entrypoints, custom_formats, (name_prefix or "data") + ".dynamic.entry-points")
+                if "dependencies" in data__dynamic_keys:
+                    data__dynamic_keys.remove("dependencies")
+                    data__dynamic__dependencies = data__dynamic["dependencies"]
+                    validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive_for_dependencies(data__dynamic__dependencies, custom_formats, (name_prefix or "data") + ".dynamic.dependencies")
+                if "optional-dependencies" in data__dynamic_keys:
+                    data__dynamic_keys.remove("optional-dependencies")
+                    data__dynamic__optionaldependencies = data__dynamic["optional-dependencies"]
+                    if not isinstance(data__dynamic__optionaldependencies, (dict)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.optional-dependencies must be object", value=data__dynamic__optionaldependencies, name="" + (name_prefix or "data") + ".dynamic.optional-dependencies", definition={'type': 'object', 'propertyNames': {'type': 'string', 'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'.+': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}}}, rule='type')
+                    data__dynamic__optionaldependencies_is_dict = isinstance(data__dynamic__optionaldependencies, dict)
+                    if data__dynamic__optionaldependencies_is_dict:
+                        data__dynamic__optionaldependencies_keys = set(data__dynamic__optionaldependencies.keys())
+                        for data__dynamic__optionaldependencies_key, data__dynamic__optionaldependencies_val in data__dynamic__optionaldependencies.items():
+                            if REGEX_PATTERNS['.+'].search(data__dynamic__optionaldependencies_key):
+                                if data__dynamic__optionaldependencies_key in data__dynamic__optionaldependencies_keys:
+                                    data__dynamic__optionaldependencies_keys.remove(data__dynamic__optionaldependencies_key)
+                                validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive_for_dependencies(data__dynamic__optionaldependencies_val, custom_formats, (name_prefix or "data") + ".dynamic.optional-dependencies.{data__dynamic__optionaldependencies_key}".format(**locals()))
+                        if data__dynamic__optionaldependencies_keys:
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.optional-dependencies must not contain "+str(data__dynamic__optionaldependencies_keys)+" properties", value=data__dynamic__optionaldependencies, name="" + (name_prefix or "data") + ".dynamic.optional-dependencies", definition={'type': 'object', 'propertyNames': {'type': 'string', 'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'.+': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}}}, rule='additionalProperties')
+                        data__dynamic__optionaldependencies_len = len(data__dynamic__optionaldependencies)
+                        if data__dynamic__optionaldependencies_len != 0:
+                            data__dynamic__optionaldependencies_property_names = True
+                            for data__dynamic__optionaldependencies_key in data__dynamic__optionaldependencies:
+                                try:
+                                    if not isinstance(data__dynamic__optionaldependencies_key, (str)):
+                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.optional-dependencies must be string", value=data__dynamic__optionaldependencies_key, name="" + (name_prefix or "data") + ".dynamic.optional-dependencies", definition={'type': 'string', 'format': 'pep508-identifier'}, rule='type')
+                                    if isinstance(data__dynamic__optionaldependencies_key, str):
+                                        if not custom_formats["pep508-identifier"](data__dynamic__optionaldependencies_key):
+                                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.optional-dependencies must be pep508-identifier", value=data__dynamic__optionaldependencies_key, name="" + (name_prefix or "data") + ".dynamic.optional-dependencies", definition={'type': 'string', 'format': 'pep508-identifier'}, rule='format')
+                                except JsonSchemaValueException:
+                                    data__dynamic__optionaldependencies_property_names = False
+                            if not data__dynamic__optionaldependencies_property_names:
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.optional-dependencies must be named by propertyName definition", value=data__dynamic__optionaldependencies, name="" + (name_prefix or "data") + ".dynamic.optional-dependencies", definition={'type': 'object', 'propertyNames': {'type': 'string', 'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'.+': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}}}, rule='propertyNames')
+                if "readme" in data__dynamic_keys:
+                    data__dynamic_keys.remove("readme")
+                    data__dynamic__readme = data__dynamic["readme"]
+                    if not isinstance(data__dynamic__readme, (dict)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.readme must be object", value=data__dynamic__readme, name="" + (name_prefix or "data") + ".dynamic.readme", definition={'type': 'object', 'anyOf': [{'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, {'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'additionalProperties': False}], 'required': ['file']}, rule='type')
+                    data__dynamic__readme_any_of_count7 = 0
+                    if not data__dynamic__readme_any_of_count7:
+                        try:
+                            validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive(data__dynamic__readme, custom_formats, (name_prefix or "data") + ".dynamic.readme")
+                            data__dynamic__readme_any_of_count7 += 1
+                        except JsonSchemaValueException: pass
+                    if not data__dynamic__readme_any_of_count7:
+                        try:
+                            if not isinstance(data__dynamic__readme, (dict)):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.readme must be object", value=data__dynamic__readme, name="" + (name_prefix or "data") + ".dynamic.readme", definition={'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'additionalProperties': False}, rule='type')
+                            data__dynamic__readme_is_dict = isinstance(data__dynamic__readme, dict)
+                            if data__dynamic__readme_is_dict:
+                                data__dynamic__readme_keys = set(data__dynamic__readme.keys())
+                                if "content-type" in data__dynamic__readme_keys:
+                                    data__dynamic__readme_keys.remove("content-type")
+                                    data__dynamic__readme__contenttype = data__dynamic__readme["content-type"]
+                                    if not isinstance(data__dynamic__readme__contenttype, (str)):
+                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.readme.content-type must be string", value=data__dynamic__readme__contenttype, name="" + (name_prefix or "data") + ".dynamic.readme.content-type", definition={'type': 'string'}, rule='type')
+                                if "file" in data__dynamic__readme_keys:
+                                    data__dynamic__readme_keys.remove("file")
+                                    data__dynamic__readme__file = data__dynamic__readme["file"]
+                                    validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive_properties_file(data__dynamic__readme__file, custom_formats, (name_prefix or "data") + ".dynamic.readme.file")
+                                if data__dynamic__readme_keys:
+                                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.readme must not contain "+str(data__dynamic__readme_keys)+" properties", value=data__dynamic__readme, name="" + (name_prefix or "data") + ".dynamic.readme", definition={'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'additionalProperties': False}, rule='additionalProperties')
+                            data__dynamic__readme_any_of_count7 += 1
+                        except JsonSchemaValueException: pass
+                    if not data__dynamic__readme_any_of_count7:
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.readme cannot be validated by any definition", value=data__dynamic__readme, name="" + (name_prefix or "data") + ".dynamic.readme", definition={'type': 'object', 'anyOf': [{'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, {'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'additionalProperties': False}], 'required': ['file']}, rule='anyOf')
+                    data__dynamic__readme_is_dict = isinstance(data__dynamic__readme, dict)
+                    if data__dynamic__readme_is_dict:
+                        data__dynamic__readme__missing_keys = set(['file']) - data__dynamic__readme.keys()
+                        if data__dynamic__readme__missing_keys:
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic.readme must contain " + (str(sorted(data__dynamic__readme__missing_keys)) + " properties"), value=data__dynamic__readme, name="" + (name_prefix or "data") + ".dynamic.readme", definition={'type': 'object', 'anyOf': [{'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, {'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'additionalProperties': False}], 'required': ['file']}, rule='required')
+                if data__dynamic_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic must not contain "+str(data__dynamic_keys)+" properties", value=data__dynamic, name="" + (name_prefix or "data") + ".dynamic", definition={'type': 'object', 'description': 'Instructions for loading :pep:`621`-related metadata dynamically', 'additionalProperties': False, 'properties': {'version': {'$$description': ['A version dynamically loaded via either the ``attr:`` or ``file:``', 'directives. Please make sure the given file or attribute respects :pep:`440`.', 'Also ensure to set ``project.dynamic`` accordingly.'], 'oneOf': [{'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}]}, 'classifiers': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'description': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'entry-points': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'dependencies': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}, 'optional-dependencies': {'type': 'object', 'propertyNames': {'type': 'string', 'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'.+': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}}}, 'readme': {'type': 'object', 'anyOf': [{'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, {'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'additionalProperties': False}], 'required': ['file']}}}, rule='additionalProperties')
+        if data_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must not contain "+str(data_keys)+" properties", value=data, name="" + (name_prefix or "data") + "", definition={'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html', 'title': '``tool.setuptools`` table', '$$description': ['``setuptools``-specific configurations that can be set by users that require', 'customization.', 'These configurations are completely optional and probably can be skipped when', 'creating simple packages. They are equivalent to some of the `Keywords', '`_', 'used by the ``setup.py`` file, and can be set via the ``tool.setuptools`` table.', 'It considers only ``setuptools`` `parameters', '`_', 'that are not covered by :pep:`621`; and intentionally excludes ``dependency_links``', 'and ``setup_requires`` (incompatible with modern workflows/standards).'], 'type': 'object', 'additionalProperties': False, 'properties': {'platforms': {'type': 'array', 'items': {'type': 'string'}}, 'provides': {'$$description': ['Package and virtual package names contained within this package', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, 'obsoletes': {'$$description': ['Packages which this package renders obsolete', '**(not supported by pip)**'], 'type': 'array', 'items': {'type': 'string', 'format': 'pep508-identifier'}}, 'zip-safe': {'$$description': ['Whether the project can be safely installed and run from a zip file.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'boolean'}, 'script-files': {'$$description': ['Legacy way of defining scripts (entry-points are preferred).', 'Equivalent to the ``script`` keyword in ``setup.py``', '(it was renamed to avoid confusion with entry-point based ``project.scripts``', 'defined in :pep:`621`).', '**DISCOURAGED**: generic script wrappers are tricky and may not work properly.', 'Whenever possible, please use ``project.scripts`` instead.'], 'type': 'array', 'items': {'type': 'string'}, '$comment': 'TODO: is this field deprecated/should be removed?'}, 'eager-resources': {'$$description': ['Resources that should be extracted together, if any of them is needed,', 'or if any C extensions included in the project are imported.', '**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and', '``setup.py install`` in the context of ``eggs`` (**DEPRECATED**).'], 'type': 'array', 'items': {'type': 'string'}}, 'packages': {'$$description': ['Packages that should be included in the distribution.', 'It can be given either as a list of package identifiers', 'or as a ``dict``-like structure with a single key ``find``', 'which corresponds to a dynamic call to', '``setuptools.config.expand.find_packages`` function.', 'The ``find`` key is associated with a nested ``dict``-like structure that can', 'contain ``where``, ``include``, ``exclude`` and ``namespaces`` keys,', 'mimicking the keyword arguments of the associated function.'], 'oneOf': [{'title': 'Array of Python package identifiers', 'type': 'array', 'items': {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}}, {'$id': '#/definitions/find-directive', 'title': "'find:' directive", 'type': 'object', 'additionalProperties': False, 'properties': {'find': {'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}}}]}, 'package-dir': {'$$description': [':class:`dict`-like structure mapping from package names to directories where their', 'code can be found.', 'The empty string (as key) means that all packages are contained inside', 'the given directory will be included in the distribution.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'const': ''}, {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}]}, 'patternProperties': {'^.*$': {'type': 'string'}}}, 'package-data': {'$$description': ['Mapping from package names to lists of glob patterns.', 'Usually this option is not needed when using ``include-package-data = true``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'include-package-data': {'$$description': ['Automatically include any data files inside the package directories', 'that are specified by ``MANIFEST.in``', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'boolean'}, 'exclude-package-data': {'$$description': ['Mapping from package names to lists of glob patterns that should be excluded', 'For more information on how to include data files, check ``setuptools`` `docs', '`_.'], 'type': 'object', 'additionalProperties': False, 'propertyNames': {'anyOf': [{'type': 'string', 'format': 'python-module-name'}, {'const': '*'}]}, 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'namespace-packages': {'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'https://setuptools.pypa.io/en/latest/userguide/package_discovery.html', 'description': '**DEPRECATED**: use implicit namespaces instead (:pep:`420`).'}, 'py-modules': {'description': 'Modules that setuptools will manipulate', 'type': 'array', 'items': {'type': 'string', 'format': 'python-module-name-relaxed'}, '$comment': 'TODO: clarify the relationship with ``packages``'}, 'ext-modules': {'description': 'Extension modules to be compiled by setuptools', 'type': 'array', 'items': {'$id': '#/definitions/ext-module', 'title': 'Extension module', 'description': 'Parameters to construct a :class:`setuptools.Extension` object', 'type': 'object', 'required': ['name', 'sources'], 'additionalProperties': False, 'properties': {'name': {'type': 'string', 'format': 'python-module-name-relaxed'}, 'sources': {'type': 'array', 'items': {'type': 'string'}}, 'include-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'define-macros': {'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, 'undef-macros': {'type': 'array', 'items': {'type': 'string'}}, 'library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'libraries': {'type': 'array', 'items': {'type': 'string'}}, 'runtime-library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'extra-objects': {'type': 'array', 'items': {'type': 'string'}}, 'extra-compile-args': {'type': 'array', 'items': {'type': 'string'}}, 'extra-link-args': {'type': 'array', 'items': {'type': 'string'}}, 'export-symbols': {'type': 'array', 'items': {'type': 'string'}}, 'swig-opts': {'type': 'array', 'items': {'type': 'string'}}, 'depends': {'type': 'array', 'items': {'type': 'string'}}, 'language': {'type': 'string'}, 'optional': {'type': 'boolean'}, 'py-limited-api': {'type': 'boolean'}}}}, 'data-files': {'$$description': ['``dict``-like structure where each key represents a directory and', 'the value is a list of glob patterns that should be installed in them.', '**DISCOURAGED**: please notice this might not work as expected with wheels.', 'Whenever possible, consider using data files inside the package directories', '(or create a new namespace package that only contains data files).', 'See `data files support', '`_.'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'array', 'items': {'type': 'string'}}}}, 'cmdclass': {'$$description': ['Mapping of distutils-style command names to ``setuptools.Command`` subclasses', 'which in turn should be represented by strings with a qualified class name', '(i.e., "dotted" form with module), e.g.::\n\n', '    cmdclass = {mycmd = "pkg.subpkg.module.CommandClass"}\n\n', 'The command class should be a directly defined at the top-level of the', 'containing module (no class nesting).'], 'type': 'object', 'patternProperties': {'^.*$': {'type': 'string', 'format': 'python-qualified-identifier'}}}, 'license-files': {'type': 'array', 'items': {'type': 'string'}, '$$description': ['**PROVISIONAL**: list of glob patterns for all license files being distributed.', '(likely to become standard with :pep:`639`).', "By default: ``['LICEN[CS]E*', 'COPYING*', 'NOTICE*', 'AUTHORS*']``"], '$comment': 'TODO: revise if PEP 639 is accepted. Probably ``project.license-files``?'}, 'dynamic': {'type': 'object', 'description': 'Instructions for loading :pep:`621`-related metadata dynamically', 'additionalProperties': False, 'properties': {'version': {'$$description': ['A version dynamically loaded via either the ``attr:`` or ``file:``', 'directives. Please make sure the given file or attribute respects :pep:`440`.', 'Also ensure to set ``project.dynamic`` accordingly.'], 'oneOf': [{'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}]}, 'classifiers': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'description': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'entry-points': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'dependencies': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}, 'optional-dependencies': {'type': 'object', 'propertyNames': {'type': 'string', 'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'.+': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$ref': '#/definitions/file-directive'}]}}}, 'readme': {'type': 'object', 'anyOf': [{'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, {'type': 'object', 'properties': {'content-type': {'type': 'string'}, 'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'additionalProperties': False}], 'required': ['file']}}}}, 'definitions': {'package-name': {'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}, 'ext-module': {'$id': '#/definitions/ext-module', 'title': 'Extension module', 'description': 'Parameters to construct a :class:`setuptools.Extension` object', 'type': 'object', 'required': ['name', 'sources'], 'additionalProperties': False, 'properties': {'name': {'type': 'string', 'format': 'python-module-name-relaxed'}, 'sources': {'type': 'array', 'items': {'type': 'string'}}, 'include-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'define-macros': {'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, 'undef-macros': {'type': 'array', 'items': {'type': 'string'}}, 'library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'libraries': {'type': 'array', 'items': {'type': 'string'}}, 'runtime-library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'extra-objects': {'type': 'array', 'items': {'type': 'string'}}, 'extra-compile-args': {'type': 'array', 'items': {'type': 'string'}}, 'extra-link-args': {'type': 'array', 'items': {'type': 'string'}}, 'export-symbols': {'type': 'array', 'items': {'type': 'string'}}, 'swig-opts': {'type': 'array', 'items': {'type': 'string'}}, 'depends': {'type': 'array', 'items': {'type': 'string'}}, 'language': {'type': 'string'}, 'optional': {'type': 'boolean'}, 'py-limited-api': {'type': 'boolean'}}}, 'file-directive': {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, 'file-directive-for-dependencies': {'title': "'file:' directive for dependencies", 'allOf': [{'$$description': ['**BETA**: subset of the ``requirements.txt`` format', 'without ``pip`` flags and options', '(one :pep:`508`-compliant string per line,', 'lines that are blank or start with ``#`` are excluded).', 'See `dynamic metadata', '`_.']}, {'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}]}, 'attr-directive': {'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, 'find-directive': {'$id': '#/definitions/find-directive', 'title': "'find:' directive", 'type': 'object', 'additionalProperties': False, 'properties': {'find': {'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}}}}}, rule='additionalProperties')
+    return data
+
+def validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive_properties_file(data, custom_formats={}, name_prefix=None):
+    data_one_of_count8 = 0
+    if data_one_of_count8 < 2:
+        try:
+            if not isinstance(data, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + " must be string", value=data, name="" + (name_prefix or "data") + "", definition={'type': 'string'}, rule='type')
+            data_one_of_count8 += 1
+        except JsonSchemaValueException: pass
+    if data_one_of_count8 < 2:
+        try:
+            if not isinstance(data, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + " must be array", value=data, name="" + (name_prefix or "data") + "", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data_is_list = isinstance(data, (list, tuple))
+            if data_is_list:
+                data_len = len(data)
+                for data_x, data_item in enumerate(data):
+                    if not isinstance(data_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + "[{data_x}]".format(**locals()) + " must be string", value=data_item, name="" + (name_prefix or "data") + "[{data_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+            data_one_of_count8 += 1
+        except JsonSchemaValueException: pass
+    if data_one_of_count8 != 1:
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be valid exactly by one definition" + (" (" + str(data_one_of_count8) + " matches found)"), value=data, name="" + (name_prefix or "data") + "", definition={'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}, rule='oneOf')
+    return data
+
+def validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive_for_dependencies(data, custom_formats={}, name_prefix=None):
+    validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive(data, custom_formats, (name_prefix or "data") + "")
+    return data
+
+def validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_file_directive(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (dict)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be object", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, rule='type')
+    data_is_dict = isinstance(data, dict)
+    if data_is_dict:
+        data__missing_keys = set(['file']) - data.keys()
+        if data__missing_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must contain " + (str(sorted(data__missing_keys)) + " properties"), value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, rule='required')
+        data_keys = set(data.keys())
+        if "file" in data_keys:
+            data_keys.remove("file")
+            data__file = data["file"]
+            data__file_one_of_count9 = 0
+            if data__file_one_of_count9 < 2:
+                try:
+                    if not isinstance(data__file, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".file must be string", value=data__file, name="" + (name_prefix or "data") + ".file", definition={'type': 'string'}, rule='type')
+                    data__file_one_of_count9 += 1
+                except JsonSchemaValueException: pass
+            if data__file_one_of_count9 < 2:
+                try:
+                    if not isinstance(data__file, (list, tuple)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".file must be array", value=data__file, name="" + (name_prefix or "data") + ".file", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+                    data__file_is_list = isinstance(data__file, (list, tuple))
+                    if data__file_is_list:
+                        data__file_len = len(data__file)
+                        for data__file_x, data__file_item in enumerate(data__file):
+                            if not isinstance(data__file_item, (str)):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".file[{data__file_x}]".format(**locals()) + " must be string", value=data__file_item, name="" + (name_prefix or "data") + ".file[{data__file_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+                    data__file_one_of_count9 += 1
+                except JsonSchemaValueException: pass
+            if data__file_one_of_count9 != 1:
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".file must be valid exactly by one definition" + (" (" + str(data__file_one_of_count9) + " matches found)"), value=data__file, name="" + (name_prefix or "data") + ".file", definition={'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}, rule='oneOf')
+        if data_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must not contain "+str(data_keys)+" properties", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/file-directive', 'title': "'file:' directive", 'description': 'Value is read from a file (or list of files and then concatenated)', 'type': 'object', 'additionalProperties': False, 'properties': {'file': {'oneOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}, 'required': ['file']}, rule='additionalProperties')
+    return data
+
+def validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_attr_directive(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (dict)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be object", value=data, name="" + (name_prefix or "data") + "", definition={'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, rule='type')
+    data_is_dict = isinstance(data, dict)
+    if data_is_dict:
+        data__missing_keys = set(['attr']) - data.keys()
+        if data__missing_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must contain " + (str(sorted(data__missing_keys)) + " properties"), value=data, name="" + (name_prefix or "data") + "", definition={'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, rule='required')
+        data_keys = set(data.keys())
+        if "attr" in data_keys:
+            data_keys.remove("attr")
+            data__attr = data["attr"]
+            if not isinstance(data__attr, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".attr must be string", value=data__attr, name="" + (name_prefix or "data") + ".attr", definition={'type': 'string', 'format': 'python-qualified-identifier'}, rule='type')
+            if isinstance(data__attr, str):
+                if not custom_formats["python-qualified-identifier"](data__attr):
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".attr must be python-qualified-identifier", value=data__attr, name="" + (name_prefix or "data") + ".attr", definition={'type': 'string', 'format': 'python-qualified-identifier'}, rule='format')
+        if data_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must not contain "+str(data_keys)+" properties", value=data, name="" + (name_prefix or "data") + "", definition={'title': "'attr:' directive", '$id': '#/definitions/attr-directive', '$$description': ['Value is read from a module attribute. Supports callables and iterables;', 'unsupported types are cast via ``str()``'], 'type': 'object', 'additionalProperties': False, 'properties': {'attr': {'type': 'string', 'format': 'python-qualified-identifier'}}, 'required': ['attr']}, rule='additionalProperties')
+    return data
+
+def validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_ext_module(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (dict)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be object", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/ext-module', 'title': 'Extension module', 'description': 'Parameters to construct a :class:`setuptools.Extension` object', 'type': 'object', 'required': ['name', 'sources'], 'additionalProperties': False, 'properties': {'name': {'type': 'string', 'format': 'python-module-name-relaxed'}, 'sources': {'type': 'array', 'items': {'type': 'string'}}, 'include-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'define-macros': {'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, 'undef-macros': {'type': 'array', 'items': {'type': 'string'}}, 'library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'libraries': {'type': 'array', 'items': {'type': 'string'}}, 'runtime-library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'extra-objects': {'type': 'array', 'items': {'type': 'string'}}, 'extra-compile-args': {'type': 'array', 'items': {'type': 'string'}}, 'extra-link-args': {'type': 'array', 'items': {'type': 'string'}}, 'export-symbols': {'type': 'array', 'items': {'type': 'string'}}, 'swig-opts': {'type': 'array', 'items': {'type': 'string'}}, 'depends': {'type': 'array', 'items': {'type': 'string'}}, 'language': {'type': 'string'}, 'optional': {'type': 'boolean'}, 'py-limited-api': {'type': 'boolean'}}}, rule='type')
+    data_is_dict = isinstance(data, dict)
+    if data_is_dict:
+        data__missing_keys = set(['name', 'sources']) - data.keys()
+        if data__missing_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must contain " + (str(sorted(data__missing_keys)) + " properties"), value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/ext-module', 'title': 'Extension module', 'description': 'Parameters to construct a :class:`setuptools.Extension` object', 'type': 'object', 'required': ['name', 'sources'], 'additionalProperties': False, 'properties': {'name': {'type': 'string', 'format': 'python-module-name-relaxed'}, 'sources': {'type': 'array', 'items': {'type': 'string'}}, 'include-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'define-macros': {'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, 'undef-macros': {'type': 'array', 'items': {'type': 'string'}}, 'library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'libraries': {'type': 'array', 'items': {'type': 'string'}}, 'runtime-library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'extra-objects': {'type': 'array', 'items': {'type': 'string'}}, 'extra-compile-args': {'type': 'array', 'items': {'type': 'string'}}, 'extra-link-args': {'type': 'array', 'items': {'type': 'string'}}, 'export-symbols': {'type': 'array', 'items': {'type': 'string'}}, 'swig-opts': {'type': 'array', 'items': {'type': 'string'}}, 'depends': {'type': 'array', 'items': {'type': 'string'}}, 'language': {'type': 'string'}, 'optional': {'type': 'boolean'}, 'py-limited-api': {'type': 'boolean'}}}, rule='required')
+        data_keys = set(data.keys())
+        if "name" in data_keys:
+            data_keys.remove("name")
+            data__name = data["name"]
+            if not isinstance(data__name, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".name must be string", value=data__name, name="" + (name_prefix or "data") + ".name", definition={'type': 'string', 'format': 'python-module-name-relaxed'}, rule='type')
+            if isinstance(data__name, str):
+                if not custom_formats["python-module-name-relaxed"](data__name):
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".name must be python-module-name-relaxed", value=data__name, name="" + (name_prefix or "data") + ".name", definition={'type': 'string', 'format': 'python-module-name-relaxed'}, rule='format')
+        if "sources" in data_keys:
+            data_keys.remove("sources")
+            data__sources = data["sources"]
+            if not isinstance(data__sources, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".sources must be array", value=data__sources, name="" + (name_prefix or "data") + ".sources", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__sources_is_list = isinstance(data__sources, (list, tuple))
+            if data__sources_is_list:
+                data__sources_len = len(data__sources)
+                for data__sources_x, data__sources_item in enumerate(data__sources):
+                    if not isinstance(data__sources_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".sources[{data__sources_x}]".format(**locals()) + " must be string", value=data__sources_item, name="" + (name_prefix or "data") + ".sources[{data__sources_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "include-dirs" in data_keys:
+            data_keys.remove("include-dirs")
+            data__includedirs = data["include-dirs"]
+            if not isinstance(data__includedirs, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".include-dirs must be array", value=data__includedirs, name="" + (name_prefix or "data") + ".include-dirs", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__includedirs_is_list = isinstance(data__includedirs, (list, tuple))
+            if data__includedirs_is_list:
+                data__includedirs_len = len(data__includedirs)
+                for data__includedirs_x, data__includedirs_item in enumerate(data__includedirs):
+                    if not isinstance(data__includedirs_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".include-dirs[{data__includedirs_x}]".format(**locals()) + " must be string", value=data__includedirs_item, name="" + (name_prefix or "data") + ".include-dirs[{data__includedirs_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "define-macros" in data_keys:
+            data_keys.remove("define-macros")
+            data__definemacros = data["define-macros"]
+            if not isinstance(data__definemacros, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".define-macros must be array", value=data__definemacros, name="" + (name_prefix or "data") + ".define-macros", definition={'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, rule='type')
+            data__definemacros_is_list = isinstance(data__definemacros, (list, tuple))
+            if data__definemacros_is_list:
+                data__definemacros_len = len(data__definemacros)
+                for data__definemacros_x, data__definemacros_item in enumerate(data__definemacros):
+                    if not isinstance(data__definemacros_item, (list, tuple)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}]".format(**locals()) + " must be array", value=data__definemacros_item, name="" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}]".format(**locals()) + "", definition={'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}, rule='type')
+                    data__definemacros_item_is_list = isinstance(data__definemacros_item, (list, tuple))
+                    if data__definemacros_item_is_list:
+                        data__definemacros_item_len = len(data__definemacros_item)
+                        if data__definemacros_item_len > 0:
+                            data__definemacros_item__0 = data__definemacros_item[0]
+                            if not isinstance(data__definemacros_item__0, (str)):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}][0]".format(**locals()) + " must be string", value=data__definemacros_item__0, name="" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}][0]".format(**locals()) + "", definition={'description': 'macro name', 'type': 'string'}, rule='type')
+                        if data__definemacros_item_len > 1:
+                            data__definemacros_item__1 = data__definemacros_item[1]
+                            data__definemacros_item__1_one_of_count10 = 0
+                            if data__definemacros_item__1_one_of_count10 < 2:
+                                try:
+                                    if not isinstance(data__definemacros_item__1, (str)):
+                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}][1]".format(**locals()) + " must be string", value=data__definemacros_item__1, name="" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}][1]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+                                    data__definemacros_item__1_one_of_count10 += 1
+                                except JsonSchemaValueException: pass
+                            if data__definemacros_item__1_one_of_count10 < 2:
+                                try:
+                                    if not isinstance(data__definemacros_item__1, (NoneType)):
+                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}][1]".format(**locals()) + " must be null", value=data__definemacros_item__1, name="" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}][1]".format(**locals()) + "", definition={'type': 'null'}, rule='type')
+                                    data__definemacros_item__1_one_of_count10 += 1
+                                except JsonSchemaValueException: pass
+                            if data__definemacros_item__1_one_of_count10 != 1:
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}][1]".format(**locals()) + " must be valid exactly by one definition" + (" (" + str(data__definemacros_item__1_one_of_count10) + " matches found)"), value=data__definemacros_item__1, name="" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}][1]".format(**locals()) + "", definition={'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}, rule='oneOf')
+                        if data__definemacros_item_len > 2:
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}]".format(**locals()) + " must contain only specified items", value=data__definemacros_item, name="" + (name_prefix or "data") + ".define-macros[{data__definemacros_x}]".format(**locals()) + "", definition={'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}, rule='items')
+        if "undef-macros" in data_keys:
+            data_keys.remove("undef-macros")
+            data__undefmacros = data["undef-macros"]
+            if not isinstance(data__undefmacros, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".undef-macros must be array", value=data__undefmacros, name="" + (name_prefix or "data") + ".undef-macros", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__undefmacros_is_list = isinstance(data__undefmacros, (list, tuple))
+            if data__undefmacros_is_list:
+                data__undefmacros_len = len(data__undefmacros)
+                for data__undefmacros_x, data__undefmacros_item in enumerate(data__undefmacros):
+                    if not isinstance(data__undefmacros_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".undef-macros[{data__undefmacros_x}]".format(**locals()) + " must be string", value=data__undefmacros_item, name="" + (name_prefix or "data") + ".undef-macros[{data__undefmacros_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "library-dirs" in data_keys:
+            data_keys.remove("library-dirs")
+            data__librarydirs = data["library-dirs"]
+            if not isinstance(data__librarydirs, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".library-dirs must be array", value=data__librarydirs, name="" + (name_prefix or "data") + ".library-dirs", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__librarydirs_is_list = isinstance(data__librarydirs, (list, tuple))
+            if data__librarydirs_is_list:
+                data__librarydirs_len = len(data__librarydirs)
+                for data__librarydirs_x, data__librarydirs_item in enumerate(data__librarydirs):
+                    if not isinstance(data__librarydirs_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".library-dirs[{data__librarydirs_x}]".format(**locals()) + " must be string", value=data__librarydirs_item, name="" + (name_prefix or "data") + ".library-dirs[{data__librarydirs_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "libraries" in data_keys:
+            data_keys.remove("libraries")
+            data__libraries = data["libraries"]
+            if not isinstance(data__libraries, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".libraries must be array", value=data__libraries, name="" + (name_prefix or "data") + ".libraries", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__libraries_is_list = isinstance(data__libraries, (list, tuple))
+            if data__libraries_is_list:
+                data__libraries_len = len(data__libraries)
+                for data__libraries_x, data__libraries_item in enumerate(data__libraries):
+                    if not isinstance(data__libraries_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".libraries[{data__libraries_x}]".format(**locals()) + " must be string", value=data__libraries_item, name="" + (name_prefix or "data") + ".libraries[{data__libraries_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "runtime-library-dirs" in data_keys:
+            data_keys.remove("runtime-library-dirs")
+            data__runtimelibrarydirs = data["runtime-library-dirs"]
+            if not isinstance(data__runtimelibrarydirs, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".runtime-library-dirs must be array", value=data__runtimelibrarydirs, name="" + (name_prefix or "data") + ".runtime-library-dirs", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__runtimelibrarydirs_is_list = isinstance(data__runtimelibrarydirs, (list, tuple))
+            if data__runtimelibrarydirs_is_list:
+                data__runtimelibrarydirs_len = len(data__runtimelibrarydirs)
+                for data__runtimelibrarydirs_x, data__runtimelibrarydirs_item in enumerate(data__runtimelibrarydirs):
+                    if not isinstance(data__runtimelibrarydirs_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".runtime-library-dirs[{data__runtimelibrarydirs_x}]".format(**locals()) + " must be string", value=data__runtimelibrarydirs_item, name="" + (name_prefix or "data") + ".runtime-library-dirs[{data__runtimelibrarydirs_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "extra-objects" in data_keys:
+            data_keys.remove("extra-objects")
+            data__extraobjects = data["extra-objects"]
+            if not isinstance(data__extraobjects, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".extra-objects must be array", value=data__extraobjects, name="" + (name_prefix or "data") + ".extra-objects", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__extraobjects_is_list = isinstance(data__extraobjects, (list, tuple))
+            if data__extraobjects_is_list:
+                data__extraobjects_len = len(data__extraobjects)
+                for data__extraobjects_x, data__extraobjects_item in enumerate(data__extraobjects):
+                    if not isinstance(data__extraobjects_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".extra-objects[{data__extraobjects_x}]".format(**locals()) + " must be string", value=data__extraobjects_item, name="" + (name_prefix or "data") + ".extra-objects[{data__extraobjects_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "extra-compile-args" in data_keys:
+            data_keys.remove("extra-compile-args")
+            data__extracompileargs = data["extra-compile-args"]
+            if not isinstance(data__extracompileargs, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".extra-compile-args must be array", value=data__extracompileargs, name="" + (name_prefix or "data") + ".extra-compile-args", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__extracompileargs_is_list = isinstance(data__extracompileargs, (list, tuple))
+            if data__extracompileargs_is_list:
+                data__extracompileargs_len = len(data__extracompileargs)
+                for data__extracompileargs_x, data__extracompileargs_item in enumerate(data__extracompileargs):
+                    if not isinstance(data__extracompileargs_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".extra-compile-args[{data__extracompileargs_x}]".format(**locals()) + " must be string", value=data__extracompileargs_item, name="" + (name_prefix or "data") + ".extra-compile-args[{data__extracompileargs_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "extra-link-args" in data_keys:
+            data_keys.remove("extra-link-args")
+            data__extralinkargs = data["extra-link-args"]
+            if not isinstance(data__extralinkargs, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".extra-link-args must be array", value=data__extralinkargs, name="" + (name_prefix or "data") + ".extra-link-args", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__extralinkargs_is_list = isinstance(data__extralinkargs, (list, tuple))
+            if data__extralinkargs_is_list:
+                data__extralinkargs_len = len(data__extralinkargs)
+                for data__extralinkargs_x, data__extralinkargs_item in enumerate(data__extralinkargs):
+                    if not isinstance(data__extralinkargs_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".extra-link-args[{data__extralinkargs_x}]".format(**locals()) + " must be string", value=data__extralinkargs_item, name="" + (name_prefix or "data") + ".extra-link-args[{data__extralinkargs_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "export-symbols" in data_keys:
+            data_keys.remove("export-symbols")
+            data__exportsymbols = data["export-symbols"]
+            if not isinstance(data__exportsymbols, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".export-symbols must be array", value=data__exportsymbols, name="" + (name_prefix or "data") + ".export-symbols", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__exportsymbols_is_list = isinstance(data__exportsymbols, (list, tuple))
+            if data__exportsymbols_is_list:
+                data__exportsymbols_len = len(data__exportsymbols)
+                for data__exportsymbols_x, data__exportsymbols_item in enumerate(data__exportsymbols):
+                    if not isinstance(data__exportsymbols_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".export-symbols[{data__exportsymbols_x}]".format(**locals()) + " must be string", value=data__exportsymbols_item, name="" + (name_prefix or "data") + ".export-symbols[{data__exportsymbols_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "swig-opts" in data_keys:
+            data_keys.remove("swig-opts")
+            data__swigopts = data["swig-opts"]
+            if not isinstance(data__swigopts, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".swig-opts must be array", value=data__swigopts, name="" + (name_prefix or "data") + ".swig-opts", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__swigopts_is_list = isinstance(data__swigopts, (list, tuple))
+            if data__swigopts_is_list:
+                data__swigopts_len = len(data__swigopts)
+                for data__swigopts_x, data__swigopts_item in enumerate(data__swigopts):
+                    if not isinstance(data__swigopts_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".swig-opts[{data__swigopts_x}]".format(**locals()) + " must be string", value=data__swigopts_item, name="" + (name_prefix or "data") + ".swig-opts[{data__swigopts_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "depends" in data_keys:
+            data_keys.remove("depends")
+            data__depends = data["depends"]
+            if not isinstance(data__depends, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".depends must be array", value=data__depends, name="" + (name_prefix or "data") + ".depends", definition={'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__depends_is_list = isinstance(data__depends, (list, tuple))
+            if data__depends_is_list:
+                data__depends_len = len(data__depends)
+                for data__depends_x, data__depends_item in enumerate(data__depends):
+                    if not isinstance(data__depends_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".depends[{data__depends_x}]".format(**locals()) + " must be string", value=data__depends_item, name="" + (name_prefix or "data") + ".depends[{data__depends_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "language" in data_keys:
+            data_keys.remove("language")
+            data__language = data["language"]
+            if not isinstance(data__language, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".language must be string", value=data__language, name="" + (name_prefix or "data") + ".language", definition={'type': 'string'}, rule='type')
+        if "optional" in data_keys:
+            data_keys.remove("optional")
+            data__optional = data["optional"]
+            if not isinstance(data__optional, (bool)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".optional must be boolean", value=data__optional, name="" + (name_prefix or "data") + ".optional", definition={'type': 'boolean'}, rule='type')
+        if "py-limited-api" in data_keys:
+            data_keys.remove("py-limited-api")
+            data__pylimitedapi = data["py-limited-api"]
+            if not isinstance(data__pylimitedapi, (bool)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".py-limited-api must be boolean", value=data__pylimitedapi, name="" + (name_prefix or "data") + ".py-limited-api", definition={'type': 'boolean'}, rule='type')
+        if data_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must not contain "+str(data_keys)+" properties", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/ext-module', 'title': 'Extension module', 'description': 'Parameters to construct a :class:`setuptools.Extension` object', 'type': 'object', 'required': ['name', 'sources'], 'additionalProperties': False, 'properties': {'name': {'type': 'string', 'format': 'python-module-name-relaxed'}, 'sources': {'type': 'array', 'items': {'type': 'string'}}, 'include-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'define-macros': {'type': 'array', 'items': {'type': 'array', 'items': [{'description': 'macro name', 'type': 'string'}, {'description': 'macro value', 'oneOf': [{'type': 'string'}, {'type': 'null'}]}], 'additionalItems': False}}, 'undef-macros': {'type': 'array', 'items': {'type': 'string'}}, 'library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'libraries': {'type': 'array', 'items': {'type': 'string'}}, 'runtime-library-dirs': {'type': 'array', 'items': {'type': 'string'}}, 'extra-objects': {'type': 'array', 'items': {'type': 'string'}}, 'extra-compile-args': {'type': 'array', 'items': {'type': 'string'}}, 'extra-link-args': {'type': 'array', 'items': {'type': 'string'}}, 'export-symbols': {'type': 'array', 'items': {'type': 'string'}}, 'swig-opts': {'type': 'array', 'items': {'type': 'string'}}, 'depends': {'type': 'array', 'items': {'type': 'string'}}, 'language': {'type': 'string'}, 'optional': {'type': 'boolean'}, 'py-limited-api': {'type': 'boolean'}}}, rule='additionalProperties')
+    return data
+
+def validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_find_directive(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (dict)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be object", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/find-directive', 'title': "'find:' directive", 'type': 'object', 'additionalProperties': False, 'properties': {'find': {'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}}}, rule='type')
+    data_is_dict = isinstance(data, dict)
+    if data_is_dict:
+        data_keys = set(data.keys())
+        if "find" in data_keys:
+            data_keys.remove("find")
+            data__find = data["find"]
+            if not isinstance(data__find, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".find must be object", value=data__find, name="" + (name_prefix or "data") + ".find", definition={'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}, rule='type')
+            data__find_is_dict = isinstance(data__find, dict)
+            if data__find_is_dict:
+                data__find_keys = set(data__find.keys())
+                if "where" in data__find_keys:
+                    data__find_keys.remove("where")
+                    data__find__where = data__find["where"]
+                    if not isinstance(data__find__where, (list, tuple)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".find.where must be array", value=data__find__where, name="" + (name_prefix or "data") + ".find.where", definition={'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, rule='type')
+                    data__find__where_is_list = isinstance(data__find__where, (list, tuple))
+                    if data__find__where_is_list:
+                        data__find__where_len = len(data__find__where)
+                        for data__find__where_x, data__find__where_item in enumerate(data__find__where):
+                            if not isinstance(data__find__where_item, (str)):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".find.where[{data__find__where_x}]".format(**locals()) + " must be string", value=data__find__where_item, name="" + (name_prefix or "data") + ".find.where[{data__find__where_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+                if "exclude" in data__find_keys:
+                    data__find_keys.remove("exclude")
+                    data__find__exclude = data__find["exclude"]
+                    if not isinstance(data__find__exclude, (list, tuple)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".find.exclude must be array", value=data__find__exclude, name="" + (name_prefix or "data") + ".find.exclude", definition={'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, rule='type')
+                    data__find__exclude_is_list = isinstance(data__find__exclude, (list, tuple))
+                    if data__find__exclude_is_list:
+                        data__find__exclude_len = len(data__find__exclude)
+                        for data__find__exclude_x, data__find__exclude_item in enumerate(data__find__exclude):
+                            if not isinstance(data__find__exclude_item, (str)):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".find.exclude[{data__find__exclude_x}]".format(**locals()) + " must be string", value=data__find__exclude_item, name="" + (name_prefix or "data") + ".find.exclude[{data__find__exclude_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+                if "include" in data__find_keys:
+                    data__find_keys.remove("include")
+                    data__find__include = data__find["include"]
+                    if not isinstance(data__find__include, (list, tuple)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".find.include must be array", value=data__find__include, name="" + (name_prefix or "data") + ".find.include", definition={'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, rule='type')
+                    data__find__include_is_list = isinstance(data__find__include, (list, tuple))
+                    if data__find__include_is_list:
+                        data__find__include_len = len(data__find__include)
+                        for data__find__include_x, data__find__include_item in enumerate(data__find__include):
+                            if not isinstance(data__find__include_item, (str)):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".find.include[{data__find__include_x}]".format(**locals()) + " must be string", value=data__find__include_item, name="" + (name_prefix or "data") + ".find.include[{data__find__include_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+                if "namespaces" in data__find_keys:
+                    data__find_keys.remove("namespaces")
+                    data__find__namespaces = data__find["namespaces"]
+                    if not isinstance(data__find__namespaces, (bool)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".find.namespaces must be boolean", value=data__find__namespaces, name="" + (name_prefix or "data") + ".find.namespaces", definition={'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}, rule='type')
+                if data__find_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".find must not contain "+str(data__find_keys)+" properties", value=data__find, name="" + (name_prefix or "data") + ".find", definition={'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}, rule='additionalProperties')
+        if data_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must not contain "+str(data_keys)+" properties", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/find-directive', 'title': "'find:' directive", 'type': 'object', 'additionalProperties': False, 'properties': {'find': {'type': 'object', '$$description': ['Dynamic `package discovery', '`_.'], 'additionalProperties': False, 'properties': {'where': {'description': 'Directories to be searched for packages (Unix-style relative path)', 'type': 'array', 'items': {'type': 'string'}}, 'exclude': {'type': 'array', '$$description': ['Exclude packages that match the values listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'include': {'type': 'array', '$$description': ['Restrict the found packages to just the ones listed in this field.', "Can container shell-style wildcards (e.g. ``'pkg.*'``)"], 'items': {'type': 'string'}}, 'namespaces': {'type': 'boolean', '$$description': ['When ``True``, directories without a ``__init__.py`` file will also', 'be scanned for :pep:`420`-style implicit namespaces']}}}}}, rule='additionalProperties')
+    return data
+
+def validate_https___setuptools_pypa_io_en_latest_userguide_pyproject_config_html__definitions_package_name(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (str)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be string", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}, rule='type')
+    data_any_of_count11 = 0
+    if not data_any_of_count11:
+        try:
+            if not isinstance(data, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + " must be string", value=data, name="" + (name_prefix or "data") + "", definition={'type': 'string', 'format': 'python-module-name-relaxed'}, rule='type')
+            if isinstance(data, str):
+                if not custom_formats["python-module-name-relaxed"](data):
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + " must be python-module-name-relaxed", value=data, name="" + (name_prefix or "data") + "", definition={'type': 'string', 'format': 'python-module-name-relaxed'}, rule='format')
+            data_any_of_count11 += 1
+        except JsonSchemaValueException: pass
+    if not data_any_of_count11:
+        try:
+            if not isinstance(data, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + " must be string", value=data, name="" + (name_prefix or "data") + "", definition={'type': 'string', 'format': 'pep561-stub-name'}, rule='type')
+            if isinstance(data, str):
+                if not custom_formats["pep561-stub-name"](data):
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + " must be pep561-stub-name", value=data, name="" + (name_prefix or "data") + "", definition={'type': 'string', 'format': 'pep561-stub-name'}, rule='format')
+            data_any_of_count11 += 1
+        except JsonSchemaValueException: pass
+    if not data_any_of_count11:
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " cannot be validated by any definition", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/package-name', 'title': 'Valid package name', 'description': 'Valid package name (importable or :pep:`561`).', 'type': 'string', 'anyOf': [{'type': 'string', 'format': 'python-module-name-relaxed'}, {'type': 'string', 'format': 'pep561-stub-name'}]}, rule='anyOf')
+    return data
+
+def validate_https___setuptools_pypa_io_en_latest_deprecated_distutils_configfile_html(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (dict)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be object", value=data, name="" + (name_prefix or "data") + "", definition={'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://setuptools.pypa.io/en/latest/deprecated/distutils/configfile.html', 'title': '``tool.distutils`` table', '$$description': ['**EXPERIMENTAL** (NOT OFFICIALLY SUPPORTED): Use ``tool.distutils``', 'subtables to configure arguments for ``distutils`` commands.', 'Originally, ``distutils`` allowed developers to configure arguments for', '``setup.py`` commands via `distutils configuration files', '`_.', 'See also `the old Python docs _`.'], 'type': 'object', 'properties': {'global': {'type': 'object', 'description': 'Global options applied to all ``distutils`` commands'}}, 'patternProperties': {'.+': {'type': 'object'}}, '$comment': 'TODO: Is there a practical way of making this schema more specific?'}, rule='type')
+    data_is_dict = isinstance(data, dict)
+    if data_is_dict:
+        data_keys = set(data.keys())
+        if "global" in data_keys:
+            data_keys.remove("global")
+            data__global = data["global"]
+            if not isinstance(data__global, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".global must be object", value=data__global, name="" + (name_prefix or "data") + ".global", definition={'type': 'object', 'description': 'Global options applied to all ``distutils`` commands'}, rule='type')
+        for data_key, data_val in data.items():
+            if REGEX_PATTERNS['.+'].search(data_key):
+                if data_key in data_keys:
+                    data_keys.remove(data_key)
+                if not isinstance(data_val, (dict)):
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".{data_key}".format(**locals()) + " must be object", value=data_val, name="" + (name_prefix or "data") + ".{data_key}".format(**locals()) + "", definition={'type': 'object'}, rule='type')
+    return data
+
+def validate_https___packaging_python_org_en_latest_specifications_pyproject_toml(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (dict)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be object", value=data, name="" + (name_prefix or "data") + "", definition={'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://packaging.python.org/en/latest/specifications/pyproject-toml/', 'title': 'Package metadata stored in the ``project`` table', '$$description': ['Data structure for the **project** table inside ``pyproject.toml``', '(as initially defined in :pep:`621`)'], 'type': 'object', 'properties': {'name': {'type': 'string', 'description': 'The name (primary identifier) of the project. MUST be statically defined.', 'format': 'pep508-identifier'}, 'version': {'type': 'string', 'description': 'The version of the project as supported by :pep:`440`.', 'format': 'pep440'}, 'description': {'type': 'string', '$$description': ['The `summary description of the project', '`_']}, 'readme': {'$$description': ['`Full/detailed description of the project in the form of a README', '`_', "with meaning similar to the one defined in `core metadata's Description", '`_'], 'oneOf': [{'type': 'string', '$$description': ['Relative path to a text file (UTF-8) containing the full description', 'of the project. If the file path ends in case-insensitive ``.md`` or', '``.rst`` suffixes, then the content-type is respectively', '``text/markdown`` or ``text/x-rst``']}, {'type': 'object', 'allOf': [{'anyOf': [{'properties': {'file': {'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}}, 'required': ['file']}, {'properties': {'text': {'type': 'string', 'description': 'Full text describing the project.'}}, 'required': ['text']}]}, {'properties': {'content-type': {'type': 'string', '$$description': ['Content-type (:rfc:`1341`) of the full description', '(e.g. ``text/markdown``). The ``charset`` parameter is assumed', 'UTF-8 when not present.'], '$comment': 'TODO: add regex pattern or format?'}}, 'required': ['content-type']}]}]}, 'requires-python': {'type': 'string', 'format': 'pep508-versionspec', '$$description': ['`The Python version requirements of the project', '`_.']}, 'license': {'description': '`Project license `_.', 'oneOf': [{'type': 'string', 'description': 'An SPDX license identifier', 'format': 'SPDX'}, {'type': 'object', 'properties': {'file': {'type': 'string', '$$description': ['Relative path to the file (UTF-8) which contains the license for the', 'project.']}}, 'required': ['file']}, {'type': 'object', 'properties': {'text': {'type': 'string', '$$description': ['The license of the project whose meaning is that of the', '`License field from the core metadata', '`_.']}}, 'required': ['text']}]}, 'license-files': {'description': 'Paths or globs to paths of license files', 'type': 'array', 'items': {'type': 'string'}}, 'authors': {'type': 'array', 'items': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, '$$description': ["The people or organizations considered to be the 'authors' of the project.", 'The exact meaning is open to interpretation (e.g. original or primary authors,', 'current maintainers, or owners of the package).']}, 'maintainers': {'type': 'array', 'items': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, '$$description': ["The people or organizations considered to be the 'maintainers' of the project.", 'Similarly to ``authors``, the exact meaning is open to interpretation.']}, 'keywords': {'type': 'array', 'items': {'type': 'string'}, 'description': 'List of keywords to assist searching for the distribution in a larger catalog.'}, 'classifiers': {'type': 'array', 'items': {'type': 'string', 'format': 'trove-classifier', 'description': '`PyPI classifier `_.'}, '$$description': ['`Trove classifiers `_', 'which apply to the project.']}, 'urls': {'type': 'object', 'description': 'URLs associated with the project in the form ``label => value``.', 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', 'format': 'url'}}}, 'scripts': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'gui-scripts': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'entry-points': {'$$description': ['Instruct the installer to expose the given modules/functions via', '``entry-point`` discovery mechanism (useful for plugins).', 'More information available in the `Python packaging guide', '`_.'], 'propertyNames': {'format': 'python-entrypoint-group'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}}}, 'dependencies': {'type': 'array', 'description': 'Project (mandatory) dependencies.', 'items': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}, 'optional-dependencies': {'type': 'object', 'description': 'Optional dependency for the project', 'propertyNames': {'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'array', 'items': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}}, 'dynamic': {'type': 'array', '$$description': ['Specifies which fields are intentionally unspecified and expected to be', 'dynamically provided by build tools'], 'items': {'enum': ['version', 'description', 'readme', 'requires-python', 'license', 'license-files', 'authors', 'maintainers', 'keywords', 'classifiers', 'urls', 'scripts', 'gui-scripts', 'entry-points', 'dependencies', 'optional-dependencies']}}}, 'required': ['name'], 'additionalProperties': False, 'allOf': [{'if': {'not': {'required': ['dynamic'], 'properties': {'dynamic': {'contains': {'const': 'version'}, '$$description': ['version is listed in ``dynamic``']}}}, '$$comment': ['According to :pep:`621`:', '    If the core metadata specification lists a field as "Required", then', '    the metadata MUST specify the field statically or list it in dynamic', 'In turn, `core metadata`_ defines:', '    The required fields are: Metadata-Version, Name, Version.', '    All the other fields are optional.', 'Since ``Metadata-Version`` is defined by the build back-end, ``name`` and', '``version`` are the only mandatory information in ``pyproject.toml``.', '.. _core metadata: https://packaging.python.org/specifications/core-metadata/']}, 'then': {'required': ['version'], '$$description': ['version should be statically defined in the ``version`` field']}}, {'if': {'required': ['license-files']}, 'then': {'properties': {'license': {'type': 'string'}}}}], 'definitions': {'author': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, 'entry-point-group': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'dependency': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}, rule='type')
+    try:
+        try:
+            data_is_dict = isinstance(data, dict)
+            if data_is_dict:
+                data__missing_keys = set(['dynamic']) - data.keys()
+                if data__missing_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + " must contain " + (str(sorted(data__missing_keys)) + " properties"), value=data, name="" + (name_prefix or "data") + "", definition={'required': ['dynamic'], 'properties': {'dynamic': {'contains': {'const': 'version'}, '$$description': ['version is listed in ``dynamic``']}}}, rule='required')
+                data_keys = set(data.keys())
+                if "dynamic" in data_keys:
+                    data_keys.remove("dynamic")
+                    data__dynamic = data["dynamic"]
+                    data__dynamic_is_list = isinstance(data__dynamic, (list, tuple))
+                    if data__dynamic_is_list:
+                        data__dynamic_contains = False
+                        for data__dynamic_key in data__dynamic:
+                            try:
+                                if data__dynamic_key != "version":
+                                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic must be same as const definition: version", value=data__dynamic_key, name="" + (name_prefix or "data") + ".dynamic", definition={'const': 'version'}, rule='const')
+                                data__dynamic_contains = True
+                                break
+                            except JsonSchemaValueException: pass
+                        if not data__dynamic_contains:
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic must contain one of contains definition", value=data__dynamic, name="" + (name_prefix or "data") + ".dynamic", definition={'contains': {'const': 'version'}, '$$description': ['version is listed in ``dynamic``']}, rule='contains')
+        except JsonSchemaValueException: pass
+        else:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must NOT match a disallowed definition", value=data, name="" + (name_prefix or "data") + "", definition={'not': {'required': ['dynamic'], 'properties': {'dynamic': {'contains': {'const': 'version'}, '$$description': ['version is listed in ``dynamic``']}}}, '$$comment': ['According to :pep:`621`:', '    If the core metadata specification lists a field as "Required", then', '    the metadata MUST specify the field statically or list it in dynamic', 'In turn, `core metadata`_ defines:', '    The required fields are: Metadata-Version, Name, Version.', '    All the other fields are optional.', 'Since ``Metadata-Version`` is defined by the build back-end, ``name`` and', '``version`` are the only mandatory information in ``pyproject.toml``.', '.. _core metadata: https://packaging.python.org/specifications/core-metadata/']}, rule='not')
+    except JsonSchemaValueException:
+        pass
+    else:
+        data_is_dict = isinstance(data, dict)
+        if data_is_dict:
+            data__missing_keys = set(['version']) - data.keys()
+            if data__missing_keys:
+                raise JsonSchemaValueException("" + (name_prefix or "data") + " must contain " + (str(sorted(data__missing_keys)) + " properties"), value=data, name="" + (name_prefix or "data") + "", definition={'required': ['version'], '$$description': ['version should be statically defined in the ``version`` field']}, rule='required')
+    try:
+        data_is_dict = isinstance(data, dict)
+        if data_is_dict:
+            data__missing_keys = set(['license-files']) - data.keys()
+            if data__missing_keys:
+                raise JsonSchemaValueException("" + (name_prefix or "data") + " must contain " + (str(sorted(data__missing_keys)) + " properties"), value=data, name="" + (name_prefix or "data") + "", definition={'required': ['license-files']}, rule='required')
+    except JsonSchemaValueException:
+        pass
+    else:
+        data_is_dict = isinstance(data, dict)
+        if data_is_dict:
+            data_keys = set(data.keys())
+            if "license" in data_keys:
+                data_keys.remove("license")
+                data__license = data["license"]
+                if not isinstance(data__license, (str)):
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".license must be string", value=data__license, name="" + (name_prefix or "data") + ".license", definition={'type': 'string'}, rule='type')
+    data_is_dict = isinstance(data, dict)
+    if data_is_dict:
+        data__missing_keys = set(['name']) - data.keys()
+        if data__missing_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must contain " + (str(sorted(data__missing_keys)) + " properties"), value=data, name="" + (name_prefix or "data") + "", definition={'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://packaging.python.org/en/latest/specifications/pyproject-toml/', 'title': 'Package metadata stored in the ``project`` table', '$$description': ['Data structure for the **project** table inside ``pyproject.toml``', '(as initially defined in :pep:`621`)'], 'type': 'object', 'properties': {'name': {'type': 'string', 'description': 'The name (primary identifier) of the project. MUST be statically defined.', 'format': 'pep508-identifier'}, 'version': {'type': 'string', 'description': 'The version of the project as supported by :pep:`440`.', 'format': 'pep440'}, 'description': {'type': 'string', '$$description': ['The `summary description of the project', '`_']}, 'readme': {'$$description': ['`Full/detailed description of the project in the form of a README', '`_', "with meaning similar to the one defined in `core metadata's Description", '`_'], 'oneOf': [{'type': 'string', '$$description': ['Relative path to a text file (UTF-8) containing the full description', 'of the project. If the file path ends in case-insensitive ``.md`` or', '``.rst`` suffixes, then the content-type is respectively', '``text/markdown`` or ``text/x-rst``']}, {'type': 'object', 'allOf': [{'anyOf': [{'properties': {'file': {'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}}, 'required': ['file']}, {'properties': {'text': {'type': 'string', 'description': 'Full text describing the project.'}}, 'required': ['text']}]}, {'properties': {'content-type': {'type': 'string', '$$description': ['Content-type (:rfc:`1341`) of the full description', '(e.g. ``text/markdown``). The ``charset`` parameter is assumed', 'UTF-8 when not present.'], '$comment': 'TODO: add regex pattern or format?'}}, 'required': ['content-type']}]}]}, 'requires-python': {'type': 'string', 'format': 'pep508-versionspec', '$$description': ['`The Python version requirements of the project', '`_.']}, 'license': {'description': '`Project license `_.', 'oneOf': [{'type': 'string', 'description': 'An SPDX license identifier', 'format': 'SPDX'}, {'type': 'object', 'properties': {'file': {'type': 'string', '$$description': ['Relative path to the file (UTF-8) which contains the license for the', 'project.']}}, 'required': ['file']}, {'type': 'object', 'properties': {'text': {'type': 'string', '$$description': ['The license of the project whose meaning is that of the', '`License field from the core metadata', '`_.']}}, 'required': ['text']}]}, 'license-files': {'description': 'Paths or globs to paths of license files', 'type': 'array', 'items': {'type': 'string'}}, 'authors': {'type': 'array', 'items': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, '$$description': ["The people or organizations considered to be the 'authors' of the project.", 'The exact meaning is open to interpretation (e.g. original or primary authors,', 'current maintainers, or owners of the package).']}, 'maintainers': {'type': 'array', 'items': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, '$$description': ["The people or organizations considered to be the 'maintainers' of the project.", 'Similarly to ``authors``, the exact meaning is open to interpretation.']}, 'keywords': {'type': 'array', 'items': {'type': 'string'}, 'description': 'List of keywords to assist searching for the distribution in a larger catalog.'}, 'classifiers': {'type': 'array', 'items': {'type': 'string', 'format': 'trove-classifier', 'description': '`PyPI classifier `_.'}, '$$description': ['`Trove classifiers `_', 'which apply to the project.']}, 'urls': {'type': 'object', 'description': 'URLs associated with the project in the form ``label => value``.', 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', 'format': 'url'}}}, 'scripts': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'gui-scripts': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'entry-points': {'$$description': ['Instruct the installer to expose the given modules/functions via', '``entry-point`` discovery mechanism (useful for plugins).', 'More information available in the `Python packaging guide', '`_.'], 'propertyNames': {'format': 'python-entrypoint-group'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}}}, 'dependencies': {'type': 'array', 'description': 'Project (mandatory) dependencies.', 'items': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}, 'optional-dependencies': {'type': 'object', 'description': 'Optional dependency for the project', 'propertyNames': {'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'array', 'items': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}}, 'dynamic': {'type': 'array', '$$description': ['Specifies which fields are intentionally unspecified and expected to be', 'dynamically provided by build tools'], 'items': {'enum': ['version', 'description', 'readme', 'requires-python', 'license', 'license-files', 'authors', 'maintainers', 'keywords', 'classifiers', 'urls', 'scripts', 'gui-scripts', 'entry-points', 'dependencies', 'optional-dependencies']}}}, 'required': ['name'], 'additionalProperties': False, 'allOf': [{'if': {'not': {'required': ['dynamic'], 'properties': {'dynamic': {'contains': {'const': 'version'}, '$$description': ['version is listed in ``dynamic``']}}}, '$$comment': ['According to :pep:`621`:', '    If the core metadata specification lists a field as "Required", then', '    the metadata MUST specify the field statically or list it in dynamic', 'In turn, `core metadata`_ defines:', '    The required fields are: Metadata-Version, Name, Version.', '    All the other fields are optional.', 'Since ``Metadata-Version`` is defined by the build back-end, ``name`` and', '``version`` are the only mandatory information in ``pyproject.toml``.', '.. _core metadata: https://packaging.python.org/specifications/core-metadata/']}, 'then': {'required': ['version'], '$$description': ['version should be statically defined in the ``version`` field']}}, {'if': {'required': ['license-files']}, 'then': {'properties': {'license': {'type': 'string'}}}}], 'definitions': {'author': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, 'entry-point-group': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'dependency': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}, rule='required')
+        data_keys = set(data.keys())
+        if "name" in data_keys:
+            data_keys.remove("name")
+            data__name = data["name"]
+            if not isinstance(data__name, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".name must be string", value=data__name, name="" + (name_prefix or "data") + ".name", definition={'type': 'string', 'description': 'The name (primary identifier) of the project. MUST be statically defined.', 'format': 'pep508-identifier'}, rule='type')
+            if isinstance(data__name, str):
+                if not custom_formats["pep508-identifier"](data__name):
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".name must be pep508-identifier", value=data__name, name="" + (name_prefix or "data") + ".name", definition={'type': 'string', 'description': 'The name (primary identifier) of the project. MUST be statically defined.', 'format': 'pep508-identifier'}, rule='format')
+        if "version" in data_keys:
+            data_keys.remove("version")
+            data__version = data["version"]
+            if not isinstance(data__version, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".version must be string", value=data__version, name="" + (name_prefix or "data") + ".version", definition={'type': 'string', 'description': 'The version of the project as supported by :pep:`440`.', 'format': 'pep440'}, rule='type')
+            if isinstance(data__version, str):
+                if not custom_formats["pep440"](data__version):
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".version must be pep440", value=data__version, name="" + (name_prefix or "data") + ".version", definition={'type': 'string', 'description': 'The version of the project as supported by :pep:`440`.', 'format': 'pep440'}, rule='format')
+        if "description" in data_keys:
+            data_keys.remove("description")
+            data__description = data["description"]
+            if not isinstance(data__description, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".description must be string", value=data__description, name="" + (name_prefix or "data") + ".description", definition={'type': 'string', '$$description': ['The `summary description of the project', '`_']}, rule='type')
+        if "readme" in data_keys:
+            data_keys.remove("readme")
+            data__readme = data["readme"]
+            data__readme_one_of_count12 = 0
+            if data__readme_one_of_count12 < 2:
+                try:
+                    if not isinstance(data__readme, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".readme must be string", value=data__readme, name="" + (name_prefix or "data") + ".readme", definition={'type': 'string', '$$description': ['Relative path to a text file (UTF-8) containing the full description', 'of the project. If the file path ends in case-insensitive ``.md`` or', '``.rst`` suffixes, then the content-type is respectively', '``text/markdown`` or ``text/x-rst``']}, rule='type')
+                    data__readme_one_of_count12 += 1
+                except JsonSchemaValueException: pass
+            if data__readme_one_of_count12 < 2:
+                try:
+                    if not isinstance(data__readme, (dict)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".readme must be object", value=data__readme, name="" + (name_prefix or "data") + ".readme", definition={'type': 'object', 'allOf': [{'anyOf': [{'properties': {'file': {'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}}, 'required': ['file']}, {'properties': {'text': {'type': 'string', 'description': 'Full text describing the project.'}}, 'required': ['text']}]}, {'properties': {'content-type': {'type': 'string', '$$description': ['Content-type (:rfc:`1341`) of the full description', '(e.g. ``text/markdown``). The ``charset`` parameter is assumed', 'UTF-8 when not present.'], '$comment': 'TODO: add regex pattern or format?'}}, 'required': ['content-type']}]}, rule='type')
+                    data__readme_any_of_count13 = 0
+                    if not data__readme_any_of_count13:
+                        try:
+                            data__readme_is_dict = isinstance(data__readme, dict)
+                            if data__readme_is_dict:
+                                data__readme__missing_keys = set(['file']) - data__readme.keys()
+                                if data__readme__missing_keys:
+                                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".readme must contain " + (str(sorted(data__readme__missing_keys)) + " properties"), value=data__readme, name="" + (name_prefix or "data") + ".readme", definition={'properties': {'file': {'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}}, 'required': ['file']}, rule='required')
+                                data__readme_keys = set(data__readme.keys())
+                                if "file" in data__readme_keys:
+                                    data__readme_keys.remove("file")
+                                    data__readme__file = data__readme["file"]
+                                    if not isinstance(data__readme__file, (str)):
+                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".readme.file must be string", value=data__readme__file, name="" + (name_prefix or "data") + ".readme.file", definition={'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}, rule='type')
+                            data__readme_any_of_count13 += 1
+                        except JsonSchemaValueException: pass
+                    if not data__readme_any_of_count13:
+                        try:
+                            data__readme_is_dict = isinstance(data__readme, dict)
+                            if data__readme_is_dict:
+                                data__readme__missing_keys = set(['text']) - data__readme.keys()
+                                if data__readme__missing_keys:
+                                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".readme must contain " + (str(sorted(data__readme__missing_keys)) + " properties"), value=data__readme, name="" + (name_prefix or "data") + ".readme", definition={'properties': {'text': {'type': 'string', 'description': 'Full text describing the project.'}}, 'required': ['text']}, rule='required')
+                                data__readme_keys = set(data__readme.keys())
+                                if "text" in data__readme_keys:
+                                    data__readme_keys.remove("text")
+                                    data__readme__text = data__readme["text"]
+                                    if not isinstance(data__readme__text, (str)):
+                                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".readme.text must be string", value=data__readme__text, name="" + (name_prefix or "data") + ".readme.text", definition={'type': 'string', 'description': 'Full text describing the project.'}, rule='type')
+                            data__readme_any_of_count13 += 1
+                        except JsonSchemaValueException: pass
+                    if not data__readme_any_of_count13:
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".readme cannot be validated by any definition", value=data__readme, name="" + (name_prefix or "data") + ".readme", definition={'anyOf': [{'properties': {'file': {'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}}, 'required': ['file']}, {'properties': {'text': {'type': 'string', 'description': 'Full text describing the project.'}}, 'required': ['text']}]}, rule='anyOf')
+                    data__readme_is_dict = isinstance(data__readme, dict)
+                    if data__readme_is_dict:
+                        data__readme__missing_keys = set(['content-type']) - data__readme.keys()
+                        if data__readme__missing_keys:
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".readme must contain " + (str(sorted(data__readme__missing_keys)) + " properties"), value=data__readme, name="" + (name_prefix or "data") + ".readme", definition={'properties': {'content-type': {'type': 'string', '$$description': ['Content-type (:rfc:`1341`) of the full description', '(e.g. ``text/markdown``). The ``charset`` parameter is assumed', 'UTF-8 when not present.'], '$comment': 'TODO: add regex pattern or format?'}}, 'required': ['content-type']}, rule='required')
+                        data__readme_keys = set(data__readme.keys())
+                        if "content-type" in data__readme_keys:
+                            data__readme_keys.remove("content-type")
+                            data__readme__contenttype = data__readme["content-type"]
+                            if not isinstance(data__readme__contenttype, (str)):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".readme.content-type must be string", value=data__readme__contenttype, name="" + (name_prefix or "data") + ".readme.content-type", definition={'type': 'string', '$$description': ['Content-type (:rfc:`1341`) of the full description', '(e.g. ``text/markdown``). The ``charset`` parameter is assumed', 'UTF-8 when not present.'], '$comment': 'TODO: add regex pattern or format?'}, rule='type')
+                    data__readme_one_of_count12 += 1
+                except JsonSchemaValueException: pass
+            if data__readme_one_of_count12 != 1:
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".readme must be valid exactly by one definition" + (" (" + str(data__readme_one_of_count12) + " matches found)"), value=data__readme, name="" + (name_prefix or "data") + ".readme", definition={'$$description': ['`Full/detailed description of the project in the form of a README', '`_', "with meaning similar to the one defined in `core metadata's Description", '`_'], 'oneOf': [{'type': 'string', '$$description': ['Relative path to a text file (UTF-8) containing the full description', 'of the project. If the file path ends in case-insensitive ``.md`` or', '``.rst`` suffixes, then the content-type is respectively', '``text/markdown`` or ``text/x-rst``']}, {'type': 'object', 'allOf': [{'anyOf': [{'properties': {'file': {'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}}, 'required': ['file']}, {'properties': {'text': {'type': 'string', 'description': 'Full text describing the project.'}}, 'required': ['text']}]}, {'properties': {'content-type': {'type': 'string', '$$description': ['Content-type (:rfc:`1341`) of the full description', '(e.g. ``text/markdown``). The ``charset`` parameter is assumed', 'UTF-8 when not present.'], '$comment': 'TODO: add regex pattern or format?'}}, 'required': ['content-type']}]}]}, rule='oneOf')
+        if "requires-python" in data_keys:
+            data_keys.remove("requires-python")
+            data__requirespython = data["requires-python"]
+            if not isinstance(data__requirespython, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".requires-python must be string", value=data__requirespython, name="" + (name_prefix or "data") + ".requires-python", definition={'type': 'string', 'format': 'pep508-versionspec', '$$description': ['`The Python version requirements of the project', '`_.']}, rule='type')
+            if isinstance(data__requirespython, str):
+                if not custom_formats["pep508-versionspec"](data__requirespython):
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".requires-python must be pep508-versionspec", value=data__requirespython, name="" + (name_prefix or "data") + ".requires-python", definition={'type': 'string', 'format': 'pep508-versionspec', '$$description': ['`The Python version requirements of the project', '`_.']}, rule='format')
+        if "license" in data_keys:
+            data_keys.remove("license")
+            data__license = data["license"]
+            data__license_one_of_count14 = 0
+            if data__license_one_of_count14 < 2:
+                try:
+                    if not isinstance(data__license, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".license must be string", value=data__license, name="" + (name_prefix or "data") + ".license", definition={'type': 'string', 'description': 'An SPDX license identifier', 'format': 'SPDX'}, rule='type')
+                    if isinstance(data__license, str):
+                        if not custom_formats["SPDX"](data__license):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".license must be SPDX", value=data__license, name="" + (name_prefix or "data") + ".license", definition={'type': 'string', 'description': 'An SPDX license identifier', 'format': 'SPDX'}, rule='format')
+                    data__license_one_of_count14 += 1
+                except JsonSchemaValueException: pass
+            if data__license_one_of_count14 < 2:
+                try:
+                    if not isinstance(data__license, (dict)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".license must be object", value=data__license, name="" + (name_prefix or "data") + ".license", definition={'type': 'object', 'properties': {'file': {'type': 'string', '$$description': ['Relative path to the file (UTF-8) which contains the license for the', 'project.']}}, 'required': ['file']}, rule='type')
+                    data__license_is_dict = isinstance(data__license, dict)
+                    if data__license_is_dict:
+                        data__license__missing_keys = set(['file']) - data__license.keys()
+                        if data__license__missing_keys:
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".license must contain " + (str(sorted(data__license__missing_keys)) + " properties"), value=data__license, name="" + (name_prefix or "data") + ".license", definition={'type': 'object', 'properties': {'file': {'type': 'string', '$$description': ['Relative path to the file (UTF-8) which contains the license for the', 'project.']}}, 'required': ['file']}, rule='required')
+                        data__license_keys = set(data__license.keys())
+                        if "file" in data__license_keys:
+                            data__license_keys.remove("file")
+                            data__license__file = data__license["file"]
+                            if not isinstance(data__license__file, (str)):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".license.file must be string", value=data__license__file, name="" + (name_prefix or "data") + ".license.file", definition={'type': 'string', '$$description': ['Relative path to the file (UTF-8) which contains the license for the', 'project.']}, rule='type')
+                    data__license_one_of_count14 += 1
+                except JsonSchemaValueException: pass
+            if data__license_one_of_count14 < 2:
+                try:
+                    if not isinstance(data__license, (dict)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".license must be object", value=data__license, name="" + (name_prefix or "data") + ".license", definition={'type': 'object', 'properties': {'text': {'type': 'string', '$$description': ['The license of the project whose meaning is that of the', '`License field from the core metadata', '`_.']}}, 'required': ['text']}, rule='type')
+                    data__license_is_dict = isinstance(data__license, dict)
+                    if data__license_is_dict:
+                        data__license__missing_keys = set(['text']) - data__license.keys()
+                        if data__license__missing_keys:
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".license must contain " + (str(sorted(data__license__missing_keys)) + " properties"), value=data__license, name="" + (name_prefix or "data") + ".license", definition={'type': 'object', 'properties': {'text': {'type': 'string', '$$description': ['The license of the project whose meaning is that of the', '`License field from the core metadata', '`_.']}}, 'required': ['text']}, rule='required')
+                        data__license_keys = set(data__license.keys())
+                        if "text" in data__license_keys:
+                            data__license_keys.remove("text")
+                            data__license__text = data__license["text"]
+                            if not isinstance(data__license__text, (str)):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".license.text must be string", value=data__license__text, name="" + (name_prefix or "data") + ".license.text", definition={'type': 'string', '$$description': ['The license of the project whose meaning is that of the', '`License field from the core metadata', '`_.']}, rule='type')
+                    data__license_one_of_count14 += 1
+                except JsonSchemaValueException: pass
+            if data__license_one_of_count14 != 1:
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".license must be valid exactly by one definition" + (" (" + str(data__license_one_of_count14) + " matches found)"), value=data__license, name="" + (name_prefix or "data") + ".license", definition={'description': '`Project license `_.', 'oneOf': [{'type': 'string', 'description': 'An SPDX license identifier', 'format': 'SPDX'}, {'type': 'object', 'properties': {'file': {'type': 'string', '$$description': ['Relative path to the file (UTF-8) which contains the license for the', 'project.']}}, 'required': ['file']}, {'type': 'object', 'properties': {'text': {'type': 'string', '$$description': ['The license of the project whose meaning is that of the', '`License field from the core metadata', '`_.']}}, 'required': ['text']}]}, rule='oneOf')
+        if "license-files" in data_keys:
+            data_keys.remove("license-files")
+            data__licensefiles = data["license-files"]
+            if not isinstance(data__licensefiles, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".license-files must be array", value=data__licensefiles, name="" + (name_prefix or "data") + ".license-files", definition={'description': 'Paths or globs to paths of license files', 'type': 'array', 'items': {'type': 'string'}}, rule='type')
+            data__licensefiles_is_list = isinstance(data__licensefiles, (list, tuple))
+            if data__licensefiles_is_list:
+                data__licensefiles_len = len(data__licensefiles)
+                for data__licensefiles_x, data__licensefiles_item in enumerate(data__licensefiles):
+                    if not isinstance(data__licensefiles_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".license-files[{data__licensefiles_x}]".format(**locals()) + " must be string", value=data__licensefiles_item, name="" + (name_prefix or "data") + ".license-files[{data__licensefiles_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "authors" in data_keys:
+            data_keys.remove("authors")
+            data__authors = data["authors"]
+            if not isinstance(data__authors, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".authors must be array", value=data__authors, name="" + (name_prefix or "data") + ".authors", definition={'type': 'array', 'items': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, '$$description': ["The people or organizations considered to be the 'authors' of the project.", 'The exact meaning is open to interpretation (e.g. original or primary authors,', 'current maintainers, or owners of the package).']}, rule='type')
+            data__authors_is_list = isinstance(data__authors, (list, tuple))
+            if data__authors_is_list:
+                data__authors_len = len(data__authors)
+                for data__authors_x, data__authors_item in enumerate(data__authors):
+                    validate_https___packaging_python_org_en_latest_specifications_pyproject_toml___definitions_author(data__authors_item, custom_formats, (name_prefix or "data") + ".authors[{data__authors_x}]".format(**locals()))
+        if "maintainers" in data_keys:
+            data_keys.remove("maintainers")
+            data__maintainers = data["maintainers"]
+            if not isinstance(data__maintainers, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".maintainers must be array", value=data__maintainers, name="" + (name_prefix or "data") + ".maintainers", definition={'type': 'array', 'items': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, '$$description': ["The people or organizations considered to be the 'maintainers' of the project.", 'Similarly to ``authors``, the exact meaning is open to interpretation.']}, rule='type')
+            data__maintainers_is_list = isinstance(data__maintainers, (list, tuple))
+            if data__maintainers_is_list:
+                data__maintainers_len = len(data__maintainers)
+                for data__maintainers_x, data__maintainers_item in enumerate(data__maintainers):
+                    validate_https___packaging_python_org_en_latest_specifications_pyproject_toml___definitions_author(data__maintainers_item, custom_formats, (name_prefix or "data") + ".maintainers[{data__maintainers_x}]".format(**locals()))
+        if "keywords" in data_keys:
+            data_keys.remove("keywords")
+            data__keywords = data["keywords"]
+            if not isinstance(data__keywords, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".keywords must be array", value=data__keywords, name="" + (name_prefix or "data") + ".keywords", definition={'type': 'array', 'items': {'type': 'string'}, 'description': 'List of keywords to assist searching for the distribution in a larger catalog.'}, rule='type')
+            data__keywords_is_list = isinstance(data__keywords, (list, tuple))
+            if data__keywords_is_list:
+                data__keywords_len = len(data__keywords)
+                for data__keywords_x, data__keywords_item in enumerate(data__keywords):
+                    if not isinstance(data__keywords_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".keywords[{data__keywords_x}]".format(**locals()) + " must be string", value=data__keywords_item, name="" + (name_prefix or "data") + ".keywords[{data__keywords_x}]".format(**locals()) + "", definition={'type': 'string'}, rule='type')
+        if "classifiers" in data_keys:
+            data_keys.remove("classifiers")
+            data__classifiers = data["classifiers"]
+            if not isinstance(data__classifiers, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".classifiers must be array", value=data__classifiers, name="" + (name_prefix or "data") + ".classifiers", definition={'type': 'array', 'items': {'type': 'string', 'format': 'trove-classifier', 'description': '`PyPI classifier `_.'}, '$$description': ['`Trove classifiers `_', 'which apply to the project.']}, rule='type')
+            data__classifiers_is_list = isinstance(data__classifiers, (list, tuple))
+            if data__classifiers_is_list:
+                data__classifiers_len = len(data__classifiers)
+                for data__classifiers_x, data__classifiers_item in enumerate(data__classifiers):
+                    if not isinstance(data__classifiers_item, (str)):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".classifiers[{data__classifiers_x}]".format(**locals()) + " must be string", value=data__classifiers_item, name="" + (name_prefix or "data") + ".classifiers[{data__classifiers_x}]".format(**locals()) + "", definition={'type': 'string', 'format': 'trove-classifier', 'description': '`PyPI classifier `_.'}, rule='type')
+                    if isinstance(data__classifiers_item, str):
+                        if not custom_formats["trove-classifier"](data__classifiers_item):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".classifiers[{data__classifiers_x}]".format(**locals()) + " must be trove-classifier", value=data__classifiers_item, name="" + (name_prefix or "data") + ".classifiers[{data__classifiers_x}]".format(**locals()) + "", definition={'type': 'string', 'format': 'trove-classifier', 'description': '`PyPI classifier `_.'}, rule='format')
+        if "urls" in data_keys:
+            data_keys.remove("urls")
+            data__urls = data["urls"]
+            if not isinstance(data__urls, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".urls must be object", value=data__urls, name="" + (name_prefix or "data") + ".urls", definition={'type': 'object', 'description': 'URLs associated with the project in the form ``label => value``.', 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', 'format': 'url'}}}, rule='type')
+            data__urls_is_dict = isinstance(data__urls, dict)
+            if data__urls_is_dict:
+                data__urls_keys = set(data__urls.keys())
+                for data__urls_key, data__urls_val in data__urls.items():
+                    if REGEX_PATTERNS['^.+$'].search(data__urls_key):
+                        if data__urls_key in data__urls_keys:
+                            data__urls_keys.remove(data__urls_key)
+                        if not isinstance(data__urls_val, (str)):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".urls.{data__urls_key}".format(**locals()) + " must be string", value=data__urls_val, name="" + (name_prefix or "data") + ".urls.{data__urls_key}".format(**locals()) + "", definition={'type': 'string', 'format': 'url'}, rule='type')
+                        if isinstance(data__urls_val, str):
+                            if not custom_formats["url"](data__urls_val):
+                                raise JsonSchemaValueException("" + (name_prefix or "data") + ".urls.{data__urls_key}".format(**locals()) + " must be url", value=data__urls_val, name="" + (name_prefix or "data") + ".urls.{data__urls_key}".format(**locals()) + "", definition={'type': 'string', 'format': 'url'}, rule='format')
+                if data__urls_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".urls must not contain "+str(data__urls_keys)+" properties", value=data__urls, name="" + (name_prefix or "data") + ".urls", definition={'type': 'object', 'description': 'URLs associated with the project in the form ``label => value``.', 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', 'format': 'url'}}}, rule='additionalProperties')
+        if "scripts" in data_keys:
+            data_keys.remove("scripts")
+            data__scripts = data["scripts"]
+            validate_https___packaging_python_org_en_latest_specifications_pyproject_toml___definitions_entry_point_group(data__scripts, custom_formats, (name_prefix or "data") + ".scripts")
+        if "gui-scripts" in data_keys:
+            data_keys.remove("gui-scripts")
+            data__guiscripts = data["gui-scripts"]
+            validate_https___packaging_python_org_en_latest_specifications_pyproject_toml___definitions_entry_point_group(data__guiscripts, custom_formats, (name_prefix or "data") + ".gui-scripts")
+        if "entry-points" in data_keys:
+            data_keys.remove("entry-points")
+            data__entrypoints = data["entry-points"]
+            data__entrypoints_is_dict = isinstance(data__entrypoints, dict)
+            if data__entrypoints_is_dict:
+                data__entrypoints_keys = set(data__entrypoints.keys())
+                for data__entrypoints_key, data__entrypoints_val in data__entrypoints.items():
+                    if REGEX_PATTERNS['^.+$'].search(data__entrypoints_key):
+                        if data__entrypoints_key in data__entrypoints_keys:
+                            data__entrypoints_keys.remove(data__entrypoints_key)
+                        validate_https___packaging_python_org_en_latest_specifications_pyproject_toml___definitions_entry_point_group(data__entrypoints_val, custom_formats, (name_prefix or "data") + ".entry-points.{data__entrypoints_key}".format(**locals()))
+                if data__entrypoints_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".entry-points must not contain "+str(data__entrypoints_keys)+" properties", value=data__entrypoints, name="" + (name_prefix or "data") + ".entry-points", definition={'$$description': ['Instruct the installer to expose the given modules/functions via', '``entry-point`` discovery mechanism (useful for plugins).', 'More information available in the `Python packaging guide', '`_.'], 'propertyNames': {'format': 'python-entrypoint-group'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}}}, rule='additionalProperties')
+                data__entrypoints_len = len(data__entrypoints)
+                if data__entrypoints_len != 0:
+                    data__entrypoints_property_names = True
+                    for data__entrypoints_key in data__entrypoints:
+                        try:
+                            if isinstance(data__entrypoints_key, str):
+                                if not custom_formats["python-entrypoint-group"](data__entrypoints_key):
+                                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".entry-points must be python-entrypoint-group", value=data__entrypoints_key, name="" + (name_prefix or "data") + ".entry-points", definition={'format': 'python-entrypoint-group'}, rule='format')
+                        except JsonSchemaValueException:
+                            data__entrypoints_property_names = False
+                    if not data__entrypoints_property_names:
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".entry-points must be named by propertyName definition", value=data__entrypoints, name="" + (name_prefix or "data") + ".entry-points", definition={'$$description': ['Instruct the installer to expose the given modules/functions via', '``entry-point`` discovery mechanism (useful for plugins).', 'More information available in the `Python packaging guide', '`_.'], 'propertyNames': {'format': 'python-entrypoint-group'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}}}, rule='propertyNames')
+        if "dependencies" in data_keys:
+            data_keys.remove("dependencies")
+            data__dependencies = data["dependencies"]
+            if not isinstance(data__dependencies, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".dependencies must be array", value=data__dependencies, name="" + (name_prefix or "data") + ".dependencies", definition={'type': 'array', 'description': 'Project (mandatory) dependencies.', 'items': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}, rule='type')
+            data__dependencies_is_list = isinstance(data__dependencies, (list, tuple))
+            if data__dependencies_is_list:
+                data__dependencies_len = len(data__dependencies)
+                for data__dependencies_x, data__dependencies_item in enumerate(data__dependencies):
+                    validate_https___packaging_python_org_en_latest_specifications_pyproject_toml___definitions_dependency(data__dependencies_item, custom_formats, (name_prefix or "data") + ".dependencies[{data__dependencies_x}]".format(**locals()))
+        if "optional-dependencies" in data_keys:
+            data_keys.remove("optional-dependencies")
+            data__optionaldependencies = data["optional-dependencies"]
+            if not isinstance(data__optionaldependencies, (dict)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".optional-dependencies must be object", value=data__optionaldependencies, name="" + (name_prefix or "data") + ".optional-dependencies", definition={'type': 'object', 'description': 'Optional dependency for the project', 'propertyNames': {'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'array', 'items': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}}, rule='type')
+            data__optionaldependencies_is_dict = isinstance(data__optionaldependencies, dict)
+            if data__optionaldependencies_is_dict:
+                data__optionaldependencies_keys = set(data__optionaldependencies.keys())
+                for data__optionaldependencies_key, data__optionaldependencies_val in data__optionaldependencies.items():
+                    if REGEX_PATTERNS['^.+$'].search(data__optionaldependencies_key):
+                        if data__optionaldependencies_key in data__optionaldependencies_keys:
+                            data__optionaldependencies_keys.remove(data__optionaldependencies_key)
+                        if not isinstance(data__optionaldependencies_val, (list, tuple)):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + ".optional-dependencies.{data__optionaldependencies_key}".format(**locals()) + " must be array", value=data__optionaldependencies_val, name="" + (name_prefix or "data") + ".optional-dependencies.{data__optionaldependencies_key}".format(**locals()) + "", definition={'type': 'array', 'items': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}, rule='type')
+                        data__optionaldependencies_val_is_list = isinstance(data__optionaldependencies_val, (list, tuple))
+                        if data__optionaldependencies_val_is_list:
+                            data__optionaldependencies_val_len = len(data__optionaldependencies_val)
+                            for data__optionaldependencies_val_x, data__optionaldependencies_val_item in enumerate(data__optionaldependencies_val):
+                                validate_https___packaging_python_org_en_latest_specifications_pyproject_toml___definitions_dependency(data__optionaldependencies_val_item, custom_formats, (name_prefix or "data") + ".optional-dependencies.{data__optionaldependencies_key}[{data__optionaldependencies_val_x}]".format(**locals()))
+                if data__optionaldependencies_keys:
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".optional-dependencies must not contain "+str(data__optionaldependencies_keys)+" properties", value=data__optionaldependencies, name="" + (name_prefix or "data") + ".optional-dependencies", definition={'type': 'object', 'description': 'Optional dependency for the project', 'propertyNames': {'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'array', 'items': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}}, rule='additionalProperties')
+                data__optionaldependencies_len = len(data__optionaldependencies)
+                if data__optionaldependencies_len != 0:
+                    data__optionaldependencies_property_names = True
+                    for data__optionaldependencies_key in data__optionaldependencies:
+                        try:
+                            if isinstance(data__optionaldependencies_key, str):
+                                if not custom_formats["pep508-identifier"](data__optionaldependencies_key):
+                                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".optional-dependencies must be pep508-identifier", value=data__optionaldependencies_key, name="" + (name_prefix or "data") + ".optional-dependencies", definition={'format': 'pep508-identifier'}, rule='format')
+                        except JsonSchemaValueException:
+                            data__optionaldependencies_property_names = False
+                    if not data__optionaldependencies_property_names:
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".optional-dependencies must be named by propertyName definition", value=data__optionaldependencies, name="" + (name_prefix or "data") + ".optional-dependencies", definition={'type': 'object', 'description': 'Optional dependency for the project', 'propertyNames': {'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'array', 'items': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}}, rule='propertyNames')
+        if "dynamic" in data_keys:
+            data_keys.remove("dynamic")
+            data__dynamic = data["dynamic"]
+            if not isinstance(data__dynamic, (list, tuple)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic must be array", value=data__dynamic, name="" + (name_prefix or "data") + ".dynamic", definition={'type': 'array', '$$description': ['Specifies which fields are intentionally unspecified and expected to be', 'dynamically provided by build tools'], 'items': {'enum': ['version', 'description', 'readme', 'requires-python', 'license', 'license-files', 'authors', 'maintainers', 'keywords', 'classifiers', 'urls', 'scripts', 'gui-scripts', 'entry-points', 'dependencies', 'optional-dependencies']}}, rule='type')
+            data__dynamic_is_list = isinstance(data__dynamic, (list, tuple))
+            if data__dynamic_is_list:
+                data__dynamic_len = len(data__dynamic)
+                for data__dynamic_x, data__dynamic_item in enumerate(data__dynamic):
+                    if data__dynamic_item not in ['version', 'description', 'readme', 'requires-python', 'license', 'license-files', 'authors', 'maintainers', 'keywords', 'classifiers', 'urls', 'scripts', 'gui-scripts', 'entry-points', 'dependencies', 'optional-dependencies']:
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".dynamic[{data__dynamic_x}]".format(**locals()) + " must be one of ['version', 'description', 'readme', 'requires-python', 'license', 'license-files', 'authors', 'maintainers', 'keywords', 'classifiers', 'urls', 'scripts', 'gui-scripts', 'entry-points', 'dependencies', 'optional-dependencies']", value=data__dynamic_item, name="" + (name_prefix or "data") + ".dynamic[{data__dynamic_x}]".format(**locals()) + "", definition={'enum': ['version', 'description', 'readme', 'requires-python', 'license', 'license-files', 'authors', 'maintainers', 'keywords', 'classifiers', 'urls', 'scripts', 'gui-scripts', 'entry-points', 'dependencies', 'optional-dependencies']}, rule='enum')
+        if data_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must not contain "+str(data_keys)+" properties", value=data, name="" + (name_prefix or "data") + "", definition={'$schema': 'http://json-schema.org/draft-07/schema#', '$id': 'https://packaging.python.org/en/latest/specifications/pyproject-toml/', 'title': 'Package metadata stored in the ``project`` table', '$$description': ['Data structure for the **project** table inside ``pyproject.toml``', '(as initially defined in :pep:`621`)'], 'type': 'object', 'properties': {'name': {'type': 'string', 'description': 'The name (primary identifier) of the project. MUST be statically defined.', 'format': 'pep508-identifier'}, 'version': {'type': 'string', 'description': 'The version of the project as supported by :pep:`440`.', 'format': 'pep440'}, 'description': {'type': 'string', '$$description': ['The `summary description of the project', '`_']}, 'readme': {'$$description': ['`Full/detailed description of the project in the form of a README', '`_', "with meaning similar to the one defined in `core metadata's Description", '`_'], 'oneOf': [{'type': 'string', '$$description': ['Relative path to a text file (UTF-8) containing the full description', 'of the project. If the file path ends in case-insensitive ``.md`` or', '``.rst`` suffixes, then the content-type is respectively', '``text/markdown`` or ``text/x-rst``']}, {'type': 'object', 'allOf': [{'anyOf': [{'properties': {'file': {'type': 'string', '$$description': ['Relative path to a text file containing the full description', 'of the project.']}}, 'required': ['file']}, {'properties': {'text': {'type': 'string', 'description': 'Full text describing the project.'}}, 'required': ['text']}]}, {'properties': {'content-type': {'type': 'string', '$$description': ['Content-type (:rfc:`1341`) of the full description', '(e.g. ``text/markdown``). The ``charset`` parameter is assumed', 'UTF-8 when not present.'], '$comment': 'TODO: add regex pattern or format?'}}, 'required': ['content-type']}]}]}, 'requires-python': {'type': 'string', 'format': 'pep508-versionspec', '$$description': ['`The Python version requirements of the project', '`_.']}, 'license': {'description': '`Project license `_.', 'oneOf': [{'type': 'string', 'description': 'An SPDX license identifier', 'format': 'SPDX'}, {'type': 'object', 'properties': {'file': {'type': 'string', '$$description': ['Relative path to the file (UTF-8) which contains the license for the', 'project.']}}, 'required': ['file']}, {'type': 'object', 'properties': {'text': {'type': 'string', '$$description': ['The license of the project whose meaning is that of the', '`License field from the core metadata', '`_.']}}, 'required': ['text']}]}, 'license-files': {'description': 'Paths or globs to paths of license files', 'type': 'array', 'items': {'type': 'string'}}, 'authors': {'type': 'array', 'items': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, '$$description': ["The people or organizations considered to be the 'authors' of the project.", 'The exact meaning is open to interpretation (e.g. original or primary authors,', 'current maintainers, or owners of the package).']}, 'maintainers': {'type': 'array', 'items': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, '$$description': ["The people or organizations considered to be the 'maintainers' of the project.", 'Similarly to ``authors``, the exact meaning is open to interpretation.']}, 'keywords': {'type': 'array', 'items': {'type': 'string'}, 'description': 'List of keywords to assist searching for the distribution in a larger catalog.'}, 'classifiers': {'type': 'array', 'items': {'type': 'string', 'format': 'trove-classifier', 'description': '`PyPI classifier `_.'}, '$$description': ['`Trove classifiers `_', 'which apply to the project.']}, 'urls': {'type': 'object', 'description': 'URLs associated with the project in the form ``label => value``.', 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', 'format': 'url'}}}, 'scripts': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'gui-scripts': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'entry-points': {'$$description': ['Instruct the installer to expose the given modules/functions via', '``entry-point`` discovery mechanism (useful for plugins).', 'More information available in the `Python packaging guide', '`_.'], 'propertyNames': {'format': 'python-entrypoint-group'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}}}, 'dependencies': {'type': 'array', 'description': 'Project (mandatory) dependencies.', 'items': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}, 'optional-dependencies': {'type': 'object', 'description': 'Optional dependency for the project', 'propertyNames': {'format': 'pep508-identifier'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'array', 'items': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}}, 'dynamic': {'type': 'array', '$$description': ['Specifies which fields are intentionally unspecified and expected to be', 'dynamically provided by build tools'], 'items': {'enum': ['version', 'description', 'readme', 'requires-python', 'license', 'license-files', 'authors', 'maintainers', 'keywords', 'classifiers', 'urls', 'scripts', 'gui-scripts', 'entry-points', 'dependencies', 'optional-dependencies']}}}, 'required': ['name'], 'additionalProperties': False, 'allOf': [{'if': {'not': {'required': ['dynamic'], 'properties': {'dynamic': {'contains': {'const': 'version'}, '$$description': ['version is listed in ``dynamic``']}}}, '$$comment': ['According to :pep:`621`:', '    If the core metadata specification lists a field as "Required", then', '    the metadata MUST specify the field statically or list it in dynamic', 'In turn, `core metadata`_ defines:', '    The required fields are: Metadata-Version, Name, Version.', '    All the other fields are optional.', 'Since ``Metadata-Version`` is defined by the build back-end, ``name`` and', '``version`` are the only mandatory information in ``pyproject.toml``.', '.. _core metadata: https://packaging.python.org/specifications/core-metadata/']}, 'then': {'required': ['version'], '$$description': ['version should be statically defined in the ``version`` field']}}, {'if': {'required': ['license-files']}, 'then': {'properties': {'license': {'type': 'string'}}}}], 'definitions': {'author': {'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, 'entry-point-group': {'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, 'dependency': {'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}}}, rule='additionalProperties')
+    return data
+
+def validate_https___packaging_python_org_en_latest_specifications_pyproject_toml___definitions_dependency(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (str)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be string", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}, rule='type')
+    if isinstance(data, str):
+        if not custom_formats["pep508"](data):
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must be pep508", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/dependency', 'title': 'Dependency', 'type': 'string', 'description': 'Project dependency specification according to PEP 508', 'format': 'pep508'}, rule='format')
+    return data
+
+def validate_https___packaging_python_org_en_latest_specifications_pyproject_toml___definitions_entry_point_group(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (dict)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be object", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, rule='type')
+    data_is_dict = isinstance(data, dict)
+    if data_is_dict:
+        data_keys = set(data.keys())
+        for data_key, data_val in data.items():
+            if REGEX_PATTERNS['^.+$'].search(data_key):
+                if data_key in data_keys:
+                    data_keys.remove(data_key)
+                if not isinstance(data_val, (str)):
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".{data_key}".format(**locals()) + " must be string", value=data_val, name="" + (name_prefix or "data") + ".{data_key}".format(**locals()) + "", definition={'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}, rule='type')
+                if isinstance(data_val, str):
+                    if not custom_formats["python-entrypoint-reference"](data_val):
+                        raise JsonSchemaValueException("" + (name_prefix or "data") + ".{data_key}".format(**locals()) + " must be python-entrypoint-reference", value=data_val, name="" + (name_prefix or "data") + ".{data_key}".format(**locals()) + "", definition={'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}, rule='format')
+        if data_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must not contain "+str(data_keys)+" properties", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, rule='additionalProperties')
+        data_len = len(data)
+        if data_len != 0:
+            data_property_names = True
+            for data_key in data:
+                try:
+                    if isinstance(data_key, str):
+                        if not custom_formats["python-entrypoint-name"](data_key):
+                            raise JsonSchemaValueException("" + (name_prefix or "data") + " must be python-entrypoint-name", value=data_key, name="" + (name_prefix or "data") + "", definition={'format': 'python-entrypoint-name'}, rule='format')
+                except JsonSchemaValueException:
+                    data_property_names = False
+            if not data_property_names:
+                raise JsonSchemaValueException("" + (name_prefix or "data") + " must be named by propertyName definition", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/entry-point-group', 'title': 'Entry-points', 'type': 'object', '$$description': ['Entry-points are grouped together to indicate what sort of capabilities they', 'provide.', 'See the `packaging guides', '`_', 'and `setuptools docs', '`_', 'for more information.'], 'propertyNames': {'format': 'python-entrypoint-name'}, 'additionalProperties': False, 'patternProperties': {'^.+$': {'type': 'string', '$$description': ['Reference to a Python object. It is either in the form', '``importable.module``, or ``importable.module:object.attr``.'], 'format': 'python-entrypoint-reference', '$comment': 'https://packaging.python.org/specifications/entry-points/'}}}, rule='propertyNames')
+    return data
+
+def validate_https___packaging_python_org_en_latest_specifications_pyproject_toml___definitions_author(data, custom_formats={}, name_prefix=None):
+    if not isinstance(data, (dict)):
+        raise JsonSchemaValueException("" + (name_prefix or "data") + " must be object", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, rule='type')
+    data_is_dict = isinstance(data, dict)
+    if data_is_dict:
+        data_keys = set(data.keys())
+        if "name" in data_keys:
+            data_keys.remove("name")
+            data__name = data["name"]
+            if not isinstance(data__name, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".name must be string", value=data__name, name="" + (name_prefix or "data") + ".name", definition={'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, rule='type')
+        if "email" in data_keys:
+            data_keys.remove("email")
+            data__email = data["email"]
+            if not isinstance(data__email, (str)):
+                raise JsonSchemaValueException("" + (name_prefix or "data") + ".email must be string", value=data__email, name="" + (name_prefix or "data") + ".email", definition={'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}, rule='type')
+            if isinstance(data__email, str):
+                if not REGEX_PATTERNS["idn-email_re_pattern"].match(data__email):
+                    raise JsonSchemaValueException("" + (name_prefix or "data") + ".email must be idn-email", value=data__email, name="" + (name_prefix or "data") + ".email", definition={'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}, rule='format')
+        if data_keys:
+            raise JsonSchemaValueException("" + (name_prefix or "data") + " must not contain "+str(data_keys)+" properties", value=data, name="" + (name_prefix or "data") + "", definition={'$id': '#/definitions/author', 'title': 'Author or Maintainer', '$comment': 'https://peps.python.org/pep-0621/#authors-maintainers', 'type': 'object', 'additionalProperties': False, 'properties': {'name': {'type': 'string', '$$description': ['MUST be a valid email name, i.e. whatever can be put as a name, before an', 'email, in :rfc:`822`.']}, 'email': {'type': 'string', 'format': 'idn-email', 'description': 'MUST be a valid email address'}}}, rule='additionalProperties')
+    return data
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/formats.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/formats.py
new file mode 100644
index 0000000000000000000000000000000000000000..1cf4a465ef0156deef5bd4d1fc02350e40ff2fe5
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/_validate_pyproject/formats.py
@@ -0,0 +1,402 @@
+"""
+The functions in this module are used to validate schemas with the
+`format JSON Schema keyword
+`_.
+
+The correspondence is given by replacing the ``_`` character in the name of the
+function with a ``-`` to obtain the format name and vice versa.
+"""
+
+import builtins
+import logging
+import os
+import re
+import string
+import typing
+from itertools import chain as _chain
+
+if typing.TYPE_CHECKING:
+    from typing_extensions import Literal
+
+_logger = logging.getLogger(__name__)
+
+# -------------------------------------------------------------------------------------
+# PEP 440
+
+VERSION_PATTERN = r"""
+    v?
+    (?:
+        (?:(?P[0-9]+)!)?                           # epoch
+        (?P[0-9]+(?:\.[0-9]+)*)                  # release segment
+        (?P
                                          # pre-release
+            [-_\.]?
+            (?Palpha|a|beta|b|preview|pre|c|rc)
+            [-_\.]?
+            (?P[0-9]+)?
+        )?
+        (?P                                         # post release
+            (?:-(?P[0-9]+))
+            |
+            (?:
+                [-_\.]?
+                (?Ppost|rev|r)
+                [-_\.]?
+                (?P[0-9]+)?
+            )
+        )?
+        (?P                                          # dev release
+            [-_\.]?
+            (?Pdev)
+            [-_\.]?
+            (?P[0-9]+)?
+        )?
+    )
+    (?:\+(?P[a-z0-9]+(?:[-_\.][a-z0-9]+)*))?       # local version
+"""
+
+VERSION_REGEX = re.compile(r"^\s*" + VERSION_PATTERN + r"\s*$", re.X | re.I)
+
+
+def pep440(version: str) -> bool:
+    """See :ref:`PyPA's version specification `
+    (initially introduced in :pep:`440`).
+    """
+    return VERSION_REGEX.match(version) is not None
+
+
+# -------------------------------------------------------------------------------------
+# PEP 508
+
+PEP508_IDENTIFIER_PATTERN = r"([A-Z0-9]|[A-Z0-9][A-Z0-9._-]*[A-Z0-9])"
+PEP508_IDENTIFIER_REGEX = re.compile(f"^{PEP508_IDENTIFIER_PATTERN}$", re.I)
+
+
+def pep508_identifier(name: str) -> bool:
+    """See :ref:`PyPA's name specification `
+    (initially introduced in :pep:`508#names`).
+    """
+    return PEP508_IDENTIFIER_REGEX.match(name) is not None
+
+
+try:
+    try:
+        from packaging import requirements as _req
+    except ImportError:  # pragma: no cover
+        # let's try setuptools vendored version
+        from setuptools._vendor.packaging import (  # type: ignore[no-redef]
+            requirements as _req,
+        )
+
+    def pep508(value: str) -> bool:
+        """See :ref:`PyPA's dependency specifiers `
+        (initially introduced in :pep:`508`).
+        """
+        try:
+            _req.Requirement(value)
+            return True
+        except _req.InvalidRequirement:
+            return False
+
+except ImportError:  # pragma: no cover
+    _logger.warning(
+        "Could not find an installation of `packaging`. Requirements, dependencies and "
+        "versions might not be validated. "
+        "To enforce validation, please install `packaging`."
+    )
+
+    def pep508(value: str) -> bool:
+        return True
+
+
+def pep508_versionspec(value: str) -> bool:
+    """Expression that can be used to specify/lock versions (including ranges)
+    See ``versionspec`` in :ref:`PyPA's dependency specifiers
+    ` (initially introduced in :pep:`508`).
+    """
+    if any(c in value for c in (";", "]", "@")):
+        # In PEP 508:
+        # conditional markers, extras and URL specs are not included in the
+        # versionspec
+        return False
+    # Let's pretend we have a dependency called `requirement` with the given
+    # version spec, then we can reuse the pep508 function for validation:
+    return pep508(f"requirement{value}")
+
+
+# -------------------------------------------------------------------------------------
+# PEP 517
+
+
+def pep517_backend_reference(value: str) -> bool:
+    """See PyPA's specification for defining build-backend references
+    introduced in :pep:`517#source-trees`.
+
+    This is similar to an entry-point reference (e.g., ``package.module:object``).
+    """
+    module, _, obj = value.partition(":")
+    identifiers = (i.strip() for i in _chain(module.split("."), obj.split(".")))
+    return all(python_identifier(i) for i in identifiers if i)
+
+
+# -------------------------------------------------------------------------------------
+# Classifiers - PEP 301
+
+
+def _download_classifiers() -> str:
+    import ssl
+    from email.message import Message
+    from urllib.request import urlopen
+
+    url = "https://pypi.org/pypi?:action=list_classifiers"
+    context = ssl.create_default_context()
+    with urlopen(url, context=context) as response:  # noqa: S310 (audit URLs)
+        headers = Message()
+        headers["content_type"] = response.getheader("content-type", "text/plain")
+        return response.read().decode(headers.get_param("charset", "utf-8"))  # type: ignore[no-any-return]
+
+
+class _TroveClassifier:
+    """The ``trove_classifiers`` package is the official way of validating classifiers,
+    however this package might not be always available.
+    As a workaround we can still download a list from PyPI.
+    We also don't want to be over strict about it, so simply skipping silently is an
+    option (classifiers will be validated anyway during the upload to PyPI).
+    """
+
+    downloaded: typing.Union[None, "Literal[False]", typing.Set[str]]
+    """
+    None => not cached yet
+    False => unavailable
+    set => cached values
+    """
+
+    def __init__(self) -> None:
+        self.downloaded = None
+        self._skip_download = False
+        self.__name__ = "trove_classifier"  # Emulate a public function
+
+    def _disable_download(self) -> None:
+        # This is a private API. Only setuptools has the consent of using it.
+        self._skip_download = True
+
+    def __call__(self, value: str) -> bool:
+        if self.downloaded is False or self._skip_download is True:
+            return True
+
+        if os.getenv("NO_NETWORK") or os.getenv("VALIDATE_PYPROJECT_NO_NETWORK"):
+            self.downloaded = False
+            msg = (
+                "Install ``trove-classifiers`` to ensure proper validation. "
+                "Skipping download of classifiers list from PyPI (NO_NETWORK)."
+            )
+            _logger.debug(msg)
+            return True
+
+        if self.downloaded is None:
+            msg = (
+                "Install ``trove-classifiers`` to ensure proper validation. "
+                "Meanwhile a list of classifiers will be downloaded from PyPI."
+            )
+            _logger.debug(msg)
+            try:
+                self.downloaded = set(_download_classifiers().splitlines())
+            except Exception:
+                self.downloaded = False
+                _logger.debug("Problem with download, skipping validation")
+                return True
+
+        return value in self.downloaded or value.lower().startswith("private ::")
+
+
+try:
+    from trove_classifiers import classifiers as _trove_classifiers
+
+    def trove_classifier(value: str) -> bool:
+        """See https://pypi.org/classifiers/"""
+        return value in _trove_classifiers or value.lower().startswith("private ::")
+
+except ImportError:  # pragma: no cover
+    trove_classifier = _TroveClassifier()
+
+
+# -------------------------------------------------------------------------------------
+# Stub packages - PEP 561
+
+
+def pep561_stub_name(value: str) -> bool:
+    """Name of a directory containing type stubs.
+    It must follow the name scheme ``-stubs`` as defined in
+    :pep:`561#stub-only-packages`.
+    """
+    top, *children = value.split(".")
+    if not top.endswith("-stubs"):
+        return False
+    return python_module_name(".".join([top[: -len("-stubs")], *children]))
+
+
+# -------------------------------------------------------------------------------------
+# Non-PEP related
+
+
+def url(value: str) -> bool:
+    """Valid URL (validation uses :obj:`urllib.parse`).
+    For maximum compatibility please make sure to include a ``scheme`` prefix
+    in your URL (e.g. ``http://``).
+    """
+    from urllib.parse import urlparse
+
+    try:
+        parts = urlparse(value)
+        if not parts.scheme:
+            _logger.warning(
+                "For maximum compatibility please make sure to include a "
+                "`scheme` prefix in your URL (e.g. 'http://'). "
+                f"Given value: {value}"
+            )
+            if not (value.startswith("/") or value.startswith("\\") or "@" in value):
+                parts = urlparse(f"http://{value}")
+
+        return bool(parts.scheme and parts.netloc)
+    except Exception:
+        return False
+
+
+# https://packaging.python.org/specifications/entry-points/
+ENTRYPOINT_PATTERN = r"[^\[\s=]([^=]*[^\s=])?"
+ENTRYPOINT_REGEX = re.compile(f"^{ENTRYPOINT_PATTERN}$", re.I)
+RECOMMEDED_ENTRYPOINT_PATTERN = r"[\w.-]+"
+RECOMMEDED_ENTRYPOINT_REGEX = re.compile(f"^{RECOMMEDED_ENTRYPOINT_PATTERN}$", re.I)
+ENTRYPOINT_GROUP_PATTERN = r"\w+(\.\w+)*"
+ENTRYPOINT_GROUP_REGEX = re.compile(f"^{ENTRYPOINT_GROUP_PATTERN}$", re.I)
+
+
+def python_identifier(value: str) -> bool:
+    """Can be used as identifier in Python.
+    (Validation uses :obj:`str.isidentifier`).
+    """
+    return value.isidentifier()
+
+
+def python_qualified_identifier(value: str) -> bool:
+    """
+    Python "dotted identifier", i.e. a sequence of :obj:`python_identifier`
+    concatenated with ``"."`` (e.g.: ``package.module.submodule``).
+    """
+    if value.startswith(".") or value.endswith("."):
+        return False
+    return all(python_identifier(m) for m in value.split("."))
+
+
+def python_module_name(value: str) -> bool:
+    """Module name that can be used in an ``import``-statement in Python.
+    See :obj:`python_qualified_identifier`.
+    """
+    return python_qualified_identifier(value)
+
+
+def python_module_name_relaxed(value: str) -> bool:
+    """Similar to :obj:`python_module_name`, but relaxed to also accept
+    dash characters (``-``) and cover special cases like ``pip-run``.
+
+    It is recommended, however, that beginners avoid dash characters,
+    as they require advanced knowledge about Python internals.
+
+    The following are disallowed:
+
+    * names starting/ending in dashes,
+    * names ending in ``-stubs`` (potentially collide with :obj:`pep561_stub_name`).
+    """
+    if value.startswith("-") or value.endswith("-"):
+        return False
+    if value.endswith("-stubs"):
+        return False  # Avoid collision with PEP 561
+    return python_module_name(value.replace("-", "_"))
+
+
+def python_entrypoint_group(value: str) -> bool:
+    """See ``Data model > group`` in the :ref:`PyPA's entry-points specification
+    `.
+    """
+    return ENTRYPOINT_GROUP_REGEX.match(value) is not None
+
+
+def python_entrypoint_name(value: str) -> bool:
+    """See ``Data model > name`` in the :ref:`PyPA's entry-points specification
+    `.
+    """
+    if not ENTRYPOINT_REGEX.match(value):
+        return False
+    if not RECOMMEDED_ENTRYPOINT_REGEX.match(value):
+        msg = f"Entry point `{value}` does not follow recommended pattern: "
+        msg += RECOMMEDED_ENTRYPOINT_PATTERN
+        _logger.warning(msg)
+    return True
+
+
+def python_entrypoint_reference(value: str) -> bool:
+    """Reference to a Python object using in the format::
+
+        importable.module:object.attr
+
+    See ``Data model >object reference`` in the :ref:`PyPA's entry-points specification
+    `.
+    """
+    module, _, rest = value.partition(":")
+    if "[" in rest:
+        obj, _, extras_ = rest.partition("[")
+        if extras_.strip()[-1] != "]":
+            return False
+        extras = (x.strip() for x in extras_.strip(string.whitespace + "[]").split(","))
+        if not all(pep508_identifier(e) for e in extras):
+            return False
+        _logger.warning(f"`{value}` - using extras for entry points is not recommended")
+    else:
+        obj = rest
+
+    module_parts = module.split(".")
+    identifiers = _chain(module_parts, obj.split(".")) if rest else iter(module_parts)
+    return all(python_identifier(i.strip()) for i in identifiers)
+
+
+def uint8(value: builtins.int) -> bool:
+    r"""Unsigned 8-bit integer (:math:`0 \leq x < 2^8`)"""
+    return 0 <= value < 2**8
+
+
+def uint16(value: builtins.int) -> bool:
+    r"""Unsigned 16-bit integer (:math:`0 \leq x < 2^{16}`)"""
+    return 0 <= value < 2**16
+
+
+def uint(value: builtins.int) -> bool:
+    r"""Unsigned 64-bit integer (:math:`0 \leq x < 2^{64}`)"""
+    return 0 <= value < 2**64
+
+
+def int(value: builtins.int) -> bool:
+    r"""Signed 64-bit integer (:math:`-2^{63} \leq x < 2^{63}`)"""
+    return -(2**63) <= value < 2**63
+
+
+try:
+    from packaging import licenses as _licenses
+
+    def SPDX(value: str) -> bool:
+        """See :ref:`PyPA's License-Expression specification
+        ` (added in :pep:`639`).
+        """
+        try:
+            _licenses.canonicalize_license_expression(value)
+            return True
+        except _licenses.InvalidLicenseExpression:
+            return False
+
+except ImportError:  # pragma: no cover
+    _logger.warning(
+        "Could not find an up-to-date installation of `packaging`. "
+        "License expressions might not be validated. "
+        "To enforce validation, please install `packaging>=24.2`."
+    )
+
+    def SPDX(value: str) -> bool:
+        return True
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/distutils.schema.json b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/distutils.schema.json
new file mode 100644
index 0000000000000000000000000000000000000000..93cd2e868acdaf41bf8b1f77026e84c02a5af3f8
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/distutils.schema.json
@@ -0,0 +1,26 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+
+  "$id": "https://setuptools.pypa.io/en/latest/deprecated/distutils/configfile.html",
+  "title": "``tool.distutils`` table",
+  "$$description": [
+    "**EXPERIMENTAL** (NOT OFFICIALLY SUPPORTED): Use ``tool.distutils``",
+    "subtables to configure arguments for ``distutils`` commands.",
+    "Originally, ``distutils`` allowed developers to configure arguments for",
+    "``setup.py`` commands via `distutils configuration files",
+    "`_.",
+    "See also `the old Python docs _`."
+  ],
+
+  "type": "object",
+  "properties": {
+    "global": {
+      "type": "object",
+      "description": "Global options applied to all ``distutils`` commands"
+    }
+  },
+  "patternProperties": {
+    ".+": {"type": "object"}
+  },
+  "$comment": "TODO: Is there a practical way of making this schema more specific?"
+}
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/expand.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/expand.py
new file mode 100644
index 0000000000000000000000000000000000000000..d9a2ded430eb2720d2dac0da125105befe9e222e
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/expand.py
@@ -0,0 +1,452 @@
+"""Utility functions to expand configuration directives or special values
+(such glob patterns).
+
+We can split the process of interpreting configuration files into 2 steps:
+
+1. The parsing the file contents from strings to value objects
+   that can be understand by Python (for example a string with a comma
+   separated list of keywords into an actual Python list of strings).
+
+2. The expansion (or post-processing) of these values according to the
+   semantics ``setuptools`` assign to them (for example a configuration field
+   with the ``file:`` directive should be expanded from a list of file paths to
+   a single string with the contents of those files concatenated)
+
+This module focus on the second step, and therefore allow sharing the expansion
+functions among several configuration file formats.
+
+**PRIVATE MODULE**: API reserved for setuptools internal usage only.
+"""
+
+from __future__ import annotations
+
+import ast
+import importlib
+import os
+import pathlib
+import sys
+from collections.abc import Iterable, Iterator, Mapping
+from configparser import ConfigParser
+from glob import iglob
+from importlib.machinery import ModuleSpec, all_suffixes
+from itertools import chain
+from pathlib import Path
+from types import ModuleType, TracebackType
+from typing import TYPE_CHECKING, Any, Callable, TypeVar
+
+from .. import _static
+from .._path import StrPath, same_path as _same_path
+from ..discovery import find_package_path
+from ..warnings import SetuptoolsWarning
+
+from distutils.errors import DistutilsOptionError
+
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
+    from setuptools.dist import Distribution
+
+_K = TypeVar("_K")
+_V_co = TypeVar("_V_co", covariant=True)
+
+
+class StaticModule:
+    """Proxy to a module object that avoids executing arbitrary code."""
+
+    def __init__(self, name: str, spec: ModuleSpec) -> None:
+        module = ast.parse(pathlib.Path(spec.origin).read_bytes())  # type: ignore[arg-type] # Let it raise an error on None
+        vars(self).update(locals())
+        del self.self
+
+    def _find_assignments(self) -> Iterator[tuple[ast.AST, ast.AST]]:
+        for statement in self.module.body:
+            if isinstance(statement, ast.Assign):
+                yield from ((target, statement.value) for target in statement.targets)
+            elif isinstance(statement, ast.AnnAssign) and statement.value:
+                yield (statement.target, statement.value)
+
+    def __getattr__(self, attr: str) -> Any:
+        """Attempt to load an attribute "statically", via :func:`ast.literal_eval`."""
+        try:
+            return next(
+                ast.literal_eval(value)
+                for target, value in self._find_assignments()
+                if isinstance(target, ast.Name) and target.id == attr
+            )
+        except Exception as e:
+            raise AttributeError(f"{self.name} has no attribute {attr}") from e
+
+
+def glob_relative(
+    patterns: Iterable[str], root_dir: StrPath | None = None
+) -> list[str]:
+    """Expand the list of glob patterns, but preserving relative paths.
+
+    :param list[str] patterns: List of glob patterns
+    :param str root_dir: Path to which globs should be relative
+                         (current directory by default)
+    :rtype: list
+    """
+    glob_characters = {'*', '?', '[', ']', '{', '}'}
+    expanded_values = []
+    root_dir = root_dir or os.getcwd()
+    for value in patterns:
+        # Has globby characters?
+        if any(char in value for char in glob_characters):
+            # then expand the glob pattern while keeping paths *relative*:
+            glob_path = os.path.abspath(os.path.join(root_dir, value))
+            expanded_values.extend(
+                sorted(
+                    os.path.relpath(path, root_dir).replace(os.sep, "/")
+                    for path in iglob(glob_path, recursive=True)
+                )
+            )
+
+        else:
+            # take the value as-is
+            path = os.path.relpath(value, root_dir).replace(os.sep, "/")
+            expanded_values.append(path)
+
+    return expanded_values
+
+
+def read_files(
+    filepaths: StrPath | Iterable[StrPath], root_dir: StrPath | None = None
+) -> str:
+    """Return the content of the files concatenated using ``\n`` as str
+
+    This function is sandboxed and won't reach anything outside ``root_dir``
+
+    (By default ``root_dir`` is the current directory).
+    """
+    from more_itertools import always_iterable
+
+    root_dir = os.path.abspath(root_dir or os.getcwd())
+    _filepaths = (os.path.join(root_dir, path) for path in always_iterable(filepaths))
+    return '\n'.join(
+        _read_file(path)
+        for path in _filter_existing_files(_filepaths)
+        if _assert_local(path, root_dir)
+    )
+
+
+def _filter_existing_files(filepaths: Iterable[StrPath]) -> Iterator[StrPath]:
+    for path in filepaths:
+        if os.path.isfile(path):
+            yield path
+        else:
+            SetuptoolsWarning.emit(f"File {path!r} cannot be found")
+
+
+def _read_file(filepath: bytes | StrPath) -> str:
+    with open(filepath, encoding='utf-8') as f:
+        return f.read()
+
+
+def _assert_local(filepath: StrPath, root_dir: str):
+    if Path(os.path.abspath(root_dir)) not in Path(os.path.abspath(filepath)).parents:
+        msg = f"Cannot access {filepath!r} (or anything outside {root_dir!r})"
+        raise DistutilsOptionError(msg)
+
+    return True
+
+
+def read_attr(
+    attr_desc: str,
+    package_dir: Mapping[str, str] | None = None,
+    root_dir: StrPath | None = None,
+) -> Any:
+    """Reads the value of an attribute from a module.
+
+    This function will try to read the attributed statically first
+    (via :func:`ast.literal_eval`), and only evaluate the module if it fails.
+
+    Examples:
+        read_attr("package.attr")
+        read_attr("package.module.attr")
+
+    :param str attr_desc: Dot-separated string describing how to reach the
+        attribute (see examples above)
+    :param dict[str, str] package_dir: Mapping of package names to their
+        location in disk (represented by paths relative to ``root_dir``).
+    :param str root_dir: Path to directory containing all the packages in
+        ``package_dir`` (current directory by default).
+    :rtype: str
+    """
+    root_dir = root_dir or os.getcwd()
+    attrs_path = attr_desc.strip().split('.')
+    attr_name = attrs_path.pop()
+    module_name = '.'.join(attrs_path)
+    module_name = module_name or '__init__'
+    path = _find_module(module_name, package_dir, root_dir)
+    spec = _find_spec(module_name, path)
+
+    try:
+        value = getattr(StaticModule(module_name, spec), attr_name)
+        # XXX: Is marking as static contents coming from modules too optimistic?
+        return _static.attempt_conversion(value)
+    except Exception:
+        # fallback to evaluate module
+        module = _load_spec(spec, module_name)
+        return getattr(module, attr_name)
+
+
+def _find_spec(module_name: str, module_path: StrPath | None) -> ModuleSpec:
+    spec = importlib.util.spec_from_file_location(module_name, module_path)
+    spec = spec or importlib.util.find_spec(module_name)
+
+    if spec is None:
+        raise ModuleNotFoundError(module_name)
+
+    return spec
+
+
+def _load_spec(spec: ModuleSpec, module_name: str) -> ModuleType:
+    name = getattr(spec, "__name__", module_name)
+    if name in sys.modules:
+        return sys.modules[name]
+    module = importlib.util.module_from_spec(spec)
+    sys.modules[name] = module  # cache (it also ensures `==` works on loaded items)
+    assert spec.loader is not None
+    spec.loader.exec_module(module)
+    return module
+
+
+def _find_module(
+    module_name: str, package_dir: Mapping[str, str] | None, root_dir: StrPath
+) -> str | None:
+    """Find the path to the module named ``module_name``,
+    considering the ``package_dir`` in the build configuration and ``root_dir``.
+
+    >>> tmp = getfixture('tmpdir')
+    >>> _ = tmp.ensure("a/b/c.py")
+    >>> _ = tmp.ensure("a/b/d/__init__.py")
+    >>> r = lambda x: x.replace(str(tmp), "tmp").replace(os.sep, "/")
+    >>> r(_find_module("a.b.c", None, tmp))
+    'tmp/a/b/c.py'
+    >>> r(_find_module("f.g.h", {"": "1", "f": "2", "f.g": "3", "f.g.h": "a/b/d"}, tmp))
+    'tmp/a/b/d/__init__.py'
+    """
+    path_start = find_package_path(module_name, package_dir or {}, root_dir)
+    candidates = chain.from_iterable(
+        (f"{path_start}{ext}", os.path.join(path_start, f"__init__{ext}"))
+        for ext in all_suffixes()
+    )
+    return next((x for x in candidates if os.path.isfile(x)), None)
+
+
+def resolve_class(
+    qualified_class_name: str,
+    package_dir: Mapping[str, str] | None = None,
+    root_dir: StrPath | None = None,
+) -> Callable:
+    """Given a qualified class name, return the associated class object"""
+    root_dir = root_dir or os.getcwd()
+    idx = qualified_class_name.rfind('.')
+    class_name = qualified_class_name[idx + 1 :]
+    pkg_name = qualified_class_name[:idx]
+
+    path = _find_module(pkg_name, package_dir, root_dir)
+    module = _load_spec(_find_spec(pkg_name, path), pkg_name)
+    return getattr(module, class_name)
+
+
+def cmdclass(
+    values: dict[str, str],
+    package_dir: Mapping[str, str] | None = None,
+    root_dir: StrPath | None = None,
+) -> dict[str, Callable]:
+    """Given a dictionary mapping command names to strings for qualified class
+    names, apply :func:`resolve_class` to the dict values.
+    """
+    return {k: resolve_class(v, package_dir, root_dir) for k, v in values.items()}
+
+
+def find_packages(
+    *,
+    namespaces=True,
+    fill_package_dir: dict[str, str] | None = None,
+    root_dir: StrPath | None = None,
+    **kwargs,
+) -> list[str]:
+    """Works similarly to :func:`setuptools.find_packages`, but with all
+    arguments given as keyword arguments. Moreover, ``where`` can be given
+    as a list (the results will be simply concatenated).
+
+    When the additional keyword argument ``namespaces`` is ``True``, it will
+    behave like :func:`setuptools.find_namespace_packages`` (i.e. include
+    implicit namespaces as per :pep:`420`).
+
+    The ``where`` argument will be considered relative to ``root_dir`` (or the current
+    working directory when ``root_dir`` is not given).
+
+    If the ``fill_package_dir`` argument is passed, this function will consider it as a
+    similar data structure to the ``package_dir`` configuration parameter add fill-in
+    any missing package location.
+
+    :rtype: list
+    """
+    from more_itertools import always_iterable, unique_everseen
+
+    from setuptools.discovery import construct_package_dir
+
+    # check "not namespaces" first due to python/mypy#6232
+    if not namespaces:
+        from setuptools.discovery import PackageFinder
+    else:
+        from setuptools.discovery import PEP420PackageFinder as PackageFinder
+
+    root_dir = root_dir or os.curdir
+    where = kwargs.pop('where', ['.'])
+    packages: list[str] = []
+    fill_package_dir = {} if fill_package_dir is None else fill_package_dir
+    search = list(unique_everseen(always_iterable(where)))
+
+    if len(search) == 1 and all(not _same_path(search[0], x) for x in (".", root_dir)):
+        fill_package_dir.setdefault("", search[0])
+
+    for path in search:
+        package_path = _nest_path(root_dir, path)
+        pkgs = PackageFinder.find(package_path, **kwargs)
+        packages.extend(pkgs)
+        if pkgs and not (
+            fill_package_dir.get("") == path or os.path.samefile(package_path, root_dir)
+        ):
+            fill_package_dir.update(construct_package_dir(pkgs, path))
+
+    return packages
+
+
+def _nest_path(parent: StrPath, path: StrPath) -> str:
+    path = parent if path in {".", ""} else os.path.join(parent, path)
+    return os.path.normpath(path)
+
+
+def version(value: Callable | Iterable[str | int] | str) -> str:
+    """When getting the version directly from an attribute,
+    it should be normalised to string.
+    """
+    _value = value() if callable(value) else value
+
+    if isinstance(_value, str):
+        return _value
+    if hasattr(_value, '__iter__'):
+        return '.'.join(map(str, _value))
+    return f'{_value}'
+
+
+def canonic_package_data(package_data: dict) -> dict:
+    if "*" in package_data:
+        package_data[""] = package_data.pop("*")
+    return package_data
+
+
+def canonic_data_files(
+    data_files: list | dict, root_dir: StrPath | None = None
+) -> list[tuple[str, list[str]]]:
+    """For compatibility with ``setup.py``, ``data_files`` should be a list
+    of pairs instead of a dict.
+
+    This function also expands glob patterns.
+    """
+    if isinstance(data_files, list):
+        return data_files
+
+    return [
+        (dest, glob_relative(patterns, root_dir))
+        for dest, patterns in data_files.items()
+    ]
+
+
+def entry_points(
+    text: str, text_source: str = "entry-points"
+) -> dict[str, dict[str, str]]:
+    """Given the contents of entry-points file,
+    process it into a 2-level dictionary (``dict[str, dict[str, str]]``).
+    The first level keys are entry-point groups, the second level keys are
+    entry-point names, and the second level values are references to objects
+    (that correspond to the entry-point value).
+    """
+    # Using undocumented behaviour, see python/typeshed#12700
+    parser = ConfigParser(default_section=None, delimiters=("=",))  # type: ignore[call-overload]
+    parser.optionxform = str  # case sensitive
+    parser.read_string(text, text_source)
+    groups = {k: dict(v.items()) for k, v in parser.items()}
+    groups.pop(parser.default_section, None)
+    return groups
+
+
+class EnsurePackagesDiscovered:
+    """Some expand functions require all the packages to already be discovered before
+    they run, e.g. :func:`read_attr`, :func:`resolve_class`, :func:`cmdclass`.
+
+    Therefore in some cases we will need to run autodiscovery during the evaluation of
+    the configuration. However, it is better to postpone calling package discovery as
+    much as possible, because some parameters can influence it (e.g. ``package_dir``),
+    and those might not have been processed yet.
+    """
+
+    def __init__(self, distribution: Distribution) -> None:
+        self._dist = distribution
+        self._called = False
+
+    def __call__(self) -> None:
+        """Trigger the automatic package discovery, if it is still necessary."""
+        if not self._called:
+            self._called = True
+            self._dist.set_defaults(name=False)  # Skip name, we can still be parsing
+
+    def __enter__(self) -> Self:
+        return self
+
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_value: BaseException | None,
+        traceback: TracebackType | None,
+    ) -> None:
+        if self._called:
+            self._dist.set_defaults.analyse_name()  # Now we can set a default name
+
+    def _get_package_dir(self) -> Mapping[str, str]:
+        self()
+        pkg_dir = self._dist.package_dir
+        return {} if pkg_dir is None else pkg_dir
+
+    @property
+    def package_dir(self) -> Mapping[str, str]:
+        """Proxy to ``package_dir`` that may trigger auto-discovery when used."""
+        return LazyMappingProxy(self._get_package_dir)
+
+
+class LazyMappingProxy(Mapping[_K, _V_co]):
+    """Mapping proxy that delays resolving the target object, until really needed.
+
+    >>> def obtain_mapping():
+    ...     print("Running expensive function!")
+    ...     return {"key": "value", "other key": "other value"}
+    >>> mapping = LazyMappingProxy(obtain_mapping)
+    >>> mapping["key"]
+    Running expensive function!
+    'value'
+    >>> mapping["other key"]
+    'other value'
+    """
+
+    def __init__(self, obtain_mapping_value: Callable[[], Mapping[_K, _V_co]]) -> None:
+        self._obtain = obtain_mapping_value
+        self._value: Mapping[_K, _V_co] | None = None
+
+    def _target(self) -> Mapping[_K, _V_co]:
+        if self._value is None:
+            self._value = self._obtain()
+        return self._value
+
+    def __getitem__(self, key: _K) -> _V_co:
+        return self._target()[key]
+
+    def __len__(self) -> int:
+        return len(self._target())
+
+    def __iter__(self) -> Iterator[_K]:
+        return iter(self._target())
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/pyprojecttoml.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/pyprojecttoml.py
new file mode 100644
index 0000000000000000000000000000000000000000..fd6c5968c820435a0a8a82ecfacbe94abd7e8d3d
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/pyprojecttoml.py
@@ -0,0 +1,468 @@
+"""
+Load setuptools configuration from ``pyproject.toml`` files.
+
+**PRIVATE MODULE**: API reserved for setuptools internal usage only.
+
+To read project metadata, consider using
+``build.util.project_wheel_metadata`` (https://pypi.org/project/build/).
+For simple scenarios, you can also try parsing the file directly
+with the help of ``tomllib`` or ``tomli``.
+"""
+
+from __future__ import annotations
+
+import logging
+import os
+from collections.abc import Mapping
+from contextlib import contextmanager
+from functools import partial
+from types import TracebackType
+from typing import TYPE_CHECKING, Any, Callable
+
+from .._path import StrPath
+from ..errors import FileError, InvalidConfigError
+from ..warnings import SetuptoolsWarning
+from . import expand as _expand
+from ._apply_pyprojecttoml import _PREVIOUSLY_DEFINED, _MissingDynamic, apply as _apply
+
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
+    from setuptools.dist import Distribution
+
+_logger = logging.getLogger(__name__)
+
+
+def load_file(filepath: StrPath) -> dict:
+    from ..compat.py310 import tomllib
+
+    with open(filepath, "rb") as file:
+        return tomllib.load(file)
+
+
+def validate(config: dict, filepath: StrPath) -> bool:
+    from . import _validate_pyproject as validator
+
+    trove_classifier = validator.FORMAT_FUNCTIONS.get("trove-classifier")
+    if hasattr(trove_classifier, "_disable_download"):
+        # Improve reproducibility by default. See abravalheri/validate-pyproject#31
+        trove_classifier._disable_download()  # type: ignore[union-attr]
+
+    try:
+        return validator.validate(config)
+    except validator.ValidationError as ex:
+        summary = f"configuration error: {ex.summary}"
+        if ex.name.strip("`") != "project":
+            # Probably it is just a field missing/misnamed, not worthy the verbosity...
+            _logger.debug(summary)
+            _logger.debug(ex.details)
+
+        error = f"invalid pyproject.toml config: {ex.name}."
+        raise ValueError(f"{error}\n{summary}") from None
+
+
+def apply_configuration(
+    dist: Distribution,
+    filepath: StrPath,
+    ignore_option_errors: bool = False,
+) -> Distribution:
+    """Apply the configuration from a ``pyproject.toml`` file into an existing
+    distribution object.
+    """
+    config = read_configuration(filepath, True, ignore_option_errors, dist)
+    return _apply(dist, config, filepath)
+
+
+def read_configuration(
+    filepath: StrPath,
+    expand: bool = True,
+    ignore_option_errors: bool = False,
+    dist: Distribution | None = None,
+) -> dict[str, Any]:
+    """Read given configuration file and returns options from it as a dict.
+
+    :param str|unicode filepath: Path to configuration file in the ``pyproject.toml``
+        format.
+
+    :param bool expand: Whether to expand directives and other computed values
+        (i.e. post-process the given configuration)
+
+    :param bool ignore_option_errors: Whether to silently ignore
+        options, values of which could not be resolved (e.g. due to exceptions
+        in directives such as file:, attr:, etc.).
+        If False exceptions are propagated as expected.
+
+    :param Distribution|None: Distribution object to which the configuration refers.
+        If not given a dummy object will be created and discarded after the
+        configuration is read. This is used for auto-discovery of packages and in the
+        case a dynamic configuration (e.g. ``attr`` or ``cmdclass``) is expanded.
+        When ``expand=False`` this object is simply ignored.
+
+    :rtype: dict
+    """
+    filepath = os.path.abspath(filepath)
+
+    if not os.path.isfile(filepath):
+        raise FileError(f"Configuration file {filepath!r} does not exist.")
+
+    asdict = load_file(filepath) or {}
+    project_table = asdict.get("project", {})
+    tool_table = asdict.get("tool", {})
+    setuptools_table = tool_table.get("setuptools", {})
+    if not asdict or not (project_table or setuptools_table):
+        return {}  # User is not using pyproject to configure setuptools
+
+    if "setuptools" in asdict.get("tools", {}):
+        # let the user know they probably have a typo in their metadata
+        _ToolsTypoInMetadata.emit()
+
+    if "distutils" in tool_table:
+        _ExperimentalConfiguration.emit(subject="[tool.distutils]")
+
+    # There is an overall sense in the community that making include_package_data=True
+    # the default would be an improvement.
+    # `ini2toml` backfills include_package_data=False when nothing is explicitly given,
+    # therefore setting a default here is backwards compatible.
+    if dist and dist.include_package_data is not None:
+        setuptools_table.setdefault("include-package-data", dist.include_package_data)
+    else:
+        setuptools_table.setdefault("include-package-data", True)
+    # Persist changes:
+    asdict["tool"] = tool_table
+    tool_table["setuptools"] = setuptools_table
+
+    if "ext-modules" in setuptools_table:
+        _ExperimentalConfiguration.emit(subject="[tool.setuptools.ext-modules]")
+
+    with _ignore_errors(ignore_option_errors):
+        # Don't complain about unrelated errors (e.g. tools not using the "tool" table)
+        subset = {"project": project_table, "tool": {"setuptools": setuptools_table}}
+        validate(subset, filepath)
+
+    if expand:
+        root_dir = os.path.dirname(filepath)
+        return expand_configuration(asdict, root_dir, ignore_option_errors, dist)
+
+    return asdict
+
+
+def expand_configuration(
+    config: dict,
+    root_dir: StrPath | None = None,
+    ignore_option_errors: bool = False,
+    dist: Distribution | None = None,
+) -> dict:
+    """Given a configuration with unresolved fields (e.g. dynamic, cmdclass, ...)
+    find their final values.
+
+    :param dict config: Dict containing the configuration for the distribution
+    :param str root_dir: Top-level directory for the distribution/project
+        (the same directory where ``pyproject.toml`` is place)
+    :param bool ignore_option_errors: see :func:`read_configuration`
+    :param Distribution|None: Distribution object to which the configuration refers.
+        If not given a dummy object will be created and discarded after the
+        configuration is read. Used in the case a dynamic configuration
+        (e.g. ``attr`` or ``cmdclass``).
+
+    :rtype: dict
+    """
+    return _ConfigExpander(config, root_dir, ignore_option_errors, dist).expand()
+
+
+class _ConfigExpander:
+    def __init__(
+        self,
+        config: dict,
+        root_dir: StrPath | None = None,
+        ignore_option_errors: bool = False,
+        dist: Distribution | None = None,
+    ) -> None:
+        self.config = config
+        self.root_dir = root_dir or os.getcwd()
+        self.project_cfg = config.get("project", {})
+        self.dynamic = self.project_cfg.get("dynamic", [])
+        self.setuptools_cfg = config.get("tool", {}).get("setuptools", {})
+        self.dynamic_cfg = self.setuptools_cfg.get("dynamic", {})
+        self.ignore_option_errors = ignore_option_errors
+        self._dist = dist
+        self._referenced_files = set[str]()
+
+    def _ensure_dist(self) -> Distribution:
+        from setuptools.dist import Distribution
+
+        attrs = {"src_root": self.root_dir, "name": self.project_cfg.get("name", None)}
+        return self._dist or Distribution(attrs)
+
+    def _process_field(self, container: dict, field: str, fn: Callable):
+        if field in container:
+            with _ignore_errors(self.ignore_option_errors):
+                container[field] = fn(container[field])
+
+    def _canonic_package_data(self, field="package-data"):
+        package_data = self.setuptools_cfg.get(field, {})
+        return _expand.canonic_package_data(package_data)
+
+    def expand(self):
+        self._expand_packages()
+        self._canonic_package_data()
+        self._canonic_package_data("exclude-package-data")
+
+        # A distribution object is required for discovering the correct package_dir
+        dist = self._ensure_dist()
+        ctx = _EnsurePackagesDiscovered(dist, self.project_cfg, self.setuptools_cfg)
+        with ctx as ensure_discovered:
+            package_dir = ensure_discovered.package_dir
+            self._expand_data_files()
+            self._expand_cmdclass(package_dir)
+            self._expand_all_dynamic(dist, package_dir)
+
+        dist._referenced_files.update(self._referenced_files)
+        return self.config
+
+    def _expand_packages(self):
+        packages = self.setuptools_cfg.get("packages")
+        if packages is None or isinstance(packages, (list, tuple)):
+            return
+
+        find = packages.get("find")
+        if isinstance(find, dict):
+            find["root_dir"] = self.root_dir
+            find["fill_package_dir"] = self.setuptools_cfg.setdefault("package-dir", {})
+            with _ignore_errors(self.ignore_option_errors):
+                self.setuptools_cfg["packages"] = _expand.find_packages(**find)
+
+    def _expand_data_files(self):
+        data_files = partial(_expand.canonic_data_files, root_dir=self.root_dir)
+        self._process_field(self.setuptools_cfg, "data-files", data_files)
+
+    def _expand_cmdclass(self, package_dir: Mapping[str, str]):
+        root_dir = self.root_dir
+        cmdclass = partial(_expand.cmdclass, package_dir=package_dir, root_dir=root_dir)
+        self._process_field(self.setuptools_cfg, "cmdclass", cmdclass)
+
+    def _expand_all_dynamic(self, dist: Distribution, package_dir: Mapping[str, str]):
+        special = (  # need special handling
+            "version",
+            "readme",
+            "entry-points",
+            "scripts",
+            "gui-scripts",
+            "classifiers",
+            "dependencies",
+            "optional-dependencies",
+        )
+        # `_obtain` functions are assumed to raise appropriate exceptions/warnings.
+        obtained_dynamic = {
+            field: self._obtain(dist, field, package_dir)
+            for field in self.dynamic
+            if field not in special
+        }
+        obtained_dynamic.update(
+            self._obtain_entry_points(dist, package_dir) or {},
+            version=self._obtain_version(dist, package_dir),
+            readme=self._obtain_readme(dist),
+            classifiers=self._obtain_classifiers(dist),
+            dependencies=self._obtain_dependencies(dist),
+            optional_dependencies=self._obtain_optional_dependencies(dist),
+        )
+        # `None` indicates there is nothing in `tool.setuptools.dynamic` but the value
+        # might have already been set by setup.py/extensions, so avoid overwriting.
+        updates = {k: v for k, v in obtained_dynamic.items() if v is not None}
+        self.project_cfg.update(updates)
+
+    def _ensure_previously_set(self, dist: Distribution, field: str):
+        previous = _PREVIOUSLY_DEFINED[field](dist)
+        if previous is None and not self.ignore_option_errors:
+            msg = (
+                f"No configuration found for dynamic {field!r}.\n"
+                "Some dynamic fields need to be specified via `tool.setuptools.dynamic`"
+                "\nothers must be specified via the equivalent attribute in `setup.py`."
+            )
+            raise InvalidConfigError(msg)
+
+    def _expand_directive(
+        self, specifier: str, directive, package_dir: Mapping[str, str]
+    ):
+        from more_itertools import always_iterable
+
+        with _ignore_errors(self.ignore_option_errors):
+            root_dir = self.root_dir
+            if "file" in directive:
+                self._referenced_files.update(always_iterable(directive["file"]))
+                return _expand.read_files(directive["file"], root_dir)
+            if "attr" in directive:
+                return _expand.read_attr(directive["attr"], package_dir, root_dir)
+            raise ValueError(f"invalid `{specifier}`: {directive!r}")
+        return None
+
+    def _obtain(self, dist: Distribution, field: str, package_dir: Mapping[str, str]):
+        if field in self.dynamic_cfg:
+            return self._expand_directive(
+                f"tool.setuptools.dynamic.{field}",
+                self.dynamic_cfg[field],
+                package_dir,
+            )
+        self._ensure_previously_set(dist, field)
+        return None
+
+    def _obtain_version(self, dist: Distribution, package_dir: Mapping[str, str]):
+        # Since plugins can set version, let's silently skip if it cannot be obtained
+        if "version" in self.dynamic and "version" in self.dynamic_cfg:
+            return _expand.version(
+                # We already do an early check for the presence of "version"
+                self._obtain(dist, "version", package_dir)  # pyright: ignore[reportArgumentType]
+            )
+        return None
+
+    def _obtain_readme(self, dist: Distribution) -> dict[str, str] | None:
+        if "readme" not in self.dynamic:
+            return None
+
+        dynamic_cfg = self.dynamic_cfg
+        if "readme" in dynamic_cfg:
+            return {
+                # We already do an early check for the presence of "readme"
+                "text": self._obtain(dist, "readme", {}),
+                "content-type": dynamic_cfg["readme"].get("content-type", "text/x-rst"),
+            }  # pyright: ignore[reportReturnType]
+
+        self._ensure_previously_set(dist, "readme")
+        return None
+
+    def _obtain_entry_points(
+        self, dist: Distribution, package_dir: Mapping[str, str]
+    ) -> dict[str, dict[str, Any]] | None:
+        fields = ("entry-points", "scripts", "gui-scripts")
+        if not any(field in self.dynamic for field in fields):
+            return None
+
+        text = self._obtain(dist, "entry-points", package_dir)
+        if text is None:
+            return None
+
+        groups = _expand.entry_points(text)
+        # Any is str | dict[str, str], but causes variance issues
+        expanded: dict[str, dict[str, Any]] = {"entry-points": groups}
+
+        def _set_scripts(field: str, group: str):
+            if group in groups:
+                value = groups.pop(group)
+                if field not in self.dynamic:
+                    raise InvalidConfigError(_MissingDynamic.details(field, value))
+                expanded[field] = value
+
+        _set_scripts("scripts", "console_scripts")
+        _set_scripts("gui-scripts", "gui_scripts")
+
+        return expanded
+
+    def _obtain_classifiers(self, dist: Distribution):
+        if "classifiers" in self.dynamic:
+            value = self._obtain(dist, "classifiers", {})
+            if value:
+                return value.splitlines()
+        return None
+
+    def _obtain_dependencies(self, dist: Distribution):
+        if "dependencies" in self.dynamic:
+            value = self._obtain(dist, "dependencies", {})
+            if value:
+                return _parse_requirements_list(value)
+        return None
+
+    def _obtain_optional_dependencies(self, dist: Distribution):
+        if "optional-dependencies" not in self.dynamic:
+            return None
+        if "optional-dependencies" in self.dynamic_cfg:
+            optional_dependencies_map = self.dynamic_cfg["optional-dependencies"]
+            assert isinstance(optional_dependencies_map, dict)
+            return {
+                group: _parse_requirements_list(
+                    self._expand_directive(
+                        f"tool.setuptools.dynamic.optional-dependencies.{group}",
+                        directive,
+                        {},
+                    )
+                )
+                for group, directive in optional_dependencies_map.items()
+            }
+        self._ensure_previously_set(dist, "optional-dependencies")
+        return None
+
+
+def _parse_requirements_list(value):
+    return [
+        line
+        for line in value.splitlines()
+        if line.strip() and not line.strip().startswith("#")
+    ]
+
+
+@contextmanager
+def _ignore_errors(ignore_option_errors: bool):
+    if not ignore_option_errors:
+        yield
+        return
+
+    try:
+        yield
+    except Exception as ex:
+        _logger.debug(f"ignored error: {ex.__class__.__name__} - {ex}")
+
+
+class _EnsurePackagesDiscovered(_expand.EnsurePackagesDiscovered):
+    def __init__(
+        self, distribution: Distribution, project_cfg: dict, setuptools_cfg: dict
+    ) -> None:
+        super().__init__(distribution)
+        self._project_cfg = project_cfg
+        self._setuptools_cfg = setuptools_cfg
+
+    def __enter__(self) -> Self:
+        """When entering the context, the values of ``packages``, ``py_modules`` and
+        ``package_dir`` that are missing in ``dist`` are copied from ``setuptools_cfg``.
+        """
+        dist, cfg = self._dist, self._setuptools_cfg
+        package_dir: dict[str, str] = cfg.setdefault("package-dir", {})
+        package_dir.update(dist.package_dir or {})
+        dist.package_dir = package_dir  # needs to be the same object
+
+        dist.set_defaults._ignore_ext_modules()  # pyproject.toml-specific behaviour
+
+        # Set `name`, `py_modules` and `packages` in dist to short-circuit
+        # auto-discovery, but avoid overwriting empty lists purposefully set by users.
+        if dist.metadata.name is None:
+            dist.metadata.name = self._project_cfg.get("name")
+        if dist.py_modules is None:
+            dist.py_modules = cfg.get("py-modules")
+        if dist.packages is None:
+            dist.packages = cfg.get("packages")
+
+        return super().__enter__()
+
+    def __exit__(
+        self,
+        exc_type: type[BaseException] | None,
+        exc_value: BaseException | None,
+        traceback: TracebackType | None,
+    ) -> None:
+        """When exiting the context, if values of ``packages``, ``py_modules`` and
+        ``package_dir`` are missing in ``setuptools_cfg``, copy from ``dist``.
+        """
+        # If anything was discovered set them back, so they count in the final config.
+        self._setuptools_cfg.setdefault("packages", self._dist.packages)
+        self._setuptools_cfg.setdefault("py-modules", self._dist.py_modules)
+        return super().__exit__(exc_type, exc_value, traceback)
+
+
+class _ExperimentalConfiguration(SetuptoolsWarning):
+    _SUMMARY = (
+        "`{subject}` in `pyproject.toml` is still *experimental* "
+        "and likely to change in future releases."
+    )
+
+
+class _ToolsTypoInMetadata(SetuptoolsWarning):
+    _SUMMARY = (
+        "Ignoring [tools.setuptools] in pyproject.toml, did you mean [tool.setuptools]?"
+    )
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/setupcfg.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/setupcfg.py
new file mode 100644
index 0000000000000000000000000000000000000000..121a0febda1b37523da5074f14cc04301efa60bf
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/setupcfg.py
@@ -0,0 +1,782 @@
+"""
+Load setuptools configuration from ``setup.cfg`` files.
+
+**API will be made private in the future**
+
+To read project metadata, consider using
+``build.util.project_wheel_metadata`` (https://pypi.org/project/build/).
+For simple scenarios, you can also try parsing the file directly
+with the help of ``configparser``.
+"""
+
+from __future__ import annotations
+
+import contextlib
+import functools
+import os
+from abc import abstractmethod
+from collections import defaultdict
+from collections.abc import Iterable, Iterator
+from functools import partial, wraps
+from typing import TYPE_CHECKING, Any, Callable, ClassVar, Generic, TypeVar, cast
+
+from packaging.markers import default_environment as marker_env
+from packaging.requirements import InvalidRequirement, Requirement
+from packaging.version import InvalidVersion, Version
+
+from .. import _static
+from .._path import StrPath
+from ..errors import FileError, OptionError
+from ..warnings import SetuptoolsDeprecationWarning
+from . import expand
+
+if TYPE_CHECKING:
+    from typing_extensions import TypeAlias
+
+    from setuptools.dist import Distribution
+
+    from distutils.dist import DistributionMetadata
+
+SingleCommandOptions: TypeAlias = dict[str, tuple[str, Any]]
+"""Dict that associate the name of the options of a particular command to a
+tuple. The first element of the tuple indicates the origin of the option value
+(e.g. the name of the configuration file where it was read from),
+while the second element of the tuple is the option value itself
+"""
+AllCommandOptions: TypeAlias = dict[str, SingleCommandOptions]
+"""cmd name => its options"""
+Target = TypeVar("Target", "Distribution", "DistributionMetadata")
+
+
+def read_configuration(
+    filepath: StrPath, find_others: bool = False, ignore_option_errors: bool = False
+) -> dict:
+    """Read given configuration file and returns options from it as a dict.
+
+    :param str|unicode filepath: Path to configuration file
+        to get options from.
+
+    :param bool find_others: Whether to search for other configuration files
+        which could be on in various places.
+
+    :param bool ignore_option_errors: Whether to silently ignore
+        options, values of which could not be resolved (e.g. due to exceptions
+        in directives such as file:, attr:, etc.).
+        If False exceptions are propagated as expected.
+
+    :rtype: dict
+    """
+    from setuptools.dist import Distribution
+
+    dist = Distribution()
+    filenames = dist.find_config_files() if find_others else []
+    handlers = _apply(dist, filepath, filenames, ignore_option_errors)
+    return configuration_to_dict(handlers)
+
+
+def apply_configuration(dist: Distribution, filepath: StrPath) -> Distribution:
+    """Apply the configuration from a ``setup.cfg`` file into an existing
+    distribution object.
+    """
+    _apply(dist, filepath)
+    dist._finalize_requires()
+    return dist
+
+
+def _apply(
+    dist: Distribution,
+    filepath: StrPath,
+    other_files: Iterable[StrPath] = (),
+    ignore_option_errors: bool = False,
+) -> tuple[ConfigMetadataHandler, ConfigOptionsHandler]:
+    """Read configuration from ``filepath`` and applies to the ``dist`` object."""
+    from setuptools.dist import _Distribution
+
+    filepath = os.path.abspath(filepath)
+
+    if not os.path.isfile(filepath):
+        raise FileError(f'Configuration file {filepath} does not exist.')
+
+    current_directory = os.getcwd()
+    os.chdir(os.path.dirname(filepath))
+    filenames = [*other_files, filepath]
+
+    try:
+        # TODO: Temporary cast until mypy 1.12 is released with upstream fixes from typeshed
+        _Distribution.parse_config_files(dist, filenames=cast(list[str], filenames))
+        handlers = parse_configuration(
+            dist, dist.command_options, ignore_option_errors=ignore_option_errors
+        )
+        dist._finalize_license_files()
+    finally:
+        os.chdir(current_directory)
+
+    return handlers
+
+
+def _get_option(target_obj: Distribution | DistributionMetadata, key: str):
+    """
+    Given a target object and option key, get that option from
+    the target object, either through a get_{key} method or
+    from an attribute directly.
+    """
+    getter_name = f'get_{key}'
+    by_attribute = functools.partial(getattr, target_obj, key)
+    getter = getattr(target_obj, getter_name, by_attribute)
+    return getter()
+
+
+def configuration_to_dict(
+    handlers: Iterable[
+        ConfigHandler[Distribution] | ConfigHandler[DistributionMetadata]
+    ],
+) -> dict:
+    """Returns configuration data gathered by given handlers as a dict.
+
+    :param Iterable[ConfigHandler] handlers: Handlers list,
+        usually from parse_configuration()
+
+    :rtype: dict
+    """
+    config_dict: dict = defaultdict(dict)
+
+    for handler in handlers:
+        for option in handler.set_options:
+            value = _get_option(handler.target_obj, option)
+            config_dict[handler.section_prefix][option] = value
+
+    return config_dict
+
+
+def parse_configuration(
+    distribution: Distribution,
+    command_options: AllCommandOptions,
+    ignore_option_errors: bool = False,
+) -> tuple[ConfigMetadataHandler, ConfigOptionsHandler]:
+    """Performs additional parsing of configuration options
+    for a distribution.
+
+    Returns a list of used option handlers.
+
+    :param Distribution distribution:
+    :param dict command_options:
+    :param bool ignore_option_errors: Whether to silently ignore
+        options, values of which could not be resolved (e.g. due to exceptions
+        in directives such as file:, attr:, etc.).
+        If False exceptions are propagated as expected.
+    :rtype: list
+    """
+    with expand.EnsurePackagesDiscovered(distribution) as ensure_discovered:
+        options = ConfigOptionsHandler(
+            distribution,
+            command_options,
+            ignore_option_errors,
+            ensure_discovered,
+        )
+
+        options.parse()
+        if not distribution.package_dir:
+            distribution.package_dir = options.package_dir  # Filled by `find_packages`
+
+        meta = ConfigMetadataHandler(
+            distribution.metadata,
+            command_options,
+            ignore_option_errors,
+            ensure_discovered,
+            distribution.package_dir,
+            distribution.src_root,
+        )
+        meta.parse()
+        distribution._referenced_files.update(
+            options._referenced_files, meta._referenced_files
+        )
+
+    return meta, options
+
+
+def _warn_accidental_env_marker_misconfig(label: str, orig_value: str, parsed: list):
+    """Because users sometimes misinterpret this configuration:
+
+    [options.extras_require]
+    foo = bar;python_version<"4"
+
+    It looks like one requirement with an environment marker
+    but because there is no newline, it's parsed as two requirements
+    with a semicolon as separator.
+
+    Therefore, if:
+        * input string does not contain a newline AND
+        * parsed result contains two requirements AND
+        * parsing of the two parts from the result (";")
+        leads in a valid Requirement with a valid marker
+    a UserWarning is shown to inform the user about the possible problem.
+    """
+    if "\n" in orig_value or len(parsed) != 2:
+        return
+
+    markers = marker_env().keys()
+
+    try:
+        req = Requirement(parsed[1])
+        if req.name in markers:
+            _AmbiguousMarker.emit(field=label, req=parsed[1])
+    except InvalidRequirement as ex:
+        if any(parsed[1].startswith(marker) for marker in markers):
+            msg = _AmbiguousMarker.message(field=label, req=parsed[1])
+            raise InvalidRequirement(msg) from ex
+
+
+class ConfigHandler(Generic[Target]):
+    """Handles metadata supplied in configuration files."""
+
+    section_prefix: str
+    """Prefix for config sections handled by this handler.
+    Must be provided by class heirs.
+
+    """
+
+    aliases: ClassVar[dict[str, str]] = {}
+    """Options aliases.
+    For compatibility with various packages. E.g.: d2to1 and pbr.
+    Note: `-` in keys is replaced with `_` by config parser.
+
+    """
+
+    def __init__(
+        self,
+        target_obj: Target,
+        options: AllCommandOptions,
+        ignore_option_errors,
+        ensure_discovered: expand.EnsurePackagesDiscovered,
+    ) -> None:
+        self.ignore_option_errors = ignore_option_errors
+        self.target_obj: Target = target_obj
+        self.sections = dict(self._section_options(options))
+        self.set_options: list[str] = []
+        self.ensure_discovered = ensure_discovered
+        self._referenced_files = set[str]()
+        """After parsing configurations, this property will enumerate
+        all files referenced by the "file:" directive. Private API for setuptools only.
+        """
+
+    @classmethod
+    def _section_options(
+        cls, options: AllCommandOptions
+    ) -> Iterator[tuple[str, SingleCommandOptions]]:
+        for full_name, value in options.items():
+            pre, _sep, name = full_name.partition(cls.section_prefix)
+            if pre:
+                continue
+            yield name.lstrip('.'), value
+
+    @property
+    @abstractmethod
+    def parsers(self) -> dict[str, Callable]:
+        """Metadata item name to parser function mapping."""
+        raise NotImplementedError(
+            f'{self.__class__.__name__} must provide .parsers property'
+        )
+
+    def __setitem__(self, option_name, value) -> None:
+        target_obj = self.target_obj
+
+        # Translate alias into real name.
+        option_name = self.aliases.get(option_name, option_name)
+
+        try:
+            current_value = getattr(target_obj, option_name)
+        except AttributeError as e:
+            raise KeyError(option_name) from e
+
+        if current_value:
+            # Already inhabited. Skipping.
+            return
+
+        try:
+            parsed = self.parsers.get(option_name, lambda x: x)(value)
+        except (Exception,) * self.ignore_option_errors:
+            return
+
+        simple_setter = functools.partial(target_obj.__setattr__, option_name)
+        setter = getattr(target_obj, f"set_{option_name}", simple_setter)
+        setter(parsed)
+
+        self.set_options.append(option_name)
+
+    @classmethod
+    def _parse_list(cls, value, separator=','):
+        """Represents value as a list.
+
+        Value is split either by separator (defaults to comma) or by lines.
+
+        :param value:
+        :param separator: List items separator character.
+        :rtype: list
+        """
+        if isinstance(value, list):  # _get_parser_compound case
+            return value
+
+        if '\n' in value:
+            value = value.splitlines()
+        else:
+            value = value.split(separator)
+
+        return [chunk.strip() for chunk in value if chunk.strip()]
+
+    @classmethod
+    def _parse_dict(cls, value):
+        """Represents value as a dict.
+
+        :param value:
+        :rtype: dict
+        """
+        separator = '='
+        result = {}
+        for line in cls._parse_list(value):
+            key, sep, val = line.partition(separator)
+            if sep != separator:
+                raise OptionError(f"Unable to parse option value to dict: {value}")
+            result[key.strip()] = val.strip()
+
+        return result
+
+    @classmethod
+    def _parse_bool(cls, value):
+        """Represents value as boolean.
+
+        :param value:
+        :rtype: bool
+        """
+        value = value.lower()
+        return value in ('1', 'true', 'yes')
+
+    @classmethod
+    def _exclude_files_parser(cls, key):
+        """Returns a parser function to make sure field inputs
+        are not files.
+
+        Parses a value after getting the key so error messages are
+        more informative.
+
+        :param key:
+        :rtype: callable
+        """
+
+        def parser(value):
+            exclude_directive = 'file:'
+            if value.startswith(exclude_directive):
+                raise ValueError(
+                    f'Only strings are accepted for the {key} field, '
+                    'files are not accepted'
+                )
+            return _static.Str(value)
+
+        return parser
+
+    def _parse_file(self, value, root_dir: StrPath | None):
+        """Represents value as a string, allowing including text
+        from nearest files using `file:` directive.
+
+        Directive is sandboxed and won't reach anything outside
+        directory with setup.py.
+
+        Examples:
+            file: README.rst, CHANGELOG.md, src/file.txt
+
+        :param str value:
+        :rtype: str
+        """
+        include_directive = 'file:'
+
+        if not isinstance(value, str):
+            return value
+
+        if not value.startswith(include_directive):
+            return _static.Str(value)
+
+        spec = value[len(include_directive) :]
+        filepaths = [path.strip() for path in spec.split(',')]
+        self._referenced_files.update(filepaths)
+        # XXX: Is marking as static contents coming from files too optimistic?
+        return _static.Str(expand.read_files(filepaths, root_dir))
+
+    def _parse_attr(self, value, package_dir, root_dir: StrPath):
+        """Represents value as a module attribute.
+
+        Examples:
+            attr: package.attr
+            attr: package.module.attr
+
+        :param str value:
+        :rtype: str
+        """
+        attr_directive = 'attr:'
+        if not value.startswith(attr_directive):
+            return _static.Str(value)
+
+        attr_desc = value.replace(attr_directive, '')
+
+        # Make sure package_dir is populated correctly, so `attr:` directives can work
+        package_dir.update(self.ensure_discovered.package_dir)
+        return expand.read_attr(attr_desc, package_dir, root_dir)
+
+    @classmethod
+    def _get_parser_compound(cls, *parse_methods):
+        """Returns parser function to represents value as a list.
+
+        Parses a value applying given methods one after another.
+
+        :param parse_methods:
+        :rtype: callable
+        """
+
+        def parse(value):
+            parsed = value
+
+            for method in parse_methods:
+                parsed = method(parsed)
+
+            return parsed
+
+        return parse
+
+    @classmethod
+    def _parse_section_to_dict_with_key(cls, section_options, values_parser):
+        """Parses section options into a dictionary.
+
+        Applies a given parser to each option in a section.
+
+        :param dict section_options:
+        :param callable values_parser: function with 2 args corresponding to key, value
+        :rtype: dict
+        """
+        value = {}
+        for key, (_, val) in section_options.items():
+            value[key] = values_parser(key, val)
+        return value
+
+    @classmethod
+    def _parse_section_to_dict(cls, section_options, values_parser=None):
+        """Parses section options into a dictionary.
+
+        Optionally applies a given parser to each value.
+
+        :param dict section_options:
+        :param callable values_parser: function with 1 arg corresponding to option value
+        :rtype: dict
+        """
+        parser = (lambda _, v: values_parser(v)) if values_parser else (lambda _, v: v)
+        return cls._parse_section_to_dict_with_key(section_options, parser)
+
+    def parse_section(self, section_options) -> None:
+        """Parses configuration file section.
+
+        :param dict section_options:
+        """
+        for name, (_, value) in section_options.items():
+            with contextlib.suppress(KeyError):
+                # Keep silent for a new option may appear anytime.
+                self[name] = value
+
+    def parse(self) -> None:
+        """Parses configuration file items from one
+        or more related sections.
+
+        """
+        for section_name, section_options in self.sections.items():
+            method_postfix = ''
+            if section_name:  # [section.option] variant
+                method_postfix = f"_{section_name}"
+
+            section_parser_method: Callable | None = getattr(
+                self,
+                # Dots in section names are translated into dunderscores.
+                f'parse_section{method_postfix}'.replace('.', '__'),
+                None,
+            )
+
+            if section_parser_method is None:
+                raise OptionError(
+                    "Unsupported distribution option section: "
+                    f"[{self.section_prefix}.{section_name}]"
+                )
+
+            section_parser_method(section_options)
+
+    def _deprecated_config_handler(self, func, msg, **kw):
+        """this function will wrap around parameters that are deprecated
+
+        :param msg: deprecation message
+        :param func: function to be wrapped around
+        """
+
+        @wraps(func)
+        def config_handler(*args, **kwargs):
+            kw.setdefault("stacklevel", 2)
+            _DeprecatedConfig.emit("Deprecated config in `setup.cfg`", msg, **kw)
+            return func(*args, **kwargs)
+
+        return config_handler
+
+
+class ConfigMetadataHandler(ConfigHandler["DistributionMetadata"]):
+    section_prefix = 'metadata'
+
+    aliases = {
+        'home_page': 'url',
+        'summary': 'description',
+        'classifier': 'classifiers',
+        'platform': 'platforms',
+    }
+
+    strict_mode = False
+    """We need to keep it loose, to be partially compatible with
+    `pbr` and `d2to1` packages which also uses `metadata` section.
+
+    """
+
+    def __init__(
+        self,
+        target_obj: DistributionMetadata,
+        options: AllCommandOptions,
+        ignore_option_errors: bool,
+        ensure_discovered: expand.EnsurePackagesDiscovered,
+        package_dir: dict | None = None,
+        root_dir: StrPath | None = os.curdir,
+    ) -> None:
+        super().__init__(target_obj, options, ignore_option_errors, ensure_discovered)
+        self.package_dir = package_dir
+        self.root_dir = root_dir
+
+    @property
+    def parsers(self) -> dict[str, Callable]:
+        """Metadata item name to parser function mapping."""
+        parse_list_static = self._get_parser_compound(self._parse_list, _static.List)
+        parse_dict_static = self._get_parser_compound(self._parse_dict, _static.Dict)
+        parse_file = partial(self._parse_file, root_dir=self.root_dir)
+        exclude_files_parser = self._exclude_files_parser
+
+        return {
+            'author': _static.Str,
+            'author_email': _static.Str,
+            'maintainer': _static.Str,
+            'maintainer_email': _static.Str,
+            'platforms': parse_list_static,
+            'keywords': parse_list_static,
+            'provides': parse_list_static,
+            'obsoletes': parse_list_static,
+            'classifiers': self._get_parser_compound(parse_file, parse_list_static),
+            'license': exclude_files_parser('license'),
+            'license_files': parse_list_static,
+            'description': parse_file,
+            'long_description': parse_file,
+            'long_description_content_type': _static.Str,
+            'version': self._parse_version,  # Cannot be marked as dynamic
+            'url': _static.Str,
+            'project_urls': parse_dict_static,
+        }
+
+    def _parse_version(self, value):
+        """Parses `version` option value.
+
+        :param value:
+        :rtype: str
+
+        """
+        version = self._parse_file(value, self.root_dir)
+
+        if version != value:
+            version = version.strip()
+            # Be strict about versions loaded from file because it's easy to
+            # accidentally include newlines and other unintended content
+            try:
+                Version(version)
+            except InvalidVersion as e:
+                raise OptionError(
+                    f'Version loaded from {value} does not '
+                    f'comply with PEP 440: {version}'
+                ) from e
+
+            return version
+
+        return expand.version(self._parse_attr(value, self.package_dir, self.root_dir))
+
+
+class ConfigOptionsHandler(ConfigHandler["Distribution"]):
+    section_prefix = 'options'
+
+    def __init__(
+        self,
+        target_obj: Distribution,
+        options: AllCommandOptions,
+        ignore_option_errors: bool,
+        ensure_discovered: expand.EnsurePackagesDiscovered,
+    ) -> None:
+        super().__init__(target_obj, options, ignore_option_errors, ensure_discovered)
+        self.root_dir = target_obj.src_root
+        self.package_dir: dict[str, str] = {}  # To be filled by `find_packages`
+
+    @classmethod
+    def _parse_list_semicolon(cls, value):
+        return cls._parse_list(value, separator=';')
+
+    def _parse_file_in_root(self, value):
+        return self._parse_file(value, root_dir=self.root_dir)
+
+    def _parse_requirements_list(self, label: str, value: str):
+        # Parse a requirements list, either by reading in a `file:`, or a list.
+        parsed = self._parse_list_semicolon(self._parse_file_in_root(value))
+        _warn_accidental_env_marker_misconfig(label, value, parsed)
+        # Filter it to only include lines that are not comments. `parse_list`
+        # will have stripped each line and filtered out empties.
+        return _static.List(line for line in parsed if not line.startswith("#"))
+        # ^-- Use `_static.List` to mark a non-`Dynamic` Core Metadata
+
+    @property
+    def parsers(self) -> dict[str, Callable]:
+        """Metadata item name to parser function mapping."""
+        parse_list = self._parse_list
+        parse_bool = self._parse_bool
+        parse_cmdclass = self._parse_cmdclass
+
+        return {
+            'zip_safe': parse_bool,
+            'include_package_data': parse_bool,
+            'package_dir': self._parse_dict,
+            'scripts': parse_list,
+            'eager_resources': parse_list,
+            'dependency_links': parse_list,
+            'namespace_packages': self._deprecated_config_handler(
+                parse_list,
+                "The namespace_packages parameter is deprecated, "
+                "consider using implicit namespaces instead (PEP 420).",
+                # TODO: define due date, see setuptools.dist:check_nsp.
+            ),
+            'install_requires': partial(  # Core Metadata
+                self._parse_requirements_list, "install_requires"
+            ),
+            'setup_requires': self._parse_list_semicolon,
+            'packages': self._parse_packages,
+            'entry_points': self._parse_file_in_root,
+            'py_modules': parse_list,
+            'python_requires': _static.SpecifierSet,  # Core Metadata
+            'cmdclass': parse_cmdclass,
+        }
+
+    def _parse_cmdclass(self, value):
+        package_dir = self.ensure_discovered.package_dir
+        return expand.cmdclass(self._parse_dict(value), package_dir, self.root_dir)
+
+    def _parse_packages(self, value):
+        """Parses `packages` option value.
+
+        :param value:
+        :rtype: list
+        """
+        find_directives = ['find:', 'find_namespace:']
+        trimmed_value = value.strip()
+
+        if trimmed_value not in find_directives:
+            return self._parse_list(value)
+
+        # Read function arguments from a dedicated section.
+        find_kwargs = self.parse_section_packages__find(
+            self.sections.get('packages.find', {})
+        )
+
+        find_kwargs.update(
+            namespaces=(trimmed_value == find_directives[1]),
+            root_dir=self.root_dir,
+            fill_package_dir=self.package_dir,
+        )
+
+        return expand.find_packages(**find_kwargs)
+
+    def parse_section_packages__find(self, section_options):
+        """Parses `packages.find` configuration file section.
+
+        To be used in conjunction with _parse_packages().
+
+        :param dict section_options:
+        """
+        section_data = self._parse_section_to_dict(section_options, self._parse_list)
+
+        valid_keys = ['where', 'include', 'exclude']
+        find_kwargs = {k: v for k, v in section_data.items() if k in valid_keys and v}
+
+        where = find_kwargs.get('where')
+        if where is not None:
+            find_kwargs['where'] = where[0]  # cast list to single val
+
+        return find_kwargs
+
+    def parse_section_entry_points(self, section_options) -> None:
+        """Parses `entry_points` configuration file section.
+
+        :param dict section_options:
+        """
+        parsed = self._parse_section_to_dict(section_options, self._parse_list)
+        self['entry_points'] = parsed
+
+    def _parse_package_data(self, section_options):
+        package_data = self._parse_section_to_dict(section_options, self._parse_list)
+        return expand.canonic_package_data(package_data)
+
+    def parse_section_package_data(self, section_options) -> None:
+        """Parses `package_data` configuration file section.
+
+        :param dict section_options:
+        """
+        self['package_data'] = self._parse_package_data(section_options)
+
+    def parse_section_exclude_package_data(self, section_options) -> None:
+        """Parses `exclude_package_data` configuration file section.
+
+        :param dict section_options:
+        """
+        self['exclude_package_data'] = self._parse_package_data(section_options)
+
+    def parse_section_extras_require(self, section_options) -> None:  # Core Metadata
+        """Parses `extras_require` configuration file section.
+
+        :param dict section_options:
+        """
+        parsed = self._parse_section_to_dict_with_key(
+            section_options,
+            lambda k, v: self._parse_requirements_list(f"extras_require[{k}]", v),
+        )
+
+        self['extras_require'] = _static.Dict(parsed)
+        # ^-- Use `_static.Dict` to mark a non-`Dynamic` Core Metadata
+
+    def parse_section_data_files(self, section_options) -> None:
+        """Parses `data_files` configuration file section.
+
+        :param dict section_options:
+        """
+        parsed = self._parse_section_to_dict(section_options, self._parse_list)
+        self['data_files'] = expand.canonic_data_files(parsed, self.root_dir)
+
+
+class _AmbiguousMarker(SetuptoolsDeprecationWarning):
+    _SUMMARY = "Ambiguous requirement marker."
+    _DETAILS = """
+    One of the parsed requirements in `{field}` looks like a valid environment marker:
+
+        {req!r}
+
+    Please make sure that the configuration file is correct.
+    You can use dangling lines to avoid this problem.
+    """
+    _SEE_DOCS = "userguide/declarative_config.html#opt-2"
+    # TODO: should we include due_date here? Initially introduced in 6 Aug 2022.
+    # Does this make sense with latest version of packaging?
+
+    @classmethod
+    def message(cls, **kw):
+        docs = f"https://setuptools.pypa.io/en/latest/{cls._SEE_DOCS}"
+        return cls._format(cls._SUMMARY, cls._DETAILS, see_url=docs, format_args=kw)
+
+
+class _DeprecatedConfig(SetuptoolsDeprecationWarning):
+    _SEE_DOCS = "userguide/declarative_config.html"
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/setuptools.schema.json b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/setuptools.schema.json
new file mode 100644
index 0000000000000000000000000000000000000000..ec887b35736e4ede6265e95e3a9e2520b43cc40f
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/config/setuptools.schema.json
@@ -0,0 +1,433 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+
+  "$id": "https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html",
+  "title": "``tool.setuptools`` table",
+  "$$description": [
+    "``setuptools``-specific configurations that can be set by users that require",
+    "customization.",
+    "These configurations are completely optional and probably can be skipped when",
+    "creating simple packages. They are equivalent to some of the `Keywords",
+    "`_",
+    "used by the ``setup.py`` file, and can be set via the ``tool.setuptools`` table.",
+    "It considers only ``setuptools`` `parameters",
+    "`_",
+    "that are not covered by :pep:`621`; and intentionally excludes ``dependency_links``",
+    "and ``setup_requires`` (incompatible with modern workflows/standards)."
+  ],
+
+  "type": "object",
+  "additionalProperties": false,
+  "properties": {
+    "platforms": {
+      "type": "array",
+      "items": {"type": "string"}
+    },
+    "provides": {
+      "$$description": [
+        "Package and virtual package names contained within this package",
+        "**(not supported by pip)**"
+      ],
+      "type": "array",
+      "items": {"type": "string", "format": "pep508-identifier"}
+    },
+    "obsoletes": {
+      "$$description": [
+        "Packages which this package renders obsolete",
+        "**(not supported by pip)**"
+      ],
+      "type": "array",
+      "items": {"type": "string", "format": "pep508-identifier"}
+    },
+    "zip-safe": {
+      "$$description": [
+        "Whether the project can be safely installed and run from a zip file.",
+        "**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and",
+        "``setup.py install`` in the context of ``eggs`` (**DEPRECATED**)."
+      ],
+      "type": "boolean"
+    },
+    "script-files": {
+      "$$description": [
+        "Legacy way of defining scripts (entry-points are preferred).",
+        "Equivalent to the ``script`` keyword in ``setup.py``",
+        "(it was renamed to avoid confusion with entry-point based ``project.scripts``",
+        "defined in :pep:`621`).",
+        "**DISCOURAGED**: generic script wrappers are tricky and may not work properly.",
+        "Whenever possible, please use ``project.scripts`` instead."
+      ],
+      "type": "array",
+      "items": {"type": "string"},
+      "$comment": "TODO: is this field deprecated/should be removed?"
+    },
+    "eager-resources": {
+      "$$description": [
+        "Resources that should be extracted together, if any of them is needed,",
+        "or if any C extensions included in the project are imported.",
+        "**OBSOLETE**: only relevant for ``pkg_resources``, ``easy_install`` and",
+        "``setup.py install`` in the context of ``eggs`` (**DEPRECATED**)."
+      ],
+      "type": "array",
+      "items": {"type": "string"}
+    },
+    "packages": {
+      "$$description": [
+        "Packages that should be included in the distribution.",
+        "It can be given either as a list of package identifiers",
+        "or as a ``dict``-like structure with a single key ``find``",
+        "which corresponds to a dynamic call to",
+        "``setuptools.config.expand.find_packages`` function.",
+        "The ``find`` key is associated with a nested ``dict``-like structure that can",
+        "contain ``where``, ``include``, ``exclude`` and ``namespaces`` keys,",
+        "mimicking the keyword arguments of the associated function."
+      ],
+      "oneOf": [
+        {
+          "title": "Array of Python package identifiers",
+          "type": "array",
+          "items": {"$ref": "#/definitions/package-name"}
+        },
+        {"$ref": "#/definitions/find-directive"}
+      ]
+    },
+    "package-dir": {
+      "$$description": [
+        ":class:`dict`-like structure mapping from package names to directories where their",
+        "code can be found.",
+        "The empty string (as key) means that all packages are contained inside",
+        "the given directory will be included in the distribution."
+      ],
+      "type": "object",
+      "additionalProperties": false,
+      "propertyNames": {
+        "anyOf": [{"const": ""}, {"$ref": "#/definitions/package-name"}]
+      },
+      "patternProperties": {
+        "^.*$": {"type": "string" }
+      }
+    },
+    "package-data": {
+      "$$description": [
+        "Mapping from package names to lists of glob patterns.",
+        "Usually this option is not needed when using ``include-package-data = true``",
+        "For more information on how to include data files, check ``setuptools`` `docs",
+        "`_."
+      ],
+      "type": "object",
+      "additionalProperties": false,
+      "propertyNames": {
+        "anyOf": [{"type": "string", "format": "python-module-name"}, {"const": "*"}]
+      },
+      "patternProperties": {
+        "^.*$": {"type": "array", "items": {"type": "string"}}
+      }
+    },
+    "include-package-data": {
+      "$$description": [
+        "Automatically include any data files inside the package directories",
+        "that are specified by ``MANIFEST.in``",
+        "For more information on how to include data files, check ``setuptools`` `docs",
+        "`_."
+      ],
+      "type": "boolean"
+    },
+    "exclude-package-data": {
+      "$$description": [
+        "Mapping from package names to lists of glob patterns that should be excluded",
+        "For more information on how to include data files, check ``setuptools`` `docs",
+        "`_."
+      ],
+      "type": "object",
+      "additionalProperties": false,
+      "propertyNames": {
+        "anyOf": [{"type": "string", "format": "python-module-name"}, {"const": "*"}]
+      },
+      "patternProperties": {
+          "^.*$": {"type": "array", "items": {"type": "string"}}
+      }
+    },
+    "namespace-packages": {
+      "type": "array",
+      "items": {"type": "string", "format": "python-module-name-relaxed"},
+      "$comment": "https://setuptools.pypa.io/en/latest/userguide/package_discovery.html",
+      "description": "**DEPRECATED**: use implicit namespaces instead (:pep:`420`)."
+    },
+    "py-modules": {
+      "description": "Modules that setuptools will manipulate",
+      "type": "array",
+      "items": {"type": "string", "format": "python-module-name-relaxed"},
+      "$comment": "TODO: clarify the relationship with ``packages``"
+    },
+    "ext-modules": {
+      "description": "Extension modules to be compiled by setuptools",
+      "type": "array",
+      "items": {"$ref": "#/definitions/ext-module"}
+    },
+    "data-files": {
+      "$$description": [
+        "``dict``-like structure where each key represents a directory and",
+        "the value is a list of glob patterns that should be installed in them.",
+        "**DISCOURAGED**: please notice this might not work as expected with wheels.",
+        "Whenever possible, consider using data files inside the package directories",
+        "(or create a new namespace package that only contains data files).",
+        "See `data files support",
+        "`_."
+      ],
+      "type": "object",
+      "patternProperties": {
+          "^.*$": {"type": "array", "items": {"type": "string"}}
+      }
+    },
+    "cmdclass": {
+      "$$description": [
+        "Mapping of distutils-style command names to ``setuptools.Command`` subclasses",
+        "which in turn should be represented by strings with a qualified class name",
+        "(i.e., \"dotted\" form with module), e.g.::\n\n",
+        "    cmdclass = {mycmd = \"pkg.subpkg.module.CommandClass\"}\n\n",
+        "The command class should be a directly defined at the top-level of the",
+        "containing module (no class nesting)."
+      ],
+      "type": "object",
+      "patternProperties": {
+          "^.*$": {"type": "string", "format": "python-qualified-identifier"}
+      }
+    },
+    "license-files": {
+      "type": "array",
+      "items": {"type": "string"},
+      "$$description": [
+        "**PROVISIONAL**: list of glob patterns for all license files being distributed.",
+        "(likely to become standard with :pep:`639`).",
+        "By default: ``['LICEN[CS]E*', 'COPYING*', 'NOTICE*', 'AUTHORS*']``"
+      ],
+      "$comment": "TODO: revise if PEP 639 is accepted. Probably ``project.license-files``?"
+    },
+    "dynamic": {
+      "type": "object",
+      "description": "Instructions for loading :pep:`621`-related metadata dynamically",
+      "additionalProperties": false,
+      "properties": {
+        "version": {
+          "$$description": [
+            "A version dynamically loaded via either the ``attr:`` or ``file:``",
+            "directives. Please make sure the given file or attribute respects :pep:`440`.",
+            "Also ensure to set ``project.dynamic`` accordingly."
+          ],
+          "oneOf": [
+            {"$ref": "#/definitions/attr-directive"},
+            {"$ref": "#/definitions/file-directive"}
+          ]
+        },
+        "classifiers": {"$ref": "#/definitions/file-directive"},
+        "description": {"$ref": "#/definitions/file-directive"},
+        "entry-points": {"$ref": "#/definitions/file-directive"},
+        "dependencies": {"$ref": "#/definitions/file-directive-for-dependencies"},
+        "optional-dependencies": {
+          "type": "object",
+          "propertyNames": {"type": "string", "format": "pep508-identifier"},
+          "additionalProperties": false,
+          "patternProperties": {
+            ".+": {"$ref": "#/definitions/file-directive-for-dependencies"}
+          }
+        },
+        "readme": {
+          "type": "object",
+          "anyOf": [
+            {"$ref": "#/definitions/file-directive"},
+            {
+              "type": "object",
+              "properties": {
+                "content-type": {"type": "string"},
+                "file": { "$ref": "#/definitions/file-directive/properties/file" }
+              },
+              "additionalProperties": false}
+          ],
+          "required": ["file"]
+        }
+      }
+    }
+  },
+
+  "definitions": {
+    "package-name": {
+      "$id": "#/definitions/package-name",
+      "title": "Valid package name",
+      "description": "Valid package name (importable or :pep:`561`).",
+      "type": "string",
+      "anyOf": [
+        {"type": "string", "format": "python-module-name-relaxed"},
+        {"type": "string", "format": "pep561-stub-name"}
+      ]
+    },
+    "ext-module": {
+      "$id": "#/definitions/ext-module",
+      "title": "Extension module",
+      "description": "Parameters to construct a :class:`setuptools.Extension` object",
+      "type": "object",
+      "required": ["name", "sources"],
+      "additionalProperties": false,
+      "properties": {
+        "name": {
+          "type": "string",
+          "format": "python-module-name-relaxed"
+        },
+        "sources": {
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "include-dirs":{
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "define-macros": {
+          "type": "array",
+          "items": {
+            "type": "array",
+            "items": [
+              {"description": "macro name", "type": "string"},
+              {"description": "macro value", "oneOf": [{"type": "string"}, {"type": "null"}]}
+            ],
+            "additionalItems": false
+          }
+        },
+        "undef-macros": {
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "library-dirs": {
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "libraries": {
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "runtime-library-dirs": {
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "extra-objects": {
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "extra-compile-args": {
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "extra-link-args": {
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "export-symbols": {
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "swig-opts": {
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "depends": {
+          "type": "array",
+          "items": {"type": "string"}
+        },
+        "language": {"type": "string"},
+        "optional": {"type": "boolean"},
+        "py-limited-api": {"type": "boolean"}
+      }
+    },
+    "file-directive": {
+      "$id": "#/definitions/file-directive",
+      "title": "'file:' directive",
+      "description":
+        "Value is read from a file (or list of files and then concatenated)",
+      "type": "object",
+      "additionalProperties": false,
+      "properties": {
+        "file": {
+          "oneOf": [
+            {"type": "string"},
+            {"type": "array", "items": {"type": "string"}}
+          ]
+        }
+      },
+      "required": ["file"]
+    },
+    "file-directive-for-dependencies": {
+      "title": "'file:' directive for dependencies",
+      "allOf": [
+        {
+          "$$description": [
+            "**BETA**: subset of the ``requirements.txt`` format",
+            "without ``pip`` flags and options",
+            "(one :pep:`508`-compliant string per line,",
+            "lines that are blank or start with ``#`` are excluded).",
+            "See `dynamic metadata",
+            "`_."
+          ]
+        },
+        {"$ref": "#/definitions/file-directive"}
+      ]
+    },
+    "attr-directive": {
+      "title": "'attr:' directive",
+      "$id": "#/definitions/attr-directive",
+      "$$description": [
+        "Value is read from a module attribute. Supports callables and iterables;",
+        "unsupported types are cast via ``str()``"
+      ],
+      "type": "object",
+      "additionalProperties": false,
+      "properties": {
+        "attr": {"type": "string", "format": "python-qualified-identifier"}
+      },
+      "required": ["attr"]
+    },
+    "find-directive": {
+      "$id": "#/definitions/find-directive",
+      "title": "'find:' directive",
+      "type": "object",
+      "additionalProperties": false,
+      "properties": {
+        "find": {
+          "type": "object",
+          "$$description": [
+            "Dynamic `package discovery",
+            "`_."
+          ],
+          "additionalProperties": false,
+          "properties": {
+            "where": {
+              "description":
+                "Directories to be searched for packages (Unix-style relative path)",
+              "type": "array",
+              "items": {"type": "string"}
+            },
+            "exclude": {
+              "type": "array",
+              "$$description": [
+                "Exclude packages that match the values listed in this field.",
+                "Can container shell-style wildcards (e.g. ``'pkg.*'``)"
+              ],
+              "items": {"type": "string"}
+            },
+            "include": {
+              "type": "array",
+              "$$description": [
+                "Restrict the found packages to just the ones listed in this field.",
+                "Can container shell-style wildcards (e.g. ``'pkg.*'``)"
+              ],
+              "items": {"type": "string"}
+            },
+            "namespaces": {
+              "type": "boolean",
+              "$$description": [
+                "When ``True``, directories without a ``__init__.py`` file will also",
+                "be scanned for :pep:`420`-style implicit namespaces"
+              ]
+            }
+          }
+        }
+      }
+    }
+  }
+}
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..eb70bfb7115a2a94a8b942b31cafc3a550f0c005
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/__init__.py
@@ -0,0 +1,13 @@
+import locale
+import sys
+
+import pytest
+
+__all__ = ['fail_on_ascii']
+
+if sys.version_info >= (3, 11):
+    locale_encoding = locale.getencoding()
+else:
+    locale_encoding = locale.getpreferredencoding(False)
+is_ascii = locale_encoding == 'ANSI_X3.4-1968'
+fail_on_ascii = pytest.mark.xfail(is_ascii, reason="Test fails in this locale")
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/compat/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/compat/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/compat/py39.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/compat/py39.py
new file mode 100644
index 0000000000000000000000000000000000000000..1fdb9dac1fa3f121a634082515d1a305fc09793c
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/compat/py39.py
@@ -0,0 +1,3 @@
+from jaraco.test.cpython import from_test_support, try_import
+
+os_helper = try_import('os_helper') or from_test_support('can_symlink')
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/downloads/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/downloads/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..00a16423f448e7773f5e6dc9b365efe80f40a778
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/downloads/__init__.py
@@ -0,0 +1,59 @@
+from __future__ import annotations
+
+import re
+import time
+from pathlib import Path
+from urllib.error import HTTPError
+from urllib.request import urlopen
+
+__all__ = ["DOWNLOAD_DIR", "retrieve_file", "output_file", "urls_from_file"]
+
+
+NAME_REMOVE = ("http://", "https://", "github.com/", "/raw/")
+DOWNLOAD_DIR = Path(__file__).parent
+
+
+# ----------------------------------------------------------------------
+# Please update ./preload.py accordingly when modifying this file
+# ----------------------------------------------------------------------
+
+
+def output_file(url: str, download_dir: Path = DOWNLOAD_DIR) -> Path:
+    file_name = url.strip()
+    for part in NAME_REMOVE:
+        file_name = file_name.replace(part, '').strip().strip('/:').strip()
+    return Path(download_dir, re.sub(r"[^\-_\.\w\d]+", "_", file_name))
+
+
+def retrieve_file(url: str, download_dir: Path = DOWNLOAD_DIR, wait: float = 5) -> Path:
+    path = output_file(url, download_dir)
+    if path.exists():
+        print(f"Skipping {url} (already exists: {path})")
+    else:
+        download_dir.mkdir(exist_ok=True, parents=True)
+        print(f"Downloading {url} to {path}")
+        try:
+            download(url, path)
+        except HTTPError:
+            time.sleep(wait)  # wait a few seconds and try again.
+            download(url, path)
+    return path
+
+
+def urls_from_file(list_file: Path) -> list[str]:
+    """``list_file`` should be a text file where each line corresponds to a URL to
+    download.
+    """
+    print(f"file: {list_file}")
+    content = list_file.read_text(encoding="utf-8")
+    return [url for url in content.splitlines() if not url.startswith("#")]
+
+
+def download(url: str, dest: Path):
+    with urlopen(url) as f:
+        data = f.read()
+
+    with open(dest, "wb") as f:
+        f.write(data)
+
+    assert Path(dest).exists()
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/downloads/preload.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/downloads/preload.py
new file mode 100644
index 0000000000000000000000000000000000000000..8eeb5dd75d3dcb375cee5acaf11ad385084bff5a
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/downloads/preload.py
@@ -0,0 +1,18 @@
+"""This file can be used to preload files needed for testing.
+
+For example you can use::
+
+    cd setuptools/tests/config
+    python -m downloads.preload setupcfg_examples.txt
+
+to make sure the `setup.cfg` examples are downloaded before starting the tests.
+"""
+
+import sys
+from pathlib import Path
+
+from . import retrieve_file, urls_from_file
+
+if __name__ == "__main__":
+    urls = urls_from_file(Path(sys.argv[1]))
+    list(map(retrieve_file, urls))
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/setupcfg_examples.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/setupcfg_examples.txt
new file mode 100644
index 0000000000000000000000000000000000000000..6aab887ff1fe631d97f1abea90a8448040746a12
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/setupcfg_examples.txt
@@ -0,0 +1,22 @@
+# ====================================================================
+# Some popular packages that use setup.cfg (and others not so popular)
+# Reference: https://hugovk.github.io/top-pypi-packages/
+# ====================================================================
+https://github.com/pypa/setuptools/raw/52c990172fec37766b3566679724aa8bf70ae06d/setup.cfg
+https://github.com/pypa/wheel/raw/0acd203cd896afec7f715aa2ff5980a403459a3b/setup.cfg
+https://github.com/python/importlib_metadata/raw/2f05392ca980952a6960d82b2f2d2ea10aa53239/setup.cfg
+https://github.com/jaraco/skeleton/raw/d9008b5c510cd6969127a6a2ab6f832edddef296/setup.cfg
+https://github.com/jaraco/zipp/raw/700d3a96390e970b6b962823bfea78b4f7e1c537/setup.cfg
+https://github.com/pallets/jinja/raw/7d72eb7fefb7dce065193967f31f805180508448/setup.cfg
+https://github.com/tkem/cachetools/raw/2fd87a94b8d3861d80e9e4236cd480bfdd21c90d/setup.cfg
+https://github.com/aio-libs/aiohttp/raw/5e0e6b7080f2408d5f1dd544c0e1cf88378b7b10/setup.cfg
+https://github.com/pallets/flask/raw/9486b6cf57bd6a8a261f67091aca8ca78eeec1e3/setup.cfg
+https://github.com/pallets/click/raw/6411f425fae545f42795665af4162006b36c5e4a/setup.cfg
+https://github.com/sqlalchemy/sqlalchemy/raw/533f5718904b620be8d63f2474229945d6f8ba5d/setup.cfg
+https://github.com/pytest-dev/pluggy/raw/461ef63291d13589c4e21aa182cd1529257e9a0a/setup.cfg
+https://github.com/pytest-dev/pytest/raw/c7be96dae487edbd2f55b561b31b68afac1dabe6/setup.cfg
+https://github.com/platformdirs/platformdirs/raw/7b7852128dd6f07511b618d6edea35046bd0c6ff/setup.cfg
+https://github.com/pandas-dev/pandas/raw/bc17343f934a33dc231c8c74be95d8365537c376/setup.cfg
+https://github.com/django/django/raw/4e249d11a6e56ca8feb4b055b681cec457ef3a3d/setup.cfg
+https://github.com/pyscaffold/pyscaffold/raw/de7aa5dc059fbd04307419c667cc4961bc9df4b8/setup.cfg
+https://github.com/pypa/virtualenv/raw/f92eda6e3da26a4d28c2663ffb85c4960bdb990c/setup.cfg
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_apply_pyprojecttoml.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_apply_pyprojecttoml.py
new file mode 100644
index 0000000000000000000000000000000000000000..8f48c4316d9e9c3d09fe2abda9bd4aab63d90355
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_apply_pyprojecttoml.py
@@ -0,0 +1,774 @@
+"""Make sure that applying the configuration from pyproject.toml is equivalent to
+applying a similar configuration from setup.cfg
+
+To run these tests offline, please have a look on ``./downloads/preload.py``
+"""
+
+from __future__ import annotations
+
+import io
+import re
+import tarfile
+from inspect import cleandoc
+from pathlib import Path
+from unittest.mock import Mock
+
+import pytest
+from ini2toml.api import LiteTranslator
+from packaging.metadata import Metadata
+
+import setuptools  # noqa: F401 # ensure monkey patch to metadata
+from setuptools._static import is_static
+from setuptools.command.egg_info import write_requirements
+from setuptools.config import expand, pyprojecttoml, setupcfg
+from setuptools.config._apply_pyprojecttoml import _MissingDynamic, _some_attrgetter
+from setuptools.dist import Distribution
+from setuptools.errors import InvalidConfigError, RemovedConfigError
+from setuptools.warnings import InformationOnly, SetuptoolsDeprecationWarning
+
+from .downloads import retrieve_file, urls_from_file
+
+HERE = Path(__file__).parent
+EXAMPLES_FILE = "setupcfg_examples.txt"
+
+
+def makedist(path, **attrs):
+    return Distribution({"src_root": path, **attrs})
+
+
+def _mock_expand_patterns(patterns, *_, **__):
+    """
+    Allow comparing the given patterns for 2 dist objects.
+    We need to strip special chars to avoid errors when validating.
+    """
+    return [
+        re.sub("[^a-z0-9]+", "", p, flags=re.IGNORECASE) or "empty" for p in patterns
+    ]
+
+
+@pytest.mark.parametrize("url", urls_from_file(HERE / EXAMPLES_FILE))
+@pytest.mark.filterwarnings("ignore")
+@pytest.mark.uses_network
+def test_apply_pyproject_equivalent_to_setupcfg(url, monkeypatch, tmp_path):
+    monkeypatch.setattr(expand, "read_attr", Mock(return_value="0.0.1"))
+    monkeypatch.setattr(
+        Distribution, "_expand_patterns", Mock(side_effect=_mock_expand_patterns)
+    )
+    setupcfg_example = retrieve_file(url)
+    pyproject_example = Path(tmp_path, "pyproject.toml")
+    setupcfg_text = setupcfg_example.read_text(encoding="utf-8")
+    toml_config = LiteTranslator().translate(setupcfg_text, "setup.cfg")
+    pyproject_example.write_text(toml_config, encoding="utf-8")
+
+    dist_toml = pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject_example)
+    dist_cfg = setupcfg.apply_configuration(makedist(tmp_path), setupcfg_example)
+
+    pkg_info_toml = core_metadata(dist_toml)
+    pkg_info_cfg = core_metadata(dist_cfg)
+    assert pkg_info_toml == pkg_info_cfg
+
+    if any(getattr(d, "license_files", None) for d in (dist_toml, dist_cfg)):
+        assert set(dist_toml.license_files) == set(dist_cfg.license_files)
+
+    if any(getattr(d, "entry_points", None) for d in (dist_toml, dist_cfg)):
+        print(dist_cfg.entry_points)
+        ep_toml = {
+            (k, *sorted(i.replace(" ", "") for i in v))
+            for k, v in dist_toml.entry_points.items()
+        }
+        ep_cfg = {
+            (k, *sorted(i.replace(" ", "") for i in v))
+            for k, v in dist_cfg.entry_points.items()
+        }
+        assert ep_toml == ep_cfg
+
+    if any(getattr(d, "package_data", None) for d in (dist_toml, dist_cfg)):
+        pkg_data_toml = {(k, *sorted(v)) for k, v in dist_toml.package_data.items()}
+        pkg_data_cfg = {(k, *sorted(v)) for k, v in dist_cfg.package_data.items()}
+        assert pkg_data_toml == pkg_data_cfg
+
+    if any(getattr(d, "data_files", None) for d in (dist_toml, dist_cfg)):
+        data_files_toml = {(k, *sorted(v)) for k, v in dist_toml.data_files}
+        data_files_cfg = {(k, *sorted(v)) for k, v in dist_cfg.data_files}
+        assert data_files_toml == data_files_cfg
+
+    assert set(dist_toml.install_requires) == set(dist_cfg.install_requires)
+    if any(getattr(d, "extras_require", None) for d in (dist_toml, dist_cfg)):
+        extra_req_toml = {(k, *sorted(v)) for k, v in dist_toml.extras_require.items()}
+        extra_req_cfg = {(k, *sorted(v)) for k, v in dist_cfg.extras_require.items()}
+        assert extra_req_toml == extra_req_cfg
+
+
+PEP621_EXAMPLE = """\
+[project]
+name = "spam"
+version = "2020.0.0"
+description = "Lovely Spam! Wonderful Spam!"
+readme = "README.rst"
+requires-python = ">=3.8"
+license-files = ["LICENSE.txt"]  # Updated to be PEP 639 compliant
+keywords = ["egg", "bacon", "sausage", "tomatoes", "Lobster Thermidor"]
+authors = [
+  {email = "hi@pradyunsg.me"},
+  {name = "Tzu-Ping Chung"}
+]
+maintainers = [
+  {name = "Brett Cannon", email = "brett@python.org"},
+  {name = "John X. Ãørçeč", email = "john@utf8.org"},
+  {name = "Γαμα קּ 東", email = "gama@utf8.org"},
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Programming Language :: Python"
+]
+
+dependencies = [
+  "httpx",
+  "gidgethub[httpx]>4.0.0",
+  "django>2.1; os_name != 'nt'",
+  "django>2.0; os_name == 'nt'"
+]
+
+[project.optional-dependencies]
+test = [
+  "pytest < 5.0.0",
+  "pytest-cov[all]"
+]
+
+[project.urls]
+homepage = "http://example.com"
+documentation = "http://readthedocs.org"
+repository = "http://github.com"
+changelog = "http://github.com/me/spam/blob/master/CHANGELOG.md"
+
+[project.scripts]
+spam-cli = "spam:main_cli"
+
+[project.gui-scripts]
+spam-gui = "spam:main_gui"
+
+[project.entry-points."spam.magical"]
+tomatoes = "spam:main_tomatoes"
+"""
+
+PEP621_INTERNATIONAL_EMAIL_EXAMPLE = """\
+[project]
+name = "spam"
+version = "2020.0.0"
+authors = [
+  {email = "hi@pradyunsg.me"},
+  {name = "Tzu-Ping Chung"}
+]
+maintainers = [
+  {name = "अंकित अहलावत", email = "ankit@example.com"},
+]
+"""
+
+PEP621_EXAMPLE_SCRIPT = """
+def main_cli(): pass
+def main_gui(): pass
+def main_tomatoes(): pass
+"""
+
+PEP639_LICENSE_TEXT = """\
+[project]
+name = "spam"
+version = "2020.0.0"
+authors = [
+  {email = "hi@pradyunsg.me"},
+  {name = "Tzu-Ping Chung"}
+]
+license = {text = "MIT"}
+"""
+
+PEP639_LICENSE_EXPRESSION = """\
+[project]
+name = "spam"
+version = "2020.0.0"
+authors = [
+  {email = "hi@pradyunsg.me"},
+  {name = "Tzu-Ping Chung"}
+]
+license = "mit or apache-2.0"  # should be normalized in metadata
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Programming Language :: Python",
+]
+"""
+
+
+def _pep621_example_project(
+    tmp_path,
+    readme="README.rst",
+    pyproject_text=PEP621_EXAMPLE,
+):
+    pyproject = tmp_path / "pyproject.toml"
+    text = pyproject_text
+    replacements = {'readme = "README.rst"': f'readme = "{readme}"'}
+    for orig, subst in replacements.items():
+        text = text.replace(orig, subst)
+    pyproject.write_text(text, encoding="utf-8")
+
+    (tmp_path / readme).write_text("hello world", encoding="utf-8")
+    (tmp_path / "LICENSE.txt").write_text("--- LICENSE stub ---", encoding="utf-8")
+    (tmp_path / "spam.py").write_text(PEP621_EXAMPLE_SCRIPT, encoding="utf-8")
+    return pyproject
+
+
+def test_pep621_example(tmp_path):
+    """Make sure the example in PEP 621 works"""
+    pyproject = _pep621_example_project(tmp_path)
+    dist = pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+    assert set(dist.metadata.license_files) == {"LICENSE.txt"}
+
+
+@pytest.mark.parametrize(
+    ("readme", "ctype"),
+    [
+        ("Readme.txt", "text/plain"),
+        ("readme.md", "text/markdown"),
+        ("text.rst", "text/x-rst"),
+    ],
+)
+def test_readme_content_type(tmp_path, readme, ctype):
+    pyproject = _pep621_example_project(tmp_path, readme)
+    dist = pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+    assert dist.metadata.long_description_content_type == ctype
+
+
+def test_undefined_content_type(tmp_path):
+    pyproject = _pep621_example_project(tmp_path, "README.tex")
+    with pytest.raises(ValueError, match="Undefined content type for README.tex"):
+        pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+
+
+def test_no_explicit_content_type_for_missing_extension(tmp_path):
+    pyproject = _pep621_example_project(tmp_path, "README")
+    dist = pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+    assert dist.metadata.long_description_content_type is None
+
+
+@pytest.mark.parametrize(
+    ("pyproject_text", "expected_maintainers_meta_value"),
+    (
+        pytest.param(
+            PEP621_EXAMPLE,
+            (
+                'Brett Cannon , "John X. Ãørçeč" , '
+                'Γαμα קּ 東 '
+            ),
+            id='non-international-emails',
+        ),
+        pytest.param(
+            PEP621_INTERNATIONAL_EMAIL_EXAMPLE,
+            'Ankit Ahlawat <अंकित@उदाहरण.भारत>',
+            marks=pytest.mark.xfail(
+                reason="CPython's `email.headerregistry.Address` only supports "
+                'RFC 5322, as of Oct 20, 2025 and latest Python 3.13.0',
+                strict=True,
+            ),
+            id='international-email',
+        ),
+    ),
+)
+def test_utf8_maintainer_in_metadata(  # issue-3663
+    expected_maintainers_meta_value,
+    pyproject_text,
+    tmp_path,
+):
+    pyproject = _pep621_example_project(
+        tmp_path,
+        "README",
+        pyproject_text=pyproject_text,
+    )
+    dist = pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+    assert dist.metadata.maintainer_email == expected_maintainers_meta_value
+    pkg_file = tmp_path / "PKG-FILE"
+    with open(pkg_file, "w", encoding="utf-8") as fh:
+        dist.metadata.write_pkg_file(fh)
+    content = pkg_file.read_text(encoding="utf-8")
+    assert f"Maintainer-email: {expected_maintainers_meta_value}" in content
+
+
+@pytest.mark.parametrize(
+    (
+        'pyproject_text',
+        'license',
+        'license_expression',
+        'content_str',
+        'not_content_str',
+    ),
+    (
+        pytest.param(
+            PEP639_LICENSE_TEXT,
+            'MIT',
+            None,
+            'License: MIT',
+            'License-Expression: ',
+            id='license-text',
+            marks=[
+                pytest.mark.filterwarnings(
+                    "ignore:.project.license. as a TOML table is deprecated",
+                )
+            ],
+        ),
+        pytest.param(
+            PEP639_LICENSE_EXPRESSION,
+            None,
+            'MIT OR Apache-2.0',
+            'License-Expression: MIT OR Apache-2.0',
+            'License: ',
+            id='license-expression',
+        ),
+    ),
+)
+def test_license_in_metadata(
+    license,
+    license_expression,
+    content_str,
+    not_content_str,
+    pyproject_text,
+    tmp_path,
+):
+    pyproject = _pep621_example_project(
+        tmp_path,
+        "README",
+        pyproject_text=pyproject_text,
+    )
+    dist = pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+    assert dist.metadata.license == license
+    assert dist.metadata.license_expression == license_expression
+    pkg_file = tmp_path / "PKG-FILE"
+    with open(pkg_file, "w", encoding="utf-8") as fh:
+        dist.metadata.write_pkg_file(fh)
+    content = pkg_file.read_text(encoding="utf-8")
+    assert "Metadata-Version: 2.4" in content
+    assert content_str in content
+    assert not_content_str not in content
+
+
+def test_license_classifier_with_license_expression(tmp_path):
+    text = PEP639_LICENSE_EXPRESSION.rsplit("\n", 2)[0]
+    pyproject = _pep621_example_project(
+        tmp_path,
+        "README",
+        f"{text}\n    \"License :: OSI Approved :: MIT License\"\n]",
+    )
+    msg = "License classifiers have been superseded by license expressions"
+    with pytest.raises(InvalidConfigError, match=msg) as exc:
+        pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+
+    assert "License :: OSI Approved :: MIT License" in str(exc.value)
+
+
+def test_license_classifier_without_license_expression(tmp_path):
+    text = """\
+    [project]
+    name = "spam"
+    version = "2020.0.0"
+    license = {text = "mit or apache-2.0"}
+    classifiers = ["License :: OSI Approved :: MIT License"]
+    """
+    pyproject = _pep621_example_project(tmp_path, "README", text)
+
+    msg1 = "License classifiers are deprecated(?:.|\n)*MIT License"
+    msg2 = ".project.license. as a TOML table is deprecated"
+    with (
+        pytest.warns(SetuptoolsDeprecationWarning, match=msg1),
+        pytest.warns(SetuptoolsDeprecationWarning, match=msg2),
+    ):
+        dist = pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+
+    # Check license classifier is still included
+    assert dist.metadata.get_classifiers() == ["License :: OSI Approved :: MIT License"]
+
+
+class TestLicenseFiles:
+    def base_pyproject(
+        self,
+        tmp_path,
+        additional_text="",
+        license_toml='license = {file = "LICENSE.txt"}\n',
+    ):
+        text = PEP639_LICENSE_EXPRESSION
+
+        # Sanity-check
+        assert 'license = "mit or apache-2.0"' in text
+        assert 'license-files' not in text
+        assert "[tool.setuptools]" not in text
+
+        text = re.sub(
+            r"(license = .*)\n",
+            license_toml,
+            text,
+            count=1,
+        )
+        assert license_toml in text  # sanity check
+        text = f"{text}\n{additional_text}\n"
+        pyproject = _pep621_example_project(tmp_path, "README", pyproject_text=text)
+        return pyproject
+
+    def base_pyproject_license_pep639(self, tmp_path, additional_text=""):
+        return self.base_pyproject(
+            tmp_path,
+            additional_text=additional_text,
+            license_toml='license = "licenseref-Proprietary"'
+            '\nlicense-files = ["_FILE*"]\n',
+        )
+
+    def test_both_license_and_license_files_defined(self, tmp_path):
+        setuptools_config = '[tool.setuptools]\nlicense-files = ["_FILE*"]'
+        pyproject = self.base_pyproject(tmp_path, setuptools_config)
+
+        (tmp_path / "_FILE.txt").touch()
+        (tmp_path / "_FILE.rst").touch()
+
+        # Would normally match the `license_files` patterns, but we want to exclude it
+        # by being explicit. On the other hand, contents should be added to `license`
+        license = tmp_path / "LICENSE.txt"
+        license.write_text("LicenseRef-Proprietary\n", encoding="utf-8")
+
+        msg1 = "'tool.setuptools.license-files' is deprecated in favor of 'project.license-files'"
+        msg2 = ".project.license. as a TOML table is deprecated"
+        with (
+            pytest.warns(SetuptoolsDeprecationWarning, match=msg1),
+            pytest.warns(SetuptoolsDeprecationWarning, match=msg2),
+        ):
+            dist = pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+        assert set(dist.metadata.license_files) == {"_FILE.rst", "_FILE.txt"}
+        assert dist.metadata.license == "LicenseRef-Proprietary\n"
+
+    def test_both_license_and_license_files_defined_pep639(self, tmp_path):
+        # Set license and license-files
+        pyproject = self.base_pyproject_license_pep639(tmp_path)
+
+        (tmp_path / "_FILE.txt").touch()
+        (tmp_path / "_FILE.rst").touch()
+
+        msg = "Normalizing.*LicenseRef"
+        with pytest.warns(InformationOnly, match=msg):
+            dist = pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+
+        assert set(dist.metadata.license_files) == {"_FILE.rst", "_FILE.txt"}
+        assert dist.metadata.license is None
+        assert dist.metadata.license_expression == "LicenseRef-Proprietary"
+
+    def test_license_files_defined_twice(self, tmp_path):
+        # Set project.license-files and tools.setuptools.license-files
+        setuptools_config = '[tool.setuptools]\nlicense-files = ["_FILE*"]'
+        pyproject = self.base_pyproject_license_pep639(tmp_path, setuptools_config)
+
+        msg = "'project.license-files' is defined already. Remove 'tool.setuptools.license-files'"
+        with pytest.raises(InvalidConfigError, match=msg):
+            pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+
+    def test_default_patterns(self, tmp_path):
+        setuptools_config = '[tool.setuptools]\nzip-safe = false'
+        # ^ used just to trigger section validation
+        pyproject = self.base_pyproject(tmp_path, setuptools_config, license_toml="")
+
+        license_files = "LICENCE-a.html COPYING-abc.txt AUTHORS-xyz NOTICE,def".split()
+
+        for fname in license_files:
+            (tmp_path / fname).write_text(f"{fname}\n", encoding="utf-8")
+
+        dist = pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+
+        assert (tmp_path / "LICENSE.txt").exists()  # from base example
+        assert set(dist.metadata.license_files) == {*license_files, "LICENSE.txt"}
+
+    def test_missing_patterns(self, tmp_path):
+        pyproject = self.base_pyproject_license_pep639(tmp_path)
+        assert list(tmp_path.glob("_FILE*")) == []  # sanity check
+
+        msg1 = "Cannot find any files for the given pattern.*"
+        msg2 = "Normalizing 'licenseref-Proprietary' to 'LicenseRef-Proprietary'"
+        with (
+            pytest.warns(SetuptoolsDeprecationWarning, match=msg1),
+            pytest.warns(InformationOnly, match=msg2),
+        ):
+            pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+
+    def test_deprecated_file_expands_to_text(self, tmp_path):
+        """Make sure the old example with ``license = {text = ...}`` works"""
+
+        assert 'license-files = ["LICENSE.txt"]' in PEP621_EXAMPLE  # sanity check
+        text = PEP621_EXAMPLE.replace(
+            'license-files = ["LICENSE.txt"]',
+            'license = {file = "LICENSE.txt"}',
+        )
+        pyproject = _pep621_example_project(tmp_path, pyproject_text=text)
+
+        msg = ".project.license. as a TOML table is deprecated"
+        with pytest.warns(SetuptoolsDeprecationWarning, match=msg):
+            dist = pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+
+        assert dist.metadata.license == "--- LICENSE stub ---"
+        assert set(dist.metadata.license_files) == {"LICENSE.txt"}  # auto-filled
+
+
+class TestPyModules:
+    # https://github.com/pypa/setuptools/issues/4316
+
+    def dist(self, name):
+        toml_config = f"""
+        [project]
+        name = "test"
+        version = "42.0"
+        [tool.setuptools]
+        py-modules = [{name!r}]
+        """
+        pyproject = Path("pyproject.toml")
+        pyproject.write_text(cleandoc(toml_config), encoding="utf-8")
+        return pyprojecttoml.apply_configuration(Distribution({}), pyproject)
+
+    @pytest.mark.parametrize("module", ["pip-run", "abc-d.λ-xyz-e"])
+    def test_valid_module_name(self, tmp_path, monkeypatch, module):
+        monkeypatch.chdir(tmp_path)
+        assert module in self.dist(module).py_modules
+
+    @pytest.mark.parametrize("module", ["pip run", "-pip-run", "pip-run-stubs"])
+    def test_invalid_module_name(self, tmp_path, monkeypatch, module):
+        monkeypatch.chdir(tmp_path)
+        with pytest.raises(ValueError, match="py-modules"):
+            self.dist(module).py_modules
+
+
+class TestExtModules:
+    def test_pyproject_sets_attribute(self, tmp_path, monkeypatch):
+        monkeypatch.chdir(tmp_path)
+        pyproject = Path("pyproject.toml")
+        toml_config = """
+        [project]
+        name = "test"
+        version = "42.0"
+        [tool.setuptools]
+        ext-modules = [
+          {name = "my.ext", sources = ["hello.c", "world.c"]}
+        ]
+        """
+        pyproject.write_text(cleandoc(toml_config), encoding="utf-8")
+        with pytest.warns(pyprojecttoml._ExperimentalConfiguration):
+            dist = pyprojecttoml.apply_configuration(Distribution({}), pyproject)
+        assert len(dist.ext_modules) == 1
+        assert dist.ext_modules[0].name == "my.ext"
+        assert set(dist.ext_modules[0].sources) == {"hello.c", "world.c"}
+
+
+class TestDeprecatedFields:
+    def test_namespace_packages(self, tmp_path):
+        pyproject = tmp_path / "pyproject.toml"
+        config = """
+        [project]
+        name = "myproj"
+        version = "42"
+        [tool.setuptools]
+        namespace-packages = ["myproj.pkg"]
+        """
+        pyproject.write_text(cleandoc(config), encoding="utf-8")
+        with pytest.raises(RemovedConfigError, match="namespace-packages"):
+            pyprojecttoml.apply_configuration(makedist(tmp_path), pyproject)
+
+
+class TestPresetField:
+    def pyproject(self, tmp_path, dynamic, extra_content=""):
+        content = f"[project]\nname = 'proj'\ndynamic = {dynamic!r}\n"
+        if "version" not in dynamic:
+            content += "version = '42'\n"
+        file = tmp_path / "pyproject.toml"
+        file.write_text(content + extra_content, encoding="utf-8")
+        return file
+
+    @pytest.mark.parametrize(
+        ("attr", "field", "value"),
+        [
+            ("license_expression", "license", "MIT"),
+            pytest.param(
+                *("license", "license", "Not SPDX"),
+                marks=[pytest.mark.filterwarnings("ignore:.*license. overwritten")],
+            ),
+            ("classifiers", "classifiers", ["Private :: Classifier"]),
+            ("entry_points", "scripts", {"console_scripts": ["foobar=foobar:main"]}),
+            ("entry_points", "gui-scripts", {"gui_scripts": ["bazquux=bazquux:main"]}),
+            pytest.param(
+                *("install_requires", "dependencies", ["six"]),
+                marks=[
+                    pytest.mark.filterwarnings("ignore:.*install_requires. overwritten")
+                ],
+            ),
+        ],
+    )
+    def test_not_listed_in_dynamic(self, tmp_path, attr, field, value):
+        """Setuptools cannot set a field if not listed in ``dynamic``"""
+        pyproject = self.pyproject(tmp_path, [])
+        dist = makedist(tmp_path, **{attr: value})
+        msg = re.compile(f"defined outside of `pyproject.toml`:.*{field}", re.DOTALL)
+        with pytest.warns(_MissingDynamic, match=msg):
+            dist = pyprojecttoml.apply_configuration(dist, pyproject)
+
+        dist_value = _some_attrgetter(f"metadata.{attr}", attr)(dist)
+        assert not dist_value
+
+    @pytest.mark.parametrize(
+        ("attr", "field", "value"),
+        [
+            ("license_expression", "license", "MIT"),
+            ("install_requires", "dependencies", []),
+            ("extras_require", "optional-dependencies", {}),
+            ("install_requires", "dependencies", ["six"]),
+            ("classifiers", "classifiers", ["Private :: Classifier"]),
+        ],
+    )
+    def test_listed_in_dynamic(self, tmp_path, attr, field, value):
+        pyproject = self.pyproject(tmp_path, [field])
+        dist = makedist(tmp_path, **{attr: value})
+        dist = pyprojecttoml.apply_configuration(dist, pyproject)
+        dist_value = _some_attrgetter(f"metadata.{attr}", attr)(dist)
+        assert dist_value == value
+
+    def test_license_files_exempt_from_dynamic(self, monkeypatch, tmp_path):
+        """
+        license-file is currently not considered in the context of dynamic.
+        As per 2025-02-19, https://packaging.python.org/en/latest/specifications/pyproject-toml/#license-files
+        allows setuptools to fill-in `license-files` the way it sees fit:
+
+        > If the license-files key is not defined, tools can decide how to handle license files.
+        > For example they can choose not to include any files or use their own
+        > logic to discover the appropriate files in the distribution.
+
+        Using license_files from setup.py to fill-in the value is in accordance
+        with this rule.
+        """
+        monkeypatch.chdir(tmp_path)
+        pyproject = self.pyproject(tmp_path, [])
+        dist = makedist(tmp_path, license_files=["LIC*"])
+        (tmp_path / "LIC1").write_text("42", encoding="utf-8")
+        dist = pyprojecttoml.apply_configuration(dist, pyproject)
+        assert dist.metadata.license_files == ["LIC1"]
+
+    def test_warning_overwritten_dependencies(self, tmp_path):
+        src = "[project]\nname='pkg'\nversion='0.1'\ndependencies=['click']\n"
+        pyproject = tmp_path / "pyproject.toml"
+        pyproject.write_text(src, encoding="utf-8")
+        dist = makedist(tmp_path, install_requires=["wheel"])
+        with pytest.warns(match="`install_requires` overwritten"):
+            dist = pyprojecttoml.apply_configuration(dist, pyproject)
+        assert "wheel" not in dist.install_requires
+
+    def test_optional_dependencies_dont_remove_env_markers(self, tmp_path):
+        """
+        Internally setuptools converts dependencies with markers to "extras".
+        If ``install_requires`` is given by ``setup.py``, we have to ensure that
+        applying ``optional-dependencies`` does not overwrite the mandatory
+        dependencies with markers (see #3204).
+        """
+        # If setuptools replace its internal mechanism that uses `requires.txt`
+        # this test has to be rewritten to adapt accordingly
+        extra = "\n[project.optional-dependencies]\nfoo = ['bar>1']\n"
+        pyproject = self.pyproject(tmp_path, ["dependencies"], extra)
+        install_req = ['importlib-resources (>=3.0.0) ; python_version < "3.7"']
+        dist = makedist(tmp_path, install_requires=install_req)
+        dist = pyprojecttoml.apply_configuration(dist, pyproject)
+        assert "foo" in dist.extras_require
+        egg_info = dist.get_command_obj("egg_info")
+        write_requirements(egg_info, tmp_path, tmp_path / "requires.txt")
+        reqs = (tmp_path / "requires.txt").read_text(encoding="utf-8")
+        assert "importlib-resources" in reqs
+        assert "bar" in reqs
+        assert ':python_version < "3.7"' in reqs
+
+    @pytest.mark.parametrize(
+        ("field", "group"),
+        [("scripts", "console_scripts"), ("gui-scripts", "gui_scripts")],
+    )
+    @pytest.mark.filterwarnings("error")
+    def test_scripts_dont_require_dynamic_entry_points(self, tmp_path, field, group):
+        # Issue 3862
+        pyproject = self.pyproject(tmp_path, [field])
+        dist = makedist(tmp_path, entry_points={group: ["foobar=foobar:main"]})
+        dist = pyprojecttoml.apply_configuration(dist, pyproject)
+        assert group in dist.entry_points
+
+
+class TestMeta:
+    def test_example_file_in_sdist(self, setuptools_sdist):
+        """Meta test to ensure tests can run from sdist"""
+        with tarfile.open(setuptools_sdist) as tar:
+            assert any(name.endswith(EXAMPLES_FILE) for name in tar.getnames())
+
+
+class TestInteropCommandLineParsing:
+    def test_version(self, tmp_path, monkeypatch, capsys):
+        # See pypa/setuptools#4047
+        # This test can be removed once the CLI interface of setup.py is removed
+        monkeypatch.chdir(tmp_path)
+        toml_config = """
+        [project]
+        name = "test"
+        version = "42.0"
+        """
+        pyproject = Path(tmp_path, "pyproject.toml")
+        pyproject.write_text(cleandoc(toml_config), encoding="utf-8")
+        opts = {"script_args": ["--version"]}
+        dist = pyprojecttoml.apply_configuration(Distribution(opts), pyproject)
+        dist.parse_command_line()  # <-- there should be no exception here.
+        captured = capsys.readouterr()
+        assert "42.0" in captured.out
+
+
+class TestStaticConfig:
+    def test_mark_static_fields(self, tmp_path, monkeypatch):
+        monkeypatch.chdir(tmp_path)
+        toml_config = """
+        [project]
+        name = "test"
+        version = "42.0"
+        dependencies = ["hello"]
+        keywords = ["world"]
+        classifiers = ["private :: hello world"]
+        [tool.setuptools]
+        obsoletes = ["abcd"]
+        provides = ["abcd"]
+        platforms = ["abcd"]
+        """
+        pyproject = Path(tmp_path, "pyproject.toml")
+        pyproject.write_text(cleandoc(toml_config), encoding="utf-8")
+        dist = pyprojecttoml.apply_configuration(Distribution({}), pyproject)
+        assert is_static(dist.install_requires)
+        assert is_static(dist.metadata.keywords)
+        assert is_static(dist.metadata.classifiers)
+        assert is_static(dist.metadata.obsoletes)
+        assert is_static(dist.metadata.provides)
+        assert is_static(dist.metadata.platforms)
+
+
+# --- Auxiliary Functions ---
+
+
+def core_metadata(dist) -> str:
+    with io.StringIO() as buffer:
+        dist.metadata.write_pkg_file(buffer)
+        pkg_file_txt = buffer.getvalue()
+
+    # Make sure core metadata is valid
+    Metadata.from_email(pkg_file_txt, validate=True)  # can raise exceptions
+
+    skip_prefixes: tuple[str, ...] = ()
+    skip_lines = set()
+    # ---- DIFF NORMALISATION ----
+    # PEP 621 is very particular about author/maintainer metadata conversion, so skip
+    skip_prefixes += ("Author:", "Author-email:", "Maintainer:", "Maintainer-email:")
+    # May be redundant with Home-page
+    skip_prefixes += ("Project-URL: Homepage,", "Home-page:")
+    # May be missing in original (relying on default) but backfilled in the TOML
+    skip_prefixes += ("Description-Content-Type:",)
+    # Remove empty lines
+    skip_lines.add("")
+
+    result = []
+    for line in pkg_file_txt.splitlines():
+        if line.startswith(skip_prefixes) or line in skip_lines:
+            continue
+        result.append(line + "\n")
+
+    return "".join(result)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_expand.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_expand.py
new file mode 100644
index 0000000000000000000000000000000000000000..c5710ec63d7d9d4ed7b709203bb2fc4b512f2093
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_expand.py
@@ -0,0 +1,247 @@
+import os
+import sys
+from pathlib import Path
+
+import pytest
+
+from setuptools._static import is_static
+from setuptools.config import expand
+from setuptools.discovery import find_package_path
+
+from distutils.errors import DistutilsOptionError
+
+
+def write_files(files, root_dir):
+    for file, content in files.items():
+        path = root_dir / file
+        path.parent.mkdir(exist_ok=True, parents=True)
+        path.write_text(content, encoding="utf-8")
+
+
+def test_glob_relative(tmp_path, monkeypatch):
+    files = {
+        "dir1/dir2/dir3/file1.txt",
+        "dir1/dir2/file2.txt",
+        "dir1/file3.txt",
+        "a.ini",
+        "b.ini",
+        "dir1/c.ini",
+        "dir1/dir2/a.ini",
+    }
+
+    write_files({k: "" for k in files}, tmp_path)
+    patterns = ["**/*.txt", "[ab].*", "**/[ac].ini"]
+    monkeypatch.chdir(tmp_path)
+    assert set(expand.glob_relative(patterns)) == files
+    # Make sure the same APIs work outside cwd
+    assert set(expand.glob_relative(patterns, tmp_path)) == files
+
+
+def test_read_files(tmp_path, monkeypatch):
+    dir_ = tmp_path / "dir_"
+    (tmp_path / "_dir").mkdir(exist_ok=True)
+    (tmp_path / "a.txt").touch()
+    files = {"a.txt": "a", "dir1/b.txt": "b", "dir1/dir2/c.txt": "c"}
+    write_files(files, dir_)
+
+    secrets = Path(str(dir_) + "secrets")
+    secrets.mkdir(exist_ok=True)
+    write_files({"secrets.txt": "secret keys"}, secrets)
+
+    with monkeypatch.context() as m:
+        m.chdir(dir_)
+        assert expand.read_files(list(files)) == "a\nb\nc"
+
+        cannot_access_msg = r"Cannot access '.*\.\..a\.txt'"
+        with pytest.raises(DistutilsOptionError, match=cannot_access_msg):
+            expand.read_files(["../a.txt"])
+
+        cannot_access_secrets_msg = r"Cannot access '.*secrets\.txt'"
+        with pytest.raises(DistutilsOptionError, match=cannot_access_secrets_msg):
+            expand.read_files(["../dir_secrets/secrets.txt"])
+
+    # Make sure the same APIs work outside cwd
+    assert expand.read_files(list(files), dir_) == "a\nb\nc"
+    with pytest.raises(DistutilsOptionError, match=cannot_access_msg):
+        expand.read_files(["../a.txt"], dir_)
+
+
+class TestReadAttr:
+    @pytest.mark.parametrize(
+        "example",
+        [
+            # No cookie means UTF-8:
+            b"__version__ = '\xc3\xa9'\nraise SystemExit(1)\n",
+            # If a cookie is present, honor it:
+            b"# -*- coding: utf-8 -*-\n__version__ = '\xc3\xa9'\nraise SystemExit(1)\n",
+            b"# -*- coding: latin1 -*-\n__version__ = '\xe9'\nraise SystemExit(1)\n",
+        ],
+    )
+    def test_read_attr_encoding_cookie(self, example, tmp_path):
+        (tmp_path / "mod.py").write_bytes(example)
+        assert expand.read_attr('mod.__version__', root_dir=tmp_path) == 'é'
+
+    def test_read_attr(self, tmp_path, monkeypatch):
+        files = {
+            "pkg/__init__.py": "",
+            "pkg/sub/__init__.py": "VERSION = '0.1.1'",
+            "pkg/sub/mod.py": (
+                "VALUES = {'a': 0, 'b': {42}, 'c': (0, 1, 1)}\nraise SystemExit(1)"
+            ),
+        }
+        write_files(files, tmp_path)
+
+        with monkeypatch.context() as m:
+            m.chdir(tmp_path)
+            # Make sure it can read the attr statically without evaluating the module
+            version = expand.read_attr('pkg.sub.VERSION')
+            values = expand.read_attr('lib.mod.VALUES', {'lib': 'pkg/sub'})
+
+        assert version == '0.1.1'
+        assert is_static(values)
+
+        assert values['a'] == 0
+        assert values['b'] == {42}
+        assert is_static(values)
+
+        # Make sure the same APIs work outside cwd
+        assert expand.read_attr('pkg.sub.VERSION', root_dir=tmp_path) == '0.1.1'
+        values = expand.read_attr('lib.mod.VALUES', {'lib': 'pkg/sub'}, tmp_path)
+        assert values['c'] == (0, 1, 1)
+
+    @pytest.mark.parametrize(
+        "example",
+        [
+            "VERSION: str\nVERSION = '0.1.1'\nraise SystemExit(1)\n",
+            "VERSION: str = '0.1.1'\nraise SystemExit(1)\n",
+        ],
+    )
+    def test_read_annotated_attr(self, tmp_path, example):
+        files = {
+            "pkg/__init__.py": "",
+            "pkg/sub/__init__.py": example,
+        }
+        write_files(files, tmp_path)
+        # Make sure this attribute can be read statically
+        version = expand.read_attr('pkg.sub.VERSION', root_dir=tmp_path)
+        assert version == '0.1.1'
+        assert is_static(version)
+
+    @pytest.mark.parametrize(
+        "example",
+        [
+            "VERSION = (lambda: '0.1.1')()\n",
+            "def fn(): return '0.1.1'\nVERSION = fn()\n",
+            "VERSION: str = (lambda: '0.1.1')()\n",
+        ],
+    )
+    def test_read_dynamic_attr(self, tmp_path, monkeypatch, example):
+        files = {
+            "pkg/__init__.py": "",
+            "pkg/sub/__init__.py": example,
+        }
+        write_files(files, tmp_path)
+        monkeypatch.chdir(tmp_path)
+        version = expand.read_attr('pkg.sub.VERSION')
+        assert version == '0.1.1'
+        assert not is_static(version)
+
+    def test_import_order(self, tmp_path):
+        """
+        Sometimes the import machinery will import the parent package of a nested
+        module, which triggers side-effects and might create problems (see issue #3176)
+
+        ``read_attr`` should bypass these limitations by resolving modules statically
+        (via ast.literal_eval).
+        """
+        files = {
+            "src/pkg/__init__.py": "from .main import func\nfrom .about import version",
+            "src/pkg/main.py": "import super_complicated_dep\ndef func(): return 42",
+            "src/pkg/about.py": "version = '42'",
+        }
+        write_files(files, tmp_path)
+        attr_desc = "pkg.about.version"
+        package_dir = {"": "src"}
+        # `import super_complicated_dep` should not run, otherwise the build fails
+        assert expand.read_attr(attr_desc, package_dir, tmp_path) == "42"
+
+
+@pytest.mark.parametrize(
+    ("package_dir", "file", "module", "return_value"),
+    [
+        ({"": "src"}, "src/pkg/main.py", "pkg.main", 42),
+        ({"pkg": "lib"}, "lib/main.py", "pkg.main", 13),
+        ({}, "single_module.py", "single_module", 70),
+        ({}, "flat_layout/pkg.py", "flat_layout.pkg", 836),
+    ],
+)
+def test_resolve_class(monkeypatch, tmp_path, package_dir, file, module, return_value):
+    monkeypatch.setattr(sys, "modules", {})  # reproducibility
+    files = {file: f"class Custom:\n    def testing(self): return {return_value}"}
+    write_files(files, tmp_path)
+    cls = expand.resolve_class(f"{module}.Custom", package_dir, tmp_path)
+    assert cls().testing() == return_value
+
+
+@pytest.mark.parametrize(
+    ("args", "pkgs"),
+    [
+        ({"where": ["."], "namespaces": False}, {"pkg", "other"}),
+        ({"where": [".", "dir1"], "namespaces": False}, {"pkg", "other", "dir2"}),
+        ({"namespaces": True}, {"pkg", "other", "dir1", "dir1.dir2"}),
+        ({}, {"pkg", "other", "dir1", "dir1.dir2"}),  # default value for `namespaces`
+    ],
+)
+def test_find_packages(tmp_path, args, pkgs):
+    files = {
+        "pkg/__init__.py",
+        "other/__init__.py",
+        "dir1/dir2/__init__.py",
+    }
+    write_files({k: "" for k in files}, tmp_path)
+
+    package_dir = {}
+    kwargs = {"root_dir": tmp_path, "fill_package_dir": package_dir, **args}
+    where = kwargs.get("where", ["."])
+    assert set(expand.find_packages(**kwargs)) == pkgs
+    for pkg in pkgs:
+        pkg_path = find_package_path(pkg, package_dir, tmp_path)
+        assert os.path.exists(pkg_path)
+
+    # Make sure the same APIs work outside cwd
+    where = [
+        str((tmp_path / p).resolve()).replace(os.sep, "/")  # ensure posix-style paths
+        for p in args.pop("where", ["."])
+    ]
+
+    assert set(expand.find_packages(where=where, **args)) == pkgs
+
+
+@pytest.mark.parametrize(
+    ("files", "where", "expected_package_dir"),
+    [
+        (["pkg1/__init__.py", "pkg1/other.py"], ["."], {}),
+        (["pkg1/__init__.py", "pkg2/__init__.py"], ["."], {}),
+        (["src/pkg1/__init__.py", "src/pkg1/other.py"], ["src"], {"": "src"}),
+        (["src/pkg1/__init__.py", "src/pkg2/__init__.py"], ["src"], {"": "src"}),
+        (
+            ["src1/pkg1/__init__.py", "src2/pkg2/__init__.py"],
+            ["src1", "src2"],
+            {"pkg1": "src1/pkg1", "pkg2": "src2/pkg2"},
+        ),
+        (
+            ["src/pkg1/__init__.py", "pkg2/__init__.py"],
+            ["src", "."],
+            {"pkg1": "src/pkg1"},
+        ),
+    ],
+)
+def test_fill_package_dir(tmp_path, files, where, expected_package_dir):
+    write_files({k: "" for k in files}, tmp_path)
+    pkg_dir = {}
+    kwargs = {"root_dir": tmp_path, "fill_package_dir": pkg_dir, "namespaces": False}
+    pkgs = expand.find_packages(where=where, **kwargs)
+    assert set(pkg_dir.items()) == set(expected_package_dir.items())
+    for pkg in pkgs:
+        pkg_path = find_package_path(pkg, pkg_dir, tmp_path)
+        assert os.path.exists(pkg_path)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_pyprojecttoml.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_pyprojecttoml.py
new file mode 100644
index 0000000000000000000000000000000000000000..6d995d23af12b4f103dbb310635d14687ab1a0be
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_pyprojecttoml.py
@@ -0,0 +1,398 @@
+import re
+from configparser import ConfigParser
+from inspect import cleandoc
+
+import jaraco.path
+import pytest
+import tomli_w
+from path import Path
+
+import setuptools  # noqa: F401 # force distutils.core to be patched
+from setuptools.config.pyprojecttoml import (
+    _ToolsTypoInMetadata,
+    apply_configuration,
+    expand_configuration,
+    read_configuration,
+    validate,
+)
+from setuptools.dist import Distribution
+from setuptools.errors import OptionError
+
+import distutils.core
+
+EXAMPLE = """
+[project]
+name = "myproj"
+keywords = ["some", "key", "words"]
+dynamic = ["version", "readme"]
+requires-python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+dependencies = [
+    'importlib-metadata>=0.12;python_version<"3.8"',
+    'importlib-resources>=1.0;python_version<"3.7"',
+    'pathlib2>=2.3.3,<3;python_version < "3.4" and sys.platform != "win32"',
+]
+
+[project.optional-dependencies]
+docs = [
+    "sphinx>=3",
+    "sphinx-argparse>=0.2.5",
+    "sphinx-rtd-theme>=0.4.3",
+]
+testing = [
+    "pytest>=1",
+    "coverage>=3,<5",
+]
+
+[project.scripts]
+exec = "pkg.__main__:exec"
+
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+zip-safe = true
+platforms = ["any"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.cmdclass]
+sdist = "pkg.mod.CustomSdist"
+
+[tool.setuptools.dynamic.version]
+attr = "pkg.__version__.VERSION"
+
+[tool.setuptools.dynamic.readme]
+file = ["README.md"]
+content-type = "text/markdown"
+
+[tool.setuptools.package-data]
+"*" = ["*.txt"]
+
+[tool.setuptools.data-files]
+"data" = ["_files/*.txt"]
+
+[tool.distutils.sdist]
+formats = "gztar"
+
+[tool.distutils.bdist_wheel]
+universal = true
+"""
+
+
+def create_example(path, pkg_root):
+    files = {
+        "pyproject.toml": EXAMPLE,
+        "README.md": "hello world",
+        "_files": {
+            "file.txt": "",
+        },
+    }
+    packages = {
+        "pkg": {
+            "__init__.py": "",
+            "mod.py": "class CustomSdist: pass",
+            "__version__.py": "VERSION = (3, 10)",
+            "__main__.py": "def exec(): print('hello')",
+        },
+    }
+
+    assert pkg_root  # Meta-test: cannot be empty string.
+
+    if pkg_root == ".":
+        files = {**files, **packages}
+        # skip other files: flat-layout will raise error for multi-package dist
+    else:
+        # Use this opportunity to ensure namespaces are discovered
+        files[pkg_root] = {**packages, "other": {"nested": {"__init__.py": ""}}}
+
+    jaraco.path.build(files, prefix=path)
+
+
+def verify_example(config, path, pkg_root):
+    pyproject = path / "pyproject.toml"
+    pyproject.write_text(tomli_w.dumps(config), encoding="utf-8")
+    expanded = expand_configuration(config, path)
+    expanded_project = expanded["project"]
+    assert read_configuration(pyproject, expand=True) == expanded
+    assert expanded_project["version"] == "3.10"
+    assert expanded_project["readme"]["text"] == "hello world"
+    assert "packages" in expanded["tool"]["setuptools"]
+    if pkg_root == ".":
+        # Auto-discovery will raise error for multi-package dist
+        assert set(expanded["tool"]["setuptools"]["packages"]) == {"pkg"}
+    else:
+        assert set(expanded["tool"]["setuptools"]["packages"]) == {
+            "pkg",
+            "other",
+            "other.nested",
+        }
+    assert expanded["tool"]["setuptools"]["include-package-data"] is True
+    assert "" in expanded["tool"]["setuptools"]["package-data"]
+    assert "*" not in expanded["tool"]["setuptools"]["package-data"]
+    assert expanded["tool"]["setuptools"]["data-files"] == [
+        ("data", ["_files/file.txt"])
+    ]
+
+
+def test_read_configuration(tmp_path):
+    create_example(tmp_path, "src")
+    pyproject = tmp_path / "pyproject.toml"
+
+    config = read_configuration(pyproject, expand=False)
+    assert config["project"].get("version") is None
+    assert config["project"].get("readme") is None
+
+    verify_example(config, tmp_path, "src")
+
+
+@pytest.mark.parametrize(
+    ("pkg_root", "opts"),
+    [
+        (".", {}),
+        ("src", {}),
+        ("lib", {"packages": {"find": {"where": ["lib"]}}}),
+    ],
+)
+def test_discovered_package_dir_with_attr_directive_in_config(tmp_path, pkg_root, opts):
+    create_example(tmp_path, pkg_root)
+
+    pyproject = tmp_path / "pyproject.toml"
+
+    config = read_configuration(pyproject, expand=False)
+    assert config["project"].get("version") is None
+    assert config["project"].get("readme") is None
+    config["tool"]["setuptools"].pop("packages", None)
+    config["tool"]["setuptools"].pop("package-dir", None)
+
+    config["tool"]["setuptools"].update(opts)
+    verify_example(config, tmp_path, pkg_root)
+
+
+ENTRY_POINTS = {
+    "console_scripts": {"a": "mod.a:func"},
+    "gui_scripts": {"b": "mod.b:func"},
+    "other": {"c": "mod.c:func [extra]"},
+}
+
+
+class TestEntryPoints:
+    def write_entry_points(self, tmp_path):
+        entry_points = ConfigParser()
+        entry_points.read_dict(ENTRY_POINTS)
+        with open(tmp_path / "entry-points.txt", "w", encoding="utf-8") as f:
+            entry_points.write(f)
+
+    def pyproject(self, dynamic=None):
+        project = {"dynamic": dynamic or ["scripts", "gui-scripts", "entry-points"]}
+        tool = {"dynamic": {"entry-points": {"file": "entry-points.txt"}}}
+        return {"project": project, "tool": {"setuptools": tool}}
+
+    def test_all_listed_in_dynamic(self, tmp_path):
+        self.write_entry_points(tmp_path)
+        expanded = expand_configuration(self.pyproject(), tmp_path)
+        expanded_project = expanded["project"]
+        assert len(expanded_project["scripts"]) == 1
+        assert expanded_project["scripts"]["a"] == "mod.a:func"
+        assert len(expanded_project["gui-scripts"]) == 1
+        assert expanded_project["gui-scripts"]["b"] == "mod.b:func"
+        assert len(expanded_project["entry-points"]) == 1
+        assert expanded_project["entry-points"]["other"]["c"] == "mod.c:func [extra]"
+
+    @pytest.mark.parametrize("missing_dynamic", ("scripts", "gui-scripts"))
+    def test_scripts_not_listed_in_dynamic(self, tmp_path, missing_dynamic):
+        self.write_entry_points(tmp_path)
+        dynamic = {"scripts", "gui-scripts", "entry-points"} - {missing_dynamic}
+
+        msg = f"defined outside of `pyproject.toml`:.*{missing_dynamic}"
+        with pytest.raises(OptionError, match=re.compile(msg, re.DOTALL)):
+            expand_configuration(self.pyproject(dynamic), tmp_path)
+
+
+class TestClassifiers:
+    def test_dynamic(self, tmp_path):
+        # Let's create a project example that has dynamic classifiers
+        # coming from a txt file.
+        create_example(tmp_path, "src")
+        classifiers = cleandoc(
+            """
+            Framework :: Flask
+            Programming Language :: Haskell
+            """
+        )
+        (tmp_path / "classifiers.txt").write_text(classifiers, encoding="utf-8")
+
+        pyproject = tmp_path / "pyproject.toml"
+        config = read_configuration(pyproject, expand=False)
+        dynamic = config["project"]["dynamic"]
+        config["project"]["dynamic"] = list({*dynamic, "classifiers"})
+        dynamic_config = config["tool"]["setuptools"]["dynamic"]
+        dynamic_config["classifiers"] = {"file": "classifiers.txt"}
+
+        # When the configuration is expanded,
+        # each line of the file should be an different classifier.
+        validate(config, pyproject)
+        expanded = expand_configuration(config, tmp_path)
+
+        assert set(expanded["project"]["classifiers"]) == {
+            "Framework :: Flask",
+            "Programming Language :: Haskell",
+        }
+
+    def test_dynamic_without_config(self, tmp_path):
+        config = """
+        [project]
+        name = "myproj"
+        version = '42'
+        dynamic = ["classifiers"]
+        """
+
+        pyproject = tmp_path / "pyproject.toml"
+        pyproject.write_text(cleandoc(config), encoding="utf-8")
+        with pytest.raises(OptionError, match="No configuration .* .classifiers."):
+            read_configuration(pyproject)
+
+    def test_dynamic_readme_from_setup_script_args(self, tmp_path):
+        config = """
+        [project]
+        name = "myproj"
+        version = '42'
+        dynamic = ["readme"]
+        """
+        pyproject = tmp_path / "pyproject.toml"
+        pyproject.write_text(cleandoc(config), encoding="utf-8")
+        dist = Distribution(attrs={"long_description": "42"})
+        # No error should occur because of missing `readme`
+        dist = apply_configuration(dist, pyproject)
+        assert dist.metadata.long_description == "42"
+
+    def test_dynamic_without_file(self, tmp_path):
+        config = """
+        [project]
+        name = "myproj"
+        version = '42'
+        dynamic = ["classifiers"]
+
+        [tool.setuptools.dynamic]
+        classifiers = {file = ["classifiers.txt"]}
+        """
+
+        pyproject = tmp_path / "pyproject.toml"
+        pyproject.write_text(cleandoc(config), encoding="utf-8")
+        with pytest.warns(UserWarning, match="File .*classifiers.txt. cannot be found"):
+            expanded = read_configuration(pyproject)
+        assert "classifiers" not in expanded["project"]
+
+
+@pytest.mark.parametrize(
+    "example",
+    (
+        """
+        [project]
+        name = "myproj"
+        version = "1.2"
+
+        [my-tool.that-disrespect.pep518]
+        value = 42
+        """,
+    ),
+)
+def test_ignore_unrelated_config(tmp_path, example):
+    pyproject = tmp_path / "pyproject.toml"
+    pyproject.write_text(cleandoc(example), encoding="utf-8")
+
+    # Make sure no error is raised due to 3rd party configs in pyproject.toml
+    assert read_configuration(pyproject) is not None
+
+
+@pytest.mark.parametrize(
+    ("example", "error_msg"),
+    [
+        (
+            """
+            [project]
+            name = "myproj"
+            version = "1.2"
+            requires = ['pywin32; platform_system=="Windows"' ]
+            """,
+            "configuration error: .project. must not contain ..requires.. properties",
+        ),
+    ],
+)
+def test_invalid_example(tmp_path, example, error_msg):
+    pyproject = tmp_path / "pyproject.toml"
+    pyproject.write_text(cleandoc(example), encoding="utf-8")
+
+    pattern = re.compile(
+        f"invalid pyproject.toml.*{error_msg}.*", re.MULTILINE | re.DOTALL
+    )
+    with pytest.raises(ValueError, match=pattern):
+        read_configuration(pyproject)
+
+
+@pytest.mark.parametrize("config", ("", "[tool.something]\nvalue = 42"))
+def test_empty(tmp_path, config):
+    pyproject = tmp_path / "pyproject.toml"
+    pyproject.write_text(config, encoding="utf-8")
+
+    # Make sure no error is raised
+    assert read_configuration(pyproject) == {}
+
+
+@pytest.mark.parametrize("config", ("[project]\nname = 'myproj'\nversion='42'\n",))
+def test_include_package_data_by_default(tmp_path, config):
+    """Builds with ``pyproject.toml`` should consider ``include-package-data=True`` as
+    default.
+    """
+    pyproject = tmp_path / "pyproject.toml"
+    pyproject.write_text(config, encoding="utf-8")
+
+    config = read_configuration(pyproject)
+    assert config["tool"]["setuptools"]["include-package-data"] is True
+
+
+def test_include_package_data_in_setuppy(tmp_path):
+    """Builds with ``pyproject.toml`` should consider ``include_package_data`` set in
+    ``setup.py``.
+
+    See https://github.com/pypa/setuptools/issues/3197#issuecomment-1079023889
+    """
+    files = {
+        "pyproject.toml": "[project]\nname = 'myproj'\nversion='42'\n",
+        "setup.py": "__import__('setuptools').setup(include_package_data=False)",
+    }
+    jaraco.path.build(files, prefix=tmp_path)
+
+    with Path(tmp_path):
+        dist = distutils.core.run_setup("setup.py", {}, stop_after="config")
+
+    assert dist.get_name() == "myproj"
+    assert dist.get_version() == "42"
+    assert dist.include_package_data is False
+
+
+def test_warn_tools_typo(tmp_path):
+    """Test that the common ``tools.setuptools`` typo in ``pyproject.toml`` issues a warning
+
+    See https://github.com/pypa/setuptools/issues/4150
+    """
+    config = """
+    [build-system]
+    requires = ["setuptools"]
+    build-backend = "setuptools.build_meta"
+
+    [project]
+    name = "myproj"
+    version = '42'
+
+    [tools.setuptools]
+    packages = ["package"]
+    """
+
+    pyproject = tmp_path / "pyproject.toml"
+    pyproject.write_text(cleandoc(config), encoding="utf-8")
+
+    with pytest.warns(_ToolsTypoInMetadata):
+        read_configuration(pyproject)
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_pyprojecttoml_dynamic_deps.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_pyprojecttoml_dynamic_deps.py
new file mode 100644
index 0000000000000000000000000000000000000000..9fc8050743c4b1a8497d5ea20c571b565d074e59
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_pyprojecttoml_dynamic_deps.py
@@ -0,0 +1,111 @@
+from inspect import cleandoc
+
+import pytest
+from jaraco import path
+
+from setuptools.config.pyprojecttoml import apply_configuration
+from setuptools.dist import Distribution
+from setuptools.warnings import SetuptoolsWarning
+
+
+def test_dynamic_dependencies(tmp_path):
+    files = {
+        "requirements.txt": "six\n  # comment\n",
+        "pyproject.toml": cleandoc(
+            """
+            [project]
+            name = "myproj"
+            version = "1.0"
+            dynamic = ["dependencies"]
+
+            [build-system]
+            requires = ["setuptools", "wheel"]
+            build-backend = "setuptools.build_meta"
+
+            [tool.setuptools.dynamic.dependencies]
+            file = ["requirements.txt"]
+            """
+        ),
+    }
+    path.build(files, prefix=tmp_path)
+    dist = Distribution()
+    dist = apply_configuration(dist, tmp_path / "pyproject.toml")
+    assert dist.install_requires == ["six"]
+
+
+def test_dynamic_optional_dependencies(tmp_path):
+    files = {
+        "requirements-docs.txt": "sphinx\n  # comment\n",
+        "pyproject.toml": cleandoc(
+            """
+            [project]
+            name = "myproj"
+            version = "1.0"
+            dynamic = ["optional-dependencies"]
+
+            [tool.setuptools.dynamic.optional-dependencies.docs]
+            file = ["requirements-docs.txt"]
+
+            [build-system]
+            requires = ["setuptools", "wheel"]
+            build-backend = "setuptools.build_meta"
+            """
+        ),
+    }
+    path.build(files, prefix=tmp_path)
+    dist = Distribution()
+    dist = apply_configuration(dist, tmp_path / "pyproject.toml")
+    assert dist.extras_require == {"docs": ["sphinx"]}
+
+
+def test_mixed_dynamic_optional_dependencies(tmp_path):
+    """
+    Test that if PEP 621 was loosened to allow mixing of dynamic and static
+    configurations in the case of fields containing sub-fields (groups),
+    things would work out.
+    """
+    files = {
+        "requirements-images.txt": "pillow~=42.0\n  # comment\n",
+        "pyproject.toml": cleandoc(
+            """
+            [project]
+            name = "myproj"
+            version = "1.0"
+            dynamic = ["optional-dependencies"]
+
+            [project.optional-dependencies]
+            docs = ["sphinx"]
+
+            [tool.setuptools.dynamic.optional-dependencies.images]
+            file = ["requirements-images.txt"]
+            """
+        ),
+    }
+
+    path.build(files, prefix=tmp_path)
+    pyproject = tmp_path / "pyproject.toml"
+    with pytest.raises(ValueError, match="project.optional-dependencies"):
+        apply_configuration(Distribution(), pyproject)
+
+
+def test_mixed_extras_require_optional_dependencies(tmp_path):
+    files = {
+        "pyproject.toml": cleandoc(
+            """
+            [project]
+            name = "myproj"
+            version = "1.0"
+            optional-dependencies.docs = ["sphinx"]
+            """
+        ),
+    }
+
+    path.build(files, prefix=tmp_path)
+    pyproject = tmp_path / "pyproject.toml"
+
+    dist = Distribution({"extras_require": {"hello": ["world"]}})
+
+    with pytest.warns(SetuptoolsWarning, match=".extras_require. overwritten"):
+        dist = apply_configuration(dist, pyproject)
+
+    assert dist.extras_require == {"docs": ["sphinx"]}
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_setupcfg.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_setupcfg.py
new file mode 100644
index 0000000000000000000000000000000000000000..495337a9a5815e3d2a0aefa584b8ee81f5136d95
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/config/test_setupcfg.py
@@ -0,0 +1,987 @@
+import configparser
+import contextlib
+import inspect
+import re
+import sys
+from pathlib import Path
+from unittest.mock import Mock, patch
+
+import pytest
+from packaging.requirements import InvalidRequirement
+
+from setuptools.config.setupcfg import ConfigHandler, Target, read_configuration
+from setuptools.dist import Distribution, _Distribution
+from setuptools.warnings import SetuptoolsDeprecationWarning
+
+from ..textwrap import DALS
+
+from distutils.errors import DistutilsFileError, DistutilsOptionError
+
+IS_PYPY = '__pypy__' in sys.builtin_module_names
+
+
+class ErrConfigHandler(ConfigHandler[Target]):
+    """Erroneous handler. Fails to implement required methods."""
+
+    section_prefix = "**err**"
+
+
+def make_package_dir(name, base_dir, ns=False):
+    dir_package = base_dir
+    for dir_name in name.split('/'):
+        dir_package = dir_package.mkdir(dir_name)
+    init_file = None
+    if not ns:
+        init_file = dir_package.join('__init__.py')
+        init_file.write('')
+    return dir_package, init_file
+
+
+def fake_env(
+    tmpdir, setup_cfg, setup_py=None, encoding='ascii', package_path='fake_package'
+):
+    if setup_py is None:
+        setup_py = 'from setuptools import setup\nsetup()\n'
+
+    tmpdir.join('setup.py').write(setup_py)
+    config = tmpdir.join('setup.cfg')
+    config.write(setup_cfg.encode(encoding), mode='wb')
+
+    package_dir, init_file = make_package_dir(package_path, tmpdir)
+
+    init_file.write(
+        'VERSION = (1, 2, 3)\n'
+        '\n'
+        'VERSION_MAJOR = 1'
+        '\n'
+        'def get_version():\n'
+        '    return [3, 4, 5, "dev"]\n'
+        '\n'
+    )
+
+    return package_dir, config
+
+
+@contextlib.contextmanager
+def get_dist(tmpdir, kwargs_initial=None, parse=True):
+    kwargs_initial = kwargs_initial or {}
+
+    with tmpdir.as_cwd():
+        dist = Distribution(kwargs_initial)
+        dist.script_name = 'setup.py'
+        parse and dist.parse_config_files()
+
+        yield dist
+
+
+def test_parsers_implemented():
+    with pytest.raises(NotImplementedError):
+        handler = ErrConfigHandler(None, {}, False, Mock())
+        handler.parsers
+
+
+class TestConfigurationReader:
+    def test_basic(self, tmpdir):
+        _, config = fake_env(
+            tmpdir,
+            '[metadata]\n'
+            'version = 10.1.1\n'
+            'keywords = one, two\n'
+            '\n'
+            '[options]\n'
+            'scripts = bin/a.py, bin/b.py\n',
+        )
+        config_dict = read_configuration(str(config))
+        assert config_dict['metadata']['version'] == '10.1.1'
+        assert config_dict['metadata']['keywords'] == ['one', 'two']
+        assert config_dict['options']['scripts'] == ['bin/a.py', 'bin/b.py']
+
+    def test_no_config(self, tmpdir):
+        with pytest.raises(DistutilsFileError):
+            read_configuration(str(tmpdir.join('setup.cfg')))
+
+    def test_ignore_errors(self, tmpdir):
+        _, config = fake_env(
+            tmpdir,
+            '[metadata]\nversion = attr: none.VERSION\nkeywords = one, two\n',
+        )
+        with pytest.raises(ImportError):
+            read_configuration(str(config))
+
+        config_dict = read_configuration(str(config), ignore_option_errors=True)
+
+        assert config_dict['metadata']['keywords'] == ['one', 'two']
+        assert 'version' not in config_dict['metadata']
+
+        config.remove()
+
+
+class TestMetadata:
+    def test_basic(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[metadata]\n'
+            'version = 10.1.1\n'
+            'description = Some description\n'
+            'long_description_content_type = text/something\n'
+            'long_description = file: README\n'
+            'name = fake_name\n'
+            'keywords = one, two\n'
+            'provides = package, package.sub\n'
+            'license = otherlic\n'
+            'download_url = http://test.test.com/test/\n'
+            'maintainer_email = test@test.com\n',
+        )
+
+        tmpdir.join('README').write('readme contents\nline2')
+
+        meta_initial = {
+            # This will be used so `otherlic` won't replace it.
+            'license': 'BSD 3-Clause License',
+        }
+
+        with get_dist(tmpdir, meta_initial) as dist:
+            metadata = dist.metadata
+
+            assert metadata.version == '10.1.1'
+            assert metadata.description == 'Some description'
+            assert metadata.long_description_content_type == 'text/something'
+            assert metadata.long_description == 'readme contents\nline2'
+            assert metadata.provides == ['package', 'package.sub']
+            assert metadata.license == 'BSD 3-Clause License'
+            assert metadata.name == 'fake_name'
+            assert metadata.keywords == ['one', 'two']
+            assert metadata.download_url == 'http://test.test.com/test/'
+            assert metadata.maintainer_email == 'test@test.com'
+
+    def test_license_cfg(self, tmpdir):
+        fake_env(
+            tmpdir,
+            DALS(
+                """
+            [metadata]
+            name=foo
+            version=0.0.1
+            license=Apache 2.0
+            """
+            ),
+        )
+
+        with get_dist(tmpdir) as dist:
+            metadata = dist.metadata
+
+            assert metadata.name == "foo"
+            assert metadata.version == "0.0.1"
+            assert metadata.license == "Apache 2.0"
+
+    def test_file_mixed(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[metadata]\nlong_description = file: README.rst, CHANGES.rst\n\n',
+        )
+
+        tmpdir.join('README.rst').write('readme contents\nline2')
+        tmpdir.join('CHANGES.rst').write('changelog contents\nand stuff')
+
+        with get_dist(tmpdir) as dist:
+            assert dist.metadata.long_description == (
+                'readme contents\nline2\nchangelog contents\nand stuff'
+            )
+
+    def test_file_sandboxed(self, tmpdir):
+        tmpdir.ensure("README")
+        project = tmpdir.join('depth1', 'depth2')
+        project.ensure(dir=True)
+        fake_env(project, '[metadata]\nlong_description = file: ../../README\n')
+
+        with get_dist(project, parse=False) as dist:
+            with pytest.raises(DistutilsOptionError):
+                dist.parse_config_files()  # file: out of sandbox
+
+    def test_aliases(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[metadata]\n'
+            'author_email = test@test.com\n'
+            'home_page = http://test.test.com/test/\n'
+            'summary = Short summary\n'
+            'platform = a, b\n'
+            'classifier =\n'
+            '  Framework :: Django\n'
+            '  Programming Language :: Python :: 3.5\n',
+        )
+
+        with get_dist(tmpdir) as dist:
+            metadata = dist.metadata
+            assert metadata.author_email == 'test@test.com'
+            assert metadata.url == 'http://test.test.com/test/'
+            assert metadata.description == 'Short summary'
+            assert metadata.platforms == ['a', 'b']
+            assert metadata.classifiers == [
+                'Framework :: Django',
+                'Programming Language :: Python :: 3.5',
+            ]
+
+    def test_multiline(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[metadata]\n'
+            'name = fake_name\n'
+            'keywords =\n'
+            '  one\n'
+            '  two\n'
+            'classifiers =\n'
+            '  Framework :: Django\n'
+            '  Programming Language :: Python :: 3.5\n',
+        )
+        with get_dist(tmpdir) as dist:
+            metadata = dist.metadata
+            assert metadata.keywords == ['one', 'two']
+            assert metadata.classifiers == [
+                'Framework :: Django',
+                'Programming Language :: Python :: 3.5',
+            ]
+
+    def test_dict(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[metadata]\n'
+            'project_urls =\n'
+            '  Link One = https://example.com/one/\n'
+            '  Link Two = https://example.com/two/\n',
+        )
+        with get_dist(tmpdir) as dist:
+            metadata = dist.metadata
+            assert metadata.project_urls == {
+                'Link One': 'https://example.com/one/',
+                'Link Two': 'https://example.com/two/',
+            }
+
+    def test_version(self, tmpdir):
+        package_dir, config = fake_env(
+            tmpdir, '[metadata]\nversion = attr: fake_package.VERSION\n'
+        )
+
+        sub_a = package_dir.mkdir('subpkg_a')
+        sub_a.join('__init__.py').write('')
+        sub_a.join('mod.py').write('VERSION = (2016, 11, 26)')
+
+        sub_b = package_dir.mkdir('subpkg_b')
+        sub_b.join('__init__.py').write('')
+        sub_b.join('mod.py').write(
+            'import third_party_module\nVERSION = (2016, 11, 26)'
+        )
+
+        with get_dist(tmpdir) as dist:
+            assert dist.metadata.version == '1.2.3'
+
+        config.write('[metadata]\nversion = attr: fake_package.get_version\n')
+        with get_dist(tmpdir) as dist:
+            assert dist.metadata.version == '3.4.5.dev'
+
+        config.write('[metadata]\nversion = attr: fake_package.VERSION_MAJOR\n')
+        with get_dist(tmpdir) as dist:
+            assert dist.metadata.version == '1'
+
+        config.write('[metadata]\nversion = attr: fake_package.subpkg_a.mod.VERSION\n')
+        with get_dist(tmpdir) as dist:
+            assert dist.metadata.version == '2016.11.26'
+
+        config.write('[metadata]\nversion = attr: fake_package.subpkg_b.mod.VERSION\n')
+        with get_dist(tmpdir) as dist:
+            assert dist.metadata.version == '2016.11.26'
+
+    def test_version_file(self, tmpdir):
+        fake_env(tmpdir, '[metadata]\nversion = file: fake_package/version.txt\n')
+        tmpdir.join('fake_package', 'version.txt').write('1.2.3\n')
+
+        with get_dist(tmpdir) as dist:
+            assert dist.metadata.version == '1.2.3'
+
+        tmpdir.join('fake_package', 'version.txt').write('1.2.3\n4.5.6\n')
+        with pytest.raises(DistutilsOptionError):
+            with get_dist(tmpdir) as dist:
+                dist.metadata.version
+
+    def test_version_with_package_dir_simple(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[metadata]\n'
+            'version = attr: fake_package_simple.VERSION\n'
+            '[options]\n'
+            'package_dir =\n'
+            '    = src\n',
+            package_path='src/fake_package_simple',
+        )
+
+        with get_dist(tmpdir) as dist:
+            assert dist.metadata.version == '1.2.3'
+
+    def test_version_with_package_dir_rename(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[metadata]\n'
+            'version = attr: fake_package_rename.VERSION\n'
+            '[options]\n'
+            'package_dir =\n'
+            '    fake_package_rename = fake_dir\n',
+            package_path='fake_dir',
+        )
+
+        with get_dist(tmpdir) as dist:
+            assert dist.metadata.version == '1.2.3'
+
+    def test_version_with_package_dir_complex(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[metadata]\n'
+            'version = attr: fake_package_complex.VERSION\n'
+            '[options]\n'
+            'package_dir =\n'
+            '    fake_package_complex = src/fake_dir\n',
+            package_path='src/fake_dir',
+        )
+
+        with get_dist(tmpdir) as dist:
+            assert dist.metadata.version == '1.2.3'
+
+    def test_unknown_meta_item(self, tmpdir):
+        fake_env(tmpdir, '[metadata]\nname = fake_name\nunknown = some\n')
+        with get_dist(tmpdir, parse=False) as dist:
+            dist.parse_config_files()  # Skip unknown.
+
+    def test_usupported_section(self, tmpdir):
+        fake_env(tmpdir, '[metadata.some]\nkey = val\n')
+        with get_dist(tmpdir, parse=False) as dist:
+            with pytest.raises(DistutilsOptionError):
+                dist.parse_config_files()
+
+    def test_classifiers(self, tmpdir):
+        expected = set([
+            'Framework :: Django',
+            'Programming Language :: Python :: 3',
+            'Programming Language :: Python :: 3.5',
+        ])
+
+        # From file.
+        _, config = fake_env(tmpdir, '[metadata]\nclassifiers = file: classifiers\n')
+
+        tmpdir.join('classifiers').write(
+            'Framework :: Django\n'
+            'Programming Language :: Python :: 3\n'
+            'Programming Language :: Python :: 3.5\n'
+        )
+
+        with get_dist(tmpdir) as dist:
+            assert set(dist.metadata.classifiers) == expected
+
+        # From list notation
+        config.write(
+            '[metadata]\n'
+            'classifiers =\n'
+            '    Framework :: Django\n'
+            '    Programming Language :: Python :: 3\n'
+            '    Programming Language :: Python :: 3.5\n'
+        )
+        with get_dist(tmpdir) as dist:
+            assert set(dist.metadata.classifiers) == expected
+
+    def test_interpolation(self, tmpdir):
+        fake_env(tmpdir, '[metadata]\ndescription = %(message)s\n')
+        with pytest.raises(configparser.InterpolationMissingOptionError):
+            with get_dist(tmpdir):
+                pass
+
+    def test_non_ascii_1(self, tmpdir):
+        fake_env(tmpdir, '[metadata]\ndescription = éàïôñ\n', encoding='utf-8')
+        with get_dist(tmpdir):
+            pass
+
+    def test_non_ascii_3(self, tmpdir):
+        fake_env(tmpdir, '\n# -*- coding: invalid\n')
+        with get_dist(tmpdir):
+            pass
+
+    def test_non_ascii_4(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '# -*- coding: utf-8\n[metadata]\ndescription = éàïôñ\n',
+            encoding='utf-8',
+        )
+        with get_dist(tmpdir) as dist:
+            assert dist.metadata.description == 'éàïôñ'
+
+    def test_not_utf8(self, tmpdir):
+        """
+        Config files encoded not in UTF-8 will fail
+        """
+        fake_env(
+            tmpdir,
+            '# vim: set fileencoding=iso-8859-15 :\n[metadata]\ndescription = éàïôñ\n',
+            encoding='iso-8859-15',
+        )
+        with pytest.raises(UnicodeDecodeError):
+            with get_dist(tmpdir):
+                pass
+
+    @pytest.mark.parametrize(
+        ("error_msg", "config", "invalid"),
+        [
+            (
+                "Invalid dash-separated key 'author-email' in 'metadata' (setup.cfg)",
+                DALS(
+                    """
+                    [metadata]
+                    author-email = test@test.com
+                    maintainer_email = foo@foo.com
+                    """
+                ),
+                {"author-email": "test@test.com"},
+            ),
+            (
+                "Invalid uppercase key 'Name' in 'metadata' (setup.cfg)",
+                DALS(
+                    """
+                    [metadata]
+                    Name = foo
+                    description = Some description
+                    """
+                ),
+                {"Name": "foo"},
+            ),
+        ],
+    )
+    def test_invalid_options_previously_deprecated(
+        self, tmpdir, error_msg, config, invalid
+    ):
+        # This test and related methods can be removed when no longer needed.
+        # Deprecation postponed due to push-back from the community in
+        # https://github.com/pypa/setuptools/issues/4910
+        fake_env(tmpdir, config)
+        with pytest.warns(SetuptoolsDeprecationWarning, match=re.escape(error_msg)):
+            dist = get_dist(tmpdir).__enter__()
+
+        tmpdir.join('setup.cfg').remove()
+
+        for field, value in invalid.items():
+            attr = field.replace("-", "_").lower()
+            assert getattr(dist.metadata, attr) == value
+
+
+class TestOptions:
+    def test_basic(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[options]\n'
+            'zip_safe = True\n'
+            'include_package_data = yes\n'
+            'package_dir = b=c, =src\n'
+            'packages = pack_a, pack_b.subpack\n'
+            'namespace_packages = pack1, pack2\n'
+            'scripts = bin/one.py, bin/two.py\n'
+            'eager_resources = bin/one.py, bin/two.py\n'
+            'install_requires = docutils>=0.3; pack ==1.1, ==1.3; hey\n'
+            'setup_requires = docutils>=0.3; spack ==1.1, ==1.3; there\n'
+            'dependency_links = http://some.com/here/1, '
+            'http://some.com/there/2\n'
+            'python_requires = >=1.0, !=2.8\n'
+            'py_modules = module1, module2\n',
+        )
+        deprec = pytest.warns(SetuptoolsDeprecationWarning, match="namespace_packages")
+        with deprec, get_dist(tmpdir) as dist:
+            assert dist.zip_safe
+            assert dist.include_package_data
+            assert dist.package_dir == {'': 'src', 'b': 'c'}
+            assert dist.packages == ['pack_a', 'pack_b.subpack']
+            assert dist.namespace_packages == ['pack1', 'pack2']
+            assert dist.scripts == ['bin/one.py', 'bin/two.py']
+            assert dist.dependency_links == ([
+                'http://some.com/here/1',
+                'http://some.com/there/2',
+            ])
+            assert dist.install_requires == ([
+                'docutils>=0.3',
+                'pack==1.1,==1.3',
+                'hey',
+            ])
+            assert dist.setup_requires == ([
+                'docutils>=0.3',
+                'spack ==1.1, ==1.3',
+                'there',
+            ])
+            assert dist.python_requires == '>=1.0, !=2.8'
+            assert dist.py_modules == ['module1', 'module2']
+
+    def test_multiline(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[options]\n'
+            'package_dir = \n'
+            '  b=c\n'
+            '  =src\n'
+            'packages = \n'
+            '  pack_a\n'
+            '  pack_b.subpack\n'
+            'namespace_packages = \n'
+            '  pack1\n'
+            '  pack2\n'
+            'scripts = \n'
+            '  bin/one.py\n'
+            '  bin/two.py\n'
+            'eager_resources = \n'
+            '  bin/one.py\n'
+            '  bin/two.py\n'
+            'install_requires = \n'
+            '  docutils>=0.3\n'
+            '  pack ==1.1, ==1.3\n'
+            '  hey\n'
+            'setup_requires = \n'
+            '  docutils>=0.3\n'
+            '  spack ==1.1, ==1.3\n'
+            '  there\n'
+            'dependency_links = \n'
+            '  http://some.com/here/1\n'
+            '  http://some.com/there/2\n',
+        )
+        deprec = pytest.warns(SetuptoolsDeprecationWarning, match="namespace_packages")
+        with deprec, get_dist(tmpdir) as dist:
+            assert dist.package_dir == {'': 'src', 'b': 'c'}
+            assert dist.packages == ['pack_a', 'pack_b.subpack']
+            assert dist.namespace_packages == ['pack1', 'pack2']
+            assert dist.scripts == ['bin/one.py', 'bin/two.py']
+            assert dist.dependency_links == ([
+                'http://some.com/here/1',
+                'http://some.com/there/2',
+            ])
+            assert dist.install_requires == ([
+                'docutils>=0.3',
+                'pack==1.1,==1.3',
+                'hey',
+            ])
+            assert dist.setup_requires == ([
+                'docutils>=0.3',
+                'spack ==1.1, ==1.3',
+                'there',
+            ])
+
+    def test_package_dir_fail(self, tmpdir):
+        fake_env(tmpdir, '[options]\npackage_dir = a b\n')
+        with get_dist(tmpdir, parse=False) as dist:
+            with pytest.raises(DistutilsOptionError):
+                dist.parse_config_files()
+
+    def test_package_data(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[options.package_data]\n'
+            '* = *.txt, *.rst\n'
+            'hello = *.msg\n'
+            '\n'
+            '[options.exclude_package_data]\n'
+            '* = fake1.txt, fake2.txt\n'
+            'hello = *.dat\n',
+        )
+
+        with get_dist(tmpdir) as dist:
+            assert dist.package_data == {
+                '': ['*.txt', '*.rst'],
+                'hello': ['*.msg'],
+            }
+            assert dist.exclude_package_data == {
+                '': ['fake1.txt', 'fake2.txt'],
+                'hello': ['*.dat'],
+            }
+
+    def test_packages(self, tmpdir):
+        fake_env(tmpdir, '[options]\npackages = find:\n')
+
+        with get_dist(tmpdir) as dist:
+            assert dist.packages == ['fake_package']
+
+    def test_find_directive(self, tmpdir):
+        dir_package, config = fake_env(tmpdir, '[options]\npackages = find:\n')
+
+        make_package_dir('sub_one', dir_package)
+        make_package_dir('sub_two', dir_package)
+
+        with get_dist(tmpdir) as dist:
+            assert set(dist.packages) == set([
+                'fake_package',
+                'fake_package.sub_two',
+                'fake_package.sub_one',
+            ])
+
+        config.write(
+            '[options]\n'
+            'packages = find:\n'
+            '\n'
+            '[options.packages.find]\n'
+            'where = .\n'
+            'include =\n'
+            '    fake_package.sub_one\n'
+            '    two\n'
+        )
+        with get_dist(tmpdir) as dist:
+            assert dist.packages == ['fake_package.sub_one']
+
+        config.write(
+            '[options]\n'
+            'packages = find:\n'
+            '\n'
+            '[options.packages.find]\n'
+            'exclude =\n'
+            '    fake_package.sub_one\n'
+        )
+        with get_dist(tmpdir) as dist:
+            assert set(dist.packages) == set(['fake_package', 'fake_package.sub_two'])
+
+    def test_find_namespace_directive(self, tmpdir):
+        dir_package, config = fake_env(
+            tmpdir, '[options]\npackages = find_namespace:\n'
+        )
+
+        make_package_dir('sub_one', dir_package)
+        make_package_dir('sub_two', dir_package, ns=True)
+
+        with get_dist(tmpdir) as dist:
+            assert set(dist.packages) == {
+                'fake_package',
+                'fake_package.sub_two',
+                'fake_package.sub_one',
+            }
+
+        config.write(
+            '[options]\n'
+            'packages = find_namespace:\n'
+            '\n'
+            '[options.packages.find]\n'
+            'where = .\n'
+            'include =\n'
+            '    fake_package.sub_one\n'
+            '    two\n'
+        )
+        with get_dist(tmpdir) as dist:
+            assert dist.packages == ['fake_package.sub_one']
+
+        config.write(
+            '[options]\n'
+            'packages = find_namespace:\n'
+            '\n'
+            '[options.packages.find]\n'
+            'exclude =\n'
+            '    fake_package.sub_one\n'
+        )
+        with get_dist(tmpdir) as dist:
+            assert set(dist.packages) == {'fake_package', 'fake_package.sub_two'}
+
+    def test_extras_require(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[options.extras_require]\n'
+            'pdf = ReportLab>=1.2; RXP\n'
+            'rest = \n'
+            '  docutils>=0.3\n'
+            '  pack ==1.1, ==1.3\n',
+        )
+
+        with get_dist(tmpdir) as dist:
+            assert dist.extras_require == {
+                'pdf': ['ReportLab>=1.2', 'RXP'],
+                'rest': ['docutils>=0.3', 'pack==1.1,==1.3'],
+            }
+            assert set(dist.metadata.provides_extras) == {'pdf', 'rest'}
+
+    @pytest.mark.parametrize(
+        "config",
+        [
+            "[options.extras_require]\nfoo = bar;python_version<'3'",
+            "[options.extras_require]\nfoo = bar;os_name=='linux'",
+            "[options.extras_require]\nfoo = bar;python_version<'3'\n",
+            "[options.extras_require]\nfoo = bar;os_name=='linux'\n",
+            "[options]\ninstall_requires = bar;python_version<'3'",
+            "[options]\ninstall_requires = bar;os_name=='linux'",
+            "[options]\ninstall_requires = bar;python_version<'3'\n",
+            "[options]\ninstall_requires = bar;os_name=='linux'\n",
+        ],
+    )
+    @pytest.mark.xfail(IS_PYPY, reason="Exceptions missing on PyPy")
+    # TODO: investigate PyPy problem
+    def test_raises_accidental_env_marker_misconfig(self, config, tmpdir):
+        fake_env(tmpdir, config)
+        match = (
+            r"One of the parsed requirements in `(install_requires|extras_require.+)` "
+            "looks like a valid environment marker.*"
+        )
+        with pytest.raises(InvalidRequirement, match=match):
+            with get_dist(tmpdir) as _:
+                pass
+
+    @pytest.mark.parametrize(
+        "config",
+        [
+            "[options.extras_require]\nfoo = bar;python_version<3",
+            "[options.extras_require]\nfoo = bar;python_version<3\n",
+            "[options]\ninstall_requires = bar;python_version<3",
+            "[options]\ninstall_requires = bar;python_version<3\n",
+        ],
+    )
+    @pytest.mark.xfail(IS_PYPY, reason="Warnings missing on PyPy (minor issue)")
+    # TODO: investigate PyPy problem
+    def test_warn_accidental_env_marker_misconfig(self, config, tmpdir):
+        fake_env(tmpdir, config)
+        match = (
+            r"One of the parsed requirements in `(install_requires|extras_require.+)` "
+            "looks like a valid environment marker.*"
+        )
+        with pytest.warns(SetuptoolsDeprecationWarning, match=match):
+            with get_dist(tmpdir) as _:
+                pass
+
+    @pytest.mark.parametrize(
+        "config",
+        [
+            "[options.extras_require]\nfoo =\n    bar;python_version<'3'",
+            "[options.extras_require]\nfoo = bar;baz\nboo = xxx;yyy",
+            "[options.extras_require]\nfoo =\n    bar;python_version<'3'\n",
+            "[options.extras_require]\nfoo = bar;baz\nboo = xxx;yyy\n",
+            "[options.extras_require]\nfoo =\n    bar\n    python_version<3\n",
+            "[options]\ninstall_requires =\n    bar;python_version<'3'",
+            "[options]\ninstall_requires = bar;baz\nboo = xxx;yyy",
+            "[options]\ninstall_requires =\n    bar;python_version<'3'\n",
+            "[options]\ninstall_requires = bar;baz\nboo = xxx;yyy\n",
+            "[options]\ninstall_requires =\n    bar\n    python_version<3\n",
+        ],
+    )
+    @pytest.mark.filterwarnings("error::setuptools.SetuptoolsDeprecationWarning")
+    def test_nowarn_accidental_env_marker_misconfig(self, config, tmpdir, recwarn):
+        fake_env(tmpdir, config)
+        num_warnings = len(recwarn)
+        with get_dist(tmpdir) as _:
+            pass
+        # The examples are valid, no warnings shown
+        assert len(recwarn) == num_warnings
+
+    def test_dash_preserved_extras_require(self, tmpdir):
+        fake_env(tmpdir, '[options.extras_require]\nfoo-a = foo\nfoo_b = test\n')
+
+        with get_dist(tmpdir) as dist:
+            assert dist.extras_require == {'foo-a': ['foo'], 'foo_b': ['test']}
+
+    def test_entry_points(self, tmpdir):
+        _, config = fake_env(
+            tmpdir,
+            '[options.entry_points]\n'
+            'group1 = point1 = pack.module:func, '
+            '.point2 = pack.module2:func_rest [rest]\n'
+            'group2 = point3 = pack.module:func2\n',
+        )
+
+        with get_dist(tmpdir) as dist:
+            assert dist.entry_points == {
+                'group1': [
+                    'point1 = pack.module:func',
+                    '.point2 = pack.module2:func_rest [rest]',
+                ],
+                'group2': ['point3 = pack.module:func2'],
+            }
+
+        expected = (
+            '[blogtool.parsers]\n'
+            '.rst = some.nested.module:SomeClass.some_classmethod[reST]\n'
+        )
+
+        tmpdir.join('entry_points').write(expected)
+
+        # From file.
+        config.write('[options]\nentry_points = file: entry_points\n')
+
+        with get_dist(tmpdir) as dist:
+            assert dist.entry_points == expected
+
+    def test_case_sensitive_entry_points(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[options.entry_points]\n'
+            'GROUP1 = point1 = pack.module:func, '
+            '.point2 = pack.module2:func_rest [rest]\n'
+            'group2 = point3 = pack.module:func2\n',
+        )
+
+        with get_dist(tmpdir) as dist:
+            assert dist.entry_points == {
+                'GROUP1': [
+                    'point1 = pack.module:func',
+                    '.point2 = pack.module2:func_rest [rest]',
+                ],
+                'group2': ['point3 = pack.module:func2'],
+            }
+
+    def test_data_files(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[options.data_files]\n'
+            'cfg =\n'
+            '      a/b.conf\n'
+            '      c/d.conf\n'
+            'data = e/f.dat, g/h.dat\n',
+        )
+
+        with get_dist(tmpdir) as dist:
+            expected = [
+                ('cfg', ['a/b.conf', 'c/d.conf']),
+                ('data', ['e/f.dat', 'g/h.dat']),
+            ]
+            assert sorted(dist.data_files) == sorted(expected)
+
+    def test_data_files_globby(self, tmpdir):
+        fake_env(
+            tmpdir,
+            '[options.data_files]\n'
+            'cfg =\n'
+            '      a/b.conf\n'
+            '      c/d.conf\n'
+            'data = *.dat\n'
+            'icons = \n'
+            '      *.ico\n'
+            'audio = \n'
+            '      *.wav\n'
+            '      sounds.db\n',
+        )
+
+        # Create dummy files for glob()'s sake:
+        tmpdir.join('a.dat').write('')
+        tmpdir.join('b.dat').write('')
+        tmpdir.join('c.dat').write('')
+        tmpdir.join('a.ico').write('')
+        tmpdir.join('b.ico').write('')
+        tmpdir.join('c.ico').write('')
+        tmpdir.join('beep.wav').write('')
+        tmpdir.join('boop.wav').write('')
+        tmpdir.join('sounds.db').write('')
+
+        with get_dist(tmpdir) as dist:
+            expected = [
+                ('cfg', ['a/b.conf', 'c/d.conf']),
+                ('data', ['a.dat', 'b.dat', 'c.dat']),
+                ('icons', ['a.ico', 'b.ico', 'c.ico']),
+                ('audio', ['beep.wav', 'boop.wav', 'sounds.db']),
+            ]
+            assert sorted(dist.data_files) == sorted(expected)
+
+    def test_python_requires_simple(self, tmpdir):
+        fake_env(
+            tmpdir,
+            DALS(
+                """
+            [options]
+            python_requires=>=2.7
+            """
+            ),
+        )
+        with get_dist(tmpdir) as dist:
+            dist.parse_config_files()
+
+    def test_python_requires_compound(self, tmpdir):
+        fake_env(
+            tmpdir,
+            DALS(
+                """
+            [options]
+            python_requires=>=2.7,!=3.0.*
+            """
+            ),
+        )
+        with get_dist(tmpdir) as dist:
+            dist.parse_config_files()
+
+    def test_python_requires_invalid(self, tmpdir):
+        fake_env(
+            tmpdir,
+            DALS(
+                """
+            [options]
+            python_requires=invalid
+            """
+            ),
+        )
+        with pytest.raises(Exception):
+            with get_dist(tmpdir) as dist:
+                dist.parse_config_files()
+
+    def test_cmdclass(self, tmpdir):
+        module_path = Path(tmpdir, "src/custom_build.py")  # auto discovery for src
+        module_path.parent.mkdir(parents=True, exist_ok=True)
+        module_path.write_text(
+            "from distutils.core import Command\nclass CustomCmd(Command): pass\n",
+            encoding="utf-8",
+        )
+
+        setup_cfg = """
+            [options]
+            cmdclass =
+                customcmd = custom_build.CustomCmd
+        """
+        fake_env(tmpdir, inspect.cleandoc(setup_cfg))
+
+        with get_dist(tmpdir) as dist:
+            cmdclass = dist.cmdclass['customcmd']
+            assert cmdclass.__name__ == "CustomCmd"
+            assert cmdclass.__module__ == "custom_build"
+            assert module_path.samefile(inspect.getfile(cmdclass))
+
+    def test_requirements_file(self, tmpdir):
+        fake_env(
+            tmpdir,
+            DALS(
+                """
+            [options]
+            install_requires = file:requirements.txt
+            [options.extras_require]
+            colors = file:requirements-extra.txt
+            """
+            ),
+        )
+
+        tmpdir.join('requirements.txt').write('\ndocutils>=0.3\n\n')
+        tmpdir.join('requirements-extra.txt').write('colorama')
+
+        with get_dist(tmpdir) as dist:
+            assert dist.install_requires == ['docutils>=0.3']
+            assert dist.extras_require == {'colors': ['colorama']}
+
+
+saved_dist_init = _Distribution.__init__
+
+
+class TestExternalSetters:
+    # During creation of the setuptools Distribution() object, we call
+    # the init of the parent distutils Distribution object via
+    # _Distribution.__init__ ().
+    #
+    # It's possible distutils calls out to various keyword
+    # implementations (i.e. distutils.setup_keywords entry points)
+    # that may set a range of variables.
+    #
+    # This wraps distutil's Distribution.__init__ and simulates
+    # pbr or something else setting these values.
+    def _fake_distribution_init(self, dist, attrs):
+        saved_dist_init(dist, attrs)
+        # see self._DISTUTILS_UNSUPPORTED_METADATA
+        dist.metadata.long_description_content_type = 'text/something'
+        # Test overwrite setup() args
+        dist.metadata.project_urls = {
+            'Link One': 'https://example.com/one/',
+            'Link Two': 'https://example.com/two/',
+        }
+
+    @patch.object(_Distribution, '__init__', autospec=True)
+    def test_external_setters(self, mock_parent_init, tmpdir):
+        mock_parent_init.side_effect = self._fake_distribution_init
+
+        dist = Distribution(attrs={'project_urls': {'will_be': 'ignored'}})
+
+        assert dist.metadata.long_description_content_type == 'text/something'
+        assert dist.metadata.project_urls == {
+            'Link One': 'https://example.com/one/',
+            'Link Two': 'https://example.com/two/',
+        }
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/contexts.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/contexts.py
new file mode 100644
index 0000000000000000000000000000000000000000..3c931bbd4fd9046702d850a18877622651882d7a
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/contexts.py
@@ -0,0 +1,131 @@
+import contextlib
+import io
+import os
+import shutil
+import site
+import sys
+import tempfile
+
+from filelock import FileLock
+
+
+@contextlib.contextmanager
+def tempdir(cd=lambda dir: None, **kwargs):
+    temp_dir = tempfile.mkdtemp(**kwargs)
+    orig_dir = os.getcwd()
+    try:
+        cd(temp_dir)
+        yield temp_dir
+    finally:
+        cd(orig_dir)
+        shutil.rmtree(temp_dir)
+
+
+@contextlib.contextmanager
+def environment(**replacements):
+    """
+    In a context, patch the environment with replacements. Pass None values
+    to clear the values.
+    """
+    saved = dict((key, os.environ[key]) for key in replacements if key in os.environ)
+
+    # remove values that are null
+    remove = (key for (key, value) in replacements.items() if value is None)
+    for key in list(remove):
+        os.environ.pop(key, None)
+        replacements.pop(key)
+
+    os.environ.update(replacements)
+
+    try:
+        yield saved
+    finally:
+        for key in replacements:
+            os.environ.pop(key, None)
+        os.environ.update(saved)
+
+
+@contextlib.contextmanager
+def quiet():
+    """
+    Redirect stdout/stderr to StringIO objects to prevent console output from
+    distutils commands.
+    """
+
+    old_stdout = sys.stdout
+    old_stderr = sys.stderr
+    new_stdout = sys.stdout = io.StringIO()
+    new_stderr = sys.stderr = io.StringIO()
+    try:
+        yield new_stdout, new_stderr
+    finally:
+        new_stdout.seek(0)
+        new_stderr.seek(0)
+        sys.stdout = old_stdout
+        sys.stderr = old_stderr
+
+
+@contextlib.contextmanager
+def save_user_site_setting():
+    saved = site.ENABLE_USER_SITE
+    try:
+        yield saved
+    finally:
+        site.ENABLE_USER_SITE = saved
+
+
+@contextlib.contextmanager
+def suppress_exceptions(*excs):
+    try:
+        yield
+    except excs:
+        pass
+
+
+def multiproc(request):
+    """
+    Return True if running under xdist and multiple
+    workers are used.
+    """
+    try:
+        worker_id = request.getfixturevalue('worker_id')
+    except Exception:
+        return False
+    return worker_id != 'master'
+
+
+@contextlib.contextmanager
+def session_locked_tmp_dir(request, tmp_path_factory, name):
+    """Uses a file lock to guarantee only one worker can access a temp dir"""
+    # get the temp directory shared by all workers
+    base = tmp_path_factory.getbasetemp()
+    shared_dir = base.parent if multiproc(request) else base
+
+    locked_dir = shared_dir / name
+    with FileLock(locked_dir.with_suffix(".lock")):
+        # ^-- prevent multiple workers to access the directory at once
+        locked_dir.mkdir(exist_ok=True, parents=True)
+        yield locked_dir
+
+
+@contextlib.contextmanager
+def save_paths():
+    """Make sure ``sys.path``, ``sys.meta_path`` and ``sys.path_hooks`` are preserved"""
+    prev = sys.path[:], sys.meta_path[:], sys.path_hooks[:]
+
+    try:
+        yield
+    finally:
+        sys.path, sys.meta_path, sys.path_hooks = prev
+
+
+@contextlib.contextmanager
+def save_sys_modules():
+    """Make sure initial ``sys.modules`` is preserved"""
+    prev_modules = sys.modules
+
+    try:
+        sys.modules = sys.modules.copy()
+        yield
+    finally:
+        sys.modules = prev_modules
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/environment.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/environment.py
new file mode 100644
index 0000000000000000000000000000000000000000..ed5499ef7d73762d033a4877bfe586d6c0b82235
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/environment.py
@@ -0,0 +1,95 @@
+import os
+import subprocess
+import sys
+import unicodedata
+from subprocess import PIPE as _PIPE, Popen as _Popen
+
+import jaraco.envs
+
+
+class VirtualEnv(jaraco.envs.VirtualEnv):
+    name = '.env'
+    # Some version of PyPy will import distutils on startup, implicitly
+    # importing setuptools, and thus leading to BackendInvalid errors
+    # when upgrading Setuptools. Bypass this behavior by avoiding the
+    # early availability and need to upgrade.
+    create_opts = ['--no-setuptools']
+
+    def run(self, cmd, *args, **kwargs):
+        cmd = [self.exe(cmd[0])] + cmd[1:]
+        kwargs = {"cwd": self.root, "encoding": "utf-8", **kwargs}  # Allow overriding
+        # In some environments (eg. downstream distro packaging), where:
+        # - tox isn't used to run tests and
+        # - PYTHONPATH is set to point to a specific setuptools codebase and
+        # - no custom env is explicitly set by a test
+        # PYTHONPATH will leak into the spawned processes.
+        # In that case tests look for module in the wrong place (on PYTHONPATH).
+        # Unless the test sets its own special env, pass a copy of the existing
+        # environment with removed PYTHONPATH to the subprocesses.
+        if "env" not in kwargs:
+            env = dict(os.environ)
+            if "PYTHONPATH" in env:
+                del env["PYTHONPATH"]
+            kwargs["env"] = env
+        return subprocess.check_output(cmd, *args, **kwargs)
+
+
+def _which_dirs(cmd):
+    result = set()
+    for path in os.environ.get('PATH', '').split(os.pathsep):
+        filename = os.path.join(path, cmd)
+        if os.access(filename, os.X_OK):
+            result.add(path)
+    return result
+
+
+def run_setup_py(cmd, pypath=None, path=None, data_stream=0, env=None):
+    """
+    Execution command for tests, separate from those used by the
+    code directly to prevent accidental behavior issues
+    """
+    if env is None:
+        env = dict()
+        for envname in os.environ:
+            env[envname] = os.environ[envname]
+
+    # override the python path if needed
+    if pypath is not None:
+        env["PYTHONPATH"] = pypath
+
+    # override the execution path if needed
+    if path is not None:
+        env["PATH"] = path
+    if not env.get("PATH", ""):
+        env["PATH"] = _which_dirs("tar").union(_which_dirs("gzip"))
+        env["PATH"] = os.pathsep.join(env["PATH"])
+
+    cmd = [sys.executable, "setup.py"] + list(cmd)
+
+    # https://bugs.python.org/issue8557
+    shell = sys.platform == 'win32'
+
+    try:
+        proc = _Popen(
+            cmd,
+            stdout=_PIPE,
+            stderr=_PIPE,
+            shell=shell,
+            env=env,
+            encoding="utf-8",
+        )
+
+        if isinstance(data_stream, tuple):
+            data_stream = slice(*data_stream)
+        data = proc.communicate()[data_stream]
+    except OSError:
+        return 1, ''
+
+    # decode the console string if needed
+    if hasattr(data, "decode"):
+        # use the default encoding
+        data = data.decode()
+        data = unicodedata.normalize('NFC', data)
+
+    # communicate calls wait()
+    return proc.returncode, data
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/fixtures.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/fixtures.py
new file mode 100644
index 0000000000000000000000000000000000000000..20b31d4681377745bc2ddaeaf5f0074b4050e5ba
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/fixtures.py
@@ -0,0 +1,406 @@
+import contextlib
+import io
+import os
+import subprocess
+import sys
+import tarfile
+import time
+from pathlib import Path
+
+import jaraco.path
+import path
+import pytest
+
+from setuptools._normalization import safer_name
+
+from . import contexts, environment
+from .textwrap import DALS
+
+
+@pytest.fixture
+def user_override(monkeypatch):
+    """
+    Override site.USER_BASE and site.USER_SITE with temporary directories in
+    a context.
+    """
+    with contexts.tempdir() as user_base:
+        monkeypatch.setattr('site.USER_BASE', user_base)
+        with contexts.tempdir() as user_site:
+            monkeypatch.setattr('site.USER_SITE', user_site)
+            with contexts.save_user_site_setting():
+                yield
+
+
+@pytest.fixture
+def tmpdir_cwd(tmpdir):
+    with tmpdir.as_cwd() as orig:
+        yield orig
+
+
+@pytest.fixture(autouse=True, scope="session")
+def workaround_xdist_376(request):
+    """
+    Workaround pytest-dev/pytest-xdist#376
+
+    ``pytest-xdist`` tends to inject '' into ``sys.path``,
+    which may break certain isolation expectations.
+    Remove the entry so the import
+    machinery behaves the same irrespective of xdist.
+    """
+    if not request.config.pluginmanager.has_plugin('xdist'):
+        return
+
+    with contextlib.suppress(ValueError):
+        sys.path.remove('')
+
+
+@pytest.fixture
+def sample_project(tmp_path):
+    """
+    Clone the 'sampleproject' and return a path to it.
+    """
+    cmd = ['git', 'clone', 'https://github.com/pypa/sampleproject']
+    try:
+        subprocess.check_call(cmd, cwd=str(tmp_path))
+    except Exception:
+        pytest.skip("Unable to clone sampleproject")
+    return tmp_path / 'sampleproject'
+
+
+@pytest.fixture
+def sample_project_cwd(sample_project):
+    with path.Path(sample_project):
+        yield
+
+
+# sdist and wheel artifacts should be stable across a round of tests
+# so we can build them once per session and use the files as "readonly"
+
+# In the case of setuptools, building the wheel without sdist may cause
+# it to contain the `build` directory, and therefore create situations with
+# `setuptools/build/lib/build/lib/...`. To avoid that, build both artifacts at once.
+
+
+def _build_distributions(tmp_path_factory, request):
+    with contexts.session_locked_tmp_dir(
+        request, tmp_path_factory, "dist_build"
+    ) as tmp:  # pragma: no cover
+        sdist = next(tmp.glob("*.tar.gz"), None)
+        wheel = next(tmp.glob("*.whl"), None)
+        if sdist and wheel:
+            return (sdist, wheel)
+
+        # Sanity check: should not create recursive setuptools/build/lib/build/lib/...
+        assert not Path(request.config.rootdir, "build/lib/build").exists()
+
+        subprocess.check_output([
+            sys.executable,
+            "-m",
+            "build",
+            "--outdir",
+            str(tmp),
+            str(request.config.rootdir),
+        ])
+
+        # Sanity check: should not create recursive setuptools/build/lib/build/lib/...
+        assert not Path(request.config.rootdir, "build/lib/build").exists()
+
+        return next(tmp.glob("*.tar.gz")), next(tmp.glob("*.whl"))
+
+
+@pytest.fixture(scope="session")
+def setuptools_sdist(tmp_path_factory, request):
+    prebuilt = os.getenv("PRE_BUILT_SETUPTOOLS_SDIST")
+    if prebuilt and os.path.exists(prebuilt):  # pragma: no cover
+        return Path(prebuilt).resolve()
+
+    sdist, _ = _build_distributions(tmp_path_factory, request)
+    return sdist
+
+
+@pytest.fixture(scope="session")
+def setuptools_wheel(tmp_path_factory, request):
+    prebuilt = os.getenv("PRE_BUILT_SETUPTOOLS_WHEEL")
+    if prebuilt and os.path.exists(prebuilt):  # pragma: no cover
+        return Path(prebuilt).resolve()
+
+    _, wheel = _build_distributions(tmp_path_factory, request)
+    return wheel
+
+
+@pytest.fixture
+def venv(tmp_path, setuptools_wheel):
+    """Virtual env with the version of setuptools under test installed"""
+    env = environment.VirtualEnv()
+    env.root = path.Path(tmp_path / 'venv')
+    env.create_opts = ['--no-setuptools', '--wheel=bundle']
+    # TODO: Use `--no-wheel` when setuptools implements its own bdist_wheel
+    env.req = str(setuptools_wheel)
+    # In some environments (eg. downstream distro packaging),
+    # where tox isn't used to run tests and PYTHONPATH is set to point to
+    # a specific setuptools codebase, PYTHONPATH will leak into the spawned
+    # processes.
+    # env.create() should install the just created setuptools
+    # wheel, but it doesn't if it finds another existing matching setuptools
+    # installation present on PYTHONPATH:
+    # `setuptools is already installed with the same version as the provided
+    # wheel. Use --force-reinstall to force an installation of the wheel.`
+    # This prevents leaking PYTHONPATH to the created environment.
+    with contexts.environment(PYTHONPATH=None):
+        return env.create()
+
+
+@pytest.fixture
+def venv_without_setuptools(tmp_path):
+    """Virtual env without any version of setuptools installed"""
+    env = environment.VirtualEnv()
+    env.root = path.Path(tmp_path / 'venv_without_setuptools')
+    env.create_opts = ['--no-setuptools', '--no-wheel']
+    env.ensure_env()
+    return env
+
+
+@pytest.fixture
+def bare_venv(tmp_path):
+    """Virtual env without any common packages installed"""
+    env = environment.VirtualEnv()
+    env.root = path.Path(tmp_path / 'bare_venv')
+    env.create_opts = ['--no-setuptools', '--no-pip', '--no-wheel', '--no-seed']
+    env.ensure_env()
+    return env
+
+
+def make_sdist(dist_path, files):
+    """
+    Create a simple sdist tarball at dist_path, containing the files
+    listed in ``files`` as ``(filename, content)`` tuples.
+    """
+
+    # Distributions with only one file don't play well with pip.
+    assert len(files) > 1
+    with tarfile.open(dist_path, 'w:gz') as dist:
+        for filename, content in files:
+            file_bytes = io.BytesIO(content.encode('utf-8'))
+            file_info = tarfile.TarInfo(name=filename)
+            file_info.size = len(file_bytes.getvalue())
+            file_info.mtime = int(time.time())
+            dist.addfile(file_info, fileobj=file_bytes)
+
+
+def make_trivial_sdist(dist_path, distname, version, setuptools_wheel=None):
+    """
+    Create a simple sdist tarball at dist_path, containing just a simple
+    setup.py.
+
+    If ``setuptools_wheel`` is passed, a ``pyproject.toml`` file will also
+    be generated and the passed value will be used as location for
+    setuptools (as build dependency).
+    """
+    files = [
+        (
+            'setup.py',
+            DALS(
+                f"""\
+                 import setuptools
+                 setuptools.setup(
+                     name={distname!r},
+                     version={version!r}
+                 )
+                 """
+            ),
+        ),
+        ('setup.cfg', ''),
+    ]
+
+    if setuptools_wheel:
+        files.append((
+            "pyproject.toml",
+            DALS(
+                f"""\
+                [build-system]
+                requires = ["setuptools @ {setuptools_wheel.as_uri()}"]
+                build-backend = "setuptools.build_meta"
+                """
+            ),
+        ))
+
+    make_sdist(dist_path, files)
+
+
+def make_nspkg_sdist(dist_path, distname, version):
+    """
+    Make an sdist tarball with distname and version which also contains one
+    package with the same name as distname.  The top-level package is
+    designated a namespace package).
+    """
+    # Assert that the distname contains at least one period
+    assert '.' in distname
+
+    parts = distname.split('.')
+    nspackage = parts[0]
+
+    packages = ['.'.join(parts[:idx]) for idx in range(1, len(parts) + 1)]
+
+    setup_py = DALS(
+        f"""\
+        import setuptools
+        setuptools.setup(
+            name={distname!r},
+            version={version!r},
+            packages={packages!r},
+            namespace_packages=[{nspackage!r}]
+        )
+    """
+    )
+
+    init = "__import__('pkg_resources').declare_namespace(__name__)"
+
+    files = [('setup.py', setup_py), (os.path.join(nspackage, '__init__.py'), init)]
+    for package in packages[1:]:
+        filename = os.path.join(*(package.split('.') + ['__init__.py']))
+        files.append((filename, ''))
+
+    make_sdist(dist_path, files)
+
+
+def make_python_requires_sdist(dist_path, distname, version, python_requires):
+    make_sdist(
+        dist_path,
+        [
+            (
+                'setup.py',
+                DALS(
+                    """\
+                import setuptools
+                setuptools.setup(
+                  name={name!r},
+                  version={version!r},
+                  python_requires={python_requires!r},
+                )
+                """
+                ).format(
+                    name=distname, version=version, python_requires=python_requires
+                ),
+            ),
+            ('setup.cfg', ''),
+        ],
+    )
+
+
+def create_setup_requires_package(
+    path,
+    distname='foobar',
+    version='0.1',
+    make_package=make_trivial_sdist,
+    setup_py_template=None,
+    setup_attrs=None,
+    use_setup_cfg=(),
+):
+    """Creates a source tree under path for a trivial test package that has a
+    single requirement in setup_requires--a tarball for that requirement is
+    also created and added to the dependency_links argument.
+
+    ``distname`` and ``version`` refer to the name/version of the package that
+    the test package requires via ``setup_requires``.  The name of the test
+    package itself is just 'test_pkg'.
+    """
+
+    normalized_distname = safer_name(distname)
+    test_setup_attrs = {
+        'name': 'test_pkg',
+        'version': '0.0',
+        'setup_requires': [f'{normalized_distname}=={version}'],
+        'dependency_links': [os.path.abspath(path)],
+    }
+    if setup_attrs:
+        test_setup_attrs.update(setup_attrs)
+
+    test_pkg = os.path.join(path, 'test_pkg')
+    os.mkdir(test_pkg)
+
+    # setup.cfg
+    if use_setup_cfg:
+        options = []
+        metadata = []
+        for name in use_setup_cfg:
+            value = test_setup_attrs.pop(name)
+            if name in 'name version'.split():
+                section = metadata
+            else:
+                section = options
+            if isinstance(value, (tuple, list)):
+                value = ';'.join(value)
+            section.append(f'{name}: {value}')
+        test_setup_cfg_contents = DALS(
+            """
+            [metadata]
+            {metadata}
+            [options]
+            {options}
+            """
+        ).format(
+            options='\n'.join(options),
+            metadata='\n'.join(metadata),
+        )
+    else:
+        test_setup_cfg_contents = ''
+    with open(os.path.join(test_pkg, 'setup.cfg'), 'w', encoding="utf-8") as f:
+        f.write(test_setup_cfg_contents)
+
+    # setup.py
+    if setup_py_template is None:
+        setup_py_template = DALS(
+            """\
+            import setuptools
+            setuptools.setup(**%r)
+        """
+        )
+    with open(os.path.join(test_pkg, 'setup.py'), 'w', encoding="utf-8") as f:
+        f.write(setup_py_template % test_setup_attrs)
+
+    foobar_path = os.path.join(path, f'{normalized_distname}-{version}.tar.gz')
+    make_package(foobar_path, distname, version)
+
+    return test_pkg
+
+
+@pytest.fixture
+def pbr_package(tmp_path, monkeypatch, venv):
+    files = {
+        "pyproject.toml": DALS(
+            """
+            [build-system]
+            requires = ["setuptools"]
+            build-backend = "setuptools.build_meta"
+            """
+        ),
+        "setup.py": DALS(
+            """
+            __import__('setuptools').setup(
+                pbr=True,
+                setup_requires=["pbr"],
+            )
+            """
+        ),
+        "setup.cfg": DALS(
+            """
+            [metadata]
+            name = mypkg
+
+            [files]
+            packages =
+                mypkg
+            """
+        ),
+        "mypkg": {
+            "__init__.py": "",
+            "hello.py": "print('Hello world!')",
+        },
+        "other": {"test.txt": "Another file in here."},
+    }
+    venv.run(["python", "-m", "pip", "install", "pbr"])
+    prefix = tmp_path / 'mypkg'
+    prefix.mkdir()
+    jaraco.path.build(files, prefix=prefix)
+    monkeypatch.setenv('PBR_VERSION', "0.42")
+    return prefix
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/indexes/test_links_priority/external.html b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/indexes/test_links_priority/external.html
new file mode 100644
index 0000000000000000000000000000000000000000..92e4702f634dfb37a404bec3103b76f6afcaa917
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/indexes/test_links_priority/external.html
@@ -0,0 +1,3 @@
+
+bad old link
+
diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/indexes/test_links_priority/simple/foobar/index.html b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/indexes/test_links_priority/simple/foobar/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..fefb028bd3ee7d45a414d6e96a7b2a21ffd7eda7
--- /dev/null
+++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/indexes/test_links_priority/simple/foobar/index.html
@@ -0,0 +1,4 @@
+
+foobar-0.1.tar.gz
+external homepage
+ diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/integration/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/integration/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/integration/helpers.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/integration/helpers.py new file mode 100644 index 0000000000000000000000000000000000000000..16b13022913f62ba86df6b2480d22e3119cdb8cc --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/integration/helpers.py @@ -0,0 +1,80 @@ +"""Reusable functions and classes for different types of integration tests. + +For example ``Archive`` can be used to check the contents of distribution built +with setuptools, and ``run`` will always try to be as verbose as possible to +facilitate debugging. +""" + +from __future__ import annotations + +import os +import subprocess +import tarfile +from collections.abc import Iterator +from pathlib import Path +from zipfile import ZipFile, ZipInfo + + +def run(cmd, env=None): + r = subprocess.run( + cmd, + capture_output=True, + text=True, + encoding="utf-8", + env={**os.environ, **(env or {})}, + # ^-- allow overwriting instead of discarding the current env + ) + + out = r.stdout + "\n" + r.stderr + # pytest omits stdout/err by default, if the test fails they help debugging + print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~") + print(f"Command: {cmd}\nreturn code: {r.returncode}\n\n{out}") + + if r.returncode == 0: + return out + raise subprocess.CalledProcessError(r.returncode, cmd, r.stdout, r.stderr) + + +class Archive: + """Compatibility layer for ZipFile/Info and TarFile/Info""" + + def __init__(self, filename) -> None: + self._filename = filename + if filename.endswith("tar.gz"): + self._obj: tarfile.TarFile | ZipFile = tarfile.open(filename, "r:gz") + elif filename.endswith("zip"): + self._obj = ZipFile(filename) + else: + raise ValueError(f"{filename} doesn't seem to be a zip or tar.gz") + + def __iter__(self) -> Iterator[ZipInfo] | Iterator[tarfile.TarInfo]: + if hasattr(self._obj, "infolist"): + return iter(self._obj.infolist()) + return iter(self._obj) + + def get_name(self, zip_or_tar_info): + if hasattr(zip_or_tar_info, "filename"): + return zip_or_tar_info.filename + return zip_or_tar_info.name + + def get_content(self, zip_or_tar_info): + if hasattr(self._obj, "extractfile"): + content = self._obj.extractfile(zip_or_tar_info) + if content is None: + msg = f"Invalid {zip_or_tar_info.name} in {self._filename}" + raise ValueError(msg) + return str(content.read(), "utf-8") + return str(self._obj.read(zip_or_tar_info), "utf-8") + + +def get_sdist_members(sdist_path): + with tarfile.open(sdist_path, "r:gz") as tar: + files = [Path(f) for f in tar.getnames()] + # remove root folder + relative_files = ("/".join(f.parts[1:]) for f in files) + return {f for f in relative_files if f} + + +def get_wheel_members(wheel_path): + with ZipFile(wheel_path) as zipfile: + return set(zipfile.namelist()) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/integration/test_pbr.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/integration/test_pbr.py new file mode 100644 index 0000000000000000000000000000000000000000..f89e5b8b2151430d0994836dd609f1b75490a336 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/integration/test_pbr.py @@ -0,0 +1,20 @@ +import subprocess + +import pytest + + +@pytest.mark.uses_network +def test_pbr_integration(pbr_package, venv): + """Ensure pbr packages install.""" + cmd = [ + 'python', + '-m', + 'pip', + '-v', + 'install', + '--no-build-isolation', + pbr_package, + ] + venv.run(cmd, stderr=subprocess.STDOUT) + out = venv.run(["python", "-c", "import mypkg.hello"]) + assert "Hello world!" in out diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/integration/test_pip_install_sdist.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/integration/test_pip_install_sdist.py new file mode 100644 index 0000000000000000000000000000000000000000..4e84f218323e6ad67adfbce07cea5a16e91a311c --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/integration/test_pip_install_sdist.py @@ -0,0 +1,223 @@ +# https://github.com/python/mypy/issues/16936 +# mypy: disable-error-code="has-type" +"""Integration tests for setuptools that focus on building packages via pip. + +The idea behind these tests is not to exhaustively check all the possible +combinations of packages, operating systems, supporting libraries, etc, but +rather check a limited number of popular packages and how they interact with +the exposed public API. This way if any change in API is introduced, we hope to +identify backward compatibility problems before publishing a release. + +The number of tested packages is purposefully kept small, to minimise duration +and the associated maintenance cost (changes in the way these packages define +their build process may require changes in the tests). +""" + +import json +import os +import shutil +import sys +from enum import Enum +from glob import glob +from hashlib import md5 +from urllib.request import urlopen + +import pytest +from packaging.requirements import Requirement + +from .helpers import Archive, run + +pytestmark = pytest.mark.integration + + +(LATEST,) = Enum("v", "LATEST") # type: ignore[misc] # https://github.com/python/mypy/issues/16936 +"""Default version to be checked""" +# There are positive and negative aspects of checking the latest version of the +# packages. +# The main positive aspect is that the latest version might have already +# removed the use of APIs deprecated in previous releases of setuptools. + + +# Packages to be tested: +# (Please notice the test environment cannot support EVERY library required for +# compiling binary extensions. In Ubuntu/Debian nomenclature, we only assume +# that `build-essential`, `gfortran` and `libopenblas-dev` are installed, +# due to their relevance to the numerical/scientific programming ecosystem) +EXAMPLES = [ + ("pip", LATEST), # just in case... + ("pytest", LATEST), # uses setuptools_scm + ("mypy", LATEST), # custom build_py + ext_modules + # --- Popular packages: https://hugovk.github.io/top-pypi-packages/ --- + ("botocore", LATEST), + ("kiwisolver", LATEST), # build_ext + ("brotli", LATEST), # not in the list but used by urllib3 + ("pyyaml", LATEST), # cython + custom build_ext + custom distclass + ("charset-normalizer", LATEST), # uses mypyc, used by aiohttp + ("protobuf", LATEST), + # ("requests", LATEST), # XXX: https://github.com/psf/requests/pull/6920 + ("celery", LATEST), + # When adding packages to this list, make sure they expose a `__version__` + # attribute, or modify the tests below +] + + +# Some packages have "optional" dependencies that modify their build behaviour +# and are not listed in pyproject.toml, others still use `setup_requires` +EXTRA_BUILD_DEPS = { + "pyyaml": ("Cython<3.0",), # constraint to avoid errors + "charset-normalizer": ("mypy>=1.4.1",), # no pyproject.toml available +} + +EXTRA_ENV_VARS = { + "pyyaml": {"PYYAML_FORCE_CYTHON": "1"}, + "charset-normalizer": {"CHARSET_NORMALIZER_USE_MYPYC": "1"}, +} + +IMPORT_NAME = { + "pyyaml": "yaml", + "protobuf": "google.protobuf", +} + + +VIRTUALENV = (sys.executable, "-m", "virtualenv") + + +# By default, pip will try to build packages in isolation (PEP 517), which +# means it will download the previous stable version of setuptools. +# `pip` flags can avoid that (the version of setuptools under test +# should be the one to be used) +INSTALL_OPTIONS = ( + "--ignore-installed", + "--no-build-isolation", + # Omit "--no-binary :all:" the sdist is supplied directly. + # Allows dependencies as wheels. +) +# The downside of `--no-build-isolation` is that pip will not download build +# dependencies. The test script will have to also handle that. + + +@pytest.fixture +def venv_python(tmp_path): + run([*VIRTUALENV, str(tmp_path / ".venv")]) + possible_path = (str(p.parent) for p in tmp_path.glob(".venv/*/python*")) + return shutil.which("python", path=os.pathsep.join(possible_path)) + + +@pytest.fixture(autouse=True) +def _prepare(tmp_path, venv_python, monkeypatch): + download_path = os.getenv("DOWNLOAD_PATH", str(tmp_path)) + os.makedirs(download_path, exist_ok=True) + + # Environment vars used for building some of the packages + monkeypatch.setenv("USE_MYPYC", "1") + + yield + + # Let's provide the maximum amount of information possible in the case + # it is necessary to debug the tests directly from the CI logs. + print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~") + print("Temporary directory:") + map(print, tmp_path.glob("*")) + print("Virtual environment:") + run([venv_python, "-m", "pip", "freeze"]) + + +@pytest.mark.parametrize(("package", "version"), EXAMPLES) +@pytest.mark.uses_network +def test_install_sdist(package, version, tmp_path, venv_python, setuptools_wheel): + venv_pip = (venv_python, "-m", "pip") + sdist = retrieve_sdist(package, version, tmp_path) + deps = build_deps(package, sdist) + if deps: + print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~") + print("Dependencies:", deps) + run([*venv_pip, "install", *deps]) + + # Use a virtualenv to simulate PEP 517 isolation + # but install fresh setuptools wheel to ensure the version under development + env = EXTRA_ENV_VARS.get(package, {}) + run([*venv_pip, "install", "--force-reinstall", setuptools_wheel]) + run([*venv_pip, "install", *INSTALL_OPTIONS, sdist], env) + + # Execute a simple script to make sure the package was installed correctly + pkg = IMPORT_NAME.get(package, package).replace("-", "_") + script = f"import {pkg}; print(getattr({pkg}, '__version__', 0))" + run([venv_python, "-c", script]) + + +# ---- Helper Functions ---- + + +def retrieve_sdist(package, version, tmp_path): + """Either use cached sdist file or download it from PyPI""" + # `pip download` cannot be used due to + # https://github.com/pypa/pip/issues/1884 + # https://discuss.python.org/t/pep-625-file-name-of-a-source-distribution/4686 + # We have to find the correct distribution file and download it + download_path = os.getenv("DOWNLOAD_PATH", str(tmp_path)) + dist = retrieve_pypi_sdist_metadata(package, version) + + # Remove old files to prevent cache to grow indefinitely + for file in glob(os.path.join(download_path, f"{package}*")): + if dist["filename"] != file: + os.unlink(file) + + dist_file = os.path.join(download_path, dist["filename"]) + if not os.path.exists(dist_file): + download(dist["url"], dist_file, dist["md5_digest"]) + return dist_file + + +def retrieve_pypi_sdist_metadata(package, version): + # https://warehouse.pypa.io/api-reference/json.html + id_ = package if version is LATEST else f"{package}/{version}" + with urlopen(f"https://pypi.org/pypi/{id_}/json") as f: + metadata = json.load(f) + + if metadata["info"]["yanked"]: + raise ValueError(f"Release for {package} {version} was yanked") + + version = metadata["info"]["version"] + release = metadata["releases"][version] if version is LATEST else metadata["urls"] + (sdist,) = filter(lambda d: d["packagetype"] == "sdist", release) + return sdist + + +def download(url, dest, md5_digest): + with urlopen(url) as f: + data = f.read() + + assert md5(data).hexdigest() == md5_digest + + with open(dest, "wb") as f: + f.write(data) + + assert os.path.exists(dest) + + +def build_deps(package, sdist_file): + """Find out what are the build dependencies for a package. + + "Manually" install them, since pip will not install build + deps with `--no-build-isolation`. + """ + # delay importing, since pytest discovery phase may hit this file from a + # testenv without tomli + from setuptools.compat.py310 import tomllib + + archive = Archive(sdist_file) + info = tomllib.loads(_read_pyproject(archive)) + deps = info.get("build-system", {}).get("requires", []) + deps += EXTRA_BUILD_DEPS.get(package, []) + # Remove setuptools from requirements (and deduplicate) + requirements = {Requirement(d).name: d for d in deps} + return [v for k, v in requirements.items() if k != "setuptools"] + + +def _read_pyproject(archive): + contents = ( + archive.get_content(member) + for member in archive + if os.path.basename(archive.get_name(member)) == "pyproject.toml" + ) + return next(contents, "") diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/mod_with_constant.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/mod_with_constant.py new file mode 100644 index 0000000000000000000000000000000000000000..ef755dd1c7a8d1f116fe51f1b43315057f03379d --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/mod_with_constant.py @@ -0,0 +1 @@ +value = 'three, sir!' diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/namespaces.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/namespaces.py new file mode 100644 index 0000000000000000000000000000000000000000..248db98f97951aeeee0222131417e73074cc72d2 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/namespaces.py @@ -0,0 +1,90 @@ +import ast +import json +import textwrap +from pathlib import Path + + +def iter_namespace_pkgs(namespace): + parts = namespace.split(".") + for i in range(len(parts)): + yield ".".join(parts[: i + 1]) + + +def build_namespace_package(tmpdir, name, version="1.0", impl="pkg_resources"): + src_dir = tmpdir / name + src_dir.mkdir() + setup_py = src_dir / 'setup.py' + namespace, _, rest = name.rpartition('.') + namespaces = list(iter_namespace_pkgs(namespace)) + setup_args = { + "name": name, + "version": version, + "packages": namespaces, + } + + if impl == "pkg_resources": + tmpl = '__import__("pkg_resources").declare_namespace(__name__)' + setup_args["namespace_packages"] = namespaces + elif impl == "pkgutil": + tmpl = '__path__ = __import__("pkgutil").extend_path(__path__, __name__)' + else: + raise ValueError(f"Cannot recognise {impl=} when creating namespaces") + + args = json.dumps(setup_args, indent=4) + assert ast.literal_eval(args) # ensure it is valid Python + + script = textwrap.dedent( + """\ + import setuptools + args = {args} + setuptools.setup(**args) + """ + ).format(args=args) + setup_py.write_text(script, encoding='utf-8') + + ns_pkg_dir = Path(src_dir, namespace.replace(".", "/")) + ns_pkg_dir.mkdir(parents=True) + + for ns in namespaces: + pkg_init = src_dir / ns.replace(".", "/") / '__init__.py' + pkg_init.write_text(tmpl, encoding='utf-8') + + pkg_mod = ns_pkg_dir / (rest + '.py') + some_functionality = 'name = {rest!r}'.format(**locals()) + pkg_mod.write_text(some_functionality, encoding='utf-8') + return src_dir + + +def build_pep420_namespace_package(tmpdir, name): + src_dir = tmpdir / name + src_dir.mkdir() + pyproject = src_dir / "pyproject.toml" + namespace, _, rest = name.rpartition(".") + script = f"""\ + [build-system] + requires = ["setuptools"] + build-backend = "setuptools.build_meta" + + [project] + name = "{name}" + version = "3.14159" + """ + pyproject.write_text(textwrap.dedent(script), encoding='utf-8') + ns_pkg_dir = Path(src_dir, namespace.replace(".", "/")) + ns_pkg_dir.mkdir(parents=True) + pkg_mod = ns_pkg_dir / (rest + ".py") + some_functionality = f"name = {rest!r}" + pkg_mod.write_text(some_functionality, encoding='utf-8') + return src_dir + + +def make_site_dir(target): + """ + Add a sitecustomize.py module in target to cause + target to be added to site dirs such that .pth files + are processed there. + """ + sc = target / 'sitecustomize.py' + target_str = str(target) + tmpl = '__import__("site").addsitedir({target_str!r})' + sc.write_text(tmpl.format(**locals()), encoding='utf-8') diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/script-with-bom.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/script-with-bom.py new file mode 100644 index 0000000000000000000000000000000000000000..c074d263c45bcaebe32fdba328d975c73d1ad5ca --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/script-with-bom.py @@ -0,0 +1 @@ +result = 'passed' diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_archive_util.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_archive_util.py new file mode 100644 index 0000000000000000000000000000000000000000..e3efc62889994fa68bc9170e8a0e403f48a204e1 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_archive_util.py @@ -0,0 +1,36 @@ +import io +import tarfile + +import pytest + +from setuptools import archive_util + + +@pytest.fixture +def tarfile_with_unicode(tmpdir): + """ + Create a tarfile containing only a file whose name is + a zero byte file called testimäge.png. + """ + tarobj = io.BytesIO() + + with tarfile.open(fileobj=tarobj, mode="w:gz") as tgz: + data = b"" + + filename = "testimäge.png" + + t = tarfile.TarInfo(filename) + t.size = len(data) + + tgz.addfile(t, io.BytesIO(data)) + + target = tmpdir / 'unicode-pkg-1.0.tar.gz' + with open(str(target), mode='wb') as tf: + tf.write(tarobj.getvalue()) + return str(target) + + +@pytest.mark.xfail(reason="#710 and #712") +def test_unicode_files(tarfile_with_unicode, tmpdir): + target = tmpdir / 'out' + archive_util.unpack_archive(tarfile_with_unicode, str(target)) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_bdist_deprecations.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_bdist_deprecations.py new file mode 100644 index 0000000000000000000000000000000000000000..d9d67b06161a2b36e7b15fab09f797c5c15575c2 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_bdist_deprecations.py @@ -0,0 +1,28 @@ +"""develop tests""" + +import sys +from unittest import mock + +import pytest + +from setuptools import SetuptoolsDeprecationWarning +from setuptools.dist import Distribution + + +@pytest.mark.skipif(sys.platform == 'win32', reason='non-Windows only') +@pytest.mark.xfail(reason="bdist_rpm is long deprecated, should we remove it? #1988") +@mock.patch('distutils.command.bdist_rpm.bdist_rpm') +def test_bdist_rpm_warning(distutils_cmd, tmpdir_cwd): + dist = Distribution( + dict( + script_name='setup.py', + script_args=['bdist_rpm'], + name='foo', + py_modules=['hi'], + ) + ) + dist.parse_command_line() + with pytest.warns(SetuptoolsDeprecationWarning): + dist.run_commands() + + distutils_cmd.run.assert_called_once() diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_bdist_egg.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_bdist_egg.py new file mode 100644 index 0000000000000000000000000000000000000000..036167dd951e70ad543775529d5ce3f6d6544c71 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_bdist_egg.py @@ -0,0 +1,73 @@ +"""develop tests""" + +import os +import re +import zipfile + +import pytest + +from setuptools.dist import Distribution + +from . import contexts + +SETUP_PY = """\ +from setuptools import setup + +setup(py_modules=['hi']) +""" + + +@pytest.fixture +def setup_context(tmpdir): + with (tmpdir / 'setup.py').open('w') as f: + f.write(SETUP_PY) + with (tmpdir / 'hi.py').open('w') as f: + f.write('1\n') + with tmpdir.as_cwd(): + yield tmpdir + + +class Test: + @pytest.mark.usefixtures("user_override") + @pytest.mark.usefixtures("setup_context") + def test_bdist_egg(self): + dist = Distribution( + dict( + script_name='setup.py', + script_args=['bdist_egg'], + name='foo', + py_modules=['hi'], + ) + ) + os.makedirs(os.path.join('build', 'src')) + with contexts.quiet(): + dist.parse_command_line() + dist.run_commands() + + # let's see if we got our egg link at the right place + [content] = os.listdir('dist') + assert re.match(r'foo-0.0.0-py[23].\d+.egg$', content) + + @pytest.mark.xfail( + os.environ.get('PYTHONDONTWRITEBYTECODE', False), + reason="Byte code disabled", + ) + @pytest.mark.usefixtures("user_override") + @pytest.mark.usefixtures("setup_context") + def test_exclude_source_files(self): + dist = Distribution( + dict( + script_name='setup.py', + script_args=['bdist_egg', '--exclude-source-files'], + py_modules=['hi'], + ) + ) + with contexts.quiet(): + dist.parse_command_line() + dist.run_commands() + [dist_name] = os.listdir('dist') + dist_filename = os.path.join('dist', dist_name) + zip = zipfile.ZipFile(dist_filename) + names = list(zi.filename for zi in zip.filelist) + assert 'hi.pyc' in names + assert 'hi.py' not in names diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_bdist_wheel.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_bdist_wheel.py new file mode 100644 index 0000000000000000000000000000000000000000..68cc0c4d3662bcf6f0881df54105ebaf38403564 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_bdist_wheel.py @@ -0,0 +1,708 @@ +from __future__ import annotations + +import builtins +import importlib +import os.path +import platform +import shutil +import stat +import struct +import sys +import sysconfig +from contextlib import suppress +from inspect import cleandoc +from zipfile import ZipFile + +import jaraco.path +import pytest +from packaging import tags + +import setuptools +from setuptools.command.bdist_wheel import bdist_wheel, get_abi_tag +from setuptools.dist import Distribution +from setuptools.warnings import SetuptoolsDeprecationWarning + +from distutils.core import run_setup + +DEFAULT_FILES = { + "dummy_dist-1.0.dist-info/top_level.txt", + "dummy_dist-1.0.dist-info/METADATA", + "dummy_dist-1.0.dist-info/WHEEL", + "dummy_dist-1.0.dist-info/RECORD", +} +DEFAULT_LICENSE_FILES = { + "LICENSE", + "LICENSE.txt", + "LICENCE", + "LICENCE.txt", + "COPYING", + "COPYING.md", + "NOTICE", + "NOTICE.rst", + "AUTHORS", + "AUTHORS.txt", +} +OTHER_IGNORED_FILES = { + "LICENSE~", + "AUTHORS~", +} +SETUPPY_EXAMPLE = """\ +from setuptools import setup + +setup( + name='dummy_dist', + version='1.0', +) +""" + + +EXAMPLES = { + "dummy-dist": { + "setup.py": SETUPPY_EXAMPLE, + "licenses_dir": {"DUMMYFILE": ""}, + **dict.fromkeys(DEFAULT_LICENSE_FILES | OTHER_IGNORED_FILES, ""), + }, + "simple-dist": { + "setup.py": cleandoc( + """ + from setuptools import setup + + setup( + name="simple.dist", + version="0.1", + description="A testing distribution \N{SNOWMAN}", + extras_require={"voting": ["beaglevote"]}, + ) + """ + ), + "simpledist": "", + }, + "complex-dist": { + "setup.py": cleandoc( + """ + from setuptools import setup + + setup( + name="complex-dist", + version="0.1", + description="Another testing distribution \N{SNOWMAN}", + long_description="Another testing distribution \N{SNOWMAN}", + author="Illustrious Author", + author_email="illustrious@example.org", + url="http://example.org/exemplary", + packages=["complexdist"], + setup_requires=["setuptools"], + install_requires=["quux", "splort"], + extras_require={"simple": ["simple.dist"]}, + entry_points={ + "console_scripts": [ + "complex-dist=complexdist:main", + "complex-dist2=complexdist:main", + ], + }, + ) + """ + ), + "complexdist": {"__init__.py": "def main(): return"}, + }, + "headers-dist": { + "setup.py": cleandoc( + """ + from setuptools import setup + + setup( + name="headers.dist", + version="0.1", + description="A distribution with headers", + headers=["header.h"], + ) + """ + ), + "headersdist.py": "", + "header.h": "", + }, + "commasinfilenames-dist": { + "setup.py": cleandoc( + """ + from setuptools import setup + + setup( + name="testrepo", + version="0.1", + packages=["mypackage"], + description="A test package with commas in file names", + include_package_data=True, + package_data={"mypackage.data": ["*"]}, + ) + """ + ), + "mypackage": { + "__init__.py": "", + "data": {"__init__.py": "", "1,2,3.txt": ""}, + }, + "testrepo-0.1.0": { + "mypackage": {"__init__.py": ""}, + }, + }, + "unicode-dist": { + "setup.py": cleandoc( + """ + from setuptools import setup + + setup( + name="unicode.dist", + version="0.1", + description="A testing distribution \N{SNOWMAN}", + packages=["unicodedist"], + zip_safe=True, + ) + """ + ), + "unicodedist": {"__init__.py": "", "åäö_日本語.py": ""}, + }, + "utf8-metadata-dist": { + "setup.cfg": cleandoc( + """ + [metadata] + name = utf8-metadata-dist + version = 42 + author_email = "John X. Ãørçeč" , Γαμα קּ 東 + long_description = file: README.rst + """ + ), + "README.rst": "UTF-8 描述 説明", + }, + "licenses-dist": { + "setup.cfg": cleandoc( + """ + [metadata] + name = licenses-dist + version = 1.0 + license_files = **/LICENSE + """ + ), + "LICENSE": "", + "src": { + "vendor": {"LICENSE": ""}, + }, + }, +} + + +if sys.platform != "win32": + # ABI3 extensions don't really work on Windows + EXAMPLES["abi3extension-dist"] = { + "setup.py": cleandoc( + """ + from setuptools import Extension, setup + + setup( + name="extension.dist", + version="0.1", + description="A testing distribution \N{SNOWMAN}", + ext_modules=[ + Extension( + name="extension", sources=["extension.c"], py_limited_api=True + ) + ], + ) + """ + ), + "setup.cfg": "[bdist_wheel]\npy_limited_api=cp32", + "extension.c": "#define Py_LIMITED_API 0x03020000\n#include ", + } + + +def bdist_wheel_cmd(**kwargs): + """Run command in the same process so that it is easier to collect coverage""" + dist_obj = ( + run_setup("setup.py", stop_after="init") + if os.path.exists("setup.py") + else Distribution({"script_name": "%%build_meta%%"}) + ) + dist_obj.parse_config_files() + cmd = bdist_wheel(dist_obj) + for attr, value in kwargs.items(): + setattr(cmd, attr, value) + cmd.finalize_options() + return cmd + + +def mkexample(tmp_path_factory, name): + basedir = tmp_path_factory.mktemp(name) + jaraco.path.build(EXAMPLES[name], prefix=str(basedir)) + return basedir + + +@pytest.fixture(scope="session") +def wheel_paths(tmp_path_factory): + build_base = tmp_path_factory.mktemp("build") + dist_dir = tmp_path_factory.mktemp("dist") + for name in EXAMPLES: + example_dir = mkexample(tmp_path_factory, name) + build_dir = build_base / name + with jaraco.path.DirectoryStack().context(example_dir): + bdist_wheel_cmd(bdist_dir=str(build_dir), dist_dir=str(dist_dir)).run() + + return sorted(str(fname) for fname in dist_dir.glob("*.whl")) + + +@pytest.fixture +def dummy_dist(tmp_path_factory): + return mkexample(tmp_path_factory, "dummy-dist") + + +@pytest.fixture +def licenses_dist(tmp_path_factory): + return mkexample(tmp_path_factory, "licenses-dist") + + +def test_no_scripts(wheel_paths): + """Make sure entry point scripts are not generated.""" + path = next(path for path in wheel_paths if "complex_dist" in path) + for entry in ZipFile(path).infolist(): + assert ".data/scripts/" not in entry.filename + + +def test_unicode_record(wheel_paths): + path = next(path for path in wheel_paths if "unicode_dist" in path) + with ZipFile(path) as zf: + record = zf.read("unicode_dist-0.1.dist-info/RECORD") + + assert "åäö_日本語.py".encode() in record + + +UTF8_PKG_INFO = """\ +Metadata-Version: 2.1 +Name: helloworld +Version: 42 +Author-email: "John X. Ãørçeč" , Γαμα קּ 東 + + +UTF-8 描述 説明 +""" + + +def test_preserve_unicode_metadata(monkeypatch, tmp_path): + monkeypatch.chdir(tmp_path) + egginfo = tmp_path / "dummy_dist.egg-info" + distinfo = tmp_path / "dummy_dist.dist-info" + + egginfo.mkdir() + (egginfo / "PKG-INFO").write_text(UTF8_PKG_INFO, encoding="utf-8") + (egginfo / "dependency_links.txt").touch() + + class simpler_bdist_wheel(bdist_wheel): + """Avoid messing with setuptools/distutils internals""" + + def __init__(self) -> None: + pass + + @property + def license_paths(self): + return [] + + cmd_obj = simpler_bdist_wheel() + cmd_obj.egg2dist(egginfo, distinfo) + + metadata = (distinfo / "METADATA").read_text(encoding="utf-8") + assert 'Author-email: "John X. Ãørçeč"' in metadata + assert "Γαμα קּ 東 " in metadata + assert "UTF-8 描述 説明" in metadata + + +def test_licenses_default(dummy_dist, monkeypatch, tmp_path): + monkeypatch.chdir(dummy_dist) + bdist_wheel_cmd(bdist_dir=str(tmp_path)).run() + with ZipFile("dist/dummy_dist-1.0-py3-none-any.whl") as wf: + license_files = { + "dummy_dist-1.0.dist-info/licenses/" + fname + for fname in DEFAULT_LICENSE_FILES + } + assert set(wf.namelist()) == DEFAULT_FILES | license_files + + +def test_licenses_deprecated(dummy_dist, monkeypatch, tmp_path): + dummy_dist.joinpath("setup.cfg").write_text( + "[metadata]\nlicense_file=licenses_dir/DUMMYFILE", encoding="utf-8" + ) + monkeypatch.chdir(dummy_dist) + + bdist_wheel_cmd(bdist_dir=str(tmp_path)).run() + + with ZipFile("dist/dummy_dist-1.0-py3-none-any.whl") as wf: + license_files = {"dummy_dist-1.0.dist-info/licenses/licenses_dir/DUMMYFILE"} + assert set(wf.namelist()) == DEFAULT_FILES | license_files + + +@pytest.mark.parametrize( + ("config_file", "config"), + [ + ("setup.cfg", "[metadata]\nlicense_files=licenses_dir/*\n LICENSE"), + ("setup.cfg", "[metadata]\nlicense_files=licenses_dir/*, LICENSE"), + ( + "setup.py", + SETUPPY_EXAMPLE.replace( + ")", " license_files=['licenses_dir/DUMMYFILE', 'LICENSE'])" + ), + ), + ], +) +def test_licenses_override(dummy_dist, monkeypatch, tmp_path, config_file, config): + dummy_dist.joinpath(config_file).write_text(config, encoding="utf-8") + monkeypatch.chdir(dummy_dist) + bdist_wheel_cmd(bdist_dir=str(tmp_path)).run() + with ZipFile("dist/dummy_dist-1.0-py3-none-any.whl") as wf: + license_files = { + "dummy_dist-1.0.dist-info/licenses/" + fname + for fname in {"licenses_dir/DUMMYFILE", "LICENSE"} + } + assert set(wf.namelist()) == DEFAULT_FILES | license_files + metadata = wf.read("dummy_dist-1.0.dist-info/METADATA").decode("utf8") + assert "License-File: licenses_dir/DUMMYFILE" in metadata + assert "License-File: LICENSE" in metadata + + +def test_licenses_preserve_folder_structure(licenses_dist, monkeypatch, tmp_path): + monkeypatch.chdir(licenses_dist) + bdist_wheel_cmd(bdist_dir=str(tmp_path)).run() + print(os.listdir("dist")) + with ZipFile("dist/licenses_dist-1.0-py3-none-any.whl") as wf: + default_files = {name.replace("dummy_", "licenses_") for name in DEFAULT_FILES} + license_files = { + "licenses_dist-1.0.dist-info/licenses/LICENSE", + "licenses_dist-1.0.dist-info/licenses/src/vendor/LICENSE", + } + assert set(wf.namelist()) == default_files | license_files + metadata = wf.read("licenses_dist-1.0.dist-info/METADATA").decode("utf8") + assert "License-File: src/vendor/LICENSE" in metadata + assert "License-File: LICENSE" in metadata + + +def test_licenses_disabled(dummy_dist, monkeypatch, tmp_path): + dummy_dist.joinpath("setup.cfg").write_text( + "[metadata]\nlicense_files=\n", encoding="utf-8" + ) + monkeypatch.chdir(dummy_dist) + bdist_wheel_cmd(bdist_dir=str(tmp_path)).run() + with ZipFile("dist/dummy_dist-1.0-py3-none-any.whl") as wf: + assert set(wf.namelist()) == DEFAULT_FILES + + +def test_build_number(dummy_dist, monkeypatch, tmp_path): + monkeypatch.chdir(dummy_dist) + bdist_wheel_cmd(bdist_dir=str(tmp_path), build_number="2").run() + with ZipFile("dist/dummy_dist-1.0-2-py3-none-any.whl") as wf: + filenames = set(wf.namelist()) + assert "dummy_dist-1.0.dist-info/RECORD" in filenames + assert "dummy_dist-1.0.dist-info/METADATA" in filenames + + +def test_universal_deprecated(dummy_dist, monkeypatch, tmp_path): + monkeypatch.chdir(dummy_dist) + with pytest.warns(SetuptoolsDeprecationWarning, match=".*universal is deprecated"): + bdist_wheel_cmd(bdist_dir=str(tmp_path), universal=True).run() + + # For now we still respect the option + assert os.path.exists("dist/dummy_dist-1.0-py2.py3-none-any.whl") + + +EXTENSION_EXAMPLE = """\ +#include + +static PyMethodDef methods[] = { + { NULL, NULL, 0, NULL } +}; + +static struct PyModuleDef module_def = { + PyModuleDef_HEAD_INIT, + "extension", + "Dummy extension module", + -1, + methods +}; + +PyMODINIT_FUNC PyInit_extension(void) { + return PyModule_Create(&module_def); +} +""" +EXTENSION_SETUPPY = """\ +from __future__ import annotations + +from setuptools import Extension, setup + +setup( + name="extension.dist", + version="0.1", + description="A testing distribution \N{SNOWMAN}", + ext_modules=[Extension(name="extension", sources=["extension.c"])], +) +""" + + +@pytest.mark.filterwarnings( + "once:Config variable '.*' is unset.*, Python ABI tag may be incorrect" +) +def test_limited_abi(monkeypatch, tmp_path, tmp_path_factory): + """Test that building a binary wheel with the limited ABI works.""" + source_dir = tmp_path_factory.mktemp("extension_dist") + (source_dir / "setup.py").write_text(EXTENSION_SETUPPY, encoding="utf-8") + (source_dir / "extension.c").write_text(EXTENSION_EXAMPLE, encoding="utf-8") + build_dir = tmp_path.joinpath("build") + dist_dir = tmp_path.joinpath("dist") + monkeypatch.chdir(source_dir) + bdist_wheel_cmd(bdist_dir=str(build_dir), dist_dir=str(dist_dir)).run() + + +def test_build_from_readonly_tree(dummy_dist, monkeypatch, tmp_path): + basedir = str(tmp_path.joinpath("dummy")) + shutil.copytree(str(dummy_dist), basedir) + monkeypatch.chdir(basedir) + + # Make the tree read-only + for root, _dirs, files in os.walk(basedir): + for fname in files: + os.chmod(os.path.join(root, fname), stat.S_IREAD) + + bdist_wheel_cmd().run() + + +@pytest.mark.parametrize( + ("option", "compress_type"), + list(bdist_wheel.supported_compressions.items()), + ids=list(bdist_wheel.supported_compressions), +) +def test_compression(dummy_dist, monkeypatch, tmp_path, option, compress_type): + monkeypatch.chdir(dummy_dist) + bdist_wheel_cmd(bdist_dir=str(tmp_path), compression=option).run() + with ZipFile("dist/dummy_dist-1.0-py3-none-any.whl") as wf: + filenames = set(wf.namelist()) + assert "dummy_dist-1.0.dist-info/RECORD" in filenames + assert "dummy_dist-1.0.dist-info/METADATA" in filenames + for zinfo in wf.filelist: + assert zinfo.compress_type == compress_type + + +def test_wheelfile_line_endings(wheel_paths): + for path in wheel_paths: + with ZipFile(path) as wf: + wheelfile = next(fn for fn in wf.filelist if fn.filename.endswith("WHEEL")) + wheelfile_contents = wf.read(wheelfile) + assert b"\r" not in wheelfile_contents + + +def test_unix_epoch_timestamps(dummy_dist, monkeypatch, tmp_path): + monkeypatch.setenv("SOURCE_DATE_EPOCH", "0") + monkeypatch.chdir(dummy_dist) + bdist_wheel_cmd(bdist_dir=str(tmp_path), build_number="2a").run() + with ZipFile("dist/dummy_dist-1.0-2a-py3-none-any.whl") as wf: + for zinfo in wf.filelist: + assert zinfo.date_time >= (1980, 1, 1, 0, 0, 0) # min epoch is used + + +def test_get_abi_tag_windows(monkeypatch): + monkeypatch.setattr(tags, "interpreter_name", lambda: "cp") + monkeypatch.setattr(sysconfig, "get_config_var", lambda x: "cp313-win_amd64") + assert get_abi_tag() == "cp313" + monkeypatch.setattr(sys, "gettotalrefcount", lambda: 1, False) + assert get_abi_tag() == "cp313d" + monkeypatch.setattr(sysconfig, "get_config_var", lambda x: "cp313t-win_amd64") + assert get_abi_tag() == "cp313td" + monkeypatch.delattr(sys, "gettotalrefcount") + assert get_abi_tag() == "cp313t" + + +def test_get_abi_tag_pypy_old(monkeypatch): + monkeypatch.setattr(tags, "interpreter_name", lambda: "pp") + monkeypatch.setattr(sysconfig, "get_config_var", lambda x: "pypy36-pp73") + assert get_abi_tag() == "pypy36_pp73" + + +def test_get_abi_tag_pypy_new(monkeypatch): + monkeypatch.setattr(sysconfig, "get_config_var", lambda x: "pypy37-pp73-darwin") + monkeypatch.setattr(tags, "interpreter_name", lambda: "pp") + assert get_abi_tag() == "pypy37_pp73" + + +def test_get_abi_tag_graalpy(monkeypatch): + monkeypatch.setattr( + sysconfig, "get_config_var", lambda x: "graalpy231-310-native-x86_64-linux" + ) + monkeypatch.setattr(tags, "interpreter_name", lambda: "graalpy") + assert get_abi_tag() == "graalpy231_310_native" + + +def test_get_abi_tag_fallback(monkeypatch): + monkeypatch.setattr(sysconfig, "get_config_var", lambda x: "unknown-python-310") + monkeypatch.setattr(tags, "interpreter_name", lambda: "unknown-python") + assert get_abi_tag() == "unknown_python_310" + + +def test_platform_with_space(dummy_dist, monkeypatch): + """Ensure building on platforms with a space in the name succeed.""" + monkeypatch.chdir(dummy_dist) + bdist_wheel_cmd(plat_name="isilon onefs").run() + + +def test_data_dir_with_tag_build(monkeypatch, tmp_path): + """ + Setuptools allow authors to set PEP 440's local version segments + using ``egg_info.tag_build``. This should be reflected not only in the + ``.whl`` file name, but also in the ``.dist-info`` and ``.data`` dirs. + See pypa/setuptools#3997. + """ + monkeypatch.chdir(tmp_path) + files = { + "setup.py": """ + from setuptools import setup + setup(headers=["hello.h"]) + """, + "setup.cfg": """ + [metadata] + name = test + version = 1.0 + + [options.data_files] + hello/world = file.txt + + [egg_info] + tag_build = +what + tag_date = 0 + """, + "file.txt": "", + "hello.h": "", + } + for file, content in files.items(): + with open(file, "w", encoding="utf-8") as fh: + fh.write(cleandoc(content)) + + bdist_wheel_cmd().run() + + # Ensure .whl, .dist-info and .data contain the local segment + wheel_path = "dist/test-1.0+what-py3-none-any.whl" + assert os.path.exists(wheel_path) + entries = set(ZipFile(wheel_path).namelist()) + for expected in ( + "test-1.0+what.data/headers/hello.h", + "test-1.0+what.data/data/hello/world/file.txt", + "test-1.0+what.dist-info/METADATA", + "test-1.0+what.dist-info/WHEEL", + ): + assert expected in entries + + for not_expected in ( + "test.data/headers/hello.h", + "test-1.0.data/data/hello/world/file.txt", + "test.dist-info/METADATA", + "test-1.0.dist-info/WHEEL", + ): + assert not_expected not in entries + + +@pytest.mark.parametrize( + ("reported", "expected"), + [("linux-x86_64", "linux_i686"), ("linux-aarch64", "linux_armv7l")], +) +@pytest.mark.skipif( + platform.system() != "Linux", reason="Only makes sense to test on Linux" +) +def test_platform_linux32(reported, expected, monkeypatch): + monkeypatch.setattr(struct, "calcsize", lambda x: 4) + dist = setuptools.Distribution() + cmd = bdist_wheel(dist) + cmd.plat_name = reported + cmd.root_is_pure = False + _, _, actual = cmd.get_tag() + assert actual == expected + + +def test_no_ctypes(monkeypatch) -> None: + def _fake_import(name: str, *args, **kwargs): + if name == "ctypes": + raise ModuleNotFoundError(f"No module named {name}") + + return importlib.__import__(name, *args, **kwargs) + + with suppress(KeyError): + monkeypatch.delitem(sys.modules, "wheel.macosx_libfile") + + # Install an importer shim that refuses to load ctypes + monkeypatch.setattr(builtins, "__import__", _fake_import) + with pytest.raises(ModuleNotFoundError, match="No module named ctypes"): + import wheel.macosx_libfile # noqa: F401 + + # Unload and reimport the bdist_wheel command module to make sure it won't try to + # import ctypes + monkeypatch.delitem(sys.modules, "setuptools.command.bdist_wheel") + + import setuptools.command.bdist_wheel # noqa: F401 + + +def test_dist_info_provided(dummy_dist, monkeypatch, tmp_path): + monkeypatch.chdir(dummy_dist) + distinfo = tmp_path / "dummy_dist.dist-info" + + distinfo.mkdir() + (distinfo / "METADATA").write_text("name: helloworld", encoding="utf-8") + + # We don't control the metadata. According to PEP-517, "The hook MAY also + # create other files inside this directory, and a build frontend MUST + # preserve". + (distinfo / "FOO").write_text("bar", encoding="utf-8") + + bdist_wheel_cmd(bdist_dir=str(tmp_path), dist_info_dir=str(distinfo)).run() + expected = { + "dummy_dist-1.0.dist-info/FOO", + "dummy_dist-1.0.dist-info/RECORD", + } + with ZipFile("dist/dummy_dist-1.0-py3-none-any.whl") as wf: + files_found = set(wf.namelist()) + # Check that all expected files are there. + assert expected - files_found == set() + # Make sure there is no accidental egg-info bleeding into the wheel. + assert not [path for path in files_found if 'egg-info' in str(path)] + + +def test_allow_grace_period_parent_directory_license(monkeypatch, tmp_path): + # Motivation: https://github.com/pypa/setuptools/issues/4892 + # TODO: Remove this test after deprecation period is over + files = { + "LICENSE.txt": "parent license", # <---- the license files are outside + "NOTICE.txt": "parent notice", + "python": { + "pyproject.toml": cleandoc( + """ + [project] + name = "test-proj" + dynamic = ["version"] # <---- testing dynamic will not break + [tool.setuptools.dynamic] + version.file = "VERSION" + """ + ), + "setup.cfg": cleandoc( + """ + [metadata] + license_files = + ../LICENSE.txt + ../NOTICE.txt + """ + ), + "VERSION": "42", + }, + } + jaraco.path.build(files, prefix=str(tmp_path)) + monkeypatch.chdir(tmp_path / "python") + msg = "Pattern '../.*.txt' cannot contain '..'" + with pytest.warns(SetuptoolsDeprecationWarning, match=msg): + bdist_wheel_cmd().run() + with ZipFile("dist/test_proj-42-py3-none-any.whl") as wf: + files_found = set(wf.namelist()) + expected_files = { + "test_proj-42.dist-info/licenses/LICENSE.txt", + "test_proj-42.dist-info/licenses/NOTICE.txt", + } + assert expected_files <= files_found + + metadata = wf.read("test_proj-42.dist-info/METADATA").decode("utf8") + assert "License-File: LICENSE.txt" in metadata + assert "License-File: NOTICE.txt" in metadata diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build.py new file mode 100644 index 0000000000000000000000000000000000000000..f0f1d9dcf21bafe9dc82a76d373b366ddeecfcec --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build.py @@ -0,0 +1,33 @@ +from setuptools import Command +from setuptools.command.build import build +from setuptools.dist import Distribution + + +def test_distribution_gives_setuptools_build_obj(tmpdir_cwd): + """ + Check that the setuptools Distribution uses the + setuptools specific build object. + """ + + dist = Distribution( + dict( + script_name='setup.py', + script_args=['build'], + packages=[], + package_data={'': ['path/*']}, + ) + ) + assert isinstance(dist.get_command_obj("build"), build) + + +class Subcommand(Command): + """Dummy command to be used in tests""" + + def initialize_options(self): + pass + + def finalize_options(self): + pass + + def run(self): + raise NotImplementedError("just to check if the command runs") diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_clib.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_clib.py new file mode 100644 index 0000000000000000000000000000000000000000..b5315df4f6599cd376e628c0d74cb14129cd89b8 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_clib.py @@ -0,0 +1,84 @@ +import random +from unittest import mock + +import pytest + +from setuptools.command.build_clib import build_clib +from setuptools.dist import Distribution + +from distutils.errors import DistutilsSetupError + + +class TestBuildCLib: + @mock.patch('setuptools.command.build_clib.newer_pairwise_group') + def test_build_libraries(self, mock_newer): + dist = Distribution() + cmd = build_clib(dist) + + # this will be a long section, just making sure all + # exceptions are properly raised + libs = [('example', {'sources': 'broken.c'})] + with pytest.raises(DistutilsSetupError): + cmd.build_libraries(libs) + + obj_deps = 'some_string' + libs = [('example', {'sources': ['source.c'], 'obj_deps': obj_deps})] + with pytest.raises(DistutilsSetupError): + cmd.build_libraries(libs) + + obj_deps = {'': ''} + libs = [('example', {'sources': ['source.c'], 'obj_deps': obj_deps})] + with pytest.raises(DistutilsSetupError): + cmd.build_libraries(libs) + + obj_deps = {'source.c': ''} + libs = [('example', {'sources': ['source.c'], 'obj_deps': obj_deps})] + with pytest.raises(DistutilsSetupError): + cmd.build_libraries(libs) + + # with that out of the way, let's see if the crude dependency + # system works + cmd.compiler = mock.MagicMock(spec=cmd.compiler) + mock_newer.return_value = ([], []) + + obj_deps = {'': ('global.h',), 'example.c': ('example.h',)} + libs = [('example', {'sources': ['example.c'], 'obj_deps': obj_deps})] + + cmd.build_libraries(libs) + assert [['example.c', 'global.h', 'example.h']] in mock_newer.call_args[0] + assert not cmd.compiler.compile.called + assert cmd.compiler.create_static_lib.call_count == 1 + + # reset the call numbers so we can test again + cmd.compiler.reset_mock() + + mock_newer.return_value = '' # anything as long as it's not ([],[]) + cmd.build_libraries(libs) + assert cmd.compiler.compile.call_count == 1 + assert cmd.compiler.create_static_lib.call_count == 1 + + @mock.patch('setuptools.command.build_clib.newer_pairwise_group') + def test_build_libraries_reproducible(self, mock_newer): + dist = Distribution() + cmd = build_clib(dist) + + # with that out of the way, let's see if the crude dependency + # system works + cmd.compiler = mock.MagicMock(spec=cmd.compiler) + mock_newer.return_value = ([], []) + + original_sources = ['a-example.c', 'example.c'] + sources = original_sources + + obj_deps = {'': ('global.h',), 'example.c': ('example.h',)} + libs = [('example', {'sources': sources, 'obj_deps': obj_deps})] + + cmd.build_libraries(libs) + computed_call_args = mock_newer.call_args[0] + + while sources == original_sources: + sources = random.sample(original_sources, len(original_sources)) + libs = [('example', {'sources': sources, 'obj_deps': obj_deps})] + + cmd.build_libraries(libs) + assert computed_call_args == mock_newer.call_args[0] diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_ext.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_ext.py new file mode 100644 index 0000000000000000000000000000000000000000..c7b60ac32fcd6628cf96396a7e5d8fdb50f67c19 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_ext.py @@ -0,0 +1,293 @@ +from __future__ import annotations + +import os +import sys +from importlib.util import cache_from_source as _compiled_file_name + +import pytest +from jaraco import path + +from setuptools.command.build_ext import build_ext, get_abi3_suffix +from setuptools.dist import Distribution +from setuptools.errors import CompileError +from setuptools.extension import Extension + +from . import environment +from .textwrap import DALS + +import distutils.command.build_ext as orig +from distutils.sysconfig import get_config_var + +IS_PYPY = '__pypy__' in sys.builtin_module_names + + +class TestBuildExt: + def test_get_ext_filename(self): + """ + Setuptools needs to give back the same + result as distutils, even if the fullname + is not in ext_map. + """ + dist = Distribution() + cmd = build_ext(dist) + cmd.ext_map['foo/bar'] = '' + res = cmd.get_ext_filename('foo') + wanted = orig.build_ext.get_ext_filename(cmd, 'foo') + assert res == wanted + + def test_abi3_filename(self): + """ + Filename needs to be loadable by several versions + of Python 3 if 'is_abi3' is truthy on Extension() + """ + print(get_abi3_suffix()) + + extension = Extension('spam.eggs', ['eggs.c'], py_limited_api=True) + dist = Distribution(dict(ext_modules=[extension])) + cmd = build_ext(dist) + cmd.finalize_options() + assert 'spam.eggs' in cmd.ext_map + res = cmd.get_ext_filename('spam.eggs') + + if not get_abi3_suffix(): + assert res.endswith(get_config_var('EXT_SUFFIX')) + elif sys.platform == 'win32': + assert res.endswith('eggs.pyd') + else: + assert 'abi3' in res + + def test_ext_suffix_override(self): + """ + SETUPTOOLS_EXT_SUFFIX variable always overrides + default extension options. + """ + dist = Distribution() + cmd = build_ext(dist) + cmd.ext_map['for_abi3'] = ext = Extension( + 'for_abi3', + ['s.c'], + # Override shouldn't affect abi3 modules + py_limited_api=True, + ) + # Mock value needed to pass tests + ext._links_to_dynamic = False + + if not IS_PYPY: + expect = cmd.get_ext_filename('for_abi3') + else: + # PyPy builds do not use ABI3 tag, so they will + # also get the overridden suffix. + expect = 'for_abi3.test-suffix' + + try: + os.environ['SETUPTOOLS_EXT_SUFFIX'] = '.test-suffix' + res = cmd.get_ext_filename('normal') + assert 'normal.test-suffix' == res + res = cmd.get_ext_filename('for_abi3') + assert expect == res + finally: + del os.environ['SETUPTOOLS_EXT_SUFFIX'] + + def dist_with_example(self): + files = { + "src": {"mypkg": {"subpkg": {"ext2.c": ""}}}, + "c-extensions": {"ext1": {"main.c": ""}}, + } + + ext1 = Extension("mypkg.ext1", ["c-extensions/ext1/main.c"]) + ext2 = Extension("mypkg.subpkg.ext2", ["src/mypkg/subpkg/ext2.c"]) + ext3 = Extension("ext3", ["c-extension/ext3.c"]) + + path.build(files) + return Distribution({ + "script_name": "%test%", + "ext_modules": [ext1, ext2, ext3], + "package_dir": {"": "src"}, + }) + + def test_get_outputs(self, tmpdir_cwd, monkeypatch): + monkeypatch.setenv('SETUPTOOLS_EXT_SUFFIX', '.mp3') # make test OS-independent + monkeypatch.setattr('setuptools.command.build_ext.use_stubs', False) + dist = self.dist_with_example() + + # Regular build: get_outputs not empty, but get_output_mappings is empty + build_ext = dist.get_command_obj("build_ext") + build_ext.editable_mode = False + build_ext.ensure_finalized() + build_lib = build_ext.build_lib.replace(os.sep, "/") + outputs = [x.replace(os.sep, "/") for x in build_ext.get_outputs()] + assert outputs == [ + f"{build_lib}/ext3.mp3", + f"{build_lib}/mypkg/ext1.mp3", + f"{build_lib}/mypkg/subpkg/ext2.mp3", + ] + assert build_ext.get_output_mapping() == {} + + # Editable build: get_output_mappings should contain everything in get_outputs + dist.reinitialize_command("build_ext") + build_ext.editable_mode = True + build_ext.ensure_finalized() + mapping = { + k.replace(os.sep, "/"): v.replace(os.sep, "/") + for k, v in build_ext.get_output_mapping().items() + } + assert mapping == { + f"{build_lib}/ext3.mp3": "src/ext3.mp3", + f"{build_lib}/mypkg/ext1.mp3": "src/mypkg/ext1.mp3", + f"{build_lib}/mypkg/subpkg/ext2.mp3": "src/mypkg/subpkg/ext2.mp3", + } + + def test_get_output_mapping_with_stub(self, tmpdir_cwd, monkeypatch): + monkeypatch.setenv('SETUPTOOLS_EXT_SUFFIX', '.mp3') # make test OS-independent + monkeypatch.setattr('setuptools.command.build_ext.use_stubs', True) + dist = self.dist_with_example() + + # Editable build should create compiled stubs (.pyc files only, no .py) + build_ext = dist.get_command_obj("build_ext") + build_ext.editable_mode = True + build_ext.ensure_finalized() + for ext in build_ext.extensions: + monkeypatch.setattr(ext, "_needs_stub", True) + + build_lib = build_ext.build_lib.replace(os.sep, "/") + mapping = { + k.replace(os.sep, "/"): v.replace(os.sep, "/") + for k, v in build_ext.get_output_mapping().items() + } + + def C(file): + """Make it possible to do comparisons and tests in a OS-independent way""" + return _compiled_file_name(file).replace(os.sep, "/") + + assert mapping == { + C(f"{build_lib}/ext3.py"): C("src/ext3.py"), + f"{build_lib}/ext3.mp3": "src/ext3.mp3", + C(f"{build_lib}/mypkg/ext1.py"): C("src/mypkg/ext1.py"), + f"{build_lib}/mypkg/ext1.mp3": "src/mypkg/ext1.mp3", + C(f"{build_lib}/mypkg/subpkg/ext2.py"): C("src/mypkg/subpkg/ext2.py"), + f"{build_lib}/mypkg/subpkg/ext2.mp3": "src/mypkg/subpkg/ext2.mp3", + } + + # Ensure only the compiled stubs are present not the raw .py stub + assert f"{build_lib}/mypkg/ext1.py" not in mapping + assert f"{build_lib}/mypkg/subpkg/ext2.py" not in mapping + + # Visualize what the cached stub files look like + example_stub = C(f"{build_lib}/mypkg/ext1.py") + assert example_stub in mapping + assert example_stub.startswith(f"{build_lib}/mypkg/__pycache__/ext1") + assert example_stub.endswith(".pyc") + + +class TestBuildExtInplace: + def get_build_ext_cmd(self, optional: bool, **opts) -> build_ext: + files: dict[str, str | dict[str, dict[str, str]]] = { + "eggs.c": "#include missingheader.h\n", + ".build": {"lib": {}, "tmp": {}}, + } + path.build(files) + extension = Extension('spam.eggs', ['eggs.c'], optional=optional) + dist = Distribution(dict(ext_modules=[extension])) + dist.script_name = 'setup.py' + cmd = build_ext(dist) + vars(cmd).update(build_lib=".build/lib", build_temp=".build/tmp", **opts) + cmd.ensure_finalized() + return cmd + + def get_log_messages(self, caplog, capsys): + """ + Historically, distutils "logged" by printing to sys.std*. + Later versions adopted the logging framework. Grab + messages regardless of how they were captured. + """ + std = capsys.readouterr() + return std.out.splitlines() + std.err.splitlines() + caplog.messages + + def test_optional(self, tmpdir_cwd, caplog, capsys): + """ + If optional extensions fail to build, setuptools should show the error + in the logs but not fail to build + """ + cmd = self.get_build_ext_cmd(optional=True, inplace=True) + cmd.run() + assert any( + 'build_ext: building extension "spam.eggs" failed' + for msg in self.get_log_messages(caplog, capsys) + ) + # No compile error exception should be raised + + def test_non_optional(self, tmpdir_cwd): + # Non-optional extensions should raise an exception + cmd = self.get_build_ext_cmd(optional=False, inplace=True) + with pytest.raises(CompileError): + cmd.run() + + +def test_build_ext_config_handling(tmpdir_cwd): + files = { + 'setup.py': DALS( + """ + from setuptools import Extension, setup + setup( + name='foo', + version='0.0.0', + ext_modules=[Extension('foo', ['foo.c'])], + ) + """ + ), + 'foo.c': DALS( + """ + #include "Python.h" + + #if PY_MAJOR_VERSION >= 3 + + static struct PyModuleDef moduledef = { + PyModuleDef_HEAD_INIT, + "foo", + NULL, + 0, + NULL, + NULL, + NULL, + NULL, + NULL + }; + + #define INITERROR return NULL + + PyMODINIT_FUNC PyInit_foo(void) + + #else + + #define INITERROR return + + void initfoo(void) + + #endif + { + #if PY_MAJOR_VERSION >= 3 + PyObject *module = PyModule_Create(&moduledef); + #else + PyObject *module = Py_InitModule("extension", NULL); + #endif + if (module == NULL) + INITERROR; + #if PY_MAJOR_VERSION >= 3 + return module; + #endif + } + """ + ), + 'setup.cfg': DALS( + """ + [build] + build_base = foo_build + """ + ), + } + path.build(files) + code, (stdout, stderr) = environment.run_setup_py( + cmd=['build'], + data_stream=(0, 2), + ) + assert code == 0, f'\nSTDOUT:\n{stdout}\nSTDERR:\n{stderr}' diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_meta.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_meta.py new file mode 100644 index 0000000000000000000000000000000000000000..2cd0a0a8ede8ecb8d0c5ae55c8c3b09559239ed5 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_meta.py @@ -0,0 +1,959 @@ +import contextlib +import importlib +import os +import re +import shutil +import signal +import sys +import tarfile +import warnings +from concurrent import futures +from pathlib import Path +from typing import Any, Callable +from zipfile import ZipFile + +import pytest +from jaraco import path +from packaging.requirements import Requirement + +from setuptools.warnings import SetuptoolsDeprecationWarning + +from .textwrap import DALS + +SETUP_SCRIPT_STUB = "__import__('setuptools').setup()" + + +TIMEOUT = int(os.getenv("TIMEOUT_BACKEND_TEST", "180")) # in seconds +IS_PYPY = '__pypy__' in sys.builtin_module_names + + +pytestmark = pytest.mark.skipif( + sys.platform == "win32" and IS_PYPY, + reason="The combination of PyPy + Windows + pytest-xdist + ProcessPoolExecutor " + "is flaky and problematic", +) + + +class BuildBackendBase: + def __init__(self, cwd='.', env=None, backend_name='setuptools.build_meta') -> None: + self.cwd = cwd + self.env = env or {} + self.backend_name = backend_name + + +class BuildBackend(BuildBackendBase): + """PEP 517 Build Backend""" + + def __init__(self, *args, **kwargs) -> None: + super().__init__(*args, **kwargs) + self.pool = futures.ProcessPoolExecutor(max_workers=1) + + def __getattr__(self, name: str) -> Callable[..., Any]: + """Handles arbitrary function invocations on the build backend.""" + + def method(*args, **kw): + root = os.path.abspath(self.cwd) + caller = BuildBackendCaller(root, self.env, self.backend_name) + pid = None + try: + pid = self.pool.submit(os.getpid).result(TIMEOUT) + return self.pool.submit(caller, name, *args, **kw).result(TIMEOUT) + except futures.TimeoutError: + self.pool.shutdown(wait=False) # doesn't stop already running processes + self._kill(pid) + pytest.xfail(f"Backend did not respond before timeout ({TIMEOUT} s)") + except (futures.process.BrokenProcessPool, MemoryError, OSError): + if IS_PYPY: + pytest.xfail("PyPy frequently fails tests with ProcessPoolExector") + raise + + return method + + def _kill(self, pid): + if pid is None: + return + with contextlib.suppress(ProcessLookupError, OSError): + os.kill(pid, signal.SIGTERM if os.name == "nt" else signal.SIGKILL) + + +class BuildBackendCaller(BuildBackendBase): + def __init__(self, *args, **kwargs) -> None: + super().__init__(*args, **kwargs) + + (self.backend_name, _, self.backend_obj) = self.backend_name.partition(':') + + def __call__(self, name, *args, **kw) -> Any: + """Handles arbitrary function invocations on the build backend.""" + os.chdir(self.cwd) + os.environ.update(self.env) + mod = importlib.import_module(self.backend_name) + + if self.backend_obj: + backend = getattr(mod, self.backend_obj) + else: + backend = mod + + return getattr(backend, name)(*args, **kw) + + +defns = [ + { # simple setup.py script + 'setup.py': DALS( + """ + __import__('setuptools').setup( + name='foo', + version='0.0.0', + py_modules=['hello'], + setup_requires=['six'], + ) + """ + ), + 'hello.py': DALS( + """ + def run(): + print('hello') + """ + ), + }, + { # setup.py that relies on __name__ + 'setup.py': DALS( + """ + assert __name__ == '__main__' + __import__('setuptools').setup( + name='foo', + version='0.0.0', + py_modules=['hello'], + setup_requires=['six'], + ) + """ + ), + 'hello.py': DALS( + """ + def run(): + print('hello') + """ + ), + }, + { # setup.py script that runs arbitrary code + 'setup.py': DALS( + """ + variable = True + def function(): + return variable + assert variable + __import__('setuptools').setup( + name='foo', + version='0.0.0', + py_modules=['hello'], + setup_requires=['six'], + ) + """ + ), + 'hello.py': DALS( + """ + def run(): + print('hello') + """ + ), + }, + { # setup.py script that constructs temp files to be included in the distribution + 'setup.py': DALS( + """ + # Some packages construct files on the fly, include them in the package, + # and immediately remove them after `setup()` (e.g. pybind11==2.9.1). + # Therefore, we cannot use `distutils.core.run_setup(..., stop_after=...)` + # to obtain a distribution object first, and then run the distutils + # commands later, because these files will be removed in the meantime. + + with open('world.py', 'w', encoding="utf-8") as f: + f.write('x = 42') + + try: + __import__('setuptools').setup( + name='foo', + version='0.0.0', + py_modules=['world'], + setup_requires=['six'], + ) + finally: + # Some packages will clean temporary files + __import__('os').unlink('world.py') + """ + ), + }, + { # setup.cfg only + 'setup.cfg': DALS( + """ + [metadata] + name = foo + version = 0.0.0 + + [options] + py_modules=hello + setup_requires=six + """ + ), + 'hello.py': DALS( + """ + def run(): + print('hello') + """ + ), + }, + { # setup.cfg and setup.py + 'setup.cfg': DALS( + """ + [metadata] + name = foo + version = 0.0.0 + + [options] + py_modules=hello + setup_requires=six + """ + ), + 'setup.py': "__import__('setuptools').setup()", + 'hello.py': DALS( + """ + def run(): + print('hello') + """ + ), + }, +] + + +class TestBuildMetaBackend: + backend_name = 'setuptools.build_meta' + + def get_build_backend(self): + return BuildBackend(backend_name=self.backend_name) + + @pytest.fixture(params=defns) + def build_backend(self, tmpdir, request): + path.build(request.param, prefix=str(tmpdir)) + with tmpdir.as_cwd(): + yield self.get_build_backend() + + def test_get_requires_for_build_wheel(self, build_backend): + actual = build_backend.get_requires_for_build_wheel() + expected = ['six'] + assert sorted(actual) == sorted(expected) + + def test_get_requires_for_build_sdist(self, build_backend): + actual = build_backend.get_requires_for_build_sdist() + expected = ['six'] + assert sorted(actual) == sorted(expected) + + def test_build_wheel(self, build_backend): + dist_dir = os.path.abspath('pip-wheel') + os.makedirs(dist_dir) + wheel_name = build_backend.build_wheel(dist_dir) + + wheel_file = os.path.join(dist_dir, wheel_name) + assert os.path.isfile(wheel_file) + + # Temporary files should be removed + assert not os.path.isfile('world.py') + + with ZipFile(wheel_file) as zipfile: + wheel_contents = set(zipfile.namelist()) + + # Each one of the examples have a single module + # that should be included in the distribution + python_scripts = (f for f in wheel_contents if f.endswith('.py')) + modules = [f for f in python_scripts if not f.endswith('setup.py')] + assert len(modules) == 1 + + @pytest.mark.parametrize('build_type', ('wheel', 'sdist')) + def test_build_with_existing_file_present(self, build_type, tmpdir_cwd): + # Building a sdist/wheel should still succeed if there's + # already a sdist/wheel in the destination directory. + files = { + 'setup.py': "from setuptools import setup\nsetup()", + 'VERSION': "0.0.1", + 'setup.cfg': DALS( + """ + [metadata] + name = foo + version = file: VERSION + """ + ), + 'pyproject.toml': DALS( + """ + [build-system] + requires = ["setuptools", "wheel"] + build-backend = "setuptools.build_meta" + """ + ), + } + + path.build(files) + + dist_dir = os.path.abspath('preexisting-' + build_type) + + build_backend = self.get_build_backend() + build_method = getattr(build_backend, 'build_' + build_type) + + # Build a first sdist/wheel. + # Note: this also check the destination directory is + # successfully created if it does not exist already. + first_result = build_method(dist_dir) + + # Change version. + with open("VERSION", "wt", encoding="utf-8") as version_file: + version_file.write("0.0.2") + + # Build a *second* sdist/wheel. + second_result = build_method(dist_dir) + + assert os.path.isfile(os.path.join(dist_dir, first_result)) + assert first_result != second_result + + # And if rebuilding the exact same sdist/wheel? + open(os.path.join(dist_dir, second_result), 'wb').close() + third_result = build_method(dist_dir) + assert third_result == second_result + assert os.path.getsize(os.path.join(dist_dir, third_result)) > 0 + + @pytest.mark.parametrize("setup_script", [None, SETUP_SCRIPT_STUB]) + def test_build_with_pyproject_config(self, tmpdir, setup_script): + files = { + 'pyproject.toml': DALS( + """ + [build-system] + requires = ["setuptools", "wheel"] + build-backend = "setuptools.build_meta" + + [project] + name = "foo" + license = {text = "MIT"} + description = "This is a Python package" + dynamic = ["version", "readme"] + classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Developers" + ] + urls = {Homepage = "http://github.com"} + dependencies = [ + "appdirs", + ] + + [project.optional-dependencies] + all = [ + "tomli>=1", + "pyscaffold>=4,<5", + 'importlib; python_version == "2.6"', + ] + + [project.scripts] + foo = "foo.cli:main" + + [tool.setuptools] + zip-safe = false + package-dir = {"" = "src"} + packages = {find = {where = ["src"]}} + license-files = ["LICENSE*"] + + [tool.setuptools.dynamic] + version = {attr = "foo.__version__"} + readme = {file = "README.rst"} + + [tool.distutils.sdist] + formats = "gztar" + """ + ), + "MANIFEST.in": DALS( + """ + global-include *.py *.txt + global-exclude *.py[cod] + """ + ), + "README.rst": "This is a ``README``", + "LICENSE.txt": "---- placeholder MIT license ----", + "src": { + "foo": { + "__init__.py": "__version__ = '0.1'", + "__init__.pyi": "__version__: str", + "cli.py": "def main(): print('hello world')", + "data.txt": "def main(): print('hello world')", + "py.typed": "", + } + }, + } + if setup_script: + files["setup.py"] = setup_script + + build_backend = self.get_build_backend() + with tmpdir.as_cwd(): + path.build(files) + msgs = [ + "'tool.setuptools.license-files' is deprecated in favor of 'project.license-files'", + "`project.license` as a TOML table is deprecated", + ] + with warnings.catch_warnings(): + for msg in msgs: + warnings.filterwarnings("ignore", msg, SetuptoolsDeprecationWarning) + sdist_path = build_backend.build_sdist("temp") + wheel_file = build_backend.build_wheel("temp") + + with tarfile.open(os.path.join(tmpdir, "temp", sdist_path)) as tar: + sdist_contents = set(tar.getnames()) + + with ZipFile(os.path.join(tmpdir, "temp", wheel_file)) as zipfile: + wheel_contents = set(zipfile.namelist()) + metadata = str(zipfile.read("foo-0.1.dist-info/METADATA"), "utf-8") + license = str( + zipfile.read("foo-0.1.dist-info/licenses/LICENSE.txt"), "utf-8" + ) + epoints = str(zipfile.read("foo-0.1.dist-info/entry_points.txt"), "utf-8") + + assert sdist_contents - {"foo-0.1/setup.py"} == { + 'foo-0.1', + 'foo-0.1/LICENSE.txt', + 'foo-0.1/MANIFEST.in', + 'foo-0.1/PKG-INFO', + 'foo-0.1/README.rst', + 'foo-0.1/pyproject.toml', + 'foo-0.1/setup.cfg', + 'foo-0.1/src', + 'foo-0.1/src/foo', + 'foo-0.1/src/foo/__init__.py', + 'foo-0.1/src/foo/__init__.pyi', + 'foo-0.1/src/foo/cli.py', + 'foo-0.1/src/foo/data.txt', + 'foo-0.1/src/foo/py.typed', + 'foo-0.1/src/foo.egg-info', + 'foo-0.1/src/foo.egg-info/PKG-INFO', + 'foo-0.1/src/foo.egg-info/SOURCES.txt', + 'foo-0.1/src/foo.egg-info/dependency_links.txt', + 'foo-0.1/src/foo.egg-info/entry_points.txt', + 'foo-0.1/src/foo.egg-info/requires.txt', + 'foo-0.1/src/foo.egg-info/top_level.txt', + 'foo-0.1/src/foo.egg-info/not-zip-safe', + } + assert wheel_contents == { + "foo/__init__.py", + "foo/__init__.pyi", # include type information by default + "foo/cli.py", + "foo/data.txt", # include_package_data defaults to True + "foo/py.typed", # include type information by default + "foo-0.1.dist-info/licenses/LICENSE.txt", + "foo-0.1.dist-info/METADATA", + "foo-0.1.dist-info/WHEEL", + "foo-0.1.dist-info/entry_points.txt", + "foo-0.1.dist-info/top_level.txt", + "foo-0.1.dist-info/RECORD", + } + assert license == "---- placeholder MIT license ----" + + for line in ( + "Summary: This is a Python package", + "License: MIT", + "License-File: LICENSE.txt", + "Classifier: Intended Audience :: Developers", + "Requires-Dist: appdirs", + "Requires-Dist: " + str(Requirement('tomli>=1 ; extra == "all"')), + "Requires-Dist: " + + str(Requirement('importlib; python_version=="2.6" and extra =="all"')), + ): + assert line in metadata, (line, metadata) + + assert metadata.strip().endswith("This is a ``README``") + assert epoints.strip() == "[console_scripts]\nfoo = foo.cli:main" + + def test_static_metadata_in_pyproject_config(self, tmpdir): + # Make sure static metadata in pyproject.toml is not overwritten by setup.py + # as required by PEP 621 + files = { + 'pyproject.toml': DALS( + """ + [build-system] + requires = ["setuptools", "wheel"] + build-backend = "setuptools.build_meta" + + [project] + name = "foo" + description = "This is a Python package" + version = "42" + dependencies = ["six"] + """ + ), + 'hello.py': DALS( + """ + def run(): + print('hello') + """ + ), + 'setup.py': DALS( + """ + __import__('setuptools').setup( + name='bar', + version='13', + ) + """ + ), + } + build_backend = self.get_build_backend() + with tmpdir.as_cwd(): + path.build(files) + sdist_path = build_backend.build_sdist("temp") + wheel_file = build_backend.build_wheel("temp") + + assert (tmpdir / "temp/foo-42.tar.gz").exists() + assert (tmpdir / "temp/foo-42-py3-none-any.whl").exists() + assert not (tmpdir / "temp/bar-13.tar.gz").exists() + assert not (tmpdir / "temp/bar-42.tar.gz").exists() + assert not (tmpdir / "temp/foo-13.tar.gz").exists() + assert not (tmpdir / "temp/bar-13-py3-none-any.whl").exists() + assert not (tmpdir / "temp/bar-42-py3-none-any.whl").exists() + assert not (tmpdir / "temp/foo-13-py3-none-any.whl").exists() + + with tarfile.open(os.path.join(tmpdir, "temp", sdist_path)) as tar: + pkg_info = str(tar.extractfile('foo-42/PKG-INFO').read(), "utf-8") + members = tar.getnames() + assert "bar-13/PKG-INFO" not in members + + with ZipFile(os.path.join(tmpdir, "temp", wheel_file)) as zipfile: + metadata = str(zipfile.read("foo-42.dist-info/METADATA"), "utf-8") + members = zipfile.namelist() + assert "bar-13.dist-info/METADATA" not in members + + for file in pkg_info, metadata: + for line in ("Name: foo", "Version: 42"): + assert line in file + for line in ("Name: bar", "Version: 13"): + assert line not in file + + def test_build_sdist(self, build_backend): + dist_dir = os.path.abspath('pip-sdist') + os.makedirs(dist_dir) + sdist_name = build_backend.build_sdist(dist_dir) + + assert os.path.isfile(os.path.join(dist_dir, sdist_name)) + + def test_prepare_metadata_for_build_wheel(self, build_backend): + dist_dir = os.path.abspath('pip-dist-info') + os.makedirs(dist_dir) + + dist_info = build_backend.prepare_metadata_for_build_wheel(dist_dir) + + assert os.path.isfile(os.path.join(dist_dir, dist_info, 'METADATA')) + + def test_prepare_metadata_inplace(self, build_backend): + """ + Some users might pass metadata_directory pre-populated with `.tox` or `.venv`. + See issue #3523. + """ + for pre_existing in [ + ".tox/python/lib/python3.10/site-packages/attrs-22.1.0.dist-info", + ".tox/python/lib/python3.10/site-packages/autocommand-2.2.1.dist-info", + ".nox/python/lib/python3.10/site-packages/build-0.8.0.dist-info", + ".venv/python3.10/site-packages/click-8.1.3.dist-info", + "venv/python3.10/site-packages/distlib-0.3.5.dist-info", + "env/python3.10/site-packages/docutils-0.19.dist-info", + ]: + os.makedirs(pre_existing, exist_ok=True) + dist_info = build_backend.prepare_metadata_for_build_wheel(".") + assert os.path.isfile(os.path.join(dist_info, 'METADATA')) + + def test_build_sdist_explicit_dist(self, build_backend): + # explicitly specifying the dist folder should work + # the folder sdist_directory and the ``--dist-dir`` can be the same + dist_dir = os.path.abspath('dist') + sdist_name = build_backend.build_sdist(dist_dir) + assert os.path.isfile(os.path.join(dist_dir, sdist_name)) + + def test_build_sdist_version_change(self, build_backend): + sdist_into_directory = os.path.abspath("out_sdist") + os.makedirs(sdist_into_directory) + + sdist_name = build_backend.build_sdist(sdist_into_directory) + assert os.path.isfile(os.path.join(sdist_into_directory, sdist_name)) + + # if the setup.py changes subsequent call of the build meta + # should still succeed, given the + # sdist_directory the frontend specifies is empty + setup_loc = os.path.abspath("setup.py") + if not os.path.exists(setup_loc): + setup_loc = os.path.abspath("setup.cfg") + + with open(setup_loc, 'rt', encoding="utf-8") as file_handler: + content = file_handler.read() + with open(setup_loc, 'wt', encoding="utf-8") as file_handler: + file_handler.write(content.replace("version='0.0.0'", "version='0.0.1'")) + + shutil.rmtree(sdist_into_directory) + os.makedirs(sdist_into_directory) + + sdist_name = build_backend.build_sdist("out_sdist") + assert os.path.isfile(os.path.join(os.path.abspath("out_sdist"), sdist_name)) + + def test_build_sdist_pyproject_toml_exists(self, tmpdir_cwd): + files = { + 'setup.py': DALS( + """ + __import__('setuptools').setup( + name='foo', + version='0.0.0', + py_modules=['hello'] + )""" + ), + 'hello.py': '', + 'pyproject.toml': DALS( + """ + [build-system] + requires = ["setuptools", "wheel"] + build-backend = "setuptools.build_meta" + """ + ), + } + path.build(files) + build_backend = self.get_build_backend() + targz_path = build_backend.build_sdist("temp") + with tarfile.open(os.path.join("temp", targz_path)) as tar: + assert any('pyproject.toml' in name for name in tar.getnames()) + + def test_build_sdist_setup_py_exists(self, tmpdir_cwd): + # If build_sdist is called from a script other than setup.py, + # ensure setup.py is included + path.build(defns[0]) + + build_backend = self.get_build_backend() + targz_path = build_backend.build_sdist("temp") + with tarfile.open(os.path.join("temp", targz_path)) as tar: + assert any('setup.py' in name for name in tar.getnames()) + + def test_build_sdist_setup_py_manifest_excluded(self, tmpdir_cwd): + # Ensure that MANIFEST.in can exclude setup.py + files = { + 'setup.py': DALS( + """ + __import__('setuptools').setup( + name='foo', + version='0.0.0', + py_modules=['hello'] + )""" + ), + 'hello.py': '', + 'MANIFEST.in': DALS( + """ + exclude setup.py + """ + ), + } + + path.build(files) + + build_backend = self.get_build_backend() + targz_path = build_backend.build_sdist("temp") + with tarfile.open(os.path.join("temp", targz_path)) as tar: + assert not any('setup.py' in name for name in tar.getnames()) + + def test_build_sdist_builds_targz_even_if_zip_indicated(self, tmpdir_cwd): + files = { + 'setup.py': DALS( + """ + __import__('setuptools').setup( + name='foo', + version='0.0.0', + py_modules=['hello'] + )""" + ), + 'hello.py': '', + 'setup.cfg': DALS( + """ + [sdist] + formats=zip + """ + ), + } + + path.build(files) + + build_backend = self.get_build_backend() + build_backend.build_sdist("temp") + + _relative_path_import_files = { + 'setup.py': DALS( + """ + __import__('setuptools').setup( + name='foo', + version=__import__('hello').__version__, + py_modules=['hello'] + )""" + ), + 'hello.py': '__version__ = "0.0.0"', + 'setup.cfg': DALS( + """ + [sdist] + formats=zip + """ + ), + } + + def test_build_sdist_relative_path_import(self, tmpdir_cwd): + path.build(self._relative_path_import_files) + build_backend = self.get_build_backend() + with pytest.raises(ImportError, match="^No module named 'hello'$"): + build_backend.build_sdist("temp") + + _simple_pyproject_example = { + "pyproject.toml": DALS( + """ + [project] + name = "proj" + version = "42" + """ + ), + "src": {"proj": {"__init__.py": ""}}, + } + + def _assert_link_tree(self, parent_dir): + """All files in the directory should be either links or hard links""" + files = list(Path(parent_dir).glob("**/*")) + assert files # Should not be empty + for file in files: + assert file.is_symlink() or os.stat(file).st_nlink > 0 + + def test_editable_without_config_settings(self, tmpdir_cwd): + """ + Sanity check to ensure tests with --mode=strict are different from the ones + without --mode. + + --mode=strict should create a local directory with a package tree. + The directory should not get created otherwise. + """ + path.build(self._simple_pyproject_example) + build_backend = self.get_build_backend() + assert not Path("build").exists() + build_backend.build_editable("temp") + assert not Path("build").exists() + + def test_build_wheel_inplace(self, tmpdir_cwd): + config_settings = {"--build-option": ["build_ext", "--inplace"]} + path.build(self._simple_pyproject_example) + build_backend = self.get_build_backend() + assert not Path("build").exists() + Path("build").mkdir() + build_backend.prepare_metadata_for_build_wheel("build", config_settings) + build_backend.build_wheel("build", config_settings) + assert Path("build/proj-42-py3-none-any.whl").exists() + + @pytest.mark.parametrize("config_settings", [{"editable-mode": "strict"}]) + def test_editable_with_config_settings(self, tmpdir_cwd, config_settings): + path.build({**self._simple_pyproject_example, '_meta': {}}) + assert not Path("build").exists() + build_backend = self.get_build_backend() + build_backend.prepare_metadata_for_build_editable("_meta", config_settings) + build_backend.build_editable("temp", config_settings, "_meta") + self._assert_link_tree(next(Path("build").glob("__editable__.*"))) + + @pytest.mark.parametrize( + ("setup_literal", "requirements"), + [ + ("'foo'", ['foo']), + ("['foo']", ['foo']), + (r"'foo\n'", ['foo']), + (r"'foo\n\n'", ['foo']), + ("['foo', 'bar']", ['foo', 'bar']), + (r"'# Has a comment line\nfoo'", ['foo']), + (r"'foo # Has an inline comment'", ['foo']), + (r"'foo \\\n >=3.0'", ['foo>=3.0']), + (r"'foo\nbar'", ['foo', 'bar']), + (r"'foo\nbar\n'", ['foo', 'bar']), + (r"['foo\n', 'bar\n']", ['foo', 'bar']), + ], + ) + @pytest.mark.parametrize('use_wheel', [True, False]) + def test_setup_requires(self, setup_literal, requirements, use_wheel, tmpdir_cwd): + files = { + 'setup.py': DALS( + """ + from setuptools import setup + + setup( + name="qux", + version="0.0.0", + py_modules=["hello"], + setup_requires={setup_literal}, + ) + """ + ).format(setup_literal=setup_literal), + 'hello.py': DALS( + """ + def run(): + print('hello') + """ + ), + } + + path.build(files) + + build_backend = self.get_build_backend() + + if use_wheel: + get_requires = build_backend.get_requires_for_build_wheel + else: + get_requires = build_backend.get_requires_for_build_sdist + + # Ensure that the build requirements are properly parsed + expected = sorted(requirements) + actual = get_requires() + + assert expected == sorted(actual) + + def test_setup_requires_with_auto_discovery(self, tmpdir_cwd): + # Make sure patches introduced to retrieve setup_requires don't accidentally + # activate auto-discovery and cause problems due to the incomplete set of + # attributes passed to MinimalDistribution + files = { + 'pyproject.toml': DALS( + """ + [project] + name = "proj" + version = "42" + """ + ), + "setup.py": DALS( + """ + __import__('setuptools').setup( + setup_requires=["foo"], + py_modules = ["hello", "world"] + ) + """ + ), + 'hello.py': "'hello'", + 'world.py': "'world'", + } + path.build(files) + build_backend = self.get_build_backend() + setup_requires = build_backend.get_requires_for_build_wheel() + assert setup_requires == ["foo"] + + def test_dont_install_setup_requires(self, tmpdir_cwd): + files = { + 'setup.py': DALS( + """ + from setuptools import setup + + setup( + name="qux", + version="0.0.0", + py_modules=["hello"], + setup_requires=["does-not-exist >99"], + ) + """ + ), + 'hello.py': DALS( + """ + def run(): + print('hello') + """ + ), + } + + path.build(files) + + build_backend = self.get_build_backend() + + dist_dir = os.path.abspath('pip-dist-info') + os.makedirs(dist_dir) + + # does-not-exist can't be satisfied, so if it attempts to install + # setup_requires, it will fail. + build_backend.prepare_metadata_for_build_wheel(dist_dir) + + _sys_argv_0_passthrough = { + 'setup.py': DALS( + """ + import os + import sys + + __import__('setuptools').setup( + name='foo', + version='0.0.0', + ) + + sys_argv = os.path.abspath(sys.argv[0]) + file_path = os.path.abspath('setup.py') + assert sys_argv == file_path + """ + ) + } + + def test_sys_argv_passthrough(self, tmpdir_cwd): + path.build(self._sys_argv_0_passthrough) + build_backend = self.get_build_backend() + with pytest.raises(AssertionError): + build_backend.build_sdist("temp") + + _setup_py_file_abspath = { + 'setup.py': DALS( + """ + import os + assert os.path.isabs(__file__) + __import__('setuptools').setup( + name='foo', + version='0.0.0', + py_modules=['hello'], + setup_requires=['six'], + ) + """ + ) + } + + def test_setup_py_file_abspath(self, tmpdir_cwd): + path.build(self._setup_py_file_abspath) + build_backend = self.get_build_backend() + build_backend.build_sdist("temp") + + @pytest.mark.parametrize('build_hook', ('build_sdist', 'build_wheel')) + def test_build_with_empty_setuppy(self, build_backend, build_hook): + files = {'setup.py': ''} + path.build(files) + + msg = re.escape('No distribution was found.') + with pytest.raises(ValueError, match=msg): + getattr(build_backend, build_hook)("temp") + + +class TestBuildMetaLegacyBackend(TestBuildMetaBackend): + backend_name = 'setuptools.build_meta:__legacy__' + + # build_meta_legacy-specific tests + def test_build_sdist_relative_path_import(self, tmpdir_cwd): + # This must fail in build_meta, but must pass in build_meta_legacy + path.build(self._relative_path_import_files) + + build_backend = self.get_build_backend() + build_backend.build_sdist("temp") + + def test_sys_argv_passthrough(self, tmpdir_cwd): + path.build(self._sys_argv_0_passthrough) + + build_backend = self.get_build_backend() + build_backend.build_sdist("temp") + + +@pytest.mark.filterwarnings("ignore::setuptools.SetuptoolsDeprecationWarning") +def test_sys_exit_0_in_setuppy(monkeypatch, tmp_path): + """Setuptools should be resilient to setup.py with ``sys.exit(0)`` (#3973).""" + monkeypatch.chdir(tmp_path) + setuppy = """ + import sys, setuptools + setuptools.setup(name='foo', version='0.0.0') + sys.exit(0) + """ + (tmp_path / "setup.py").write_text(DALS(setuppy), encoding="utf-8") + backend = BuildBackend(backend_name="setuptools.build_meta") + assert backend.get_requires_for_build_wheel() == [] + + +def test_system_exit_in_setuppy(monkeypatch, tmp_path): + monkeypatch.chdir(tmp_path) + setuppy = "import sys; sys.exit('some error')" + (tmp_path / "setup.py").write_text(setuppy, encoding="utf-8") + with pytest.raises(SystemExit, match="some error"): + backend = BuildBackend(backend_name="setuptools.build_meta") + backend.get_requires_for_build_wheel() diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_py.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_py.py new file mode 100644 index 0000000000000000000000000000000000000000..78848f718281cce38df5deb82b7afa855c6e0d07 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_build_py.py @@ -0,0 +1,480 @@ +import os +import shutil +import stat +import warnings +from pathlib import Path +from unittest.mock import Mock + +import jaraco.path +import pytest + +from setuptools import SetuptoolsDeprecationWarning +from setuptools.dist import Distribution + +from .textwrap import DALS + + +def test_directories_in_package_data_glob(tmpdir_cwd): + """ + Directories matching the glob in package_data should + not be included in the package data. + + Regression test for #261. + """ + dist = Distribution( + dict( + script_name='setup.py', + script_args=['build_py'], + packages=[''], + package_data={'': ['path/*']}, + ) + ) + os.makedirs('path/subpath') + dist.parse_command_line() + dist.run_commands() + + +def test_recursive_in_package_data_glob(tmpdir_cwd): + """ + Files matching recursive globs (**) in package_data should + be included in the package data. + + #1806 + """ + dist = Distribution( + dict( + script_name='setup.py', + script_args=['build_py'], + packages=[''], + package_data={'': ['path/**/data']}, + ) + ) + os.makedirs('path/subpath/subsubpath') + open('path/subpath/subsubpath/data', 'wb').close() + + dist.parse_command_line() + dist.run_commands() + + assert stat.S_ISREG(os.stat('build/lib/path/subpath/subsubpath/data').st_mode), ( + "File is not included" + ) + + +def test_read_only(tmpdir_cwd): + """ + Ensure read-only flag is not preserved in copy + for package modules and package data, as that + causes problems with deleting read-only files on + Windows. + + #1451 + """ + dist = Distribution( + dict( + script_name='setup.py', + script_args=['build_py'], + packages=['pkg'], + package_data={'pkg': ['data.dat']}, + ) + ) + os.makedirs('pkg') + open('pkg/__init__.py', 'wb').close() + open('pkg/data.dat', 'wb').close() + os.chmod('pkg/__init__.py', stat.S_IREAD) + os.chmod('pkg/data.dat', stat.S_IREAD) + dist.parse_command_line() + dist.run_commands() + shutil.rmtree('build') + + +@pytest.mark.xfail( + 'platform.system() == "Windows"', + reason="On Windows, files do not have executable bits", + raises=AssertionError, + strict=True, +) +def test_executable_data(tmpdir_cwd): + """ + Ensure executable bit is preserved in copy for + package data, as users rely on it for scripts. + + #2041 + """ + dist = Distribution( + dict( + script_name='setup.py', + script_args=['build_py'], + packages=['pkg'], + package_data={'pkg': ['run-me']}, + ) + ) + os.makedirs('pkg') + open('pkg/__init__.py', 'wb').close() + open('pkg/run-me', 'wb').close() + os.chmod('pkg/run-me', 0o700) + + dist.parse_command_line() + dist.run_commands() + + assert os.stat('build/lib/pkg/run-me').st_mode & stat.S_IEXEC, ( + "Script is not executable" + ) + + +EXAMPLE_WITH_MANIFEST = { + "setup.cfg": DALS( + """ + [metadata] + name = mypkg + version = 42 + + [options] + include_package_data = True + packages = find: + + [options.packages.find] + exclude = *.tests* + """ + ), + "mypkg": { + "__init__.py": "", + "resource_file.txt": "", + "tests": { + "__init__.py": "", + "test_mypkg.py": "", + "test_file.txt": "", + }, + }, + "MANIFEST.in": DALS( + """ + global-include *.py *.txt + global-exclude *.py[cod] + prune dist + prune build + prune *.egg-info + """ + ), +} + + +def test_excluded_subpackages(tmpdir_cwd): + jaraco.path.build(EXAMPLE_WITH_MANIFEST) + dist = Distribution({"script_name": "%PEP 517%"}) + dist.parse_config_files() + + build_py = dist.get_command_obj("build_py") + + msg = r"Python recognizes 'mypkg\.tests' as an importable package" + with pytest.warns(SetuptoolsDeprecationWarning, match=msg): # noqa: PT031 + # TODO: To fix #3260 we need some transition period to deprecate the + # existing behavior of `include_package_data`. After the transition, we + # should remove the warning and fix the behavior. + + if os.getenv("SETUPTOOLS_USE_DISTUTILS") == "stdlib": + # pytest.warns reset the warning filter temporarily + # https://github.com/pytest-dev/pytest/issues/4011#issuecomment-423494810 + warnings.filterwarnings( + "ignore", + "'encoding' argument not specified", + module="distutils.text_file", + # This warning is already fixed in pypa/distutils but not in stdlib + ) + + build_py.finalize_options() + build_py.run() + + build_dir = Path(dist.get_command_obj("build_py").build_lib) + assert (build_dir / "mypkg/__init__.py").exists() + assert (build_dir / "mypkg/resource_file.txt").exists() + + # Setuptools is configured to ignore `mypkg.tests`, therefore the following + # files/dirs should not be included in the distribution. + for f in [ + "mypkg/tests/__init__.py", + "mypkg/tests/test_mypkg.py", + "mypkg/tests/test_file.txt", + "mypkg/tests", + ]: + with pytest.raises(AssertionError): + # TODO: Enforce the following assertion once #3260 is fixed + # (remove context manager and the following xfail). + assert not (build_dir / f).exists() + + pytest.xfail("#3260") + + +@pytest.mark.filterwarnings("ignore::setuptools.SetuptoolsDeprecationWarning") +def test_existing_egg_info(tmpdir_cwd, monkeypatch): + """When provided with the ``existing_egg_info_dir`` attribute, build_py should not + attempt to run egg_info again. + """ + # == Pre-condition == + # Generate an egg-info dir + jaraco.path.build(EXAMPLE_WITH_MANIFEST) + dist = Distribution({"script_name": "%PEP 517%"}) + dist.parse_config_files() + assert dist.include_package_data + + egg_info = dist.get_command_obj("egg_info") + dist.run_command("egg_info") + egg_info_dir = next(Path(egg_info.egg_base).glob("*.egg-info")) + assert egg_info_dir.is_dir() + + # == Setup == + build_py = dist.get_command_obj("build_py") + build_py.finalize_options() + egg_info = dist.get_command_obj("egg_info") + egg_info_run = Mock(side_effect=egg_info.run) + monkeypatch.setattr(egg_info, "run", egg_info_run) + + # == Remove caches == + # egg_info is called when build_py looks for data_files, which gets cached. + # We need to ensure it is not cached yet, otherwise it may impact on the tests + build_py.__dict__.pop('data_files', None) + dist.reinitialize_command(egg_info) + + # == Sanity check == + # Ensure that if existing_egg_info is not given, build_py attempts to run egg_info + build_py.existing_egg_info_dir = None + build_py.run() + egg_info_run.assert_called() + + # == Remove caches == + egg_info_run.reset_mock() + build_py.__dict__.pop('data_files', None) + dist.reinitialize_command(egg_info) + + # == Actual test == + # Ensure that if existing_egg_info_dir is given, egg_info doesn't run + build_py.existing_egg_info_dir = egg_info_dir + build_py.run() + egg_info_run.assert_not_called() + assert build_py.data_files + + # Make sure the list of outputs is actually OK + outputs = map(lambda x: x.replace(os.sep, "/"), build_py.get_outputs()) + assert outputs + example = str(Path(build_py.build_lib, "mypkg/__init__.py")).replace(os.sep, "/") + assert example in outputs + + +EXAMPLE_ARBITRARY_MAPPING = { + "pyproject.toml": DALS( + """ + [project] + name = "mypkg" + version = "42" + + [tool.setuptools] + packages = ["mypkg", "mypkg.sub1", "mypkg.sub2", "mypkg.sub2.nested"] + + [tool.setuptools.package-dir] + "" = "src" + "mypkg.sub2" = "src/mypkg/_sub2" + "mypkg.sub2.nested" = "other" + """ + ), + "src": { + "mypkg": { + "__init__.py": "", + "resource_file.txt": "", + "sub1": { + "__init__.py": "", + "mod1.py": "", + }, + "_sub2": { + "mod2.py": "", + }, + }, + }, + "other": { + "__init__.py": "", + "mod3.py": "", + }, + "MANIFEST.in": DALS( + """ + global-include *.py *.txt + global-exclude *.py[cod] + """ + ), +} + + +def test_get_outputs(tmpdir_cwd): + jaraco.path.build(EXAMPLE_ARBITRARY_MAPPING) + dist = Distribution({"script_name": "%test%"}) + dist.parse_config_files() + + build_py = dist.get_command_obj("build_py") + build_py.editable_mode = True + build_py.ensure_finalized() + build_lib = build_py.build_lib.replace(os.sep, "/") + outputs = {x.replace(os.sep, "/") for x in build_py.get_outputs()} + assert outputs == { + f"{build_lib}/mypkg/__init__.py", + f"{build_lib}/mypkg/resource_file.txt", + f"{build_lib}/mypkg/sub1/__init__.py", + f"{build_lib}/mypkg/sub1/mod1.py", + f"{build_lib}/mypkg/sub2/mod2.py", + f"{build_lib}/mypkg/sub2/nested/__init__.py", + f"{build_lib}/mypkg/sub2/nested/mod3.py", + } + mapping = { + k.replace(os.sep, "/"): v.replace(os.sep, "/") + for k, v in build_py.get_output_mapping().items() + } + assert mapping == { + f"{build_lib}/mypkg/__init__.py": "src/mypkg/__init__.py", + f"{build_lib}/mypkg/resource_file.txt": "src/mypkg/resource_file.txt", + f"{build_lib}/mypkg/sub1/__init__.py": "src/mypkg/sub1/__init__.py", + f"{build_lib}/mypkg/sub1/mod1.py": "src/mypkg/sub1/mod1.py", + f"{build_lib}/mypkg/sub2/mod2.py": "src/mypkg/_sub2/mod2.py", + f"{build_lib}/mypkg/sub2/nested/__init__.py": "other/__init__.py", + f"{build_lib}/mypkg/sub2/nested/mod3.py": "other/mod3.py", + } + + +class TestTypeInfoFiles: + PYPROJECTS = { + "default_pyproject": DALS( + """ + [project] + name = "foo" + version = "1" + """ + ), + "dont_include_package_data": DALS( + """ + [project] + name = "foo" + version = "1" + + [tool.setuptools] + include-package-data = false + """ + ), + "exclude_type_info": DALS( + """ + [project] + name = "foo" + version = "1" + + [tool.setuptools] + include-package-data = false + + [tool.setuptools.exclude-package-data] + "*" = ["py.typed", "*.pyi"] + """ + ), + } + + EXAMPLES = { + "simple_namespace": { + "directory_structure": { + "foo": { + "bar.pyi": "", + "py.typed": "", + "__init__.py": "", + } + }, + "expected_type_files": {"foo/bar.pyi", "foo/py.typed"}, + }, + "nested_inside_namespace": { + "directory_structure": { + "foo": { + "bar": { + "py.typed": "", + "mod.pyi": "", + } + } + }, + "expected_type_files": {"foo/bar/mod.pyi", "foo/bar/py.typed"}, + }, + "namespace_nested_inside_regular": { + "directory_structure": { + "foo": { + "namespace": { + "foo.pyi": "", + }, + "__init__.pyi": "", + "py.typed": "", + } + }, + "expected_type_files": { + "foo/namespace/foo.pyi", + "foo/__init__.pyi", + "foo/py.typed", + }, + }, + } + + @pytest.mark.parametrize( + "pyproject", + [ + "default_pyproject", + pytest.param( + "dont_include_package_data", + marks=pytest.mark.xfail(reason="pypa/setuptools#4350"), + ), + ], + ) + @pytest.mark.parametrize("example", EXAMPLES.keys()) + def test_type_files_included_by_default(self, tmpdir_cwd, pyproject, example): + structure = { + **self.EXAMPLES[example]["directory_structure"], + "pyproject.toml": self.PYPROJECTS[pyproject], + } + expected_type_files = self.EXAMPLES[example]["expected_type_files"] + jaraco.path.build(structure) + + build_py = get_finalized_build_py() + outputs = get_outputs(build_py) + assert expected_type_files <= outputs + + @pytest.mark.parametrize("pyproject", ["exclude_type_info"]) + @pytest.mark.parametrize("example", EXAMPLES.keys()) + def test_type_files_can_be_excluded(self, tmpdir_cwd, pyproject, example): + structure = { + **self.EXAMPLES[example]["directory_structure"], + "pyproject.toml": self.PYPROJECTS[pyproject], + } + expected_type_files = self.EXAMPLES[example]["expected_type_files"] + jaraco.path.build(structure) + + build_py = get_finalized_build_py() + outputs = get_outputs(build_py) + assert expected_type_files.isdisjoint(outputs) + + def test_stub_only_package(self, tmpdir_cwd): + structure = { + "pyproject.toml": DALS( + """ + [project] + name = "foo-stubs" + version = "1" + """ + ), + "foo-stubs": {"__init__.pyi": "", "bar.pyi": ""}, + } + expected_type_files = {"foo-stubs/__init__.pyi", "foo-stubs/bar.pyi"} + jaraco.path.build(structure) + + build_py = get_finalized_build_py() + outputs = get_outputs(build_py) + assert expected_type_files <= outputs + + +def get_finalized_build_py(script_name="%build_py-test%"): + dist = Distribution({"script_name": script_name}) + dist.parse_config_files() + build_py = dist.get_command_obj("build_py") + build_py.finalize_options() + return build_py + + +def get_outputs(build_py): + build_dir = Path(build_py.build_lib) + return { + os.path.relpath(x, build_dir).replace(os.sep, "/") + for x in build_py.get_outputs() + } diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_config_discovery.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_config_discovery.py new file mode 100644 index 0000000000000000000000000000000000000000..b5df8203cdb6f9129a65d0c503c4f51e21315b1f --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_config_discovery.py @@ -0,0 +1,647 @@ +import os +import sys +from configparser import ConfigParser +from itertools import product +from typing import cast + +import jaraco.path +import pytest +from path import Path + +import setuptools # noqa: F401 # force distutils.core to be patched +from setuptools.command.sdist import sdist +from setuptools.discovery import find_package_path, find_parent_package +from setuptools.dist import Distribution +from setuptools.errors import PackageDiscoveryError + +from .contexts import quiet +from .integration.helpers import get_sdist_members, get_wheel_members, run +from .textwrap import DALS + +import distutils.core + + +class TestFindParentPackage: + def test_single_package(self, tmp_path): + # find_parent_package should find a non-namespace parent package + (tmp_path / "src/namespace/pkg/nested").mkdir(exist_ok=True, parents=True) + (tmp_path / "src/namespace/pkg/nested/__init__.py").touch() + (tmp_path / "src/namespace/pkg/__init__.py").touch() + packages = ["namespace", "namespace.pkg", "namespace.pkg.nested"] + assert find_parent_package(packages, {"": "src"}, tmp_path) == "namespace.pkg" + + def test_multiple_toplevel(self, tmp_path): + # find_parent_package should return null if the given list of packages does not + # have a single parent package + multiple = ["pkg", "pkg1", "pkg2"] + for name in multiple: + (tmp_path / f"src/{name}").mkdir(exist_ok=True, parents=True) + (tmp_path / f"src/{name}/__init__.py").touch() + assert find_parent_package(multiple, {"": "src"}, tmp_path) is None + + +class TestDiscoverPackagesAndPyModules: + """Make sure discovered values for ``packages`` and ``py_modules`` work + similarly to explicit configuration for the simple scenarios. + """ + + OPTIONS = { + # Different options according to the circumstance being tested + "explicit-src": {"package_dir": {"": "src"}, "packages": ["pkg"]}, + "variation-lib": { + "package_dir": {"": "lib"}, # variation of the source-layout + }, + "explicit-flat": {"packages": ["pkg"]}, + "explicit-single_module": {"py_modules": ["pkg"]}, + "explicit-namespace": {"packages": ["ns", "ns.pkg"]}, + "automatic-src": {}, + "automatic-flat": {}, + "automatic-single_module": {}, + "automatic-namespace": {}, + } + FILES = { + "src": ["src/pkg/__init__.py", "src/pkg/main.py"], + "lib": ["lib/pkg/__init__.py", "lib/pkg/main.py"], + "flat": ["pkg/__init__.py", "pkg/main.py"], + "single_module": ["pkg.py"], + "namespace": ["ns/pkg/__init__.py"], + } + + def _get_info(self, circumstance): + _, _, layout = circumstance.partition("-") + files = self.FILES[layout] + options = self.OPTIONS[circumstance] + return files, options + + @pytest.mark.parametrize("circumstance", OPTIONS.keys()) + def test_sdist_filelist(self, tmp_path, circumstance): + files, options = self._get_info(circumstance) + _populate_project_dir(tmp_path, files, options) + + _, cmd = _run_sdist_programatically(tmp_path, options) + + manifest = [f.replace(os.sep, "/") for f in cmd.filelist.files] + for file in files: + assert any(f.endswith(file) for f in manifest) + + @pytest.mark.parametrize("circumstance", OPTIONS.keys()) + def test_project(self, tmp_path, circumstance): + files, options = self._get_info(circumstance) + _populate_project_dir(tmp_path, files, options) + + # Simulate a pre-existing `build` directory + (tmp_path / "build").mkdir() + (tmp_path / "build/lib").mkdir() + (tmp_path / "build/bdist.linux-x86_64").mkdir() + (tmp_path / "build/bdist.linux-x86_64/file.py").touch() + (tmp_path / "build/lib/__init__.py").touch() + (tmp_path / "build/lib/file.py").touch() + (tmp_path / "dist").mkdir() + (tmp_path / "dist/file.py").touch() + + _run_build(tmp_path) + + sdist_files = get_sdist_members(next(tmp_path.glob("dist/*.tar.gz"))) + print("~~~~~ sdist_members ~~~~~") + print('\n'.join(sdist_files)) + assert sdist_files >= set(files) + + wheel_files = get_wheel_members(next(tmp_path.glob("dist/*.whl"))) + print("~~~~~ wheel_members ~~~~~") + print('\n'.join(wheel_files)) + orig_files = {f.replace("src/", "").replace("lib/", "") for f in files} + assert wheel_files >= orig_files + + # Make sure build files are not included by mistake + for file in wheel_files: + assert "build" not in files + assert "dist" not in files + + PURPOSEFULLY_EMPY = { + "setup.cfg": DALS( + """ + [metadata] + name = myproj + version = 0.0.0 + + [options] + {param} = + """ + ), + "setup.py": DALS( + """ + __import__('setuptools').setup( + name="myproj", + version="0.0.0", + {param}=[] + ) + """ + ), + "pyproject.toml": DALS( + """ + [build-system] + requires = [] + build-backend = 'setuptools.build_meta' + + [project] + name = "myproj" + version = "0.0.0" + + [tool.setuptools] + {param} = [] + """ + ), + "template-pyproject.toml": DALS( + """ + [build-system] + requires = [] + build-backend = 'setuptools.build_meta' + """ + ), + } + + @pytest.mark.parametrize( + ("config_file", "param", "circumstance"), + product( + ["setup.cfg", "setup.py", "pyproject.toml"], + ["packages", "py_modules"], + FILES.keys(), + ), + ) + def test_purposefully_empty(self, tmp_path, config_file, param, circumstance): + files = self.FILES[circumstance] + ["mod.py", "other.py", "src/pkg/__init__.py"] + _populate_project_dir(tmp_path, files, {}) + + if config_file == "pyproject.toml": + template_param = param.replace("_", "-") + else: + # Make sure build works with or without setup.cfg + pyproject = self.PURPOSEFULLY_EMPY["template-pyproject.toml"] + (tmp_path / "pyproject.toml").write_text(pyproject, encoding="utf-8") + template_param = param + + config = self.PURPOSEFULLY_EMPY[config_file].format(param=template_param) + (tmp_path / config_file).write_text(config, encoding="utf-8") + + dist = _get_dist(tmp_path, {}) + # When either parameter package or py_modules is an empty list, + # then there should be no discovery + assert getattr(dist, param) == [] + other = {"py_modules": "packages", "packages": "py_modules"}[param] + assert getattr(dist, other) is None + + @pytest.mark.parametrize( + ("extra_files", "pkgs"), + [ + (["venv/bin/simulate_venv"], {"pkg"}), + (["pkg-stubs/__init__.pyi"], {"pkg", "pkg-stubs"}), + (["other-stubs/__init__.pyi"], {"pkg", "other-stubs"}), + ( + # Type stubs can also be namespaced + ["namespace-stubs/pkg/__init__.pyi"], + {"pkg", "namespace-stubs", "namespace-stubs.pkg"}, + ), + ( + # Just the top-level package can have `-stubs`, ignore nested ones + ["namespace-stubs/pkg-stubs/__init__.pyi"], + {"pkg", "namespace-stubs"}, + ), + (["_hidden/file.py"], {"pkg"}), + (["news/finalize.py"], {"pkg"}), + ], + ) + def test_flat_layout_with_extra_files(self, tmp_path, extra_files, pkgs): + files = self.FILES["flat"] + extra_files + _populate_project_dir(tmp_path, files, {}) + dist = _get_dist(tmp_path, {}) + assert set(dist.packages) == pkgs + + @pytest.mark.parametrize( + "extra_files", + [ + ["other/__init__.py"], + ["other/finalize.py"], + ], + ) + def test_flat_layout_with_dangerous_extra_files(self, tmp_path, extra_files): + files = self.FILES["flat"] + extra_files + _populate_project_dir(tmp_path, files, {}) + with pytest.raises(PackageDiscoveryError, match="multiple (packages|modules)"): + _get_dist(tmp_path, {}) + + def test_flat_layout_with_single_module(self, tmp_path): + files = self.FILES["single_module"] + ["invalid-module-name.py"] + _populate_project_dir(tmp_path, files, {}) + dist = _get_dist(tmp_path, {}) + assert set(dist.py_modules) == {"pkg"} + + def test_flat_layout_with_multiple_modules(self, tmp_path): + files = self.FILES["single_module"] + ["valid_module_name.py"] + _populate_project_dir(tmp_path, files, {}) + with pytest.raises(PackageDiscoveryError, match="multiple (packages|modules)"): + _get_dist(tmp_path, {}) + + def test_py_modules_when_wheel_dir_is_cwd(self, tmp_path): + """Regression for issue 3692""" + from setuptools import build_meta + + pyproject = '[project]\nname = "test"\nversion = "1"' + (tmp_path / "pyproject.toml").write_text(DALS(pyproject), encoding="utf-8") + (tmp_path / "foo.py").touch() + with jaraco.path.DirectoryStack().context(tmp_path): + build_meta.build_wheel(".") + # Ensure py_modules are found + wheel_files = get_wheel_members(next(tmp_path.glob("*.whl"))) + assert "foo.py" in wheel_files + + +class TestNoConfig: + DEFAULT_VERSION = "0.0.0" # Default version given by setuptools + + EXAMPLES = { + "pkg1": ["src/pkg1.py"], + "pkg2": ["src/pkg2/__init__.py"], + "pkg3": ["src/pkg3/__init__.py", "src/pkg3-stubs/__init__.py"], + "pkg4": ["pkg4/__init__.py", "pkg4-stubs/__init__.py"], + "ns.nested.pkg1": ["src/ns/nested/pkg1/__init__.py"], + "ns.nested.pkg2": ["ns/nested/pkg2/__init__.py"], + } + + @pytest.mark.parametrize("example", EXAMPLES.keys()) + def test_discover_name(self, tmp_path, example): + _populate_project_dir(tmp_path, self.EXAMPLES[example], {}) + dist = _get_dist(tmp_path, {}) + assert dist.get_name() == example + + def test_build_with_discovered_name(self, tmp_path): + files = ["src/ns/nested/pkg/__init__.py"] + _populate_project_dir(tmp_path, files, {}) + _run_build(tmp_path, "--sdist") + # Expected distribution file + dist_file = tmp_path / f"dist/ns_nested_pkg-{self.DEFAULT_VERSION}.tar.gz" + assert dist_file.is_file() + + +class TestWithAttrDirective: + @pytest.mark.parametrize( + ("folder", "opts"), + [ + ("src", {}), + ("lib", {"packages": "find:", "packages.find": {"where": "lib"}}), + ], + ) + def test_setupcfg_metadata(self, tmp_path, folder, opts): + files = [f"{folder}/pkg/__init__.py", "setup.cfg"] + _populate_project_dir(tmp_path, files, opts) + + config = (tmp_path / "setup.cfg").read_text(encoding="utf-8") + overwrite = { + folder: {"pkg": {"__init__.py": "version = 42"}}, + "setup.cfg": "[metadata]\nversion = attr: pkg.version\n" + config, + } + jaraco.path.build(overwrite, prefix=tmp_path) + + dist = _get_dist(tmp_path, {}) + assert dist.get_name() == "pkg" + assert dist.get_version() == "42" + assert dist.package_dir + package_path = find_package_path("pkg", dist.package_dir, tmp_path) + assert os.path.exists(package_path) + assert folder in Path(package_path).parts() + + _run_build(tmp_path, "--sdist") + dist_file = tmp_path / "dist/pkg-42.tar.gz" + assert dist_file.is_file() + + def test_pyproject_metadata(self, tmp_path): + _populate_project_dir(tmp_path, ["src/pkg/__init__.py"], {}) + + overwrite = { + "src": {"pkg": {"__init__.py": "version = 42"}}, + "pyproject.toml": ( + "[project]\nname = 'pkg'\ndynamic = ['version']\n" + "[tool.setuptools.dynamic]\nversion = {attr = 'pkg.version'}\n" + ), + } + jaraco.path.build(overwrite, prefix=tmp_path) + + dist = _get_dist(tmp_path, {}) + assert dist.get_version() == "42" + assert dist.package_dir == {"": "src"} + + +class TestWithCExtension: + def _simulate_package_with_extension(self, tmp_path): + # This example is based on: https://github.com/nucleic/kiwi/tree/1.4.0 + files = [ + "benchmarks/file.py", + "docs/Makefile", + "docs/requirements.txt", + "docs/source/conf.py", + "proj/header.h", + "proj/file.py", + "py/proj.cpp", + "py/other.cpp", + "py/file.py", + "py/py.typed", + "py/tests/test_proj.py", + "README.rst", + ] + _populate_project_dir(tmp_path, files, {}) + + setup_script = """ + from setuptools import Extension, setup + + ext_modules = [ + Extension( + "proj", + ["py/proj.cpp", "py/other.cpp"], + include_dirs=["."], + language="c++", + ), + ] + setup(ext_modules=ext_modules) + """ + (tmp_path / "setup.py").write_text(DALS(setup_script), encoding="utf-8") + + def test_skip_discovery_with_setupcfg_metadata(self, tmp_path): + """Ensure that auto-discovery is not triggered when the project is based on + C-extensions only, for backward compatibility. + """ + self._simulate_package_with_extension(tmp_path) + + pyproject = """ + [build-system] + requires = [] + build-backend = 'setuptools.build_meta' + """ + (tmp_path / "pyproject.toml").write_text(DALS(pyproject), encoding="utf-8") + + setupcfg = """ + [metadata] + name = proj + version = 42 + """ + (tmp_path / "setup.cfg").write_text(DALS(setupcfg), encoding="utf-8") + + dist = _get_dist(tmp_path, {}) + assert dist.get_name() == "proj" + assert dist.get_version() == "42" + assert dist.py_modules is None + assert dist.packages is None + assert len(dist.ext_modules) == 1 + assert dist.ext_modules[0].name == "proj" + + def test_dont_skip_discovery_with_pyproject_metadata(self, tmp_path): + """When opting-in to pyproject.toml metadata, auto-discovery will be active if + the package lists C-extensions, but does not configure py-modules or packages. + + This way we ensure users with complex package layouts that would lead to the + discovery of multiple top-level modules/packages see errors and are forced to + explicitly set ``packages`` or ``py-modules``. + """ + self._simulate_package_with_extension(tmp_path) + + pyproject = """ + [project] + name = 'proj' + version = '42' + """ + (tmp_path / "pyproject.toml").write_text(DALS(pyproject), encoding="utf-8") + with pytest.raises(PackageDiscoveryError, match="multiple (packages|modules)"): + _get_dist(tmp_path, {}) + + +class TestWithPackageData: + def _simulate_package_with_data_files(self, tmp_path, src_root): + files = [ + f"{src_root}/proj/__init__.py", + f"{src_root}/proj/file1.txt", + f"{src_root}/proj/nested/file2.txt", + ] + _populate_project_dir(tmp_path, files, {}) + + manifest = """ + global-include *.py *.txt + """ + (tmp_path / "MANIFEST.in").write_text(DALS(manifest), encoding="utf-8") + + EXAMPLE_SETUPCFG = """ + [metadata] + name = proj + version = 42 + + [options] + include_package_data = True + """ + EXAMPLE_PYPROJECT = """ + [project] + name = "proj" + version = "42" + """ + + PYPROJECT_PACKAGE_DIR = """ + [tool.setuptools] + package-dir = {"" = "src"} + """ + + @pytest.mark.parametrize( + ("src_root", "files"), + [ + (".", {"setup.cfg": DALS(EXAMPLE_SETUPCFG)}), + (".", {"pyproject.toml": DALS(EXAMPLE_PYPROJECT)}), + ("src", {"setup.cfg": DALS(EXAMPLE_SETUPCFG)}), + ("src", {"pyproject.toml": DALS(EXAMPLE_PYPROJECT)}), + ( + "src", + { + "setup.cfg": DALS(EXAMPLE_SETUPCFG) + + DALS( + """ + packages = find: + package_dir = + =src + + [options.packages.find] + where = src + """ + ) + }, + ), + ( + "src", + { + "pyproject.toml": DALS(EXAMPLE_PYPROJECT) + + DALS( + """ + [tool.setuptools] + package-dir = {"" = "src"} + """ + ) + }, + ), + ], + ) + def test_include_package_data(self, tmp_path, src_root, files): + """ + Make sure auto-discovery does not affect package include_package_data. + See issue #3196. + """ + jaraco.path.build(files, prefix=str(tmp_path)) + self._simulate_package_with_data_files(tmp_path, src_root) + + expected = { + os.path.normpath(f"{src_root}/proj/file1.txt").replace(os.sep, "/"), + os.path.normpath(f"{src_root}/proj/nested/file2.txt").replace(os.sep, "/"), + } + + _run_build(tmp_path) + + sdist_files = get_sdist_members(next(tmp_path.glob("dist/*.tar.gz"))) + print("~~~~~ sdist_members ~~~~~") + print('\n'.join(sdist_files)) + assert sdist_files >= expected + + wheel_files = get_wheel_members(next(tmp_path.glob("dist/*.whl"))) + print("~~~~~ wheel_members ~~~~~") + print('\n'.join(wheel_files)) + orig_files = {f.replace("src/", "").replace("lib/", "") for f in expected} + assert wheel_files >= orig_files + + +def test_compatible_with_numpy_configuration(tmp_path): + files = [ + "dir1/__init__.py", + "dir2/__init__.py", + "file.py", + ] + _populate_project_dir(tmp_path, files, {}) + dist = Distribution({}) + dist.configuration = object() + dist.set_defaults() + assert dist.py_modules is None + assert dist.packages is None + + +def test_name_discovery_doesnt_break_cli(tmpdir_cwd): + jaraco.path.build({"pkg.py": ""}) + dist = Distribution({}) + dist.script_args = ["--name"] + dist.set_defaults() + dist.parse_command_line() # <-- no exception should be raised here. + assert dist.get_name() == "pkg" + + +def test_preserve_explicit_name_with_dynamic_version(tmpdir_cwd, monkeypatch): + """According to #3545 it seems that ``name`` discovery is running, + even when the project already explicitly sets it. + This seems to be related to parsing of dynamic versions (via ``attr`` directive), + which requires the auto-discovery of ``package_dir``. + """ + files = { + "src": { + "pkg": {"__init__.py": "__version__ = 42\n"}, + }, + "pyproject.toml": DALS( + """ + [project] + name = "myproj" # purposefully different from package name + dynamic = ["version"] + [tool.setuptools.dynamic] + version = {"attr" = "pkg.__version__"} + """ + ), + } + jaraco.path.build(files) + dist = Distribution({}) + orig_analyse_name = dist.set_defaults.analyse_name + + def spy_analyse_name(): + # We can check if name discovery was triggered by ensuring the original + # name remains instead of the package name. + orig_analyse_name() + assert dist.get_name() == "myproj" + + monkeypatch.setattr(dist.set_defaults, "analyse_name", spy_analyse_name) + dist.parse_config_files() + assert dist.get_version() == "42" + assert set(dist.packages) == {"pkg"} + + +def _populate_project_dir(root, files, options): + # NOTE: Currently pypa/build will refuse to build the project if no + # `pyproject.toml` or `setup.py` is found. So it is impossible to do + # completely "config-less" projects. + basic = { + "setup.py": "import setuptools\nsetuptools.setup()", + "README.md": "# Example Package", + "LICENSE": "Copyright (c) 2018", + } + jaraco.path.build(basic, prefix=root) + _write_setupcfg(root, options) + paths = (root / f for f in files) + for path in paths: + path.parent.mkdir(exist_ok=True, parents=True) + path.touch() + + +def _write_setupcfg(root, options): + if not options: + print("~~~~~ **NO** setup.cfg ~~~~~") + return + setupcfg = ConfigParser() + setupcfg.add_section("options") + for key, value in options.items(): + if key == "packages.find": + setupcfg.add_section(f"options.{key}") + setupcfg[f"options.{key}"].update(value) + elif isinstance(value, list): + setupcfg["options"][key] = ", ".join(value) + elif isinstance(value, dict): + str_value = "\n".join(f"\t{k} = {v}" for k, v in value.items()) + setupcfg["options"][key] = "\n" + str_value + else: + setupcfg["options"][key] = str(value) + with open(root / "setup.cfg", "w", encoding="utf-8") as f: + setupcfg.write(f) + print("~~~~~ setup.cfg ~~~~~") + print((root / "setup.cfg").read_text(encoding="utf-8")) + + +def _run_build(path, *flags): + cmd = [sys.executable, "-m", "build", "--no-isolation", *flags, str(path)] + return run(cmd, env={'DISTUTILS_DEBUG': ''}) + + +def _get_dist(dist_path, attrs): + root = "/".join(os.path.split(dist_path)) # POSIX-style + + script = dist_path / 'setup.py' + if script.exists(): + with Path(dist_path): + dist = cast( + Distribution, + distutils.core.run_setup("setup.py", {}, stop_after="init"), + ) + else: + dist = Distribution(attrs) + + dist.src_root = root + dist.script_name = "setup.py" + with Path(dist_path): + dist.parse_config_files() + + dist.set_defaults() + return dist + + +def _run_sdist_programatically(dist_path, attrs): + dist = _get_dist(dist_path, attrs) + cmd = sdist(dist) + cmd.ensure_finalized() + assert cmd.distribution.packages or cmd.distribution.py_modules + + with quiet(), Path(dist_path): + cmd.run() + + return dist, cmd diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_core_metadata.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_core_metadata.py new file mode 100644 index 0000000000000000000000000000000000000000..0d925111fa6e611ae919df8bb30bcda0f248c5b6 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_core_metadata.py @@ -0,0 +1,622 @@ +from __future__ import annotations + +import functools +import importlib +import io +from email import message_from_string +from email.generator import Generator +from email.message import EmailMessage, Message +from email.parser import Parser +from email.policy import EmailPolicy +from inspect import cleandoc +from pathlib import Path +from unittest.mock import Mock + +import jaraco.path +import pytest +from packaging.metadata import Metadata +from packaging.requirements import Requirement + +from setuptools import _reqs, sic +from setuptools._core_metadata import rfc822_escape, rfc822_unescape +from setuptools.command.egg_info import egg_info, write_requirements +from setuptools.config import expand, setupcfg +from setuptools.dist import Distribution + +from .config.downloads import retrieve_file, urls_from_file + +EXAMPLE_BASE_INFO = dict( + name="package", + version="0.0.1", + author="Foo Bar", + author_email="foo@bar.net", + long_description="Long\ndescription", + description="Short description", + keywords=["one", "two"], +) + + +@pytest.mark.parametrize( + ("content", "result"), + ( + pytest.param( + "Just a single line", + None, + id="single_line", + ), + pytest.param( + "Multiline\nText\nwithout\nextra indents\n", + None, + id="multiline", + ), + pytest.param( + "Multiline\n With\n\nadditional\n indentation", + None, + id="multiline_with_indentation", + ), + pytest.param( + " Leading whitespace", + "Leading whitespace", + id="remove_leading_whitespace", + ), + pytest.param( + " Leading whitespace\nIn\n Multiline comment", + "Leading whitespace\nIn\n Multiline comment", + id="remove_leading_whitespace_multiline", + ), + ), +) +def test_rfc822_unescape(content, result): + assert (result or content) == rfc822_unescape(rfc822_escape(content)) + + +def __read_test_cases(): + base = EXAMPLE_BASE_INFO + + params = functools.partial(dict, base) + + return [ + ('Metadata version 1.0', params()), + ( + 'Metadata Version 1.0: Short long description', + params( + long_description='Short long description', + ), + ), + ( + 'Metadata version 1.1: Classifiers', + params( + classifiers=[ + 'Programming Language :: Python :: 3', + 'Programming Language :: Python :: 3.7', + 'License :: OSI Approved :: MIT License', + ], + ), + ), + ( + 'Metadata version 1.1: Download URL', + params( + download_url='https://example.com', + ), + ), + ( + 'Metadata Version 1.2: Requires-Python', + params( + python_requires='>=3.7', + ), + ), + pytest.param( + 'Metadata Version 1.2: Project-Url', + params(project_urls=dict(Foo='https://example.bar')), + marks=pytest.mark.xfail( + reason="Issue #1578: project_urls not read", + ), + ), + ( + 'Metadata Version 2.1: Long Description Content Type', + params( + long_description_content_type='text/x-rst; charset=UTF-8', + ), + ), + ( + 'License', + params( + license='MIT', + ), + ), + ( + 'License multiline', + params( + license='This is a long license \nover multiple lines', + ), + ), + pytest.param( + 'Metadata Version 2.1: Provides Extra', + params(provides_extras=['foo', 'bar']), + marks=pytest.mark.xfail(reason="provides_extras not read"), + ), + ( + 'Missing author', + dict( + name='foo', + version='1.0.0', + author_email='snorri@sturluson.name', + ), + ), + ( + 'Missing author e-mail', + dict( + name='foo', + version='1.0.0', + author='Snorri Sturluson', + ), + ), + ( + 'Missing author and e-mail', + dict( + name='foo', + version='1.0.0', + ), + ), + ( + 'Bypass normalized version', + dict( + name='foo', + version=sic('1.0.0a'), + ), + ), + ] + + +@pytest.mark.parametrize(("name", "attrs"), __read_test_cases()) +def test_read_metadata(name, attrs): + dist = Distribution(attrs) + metadata_out = dist.metadata + dist_class = metadata_out.__class__ + + # Write to PKG_INFO and then load into a new metadata object + PKG_INFO = io.StringIO() + + metadata_out.write_pkg_file(PKG_INFO) + PKG_INFO.seek(0) + pkg_info = PKG_INFO.read() + assert _valid_metadata(pkg_info) + + PKG_INFO.seek(0) + metadata_in = dist_class() + metadata_in.read_pkg_file(PKG_INFO) + + tested_attrs = [ + ('name', dist_class.get_name), + ('version', dist_class.get_version), + ('author', dist_class.get_contact), + ('author_email', dist_class.get_contact_email), + ('metadata_version', dist_class.get_metadata_version), + ('provides', dist_class.get_provides), + ('description', dist_class.get_description), + ('long_description', dist_class.get_long_description), + ('download_url', dist_class.get_download_url), + ('keywords', dist_class.get_keywords), + ('platforms', dist_class.get_platforms), + ('obsoletes', dist_class.get_obsoletes), + ('requires', dist_class.get_requires), + ('classifiers', dist_class.get_classifiers), + ('project_urls', lambda s: getattr(s, 'project_urls', {})), + ('provides_extras', lambda s: getattr(s, 'provides_extras', {})), + ] + + for attr, getter in tested_attrs: + assert getter(metadata_in) == getter(metadata_out) + + +def __maintainer_test_cases(): + attrs = {"name": "package", "version": "1.0", "description": "xxx"} + + def merge_dicts(d1, d2): + d1 = d1.copy() + d1.update(d2) + + return d1 + + return [ + ('No author, no maintainer', attrs.copy()), + ( + 'Author (no e-mail), no maintainer', + merge_dicts(attrs, {'author': 'Author Name'}), + ), + ( + 'Author (e-mail), no maintainer', + merge_dicts( + attrs, {'author': 'Author Name', 'author_email': 'author@name.com'} + ), + ), + ( + 'No author, maintainer (no e-mail)', + merge_dicts(attrs, {'maintainer': 'Maintainer Name'}), + ), + ( + 'No author, maintainer (e-mail)', + merge_dicts( + attrs, + { + 'maintainer': 'Maintainer Name', + 'maintainer_email': 'maintainer@name.com', + }, + ), + ), + ( + 'Author (no e-mail), Maintainer (no-email)', + merge_dicts( + attrs, {'author': 'Author Name', 'maintainer': 'Maintainer Name'} + ), + ), + ( + 'Author (e-mail), Maintainer (e-mail)', + merge_dicts( + attrs, + { + 'author': 'Author Name', + 'author_email': 'author@name.com', + 'maintainer': 'Maintainer Name', + 'maintainer_email': 'maintainer@name.com', + }, + ), + ), + ( + 'No author (e-mail), no maintainer (e-mail)', + merge_dicts( + attrs, + { + 'author_email': 'author@name.com', + 'maintainer_email': 'maintainer@name.com', + }, + ), + ), + ('Author unicode', merge_dicts(attrs, {'author': '鉄沢寛'})), + ('Maintainer unicode', merge_dicts(attrs, {'maintainer': 'Jan Łukasiewicz'})), + ] + + +@pytest.mark.parametrize(("name", "attrs"), __maintainer_test_cases()) +def test_maintainer_author(name, attrs, tmpdir): + tested_keys = { + 'author': 'Author', + 'author_email': 'Author-email', + 'maintainer': 'Maintainer', + 'maintainer_email': 'Maintainer-email', + } + + # Generate a PKG-INFO file + dist = Distribution(attrs) + fn = tmpdir.mkdir('pkg_info') + fn_s = str(fn) + + dist.metadata.write_pkg_info(fn_s) + + with open(str(fn.join('PKG-INFO')), 'r', encoding='utf-8') as f: + pkg_info = f.read() + + assert _valid_metadata(pkg_info) + + # Drop blank lines and strip lines from default description + raw_pkg_lines = pkg_info.splitlines() + pkg_lines = list(filter(None, raw_pkg_lines[:-2])) + + pkg_lines_set = set(pkg_lines) + + # Duplicate lines should not be generated + assert len(pkg_lines) == len(pkg_lines_set) + + for fkey, dkey in tested_keys.items(): + val = attrs.get(dkey, None) + if val is None: + for line in pkg_lines: + assert not line.startswith(fkey + ':') + else: + line = f'{fkey}: {val}' + assert line in pkg_lines_set + + +class TestParityWithMetadataFromPyPaWheel: + def base_example(self): + attrs = dict( + **EXAMPLE_BASE_INFO, + # Example with complex requirement definition + python_requires=">=3.8", + install_requires=""" + packaging==23.2 + more-itertools==8.8.0; extra == "other" + jaraco.text==3.7.0 + importlib-resources==5.10.2; python_version<"3.8" + importlib-metadata==6.0.0 ; python_version<"3.8" + colorama>=0.4.4; sys_platform == "win32" + """, + extras_require={ + "testing": """ + pytest >= 6 + pytest-checkdocs >= 2.4 + tomli ; \\ + # Using stdlib when possible + python_version < "3.11" + ini2toml[lite]>=0.9 + """, + "other": [], + }, + ) + # Generate a PKG-INFO file using setuptools + return Distribution(attrs) + + def test_requires_dist(self, tmp_path): + dist = self.base_example() + pkg_info = _get_pkginfo(dist) + assert _valid_metadata(pkg_info) + + # Ensure Requires-Dist is present + expected = [ + 'Metadata-Version:', + 'Requires-Python: >=3.8', + 'Provides-Extra: other', + 'Provides-Extra: testing', + 'Requires-Dist: tomli; python_version < "3.11" and extra == "testing"', + 'Requires-Dist: more-itertools==8.8.0; extra == "other"', + 'Requires-Dist: ini2toml[lite]>=0.9; extra == "testing"', + ] + for line in expected: + assert line in pkg_info + + HERE = Path(__file__).parent + EXAMPLES_FILE = HERE / "config/setupcfg_examples.txt" + + @pytest.fixture(params=[None, *urls_from_file(EXAMPLES_FILE)]) + def dist(self, request, monkeypatch, tmp_path): + """Example of distribution with arbitrary configuration""" + monkeypatch.chdir(tmp_path) + monkeypatch.setattr(expand, "read_attr", Mock(return_value="0.42")) + monkeypatch.setattr(expand, "read_files", Mock(return_value="hello world")) + monkeypatch.setattr( + Distribution, "_finalize_license_files", Mock(return_value=None) + ) + if request.param is None: + yield self.base_example() + else: + # Real-world usage + config = retrieve_file(request.param) + yield setupcfg.apply_configuration(Distribution({}), config) + + @pytest.mark.uses_network + def test_equivalent_output(self, tmp_path, dist): + """Ensure output from setuptools is equivalent to the one from `pypa/wheel`""" + # Generate a METADATA file using pypa/wheel for comparison + wheel_metadata = importlib.import_module("wheel.metadata") + pkginfo_to_metadata = getattr(wheel_metadata, "pkginfo_to_metadata", None) + + if pkginfo_to_metadata is None: # pragma: nocover + pytest.xfail( + "wheel.metadata.pkginfo_to_metadata is undefined, " + "(this is likely to be caused by API changes in pypa/wheel" + ) + + # Generate an simplified "egg-info" dir for pypa/wheel to convert + pkg_info = _get_pkginfo(dist) + egg_info_dir = tmp_path / "pkg.egg-info" + egg_info_dir.mkdir(parents=True) + (egg_info_dir / "PKG-INFO").write_text(pkg_info, encoding="utf-8") + write_requirements(egg_info(dist), egg_info_dir, egg_info_dir / "requires.txt") + + # Get pypa/wheel generated METADATA but normalize requirements formatting + metadata_msg = pkginfo_to_metadata(egg_info_dir, egg_info_dir / "PKG-INFO") + metadata_str = _normalize_metadata(metadata_msg) + pkg_info_msg = message_from_string(pkg_info) + pkg_info_str = _normalize_metadata(pkg_info_msg) + + # Compare setuptools PKG-INFO x pypa/wheel METADATA + assert metadata_str == pkg_info_str + + # Make sure it parses/serializes well in pypa/wheel + _assert_roundtrip_message(pkg_info) + + +class TestPEP643: + STATIC_CONFIG = { + "setup.cfg": cleandoc( + """ + [metadata] + name = package + version = 0.0.1 + author = Foo Bar + author_email = foo@bar.net + long_description = Long + description + description = Short description + keywords = one, two + platforms = abcd + [options] + install_requires = requests + """ + ), + "pyproject.toml": cleandoc( + """ + [project] + name = "package" + version = "0.0.1" + authors = [ + {name = "Foo Bar", email = "foo@bar.net"} + ] + description = "Short description" + readme = {text = "Long\\ndescription", content-type = "text/plain"} + keywords = ["one", "two"] + dependencies = ["requests"] + license = "AGPL-3.0-or-later" + [tool.setuptools] + provides = ["abcd"] + obsoletes = ["abcd"] + """ + ), + } + + @pytest.mark.parametrize("file", STATIC_CONFIG.keys()) + def test_static_config_has_no_dynamic(self, file, tmpdir_cwd): + Path(file).write_text(self.STATIC_CONFIG[file], encoding="utf-8") + metadata = _get_metadata() + assert metadata.get_all("Dynamic") is None + assert metadata.get_all("dynamic") is None + + @pytest.mark.parametrize("file", STATIC_CONFIG.keys()) + @pytest.mark.parametrize( + "fields", + [ + # Single dynamic field + {"requires-python": ("python_requires", ">=3.12")}, + {"author-email": ("author_email", "snoopy@peanuts.com")}, + {"keywords": ("keywords", ["hello", "world"])}, + {"platform": ("platforms", ["abcd"])}, + # Multiple dynamic fields + { + "summary": ("description", "hello world"), + "description": ("long_description", "bla bla bla bla"), + "requires-dist": ("install_requires", ["hello-world"]), + }, + ], + ) + def test_modified_fields_marked_as_dynamic(self, file, fields, tmpdir_cwd): + # We start with a static config + Path(file).write_text(self.STATIC_CONFIG[file], encoding="utf-8") + dist = _makedist() + + # ... but then we simulate the effects of a plugin modifying the distribution + for attr, value in fields.values(): + # `dist` and `dist.metadata` are complicated... + # Some attributes work when set on `dist`, others on `dist.metadata`... + # Here we set in both just in case (this also avoids calling `_finalize_*`) + setattr(dist, attr, value) + setattr(dist.metadata, attr, value) + + # Then we should be able to list the modified fields as Dynamic + metadata = _get_metadata(dist) + assert set(metadata.get_all("Dynamic")) == set(fields) + + @pytest.mark.parametrize( + "extra_toml", + [ + "# Let setuptools autofill license-files", + "license-files = ['LICENSE*', 'AUTHORS*', 'NOTICE']", + ], + ) + def test_license_files_dynamic(self, extra_toml, tmpdir_cwd): + # For simplicity (and for the time being) setuptools is not making + # any special handling to guarantee `License-File` is considered static. + # Instead we rely in the fact that, although suboptimal, it is OK to have + # it as dynamics, as per: + # https://github.com/pypa/setuptools/issues/4629#issuecomment-2331233677 + files = { + "pyproject.toml": self.STATIC_CONFIG["pyproject.toml"].replace( + 'license = "AGPL-3.0-or-later"', + f"dynamic = ['license']\n{extra_toml}", + ), + "LICENSE.md": "--- mock license ---", + "NOTICE": "--- mock notice ---", + "AUTHORS.txt": "--- me ---", + } + # Sanity checks: + assert extra_toml in files["pyproject.toml"] + assert 'license = "AGPL-3.0-or-later"' not in extra_toml + + jaraco.path.build(files) + dist = _makedist(license_expression="AGPL-3.0-or-later") + metadata = _get_metadata(dist) + assert set(metadata.get_all("Dynamic")) == { + 'license-file', + 'license-expression', + } + assert metadata.get("License-Expression") == "AGPL-3.0-or-later" + assert set(metadata.get_all("License-File")) == { + "NOTICE", + "AUTHORS.txt", + "LICENSE.md", + } + + +def _makedist(**attrs): + dist = Distribution(attrs) + dist.parse_config_files() + return dist + + +def _assert_roundtrip_message(metadata: str) -> None: + """Emulate the way wheel.bdist_wheel parses and regenerates the message, + then ensures the metadata generated by setuptools is compatible. + """ + with io.StringIO(metadata) as buffer: + msg = Parser(EmailMessage).parse(buffer) + + serialization_policy = EmailPolicy( + utf8=True, + mangle_from_=False, + max_line_length=0, + ) + with io.BytesIO() as buffer: + out = io.TextIOWrapper(buffer, encoding="utf-8") + Generator(out, policy=serialization_policy).flatten(msg) + out.flush() + regenerated = buffer.getvalue() + + raw_metadata = bytes(metadata, "utf-8") + # Normalise newlines to avoid test errors on Windows: + raw_metadata = b"\n".join(raw_metadata.splitlines()) + regenerated = b"\n".join(regenerated.splitlines()) + assert regenerated == raw_metadata + + +def _normalize_metadata(msg: Message) -> str: + """Allow equivalent metadata to be compared directly""" + # The main challenge regards the requirements and extras. + # Both setuptools and wheel already apply some level of normalization + # but they differ regarding which character is chosen, according to the + # following spec it should be "-": + # https://packaging.python.org/en/latest/specifications/name-normalization/ + + # Related issues: + # https://github.com/pypa/packaging/issues/845 + # https://github.com/pypa/packaging/issues/644#issuecomment-2429813968 + + extras = {x.replace("_", "-"): x for x in msg.get_all("Provides-Extra", [])} + reqs = [ + _normalize_req(req, extras) + for req in _reqs.parse(msg.get_all("Requires-Dist", [])) + ] + del msg["Requires-Dist"] + del msg["Provides-Extra"] + + # Ensure consistent ord + for req in sorted(reqs): + msg["Requires-Dist"] = req + for extra in sorted(extras): + msg["Provides-Extra"] = extra + + # TODO: Handle lack of PEP 643 implementation in pypa/wheel? + del msg["Metadata-Version"] + + return msg.as_string() + + +def _normalize_req(req: Requirement, extras: dict[str, str]) -> str: + """Allow equivalent requirement objects to be compared directly""" + as_str = str(req).replace(req.name, req.name.replace("_", "-")) + for norm, orig in extras.items(): + as_str = as_str.replace(orig, norm) + return as_str + + +def _get_pkginfo(dist: Distribution): + with io.StringIO() as fp: + dist.metadata.write_pkg_file(fp) + return fp.getvalue() + + +def _get_metadata(dist: Distribution | None = None): + return message_from_string(_get_pkginfo(dist or _makedist())) + + +def _valid_metadata(text: str) -> bool: + metadata = Metadata.from_email(text, validate=True) # can raise exceptions + return metadata is not None diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_depends.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_depends.py new file mode 100644 index 0000000000000000000000000000000000000000..1714c041f7a23e1ecbfc3245bf964f75c13734ca --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_depends.py @@ -0,0 +1,15 @@ +import sys + +from setuptools import depends + + +class TestGetModuleConstant: + def test_basic(self): + """ + Invoke get_module_constant on a module in + the test package. + """ + mod_name = 'setuptools.tests.mod_with_constant' + val = depends.get_module_constant(mod_name, 'value') + assert val == 'three, sir!' + assert 'setuptools.tests.mod_with_constant' not in sys.modules diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_develop.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_develop.py new file mode 100644 index 0000000000000000000000000000000000000000..354c51fc3c7888de2161122f6f3cafa55b181594 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_develop.py @@ -0,0 +1,112 @@ +"""develop tests""" + +import os +import platform +import subprocess +import sys + +import pytest + +from setuptools._path import paths_on_pythonpath + +from . import contexts, namespaces + +SETUP_PY = """\ +from setuptools import setup + +setup(name='foo', + packages=['foo'], +) +""" + +INIT_PY = """print "foo" +""" + + +@pytest.fixture +def temp_user(monkeypatch): + with contexts.tempdir() as user_base: + with contexts.tempdir() as user_site: + monkeypatch.setattr('site.USER_BASE', user_base) + monkeypatch.setattr('site.USER_SITE', user_site) + yield + + +@pytest.fixture +def test_env(tmpdir, temp_user): + target = tmpdir + foo = target.mkdir('foo') + setup = target / 'setup.py' + if setup.isfile(): + raise ValueError(dir(target)) + with setup.open('w') as f: + f.write(SETUP_PY) + init = foo / '__init__.py' + with init.open('w') as f: + f.write(INIT_PY) + with target.as_cwd(): + yield target + + +class TestNamespaces: + @staticmethod + def install_develop(src_dir, target): + develop_cmd = [ + sys.executable, + 'setup.py', + 'develop', + '--install-dir', + str(target), + ] + with src_dir.as_cwd(): + with paths_on_pythonpath([str(target)]): + subprocess.check_call(develop_cmd) + + @pytest.mark.skipif( + bool(os.environ.get("APPVEYOR")), + reason="https://github.com/pypa/setuptools/issues/851", + ) + @pytest.mark.skipif( + platform.python_implementation() == 'PyPy', + reason="https://github.com/pypa/setuptools/issues/1202", + ) + @pytest.mark.uses_network + def test_namespace_package_importable(self, tmpdir): + """ + Installing two packages sharing the same namespace, one installed + naturally using pip or `--single-version-externally-managed` + and the other installed using `develop` should leave the namespace + in tact and both packages reachable by import. + """ + pkg_A = namespaces.build_namespace_package(tmpdir, 'myns.pkgA') + pkg_B = namespaces.build_namespace_package(tmpdir, 'myns.pkgB') + target = tmpdir / 'packages' + # use pip to install to the target directory + install_cmd = [ + sys.executable, + '-m', + 'pip', + 'install', + str(pkg_A), + '-t', + str(target), + ] + subprocess.check_call(install_cmd) + self.install_develop(pkg_B, target) + namespaces.make_site_dir(target) + try_import = [ + sys.executable, + '-c', + 'import myns.pkgA; import myns.pkgB', + ] + with paths_on_pythonpath([str(target)]): + subprocess.check_call(try_import) + + # additionally ensure that pkg_resources import works + pkg_resources_imp = [ + sys.executable, + '-c', + 'import pkg_resources', + ] + with paths_on_pythonpath([str(target)]): + subprocess.check_call(pkg_resources_imp) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_dist.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_dist.py new file mode 100644 index 0000000000000000000000000000000000000000..9685dcd7cbbeceb1e35d69de30b9e2fdc3f06227 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_dist.py @@ -0,0 +1,280 @@ +import os +import re +import urllib.parse +import urllib.request + +import pytest + +from setuptools import Distribution +from setuptools.dist import check_package_data, check_specifier + +from .fixtures import make_trivial_sdist +from .test_find_packages import ensure_files +from .textwrap import DALS + +from distutils.errors import DistutilsSetupError + + +def test_dist_fetch_build_egg(tmpdir, setuptools_wheel): + """ + Check multiple calls to `Distribution.fetch_build_egg` work as expected. + """ + index = tmpdir.mkdir('index') + index_url = urllib.parse.urljoin('file://', urllib.request.pathname2url(str(index))) + + def sdist_with_index(distname, version): + dist_dir = index.mkdir(distname) + dist_sdist = f'{distname}-{version}.tar.gz' + make_trivial_sdist( + str(dist_dir.join(dist_sdist)), distname, version, setuptools_wheel + ) + with dist_dir.join('index.html').open('w') as fp: + fp.write( + DALS( + """ + + {dist_sdist}
+ + """ + ).format(dist_sdist=dist_sdist) + ) + + sdist_with_index('barbazquux', '3.2.0') + sdist_with_index('barbazquux-runner', '2.11.1') + with tmpdir.join('setup.cfg').open('w') as fp: + fp.write( + DALS( + """ + [easy_install] + index_url = {index_url} + """ + ).format(index_url=index_url) + ) + reqs = """ + barbazquux-runner + barbazquux + """.split() + with tmpdir.as_cwd(): + dist = Distribution() + dist.parse_config_files() + resolved_dists = [dist.fetch_build_egg(r) for r in reqs] + assert [dist.name for dist in resolved_dists if dist] == reqs + + +EXAMPLE_BASE_INFO = dict( + name="package", + version="0.0.1", + author="Foo Bar", + author_email="foo@bar.net", + long_description="Long\ndescription", + description="Short description", + keywords=["one", "two"], +) + + +def test_provides_extras_deterministic_order(): + attrs = dict(extras_require=dict(a=['foo'], b=['bar'])) + dist = Distribution(attrs) + assert list(dist.metadata.provides_extras) == ['a', 'b'] + attrs['extras_require'] = dict(reversed(attrs['extras_require'].items())) + dist = Distribution(attrs) + assert list(dist.metadata.provides_extras) == ['b', 'a'] + + +CHECK_PACKAGE_DATA_TESTS = ( + # Valid. + ( + { + '': ['*.txt', '*.rst'], + 'hello': ['*.msg'], + }, + None, + ), + # Not a dictionary. + ( + ( + ('', ['*.txt', '*.rst']), + ('hello', ['*.msg']), + ), + ( + "'package_data' must be a dictionary mapping package" + " names to lists of string wildcard patterns" + ), + ), + # Invalid key type. + ( + { + 400: ['*.txt', '*.rst'], + }, + ("keys of 'package_data' dict must be strings (got 400)"), + ), + # Invalid value type. + ( + { + 'hello': '*.msg', + }, + ( + "\"values of 'package_data' dict\" must be of type " + " (got '*.msg')" + ), + ), + # Invalid value type (generators are single use) + ( + { + 'hello': (x for x in "generator"), + }, + ( + "\"values of 'package_data' dict\" must be of type " + " (got =3.0, !=3.1'} + dist = Distribution(attrs) + check_specifier(dist, attrs, attrs['python_requires']) + + attrs = {'name': 'foo', 'python_requires': ['>=3.0', '!=3.1']} + dist = Distribution(attrs) + check_specifier(dist, attrs, attrs['python_requires']) + + # invalid specifier value + attrs = {'name': 'foo', 'python_requires': '>=invalid-version'} + with pytest.raises(DistutilsSetupError): + dist = Distribution(attrs) + + +def test_metadata_name(): + with pytest.raises(DistutilsSetupError, match='missing.*name'): + Distribution()._validate_metadata() + + +@pytest.mark.parametrize( + ('dist_name', 'py_module'), + [ + ("my.pkg", "my_pkg"), + ("my-pkg", "my_pkg"), + ("my_pkg", "my_pkg"), + ("pkg", "pkg"), + ], +) +def test_dist_default_py_modules(tmp_path, dist_name, py_module): + (tmp_path / f"{py_module}.py").touch() + + (tmp_path / "setup.py").touch() + (tmp_path / "noxfile.py").touch() + # ^-- make sure common tool files are ignored + + attrs = {**EXAMPLE_BASE_INFO, "name": dist_name, "src_root": str(tmp_path)} + # Find `py_modules` corresponding to dist_name if not given + dist = Distribution(attrs) + dist.set_defaults() + assert dist.py_modules == [py_module] + # When `py_modules` is given, don't do anything + dist = Distribution({**attrs, "py_modules": ["explicity_py_module"]}) + dist.set_defaults() + assert dist.py_modules == ["explicity_py_module"] + # When `packages` is given, don't do anything + dist = Distribution({**attrs, "packages": ["explicity_package"]}) + dist.set_defaults() + assert not dist.py_modules + + +@pytest.mark.parametrize( + ('dist_name', 'package_dir', 'package_files', 'packages'), + [ + ("my.pkg", None, ["my_pkg/__init__.py", "my_pkg/mod.py"], ["my_pkg"]), + ("my-pkg", None, ["my_pkg/__init__.py", "my_pkg/mod.py"], ["my_pkg"]), + ("my_pkg", None, ["my_pkg/__init__.py", "my_pkg/mod.py"], ["my_pkg"]), + ("my.pkg", None, ["my/pkg/__init__.py"], ["my", "my.pkg"]), + ( + "my_pkg", + None, + ["src/my_pkg/__init__.py", "src/my_pkg2/__init__.py"], + ["my_pkg", "my_pkg2"], + ), + ( + "my_pkg", + {"pkg": "lib", "pkg2": "lib2"}, + ["lib/__init__.py", "lib/nested/__init__.pyt", "lib2/__init__.py"], + ["pkg", "pkg.nested", "pkg2"], + ), + ], +) +def test_dist_default_packages( + tmp_path, dist_name, package_dir, package_files, packages +): + ensure_files(tmp_path, package_files) + + (tmp_path / "setup.py").touch() + (tmp_path / "noxfile.py").touch() + # ^-- should not be included by default + + attrs = { + **EXAMPLE_BASE_INFO, + "name": dist_name, + "src_root": str(tmp_path), + "package_dir": package_dir, + } + # Find `packages` either corresponding to dist_name or inside src + dist = Distribution(attrs) + dist.set_defaults() + assert not dist.py_modules + assert not dist.py_modules + assert set(dist.packages) == set(packages) + # When `py_modules` is given, don't do anything + dist = Distribution({**attrs, "py_modules": ["explicit_py_module"]}) + dist.set_defaults() + assert not dist.packages + assert set(dist.py_modules) == {"explicit_py_module"} + # When `packages` is given, don't do anything + dist = Distribution({**attrs, "packages": ["explicit_package"]}) + dist.set_defaults() + assert not dist.py_modules + assert set(dist.packages) == {"explicit_package"} + + +@pytest.mark.parametrize( + ('dist_name', 'package_dir', 'package_files'), + [ + ("my.pkg.nested", None, ["my/pkg/nested/__init__.py"]), + ("my.pkg", None, ["my/pkg/__init__.py", "my/pkg/file.py"]), + ("my_pkg", None, ["my_pkg.py"]), + ("my_pkg", None, ["my_pkg/__init__.py", "my_pkg/nested/__init__.py"]), + ("my_pkg", None, ["src/my_pkg/__init__.py", "src/my_pkg/nested/__init__.py"]), + ( + "my_pkg", + {"my_pkg": "lib", "my_pkg.lib2": "lib2"}, + ["lib/__init__.py", "lib/nested/__init__.pyt", "lib2/__init__.py"], + ), + # Should not try to guess a name from multiple py_modules/packages + ("UNKNOWN", None, ["src/mod1.py", "src/mod2.py"]), + ("UNKNOWN", None, ["src/pkg1/__ini__.py", "src/pkg2/__init__.py"]), + ], +) +def test_dist_default_name(tmp_path, dist_name, package_dir, package_files): + """Make sure dist.name is discovered from packages/py_modules""" + ensure_files(tmp_path, package_files) + attrs = { + **EXAMPLE_BASE_INFO, + "src_root": "/".join(os.path.split(tmp_path)), # POSIX-style + "package_dir": package_dir, + } + del attrs["name"] + + dist = Distribution(attrs) + dist.set_defaults() + assert dist.py_modules or dist.packages + assert dist.get_name() == dist_name diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_dist_info.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_dist_info.py new file mode 100644 index 0000000000000000000000000000000000000000..f65d0afbe46299fa816b2c64dc538dbd66880dab --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_dist_info.py @@ -0,0 +1,147 @@ +"""Test .dist-info style distributions.""" + +import pathlib +import re +import shutil +import subprocess +import sys +from functools import partial + +import pytest + +from setuptools.archive_util import unpack_archive + +from .textwrap import DALS + +read = partial(pathlib.Path.read_text, encoding="utf-8") + + +class TestDistInfo: + def test_invalid_version(self, tmp_path): + """ + Supplying an invalid version crashes dist_info. + """ + config = "[metadata]\nname=proj\nversion=42\n[egg_info]\ntag_build=invalid!!!\n" + (tmp_path / "setup.cfg").write_text(config, encoding="utf-8") + msg = re.compile("invalid version", re.MULTILINE | re.IGNORECASE) + proc = run_command_inner("dist_info", cwd=tmp_path, check=False) + assert proc.returncode + assert msg.search(proc.stdout) + assert not list(tmp_path.glob("*.dist-info")) + + def test_tag_arguments(self, tmp_path): + config = """ + [metadata] + name=proj + version=42 + [egg_info] + tag_date=1 + tag_build=.post + """ + (tmp_path / "setup.cfg").write_text(config, encoding="utf-8") + + print(run_command("dist_info", "--no-date", cwd=tmp_path)) + dist_info = next(tmp_path.glob("*.dist-info")) + assert dist_info.name.startswith("proj-42") + shutil.rmtree(dist_info) + + print(run_command("dist_info", "--tag-build", ".a", cwd=tmp_path)) + dist_info = next(tmp_path.glob("*.dist-info")) + assert dist_info.name.startswith("proj-42a") + + @pytest.mark.parametrize("keep_egg_info", (False, True)) + def test_output_dir(self, tmp_path, keep_egg_info): + config = "[metadata]\nname=proj\nversion=42\n" + (tmp_path / "setup.cfg").write_text(config, encoding="utf-8") + out = tmp_path / "__out" + out.mkdir() + opts = ["--keep-egg-info"] if keep_egg_info else [] + run_command("dist_info", "--output-dir", out, *opts, cwd=tmp_path) + assert len(list(out.glob("*.dist-info"))) == 1 + assert len(list(tmp_path.glob("*.dist-info"))) == 0 + expected_egg_info = int(keep_egg_info) + assert len(list(out.glob("*.egg-info"))) == expected_egg_info + assert len(list(tmp_path.glob("*.egg-info"))) == 0 + assert len(list(out.glob("*.__bkp__"))) == 0 + assert len(list(tmp_path.glob("*.__bkp__"))) == 0 + + +class TestWheelCompatibility: + """Make sure the .dist-info directory produced with the ``dist_info`` command + is the same as the one produced by ``bdist_wheel``. + """ + + SETUPCFG = DALS( + """ + [metadata] + name = {name} + version = {version} + + [options] + install_requires = + foo>=12; sys_platform != "linux" + + [options.extras_require] + test = pytest + + [options.entry_points] + console_scripts = + executable-name = my_package.module:function + discover = + myproj = my_package.other_module:function + """ + ) + + EGG_INFO_OPTS = [ + # Related: #3088 #2872 + ("", ""), + (".post", "[egg_info]\ntag_build = post\n"), + (".post", "[egg_info]\ntag_build = .post\n"), + (".post", "[egg_info]\ntag_build = post\ntag_date = 1\n"), + (".dev", "[egg_info]\ntag_build = .dev\n"), + (".dev", "[egg_info]\ntag_build = .dev\ntag_date = 1\n"), + ("a1", "[egg_info]\ntag_build = .a1\n"), + ("+local", "[egg_info]\ntag_build = +local\n"), + ] + + @pytest.mark.parametrize("name", "my-proj my_proj my.proj My.Proj".split()) + @pytest.mark.parametrize("version", ["0.42.13"]) + @pytest.mark.parametrize(("suffix", "cfg"), EGG_INFO_OPTS) + def test_dist_info_is_the_same_as_in_wheel( + self, name, version, tmp_path, suffix, cfg + ): + config = self.SETUPCFG.format(name=name, version=version) + cfg + + for i in "dir_wheel", "dir_dist": + (tmp_path / i).mkdir() + (tmp_path / i / "setup.cfg").write_text(config, encoding="utf-8") + + run_command("bdist_wheel", cwd=tmp_path / "dir_wheel") + wheel = next(tmp_path.glob("dir_wheel/dist/*.whl")) + unpack_archive(wheel, tmp_path / "unpack") + wheel_dist_info = next(tmp_path.glob("unpack/*.dist-info")) + + run_command("dist_info", cwd=tmp_path / "dir_dist") + dist_info = next(tmp_path.glob("dir_dist/*.dist-info")) + + assert dist_info.name == wheel_dist_info.name + assert dist_info.name.startswith(f"my_proj-{version}{suffix}") + for file in "METADATA", "entry_points.txt": + assert read(dist_info / file) == read(wheel_dist_info / file) + + +def run_command_inner(*cmd, **kwargs): + opts = { + "stderr": subprocess.STDOUT, + "stdout": subprocess.PIPE, + "text": True, + "encoding": "utf-8", + "check": True, + **kwargs, + } + cmd = [sys.executable, "-c", "__import__('setuptools').setup()", *map(str, cmd)] + return subprocess.run(cmd, **opts) + + +def run_command(*args, **kwargs): + return run_command_inner(*args, **kwargs).stdout diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_distutils_adoption.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_distutils_adoption.py new file mode 100644 index 0000000000000000000000000000000000000000..f99a58849950029f53322c19cde1c171fe26622c --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_distutils_adoption.py @@ -0,0 +1,198 @@ +import os +import platform +import sys +import textwrap + +import pytest + +IS_PYPY = '__pypy__' in sys.builtin_module_names + +_TEXT_KWARGS = {"text": True, "encoding": "utf-8"} # For subprocess.run + + +def win_sr(env): + """ + On Windows, SYSTEMROOT must be present to avoid + + > Fatal Python error: _Py_HashRandomization_Init: failed to + > get random numbers to initialize Python + """ + if env and platform.system() == 'Windows': + env['SYSTEMROOT'] = os.environ['SYSTEMROOT'] + return env + + +def find_distutils(venv, imports='distutils', env=None, **kwargs): + py_cmd = 'import {imports}; print(distutils.__file__)'.format(**locals()) + cmd = ['python', '-c', py_cmd] + return venv.run(cmd, env=win_sr(env), **_TEXT_KWARGS, **kwargs) + + +def count_meta_path(venv, env=None): + py_cmd = textwrap.dedent( + """ + import sys + is_distutils = lambda finder: finder.__class__.__name__ == "DistutilsMetaFinder" + print(len(list(filter(is_distutils, sys.meta_path)))) + """ + ) + cmd = ['python', '-c', py_cmd] + return int(venv.run(cmd, env=win_sr(env), **_TEXT_KWARGS)) + + +skip_without_stdlib_distutils = pytest.mark.skipif( + sys.version_info >= (3, 12), + reason='stdlib distutils is removed from Python 3.12+', +) + + +@skip_without_stdlib_distutils +def test_distutils_stdlib(venv): + """ + Ensure stdlib distutils is used when appropriate. + """ + env = dict(SETUPTOOLS_USE_DISTUTILS='stdlib') + assert venv.name not in find_distutils(venv, env=env).split(os.sep) + assert count_meta_path(venv, env=env) == 0 + + +def test_distutils_local_with_setuptools(venv): + """ + Ensure local distutils is used when appropriate. + """ + env = dict(SETUPTOOLS_USE_DISTUTILS='local') + loc = find_distutils(venv, imports='setuptools, distutils', env=env) + assert venv.name in loc.split(os.sep) + assert count_meta_path(venv, env=env) <= 1 + + +@pytest.mark.xfail('IS_PYPY', reason='pypy imports distutils on startup') +def test_distutils_local(venv): + """ + Even without importing, the setuptools-local copy of distutils is + preferred. + """ + env = dict(SETUPTOOLS_USE_DISTUTILS='local') + assert venv.name in find_distutils(venv, env=env).split(os.sep) + assert count_meta_path(venv, env=env) <= 1 + + +def test_pip_import(venv): + """ + Ensure pip can be imported. + Regression test for #3002. + """ + cmd = ['python', '-c', 'import pip'] + venv.run(cmd, **_TEXT_KWARGS) + + +def test_distutils_has_origin(): + """ + Distutils module spec should have an origin. #2990. + """ + assert __import__('distutils').__spec__.origin + + +ENSURE_IMPORTS_ARE_NOT_DUPLICATED = r""" +# Depending on the importlib machinery and _distutils_hack, some imports are +# duplicated resulting in different module objects being loaded, which prevents +# patches as shown in #3042. +# This script provides a way of verifying if this duplication is happening. + +from distutils import cmd +import distutils.command.sdist as sdist + +# import last to prevent caching +from distutils import {imported_module} + +for mod in (cmd, sdist): + assert mod.{imported_module} == {imported_module}, ( + f"\n{{mod.dir_util}}\n!=\n{{{imported_module}}}" + ) + +print("success") +""" + + +@pytest.mark.usefixtures("tmpdir_cwd") +@pytest.mark.parametrize( + ('distutils_version', 'imported_module'), + [ + pytest.param("stdlib", "dir_util", marks=skip_without_stdlib_distutils), + pytest.param("stdlib", "file_util", marks=skip_without_stdlib_distutils), + pytest.param("stdlib", "archive_util", marks=skip_without_stdlib_distutils), + ("local", "dir_util"), + ("local", "file_util"), + ("local", "archive_util"), + ], +) +def test_modules_are_not_duplicated_on_import(distutils_version, imported_module, venv): + env = dict(SETUPTOOLS_USE_DISTUTILS=distutils_version) + script = ENSURE_IMPORTS_ARE_NOT_DUPLICATED.format(imported_module=imported_module) + cmd = ['python', '-c', script] + output = venv.run(cmd, env=win_sr(env), **_TEXT_KWARGS).strip() + assert output == "success" + + +ENSURE_LOG_IMPORT_IS_NOT_DUPLICATED = r""" +import types +import distutils.dist as dist +from distutils import log +if isinstance(dist.log, types.ModuleType): + assert dist.log == log, f"\n{dist.log}\n!=\n{log}" +print("success") +""" + + +@pytest.mark.usefixtures("tmpdir_cwd") +@pytest.mark.parametrize( + "distutils_version", + [ + "local", + pytest.param("stdlib", marks=skip_without_stdlib_distutils), + ], +) +def test_log_module_is_not_duplicated_on_import(distutils_version, venv): + env = dict(SETUPTOOLS_USE_DISTUTILS=distutils_version) + cmd = ['python', '-c', ENSURE_LOG_IMPORT_IS_NOT_DUPLICATED] + output = venv.run(cmd, env=win_sr(env), **_TEXT_KWARGS).strip() + assert output == "success" + + +ENSURE_CONSISTENT_ERROR_FROM_MODIFIED_PY = r""" +from setuptools.modified import newer +from {imported_module}.errors import DistutilsError + +# Can't use pytest.raises in this context +try: + newer("", "") +except DistutilsError: + print("success") +else: + raise AssertionError("Expected to raise") +""" + + +@pytest.mark.usefixtures("tmpdir_cwd") +@pytest.mark.parametrize( + ('distutils_version', 'imported_module'), + [ + ("local", "distutils"), + # Unfortunately we still get ._distutils.errors.DistutilsError with SETUPTOOLS_USE_DISTUTILS=stdlib + # But that's a deprecated use-case we don't mind not fully supporting in newer code + pytest.param( + "stdlib", "setuptools._distutils", marks=skip_without_stdlib_distutils + ), + ], +) +def test_consistent_error_from_modified_py(distutils_version, imported_module, venv): + env = dict(SETUPTOOLS_USE_DISTUTILS=distutils_version) + cmd = [ + 'python', + '-c', + ENSURE_CONSISTENT_ERROR_FROM_MODIFIED_PY.format( + imported_module=imported_module + ), + ] + output = venv.run(cmd, env=win_sr(env), **_TEXT_KWARGS).strip() + assert output == "success" diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_editable_install.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_editable_install.py new file mode 100644 index 0000000000000000000000000000000000000000..225fc6a2f501e46e6b8f0c0010bf332dd1e59c54 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_editable_install.py @@ -0,0 +1,1263 @@ +from __future__ import annotations + +import os +import platform +import stat +import subprocess +import sys +from copy import deepcopy +from importlib import import_module +from importlib.machinery import EXTENSION_SUFFIXES +from pathlib import Path +from textwrap import dedent +from typing import Any +from unittest.mock import Mock +from uuid import uuid4 + +import jaraco.envs +import jaraco.path +import pytest +from path import Path as _Path + +from setuptools._importlib import resources as importlib_resources +from setuptools.command.editable_wheel import ( + _encode_pth, + _find_namespaces, + _find_package_roots, + _find_virtual_namespaces, + _finder_template, + _LinkTree, + _TopLevelFinder, + editable_wheel, +) +from setuptools.dist import Distribution +from setuptools.extension import Extension +from setuptools.warnings import SetuptoolsDeprecationWarning + +from . import contexts, namespaces + +from distutils.core import run_setup + + +@pytest.fixture(params=["strict", "lenient"]) +def editable_opts(request): + if request.param == "strict": + return ["--config-settings", "editable-mode=strict"] + return [] + + +EXAMPLE = { + 'pyproject.toml': dedent( + """\ + [build-system] + requires = ["setuptools"] + build-backend = "setuptools.build_meta" + + [project] + name = "mypkg" + version = "3.14159" + license = {text = "MIT"} + description = "This is a Python package" + dynamic = ["readme"] + classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Developers" + ] + urls = {Homepage = "https://github.com"} + + [tool.setuptools] + package-dir = {"" = "src"} + packages = {find = {where = ["src"]}} + license-files = ["LICENSE*"] + + [tool.setuptools.dynamic] + readme = {file = "README.rst"} + + [tool.distutils.egg_info] + tag-build = ".post0" + """ + ), + "MANIFEST.in": dedent( + """\ + global-include *.py *.txt + global-exclude *.py[cod] + prune dist + prune build + """ + ).strip(), + "README.rst": "This is a ``README``", + "LICENSE.txt": "---- placeholder MIT license ----", + "src": { + "mypkg": { + "__init__.py": dedent( + """\ + import sys + from importlib.metadata import PackageNotFoundError, version + + try: + __version__ = version(__name__) + except PackageNotFoundError: + __version__ = "unknown" + """ + ), + "__main__.py": dedent( + """\ + from importlib.resources import read_text + from . import __version__, __name__ as parent + from .mod import x + + data = read_text(parent, "data.txt") + print(__version__, data, x) + """ + ), + "mod.py": "x = ''", + "data.txt": "Hello World", + } + }, +} + + +SETUP_SCRIPT_STUB = "__import__('setuptools').setup()" + + +@pytest.mark.xfail(sys.platform == "darwin", reason="pypa/setuptools#4328") +@pytest.mark.parametrize( + "files", + [ + {**EXAMPLE, "setup.py": SETUP_SCRIPT_STUB}, + EXAMPLE, # No setup.py script + ], +) +def test_editable_with_pyproject(tmp_path, venv, files, editable_opts): + project = tmp_path / "mypkg" + project.mkdir() + jaraco.path.build(files, prefix=project) + + cmd = [ + "python", + "-m", + "pip", + "install", + "--no-build-isolation", # required to force current version of setuptools + "-e", + str(project), + *editable_opts, + ] + print(venv.run(cmd)) + + cmd = ["python", "-m", "mypkg"] + assert venv.run(cmd).strip() == "3.14159.post0 Hello World" + + (project / "src/mypkg/data.txt").write_text("foobar", encoding="utf-8") + (project / "src/mypkg/mod.py").write_text("x = 42", encoding="utf-8") + assert venv.run(cmd).strip() == "3.14159.post0 foobar 42" + + +def test_editable_with_flat_layout(tmp_path, venv, editable_opts): + files = { + "mypkg": { + "pyproject.toml": dedent( + """\ + [build-system] + requires = ["setuptools", "wheel"] + build-backend = "setuptools.build_meta" + + [project] + name = "mypkg" + version = "3.14159" + + [tool.setuptools] + packages = ["pkg"] + py-modules = ["mod"] + """ + ), + "pkg": {"__init__.py": "a = 4"}, + "mod.py": "b = 2", + }, + } + jaraco.path.build(files, prefix=tmp_path) + project = tmp_path / "mypkg" + + cmd = [ + "python", + "-m", + "pip", + "install", + "--no-build-isolation", # required to force current version of setuptools + "-e", + str(project), + *editable_opts, + ] + print(venv.run(cmd)) + cmd = ["python", "-c", "import pkg, mod; print(pkg.a, mod.b)"] + assert venv.run(cmd).strip() == "4 2" + + +def test_editable_with_single_module(tmp_path, venv, editable_opts): + files = { + "mypkg": { + "pyproject.toml": dedent( + """\ + [build-system] + requires = ["setuptools", "wheel"] + build-backend = "setuptools.build_meta" + + [project] + name = "mod" + version = "3.14159" + + [tool.setuptools] + py-modules = ["mod"] + """ + ), + "mod.py": "b = 2", + }, + } + jaraco.path.build(files, prefix=tmp_path) + project = tmp_path / "mypkg" + + cmd = [ + "python", + "-m", + "pip", + "install", + "--no-build-isolation", # required to force current version of setuptools + "-e", + str(project), + *editable_opts, + ] + print(venv.run(cmd)) + cmd = ["python", "-c", "import mod; print(mod.b)"] + assert venv.run(cmd).strip() == "2" + + +class TestLegacyNamespaces: + # legacy => pkg_resources.declare_namespace(...) + setup(namespace_packages=...) + + def test_nspkg_file_is_unique(self, tmp_path, monkeypatch): + deprecation = pytest.warns( + SetuptoolsDeprecationWarning, match=".*namespace_packages parameter.*" + ) + installation_dir = tmp_path / ".installation_dir" + installation_dir.mkdir() + examples = ( + "myns.pkgA", + "myns.pkgB", + "myns.n.pkgA", + "myns.n.pkgB", + ) + + for name in examples: + pkg = namespaces.build_namespace_package(tmp_path, name, version="42") + with deprecation, monkeypatch.context() as ctx: + ctx.chdir(pkg) + dist = run_setup("setup.py", stop_after="config") + cmd = editable_wheel(dist) + cmd.finalize_options() + editable_name = cmd.get_finalized_command("dist_info").name + cmd._install_namespaces(installation_dir, editable_name) + + files = list(installation_dir.glob("*-nspkg.pth")) + assert len(files) == len(examples) + + @pytest.mark.parametrize( + "impl", + ( + "pkg_resources", + # "pkgutil", => does not work + ), + ) + @pytest.mark.parametrize("ns", ("myns.n",)) + def test_namespace_package_importable( + self, venv, tmp_path, ns, impl, editable_opts + ): + """ + Installing two packages sharing the same namespace, one installed + naturally using pip or `--single-version-externally-managed` + and the other installed in editable mode should leave the namespace + intact and both packages reachable by import. + (Ported from test_develop). + """ + build_system = """\ + [build-system] + requires = ["setuptools"] + build-backend = "setuptools.build_meta" + """ + pkg_A = namespaces.build_namespace_package(tmp_path, f"{ns}.pkgA", impl=impl) + pkg_B = namespaces.build_namespace_package(tmp_path, f"{ns}.pkgB", impl=impl) + (pkg_A / "pyproject.toml").write_text(build_system, encoding="utf-8") + (pkg_B / "pyproject.toml").write_text(build_system, encoding="utf-8") + # use pip to install to the target directory + opts = editable_opts[:] + opts.append("--no-build-isolation") # force current version of setuptools + venv.run(["python", "-m", "pip", "install", str(pkg_A), *opts]) + venv.run(["python", "-m", "pip", "install", "-e", str(pkg_B), *opts]) + venv.run(["python", "-c", f"import {ns}.pkgA; import {ns}.pkgB"]) + # additionally ensure that pkg_resources import works + venv.run(["python", "-c", "import pkg_resources"]) + + +class TestPep420Namespaces: + def test_namespace_package_importable(self, venv, tmp_path, editable_opts): + """ + Installing two packages sharing the same namespace, one installed + normally using pip and the other installed in editable mode + should allow importing both packages. + """ + pkg_A = namespaces.build_pep420_namespace_package(tmp_path, 'myns.n.pkgA') + pkg_B = namespaces.build_pep420_namespace_package(tmp_path, 'myns.n.pkgB') + # use pip to install to the target directory + opts = editable_opts[:] + opts.append("--no-build-isolation") # force current version of setuptools + venv.run(["python", "-m", "pip", "install", str(pkg_A), *opts]) + venv.run(["python", "-m", "pip", "install", "-e", str(pkg_B), *opts]) + venv.run(["python", "-c", "import myns.n.pkgA; import myns.n.pkgB"]) + + def test_namespace_created_via_package_dir(self, venv, tmp_path, editable_opts): + """Currently users can create a namespace by tweaking `package_dir`""" + files = { + "pkgA": { + "pyproject.toml": dedent( + """\ + [build-system] + requires = ["setuptools", "wheel"] + build-backend = "setuptools.build_meta" + + [project] + name = "pkgA" + version = "3.14159" + + [tool.setuptools] + package-dir = {"myns.n.pkgA" = "src"} + """ + ), + "src": {"__init__.py": "a = 1"}, + }, + } + jaraco.path.build(files, prefix=tmp_path) + pkg_A = tmp_path / "pkgA" + pkg_B = namespaces.build_pep420_namespace_package(tmp_path, 'myns.n.pkgB') + pkg_C = namespaces.build_pep420_namespace_package(tmp_path, 'myns.n.pkgC') + + # use pip to install to the target directory + opts = editable_opts[:] + opts.append("--no-build-isolation") # force current version of setuptools + venv.run(["python", "-m", "pip", "install", str(pkg_A), *opts]) + venv.run(["python", "-m", "pip", "install", "-e", str(pkg_B), *opts]) + venv.run(["python", "-m", "pip", "install", "-e", str(pkg_C), *opts]) + venv.run(["python", "-c", "from myns.n import pkgA, pkgB, pkgC"]) + + def test_namespace_accidental_config_in_lenient_mode(self, venv, tmp_path): + """Sometimes users might specify an ``include`` pattern that ignores parent + packages. In a normal installation this would ignore all modules inside the + parent packages, and make them namespaces (reported in issue #3504), + so the editable mode should preserve this behaviour. + """ + files = { + "pkgA": { + "pyproject.toml": dedent( + """\ + [build-system] + requires = ["setuptools", "wheel"] + build-backend = "setuptools.build_meta" + + [project] + name = "pkgA" + version = "3.14159" + + [tool.setuptools] + packages.find.include = ["mypkg.*"] + """ + ), + "mypkg": { + "__init__.py": "", + "other.py": "b = 1", + "n": { + "__init__.py": "", + "pkgA.py": "a = 1", + }, + }, + "MANIFEST.in": EXAMPLE["MANIFEST.in"], + }, + } + jaraco.path.build(files, prefix=tmp_path) + pkg_A = tmp_path / "pkgA" + + # use pip to install to the target directory + opts = ["--no-build-isolation"] # force current version of setuptools + venv.run(["python", "-m", "pip", "-v", "install", "-e", str(pkg_A), *opts]) + out = venv.run(["python", "-c", "from mypkg.n import pkgA; print(pkgA.a)"]) + assert out.strip() == "1" + cmd = """\ + try: + import mypkg.other + except ImportError: + print("mypkg.other not defined") + """ + out = venv.run(["python", "-c", dedent(cmd)]) + assert "mypkg.other not defined" in out + + +def test_editable_with_prefix(tmp_path, sample_project, editable_opts): + """ + Editable install to a prefix should be discoverable. + """ + prefix = tmp_path / 'prefix' + + # figure out where pip will likely install the package + site_packages_all = [ + prefix / Path(path).relative_to(sys.prefix) + for path in sys.path + if 'site-packages' in path and path.startswith(sys.prefix) + ] + + for sp in site_packages_all: + sp.mkdir(parents=True) + + # install workaround + _addsitedirs(site_packages_all) + + env = dict(os.environ, PYTHONPATH=os.pathsep.join(map(str, site_packages_all))) + cmd = [ + sys.executable, + '-m', + 'pip', + 'install', + '--editable', + str(sample_project), + '--prefix', + str(prefix), + '--no-build-isolation', + *editable_opts, + ] + subprocess.check_call(cmd, env=env) + + # now run 'sample' with the prefix on the PYTHONPATH + bin = 'Scripts' if platform.system() == 'Windows' else 'bin' + exe = prefix / bin / 'sample' + subprocess.check_call([exe], env=env) + + +class TestFinderTemplate: + """This test focus in getting a particular implementation detail right. + If at some point in time the implementation is changed for something different, + this test can be modified or even excluded. + """ + + def install_finder(self, finder): + loc = {} + exec(finder, loc, loc) + loc["install"]() + + def test_packages(self, tmp_path): + files = { + "src1": { + "pkg1": { + "__init__.py": "", + "subpkg": {"mod1.py": "a = 42"}, + }, + }, + "src2": {"mod2.py": "a = 43"}, + } + jaraco.path.build(files, prefix=tmp_path) + + mapping = { + "pkg1": str(tmp_path / "src1/pkg1"), + "mod2": str(tmp_path / "src2/mod2"), + } + template = _finder_template(str(uuid4()), mapping, {}) + + with contexts.save_paths(), contexts.save_sys_modules(): + for mod in ("pkg1", "pkg1.subpkg", "pkg1.subpkg.mod1", "mod2"): + sys.modules.pop(mod, None) + + self.install_finder(template) + mod1 = import_module("pkg1.subpkg.mod1") + mod2 = import_module("mod2") + subpkg = import_module("pkg1.subpkg") + + assert mod1.a == 42 + assert mod2.a == 43 + expected = str((tmp_path / "src1/pkg1/subpkg").resolve()) + assert_path(subpkg, expected) + + def test_namespace(self, tmp_path): + files = {"pkg": {"__init__.py": "a = 13", "text.txt": "abc"}} + jaraco.path.build(files, prefix=tmp_path) + + mapping = {"ns.othername": str(tmp_path / "pkg")} + namespaces = {"ns": []} + + template = _finder_template(str(uuid4()), mapping, namespaces) + with contexts.save_paths(), contexts.save_sys_modules(): + for mod in ("ns", "ns.othername"): + sys.modules.pop(mod, None) + + self.install_finder(template) + pkg = import_module("ns.othername") + text = importlib_resources.files(pkg) / "text.txt" + + expected = str((tmp_path / "pkg").resolve()) + assert_path(pkg, expected) + assert pkg.a == 13 + + # Make sure resources can also be found + assert text.read_text(encoding="utf-8") == "abc" + + def test_combine_namespaces(self, tmp_path): + files = { + "src1": {"ns": {"pkg1": {"__init__.py": "a = 13"}}}, + "src2": {"ns": {"mod2.py": "b = 37"}}, + } + jaraco.path.build(files, prefix=tmp_path) + + mapping = { + "ns.pkgA": str(tmp_path / "src1/ns/pkg1"), + "ns": str(tmp_path / "src2/ns"), + } + namespaces_ = {"ns": [str(tmp_path / "src1"), str(tmp_path / "src2")]} + template = _finder_template(str(uuid4()), mapping, namespaces_) + + with contexts.save_paths(), contexts.save_sys_modules(): + for mod in ("ns", "ns.pkgA", "ns.mod2"): + sys.modules.pop(mod, None) + + self.install_finder(template) + pkgA = import_module("ns.pkgA") + mod2 = import_module("ns.mod2") + + expected = str((tmp_path / "src1/ns/pkg1").resolve()) + assert_path(pkgA, expected) + assert pkgA.a == 13 + assert mod2.b == 37 + + def test_combine_namespaces_nested(self, tmp_path): + """ + Users may attempt to combine namespace packages in a nested way via + ``package_dir`` as shown in pypa/setuptools#4248. + """ + + files = { + "src": {"my_package": {"my_module.py": "a = 13"}}, + "src2": {"my_package2": {"my_module2.py": "b = 37"}}, + } + + stack = jaraco.path.DirectoryStack() + with stack.context(tmp_path): + jaraco.path.build(files) + attrs = { + "script_name": "%PEP 517%", + "package_dir": { + "different_name": "src/my_package", + "different_name.subpkg": "src2/my_package2", + }, + "packages": ["different_name", "different_name.subpkg"], + } + dist = Distribution(attrs) + finder = _TopLevelFinder(dist, str(uuid4())) + code = next(v for k, v in finder.get_implementation() if k.endswith(".py")) + + with contexts.save_paths(), contexts.save_sys_modules(): + for mod in attrs["packages"]: + sys.modules.pop(mod, None) + + self.install_finder(code) + mod1 = import_module("different_name.my_module") + mod2 = import_module("different_name.subpkg.my_module2") + + expected = str((tmp_path / "src/my_package/my_module.py").resolve()) + assert str(Path(mod1.__file__).resolve()) == expected + + expected = str((tmp_path / "src2/my_package2/my_module2.py").resolve()) + assert str(Path(mod2.__file__).resolve()) == expected + + assert mod1.a == 13 + assert mod2.b == 37 + + def test_dynamic_path_computation(self, tmp_path): + # Follows the example in PEP 420 + files = { + "project1": {"parent": {"child": {"one.py": "x = 1"}}}, + "project2": {"parent": {"child": {"two.py": "x = 2"}}}, + "project3": {"parent": {"child": {"three.py": "x = 3"}}}, + } + jaraco.path.build(files, prefix=tmp_path) + mapping = {} + namespaces_ = {"parent": [str(tmp_path / "project1/parent")]} + template = _finder_template(str(uuid4()), mapping, namespaces_) + + mods = (f"parent.child.{name}" for name in ("one", "two", "three")) + with contexts.save_paths(), contexts.save_sys_modules(): + for mod in ("parent", "parent.child", "parent.child", *mods): + sys.modules.pop(mod, None) + + self.install_finder(template) + + one = import_module("parent.child.one") + assert one.x == 1 + + with pytest.raises(ImportError): + import_module("parent.child.two") + + sys.path.append(str(tmp_path / "project2")) + two = import_module("parent.child.two") + assert two.x == 2 + + with pytest.raises(ImportError): + import_module("parent.child.three") + + sys.path.append(str(tmp_path / "project3")) + three = import_module("parent.child.three") + assert three.x == 3 + + def test_no_recursion(self, tmp_path): + # See issue #3550 + files = { + "pkg": { + "__init__.py": "from . import pkg", + }, + } + jaraco.path.build(files, prefix=tmp_path) + + mapping = { + "pkg": str(tmp_path / "pkg"), + } + template = _finder_template(str(uuid4()), mapping, {}) + + with contexts.save_paths(), contexts.save_sys_modules(): + sys.modules.pop("pkg", None) + + self.install_finder(template) + with pytest.raises(ImportError, match="pkg"): + import_module("pkg") + + def test_similar_name(self, tmp_path): + files = { + "foo": { + "__init__.py": "", + "bar": { + "__init__.py": "", + }, + }, + } + jaraco.path.build(files, prefix=tmp_path) + + mapping = { + "foo": str(tmp_path / "foo"), + } + template = _finder_template(str(uuid4()), mapping, {}) + + with contexts.save_paths(), contexts.save_sys_modules(): + sys.modules.pop("foo", None) + sys.modules.pop("foo.bar", None) + + self.install_finder(template) + with pytest.raises(ImportError, match="foobar"): + import_module("foobar") + + def test_case_sensitivity(self, tmp_path): + files = { + "foo": { + "__init__.py": "", + "lowercase.py": "x = 1", + "bar": { + "__init__.py": "", + "lowercase.py": "x = 2", + }, + }, + } + jaraco.path.build(files, prefix=tmp_path) + mapping = { + "foo": str(tmp_path / "foo"), + } + template = _finder_template(str(uuid4()), mapping, {}) + with contexts.save_paths(), contexts.save_sys_modules(): + sys.modules.pop("foo", None) + + self.install_finder(template) + with pytest.raises(ImportError, match="'FOO'"): + import_module("FOO") + + with pytest.raises(ImportError, match="'foo\\.LOWERCASE'"): + import_module("foo.LOWERCASE") + + with pytest.raises(ImportError, match="'foo\\.bar\\.Lowercase'"): + import_module("foo.bar.Lowercase") + + with pytest.raises(ImportError, match="'foo\\.BAR'"): + import_module("foo.BAR.lowercase") + + with pytest.raises(ImportError, match="'FOO'"): + import_module("FOO.bar.lowercase") + + mod = import_module("foo.lowercase") + assert mod.x == 1 + + mod = import_module("foo.bar.lowercase") + assert mod.x == 2 + + def test_namespace_case_sensitivity(self, tmp_path): + files = { + "pkg": { + "__init__.py": "a = 13", + "foo": { + "__init__.py": "b = 37", + "bar.py": "c = 42", + }, + }, + } + jaraco.path.build(files, prefix=tmp_path) + + mapping = {"ns.othername": str(tmp_path / "pkg")} + namespaces = {"ns": []} + + template = _finder_template(str(uuid4()), mapping, namespaces) + with contexts.save_paths(), contexts.save_sys_modules(): + for mod in ("ns", "ns.othername"): + sys.modules.pop(mod, None) + + self.install_finder(template) + pkg = import_module("ns.othername") + expected = str((tmp_path / "pkg").resolve()) + assert_path(pkg, expected) + assert pkg.a == 13 + + foo = import_module("ns.othername.foo") + assert foo.b == 37 + + bar = import_module("ns.othername.foo.bar") + assert bar.c == 42 + + with pytest.raises(ImportError, match="'NS'"): + import_module("NS.othername.foo") + + with pytest.raises(ImportError, match="'ns\\.othername\\.FOO\\'"): + import_module("ns.othername.FOO") + + with pytest.raises(ImportError, match="'ns\\.othername\\.foo\\.BAR\\'"): + import_module("ns.othername.foo.BAR") + + def test_intermediate_packages(self, tmp_path): + """ + The finder should not import ``fullname`` if the intermediate segments + don't exist (see pypa/setuptools#4019). + """ + files = { + "src": { + "mypkg": { + "__init__.py": "", + "config.py": "a = 13", + "helloworld.py": "b = 13", + "components": { + "config.py": "a = 37", + }, + }, + } + } + jaraco.path.build(files, prefix=tmp_path) + + mapping = {"mypkg": str(tmp_path / "src/mypkg")} + template = _finder_template(str(uuid4()), mapping, {}) + + with contexts.save_paths(), contexts.save_sys_modules(): + for mod in ( + "mypkg", + "mypkg.config", + "mypkg.helloworld", + "mypkg.components", + "mypkg.components.config", + "mypkg.components.helloworld", + ): + sys.modules.pop(mod, None) + + self.install_finder(template) + + config = import_module("mypkg.components.config") + assert config.a == 37 + + helloworld = import_module("mypkg.helloworld") + assert helloworld.b == 13 + + with pytest.raises(ImportError): + import_module("mypkg.components.helloworld") + + +def test_pkg_roots(tmp_path): + """This test focus in getting a particular implementation detail right. + If at some point in time the implementation is changed for something different, + this test can be modified or even excluded. + """ + files = { + "a": {"b": {"__init__.py": "ab = 1"}, "__init__.py": "a = 1"}, + "d": {"__init__.py": "d = 1", "e": {"__init__.py": "de = 1"}}, + "f": {"g": {"h": {"__init__.py": "fgh = 1"}}}, + "other": {"__init__.py": "abc = 1"}, + "another": {"__init__.py": "abcxyz = 1"}, + "yet_another": {"__init__.py": "mnopq = 1"}, + } + jaraco.path.build(files, prefix=tmp_path) + package_dir = { + "a.b.c": "other", + "a.b.c.x.y.z": "another", + "m.n.o.p.q": "yet_another", + } + packages = [ + "a", + "a.b", + "a.b.c", + "a.b.c.x.y", + "a.b.c.x.y.z", + "d", + "d.e", + "f", + "f.g", + "f.g.h", + "m.n.o.p.q", + ] + roots = _find_package_roots(packages, package_dir, tmp_path) + assert roots == { + "a": str(tmp_path / "a"), + "a.b.c": str(tmp_path / "other"), + "a.b.c.x.y.z": str(tmp_path / "another"), + "d": str(tmp_path / "d"), + "f": str(tmp_path / "f"), + "m.n.o.p.q": str(tmp_path / "yet_another"), + } + + ns = set(dict(_find_namespaces(packages, roots))) + assert ns == {"f", "f.g"} + + ns = set(_find_virtual_namespaces(roots)) + assert ns == {"a.b", "a.b.c.x", "a.b.c.x.y", "m", "m.n", "m.n.o", "m.n.o.p"} + + +class TestOverallBehaviour: + PYPROJECT = """\ + [build-system] + requires = ["setuptools"] + build-backend = "setuptools.build_meta" + + [project] + name = "mypkg" + version = "3.14159" + """ + + # Any: Would need a TypedDict. Keep it simple for tests + FLAT_LAYOUT: dict[str, Any] = { + "pyproject.toml": dedent(PYPROJECT), + "MANIFEST.in": EXAMPLE["MANIFEST.in"], + "otherfile.py": "", + "mypkg": { + "__init__.py": "", + "mod1.py": "var = 42", + "subpackage": { + "__init__.py": "", + "mod2.py": "var = 13", + "resource_file.txt": "resource 39", + }, + }, + } + + EXAMPLES = { + "flat-layout": FLAT_LAYOUT, + "src-layout": { + "pyproject.toml": dedent(PYPROJECT), + "MANIFEST.in": EXAMPLE["MANIFEST.in"], + "otherfile.py": "", + "src": {"mypkg": FLAT_LAYOUT["mypkg"]}, + }, + "custom-layout": { + "pyproject.toml": dedent(PYPROJECT) + + dedent( + """\ + [tool.setuptools] + packages = ["mypkg", "mypkg.subpackage"] + + [tool.setuptools.package-dir] + "mypkg.subpackage" = "other" + """ + ), + "MANIFEST.in": EXAMPLE["MANIFEST.in"], + "otherfile.py": "", + "mypkg": { + "__init__.py": "", + "mod1.py": FLAT_LAYOUT["mypkg"]["mod1.py"], + }, + "other": FLAT_LAYOUT["mypkg"]["subpackage"], + }, + "namespace": { + "pyproject.toml": dedent(PYPROJECT), + "MANIFEST.in": EXAMPLE["MANIFEST.in"], + "otherfile.py": "", + "src": { + "mypkg": { + "mod1.py": FLAT_LAYOUT["mypkg"]["mod1.py"], + "subpackage": FLAT_LAYOUT["mypkg"]["subpackage"], + }, + }, + }, + } + + @pytest.mark.xfail(sys.platform == "darwin", reason="pypa/setuptools#4328") + @pytest.mark.parametrize("layout", EXAMPLES.keys()) + def test_editable_install(self, tmp_path, venv, layout, editable_opts): + project, _ = install_project( + "mypkg", venv, tmp_path, self.EXAMPLES[layout], *editable_opts + ) + + # Ensure stray files are not importable + cmd_import_error = """\ + try: + import otherfile + except ImportError as ex: + print(ex) + """ + out = venv.run(["python", "-c", dedent(cmd_import_error)]) + assert "No module named 'otherfile'" in out + + # Ensure the modules are importable + cmd_get_vars = """\ + import mypkg, mypkg.mod1, mypkg.subpackage.mod2 + print(mypkg.mod1.var, mypkg.subpackage.mod2.var) + """ + out = venv.run(["python", "-c", dedent(cmd_get_vars)]) + assert "42 13" in out + + # Ensure resources are reachable + cmd_get_resource = """\ + import mypkg.subpackage + from setuptools._importlib import resources as importlib_resources + text = importlib_resources.files(mypkg.subpackage) / "resource_file.txt" + print(text.read_text(encoding="utf-8")) + """ + out = venv.run(["python", "-c", dedent(cmd_get_resource)]) + assert "resource 39" in out + + # Ensure files are editable + mod1 = next(project.glob("**/mod1.py")) + mod2 = next(project.glob("**/mod2.py")) + resource_file = next(project.glob("**/resource_file.txt")) + + mod1.write_text("var = 17", encoding="utf-8") + mod2.write_text("var = 781", encoding="utf-8") + resource_file.write_text("resource 374", encoding="utf-8") + + out = venv.run(["python", "-c", dedent(cmd_get_vars)]) + assert "42 13" not in out + assert "17 781" in out + + out = venv.run(["python", "-c", dedent(cmd_get_resource)]) + assert "resource 39" not in out + assert "resource 374" in out + + +class TestLinkTree: + FILES = deepcopy(TestOverallBehaviour.EXAMPLES["src-layout"]) + FILES["pyproject.toml"] += dedent( + """\ + [tool.setuptools] + # Temporary workaround: both `include-package-data` and `package-data` configs + # can be removed after #3260 is fixed. + include-package-data = false + package-data = {"*" = ["*.txt"]} + + [tool.setuptools.packages.find] + where = ["src"] + exclude = ["*.subpackage*"] + """ + ) + FILES["src"]["mypkg"]["resource.not_in_manifest"] = "abc" + + def test_generated_tree(self, tmp_path): + jaraco.path.build(self.FILES, prefix=tmp_path) + + with _Path(tmp_path): + name = "mypkg-3.14159" + dist = Distribution({"script_name": "%PEP 517%"}) + dist.parse_config_files() + + wheel = Mock() + aux = tmp_path / ".aux" + build = tmp_path / ".build" + aux.mkdir() + build.mkdir() + + build_py = dist.get_command_obj("build_py") + build_py.editable_mode = True + build_py.build_lib = str(build) + build_py.ensure_finalized() + outputs = build_py.get_outputs() + output_mapping = build_py.get_output_mapping() + + make_tree = _LinkTree(dist, name, aux, build) + make_tree(wheel, outputs, output_mapping) + + mod1 = next(aux.glob("**/mod1.py")) + expected = tmp_path / "src/mypkg/mod1.py" + assert_link_to(mod1, expected) + + assert next(aux.glob("**/subpackage"), None) is None + assert next(aux.glob("**/mod2.py"), None) is None + assert next(aux.glob("**/resource_file.txt"), None) is None + + assert next(aux.glob("**/resource.not_in_manifest"), None) is None + + def test_strict_install(self, tmp_path, venv): + opts = ["--config-settings", "editable-mode=strict"] + install_project("mypkg", venv, tmp_path, self.FILES, *opts) + + out = venv.run(["python", "-c", "import mypkg.mod1; print(mypkg.mod1.var)"]) + assert "42" in out + + # Ensure packages excluded from distribution are not importable + cmd_import_error = """\ + try: + from mypkg import subpackage + except ImportError as ex: + print(ex) + """ + out = venv.run(["python", "-c", dedent(cmd_import_error)]) + assert "cannot import name 'subpackage'" in out + + # Ensure resource files excluded from distribution are not reachable + cmd_get_resource = """\ + import mypkg + from setuptools._importlib import resources as importlib_resources + try: + text = importlib_resources.files(mypkg) / "resource.not_in_manifest" + print(text.read_text(encoding="utf-8")) + except FileNotFoundError as ex: + print(ex) + """ + out = venv.run(["python", "-c", dedent(cmd_get_resource)]) + assert "No such file or directory" in out + assert "resource.not_in_manifest" in out + + +@pytest.mark.filterwarnings("ignore:.*compat.*:setuptools.SetuptoolsDeprecationWarning") +def test_compat_install(tmp_path, venv): + # TODO: Remove `compat` after Dec/2022. + opts = ["--config-settings", "editable-mode=compat"] + files = TestOverallBehaviour.EXAMPLES["custom-layout"] + install_project("mypkg", venv, tmp_path, files, *opts) + + out = venv.run(["python", "-c", "import mypkg.mod1; print(mypkg.mod1.var)"]) + assert "42" in out + + expected_path = comparable_path(str(tmp_path)) + + # Compatible behaviour will make spurious modules and excluded + # files importable directly from the original path + for cmd in ( + "import otherfile; print(otherfile)", + "import other; print(other)", + "import mypkg; print(mypkg)", + ): + out = comparable_path(venv.run(["python", "-c", cmd])) + assert expected_path in out + + # Compatible behaviour will not consider custom mappings + cmd = """\ + try: + from mypkg import subpackage; + except ImportError as ex: + print(ex) + """ + out = venv.run(["python", "-c", dedent(cmd)]) + assert "cannot import name 'subpackage'" in out + + +@pytest.mark.uses_network +def test_pbr_integration(pbr_package, venv, editable_opts): + """Ensure editable installs work with pbr, issue #3500""" + cmd = [ + 'python', + '-m', + 'pip', + '-v', + 'install', + '--editable', + pbr_package, + *editable_opts, + ] + venv.run(cmd, stderr=subprocess.STDOUT) + out = venv.run(["python", "-c", "import mypkg.hello"]) + assert "Hello world!" in out + + +class TestCustomBuildPy: + """ + Issue #3501 indicates that some plugins/customizations might rely on: + + 1. ``build_py`` not running + 2. ``build_py`` always copying files to ``build_lib`` + + During the transition period setuptools should prevent potential errors from + happening due to those assumptions. + """ + + # TODO: Remove tests after _run_build_steps is removed. + + FILES = { + **TestOverallBehaviour.EXAMPLES["flat-layout"], + "setup.py": dedent( + """\ + import pathlib + from setuptools import setup + from setuptools.command.build_py import build_py as orig + + class my_build_py(orig): + def run(self): + super().run() + raise ValueError("TEST_RAISE") + + setup(cmdclass={"build_py": my_build_py}) + """ + ), + } + + def test_safeguarded_from_errors(self, tmp_path, venv): + """Ensure that errors in custom build_py are reported as warnings""" + # Warnings should show up + _, out = install_project("mypkg", venv, tmp_path, self.FILES) + assert "SetuptoolsDeprecationWarning" in out + assert "ValueError: TEST_RAISE" in out + # but installation should be successful + out = venv.run(["python", "-c", "import mypkg.mod1; print(mypkg.mod1.var)"]) + assert "42" in out + + +class TestCustomBuildWheel: + def install_custom_build_wheel(self, dist): + bdist_wheel_cls = dist.get_command_class("bdist_wheel") + + class MyBdistWheel(bdist_wheel_cls): + def get_tag(self): + # In issue #3513, we can see that some extensions may try to access + # the `plat_name` property in bdist_wheel + if self.plat_name.startswith("macosx-"): + _ = "macOS platform" + return super().get_tag() + + dist.cmdclass["bdist_wheel"] = MyBdistWheel + + def test_access_plat_name(self, tmpdir_cwd): + # Even when a custom bdist_wheel tries to access plat_name the build should + # be successful + jaraco.path.build({"module.py": "x = 42"}) + dist = Distribution() + dist.script_name = "setup.py" + dist.set_defaults() + self.install_custom_build_wheel(dist) + cmd = editable_wheel(dist) + cmd.ensure_finalized() + cmd.run() + wheel_file = str(next(Path().glob('dist/*.whl'))) + assert "editable" in wheel_file + + +class TestCustomBuildExt: + def install_custom_build_ext_distutils(self, dist): + from distutils.command.build_ext import build_ext as build_ext_cls + + class MyBuildExt(build_ext_cls): + pass + + dist.cmdclass["build_ext"] = MyBuildExt + + @pytest.mark.skipif( + sys.platform != "linux", reason="compilers may fail without correct setup" + ) + def test_distutils_leave_inplace_files(self, tmpdir_cwd): + jaraco.path.build({"module.c": ""}) + attrs = { + "ext_modules": [Extension("module", ["module.c"])], + } + dist = Distribution(attrs) + dist.script_name = "setup.py" + dist.set_defaults() + self.install_custom_build_ext_distutils(dist) + cmd = editable_wheel(dist) + cmd.ensure_finalized() + cmd.run() + wheel_file = str(next(Path().glob('dist/*.whl'))) + assert "editable" in wheel_file + files = [p for p in Path().glob("module.*") if p.suffix != ".c"] + assert len(files) == 1 + name = files[0].name + assert any(name.endswith(ext) for ext in EXTENSION_SUFFIXES) + + +def test_debugging_tips(tmpdir_cwd, monkeypatch): + """Make sure to display useful debugging tips to the user.""" + jaraco.path.build({"module.py": "x = 42"}) + dist = Distribution() + dist.script_name = "setup.py" + dist.set_defaults() + cmd = editable_wheel(dist) + cmd.ensure_finalized() + + SimulatedErr = type("SimulatedErr", (Exception,), {}) + simulated_failure = Mock(side_effect=SimulatedErr()) + monkeypatch.setattr(cmd, "get_finalized_command", simulated_failure) + + with pytest.raises(SimulatedErr) as ctx: + cmd.run() + assert any('debugging-tips' in note for note in ctx.value.__notes__) + + +@pytest.mark.filterwarnings("error") +def test_encode_pth(): + """Ensure _encode_pth function does not produce encoding warnings""" + content = _encode_pth("tkmilan_ç_utf8") # no warnings (would be turned into errors) + assert isinstance(content, bytes) + + +def install_project(name, venv, tmp_path, files, *opts): + project = tmp_path / name + project.mkdir() + jaraco.path.build(files, prefix=project) + opts = [*opts, "--no-build-isolation"] # force current version of setuptools + out = venv.run( + ["python", "-m", "pip", "-v", "install", "-e", str(project), *opts], + stderr=subprocess.STDOUT, + ) + return project, out + + +def _addsitedirs(new_dirs): + """To use this function, it is necessary to insert new_dir in front of sys.path. + The Python process will try to import a ``sitecustomize`` module on startup. + If we manipulate sys.path/PYTHONPATH, we can force it to run our code, + which invokes ``addsitedir`` and ensure ``.pth`` files are loaded. + """ + content = '\n'.join( + ("import site",) + + tuple(f"site.addsitedir({os.fspath(new_dir)!r})" for new_dir in new_dirs) + ) + (new_dirs[0] / "sitecustomize.py").write_text(content, encoding="utf-8") + + +# ---- Assertion Helpers ---- + + +def assert_path(pkg, expected): + # __path__ is not guaranteed to exist, so we have to account for that + if pkg.__path__: + path = next(iter(pkg.__path__), None) + if path: + assert str(Path(path).resolve()) == expected + + +def assert_link_to(file: Path, other: Path) -> None: + if file.is_symlink(): + assert str(file.resolve()) == str(other.resolve()) + else: + file_stat = file.stat() + other_stat = other.stat() + assert file_stat[stat.ST_INO] == other_stat[stat.ST_INO] + assert file_stat[stat.ST_DEV] == other_stat[stat.ST_DEV] + + +def comparable_path(str_with_path: str) -> str: + return str_with_path.lower().replace(os.sep, "/").replace("//", "/") diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_egg_info.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_egg_info.py new file mode 100644 index 0000000000000000000000000000000000000000..3653be096f11b77c71f58679d6e4a108903668a5 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_egg_info.py @@ -0,0 +1,1306 @@ +from __future__ import annotations + +import ast +import glob +import os +import re +import stat +import sys +import time +from pathlib import Path +from unittest import mock + +import pytest +from jaraco import path + +from setuptools import errors +from setuptools.command.egg_info import egg_info, manifest_maker, write_entries +from setuptools.dist import Distribution + +from . import contexts, environment +from .textwrap import DALS + + +class Environment(str): + pass + + +@pytest.fixture +def env(): + with contexts.tempdir(prefix='setuptools-test.') as env_dir: + env = Environment(env_dir) + os.chmod(env_dir, stat.S_IRWXU) + subs = 'home', 'lib', 'scripts', 'data', 'egg-base' + env.paths = dict((dirname, os.path.join(env_dir, dirname)) for dirname in subs) + list(map(os.mkdir, env.paths.values())) + path.build({ + env.paths['home']: { + '.pydistutils.cfg': DALS( + """ + [egg_info] + egg-base = {egg-base} + """.format(**env.paths) + ) + } + }) + yield env + + +class TestEggInfo: + setup_script = DALS( + """ + from setuptools import setup + + setup( + name='foo', + py_modules=['hello'], + entry_points={'console_scripts': ['hi = hello.run']}, + zip_safe=False, + ) + """ + ) + + def _create_project(self): + path.build({ + 'setup.py': self.setup_script, + 'hello.py': DALS( + """ + def run(): + print('hello') + """ + ), + }) + + @staticmethod + def _extract_mv_version(pkg_info_lines: list[str]) -> tuple[int, int]: + version_str = pkg_info_lines[0].split(' ')[1] + major, minor = map(int, version_str.split('.')[:2]) + return major, minor + + def test_egg_info_save_version_info_setup_empty(self, tmpdir_cwd, env): + """ + When the egg_info section is empty or not present, running + save_version_info should add the settings to the setup.cfg + in a deterministic order. + """ + setup_cfg = os.path.join(env.paths['home'], 'setup.cfg') + dist = Distribution() + ei = egg_info(dist) + ei.initialize_options() + ei.save_version_info(setup_cfg) + + with open(setup_cfg, 'r', encoding="utf-8") as f: + content = f.read() + + assert '[egg_info]' in content + assert 'tag_build =' in content + assert 'tag_date = 0' in content + + expected_order = ( + 'tag_build', + 'tag_date', + ) + + self._validate_content_order(content, expected_order) + + @staticmethod + def _validate_content_order(content, expected): + """ + Assert that the strings in expected appear in content + in order. + """ + pattern = '.*'.join(expected) + flags = re.MULTILINE | re.DOTALL + assert re.search(pattern, content, flags) + + def test_egg_info_save_version_info_setup_defaults(self, tmpdir_cwd, env): + """ + When running save_version_info on an existing setup.cfg + with the 'default' values present from a previous run, + the file should remain unchanged. + """ + setup_cfg = os.path.join(env.paths['home'], 'setup.cfg') + path.build({ + setup_cfg: DALS( + """ + [egg_info] + tag_build = + tag_date = 0 + """ + ), + }) + dist = Distribution() + ei = egg_info(dist) + ei.initialize_options() + ei.save_version_info(setup_cfg) + + with open(setup_cfg, 'r', encoding="utf-8") as f: + content = f.read() + + assert '[egg_info]' in content + assert 'tag_build =' in content + assert 'tag_date = 0' in content + + expected_order = ( + 'tag_build', + 'tag_date', + ) + + self._validate_content_order(content, expected_order) + + def test_expected_files_produced(self, tmpdir_cwd, env): + self._create_project() + + self._run_egg_info_command(tmpdir_cwd, env) + actual = os.listdir('foo.egg-info') + + expected = [ + 'PKG-INFO', + 'SOURCES.txt', + 'dependency_links.txt', + 'entry_points.txt', + 'not-zip-safe', + 'top_level.txt', + ] + assert sorted(actual) == expected + + def test_handling_utime_error(self, tmpdir_cwd, env): + dist = Distribution() + ei = egg_info(dist) + utime_patch = mock.patch('os.utime', side_effect=OSError("TEST")) + mkpath_patch = mock.patch( + 'setuptools.command.egg_info.egg_info.mkpath', return_val=None + ) + + with utime_patch, mkpath_patch: + import distutils.errors + + msg = r"Cannot update time stamp of directory 'None'" + with pytest.raises(distutils.errors.DistutilsFileError, match=msg): + ei.run() + + def test_license_is_a_string(self, tmpdir_cwd, env): + setup_config = DALS( + """ + [metadata] + name=foo + version=0.0.1 + license=file:MIT + """ + ) + + setup_script = DALS( + """ + from setuptools import setup + + setup() + """ + ) + + path.build({ + 'setup.py': setup_script, + 'setup.cfg': setup_config, + }) + + # This command should fail with a ValueError, but because it's + # currently configured to use a subprocess, the actual traceback + # object is lost and we need to parse it from stderr + with pytest.raises(AssertionError) as exc: + self._run_egg_info_command(tmpdir_cwd, env) + + # The only argument to the assertion error should be a traceback + # containing a ValueError + assert 'ValueError' in exc.value.args[0] + + def test_rebuilt(self, tmpdir_cwd, env): + """Ensure timestamps are updated when the command is re-run.""" + self._create_project() + + self._run_egg_info_command(tmpdir_cwd, env) + timestamp_a = os.path.getmtime('foo.egg-info') + + # arbitrary sleep just to handle *really* fast systems + time.sleep(0.001) + + self._run_egg_info_command(tmpdir_cwd, env) + timestamp_b = os.path.getmtime('foo.egg-info') + + assert timestamp_a != timestamp_b + + def test_manifest_template_is_read(self, tmpdir_cwd, env): + self._create_project() + path.build({ + 'MANIFEST.in': DALS( + """ + recursive-include docs *.rst + """ + ), + 'docs': { + 'usage.rst': "Run 'hi'", + }, + }) + self._run_egg_info_command(tmpdir_cwd, env) + egg_info_dir = os.path.join('.', 'foo.egg-info') + sources_txt = os.path.join(egg_info_dir, 'SOURCES.txt') + with open(sources_txt, encoding="utf-8") as f: + assert 'docs/usage.rst' in f.read().split('\n') + + def _setup_script_with_requires(self, requires, use_setup_cfg=False): + setup_script = DALS( + """ + from setuptools import setup + + setup(name='foo', zip_safe=False, %s) + """ + ) % ('' if use_setup_cfg else requires) + setup_config = requires if use_setup_cfg else '' + path.build({ + 'setup.py': setup_script, + 'setup.cfg': setup_config, + }) + + mismatch_marker = f"python_version<'{sys.version_info[0]}'" + # Alternate equivalent syntax. + mismatch_marker_alternate = f'python_version < "{sys.version_info[0]}"' + invalid_marker = "<=>++" + + class RequiresTestHelper: + @staticmethod + def parametrize(*test_list, **format_dict): + idlist = [] + argvalues = [] + for test in test_list: + test_params = test.lstrip().split('\n\n', 3) + name_kwargs = test_params.pop(0).split('\n') + if len(name_kwargs) > 1: + val = name_kwargs[1].strip() + install_cmd_kwargs = ast.literal_eval(val) + else: + install_cmd_kwargs = {} + name = name_kwargs[0].strip() + setup_py_requires, setup_cfg_requires, expected_requires = [ + DALS(a).format(**format_dict) for a in test_params + ] + for id_, requires, use_cfg in ( + (name, setup_py_requires, False), + (name + '_in_setup_cfg', setup_cfg_requires, True), + ): + idlist.append(id_) + marks = () + if requires.startswith('@xfail\n'): + requires = requires[7:] + marks = pytest.mark.xfail + argvalues.append( + pytest.param( + requires, + use_cfg, + expected_requires, + install_cmd_kwargs, + marks=marks, + ) + ) + return pytest.mark.parametrize( + ( + "requires", + "use_setup_cfg", + "expected_requires", + "install_cmd_kwargs", + ), + argvalues, + ids=idlist, + ) + + @RequiresTestHelper.parametrize( + # Format of a test: + # + # id + # install_cmd_kwargs [optional] + # + # requires block (when used in setup.py) + # + # requires block (when used in setup.cfg) + # + # expected contents of requires.txt + """ + install_requires_deterministic + + install_requires=["wheel>=0.5", "pytest"] + + [options] + install_requires = + wheel>=0.5 + pytest + + wheel>=0.5 + pytest + """, + """ + install_requires_ordered + + install_requires=["pytest>=3.0.2,!=10.9999"] + + [options] + install_requires = + pytest>=3.0.2,!=10.9999 + + pytest!=10.9999,>=3.0.2 + """, + """ + install_requires_with_marker + + install_requires=["barbazquux;{mismatch_marker}"], + + [options] + install_requires = + barbazquux; {mismatch_marker} + + [:{mismatch_marker_alternate}] + barbazquux + """, + """ + install_requires_with_extra + {'cmd': ['egg_info']} + + install_requires=["barbazquux [test]"], + + [options] + install_requires = + barbazquux [test] + + barbazquux[test] + """, + """ + install_requires_with_extra_and_marker + + install_requires=["barbazquux [test]; {mismatch_marker}"], + + [options] + install_requires = + barbazquux [test]; {mismatch_marker} + + [:{mismatch_marker_alternate}] + barbazquux[test] + """, + """ + setup_requires_with_markers + + setup_requires=["barbazquux;{mismatch_marker}"], + + [options] + setup_requires = + barbazquux; {mismatch_marker} + + """, + """ + extras_require_with_extra + {'cmd': ['egg_info']} + + extras_require={{"extra": ["barbazquux [test]"]}}, + + [options.extras_require] + extra = barbazquux [test] + + [extra] + barbazquux[test] + """, + """ + extras_require_with_extra_and_marker_in_req + + extras_require={{"extra": ["barbazquux [test]; {mismatch_marker}"]}}, + + [options.extras_require] + extra = + barbazquux [test]; {mismatch_marker} + + [extra] + + [extra:{mismatch_marker_alternate}] + barbazquux[test] + """, + # FIXME: ConfigParser does not allow : in key names! + """ + extras_require_with_marker + + extras_require={{":{mismatch_marker}": ["barbazquux"]}}, + + @xfail + [options.extras_require] + :{mismatch_marker} = barbazquux + + [:{mismatch_marker}] + barbazquux + """, + """ + extras_require_with_marker_in_req + + extras_require={{"extra": ["barbazquux; {mismatch_marker}"]}}, + + [options.extras_require] + extra = + barbazquux; {mismatch_marker} + + [extra] + + [extra:{mismatch_marker_alternate}] + barbazquux + """, + """ + extras_require_with_empty_section + + extras_require={{"empty": []}}, + + [options.extras_require] + empty = + + [empty] + """, + # Format arguments. + invalid_marker=invalid_marker, + mismatch_marker=mismatch_marker, + mismatch_marker_alternate=mismatch_marker_alternate, + ) + def test_requires( + self, + tmpdir_cwd, + env, + requires, + use_setup_cfg, + expected_requires, + install_cmd_kwargs, + ): + self._setup_script_with_requires(requires, use_setup_cfg) + self._run_egg_info_command(tmpdir_cwd, env, **install_cmd_kwargs) + egg_info_dir = os.path.join('.', 'foo.egg-info') + requires_txt = os.path.join(egg_info_dir, 'requires.txt') + if os.path.exists(requires_txt): + with open(requires_txt, encoding="utf-8") as fp: + install_requires = fp.read() + else: + install_requires = '' + assert install_requires.lstrip() == expected_requires + assert glob.glob(os.path.join(env.paths['lib'], 'barbazquux*')) == [] + + def test_install_requires_unordered_disallowed(self, tmpdir_cwd, env): + """ + Packages that pass unordered install_requires sequences + should be rejected as they produce non-deterministic + builds. See #458. + """ + req = 'install_requires={"fake-factory==0.5.2", "pytz"}' + self._setup_script_with_requires(req) + with pytest.raises(AssertionError): + self._run_egg_info_command(tmpdir_cwd, env) + + def test_extras_require_with_invalid_marker(self, tmpdir_cwd, env): + tmpl = 'extras_require={{":{marker}": ["barbazquux"]}},' + req = tmpl.format(marker=self.invalid_marker) + self._setup_script_with_requires(req) + with pytest.raises(AssertionError): + self._run_egg_info_command(tmpdir_cwd, env) + assert glob.glob(os.path.join(env.paths['lib'], 'barbazquux*')) == [] + + def test_extras_require_with_invalid_marker_in_req(self, tmpdir_cwd, env): + tmpl = 'extras_require={{"extra": ["barbazquux; {marker}"]}},' + req = tmpl.format(marker=self.invalid_marker) + self._setup_script_with_requires(req) + with pytest.raises(AssertionError): + self._run_egg_info_command(tmpdir_cwd, env) + assert glob.glob(os.path.join(env.paths['lib'], 'barbazquux*')) == [] + + def test_provides_extra(self, tmpdir_cwd, env): + self._setup_script_with_requires('extras_require={"foobar": ["barbazquux"]},') + environ = os.environ.copy().update( + HOME=env.paths['home'], + ) + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + data_stream=1, + env=environ, + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + with open(os.path.join(egg_info_dir, 'PKG-INFO'), encoding="utf-8") as fp: + pkg_info_lines = fp.read().split('\n') + assert 'Provides-Extra: foobar' in pkg_info_lines + assert 'Metadata-Version: 2.4' in pkg_info_lines + + def test_doesnt_provides_extra(self, tmpdir_cwd, env): + self._setup_script_with_requires( + """install_requires=["spam ; python_version<'3.6'"]""" + ) + environ = os.environ.copy().update( + HOME=env.paths['home'], + ) + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + data_stream=1, + env=environ, + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + with open(os.path.join(egg_info_dir, 'PKG-INFO'), encoding="utf-8") as fp: + pkg_info_text = fp.read() + assert 'Provides-Extra:' not in pkg_info_text + + @pytest.mark.parametrize( + ('files', 'license_in_sources'), + [ + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = LICENSE + """ + ), + 'LICENSE': "Test license", + }, + True, + ), # with license + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = INVALID_LICENSE + """ + ), + 'LICENSE': "Test license", + }, + False, + ), # with an invalid license + ( + { + 'setup.cfg': DALS( + """ + """ + ), + 'LICENSE': "Test license", + }, + True, + ), # no license_file attribute, LICENSE auto-included + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = LICENSE + """ + ), + 'MANIFEST.in': "exclude LICENSE", + 'LICENSE': "Test license", + }, + True, + ), # manifest is overwritten by license_file + pytest.param( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = LICEN[CS]E* + """ + ), + 'LICENSE': "Test license", + }, + True, + id="glob_pattern", + ), + ], + ) + def test_setup_cfg_license_file(self, tmpdir_cwd, env, files, license_in_sources): + self._create_project() + path.build(files) + + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + + sources_text = Path(egg_info_dir, "SOURCES.txt").read_text(encoding="utf-8") + + if license_in_sources: + assert 'LICENSE' in sources_text + else: + assert 'LICENSE' not in sources_text + # for invalid license test + assert 'INVALID_LICENSE' not in sources_text + + @pytest.mark.parametrize( + ('files', 'incl_licenses', 'excl_licenses'), + [ + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_files = + LICENSE-ABC + LICENSE-XYZ + """ + ), + 'LICENSE-ABC': "ABC license", + 'LICENSE-XYZ': "XYZ license", + }, + ['LICENSE-ABC', 'LICENSE-XYZ'], + [], + ), # with licenses + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_files = LICENSE-ABC, LICENSE-XYZ + """ + ), + 'LICENSE-ABC': "ABC license", + 'LICENSE-XYZ': "XYZ license", + }, + ['LICENSE-ABC', 'LICENSE-XYZ'], + [], + ), # with commas + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_files = + LICENSE-ABC + """ + ), + 'LICENSE-ABC': "ABC license", + 'LICENSE-XYZ': "XYZ license", + }, + ['LICENSE-ABC'], + ['LICENSE-XYZ'], + ), # with one license + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_files = + """ + ), + 'LICENSE-ABC': "ABC license", + 'LICENSE-XYZ': "XYZ license", + }, + [], + ['LICENSE-ABC', 'LICENSE-XYZ'], + ), # empty + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_files = LICENSE-XYZ + """ + ), + 'LICENSE-ABC': "ABC license", + 'LICENSE-XYZ': "XYZ license", + }, + ['LICENSE-XYZ'], + ['LICENSE-ABC'], + ), # on same line + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_files = + LICENSE-ABC + INVALID_LICENSE + """ + ), + 'LICENSE-ABC': "Test license", + }, + ['LICENSE-ABC'], + ['INVALID_LICENSE'], + ), # with an invalid license + ( + { + 'setup.cfg': DALS( + """ + """ + ), + 'LICENSE': "Test license", + }, + ['LICENSE'], + [], + ), # no license_files attribute, LICENSE auto-included + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_files = LICENSE + """ + ), + 'MANIFEST.in': "exclude LICENSE", + 'LICENSE': "Test license", + }, + ['LICENSE'], + [], + ), # manifest is overwritten by license_files + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_files = + LICENSE-ABC + LICENSE-XYZ + """ + ), + 'MANIFEST.in': "exclude LICENSE-XYZ", + 'LICENSE-ABC': "ABC license", + 'LICENSE-XYZ': "XYZ license", + # manifest is overwritten by license_files + }, + ['LICENSE-ABC', 'LICENSE-XYZ'], + [], + ), + pytest.param( + { + 'setup.cfg': "", + 'LICENSE-ABC': "ABC license", + 'COPYING-ABC': "ABC copying", + 'NOTICE-ABC': "ABC notice", + 'AUTHORS-ABC': "ABC authors", + 'LICENCE-XYZ': "XYZ license", + 'LICENSE': "License", + 'INVALID-LICENSE': "Invalid license", + }, + [ + 'LICENSE-ABC', + 'COPYING-ABC', + 'NOTICE-ABC', + 'AUTHORS-ABC', + 'LICENCE-XYZ', + 'LICENSE', + ], + ['INVALID-LICENSE'], + # ('LICEN[CS]E*', 'COPYING*', 'NOTICE*', 'AUTHORS*') + id="default_glob_patterns", + ), + pytest.param( + { + 'setup.cfg': DALS( + """ + [metadata] + license_files = + LICENSE* + """ + ), + 'LICENSE-ABC': "ABC license", + 'NOTICE-XYZ': "XYZ notice", + }, + ['LICENSE-ABC'], + ['NOTICE-XYZ'], + id="no_default_glob_patterns", + ), + pytest.param( + { + 'setup.cfg': DALS( + """ + [metadata] + license_files = + LICENSE-ABC + LICENSE* + """ + ), + 'LICENSE-ABC': "ABC license", + }, + ['LICENSE-ABC'], + [], + id="files_only_added_once", + ), + pytest.param( + { + 'setup.cfg': DALS( + """ + [metadata] + license_files = **/LICENSE + """ + ), + 'LICENSE': "ABC license", + 'LICENSE-OTHER': "Don't include", + 'vendor': {'LICENSE': "Vendor license"}, + }, + ['LICENSE', 'vendor/LICENSE'], + ['LICENSE-OTHER'], + id="recursive_glob", + ), + ], + ) + def test_setup_cfg_license_files( + self, tmpdir_cwd, env, files, incl_licenses, excl_licenses + ): + self._create_project() + path.build(files) + + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + + sources_text = Path(egg_info_dir, "SOURCES.txt").read_text(encoding="utf-8") + sources_lines = [line.strip() for line in sources_text.splitlines()] + + for lf in incl_licenses: + assert sources_lines.count(lf) == 1 + + for lf in excl_licenses: + assert sources_lines.count(lf) == 0 + + @pytest.mark.parametrize( + ('files', 'incl_licenses', 'excl_licenses'), + [ + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = + license_files = + """ + ), + 'LICENSE-ABC': "ABC license", + 'LICENSE-XYZ': "XYZ license", + }, + [], + ['LICENSE-ABC', 'LICENSE-XYZ'], + ), # both empty + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = + LICENSE-ABC + LICENSE-XYZ + """ + ), + 'LICENSE-ABC': "ABC license", + 'LICENSE-XYZ': "XYZ license", + # license_file is still singular + }, + [], + ['LICENSE-ABC', 'LICENSE-XYZ'], + ), + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = LICENSE-ABC + license_files = + LICENSE-XYZ + LICENSE-PQR + """ + ), + 'LICENSE-ABC': "ABC license", + 'LICENSE-PQR': "PQR license", + 'LICENSE-XYZ': "XYZ license", + }, + ['LICENSE-ABC', 'LICENSE-PQR', 'LICENSE-XYZ'], + [], + ), # combined + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = LICENSE-ABC + license_files = + LICENSE-ABC + LICENSE-XYZ + LICENSE-PQR + """ + ), + 'LICENSE-ABC': "ABC license", + 'LICENSE-PQR': "PQR license", + 'LICENSE-XYZ': "XYZ license", + # duplicate license + }, + ['LICENSE-ABC', 'LICENSE-PQR', 'LICENSE-XYZ'], + [], + ), + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = LICENSE-ABC + license_files = + LICENSE-XYZ + """ + ), + 'LICENSE-ABC': "ABC license", + 'LICENSE-PQR': "PQR license", + 'LICENSE-XYZ': "XYZ license", + # combined subset + }, + ['LICENSE-ABC', 'LICENSE-XYZ'], + ['LICENSE-PQR'], + ), + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = LICENSE-ABC + license_files = + LICENSE-XYZ + LICENSE-PQR + """ + ), + 'LICENSE-PQR': "Test license", + # with invalid licenses + }, + ['LICENSE-PQR'], + ['LICENSE-ABC', 'LICENSE-XYZ'], + ), + ( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = LICENSE-ABC + license_files = + LICENSE-PQR + LICENSE-XYZ + """ + ), + 'MANIFEST.in': "exclude LICENSE-ABC\nexclude LICENSE-PQR", + 'LICENSE-ABC': "ABC license", + 'LICENSE-PQR': "PQR license", + 'LICENSE-XYZ': "XYZ license", + # manifest is overwritten + }, + ['LICENSE-ABC', 'LICENSE-PQR', 'LICENSE-XYZ'], + [], + ), + pytest.param( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = LICENSE* + """ + ), + 'LICENSE-ABC': "ABC license", + 'NOTICE-XYZ': "XYZ notice", + }, + ['LICENSE-ABC'], + ['NOTICE-XYZ'], + id="no_default_glob_patterns", + ), + pytest.param( + { + 'setup.cfg': DALS( + """ + [metadata] + license_file = LICENSE* + license_files = + NOTICE* + """ + ), + 'LICENSE-ABC': "ABC license", + 'NOTICE-ABC': "ABC notice", + 'AUTHORS-ABC': "ABC authors", + }, + ['LICENSE-ABC', 'NOTICE-ABC'], + ['AUTHORS-ABC'], + id="combined_glob_patterrns", + ), + ], + ) + def test_setup_cfg_license_file_license_files( + self, tmpdir_cwd, env, files, incl_licenses, excl_licenses + ): + self._create_project() + path.build(files) + + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + + sources_text = Path(egg_info_dir, "SOURCES.txt").read_text(encoding="utf-8") + sources_lines = [line.strip() for line in sources_text.splitlines()] + + for lf in incl_licenses: + assert sources_lines.count(lf) == 1 + + for lf in excl_licenses: + assert sources_lines.count(lf) == 0 + + def test_license_file_attr_pkg_info(self, tmpdir_cwd, env): + """All matched license files should have a corresponding License-File.""" + self._create_project() + path.build({ + "setup.cfg": DALS( + """ + [metadata] + license_files = + NOTICE* + LICENSE* + **/LICENSE + """ + ), + "LICENSE-ABC": "ABC license", + "LICENSE-XYZ": "XYZ license", + "NOTICE": "included", + "IGNORE": "not include", + "vendor": {'LICENSE': "Vendor license"}, + }) + + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + with open(os.path.join(egg_info_dir, 'PKG-INFO'), encoding="utf-8") as fp: + pkg_info_lines = fp.read().split('\n') + license_file_lines = [ + line for line in pkg_info_lines if line.startswith('License-File:') + ] + + # Only 'NOTICE', LICENSE-ABC', and 'LICENSE-XYZ' should have been matched + # Also assert that order from license_files is keeped + assert len(license_file_lines) == 4 + assert "License-File: NOTICE" == license_file_lines[0] + assert "License-File: LICENSE-ABC" in license_file_lines[1:] + assert "License-File: LICENSE-XYZ" in license_file_lines[1:] + assert "License-File: vendor/LICENSE" in license_file_lines[3] + + def test_metadata_version(self, tmpdir_cwd, env): + """Make sure latest metadata version is used by default.""" + self._setup_script_with_requires("") + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + data_stream=1, + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + with open(os.path.join(egg_info_dir, 'PKG-INFO'), encoding="utf-8") as fp: + pkg_info_lines = fp.read().split('\n') + # Update metadata version if changed + assert self._extract_mv_version(pkg_info_lines) == (2, 4) + + def test_long_description_content_type(self, tmpdir_cwd, env): + # Test that specifying a `long_description_content_type` keyword arg to + # the `setup` function results in writing a `Description-Content-Type` + # line to the `PKG-INFO` file in the `.egg-info` + # directory. + # `Description-Content-Type` is described at + # https://github.com/pypa/python-packaging-user-guide/pull/258 + + self._setup_script_with_requires( + """long_description_content_type='text/markdown',""" + ) + environ = os.environ.copy().update( + HOME=env.paths['home'], + ) + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + data_stream=1, + env=environ, + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + with open(os.path.join(egg_info_dir, 'PKG-INFO'), encoding="utf-8") as fp: + pkg_info_lines = fp.read().split('\n') + expected_line = 'Description-Content-Type: text/markdown' + assert expected_line in pkg_info_lines + assert 'Metadata-Version: 2.4' in pkg_info_lines + + def test_long_description(self, tmpdir_cwd, env): + # Test that specifying `long_description` and `long_description_content_type` + # keyword args to the `setup` function results in writing + # the description in the message payload of the `PKG-INFO` file + # in the `.egg-info` directory. + self._setup_script_with_requires( + "long_description='This is a long description\\nover multiple lines'," + "long_description_content_type='text/markdown'," + ) + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + data_stream=1, + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + with open(os.path.join(egg_info_dir, 'PKG-INFO'), encoding="utf-8") as fp: + pkg_info_lines = fp.read().split('\n') + assert 'Metadata-Version: 2.4' in pkg_info_lines + assert '' == pkg_info_lines[-1] # last line should be empty + long_desc_lines = pkg_info_lines[pkg_info_lines.index('') :] + assert 'This is a long description' in long_desc_lines + assert 'over multiple lines' in long_desc_lines + + def test_project_urls(self, tmpdir_cwd, env): + # Test that specifying a `project_urls` dict to the `setup` + # function results in writing multiple `Project-URL` lines to + # the `PKG-INFO` file in the `.egg-info` + # directory. + # `Project-URL` is described at https://packaging.python.org + # /specifications/core-metadata/#project-url-multiple-use + + self._setup_script_with_requires( + """project_urls={ + 'Link One': 'https://example.com/one/', + 'Link Two': 'https://example.com/two/', + },""" + ) + environ = os.environ.copy().update( + HOME=env.paths['home'], + ) + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + data_stream=1, + env=environ, + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + with open(os.path.join(egg_info_dir, 'PKG-INFO'), encoding="utf-8") as fp: + pkg_info_lines = fp.read().split('\n') + expected_line = 'Project-URL: Link One, https://example.com/one/' + assert expected_line in pkg_info_lines + expected_line = 'Project-URL: Link Two, https://example.com/two/' + assert expected_line in pkg_info_lines + assert self._extract_mv_version(pkg_info_lines) >= (1, 2) + + def test_license(self, tmpdir_cwd, env): + """Test single line license.""" + self._setup_script_with_requires("license='MIT',") + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + data_stream=1, + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + with open(os.path.join(egg_info_dir, 'PKG-INFO'), encoding="utf-8") as fp: + pkg_info_lines = fp.read().split('\n') + assert 'License: MIT' in pkg_info_lines + + def test_license_escape(self, tmpdir_cwd, env): + """Test license is escaped correctly if longer than one line.""" + self._setup_script_with_requires( + "license='This is a long license text \\nover multiple lines'," + ) + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + data_stream=1, + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + with open(os.path.join(egg_info_dir, 'PKG-INFO'), encoding="utf-8") as fp: + pkg_info_lines = fp.read().split('\n') + + assert 'License: This is a long license text ' in pkg_info_lines + assert ' over multiple lines' in pkg_info_lines + assert 'text \n over multiple' in '\n'.join(pkg_info_lines) + + def test_python_requires_egg_info(self, tmpdir_cwd, env): + self._setup_script_with_requires("""python_requires='>=2.7.12',""") + environ = os.environ.copy().update( + HOME=env.paths['home'], + ) + environment.run_setup_py( + cmd=['egg_info'], + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + data_stream=1, + env=environ, + ) + egg_info_dir = os.path.join('.', 'foo.egg-info') + with open(os.path.join(egg_info_dir, 'PKG-INFO'), encoding="utf-8") as fp: + pkg_info_lines = fp.read().split('\n') + assert 'Requires-Python: >=2.7.12' in pkg_info_lines + assert self._extract_mv_version(pkg_info_lines) >= (1, 2) + + def test_manifest_maker_warning_suppression(self): + fixtures = [ + "standard file not found: should have one of foo.py, bar.py", + "standard file 'setup.py' not found", + ] + + for msg in fixtures: + assert manifest_maker._should_suppress_warning(msg) + + def test_egg_info_includes_setup_py(self, tmpdir_cwd): + self._create_project() + dist = Distribution({"name": "foo", "version": "0.0.1"}) + dist.script_name = "non_setup.py" + egg_info_instance = egg_info(dist) + egg_info_instance.finalize_options() + egg_info_instance.run() + + assert 'setup.py' in egg_info_instance.filelist.files + + with open(egg_info_instance.egg_info + "/SOURCES.txt", encoding="utf-8") as f: + sources = f.read().split('\n') + assert 'setup.py' in sources + + def _run_egg_info_command(self, tmpdir_cwd, env, cmd=None, output=None): + environ = os.environ.copy().update( + HOME=env.paths['home'], + ) + if cmd is None: + cmd = [ + 'egg_info', + ] + code, data = environment.run_setup_py( + cmd=cmd, + pypath=os.pathsep.join([env.paths['lib'], str(tmpdir_cwd)]), + data_stream=1, + env=environ, + ) + assert not code, data + + if output: + assert output in data + + def test_egg_info_tag_only_once(self, tmpdir_cwd, env): + self._create_project() + path.build({ + 'setup.cfg': DALS( + """ + [egg_info] + tag_build = dev + tag_date = 0 + tag_svn_revision = 0 + """ + ), + }) + self._run_egg_info_command(tmpdir_cwd, env) + egg_info_dir = os.path.join('.', 'foo.egg-info') + with open(os.path.join(egg_info_dir, 'PKG-INFO'), encoding="utf-8") as fp: + pkg_info_lines = fp.read().split('\n') + assert 'Version: 0.0.0.dev0' in pkg_info_lines + + +class TestWriteEntries: + def test_invalid_entry_point(self, tmpdir_cwd, env): + dist = Distribution({"name": "foo", "version": "0.0.1"}) + dist.entry_points = {"foo": "foo = invalid-identifier:foo"} + cmd = dist.get_command_obj("egg_info") + expected_msg = r"(Invalid object reference|Problems to parse)" + with pytest.raises((errors.OptionError, ValueError), match=expected_msg) as ex: + write_entries(cmd, "entry_points", "entry_points.txt") + assert "ensure entry-point follows the spec" in ex.value.args[0] + assert "invalid-identifier" in str(ex.value) + + def test_valid_entry_point(self, tmpdir_cwd, env): + dist = Distribution({"name": "foo", "version": "0.0.1"}) + dist.entry_points = { + "abc": "foo = bar:baz", + "def": ["faa = bor:boz"], + } + cmd = dist.get_command_obj("egg_info") + write_entries(cmd, "entry_points", "entry_points.txt") + content = Path("entry_points.txt").read_text(encoding="utf-8") + assert "[abc]\nfoo = bar:baz\n" in content + assert "[def]\nfaa = bor:boz\n" in content diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_extern.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_extern.py new file mode 100644 index 0000000000000000000000000000000000000000..d7eb3c62c190dacdd4a054d2934962be2f4ee860 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_extern.py @@ -0,0 +1,15 @@ +import importlib +import pickle + +import packaging + +from setuptools import Distribution + + +def test_reimport_extern(): + packaging2 = importlib.import_module(packaging.__name__) + assert packaging is packaging2 + + +def test_distribution_picklable(): + pickle.loads(pickle.dumps(Distribution())) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_find_packages.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_find_packages.py new file mode 100644 index 0000000000000000000000000000000000000000..9fd9f8f6637d13cb898fcd446a6b090323d02014 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_find_packages.py @@ -0,0 +1,218 @@ +"""Tests for automatic package discovery""" + +import os +import shutil +import tempfile + +import pytest + +from setuptools import find_namespace_packages, find_packages +from setuptools.discovery import FlatLayoutPackageFinder + +from .compat.py39 import os_helper + + +class TestFindPackages: + def setup_method(self, method): + self.dist_dir = tempfile.mkdtemp() + self._make_pkg_structure() + + def teardown_method(self, method): + shutil.rmtree(self.dist_dir) + + def _make_pkg_structure(self): + """Make basic package structure. + + dist/ + docs/ + conf.py + pkg/ + __pycache__/ + nspkg/ + mod.py + subpkg/ + assets/ + asset + __init__.py + setup.py + + """ + self.docs_dir = self._mkdir('docs', self.dist_dir) + self._touch('conf.py', self.docs_dir) + self.pkg_dir = self._mkdir('pkg', self.dist_dir) + self._mkdir('__pycache__', self.pkg_dir) + self.ns_pkg_dir = self._mkdir('nspkg', self.pkg_dir) + self._touch('mod.py', self.ns_pkg_dir) + self.sub_pkg_dir = self._mkdir('subpkg', self.pkg_dir) + self.asset_dir = self._mkdir('assets', self.sub_pkg_dir) + self._touch('asset', self.asset_dir) + self._touch('__init__.py', self.sub_pkg_dir) + self._touch('setup.py', self.dist_dir) + + def _mkdir(self, path, parent_dir=None): + if parent_dir: + path = os.path.join(parent_dir, path) + os.mkdir(path) + return path + + def _touch(self, path, dir_=None): + if dir_: + path = os.path.join(dir_, path) + open(path, 'wb').close() + return path + + def test_regular_package(self): + self._touch('__init__.py', self.pkg_dir) + packages = find_packages(self.dist_dir) + assert packages == ['pkg', 'pkg.subpkg'] + + def test_exclude(self): + self._touch('__init__.py', self.pkg_dir) + packages = find_packages(self.dist_dir, exclude=('pkg.*',)) + assert packages == ['pkg'] + + def test_exclude_recursive(self): + """ + Excluding a parent package should not exclude child packages as well. + """ + self._touch('__init__.py', self.pkg_dir) + self._touch('__init__.py', self.sub_pkg_dir) + packages = find_packages(self.dist_dir, exclude=('pkg',)) + assert packages == ['pkg.subpkg'] + + def test_include_excludes_other(self): + """ + If include is specified, other packages should be excluded. + """ + self._touch('__init__.py', self.pkg_dir) + alt_dir = self._mkdir('other_pkg', self.dist_dir) + self._touch('__init__.py', alt_dir) + packages = find_packages(self.dist_dir, include=['other_pkg']) + assert packages == ['other_pkg'] + + def test_dir_with_dot_is_skipped(self): + shutil.rmtree(os.path.join(self.dist_dir, 'pkg/subpkg/assets')) + data_dir = self._mkdir('some.data', self.pkg_dir) + self._touch('__init__.py', data_dir) + self._touch('file.dat', data_dir) + packages = find_packages(self.dist_dir) + assert 'pkg.some.data' not in packages + + def test_dir_with_packages_in_subdir_is_excluded(self): + """ + Ensure that a package in a non-package such as build/pkg/__init__.py + is excluded. + """ + build_dir = self._mkdir('build', self.dist_dir) + build_pkg_dir = self._mkdir('pkg', build_dir) + self._touch('__init__.py', build_pkg_dir) + packages = find_packages(self.dist_dir) + assert 'build.pkg' not in packages + + @pytest.mark.skipif(not os_helper.can_symlink(), reason='Symlink support required') + def test_symlinked_packages_are_included(self): + """ + A symbolically-linked directory should be treated like any other + directory when matched as a package. + + Create a link from lpkg -> pkg. + """ + self._touch('__init__.py', self.pkg_dir) + linked_pkg = os.path.join(self.dist_dir, 'lpkg') + os.symlink('pkg', linked_pkg) + assert os.path.isdir(linked_pkg) + packages = find_packages(self.dist_dir) + assert 'lpkg' in packages + + def _assert_packages(self, actual, expected): + assert set(actual) == set(expected) + + def test_pep420_ns_package(self): + packages = find_namespace_packages( + self.dist_dir, include=['pkg*'], exclude=['pkg.subpkg.assets'] + ) + self._assert_packages(packages, ['pkg', 'pkg.nspkg', 'pkg.subpkg']) + + def test_pep420_ns_package_no_includes(self): + packages = find_namespace_packages(self.dist_dir, exclude=['pkg.subpkg.assets']) + self._assert_packages(packages, ['docs', 'pkg', 'pkg.nspkg', 'pkg.subpkg']) + + def test_pep420_ns_package_no_includes_or_excludes(self): + packages = find_namespace_packages(self.dist_dir) + expected = ['docs', 'pkg', 'pkg.nspkg', 'pkg.subpkg', 'pkg.subpkg.assets'] + self._assert_packages(packages, expected) + + def test_regular_package_with_nested_pep420_ns_packages(self): + self._touch('__init__.py', self.pkg_dir) + packages = find_namespace_packages( + self.dist_dir, exclude=['docs', 'pkg.subpkg.assets'] + ) + self._assert_packages(packages, ['pkg', 'pkg.nspkg', 'pkg.subpkg']) + + def test_pep420_ns_package_no_non_package_dirs(self): + shutil.rmtree(self.docs_dir) + shutil.rmtree(os.path.join(self.dist_dir, 'pkg/subpkg/assets')) + packages = find_namespace_packages(self.dist_dir) + self._assert_packages(packages, ['pkg', 'pkg.nspkg', 'pkg.subpkg']) + + +class TestFlatLayoutPackageFinder: + EXAMPLES = { + "hidden-folders": ( + [".pkg/__init__.py", "pkg/__init__.py", "pkg/nested/file.txt"], + ["pkg", "pkg.nested"], + ), + "private-packages": ( + ["_pkg/__init__.py", "pkg/_private/__init__.py"], + ["pkg", "pkg._private"], + ), + "invalid-name": ( + ["invalid-pkg/__init__.py", "other.pkg/__init__.py", "yet,another/file.py"], + [], + ), + "docs": (["pkg/__init__.py", "docs/conf.py", "docs/readme.rst"], ["pkg"]), + "tests": ( + ["pkg/__init__.py", "tests/test_pkg.py", "tests/__init__.py"], + ["pkg"], + ), + "examples": ( + [ + "pkg/__init__.py", + "examples/__init__.py", + "examples/file.py", + "example/other_file.py", + # Sub-packages should always be fine + "pkg/example/__init__.py", + "pkg/examples/__init__.py", + ], + ["pkg", "pkg.examples", "pkg.example"], + ), + "tool-specific": ( + [ + "htmlcov/index.html", + "pkg/__init__.py", + "tasks/__init__.py", + "tasks/subpackage/__init__.py", + "fabfile/__init__.py", + "fabfile/subpackage/__init__.py", + # Sub-packages should always be fine + "pkg/tasks/__init__.py", + "pkg/fabfile/__init__.py", + ], + ["pkg", "pkg.tasks", "pkg.fabfile"], + ), + } + + @pytest.mark.parametrize("example", EXAMPLES.keys()) + def test_unwanted_directories_not_included(self, tmp_path, example): + files, expected_packages = self.EXAMPLES[example] + ensure_files(tmp_path, files) + found_packages = FlatLayoutPackageFinder.find(str(tmp_path)) + assert set(found_packages) == set(expected_packages) + + +def ensure_files(root_path, files): + for file in files: + path = root_path / file + path.parent.mkdir(parents=True, exist_ok=True) + path.touch() diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_find_py_modules.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_find_py_modules.py new file mode 100644 index 0000000000000000000000000000000000000000..8034b544294e5d30274bac82f24f93613120a0d4 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_find_py_modules.py @@ -0,0 +1,73 @@ +"""Tests for automatic discovery of modules""" + +import os + +import pytest + +from setuptools.discovery import FlatLayoutModuleFinder, ModuleFinder + +from .compat.py39 import os_helper +from .test_find_packages import ensure_files + + +class TestModuleFinder: + def find(self, path, *args, **kwargs): + return set(ModuleFinder.find(str(path), *args, **kwargs)) + + EXAMPLES = { + # circumstance: (files, kwargs, expected_modules) + "simple_folder": ( + ["file.py", "other.py"], + {}, # kwargs + ["file", "other"], + ), + "exclude": ( + ["file.py", "other.py"], + {"exclude": ["f*"]}, + ["other"], + ), + "include": ( + ["file.py", "fole.py", "other.py"], + {"include": ["f*"], "exclude": ["fo*"]}, + ["file"], + ), + "invalid-name": (["my-file.py", "other.file.py"], {}, []), + } + + @pytest.mark.parametrize("example", EXAMPLES.keys()) + def test_finder(self, tmp_path, example): + files, kwargs, expected_modules = self.EXAMPLES[example] + ensure_files(tmp_path, files) + assert self.find(tmp_path, **kwargs) == set(expected_modules) + + @pytest.mark.skipif(not os_helper.can_symlink(), reason='Symlink support required') + def test_symlinked_packages_are_included(self, tmp_path): + src = "_myfiles/file.py" + ensure_files(tmp_path, [src]) + os.symlink(tmp_path / src, tmp_path / "link.py") + assert self.find(tmp_path) == {"link"} + + +class TestFlatLayoutModuleFinder: + def find(self, path, *args, **kwargs): + return set(FlatLayoutModuleFinder.find(str(path))) + + EXAMPLES = { + # circumstance: (files, expected_modules) + "hidden-files": ([".module.py"], []), + "private-modules": (["_module.py"], []), + "common-names": ( + ["setup.py", "conftest.py", "test.py", "tests.py", "example.py", "mod.py"], + ["mod"], + ), + "tool-specific": ( + ["tasks.py", "fabfile.py", "noxfile.py", "dodo.py", "manage.py", "mod.py"], + ["mod"], + ), + } + + @pytest.mark.parametrize("example", EXAMPLES.keys()) + def test_unwanted_files_not_included(self, tmp_path, example): + files, expected_modules = self.EXAMPLES[example] + ensure_files(tmp_path, files) + assert self.find(tmp_path) == set(expected_modules) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_glob.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_glob.py new file mode 100644 index 0000000000000000000000000000000000000000..8d225a44610163c7d56d65b07c06f0f598ccfe84 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_glob.py @@ -0,0 +1,45 @@ +import pytest +from jaraco import path + +from setuptools.glob import glob + + +@pytest.mark.parametrize( + ('tree', 'pattern', 'matches'), + ( + ('', b'', []), + ('', '', []), + ( + """ + appveyor.yml + CHANGES.rst + LICENSE + MANIFEST.in + pyproject.toml + README.rst + setup.cfg + setup.py + """, + '*.rst', + ('CHANGES.rst', 'README.rst'), + ), + ( + """ + appveyor.yml + CHANGES.rst + LICENSE + MANIFEST.in + pyproject.toml + README.rst + setup.cfg + setup.py + """, + b'*.rst', + (b'CHANGES.rst', b'README.rst'), + ), + ), +) +def test_glob(monkeypatch, tmpdir, tree, pattern, matches): + monkeypatch.chdir(tmpdir) + path.build({name: '' for name in tree.split()}) + assert list(sorted(glob(pattern))) == list(sorted(matches)) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_install_scripts.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_install_scripts.py new file mode 100644 index 0000000000000000000000000000000000000000..e62a6b7f318df2da0cf29e53c41f74e5525e78ac --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_install_scripts.py @@ -0,0 +1,89 @@ +"""install_scripts tests""" + +import sys + +import pytest + +from setuptools.command.install_scripts import install_scripts +from setuptools.dist import Distribution + +from . import contexts + + +class TestInstallScripts: + settings = dict( + name='foo', + entry_points={'console_scripts': ['foo=foo:foo']}, + version='0.0', + ) + unix_exe = '/usr/dummy-test-path/local/bin/python' + unix_spaces_exe = '/usr/bin/env dummy-test-python' + win32_exe = 'C:\\Dummy Test Path\\Program Files\\Python 3.6\\python.exe' + + def _run_install_scripts(self, install_dir, executable=None): + dist = Distribution(self.settings) + dist.script_name = 'setup.py' + cmd = install_scripts(dist) + cmd.install_dir = install_dir + if executable is not None: + bs = cmd.get_finalized_command('build_scripts') + bs.executable = executable + cmd.ensure_finalized() + with contexts.quiet(): + cmd.run() + + @pytest.mark.skipif(sys.platform == 'win32', reason='non-Windows only') + def test_sys_executable_escaping_unix(self, tmpdir, monkeypatch): + """ + Ensure that shebang is not quoted on Unix when getting the Python exe + from sys.executable. + """ + expected = f'#!{self.unix_exe}\n' + monkeypatch.setattr('sys.executable', self.unix_exe) + with tmpdir.as_cwd(): + self._run_install_scripts(str(tmpdir)) + with open(str(tmpdir.join('foo')), 'r', encoding="utf-8") as f: + actual = f.readline() + assert actual == expected + + @pytest.mark.skipif(sys.platform != 'win32', reason='Windows only') + def test_sys_executable_escaping_win32(self, tmpdir, monkeypatch): + """ + Ensure that shebang is quoted on Windows when getting the Python exe + from sys.executable and it contains a space. + """ + expected = f'#!"{self.win32_exe}"\n' + monkeypatch.setattr('sys.executable', self.win32_exe) + with tmpdir.as_cwd(): + self._run_install_scripts(str(tmpdir)) + with open(str(tmpdir.join('foo-script.py')), 'r', encoding="utf-8") as f: + actual = f.readline() + assert actual == expected + + @pytest.mark.skipif(sys.platform == 'win32', reason='non-Windows only') + def test_executable_with_spaces_escaping_unix(self, tmpdir): + """ + Ensure that shebang on Unix is not quoted, even when + a value with spaces + is specified using --executable. + """ + expected = f'#!{self.unix_spaces_exe}\n' + with tmpdir.as_cwd(): + self._run_install_scripts(str(tmpdir), self.unix_spaces_exe) + with open(str(tmpdir.join('foo')), 'r', encoding="utf-8") as f: + actual = f.readline() + assert actual == expected + + @pytest.mark.skipif(sys.platform != 'win32', reason='Windows only') + def test_executable_arg_escaping_win32(self, tmpdir): + """ + Ensure that shebang on Windows is quoted when + getting a path with spaces + from --executable, that is itself properly quoted. + """ + expected = f'#!"{self.win32_exe}"\n' + with tmpdir.as_cwd(): + self._run_install_scripts(str(tmpdir), '"' + self.win32_exe + '"') + with open(str(tmpdir.join('foo-script.py')), 'r', encoding="utf-8") as f: + actual = f.readline() + assert actual == expected diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_logging.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_logging.py new file mode 100644 index 0000000000000000000000000000000000000000..ea58001e93d8e4bcbd50bfd49303324d71858d16 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_logging.py @@ -0,0 +1,76 @@ +import functools +import inspect +import logging +import sys + +import pytest + +IS_PYPY = '__pypy__' in sys.builtin_module_names + + +setup_py = """\ +from setuptools import setup + +setup( + name="test_logging", + version="0.0" +) +""" + + +@pytest.mark.parametrize( + ('flag', 'expected_level'), [("--dry-run", "INFO"), ("--verbose", "DEBUG")] +) +def test_verbosity_level(tmp_path, monkeypatch, flag, expected_level): + """Make sure the correct verbosity level is set (issue #3038)""" + import setuptools # noqa: F401 # import setuptools to monkeypatch distutils + + import distutils # <- load distutils after all the patches take place + + logger = logging.Logger(__name__) + monkeypatch.setattr(logging, "root", logger) + unset_log_level = logger.getEffectiveLevel() + assert logging.getLevelName(unset_log_level) == "NOTSET" + + setup_script = tmp_path / "setup.py" + setup_script.write_text(setup_py, encoding="utf-8") + dist = distutils.core.run_setup(setup_script, stop_after="init") + dist.script_args = [flag, "sdist"] + dist.parse_command_line() # <- where the log level is set + log_level = logger.getEffectiveLevel() + log_level_name = logging.getLevelName(log_level) + assert log_level_name == expected_level + + +def flaky_on_pypy(func): + @functools.wraps(func) + def _func(): + try: + func() + except AssertionError: # pragma: no cover + if IS_PYPY: + msg = "Flaky monkeypatch on PyPy (#4124)" + pytest.xfail(f"{msg}. Original discussion in #3707, #3709.") + raise + + return _func + + +@flaky_on_pypy +def test_patching_does_not_cause_problems(): + # Ensure `dist.log` is only patched if necessary + + import _distutils_hack + + import setuptools.logging + + from distutils import dist + + setuptools.logging.configure() + + if _distutils_hack.enabled(): + # Modern logging infra, no problematic patching. + assert dist.__file__ is None or "setuptools" in dist.__file__ + assert isinstance(dist.log, logging.Logger) + else: + assert inspect.ismodule(dist.log) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_manifest.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_manifest.py new file mode 100644 index 0000000000000000000000000000000000000000..903a528db0cc2bba27bbcef24aa1c59dc4156528 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_manifest.py @@ -0,0 +1,622 @@ +"""sdist tests""" + +from __future__ import annotations + +import contextlib +import io +import itertools +import logging +import os +import shutil +import sys +import tempfile + +import pytest + +from setuptools.command.egg_info import FileList, egg_info, translate_pattern +from setuptools.dist import Distribution +from setuptools.tests.textwrap import DALS + +from distutils import log +from distutils.errors import DistutilsTemplateError + +IS_PYPY = '__pypy__' in sys.builtin_module_names + + +def make_local_path(s): + """Converts '/' in a string to os.sep""" + return s.replace('/', os.sep) + + +SETUP_ATTRS = { + 'name': 'app', + 'version': '0.0', + 'packages': ['app'], +} + +SETUP_PY = f"""\ +from setuptools import setup + +setup(**{SETUP_ATTRS!r}) +""" + + +@contextlib.contextmanager +def quiet(): + old_stdout, old_stderr = sys.stdout, sys.stderr + sys.stdout, sys.stderr = io.StringIO(), io.StringIO() + try: + yield + finally: + sys.stdout, sys.stderr = old_stdout, old_stderr + + +def touch(filename): + open(filename, 'wb').close() + + +# The set of files always in the manifest, including all files in the +# .egg-info directory +default_files = frozenset( + map( + make_local_path, + [ + 'README.rst', + 'MANIFEST.in', + 'setup.py', + 'app.egg-info/PKG-INFO', + 'app.egg-info/SOURCES.txt', + 'app.egg-info/dependency_links.txt', + 'app.egg-info/top_level.txt', + 'app/__init__.py', + ], + ) +) + + +translate_specs: list[tuple[str, list[str], list[str]]] = [ + ('foo', ['foo'], ['bar', 'foobar']), + ('foo/bar', ['foo/bar'], ['foo/bar/baz', './foo/bar', 'foo']), + # Glob matching + ('*.txt', ['foo.txt', 'bar.txt'], ['foo/foo.txt']), + ('dir/*.txt', ['dir/foo.txt', 'dir/bar.txt', 'dir/.txt'], ['notdir/foo.txt']), + ('*/*.py', ['bin/start.py'], []), + ('docs/page-?.txt', ['docs/page-9.txt'], ['docs/page-10.txt']), + # Globstars change what they mean depending upon where they are + ( + 'foo/**/bar', + ['foo/bing/bar', 'foo/bing/bang/bar', 'foo/bar'], + ['foo/abar'], + ), + ( + 'foo/**', + ['foo/bar/bing.py', 'foo/x'], + ['/foo/x'], + ), + ( + '**', + ['x', 'abc/xyz', '@nything'], + [], + ), + # Character classes + ( + 'pre[one]post', + ['preopost', 'prenpost', 'preepost'], + ['prepost', 'preonepost'], + ), + ( + 'hello[!one]world', + ['helloxworld', 'helloyworld'], + ['hellooworld', 'helloworld', 'hellooneworld'], + ), + ( + '[]one].txt', + ['o.txt', '].txt', 'e.txt'], + ['one].txt'], + ), + ( + 'foo[!]one]bar', + ['fooybar'], + ['foo]bar', 'fooobar', 'fooebar'], + ), +] +""" +A spec of inputs for 'translate_pattern' and matches and mismatches +for that input. +""" + +match_params = itertools.chain.from_iterable( + zip(itertools.repeat(pattern), matches) + for pattern, matches, mismatches in translate_specs +) + + +@pytest.fixture(params=match_params) +def pattern_match(request): + return map(make_local_path, request.param) + + +mismatch_params = itertools.chain.from_iterable( + zip(itertools.repeat(pattern), mismatches) + for pattern, matches, mismatches in translate_specs +) + + +@pytest.fixture(params=mismatch_params) +def pattern_mismatch(request): + return map(make_local_path, request.param) + + +def test_translated_pattern_match(pattern_match): + pattern, target = pattern_match + assert translate_pattern(pattern).match(target) + + +def test_translated_pattern_mismatch(pattern_mismatch): + pattern, target = pattern_mismatch + assert not translate_pattern(pattern).match(target) + + +class TempDirTestCase: + def setup_method(self, method): + self.temp_dir = tempfile.mkdtemp() + self.old_cwd = os.getcwd() + os.chdir(self.temp_dir) + + def teardown_method(self, method): + os.chdir(self.old_cwd) + shutil.rmtree(self.temp_dir) + + +class TestManifestTest(TempDirTestCase): + def setup_method(self, method): + super().setup_method(method) + + f = open(os.path.join(self.temp_dir, 'setup.py'), 'w', encoding="utf-8") + f.write(SETUP_PY) + f.close() + """ + Create a file tree like: + - LICENSE + - README.rst + - testing.rst + - .hidden.rst + - app/ + - __init__.py + - a.txt + - b.txt + - c.rst + - static/ + - app.js + - app.js.map + - app.css + - app.css.map + """ + + for fname in ['README.rst', '.hidden.rst', 'testing.rst', 'LICENSE']: + touch(os.path.join(self.temp_dir, fname)) + + # Set up the rest of the test package + test_pkg = os.path.join(self.temp_dir, 'app') + os.mkdir(test_pkg) + for fname in ['__init__.py', 'a.txt', 'b.txt', 'c.rst']: + touch(os.path.join(test_pkg, fname)) + + # Some compiled front-end assets to include + static = os.path.join(test_pkg, 'static') + os.mkdir(static) + for fname in ['app.js', 'app.js.map', 'app.css', 'app.css.map']: + touch(os.path.join(static, fname)) + + def make_manifest(self, contents): + """Write a MANIFEST.in.""" + manifest = os.path.join(self.temp_dir, 'MANIFEST.in') + with open(manifest, 'w', encoding="utf-8") as f: + f.write(DALS(contents)) + + def get_files(self): + """Run egg_info and get all the files to include, as a set""" + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'setup.py' + cmd = egg_info(dist) + cmd.ensure_finalized() + + cmd.run() + + return set(cmd.filelist.files) + + def test_no_manifest(self): + """Check a missing MANIFEST.in includes only the standard files.""" + assert (default_files - set(['MANIFEST.in'])) == self.get_files() + + def test_empty_files(self): + """Check an empty MANIFEST.in includes only the standard files.""" + self.make_manifest("") + assert default_files == self.get_files() + + def test_include(self): + """Include extra rst files in the project root.""" + self.make_manifest("include *.rst") + files = default_files | set(['testing.rst', '.hidden.rst']) + assert files == self.get_files() + + def test_exclude(self): + """Include everything in app/ except the text files""" + ml = make_local_path + self.make_manifest( + """ + include app/* + exclude app/*.txt + """ + ) + files = default_files | set([ml('app/c.rst')]) + assert files == self.get_files() + + def test_include_multiple(self): + """Include with multiple patterns.""" + ml = make_local_path + self.make_manifest("include app/*.txt app/static/*") + files = default_files | set([ + ml('app/a.txt'), + ml('app/b.txt'), + ml('app/static/app.js'), + ml('app/static/app.js.map'), + ml('app/static/app.css'), + ml('app/static/app.css.map'), + ]) + assert files == self.get_files() + + def test_graft(self): + """Include the whole app/static/ directory.""" + ml = make_local_path + self.make_manifest("graft app/static") + files = default_files | set([ + ml('app/static/app.js'), + ml('app/static/app.js.map'), + ml('app/static/app.css'), + ml('app/static/app.css.map'), + ]) + assert files == self.get_files() + + def test_graft_glob_syntax(self): + """Include the whole app/static/ directory.""" + ml = make_local_path + self.make_manifest("graft */static") + files = default_files | set([ + ml('app/static/app.js'), + ml('app/static/app.js.map'), + ml('app/static/app.css'), + ml('app/static/app.css.map'), + ]) + assert files == self.get_files() + + def test_graft_global_exclude(self): + """Exclude all *.map files in the project.""" + ml = make_local_path + self.make_manifest( + """ + graft app/static + global-exclude *.map + """ + ) + files = default_files | set([ml('app/static/app.js'), ml('app/static/app.css')]) + assert files == self.get_files() + + def test_global_include(self): + """Include all *.rst, *.js, and *.css files in the whole tree.""" + ml = make_local_path + self.make_manifest( + """ + global-include *.rst *.js *.css + """ + ) + files = default_files | set([ + '.hidden.rst', + 'testing.rst', + ml('app/c.rst'), + ml('app/static/app.js'), + ml('app/static/app.css'), + ]) + assert files == self.get_files() + + def test_graft_prune(self): + """Include all files in app/, except for the whole app/static/ dir.""" + ml = make_local_path + self.make_manifest( + """ + graft app + prune app/static + """ + ) + files = default_files | set([ml('app/a.txt'), ml('app/b.txt'), ml('app/c.rst')]) + assert files == self.get_files() + + +class TestFileListTest(TempDirTestCase): + """ + A copy of the relevant bits of distutils/tests/test_filelist.py, + to ensure setuptools' version of FileList keeps parity with distutils. + """ + + @pytest.fixture(autouse=os.getenv("SETUPTOOLS_USE_DISTUTILS") == "stdlib") + def _compat_record_logs(self, monkeypatch, caplog): + """Account for stdlib compatibility""" + + def _log(_logger, level, msg, args): + exc = sys.exc_info() + rec = logging.LogRecord("distutils", level, "", 0, msg, args, exc) + caplog.records.append(rec) + + monkeypatch.setattr(log.Log, "_log", _log) + + def get_records(self, caplog, *levels): + return [r for r in caplog.records if r.levelno in levels] + + def assertNoWarnings(self, caplog): + assert self.get_records(caplog, log.WARN) == [] + caplog.clear() + + def assertWarnings(self, caplog): + if IS_PYPY and not caplog.records: + pytest.xfail("caplog checks may not work well in PyPy") + else: + assert len(self.get_records(caplog, log.WARN)) > 0 + caplog.clear() + + def make_files(self, files): + for file in files: + file = os.path.join(self.temp_dir, file) + dirname, _basename = os.path.split(file) + os.makedirs(dirname, exist_ok=True) + touch(file) + + def test_process_template_line(self): + # testing all MANIFEST.in template patterns + file_list = FileList() + ml = make_local_path + + # simulated file list + self.make_files([ + 'foo.tmp', + 'ok', + 'xo', + 'four.txt', + 'buildout.cfg', + # filelist does not filter out VCS directories, + # it's sdist that does + ml('.hg/last-message.txt'), + ml('global/one.txt'), + ml('global/two.txt'), + ml('global/files.x'), + ml('global/here.tmp'), + ml('f/o/f.oo'), + ml('dir/graft-one'), + ml('dir/dir2/graft2'), + ml('dir3/ok'), + ml('dir3/sub/ok.txt'), + ]) + + MANIFEST_IN = DALS( + """\ + include ok + include xo + exclude xo + include foo.tmp + include buildout.cfg + global-include *.x + global-include *.txt + global-exclude *.tmp + recursive-include f *.oo + recursive-exclude global *.x + graft dir + prune dir3 + """ + ) + + for line in MANIFEST_IN.split('\n'): + if not line: + continue + file_list.process_template_line(line) + + wanted = [ + 'buildout.cfg', + 'four.txt', + 'ok', + ml('.hg/last-message.txt'), + ml('dir/graft-one'), + ml('dir/dir2/graft2'), + ml('f/o/f.oo'), + ml('global/one.txt'), + ml('global/two.txt'), + ] + + file_list.sort() + assert file_list.files == wanted + + def test_exclude_pattern(self): + # return False if no match + file_list = FileList() + assert not file_list.exclude_pattern('*.py') + + # return True if files match + file_list = FileList() + file_list.files = ['a.py', 'b.py'] + assert file_list.exclude_pattern('*.py') + + # test excludes + file_list = FileList() + file_list.files = ['a.py', 'a.txt'] + file_list.exclude_pattern('*.py') + file_list.sort() + assert file_list.files == ['a.txt'] + + def test_include_pattern(self): + # return False if no match + file_list = FileList() + self.make_files([]) + assert not file_list.include_pattern('*.py') + + # return True if files match + file_list = FileList() + self.make_files(['a.py', 'b.txt']) + assert file_list.include_pattern('*.py') + + # test * matches all files + file_list = FileList() + self.make_files(['a.py', 'b.txt']) + file_list.include_pattern('*') + file_list.sort() + assert file_list.files == ['a.py', 'b.txt'] + + def test_process_template_line_invalid(self): + # invalid lines + file_list = FileList() + for action in ( + 'include', + 'exclude', + 'global-include', + 'global-exclude', + 'recursive-include', + 'recursive-exclude', + 'graft', + 'prune', + 'blarg', + ): + with pytest.raises(DistutilsTemplateError): + file_list.process_template_line(action) + + def test_include(self, caplog): + caplog.set_level(logging.DEBUG) + ml = make_local_path + # include + file_list = FileList() + self.make_files(['a.py', 'b.txt', ml('d/c.py')]) + + file_list.process_template_line('include *.py') + file_list.sort() + assert file_list.files == ['a.py'] + self.assertNoWarnings(caplog) + + file_list.process_template_line('include *.rb') + file_list.sort() + assert file_list.files == ['a.py'] + self.assertWarnings(caplog) + + def test_exclude(self, caplog): + caplog.set_level(logging.DEBUG) + ml = make_local_path + # exclude + file_list = FileList() + file_list.files = ['a.py', 'b.txt', ml('d/c.py')] + + file_list.process_template_line('exclude *.py') + file_list.sort() + assert file_list.files == ['b.txt', ml('d/c.py')] + self.assertNoWarnings(caplog) + + file_list.process_template_line('exclude *.rb') + file_list.sort() + assert file_list.files == ['b.txt', ml('d/c.py')] + self.assertWarnings(caplog) + + def test_global_include(self, caplog): + caplog.set_level(logging.DEBUG) + ml = make_local_path + # global-include + file_list = FileList() + self.make_files(['a.py', 'b.txt', ml('d/c.py')]) + + file_list.process_template_line('global-include *.py') + file_list.sort() + assert file_list.files == ['a.py', ml('d/c.py')] + self.assertNoWarnings(caplog) + + file_list.process_template_line('global-include *.rb') + file_list.sort() + assert file_list.files == ['a.py', ml('d/c.py')] + self.assertWarnings(caplog) + + def test_global_exclude(self, caplog): + caplog.set_level(logging.DEBUG) + ml = make_local_path + # global-exclude + file_list = FileList() + file_list.files = ['a.py', 'b.txt', ml('d/c.py')] + + file_list.process_template_line('global-exclude *.py') + file_list.sort() + assert file_list.files == ['b.txt'] + self.assertNoWarnings(caplog) + + file_list.process_template_line('global-exclude *.rb') + file_list.sort() + assert file_list.files == ['b.txt'] + self.assertWarnings(caplog) + + def test_recursive_include(self, caplog): + caplog.set_level(logging.DEBUG) + ml = make_local_path + # recursive-include + file_list = FileList() + self.make_files(['a.py', ml('d/b.py'), ml('d/c.txt'), ml('d/d/e.py')]) + + file_list.process_template_line('recursive-include d *.py') + file_list.sort() + assert file_list.files == [ml('d/b.py'), ml('d/d/e.py')] + self.assertNoWarnings(caplog) + + file_list.process_template_line('recursive-include e *.py') + file_list.sort() + assert file_list.files == [ml('d/b.py'), ml('d/d/e.py')] + self.assertWarnings(caplog) + + def test_recursive_exclude(self, caplog): + caplog.set_level(logging.DEBUG) + ml = make_local_path + # recursive-exclude + file_list = FileList() + file_list.files = ['a.py', ml('d/b.py'), ml('d/c.txt'), ml('d/d/e.py')] + + file_list.process_template_line('recursive-exclude d *.py') + file_list.sort() + assert file_list.files == ['a.py', ml('d/c.txt')] + self.assertNoWarnings(caplog) + + file_list.process_template_line('recursive-exclude e *.py') + file_list.sort() + assert file_list.files == ['a.py', ml('d/c.txt')] + self.assertWarnings(caplog) + + def test_graft(self, caplog): + caplog.set_level(logging.DEBUG) + ml = make_local_path + # graft + file_list = FileList() + self.make_files(['a.py', ml('d/b.py'), ml('d/d/e.py'), ml('f/f.py')]) + + file_list.process_template_line('graft d') + file_list.sort() + assert file_list.files == [ml('d/b.py'), ml('d/d/e.py')] + self.assertNoWarnings(caplog) + + file_list.process_template_line('graft e') + file_list.sort() + assert file_list.files == [ml('d/b.py'), ml('d/d/e.py')] + self.assertWarnings(caplog) + + def test_prune(self, caplog): + caplog.set_level(logging.DEBUG) + ml = make_local_path + # prune + file_list = FileList() + file_list.files = ['a.py', ml('d/b.py'), ml('d/d/e.py'), ml('f/f.py')] + + file_list.process_template_line('prune d') + file_list.sort() + assert file_list.files == ['a.py', ml('f/f.py')] + self.assertNoWarnings(caplog) + + file_list.process_template_line('prune e') + file_list.sort() + assert file_list.files == ['a.py', ml('f/f.py')] + self.assertWarnings(caplog) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_namespaces.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_namespaces.py new file mode 100644 index 0000000000000000000000000000000000000000..a0f4120bf7900b2118cc066034e036ab7af1798b --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_namespaces.py @@ -0,0 +1,138 @@ +import subprocess +import sys + +from setuptools._path import paths_on_pythonpath + +from . import namespaces + + +class TestNamespaces: + def test_mixed_site_and_non_site(self, tmpdir): + """ + Installing two packages sharing the same namespace, one installed + to a site dir and the other installed just to a path on PYTHONPATH + should leave the namespace in tact and both packages reachable by + import. + """ + pkg_A = namespaces.build_namespace_package(tmpdir, 'myns.pkgA') + pkg_B = namespaces.build_namespace_package(tmpdir, 'myns.pkgB') + site_packages = tmpdir / 'site-packages' + path_packages = tmpdir / 'path-packages' + targets = site_packages, path_packages + # use pip to install to the target directory + install_cmd = [ + sys.executable, + '-m', + 'pip.__main__', + 'install', + str(pkg_A), + '-t', + str(site_packages), + ] + subprocess.check_call(install_cmd) + namespaces.make_site_dir(site_packages) + install_cmd = [ + sys.executable, + '-m', + 'pip.__main__', + 'install', + str(pkg_B), + '-t', + str(path_packages), + ] + subprocess.check_call(install_cmd) + try_import = [ + sys.executable, + '-c', + 'import myns.pkgA; import myns.pkgB', + ] + with paths_on_pythonpath(map(str, targets)): + subprocess.check_call(try_import) + + def test_pkg_resources_import(self, tmpdir): + """ + Ensure that a namespace package doesn't break on import + of pkg_resources. + """ + pkg = namespaces.build_namespace_package(tmpdir, 'myns.pkgA') + target = tmpdir / 'packages' + target.mkdir() + install_cmd = [ + sys.executable, + '-m', + 'pip', + 'install', + '-t', + str(target), + str(pkg), + ] + with paths_on_pythonpath([str(target)]): + subprocess.check_call(install_cmd) + namespaces.make_site_dir(target) + try_import = [ + sys.executable, + '-c', + 'import pkg_resources', + ] + with paths_on_pythonpath([str(target)]): + subprocess.check_call(try_import) + + def test_namespace_package_installed_and_cwd(self, tmpdir): + """ + Installing a namespace packages but also having it in the current + working directory, only one version should take precedence. + """ + pkg_A = namespaces.build_namespace_package(tmpdir, 'myns.pkgA') + target = tmpdir / 'packages' + # use pip to install to the target directory + install_cmd = [ + sys.executable, + '-m', + 'pip.__main__', + 'install', + str(pkg_A), + '-t', + str(target), + ] + subprocess.check_call(install_cmd) + namespaces.make_site_dir(target) + + # ensure that package imports and pkg_resources imports + pkg_resources_imp = [ + sys.executable, + '-c', + 'import pkg_resources; import myns.pkgA', + ] + with paths_on_pythonpath([str(target)]): + subprocess.check_call(pkg_resources_imp, cwd=str(pkg_A)) + + def test_packages_in_the_same_namespace_installed_and_cwd(self, tmpdir): + """ + Installing one namespace package and also have another in the same + namespace in the current working directory, both of them must be + importable. + """ + pkg_A = namespaces.build_namespace_package(tmpdir, 'myns.pkgA') + pkg_B = namespaces.build_namespace_package(tmpdir, 'myns.pkgB') + target = tmpdir / 'packages' + # use pip to install to the target directory + install_cmd = [ + sys.executable, + '-m', + 'pip.__main__', + 'install', + str(pkg_A), + '-t', + str(target), + ] + subprocess.check_call(install_cmd) + namespaces.make_site_dir(target) + + # ensure that all packages import and pkg_resources imports + pkg_resources_imp = [ + sys.executable, + '-c', + 'import pkg_resources; import myns.pkgA; import myns.pkgB', + ] + with paths_on_pythonpath([str(target)]): + subprocess.check_call(pkg_resources_imp, cwd=str(pkg_B)) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_scripts.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_scripts.py new file mode 100644 index 0000000000000000000000000000000000000000..8641f7b639161525e2fff3100744d7fa55d9d718 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_scripts.py @@ -0,0 +1,12 @@ +from setuptools import _scripts + + +class TestWindowsScriptWriter: + def test_header(self): + hdr = _scripts.WindowsScriptWriter.get_header('') + assert hdr.startswith('#!') + assert hdr.endswith('\n') + hdr = hdr.lstrip('#!') + hdr = hdr.rstrip('\n') + # header should not start with an escaped quote + assert not hdr.startswith('\\"') diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_sdist.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_sdist.py new file mode 100644 index 0000000000000000000000000000000000000000..5b435fe111346d026ba20bbbf68994282e8b64c7 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_sdist.py @@ -0,0 +1,980 @@ +"""sdist tests""" + +import contextlib +import io +import logging +import os +import pathlib +import sys +import tarfile +import tempfile +import unicodedata +from inspect import cleandoc +from pathlib import Path +from unittest import mock + +import jaraco.path +import pytest + +from setuptools import Command, SetuptoolsDeprecationWarning +from setuptools._importlib import metadata +from setuptools.command.egg_info import manifest_maker +from setuptools.command.sdist import sdist +from setuptools.dist import Distribution +from setuptools.extension import Extension +from setuptools.tests import fail_on_ascii + +from .text import Filenames + +import distutils +from distutils.core import run_setup + +SETUP_ATTRS = { + 'name': 'sdist_test', + 'version': '0.0', + 'packages': ['sdist_test'], + 'package_data': {'sdist_test': ['*.txt']}, + 'data_files': [("data", [os.path.join("d", "e.dat")])], +} + +SETUP_PY = f"""\ +from setuptools import setup + +setup(**{SETUP_ATTRS!r}) +""" + +EXTENSION = Extension( + name="sdist_test.f", + sources=[os.path.join("sdist_test", "f.c")], + depends=[os.path.join("sdist_test", "f.h")], +) +EXTENSION_SOURCES = EXTENSION.sources + EXTENSION.depends + + +@contextlib.contextmanager +def quiet(): + old_stdout, old_stderr = sys.stdout, sys.stderr + sys.stdout, sys.stderr = io.StringIO(), io.StringIO() + try: + yield + finally: + sys.stdout, sys.stderr = old_stdout, old_stderr + + +# Convert to POSIX path +def posix(path): + if not isinstance(path, str): + return path.replace(os.sep.encode('ascii'), b'/') + else: + return path.replace(os.sep, '/') + + +# HFS Plus uses decomposed UTF-8 +def decompose(path): + if isinstance(path, str): + return unicodedata.normalize('NFD', path) + try: + path = path.decode('utf-8') + path = unicodedata.normalize('NFD', path) + path = path.encode('utf-8') + except UnicodeError: + pass # Not UTF-8 + return path + + +def read_all_bytes(filename): + with open(filename, 'rb') as fp: + return fp.read() + + +def latin1_fail(): + try: + desc, filename = tempfile.mkstemp(suffix=Filenames.latin_1) + os.close(desc) + os.remove(filename) + except Exception: + return True + + +fail_on_latin1_encoded_filenames = pytest.mark.xfail( + latin1_fail(), + reason="System does not support latin-1 filenames", +) + + +skip_under_xdist = pytest.mark.skipif( + "os.environ.get('PYTEST_XDIST_WORKER')", + reason="pytest-dev/pytest-xdist#843", +) +skip_under_stdlib_distutils = pytest.mark.skipif( + not distutils.__package__.startswith('setuptools'), + reason="the test is not supported with stdlib distutils", +) + + +def touch(path): + open(path, 'wb').close() + return path + + +def symlink_or_skip_test(src, dst): + try: + os.symlink(src, dst) + except (OSError, NotImplementedError): + pytest.skip("symlink not supported in OS") + return None + return dst + + +class TestSdistTest: + @pytest.fixture(autouse=True) + def source_dir(self, tmpdir): + tmpdir = tmpdir / "project_root" + tmpdir.mkdir() + + (tmpdir / 'setup.py').write_text(SETUP_PY, encoding='utf-8') + + # Set up the rest of the test package + test_pkg = tmpdir / 'sdist_test' + test_pkg.mkdir() + data_folder = tmpdir / 'd' + data_folder.mkdir() + # *.rst was not included in package_data, so c.rst should not be + # automatically added to the manifest when not under version control + for fname in ['__init__.py', 'a.txt', 'b.txt', 'c.rst']: + touch(test_pkg / fname) + touch(data_folder / 'e.dat') + # C sources are not included by default, but they will be, + # if an extension module uses them as sources or depends + for fname in EXTENSION_SOURCES: + touch(tmpdir / fname) + + with tmpdir.as_cwd(): + yield tmpdir + + def assert_package_data_in_manifest(self, cmd): + manifest = cmd.filelist.files + assert os.path.join('sdist_test', 'a.txt') in manifest + assert os.path.join('sdist_test', 'b.txt') in manifest + assert os.path.join('sdist_test', 'c.rst') not in manifest + assert os.path.join('d', 'e.dat') in manifest + + def setup_with_extension(self): + setup_attrs = {**SETUP_ATTRS, 'ext_modules': [EXTENSION]} + + dist = Distribution(setup_attrs) + dist.script_name = 'setup.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + with quiet(): + cmd.run() + + return cmd + + def test_package_data_in_sdist(self): + """Regression test for pull request #4: ensures that files listed in + package_data are included in the manifest even if they're not added to + version control. + """ + + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'setup.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + with quiet(): + cmd.run() + + self.assert_package_data_in_manifest(cmd) + + def test_package_data_and_include_package_data_in_sdist(self): + """ + Ensure package_data and include_package_data work + together. + """ + setup_attrs = {**SETUP_ATTRS, 'include_package_data': True} + assert setup_attrs['package_data'] + + dist = Distribution(setup_attrs) + dist.script_name = 'setup.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + with quiet(): + cmd.run() + + self.assert_package_data_in_manifest(cmd) + + def test_extension_sources_in_sdist(self): + """ + Ensure that the files listed in Extension.sources and Extension.depends + are automatically included in the manifest. + """ + cmd = self.setup_with_extension() + self.assert_package_data_in_manifest(cmd) + manifest = cmd.filelist.files + for path in EXTENSION_SOURCES: + assert path in manifest + + def test_missing_extension_sources(self): + """ + Similar to test_extension_sources_in_sdist but the referenced files don't exist. + Missing files should not be included in distribution (with no error raised). + """ + for path in EXTENSION_SOURCES: + os.remove(path) + + cmd = self.setup_with_extension() + self.assert_package_data_in_manifest(cmd) + manifest = cmd.filelist.files + for path in EXTENSION_SOURCES: + assert path not in manifest + + def test_symlinked_extension_sources(self): + """ + Similar to test_extension_sources_in_sdist but the referenced files are + instead symbolic links to project-local files. Referenced file paths + should be included. Symlink targets themselves should NOT be included. + """ + symlinked = [] + for path in EXTENSION_SOURCES: + base, ext = os.path.splitext(path) + target = base + "_target." + ext + + os.rename(path, target) + symlink_or_skip_test(os.path.basename(target), path) + symlinked.append(target) + + cmd = self.setup_with_extension() + self.assert_package_data_in_manifest(cmd) + manifest = cmd.filelist.files + for path in EXTENSION_SOURCES: + assert path in manifest + for path in symlinked: + assert path not in manifest + + _INVALID_PATHS = { + "must be relative": lambda: os.path.abspath(os.path.join("sdist_test", "f.h")), + "can't have `..` segments": lambda: os.path.join( + "sdist_test", "..", "sdist_test", "f.h" + ), + "doesn't exist": lambda: os.path.join( + "sdist_test", "this_file_does_not_exist.h" + ), + "must be inside the project root": lambda: symlink_or_skip_test( + touch(os.path.join("..", "outside_of_project_root.h")), + "symlink.h", + ), + } + + @skip_under_stdlib_distutils + @pytest.mark.parametrize("reason", _INVALID_PATHS.keys()) + def test_invalid_extension_depends(self, reason, caplog): + """ + Due to backwards compatibility reasons, `Extension.depends` should accept + invalid/weird paths, but then ignore them when building a sdist. + + This test verifies that the source distribution is still built + successfully with such paths, but that instead of adding these paths to + the manifest, we emit an informational message, notifying the user that + the invalid path won't be automatically included. + """ + invalid_path = self._INVALID_PATHS[reason]() + extension = Extension( + name="sdist_test.f", + sources=[], + depends=[invalid_path], + ) + setup_attrs = {**SETUP_ATTRS, 'ext_modules': [extension]} + + dist = Distribution(setup_attrs) + dist.script_name = 'setup.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + with quiet(), caplog.at_level(logging.INFO): + cmd.run() + + self.assert_package_data_in_manifest(cmd) + manifest = cmd.filelist.files + assert invalid_path not in manifest + + expected_message = [ + message + for (logger, level, message) in caplog.record_tuples + if ( + logger == "root" # + and level == logging.INFO # + and invalid_path in message # + ) + ] + assert len(expected_message) == 1 + (expected_message,) = expected_message + assert reason in expected_message + + def test_custom_build_py(self): + """ + Ensure projects defining custom build_py don't break + when creating sdists (issue #2849) + """ + from distutils.command.build_py import build_py as OrigBuildPy + + using_custom_command_guard = mock.Mock() + + class CustomBuildPy(OrigBuildPy): + """ + Some projects have custom commands inheriting from `distutils` + """ + + def get_data_files(self): + using_custom_command_guard() + return super().get_data_files() + + setup_attrs = {**SETUP_ATTRS, 'include_package_data': True} + assert setup_attrs['package_data'] + + dist = Distribution(setup_attrs) + dist.script_name = 'setup.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + # Make sure we use the custom command + cmd.cmdclass = {'build_py': CustomBuildPy} + cmd.distribution.cmdclass = {'build_py': CustomBuildPy} + assert cmd.distribution.get_command_class('build_py') == CustomBuildPy + + msg = "setuptools instead of distutils" + with quiet(), pytest.warns(SetuptoolsDeprecationWarning, match=msg): + cmd.run() + + using_custom_command_guard.assert_called() + self.assert_package_data_in_manifest(cmd) + + def test_setup_py_exists(self): + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'foo.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + with quiet(): + cmd.run() + + manifest = cmd.filelist.files + assert 'setup.py' in manifest + + def test_setup_py_missing(self): + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'foo.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + if os.path.exists("setup.py"): + os.remove("setup.py") + with quiet(): + cmd.run() + + manifest = cmd.filelist.files + assert 'setup.py' not in manifest + + def test_setup_py_excluded(self): + with open("MANIFEST.in", "w", encoding="utf-8") as manifest_file: + manifest_file.write("exclude setup.py") + + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'foo.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + with quiet(): + cmd.run() + + manifest = cmd.filelist.files + assert 'setup.py' not in manifest + + def test_defaults_case_sensitivity(self, source_dir): + """ + Make sure default files (README.*, etc.) are added in a case-sensitive + way to avoid problems with packages built on Windows. + """ + + touch(source_dir / 'readme.rst') + touch(source_dir / 'SETUP.cfg') + + dist = Distribution(SETUP_ATTRS) + # the extension deliberately capitalized for this test + # to make sure the actual filename (not capitalized) gets added + # to the manifest + dist.script_name = 'setup.PY' + cmd = sdist(dist) + cmd.ensure_finalized() + + with quiet(): + cmd.run() + + # lowercase all names so we can test in a + # case-insensitive way to make sure the files + # are not included. + manifest = map(lambda x: x.lower(), cmd.filelist.files) + assert 'readme.rst' not in manifest, manifest + assert 'setup.py' not in manifest, manifest + assert 'setup.cfg' not in manifest, manifest + + def test_exclude_dev_only_cache_folders(self, source_dir): + included = { + # Emulate problem in https://github.com/pypa/setuptools/issues/4601 + "MANIFEST.in": ( + "global-include LICEN[CS]E* COPYING* NOTICE* AUTHORS*\n" + "global-include *.txt\n" + ), + # For the sake of being conservative and limiting unforeseen side-effects + # we just exclude dev-only cache folders at the root of the repository: + "test/.venv/lib/python3.9/site-packages/bar-2.dist-info/AUTHORS.rst": "", + "src/.nox/py/lib/python3.12/site-packages/bar-2.dist-info/COPYING.txt": "", + "doc/.tox/default/lib/python3.11/site-packages/foo-4.dist-info/LICENSE": "", + # Let's test against false positives with similarly named files: + ".venv-requirements.txt": "", + ".tox-coveragerc.txt": "", + ".noxy/coveragerc.txt": "", + } + + excluded = { + # .tox/.nox/.venv are well-know folders present at the root of Python repos + # and therefore should be excluded + ".tox/release/lib/python3.11/site-packages/foo-4.dist-info/LICENSE": "", + ".nox/py/lib/python3.12/site-packages/bar-2.dist-info/COPYING.txt": "", + ".venv/lib/python3.9/site-packages/bar-2.dist-info/AUTHORS.rst": "", + } + + for file, content in {**excluded, **included}.items(): + Path(source_dir, file).parent.mkdir(parents=True, exist_ok=True) + Path(source_dir, file).write_text(content, encoding="utf-8") + + cmd = self.setup_with_extension() + self.assert_package_data_in_manifest(cmd) + manifest = {f.replace(os.sep, '/') for f in cmd.filelist.files} + for path in excluded: + assert os.path.exists(path) + assert path not in manifest, (path, manifest) + for path in included: + assert os.path.exists(path) + assert path in manifest, (path, manifest) + + @fail_on_ascii + def test_manifest_is_written_with_utf8_encoding(self): + # Test for #303. + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'setup.py' + mm = manifest_maker(dist) + mm.manifest = os.path.join('sdist_test.egg-info', 'SOURCES.txt') + os.mkdir('sdist_test.egg-info') + + # UTF-8 filename + filename = os.path.join('sdist_test', 'smörbröd.py') + + # Must create the file or it will get stripped. + touch(filename) + + # Add UTF-8 filename and write manifest + with quiet(): + mm.run() + mm.filelist.append(filename) + mm.write_manifest() + + contents = read_all_bytes(mm.manifest) + + # The manifest should be UTF-8 encoded + u_contents = contents.decode('UTF-8') + + # The manifest should contain the UTF-8 filename + assert posix(filename) in u_contents + + @fail_on_ascii + def test_write_manifest_allows_utf8_filenames(self): + # Test for #303. + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'setup.py' + mm = manifest_maker(dist) + mm.manifest = os.path.join('sdist_test.egg-info', 'SOURCES.txt') + os.mkdir('sdist_test.egg-info') + + filename = os.path.join(b'sdist_test', Filenames.utf_8) + + # Must touch the file or risk removal + touch(filename) + + # Add filename and write manifest + with quiet(): + mm.run() + u_filename = filename.decode('utf-8') + mm.filelist.files.append(u_filename) + # Re-write manifest + mm.write_manifest() + + contents = read_all_bytes(mm.manifest) + + # The manifest should be UTF-8 encoded + contents.decode('UTF-8') + + # The manifest should contain the UTF-8 filename + assert posix(filename) in contents + + # The filelist should have been updated as well + assert u_filename in mm.filelist.files + + @skip_under_xdist + def test_write_manifest_skips_non_utf8_filenames(self): + """ + Files that cannot be encoded to UTF-8 (specifically, those that + weren't originally successfully decoded and have surrogate + escapes) should be omitted from the manifest. + See https://bitbucket.org/tarek/distribute/issue/303 for history. + """ + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'setup.py' + mm = manifest_maker(dist) + mm.manifest = os.path.join('sdist_test.egg-info', 'SOURCES.txt') + os.mkdir('sdist_test.egg-info') + + # Latin-1 filename + filename = os.path.join(b'sdist_test', Filenames.latin_1) + + # Add filename with surrogates and write manifest + with quiet(): + mm.run() + u_filename = filename.decode('utf-8', 'surrogateescape') + mm.filelist.append(u_filename) + # Re-write manifest + mm.write_manifest() + + contents = read_all_bytes(mm.manifest) + + # The manifest should be UTF-8 encoded + contents.decode('UTF-8') + + # The Latin-1 filename should have been skipped + assert posix(filename) not in contents + + # The filelist should have been updated as well + assert u_filename not in mm.filelist.files + + @fail_on_ascii + def test_manifest_is_read_with_utf8_encoding(self): + # Test for #303. + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'setup.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + # Create manifest + with quiet(): + cmd.run() + + # Add UTF-8 filename to manifest + filename = os.path.join(b'sdist_test', Filenames.utf_8) + cmd.manifest = os.path.join('sdist_test.egg-info', 'SOURCES.txt') + manifest = open(cmd.manifest, 'ab') + manifest.write(b'\n' + filename) + manifest.close() + + # The file must exist to be included in the filelist + touch(filename) + + # Re-read manifest + cmd.filelist.files = [] + with quiet(): + cmd.read_manifest() + + # The filelist should contain the UTF-8 filename + filename = filename.decode('utf-8') + assert filename in cmd.filelist.files + + @fail_on_latin1_encoded_filenames + def test_read_manifest_skips_non_utf8_filenames(self): + # Test for #303. + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'setup.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + # Create manifest + with quiet(): + cmd.run() + + # Add Latin-1 filename to manifest + filename = os.path.join(b'sdist_test', Filenames.latin_1) + cmd.manifest = os.path.join('sdist_test.egg-info', 'SOURCES.txt') + manifest = open(cmd.manifest, 'ab') + manifest.write(b'\n' + filename) + manifest.close() + + # The file must exist to be included in the filelist + touch(filename) + + # Re-read manifest + cmd.filelist.files = [] + with quiet(): + cmd.read_manifest() + + # The Latin-1 filename should have been skipped + filename = filename.decode('latin-1') + assert filename not in cmd.filelist.files + + @fail_on_ascii + @fail_on_latin1_encoded_filenames + def test_sdist_with_utf8_encoded_filename(self): + # Test for #303. + dist = Distribution(self.make_strings(SETUP_ATTRS)) + dist.script_name = 'setup.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + filename = os.path.join(b'sdist_test', Filenames.utf_8) + touch(filename) + + with quiet(): + cmd.run() + + if sys.platform == 'darwin': + filename = decompose(filename) + + fs_enc = sys.getfilesystemencoding() + + if sys.platform == 'win32': + if fs_enc == 'cp1252': + # Python mangles the UTF-8 filename + filename = filename.decode('cp1252') + assert filename in cmd.filelist.files + else: + filename = filename.decode('mbcs') + assert filename in cmd.filelist.files + else: + filename = filename.decode('utf-8') + assert filename in cmd.filelist.files + + @classmethod + def make_strings(cls, item): + if isinstance(item, dict): + return {key: cls.make_strings(value) for key, value in item.items()} + if isinstance(item, list): + return list(map(cls.make_strings, item)) + return str(item) + + @fail_on_latin1_encoded_filenames + @skip_under_xdist + def test_sdist_with_latin1_encoded_filename(self): + # Test for #303. + dist = Distribution(self.make_strings(SETUP_ATTRS)) + dist.script_name = 'setup.py' + cmd = sdist(dist) + cmd.ensure_finalized() + + # Latin-1 filename + filename = os.path.join(b'sdist_test', Filenames.latin_1) + touch(filename) + assert os.path.isfile(filename) + + with quiet(): + cmd.run() + + # not all windows systems have a default FS encoding of cp1252 + if sys.platform == 'win32': + # Latin-1 is similar to Windows-1252 however + # on mbcs filesys it is not in latin-1 encoding + fs_enc = sys.getfilesystemencoding() + if fs_enc != 'mbcs': + fs_enc = 'latin-1' + filename = filename.decode(fs_enc) + + assert filename in cmd.filelist.files + else: + # The Latin-1 filename should have been skipped + filename = filename.decode('latin-1') + assert filename not in cmd.filelist.files + + _EXAMPLE_DIRECTIVES = { + "setup.cfg - long_description and version": """ + [metadata] + name = testing + version = file: src/VERSION.txt + license_files = DOWHATYOUWANT + long_description = file: README.rst, USAGE.rst + """, + "pyproject.toml - static readme/license files and dynamic version": """ + [project] + name = "testing" + readme = "USAGE.rst" + license-files = ["DOWHATYOUWANT"] + dynamic = ["version"] + [tool.setuptools.dynamic] + version = {file = ["src/VERSION.txt"]} + """, + "pyproject.toml - directive with str instead of list": """ + [project] + name = "testing" + readme = "USAGE.rst" + license-files = ["DOWHATYOUWANT"] + dynamic = ["version"] + [tool.setuptools.dynamic] + version = {file = "src/VERSION.txt"} + """, + "pyproject.toml - deprecated license table with file entry": """ + [project] + name = "testing" + readme = "USAGE.rst" + license = {file = "DOWHATYOUWANT"} + dynamic = ["version"] + [tool.setuptools.dynamic] + version = {file = "src/VERSION.txt"} + """, + } + + @pytest.mark.parametrize("config", _EXAMPLE_DIRECTIVES.keys()) + @pytest.mark.filterwarnings( + "ignore:.project.license. as a TOML table is deprecated" + ) + def test_add_files_referenced_by_config_directives(self, source_dir, config): + config_file, _, _ = config.partition(" - ") + config_text = self._EXAMPLE_DIRECTIVES[config] + (source_dir / 'src').mkdir() + (source_dir / 'src/VERSION.txt').write_text("0.42", encoding="utf-8") + (source_dir / 'README.rst').write_text("hello world!", encoding="utf-8") + (source_dir / 'USAGE.rst').write_text("hello world!", encoding="utf-8") + (source_dir / 'DOWHATYOUWANT').write_text("hello world!", encoding="utf-8") + (source_dir / config_file).write_text(config_text, encoding="utf-8") + + dist = Distribution({"packages": []}) + dist.script_name = 'setup.py' + dist.parse_config_files() + + cmd = sdist(dist) + cmd.ensure_finalized() + with quiet(): + cmd.run() + + assert ( + 'src/VERSION.txt' in cmd.filelist.files + or 'src\\VERSION.txt' in cmd.filelist.files + ) + assert 'USAGE.rst' in cmd.filelist.files + assert 'DOWHATYOUWANT' in cmd.filelist.files + assert '/' not in cmd.filelist.files + assert '\\' not in cmd.filelist.files + + def test_pyproject_toml_in_sdist(self, source_dir): + """ + Check if pyproject.toml is included in source distribution if present + """ + touch(source_dir / 'pyproject.toml') + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'setup.py' + cmd = sdist(dist) + cmd.ensure_finalized() + with quiet(): + cmd.run() + manifest = cmd.filelist.files + assert 'pyproject.toml' in manifest + + def test_pyproject_toml_excluded(self, source_dir): + """ + Check that pyproject.toml can excluded even if present + """ + touch(source_dir / 'pyproject.toml') + with open('MANIFEST.in', 'w', encoding="utf-8") as mts: + print('exclude pyproject.toml', file=mts) + dist = Distribution(SETUP_ATTRS) + dist.script_name = 'setup.py' + cmd = sdist(dist) + cmd.ensure_finalized() + with quiet(): + cmd.run() + manifest = cmd.filelist.files + assert 'pyproject.toml' not in manifest + + def test_build_subcommand_source_files(self, source_dir): + touch(source_dir / '.myfile~') + + # Sanity check: without custom commands file list should not be affected + dist = Distribution({**SETUP_ATTRS, "script_name": "setup.py"}) + cmd = sdist(dist) + cmd.ensure_finalized() + with quiet(): + cmd.run() + manifest = cmd.filelist.files + assert '.myfile~' not in manifest + + # Test: custom command should be able to augment file list + dist = Distribution({**SETUP_ATTRS, "script_name": "setup.py"}) + build = dist.get_command_obj("build") + build.sub_commands = [*build.sub_commands, ("build_custom", None)] + + class build_custom(Command): + def initialize_options(self): ... + + def finalize_options(self): ... + + def run(self): ... + + def get_source_files(self): + return ['.myfile~'] + + dist.cmdclass.update(build_custom=build_custom) + + cmd = sdist(dist) + cmd.use_defaults = True + cmd.ensure_finalized() + with quiet(): + cmd.run() + manifest = cmd.filelist.files + assert '.myfile~' in manifest + + @pytest.mark.skipif("os.environ.get('SETUPTOOLS_USE_DISTUTILS') == 'stdlib'") + def test_build_base_pathlib(self, source_dir): + """ + Ensure if build_base is a pathlib.Path, the build still succeeds. + """ + dist = Distribution({ + **SETUP_ATTRS, + "script_name": "setup.py", + "options": {"build": {"build_base": pathlib.Path('build')}}, + }) + cmd = sdist(dist) + cmd.ensure_finalized() + with quiet(): + cmd.run() + + +def test_default_revctrl(): + """ + When _default_revctrl was removed from the `setuptools.command.sdist` + module in 10.0, it broke some systems which keep an old install of + setuptools (Distribute) around. Those old versions require that the + setuptools package continue to implement that interface, so this + function provides that interface, stubbed. See #320 for details. + + This interface must be maintained until Ubuntu 12.04 is no longer + supported (by Setuptools). + """ + (ep,) = metadata.EntryPoints._from_text( + """ + [setuptools.file_finders] + svn_cvs = setuptools.command.sdist:_default_revctrl + """ + ) + res = ep.load() + assert hasattr(res, '__iter__') + + +class TestRegressions: + """ + Can be removed/changed if the project decides to change how it handles symlinks + or external files. + """ + + @staticmethod + def files_for_symlink_in_extension_depends(tmp_path, dep_path): + return { + "external": { + "dir": {"file.h": ""}, + }, + "project": { + "setup.py": cleandoc( + f""" + from setuptools import Extension, setup + setup( + name="myproj", + version="42", + ext_modules=[ + Extension( + "hello", sources=["hello.pyx"], + depends=[{dep_path!r}] + ) + ], + ) + """ + ), + "hello.pyx": "", + "MANIFEST.in": "global-include *.h", + }, + } + + @pytest.mark.parametrize( + "dep_path", ("myheaders/dir/file.h", "myheaders/dir/../dir/file.h") + ) + def test_symlink_in_extension_depends(self, monkeypatch, tmp_path, dep_path): + # Given a project with a symlinked dir and a "depends" targeting that dir + files = self.files_for_symlink_in_extension_depends(tmp_path, dep_path) + jaraco.path.build(files, prefix=str(tmp_path)) + symlink_or_skip_test(tmp_path / "external", tmp_path / "project/myheaders") + + # When `sdist` runs, there should be no error + members = run_sdist(monkeypatch, tmp_path / "project") + # and the sdist should contain the symlinked files + for expected in ( + "myproj-42/hello.pyx", + "myproj-42/myheaders/dir/file.h", + ): + assert expected in members + + @staticmethod + def files_for_external_path_in_extension_depends(tmp_path, dep_path): + head, _, tail = dep_path.partition("$tmp_path$/") + dep_path = tmp_path / tail if tail else head + + return { + "external": { + "dir": {"file.h": ""}, + }, + "project": { + "setup.py": cleandoc( + f""" + from setuptools import Extension, setup + setup( + name="myproj", + version="42", + ext_modules=[ + Extension( + "hello", sources=["hello.pyx"], + depends=[{str(dep_path)!r}] + ) + ], + ) + """ + ), + "hello.pyx": "", + "MANIFEST.in": "global-include *.h", + }, + } + + @pytest.mark.parametrize( + "dep_path", ("$tmp_path$/external/dir/file.h", "../external/dir/file.h") + ) + def test_external_path_in_extension_depends(self, monkeypatch, tmp_path, dep_path): + # Given a project with a "depends" targeting an external dir + files = self.files_for_external_path_in_extension_depends(tmp_path, dep_path) + jaraco.path.build(files, prefix=str(tmp_path)) + # When `sdist` runs, there should be no error + members = run_sdist(monkeypatch, tmp_path / "project") + # and the sdist should not contain the external file + for name in members: + assert "file.h" not in name + + +def run_sdist(monkeypatch, project): + """Given a project directory, run the sdist and return its contents""" + monkeypatch.chdir(project) + with quiet(): + run_setup("setup.py", ["sdist"]) + + archive = next((project / "dist").glob("*.tar.gz")) + with tarfile.open(str(archive)) as tar: + return set(tar.getnames()) + + +def test_sanity_check_setuptools_own_sdist(setuptools_sdist): + with tarfile.open(setuptools_sdist) as tar: + files = tar.getnames() + + # setuptools sdist should not include the .tox folder + tox_files = [name for name in files if ".tox" in name] + assert len(tox_files) == 0, f"not empty {tox_files}" diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_setopt.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_setopt.py new file mode 100644 index 0000000000000000000000000000000000000000..ccf25618a5d6e255ad0be0fbed51fc29c179dcfe --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_setopt.py @@ -0,0 +1,40 @@ +import configparser + +from setuptools.command import setopt + + +class TestEdit: + @staticmethod + def parse_config(filename): + parser = configparser.ConfigParser() + with open(filename, encoding='utf-8') as reader: + parser.read_file(reader) + return parser + + @staticmethod + def write_text(file, content): + with open(file, 'wb') as strm: + strm.write(content.encode('utf-8')) + + def test_utf8_encoding_retained(self, tmpdir): + """ + When editing a file, non-ASCII characters encoded in + UTF-8 should be retained. + """ + config = tmpdir.join('setup.cfg') + self.write_text(str(config), '[names]\njaraco=джарако') + setopt.edit_config(str(config), dict(names=dict(other='yes'))) + parser = self.parse_config(str(config)) + assert parser.get('names', 'jaraco') == 'джарако' + assert parser.get('names', 'other') == 'yes' + + def test_case_retained(self, tmpdir): + """ + When editing a file, case of keys should be retained. + """ + config = tmpdir.join('setup.cfg') + self.write_text(str(config), '[names]\nFoO=bAr') + setopt.edit_config(str(config), dict(names=dict(oTher='yes'))) + actual = config.read_text(encoding='ascii') + assert 'FoO' in actual + assert 'oTher' in actual diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_setuptools.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_setuptools.py new file mode 100644 index 0000000000000000000000000000000000000000..1d56e1a8a4ebc5c7aaeb9902ef9972f7de97ecbf --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_setuptools.py @@ -0,0 +1,290 @@ +"""Tests for the 'setuptools' package""" + +import os +import re +import sys +from zipfile import ZipFile + +import pytest +from packaging.version import Version + +import setuptools +import setuptools.depends as dep +import setuptools.dist +from setuptools.depends import Require + +import distutils.cmd +import distutils.core +from distutils.core import Extension +from distutils.errors import DistutilsSetupError + + +@pytest.fixture(autouse=True) +def isolated_dir(tmpdir_cwd): + return + + +def makeSetup(**args): + """Return distribution from 'setup(**args)', without executing commands""" + + distutils.core._setup_stop_after = "commandline" + + # Don't let system command line leak into tests! + args.setdefault('script_args', ['install']) + + try: + return setuptools.setup(**args) + finally: + distutils.core._setup_stop_after = None + + +needs_bytecode = pytest.mark.skipif( + not hasattr(dep, 'get_module_constant'), + reason="bytecode support not available", +) + + +class TestDepends: + def testExtractConst(self): + if not hasattr(dep, 'extract_constant'): + # skip on non-bytecode platforms + return + + def f1(): + global x, y, z + x = "test" + y = z # pyright: ignore[reportUnboundVariable] # Explicitly testing for this runtime issue + + fc = f1.__code__ + + # unrecognized name + assert dep.extract_constant(fc, 'q', -1) is None + + # constant assigned + assert dep.extract_constant(fc, 'x', -1) == "test" + + # expression assigned + assert dep.extract_constant(fc, 'y', -1) == -1 + + # recognized name, not assigned + assert dep.extract_constant(fc, 'z', -1) is None + + def testFindModule(self): + with pytest.raises(ImportError): + dep.find_module('no-such.-thing') + with pytest.raises(ImportError): + dep.find_module('setuptools.non-existent') + f, _p, _i = dep.find_module('setuptools.tests') + f.close() + + @needs_bytecode + def testModuleExtract(self): + from json import __version__ + + assert dep.get_module_constant('json', '__version__') == __version__ + assert dep.get_module_constant('sys', 'version') == sys.version + assert ( + dep.get_module_constant('setuptools.tests.test_setuptools', '__doc__') + == __doc__ + ) + + @needs_bytecode + def testRequire(self): + req = Require('Json', '1.0.3', 'json') + + assert req.name == 'Json' + assert req.module == 'json' + assert req.requested_version == Version('1.0.3') + assert req.attribute == '__version__' + assert req.full_name() == 'Json-1.0.3' + + from json import __version__ + + assert str(req.get_version()) == __version__ + assert req.version_ok('1.0.9') + assert not req.version_ok('0.9.1') + assert not req.version_ok('unknown') + + assert req.is_present() + assert req.is_current() + + req = Require('Do-what-I-mean', '1.0', 'd-w-i-m') + assert not req.is_present() + assert not req.is_current() + + @needs_bytecode + def test_require_present(self): + # In #1896, this test was failing for months with the only + # complaint coming from test runners (not end users). + # TODO: Evaluate if this code is needed at all. + req = Require('Tests', None, 'tests', homepage="http://example.com") + assert req.format is None + assert req.attribute is None + assert req.requested_version is None + assert req.full_name() == 'Tests' + assert req.homepage == 'http://example.com' + + from setuptools.tests import __path__ + + paths = [os.path.dirname(p) for p in __path__] + assert req.is_present(paths) + assert req.is_current(paths) + + +class TestDistro: + def setup_method(self, method): + self.e1 = Extension('bar.ext', ['bar.c']) + self.e2 = Extension('c.y', ['y.c']) + + self.dist = makeSetup( + packages=['a', 'a.b', 'a.b.c', 'b', 'c'], + py_modules=['b.d', 'x'], + ext_modules=(self.e1, self.e2), + package_dir={}, + ) + + def testDistroType(self): + assert isinstance(self.dist, setuptools.dist.Distribution) + + def testExcludePackage(self): + self.dist.exclude_package('a') + assert self.dist.packages == ['b', 'c'] + + self.dist.exclude_package('b') + assert self.dist.packages == ['c'] + assert self.dist.py_modules == ['x'] + assert self.dist.ext_modules == [self.e1, self.e2] + + self.dist.exclude_package('c') + assert self.dist.packages == [] + assert self.dist.py_modules == ['x'] + assert self.dist.ext_modules == [self.e1] + + # test removals from unspecified options + makeSetup().exclude_package('x') + + def testIncludeExclude(self): + # remove an extension + self.dist.exclude(ext_modules=[self.e1]) + assert self.dist.ext_modules == [self.e2] + + # add it back in + self.dist.include(ext_modules=[self.e1]) + assert self.dist.ext_modules == [self.e2, self.e1] + + # should not add duplicate + self.dist.include(ext_modules=[self.e1]) + assert self.dist.ext_modules == [self.e2, self.e1] + + def testExcludePackages(self): + self.dist.exclude(packages=['c', 'b', 'a']) + assert self.dist.packages == [] + assert self.dist.py_modules == ['x'] + assert self.dist.ext_modules == [self.e1] + + def testEmpty(self): + dist = makeSetup() + dist.include(packages=['a'], py_modules=['b'], ext_modules=[self.e2]) + dist = makeSetup() + dist.exclude(packages=['a'], py_modules=['b'], ext_modules=[self.e2]) + + def testContents(self): + assert self.dist.has_contents_for('a') + self.dist.exclude_package('a') + assert not self.dist.has_contents_for('a') + + assert self.dist.has_contents_for('b') + self.dist.exclude_package('b') + assert not self.dist.has_contents_for('b') + + assert self.dist.has_contents_for('c') + self.dist.exclude_package('c') + assert not self.dist.has_contents_for('c') + + def testInvalidIncludeExclude(self): + with pytest.raises(DistutilsSetupError): + self.dist.include(nonexistent_option='x') + with pytest.raises(DistutilsSetupError): + self.dist.exclude(nonexistent_option='x') + with pytest.raises(DistutilsSetupError): + self.dist.include(packages={'x': 'y'}) + with pytest.raises(DistutilsSetupError): + self.dist.exclude(packages={'x': 'y'}) + with pytest.raises(DistutilsSetupError): + self.dist.include(ext_modules={'x': 'y'}) + with pytest.raises(DistutilsSetupError): + self.dist.exclude(ext_modules={'x': 'y'}) + + with pytest.raises(DistutilsSetupError): + self.dist.include(package_dir=['q']) + with pytest.raises(DistutilsSetupError): + self.dist.exclude(package_dir=['q']) + + +@pytest.fixture +def example_source(tmpdir): + tmpdir.mkdir('foo') + (tmpdir / 'foo/bar.py').write('') + (tmpdir / 'readme.txt').write('') + return tmpdir + + +def test_findall(example_source): + found = list(setuptools.findall(str(example_source))) + expected = ['readme.txt', 'foo/bar.py'] + expected = [example_source.join(fn) for fn in expected] + assert found == expected + + +def test_findall_curdir(example_source): + with example_source.as_cwd(): + found = list(setuptools.findall()) + expected = ['readme.txt', os.path.join('foo', 'bar.py')] + assert found == expected + + +@pytest.fixture +def can_symlink(tmpdir): + """ + Skip if cannot create a symbolic link + """ + link_fn = 'link' + target_fn = 'target' + try: + os.symlink(target_fn, link_fn) + except (OSError, NotImplementedError, AttributeError): + pytest.skip("Cannot create symbolic links") + os.remove(link_fn) + + +@pytest.mark.usefixtures("can_symlink") +def test_findall_missing_symlink(tmpdir): + with tmpdir.as_cwd(): + os.symlink('foo', 'bar') + found = list(setuptools.findall()) + assert found == [] + + +@pytest.mark.xfail(reason="unable to exclude tests; #4475 #3260") +def test_its_own_wheel_does_not_contain_tests(setuptools_wheel): + with ZipFile(setuptools_wheel) as zipfile: + contents = [f.replace(os.sep, '/') for f in zipfile.namelist()] + + for member in contents: + assert '/tests/' not in member + + +def test_wheel_includes_cli_scripts(setuptools_wheel): + with ZipFile(setuptools_wheel) as zipfile: + contents = [f.replace(os.sep, '/') for f in zipfile.namelist()] + + assert any('cli-64.exe' in member for member in contents) + + +def test_wheel_includes_vendored_metadata(setuptools_wheel): + with ZipFile(setuptools_wheel) as zipfile: + contents = [f.replace(os.sep, '/') for f in zipfile.namelist()] + + assert any( + re.search(r'_vendor/.*\.dist-info/METADATA', member) for member in contents + ) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_shutil_wrapper.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_shutil_wrapper.py new file mode 100644 index 0000000000000000000000000000000000000000..74ff7e9a896328a3d57ca3639658e3b9d538585f --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_shutil_wrapper.py @@ -0,0 +1,23 @@ +import stat +import sys +from unittest.mock import Mock + +from setuptools import _shutil + + +def test_rmtree_readonly(monkeypatch, tmp_path): + """Verify onerr works as expected""" + + tmp_dir = tmp_path / "with_readonly" + tmp_dir.mkdir() + some_file = tmp_dir.joinpath("file.txt") + some_file.touch() + some_file.chmod(stat.S_IREAD) + + expected_count = 1 if sys.platform.startswith("win") else 0 + chmod_fn = Mock(wraps=_shutil.attempt_chmod_verbose) + monkeypatch.setattr(_shutil, "attempt_chmod_verbose", chmod_fn) + + _shutil.rmtree(tmp_dir) + assert chmod_fn.call_count == expected_count + assert not tmp_dir.is_dir() diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_unicode_utils.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_unicode_utils.py new file mode 100644 index 0000000000000000000000000000000000000000..a24a9bd5305d1de7c1c925466bb7d222c85864a7 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_unicode_utils.py @@ -0,0 +1,10 @@ +from setuptools import unicode_utils + + +def test_filesys_decode_fs_encoding_is_None(monkeypatch): + """ + Test filesys_decode does not raise TypeError when + getfilesystemencoding returns None. + """ + monkeypatch.setattr('sys.getfilesystemencoding', lambda: None) + unicode_utils.filesys_decode(b'test') diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_virtualenv.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_virtualenv.py new file mode 100644 index 0000000000000000000000000000000000000000..b02949baf9cef8eb4df9c697add28f79a93b64d4 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_virtualenv.py @@ -0,0 +1,113 @@ +import os +import subprocess +import sys +from urllib.error import URLError +from urllib.request import urlopen + +import pytest + + +@pytest.fixture(autouse=True) +def pytest_virtualenv_works(venv): + """ + pytest_virtualenv may not work. if it doesn't, skip these + tests. See #1284. + """ + venv_prefix = venv.run(["python", "-c", "import sys; print(sys.prefix)"]).strip() + if venv_prefix == sys.prefix: + pytest.skip("virtualenv is broken (see pypa/setuptools#1284)") + + +def test_clean_env_install(venv_without_setuptools, setuptools_wheel): + """ + Check setuptools can be installed in a clean environment. + """ + cmd = ["python", "-m", "pip", "install", str(setuptools_wheel)] + venv_without_setuptools.run(cmd) + + +def access_pypi(): + # Detect if tests are being run without connectivity + if not os.environ.get('NETWORK_REQUIRED', False): # pragma: nocover + try: + urlopen('https://pypi.org', timeout=1) + except URLError: + # No network, disable most of these tests + return False + + return True + + +@pytest.mark.skipif( + 'platform.python_implementation() == "PyPy"', + reason="https://github.com/pypa/setuptools/pull/2865#issuecomment-965834995", +) +@pytest.mark.skipif(not access_pypi(), reason="no network") +# ^-- Even when it is not necessary to install a different version of `pip` +# the build process will still try to download `wheel`, see #3147 and #2986. +@pytest.mark.parametrize( + 'pip_version', + [ + None, + pytest.param( + 'pip<20.1', + marks=pytest.mark.xfail( + 'sys.version_info >= (3, 12)', + reason="pip 23.1.2 required for Python 3.12 and later", + ), + ), + pytest.param( + 'pip<21', + marks=pytest.mark.xfail( + 'sys.version_info >= (3, 12)', + reason="pip 23.1.2 required for Python 3.12 and later", + ), + ), + pytest.param( + 'pip<22', + marks=pytest.mark.xfail( + 'sys.version_info >= (3, 12)', + reason="pip 23.1.2 required for Python 3.12 and later", + ), + ), + pytest.param( + 'pip<23', + marks=pytest.mark.xfail( + 'sys.version_info >= (3, 12)', + reason="pip 23.1.2 required for Python 3.12 and later", + ), + ), + pytest.param( + 'https://github.com/pypa/pip/archive/main.zip', + marks=pytest.mark.xfail(reason='#2975'), + ), + ], +) +def test_pip_upgrade_from_source( + pip_version, venv_without_setuptools, setuptools_wheel, setuptools_sdist +): + """ + Check pip can upgrade setuptools from source. + """ + # Install pip/wheel, in a venv without setuptools (as it + # should not be needed for bootstrapping from source) + venv = venv_without_setuptools + venv.run(["pip", "install", "-U", "wheel"]) + if pip_version is not None: + venv.run(["python", "-m", "pip", "install", "-U", pip_version, "--retries=1"]) + with pytest.raises(subprocess.CalledProcessError): + # Meta-test to make sure setuptools is not installed + venv.run(["python", "-c", "import setuptools"]) + + # Then install from wheel. + venv.run(["pip", "install", str(setuptools_wheel)]) + # And finally try to upgrade from source. + venv.run(["pip", "install", "--no-cache-dir", "--upgrade", str(setuptools_sdist)]) + + +def test_no_missing_dependencies(bare_venv, request): + """ + Quick and dirty test to ensure all external dependencies are vendored. + """ + setuptools_dir = request.config.rootdir + bare_venv.run(['python', 'setup.py', '--help'], cwd=setuptools_dir) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_warnings.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_warnings.py new file mode 100644 index 0000000000000000000000000000000000000000..41193d4f717344546f8c70ad18b268a04740129b --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_warnings.py @@ -0,0 +1,106 @@ +from inspect import cleandoc + +import pytest + +from setuptools.warnings import SetuptoolsDeprecationWarning, SetuptoolsWarning + +_EXAMPLES = { + "default": dict( + args=("Hello {x}", "\n\t{target} {v:.1f}"), + kwargs={"x": 5, "v": 3, "target": "World"}, + expected=""" + Hello 5 + !! + + ******************************************************************************** + World 3.0 + ******************************************************************************** + + !! + """, + ), + "futue_due_date": dict( + args=("Summary", "Lorem ipsum"), + kwargs={"due_date": (9999, 11, 22)}, + expected=""" + Summary + !! + + ******************************************************************************** + Lorem ipsum + + By 9999-Nov-22, you need to update your project and remove deprecated calls + or your builds will no longer be supported. + ******************************************************************************** + + !! + """, + ), + "past_due_date_with_docs": dict( + args=("Summary", "Lorem ipsum"), + kwargs={"due_date": (2000, 11, 22), "see_docs": "some_page.html"}, + expected=""" + Summary + !! + + ******************************************************************************** + Lorem ipsum + + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. + + See https://setuptools.pypa.io/en/latest/some_page.html for details. + ******************************************************************************** + + !! + """, + ), +} + + +@pytest.mark.parametrize("example_name", _EXAMPLES.keys()) +def test_formatting(monkeypatch, example_name): + """ + It should automatically handle indentation, interpolation and things like due date. + """ + args = _EXAMPLES[example_name]["args"] + kwargs = _EXAMPLES[example_name]["kwargs"] + expected = _EXAMPLES[example_name]["expected"] + + monkeypatch.setenv("SETUPTOOLS_ENFORCE_DEPRECATION", "false") + with pytest.warns(SetuptoolsWarning) as warn_info: + SetuptoolsWarning.emit(*args, **kwargs) + assert _get_message(warn_info) == cleandoc(expected) + + +def test_due_date_enforcement(monkeypatch): + class _MyDeprecation(SetuptoolsDeprecationWarning): + _SUMMARY = "Summary" + _DETAILS = "Lorem ipsum" + _DUE_DATE = (2000, 11, 22) + _SEE_DOCS = "some_page.html" + + monkeypatch.setenv("SETUPTOOLS_ENFORCE_DEPRECATION", "true") + with pytest.raises(SetuptoolsDeprecationWarning) as exc_info: + _MyDeprecation.emit() + + expected = """ + Summary + !! + + ******************************************************************************** + Lorem ipsum + + This deprecation is overdue, please update your project and remove deprecated + calls to avoid build errors in the future. + + See https://setuptools.pypa.io/en/latest/some_page.html for details. + ******************************************************************************** + + !! + """ + assert str(exc_info.value) == cleandoc(expected) + + +def _get_message(warn_info): + return next(warn.message.args[0] for warn in warn_info) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_wheel.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_wheel.py new file mode 100644 index 0000000000000000000000000000000000000000..c3b215a4744c8118f2667c8a6cc1e1a2ebdce138 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_wheel.py @@ -0,0 +1,690 @@ +"""wheel tests""" + +from __future__ import annotations + +import contextlib +import glob +import inspect +import os +import pathlib +import stat +import subprocess +import sys +import sysconfig +import zipfile +from typing import Any + +import pytest +from jaraco import path +from packaging.tags import parse_tag + +from setuptools._importlib import metadata +from setuptools.wheel import Wheel + +from .contexts import tempdir +from .textwrap import DALS + +from distutils.sysconfig import get_config_var +from distutils.util import get_platform + +WHEEL_INFO_TESTS = ( + ('invalid.whl', ValueError), + ( + 'simplewheel-2.0-1-py2.py3-none-any.whl', + { + 'project_name': 'simplewheel', + 'version': '2.0', + 'build': '1', + 'py_version': 'py2.py3', + 'abi': 'none', + 'platform': 'any', + }, + ), + ( + 'simple.dist-0.1-py2.py3-none-any.whl', + { + 'project_name': 'simple.dist', + 'version': '0.1', + 'build': None, + 'py_version': 'py2.py3', + 'abi': 'none', + 'platform': 'any', + }, + ), + ( + 'example_pkg_a-1-py3-none-any.whl', + { + 'project_name': 'example_pkg_a', + 'version': '1', + 'build': None, + 'py_version': 'py3', + 'abi': 'none', + 'platform': 'any', + }, + ), + ( + 'PyQt5-5.9-5.9.1-cp35.cp36.cp37-abi3-manylinux1_x86_64.whl', + { + 'project_name': 'PyQt5', + 'version': '5.9', + 'build': '5.9.1', + 'py_version': 'cp35.cp36.cp37', + 'abi': 'abi3', + 'platform': 'manylinux1_x86_64', + }, + ), +) + + +@pytest.mark.parametrize( + ('filename', 'info'), WHEEL_INFO_TESTS, ids=[t[0] for t in WHEEL_INFO_TESTS] +) +def test_wheel_info(filename, info): + if inspect.isclass(info): + with pytest.raises(info): + Wheel(filename) + return + w = Wheel(filename) + assert {k: getattr(w, k) for k in info.keys()} == info + + +@contextlib.contextmanager +def build_wheel(extra_file_defs=None, **kwargs): + file_defs = { + 'setup.py': ( + DALS( + """ + # -*- coding: utf-8 -*- + from setuptools import setup + import setuptools + setup(**%r) + """ + ) + % kwargs + ).encode('utf-8'), + } + if extra_file_defs: + file_defs.update(extra_file_defs) + with tempdir() as source_dir: + path.build(file_defs, source_dir) + subprocess.check_call( + (sys.executable, 'setup.py', '-q', 'bdist_wheel'), cwd=source_dir + ) + yield glob.glob(os.path.join(source_dir, 'dist', '*.whl'))[0] + + +def tree_set(root): + return { + os.path.join(os.path.relpath(dirpath, root), filename) + for dirpath, dirnames, filenames in os.walk(root) + for filename in filenames + } + + +def flatten_tree(tree): + """Flatten nested dicts and lists into a full list of paths""" + output = set() + for node, contents in tree.items(): + if isinstance(contents, dict): + contents = flatten_tree(contents) + + for elem in contents: + if isinstance(elem, dict): + output |= {os.path.join(node, val) for val in flatten_tree(elem)} + else: + output.add(os.path.join(node, elem)) + return output + + +def format_install_tree(tree): + return { + x.format( + py_version=sysconfig.get_python_version(), + platform=get_platform(), + shlib_ext=get_config_var('EXT_SUFFIX') or get_config_var('SO'), + ) + for x in tree + } + + +def _check_wheel_install( + filename, install_dir, install_tree_includes, project_name, version, requires_txt +): + w = Wheel(filename) + egg_path = os.path.join(install_dir, w.egg_name()) + w.install_as_egg(egg_path) + if install_tree_includes is not None: + install_tree = format_install_tree(install_tree_includes) + exp = tree_set(install_dir) + assert install_tree.issubset(exp), install_tree - exp + + (dist,) = metadata.Distribution.discover(path=[egg_path]) + + # pyright is nitpicky; fine to assume dist.metadata.__getitem__ will fail or return None + # (https://github.com/pypa/setuptools/pull/5006#issuecomment-2894774288) + assert dist.metadata['Name'] == project_name # pyright: ignore # noqa: PGH003 + assert dist.metadata['Version'] == version # pyright: ignore # noqa: PGH003 + assert dist.read_text('requires.txt') == requires_txt + + +class Record: + def __init__(self, id, **kwargs) -> None: + self._id = id + self._fields = kwargs + + def __repr__(self) -> str: + return f'{self._id}(**{self._fields!r})' + + +# Using Any to avoid possible type union issues later in test +# making a TypedDict is not worth in a test and anonymous/inline TypedDict are experimental +# https://github.com/python/mypy/issues/9884 +WHEEL_INSTALL_TESTS: tuple[dict[str, Any], ...] = ( + dict( + id='basic', + file_defs={'foo': {'__init__.py': ''}}, + setup_kwargs=dict( + packages=['foo'], + ), + install_tree=flatten_tree({ + 'foo-1.0-py{py_version}.egg': { + 'EGG-INFO': ['PKG-INFO', 'RECORD', 'WHEEL', 'top_level.txt'], + 'foo': ['__init__.py'], + } + }), + ), + dict( + id='utf-8', + setup_kwargs=dict( + description='Description accentuée', + ), + ), + dict( + id='data', + file_defs={ + 'data.txt': DALS( + """ + Some data... + """ + ), + }, + setup_kwargs=dict( + data_files=[('data_dir', ['data.txt'])], + ), + install_tree=flatten_tree({ + 'foo-1.0-py{py_version}.egg': { + 'EGG-INFO': ['PKG-INFO', 'RECORD', 'WHEEL', 'top_level.txt'], + 'data_dir': ['data.txt'], + } + }), + ), + dict( + id='extension', + file_defs={ + 'extension.c': DALS( + """ + #include "Python.h" + + #if PY_MAJOR_VERSION >= 3 + + static struct PyModuleDef moduledef = { + PyModuleDef_HEAD_INIT, + "extension", + NULL, + 0, + NULL, + NULL, + NULL, + NULL, + NULL + }; + + #define INITERROR return NULL + + PyMODINIT_FUNC PyInit_extension(void) + + #else + + #define INITERROR return + + void initextension(void) + + #endif + { + #if PY_MAJOR_VERSION >= 3 + PyObject *module = PyModule_Create(&moduledef); + #else + PyObject *module = Py_InitModule("extension", NULL); + #endif + if (module == NULL) + INITERROR; + #if PY_MAJOR_VERSION >= 3 + return module; + #endif + } + """ + ), + }, + setup_kwargs=dict( + ext_modules=[ + Record( + 'setuptools.Extension', name='extension', sources=['extension.c'] + ) + ], + ), + install_tree=flatten_tree({ + 'foo-1.0-py{py_version}-{platform}.egg': [ + 'extension{shlib_ext}', + { + 'EGG-INFO': [ + 'PKG-INFO', + 'RECORD', + 'WHEEL', + 'top_level.txt', + ] + }, + ] + }), + ), + dict( + id='header', + file_defs={ + 'header.h': DALS( + """ + """ + ), + }, + setup_kwargs=dict( + headers=['header.h'], + ), + install_tree=flatten_tree({ + 'foo-1.0-py{py_version}.egg': [ + 'header.h', + { + 'EGG-INFO': [ + 'PKG-INFO', + 'RECORD', + 'WHEEL', + 'top_level.txt', + ] + }, + ] + }), + ), + dict( + id='script', + file_defs={ + 'script.py': DALS( + """ + #/usr/bin/python + print('hello world!') + """ + ), + 'script.sh': DALS( + """ + #/bin/sh + echo 'hello world!' + """ + ), + }, + setup_kwargs=dict( + scripts=['script.py', 'script.sh'], + ), + install_tree=flatten_tree({ + 'foo-1.0-py{py_version}.egg': { + 'EGG-INFO': [ + 'PKG-INFO', + 'RECORD', + 'WHEEL', + 'top_level.txt', + {'scripts': ['script.py', 'script.sh']}, + ] + } + }), + ), + dict( + id='requires1', + install_requires='foobar==2.0', + install_tree=flatten_tree({ + 'foo-1.0-py{py_version}.egg': { + 'EGG-INFO': [ + 'PKG-INFO', + 'RECORD', + 'WHEEL', + 'requires.txt', + 'top_level.txt', + ] + } + }), + requires_txt=DALS( + """ + foobar==2.0 + """ + ), + ), + dict( + id='requires2', + install_requires=f""" + bar + foo<=2.0; {sys.platform!r} in sys_platform + """, + requires_txt=DALS( + """ + bar + foo<=2.0 + """ + ), + ), + dict( + id='requires3', + install_requires=f""" + bar; {sys.platform!r} != sys_platform + """, + ), + dict( + id='requires4', + install_requires=""" + foo + """, + extras_require={ + 'extra': 'foobar>3', + }, + requires_txt=DALS( + """ + foo + + [extra] + foobar>3 + """ + ), + ), + dict( + id='requires5', + extras_require={ + 'extra': f'foobar; {sys.platform!r} != sys_platform', + }, + requires_txt='\n' + + DALS( + """ + [extra] + """ + ), + ), + dict( + id='requires_ensure_order', + install_requires=""" + foo + bar + baz + qux + """, + extras_require={ + 'extra': """ + foobar>3 + barbaz>4 + bazqux>5 + quxzap>6 + """, + }, + requires_txt=DALS( + """ + foo + bar + baz + qux + + [extra] + foobar>3 + barbaz>4 + bazqux>5 + quxzap>6 + """ + ), + ), + dict( + id='namespace_package', + file_defs={ + 'foo': { + 'bar': {'__init__.py': ''}, + }, + }, + setup_kwargs=dict( + namespace_packages=['foo'], + packages=['foo.bar'], + ), + install_tree=flatten_tree({ + 'foo-1.0-py{py_version}.egg': [ + 'foo-1.0-py{py_version}-nspkg.pth', + { + 'EGG-INFO': [ + 'PKG-INFO', + 'RECORD', + 'WHEEL', + 'namespace_packages.txt', + 'top_level.txt', + ] + }, + { + 'foo': [ + '__init__.py', + {'bar': ['__init__.py']}, + ] + }, + ] + }), + ), + dict( + id='empty_namespace_package', + file_defs={ + 'foobar': { + '__init__.py': ( + "__import__('pkg_resources').declare_namespace(__name__)" + ) + }, + }, + setup_kwargs=dict( + namespace_packages=['foobar'], + packages=['foobar'], + ), + install_tree=flatten_tree({ + 'foo-1.0-py{py_version}.egg': [ + 'foo-1.0-py{py_version}-nspkg.pth', + { + 'EGG-INFO': [ + 'PKG-INFO', + 'RECORD', + 'WHEEL', + 'namespace_packages.txt', + 'top_level.txt', + ] + }, + { + 'foobar': [ + '__init__.py', + ] + }, + ] + }), + ), + dict( + id='data_in_package', + file_defs={ + 'foo': { + '__init__.py': '', + 'data_dir': { + 'data.txt': DALS( + """ + Some data... + """ + ), + }, + } + }, + setup_kwargs=dict( + packages=['foo'], + data_files=[('foo/data_dir', ['foo/data_dir/data.txt'])], + ), + install_tree=flatten_tree({ + 'foo-1.0-py{py_version}.egg': { + 'EGG-INFO': [ + 'PKG-INFO', + 'RECORD', + 'WHEEL', + 'top_level.txt', + ], + 'foo': [ + '__init__.py', + { + 'data_dir': [ + 'data.txt', + ] + }, + ], + } + }), + ), +) + + +@pytest.mark.parametrize( + 'params', + WHEEL_INSTALL_TESTS, + ids=[params['id'] for params in WHEEL_INSTALL_TESTS], +) +def test_wheel_install(params): + project_name = params.get('name', 'foo') + version = params.get('version', '1.0') + install_requires = params.get('install_requires', []) + extras_require = params.get('extras_require', {}) + requires_txt = params.get('requires_txt', None) + install_tree = params.get('install_tree') + file_defs = params.get('file_defs', {}) + setup_kwargs = params.get('setup_kwargs', {}) + with ( + build_wheel( + name=project_name, + version=version, + install_requires=install_requires, + extras_require=extras_require, + extra_file_defs=file_defs, + **setup_kwargs, + ) as filename, + tempdir() as install_dir, + ): + _check_wheel_install( + filename, install_dir, install_tree, project_name, version, requires_txt + ) + + +def test_wheel_no_dist_dir(): + project_name = 'nodistinfo' + version = '1.0' + wheel_name = f'{project_name}-{version}-py2.py3-none-any.whl' + with tempdir() as source_dir: + wheel_path = os.path.join(source_dir, wheel_name) + # create an empty zip file + zipfile.ZipFile(wheel_path, 'w').close() + with tempdir() as install_dir: + with pytest.raises(ValueError): + _check_wheel_install( + wheel_path, install_dir, None, project_name, version, None + ) + + +def test_wheel_is_compatible(monkeypatch): + def sys_tags(): + return { + (t.interpreter, t.abi, t.platform) + for t in parse_tag('cp36-cp36m-manylinux1_x86_64') + } + + monkeypatch.setattr('setuptools.wheel._get_supported_tags', sys_tags) + assert Wheel('onnxruntime-0.1.2-cp36-cp36m-manylinux1_x86_64.whl').is_compatible() + + +def test_wheel_mode(): + @contextlib.contextmanager + def build_wheel(extra_file_defs=None, **kwargs): + file_defs = { + 'setup.py': ( + DALS( + """ + # -*- coding: utf-8 -*- + from setuptools import setup + import setuptools + setup(**%r) + """ + ) + % kwargs + ).encode('utf-8'), + } + if extra_file_defs: + file_defs.update(extra_file_defs) + with tempdir() as source_dir: + path.build(file_defs, source_dir) + runsh = pathlib.Path(source_dir) / "script.sh" + os.chmod(runsh, 0o777) + subprocess.check_call( + (sys.executable, 'setup.py', '-q', 'bdist_wheel'), cwd=source_dir + ) + yield glob.glob(os.path.join(source_dir, 'dist', '*.whl'))[0] + + params = dict( + id='script', + file_defs={ + 'script.py': DALS( + """ + #/usr/bin/python + print('hello world!') + """ + ), + 'script.sh': DALS( + """ + #/bin/sh + echo 'hello world!' + """ + ), + }, + setup_kwargs=dict( + scripts=['script.py', 'script.sh'], + ), + install_tree=flatten_tree({ + 'foo-1.0-py{py_version}.egg': { + 'EGG-INFO': [ + 'PKG-INFO', + 'RECORD', + 'WHEEL', + 'top_level.txt', + {'scripts': ['script.py', 'script.sh']}, + ] + } + }), + ) + + project_name = params.get('name', 'foo') + version = params.get('version', '1.0') + install_tree = params.get('install_tree') + file_defs = params.get('file_defs', {}) + setup_kwargs = params.get('setup_kwargs', {}) + + with ( + build_wheel( + name=project_name, + version=version, + install_requires=[], + extras_require={}, + extra_file_defs=file_defs, + **setup_kwargs, + ) as filename, + tempdir() as install_dir, + ): + _check_wheel_install( + filename, install_dir, install_tree, project_name, version, None + ) + w = Wheel(filename) + base = pathlib.Path(install_dir) / w.egg_name() + script_sh = base / "EGG-INFO" / "scripts" / "script.sh" + assert script_sh.exists() + if sys.platform != 'win32': + # Editable file mode has no effect on Windows + assert oct(stat.S_IMODE(script_sh.stat().st_mode)) == "0o777" diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_windows_wrappers.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_windows_wrappers.py new file mode 100644 index 0000000000000000000000000000000000000000..4f990eb1c3cc67c61ea17f791430651e91040f18 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/test_windows_wrappers.py @@ -0,0 +1,258 @@ +""" +Python Script Wrapper for Windows +================================= + +setuptools includes wrappers for Python scripts that allows them to be +executed like regular windows programs. There are 2 wrappers, one +for command-line programs, cli.exe, and one for graphical programs, +gui.exe. These programs are almost identical, function pretty much +the same way, and are generated from the same source file. The +wrapper programs are used by copying them to the directory containing +the script they are to wrap and with the same name as the script they +are to wrap. +""" + +import pathlib +import platform +import subprocess +import sys +import textwrap + +import pytest + +from setuptools._importlib import resources + +pytestmark = pytest.mark.skipif(sys.platform != 'win32', reason="Windows only") + + +class WrapperTester: + @classmethod + def prep_script(cls, template): + python_exe = subprocess.list2cmdline([sys.executable]) + return template % locals() + + @classmethod + def create_script(cls, tmpdir): + """ + Create a simple script, foo-script.py + + Note that the script starts with a Unix-style '#!' line saying which + Python executable to run. The wrapper will use this line to find the + correct Python executable. + """ + + script = cls.prep_script(cls.script_tmpl) + + with (tmpdir / cls.script_name).open('w') as f: + f.write(script) + + # also copy cli.exe to the sample directory + with (tmpdir / cls.wrapper_name).open('wb') as f: + w = resources.files('setuptools').joinpath(cls.wrapper_source).read_bytes() + f.write(w) + + +def win_launcher_exe(prefix): + """A simple routine to select launcher script based on platform.""" + assert prefix in ('cli', 'gui') + if platform.machine() == "ARM64": + return f"{prefix}-arm64.exe" + else: + return f"{prefix}-32.exe" + + +class TestCLI(WrapperTester): + script_name = 'foo-script.py' + wrapper_name = 'foo.exe' + wrapper_source = win_launcher_exe('cli') + + script_tmpl = textwrap.dedent( + """ + #!%(python_exe)s + import sys + input = repr(sys.stdin.read()) + print(sys.argv[0][-14:]) + print(sys.argv[1:]) + print(input) + if __debug__: + print('non-optimized') + """ + ).lstrip() + + def test_basic(self, tmpdir): + """ + When the copy of cli.exe, foo.exe in this example, runs, it examines + the path name it was run with and computes a Python script path name + by removing the '.exe' suffix and adding the '-script.py' suffix. (For + GUI programs, the suffix '-script.pyw' is added.) This is why we + named out script the way we did. Now we can run out script by running + the wrapper: + + This example was a little pathological in that it exercised windows + (MS C runtime) quoting rules: + + - Strings containing spaces are surrounded by double quotes. + + - Double quotes in strings need to be escaped by preceding them with + back slashes. + + - One or more backslashes preceding double quotes need to be escaped + by preceding each of them with back slashes. + """ + self.create_script(tmpdir) + cmd = [ + str(tmpdir / 'foo.exe'), + 'arg1', + 'arg 2', + 'arg "2\\"', + 'arg 4\\', + 'arg5 a\\\\b', + ] + proc = subprocess.Popen( + cmd, + stdout=subprocess.PIPE, + stdin=subprocess.PIPE, + text=True, + encoding="utf-8", + ) + stdout, _stderr = proc.communicate('hello\nworld\n') + actual = stdout.replace('\r\n', '\n') + expected = textwrap.dedent( + r""" + \foo-script.py + ['arg1', 'arg 2', 'arg "2\\"', 'arg 4\\', 'arg5 a\\\\b'] + 'hello\nworld\n' + non-optimized + """ + ).lstrip() + assert actual == expected + + def test_symlink(self, tmpdir): + """ + Ensure that symlink for the foo.exe is working correctly. + """ + script_dir = tmpdir / "script_dir" + script_dir.mkdir() + self.create_script(script_dir) + symlink = pathlib.Path(tmpdir / "foo.exe") + symlink.symlink_to(script_dir / "foo.exe") + + cmd = [ + str(tmpdir / 'foo.exe'), + 'arg1', + 'arg 2', + 'arg "2\\"', + 'arg 4\\', + 'arg5 a\\\\b', + ] + proc = subprocess.Popen( + cmd, + stdout=subprocess.PIPE, + stdin=subprocess.PIPE, + text=True, + encoding="utf-8", + ) + stdout, _stderr = proc.communicate('hello\nworld\n') + actual = stdout.replace('\r\n', '\n') + expected = textwrap.dedent( + r""" + \foo-script.py + ['arg1', 'arg 2', 'arg "2\\"', 'arg 4\\', 'arg5 a\\\\b'] + 'hello\nworld\n' + non-optimized + """ + ).lstrip() + assert actual == expected + + def test_with_options(self, tmpdir): + """ + Specifying Python Command-line Options + -------------------------------------- + + You can specify a single argument on the '#!' line. This can be used + to specify Python options like -O, to run in optimized mode or -i + to start the interactive interpreter. You can combine multiple + options as usual. For example, to run in optimized mode and + enter the interpreter after running the script, you could use -Oi: + """ + self.create_script(tmpdir) + tmpl = textwrap.dedent( + """ + #!%(python_exe)s -Oi + import sys + input = repr(sys.stdin.read()) + print(sys.argv[0][-14:]) + print(sys.argv[1:]) + print(input) + if __debug__: + print('non-optimized') + sys.ps1 = '---' + """ + ).lstrip() + with (tmpdir / 'foo-script.py').open('w') as f: + f.write(self.prep_script(tmpl)) + cmd = [str(tmpdir / 'foo.exe')] + proc = subprocess.Popen( + cmd, + stdout=subprocess.PIPE, + stdin=subprocess.PIPE, + stderr=subprocess.STDOUT, + text=True, + encoding="utf-8", + ) + stdout, _stderr = proc.communicate() + actual = stdout.replace('\r\n', '\n') + expected = textwrap.dedent( + r""" + \foo-script.py + [] + '' + --- + """ + ).lstrip() + assert actual == expected + + +class TestGUI(WrapperTester): + """ + Testing the GUI Version + ----------------------- + """ + + script_name = 'bar-script.pyw' + wrapper_source = win_launcher_exe('gui') + wrapper_name = 'bar.exe' + + script_tmpl = textwrap.dedent( + """ + #!%(python_exe)s + import sys + f = open(sys.argv[1], 'wb') + bytes_written = f.write(repr(sys.argv[2]).encode('utf-8')) + f.close() + """ + ).strip() + + def test_basic(self, tmpdir): + """Test the GUI version with the simple script, bar-script.py""" + self.create_script(tmpdir) + + cmd = [ + str(tmpdir / 'bar.exe'), + str(tmpdir / 'test_output.txt'), + 'Test Argument', + ] + proc = subprocess.Popen( + cmd, + stdout=subprocess.PIPE, + stdin=subprocess.PIPE, + stderr=subprocess.STDOUT, + text=True, + encoding="utf-8", + ) + stdout, stderr = proc.communicate() + assert not stdout + assert not stderr + with (tmpdir / 'test_output.txt').open('rb') as f_out: + actual = f_out.read().decode('ascii') + assert actual == repr('Test Argument') diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/text.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/text.py new file mode 100644 index 0000000000000000000000000000000000000000..e05cc633ede9e5ce4f74b66a7bf76327c2000caa --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/text.py @@ -0,0 +1,4 @@ +class Filenames: + unicode = 'smörbröd.py' + latin_1 = unicode.encode('latin-1') + utf_8 = unicode.encode('utf-8') diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/textwrap.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/textwrap.py new file mode 100644 index 0000000000000000000000000000000000000000..5e39618dca4ad6c3f0d4c8cb20af59ab85fb0eba --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/setuptools/tests/textwrap.py @@ -0,0 +1,6 @@ +import textwrap + + +def DALS(s): + "dedent and left-strip" + return textwrap.dedent(s).lstrip() diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/INSTALLER new file mode 100644 index 0000000000000000000000000000000000000000..a1b589e38a32041e49332e5e81c2d363dc418d68 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/INSTALLER @@ -0,0 +1 @@ +pip diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..b9077766e9b9bdcae49ea5c8fced750ed13ec8f7 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/LICENSE @@ -0,0 +1,13 @@ +Copyright (c) 2018, Tzu-ping Chung + +Permission to use, copy, modify, and distribute this software for any +purpose with or without fee is hereby granted, provided that the above +copyright notice and this permission notice appear in all copies. + +THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES +WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR +ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES +WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN +ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF +OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/METADATA new file mode 100644 index 0000000000000000000000000000000000000000..52118f1e5c83bd7ef39196a749651fc87d176812 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/METADATA @@ -0,0 +1,106 @@ +Metadata-Version: 2.1 +Name: shellingham +Version: 1.5.4 +Summary: Tool to Detect Surrounding Shell +Home-page: https://github.com/sarugaku/shellingham +Author: Tzu-ping Chung +Author-email: uranusjr@gmail.com +License: ISC License +Keywords: shell +Classifier: Development Status :: 3 - Alpha +Classifier: Environment :: Console +Classifier: Intended Audience :: Developers +Classifier: License :: OSI Approved :: ISC License (ISCL) +Classifier: Operating System :: OS Independent +Classifier: Programming Language :: Python :: 3 :: Only +Classifier: Programming Language :: Python :: 3.7 +Classifier: Programming Language :: Python :: 3.8 +Classifier: Programming Language :: Python :: 3.9 +Classifier: Programming Language :: Python :: 3.10 +Classifier: Programming Language :: Python :: 3.11 +Classifier: Programming Language :: Python :: 3.12 +Classifier: Topic :: Software Development :: Libraries :: Python Modules +Requires-Python: >=3.7 +Description-Content-Type: text/x-rst +License-File: LICENSE + +============================================= +Shellingham: Tool to Detect Surrounding Shell +============================================= + +.. image:: https://img.shields.io/pypi/v/shellingham.svg + :target: https://pypi.org/project/shellingham/ + +Shellingham detects what shell the current Python executable is running in. + + +Usage +===== + +.. code-block:: python + + >>> import shellingham + >>> shellingham.detect_shell() + ('bash', '/bin/bash') + +``detect_shell`` pokes around the process's running environment to determine +what shell it is run in. It returns a 2-tuple: + +* The shell name, always lowercased. +* The command used to run the shell. + +``ShellDetectionFailure`` is raised if ``detect_shell`` fails to detect the +surrounding shell. + + +Notes +===== + +* The shell name is always lowercased. +* On Windows, the shell name is the name of the executable, minus the file + extension. + + +Notes for Application Developers +================================ + +Remember, your application's user is not necessarily using a shell. +Shellingham raises ``ShellDetectionFailure`` if there is no shell to detect, +but *your application should almost never do this to your user*. + +A practical approach to this is to wrap ``detect_shell`` in a try block, and +provide a sane default on failure + +.. code-block:: python + + try: + shell = shellingham.detect_shell() + except shellingham.ShellDetectionFailure: + shell = provide_default() + + +There are a few choices for you to choose from. + +* The POSIX standard mandates the environment variable ``SHELL`` to refer to + "the user's preferred command language interpreter". This is always available + (even if the user is not in an interactive session), and likely the correct + choice to launch an interactive sub-shell with. +* A command ``sh`` is almost guaranteed to exist, likely at ``/bin/sh``, since + several POSIX tools rely on it. This should be suitable if you want to run a + (possibly non-interactive) script. +* All versions of DOS and Windows have an environment variable ``COMSPEC``. + This can always be used to launch a usable command prompt (e.g. `cmd.exe` on + Windows). + +Here's a simple implementation to provide a default shell + +.. code-block:: python + + import os + + def provide_default(): + if os.name == 'posix': + return os.environ['SHELL'] + elif os.name == 'nt': + return os.environ['COMSPEC'] + raise NotImplementedError(f'OS {os.name!r} support not available') diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/RECORD new file mode 100644 index 0000000000000000000000000000000000000000..a03e85926af1ddd60a801034a230b4812a4b9ffd --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/RECORD @@ -0,0 +1,21 @@ +shellingham-1.5.4.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4 +shellingham-1.5.4.dist-info/LICENSE,sha256=84j9OMrRMRLB3A9mm76A5_hFQe26-3LzAw0sp2QsPJ0,751 +shellingham-1.5.4.dist-info/METADATA,sha256=GD2AIgo3STJieVc53TV8xbs_Sb05DMkZjVGA5UUaB_o,3461 +shellingham-1.5.4.dist-info/RECORD,, +shellingham-1.5.4.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110 +shellingham-1.5.4.dist-info/top_level.txt,sha256=uKMQL5AKxPi4O9_Rbd838QeEs4ImpGQKNbEDZYqgBgk,12 +shellingham-1.5.4.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1 +shellingham/__init__.py,sha256=pAKXUPKUdwyErC0ZjS-5w-fRdSbmdcfvnpt_x1yWqtA,635 +shellingham/__pycache__/__init__.cpython-310.pyc,, +shellingham/__pycache__/_core.cpython-310.pyc,, +shellingham/__pycache__/nt.cpython-310.pyc,, +shellingham/_core.py,sha256=v-CTr_7F7cJAtNnzpa1N_Hl8afkY5yiDA4joGmsUBu0,300 +shellingham/nt.py,sha256=m6J6SuwyqVVlxXT9Bc-9F_1x-T5u0gCFFrRAF2LIkeg,4516 +shellingham/posix/__init__.py,sha256=pB69qtvZJ_yIf48nl4-ZfS3wLwwuXuknXOZhBnC2T1o,3129 +shellingham/posix/__pycache__/__init__.cpython-310.pyc,, +shellingham/posix/__pycache__/_core.cpython-310.pyc,, +shellingham/posix/__pycache__/proc.cpython-310.pyc,, +shellingham/posix/__pycache__/ps.cpython-310.pyc,, +shellingham/posix/_core.py,sha256=_v18UaXbzr4muNhr3-mH1FdSdjZ_dOXQrtUyomIbKYQ,81 +shellingham/posix/proc.py,sha256=nSUxIuQSotvaDW76i0oTQAM9aZ9PXBLFAEktWljSKCo,2659 +shellingham/posix/ps.py,sha256=NGmDKCukhNp0lahwYCaMXphBYaVbhbiR9BtE0OkT8qU,1770 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/WHEEL new file mode 100644 index 0000000000000000000000000000000000000000..c34f1162ef9a50c355df1261ef6194ffc1b39975 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/WHEEL @@ -0,0 +1,6 @@ +Wheel-Version: 1.0 +Generator: bdist_wheel (0.41.2) +Root-Is-Purelib: true +Tag: py2-none-any +Tag: py3-none-any + diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/top_level.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/top_level.txt new file mode 100644 index 0000000000000000000000000000000000000000..d4e44ce0299bb38463f8491ec8850910235c2709 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/top_level.txt @@ -0,0 +1 @@ +shellingham diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/zip-safe b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/zip-safe new file mode 100644 index 0000000000000000000000000000000000000000..8b137891791fe96927ad78e64b0aad7bded08bdc --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham-1.5.4.dist-info/zip-safe @@ -0,0 +1 @@ + diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..15f7a90cbd02e5c2cc933cf6aa0374cca68035f1 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/__init__.py @@ -0,0 +1,23 @@ +import importlib +import os + +from ._core import ShellDetectionFailure + +__version__ = "1.5.4" + + +def detect_shell(pid=None, max_depth=10): + name = os.name + try: + impl = importlib.import_module(".{}".format(name), __name__) + except ImportError: + message = "Shell detection not implemented for {0!r}".format(name) + raise RuntimeError(message) + try: + get_shell = impl.get_shell + except AttributeError: + raise RuntimeError("get_shell not implemented for {0!r}".format(name)) + shell = get_shell(pid, max_depth=max_depth) + if shell: + return shell + raise ShellDetectionFailure() diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/_core.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/_core.py new file mode 100644 index 0000000000000000000000000000000000000000..13b65417c733b54e48b120e37f573c2baa6ef72b --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/_core.py @@ -0,0 +1,11 @@ +SHELL_NAMES = ( + {"sh", "bash", "dash", "ash"} # Bourne. + | {"csh", "tcsh"} # C. + | {"ksh", "zsh", "fish"} # Common alternatives. + | {"cmd", "powershell", "pwsh"} # Microsoft. + | {"elvish", "xonsh", "nu"} # More exotic. +) + + +class ShellDetectionFailure(EnvironmentError): + pass diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/nt.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/nt.py new file mode 100644 index 0000000000000000000000000000000000000000..389551b223a761fa2f97e929b60bf3ca5baed94c --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/nt.py @@ -0,0 +1,163 @@ +import contextlib +import ctypes +import os + +from ctypes.wintypes import ( + BOOL, + CHAR, + DWORD, + HANDLE, + LONG, + LPWSTR, + MAX_PATH, + PDWORD, + ULONG, +) + +from shellingham._core import SHELL_NAMES + + +INVALID_HANDLE_VALUE = HANDLE(-1).value +ERROR_NO_MORE_FILES = 18 +ERROR_INSUFFICIENT_BUFFER = 122 +TH32CS_SNAPPROCESS = 2 +PROCESS_QUERY_LIMITED_INFORMATION = 0x1000 + + +kernel32 = ctypes.windll.kernel32 + + +def _check_handle(error_val=0): + def check(ret, func, args): + if ret == error_val: + raise ctypes.WinError() + return ret + + return check + + +def _check_expected(expected): + def check(ret, func, args): + if ret: + return True + code = ctypes.GetLastError() + if code == expected: + return False + raise ctypes.WinError(code) + + return check + + +class ProcessEntry32(ctypes.Structure): + _fields_ = ( + ("dwSize", DWORD), + ("cntUsage", DWORD), + ("th32ProcessID", DWORD), + ("th32DefaultHeapID", ctypes.POINTER(ULONG)), + ("th32ModuleID", DWORD), + ("cntThreads", DWORD), + ("th32ParentProcessID", DWORD), + ("pcPriClassBase", LONG), + ("dwFlags", DWORD), + ("szExeFile", CHAR * MAX_PATH), + ) + + +kernel32.CloseHandle.argtypes = [HANDLE] +kernel32.CloseHandle.restype = BOOL + +kernel32.CreateToolhelp32Snapshot.argtypes = [DWORD, DWORD] +kernel32.CreateToolhelp32Snapshot.restype = HANDLE +kernel32.CreateToolhelp32Snapshot.errcheck = _check_handle( # type: ignore + INVALID_HANDLE_VALUE, +) + +kernel32.Process32First.argtypes = [HANDLE, ctypes.POINTER(ProcessEntry32)] +kernel32.Process32First.restype = BOOL +kernel32.Process32First.errcheck = _check_expected( # type: ignore + ERROR_NO_MORE_FILES, +) + +kernel32.Process32Next.argtypes = [HANDLE, ctypes.POINTER(ProcessEntry32)] +kernel32.Process32Next.restype = BOOL +kernel32.Process32Next.errcheck = _check_expected( # type: ignore + ERROR_NO_MORE_FILES, +) + +kernel32.GetCurrentProcessId.argtypes = [] +kernel32.GetCurrentProcessId.restype = DWORD + +kernel32.OpenProcess.argtypes = [DWORD, BOOL, DWORD] +kernel32.OpenProcess.restype = HANDLE +kernel32.OpenProcess.errcheck = _check_handle( # type: ignore + INVALID_HANDLE_VALUE, +) + +kernel32.QueryFullProcessImageNameW.argtypes = [HANDLE, DWORD, LPWSTR, PDWORD] +kernel32.QueryFullProcessImageNameW.restype = BOOL +kernel32.QueryFullProcessImageNameW.errcheck = _check_expected( # type: ignore + ERROR_INSUFFICIENT_BUFFER, +) + + +@contextlib.contextmanager +def _handle(f, *args, **kwargs): + handle = f(*args, **kwargs) + try: + yield handle + finally: + kernel32.CloseHandle(handle) + + +def _iter_processes(): + f = kernel32.CreateToolhelp32Snapshot + with _handle(f, TH32CS_SNAPPROCESS, 0) as snap: + entry = ProcessEntry32() + entry.dwSize = ctypes.sizeof(entry) + ret = kernel32.Process32First(snap, entry) + while ret: + yield entry + ret = kernel32.Process32Next(snap, entry) + + +def _get_full_path(proch): + size = DWORD(MAX_PATH) + while True: + path_buff = ctypes.create_unicode_buffer("", size.value) + if kernel32.QueryFullProcessImageNameW(proch, 0, path_buff, size): + return path_buff.value + size.value *= 2 + + +def get_shell(pid=None, max_depth=10): + proc_map = { + proc.th32ProcessID: (proc.th32ParentProcessID, proc.szExeFile) + for proc in _iter_processes() + } + pid = pid or os.getpid() + + for _ in range(0, max_depth + 1): + try: + ppid, executable = proc_map[pid] + except KeyError: # No such process? Give up. + break + + # The executable name would be encoded with the current code page if + # we're in ANSI mode (usually). Try to decode it into str/unicode, + # replacing invalid characters to be safe (not thoeratically necessary, + # I think). Note that we need to use 'mbcs' instead of encoding + # settings from sys because this is from the Windows API, not Python + # internals (which those settings reflect). (pypa/pipenv#3382) + if isinstance(executable, bytes): + executable = executable.decode("mbcs", "replace") + + name = executable.rpartition(".")[0].lower() + if name not in SHELL_NAMES: + pid = ppid + continue + + key = PROCESS_QUERY_LIMITED_INFORMATION + with _handle(kernel32.OpenProcess, key, 0, pid) as proch: + return (name, _get_full_path(proch)) + + return None diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..5bd2070db27189e62a1867e4de49f16f8c8841ff --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/__init__.py @@ -0,0 +1,112 @@ +import os +import re + +from .._core import SHELL_NAMES, ShellDetectionFailure +from . import proc, ps + +# Based on QEMU docs: https://www.qemu.org/docs/master/user/main.html +QEMU_BIN_REGEX = re.compile( + r"""qemu- + (alpha + |armeb + |arm + |m68k + |cris + |i386 + |x86_64 + |microblaze + |mips + |mipsel + |mips64 + |mips64el + |mipsn32 + |mipsn32el + |nios2 + |ppc64 + |ppc + |sh4eb + |sh4 + |sparc + |sparc32plus + |sparc64 + )""", + re.VERBOSE, +) + + +def _iter_process_parents(pid, max_depth=10): + """Select a way to obtain process information from the system. + + * `/proc` is used if supported. + * The system `ps` utility is used as a fallback option. + """ + for impl in (proc, ps): + try: + iterator = impl.iter_process_parents(pid, max_depth) + except EnvironmentError: + continue + return iterator + raise ShellDetectionFailure("compatible proc fs or ps utility is required") + + +def _get_login_shell(proc_cmd): + """Form shell information from SHELL environ if possible.""" + login_shell = os.environ.get("SHELL", "") + if login_shell: + proc_cmd = login_shell + else: + proc_cmd = proc_cmd[1:] + return (os.path.basename(proc_cmd).lower(), proc_cmd) + + +_INTERPRETER_SHELL_NAMES = [ + (re.compile(r"^python(\d+(\.\d+)?)?$"), {"xonsh"}), +] + + +def _get_interpreter_shell(proc_name, proc_args): + """Get shell invoked via an interpreter. + + Some shells are implemented on, and invoked with an interpreter, e.g. xonsh + is commonly executed with an executable Python script. This detects what + script the interpreter is actually running, and check whether that looks + like a shell. + + See sarugaku/shellingham#26 for rational. + """ + for pattern, shell_names in _INTERPRETER_SHELL_NAMES: + if not pattern.match(proc_name): + continue + for arg in proc_args: + name = os.path.basename(arg).lower() + if os.path.isfile(arg) and name in shell_names: + return (name, arg) + return None + + +def _get_shell(cmd, *args): + if cmd.startswith("-"): # Login shell! Let's use this. + return _get_login_shell(cmd) + name = os.path.basename(cmd).lower() + if name == "rosetta" or QEMU_BIN_REGEX.fullmatch(name): + # If the current process is Rosetta or QEMU, this likely is a + # containerized process. Parse out the actual command instead. + cmd = args[0] + args = args[1:] + name = os.path.basename(cmd).lower() + if name in SHELL_NAMES: # Command looks like a shell. + return (name, cmd) + shell = _get_interpreter_shell(name, args) + if shell: + return shell + return None + + +def get_shell(pid=None, max_depth=10): + """Get the shell that the supplied pid or os.getpid() is running in.""" + pid = str(pid or os.getpid()) + for proc_args, _, _ in _iter_process_parents(pid, max_depth): + shell = _get_shell(*proc_args) + if shell: + return shell + return None diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/_core.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/_core.py new file mode 100644 index 0000000000000000000000000000000000000000..adc49e6e7a9d3edf062c55e0078136899f78d30d --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/_core.py @@ -0,0 +1,3 @@ +import collections + +Process = collections.namedtuple("Process", "args pid ppid") diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/proc.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/proc.py new file mode 100644 index 0000000000000000000000000000000000000000..950f63228e5b328f82b70da8851ec60c6a2ff029 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/proc.py @@ -0,0 +1,83 @@ +import io +import os +import re +import sys + +from ._core import Process + +# FreeBSD: https://www.freebsd.org/cgi/man.cgi?query=procfs +# NetBSD: https://man.netbsd.org/NetBSD-9.3-STABLE/mount_procfs.8 +# DragonFlyBSD: https://www.dragonflybsd.org/cgi/web-man?command=procfs +BSD_STAT_PPID = 2 + +# See https://docs.kernel.org/filesystems/proc.html +LINUX_STAT_PPID = 3 + +STAT_PATTERN = re.compile(r"\(.+\)|\S+") + + +def detect_proc(): + """Detect /proc filesystem style. + + This checks the /proc/{pid} directory for possible formats. Returns one of + the following as str: + + * `stat`: Linux-style, i.e. ``/proc/{pid}/stat``. + * `status`: BSD-style, i.e. ``/proc/{pid}/status``. + """ + pid = os.getpid() + for name in ("stat", "status"): + if os.path.exists(os.path.join("/proc", str(pid), name)): + return name + raise ProcFormatError("unsupported proc format") + + +def _use_bsd_stat_format(): + try: + return os.uname().sysname.lower() in ("freebsd", "netbsd", "dragonfly") + except Exception: + return False + + +def _get_ppid(pid, name): + path = os.path.join("/proc", str(pid), name) + with io.open(path, encoding="ascii", errors="replace") as f: + parts = STAT_PATTERN.findall(f.read()) + # We only care about TTY and PPID -- both are numbers. + if _use_bsd_stat_format(): + return parts[BSD_STAT_PPID] + return parts[LINUX_STAT_PPID] + + +def _get_cmdline(pid): + path = os.path.join("/proc", str(pid), "cmdline") + encoding = sys.getfilesystemencoding() or "utf-8" + with io.open(path, encoding=encoding, errors="replace") as f: + # XXX: Command line arguments can be arbitrary byte sequences, not + # necessarily decodable. For Shellingham's purpose, however, we don't + # care. (pypa/pipenv#2820) + # cmdline appends an extra NULL at the end, hence the [:-1]. + return tuple(f.read().split("\0")[:-1]) + + +class ProcFormatError(EnvironmentError): + pass + + +def iter_process_parents(pid, max_depth=10): + """Try to look up the process tree via the /proc interface.""" + stat_name = detect_proc() + + # Inner generator function so we correctly throw an error eagerly if proc + # is not supported, rather than on the first call to the iterator. This + # allows the call site detects the correct implementation. + def _iter_process_parents(pid, max_depth): + for _ in range(max_depth): + ppid = _get_ppid(pid, stat_name) + args = _get_cmdline(pid) + yield Process(args=args, pid=pid, ppid=ppid) + if ppid == "0": + break + pid = ppid + + return _iter_process_parents(pid, max_depth) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/ps.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/ps.py new file mode 100644 index 0000000000000000000000000000000000000000..3bc39a74a56390c263e63bfead028f6bce4df3cb --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/shellingham/posix/ps.py @@ -0,0 +1,51 @@ +import errno +import subprocess +import sys + +from ._core import Process + + +class PsNotAvailable(EnvironmentError): + pass + + +def iter_process_parents(pid, max_depth=10): + """Try to look up the process tree via the output of `ps`.""" + try: + cmd = ["ps", "-ww", "-o", "pid=", "-o", "ppid=", "-o", "args="] + output = subprocess.check_output(cmd) + except OSError as e: # Python 2-compatible FileNotFoundError. + if e.errno != errno.ENOENT: + raise + raise PsNotAvailable("ps not found") + except subprocess.CalledProcessError as e: + # `ps` can return 1 if the process list is completely empty. + # (sarugaku/shellingham#15) + if not e.output.strip(): + return + raise + if not isinstance(output, str): + encoding = sys.getfilesystemencoding() or sys.getdefaultencoding() + output = output.decode(encoding) + + processes_mapping = {} + for line in output.split("\n"): + try: + _pid, ppid, args = line.strip().split(None, 2) + # XXX: This is not right, but we are really out of options. + # ps does not offer a sane way to decode the argument display, + # and this is "Good Enough" for obtaining shell names. Hopefully + # people don't name their shell with a space, or have something + # like "/usr/bin/xonsh is uber". (sarugaku/shellingham#14) + args = tuple(a.strip() for a in args.split(" ")) + except ValueError: + continue + processes_mapping[_pid] = Process(args=args, pid=_pid, ppid=ppid) + + for _ in range(max_depth): + try: + process = processes_mapping[pid] + except KeyError: + return + yield process + pid = process.ppid diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/INSTALLER b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/INSTALLER new file mode 100644 index 0000000000000000000000000000000000000000..a1b589e38a32041e49332e5e81c2d363dc418d68 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/INSTALLER @@ -0,0 +1 @@ +pip diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/LICENSE b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..1cc22a5aa7679ebaa10934212f356823931bdc3e --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/LICENSE @@ -0,0 +1,18 @@ +Copyright (c) 2010-2024 Benjamin Peterson + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of +the Software, and to permit persons to whom the Software is furnished to do so, +subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS +FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR +COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER +IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/METADATA b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/METADATA new file mode 100644 index 0000000000000000000000000000000000000000..cfde03c2631c5c1d5cdc0949d0ee3379e7110f0e --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/METADATA @@ -0,0 +1,43 @@ +Metadata-Version: 2.1 +Name: six +Version: 1.17.0 +Summary: Python 2 and 3 compatibility utilities +Home-page: https://github.com/benjaminp/six +Author: Benjamin Peterson +Author-email: benjamin@python.org +License: MIT +Classifier: Development Status :: 5 - Production/Stable +Classifier: Programming Language :: Python :: 2 +Classifier: Programming Language :: Python :: 3 +Classifier: Intended Audience :: Developers +Classifier: License :: OSI Approved :: MIT License +Classifier: Topic :: Software Development :: Libraries +Classifier: Topic :: Utilities +Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.* +License-File: LICENSE + +.. image:: https://img.shields.io/pypi/v/six.svg + :target: https://pypi.org/project/six/ + :alt: six on PyPI + +.. image:: https://readthedocs.org/projects/six/badge/?version=latest + :target: https://six.readthedocs.io/ + :alt: six's documentation on Read the Docs + +.. image:: https://img.shields.io/badge/license-MIT-green.svg + :target: https://github.com/benjaminp/six/blob/master/LICENSE + :alt: MIT License badge + +Six is a Python 2 and 3 compatibility library. It provides utility functions +for smoothing over the differences between the Python versions with the goal of +writing Python code that is compatible on both Python versions. See the +documentation for more information on what is provided. + +Six supports Python 2.7 and 3.3+. It is contained in only one Python +file, so it can be easily copied into your project. (The copyright and license +notice must be retained.) + +Online documentation is at https://six.readthedocs.io/. + +Bugs can be reported to https://github.com/benjaminp/six. The code can also +be found there. diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/RECORD b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/RECORD new file mode 100644 index 0000000000000000000000000000000000000000..888d9850e5c78ed5c5e19c3974b6311297fb3bae --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/RECORD @@ -0,0 +1,8 @@ +__pycache__/six.cpython-310.pyc,, +six-1.17.0.dist-info/INSTALLER,sha256=zuuue4knoyJ-UwPPXg8fezS7VCrXJQrAP7zeNuwvFQg,4 +six-1.17.0.dist-info/LICENSE,sha256=Q3W6IOK5xsTnytKUCmKP2Q6VzD1Q7pKq51VxXYuh-9A,1066 +six-1.17.0.dist-info/METADATA,sha256=ViBCB4wnUlSfbYp8htvF3XCAiKe-bYBnLsewcQC3JGg,1658 +six-1.17.0.dist-info/RECORD,, +six-1.17.0.dist-info/WHEEL,sha256=pxeNX5JdtCe58PUSYP9upmc7jdRPgvT0Gm9kb1SHlVw,109 +six-1.17.0.dist-info/top_level.txt,sha256=_iVH_iYEtEXnD8nYGQYpYFUvkUW9sEO1GYbkeKSAais,4 +six.py,sha256=xRyR9wPT1LNpbJI8tf7CE-BeddkhU5O--sfy-mo5BN8,34703 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/WHEEL b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/WHEEL new file mode 100644 index 0000000000000000000000000000000000000000..104f3874635f24f0d2918dfeaf6a59652274460c --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/WHEEL @@ -0,0 +1,6 @@ +Wheel-Version: 1.0 +Generator: setuptools (75.6.0) +Root-Is-Purelib: true +Tag: py2-none-any +Tag: py3-none-any + diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/top_level.txt b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/top_level.txt new file mode 100644 index 0000000000000000000000000000000000000000..ffe2fce498955b628014618b28c6bcf152466a4a --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/six-1.17.0.dist-info/top_level.txt @@ -0,0 +1 @@ +six diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..6e06d16bd4d506966ccc5a6ea42de1a608d8e99e --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/__init__.py @@ -0,0 +1,54 @@ +"""Module to give helpful messages to the user that did not +compile scikit-learn properly. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import os + +INPLACE_MSG = """ +It appears that you are importing a local scikit-learn source tree. For +this, you need to have an inplace install. Maybe you are in the source +directory and you need to try from another location.""" + +STANDARD_MSG = """ +If you have used an installer, please check that it is suited for your +Python version, your operating system and your platform.""" + + +def raise_build_error(e): + # Raise a comprehensible error and list the contents of the + # directory to help debugging on the mailing list. + local_dir = os.path.split(__file__)[0] + msg = STANDARD_MSG + if local_dir == "sklearn/__check_build": + # Picking up the local install: this will work only if the + # install is an 'inplace build' + msg = INPLACE_MSG + dir_content = list() + for i, filename in enumerate(os.listdir(local_dir)): + if (i + 1) % 3: + dir_content.append(filename.ljust(26)) + else: + dir_content.append(filename + "\n") + raise ImportError( + """%s +___________________________________________________________________________ +Contents of %s: +%s +___________________________________________________________________________ +It seems that scikit-learn has not been built correctly. + +If you have installed scikit-learn from source, please do not forget +to build the package before using it. For detailed instructions, see: +https://scikit-learn.org/dev/developers/advanced_installation.html#building-from-source +%s""" + % (e, local_dir, "".join(dir_content).strip(), msg) + ) + + +try: + from ._check_build import check_build # noqa: F401 +except ImportError as e: + raise_build_error(e) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/_check_build.cpython-310-x86_64-linux-gnu.so b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/_check_build.cpython-310-x86_64-linux-gnu.so new file mode 100644 index 0000000000000000000000000000000000000000..f4d3fef213e165e748073d223fc2b3af9bd30dff Binary files /dev/null and b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/_check_build.cpython-310-x86_64-linux-gnu.so differ diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/_check_build.pyx b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/_check_build.pyx new file mode 100644 index 0000000000000000000000000000000000000000..0409e73f5e96dc3a4c27889fa44eda8a17d36ef9 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/_check_build.pyx @@ -0,0 +1,2 @@ +def check_build(): + return diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/meson.build b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/meson.build new file mode 100644 index 0000000000000000000000000000000000000000..5f6115d9765499dc28f477a1506a8298492003f5 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__check_build/meson.build @@ -0,0 +1,6 @@ +py.extension_module( + '_check_build', + cython_gen.process('_check_build.pyx'), + install: true, + subdir: 'sklearn/__check_build', +) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..1064d6564ce6d5bd256386cc1b928d46a60f2b50 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/__init__.py @@ -0,0 +1,162 @@ +"""Configure global settings and get information about the working environment.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +# Machine learning module for Python +# ================================== +# +# sklearn is a Python module integrating classical machine +# learning algorithms in the tightly-knit world of scientific Python +# packages (numpy, scipy, matplotlib). +# +# It aims to provide simple and efficient solutions to learning problems +# that are accessible to everybody and reusable in various contexts: +# machine-learning as a versatile tool for science and engineering. +# +# See https://scikit-learn.org for complete documentation. + +import importlib as _importlib +import logging +import os +import random + +from ._config import config_context, get_config, set_config + +logger = logging.getLogger(__name__) + + +# PEP0440 compatible formatted version, see: +# https://www.python.org/dev/peps/pep-0440/ +# +# Generic release markers: +# X.Y.0 # For first release after an increment in Y +# X.Y.Z # For bugfix releases +# +# Admissible pre-release markers: +# X.Y.ZaN # Alpha release +# X.Y.ZbN # Beta release +# X.Y.ZrcN # Release Candidate +# X.Y.Z # Final release +# +# Dev branch marker is: 'X.Y.dev' or 'X.Y.devN' where N is an integer. +# 'X.Y.dev0' is the canonical version of 'X.Y.dev' +# +__version__ = "1.7.2" + + +# On OSX, we can get a runtime error due to multiple OpenMP libraries loaded +# simultaneously. This can happen for instance when calling BLAS inside a +# prange. Setting the following environment variable allows multiple OpenMP +# libraries to be loaded. It should not degrade performances since we manually +# take care of potential over-subcription performance issues, in sections of +# the code where nested OpenMP loops can happen, by dynamically reconfiguring +# the inner OpenMP runtime to temporarily disable it while under the scope of +# the outer OpenMP parallel section. +os.environ.setdefault("KMP_DUPLICATE_LIB_OK", "True") + +# Workaround issue discovered in intel-openmp 2019.5: +# https://github.com/ContinuumIO/anaconda-issues/issues/11294 +os.environ.setdefault("KMP_INIT_AT_FORK", "FALSE") + +# `_distributor_init` allows distributors to run custom init code. +# For instance, for the Windows wheel, this is used to pre-load the +# vcomp shared library runtime for OpenMP embedded in the sklearn/.libs +# sub-folder. +# It is necessary to do this prior to importing show_versions as the +# later is linked to the OpenMP runtime to make it possible to introspect +# it and importing it first would fail if the OpenMP dll cannot be found. +from . import ( # noqa: F401 E402 + __check_build, + _distributor_init, +) +from .base import clone # noqa: E402 +from .utils._show_versions import show_versions # noqa: E402 + +_submodules = [ + "calibration", + "cluster", + "covariance", + "cross_decomposition", + "datasets", + "decomposition", + "dummy", + "ensemble", + "exceptions", + "experimental", + "externals", + "feature_extraction", + "feature_selection", + "frozen", + "gaussian_process", + "inspection", + "isotonic", + "kernel_approximation", + "kernel_ridge", + "linear_model", + "manifold", + "metrics", + "mixture", + "model_selection", + "multiclass", + "multioutput", + "naive_bayes", + "neighbors", + "neural_network", + "pipeline", + "preprocessing", + "random_projection", + "semi_supervised", + "svm", + "tree", + "discriminant_analysis", + "impute", + "compose", +] + +__all__ = _submodules + [ + # Non-modules: + "clone", + "get_config", + "set_config", + "config_context", + "show_versions", +] + + +def __dir__(): + return __all__ + + +def __getattr__(name): + if name in _submodules: + return _importlib.import_module(f"sklearn.{name}") + else: + try: + return globals()[name] + except KeyError: + raise AttributeError(f"Module 'sklearn' has no attribute '{name}'") + + +_BUILT_WITH_MESON = False +try: + import sklearn._built_with_meson # noqa: F401 + + _BUILT_WITH_MESON = True +except ModuleNotFoundError: + pass + + +def setup_module(module): + """Fixture for the tests to assure globally controllable seeding of RNGs""" + + import numpy as np + + # Check if a random seed exists in the environment, if not create one. + _random_seed = os.environ.get("SKLEARN_SEED", None) + if _random_seed is None: + _random_seed = np.random.uniform() * np.iinfo(np.int32).max + _random_seed = int(_random_seed) + print("I: Seeding RNGs with %r" % _random_seed) + np.random.seed(_random_seed) + random.seed(_random_seed) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_build_utils/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_build_utils/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_build_utils/tempita.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_build_utils/tempita.py new file mode 100644 index 0000000000000000000000000000000000000000..c8a7a35a62feeed47fbb10ace87411c9bdc16370 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_build_utils/tempita.py @@ -0,0 +1,62 @@ +#!/usr/bin/env python3 + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import argparse +import os + +from Cython import Tempita as tempita + +# XXX: If this import ever fails (does it really?), vendor either +# cython.tempita or numpy/npy_tempita. + + +def process_tempita(fromfile, outfile=None): + """Process tempita templated file and write out the result. + + The template file is expected to end in `.c.tp` or `.pyx.tp`: + E.g. processing `template.c.in` generates `template.c`. + + """ + with open(fromfile, "r", encoding="utf-8") as f: + template_content = f.read() + + template = tempita.Template(template_content) + content = template.substitute() + + with open(outfile, "w", encoding="utf-8") as f: + f.write(content) + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument("infile", type=str, help="Path to the input file") + parser.add_argument("-o", "--outdir", type=str, help="Path to the output directory") + parser.add_argument( + "-i", + "--ignore", + type=str, + help=( + "An ignored input - may be useful to add a " + "dependency between custom targets" + ), + ) + args = parser.parse_args() + + if not args.infile.endswith(".tp"): + raise ValueError(f"Unexpected extension: {args.infile}") + + if not args.outdir: + raise ValueError("Missing `--outdir` argument to tempita.py") + + outdir_abs = os.path.join(os.getcwd(), args.outdir) + outfile = os.path.join( + outdir_abs, os.path.splitext(os.path.split(args.infile)[1])[0] + ) + + process_tempita(args.infile, outfile) + + +if __name__ == "__main__": + main() diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_build_utils/version.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_build_utils/version.py new file mode 100644 index 0000000000000000000000000000000000000000..922a14917bf3fd2d395a4f5002a39c4d9d9c7ee2 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_build_utils/version.py @@ -0,0 +1,16 @@ +#!/usr/bin/env python3 +"""Extract version number from __init__.py""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import os + +sklearn_init = os.path.join(os.path.dirname(__file__), "../__init__.py") + +data = open(sklearn_init).readlines() +version_line = next(line for line in data if line.startswith("__version__")) + +version = version_line.strip().split(" = ")[1].replace('"', "").replace("'", "") + +print(version) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_built_with_meson.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_built_with_meson.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_config.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_config.py new file mode 100644 index 0000000000000000000000000000000000000000..66d119e02d1a3992ac59b86cef9b15d4e4e5b670 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_config.py @@ -0,0 +1,407 @@ +"""Global configuration state and functions for management""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import os +import threading +from contextlib import contextmanager as contextmanager + +_global_config = { + "assume_finite": bool(os.environ.get("SKLEARN_ASSUME_FINITE", False)), + "working_memory": int(os.environ.get("SKLEARN_WORKING_MEMORY", 1024)), + "print_changed_only": True, + "display": "diagram", + "pairwise_dist_chunk_size": int( + os.environ.get("SKLEARN_PAIRWISE_DIST_CHUNK_SIZE", 256) + ), + "enable_cython_pairwise_dist": True, + "array_api_dispatch": False, + "transform_output": "default", + "enable_metadata_routing": False, + "skip_parameter_validation": False, +} +_threadlocal = threading.local() + + +def _get_threadlocal_config(): + """Get a threadlocal **mutable** configuration. If the configuration + does not exist, copy the default global configuration.""" + if not hasattr(_threadlocal, "global_config"): + _threadlocal.global_config = _global_config.copy() + return _threadlocal.global_config + + +def get_config(): + """Retrieve the current scikit-learn configuration. + + This reflects the effective global configurations as established by default upon + library import, or modified via :func:`set_config` or :func:`config_context`. + + Returns + ------- + config : dict + Keys are parameter names that can be passed to :func:`set_config`. + + See Also + -------- + config_context : Context manager for global scikit-learn configuration. + set_config : Set global scikit-learn configuration. + + Examples + -------- + >>> import sklearn + >>> config = sklearn.get_config() + >>> config.keys() + dict_keys([...]) + """ + # Return a copy of the threadlocal configuration so that users will + # not be able to modify the configuration with the returned dict. + return _get_threadlocal_config().copy() + + +def set_config( + assume_finite=None, + working_memory=None, + print_changed_only=None, + display=None, + pairwise_dist_chunk_size=None, + enable_cython_pairwise_dist=None, + array_api_dispatch=None, + transform_output=None, + enable_metadata_routing=None, + skip_parameter_validation=None, +): + """Set global scikit-learn configuration. + + These settings control the behaviour of scikit-learn functions during a library + usage session. Global configuration defaults (as described in the parameter list + below) take effect when scikit-learn is imported. + + This function can be used to modify the global scikit-learn configuration at + runtime. Passing `None` as an argument (the default) leaves the corresponding + setting unchanged. This allows users to selectively update the global configuration + values without affecting the others. + + .. versionadded:: 0.19 + + Parameters + ---------- + assume_finite : bool, default=None + If True, validation for finiteness will be skipped, + saving time, but leading to potential crashes. If + False, validation for finiteness will be performed, + avoiding error. Global default: False. + + .. versionadded:: 0.19 + + working_memory : int, default=None + If set, scikit-learn will attempt to limit the size of temporary arrays + to this number of MiB (per job when parallelised), often saving both + computation time and memory on expensive operations that can be + performed in chunks. Global default: 1024. + + .. versionadded:: 0.20 + + print_changed_only : bool, default=None + If True, only the parameters that were set to non-default + values will be printed when printing an estimator. For example, + ``print(SVC())`` while True will only print 'SVC()' while the default + behaviour would be to print 'SVC(C=1.0, cache_size=200, ...)' with + all the non-changed parameters. Global default: True. + + .. versionadded:: 0.21 + .. versionchanged:: 0.23 + Global default configuration changed from False to True. + + display : {'text', 'diagram'}, default=None + If 'diagram', estimators will be displayed as a diagram in a Jupyter + lab or notebook context. If 'text', estimators will be displayed as + text. Global default: 'diagram'. + + .. versionadded:: 0.23 + + pairwise_dist_chunk_size : int, default=None + The number of row vectors per chunk for the accelerated pairwise- + distances reduction backend. Global default: 256 (suitable for most of + modern laptops' caches and architectures). + + Intended for easier benchmarking and testing of scikit-learn internals. + End users are not expected to benefit from customizing this configuration + setting. + + .. versionadded:: 1.1 + + enable_cython_pairwise_dist : bool, default=None + Use the accelerated pairwise-distances reduction backend when + possible. Global default: True. + + Intended for easier benchmarking and testing of scikit-learn internals. + End users are not expected to benefit from customizing this configuration + setting. + + .. versionadded:: 1.1 + + array_api_dispatch : bool, default=None + Use Array API dispatching when inputs follow the Array API standard. + Global default: False. + + See the :ref:`User Guide ` for more details. + + .. versionadded:: 1.2 + + transform_output : str, default=None + Configure output of `transform` and `fit_transform`. + + See :ref:`sphx_glr_auto_examples_miscellaneous_plot_set_output.py` + for an example on how to use the API. + + - `"default"`: Default output format of a transformer + - `"pandas"`: DataFrame output + - `"polars"`: Polars output + - `None`: Transform configuration is unchanged + + Global default: "default". + + .. versionadded:: 1.2 + .. versionadded:: 1.4 + `"polars"` option was added. + + enable_metadata_routing : bool, default=None + Enable metadata routing. By default this feature is disabled. + + Refer to :ref:`metadata routing user guide ` for more + details. + + - `True`: Metadata routing is enabled + - `False`: Metadata routing is disabled, use the old syntax. + - `None`: Configuration is unchanged + + Global default: False. + + .. versionadded:: 1.3 + + skip_parameter_validation : bool, default=None + If `True`, disable the validation of the hyper-parameters' types and values in + the fit method of estimators and for arguments passed to public helper + functions. It can save time in some situations but can lead to low level + crashes and exceptions with confusing error messages. + Global default: False. + + Note that for data parameters, such as `X` and `y`, only type validation is + skipped but validation with `check_array` will continue to run. + + .. versionadded:: 1.3 + + See Also + -------- + config_context : Context manager for global scikit-learn configuration. + get_config : Retrieve current values of the global configuration. + + Examples + -------- + >>> from sklearn import set_config + >>> set_config(display='diagram') # doctest: +SKIP + """ + local_config = _get_threadlocal_config() + + if assume_finite is not None: + local_config["assume_finite"] = assume_finite + if working_memory is not None: + local_config["working_memory"] = working_memory + if print_changed_only is not None: + local_config["print_changed_only"] = print_changed_only + if display is not None: + local_config["display"] = display + if pairwise_dist_chunk_size is not None: + local_config["pairwise_dist_chunk_size"] = pairwise_dist_chunk_size + if enable_cython_pairwise_dist is not None: + local_config["enable_cython_pairwise_dist"] = enable_cython_pairwise_dist + if array_api_dispatch is not None: + from .utils._array_api import _check_array_api_dispatch + + _check_array_api_dispatch(array_api_dispatch) + local_config["array_api_dispatch"] = array_api_dispatch + if transform_output is not None: + local_config["transform_output"] = transform_output + if enable_metadata_routing is not None: + local_config["enable_metadata_routing"] = enable_metadata_routing + if skip_parameter_validation is not None: + local_config["skip_parameter_validation"] = skip_parameter_validation + + +@contextmanager +def config_context( + *, + assume_finite=None, + working_memory=None, + print_changed_only=None, + display=None, + pairwise_dist_chunk_size=None, + enable_cython_pairwise_dist=None, + array_api_dispatch=None, + transform_output=None, + enable_metadata_routing=None, + skip_parameter_validation=None, +): + """Context manager to temporarily change the global scikit-learn configuration. + + This context manager can be used to apply scikit-learn configuration changes within + the scope of the with statement. Once the context exits, the global configuration is + restored again. + + The default global configurations (which take effect when scikit-learn is imported) + are defined below in the parameter list. + + Parameters + ---------- + assume_finite : bool, default=None + If True, validation for finiteness will be skipped, + saving time, but leading to potential crashes. If + False, validation for finiteness will be performed, + avoiding error. If None, the existing configuration won't change. + Global default: False. + + working_memory : int, default=None + If set, scikit-learn will attempt to limit the size of temporary arrays + to this number of MiB (per job when parallelised), often saving both + computation time and memory on expensive operations that can be + performed in chunks. If None, the existing configuration won't change. + Global default: 1024. + + print_changed_only : bool, default=None + If True, only the parameters that were set to non-default + values will be printed when printing an estimator. For example, + ``print(SVC())`` while True will only print 'SVC()', but would print + 'SVC(C=1.0, cache_size=200, ...)' with all the non-changed parameters + when False. If None, the existing configuration won't change. + Global default: True. + + .. versionchanged:: 0.23 + Global default configuration changed from False to True. + + display : {'text', 'diagram'}, default=None + If 'diagram', estimators will be displayed as a diagram in a Jupyter + lab or notebook context. If 'text', estimators will be displayed as + text. If None, the existing configuration won't change. + Global default: 'diagram'. + + .. versionadded:: 0.23 + + pairwise_dist_chunk_size : int, default=None + The number of row vectors per chunk for the accelerated pairwise- + distances reduction backend. Global default: 256 (suitable for most of + modern laptops' caches and architectures). + + Intended for easier benchmarking and testing of scikit-learn internals. + End users are not expected to benefit from customizing this configuration + setting. + + .. versionadded:: 1.1 + + enable_cython_pairwise_dist : bool, default=None + Use the accelerated pairwise-distances reduction backend when + possible. Global default: True. + + Intended for easier benchmarking and testing of scikit-learn internals. + End users are not expected to benefit from customizing this configuration + setting. + + .. versionadded:: 1.1 + + array_api_dispatch : bool, default=None + Use Array API dispatching when inputs follow the Array API standard. + Global default: False. + + See the :ref:`User Guide ` for more details. + + .. versionadded:: 1.2 + + transform_output : str, default=None + Configure output of `transform` and `fit_transform`. + + See :ref:`sphx_glr_auto_examples_miscellaneous_plot_set_output.py` + for an example on how to use the API. + + - `"default"`: Default output format of a transformer + - `"pandas"`: DataFrame output + - `"polars"`: Polars output + - `None`: Transform configuration is unchanged + + Global default: "default". + + .. versionadded:: 1.2 + .. versionadded:: 1.4 + `"polars"` option was added. + + enable_metadata_routing : bool, default=None + Enable metadata routing. By default this feature is disabled. + + Refer to :ref:`metadata routing user guide ` for more + details. + + - `True`: Metadata routing is enabled + - `False`: Metadata routing is disabled, use the old syntax. + - `None`: Configuration is unchanged + + Global default: False. + + .. versionadded:: 1.3 + + skip_parameter_validation : bool, default=None + If `True`, disable the validation of the hyper-parameters' types and values in + the fit method of estimators and for arguments passed to public helper + functions. It can save time in some situations but can lead to low level + crashes and exceptions with confusing error messages. + Global default: False. + + Note that for data parameters, such as `X` and `y`, only type validation is + skipped but validation with `check_array` will continue to run. + + .. versionadded:: 1.3 + + Yields + ------ + None. + + See Also + -------- + set_config : Set global scikit-learn configuration. + get_config : Retrieve current values of the global configuration. + + Notes + ----- + All settings, not just those presently modified, will be returned to + their previous values when the context manager is exited. + + Examples + -------- + >>> import sklearn + >>> from sklearn.utils.validation import assert_all_finite + >>> with sklearn.config_context(assume_finite=True): + ... assert_all_finite([float('nan')]) + >>> with sklearn.config_context(assume_finite=True): + ... with sklearn.config_context(assume_finite=False): + ... assert_all_finite([float('nan')]) + Traceback (most recent call last): + ... + ValueError: Input contains NaN... + """ + old_config = get_config() + set_config( + assume_finite=assume_finite, + working_memory=working_memory, + print_changed_only=print_changed_only, + display=display, + pairwise_dist_chunk_size=pairwise_dist_chunk_size, + enable_cython_pairwise_dist=enable_cython_pairwise_dist, + array_api_dispatch=array_api_dispatch, + transform_output=transform_output, + enable_metadata_routing=enable_metadata_routing, + skip_parameter_validation=skip_parameter_validation, + ) + + try: + yield + finally: + set_config(**old_config) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_distributor_init.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_distributor_init.py new file mode 100644 index 0000000000000000000000000000000000000000..d66d5d36955c1ca5debf5821e2a2f265ef1f98ed --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_distributor_init.py @@ -0,0 +1,13 @@ +"""Distributor init file + +Distributors: you can add custom code here to support particular distributions +of scikit-learn. + +For example, this is a good place to put any checks for hardware requirements. + +The scikit-learn standard source distribution will not put code in this file, +so you can safely replace this file with your own version. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_isotonic.pyx b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_isotonic.pyx new file mode 100644 index 0000000000000000000000000000000000000000..3dfb0421f0c190b293ce4121fc21cc68bc54f79c --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_isotonic.pyx @@ -0,0 +1,116 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +# Uses the pool adjacent violators algorithm (PAVA), with the +# enhancement of searching for the longest decreasing subsequence to +# pool at each step. + +import numpy as np +from cython cimport floating + + +def _inplace_contiguous_isotonic_regression(floating[::1] y, floating[::1] w): + cdef: + Py_ssize_t n = y.shape[0], i, k + floating prev_y, sum_wy, sum_w + Py_ssize_t[::1] target = np.arange(n, dtype=np.intp) + + # target describes a list of blocks. At any time, if [i..j] (inclusive) is + # an active block, then target[i] := j and target[j] := i. + + # For "active" indices (block starts): + # w[i] := sum{w_orig[j], j=[i..target[i]]} + # y[i] := sum{y_orig[j]*w_orig[j], j=[i..target[i]]} / w[i] + + with nogil: + i = 0 + while i < n: + k = target[i] + 1 + if k == n: + break + if y[i] < y[k]: + i = k + continue + sum_wy = w[i] * y[i] + sum_w = w[i] + while True: + # We are within a decreasing subsequence. + prev_y = y[k] + sum_wy += w[k] * y[k] + sum_w += w[k] + k = target[k] + 1 + if k == n or prev_y < y[k]: + # Non-singleton decreasing subsequence is finished, + # update first entry. + y[i] = sum_wy / sum_w + w[i] = sum_w + target[i] = k - 1 + target[k - 1] = i + if i > 0: + # Backtrack if we can. This makes the algorithm + # single-pass and ensures O(n) complexity. + i = target[i - 1] + # Otherwise, restart from the same point. + break + # Reconstruct the solution. + i = 0 + while i < n: + k = target[i] + 1 + y[i + 1 : k] = y[i] + i = k + + +def _make_unique(const floating[::1] X, + const floating[::1] y, + const floating[::1] sample_weights): + """Average targets for duplicate X, drop duplicates. + + Aggregates duplicate X values into a single X value where + the target y is a (sample_weighted) average of the individual + targets. + + Assumes that X is ordered, so that all duplicates follow each other. + """ + unique_values = len(np.unique(X)) + + if floating is float: + dtype = np.float32 + else: + dtype = np.float64 + + cdef floating[::1] y_out = np.empty(unique_values, dtype=dtype) + cdef floating[::1] x_out = np.empty_like(y_out) + cdef floating[::1] weights_out = np.empty_like(y_out) + + cdef floating current_x = X[0] + cdef floating current_y = 0 + cdef floating current_weight = 0 + cdef int i = 0 + cdef int j + cdef floating x + cdef int n_samples = len(X) + cdef floating eps = np.finfo(dtype).resolution + + for j in range(n_samples): + x = X[j] + if x - current_x >= eps: + # next unique value + x_out[i] = current_x + weights_out[i] = current_weight + y_out[i] = current_y / current_weight + i += 1 + current_x = x + current_weight = sample_weights[j] + current_y = y[j] * sample_weights[j] + else: + current_weight += sample_weights[j] + current_y += y[j] * sample_weights[j] + + x_out[i] = current_x + weights_out[i] = current_weight + y_out[i] = current_y / current_weight + return( + np.asarray(x_out[:i+1]), + np.asarray(y_out[:i+1]), + np.asarray(weights_out[:i+1]), + ) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..97fdd884e517c4a623e6fc180526bde227af0c21 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/__init__.py @@ -0,0 +1,33 @@ +""" +The :mod:`sklearn._loss` module includes loss function classes suitable for +fitting classification and regression tasks. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +from .loss import ( + AbsoluteError, + HalfBinomialLoss, + HalfGammaLoss, + HalfMultinomialLoss, + HalfPoissonLoss, + HalfSquaredError, + HalfTweedieLoss, + HalfTweedieLossIdentity, + HuberLoss, + PinballLoss, +) + +__all__ = [ + "AbsoluteError", + "HalfBinomialLoss", + "HalfGammaLoss", + "HalfMultinomialLoss", + "HalfPoissonLoss", + "HalfSquaredError", + "HalfTweedieLoss", + "HalfTweedieLossIdentity", + "HuberLoss", + "PinballLoss", +] diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/_loss.pxd b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/_loss.pxd new file mode 100644 index 0000000000000000000000000000000000000000..ac01b122a0941c35bc4d440543cf5c981943952a --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/_loss.pxd @@ -0,0 +1,101 @@ +# Fused types for input like y_true, raw_prediction, sample_weights. +ctypedef fused floating_in: + double + float + + +# Fused types for output like gradient and hessian +# We use a different fused types for input (floating_in) and output (floating_out), such +# that input and output can have different dtypes in the same function call. A single +# fused type can only take on one single value (type) for all arguments in one function +# call. +ctypedef fused floating_out: + double + float + + +# Struct to return 2 doubles +ctypedef struct double_pair: + double val1 + double val2 + + +# C base class for loss functions +cdef class CyLossFunction: + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil + cdef double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil + + +cdef class CyHalfSquaredError(CyLossFunction): + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil + cdef double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil + + +cdef class CyAbsoluteError(CyLossFunction): + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil + cdef double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil + + +cdef class CyPinballLoss(CyLossFunction): + cdef readonly double quantile # readonly makes it accessible from Python + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil + cdef double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil + + +cdef class CyHuberLoss(CyLossFunction): + cdef public double delta # public makes it accessible from Python + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil + cdef double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil + + +cdef class CyHalfPoissonLoss(CyLossFunction): + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil + cdef double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil + + +cdef class CyHalfGammaLoss(CyLossFunction): + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil + cdef double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil + + +cdef class CyHalfTweedieLoss(CyLossFunction): + cdef readonly double power # readonly makes it accessible from Python + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil + cdef double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil + + +cdef class CyHalfTweedieLossIdentity(CyLossFunction): + cdef readonly double power # readonly makes it accessible from Python + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil + cdef double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil + + +cdef class CyHalfBinomialLoss(CyLossFunction): + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil + cdef double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil + + +cdef class CyExponentialLoss(CyLossFunction): + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil + cdef double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil + + +cdef class CyHalfMultinomialLoss(): + cdef void cy_gradient( + self, + const floating_in y_true, + const floating_in[::1] raw_prediction, + const floating_in sample_weight, + floating_out[::1] gradient_out, + ) noexcept nogil diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/_loss.pyx.tp b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/_loss.pyx.tp new file mode 100644 index 0000000000000000000000000000000000000000..44d5acd530a7f60ac6e08174c5e5197f3fb00735 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/_loss.pyx.tp @@ -0,0 +1,1505 @@ +{{py: + +""" +Template file to easily generate loops over samples using Tempita +(https://github.com/cython/cython/blob/master/Cython/Tempita/_tempita.py). + +Generated file: _loss.pyx + +Each loss class is generated by a cdef functions on single samples. +The keywords between double braces are substituted during the build. +""" + +doc_HalfSquaredError = ( + """Half Squared Error with identity link. + + Domain: + y_true and y_pred all real numbers + + Link: + y_pred = raw_prediction + """ +) + +doc_AbsoluteError = ( + """Absolute Error with identity link. + + Domain: + y_true and y_pred all real numbers + + Link: + y_pred = raw_prediction + """ +) + +doc_PinballLoss = ( + """Quantile Loss aka Pinball Loss with identity link. + + Domain: + y_true and y_pred all real numbers + quantile in (0, 1) + + Link: + y_pred = raw_prediction + + Note: 2 * cPinballLoss(quantile=0.5) equals cAbsoluteError() + """ +) + +doc_HuberLoss = ( + """Huber Loss with identity link. + + Domain: + y_true and y_pred all real numbers + delta in positive real numbers + + Link: + y_pred = raw_prediction + """ +) + +doc_HalfPoissonLoss = ( + """Half Poisson deviance loss with log-link. + + Domain: + y_true in non-negative real numbers + y_pred in positive real numbers + + Link: + y_pred = exp(raw_prediction) + + Half Poisson deviance with log-link is + y_true * log(y_true/y_pred) + y_pred - y_true + = y_true * log(y_true) - y_true * raw_prediction + + exp(raw_prediction) - y_true + + Dropping constant terms, this gives: + exp(raw_prediction) - y_true * raw_prediction + """ +) + +doc_HalfGammaLoss = ( + """Half Gamma deviance loss with log-link. + + Domain: + y_true and y_pred in positive real numbers + + Link: + y_pred = exp(raw_prediction) + + Half Gamma deviance with log-link is + log(y_pred/y_true) + y_true/y_pred - 1 + = raw_prediction - log(y_true) + y_true * exp(-raw_prediction) - 1 + + Dropping constant terms, this gives: + raw_prediction + y_true * exp(-raw_prediction) + """ +) + +doc_HalfTweedieLoss = ( + """Half Tweedie deviance loss with log-link. + + Domain: + y_true in real numbers if p <= 0 + y_true in non-negative real numbers if 0 < p < 2 + y_true in positive real numbers if p >= 2 + y_pred and power in positive real numbers + + Link: + y_pred = exp(raw_prediction) + + Half Tweedie deviance with log-link and p=power is + max(y_true, 0)**(2-p) / (1-p) / (2-p) + - y_true * y_pred**(1-p) / (1-p) + + y_pred**(2-p) / (2-p) + = max(y_true, 0)**(2-p) / (1-p) / (2-p) + - y_true * exp((1-p) * raw_prediction) / (1-p) + + exp((2-p) * raw_prediction) / (2-p) + + Dropping constant terms, this gives: + exp((2-p) * raw_prediction) / (2-p) + - y_true * exp((1-p) * raw_prediction) / (1-p) + + Notes: + - Poisson with p=1 and Gamma with p=2 have different terms dropped such + that cHalfTweedieLoss is not continuous in p=power at p=1 and p=2. + - While the Tweedie distribution only exists for p<=0 or p>=1, the range + 0= 2 + y_pred and power in positive real numbers, y_pred may be negative for p=0. + + Link: + y_pred = raw_prediction + + Half Tweedie deviance with identity link and p=power is + max(y_true, 0)**(2-p) / (1-p) / (2-p) + - y_true * y_pred**(1-p) / (1-p) + + y_pred**(2-p) / (2-p) + + Notes: + - Here, we do not drop constant terms in contrast to the version with log-link. + """ +) + +doc_HalfBinomialLoss = ( + """Half Binomial deviance loss with logit link. + + Domain: + y_true in [0, 1] + y_pred in (0, 1), i.e. boundaries excluded + + Link: + y_pred = expit(raw_prediction) + """ +) + +doc_ExponentialLoss = ( + """"Exponential loss with (half) logit link + + Domain: + y_true in [0, 1] + y_pred in (0, 1), i.e. boundaries excluded + + Link: + y_pred = expit(2 * raw_prediction) + """ +) + +# loss class name, docstring, param, +# cy_loss, cy_loss_grad, +# cy_grad, cy_grad_hess, +class_list = [ + ("CyHalfSquaredError", doc_HalfSquaredError, None, + "closs_half_squared_error", None, + "cgradient_half_squared_error", "cgrad_hess_half_squared_error"), + ("CyAbsoluteError", doc_AbsoluteError, None, + "closs_absolute_error", None, + "cgradient_absolute_error", "cgrad_hess_absolute_error"), + ("CyPinballLoss", doc_PinballLoss, "quantile", + "closs_pinball_loss", None, + "cgradient_pinball_loss", "cgrad_hess_pinball_loss"), + ("CyHuberLoss", doc_HuberLoss, "delta", + "closs_huber_loss", None, + "cgradient_huber_loss", "cgrad_hess_huber_loss"), + ("CyHalfPoissonLoss", doc_HalfPoissonLoss, None, + "closs_half_poisson", "closs_grad_half_poisson", + "cgradient_half_poisson", "cgrad_hess_half_poisson"), + ("CyHalfGammaLoss", doc_HalfGammaLoss, None, + "closs_half_gamma", "closs_grad_half_gamma", + "cgradient_half_gamma", "cgrad_hess_half_gamma"), + ("CyHalfTweedieLoss", doc_HalfTweedieLoss, "power", + "closs_half_tweedie", "closs_grad_half_tweedie", + "cgradient_half_tweedie", "cgrad_hess_half_tweedie"), + ("CyHalfTweedieLossIdentity", doc_HalfTweedieLossIdentity, "power", + "closs_half_tweedie_identity", "closs_grad_half_tweedie_identity", + "cgradient_half_tweedie_identity", "cgrad_hess_half_tweedie_identity"), + ("CyHalfBinomialLoss", doc_HalfBinomialLoss, None, + "closs_half_binomial", "closs_grad_half_binomial", + "cgradient_half_binomial", "cgrad_hess_half_binomial"), + ("CyExponentialLoss", doc_ExponentialLoss, None, + "closs_exponential", "closs_grad_exponential", + "cgradient_exponential", "cgrad_hess_exponential"), +] +}} + +# Design: +# See https://github.com/scikit-learn/scikit-learn/issues/15123 for reasons. +# a) Merge link functions into loss functions for speed and numerical +# stability, i.e. use raw_prediction instead of y_pred in signature. +# b) Pure C functions (nogil) calculate single points (single sample) +# c) Wrap C functions in a loop to get Python functions operating on ndarrays. +# - Write loops manually---use Tempita for this. +# Reason: There is still some performance overhead when using a wrapper +# function "wrap" that carries out the loop and gets as argument a function +# pointer to one of the C functions from b), e.g. +# wrap(closs_half_poisson, y_true, ...) +# - Pass n_threads as argument to prange and propagate option to all callers. +# d) Provide classes (Cython extension types) per loss (names start with Cy) in +# order to have semantical structured objects. +# - Member functions for single points just call the C function from b). +# These are used e.g. in SGD `_plain_sgd`. +# - Member functions operating on ndarrays, see c), looping over calls to C +# functions from b). +# e) Provide convenience Python classes that compose from these extension types +# elsewhere (see loss.py) +# - Example: loss.gradient calls CyLoss.gradient but does some input +# checking like None -> np.empty(). +# +# Note: We require 1-dim ndarrays to be contiguous. + +from cython.parallel import parallel, prange +import numpy as np + +from libc.math cimport exp, fabs, log, log1p, pow +from libc.stdlib cimport malloc, free + + +# ------------------------------------- +# Helper functions +# ------------------------------------- +# Numerically stable version of log(1 + exp(x)) for double precision, see Eq. (10) of +# https://cran.r-project.org/web/packages/Rmpfr/vignettes/log1mexp-note.pdf +# Note: The only important cutoff is at x = 18. All others are to save computation +# time. Compared to the reference, we add the additional case distinction x <= -2 in +# order to use log instead of log1p for improved performance. As with the other +# cutoffs, this is accurate within machine precision of double. +cdef inline double log1pexp(double x) noexcept nogil: + if x <= -37: + return exp(x) + elif x <= -2: + return log1p(exp(x)) + elif x <= 18: + return log(1. + exp(x)) + elif x <= 33.3: + return x + exp(-x) + else: + return x + + +cdef inline double_pair sum_exp_minus_max( + const int i, + const floating_in[:, :] raw_prediction, # IN + floating_out *p # OUT +) noexcept nogil: + # Thread local buffers are used to store part of the results via p. + # The results are stored as follows: + # p[k] = exp(raw_prediction_i_k - max_value) for k = 0 to n_classes-1 + # return.val1 = max_value = max(raw_prediction_i_k, k = 0 to n_classes-1) + # return.val2 = sum_exps = sum(p[k], k = 0 to n_classes-1) = sum of exponentials + # len(p) must be n_classes + # Notes: + # - We return the max value and sum of exps (stored in p) as a double_pair. + # - i needs to be passed (and stays constant) because otherwise Cython does + # not generate optimal code, see + # https://github.com/scikit-learn/scikit-learn/issues/17299 + # - We do not normalize p by calculating p[k] = p[k] / sum_exps. + # This helps to save one loop over k. + cdef: + int k + int n_classes = raw_prediction.shape[1] + double_pair max_value_and_sum_exps # val1 = max_value, val2 = sum_exps + + max_value_and_sum_exps.val1 = raw_prediction[i, 0] + max_value_and_sum_exps.val2 = 0 + for k in range(1, n_classes): + # Compute max value of array for numerical stability + if max_value_and_sum_exps.val1 < raw_prediction[i, k]: + max_value_and_sum_exps.val1 = raw_prediction[i, k] + + for k in range(n_classes): + p[k] = exp(raw_prediction[i, k] - max_value_and_sum_exps.val1) + max_value_and_sum_exps.val2 += p[k] + + return max_value_and_sum_exps + + +# ------------------------------------- +# Single point inline C functions +# ------------------------------------- +# Half Squared Error +cdef inline double closs_half_squared_error( + double y_true, + double raw_prediction +) noexcept nogil: + return 0.5 * (raw_prediction - y_true) * (raw_prediction - y_true) + + +cdef inline double cgradient_half_squared_error( + double y_true, + double raw_prediction +) noexcept nogil: + return raw_prediction - y_true + + +cdef inline double_pair cgrad_hess_half_squared_error( + double y_true, + double raw_prediction +) noexcept nogil: + cdef double_pair gh + gh.val1 = raw_prediction - y_true # gradient + gh.val2 = 1. # hessian + return gh + + +# Absolute Error +cdef inline double closs_absolute_error( + double y_true, + double raw_prediction +) noexcept nogil: + return fabs(raw_prediction - y_true) + + +cdef inline double cgradient_absolute_error( + double y_true, + double raw_prediction +) noexcept nogil: + return 1. if raw_prediction > y_true else -1. + + +cdef inline double_pair cgrad_hess_absolute_error( + double y_true, + double raw_prediction +) noexcept nogil: + cdef double_pair gh + # Note that exact hessian = 0 almost everywhere. Optimization routines like + # in HGBT, however, need a hessian > 0. Therefore, we assign 1. + gh.val1 = 1. if raw_prediction > y_true else -1. # gradient + gh.val2 = 1. # hessian + return gh + + +# Quantile Loss / Pinball Loss +cdef inline double closs_pinball_loss( + double y_true, + double raw_prediction, + double quantile +) noexcept nogil: + return (quantile * (y_true - raw_prediction) if y_true >= raw_prediction + else (1. - quantile) * (raw_prediction - y_true)) + + +cdef inline double cgradient_pinball_loss( + double y_true, + double raw_prediction, + double quantile +) noexcept nogil: + return -quantile if y_true >=raw_prediction else 1. - quantile + + +cdef inline double_pair cgrad_hess_pinball_loss( + double y_true, + double raw_prediction, + double quantile +) noexcept nogil: + cdef double_pair gh + # Note that exact hessian = 0 almost everywhere. Optimization routines like + # in HGBT, however, need a hessian > 0. Therefore, we assign 1. + gh.val1 = -quantile if y_true >=raw_prediction else 1. - quantile # gradient + gh.val2 = 1. # hessian + return gh + + +# Huber Loss +cdef inline double closs_huber_loss( + double y_true, + double raw_prediction, + double delta, +) noexcept nogil: + cdef double abserr = fabs(y_true - raw_prediction) + if abserr <= delta: + return 0.5 * abserr**2 + else: + return delta * (abserr - 0.5 * delta) + + +cdef inline double cgradient_huber_loss( + double y_true, + double raw_prediction, + double delta, +) noexcept nogil: + cdef double res = raw_prediction - y_true + if fabs(res) <= delta: + return res + else: + return delta if res >=0 else -delta + + +cdef inline double_pair cgrad_hess_huber_loss( + double y_true, + double raw_prediction, + double delta, +) noexcept nogil: + cdef double_pair gh + gh.val2 = raw_prediction - y_true # used as temporary + if fabs(gh.val2) <= delta: + gh.val1 = gh.val2 # gradient + gh.val2 = 1 # hessian + else: + gh.val1 = delta if gh.val2 >=0 else -delta # gradient + gh.val2 = 0 # hessian + return gh + + +# Half Poisson Deviance with Log-Link, dropping constant terms +cdef inline double closs_half_poisson( + double y_true, + double raw_prediction +) noexcept nogil: + return exp(raw_prediction) - y_true * raw_prediction + + +cdef inline double cgradient_half_poisson( + double y_true, + double raw_prediction +) noexcept nogil: + # y_pred - y_true + return exp(raw_prediction) - y_true + + +cdef inline double_pair closs_grad_half_poisson( + double y_true, + double raw_prediction +) noexcept nogil: + cdef double_pair lg + lg.val2 = exp(raw_prediction) # used as temporary + lg.val1 = lg.val2 - y_true * raw_prediction # loss + lg.val2 -= y_true # gradient + return lg + + +cdef inline double_pair cgrad_hess_half_poisson( + double y_true, + double raw_prediction +) noexcept nogil: + cdef double_pair gh + gh.val2 = exp(raw_prediction) # hessian + gh.val1 = gh.val2 - y_true # gradient + return gh + + +# Half Gamma Deviance with Log-Link, dropping constant terms +cdef inline double closs_half_gamma( + double y_true, + double raw_prediction +) noexcept nogil: + return raw_prediction + y_true * exp(-raw_prediction) + + +cdef inline double cgradient_half_gamma( + double y_true, + double raw_prediction +) noexcept nogil: + return 1. - y_true * exp(-raw_prediction) + + +cdef inline double_pair closs_grad_half_gamma( + double y_true, + double raw_prediction +) noexcept nogil: + cdef double_pair lg + lg.val2 = exp(-raw_prediction) # used as temporary + lg.val1 = raw_prediction + y_true * lg.val2 # loss + lg.val2 = 1. - y_true * lg.val2 # gradient + return lg + + +cdef inline double_pair cgrad_hess_half_gamma( + double y_true, + double raw_prediction +) noexcept nogil: + cdef double_pair gh + gh.val2 = exp(-raw_prediction) # used as temporary + gh.val1 = 1. - y_true * gh.val2 # gradient + gh.val2 *= y_true # hessian + return gh + + +# Half Tweedie Deviance with Log-Link, dropping constant terms +# Note that by dropping constants this is no longer continuous in parameter power. +cdef inline double closs_half_tweedie( + double y_true, + double raw_prediction, + double power +) noexcept nogil: + if power == 0.: + return closs_half_squared_error(y_true, exp(raw_prediction)) + elif power == 1.: + return closs_half_poisson(y_true, raw_prediction) + elif power == 2.: + return closs_half_gamma(y_true, raw_prediction) + else: + return (exp((2. - power) * raw_prediction) / (2. - power) + - y_true * exp((1. - power) * raw_prediction) / (1. - power)) + + +cdef inline double cgradient_half_tweedie( + double y_true, + double raw_prediction, + double power +) noexcept nogil: + cdef double exp1 + if power == 0.: + exp1 = exp(raw_prediction) + return exp1 * (exp1 - y_true) + elif power == 1.: + return cgradient_half_poisson(y_true, raw_prediction) + elif power == 2.: + return cgradient_half_gamma(y_true, raw_prediction) + else: + return (exp((2. - power) * raw_prediction) + - y_true * exp((1. - power) * raw_prediction)) + + +cdef inline double_pair closs_grad_half_tweedie( + double y_true, + double raw_prediction, + double power +) noexcept nogil: + cdef double_pair lg + cdef double exp1, exp2 + if power == 0.: + exp1 = exp(raw_prediction) + lg.val1 = closs_half_squared_error(y_true, exp1) # loss + lg.val2 = exp1 * (exp1 - y_true) # gradient + elif power == 1.: + return closs_grad_half_poisson(y_true, raw_prediction) + elif power == 2.: + return closs_grad_half_gamma(y_true, raw_prediction) + else: + exp1 = exp((1. - power) * raw_prediction) + exp2 = exp((2. - power) * raw_prediction) + lg.val1 = exp2 / (2. - power) - y_true * exp1 / (1. - power) # loss + lg.val2 = exp2 - y_true * exp1 # gradient + return lg + + +cdef inline double_pair cgrad_hess_half_tweedie( + double y_true, + double raw_prediction, + double power +) noexcept nogil: + cdef double_pair gh + cdef double exp1, exp2 + if power == 0.: + exp1 = exp(raw_prediction) + gh.val1 = exp1 * (exp1 - y_true) # gradient + gh.val2 = exp1 * (2 * exp1 - y_true) # hessian + elif power == 1.: + return cgrad_hess_half_poisson(y_true, raw_prediction) + elif power == 2.: + return cgrad_hess_half_gamma(y_true, raw_prediction) + else: + exp1 = exp((1. - power) * raw_prediction) + exp2 = exp((2. - power) * raw_prediction) + gh.val1 = exp2 - y_true * exp1 # gradient + gh.val2 = (2. - power) * exp2 - (1. - power) * y_true * exp1 # hessian + return gh + + +# Half Tweedie Deviance with identity link, without dropping constant terms! +# Therefore, best loss value is zero. +cdef inline double closs_half_tweedie_identity( + double y_true, + double raw_prediction, + double power +) noexcept nogil: + cdef double tmp + if power == 0.: + return closs_half_squared_error(y_true, raw_prediction) + elif power == 1.: + if y_true == 0: + return raw_prediction + else: + return y_true * log(y_true/raw_prediction) + raw_prediction - y_true + elif power == 2.: + return log(raw_prediction/y_true) + y_true/raw_prediction - 1. + else: + tmp = pow(raw_prediction, 1. - power) + tmp = raw_prediction * tmp / (2. - power) - y_true * tmp / (1. - power) + if y_true > 0: + tmp += pow(y_true, 2. - power) / ((1. - power) * (2. - power)) + return tmp + + +cdef inline double cgradient_half_tweedie_identity( + double y_true, + double raw_prediction, + double power +) noexcept nogil: + if power == 0.: + return raw_prediction - y_true + elif power == 1.: + return 1. - y_true / raw_prediction + elif power == 2.: + return (raw_prediction - y_true) / (raw_prediction * raw_prediction) + else: + return pow(raw_prediction, -power) * (raw_prediction - y_true) + + +cdef inline double_pair closs_grad_half_tweedie_identity( + double y_true, + double raw_prediction, + double power +) noexcept nogil: + cdef double_pair lg + cdef double tmp + if power == 0.: + lg.val2 = raw_prediction - y_true # gradient + lg.val1 = 0.5 * lg.val2 * lg.val2 # loss + elif power == 1.: + if y_true == 0: + lg.val1 = raw_prediction + else: + lg.val1 = (y_true * log(y_true/raw_prediction) # loss + + raw_prediction - y_true) + lg.val2 = 1. - y_true / raw_prediction # gradient + elif power == 2.: + lg.val1 = log(raw_prediction/y_true) + y_true/raw_prediction - 1. # loss + tmp = raw_prediction * raw_prediction + lg.val2 = (raw_prediction - y_true) / tmp # gradient + else: + tmp = pow(raw_prediction, 1. - power) + lg.val1 = (raw_prediction * tmp / (2. - power) # loss + - y_true * tmp / (1. - power)) + if y_true > 0: + lg.val1 += (pow(y_true, 2. - power) + / ((1. - power) * (2. - power))) + lg.val2 = tmp * (1. - y_true / raw_prediction) # gradient + return lg + + +cdef inline double_pair cgrad_hess_half_tweedie_identity( + double y_true, + double raw_prediction, + double power +) noexcept nogil: + cdef double_pair gh + cdef double tmp + if power == 0.: + gh.val1 = raw_prediction - y_true # gradient + gh.val2 = 1. # hessian + elif power == 1.: + gh.val1 = 1. - y_true / raw_prediction # gradient + gh.val2 = y_true / (raw_prediction * raw_prediction) # hessian + elif power == 2.: + tmp = raw_prediction * raw_prediction + gh.val1 = (raw_prediction - y_true) / tmp # gradient + gh.val2 = (-1. + 2. * y_true / raw_prediction) / tmp # hessian + else: + tmp = pow(raw_prediction, -power) + gh.val1 = tmp * (raw_prediction - y_true) # gradient + gh.val2 = tmp * ((1. - power) + power * y_true / raw_prediction) # hessian + return gh + + +# Half Binomial deviance with logit-link, aka log-loss or binary cross entropy +cdef inline double closs_half_binomial( + double y_true, + double raw_prediction +) noexcept nogil: + # log1p(exp(raw_prediction)) - y_true * raw_prediction + return log1pexp(raw_prediction) - y_true * raw_prediction + + +cdef inline double cgradient_half_binomial( + double y_true, + double raw_prediction +) noexcept nogil: + # gradient = y_pred - y_true = expit(raw_prediction) - y_true + # Numerically more stable, see http://fa.bianp.net/blog/2019/evaluate_logistic/ + # if raw_prediction < 0: + # exp_tmp = exp(raw_prediction) + # return ((1 - y_true) * exp_tmp - y_true) / (1 + exp_tmp) + # else: + # exp_tmp = exp(-raw_prediction) + # return ((1 - y_true) - y_true * exp_tmp) / (1 + exp_tmp) + # Note that optimal speed would be achieved, at the cost of precision, by + # return expit(raw_prediction) - y_true + # i.e. no "if else" and an own inline implementation of expit instead of + # from scipy.special.cython_special cimport expit + # The case distinction raw_prediction < 0 in the stable implementation does not + # provide significant better precision apart from protecting overflow of exp(..). + # The branch (if else), however, can incur runtime costs of up to 30%. + # Instead, we help branch prediction by almost always ending in the first if clause + # and making the second branch (else) a bit simpler. This has the exact same + # precision but is faster than the stable implementation. + # As branching criteria, we use the same cutoff as in log1pexp. Note that the + # maximal value to get gradient = -1 with y_true = 1 is -37.439198610162731 + # (based on mpmath), and scipy.special.logit(np.finfo(float).eps) ~ -36.04365. + cdef double exp_tmp + if raw_prediction > -37: + exp_tmp = exp(-raw_prediction) + return ((1 - y_true) - y_true * exp_tmp) / (1 + exp_tmp) + else: + # expit(raw_prediction) = exp(raw_prediction) for raw_prediction <= -37 + return exp(raw_prediction) - y_true + + +cdef inline double_pair closs_grad_half_binomial( + double y_true, + double raw_prediction +) noexcept nogil: + cdef double_pair lg + # Same if else conditions as in log1pexp. + if raw_prediction <= -37: + lg.val2 = exp(raw_prediction) # used as temporary + lg.val1 = lg.val2 - y_true * raw_prediction # loss + lg.val2 -= y_true # gradient + elif raw_prediction <= -2: + lg.val2 = exp(raw_prediction) # used as temporary + lg.val1 = log1p(lg.val2) - y_true * raw_prediction # loss + lg.val2 = ((1 - y_true) * lg.val2 - y_true) / (1 + lg.val2) # gradient + elif raw_prediction <= 18: + lg.val2 = exp(-raw_prediction) # used as temporary + # log1p(exp(x)) = log(1 + exp(x)) = x + log1p(exp(-x)) + lg.val1 = log1p(lg.val2) + (1 - y_true) * raw_prediction # loss + lg.val2 = ((1 - y_true) - y_true * lg.val2) / (1 + lg.val2) # gradient + else: + lg.val2 = exp(-raw_prediction) # used as temporary + lg.val1 = lg.val2 + (1 - y_true) * raw_prediction # loss + lg.val2 = ((1 - y_true) - y_true * lg.val2) / (1 + lg.val2) # gradient + return lg + + +cdef inline double_pair cgrad_hess_half_binomial( + double y_true, + double raw_prediction +) noexcept nogil: + # with y_pred = expit(raw) + # hessian = y_pred * (1 - y_pred) = exp( raw) / (1 + exp( raw))**2 + # = exp(-raw) / (1 + exp(-raw))**2 + cdef double_pair gh + # See comment in cgradient_half_binomial. + if raw_prediction > -37: + gh.val2 = exp(-raw_prediction) # used as temporary + gh.val1 = ((1 - y_true) - y_true * gh.val2) / (1 + gh.val2) # gradient + gh.val2 = gh.val2 / (1 + gh.val2)**2 # hessian + else: + gh.val2 = exp(raw_prediction) # = 1. order Taylor in exp(raw_prediction) + gh.val1 = gh.val2 - y_true + return gh + + +# Exponential loss with (half) logit-link, aka boosting loss +cdef inline double closs_exponential( + double y_true, + double raw_prediction +) noexcept nogil: + cdef double tmp = exp(raw_prediction) + return y_true / tmp + (1 - y_true) * tmp + + +cdef inline double cgradient_exponential( + double y_true, + double raw_prediction +) noexcept nogil: + cdef double tmp = exp(raw_prediction) + return -y_true / tmp + (1 - y_true) * tmp + + +cdef inline double_pair closs_grad_exponential( + double y_true, + double raw_prediction +) noexcept nogil: + cdef double_pair lg + lg.val2 = exp(raw_prediction) # used as temporary + + lg.val1 = y_true / lg.val2 + (1 - y_true) * lg.val2 # loss + lg.val2 = -y_true / lg.val2 + (1 - y_true) * lg.val2 # gradient + return lg + + +cdef inline double_pair cgrad_hess_exponential( + double y_true, + double raw_prediction +) noexcept nogil: + # Note that hessian = loss + cdef double_pair gh + gh.val2 = exp(raw_prediction) # used as temporary + + gh.val1 = -y_true / gh.val2 + (1 - y_true) * gh.val2 # gradient + gh.val2 = y_true / gh.val2 + (1 - y_true) * gh.val2 # hessian + return gh + + +# --------------------------------------------------- +# Extension Types for Loss Functions of 1-dim targets +# --------------------------------------------------- +cdef class CyLossFunction: + """Base class for convex loss functions.""" + + def __reduce__(self): + return (self.__class__, ()) + + cdef double cy_loss(self, double y_true, double raw_prediction) noexcept nogil: + """Compute the loss for a single sample. + + Parameters + ---------- + y_true : double + Observed, true target value. + raw_prediction : double + Raw prediction value (in link space). + + Returns + ------- + double + The loss evaluated at `y_true` and `raw_prediction`. + """ + pass + + cdef double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil: + """Compute gradient of loss w.r.t. raw_prediction for a single sample. + + Parameters + ---------- + y_true : double + Observed, true target value. + raw_prediction : double + Raw prediction value (in link space). + + Returns + ------- + double + The derivative of the loss function w.r.t. `raw_prediction`. + """ + pass + + cdef double_pair cy_grad_hess( + self, double y_true, double raw_prediction + ) noexcept nogil: + """Compute gradient and hessian. + + Gradient and hessian of loss w.r.t. raw_prediction for a single sample. + + This is usually diagonal in raw_prediction_i and raw_prediction_j. + Therefore, we return the diagonal element i=j. + + For a loss with a non-canonical link, this might implement the diagonal + of the Fisher matrix (=expected hessian) instead of the hessian. + + Parameters + ---------- + y_true : double + Observed, true target value. + raw_prediction : double + Raw prediction value (in link space). + + Returns + ------- + double_pair + Gradient and hessian of the loss function w.r.t. `raw_prediction`. + """ + pass + + def loss( + self, + const floating_in[::1] y_true, # IN + const floating_in[::1] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[::1] loss_out, # OUT + int n_threads=1 + ): + """Compute the point-wise loss value for each input. + + The point-wise loss is written to `loss_out` and no array is returned. + + Parameters + ---------- + y_true : array of shape (n_samples,) + Observed, true target values. + raw_prediction : array of shape (n_samples,) + Raw prediction values (in link space). + sample_weight : array of shape (n_samples,) or None + Sample weights. + loss_out : array of shape (n_samples,) + A location into which the result is stored. + n_threads : int + Number of threads used by OpenMP (if any). + """ + pass + + def gradient( + self, + const floating_in[::1] y_true, # IN + const floating_in[::1] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[::1] gradient_out, # OUT + int n_threads=1 + ): + """Compute gradient of loss w.r.t raw_prediction for each input. + + The gradient is written to `gradient_out` and no array is returned. + + Parameters + ---------- + y_true : array of shape (n_samples,) + Observed, true target values. + raw_prediction : array of shape (n_samples,) + Raw prediction values (in link space). + sample_weight : array of shape (n_samples,) or None + Sample weights. + gradient_out : array of shape (n_samples,) + A location into which the result is stored. + n_threads : int + Number of threads used by OpenMP (if any). + """ + pass + + def loss_gradient( + self, + const floating_in[::1] y_true, # IN + const floating_in[::1] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[::1] loss_out, # OUT + floating_out[::1] gradient_out, # OUT + int n_threads=1 + ): + """Compute loss and gradient of loss w.r.t raw_prediction. + + The loss and gradient are written to `loss_out` and `gradient_out` and no arrays + are returned. + + Parameters + ---------- + y_true : array of shape (n_samples,) + Observed, true target values. + raw_prediction : array of shape (n_samples,) + Raw prediction values (in link space). + sample_weight : array of shape (n_samples,) or None + Sample weights. + loss_out : array of shape (n_samples,) or None + A location into which the element-wise loss is stored. + gradient_out : array of shape (n_samples,) + A location into which the gradient is stored. + n_threads : int + Number of threads used by OpenMP (if any). + """ + self.loss(y_true, raw_prediction, sample_weight, loss_out, n_threads) + self.gradient(y_true, raw_prediction, sample_weight, gradient_out, n_threads) + + def gradient_hessian( + self, + const floating_in[::1] y_true, # IN + const floating_in[::1] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[::1] gradient_out, # OUT + floating_out[::1] hessian_out, # OUT + int n_threads=1 + ): + """Compute gradient and hessian of loss w.r.t raw_prediction. + + The gradient and hessian are written to `gradient_out` and `hessian_out` and no + arrays are returned. + + Parameters + ---------- + y_true : array of shape (n_samples,) + Observed, true target values. + raw_prediction : array of shape (n_samples,) + Raw prediction values (in link space). + sample_weight : array of shape (n_samples,) or None + Sample weights. + gradient_out : array of shape (n_samples,) + A location into which the gradient is stored. + hessian_out : array of shape (n_samples,) + A location into which the hessian is stored. + n_threads : int + Number of threads used by OpenMP (if any). + """ + pass + + +{{for name, docstring, param, closs, closs_grad, cgrad, cgrad_hess, in class_list}} +{{py: +if param is None: + with_param = "" +else: + with_param = ", self." + param +}} + +cdef class {{name}}(CyLossFunction): + """{{docstring}}""" + + {{if param is not None}} + def __init__(self, {{param}}): + self.{{param}} = {{param}} + {{endif}} + + {{if param is not None}} + def __reduce__(self): + return (self.__class__, (self.{{param}},)) + {{endif}} + + cdef inline double cy_loss(self, double y_true, double raw_prediction) noexcept nogil: + return {{closs}}(y_true, raw_prediction{{with_param}}) + + cdef inline double cy_gradient(self, double y_true, double raw_prediction) noexcept nogil: + return {{cgrad}}(y_true, raw_prediction{{with_param}}) + + cdef inline double_pair cy_grad_hess(self, double y_true, double raw_prediction) noexcept nogil: + return {{cgrad_hess}}(y_true, raw_prediction{{with_param}}) + + def loss( + self, + const floating_in[::1] y_true, # IN + const floating_in[::1] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[::1] loss_out, # OUT + int n_threads=1 + ): + cdef: + int i + int n_samples = y_true.shape[0] + + if sample_weight is None: + for i in prange( + n_samples, schedule='static', nogil=True, num_threads=n_threads + ): + loss_out[i] = {{closs}}(y_true[i], raw_prediction[i]{{with_param}}) + else: + for i in prange( + n_samples, schedule='static', nogil=True, num_threads=n_threads + ): + loss_out[i] = sample_weight[i] * {{closs}}(y_true[i], raw_prediction[i]{{with_param}}) + + {{if closs_grad is not None}} + def loss_gradient( + self, + const floating_in[::1] y_true, # IN + const floating_in[::1] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[::1] loss_out, # OUT + floating_out[::1] gradient_out, # OUT + int n_threads=1 + ): + cdef: + int i + int n_samples = y_true.shape[0] + double_pair dbl2 + + if sample_weight is None: + for i in prange( + n_samples, schedule='static', nogil=True, num_threads=n_threads + ): + dbl2 = {{closs_grad}}(y_true[i], raw_prediction[i]{{with_param}}) + loss_out[i] = dbl2.val1 + gradient_out[i] = dbl2.val2 + else: + for i in prange( + n_samples, schedule='static', nogil=True, num_threads=n_threads + ): + dbl2 = {{closs_grad}}(y_true[i], raw_prediction[i]{{with_param}}) + loss_out[i] = sample_weight[i] * dbl2.val1 + gradient_out[i] = sample_weight[i] * dbl2.val2 + + {{endif}} + + def gradient( + self, + const floating_in[::1] y_true, # IN + const floating_in[::1] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[::1] gradient_out, # OUT + int n_threads=1 + ): + cdef: + int i + int n_samples = y_true.shape[0] + + if sample_weight is None: + for i in prange( + n_samples, schedule='static', nogil=True, num_threads=n_threads + ): + gradient_out[i] = {{cgrad}}(y_true[i], raw_prediction[i]{{with_param}}) + else: + for i in prange( + n_samples, schedule='static', nogil=True, num_threads=n_threads + ): + gradient_out[i] = sample_weight[i] * {{cgrad}}(y_true[i], raw_prediction[i]{{with_param}}) + + def gradient_hessian( + self, + const floating_in[::1] y_true, # IN + const floating_in[::1] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[::1] gradient_out, # OUT + floating_out[::1] hessian_out, # OUT + int n_threads=1 + ): + cdef: + int i + int n_samples = y_true.shape[0] + double_pair dbl2 + + if sample_weight is None: + for i in prange( + n_samples, schedule='static', nogil=True, num_threads=n_threads + ): + dbl2 = {{cgrad_hess}}(y_true[i], raw_prediction[i]{{with_param}}) + gradient_out[i] = dbl2.val1 + hessian_out[i] = dbl2.val2 + else: + for i in prange( + n_samples, schedule='static', nogil=True, num_threads=n_threads + ): + dbl2 = {{cgrad_hess}}(y_true[i], raw_prediction[i]{{with_param}}) + gradient_out[i] = sample_weight[i] * dbl2.val1 + hessian_out[i] = sample_weight[i] * dbl2.val2 + +{{endfor}} + + +# The multinomial deviance loss is also known as categorical cross-entropy or +# multinomial log-likelihood. +# Here, we do not inherit from CyLossFunction as its cy_gradient method deviates +# from the API. +cdef class CyHalfMultinomialLoss(): + """Half Multinomial deviance loss with multinomial logit link. + + Domain: + y_true in {0, 1, 2, 3, .., n_classes - 1} + y_pred in (0, 1)**n_classes, i.e. interval with boundaries excluded + + Link: + y_pred = softmax(raw_prediction) + + Note: Label encoding is built-in, i.e. {0, 1, 2, 3, .., n_classes - 1} is + mapped to (y_true == k) for k = 0 .. n_classes - 1 which is either 0 or 1. + """ + + # Here we deviate from the CyLossFunction API. SAG/SAGA needs direct access to + # sample-wise gradients which we provide here. + cdef inline void cy_gradient( + self, + const floating_in y_true, + const floating_in[::1] raw_prediction, # IN + const floating_in sample_weight, + floating_out[::1] gradient_out, # OUT + ) noexcept nogil: + """Compute gradient of loss w.r.t. `raw_prediction` for a single sample. + + The gradient of the multinomial logistic loss with respect to a class k, + and for one sample is: + grad_k = - sw * (p[k] - (y==k)) + + where: + p[k] = proba[k] = exp(raw_prediction[k] - logsumexp(raw_prediction)) + sw = sample_weight + + Parameters + ---------- + y_true : double + Observed, true target value. + raw_prediction : array of shape (n_classes,) + Raw prediction values (in link space). + sample_weight : double + Sample weight. + gradient_out : array of shape (n_classs,) + A location into which the gradient is stored. + + Returns + ------- + gradient : double + The derivative of the loss function w.r.t. `raw_prediction`. + """ + cdef: + int k + int n_classes = raw_prediction.shape[0] + double_pair max_value_and_sum_exps + const floating_in[:, :] raw = raw_prediction[None, :] + + max_value_and_sum_exps = sum_exp_minus_max(0, raw, &gradient_out[0]) + for k in range(n_classes): + # gradient_out[k] = p_k = y_pred_k = prob of class k + gradient_out[k] /= max_value_and_sum_exps.val2 + # gradient_k = (p_k - (y_true == k)) * sw + gradient_out[k] = (gradient_out[k] - (y_true == k)) * sample_weight + + def _test_cy_gradient( + self, + const floating_in[::1] y_true, # IN + const floating_in[:, ::1] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + ): + """For testing only.""" + cdef: + int i, k + int n_samples = y_true.shape[0] + int n_classes = raw_prediction.shape[1] + floating_in [:, ::1] gradient_out + gradient = np.empty((n_samples, n_classes), dtype=np.float64) + gradient_out = gradient + + for i in range(n_samples): + self.cy_gradient( + y_true=y_true[i], + raw_prediction=raw_prediction[i, :], + sample_weight=1.0 if sample_weight is None else sample_weight[i], + gradient_out=gradient_out[i, :], + ) + return gradient + + # Note that we do not assume memory alignment/contiguity of 2d arrays. + # There seems to be little benefit in doing so. Benchmarks proofing the + # opposite are welcome. + def loss( + self, + const floating_in[::1] y_true, # IN + const floating_in[:, :] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[::1] loss_out, # OUT + int n_threads=1 + ): + cdef: + int i, k + int n_samples = y_true.shape[0] + int n_classes = raw_prediction.shape[1] + floating_in max_value, sum_exps + floating_in* p # temporary buffer + double_pair max_value_and_sum_exps + + # We assume n_samples > n_classes. In this case having the inner loop + # over n_classes is a good default. + # TODO: If every memoryview is contiguous and raw_prediction is + # f-contiguous, can we write a better algo (loops) to improve + # performance? + if sample_weight is None: + # inner loop over n_classes + with nogil, parallel(num_threads=n_threads): + # Define private buffer variables as each thread might use its + # own. + p = malloc(sizeof(floating_in) * (n_classes)) + + for i in prange(n_samples, schedule='static'): + max_value_and_sum_exps = sum_exp_minus_max(i, raw_prediction, p) + max_value = max_value_and_sum_exps.val1 + sum_exps = max_value_and_sum_exps.val2 + loss_out[i] = log(sum_exps) + max_value + + # label encoded y_true + k = int(y_true[i]) + loss_out[i] -= raw_prediction[i, k] + + free(p) + else: + with nogil, parallel(num_threads=n_threads): + p = malloc(sizeof(floating_in) * (n_classes)) + + for i in prange(n_samples, schedule='static'): + max_value_and_sum_exps = sum_exp_minus_max(i, raw_prediction, p) + max_value = max_value_and_sum_exps.val1 + sum_exps = max_value_and_sum_exps.val2 + loss_out[i] = log(sum_exps) + max_value + + # label encoded y_true + k = int(y_true[i]) + loss_out[i] -= raw_prediction[i, k] + + loss_out[i] *= sample_weight[i] + + free(p) + + def loss_gradient( + self, + const floating_in[::1] y_true, # IN + const floating_in[:, :] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[::1] loss_out, # OUT + floating_out[:, :] gradient_out, # OUT + int n_threads=1 + ): + cdef: + int i, k + int n_samples = y_true.shape[0] + int n_classes = raw_prediction.shape[1] + floating_in max_value, sum_exps + floating_in* p # temporary buffer + double_pair max_value_and_sum_exps + + if sample_weight is None: + # inner loop over n_classes + with nogil, parallel(num_threads=n_threads): + # Define private buffer variables as each thread might use its + # own. + p = malloc(sizeof(floating_in) * (n_classes)) + + for i in prange(n_samples, schedule='static'): + max_value_and_sum_exps = sum_exp_minus_max(i, raw_prediction, p) + max_value = max_value_and_sum_exps.val1 + sum_exps = max_value_and_sum_exps.val2 + loss_out[i] = log(sum_exps) + max_value + + for k in range(n_classes): + # label decode y_true + if y_true[i] == k: + loss_out[i] -= raw_prediction[i, k] + p[k] /= sum_exps # p_k = y_pred_k = prob of class k + # gradient_k = p_k - (y_true == k) + gradient_out[i, k] = p[k] - (y_true[i] == k) + + free(p) + else: + with nogil, parallel(num_threads=n_threads): + p = malloc(sizeof(floating_in) * (n_classes)) + + for i in prange(n_samples, schedule='static'): + max_value_and_sum_exps = sum_exp_minus_max(i, raw_prediction, p) + max_value = max_value_and_sum_exps.val1 + sum_exps = max_value_and_sum_exps.val2 + loss_out[i] = log(sum_exps) + max_value + + for k in range(n_classes): + # label decode y_true + if y_true[i] == k: + loss_out[i] -= raw_prediction[i, k] + p[k] /= sum_exps # p_k = y_pred_k = prob of class k + # gradient_k = (p_k - (y_true == k)) * sw + gradient_out[i, k] = (p[k] - (y_true[i] == k)) * sample_weight[i] + + loss_out[i] *= sample_weight[i] + + free(p) + + def gradient( + self, + const floating_in[::1] y_true, # IN + const floating_in[:, :] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[:, :] gradient_out, # OUT + int n_threads=1 + ): + cdef: + int i, k + int n_samples = y_true.shape[0] + int n_classes = raw_prediction.shape[1] + floating_in sum_exps + floating_in* p # temporary buffer + double_pair max_value_and_sum_exps + + if sample_weight is None: + # inner loop over n_classes + with nogil, parallel(num_threads=n_threads): + # Define private buffer variables as each thread might use its + # own. + p = malloc(sizeof(floating_in) * (n_classes)) + + for i in prange(n_samples, schedule='static'): + max_value_and_sum_exps = sum_exp_minus_max(i, raw_prediction, p) + sum_exps = max_value_and_sum_exps.val2 + + for k in range(n_classes): + p[k] /= sum_exps # p_k = y_pred_k = prob of class k + # gradient_k = y_pred_k - (y_true == k) + gradient_out[i, k] = p[k] - (y_true[i] == k) + + free(p) + else: + with nogil, parallel(num_threads=n_threads): + p = malloc(sizeof(floating_in) * (n_classes)) + + for i in prange(n_samples, schedule='static'): + max_value_and_sum_exps = sum_exp_minus_max(i, raw_prediction, p) + sum_exps = max_value_and_sum_exps.val2 + + for k in range(n_classes): + p[k] /= sum_exps # p_k = y_pred_k = prob of class k + # gradient_k = (p_k - (y_true == k)) * sw + gradient_out[i, k] = (p[k] - (y_true[i] == k)) * sample_weight[i] + + free(p) + + def gradient_hessian( + self, + const floating_in[::1] y_true, # IN + const floating_in[:, :] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[:, :] gradient_out, # OUT + floating_out[:, :] hessian_out, # OUT + int n_threads=1 + ): + cdef: + int i, k + int n_samples = y_true.shape[0] + int n_classes = raw_prediction.shape[1] + floating_in sum_exps + floating_in* p # temporary buffer + double_pair max_value_and_sum_exps + + if sample_weight is None: + # inner loop over n_classes + with nogil, parallel(num_threads=n_threads): + # Define private buffer variables as each thread might use its + # own. + p = malloc(sizeof(floating_in) * (n_classes)) + + for i in prange(n_samples, schedule='static'): + max_value_and_sum_exps = sum_exp_minus_max(i, raw_prediction, p) + sum_exps = max_value_and_sum_exps.val2 + + for k in range(n_classes): + p[k] /= sum_exps # p_k = y_pred_k = prob of class k + # hessian_k = p_k * (1 - p_k) + # gradient_k = p_k - (y_true == k) + gradient_out[i, k] = p[k] - (y_true[i] == k) + hessian_out[i, k] = p[k] * (1. - p[k]) + + free(p) + else: + with nogil, parallel(num_threads=n_threads): + p = malloc(sizeof(floating_in) * (n_classes)) + + for i in prange(n_samples, schedule='static'): + max_value_and_sum_exps = sum_exp_minus_max(i, raw_prediction, p) + sum_exps = max_value_and_sum_exps.val2 + + for k in range(n_classes): + p[k] /= sum_exps # p_k = y_pred_k = prob of class k + # gradient_k = (p_k - (y_true == k)) * sw + # hessian_k = p_k * (1 - p_k) * sw + gradient_out[i, k] = (p[k] - (y_true[i] == k)) * sample_weight[i] + hessian_out[i, k] = (p[k] * (1. - p[k])) * sample_weight[i] + + free(p) + + # This method simplifies the implementation of hessp in linear models, + # i.e. the matrix-vector product of the full hessian, not only of the + # diagonal (in the classes) approximation as implemented above. + def gradient_proba( + self, + const floating_in[::1] y_true, # IN + const floating_in[:, :] raw_prediction, # IN + const floating_in[::1] sample_weight, # IN + floating_out[:, :] gradient_out, # OUT + floating_out[:, :] proba_out, # OUT + int n_threads=1 + ): + cdef: + int i, k + int n_samples = y_true.shape[0] + int n_classes = raw_prediction.shape[1] + floating_in sum_exps + floating_in* p # temporary buffer + double_pair max_value_and_sum_exps + + if sample_weight is None: + # inner loop over n_classes + with nogil, parallel(num_threads=n_threads): + # Define private buffer variables as each thread might use its + # own. + p = malloc(sizeof(floating_in) * (n_classes)) + + for i in prange(n_samples, schedule='static'): + max_value_and_sum_exps = sum_exp_minus_max(i, raw_prediction, p) + sum_exps = max_value_and_sum_exps.val2 + + for k in range(n_classes): + proba_out[i, k] = p[k] / sum_exps # y_pred_k = prob of class k + # gradient_k = y_pred_k - (y_true == k) + gradient_out[i, k] = proba_out[i, k] - (y_true[i] == k) + + free(p) + else: + with nogil, parallel(num_threads=n_threads): + p = malloc(sizeof(floating_in) * (n_classes)) + + for i in prange(n_samples, schedule='static'): + max_value_and_sum_exps = sum_exp_minus_max(i, raw_prediction, p) + sum_exps = max_value_and_sum_exps.val2 + + for k in range(n_classes): + proba_out[i, k] = p[k] / sum_exps # y_pred_k = prob of class k + # gradient_k = (p_k - (y_true == k)) * sw + gradient_out[i, k] = (proba_out[i, k] - (y_true[i] == k)) * sample_weight[i] + + free(p) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/link.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/link.py new file mode 100644 index 0000000000000000000000000000000000000000..53dff6c2e928541ce58bb71c484e59622143104d --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/link.py @@ -0,0 +1,282 @@ +""" +Module contains classes for invertible (and differentiable) link functions. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +from abc import ABC, abstractmethod +from dataclasses import dataclass + +import numpy as np +from scipy.special import expit, logit +from scipy.stats import gmean + +from ..utils.extmath import softmax + + +@dataclass +class Interval: + low: float + high: float + low_inclusive: bool + high_inclusive: bool + + def __post_init__(self): + """Check that low <= high""" + if self.low > self.high: + raise ValueError( + f"One must have low <= high; got low={self.low}, high={self.high}." + ) + + def includes(self, x): + """Test whether all values of x are in interval range. + + Parameters + ---------- + x : ndarray + Array whose elements are tested to be in interval range. + + Returns + ------- + result : bool + """ + if self.low_inclusive: + low = np.greater_equal(x, self.low) + else: + low = np.greater(x, self.low) + + if not np.all(low): + return False + + if self.high_inclusive: + high = np.less_equal(x, self.high) + else: + high = np.less(x, self.high) + + # Note: np.all returns numpy.bool_ + return bool(np.all(high)) + + +def _inclusive_low_high(interval, dtype=np.float64): + """Generate values low and high to be within the interval range. + + This is used in tests only. + + Returns + ------- + low, high : tuple + The returned values low and high lie within the interval. + """ + eps = 10 * np.finfo(dtype).eps + if interval.low == -np.inf: + low = -1e10 + elif interval.low < 0: + low = interval.low * (1 - eps) + eps + else: + low = interval.low * (1 + eps) + eps + + if interval.high == np.inf: + high = 1e10 + elif interval.high < 0: + high = interval.high * (1 + eps) - eps + else: + high = interval.high * (1 - eps) - eps + + return low, high + + +class BaseLink(ABC): + """Abstract base class for differentiable, invertible link functions. + + Convention: + - link function g: raw_prediction = g(y_pred) + - inverse link h: y_pred = h(raw_prediction) + + For (generalized) linear models, `raw_prediction = X @ coef` is the so + called linear predictor, and `y_pred = h(raw_prediction)` is the predicted + conditional (on X) expected value of the target `y_true`. + + The methods are not implemented as staticmethods in case a link function needs + parameters. + """ + + is_multiclass = False # used for testing only + + # Usually, raw_prediction may be any real number and y_pred is an open + # interval. + # interval_raw_prediction = Interval(-np.inf, np.inf, False, False) + interval_y_pred = Interval(-np.inf, np.inf, False, False) + + @abstractmethod + def link(self, y_pred, out=None): + """Compute the link function g(y_pred). + + The link function maps (predicted) target values to raw predictions, + i.e. `g(y_pred) = raw_prediction`. + + Parameters + ---------- + y_pred : array + Predicted target values. + out : array + A location into which the result is stored. If provided, it must + have a shape that the inputs broadcast to. If not provided or None, + a freshly-allocated array is returned. + + Returns + ------- + out : array + Output array, element-wise link function. + """ + + @abstractmethod + def inverse(self, raw_prediction, out=None): + """Compute the inverse link function h(raw_prediction). + + The inverse link function maps raw predictions to predicted target + values, i.e. `h(raw_prediction) = y_pred`. + + Parameters + ---------- + raw_prediction : array + Raw prediction values (in link space). + out : array + A location into which the result is stored. If provided, it must + have a shape that the inputs broadcast to. If not provided or None, + a freshly-allocated array is returned. + + Returns + ------- + out : array + Output array, element-wise inverse link function. + """ + + +class IdentityLink(BaseLink): + """The identity link function g(x)=x.""" + + def link(self, y_pred, out=None): + if out is not None: + np.copyto(out, y_pred) + return out + else: + return y_pred + + inverse = link + + +class LogLink(BaseLink): + """The log link function g(x)=log(x).""" + + interval_y_pred = Interval(0, np.inf, False, False) + + def link(self, y_pred, out=None): + return np.log(y_pred, out=out) + + def inverse(self, raw_prediction, out=None): + return np.exp(raw_prediction, out=out) + + +class LogitLink(BaseLink): + """The logit link function g(x)=logit(x).""" + + interval_y_pred = Interval(0, 1, False, False) + + def link(self, y_pred, out=None): + return logit(y_pred, out=out) + + def inverse(self, raw_prediction, out=None): + return expit(raw_prediction, out=out) + + +class HalfLogitLink(BaseLink): + """Half the logit link function g(x)=1/2 * logit(x). + + Used for the exponential loss. + """ + + interval_y_pred = Interval(0, 1, False, False) + + def link(self, y_pred, out=None): + out = logit(y_pred, out=out) + out *= 0.5 + return out + + def inverse(self, raw_prediction, out=None): + return expit(2 * raw_prediction, out) + + +class MultinomialLogit(BaseLink): + """The symmetric multinomial logit function. + + Convention: + - y_pred.shape = raw_prediction.shape = (n_samples, n_classes) + + Notes: + - The inverse link h is the softmax function. + - The sum is over the second axis, i.e. axis=1 (n_classes). + + We have to choose additional constraints in order to make + + y_pred[k] = exp(raw_pred[k]) / sum(exp(raw_pred[k]), k=0..n_classes-1) + + for n_classes classes identifiable and invertible. + We choose the symmetric side constraint where the geometric mean response + is set as reference category, see [2]: + + The symmetric multinomial logit link function for a single data point is + then defined as + + raw_prediction[k] = g(y_pred[k]) = log(y_pred[k]/gmean(y_pred)) + = log(y_pred[k]) - mean(log(y_pred)). + + Note that this is equivalent to the definition in [1] and implies mean + centered raw predictions: + + sum(raw_prediction[k], k=0..n_classes-1) = 0. + + For linear models with raw_prediction = X @ coef, this corresponds to + sum(coef[k], k=0..n_classes-1) = 0, i.e. the sum over classes for every + feature is zero. + + Reference + --------- + .. [1] Friedman, Jerome; Hastie, Trevor; Tibshirani, Robert. "Additive + logistic regression: a statistical view of boosting" Ann. Statist. + 28 (2000), no. 2, 337--407. doi:10.1214/aos/1016218223. + https://projecteuclid.org/euclid.aos/1016218223 + + .. [2] Zahid, Faisal Maqbool and Gerhard Tutz. "Ridge estimation for + multinomial logit models with symmetric side constraints." + Computational Statistics 28 (2013): 1017-1034. + http://epub.ub.uni-muenchen.de/11001/1/tr067.pdf + """ + + is_multiclass = True + interval_y_pred = Interval(0, 1, False, False) + + def symmetrize_raw_prediction(self, raw_prediction): + return raw_prediction - np.mean(raw_prediction, axis=1)[:, np.newaxis] + + def link(self, y_pred, out=None): + # geometric mean as reference category + gm = gmean(y_pred, axis=1) + return np.log(y_pred / gm[:, np.newaxis], out=out) + + def inverse(self, raw_prediction, out=None): + if out is None: + return softmax(raw_prediction, copy=True) + else: + np.copyto(out, raw_prediction) + softmax(out, copy=False) + return out + + +_LINKS = { + "identity": IdentityLink, + "log": LogLink, + "logit": LogitLink, + "half_logit": HalfLogitLink, + "multinomial_logit": MultinomialLogit, +} diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/loss.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/loss.py new file mode 100644 index 0000000000000000000000000000000000000000..b45ff3322699aa26533d504be6407f9d5acbb5b8 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/loss.py @@ -0,0 +1,1181 @@ +""" +This module contains loss classes suitable for fitting. + +It is not part of the public API. +Specific losses are used for regression, binary classification or multiclass +classification. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +# Goals: +# - Provide a common private module for loss functions/classes. +# - To be used in: +# - LogisticRegression +# - PoissonRegressor, GammaRegressor, TweedieRegressor +# - HistGradientBoostingRegressor, HistGradientBoostingClassifier +# - GradientBoostingRegressor, GradientBoostingClassifier +# - SGDRegressor, SGDClassifier +# - Replace link module of GLMs. + +import numbers + +import numpy as np +from scipy.special import xlogy + +from ..utils import check_scalar +from ..utils.stats import _weighted_percentile +from ._loss import ( + CyAbsoluteError, + CyExponentialLoss, + CyHalfBinomialLoss, + CyHalfGammaLoss, + CyHalfMultinomialLoss, + CyHalfPoissonLoss, + CyHalfSquaredError, + CyHalfTweedieLoss, + CyHalfTweedieLossIdentity, + CyHuberLoss, + CyPinballLoss, +) +from .link import ( + HalfLogitLink, + IdentityLink, + Interval, + LogitLink, + LogLink, + MultinomialLogit, +) + + +# Note: The shape of raw_prediction for multiclass classifications are +# - GradientBoostingClassifier: (n_samples, n_classes) +# - HistGradientBoostingClassifier: (n_classes, n_samples) +# +# Note: Instead of inheritance like +# +# class BaseLoss(BaseLink, CyLossFunction): +# ... +# +# # Note: Naturally, we would inherit in the following order +# # class HalfSquaredError(IdentityLink, CyHalfSquaredError, BaseLoss) +# # But because of https://github.com/cython/cython/issues/4350 we set BaseLoss as +# # the last one. This, of course, changes the MRO. +# class HalfSquaredError(IdentityLink, CyHalfSquaredError, BaseLoss): +# +# we use composition. This way we improve maintainability by avoiding the above +# mentioned Cython edge case and have easier to understand code (which method calls +# which code). +class BaseLoss: + """Base class for a loss function of 1-dimensional targets. + + Conventions: + + - y_true.shape = sample_weight.shape = (n_samples,) + - y_pred.shape = raw_prediction.shape = (n_samples,) + - If is_multiclass is true (multiclass classification), then + y_pred.shape = raw_prediction.shape = (n_samples, n_classes) + Note that this corresponds to the return value of decision_function. + + y_true, y_pred, sample_weight and raw_prediction must either be all float64 + or all float32. + gradient and hessian must be either both float64 or both float32. + + Note that y_pred = link.inverse(raw_prediction). + + Specific loss classes can inherit specific link classes to satisfy + BaseLink's abstractmethods. + + Parameters + ---------- + sample_weight : {None, ndarray} + If sample_weight is None, the hessian might be constant. + n_classes : {None, int} + The number of classes for classification, else None. + + Attributes + ---------- + closs: CyLossFunction + link : BaseLink + interval_y_true : Interval + Valid interval for y_true + interval_y_pred : Interval + Valid Interval for y_pred + differentiable : bool + Indicates whether or not loss function is differentiable in + raw_prediction everywhere. + need_update_leaves_values : bool + Indicates whether decision trees in gradient boosting need to uptade + leave values after having been fit to the (negative) gradients. + approx_hessian : bool + Indicates whether the hessian is approximated or exact. If, + approximated, it should be larger or equal to the exact one. + constant_hessian : bool + Indicates whether the hessian is one for this loss. + is_multiclass : bool + Indicates whether n_classes > 2 is allowed. + """ + + # For gradient boosted decision trees: + # This variable indicates whether the loss requires the leaves values to + # be updated once the tree has been trained. The trees are trained to + # predict a Newton-Raphson step (see grower._finalize_leaf()). But for + # some losses (e.g. least absolute deviation) we need to adjust the tree + # values to account for the "line search" of the gradient descent + # procedure. See the original paper Greedy Function Approximation: A + # Gradient Boosting Machine by Friedman + # (https://statweb.stanford.edu/~jhf/ftp/trebst.pdf) for the theory. + differentiable = True + need_update_leaves_values = False + is_multiclass = False + + def __init__(self, closs, link, n_classes=None): + self.closs = closs + self.link = link + self.approx_hessian = False + self.constant_hessian = False + self.n_classes = n_classes + self.interval_y_true = Interval(-np.inf, np.inf, False, False) + self.interval_y_pred = self.link.interval_y_pred + + def in_y_true_range(self, y): + """Return True if y is in the valid range of y_true. + + Parameters + ---------- + y : ndarray + """ + return self.interval_y_true.includes(y) + + def in_y_pred_range(self, y): + """Return True if y is in the valid range of y_pred. + + Parameters + ---------- + y : ndarray + """ + return self.interval_y_pred.includes(y) + + def loss( + self, + y_true, + raw_prediction, + sample_weight=None, + loss_out=None, + n_threads=1, + ): + """Compute the pointwise loss value for each input. + + Parameters + ---------- + y_true : C-contiguous array of shape (n_samples,) + Observed, true target values. + raw_prediction : C-contiguous array of shape (n_samples,) or array of \ + shape (n_samples, n_classes) + Raw prediction values (in link space). + sample_weight : None or C-contiguous array of shape (n_samples,) + Sample weights. + loss_out : None or C-contiguous array of shape (n_samples,) + A location into which the result is stored. If None, a new array + might be created. + n_threads : int, default=1 + Might use openmp thread parallelism. + + Returns + ------- + loss : array of shape (n_samples,) + Element-wise loss function. + """ + if loss_out is None: + loss_out = np.empty_like(y_true) + # Be graceful to shape (n_samples, 1) -> (n_samples,) + if raw_prediction.ndim == 2 and raw_prediction.shape[1] == 1: + raw_prediction = raw_prediction.squeeze(1) + + self.closs.loss( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + loss_out=loss_out, + n_threads=n_threads, + ) + return loss_out + + def loss_gradient( + self, + y_true, + raw_prediction, + sample_weight=None, + loss_out=None, + gradient_out=None, + n_threads=1, + ): + """Compute loss and gradient w.r.t. raw_prediction for each input. + + Parameters + ---------- + y_true : C-contiguous array of shape (n_samples,) + Observed, true target values. + raw_prediction : C-contiguous array of shape (n_samples,) or array of \ + shape (n_samples, n_classes) + Raw prediction values (in link space). + sample_weight : None or C-contiguous array of shape (n_samples,) + Sample weights. + loss_out : None or C-contiguous array of shape (n_samples,) + A location into which the loss is stored. If None, a new array + might be created. + gradient_out : None or C-contiguous array of shape (n_samples,) or array \ + of shape (n_samples, n_classes) + A location into which the gradient is stored. If None, a new array + might be created. + n_threads : int, default=1 + Might use openmp thread parallelism. + + Returns + ------- + loss : array of shape (n_samples,) + Element-wise loss function. + + gradient : array of shape (n_samples,) or (n_samples, n_classes) + Element-wise gradients. + """ + if loss_out is None: + if gradient_out is None: + loss_out = np.empty_like(y_true) + gradient_out = np.empty_like(raw_prediction) + else: + loss_out = np.empty_like(y_true, dtype=gradient_out.dtype) + elif gradient_out is None: + gradient_out = np.empty_like(raw_prediction, dtype=loss_out.dtype) + + # Be graceful to shape (n_samples, 1) -> (n_samples,) + if raw_prediction.ndim == 2 and raw_prediction.shape[1] == 1: + raw_prediction = raw_prediction.squeeze(1) + if gradient_out.ndim == 2 and gradient_out.shape[1] == 1: + gradient_out = gradient_out.squeeze(1) + + self.closs.loss_gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + loss_out=loss_out, + gradient_out=gradient_out, + n_threads=n_threads, + ) + return loss_out, gradient_out + + def gradient( + self, + y_true, + raw_prediction, + sample_weight=None, + gradient_out=None, + n_threads=1, + ): + """Compute gradient of loss w.r.t raw_prediction for each input. + + Parameters + ---------- + y_true : C-contiguous array of shape (n_samples,) + Observed, true target values. + raw_prediction : C-contiguous array of shape (n_samples,) or array of \ + shape (n_samples, n_classes) + Raw prediction values (in link space). + sample_weight : None or C-contiguous array of shape (n_samples,) + Sample weights. + gradient_out : None or C-contiguous array of shape (n_samples,) or array \ + of shape (n_samples, n_classes) + A location into which the result is stored. If None, a new array + might be created. + n_threads : int, default=1 + Might use openmp thread parallelism. + + Returns + ------- + gradient : array of shape (n_samples,) or (n_samples, n_classes) + Element-wise gradients. + """ + if gradient_out is None: + gradient_out = np.empty_like(raw_prediction) + + # Be graceful to shape (n_samples, 1) -> (n_samples,) + if raw_prediction.ndim == 2 and raw_prediction.shape[1] == 1: + raw_prediction = raw_prediction.squeeze(1) + if gradient_out.ndim == 2 and gradient_out.shape[1] == 1: + gradient_out = gradient_out.squeeze(1) + + self.closs.gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=gradient_out, + n_threads=n_threads, + ) + return gradient_out + + def gradient_hessian( + self, + y_true, + raw_prediction, + sample_weight=None, + gradient_out=None, + hessian_out=None, + n_threads=1, + ): + """Compute gradient and hessian of loss w.r.t raw_prediction. + + Parameters + ---------- + y_true : C-contiguous array of shape (n_samples,) + Observed, true target values. + raw_prediction : C-contiguous array of shape (n_samples,) or array of \ + shape (n_samples, n_classes) + Raw prediction values (in link space). + sample_weight : None or C-contiguous array of shape (n_samples,) + Sample weights. + gradient_out : None or C-contiguous array of shape (n_samples,) or array \ + of shape (n_samples, n_classes) + A location into which the gradient is stored. If None, a new array + might be created. + hessian_out : None or C-contiguous array of shape (n_samples,) or array \ + of shape (n_samples, n_classes) + A location into which the hessian is stored. If None, a new array + might be created. + n_threads : int, default=1 + Might use openmp thread parallelism. + + Returns + ------- + gradient : arrays of shape (n_samples,) or (n_samples, n_classes) + Element-wise gradients. + + hessian : arrays of shape (n_samples,) or (n_samples, n_classes) + Element-wise hessians. + """ + if gradient_out is None: + if hessian_out is None: + gradient_out = np.empty_like(raw_prediction) + hessian_out = np.empty_like(raw_prediction) + else: + gradient_out = np.empty_like(hessian_out) + elif hessian_out is None: + hessian_out = np.empty_like(gradient_out) + + # Be graceful to shape (n_samples, 1) -> (n_samples,) + if raw_prediction.ndim == 2 and raw_prediction.shape[1] == 1: + raw_prediction = raw_prediction.squeeze(1) + if gradient_out.ndim == 2 and gradient_out.shape[1] == 1: + gradient_out = gradient_out.squeeze(1) + if hessian_out.ndim == 2 and hessian_out.shape[1] == 1: + hessian_out = hessian_out.squeeze(1) + + self.closs.gradient_hessian( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=gradient_out, + hessian_out=hessian_out, + n_threads=n_threads, + ) + return gradient_out, hessian_out + + def __call__(self, y_true, raw_prediction, sample_weight=None, n_threads=1): + """Compute the weighted average loss. + + Parameters + ---------- + y_true : C-contiguous array of shape (n_samples,) + Observed, true target values. + raw_prediction : C-contiguous array of shape (n_samples,) or array of \ + shape (n_samples, n_classes) + Raw prediction values (in link space). + sample_weight : None or C-contiguous array of shape (n_samples,) + Sample weights. + n_threads : int, default=1 + Might use openmp thread parallelism. + + Returns + ------- + loss : float + Mean or averaged loss function. + """ + return np.average( + self.loss( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=None, + loss_out=None, + n_threads=n_threads, + ), + weights=sample_weight, + ) + + def fit_intercept_only(self, y_true, sample_weight=None): + """Compute raw_prediction of an intercept-only model. + + This can be used as initial estimates of predictions, i.e. before the + first iteration in fit. + + Parameters + ---------- + y_true : array-like of shape (n_samples,) + Observed, true target values. + sample_weight : None or array of shape (n_samples,) + Sample weights. + + Returns + ------- + raw_prediction : numpy scalar or array of shape (n_classes,) + Raw predictions of an intercept-only model. + """ + # As default, take weighted average of the target over the samples + # axis=0 and then transform into link-scale (raw_prediction). + y_pred = np.average(y_true, weights=sample_weight, axis=0) + eps = 10 * np.finfo(y_pred.dtype).eps + + if self.interval_y_pred.low == -np.inf: + a_min = None + elif self.interval_y_pred.low_inclusive: + a_min = self.interval_y_pred.low + else: + a_min = self.interval_y_pred.low + eps + + if self.interval_y_pred.high == np.inf: + a_max = None + elif self.interval_y_pred.high_inclusive: + a_max = self.interval_y_pred.high + else: + a_max = self.interval_y_pred.high - eps + + if a_min is None and a_max is None: + return self.link.link(y_pred) + else: + return self.link.link(np.clip(y_pred, a_min, a_max)) + + def constant_to_optimal_zero(self, y_true, sample_weight=None): + """Calculate term dropped in loss. + + With this term added, the loss of perfect predictions is zero. + """ + return np.zeros_like(y_true) + + def init_gradient_and_hessian(self, n_samples, dtype=np.float64, order="F"): + """Initialize arrays for gradients and hessians. + + Unless hessians are constant, arrays are initialized with undefined values. + + Parameters + ---------- + n_samples : int + The number of samples, usually passed to `fit()`. + dtype : {np.float64, np.float32}, default=np.float64 + The dtype of the arrays gradient and hessian. + order : {'C', 'F'}, default='F' + Order of the arrays gradient and hessian. The default 'F' makes the arrays + contiguous along samples. + + Returns + ------- + gradient : C-contiguous array of shape (n_samples,) or array of shape \ + (n_samples, n_classes) + Empty array (allocated but not initialized) to be used as argument + gradient_out. + hessian : C-contiguous array of shape (n_samples,), array of shape + (n_samples, n_classes) or shape (1,) + Empty (allocated but not initialized) array to be used as argument + hessian_out. + If constant_hessian is True (e.g. `HalfSquaredError`), the array is + initialized to ``1``. + """ + if dtype not in (np.float32, np.float64): + raise ValueError( + "Valid options for 'dtype' are np.float32 and np.float64. " + f"Got dtype={dtype} instead." + ) + + if self.is_multiclass: + shape = (n_samples, self.n_classes) + else: + shape = (n_samples,) + gradient = np.empty(shape=shape, dtype=dtype, order=order) + + if self.constant_hessian: + # If the hessians are constant, we consider them equal to 1. + # - This is correct for HalfSquaredError + # - For AbsoluteError, hessians are actually 0, but they are + # always ignored anyway. + hessian = np.ones(shape=(1,), dtype=dtype) + else: + hessian = np.empty(shape=shape, dtype=dtype, order=order) + + return gradient, hessian + + +# Note: Naturally, we would inherit in the following order +# class HalfSquaredError(IdentityLink, CyHalfSquaredError, BaseLoss) +# But because of https://github.com/cython/cython/issues/4350 we +# set BaseLoss as the last one. This, of course, changes the MRO. +class HalfSquaredError(BaseLoss): + """Half squared error with identity link, for regression. + + Domain: + y_true and y_pred all real numbers + + Link: + y_pred = raw_prediction + + For a given sample x_i, half squared error is defined as:: + + loss(x_i) = 0.5 * (y_true_i - raw_prediction_i)**2 + + The factor of 0.5 simplifies the computation of gradients and results in a + unit hessian (and is consistent with what is done in LightGBM). It is also + half the Normal distribution deviance. + """ + + def __init__(self, sample_weight=None): + super().__init__(closs=CyHalfSquaredError(), link=IdentityLink()) + self.constant_hessian = sample_weight is None + + +class AbsoluteError(BaseLoss): + """Absolute error with identity link, for regression. + + Domain: + y_true and y_pred all real numbers + + Link: + y_pred = raw_prediction + + For a given sample x_i, the absolute error is defined as:: + + loss(x_i) = |y_true_i - raw_prediction_i| + + Note that the exact hessian = 0 almost everywhere (except at one point, therefore + differentiable = False). Optimization routines like in HGBT, however, need a + hessian > 0. Therefore, we assign 1. + """ + + differentiable = False + need_update_leaves_values = True + + def __init__(self, sample_weight=None): + super().__init__(closs=CyAbsoluteError(), link=IdentityLink()) + self.approx_hessian = True + self.constant_hessian = sample_weight is None + + def fit_intercept_only(self, y_true, sample_weight=None): + """Compute raw_prediction of an intercept-only model. + + This is the weighted median of the target, i.e. over the samples + axis=0. + """ + if sample_weight is None: + return np.median(y_true, axis=0) + else: + return _weighted_percentile(y_true, sample_weight, 50) + + +class PinballLoss(BaseLoss): + """Quantile loss aka pinball loss, for regression. + + Domain: + y_true and y_pred all real numbers + quantile in (0, 1) + + Link: + y_pred = raw_prediction + + For a given sample x_i, the pinball loss is defined as:: + + loss(x_i) = rho_{quantile}(y_true_i - raw_prediction_i) + + rho_{quantile}(u) = u * (quantile - 1_{u<0}) + = -u *(1 - quantile) if u < 0 + u * quantile if u >= 0 + + Note: 2 * PinballLoss(quantile=0.5) equals AbsoluteError(). + + Note that the exact hessian = 0 almost everywhere (except at one point, therefore + differentiable = False). Optimization routines like in HGBT, however, need a + hessian > 0. Therefore, we assign 1. + + Additional Attributes + --------------------- + quantile : float + The quantile level of the quantile to be estimated. Must be in range (0, 1). + """ + + differentiable = False + need_update_leaves_values = True + + def __init__(self, sample_weight=None, quantile=0.5): + check_scalar( + quantile, + "quantile", + target_type=numbers.Real, + min_val=0, + max_val=1, + include_boundaries="neither", + ) + super().__init__( + closs=CyPinballLoss(quantile=float(quantile)), + link=IdentityLink(), + ) + self.approx_hessian = True + self.constant_hessian = sample_weight is None + + def fit_intercept_only(self, y_true, sample_weight=None): + """Compute raw_prediction of an intercept-only model. + + This is the weighted median of the target, i.e. over the samples + axis=0. + """ + if sample_weight is None: + return np.percentile(y_true, 100 * self.closs.quantile, axis=0) + else: + return _weighted_percentile( + y_true, sample_weight, 100 * self.closs.quantile + ) + + +class HuberLoss(BaseLoss): + """Huber loss, for regression. + + Domain: + y_true and y_pred all real numbers + quantile in (0, 1) + + Link: + y_pred = raw_prediction + + For a given sample x_i, the Huber loss is defined as:: + + loss(x_i) = 1/2 * abserr**2 if abserr <= delta + delta * (abserr - delta/2) if abserr > delta + + abserr = |y_true_i - raw_prediction_i| + delta = quantile(abserr, self.quantile) + + Note: HuberLoss(quantile=1) equals HalfSquaredError and HuberLoss(quantile=0) + equals delta * (AbsoluteError() - delta/2). + + Additional Attributes + --------------------- + quantile : float + The quantile level which defines the breaking point `delta` to distinguish + between absolute error and squared error. Must be in range (0, 1). + + Reference + --------- + .. [1] Friedman, J.H. (2001). :doi:`Greedy function approximation: A gradient + boosting machine <10.1214/aos/1013203451>`. + Annals of Statistics, 29, 1189-1232. + """ + + differentiable = False + need_update_leaves_values = True + + def __init__(self, sample_weight=None, quantile=0.9, delta=0.5): + check_scalar( + quantile, + "quantile", + target_type=numbers.Real, + min_val=0, + max_val=1, + include_boundaries="neither", + ) + self.quantile = quantile # This is better stored outside of Cython. + super().__init__( + closs=CyHuberLoss(delta=float(delta)), + link=IdentityLink(), + ) + self.approx_hessian = True + self.constant_hessian = False + + def fit_intercept_only(self, y_true, sample_weight=None): + """Compute raw_prediction of an intercept-only model. + + This is the weighted median of the target, i.e. over the samples + axis=0. + """ + # See formula before algo 4 in Friedman (2001), but we apply it to y_true, + # not to the residual y_true - raw_prediction. An estimator like + # HistGradientBoostingRegressor might then call it on the residual, e.g. + # fit_intercept_only(y_true - raw_prediction). + if sample_weight is None: + median = np.percentile(y_true, 50, axis=0) + else: + median = _weighted_percentile(y_true, sample_weight, 50) + diff = y_true - median + term = np.sign(diff) * np.minimum(self.closs.delta, np.abs(diff)) + return median + np.average(term, weights=sample_weight) + + +class HalfPoissonLoss(BaseLoss): + """Half Poisson deviance loss with log-link, for regression. + + Domain: + y_true in non-negative real numbers + y_pred in positive real numbers + + Link: + y_pred = exp(raw_prediction) + + For a given sample x_i, half the Poisson deviance is defined as:: + + loss(x_i) = y_true_i * log(y_true_i/exp(raw_prediction_i)) + - y_true_i + exp(raw_prediction_i) + + Half the Poisson deviance is actually the negative log-likelihood up to + constant terms (not involving raw_prediction) and simplifies the + computation of the gradients. + We also skip the constant term `y_true_i * log(y_true_i) - y_true_i`. + """ + + def __init__(self, sample_weight=None): + super().__init__(closs=CyHalfPoissonLoss(), link=LogLink()) + self.interval_y_true = Interval(0, np.inf, True, False) + + def constant_to_optimal_zero(self, y_true, sample_weight=None): + term = xlogy(y_true, y_true) - y_true + if sample_weight is not None: + term *= sample_weight + return term + + +class HalfGammaLoss(BaseLoss): + """Half Gamma deviance loss with log-link, for regression. + + Domain: + y_true and y_pred in positive real numbers + + Link: + y_pred = exp(raw_prediction) + + For a given sample x_i, half Gamma deviance loss is defined as:: + + loss(x_i) = log(exp(raw_prediction_i)/y_true_i) + + y_true/exp(raw_prediction_i) - 1 + + Half the Gamma deviance is actually proportional to the negative log- + likelihood up to constant terms (not involving raw_prediction) and + simplifies the computation of the gradients. + We also skip the constant term `-log(y_true_i) - 1`. + """ + + def __init__(self, sample_weight=None): + super().__init__(closs=CyHalfGammaLoss(), link=LogLink()) + self.interval_y_true = Interval(0, np.inf, False, False) + + def constant_to_optimal_zero(self, y_true, sample_weight=None): + term = -np.log(y_true) - 1 + if sample_weight is not None: + term *= sample_weight + return term + + +class HalfTweedieLoss(BaseLoss): + """Half Tweedie deviance loss with log-link, for regression. + + Domain: + y_true in real numbers for power <= 0 + y_true in non-negative real numbers for 0 < power < 2 + y_true in positive real numbers for 2 <= power + y_pred in positive real numbers + power in real numbers + + Link: + y_pred = exp(raw_prediction) + + For a given sample x_i, half Tweedie deviance loss with p=power is defined + as:: + + loss(x_i) = max(y_true_i, 0)**(2-p) / (1-p) / (2-p) + - y_true_i * exp(raw_prediction_i)**(1-p) / (1-p) + + exp(raw_prediction_i)**(2-p) / (2-p) + + Taking the limits for p=0, 1, 2 gives HalfSquaredError with a log link, + HalfPoissonLoss and HalfGammaLoss. + + We also skip constant terms, but those are different for p=0, 1, 2. + Therefore, the loss is not continuous in `power`. + + Note furthermore that although no Tweedie distribution exists for + 0 < power < 1, it still gives a strictly consistent scoring function for + the expectation. + """ + + def __init__(self, sample_weight=None, power=1.5): + super().__init__( + closs=CyHalfTweedieLoss(power=float(power)), + link=LogLink(), + ) + if self.closs.power <= 0: + self.interval_y_true = Interval(-np.inf, np.inf, False, False) + elif self.closs.power < 2: + self.interval_y_true = Interval(0, np.inf, True, False) + else: + self.interval_y_true = Interval(0, np.inf, False, False) + + def constant_to_optimal_zero(self, y_true, sample_weight=None): + if self.closs.power == 0: + return HalfSquaredError().constant_to_optimal_zero( + y_true=y_true, sample_weight=sample_weight + ) + elif self.closs.power == 1: + return HalfPoissonLoss().constant_to_optimal_zero( + y_true=y_true, sample_weight=sample_weight + ) + elif self.closs.power == 2: + return HalfGammaLoss().constant_to_optimal_zero( + y_true=y_true, sample_weight=sample_weight + ) + else: + p = self.closs.power + term = np.power(np.maximum(y_true, 0), 2 - p) / (1 - p) / (2 - p) + if sample_weight is not None: + term *= sample_weight + return term + + +class HalfTweedieLossIdentity(BaseLoss): + """Half Tweedie deviance loss with identity link, for regression. + + Domain: + y_true in real numbers for power <= 0 + y_true in non-negative real numbers for 0 < power < 2 + y_true in positive real numbers for 2 <= power + y_pred in positive real numbers for power != 0 + y_pred in real numbers for power = 0 + power in real numbers + + Link: + y_pred = raw_prediction + + For a given sample x_i, half Tweedie deviance loss with p=power is defined + as:: + + loss(x_i) = max(y_true_i, 0)**(2-p) / (1-p) / (2-p) + - y_true_i * raw_prediction_i**(1-p) / (1-p) + + raw_prediction_i**(2-p) / (2-p) + + Note that the minimum value of this loss is 0. + + Note furthermore that although no Tweedie distribution exists for + 0 < power < 1, it still gives a strictly consistent scoring function for + the expectation. + """ + + def __init__(self, sample_weight=None, power=1.5): + super().__init__( + closs=CyHalfTweedieLossIdentity(power=float(power)), + link=IdentityLink(), + ) + if self.closs.power <= 0: + self.interval_y_true = Interval(-np.inf, np.inf, False, False) + elif self.closs.power < 2: + self.interval_y_true = Interval(0, np.inf, True, False) + else: + self.interval_y_true = Interval(0, np.inf, False, False) + + if self.closs.power == 0: + self.interval_y_pred = Interval(-np.inf, np.inf, False, False) + else: + self.interval_y_pred = Interval(0, np.inf, False, False) + + +class HalfBinomialLoss(BaseLoss): + """Half Binomial deviance loss with logit link, for binary classification. + + This is also know as binary cross entropy, log-loss and logistic loss. + + Domain: + y_true in [0, 1], i.e. regression on the unit interval + y_pred in (0, 1), i.e. boundaries excluded + + Link: + y_pred = expit(raw_prediction) + + For a given sample x_i, half Binomial deviance is defined as the negative + log-likelihood of the Binomial/Bernoulli distribution and can be expressed + as:: + + loss(x_i) = log(1 + exp(raw_pred_i)) - y_true_i * raw_pred_i + + See The Elements of Statistical Learning, by Hastie, Tibshirani, Friedman, + section 4.4.1 (about logistic regression). + + Note that the formulation works for classification, y = {0, 1}, as well as + logistic regression, y = [0, 1]. + If you add `constant_to_optimal_zero` to the loss, you get half the + Bernoulli/binomial deviance. + + More details: Inserting the predicted probability y_pred = expit(raw_prediction) + in the loss gives the well known:: + + loss(x_i) = - y_true_i * log(y_pred_i) - (1 - y_true_i) * log(1 - y_pred_i) + """ + + def __init__(self, sample_weight=None): + super().__init__( + closs=CyHalfBinomialLoss(), + link=LogitLink(), + n_classes=2, + ) + self.interval_y_true = Interval(0, 1, True, True) + + def constant_to_optimal_zero(self, y_true, sample_weight=None): + # This is non-zero only if y_true is neither 0 nor 1. + term = xlogy(y_true, y_true) + xlogy(1 - y_true, 1 - y_true) + if sample_weight is not None: + term *= sample_weight + return term + + def predict_proba(self, raw_prediction): + """Predict probabilities. + + Parameters + ---------- + raw_prediction : array of shape (n_samples,) or (n_samples, 1) + Raw prediction values (in link space). + + Returns + ------- + proba : array of shape (n_samples, 2) + Element-wise class probabilities. + """ + # Be graceful to shape (n_samples, 1) -> (n_samples,) + if raw_prediction.ndim == 2 and raw_prediction.shape[1] == 1: + raw_prediction = raw_prediction.squeeze(1) + proba = np.empty((raw_prediction.shape[0], 2), dtype=raw_prediction.dtype) + proba[:, 1] = self.link.inverse(raw_prediction) + proba[:, 0] = 1 - proba[:, 1] + return proba + + +class HalfMultinomialLoss(BaseLoss): + """Categorical cross-entropy loss, for multiclass classification. + + Domain: + y_true in {0, 1, 2, 3, .., n_classes - 1} + y_pred has n_classes elements, each element in (0, 1) + + Link: + y_pred = softmax(raw_prediction) + + Note: We assume y_true to be already label encoded. The inverse link is + softmax. But the full link function is the symmetric multinomial logit + function. + + For a given sample x_i, the categorical cross-entropy loss is defined as + the negative log-likelihood of the multinomial distribution, it + generalizes the binary cross-entropy to more than 2 classes:: + + loss_i = log(sum(exp(raw_pred_{i, k}), k=0..n_classes-1)) + - sum(y_true_{i, k} * raw_pred_{i, k}, k=0..n_classes-1) + + See [1]. + + Note that for the hessian, we calculate only the diagonal part in the + classes: If the full hessian for classes k and l and sample i is H_i_k_l, + we calculate H_i_k_k, i.e. k=l. + + Reference + --------- + .. [1] :arxiv:`Simon, Noah, J. Friedman and T. Hastie. + "A Blockwise Descent Algorithm for Group-penalized Multiresponse and + Multinomial Regression". + <1311.6529>` + """ + + is_multiclass = True + + def __init__(self, sample_weight=None, n_classes=3): + super().__init__( + closs=CyHalfMultinomialLoss(), + link=MultinomialLogit(), + n_classes=n_classes, + ) + self.interval_y_true = Interval(0, np.inf, True, False) + self.interval_y_pred = Interval(0, 1, False, False) + + def in_y_true_range(self, y): + """Return True if y is in the valid range of y_true. + + Parameters + ---------- + y : ndarray + """ + return self.interval_y_true.includes(y) and np.all(y.astype(int) == y) + + def fit_intercept_only(self, y_true, sample_weight=None): + """Compute raw_prediction of an intercept-only model. + + This is the softmax of the weighted average of the target, i.e. over + the samples axis=0. + """ + out = np.zeros(self.n_classes, dtype=y_true.dtype) + eps = np.finfo(y_true.dtype).eps + for k in range(self.n_classes): + out[k] = np.average(y_true == k, weights=sample_weight, axis=0) + out[k] = np.clip(out[k], eps, 1 - eps) + return self.link.link(out[None, :]).reshape(-1) + + def predict_proba(self, raw_prediction): + """Predict probabilities. + + Parameters + ---------- + raw_prediction : array of shape (n_samples, n_classes) + Raw prediction values (in link space). + + Returns + ------- + proba : array of shape (n_samples, n_classes) + Element-wise class probabilities. + """ + return self.link.inverse(raw_prediction) + + def gradient_proba( + self, + y_true, + raw_prediction, + sample_weight=None, + gradient_out=None, + proba_out=None, + n_threads=1, + ): + """Compute gradient and class probabilities fow raw_prediction. + + Parameters + ---------- + y_true : C-contiguous array of shape (n_samples,) + Observed, true target values. + raw_prediction : array of shape (n_samples, n_classes) + Raw prediction values (in link space). + sample_weight : None or C-contiguous array of shape (n_samples,) + Sample weights. + gradient_out : None or array of shape (n_samples, n_classes) + A location into which the gradient is stored. If None, a new array + might be created. + proba_out : None or array of shape (n_samples, n_classes) + A location into which the class probabilities are stored. If None, + a new array might be created. + n_threads : int, default=1 + Might use openmp thread parallelism. + + Returns + ------- + gradient : array of shape (n_samples, n_classes) + Element-wise gradients. + + proba : array of shape (n_samples, n_classes) + Element-wise class probabilities. + """ + if gradient_out is None: + if proba_out is None: + gradient_out = np.empty_like(raw_prediction) + proba_out = np.empty_like(raw_prediction) + else: + gradient_out = np.empty_like(proba_out) + elif proba_out is None: + proba_out = np.empty_like(gradient_out) + + self.closs.gradient_proba( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=gradient_out, + proba_out=proba_out, + n_threads=n_threads, + ) + return gradient_out, proba_out + + +class ExponentialLoss(BaseLoss): + """Exponential loss with (half) logit link, for binary classification. + + This is also know as boosting loss. + + Domain: + y_true in [0, 1], i.e. regression on the unit interval + y_pred in (0, 1), i.e. boundaries excluded + + Link: + y_pred = expit(2 * raw_prediction) + + For a given sample x_i, the exponential loss is defined as:: + + loss(x_i) = y_true_i * exp(-raw_pred_i)) + (1 - y_true_i) * exp(raw_pred_i) + + See: + - J. Friedman, T. Hastie, R. Tibshirani. + "Additive logistic regression: a statistical view of boosting (With discussion + and a rejoinder by the authors)." Ann. Statist. 28 (2) 337 - 407, April 2000. + https://doi.org/10.1214/aos/1016218223 + - A. Buja, W. Stuetzle, Y. Shen. (2005). + "Loss Functions for Binary Class Probability Estimation and Classification: + Structure and Applications." + + Note that the formulation works for classification, y = {0, 1}, as well as + "exponential logistic" regression, y = [0, 1]. + Note that this is a proper scoring rule, but without it's canonical link. + + More details: Inserting the predicted probability + y_pred = expit(2 * raw_prediction) in the loss gives:: + + loss(x_i) = y_true_i * sqrt((1 - y_pred_i) / y_pred_i) + + (1 - y_true_i) * sqrt(y_pred_i / (1 - y_pred_i)) + """ + + def __init__(self, sample_weight=None): + super().__init__( + closs=CyExponentialLoss(), + link=HalfLogitLink(), + n_classes=2, + ) + self.interval_y_true = Interval(0, 1, True, True) + + def constant_to_optimal_zero(self, y_true, sample_weight=None): + # This is non-zero only if y_true is neither 0 nor 1. + term = -2 * np.sqrt(y_true * (1 - y_true)) + if sample_weight is not None: + term *= sample_weight + return term + + def predict_proba(self, raw_prediction): + """Predict probabilities. + + Parameters + ---------- + raw_prediction : array of shape (n_samples,) or (n_samples, 1) + Raw prediction values (in link space). + + Returns + ------- + proba : array of shape (n_samples, 2) + Element-wise class probabilities. + """ + # Be graceful to shape (n_samples, 1) -> (n_samples,) + if raw_prediction.ndim == 2 and raw_prediction.shape[1] == 1: + raw_prediction = raw_prediction.squeeze(1) + proba = np.empty((raw_prediction.shape[0], 2), dtype=raw_prediction.dtype) + proba[:, 1] = self.link.inverse(raw_prediction) + proba[:, 0] = 1 - proba[:, 1] + return proba + + +_LOSSES = { + "squared_error": HalfSquaredError, + "absolute_error": AbsoluteError, + "pinball_loss": PinballLoss, + "huber_loss": HuberLoss, + "poisson_loss": HalfPoissonLoss, + "gamma_loss": HalfGammaLoss, + "tweedie_loss": HalfTweedieLoss, + "binomial_loss": HalfBinomialLoss, + "multinomial_loss": HalfMultinomialLoss, + "exponential_loss": ExponentialLoss, +} diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/meson.build b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/meson.build new file mode 100644 index 0000000000000000000000000000000000000000..a4b3425a21cd21b6dfa69d28ac688ede94ef2bea --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/meson.build @@ -0,0 +1,23 @@ +# .pyx is generated, so this is needed to make Cython compilation work +_loss_cython_tree = [ + fs.copyfile('_loss.pxd') +] + +_loss_pyx = custom_target( + '_loss_pyx', + output: '_loss.pyx', + input: '_loss.pyx.tp', + command: [tempita, '@INPUT@', '-o', '@OUTDIR@'], + # TODO in principle this should go in py.exension_module below. This is + # temporary work-around for dependency issue with .pyx.tp files. For more + # details, see https://github.com/mesonbuild/meson/issues/13212 + depends: _loss_cython_tree, +) + +py.extension_module( + '_loss', + cython_gen.process(_loss_pyx), + dependencies: [openmp_dep], + install: true, + subdir: 'sklearn/_loss', +) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/tests/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/tests/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/tests/test_link.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/tests/test_link.py new file mode 100644 index 0000000000000000000000000000000000000000..e5a665f8d48ac9e356971346774a125b18d234d9 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/tests/test_link.py @@ -0,0 +1,111 @@ +import numpy as np +import pytest +from numpy.testing import assert_allclose, assert_array_equal + +from sklearn._loss.link import ( + _LINKS, + HalfLogitLink, + Interval, + MultinomialLogit, + _inclusive_low_high, +) + +LINK_FUNCTIONS = list(_LINKS.values()) + + +def test_interval_raises(): + """Test that interval with low > high raises ValueError.""" + with pytest.raises( + ValueError, match="One must have low <= high; got low=1, high=0." + ): + Interval(1, 0, False, False) + + +@pytest.mark.parametrize( + "interval", + [ + Interval(0, 1, False, False), + Interval(0, 1, False, True), + Interval(0, 1, True, False), + Interval(0, 1, True, True), + Interval(-np.inf, np.inf, False, False), + Interval(-np.inf, np.inf, False, True), + Interval(-np.inf, np.inf, True, False), + Interval(-np.inf, np.inf, True, True), + Interval(-10, -1, False, False), + Interval(-10, -1, False, True), + Interval(-10, -1, True, False), + Interval(-10, -1, True, True), + ], +) +def test_is_in_range(interval): + # make sure low and high are always within the interval, used for linspace + low, high = _inclusive_low_high(interval) + + x = np.linspace(low, high, num=10) + assert interval.includes(x) + + # x contains lower bound + assert interval.includes(np.r_[x, interval.low]) == interval.low_inclusive + + # x contains upper bound + assert interval.includes(np.r_[x, interval.high]) == interval.high_inclusive + + # x contains upper and lower bound + assert interval.includes(np.r_[x, interval.low, interval.high]) == ( + interval.low_inclusive and interval.high_inclusive + ) + + +@pytest.mark.parametrize("link", LINK_FUNCTIONS) +def test_link_inverse_identity(link, global_random_seed): + # Test that link of inverse gives identity. + rng = np.random.RandomState(global_random_seed) + link = link() + n_samples, n_classes = 100, None + # The values for `raw_prediction` are limited from -20 to 20 because in the + # class `LogitLink` the term `expit(x)` comes very close to 1 for large + # positive x and therefore loses precision. + if link.is_multiclass: + n_classes = 10 + raw_prediction = rng.uniform(low=-20, high=20, size=(n_samples, n_classes)) + if isinstance(link, MultinomialLogit): + raw_prediction = link.symmetrize_raw_prediction(raw_prediction) + elif isinstance(link, HalfLogitLink): + raw_prediction = rng.uniform(low=-10, high=10, size=(n_samples)) + else: + raw_prediction = rng.uniform(low=-20, high=20, size=(n_samples)) + + assert_allclose(link.link(link.inverse(raw_prediction)), raw_prediction) + y_pred = link.inverse(raw_prediction) + assert_allclose(link.inverse(link.link(y_pred)), y_pred) + + +@pytest.mark.parametrize("link", LINK_FUNCTIONS) +def test_link_out_argument(link): + # Test that out argument gets assigned the result. + rng = np.random.RandomState(42) + link = link() + n_samples, n_classes = 100, None + if link.is_multiclass: + n_classes = 10 + raw_prediction = rng.normal(loc=0, scale=10, size=(n_samples, n_classes)) + if isinstance(link, MultinomialLogit): + raw_prediction = link.symmetrize_raw_prediction(raw_prediction) + else: + # So far, the valid interval of raw_prediction is (-inf, inf) and + # we do not need to distinguish. + raw_prediction = rng.uniform(low=-10, high=10, size=(n_samples)) + + y_pred = link.inverse(raw_prediction, out=None) + out = np.empty_like(raw_prediction) + y_pred_2 = link.inverse(raw_prediction, out=out) + assert_allclose(y_pred, out) + assert_array_equal(out, y_pred_2) + assert np.shares_memory(out, y_pred_2) + + out = np.empty_like(y_pred) + raw_prediction_2 = link.link(y_pred, out=out) + assert_allclose(raw_prediction, out) + assert_array_equal(out, raw_prediction_2) + assert np.shares_memory(out, raw_prediction_2) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/tests/test_loss.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/tests/test_loss.py new file mode 100644 index 0000000000000000000000000000000000000000..4fea32572902366ed70490d67431cab1d1a29f80 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_loss/tests/test_loss.py @@ -0,0 +1,1358 @@ +import pickle + +import numpy as np +import pytest +from numpy.testing import assert_allclose, assert_array_equal +from pytest import approx +from scipy.optimize import ( + LinearConstraint, + minimize, + minimize_scalar, + newton, +) +from scipy.special import logsumexp + +from sklearn._loss.link import IdentityLink, _inclusive_low_high +from sklearn._loss.loss import ( + _LOSSES, + AbsoluteError, + BaseLoss, + HalfBinomialLoss, + HalfGammaLoss, + HalfMultinomialLoss, + HalfPoissonLoss, + HalfSquaredError, + HalfTweedieLoss, + HalfTweedieLossIdentity, + HuberLoss, + PinballLoss, +) +from sklearn.utils import assert_all_finite +from sklearn.utils._testing import create_memmap_backed_data, skip_if_32bit + +ALL_LOSSES = list(_LOSSES.values()) + +LOSS_INSTANCES = [loss() for loss in ALL_LOSSES] +# HalfTweedieLoss(power=1.5) is already there as default +LOSS_INSTANCES += [ + PinballLoss(quantile=0.25), + HuberLoss(quantile=0.75), + HalfTweedieLoss(power=-1.5), + HalfTweedieLoss(power=0), + HalfTweedieLoss(power=1), + HalfTweedieLoss(power=2), + HalfTweedieLoss(power=3.0), + HalfTweedieLossIdentity(power=0), + HalfTweedieLossIdentity(power=1), + HalfTweedieLossIdentity(power=2), + HalfTweedieLossIdentity(power=3.0), +] + + +def loss_instance_name(param): + if isinstance(param, BaseLoss): + loss = param + name = loss.__class__.__name__ + if isinstance(loss, PinballLoss): + name += f"(quantile={loss.closs.quantile})" + elif isinstance(loss, HuberLoss): + name += f"(quantile={loss.quantile}" + elif hasattr(loss, "closs") and hasattr(loss.closs, "power"): + name += f"(power={loss.closs.power})" + return name + else: + return str(param) + + +def random_y_true_raw_prediction( + loss, n_samples, y_bound=(-100, 100), raw_bound=(-5, 5), seed=42 +): + """Random generate y_true and raw_prediction in valid range.""" + rng = np.random.RandomState(seed) + if loss.is_multiclass: + raw_prediction = np.empty((n_samples, loss.n_classes)) + raw_prediction.flat[:] = rng.uniform( + low=raw_bound[0], + high=raw_bound[1], + size=n_samples * loss.n_classes, + ) + y_true = np.arange(n_samples).astype(float) % loss.n_classes + else: + # If link is identity, we must respect the interval of y_pred: + if isinstance(loss.link, IdentityLink): + low, high = _inclusive_low_high(loss.interval_y_pred) + low = np.amax([low, raw_bound[0]]) + high = np.amin([high, raw_bound[1]]) + raw_bound = (low, high) + raw_prediction = rng.uniform( + low=raw_bound[0], high=raw_bound[1], size=n_samples + ) + # generate a y_true in valid range + low, high = _inclusive_low_high(loss.interval_y_true) + low = max(low, y_bound[0]) + high = min(high, y_bound[1]) + y_true = rng.uniform(low, high, size=n_samples) + # set some values at special boundaries + if loss.interval_y_true.low == 0 and loss.interval_y_true.low_inclusive: + y_true[:: (n_samples // 3)] = 0 + if loss.interval_y_true.high == 1 and loss.interval_y_true.high_inclusive: + y_true[1 :: (n_samples // 3)] = 1 + + return y_true, raw_prediction + + +def numerical_derivative(func, x, eps): + """Helper function for numerical (first) derivatives.""" + # For numerical derivatives, see + # https://en.wikipedia.org/wiki/Numerical_differentiation + # https://en.wikipedia.org/wiki/Finite_difference_coefficient + # We use central finite differences of accuracy 4. + h = np.full_like(x, fill_value=eps) + f_minus_2h = func(x - 2 * h) + f_minus_1h = func(x - h) + f_plus_1h = func(x + h) + f_plus_2h = func(x + 2 * h) + return (-f_plus_2h + 8 * f_plus_1h - 8 * f_minus_1h + f_minus_2h) / (12.0 * eps) + + +@pytest.mark.parametrize("loss", LOSS_INSTANCES, ids=loss_instance_name) +def test_loss_boundary(loss): + """Test interval ranges of y_true and y_pred in losses.""" + # make sure low and high are always within the interval, used for linspace + if loss.is_multiclass: + n_classes = 3 # default value + y_true = np.tile(np.linspace(0, n_classes - 1, num=n_classes), 3) + else: + low, high = _inclusive_low_high(loss.interval_y_true) + y_true = np.linspace(low, high, num=10) + + # add boundaries if they are included + if loss.interval_y_true.low_inclusive: + y_true = np.r_[y_true, loss.interval_y_true.low] + if loss.interval_y_true.high_inclusive: + y_true = np.r_[y_true, loss.interval_y_true.high] + + assert loss.in_y_true_range(y_true) + + n = y_true.shape[0] + low, high = _inclusive_low_high(loss.interval_y_pred) + if loss.is_multiclass: + y_pred = np.empty((n, n_classes)) + y_pred[:, 0] = np.linspace(low, high, num=n) + y_pred[:, 1] = 0.5 * (1 - y_pred[:, 0]) + y_pred[:, 2] = 0.5 * (1 - y_pred[:, 0]) + else: + y_pred = np.linspace(low, high, num=n) + + assert loss.in_y_pred_range(y_pred) + + # calculating losses should not fail + raw_prediction = loss.link.link(y_pred) + loss.loss(y_true=y_true, raw_prediction=raw_prediction) + + +# Fixture to test valid value ranges. +Y_COMMON_PARAMS = [ + # (loss, [y success], [y fail]) + (HalfSquaredError(), [-100, 0, 0.1, 100], [-np.inf, np.inf]), + (AbsoluteError(), [-100, 0, 0.1, 100], [-np.inf, np.inf]), + (PinballLoss(), [-100, 0, 0.1, 100], [-np.inf, np.inf]), + (HuberLoss(), [-100, 0, 0.1, 100], [-np.inf, np.inf]), + (HalfPoissonLoss(), [0.1, 100], [-np.inf, -3, -0.1, np.inf]), + (HalfGammaLoss(), [0.1, 100], [-np.inf, -3, -0.1, 0, np.inf]), + (HalfTweedieLoss(power=-3), [0.1, 100], [-np.inf, np.inf]), + (HalfTweedieLoss(power=0), [0.1, 100], [-np.inf, np.inf]), + (HalfTweedieLoss(power=1.5), [0.1, 100], [-np.inf, -3, -0.1, np.inf]), + (HalfTweedieLoss(power=2), [0.1, 100], [-np.inf, -3, -0.1, 0, np.inf]), + (HalfTweedieLoss(power=3), [0.1, 100], [-np.inf, -3, -0.1, 0, np.inf]), + (HalfTweedieLossIdentity(power=-3), [0.1, 100], [-np.inf, np.inf]), + (HalfTweedieLossIdentity(power=0), [-3, -0.1, 0, 0.1, 100], [-np.inf, np.inf]), + (HalfTweedieLossIdentity(power=1.5), [0.1, 100], [-np.inf, -3, -0.1, np.inf]), + (HalfTweedieLossIdentity(power=2), [0.1, 100], [-np.inf, -3, -0.1, 0, np.inf]), + (HalfTweedieLossIdentity(power=3), [0.1, 100], [-np.inf, -3, -0.1, 0, np.inf]), + (HalfBinomialLoss(), [0.1, 0.5, 0.9], [-np.inf, -1, 2, np.inf]), + (HalfMultinomialLoss(), [], [-np.inf, -1, 1.1, np.inf]), +] +# y_pred and y_true do not always have the same domain (valid value range). +# Hence, we define extra sets of parameters for each of them. +Y_TRUE_PARAMS = [ # type: ignore[var-annotated] + # (loss, [y success], [y fail]) + (HalfPoissonLoss(), [0], []), + (HuberLoss(), [0], []), + (HalfTweedieLoss(power=-3), [-100, -0.1, 0], []), + (HalfTweedieLoss(power=0), [-100, 0], []), + (HalfTweedieLoss(power=1.5), [0], []), + (HalfTweedieLossIdentity(power=-3), [-100, -0.1, 0], []), + (HalfTweedieLossIdentity(power=0), [-100, 0], []), + (HalfTweedieLossIdentity(power=1.5), [0], []), + (HalfBinomialLoss(), [0, 1], []), + (HalfMultinomialLoss(), [0.0, 1.0, 2], []), +] +Y_PRED_PARAMS = [ + # (loss, [y success], [y fail]) + (HalfPoissonLoss(), [], [0]), + (HalfTweedieLoss(power=-3), [], [-3, -0.1, 0]), + (HalfTweedieLoss(power=0), [], [-3, -0.1, 0]), + (HalfTweedieLoss(power=1.5), [], [0]), + (HalfTweedieLossIdentity(power=-3), [], [-3, -0.1, 0]), + (HalfTweedieLossIdentity(power=0), [-3, -0.1, 0], []), + (HalfTweedieLossIdentity(power=1.5), [], [0]), + (HalfBinomialLoss(), [], [0, 1]), + (HalfMultinomialLoss(), [0.1, 0.5], [0, 1]), +] + + +@pytest.mark.parametrize( + "loss, y_true_success, y_true_fail", + Y_COMMON_PARAMS + Y_TRUE_PARAMS, # type: ignore[operator] +) +def test_loss_boundary_y_true(loss, y_true_success, y_true_fail): + """Test boundaries of y_true for loss functions.""" + for y in y_true_success: + assert loss.in_y_true_range(np.array([y])) + for y in y_true_fail: + assert not loss.in_y_true_range(np.array([y])) + + +@pytest.mark.parametrize( + "loss, y_pred_success, y_pred_fail", + Y_COMMON_PARAMS + Y_PRED_PARAMS, # type: ignore[operator] +) +def test_loss_boundary_y_pred(loss, y_pred_success, y_pred_fail): + """Test boundaries of y_pred for loss functions.""" + for y in y_pred_success: + assert loss.in_y_pred_range(np.array([y])) + for y in y_pred_fail: + assert not loss.in_y_pred_range(np.array([y])) + + +@pytest.mark.parametrize( + "loss, y_true, raw_prediction, loss_true, gradient_true, hessian_true", + [ + (HalfSquaredError(), 1.0, 5.0, 8, 4, 1), + (AbsoluteError(), 1.0, 5.0, 4.0, 1.0, None), + (PinballLoss(quantile=0.5), 1.0, 5.0, 2, 0.5, None), + (PinballLoss(quantile=0.25), 1.0, 5.0, 4 * (1 - 0.25), 1 - 0.25, None), + (PinballLoss(quantile=0.25), 5.0, 1.0, 4 * 0.25, -0.25, None), + (HuberLoss(quantile=0.5, delta=3), 1.0, 5.0, 3 * (4 - 3 / 2), None, None), + (HuberLoss(quantile=0.5, delta=3), 1.0, 3.0, 0.5 * 2**2, None, None), + (HalfPoissonLoss(), 2.0, np.log(4), 4 - 2 * np.log(4), 4 - 2, 4), + (HalfGammaLoss(), 2.0, np.log(4), np.log(4) + 2 / 4, 1 - 2 / 4, 2 / 4), + (HalfTweedieLoss(power=3), 2.0, np.log(4), -1 / 4 + 1 / 4**2, None, None), + (HalfTweedieLossIdentity(power=1), 2.0, 4.0, 2 - 2 * np.log(2), None, None), + (HalfTweedieLossIdentity(power=2), 2.0, 4.0, np.log(2) - 1 / 2, None, None), + ( + HalfTweedieLossIdentity(power=3), + 2.0, + 4.0, + -1 / 4 + 1 / 4**2 + 1 / 2 / 2, + None, + None, + ), + ( + HalfBinomialLoss(), + 0.25, + np.log(4), + np.log1p(4) - 0.25 * np.log(4), + None, + None, + ), + # Extreme log loss cases, checked with mpmath: + # import mpmath as mp + # + # # Stolen from scipy + # def mpf2float(x): + # return float(mp.nstr(x, 17, min_fixed=0, max_fixed=0)) + # + # def mp_logloss(y_true, raw): + # with mp.workdps(100): + # y_true, raw = mp.mpf(float(y_true)), mp.mpf(float(raw)) + # out = mp.log1p(mp.exp(raw)) - y_true * raw + # return mpf2float(out) + # + # def mp_gradient(y_true, raw): + # with mp.workdps(100): + # y_true, raw = mp.mpf(float(y_true)), mp.mpf(float(raw)) + # out = mp.mpf(1) / (mp.mpf(1) + mp.exp(-raw)) - y_true + # return mpf2float(out) + # + # def mp_hessian(y_true, raw): + # with mp.workdps(100): + # y_true, raw = mp.mpf(float(y_true)), mp.mpf(float(raw)) + # p = mp.mpf(1) / (mp.mpf(1) + mp.exp(-raw)) + # out = p * (mp.mpf(1) - p) + # return mpf2float(out) + # + # y, raw = 0.0, 37. + # mp_logloss(y, raw), mp_gradient(y, raw), mp_hessian(y, raw) + (HalfBinomialLoss(), 0.0, -1e20, 0, 0, 0), + (HalfBinomialLoss(), 1.0, -1e20, 1e20, -1, 0), + (HalfBinomialLoss(), 0.0, -1e3, 0, 0, 0), + (HalfBinomialLoss(), 1.0, -1e3, 1e3, -1, 0), + (HalfBinomialLoss(), 1.0, -37.5, 37.5, -1, 0), + (HalfBinomialLoss(), 1.0, -37.0, 37, 1e-16 - 1, 8.533047625744065e-17), + (HalfBinomialLoss(), 0.0, -37.0, *[8.533047625744065e-17] * 3), + (HalfBinomialLoss(), 1.0, -36.9, 36.9, 1e-16 - 1, 9.430476078526806e-17), + (HalfBinomialLoss(), 0.0, -36.9, *[9.430476078526806e-17] * 3), + (HalfBinomialLoss(), 0.0, 37.0, 37, 1 - 1e-16, 8.533047625744065e-17), + (HalfBinomialLoss(), 1.0, 37.0, *[8.533047625744066e-17] * 3), + (HalfBinomialLoss(), 0.0, 37.5, 37.5, 1, 5.175555005801868e-17), + (HalfBinomialLoss(), 0.0, 232.8, 232.8, 1, 1.4287342391028437e-101), + (HalfBinomialLoss(), 1.0, 1e20, 0, 0, 0), + (HalfBinomialLoss(), 0.0, 1e20, 1e20, 1, 0), + ( + HalfBinomialLoss(), + 1.0, + 232.8, + 0, + -1.4287342391028437e-101, + 1.4287342391028437e-101, + ), + (HalfBinomialLoss(), 1.0, 232.9, 0, 0, 0), + (HalfBinomialLoss(), 1.0, 1e3, 0, 0, 0), + (HalfBinomialLoss(), 0.0, 1e3, 1e3, 1, 0), + ( + HalfMultinomialLoss(n_classes=3), + 0.0, + [0.2, 0.5, 0.3], + logsumexp([0.2, 0.5, 0.3]) - 0.2, + None, + None, + ), + ( + HalfMultinomialLoss(n_classes=3), + 1.0, + [0.2, 0.5, 0.3], + logsumexp([0.2, 0.5, 0.3]) - 0.5, + None, + None, + ), + ( + HalfMultinomialLoss(n_classes=3), + 2.0, + [0.2, 0.5, 0.3], + logsumexp([0.2, 0.5, 0.3]) - 0.3, + None, + None, + ), + ( + HalfMultinomialLoss(n_classes=3), + 2.0, + [1e4, 0, 7e-7], + logsumexp([1e4, 0, 7e-7]) - (7e-7), + None, + None, + ), + ], + ids=loss_instance_name, +) +def test_loss_on_specific_values( + loss, y_true, raw_prediction, loss_true, gradient_true, hessian_true +): + """Test losses, gradients and hessians at specific values.""" + loss1 = loss(y_true=np.array([y_true]), raw_prediction=np.array([raw_prediction])) + grad1 = loss.gradient( + y_true=np.array([y_true]), raw_prediction=np.array([raw_prediction]) + ) + loss2, grad2 = loss.loss_gradient( + y_true=np.array([y_true]), raw_prediction=np.array([raw_prediction]) + ) + grad3, hess = loss.gradient_hessian( + y_true=np.array([y_true]), raw_prediction=np.array([raw_prediction]) + ) + + assert loss1 == approx(loss_true, rel=1e-15, abs=1e-15) + assert loss2 == approx(loss_true, rel=1e-15, abs=1e-15) + + if gradient_true is not None: + assert grad1 == approx(gradient_true, rel=1e-15, abs=1e-15) + assert grad2 == approx(gradient_true, rel=1e-15, abs=1e-15) + assert grad3 == approx(gradient_true, rel=1e-15, abs=1e-15) + + if hessian_true is not None: + assert hess == approx(hessian_true, rel=1e-15, abs=1e-15) + + +@pytest.mark.parametrize("loss", ALL_LOSSES) +@pytest.mark.parametrize("readonly_memmap", [False, True]) +@pytest.mark.parametrize("dtype_in", [np.float32, np.float64]) +@pytest.mark.parametrize("dtype_out", [np.float32, np.float64]) +@pytest.mark.parametrize("sample_weight", [None, 1]) +@pytest.mark.parametrize("out1", [None, 1]) +@pytest.mark.parametrize("out2", [None, 1]) +@pytest.mark.parametrize("n_threads", [1, 2]) +def test_loss_dtype( + loss, readonly_memmap, dtype_in, dtype_out, sample_weight, out1, out2, n_threads +): + """Test acceptance of dtypes, readonly and writeable arrays in loss functions. + + Check that loss accepts if all input arrays are either all float32 or all + float64, and all output arrays are either all float32 or all float64. + + Also check that input arrays can be readonly, e.g. memory mapped. + """ + loss = loss() + # generate a y_true and raw_prediction in valid range + n_samples = 5 + y_true, raw_prediction = random_y_true_raw_prediction( + loss=loss, + n_samples=n_samples, + y_bound=(-100, 100), + raw_bound=(-10, 10), + seed=42, + ) + y_true = y_true.astype(dtype_in) + raw_prediction = raw_prediction.astype(dtype_in) + + if sample_weight is not None: + sample_weight = np.array([2.0] * n_samples, dtype=dtype_in) + if out1 is not None: + out1 = np.empty_like(y_true, dtype=dtype_out) + if out2 is not None: + out2 = np.empty_like(raw_prediction, dtype=dtype_out) + + if readonly_memmap: + y_true = create_memmap_backed_data(y_true) + raw_prediction = create_memmap_backed_data(raw_prediction) + if sample_weight is not None: + sample_weight = create_memmap_backed_data(sample_weight) + + l = loss.loss( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + loss_out=out1, + n_threads=n_threads, + ) + assert l is out1 if out1 is not None else True + g = loss.gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=out2, + n_threads=n_threads, + ) + assert g is out2 if out2 is not None else True + l, g = loss.loss_gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + loss_out=out1, + gradient_out=out2, + n_threads=n_threads, + ) + assert l is out1 if out1 is not None else True + assert g is out2 if out2 is not None else True + if out1 is not None and loss.is_multiclass: + out1 = np.empty_like(raw_prediction, dtype=dtype_out) + g, h = loss.gradient_hessian( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=out1, + hessian_out=out2, + n_threads=n_threads, + ) + assert g is out1 if out1 is not None else True + assert h is out2 if out2 is not None else True + loss(y_true=y_true, raw_prediction=raw_prediction, sample_weight=sample_weight) + loss.fit_intercept_only(y_true=y_true, sample_weight=sample_weight) + loss.constant_to_optimal_zero(y_true=y_true, sample_weight=sample_weight) + if hasattr(loss, "predict_proba"): + loss.predict_proba(raw_prediction=raw_prediction) + if hasattr(loss, "gradient_proba"): + g, p = loss.gradient_proba( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=out1, + proba_out=out2, + n_threads=n_threads, + ) + assert g is out1 if out1 is not None else True + assert p is out2 if out2 is not None else True + + +@pytest.mark.parametrize("loss", LOSS_INSTANCES, ids=loss_instance_name) +@pytest.mark.parametrize("sample_weight", [None, "range"]) +def test_loss_same_as_C_functions(loss, sample_weight): + """Test that Python and Cython functions return same results.""" + y_true, raw_prediction = random_y_true_raw_prediction( + loss=loss, + n_samples=20, + y_bound=(-100, 100), + raw_bound=(-10, 10), + seed=42, + ) + if sample_weight == "range": + sample_weight = np.linspace(1, y_true.shape[0], num=y_true.shape[0]) + + out_l1 = np.empty_like(y_true) + out_l2 = np.empty_like(y_true) + out_g1 = np.empty_like(raw_prediction) + out_g2 = np.empty_like(raw_prediction) + out_h1 = np.empty_like(raw_prediction) + out_h2 = np.empty_like(raw_prediction) + loss.loss( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + loss_out=out_l1, + ) + loss.closs.loss( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + loss_out=out_l2, + ) + assert_allclose(out_l1, out_l2) + loss.gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=out_g1, + ) + loss.closs.gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=out_g2, + ) + assert_allclose(out_g1, out_g2) + loss.closs.loss_gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + loss_out=out_l1, + gradient_out=out_g1, + ) + loss.closs.loss_gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + loss_out=out_l2, + gradient_out=out_g2, + ) + assert_allclose(out_l1, out_l2) + assert_allclose(out_g1, out_g2) + loss.gradient_hessian( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=out_g1, + hessian_out=out_h1, + ) + loss.closs.gradient_hessian( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=out_g2, + hessian_out=out_h2, + ) + assert_allclose(out_g1, out_g2) + assert_allclose(out_h1, out_h2) + + +@pytest.mark.parametrize("loss", LOSS_INSTANCES, ids=loss_instance_name) +@pytest.mark.parametrize("sample_weight", [None, "range"]) +def test_loss_gradients_are_the_same(loss, sample_weight, global_random_seed): + """Test that loss and gradient are the same across different functions. + + Also test that output arguments contain correct results. + """ + y_true, raw_prediction = random_y_true_raw_prediction( + loss=loss, + n_samples=20, + y_bound=(-100, 100), + raw_bound=(-10, 10), + seed=global_random_seed, + ) + if sample_weight == "range": + sample_weight = np.linspace(1, y_true.shape[0], num=y_true.shape[0]) + + out_l1 = np.empty_like(y_true) + out_l2 = np.empty_like(y_true) + out_g1 = np.empty_like(raw_prediction) + out_g2 = np.empty_like(raw_prediction) + out_g3 = np.empty_like(raw_prediction) + out_h3 = np.empty_like(raw_prediction) + + l1 = loss.loss( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + loss_out=out_l1, + ) + g1 = loss.gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=out_g1, + ) + l2, g2 = loss.loss_gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + loss_out=out_l2, + gradient_out=out_g2, + ) + g3, h3 = loss.gradient_hessian( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=out_g3, + hessian_out=out_h3, + ) + assert_allclose(l1, l2) + assert_array_equal(l1, out_l1) + assert np.shares_memory(l1, out_l1) + assert_array_equal(l2, out_l2) + assert np.shares_memory(l2, out_l2) + assert_allclose(g1, g2) + assert_allclose(g1, g3) + assert_array_equal(g1, out_g1) + assert np.shares_memory(g1, out_g1) + assert_array_equal(g2, out_g2) + assert np.shares_memory(g2, out_g2) + assert_array_equal(g3, out_g3) + assert np.shares_memory(g3, out_g3) + + if hasattr(loss, "gradient_proba"): + assert loss.is_multiclass # only for HalfMultinomialLoss + out_g4 = np.empty_like(raw_prediction) + out_proba = np.empty_like(raw_prediction) + g4, proba = loss.gradient_proba( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + gradient_out=out_g4, + proba_out=out_proba, + ) + assert_allclose(g1, out_g4) + assert_allclose(g1, g4) + assert_allclose(proba, out_proba) + assert_allclose(np.sum(proba, axis=1), 1, rtol=1e-11) + + +@pytest.mark.parametrize("loss", LOSS_INSTANCES, ids=loss_instance_name) +@pytest.mark.parametrize("sample_weight", ["ones", "random"]) +def test_sample_weight_multiplies(loss, sample_weight, global_random_seed): + """Test sample weights in loss, gradients and hessians. + + Make sure that passing sample weights to loss, gradient and hessian + computation methods is equivalent to multiplying by the weights. + """ + n_samples = 100 + y_true, raw_prediction = random_y_true_raw_prediction( + loss=loss, + n_samples=n_samples, + y_bound=(-100, 100), + raw_bound=(-5, 5), + seed=global_random_seed, + ) + + if sample_weight == "ones": + sample_weight = np.ones(shape=n_samples, dtype=np.float64) + else: + rng = np.random.RandomState(global_random_seed) + sample_weight = rng.normal(size=n_samples).astype(np.float64) + + assert_allclose( + loss.loss( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + ), + sample_weight + * loss.loss( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=None, + ), + ) + + losses, gradient = loss.loss_gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=None, + ) + losses_sw, gradient_sw = loss.loss_gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + ) + assert_allclose(losses * sample_weight, losses_sw) + if not loss.is_multiclass: + assert_allclose(gradient * sample_weight, gradient_sw) + else: + assert_allclose(gradient * sample_weight[:, None], gradient_sw) + + gradient, hessian = loss.gradient_hessian( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=None, + ) + gradient_sw, hessian_sw = loss.gradient_hessian( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + ) + if not loss.is_multiclass: + assert_allclose(gradient * sample_weight, gradient_sw) + assert_allclose(hessian * sample_weight, hessian_sw) + else: + assert_allclose(gradient * sample_weight[:, None], gradient_sw) + assert_allclose(hessian * sample_weight[:, None], hessian_sw) + + +@pytest.mark.parametrize("loss", LOSS_INSTANCES, ids=loss_instance_name) +def test_graceful_squeezing(loss): + """Test that reshaped raw_prediction gives same results.""" + y_true, raw_prediction = random_y_true_raw_prediction( + loss=loss, + n_samples=20, + y_bound=(-100, 100), + raw_bound=(-10, 10), + seed=42, + ) + + if raw_prediction.ndim == 1: + raw_prediction_2d = raw_prediction[:, None] + assert_allclose( + loss.loss(y_true=y_true, raw_prediction=raw_prediction_2d), + loss.loss(y_true=y_true, raw_prediction=raw_prediction), + ) + assert_allclose( + loss.loss_gradient(y_true=y_true, raw_prediction=raw_prediction_2d), + loss.loss_gradient(y_true=y_true, raw_prediction=raw_prediction), + ) + assert_allclose( + loss.gradient(y_true=y_true, raw_prediction=raw_prediction_2d), + loss.gradient(y_true=y_true, raw_prediction=raw_prediction), + ) + assert_allclose( + loss.gradient_hessian(y_true=y_true, raw_prediction=raw_prediction_2d), + loss.gradient_hessian(y_true=y_true, raw_prediction=raw_prediction), + ) + + +@pytest.mark.parametrize("loss", LOSS_INSTANCES, ids=loss_instance_name) +@pytest.mark.parametrize("sample_weight", [None, "range"]) +def test_loss_of_perfect_prediction(loss, sample_weight): + """Test value of perfect predictions. + + Loss of y_pred = y_true plus constant_to_optimal_zero should sums up to + zero. + """ + if not loss.is_multiclass: + # Use small values such that exp(value) is not nan. + raw_prediction = np.array([-10, -0.1, 0, 0.1, 3, 10]) + # If link is identity, we must respect the interval of y_pred: + if isinstance(loss.link, IdentityLink): + eps = 1e-10 + low = loss.interval_y_pred.low + if not loss.interval_y_pred.low_inclusive: + low = low + eps + high = loss.interval_y_pred.high + if not loss.interval_y_pred.high_inclusive: + high = high - eps + raw_prediction = np.clip(raw_prediction, low, high) + y_true = loss.link.inverse(raw_prediction) + else: + # HalfMultinomialLoss + y_true = np.arange(loss.n_classes).astype(float) + # raw_prediction with entries -exp(10), but +exp(10) on the diagonal + # this is close enough to np.inf which would produce nan + raw_prediction = np.full( + shape=(loss.n_classes, loss.n_classes), + fill_value=-np.exp(10), + dtype=float, + ) + raw_prediction.flat[:: loss.n_classes + 1] = np.exp(10) + + if sample_weight == "range": + sample_weight = np.linspace(1, y_true.shape[0], num=y_true.shape[0]) + + loss_value = loss.loss( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + ) + constant_term = loss.constant_to_optimal_zero( + y_true=y_true, sample_weight=sample_weight + ) + # Comparing loss_value + constant_term to zero would result in large + # round-off errors. + assert_allclose(loss_value, -constant_term, atol=1e-14, rtol=1e-15) + + +@pytest.mark.parametrize("loss", LOSS_INSTANCES, ids=loss_instance_name) +@pytest.mark.parametrize("sample_weight", [None, "range"]) +def test_gradients_hessians_numerically(loss, sample_weight, global_random_seed): + """Test gradients and hessians with numerical derivatives. + + Gradient should equal the numerical derivatives of the loss function. + Hessians should equal the numerical derivatives of gradients. + """ + n_samples = 20 + y_true, raw_prediction = random_y_true_raw_prediction( + loss=loss, + n_samples=n_samples, + y_bound=(-100, 100), + raw_bound=(-5, 5), + seed=global_random_seed, + ) + + if sample_weight == "range": + sample_weight = np.linspace(1, y_true.shape[0], num=y_true.shape[0]) + + g, h = loss.gradient_hessian( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + ) + + assert g.shape == raw_prediction.shape + assert h.shape == raw_prediction.shape + + if not loss.is_multiclass: + + def loss_func(x): + return loss.loss( + y_true=y_true, + raw_prediction=x, + sample_weight=sample_weight, + ) + + g_numeric = numerical_derivative(loss_func, raw_prediction, eps=1e-6) + assert_allclose(g, g_numeric, rtol=5e-6, atol=1e-10) + + def grad_func(x): + return loss.gradient( + y_true=y_true, + raw_prediction=x, + sample_weight=sample_weight, + ) + + h_numeric = numerical_derivative(grad_func, raw_prediction, eps=1e-6) + if loss.approx_hessian: + # TODO: What could we test if loss.approx_hessian? + pass + else: + assert_allclose(h, h_numeric, rtol=5e-6, atol=1e-10) + else: + # For multiclass loss, we should only change the predictions of the + # class for which the derivative is taken for, e.g. offset[:, k] = eps + # for class k. + # As a softmax is computed, offsetting the whole array by a constant + # would have no effect on the probabilities, and thus on the loss. + for k in range(loss.n_classes): + + def loss_func(x): + raw = raw_prediction.copy() + raw[:, k] = x + return loss.loss( + y_true=y_true, + raw_prediction=raw, + sample_weight=sample_weight, + ) + + g_numeric = numerical_derivative(loss_func, raw_prediction[:, k], eps=1e-5) + assert_allclose(g[:, k], g_numeric, rtol=5e-6, atol=1e-10) + + def grad_func(x): + raw = raw_prediction.copy() + raw[:, k] = x + return loss.gradient( + y_true=y_true, + raw_prediction=raw, + sample_weight=sample_weight, + )[:, k] + + h_numeric = numerical_derivative(grad_func, raw_prediction[:, k], eps=1e-6) + if loss.approx_hessian: + # TODO: What could we test if loss.approx_hessian? + pass + else: + assert_allclose(h[:, k], h_numeric, rtol=5e-6, atol=1e-10) + + +@pytest.mark.parametrize( + "loss, x0, y_true", + [ + ("squared_error", -2.0, 42), + ("squared_error", 117.0, 1.05), + ("squared_error", 0.0, 0.0), + # The argmin of binomial_loss for y_true=0 and y_true=1 is resp. + # -inf and +inf due to logit, cf. "complete separation". Therefore, we + # use 0 < y_true < 1. + ("binomial_loss", 0.3, 0.1), + ("binomial_loss", -12, 0.2), + ("binomial_loss", 30, 0.9), + ("poisson_loss", 12.0, 1.0), + ("poisson_loss", 0.0, 2.0), + ("poisson_loss", -22.0, 10.0), + ], +) +@skip_if_32bit +def test_derivatives(loss, x0, y_true): + """Test that gradients are zero at the minimum of the loss. + + We check this on a single value/sample using Halley's method with the + first and second order derivatives computed by the Loss instance. + Note that methods of Loss instances operate on arrays while the newton + root finder expects a scalar or a one-element array for this purpose. + """ + loss = _LOSSES[loss](sample_weight=None) + y_true = np.array([y_true], dtype=np.float64) + x0 = np.array([x0], dtype=np.float64) + + def func(x: np.ndarray) -> np.ndarray: + """Compute loss plus constant term. + + The constant term is such that the minimum function value is zero, + which is required by the Newton method. + """ + return loss.loss( + y_true=y_true, raw_prediction=x + ) + loss.constant_to_optimal_zero(y_true=y_true) + + def fprime(x: np.ndarray) -> np.ndarray: + return loss.gradient(y_true=y_true, raw_prediction=x) + + def fprime2(x: np.ndarray) -> np.ndarray: + return loss.gradient_hessian(y_true=y_true, raw_prediction=x)[1] + + optimum = newton( + func, + x0=x0, + fprime=fprime, + fprime2=fprime2, + maxiter=100, + tol=5e-8, + ) + + # Need to ravel arrays because assert_allclose requires matching + # dimensions. + y_true = y_true.ravel() + optimum = optimum.ravel() + assert_allclose(loss.link.inverse(optimum), y_true) + assert_allclose(func(optimum), 0, atol=1e-14) + assert_allclose(loss.gradient(y_true=y_true, raw_prediction=optimum), 0, atol=5e-7) + + +@pytest.mark.parametrize("loss", LOSS_INSTANCES, ids=loss_instance_name) +@pytest.mark.parametrize("sample_weight", [None, "range"]) +def test_loss_intercept_only(loss, sample_weight): + """Test that fit_intercept_only returns the argmin of the loss. + + Also test that the gradient is zero at the minimum. + """ + n_samples = 50 + if not loss.is_multiclass: + y_true = loss.link.inverse(np.linspace(-4, 4, num=n_samples)) + else: + y_true = np.arange(n_samples).astype(np.float64) % loss.n_classes + y_true[::5] = 0 # exceedance of class 0 + + if sample_weight == "range": + sample_weight = np.linspace(0.1, 2, num=n_samples) + + a = loss.fit_intercept_only(y_true=y_true, sample_weight=sample_weight) + + # find minimum by optimization + def fun(x): + if not loss.is_multiclass: + raw_prediction = np.full(shape=(n_samples), fill_value=x) + else: + raw_prediction = np.ascontiguousarray( + np.broadcast_to(x, shape=(n_samples, loss.n_classes)) + ) + return loss( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + ) + + if not loss.is_multiclass: + opt = minimize_scalar(fun, tol=1e-7, options={"maxiter": 100}) + grad = loss.gradient( + y_true=y_true, + raw_prediction=np.full_like(y_true, a), + sample_weight=sample_weight, + ) + assert a.shape == tuple() # scalar + assert a.dtype == y_true.dtype + assert_all_finite(a) + a == approx(opt.x, rel=1e-7) + grad.sum() == approx(0, abs=1e-12) + else: + # The constraint corresponds to sum(raw_prediction) = 0. Without it, we would + # need to apply loss.symmetrize_raw_prediction to opt.x before comparing. + opt = minimize( + fun, + np.zeros((loss.n_classes)), + tol=1e-13, + options={"maxiter": 100}, + method="SLSQP", + constraints=LinearConstraint(np.ones((1, loss.n_classes)), 0, 0), + ) + grad = loss.gradient( + y_true=y_true, + raw_prediction=np.tile(a, (n_samples, 1)), + sample_weight=sample_weight, + ) + assert a.dtype == y_true.dtype + assert_all_finite(a) + assert_allclose(a, opt.x, rtol=5e-6, atol=1e-12) + assert_allclose(grad.sum(axis=0), 0, atol=1e-12) + + +@pytest.mark.parametrize( + "loss, func, random_dist", + [ + (HalfSquaredError(), np.mean, "normal"), + (AbsoluteError(), np.median, "normal"), + (PinballLoss(quantile=0.25), lambda x: np.percentile(x, q=25), "normal"), + (HalfPoissonLoss(), np.mean, "poisson"), + (HalfGammaLoss(), np.mean, "exponential"), + (HalfTweedieLoss(), np.mean, "exponential"), + (HalfBinomialLoss(), np.mean, "binomial"), + ], +) +def test_specific_fit_intercept_only(loss, func, random_dist, global_random_seed): + """Test that fit_intercept_only returns the correct functional. + + We test the functional for specific, meaningful distributions, e.g. + squared error estimates the expectation of a probability distribution. + """ + rng = np.random.RandomState(global_random_seed) + if random_dist == "binomial": + y_train = rng.binomial(1, 0.5, size=100) + else: + y_train = getattr(rng, random_dist)(size=100) + baseline_prediction = loss.fit_intercept_only(y_true=y_train) + # Make sure baseline prediction is the expected functional=func, e.g. mean + # or median. + assert_all_finite(baseline_prediction) + assert baseline_prediction == approx(loss.link.link(func(y_train))) + assert loss.link.inverse(baseline_prediction) == approx(func(y_train)) + if isinstance(loss, IdentityLink): + assert_allclose(loss.link.inverse(baseline_prediction), baseline_prediction) + + # Test baseline at boundary + if loss.interval_y_true.low_inclusive: + y_train.fill(loss.interval_y_true.low) + baseline_prediction = loss.fit_intercept_only(y_true=y_train) + assert_all_finite(baseline_prediction) + if loss.interval_y_true.high_inclusive: + y_train.fill(loss.interval_y_true.high) + baseline_prediction = loss.fit_intercept_only(y_true=y_train) + assert_all_finite(baseline_prediction) + + +def test_multinomial_loss_fit_intercept_only(): + """Test that fit_intercept_only returns the mean functional for CCE.""" + rng = np.random.RandomState(0) + n_classes = 4 + loss = HalfMultinomialLoss(n_classes=n_classes) + # Same logic as test_specific_fit_intercept_only. Here inverse link + # function = softmax and link function = log - symmetry term. + y_train = rng.randint(0, n_classes + 1, size=100).astype(np.float64) + baseline_prediction = loss.fit_intercept_only(y_true=y_train) + assert baseline_prediction.shape == (n_classes,) + p = np.zeros(n_classes, dtype=y_train.dtype) + for k in range(n_classes): + p[k] = (y_train == k).mean() + assert_allclose(baseline_prediction, np.log(p) - np.mean(np.log(p))) + assert_allclose(baseline_prediction[None, :], loss.link.link(p[None, :])) + + for y_train in (np.zeros(shape=10), np.ones(shape=10)): + y_train = y_train.astype(np.float64) + baseline_prediction = loss.fit_intercept_only(y_true=y_train) + assert baseline_prediction.dtype == y_train.dtype + assert_all_finite(baseline_prediction) + + +def test_multinomial_cy_gradient(global_random_seed): + """Test that Multinomial cy_gradient gives the same result as gradient. + + CyHalfMultinomialLoss does not inherit from CyLossFunction and has a different API. + As a consequence, the functions like `loss` and `gradient` do not rely on `cy_loss` + and `cy_gradient`. + """ + n_samples = 100 + n_classes = 5 + loss = HalfMultinomialLoss(n_classes=n_classes) + y_true, raw_prediction = random_y_true_raw_prediction( + loss=loss, + n_samples=n_samples, + seed=global_random_seed, + ) + sample_weight = np.linspace(0.1, 2, num=n_samples) + + grad1 = loss.closs._test_cy_gradient( + y_true=y_true, + raw_prediction=raw_prediction, # needs to be C-contiguous + sample_weight=sample_weight, + ) + grad2 = loss.gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + ) + assert_allclose(grad1, grad2) + + +def test_binomial_and_multinomial_loss(global_random_seed): + """Test that multinomial loss with n_classes = 2 is the same as binomial loss.""" + rng = np.random.RandomState(global_random_seed) + n_samples = 20 + binom = HalfBinomialLoss() + multinom = HalfMultinomialLoss(n_classes=2) + y_train = rng.randint(0, 2, size=n_samples).astype(np.float64) + raw_prediction = rng.normal(size=n_samples) + raw_multinom = np.empty((n_samples, 2)) + raw_multinom[:, 0] = -0.5 * raw_prediction + raw_multinom[:, 1] = 0.5 * raw_prediction + assert_allclose( + binom.loss(y_true=y_train, raw_prediction=raw_prediction), + multinom.loss(y_true=y_train, raw_prediction=raw_multinom), + ) + + +@pytest.mark.parametrize("y_true", (np.array([0.0, 0, 0]), np.array([1.0, 1, 1]))) +@pytest.mark.parametrize("y_pred", (np.array([-5.0, -5, -5]), np.array([3.0, 3, 3]))) +def test_binomial_vs_alternative_formulation(y_true, y_pred, global_dtype): + """Test that both formulations of the binomial deviance agree. + + Often, the binomial deviance or log loss is written in terms of a variable + z in {-1, +1}, but we use y in {0, 1}, hence z = 2 * y - 1. + ESL II Eq. (10.18): + + -loglike(z, f) = log(1 + exp(-2 * z * f)) + + Note: + - ESL 2*f = raw_prediction, hence the factor 2 of ESL disappears. + - Deviance = -2*loglike + .., but HalfBinomialLoss is half of the + deviance, hence the factor of 2 cancels in the comparison. + """ + + def alt_loss(y, raw_pred): + z = 2 * y - 1 + return np.mean(np.log(1 + np.exp(-z * raw_pred))) + + def alt_gradient(y, raw_pred): + # alternative gradient formula according to ESL + z = 2 * y - 1 + return -z / (1 + np.exp(z * raw_pred)) + + bin_loss = HalfBinomialLoss() + + y_true = y_true.astype(global_dtype) + y_pred = y_pred.astype(global_dtype) + datum = (y_true, y_pred) + + assert bin_loss(*datum) == approx(alt_loss(*datum)) + assert_allclose(bin_loss.gradient(*datum), alt_gradient(*datum)) + + +@pytest.mark.parametrize("loss", LOSS_INSTANCES, ids=loss_instance_name) +def test_predict_proba(loss, global_random_seed): + """Test that predict_proba and gradient_proba work as expected.""" + n_samples = 20 + y_true, raw_prediction = random_y_true_raw_prediction( + loss=loss, + n_samples=n_samples, + y_bound=(-100, 100), + raw_bound=(-5, 5), + seed=global_random_seed, + ) + + if hasattr(loss, "predict_proba"): + proba = loss.predict_proba(raw_prediction) + assert proba.shape == (n_samples, loss.n_classes) + assert np.sum(proba, axis=1) == approx(1, rel=1e-11) + + if hasattr(loss, "gradient_proba"): + for grad, proba in ( + (None, None), + (None, np.empty_like(raw_prediction)), + (np.empty_like(raw_prediction), None), + (np.empty_like(raw_prediction), np.empty_like(raw_prediction)), + ): + grad, proba = loss.gradient_proba( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=None, + gradient_out=grad, + proba_out=proba, + ) + assert proba.shape == (n_samples, loss.n_classes) + assert np.sum(proba, axis=1) == approx(1, rel=1e-11) + assert_allclose( + grad, + loss.gradient( + y_true=y_true, + raw_prediction=raw_prediction, + sample_weight=None, + gradient_out=None, + ), + ) + + +@pytest.mark.parametrize("loss", ALL_LOSSES) +@pytest.mark.parametrize("sample_weight", [None, "range"]) +@pytest.mark.parametrize("dtype", (np.float32, np.float64)) +@pytest.mark.parametrize("order", ("C", "F")) +def test_init_gradient_and_hessians(loss, sample_weight, dtype, order): + """Test that init_gradient_and_hessian works as expected. + + passing sample_weight to a loss correctly influences the constant_hessian + attribute, and consequently the shape of the hessian array. + """ + n_samples = 5 + if sample_weight == "range": + sample_weight = np.ones(n_samples) + loss = loss(sample_weight=sample_weight) + gradient, hessian = loss.init_gradient_and_hessian( + n_samples=n_samples, + dtype=dtype, + order=order, + ) + if loss.constant_hessian: + assert gradient.shape == (n_samples,) + assert hessian.shape == (1,) + elif loss.is_multiclass: + assert gradient.shape == (n_samples, loss.n_classes) + assert hessian.shape == (n_samples, loss.n_classes) + else: + assert hessian.shape == (n_samples,) + assert hessian.shape == (n_samples,) + + assert gradient.dtype == dtype + assert hessian.dtype == dtype + + if order == "C": + assert gradient.flags.c_contiguous + assert hessian.flags.c_contiguous + else: + assert gradient.flags.f_contiguous + assert hessian.flags.f_contiguous + + +@pytest.mark.parametrize("loss", ALL_LOSSES) +@pytest.mark.parametrize( + "params, err_msg", + [ + ( + {"dtype": np.int64}, + f"Valid options for 'dtype' are .* Got dtype={np.int64} instead.", + ), + ], +) +def test_init_gradient_and_hessian_raises(loss, params, err_msg): + """Test that init_gradient_and_hessian raises errors for invalid input.""" + loss = loss() + with pytest.raises((ValueError, TypeError), match=err_msg): + gradient, hessian = loss.init_gradient_and_hessian(n_samples=5, **params) + + +@pytest.mark.parametrize( + "loss, params, err_type, err_msg", + [ + ( + PinballLoss, + {"quantile": None}, + TypeError, + "quantile must be an instance of float, not NoneType.", + ), + ( + PinballLoss, + {"quantile": 0}, + ValueError, + "quantile == 0, must be > 0.", + ), + (PinballLoss, {"quantile": 1.1}, ValueError, "quantile == 1.1, must be < 1."), + ( + HuberLoss, + {"quantile": None}, + TypeError, + "quantile must be an instance of float, not NoneType.", + ), + ( + HuberLoss, + {"quantile": 0}, + ValueError, + "quantile == 0, must be > 0.", + ), + (HuberLoss, {"quantile": 1.1}, ValueError, "quantile == 1.1, must be < 1."), + ], +) +def test_loss_init_parameter_validation(loss, params, err_type, err_msg): + """Test that loss raises errors for invalid input.""" + with pytest.raises(err_type, match=err_msg): + loss(**params) + + +@pytest.mark.parametrize("loss", LOSS_INSTANCES, ids=loss_instance_name) +def test_loss_pickle(loss): + """Test that losses can be pickled.""" + n_samples = 20 + y_true, raw_prediction = random_y_true_raw_prediction( + loss=loss, + n_samples=n_samples, + y_bound=(-100, 100), + raw_bound=(-5, 5), + seed=42, + ) + pickled_loss = pickle.dumps(loss) + unpickled_loss = pickle.loads(pickled_loss) + assert loss(y_true=y_true, raw_prediction=raw_prediction) == approx( + unpickled_loss(y_true=y_true, raw_prediction=raw_prediction) + ) + + +@pytest.mark.parametrize("p", [-1.5, 0, 1, 1.5, 2, 3]) +def test_tweedie_log_identity_consistency(p): + """Test for identical losses when only the link function is different.""" + half_tweedie_log = HalfTweedieLoss(power=p) + half_tweedie_identity = HalfTweedieLossIdentity(power=p) + n_samples = 10 + y_true, raw_prediction = random_y_true_raw_prediction( + loss=half_tweedie_log, n_samples=n_samples, seed=42 + ) + y_pred = half_tweedie_log.link.inverse(raw_prediction) # exp(raw_prediction) + + # Let's compare the loss values, up to some constant term that is dropped + # in HalfTweedieLoss but not in HalfTweedieLossIdentity. + loss_log = half_tweedie_log.loss( + y_true=y_true, raw_prediction=raw_prediction + ) + half_tweedie_log.constant_to_optimal_zero(y_true) + loss_identity = half_tweedie_identity.loss( + y_true=y_true, raw_prediction=y_pred + ) + half_tweedie_identity.constant_to_optimal_zero(y_true) + # Note that HalfTweedieLoss ignores different constant terms than + # HalfTweedieLossIdentity. Constant terms means terms not depending on + # raw_prediction. By adding these terms, `constant_to_optimal_zero`, both losses + # give the same values. + assert_allclose(loss_log, loss_identity) + + # For gradients and hessians, the constant terms do not matter. We have, however, + # to account for the chain rule, i.e. with x=raw_prediction + # gradient_log(x) = d/dx loss_log(x) + # = d/dx loss_identity(exp(x)) + # = exp(x) * gradient_identity(exp(x)) + # Similarly, + # hessian_log(x) = exp(x) * gradient_identity(exp(x)) + # + exp(x)**2 * hessian_identity(x) + gradient_log, hessian_log = half_tweedie_log.gradient_hessian( + y_true=y_true, raw_prediction=raw_prediction + ) + gradient_identity, hessian_identity = half_tweedie_identity.gradient_hessian( + y_true=y_true, raw_prediction=y_pred + ) + assert_allclose(gradient_log, y_pred * gradient_identity) + assert_allclose( + hessian_log, y_pred * gradient_identity + y_pred**2 * hessian_identity + ) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_min_dependencies.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_min_dependencies.py new file mode 100644 index 0000000000000000000000000000000000000000..ac588206869144b4839496f694fd94744967f26a --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/_min_dependencies.py @@ -0,0 +1,74 @@ +"""All minimum dependencies for scikit-learn.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import argparse +from collections import defaultdict + +# scipy and cython should by in sync with pyproject.toml +NUMPY_MIN_VERSION = "1.22.0" +SCIPY_MIN_VERSION = "1.8.0" +JOBLIB_MIN_VERSION = "1.2.0" +THREADPOOLCTL_MIN_VERSION = "3.1.0" +PYTEST_MIN_VERSION = "7.1.2" +CYTHON_MIN_VERSION = "3.0.10" + + +# 'build' and 'install' is included to have structured metadata for CI. +# It will NOT be included in setup's extras_require +# The values are (version_spec, comma separated tags) +dependent_packages = { + "numpy": (NUMPY_MIN_VERSION, "build, install"), + "scipy": (SCIPY_MIN_VERSION, "build, install"), + "joblib": (JOBLIB_MIN_VERSION, "install"), + "threadpoolctl": (THREADPOOLCTL_MIN_VERSION, "install"), + "cython": (CYTHON_MIN_VERSION, "build"), + "meson-python": ("0.17.1", "build"), + "matplotlib": ("3.5.0", "benchmark, docs, examples, tests"), + "scikit-image": ("0.19.0", "docs, examples, tests"), + "pandas": ("1.4.0", "benchmark, docs, examples, tests"), + "seaborn": ("0.9.0", "docs, examples"), + "memory_profiler": ("0.57.0", "benchmark, docs"), + "pytest": (PYTEST_MIN_VERSION, "tests"), + "pytest-cov": ("2.9.0", "tests"), + "ruff": ("0.11.7", "tests"), + "mypy": ("1.15", "tests"), + "pyamg": ("4.2.1", "tests"), + "polars": ("0.20.30", "docs, tests"), + "pyarrow": ("12.0.0", "tests"), + "sphinx": ("7.3.7", "docs"), + "sphinx-copybutton": ("0.5.2", "docs"), + "sphinx-gallery": ("0.17.1", "docs"), + "numpydoc": ("1.2.0", "docs, tests"), + "Pillow": ("8.4.0", "docs"), + "pooch": ("1.6.0", "docs, examples, tests"), + "sphinx-prompt": ("1.4.0", "docs"), + "sphinxext-opengraph": ("0.9.1", "docs"), + "plotly": ("5.14.0", "docs, examples"), + "sphinxcontrib-sass": ("0.3.4", "docs"), + "sphinx-remove-toctrees": ("1.0.0.post1", "docs"), + "sphinx-design": ("0.6.0", "docs"), + "pydata-sphinx-theme": ("0.15.3", "docs"), + "towncrier": ("24.8.0", "docs"), + # XXX: Pin conda-lock to the latest released version (needs manual update + # from time to time) + "conda-lock": ("3.0.1", "maintenance"), +} + + +# create inverse mapping for setuptools +tag_to_packages: dict = defaultdict(list) +for package, (min_version, extras) in dependent_packages.items(): + for extra in extras.split(", "): + tag_to_packages[extra].append("{}>={}".format(package, min_version)) + + +# Used by CI to get the min dependencies +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Get min dependencies for a package") + + parser.add_argument("package", choices=dependent_packages) + args = parser.parse_args() + min_version = dependent_packages[args.package][0] + print(min_version) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/base.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/base.py new file mode 100644 index 0000000000000000000000000000000000000000..e9308d8f1376f53bf8144acc918cac71d7f58bae --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/base.py @@ -0,0 +1,1369 @@ +"""Base classes for all estimators and various utility functions.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import copy +import functools +import inspect +import platform +import re +import warnings +from collections import defaultdict + +import numpy as np + +from . import __version__ +from ._config import config_context, get_config +from .exceptions import InconsistentVersionWarning +from .utils._metadata_requests import _MetadataRequester, _routing_enabled +from .utils._missing import is_scalar_nan +from .utils._param_validation import validate_parameter_constraints +from .utils._repr_html.base import ReprHTMLMixin, _HTMLDocumentationLinkMixin +from .utils._repr_html.estimator import estimator_html_repr +from .utils._repr_html.params import ParamsDict +from .utils._set_output import _SetOutputMixin +from .utils._tags import ( + ClassifierTags, + RegressorTags, + Tags, + TargetTags, + TransformerTags, + get_tags, +) +from .utils.fixes import _IS_32BIT +from .utils.validation import ( + _check_feature_names_in, + _generate_get_feature_names_out, + _is_fitted, + check_array, + check_is_fitted, +) + + +def clone(estimator, *, safe=True): + """Construct a new unfitted estimator with the same parameters. + + Clone does a deep copy of the model in an estimator + without actually copying attached data. It returns a new estimator + with the same parameters that has not been fitted on any data. + + .. versionchanged:: 1.3 + Delegates to `estimator.__sklearn_clone__` if the method exists. + + Parameters + ---------- + estimator : {list, tuple, set} of estimator instance or a single \ + estimator instance + The estimator or group of estimators to be cloned. + safe : bool, default=True + If safe is False, clone will fall back to a deep copy on objects + that are not estimators. Ignored if `estimator.__sklearn_clone__` + exists. + + Returns + ------- + estimator : object + The deep copy of the input, an estimator if input is an estimator. + + Notes + ----- + If the estimator's `random_state` parameter is an integer (or if the + estimator doesn't have a `random_state` parameter), an *exact clone* is + returned: the clone and the original estimator will give the exact same + results. Otherwise, *statistical clone* is returned: the clone might + return different results from the original estimator. More details can be + found in :ref:`randomness`. + + Examples + -------- + >>> from sklearn.base import clone + >>> from sklearn.linear_model import LogisticRegression + >>> X = [[-1, 0], [0, 1], [0, -1], [1, 0]] + >>> y = [0, 0, 1, 1] + >>> classifier = LogisticRegression().fit(X, y) + >>> cloned_classifier = clone(classifier) + >>> hasattr(classifier, "classes_") + True + >>> hasattr(cloned_classifier, "classes_") + False + >>> classifier is cloned_classifier + False + """ + if hasattr(estimator, "__sklearn_clone__") and not inspect.isclass(estimator): + return estimator.__sklearn_clone__() + return _clone_parametrized(estimator, safe=safe) + + +def _clone_parametrized(estimator, *, safe=True): + """Default implementation of clone. See :func:`sklearn.base.clone` for details.""" + + estimator_type = type(estimator) + if estimator_type is dict: + return {k: clone(v, safe=safe) for k, v in estimator.items()} + elif estimator_type in (list, tuple, set, frozenset): + return estimator_type([clone(e, safe=safe) for e in estimator]) + elif not hasattr(estimator, "get_params") or isinstance(estimator, type): + if not safe: + return copy.deepcopy(estimator) + else: + if isinstance(estimator, type): + raise TypeError( + "Cannot clone object. " + "You should provide an instance of " + "scikit-learn estimator instead of a class." + ) + else: + raise TypeError( + "Cannot clone object '%s' (type %s): " + "it does not seem to be a scikit-learn " + "estimator as it does not implement a " + "'get_params' method." % (repr(estimator), type(estimator)) + ) + + klass = estimator.__class__ + new_object_params = estimator.get_params(deep=False) + for name, param in new_object_params.items(): + new_object_params[name] = clone(param, safe=False) + + new_object = klass(**new_object_params) + try: + new_object._metadata_request = copy.deepcopy(estimator._metadata_request) + except AttributeError: + pass + + params_set = new_object.get_params(deep=False) + + # quick sanity check of the parameters of the clone + for name in new_object_params: + param1 = new_object_params[name] + param2 = params_set[name] + if param1 is not param2: + raise RuntimeError( + "Cannot clone object %s, as the constructor " + "either does not set or modifies parameter %s" % (estimator, name) + ) + + # _sklearn_output_config is used by `set_output` to configure the output + # container of an estimator. + if hasattr(estimator, "_sklearn_output_config"): + new_object._sklearn_output_config = copy.deepcopy( + estimator._sklearn_output_config + ) + return new_object + + +class BaseEstimator(ReprHTMLMixin, _HTMLDocumentationLinkMixin, _MetadataRequester): + """Base class for all estimators in scikit-learn. + + Inheriting from this class provides default implementations of: + + - setting and getting parameters used by `GridSearchCV` and friends; + - textual and HTML representation displayed in terminals and IDEs; + - estimator serialization; + - parameters validation; + - data validation; + - feature names validation. + + Read more in the :ref:`User Guide `. + + + Notes + ----- + All estimators should specify all the parameters that can be set + at the class level in their ``__init__`` as explicit keyword + arguments (no ``*args`` or ``**kwargs``). + + Examples + -------- + >>> import numpy as np + >>> from sklearn.base import BaseEstimator + >>> class MyEstimator(BaseEstimator): + ... def __init__(self, *, param=1): + ... self.param = param + ... def fit(self, X, y=None): + ... self.is_fitted_ = True + ... return self + ... def predict(self, X): + ... return np.full(shape=X.shape[0], fill_value=self.param) + >>> estimator = MyEstimator(param=2) + >>> estimator.get_params() + {'param': 2} + >>> X = np.array([[1, 2], [2, 3], [3, 4]]) + >>> y = np.array([1, 0, 1]) + >>> estimator.fit(X, y).predict(X) + array([2, 2, 2]) + >>> estimator.set_params(param=3).fit(X, y).predict(X) + array([3, 3, 3]) + """ + + _html_repr = estimator_html_repr + + @classmethod + def _get_param_names(cls): + """Get parameter names for the estimator""" + # fetch the constructor or the original constructor before + # deprecation wrapping if any + init = getattr(cls.__init__, "deprecated_original", cls.__init__) + if init is object.__init__: + # No explicit constructor to introspect + return [] + + # introspect the constructor arguments to find the model parameters + # to represent + init_signature = inspect.signature(init) + # Consider the constructor parameters excluding 'self' + parameters = [ + p + for p in init_signature.parameters.values() + if p.name != "self" and p.kind != p.VAR_KEYWORD + ] + for p in parameters: + if p.kind == p.VAR_POSITIONAL: + raise RuntimeError( + "scikit-learn estimators should always " + "specify their parameters in the signature" + " of their __init__ (no varargs)." + " %s with constructor %s doesn't " + " follow this convention." % (cls, init_signature) + ) + # Extract and sort argument names excluding 'self' + return sorted([p.name for p in parameters]) + + def get_params(self, deep=True): + """ + Get parameters for this estimator. + + Parameters + ---------- + deep : bool, default=True + If True, will return the parameters for this estimator and + contained subobjects that are estimators. + + Returns + ------- + params : dict + Parameter names mapped to their values. + """ + out = dict() + for key in self._get_param_names(): + value = getattr(self, key) + if deep and hasattr(value, "get_params") and not isinstance(value, type): + deep_items = value.get_params().items() + out.update((key + "__" + k, val) for k, val in deep_items) + out[key] = value + return out + + def _get_params_html(self, deep=True): + """ + Get parameters for this estimator with a specific HTML representation. + + Parameters + ---------- + deep : bool, default=True + If True, will return the parameters for this estimator and + contained subobjects that are estimators. + + Returns + ------- + params : ParamsDict + Parameter names mapped to their values. We return a `ParamsDict` + dictionary, which renders a specific HTML representation in table + form. + """ + out = self.get_params(deep=deep) + + init_func = getattr(self.__init__, "deprecated_original", self.__init__) + init_default_params = inspect.signature(init_func).parameters + init_default_params = { + name: param.default for name, param in init_default_params.items() + } + + def is_non_default(param_name, param_value): + """Finds the parameters that have been set by the user.""" + if param_name not in init_default_params: + # happens if k is part of a **kwargs + return True + if init_default_params[param_name] == inspect._empty: + # k has no default value + return True + # avoid calling repr on nested estimators + if isinstance(param_value, BaseEstimator) and type(param_value) is not type( + init_default_params[param_name] + ): + return True + if not np.array_equal( + param_value, init_default_params[param_name] + ) and not ( + is_scalar_nan(init_default_params[param_name]) + and is_scalar_nan(param_value) + ): + return True + + return False + + # reorder the parameters from `self.get_params` using the `__init__` + # signature + remaining_params = [name for name in out if name not in init_default_params] + ordered_out = {name: out[name] for name in init_default_params if name in out} + ordered_out.update({name: out[name] for name in remaining_params}) + + non_default_ls = tuple( + [name for name, value in ordered_out.items() if is_non_default(name, value)] + ) + + return ParamsDict(ordered_out, non_default=non_default_ls) + + def set_params(self, **params): + """Set the parameters of this estimator. + + The method works on simple estimators as well as on nested objects + (such as :class:`~sklearn.pipeline.Pipeline`). The latter have + parameters of the form ``__`` so that it's + possible to update each component of a nested object. + + Parameters + ---------- + **params : dict + Estimator parameters. + + Returns + ------- + self : estimator instance + Estimator instance. + """ + if not params: + # Simple optimization to gain speed (inspect is slow) + return self + valid_params = self.get_params(deep=True) + + nested_params = defaultdict(dict) # grouped by prefix + for key, value in params.items(): + key, delim, sub_key = key.partition("__") + if key not in valid_params: + local_valid_params = self._get_param_names() + raise ValueError( + f"Invalid parameter {key!r} for estimator {self}. " + f"Valid parameters are: {local_valid_params!r}." + ) + + if delim: + nested_params[key][sub_key] = value + else: + setattr(self, key, value) + valid_params[key] = value + + for key, sub_params in nested_params.items(): + valid_params[key].set_params(**sub_params) + + return self + + def __sklearn_clone__(self): + return _clone_parametrized(self) + + def __repr__(self, N_CHAR_MAX=700): + # N_CHAR_MAX is the (approximate) maximum number of non-blank + # characters to render. We pass it as an optional parameter to ease + # the tests. + + from .utils._pprint import _EstimatorPrettyPrinter + + N_MAX_ELEMENTS_TO_SHOW = 30 # number of elements to show in sequences + + # use ellipsis for sequences with a lot of elements + pp = _EstimatorPrettyPrinter( + compact=True, + indent=1, + indent_at_name=True, + n_max_elements_to_show=N_MAX_ELEMENTS_TO_SHOW, + ) + + repr_ = pp.pformat(self) + + # Use bruteforce ellipsis when there are a lot of non-blank characters + n_nonblank = len("".join(repr_.split())) + if n_nonblank > N_CHAR_MAX: + lim = N_CHAR_MAX // 2 # apprx number of chars to keep on both ends + regex = r"^(\s*\S){%d}" % lim + # The regex '^(\s*\S){%d}' % n + # matches from the start of the string until the nth non-blank + # character: + # - ^ matches the start of string + # - (pattern){n} matches n repetitions of pattern + # - \s*\S matches a non-blank char following zero or more blanks + left_lim = re.match(regex, repr_).end() + right_lim = re.match(regex, repr_[::-1]).end() + + if "\n" in repr_[left_lim:-right_lim]: + # The left side and right side aren't on the same line. + # To avoid weird cuts, e.g.: + # categoric...ore', + # we need to start the right side with an appropriate newline + # character so that it renders properly as: + # categoric... + # handle_unknown='ignore', + # so we add [^\n]*\n which matches until the next \n + regex += r"[^\n]*\n" + right_lim = re.match(regex, repr_[::-1]).end() + + ellipsis = "..." + if left_lim + len(ellipsis) < len(repr_) - right_lim: + # Only add ellipsis if it results in a shorter repr + repr_ = repr_[:left_lim] + "..." + repr_[-right_lim:] + + return repr_ + + def __getstate__(self): + if getattr(self, "__slots__", None): + raise TypeError( + "You cannot use `__slots__` in objects inheriting from " + "`sklearn.base.BaseEstimator`." + ) + + try: + state = super().__getstate__() + if state is None: + # For Python 3.11+, empty instance (no `__slots__`, + # and `__dict__`) will return a state equal to `None`. + state = self.__dict__.copy() + except AttributeError: + # Python < 3.11 + state = self.__dict__.copy() + + if type(self).__module__.startswith("sklearn."): + return dict(state.items(), _sklearn_version=__version__) + else: + return state + + def __setstate__(self, state): + if type(self).__module__.startswith("sklearn."): + pickle_version = state.pop("_sklearn_version", "pre-0.18") + if pickle_version != __version__: + warnings.warn( + InconsistentVersionWarning( + estimator_name=self.__class__.__name__, + current_sklearn_version=__version__, + original_sklearn_version=pickle_version, + ), + ) + try: + super().__setstate__(state) + except AttributeError: + self.__dict__.update(state) + + def __sklearn_tags__(self): + return Tags( + estimator_type=None, + target_tags=TargetTags(required=False), + transformer_tags=None, + regressor_tags=None, + classifier_tags=None, + ) + + def _validate_params(self): + """Validate types and values of constructor parameters + + The expected type and values must be defined in the `_parameter_constraints` + class attribute, which is a dictionary `param_name: list of constraints`. See + the docstring of `validate_parameter_constraints` for a description of the + accepted constraints. + """ + validate_parameter_constraints( + self._parameter_constraints, + self.get_params(deep=False), + caller_name=self.__class__.__name__, + ) + + +class ClassifierMixin: + """Mixin class for all classifiers in scikit-learn. + + This mixin defines the following functionality: + + - set estimator type to `"classifier"` through the `estimator_type` tag; + - `score` method that default to :func:`~sklearn.metrics.accuracy_score`. + - enforce that `fit` requires `y` to be passed through the `requires_y` tag, + which is done by setting the classifier type tag. + + Read more in the :ref:`User Guide `. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.base import BaseEstimator, ClassifierMixin + >>> # Mixin classes should always be on the left-hand side for a correct MRO + >>> class MyEstimator(ClassifierMixin, BaseEstimator): + ... def __init__(self, *, param=1): + ... self.param = param + ... def fit(self, X, y=None): + ... self.is_fitted_ = True + ... return self + ... def predict(self, X): + ... return np.full(shape=X.shape[0], fill_value=self.param) + >>> estimator = MyEstimator(param=1) + >>> X = np.array([[1, 2], [2, 3], [3, 4]]) + >>> y = np.array([1, 0, 1]) + >>> estimator.fit(X, y).predict(X) + array([1, 1, 1]) + >>> estimator.score(X, y) + 0.66... + """ + + # TODO(1.8): Remove this attribute + _estimator_type = "classifier" + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.estimator_type = "classifier" + tags.classifier_tags = ClassifierTags() + tags.target_tags.required = True + return tags + + def score(self, X, y, sample_weight=None): + """ + Return :ref:`accuracy ` on provided data and labels. + + In multi-label classification, this is the subset accuracy + which is a harsh metric since you require for each sample that + each label set be correctly predicted. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Test samples. + + y : array-like of shape (n_samples,) or (n_samples, n_outputs) + True labels for `X`. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. + + Returns + ------- + score : float + Mean accuracy of ``self.predict(X)`` w.r.t. `y`. + """ + from .metrics import accuracy_score + + return accuracy_score(y, self.predict(X), sample_weight=sample_weight) + + +class RegressorMixin: + """Mixin class for all regression estimators in scikit-learn. + + This mixin defines the following functionality: + + - set estimator type to `"regressor"` through the `estimator_type` tag; + - `score` method that default to :func:`~sklearn.metrics.r2_score`. + - enforce that `fit` requires `y` to be passed through the `requires_y` tag, + which is done by setting the regressor type tag. + + Read more in the :ref:`User Guide `. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.base import BaseEstimator, RegressorMixin + >>> # Mixin classes should always be on the left-hand side for a correct MRO + >>> class MyEstimator(RegressorMixin, BaseEstimator): + ... def __init__(self, *, param=1): + ... self.param = param + ... def fit(self, X, y=None): + ... self.is_fitted_ = True + ... return self + ... def predict(self, X): + ... return np.full(shape=X.shape[0], fill_value=self.param) + >>> estimator = MyEstimator(param=0) + >>> X = np.array([[1, 2], [2, 3], [3, 4]]) + >>> y = np.array([-1, 0, 1]) + >>> estimator.fit(X, y).predict(X) + array([0, 0, 0]) + >>> estimator.score(X, y) + 0.0 + """ + + # TODO(1.8): Remove this attribute + _estimator_type = "regressor" + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.estimator_type = "regressor" + tags.regressor_tags = RegressorTags() + tags.target_tags.required = True + return tags + + def score(self, X, y, sample_weight=None): + """Return :ref:`coefficient of determination ` on test data. + + The coefficient of determination, :math:`R^2`, is defined as + :math:`(1 - \\frac{u}{v})`, where :math:`u` is the residual + sum of squares ``((y_true - y_pred)** 2).sum()`` and :math:`v` + is the total sum of squares ``((y_true - y_true.mean()) ** 2).sum()``. + The best possible score is 1.0 and it can be negative (because the + model can be arbitrarily worse). A constant model that always predicts + the expected value of `y`, disregarding the input features, would get + a :math:`R^2` score of 0.0. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Test samples. For some estimators this may be a precomputed + kernel matrix or a list of generic objects instead with shape + ``(n_samples, n_samples_fitted)``, where ``n_samples_fitted`` + is the number of samples used in the fitting for the estimator. + + y : array-like of shape (n_samples,) or (n_samples, n_outputs) + True values for `X`. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. + + Returns + ------- + score : float + :math:`R^2` of ``self.predict(X)`` w.r.t. `y`. + + Notes + ----- + The :math:`R^2` score used when calling ``score`` on a regressor uses + ``multioutput='uniform_average'`` from version 0.23 to keep consistent + with default value of :func:`~sklearn.metrics.r2_score`. + This influences the ``score`` method of all the multioutput + regressors (except for + :class:`~sklearn.multioutput.MultiOutputRegressor`). + """ + + from .metrics import r2_score + + y_pred = self.predict(X) + return r2_score(y, y_pred, sample_weight=sample_weight) + + +class ClusterMixin: + """Mixin class for all cluster estimators in scikit-learn. + + - set estimator type to `"clusterer"` through the `estimator_type` tag; + - `fit_predict` method returning the cluster labels associated to each sample. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.base import BaseEstimator, ClusterMixin + >>> class MyClusterer(ClusterMixin, BaseEstimator): + ... def fit(self, X, y=None): + ... self.labels_ = np.ones(shape=(len(X),), dtype=np.int64) + ... return self + >>> X = [[1, 2], [2, 3], [3, 4]] + >>> MyClusterer().fit_predict(X) + array([1, 1, 1]) + """ + + # TODO(1.8): Remove this attribute + _estimator_type = "clusterer" + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.estimator_type = "clusterer" + if tags.transformer_tags is not None: + tags.transformer_tags.preserves_dtype = [] + return tags + + def fit_predict(self, X, y=None, **kwargs): + """ + Perform clustering on `X` and returns cluster labels. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Input data. + + y : Ignored + Not used, present for API consistency by convention. + + **kwargs : dict + Arguments to be passed to ``fit``. + + .. versionadded:: 1.4 + + Returns + ------- + labels : ndarray of shape (n_samples,), dtype=np.int64 + Cluster labels. + """ + # non-optimized default implementation; override when a better + # method is possible for a given clustering algorithm + self.fit(X, **kwargs) + return self.labels_ + + +class BiclusterMixin: + """Mixin class for all bicluster estimators in scikit-learn. + + This mixin defines the following functionality: + + - `biclusters_` property that returns the row and column indicators; + - `get_indices` method that returns the row and column indices of a bicluster; + - `get_shape` method that returns the shape of a bicluster; + - `get_submatrix` method that returns the submatrix corresponding to a bicluster. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.base import BaseEstimator, BiclusterMixin + >>> class DummyBiClustering(BiclusterMixin, BaseEstimator): + ... def fit(self, X, y=None): + ... self.rows_ = np.ones(shape=(1, X.shape[0]), dtype=bool) + ... self.columns_ = np.ones(shape=(1, X.shape[1]), dtype=bool) + ... return self + >>> X = np.array([[1, 1], [2, 1], [1, 0], + ... [4, 7], [3, 5], [3, 6]]) + >>> bicluster = DummyBiClustering().fit(X) + >>> hasattr(bicluster, "biclusters_") + True + >>> bicluster.get_indices(0) + (array([0, 1, 2, 3, 4, 5]), array([0, 1])) + """ + + @property + def biclusters_(self): + """Convenient way to get row and column indicators together. + + Returns the ``rows_`` and ``columns_`` members. + """ + return self.rows_, self.columns_ + + def get_indices(self, i): + """Row and column indices of the `i`'th bicluster. + + Only works if ``rows_`` and ``columns_`` attributes exist. + + Parameters + ---------- + i : int + The index of the cluster. + + Returns + ------- + row_ind : ndarray, dtype=np.intp + Indices of rows in the dataset that belong to the bicluster. + col_ind : ndarray, dtype=np.intp + Indices of columns in the dataset that belong to the bicluster. + """ + rows = self.rows_[i] + columns = self.columns_[i] + return np.nonzero(rows)[0], np.nonzero(columns)[0] + + def get_shape(self, i): + """Shape of the `i`'th bicluster. + + Parameters + ---------- + i : int + The index of the cluster. + + Returns + ------- + n_rows : int + Number of rows in the bicluster. + + n_cols : int + Number of columns in the bicluster. + """ + indices = self.get_indices(i) + return tuple(len(i) for i in indices) + + def get_submatrix(self, i, data): + """Return the submatrix corresponding to bicluster `i`. + + Parameters + ---------- + i : int + The index of the cluster. + data : array-like of shape (n_samples, n_features) + The data. + + Returns + ------- + submatrix : ndarray of shape (n_rows, n_cols) + The submatrix corresponding to bicluster `i`. + + Notes + ----- + Works with sparse matrices. Only works if ``rows_`` and + ``columns_`` attributes exist. + """ + + data = check_array(data, accept_sparse="csr") + row_ind, col_ind = self.get_indices(i) + return data[row_ind[:, np.newaxis], col_ind] + + +class TransformerMixin(_SetOutputMixin): + """Mixin class for all transformers in scikit-learn. + + This mixin defines the following functionality: + + - a `fit_transform` method that delegates to `fit` and `transform`; + - a `set_output` method to output `X` as a specific container type. + + If :term:`get_feature_names_out` is defined, then :class:`BaseEstimator` will + automatically wrap `transform` and `fit_transform` to follow the `set_output` + API. See the :ref:`developer_api_set_output` for details. + + :class:`OneToOneFeatureMixin` and + :class:`ClassNamePrefixFeaturesOutMixin` are helpful mixins for + defining :term:`get_feature_names_out`. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.base import BaseEstimator, TransformerMixin + >>> class MyTransformer(TransformerMixin, BaseEstimator): + ... def __init__(self, *, param=1): + ... self.param = param + ... def fit(self, X, y=None): + ... return self + ... def transform(self, X): + ... return np.full(shape=len(X), fill_value=self.param) + >>> transformer = MyTransformer() + >>> X = [[1, 2], [2, 3], [3, 4]] + >>> transformer.fit_transform(X) + array([1, 1, 1]) + """ + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.transformer_tags = TransformerTags() + return tags + + def fit_transform(self, X, y=None, **fit_params): + """ + Fit to data, then transform it. + + Fits transformer to `X` and `y` with optional parameters `fit_params` + and returns a transformed version of `X`. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Input samples. + + y : array-like of shape (n_samples,) or (n_samples, n_outputs), \ + default=None + Target values (None for unsupervised transformations). + + **fit_params : dict + Additional fit parameters. + + Returns + ------- + X_new : ndarray array of shape (n_samples, n_features_new) + Transformed array. + """ + # non-optimized default implementation; override when a better + # method is possible for a given clustering algorithm + + # we do not route parameters here, since consumers don't route. But + # since it's possible for a `transform` method to also consume + # metadata, we check if that's the case, and we raise a warning telling + # users that they should implement a custom `fit_transform` method + # to forward metadata to `transform` as well. + # + # For that, we calculate routing and check if anything would be routed + # to `transform` if we were to route them. + if _routing_enabled(): + transform_params = self.get_metadata_routing().consumes( + method="transform", params=fit_params.keys() + ) + if transform_params: + warnings.warn( + ( + f"This object ({self.__class__.__name__}) has a `transform`" + " method which consumes metadata, but `fit_transform` does not" + " forward metadata to `transform`. Please implement a custom" + " `fit_transform` method to forward metadata to `transform` as" + " well. Alternatively, you can explicitly do" + " `set_transform_request`and set all values to `False` to" + " disable metadata routed to `transform`, if that's an option." + ), + UserWarning, + ) + + if y is None: + # fit method of arity 1 (unsupervised transformation) + return self.fit(X, **fit_params).transform(X) + else: + # fit method of arity 2 (supervised transformation) + return self.fit(X, y, **fit_params).transform(X) + + +class OneToOneFeatureMixin: + """Provides `get_feature_names_out` for simple transformers. + + This mixin assumes there's a 1-to-1 correspondence between input features + and output features, such as :class:`~sklearn.preprocessing.StandardScaler`. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.base import OneToOneFeatureMixin, BaseEstimator + >>> class MyEstimator(OneToOneFeatureMixin, BaseEstimator): + ... def fit(self, X, y=None): + ... self.n_features_in_ = X.shape[1] + ... return self + >>> X = np.array([[1, 2], [3, 4]]) + >>> MyEstimator().fit(X).get_feature_names_out() + array(['x0', 'x1'], dtype=object) + """ + + def get_feature_names_out(self, input_features=None): + """Get output feature names for transformation. + + Parameters + ---------- + input_features : array-like of str or None, default=None + Input features. + + - If `input_features` is `None`, then `feature_names_in_` is + used as feature names in. If `feature_names_in_` is not defined, + then the following input feature names are generated: + `["x0", "x1", ..., "x(n_features_in_ - 1)"]`. + - If `input_features` is an array-like, then `input_features` must + match `feature_names_in_` if `feature_names_in_` is defined. + + Returns + ------- + feature_names_out : ndarray of str objects + Same as input features. + """ + # Note that passing attributes="n_features_in_" forces check_is_fitted + # to check if the attribute is present. Otherwise it will pass on + # stateless estimators (requires_fit=False) + check_is_fitted(self, attributes="n_features_in_") + return _check_feature_names_in(self, input_features) + + +class ClassNamePrefixFeaturesOutMixin: + """Mixin class for transformers that generate their own names by prefixing. + + This mixin is useful when the transformer needs to generate its own feature + names out, such as :class:`~sklearn.decomposition.PCA`. For example, if + :class:`~sklearn.decomposition.PCA` outputs 3 features, then the generated feature + names out are: `["pca0", "pca1", "pca2"]`. + + This mixin assumes that a `_n_features_out` attribute is defined when the + transformer is fitted. `_n_features_out` is the number of output features + that the transformer will return in `transform` of `fit_transform`. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.base import ClassNamePrefixFeaturesOutMixin, BaseEstimator + >>> class MyEstimator(ClassNamePrefixFeaturesOutMixin, BaseEstimator): + ... def fit(self, X, y=None): + ... self._n_features_out = X.shape[1] + ... return self + >>> X = np.array([[1, 2], [3, 4]]) + >>> MyEstimator().fit(X).get_feature_names_out() + array(['myestimator0', 'myestimator1'], dtype=object) + """ + + def get_feature_names_out(self, input_features=None): + """Get output feature names for transformation. + + The feature names out will prefixed by the lowercased class name. For + example, if the transformer outputs 3 features, then the feature names + out are: `["class_name0", "class_name1", "class_name2"]`. + + Parameters + ---------- + input_features : array-like of str or None, default=None + Only used to validate feature names with the names seen in `fit`. + + Returns + ------- + feature_names_out : ndarray of str objects + Transformed feature names. + """ + check_is_fitted(self, "_n_features_out") + return _generate_get_feature_names_out( + self, self._n_features_out, input_features=input_features + ) + + +class DensityMixin: + """Mixin class for all density estimators in scikit-learn. + + This mixin defines the following functionality: + + - sets estimator type to `"density_estimator"` through the `estimator_type` tag; + - `score` method that default that do no-op. + + Examples + -------- + >>> from sklearn.base import DensityMixin + >>> class MyEstimator(DensityMixin): + ... def fit(self, X, y=None): + ... self.is_fitted_ = True + ... return self + >>> estimator = MyEstimator() + >>> hasattr(estimator, "score") + True + """ + + # TODO(1.8): Remove this attribute + _estimator_type = "DensityEstimator" + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.estimator_type = "density_estimator" + return tags + + def score(self, X, y=None): + """Return the score of the model on the data `X`. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Test samples. + + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + score : float + """ + pass + + +class OutlierMixin: + """Mixin class for all outlier detection estimators in scikit-learn. + + This mixin defines the following functionality: + + - set estimator type to `"outlier_detector"` through the `estimator_type` tag; + - `fit_predict` method that default to `fit` and `predict`. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.base import BaseEstimator, OutlierMixin + >>> class MyEstimator(OutlierMixin): + ... def fit(self, X, y=None): + ... self.is_fitted_ = True + ... return self + ... def predict(self, X): + ... return np.ones(shape=len(X)) + >>> estimator = MyEstimator() + >>> X = np.array([[1, 2], [2, 3], [3, 4]]) + >>> estimator.fit_predict(X) + array([1., 1., 1.]) + """ + + # TODO(1.8): Remove this attribute + _estimator_type = "outlier_detector" + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.estimator_type = "outlier_detector" + return tags + + def fit_predict(self, X, y=None, **kwargs): + """Perform fit on X and returns labels for X. + + Returns -1 for outliers and 1 for inliers. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input samples. + + y : Ignored + Not used, present for API consistency by convention. + + **kwargs : dict + Arguments to be passed to ``fit``. + + .. versionadded:: 1.4 + + Returns + ------- + y : ndarray of shape (n_samples,) + 1 for inliers, -1 for outliers. + """ + # we do not route parameters here, since consumers don't route. But + # since it's possible for a `predict` method to also consume + # metadata, we check if that's the case, and we raise a warning telling + # users that they should implement a custom `fit_predict` method + # to forward metadata to `predict` as well. + # + # For that, we calculate routing and check if anything would be routed + # to `predict` if we were to route them. + if _routing_enabled(): + transform_params = self.get_metadata_routing().consumes( + method="predict", params=kwargs.keys() + ) + if transform_params: + warnings.warn( + ( + f"This object ({self.__class__.__name__}) has a `predict` " + "method which consumes metadata, but `fit_predict` does not " + "forward metadata to `predict`. Please implement a custom " + "`fit_predict` method to forward metadata to `predict` as well." + "Alternatively, you can explicitly do `set_predict_request`" + "and set all values to `False` to disable metadata routed to " + "`predict`, if that's an option." + ), + UserWarning, + ) + + # override for transductive outlier detectors like LocalOulierFactor + return self.fit(X, **kwargs).predict(X) + + +class MetaEstimatorMixin: + """Mixin class for all meta estimators in scikit-learn. + + This mixin is empty, and only exists to indicate that the estimator is a + meta-estimator. + + .. versionchanged:: 1.6 + The `_required_parameters` is now removed and is unnecessary since tests are + refactored and don't use this anymore. + + Examples + -------- + >>> from sklearn.base import MetaEstimatorMixin + >>> from sklearn.datasets import load_iris + >>> from sklearn.linear_model import LogisticRegression + >>> class MyEstimator(MetaEstimatorMixin): + ... def __init__(self, *, estimator=None): + ... self.estimator = estimator + ... def fit(self, X, y=None): + ... if self.estimator is None: + ... self.estimator_ = LogisticRegression() + ... else: + ... self.estimator_ = self.estimator + ... return self + >>> X, y = load_iris(return_X_y=True) + >>> estimator = MyEstimator().fit(X, y) + >>> estimator.estimator_ + LogisticRegression() + """ + + +class MultiOutputMixin: + """Mixin to mark estimators that support multioutput.""" + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.target_tags.multi_output = True + return tags + + +class _UnstableArchMixin: + """Mark estimators that are non-determinstic on 32bit or PowerPC""" + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.non_deterministic = _IS_32BIT or platform.machine().startswith( + ("ppc", "powerpc") + ) + return tags + + +def is_classifier(estimator): + """Return True if the given estimator is (probably) a classifier. + + Parameters + ---------- + estimator : object + Estimator object to test. + + Returns + ------- + out : bool + True if estimator is a classifier and False otherwise. + + Examples + -------- + >>> from sklearn.base import is_classifier + >>> from sklearn.cluster import KMeans + >>> from sklearn.svm import SVC, SVR + >>> classifier = SVC() + >>> regressor = SVR() + >>> kmeans = KMeans() + >>> is_classifier(classifier) + True + >>> is_classifier(regressor) + False + >>> is_classifier(kmeans) + False + """ + # TODO(1.8): Remove this check + if isinstance(estimator, type): + warnings.warn( + f"passing a class to {print(inspect.stack()[0][3])} is deprecated and " + "will be removed in 1.8. Use an instance of the class instead.", + FutureWarning, + ) + return getattr(estimator, "_estimator_type", None) == "classifier" + + return get_tags(estimator).estimator_type == "classifier" + + +def is_regressor(estimator): + """Return True if the given estimator is (probably) a regressor. + + Parameters + ---------- + estimator : estimator instance + Estimator object to test. + + Returns + ------- + out : bool + True if estimator is a regressor and False otherwise. + + Examples + -------- + >>> from sklearn.base import is_regressor + >>> from sklearn.cluster import KMeans + >>> from sklearn.svm import SVC, SVR + >>> classifier = SVC() + >>> regressor = SVR() + >>> kmeans = KMeans() + >>> is_regressor(classifier) + False + >>> is_regressor(regressor) + True + >>> is_regressor(kmeans) + False + """ + # TODO(1.8): Remove this check + if isinstance(estimator, type): + warnings.warn( + f"passing a class to {print(inspect.stack()[0][3])} is deprecated and " + "will be removed in 1.8. Use an instance of the class instead.", + FutureWarning, + ) + return getattr(estimator, "_estimator_type", None) == "regressor" + + return get_tags(estimator).estimator_type == "regressor" + + +def is_clusterer(estimator): + """Return True if the given estimator is (probably) a clusterer. + + .. versionadded:: 1.6 + + Parameters + ---------- + estimator : object + Estimator object to test. + + Returns + ------- + out : bool + True if estimator is a clusterer and False otherwise. + + Examples + -------- + >>> from sklearn.base import is_clusterer + >>> from sklearn.cluster import KMeans + >>> from sklearn.svm import SVC, SVR + >>> classifier = SVC() + >>> regressor = SVR() + >>> kmeans = KMeans() + >>> is_clusterer(classifier) + False + >>> is_clusterer(regressor) + False + >>> is_clusterer(kmeans) + True + """ + # TODO(1.8): Remove this check + if isinstance(estimator, type): + warnings.warn( + f"passing a class to {print(inspect.stack()[0][3])} is deprecated and " + "will be removed in 1.8. Use an instance of the class instead.", + FutureWarning, + ) + return getattr(estimator, "_estimator_type", None) == "clusterer" + + return get_tags(estimator).estimator_type == "clusterer" + + +def is_outlier_detector(estimator): + """Return True if the given estimator is (probably) an outlier detector. + + Parameters + ---------- + estimator : estimator instance + Estimator object to test. + + Returns + ------- + out : bool + True if estimator is an outlier detector and False otherwise. + """ + # TODO(1.8): Remove this check + if isinstance(estimator, type): + warnings.warn( + f"passing a class to {print(inspect.stack()[0][3])} is deprecated and " + "will be removed in 1.8. Use an instance of the class instead.", + FutureWarning, + ) + return getattr(estimator, "_estimator_type", None) == "outlier_detector" + + return get_tags(estimator).estimator_type == "outlier_detector" + + +def _fit_context(*, prefer_skip_nested_validation): + """Decorator to run the fit methods of estimators within context managers. + + Parameters + ---------- + prefer_skip_nested_validation : bool + If True, the validation of parameters of inner estimators or functions + called during fit will be skipped. + + This is useful to avoid validating many times the parameters passed by the + user from the public facing API. It's also useful to avoid validating + parameters that we pass internally to inner functions that are guaranteed to + be valid by the test suite. + + It should be set to True for most estimators, except for those that receive + non-validated objects as parameters, such as meta-estimators that are given + estimator objects. + + Returns + ------- + decorated_fit : method + The decorated fit method. + """ + + def decorator(fit_method): + @functools.wraps(fit_method) + def wrapper(estimator, *args, **kwargs): + global_skip_validation = get_config()["skip_parameter_validation"] + + # we don't want to validate again for each call to partial_fit + partial_fit_and_fitted = ( + fit_method.__name__ == "partial_fit" and _is_fitted(estimator) + ) + + if not global_skip_validation and not partial_fit_and_fitted: + estimator._validate_params() + + with config_context( + skip_parameter_validation=( + prefer_skip_nested_validation or global_skip_validation + ) + ): + return fit_method(estimator, *args, **kwargs) + + return wrapper + + return decorator diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/calibration.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/calibration.py new file mode 100644 index 0000000000000000000000000000000000000000..5b2bca2edfcc01bdec5ad60906061888d4fd7f8d --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/calibration.py @@ -0,0 +1,1448 @@ +"""Methods for calibrating predicted probabilities.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from inspect import signature +from math import log +from numbers import Integral, Real + +import numpy as np +from scipy.optimize import minimize +from scipy.special import expit + +from sklearn.utils import Bunch + +from ._loss import HalfBinomialLoss +from .base import ( + BaseEstimator, + ClassifierMixin, + MetaEstimatorMixin, + RegressorMixin, + _fit_context, + clone, +) +from .frozen import FrozenEstimator +from .isotonic import IsotonicRegression +from .model_selection import LeaveOneOut, check_cv, cross_val_predict +from .preprocessing import LabelEncoder, label_binarize +from .svm import LinearSVC +from .utils import _safe_indexing, column_or_1d, get_tags, indexable +from .utils._param_validation import ( + HasMethods, + Hidden, + Interval, + StrOptions, + validate_params, +) +from .utils._plotting import _BinaryClassifierCurveDisplayMixin, _validate_style_kwargs +from .utils._response import _get_response_values, _process_predict_proba +from .utils.metadata_routing import ( + MetadataRouter, + MethodMapping, + _routing_enabled, + process_routing, +) +from .utils.multiclass import check_classification_targets +from .utils.parallel import Parallel, delayed +from .utils.validation import ( + _check_method_params, + _check_pos_label_consistency, + _check_response_method, + _check_sample_weight, + _num_samples, + check_consistent_length, + check_is_fitted, +) + + +class CalibratedClassifierCV(ClassifierMixin, MetaEstimatorMixin, BaseEstimator): + """Probability calibration with isotonic regression or logistic regression. + + This class uses cross-validation to both estimate the parameters of a + classifier and subsequently calibrate a classifier. With + `ensemble=True`, for each cv split it + fits a copy of the base estimator to the training subset, and calibrates it + using the testing subset. For prediction, predicted probabilities are + averaged across these individual calibrated classifiers. When + `ensemble=False`, cross-validation is used to obtain unbiased predictions, + via :func:`~sklearn.model_selection.cross_val_predict`, which are then + used for calibration. For prediction, the base estimator, trained using all + the data, is used. This is the prediction method implemented when + `probabilities=True` for :class:`~sklearn.svm.SVC` and :class:`~sklearn.svm.NuSVC` + estimators (see :ref:`User Guide ` for details). + + Already fitted classifiers can be calibrated by wrapping the model in a + :class:`~sklearn.frozen.FrozenEstimator`. In this case all provided + data is used for calibration. The user has to take care manually that data + for model fitting and calibration are disjoint. + + The calibration is based on the :term:`decision_function` method of the + `estimator` if it exists, else on :term:`predict_proba`. + + Read more in the :ref:`User Guide `. + In order to learn more on the CalibratedClassifierCV class, see the + following calibration examples: + :ref:`sphx_glr_auto_examples_calibration_plot_calibration.py`, + :ref:`sphx_glr_auto_examples_calibration_plot_calibration_curve.py`, and + :ref:`sphx_glr_auto_examples_calibration_plot_calibration_multiclass.py`. + + Parameters + ---------- + estimator : estimator instance, default=None + The classifier whose output need to be calibrated to provide more + accurate `predict_proba` outputs. The default classifier is + a :class:`~sklearn.svm.LinearSVC`. + + .. versionadded:: 1.2 + + method : {'sigmoid', 'isotonic'}, default='sigmoid' + The method to use for calibration. Can be 'sigmoid' which + corresponds to Platt's method (i.e. a logistic regression model) or + 'isotonic' which is a non-parametric approach. It is not advised to + use isotonic calibration with too few calibration samples + ``(<<1000)`` since it tends to overfit. + + cv : int, cross-validation generator, or iterable, default=None + Determines the cross-validation splitting strategy. + Possible inputs for cv are: + + - None, to use the default 5-fold cross-validation, + - integer, to specify the number of folds. + - :term:`CV splitter`, + - An iterable yielding (train, test) splits as arrays of indices. + + For integer/None inputs, if ``y`` is binary or multiclass, + :class:`~sklearn.model_selection.StratifiedKFold` is used. If ``y`` is + neither binary nor multiclass, :class:`~sklearn.model_selection.KFold` + is used. + + Refer to the :ref:`User Guide ` for the various + cross-validation strategies that can be used here. + + .. versionchanged:: 0.22 + ``cv`` default value if None changed from 3-fold to 5-fold. + + .. versionchanged:: 1.6 + `"prefit"` is deprecated. Use :class:`~sklearn.frozen.FrozenEstimator` + instead. + + n_jobs : int, default=None + Number of jobs to run in parallel. + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. + + Base estimator clones are fitted in parallel across cross-validation + iterations. Therefore parallelism happens only when `cv != "prefit"`. + + See :term:`Glossary ` for more details. + + .. versionadded:: 0.24 + + ensemble : bool, or "auto", default="auto" + Determines how the calibrator is fitted. + + "auto" will use `False` if the `estimator` is a + :class:`~sklearn.frozen.FrozenEstimator`, and `True` otherwise. + + If `True`, the `estimator` is fitted using training data, and + calibrated using testing data, for each `cv` fold. The final estimator + is an ensemble of `n_cv` fitted classifier and calibrator pairs, where + `n_cv` is the number of cross-validation folds. The output is the + average predicted probabilities of all pairs. + + If `False`, `cv` is used to compute unbiased predictions, via + :func:`~sklearn.model_selection.cross_val_predict`, which are then + used for calibration. At prediction time, the classifier used is the + `estimator` trained on all the data. + Note that this method is also internally implemented in + :mod:`sklearn.svm` estimators with the `probabilities=True` parameter. + + .. versionadded:: 0.24 + + .. versionchanged:: 1.6 + `"auto"` option is added and is the default. + + Attributes + ---------- + classes_ : ndarray of shape (n_classes,) + The class labels. + + n_features_in_ : int + Number of features seen during :term:`fit`. Only defined if the + underlying estimator exposes such an attribute when fit. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Only defined if the + underlying estimator exposes such an attribute when fit. + + .. versionadded:: 1.0 + + calibrated_classifiers_ : list (len() equal to cv or 1 if `ensemble=False`) + The list of classifier and calibrator pairs. + + - When `ensemble=True`, `n_cv` fitted `estimator` and calibrator pairs. + `n_cv` is the number of cross-validation folds. + - When `ensemble=False`, the `estimator`, fitted on all the data, and fitted + calibrator. + + .. versionchanged:: 0.24 + Single calibrated classifier case when `ensemble=False`. + + See Also + -------- + calibration_curve : Compute true and predicted probabilities + for a calibration curve. + + References + ---------- + .. [1] Obtaining calibrated probability estimates from decision trees + and naive Bayesian classifiers, B. Zadrozny & C. Elkan, ICML 2001 + + .. [2] Transforming Classifier Scores into Accurate Multiclass + Probability Estimates, B. Zadrozny & C. Elkan, (KDD 2002) + + .. [3] Probabilistic Outputs for Support Vector Machines and Comparisons to + Regularized Likelihood Methods, J. Platt, (1999) + + .. [4] Predicting Good Probabilities with Supervised Learning, + A. Niculescu-Mizil & R. Caruana, ICML 2005 + + Examples + -------- + >>> from sklearn.datasets import make_classification + >>> from sklearn.naive_bayes import GaussianNB + >>> from sklearn.calibration import CalibratedClassifierCV + >>> X, y = make_classification(n_samples=100, n_features=2, + ... n_redundant=0, random_state=42) + >>> base_clf = GaussianNB() + >>> calibrated_clf = CalibratedClassifierCV(base_clf, cv=3) + >>> calibrated_clf.fit(X, y) + CalibratedClassifierCV(...) + >>> len(calibrated_clf.calibrated_classifiers_) + 3 + >>> calibrated_clf.predict_proba(X)[:5, :] + array([[0.110, 0.889], + [0.072, 0.927], + [0.928, 0.072], + [0.928, 0.072], + [0.072, 0.928]]) + >>> from sklearn.model_selection import train_test_split + >>> X, y = make_classification(n_samples=100, n_features=2, + ... n_redundant=0, random_state=42) + >>> X_train, X_calib, y_train, y_calib = train_test_split( + ... X, y, random_state=42 + ... ) + >>> base_clf = GaussianNB() + >>> base_clf.fit(X_train, y_train) + GaussianNB() + >>> from sklearn.frozen import FrozenEstimator + >>> calibrated_clf = CalibratedClassifierCV(FrozenEstimator(base_clf)) + >>> calibrated_clf.fit(X_calib, y_calib) + CalibratedClassifierCV(...) + >>> len(calibrated_clf.calibrated_classifiers_) + 1 + >>> calibrated_clf.predict_proba([[-0.5, 0.5]]) + array([[0.936, 0.063]]) + """ + + _parameter_constraints: dict = { + "estimator": [ + HasMethods(["fit", "predict_proba"]), + HasMethods(["fit", "decision_function"]), + None, + ], + "method": [StrOptions({"isotonic", "sigmoid"})], + "cv": ["cv_object", Hidden(StrOptions({"prefit"}))], + "n_jobs": [Integral, None], + "ensemble": ["boolean", StrOptions({"auto"})], + } + + def __init__( + self, + estimator=None, + *, + method="sigmoid", + cv=None, + n_jobs=None, + ensemble="auto", + ): + self.estimator = estimator + self.method = method + self.cv = cv + self.n_jobs = n_jobs + self.ensemble = ensemble + + def _get_estimator(self): + """Resolve which estimator to return (default is LinearSVC)""" + if self.estimator is None: + # we want all classifiers that don't expose a random_state + # to be deterministic (and we don't want to expose this one). + estimator = LinearSVC(random_state=0) + if _routing_enabled(): + estimator.set_fit_request(sample_weight=True) + else: + estimator = self.estimator + + return estimator + + @_fit_context( + # CalibratedClassifierCV.estimator is not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, y, sample_weight=None, **fit_params): + """Fit the calibrated model. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data. + + y : array-like of shape (n_samples,) + Target values. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. If None, then samples are equally weighted. + + **fit_params : dict + Parameters to pass to the `fit` method of the underlying + classifier. + + Returns + ------- + self : object + Returns an instance of self. + """ + check_classification_targets(y) + X, y = indexable(X, y) + estimator = self._get_estimator() + + _ensemble = self.ensemble + if _ensemble == "auto": + _ensemble = not isinstance(estimator, FrozenEstimator) + + self.calibrated_classifiers_ = [] + if self.cv == "prefit": + # TODO(1.8): Remove this code branch and cv='prefit' + warnings.warn( + "The `cv='prefit'` option is deprecated in 1.6 and will be removed in" + " 1.8. You can use CalibratedClassifierCV(FrozenEstimator(estimator))" + " instead.", + category=FutureWarning, + ) + # `classes_` should be consistent with that of estimator + check_is_fitted(self.estimator, attributes=["classes_"]) + self.classes_ = self.estimator.classes_ + + predictions, _ = _get_response_values( + estimator, + X, + response_method=["decision_function", "predict_proba"], + ) + if predictions.ndim == 1: + # Reshape binary output from `(n_samples,)` to `(n_samples, 1)` + predictions = predictions.reshape(-1, 1) + + if sample_weight is not None: + # Check that the sample_weight dtype is consistent with the predictions + # to avoid unintentional upcasts. + sample_weight = _check_sample_weight( + sample_weight, predictions, dtype=predictions.dtype + ) + + calibrated_classifier = _fit_calibrator( + estimator, + predictions, + y, + self.classes_, + self.method, + sample_weight, + ) + self.calibrated_classifiers_.append(calibrated_classifier) + else: + # Set `classes_` using all `y` + label_encoder_ = LabelEncoder().fit(y) + self.classes_ = label_encoder_.classes_ + + if _routing_enabled(): + routed_params = process_routing( + self, + "fit", + sample_weight=sample_weight, + **fit_params, + ) + else: + # sample_weight checks + fit_parameters = signature(estimator.fit).parameters + supports_sw = "sample_weight" in fit_parameters + if sample_weight is not None and not supports_sw: + estimator_name = type(estimator).__name__ + warnings.warn( + f"Since {estimator_name} does not appear to accept" + " sample_weight, sample weights will only be used for the" + " calibration itself. This can be caused by a limitation of" + " the current scikit-learn API. See the following issue for" + " more details:" + " https://github.com/scikit-learn/scikit-learn/issues/21134." + " Be warned that the result of the calibration is likely to be" + " incorrect." + ) + routed_params = Bunch() + routed_params.splitter = Bunch(split={}) # no routing for splitter + routed_params.estimator = Bunch(fit=fit_params) + if sample_weight is not None and supports_sw: + routed_params.estimator.fit["sample_weight"] = sample_weight + + # Check that each cross-validation fold can have at least one + # example per class + if isinstance(self.cv, int): + n_folds = self.cv + elif hasattr(self.cv, "n_splits"): + n_folds = self.cv.n_splits + else: + n_folds = None + if n_folds and np.any(np.unique(y, return_counts=True)[1] < n_folds): + raise ValueError( + f"Requesting {n_folds}-fold " + "cross-validation but provided less than " + f"{n_folds} examples for at least one class." + ) + if isinstance(self.cv, LeaveOneOut): + raise ValueError( + "LeaveOneOut cross-validation does not allow" + "all classes to be present in test splits. " + "Please use a cross-validation generator that allows " + "all classes to appear in every test and train split." + ) + cv = check_cv(self.cv, y, classifier=True) + + if _ensemble: + parallel = Parallel(n_jobs=self.n_jobs) + self.calibrated_classifiers_ = parallel( + delayed(_fit_classifier_calibrator_pair)( + clone(estimator), + X, + y, + train=train, + test=test, + method=self.method, + classes=self.classes_, + sample_weight=sample_weight, + fit_params=routed_params.estimator.fit, + ) + for train, test in cv.split(X, y, **routed_params.splitter.split) + ) + else: + this_estimator = clone(estimator) + method_name = _check_response_method( + this_estimator, + ["decision_function", "predict_proba"], + ).__name__ + predictions = cross_val_predict( + estimator=this_estimator, + X=X, + y=y, + cv=cv, + method=method_name, + n_jobs=self.n_jobs, + params=routed_params.estimator.fit, + ) + if len(self.classes_) == 2: + # Ensure shape (n_samples, 1) in the binary case + if method_name == "predict_proba": + # Select the probability column of the positive class + predictions = _process_predict_proba( + y_pred=predictions, + target_type="binary", + classes=self.classes_, + pos_label=self.classes_[1], + ) + predictions = predictions.reshape(-1, 1) + + if sample_weight is not None: + # Check that the sample_weight dtype is consistent with the + # predictions to avoid unintentional upcasts. + sample_weight = _check_sample_weight( + sample_weight, predictions, dtype=predictions.dtype + ) + + this_estimator.fit(X, y, **routed_params.estimator.fit) + # Note: Here we don't pass on fit_params because the supported + # calibrators don't support fit_params anyway + calibrated_classifier = _fit_calibrator( + this_estimator, + predictions, + y, + self.classes_, + self.method, + sample_weight, + ) + self.calibrated_classifiers_.append(calibrated_classifier) + + first_clf = self.calibrated_classifiers_[0].estimator + if hasattr(first_clf, "n_features_in_"): + self.n_features_in_ = first_clf.n_features_in_ + if hasattr(first_clf, "feature_names_in_"): + self.feature_names_in_ = first_clf.feature_names_in_ + return self + + def predict_proba(self, X): + """Calibrated probabilities of classification. + + This function returns calibrated probabilities of classification + according to each class on an array of test vectors X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The samples, as accepted by `estimator.predict_proba`. + + Returns + ------- + C : ndarray of shape (n_samples, n_classes) + The predicted probas. + """ + check_is_fitted(self) + # Compute the arithmetic mean of the predictions of the calibrated + # classifiers + mean_proba = np.zeros((_num_samples(X), len(self.classes_))) + for calibrated_classifier in self.calibrated_classifiers_: + proba = calibrated_classifier.predict_proba(X) + mean_proba += proba + + mean_proba /= len(self.calibrated_classifiers_) + + return mean_proba + + def predict(self, X): + """Predict the target of new samples. + + The predicted class is the class that has the highest probability, + and can thus be different from the prediction of the uncalibrated classifier. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The samples, as accepted by `estimator.predict`. + + Returns + ------- + C : ndarray of shape (n_samples,) + The predicted class. + """ + check_is_fitted(self) + return self.classes_[np.argmax(self.predict_proba(X), axis=1)] + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + router = ( + MetadataRouter(owner=self.__class__.__name__) + .add_self_request(self) + .add( + estimator=self._get_estimator(), + method_mapping=MethodMapping().add(caller="fit", callee="fit"), + ) + .add( + splitter=self.cv, + method_mapping=MethodMapping().add(caller="fit", callee="split"), + ) + ) + return router + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = get_tags(self._get_estimator()).input_tags.sparse + return tags + + +def _fit_classifier_calibrator_pair( + estimator, + X, + y, + train, + test, + method, + classes, + sample_weight=None, + fit_params=None, +): + """Fit a classifier/calibration pair on a given train/test split. + + Fit the classifier on the train set, compute its predictions on the test + set and use the predictions as input to fit the calibrator along with the + test labels. + + Parameters + ---------- + estimator : estimator instance + Cloned base estimator. + + X : array-like, shape (n_samples, n_features) + Sample data. + + y : array-like, shape (n_samples,) + Targets. + + train : ndarray, shape (n_train_indices,) + Indices of the training subset. + + test : ndarray, shape (n_test_indices,) + Indices of the testing subset. + + method : {'sigmoid', 'isotonic'} + Method to use for calibration. + + classes : ndarray, shape (n_classes,) + The target classes. + + sample_weight : array-like, default=None + Sample weights for `X`. + + fit_params : dict, default=None + Parameters to pass to the `fit` method of the underlying + classifier. + + Returns + ------- + calibrated_classifier : _CalibratedClassifier instance + """ + fit_params_train = _check_method_params(X, params=fit_params, indices=train) + X_train, y_train = _safe_indexing(X, train), _safe_indexing(y, train) + X_test, y_test = _safe_indexing(X, test), _safe_indexing(y, test) + + estimator.fit(X_train, y_train, **fit_params_train) + + predictions, _ = _get_response_values( + estimator, + X_test, + response_method=["decision_function", "predict_proba"], + ) + if predictions.ndim == 1: + # Reshape binary output from `(n_samples,)` to `(n_samples, 1)` + predictions = predictions.reshape(-1, 1) + + if sample_weight is not None: + # Check that the sample_weight dtype is consistent with the predictions + # to avoid unintentional upcasts. + sample_weight = _check_sample_weight(sample_weight, X, dtype=predictions.dtype) + sw_test = _safe_indexing(sample_weight, test) + else: + sw_test = None + calibrated_classifier = _fit_calibrator( + estimator, predictions, y_test, classes, method, sample_weight=sw_test + ) + return calibrated_classifier + + +def _fit_calibrator(clf, predictions, y, classes, method, sample_weight=None): + """Fit calibrator(s) and return a `_CalibratedClassifier` + instance. + + `n_classes` (i.e. `len(clf.classes_)`) calibrators are fitted. + However, if `n_classes` equals 2, one calibrator is fitted. + + Parameters + ---------- + clf : estimator instance + Fitted classifier. + + predictions : array-like, shape (n_samples, n_classes) or (n_samples, 1) \ + when binary. + Raw predictions returned by the un-calibrated base classifier. + + y : array-like, shape (n_samples,) + The targets. + + classes : ndarray, shape (n_classes,) + All the prediction classes. + + method : {'sigmoid', 'isotonic'} + The method to use for calibration. + + sample_weight : ndarray, shape (n_samples,), default=None + Sample weights. If None, then samples are equally weighted. + + Returns + ------- + pipeline : _CalibratedClassifier instance + """ + Y = label_binarize(y, classes=classes) + label_encoder = LabelEncoder().fit(classes) + pos_class_indices = label_encoder.transform(clf.classes_) + calibrators = [] + for class_idx, this_pred in zip(pos_class_indices, predictions.T): + if method == "isotonic": + calibrator = IsotonicRegression(out_of_bounds="clip") + else: # "sigmoid" + calibrator = _SigmoidCalibration() + calibrator.fit(this_pred, Y[:, class_idx], sample_weight) + calibrators.append(calibrator) + + pipeline = _CalibratedClassifier(clf, calibrators, method=method, classes=classes) + return pipeline + + +class _CalibratedClassifier: + """Pipeline-like chaining a fitted classifier and its fitted calibrators. + + Parameters + ---------- + estimator : estimator instance + Fitted classifier. + + calibrators : list of fitted estimator instances + List of fitted calibrators (either 'IsotonicRegression' or + '_SigmoidCalibration'). The number of calibrators equals the number of + classes. However, if there are 2 classes, the list contains only one + fitted calibrator. + + classes : array-like of shape (n_classes,) + All the prediction classes. + + method : {'sigmoid', 'isotonic'}, default='sigmoid' + The method to use for calibration. Can be 'sigmoid' which + corresponds to Platt's method or 'isotonic' which is a + non-parametric approach based on isotonic regression. + """ + + def __init__(self, estimator, calibrators, *, classes, method="sigmoid"): + self.estimator = estimator + self.calibrators = calibrators + self.classes = classes + self.method = method + + def predict_proba(self, X): + """Calculate calibrated probabilities. + + Calculates classification calibrated probabilities + for each class, in a one-vs-all manner, for `X`. + + Parameters + ---------- + X : ndarray of shape (n_samples, n_features) + The sample data. + + Returns + ------- + proba : array, shape (n_samples, n_classes) + The predicted probabilities. Can be exact zeros. + """ + predictions, _ = _get_response_values( + self.estimator, + X, + response_method=["decision_function", "predict_proba"], + ) + if predictions.ndim == 1: + # Reshape binary output from `(n_samples,)` to `(n_samples, 1)` + predictions = predictions.reshape(-1, 1) + + n_classes = len(self.classes) + + label_encoder = LabelEncoder().fit(self.classes) + pos_class_indices = label_encoder.transform(self.estimator.classes_) + + proba = np.zeros((_num_samples(X), n_classes)) + for class_idx, this_pred, calibrator in zip( + pos_class_indices, predictions.T, self.calibrators + ): + if n_classes == 2: + # When binary, `predictions` consists only of predictions for + # clf.classes_[1] but `pos_class_indices` = 0 + class_idx += 1 + proba[:, class_idx] = calibrator.predict(this_pred) + + # Normalize the probabilities + if n_classes == 2: + proba[:, 0] = 1.0 - proba[:, 1] + else: + denominator = np.sum(proba, axis=1)[:, np.newaxis] + # In the edge case where for each class calibrator returns a null + # probability for a given sample, use the uniform distribution + # instead. + uniform_proba = np.full_like(proba, 1 / n_classes) + proba = np.divide( + proba, denominator, out=uniform_proba, where=denominator != 0 + ) + + # Deal with cases where the predicted probability minimally exceeds 1.0 + proba[(1.0 < proba) & (proba <= 1.0 + 1e-5)] = 1.0 + + return proba + + +# The max_abs_prediction_threshold was approximated using +# logit(np.finfo(np.float64).eps) which is about -36 +def _sigmoid_calibration( + predictions, y, sample_weight=None, max_abs_prediction_threshold=30 +): + """Probability Calibration with sigmoid method (Platt 2000) + + Parameters + ---------- + predictions : ndarray of shape (n_samples,) + The decision function or predict proba for the samples. + + y : ndarray of shape (n_samples,) + The targets. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. If None, then samples are equally weighted. + + Returns + ------- + a : float + The slope. + + b : float + The intercept. + + References + ---------- + Platt, "Probabilistic Outputs for Support Vector Machines" + """ + predictions = column_or_1d(predictions) + y = column_or_1d(y) + + F = predictions # F follows Platt's notations + + scale_constant = 1.0 + max_prediction = np.max(np.abs(F)) + + # If the predictions have large values we scale them in order to bring + # them within a suitable range. This has no effect on the final + # (prediction) result because linear models like Logisitic Regression + # without a penalty are invariant to multiplying the features by a + # constant. + if max_prediction >= max_abs_prediction_threshold: + scale_constant = max_prediction + # We rescale the features in a copy: inplace rescaling could confuse + # the caller and make the code harder to reason about. + F = F / scale_constant + + # Bayesian priors (see Platt end of section 2.2): + # It corresponds to the number of samples, taking into account the + # `sample_weight`. + mask_negative_samples = y <= 0 + if sample_weight is not None: + prior0 = (sample_weight[mask_negative_samples]).sum() + prior1 = (sample_weight[~mask_negative_samples]).sum() + else: + prior0 = float(np.sum(mask_negative_samples)) + prior1 = y.shape[0] - prior0 + T = np.zeros_like(y, dtype=predictions.dtype) + T[y > 0] = (prior1 + 1.0) / (prior1 + 2.0) + T[y <= 0] = 1.0 / (prior0 + 2.0) + + bin_loss = HalfBinomialLoss() + + def loss_grad(AB): + # .astype below is needed to ensure y_true and raw_prediction have the + # same dtype. With result = np.float64(0) * np.array([1, 2], dtype=np.float32) + # - in Numpy 2, result.dtype is float64 + # - in Numpy<2, result.dtype is float32 + raw_prediction = -(AB[0] * F + AB[1]).astype(dtype=predictions.dtype) + l, g = bin_loss.loss_gradient( + y_true=T, + raw_prediction=raw_prediction, + sample_weight=sample_weight, + ) + loss = l.sum() + # TODO: Remove casting to np.float64 when minimum supported SciPy is 1.11.2 + # With SciPy >= 1.11.2, the LBFGS implementation will cast to float64 + # https://github.com/scipy/scipy/pull/18825. + # Here we cast to float64 to support SciPy < 1.11.2 + grad = np.asarray([-g @ F, -g.sum()], dtype=np.float64) + return loss, grad + + AB0 = np.array([0.0, log((prior0 + 1.0) / (prior1 + 1.0))]) + + opt_result = minimize( + loss_grad, + AB0, + method="L-BFGS-B", + jac=True, + options={ + "gtol": 1e-6, + "ftol": 64 * np.finfo(float).eps, + }, + ) + AB_ = opt_result.x + + # The tuned multiplicative parameter is converted back to the original + # input feature scale. The offset parameter does not need rescaling since + # we did not rescale the outcome variable. + return AB_[0] / scale_constant, AB_[1] + + +class _SigmoidCalibration(RegressorMixin, BaseEstimator): + """Sigmoid regression model. + + Attributes + ---------- + a_ : float + The slope. + + b_ : float + The intercept. + """ + + def fit(self, X, y, sample_weight=None): + """Fit the model using X, y as training data. + + Parameters + ---------- + X : array-like of shape (n_samples,) + Training data. + + y : array-like of shape (n_samples,) + Training target. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. If None, then samples are equally weighted. + + Returns + ------- + self : object + Returns an instance of self. + """ + X = column_or_1d(X) + y = column_or_1d(y) + X, y = indexable(X, y) + + self.a_, self.b_ = _sigmoid_calibration(X, y, sample_weight) + return self + + def predict(self, T): + """Predict new data by linear interpolation. + + Parameters + ---------- + T : array-like of shape (n_samples,) + Data to predict from. + + Returns + ------- + T_ : ndarray of shape (n_samples,) + The predicted data. + """ + T = column_or_1d(T) + return expit(-(self.a_ * T + self.b_)) + + +@validate_params( + { + "y_true": ["array-like"], + "y_prob": ["array-like"], + "pos_label": [Real, str, "boolean", None], + "n_bins": [Interval(Integral, 1, None, closed="left")], + "strategy": [StrOptions({"uniform", "quantile"})], + }, + prefer_skip_nested_validation=True, +) +def calibration_curve( + y_true, + y_prob, + *, + pos_label=None, + n_bins=5, + strategy="uniform", +): + """Compute true and predicted probabilities for a calibration curve. + + The method assumes the inputs come from a binary classifier, and + discretize the [0, 1] interval into bins. + + Calibration curves may also be referred to as reliability diagrams. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + y_true : array-like of shape (n_samples,) + True targets. + + y_prob : array-like of shape (n_samples,) + Probabilities of the positive class. + + pos_label : int, float, bool or str, default=None + The label of the positive class. + + .. versionadded:: 1.1 + + n_bins : int, default=5 + Number of bins to discretize the [0, 1] interval. A bigger number + requires more data. Bins with no samples (i.e. without + corresponding values in `y_prob`) will not be returned, thus the + returned arrays may have less than `n_bins` values. + + strategy : {'uniform', 'quantile'}, default='uniform' + Strategy used to define the widths of the bins. + + uniform + The bins have identical widths. + quantile + The bins have the same number of samples and depend on `y_prob`. + + Returns + ------- + prob_true : ndarray of shape (n_bins,) or smaller + The proportion of samples whose class is the positive class, in each + bin (fraction of positives). + + prob_pred : ndarray of shape (n_bins,) or smaller + The mean predicted probability in each bin. + + See Also + -------- + CalibrationDisplay.from_predictions : Plot calibration curve using true + and predicted labels. + CalibrationDisplay.from_estimator : Plot calibration curve using an + estimator and data. + + References + ---------- + Alexandru Niculescu-Mizil and Rich Caruana (2005) Predicting Good + Probabilities With Supervised Learning, in Proceedings of the 22nd + International Conference on Machine Learning (ICML). + See section 4 (Qualitative Analysis of Predictions). + + Examples + -------- + >>> import numpy as np + >>> from sklearn.calibration import calibration_curve + >>> y_true = np.array([0, 0, 0, 0, 1, 1, 1, 1, 1]) + >>> y_pred = np.array([0.1, 0.2, 0.3, 0.4, 0.65, 0.7, 0.8, 0.9, 1.]) + >>> prob_true, prob_pred = calibration_curve(y_true, y_pred, n_bins=3) + >>> prob_true + array([0. , 0.5, 1. ]) + >>> prob_pred + array([0.2 , 0.525, 0.85 ]) + """ + y_true = column_or_1d(y_true) + y_prob = column_or_1d(y_prob) + check_consistent_length(y_true, y_prob) + pos_label = _check_pos_label_consistency(pos_label, y_true) + + if y_prob.min() < 0 or y_prob.max() > 1: + raise ValueError("y_prob has values outside [0, 1].") + + labels = np.unique(y_true) + if len(labels) > 2: + raise ValueError( + f"Only binary classification is supported. Provided labels {labels}." + ) + y_true = y_true == pos_label + + if strategy == "quantile": # Determine bin edges by distribution of data + quantiles = np.linspace(0, 1, n_bins + 1) + bins = np.percentile(y_prob, quantiles * 100) + elif strategy == "uniform": + bins = np.linspace(0.0, 1.0, n_bins + 1) + else: + raise ValueError( + "Invalid entry to 'strategy' input. Strategy " + "must be either 'quantile' or 'uniform'." + ) + + binids = np.searchsorted(bins[1:-1], y_prob) + + bin_sums = np.bincount(binids, weights=y_prob, minlength=len(bins)) + bin_true = np.bincount(binids, weights=y_true, minlength=len(bins)) + bin_total = np.bincount(binids, minlength=len(bins)) + + nonzero = bin_total != 0 + prob_true = bin_true[nonzero] / bin_total[nonzero] + prob_pred = bin_sums[nonzero] / bin_total[nonzero] + + return prob_true, prob_pred + + +class CalibrationDisplay(_BinaryClassifierCurveDisplayMixin): + """Calibration curve (also known as reliability diagram) visualization. + + It is recommended to use + :func:`~sklearn.calibration.CalibrationDisplay.from_estimator` or + :func:`~sklearn.calibration.CalibrationDisplay.from_predictions` + to create a `CalibrationDisplay`. All parameters are stored as attributes. + + Read more about calibration in the :ref:`User Guide ` and + more about the scikit-learn visualization API in :ref:`visualizations`. + + For an example on how to use the visualization, see + :ref:`sphx_glr_auto_examples_calibration_plot_calibration_curve.py`. + + .. versionadded:: 1.0 + + Parameters + ---------- + prob_true : ndarray of shape (n_bins,) + The proportion of samples whose class is the positive class (fraction + of positives), in each bin. + + prob_pred : ndarray of shape (n_bins,) + The mean predicted probability in each bin. + + y_prob : ndarray of shape (n_samples,) + Probability estimates for the positive class, for each sample. + + estimator_name : str, default=None + Name of estimator. If None, the estimator name is not shown. + + pos_label : int, float, bool or str, default=None + The positive class when computing the calibration curve. + By default, `pos_label` is set to `estimators.classes_[1]` when using + `from_estimator` and set to 1 when using `from_predictions`. + + .. versionadded:: 1.1 + + Attributes + ---------- + line_ : matplotlib Artist + Calibration curve. + + ax_ : matplotlib Axes + Axes with calibration curve. + + figure_ : matplotlib Figure + Figure containing the curve. + + See Also + -------- + calibration_curve : Compute true and predicted probabilities for a + calibration curve. + CalibrationDisplay.from_predictions : Plot calibration curve using true + and predicted labels. + CalibrationDisplay.from_estimator : Plot calibration curve using an + estimator and data. + + Examples + -------- + >>> from sklearn.datasets import make_classification + >>> from sklearn.model_selection import train_test_split + >>> from sklearn.linear_model import LogisticRegression + >>> from sklearn.calibration import calibration_curve, CalibrationDisplay + >>> X, y = make_classification(random_state=0) + >>> X_train, X_test, y_train, y_test = train_test_split( + ... X, y, random_state=0) + >>> clf = LogisticRegression(random_state=0) + >>> clf.fit(X_train, y_train) + LogisticRegression(random_state=0) + >>> y_prob = clf.predict_proba(X_test)[:, 1] + >>> prob_true, prob_pred = calibration_curve(y_test, y_prob, n_bins=10) + >>> disp = CalibrationDisplay(prob_true, prob_pred, y_prob) + >>> disp.plot() + <...> + """ + + def __init__( + self, prob_true, prob_pred, y_prob, *, estimator_name=None, pos_label=None + ): + self.prob_true = prob_true + self.prob_pred = prob_pred + self.y_prob = y_prob + self.estimator_name = estimator_name + self.pos_label = pos_label + + def plot(self, *, ax=None, name=None, ref_line=True, **kwargs): + """Plot visualization. + + Extra keyword arguments will be passed to + :func:`matplotlib.pyplot.plot`. + + Parameters + ---------- + ax : Matplotlib Axes, default=None + Axes object to plot on. If `None`, a new figure and axes is + created. + + name : str, default=None + Name for labeling curve. If `None`, use `estimator_name` if + not `None`, otherwise no labeling is shown. + + ref_line : bool, default=True + If `True`, plots a reference line representing a perfectly + calibrated classifier. + + **kwargs : dict + Keyword arguments to be passed to :func:`matplotlib.pyplot.plot`. + + Returns + ------- + display : :class:`~sklearn.calibration.CalibrationDisplay` + Object that stores computed values. + """ + self.ax_, self.figure_, name = self._validate_plot_params(ax=ax, name=name) + + info_pos_label = ( + f"(Positive class: {self.pos_label})" if self.pos_label is not None else "" + ) + + default_line_kwargs = {"marker": "s", "linestyle": "-"} + if name is not None: + default_line_kwargs["label"] = name + line_kwargs = _validate_style_kwargs(default_line_kwargs, kwargs) + + ref_line_label = "Perfectly calibrated" + existing_ref_line = ref_line_label in self.ax_.get_legend_handles_labels()[1] + if ref_line and not existing_ref_line: + self.ax_.plot([0, 1], [0, 1], "k:", label=ref_line_label) + self.line_ = self.ax_.plot(self.prob_pred, self.prob_true, **line_kwargs)[0] + + # We always have to show the legend for at least the reference line + self.ax_.legend(loc="lower right") + + xlabel = f"Mean predicted probability {info_pos_label}" + ylabel = f"Fraction of positives {info_pos_label}" + self.ax_.set(xlabel=xlabel, ylabel=ylabel) + + return self + + @classmethod + def from_estimator( + cls, + estimator, + X, + y, + *, + n_bins=5, + strategy="uniform", + pos_label=None, + name=None, + ax=None, + ref_line=True, + **kwargs, + ): + """Plot calibration curve using a binary classifier and data. + + A calibration curve, also known as a reliability diagram, uses inputs + from a binary classifier and plots the average predicted probability + for each bin against the fraction of positive classes, on the + y-axis. + + Extra keyword arguments will be passed to + :func:`matplotlib.pyplot.plot`. + + Read more about calibration in the :ref:`User Guide ` and + more about the scikit-learn visualization API in :ref:`visualizations`. + + .. versionadded:: 1.0 + + Parameters + ---------- + estimator : estimator instance + Fitted classifier or a fitted :class:`~sklearn.pipeline.Pipeline` + in which the last estimator is a classifier. The classifier must + have a :term:`predict_proba` method. + + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Input values. + + y : array-like of shape (n_samples,) + Binary target values. + + n_bins : int, default=5 + Number of bins to discretize the [0, 1] interval into when + calculating the calibration curve. A bigger number requires more + data. + + strategy : {'uniform', 'quantile'}, default='uniform' + Strategy used to define the widths of the bins. + + - `'uniform'`: The bins have identical widths. + - `'quantile'`: The bins have the same number of samples and depend + on predicted probabilities. + + pos_label : int, float, bool or str, default=None + The positive class when computing the calibration curve. + By default, `estimators.classes_[1]` is considered as the + positive class. + + .. versionadded:: 1.1 + + name : str, default=None + Name for labeling curve. If `None`, the name of the estimator is + used. + + ax : matplotlib axes, default=None + Axes object to plot on. If `None`, a new figure and axes is + created. + + ref_line : bool, default=True + If `True`, plots a reference line representing a perfectly + calibrated classifier. + + **kwargs : dict + Keyword arguments to be passed to :func:`matplotlib.pyplot.plot`. + + Returns + ------- + display : :class:`~sklearn.calibration.CalibrationDisplay`. + Object that stores computed values. + + See Also + -------- + CalibrationDisplay.from_predictions : Plot calibration curve using true + and predicted labels. + + Examples + -------- + >>> import matplotlib.pyplot as plt + >>> from sklearn.datasets import make_classification + >>> from sklearn.model_selection import train_test_split + >>> from sklearn.linear_model import LogisticRegression + >>> from sklearn.calibration import CalibrationDisplay + >>> X, y = make_classification(random_state=0) + >>> X_train, X_test, y_train, y_test = train_test_split( + ... X, y, random_state=0) + >>> clf = LogisticRegression(random_state=0) + >>> clf.fit(X_train, y_train) + LogisticRegression(random_state=0) + >>> disp = CalibrationDisplay.from_estimator(clf, X_test, y_test) + >>> plt.show() + """ + y_prob, pos_label, name = cls._validate_and_get_response_values( + estimator, + X, + y, + response_method="predict_proba", + pos_label=pos_label, + name=name, + ) + + return cls.from_predictions( + y, + y_prob, + n_bins=n_bins, + strategy=strategy, + pos_label=pos_label, + name=name, + ref_line=ref_line, + ax=ax, + **kwargs, + ) + + @classmethod + def from_predictions( + cls, + y_true, + y_prob, + *, + n_bins=5, + strategy="uniform", + pos_label=None, + name=None, + ax=None, + ref_line=True, + **kwargs, + ): + """Plot calibration curve using true labels and predicted probabilities. + + Calibration curve, also known as reliability diagram, uses inputs + from a binary classifier and plots the average predicted probability + for each bin against the fraction of positive classes, on the + y-axis. + + Extra keyword arguments will be passed to + :func:`matplotlib.pyplot.plot`. + + Read more about calibration in the :ref:`User Guide ` and + more about the scikit-learn visualization API in :ref:`visualizations`. + + .. versionadded:: 1.0 + + Parameters + ---------- + y_true : array-like of shape (n_samples,) + True labels. + + y_prob : array-like of shape (n_samples,) + The predicted probabilities of the positive class. + + n_bins : int, default=5 + Number of bins to discretize the [0, 1] interval into when + calculating the calibration curve. A bigger number requires more + data. + + strategy : {'uniform', 'quantile'}, default='uniform' + Strategy used to define the widths of the bins. + + - `'uniform'`: The bins have identical widths. + - `'quantile'`: The bins have the same number of samples and depend + on predicted probabilities. + + pos_label : int, float, bool or str, default=None + The positive class when computing the calibration curve. + By default `pos_label` is set to 1. + + .. versionadded:: 1.1 + + name : str, default=None + Name for labeling curve. + + ax : matplotlib axes, default=None + Axes object to plot on. If `None`, a new figure and axes is + created. + + ref_line : bool, default=True + If `True`, plots a reference line representing a perfectly + calibrated classifier. + + **kwargs : dict + Keyword arguments to be passed to :func:`matplotlib.pyplot.plot`. + + Returns + ------- + display : :class:`~sklearn.calibration.CalibrationDisplay`. + Object that stores computed values. + + See Also + -------- + CalibrationDisplay.from_estimator : Plot calibration curve using an + estimator and data. + + Examples + -------- + >>> import matplotlib.pyplot as plt + >>> from sklearn.datasets import make_classification + >>> from sklearn.model_selection import train_test_split + >>> from sklearn.linear_model import LogisticRegression + >>> from sklearn.calibration import CalibrationDisplay + >>> X, y = make_classification(random_state=0) + >>> X_train, X_test, y_train, y_test = train_test_split( + ... X, y, random_state=0) + >>> clf = LogisticRegression(random_state=0) + >>> clf.fit(X_train, y_train) + LogisticRegression(random_state=0) + >>> y_prob = clf.predict_proba(X_test)[:, 1] + >>> disp = CalibrationDisplay.from_predictions(y_test, y_prob) + >>> plt.show() + """ + pos_label_validated, name = cls._validate_from_predictions_params( + y_true, y_prob, sample_weight=None, pos_label=pos_label, name=name + ) + + prob_true, prob_pred = calibration_curve( + y_true, y_prob, n_bins=n_bins, strategy=strategy, pos_label=pos_label + ) + + disp = cls( + prob_true=prob_true, + prob_pred=prob_pred, + y_prob=y_prob, + estimator_name=name, + pos_label=pos_label_validated, + ) + return disp.plot(ax=ax, ref_line=ref_line, **kwargs) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..de86a59e07113dcc7f9c656e65c7708ee230afa6 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/__init__.py @@ -0,0 +1,56 @@ +"""Popular unsupervised clustering algorithms.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +from ._affinity_propagation import AffinityPropagation, affinity_propagation +from ._agglomerative import ( + AgglomerativeClustering, + FeatureAgglomeration, + linkage_tree, + ward_tree, +) +from ._bicluster import SpectralBiclustering, SpectralCoclustering +from ._birch import Birch +from ._bisect_k_means import BisectingKMeans +from ._dbscan import DBSCAN, dbscan +from ._hdbscan.hdbscan import HDBSCAN +from ._kmeans import KMeans, MiniBatchKMeans, k_means, kmeans_plusplus +from ._mean_shift import MeanShift, estimate_bandwidth, get_bin_seeds, mean_shift +from ._optics import ( + OPTICS, + cluster_optics_dbscan, + cluster_optics_xi, + compute_optics_graph, +) +from ._spectral import SpectralClustering, spectral_clustering + +__all__ = [ + "DBSCAN", + "HDBSCAN", + "OPTICS", + "AffinityPropagation", + "AgglomerativeClustering", + "Birch", + "BisectingKMeans", + "FeatureAgglomeration", + "KMeans", + "MeanShift", + "MiniBatchKMeans", + "SpectralBiclustering", + "SpectralClustering", + "SpectralCoclustering", + "affinity_propagation", + "cluster_optics_dbscan", + "cluster_optics_xi", + "compute_optics_graph", + "dbscan", + "estimate_bandwidth", + "get_bin_seeds", + "k_means", + "kmeans_plusplus", + "linkage_tree", + "mean_shift", + "spectral_clustering", + "ward_tree", +] diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_affinity_propagation.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_affinity_propagation.py new file mode 100644 index 0000000000000000000000000000000000000000..c7ae6ed63580d60eb2d889c11cfe84875380c55c --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_affinity_propagation.py @@ -0,0 +1,607 @@ +"""Affinity Propagation clustering algorithm.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from numbers import Integral, Real + +import numpy as np + +from .._config import config_context +from ..base import BaseEstimator, ClusterMixin, _fit_context +from ..exceptions import ConvergenceWarning +from ..metrics import euclidean_distances, pairwise_distances_argmin +from ..utils import check_random_state +from ..utils._param_validation import Interval, StrOptions, validate_params +from ..utils.validation import check_is_fitted, validate_data + + +def _equal_similarities_and_preferences(S, preference): + def all_equal_preferences(): + return np.all(preference == preference.flat[0]) + + def all_equal_similarities(): + # Create mask to ignore diagonal of S + mask = np.ones(S.shape, dtype=bool) + np.fill_diagonal(mask, 0) + + return np.all(S[mask].flat == S[mask].flat[0]) + + return all_equal_preferences() and all_equal_similarities() + + +def _affinity_propagation( + S, + *, + preference, + convergence_iter, + max_iter, + damping, + verbose, + return_n_iter, + random_state, +): + """Main affinity propagation algorithm.""" + n_samples = S.shape[0] + if n_samples == 1 or _equal_similarities_and_preferences(S, preference): + # It makes no sense to run the algorithm in this case, so return 1 or + # n_samples clusters, depending on preferences + warnings.warn( + "All samples have mutually equal similarities. " + "Returning arbitrary cluster center(s)." + ) + if preference.flat[0] > S.flat[n_samples - 1]: + return ( + (np.arange(n_samples), np.arange(n_samples), 0) + if return_n_iter + else (np.arange(n_samples), np.arange(n_samples)) + ) + else: + return ( + (np.array([0]), np.array([0] * n_samples), 0) + if return_n_iter + else (np.array([0]), np.array([0] * n_samples)) + ) + + # Place preference on the diagonal of S + S.flat[:: (n_samples + 1)] = preference + + A = np.zeros((n_samples, n_samples)) + R = np.zeros((n_samples, n_samples)) # Initialize messages + # Intermediate results + tmp = np.zeros((n_samples, n_samples)) + + # Remove degeneracies + S += ( + np.finfo(S.dtype).eps * S + np.finfo(S.dtype).tiny * 100 + ) * random_state.standard_normal(size=(n_samples, n_samples)) + + # Execute parallel affinity propagation updates + e = np.zeros((n_samples, convergence_iter)) + + ind = np.arange(n_samples) + + for it in range(max_iter): + # tmp = A + S; compute responsibilities + np.add(A, S, tmp) + I = np.argmax(tmp, axis=1) + Y = tmp[ind, I] # np.max(A + S, axis=1) + tmp[ind, I] = -np.inf + Y2 = np.max(tmp, axis=1) + + # tmp = Rnew + np.subtract(S, Y[:, None], tmp) + tmp[ind, I] = S[ind, I] - Y2 + + # Damping + tmp *= 1 - damping + R *= damping + R += tmp + + # tmp = Rp; compute availabilities + np.maximum(R, 0, tmp) + tmp.flat[:: n_samples + 1] = R.flat[:: n_samples + 1] + + # tmp = -Anew + tmp -= np.sum(tmp, axis=0) + dA = np.diag(tmp).copy() + tmp.clip(0, np.inf, tmp) + tmp.flat[:: n_samples + 1] = dA + + # Damping + tmp *= 1 - damping + A *= damping + A -= tmp + + # Check for convergence + E = (np.diag(A) + np.diag(R)) > 0 + e[:, it % convergence_iter] = E + K = np.sum(E, axis=0) + + if it >= convergence_iter: + se = np.sum(e, axis=1) + unconverged = np.sum((se == convergence_iter) + (se == 0)) != n_samples + if (not unconverged and (K > 0)) or (it == max_iter): + never_converged = False + if verbose: + print("Converged after %d iterations." % it) + break + else: + never_converged = True + if verbose: + print("Did not converge") + + I = np.flatnonzero(E) + K = I.size # Identify exemplars + + if K > 0: + if never_converged: + warnings.warn( + ( + "Affinity propagation did not converge, this model " + "may return degenerate cluster centers and labels." + ), + ConvergenceWarning, + ) + c = np.argmax(S[:, I], axis=1) + c[I] = np.arange(K) # Identify clusters + # Refine the final set of exemplars and clusters and return results + for k in range(K): + ii = np.asarray(c == k).nonzero()[0] + j = np.argmax(np.sum(S[ii[:, np.newaxis], ii], axis=0)) + I[k] = ii[j] + + c = np.argmax(S[:, I], axis=1) + c[I] = np.arange(K) + labels = I[c] + # Reduce labels to a sorted, gapless, list + cluster_centers_indices = np.unique(labels) + labels = np.searchsorted(cluster_centers_indices, labels) + else: + warnings.warn( + ( + "Affinity propagation did not converge and this model " + "will not have any cluster centers." + ), + ConvergenceWarning, + ) + labels = np.array([-1] * n_samples) + cluster_centers_indices = [] + + if return_n_iter: + return cluster_centers_indices, labels, it + 1 + else: + return cluster_centers_indices, labels + + +############################################################################### +# Public API + + +@validate_params( + { + "S": ["array-like"], + "return_n_iter": ["boolean"], + }, + prefer_skip_nested_validation=False, +) +def affinity_propagation( + S, + *, + preference=None, + convergence_iter=15, + max_iter=200, + damping=0.5, + copy=True, + verbose=False, + return_n_iter=False, + random_state=None, +): + """Perform Affinity Propagation Clustering of data. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + S : array-like of shape (n_samples, n_samples) + Matrix of similarities between points. + + preference : array-like of shape (n_samples,) or float, default=None + Preferences for each point - points with larger values of + preferences are more likely to be chosen as exemplars. The number of + exemplars, i.e. of clusters, is influenced by the input preferences + value. If the preferences are not passed as arguments, they will be + set to the median of the input similarities (resulting in a moderate + number of clusters). For a smaller amount of clusters, this can be set + to the minimum value of the similarities. + + convergence_iter : int, default=15 + Number of iterations with no change in the number + of estimated clusters that stops the convergence. + + max_iter : int, default=200 + Maximum number of iterations. + + damping : float, default=0.5 + Damping factor between 0.5 and 1. + + copy : bool, default=True + If copy is False, the affinity matrix is modified inplace by the + algorithm, for memory efficiency. + + verbose : bool, default=False + The verbosity level. + + return_n_iter : bool, default=False + Whether or not to return the number of iterations. + + random_state : int, RandomState instance or None, default=None + Pseudo-random number generator to control the starting state. + Use an int for reproducible results across function calls. + See the :term:`Glossary `. + + .. versionadded:: 0.23 + this parameter was previously hardcoded as 0. + + Returns + ------- + cluster_centers_indices : ndarray of shape (n_clusters,) + Index of clusters centers. + + labels : ndarray of shape (n_samples,) + Cluster labels for each point. + + n_iter : int + Number of iterations run. Returned only if `return_n_iter` is + set to True. + + Notes + ----- + For an example usage, + see :ref:`sphx_glr_auto_examples_cluster_plot_affinity_propagation.py`. + You may also check out, + :ref:`sphx_glr_auto_examples_applications_plot_stock_market.py` + + When the algorithm does not converge, it will still return a arrays of + ``cluster_center_indices`` and labels if there are any exemplars/clusters, + however they may be degenerate and should be used with caution. + + When all training samples have equal similarities and equal preferences, + the assignment of cluster centers and labels depends on the preference. + If the preference is smaller than the similarities, a single cluster center + and label ``0`` for every sample will be returned. Otherwise, every + training sample becomes its own cluster center and is assigned a unique + label. + + References + ---------- + Brendan J. Frey and Delbert Dueck, "Clustering by Passing Messages + Between Data Points", Science Feb. 2007 + + Examples + -------- + >>> import numpy as np + >>> from sklearn.cluster import affinity_propagation + >>> from sklearn.metrics.pairwise import euclidean_distances + >>> X = np.array([[1, 2], [1, 4], [1, 0], + ... [4, 2], [4, 4], [4, 0]]) + >>> S = -euclidean_distances(X, squared=True) + >>> cluster_centers_indices, labels = affinity_propagation(S, random_state=0) + >>> cluster_centers_indices + array([0, 3]) + >>> labels + array([0, 0, 0, 1, 1, 1]) + """ + estimator = AffinityPropagation( + damping=damping, + max_iter=max_iter, + convergence_iter=convergence_iter, + copy=copy, + preference=preference, + affinity="precomputed", + verbose=verbose, + random_state=random_state, + ).fit(S) + + if return_n_iter: + return estimator.cluster_centers_indices_, estimator.labels_, estimator.n_iter_ + return estimator.cluster_centers_indices_, estimator.labels_ + + +class AffinityPropagation(ClusterMixin, BaseEstimator): + """Perform Affinity Propagation Clustering of data. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + damping : float, default=0.5 + Damping factor in the range `[0.5, 1.0)` is the extent to + which the current value is maintained relative to + incoming values (weighted 1 - damping). This in order + to avoid numerical oscillations when updating these + values (messages). + + max_iter : int, default=200 + Maximum number of iterations. + + convergence_iter : int, default=15 + Number of iterations with no change in the number + of estimated clusters that stops the convergence. + + copy : bool, default=True + Make a copy of input data. + + preference : array-like of shape (n_samples,) or float, default=None + Preferences for each point - points with larger values of + preferences are more likely to be chosen as exemplars. The number + of exemplars, ie of clusters, is influenced by the input + preferences value. If the preferences are not passed as arguments, + they will be set to the median of the input similarities. + + affinity : {'euclidean', 'precomputed'}, default='euclidean' + Which affinity to use. At the moment 'precomputed' and + ``euclidean`` are supported. 'euclidean' uses the + negative squared euclidean distance between points. + + verbose : bool, default=False + Whether to be verbose. + + random_state : int, RandomState instance or None, default=None + Pseudo-random number generator to control the starting state. + Use an int for reproducible results across function calls. + See the :term:`Glossary `. + + .. versionadded:: 0.23 + this parameter was previously hardcoded as 0. + + Attributes + ---------- + cluster_centers_indices_ : ndarray of shape (n_clusters,) + Indices of cluster centers. + + cluster_centers_ : ndarray of shape (n_clusters, n_features) + Cluster centers (if affinity != ``precomputed``). + + labels_ : ndarray of shape (n_samples,) + Labels of each point. + + affinity_matrix_ : ndarray of shape (n_samples, n_samples) + Stores the affinity matrix used in ``fit``. + + n_iter_ : int + Number of iterations taken to converge. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + AgglomerativeClustering : Recursively merges the pair of + clusters that minimally increases a given linkage distance. + FeatureAgglomeration : Similar to AgglomerativeClustering, + but recursively merges features instead of samples. + KMeans : K-Means clustering. + MiniBatchKMeans : Mini-Batch K-Means clustering. + MeanShift : Mean shift clustering using a flat kernel. + SpectralClustering : Apply clustering to a projection + of the normalized Laplacian. + + Notes + ----- + The algorithmic complexity of affinity propagation is quadratic + in the number of points. + + When the algorithm does not converge, it will still return a arrays of + ``cluster_center_indices`` and labels if there are any exemplars/clusters, + however they may be degenerate and should be used with caution. + + When ``fit`` does not converge, ``cluster_centers_`` is still populated + however it may be degenerate. In such a case, proceed with caution. + If ``fit`` does not converge and fails to produce any ``cluster_centers_`` + then ``predict`` will label every sample as ``-1``. + + When all training samples have equal similarities and equal preferences, + the assignment of cluster centers and labels depends on the preference. + If the preference is smaller than the similarities, ``fit`` will result in + a single cluster center and label ``0`` for every sample. Otherwise, every + training sample becomes its own cluster center and is assigned a unique + label. + + References + ---------- + + Brendan J. Frey and Delbert Dueck, "Clustering by Passing Messages + Between Data Points", Science Feb. 2007 + + Examples + -------- + >>> from sklearn.cluster import AffinityPropagation + >>> import numpy as np + >>> X = np.array([[1, 2], [1, 4], [1, 0], + ... [4, 2], [4, 4], [4, 0]]) + >>> clustering = AffinityPropagation(random_state=5).fit(X) + >>> clustering + AffinityPropagation(random_state=5) + >>> clustering.labels_ + array([0, 0, 0, 1, 1, 1]) + >>> clustering.predict([[0, 0], [4, 4]]) + array([0, 1]) + >>> clustering.cluster_centers_ + array([[1, 2], + [4, 2]]) + + For an example usage, + see :ref:`sphx_glr_auto_examples_cluster_plot_affinity_propagation.py`. + + For a comparison of Affinity Propagation with other clustering algorithms, see + :ref:`sphx_glr_auto_examples_cluster_plot_cluster_comparison.py` + """ + + _parameter_constraints: dict = { + "damping": [Interval(Real, 0.5, 1.0, closed="left")], + "max_iter": [Interval(Integral, 1, None, closed="left")], + "convergence_iter": [Interval(Integral, 1, None, closed="left")], + "copy": ["boolean"], + "preference": [ + "array-like", + Interval(Real, None, None, closed="neither"), + None, + ], + "affinity": [StrOptions({"euclidean", "precomputed"})], + "verbose": ["verbose"], + "random_state": ["random_state"], + } + + def __init__( + self, + *, + damping=0.5, + max_iter=200, + convergence_iter=15, + copy=True, + preference=None, + affinity="euclidean", + verbose=False, + random_state=None, + ): + self.damping = damping + self.max_iter = max_iter + self.convergence_iter = convergence_iter + self.copy = copy + self.verbose = verbose + self.preference = preference + self.affinity = affinity + self.random_state = random_state + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.pairwise = self.affinity == "precomputed" + tags.input_tags.sparse = self.affinity != "precomputed" + return tags + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the clustering from features, or affinity matrix. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features), or \ + array-like of shape (n_samples, n_samples) + Training instances to cluster, or similarities / affinities between + instances if ``affinity='precomputed'``. If a sparse feature matrix + is provided, it will be converted into a sparse ``csr_matrix``. + + y : Ignored + Not used, present here for API consistency by convention. + + Returns + ------- + self + Returns the instance itself. + """ + if self.affinity == "precomputed": + X = validate_data(self, X, copy=self.copy, force_writeable=True) + self.affinity_matrix_ = X + else: # self.affinity == "euclidean" + X = validate_data(self, X, accept_sparse="csr") + self.affinity_matrix_ = -euclidean_distances(X, squared=True) + + if self.affinity_matrix_.shape[0] != self.affinity_matrix_.shape[1]: + raise ValueError( + "The matrix of similarities must be a square array. " + f"Got {self.affinity_matrix_.shape} instead." + ) + + if self.preference is None: + preference = np.median(self.affinity_matrix_) + else: + preference = self.preference + preference = np.asarray(preference) + + random_state = check_random_state(self.random_state) + + ( + self.cluster_centers_indices_, + self.labels_, + self.n_iter_, + ) = _affinity_propagation( + self.affinity_matrix_, + max_iter=self.max_iter, + convergence_iter=self.convergence_iter, + preference=preference, + damping=self.damping, + verbose=self.verbose, + return_n_iter=True, + random_state=random_state, + ) + + if self.affinity != "precomputed": + self.cluster_centers_ = X[self.cluster_centers_indices_].copy() + + return self + + def predict(self, X): + """Predict the closest cluster each sample in X belongs to. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + New data to predict. If a sparse matrix is provided, it will be + converted into a sparse ``csr_matrix``. + + Returns + ------- + labels : ndarray of shape (n_samples,) + Cluster labels. + """ + check_is_fitted(self) + X = validate_data(self, X, reset=False, accept_sparse="csr") + if not hasattr(self, "cluster_centers_"): + raise ValueError( + "Predict method is not supported when affinity='precomputed'." + ) + + if self.cluster_centers_.shape[0] > 0: + with config_context(assume_finite=True): + return pairwise_distances_argmin(X, self.cluster_centers_) + else: + warnings.warn( + ( + "This model does not have any cluster centers " + "because affinity propagation did not converge. " + "Labeling every sample as '-1'." + ), + ConvergenceWarning, + ) + return np.array([-1] * X.shape[0]) + + def fit_predict(self, X, y=None): + """Fit clustering from features/affinity matrix; return cluster labels. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features), or \ + array-like of shape (n_samples, n_samples) + Training instances to cluster, or similarities / affinities between + instances if ``affinity='precomputed'``. If a sparse feature matrix + is provided, it will be converted into a sparse ``csr_matrix``. + + y : Ignored + Not used, present here for API consistency by convention. + + Returns + ------- + labels : ndarray of shape (n_samples,) + Cluster labels. + """ + return super().fit_predict(X, y) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_agglomerative.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_agglomerative.py new file mode 100644 index 0000000000000000000000000000000000000000..f068dc934151d0f4a03f32000fb79e2d657f45a2 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_agglomerative.py @@ -0,0 +1,1333 @@ +"""Hierarchical Agglomerative Clustering + +These routines perform some hierarchical agglomerative clustering of some +input data. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from heapq import heapify, heappop, heappush, heappushpop +from numbers import Integral, Real + +import numpy as np +from scipy import sparse +from scipy.sparse.csgraph import connected_components + +from ..base import ( + BaseEstimator, + ClassNamePrefixFeaturesOutMixin, + ClusterMixin, + _fit_context, +) +from ..metrics import DistanceMetric +from ..metrics._dist_metrics import METRIC_MAPPING64 +from ..metrics.pairwise import _VALID_METRICS, paired_distances +from ..utils import check_array +from ..utils._fast_dict import IntFloatDict +from ..utils._param_validation import ( + HasMethods, + Interval, + StrOptions, + validate_params, +) +from ..utils.graph import _fix_connected_components +from ..utils.validation import check_memory, validate_data + +# mypy error: Module 'sklearn.cluster' has no attribute '_hierarchical_fast' +from . import _hierarchical_fast as _hierarchical # type: ignore[attr-defined] +from ._feature_agglomeration import AgglomerationTransform + +############################################################################### +# For non fully-connected graphs + + +def _fix_connectivity(X, connectivity, affinity): + """ + Fixes the connectivity matrix. + + The different steps are: + + - copies it + - makes it symmetric + - converts it to LIL if necessary + - completes it if necessary. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Feature matrix representing `n_samples` samples to be clustered. + + connectivity : sparse matrix, default=None + Connectivity matrix. Defines for each sample the neighboring samples + following a given structure of the data. The matrix is assumed to + be symmetric and only the upper triangular half is used. + Default is `None`, i.e, the Ward algorithm is unstructured. + + affinity : {"euclidean", "precomputed"}, default="euclidean" + Which affinity to use. At the moment `precomputed` and + ``euclidean`` are supported. `euclidean` uses the + negative squared Euclidean distance between points. + + Returns + ------- + connectivity : sparse matrix + The fixed connectivity matrix. + + n_connected_components : int + The number of connected components in the graph. + """ + n_samples = X.shape[0] + if connectivity.shape[0] != n_samples or connectivity.shape[1] != n_samples: + raise ValueError( + "Wrong shape for connectivity matrix: %s when X is %s" + % (connectivity.shape, X.shape) + ) + + # Make the connectivity matrix symmetric: + connectivity = connectivity + connectivity.T + + # Convert connectivity matrix to LIL + if not sparse.issparse(connectivity): + connectivity = sparse.lil_matrix(connectivity) + + # `connectivity` is a sparse matrix at this point + if connectivity.format != "lil": + connectivity = connectivity.tolil() + + # Compute the number of nodes + n_connected_components, labels = connected_components(connectivity) + + if n_connected_components > 1: + warnings.warn( + "the number of connected components of the " + "connectivity matrix is %d > 1. Completing it to avoid " + "stopping the tree early." % n_connected_components, + stacklevel=2, + ) + # XXX: Can we do without completing the matrix? + connectivity = _fix_connected_components( + X=X, + graph=connectivity, + n_connected_components=n_connected_components, + component_labels=labels, + metric=affinity, + mode="connectivity", + ) + + return connectivity, n_connected_components + + +def _single_linkage_tree( + connectivity, + n_samples, + n_nodes, + n_clusters, + n_connected_components, + return_distance, +): + """ + Perform single linkage clustering on sparse data via the minimum + spanning tree from scipy.sparse.csgraph, then using union-find to label. + The parent array is then generated by walking through the tree. + """ + from scipy.sparse.csgraph import minimum_spanning_tree + + # explicitly cast connectivity to ensure safety + connectivity = connectivity.astype(np.float64, copy=False) + + # Ensure zero distances aren't ignored by setting them to "epsilon" + epsilon_value = np.finfo(dtype=connectivity.data.dtype).eps + connectivity.data[connectivity.data == 0] = epsilon_value + + # Use scipy.sparse.csgraph to generate a minimum spanning tree + mst = minimum_spanning_tree(connectivity.tocsr()) + + # Convert the graph to scipy.cluster.hierarchy array format + mst = mst.tocoo() + + # Undo the epsilon values + mst.data[mst.data == epsilon_value] = 0 + + mst_array = np.vstack([mst.row, mst.col, mst.data]).T + + # Sort edges of the min_spanning_tree by weight + mst_array = mst_array[np.argsort(mst_array.T[2], kind="mergesort"), :] + + # Convert edge list into standard hierarchical clustering format + single_linkage_tree = _hierarchical._single_linkage_label(mst_array) + children_ = single_linkage_tree[:, :2].astype(int) + + # Compute parents + parent = np.arange(n_nodes, dtype=np.intp) + for i, (left, right) in enumerate(children_, n_samples): + if n_clusters is not None and i >= n_nodes: + break + if left < n_nodes: + parent[left] = i + if right < n_nodes: + parent[right] = i + + if return_distance: + distances = single_linkage_tree[:, 2] + return children_, n_connected_components, n_samples, parent, distances + return children_, n_connected_components, n_samples, parent + + +############################################################################### +# Hierarchical tree building functions + + +@validate_params( + { + "X": ["array-like"], + "connectivity": ["array-like", "sparse matrix", None], + "n_clusters": [Interval(Integral, 1, None, closed="left"), None], + "return_distance": ["boolean"], + }, + prefer_skip_nested_validation=True, +) +def ward_tree(X, *, connectivity=None, n_clusters=None, return_distance=False): + """Ward clustering based on a Feature matrix. + + Recursively merges the pair of clusters that minimally increases + within-cluster variance. + + The inertia matrix uses a Heapq-based representation. + + This is the structured version, that takes into account some topological + structure between samples. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Feature matrix representing `n_samples` samples to be clustered. + + connectivity : {array-like, sparse matrix}, default=None + Connectivity matrix. Defines for each sample the neighboring samples + following a given structure of the data. The matrix is assumed to + be symmetric and only the upper triangular half is used. + Default is None, i.e, the Ward algorithm is unstructured. + + n_clusters : int, default=None + `n_clusters` should be less than `n_samples`. Stop early the + construction of the tree at `n_clusters.` This is useful to decrease + computation time if the number of clusters is not small compared to the + number of samples. In this case, the complete tree is not computed, thus + the 'children' output is of limited use, and the 'parents' output should + rather be used. This option is valid only when specifying a connectivity + matrix. + + return_distance : bool, default=False + If `True`, return the distance between the clusters. + + Returns + ------- + children : ndarray of shape (n_nodes-1, 2) + The children of each non-leaf node. Values less than `n_samples` + correspond to leaves of the tree which are the original samples. + A node `i` greater than or equal to `n_samples` is a non-leaf + node and has children `children_[i - n_samples]`. Alternatively + at the i-th iteration, children[i][0] and children[i][1] + are merged to form node `n_samples + i`. + + n_connected_components : int + The number of connected components in the graph. + + n_leaves : int + The number of leaves in the tree. + + parents : ndarray of shape (n_nodes,) or None + The parent of each node. Only returned when a connectivity matrix + is specified, elsewhere 'None' is returned. + + distances : ndarray of shape (n_nodes-1,) + Only returned if `return_distance` is set to `True` (for compatibility). + The distances between the centers of the nodes. `distances[i]` + corresponds to a weighted Euclidean distance between + the nodes `children[i, 1]` and `children[i, 2]`. If the nodes refer to + leaves of the tree, then `distances[i]` is their unweighted Euclidean + distance. Distances are updated in the following way + (from scipy.hierarchy.linkage): + + The new entry :math:`d(u,v)` is computed as follows, + + .. math:: + + d(u,v) = \\sqrt{\\frac{|v|+|s|} + {T}d(v,s)^2 + + \\frac{|v|+|t|} + {T}d(v,t)^2 + - \\frac{|v|} + {T}d(s,t)^2} + + where :math:`u` is the newly joined cluster consisting of + clusters :math:`s` and :math:`t`, :math:`v` is an unused + cluster in the forest, :math:`T=|v|+|s|+|t|`, and + :math:`|*|` is the cardinality of its argument. This is also + known as the incremental algorithm. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.cluster import ward_tree + >>> X = np.array([[1, 2], [1, 4], [1, 0], + ... [4, 2], [4, 4], [4, 0]]) + >>> children, n_connected_components, n_leaves, parents = ward_tree(X) + >>> children + array([[0, 1], + [3, 5], + [2, 6], + [4, 7], + [8, 9]]) + >>> n_connected_components + 1 + >>> n_leaves + 6 + """ + X = np.asarray(X) + if X.ndim == 1: + X = np.reshape(X, (-1, 1)) + n_samples, n_features = X.shape + + if connectivity is None: + from scipy.cluster import hierarchy # imports PIL + + if n_clusters is not None: + warnings.warn( + ( + "Partial build of the tree is implemented " + "only for structured clustering (i.e. with " + "explicit connectivity). The algorithm " + "will build the full tree and only " + "retain the lower branches required " + "for the specified number of clusters" + ), + stacklevel=2, + ) + X = np.require(X, requirements="W") + out = hierarchy.ward(X) + children_ = out[:, :2].astype(np.intp) + + if return_distance: + distances = out[:, 2] + return children_, 1, n_samples, None, distances + else: + return children_, 1, n_samples, None + + connectivity, n_connected_components = _fix_connectivity( + X, connectivity, affinity="euclidean" + ) + if n_clusters is None: + n_nodes = 2 * n_samples - 1 + else: + if n_clusters > n_samples: + raise ValueError( + "Cannot provide more clusters than samples. " + "%i n_clusters was asked, and there are %i " + "samples." % (n_clusters, n_samples) + ) + n_nodes = 2 * n_samples - n_clusters + + # create inertia matrix + coord_row = [] + coord_col = [] + A = [] + for ind, row in enumerate(connectivity.rows): + A.append(row) + # We keep only the upper triangular for the moments + # Generator expressions are faster than arrays on the following + row = [i for i in row if i < ind] + coord_row.extend( + len(row) + * [ + ind, + ] + ) + coord_col.extend(row) + + coord_row = np.array(coord_row, dtype=np.intp, order="C") + coord_col = np.array(coord_col, dtype=np.intp, order="C") + + # build moments as a list + moments_1 = np.zeros(n_nodes, order="C") + moments_1[:n_samples] = 1 + moments_2 = np.zeros((n_nodes, n_features), order="C") + moments_2[:n_samples] = X + inertia = np.empty(len(coord_row), dtype=np.float64, order="C") + _hierarchical.compute_ward_dist(moments_1, moments_2, coord_row, coord_col, inertia) + inertia = list(zip(inertia, coord_row, coord_col)) + heapify(inertia) + + # prepare the main fields + parent = np.arange(n_nodes, dtype=np.intp) + used_node = np.ones(n_nodes, dtype=bool) + children = [] + if return_distance: + distances = np.empty(n_nodes - n_samples) + + not_visited = np.empty(n_nodes, dtype=bool, order="C") + + # recursive merge loop + for k in range(n_samples, n_nodes): + # identify the merge + while True: + inert, i, j = heappop(inertia) + if used_node[i] and used_node[j]: + break + parent[i], parent[j] = k, k + children.append((i, j)) + used_node[i] = used_node[j] = False + if return_distance: # store inertia value + distances[k - n_samples] = inert + + # update the moments + moments_1[k] = moments_1[i] + moments_1[j] + moments_2[k] = moments_2[i] + moments_2[j] + + # update the structure matrix A and the inertia matrix + coord_col = [] + not_visited.fill(1) + not_visited[k] = 0 + _hierarchical._get_parents(A[i], coord_col, parent, not_visited) + _hierarchical._get_parents(A[j], coord_col, parent, not_visited) + # List comprehension is faster than a for loop + [A[col].append(k) for col in coord_col] + A.append(coord_col) + coord_col = np.array(coord_col, dtype=np.intp, order="C") + coord_row = np.empty(coord_col.shape, dtype=np.intp, order="C") + coord_row.fill(k) + n_additions = len(coord_row) + ini = np.empty(n_additions, dtype=np.float64, order="C") + + _hierarchical.compute_ward_dist(moments_1, moments_2, coord_row, coord_col, ini) + + # List comprehension is faster than a for loop + [heappush(inertia, (ini[idx], k, coord_col[idx])) for idx in range(n_additions)] + + # Separate leaves in children (empty lists up to now) + n_leaves = n_samples + # sort children to get consistent output with unstructured version + children = [c[::-1] for c in children] + children = np.array(children) # return numpy array for efficient caching + + if return_distance: + # 2 is scaling factor to compare w/ unstructured version + distances = np.sqrt(2.0 * distances) + return children, n_connected_components, n_leaves, parent, distances + else: + return children, n_connected_components, n_leaves, parent + + +# single average and complete linkage +def linkage_tree( + X, + connectivity=None, + n_clusters=None, + linkage="complete", + affinity="euclidean", + return_distance=False, +): + """Linkage agglomerative clustering based on a Feature matrix. + + The inertia matrix uses a Heapq-based representation. + + This is the structured version, that takes into account some topological + structure between samples. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Feature matrix representing `n_samples` samples to be clustered. + + connectivity : sparse matrix, default=None + Connectivity matrix. Defines for each sample the neighboring samples + following a given structure of the data. The matrix is assumed to + be symmetric and only the upper triangular half is used. + Default is `None`, i.e, the Ward algorithm is unstructured. + + n_clusters : int, default=None + Stop early the construction of the tree at `n_clusters`. This is + useful to decrease computation time if the number of clusters is + not small compared to the number of samples. In this case, the + complete tree is not computed, thus the 'children' output is of + limited use, and the 'parents' output should rather be used. + This option is valid only when specifying a connectivity matrix. + + linkage : {"average", "complete", "single"}, default="complete" + Which linkage criteria to use. The linkage criterion determines which + distance to use between sets of observation. + - "average" uses the average of the distances of each observation of + the two sets. + - "complete" or maximum linkage uses the maximum distances between + all observations of the two sets. + - "single" uses the minimum of the distances between all + observations of the two sets. + + affinity : str or callable, default='euclidean' + Which metric to use. Can be 'euclidean', 'manhattan', or any + distance known to paired distance (see metric.pairwise). + + return_distance : bool, default=False + Whether or not to return the distances between the clusters. + + Returns + ------- + children : ndarray of shape (n_nodes-1, 2) + The children of each non-leaf node. Values less than `n_samples` + correspond to leaves of the tree which are the original samples. + A node `i` greater than or equal to `n_samples` is a non-leaf + node and has children `children_[i - n_samples]`. Alternatively + at the i-th iteration, children[i][0] and children[i][1] + are merged to form node `n_samples + i`. + + n_connected_components : int + The number of connected components in the graph. + + n_leaves : int + The number of leaves in the tree. + + parents : ndarray of shape (n_nodes, ) or None + The parent of each node. Only returned when a connectivity matrix + is specified, elsewhere 'None' is returned. + + distances : ndarray of shape (n_nodes-1,) + Returned when `return_distance` is set to `True`. + + distances[i] refers to the distance between children[i][0] and + children[i][1] when they are merged. + + See Also + -------- + ward_tree : Hierarchical clustering with ward linkage. + """ + X = np.asarray(X) + if X.ndim == 1: + X = np.reshape(X, (-1, 1)) + n_samples, n_features = X.shape + + linkage_choices = { + "complete": _hierarchical.max_merge, + "average": _hierarchical.average_merge, + "single": None, + } # Single linkage is handled differently + try: + join_func = linkage_choices[linkage] + except KeyError as e: + raise ValueError( + "Unknown linkage option, linkage should be one of %s, but %s was given" + % (linkage_choices.keys(), linkage) + ) from e + + if affinity == "cosine" and np.any(~np.any(X, axis=1)): + raise ValueError("Cosine affinity cannot be used when X contains zero vectors") + + if connectivity is None: + from scipy.cluster import hierarchy # imports PIL + + if n_clusters is not None: + warnings.warn( + ( + "Partial build of the tree is implemented " + "only for structured clustering (i.e. with " + "explicit connectivity). The algorithm " + "will build the full tree and only " + "retain the lower branches required " + "for the specified number of clusters" + ), + stacklevel=2, + ) + + if affinity == "precomputed": + # for the linkage function of hierarchy to work on precomputed + # data, provide as first argument an ndarray of the shape returned + # by sklearn.metrics.pairwise_distances. + if X.shape[0] != X.shape[1]: + raise ValueError( + f"Distance matrix should be square, got matrix of shape {X.shape}" + ) + i, j = np.triu_indices(X.shape[0], k=1) + X = X[i, j] + elif affinity == "l2": + # Translate to something understood by scipy + affinity = "euclidean" + elif affinity in ("l1", "manhattan"): + affinity = "cityblock" + elif callable(affinity): + X = affinity(X) + i, j = np.triu_indices(X.shape[0], k=1) + X = X[i, j] + if ( + linkage == "single" + and affinity != "precomputed" + and not callable(affinity) + and affinity in METRIC_MAPPING64 + ): + # We need the fast cythonized metric from neighbors + dist_metric = DistanceMetric.get_metric(affinity) + + # The Cython routines used require contiguous arrays + X = np.ascontiguousarray(X, dtype=np.double) + + mst = _hierarchical.mst_linkage_core(X, dist_metric) + # Sort edges of the min_spanning_tree by weight + mst = mst[np.argsort(mst.T[2], kind="mergesort"), :] + + # Convert edge list into standard hierarchical clustering format + out = _hierarchical.single_linkage_label(mst) + else: + out = hierarchy.linkage(X, method=linkage, metric=affinity) + children_ = out[:, :2].astype(int, copy=False) + + if return_distance: + distances = out[:, 2] + return children_, 1, n_samples, None, distances + return children_, 1, n_samples, None + + connectivity, n_connected_components = _fix_connectivity( + X, connectivity, affinity=affinity + ) + connectivity = connectivity.tocoo() + # Put the diagonal to zero + diag_mask = connectivity.row != connectivity.col + connectivity.row = connectivity.row[diag_mask] + connectivity.col = connectivity.col[diag_mask] + connectivity.data = connectivity.data[diag_mask] + del diag_mask + + if affinity == "precomputed": + distances = X[connectivity.row, connectivity.col].astype(np.float64, copy=False) + else: + # FIXME We compute all the distances, while we could have only computed + # the "interesting" distances + distances = paired_distances( + X[connectivity.row], X[connectivity.col], metric=affinity + ) + connectivity.data = distances + + if n_clusters is None: + n_nodes = 2 * n_samples - 1 + else: + assert n_clusters <= n_samples + n_nodes = 2 * n_samples - n_clusters + + if linkage == "single": + return _single_linkage_tree( + connectivity, + n_samples, + n_nodes, + n_clusters, + n_connected_components, + return_distance, + ) + + if return_distance: + distances = np.empty(n_nodes - n_samples) + # create inertia heap and connection matrix + A = np.empty(n_nodes, dtype=object) + inertia = list() + + # LIL seems to the best format to access the rows quickly, + # without the numpy overhead of slicing CSR indices and data. + connectivity = connectivity.tolil() + # We are storing the graph in a list of IntFloatDict + for ind, (data, row) in enumerate(zip(connectivity.data, connectivity.rows)): + A[ind] = IntFloatDict( + np.asarray(row, dtype=np.intp), np.asarray(data, dtype=np.float64) + ) + # We keep only the upper triangular for the heap + # Generator expressions are faster than arrays on the following + inertia.extend( + _hierarchical.WeightedEdge(d, ind, r) for r, d in zip(row, data) if r < ind + ) + del connectivity + + heapify(inertia) + + # prepare the main fields + parent = np.arange(n_nodes, dtype=np.intp) + used_node = np.ones(n_nodes, dtype=np.intp) + children = [] + + # recursive merge loop + for k in range(n_samples, n_nodes): + # identify the merge + while True: + edge = heappop(inertia) + if used_node[edge.a] and used_node[edge.b]: + break + i = edge.a + j = edge.b + + if return_distance: + # store distances + distances[k - n_samples] = edge.weight + + parent[i] = parent[j] = k + children.append((i, j)) + # Keep track of the number of elements per cluster + n_i = used_node[i] + n_j = used_node[j] + used_node[k] = n_i + n_j + used_node[i] = used_node[j] = False + + # update the structure matrix A and the inertia matrix + # a clever 'min', or 'max' operation between A[i] and A[j] + coord_col = join_func(A[i], A[j], used_node, n_i, n_j) + for col, d in coord_col: + A[col].append(k, d) + # Here we use the information from coord_col (containing the + # distances) to update the heap + heappush(inertia, _hierarchical.WeightedEdge(d, k, col)) + A[k] = coord_col + # Clear A[i] and A[j] to save memory + A[i] = A[j] = 0 + + # Separate leaves in children (empty lists up to now) + n_leaves = n_samples + + # # return numpy array for efficient caching + children = np.array(children)[:, ::-1] + + if return_distance: + return children, n_connected_components, n_leaves, parent, distances + return children, n_connected_components, n_leaves, parent + + +# Matching names to tree-building strategies +def _complete_linkage(*args, **kwargs): + kwargs["linkage"] = "complete" + return linkage_tree(*args, **kwargs) + + +def _average_linkage(*args, **kwargs): + kwargs["linkage"] = "average" + return linkage_tree(*args, **kwargs) + + +def _single_linkage(*args, **kwargs): + kwargs["linkage"] = "single" + return linkage_tree(*args, **kwargs) + + +_TREE_BUILDERS = dict( + ward=ward_tree, + complete=_complete_linkage, + average=_average_linkage, + single=_single_linkage, +) + +############################################################################### +# Functions for cutting hierarchical clustering tree + + +def _hc_cut(n_clusters, children, n_leaves): + """Function cutting the ward tree for a given number of clusters. + + Parameters + ---------- + n_clusters : int or ndarray + The number of clusters to form. + + children : ndarray of shape (n_nodes-1, 2) + The children of each non-leaf node. Values less than `n_samples` + correspond to leaves of the tree which are the original samples. + A node `i` greater than or equal to `n_samples` is a non-leaf + node and has children `children_[i - n_samples]`. Alternatively + at the i-th iteration, children[i][0] and children[i][1] + are merged to form node `n_samples + i`. + + n_leaves : int + Number of leaves of the tree. + + Returns + ------- + labels : array [n_samples] + Cluster labels for each point. + """ + if n_clusters > n_leaves: + raise ValueError( + "Cannot extract more clusters than samples: " + f"{n_clusters} clusters were given for a tree with {n_leaves} leaves." + ) + # In this function, we store nodes as a heap to avoid recomputing + # the max of the nodes: the first element is always the smallest + # We use negated indices as heaps work on smallest elements, and we + # are interested in largest elements + # children[-1] is the root of the tree + nodes = [-(max(children[-1]) + 1)] + for _ in range(n_clusters - 1): + # As we have a heap, nodes[0] is the smallest element + these_children = children[-nodes[0] - n_leaves] + # Insert the 2 children and remove the largest node + heappush(nodes, -these_children[0]) + heappushpop(nodes, -these_children[1]) + label = np.zeros(n_leaves, dtype=np.intp) + for i, node in enumerate(nodes): + label[_hierarchical._hc_get_descendent(-node, children, n_leaves)] = i + return label + + +############################################################################### + + +class AgglomerativeClustering(ClusterMixin, BaseEstimator): + """ + Agglomerative Clustering. + + Recursively merges pair of clusters of sample data; uses linkage distance. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + n_clusters : int or None, default=2 + The number of clusters to find. It must be ``None`` if + ``distance_threshold`` is not ``None``. + + metric : str or callable, default="euclidean" + Metric used to compute the linkage. Can be "euclidean", "l1", "l2", + "manhattan", "cosine", or "precomputed". If linkage is "ward", only + "euclidean" is accepted. If "precomputed", a distance matrix is needed + as input for the fit method. If connectivity is None, linkage is + "single" and affinity is not "precomputed" any valid pairwise distance + metric can be assigned. + + For an example of agglomerative clustering with different metrics, see + :ref:`sphx_glr_auto_examples_cluster_plot_agglomerative_clustering_metrics.py`. + + .. versionadded:: 1.2 + + memory : str or object with the joblib.Memory interface, default=None + Used to cache the output of the computation of the tree. + By default, no caching is done. If a string is given, it is the + path to the caching directory. + + connectivity : array-like, sparse matrix, or callable, default=None + Connectivity matrix. Defines for each sample the neighboring + samples following a given structure of the data. + This can be a connectivity matrix itself or a callable that transforms + the data into a connectivity matrix, such as derived from + `kneighbors_graph`. Default is ``None``, i.e, the + hierarchical clustering algorithm is unstructured. + + For an example of connectivity matrix using + :class:`~sklearn.neighbors.kneighbors_graph`, see + :ref:`sphx_glr_auto_examples_cluster_plot_agglomerative_clustering.py`. + + compute_full_tree : 'auto' or bool, default='auto' + Stop early the construction of the tree at ``n_clusters``. This is + useful to decrease computation time if the number of clusters is not + small compared to the number of samples. This option is useful only + when specifying a connectivity matrix. Note also that when varying the + number of clusters and using caching, it may be advantageous to compute + the full tree. It must be ``True`` if ``distance_threshold`` is not + ``None``. By default `compute_full_tree` is "auto", which is equivalent + to `True` when `distance_threshold` is not `None` or that `n_clusters` + is inferior to the maximum between 100 or `0.02 * n_samples`. + Otherwise, "auto" is equivalent to `False`. + + linkage : {'ward', 'complete', 'average', 'single'}, default='ward' + Which linkage criterion to use. The linkage criterion determines which + distance to use between sets of observation. The algorithm will merge + the pairs of cluster that minimize this criterion. + + - 'ward' minimizes the variance of the clusters being merged. + - 'average' uses the average of the distances of each observation of + the two sets. + - 'complete' or 'maximum' linkage uses the maximum distances between + all observations of the two sets. + - 'single' uses the minimum of the distances between all observations + of the two sets. + + .. versionadded:: 0.20 + Added the 'single' option + + For examples comparing different `linkage` criteria, see + :ref:`sphx_glr_auto_examples_cluster_plot_linkage_comparison.py`. + + distance_threshold : float, default=None + The linkage distance threshold at or above which clusters will not be + merged. If not ``None``, ``n_clusters`` must be ``None`` and + ``compute_full_tree`` must be ``True``. + + .. versionadded:: 0.21 + + compute_distances : bool, default=False + Computes distances between clusters even if `distance_threshold` is not + used. This can be used to make dendrogram visualization, but introduces + a computational and memory overhead. + + .. versionadded:: 0.24 + + For an example of dendrogram visualization, see + :ref:`sphx_glr_auto_examples_cluster_plot_agglomerative_dendrogram.py`. + + Attributes + ---------- + n_clusters_ : int + The number of clusters found by the algorithm. If + ``distance_threshold=None``, it will be equal to the given + ``n_clusters``. + + labels_ : ndarray of shape (n_samples) + Cluster labels for each point. + + n_leaves_ : int + Number of leaves in the hierarchical tree. + + n_connected_components_ : int + The estimated number of connected components in the graph. + + .. versionadded:: 0.21 + ``n_connected_components_`` was added to replace ``n_components_``. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + children_ : array-like of shape (n_samples-1, 2) + The children of each non-leaf node. Values less than `n_samples` + correspond to leaves of the tree which are the original samples. + A node `i` greater than or equal to `n_samples` is a non-leaf + node and has children `children_[i - n_samples]`. Alternatively + at the i-th iteration, children[i][0] and children[i][1] + are merged to form node `n_samples + i`. + + distances_ : array-like of shape (n_nodes-1,) + Distances between nodes in the corresponding place in `children_`. + Only computed if `distance_threshold` is used or `compute_distances` + is set to `True`. + + See Also + -------- + FeatureAgglomeration : Agglomerative clustering but for features instead of + samples. + ward_tree : Hierarchical clustering with ward linkage. + + Examples + -------- + >>> from sklearn.cluster import AgglomerativeClustering + >>> import numpy as np + >>> X = np.array([[1, 2], [1, 4], [1, 0], + ... [4, 2], [4, 4], [4, 0]]) + >>> clustering = AgglomerativeClustering().fit(X) + >>> clustering + AgglomerativeClustering() + >>> clustering.labels_ + array([1, 1, 1, 0, 0, 0]) + + For a comparison of Agglomerative clustering with other clustering algorithms, see + :ref:`sphx_glr_auto_examples_cluster_plot_cluster_comparison.py` + """ + + _parameter_constraints: dict = { + "n_clusters": [Interval(Integral, 1, None, closed="left"), None], + "metric": [ + StrOptions(set(_VALID_METRICS) | {"precomputed"}), + callable, + ], + "memory": [str, HasMethods("cache"), None], + "connectivity": ["array-like", "sparse matrix", callable, None], + "compute_full_tree": [StrOptions({"auto"}), "boolean"], + "linkage": [StrOptions(set(_TREE_BUILDERS.keys()))], + "distance_threshold": [Interval(Real, 0, None, closed="left"), None], + "compute_distances": ["boolean"], + } + + def __init__( + self, + n_clusters=2, + *, + metric="euclidean", + memory=None, + connectivity=None, + compute_full_tree="auto", + linkage="ward", + distance_threshold=None, + compute_distances=False, + ): + self.n_clusters = n_clusters + self.distance_threshold = distance_threshold + self.memory = memory + self.connectivity = connectivity + self.compute_full_tree = compute_full_tree + self.linkage = linkage + self.metric = metric + self.compute_distances = compute_distances + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the hierarchical clustering from features, or distance matrix. + + Parameters + ---------- + X : array-like, shape (n_samples, n_features) or \ + (n_samples, n_samples) + Training instances to cluster, or distances between instances if + ``metric='precomputed'``. + + y : Ignored + Not used, present here for API consistency by convention. + + Returns + ------- + self : object + Returns the fitted instance. + """ + X = validate_data(self, X, ensure_min_samples=2) + return self._fit(X) + + def _fit(self, X): + """Fit without validation + + Parameters + ---------- + X : ndarray of shape (n_samples, n_features) or (n_samples, n_samples) + Training instances to cluster, or distances between instances if + ``metric='precomputed'``. + + Returns + ------- + self : object + Returns the fitted instance. + """ + memory = check_memory(self.memory) + + if not ((self.n_clusters is None) ^ (self.distance_threshold is None)): + raise ValueError( + "Exactly one of n_clusters and " + "distance_threshold has to be set, and the other " + "needs to be None." + ) + + if self.distance_threshold is not None and not self.compute_full_tree: + raise ValueError( + "compute_full_tree must be True if distance_threshold is set." + ) + + if self.linkage == "ward" and self.metric != "euclidean": + raise ValueError( + f"{self.metric} was provided as metric. Ward can only " + "work with euclidean distances." + ) + + tree_builder = _TREE_BUILDERS[self.linkage] + + connectivity = self.connectivity + if self.connectivity is not None: + if callable(self.connectivity): + connectivity = self.connectivity(X) + connectivity = check_array( + connectivity, accept_sparse=["csr", "coo", "lil"] + ) + + n_samples = len(X) + compute_full_tree = self.compute_full_tree + if self.connectivity is None: + compute_full_tree = True + if compute_full_tree == "auto": + if self.distance_threshold is not None: + compute_full_tree = True + else: + # Early stopping is likely to give a speed up only for + # a large number of clusters. The actual threshold + # implemented here is heuristic + compute_full_tree = self.n_clusters < max(100, 0.02 * n_samples) + n_clusters = self.n_clusters + if compute_full_tree: + n_clusters = None + + # Construct the tree + kwargs = {} + if self.linkage != "ward": + kwargs["linkage"] = self.linkage + kwargs["affinity"] = self.metric + + distance_threshold = self.distance_threshold + + return_distance = (distance_threshold is not None) or self.compute_distances + + out = memory.cache(tree_builder)( + X, + connectivity=connectivity, + n_clusters=n_clusters, + return_distance=return_distance, + **kwargs, + ) + (self.children_, self.n_connected_components_, self.n_leaves_, parents) = out[ + :4 + ] + + if return_distance: + self.distances_ = out[-1] + + if self.distance_threshold is not None: # distance_threshold is used + self.n_clusters_ = ( + np.count_nonzero(self.distances_ >= distance_threshold) + 1 + ) + else: # n_clusters is used + self.n_clusters_ = self.n_clusters + + # Cut the tree + if compute_full_tree: + self.labels_ = _hc_cut(self.n_clusters_, self.children_, self.n_leaves_) + else: + labels = _hierarchical.hc_get_heads(parents, copy=False) + # copy to avoid holding a reference on the original array + labels = np.copy(labels[:n_samples]) + # Reassign cluster numbers + self.labels_ = np.searchsorted(np.unique(labels), labels) + return self + + def fit_predict(self, X, y=None): + """Fit and return the result of each sample's clustering assignment. + + In addition to fitting, this method also return the result of the + clustering assignment for each sample in the training set. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) or \ + (n_samples, n_samples) + Training instances to cluster, or distances between instances if + ``affinity='precomputed'``. + + y : Ignored + Not used, present here for API consistency by convention. + + Returns + ------- + labels : ndarray of shape (n_samples,) + Cluster labels. + """ + return super().fit_predict(X, y) + + +class FeatureAgglomeration( + ClassNamePrefixFeaturesOutMixin, AgglomerationTransform, AgglomerativeClustering +): + """Agglomerate features. + + Recursively merges pair of clusters of features. + + Refer to + :ref:`sphx_glr_auto_examples_cluster_plot_feature_agglomeration_vs_univariate_selection.py` + for an example comparison of :class:`FeatureAgglomeration` strategy with a + univariate feature selection strategy (based on ANOVA). + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + n_clusters : int or None, default=2 + The number of clusters to find. It must be ``None`` if + ``distance_threshold`` is not ``None``. + + metric : str or callable, default="euclidean" + Metric used to compute the linkage. Can be "euclidean", "l1", "l2", + "manhattan", "cosine", or "precomputed". If linkage is "ward", only + "euclidean" is accepted. If "precomputed", a distance matrix is needed + as input for the fit method. + + .. versionadded:: 1.2 + + memory : str or object with the joblib.Memory interface, default=None + Used to cache the output of the computation of the tree. + By default, no caching is done. If a string is given, it is the + path to the caching directory. + + connectivity : array-like, sparse matrix, or callable, default=None + Connectivity matrix. Defines for each feature the neighboring + features following a given structure of the data. + This can be a connectivity matrix itself or a callable that transforms + the data into a connectivity matrix, such as derived from + `kneighbors_graph`. Default is `None`, i.e, the + hierarchical clustering algorithm is unstructured. + + compute_full_tree : 'auto' or bool, default='auto' + Stop early the construction of the tree at `n_clusters`. This is useful + to decrease computation time if the number of clusters is not small + compared to the number of features. This option is useful only when + specifying a connectivity matrix. Note also that when varying the + number of clusters and using caching, it may be advantageous to compute + the full tree. It must be ``True`` if ``distance_threshold`` is not + ``None``. By default `compute_full_tree` is "auto", which is equivalent + to `True` when `distance_threshold` is not `None` or that `n_clusters` + is inferior to the maximum between 100 or `0.02 * n_samples`. + Otherwise, "auto" is equivalent to `False`. + + linkage : {"ward", "complete", "average", "single"}, default="ward" + Which linkage criterion to use. The linkage criterion determines which + distance to use between sets of features. The algorithm will merge + the pairs of cluster that minimize this criterion. + + - "ward" minimizes the variance of the clusters being merged. + - "complete" or maximum linkage uses the maximum distances between + all features of the two sets. + - "average" uses the average of the distances of each feature of + the two sets. + - "single" uses the minimum of the distances between all features + of the two sets. + + pooling_func : callable, default=np.mean + This combines the values of agglomerated features into a single + value, and should accept an array of shape [M, N] and the keyword + argument `axis=1`, and reduce it to an array of size [M]. + + distance_threshold : float, default=None + The linkage distance threshold at or above which clusters will not be + merged. If not ``None``, ``n_clusters`` must be ``None`` and + ``compute_full_tree`` must be ``True``. + + .. versionadded:: 0.21 + + compute_distances : bool, default=False + Computes distances between clusters even if `distance_threshold` is not + used. This can be used to make dendrogram visualization, but introduces + a computational and memory overhead. + + .. versionadded:: 0.24 + + Attributes + ---------- + n_clusters_ : int + The number of clusters found by the algorithm. If + ``distance_threshold=None``, it will be equal to the given + ``n_clusters``. + + labels_ : array-like of (n_features,) + Cluster labels for each feature. + + n_leaves_ : int + Number of leaves in the hierarchical tree. + + n_connected_components_ : int + The estimated number of connected components in the graph. + + .. versionadded:: 0.21 + ``n_connected_components_`` was added to replace ``n_components_``. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + children_ : array-like of shape (n_nodes-1, 2) + The children of each non-leaf node. Values less than `n_features` + correspond to leaves of the tree which are the original samples. + A node `i` greater than or equal to `n_features` is a non-leaf + node and has children `children_[i - n_features]`. Alternatively + at the i-th iteration, children[i][0] and children[i][1] + are merged to form node `n_features + i`. + + distances_ : array-like of shape (n_nodes-1,) + Distances between nodes in the corresponding place in `children_`. + Only computed if `distance_threshold` is used or `compute_distances` + is set to `True`. + + See Also + -------- + AgglomerativeClustering : Agglomerative clustering samples instead of + features. + ward_tree : Hierarchical clustering with ward linkage. + + Examples + -------- + >>> import numpy as np + >>> from sklearn import datasets, cluster + >>> digits = datasets.load_digits() + >>> images = digits.images + >>> X = np.reshape(images, (len(images), -1)) + >>> agglo = cluster.FeatureAgglomeration(n_clusters=32) + >>> agglo.fit(X) + FeatureAgglomeration(n_clusters=32) + >>> X_reduced = agglo.transform(X) + >>> X_reduced.shape + (1797, 32) + """ + + _parameter_constraints: dict = { + "n_clusters": [Interval(Integral, 1, None, closed="left"), None], + "metric": [ + StrOptions(set(_VALID_METRICS) | {"precomputed"}), + callable, + ], + "memory": [str, HasMethods("cache"), None], + "connectivity": ["array-like", "sparse matrix", callable, None], + "compute_full_tree": [StrOptions({"auto"}), "boolean"], + "linkage": [StrOptions(set(_TREE_BUILDERS.keys()))], + "pooling_func": [callable], + "distance_threshold": [Interval(Real, 0, None, closed="left"), None], + "compute_distances": ["boolean"], + } + + def __init__( + self, + n_clusters=2, + *, + metric="euclidean", + memory=None, + connectivity=None, + compute_full_tree="auto", + linkage="ward", + pooling_func=np.mean, + distance_threshold=None, + compute_distances=False, + ): + super().__init__( + n_clusters=n_clusters, + memory=memory, + connectivity=connectivity, + compute_full_tree=compute_full_tree, + linkage=linkage, + metric=metric, + distance_threshold=distance_threshold, + compute_distances=compute_distances, + ) + self.pooling_func = pooling_func + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the hierarchical clustering on the data. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The data. + + y : Ignored + Not used, present here for API consistency by convention. + + Returns + ------- + self : object + Returns the transformer. + """ + X = validate_data(self, X, ensure_min_features=2) + super()._fit(X.T) + self._n_features_out = self.n_clusters_ + return self + + @property + def fit_predict(self): + """Fit and return the result of each sample's clustering assignment.""" + raise AttributeError diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_bicluster.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_bicluster.py new file mode 100644 index 0000000000000000000000000000000000000000..04a4e68024d33350b9fdd844f6bc614e4c22f39a --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_bicluster.py @@ -0,0 +1,621 @@ +"""Spectral biclustering algorithms.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +from abc import ABCMeta, abstractmethod +from numbers import Integral + +import numpy as np +from scipy.linalg import norm +from scipy.sparse import dia_matrix, issparse +from scipy.sparse.linalg import eigsh, svds + +from ..base import BaseEstimator, BiclusterMixin, _fit_context +from ..utils import check_random_state, check_scalar +from ..utils._param_validation import Interval, StrOptions +from ..utils.extmath import _randomized_svd, make_nonnegative, safe_sparse_dot +from ..utils.validation import assert_all_finite, validate_data +from ._kmeans import KMeans, MiniBatchKMeans + +__all__ = ["SpectralBiclustering", "SpectralCoclustering"] + + +def _scale_normalize(X): + """Normalize ``X`` by scaling rows and columns independently. + + Returns the normalized matrix and the row and column scaling + factors. + """ + X = make_nonnegative(X) + row_diag = np.asarray(1.0 / np.sqrt(X.sum(axis=1))).squeeze() + col_diag = np.asarray(1.0 / np.sqrt(X.sum(axis=0))).squeeze() + row_diag = np.where(np.isnan(row_diag), 0, row_diag) + col_diag = np.where(np.isnan(col_diag), 0, col_diag) + if issparse(X): + n_rows, n_cols = X.shape + r = dia_matrix((row_diag, [0]), shape=(n_rows, n_rows)) + c = dia_matrix((col_diag, [0]), shape=(n_cols, n_cols)) + an = r @ X @ c + else: + an = row_diag[:, np.newaxis] * X * col_diag + return an, row_diag, col_diag + + +def _bistochastic_normalize(X, max_iter=1000, tol=1e-5): + """Normalize rows and columns of ``X`` simultaneously so that all + rows sum to one constant and all columns sum to a different + constant. + """ + # According to paper, this can also be done more efficiently with + # deviation reduction and balancing algorithms. + X = make_nonnegative(X) + X_scaled = X + for _ in range(max_iter): + X_new, _, _ = _scale_normalize(X_scaled) + if issparse(X): + dist = norm(X_scaled.data - X.data) + else: + dist = norm(X_scaled - X_new) + X_scaled = X_new + if dist is not None and dist < tol: + break + return X_scaled + + +def _log_normalize(X): + """Normalize ``X`` according to Kluger's log-interactions scheme.""" + X = make_nonnegative(X, min_value=1) + if issparse(X): + raise ValueError( + "Cannot compute log of a sparse matrix," + " because log(x) diverges to -infinity as x" + " goes to 0." + ) + L = np.log(X) + row_avg = L.mean(axis=1)[:, np.newaxis] + col_avg = L.mean(axis=0) + avg = L.mean() + return L - row_avg - col_avg + avg + + +class BaseSpectral(BiclusterMixin, BaseEstimator, metaclass=ABCMeta): + """Base class for spectral biclustering.""" + + _parameter_constraints: dict = { + "svd_method": [StrOptions({"randomized", "arpack"})], + "n_svd_vecs": [Interval(Integral, 0, None, closed="left"), None], + "mini_batch": ["boolean"], + "init": [StrOptions({"k-means++", "random"}), np.ndarray], + "n_init": [Interval(Integral, 1, None, closed="left")], + "random_state": ["random_state"], + } + + @abstractmethod + def __init__( + self, + n_clusters=3, + svd_method="randomized", + n_svd_vecs=None, + mini_batch=False, + init="k-means++", + n_init=10, + random_state=None, + ): + self.n_clusters = n_clusters + self.svd_method = svd_method + self.n_svd_vecs = n_svd_vecs + self.mini_batch = mini_batch + self.init = init + self.n_init = n_init + self.random_state = random_state + + @abstractmethod + def _check_parameters(self, n_samples): + """Validate parameters depending on the input data.""" + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Create a biclustering for X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data. + + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + self : object + SpectralBiclustering instance. + """ + X = validate_data(self, X, accept_sparse="csr", dtype=np.float64) + self._check_parameters(X.shape[0]) + self._fit(X) + return self + + def _svd(self, array, n_components, n_discard): + """Returns first `n_components` left and right singular + vectors u and v, discarding the first `n_discard`. + """ + if self.svd_method == "randomized": + kwargs = {} + if self.n_svd_vecs is not None: + kwargs["n_oversamples"] = self.n_svd_vecs + u, _, vt = _randomized_svd( + array, n_components, random_state=self.random_state, **kwargs + ) + + elif self.svd_method == "arpack": + u, _, vt = svds(array, k=n_components, ncv=self.n_svd_vecs) + if np.any(np.isnan(vt)): + # some eigenvalues of A * A.T are negative, causing + # sqrt() to be np.nan. This causes some vectors in vt + # to be np.nan. + A = safe_sparse_dot(array.T, array) + random_state = check_random_state(self.random_state) + # initialize with [-1,1] as in ARPACK + v0 = random_state.uniform(-1, 1, A.shape[0]) + _, v = eigsh(A, ncv=self.n_svd_vecs, v0=v0) + vt = v.T + if np.any(np.isnan(u)): + A = safe_sparse_dot(array, array.T) + random_state = check_random_state(self.random_state) + # initialize with [-1,1] as in ARPACK + v0 = random_state.uniform(-1, 1, A.shape[0]) + _, u = eigsh(A, ncv=self.n_svd_vecs, v0=v0) + + assert_all_finite(u) + assert_all_finite(vt) + u = u[:, n_discard:] + vt = vt[n_discard:] + return u, vt.T + + def _k_means(self, data, n_clusters): + if self.mini_batch: + model = MiniBatchKMeans( + n_clusters, + init=self.init, + n_init=self.n_init, + random_state=self.random_state, + ) + else: + model = KMeans( + n_clusters, + init=self.init, + n_init=self.n_init, + random_state=self.random_state, + ) + model.fit(data) + centroid = model.cluster_centers_ + labels = model.labels_ + return centroid, labels + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + return tags + + +class SpectralCoclustering(BaseSpectral): + """Spectral Co-Clustering algorithm (Dhillon, 2001). + + Clusters rows and columns of an array `X` to solve the relaxed + normalized cut of the bipartite graph created from `X` as follows: + the edge between row vertex `i` and column vertex `j` has weight + `X[i, j]`. + + The resulting bicluster structure is block-diagonal, since each + row and each column belongs to exactly one bicluster. + + Supports sparse matrices, as long as they are nonnegative. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + n_clusters : int, default=3 + The number of biclusters to find. + + svd_method : {'randomized', 'arpack'}, default='randomized' + Selects the algorithm for finding singular vectors. May be + 'randomized' or 'arpack'. If 'randomized', use + :func:`sklearn.utils.extmath.randomized_svd`, which may be faster + for large matrices. If 'arpack', use + :func:`scipy.sparse.linalg.svds`, which is more accurate, but + possibly slower in some cases. + + n_svd_vecs : int, default=None + Number of vectors to use in calculating the SVD. Corresponds + to `ncv` when `svd_method=arpack` and `n_oversamples` when + `svd_method` is 'randomized`. + + mini_batch : bool, default=False + Whether to use mini-batch k-means, which is faster but may get + different results. + + init : {'k-means++', 'random'}, or ndarray of shape \ + (n_clusters, n_features), default='k-means++' + Method for initialization of k-means algorithm; defaults to + 'k-means++'. + + n_init : int, default=10 + Number of random initializations that are tried with the + k-means algorithm. + + If mini-batch k-means is used, the best initialization is + chosen and the algorithm runs once. Otherwise, the algorithm + is run for each initialization and the best solution chosen. + + random_state : int, RandomState instance, default=None + Used for randomizing the singular value decomposition and the k-means + initialization. Use an int to make the randomness deterministic. + See :term:`Glossary `. + + Attributes + ---------- + rows_ : array-like of shape (n_row_clusters, n_rows) + Results of the clustering. `rows[i, r]` is True if + cluster `i` contains row `r`. Available only after calling ``fit``. + + columns_ : array-like of shape (n_column_clusters, n_columns) + Results of the clustering, like `rows`. + + row_labels_ : array-like of shape (n_rows,) + The bicluster label of each row. + + column_labels_ : array-like of shape (n_cols,) + The bicluster label of each column. + + biclusters_ : tuple of two ndarrays + The tuple contains the `rows_` and `columns_` arrays. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + SpectralBiclustering : Partitions rows and columns under the assumption + that the data has an underlying checkerboard structure. + + References + ---------- + * :doi:`Dhillon, Inderjit S, 2001. Co-clustering documents and words using + bipartite spectral graph partitioning. + <10.1145/502512.502550>` + + Examples + -------- + >>> from sklearn.cluster import SpectralCoclustering + >>> import numpy as np + >>> X = np.array([[1, 1], [2, 1], [1, 0], + ... [4, 7], [3, 5], [3, 6]]) + >>> clustering = SpectralCoclustering(n_clusters=2, random_state=0).fit(X) + >>> clustering.row_labels_ #doctest: +SKIP + array([0, 1, 1, 0, 0, 0], dtype=int32) + >>> clustering.column_labels_ #doctest: +SKIP + array([0, 0], dtype=int32) + >>> clustering + SpectralCoclustering(n_clusters=2, random_state=0) + + For a more detailed example, see the following: + :ref:`sphx_glr_auto_examples_bicluster_plot_spectral_coclustering.py`. + """ + + _parameter_constraints: dict = { + **BaseSpectral._parameter_constraints, + "n_clusters": [Interval(Integral, 1, None, closed="left")], + } + + def __init__( + self, + n_clusters=3, + *, + svd_method="randomized", + n_svd_vecs=None, + mini_batch=False, + init="k-means++", + n_init=10, + random_state=None, + ): + super().__init__( + n_clusters, svd_method, n_svd_vecs, mini_batch, init, n_init, random_state + ) + + def _check_parameters(self, n_samples): + if self.n_clusters > n_samples: + raise ValueError( + f"n_clusters should be <= n_samples={n_samples}. Got" + f" {self.n_clusters} instead." + ) + + def _fit(self, X): + normalized_data, row_diag, col_diag = _scale_normalize(X) + n_sv = 1 + int(np.ceil(np.log2(self.n_clusters))) + u, v = self._svd(normalized_data, n_sv, n_discard=1) + z = np.vstack((row_diag[:, np.newaxis] * u, col_diag[:, np.newaxis] * v)) + + _, labels = self._k_means(z, self.n_clusters) + + n_rows = X.shape[0] + self.row_labels_ = labels[:n_rows] + self.column_labels_ = labels[n_rows:] + + self.rows_ = np.vstack([self.row_labels_ == c for c in range(self.n_clusters)]) + self.columns_ = np.vstack( + [self.column_labels_ == c for c in range(self.n_clusters)] + ) + + +class SpectralBiclustering(BaseSpectral): + """Spectral biclustering (Kluger, 2003). + + Partitions rows and columns under the assumption that the data has + an underlying checkerboard structure. For instance, if there are + two row partitions and three column partitions, each row will + belong to three biclusters, and each column will belong to two + biclusters. The outer product of the corresponding row and column + label vectors gives this checkerboard structure. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + n_clusters : int or tuple (n_row_clusters, n_column_clusters), default=3 + The number of row and column clusters in the checkerboard + structure. + + method : {'bistochastic', 'scale', 'log'}, default='bistochastic' + Method of normalizing and converting singular vectors into + biclusters. May be one of 'scale', 'bistochastic', or 'log'. + The authors recommend using 'log'. If the data is sparse, + however, log normalization will not work, which is why the + default is 'bistochastic'. + + .. warning:: + if `method='log'`, the data must not be sparse. + + n_components : int, default=6 + Number of singular vectors to check. + + n_best : int, default=3 + Number of best singular vectors to which to project the data + for clustering. + + svd_method : {'randomized', 'arpack'}, default='randomized' + Selects the algorithm for finding singular vectors. May be + 'randomized' or 'arpack'. If 'randomized', uses + :func:`~sklearn.utils.extmath.randomized_svd`, which may be faster + for large matrices. If 'arpack', uses + `scipy.sparse.linalg.svds`, which is more accurate, but + possibly slower in some cases. + + n_svd_vecs : int, default=None + Number of vectors to use in calculating the SVD. Corresponds + to `ncv` when `svd_method=arpack` and `n_oversamples` when + `svd_method` is 'randomized`. + + mini_batch : bool, default=False + Whether to use mini-batch k-means, which is faster but may get + different results. + + init : {'k-means++', 'random'} or ndarray of shape (n_clusters, n_features), \ + default='k-means++' + Method for initialization of k-means algorithm; defaults to + 'k-means++'. + + n_init : int, default=10 + Number of random initializations that are tried with the + k-means algorithm. + + If mini-batch k-means is used, the best initialization is + chosen and the algorithm runs once. Otherwise, the algorithm + is run for each initialization and the best solution chosen. + + random_state : int, RandomState instance, default=None + Used for randomizing the singular value decomposition and the k-means + initialization. Use an int to make the randomness deterministic. + See :term:`Glossary `. + + Attributes + ---------- + rows_ : array-like of shape (n_row_clusters, n_rows) + Results of the clustering. `rows[i, r]` is True if + cluster `i` contains row `r`. Available only after calling ``fit``. + + columns_ : array-like of shape (n_column_clusters, n_columns) + Results of the clustering, like `rows`. + + row_labels_ : array-like of shape (n_rows,) + Row partition labels. + + column_labels_ : array-like of shape (n_cols,) + Column partition labels. + + biclusters_ : tuple of two ndarrays + The tuple contains the `rows_` and `columns_` arrays. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + SpectralCoclustering : Spectral Co-Clustering algorithm (Dhillon, 2001). + + References + ---------- + + * :doi:`Kluger, Yuval, et. al., 2003. Spectral biclustering of microarray + data: coclustering genes and conditions. + <10.1101/gr.648603>` + + Examples + -------- + >>> from sklearn.cluster import SpectralBiclustering + >>> import numpy as np + >>> X = np.array([[1, 1], [2, 1], [1, 0], + ... [4, 7], [3, 5], [3, 6]]) + >>> clustering = SpectralBiclustering(n_clusters=2, random_state=0).fit(X) + >>> clustering.row_labels_ + array([1, 1, 1, 0, 0, 0], dtype=int32) + >>> clustering.column_labels_ + array([1, 0], dtype=int32) + >>> clustering + SpectralBiclustering(n_clusters=2, random_state=0) + + For a more detailed example, see + :ref:`sphx_glr_auto_examples_bicluster_plot_spectral_biclustering.py` + """ + + _parameter_constraints: dict = { + **BaseSpectral._parameter_constraints, + "n_clusters": [Interval(Integral, 1, None, closed="left"), tuple], + "method": [StrOptions({"bistochastic", "scale", "log"})], + "n_components": [Interval(Integral, 1, None, closed="left")], + "n_best": [Interval(Integral, 1, None, closed="left")], + } + + def __init__( + self, + n_clusters=3, + *, + method="bistochastic", + n_components=6, + n_best=3, + svd_method="randomized", + n_svd_vecs=None, + mini_batch=False, + init="k-means++", + n_init=10, + random_state=None, + ): + super().__init__( + n_clusters, svd_method, n_svd_vecs, mini_batch, init, n_init, random_state + ) + self.method = method + self.n_components = n_components + self.n_best = n_best + + def _check_parameters(self, n_samples): + if isinstance(self.n_clusters, Integral): + if self.n_clusters > n_samples: + raise ValueError( + f"n_clusters should be <= n_samples={n_samples}. Got" + f" {self.n_clusters} instead." + ) + else: # tuple + try: + n_row_clusters, n_column_clusters = self.n_clusters + check_scalar( + n_row_clusters, + "n_row_clusters", + target_type=Integral, + min_val=1, + max_val=n_samples, + ) + check_scalar( + n_column_clusters, + "n_column_clusters", + target_type=Integral, + min_val=1, + max_val=n_samples, + ) + except (ValueError, TypeError) as e: + raise ValueError( + "Incorrect parameter n_clusters has value:" + f" {self.n_clusters}. It should either be a single integer" + " or an iterable with two integers:" + " (n_row_clusters, n_column_clusters)" + " And the values are should be in the" + " range: (1, n_samples)" + ) from e + + if self.n_best > self.n_components: + raise ValueError( + f"n_best={self.n_best} must be <= n_components={self.n_components}." + ) + + def _fit(self, X): + n_sv = self.n_components + if self.method == "bistochastic": + normalized_data = _bistochastic_normalize(X) + n_sv += 1 + elif self.method == "scale": + normalized_data, _, _ = _scale_normalize(X) + n_sv += 1 + elif self.method == "log": + normalized_data = _log_normalize(X) + n_discard = 0 if self.method == "log" else 1 + u, v = self._svd(normalized_data, n_sv, n_discard) + ut = u.T + vt = v.T + + try: + n_row_clusters, n_col_clusters = self.n_clusters + except TypeError: + n_row_clusters = n_col_clusters = self.n_clusters + + best_ut = self._fit_best_piecewise(ut, self.n_best, n_row_clusters) + + best_vt = self._fit_best_piecewise(vt, self.n_best, n_col_clusters) + + self.row_labels_ = self._project_and_cluster(X, best_vt.T, n_row_clusters) + + self.column_labels_ = self._project_and_cluster(X.T, best_ut.T, n_col_clusters) + + self.rows_ = np.vstack( + [ + self.row_labels_ == label + for label in range(n_row_clusters) + for _ in range(n_col_clusters) + ] + ) + self.columns_ = np.vstack( + [ + self.column_labels_ == label + for _ in range(n_row_clusters) + for label in range(n_col_clusters) + ] + ) + + def _fit_best_piecewise(self, vectors, n_best, n_clusters): + """Find the ``n_best`` vectors that are best approximated by piecewise + constant vectors. + + The piecewise vectors are found by k-means; the best is chosen + according to Euclidean distance. + + """ + + def make_piecewise(v): + centroid, labels = self._k_means(v.reshape(-1, 1), n_clusters) + return centroid[labels].ravel() + + piecewise_vectors = np.apply_along_axis(make_piecewise, axis=1, arr=vectors) + dists = np.apply_along_axis(norm, axis=1, arr=(vectors - piecewise_vectors)) + result = vectors[np.argsort(dists)[:n_best]] + return result + + def _project_and_cluster(self, data, vectors, n_clusters): + """Project ``data`` to ``vectors`` and cluster the result.""" + projected = safe_sparse_dot(data, vectors) + _, labels = self._k_means(projected, n_clusters) + return labels diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_birch.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_birch.py new file mode 100644 index 0000000000000000000000000000000000000000..4c894a644c8bc8b96b1c285358fd6a9cbf803a47 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_birch.py @@ -0,0 +1,749 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from math import sqrt +from numbers import Integral, Real + +import numpy as np +from scipy import sparse + +from .._config import config_context +from ..base import ( + BaseEstimator, + ClassNamePrefixFeaturesOutMixin, + ClusterMixin, + TransformerMixin, + _fit_context, +) +from ..exceptions import ConvergenceWarning +from ..metrics import pairwise_distances_argmin +from ..metrics.pairwise import euclidean_distances +from ..utils._param_validation import Hidden, Interval, StrOptions +from ..utils.extmath import row_norms +from ..utils.validation import check_is_fitted, validate_data +from . import AgglomerativeClustering + + +def _iterate_sparse_X(X): + """This little hack returns a densified row when iterating over a sparse + matrix, instead of constructing a sparse matrix for every row that is + expensive. + """ + n_samples = X.shape[0] + X_indices = X.indices + X_data = X.data + X_indptr = X.indptr + + for i in range(n_samples): + row = np.zeros(X.shape[1]) + startptr, endptr = X_indptr[i], X_indptr[i + 1] + nonzero_indices = X_indices[startptr:endptr] + row[nonzero_indices] = X_data[startptr:endptr] + yield row + + +def _split_node(node, threshold, branching_factor): + """The node has to be split if there is no place for a new subcluster + in the node. + 1. Two empty nodes and two empty subclusters are initialized. + 2. The pair of distant subclusters are found. + 3. The properties of the empty subclusters and nodes are updated + according to the nearest distance between the subclusters to the + pair of distant subclusters. + 4. The two nodes are set as children to the two subclusters. + """ + new_subcluster1 = _CFSubcluster() + new_subcluster2 = _CFSubcluster() + new_node1 = _CFNode( + threshold=threshold, + branching_factor=branching_factor, + is_leaf=node.is_leaf, + n_features=node.n_features, + dtype=node.init_centroids_.dtype, + ) + new_node2 = _CFNode( + threshold=threshold, + branching_factor=branching_factor, + is_leaf=node.is_leaf, + n_features=node.n_features, + dtype=node.init_centroids_.dtype, + ) + new_subcluster1.child_ = new_node1 + new_subcluster2.child_ = new_node2 + + if node.is_leaf: + if node.prev_leaf_ is not None: + node.prev_leaf_.next_leaf_ = new_node1 + new_node1.prev_leaf_ = node.prev_leaf_ + new_node1.next_leaf_ = new_node2 + new_node2.prev_leaf_ = new_node1 + new_node2.next_leaf_ = node.next_leaf_ + if node.next_leaf_ is not None: + node.next_leaf_.prev_leaf_ = new_node2 + + dist = euclidean_distances( + node.centroids_, Y_norm_squared=node.squared_norm_, squared=True + ) + n_clusters = dist.shape[0] + + farthest_idx = np.unravel_index(dist.argmax(), (n_clusters, n_clusters)) + node1_dist, node2_dist = dist[(farthest_idx,)] + + node1_closer = node1_dist < node2_dist + # make sure node1 is closest to itself even if all distances are equal. + # This can only happen when all node.centroids_ are duplicates leading to all + # distances between centroids being zero. + node1_closer[farthest_idx[0]] = True + + for idx, subcluster in enumerate(node.subclusters_): + if node1_closer[idx]: + new_node1.append_subcluster(subcluster) + new_subcluster1.update(subcluster) + else: + new_node2.append_subcluster(subcluster) + new_subcluster2.update(subcluster) + return new_subcluster1, new_subcluster2 + + +class _CFNode: + """Each node in a CFTree is called a CFNode. + + The CFNode can have a maximum of branching_factor + number of CFSubclusters. + + Parameters + ---------- + threshold : float + Threshold needed for a new subcluster to enter a CFSubcluster. + + branching_factor : int + Maximum number of CF subclusters in each node. + + is_leaf : bool + We need to know if the CFNode is a leaf or not, in order to + retrieve the final subclusters. + + n_features : int + The number of features. + + Attributes + ---------- + subclusters_ : list + List of subclusters for a particular CFNode. + + prev_leaf_ : _CFNode + Useful only if is_leaf is True. + + next_leaf_ : _CFNode + next_leaf. Useful only if is_leaf is True. + the final subclusters. + + init_centroids_ : ndarray of shape (branching_factor + 1, n_features) + Manipulate ``init_centroids_`` throughout rather than centroids_ since + the centroids are just a view of the ``init_centroids_`` . + + init_sq_norm_ : ndarray of shape (branching_factor + 1,) + manipulate init_sq_norm_ throughout. similar to ``init_centroids_``. + + centroids_ : ndarray of shape (branching_factor + 1, n_features) + View of ``init_centroids_``. + + squared_norm_ : ndarray of shape (branching_factor + 1,) + View of ``init_sq_norm_``. + + """ + + def __init__(self, *, threshold, branching_factor, is_leaf, n_features, dtype): + self.threshold = threshold + self.branching_factor = branching_factor + self.is_leaf = is_leaf + self.n_features = n_features + + # The list of subclusters, centroids and squared norms + # to manipulate throughout. + self.subclusters_ = [] + self.init_centroids_ = np.zeros((branching_factor + 1, n_features), dtype=dtype) + self.init_sq_norm_ = np.zeros((branching_factor + 1), dtype) + self.squared_norm_ = [] + self.prev_leaf_ = None + self.next_leaf_ = None + + def append_subcluster(self, subcluster): + n_samples = len(self.subclusters_) + self.subclusters_.append(subcluster) + self.init_centroids_[n_samples] = subcluster.centroid_ + self.init_sq_norm_[n_samples] = subcluster.sq_norm_ + + # Keep centroids and squared norm as views. In this way + # if we change init_centroids and init_sq_norm_, it is + # sufficient, + self.centroids_ = self.init_centroids_[: n_samples + 1, :] + self.squared_norm_ = self.init_sq_norm_[: n_samples + 1] + + def update_split_subclusters(self, subcluster, new_subcluster1, new_subcluster2): + """Remove a subcluster from a node and update it with the + split subclusters. + """ + ind = self.subclusters_.index(subcluster) + self.subclusters_[ind] = new_subcluster1 + self.init_centroids_[ind] = new_subcluster1.centroid_ + self.init_sq_norm_[ind] = new_subcluster1.sq_norm_ + self.append_subcluster(new_subcluster2) + + def insert_cf_subcluster(self, subcluster): + """Insert a new subcluster into the node.""" + if not self.subclusters_: + self.append_subcluster(subcluster) + return False + + threshold = self.threshold + branching_factor = self.branching_factor + # We need to find the closest subcluster among all the + # subclusters so that we can insert our new subcluster. + dist_matrix = np.dot(self.centroids_, subcluster.centroid_) + dist_matrix *= -2.0 + dist_matrix += self.squared_norm_ + closest_index = np.argmin(dist_matrix) + closest_subcluster = self.subclusters_[closest_index] + + # If the subcluster has a child, we need a recursive strategy. + if closest_subcluster.child_ is not None: + split_child = closest_subcluster.child_.insert_cf_subcluster(subcluster) + + if not split_child: + # If it is determined that the child need not be split, we + # can just update the closest_subcluster + closest_subcluster.update(subcluster) + self.init_centroids_[closest_index] = self.subclusters_[ + closest_index + ].centroid_ + self.init_sq_norm_[closest_index] = self.subclusters_[ + closest_index + ].sq_norm_ + return False + + # things not too good. we need to redistribute the subclusters in + # our child node, and add a new subcluster in the parent + # subcluster to accommodate the new child. + else: + new_subcluster1, new_subcluster2 = _split_node( + closest_subcluster.child_, + threshold, + branching_factor, + ) + self.update_split_subclusters( + closest_subcluster, new_subcluster1, new_subcluster2 + ) + + if len(self.subclusters_) > self.branching_factor: + return True + return False + + # good to go! + else: + merged = closest_subcluster.merge_subcluster(subcluster, self.threshold) + if merged: + self.init_centroids_[closest_index] = closest_subcluster.centroid_ + self.init_sq_norm_[closest_index] = closest_subcluster.sq_norm_ + return False + + # not close to any other subclusters, and we still + # have space, so add. + elif len(self.subclusters_) < self.branching_factor: + self.append_subcluster(subcluster) + return False + + # We do not have enough space nor is it closer to an + # other subcluster. We need to split. + else: + self.append_subcluster(subcluster) + return True + + +class _CFSubcluster: + """Each subcluster in a CFNode is called a CFSubcluster. + + A CFSubcluster can have a CFNode has its child. + + Parameters + ---------- + linear_sum : ndarray of shape (n_features,), default=None + Sample. This is kept optional to allow initialization of empty + subclusters. + + Attributes + ---------- + n_samples_ : int + Number of samples that belong to each subcluster. + + linear_sum_ : ndarray + Linear sum of all the samples in a subcluster. Prevents holding + all sample data in memory. + + squared_sum_ : float + Sum of the squared l2 norms of all samples belonging to a subcluster. + + centroid_ : ndarray of shape (branching_factor + 1, n_features) + Centroid of the subcluster. Prevent recomputing of centroids when + ``CFNode.centroids_`` is called. + + child_ : _CFNode + Child Node of the subcluster. Once a given _CFNode is set as the child + of the _CFNode, it is set to ``self.child_``. + + sq_norm_ : ndarray of shape (branching_factor + 1,) + Squared norm of the subcluster. Used to prevent recomputing when + pairwise minimum distances are computed. + """ + + def __init__(self, *, linear_sum=None): + if linear_sum is None: + self.n_samples_ = 0 + self.squared_sum_ = 0.0 + self.centroid_ = self.linear_sum_ = 0 + else: + self.n_samples_ = 1 + self.centroid_ = self.linear_sum_ = linear_sum + self.squared_sum_ = self.sq_norm_ = np.dot( + self.linear_sum_, self.linear_sum_ + ) + self.child_ = None + + def update(self, subcluster): + self.n_samples_ += subcluster.n_samples_ + self.linear_sum_ += subcluster.linear_sum_ + self.squared_sum_ += subcluster.squared_sum_ + self.centroid_ = self.linear_sum_ / self.n_samples_ + self.sq_norm_ = np.dot(self.centroid_, self.centroid_) + + def merge_subcluster(self, nominee_cluster, threshold): + """Check if a cluster is worthy enough to be merged. If + yes then merge. + """ + new_ss = self.squared_sum_ + nominee_cluster.squared_sum_ + new_ls = self.linear_sum_ + nominee_cluster.linear_sum_ + new_n = self.n_samples_ + nominee_cluster.n_samples_ + new_centroid = (1 / new_n) * new_ls + new_sq_norm = np.dot(new_centroid, new_centroid) + + # The squared radius of the cluster is defined: + # r^2 = sum_i ||x_i - c||^2 / n + # with x_i the n points assigned to the cluster and c its centroid: + # c = sum_i x_i / n + # This can be expanded to: + # r^2 = sum_i ||x_i||^2 / n - 2 < sum_i x_i / n, c> + n ||c||^2 / n + # and therefore simplifies to: + # r^2 = sum_i ||x_i||^2 / n - ||c||^2 + sq_radius = new_ss / new_n - new_sq_norm + + if sq_radius <= threshold**2: + ( + self.n_samples_, + self.linear_sum_, + self.squared_sum_, + self.centroid_, + self.sq_norm_, + ) = (new_n, new_ls, new_ss, new_centroid, new_sq_norm) + return True + return False + + @property + def radius(self): + """Return radius of the subcluster""" + # Because of numerical issues, this could become negative + sq_radius = self.squared_sum_ / self.n_samples_ - self.sq_norm_ + return sqrt(max(0, sq_radius)) + + +class Birch( + ClassNamePrefixFeaturesOutMixin, ClusterMixin, TransformerMixin, BaseEstimator +): + """Implements the BIRCH clustering algorithm. + + It is a memory-efficient, online-learning algorithm provided as an + alternative to :class:`MiniBatchKMeans`. It constructs a tree + data structure with the cluster centroids being read off the leaf. + These can be either the final cluster centroids or can be provided as input + to another clustering algorithm such as :class:`AgglomerativeClustering`. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.16 + + Parameters + ---------- + threshold : float, default=0.5 + The radius of the subcluster obtained by merging a new sample and the + closest subcluster should be lesser than the threshold. Otherwise a new + subcluster is started. Setting this value to be very low promotes + splitting and vice-versa. + + branching_factor : int, default=50 + Maximum number of CF subclusters in each node. If a new samples enters + such that the number of subclusters exceed the branching_factor then + that node is split into two nodes with the subclusters redistributed + in each. The parent subcluster of that node is removed and two new + subclusters are added as parents of the 2 split nodes. + + n_clusters : int, instance of sklearn.cluster model or None, default=3 + Number of clusters after the final clustering step, which treats the + subclusters from the leaves as new samples. + + - `None` : the final clustering step is not performed and the + subclusters are returned as they are. + + - :mod:`sklearn.cluster` Estimator : If a model is provided, the model + is fit treating the subclusters as new samples and the initial data + is mapped to the label of the closest subcluster. + + - `int` : the model fit is :class:`AgglomerativeClustering` with + `n_clusters` set to be equal to the int. + + compute_labels : bool, default=True + Whether or not to compute labels for each fit. + + copy : bool, default=True + Whether or not to make a copy of the given data. If set to False, + the initial data will be overwritten. + + .. deprecated:: 1.6 + `copy` was deprecated in 1.6 and will be removed in 1.8. It has no effect + as the estimator does not perform in-place operations on the input data. + + Attributes + ---------- + root_ : _CFNode + Root of the CFTree. + + dummy_leaf_ : _CFNode + Start pointer to all the leaves. + + subcluster_centers_ : ndarray + Centroids of all subclusters read directly from the leaves. + + subcluster_labels_ : ndarray + Labels assigned to the centroids of the subclusters after + they are clustered globally. + + labels_ : ndarray of shape (n_samples,) + Array of labels assigned to the input data. + if partial_fit is used instead of fit, they are assigned to the + last batch of data. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + MiniBatchKMeans : Alternative implementation that does incremental updates + of the centers' positions using mini-batches. + + Notes + ----- + The tree data structure consists of nodes with each node consisting of + a number of subclusters. The maximum number of subclusters in a node + is determined by the branching factor. Each subcluster maintains a + linear sum, squared sum and the number of samples in that subcluster. + In addition, each subcluster can also have a node as its child, if the + subcluster is not a member of a leaf node. + + For a new point entering the root, it is merged with the subcluster closest + to it and the linear sum, squared sum and the number of samples of that + subcluster are updated. This is done recursively till the properties of + the leaf node are updated. + + See :ref:`sphx_glr_auto_examples_cluster_plot_birch_vs_minibatchkmeans.py` for a + comparison with :class:`~sklearn.cluster.MiniBatchKMeans`. + + References + ---------- + * Tian Zhang, Raghu Ramakrishnan, Maron Livny + BIRCH: An efficient data clustering method for large databases. + https://www.cs.sfu.ca/CourseCentral/459/han/papers/zhang96.pdf + + * Roberto Perdisci + JBirch - Java implementation of BIRCH clustering algorithm + https://code.google.com/archive/p/jbirch + + Examples + -------- + >>> from sklearn.cluster import Birch + >>> X = [[0, 1], [0.3, 1], [-0.3, 1], [0, -1], [0.3, -1], [-0.3, -1]] + >>> brc = Birch(n_clusters=None) + >>> brc.fit(X) + Birch(n_clusters=None) + >>> brc.predict(X) + array([0, 0, 0, 1, 1, 1]) + + For a comparison of the BIRCH clustering algorithm with other clustering algorithms, + see :ref:`sphx_glr_auto_examples_cluster_plot_cluster_comparison.py` + """ + + _parameter_constraints: dict = { + "threshold": [Interval(Real, 0.0, None, closed="neither")], + "branching_factor": [Interval(Integral, 1, None, closed="neither")], + "n_clusters": [None, ClusterMixin, Interval(Integral, 1, None, closed="left")], + "compute_labels": ["boolean"], + "copy": ["boolean", Hidden(StrOptions({"deprecated"}))], + } + + def __init__( + self, + *, + threshold=0.5, + branching_factor=50, + n_clusters=3, + compute_labels=True, + copy="deprecated", + ): + self.threshold = threshold + self.branching_factor = branching_factor + self.n_clusters = n_clusters + self.compute_labels = compute_labels + self.copy = copy + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """ + Build a CF Tree for the input data. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Input data. + + y : Ignored + Not used, present here for API consistency by convention. + + Returns + ------- + self + Fitted estimator. + """ + return self._fit(X, partial=False) + + def _fit(self, X, partial): + has_root = getattr(self, "root_", None) + first_call = not (partial and has_root) + + if self.copy != "deprecated" and first_call: + warnings.warn( + "`copy` was deprecated in 1.6 and will be removed in 1.8 since it " + "has no effect internally. Simply leave this parameter to its default " + "value to avoid this warning.", + FutureWarning, + ) + + X = validate_data( + self, + X, + accept_sparse="csr", + reset=first_call, + dtype=[np.float64, np.float32], + ) + threshold = self.threshold + branching_factor = self.branching_factor + + n_samples, n_features = X.shape + + # If partial_fit is called for the first time or fit is called, we + # start a new tree. + if first_call: + # The first root is the leaf. Manipulate this object throughout. + self.root_ = _CFNode( + threshold=threshold, + branching_factor=branching_factor, + is_leaf=True, + n_features=n_features, + dtype=X.dtype, + ) + + # To enable getting back subclusters. + self.dummy_leaf_ = _CFNode( + threshold=threshold, + branching_factor=branching_factor, + is_leaf=True, + n_features=n_features, + dtype=X.dtype, + ) + self.dummy_leaf_.next_leaf_ = self.root_ + self.root_.prev_leaf_ = self.dummy_leaf_ + + # Cannot vectorize. Enough to convince to use cython. + if not sparse.issparse(X): + iter_func = iter + else: + iter_func = _iterate_sparse_X + + for sample in iter_func(X): + subcluster = _CFSubcluster(linear_sum=sample) + split = self.root_.insert_cf_subcluster(subcluster) + + if split: + new_subcluster1, new_subcluster2 = _split_node( + self.root_, threshold, branching_factor + ) + del self.root_ + self.root_ = _CFNode( + threshold=threshold, + branching_factor=branching_factor, + is_leaf=False, + n_features=n_features, + dtype=X.dtype, + ) + self.root_.append_subcluster(new_subcluster1) + self.root_.append_subcluster(new_subcluster2) + + centroids = np.concatenate([leaf.centroids_ for leaf in self._get_leaves()]) + self.subcluster_centers_ = centroids + self._n_features_out = self.subcluster_centers_.shape[0] + + self._global_clustering(X) + return self + + def _get_leaves(self): + """ + Retrieve the leaves of the CF Node. + + Returns + ------- + leaves : list of shape (n_leaves,) + List of the leaf nodes. + """ + leaf_ptr = self.dummy_leaf_.next_leaf_ + leaves = [] + while leaf_ptr is not None: + leaves.append(leaf_ptr) + leaf_ptr = leaf_ptr.next_leaf_ + return leaves + + @_fit_context(prefer_skip_nested_validation=True) + def partial_fit(self, X=None, y=None): + """ + Online learning. Prevents rebuilding of CFTree from scratch. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features), \ + default=None + Input data. If X is not provided, only the global clustering + step is done. + + y : Ignored + Not used, present here for API consistency by convention. + + Returns + ------- + self + Fitted estimator. + """ + if X is None: + # Perform just the final global clustering step. + self._global_clustering() + return self + else: + return self._fit(X, partial=True) + + def predict(self, X): + """ + Predict data using the ``centroids_`` of subclusters. + + Avoid computation of the row norms of X. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Input data. + + Returns + ------- + labels : ndarray of shape(n_samples,) + Labelled data. + """ + check_is_fitted(self) + X = validate_data(self, X, accept_sparse="csr", reset=False) + return self._predict(X) + + def _predict(self, X): + """Predict data using the ``centroids_`` of subclusters.""" + kwargs = {"Y_norm_squared": self._subcluster_norms} + + with config_context(assume_finite=True): + argmin = pairwise_distances_argmin( + X, self.subcluster_centers_, metric_kwargs=kwargs + ) + return self.subcluster_labels_[argmin] + + def transform(self, X): + """ + Transform X into subcluster centroids dimension. + + Each dimension represents the distance from the sample point to each + cluster centroid. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Input data. + + Returns + ------- + X_trans : {array-like, sparse matrix} of shape (n_samples, n_clusters) + Transformed data. + """ + check_is_fitted(self) + X = validate_data(self, X, accept_sparse="csr", reset=False) + with config_context(assume_finite=True): + return euclidean_distances(X, self.subcluster_centers_) + + def _global_clustering(self, X=None): + """ + Global clustering for the subclusters obtained after fitting + """ + clusterer = self.n_clusters + centroids = self.subcluster_centers_ + compute_labels = (X is not None) and self.compute_labels + + # Preprocessing for the global clustering. + not_enough_centroids = False + if isinstance(clusterer, Integral): + clusterer = AgglomerativeClustering(n_clusters=self.n_clusters) + # There is no need to perform the global clustering step. + if len(centroids) < self.n_clusters: + not_enough_centroids = True + + # To use in predict to avoid recalculation. + self._subcluster_norms = row_norms(self.subcluster_centers_, squared=True) + + if clusterer is None or not_enough_centroids: + self.subcluster_labels_ = np.arange(len(centroids)) + if not_enough_centroids: + warnings.warn( + "Number of subclusters found (%d) by BIRCH is less " + "than (%d). Decrease the threshold." + % (len(centroids), self.n_clusters), + ConvergenceWarning, + ) + else: + # The global clustering step that clusters the subclusters of + # the leaves. It assumes the centroids of the subclusters as + # samples and finds the final centroids. + self.subcluster_labels_ = clusterer.fit_predict(self.subcluster_centers_) + + if compute_labels: + self.labels_ = self._predict(X) + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.transformer_tags.preserves_dtype = ["float64", "float32"] + tags.input_tags.sparse = True + return tags diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_bisect_k_means.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_bisect_k_means.py new file mode 100644 index 0000000000000000000000000000000000000000..77e24adbf80848b13f36adc1151686746024bf25 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_bisect_k_means.py @@ -0,0 +1,543 @@ +"""Bisecting K-means clustering.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings + +import numpy as np +import scipy.sparse as sp + +from ..base import _fit_context +from ..utils._openmp_helpers import _openmp_effective_n_threads +from ..utils._param_validation import Integral, Interval, StrOptions +from ..utils.extmath import row_norms +from ..utils.validation import ( + _check_sample_weight, + check_is_fitted, + check_random_state, + validate_data, +) +from ._k_means_common import _inertia_dense, _inertia_sparse +from ._kmeans import ( + _BaseKMeans, + _kmeans_single_elkan, + _kmeans_single_lloyd, + _labels_inertia_threadpool_limit, +) + + +class _BisectingTree: + """Tree structure representing the hierarchical clusters of BisectingKMeans.""" + + def __init__(self, center, indices, score): + """Create a new cluster node in the tree. + + The node holds the center of this cluster and the indices of the data points + that belong to it. + """ + self.center = center + self.indices = indices + self.score = score + + self.left = None + self.right = None + + def split(self, labels, centers, scores): + """Split the cluster node into two subclusters.""" + self.left = _BisectingTree( + indices=self.indices[labels == 0], center=centers[0], score=scores[0] + ) + self.right = _BisectingTree( + indices=self.indices[labels == 1], center=centers[1], score=scores[1] + ) + + # reset the indices attribute to save memory + self.indices = None + + def get_cluster_to_bisect(self): + """Return the cluster node to bisect next. + + It's based on the score of the cluster, which can be either the number of + data points assigned to that cluster or the inertia of that cluster + (see `bisecting_strategy` for details). + """ + max_score = None + + for cluster_leaf in self.iter_leaves(): + if max_score is None or cluster_leaf.score > max_score: + max_score = cluster_leaf.score + best_cluster_leaf = cluster_leaf + + return best_cluster_leaf + + def iter_leaves(self): + """Iterate over all the cluster leaves in the tree.""" + if self.left is None: + yield self + else: + yield from self.left.iter_leaves() + yield from self.right.iter_leaves() + + +class BisectingKMeans(_BaseKMeans): + """Bisecting K-Means clustering. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 1.1 + + Parameters + ---------- + n_clusters : int, default=8 + The number of clusters to form as well as the number of + centroids to generate. + + init : {'k-means++', 'random'} or callable, default='random' + Method for initialization: + + 'k-means++' : selects initial cluster centers for k-mean + clustering in a smart way to speed up convergence. See section + Notes in k_init for more details. + + 'random': choose `n_clusters` observations (rows) at random from data + for the initial centroids. + + If a callable is passed, it should take arguments X, n_clusters and a + random state and return an initialization. + + n_init : int, default=1 + Number of time the inner k-means algorithm will be run with different + centroid seeds in each bisection. + That will result producing for each bisection best output of n_init + consecutive runs in terms of inertia. + + random_state : int, RandomState instance or None, default=None + Determines random number generation for centroid initialization + in inner K-Means. Use an int to make the randomness deterministic. + See :term:`Glossary `. + + max_iter : int, default=300 + Maximum number of iterations of the inner k-means algorithm at each + bisection. + + verbose : int, default=0 + Verbosity mode. + + tol : float, default=1e-4 + Relative tolerance with regards to Frobenius norm of the difference + in the cluster centers of two consecutive iterations to declare + convergence. Used in inner k-means algorithm at each bisection to pick + best possible clusters. + + copy_x : bool, default=True + When pre-computing distances it is more numerically accurate to center + the data first. If copy_x is True (default), then the original data is + not modified. If False, the original data is modified, and put back + before the function returns, but small numerical differences may be + introduced by subtracting and then adding the data mean. Note that if + the original data is not C-contiguous, a copy will be made even if + copy_x is False. If the original data is sparse, but not in CSR format, + a copy will be made even if copy_x is False. + + algorithm : {"lloyd", "elkan"}, default="lloyd" + Inner K-means algorithm used in bisection. + The classical EM-style algorithm is `"lloyd"`. + The `"elkan"` variation can be more efficient on some datasets with + well-defined clusters, by using the triangle inequality. However it's + more memory intensive due to the allocation of an extra array of shape + `(n_samples, n_clusters)`. + + bisecting_strategy : {"biggest_inertia", "largest_cluster"},\ + default="biggest_inertia" + Defines how bisection should be performed: + + - "biggest_inertia" means that BisectingKMeans will always check + all calculated cluster for cluster with biggest SSE + (Sum of squared errors) and bisect it. This approach concentrates on + precision, but may be costly in terms of execution time (especially for + larger amount of data points). + + - "largest_cluster" - BisectingKMeans will always split cluster with + largest amount of points assigned to it from all clusters + previously calculated. That should work faster than picking by SSE + ('biggest_inertia') and may produce similar results in most cases. + + Attributes + ---------- + cluster_centers_ : ndarray of shape (n_clusters, n_features) + Coordinates of cluster centers. If the algorithm stops before fully + converging (see ``tol`` and ``max_iter``), these will not be + consistent with ``labels_``. + + labels_ : ndarray of shape (n_samples,) + Labels of each point. + + inertia_ : float + Sum of squared distances of samples to their closest cluster center, + weighted by the sample weights if provided. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + See Also + -------- + KMeans : Original implementation of K-Means algorithm. + + Notes + ----- + It might be inefficient when n_cluster is less than 3, due to unnecessary + calculations for that case. + + Examples + -------- + >>> from sklearn.cluster import BisectingKMeans + >>> import numpy as np + >>> X = np.array([[1, 1], [10, 1], [3, 1], + ... [10, 0], [2, 1], [10, 2], + ... [10, 8], [10, 9], [10, 10]]) + >>> bisect_means = BisectingKMeans(n_clusters=3, random_state=0).fit(X) + >>> bisect_means.labels_ + array([0, 2, 0, 2, 0, 2, 1, 1, 1], dtype=int32) + >>> bisect_means.predict([[0, 0], [12, 3]]) + array([0, 2], dtype=int32) + >>> bisect_means.cluster_centers_ + array([[ 2., 1.], + [10., 9.], + [10., 1.]]) + + For a comparison between BisectingKMeans and K-Means refer to example + :ref:`sphx_glr_auto_examples_cluster_plot_bisect_kmeans.py`. + """ + + _parameter_constraints: dict = { + **_BaseKMeans._parameter_constraints, + "init": [StrOptions({"k-means++", "random"}), callable], + "n_init": [Interval(Integral, 1, None, closed="left")], + "copy_x": ["boolean"], + "algorithm": [StrOptions({"lloyd", "elkan"})], + "bisecting_strategy": [StrOptions({"biggest_inertia", "largest_cluster"})], + } + + def __init__( + self, + n_clusters=8, + *, + init="random", + n_init=1, + random_state=None, + max_iter=300, + verbose=0, + tol=1e-4, + copy_x=True, + algorithm="lloyd", + bisecting_strategy="biggest_inertia", + ): + super().__init__( + n_clusters=n_clusters, + init=init, + max_iter=max_iter, + verbose=verbose, + random_state=random_state, + tol=tol, + n_init=n_init, + ) + + self.copy_x = copy_x + self.algorithm = algorithm + self.bisecting_strategy = bisecting_strategy + + def _warn_mkl_vcomp(self, n_active_threads): + """Warn when vcomp and mkl are both present""" + warnings.warn( + "BisectingKMeans is known to have a memory leak on Windows " + "with MKL, when there are less chunks than available " + "threads. You can avoid it by setting the environment" + f" variable OMP_NUM_THREADS={n_active_threads}." + ) + + def _inertia_per_cluster(self, X, centers, labels, sample_weight): + """Calculate the sum of squared errors (inertia) per cluster. + + Parameters + ---------- + X : {ndarray, csr_matrix} of shape (n_samples, n_features) + The input samples. + + centers : ndarray of shape (n_clusters=2, n_features) + The cluster centers. + + labels : ndarray of shape (n_samples,) + Index of the cluster each sample belongs to. + + sample_weight : ndarray of shape (n_samples,) + The weights for each observation in X. + + Returns + ------- + inertia_per_cluster : ndarray of shape (n_clusters=2,) + Sum of squared errors (inertia) for each cluster. + """ + n_clusters = centers.shape[0] # = 2 since centers comes from a bisection + _inertia = _inertia_sparse if sp.issparse(X) else _inertia_dense + + inertia_per_cluster = np.empty(n_clusters) + for label in range(n_clusters): + inertia_per_cluster[label] = _inertia( + X, sample_weight, centers, labels, self._n_threads, single_label=label + ) + + return inertia_per_cluster + + def _bisect(self, X, x_squared_norms, sample_weight, cluster_to_bisect): + """Split a cluster into 2 subsclusters. + + Parameters + ---------- + X : {ndarray, csr_matrix} of shape (n_samples, n_features) + Training instances to cluster. + + x_squared_norms : ndarray of shape (n_samples,) + Squared euclidean norm of each data point. + + sample_weight : ndarray of shape (n_samples,) + The weights for each observation in X. + + cluster_to_bisect : _BisectingTree node object + The cluster node to split. + """ + X = X[cluster_to_bisect.indices] + x_squared_norms = x_squared_norms[cluster_to_bisect.indices] + sample_weight = sample_weight[cluster_to_bisect.indices] + + best_inertia = None + + # Split samples in X into 2 clusters. + # Repeating `n_init` times to obtain best clusters + for _ in range(self.n_init): + centers_init = self._init_centroids( + X, + x_squared_norms=x_squared_norms, + init=self.init, + random_state=self._random_state, + n_centroids=2, + sample_weight=sample_weight, + ) + + labels, inertia, centers, _ = self._kmeans_single( + X, + sample_weight, + centers_init, + max_iter=self.max_iter, + verbose=self.verbose, + tol=self.tol, + n_threads=self._n_threads, + ) + + # allow small tolerance on the inertia to accommodate for + # non-deterministic rounding errors due to parallel computation + if best_inertia is None or inertia < best_inertia * (1 - 1e-6): + best_labels = labels + best_centers = centers + best_inertia = inertia + + if self.verbose: + print(f"New centroids from bisection: {best_centers}") + + if self.bisecting_strategy == "biggest_inertia": + scores = self._inertia_per_cluster( + X, best_centers, best_labels, sample_weight + ) + else: # bisecting_strategy == "largest_cluster" + # Using minlength to make sure that we have the counts for both labels even + # if all samples are labelled 0. + scores = np.bincount(best_labels, minlength=2) + + cluster_to_bisect.split(best_labels, best_centers, scores) + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None, sample_weight=None): + """Compute bisecting k-means clustering. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + + Training instances to cluster. + + .. note:: The data will be converted to C ordering, + which will cause a memory copy + if the given data is not C-contiguous. + + y : Ignored + Not used, present here for API consistency by convention. + + sample_weight : array-like of shape (n_samples,), default=None + The weights for each observation in X. If None, all observations + are assigned equal weight. `sample_weight` is not used during + initialization if `init` is a callable. + + Returns + ------- + self + Fitted estimator. + """ + X = validate_data( + self, + X, + accept_sparse="csr", + dtype=[np.float64, np.float32], + order="C", + copy=self.copy_x, + accept_large_sparse=False, + ) + + self._check_params_vs_input(X) + + self._random_state = check_random_state(self.random_state) + sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype) + self._n_threads = _openmp_effective_n_threads() + + if self.algorithm == "lloyd" or self.n_clusters == 1: + self._kmeans_single = _kmeans_single_lloyd + self._check_mkl_vcomp(X, X.shape[0]) + else: + self._kmeans_single = _kmeans_single_elkan + + # Subtract of mean of X for more accurate distance computations + if not sp.issparse(X): + self._X_mean = X.mean(axis=0) + X -= self._X_mean + + # Initialize the hierarchical clusters tree + self._bisecting_tree = _BisectingTree( + indices=np.arange(X.shape[0]), + center=X.mean(axis=0), + score=0, + ) + + x_squared_norms = row_norms(X, squared=True) + + for _ in range(self.n_clusters - 1): + # Chose cluster to bisect + cluster_to_bisect = self._bisecting_tree.get_cluster_to_bisect() + + # Split this cluster into 2 subclusters + self._bisect(X, x_squared_norms, sample_weight, cluster_to_bisect) + + # Aggregate final labels and centers from the bisecting tree + self.labels_ = np.full(X.shape[0], -1, dtype=np.int32) + self.cluster_centers_ = np.empty((self.n_clusters, X.shape[1]), dtype=X.dtype) + + for i, cluster_node in enumerate(self._bisecting_tree.iter_leaves()): + self.labels_[cluster_node.indices] = i + self.cluster_centers_[i] = cluster_node.center + cluster_node.label = i # label final clusters for future prediction + cluster_node.indices = None # release memory + + # Restore original data + if not sp.issparse(X): + X += self._X_mean + self.cluster_centers_ += self._X_mean + + _inertia = _inertia_sparse if sp.issparse(X) else _inertia_dense + self.inertia_ = _inertia( + X, sample_weight, self.cluster_centers_, self.labels_, self._n_threads + ) + + self._n_features_out = self.cluster_centers_.shape[0] + + return self + + def predict(self, X): + """Predict which cluster each sample in X belongs to. + + Prediction is made by going down the hierarchical tree + in searching of closest leaf cluster. + + In the vector quantization literature, `cluster_centers_` is called + the code book and each value returned by `predict` is the index of + the closest code in the code book. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + New data to predict. + + Returns + ------- + labels : ndarray of shape (n_samples,) + Index of the cluster each sample belongs to. + """ + check_is_fitted(self) + + X = self._check_test_data(X) + x_squared_norms = row_norms(X, squared=True) + + # sample weights are unused but necessary in cython helpers + sample_weight = np.ones_like(x_squared_norms) + + labels = self._predict_recursive(X, sample_weight, self._bisecting_tree) + + return labels + + def _predict_recursive(self, X, sample_weight, cluster_node): + """Predict recursively by going down the hierarchical tree. + + Parameters + ---------- + X : {ndarray, csr_matrix} of shape (n_samples, n_features) + The data points, currently assigned to `cluster_node`, to predict between + the subclusters of this node. + + sample_weight : ndarray of shape (n_samples,) + The weights for each observation in X. + + cluster_node : _BisectingTree node object + The cluster node of the hierarchical tree. + + Returns + ------- + labels : ndarray of shape (n_samples,) + Index of the cluster each sample belongs to. + """ + if cluster_node.left is None: + # This cluster has no subcluster. Labels are just the label of the cluster. + return np.full(X.shape[0], cluster_node.label, dtype=np.int32) + + # Determine if data points belong to the left or right subcluster + centers = np.vstack((cluster_node.left.center, cluster_node.right.center)) + if hasattr(self, "_X_mean"): + centers += self._X_mean + + cluster_labels = _labels_inertia_threadpool_limit( + X, + sample_weight, + centers, + self._n_threads, + return_inertia=False, + ) + mask = cluster_labels == 0 + + # Compute the labels for each subset of the data points. + labels = np.full(X.shape[0], -1, dtype=np.int32) + + labels[mask] = self._predict_recursive( + X[mask], sample_weight[mask], cluster_node.left + ) + + labels[~mask] = self._predict_recursive( + X[~mask], sample_weight[~mask], cluster_node.right + ) + + return labels + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + tags.transformer_tags.preserves_dtype = ["float64", "float32"] + return tags diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_dbscan.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_dbscan.py new file mode 100644 index 0000000000000000000000000000000000000000..857a332cc2371a6cbbcc8b69c21cd7e432ccbcc6 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_dbscan.py @@ -0,0 +1,480 @@ +""" +DBSCAN: Density-Based Spatial Clustering of Applications with Noise +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from numbers import Integral, Real + +import numpy as np +from scipy import sparse + +from ..base import BaseEstimator, ClusterMixin, _fit_context +from ..metrics.pairwise import _VALID_METRICS +from ..neighbors import NearestNeighbors +from ..utils._param_validation import Interval, StrOptions, validate_params +from ..utils.validation import _check_sample_weight, validate_data +from ._dbscan_inner import dbscan_inner + + +@validate_params( + { + "X": ["array-like", "sparse matrix"], + "sample_weight": ["array-like", None], + }, + prefer_skip_nested_validation=False, +) +def dbscan( + X, + eps=0.5, + *, + min_samples=5, + metric="minkowski", + metric_params=None, + algorithm="auto", + leaf_size=30, + p=2, + sample_weight=None, + n_jobs=None, +): + """Perform DBSCAN clustering from vector array or distance matrix. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + X : {array-like, sparse (CSR) matrix} of shape (n_samples, n_features) or \ + (n_samples, n_samples) + A feature array, or array of distances between samples if + ``metric='precomputed'``. + + eps : float, default=0.5 + The maximum distance between two samples for one to be considered + as in the neighborhood of the other. This is not a maximum bound + on the distances of points within a cluster. This is the most + important DBSCAN parameter to choose appropriately for your data set + and distance function. + + min_samples : int, default=5 + The number of samples (or total weight) in a neighborhood for a point + to be considered as a core point. This includes the point itself. + + metric : str or callable, default='minkowski' + The metric to use when calculating distance between instances in a + feature array. If metric is a string or callable, it must be one of + the options allowed by :func:`sklearn.metrics.pairwise_distances` for + its metric parameter. + If metric is "precomputed", X is assumed to be a distance matrix and + must be square during fit. + X may be a :term:`sparse graph `, + in which case only "nonzero" elements may be considered neighbors. + + metric_params : dict, default=None + Additional keyword arguments for the metric function. + + .. versionadded:: 0.19 + + algorithm : {'auto', 'ball_tree', 'kd_tree', 'brute'}, default='auto' + The algorithm to be used by the NearestNeighbors module + to compute pointwise distances and find nearest neighbors. + See NearestNeighbors module documentation for details. + + leaf_size : int, default=30 + Leaf size passed to BallTree or cKDTree. This can affect the speed + of the construction and query, as well as the memory required + to store the tree. The optimal value depends + on the nature of the problem. + + p : float, default=2 + The power of the Minkowski metric to be used to calculate distance + between points. + + sample_weight : array-like of shape (n_samples,), default=None + Weight of each sample, such that a sample with a weight of at least + ``min_samples`` is by itself a core sample; a sample with negative + weight may inhibit its eps-neighbor from being core. + Note that weights are absolute, and default to 1. + + n_jobs : int, default=None + The number of parallel jobs to run for neighbors search. ``None`` means + 1 unless in a :obj:`joblib.parallel_backend` context. ``-1`` means + using all processors. See :term:`Glossary ` for more details. + If precomputed distance are used, parallel execution is not available + and thus n_jobs will have no effect. + + Returns + ------- + core_samples : ndarray of shape (n_core_samples,) + Indices of core samples. + + labels : ndarray of shape (n_samples,) + Cluster labels for each point. Noisy samples are given the label -1. + + See Also + -------- + DBSCAN : An estimator interface for this clustering algorithm. + OPTICS : A similar estimator interface clustering at multiple values of + eps. Our implementation is optimized for memory usage. + + Notes + ----- + For an example, see :ref:`sphx_glr_auto_examples_cluster_plot_dbscan.py`. + + This implementation bulk-computes all neighborhood queries, which increases + the memory complexity to O(n.d) where d is the average number of neighbors, + while original DBSCAN had memory complexity O(n). It may attract a higher + memory complexity when querying these nearest neighborhoods, depending + on the ``algorithm``. + + One way to avoid the query complexity is to pre-compute sparse + neighborhoods in chunks using + :func:`NearestNeighbors.radius_neighbors_graph + ` with + ``mode='distance'``, then using ``metric='precomputed'`` here. + + Another way to reduce memory and computation time is to remove + (near-)duplicate points and use ``sample_weight`` instead. + + :class:`~sklearn.cluster.OPTICS` provides a similar clustering with lower + memory usage. + + References + ---------- + Ester, M., H. P. Kriegel, J. Sander, and X. Xu, `"A Density-Based + Algorithm for Discovering Clusters in Large Spatial Databases with Noise" + `_. + In: Proceedings of the 2nd International Conference on Knowledge Discovery + and Data Mining, Portland, OR, AAAI Press, pp. 226-231. 1996 + + Schubert, E., Sander, J., Ester, M., Kriegel, H. P., & Xu, X. (2017). + :doi:`"DBSCAN revisited, revisited: why and how you should (still) use DBSCAN." + <10.1145/3068335>` + ACM Transactions on Database Systems (TODS), 42(3), 19. + + Examples + -------- + >>> from sklearn.cluster import dbscan + >>> X = [[1, 2], [2, 2], [2, 3], [8, 7], [8, 8], [25, 80]] + >>> core_samples, labels = dbscan(X, eps=3, min_samples=2) + >>> core_samples + array([0, 1, 2, 3, 4]) + >>> labels + array([ 0, 0, 0, 1, 1, -1]) + """ + + est = DBSCAN( + eps=eps, + min_samples=min_samples, + metric=metric, + metric_params=metric_params, + algorithm=algorithm, + leaf_size=leaf_size, + p=p, + n_jobs=n_jobs, + ) + est.fit(X, sample_weight=sample_weight) + return est.core_sample_indices_, est.labels_ + + +class DBSCAN(ClusterMixin, BaseEstimator): + """Perform DBSCAN clustering from vector array or distance matrix. + + DBSCAN - Density-Based Spatial Clustering of Applications with Noise. + Finds core samples of high density and expands clusters from them. + Good for data which contains clusters of similar density. + + This implementation has a worst case memory complexity of :math:`O({n}^2)`, + which can occur when the `eps` param is large and `min_samples` is low, + while the original DBSCAN only uses linear memory. + For further details, see the Notes below. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + eps : float, default=0.5 + The maximum distance between two samples for one to be considered + as in the neighborhood of the other. This is not a maximum bound + on the distances of points within a cluster. This is the most + important DBSCAN parameter to choose appropriately for your data set + and distance function. + + min_samples : int, default=5 + The number of samples (or total weight) in a neighborhood for a point to + be considered as a core point. This includes the point itself. If + `min_samples` is set to a higher value, DBSCAN will find denser clusters, + whereas if it is set to a lower value, the found clusters will be more + sparse. + + metric : str, or callable, default='euclidean' + The metric to use when calculating distance between instances in a + feature array. If metric is a string or callable, it must be one of + the options allowed by :func:`sklearn.metrics.pairwise_distances` for + its metric parameter. + If metric is "precomputed", X is assumed to be a distance matrix and + must be square. X may be a :term:`sparse graph`, in which + case only "nonzero" elements may be considered neighbors for DBSCAN. + + .. versionadded:: 0.17 + metric *precomputed* to accept precomputed sparse matrix. + + metric_params : dict, default=None + Additional keyword arguments for the metric function. + + .. versionadded:: 0.19 + + algorithm : {'auto', 'ball_tree', 'kd_tree', 'brute'}, default='auto' + The algorithm to be used by the NearestNeighbors module + to compute pointwise distances and find nearest neighbors. + See NearestNeighbors module documentation for details. + + leaf_size : int, default=30 + Leaf size passed to BallTree or cKDTree. This can affect the speed + of the construction and query, as well as the memory required + to store the tree. The optimal value depends + on the nature of the problem. + + p : float, default=None + The power of the Minkowski metric to be used to calculate distance + between points. If None, then ``p=2`` (equivalent to the Euclidean + distance). + + n_jobs : int, default=None + The number of parallel jobs to run. + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + Attributes + ---------- + core_sample_indices_ : ndarray of shape (n_core_samples,) + Indices of core samples. + + components_ : ndarray of shape (n_core_samples, n_features) + Copy of each core sample found by training. + + labels_ : ndarray of shape (n_samples) + Cluster labels for each point in the dataset given to fit(). + Noisy samples are given the label -1. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + OPTICS : A similar clustering at multiple values of eps. Our implementation + is optimized for memory usage. + + Notes + ----- + This implementation bulk-computes all neighborhood queries, which increases + the memory complexity to O(n.d) where d is the average number of neighbors, + while original DBSCAN had memory complexity O(n). It may attract a higher + memory complexity when querying these nearest neighborhoods, depending + on the ``algorithm``. + + One way to avoid the query complexity is to pre-compute sparse + neighborhoods in chunks using + :func:`NearestNeighbors.radius_neighbors_graph + ` with + ``mode='distance'``, then using ``metric='precomputed'`` here. + + Another way to reduce memory and computation time is to remove + (near-)duplicate points and use ``sample_weight`` instead. + + :class:`~sklearn.cluster.OPTICS` provides a similar clustering with lower memory + usage. + + References + ---------- + Ester, M., H. P. Kriegel, J. Sander, and X. Xu, `"A Density-Based + Algorithm for Discovering Clusters in Large Spatial Databases with Noise" + `_. + In: Proceedings of the 2nd International Conference on Knowledge Discovery + and Data Mining, Portland, OR, AAAI Press, pp. 226-231. 1996 + + Schubert, E., Sander, J., Ester, M., Kriegel, H. P., & Xu, X. (2017). + :doi:`"DBSCAN revisited, revisited: why and how you should (still) use DBSCAN." + <10.1145/3068335>` + ACM Transactions on Database Systems (TODS), 42(3), 19. + + Examples + -------- + >>> from sklearn.cluster import DBSCAN + >>> import numpy as np + >>> X = np.array([[1, 2], [2, 2], [2, 3], + ... [8, 7], [8, 8], [25, 80]]) + >>> clustering = DBSCAN(eps=3, min_samples=2).fit(X) + >>> clustering.labels_ + array([ 0, 0, 0, 1, 1, -1]) + >>> clustering + DBSCAN(eps=3, min_samples=2) + + For an example, see + :ref:`sphx_glr_auto_examples_cluster_plot_dbscan.py`. + + For a comparison of DBSCAN with other clustering algorithms, see + :ref:`sphx_glr_auto_examples_cluster_plot_cluster_comparison.py` + """ + + _parameter_constraints: dict = { + "eps": [Interval(Real, 0.0, None, closed="neither")], + "min_samples": [Interval(Integral, 1, None, closed="left")], + "metric": [ + StrOptions(set(_VALID_METRICS) | {"precomputed"}), + callable, + ], + "metric_params": [dict, None], + "algorithm": [StrOptions({"auto", "ball_tree", "kd_tree", "brute"})], + "leaf_size": [Interval(Integral, 1, None, closed="left")], + "p": [Interval(Real, 0.0, None, closed="left"), None], + "n_jobs": [Integral, None], + } + + def __init__( + self, + eps=0.5, + *, + min_samples=5, + metric="euclidean", + metric_params=None, + algorithm="auto", + leaf_size=30, + p=None, + n_jobs=None, + ): + self.eps = eps + self.min_samples = min_samples + self.metric = metric + self.metric_params = metric_params + self.algorithm = algorithm + self.leaf_size = leaf_size + self.p = p + self.n_jobs = n_jobs + + @_fit_context( + # DBSCAN.metric is not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, y=None, sample_weight=None): + """Perform DBSCAN clustering from features, or distance matrix. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features), or \ + (n_samples, n_samples) + Training instances to cluster, or distances between instances if + ``metric='precomputed'``. If a sparse matrix is provided, it will + be converted into a sparse ``csr_matrix``. + + y : Ignored + Not used, present here for API consistency by convention. + + sample_weight : array-like of shape (n_samples,), default=None + Weight of each sample, such that a sample with a weight of at least + ``min_samples`` is by itself a core sample; a sample with a + negative weight may inhibit its eps-neighbor from being core. + Note that weights are absolute, and default to 1. + + Returns + ------- + self : object + Returns a fitted instance of self. + """ + X = validate_data(self, X, accept_sparse="csr") + + if sample_weight is not None: + sample_weight = _check_sample_weight(sample_weight, X) + + # Calculate neighborhood for all samples. This leaves the original + # point in, which needs to be considered later (i.e. point i is in the + # neighborhood of point i. While True, its useless information) + if self.metric == "precomputed" and sparse.issparse(X): + # set the diagonal to explicit values, as a point is its own + # neighbor + X = X.copy() # copy to avoid in-place modification + with warnings.catch_warnings(): + warnings.simplefilter("ignore", sparse.SparseEfficiencyWarning) + X.setdiag(X.diagonal()) + + neighbors_model = NearestNeighbors( + radius=self.eps, + algorithm=self.algorithm, + leaf_size=self.leaf_size, + metric=self.metric, + metric_params=self.metric_params, + p=self.p, + n_jobs=self.n_jobs, + ) + neighbors_model.fit(X) + # This has worst case O(n^2) memory complexity + neighborhoods = neighbors_model.radius_neighbors(X, return_distance=False) + + if sample_weight is None: + n_neighbors = np.array([len(neighbors) for neighbors in neighborhoods]) + else: + n_neighbors = np.array( + [np.sum(sample_weight[neighbors]) for neighbors in neighborhoods] + ) + + # Initially, all samples are noise. + labels = np.full(X.shape[0], -1, dtype=np.intp) + + # A list of all core samples found. + core_samples = np.asarray(n_neighbors >= self.min_samples, dtype=np.uint8) + dbscan_inner(core_samples, neighborhoods, labels) + + self.core_sample_indices_ = np.where(core_samples)[0] + self.labels_ = labels + + if len(self.core_sample_indices_): + # fix for scipy sparse indexing issue + self.components_ = X[self.core_sample_indices_].copy() + else: + # no core samples + self.components_ = np.empty((0, X.shape[1])) + return self + + def fit_predict(self, X, y=None, sample_weight=None): + """Compute clusters from a data or distance matrix and predict labels. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features), or \ + (n_samples, n_samples) + Training instances to cluster, or distances between instances if + ``metric='precomputed'``. If a sparse matrix is provided, it will + be converted into a sparse ``csr_matrix``. + + y : Ignored + Not used, present here for API consistency by convention. + + sample_weight : array-like of shape (n_samples,), default=None + Weight of each sample, such that a sample with a weight of at least + ``min_samples`` is by itself a core sample; a sample with a + negative weight may inhibit its eps-neighbor from being core. + Note that weights are absolute, and default to 1. + + Returns + ------- + labels : ndarray of shape (n_samples,) + Cluster labels. Noisy samples are given the label -1. + """ + self.fit(X, sample_weight=sample_weight) + return self.labels_ + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.pairwise = self.metric == "precomputed" + tags.input_tags.sparse = True + return tags diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_dbscan_inner.cpython-310-x86_64-linux-gnu.so b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_dbscan_inner.cpython-310-x86_64-linux-gnu.so new file mode 100644 index 0000000000000000000000000000000000000000..ce45bf1d355ade266248a0f433e97bac698c22b8 Binary files /dev/null and b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_dbscan_inner.cpython-310-x86_64-linux-gnu.so differ diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_dbscan_inner.pyx b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_dbscan_inner.pyx new file mode 100644 index 0000000000000000000000000000000000000000..266b214bb269a717fd2eea300fe7445b96bd7cba --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_dbscan_inner.pyx @@ -0,0 +1,41 @@ +# Fast inner loop for DBSCAN. + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +from libcpp.vector cimport vector + +from ..utils._typedefs cimport uint8_t, intp_t + + +def dbscan_inner(const uint8_t[::1] is_core, + object[:] neighborhoods, + intp_t[::1] labels): + cdef intp_t i, label_num = 0, v + cdef intp_t[:] neighb + cdef vector[intp_t] stack + + for i in range(labels.shape[0]): + if labels[i] != -1 or not is_core[i]: + continue + + # Depth-first search starting from i, ending at the non-core points. + # This is very similar to the classic algorithm for computing connected + # components, the difference being that we label non-core points as + # part of a cluster (component), but don't expand their neighborhoods. + while True: + if labels[i] == -1: + labels[i] = label_num + if is_core[i]: + neighb = neighborhoods[i] + for i in range(neighb.shape[0]): + v = neighb[i] + if labels[v] == -1: + stack.push_back(v) + + if stack.size() == 0: + break + i = stack.back() + stack.pop_back() + + label_num += 1 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_feature_agglomeration.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_feature_agglomeration.py new file mode 100644 index 0000000000000000000000000000000000000000..32fcb85625f354bf0dcece88453e7e8f931e03cb --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_feature_agglomeration.py @@ -0,0 +1,76 @@ +""" +Feature agglomeration. Base classes and functions for performing feature +agglomeration. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import numpy as np +from scipy.sparse import issparse + +from ..base import TransformerMixin +from ..utils.validation import check_is_fitted, validate_data + +############################################################################### +# Mixin class for feature agglomeration. + + +class AgglomerationTransform(TransformerMixin): + """ + A class for feature agglomeration via the transform interface. + """ + + def transform(self, X): + """ + Transform a new matrix using the built clustering. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) or \ + (n_samples, n_samples) + A M by N array of M observations in N dimensions or a length + M array of M one-dimensional observations. + + Returns + ------- + Y : ndarray of shape (n_samples, n_clusters) or (n_clusters,) + The pooled values for each feature cluster. + """ + check_is_fitted(self) + + X = validate_data(self, X, reset=False) + if self.pooling_func == np.mean and not issparse(X): + size = np.bincount(self.labels_) + n_samples = X.shape[0] + # a fast way to compute the mean of grouped features + nX = np.array( + [np.bincount(self.labels_, X[i, :]) / size for i in range(n_samples)] + ) + else: + nX = [ + self.pooling_func(X[:, self.labels_ == l], axis=1) + for l in np.unique(self.labels_) + ] + nX = np.array(nX).T + return nX + + def inverse_transform(self, X): + """ + Inverse the transformation and return a vector of size `n_features`. + + Parameters + ---------- + X : array-like of shape (n_samples, n_clusters) or (n_clusters,) + The values to be assigned to each cluster of samples. + + Returns + ------- + X_original : ndarray of shape (n_samples, n_features) or (n_features,) + A vector of size `n_samples` with the values of `X` assigned to + each of the cluster of samples. + """ + check_is_fitted(self) + + unil, inverse = np.unique(self.labels_, return_inverse=True) + return X[..., inverse] diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..67dd18fb94b593f0a3125c1f5833f3b9597614ba --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/__init__.py @@ -0,0 +1,2 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_linkage.pyx b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_linkage.pyx new file mode 100644 index 0000000000000000000000000000000000000000..5684193a13d40ed68cabe9b8502a4b59b18d4e1b --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_linkage.pyx @@ -0,0 +1,274 @@ +# Minimum spanning tree single linkage implementation for hdbscan + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are met: + +# 1. Redistributions of source code must retain the above copyright notice, +# this list of conditions and the following disclaimer. + +# 2. Redistributions in binary form must reproduce the above copyright notice, +# this list of conditions and the following disclaimer in the documentation +# and/or other materials provided with the distribution. + +# 3. Neither the name of the copyright holder nor the names of its contributors +# may be used to endorse or promote products derived from this software without +# specific prior written permission. + +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +# POSSIBILITY OF SUCH DAMAGE. + +cimport numpy as cnp +from libc.float cimport DBL_MAX + +import numpy as np +from ...metrics._dist_metrics cimport DistanceMetric64 +from ...cluster._hierarchical_fast cimport UnionFind +from ...cluster._hdbscan._tree cimport HIERARCHY_t +from ...cluster._hdbscan._tree import HIERARCHY_dtype +from ...utils._typedefs cimport intp_t, float64_t, int64_t, uint8_t + +cnp.import_array() + +cdef extern from "numpy/arrayobject.h": + intp_t * PyArray_SHAPE(cnp.PyArrayObject *) + +# Numpy structured dtype representing a single ordered edge in Prim's algorithm +MST_edge_dtype = np.dtype([ + ("current_node", np.int64), + ("next_node", np.int64), + ("distance", np.float64), +]) + +# Packed shouldn't make a difference since they're all 8-byte quantities, +# but it's included just to be safe. +ctypedef packed struct MST_edge_t: + int64_t current_node + int64_t next_node + float64_t distance + +cpdef cnp.ndarray[MST_edge_t, ndim=1, mode='c'] mst_from_mutual_reachability( + cnp.ndarray[float64_t, ndim=2] mutual_reachability +): + """Compute the Minimum Spanning Tree (MST) representation of the mutual- + reachability graph using Prim's algorithm. + + Parameters + ---------- + mutual_reachability : ndarray of shape (n_samples, n_samples) + Array of mutual-reachabilities between samples. + + Returns + ------- + mst : ndarray of shape (n_samples - 1,), dtype=MST_edge_dtype + The MST representation of the mutual-reachability graph. The MST is + represented as a collection of edges. + """ + cdef: + # Note: we utilize ndarray's over memory-views to make use of numpy + # binary indexing and sub-selection below. + cnp.ndarray[int64_t, ndim=1, mode='c'] current_labels + cnp.ndarray[float64_t, ndim=1, mode='c'] min_reachability, left, right + cnp.ndarray[MST_edge_t, ndim=1, mode='c'] mst + + cnp.ndarray[uint8_t, mode='c'] label_filter + + int64_t n_samples = PyArray_SHAPE( mutual_reachability)[0] + int64_t current_node, new_node_index, new_node, i + + mst = np.empty(n_samples - 1, dtype=MST_edge_dtype) + current_labels = np.arange(n_samples, dtype=np.int64) + current_node = 0 + min_reachability = np.full(n_samples, fill_value=np.inf, dtype=np.float64) + for i in range(0, n_samples - 1): + label_filter = current_labels != current_node + current_labels = current_labels[label_filter] + left = min_reachability[label_filter] + right = mutual_reachability[current_node][current_labels] + min_reachability = np.minimum(left, right) + + new_node_index = np.argmin(min_reachability) + new_node = current_labels[new_node_index] + mst[i].current_node = current_node + mst[i].next_node = new_node + mst[i].distance = min_reachability[new_node_index] + current_node = new_node + + return mst + + +cpdef cnp.ndarray[MST_edge_t, ndim=1, mode='c'] mst_from_data_matrix( + const float64_t[:, ::1] raw_data, + const float64_t[::1] core_distances, + DistanceMetric64 dist_metric, + float64_t alpha=1.0 +): + """Compute the Minimum Spanning Tree (MST) representation of the mutual- + reachability graph generated from the provided `raw_data` and + `core_distances` using Prim's algorithm. + + Parameters + ---------- + raw_data : ndarray of shape (n_samples, n_features) + Input array of data samples. + + core_distances : ndarray of shape (n_samples,) + An array containing the core-distance calculated for each corresponding + sample. + + dist_metric : DistanceMetric + The distance metric to use when calculating pairwise distances for + determining mutual-reachability. + + Returns + ------- + mst : ndarray of shape (n_samples - 1,), dtype=MST_edge_dtype + The MST representation of the mutual-reachability graph. The MST is + represented as a collection of edges. + """ + + cdef: + uint8_t[::1] in_tree + float64_t[::1] min_reachability + int64_t[::1] current_sources + cnp.ndarray[MST_edge_t, ndim=1, mode='c'] mst + + int64_t current_node, source_node, new_node, next_node_source + int64_t i, j, n_samples, num_features + + float64_t current_node_core_dist, new_reachability, mutual_reachability_distance + float64_t next_node_min_reach, pair_distance, next_node_core_dist + + n_samples = raw_data.shape[0] + num_features = raw_data.shape[1] + + mst = np.empty(n_samples - 1, dtype=MST_edge_dtype) + + in_tree = np.zeros(n_samples, dtype=np.uint8) + min_reachability = np.full(n_samples, fill_value=np.inf, dtype=np.float64) + current_sources = np.ones(n_samples, dtype=np.int64) + + current_node = 0 + + # The following loop dynamically updates minimum reachability node-by-node, + # avoiding unnecessary computation where possible. + for i in range(0, n_samples - 1): + + in_tree[current_node] = 1 + + current_node_core_dist = core_distances[current_node] + + new_reachability = DBL_MAX + source_node = 0 + new_node = 0 + + for j in range(n_samples): + if in_tree[j]: + continue + + next_node_min_reach = min_reachability[j] + next_node_source = current_sources[j] + + pair_distance = dist_metric.dist( + &raw_data[current_node, 0], + &raw_data[j, 0], + num_features + ) + + pair_distance /= alpha + + next_node_core_dist = core_distances[j] + mutual_reachability_distance = max( + current_node_core_dist, + next_node_core_dist, + pair_distance + ) + + # If MRD(i, j) is smaller than node j's min_reachability, we update + # node j's min_reachability for future reference. + if mutual_reachability_distance < next_node_min_reach: + min_reachability[j] = mutual_reachability_distance + current_sources[j] = current_node + + # If MRD(i, j) is also smaller than node i's current + # min_reachability, we update and set their edge as the current + # MST edge candidate. + if mutual_reachability_distance < new_reachability: + new_reachability = mutual_reachability_distance + source_node = current_node + new_node = j + + # If the node j is closer to another node already in the tree, we + # make their edge the current MST candidate edge. + elif next_node_min_reach < new_reachability: + new_reachability = next_node_min_reach + source_node = next_node_source + new_node = j + + mst[i].current_node = source_node + mst[i].next_node = new_node + mst[i].distance = new_reachability + current_node = new_node + + return mst + +cpdef cnp.ndarray[HIERARCHY_t, ndim=1, mode="c"] make_single_linkage(const MST_edge_t[::1] mst): + """Construct a single-linkage tree from an MST. + + Parameters + ---------- + mst : ndarray of shape (n_samples - 1,), dtype=MST_edge_dtype + The MST representation of the mutual-reachability graph. The MST is + represented as a collection of edges. + + Returns + ------- + single_linkage : ndarray of shape (n_samples - 1,), dtype=HIERARCHY_dtype + The single-linkage tree tree (dendrogram) built from the MST. Each + of the array represents the following: + + - left node/cluster + - right node/cluster + - distance + - new cluster size + """ + cdef: + cnp.ndarray[HIERARCHY_t, ndim=1, mode="c"] single_linkage + + # Note mst.shape[0] is one fewer than the number of samples + int64_t n_samples = mst.shape[0] + 1 + intp_t current_node_cluster, next_node_cluster + int64_t current_node, next_node, i + float64_t distance + UnionFind U = UnionFind(n_samples) + + single_linkage = np.zeros(n_samples - 1, dtype=HIERARCHY_dtype) + + for i in range(n_samples - 1): + + current_node = mst[i].current_node + next_node = mst[i].next_node + distance = mst[i].distance + + current_node_cluster = U.fast_find(current_node) + next_node_cluster = U.fast_find(next_node) + + single_linkage[i].left_node = current_node_cluster + single_linkage[i].right_node = next_node_cluster + single_linkage[i].value = distance + single_linkage[i].cluster_size = U.size[current_node_cluster] + U.size[next_node_cluster] + + U.union(current_node_cluster, next_node_cluster) + + return single_linkage diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_reachability.pyx b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_reachability.pyx new file mode 100644 index 0000000000000000000000000000000000000000..bff686ae0a6369a7891525433a3fd79341dd2022 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_reachability.pyx @@ -0,0 +1,210 @@ +# mutual reachability distance computations + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are met: + +# 1. Redistributions of source code must retain the above copyright notice, +# this list of conditions and the following disclaimer. + +# 2. Redistributions in binary form must reproduce the above copyright notice, +# this list of conditions and the following disclaimer in the documentation +# and/or other materials provided with the distribution. + +# 3. Neither the name of the copyright holder nor the names of its contributors +# may be used to endorse or promote products derived from this software without +# specific prior written permission. + +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +# POSSIBILITY OF SUCH DAMAGE. + +cimport numpy as cnp + +import numpy as np +from scipy.sparse import issparse +from cython cimport floating, integral +from libc.math cimport isfinite, INFINITY +from ...utils._typedefs cimport intp_t +cnp.import_array() + + +def mutual_reachability_graph( + distance_matrix, min_samples=5, max_distance=0.0 +): + """Compute the weighted adjacency matrix of the mutual reachability graph. + + The mutual reachability distance used to build the graph is defined as:: + + max(d_core(x_p), d_core(x_q), d(x_p, x_q)) + + and the core distance `d_core` is defined as the distance between a point + `x_p` and its k-th nearest neighbor. + + Note that all computations are done in-place. + + Parameters + ---------- + distance_matrix : {ndarray, sparse matrix} of shape (n_samples, n_samples) + Array of distances between samples. If sparse, the array must be in + `CSR` format. + + min_samples : int, default=5 + The parameter `k` used to calculate the distance between a point + `x_p` and its k-th nearest neighbor. + + max_distance : float, default=0.0 + The distance which `np.inf` is replaced with. When the true mutual- + reachability distance is measured to be infinite, it is instead + truncated to `max_dist`. Only used when `distance_matrix` is a sparse + matrix. + + Returns + ------- + mututal_reachability_graph: {ndarray, sparse matrix} of shape \ + (n_samples, n_samples) + Weighted adjacency matrix of the mutual reachability graph. + + References + ---------- + .. [1] Campello, R. J., Moulavi, D., & Sander, J. (2013, April). + Density-based clustering based on hierarchical density estimates. + In Pacific-Asia Conference on Knowledge Discovery and Data Mining + (pp. 160-172). Springer Berlin Heidelberg. + """ + further_neighbor_idx = min_samples - 1 + if issparse(distance_matrix): + if distance_matrix.format != "csr": + raise ValueError( + "Only sparse CSR matrices are supported for `distance_matrix`." + ) + _sparse_mutual_reachability_graph( + distance_matrix.data, + distance_matrix.indices, + distance_matrix.indptr, + distance_matrix.shape[0], + further_neighbor_idx=further_neighbor_idx, + max_distance=max_distance, + ) + else: + _dense_mutual_reachability_graph( + distance_matrix, further_neighbor_idx=further_neighbor_idx + ) + return distance_matrix + + +def _dense_mutual_reachability_graph( + floating[:, :] distance_matrix, + intp_t further_neighbor_idx, +): + """Dense implementation of mutual reachability graph. + + The computation is done in-place, i.e. the distance matrix is modified + directly. + + Parameters + ---------- + distance_matrix : ndarray of shape (n_samples, n_samples) + Array of distances between samples. + + further_neighbor_idx : int + The index of the furthest neighbor to use to define the core distances. + """ + cdef: + intp_t i, j, n_samples = distance_matrix.shape[0] + floating mutual_reachability_distance + floating[::1] core_distances + + # We assume that the distance matrix is symmetric. We choose to sort every + # row to have the same implementation than the sparse case that requires + # CSR matrix. + core_distances = np.ascontiguousarray( + np.partition( + distance_matrix, further_neighbor_idx, axis=1 + )[:, further_neighbor_idx] + ) + + with nogil: + # TODO: Update w/ prange with thread count based on + # _openmp_effective_n_threads + for i in range(n_samples): + for j in range(n_samples): + mutual_reachability_distance = max( + core_distances[i], + core_distances[j], + distance_matrix[i, j], + ) + distance_matrix[i, j] = mutual_reachability_distance + + +def _sparse_mutual_reachability_graph( + cnp.ndarray[floating, ndim=1, mode="c"] data, + cnp.ndarray[integral, ndim=1, mode="c"] indices, + cnp.ndarray[integral, ndim=1, mode="c"] indptr, + intp_t n_samples, + intp_t further_neighbor_idx, + floating max_distance, +): + """Sparse implementation of mutual reachability graph. + + The computation is done in-place, i.e. the distance matrix is modified + directly. This implementation only accepts `CSR` format sparse matrices. + + Parameters + ---------- + distance_matrix : sparse matrix of shape (n_samples, n_samples) + Sparse matrix of distances between samples. The sparse format should + be `CSR`. + + further_neighbor_idx : int + The index of the furthest neighbor to use to define the core distances. + + max_distance : float + The distance which `np.inf` is replaced with. When the true mutual- + reachability distance is measured to be infinite, it is instead + truncated to `max_dist`. Only used when `distance_matrix` is a sparse + matrix. + """ + cdef: + integral i, col_ind, row_ind + floating mutual_reachability_distance + floating[:] core_distances + floating[:] row_data + + if floating is float: + dtype = np.float32 + else: + dtype = np.float64 + + core_distances = np.empty(n_samples, dtype=dtype) + + for i in range(n_samples): + row_data = data[indptr[i]:indptr[i + 1]] + if further_neighbor_idx < row_data.size: + core_distances[i] = np.partition( + row_data, further_neighbor_idx + )[further_neighbor_idx] + else: + core_distances[i] = INFINITY + + with nogil: + for row_ind in range(n_samples): + for i in range(indptr[row_ind], indptr[row_ind + 1]): + col_ind = indices[i] + mutual_reachability_distance = max( + core_distances[row_ind], core_distances[col_ind], data[i] + ) + if isfinite(mutual_reachability_distance): + data[i] = mutual_reachability_distance + elif max_distance > 0: + data[i] = max_distance diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_tree.pxd b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_tree.pxd new file mode 100644 index 0000000000000000000000000000000000000000..23708b9a38d07884c035b88e260821146075f861 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_tree.pxd @@ -0,0 +1,49 @@ +# Copyright (c) 2015, Leland McInnes +# All rights reserved. + +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are met: + +# 1. Redistributions of source code must retain the above copyright notice, +# this list of conditions and the following disclaimer. + +# 2. Redistributions in binary form must reproduce the above copyright notice, +# this list of conditions and the following disclaimer in the documentation +# and/or other materials provided with the distribution. + +# 3. Neither the name of the copyright holder nor the names of its contributors +# may be used to endorse or promote products derived from this software without +# specific prior written permission. + +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +# POSSIBILITY OF SUCH DAMAGE. + +from ...utils._typedefs cimport intp_t, float64_t, uint8_t +cimport numpy as cnp + +# This corresponds to the scipy.cluster.hierarchy format +ctypedef packed struct HIERARCHY_t: + intp_t left_node + intp_t right_node + float64_t value + intp_t cluster_size + +# Effectively an edgelist encoding a parent/child pair, along with a value and +# the corresponding cluster_size in each row providing a tree structure. +ctypedef packed struct CONDENSED_t: + intp_t parent + intp_t child + float64_t value + intp_t cluster_size + +cdef extern from "numpy/arrayobject.h": + intp_t * PyArray_SHAPE(cnp.PyArrayObject *) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_tree.pyx b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_tree.pyx new file mode 100644 index 0000000000000000000000000000000000000000..161092033b915bd9bb51f87750fb156c6a598833 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/_tree.pyx @@ -0,0 +1,799 @@ +# Tree handling (condensing, finding stable clusters) for hdbscan + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are met: + +# 1. Redistributions of source code must retain the above copyright notice, +# this list of conditions and the following disclaimer. + +# 2. Redistributions in binary form must reproduce the above copyright notice, +# this list of conditions and the following disclaimer in the documentation +# and/or other materials provided with the distribution. + +# 3. Neither the name of the copyright holder nor the names of its contributors +# may be used to endorse or promote products derived from this software without +# specific prior written permission. + +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +# POSSIBILITY OF SUCH DAMAGE. + + +cimport numpy as cnp +from libc.math cimport isinf +import cython + +import numpy as np + +cnp.import_array() + +cdef extern from "numpy/arrayobject.h": + intp_t * PyArray_SHAPE(cnp.PyArrayObject *) + +cdef cnp.float64_t INFTY = np.inf +cdef cnp.intp_t NOISE = -1 + +HIERARCHY_dtype = np.dtype([ + ("left_node", np.intp), + ("right_node", np.intp), + ("value", np.float64), + ("cluster_size", np.intp), +]) + +CONDENSED_dtype = np.dtype([ + ("parent", np.intp), + ("child", np.intp), + ("value", np.float64), + ("cluster_size", np.intp), +]) + +cpdef tuple tree_to_labels( + const HIERARCHY_t[::1] single_linkage_tree, + cnp.intp_t min_cluster_size=10, + cluster_selection_method="eom", + bint allow_single_cluster=False, + cnp.float64_t cluster_selection_epsilon=0.0, + max_cluster_size=None, +): + cdef: + cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] condensed_tree + cnp.ndarray[cnp.intp_t, ndim=1, mode='c'] labels + cnp.ndarray[cnp.float64_t, ndim=1, mode='c'] probabilities + + condensed_tree = _condense_tree(single_linkage_tree, min_cluster_size) + labels, probabilities = _get_clusters( + condensed_tree, + _compute_stability(condensed_tree), + cluster_selection_method, + allow_single_cluster, + cluster_selection_epsilon, + max_cluster_size, + ) + + return (labels, probabilities) + +cdef list bfs_from_hierarchy( + const HIERARCHY_t[::1] hierarchy, + cnp.intp_t bfs_root +): + """ + Perform a breadth first search on a tree in scipy hclust format. + """ + + cdef list process_queue, next_queue, result + cdef cnp.intp_t n_samples = hierarchy.shape[0] + 1 + cdef cnp.intp_t node + process_queue = [bfs_root] + result = [] + + while process_queue: + result.extend(process_queue) + # By construction, node i is formed by the union of nodes + # hierarchy[i - n_samples, 0] and hierarchy[i - n_samples, 1] + process_queue = [ + x - n_samples + for x in process_queue + if x >= n_samples + ] + if process_queue: + next_queue = [] + for node in process_queue: + next_queue.extend( + [ + hierarchy[node].left_node, + hierarchy[node].right_node, + ] + ) + process_queue = next_queue + return result + + +cpdef cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] _condense_tree( + const HIERARCHY_t[::1] hierarchy, + cnp.intp_t min_cluster_size=10 +): + """Condense a tree according to a minimum cluster size. This is akin + to the runt pruning procedure of Stuetzle. The result is a much simpler + tree that is easier to visualize. We include extra information on the + lambda value at which individual points depart clusters for later + analysis and computation. + + Parameters + ---------- + hierarchy : ndarray of shape (n_samples,), dtype=HIERARCHY_dtype + A single linkage hierarchy in scipy.cluster.hierarchy format. + + min_cluster_size : int, optional (default 10) + The minimum size of clusters to consider. Clusters smaller than this + are pruned from the tree. + + Returns + ------- + condensed_tree : ndarray of shape (n_samples,), dtype=CONDENSED_dtype + Effectively an edgelist encoding a parent/child pair, along with a + value and the corresponding cluster_size in each row providing a tree + structure. + """ + + cdef: + cnp.intp_t root = 2 * hierarchy.shape[0] + cnp.intp_t n_samples = hierarchy.shape[0] + 1 + cnp.intp_t next_label = n_samples + 1 + list result_list, node_list = bfs_from_hierarchy(hierarchy, root) + + cnp.intp_t[::1] relabel + cnp.uint8_t[::1] ignore + + cnp.intp_t node, sub_node, left, right + cnp.float64_t lambda_value, distance + cnp.intp_t left_count, right_count + HIERARCHY_t children + + relabel = np.empty(root + 1, dtype=np.intp) + relabel[root] = n_samples + result_list = [] + ignore = np.zeros(len(node_list), dtype=bool) + + for node in node_list: + if ignore[node] or node < n_samples: + continue + + children = hierarchy[node - n_samples] + left = children.left_node + right = children.right_node + distance = children.value + if distance > 0.0: + lambda_value = 1.0 / distance + else: + lambda_value = INFTY + + if left >= n_samples: + left_count = hierarchy[left - n_samples].cluster_size + else: + left_count = 1 + + if right >= n_samples: + right_count = hierarchy[right - n_samples].cluster_size + else: + right_count = 1 + + if left_count >= min_cluster_size and right_count >= min_cluster_size: + relabel[left] = next_label + next_label += 1 + result_list.append( + (relabel[node], relabel[left], lambda_value, left_count) + ) + + relabel[right] = next_label + next_label += 1 + result_list.append( + (relabel[node], relabel[right], lambda_value, right_count) + ) + + elif left_count < min_cluster_size and right_count < min_cluster_size: + for sub_node in bfs_from_hierarchy(hierarchy, left): + if sub_node < n_samples: + result_list.append( + (relabel[node], sub_node, lambda_value, 1) + ) + ignore[sub_node] = True + + for sub_node in bfs_from_hierarchy(hierarchy, right): + if sub_node < n_samples: + result_list.append( + (relabel[node], sub_node, lambda_value, 1) + ) + ignore[sub_node] = True + + elif left_count < min_cluster_size: + relabel[right] = relabel[node] + for sub_node in bfs_from_hierarchy(hierarchy, left): + if sub_node < n_samples: + result_list.append( + (relabel[node], sub_node, lambda_value, 1) + ) + ignore[sub_node] = True + + else: + relabel[left] = relabel[node] + for sub_node in bfs_from_hierarchy(hierarchy, right): + if sub_node < n_samples: + result_list.append( + (relabel[node], sub_node, lambda_value, 1) + ) + ignore[sub_node] = True + + return np.array(result_list, dtype=CONDENSED_dtype) + + +cdef dict _compute_stability( + cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] condensed_tree +): + + cdef: + cnp.float64_t[::1] result, births + cnp.intp_t[:] parents = condensed_tree['parent'] + + cnp.intp_t parent, cluster_size, result_index, idx + cnp.float64_t lambda_val + CONDENSED_t condensed_node + cnp.intp_t largest_child = condensed_tree['child'].max() + cnp.intp_t smallest_cluster = np.min(parents) + cnp.intp_t num_clusters = np.max(parents) - smallest_cluster + 1 + dict stability_dict = {} + + largest_child = max(largest_child, smallest_cluster) + births = np.full(largest_child + 1, np.nan, dtype=np.float64) + + for idx in range(PyArray_SHAPE( condensed_tree)[0]): + condensed_node = condensed_tree[idx] + births[condensed_node.child] = condensed_node.value + + births[smallest_cluster] = 0.0 + + result = np.zeros(num_clusters, dtype=np.float64) + for idx in range(PyArray_SHAPE( condensed_tree)[0]): + condensed_node = condensed_tree[idx] + parent = condensed_node.parent + lambda_val = condensed_node.value + cluster_size = condensed_node.cluster_size + + result_index = parent - smallest_cluster + result[result_index] += (lambda_val - births[parent]) * cluster_size + + for idx in range(num_clusters): + stability_dict[idx + smallest_cluster] = result[idx] + + return stability_dict + + +cdef list bfs_from_cluster_tree( + cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] condensed_tree, + cnp.intp_t bfs_root +): + + cdef: + list result = [] + cnp.ndarray[cnp.intp_t, ndim=1] process_queue = ( + np.array([bfs_root], dtype=np.intp) + ) + cnp.ndarray[cnp.intp_t, ndim=1] children = condensed_tree['child'] + cnp.intp_t[:] parents = condensed_tree['parent'] + + while len(process_queue) > 0: + result.extend(process_queue.tolist()) + process_queue = children[np.isin(parents, process_queue)] + + return result + + +cdef cnp.float64_t[::1] max_lambdas(cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] condensed_tree): + + cdef: + cnp.intp_t parent, current_parent, idx + cnp.float64_t lambda_val, max_lambda + cnp.float64_t[::1] deaths + cnp.intp_t largest_parent = condensed_tree['parent'].max() + + deaths = np.zeros(largest_parent + 1, dtype=np.float64) + current_parent = condensed_tree[0].parent + max_lambda = condensed_tree[0].value + + for idx in range(1, PyArray_SHAPE( condensed_tree)[0]): + parent = condensed_tree[idx].parent + lambda_val = condensed_tree[idx].value + + if parent == current_parent: + max_lambda = max(max_lambda, lambda_val) + else: + deaths[current_parent] = max_lambda + current_parent = parent + max_lambda = lambda_val + + deaths[current_parent] = max_lambda # value for last parent + return deaths + + +@cython.final +cdef class TreeUnionFind: + + cdef cnp.intp_t[:, ::1] data + cdef cnp.uint8_t[::1] is_component + + def __init__(self, size): + cdef cnp.intp_t idx + self.data = np.zeros((size, 2), dtype=np.intp) + for idx in range(size): + self.data[idx, 0] = idx + self.is_component = np.ones(size, dtype=np.uint8) + + cdef void union(self, cnp.intp_t x, cnp.intp_t y): + cdef cnp.intp_t x_root = self.find(x) + cdef cnp.intp_t y_root = self.find(y) + + if self.data[x_root, 1] < self.data[y_root, 1]: + self.data[x_root, 0] = y_root + elif self.data[x_root, 1] > self.data[y_root, 1]: + self.data[y_root, 0] = x_root + else: + self.data[y_root, 0] = x_root + self.data[x_root, 1] += 1 + return + + cdef cnp.intp_t find(self, cnp.intp_t x): + if self.data[x, 0] != x: + self.data[x, 0] = self.find(self.data[x, 0]) + self.is_component[x] = False + return self.data[x, 0] + + +cpdef cnp.ndarray[cnp.intp_t, ndim=1, mode='c'] labelling_at_cut( + const HIERARCHY_t[::1] linkage, + cnp.float64_t cut, + cnp.intp_t min_cluster_size +): + """Given a single linkage tree and a cut value, return the + vector of cluster labels at that cut value. This is useful + for Robust Single Linkage, and extracting DBSCAN results + from a single HDBSCAN run. + + Parameters + ---------- + linkage : ndarray of shape (n_samples,), dtype=HIERARCHY_dtype + The single linkage tree in scipy.cluster.hierarchy format. + + cut : double + The cut value at which to find clusters. + + min_cluster_size : int + The minimum cluster size; clusters below this size at + the cut will be considered noise. + + Returns + ------- + labels : ndarray of shape (n_samples,) + The cluster labels for each point in the data set; + a label of -1 denotes a noise assignment. + """ + + cdef: + cnp.intp_t n, cluster, root, n_samples, cluster_label + cnp.intp_t[::1] unique_labels, cluster_size + cnp.ndarray[cnp.intp_t, ndim=1, mode='c'] result + TreeUnionFind union_find + dict cluster_label_map + HIERARCHY_t node + + root = 2 * linkage.shape[0] + n_samples = root // 2 + 1 + result = np.empty(n_samples, dtype=np.intp) + union_find = TreeUnionFind(root + 1) + + cluster = n_samples + for node in linkage: + if node.value < cut: + union_find.union(node.left_node, cluster) + union_find.union(node.right_node, cluster) + cluster += 1 + + cluster_size = np.zeros(cluster, dtype=np.intp) + for n in range(n_samples): + cluster = union_find.find(n) + cluster_size[cluster] += 1 + result[n] = cluster + + cluster_label_map = {-1: NOISE} + cluster_label = 0 + unique_labels = np.unique(result) + + for cluster in unique_labels: + if cluster_size[cluster] < min_cluster_size: + cluster_label_map[cluster] = NOISE + else: + cluster_label_map[cluster] = cluster_label + cluster_label += 1 + + for n in range(n_samples): + result[n] = cluster_label_map[result[n]] + + return result + + +cpdef cnp.ndarray[cnp.intp_t, ndim=1, mode='c'] _do_labelling( + cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] condensed_tree, + set clusters, + dict cluster_label_map, + cnp.intp_t allow_single_cluster, + cnp.float64_t cluster_selection_epsilon +): + """Given a condensed tree, clusters and a labeling map for the clusters, + return an array containing the labels of each point based on cluster + membership. Note that this is where points may be marked as noisy + outliers. The determination of some points as noise is in large, single- + cluster datasets is controlled by the `allow_single_cluster` and + `cluster_selection_epsilon` parameters. + + Parameters + ---------- + condensed_tree : ndarray of shape (n_samples,), dtype=CONDENSED_dtype + Effectively an edgelist encoding a parent/child pair, along with a + value and the corresponding cluster_size in each row providing a tree + structure. + + clusters : set + The set of nodes corresponding to identified clusters. These node + values should be the same as those present in `condensed_tree`. + + cluster_label_map : dict + A mapping from the node values present in `clusters` to the labels + which will be returned. + + Returns + ------- + labels : ndarray of shape (n_samples,) + The cluster labels for each point in the data set; + a label of -1 denotes a noise assignment. + """ + + cdef: + cnp.intp_t root_cluster + cnp.ndarray[cnp.intp_t, ndim=1, mode='c'] result + cnp.ndarray[cnp.intp_t, ndim=1] parent_array, child_array + cnp.ndarray[cnp.float64_t, ndim=1] lambda_array + TreeUnionFind union_find + cnp.intp_t n, parent, child, cluster + cnp.float64_t threshold + + child_array = condensed_tree['child'] + parent_array = condensed_tree['parent'] + lambda_array = condensed_tree['value'] + + root_cluster = np.min(parent_array) + result = np.empty(root_cluster, dtype=np.intp) + union_find = TreeUnionFind(np.max(parent_array) + 1) + + for n in range(PyArray_SHAPE( condensed_tree)[0]): + child = child_array[n] + parent = parent_array[n] + if child not in clusters: + union_find.union(parent, child) + + for n in range(root_cluster): + cluster = union_find.find(n) + label = NOISE + if cluster != root_cluster: + label = cluster_label_map[cluster] + elif len(clusters) == 1 and allow_single_cluster: + # There can only be one edge with this particular child hence this + # expression extracts a unique, scalar lambda value. + parent_lambda = lambda_array[child_array == n] + if cluster_selection_epsilon != 0.0: + threshold = 1 / cluster_selection_epsilon + else: + # The threshold should be calculated per-sample based on the + # largest lambda of any simbling node. + threshold = lambda_array[parent_array == cluster].max() + if parent_lambda >= threshold: + label = cluster_label_map[cluster] + + result[n] = label + + return result + + +cdef cnp.ndarray[cnp.float64_t, ndim=1, mode='c'] get_probabilities( + cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] condensed_tree, + dict cluster_map, + cnp.intp_t[::1] labels +): + + cdef: + cnp.ndarray[cnp.float64_t, ndim=1, mode='c'] result + cnp.float64_t[:] lambda_array + cnp.float64_t[::1] deaths + cnp.intp_t[:] child_array, parent_array + cnp.intp_t root_cluster, n, point, cluster_num, cluster + cnp.float64_t max_lambda, lambda_val + + child_array = condensed_tree['child'] + parent_array = condensed_tree['parent'] + lambda_array = condensed_tree['value'] + + result = np.zeros(labels.shape[0]) + deaths = max_lambdas(condensed_tree) + root_cluster = np.min(parent_array) + + for n in range(PyArray_SHAPE( condensed_tree)[0]): + point = child_array[n] + if point >= root_cluster: + continue + + cluster_num = labels[point] + if cluster_num == -1: + continue + + cluster = cluster_map[cluster_num] + max_lambda = deaths[cluster] + if max_lambda == 0.0 or isinf(lambda_array[n]): + result[point] = 1.0 + else: + lambda_val = min(lambda_array[n], max_lambda) + result[point] = lambda_val / max_lambda + + return result + + +cpdef list recurse_leaf_dfs( + cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] cluster_tree, + cnp.intp_t current_node +): + cdef cnp.intp_t[:] children + cdef cnp.intp_t child + + children = cluster_tree[cluster_tree['parent'] == current_node]['child'] + if children.shape[0] == 0: + return [current_node,] + else: + return sum([recurse_leaf_dfs(cluster_tree, child) for child in children], []) + + +cpdef list get_cluster_tree_leaves(cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] cluster_tree): + cdef cnp.intp_t root + if PyArray_SHAPE( cluster_tree)[0] == 0: + return [] + root = cluster_tree['parent'].min() + return recurse_leaf_dfs(cluster_tree, root) + +cdef cnp.intp_t traverse_upwards( + cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] cluster_tree, + cnp.float64_t cluster_selection_epsilon, + cnp.intp_t leaf, + cnp.intp_t allow_single_cluster +): + cdef cnp.intp_t root, parent + cdef cnp.float64_t parent_eps + + root = cluster_tree['parent'].min() + parent = cluster_tree[cluster_tree['child'] == leaf]['parent'] + if parent == root: + if allow_single_cluster: + return parent + else: + return leaf # return node closest to root + + parent_eps = 1 / cluster_tree[cluster_tree['child'] == parent]['value'] + if parent_eps > cluster_selection_epsilon: + return parent + else: + return traverse_upwards( + cluster_tree, + cluster_selection_epsilon, + parent, + allow_single_cluster + ) + +cdef set epsilon_search( + set leaves, + cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] cluster_tree, + cnp.float64_t cluster_selection_epsilon, + cnp.intp_t allow_single_cluster +): + cdef: + list selected_clusters = list() + list processed = list() + cnp.intp_t leaf, epsilon_child, sub_node + cnp.float64_t eps + cnp.uint8_t[:] leaf_nodes + cnp.ndarray[cnp.intp_t, ndim=1] children = cluster_tree['child'] + cnp.ndarray[cnp.float64_t, ndim=1] distances = cluster_tree['value'] + + for leaf in leaves: + leaf_nodes = children == leaf + eps = 1 / distances[leaf_nodes][0] + if eps < cluster_selection_epsilon: + if leaf not in processed: + epsilon_child = traverse_upwards( + cluster_tree, + cluster_selection_epsilon, + leaf, + allow_single_cluster + ) + selected_clusters.append(epsilon_child) + + for sub_node in bfs_from_cluster_tree(cluster_tree, epsilon_child): + if sub_node != epsilon_child: + processed.append(sub_node) + else: + selected_clusters.append(leaf) + + return set(selected_clusters) + + +@cython.wraparound(True) +cdef tuple _get_clusters( + cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] condensed_tree, + dict stability, + cluster_selection_method='eom', + cnp.uint8_t allow_single_cluster=False, + cnp.float64_t cluster_selection_epsilon=0.0, + max_cluster_size=None +): + """Given a tree and stability dict, produce the cluster labels + (and probabilities) for a flat clustering based on the chosen + cluster selection method. + + Parameters + ---------- + condensed_tree : ndarray of shape (n_samples,), dtype=CONDENSED_dtype + Effectively an edgelist encoding a parent/child pair, along with a + value and the corresponding cluster_size in each row providing a tree + structure. + + stability : dict + A dictionary mapping cluster_ids to stability values + + cluster_selection_method : string, optional (default 'eom') + The method of selecting clusters. The default is the + Excess of Mass algorithm specified by 'eom'. The alternate + option is 'leaf'. + + allow_single_cluster : boolean, optional (default False) + Whether to allow a single cluster to be selected by the + Excess of Mass algorithm. + + cluster_selection_epsilon: double, optional (default 0.0) + A distance threshold for cluster splits. + + max_cluster_size: int, default=None + The maximum size for clusters located by the EOM clusterer. Can + be overridden by the cluster_selection_epsilon parameter in + rare cases. + + Returns + ------- + labels : ndarray of shape (n_samples,) + An integer array of cluster labels, with -1 denoting noise. + + probabilities : ndarray (n_samples,) + The cluster membership strength of each sample. + + stabilities : ndarray (n_clusters,) + The cluster coherence strengths of each cluster. + """ + cdef: + list node_list + cnp.ndarray[CONDENSED_t, ndim=1, mode='c'] cluster_tree + cnp.uint8_t[::1] child_selection + cnp.ndarray[cnp.intp_t, ndim=1, mode='c'] labels + dict is_cluster, cluster_sizes + cnp.float64_t subtree_stability + cnp.intp_t node, sub_node, cluster, n_samples + cnp.ndarray[cnp.float64_t, ndim=1, mode='c'] probs + + # Assume clusters are ordered by numeric id equivalent to + # a topological sort of the tree; This is valid given the + # current implementation above, so don't change that ... or + # if you do, change this accordingly! + if allow_single_cluster: + node_list = sorted(stability.keys(), reverse=True) + else: + node_list = sorted(stability.keys(), reverse=True)[:-1] + # (exclude root) + + cluster_tree = condensed_tree[condensed_tree['cluster_size'] > 1] + is_cluster = {cluster: True for cluster in node_list} + n_samples = np.max(condensed_tree[condensed_tree['cluster_size'] == 1]['child']) + 1 + + if max_cluster_size is None: + max_cluster_size = n_samples + 1 # Set to a value that will never be triggered + cluster_sizes = { + child: cluster_size for child, cluster_size + in zip(cluster_tree['child'], cluster_tree['cluster_size']) + } + if allow_single_cluster: + # Compute cluster size for the root node + cluster_sizes[node_list[-1]] = np.sum( + cluster_tree[cluster_tree['parent'] == node_list[-1]]['cluster_size']) + + if cluster_selection_method == 'eom': + for node in node_list: + child_selection = (cluster_tree['parent'] == node) + subtree_stability = np.sum([ + stability[child] for + child in cluster_tree['child'][child_selection]]) + if subtree_stability > stability[node] or cluster_sizes[node] > max_cluster_size: + is_cluster[node] = False + stability[node] = subtree_stability + else: + for sub_node in bfs_from_cluster_tree(cluster_tree, node): + if sub_node != node: + is_cluster[sub_node] = False + + if cluster_selection_epsilon != 0.0 and PyArray_SHAPE( cluster_tree)[0] > 0: + eom_clusters = [c for c in is_cluster if is_cluster[c]] + selected_clusters = [] + # first check if eom_clusters only has root node, which skips epsilon check. + if (len(eom_clusters) == 1 and eom_clusters[0] == cluster_tree['parent'].min()): + if allow_single_cluster: + selected_clusters = eom_clusters + else: + selected_clusters = epsilon_search( + set(eom_clusters), + cluster_tree, + cluster_selection_epsilon, + allow_single_cluster + ) + for c in is_cluster: + if c in selected_clusters: + is_cluster[c] = True + else: + is_cluster[c] = False + + elif cluster_selection_method == 'leaf': + leaves = set(get_cluster_tree_leaves(cluster_tree)) + if len(leaves) == 0: + for c in is_cluster: + is_cluster[c] = False + is_cluster[condensed_tree['parent'].min()] = True + + if cluster_selection_epsilon != 0.0: + selected_clusters = epsilon_search( + leaves, + cluster_tree, + cluster_selection_epsilon, + allow_single_cluster + ) + else: + selected_clusters = leaves + + for c in is_cluster: + if c in selected_clusters: + is_cluster[c] = True + else: + is_cluster[c] = False + + clusters = set([c for c in is_cluster if is_cluster[c]]) + cluster_map = {c: n for n, c in enumerate(sorted(list(clusters)))} + reverse_cluster_map = {n: c for c, n in cluster_map.items()} + + labels = _do_labelling( + condensed_tree, + clusters, + cluster_map, + allow_single_cluster, + cluster_selection_epsilon + ) + probs = get_probabilities(condensed_tree, reverse_cluster_map, labels) + + return (labels, probs) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/hdbscan.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/hdbscan.py new file mode 100644 index 0000000000000000000000000000000000000000..f292a1f65909b6a5a1a0287adbc2996a3dc36381 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/hdbscan.py @@ -0,0 +1,1000 @@ +""" +HDBSCAN: Hierarchical Density-Based Spatial Clustering + of Applications with Noise +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are met: + +# 1. Redistributions of source code must retain the above copyright notice, +# this list of conditions and the following disclaimer. + +# 2. Redistributions in binary form must reproduce the above copyright notice, +# this list of conditions and the following disclaimer in the documentation +# and/or other materials provided with the distribution. + +# 3. Neither the name of the copyright holder nor the names of its contributors +# may be used to endorse or promote products derived from this software without +# specific prior written permission. + +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +# POSSIBILITY OF SUCH DAMAGE. + +from numbers import Integral, Real +from warnings import warn + +import numpy as np +from scipy.sparse import csgraph, issparse + +from ...base import BaseEstimator, ClusterMixin, _fit_context +from ...metrics import pairwise_distances +from ...metrics._dist_metrics import DistanceMetric +from ...metrics.pairwise import _VALID_METRICS +from ...neighbors import BallTree, KDTree, NearestNeighbors +from ...utils._param_validation import Interval, StrOptions +from ...utils.validation import ( + _allclose_dense_sparse, + _assert_all_finite, + validate_data, +) +from ._linkage import ( + MST_edge_dtype, + make_single_linkage, + mst_from_data_matrix, + mst_from_mutual_reachability, +) +from ._reachability import mutual_reachability_graph +from ._tree import HIERARCHY_dtype, labelling_at_cut, tree_to_labels + +FAST_METRICS = set(KDTree.valid_metrics + BallTree.valid_metrics) + +# Encodings are arbitrary but must be strictly negative. +# The current encodings are chosen as extensions to the -1 noise label. +# Avoided enums so that the end user only deals with simple labels. +_OUTLIER_ENCODING: dict = { + "infinite": { + "label": -2, + # The probability could also be 1, since infinite points are certainly + # infinite outliers, however 0 is convention from the HDBSCAN library + # implementation. + "prob": 0, + }, + "missing": { + "label": -3, + # A nan probability is chosen to emphasize the fact that the + # corresponding data was not considered in the clustering problem. + "prob": np.nan, + }, +} + + +def _brute_mst(mutual_reachability, min_samples): + """ + Builds a minimum spanning tree (MST) from the provided mutual-reachability + values. This function dispatches to a custom Cython implementation for + dense arrays, and `scipy.sparse.csgraph.minimum_spanning_tree` for sparse + arrays/matrices. + + Parameters + ---------- + mututal_reachability_graph: {ndarray, sparse matrix} of shape \ + (n_samples, n_samples) + Weighted adjacency matrix of the mutual reachability graph. + + min_samples : int, default=None + The number of samples in a neighborhood for a point + to be considered as a core point. This includes the point itself. + + Returns + ------- + mst : ndarray of shape (n_samples - 1,), dtype=MST_edge_dtype + The MST representation of the mutual-reachability graph. The MST is + represented as a collection of edges. + """ + if not issparse(mutual_reachability): + return mst_from_mutual_reachability(mutual_reachability) + + # Check if the mutual reachability matrix has any rows which have + # less than `min_samples` non-zero elements. + indptr = mutual_reachability.indptr + num_points = mutual_reachability.shape[0] + if any((indptr[i + 1] - indptr[i]) < min_samples for i in range(num_points)): + raise ValueError( + f"There exists points with fewer than {min_samples} neighbors. Ensure" + " your distance matrix has non-zero values for at least" + f" `min_sample`={min_samples} neighbors for each points (i.e. K-nn" + " graph), or specify a `max_distance` in `metric_params` to use when" + " distances are missing." + ) + # Check connected component on mutual reachability. + # If more than one connected component is present, + # it means that the graph is disconnected. + n_components = csgraph.connected_components( + mutual_reachability, directed=False, return_labels=False + ) + if n_components > 1: + raise ValueError( + f"Sparse mutual reachability matrix has {n_components} connected" + " components. HDBSCAN cannot be performed on a disconnected graph. Ensure" + " that the sparse distance matrix has only one connected component." + ) + + # Compute the minimum spanning tree for the sparse graph + sparse_min_spanning_tree = csgraph.minimum_spanning_tree(mutual_reachability) + rows, cols = sparse_min_spanning_tree.nonzero() + mst = np.rec.fromarrays( + [rows, cols, sparse_min_spanning_tree.data], + dtype=MST_edge_dtype, + ) + return mst + + +def _process_mst(min_spanning_tree): + """ + Builds a single-linkage tree (SLT) from the provided minimum spanning tree + (MST). The MST is first sorted then processed by a custom Cython routine. + + Parameters + ---------- + min_spanning_tree : ndarray of shape (n_samples - 1,), dtype=MST_edge_dtype + The MST representation of the mutual-reachability graph. The MST is + represented as a collection of edges. + + Returns + ------- + single_linkage : ndarray of shape (n_samples - 1,), dtype=HIERARCHY_dtype + The single-linkage tree tree (dendrogram) built from the MST. + """ + # Sort edges of the min_spanning_tree by weight + row_order = np.argsort(min_spanning_tree["distance"]) + min_spanning_tree = min_spanning_tree[row_order] + # Convert edge list into standard hierarchical clustering format + return make_single_linkage(min_spanning_tree) + + +def _hdbscan_brute( + X, + min_samples=5, + alpha=None, + metric="euclidean", + n_jobs=None, + copy=False, + **metric_params, +): + """ + Builds a single-linkage tree (SLT) from the input data `X`. If + `metric="precomputed"` then `X` must be a symmetric array of distances. + Otherwise, the pairwise distances are calculated directly and passed to + `mutual_reachability_graph`. + + Parameters + ---------- + X : ndarray of shape (n_samples, n_features) or (n_samples, n_samples) + Either the raw data from which to compute the pairwise distances, + or the precomputed distances. + + min_samples : int, default=None + The number of samples in a neighborhood for a point + to be considered as a core point. This includes the point itself. + + alpha : float, default=1.0 + A distance scaling parameter as used in robust single linkage. + + metric : str or callable, default='euclidean' + The metric to use when calculating distance between instances in a + feature array. + + - If metric is a string or callable, it must be one of + the options allowed by :func:`~sklearn.metrics.pairwise_distances` + for its metric parameter. + + - If metric is "precomputed", X is assumed to be a distance matrix and + must be square. + + n_jobs : int, default=None + The number of jobs to use for computing the pairwise distances. This + works by breaking down the pairwise matrix into n_jobs even slices and + computing them in parallel. This parameter is passed directly to + :func:`~sklearn.metrics.pairwise_distances`. + + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + copy : bool, default=False + If `copy=True` then any time an in-place modifications would be made + that would overwrite `X`, a copy will first be made, guaranteeing that + the original data will be unchanged. Currently, it only applies when + `metric="precomputed"`, when passing a dense array or a CSR sparse + array/matrix. + + metric_params : dict, default=None + Arguments passed to the distance metric. + + Returns + ------- + single_linkage : ndarray of shape (n_samples - 1,), dtype=HIERARCHY_dtype + The single-linkage tree tree (dendrogram) built from the MST. + """ + if metric == "precomputed": + if X.shape[0] != X.shape[1]: + raise ValueError( + "The precomputed distance matrix is expected to be symmetric, however" + f" it has shape {X.shape}. Please verify that the" + " distance matrix was constructed correctly." + ) + if not _allclose_dense_sparse(X, X.T): + raise ValueError( + "The precomputed distance matrix is expected to be symmetric, however" + " its values appear to be asymmetric. Please verify that the distance" + " matrix was constructed correctly." + ) + + distance_matrix = X.copy() if copy else X + else: + distance_matrix = pairwise_distances( + X, metric=metric, n_jobs=n_jobs, **metric_params + ) + distance_matrix /= alpha + + max_distance = metric_params.get("max_distance", 0.0) + if issparse(distance_matrix) and distance_matrix.format != "csr": + # we need CSR format to avoid a conversion in `_brute_mst` when calling + # `csgraph.connected_components` + distance_matrix = distance_matrix.tocsr() + + # Note that `distance_matrix` is manipulated in-place, however we do not + # need it for anything else past this point, hence the operation is safe. + mutual_reachability_ = mutual_reachability_graph( + distance_matrix, min_samples=min_samples, max_distance=max_distance + ) + min_spanning_tree = _brute_mst(mutual_reachability_, min_samples=min_samples) + # Warn if the MST couldn't be constructed around the missing distances + if np.isinf(min_spanning_tree["distance"]).any(): + warn( + ( + "The minimum spanning tree contains edge weights with value " + "infinity. Potentially, you are missing too many distances " + "in the initial distance matrix for the given neighborhood " + "size." + ), + UserWarning, + ) + return _process_mst(min_spanning_tree) + + +def _hdbscan_prims( + X, + algo, + min_samples=5, + alpha=1.0, + metric="euclidean", + leaf_size=40, + n_jobs=None, + **metric_params, +): + """ + Builds a single-linkage tree (SLT) from the input data `X`. If + `metric="precomputed"` then `X` must be a symmetric array of distances. + Otherwise, the pairwise distances are calculated directly and passed to + `mutual_reachability_graph`. + + Parameters + ---------- + X : ndarray of shape (n_samples, n_features) + The raw data. + + min_samples : int, default=None + The number of samples in a neighborhood for a point + to be considered as a core point. This includes the point itself. + + alpha : float, default=1.0 + A distance scaling parameter as used in robust single linkage. + + metric : str or callable, default='euclidean' + The metric to use when calculating distance between instances in a + feature array. `metric` must be one of the options allowed by + :func:`~sklearn.metrics.pairwise_distances` for its metric + parameter. + + n_jobs : int, default=None + The number of jobs to use for computing the pairwise distances. This + works by breaking down the pairwise matrix into n_jobs even slices and + computing them in parallel. This parameter is passed directly to + :func:`~sklearn.metrics.pairwise_distances`. + + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + copy : bool, default=False + If `copy=True` then any time an in-place modifications would be made + that would overwrite `X`, a copy will first be made, guaranteeing that + the original data will be unchanged. Currently, it only applies when + `metric="precomputed"`, when passing a dense array or a CSR sparse + array/matrix. + + metric_params : dict, default=None + Arguments passed to the distance metric. + + Returns + ------- + single_linkage : ndarray of shape (n_samples - 1,), dtype=HIERARCHY_dtype + The single-linkage tree tree (dendrogram) built from the MST. + """ + # The Cython routines used require contiguous arrays + X = np.asarray(X, order="C") + + # Get distance to kth nearest neighbour + nbrs = NearestNeighbors( + n_neighbors=min_samples, + algorithm=algo, + leaf_size=leaf_size, + metric=metric, + metric_params=metric_params, + n_jobs=n_jobs, + p=None, + ).fit(X) + + neighbors_distances, _ = nbrs.kneighbors(X, min_samples, return_distance=True) + core_distances = np.ascontiguousarray(neighbors_distances[:, -1]) + dist_metric = DistanceMetric.get_metric(metric, **metric_params) + + # Mutual reachability distance is implicit in mst_from_data_matrix + min_spanning_tree = mst_from_data_matrix(X, core_distances, dist_metric, alpha) + return _process_mst(min_spanning_tree) + + +def remap_single_linkage_tree(tree, internal_to_raw, non_finite): + """ + Takes an internal single_linkage_tree structure and adds back in a set of points + that were initially detected as non-finite and returns that new tree. + These points will all be merged into the final node at np.inf distance and + considered noise points. + + Parameters + ---------- + tree : ndarray of shape (n_samples - 1,), dtype=HIERARCHY_dtype + The single-linkage tree tree (dendrogram) built from the MST. + internal_to_raw: dict + A mapping from internal integer index to the raw integer index + non_finite : ndarray + Boolean array of which entries in the raw data are non-finite + """ + finite_count = len(internal_to_raw) + + outlier_count = len(non_finite) + for i, _ in enumerate(tree): + left = tree[i]["left_node"] + right = tree[i]["right_node"] + + if left < finite_count: + tree[i]["left_node"] = internal_to_raw[left] + else: + tree[i]["left_node"] = left + outlier_count + if right < finite_count: + tree[i]["right_node"] = internal_to_raw[right] + else: + tree[i]["right_node"] = right + outlier_count + + outlier_tree = np.zeros(len(non_finite), dtype=HIERARCHY_dtype) + last_cluster_id = max( + tree[tree.shape[0] - 1]["left_node"], tree[tree.shape[0] - 1]["right_node"] + ) + last_cluster_size = tree[tree.shape[0] - 1]["cluster_size"] + for i, outlier in enumerate(non_finite): + outlier_tree[i] = (outlier, last_cluster_id + 1, np.inf, last_cluster_size + 1) + last_cluster_id += 1 + last_cluster_size += 1 + tree = np.concatenate([tree, outlier_tree]) + return tree + + +def _get_finite_row_indices(matrix): + """ + Returns the indices of the purely finite rows of a + sparse matrix or dense ndarray + """ + if issparse(matrix): + row_indices = np.array( + [i for i, row in enumerate(matrix.tolil().data) if np.all(np.isfinite(row))] + ) + else: + (row_indices,) = np.isfinite(matrix.sum(axis=1)).nonzero() + return row_indices + + +class HDBSCAN(ClusterMixin, BaseEstimator): + """Cluster data using hierarchical density-based clustering. + + HDBSCAN - Hierarchical Density-Based Spatial Clustering of Applications + with Noise. Performs :class:`~sklearn.cluster.DBSCAN` over varying epsilon + values and integrates the result to find a clustering that gives the best + stability over epsilon. + This allows HDBSCAN to find clusters of varying densities (unlike + :class:`~sklearn.cluster.DBSCAN`), and be more robust to parameter selection. + Read more in the :ref:`User Guide `. + + .. versionadded:: 1.3 + + Parameters + ---------- + min_cluster_size : int, default=5 + The minimum number of samples in a group for that group to be + considered a cluster; groupings smaller than this size will be left + as noise. + + min_samples : int, default=None + The parameter `k` used to calculate the distance between a point + `x_p` and its k-th nearest neighbor. + When `None`, defaults to `min_cluster_size`. + + cluster_selection_epsilon : float, default=0.0 + A distance threshold. Clusters below this value will be merged. + See [5]_ for more information. + + max_cluster_size : int, default=None + A limit to the size of clusters returned by the `"eom"` cluster + selection algorithm. There is no limit when `max_cluster_size=None`. + Has no effect if `cluster_selection_method="leaf"`. + + metric : str or callable, default='euclidean' + The metric to use when calculating distance between instances in a + feature array. + + - If metric is a string or callable, it must be one of + the options allowed by :func:`~sklearn.metrics.pairwise_distances` + for its metric parameter. + + - If metric is "precomputed", X is assumed to be a distance matrix and + must be square. + + metric_params : dict, default=None + Arguments passed to the distance metric. + + alpha : float, default=1.0 + A distance scaling parameter as used in robust single linkage. + See [3]_ for more information. + + algorithm : {"auto", "brute", "kd_tree", "ball_tree"}, default="auto" + Exactly which algorithm to use for computing core distances; By default + this is set to `"auto"` which attempts to use a + :class:`~sklearn.neighbors.KDTree` tree if possible, otherwise it uses + a :class:`~sklearn.neighbors.BallTree` tree. Both `"kd_tree"` and + `"ball_tree"` algorithms use the + :class:`~sklearn.neighbors.NearestNeighbors` estimator. + + If the `X` passed during `fit` is sparse or `metric` is invalid for + both :class:`~sklearn.neighbors.KDTree` and + :class:`~sklearn.neighbors.BallTree`, then it resolves to use the + `"brute"` algorithm. + + leaf_size : int, default=40 + Leaf size for trees responsible for fast nearest neighbour queries when + a KDTree or a BallTree are used as core-distance algorithms. A large + dataset size and small `leaf_size` may induce excessive memory usage. + If you are running out of memory consider increasing the `leaf_size` + parameter. Ignored for `algorithm="brute"`. + + n_jobs : int, default=None + Number of jobs to run in parallel to calculate distances. + `None` means 1 unless in a :obj:`joblib.parallel_backend` context. + `-1` means using all processors. See :term:`Glossary ` + for more details. + + cluster_selection_method : {"eom", "leaf"}, default="eom" + The method used to select clusters from the condensed tree. The + standard approach for HDBSCAN* is to use an Excess of Mass (`"eom"`) + algorithm to find the most persistent clusters. Alternatively you can + instead select the clusters at the leaves of the tree -- this provides + the most fine grained and homogeneous clusters. + + allow_single_cluster : bool, default=False + By default HDBSCAN* will not produce a single cluster, setting this + to True will override this and allow single cluster results in + the case that you feel this is a valid result for your dataset. + + store_centers : str, default=None + Which, if any, cluster centers to compute and store. The options are: + + - `None` which does not compute nor store any centers. + - `"centroid"` which calculates the center by taking the weighted + average of their positions. Note that the algorithm uses the + euclidean metric and does not guarantee that the output will be + an observed data point. + - `"medoid"` which calculates the center by taking the point in the + fitted data which minimizes the distance to all other points in + the cluster. This is slower than "centroid" since it requires + computing additional pairwise distances between points of the + same cluster but guarantees the output is an observed data point. + The medoid is also well-defined for arbitrary metrics, and does not + depend on a euclidean metric. + - `"both"` which computes and stores both forms of centers. + + copy : bool, default=False + If `copy=True` then any time an in-place modifications would be made + that would overwrite data passed to :term:`fit`, a copy will first be + made, guaranteeing that the original data will be unchanged. + Currently, it only applies when `metric="precomputed"`, when passing + a dense array or a CSR sparse matrix and when `algorithm="brute"`. + + Attributes + ---------- + labels_ : ndarray of shape (n_samples,) + Cluster labels for each point in the dataset given to :term:`fit`. + Outliers are labeled as follows: + + - Noisy samples are given the label -1. + - Samples with infinite elements (+/- np.inf) are given the label -2. + - Samples with missing data are given the label -3, even if they + also have infinite elements. + + probabilities_ : ndarray of shape (n_samples,) + The strength with which each sample is a member of its assigned + cluster. + + - Clustered samples have probabilities proportional to the degree that + they persist as part of the cluster. + - Noisy samples have probability zero. + - Samples with infinite elements (+/- np.inf) have probability 0. + - Samples with missing data have probability `np.nan`. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + centroids_ : ndarray of shape (n_clusters, n_features) + A collection containing the centroid of each cluster calculated under + the standard euclidean metric. The centroids may fall "outside" their + respective clusters if the clusters themselves are non-convex. + + Note that `n_clusters` only counts non-outlier clusters. That is to + say, the `-1, -2, -3` labels for the outlier clusters are excluded. + + medoids_ : ndarray of shape (n_clusters, n_features) + A collection containing the medoid of each cluster calculated under + the whichever metric was passed to the `metric` parameter. The + medoids are points in the original cluster which minimize the average + distance to all other points in that cluster under the chosen metric. + These can be thought of as the result of projecting the `metric`-based + centroid back onto the cluster. + + Note that `n_clusters` only counts non-outlier clusters. That is to + say, the `-1, -2, -3` labels for the outlier clusters are excluded. + + See Also + -------- + DBSCAN : Density-Based Spatial Clustering of Applications + with Noise. + OPTICS : Ordering Points To Identify the Clustering Structure. + Birch : Memory-efficient, online-learning algorithm. + + Notes + ----- + The `min_samples` parameter includes the point itself, whereas the implementation in + `scikit-learn-contrib/hdbscan `_ + does not. To get the same results in both versions, the value of `min_samples` here + must be 1 greater than the value used in `scikit-learn-contrib/hdbscan + `_. + + References + ---------- + + .. [1] :doi:`Campello, R. J., Moulavi, D., & Sander, J. Density-based clustering + based on hierarchical density estimates. + <10.1007/978-3-642-37456-2_14>` + .. [2] :doi:`Campello, R. J., Moulavi, D., Zimek, A., & Sander, J. + Hierarchical density estimates for data clustering, visualization, + and outlier detection.<10.1145/2733381>` + + .. [3] `Chaudhuri, K., & Dasgupta, S. Rates of convergence for the + cluster tree. + `_ + + .. [4] `Moulavi, D., Jaskowiak, P.A., Campello, R.J., Zimek, A. and + Sander, J. Density-Based Clustering Validation. + `_ + + .. [5] :arxiv:`Malzer, C., & Baum, M. "A Hybrid Approach To Hierarchical + Density-based Cluster Selection."<1911.02282>`. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.cluster import HDBSCAN + >>> from sklearn.datasets import load_digits + >>> X, _ = load_digits(return_X_y=True) + >>> hdb = HDBSCAN(min_cluster_size=20) + >>> hdb.fit(X) + HDBSCAN(min_cluster_size=20) + >>> hdb.labels_.shape == (X.shape[0],) + True + >>> np.unique(hdb.labels_).tolist() + [-1, 0, 1, 2, 3, 4, 5, 6, 7] + """ + + _parameter_constraints = { + "min_cluster_size": [Interval(Integral, left=2, right=None, closed="left")], + "min_samples": [Interval(Integral, left=1, right=None, closed="left"), None], + "cluster_selection_epsilon": [ + Interval(Real, left=0, right=None, closed="left") + ], + "max_cluster_size": [ + None, + Interval(Integral, left=1, right=None, closed="left"), + ], + "metric": [ + StrOptions(FAST_METRICS | set(_VALID_METRICS) | {"precomputed"}), + callable, + ], + "metric_params": [dict, None], + "alpha": [Interval(Real, left=0, right=None, closed="neither")], + "algorithm": [StrOptions({"auto", "brute", "kd_tree", "ball_tree"})], + "leaf_size": [Interval(Integral, left=1, right=None, closed="left")], + "n_jobs": [Integral, None], + "cluster_selection_method": [StrOptions({"eom", "leaf"})], + "allow_single_cluster": ["boolean"], + "store_centers": [None, StrOptions({"centroid", "medoid", "both"})], + "copy": ["boolean"], + } + + def __init__( + self, + min_cluster_size=5, + min_samples=None, + cluster_selection_epsilon=0.0, + max_cluster_size=None, + metric="euclidean", + metric_params=None, + alpha=1.0, + algorithm="auto", + leaf_size=40, + n_jobs=None, + cluster_selection_method="eom", + allow_single_cluster=False, + store_centers=None, + copy=False, + ): + self.min_cluster_size = min_cluster_size + self.min_samples = min_samples + self.alpha = alpha + self.max_cluster_size = max_cluster_size + self.cluster_selection_epsilon = cluster_selection_epsilon + self.metric = metric + self.metric_params = metric_params + self.algorithm = algorithm + self.leaf_size = leaf_size + self.n_jobs = n_jobs + self.cluster_selection_method = cluster_selection_method + self.allow_single_cluster = allow_single_cluster + self.store_centers = store_centers + self.copy = copy + + @_fit_context( + # HDBSCAN.metric is not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, y=None): + """Find clusters based on hierarchical density-based clustering. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features), or \ + ndarray of shape (n_samples, n_samples) + A feature array, or array of distances between samples if + `metric='precomputed'`. + + y : None + Ignored. + + Returns + ------- + self : object + Returns self. + """ + if self.metric == "precomputed" and self.store_centers is not None: + raise ValueError( + "Cannot store centers when using a precomputed distance matrix." + ) + + self._metric_params = self.metric_params or {} + if self.metric != "precomputed": + # Non-precomputed matrices may contain non-finite values. + X = validate_data( + self, + X, + accept_sparse=["csr", "lil"], + ensure_all_finite=False, + dtype=np.float64, + ) + self._raw_data = X + all_finite = True + try: + _assert_all_finite(X.data if issparse(X) else X) + except ValueError: + all_finite = False + + if not all_finite: + # Pass only the purely finite indices into hdbscan + # We will later assign all non-finite points their + # corresponding labels, as specified in `_OUTLIER_ENCODING` + + # Reduce X to make the checks for missing/outlier samples more + # convenient. + reduced_X = X.sum(axis=1) + + # Samples with missing data are denoted by the presence of + # `np.nan` + missing_index = np.isnan(reduced_X).nonzero()[0] + + # Outlier samples are denoted by the presence of `np.inf` + infinite_index = np.isinf(reduced_X).nonzero()[0] + + # Continue with only finite samples + finite_index = _get_finite_row_indices(X) + internal_to_raw = {x: y for x, y in enumerate(finite_index)} + X = X[finite_index] + elif issparse(X): + # Handle sparse precomputed distance matrices separately + X = validate_data( + self, + X, + accept_sparse=["csr", "lil"], + dtype=np.float64, + force_writeable=True, + ) + else: + # Only non-sparse, precomputed distance matrices are handled here + # and thereby allowed to contain numpy.inf for missing distances + + # Perform data validation after removing infinite values (numpy.inf) + # from the given distance matrix. + X = validate_data( + self, X, ensure_all_finite=False, dtype=np.float64, force_writeable=True + ) + if np.isnan(X).any(): + # TODO: Support np.nan in Cython implementation for precomputed + # dense HDBSCAN + raise ValueError("np.nan values found in precomputed-dense") + if X.shape[0] == 1: + raise ValueError("n_samples=1 while HDBSCAN requires more than one sample") + self._min_samples = ( + self.min_cluster_size if self.min_samples is None else self.min_samples + ) + + if self._min_samples > X.shape[0]: + raise ValueError( + f"min_samples ({self._min_samples}) must be at most the number of" + f" samples in X ({X.shape[0]})" + ) + + mst_func = None + kwargs = dict( + X=X, + min_samples=self._min_samples, + alpha=self.alpha, + metric=self.metric, + n_jobs=self.n_jobs, + **self._metric_params, + ) + if self.algorithm == "kd_tree" and self.metric not in KDTree.valid_metrics: + raise ValueError( + f"{self.metric} is not a valid metric for a KDTree-based algorithm." + " Please select a different metric." + ) + elif ( + self.algorithm == "ball_tree" and self.metric not in BallTree.valid_metrics + ): + raise ValueError( + f"{self.metric} is not a valid metric for a BallTree-based algorithm." + " Please select a different metric." + ) + + if self.algorithm != "auto": + if ( + self.metric != "precomputed" + and issparse(X) + and self.algorithm != "brute" + ): + raise ValueError("Sparse data matrices only support algorithm `brute`.") + + if self.algorithm == "brute": + mst_func = _hdbscan_brute + kwargs["copy"] = self.copy + elif self.algorithm == "kd_tree": + mst_func = _hdbscan_prims + kwargs["algo"] = "kd_tree" + kwargs["leaf_size"] = self.leaf_size + else: + mst_func = _hdbscan_prims + kwargs["algo"] = "ball_tree" + kwargs["leaf_size"] = self.leaf_size + else: + if issparse(X) or self.metric not in FAST_METRICS: + # We can't do much with sparse matrices ... + mst_func = _hdbscan_brute + kwargs["copy"] = self.copy + elif self.metric in KDTree.valid_metrics: + # TODO: Benchmark KD vs Ball Tree efficiency + mst_func = _hdbscan_prims + kwargs["algo"] = "kd_tree" + kwargs["leaf_size"] = self.leaf_size + else: + # Metric is a valid BallTree metric + mst_func = _hdbscan_prims + kwargs["algo"] = "ball_tree" + kwargs["leaf_size"] = self.leaf_size + + self._single_linkage_tree_ = mst_func(**kwargs) + + self.labels_, self.probabilities_ = tree_to_labels( + self._single_linkage_tree_, + self.min_cluster_size, + self.cluster_selection_method, + self.allow_single_cluster, + self.cluster_selection_epsilon, + self.max_cluster_size, + ) + if self.metric != "precomputed" and not all_finite: + # Remap indices to align with original data in the case of + # non-finite entries. Samples with np.inf are mapped to -1 and + # those with np.nan are mapped to -2. + self._single_linkage_tree_ = remap_single_linkage_tree( + self._single_linkage_tree_, + internal_to_raw, + # There may be overlap for points w/ both `np.inf` and `np.nan` + non_finite=set(np.hstack([infinite_index, missing_index])), + ) + new_labels = np.empty(self._raw_data.shape[0], dtype=np.int32) + new_labels[finite_index] = self.labels_ + new_labels[infinite_index] = _OUTLIER_ENCODING["infinite"]["label"] + new_labels[missing_index] = _OUTLIER_ENCODING["missing"]["label"] + self.labels_ = new_labels + + new_probabilities = np.zeros(self._raw_data.shape[0], dtype=np.float64) + new_probabilities[finite_index] = self.probabilities_ + # Infinite outliers have probability 0 by convention, though this + # is arbitrary. + new_probabilities[infinite_index] = _OUTLIER_ENCODING["infinite"]["prob"] + new_probabilities[missing_index] = _OUTLIER_ENCODING["missing"]["prob"] + self.probabilities_ = new_probabilities + + if self.store_centers: + self._weighted_cluster_center(X) + return self + + def fit_predict(self, X, y=None): + """Cluster X and return the associated cluster labels. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features), or \ + ndarray of shape (n_samples, n_samples) + A feature array, or array of distances between samples if + `metric='precomputed'`. + + y : None + Ignored. + + Returns + ------- + y : ndarray of shape (n_samples,) + Cluster labels. + """ + self.fit(X) + return self.labels_ + + def _weighted_cluster_center(self, X): + """Calculate and store the centroids/medoids of each cluster. + + This requires `X` to be a raw feature array, not precomputed + distances. Rather than return outputs directly, this helper method + instead stores them in the `self.{centroids, medoids}_` attributes. + The choice for which attributes are calculated and stored is mediated + by the value of `self.store_centers`. + + Parameters + ---------- + X : ndarray of shape (n_samples, n_features) + The feature array that the estimator was fit with. + + """ + # Number of non-noise clusters + n_clusters = len(set(self.labels_) - {-1, -2}) + mask = np.empty((X.shape[0],), dtype=np.bool_) + make_centroids = self.store_centers in ("centroid", "both") + make_medoids = self.store_centers in ("medoid", "both") + + if make_centroids: + self.centroids_ = np.empty((n_clusters, X.shape[1]), dtype=np.float64) + if make_medoids: + self.medoids_ = np.empty((n_clusters, X.shape[1]), dtype=np.float64) + + # Need to handle iteratively seen each cluster may have a different + # number of samples, hence we can't create a homogeneous 3D array. + for idx in range(n_clusters): + mask = self.labels_ == idx + data = X[mask] + strength = self.probabilities_[mask] + if make_centroids: + self.centroids_[idx] = np.average(data, weights=strength, axis=0) + if make_medoids: + # TODO: Implement weighted argmin PWD backend + dist_mat = pairwise_distances( + data, metric=self.metric, **self._metric_params + ) + dist_mat = dist_mat * strength + medoid_index = np.argmin(dist_mat.sum(axis=1)) + self.medoids_[idx] = data[medoid_index] + return + + def dbscan_clustering(self, cut_distance, min_cluster_size=5): + """Return clustering given by DBSCAN without border points. + + Return clustering that would be equivalent to running DBSCAN* for a + particular cut_distance (or epsilon) DBSCAN* can be thought of as + DBSCAN without the border points. As such these results may differ + slightly from `cluster.DBSCAN` due to the difference in implementation + over the non-core points. + + This can also be thought of as a flat clustering derived from constant + height cut through the single linkage tree. + + This represents the result of selecting a cut value for robust single linkage + clustering. The `min_cluster_size` allows the flat clustering to declare noise + points (and cluster smaller than `min_cluster_size`). + + Parameters + ---------- + cut_distance : float + The mutual reachability distance cut value to use to generate a + flat clustering. + + min_cluster_size : int, default=5 + Clusters smaller than this value with be called 'noise' and remain + unclustered in the resulting flat clustering. + + Returns + ------- + labels : ndarray of shape (n_samples,) + An array of cluster labels, one per datapoint. + Outliers are labeled as follows: + + - Noisy samples are given the label -1. + - Samples with infinite elements (+/- np.inf) are given the label -2. + - Samples with missing data are given the label -3, even if they + also have infinite elements. + """ + labels = labelling_at_cut( + self._single_linkage_tree_, cut_distance, min_cluster_size + ) + # Infer indices from labels generated during `fit` + infinite_index = self.labels_ == _OUTLIER_ENCODING["infinite"]["label"] + missing_index = self.labels_ == _OUTLIER_ENCODING["missing"]["label"] + + # Overwrite infinite/missing outlier samples (otherwise simple noise) + labels[infinite_index] = _OUTLIER_ENCODING["infinite"]["label"] + labels[missing_index] = _OUTLIER_ENCODING["missing"]["label"] + return labels + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + tags.input_tags.allow_nan = self.metric != "precomputed" + return tags diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/meson.build b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/meson.build new file mode 100644 index 0000000000000000000000000000000000000000..8d880b39a4db58dffa1b282c3633c873755f5245 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/meson.build @@ -0,0 +1,15 @@ +cluster_hdbscan_extension_metadata = { + '_linkage': {'sources': [cython_gen.process('_linkage.pyx'), metrics_cython_tree]}, + '_reachability': {'sources': [cython_gen.process('_reachability.pyx')]}, + '_tree': {'sources': [cython_gen.process('_tree.pyx')]} +} + +foreach ext_name, ext_dict : cluster_hdbscan_extension_metadata + py.extension_module( + ext_name, + ext_dict.get('sources'), + dependencies: [np_dep], + subdir: 'sklearn/cluster/_hdbscan', + install: true + ) +endforeach diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/tests/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/tests/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/tests/test_reachibility.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/tests/test_reachibility.py new file mode 100644 index 0000000000000000000000000000000000000000..a336e6be6116d1345a1d4eb0448c2e2f58cd8ecd --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hdbscan/tests/test_reachibility.py @@ -0,0 +1,63 @@ +import numpy as np +import pytest + +from sklearn.cluster._hdbscan._reachability import mutual_reachability_graph +from sklearn.utils._testing import ( + _convert_container, + assert_allclose, +) + + +def test_mutual_reachability_graph_error_sparse_format(): + """Check that we raise an error if the sparse format is not CSR.""" + rng = np.random.RandomState(0) + X = rng.randn(10, 10) + X = X.T @ X + np.fill_diagonal(X, 0.0) + X = _convert_container(X, "sparse_csc") + + err_msg = "Only sparse CSR matrices are supported" + with pytest.raises(ValueError, match=err_msg): + mutual_reachability_graph(X) + + +@pytest.mark.parametrize("array_type", ["array", "sparse_csr"]) +def test_mutual_reachability_graph_inplace(array_type): + """Check that the operation is happening inplace.""" + rng = np.random.RandomState(0) + X = rng.randn(10, 10) + X = X.T @ X + np.fill_diagonal(X, 0.0) + X = _convert_container(X, array_type) + + mr_graph = mutual_reachability_graph(X) + + assert id(mr_graph) == id(X) + + +def test_mutual_reachability_graph_equivalence_dense_sparse(): + """Check that we get the same results for dense and sparse implementation.""" + rng = np.random.RandomState(0) + X = rng.randn(5, 5) + X_dense = X.T @ X + X_sparse = _convert_container(X_dense, "sparse_csr") + + mr_graph_dense = mutual_reachability_graph(X_dense, min_samples=3) + mr_graph_sparse = mutual_reachability_graph(X_sparse, min_samples=3) + + assert_allclose(mr_graph_dense, mr_graph_sparse.toarray()) + + +@pytest.mark.parametrize("array_type", ["array", "sparse_csr"]) +@pytest.mark.parametrize("dtype", [np.float32, np.float64]) +def test_mutual_reachability_graph_preserves_dtype(array_type, dtype): + """Check that the computation preserve dtype thanks to fused types.""" + rng = np.random.RandomState(0) + X = rng.randn(10, 10) + X = (X.T @ X).astype(dtype) + np.fill_diagonal(X, 0.0) + X = _convert_container(X, array_type) + + assert X.dtype == dtype + mr_graph = mutual_reachability_graph(X) + assert mr_graph.dtype == dtype diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hierarchical_fast.pxd b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hierarchical_fast.pxd new file mode 100644 index 0000000000000000000000000000000000000000..a10f8c12f34402c872ccc3bd7c14266dcc9b5e7a --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hierarchical_fast.pxd @@ -0,0 +1,9 @@ +from ..utils._typedefs cimport intp_t + +cdef class UnionFind: + cdef intp_t next_label + cdef intp_t[:] parent + cdef intp_t[:] size + + cdef void union(self, intp_t m, intp_t n) noexcept + cdef intp_t fast_find(self, intp_t n) noexcept diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hierarchical_fast.pyx b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hierarchical_fast.pyx new file mode 100644 index 0000000000000000000000000000000000000000..36ae0ab0d241432df9f5833901580dc88c30d925 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_hierarchical_fast.pyx @@ -0,0 +1,507 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import numpy as np +cimport cython + +from ..metrics._dist_metrics cimport DistanceMetric64 +from ..utils._fast_dict cimport IntFloatDict +from ..utils._typedefs cimport float64_t, intp_t, uint8_t + +# C++ +from cython.operator cimport dereference as deref, preincrement as inc +from libcpp.map cimport map as cpp_map +from libc.math cimport fmax, INFINITY + + +############################################################################### +# Utilities for computing the ward momentum + +def compute_ward_dist( + const float64_t[::1] m_1, + const float64_t[:, ::1] m_2, + const intp_t[::1] coord_row, + const intp_t[::1] coord_col, + float64_t[::1] res +): + cdef intp_t size_max = coord_row.shape[0] + cdef intp_t n_features = m_2.shape[1] + cdef intp_t i, j, row, col + cdef float64_t pa, n + + for i in range(size_max): + row = coord_row[i] + col = coord_col[i] + n = (m_1[row] * m_1[col]) / (m_1[row] + m_1[col]) + pa = 0. + for j in range(n_features): + pa += (m_2[row, j] / m_1[row] - m_2[col, j] / m_1[col]) ** 2 + res[i] = pa * n + + +############################################################################### +# Utilities for cutting and exploring a hierarchical tree + +def _hc_get_descendent(intp_t node, children, intp_t n_leaves): + """ + Function returning all the descendent leaves of a set of nodes in the tree. + + Parameters + ---------- + node : integer + The node for which we want the descendents. + + children : list of pairs, length n_nodes + The children of each non-leaf node. Values less than `n_samples` refer + to leaves of the tree. A greater value `i` indicates a node with + children `children[i - n_samples]`. + + n_leaves : integer + Number of leaves. + + Returns + ------- + descendent : list of int + """ + ind = [node] + if node < n_leaves: + return ind + descendent = [] + + # It is actually faster to do the accounting of the number of + # elements is the list ourselves: len is a lengthy operation on a + # chained list + cdef intp_t i, n_indices = 1 + + while n_indices: + i = ind.pop() + if i < n_leaves: + descendent.append(i) + n_indices -= 1 + else: + ind.extend(children[i - n_leaves]) + n_indices += 1 + return descendent + + +def hc_get_heads(intp_t[:] parents, copy=True): + """Returns the heads of the forest, as defined by parents. + + Parameters + ---------- + parents : array of integers + The parent structure defining the forest (ensemble of trees) + copy : boolean + If copy is False, the input 'parents' array is modified inplace + + Returns + ------- + heads : array of integers of same shape as parents + The indices in the 'parents' of the tree heads + + """ + cdef intp_t parent, node0, node, size + if copy: + parents = np.copy(parents) + size = parents.size + + # Start from the top of the tree and go down + for node0 in range(size - 1, -1, -1): + node = node0 + parent = parents[node] + while parent != node: + parents[node0] = parent + node = parent + parent = parents[node] + return parents + + +def _get_parents( + nodes, + heads, + const intp_t[:] parents, + uint8_t[::1] not_visited +): + """Returns the heads of the given nodes, as defined by parents. + + Modifies 'heads' and 'not_visited' in-place. + + Parameters + ---------- + nodes : list of integers + The nodes to start from + heads : list of integers + A list to hold the results (modified inplace) + parents : array of integers + The parent structure defining the tree + not_visited + The tree nodes to consider (modified inplace) + + """ + cdef intp_t parent, node + + for node in nodes: + parent = parents[node] + while parent != node: + node = parent + parent = parents[node] + if not_visited[node]: + not_visited[node] = 0 + heads.append(node) + + +############################################################################### +# merge strategies implemented on IntFloatDicts + +# These are used in the hierarchical clustering code, to implement +# merging between two clusters, defined as a dict containing node number +# as keys and edge weights as values. + + +def max_merge( + IntFloatDict a, + IntFloatDict b, + const intp_t[:] mask, + intp_t n_a, + intp_t n_b +): + """Merge two IntFloatDicts with the max strategy: when the same key is + present in the two dicts, the max of the two values is used. + + Parameters + ========== + a, b : IntFloatDict object + The IntFloatDicts to merge + mask : ndarray array of dtype integer and of dimension 1 + a mask for keys to ignore: if not mask[key] the corresponding key + is skipped in the output dictionary + n_a, n_b : float + n_a and n_b are weights for a and b for the merge strategy. + They are not used in the case of a max merge. + + Returns + ======= + out : IntFloatDict object + The IntFloatDict resulting from the merge + """ + cdef IntFloatDict out_obj = IntFloatDict.__new__(IntFloatDict) + cdef cpp_map[intp_t, float64_t].iterator a_it = a.my_map.begin() + cdef cpp_map[intp_t, float64_t].iterator a_end = a.my_map.end() + cdef intp_t key + cdef float64_t value + # First copy a into out + while a_it != a_end: + key = deref(a_it).first + if mask[key]: + out_obj.my_map[key] = deref(a_it).second + inc(a_it) + + # Then merge b into out + cdef cpp_map[intp_t, float64_t].iterator out_it = out_obj.my_map.begin() + cdef cpp_map[intp_t, float64_t].iterator out_end = out_obj.my_map.end() + cdef cpp_map[intp_t, float64_t].iterator b_it = b.my_map.begin() + cdef cpp_map[intp_t, float64_t].iterator b_end = b.my_map.end() + while b_it != b_end: + key = deref(b_it).first + value = deref(b_it).second + if mask[key]: + out_it = out_obj.my_map.find(key) + if out_it == out_end: + # Key not found + out_obj.my_map[key] = value + else: + deref(out_it).second = fmax(deref(out_it).second, value) + inc(b_it) + return out_obj + + +def average_merge( + IntFloatDict a, + IntFloatDict b, + const intp_t[:] mask, + intp_t n_a, + intp_t n_b +): + """Merge two IntFloatDicts with the average strategy: when the + same key is present in the two dicts, the weighted average of the two + values is used. + + Parameters + ========== + a, b : IntFloatDict object + The IntFloatDicts to merge + mask : ndarray array of dtype integer and of dimension 1 + a mask for keys to ignore: if not mask[key] the corresponding key + is skipped in the output dictionary + n_a, n_b : float + n_a and n_b are weights for a and b for the merge strategy. + They are used for a weighted mean. + + Returns + ======= + out : IntFloatDict object + The IntFloatDict resulting from the merge + """ + cdef IntFloatDict out_obj = IntFloatDict.__new__(IntFloatDict) + cdef cpp_map[intp_t, float64_t].iterator a_it = a.my_map.begin() + cdef cpp_map[intp_t, float64_t].iterator a_end = a.my_map.end() + cdef intp_t key + cdef float64_t value + cdef float64_t n_out = (n_a + n_b) + # First copy a into out + while a_it != a_end: + key = deref(a_it).first + if mask[key]: + out_obj.my_map[key] = deref(a_it).second + inc(a_it) + + # Then merge b into out + cdef cpp_map[intp_t, float64_t].iterator out_it = out_obj.my_map.begin() + cdef cpp_map[intp_t, float64_t].iterator out_end = out_obj.my_map.end() + cdef cpp_map[intp_t, float64_t].iterator b_it = b.my_map.begin() + cdef cpp_map[intp_t, float64_t].iterator b_end = b.my_map.end() + while b_it != b_end: + key = deref(b_it).first + value = deref(b_it).second + if mask[key]: + out_it = out_obj.my_map.find(key) + if out_it == out_end: + # Key not found + out_obj.my_map[key] = value + else: + deref(out_it).second = (n_a * deref(out_it).second + + n_b * value) / n_out + inc(b_it) + return out_obj + + +############################################################################### +# An edge object for fast comparisons + +cdef class WeightedEdge: + cdef public intp_t a + cdef public intp_t b + cdef public float64_t weight + + def __init__(self, float64_t weight, intp_t a, intp_t b): + self.weight = weight + self.a = a + self.b = b + + def __richcmp__(self, WeightedEdge other, int op): + """Cython-specific comparison method. + + op is the comparison code:: + < 0 + == 2 + > 4 + <= 1 + != 3 + >= 5 + """ + if op == 0: + return self.weight < other.weight + elif op == 1: + return self.weight <= other.weight + elif op == 2: + return self.weight == other.weight + elif op == 3: + return self.weight != other.weight + elif op == 4: + return self.weight > other.weight + elif op == 5: + return self.weight >= other.weight + + def __repr__(self): + return "%s(weight=%f, a=%i, b=%i)" % (self.__class__.__name__, + self.weight, + self.a, self.b) + + +################################################################################ +# Efficient labelling/conversion of MSTs to single linkage hierarchies + +cdef class UnionFind(object): + + def __init__(self, N): + self.parent = np.full(2 * N - 1, -1., dtype=np.intp, order='C') + self.next_label = N + self.size = np.hstack((np.ones(N, dtype=np.intp), + np.zeros(N - 1, dtype=np.intp))) + + cdef void union(self, intp_t m, intp_t n) noexcept: + self.parent[m] = self.next_label + self.parent[n] = self.next_label + self.size[self.next_label] = self.size[m] + self.size[n] + self.next_label += 1 + return + + @cython.wraparound(True) + cdef intp_t fast_find(self, intp_t n) noexcept: + cdef intp_t p + p = n + # find the highest node in the linkage graph so far + while self.parent[n] != -1: + n = self.parent[n] + # provide a shortcut up to the highest node + while self.parent[p] != n: + p, self.parent[p] = self.parent[p], n + return n + + +def _single_linkage_label(const float64_t[:, :] L): + """ + Convert an linkage array or MST to a tree by labelling clusters at merges. + This is done by using a Union find structure to keep track of merges + efficiently. This is the private version of the function that assumes that + ``L`` has been properly validated. See ``single_linkage_label`` for the + user facing version of this function. + + Parameters + ---------- + L: array of shape (n_samples - 1, 3) + The linkage array or MST where each row specifies two samples + to be merged and a distance or weight at which the merge occurs. This + array is assumed to be sorted by the distance/weight. + + Returns + ------- + A tree in the format used by scipy.cluster.hierarchy. + """ + + cdef float64_t[:, ::1] result_arr + + cdef intp_t left, left_cluster, right, right_cluster, index + cdef float64_t delta + + result_arr = np.zeros((L.shape[0], 4), dtype=np.float64) + U = UnionFind(L.shape[0] + 1) + + for index in range(L.shape[0]): + + left = L[index, 0] + right = L[index, 1] + delta = L[index, 2] + + left_cluster = U.fast_find(left) + right_cluster = U.fast_find(right) + + result_arr[index][0] = left_cluster + result_arr[index][1] = right_cluster + result_arr[index][2] = delta + result_arr[index][3] = U.size[left_cluster] + U.size[right_cluster] + + U.union(left_cluster, right_cluster) + + return np.asarray(result_arr) + + +@cython.wraparound(True) +def single_linkage_label(L): + """ + Convert an linkage array or MST to a tree by labelling clusters at merges. + This is done by using a Union find structure to keep track of merges + efficiently. + + Parameters + ---------- + L: array of shape (n_samples - 1, 3) + The linkage array or MST where each row specifies two samples + to be merged and a distance or weight at which the merge occurs. This + array is assumed to be sorted by the distance/weight. + + Returns + ------- + A tree in the format used by scipy.cluster.hierarchy. + """ + # Validate L + if L[:, :2].min() < 0 or L[:, :2].max() >= 2 * L.shape[0] + 1: + raise ValueError("Input MST array is not a validly formatted MST array") + + is_sorted = lambda x: np.all(x[:-1] <= x[1:]) + if not is_sorted(L[:, 2]): + raise ValueError("Input MST array must be sorted by weight") + + return _single_linkage_label(L) + + +# Implements MST-LINKAGE-CORE from https://arxiv.org/abs/1109.2378 +def mst_linkage_core( + const float64_t [:, ::1] raw_data, + DistanceMetric64 dist_metric): + """ + Compute the necessary elements of a minimum spanning + tree for computation of single linkage clustering. This + represents the MST-LINKAGE-CORE algorithm (Figure 6) from + :arxiv:`Daniel Mullner, "Modern hierarchical, agglomerative clustering + algorithms" <1109.2378>`. + + In contrast to the scipy implementation is never computes + a full distance matrix, generating distances only as they + are needed and releasing them when no longer needed. + + Parameters + ---------- + raw_data: array of shape (n_samples, n_features) + The array of feature data to be clustered. Must be C-aligned + + dist_metric: DistanceMetric64 + A DistanceMetric64 object conforming to the API from + ``sklearn.metrics._dist_metrics.pxd`` that will be + used to compute distances. + + Returns + ------- + mst_core_data: array of shape (n_samples, 3) + An array providing information from which one + can either compute an MST, or the linkage hierarchy + very efficiently. See :arxiv:`Daniel Mullner, "Modern hierarchical, + agglomerative clustering algorithms" <1109.2378>` algorithm + MST-LINKAGE-CORE for more details. + """ + cdef: + intp_t n_samples = raw_data.shape[0] + uint8_t[:] in_tree = np.zeros(n_samples, dtype=bool) + float64_t[:, ::1] result = np.zeros((n_samples - 1, 3)) + + intp_t current_node = 0 + intp_t new_node + intp_t i + intp_t j + intp_t num_features = raw_data.shape[1] + + float64_t right_value + float64_t left_value + float64_t new_distance + + float64_t[:] current_distances = np.full(n_samples, INFINITY) + + for i in range(n_samples - 1): + + in_tree[current_node] = 1 + + new_distance = INFINITY + new_node = 0 + + for j in range(n_samples): + if in_tree[j]: + continue + + right_value = current_distances[j] + left_value = dist_metric.dist(&raw_data[current_node, 0], + &raw_data[j, 0], + num_features) + + if left_value < right_value: + current_distances[j] = left_value + + if current_distances[j] < new_distance: + new_distance = current_distances[j] + new_node = j + + result[i, 0] = current_node + result[i, 1] = new_node + result[i, 2] = new_distance + current_node = new_node + + return np.array(result) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_common.pxd b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_common.pxd new file mode 100644 index 0000000000000000000000000000000000000000..9a41ea68d1bafc0cad55c028e0413e463ddb6d2e --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_common.pxd @@ -0,0 +1,48 @@ +from cython cimport floating + + +cdef floating _euclidean_dense_dense( + const floating*, + const floating*, + int, + bint +) noexcept nogil + +cdef floating _euclidean_sparse_dense( + const floating[::1], + const int[::1], + const floating[::1], + floating, + bint +) noexcept nogil + +cpdef void _relocate_empty_clusters_dense( + const floating[:, ::1], + const floating[::1], + const floating[:, ::1], + floating[:, ::1], + floating[::1], + const int[::1] +) + +cpdef void _relocate_empty_clusters_sparse( + const floating[::1], + const int[::1], + const int[::1], + const floating[::1], + const floating[:, ::1], + floating[:, ::1], + floating[::1], + const int[::1] +) + +cdef void _average_centers( + floating[:, ::1], + const floating[::1] +) + +cdef void _center_shift( + const floating[:, ::1], + const floating[:, ::1], + floating[::1] +) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_common.pyx b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_common.pyx new file mode 100644 index 0000000000000000000000000000000000000000..674d4026a67564f266ec709a9f47d77f8f912386 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_common.pyx @@ -0,0 +1,328 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import numpy as np +from cython cimport floating +from cython.parallel cimport prange +from libc.math cimport sqrt + +from ..utils.extmath import row_norms + + +# Number of samples per data chunk defined as a global constant. +CHUNK_SIZE = 256 + + +cdef floating _euclidean_dense_dense( + const floating* a, # IN + const floating* b, # IN + int n_features, + bint squared +) noexcept nogil: + """Euclidean distance between a dense and b dense""" + cdef: + int i + int n = n_features // 4 + int rem = n_features % 4 + floating result = 0 + + # We manually unroll the loop for better cache optimization. + for i in range(n): + result += ( + (a[0] - b[0]) * (a[0] - b[0]) + + (a[1] - b[1]) * (a[1] - b[1]) + + (a[2] - b[2]) * (a[2] - b[2]) + + (a[3] - b[3]) * (a[3] - b[3]) + ) + a += 4 + b += 4 + + for i in range(rem): + result += (a[i] - b[i]) * (a[i] - b[i]) + + return result if squared else sqrt(result) + + +def _euclidean_dense_dense_wrapper( + const floating[::1] a, + const floating[::1] b, + bint squared +): + """Wrapper of _euclidean_dense_dense for testing purpose""" + return _euclidean_dense_dense(&a[0], &b[0], a.shape[0], squared) + + +cdef floating _euclidean_sparse_dense( + const floating[::1] a_data, # IN + const int[::1] a_indices, # IN + const floating[::1] b, # IN + floating b_squared_norm, + bint squared +) noexcept nogil: + """Euclidean distance between a sparse and b dense""" + cdef: + int nnz = a_indices.shape[0] + int i + floating tmp, bi + floating result = 0.0 + + for i in range(nnz): + bi = b[a_indices[i]] + tmp = a_data[i] - bi + result += tmp * tmp - bi * bi + + result += b_squared_norm + + if result < 0: + result = 0.0 + + return result if squared else sqrt(result) + + +def _euclidean_sparse_dense_wrapper( + const floating[::1] a_data, + const int[::1] a_indices, + const floating[::1] b, + floating b_squared_norm, + bint squared +): + """Wrapper of _euclidean_sparse_dense for testing purpose""" + return _euclidean_sparse_dense( + a_data, a_indices, b, b_squared_norm, squared) + + +cpdef floating _inertia_dense( + const floating[:, ::1] X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers, # IN + const int[::1] labels, # IN + int n_threads, + int single_label=-1, +): + """Compute inertia for dense input data + + Sum of squared distance between each sample and its assigned center. + + If single_label is >= 0, the inertia is computed only for that label. + """ + cdef: + int n_samples = X.shape[0] + int n_features = X.shape[1] + int i, j + + floating sq_dist = 0.0 + floating inertia = 0.0 + + for i in prange(n_samples, nogil=True, num_threads=n_threads, + schedule='static'): + j = labels[i] + if single_label < 0 or single_label == j: + sq_dist = _euclidean_dense_dense(&X[i, 0], ¢ers[j, 0], + n_features, True) + inertia += sq_dist * sample_weight[i] + + return inertia + + +cpdef floating _inertia_sparse( + X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers, # IN + const int[::1] labels, # IN + int n_threads, + int single_label=-1, +): + """Compute inertia for sparse input data + + Sum of squared distance between each sample and its assigned center. + + If single_label is >= 0, the inertia is computed only for that label. + """ + cdef: + floating[::1] X_data = X.data + int[::1] X_indices = X.indices + int[::1] X_indptr = X.indptr + + int n_samples = X.shape[0] + int i, j + + floating sq_dist = 0.0 + floating inertia = 0.0 + + floating[::1] centers_squared_norms = row_norms(centers, squared=True) + + for i in prange(n_samples, nogil=True, num_threads=n_threads, + schedule='static'): + j = labels[i] + if single_label < 0 or single_label == j: + sq_dist = _euclidean_sparse_dense( + X_data[X_indptr[i]: X_indptr[i + 1]], + X_indices[X_indptr[i]: X_indptr[i + 1]], + centers[j], centers_squared_norms[j], True) + inertia += sq_dist * sample_weight[i] + + return inertia + + +cpdef void _relocate_empty_clusters_dense( + const floating[:, ::1] X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + floating[:, ::1] centers_new, # INOUT + floating[::1] weight_in_clusters, # INOUT + const int[::1] labels # IN +): + """Relocate centers which have no sample assigned to them.""" + cdef: + int[::1] empty_clusters = np.where(np.equal(weight_in_clusters, 0))[0].astype(np.int32) + int n_empty = empty_clusters.shape[0] + + if n_empty == 0: + return + + cdef: + int n_features = X.shape[1] + + floating[::1] distances = ((np.asarray(X) - np.asarray(centers_old)[labels])**2).sum(axis=1) + int[::1] far_from_centers = np.argpartition(distances, -n_empty)[:-n_empty-1:-1].astype(np.int32) + + int new_cluster_id, old_cluster_id, far_idx, idx, k + floating weight + + if np.max(distances) == 0: + # Happens when there are more clusters than non-duplicate samples. Relocating + # is pointless in this case. + return + + for idx in range(n_empty): + + new_cluster_id = empty_clusters[idx] + + far_idx = far_from_centers[idx] + weight = sample_weight[far_idx] + + old_cluster_id = labels[far_idx] + + for k in range(n_features): + centers_new[old_cluster_id, k] -= X[far_idx, k] * weight + centers_new[new_cluster_id, k] = X[far_idx, k] * weight + + weight_in_clusters[new_cluster_id] = weight + weight_in_clusters[old_cluster_id] -= weight + + +cpdef void _relocate_empty_clusters_sparse( + const floating[::1] X_data, # IN + const int[::1] X_indices, # IN + const int[::1] X_indptr, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + floating[:, ::1] centers_new, # INOUT + floating[::1] weight_in_clusters, # INOUT + const int[::1] labels # IN +): + """Relocate centers which have no sample assigned to them.""" + cdef: + int[::1] empty_clusters = np.where(np.equal(weight_in_clusters, 0))[0].astype(np.int32) + int n_empty = empty_clusters.shape[0] + + if n_empty == 0: + return + + cdef: + int n_samples = X_indptr.shape[0] - 1 + int i, j, k + + floating[::1] distances = np.zeros(n_samples, dtype=X_data.base.dtype) + floating[::1] centers_squared_norms = row_norms(centers_old, squared=True) + + for i in range(n_samples): + j = labels[i] + distances[i] = _euclidean_sparse_dense( + X_data[X_indptr[i]: X_indptr[i + 1]], + X_indices[X_indptr[i]: X_indptr[i + 1]], + centers_old[j], centers_squared_norms[j], True) + + if np.max(distances) == 0: + # Happens when there are more clusters than non-duplicate samples. Relocating + # is pointless in this case. + return + + cdef: + int[::1] far_from_centers = np.argpartition(distances, -n_empty)[:-n_empty-1:-1].astype(np.int32) + + int new_cluster_id, old_cluster_id, far_idx, idx + floating weight + + for idx in range(n_empty): + + new_cluster_id = empty_clusters[idx] + + far_idx = far_from_centers[idx] + weight = sample_weight[far_idx] + + old_cluster_id = labels[far_idx] + + for k in range(X_indptr[far_idx], X_indptr[far_idx + 1]): + centers_new[old_cluster_id, X_indices[k]] -= X_data[k] * weight + centers_new[new_cluster_id, X_indices[k]] = X_data[k] * weight + + weight_in_clusters[new_cluster_id] = weight + weight_in_clusters[old_cluster_id] -= weight + + +cdef void _average_centers( + floating[:, ::1] centers, # INOUT + const floating[::1] weight_in_clusters # IN +): + """Average new centers wrt weights.""" + cdef: + int n_clusters = centers.shape[0] + int n_features = centers.shape[1] + int j, k + floating alpha + int argmax_weight = np.argmax(weight_in_clusters) + + for j in range(n_clusters): + if weight_in_clusters[j] > 0: + alpha = 1.0 / weight_in_clusters[j] + for k in range(n_features): + centers[j, k] *= alpha + else: + # For convenience, we avoid setting empty clusters at the origin but place + # them at the location of the biggest cluster. + for k in range(n_features): + centers[j, k] = centers[argmax_weight, k] + + +cdef void _center_shift( + const floating[:, ::1] centers_old, # IN + const floating[:, ::1] centers_new, # IN + floating[::1] center_shift # OUT +): + """Compute shift between old and new centers.""" + cdef: + int n_clusters = centers_old.shape[0] + int n_features = centers_old.shape[1] + int j + + for j in range(n_clusters): + center_shift[j] = _euclidean_dense_dense( + ¢ers_new[j, 0], ¢ers_old[j, 0], n_features, False) + + +def _is_same_clustering( + const int[::1] labels1, + const int[::1] labels2, + n_clusters +): + """Check if two arrays of labels are the same up to a permutation of the labels""" + cdef int[::1] mapping = np.full(fill_value=-1, shape=(n_clusters,), dtype=np.int32) + cdef int i + + for i in range(labels1.shape[0]): + if mapping[labels1[i]] == -1: + mapping[labels1[i]] = labels2[i] + elif mapping[labels1[i]] != labels2[i]: + return False + return True diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_elkan.pyx b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_elkan.pyx new file mode 100644 index 0000000000000000000000000000000000000000..564218a17f7018241d43dd33f55d3f516746a145 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_elkan.pyx @@ -0,0 +1,686 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +from cython cimport floating +from cython.parallel import prange, parallel +from libc.stdlib cimport calloc, free +from libc.string cimport memset + +from ..utils._openmp_helpers cimport omp_lock_t +from ..utils._openmp_helpers cimport omp_init_lock +from ..utils._openmp_helpers cimport omp_destroy_lock +from ..utils._openmp_helpers cimport omp_set_lock +from ..utils._openmp_helpers cimport omp_unset_lock +from ..utils.extmath import row_norms +from ._k_means_common import CHUNK_SIZE +from ._k_means_common cimport _relocate_empty_clusters_dense +from ._k_means_common cimport _relocate_empty_clusters_sparse +from ._k_means_common cimport _euclidean_dense_dense +from ._k_means_common cimport _euclidean_sparse_dense +from ._k_means_common cimport _average_centers +from ._k_means_common cimport _center_shift + + +def init_bounds_dense( + const floating[:, ::1] X, # IN + const floating[:, ::1] centers, # IN + const floating[:, ::1] center_half_distances, # IN + int[::1] labels, # OUT + floating[::1] upper_bounds, # OUT + floating[:, ::1] lower_bounds, # OUT + int n_threads): + """Initialize upper and lower bounds for each sample for dense input data. + + Given X, centers and the pairwise distances divided by 2.0 between the + centers this calculates the upper bounds and lower bounds for each sample. + The upper bound for each sample is set to the distance between the sample + and the closest center. + + The lower bound for each sample is a one-dimensional array of n_clusters. + For each sample i assume that the previously assigned cluster is c1 and the + previous closest distance is dist, for a new cluster c2, the + lower_bound[i][c2] is set to distance between the sample and this new + cluster, if and only if dist > center_half_distances[c1][c2]. This prevents + computation of unnecessary distances for each sample to the clusters that + it is unlikely to be assigned to. + + Parameters + ---------- + X : ndarray of shape (n_samples, n_features), dtype=floating + The input data. + + centers : ndarray of shape (n_clusters, n_features), dtype=floating + The cluster centers. + + center_half_distances : ndarray of shape (n_clusters, n_clusters), \ + dtype=floating + The half of the distance between any 2 clusters centers. + + labels : ndarray of shape(n_samples), dtype=int + The label for each sample. This array is modified in place. + + upper_bounds : ndarray of shape(n_samples,), dtype=floating + The upper bound on the distance between each sample and its closest + cluster center. This array is modified in place. + + lower_bounds : ndarray, of shape(n_samples, n_clusters), dtype=floating + The lower bound on the distance between each sample and each cluster + center. This array is modified in place. + + n_threads : int + The number of threads to be used by openmp. + """ + cdef: + int n_samples = X.shape[0] + int n_clusters = centers.shape[0] + int n_features = X.shape[1] + + floating min_dist, dist + int best_cluster, i, j + + for i in prange( + n_samples, num_threads=n_threads, schedule='static', nogil=True + ): + best_cluster = 0 + min_dist = _euclidean_dense_dense(&X[i, 0], ¢ers[0, 0], + n_features, False) + lower_bounds[i, 0] = min_dist + for j in range(1, n_clusters): + if min_dist > center_half_distances[best_cluster, j]: + dist = _euclidean_dense_dense(&X[i, 0], ¢ers[j, 0], + n_features, False) + lower_bounds[i, j] = dist + if dist < min_dist: + min_dist = dist + best_cluster = j + labels[i] = best_cluster + upper_bounds[i] = min_dist + + +def init_bounds_sparse( + X, # IN + const floating[:, ::1] centers, # IN + const floating[:, ::1] center_half_distances, # IN + int[::1] labels, # OUT + floating[::1] upper_bounds, # OUT + floating[:, ::1] lower_bounds, # OUT + int n_threads): + """Initialize upper and lower bounds for each sample for sparse input data. + + Given X, centers and the pairwise distances divided by 2.0 between the + centers this calculates the upper bounds and lower bounds for each sample. + The upper bound for each sample is set to the distance between the sample + and the closest center. + + The lower bound for each sample is a one-dimensional array of n_clusters. + For each sample i assume that the previously assigned cluster is c1 and the + previous closest distance is dist, for a new cluster c2, the + lower_bound[i][c2] is set to distance between the sample and this new + cluster, if and only if dist > center_half_distances[c1][c2]. This prevents + computation of unnecessary distances for each sample to the clusters that + it is unlikely to be assigned to. + + Parameters + ---------- + X : sparse matrix of shape (n_samples, n_features), dtype=floating + The input data. Must be in CSR format. + + centers : ndarray of shape (n_clusters, n_features), dtype=floating + The cluster centers. + + center_half_distances : ndarray of shape (n_clusters, n_clusters), \ + dtype=floating + The half of the distance between any 2 clusters centers. + + labels : ndarray of shape(n_samples), dtype=int + The label for each sample. This array is modified in place. + + upper_bounds : ndarray of shape(n_samples,), dtype=floating + The upper bound on the distance between each sample and its closest + cluster center. This array is modified in place. + + lower_bounds : ndarray of shape(n_samples, n_clusters), dtype=floating + The lower bound on the distance between each sample and each cluster + center. This array is modified in place. + + n_threads : int + The number of threads to be used by openmp. + """ + cdef: + int n_samples = X.shape[0] + int n_clusters = centers.shape[0] + + floating[::1] X_data = X.data + int[::1] X_indices = X.indices + int[::1] X_indptr = X.indptr + + floating min_dist, dist + int best_cluster, i, j + + floating[::1] centers_squared_norms = row_norms(centers, squared=True) + + for i in prange( + n_samples, num_threads=n_threads, schedule='static', nogil=True + ): + best_cluster = 0 + min_dist = _euclidean_sparse_dense( + X_data[X_indptr[i]: X_indptr[i + 1]], + X_indices[X_indptr[i]: X_indptr[i + 1]], + centers[0], centers_squared_norms[0], False) + + lower_bounds[i, 0] = min_dist + for j in range(1, n_clusters): + if min_dist > center_half_distances[best_cluster, j]: + dist = _euclidean_sparse_dense( + X_data[X_indptr[i]: X_indptr[i + 1]], + X_indices[X_indptr[i]: X_indptr[i + 1]], + centers[j], centers_squared_norms[j], False) + lower_bounds[i, j] = dist + if dist < min_dist: + min_dist = dist + best_cluster = j + labels[i] = best_cluster + upper_bounds[i] = min_dist + + +def elkan_iter_chunked_dense( + const floating[:, ::1] X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + floating[:, ::1] centers_new, # OUT + floating[::1] weight_in_clusters, # OUT + const floating[:, ::1] center_half_distances, # IN + const floating[::1] distance_next_center, # IN + floating[::1] upper_bounds, # INOUT + floating[:, ::1] lower_bounds, # INOUT + int[::1] labels, # INOUT + floating[::1] center_shift, # OUT + int n_threads, + bint update_centers=True): + """Single iteration of K-means Elkan algorithm with dense input. + + Update labels and centers (inplace), for one iteration, distributed + over data chunks. + + Parameters + ---------- + X : ndarray of shape (n_samples, n_features), dtype=floating + The observations to cluster. + + sample_weight : ndarray of shape (n_samples,), dtype=floating + The weights for each observation in X. + + centers_old : ndarray of shape (n_clusters, n_features), dtype=floating + Centers before previous iteration, placeholder for the centers after + previous iteration. + + centers_new : ndarray of shape (n_clusters, n_features), dtype=floating + Centers after previous iteration, placeholder for the new centers + computed during this iteration. + + weight_in_clusters : ndarray of shape (n_clusters,), dtype=floating + Placeholder for the sums of the weights of every observation assigned + to each center. + + center_half_distances : ndarray of shape (n_clusters, n_clusters), \ + dtype=floating + Half pairwise distances between centers. + + distance_next_center : ndarray of shape (n_clusters,), dtype=floating + Distance between each center its closest center. + + upper_bounds : ndarray of shape (n_samples,), dtype=floating + Upper bound for the distance between each sample and its center, + updated inplace. + + lower_bounds : ndarray of shape (n_samples, n_clusters), dtype=floating + Lower bound for the distance between each sample and each center, + updated inplace. + + labels : ndarray of shape (n_samples,), dtype=int + labels assignment. + + center_shift : ndarray of shape (n_clusters,), dtype=floating + Distance between old and new centers. + + n_threads : int + The number of threads to be used by openmp. + + update_centers : bool + - If True, the labels and the new centers will be computed, i.e. runs + the E-step and the M-step of the algorithm. + - If False, only the labels will be computed, i.e runs the E-step of + the algorithm. This is useful especially when calling predict on a + fitted model. + """ + cdef: + int n_samples = X.shape[0] + int n_features = X.shape[1] + int n_clusters = centers_new.shape[0] + + if n_samples == 0: + # An empty array was passed, do nothing and return early (before + # attempting to compute n_chunks). This can typically happen when + # calling the prediction function of a bisecting k-means model with a + # large fraction of outliers. + return + + cdef: + # hard-coded number of samples per chunk. Splitting in chunks is + # necessary to get parallelism. Chunk size chosen to be same as lloyd's + int n_samples_chunk = CHUNK_SIZE if n_samples > CHUNK_SIZE else n_samples + int n_chunks = n_samples // n_samples_chunk + int n_samples_rem = n_samples % n_samples_chunk + int chunk_idx + int start, end + + int i, j, k + + floating *centers_new_chunk + floating *weight_in_clusters_chunk + + omp_lock_t lock + + # count remainder chunk in total number of chunks + n_chunks += n_samples != n_chunks * n_samples_chunk + + # number of threads should not be bigger than number of chunks + n_threads = min(n_threads, n_chunks) + + if update_centers: + memset(¢ers_new[0, 0], 0, n_clusters * n_features * sizeof(floating)) + memset(&weight_in_clusters[0], 0, n_clusters * sizeof(floating)) + omp_init_lock(&lock) + + with nogil, parallel(num_threads=n_threads): + # thread local buffers + centers_new_chunk = calloc(n_clusters * n_features, sizeof(floating)) + weight_in_clusters_chunk = calloc(n_clusters, sizeof(floating)) + + for chunk_idx in prange(n_chunks, schedule='static'): + start = chunk_idx * n_samples_chunk + if chunk_idx == n_chunks - 1 and n_samples_rem > 0: + end = start + n_samples_rem + else: + end = start + n_samples_chunk + + _update_chunk_dense( + X[start: end], + sample_weight[start: end], + centers_old, + center_half_distances, + distance_next_center, + labels[start: end], + upper_bounds[start: end], + lower_bounds[start: end], + centers_new_chunk, + weight_in_clusters_chunk, + update_centers) + + # reduction from local buffers. + if update_centers: + # The lock is necessary to avoid race conditions when aggregating + # info from different thread-local buffers. + omp_set_lock(&lock) + for j in range(n_clusters): + weight_in_clusters[j] += weight_in_clusters_chunk[j] + for k in range(n_features): + centers_new[j, k] += centers_new_chunk[j * n_features + k] + omp_unset_lock(&lock) + + free(centers_new_chunk) + free(weight_in_clusters_chunk) + + if update_centers: + omp_destroy_lock(&lock) + _relocate_empty_clusters_dense(X, sample_weight, centers_old, + centers_new, weight_in_clusters, labels) + + _average_centers(centers_new, weight_in_clusters) + _center_shift(centers_old, centers_new, center_shift) + + # update lower and upper bounds + for i in range(n_samples): + upper_bounds[i] += center_shift[labels[i]] + + for j in range(n_clusters): + lower_bounds[i, j] -= center_shift[j] + if lower_bounds[i, j] < 0: + lower_bounds[i, j] = 0 + + +cdef void _update_chunk_dense( + const floating[:, ::1] X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + const floating[:, ::1] center_half_distances, # IN + const floating[::1] distance_next_center, # IN + int[::1] labels, # INOUT + floating[::1] upper_bounds, # INOUT + floating[:, ::1] lower_bounds, # INOUT + floating *centers_new, # OUT + floating *weight_in_clusters, # OUT + bint update_centers) noexcept nogil: + """K-means combined EM step for one dense data chunk. + + Compute the partial contribution of a single data chunk to the labels and + centers. + """ + cdef: + int n_samples = labels.shape[0] + int n_clusters = centers_old.shape[0] + int n_features = centers_old.shape[1] + + floating upper_bound, distance + int i, j, k, label + + for i in range(n_samples): + upper_bound = upper_bounds[i] + bounds_tight = 0 + label = labels[i] + + # Next center is not far away from the currently assigned center. + # Sample might need to be assigned to another center. + if not distance_next_center[label] >= upper_bound: + + for j in range(n_clusters): + + # If this holds, then center_index is a good candidate for the + # sample to be relabelled, and we need to confirm this by + # recomputing the upper and lower bounds. + if ( + j != label + and (upper_bound > lower_bounds[i, j]) + and (upper_bound > center_half_distances[label, j]) + ): + + # Recompute upper bound by calculating the actual distance + # between the sample and its current assigned center. + if not bounds_tight: + upper_bound = _euclidean_dense_dense( + &X[i, 0], ¢ers_old[label, 0], n_features, False) + lower_bounds[i, label] = upper_bound + bounds_tight = 1 + + # If the condition still holds, then compute the actual + # distance between the sample and center. If this is less + # than the previous distance, reassign label. + if ( + upper_bound > lower_bounds[i, j] + or (upper_bound > center_half_distances[label, j]) + ): + + distance = _euclidean_dense_dense( + &X[i, 0], ¢ers_old[j, 0], n_features, False) + lower_bounds[i, j] = distance + if distance < upper_bound: + label = j + upper_bound = distance + + labels[i] = label + upper_bounds[i] = upper_bound + + if update_centers: + weight_in_clusters[label] += sample_weight[i] + for k in range(n_features): + centers_new[label * n_features + k] += X[i, k] * sample_weight[i] + + +def elkan_iter_chunked_sparse( + X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + floating[:, ::1] centers_new, # OUT + floating[::1] weight_in_clusters, # OUT + const floating[:, ::1] center_half_distances, # IN + const floating[::1] distance_next_center, # IN + floating[::1] upper_bounds, # INOUT + floating[:, ::1] lower_bounds, # INOUT + int[::1] labels, # INOUT + floating[::1] center_shift, # OUT + int n_threads, + bint update_centers=True): + """Single iteration of K-means Elkan algorithm with sparse input. + + Update labels and centers (inplace), for one iteration, distributed + over data chunks. + + Parameters + ---------- + X : sparse matrix of shape (n_samples, n_features) + The observations to cluster. Must be in CSR format. + + sample_weight : ndarray of shape (n_samples,), dtype=floating + The weights for each observation in X. + + centers_old : ndarray of shape (n_clusters, n_features), dtype=floating + Centers before previous iteration, placeholder for the centers after + previous iteration. + + centers_new : ndarray of shape (n_clusters, n_features), dtype=floating + Centers after previous iteration, placeholder for the new centers + computed during this iteration. + + weight_in_clusters : ndarray of shape (n_clusters,), dtype=floating + Placeholder for the sums of the weights of every observation assigned + to each center. + + center_half_distances : ndarray of shape (n_clusters, n_clusters), \ + dtype=floating + Half pairwise distances between centers. + + distance_next_center : ndarray of shape (n_clusters,), dtype=floating + Distance between each center its closest center. + + upper_bounds : ndarray of shape (n_samples,), dtype=floating + Upper bound for the distance between each sample and its center, + updated inplace. + + lower_bounds : ndarray of shape (n_samples, n_clusters), dtype=floating + Lower bound for the distance between each sample and each center, + updated inplace. + + labels : ndarray of shape (n_samples,), dtype=int + labels assignment. + + center_shift : ndarray of shape (n_clusters,), dtype=floating + Distance between old and new centers. + + n_threads : int + The number of threads to be used by openmp. + + update_centers : bool + - If True, the labels and the new centers will be computed, i.e. runs + the E-step and the M-step of the algorithm. + - If False, only the labels will be computed, i.e runs the E-step of + the algorithm. This is useful especially when calling predict on a + fitted model. + """ + cdef: + int n_samples = X.shape[0] + int n_features = X.shape[1] + int n_clusters = centers_new.shape[0] + + if n_samples == 0: + # An empty array was passed, do nothing and return early (before + # attempting to compute n_chunks). This can typically happen when + # calling the prediction function of a bisecting k-means model with a + # large fraction of outliers. + return + + cdef: + floating[::1] X_data = X.data + int[::1] X_indices = X.indices + int[::1] X_indptr = X.indptr + + # hard-coded number of samples per chunk. Splitting in chunks is + # necessary to get parallelism. Chunk size chosen to be same as lloyd's + int n_samples_chunk = CHUNK_SIZE if n_samples > CHUNK_SIZE else n_samples + int n_chunks = n_samples // n_samples_chunk + int n_samples_rem = n_samples % n_samples_chunk + int chunk_idx + int start, end + + int i, j, k + + floating[::1] centers_squared_norms = row_norms(centers_old, squared=True) + + floating *centers_new_chunk + floating *weight_in_clusters_chunk + + omp_lock_t lock + + # count remainder chunk in total number of chunks + n_chunks += n_samples != n_chunks * n_samples_chunk + + # number of threads should not be bigger than number of chunks + n_threads = min(n_threads, n_chunks) + + if update_centers: + memset(¢ers_new[0, 0], 0, n_clusters * n_features * sizeof(floating)) + memset(&weight_in_clusters[0], 0, n_clusters * sizeof(floating)) + omp_init_lock(&lock) + + with nogil, parallel(num_threads=n_threads): + # thread local buffers + centers_new_chunk = calloc(n_clusters * n_features, sizeof(floating)) + weight_in_clusters_chunk = calloc(n_clusters, sizeof(floating)) + + for chunk_idx in prange(n_chunks, schedule='static'): + start = chunk_idx * n_samples_chunk + if chunk_idx == n_chunks - 1 and n_samples_rem > 0: + end = start + n_samples_rem + else: + end = start + n_samples_chunk + + _update_chunk_sparse( + X_data[X_indptr[start]: X_indptr[end]], + X_indices[X_indptr[start]: X_indptr[end]], + X_indptr[start: end+1], + sample_weight[start: end], + centers_old, + centers_squared_norms, + center_half_distances, + distance_next_center, + labels[start: end], + upper_bounds[start: end], + lower_bounds[start: end], + centers_new_chunk, + weight_in_clusters_chunk, + update_centers) + + # reduction from local buffers. + if update_centers: + # The lock is necessary to avoid race conditions when aggregating + # info from different thread-local buffers. + omp_set_lock(&lock) + for j in range(n_clusters): + weight_in_clusters[j] += weight_in_clusters_chunk[j] + for k in range(n_features): + centers_new[j, k] += centers_new_chunk[j * n_features + k] + omp_unset_lock(&lock) + + free(centers_new_chunk) + free(weight_in_clusters_chunk) + + if update_centers: + omp_destroy_lock(&lock) + _relocate_empty_clusters_sparse( + X_data, X_indices, X_indptr, sample_weight, + centers_old, centers_new, weight_in_clusters, labels) + + _average_centers(centers_new, weight_in_clusters) + _center_shift(centers_old, centers_new, center_shift) + + # update lower and upper bounds + for i in range(n_samples): + upper_bounds[i] += center_shift[labels[i]] + + for j in range(n_clusters): + lower_bounds[i, j] -= center_shift[j] + if lower_bounds[i, j] < 0: + lower_bounds[i, j] = 0 + + +cdef void _update_chunk_sparse( + const floating[::1] X_data, # IN + const int[::1] X_indices, # IN + const int[::1] X_indptr, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + const floating[::1] centers_squared_norms, # IN + const floating[:, ::1] center_half_distances, # IN + const floating[::1] distance_next_center, # IN + int[::1] labels, # INOUT + floating[::1] upper_bounds, # INOUT + floating[:, ::1] lower_bounds, # INOUT + floating *centers_new, # OUT + floating *weight_in_clusters, # OUT + bint update_centers) noexcept nogil: + """K-means combined EM step for one sparse data chunk. + + Compute the partial contribution of a single data chunk to the labels and + centers. + """ + cdef: + int n_samples = labels.shape[0] + int n_clusters = centers_old.shape[0] + int n_features = centers_old.shape[1] + + floating upper_bound, distance + int i, j, k, label + int s = X_indptr[0] + + for i in range(n_samples): + upper_bound = upper_bounds[i] + bounds_tight = 0 + label = labels[i] + + # Next center is not far away from the currently assigned center. + # Sample might need to be assigned to another center. + if not distance_next_center[label] >= upper_bound: + + for j in range(n_clusters): + + # If this holds, then center_index is a good candidate for the + # sample to be relabelled, and we need to confirm this by + # recomputing the upper and lower bounds. + if ( + j != label + and (upper_bound > lower_bounds[i, j]) + and (upper_bound > center_half_distances[label, j]) + ): + + # Recompute upper bound by calculating the actual distance + # between the sample and its current assigned center. + if not bounds_tight: + upper_bound = _euclidean_sparse_dense( + X_data[X_indptr[i] - s: X_indptr[i + 1] - s], + X_indices[X_indptr[i] - s: X_indptr[i + 1] - s], + centers_old[label], centers_squared_norms[label], False) + lower_bounds[i, label] = upper_bound + bounds_tight = 1 + + # If the condition still holds, then compute the actual + # distance between the sample and center. If this is less + # than the previous distance, reassign label. + if ( + upper_bound > lower_bounds[i, j] + or (upper_bound > center_half_distances[label, j]) + ): + distance = _euclidean_sparse_dense( + X_data[X_indptr[i] - s: X_indptr[i + 1] - s], + X_indices[X_indptr[i] - s: X_indptr[i + 1] - s], + centers_old[j], centers_squared_norms[j], False) + lower_bounds[i, j] = distance + if distance < upper_bound: + label = j + upper_bound = distance + + labels[i] = label + upper_bounds[i] = upper_bound + + if update_centers: + weight_in_clusters[label] += sample_weight[i] + for k in range(X_indptr[i] - s, X_indptr[i + 1] - s): + centers_new[label * n_features + X_indices[k]] += X_data[k] * sample_weight[i] diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_lloyd.pyx b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_lloyd.pyx new file mode 100644 index 0000000000000000000000000000000000000000..a507a6239ab5f836e8c7d23ac0e3e2ab2f7f4d11 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_lloyd.pyx @@ -0,0 +1,420 @@ +# Licence: BSD 3 clause + +from cython cimport floating +from cython.parallel import prange, parallel +from libc.stdlib cimport malloc, calloc, free +from libc.string cimport memset +from libc.float cimport DBL_MAX, FLT_MAX + +from ..utils._openmp_helpers cimport omp_lock_t +from ..utils._openmp_helpers cimport omp_init_lock +from ..utils._openmp_helpers cimport omp_destroy_lock +from ..utils._openmp_helpers cimport omp_set_lock +from ..utils._openmp_helpers cimport omp_unset_lock +from ..utils.extmath import row_norms +from ..utils._cython_blas cimport _gemm +from ..utils._cython_blas cimport RowMajor, Trans, NoTrans +from ._k_means_common import CHUNK_SIZE +from ._k_means_common cimport _relocate_empty_clusters_dense +from ._k_means_common cimport _relocate_empty_clusters_sparse +from ._k_means_common cimport _average_centers, _center_shift + + +def lloyd_iter_chunked_dense( + const floating[:, ::1] X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + floating[:, ::1] centers_new, # OUT + floating[::1] weight_in_clusters, # OUT + int[::1] labels, # OUT + floating[::1] center_shift, # OUT + int n_threads, + bint update_centers=True): + """Single iteration of K-means lloyd algorithm with dense input. + + Update labels and centers (inplace), for one iteration, distributed + over data chunks. + + Parameters + ---------- + X : ndarray of shape (n_samples, n_features), dtype=floating + The observations to cluster. + + sample_weight : ndarray of shape (n_samples,), dtype=floating + The weights for each observation in X. + + centers_old : ndarray of shape (n_clusters, n_features), dtype=floating + Centers before previous iteration, placeholder for the centers after + previous iteration. + + centers_new : ndarray of shape (n_clusters, n_features), dtype=floating + Centers after previous iteration, placeholder for the new centers + computed during this iteration. `centers_new` can be `None` if + `update_centers` is False. + + weight_in_clusters : ndarray of shape (n_clusters,), dtype=floating + Placeholder for the sums of the weights of every observation assigned + to each center. `weight_in_clusters` can be `None` if `update_centers` + is False. + + labels : ndarray of shape (n_samples,), dtype=int + labels assignment. + + center_shift : ndarray of shape (n_clusters,), dtype=floating + Distance between old and new centers. + + n_threads : int + The number of threads to be used by openmp. + + update_centers : bool + - If True, the labels and the new centers will be computed, i.e. runs + the E-step and the M-step of the algorithm. + - If False, only the labels will be computed, i.e runs the E-step of + the algorithm. This is useful especially when calling predict on a + fitted model. + """ + cdef: + int n_samples = X.shape[0] + int n_features = X.shape[1] + int n_clusters = centers_old.shape[0] + + if n_samples == 0: + # An empty array was passed, do nothing and return early (before + # attempting to compute n_chunks). This can typically happen when + # calling the prediction function of a bisecting k-means model with a + # large fraction of outliers. + return + + cdef: + # hard-coded number of samples per chunk. Appeared to be close to + # optimal in all situations. + int n_samples_chunk = CHUNK_SIZE if n_samples > CHUNK_SIZE else n_samples + int n_chunks = n_samples // n_samples_chunk + int n_samples_rem = n_samples % n_samples_chunk + int chunk_idx + int start, end + + int j, k + + floating[::1] centers_squared_norms = row_norms(centers_old, squared=True) + + floating *centers_new_chunk + floating *weight_in_clusters_chunk + floating *pairwise_distances_chunk + + omp_lock_t lock + + # count remainder chunk in total number of chunks + n_chunks += n_samples != n_chunks * n_samples_chunk + + # number of threads should not be bigger than number of chunks + n_threads = min(n_threads, n_chunks) + + if update_centers: + memset(¢ers_new[0, 0], 0, n_clusters * n_features * sizeof(floating)) + memset(&weight_in_clusters[0], 0, n_clusters * sizeof(floating)) + omp_init_lock(&lock) + + with nogil, parallel(num_threads=n_threads): + # thread local buffers + centers_new_chunk = calloc(n_clusters * n_features, sizeof(floating)) + weight_in_clusters_chunk = calloc(n_clusters, sizeof(floating)) + pairwise_distances_chunk = malloc(n_samples_chunk * n_clusters * sizeof(floating)) + + for chunk_idx in prange(n_chunks, schedule='static'): + start = chunk_idx * n_samples_chunk + if chunk_idx == n_chunks - 1 and n_samples_rem > 0: + end = start + n_samples_rem + else: + end = start + n_samples_chunk + + _update_chunk_dense( + X[start: end], + sample_weight[start: end], + centers_old, + centers_squared_norms, + labels[start: end], + centers_new_chunk, + weight_in_clusters_chunk, + pairwise_distances_chunk, + update_centers) + + # reduction from local buffers. + if update_centers: + # The lock is necessary to avoid race conditions when aggregating + # info from different thread-local buffers. + omp_set_lock(&lock) + for j in range(n_clusters): + weight_in_clusters[j] += weight_in_clusters_chunk[j] + for k in range(n_features): + centers_new[j, k] += centers_new_chunk[j * n_features + k] + + omp_unset_lock(&lock) + + free(centers_new_chunk) + free(weight_in_clusters_chunk) + free(pairwise_distances_chunk) + + if update_centers: + omp_destroy_lock(&lock) + _relocate_empty_clusters_dense( + X, sample_weight, centers_old, centers_new, weight_in_clusters, labels + ) + + _average_centers(centers_new, weight_in_clusters) + _center_shift(centers_old, centers_new, center_shift) + + +cdef void _update_chunk_dense( + const floating[:, ::1] X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + const floating[::1] centers_squared_norms, # IN + int[::1] labels, # OUT + floating *centers_new, # OUT + floating *weight_in_clusters, # OUT + floating *pairwise_distances, # OUT + bint update_centers) noexcept nogil: + """K-means combined EM step for one dense data chunk. + + Compute the partial contribution of a single data chunk to the labels and + centers. + """ + cdef: + int n_samples = labels.shape[0] + int n_clusters = centers_old.shape[0] + int n_features = centers_old.shape[1] + + floating sq_dist, min_sq_dist + int i, j, k, label + + # Instead of computing the full pairwise squared distances matrix, + # ||X - C||² = ||X||² - 2 X.C^T + ||C||², we only need to store + # the - 2 X.C^T + ||C||² term since the argmin for a given sample only + # depends on the centers. + # pairwise_distances = ||C||² + for i in range(n_samples): + for j in range(n_clusters): + pairwise_distances[i * n_clusters + j] = centers_squared_norms[j] + + # pairwise_distances += -2 * X.dot(C.T) + _gemm(RowMajor, NoTrans, Trans, n_samples, n_clusters, n_features, + -2.0, &X[0, 0], n_features, ¢ers_old[0, 0], n_features, + 1.0, pairwise_distances, n_clusters) + + for i in range(n_samples): + min_sq_dist = pairwise_distances[i * n_clusters] + label = 0 + for j in range(1, n_clusters): + sq_dist = pairwise_distances[i * n_clusters + j] + if sq_dist < min_sq_dist: + min_sq_dist = sq_dist + label = j + labels[i] = label + + if update_centers: + weight_in_clusters[label] += sample_weight[i] + for k in range(n_features): + centers_new[label * n_features + k] += X[i, k] * sample_weight[i] + + +def lloyd_iter_chunked_sparse( + X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + floating[:, ::1] centers_new, # OUT + floating[::1] weight_in_clusters, # OUT + int[::1] labels, # OUT + floating[::1] center_shift, # OUT + int n_threads, + bint update_centers=True): + """Single iteration of K-means lloyd algorithm with sparse input. + + Update labels and centers (inplace), for one iteration, distributed + over data chunks. + + Parameters + ---------- + X : sparse matrix of shape (n_samples, n_features), dtype=floating + The observations to cluster. Must be in CSR format. + + sample_weight : ndarray of shape (n_samples,), dtype=floating + The weights for each observation in X. + + centers_old : ndarray of shape (n_clusters, n_features), dtype=floating + Centers before previous iteration, placeholder for the centers after + previous iteration. + + centers_new : ndarray of shape (n_clusters, n_features), dtype=floating + Centers after previous iteration, placeholder for the new centers + computed during this iteration. `centers_new` can be `None` if + `update_centers` is False. + + weight_in_clusters : ndarray of shape (n_clusters,), dtype=floating + Placeholder for the sums of the weights of every observation assigned + to each center. `weight_in_clusters` can be `None` if `update_centers` + is False. + + labels : ndarray of shape (n_samples,), dtype=int + labels assignment. + + center_shift : ndarray of shape (n_clusters,), dtype=floating + Distance between old and new centers. + + n_threads : int + The number of threads to be used by openmp. + + update_centers : bool + - If True, the labels and the new centers will be computed, i.e. runs + the E-step and the M-step of the algorithm. + - If False, only the labels will be computed, i.e runs the E-step of + the algorithm. This is useful especially when calling predict on a + fitted model. + """ + cdef: + int n_samples = X.shape[0] + int n_features = X.shape[1] + int n_clusters = centers_old.shape[0] + + if n_samples == 0: + # An empty array was passed, do nothing and return early (before + # attempting to compute n_chunks). This can typically happen when + # calling the prediction function of a bisecting k-means model with a + # large fraction of outliers. + return + + cdef: + # Choose same as for dense. Does not have the same impact since with + # sparse data the pairwise distances matrix is not precomputed. + # However, splitting in chunks is necessary to get parallelism. + int n_samples_chunk = CHUNK_SIZE if n_samples > CHUNK_SIZE else n_samples + int n_chunks = n_samples // n_samples_chunk + int n_samples_rem = n_samples % n_samples_chunk + int chunk_idx + int start = 0, end = 0 + + int j, k + + floating[::1] X_data = X.data + int[::1] X_indices = X.indices + int[::1] X_indptr = X.indptr + + floating[::1] centers_squared_norms = row_norms(centers_old, squared=True) + + floating *centers_new_chunk + floating *weight_in_clusters_chunk + + omp_lock_t lock + + # count remainder chunk in total number of chunks + n_chunks += n_samples != n_chunks * n_samples_chunk + + # number of threads should not be bigger than number of chunks + n_threads = min(n_threads, n_chunks) + + if update_centers: + memset(¢ers_new[0, 0], 0, n_clusters * n_features * sizeof(floating)) + memset(&weight_in_clusters[0], 0, n_clusters * sizeof(floating)) + omp_init_lock(&lock) + + with nogil, parallel(num_threads=n_threads): + # thread local buffers + centers_new_chunk = calloc(n_clusters * n_features, sizeof(floating)) + weight_in_clusters_chunk = calloc(n_clusters, sizeof(floating)) + + for chunk_idx in prange(n_chunks, schedule='static'): + start = chunk_idx * n_samples_chunk + if chunk_idx == n_chunks - 1 and n_samples_rem > 0: + end = start + n_samples_rem + else: + end = start + n_samples_chunk + + _update_chunk_sparse( + X_data[X_indptr[start]: X_indptr[end]], + X_indices[X_indptr[start]: X_indptr[end]], + X_indptr[start: end+1], + sample_weight[start: end], + centers_old, + centers_squared_norms, + labels[start: end], + centers_new_chunk, + weight_in_clusters_chunk, + update_centers) + + # reduction from local buffers. + if update_centers: + # The lock is necessary to avoid race conditions when aggregating + # info from different thread-local buffers. + omp_set_lock(&lock) + for j in range(n_clusters): + weight_in_clusters[j] += weight_in_clusters_chunk[j] + for k in range(n_features): + centers_new[j, k] += centers_new_chunk[j * n_features + k] + omp_unset_lock(&lock) + + free(centers_new_chunk) + free(weight_in_clusters_chunk) + + if update_centers: + omp_destroy_lock(&lock) + _relocate_empty_clusters_sparse( + X_data, X_indices, X_indptr, sample_weight, + centers_old, centers_new, weight_in_clusters, labels) + + _average_centers(centers_new, weight_in_clusters) + _center_shift(centers_old, centers_new, center_shift) + + +cdef void _update_chunk_sparse( + const floating[::1] X_data, # IN + const int[::1] X_indices, # IN + const int[::1] X_indptr, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + const floating[::1] centers_squared_norms, # IN + int[::1] labels, # OUT + floating *centers_new, # OUT + floating *weight_in_clusters, # OUT + bint update_centers) noexcept nogil: + """K-means combined EM step for one sparse data chunk. + + Compute the partial contribution of a single data chunk to the labels and + centers. + """ + cdef: + int n_samples = labels.shape[0] + int n_clusters = centers_old.shape[0] + int n_features = centers_old.shape[1] + + floating sq_dist, min_sq_dist + int i, j, k, label + floating max_floating = FLT_MAX if floating is float else DBL_MAX + int s = X_indptr[0] + + # XXX Precompute the pairwise distances matrix is not worth for sparse + # currently. Should be tested when BLAS (sparse x dense) matrix + # multiplication is available. + for i in range(n_samples): + min_sq_dist = max_floating + label = 0 + + for j in range(n_clusters): + sq_dist = 0.0 + for k in range(X_indptr[i] - s, X_indptr[i + 1] - s): + sq_dist += centers_old[j, X_indices[k]] * X_data[k] + + # Instead of computing the full squared distance with each cluster, + # ||X - C||² = ||X||² - 2 X.C^T + ||C||², we only need to compute + # the - 2 X.C^T + ||C||² term since the argmin for a given sample + # only depends on the centers C. + sq_dist = centers_squared_norms[j] -2 * sq_dist + if sq_dist < min_sq_dist: + min_sq_dist = sq_dist + label = j + + labels[i] = label + + if update_centers: + weight_in_clusters[label] += sample_weight[i] + for k in range(X_indptr[i] - s, X_indptr[i + 1] - s): + centers_new[label * n_features + X_indices[k]] += X_data[k] * sample_weight[i] diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_minibatch.pyx b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_minibatch.pyx new file mode 100644 index 0000000000000000000000000000000000000000..22ca5255e3889574d7155f1e077f84111832cf92 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_k_means_minibatch.pyx @@ -0,0 +1,218 @@ +from cython cimport floating +from cython.parallel cimport parallel, prange +from libc.stdlib cimport malloc, free + + +def _minibatch_update_dense( + const floating[:, ::1] X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + floating[:, ::1] centers_new, # OUT + floating[::1] weight_sums, # INOUT + const int[::1] labels, # IN + int n_threads): + """Update of the centers for dense MiniBatchKMeans. + + Parameters + ---------- + X : ndarray of shape (n_samples, n_features), dtype=floating + The observations to cluster. + + sample_weight : ndarray of shape (n_samples,), dtype=floating + The weights for each observation in X. + + centers_old : ndarray of shape (n_clusters, n_features), dtype=floating + Centers before previous iteration, placeholder for the centers after + previous iteration. + + centers_new : ndarray of shape (n_clusters, n_features), dtype=floating + Centers after previous iteration, placeholder for the new centers + computed during this iteration. + + weight_sums : ndarray of shape (n_clusters,), dtype=floating + Current sums of the accumulated weights for each center. + + labels : ndarray of shape (n_samples,), dtype=int + labels assignment. + + n_threads : int + The number of threads to be used by openmp. + """ + cdef: + int n_samples = X.shape[0] + int n_clusters = centers_old.shape[0] + int cluster_idx + + int *indices + + with nogil, parallel(num_threads=n_threads): + indices = malloc(n_samples * sizeof(int)) + + for cluster_idx in prange(n_clusters, schedule="static"): + update_center_dense(cluster_idx, X, sample_weight, + centers_old, centers_new, weight_sums, labels, + indices) + + free(indices) + + +cdef void update_center_dense( + int cluster_idx, + const floating[:, ::1] X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + floating[:, ::1] centers_new, # OUT + floating[::1] weight_sums, # INOUT + const int[::1] labels, # IN + int *indices) noexcept nogil: # TMP + """Update of a single center for dense MinibatchKMeans""" + cdef: + int n_samples = sample_weight.shape[0] + int n_features = centers_old.shape[1] + floating alpha + int n_indices + int k, sample_idx, feature_idx + + floating wsum = 0 + + # indices = np.where(labels == cluster_idx)[0] + k = 0 + for sample_idx in range(n_samples): + if labels[sample_idx] == cluster_idx: + indices[k] = sample_idx + wsum += sample_weight[sample_idx] + k += 1 + n_indices = k + + if wsum > 0: + # Undo the previous count-based scaling for this cluster center + for feature_idx in range(n_features): + centers_new[cluster_idx, feature_idx] = centers_old[cluster_idx, feature_idx] * weight_sums[cluster_idx] + + # Update cluster with new point members + for k in range(n_indices): + sample_idx = indices[k] + for feature_idx in range(n_features): + centers_new[cluster_idx, feature_idx] += X[sample_idx, feature_idx] * sample_weight[sample_idx] + + # Update the count statistics for this center + weight_sums[cluster_idx] += wsum + + # Rescale to compute mean of all points (old and new) + alpha = 1 / weight_sums[cluster_idx] + for feature_idx in range(n_features): + centers_new[cluster_idx, feature_idx] *= alpha + else: + # No sample was assigned to this cluster in this batch of data + for feature_idx in range(n_features): + centers_new[cluster_idx, feature_idx] = centers_old[cluster_idx, feature_idx] + + +def _minibatch_update_sparse( + X, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + floating[:, ::1] centers_new, # OUT + floating[::1] weight_sums, # INOUT + const int[::1] labels, # IN + int n_threads): + """Update of the centers for sparse MiniBatchKMeans. + + Parameters + ---------- + X : sparse matrix of shape (n_samples, n_features), dtype=floating + The observations to cluster. Must be in CSR format. + + sample_weight : ndarray of shape (n_samples,), dtype=floating + The weights for each observation in X. + + centers_old : ndarray of shape (n_clusters, n_features), dtype=floating + Centers before previous iteration, placeholder for the centers after + previous iteration. + + centers_new : ndarray of shape (n_clusters, n_features), dtype=floating + Centers after previous iteration, placeholder for the new centers + computed during this iteration. + + weight_sums : ndarray of shape (n_clusters,), dtype=floating + Current sums of the accumulated weights for each center. + + labels : ndarray of shape (n_samples,), dtype=int + labels assignment. + + n_threads : int + The number of threads to be used by openmp. + """ + cdef: + floating[::1] X_data = X.data + int[::1] X_indices = X.indices + int[::1] X_indptr = X.indptr + int n_samples = X.shape[0] + int n_clusters = centers_old.shape[0] + int cluster_idx + + int *indices + + with nogil, parallel(num_threads=n_threads): + indices = malloc(n_samples * sizeof(int)) + + for cluster_idx in prange(n_clusters, schedule="static"): + update_center_sparse(cluster_idx, X_data, X_indices, X_indptr, + sample_weight, centers_old, centers_new, + weight_sums, labels, indices) + + free(indices) + + +cdef void update_center_sparse( + int cluster_idx, + const floating[::1] X_data, # IN + const int[::1] X_indices, # IN + const int[::1] X_indptr, # IN + const floating[::1] sample_weight, # IN + const floating[:, ::1] centers_old, # IN + floating[:, ::1] centers_new, # OUT + floating[::1] weight_sums, # INOUT + const int[::1] labels, # IN + int *indices) noexcept nogil: # TMP + """Update of a single center for sparse MinibatchKMeans""" + cdef: + int n_samples = sample_weight.shape[0] + int n_features = centers_old.shape[1] + floating alpha + int n_indices + int k, sample_idx, feature_idx + + floating wsum = 0 + + # indices = np.where(labels == cluster_idx)[0] + k = 0 + for sample_idx in range(n_samples): + if labels[sample_idx] == cluster_idx: + indices[k] = sample_idx + wsum += sample_weight[sample_idx] + k += 1 + n_indices = k + + if wsum > 0: + # Undo the previous count-based scaling for this cluster center: + for feature_idx in range(n_features): + centers_new[cluster_idx, feature_idx] = centers_old[cluster_idx, feature_idx] * weight_sums[cluster_idx] + + # Update cluster with new point members + for k in range(n_indices): + sample_idx = indices[k] + for feature_idx in range(X_indptr[sample_idx], X_indptr[sample_idx + 1]): + centers_new[cluster_idx, X_indices[feature_idx]] += X_data[feature_idx] * sample_weight[sample_idx] + + # Update the count statistics for this center + weight_sums[cluster_idx] += wsum + + # Rescale to compute mean of all points (old and new) + alpha = 1 / weight_sums[cluster_idx] + for feature_idx in range(n_features): + centers_new[cluster_idx, feature_idx] *= alpha + else: + # No sample was assigned to this cluster in this batch of data + for feature_idx in range(n_features): + centers_new[cluster_idx, feature_idx] = centers_old[cluster_idx, feature_idx] diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_kmeans.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_kmeans.py new file mode 100644 index 0000000000000000000000000000000000000000..11c85610239ccae163137a1ced0f990325864390 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_kmeans.py @@ -0,0 +1,2303 @@ +"""K-means clustering.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from abc import ABC, abstractmethod +from numbers import Integral, Real + +import numpy as np +import scipy.sparse as sp + +from ..base import ( + BaseEstimator, + ClassNamePrefixFeaturesOutMixin, + ClusterMixin, + TransformerMixin, + _fit_context, +) +from ..exceptions import ConvergenceWarning +from ..metrics.pairwise import _euclidean_distances, euclidean_distances +from ..utils import check_array, check_random_state +from ..utils._openmp_helpers import _openmp_effective_n_threads +from ..utils._param_validation import Interval, StrOptions, validate_params +from ..utils.extmath import row_norms, stable_cumsum +from ..utils.parallel import ( + _get_threadpool_controller, + _threadpool_controller_decorator, +) +from ..utils.sparsefuncs import mean_variance_axis +from ..utils.sparsefuncs_fast import assign_rows_csr +from ..utils.validation import ( + _check_sample_weight, + _is_arraylike_not_scalar, + check_is_fitted, + validate_data, +) +from ._k_means_common import ( + CHUNK_SIZE, + _inertia_dense, + _inertia_sparse, + _is_same_clustering, +) +from ._k_means_elkan import ( + elkan_iter_chunked_dense, + elkan_iter_chunked_sparse, + init_bounds_dense, + init_bounds_sparse, +) +from ._k_means_lloyd import lloyd_iter_chunked_dense, lloyd_iter_chunked_sparse +from ._k_means_minibatch import _minibatch_update_dense, _minibatch_update_sparse + +############################################################################### +# Initialization heuristic + + +@validate_params( + { + "X": ["array-like", "sparse matrix"], + "n_clusters": [Interval(Integral, 1, None, closed="left")], + "sample_weight": ["array-like", None], + "x_squared_norms": ["array-like", None], + "random_state": ["random_state"], + "n_local_trials": [Interval(Integral, 1, None, closed="left"), None], + }, + prefer_skip_nested_validation=True, +) +def kmeans_plusplus( + X, + n_clusters, + *, + sample_weight=None, + x_squared_norms=None, + random_state=None, + n_local_trials=None, +): + """Init n_clusters seeds according to k-means++. + + .. versionadded:: 0.24 + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The data to pick seeds from. + + n_clusters : int + The number of centroids to initialize. + + sample_weight : array-like of shape (n_samples,), default=None + The weights for each observation in `X`. If `None`, all observations + are assigned equal weight. `sample_weight` is ignored if `init` + is a callable or a user provided array. + + .. versionadded:: 1.3 + + x_squared_norms : array-like of shape (n_samples,), default=None + Squared Euclidean norm of each data point. + + random_state : int or RandomState instance, default=None + Determines random number generation for centroid initialization. Pass + an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + n_local_trials : int, default=None + The number of seeding trials for each center (except the first), + of which the one reducing inertia the most is greedily chosen. + Set to None to make the number of trials depend logarithmically + on the number of seeds (2+log(k)) which is the recommended setting. + Setting to 1 disables the greedy cluster selection and recovers the + vanilla k-means++ algorithm which was empirically shown to work less + well than its greedy variant. + + Returns + ------- + centers : ndarray of shape (n_clusters, n_features) + The initial centers for k-means. + + indices : ndarray of shape (n_clusters,) + The index location of the chosen centers in the data array X. For a + given index and center, X[index] = center. + + Notes + ----- + Selects initial cluster centers for k-mean clustering in a smart way + to speed up convergence. see: Arthur, D. and Vassilvitskii, S. + "k-means++: the advantages of careful seeding". ACM-SIAM symposium + on Discrete algorithms. 2007 + + Examples + -------- + + >>> from sklearn.cluster import kmeans_plusplus + >>> import numpy as np + >>> X = np.array([[1, 2], [1, 4], [1, 0], + ... [10, 2], [10, 4], [10, 0]]) + >>> centers, indices = kmeans_plusplus(X, n_clusters=2, random_state=0) + >>> centers + array([[10, 2], + [ 1, 0]]) + >>> indices + array([3, 2]) + """ + # Check data + check_array(X, accept_sparse="csr", dtype=[np.float64, np.float32]) + sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype) + + if X.shape[0] < n_clusters: + raise ValueError( + f"n_samples={X.shape[0]} should be >= n_clusters={n_clusters}." + ) + + # Check parameters + if x_squared_norms is None: + x_squared_norms = row_norms(X, squared=True) + else: + x_squared_norms = check_array(x_squared_norms, dtype=X.dtype, ensure_2d=False) + + if x_squared_norms.shape[0] != X.shape[0]: + raise ValueError( + f"The length of x_squared_norms {x_squared_norms.shape[0]} should " + f"be equal to the length of n_samples {X.shape[0]}." + ) + + random_state = check_random_state(random_state) + + # Call private k-means++ + centers, indices = _kmeans_plusplus( + X, n_clusters, x_squared_norms, sample_weight, random_state, n_local_trials + ) + + return centers, indices + + +def _kmeans_plusplus( + X, n_clusters, x_squared_norms, sample_weight, random_state, n_local_trials=None +): + """Computational component for initialization of n_clusters by + k-means++. Prior validation of data is assumed. + + Parameters + ---------- + X : {ndarray, sparse matrix} of shape (n_samples, n_features) + The data to pick seeds for. + + n_clusters : int + The number of seeds to choose. + + sample_weight : ndarray of shape (n_samples,) + The weights for each observation in `X`. + + x_squared_norms : ndarray of shape (n_samples,) + Squared Euclidean norm of each data point. + + random_state : RandomState instance + The generator used to initialize the centers. + See :term:`Glossary `. + + n_local_trials : int, default=None + The number of seeding trials for each center (except the first), + of which the one reducing inertia the most is greedily chosen. + Set to None to make the number of trials depend logarithmically + on the number of seeds (2+log(k)); this is the default. + + Returns + ------- + centers : ndarray of shape (n_clusters, n_features) + The initial centers for k-means. + + indices : ndarray of shape (n_clusters,) + The index location of the chosen centers in the data array X. For a + given index and center, X[index] = center. + """ + n_samples, n_features = X.shape + + centers = np.empty((n_clusters, n_features), dtype=X.dtype) + + # Set the number of local seeding trials if none is given + if n_local_trials is None: + # This is what Arthur/Vassilvitskii tried, but did not report + # specific results for other than mentioning in the conclusion + # that it helped. + n_local_trials = 2 + int(np.log(n_clusters)) + + # Pick first center randomly and track index of point + center_id = random_state.choice(n_samples, p=sample_weight / sample_weight.sum()) + indices = np.full(n_clusters, -1, dtype=int) + if sp.issparse(X): + centers[0] = X[[center_id]].toarray() + else: + centers[0] = X[center_id] + indices[0] = center_id + + # Initialize list of closest distances and calculate current potential + closest_dist_sq = _euclidean_distances( + centers[0, np.newaxis], X, Y_norm_squared=x_squared_norms, squared=True + ) + current_pot = closest_dist_sq @ sample_weight + + # Pick the remaining n_clusters-1 points + for c in range(1, n_clusters): + # Choose center candidates by sampling with probability proportional + # to the squared distance to the closest existing center + rand_vals = random_state.uniform(size=n_local_trials) * current_pot + candidate_ids = np.searchsorted( + stable_cumsum(sample_weight * closest_dist_sq), rand_vals + ) + # XXX: numerical imprecision can result in a candidate_id out of range + np.clip(candidate_ids, None, closest_dist_sq.size - 1, out=candidate_ids) + + # Compute distances to center candidates + distance_to_candidates = _euclidean_distances( + X[candidate_ids], X, Y_norm_squared=x_squared_norms, squared=True + ) + + # update closest distances squared and potential for each candidate + np.minimum(closest_dist_sq, distance_to_candidates, out=distance_to_candidates) + candidates_pot = distance_to_candidates @ sample_weight.reshape(-1, 1) + + # Decide which candidate is the best + best_candidate = np.argmin(candidates_pot) + current_pot = candidates_pot[best_candidate] + closest_dist_sq = distance_to_candidates[best_candidate] + best_candidate = candidate_ids[best_candidate] + + # Permanently add best center candidate found in local tries + if sp.issparse(X): + centers[c] = X[[best_candidate]].toarray() + else: + centers[c] = X[best_candidate] + indices[c] = best_candidate + + return centers, indices + + +############################################################################### +# K-means batch estimation by EM (expectation maximization) + + +def _tolerance(X, tol): + """Return a tolerance which is dependent on the dataset.""" + if tol == 0: + return 0 + if sp.issparse(X): + variances = mean_variance_axis(X, axis=0)[1] + else: + variances = np.var(X, axis=0) + return np.mean(variances) * tol + + +@validate_params( + { + "X": ["array-like", "sparse matrix"], + "sample_weight": ["array-like", None], + "return_n_iter": [bool], + }, + prefer_skip_nested_validation=False, +) +def k_means( + X, + n_clusters, + *, + sample_weight=None, + init="k-means++", + n_init="auto", + max_iter=300, + verbose=False, + tol=1e-4, + random_state=None, + copy_x=True, + algorithm="lloyd", + return_n_iter=False, +): + """Perform K-means clustering algorithm. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The observations to cluster. It must be noted that the data + will be converted to C ordering, which will cause a memory copy + if the given data is not C-contiguous. + + n_clusters : int + The number of clusters to form as well as the number of + centroids to generate. + + sample_weight : array-like of shape (n_samples,), default=None + The weights for each observation in `X`. If `None`, all observations + are assigned equal weight. `sample_weight` is not used during + initialization if `init` is a callable or a user provided array. + + init : {'k-means++', 'random'}, callable or array-like of shape \ + (n_clusters, n_features), default='k-means++' + Method for initialization: + + - `'k-means++'` : selects initial cluster centers for k-mean + clustering in a smart way to speed up convergence. See section + Notes in k_init for more details. + - `'random'`: choose `n_clusters` observations (rows) at random from data + for the initial centroids. + - If an array is passed, it should be of shape `(n_clusters, n_features)` + and gives the initial centers. + - If a callable is passed, it should take arguments `X`, `n_clusters` and a + random state and return an initialization. + + n_init : 'auto' or int, default="auto" + Number of time the k-means algorithm will be run with different + centroid seeds. The final results will be the best output of + n_init consecutive runs in terms of inertia. + + When `n_init='auto'`, the number of runs depends on the value of init: + 10 if using `init='random'` or `init` is a callable; + 1 if using `init='k-means++'` or `init` is an array-like. + + .. versionadded:: 1.2 + Added 'auto' option for `n_init`. + + .. versionchanged:: 1.4 + Default value for `n_init` changed to `'auto'`. + + max_iter : int, default=300 + Maximum number of iterations of the k-means algorithm to run. + + verbose : bool, default=False + Verbosity mode. + + tol : float, default=1e-4 + Relative tolerance with regards to Frobenius norm of the difference + in the cluster centers of two consecutive iterations to declare + convergence. + + random_state : int, RandomState instance or None, default=None + Determines random number generation for centroid initialization. Use + an int to make the randomness deterministic. + See :term:`Glossary `. + + copy_x : bool, default=True + When pre-computing distances it is more numerically accurate to center + the data first. If `copy_x` is True (default), then the original data is + not modified. If False, the original data is modified, and put back + before the function returns, but small numerical differences may be + introduced by subtracting and then adding the data mean. Note that if + the original data is not C-contiguous, a copy will be made even if + `copy_x` is False. If the original data is sparse, but not in CSR format, + a copy will be made even if `copy_x` is False. + + algorithm : {"lloyd", "elkan"}, default="lloyd" + K-means algorithm to use. The classical EM-style algorithm is `"lloyd"`. + The `"elkan"` variation can be more efficient on some datasets with + well-defined clusters, by using the triangle inequality. However it's + more memory intensive due to the allocation of an extra array of shape + `(n_samples, n_clusters)`. + + .. versionchanged:: 0.18 + Added Elkan algorithm + + .. versionchanged:: 1.1 + Renamed "full" to "lloyd", and deprecated "auto" and "full". + Changed "auto" to use "lloyd" instead of "elkan". + + return_n_iter : bool, default=False + Whether or not to return the number of iterations. + + Returns + ------- + centroid : ndarray of shape (n_clusters, n_features) + Centroids found at the last iteration of k-means. + + label : ndarray of shape (n_samples,) + The `label[i]` is the code or index of the centroid the + i'th observation is closest to. + + inertia : float + The final value of the inertia criterion (sum of squared distances to + the closest centroid for all observations in the training set). + + best_n_iter : int + Number of iterations corresponding to the best results. + Returned only if `return_n_iter` is set to True. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.cluster import k_means + >>> X = np.array([[1, 2], [1, 4], [1, 0], + ... [10, 2], [10, 4], [10, 0]]) + >>> centroid, label, inertia = k_means( + ... X, n_clusters=2, n_init="auto", random_state=0 + ... ) + >>> centroid + array([[10., 2.], + [ 1., 2.]]) + >>> label + array([1, 1, 1, 0, 0, 0], dtype=int32) + >>> inertia + 16.0 + """ + est = KMeans( + n_clusters=n_clusters, + init=init, + n_init=n_init, + max_iter=max_iter, + verbose=verbose, + tol=tol, + random_state=random_state, + copy_x=copy_x, + algorithm=algorithm, + ).fit(X, sample_weight=sample_weight) + if return_n_iter: + return est.cluster_centers_, est.labels_, est.inertia_, est.n_iter_ + else: + return est.cluster_centers_, est.labels_, est.inertia_ + + +def _kmeans_single_elkan( + X, + sample_weight, + centers_init, + max_iter=300, + verbose=False, + tol=1e-4, + n_threads=1, +): + """A single run of k-means elkan, assumes preparation completed prior. + + Parameters + ---------- + X : {ndarray, sparse matrix} of shape (n_samples, n_features) + The observations to cluster. If sparse matrix, must be in CSR format. + + sample_weight : array-like of shape (n_samples,) + The weights for each observation in X. + + centers_init : ndarray of shape (n_clusters, n_features) + The initial centers. + + max_iter : int, default=300 + Maximum number of iterations of the k-means algorithm to run. + + verbose : bool, default=False + Verbosity mode. + + tol : float, default=1e-4 + Relative tolerance with regards to Frobenius norm of the difference + in the cluster centers of two consecutive iterations to declare + convergence. + It's not advised to set `tol=0` since convergence might never be + declared due to rounding errors. Use a very small number instead. + + n_threads : int, default=1 + The number of OpenMP threads to use for the computation. Parallelism is + sample-wise on the main cython loop which assigns each sample to its + closest center. + + Returns + ------- + centroid : ndarray of shape (n_clusters, n_features) + Centroids found at the last iteration of k-means. + + label : ndarray of shape (n_samples,) + label[i] is the code or index of the centroid the + i'th observation is closest to. + + inertia : float + The final value of the inertia criterion (sum of squared distances to + the closest centroid for all observations in the training set). + + n_iter : int + Number of iterations run. + """ + n_samples = X.shape[0] + n_clusters = centers_init.shape[0] + + # Buffers to avoid new allocations at each iteration. + centers = centers_init + centers_new = np.zeros_like(centers) + weight_in_clusters = np.zeros(n_clusters, dtype=X.dtype) + labels = np.full(n_samples, -1, dtype=np.int32) + labels_old = labels.copy() + center_half_distances = euclidean_distances(centers) / 2 + distance_next_center = np.partition( + np.asarray(center_half_distances), kth=1, axis=0 + )[1] + upper_bounds = np.zeros(n_samples, dtype=X.dtype) + lower_bounds = np.zeros((n_samples, n_clusters), dtype=X.dtype) + center_shift = np.zeros(n_clusters, dtype=X.dtype) + + if sp.issparse(X): + init_bounds = init_bounds_sparse + elkan_iter = elkan_iter_chunked_sparse + _inertia = _inertia_sparse + else: + init_bounds = init_bounds_dense + elkan_iter = elkan_iter_chunked_dense + _inertia = _inertia_dense + + init_bounds( + X, + centers, + center_half_distances, + labels, + upper_bounds, + lower_bounds, + n_threads=n_threads, + ) + + strict_convergence = False + + for i in range(max_iter): + elkan_iter( + X, + sample_weight, + centers, + centers_new, + weight_in_clusters, + center_half_distances, + distance_next_center, + upper_bounds, + lower_bounds, + labels, + center_shift, + n_threads, + ) + + # compute new pairwise distances between centers and closest other + # center of each center for next iterations + center_half_distances = euclidean_distances(centers_new) / 2 + distance_next_center = np.partition( + np.asarray(center_half_distances), kth=1, axis=0 + )[1] + + if verbose: + inertia = _inertia(X, sample_weight, centers, labels, n_threads) + print(f"Iteration {i}, inertia {inertia}") + + centers, centers_new = centers_new, centers + + if np.array_equal(labels, labels_old): + # First check the labels for strict convergence. + if verbose: + print(f"Converged at iteration {i}: strict convergence.") + strict_convergence = True + break + else: + # No strict convergence, check for tol based convergence. + center_shift_tot = (center_shift**2).sum() + if center_shift_tot <= tol: + if verbose: + print( + f"Converged at iteration {i}: center shift " + f"{center_shift_tot} within tolerance {tol}." + ) + break + + labels_old[:] = labels + + if not strict_convergence: + # rerun E-step so that predicted labels match cluster centers + elkan_iter( + X, + sample_weight, + centers, + centers, + weight_in_clusters, + center_half_distances, + distance_next_center, + upper_bounds, + lower_bounds, + labels, + center_shift, + n_threads, + update_centers=False, + ) + + inertia = _inertia(X, sample_weight, centers, labels, n_threads) + + return labels, inertia, centers, i + 1 + + +# Threadpoolctl context to limit the number of threads in second level of +# nested parallelism (i.e. BLAS) to avoid oversubscription. +@_threadpool_controller_decorator(limits=1, user_api="blas") +def _kmeans_single_lloyd( + X, + sample_weight, + centers_init, + max_iter=300, + verbose=False, + tol=1e-4, + n_threads=1, +): + """A single run of k-means lloyd, assumes preparation completed prior. + + Parameters + ---------- + X : {ndarray, sparse matrix} of shape (n_samples, n_features) + The observations to cluster. If sparse matrix, must be in CSR format. + + sample_weight : ndarray of shape (n_samples,) + The weights for each observation in X. + + centers_init : ndarray of shape (n_clusters, n_features) + The initial centers. + + max_iter : int, default=300 + Maximum number of iterations of the k-means algorithm to run. + + verbose : bool, default=False + Verbosity mode + + tol : float, default=1e-4 + Relative tolerance with regards to Frobenius norm of the difference + in the cluster centers of two consecutive iterations to declare + convergence. + It's not advised to set `tol=0` since convergence might never be + declared due to rounding errors. Use a very small number instead. + + n_threads : int, default=1 + The number of OpenMP threads to use for the computation. Parallelism is + sample-wise on the main cython loop which assigns each sample to its + closest center. + + Returns + ------- + centroid : ndarray of shape (n_clusters, n_features) + Centroids found at the last iteration of k-means. + + label : ndarray of shape (n_samples,) + label[i] is the code or index of the centroid the + i'th observation is closest to. + + inertia : float + The final value of the inertia criterion (sum of squared distances to + the closest centroid for all observations in the training set). + + n_iter : int + Number of iterations run. + """ + n_clusters = centers_init.shape[0] + + # Buffers to avoid new allocations at each iteration. + centers = centers_init + centers_new = np.zeros_like(centers) + labels = np.full(X.shape[0], -1, dtype=np.int32) + labels_old = labels.copy() + weight_in_clusters = np.zeros(n_clusters, dtype=X.dtype) + center_shift = np.zeros(n_clusters, dtype=X.dtype) + + if sp.issparse(X): + lloyd_iter = lloyd_iter_chunked_sparse + _inertia = _inertia_sparse + else: + lloyd_iter = lloyd_iter_chunked_dense + _inertia = _inertia_dense + + strict_convergence = False + + for i in range(max_iter): + lloyd_iter( + X, + sample_weight, + centers, + centers_new, + weight_in_clusters, + labels, + center_shift, + n_threads, + ) + + if verbose: + inertia = _inertia(X, sample_weight, centers, labels, n_threads) + print(f"Iteration {i}, inertia {inertia}.") + + centers, centers_new = centers_new, centers + + if np.array_equal(labels, labels_old): + # First check the labels for strict convergence. + if verbose: + print(f"Converged at iteration {i}: strict convergence.") + strict_convergence = True + break + else: + # No strict convergence, check for tol based convergence. + center_shift_tot = (center_shift**2).sum() + if center_shift_tot <= tol: + if verbose: + print( + f"Converged at iteration {i}: center shift " + f"{center_shift_tot} within tolerance {tol}." + ) + break + + labels_old[:] = labels + + if not strict_convergence: + # rerun E-step so that predicted labels match cluster centers + lloyd_iter( + X, + sample_weight, + centers, + centers, + weight_in_clusters, + labels, + center_shift, + n_threads, + update_centers=False, + ) + + inertia = _inertia(X, sample_weight, centers, labels, n_threads) + + return labels, inertia, centers, i + 1 + + +def _labels_inertia(X, sample_weight, centers, n_threads=1, return_inertia=True): + """E step of the K-means EM algorithm. + + Compute the labels and the inertia of the given samples and centers. + + Parameters + ---------- + X : {ndarray, sparse matrix} of shape (n_samples, n_features) + The input samples to assign to the labels. If sparse matrix, must + be in CSR format. + + sample_weight : ndarray of shape (n_samples,) + The weights for each observation in X. + + x_squared_norms : ndarray of shape (n_samples,) + Precomputed squared euclidean norm of each data point, to speed up + computations. + + centers : ndarray of shape (n_clusters, n_features) + The cluster centers. + + n_threads : int, default=1 + The number of OpenMP threads to use for the computation. Parallelism is + sample-wise on the main cython loop which assigns each sample to its + closest center. + + return_inertia : bool, default=True + Whether to compute and return the inertia. + + Returns + ------- + labels : ndarray of shape (n_samples,) + The resulting assignment. + + inertia : float + Sum of squared distances of samples to their closest cluster center. + Inertia is only returned if return_inertia is True. + """ + n_samples = X.shape[0] + n_clusters = centers.shape[0] + + labels = np.full(n_samples, -1, dtype=np.int32) + center_shift = np.zeros(n_clusters, dtype=centers.dtype) + + if sp.issparse(X): + _labels = lloyd_iter_chunked_sparse + _inertia = _inertia_sparse + else: + _labels = lloyd_iter_chunked_dense + _inertia = _inertia_dense + + _labels( + X, + sample_weight, + centers, + centers_new=None, + weight_in_clusters=None, + labels=labels, + center_shift=center_shift, + n_threads=n_threads, + update_centers=False, + ) + + if return_inertia: + inertia = _inertia(X, sample_weight, centers, labels, n_threads) + return labels, inertia + + return labels + + +# Same as _labels_inertia but in a threadpool_limits context. +_labels_inertia_threadpool_limit = _threadpool_controller_decorator( + limits=1, user_api="blas" +)(_labels_inertia) + + +class _BaseKMeans( + ClassNamePrefixFeaturesOutMixin, TransformerMixin, ClusterMixin, BaseEstimator, ABC +): + """Base class for KMeans and MiniBatchKMeans""" + + _parameter_constraints: dict = { + "n_clusters": [Interval(Integral, 1, None, closed="left")], + "init": [StrOptions({"k-means++", "random"}), callable, "array-like"], + "n_init": [ + StrOptions({"auto"}), + Interval(Integral, 1, None, closed="left"), + ], + "max_iter": [Interval(Integral, 1, None, closed="left")], + "tol": [Interval(Real, 0, None, closed="left")], + "verbose": ["verbose"], + "random_state": ["random_state"], + } + + def __init__( + self, + n_clusters, + *, + init, + n_init, + max_iter, + tol, + verbose, + random_state, + ): + self.n_clusters = n_clusters + self.init = init + self.max_iter = max_iter + self.tol = tol + self.n_init = n_init + self.verbose = verbose + self.random_state = random_state + + def _check_params_vs_input(self, X, default_n_init=None): + # n_clusters + if X.shape[0] < self.n_clusters: + raise ValueError( + f"n_samples={X.shape[0]} should be >= n_clusters={self.n_clusters}." + ) + + # tol + self._tol = _tolerance(X, self.tol) + + # n-init + if self.n_init == "auto": + if isinstance(self.init, str) and self.init == "k-means++": + self._n_init = 1 + elif isinstance(self.init, str) and self.init == "random": + self._n_init = default_n_init + elif callable(self.init): + self._n_init = default_n_init + else: # array-like + self._n_init = 1 + else: + self._n_init = self.n_init + + if _is_arraylike_not_scalar(self.init) and self._n_init != 1: + warnings.warn( + ( + "Explicit initial center position passed: performing only" + f" one init in {self.__class__.__name__} instead of " + f"n_init={self._n_init}." + ), + RuntimeWarning, + stacklevel=2, + ) + self._n_init = 1 + + @abstractmethod + def _warn_mkl_vcomp(self, n_active_threads): + """Issue an estimator specific warning when vcomp and mkl are both present + + This method is called by `_check_mkl_vcomp`. + """ + + def _check_mkl_vcomp(self, X, n_samples): + """Check when vcomp and mkl are both present""" + # The BLAS call inside a prange in lloyd_iter_chunked_dense is known to + # cause a small memory leak when there are less chunks than the number + # of available threads. It only happens when the OpenMP library is + # vcomp (microsoft OpenMP) and the BLAS library is MKL. see #18653 + if sp.issparse(X): + return + + n_active_threads = int(np.ceil(n_samples / CHUNK_SIZE)) + if n_active_threads < self._n_threads: + modules = _get_threadpool_controller().info() + has_vcomp = "vcomp" in [module["prefix"] for module in modules] + has_mkl = ("mkl", "intel") in [ + (module["internal_api"], module.get("threading_layer", None)) + for module in modules + ] + if has_vcomp and has_mkl: + self._warn_mkl_vcomp(n_active_threads) + + def _validate_center_shape(self, X, centers): + """Check if centers is compatible with X and n_clusters.""" + if centers.shape[0] != self.n_clusters: + raise ValueError( + f"The shape of the initial centers {centers.shape} does not " + f"match the number of clusters {self.n_clusters}." + ) + if centers.shape[1] != X.shape[1]: + raise ValueError( + f"The shape of the initial centers {centers.shape} does not " + f"match the number of features of the data {X.shape[1]}." + ) + + def _check_test_data(self, X): + X = validate_data( + self, + X, + accept_sparse="csr", + reset=False, + dtype=[np.float64, np.float32], + order="C", + accept_large_sparse=False, + ) + return X + + def _init_centroids( + self, + X, + x_squared_norms, + init, + random_state, + sample_weight, + init_size=None, + n_centroids=None, + ): + """Compute the initial centroids. + + Parameters + ---------- + X : {ndarray, sparse matrix} of shape (n_samples, n_features) + The input samples. + + x_squared_norms : ndarray of shape (n_samples,) + Squared euclidean norm of each data point. Pass it if you have it + at hands already to avoid it being recomputed here. + + init : {'k-means++', 'random'}, callable or ndarray of shape \ + (n_clusters, n_features) + Method for initialization. + + random_state : RandomState instance + Determines random number generation for centroid initialization. + See :term:`Glossary `. + + sample_weight : ndarray of shape (n_samples,) + The weights for each observation in X. `sample_weight` is not used + during initialization if `init` is a callable or a user provided + array. + + init_size : int, default=None + Number of samples to randomly sample for speeding up the + initialization (sometimes at the expense of accuracy). + + n_centroids : int, default=None + Number of centroids to initialize. + If left to 'None' the number of centroids will be equal to + number of clusters to form (self.n_clusters). + + Returns + ------- + centers : ndarray of shape (n_clusters, n_features) + Initial centroids of clusters. + """ + n_samples = X.shape[0] + n_clusters = self.n_clusters if n_centroids is None else n_centroids + + if init_size is not None and init_size < n_samples: + init_indices = random_state.randint(0, n_samples, init_size) + X = X[init_indices] + x_squared_norms = x_squared_norms[init_indices] + n_samples = X.shape[0] + sample_weight = sample_weight[init_indices] + + if isinstance(init, str) and init == "k-means++": + centers, _ = _kmeans_plusplus( + X, + n_clusters, + random_state=random_state, + x_squared_norms=x_squared_norms, + sample_weight=sample_weight, + ) + elif isinstance(init, str) and init == "random": + seeds = random_state.choice( + n_samples, + size=n_clusters, + replace=False, + p=sample_weight / sample_weight.sum(), + ) + centers = X[seeds] + elif _is_arraylike_not_scalar(self.init): + centers = init + elif callable(init): + centers = init(X, n_clusters, random_state=random_state) + centers = check_array(centers, dtype=X.dtype, copy=False, order="C") + self._validate_center_shape(X, centers) + + if sp.issparse(centers): + centers = centers.toarray() + + return centers + + def fit_predict(self, X, y=None, sample_weight=None): + """Compute cluster centers and predict cluster index for each sample. + + Convenience method; equivalent to calling fit(X) followed by + predict(X). + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + New data to transform. + + y : Ignored + Not used, present here for API consistency by convention. + + sample_weight : array-like of shape (n_samples,), default=None + The weights for each observation in X. If None, all observations + are assigned equal weight. + + Returns + ------- + labels : ndarray of shape (n_samples,) + Index of the cluster each sample belongs to. + """ + return self.fit(X, sample_weight=sample_weight).labels_ + + def predict(self, X): + """Predict the closest cluster each sample in X belongs to. + + In the vector quantization literature, `cluster_centers_` is called + the code book and each value returned by `predict` is the index of + the closest code in the code book. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + New data to predict. + + Returns + ------- + labels : ndarray of shape (n_samples,) + Index of the cluster each sample belongs to. + """ + check_is_fitted(self) + + X = self._check_test_data(X) + + # sample weights are not used by predict but cython helpers expect an array + sample_weight = np.ones(X.shape[0], dtype=X.dtype) + + labels = _labels_inertia_threadpool_limit( + X, + sample_weight, + self.cluster_centers_, + n_threads=self._n_threads, + return_inertia=False, + ) + + return labels + + def fit_transform(self, X, y=None, sample_weight=None): + """Compute clustering and transform X to cluster-distance space. + + Equivalent to fit(X).transform(X), but more efficiently implemented. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + New data to transform. + + y : Ignored + Not used, present here for API consistency by convention. + + sample_weight : array-like of shape (n_samples,), default=None + The weights for each observation in X. If None, all observations + are assigned equal weight. + + Returns + ------- + X_new : ndarray of shape (n_samples, n_clusters) + X transformed in the new space. + """ + return self.fit(X, sample_weight=sample_weight)._transform(X) + + def transform(self, X): + """Transform X to a cluster-distance space. + + In the new space, each dimension is the distance to the cluster + centers. Note that even if X is sparse, the array returned by + `transform` will typically be dense. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + New data to transform. + + Returns + ------- + X_new : ndarray of shape (n_samples, n_clusters) + X transformed in the new space. + """ + check_is_fitted(self) + + X = self._check_test_data(X) + return self._transform(X) + + def _transform(self, X): + """Guts of transform method; no input validation.""" + return euclidean_distances(X, self.cluster_centers_) + + def score(self, X, y=None, sample_weight=None): + """Opposite of the value of X on the K-means objective. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + New data. + + y : Ignored + Not used, present here for API consistency by convention. + + sample_weight : array-like of shape (n_samples,), default=None + The weights for each observation in X. If None, all observations + are assigned equal weight. + + Returns + ------- + score : float + Opposite of the value of X on the K-means objective. + """ + check_is_fitted(self) + + X = self._check_test_data(X) + sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype) + + _, scores = _labels_inertia_threadpool_limit( + X, sample_weight, self.cluster_centers_, self._n_threads + ) + return -scores + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + return tags + + +class KMeans(_BaseKMeans): + """K-Means clustering. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + + n_clusters : int, default=8 + The number of clusters to form as well as the number of + centroids to generate. + + For an example of how to choose an optimal value for `n_clusters` refer to + :ref:`sphx_glr_auto_examples_cluster_plot_kmeans_silhouette_analysis.py`. + + init : {'k-means++', 'random'}, callable or array-like of shape \ + (n_clusters, n_features), default='k-means++' + Method for initialization: + + * 'k-means++' : selects initial cluster centroids using sampling \ + based on an empirical probability distribution of the points' \ + contribution to the overall inertia. This technique speeds up \ + convergence. The algorithm implemented is "greedy k-means++". It \ + differs from the vanilla k-means++ by making several trials at \ + each sampling step and choosing the best centroid among them. + + * 'random': choose `n_clusters` observations (rows) at random from \ + data for the initial centroids. + + * If an array is passed, it should be of shape (n_clusters, n_features)\ + and gives the initial centers. + + * If a callable is passed, it should take arguments X, n_clusters and a\ + random state and return an initialization. + + For an example of how to use the different `init` strategies, see + :ref:`sphx_glr_auto_examples_cluster_plot_kmeans_digits.py`. + + For an evaluation of the impact of initialization, see the example + :ref:`sphx_glr_auto_examples_cluster_plot_kmeans_stability_low_dim_dense.py`. + + n_init : 'auto' or int, default='auto' + Number of times the k-means algorithm is run with different centroid + seeds. The final results is the best output of `n_init` consecutive runs + in terms of inertia. Several runs are recommended for sparse + high-dimensional problems (see :ref:`kmeans_sparse_high_dim`). + + When `n_init='auto'`, the number of runs depends on the value of init: + 10 if using `init='random'` or `init` is a callable; + 1 if using `init='k-means++'` or `init` is an array-like. + + .. versionadded:: 1.2 + Added 'auto' option for `n_init`. + + .. versionchanged:: 1.4 + Default value for `n_init` changed to `'auto'`. + + max_iter : int, default=300 + Maximum number of iterations of the k-means algorithm for a + single run. + + tol : float, default=1e-4 + Relative tolerance with regards to Frobenius norm of the difference + in the cluster centers of two consecutive iterations to declare + convergence. + + verbose : int, default=0 + Verbosity mode. + + random_state : int, RandomState instance or None, default=None + Determines random number generation for centroid initialization. Use + an int to make the randomness deterministic. + See :term:`Glossary `. + + copy_x : bool, default=True + When pre-computing distances it is more numerically accurate to center + the data first. If copy_x is True (default), then the original data is + not modified. If False, the original data is modified, and put back + before the function returns, but small numerical differences may be + introduced by subtracting and then adding the data mean. Note that if + the original data is not C-contiguous, a copy will be made even if + copy_x is False. If the original data is sparse, but not in CSR format, + a copy will be made even if copy_x is False. + + algorithm : {"lloyd", "elkan"}, default="lloyd" + K-means algorithm to use. The classical EM-style algorithm is `"lloyd"`. + The `"elkan"` variation can be more efficient on some datasets with + well-defined clusters, by using the triangle inequality. However it's + more memory intensive due to the allocation of an extra array of shape + `(n_samples, n_clusters)`. + + .. versionchanged:: 0.18 + Added Elkan algorithm + + .. versionchanged:: 1.1 + Renamed "full" to "lloyd", and deprecated "auto" and "full". + Changed "auto" to use "lloyd" instead of "elkan". + + Attributes + ---------- + cluster_centers_ : ndarray of shape (n_clusters, n_features) + Coordinates of cluster centers. If the algorithm stops before fully + converging (see ``tol`` and ``max_iter``), these will not be + consistent with ``labels_``. + + labels_ : ndarray of shape (n_samples,) + Labels of each point + + inertia_ : float + Sum of squared distances of samples to their closest cluster center, + weighted by the sample weights if provided. + + n_iter_ : int + Number of iterations run. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + MiniBatchKMeans : Alternative online implementation that does incremental + updates of the centers positions using mini-batches. + For large scale learning (say n_samples > 10k) MiniBatchKMeans is + probably much faster than the default batch implementation. + + Notes + ----- + The k-means problem is solved using either Lloyd's or Elkan's algorithm. + + The average complexity is given by O(k n T), where n is the number of + samples and T is the number of iteration. + + The worst case complexity is given by O(n^(k+2/p)) with + n = n_samples, p = n_features. + Refer to :doi:`"How slow is the k-means method?" D. Arthur and S. Vassilvitskii - + SoCG2006.<10.1145/1137856.1137880>` for more details. + + In practice, the k-means algorithm is very fast (one of the fastest + clustering algorithms available), but it falls in local minima. That's why + it can be useful to restart it several times. + + If the algorithm stops before fully converging (because of ``tol`` or + ``max_iter``), ``labels_`` and ``cluster_centers_`` will not be consistent, + i.e. the ``cluster_centers_`` will not be the means of the points in each + cluster. Also, the estimator will reassign ``labels_`` after the last + iteration to make ``labels_`` consistent with ``predict`` on the training + set. + + Examples + -------- + + >>> from sklearn.cluster import KMeans + >>> import numpy as np + >>> X = np.array([[1, 2], [1, 4], [1, 0], + ... [10, 2], [10, 4], [10, 0]]) + >>> kmeans = KMeans(n_clusters=2, random_state=0, n_init="auto").fit(X) + >>> kmeans.labels_ + array([1, 1, 1, 0, 0, 0], dtype=int32) + >>> kmeans.predict([[0, 0], [12, 3]]) + array([1, 0], dtype=int32) + >>> kmeans.cluster_centers_ + array([[10., 2.], + [ 1., 2.]]) + + For examples of common problems with K-Means and how to address them see + :ref:`sphx_glr_auto_examples_cluster_plot_kmeans_assumptions.py`. + + For a demonstration of how K-Means can be used to cluster text documents see + :ref:`sphx_glr_auto_examples_text_plot_document_clustering.py`. + + For a comparison between K-Means and MiniBatchKMeans refer to example + :ref:`sphx_glr_auto_examples_cluster_plot_mini_batch_kmeans.py`. + + For a comparison between K-Means and BisectingKMeans refer to example + :ref:`sphx_glr_auto_examples_cluster_plot_bisect_kmeans.py`. + """ + + _parameter_constraints: dict = { + **_BaseKMeans._parameter_constraints, + "copy_x": ["boolean"], + "algorithm": [StrOptions({"lloyd", "elkan"})], + } + + def __init__( + self, + n_clusters=8, + *, + init="k-means++", + n_init="auto", + max_iter=300, + tol=1e-4, + verbose=0, + random_state=None, + copy_x=True, + algorithm="lloyd", + ): + super().__init__( + n_clusters=n_clusters, + init=init, + n_init=n_init, + max_iter=max_iter, + tol=tol, + verbose=verbose, + random_state=random_state, + ) + + self.copy_x = copy_x + self.algorithm = algorithm + + def _check_params_vs_input(self, X): + super()._check_params_vs_input(X, default_n_init=10) + + self._algorithm = self.algorithm + if self._algorithm == "elkan" and self.n_clusters == 1: + warnings.warn( + ( + "algorithm='elkan' doesn't make sense for a single " + "cluster. Using 'lloyd' instead." + ), + RuntimeWarning, + ) + self._algorithm = "lloyd" + + def _warn_mkl_vcomp(self, n_active_threads): + """Warn when vcomp and mkl are both present""" + warnings.warn( + "KMeans is known to have a memory leak on Windows " + "with MKL, when there are less chunks than available " + "threads. You can avoid it by setting the environment" + f" variable OMP_NUM_THREADS={n_active_threads}." + ) + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None, sample_weight=None): + """Compute k-means clustering. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Training instances to cluster. It must be noted that the data + will be converted to C ordering, which will cause a memory + copy if the given data is not C-contiguous. + If a sparse matrix is passed, a copy will be made if it's not in + CSR format. + + y : Ignored + Not used, present here for API consistency by convention. + + sample_weight : array-like of shape (n_samples,), default=None + The weights for each observation in X. If None, all observations + are assigned equal weight. `sample_weight` is not used during + initialization if `init` is a callable or a user provided array. + + .. versionadded:: 0.20 + + Returns + ------- + self : object + Fitted estimator. + """ + X = validate_data( + self, + X, + accept_sparse="csr", + dtype=[np.float64, np.float32], + order="C", + copy=self.copy_x, + accept_large_sparse=False, + ) + + self._check_params_vs_input(X) + + random_state = check_random_state(self.random_state) + sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype) + self._n_threads = _openmp_effective_n_threads() + + # Validate init array + init = self.init + init_is_array_like = _is_arraylike_not_scalar(init) + if init_is_array_like: + init = check_array(init, dtype=X.dtype, copy=True, order="C") + self._validate_center_shape(X, init) + + # subtract of mean of x for more accurate distance computations + if not sp.issparse(X): + X_mean = X.mean(axis=0) + # The copy was already done above + X -= X_mean + + if init_is_array_like: + init -= X_mean + + # precompute squared norms of data points + x_squared_norms = row_norms(X, squared=True) + + if self._algorithm == "elkan": + kmeans_single = _kmeans_single_elkan + else: + kmeans_single = _kmeans_single_lloyd + self._check_mkl_vcomp(X, X.shape[0]) + + best_inertia, best_labels = None, None + + for i in range(self._n_init): + # Initialize centers + centers_init = self._init_centroids( + X, + x_squared_norms=x_squared_norms, + init=init, + random_state=random_state, + sample_weight=sample_weight, + ) + if self.verbose: + print("Initialization complete") + + # run a k-means once + labels, inertia, centers, n_iter_ = kmeans_single( + X, + sample_weight, + centers_init, + max_iter=self.max_iter, + verbose=self.verbose, + tol=self._tol, + n_threads=self._n_threads, + ) + + # determine if these results are the best so far + # we chose a new run if it has a better inertia and the clustering is + # different from the best so far (it's possible that the inertia is + # slightly better even if the clustering is the same with potentially + # permuted labels, due to rounding errors) + if best_inertia is None or ( + inertia < best_inertia + and not _is_same_clustering(labels, best_labels, self.n_clusters) + ): + best_labels = labels + best_centers = centers + best_inertia = inertia + best_n_iter = n_iter_ + + if not sp.issparse(X): + if not self.copy_x: + X += X_mean + best_centers += X_mean + + distinct_clusters = len(set(best_labels)) + if distinct_clusters < self.n_clusters: + warnings.warn( + "Number of distinct clusters ({}) found smaller than " + "n_clusters ({}). Possibly due to duplicate points " + "in X.".format(distinct_clusters, self.n_clusters), + ConvergenceWarning, + stacklevel=2, + ) + + self.cluster_centers_ = best_centers + self._n_features_out = self.cluster_centers_.shape[0] + self.labels_ = best_labels + self.inertia_ = best_inertia + self.n_iter_ = best_n_iter + return self + + +def _mini_batch_step( + X, + sample_weight, + centers, + centers_new, + weight_sums, + random_state, + random_reassign=False, + reassignment_ratio=0.01, + verbose=False, + n_threads=1, +): + """Incremental update of the centers for the Minibatch K-Means algorithm. + + Parameters + ---------- + + X : {ndarray, sparse matrix} of shape (n_samples, n_features) + The original data array. If sparse, must be in CSR format. + + x_squared_norms : ndarray of shape (n_samples,) + Squared euclidean norm of each data point. + + sample_weight : ndarray of shape (n_samples,) + The weights for each observation in `X`. + + centers : ndarray of shape (n_clusters, n_features) + The cluster centers before the current iteration + + centers_new : ndarray of shape (n_clusters, n_features) + The cluster centers after the current iteration. Modified in-place. + + weight_sums : ndarray of shape (n_clusters,) + The vector in which we keep track of the numbers of points in a + cluster. This array is modified in place. + + random_state : RandomState instance + Determines random number generation for low count centers reassignment. + See :term:`Glossary `. + + random_reassign : boolean, default=False + If True, centers with very low counts are randomly reassigned + to observations. + + reassignment_ratio : float, default=0.01 + Control the fraction of the maximum number of counts for a + center to be reassigned. A higher value means that low count + centers are more likely to be reassigned, which means that the + model will take longer to converge, but should converge in a + better clustering. + + verbose : bool, default=False + Controls the verbosity. + + n_threads : int, default=1 + The number of OpenMP threads to use for the computation. + + Returns + ------- + inertia : float + Sum of squared distances of samples to their closest cluster center. + The inertia is computed after finding the labels and before updating + the centers. + """ + # Perform label assignment to nearest centers + # For better efficiency, it's better to run _mini_batch_step in a + # threadpool_limit context than using _labels_inertia_threadpool_limit here + labels, inertia = _labels_inertia(X, sample_weight, centers, n_threads=n_threads) + + # Update centers according to the labels + if sp.issparse(X): + _minibatch_update_sparse( + X, sample_weight, centers, centers_new, weight_sums, labels, n_threads + ) + else: + _minibatch_update_dense( + X, + sample_weight, + centers, + centers_new, + weight_sums, + labels, + n_threads, + ) + + # Reassign clusters that have very low weight + if random_reassign and reassignment_ratio > 0: + to_reassign = weight_sums < reassignment_ratio * weight_sums.max() + + # pick at most .5 * batch_size samples as new centers + if to_reassign.sum() > 0.5 * X.shape[0]: + indices_dont_reassign = np.argsort(weight_sums)[int(0.5 * X.shape[0]) :] + to_reassign[indices_dont_reassign] = False + n_reassigns = to_reassign.sum() + + if n_reassigns: + # Pick new clusters amongst observations with uniform probability + new_centers = random_state.choice( + X.shape[0], replace=False, size=n_reassigns + ) + if verbose: + print(f"[MiniBatchKMeans] Reassigning {n_reassigns} cluster centers.") + + if sp.issparse(X): + assign_rows_csr( + X, + new_centers.astype(np.intp, copy=False), + np.where(to_reassign)[0].astype(np.intp, copy=False), + centers_new, + ) + else: + centers_new[to_reassign] = X[new_centers] + + # reset counts of reassigned centers, but don't reset them too small + # to avoid instant reassignment. This is a pretty dirty hack as it + # also modifies the learning rates. + weight_sums[to_reassign] = np.min(weight_sums[~to_reassign]) + + return inertia + + +class MiniBatchKMeans(_BaseKMeans): + """ + Mini-Batch K-Means clustering. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + + n_clusters : int, default=8 + The number of clusters to form as well as the number of + centroids to generate. + + init : {'k-means++', 'random'}, callable or array-like of shape \ + (n_clusters, n_features), default='k-means++' + Method for initialization: + + 'k-means++' : selects initial cluster centroids using sampling based on + an empirical probability distribution of the points' contribution to the + overall inertia. This technique speeds up convergence. The algorithm + implemented is "greedy k-means++". It differs from the vanilla k-means++ + by making several trials at each sampling step and choosing the best centroid + among them. + + 'random': choose `n_clusters` observations (rows) at random from data + for the initial centroids. + + If an array is passed, it should be of shape (n_clusters, n_features) + and gives the initial centers. + + If a callable is passed, it should take arguments X, n_clusters and a + random state and return an initialization. + + For an evaluation of the impact of initialization, see the example + :ref:`sphx_glr_auto_examples_cluster_plot_kmeans_stability_low_dim_dense.py`. + + max_iter : int, default=100 + Maximum number of iterations over the complete dataset before + stopping independently of any early stopping criterion heuristics. + + batch_size : int, default=1024 + Size of the mini batches. + For faster computations, you can set the ``batch_size`` greater than + 256 * number of cores to enable parallelism on all cores. + + .. versionchanged:: 1.0 + `batch_size` default changed from 100 to 1024. + + verbose : int, default=0 + Verbosity mode. + + compute_labels : bool, default=True + Compute label assignment and inertia for the complete dataset + once the minibatch optimization has converged in fit. + + random_state : int, RandomState instance or None, default=None + Determines random number generation for centroid initialization and + random reassignment. Use an int to make the randomness deterministic. + See :term:`Glossary `. + + tol : float, default=0.0 + Control early stopping based on the relative center changes as + measured by a smoothed, variance-normalized of the mean center + squared position changes. This early stopping heuristics is + closer to the one used for the batch variant of the algorithms + but induces a slight computational and memory overhead over the + inertia heuristic. + + To disable convergence detection based on normalized center + change, set tol to 0.0 (default). + + max_no_improvement : int, default=10 + Control early stopping based on the consecutive number of mini + batches that does not yield an improvement on the smoothed inertia. + + To disable convergence detection based on inertia, set + max_no_improvement to None. + + init_size : int, default=None + Number of samples to randomly sample for speeding up the + initialization (sometimes at the expense of accuracy): the + only algorithm is initialized by running a batch KMeans on a + random subset of the data. This needs to be larger than n_clusters. + + If `None`, the heuristic is `init_size = 3 * batch_size` if + `3 * batch_size < n_clusters`, else `init_size = 3 * n_clusters`. + + n_init : 'auto' or int, default="auto" + Number of random initializations that are tried. + In contrast to KMeans, the algorithm is only run once, using the best of + the `n_init` initializations as measured by inertia. Several runs are + recommended for sparse high-dimensional problems (see + :ref:`kmeans_sparse_high_dim`). + + When `n_init='auto'`, the number of runs depends on the value of init: + 3 if using `init='random'` or `init` is a callable; + 1 if using `init='k-means++'` or `init` is an array-like. + + .. versionadded:: 1.2 + Added 'auto' option for `n_init`. + + .. versionchanged:: 1.4 + Default value for `n_init` changed to `'auto'` in version. + + reassignment_ratio : float, default=0.01 + Control the fraction of the maximum number of counts for a center to + be reassigned. A higher value means that low count centers are more + easily reassigned, which means that the model will take longer to + converge, but should converge in a better clustering. However, too high + a value may cause convergence issues, especially with a small batch + size. + + Attributes + ---------- + + cluster_centers_ : ndarray of shape (n_clusters, n_features) + Coordinates of cluster centers. + + labels_ : ndarray of shape (n_samples,) + Labels of each point (if compute_labels is set to True). + + inertia_ : float + The value of the inertia criterion associated with the chosen + partition if compute_labels is set to True. If compute_labels is set to + False, it's an approximation of the inertia based on an exponentially + weighted average of the batch inertiae. + The inertia is defined as the sum of square distances of samples to + their cluster center, weighted by the sample weights if provided. + + n_iter_ : int + Number of iterations over the full dataset. + + n_steps_ : int + Number of minibatches processed. + + .. versionadded:: 1.0 + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + KMeans : The classic implementation of the clustering method based on the + Lloyd's algorithm. It consumes the whole set of input data at each + iteration. + + Notes + ----- + See https://www.eecs.tufts.edu/~dsculley/papers/fastkmeans.pdf + + When there are too few points in the dataset, some centers may be + duplicated, which means that a proper clustering in terms of the number + of requesting clusters and the number of returned clusters will not + always match. One solution is to set `reassignment_ratio=0`, which + prevents reassignments of clusters that are too small. + + See :ref:`sphx_glr_auto_examples_cluster_plot_birch_vs_minibatchkmeans.py` for a + comparison with :class:`~sklearn.cluster.BIRCH`. + + Examples + -------- + >>> from sklearn.cluster import MiniBatchKMeans + >>> import numpy as np + >>> X = np.array([[1, 2], [1, 4], [1, 0], + ... [4, 2], [4, 0], [4, 4], + ... [4, 5], [0, 1], [2, 2], + ... [3, 2], [5, 5], [1, -1]]) + >>> # manually fit on batches + >>> kmeans = MiniBatchKMeans(n_clusters=2, + ... random_state=0, + ... batch_size=6, + ... n_init="auto") + >>> kmeans = kmeans.partial_fit(X[0:6,:]) + >>> kmeans = kmeans.partial_fit(X[6:12,:]) + >>> kmeans.cluster_centers_ + array([[3.375, 3. ], + [0.75 , 0.5 ]]) + >>> kmeans.predict([[0, 0], [4, 4]]) + array([1, 0], dtype=int32) + >>> # fit on the whole data + >>> kmeans = MiniBatchKMeans(n_clusters=2, + ... random_state=0, + ... batch_size=6, + ... max_iter=10, + ... n_init="auto").fit(X) + >>> kmeans.cluster_centers_ + array([[3.55102041, 2.48979592], + [1.06896552, 1. ]]) + >>> kmeans.predict([[0, 0], [4, 4]]) + array([1, 0], dtype=int32) + + For a comparison of Mini-Batch K-Means clustering with other clustering algorithms, + see :ref:`sphx_glr_auto_examples_cluster_plot_cluster_comparison.py` + """ + + _parameter_constraints: dict = { + **_BaseKMeans._parameter_constraints, + "batch_size": [Interval(Integral, 1, None, closed="left")], + "compute_labels": ["boolean"], + "max_no_improvement": [Interval(Integral, 0, None, closed="left"), None], + "init_size": [Interval(Integral, 1, None, closed="left"), None], + "reassignment_ratio": [Interval(Real, 0, None, closed="left")], + } + + def __init__( + self, + n_clusters=8, + *, + init="k-means++", + max_iter=100, + batch_size=1024, + verbose=0, + compute_labels=True, + random_state=None, + tol=0.0, + max_no_improvement=10, + init_size=None, + n_init="auto", + reassignment_ratio=0.01, + ): + super().__init__( + n_clusters=n_clusters, + init=init, + max_iter=max_iter, + verbose=verbose, + random_state=random_state, + tol=tol, + n_init=n_init, + ) + + self.max_no_improvement = max_no_improvement + self.batch_size = batch_size + self.compute_labels = compute_labels + self.init_size = init_size + self.reassignment_ratio = reassignment_ratio + + def _check_params_vs_input(self, X): + super()._check_params_vs_input(X, default_n_init=3) + + self._batch_size = min(self.batch_size, X.shape[0]) + + # init_size + self._init_size = self.init_size + if self._init_size is None: + self._init_size = 3 * self._batch_size + if self._init_size < self.n_clusters: + self._init_size = 3 * self.n_clusters + elif self._init_size < self.n_clusters: + warnings.warn( + ( + f"init_size={self._init_size} should be larger than " + f"n_clusters={self.n_clusters}. Setting it to " + "min(3*n_clusters, n_samples)" + ), + RuntimeWarning, + stacklevel=2, + ) + self._init_size = 3 * self.n_clusters + self._init_size = min(self._init_size, X.shape[0]) + + # reassignment_ratio + if self.reassignment_ratio < 0: + raise ValueError( + "reassignment_ratio should be >= 0, got " + f"{self.reassignment_ratio} instead." + ) + + def _warn_mkl_vcomp(self, n_active_threads): + """Warn when vcomp and mkl are both present""" + warnings.warn( + "MiniBatchKMeans is known to have a memory leak on " + "Windows with MKL, when there are less chunks than " + "available threads. You can prevent it by setting " + f"batch_size >= {self._n_threads * CHUNK_SIZE} or by " + "setting the environment variable " + f"OMP_NUM_THREADS={n_active_threads}" + ) + + def _mini_batch_convergence( + self, step, n_steps, n_samples, centers_squared_diff, batch_inertia + ): + """Helper function to encapsulate the early stopping logic""" + # Normalize inertia to be able to compare values when + # batch_size changes + batch_inertia /= self._batch_size + + # count steps starting from 1 for user friendly verbose mode. + step = step + 1 + + # Ignore first iteration because it's inertia from initialization. + if step == 1: + if self.verbose: + print( + f"Minibatch step {step}/{n_steps}: mean batch " + f"inertia: {batch_inertia}" + ) + return False + + # Compute an Exponentially Weighted Average of the inertia to + # monitor the convergence while discarding minibatch-local stochastic + # variability: https://en.wikipedia.org/wiki/Moving_average + if self._ewa_inertia is None: + self._ewa_inertia = batch_inertia + else: + alpha = self._batch_size * 2.0 / (n_samples + 1) + alpha = min(alpha, 1) + self._ewa_inertia = self._ewa_inertia * (1 - alpha) + batch_inertia * alpha + + # Log progress to be able to monitor convergence + if self.verbose: + print( + f"Minibatch step {step}/{n_steps}: mean batch inertia: " + f"{batch_inertia}, ewa inertia: {self._ewa_inertia}" + ) + + # Early stopping based on absolute tolerance on squared change of + # centers position + if self._tol > 0.0 and centers_squared_diff <= self._tol: + if self.verbose: + print(f"Converged (small centers change) at step {step}/{n_steps}") + return True + + # Early stopping heuristic due to lack of improvement on smoothed + # inertia + if self._ewa_inertia_min is None or self._ewa_inertia < self._ewa_inertia_min: + self._no_improvement = 0 + self._ewa_inertia_min = self._ewa_inertia + else: + self._no_improvement += 1 + + if ( + self.max_no_improvement is not None + and self._no_improvement >= self.max_no_improvement + ): + if self.verbose: + print( + "Converged (lack of improvement in inertia) at step " + f"{step}/{n_steps}" + ) + return True + + return False + + def _random_reassign(self): + """Check if a random reassignment needs to be done. + + Do random reassignments each time 10 * n_clusters samples have been + processed. + + If there are empty clusters we always want to reassign. + """ + self._n_since_last_reassign += self._batch_size + if (self._counts == 0).any() or self._n_since_last_reassign >= ( + 10 * self.n_clusters + ): + self._n_since_last_reassign = 0 + return True + return False + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None, sample_weight=None): + """Compute the centroids on X by chunking it into mini-batches. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Training instances to cluster. It must be noted that the data + will be converted to C ordering, which will cause a memory copy + if the given data is not C-contiguous. + If a sparse matrix is passed, a copy will be made if it's not in + CSR format. + + y : Ignored + Not used, present here for API consistency by convention. + + sample_weight : array-like of shape (n_samples,), default=None + The weights for each observation in X. If None, all observations + are assigned equal weight. `sample_weight` is not used during + initialization if `init` is a callable or a user provided array. + + .. versionadded:: 0.20 + + Returns + ------- + self : object + Fitted estimator. + """ + X = validate_data( + self, + X, + accept_sparse="csr", + dtype=[np.float64, np.float32], + order="C", + accept_large_sparse=False, + ) + + self._check_params_vs_input(X) + random_state = check_random_state(self.random_state) + sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype) + self._n_threads = _openmp_effective_n_threads() + n_samples, n_features = X.shape + + # Validate init array + init = self.init + if _is_arraylike_not_scalar(init): + init = check_array(init, dtype=X.dtype, copy=True, order="C") + self._validate_center_shape(X, init) + + self._check_mkl_vcomp(X, self._batch_size) + + # precompute squared norms of data points + x_squared_norms = row_norms(X, squared=True) + + # Validation set for the init + validation_indices = random_state.randint(0, n_samples, self._init_size) + X_valid = X[validation_indices] + sample_weight_valid = sample_weight[validation_indices] + + # perform several inits with random subsets + best_inertia = None + for init_idx in range(self._n_init): + if self.verbose: + print(f"Init {init_idx + 1}/{self._n_init} with method {init}") + + # Initialize the centers using only a fraction of the data as we + # expect n_samples to be very large when using MiniBatchKMeans. + cluster_centers = self._init_centroids( + X, + x_squared_norms=x_squared_norms, + init=init, + random_state=random_state, + init_size=self._init_size, + sample_weight=sample_weight, + ) + + # Compute inertia on a validation set. + _, inertia = _labels_inertia_threadpool_limit( + X_valid, + sample_weight_valid, + cluster_centers, + n_threads=self._n_threads, + ) + + if self.verbose: + print(f"Inertia for init {init_idx + 1}/{self._n_init}: {inertia}") + if best_inertia is None or inertia < best_inertia: + init_centers = cluster_centers + best_inertia = inertia + + centers = init_centers + centers_new = np.empty_like(centers) + + # Initialize counts + self._counts = np.zeros(self.n_clusters, dtype=X.dtype) + + # Attributes to monitor the convergence + self._ewa_inertia = None + self._ewa_inertia_min = None + self._no_improvement = 0 + + # Initialize number of samples seen since last reassignment + self._n_since_last_reassign = 0 + + n_steps = (self.max_iter * n_samples) // self._batch_size + + with _get_threadpool_controller().limit(limits=1, user_api="blas"): + # Perform the iterative optimization until convergence + for i in range(n_steps): + # Sample a minibatch from the full dataset + minibatch_indices = random_state.randint(0, n_samples, self._batch_size) + + # Perform the actual update step on the minibatch data + batch_inertia = _mini_batch_step( + X=X[minibatch_indices], + sample_weight=sample_weight[minibatch_indices], + centers=centers, + centers_new=centers_new, + weight_sums=self._counts, + random_state=random_state, + random_reassign=self._random_reassign(), + reassignment_ratio=self.reassignment_ratio, + verbose=self.verbose, + n_threads=self._n_threads, + ) + + if self._tol > 0.0: + centers_squared_diff = np.sum((centers_new - centers) ** 2) + else: + centers_squared_diff = 0 + + centers, centers_new = centers_new, centers + + # Monitor convergence and do early stopping if necessary + if self._mini_batch_convergence( + i, n_steps, n_samples, centers_squared_diff, batch_inertia + ): + break + + self.cluster_centers_ = centers + self._n_features_out = self.cluster_centers_.shape[0] + + self.n_steps_ = i + 1 + self.n_iter_ = int(np.ceil(((i + 1) * self._batch_size) / n_samples)) + + if self.compute_labels: + self.labels_, self.inertia_ = _labels_inertia_threadpool_limit( + X, + sample_weight, + self.cluster_centers_, + n_threads=self._n_threads, + ) + else: + self.inertia_ = self._ewa_inertia * n_samples + + return self + + @_fit_context(prefer_skip_nested_validation=True) + def partial_fit(self, X, y=None, sample_weight=None): + """Update k means estimate on a single mini-batch X. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Training instances to cluster. It must be noted that the data + will be converted to C ordering, which will cause a memory copy + if the given data is not C-contiguous. + If a sparse matrix is passed, a copy will be made if it's not in + CSR format. + + y : Ignored + Not used, present here for API consistency by convention. + + sample_weight : array-like of shape (n_samples,), default=None + The weights for each observation in X. If None, all observations + are assigned equal weight. `sample_weight` is not used during + initialization if `init` is a callable or a user provided array. + + Returns + ------- + self : object + Return updated estimator. + """ + has_centers = hasattr(self, "cluster_centers_") + + X = validate_data( + self, + X, + accept_sparse="csr", + dtype=[np.float64, np.float32], + order="C", + accept_large_sparse=False, + reset=not has_centers, + ) + + self._random_state = getattr( + self, "_random_state", check_random_state(self.random_state) + ) + sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype) + self.n_steps_ = getattr(self, "n_steps_", 0) + + # precompute squared norms of data points + x_squared_norms = row_norms(X, squared=True) + + if not has_centers: + # this instance has not been fitted yet (fit or partial_fit) + self._check_params_vs_input(X) + self._n_threads = _openmp_effective_n_threads() + + # Validate init array + init = self.init + if _is_arraylike_not_scalar(init): + init = check_array(init, dtype=X.dtype, copy=True, order="C") + self._validate_center_shape(X, init) + + self._check_mkl_vcomp(X, X.shape[0]) + + # initialize the cluster centers + self.cluster_centers_ = self._init_centroids( + X, + x_squared_norms=x_squared_norms, + init=init, + random_state=self._random_state, + init_size=self._init_size, + sample_weight=sample_weight, + ) + + # Initialize counts + self._counts = np.zeros(self.n_clusters, dtype=X.dtype) + + # Initialize number of samples seen since last reassignment + self._n_since_last_reassign = 0 + + with _get_threadpool_controller().limit(limits=1, user_api="blas"): + _mini_batch_step( + X, + sample_weight=sample_weight, + centers=self.cluster_centers_, + centers_new=self.cluster_centers_, + weight_sums=self._counts, + random_state=self._random_state, + random_reassign=self._random_reassign(), + reassignment_ratio=self.reassignment_ratio, + verbose=self.verbose, + n_threads=self._n_threads, + ) + + if self.compute_labels: + self.labels_, self.inertia_ = _labels_inertia_threadpool_limit( + X, + sample_weight, + self.cluster_centers_, + n_threads=self._n_threads, + ) + + self.n_steps_ += 1 + self._n_features_out = self.cluster_centers_.shape[0] + + return self diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_mean_shift.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_mean_shift.py new file mode 100644 index 0000000000000000000000000000000000000000..1ba4409d14698b482a6854fd1558f014ea3d9f70 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_mean_shift.py @@ -0,0 +1,579 @@ +"""Mean shift clustering algorithm. + +Mean shift clustering aims to discover *blobs* in a smooth density of +samples. It is a centroid based algorithm, which works by updating candidates +for centroids to be the mean of the points within a given region. These +candidates are then filtered in a post-processing stage to eliminate +near-duplicates to form the final set of centroids. + +Seeding is performed using a binning technique for scalability. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from collections import defaultdict +from numbers import Integral, Real + +import numpy as np + +from .._config import config_context +from ..base import BaseEstimator, ClusterMixin, _fit_context +from ..metrics.pairwise import pairwise_distances_argmin +from ..neighbors import NearestNeighbors +from ..utils import check_array, check_random_state, gen_batches +from ..utils._param_validation import Interval, validate_params +from ..utils.parallel import Parallel, delayed +from ..utils.validation import check_is_fitted, validate_data + + +@validate_params( + { + "X": ["array-like"], + "quantile": [Interval(Real, 0, 1, closed="both")], + "n_samples": [Interval(Integral, 1, None, closed="left"), None], + "random_state": ["random_state"], + "n_jobs": [Integral, None], + }, + prefer_skip_nested_validation=True, +) +def estimate_bandwidth(X, *, quantile=0.3, n_samples=None, random_state=0, n_jobs=None): + """Estimate the bandwidth to use with the mean-shift algorithm. + + This function takes time at least quadratic in `n_samples`. For large + datasets, it is wise to subsample by setting `n_samples`. Alternatively, + the parameter `bandwidth` can be set to a small value without estimating + it. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Input points. + + quantile : float, default=0.3 + Should be between [0, 1] + 0.5 means that the median of all pairwise distances is used. + + n_samples : int, default=None + The number of samples to use. If not given, all samples are used. + + random_state : int, RandomState instance, default=None + The generator used to randomly select the samples from input points + for bandwidth estimation. Use an int to make the randomness + deterministic. + See :term:`Glossary `. + + n_jobs : int, default=None + The number of parallel jobs to run for neighbors search. + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + Returns + ------- + bandwidth : float + The bandwidth parameter. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.cluster import estimate_bandwidth + >>> X = np.array([[1, 1], [2, 1], [1, 0], + ... [4, 7], [3, 5], [3, 6]]) + >>> estimate_bandwidth(X, quantile=0.5) + np.float64(1.61) + """ + X = check_array(X) + + random_state = check_random_state(random_state) + if n_samples is not None: + idx = random_state.permutation(X.shape[0])[:n_samples] + X = X[idx] + n_neighbors = int(X.shape[0] * quantile) + if n_neighbors < 1: # cannot fit NearestNeighbors with n_neighbors = 0 + n_neighbors = 1 + nbrs = NearestNeighbors(n_neighbors=n_neighbors, n_jobs=n_jobs) + nbrs.fit(X) + + bandwidth = 0.0 + for batch in gen_batches(len(X), 500): + d, _ = nbrs.kneighbors(X[batch, :], return_distance=True) + bandwidth += np.max(d, axis=1).sum() + + return bandwidth / X.shape[0] + + +# separate function for each seed's iterative loop +def _mean_shift_single_seed(my_mean, X, nbrs, max_iter): + # For each seed, climb gradient until convergence or max_iter + bandwidth = nbrs.get_params()["radius"] + stop_thresh = 1e-3 * bandwidth # when mean has converged + completed_iterations = 0 + while True: + # Find mean of points within bandwidth + i_nbrs = nbrs.radius_neighbors([my_mean], bandwidth, return_distance=False)[0] + points_within = X[i_nbrs] + if len(points_within) == 0: + break # Depending on seeding strategy this condition may occur + my_old_mean = my_mean # save the old mean + my_mean = np.mean(points_within, axis=0) + # If converged or at max_iter, adds the cluster + if ( + np.linalg.norm(my_mean - my_old_mean) <= stop_thresh + or completed_iterations == max_iter + ): + break + completed_iterations += 1 + return tuple(my_mean), len(points_within), completed_iterations + + +@validate_params( + {"X": ["array-like"]}, + prefer_skip_nested_validation=False, +) +def mean_shift( + X, + *, + bandwidth=None, + seeds=None, + bin_seeding=False, + min_bin_freq=1, + cluster_all=True, + max_iter=300, + n_jobs=None, +): + """Perform mean shift clustering of data using a flat kernel. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + + X : array-like of shape (n_samples, n_features) + Input data. + + bandwidth : float, default=None + Kernel bandwidth. If not None, must be in the range [0, +inf). + + If None, the bandwidth is determined using a heuristic based on + the median of all pairwise distances. This will take quadratic time in + the number of samples. The sklearn.cluster.estimate_bandwidth function + can be used to do this more efficiently. + + seeds : array-like of shape (n_seeds, n_features) or None + Point used as initial kernel locations. If None and bin_seeding=False, + each data point is used as a seed. If None and bin_seeding=True, + see bin_seeding. + + bin_seeding : bool, default=False + If true, initial kernel locations are not locations of all + points, but rather the location of the discretized version of + points, where points are binned onto a grid whose coarseness + corresponds to the bandwidth. Setting this option to True will speed + up the algorithm because fewer seeds will be initialized. + Ignored if seeds argument is not None. + + min_bin_freq : int, default=1 + To speed up the algorithm, accept only those bins with at least + min_bin_freq points as seeds. + + cluster_all : bool, default=True + If true, then all points are clustered, even those orphans that are + not within any kernel. Orphans are assigned to the nearest kernel. + If false, then orphans are given cluster label -1. + + max_iter : int, default=300 + Maximum number of iterations, per seed point before the clustering + operation terminates (for that seed point), if has not converged yet. + + n_jobs : int, default=None + The number of jobs to use for the computation. The following tasks benefit + from the parallelization: + + - The search of nearest neighbors for bandwidth estimation and label + assignments. See the details in the docstring of the + ``NearestNeighbors`` class. + - Hill-climbing optimization for all seeds. + + See :term:`Glossary ` for more details. + + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + .. versionadded:: 0.17 + Parallel Execution using *n_jobs*. + + Returns + ------- + + cluster_centers : ndarray of shape (n_clusters, n_features) + Coordinates of cluster centers. + + labels : ndarray of shape (n_samples,) + Cluster labels for each point. + + Notes + ----- + For a usage example, see + :ref:`sphx_glr_auto_examples_cluster_plot_mean_shift.py`. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.cluster import mean_shift + >>> X = np.array([[1, 1], [2, 1], [1, 0], + ... [4, 7], [3, 5], [3, 6]]) + >>> cluster_centers, labels = mean_shift(X, bandwidth=2) + >>> cluster_centers + array([[3.33, 6. ], + [1.33, 0.66]]) + >>> labels + array([1, 1, 1, 0, 0, 0]) + """ + model = MeanShift( + bandwidth=bandwidth, + seeds=seeds, + min_bin_freq=min_bin_freq, + bin_seeding=bin_seeding, + cluster_all=cluster_all, + n_jobs=n_jobs, + max_iter=max_iter, + ).fit(X) + return model.cluster_centers_, model.labels_ + + +def get_bin_seeds(X, bin_size, min_bin_freq=1): + """Find seeds for mean_shift. + + Finds seeds by first binning data onto a grid whose lines are + spaced bin_size apart, and then choosing those bins with at least + min_bin_freq points. + + Parameters + ---------- + + X : array-like of shape (n_samples, n_features) + Input points, the same points that will be used in mean_shift. + + bin_size : float + Controls the coarseness of the binning. Smaller values lead + to more seeding (which is computationally more expensive). If you're + not sure how to set this, set it to the value of the bandwidth used + in clustering.mean_shift. + + min_bin_freq : int, default=1 + Only bins with at least min_bin_freq will be selected as seeds. + Raising this value decreases the number of seeds found, which + makes mean_shift computationally cheaper. + + Returns + ------- + bin_seeds : array-like of shape (n_samples, n_features) + Points used as initial kernel positions in clustering.mean_shift. + """ + if bin_size == 0: + return X + + # Bin points + bin_sizes = defaultdict(int) + for point in X: + binned_point = np.round(point / bin_size) + bin_sizes[tuple(binned_point)] += 1 + + # Select only those bins as seeds which have enough members + bin_seeds = np.array( + [point for point, freq in bin_sizes.items() if freq >= min_bin_freq], + dtype=np.float32, + ) + if len(bin_seeds) == len(X): + warnings.warn( + "Binning data failed with provided bin_size=%f, using data points as seeds." + % bin_size + ) + return X + bin_seeds = bin_seeds * bin_size + return bin_seeds + + +class MeanShift(ClusterMixin, BaseEstimator): + """Mean shift clustering using a flat kernel. + + Mean shift clustering aims to discover "blobs" in a smooth density of + samples. It is a centroid-based algorithm, which works by updating + candidates for centroids to be the mean of the points within a given + region. These candidates are then filtered in a post-processing stage to + eliminate near-duplicates to form the final set of centroids. + + Seeding is performed using a binning technique for scalability. + + For an example of how to use MeanShift clustering, refer to: + :ref:`sphx_glr_auto_examples_cluster_plot_mean_shift.py`. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + bandwidth : float, default=None + Bandwidth used in the flat kernel. + + If not given, the bandwidth is estimated using + sklearn.cluster.estimate_bandwidth; see the documentation for that + function for hints on scalability (see also the Notes, below). + + seeds : array-like of shape (n_samples, n_features), default=None + Seeds used to initialize kernels. If not set, + the seeds are calculated by clustering.get_bin_seeds + with bandwidth as the grid size and default values for + other parameters. + + bin_seeding : bool, default=False + If true, initial kernel locations are not locations of all + points, but rather the location of the discretized version of + points, where points are binned onto a grid whose coarseness + corresponds to the bandwidth. Setting this option to True will speed + up the algorithm because fewer seeds will be initialized. + The default value is False. + Ignored if seeds argument is not None. + + min_bin_freq : int, default=1 + To speed up the algorithm, accept only those bins with at least + min_bin_freq points as seeds. + + cluster_all : bool, default=True + If true, then all points are clustered, even those orphans that are + not within any kernel. Orphans are assigned to the nearest kernel. + If false, then orphans are given cluster label -1. + + n_jobs : int, default=None + The number of jobs to use for the computation. The following tasks benefit + from the parallelization: + + - The search of nearest neighbors for bandwidth estimation and label + assignments. See the details in the docstring of the + ``NearestNeighbors`` class. + - Hill-climbing optimization for all seeds. + + See :term:`Glossary ` for more details. + + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + max_iter : int, default=300 + Maximum number of iterations, per seed point before the clustering + operation terminates (for that seed point), if has not converged yet. + + .. versionadded:: 0.22 + + Attributes + ---------- + cluster_centers_ : ndarray of shape (n_clusters, n_features) + Coordinates of cluster centers. + + labels_ : ndarray of shape (n_samples,) + Labels of each point. + + n_iter_ : int + Maximum number of iterations performed on each seed. + + .. versionadded:: 0.22 + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + KMeans : K-Means clustering. + + Notes + ----- + + Scalability: + + Because this implementation uses a flat kernel and + a Ball Tree to look up members of each kernel, the complexity will tend + towards O(T*n*log(n)) in lower dimensions, with n the number of samples + and T the number of points. In higher dimensions the complexity will + tend towards O(T*n^2). + + Scalability can be boosted by using fewer seeds, for example by using + a higher value of min_bin_freq in the get_bin_seeds function. + + Note that the estimate_bandwidth function is much less scalable than the + mean shift algorithm and will be the bottleneck if it is used. + + References + ---------- + + Dorin Comaniciu and Peter Meer, "Mean Shift: A robust approach toward + feature space analysis". IEEE Transactions on Pattern Analysis and + Machine Intelligence. 2002. pp. 603-619. + + Examples + -------- + >>> from sklearn.cluster import MeanShift + >>> import numpy as np + >>> X = np.array([[1, 1], [2, 1], [1, 0], + ... [4, 7], [3, 5], [3, 6]]) + >>> clustering = MeanShift(bandwidth=2).fit(X) + >>> clustering.labels_ + array([1, 1, 1, 0, 0, 0]) + >>> clustering.predict([[0, 0], [5, 5]]) + array([1, 0]) + >>> clustering + MeanShift(bandwidth=2) + + For a comparison of Mean Shift clustering with other clustering algorithms, see + :ref:`sphx_glr_auto_examples_cluster_plot_cluster_comparison.py` + """ + + _parameter_constraints: dict = { + "bandwidth": [Interval(Real, 0, None, closed="neither"), None], + "seeds": ["array-like", None], + "bin_seeding": ["boolean"], + "min_bin_freq": [Interval(Integral, 1, None, closed="left")], + "cluster_all": ["boolean"], + "n_jobs": [Integral, None], + "max_iter": [Interval(Integral, 0, None, closed="left")], + } + + def __init__( + self, + *, + bandwidth=None, + seeds=None, + bin_seeding=False, + min_bin_freq=1, + cluster_all=True, + n_jobs=None, + max_iter=300, + ): + self.bandwidth = bandwidth + self.seeds = seeds + self.bin_seeding = bin_seeding + self.cluster_all = cluster_all + self.min_bin_freq = min_bin_freq + self.n_jobs = n_jobs + self.max_iter = max_iter + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Perform clustering. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Samples to cluster. + + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + self : object + Fitted instance. + """ + X = validate_data(self, X) + bandwidth = self.bandwidth + if bandwidth is None: + bandwidth = estimate_bandwidth(X, n_jobs=self.n_jobs) + + seeds = self.seeds + if seeds is None: + if self.bin_seeding: + seeds = get_bin_seeds(X, bandwidth, self.min_bin_freq) + else: + seeds = X + n_samples, n_features = X.shape + center_intensity_dict = {} + + # We use n_jobs=1 because this will be used in nested calls under + # parallel calls to _mean_shift_single_seed so there is no need for + # for further parallelism. + nbrs = NearestNeighbors(radius=bandwidth, n_jobs=1).fit(X) + + # execute iterations on all seeds in parallel + all_res = Parallel(n_jobs=self.n_jobs)( + delayed(_mean_shift_single_seed)(seed, X, nbrs, self.max_iter) + for seed in seeds + ) + # copy results in a dictionary + for i in range(len(seeds)): + if all_res[i][1]: # i.e. len(points_within) > 0 + center_intensity_dict[all_res[i][0]] = all_res[i][1] + + self.n_iter_ = max([x[2] for x in all_res]) + + if not center_intensity_dict: + # nothing near seeds + raise ValueError( + "No point was within bandwidth=%f of any seed. Try a different seeding" + " strategy or increase the bandwidth." + % bandwidth + ) + + # POST PROCESSING: remove near duplicate points + # If the distance between two kernels is less than the bandwidth, + # then we have to remove one because it is a duplicate. Remove the + # one with fewer points. + + sorted_by_intensity = sorted( + center_intensity_dict.items(), + key=lambda tup: (tup[1], tup[0]), + reverse=True, + ) + sorted_centers = np.array([tup[0] for tup in sorted_by_intensity]) + unique = np.ones(len(sorted_centers), dtype=bool) + nbrs = NearestNeighbors(radius=bandwidth, n_jobs=self.n_jobs).fit( + sorted_centers + ) + for i, center in enumerate(sorted_centers): + if unique[i]: + neighbor_idxs = nbrs.radius_neighbors([center], return_distance=False)[ + 0 + ] + unique[neighbor_idxs] = 0 + unique[i] = 1 # leave the current point as unique + cluster_centers = sorted_centers[unique] + + # ASSIGN LABELS: a point belongs to the cluster that it is closest to + nbrs = NearestNeighbors(n_neighbors=1, n_jobs=self.n_jobs).fit(cluster_centers) + labels = np.zeros(n_samples, dtype=int) + distances, idxs = nbrs.kneighbors(X) + if self.cluster_all: + labels = idxs.flatten() + else: + labels.fill(-1) + bool_selector = distances.flatten() <= bandwidth + labels[bool_selector] = idxs.flatten()[bool_selector] + + self.cluster_centers_, self.labels_ = cluster_centers, labels + return self + + def predict(self, X): + """Predict the closest cluster each sample in X belongs to. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + New data to predict. + + Returns + ------- + labels : ndarray of shape (n_samples,) + Index of the cluster each sample belongs to. + """ + check_is_fitted(self) + X = validate_data(self, X, reset=False) + with config_context(assume_finite=True): + return pairwise_distances_argmin(X, self.cluster_centers_) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_optics.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_optics.py new file mode 100644 index 0000000000000000000000000000000000000000..4a1a80c9065c2d1504a6c97a926b919374e0a1ee --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_optics.py @@ -0,0 +1,1202 @@ +"""Ordering Points To Identify the Clustering Structure (OPTICS) + +These routines execute the OPTICS algorithm, and implement various +cluster extraction methods of the ordered list. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from numbers import Integral, Real + +import numpy as np +from scipy.sparse import SparseEfficiencyWarning, issparse + +from ..base import BaseEstimator, ClusterMixin, _fit_context +from ..exceptions import DataConversionWarning +from ..metrics import pairwise_distances +from ..metrics.pairwise import _VALID_METRICS, PAIRWISE_BOOLEAN_FUNCTIONS +from ..neighbors import NearestNeighbors +from ..utils import gen_batches +from ..utils._chunking import get_chunk_n_rows +from ..utils._param_validation import ( + HasMethods, + Interval, + RealNotInt, + StrOptions, + validate_params, +) +from ..utils.validation import check_memory, validate_data + + +class OPTICS(ClusterMixin, BaseEstimator): + """Estimate clustering structure from vector array. + + OPTICS (Ordering Points To Identify the Clustering Structure), closely + related to DBSCAN, finds core samples of high density and expands clusters + from them [1]_. Unlike DBSCAN, it keeps cluster hierarchy for a variable + neighborhood radius. Better suited for usage on large datasets than the + current scikit-learn implementation of DBSCAN. + + Clusters are then extracted from the cluster-order using a + DBSCAN-like method (cluster_method = 'dbscan') or an automatic + technique proposed in [1]_ (cluster_method = 'xi'). + + This implementation deviates from the original OPTICS by first performing + k-nearest-neighborhood searches on all points to identify core sizes of + all points (instead of computing neighbors while looping through points). + Reachability distances to only unprocessed points are then computed, to + construct the cluster order, similar to the original OPTICS. + Note that we do not employ a heap to manage the expansion + candidates, so the time complexity will be O(n^2). + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + min_samples : int > 1 or float between 0 and 1, default=5 + The number of samples in a neighborhood for a point to be considered as + a core point. Also, up and down steep regions can't have more than + ``min_samples`` consecutive non-steep points. Expressed as an absolute + number or a fraction of the number of samples (rounded to be at least + 2). + + max_eps : float, default=np.inf + The maximum distance between two samples for one to be considered as + in the neighborhood of the other. Default value of ``np.inf`` will + identify clusters across all scales; reducing ``max_eps`` will result + in shorter run times. + + metric : str or callable, default='minkowski' + Metric to use for distance computation. Any metric from scikit-learn + or :mod:`scipy.spatial.distance` can be used. + + If `metric` is a callable function, it is called on each + pair of instances (rows) and the resulting value recorded. The callable + should take two arrays as input and return one value indicating the + distance between them. This works for Scipy's metrics, but is less + efficient than passing the metric name as a string. If metric is + "precomputed", `X` is assumed to be a distance matrix and must be + square. + + Valid values for metric are: + + - from scikit-learn: ['cityblock', 'cosine', 'euclidean', 'l1', 'l2', + 'manhattan'] + + - from scipy.spatial.distance: ['braycurtis', 'canberra', 'chebyshev', + 'correlation', 'dice', 'hamming', 'jaccard', 'kulsinski', + 'mahalanobis', 'minkowski', 'rogerstanimoto', 'russellrao', + 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', + 'yule'] + + Sparse matrices are only supported by scikit-learn metrics. + See :mod:`scipy.spatial.distance` for details on these metrics. + + .. note:: + `'kulsinski'` is deprecated from SciPy 1.9 and will be removed in SciPy 1.11. + + p : float, default=2 + Parameter for the Minkowski metric from + :class:`~sklearn.metrics.pairwise_distances`. When p = 1, this is + equivalent to using manhattan_distance (l1), and euclidean_distance + (l2) for p = 2. For arbitrary p, minkowski_distance (l_p) is used. + + metric_params : dict, default=None + Additional keyword arguments for the metric function. + + cluster_method : {'xi', 'dbscan'}, default='xi' + The extraction method used to extract clusters using the calculated + reachability and ordering. + + eps : float, default=None + The maximum distance between two samples for one to be considered as + in the neighborhood of the other. By default it assumes the same value + as ``max_eps``. + Used only when ``cluster_method='dbscan'``. + + xi : float between 0 and 1, default=0.05 + Determines the minimum steepness on the reachability plot that + constitutes a cluster boundary. For example, an upwards point in the + reachability plot is defined by the ratio from one point to its + successor being at most 1-xi. + Used only when ``cluster_method='xi'``. + + predecessor_correction : bool, default=True + Correct clusters according to the predecessors calculated by OPTICS + [2]_. This parameter has minimal effect on most datasets. + Used only when ``cluster_method='xi'``. + + min_cluster_size : int > 1 or float between 0 and 1, default=None + Minimum number of samples in an OPTICS cluster, expressed as an + absolute number or a fraction of the number of samples (rounded to be + at least 2). If ``None``, the value of ``min_samples`` is used instead. + Used only when ``cluster_method='xi'``. + + algorithm : {'auto', 'ball_tree', 'kd_tree', 'brute'}, default='auto' + Algorithm used to compute the nearest neighbors: + + - 'ball_tree' will use :class:`~sklearn.neighbors.BallTree`. + - 'kd_tree' will use :class:`~sklearn.neighbors.KDTree`. + - 'brute' will use a brute-force search. + - 'auto' (default) will attempt to decide the most appropriate + algorithm based on the values passed to :meth:`fit` method. + + Note: fitting on sparse input will override the setting of + this parameter, using brute force. + + leaf_size : int, default=30 + Leaf size passed to :class:`~sklearn.neighbors.BallTree` or + :class:`~sklearn.neighbors.KDTree`. This can affect the speed of the + construction and query, as well as the memory required to store the + tree. The optimal value depends on the nature of the problem. + + memory : str or object with the joblib.Memory interface, default=None + Used to cache the output of the computation of the tree. + By default, no caching is done. If a string is given, it is the + path to the caching directory. + + n_jobs : int, default=None + The number of parallel jobs to run for neighbors search. + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + Attributes + ---------- + labels_ : ndarray of shape (n_samples,) + Cluster labels for each point in the dataset given to fit(). + Noisy samples and points which are not included in a leaf cluster + of ``cluster_hierarchy_`` are labeled as -1. + + reachability_ : ndarray of shape (n_samples,) + Reachability distances per sample, indexed by object order. Use + ``clust.reachability_[clust.ordering_]`` to access in cluster order. + + ordering_ : ndarray of shape (n_samples,) + The cluster ordered list of sample indices. + + core_distances_ : ndarray of shape (n_samples,) + Distance at which each sample becomes a core point, indexed by object + order. Points which will never be core have a distance of inf. Use + ``clust.core_distances_[clust.ordering_]`` to access in cluster order. + + predecessor_ : ndarray of shape (n_samples,) + Point that a sample was reached from, indexed by object order. + Seed points have a predecessor of -1. + + cluster_hierarchy_ : ndarray of shape (n_clusters, 2) + The list of clusters in the form of ``[start, end]`` in each row, with + all indices inclusive. The clusters are ordered according to + ``(end, -start)`` (ascending) so that larger clusters encompassing + smaller clusters come after those smaller ones. Since ``labels_`` does + not reflect the hierarchy, usually + ``len(cluster_hierarchy_) > np.unique(optics.labels_)``. Please also + note that these indices are of the ``ordering_``, i.e. + ``X[ordering_][start:end + 1]`` form a cluster. + Only available when ``cluster_method='xi'``. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + DBSCAN : A similar clustering for a specified neighborhood radius (eps). + Our implementation is optimized for runtime. + + References + ---------- + .. [1] Ankerst, Mihael, Markus M. Breunig, Hans-Peter Kriegel, + and Jörg Sander. "OPTICS: ordering points to identify the clustering + structure." ACM SIGMOD Record 28, no. 2 (1999): 49-60. + + .. [2] Schubert, Erich, Michael Gertz. + "Improving the Cluster Structure Extracted from OPTICS Plots." Proc. of + the Conference "Lernen, Wissen, Daten, Analysen" (LWDA) (2018): 318-329. + + Examples + -------- + >>> from sklearn.cluster import OPTICS + >>> import numpy as np + >>> X = np.array([[1, 2], [2, 5], [3, 6], + ... [8, 7], [8, 8], [7, 3]]) + >>> clustering = OPTICS(min_samples=2).fit(X) + >>> clustering.labels_ + array([0, 0, 0, 1, 1, 1]) + + For a more detailed example see + :ref:`sphx_glr_auto_examples_cluster_plot_optics.py`. + + For a comparison of OPTICS with other clustering algorithms, see + :ref:`sphx_glr_auto_examples_cluster_plot_cluster_comparison.py` + """ + + _parameter_constraints: dict = { + "min_samples": [ + Interval(Integral, 2, None, closed="left"), + Interval(RealNotInt, 0, 1, closed="both"), + ], + "max_eps": [Interval(Real, 0, None, closed="both")], + "metric": [StrOptions(set(_VALID_METRICS) | {"precomputed"}), callable], + "p": [Interval(Real, 1, None, closed="left")], + "metric_params": [dict, None], + "cluster_method": [StrOptions({"dbscan", "xi"})], + "eps": [Interval(Real, 0, None, closed="both"), None], + "xi": [Interval(Real, 0, 1, closed="both")], + "predecessor_correction": ["boolean"], + "min_cluster_size": [ + Interval(Integral, 2, None, closed="left"), + Interval(RealNotInt, 0, 1, closed="right"), + None, + ], + "algorithm": [StrOptions({"auto", "brute", "ball_tree", "kd_tree"})], + "leaf_size": [Interval(Integral, 1, None, closed="left")], + "memory": [str, HasMethods("cache"), None], + "n_jobs": [Integral, None], + } + + def __init__( + self, + *, + min_samples=5, + max_eps=np.inf, + metric="minkowski", + p=2, + metric_params=None, + cluster_method="xi", + eps=None, + xi=0.05, + predecessor_correction=True, + min_cluster_size=None, + algorithm="auto", + leaf_size=30, + memory=None, + n_jobs=None, + ): + self.max_eps = max_eps + self.min_samples = min_samples + self.min_cluster_size = min_cluster_size + self.algorithm = algorithm + self.metric = metric + self.metric_params = metric_params + self.p = p + self.leaf_size = leaf_size + self.cluster_method = cluster_method + self.eps = eps + self.xi = xi + self.predecessor_correction = predecessor_correction + self.memory = memory + self.n_jobs = n_jobs + + @_fit_context( + # Optics.metric is not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, y=None): + """Perform OPTICS clustering. + + Extracts an ordered list of points and reachability distances, and + performs initial clustering using ``max_eps`` distance specified at + OPTICS object instantiation. + + Parameters + ---------- + X : {ndarray, sparse matrix} of shape (n_samples, n_features), or \ + (n_samples, n_samples) if metric='precomputed' + A feature array, or array of distances between samples if + metric='precomputed'. If a sparse matrix is provided, it will be + converted into CSR format. + + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + self : object + Returns a fitted instance of self. + """ + dtype = bool if self.metric in PAIRWISE_BOOLEAN_FUNCTIONS else float + if dtype is bool and X.dtype != bool: + msg = ( + "Data will be converted to boolean for" + f" metric {self.metric}, to avoid this warning," + " you may convert the data prior to calling fit." + ) + warnings.warn(msg, DataConversionWarning) + + X = validate_data(self, X, dtype=dtype, accept_sparse="csr") + if self.metric == "precomputed" and issparse(X): + X = X.copy() # copy to avoid in-place modification + with warnings.catch_warnings(): + warnings.simplefilter("ignore", SparseEfficiencyWarning) + # Set each diagonal to an explicit value so each point is its + # own neighbor + X.setdiag(X.diagonal()) + memory = check_memory(self.memory) + + ( + self.ordering_, + self.core_distances_, + self.reachability_, + self.predecessor_, + ) = memory.cache(compute_optics_graph)( + X=X, + min_samples=self.min_samples, + algorithm=self.algorithm, + leaf_size=self.leaf_size, + metric=self.metric, + metric_params=self.metric_params, + p=self.p, + n_jobs=self.n_jobs, + max_eps=self.max_eps, + ) + + # Extract clusters from the calculated orders and reachability + if self.cluster_method == "xi": + labels_, clusters_ = cluster_optics_xi( + reachability=self.reachability_, + predecessor=self.predecessor_, + ordering=self.ordering_, + min_samples=self.min_samples, + min_cluster_size=self.min_cluster_size, + xi=self.xi, + predecessor_correction=self.predecessor_correction, + ) + self.cluster_hierarchy_ = clusters_ + elif self.cluster_method == "dbscan": + if self.eps is None: + eps = self.max_eps + else: + eps = self.eps + + if eps > self.max_eps: + raise ValueError( + "Specify an epsilon smaller than %s. Got %s." % (self.max_eps, eps) + ) + + labels_ = cluster_optics_dbscan( + reachability=self.reachability_, + core_distances=self.core_distances_, + ordering=self.ordering_, + eps=eps, + ) + + self.labels_ = labels_ + return self + + +def _validate_size(size, n_samples, param_name): + if size > n_samples: + raise ValueError( + "%s must be no greater than the number of samples (%d). Got %d" + % (param_name, n_samples, size) + ) + + +# OPTICS helper functions +def _compute_core_distances_(X, neighbors, min_samples, working_memory): + """Compute the k-th nearest neighbor of each sample. + + Equivalent to neighbors.kneighbors(X, self.min_samples)[0][:, -1] + but with more memory efficiency. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The data. + neighbors : NearestNeighbors instance + The fitted nearest neighbors estimator. + working_memory : int, default=None + The sought maximum memory for temporary distance matrix chunks. + When None (default), the value of + ``sklearn.get_config()['working_memory']`` is used. + + Returns + ------- + core_distances : ndarray of shape (n_samples,) + Distance at which each sample becomes a core point. + Points which will never be core have a distance of inf. + """ + n_samples = X.shape[0] + core_distances = np.empty(n_samples) + core_distances.fill(np.nan) + + chunk_n_rows = get_chunk_n_rows( + row_bytes=16 * min_samples, max_n_rows=n_samples, working_memory=working_memory + ) + slices = gen_batches(n_samples, chunk_n_rows) + for sl in slices: + core_distances[sl] = neighbors.kneighbors(X[sl], min_samples)[0][:, -1] + return core_distances + + +@validate_params( + { + "X": [np.ndarray, "sparse matrix"], + "min_samples": [ + Interval(Integral, 2, None, closed="left"), + Interval(RealNotInt, 0, 1, closed="both"), + ], + "max_eps": [Interval(Real, 0, None, closed="both")], + "metric": [StrOptions(set(_VALID_METRICS) | {"precomputed"}), callable], + "p": [Interval(Real, 0, None, closed="right"), None], + "metric_params": [dict, None], + "algorithm": [StrOptions({"auto", "brute", "ball_tree", "kd_tree"})], + "leaf_size": [Interval(Integral, 1, None, closed="left")], + "n_jobs": [Integral, None], + }, + prefer_skip_nested_validation=False, # metric is not validated yet +) +def compute_optics_graph( + X, *, min_samples, max_eps, metric, p, metric_params, algorithm, leaf_size, n_jobs +): + """Compute the OPTICS reachability graph. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + X : {ndarray, sparse matrix} of shape (n_samples, n_features), or \ + (n_samples, n_samples) if metric='precomputed' + A feature array, or array of distances between samples if + metric='precomputed'. + + min_samples : int > 1 or float between 0 and 1 + The number of samples in a neighborhood for a point to be considered + as a core point. Expressed as an absolute number or a fraction of the + number of samples (rounded to be at least 2). + + max_eps : float, default=np.inf + The maximum distance between two samples for one to be considered as + in the neighborhood of the other. Default value of ``np.inf`` will + identify clusters across all scales; reducing ``max_eps`` will result + in shorter run times. + + metric : str or callable, default='minkowski' + Metric to use for distance computation. Any metric from scikit-learn + or scipy.spatial.distance can be used. + + If metric is a callable function, it is called on each + pair of instances (rows) and the resulting value recorded. The callable + should take two arrays as input and return one value indicating the + distance between them. This works for Scipy's metrics, but is less + efficient than passing the metric name as a string. If metric is + "precomputed", X is assumed to be a distance matrix and must be square. + + Valid values for metric are: + + - from scikit-learn: ['cityblock', 'cosine', 'euclidean', 'l1', 'l2', + 'manhattan'] + + - from scipy.spatial.distance: ['braycurtis', 'canberra', 'chebyshev', + 'correlation', 'dice', 'hamming', 'jaccard', 'kulsinski', + 'mahalanobis', 'minkowski', 'rogerstanimoto', 'russellrao', + 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', + 'yule'] + + See the documentation for scipy.spatial.distance for details on these + metrics. + + .. note:: + `'kulsinski'` is deprecated from SciPy 1.9 and will be removed in SciPy 1.11. + + p : float, default=2 + Parameter for the Minkowski metric from + :class:`~sklearn.metrics.pairwise_distances`. When p = 1, this is + equivalent to using manhattan_distance (l1), and euclidean_distance + (l2) for p = 2. For arbitrary p, minkowski_distance (l_p) is used. + + metric_params : dict, default=None + Additional keyword arguments for the metric function. + + algorithm : {'auto', 'ball_tree', 'kd_tree', 'brute'}, default='auto' + Algorithm used to compute the nearest neighbors: + + - 'ball_tree' will use :class:`~sklearn.neighbors.BallTree`. + - 'kd_tree' will use :class:`~sklearn.neighbors.KDTree`. + - 'brute' will use a brute-force search. + - 'auto' will attempt to decide the most appropriate algorithm + based on the values passed to `fit` method. (default) + + Note: fitting on sparse input will override the setting of + this parameter, using brute force. + + leaf_size : int, default=30 + Leaf size passed to :class:`~sklearn.neighbors.BallTree` or + :class:`~sklearn.neighbors.KDTree`. This can affect the speed of the + construction and query, as well as the memory required to store the + tree. The optimal value depends on the nature of the problem. + + n_jobs : int, default=None + The number of parallel jobs to run for neighbors search. + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + Returns + ------- + ordering_ : array of shape (n_samples,) + The cluster ordered list of sample indices. + + core_distances_ : array of shape (n_samples,) + Distance at which each sample becomes a core point, indexed by object + order. Points which will never be core have a distance of inf. Use + ``clust.core_distances_[clust.ordering_]`` to access in cluster order. + + reachability_ : array of shape (n_samples,) + Reachability distances per sample, indexed by object order. Use + ``clust.reachability_[clust.ordering_]`` to access in cluster order. + + predecessor_ : array of shape (n_samples,) + Point that a sample was reached from, indexed by object order. + Seed points have a predecessor of -1. + + References + ---------- + .. [1] Ankerst, Mihael, Markus M. Breunig, Hans-Peter Kriegel, + and Jörg Sander. "OPTICS: ordering points to identify the clustering + structure." ACM SIGMOD Record 28, no. 2 (1999): 49-60. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.cluster import compute_optics_graph + >>> X = np.array([[1, 2], [2, 5], [3, 6], + ... [8, 7], [8, 8], [7, 3]]) + >>> ordering, core_distances, reachability, predecessor = compute_optics_graph( + ... X, + ... min_samples=2, + ... max_eps=np.inf, + ... metric="minkowski", + ... p=2, + ... metric_params=None, + ... algorithm="auto", + ... leaf_size=30, + ... n_jobs=None, + ... ) + >>> ordering + array([0, 1, 2, 5, 3, 4]) + >>> core_distances + array([3.16, 1.41, 1.41, 1. , 1. , + 4.12]) + >>> reachability + array([ inf, 3.16, 1.41, 4.12, 1. , + 5. ]) + >>> predecessor + array([-1, 0, 1, 5, 3, 2]) + """ + n_samples = X.shape[0] + _validate_size(min_samples, n_samples, "min_samples") + if min_samples <= 1: + min_samples = max(2, int(min_samples * n_samples)) + + # Start all points as 'unprocessed' ## + reachability_ = np.empty(n_samples) + reachability_.fill(np.inf) + predecessor_ = np.empty(n_samples, dtype=int) + predecessor_.fill(-1) + + nbrs = NearestNeighbors( + n_neighbors=min_samples, + algorithm=algorithm, + leaf_size=leaf_size, + metric=metric, + metric_params=metric_params, + p=p, + n_jobs=n_jobs, + ) + + nbrs.fit(X) + # Here we first do a kNN query for each point, this differs from + # the original OPTICS that only used epsilon range queries. + # TODO: handle working_memory somehow? + core_distances_ = _compute_core_distances_( + X=X, neighbors=nbrs, min_samples=min_samples, working_memory=None + ) + # OPTICS puts an upper limit on these, use inf for undefined. + core_distances_[core_distances_ > max_eps] = np.inf + np.around( + core_distances_, + decimals=np.finfo(core_distances_.dtype).precision, + out=core_distances_, + ) + + # Main OPTICS loop. Not parallelizable. The order that entries are + # written to the 'ordering_' list is important! + # Note that this implementation is O(n^2) theoretically, but + # supposedly with very low constant factors. + processed = np.zeros(X.shape[0], dtype=bool) + ordering = np.zeros(X.shape[0], dtype=int) + for ordering_idx in range(X.shape[0]): + # Choose next based on smallest reachability distance + # (And prefer smaller ids on ties, possibly np.inf!) + index = np.where(processed == 0)[0] + point = index[np.argmin(reachability_[index])] + + processed[point] = True + ordering[ordering_idx] = point + if core_distances_[point] != np.inf: + _set_reach_dist( + core_distances_=core_distances_, + reachability_=reachability_, + predecessor_=predecessor_, + point_index=point, + processed=processed, + X=X, + nbrs=nbrs, + metric=metric, + metric_params=metric_params, + p=p, + max_eps=max_eps, + ) + if np.all(np.isinf(reachability_)): + warnings.warn( + ( + "All reachability values are inf. Set a larger" + " max_eps or all data will be considered outliers." + ), + UserWarning, + ) + return ordering, core_distances_, reachability_, predecessor_ + + +def _set_reach_dist( + core_distances_, + reachability_, + predecessor_, + point_index, + processed, + X, + nbrs, + metric, + metric_params, + p, + max_eps, +): + P = X[point_index : point_index + 1] + # Assume that radius_neighbors is faster without distances + # and we don't need all distances, nevertheless, this means + # we may be doing some work twice. + indices = nbrs.radius_neighbors(P, radius=max_eps, return_distance=False)[0] + + # Getting indices of neighbors that have not been processed + unproc = np.compress(~np.take(processed, indices), indices) + # Neighbors of current point are already processed. + if not unproc.size: + return + + # Only compute distances to unprocessed neighbors: + if metric == "precomputed": + dists = X[[point_index], unproc] + if isinstance(dists, np.matrix): + dists = np.asarray(dists) + dists = dists.ravel() + else: + _params = dict() if metric_params is None else metric_params.copy() + if metric == "minkowski" and "p" not in _params: + # the same logic as neighbors, p is ignored if explicitly set + # in the dict params + _params["p"] = p + dists = pairwise_distances(P, X[unproc], metric, n_jobs=None, **_params).ravel() + + rdists = np.maximum(dists, core_distances_[point_index]) + np.around(rdists, decimals=np.finfo(rdists.dtype).precision, out=rdists) + improved = np.where(rdists < np.take(reachability_, unproc)) + reachability_[unproc[improved]] = rdists[improved] + predecessor_[unproc[improved]] = point_index + + +@validate_params( + { + "reachability": [np.ndarray], + "core_distances": [np.ndarray], + "ordering": [np.ndarray], + "eps": [Interval(Real, 0, None, closed="both")], + }, + prefer_skip_nested_validation=True, +) +def cluster_optics_dbscan(*, reachability, core_distances, ordering, eps): + """Perform DBSCAN extraction for an arbitrary epsilon. + + Extracting the clusters runs in linear time. Note that this results in + ``labels_`` which are close to a :class:`~sklearn.cluster.DBSCAN` with + similar settings and ``eps``, only if ``eps`` is close to ``max_eps``. + + Parameters + ---------- + reachability : ndarray of shape (n_samples,) + Reachability distances calculated by OPTICS (``reachability_``). + + core_distances : ndarray of shape (n_samples,) + Distances at which points become core (``core_distances_``). + + ordering : ndarray of shape (n_samples,) + OPTICS ordered point indices (``ordering_``). + + eps : float + DBSCAN ``eps`` parameter. Must be set to < ``max_eps``. Results + will be close to DBSCAN algorithm if ``eps`` and ``max_eps`` are close + to one another. + + Returns + ------- + labels_ : array of shape (n_samples,) + The estimated labels. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.cluster import cluster_optics_dbscan, compute_optics_graph + >>> X = np.array([[1, 2], [2, 5], [3, 6], + ... [8, 7], [8, 8], [7, 3]]) + >>> ordering, core_distances, reachability, predecessor = compute_optics_graph( + ... X, + ... min_samples=2, + ... max_eps=np.inf, + ... metric="minkowski", + ... p=2, + ... metric_params=None, + ... algorithm="auto", + ... leaf_size=30, + ... n_jobs=None, + ... ) + >>> eps = 4.5 + >>> labels = cluster_optics_dbscan( + ... reachability=reachability, + ... core_distances=core_distances, + ... ordering=ordering, + ... eps=eps, + ... ) + >>> labels + array([0, 0, 0, 1, 1, 1]) + """ + n_samples = len(core_distances) + labels = np.zeros(n_samples, dtype=int) + + far_reach = reachability > eps + near_core = core_distances <= eps + labels[ordering] = np.cumsum(far_reach[ordering] & near_core[ordering]) - 1 + labels[far_reach & ~near_core] = -1 + return labels + + +@validate_params( + { + "reachability": [np.ndarray], + "predecessor": [np.ndarray], + "ordering": [np.ndarray], + "min_samples": [ + Interval(Integral, 2, None, closed="left"), + Interval(RealNotInt, 0, 1, closed="both"), + ], + "min_cluster_size": [ + Interval(Integral, 2, None, closed="left"), + Interval(RealNotInt, 0, 1, closed="both"), + None, + ], + "xi": [Interval(Real, 0, 1, closed="both")], + "predecessor_correction": ["boolean"], + }, + prefer_skip_nested_validation=True, +) +def cluster_optics_xi( + *, + reachability, + predecessor, + ordering, + min_samples, + min_cluster_size=None, + xi=0.05, + predecessor_correction=True, +): + """Automatically extract clusters according to the Xi-steep method. + + Parameters + ---------- + reachability : ndarray of shape (n_samples,) + Reachability distances calculated by OPTICS (`reachability_`). + + predecessor : ndarray of shape (n_samples,) + Predecessors calculated by OPTICS. + + ordering : ndarray of shape (n_samples,) + OPTICS ordered point indices (`ordering_`). + + min_samples : int > 1 or float between 0 and 1 + The same as the min_samples given to OPTICS. Up and down steep regions + can't have more then ``min_samples`` consecutive non-steep points. + Expressed as an absolute number or a fraction of the number of samples + (rounded to be at least 2). + + min_cluster_size : int > 1 or float between 0 and 1, default=None + Minimum number of samples in an OPTICS cluster, expressed as an + absolute number or a fraction of the number of samples (rounded to be + at least 2). If ``None``, the value of ``min_samples`` is used instead. + + xi : float between 0 and 1, default=0.05 + Determines the minimum steepness on the reachability plot that + constitutes a cluster boundary. For example, an upwards point in the + reachability plot is defined by the ratio from one point to its + successor being at most 1-xi. + + predecessor_correction : bool, default=True + Correct clusters based on the calculated predecessors. + + Returns + ------- + labels : ndarray of shape (n_samples,) + The labels assigned to samples. Points which are not included + in any cluster are labeled as -1. + + clusters : ndarray of shape (n_clusters, 2) + The list of clusters in the form of ``[start, end]`` in each row, with + all indices inclusive. The clusters are ordered according to ``(end, + -start)`` (ascending) so that larger clusters encompassing smaller + clusters come after such nested smaller clusters. Since ``labels`` does + not reflect the hierarchy, usually ``len(clusters) > + np.unique(labels)``. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.cluster import cluster_optics_xi, compute_optics_graph + >>> X = np.array([[1, 2], [2, 5], [3, 6], + ... [8, 7], [8, 8], [7, 3]]) + >>> ordering, core_distances, reachability, predecessor = compute_optics_graph( + ... X, + ... min_samples=2, + ... max_eps=np.inf, + ... metric="minkowski", + ... p=2, + ... metric_params=None, + ... algorithm="auto", + ... leaf_size=30, + ... n_jobs=None + ... ) + >>> min_samples = 2 + >>> labels, clusters = cluster_optics_xi( + ... reachability=reachability, + ... predecessor=predecessor, + ... ordering=ordering, + ... min_samples=min_samples, + ... ) + >>> labels + array([0, 0, 0, 1, 1, 1]) + >>> clusters + array([[0, 2], + [3, 5], + [0, 5]]) + """ + n_samples = len(reachability) + _validate_size(min_samples, n_samples, "min_samples") + if min_samples <= 1: + min_samples = max(2, int(min_samples * n_samples)) + if min_cluster_size is None: + min_cluster_size = min_samples + _validate_size(min_cluster_size, n_samples, "min_cluster_size") + if min_cluster_size <= 1: + min_cluster_size = max(2, int(min_cluster_size * n_samples)) + + clusters = _xi_cluster( + reachability[ordering], + predecessor[ordering], + ordering, + xi, + min_samples, + min_cluster_size, + predecessor_correction, + ) + labels = _extract_xi_labels(ordering, clusters) + return labels, clusters + + +def _extend_region(steep_point, xward_point, start, min_samples): + """Extend the area until it's maximal. + + It's the same function for both upward and downward reagions, depending on + the given input parameters. Assuming: + + - steep_{upward/downward}: bool array indicating whether a point is a + steep {upward/downward}; + - upward/downward: bool array indicating whether a point is + upward/downward; + + To extend an upward reagion, ``steep_point=steep_upward`` and + ``xward_point=downward`` are expected, and to extend a downward region, + ``steep_point=steep_downward`` and ``xward_point=upward``. + + Parameters + ---------- + steep_point : ndarray of shape (n_samples,), dtype=bool + True if the point is steep downward (upward). + + xward_point : ndarray of shape (n_samples,), dtype=bool + True if the point is an upward (respectively downward) point. + + start : int + The start of the xward region. + + min_samples : int + The same as the min_samples given to OPTICS. Up and down steep + regions can't have more then ``min_samples`` consecutive non-steep + points. + + Returns + ------- + index : int + The current index iterating over all the samples, i.e. where we are up + to in our search. + + end : int + The end of the region, which can be behind the index. The region + includes the ``end`` index. + """ + n_samples = len(steep_point) + non_xward_points = 0 + index = start + end = start + # find a maximal area + while index < n_samples: + if steep_point[index]: + non_xward_points = 0 + end = index + elif not xward_point[index]: + # it's not a steep point, but still goes up. + non_xward_points += 1 + # region should include no more than min_samples consecutive + # non steep xward points. + if non_xward_points > min_samples: + break + else: + return end + index += 1 + return end + + +def _update_filter_sdas(sdas, mib, xi_complement, reachability_plot): + """Update steep down areas (SDAs) using the new maximum in between (mib) + value, and the given complement of xi, i.e. ``1 - xi``. + """ + if np.isinf(mib): + return [] + res = [ + sda for sda in sdas if mib <= reachability_plot[sda["start"]] * xi_complement + ] + for sda in res: + sda["mib"] = max(sda["mib"], mib) + return res + + +def _correct_predecessor(reachability_plot, predecessor_plot, ordering, s, e): + """Correct for predecessors. + + Applies Algorithm 2 of [1]_. + + Input parameters are ordered by the computer OPTICS ordering. + + .. [1] Schubert, Erich, Michael Gertz. + "Improving the Cluster Structure Extracted from OPTICS Plots." Proc. of + the Conference "Lernen, Wissen, Daten, Analysen" (LWDA) (2018): 318-329. + """ + while s < e: + if reachability_plot[s] > reachability_plot[e]: + return s, e + p_e = predecessor_plot[e] + for i in range(s, e): + if p_e == ordering[i]: + return s, e + e -= 1 + return None, None + + +def _xi_cluster( + reachability_plot, + predecessor_plot, + ordering, + xi, + min_samples, + min_cluster_size, + predecessor_correction, +): + """Automatically extract clusters according to the Xi-steep method. + + This is rouphly an implementation of Figure 19 of the OPTICS paper. + + Parameters + ---------- + reachability_plot : array-like of shape (n_samples,) + The reachability plot, i.e. reachability ordered according to + the calculated ordering, all computed by OPTICS. + + predecessor_plot : array-like of shape (n_samples,) + Predecessors ordered according to the calculated ordering. + + xi : float, between 0 and 1 + Determines the minimum steepness on the reachability plot that + constitutes a cluster boundary. For example, an upwards point in the + reachability plot is defined by the ratio from one point to its + successor being at most 1-xi. + + min_samples : int > 1 + The same as the min_samples given to OPTICS. Up and down steep regions + can't have more then ``min_samples`` consecutive non-steep points. + + min_cluster_size : int > 1 + Minimum number of samples in an OPTICS cluster. + + predecessor_correction : bool + Correct clusters based on the calculated predecessors. + + Returns + ------- + clusters : ndarray of shape (n_clusters, 2) + The list of clusters in the form of [start, end] in each row, with all + indices inclusive. The clusters are ordered in a way that larger + clusters encompassing smaller clusters come after those smaller + clusters. + """ + + # Our implementation adds an inf to the end of reachability plot + # this helps to find potential clusters at the end of the + # reachability plot even if there's no upward region at the end of it. + reachability_plot = np.hstack((reachability_plot, np.inf)) + + xi_complement = 1 - xi + sdas = [] # steep down areas, introduced in section 4.3.2 of the paper + clusters = [] + index = 0 + mib = 0.0 # maximum in between, section 4.3.2 + + # Our implementation corrects a mistake in the original + # paper, i.e., in Definition 9 steep downward point, + # r(p) * (1 - x1) <= r(p + 1) should be + # r(p) * (1 - x1) >= r(p + 1) + with np.errstate(invalid="ignore"): + ratio = reachability_plot[:-1] / reachability_plot[1:] + steep_upward = ratio <= xi_complement + steep_downward = ratio >= 1 / xi_complement + downward = ratio > 1 + upward = ratio < 1 + + # the following loop is almost exactly as Figure 19 of the paper. + # it jumps over the areas which are not either steep down or up areas + for steep_index in iter(np.flatnonzero(steep_upward | steep_downward)): + # just continue if steep_index has been a part of a discovered xward + # area. + if steep_index < index: + continue + + mib = max(mib, np.max(reachability_plot[index : steep_index + 1])) + + # steep downward areas + if steep_downward[steep_index]: + sdas = _update_filter_sdas(sdas, mib, xi_complement, reachability_plot) + D_start = steep_index + D_end = _extend_region(steep_downward, upward, D_start, min_samples) + D = {"start": D_start, "end": D_end, "mib": 0.0} + sdas.append(D) + index = D_end + 1 + mib = reachability_plot[index] + + # steep upward areas + else: + sdas = _update_filter_sdas(sdas, mib, xi_complement, reachability_plot) + U_start = steep_index + U_end = _extend_region(steep_upward, downward, U_start, min_samples) + index = U_end + 1 + mib = reachability_plot[index] + + U_clusters = [] + for D in sdas: + c_start = D["start"] + c_end = U_end + + # line (**), sc2* + if reachability_plot[c_end + 1] * xi_complement < D["mib"]: + continue + + # Definition 11: criterion 4 + D_max = reachability_plot[D["start"]] + if D_max * xi_complement >= reachability_plot[c_end + 1]: + # Find the first index from the left side which is almost + # at the same level as the end of the detected cluster. + while ( + reachability_plot[c_start + 1] > reachability_plot[c_end + 1] + and c_start < D["end"] + ): + c_start += 1 + elif reachability_plot[c_end + 1] * xi_complement >= D_max: + # Find the first index from the right side which is almost + # at the same level as the beginning of the detected + # cluster. + # Our implementation corrects a mistake in the original + # paper, i.e., in Definition 11 4c, r(x) < r(sD) should be + # r(x) > r(sD). + while reachability_plot[c_end - 1] > D_max and c_end > U_start: + c_end -= 1 + + # predecessor correction + if predecessor_correction: + c_start, c_end = _correct_predecessor( + reachability_plot, predecessor_plot, ordering, c_start, c_end + ) + if c_start is None: + continue + + # Definition 11: criterion 3.a + if c_end - c_start + 1 < min_cluster_size: + continue + + # Definition 11: criterion 1 + if c_start > D["end"]: + continue + + # Definition 11: criterion 2 + if c_end < U_start: + continue + + U_clusters.append((c_start, c_end)) + + # add smaller clusters first. + U_clusters.reverse() + clusters.extend(U_clusters) + + return np.array(clusters) + + +def _extract_xi_labels(ordering, clusters): + """Extracts the labels from the clusters returned by `_xi_cluster`. + We rely on the fact that clusters are stored + with the smaller clusters coming before the larger ones. + + Parameters + ---------- + ordering : array-like of shape (n_samples,) + The ordering of points calculated by OPTICS + + clusters : array-like of shape (n_clusters, 2) + List of clusters i.e. (start, end) tuples, + as returned by `_xi_cluster`. + + Returns + ------- + labels : ndarray of shape (n_samples,) + """ + + labels = np.full(len(ordering), -1, dtype=int) + label = 0 + for c in clusters: + if not np.any(labels[c[0] : (c[1] + 1)] != -1): + labels[c[0] : (c[1] + 1)] = label + label += 1 + labels[ordering] = labels.copy() + return labels diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_spectral.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_spectral.py new file mode 100644 index 0000000000000000000000000000000000000000..00d23437504e5ad019e49583972f244d85a5dae6 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/_spectral.py @@ -0,0 +1,805 @@ +"""Algorithms for spectral clustering""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from numbers import Integral, Real + +import numpy as np +from scipy.linalg import LinAlgError, qr, svd +from scipy.sparse import csc_matrix + +from ..base import BaseEstimator, ClusterMixin, _fit_context +from ..manifold._spectral_embedding import _spectral_embedding +from ..metrics.pairwise import KERNEL_PARAMS, pairwise_kernels +from ..neighbors import NearestNeighbors, kneighbors_graph +from ..utils import as_float_array, check_random_state +from ..utils._param_validation import Interval, StrOptions, validate_params +from ..utils.validation import validate_data +from ._kmeans import k_means + + +def cluster_qr(vectors): + """Find the discrete partition closest to the eigenvector embedding. + + This implementation was proposed in [1]_. + + .. versionadded:: 1.1 + + Parameters + ---------- + vectors : array-like, shape: (n_samples, n_clusters) + The embedding space of the samples. + + Returns + ------- + labels : array of integers, shape: n_samples + The cluster labels of vectors. + + References + ---------- + .. [1] :doi:`Simple, direct, and efficient multi-way spectral clustering, 2019 + Anil Damle, Victor Minden, Lexing Ying + <10.1093/imaiai/iay008>` + + """ + + k = vectors.shape[1] + _, _, piv = qr(vectors.T, pivoting=True) + ut, _, v = svd(vectors[piv[:k], :].T) + vectors = abs(np.dot(vectors, np.dot(ut, v.conj()))) + return vectors.argmax(axis=1) + + +def discretize( + vectors, *, copy=True, max_svd_restarts=30, n_iter_max=20, random_state=None +): + """Search for a partition matrix which is closest to the eigenvector embedding. + + This implementation was proposed in [1]_. + + Parameters + ---------- + vectors : array-like of shape (n_samples, n_clusters) + The embedding space of the samples. + + copy : bool, default=True + Whether to copy vectors, or perform in-place normalization. + + max_svd_restarts : int, default=30 + Maximum number of attempts to restart SVD if convergence fails + + n_iter_max : int, default=30 + Maximum number of iterations to attempt in rotation and partition + matrix search if machine precision convergence is not reached + + random_state : int, RandomState instance, default=None + Determines random number generation for rotation matrix initialization. + Use an int to make the randomness deterministic. + See :term:`Glossary `. + + Returns + ------- + labels : array of integers, shape: n_samples + The labels of the clusters. + + References + ---------- + + .. [1] `Multiclass spectral clustering, 2003 + Stella X. Yu, Jianbo Shi + `_ + + Notes + ----- + + The eigenvector embedding is used to iteratively search for the + closest discrete partition. First, the eigenvector embedding is + normalized to the space of partition matrices. An optimal discrete + partition matrix closest to this normalized embedding multiplied by + an initial rotation is calculated. Fixing this discrete partition + matrix, an optimal rotation matrix is calculated. These two + calculations are performed until convergence. The discrete partition + matrix is returned as the clustering solution. Used in spectral + clustering, this method tends to be faster and more robust to random + initialization than k-means. + + """ + + random_state = check_random_state(random_state) + + vectors = as_float_array(vectors, copy=copy) + + eps = np.finfo(float).eps + n_samples, n_components = vectors.shape + + # Normalize the eigenvectors to an equal length of a vector of ones. + # Reorient the eigenvectors to point in the negative direction with respect + # to the first element. This may have to do with constraining the + # eigenvectors to lie in a specific quadrant to make the discretization + # search easier. + norm_ones = np.sqrt(n_samples) + for i in range(vectors.shape[1]): + vectors[:, i] = (vectors[:, i] / np.linalg.norm(vectors[:, i])) * norm_ones + if vectors[0, i] != 0: + vectors[:, i] = -1 * vectors[:, i] * np.sign(vectors[0, i]) + + # Normalize the rows of the eigenvectors. Samples should lie on the unit + # hypersphere centered at the origin. This transforms the samples in the + # embedding space to the space of partition matrices. + vectors = vectors / np.sqrt((vectors**2).sum(axis=1))[:, np.newaxis] + + svd_restarts = 0 + has_converged = False + + # If there is an exception we try to randomize and rerun SVD again + # do this max_svd_restarts times. + while (svd_restarts < max_svd_restarts) and not has_converged: + # Initialize first column of rotation matrix with a row of the + # eigenvectors + rotation = np.zeros((n_components, n_components)) + rotation[:, 0] = vectors[random_state.randint(n_samples), :].T + + # To initialize the rest of the rotation matrix, find the rows + # of the eigenvectors that are as orthogonal to each other as + # possible + c = np.zeros(n_samples) + for j in range(1, n_components): + # Accumulate c to ensure row is as orthogonal as possible to + # previous picks as well as current one + c += np.abs(np.dot(vectors, rotation[:, j - 1])) + rotation[:, j] = vectors[c.argmin(), :].T + + last_objective_value = 0.0 + n_iter = 0 + + while not has_converged: + n_iter += 1 + + t_discrete = np.dot(vectors, rotation) + + labels = t_discrete.argmax(axis=1) + vectors_discrete = csc_matrix( + (np.ones(len(labels)), (np.arange(0, n_samples), labels)), + shape=(n_samples, n_components), + ) + + t_svd = vectors_discrete.T @ vectors + + try: + U, S, Vh = np.linalg.svd(t_svd) + except LinAlgError: + svd_restarts += 1 + print("SVD did not converge, randomizing and trying again") + break + + ncut_value = 2.0 * (n_samples - S.sum()) + if (abs(ncut_value - last_objective_value) < eps) or (n_iter > n_iter_max): + has_converged = True + else: + # otherwise calculate rotation and continue + last_objective_value = ncut_value + rotation = np.dot(Vh.T, U.T) + + if not has_converged: + raise LinAlgError("SVD did not converge") + return labels + + +@validate_params( + {"affinity": ["array-like", "sparse matrix"]}, + prefer_skip_nested_validation=False, +) +def spectral_clustering( + affinity, + *, + n_clusters=8, + n_components=None, + eigen_solver=None, + random_state=None, + n_init=10, + eigen_tol="auto", + assign_labels="kmeans", + verbose=False, +): + """Apply clustering to a projection of the normalized Laplacian. + + In practice Spectral Clustering is very useful when the structure of + the individual clusters is highly non-convex or more generally when + a measure of the center and spread of the cluster is not a suitable + description of the complete cluster. For instance, when clusters are + nested circles on the 2D plane. + + If affinity is the adjacency matrix of a graph, this method can be + used to find normalized graph cuts [1]_, [2]_. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + affinity : {array-like, sparse matrix} of shape (n_samples, n_samples) + The affinity matrix describing the relationship of the samples to + embed. **Must be symmetric**. + + Possible examples: + - adjacency matrix of a graph, + - heat kernel of the pairwise distance matrix of the samples, + - symmetric k-nearest neighbours connectivity matrix of the samples. + + n_clusters : int, default=None + Number of clusters to extract. + + n_components : int, default=n_clusters + Number of eigenvectors to use for the spectral embedding. + + eigen_solver : {None, 'arpack', 'lobpcg', or 'amg'} + The eigenvalue decomposition method. If None then ``'arpack'`` is used. + See [4]_ for more details regarding ``'lobpcg'``. + Eigensolver ``'amg'`` runs ``'lobpcg'`` with optional + Algebraic MultiGrid preconditioning and requires pyamg to be installed. + It can be faster on very large sparse problems [6]_ and [7]_. + + random_state : int, RandomState instance, default=None + A pseudo random number generator used for the initialization + of the lobpcg eigenvectors decomposition when `eigen_solver == + 'amg'`, and for the K-Means initialization. Use an int to make + the results deterministic across calls (See + :term:`Glossary `). + + .. note:: + When using `eigen_solver == 'amg'`, + it is necessary to also fix the global numpy seed with + `np.random.seed(int)` to get deterministic results. See + https://github.com/pyamg/pyamg/issues/139 for further + information. + + n_init : int, default=10 + Number of time the k-means algorithm will be run with different + centroid seeds. The final results will be the best output of n_init + consecutive runs in terms of inertia. Only used if + ``assign_labels='kmeans'``. + + eigen_tol : float, default="auto" + Stopping criterion for eigendecomposition of the Laplacian matrix. + If `eigen_tol="auto"` then the passed tolerance will depend on the + `eigen_solver`: + + - If `eigen_solver="arpack"`, then `eigen_tol=0.0`; + - If `eigen_solver="lobpcg"` or `eigen_solver="amg"`, then + `eigen_tol=None` which configures the underlying `lobpcg` solver to + automatically resolve the value according to their heuristics. See, + :func:`scipy.sparse.linalg.lobpcg` for details. + + Note that when using `eigen_solver="lobpcg"` or `eigen_solver="amg"` + values of `tol<1e-5` may lead to convergence issues and should be + avoided. + + .. versionadded:: 1.2 + Added 'auto' option. + + assign_labels : {'kmeans', 'discretize', 'cluster_qr'}, default='kmeans' + The strategy to use to assign labels in the embedding + space. There are three ways to assign labels after the Laplacian + embedding. k-means can be applied and is a popular choice. But it can + also be sensitive to initialization. Discretization is another + approach which is less sensitive to random initialization [3]_. + The cluster_qr method [5]_ directly extracts clusters from eigenvectors + in spectral clustering. In contrast to k-means and discretization, cluster_qr + has no tuning parameters and is not an iterative method, yet may outperform + k-means and discretization in terms of both quality and speed. For a detailed + comparison of clustering strategies, refer to the following example: + :ref:`sphx_glr_auto_examples_cluster_plot_coin_segmentation.py`. + + .. versionchanged:: 1.1 + Added new labeling method 'cluster_qr'. + + verbose : bool, default=False + Verbosity mode. + + .. versionadded:: 0.24 + + Returns + ------- + labels : array of integers, shape: n_samples + The labels of the clusters. + + Notes + ----- + The graph should contain only one connected component, elsewhere + the results make little sense. + + This algorithm solves the normalized cut for `k=2`: it is a + normalized spectral clustering. + + References + ---------- + + .. [1] :doi:`Normalized cuts and image segmentation, 2000 + Jianbo Shi, Jitendra Malik + <10.1109/34.868688>` + + .. [2] :doi:`A Tutorial on Spectral Clustering, 2007 + Ulrike von Luxburg + <10.1007/s11222-007-9033-z>` + + .. [3] `Multiclass spectral clustering, 2003 + Stella X. Yu, Jianbo Shi + `_ + + .. [4] :doi:`Toward the Optimal Preconditioned Eigensolver: + Locally Optimal Block Preconditioned Conjugate Gradient Method, 2001 + A. V. Knyazev + SIAM Journal on Scientific Computing 23, no. 2, pp. 517-541. + <10.1137/S1064827500366124>` + + .. [5] :doi:`Simple, direct, and efficient multi-way spectral clustering, 2019 + Anil Damle, Victor Minden, Lexing Ying + <10.1093/imaiai/iay008>` + + .. [6] :doi:`Multiscale Spectral Image Segmentation Multiscale preconditioning + for computing eigenvalues of graph Laplacians in image segmentation, 2006 + Andrew Knyazev + <10.13140/RG.2.2.35280.02565>` + + .. [7] :doi:`Preconditioned spectral clustering for stochastic block partition + streaming graph challenge (Preliminary version at arXiv.) + David Zhuzhunashvili, Andrew Knyazev + <10.1109/HPEC.2017.8091045>` + + Examples + -------- + >>> import numpy as np + >>> from sklearn.metrics.pairwise import pairwise_kernels + >>> from sklearn.cluster import spectral_clustering + >>> X = np.array([[1, 1], [2, 1], [1, 0], + ... [4, 7], [3, 5], [3, 6]]) + >>> affinity = pairwise_kernels(X, metric='rbf') + >>> spectral_clustering( + ... affinity=affinity, n_clusters=2, assign_labels="discretize", random_state=0 + ... ) + array([1, 1, 1, 0, 0, 0]) + """ + + clusterer = SpectralClustering( + n_clusters=n_clusters, + n_components=n_components, + eigen_solver=eigen_solver, + random_state=random_state, + n_init=n_init, + affinity="precomputed", + eigen_tol=eigen_tol, + assign_labels=assign_labels, + verbose=verbose, + ).fit(affinity) + + return clusterer.labels_ + + +class SpectralClustering(ClusterMixin, BaseEstimator): + """Apply clustering to a projection of the normalized Laplacian. + + In practice Spectral Clustering is very useful when the structure of + the individual clusters is highly non-convex, or more generally when + a measure of the center and spread of the cluster is not a suitable + description of the complete cluster, such as when clusters are + nested circles on the 2D plane. + + If the affinity matrix is the adjacency matrix of a graph, this method + can be used to find normalized graph cuts [1]_, [2]_. + + When calling ``fit``, an affinity matrix is constructed using either + a kernel function such the Gaussian (aka RBF) kernel with Euclidean + distance ``d(X, X)``:: + + np.exp(-gamma * d(X,X) ** 2) + + or a k-nearest neighbors connectivity matrix. + + Alternatively, a user-provided affinity matrix can be specified by + setting ``affinity='precomputed'``. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + n_clusters : int, default=8 + The dimension of the projection subspace. + + eigen_solver : {'arpack', 'lobpcg', 'amg'}, default=None + The eigenvalue decomposition strategy to use. AMG requires pyamg + to be installed. It can be faster on very large, sparse problems, + but may also lead to instabilities. If None, then ``'arpack'`` is + used. See [4]_ for more details regarding `'lobpcg'`. + + n_components : int, default=None + Number of eigenvectors to use for the spectral embedding. If None, + defaults to `n_clusters`. + + random_state : int, RandomState instance, default=None + A pseudo random number generator used for the initialization + of the lobpcg eigenvectors decomposition when `eigen_solver == + 'amg'`, and for the K-Means initialization. Use an int to make + the results deterministic across calls (See + :term:`Glossary `). + + .. note:: + When using `eigen_solver == 'amg'`, + it is necessary to also fix the global numpy seed with + `np.random.seed(int)` to get deterministic results. See + https://github.com/pyamg/pyamg/issues/139 for further + information. + + n_init : int, default=10 + Number of time the k-means algorithm will be run with different + centroid seeds. The final results will be the best output of n_init + consecutive runs in terms of inertia. Only used if + ``assign_labels='kmeans'``. + + gamma : float, default=1.0 + Kernel coefficient for rbf, poly, sigmoid, laplacian and chi2 kernels. + Ignored for ``affinity='nearest_neighbors'``, ``affinity='precomputed'`` + or ``affinity='precomputed_nearest_neighbors'``. + + affinity : str or callable, default='rbf' + How to construct the affinity matrix. + - 'nearest_neighbors': construct the affinity matrix by computing a + graph of nearest neighbors. + - 'rbf': construct the affinity matrix using a radial basis function + (RBF) kernel. + - 'precomputed': interpret ``X`` as a precomputed affinity matrix, + where larger values indicate greater similarity between instances. + - 'precomputed_nearest_neighbors': interpret ``X`` as a sparse graph + of precomputed distances, and construct a binary affinity matrix + from the ``n_neighbors`` nearest neighbors of each instance. + - one of the kernels supported by + :func:`~sklearn.metrics.pairwise.pairwise_kernels`. + + Only kernels that produce similarity scores (non-negative values that + increase with similarity) should be used. This property is not checked + by the clustering algorithm. + + n_neighbors : int, default=10 + Number of neighbors to use when constructing the affinity matrix using + the nearest neighbors method. Ignored for ``affinity='rbf'``. + + eigen_tol : float, default="auto" + Stopping criterion for eigen decomposition of the Laplacian matrix. + If `eigen_tol="auto"` then the passed tolerance will depend on the + `eigen_solver`: + + - If `eigen_solver="arpack"`, then `eigen_tol=0.0`; + - If `eigen_solver="lobpcg"` or `eigen_solver="amg"`, then + `eigen_tol=None` which configures the underlying `lobpcg` solver to + automatically resolve the value according to their heuristics. See, + :func:`scipy.sparse.linalg.lobpcg` for details. + + Note that when using `eigen_solver="lobpcg"` or `eigen_solver="amg"` + values of `tol<1e-5` may lead to convergence issues and should be + avoided. + + .. versionadded:: 1.2 + Added 'auto' option. + + assign_labels : {'kmeans', 'discretize', 'cluster_qr'}, default='kmeans' + The strategy for assigning labels in the embedding space. There are two + ways to assign labels after the Laplacian embedding. k-means is a + popular choice, but it can be sensitive to initialization. + Discretization is another approach which is less sensitive to random + initialization [3]_. + The cluster_qr method [5]_ directly extract clusters from eigenvectors + in spectral clustering. In contrast to k-means and discretization, cluster_qr + has no tuning parameters and runs no iterations, yet may outperform + k-means and discretization in terms of both quality and speed. + + .. versionchanged:: 1.1 + Added new labeling method 'cluster_qr'. + + degree : float, default=3 + Degree of the polynomial kernel. Ignored by other kernels. + + coef0 : float, default=1 + Zero coefficient for polynomial and sigmoid kernels. + Ignored by other kernels. + + kernel_params : dict of str to any, default=None + Parameters (keyword arguments) and values for kernel passed as + callable object. Ignored by other kernels. + + n_jobs : int, default=None + The number of parallel jobs to run when `affinity='nearest_neighbors'` + or `affinity='precomputed_nearest_neighbors'`. The neighbors search + will be done in parallel. + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + verbose : bool, default=False + Verbosity mode. + + .. versionadded:: 0.24 + + Attributes + ---------- + affinity_matrix_ : array-like of shape (n_samples, n_samples) + Affinity matrix used for clustering. Available only after calling + ``fit``. + + labels_ : ndarray of shape (n_samples,) + Labels of each point + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + sklearn.cluster.KMeans : K-Means clustering. + sklearn.cluster.DBSCAN : Density-Based Spatial Clustering of + Applications with Noise. + + Notes + ----- + A distance matrix for which 0 indicates identical elements and high values + indicate very dissimilar elements can be transformed into an affinity / + similarity matrix that is well-suited for the algorithm by + applying the Gaussian (aka RBF, heat) kernel:: + + np.exp(- dist_matrix ** 2 / (2. * delta ** 2)) + + where ``delta`` is a free parameter representing the width of the Gaussian + kernel. + + An alternative is to take a symmetric version of the k-nearest neighbors + connectivity matrix of the points. + + If the pyamg package is installed, it is used: this greatly + speeds up computation. + + References + ---------- + .. [1] :doi:`Normalized cuts and image segmentation, 2000 + Jianbo Shi, Jitendra Malik + <10.1109/34.868688>` + + .. [2] :doi:`A Tutorial on Spectral Clustering, 2007 + Ulrike von Luxburg + <10.1007/s11222-007-9033-z>` + + .. [3] `Multiclass spectral clustering, 2003 + Stella X. Yu, Jianbo Shi + `_ + + .. [4] :doi:`Toward the Optimal Preconditioned Eigensolver: + Locally Optimal Block Preconditioned Conjugate Gradient Method, 2001 + A. V. Knyazev + SIAM Journal on Scientific Computing 23, no. 2, pp. 517-541. + <10.1137/S1064827500366124>` + + .. [5] :doi:`Simple, direct, and efficient multi-way spectral clustering, 2019 + Anil Damle, Victor Minden, Lexing Ying + <10.1093/imaiai/iay008>` + + Examples + -------- + >>> from sklearn.cluster import SpectralClustering + >>> import numpy as np + >>> X = np.array([[1, 1], [2, 1], [1, 0], + ... [4, 7], [3, 5], [3, 6]]) + >>> clustering = SpectralClustering(n_clusters=2, + ... assign_labels='discretize', + ... random_state=0).fit(X) + >>> clustering.labels_ + array([1, 1, 1, 0, 0, 0]) + >>> clustering + SpectralClustering(assign_labels='discretize', n_clusters=2, + random_state=0) + + For a comparison of Spectral clustering with other clustering algorithms, see + :ref:`sphx_glr_auto_examples_cluster_plot_cluster_comparison.py` + """ + + _parameter_constraints: dict = { + "n_clusters": [Interval(Integral, 1, None, closed="left")], + "eigen_solver": [StrOptions({"arpack", "lobpcg", "amg"}), None], + "n_components": [Interval(Integral, 1, None, closed="left"), None], + "random_state": ["random_state"], + "n_init": [Interval(Integral, 1, None, closed="left")], + "gamma": [Interval(Real, 0, None, closed="left")], + "affinity": [ + callable, + StrOptions( + set(KERNEL_PARAMS) + | {"nearest_neighbors", "precomputed", "precomputed_nearest_neighbors"} + ), + ], + "n_neighbors": [Interval(Integral, 1, None, closed="left")], + "eigen_tol": [ + Interval(Real, 0.0, None, closed="left"), + StrOptions({"auto"}), + ], + "assign_labels": [StrOptions({"kmeans", "discretize", "cluster_qr"})], + "degree": [Interval(Real, 0, None, closed="left")], + "coef0": [Interval(Real, None, None, closed="neither")], + "kernel_params": [dict, None], + "n_jobs": [Integral, None], + "verbose": ["verbose"], + } + + def __init__( + self, + n_clusters=8, + *, + eigen_solver=None, + n_components=None, + random_state=None, + n_init=10, + gamma=1.0, + affinity="rbf", + n_neighbors=10, + eigen_tol="auto", + assign_labels="kmeans", + degree=3, + coef0=1, + kernel_params=None, + n_jobs=None, + verbose=False, + ): + self.n_clusters = n_clusters + self.eigen_solver = eigen_solver + self.n_components = n_components + self.random_state = random_state + self.n_init = n_init + self.gamma = gamma + self.affinity = affinity + self.n_neighbors = n_neighbors + self.eigen_tol = eigen_tol + self.assign_labels = assign_labels + self.degree = degree + self.coef0 = coef0 + self.kernel_params = kernel_params + self.n_jobs = n_jobs + self.verbose = verbose + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Perform spectral clustering from features, or affinity matrix. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) or \ + (n_samples, n_samples) + Training instances to cluster, similarities / affinities between + instances if ``affinity='precomputed'``, or distances between + instances if ``affinity='precomputed_nearest_neighbors``. If a + sparse matrix is provided in a format other than ``csr_matrix``, + ``csc_matrix``, or ``coo_matrix``, it will be converted into a + sparse ``csr_matrix``. + + y : Ignored + Not used, present here for API consistency by convention. + + Returns + ------- + self : object + A fitted instance of the estimator. + """ + X = validate_data( + self, + X, + accept_sparse=["csr", "csc", "coo"], + dtype=np.float64, + ensure_min_samples=2, + ) + allow_squared = self.affinity in [ + "precomputed", + "precomputed_nearest_neighbors", + ] + if X.shape[0] == X.shape[1] and not allow_squared: + warnings.warn( + "The spectral clustering API has changed. ``fit``" + "now constructs an affinity matrix from data. To use" + " a custom affinity matrix, " + "set ``affinity=precomputed``." + ) + + if self.affinity == "nearest_neighbors": + connectivity = kneighbors_graph( + X, n_neighbors=self.n_neighbors, include_self=True, n_jobs=self.n_jobs + ) + self.affinity_matrix_ = 0.5 * (connectivity + connectivity.T) + elif self.affinity == "precomputed_nearest_neighbors": + estimator = NearestNeighbors( + n_neighbors=self.n_neighbors, n_jobs=self.n_jobs, metric="precomputed" + ).fit(X) + connectivity = estimator.kneighbors_graph(X=X, mode="connectivity") + self.affinity_matrix_ = 0.5 * (connectivity + connectivity.T) + elif self.affinity == "precomputed": + self.affinity_matrix_ = X + else: + params = self.kernel_params + if params is None: + params = {} + if not callable(self.affinity): + params["gamma"] = self.gamma + params["degree"] = self.degree + params["coef0"] = self.coef0 + self.affinity_matrix_ = pairwise_kernels( + X, metric=self.affinity, filter_params=True, **params + ) + + random_state = check_random_state(self.random_state) + n_components = ( + self.n_clusters if self.n_components is None else self.n_components + ) + # We now obtain the real valued solution matrix to the + # relaxed Ncut problem, solving the eigenvalue problem + # L_sym x = lambda x and recovering u = D^-1/2 x. + # The first eigenvector is constant only for fully connected graphs + # and should be kept for spectral clustering (drop_first = False) + # See spectral_embedding documentation. + maps = _spectral_embedding( + self.affinity_matrix_, + n_components=n_components, + eigen_solver=self.eigen_solver, + random_state=random_state, + eigen_tol=self.eigen_tol, + drop_first=False, + ) + if self.verbose: + print(f"Computing label assignment using {self.assign_labels}") + + if self.assign_labels == "kmeans": + _, self.labels_, _ = k_means( + maps, + self.n_clusters, + random_state=random_state, + n_init=self.n_init, + verbose=self.verbose, + ) + elif self.assign_labels == "cluster_qr": + self.labels_ = cluster_qr(maps) + else: + self.labels_ = discretize(maps, random_state=random_state) + + return self + + def fit_predict(self, X, y=None): + """Perform spectral clustering on `X` and return cluster labels. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) or \ + (n_samples, n_samples) + Training instances to cluster, similarities / affinities between + instances if ``affinity='precomputed'``, or distances between + instances if ``affinity='precomputed_nearest_neighbors``. If a + sparse matrix is provided in a format other than ``csr_matrix``, + ``csc_matrix``, or ``coo_matrix``, it will be converted into a + sparse ``csr_matrix``. + + y : Ignored + Not used, present here for API consistency by convention. + + Returns + ------- + labels : ndarray of shape (n_samples,) + Cluster labels. + """ + return super().fit_predict(X, y) + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + tags.input_tags.pairwise = self.affinity in [ + "precomputed", + "precomputed_nearest_neighbors", + ] + return tags diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/meson.build b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/meson.build new file mode 100644 index 0000000000000000000000000000000000000000..6c11619f3ca555c58ed43b1d579548d75cf6aea4 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/meson.build @@ -0,0 +1,26 @@ +cluster_extension_metadata = { + '_dbscan_inner': + {'sources': [cython_gen_cpp.process('_dbscan_inner.pyx')]}, + '_hierarchical_fast': + {'sources': [cython_gen_cpp.process('_hierarchical_fast.pyx'), metrics_cython_tree]}, + '_k_means_common': + {'sources': [cython_gen.process('_k_means_common.pyx')], 'dependencies': [openmp_dep]}, + '_k_means_lloyd': + {'sources': [cython_gen.process('_k_means_lloyd.pyx')], 'dependencies': [openmp_dep]}, + '_k_means_elkan': + {'sources': [cython_gen.process('_k_means_elkan.pyx')], 'dependencies': [openmp_dep]}, + '_k_means_minibatch': + {'sources': [cython_gen.process('_k_means_minibatch.pyx')], 'dependencies': [openmp_dep]}, +} + +foreach ext_name, ext_dict : cluster_extension_metadata + py.extension_module( + ext_name, + [ext_dict.get('sources'), utils_cython_tree], + dependencies: [np_dep] + ext_dict.get('dependencies', []), + subdir: 'sklearn/cluster', + install: true + ) +endforeach + +subdir('_hdbscan') diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/common.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/common.py new file mode 100644 index 0000000000000000000000000000000000000000..b1fe047fe230af1c3fbb2ec0b72f3ef20e5aa3aa --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/common.py @@ -0,0 +1,37 @@ +""" +Common utilities for testing clustering. + +""" + +import numpy as np + +############################################################################### +# Generate sample data + + +def generate_clustered_data( + seed=0, n_clusters=3, n_features=2, n_samples_per_cluster=20, std=0.4 +): + prng = np.random.RandomState(seed) + + # the data is voluntary shifted away from zero to check clustering + # algorithm robustness with regards to non centered data + means = ( + np.array( + [ + [1, 1, 1, 0], + [-1, -1, 0, 1], + [1, -1, 1, 1], + [-1, 1, 1, 0], + ] + ) + + 10 + ) + + X = np.empty((0, n_features)) + for i in range(n_clusters): + X = np.r_[ + X, + means[i][:n_features] + std * prng.randn(n_samples_per_cluster, n_features), + ] + return X diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_affinity_propagation.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_affinity_propagation.py new file mode 100644 index 0000000000000000000000000000000000000000..c3138e59111ed849988dd0e6d3433a4bb251e2a1 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_affinity_propagation.py @@ -0,0 +1,321 @@ +""" +Testing for Clustering methods + +""" + +import warnings + +import numpy as np +import pytest + +from sklearn.cluster import AffinityPropagation, affinity_propagation +from sklearn.cluster._affinity_propagation import _equal_similarities_and_preferences +from sklearn.datasets import make_blobs +from sklearn.exceptions import ConvergenceWarning, NotFittedError +from sklearn.metrics import euclidean_distances +from sklearn.utils._testing import assert_allclose, assert_array_equal +from sklearn.utils.fixes import CSR_CONTAINERS + +n_clusters = 3 +centers = np.array([[1, 1], [-1, -1], [1, -1]]) + 10 +X, _ = make_blobs( + n_samples=60, + n_features=2, + centers=centers, + cluster_std=0.4, + shuffle=True, + random_state=0, +) + +# TODO: AffinityPropagation must preserve dtype for its fitted attributes +# and test must be created accordingly to this new behavior. +# For more details, see: https://github.com/scikit-learn/scikit-learn/issues/11000 + + +def test_affinity_propagation(global_random_seed, global_dtype): + """Test consistency of the affinity propagations.""" + S = -euclidean_distances(X.astype(global_dtype, copy=False), squared=True) + preference = np.median(S) * 10 + cluster_centers_indices, labels = affinity_propagation( + S, preference=preference, random_state=global_random_seed + ) + + n_clusters_ = len(cluster_centers_indices) + + assert n_clusters == n_clusters_ + + +def test_affinity_propagation_precomputed(): + """Check equality of precomputed affinity matrix to internally computed affinity + matrix. + """ + S = -euclidean_distances(X, squared=True) + preference = np.median(S) * 10 + af = AffinityPropagation( + preference=preference, affinity="precomputed", random_state=28 + ) + labels_precomputed = af.fit(S).labels_ + + af = AffinityPropagation(preference=preference, verbose=True, random_state=37) + labels = af.fit(X).labels_ + + assert_array_equal(labels, labels_precomputed) + + cluster_centers_indices = af.cluster_centers_indices_ + + n_clusters_ = len(cluster_centers_indices) + assert np.unique(labels).size == n_clusters_ + assert n_clusters == n_clusters_ + + +def test_affinity_propagation_no_copy(): + """Check behaviour of not copying the input data.""" + S = -euclidean_distances(X, squared=True) + S_original = S.copy() + preference = np.median(S) * 10 + assert not np.allclose(S.diagonal(), preference) + + # with copy=True S should not be modified + affinity_propagation(S, preference=preference, copy=True, random_state=0) + assert_allclose(S, S_original) + assert not np.allclose(S.diagonal(), preference) + assert_allclose(S.diagonal(), np.zeros(S.shape[0])) + + # with copy=False S will be modified inplace + affinity_propagation(S, preference=preference, copy=False, random_state=0) + assert_allclose(S.diagonal(), preference) + + # test that copy=True and copy=False lead to the same result + S = S_original.copy() + af = AffinityPropagation(preference=preference, verbose=True, random_state=0) + + labels = af.fit(X).labels_ + _, labels_no_copy = affinity_propagation( + S, preference=preference, copy=False, random_state=74 + ) + assert_array_equal(labels, labels_no_copy) + + +def test_affinity_propagation_affinity_shape(): + """Check the shape of the affinity matrix when using `affinity_propagation.""" + S = -euclidean_distances(X, squared=True) + err_msg = "The matrix of similarities must be a square array" + with pytest.raises(ValueError, match=err_msg): + affinity_propagation(S[:, :-1]) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_affinity_propagation_precomputed_with_sparse_input(csr_container): + err_msg = "Sparse data was passed for X, but dense data is required" + with pytest.raises(TypeError, match=err_msg): + AffinityPropagation(affinity="precomputed").fit(csr_container((3, 3))) + + +def test_affinity_propagation_predict(global_random_seed, global_dtype): + # Test AffinityPropagation.predict + af = AffinityPropagation(affinity="euclidean", random_state=global_random_seed) + X_ = X.astype(global_dtype, copy=False) + labels = af.fit_predict(X_) + labels2 = af.predict(X_) + assert_array_equal(labels, labels2) + + +def test_affinity_propagation_predict_error(): + # Test exception in AffinityPropagation.predict + # Not fitted. + af = AffinityPropagation(affinity="euclidean") + with pytest.raises(NotFittedError): + af.predict(X) + + # Predict not supported when affinity="precomputed". + S = np.dot(X, X.T) + af = AffinityPropagation(affinity="precomputed", random_state=57) + af.fit(S) + with pytest.raises(ValueError, match="expecting 60 features as input"): + af.predict(X) + + +def test_affinity_propagation_fit_non_convergence(global_dtype): + # In case of non-convergence of affinity_propagation(), the cluster + # centers should be an empty array and training samples should be labelled + # as noise (-1) + X = np.array([[0, 0], [1, 1], [-2, -2]], dtype=global_dtype) + + # Force non-convergence by allowing only a single iteration + af = AffinityPropagation(preference=-10, max_iter=1, random_state=82) + + with pytest.warns(ConvergenceWarning): + af.fit(X) + assert_allclose(np.empty((0, 2)), af.cluster_centers_) + assert_array_equal(np.array([-1, -1, -1]), af.labels_) + + +def test_affinity_propagation_equal_mutual_similarities(global_dtype): + X = np.array([[-1, 1], [1, -1]], dtype=global_dtype) + S = -euclidean_distances(X, squared=True) + + # setting preference > similarity + with pytest.warns(UserWarning, match="mutually equal"): + cluster_center_indices, labels = affinity_propagation(S, preference=0) + + # expect every sample to become an exemplar + assert_array_equal([0, 1], cluster_center_indices) + assert_array_equal([0, 1], labels) + + # setting preference < similarity + with pytest.warns(UserWarning, match="mutually equal"): + cluster_center_indices, labels = affinity_propagation(S, preference=-10) + + # expect one cluster, with arbitrary (first) sample as exemplar + assert_array_equal([0], cluster_center_indices) + assert_array_equal([0, 0], labels) + + # setting different preferences + with warnings.catch_warnings(): + warnings.simplefilter("error", UserWarning) + cluster_center_indices, labels = affinity_propagation( + S, preference=[-20, -10], random_state=37 + ) + + # expect one cluster, with highest-preference sample as exemplar + assert_array_equal([1], cluster_center_indices) + assert_array_equal([0, 0], labels) + + +def test_affinity_propagation_predict_non_convergence(global_dtype): + # In case of non-convergence of affinity_propagation(), the cluster + # centers should be an empty array + X = np.array([[0, 0], [1, 1], [-2, -2]], dtype=global_dtype) + + # Force non-convergence by allowing only a single iteration + with pytest.warns(ConvergenceWarning): + af = AffinityPropagation(preference=-10, max_iter=1, random_state=75).fit(X) + + # At prediction time, consider new samples as noise since there are no + # clusters + to_predict = np.array([[2, 2], [3, 3], [4, 4]]) + with pytest.warns(ConvergenceWarning): + y = af.predict(to_predict) + assert_array_equal(np.array([-1, -1, -1]), y) + + +def test_affinity_propagation_non_convergence_regressiontest(global_dtype): + X = np.array( + [[1, 0, 0, 0, 0, 0], [0, 1, 1, 1, 0, 0], [0, 0, 1, 0, 0, 1]], dtype=global_dtype + ) + af = AffinityPropagation(affinity="euclidean", max_iter=2, random_state=34) + msg = ( + "Affinity propagation did not converge, this model may return degenerate" + " cluster centers and labels." + ) + with pytest.warns(ConvergenceWarning, match=msg): + af.fit(X) + + assert_array_equal(np.array([0, 0, 0]), af.labels_) + + +def test_equal_similarities_and_preferences(global_dtype): + # Unequal distances + X = np.array([[0, 0], [1, 1], [-2, -2]], dtype=global_dtype) + S = -euclidean_distances(X, squared=True) + + assert not _equal_similarities_and_preferences(S, np.array(0)) + assert not _equal_similarities_and_preferences(S, np.array([0, 0])) + assert not _equal_similarities_and_preferences(S, np.array([0, 1])) + + # Equal distances + X = np.array([[0, 0], [1, 1]], dtype=global_dtype) + S = -euclidean_distances(X, squared=True) + + # Different preferences + assert not _equal_similarities_and_preferences(S, np.array([0, 1])) + + # Same preferences + assert _equal_similarities_and_preferences(S, np.array([0, 0])) + assert _equal_similarities_and_preferences(S, np.array(0)) + + +def test_affinity_propagation_random_state(): + """Check that different random states lead to different initialisations + by looking at the center locations after two iterations. + """ + centers = [[1, 1], [-1, -1], [1, -1]] + X, labels_true = make_blobs( + n_samples=300, centers=centers, cluster_std=0.5, random_state=0 + ) + # random_state = 0 + ap = AffinityPropagation(convergence_iter=1, max_iter=2, random_state=0) + ap.fit(X) + centers0 = ap.cluster_centers_ + + # random_state = 76 + ap = AffinityPropagation(convergence_iter=1, max_iter=2, random_state=76) + ap.fit(X) + centers76 = ap.cluster_centers_ + # check that the centers have not yet converged to the same solution + assert np.mean((centers0 - centers76) ** 2) > 1 + + +@pytest.mark.parametrize("container", CSR_CONTAINERS + [np.array]) +def test_affinity_propagation_convergence_warning_dense_sparse(container, global_dtype): + """ + Check that having sparse or dense `centers` format should not + influence the convergence. + Non-regression test for gh-13334. + """ + centers = container(np.zeros((1, 10))) + rng = np.random.RandomState(42) + X = rng.rand(40, 10).astype(global_dtype, copy=False) + y = (4 * rng.rand(40)).astype(int) + ap = AffinityPropagation(random_state=46) + ap.fit(X, y) + ap.cluster_centers_ = centers + with warnings.catch_warnings(): + warnings.simplefilter("error", ConvergenceWarning) + assert_array_equal(ap.predict(X), np.zeros(X.shape[0], dtype=int)) + + +# FIXME; this test is broken with different random states, needs to be revisited +def test_correct_clusters(global_dtype): + # Test to fix incorrect clusters due to dtype change + # (non-regression test for issue #10832) + X = np.array( + [[1, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 1]], dtype=global_dtype + ) + afp = AffinityPropagation(preference=1, affinity="precomputed", random_state=0).fit( + X + ) + expected = np.array([0, 1, 1, 2]) + assert_array_equal(afp.labels_, expected) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_sparse_input_for_predict(csr_container): + # Test to make sure sparse inputs are accepted for predict + # (non-regression test for issue #20049) + af = AffinityPropagation(affinity="euclidean", random_state=42) + af.fit(X) + labels = af.predict(csr_container((2, 2))) + assert_array_equal(labels, (2, 2)) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_sparse_input_for_fit_predict(csr_container): + # Test to make sure sparse inputs are accepted for fit_predict + # (non-regression test for issue #20049) + af = AffinityPropagation(affinity="euclidean", random_state=42) + rng = np.random.RandomState(42) + X = csr_container(rng.randint(0, 2, size=(5, 5))) + labels = af.fit_predict(X) + assert_array_equal(labels, (0, 1, 1, 2, 3)) + + +def test_affinity_propagation_equal_points(): + """Make sure we do not assign multiple clusters to equal points. + + Non-regression test for: + https://github.com/scikit-learn/scikit-learn/pull/20043 + """ + X = np.zeros((8, 1)) + af = AffinityPropagation(affinity="euclidean", damping=0.5, random_state=42).fit(X) + assert np.all(af.labels_ == 0) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_bicluster.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_bicluster.py new file mode 100644 index 0000000000000000000000000000000000000000..ebc845a7bf262c60cf9f039e5ce021d841bdf4d4 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_bicluster.py @@ -0,0 +1,264 @@ +"""Testing for Spectral Biclustering methods""" + +import numpy as np +import pytest +from scipy.sparse import issparse + +from sklearn.base import BaseEstimator, BiclusterMixin +from sklearn.cluster import SpectralBiclustering, SpectralCoclustering +from sklearn.cluster._bicluster import ( + _bistochastic_normalize, + _log_normalize, + _scale_normalize, +) +from sklearn.datasets import make_biclusters, make_checkerboard +from sklearn.metrics import consensus_score, v_measure_score +from sklearn.model_selection import ParameterGrid +from sklearn.utils._testing import ( + assert_almost_equal, + assert_array_almost_equal, + assert_array_equal, +) +from sklearn.utils.fixes import CSR_CONTAINERS + + +class MockBiclustering(BiclusterMixin, BaseEstimator): + # Mock object for testing get_submatrix. + def __init__(self): + pass + + def get_indices(self, i): + # Overridden to reproduce old get_submatrix test. + return ( + np.where([True, True, False, False, True])[0], + np.where([False, False, True, True])[0], + ) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_get_submatrix(csr_container): + data = np.arange(20).reshape(5, 4) + model = MockBiclustering() + + for X in (data, csr_container(data), data.tolist()): + submatrix = model.get_submatrix(0, X) + if issparse(submatrix): + submatrix = submatrix.toarray() + assert_array_equal(submatrix, [[2, 3], [6, 7], [18, 19]]) + submatrix[:] = -1 + if issparse(X): + X = X.toarray() + assert np.all(X != -1) + + +def _test_shape_indices(model): + # Test get_shape and get_indices on fitted model. + for i in range(model.n_clusters): + m, n = model.get_shape(i) + i_ind, j_ind = model.get_indices(i) + assert len(i_ind) == m + assert len(j_ind) == n + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_spectral_coclustering(global_random_seed, csr_container): + # Test Dhillon's Spectral CoClustering on a simple problem. + param_grid = { + "svd_method": ["randomized", "arpack"], + "n_svd_vecs": [None, 20], + "mini_batch": [False, True], + "init": ["k-means++"], + "n_init": [10], + } + S, rows, cols = make_biclusters( + (30, 30), 3, noise=0.1, random_state=global_random_seed + ) + S -= S.min() # needs to be nonnegative before making it sparse + S = np.where(S < 1, 0, S) # threshold some values + for mat in (S, csr_container(S)): + for kwargs in ParameterGrid(param_grid): + model = SpectralCoclustering( + n_clusters=3, random_state=global_random_seed, **kwargs + ) + model.fit(mat) + + assert model.rows_.shape == (3, 30) + assert_array_equal(model.rows_.sum(axis=0), np.ones(30)) + assert_array_equal(model.columns_.sum(axis=0), np.ones(30)) + assert consensus_score(model.biclusters_, (rows, cols)) == 1 + + _test_shape_indices(model) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_spectral_biclustering(global_random_seed, csr_container): + # Test Kluger methods on a checkerboard dataset. + S, rows, cols = make_checkerboard( + (30, 30), 3, noise=0.5, random_state=global_random_seed + ) + + non_default_params = { + "method": ["scale", "log"], + "svd_method": ["arpack"], + "n_svd_vecs": [20], + "mini_batch": [True], + } + + for mat in (S, csr_container(S)): + for param_name, param_values in non_default_params.items(): + for param_value in param_values: + model = SpectralBiclustering( + n_clusters=3, + n_init=3, + init="k-means++", + random_state=global_random_seed, + ) + model.set_params(**dict([(param_name, param_value)])) + + if issparse(mat) and model.get_params().get("method") == "log": + # cannot take log of sparse matrix + with pytest.raises(ValueError): + model.fit(mat) + continue + else: + model.fit(mat) + + assert model.rows_.shape == (9, 30) + assert model.columns_.shape == (9, 30) + assert_array_equal(model.rows_.sum(axis=0), np.repeat(3, 30)) + assert_array_equal(model.columns_.sum(axis=0), np.repeat(3, 30)) + assert consensus_score(model.biclusters_, (rows, cols)) == 1 + + _test_shape_indices(model) + + +def _do_scale_test(scaled): + """Check that rows sum to one constant, and columns to another.""" + row_sum = scaled.sum(axis=1) + col_sum = scaled.sum(axis=0) + if issparse(scaled): + row_sum = np.asarray(row_sum).squeeze() + col_sum = np.asarray(col_sum).squeeze() + assert_array_almost_equal(row_sum, np.tile(row_sum.mean(), 100), decimal=1) + assert_array_almost_equal(col_sum, np.tile(col_sum.mean(), 100), decimal=1) + + +def _do_bistochastic_test(scaled): + """Check that rows and columns sum to the same constant.""" + _do_scale_test(scaled) + assert_almost_equal(scaled.sum(axis=0).mean(), scaled.sum(axis=1).mean(), decimal=1) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_scale_normalize(global_random_seed, csr_container): + generator = np.random.RandomState(global_random_seed) + X = generator.rand(100, 100) + for mat in (X, csr_container(X)): + scaled, _, _ = _scale_normalize(mat) + _do_scale_test(scaled) + if issparse(mat): + assert issparse(scaled) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_bistochastic_normalize(global_random_seed, csr_container): + generator = np.random.RandomState(global_random_seed) + X = generator.rand(100, 100) + for mat in (X, csr_container(X)): + scaled = _bistochastic_normalize(mat) + _do_bistochastic_test(scaled) + if issparse(mat): + assert issparse(scaled) + + +def test_log_normalize(global_random_seed): + # adding any constant to a log-scaled matrix should make it + # bistochastic + generator = np.random.RandomState(global_random_seed) + mat = generator.rand(100, 100) + scaled = _log_normalize(mat) + 1 + _do_bistochastic_test(scaled) + + +def test_fit_best_piecewise(global_random_seed): + model = SpectralBiclustering(random_state=global_random_seed) + vectors = np.array([[0, 0, 0, 1, 1, 1], [2, 2, 2, 3, 3, 3], [0, 1, 2, 3, 4, 5]]) + best = model._fit_best_piecewise(vectors, n_best=2, n_clusters=2) + assert_array_equal(best, vectors[:2]) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_project_and_cluster(global_random_seed, csr_container): + model = SpectralBiclustering(random_state=global_random_seed) + data = np.array([[1, 1, 1], [1, 1, 1], [3, 6, 3], [3, 6, 3]]) + vectors = np.array([[1, 0], [0, 1], [0, 0]]) + for mat in (data, csr_container(data)): + labels = model._project_and_cluster(mat, vectors, n_clusters=2) + assert_almost_equal(v_measure_score(labels, [0, 0, 1, 1]), 1.0) + + +def test_perfect_checkerboard(global_random_seed): + # XXX Previously failed on build bot (not reproducible) + model = SpectralBiclustering( + 3, svd_method="arpack", random_state=global_random_seed + ) + + S, rows, cols = make_checkerboard( + (30, 30), 3, noise=0, random_state=global_random_seed + ) + model.fit(S) + assert consensus_score(model.biclusters_, (rows, cols)) == 1 + + S, rows, cols = make_checkerboard( + (40, 30), 3, noise=0, random_state=global_random_seed + ) + model.fit(S) + assert consensus_score(model.biclusters_, (rows, cols)) == 1 + + S, rows, cols = make_checkerboard( + (30, 40), 3, noise=0, random_state=global_random_seed + ) + model.fit(S) + assert consensus_score(model.biclusters_, (rows, cols)) == 1 + + +@pytest.mark.parametrize( + "params, type_err, err_msg", + [ + ( + {"n_clusters": 6}, + ValueError, + "n_clusters should be <= n_samples=5", + ), + ( + {"n_clusters": (3, 3, 3)}, + ValueError, + "Incorrect parameter n_clusters", + ), + ( + {"n_clusters": (3, 6)}, + ValueError, + "Incorrect parameter n_clusters", + ), + ( + {"n_components": 3, "n_best": 4}, + ValueError, + "n_best=4 must be <= n_components=3", + ), + ], +) +def test_spectralbiclustering_parameter_validation(params, type_err, err_msg): + """Check parameters validation in `SpectralBiClustering`""" + data = np.arange(25).reshape((5, 5)) + model = SpectralBiclustering(**params) + with pytest.raises(type_err, match=err_msg): + model.fit(data) + + +@pytest.mark.parametrize("est", (SpectralBiclustering(), SpectralCoclustering())) +def test_n_features_in_(est): + X, _, _ = make_biclusters((3, 3), 3, random_state=0) + + assert not hasattr(est, "n_features_in_") + est.fit(X) + assert est.n_features_in_ == 3 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_birch.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_birch.py new file mode 100644 index 0000000000000000000000000000000000000000..bc87934adaecdb507126097e2de945c677587bee --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_birch.py @@ -0,0 +1,250 @@ +""" +Tests for the birch clustering algorithm. +""" + +import numpy as np +import pytest + +from sklearn.cluster import AgglomerativeClustering, Birch +from sklearn.cluster.tests.common import generate_clustered_data +from sklearn.datasets import make_blobs +from sklearn.exceptions import ConvergenceWarning +from sklearn.metrics import pairwise_distances_argmin, v_measure_score +from sklearn.utils._testing import assert_allclose, assert_array_equal +from sklearn.utils.fixes import CSR_CONTAINERS + + +def test_n_samples_leaves_roots(global_random_seed, global_dtype): + # Sanity check for the number of samples in leaves and roots + X, y = make_blobs(n_samples=10, random_state=global_random_seed) + X = X.astype(global_dtype, copy=False) + brc = Birch() + brc.fit(X) + n_samples_root = sum([sc.n_samples_ for sc in brc.root_.subclusters_]) + n_samples_leaves = sum( + [sc.n_samples_ for leaf in brc._get_leaves() for sc in leaf.subclusters_] + ) + assert n_samples_leaves == X.shape[0] + assert n_samples_root == X.shape[0] + + +def test_partial_fit(global_random_seed, global_dtype): + # Test that fit is equivalent to calling partial_fit multiple times + X, y = make_blobs(n_samples=100, random_state=global_random_seed) + X = X.astype(global_dtype, copy=False) + brc = Birch(n_clusters=3) + brc.fit(X) + brc_partial = Birch(n_clusters=None) + brc_partial.partial_fit(X[:50]) + brc_partial.partial_fit(X[50:]) + assert_allclose(brc_partial.subcluster_centers_, brc.subcluster_centers_) + + # Test that same global labels are obtained after calling partial_fit + # with None + brc_partial.set_params(n_clusters=3) + brc_partial.partial_fit(None) + assert_array_equal(brc_partial.subcluster_labels_, brc.subcluster_labels_) + + +def test_birch_predict(global_random_seed, global_dtype): + # Test the predict method predicts the nearest centroid. + rng = np.random.RandomState(global_random_seed) + X = generate_clustered_data(n_clusters=3, n_features=3, n_samples_per_cluster=10) + X = X.astype(global_dtype, copy=False) + + # n_samples * n_samples_per_cluster + shuffle_indices = np.arange(30) + rng.shuffle(shuffle_indices) + X_shuffle = X[shuffle_indices, :] + brc = Birch(n_clusters=4, threshold=1.0) + brc.fit(X_shuffle) + + # Birch must preserve inputs' dtype + assert brc.subcluster_centers_.dtype == global_dtype + + assert_array_equal(brc.labels_, brc.predict(X_shuffle)) + centroids = brc.subcluster_centers_ + nearest_centroid = brc.subcluster_labels_[ + pairwise_distances_argmin(X_shuffle, centroids) + ] + assert_allclose(v_measure_score(nearest_centroid, brc.labels_), 1.0) + + +def test_n_clusters(global_random_seed, global_dtype): + # Test that n_clusters param works properly + X, y = make_blobs(n_samples=100, centers=10, random_state=global_random_seed) + X = X.astype(global_dtype, copy=False) + brc1 = Birch(n_clusters=10) + brc1.fit(X) + assert len(brc1.subcluster_centers_) > 10 + assert len(np.unique(brc1.labels_)) == 10 + + # Test that n_clusters = Agglomerative Clustering gives + # the same results. + gc = AgglomerativeClustering(n_clusters=10) + brc2 = Birch(n_clusters=gc) + brc2.fit(X) + assert_array_equal(brc1.subcluster_labels_, brc2.subcluster_labels_) + assert_array_equal(brc1.labels_, brc2.labels_) + + # Test that a small number of clusters raises a warning. + brc4 = Birch(threshold=10000.0) + with pytest.warns(ConvergenceWarning): + brc4.fit(X) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_sparse_X(global_random_seed, global_dtype, csr_container): + # Test that sparse and dense data give same results + X, y = make_blobs(n_samples=100, centers=10, random_state=global_random_seed) + X = X.astype(global_dtype, copy=False) + brc = Birch(n_clusters=10) + brc.fit(X) + + csr = csr_container(X) + brc_sparse = Birch(n_clusters=10) + brc_sparse.fit(csr) + + # Birch must preserve inputs' dtype + assert brc_sparse.subcluster_centers_.dtype == global_dtype + + assert_array_equal(brc.labels_, brc_sparse.labels_) + assert_allclose(brc.subcluster_centers_, brc_sparse.subcluster_centers_) + + +def test_partial_fit_second_call_error_checks(): + # second partial fit calls will error when n_features is not consistent + # with the first call + X, y = make_blobs(n_samples=100) + brc = Birch(n_clusters=3) + brc.partial_fit(X, y) + + msg = "X has 1 features, but Birch is expecting 2 features" + with pytest.raises(ValueError, match=msg): + brc.partial_fit(X[:, [0]], y) + + +def check_branching_factor(node, branching_factor): + subclusters = node.subclusters_ + assert branching_factor >= len(subclusters) + for cluster in subclusters: + if cluster.child_: + check_branching_factor(cluster.child_, branching_factor) + + +def test_branching_factor(global_random_seed, global_dtype): + # Test that nodes have at max branching_factor number of subclusters + X, y = make_blobs(random_state=global_random_seed) + X = X.astype(global_dtype, copy=False) + branching_factor = 9 + + # Purposefully set a low threshold to maximize the subclusters. + brc = Birch(n_clusters=None, branching_factor=branching_factor, threshold=0.01) + brc.fit(X) + check_branching_factor(brc.root_, branching_factor) + brc = Birch(n_clusters=3, branching_factor=branching_factor, threshold=0.01) + brc.fit(X) + check_branching_factor(brc.root_, branching_factor) + + +def check_threshold(birch_instance, threshold): + """Use the leaf linked list for traversal""" + current_leaf = birch_instance.dummy_leaf_.next_leaf_ + while current_leaf: + subclusters = current_leaf.subclusters_ + for sc in subclusters: + assert threshold >= sc.radius + current_leaf = current_leaf.next_leaf_ + + +def test_threshold(global_random_seed, global_dtype): + # Test that the leaf subclusters have a threshold lesser than radius + X, y = make_blobs(n_samples=80, centers=4, random_state=global_random_seed) + X = X.astype(global_dtype, copy=False) + brc = Birch(threshold=0.5, n_clusters=None) + brc.fit(X) + check_threshold(brc, 0.5) + + brc = Birch(threshold=5.0, n_clusters=None) + brc.fit(X) + check_threshold(brc, 5.0) + + +def test_birch_n_clusters_long_int(): + # Check that birch supports n_clusters with np.int64 dtype, for instance + # coming from np.arange. #16484 + X, _ = make_blobs(random_state=0) + n_clusters = np.int64(5) + Birch(n_clusters=n_clusters).fit(X) + + +def test_feature_names_out(): + """Check `get_feature_names_out` for `Birch`.""" + X, _ = make_blobs(n_samples=80, n_features=4, random_state=0) + brc = Birch(n_clusters=4) + brc.fit(X) + n_clusters = brc.subcluster_centers_.shape[0] + + names_out = brc.get_feature_names_out() + assert_array_equal([f"birch{i}" for i in range(n_clusters)], names_out) + + +def test_transform_match_across_dtypes(global_random_seed): + X, _ = make_blobs(n_samples=80, n_features=4, random_state=global_random_seed) + brc = Birch(n_clusters=4, threshold=1.1) + Y_64 = brc.fit_transform(X) + Y_32 = brc.fit_transform(X.astype(np.float32)) + + assert_allclose(Y_64, Y_32, atol=1e-6) + + +def test_subcluster_dtype(global_dtype): + X = make_blobs(n_samples=80, n_features=4, random_state=0)[0].astype( + global_dtype, copy=False + ) + brc = Birch(n_clusters=4) + assert brc.fit(X).subcluster_centers_.dtype == global_dtype + + +def test_both_subclusters_updated(): + """Check that both subclusters are updated when a node a split, even when there are + duplicated data points. Non-regression test for #23269. + """ + + X = np.array( + [ + [-2.6192791, -1.5053215], + [-2.9993038, -1.6863596], + [-2.3724914, -1.3438171], + [-2.336792, -1.3417323], + [-2.4089134, -1.3290224], + [-2.3724914, -1.3438171], + [-3.364009, -1.8846745], + [-2.3724914, -1.3438171], + [-2.617677, -1.5003285], + [-2.2960556, -1.3260119], + [-2.3724914, -1.3438171], + [-2.5459878, -1.4533926], + [-2.25979, -1.3003055], + [-2.4089134, -1.3290224], + [-2.3724914, -1.3438171], + [-2.4089134, -1.3290224], + [-2.5459878, -1.4533926], + [-2.3724914, -1.3438171], + [-2.9720619, -1.7058647], + [-2.336792, -1.3417323], + [-2.3724914, -1.3438171], + ], + dtype=np.float32, + ) + + # no error + Birch(branching_factor=5, threshold=1e-5, n_clusters=None).fit(X) + + +# TODO(1.8): Remove +def test_birch_copy_deprecated(): + X, _ = make_blobs(n_samples=80, n_features=4, random_state=0) + brc = Birch(n_clusters=4, copy=True) + with pytest.warns(FutureWarning, match="`copy` was deprecated"): + brc.fit(X) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_bisect_k_means.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_bisect_k_means.py new file mode 100644 index 0000000000000000000000000000000000000000..799ddbc086ce0a14397fe5cb4aef607903c01228 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_bisect_k_means.py @@ -0,0 +1,158 @@ +import numpy as np +import pytest + +from sklearn.cluster import BisectingKMeans +from sklearn.metrics import v_measure_score +from sklearn.utils._testing import assert_allclose, assert_array_equal +from sklearn.utils.fixes import CSR_CONTAINERS + + +@pytest.mark.parametrize("bisecting_strategy", ["biggest_inertia", "largest_cluster"]) +@pytest.mark.parametrize("init", ["k-means++", "random"]) +def test_three_clusters(bisecting_strategy, init): + """Tries to perform bisect k-means for three clusters to check + if splitting data is performed correctly. + """ + X = np.array( + [[1, 1], [10, 1], [3, 1], [10, 0], [2, 1], [10, 2], [10, 8], [10, 9], [10, 10]] + ) + bisect_means = BisectingKMeans( + n_clusters=3, + random_state=0, + bisecting_strategy=bisecting_strategy, + init=init, + ) + bisect_means.fit(X) + + expected_centers = [[2, 1], [10, 1], [10, 9]] + expected_labels = [0, 1, 0, 1, 0, 1, 2, 2, 2] + + assert_allclose( + sorted(expected_centers), sorted(bisect_means.cluster_centers_.tolist()) + ) + assert_allclose(v_measure_score(expected_labels, bisect_means.labels_), 1.0) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_sparse(csr_container): + """Test Bisecting K-Means with sparse data. + + Checks if labels and centers are the same between dense and sparse. + """ + + rng = np.random.RandomState(0) + + X = rng.rand(20, 2) + X[X < 0.8] = 0 + X_csr = csr_container(X) + + bisect_means = BisectingKMeans(n_clusters=3, random_state=0) + + bisect_means.fit(X_csr) + sparse_centers = bisect_means.cluster_centers_ + + bisect_means.fit(X) + normal_centers = bisect_means.cluster_centers_ + + # Check if results is the same for dense and sparse data + assert_allclose(normal_centers, sparse_centers, atol=1e-8) + + +@pytest.mark.parametrize("n_clusters", [4, 5]) +def test_n_clusters(n_clusters): + """Test if resulting labels are in range [0, n_clusters - 1].""" + + rng = np.random.RandomState(0) + X = rng.rand(10, 2) + + bisect_means = BisectingKMeans(n_clusters=n_clusters, random_state=0) + bisect_means.fit(X) + + assert_array_equal(np.unique(bisect_means.labels_), np.arange(n_clusters)) + + +def test_one_cluster(): + """Test single cluster.""" + + X = np.array([[1, 2], [10, 2], [10, 8]]) + + bisect_means = BisectingKMeans(n_clusters=1, random_state=0).fit(X) + + # All labels from fit or predict should be equal 0 + assert all(bisect_means.labels_ == 0) + assert all(bisect_means.predict(X) == 0) + + assert_allclose(bisect_means.cluster_centers_, X.mean(axis=0).reshape(1, -1)) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS + [None]) +def test_fit_predict(csr_container): + """Check if labels from fit(X) method are same as from fit(X).predict(X).""" + rng = np.random.RandomState(0) + + X = rng.rand(10, 2) + + if csr_container is not None: + X[X < 0.8] = 0 + X = csr_container(X) + + bisect_means = BisectingKMeans(n_clusters=3, random_state=0) + bisect_means.fit(X) + + assert_array_equal(bisect_means.labels_, bisect_means.predict(X)) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS + [None]) +def test_dtype_preserved(csr_container, global_dtype): + """Check that centers dtype is the same as input data dtype.""" + rng = np.random.RandomState(0) + X = rng.rand(10, 2).astype(global_dtype, copy=False) + + if csr_container is not None: + X[X < 0.8] = 0 + X = csr_container(X) + + km = BisectingKMeans(n_clusters=3, random_state=0) + km.fit(X) + + assert km.cluster_centers_.dtype == global_dtype + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS + [None]) +def test_float32_float64_equivalence(csr_container): + """Check that the results are the same between float32 and float64.""" + rng = np.random.RandomState(0) + X = rng.rand(10, 2) + + if csr_container is not None: + X[X < 0.8] = 0 + X = csr_container(X) + + km64 = BisectingKMeans(n_clusters=3, random_state=0).fit(X) + km32 = BisectingKMeans(n_clusters=3, random_state=0).fit(X.astype(np.float32)) + + assert_allclose(km32.cluster_centers_, km64.cluster_centers_) + assert_array_equal(km32.labels_, km64.labels_) + + +@pytest.mark.parametrize("algorithm", ("lloyd", "elkan")) +def test_no_crash_on_empty_bisections(algorithm): + # Non-regression test for: + # https://github.com/scikit-learn/scikit-learn/issues/27081 + rng = np.random.RandomState(0) + X_train = rng.rand(3000, 10) + bkm = BisectingKMeans(n_clusters=10, algorithm=algorithm).fit(X_train) + + # predict on scaled data to trigger pathologic case + # where the inner mask leads to empty bisections. + X_test = 50 * rng.rand(100, 10) + labels = bkm.predict(X_test) # should not crash with idiv by 0 + assert np.isin(np.unique(labels), np.arange(10)).all() + + +def test_one_feature(): + # Check that no error is raised when there is only one feature + # Non-regression test for: + # https://github.com/scikit-learn/scikit-learn/issues/27236 + X = np.random.normal(size=(128, 1)) + BisectingKMeans(bisecting_strategy="biggest_inertia", random_state=0).fit(X) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_dbscan.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_dbscan.py new file mode 100644 index 0000000000000000000000000000000000000000..556f89312d2fc87ab962ab84551f4941ec8b359b --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_dbscan.py @@ -0,0 +1,434 @@ +""" +Tests for DBSCAN clustering algorithm +""" + +import pickle +import warnings + +import numpy as np +import pytest +from scipy.spatial import distance + +from sklearn.cluster import DBSCAN, dbscan +from sklearn.cluster.tests.common import generate_clustered_data +from sklearn.metrics.pairwise import pairwise_distances +from sklearn.neighbors import NearestNeighbors +from sklearn.utils._testing import assert_array_equal +from sklearn.utils.fixes import CSR_CONTAINERS, LIL_CONTAINERS + +n_clusters = 3 +X = generate_clustered_data(n_clusters=n_clusters) + + +def test_dbscan_similarity(): + # Tests the DBSCAN algorithm with a similarity array. + # Parameters chosen specifically for this task. + eps = 0.15 + min_samples = 10 + # Compute similarities + D = distance.squareform(distance.pdist(X)) + D /= np.max(D) + # Compute DBSCAN + core_samples, labels = dbscan( + D, metric="precomputed", eps=eps, min_samples=min_samples + ) + # number of clusters, ignoring noise if present + n_clusters_1 = len(set(labels)) - (1 if -1 in labels else 0) + + assert n_clusters_1 == n_clusters + + db = DBSCAN(metric="precomputed", eps=eps, min_samples=min_samples) + labels = db.fit(D).labels_ + + n_clusters_2 = len(set(labels)) - int(-1 in labels) + assert n_clusters_2 == n_clusters + + +def test_dbscan_feature(): + # Tests the DBSCAN algorithm with a feature vector array. + # Parameters chosen specifically for this task. + # Different eps to other test, because distance is not normalised. + eps = 0.8 + min_samples = 10 + metric = "euclidean" + # Compute DBSCAN + # parameters chosen for task + core_samples, labels = dbscan(X, metric=metric, eps=eps, min_samples=min_samples) + + # number of clusters, ignoring noise if present + n_clusters_1 = len(set(labels)) - int(-1 in labels) + assert n_clusters_1 == n_clusters + + db = DBSCAN(metric=metric, eps=eps, min_samples=min_samples) + labels = db.fit(X).labels_ + + n_clusters_2 = len(set(labels)) - int(-1 in labels) + assert n_clusters_2 == n_clusters + + +@pytest.mark.parametrize("lil_container", LIL_CONTAINERS) +def test_dbscan_sparse(lil_container): + core_sparse, labels_sparse = dbscan(lil_container(X), eps=0.8, min_samples=10) + core_dense, labels_dense = dbscan(X, eps=0.8, min_samples=10) + assert_array_equal(core_dense, core_sparse) + assert_array_equal(labels_dense, labels_sparse) + + +@pytest.mark.parametrize("include_self", [False, True]) +def test_dbscan_sparse_precomputed(include_self): + D = pairwise_distances(X) + nn = NearestNeighbors(radius=0.9).fit(X) + X_ = X if include_self else None + D_sparse = nn.radius_neighbors_graph(X=X_, mode="distance") + # Ensure it is sparse not merely on diagonals: + assert D_sparse.nnz < D.shape[0] * (D.shape[0] - 1) + core_sparse, labels_sparse = dbscan( + D_sparse, eps=0.8, min_samples=10, metric="precomputed" + ) + core_dense, labels_dense = dbscan(D, eps=0.8, min_samples=10, metric="precomputed") + assert_array_equal(core_dense, core_sparse) + assert_array_equal(labels_dense, labels_sparse) + + +def test_dbscan_sparse_precomputed_different_eps(): + # test that precomputed neighbors graph is filtered if computed with + # a radius larger than DBSCAN's eps. + lower_eps = 0.2 + nn = NearestNeighbors(radius=lower_eps).fit(X) + D_sparse = nn.radius_neighbors_graph(X, mode="distance") + dbscan_lower = dbscan(D_sparse, eps=lower_eps, metric="precomputed") + + higher_eps = lower_eps + 0.7 + nn = NearestNeighbors(radius=higher_eps).fit(X) + D_sparse = nn.radius_neighbors_graph(X, mode="distance") + dbscan_higher = dbscan(D_sparse, eps=lower_eps, metric="precomputed") + + assert_array_equal(dbscan_lower[0], dbscan_higher[0]) + assert_array_equal(dbscan_lower[1], dbscan_higher[1]) + + +@pytest.mark.parametrize("metric", ["precomputed", "minkowski"]) +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS + [None]) +def test_dbscan_input_not_modified(metric, csr_container): + # test that the input is not modified by dbscan + X = np.random.RandomState(0).rand(10, 10) + X = csr_container(X) if csr_container is not None else X + X_copy = X.copy() + dbscan(X, metric=metric) + + if csr_container is not None: + assert_array_equal(X.toarray(), X_copy.toarray()) + else: + assert_array_equal(X, X_copy) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_dbscan_input_not_modified_precomputed_sparse_nodiag(csr_container): + """Check that we don't modify in-place the pre-computed sparse matrix. + + Non-regression test for: + https://github.com/scikit-learn/scikit-learn/issues/27508 + """ + X = np.random.RandomState(0).rand(10, 10) + # Add zeros on the diagonal that will be implicit when creating + # the sparse matrix. If `X` is modified in-place, the zeros from + # the diagonal will be made explicit. + np.fill_diagonal(X, 0) + X = csr_container(X) + assert all(row != col for row, col in zip(*X.nonzero())) + X_copy = X.copy() + dbscan(X, metric="precomputed") + # Make sure that we did not modify `X` in-place even by creating + # explicit 0s values. + assert X.nnz == X_copy.nnz + assert_array_equal(X.toarray(), X_copy.toarray()) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_dbscan_no_core_samples(csr_container): + rng = np.random.RandomState(0) + X = rng.rand(40, 10) + X[X < 0.8] = 0 + + for X_ in [X, csr_container(X)]: + db = DBSCAN(min_samples=6).fit(X_) + assert_array_equal(db.components_, np.empty((0, X_.shape[1]))) + assert_array_equal(db.labels_, -1) + assert db.core_sample_indices_.shape == (0,) + + +def test_dbscan_callable(): + # Tests the DBSCAN algorithm with a callable metric. + # Parameters chosen specifically for this task. + # Different eps to other test, because distance is not normalised. + eps = 0.8 + min_samples = 10 + # metric is the function reference, not the string key. + metric = distance.euclidean + # Compute DBSCAN + # parameters chosen for task + core_samples, labels = dbscan( + X, metric=metric, eps=eps, min_samples=min_samples, algorithm="ball_tree" + ) + + # number of clusters, ignoring noise if present + n_clusters_1 = len(set(labels)) - int(-1 in labels) + assert n_clusters_1 == n_clusters + + db = DBSCAN(metric=metric, eps=eps, min_samples=min_samples, algorithm="ball_tree") + labels = db.fit(X).labels_ + + n_clusters_2 = len(set(labels)) - int(-1 in labels) + assert n_clusters_2 == n_clusters + + +def test_dbscan_metric_params(): + # Tests that DBSCAN works with the metrics_params argument. + eps = 0.8 + min_samples = 10 + p = 1 + + # Compute DBSCAN with metric_params arg + + with warnings.catch_warnings(record=True) as warns: + db = DBSCAN( + metric="minkowski", + metric_params={"p": p}, + eps=eps, + p=None, + min_samples=min_samples, + algorithm="ball_tree", + ).fit(X) + assert not warns, warns[0].message + core_sample_1, labels_1 = db.core_sample_indices_, db.labels_ + + # Test that sample labels are the same as passing Minkowski 'p' directly + db = DBSCAN( + metric="minkowski", eps=eps, min_samples=min_samples, algorithm="ball_tree", p=p + ).fit(X) + core_sample_2, labels_2 = db.core_sample_indices_, db.labels_ + + assert_array_equal(core_sample_1, core_sample_2) + assert_array_equal(labels_1, labels_2) + + # Minkowski with p=1 should be equivalent to Manhattan distance + db = DBSCAN( + metric="manhattan", eps=eps, min_samples=min_samples, algorithm="ball_tree" + ).fit(X) + core_sample_3, labels_3 = db.core_sample_indices_, db.labels_ + + assert_array_equal(core_sample_1, core_sample_3) + assert_array_equal(labels_1, labels_3) + + with pytest.warns( + SyntaxWarning, + match=( + "Parameter p is found in metric_params. " + "The corresponding parameter from __init__ " + "is ignored." + ), + ): + # Test that checks p is ignored in favor of metric_params={'p': } + db = DBSCAN( + metric="minkowski", + metric_params={"p": p}, + eps=eps, + p=p + 1, + min_samples=min_samples, + algorithm="ball_tree", + ).fit(X) + core_sample_4, labels_4 = db.core_sample_indices_, db.labels_ + + assert_array_equal(core_sample_1, core_sample_4) + assert_array_equal(labels_1, labels_4) + + +def test_dbscan_balltree(): + # Tests the DBSCAN algorithm with balltree for neighbor calculation. + eps = 0.8 + min_samples = 10 + + D = pairwise_distances(X) + core_samples, labels = dbscan( + D, metric="precomputed", eps=eps, min_samples=min_samples + ) + + # number of clusters, ignoring noise if present + n_clusters_1 = len(set(labels)) - int(-1 in labels) + assert n_clusters_1 == n_clusters + + db = DBSCAN(p=2.0, eps=eps, min_samples=min_samples, algorithm="ball_tree") + labels = db.fit(X).labels_ + + n_clusters_2 = len(set(labels)) - int(-1 in labels) + assert n_clusters_2 == n_clusters + + db = DBSCAN(p=2.0, eps=eps, min_samples=min_samples, algorithm="kd_tree") + labels = db.fit(X).labels_ + + n_clusters_3 = len(set(labels)) - int(-1 in labels) + assert n_clusters_3 == n_clusters + + db = DBSCAN(p=1.0, eps=eps, min_samples=min_samples, algorithm="ball_tree") + labels = db.fit(X).labels_ + + n_clusters_4 = len(set(labels)) - int(-1 in labels) + assert n_clusters_4 == n_clusters + + db = DBSCAN(leaf_size=20, eps=eps, min_samples=min_samples, algorithm="ball_tree") + labels = db.fit(X).labels_ + + n_clusters_5 = len(set(labels)) - int(-1 in labels) + assert n_clusters_5 == n_clusters + + +def test_input_validation(): + # DBSCAN.fit should accept a list of lists. + X = [[1.0, 2.0], [3.0, 4.0]] + DBSCAN().fit(X) # must not raise exception + + +def test_pickle(): + obj = DBSCAN() + s = pickle.dumps(obj) + assert type(pickle.loads(s)) is obj.__class__ + + +def test_boundaries(): + # ensure min_samples is inclusive of core point + core, _ = dbscan([[0], [1]], eps=2, min_samples=2) + assert 0 in core + # ensure eps is inclusive of circumference + core, _ = dbscan([[0], [1], [1]], eps=1, min_samples=2) + assert 0 in core + core, _ = dbscan([[0], [1], [1]], eps=0.99, min_samples=2) + assert 0 not in core + + +def test_weighted_dbscan(global_random_seed): + # ensure sample_weight is validated + with pytest.raises(ValueError): + dbscan([[0], [1]], sample_weight=[2]) + with pytest.raises(ValueError): + dbscan([[0], [1]], sample_weight=[2, 3, 4]) + + # ensure sample_weight has an effect + assert_array_equal([], dbscan([[0], [1]], sample_weight=None, min_samples=6)[0]) + assert_array_equal([], dbscan([[0], [1]], sample_weight=[5, 5], min_samples=6)[0]) + assert_array_equal([0], dbscan([[0], [1]], sample_weight=[6, 5], min_samples=6)[0]) + assert_array_equal( + [0, 1], dbscan([[0], [1]], sample_weight=[6, 6], min_samples=6)[0] + ) + + # points within eps of each other: + assert_array_equal( + [0, 1], dbscan([[0], [1]], eps=1.5, sample_weight=[5, 1], min_samples=6)[0] + ) + # and effect of non-positive and non-integer sample_weight: + assert_array_equal( + [], dbscan([[0], [1]], sample_weight=[5, 0], eps=1.5, min_samples=6)[0] + ) + assert_array_equal( + [0, 1], dbscan([[0], [1]], sample_weight=[5.9, 0.1], eps=1.5, min_samples=6)[0] + ) + assert_array_equal( + [0, 1], dbscan([[0], [1]], sample_weight=[6, 0], eps=1.5, min_samples=6)[0] + ) + assert_array_equal( + [], dbscan([[0], [1]], sample_weight=[6, -1], eps=1.5, min_samples=6)[0] + ) + + # for non-negative sample_weight, cores should be identical to repetition + rng = np.random.RandomState(global_random_seed) + sample_weight = rng.randint(0, 5, X.shape[0]) + core1, label1 = dbscan(X, sample_weight=sample_weight) + assert len(label1) == len(X) + + X_repeated = np.repeat(X, sample_weight, axis=0) + core_repeated, label_repeated = dbscan(X_repeated) + core_repeated_mask = np.zeros(X_repeated.shape[0], dtype=bool) + core_repeated_mask[core_repeated] = True + core_mask = np.zeros(X.shape[0], dtype=bool) + core_mask[core1] = True + assert_array_equal(np.repeat(core_mask, sample_weight), core_repeated_mask) + + # sample_weight should work with precomputed distance matrix + D = pairwise_distances(X) + core3, label3 = dbscan(D, sample_weight=sample_weight, metric="precomputed") + assert_array_equal(core1, core3) + assert_array_equal(label1, label3) + + # sample_weight should work with estimator + est = DBSCAN().fit(X, sample_weight=sample_weight) + core4 = est.core_sample_indices_ + label4 = est.labels_ + assert_array_equal(core1, core4) + assert_array_equal(label1, label4) + + est = DBSCAN() + label5 = est.fit_predict(X, sample_weight=sample_weight) + core5 = est.core_sample_indices_ + assert_array_equal(core1, core5) + assert_array_equal(label1, label5) + assert_array_equal(label1, est.labels_) + + +@pytest.mark.parametrize("algorithm", ["brute", "kd_tree", "ball_tree"]) +def test_dbscan_core_samples_toy(algorithm): + X = [[0], [2], [3], [4], [6], [8], [10]] + n_samples = len(X) + + # Degenerate case: every sample is a core sample, either with its own + # cluster or including other close core samples. + core_samples, labels = dbscan(X, algorithm=algorithm, eps=1, min_samples=1) + assert_array_equal(core_samples, np.arange(n_samples)) + assert_array_equal(labels, [0, 1, 1, 1, 2, 3, 4]) + + # With eps=1 and min_samples=2 only the 3 samples from the denser area + # are core samples. All other points are isolated and considered noise. + core_samples, labels = dbscan(X, algorithm=algorithm, eps=1, min_samples=2) + assert_array_equal(core_samples, [1, 2, 3]) + assert_array_equal(labels, [-1, 0, 0, 0, -1, -1, -1]) + + # Only the sample in the middle of the dense area is core. Its two + # neighbors are edge samples. Remaining samples are noise. + core_samples, labels = dbscan(X, algorithm=algorithm, eps=1, min_samples=3) + assert_array_equal(core_samples, [2]) + assert_array_equal(labels, [-1, 0, 0, 0, -1, -1, -1]) + + # It's no longer possible to extract core samples with eps=1: + # everything is noise. + core_samples, labels = dbscan(X, algorithm=algorithm, eps=1, min_samples=4) + assert_array_equal(core_samples, []) + assert_array_equal(labels, np.full(n_samples, -1.0)) + + +def test_dbscan_precomputed_metric_with_degenerate_input_arrays(): + # see https://github.com/scikit-learn/scikit-learn/issues/4641 for + # more details + X = np.eye(10) + labels = DBSCAN(eps=0.5, metric="precomputed").fit(X).labels_ + assert len(set(labels)) == 1 + + X = np.zeros((10, 10)) + labels = DBSCAN(eps=0.5, metric="precomputed").fit(X).labels_ + assert len(set(labels)) == 1 + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_dbscan_precomputed_metric_with_initial_rows_zero(csr_container): + # sample matrix with initial two row all zero + ar = np.array( + [ + [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.1, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.1, 0.0, 0.0], + [0.0, 0.0, 0.1, 0.1, 0.0, 0.0, 0.3], + [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.1], + [0.0, 0.0, 0.0, 0.0, 0.3, 0.1, 0.0], + ] + ) + matrix = csr_container(ar) + labels = DBSCAN(eps=0.2, metric="precomputed", min_samples=2).fit(matrix).labels_ + assert_array_equal(labels, [-1, -1, 0, 0, 0, 1, 1]) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_feature_agglomeration.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_feature_agglomeration.py new file mode 100644 index 0000000000000000000000000000000000000000..80aa251c358153b0771bd201067fa87f8fb6bfdc --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_feature_agglomeration.py @@ -0,0 +1,55 @@ +""" +Tests for sklearn.cluster._feature_agglomeration +""" + +import numpy as np +from numpy.testing import assert_array_equal + +from sklearn.cluster import FeatureAgglomeration +from sklearn.datasets import make_blobs +from sklearn.utils._testing import assert_array_almost_equal + + +def test_feature_agglomeration(): + n_clusters = 1 + X = np.array([0, 0, 1]).reshape(1, 3) # (n_samples, n_features) + + agglo_mean = FeatureAgglomeration(n_clusters=n_clusters, pooling_func=np.mean) + agglo_median = FeatureAgglomeration(n_clusters=n_clusters, pooling_func=np.median) + agglo_mean.fit(X) + agglo_median.fit(X) + + assert np.size(np.unique(agglo_mean.labels_)) == n_clusters + assert np.size(np.unique(agglo_median.labels_)) == n_clusters + assert np.size(agglo_mean.labels_) == X.shape[1] + assert np.size(agglo_median.labels_) == X.shape[1] + + # Test transform + Xt_mean = agglo_mean.transform(X) + Xt_median = agglo_median.transform(X) + assert Xt_mean.shape[1] == n_clusters + assert Xt_median.shape[1] == n_clusters + assert Xt_mean == np.array([1 / 3.0]) + assert Xt_median == np.array([0.0]) + + # Test inverse transform + X_full_mean = agglo_mean.inverse_transform(Xt_mean) + X_full_median = agglo_median.inverse_transform(Xt_median) + assert np.unique(X_full_mean[0]).size == n_clusters + assert np.unique(X_full_median[0]).size == n_clusters + + assert_array_almost_equal(agglo_mean.transform(X_full_mean), Xt_mean) + assert_array_almost_equal(agglo_median.transform(X_full_median), Xt_median) + + +def test_feature_agglomeration_feature_names_out(): + """Check `get_feature_names_out` for `FeatureAgglomeration`.""" + X, _ = make_blobs(n_features=6, random_state=0) + agglo = FeatureAgglomeration(n_clusters=3) + agglo.fit(X) + n_clusters = agglo.n_clusters_ + + names_out = agglo.get_feature_names_out() + assert_array_equal( + [f"featureagglomeration{i}" for i in range(n_clusters)], names_out + ) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_hdbscan.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_hdbscan.py new file mode 100644 index 0000000000000000000000000000000000000000..3b45d9d3cb7aa290e7fac62f359ac518d105579e --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_hdbscan.py @@ -0,0 +1,582 @@ +""" +Tests for HDBSCAN clustering algorithm +Based on the DBSCAN test code +""" + +import numpy as np +import pytest +from scipy import stats +from scipy.spatial import distance + +from sklearn.cluster import HDBSCAN +from sklearn.cluster._hdbscan._tree import ( + CONDENSED_dtype, + _condense_tree, + _do_labelling, +) +from sklearn.cluster._hdbscan.hdbscan import _OUTLIER_ENCODING +from sklearn.datasets import make_blobs +from sklearn.metrics import fowlkes_mallows_score +from sklearn.metrics.pairwise import _VALID_METRICS, euclidean_distances +from sklearn.neighbors import BallTree, KDTree +from sklearn.preprocessing import StandardScaler +from sklearn.utils import shuffle +from sklearn.utils._testing import assert_allclose, assert_array_equal +from sklearn.utils.fixes import CSC_CONTAINERS, CSR_CONTAINERS + +X, y = make_blobs(n_samples=200, random_state=10) +X, y = shuffle(X, y, random_state=7) +X = StandardScaler().fit_transform(X) + +ALGORITHMS = [ + "kd_tree", + "ball_tree", + "brute", + "auto", +] + +OUTLIER_SET = {-1} | {out["label"] for _, out in _OUTLIER_ENCODING.items()} + + +def check_label_quality(labels, threshold=0.99): + n_clusters = len(set(labels) - OUTLIER_SET) + assert n_clusters == 3 + assert fowlkes_mallows_score(labels, y) > threshold + + +@pytest.mark.parametrize("outlier_type", _OUTLIER_ENCODING) +def test_outlier_data(outlier_type): + """ + Tests if np.inf and np.nan data are each treated as special outliers. + """ + outlier = { + "infinite": np.inf, + "missing": np.nan, + }[outlier_type] + prob_check = { + "infinite": lambda x, y: x == y, + "missing": lambda x, y: np.isnan(x), + }[outlier_type] + label = _OUTLIER_ENCODING[outlier_type]["label"] + prob = _OUTLIER_ENCODING[outlier_type]["prob"] + + X_outlier = X.copy() + X_outlier[0] = [outlier, 1] + X_outlier[5] = [outlier, outlier] + model = HDBSCAN().fit(X_outlier) + + (missing_labels_idx,) = (model.labels_ == label).nonzero() + assert_array_equal(missing_labels_idx, [0, 5]) + + (missing_probs_idx,) = (prob_check(model.probabilities_, prob)).nonzero() + assert_array_equal(missing_probs_idx, [0, 5]) + + clean_indices = list(range(1, 5)) + list(range(6, 200)) + clean_model = HDBSCAN().fit(X_outlier[clean_indices]) + assert_array_equal(clean_model.labels_, model.labels_[clean_indices]) + + +def test_hdbscan_distance_matrix(): + """ + Tests that HDBSCAN works with precomputed distance matrices, and throws the + appropriate errors when needed. + """ + D = euclidean_distances(X) + D_original = D.copy() + labels = HDBSCAN(metric="precomputed", copy=True).fit_predict(D) + + assert_allclose(D, D_original) + check_label_quality(labels) + + msg = r"The precomputed distance matrix.*has shape" + with pytest.raises(ValueError, match=msg): + HDBSCAN(metric="precomputed", copy=True).fit_predict(X) + + msg = r"The precomputed distance matrix.*values" + # Ensure the matrix is not symmetric + D[0, 1] = 10 + D[1, 0] = 1 + with pytest.raises(ValueError, match=msg): + HDBSCAN(metric="precomputed").fit_predict(D) + + +@pytest.mark.parametrize("sparse_constructor", [*CSR_CONTAINERS, *CSC_CONTAINERS]) +def test_hdbscan_sparse_distance_matrix(sparse_constructor): + """ + Tests that HDBSCAN works with sparse distance matrices. + """ + D = distance.squareform(distance.pdist(X)) + D /= np.max(D) + + threshold = stats.scoreatpercentile(D.flatten(), 50) + + D[D >= threshold] = 0.0 + D = sparse_constructor(D) + D.eliminate_zeros() + + labels = HDBSCAN(metric="precomputed").fit_predict(D) + check_label_quality(labels) + + +def test_hdbscan_feature_array(): + """ + Tests that HDBSCAN works with feature array, including an arbitrary + goodness of fit check. Note that the check is a simple heuristic. + """ + labels = HDBSCAN().fit_predict(X) + + # Check that clustering is arbitrarily good + # This is a heuristic to guard against regression + check_label_quality(labels) + + +@pytest.mark.parametrize("algo", ALGORITHMS) +@pytest.mark.parametrize("metric", _VALID_METRICS) +def test_hdbscan_algorithms(algo, metric): + """ + Tests that HDBSCAN works with the expected combinations of algorithms and + metrics, or raises the expected errors. + """ + labels = HDBSCAN(algorithm=algo).fit_predict(X) + check_label_quality(labels) + + # Validation for brute is handled by `pairwise_distances` + if algo in ("brute", "auto"): + return + + ALGOS_TREES = { + "kd_tree": KDTree, + "ball_tree": BallTree, + } + metric_params = { + "mahalanobis": {"V": np.eye(X.shape[1])}, + "seuclidean": {"V": np.ones(X.shape[1])}, + "minkowski": {"p": 2}, + "wminkowski": {"p": 2, "w": np.ones(X.shape[1])}, + }.get(metric, None) + + hdb = HDBSCAN( + algorithm=algo, + metric=metric, + metric_params=metric_params, + ) + + if metric not in ALGOS_TREES[algo].valid_metrics: + with pytest.raises(ValueError): + hdb.fit(X) + elif metric == "wminkowski": + with pytest.warns(FutureWarning): + hdb.fit(X) + else: + hdb.fit(X) + + +def test_dbscan_clustering(): + """ + Tests that HDBSCAN can generate a sufficiently accurate dbscan clustering. + This test is more of a sanity check than a rigorous evaluation. + """ + clusterer = HDBSCAN().fit(X) + labels = clusterer.dbscan_clustering(0.3) + + # We use a looser threshold due to dbscan producing a more constrained + # clustering representation + check_label_quality(labels, threshold=0.92) + + +@pytest.mark.parametrize("cut_distance", (0.1, 0.5, 1)) +def test_dbscan_clustering_outlier_data(cut_distance): + """ + Tests if np.inf and np.nan data are each treated as special outliers. + """ + missing_label = _OUTLIER_ENCODING["missing"]["label"] + infinite_label = _OUTLIER_ENCODING["infinite"]["label"] + + X_outlier = X.copy() + X_outlier[0] = [np.inf, 1] + X_outlier[2] = [1, np.nan] + X_outlier[5] = [np.inf, np.nan] + model = HDBSCAN().fit(X_outlier) + labels = model.dbscan_clustering(cut_distance=cut_distance) + + missing_labels_idx = np.flatnonzero(labels == missing_label) + assert_array_equal(missing_labels_idx, [2, 5]) + + infinite_labels_idx = np.flatnonzero(labels == infinite_label) + assert_array_equal(infinite_labels_idx, [0]) + + clean_idx = list(set(range(200)) - set(missing_labels_idx + infinite_labels_idx)) + clean_model = HDBSCAN().fit(X_outlier[clean_idx]) + clean_labels = clean_model.dbscan_clustering(cut_distance=cut_distance) + assert_array_equal(clean_labels, labels[clean_idx]) + + +def test_hdbscan_best_balltree_metric(): + """ + Tests that HDBSCAN using `BallTree` works. + """ + labels = HDBSCAN( + metric="seuclidean", metric_params={"V": np.ones(X.shape[1])} + ).fit_predict(X) + check_label_quality(labels) + + +def test_hdbscan_no_clusters(): + """ + Tests that HDBSCAN correctly does not generate a valid cluster when the + `min_cluster_size` is too large for the data. + """ + labels = HDBSCAN(min_cluster_size=len(X) - 1).fit_predict(X) + assert set(labels).issubset(OUTLIER_SET) + + +def test_hdbscan_min_cluster_size(): + """ + Test that the smallest non-noise cluster has at least `min_cluster_size` + many points + """ + for min_cluster_size in range(2, len(X), 1): + labels = HDBSCAN(min_cluster_size=min_cluster_size).fit_predict(X) + true_labels = [label for label in labels if label != -1] + if len(true_labels) != 0: + assert np.min(np.bincount(true_labels)) >= min_cluster_size + + +def test_hdbscan_callable_metric(): + """ + Tests that HDBSCAN works when passed a callable metric. + """ + metric = distance.euclidean + labels = HDBSCAN(metric=metric).fit_predict(X) + check_label_quality(labels) + + +@pytest.mark.parametrize("tree", ["kd_tree", "ball_tree"]) +def test_hdbscan_precomputed_non_brute(tree): + """ + Tests that HDBSCAN correctly raises an error when passing precomputed data + while requesting a tree-based algorithm. + """ + hdb = HDBSCAN(metric="precomputed", algorithm=tree) + msg = "precomputed is not a valid metric for" + with pytest.raises(ValueError, match=msg): + hdb.fit(X) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_hdbscan_sparse(csr_container): + """ + Tests that HDBSCAN works correctly when passing sparse feature data. + Evaluates correctness by comparing against the same data passed as a dense + array. + """ + + dense_labels = HDBSCAN().fit(X).labels_ + check_label_quality(dense_labels) + + _X_sparse = csr_container(X) + X_sparse = _X_sparse.copy() + sparse_labels = HDBSCAN().fit(X_sparse).labels_ + assert_array_equal(dense_labels, sparse_labels) + + # Compare that the sparse and dense non-precomputed routines return the same labels + # where the 0th observation contains the outlier. + for outlier_val, outlier_type in ((np.inf, "infinite"), (np.nan, "missing")): + X_dense = X.copy() + X_dense[0, 0] = outlier_val + dense_labels = HDBSCAN().fit(X_dense).labels_ + check_label_quality(dense_labels) + assert dense_labels[0] == _OUTLIER_ENCODING[outlier_type]["label"] + + X_sparse = _X_sparse.copy() + X_sparse[0, 0] = outlier_val + sparse_labels = HDBSCAN().fit(X_sparse).labels_ + assert_array_equal(dense_labels, sparse_labels) + + msg = "Sparse data matrices only support algorithm `brute`." + with pytest.raises(ValueError, match=msg): + HDBSCAN(metric="euclidean", algorithm="ball_tree").fit(X_sparse) + + +@pytest.mark.parametrize("algorithm", ALGORITHMS) +def test_hdbscan_centers(algorithm): + """ + Tests that HDBSCAN centers are calculated and stored properly, and are + accurate to the data. + """ + centers = [(0.0, 0.0), (3.0, 3.0)] + H, _ = make_blobs(n_samples=2000, random_state=0, centers=centers, cluster_std=0.5) + hdb = HDBSCAN(store_centers="both").fit(H) + + for center, centroid, medoid in zip(centers, hdb.centroids_, hdb.medoids_): + assert_allclose(center, centroid, rtol=1, atol=0.05) + assert_allclose(center, medoid, rtol=1, atol=0.05) + + # Ensure that nothing is done for noise + hdb = HDBSCAN( + algorithm=algorithm, store_centers="both", min_cluster_size=X.shape[0] + ).fit(X) + assert hdb.centroids_.shape[0] == 0 + assert hdb.medoids_.shape[0] == 0 + + +def test_hdbscan_allow_single_cluster_with_epsilon(): + """ + Tests that HDBSCAN single-cluster selection with epsilon works correctly. + """ + rng = np.random.RandomState(0) + no_structure = rng.rand(150, 2) + # without epsilon we should see many noise points as children of root. + labels = HDBSCAN( + min_cluster_size=5, + cluster_selection_epsilon=0.0, + cluster_selection_method="eom", + allow_single_cluster=True, + ).fit_predict(no_structure) + unique_labels, counts = np.unique(labels, return_counts=True) + assert len(unique_labels) == 2 + + # Arbitrary heuristic. Would prefer something more precise. + assert counts[unique_labels == -1] > 30 + + # for this random seed an epsilon of 0.18 will produce exactly 2 noise + # points at that cut in single linkage. + labels = HDBSCAN( + min_cluster_size=5, + cluster_selection_epsilon=0.18, + cluster_selection_method="eom", + allow_single_cluster=True, + algorithm="kd_tree", + ).fit_predict(no_structure) + unique_labels, counts = np.unique(labels, return_counts=True) + assert len(unique_labels) == 2 + assert counts[unique_labels == -1] == 2 + + +def test_hdbscan_better_than_dbscan(): + """ + Validate that HDBSCAN can properly cluster this difficult synthetic + dataset. Note that DBSCAN fails on this (see HDBSCAN plotting + example) + """ + centers = [[-0.85, -0.85], [-0.85, 0.85], [3, 3], [3, -3]] + X, y = make_blobs( + n_samples=750, + centers=centers, + cluster_std=[0.2, 0.35, 1.35, 1.35], + random_state=0, + ) + labels = HDBSCAN().fit(X).labels_ + + n_clusters = len(set(labels)) - int(-1 in labels) + assert n_clusters == 4 + fowlkes_mallows_score(labels, y) > 0.99 + + +@pytest.mark.parametrize( + "kwargs, X", + [ + ({"metric": "precomputed"}, np.array([[1, np.inf], [np.inf, 1]])), + ({"metric": "precomputed"}, [[1, 2], [2, 1]]), + ({}, [[1, 2], [3, 4]]), + ], +) +def test_hdbscan_usable_inputs(X, kwargs): + """ + Tests that HDBSCAN works correctly for array-likes and precomputed inputs + with non-finite points. + """ + HDBSCAN(min_samples=1, **kwargs).fit(X) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_hdbscan_sparse_distances_too_few_nonzero(csr_container): + """ + Tests that HDBSCAN raises the correct error when there are too few + non-zero distances. + """ + X = csr_container(np.zeros((10, 10))) + + msg = "There exists points with fewer than" + with pytest.raises(ValueError, match=msg): + HDBSCAN(metric="precomputed").fit(X) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_hdbscan_sparse_distances_disconnected_graph(csr_container): + """ + Tests that HDBSCAN raises the correct error when the distance matrix + has multiple connected components. + """ + # Create symmetric sparse matrix with 2 connected components + X = np.zeros((20, 20)) + X[:5, :5] = 1 + X[5:, 15:] = 1 + X = X + X.T + X = csr_container(X) + msg = "HDBSCAN cannot be performed on a disconnected graph" + with pytest.raises(ValueError, match=msg): + HDBSCAN(metric="precomputed").fit(X) + + +def test_hdbscan_tree_invalid_metric(): + """ + Tests that HDBSCAN correctly raises an error for invalid metric choices. + """ + metric_callable = lambda x: x + msg = ( + ".* is not a valid metric for a .*-based algorithm\\. Please select a different" + " metric\\." + ) + + # Callables are not supported for either + with pytest.raises(ValueError, match=msg): + HDBSCAN(algorithm="kd_tree", metric=metric_callable).fit(X) + with pytest.raises(ValueError, match=msg): + HDBSCAN(algorithm="ball_tree", metric=metric_callable).fit(X) + + # The set of valid metrics for KDTree at the time of writing this test is a + # strict subset of those supported in BallTree + metrics_not_kd = list(set(BallTree.valid_metrics) - set(KDTree.valid_metrics)) + if len(metrics_not_kd) > 0: + with pytest.raises(ValueError, match=msg): + HDBSCAN(algorithm="kd_tree", metric=metrics_not_kd[0]).fit(X) + + +def test_hdbscan_too_many_min_samples(): + """ + Tests that HDBSCAN correctly raises an error when setting `min_samples` + larger than the number of samples. + """ + hdb = HDBSCAN(min_samples=len(X) + 1) + msg = r"min_samples (.*) must be at most" + with pytest.raises(ValueError, match=msg): + hdb.fit(X) + + +def test_hdbscan_precomputed_dense_nan(): + """ + Tests that HDBSCAN correctly raises an error when providing precomputed + distances with `np.nan` values. + """ + X_nan = X.copy() + X_nan[0, 0] = np.nan + msg = "np.nan values found in precomputed-dense" + hdb = HDBSCAN(metric="precomputed") + with pytest.raises(ValueError, match=msg): + hdb.fit(X_nan) + + +@pytest.mark.parametrize("allow_single_cluster", [True, False]) +@pytest.mark.parametrize("epsilon", [0, 0.1]) +def test_labelling_distinct(global_random_seed, allow_single_cluster, epsilon): + """ + Tests that the `_do_labelling` helper function correctly assigns labels. + """ + n_samples = 48 + X, y = make_blobs( + n_samples, + random_state=global_random_seed, + # Ensure the clusters are distinct with no overlap + centers=[ + [0, 0], + [10, 0], + [0, 10], + ], + ) + + est = HDBSCAN().fit(X) + condensed_tree = _condense_tree( + est._single_linkage_tree_, min_cluster_size=est.min_cluster_size + ) + clusters = {n_samples + 2, n_samples + 3, n_samples + 4} + cluster_label_map = {n_samples + 2: 0, n_samples + 3: 1, n_samples + 4: 2} + labels = _do_labelling( + condensed_tree=condensed_tree, + clusters=clusters, + cluster_label_map=cluster_label_map, + allow_single_cluster=allow_single_cluster, + cluster_selection_epsilon=epsilon, + ) + + first_with_label = {_y: np.where(y == _y)[0][0] for _y in list(set(y))} + y_to_labels = {_y: labels[first_with_label[_y]] for _y in list(set(y))} + aligned_target = np.vectorize(y_to_labels.get)(y) + assert_array_equal(labels, aligned_target) + + +def test_labelling_thresholding(): + """ + Tests that the `_do_labelling` helper function correctly thresholds the + incoming lambda values given various `cluster_selection_epsilon` values. + """ + n_samples = 5 + MAX_LAMBDA = 1.5 + condensed_tree = np.array( + [ + (5, 2, MAX_LAMBDA, 1), + (5, 1, 0.1, 1), + (5, 0, MAX_LAMBDA, 1), + (5, 3, 0.2, 1), + (5, 4, 0.3, 1), + ], + dtype=CONDENSED_dtype, + ) + labels = _do_labelling( + condensed_tree=condensed_tree, + clusters={n_samples}, + cluster_label_map={n_samples: 0, n_samples + 1: 1}, + allow_single_cluster=True, + cluster_selection_epsilon=1, + ) + num_noise = condensed_tree["value"] < 1 + assert sum(num_noise) == sum(labels == -1) + + labels = _do_labelling( + condensed_tree=condensed_tree, + clusters={n_samples}, + cluster_label_map={n_samples: 0, n_samples + 1: 1}, + allow_single_cluster=True, + cluster_selection_epsilon=0, + ) + # The threshold should be calculated per-sample based on the largest + # lambda of any simbling node. In this case, all points are siblings + # and the largest value is exactly MAX_LAMBDA. + num_noise = condensed_tree["value"] < MAX_LAMBDA + assert sum(num_noise) == sum(labels == -1) + + +@pytest.mark.parametrize("store_centers", ["centroid", "medoid"]) +def test_hdbscan_error_precomputed_and_store_centers(store_centers): + """Check that we raise an error if the centers are requested together with + a precomputed input matrix. + + Non-regression test for: + https://github.com/scikit-learn/scikit-learn/issues/27893 + """ + rng = np.random.RandomState(0) + X = rng.random((100, 2)) + X_dist = euclidean_distances(X) + err_msg = "Cannot store centers when using a precomputed distance matrix." + with pytest.raises(ValueError, match=err_msg): + HDBSCAN(metric="precomputed", store_centers=store_centers).fit(X_dist) + + +@pytest.mark.parametrize("valid_algo", ["auto", "brute"]) +def test_hdbscan_cosine_metric_valid_algorithm(valid_algo): + """Test that HDBSCAN works with the "cosine" metric when the algorithm is set + to "brute" or "auto". + + Non-regression test for issue #28631 + """ + HDBSCAN(metric="cosine", algorithm=valid_algo).fit_predict(X) + + +@pytest.mark.parametrize("invalid_algo", ["kd_tree", "ball_tree"]) +def test_hdbscan_cosine_metric_invalid_algorithm(invalid_algo): + """Test that HDBSCAN raises an informative error is raised when an unsupported + algorithm is used with the "cosine" metric. + """ + hdbscan = HDBSCAN(metric="cosine", algorithm=invalid_algo) + with pytest.raises(ValueError, match="cosine is not a valid metric"): + hdbscan.fit_predict(X) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_hierarchical.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_hierarchical.py new file mode 100644 index 0000000000000000000000000000000000000000..222d4f6cd92649b9d59cb3f69f3d350414493984 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_hierarchical.py @@ -0,0 +1,889 @@ +""" +Several basic tests for hierarchical clustering procedures + +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import itertools +import shutil +from functools import partial +from tempfile import mkdtemp + +import numpy as np +import pytest +from scipy.cluster import hierarchy +from scipy.sparse.csgraph import connected_components + +from sklearn.cluster import AgglomerativeClustering, FeatureAgglomeration, ward_tree +from sklearn.cluster._agglomerative import ( + _TREE_BUILDERS, + _fix_connectivity, + _hc_cut, + linkage_tree, +) +from sklearn.cluster._hierarchical_fast import ( + average_merge, + max_merge, + mst_linkage_core, +) +from sklearn.datasets import make_circles, make_moons +from sklearn.feature_extraction.image import grid_to_graph +from sklearn.metrics import DistanceMetric +from sklearn.metrics.cluster import adjusted_rand_score, normalized_mutual_info_score +from sklearn.metrics.pairwise import ( + PAIRED_DISTANCES, + cosine_distances, + manhattan_distances, + pairwise_distances, +) +from sklearn.metrics.tests.test_dist_metrics import METRICS_DEFAULT_PARAMS +from sklearn.neighbors import kneighbors_graph +from sklearn.utils._fast_dict import IntFloatDict +from sklearn.utils._testing import ( + assert_almost_equal, + assert_array_almost_equal, + assert_array_equal, + create_memmap_backed_data, + ignore_warnings, +) +from sklearn.utils.fixes import LIL_CONTAINERS + + +def test_linkage_misc(): + # Misc tests on linkage + rng = np.random.RandomState(42) + X = rng.normal(size=(5, 5)) + + with pytest.raises(ValueError): + linkage_tree(X, linkage="foo") + + with pytest.raises(ValueError): + linkage_tree(X, connectivity=np.ones((4, 4))) + + # Smoke test FeatureAgglomeration + FeatureAgglomeration().fit(X) + + # test hierarchical clustering on a precomputed distances matrix + dis = cosine_distances(X) + + res = linkage_tree(dis, affinity="precomputed") + assert_array_equal(res[0], linkage_tree(X, affinity="cosine")[0]) + + # test hierarchical clustering on a precomputed distances matrix + res = linkage_tree(X, affinity=manhattan_distances) + assert_array_equal(res[0], linkage_tree(X, affinity="manhattan")[0]) + + +def test_structured_linkage_tree(): + # Check that we obtain the correct solution for structured linkage trees. + rng = np.random.RandomState(0) + mask = np.ones([10, 10], dtype=bool) + # Avoiding a mask with only 'True' entries + mask[4:7, 4:7] = 0 + X = rng.randn(50, 100) + connectivity = grid_to_graph(*mask.shape) + for tree_builder in _TREE_BUILDERS.values(): + children, n_components, n_leaves, parent = tree_builder( + X.T, connectivity=connectivity + ) + n_nodes = 2 * X.shape[1] - 1 + assert len(children) + n_leaves == n_nodes + # Check that ward_tree raises a ValueError with a connectivity matrix + # of the wrong shape + with pytest.raises(ValueError): + tree_builder(X.T, connectivity=np.ones((4, 4))) + # Check that fitting with no samples raises an error + with pytest.raises(ValueError): + tree_builder(X.T[:0], connectivity=connectivity) + + +def test_unstructured_linkage_tree(): + # Check that we obtain the correct solution for unstructured linkage trees. + rng = np.random.RandomState(0) + X = rng.randn(50, 100) + for this_X in (X, X[0]): + # With specified a number of clusters just for the sake of + # raising a warning and testing the warning code + with ignore_warnings(): + with pytest.warns(UserWarning): + children, n_nodes, n_leaves, parent = ward_tree(this_X.T, n_clusters=10) + n_nodes = 2 * X.shape[1] - 1 + assert len(children) + n_leaves == n_nodes + + for tree_builder in _TREE_BUILDERS.values(): + for this_X in (X, X[0]): + with ignore_warnings(): + with pytest.warns(UserWarning): + children, n_nodes, n_leaves, parent = tree_builder( + this_X.T, n_clusters=10 + ) + n_nodes = 2 * X.shape[1] - 1 + assert len(children) + n_leaves == n_nodes + + +def test_height_linkage_tree(): + # Check that the height of the results of linkage tree is sorted. + rng = np.random.RandomState(0) + mask = np.ones([10, 10], dtype=bool) + X = rng.randn(50, 100) + connectivity = grid_to_graph(*mask.shape) + for linkage_func in _TREE_BUILDERS.values(): + children, n_nodes, n_leaves, parent = linkage_func( + X.T, connectivity=connectivity + ) + n_nodes = 2 * X.shape[1] - 1 + assert len(children) + n_leaves == n_nodes + + +def test_zero_cosine_linkage_tree(): + # Check that zero vectors in X produce an error when + # 'cosine' affinity is used + X = np.array([[0, 1], [0, 0]]) + msg = "Cosine affinity cannot be used when X contains zero vectors" + with pytest.raises(ValueError, match=msg): + linkage_tree(X, affinity="cosine") + + +@pytest.mark.parametrize("n_clusters, distance_threshold", [(None, 0.5), (10, None)]) +@pytest.mark.parametrize("compute_distances", [True, False]) +@pytest.mark.parametrize("linkage", ["ward", "complete", "average", "single"]) +def test_agglomerative_clustering_distances( + n_clusters, compute_distances, distance_threshold, linkage +): + # Check that when `compute_distances` is True or `distance_threshold` is + # given, the fitted model has an attribute `distances_`. + rng = np.random.RandomState(0) + mask = np.ones([10, 10], dtype=bool) + n_samples = 100 + X = rng.randn(n_samples, 50) + connectivity = grid_to_graph(*mask.shape) + + clustering = AgglomerativeClustering( + n_clusters=n_clusters, + connectivity=connectivity, + linkage=linkage, + distance_threshold=distance_threshold, + compute_distances=compute_distances, + ) + clustering.fit(X) + if compute_distances or (distance_threshold is not None): + assert hasattr(clustering, "distances_") + n_children = clustering.children_.shape[0] + n_nodes = n_children + 1 + assert clustering.distances_.shape == (n_nodes - 1,) + else: + assert not hasattr(clustering, "distances_") + + +@pytest.mark.parametrize("lil_container", LIL_CONTAINERS) +def test_agglomerative_clustering(global_random_seed, lil_container): + # Check that we obtain the correct number of clusters with + # agglomerative clustering. + rng = np.random.RandomState(global_random_seed) + mask = np.ones([10, 10], dtype=bool) + n_samples = 100 + X = rng.randn(n_samples, 50) + connectivity = grid_to_graph(*mask.shape) + for linkage in ("ward", "complete", "average", "single"): + clustering = AgglomerativeClustering( + n_clusters=10, connectivity=connectivity, linkage=linkage + ) + clustering.fit(X) + # test caching + try: + tempdir = mkdtemp() + clustering = AgglomerativeClustering( + n_clusters=10, + connectivity=connectivity, + memory=tempdir, + linkage=linkage, + ) + clustering.fit(X) + labels = clustering.labels_ + assert np.size(np.unique(labels)) == 10 + finally: + shutil.rmtree(tempdir) + # Turn caching off now + clustering = AgglomerativeClustering( + n_clusters=10, connectivity=connectivity, linkage=linkage + ) + # Check that we obtain the same solution with early-stopping of the + # tree building + clustering.compute_full_tree = False + clustering.fit(X) + assert_almost_equal(normalized_mutual_info_score(clustering.labels_, labels), 1) + clustering.connectivity = None + clustering.fit(X) + assert np.size(np.unique(clustering.labels_)) == 10 + # Check that we raise a TypeError on dense matrices + clustering = AgglomerativeClustering( + n_clusters=10, + connectivity=lil_container(connectivity.toarray()[:10, :10]), + linkage=linkage, + ) + with pytest.raises(ValueError): + clustering.fit(X) + + # Test that using ward with another metric than euclidean raises an + # exception + clustering = AgglomerativeClustering( + n_clusters=10, + connectivity=connectivity.toarray(), + metric="manhattan", + linkage="ward", + ) + with pytest.raises(ValueError): + clustering.fit(X) + + # Test using another metric than euclidean works with linkage complete + for metric in PAIRED_DISTANCES.keys(): + # Compare our (structured) implementation to scipy + clustering = AgglomerativeClustering( + n_clusters=10, + connectivity=np.ones((n_samples, n_samples)), + metric=metric, + linkage="complete", + ) + clustering.fit(X) + clustering2 = AgglomerativeClustering( + n_clusters=10, connectivity=None, metric=metric, linkage="complete" + ) + clustering2.fit(X) + assert_almost_equal( + normalized_mutual_info_score(clustering2.labels_, clustering.labels_), 1 + ) + + # Test that using a distance matrix (affinity = 'precomputed') has same + # results (with connectivity constraints) + clustering = AgglomerativeClustering( + n_clusters=10, connectivity=connectivity, linkage="complete" + ) + clustering.fit(X) + X_dist = pairwise_distances(X) + clustering2 = AgglomerativeClustering( + n_clusters=10, + connectivity=connectivity, + metric="precomputed", + linkage="complete", + ) + clustering2.fit(X_dist) + assert_array_equal(clustering.labels_, clustering2.labels_) + + +def test_agglomerative_clustering_memory_mapped(): + """AgglomerativeClustering must work on mem-mapped dataset. + + Non-regression test for issue #19875. + """ + rng = np.random.RandomState(0) + Xmm = create_memmap_backed_data(rng.randn(50, 100)) + AgglomerativeClustering(metric="euclidean", linkage="single").fit(Xmm) + + +def test_ward_agglomeration(global_random_seed): + # Check that we obtain the correct solution in a simplistic case + rng = np.random.RandomState(global_random_seed) + mask = np.ones([10, 10], dtype=bool) + X = rng.randn(50, 100) + connectivity = grid_to_graph(*mask.shape) + agglo = FeatureAgglomeration(n_clusters=5, connectivity=connectivity) + agglo.fit(X) + assert np.size(np.unique(agglo.labels_)) == 5 + + X_red = agglo.transform(X) + assert X_red.shape[1] == 5 + X_full = agglo.inverse_transform(X_red) + assert np.unique(X_full[0]).size == 5 + assert_array_almost_equal(agglo.transform(X_full), X_red) + + # Check that fitting with no samples raises a ValueError + with pytest.raises(ValueError): + agglo.fit(X[:0]) + + +def test_single_linkage_clustering(): + # Check that we get the correct result in two emblematic cases + moons, moon_labels = make_moons(noise=0.05, random_state=42) + clustering = AgglomerativeClustering(n_clusters=2, linkage="single") + clustering.fit(moons) + assert_almost_equal( + normalized_mutual_info_score(clustering.labels_, moon_labels), 1 + ) + + circles, circle_labels = make_circles(factor=0.5, noise=0.025, random_state=42) + clustering = AgglomerativeClustering(n_clusters=2, linkage="single") + clustering.fit(circles) + assert_almost_equal( + normalized_mutual_info_score(clustering.labels_, circle_labels), 1 + ) + + +def assess_same_labelling(cut1, cut2): + """Util for comparison with scipy""" + co_clust = [] + for cut in [cut1, cut2]: + n = len(cut) + k = cut.max() + 1 + ecut = np.zeros((n, k)) + ecut[np.arange(n), cut] = 1 + co_clust.append(np.dot(ecut, ecut.T)) + assert (co_clust[0] == co_clust[1]).all() + + +def test_sparse_scikit_vs_scipy(global_random_seed): + # Test scikit linkage with full connectivity (i.e. unstructured) vs scipy + n, p, k = 10, 5, 3 + rng = np.random.RandomState(global_random_seed) + + # Not using a lil_matrix here, just to check that non sparse + # matrices are well handled + connectivity = np.ones((n, n)) + for linkage in _TREE_BUILDERS.keys(): + for i in range(5): + X = 0.1 * rng.normal(size=(n, p)) + X -= 4.0 * np.arange(n)[:, np.newaxis] + X -= X.mean(axis=1)[:, np.newaxis] + + out = hierarchy.linkage(X, method=linkage) + + children_ = out[:, :2].astype(int, copy=False) + children, _, n_leaves, _ = _TREE_BUILDERS[linkage]( + X, connectivity=connectivity + ) + + # Sort the order of child nodes per row for consistency + children.sort(axis=1) + assert_array_equal( + children, + children_, + "linkage tree differs from scipy impl for linkage: " + linkage, + ) + + cut = _hc_cut(k, children, n_leaves) + cut_ = _hc_cut(k, children_, n_leaves) + assess_same_labelling(cut, cut_) + + # Test error management in _hc_cut + with pytest.raises(ValueError): + _hc_cut(n_leaves + 1, children, n_leaves) + + +# Make sure our custom mst_linkage_core gives +# the same results as scipy's builtin +def test_vector_scikit_single_vs_scipy_single(global_random_seed): + n_samples, n_features, n_clusters = 10, 5, 3 + rng = np.random.RandomState(global_random_seed) + X = 0.1 * rng.normal(size=(n_samples, n_features)) + X -= 4.0 * np.arange(n_samples)[:, np.newaxis] + X -= X.mean(axis=1)[:, np.newaxis] + + out = hierarchy.linkage(X, method="single") + children_scipy = out[:, :2].astype(int) + + children, _, n_leaves, _ = _TREE_BUILDERS["single"](X) + + # Sort the order of child nodes per row for consistency + children.sort(axis=1) + assert_array_equal( + children, + children_scipy, + "linkage tree differs from scipy impl for single linkage.", + ) + + cut = _hc_cut(n_clusters, children, n_leaves) + cut_scipy = _hc_cut(n_clusters, children_scipy, n_leaves) + assess_same_labelling(cut, cut_scipy) + + +@pytest.mark.parametrize("metric_param_grid", METRICS_DEFAULT_PARAMS) +def test_mst_linkage_core_memory_mapped(metric_param_grid): + """The MST-LINKAGE-CORE algorithm must work on mem-mapped dataset. + + Non-regression test for issue #19875. + """ + rng = np.random.RandomState(seed=1) + X = rng.normal(size=(20, 4)) + Xmm = create_memmap_backed_data(X) + metric, param_grid = metric_param_grid + keys = param_grid.keys() + for vals in itertools.product(*param_grid.values()): + kwargs = dict(zip(keys, vals)) + distance_metric = DistanceMetric.get_metric(metric, **kwargs) + mst = mst_linkage_core(X, distance_metric) + mst_mm = mst_linkage_core(Xmm, distance_metric) + np.testing.assert_equal(mst, mst_mm) + + +def test_identical_points(): + # Ensure identical points are handled correctly when using mst with + # a sparse connectivity matrix + X = np.array([[0, 0, 0], [0, 0, 0], [1, 1, 1], [1, 1, 1], [2, 2, 2], [2, 2, 2]]) + true_labels = np.array([0, 0, 1, 1, 2, 2]) + connectivity = kneighbors_graph(X, n_neighbors=3, include_self=False) + connectivity = 0.5 * (connectivity + connectivity.T) + connectivity, n_components = _fix_connectivity(X, connectivity, "euclidean") + + for linkage in ("single", "average", "average", "ward"): + clustering = AgglomerativeClustering( + n_clusters=3, linkage=linkage, connectivity=connectivity + ) + clustering.fit(X) + + assert_almost_equal( + normalized_mutual_info_score(clustering.labels_, true_labels), 1 + ) + + +def test_connectivity_propagation(): + # Check that connectivity in the ward tree is propagated correctly during + # merging. + X = np.array( + [ + (0.014, 0.120), + (0.014, 0.099), + (0.014, 0.097), + (0.017, 0.153), + (0.017, 0.153), + (0.018, 0.153), + (0.018, 0.153), + (0.018, 0.153), + (0.018, 0.153), + (0.018, 0.153), + (0.018, 0.153), + (0.018, 0.153), + (0.018, 0.152), + (0.018, 0.149), + (0.018, 0.144), + ] + ) + connectivity = kneighbors_graph(X, 10, include_self=False) + ward = AgglomerativeClustering( + n_clusters=4, connectivity=connectivity, linkage="ward" + ) + # If changes are not propagated correctly, fit crashes with an + # IndexError + ward.fit(X) + + +def test_ward_tree_children_order(global_random_seed): + # Check that children are ordered in the same way for both structured and + # unstructured versions of ward_tree. + + # test on five random datasets + n, p = 10, 5 + rng = np.random.RandomState(global_random_seed) + + connectivity = np.ones((n, n)) + for i in range(5): + X = 0.1 * rng.normal(size=(n, p)) + X -= 4.0 * np.arange(n)[:, np.newaxis] + X -= X.mean(axis=1)[:, np.newaxis] + + out_unstructured = ward_tree(X) + out_structured = ward_tree(X, connectivity=connectivity) + + assert_array_equal(out_unstructured[0], out_structured[0]) + + +def test_ward_linkage_tree_return_distance(global_random_seed): + # Test return_distance option on linkage and ward trees + + # test that return_distance when set true, gives same + # output on both structured and unstructured clustering. + n, p = 10, 5 + rng = np.random.RandomState(global_random_seed) + + connectivity = np.ones((n, n)) + for i in range(5): + X = 0.1 * rng.normal(size=(n, p)) + X -= 4.0 * np.arange(n)[:, np.newaxis] + X -= X.mean(axis=1)[:, np.newaxis] + + out_unstructured = ward_tree(X, return_distance=True) + out_structured = ward_tree(X, connectivity=connectivity, return_distance=True) + + # get children + children_unstructured = out_unstructured[0] + children_structured = out_structured[0] + + # check if we got the same clusters + assert_array_equal(children_unstructured, children_structured) + + # check if the distances are the same + dist_unstructured = out_unstructured[-1] + dist_structured = out_structured[-1] + + assert_array_almost_equal(dist_unstructured, dist_structured) + + for linkage in ["average", "complete", "single"]: + structured_items = linkage_tree( + X, connectivity=connectivity, linkage=linkage, return_distance=True + )[-1] + unstructured_items = linkage_tree(X, linkage=linkage, return_distance=True)[ + -1 + ] + structured_dist = structured_items[-1] + unstructured_dist = unstructured_items[-1] + structured_children = structured_items[0] + unstructured_children = unstructured_items[0] + assert_array_almost_equal(structured_dist, unstructured_dist) + assert_array_almost_equal(structured_children, unstructured_children) + + # test on the following dataset where we know the truth + # taken from scipy/cluster/tests/hierarchy_test_data.py + X = np.array( + [ + [1.43054825, -7.5693489], + [6.95887839, 6.82293382], + [2.87137846, -9.68248579], + [7.87974764, -6.05485803], + [8.24018364, -6.09495602], + [7.39020262, 8.54004355], + ] + ) + # truth + linkage_X_ward = np.array( + [ + [3.0, 4.0, 0.36265956, 2.0], + [1.0, 5.0, 1.77045373, 2.0], + [0.0, 2.0, 2.55760419, 2.0], + [6.0, 8.0, 9.10208346, 4.0], + [7.0, 9.0, 24.7784379, 6.0], + ] + ) + + linkage_X_complete = np.array( + [ + [3.0, 4.0, 0.36265956, 2.0], + [1.0, 5.0, 1.77045373, 2.0], + [0.0, 2.0, 2.55760419, 2.0], + [6.0, 8.0, 6.96742194, 4.0], + [7.0, 9.0, 18.77445997, 6.0], + ] + ) + + linkage_X_average = np.array( + [ + [3.0, 4.0, 0.36265956, 2.0], + [1.0, 5.0, 1.77045373, 2.0], + [0.0, 2.0, 2.55760419, 2.0], + [6.0, 8.0, 6.55832839, 4.0], + [7.0, 9.0, 15.44089605, 6.0], + ] + ) + + n_samples, n_features = np.shape(X) + connectivity_X = np.ones((n_samples, n_samples)) + + out_X_unstructured = ward_tree(X, return_distance=True) + out_X_structured = ward_tree(X, connectivity=connectivity_X, return_distance=True) + + # check that the labels are the same + assert_array_equal(linkage_X_ward[:, :2], out_X_unstructured[0]) + assert_array_equal(linkage_X_ward[:, :2], out_X_structured[0]) + + # check that the distances are correct + assert_array_almost_equal(linkage_X_ward[:, 2], out_X_unstructured[4]) + assert_array_almost_equal(linkage_X_ward[:, 2], out_X_structured[4]) + + linkage_options = ["complete", "average", "single"] + X_linkage_truth = [linkage_X_complete, linkage_X_average] + for linkage, X_truth in zip(linkage_options, X_linkage_truth): + out_X_unstructured = linkage_tree(X, return_distance=True, linkage=linkage) + out_X_structured = linkage_tree( + X, connectivity=connectivity_X, linkage=linkage, return_distance=True + ) + + # check that the labels are the same + assert_array_equal(X_truth[:, :2], out_X_unstructured[0]) + assert_array_equal(X_truth[:, :2], out_X_structured[0]) + + # check that the distances are correct + assert_array_almost_equal(X_truth[:, 2], out_X_unstructured[4]) + assert_array_almost_equal(X_truth[:, 2], out_X_structured[4]) + + +def test_connectivity_fixing_non_lil(): + # Check non regression of a bug if a non item assignable connectivity is + # provided with more than one component. + # create dummy data + x = np.array([[0, 0], [1, 1]]) + # create a mask with several components to force connectivity fixing + m = np.array([[True, False], [False, True]]) + c = grid_to_graph(n_x=2, n_y=2, mask=m) + w = AgglomerativeClustering(connectivity=c, linkage="ward") + with pytest.warns(UserWarning): + w.fit(x) + + +def test_int_float_dict(): + rng = np.random.RandomState(0) + keys = np.unique(rng.randint(100, size=10).astype(np.intp, copy=False)) + values = rng.rand(len(keys)) + + d = IntFloatDict(keys, values) + for key, value in zip(keys, values): + assert d[key] == value + + other_keys = np.arange(50, dtype=np.intp)[::2] + other_values = np.full(50, 0.5)[::2] + other = IntFloatDict(other_keys, other_values) + # Complete smoke test + max_merge(d, other, mask=np.ones(100, dtype=np.intp), n_a=1, n_b=1) + average_merge(d, other, mask=np.ones(100, dtype=np.intp), n_a=1, n_b=1) + + +def test_connectivity_callable(): + rng = np.random.RandomState(0) + X = rng.rand(20, 5) + connectivity = kneighbors_graph(X, 3, include_self=False) + aglc1 = AgglomerativeClustering(connectivity=connectivity) + aglc2 = AgglomerativeClustering( + connectivity=partial(kneighbors_graph, n_neighbors=3, include_self=False) + ) + aglc1.fit(X) + aglc2.fit(X) + assert_array_equal(aglc1.labels_, aglc2.labels_) + + +def test_connectivity_ignores_diagonal(): + rng = np.random.RandomState(0) + X = rng.rand(20, 5) + connectivity = kneighbors_graph(X, 3, include_self=False) + connectivity_include_self = kneighbors_graph(X, 3, include_self=True) + aglc1 = AgglomerativeClustering(connectivity=connectivity) + aglc2 = AgglomerativeClustering(connectivity=connectivity_include_self) + aglc1.fit(X) + aglc2.fit(X) + assert_array_equal(aglc1.labels_, aglc2.labels_) + + +def test_compute_full_tree(): + # Test that the full tree is computed if n_clusters is small + rng = np.random.RandomState(0) + X = rng.randn(10, 2) + connectivity = kneighbors_graph(X, 5, include_self=False) + + # When n_clusters is less, the full tree should be built + # that is the number of merges should be n_samples - 1 + agc = AgglomerativeClustering(n_clusters=2, connectivity=connectivity) + agc.fit(X) + n_samples = X.shape[0] + n_nodes = agc.children_.shape[0] + assert n_nodes == n_samples - 1 + + # When n_clusters is large, greater than max of 100 and 0.02 * n_samples. + # we should stop when there are n_clusters. + n_clusters = 101 + X = rng.randn(200, 2) + connectivity = kneighbors_graph(X, 10, include_self=False) + agc = AgglomerativeClustering(n_clusters=n_clusters, connectivity=connectivity) + agc.fit(X) + n_samples = X.shape[0] + n_nodes = agc.children_.shape[0] + assert n_nodes == n_samples - n_clusters + + +def test_n_components(): + # Test n_components returned by linkage, average and ward tree + rng = np.random.RandomState(0) + X = rng.rand(5, 5) + + # Connectivity matrix having five components. + connectivity = np.eye(5) + + for linkage_func in _TREE_BUILDERS.values(): + assert ignore_warnings(linkage_func)(X, connectivity=connectivity)[1] == 5 + + +def test_affinity_passed_to_fix_connectivity(): + # Test that the affinity parameter is actually passed to the pairwise + # function + + size = 2 + rng = np.random.RandomState(0) + X = rng.randn(size, size) + mask = np.array([True, False, False, True]) + + connectivity = grid_to_graph(n_x=size, n_y=size, mask=mask, return_as=np.ndarray) + + class FakeAffinity: + def __init__(self): + self.counter = 0 + + def increment(self, *args, **kwargs): + self.counter += 1 + return self.counter + + fa = FakeAffinity() + + linkage_tree(X, connectivity=connectivity, affinity=fa.increment) + + assert fa.counter == 3 + + +@pytest.mark.parametrize("linkage", ["ward", "complete", "average"]) +def test_agglomerative_clustering_with_distance_threshold(linkage, global_random_seed): + # Check that we obtain the correct number of clusters with + # agglomerative clustering with distance_threshold. + rng = np.random.RandomState(global_random_seed) + mask = np.ones([10, 10], dtype=bool) + n_samples = 100 + X = rng.randn(n_samples, 50) + connectivity = grid_to_graph(*mask.shape) + # test when distance threshold is set to 10 + distance_threshold = 10 + for conn in [None, connectivity]: + clustering = AgglomerativeClustering( + n_clusters=None, + distance_threshold=distance_threshold, + connectivity=conn, + linkage=linkage, + ) + clustering.fit(X) + clusters_produced = clustering.labels_ + num_clusters_produced = len(np.unique(clustering.labels_)) + # test if the clusters produced match the point in the linkage tree + # where the distance exceeds the threshold + tree_builder = _TREE_BUILDERS[linkage] + children, n_components, n_leaves, parent, distances = tree_builder( + X, connectivity=conn, n_clusters=None, return_distance=True + ) + num_clusters_at_threshold = ( + np.count_nonzero(distances >= distance_threshold) + 1 + ) + # test number of clusters produced + assert num_clusters_at_threshold == num_clusters_produced + # test clusters produced + clusters_at_threshold = _hc_cut( + n_clusters=num_clusters_produced, children=children, n_leaves=n_leaves + ) + assert np.array_equiv(clusters_produced, clusters_at_threshold) + + +def test_small_distance_threshold(global_random_seed): + rng = np.random.RandomState(global_random_seed) + n_samples = 10 + X = rng.randint(-300, 300, size=(n_samples, 3)) + # this should result in all data in their own clusters, given that + # their pairwise distances are bigger than .1 (which may not be the case + # with a different random seed). + clustering = AgglomerativeClustering( + n_clusters=None, distance_threshold=1.0, linkage="single" + ).fit(X) + # check that the pairwise distances are indeed all larger than .1 + all_distances = pairwise_distances(X, metric="minkowski", p=2) + np.fill_diagonal(all_distances, np.inf) + assert np.all(all_distances > 0.1) + assert clustering.n_clusters_ == n_samples + + +def test_cluster_distances_with_distance_threshold(global_random_seed): + rng = np.random.RandomState(global_random_seed) + n_samples = 100 + X = rng.randint(-10, 10, size=(n_samples, 3)) + # check the distances within the clusters and with other clusters + distance_threshold = 4 + clustering = AgglomerativeClustering( + n_clusters=None, distance_threshold=distance_threshold, linkage="single" + ).fit(X) + labels = clustering.labels_ + D = pairwise_distances(X, metric="minkowski", p=2) + # to avoid taking the 0 diagonal in min() + np.fill_diagonal(D, np.inf) + for label in np.unique(labels): + in_cluster_mask = labels == label + max_in_cluster_distance = ( + D[in_cluster_mask][:, in_cluster_mask].min(axis=0).max() + ) + min_out_cluster_distance = ( + D[in_cluster_mask][:, ~in_cluster_mask].min(axis=0).min() + ) + # single data point clusters only have that inf diagonal here + if in_cluster_mask.sum() > 1: + assert max_in_cluster_distance < distance_threshold + assert min_out_cluster_distance >= distance_threshold + + +@pytest.mark.parametrize("linkage", ["ward", "complete", "average"]) +@pytest.mark.parametrize( + ("threshold", "y_true"), [(0.5, [1, 0]), (1.0, [1, 0]), (1.5, [0, 0])] +) +def test_agglomerative_clustering_with_distance_threshold_edge_case( + linkage, threshold, y_true +): + # test boundary case of distance_threshold matching the distance + X = [[0], [1]] + clusterer = AgglomerativeClustering( + n_clusters=None, distance_threshold=threshold, linkage=linkage + ) + y_pred = clusterer.fit_predict(X) + assert adjusted_rand_score(y_true, y_pred) == 1 + + +def test_dist_threshold_invalid_parameters(): + X = [[0], [1]] + with pytest.raises(ValueError, match="Exactly one of "): + AgglomerativeClustering(n_clusters=None, distance_threshold=None).fit(X) + + with pytest.raises(ValueError, match="Exactly one of "): + AgglomerativeClustering(n_clusters=2, distance_threshold=1).fit(X) + + X = [[0], [1]] + with pytest.raises(ValueError, match="compute_full_tree must be True if"): + AgglomerativeClustering( + n_clusters=None, distance_threshold=1, compute_full_tree=False + ).fit(X) + + +def test_invalid_shape_precomputed_dist_matrix(): + # Check that an error is raised when affinity='precomputed' + # and a non square matrix is passed (PR #16257). + rng = np.random.RandomState(0) + X = rng.rand(5, 3) + with pytest.raises( + ValueError, + match=r"Distance matrix should be square, got matrix of shape \(5, 3\)", + ): + AgglomerativeClustering(metric="precomputed", linkage="complete").fit(X) + + +def test_precomputed_connectivity_metric_with_2_connected_components(): + """Check that connecting components works when connectivity and + affinity are both precomputed and the number of connected components is + greater than 1. Non-regression test for #16151. + """ + + connectivity_matrix = np.array( + [ + [0, 1, 1, 0, 0], + [0, 0, 1, 0, 0], + [0, 0, 0, 0, 0], + [0, 0, 0, 0, 1], + [0, 0, 0, 0, 0], + ] + ) + # ensure that connectivity_matrix has two connected components + assert connected_components(connectivity_matrix)[0] == 2 + + rng = np.random.RandomState(0) + X = rng.randn(5, 10) + + X_dist = pairwise_distances(X) + clusterer_precomputed = AgglomerativeClustering( + metric="precomputed", connectivity=connectivity_matrix, linkage="complete" + ) + msg = "Completing it to avoid stopping the tree early" + with pytest.warns(UserWarning, match=msg): + clusterer_precomputed.fit(X_dist) + + clusterer = AgglomerativeClustering( + connectivity=connectivity_matrix, linkage="complete" + ) + with pytest.warns(UserWarning, match=msg): + clusterer.fit(X) + + assert_array_equal(clusterer.labels_, clusterer_precomputed.labels_) + assert_array_equal(clusterer.children_, clusterer_precomputed.children_) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_k_means.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_k_means.py new file mode 100644 index 0000000000000000000000000000000000000000..0ab602d32d1330fe738ce7a24cd4b4c68cdf9c15 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_k_means.py @@ -0,0 +1,1364 @@ +"""Testing for K-means""" + +import re +import sys +from io import StringIO + +import numpy as np +import pytest +from scipy import sparse as sp + +from sklearn.base import clone +from sklearn.cluster import KMeans, MiniBatchKMeans, k_means, kmeans_plusplus +from sklearn.cluster._k_means_common import ( + _euclidean_dense_dense_wrapper, + _euclidean_sparse_dense_wrapper, + _inertia_dense, + _inertia_sparse, + _is_same_clustering, + _relocate_empty_clusters_dense, + _relocate_empty_clusters_sparse, +) +from sklearn.cluster._kmeans import _labels_inertia, _mini_batch_step +from sklearn.datasets import make_blobs +from sklearn.exceptions import ConvergenceWarning +from sklearn.metrics import pairwise_distances, pairwise_distances_argmin +from sklearn.metrics.cluster import v_measure_score +from sklearn.metrics.pairwise import euclidean_distances +from sklearn.utils._testing import ( + assert_allclose, + assert_array_equal, + create_memmap_backed_data, +) +from sklearn.utils.extmath import row_norms +from sklearn.utils.fixes import CSR_CONTAINERS +from sklearn.utils.parallel import _get_threadpool_controller + +# non centered, sparse centers to check the +centers = np.array( + [ + [0.0, 5.0, 0.0, 0.0, 0.0], + [1.0, 1.0, 4.0, 0.0, 0.0], + [1.0, 0.0, 0.0, 5.0, 1.0], + ] +) +n_samples = 100 +n_clusters, n_features = centers.shape +X, true_labels = make_blobs( + n_samples=n_samples, centers=centers, cluster_std=1.0, random_state=42 +) +X_as_any_csr = [container(X) for container in CSR_CONTAINERS] +data_containers = [np.array] + CSR_CONTAINERS +data_containers_ids = ( + ["dense", "sparse_matrix", "sparse_array"] + if len(X_as_any_csr) == 2 + else ["dense", "sparse_matrix"] +) + + +@pytest.mark.parametrize("array_constr", data_containers, ids=data_containers_ids) +@pytest.mark.parametrize("algo", ["lloyd", "elkan"]) +@pytest.mark.parametrize("dtype", [np.float32, np.float64]) +def test_kmeans_results(array_constr, algo, dtype): + # Checks that KMeans works as intended on toy dataset by comparing with + # expected results computed by hand. + X = array_constr([[0, 0], [0.5, 0], [0.5, 1], [1, 1]], dtype=dtype) + sample_weight = [3, 1, 1, 3] + init_centers = np.array([[0, 0], [1, 1]], dtype=dtype) + + expected_labels = [0, 0, 1, 1] + expected_inertia = 0.375 + expected_centers = np.array([[0.125, 0], [0.875, 1]], dtype=dtype) + expected_n_iter = 2 + + kmeans = KMeans(n_clusters=2, n_init=1, init=init_centers, algorithm=algo) + kmeans.fit(X, sample_weight=sample_weight) + + assert_array_equal(kmeans.labels_, expected_labels) + assert_allclose(kmeans.inertia_, expected_inertia) + assert_allclose(kmeans.cluster_centers_, expected_centers) + assert kmeans.n_iter_ == expected_n_iter + + +@pytest.mark.parametrize("array_constr", data_containers, ids=data_containers_ids) +@pytest.mark.parametrize("algo", ["lloyd", "elkan"]) +def test_kmeans_relocated_clusters(array_constr, algo): + # check that empty clusters are relocated as expected + X = array_constr([[0, 0], [0.5, 0], [0.5, 1], [1, 1]]) + + # second center too far from others points will be empty at first iter + init_centers = np.array([[0.5, 0.5], [3, 3]]) + + kmeans = KMeans(n_clusters=2, n_init=1, init=init_centers, algorithm=algo) + kmeans.fit(X) + + expected_n_iter = 3 + expected_inertia = 0.25 + assert_allclose(kmeans.inertia_, expected_inertia) + assert kmeans.n_iter_ == expected_n_iter + + # There are two acceptable ways of relocating clusters in this example, the output + # depends on how the argpartition strategy breaks ties. We accept both outputs. + try: + expected_labels = [0, 0, 1, 1] + expected_centers = [[0.25, 0], [0.75, 1]] + assert_array_equal(kmeans.labels_, expected_labels) + assert_allclose(kmeans.cluster_centers_, expected_centers) + except AssertionError: + expected_labels = [1, 1, 0, 0] + expected_centers = [[0.75, 1.0], [0.25, 0.0]] + assert_array_equal(kmeans.labels_, expected_labels) + assert_allclose(kmeans.cluster_centers_, expected_centers) + + +@pytest.mark.parametrize("array_constr", data_containers, ids=data_containers_ids) +def test_relocate_empty_clusters(array_constr): + # test for the _relocate_empty_clusters_(dense/sparse) helpers + + # Synthetic dataset with 3 obvious clusters of different sizes + X = np.array([-10.0, -9.5, -9, -8.5, -8, -1, 1, 9, 9.5, 10]).reshape(-1, 1) + X = array_constr(X) + sample_weight = np.ones(10) + + # centers all initialized to the first point of X + centers_old = np.array([-10.0, -10, -10]).reshape(-1, 1) + + # With this initialization, all points will be assigned to the first center + # At this point a center in centers_new is the weighted sum of the points + # it contains if it's not empty, otherwise it is the same as before. + centers_new = np.array([-16.5, -10, -10]).reshape(-1, 1) + weight_in_clusters = np.array([10.0, 0, 0]) + labels = np.zeros(10, dtype=np.int32) + + if array_constr is np.array: + _relocate_empty_clusters_dense( + X, sample_weight, centers_old, centers_new, weight_in_clusters, labels + ) + else: + _relocate_empty_clusters_sparse( + X.data, + X.indices, + X.indptr, + sample_weight, + centers_old, + centers_new, + weight_in_clusters, + labels, + ) + + # The relocation scheme will take the 2 points farthest from the center and + # assign them to the 2 empty clusters, i.e. points at 10 and at 9.9. The + # first center will be updated to contain the other 8 points. + assert_array_equal(weight_in_clusters, [8, 1, 1]) + assert_allclose(centers_new, [[-36], [10], [9.5]]) + + +@pytest.mark.parametrize("distribution", ["normal", "blobs"]) +@pytest.mark.parametrize("array_constr", data_containers, ids=data_containers_ids) +@pytest.mark.parametrize("tol", [1e-2, 1e-8, 1e-100, 0]) +def test_kmeans_elkan_results(distribution, array_constr, tol, global_random_seed): + # Check that results are identical between lloyd and elkan algorithms + rnd = np.random.RandomState(global_random_seed) + if distribution == "normal": + X = rnd.normal(size=(5000, 10)) + else: + X, _ = make_blobs(random_state=rnd) + X[X < 0] = 0 + X = array_constr(X) + + km_lloyd = KMeans(n_clusters=5, random_state=global_random_seed, n_init=1, tol=tol) + km_elkan = KMeans( + algorithm="elkan", + n_clusters=5, + random_state=global_random_seed, + n_init=1, + tol=tol, + ) + + km_lloyd.fit(X) + km_elkan.fit(X) + assert_allclose(km_elkan.cluster_centers_, km_lloyd.cluster_centers_) + assert_array_equal(km_elkan.labels_, km_lloyd.labels_) + assert km_elkan.n_iter_ == km_lloyd.n_iter_ + assert km_elkan.inertia_ == pytest.approx(km_lloyd.inertia_, rel=1e-6) + + +@pytest.mark.parametrize("algorithm", ["lloyd", "elkan"]) +def test_kmeans_convergence(algorithm, global_random_seed): + # Check that KMeans stops when convergence is reached when tol=0. (#16075) + rnd = np.random.RandomState(global_random_seed) + X = rnd.normal(size=(5000, 10)) + max_iter = 300 + + km = KMeans( + algorithm=algorithm, + n_clusters=5, + random_state=global_random_seed, + n_init=1, + tol=0, + max_iter=max_iter, + ).fit(X) + + assert km.n_iter_ < max_iter + + +@pytest.mark.parametrize("X_csr", X_as_any_csr) +def test_minibatch_update_consistency(X_csr, global_random_seed): + # Check that dense and sparse minibatch update give the same results + rng = np.random.RandomState(global_random_seed) + + centers_old = centers + rng.normal(size=centers.shape) + centers_old_csr = centers_old.copy() + + centers_new = np.zeros_like(centers_old) + centers_new_csr = np.zeros_like(centers_old_csr) + + weight_sums = np.zeros(centers_old.shape[0], dtype=X.dtype) + weight_sums_csr = np.zeros(centers_old.shape[0], dtype=X.dtype) + + sample_weight = np.ones(X.shape[0], dtype=X.dtype) + + # extract a small minibatch + X_mb = X[:10] + X_mb_csr = X_csr[:10] + sample_weight_mb = sample_weight[:10] + + # step 1: compute the dense minibatch update + old_inertia = _mini_batch_step( + X_mb, + sample_weight_mb, + centers_old, + centers_new, + weight_sums, + np.random.RandomState(global_random_seed), + random_reassign=False, + ) + assert old_inertia > 0.0 + + # compute the new inertia on the same batch to check that it decreased + labels, new_inertia = _labels_inertia(X_mb, sample_weight_mb, centers_new) + assert new_inertia > 0.0 + assert new_inertia < old_inertia + + # step 2: compute the sparse minibatch update + old_inertia_csr = _mini_batch_step( + X_mb_csr, + sample_weight_mb, + centers_old_csr, + centers_new_csr, + weight_sums_csr, + np.random.RandomState(global_random_seed), + random_reassign=False, + ) + assert old_inertia_csr > 0.0 + + # compute the new inertia on the same batch to check that it decreased + labels_csr, new_inertia_csr = _labels_inertia( + X_mb_csr, sample_weight_mb, centers_new_csr + ) + assert new_inertia_csr > 0.0 + assert new_inertia_csr < old_inertia_csr + + # step 3: check that sparse and dense updates lead to the same results + assert_array_equal(labels, labels_csr) + assert_allclose(centers_new, centers_new_csr) + assert_allclose(old_inertia, old_inertia_csr) + assert_allclose(new_inertia, new_inertia_csr) + + +def _check_fitted_model(km): + # check that the number of clusters centers and distinct labels match + # the expectation + centers = km.cluster_centers_ + assert centers.shape == (n_clusters, n_features) + + labels = km.labels_ + assert np.unique(labels).shape[0] == n_clusters + + # check that the labels assignment are perfect (up to a permutation) + assert_allclose(v_measure_score(true_labels, labels), 1.0) + assert km.inertia_ > 0.0 + + +@pytest.mark.parametrize( + "input_data", + [X] + X_as_any_csr, + ids=data_containers_ids, +) +@pytest.mark.parametrize( + "init", + ["random", "k-means++", centers, lambda X, k, random_state: centers], + ids=["random", "k-means++", "ndarray", "callable"], +) +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_all_init(Estimator, input_data, init): + # Check KMeans and MiniBatchKMeans with all possible init. + n_init = 10 if isinstance(init, str) else 1 + km = Estimator( + init=init, n_clusters=n_clusters, random_state=42, n_init=n_init + ).fit(input_data) + _check_fitted_model(km) + + +@pytest.mark.parametrize( + "init", + ["random", "k-means++", centers, lambda X, k, random_state: centers], + ids=["random", "k-means++", "ndarray", "callable"], +) +def test_minibatch_kmeans_partial_fit_init(init): + # Check MiniBatchKMeans init with partial_fit + n_init = 10 if isinstance(init, str) else 1 + km = MiniBatchKMeans( + init=init, n_clusters=n_clusters, random_state=0, n_init=n_init + ) + for i in range(100): + # "random" init requires many batches to recover the true labels. + km.partial_fit(X) + _check_fitted_model(km) + + +@pytest.mark.parametrize( + "init, expected_n_init", + [ + ("k-means++", 1), + ("random", "default"), + ( + lambda X, n_clusters, random_state: random_state.uniform( + size=(n_clusters, X.shape[1]) + ), + "default", + ), + ("array-like", 1), + ], +) +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_kmeans_init_auto_with_initial_centroids(Estimator, init, expected_n_init): + """Check that `n_init="auto"` chooses the right number of initializations. + Non-regression test for #26657: + https://github.com/scikit-learn/scikit-learn/pull/26657 + """ + n_sample, n_features, n_clusters = 100, 10, 5 + X = np.random.randn(n_sample, n_features) + if init == "array-like": + init = np.random.randn(n_clusters, n_features) + if expected_n_init == "default": + expected_n_init = 3 if Estimator is MiniBatchKMeans else 10 + + kmeans = Estimator(n_clusters=n_clusters, init=init, n_init="auto").fit(X) + assert kmeans._n_init == expected_n_init + + +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_fortran_aligned_data(Estimator, global_random_seed): + # Check that KMeans works with fortran-aligned data. + X_fortran = np.asfortranarray(X) + centers_fortran = np.asfortranarray(centers) + + km_c = Estimator( + n_clusters=n_clusters, init=centers, n_init=1, random_state=global_random_seed + ).fit(X) + km_f = Estimator( + n_clusters=n_clusters, + init=centers_fortran, + n_init=1, + random_state=global_random_seed, + ).fit(X_fortran) + assert_allclose(km_c.cluster_centers_, km_f.cluster_centers_) + assert_array_equal(km_c.labels_, km_f.labels_) + + +def test_minibatch_kmeans_verbose(): + # Check verbose mode of MiniBatchKMeans for better coverage. + km = MiniBatchKMeans(n_clusters=n_clusters, random_state=42, verbose=1) + old_stdout = sys.stdout + sys.stdout = StringIO() + try: + km.fit(X) + finally: + sys.stdout = old_stdout + + +@pytest.mark.parametrize("algorithm", ["lloyd", "elkan"]) +@pytest.mark.parametrize("tol", [1e-2, 0]) +def test_kmeans_verbose(algorithm, tol, capsys): + # Check verbose mode of KMeans for better coverage. + X = np.random.RandomState(0).normal(size=(5000, 10)) + + KMeans( + algorithm=algorithm, + n_clusters=n_clusters, + random_state=42, + init="random", + n_init=1, + tol=tol, + verbose=1, + ).fit(X) + + captured = capsys.readouterr() + + assert re.search(r"Initialization complete", captured.out) + assert re.search(r"Iteration [0-9]+, inertia", captured.out) + + if tol == 0: + assert re.search(r"strict convergence", captured.out) + else: + assert re.search(r"center shift .* within tolerance", captured.out) + + +def test_minibatch_kmeans_warning_init_size(): + # Check that a warning is raised when init_size is smaller than n_clusters + with pytest.warns( + RuntimeWarning, match=r"init_size.* should be larger than n_clusters" + ): + MiniBatchKMeans(init_size=10, n_clusters=20).fit(X) + + +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_warning_n_init_precomputed_centers(Estimator): + # Check that a warning is raised when n_init > 1 and an array is passed for + # the init parameter. + with pytest.warns( + RuntimeWarning, + match="Explicit initial center position passed: performing only one init", + ): + Estimator(init=centers, n_clusters=n_clusters, n_init=10).fit(X) + + +def test_minibatch_sensible_reassign(global_random_seed): + # check that identical initial clusters are reassigned + # also a regression test for when there are more desired reassignments than + # samples. + zeroed_X, true_labels = make_blobs( + n_samples=100, centers=5, random_state=global_random_seed + ) + zeroed_X[::2, :] = 0 + + km = MiniBatchKMeans( + n_clusters=20, batch_size=10, random_state=global_random_seed, init="random" + ).fit(zeroed_X) + # there should not be too many exact zero cluster centers + num_non_zero_clusters = km.cluster_centers_.any(axis=1).sum() + assert num_non_zero_clusters > 9, f"{num_non_zero_clusters=} is too small" + + # do the same with batch-size > X.shape[0] (regression test) + km = MiniBatchKMeans( + n_clusters=20, batch_size=200, random_state=global_random_seed, init="random" + ).fit(zeroed_X) + # there should not be too many exact zero cluster centers + num_non_zero_clusters = km.cluster_centers_.any(axis=1).sum() + assert num_non_zero_clusters > 9, f"{num_non_zero_clusters=} is too small" + + # do the same with partial_fit API + km = MiniBatchKMeans(n_clusters=20, random_state=global_random_seed, init="random") + for i in range(100): + km.partial_fit(zeroed_X) + # there should not be too many exact zero cluster centers + num_non_zero_clusters = km.cluster_centers_.any(axis=1).sum() + assert num_non_zero_clusters > 9, f"{num_non_zero_clusters=} is too small" + + +@pytest.mark.parametrize( + "input_data", + [X] + X_as_any_csr, + ids=data_containers_ids, +) +def test_minibatch_reassign(input_data, global_random_seed): + # Check the reassignment part of the minibatch step with very high or very + # low reassignment ratio. + perfect_centers = np.empty((n_clusters, n_features)) + for i in range(n_clusters): + perfect_centers[i] = X[true_labels == i].mean(axis=0) + + sample_weight = np.ones(n_samples) + centers_new = np.empty_like(perfect_centers) + + # Give a perfect initialization, but a large reassignment_ratio, as a + # result many centers should be reassigned and the model should no longer + # be good + score_before = -_labels_inertia(input_data, sample_weight, perfect_centers, 1)[1] + + _mini_batch_step( + input_data, + sample_weight, + perfect_centers, + centers_new, + np.zeros(n_clusters), + np.random.RandomState(global_random_seed), + random_reassign=True, + reassignment_ratio=1, + ) + + score_after = -_labels_inertia(input_data, sample_weight, centers_new, 1)[1] + + assert score_before > score_after + + # Give a perfect initialization, with a small reassignment_ratio, + # no center should be reassigned. + _mini_batch_step( + input_data, + sample_weight, + perfect_centers, + centers_new, + np.zeros(n_clusters), + np.random.RandomState(global_random_seed), + random_reassign=True, + reassignment_ratio=1e-15, + ) + + assert_allclose(centers_new, perfect_centers) + + +def test_minibatch_with_many_reassignments(): + # Test for the case that the number of clusters to reassign is bigger + # than the batch_size. Run the test with 100 clusters and a batch_size of + # 10 because it turned out that these values ensure that the number of + # clusters to reassign is always bigger than the batch_size. + MiniBatchKMeans( + n_clusters=100, + batch_size=10, + init_size=n_samples, + random_state=42, + verbose=True, + ).fit(X) + + +def test_minibatch_kmeans_init_size(): + # Check the internal _init_size attribute of MiniBatchKMeans + + # default init size should be 3 * batch_size + km = MiniBatchKMeans(n_clusters=10, batch_size=5, n_init=1).fit(X) + assert km._init_size == 15 + + # if 3 * batch size < n_clusters, it should then be 3 * n_clusters + km = MiniBatchKMeans(n_clusters=10, batch_size=1, n_init=1).fit(X) + assert km._init_size == 30 + + # it should not be larger than n_samples + km = MiniBatchKMeans( + n_clusters=10, batch_size=5, n_init=1, init_size=n_samples + 1 + ).fit(X) + assert km._init_size == n_samples + + +@pytest.mark.parametrize("tol, max_no_improvement", [(1e-4, None), (0, 10)]) +def test_minibatch_declared_convergence(capsys, tol, max_no_improvement): + # Check convergence detection based on ewa batch inertia or on + # small center change. + X, _, centers = make_blobs(centers=3, random_state=0, return_centers=True) + + km = MiniBatchKMeans( + n_clusters=3, + init=centers, + batch_size=20, + tol=tol, + random_state=0, + max_iter=10, + n_init=1, + verbose=1, + max_no_improvement=max_no_improvement, + ) + + km.fit(X) + assert 1 < km.n_iter_ < 10 + + captured = capsys.readouterr() + if max_no_improvement is None: + assert "Converged (small centers change)" in captured.out + if tol == 0: + assert "Converged (lack of improvement in inertia)" in captured.out + + +def test_minibatch_iter_steps(): + # Check consistency of n_iter_ and n_steps_ attributes. + batch_size = 30 + n_samples = X.shape[0] + km = MiniBatchKMeans(n_clusters=3, batch_size=batch_size, random_state=0).fit(X) + + # n_iter_ is the number of started epochs + assert km.n_iter_ == np.ceil((km.n_steps_ * batch_size) / n_samples) + assert isinstance(km.n_iter_, int) + + # without stopping condition, max_iter should be reached + km = MiniBatchKMeans( + n_clusters=3, + batch_size=batch_size, + random_state=0, + tol=0, + max_no_improvement=None, + max_iter=10, + ).fit(X) + + assert km.n_iter_ == 10 + assert km.n_steps_ == (10 * n_samples) // batch_size + assert isinstance(km.n_steps_, int) + + +def test_kmeans_copyx(): + # Check that copy_x=False returns nearly equal X after de-centering. + my_X = X.copy() + km = KMeans(copy_x=False, n_clusters=n_clusters, random_state=42) + km.fit(my_X) + _check_fitted_model(km) + + # check that my_X is de-centered + assert_allclose(my_X, X) + + +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_score_max_iter(Estimator, global_random_seed): + # Check that fitting KMeans or MiniBatchKMeans with more iterations gives + # better score + X = np.random.RandomState(global_random_seed).randn(100, 10) + + km1 = Estimator(n_init=1, random_state=global_random_seed, max_iter=1) + s1 = km1.fit(X).score(X) + km2 = Estimator(n_init=1, random_state=global_random_seed, max_iter=10) + s2 = km2.fit(X).score(X) + assert s2 > s1 + + +@pytest.mark.parametrize("array_constr", data_containers, ids=data_containers_ids) +@pytest.mark.parametrize( + "Estimator, algorithm", + [(KMeans, "lloyd"), (KMeans, "elkan"), (MiniBatchKMeans, None)], +) +@pytest.mark.parametrize("max_iter", [2, 100]) +def test_kmeans_predict( + Estimator, algorithm, array_constr, max_iter, global_dtype, global_random_seed +): + # Check the predict method and the equivalence between fit.predict and + # fit_predict. + X, _ = make_blobs( + n_samples=200, n_features=10, centers=10, random_state=global_random_seed + ) + X = array_constr(X, dtype=global_dtype) + + km = Estimator( + n_clusters=10, + init="random", + n_init=10, + max_iter=max_iter, + random_state=global_random_seed, + ) + if algorithm is not None: + km.set_params(algorithm=algorithm) + km.fit(X) + labels = km.labels_ + + # re-predict labels for training set using predict + pred = km.predict(X) + assert_array_equal(pred, labels) + + # re-predict labels for training set using fit_predict + pred = km.fit_predict(X) + assert_array_equal(pred, labels) + + # predict centroid labels + pred = km.predict(km.cluster_centers_) + assert_array_equal(pred, np.arange(10)) + + +@pytest.mark.parametrize("X_csr", X_as_any_csr) +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_dense_sparse(Estimator, X_csr, global_random_seed): + # Check that the results are the same for dense and sparse input. + sample_weight = np.random.RandomState(global_random_seed).random_sample( + (n_samples,) + ) + km_dense = Estimator( + n_clusters=n_clusters, random_state=global_random_seed, n_init=1 + ) + km_dense.fit(X, sample_weight=sample_weight) + km_sparse = Estimator( + n_clusters=n_clusters, random_state=global_random_seed, n_init=1 + ) + km_sparse.fit(X_csr, sample_weight=sample_weight) + + assert_array_equal(km_dense.labels_, km_sparse.labels_) + assert_allclose(km_dense.cluster_centers_, km_sparse.cluster_centers_) + + +@pytest.mark.parametrize("X_csr", X_as_any_csr) +@pytest.mark.parametrize( + "init", ["random", "k-means++", centers], ids=["random", "k-means++", "ndarray"] +) +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_predict_dense_sparse(Estimator, init, X_csr): + # check that models trained on sparse input also works for dense input at + # predict time and vice versa. + n_init = 10 if isinstance(init, str) else 1 + km = Estimator(n_clusters=n_clusters, init=init, n_init=n_init, random_state=0) + + km.fit(X_csr) + assert_array_equal(km.predict(X), km.labels_) + + km.fit(X) + assert_array_equal(km.predict(X_csr), km.labels_) + + +@pytest.mark.parametrize("array_constr", data_containers, ids=data_containers_ids) +@pytest.mark.parametrize("dtype", [np.int32, np.int64]) +@pytest.mark.parametrize("init", ["k-means++", "ndarray"]) +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_integer_input(Estimator, array_constr, dtype, init, global_random_seed): + # Check that KMeans and MiniBatchKMeans work with integer input. + X_dense = np.array([[0, 0], [10, 10], [12, 9], [-1, 1], [2, 0], [8, 10]]) + X = array_constr(X_dense, dtype=dtype) + + n_init = 1 if init == "ndarray" else 10 + init = X_dense[:2] if init == "ndarray" else init + + km = Estimator( + n_clusters=2, init=init, n_init=n_init, random_state=global_random_seed + ) + if Estimator is MiniBatchKMeans: + km.set_params(batch_size=2) + + km.fit(X) + + # Internally integer input should be converted to float64 + assert km.cluster_centers_.dtype == np.float64 + + expected_labels = [0, 1, 1, 0, 0, 1] + assert_allclose(v_measure_score(km.labels_, expected_labels), 1.0) + + # Same with partial_fit (#14314) + if Estimator is MiniBatchKMeans: + km = clone(km).partial_fit(X) + assert km.cluster_centers_.dtype == np.float64 + + +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_transform(Estimator, global_random_seed): + # Check the transform method + km = Estimator(n_clusters=n_clusters, random_state=global_random_seed).fit(X) + + # Transorfming cluster_centers_ should return the pairwise distances + # between centers + Xt = km.transform(km.cluster_centers_) + assert_allclose(Xt, pairwise_distances(km.cluster_centers_)) + # In particular, diagonal must be 0 + assert_array_equal(Xt.diagonal(), np.zeros(n_clusters)) + + # Transorfming X should return the pairwise distances between X and the + # centers + Xt = km.transform(X) + assert_allclose(Xt, pairwise_distances(X, km.cluster_centers_)) + + +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_fit_transform(Estimator, global_random_seed): + # Check equivalence between fit.transform and fit_transform + X1 = Estimator(random_state=global_random_seed, n_init=1).fit(X).transform(X) + X2 = Estimator(random_state=global_random_seed, n_init=1).fit_transform(X) + assert_allclose(X1, X2) + + +def test_n_init(global_random_seed): + # Check that increasing the number of init increases the quality + previous_inertia = np.inf + for n_init in [1, 5, 10]: + # set max_iter=1 to avoid finding the global minimum and get the same + # inertia each time + km = KMeans( + n_clusters=n_clusters, + init="random", + n_init=n_init, + random_state=global_random_seed, + max_iter=1, + ).fit(X) + assert km.inertia_ <= previous_inertia + + +def test_k_means_function(global_random_seed): + # test calling the k_means function directly + cluster_centers, labels, inertia = k_means( + X, n_clusters=n_clusters, sample_weight=None, random_state=global_random_seed + ) + + assert cluster_centers.shape == (n_clusters, n_features) + assert np.unique(labels).shape[0] == n_clusters + + # check that the labels assignment are perfect (up to a permutation) + assert_allclose(v_measure_score(true_labels, labels), 1.0) + assert inertia > 0.0 + + +@pytest.mark.parametrize( + "input_data", + [X] + X_as_any_csr, + ids=data_containers_ids, +) +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_float_precision(Estimator, input_data, global_random_seed): + # Check that the results are the same for single and double precision. + km = Estimator(n_init=1, random_state=global_random_seed) + + inertia = {} + Xt = {} + centers = {} + labels = {} + + for dtype in [np.float64, np.float32]: + X = input_data.astype(dtype, copy=False) + km.fit(X) + + inertia[dtype] = km.inertia_ + Xt[dtype] = km.transform(X) + centers[dtype] = km.cluster_centers_ + labels[dtype] = km.labels_ + + # dtype of cluster centers has to be the dtype of the input data + assert km.cluster_centers_.dtype == dtype + + # same with partial_fit + if Estimator is MiniBatchKMeans: + km.partial_fit(X[0:3]) + assert km.cluster_centers_.dtype == dtype + + # compare arrays with low precision since the difference between 32 and + # 64 bit comes from an accumulation of rounding errors. + assert_allclose(inertia[np.float32], inertia[np.float64], rtol=1e-4) + assert_allclose(Xt[np.float32], Xt[np.float64], atol=Xt[np.float64].max() * 1e-4) + assert_allclose( + centers[np.float32], centers[np.float64], atol=centers[np.float64].max() * 1e-4 + ) + assert_array_equal(labels[np.float32], labels[np.float64]) + + +@pytest.mark.parametrize("dtype", [np.int32, np.int64, np.float32, np.float64]) +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_centers_not_mutated(Estimator, dtype): + # Check that KMeans and MiniBatchKMeans won't mutate the user provided + # init centers silently even if input data and init centers have the same + # type. + X_new_type = X.astype(dtype, copy=False) + centers_new_type = centers.astype(dtype, copy=False) + + km = Estimator(init=centers_new_type, n_clusters=n_clusters, n_init=1) + km.fit(X_new_type) + + assert not np.may_share_memory(km.cluster_centers_, centers_new_type) + + +@pytest.mark.parametrize( + "input_data", + [X] + X_as_any_csr, + ids=data_containers_ids, +) +def test_kmeans_init_fitted_centers(input_data): + # Check that starting fitting from a local optimum shouldn't change the + # solution + km1 = KMeans(n_clusters=n_clusters).fit(input_data) + km2 = KMeans(n_clusters=n_clusters, init=km1.cluster_centers_, n_init=1).fit( + input_data + ) + + assert_allclose(km1.cluster_centers_, km2.cluster_centers_) + + +def test_kmeans_warns_less_centers_than_unique_points(global_random_seed): + # Check KMeans when the number of found clusters is smaller than expected + X = np.asarray([[0, 0], [0, 1], [1, 0], [1, 0]]) # last point is duplicated + km = KMeans(n_clusters=4, random_state=global_random_seed) + + # KMeans should warn that fewer labels than cluster centers have been used + msg = ( + r"Number of distinct clusters \(3\) found smaller than " + r"n_clusters \(4\). Possibly due to duplicate points in X." + ) + with pytest.warns(ConvergenceWarning, match=msg): + km.fit(X) + # only three distinct points, so only three clusters + # can have points assigned to them + assert set(km.labels_) == set(range(3)) + + +def _sort_centers(centers): + return np.sort(centers, axis=0) + + +def test_weighted_vs_repeated(global_random_seed): + # Check that a sample weight of N should yield the same result as an N-fold + # repetition of the sample. Valid only if init is precomputed, otherwise + # rng produces different results. Not valid for MinibatchKMeans due to rng + # to extract minibatches. + sample_weight = np.random.RandomState(global_random_seed).randint( + 1, 5, size=n_samples + ) + X_repeat = np.repeat(X, sample_weight, axis=0) + + km = KMeans( + init=centers, n_init=1, n_clusters=n_clusters, random_state=global_random_seed + ) + + km_weighted = clone(km).fit(X, sample_weight=sample_weight) + repeated_labels = np.repeat(km_weighted.labels_, sample_weight) + km_repeated = clone(km).fit(X_repeat) + + assert_array_equal(km_repeated.labels_, repeated_labels) + assert_allclose(km_weighted.inertia_, km_repeated.inertia_) + assert_allclose( + _sort_centers(km_weighted.cluster_centers_), + _sort_centers(km_repeated.cluster_centers_), + ) + + +@pytest.mark.parametrize( + "input_data", + [X] + X_as_any_csr, + ids=data_containers_ids, +) +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_unit_weights_vs_no_weights(Estimator, input_data, global_random_seed): + # Check that not passing sample weights should be equivalent to passing + # sample weights all equal to one. + sample_weight = np.ones(n_samples) + + km = Estimator(n_clusters=n_clusters, random_state=global_random_seed, n_init=1) + km_none = clone(km).fit(input_data, sample_weight=None) + km_ones = clone(km).fit(input_data, sample_weight=sample_weight) + + assert_array_equal(km_none.labels_, km_ones.labels_) + assert_allclose(km_none.cluster_centers_, km_ones.cluster_centers_) + + +@pytest.mark.parametrize( + "input_data", + [X] + X_as_any_csr, + ids=data_containers_ids, +) +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_scaled_weights(Estimator, input_data, global_random_seed): + # Check that scaling all sample weights by a common factor + # shouldn't change the result + sample_weight = np.random.RandomState(global_random_seed).uniform(size=n_samples) + + km = Estimator(n_clusters=n_clusters, random_state=global_random_seed, n_init=1) + km_orig = clone(km).fit(input_data, sample_weight=sample_weight) + km_scaled = clone(km).fit(input_data, sample_weight=0.5 * sample_weight) + + assert_array_equal(km_orig.labels_, km_scaled.labels_) + assert_allclose(km_orig.cluster_centers_, km_scaled.cluster_centers_) + + +def test_kmeans_elkan_iter_attribute(): + # Regression test on bad n_iter_ value. Previous bug n_iter_ was one off + # it's right value (#11340). + km = KMeans(algorithm="elkan", max_iter=1).fit(X) + assert km.n_iter_ == 1 + + +@pytest.mark.parametrize("array_constr", data_containers, ids=data_containers_ids) +def test_kmeans_empty_cluster_relocated(array_constr): + # check that empty clusters are correctly relocated when using sample + # weights (#13486) + X = array_constr([[-1], [1]]) + sample_weight = [1.9, 0.1] + init = np.array([[-1], [10]]) + + km = KMeans(n_clusters=2, init=init, n_init=1) + km.fit(X, sample_weight=sample_weight) + + assert len(set(km.labels_)) == 2 + assert_allclose(km.cluster_centers_, [[-1], [1]]) + + +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_result_equal_in_diff_n_threads(Estimator, global_random_seed): + # Check that KMeans/MiniBatchKMeans give the same results in parallel mode + # than in sequential mode. + rnd = np.random.RandomState(global_random_seed) + X = rnd.normal(size=(50, 10)) + + with _get_threadpool_controller().limit(limits=1, user_api="openmp"): + result_1 = ( + Estimator(n_clusters=n_clusters, random_state=global_random_seed) + .fit(X) + .labels_ + ) + with _get_threadpool_controller().limit(limits=2, user_api="openmp"): + result_2 = ( + Estimator(n_clusters=n_clusters, random_state=global_random_seed) + .fit(X) + .labels_ + ) + assert_array_equal(result_1, result_2) + + +def test_warning_elkan_1_cluster(): + # Check warning messages specific to KMeans + with pytest.warns( + RuntimeWarning, + match="algorithm='elkan' doesn't make sense for a single cluster", + ): + KMeans(n_clusters=1, algorithm="elkan").fit(X) + + +@pytest.mark.parametrize("array_constr", data_containers, ids=data_containers_ids) +@pytest.mark.parametrize("algo", ["lloyd", "elkan"]) +def test_k_means_1_iteration(array_constr, algo, global_random_seed): + # check the results after a single iteration (E-step M-step E-step) by + # comparing against a pure python implementation. + X = np.random.RandomState(global_random_seed).uniform(size=(100, 5)) + init_centers = X[:5] + X = array_constr(X) + + def py_kmeans(X, init): + new_centers = init.copy() + labels = pairwise_distances_argmin(X, init) + for label in range(init.shape[0]): + new_centers[label] = X[labels == label].mean(axis=0) + labels = pairwise_distances_argmin(X, new_centers) + return labels, new_centers + + py_labels, py_centers = py_kmeans(X, init_centers) + + cy_kmeans = KMeans( + n_clusters=5, n_init=1, init=init_centers, algorithm=algo, max_iter=1 + ).fit(X) + cy_labels = cy_kmeans.labels_ + cy_centers = cy_kmeans.cluster_centers_ + + assert_array_equal(py_labels, cy_labels) + assert_allclose(py_centers, cy_centers) + + +@pytest.mark.parametrize("dtype", [np.float32, np.float64]) +@pytest.mark.parametrize("squared", [True, False]) +def test_euclidean_distance(dtype, squared, global_random_seed): + # Check that the _euclidean_(dense/sparse)_dense helpers produce correct + # results + rng = np.random.RandomState(global_random_seed) + a_sparse = sp.random( + 1, 100, density=0.5, format="csr", random_state=rng, dtype=dtype + ) + a_dense = a_sparse.toarray().reshape(-1) + b = rng.randn(100).astype(dtype, copy=False) + b_squared_norm = (b**2).sum() + + expected = ((a_dense - b) ** 2).sum() + expected = expected if squared else np.sqrt(expected) + + distance_dense_dense = _euclidean_dense_dense_wrapper(a_dense, b, squared) + distance_sparse_dense = _euclidean_sparse_dense_wrapper( + a_sparse.data, a_sparse.indices, b, b_squared_norm, squared + ) + + rtol = 1e-4 if dtype == np.float32 else 1e-7 + assert_allclose(distance_dense_dense, distance_sparse_dense, rtol=rtol) + assert_allclose(distance_dense_dense, expected, rtol=rtol) + assert_allclose(distance_sparse_dense, expected, rtol=rtol) + + +@pytest.mark.parametrize("dtype", [np.float32, np.float64]) +def test_inertia(dtype, global_random_seed): + # Check that the _inertia_(dense/sparse) helpers produce correct results. + rng = np.random.RandomState(global_random_seed) + X_sparse = sp.random( + 100, 10, density=0.5, format="csr", random_state=rng, dtype=dtype + ) + X_dense = X_sparse.toarray() + sample_weight = rng.randn(100).astype(dtype, copy=False) + centers = rng.randn(5, 10).astype(dtype, copy=False) + labels = rng.randint(5, size=100, dtype=np.int32) + + distances = ((X_dense - centers[labels]) ** 2).sum(axis=1) + expected = np.sum(distances * sample_weight) + + inertia_dense = _inertia_dense(X_dense, sample_weight, centers, labels, n_threads=1) + inertia_sparse = _inertia_sparse( + X_sparse, sample_weight, centers, labels, n_threads=1 + ) + + rtol = 1e-4 if dtype == np.float32 else 1e-6 + assert_allclose(inertia_dense, inertia_sparse, rtol=rtol) + assert_allclose(inertia_dense, expected, rtol=rtol) + assert_allclose(inertia_sparse, expected, rtol=rtol) + + # Check the single_label parameter. + label = 1 + mask = labels == label + distances = ((X_dense[mask] - centers[label]) ** 2).sum(axis=1) + expected = np.sum(distances * sample_weight[mask]) + + inertia_dense = _inertia_dense( + X_dense, sample_weight, centers, labels, n_threads=1, single_label=label + ) + inertia_sparse = _inertia_sparse( + X_sparse, sample_weight, centers, labels, n_threads=1, single_label=label + ) + + assert_allclose(inertia_dense, inertia_sparse, rtol=rtol) + assert_allclose(inertia_dense, expected, rtol=rtol) + assert_allclose(inertia_sparse, expected, rtol=rtol) + + +@pytest.mark.parametrize("Klass, default_n_init", [(KMeans, 10), (MiniBatchKMeans, 3)]) +def test_n_init_auto(Klass, default_n_init): + est = Klass(n_init="auto", init="k-means++") + est.fit(X) + assert est._n_init == 1 + + est = Klass(n_init="auto", init="random") + est.fit(X) + assert est._n_init == 10 if Klass.__name__ == "KMeans" else 3 + + +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +def test_sample_weight_unchanged(Estimator): + # Check that sample_weight is not modified in place by KMeans (#17204) + X = np.array([[1], [2], [4]]) + sample_weight = np.array([0.5, 0.2, 0.3]) + Estimator(n_clusters=2, random_state=0).fit(X, sample_weight=sample_weight) + + assert_array_equal(sample_weight, np.array([0.5, 0.2, 0.3])) + + +@pytest.mark.parametrize("Estimator", [KMeans, MiniBatchKMeans]) +@pytest.mark.parametrize( + "param, match", + [ + ({"n_clusters": n_samples + 1}, r"n_samples.* should be >= n_clusters"), + ( + {"init": X[:2]}, + r"The shape of the initial centers .* does not match " + r"the number of clusters", + ), + ( + {"init": lambda X_, k, random_state: X_[:2]}, + r"The shape of the initial centers .* does not match " + r"the number of clusters", + ), + ( + {"init": X[:8, :2]}, + r"The shape of the initial centers .* does not match " + r"the number of features of the data", + ), + ( + {"init": lambda X_, k, random_state: X_[:8, :2]}, + r"The shape of the initial centers .* does not match " + r"the number of features of the data", + ), + ], +) +def test_wrong_params(Estimator, param, match): + # Check that error are raised with clear error message when wrong values + # are passed for the parameters + # Set n_init=1 by default to avoid warning with precomputed init + km = Estimator(n_init=1) + with pytest.raises(ValueError, match=match): + km.set_params(**param).fit(X) + + +@pytest.mark.parametrize( + "param, match", + [ + ( + {"x_squared_norms": X[:2]}, + r"The length of x_squared_norms .* should " + r"be equal to the length of n_samples", + ), + ], +) +def test_kmeans_plusplus_wrong_params(param, match): + with pytest.raises(ValueError, match=match): + kmeans_plusplus(X, n_clusters, **param) + + +@pytest.mark.parametrize( + "input_data", + [X] + X_as_any_csr, +) +@pytest.mark.parametrize("dtype", [np.float64, np.float32]) +def test_kmeans_plusplus_output(input_data, dtype, global_random_seed): + # Check for the correct number of seeds and all positive values + data = input_data.astype(dtype) + centers, indices = kmeans_plusplus( + data, n_clusters, random_state=global_random_seed + ) + + # Check there are the correct number of indices and that all indices are + # positive and within the number of samples + assert indices.shape[0] == n_clusters + assert (indices >= 0).all() + assert (indices <= data.shape[0]).all() + + # Check for the correct number of seeds and that they are bound by the data + assert centers.shape[0] == n_clusters + assert (centers.max(axis=0) <= data.max(axis=0)).all() + assert (centers.min(axis=0) >= data.min(axis=0)).all() + + # Check that indices correspond to reported centers + # Use X for comparison rather than data, test still works against centers + # calculated with sparse data. + assert_allclose(X[indices].astype(dtype), centers) + + +@pytest.mark.parametrize("x_squared_norms", [row_norms(X, squared=True), None]) +def test_kmeans_plusplus_norms(x_squared_norms): + # Check that defining x_squared_norms returns the same as default=None. + centers, indices = kmeans_plusplus(X, n_clusters, x_squared_norms=x_squared_norms) + + assert_allclose(X[indices], centers) + + +def test_kmeans_plusplus_dataorder(global_random_seed): + # Check that memory layout does not effect result + centers_c, _ = kmeans_plusplus(X, n_clusters, random_state=global_random_seed) + + X_fortran = np.asfortranarray(X) + + centers_fortran, _ = kmeans_plusplus( + X_fortran, n_clusters, random_state=global_random_seed + ) + + assert_allclose(centers_c, centers_fortran) + + +def test_is_same_clustering(): + # Sanity check for the _is_same_clustering utility function + labels1 = np.array([1, 0, 0, 1, 2, 0, 2, 1], dtype=np.int32) + assert _is_same_clustering(labels1, labels1, 3) + + # these other labels represent the same clustering since we can retrieve the first + # labels by simply renaming the labels: 0 -> 1, 1 -> 2, 2 -> 0. + labels2 = np.array([0, 2, 2, 0, 1, 2, 1, 0], dtype=np.int32) + assert _is_same_clustering(labels1, labels2, 3) + + # these other labels do not represent the same clustering since not all ones are + # mapped to a same value + labels3 = np.array([1, 0, 0, 2, 2, 0, 2, 1], dtype=np.int32) + assert not _is_same_clustering(labels1, labels3, 3) + + +@pytest.mark.parametrize( + "kwargs", ({"init": np.str_("k-means++")}, {"init": [[0, 0], [1, 1]], "n_init": 1}) +) +def test_kmeans_with_array_like_or_np_scalar_init(kwargs): + """Check that init works with numpy scalar strings. + + Non-regression test for #21964. + """ + X = np.asarray([[0, 0], [0.5, 0], [0.5, 1], [1, 1]], dtype=np.float64) + + clustering = KMeans(n_clusters=2, **kwargs) + # Does not raise + clustering.fit(X) + + +@pytest.mark.parametrize( + "Klass, method", + [(KMeans, "fit"), (MiniBatchKMeans, "fit"), (MiniBatchKMeans, "partial_fit")], +) +def test_feature_names_out(Klass, method): + """Check `feature_names_out` for `KMeans` and `MiniBatchKMeans`.""" + class_name = Klass.__name__.lower() + kmeans = Klass() + getattr(kmeans, method)(X) + n_clusters = kmeans.cluster_centers_.shape[0] + + names_out = kmeans.get_feature_names_out() + assert_array_equal([f"{class_name}{i}" for i in range(n_clusters)], names_out) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS + [None]) +def test_predict_does_not_change_cluster_centers(csr_container): + """Check that predict does not change cluster centers. + + Non-regression test for gh-24253. + """ + X, _ = make_blobs(n_samples=200, n_features=10, centers=10, random_state=0) + if csr_container is not None: + X = csr_container(X) + + kmeans = KMeans() + y_pred1 = kmeans.fit_predict(X) + # Make cluster_centers readonly + kmeans.cluster_centers_ = create_memmap_backed_data(kmeans.cluster_centers_) + kmeans.labels_ = create_memmap_backed_data(kmeans.labels_) + + y_pred2 = kmeans.predict(X) + assert_array_equal(y_pred1, y_pred2) + + +@pytest.mark.parametrize("init", ["k-means++", "random"]) +def test_sample_weight_init(init, global_random_seed): + """Check that sample weight is used during init. + + `_init_centroids` is shared across all classes inheriting from _BaseKMeans so + it's enough to check for KMeans. + """ + rng = np.random.RandomState(global_random_seed) + X, _ = make_blobs( + n_samples=200, n_features=10, centers=10, random_state=global_random_seed + ) + x_squared_norms = row_norms(X, squared=True) + + kmeans = KMeans() + clusters_weighted = kmeans._init_centroids( + X=X, + x_squared_norms=x_squared_norms, + init=init, + sample_weight=rng.uniform(size=X.shape[0]), + n_centroids=5, + random_state=np.random.RandomState(global_random_seed), + ) + clusters = kmeans._init_centroids( + X=X, + x_squared_norms=x_squared_norms, + init=init, + sample_weight=np.ones(X.shape[0]), + n_centroids=5, + random_state=np.random.RandomState(global_random_seed), + ) + with pytest.raises(AssertionError): + assert_allclose(clusters_weighted, clusters) + + +@pytest.mark.parametrize("init", ["k-means++", "random"]) +def test_sample_weight_zero(init, global_random_seed): + """Check that if sample weight is 0, this sample won't be chosen. + + `_init_centroids` is shared across all classes inheriting from _BaseKMeans so + it's enough to check for KMeans. + """ + rng = np.random.RandomState(global_random_seed) + X, _ = make_blobs( + n_samples=100, n_features=5, centers=5, random_state=global_random_seed + ) + sample_weight = rng.uniform(size=X.shape[0]) + sample_weight[::2] = 0 + x_squared_norms = row_norms(X, squared=True) + + kmeans = KMeans() + clusters_weighted = kmeans._init_centroids( + X=X, + x_squared_norms=x_squared_norms, + init=init, + sample_weight=sample_weight, + n_centroids=10, + random_state=np.random.RandomState(global_random_seed), + ) + # No center should be one of the 0 sample weight point + # (i.e. be at a distance=0 from it) + d = euclidean_distances(X[::2], clusters_weighted) + assert not np.any(np.isclose(d, 0)) + + +@pytest.mark.parametrize("array_constr", data_containers, ids=data_containers_ids) +@pytest.mark.parametrize("algorithm", ["lloyd", "elkan"]) +def test_relocating_with_duplicates(algorithm, array_constr): + """Check that kmeans stops when there are more centers than non-duplicate samples + + Non-regression test for issue: + https://github.com/scikit-learn/scikit-learn/issues/28055 + """ + X = np.array([[0, 0], [1, 1], [1, 1], [1, 0], [0, 1]]) + km = KMeans(n_clusters=5, init=X, algorithm=algorithm) + + msg = r"Number of distinct clusters \(4\) found smaller than n_clusters \(5\)" + with pytest.warns(ConvergenceWarning, match=msg): + km.fit(array_constr(X)) + + assert km.n_iter_ == 1 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_mean_shift.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_mean_shift.py new file mode 100644 index 0000000000000000000000000000000000000000..7216a064ccbc729de42688a48cae3b0be6e89bfa --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_mean_shift.py @@ -0,0 +1,215 @@ +""" +Testing for mean shift clustering methods + +""" + +import warnings + +import numpy as np +import pytest + +from sklearn.cluster import MeanShift, estimate_bandwidth, get_bin_seeds, mean_shift +from sklearn.datasets import make_blobs +from sklearn.metrics import v_measure_score +from sklearn.utils._testing import assert_allclose, assert_array_equal + +n_clusters = 3 +centers = np.array([[1, 1], [-1, -1], [1, -1]]) + 10 +X, _ = make_blobs( + n_samples=300, + n_features=2, + centers=centers, + cluster_std=0.4, + shuffle=True, + random_state=11, +) + + +def test_convergence_of_1d_constant_data(): + # Test convergence using 1D constant data + # Non-regression test for: + # https://github.com/scikit-learn/scikit-learn/issues/28926 + model = MeanShift() + n_iter = model.fit(np.ones(10).reshape(-1, 1)).n_iter_ + assert n_iter < model.max_iter + + +def test_estimate_bandwidth(): + # Test estimate_bandwidth + bandwidth = estimate_bandwidth(X, n_samples=200) + assert 0.9 <= bandwidth <= 1.5 + + +def test_estimate_bandwidth_1sample(global_dtype): + # Test estimate_bandwidth when n_samples=1 and quantile<1, so that + # n_neighbors is set to 1. + bandwidth = estimate_bandwidth( + X.astype(global_dtype, copy=False), n_samples=1, quantile=0.3 + ) + + assert bandwidth.dtype == X.dtype + assert bandwidth == pytest.approx(0.0, abs=1e-5) + + +@pytest.mark.parametrize( + "bandwidth, cluster_all, expected, first_cluster_label", + [(1.2, True, 3, 0), (1.2, False, 4, -1)], +) +def test_mean_shift( + global_dtype, bandwidth, cluster_all, expected, first_cluster_label +): + # Test MeanShift algorithm + X_with_global_dtype = X.astype(global_dtype, copy=False) + ms = MeanShift(bandwidth=bandwidth, cluster_all=cluster_all) + labels = ms.fit(X_with_global_dtype).labels_ + labels_unique = np.unique(labels) + n_clusters_ = len(labels_unique) + assert n_clusters_ == expected + assert labels_unique[0] == first_cluster_label + assert ms.cluster_centers_.dtype == global_dtype + + cluster_centers, labels_mean_shift = mean_shift( + X_with_global_dtype, cluster_all=cluster_all + ) + labels_mean_shift_unique = np.unique(labels_mean_shift) + n_clusters_mean_shift = len(labels_mean_shift_unique) + assert n_clusters_mean_shift == expected + assert labels_mean_shift_unique[0] == first_cluster_label + assert cluster_centers.dtype == global_dtype + + +def test_parallel(global_dtype, global_random_seed): + centers = np.array([[1, 1], [-1, -1], [1, -1]]) + 10 + X, _ = make_blobs( + n_samples=50, + n_features=2, + centers=centers, + cluster_std=0.4, + shuffle=True, + random_state=global_random_seed, + ) + + X = X.astype(global_dtype, copy=False) + + ms1 = MeanShift(n_jobs=2) + ms1.fit(X) + + ms2 = MeanShift() + ms2.fit(X) + + assert_allclose(ms1.cluster_centers_, ms2.cluster_centers_) + assert ms1.cluster_centers_.dtype == ms2.cluster_centers_.dtype + assert_array_equal(ms1.labels_, ms2.labels_) + + +def test_meanshift_predict(global_dtype): + # Test MeanShift.predict + ms = MeanShift(bandwidth=1.2) + X_with_global_dtype = X.astype(global_dtype, copy=False) + labels = ms.fit_predict(X_with_global_dtype) + labels2 = ms.predict(X_with_global_dtype) + assert_array_equal(labels, labels2) + + +def test_meanshift_all_orphans(): + # init away from the data, crash with a sensible warning + ms = MeanShift(bandwidth=0.1, seeds=[[-9, -9], [-10, -10]]) + msg = "No point was within bandwidth=0.1" + with pytest.raises(ValueError, match=msg): + ms.fit( + X, + ) + + +def test_unfitted(): + # Non-regression: before fit, there should be not fitted attributes. + ms = MeanShift() + assert not hasattr(ms, "cluster_centers_") + assert not hasattr(ms, "labels_") + + +def test_cluster_intensity_tie(global_dtype): + X = np.array([[1, 1], [2, 1], [1, 0], [4, 7], [3, 5], [3, 6]], dtype=global_dtype) + c1 = MeanShift(bandwidth=2).fit(X) + + X = np.array([[4, 7], [3, 5], [3, 6], [1, 1], [2, 1], [1, 0]], dtype=global_dtype) + c2 = MeanShift(bandwidth=2).fit(X) + assert_array_equal(c1.labels_, [1, 1, 1, 0, 0, 0]) + assert_array_equal(c2.labels_, [0, 0, 0, 1, 1, 1]) + + +def test_bin_seeds(global_dtype): + # Test the bin seeding technique which can be used in the mean shift + # algorithm + # Data is just 6 points in the plane + X = np.array( + [[1.0, 1.0], [1.4, 1.4], [1.8, 1.2], [2.0, 1.0], [2.1, 1.1], [0.0, 0.0]], + dtype=global_dtype, + ) + + # With a bin coarseness of 1.0 and min_bin_freq of 1, 3 bins should be + # found + ground_truth = {(1.0, 1.0), (2.0, 1.0), (0.0, 0.0)} + test_bins = get_bin_seeds(X, 1, 1) + test_result = set(tuple(p) for p in test_bins) + assert len(ground_truth.symmetric_difference(test_result)) == 0 + + # With a bin coarseness of 1.0 and min_bin_freq of 2, 2 bins should be + # found + ground_truth = {(1.0, 1.0), (2.0, 1.0)} + test_bins = get_bin_seeds(X, 1, 2) + test_result = set(tuple(p) for p in test_bins) + assert len(ground_truth.symmetric_difference(test_result)) == 0 + + # With a bin size of 0.01 and min_bin_freq of 1, 6 bins should be found + # we bail and use the whole data here. + with warnings.catch_warnings(record=True): + test_bins = get_bin_seeds(X, 0.01, 1) + assert_allclose(test_bins, X) + + # tight clusters around [0, 0] and [1, 1], only get two bins + X, _ = make_blobs( + n_samples=100, + n_features=2, + centers=[[0, 0], [1, 1]], + cluster_std=0.1, + random_state=0, + ) + X = X.astype(global_dtype, copy=False) + test_bins = get_bin_seeds(X, 1) + assert_array_equal(test_bins, [[0, 0], [1, 1]]) + + +@pytest.mark.parametrize("max_iter", [1, 100]) +def test_max_iter(max_iter): + clusters1, _ = mean_shift(X, max_iter=max_iter) + ms = MeanShift(max_iter=max_iter).fit(X) + clusters2 = ms.cluster_centers_ + + assert ms.n_iter_ <= ms.max_iter + assert len(clusters1) == len(clusters2) + + for c1, c2 in zip(clusters1, clusters2): + assert np.allclose(c1, c2) + + +def test_mean_shift_zero_bandwidth(global_dtype): + # Check that mean shift works when the estimated bandwidth is 0. + X = np.array([1, 1, 1, 2, 2, 2, 3, 3], dtype=global_dtype).reshape(-1, 1) + + # estimate_bandwidth with default args returns 0 on this dataset + bandwidth = estimate_bandwidth(X) + assert bandwidth == 0 + + # get_bin_seeds with a 0 bin_size should return the dataset itself + assert get_bin_seeds(X, bin_size=bandwidth) is X + + # MeanShift with binning and a 0 estimated bandwidth should be equivalent + # to no binning. + ms_binning = MeanShift(bin_seeding=True, bandwidth=None).fit(X) + ms_nobinning = MeanShift(bin_seeding=False).fit(X) + expected_labels = np.array([0, 0, 0, 1, 1, 1, 2, 2]) + + assert v_measure_score(ms_binning.labels_, expected_labels) == pytest.approx(1) + assert v_measure_score(ms_nobinning.labels_, expected_labels) == pytest.approx(1) + assert_allclose(ms_binning.cluster_centers_, ms_nobinning.cluster_centers_) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_optics.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_optics.py new file mode 100644 index 0000000000000000000000000000000000000000..02184ea454d65cc1f2d9d95f265e52d307c30543 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_optics.py @@ -0,0 +1,874 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings + +import numpy as np +import pytest + +from sklearn.cluster import DBSCAN, OPTICS +from sklearn.cluster._optics import _extend_region, _extract_xi_labels +from sklearn.cluster.tests.common import generate_clustered_data +from sklearn.datasets import make_blobs +from sklearn.exceptions import DataConversionWarning, EfficiencyWarning +from sklearn.metrics.cluster import contingency_matrix +from sklearn.metrics.pairwise import pairwise_distances +from sklearn.utils import shuffle +from sklearn.utils._testing import assert_allclose, assert_array_equal +from sklearn.utils.fixes import CSR_CONTAINERS + +rng = np.random.RandomState(0) +n_points_per_cluster = 10 +C1 = [-5, -2] + 0.8 * rng.randn(n_points_per_cluster, 2) +C2 = [4, -1] + 0.1 * rng.randn(n_points_per_cluster, 2) +C3 = [1, -2] + 0.2 * rng.randn(n_points_per_cluster, 2) +C4 = [-2, 3] + 0.3 * rng.randn(n_points_per_cluster, 2) +C5 = [3, -2] + 1.6 * rng.randn(n_points_per_cluster, 2) +C6 = [5, 6] + 2 * rng.randn(n_points_per_cluster, 2) +X = np.vstack((C1, C2, C3, C4, C5, C6)) + + +@pytest.mark.parametrize( + ("r_plot", "end"), + [ + [[10, 8.9, 8.8, 8.7, 7, 10], 3], + [[10, 8.9, 8.8, 8.7, 8.6, 7, 10], 0], + [[10, 8.9, 8.8, 8.7, 7, 6, np.inf], 4], + [[10, 8.9, 8.8, 8.7, 7, 6, np.inf], 4], + ], +) +def test_extend_downward(r_plot, end): + r_plot = np.array(r_plot) + ratio = r_plot[:-1] / r_plot[1:] + steep_downward = ratio >= 1 / 0.9 + upward = ratio < 1 + + e = _extend_region(steep_downward, upward, 0, 2) + assert e == end + + +@pytest.mark.parametrize( + ("r_plot", "end"), + [ + [[1, 2, 2.1, 2.2, 4, 8, 8, np.inf], 6], + [[1, 2, 2.1, 2.2, 2.3, 4, 8, 8, np.inf], 0], + [[1, 2, 2.1, 2, np.inf], 0], + [[1, 2, 2.1, np.inf], 2], + ], +) +def test_extend_upward(r_plot, end): + r_plot = np.array(r_plot) + ratio = r_plot[:-1] / r_plot[1:] + steep_upward = ratio <= 0.9 + downward = ratio > 1 + + e = _extend_region(steep_upward, downward, 0, 2) + assert e == end + + +@pytest.mark.parametrize( + ("ordering", "clusters", "expected"), + [ + [[0, 1, 2, 3], [[0, 1], [2, 3]], [0, 0, 1, 1]], + [[0, 1, 2, 3], [[0, 1], [3, 3]], [0, 0, -1, 1]], + [[0, 1, 2, 3], [[0, 1], [3, 3], [0, 3]], [0, 0, -1, 1]], + [[3, 1, 2, 0], [[0, 1], [3, 3], [0, 3]], [1, 0, -1, 0]], + ], +) +def test_the_extract_xi_labels(ordering, clusters, expected): + labels = _extract_xi_labels(ordering, clusters) + + assert_array_equal(labels, expected) + + +def test_extract_xi(global_dtype): + # small and easy test (no clusters around other clusters) + # but with a clear noise data. + # global_random_seed is not used here since the expected labels + # are hardcoded for these specific data. + rng = np.random.RandomState(0) + n_points_per_cluster = 5 + + C1 = [-5, -2] + 0.8 * rng.randn(n_points_per_cluster, 2) + C2 = [4, -1] + 0.1 * rng.randn(n_points_per_cluster, 2) + C3 = [1, -2] + 0.2 * rng.randn(n_points_per_cluster, 2) + C4 = [-2, 3] + 0.3 * rng.randn(n_points_per_cluster, 2) + C5 = [3, -2] + 0.6 * rng.randn(n_points_per_cluster, 2) + C6 = [5, 6] + 0.2 * rng.randn(n_points_per_cluster, 2) + + X = np.vstack((C1, C2, C3, C4, C5, np.array([[100, 100]]), C6)).astype( + global_dtype, copy=False + ) + expected_labels = np.r_[[2] * 5, [0] * 5, [1] * 5, [3] * 5, [1] * 5, -1, [4] * 5] + X, expected_labels = shuffle(X, expected_labels, random_state=rng) + + clust = OPTICS( + min_samples=3, min_cluster_size=2, max_eps=20, cluster_method="xi", xi=0.4 + ).fit(X) + assert_array_equal(clust.labels_, expected_labels) + + # check float min_samples and min_cluster_size + clust = OPTICS( + min_samples=0.1, min_cluster_size=0.08, max_eps=20, cluster_method="xi", xi=0.4 + ).fit(X) + assert_array_equal(clust.labels_, expected_labels) + + X = np.vstack((C1, C2, C3, C4, C5, np.array([[100, 100]] * 2), C6)).astype( + global_dtype, copy=False + ) + expected_labels = np.r_[ + [1] * 5, [3] * 5, [2] * 5, [0] * 5, [2] * 5, -1, -1, [4] * 5 + ] + X, expected_labels = shuffle(X, expected_labels, random_state=rng) + + clust = OPTICS( + min_samples=3, min_cluster_size=3, max_eps=20, cluster_method="xi", xi=0.3 + ).fit(X) + # this may fail if the predecessor correction is not at work! + assert_array_equal(clust.labels_, expected_labels) + + C1 = [[0, 0], [0, 0.1], [0, -0.1], [0.1, 0]] + C2 = [[10, 10], [10, 9], [10, 11], [9, 10]] + C3 = [[100, 100], [100, 90], [100, 110], [90, 100]] + X = np.vstack((C1, C2, C3)).astype(global_dtype, copy=False) + expected_labels = np.r_[[0] * 4, [1] * 4, [2] * 4] + X, expected_labels = shuffle(X, expected_labels, random_state=rng) + + clust = OPTICS( + min_samples=2, min_cluster_size=2, max_eps=np.inf, cluster_method="xi", xi=0.04 + ).fit(X) + assert_array_equal(clust.labels_, expected_labels) + + +def test_cluster_hierarchy(global_dtype, global_random_seed): + rng = np.random.RandomState(global_random_seed) + n_points_per_cluster = 100 + C1 = [0, 0] + 2 * rng.randn(n_points_per_cluster, 2).astype( + global_dtype, copy=False + ) + C2 = [0, 0] + 50 * rng.randn(n_points_per_cluster, 2).astype( + global_dtype, copy=False + ) + X = np.vstack((C1, C2)) + X = shuffle(X, random_state=rng) + + clusters = OPTICS(min_samples=20, xi=0.2).fit(X).cluster_hierarchy_ + assert clusters.shape == (2, 2) + + # The first cluster should contain all point from C1 but due to how the data is + # generated, some points from C2 may end up in it. + assert 100 <= np.diff(clusters[0]) + 1 <= 115 + # The second cluster should contain all points from C1 and C2. + assert np.diff(clusters[-1]) + 1 == 200 + + +@pytest.mark.parametrize( + "csr_container, metric", + [(None, "minkowski")] + [(container, "euclidean") for container in CSR_CONTAINERS], +) +def test_correct_number_of_clusters(metric, csr_container): + # in 'auto' mode + + n_clusters = 3 + X = generate_clustered_data(n_clusters=n_clusters) + # Parameters chosen specifically for this task. + # Compute OPTICS + clust = OPTICS(max_eps=5.0 * 6.0, min_samples=4, xi=0.1, metric=metric) + clust.fit(csr_container(X) if csr_container is not None else X) + # number of clusters, ignoring noise if present + n_clusters_1 = len(set(clust.labels_)) - int(-1 in clust.labels_) + assert n_clusters_1 == n_clusters + + # check attribute types and sizes + assert clust.labels_.shape == (len(X),) + assert clust.labels_.dtype.kind == "i" + + assert clust.reachability_.shape == (len(X),) + assert clust.reachability_.dtype.kind == "f" + + assert clust.core_distances_.shape == (len(X),) + assert clust.core_distances_.dtype.kind == "f" + + assert clust.ordering_.shape == (len(X),) + assert clust.ordering_.dtype.kind == "i" + assert set(clust.ordering_) == set(range(len(X))) + + +def test_minimum_number_of_sample_check(): + # test that we check a minimum number of samples + msg = "min_samples must be no greater than" + + # Compute OPTICS + X = [[1, 1]] + clust = OPTICS(max_eps=5.0 * 0.3, min_samples=10, min_cluster_size=1.0) + + # Run the fit + with pytest.raises(ValueError, match=msg): + clust.fit(X) + + +def test_bad_extract(): + # Test an extraction of eps too close to original eps + msg = "Specify an epsilon smaller than 0.15. Got 0.3." + centers = [[1, 1], [-1, -1], [1, -1]] + X, labels_true = make_blobs( + n_samples=750, centers=centers, cluster_std=0.4, random_state=0 + ) + + # Compute OPTICS + clust = OPTICS(max_eps=5.0 * 0.03, cluster_method="dbscan", eps=0.3, min_samples=10) + with pytest.raises(ValueError, match=msg): + clust.fit(X) + + +def test_bad_reachability(): + msg = "All reachability values are inf. Set a larger max_eps." + centers = [[1, 1], [-1, -1], [1, -1]] + X, labels_true = make_blobs( + n_samples=750, centers=centers, cluster_std=0.4, random_state=0 + ) + + with pytest.warns(UserWarning, match=msg): + clust = OPTICS(max_eps=5.0 * 0.003, min_samples=10, eps=0.015) + clust.fit(X) + + +def test_nowarn_if_metric_bool_data_bool(): + # make sure no warning is raised if metric and data are both boolean + # non-regression test for + # https://github.com/scikit-learn/scikit-learn/issues/18996 + + pairwise_metric = "rogerstanimoto" + X = np.random.randint(2, size=(5, 2), dtype=bool) + + with warnings.catch_warnings(): + warnings.simplefilter("error", DataConversionWarning) + + OPTICS(metric=pairwise_metric).fit(X) + + +def test_warn_if_metric_bool_data_no_bool(): + # make sure a *single* conversion warning is raised if metric is boolean + # but data isn't + # non-regression test for + # https://github.com/scikit-learn/scikit-learn/issues/18996 + + pairwise_metric = "rogerstanimoto" + X = np.random.randint(2, size=(5, 2), dtype=np.int32) + msg = f"Data will be converted to boolean for metric {pairwise_metric}" + + with pytest.warns(DataConversionWarning, match=msg) as warn_record: + # Silence a DeprecationWarning from joblib <= 1.5.1 in Python 3.14+. + warnings.filterwarnings( + "ignore", + message="'asyncio.iscoroutinefunction' is deprecated", + category=DeprecationWarning, + ) + OPTICS(metric=pairwise_metric).fit(X) + assert len(warn_record) == 1 + + +def test_nowarn_if_metric_no_bool(): + # make sure no conversion warning is raised if + # metric isn't boolean, no matter what the data type is + pairwise_metric = "minkowski" + X_bool = np.random.randint(2, size=(5, 2), dtype=bool) + X_num = np.random.randint(2, size=(5, 2), dtype=np.int32) + + with warnings.catch_warnings(): + warnings.simplefilter("error", DataConversionWarning) + + # fit boolean data + OPTICS(metric=pairwise_metric).fit(X_bool) + # fit numeric data + OPTICS(metric=pairwise_metric).fit(X_num) + + +def test_close_extract(): + # Test extract where extraction eps is close to scaled max_eps + + centers = [[1, 1], [-1, -1], [1, -1]] + X, labels_true = make_blobs( + n_samples=750, centers=centers, cluster_std=0.4, random_state=0 + ) + + # Compute OPTICS + clust = OPTICS(max_eps=1.0, cluster_method="dbscan", eps=0.3, min_samples=10).fit(X) + # Cluster ordering starts at 0; max cluster label = 2 is 3 clusters + assert max(clust.labels_) == 2 + + +@pytest.mark.parametrize("eps", [0.1, 0.3, 0.5]) +@pytest.mark.parametrize("min_samples", [3, 10, 20]) +@pytest.mark.parametrize( + "csr_container, metric", + [(None, "minkowski"), (None, "euclidean")] + + [(container, "euclidean") for container in CSR_CONTAINERS], +) +def test_dbscan_optics_parity(eps, min_samples, metric, global_dtype, csr_container): + # Test that OPTICS clustering labels are <= 5% difference of DBSCAN + + centers = [[1, 1], [-1, -1], [1, -1]] + X, labels_true = make_blobs( + n_samples=150, centers=centers, cluster_std=0.4, random_state=0 + ) + X = csr_container(X) if csr_container is not None else X + + X = X.astype(global_dtype, copy=False) + + # calculate optics with dbscan extract at 0.3 epsilon + op = OPTICS( + min_samples=min_samples, cluster_method="dbscan", eps=eps, metric=metric + ).fit(X) + + # calculate dbscan labels + db = DBSCAN(eps=eps, min_samples=min_samples).fit(X) + + contingency = contingency_matrix(db.labels_, op.labels_) + agree = min( + np.sum(np.max(contingency, axis=0)), np.sum(np.max(contingency, axis=1)) + ) + disagree = X.shape[0] - agree + + percent_mismatch = np.round((disagree - 1) / X.shape[0], 2) + + # verify label mismatch is <= 5% labels + assert percent_mismatch <= 0.05 + + +def test_min_samples_edge_case(global_dtype): + C1 = [[0, 0], [0, 0.1], [0, -0.1]] + C2 = [[10, 10], [10, 9], [10, 11]] + C3 = [[100, 100], [100, 96], [100, 106]] + X = np.vstack((C1, C2, C3)).astype(global_dtype, copy=False) + + expected_labels = np.r_[[0] * 3, [1] * 3, [2] * 3] + clust = OPTICS(min_samples=3, max_eps=7, cluster_method="xi", xi=0.04).fit(X) + assert_array_equal(clust.labels_, expected_labels) + + expected_labels = np.r_[[0] * 3, [1] * 3, [-1] * 3] + clust = OPTICS(min_samples=3, max_eps=3, cluster_method="xi", xi=0.04).fit(X) + assert_array_equal(clust.labels_, expected_labels) + + expected_labels = np.r_[[-1] * 9] + with pytest.warns(UserWarning, match="All reachability values"): + clust = OPTICS(min_samples=4, max_eps=3, cluster_method="xi", xi=0.04).fit(X) + assert_array_equal(clust.labels_, expected_labels) + + +# try arbitrary minimum sizes +@pytest.mark.parametrize("min_cluster_size", range(2, X.shape[0] // 10, 23)) +def test_min_cluster_size(min_cluster_size, global_dtype): + redX = X[::2].astype(global_dtype, copy=False) # reduce for speed + clust = OPTICS(min_samples=9, min_cluster_size=min_cluster_size).fit(redX) + cluster_sizes = np.bincount(clust.labels_[clust.labels_ != -1]) + if cluster_sizes.size: + assert min(cluster_sizes) >= min_cluster_size + # check behaviour is the same when min_cluster_size is a fraction + clust_frac = OPTICS( + min_samples=9, + min_cluster_size=min_cluster_size / redX.shape[0], + ) + clust_frac.fit(redX) + assert_array_equal(clust.labels_, clust_frac.labels_) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_min_cluster_size_invalid2(csr_container): + clust = OPTICS(min_cluster_size=len(X) + 1) + with pytest.raises(ValueError, match="must be no greater than the "): + clust.fit(X) + + clust = OPTICS(min_cluster_size=len(X) + 1, metric="euclidean") + with pytest.raises(ValueError, match="must be no greater than the "): + clust.fit(csr_container(X)) + + +def test_processing_order(): + # Ensure that we consider all unprocessed points, + # not only direct neighbors. when picking the next point. + Y = [[0], [10], [-10], [25]] + + clust = OPTICS(min_samples=3, max_eps=15).fit(Y) + assert_array_equal(clust.reachability_, [np.inf, 10, 10, 15]) + assert_array_equal(clust.core_distances_, [10, 15, np.inf, np.inf]) + assert_array_equal(clust.ordering_, [0, 1, 2, 3]) + + +def test_compare_to_ELKI(): + # Expected values, computed with (future) ELKI 0.7.5 using: + # java -jar elki.jar cli -dbc.in csv -dbc.filter FixedDBIDsFilter + # -algorithm clustering.optics.OPTICSHeap -optics.minpts 5 + # where the FixedDBIDsFilter gives 0-indexed ids. + r1 = [ + np.inf, + 1.0574896366427478, + 0.7587934993548423, + 0.7290174038973836, + 0.7290174038973836, + 0.7290174038973836, + 0.6861627576116127, + 0.7587934993548423, + 0.9280118450166668, + 1.1748022534146194, + 3.3355455741292257, + 0.49618389254482587, + 0.2552805046961355, + 0.2552805046961355, + 0.24944622248445714, + 0.24944622248445714, + 0.24944622248445714, + 0.2552805046961355, + 0.2552805046961355, + 0.3086779122185853, + 4.163024452756142, + 1.623152630340929, + 0.45315840475822655, + 0.25468325192031926, + 0.2254004358159971, + 0.18765711877083036, + 0.1821471333893275, + 0.1821471333893275, + 0.18765711877083036, + 0.18765711877083036, + 0.2240202988740153, + 1.154337614548715, + 1.342604473837069, + 1.323308536402633, + 0.8607514948648837, + 0.27219111215810565, + 0.13260875220533205, + 0.13260875220533205, + 0.09890587675958984, + 0.09890587675958984, + 0.13548790801634494, + 0.1575483940837384, + 0.17515137170530226, + 0.17575920159442388, + 0.27219111215810565, + 0.6101447895405373, + 1.3189208094864302, + 1.323308536402633, + 2.2509184159764577, + 2.4517810628594527, + 3.675977064404973, + 3.8264795626020365, + 2.9130735341510614, + 2.9130735341510614, + 2.9130735341510614, + 2.9130735341510614, + 2.8459300127258036, + 2.8459300127258036, + 2.8459300127258036, + 3.0321982337972537, + ] + o1 = [ + 0, + 3, + 6, + 4, + 7, + 8, + 2, + 9, + 5, + 1, + 31, + 30, + 32, + 34, + 33, + 38, + 39, + 35, + 37, + 36, + 44, + 21, + 23, + 24, + 22, + 25, + 27, + 29, + 26, + 28, + 20, + 40, + 45, + 46, + 10, + 15, + 11, + 13, + 17, + 19, + 18, + 12, + 16, + 14, + 47, + 49, + 43, + 48, + 42, + 41, + 53, + 57, + 51, + 52, + 56, + 59, + 54, + 55, + 58, + 50, + ] + p1 = [ + -1, + 0, + 3, + 6, + 6, + 6, + 8, + 3, + 7, + 5, + 1, + 31, + 30, + 30, + 34, + 34, + 34, + 32, + 32, + 37, + 36, + 44, + 21, + 23, + 24, + 22, + 25, + 25, + 22, + 22, + 22, + 21, + 40, + 45, + 46, + 10, + 15, + 15, + 13, + 13, + 15, + 11, + 19, + 15, + 10, + 47, + 12, + 45, + 14, + 43, + 42, + 53, + 57, + 57, + 57, + 57, + 59, + 59, + 59, + 58, + ] + + # Tests against known extraction array + # Does NOT work with metric='euclidean', because sklearn euclidean has + # worse numeric precision. 'minkowski' is slower but more accurate. + clust1 = OPTICS(min_samples=5).fit(X) + + assert_array_equal(clust1.ordering_, np.array(o1)) + assert_array_equal(clust1.predecessor_[clust1.ordering_], np.array(p1)) + assert_allclose(clust1.reachability_[clust1.ordering_], np.array(r1)) + # ELKI currently does not print the core distances (which are not used much + # in literature, but we can at least ensure to have this consistency: + for i in clust1.ordering_[1:]: + assert clust1.reachability_[i] >= clust1.core_distances_[clust1.predecessor_[i]] + + # Expected values, computed with (future) ELKI 0.7.5 using + r2 = [ + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + 0.27219111215810565, + 0.13260875220533205, + 0.13260875220533205, + 0.09890587675958984, + 0.09890587675958984, + 0.13548790801634494, + 0.1575483940837384, + 0.17515137170530226, + 0.17575920159442388, + 0.27219111215810565, + 0.4928068613197889, + np.inf, + 0.2666183922512113, + 0.18765711877083036, + 0.1821471333893275, + 0.1821471333893275, + 0.1821471333893275, + 0.18715928772277457, + 0.18765711877083036, + 0.18765711877083036, + 0.25468325192031926, + np.inf, + 0.2552805046961355, + 0.2552805046961355, + 0.24944622248445714, + 0.24944622248445714, + 0.24944622248445714, + 0.2552805046961355, + 0.2552805046961355, + 0.3086779122185853, + 0.34466409325984865, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + np.inf, + ] + o2 = [ + 0, + 1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 15, + 11, + 13, + 17, + 19, + 18, + 12, + 16, + 14, + 47, + 46, + 20, + 22, + 25, + 23, + 27, + 29, + 24, + 26, + 28, + 21, + 30, + 32, + 34, + 33, + 38, + 39, + 35, + 37, + 36, + 31, + 40, + 41, + 42, + 43, + 44, + 45, + 48, + 49, + 50, + 51, + 52, + 53, + 54, + 55, + 56, + 57, + 58, + 59, + ] + p2 = [ + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + 10, + 15, + 15, + 13, + 13, + 15, + 11, + 19, + 15, + 10, + 47, + -1, + 20, + 22, + 25, + 25, + 25, + 25, + 22, + 22, + 23, + -1, + 30, + 30, + 34, + 34, + 34, + 32, + 32, + 37, + 38, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + -1, + ] + clust2 = OPTICS(min_samples=5, max_eps=0.5).fit(X) + + assert_array_equal(clust2.ordering_, np.array(o2)) + assert_array_equal(clust2.predecessor_[clust2.ordering_], np.array(p2)) + assert_allclose(clust2.reachability_[clust2.ordering_], np.array(r2)) + + index = np.where(clust1.core_distances_ <= 0.5)[0] + assert_allclose(clust1.core_distances_[index], clust2.core_distances_[index]) + + +def test_extract_dbscan(global_dtype, global_random_seed): + # testing an easy dbscan case. Not including clusters with different + # densities. + rng = np.random.RandomState(global_random_seed) + n_points_per_cluster = 20 + C1 = [-5, -2] + 0.2 * rng.randn(n_points_per_cluster, 2) + C2 = [4, -1] + 0.2 * rng.randn(n_points_per_cluster, 2) + C3 = [1, 2] + 0.2 * rng.randn(n_points_per_cluster, 2) + C4 = [-2, 3] + 0.2 * rng.randn(n_points_per_cluster, 2) + X = np.vstack((C1, C2, C3, C4)).astype(global_dtype, copy=False) + + clust = OPTICS(cluster_method="dbscan", eps=0.5).fit(X) + assert_array_equal( + np.sort(np.unique(clust.labels_[clust.labels_ != -1])), [0, 1, 2, 3] + ) + + +@pytest.mark.parametrize("csr_container", [None] + CSR_CONTAINERS) +def test_precomputed_dists(global_dtype, csr_container): + redX = X[::2].astype(global_dtype, copy=False) + dists = pairwise_distances(redX, metric="euclidean") + dists = csr_container(dists) if csr_container is not None else dists + with warnings.catch_warnings(): + warnings.simplefilter("ignore", EfficiencyWarning) + clust1 = OPTICS(min_samples=10, algorithm="brute", metric="precomputed").fit( + dists + ) + clust2 = OPTICS(min_samples=10, algorithm="brute", metric="euclidean").fit(redX) + + assert_allclose(clust1.reachability_, clust2.reachability_) + assert_array_equal(clust1.labels_, clust2.labels_) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_optics_input_not_modified_precomputed_sparse_nodiag( + csr_container, global_random_seed +): + """Check that we don't modify in-place the pre-computed sparse matrix. + Non-regression test for: + https://github.com/scikit-learn/scikit-learn/issues/27508 + """ + X = np.random.RandomState(global_random_seed).rand(6, 6) + # Add zeros on the diagonal that will be implicit when creating + # the sparse matrix. If `X` is modified in-place, the zeros from + # the diagonal will be made explicit. + np.fill_diagonal(X, 0) + X = csr_container(X) + assert all(row != col for row, col in zip(*X.nonzero())) + X_copy = X.copy() + OPTICS(metric="precomputed").fit(X) + # Make sure that we did not modify `X` in-place even by creating + # explicit 0s values. + assert X.nnz == X_copy.nnz + assert_array_equal(X.toarray(), X_copy.toarray()) + + +def test_optics_predecessor_correction_ordering(): + """Check that cluster correction using predecessor is working as expected. + + In the following example, the predecessor correction was not working properly + since it was not using the right indices. + + This non-regression test check that reordering the data does not change the results. + + Non-regression test for: + https://github.com/scikit-learn/scikit-learn/issues/26324 + """ + X_1 = np.array([1, 2, 3, 1, 8, 8, 7, 100]).reshape(-1, 1) + reorder = [0, 1, 2, 4, 5, 6, 7, 3] + X_2 = X_1[reorder] + + optics_1 = OPTICS(min_samples=3, metric="euclidean").fit(X_1) + optics_2 = OPTICS(min_samples=3, metric="euclidean").fit(X_2) + + assert_array_equal(optics_1.labels_[reorder], optics_2.labels_) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_spectral.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_spectral.py new file mode 100644 index 0000000000000000000000000000000000000000..71b11c9fe151c310f4fd5a60f99323360e493506 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cluster/tests/test_spectral.py @@ -0,0 +1,335 @@ +"""Testing for Spectral Clustering methods""" + +import pickle +import re + +import numpy as np +import pytest +from scipy.linalg import LinAlgError + +from sklearn.cluster import SpectralClustering, spectral_clustering +from sklearn.cluster._spectral import cluster_qr, discretize +from sklearn.datasets import make_blobs +from sklearn.feature_extraction import img_to_graph +from sklearn.metrics import adjusted_rand_score +from sklearn.metrics.pairwise import kernel_metrics, rbf_kernel +from sklearn.neighbors import NearestNeighbors +from sklearn.utils import check_random_state +from sklearn.utils._testing import assert_array_equal +from sklearn.utils.fixes import COO_CONTAINERS, CSR_CONTAINERS + +try: + from pyamg import smoothed_aggregation_solver # noqa: F401 + + amg_loaded = True +except ImportError: + amg_loaded = False + +centers = np.array([[1, 1], [-1, -1], [1, -1]]) + 10 +X, _ = make_blobs( + n_samples=60, + n_features=2, + centers=centers, + cluster_std=0.4, + shuffle=True, + random_state=0, +) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +@pytest.mark.parametrize("eigen_solver", ("arpack", "lobpcg")) +@pytest.mark.parametrize("assign_labels", ("kmeans", "discretize", "cluster_qr")) +def test_spectral_clustering( + eigen_solver, assign_labels, csr_container, global_random_seed +): + S = np.array( + [ + [1.0, 1.0, 1.0, 0.2, 0.0, 0.0, 0.0], + [1.0, 1.0, 1.0, 0.2, 0.0, 0.0, 0.0], + [1.0, 1.0, 1.0, 0.2, 0.0, 0.0, 0.0], + [0.2, 0.2, 0.2, 1.0, 1.0, 1.0, 1.0], + [0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 1.0], + [0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 1.0], + [0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 1.0], + ] + ) + + for mat in (S, csr_container(S)): + model = SpectralClustering( + random_state=global_random_seed, + n_clusters=2, + affinity="precomputed", + eigen_solver=eigen_solver, + assign_labels=assign_labels, + ).fit(mat) + labels = model.labels_ + if labels[0] == 0: + labels = 1 - labels + + assert adjusted_rand_score(labels, [1, 1, 1, 0, 0, 0, 0]) == 1 + + model_copy = pickle.loads(pickle.dumps(model)) + assert model_copy.n_clusters == model.n_clusters + assert model_copy.eigen_solver == model.eigen_solver + assert_array_equal(model_copy.labels_, model.labels_) + + +@pytest.mark.parametrize("coo_container", COO_CONTAINERS) +@pytest.mark.parametrize("assign_labels", ("kmeans", "discretize", "cluster_qr")) +def test_spectral_clustering_sparse(assign_labels, coo_container, global_random_seed): + X, y = make_blobs( + n_samples=20, + random_state=global_random_seed, + centers=[[1, 1], [-1, -1]], + cluster_std=0.01, + ) + + S = rbf_kernel(X, gamma=1) + S = np.maximum(S - 1e-4, 0) + S = coo_container(S) + + labels = ( + SpectralClustering( + random_state=global_random_seed, + n_clusters=2, + affinity="precomputed", + assign_labels=assign_labels, + ) + .fit(S) + .labels_ + ) + assert adjusted_rand_score(y, labels) == 1 + + +def test_precomputed_nearest_neighbors_filtering(global_random_seed): + # Test precomputed graph filtering when containing too many neighbors + X, y = make_blobs( + n_samples=250, + random_state=global_random_seed, + centers=[[1, 1, 1], [-1, -1, -1]], + cluster_std=0.01, + ) + + n_neighbors = 2 + results = [] + for additional_neighbors in [0, 10]: + nn = NearestNeighbors(n_neighbors=n_neighbors + additional_neighbors).fit(X) + graph = nn.kneighbors_graph(X, mode="distance") + labels = ( + SpectralClustering( + random_state=global_random_seed, + n_clusters=2, + affinity="precomputed_nearest_neighbors", + n_neighbors=n_neighbors, + ) + .fit(graph) + .labels_ + ) + results.append(labels) + + assert_array_equal(results[0], results[1]) + + +def test_affinities(global_random_seed): + # Note: in the following, random_state has been selected to have + # a dataset that yields a stable eigen decomposition both when built + # on OSX and Linux + X, y = make_blobs( + n_samples=20, random_state=0, centers=[[1, 1], [-1, -1]], cluster_std=0.01 + ) + # nearest neighbors affinity + sp = SpectralClustering(n_clusters=2, affinity="nearest_neighbors", random_state=0) + with pytest.warns(UserWarning, match="not fully connected"): + sp.fit(X) + assert adjusted_rand_score(y, sp.labels_) == 1 + + sp = SpectralClustering(n_clusters=2, gamma=2, random_state=global_random_seed) + labels = sp.fit(X).labels_ + assert adjusted_rand_score(y, labels) == 1 + + X = check_random_state(10).rand(10, 5) * 10 + + kernels_available = kernel_metrics() + for kern in kernels_available: + # Additive chi^2 gives a negative similarity matrix which + # doesn't make sense for spectral clustering + if kern != "additive_chi2": + sp = SpectralClustering(n_clusters=2, affinity=kern, random_state=0) + labels = sp.fit(X).labels_ + assert (X.shape[0],) == labels.shape + + sp = SpectralClustering(n_clusters=2, affinity=lambda x, y: 1, random_state=0) + labels = sp.fit(X).labels_ + assert (X.shape[0],) == labels.shape + + def histogram(x, y, **kwargs): + # Histogram kernel implemented as a callable. + assert kwargs == {} # no kernel_params that we didn't ask for + return np.minimum(x, y).sum() + + sp = SpectralClustering(n_clusters=2, affinity=histogram, random_state=0) + labels = sp.fit(X).labels_ + assert (X.shape[0],) == labels.shape + + +def test_cluster_qr(global_random_seed): + # cluster_qr by itself should not be used for clustering generic data + # other than the rows of the eigenvectors within spectral clustering, + # but cluster_qr must still preserve the labels for different dtypes + # of the generic fixed input even if the labels may be meaningless. + random_state = np.random.RandomState(seed=global_random_seed) + n_samples, n_components = 10, 5 + data = random_state.randn(n_samples, n_components) + labels_float64 = cluster_qr(data.astype(np.float64)) + # Each sample is assigned a cluster identifier + assert labels_float64.shape == (n_samples,) + # All components should be covered by the assignment + assert np.array_equal(np.unique(labels_float64), np.arange(n_components)) + # Single precision data should yield the same cluster assignments + labels_float32 = cluster_qr(data.astype(np.float32)) + assert np.array_equal(labels_float64, labels_float32) + + +def test_cluster_qr_permutation_invariance(global_random_seed): + # cluster_qr must be invariant to sample permutation. + random_state = np.random.RandomState(seed=global_random_seed) + n_samples, n_components = 100, 5 + data = random_state.randn(n_samples, n_components) + perm = random_state.permutation(n_samples) + assert np.array_equal( + cluster_qr(data)[perm], + cluster_qr(data[perm]), + ) + + +@pytest.mark.parametrize("coo_container", COO_CONTAINERS) +@pytest.mark.parametrize("n_samples", [50, 100, 150, 500]) +def test_discretize(n_samples, coo_container, global_random_seed): + # Test the discretize using a noise assignment matrix + random_state = np.random.RandomState(seed=global_random_seed) + for n_class in range(2, 10): + # random class labels + y_true = random_state.randint(0, n_class + 1, n_samples) + y_true = np.array(y_true, float) + # noise class assignment matrix + y_indicator = coo_container( + (np.ones(n_samples), (np.arange(n_samples), y_true)), + shape=(n_samples, n_class + 1), + ) + y_true_noisy = y_indicator.toarray() + 0.1 * random_state.randn( + n_samples, n_class + 1 + ) + y_pred = discretize(y_true_noisy, random_state=random_state) + assert adjusted_rand_score(y_true, y_pred) > 0.8 + + +def test_spectral_clustering_with_arpack_amg_solvers(global_random_seed): + # Test that spectral_clustering is the same for arpack and amg solver + # Based on toy example from plot_segmentation_toy.py + + # a small two coin image + x, y = np.indices((40, 40)) + + center1, center2 = (14, 12), (20, 25) + radius1, radius2 = 8, 7 + + circle1 = (x - center1[0]) ** 2 + (y - center1[1]) ** 2 < radius1**2 + circle2 = (x - center2[0]) ** 2 + (y - center2[1]) ** 2 < radius2**2 + + circles = circle1 | circle2 + mask = circles.copy() + img = circles.astype(float) + + graph = img_to_graph(img, mask=mask) + graph.data = np.exp(-graph.data / graph.data.std()) + + labels_arpack = spectral_clustering( + graph, n_clusters=2, eigen_solver="arpack", random_state=global_random_seed + ) + + assert len(np.unique(labels_arpack)) == 2 + + if amg_loaded: + labels_amg = spectral_clustering( + graph, n_clusters=2, eigen_solver="amg", random_state=global_random_seed + ) + assert adjusted_rand_score(labels_arpack, labels_amg) == 1 + else: + with pytest.raises(ValueError): + spectral_clustering(graph, n_clusters=2, eigen_solver="amg", random_state=0) + + +def test_n_components(global_random_seed): + # Test that after adding n_components, result is different and + # n_components = n_clusters by default + X, y = make_blobs( + n_samples=20, + random_state=global_random_seed, + centers=[[1, 1], [-1, -1]], + cluster_std=0.01, + ) + sp = SpectralClustering(n_clusters=2, random_state=global_random_seed) + labels = sp.fit(X).labels_ + # set n_components = n_cluster and test if result is the same + labels_same_ncomp = ( + SpectralClustering( + n_clusters=2, n_components=2, random_state=global_random_seed + ) + .fit(X) + .labels_ + ) + # test that n_components=n_clusters by default + assert_array_equal(labels, labels_same_ncomp) + + # test that n_components affect result + # n_clusters=8 by default, and set n_components=2 + labels_diff_ncomp = ( + SpectralClustering(n_components=2, random_state=global_random_seed) + .fit(X) + .labels_ + ) + assert not np.array_equal(labels, labels_diff_ncomp) + + +@pytest.mark.parametrize("assign_labels", ("kmeans", "discretize", "cluster_qr")) +def test_verbose(assign_labels, capsys): + # Check verbose mode of KMeans for better coverage. + X, y = make_blobs( + n_samples=20, random_state=0, centers=[[1, 1], [-1, -1]], cluster_std=0.01 + ) + + SpectralClustering(n_clusters=2, random_state=42, verbose=1).fit(X) + + captured = capsys.readouterr() + + assert re.search(r"Computing label assignment using", captured.out) + + if assign_labels == "kmeans": + assert re.search(r"Initialization complete", captured.out) + assert re.search(r"Iteration [0-9]+, inertia", captured.out) + + +def test_spectral_clustering_np_matrix_raises(): + """Check that spectral_clustering raises an informative error when passed + a np.matrix. See #10993""" + X = np.matrix([[0.0, 2.0], [2.0, 0.0]]) + + msg = r"np\.matrix is not supported. Please convert to a numpy array" + with pytest.raises(TypeError, match=msg): + spectral_clustering(X) + + +def test_spectral_clustering_not_infinite_loop(capsys, monkeypatch): + """Check that discretize raises LinAlgError when svd never converges. + + Non-regression test for #21380 + """ + + def new_svd(*args, **kwargs): + raise LinAlgError() + + monkeypatch.setattr(np.linalg, "svd", new_svd) + vectors = np.ones((10, 4)) + + with pytest.raises(LinAlgError, match="SVD did not converge"): + discretize(vectors) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..842a86ba21d9b7e2e738284faf1a394e3f6ae7e9 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/__init__.py @@ -0,0 +1,23 @@ +"""Meta-estimators for building composite models with transformers. + +In addition to its current contents, this module will eventually be home to +refurbished versions of :class:`~sklearn.pipeline.Pipeline` and +:class:`~sklearn.pipeline.FeatureUnion`. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +from ._column_transformer import ( + ColumnTransformer, + make_column_selector, + make_column_transformer, +) +from ._target import TransformedTargetRegressor + +__all__ = [ + "ColumnTransformer", + "TransformedTargetRegressor", + "make_column_selector", + "make_column_transformer", +] diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/_column_transformer.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/_column_transformer.py new file mode 100644 index 0000000000000000000000000000000000000000..940d9194dd97657f0cd746b89b482ea4d75d8852 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/_column_transformer.py @@ -0,0 +1,1604 @@ +""" +The :mod:`sklearn.compose._column_transformer` module implements utilities +to work with heterogeneous data and to apply different transformers to +different columns. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from collections import Counter +from functools import partial +from itertools import chain +from numbers import Integral, Real + +import numpy as np +from scipy import sparse + +from ..base import TransformerMixin, _fit_context, clone +from ..pipeline import _fit_transform_one, _name_estimators, _transform_one +from ..preprocessing import FunctionTransformer +from ..utils import Bunch +from ..utils._indexing import _determine_key_type, _get_column_indices, _safe_indexing +from ..utils._metadata_requests import METHODS +from ..utils._param_validation import HasMethods, Hidden, Interval, StrOptions +from ..utils._repr_html.estimator import _VisualBlock +from ..utils._set_output import ( + _get_container_adapter, + _get_output_config, + _safe_set_output, +) +from ..utils._tags import get_tags +from ..utils.metadata_routing import ( + MetadataRouter, + MethodMapping, + _raise_for_params, + _routing_enabled, + process_routing, +) +from ..utils.metaestimators import _BaseComposition +from ..utils.parallel import Parallel, delayed +from ..utils.validation import ( + _check_feature_names, + _check_feature_names_in, + _check_n_features, + _get_feature_names, + _is_pandas_df, + _num_samples, + check_array, + check_is_fitted, +) + +__all__ = ["ColumnTransformer", "make_column_selector", "make_column_transformer"] + + +_ERR_MSG_1DCOLUMN = ( + "1D data passed to a transformer that expects 2D data. " + "Try to specify the column selection as a list of one " + "item instead of a scalar." +) + + +class ColumnTransformer(TransformerMixin, _BaseComposition): + """Applies transformers to columns of an array or pandas DataFrame. + + This estimator allows different columns or column subsets of the input + to be transformed separately and the features generated by each transformer + will be concatenated to form a single feature space. + This is useful for heterogeneous or columnar data, to combine several + feature extraction mechanisms or transformations into a single transformer. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.20 + + Parameters + ---------- + transformers : list of tuples + List of (name, transformer, columns) tuples specifying the + transformer objects to be applied to subsets of the data. + + name : str + Like in Pipeline and FeatureUnion, this allows the transformer and + its parameters to be set using ``set_params`` and searched in grid + search. + transformer : {'drop', 'passthrough'} or estimator + Estimator must support :term:`fit` and :term:`transform`. + Special-cased strings 'drop' and 'passthrough' are accepted as + well, to indicate to drop the columns or to pass them through + untransformed, respectively. + columns : str, array-like of str, int, array-like of int, \ + array-like of bool, slice or callable + Indexes the data on its second axis. Integers are interpreted as + positional columns, while strings can reference DataFrame columns + by name. A scalar string or int should be used where + ``transformer`` expects X to be a 1d array-like (vector), + otherwise a 2d array will be passed to the transformer. + A callable is passed the input data `X` and can return any of the + above. To select multiple columns by name or dtype, you can use + :obj:`make_column_selector`. + + remainder : {'drop', 'passthrough'} or estimator, default='drop' + By default, only the specified columns in `transformers` are + transformed and combined in the output, and the non-specified + columns are dropped. (default of ``'drop'``). + By specifying ``remainder='passthrough'``, all remaining columns that + were not specified in `transformers`, but present in the data passed + to `fit` will be automatically passed through. This subset of columns + is concatenated with the output of the transformers. For dataframes, + extra columns not seen during `fit` will be excluded from the output + of `transform`. + By setting ``remainder`` to be an estimator, the remaining + non-specified columns will use the ``remainder`` estimator. The + estimator must support :term:`fit` and :term:`transform`. + Note that using this feature requires that the DataFrame columns + input at :term:`fit` and :term:`transform` have identical order. + + sparse_threshold : float, default=0.3 + If the output of the different transformers contains sparse matrices, + these will be stacked as a sparse matrix if the overall density is + lower than this value. Use ``sparse_threshold=0`` to always return + dense. When the transformed output consists of all dense data, the + stacked result will be dense, and this keyword will be ignored. + + n_jobs : int, default=None + Number of jobs to run in parallel. + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + transformer_weights : dict, default=None + Multiplicative weights for features per transformer. The output of the + transformer is multiplied by these weights. Keys are transformer names, + values the weights. + + verbose : bool, default=False + If True, the time elapsed while fitting each transformer will be + printed as it is completed. + + verbose_feature_names_out : bool, str or Callable[[str, str], str], default=True + + - If True, :meth:`ColumnTransformer.get_feature_names_out` will prefix + all feature names with the name of the transformer that generated that + feature. It is equivalent to setting + `verbose_feature_names_out="{transformer_name}__{feature_name}"`. + - If False, :meth:`ColumnTransformer.get_feature_names_out` will not + prefix any feature names and will error if feature names are not + unique. + - If ``Callable[[str, str], str]``, + :meth:`ColumnTransformer.get_feature_names_out` will rename all the features + using the name of the transformer. The first argument of the callable is the + transformer name and the second argument is the feature name. The returned + string will be the new feature name. + - If ``str``, it must be a string ready for formatting. The given string will + be formatted using two field names: ``transformer_name`` and ``feature_name``. + e.g. ``"{feature_name}__{transformer_name}"``. See :meth:`str.format` method + from the standard library for more info. + + .. versionadded:: 1.0 + + .. versionchanged:: 1.6 + `verbose_feature_names_out` can be a callable or a string to be formatted. + + force_int_remainder_cols : bool, default=False + This parameter has no effect. + + .. note:: + If you do not access the list of columns for the remainder columns + in the `transformers_` fitted attribute, you do not need to set + this parameter. + + .. versionadded:: 1.5 + + .. versionchanged:: 1.7 + The default value for `force_int_remainder_cols` will change from + `True` to `False` in version 1.7. + + .. deprecated:: 1.7 + `force_int_remainder_cols` is deprecated and will be removed in 1.9. + + Attributes + ---------- + transformers_ : list + The collection of fitted transformers as tuples of (name, + fitted_transformer, column). `fitted_transformer` can be an estimator, + or `'drop'`; `'passthrough'` is replaced with an equivalent + :class:`~sklearn.preprocessing.FunctionTransformer`. In case there were + no columns selected, this will be the unfitted transformer. If there + are remaining columns, the final element is a tuple of the form: + ('remainder', transformer, remaining_columns) corresponding to the + ``remainder`` parameter. If there are remaining columns, then + ``len(transformers_)==len(transformers)+1``, otherwise + ``len(transformers_)==len(transformers)``. + + .. versionadded:: 1.7 + The format of the remaining columns now attempts to match that of the other + transformers: if all columns were provided as column names (`str`), the + remaining columns are stored as column names; if all columns were provided + as mask arrays (`bool`), so are the remaining columns; in all other cases + the remaining columns are stored as indices (`int`). + + named_transformers_ : :class:`~sklearn.utils.Bunch` + Read-only attribute to access any transformer by given name. + Keys are transformer names and values are the fitted transformer + objects. + + sparse_output_ : bool + Boolean flag indicating whether the output of ``transform`` is a + sparse matrix or a dense numpy array, which depends on the output + of the individual transformers and the `sparse_threshold` keyword. + + output_indices_ : dict + A dictionary from each transformer name to a slice, where the slice + corresponds to indices in the transformed output. This is useful to + inspect which transformer is responsible for which transformed + feature(s). + + .. versionadded:: 1.0 + + n_features_in_ : int + Number of features seen during :term:`fit`. Only defined if the + underlying transformers expose such an attribute when fit. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + make_column_transformer : Convenience function for + combining the outputs of multiple transformer objects applied to + column subsets of the original feature space. + make_column_selector : Convenience function for selecting + columns based on datatype or the columns name with a regex pattern. + + Notes + ----- + The order of the columns in the transformed feature matrix follows the + order of how the columns are specified in the `transformers` list. + Columns of the original feature matrix that are not specified are + dropped from the resulting transformed feature matrix, unless specified + in the `passthrough` keyword. Those columns specified with `passthrough` + are added at the right to the output of the transformers. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.compose import ColumnTransformer + >>> from sklearn.preprocessing import Normalizer + >>> ct = ColumnTransformer( + ... [("norm1", Normalizer(norm='l1'), [0, 1]), + ... ("norm2", Normalizer(norm='l1'), slice(2, 4))]) + >>> X = np.array([[0., 1., 2., 2.], + ... [1., 1., 0., 1.]]) + >>> # Normalizer scales each row of X to unit norm. A separate scaling + >>> # is applied for the two first and two last elements of each + >>> # row independently. + >>> ct.fit_transform(X) + array([[0. , 1. , 0.5, 0.5], + [0.5, 0.5, 0. , 1. ]]) + + :class:`ColumnTransformer` can be configured with a transformer that requires + a 1d array by setting the column to a string: + + >>> from sklearn.feature_extraction.text import CountVectorizer + >>> from sklearn.preprocessing import MinMaxScaler + >>> import pandas as pd # doctest: +SKIP + >>> X = pd.DataFrame({ + ... "documents": ["First item", "second one here", "Is this the last?"], + ... "width": [3, 4, 5], + ... }) # doctest: +SKIP + >>> # "documents" is a string which configures ColumnTransformer to + >>> # pass the documents column as a 1d array to the CountVectorizer + >>> ct = ColumnTransformer( + ... [("text_preprocess", CountVectorizer(), "documents"), + ... ("num_preprocess", MinMaxScaler(), ["width"])]) + >>> X_trans = ct.fit_transform(X) # doctest: +SKIP + + For a more detailed example of usage, see + :ref:`sphx_glr_auto_examples_compose_plot_column_transformer_mixed_types.py`. + """ + + _parameter_constraints: dict = { + "transformers": [list, Hidden(tuple)], + "remainder": [ + StrOptions({"drop", "passthrough"}), + HasMethods(["fit", "transform"]), + HasMethods(["fit_transform", "transform"]), + ], + "sparse_threshold": [Interval(Real, 0, 1, closed="both")], + "n_jobs": [Integral, None], + "transformer_weights": [dict, None], + "verbose": ["verbose"], + "verbose_feature_names_out": ["boolean", str, callable], + "force_int_remainder_cols": ["boolean", Hidden(StrOptions({"deprecated"}))], + } + + def __init__( + self, + transformers, + *, + remainder="drop", + sparse_threshold=0.3, + n_jobs=None, + transformer_weights=None, + verbose=False, + verbose_feature_names_out=True, + force_int_remainder_cols="deprecated", + ): + self.transformers = transformers + self.remainder = remainder + self.sparse_threshold = sparse_threshold + self.n_jobs = n_jobs + self.transformer_weights = transformer_weights + self.verbose = verbose + self.verbose_feature_names_out = verbose_feature_names_out + self.force_int_remainder_cols = force_int_remainder_cols + + @property + def _transformers(self): + """ + Internal list of transformer only containing the name and + transformers, dropping the columns. + + DO NOT USE: This is for the implementation of get_params via + BaseComposition._get_params which expects lists of tuples of len 2. + + To iterate through the transformers, use ``self._iter`` instead. + """ + try: + return [(name, trans) for name, trans, _ in self.transformers] + except (TypeError, ValueError): + return self.transformers + + @_transformers.setter + def _transformers(self, value): + """DO NOT USE: This is for the implementation of set_params via + BaseComposition._get_params which gives lists of tuples of len 2. + """ + try: + self.transformers = [ + (name, trans, col) + for ((name, trans), (_, _, col)) in zip(value, self.transformers) + ] + except (TypeError, ValueError): + self.transformers = value + + def set_output(self, *, transform=None): + """Set the output container when `"transform"` and `"fit_transform"` are called. + + Calling `set_output` will set the output of all estimators in `transformers` + and `transformers_`. + + Parameters + ---------- + transform : {"default", "pandas", "polars"}, default=None + Configure output of `transform` and `fit_transform`. + + - `"default"`: Default output format of a transformer + - `"pandas"`: DataFrame output + - `"polars"`: Polars output + - `None`: Transform configuration is unchanged + + .. versionadded:: 1.4 + `"polars"` option was added. + + Returns + ------- + self : estimator instance + Estimator instance. + """ + super().set_output(transform=transform) + + transformers = ( + trans + for _, trans, _ in chain( + self.transformers, getattr(self, "transformers_", []) + ) + if trans not in {"passthrough", "drop"} + ) + for trans in transformers: + _safe_set_output(trans, transform=transform) + + if self.remainder not in {"passthrough", "drop"}: + _safe_set_output(self.remainder, transform=transform) + + return self + + def get_params(self, deep=True): + """Get parameters for this estimator. + + Returns the parameters given in the constructor as well as the + estimators contained within the `transformers` of the + `ColumnTransformer`. + + Parameters + ---------- + deep : bool, default=True + If True, will return the parameters for this estimator and + contained subobjects that are estimators. + + Returns + ------- + params : dict + Parameter names mapped to their values. + """ + return self._get_params("_transformers", deep=deep) + + def set_params(self, **kwargs): + """Set the parameters of this estimator. + + Valid parameter keys can be listed with ``get_params()``. Note that you + can directly set the parameters of the estimators contained in + `transformers` of `ColumnTransformer`. + + Parameters + ---------- + **kwargs : dict + Estimator parameters. + + Returns + ------- + self : ColumnTransformer + This estimator. + """ + self._set_params("_transformers", **kwargs) + return self + + def _iter(self, fitted, column_as_labels, skip_drop, skip_empty_columns): + """ + Generate (name, trans, columns, weight) tuples. + + + Parameters + ---------- + fitted : bool + If True, use the fitted transformers (``self.transformers_``) to + iterate through transformers, else use the transformers passed by + the user (``self.transformers``). + + column_as_labels : bool + If True, columns are returned as string labels. If False, columns + are returned as they were given by the user. This can only be True + if the ``ColumnTransformer`` is already fitted. + + skip_drop : bool + If True, 'drop' transformers are filtered out. + + skip_empty_columns : bool + If True, transformers with empty selected columns are filtered out. + + Yields + ------ + A generator of tuples containing: + - name : the name of the transformer + - transformer : the transformer object + - columns : the columns for that transformer + - weight : the weight of the transformer + """ + if fitted: + transformers = self.transformers_ + else: + # interleave the validated column specifiers + transformers = [ + (name, trans, column) + for (name, trans, _), column in zip(self.transformers, self._columns) + ] + # add transformer tuple for remainder + if self._remainder[2]: + transformers = chain(transformers, [self._remainder]) + + get_weight = (self.transformer_weights or {}).get + + for name, trans, columns in transformers: + if skip_drop and trans == "drop": + continue + if skip_empty_columns and _is_empty_column_selection(columns): + continue + + if column_as_labels: + # Convert all columns to using their string labels + columns_is_scalar = np.isscalar(columns) + + indices = self._transformer_to_input_indices[name] + columns = self.feature_names_in_[indices] + + if columns_is_scalar: + # selection is done with one dimension + columns = columns[0] + + yield (name, trans, columns, get_weight(name)) + + def _validate_transformers(self): + """Validate names of transformers and the transformers themselves. + + This checks whether given transformers have the required methods, i.e. + `fit` or `fit_transform` and `transform` implemented. + """ + if not self.transformers: + return + + names, transformers, _ = zip(*self.transformers) + + # validate names + self._validate_names(names) + + # validate estimators + for t in transformers: + if t in ("drop", "passthrough"): + continue + if not (hasattr(t, "fit") or hasattr(t, "fit_transform")) or not hasattr( + t, "transform" + ): + # Used to validate the transformers in the `transformers` list + raise TypeError( + "All estimators should implement fit and " + "transform, or can be 'drop' or 'passthrough' " + "specifiers. '%s' (type %s) doesn't." % (t, type(t)) + ) + + def _validate_column_callables(self, X): + """ + Converts callable column specifications. + + This stores a dictionary of the form `{step_name: column_indices}` and + calls the `columns` on `X` if `columns` is a callable for a given + transformer. + + The results are then stored in `self._transformer_to_input_indices`. + """ + all_columns = [] + transformer_to_input_indices = {} + for name, _, columns in self.transformers: + if callable(columns): + columns = columns(X) + all_columns.append(columns) + transformer_to_input_indices[name] = _get_column_indices(X, columns) + + self._columns = all_columns + self._transformer_to_input_indices = transformer_to_input_indices + + def _validate_remainder(self, X): + """ + Validates ``remainder`` and defines ``_remainder`` targeting + the remaining columns. + """ + cols = set(chain(*self._transformer_to_input_indices.values())) + remaining = sorted(set(range(self.n_features_in_)) - cols) + self._transformer_to_input_indices["remainder"] = remaining + remainder_cols = self._get_remainder_cols(remaining) + self._remainder = ("remainder", self.remainder, remainder_cols) + + def _get_remainder_cols_dtype(self): + try: + all_dtypes = {_determine_key_type(c) for (*_, c) in self.transformers} + if len(all_dtypes) == 1: + return next(iter(all_dtypes)) + except ValueError: + # _determine_key_type raises a ValueError if some transformer + # columns are Callables + return "int" + return "int" + + def _get_remainder_cols(self, indices): + dtype = self._get_remainder_cols_dtype() + if dtype == "str": + return list(self.feature_names_in_[indices]) + if dtype == "bool": + return [i in indices for i in range(self.n_features_in_)] + return indices + + @property + def named_transformers_(self): + """Access the fitted transformer by name. + + Read-only attribute to access any transformer by given name. + Keys are transformer names and values are the fitted transformer + objects. + """ + # Use Bunch object to improve autocomplete + return Bunch(**{name: trans for name, trans, _ in self.transformers_}) + + def _get_feature_name_out_for_transformer(self, name, trans, feature_names_in): + """Gets feature names of transformer. + + Used in conjunction with self._iter(fitted=True) in get_feature_names_out. + """ + column_indices = self._transformer_to_input_indices[name] + names = feature_names_in[column_indices] + # An actual transformer + if not hasattr(trans, "get_feature_names_out"): + raise AttributeError( + f"Transformer {name} (type {type(trans).__name__}) does " + "not provide get_feature_names_out." + ) + return trans.get_feature_names_out(names) + + def get_feature_names_out(self, input_features=None): + """Get output feature names for transformation. + + Parameters + ---------- + input_features : array-like of str or None, default=None + Input features. + + - If `input_features` is `None`, then `feature_names_in_` is + used as feature names in. If `feature_names_in_` is not defined, + then the following input feature names are generated: + `["x0", "x1", ..., "x(n_features_in_ - 1)"]`. + - If `input_features` is an array-like, then `input_features` must + match `feature_names_in_` if `feature_names_in_` is defined. + + Returns + ------- + feature_names_out : ndarray of str objects + Transformed feature names. + """ + check_is_fitted(self) + input_features = _check_feature_names_in(self, input_features) + + # List of tuples (name, feature_names_out) + transformer_with_feature_names_out = [] + for name, trans, *_ in self._iter( + fitted=True, + column_as_labels=False, + skip_empty_columns=True, + skip_drop=True, + ): + feature_names_out = self._get_feature_name_out_for_transformer( + name, trans, input_features + ) + if feature_names_out is None: + continue + transformer_with_feature_names_out.append((name, feature_names_out)) + + if not transformer_with_feature_names_out: + # No feature names + return np.array([], dtype=object) + + return self._add_prefix_for_feature_names_out( + transformer_with_feature_names_out + ) + + def _add_prefix_for_feature_names_out(self, transformer_with_feature_names_out): + """Add prefix for feature names out that includes the transformer names. + + Parameters + ---------- + transformer_with_feature_names_out : list of tuples of (str, array-like of str) + The tuple consistent of the transformer's name and its feature names out. + + Returns + ------- + feature_names_out : ndarray of shape (n_features,), dtype=str + Transformed feature names. + """ + feature_names_out_callable = None + if callable(self.verbose_feature_names_out): + feature_names_out_callable = self.verbose_feature_names_out + elif isinstance(self.verbose_feature_names_out, str): + feature_names_out_callable = partial( + _feature_names_out_with_str_format, + str_format=self.verbose_feature_names_out, + ) + elif self.verbose_feature_names_out is True: + feature_names_out_callable = partial( + _feature_names_out_with_str_format, + str_format="{transformer_name}__{feature_name}", + ) + + if feature_names_out_callable is not None: + # Prefix the feature names out with the transformers name + names = list( + chain.from_iterable( + (feature_names_out_callable(name, i) for i in feature_names_out) + for name, feature_names_out in transformer_with_feature_names_out + ) + ) + return np.asarray(names, dtype=object) + + # verbose_feature_names_out is False + # Check that names are all unique without a prefix + feature_names_count = Counter( + chain.from_iterable(s for _, s in transformer_with_feature_names_out) + ) + top_6_overlap = [ + name for name, count in feature_names_count.most_common(6) if count > 1 + ] + top_6_overlap.sort() + if top_6_overlap: + if len(top_6_overlap) == 6: + # There are more than 5 overlapping names, we only show the 5 + # of the feature names + names_repr = str(top_6_overlap[:5])[:-1] + ", ...]" + else: + names_repr = str(top_6_overlap) + raise ValueError( + f"Output feature names: {names_repr} are not unique. Please set " + "verbose_feature_names_out=True to add prefixes to feature names" + ) + + return np.concatenate( + [name for _, name in transformer_with_feature_names_out], + ) + + def _update_fitted_transformers(self, transformers): + """Set self.transformers_ from given transformers. + + Parameters + ---------- + transformers : list of estimators + The fitted estimators as the output of + `self._call_func_on_transformers(func=_fit_transform_one, ...)`. + That function doesn't include 'drop' or transformers for which no + column is selected. 'drop' is kept as is, and for the no-column + transformers the unfitted transformer is put in + `self.transformers_`. + """ + # transformers are fitted; excludes 'drop' cases + fitted_transformers = iter(transformers) + transformers_ = [] + + for name, old, column, _ in self._iter( + fitted=False, + column_as_labels=False, + skip_drop=False, + skip_empty_columns=False, + ): + if old == "drop": + trans = "drop" + elif _is_empty_column_selection(column): + trans = old + else: + trans = next(fitted_transformers) + transformers_.append((name, trans, column)) + + # sanity check that transformers is exhausted + assert not list(fitted_transformers) + self.transformers_ = transformers_ + + def _validate_output(self, result): + """ + Ensure that the output of each transformer is 2D. Otherwise + hstack can raise an error or produce incorrect results. + """ + names = [ + name + for name, _, _, _ in self._iter( + fitted=True, + column_as_labels=False, + skip_drop=True, + skip_empty_columns=True, + ) + ] + for Xs, name in zip(result, names): + if not getattr(Xs, "ndim", 0) == 2 and not hasattr(Xs, "__dataframe__"): + raise ValueError( + "The output of the '{0}' transformer should be 2D (numpy array, " + "scipy sparse array, dataframe).".format(name) + ) + if _get_output_config("transform", self)["dense"] == "pandas": + return + try: + import pandas as pd + except ImportError: + return + for Xs, name in zip(result, names): + if not _is_pandas_df(Xs): + continue + for col_name, dtype in Xs.dtypes.to_dict().items(): + if getattr(dtype, "na_value", None) is not pd.NA: + continue + if pd.NA not in Xs[col_name].values: + continue + class_name = self.__class__.__name__ + raise ValueError( + f"The output of the '{name}' transformer for column" + f" '{col_name}' has dtype {dtype} and uses pandas.NA to" + " represent null values. Storing this output in a numpy array" + " can cause errors in downstream scikit-learn estimators, and" + " inefficiencies. To avoid this problem you can (i)" + " store the output in a pandas DataFrame by using" + f" {class_name}.set_output(transform='pandas') or (ii) modify" + f" the input data or the '{name}' transformer to avoid the" + " presence of pandas.NA (for example by using" + " pandas.DataFrame.astype)." + ) + + def _record_output_indices(self, Xs): + """ + Record which transformer produced which column. + """ + idx = 0 + self.output_indices_ = {} + + for transformer_idx, (name, _, _, _) in enumerate( + self._iter( + fitted=True, + column_as_labels=False, + skip_drop=True, + skip_empty_columns=True, + ) + ): + n_columns = Xs[transformer_idx].shape[1] + self.output_indices_[name] = slice(idx, idx + n_columns) + idx += n_columns + + # `_iter` only generates transformers that have a non empty + # selection. Here we set empty slices for transformers that + # generate no output, which are safe for indexing + all_names = [t[0] for t in self.transformers] + ["remainder"] + for name in all_names: + if name not in self.output_indices_: + self.output_indices_[name] = slice(0, 0) + + def _log_message(self, name, idx, total): + if not self.verbose: + return None + return "(%d of %d) Processing %s" % (idx, total, name) + + def _call_func_on_transformers(self, X, y, func, column_as_labels, routed_params): + """ + Private function to fit and/or transform on demand. + + Parameters + ---------- + X : {array-like, dataframe} of shape (n_samples, n_features) + The data to be used in fit and/or transform. + + y : array-like of shape (n_samples,) + Targets. + + func : callable + Function to call, which can be _fit_transform_one or + _transform_one. + + column_as_labels : bool + Used to iterate through transformers. If True, columns are returned + as strings. If False, columns are returned as they were given by + the user. Can be True only if the ``ColumnTransformer`` is already + fitted. + + routed_params : dict + The routed parameters as the output from ``process_routing``. + + Returns + ------- + Return value (transformers and/or transformed X data) depends + on the passed function. + """ + if func is _fit_transform_one: + fitted = False + else: # func is _transform_one + fitted = True + + transformers = list( + self._iter( + fitted=fitted, + column_as_labels=column_as_labels, + skip_drop=True, + skip_empty_columns=True, + ) + ) + try: + jobs = [] + for idx, (name, trans, columns, weight) in enumerate(transformers, start=1): + if func is _fit_transform_one: + if trans == "passthrough": + output_config = _get_output_config("transform", self) + trans = FunctionTransformer( + accept_sparse=True, + check_inverse=False, + feature_names_out="one-to-one", + ).set_output(transform=output_config["dense"]) + + extra_args = dict( + message_clsname="ColumnTransformer", + message=self._log_message(name, idx, len(transformers)), + ) + else: # func is _transform_one + extra_args = {} + jobs.append( + delayed(func)( + transformer=clone(trans) if not fitted else trans, + X=_safe_indexing(X, columns, axis=1), + y=y, + weight=weight, + **extra_args, + params=routed_params[name], + ) + ) + + return Parallel(n_jobs=self.n_jobs)(jobs) + + except ValueError as e: + if "Expected 2D array, got 1D array instead" in str(e): + raise ValueError(_ERR_MSG_1DCOLUMN) from e + else: + raise + + def fit(self, X, y=None, **params): + """Fit all transformers using X. + + Parameters + ---------- + X : {array-like, dataframe} of shape (n_samples, n_features) + Input data, of which specified subsets are used to fit the + transformers. + + y : array-like of shape (n_samples,...), default=None + Targets for supervised learning. + + **params : dict, default=None + Parameters to be passed to the underlying transformers' ``fit`` and + ``transform`` methods. + + You can only pass this if metadata routing is enabled, which you + can enable using ``sklearn.set_config(enable_metadata_routing=True)``. + + .. versionadded:: 1.4 + + Returns + ------- + self : ColumnTransformer + This estimator. + """ + _raise_for_params(params, self, "fit") + # we use fit_transform to make sure to set sparse_output_ (for which we + # need the transformed data) to have consistent output type in predict + self.fit_transform(X, y=y, **params) + return self + + @_fit_context( + # estimators in ColumnTransformer.transformers are not validated yet + prefer_skip_nested_validation=False + ) + def fit_transform(self, X, y=None, **params): + """Fit all transformers, transform the data and concatenate results. + + Parameters + ---------- + X : {array-like, dataframe} of shape (n_samples, n_features) + Input data, of which specified subsets are used to fit the + transformers. + + y : array-like of shape (n_samples,), default=None + Targets for supervised learning. + + **params : dict, default=None + Parameters to be passed to the underlying transformers' ``fit`` and + ``transform`` methods. + + You can only pass this if metadata routing is enabled, which you + can enable using ``sklearn.set_config(enable_metadata_routing=True)``. + + .. versionadded:: 1.4 + + Returns + ------- + X_t : {array-like, sparse matrix} of \ + shape (n_samples, sum_n_components) + Horizontally stacked results of transformers. sum_n_components is the + sum of n_components (output dimension) over transformers. If + any result is a sparse matrix, everything will be converted to + sparse matrices. + """ + _raise_for_params(params, self, "fit_transform") + _check_feature_names(self, X, reset=True) + + if self.force_int_remainder_cols != "deprecated": + warnings.warn( + "The parameter `force_int_remainder_cols` is deprecated and will be " + "removed in 1.9. It has no effect. Leave it to its default value to " + "avoid this warning.", + FutureWarning, + ) + + X = _check_X(X) + # set n_features_in_ attribute + _check_n_features(self, X, reset=True) + self._validate_transformers() + n_samples = _num_samples(X) + + self._validate_column_callables(X) + self._validate_remainder(X) + + if _routing_enabled(): + routed_params = process_routing(self, "fit_transform", **params) + else: + routed_params = self._get_empty_routing() + + result = self._call_func_on_transformers( + X, + y, + _fit_transform_one, + column_as_labels=False, + routed_params=routed_params, + ) + + if not result: + self._update_fitted_transformers([]) + # All transformers are None + return np.zeros((n_samples, 0)) + + Xs, transformers = zip(*result) + + # determine if concatenated output will be sparse or not + if any(sparse.issparse(X) for X in Xs): + nnz = sum(X.nnz if sparse.issparse(X) else X.size for X in Xs) + total = sum( + X.shape[0] * X.shape[1] if sparse.issparse(X) else X.size for X in Xs + ) + density = nnz / total + self.sparse_output_ = density < self.sparse_threshold + else: + self.sparse_output_ = False + + self._update_fitted_transformers(transformers) + self._validate_output(Xs) + self._record_output_indices(Xs) + + return self._hstack(list(Xs), n_samples=n_samples) + + def transform(self, X, **params): + """Transform X separately by each transformer, concatenate results. + + Parameters + ---------- + X : {array-like, dataframe} of shape (n_samples, n_features) + The data to be transformed by subset. + + **params : dict, default=None + Parameters to be passed to the underlying transformers' ``transform`` + method. + + You can only pass this if metadata routing is enabled, which you + can enable using ``sklearn.set_config(enable_metadata_routing=True)``. + + .. versionadded:: 1.4 + + Returns + ------- + X_t : {array-like, sparse matrix} of \ + shape (n_samples, sum_n_components) + Horizontally stacked results of transformers. sum_n_components is the + sum of n_components (output dimension) over transformers. If + any result is a sparse matrix, everything will be converted to + sparse matrices. + """ + _raise_for_params(params, self, "transform") + check_is_fitted(self) + X = _check_X(X) + + # If ColumnTransformer is fit using a dataframe, and now a dataframe is + # passed to be transformed, we select columns by name instead. This + # enables the user to pass X at transform time with extra columns which + # were not present in fit time, and the order of the columns doesn't + # matter. + fit_dataframe_and_transform_dataframe = hasattr(self, "feature_names_in_") and ( + _is_pandas_df(X) or hasattr(X, "__dataframe__") + ) + + n_samples = _num_samples(X) + column_names = _get_feature_names(X) + + if fit_dataframe_and_transform_dataframe: + named_transformers = self.named_transformers_ + # check that all names seen in fit are in transform, unless + # they were dropped + non_dropped_indices = [ + ind + for name, ind in self._transformer_to_input_indices.items() + if name in named_transformers and named_transformers[name] != "drop" + ] + + all_indices = set(chain(*non_dropped_indices)) + all_names = set(self.feature_names_in_[ind] for ind in all_indices) + + diff = all_names - set(column_names) + if diff: + raise ValueError(f"columns are missing: {diff}") + else: + # ndarray was used for fitting or transforming, thus we only + # check that n_features_in_ is consistent + _check_n_features(self, X, reset=False) + + if _routing_enabled(): + routed_params = process_routing(self, "transform", **params) + else: + routed_params = self._get_empty_routing() + + Xs = self._call_func_on_transformers( + X, + None, + _transform_one, + column_as_labels=fit_dataframe_and_transform_dataframe, + routed_params=routed_params, + ) + self._validate_output(Xs) + + if not Xs: + # All transformers are None + return np.zeros((n_samples, 0)) + + return self._hstack(list(Xs), n_samples=n_samples) + + def _hstack(self, Xs, *, n_samples): + """Stacks Xs horizontally. + + This allows subclasses to control the stacking behavior, while reusing + everything else from ColumnTransformer. + + Parameters + ---------- + Xs : list of {array-like, sparse matrix, dataframe} + The container to concatenate. + n_samples : int + The number of samples in the input data to checking the transformation + consistency. + """ + if self.sparse_output_: + try: + # since all columns should be numeric before stacking them + # in a sparse matrix, `check_array` is used for the + # dtype conversion if necessary. + converted_Xs = [ + check_array(X, accept_sparse=True, ensure_all_finite=False) + for X in Xs + ] + except ValueError as e: + raise ValueError( + "For a sparse output, all columns should " + "be a numeric or convertible to a numeric." + ) from e + + return sparse.hstack(converted_Xs).tocsr() + else: + Xs = [f.toarray() if sparse.issparse(f) else f for f in Xs] + adapter = _get_container_adapter("transform", self) + if adapter and all(adapter.is_supported_container(X) for X in Xs): + # rename before stacking as it avoids to error on temporary duplicated + # columns + transformer_names = [ + t[0] + for t in self._iter( + fitted=True, + column_as_labels=False, + skip_drop=True, + skip_empty_columns=True, + ) + ] + feature_names_outs = [X.columns for X in Xs if X.shape[1] != 0] + if self.verbose_feature_names_out: + # `_add_prefix_for_feature_names_out` takes care about raising + # an error if there are duplicated columns. + feature_names_outs = self._add_prefix_for_feature_names_out( + list(zip(transformer_names, feature_names_outs)) + ) + else: + # check for duplicated columns and raise if any + feature_names_outs = list(chain.from_iterable(feature_names_outs)) + feature_names_count = Counter(feature_names_outs) + if any(count > 1 for count in feature_names_count.values()): + duplicated_feature_names = sorted( + name + for name, count in feature_names_count.items() + if count > 1 + ) + err_msg = ( + "Duplicated feature names found before concatenating the" + " outputs of the transformers:" + f" {duplicated_feature_names}.\n" + ) + for transformer_name, X in zip(transformer_names, Xs): + if X.shape[1] == 0: + continue + dup_cols_in_transformer = sorted( + set(X.columns).intersection(duplicated_feature_names) + ) + if len(dup_cols_in_transformer): + err_msg += ( + f"Transformer {transformer_name} has conflicting " + f"columns names: {dup_cols_in_transformer}.\n" + ) + raise ValueError( + err_msg + + "Either make sure that the transformers named above " + "do not generate columns with conflicting names or set " + "verbose_feature_names_out=True to automatically " + "prefix to the output feature names with the name " + "of the transformer to prevent any conflicting " + "names." + ) + + names_idx = 0 + for X in Xs: + if X.shape[1] == 0: + continue + names_out = feature_names_outs[names_idx : names_idx + X.shape[1]] + adapter.rename_columns(X, names_out) + names_idx += X.shape[1] + + output = adapter.hstack(Xs) + output_samples = output.shape[0] + if output_samples != n_samples: + raise ValueError( + "Concatenating DataFrames from the transformer's output lead to" + " an inconsistent number of samples. The output may have Pandas" + " Indexes that do not match, or that transformers are returning" + " number of samples which are not the same as the number input" + " samples." + ) + + return output + + return np.hstack(Xs) + + def _sk_visual_block_(self): + if isinstance(self.remainder, str) and self.remainder == "drop": + transformers = self.transformers + elif hasattr(self, "_remainder"): + remainder_columns = self._remainder[2] + if ( + hasattr(self, "feature_names_in_") + and remainder_columns + and not all(isinstance(col, str) for col in remainder_columns) + ): + remainder_columns = self.feature_names_in_[remainder_columns].tolist() + transformers = chain( + self.transformers, [("remainder", self.remainder, remainder_columns)] + ) + else: + transformers = chain(self.transformers, [("remainder", self.remainder, "")]) + + names, transformers, name_details = zip(*transformers) + return _VisualBlock( + "parallel", transformers, names=names, name_details=name_details + ) + + def __getitem__(self, key): + try: + return self.named_transformers_[key] + except AttributeError as e: + raise TypeError( + "ColumnTransformer is subscriptable after it is fitted" + ) from e + except KeyError as e: + raise KeyError(f"'{key}' is not a valid transformer name") from e + + def _get_empty_routing(self): + """Return empty routing. + + Used while routing can be disabled. + + TODO: Remove when ``set_config(enable_metadata_routing=False)`` is no + more an option. + """ + return Bunch( + **{ + name: Bunch(**{method: {} for method in METHODS}) + for name, step, _, _ in self._iter( + fitted=False, + column_as_labels=False, + skip_drop=True, + skip_empty_columns=True, + ) + } + ) + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + .. versionadded:: 1.4 + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + router = MetadataRouter(owner=self.__class__.__name__) + # Here we don't care about which columns are used for which + # transformers, and whether or not a transformer is used at all, which + # might happen if no columns are selected for that transformer. We + # request all metadata requested by all transformers. + transformers = chain(self.transformers, [("remainder", self.remainder, None)]) + for name, step, _ in transformers: + method_mapping = MethodMapping() + if hasattr(step, "fit_transform"): + ( + method_mapping.add(caller="fit", callee="fit_transform").add( + caller="fit_transform", callee="fit_transform" + ) + ) + else: + ( + method_mapping.add(caller="fit", callee="fit") + .add(caller="fit", callee="transform") + .add(caller="fit_transform", callee="fit") + .add(caller="fit_transform", callee="transform") + ) + method_mapping.add(caller="transform", callee="transform") + router.add(method_mapping=method_mapping, **{name: step}) + + return router + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + try: + tags.input_tags.sparse = all( + get_tags(trans).input_tags.sparse + for name, trans, _ in self.transformers + if trans not in {"passthrough", "drop"} + ) + except Exception: + # If `transformers` does not comply with our API (list of tuples) + # then it will fail. In this case, we assume that `sparse` is False + # but the parameter validation will raise an error during `fit`. + pass # pragma: no cover + return tags + + +def _check_X(X): + """Use check_array only when necessary, e.g. on lists and other non-array-likes.""" + if ( + (hasattr(X, "__array__") and hasattr(X, "shape")) + or hasattr(X, "__dataframe__") + or sparse.issparse(X) + ): + return X + return check_array(X, ensure_all_finite="allow-nan", dtype=object) + + +def _is_empty_column_selection(column): + """ + Return True if the column selection is empty (empty list or all-False + boolean array). + + """ + if ( + hasattr(column, "dtype") + # Not necessarily a numpy dtype, can be a pandas dtype as well + and isinstance(column.dtype, np.dtype) + and np.issubdtype(column.dtype, np.bool_) + ): + return not column.any() + elif hasattr(column, "__len__"): + return len(column) == 0 or ( + all(isinstance(col, bool) for col in column) and not any(column) + ) + else: + return False + + +def _get_transformer_list(estimators): + """ + Construct (name, trans, column) tuples from list + + """ + transformers, columns = zip(*estimators) + names, _ = zip(*_name_estimators(transformers)) + + transformer_list = list(zip(names, transformers, columns)) + return transformer_list + + +# This function is not validated using validate_params because +# it's just a factory for ColumnTransformer. +def make_column_transformer( + *transformers, + remainder="drop", + sparse_threshold=0.3, + n_jobs=None, + verbose=False, + verbose_feature_names_out=True, + force_int_remainder_cols="deprecated", +): + """Construct a ColumnTransformer from the given transformers. + + This is a shorthand for the ColumnTransformer constructor; it does not + require, and does not permit, naming the transformers. Instead, they will + be given names automatically based on their types. It also does not allow + weighting with ``transformer_weights``. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + *transformers : tuples + Tuples of the form (transformer, columns) specifying the + transformer objects to be applied to subsets of the data. + + transformer : {'drop', 'passthrough'} or estimator + Estimator must support :term:`fit` and :term:`transform`. + Special-cased strings 'drop' and 'passthrough' are accepted as + well, to indicate to drop the columns or to pass them through + untransformed, respectively. + columns : str, array-like of str, int, array-like of int, slice, \ + array-like of bool or callable + Indexes the data on its second axis. Integers are interpreted as + positional columns, while strings can reference DataFrame columns + by name. A scalar string or int should be used where + ``transformer`` expects X to be a 1d array-like (vector), + otherwise a 2d array will be passed to the transformer. + A callable is passed the input data `X` and can return any of the + above. To select multiple columns by name or dtype, you can use + :obj:`make_column_selector`. + + remainder : {'drop', 'passthrough'} or estimator, default='drop' + By default, only the specified columns in `transformers` are + transformed and combined in the output, and the non-specified + columns are dropped. (default of ``'drop'``). + By specifying ``remainder='passthrough'``, all remaining columns that + were not specified in `transformers` will be automatically passed + through. This subset of columns is concatenated with the output of + the transformers. + By setting ``remainder`` to be an estimator, the remaining + non-specified columns will use the ``remainder`` estimator. The + estimator must support :term:`fit` and :term:`transform`. + + sparse_threshold : float, default=0.3 + If the transformed output consists of a mix of sparse and dense data, + it will be stacked as a sparse matrix if the density is lower than this + value. Use ``sparse_threshold=0`` to always return dense. + When the transformed output consists of all sparse or all dense data, + the stacked result will be sparse or dense, respectively, and this + keyword will be ignored. + + n_jobs : int, default=None + Number of jobs to run in parallel. + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + verbose : bool, default=False + If True, the time elapsed while fitting each transformer will be + printed as it is completed. + + verbose_feature_names_out : bool, default=True + If True, :meth:`ColumnTransformer.get_feature_names_out` will prefix + all feature names with the name of the transformer that generated that + feature. + If False, :meth:`ColumnTransformer.get_feature_names_out` will not + prefix any feature names and will error if feature names are not + unique. + + .. versionadded:: 1.0 + + force_int_remainder_cols : bool, default=True + This parameter has no effect. + + .. note:: + If you do not access the list of columns for the remainder columns + in the :attr:`ColumnTransformer.transformers_` fitted attribute, + you do not need to set this parameter. + + .. versionadded:: 1.5 + + .. versionchanged:: 1.7 + The default value for `force_int_remainder_cols` will change from + `True` to `False` in version 1.7. + + .. deprecated:: 1.7 + `force_int_remainder_cols` is deprecated and will be removed in version 1.9. + + Returns + ------- + ct : ColumnTransformer + Returns a :class:`ColumnTransformer` object. + + See Also + -------- + ColumnTransformer : Class that allows combining the + outputs of multiple transformer objects used on column subsets + of the data into a single feature space. + + Examples + -------- + >>> from sklearn.preprocessing import StandardScaler, OneHotEncoder + >>> from sklearn.compose import make_column_transformer + >>> make_column_transformer( + ... (StandardScaler(), ['numerical_column']), + ... (OneHotEncoder(), ['categorical_column'])) + ColumnTransformer(transformers=[('standardscaler', StandardScaler(...), + ['numerical_column']), + ('onehotencoder', OneHotEncoder(...), + ['categorical_column'])]) + """ + # transformer_weights keyword is not passed through because the user + # would need to know the automatically generated names of the transformers + transformer_list = _get_transformer_list(transformers) + return ColumnTransformer( + transformer_list, + n_jobs=n_jobs, + remainder=remainder, + sparse_threshold=sparse_threshold, + verbose=verbose, + verbose_feature_names_out=verbose_feature_names_out, + force_int_remainder_cols=force_int_remainder_cols, + ) + + +class make_column_selector: + """Create a callable to select columns to be used with + :class:`ColumnTransformer`. + + :func:`make_column_selector` can select columns based on datatype or the + columns name with a regex. When using multiple selection criteria, **all** + criteria must match for a column to be selected. + + For an example of how to use :func:`make_column_selector` within a + :class:`ColumnTransformer` to select columns based on data type (i.e. + `dtype`), refer to + :ref:`sphx_glr_auto_examples_compose_plot_column_transformer_mixed_types.py`. + + Parameters + ---------- + pattern : str, default=None + Name of columns containing this regex pattern will be included. If + None, column selection will not be selected based on pattern. + + dtype_include : column dtype or list of column dtypes, default=None + A selection of dtypes to include. For more details, see + :meth:`pandas.DataFrame.select_dtypes`. + + dtype_exclude : column dtype or list of column dtypes, default=None + A selection of dtypes to exclude. For more details, see + :meth:`pandas.DataFrame.select_dtypes`. + + Returns + ------- + selector : callable + Callable for column selection to be used by a + :class:`ColumnTransformer`. + + See Also + -------- + ColumnTransformer : Class that allows combining the + outputs of multiple transformer objects used on column subsets + of the data into a single feature space. + + Examples + -------- + >>> from sklearn.preprocessing import StandardScaler, OneHotEncoder + >>> from sklearn.compose import make_column_transformer + >>> from sklearn.compose import make_column_selector + >>> import numpy as np + >>> import pandas as pd # doctest: +SKIP + >>> X = pd.DataFrame({'city': ['London', 'London', 'Paris', 'Sallisaw'], + ... 'rating': [5, 3, 4, 5]}) # doctest: +SKIP + >>> ct = make_column_transformer( + ... (StandardScaler(), + ... make_column_selector(dtype_include=np.number)), # rating + ... (OneHotEncoder(), + ... make_column_selector(dtype_include=object))) # city + >>> ct.fit_transform(X) # doctest: +SKIP + array([[ 0.90453403, 1. , 0. , 0. ], + [-1.50755672, 1. , 0. , 0. ], + [-0.30151134, 0. , 1. , 0. ], + [ 0.90453403, 0. , 0. , 1. ]]) + """ + + def __init__(self, pattern=None, *, dtype_include=None, dtype_exclude=None): + self.pattern = pattern + self.dtype_include = dtype_include + self.dtype_exclude = dtype_exclude + + def __call__(self, df): + """Callable for column selection to be used by a + :class:`ColumnTransformer`. + + Parameters + ---------- + df : dataframe of shape (n_features, n_samples) + DataFrame to select columns from. + """ + if not hasattr(df, "iloc"): + raise ValueError( + "make_column_selector can only be applied to pandas dataframes" + ) + df_row = df.iloc[:1] + if self.dtype_include is not None or self.dtype_exclude is not None: + df_row = df_row.select_dtypes( + include=self.dtype_include, exclude=self.dtype_exclude + ) + cols = df_row.columns + if self.pattern is not None: + cols = cols[cols.str.contains(self.pattern, regex=True)] + return cols.tolist() + + +def _feature_names_out_with_str_format( + transformer_name: str, feature_name: str, str_format: str +) -> str: + return str_format.format( + transformer_name=transformer_name, feature_name=feature_name + ) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/_target.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/_target.py new file mode 100644 index 0000000000000000000000000000000000000000..7f713767b30cb8ce0cb5724f2252e427df05a788 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/_target.py @@ -0,0 +1,397 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings + +import numpy as np + +from ..base import BaseEstimator, RegressorMixin, _fit_context, clone +from ..exceptions import NotFittedError +from ..linear_model import LinearRegression +from ..preprocessing import FunctionTransformer +from ..utils import Bunch, _safe_indexing, check_array +from ..utils._metadata_requests import ( + MetadataRouter, + MethodMapping, + _routing_enabled, + process_routing, +) +from ..utils._param_validation import HasMethods +from ..utils._tags import get_tags +from ..utils.validation import check_is_fitted + +__all__ = ["TransformedTargetRegressor"] + + +class TransformedTargetRegressor(RegressorMixin, BaseEstimator): + """Meta-estimator to regress on a transformed target. + + Useful for applying a non-linear transformation to the target `y` in + regression problems. This transformation can be given as a Transformer + such as the :class:`~sklearn.preprocessing.QuantileTransformer` or as a + function and its inverse such as `np.log` and `np.exp`. + + The computation during :meth:`fit` is:: + + regressor.fit(X, func(y)) + + or:: + + regressor.fit(X, transformer.transform(y)) + + The computation during :meth:`predict` is:: + + inverse_func(regressor.predict(X)) + + or:: + + transformer.inverse_transform(regressor.predict(X)) + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.20 + + Parameters + ---------- + regressor : object, default=None + Regressor object such as derived from + :class:`~sklearn.base.RegressorMixin`. This regressor will + automatically be cloned each time prior to fitting. If `regressor is + None`, :class:`~sklearn.linear_model.LinearRegression` is created and used. + + transformer : object, default=None + Estimator object such as derived from + :class:`~sklearn.base.TransformerMixin`. Cannot be set at the same time + as `func` and `inverse_func`. If `transformer is None` as well as + `func` and `inverse_func`, the transformer will be an identity + transformer. Note that the transformer will be cloned during fitting. + Also, the transformer is restricting `y` to be a numpy array. + + func : function, default=None + Function to apply to `y` before passing to :meth:`fit`. Cannot be set + at the same time as `transformer`. If `func is None`, the function used will be + the identity function. If `func` is set, `inverse_func` also needs to be + provided. The function needs to return a 2-dimensional array. + + inverse_func : function, default=None + Function to apply to the prediction of the regressor. Cannot be set at + the same time as `transformer`. The inverse function is used to return + predictions to the same space of the original training labels. If + `inverse_func` is set, `func` also needs to be provided. The inverse + function needs to return a 2-dimensional array. + + check_inverse : bool, default=True + Whether to check that `transform` followed by `inverse_transform` + or `func` followed by `inverse_func` leads to the original targets. + + Attributes + ---------- + regressor_ : object + Fitted regressor. + + transformer_ : object + Transformer used in :meth:`fit` and :meth:`predict`. + + n_features_in_ : int + Number of features seen during :term:`fit`. Only defined if the + underlying regressor exposes such an attribute when fit. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + sklearn.preprocessing.FunctionTransformer : Construct a transformer from an + arbitrary callable. + + Notes + ----- + Internally, the target `y` is always converted into a 2-dimensional array + to be used by scikit-learn transformers. At the time of prediction, the + output will be reshaped to a have the same number of dimensions as `y`. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.linear_model import LinearRegression + >>> from sklearn.compose import TransformedTargetRegressor + >>> tt = TransformedTargetRegressor(regressor=LinearRegression(), + ... func=np.log, inverse_func=np.exp) + >>> X = np.arange(4).reshape(-1, 1) + >>> y = np.exp(2 * X).ravel() + >>> tt.fit(X, y) + TransformedTargetRegressor(...) + >>> tt.score(X, y) + 1.0 + >>> tt.regressor_.coef_ + array([2.]) + + For a more detailed example use case refer to + :ref:`sphx_glr_auto_examples_compose_plot_transformed_target.py`. + """ + + _parameter_constraints: dict = { + "regressor": [HasMethods(["fit", "predict"]), None], + "transformer": [HasMethods("transform"), None], + "func": [callable, None], + "inverse_func": [callable, None], + "check_inverse": ["boolean"], + } + + def __init__( + self, + regressor=None, + *, + transformer=None, + func=None, + inverse_func=None, + check_inverse=True, + ): + self.regressor = regressor + self.transformer = transformer + self.func = func + self.inverse_func = inverse_func + self.check_inverse = check_inverse + + def _fit_transformer(self, y): + """Check transformer and fit transformer. + + Create the default transformer, fit it and make additional inverse + check on a subset (optional). + + """ + if self.transformer is not None and ( + self.func is not None or self.inverse_func is not None + ): + raise ValueError( + "'transformer' and functions 'func'/'inverse_func' cannot both be set." + ) + elif self.transformer is not None: + self.transformer_ = clone(self.transformer) + else: + if (self.func is not None and self.inverse_func is None) or ( + self.func is None and self.inverse_func is not None + ): + lacking_param, existing_param = ( + ("func", "inverse_func") + if self.func is None + else ("inverse_func", "func") + ) + raise ValueError( + f"When '{existing_param}' is provided, '{lacking_param}' must also" + f" be provided. If {lacking_param} is supposed to be the default," + " you need to explicitly pass it the identity function." + ) + self.transformer_ = FunctionTransformer( + func=self.func, + inverse_func=self.inverse_func, + validate=True, + check_inverse=self.check_inverse, + ) + # We are transforming the target here and not the features, so we set the + # output of FunctionTransformer() to be a numpy array (default) and to not + # depend on the global configuration: + self.transformer_.set_output(transform="default") + # XXX: sample_weight is not currently passed to the + # transformer. However, if transformer starts using sample_weight, the + # code should be modified accordingly. At the time to consider the + # sample_prop feature, it is also a good use case to be considered. + self.transformer_.fit(y) + if self.check_inverse: + idx_selected = slice(None, None, max(1, y.shape[0] // 10)) + y_sel = _safe_indexing(y, idx_selected) + y_sel_t = self.transformer_.transform(y_sel) + if not np.allclose(y_sel, self.transformer_.inverse_transform(y_sel_t)): + warnings.warn( + ( + "The provided functions or transformer are" + " not strictly inverse of each other. If" + " you are sure you want to proceed regardless" + ", set 'check_inverse=False'" + ), + UserWarning, + ) + + @_fit_context( + # TransformedTargetRegressor.regressor/transformer are not validated yet. + prefer_skip_nested_validation=False + ) + def fit(self, X, y, **fit_params): + """Fit the model according to the given training data. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Training vector, where `n_samples` is the number of samples and + `n_features` is the number of features. + + y : array-like of shape (n_samples,) + Target values. + + **fit_params : dict + - If `enable_metadata_routing=False` (default): Parameters directly passed + to the `fit` method of the underlying regressor. + + - If `enable_metadata_routing=True`: Parameters safely routed to the `fit` + method of the underlying regressor. + + .. versionchanged:: 1.6 + See :ref:`Metadata Routing User Guide ` for + more details. + + Returns + ------- + self : object + Fitted estimator. + """ + if y is None: + raise ValueError( + f"This {self.__class__.__name__} estimator " + "requires y to be passed, but the target y is None." + ) + y = check_array( + y, + input_name="y", + accept_sparse=False, + ensure_all_finite=True, + ensure_2d=False, + dtype="numeric", + allow_nd=True, + ) + + # store the number of dimension of the target to predict an array of + # similar shape at predict + self._training_dim = y.ndim + + # transformers are designed to modify X which is 2d dimensional, we + # need to modify y accordingly. + if y.ndim == 1: + y_2d = y.reshape(-1, 1) + else: + y_2d = y + self._fit_transformer(y_2d) + + # transform y and convert back to 1d array if needed + y_trans = self.transformer_.transform(y_2d) + # FIXME: a FunctionTransformer can return a 1D array even when validate + # is set to True. Therefore, we need to check the number of dimension + # first. + if y_trans.ndim == 2 and y_trans.shape[1] == 1 and self._training_dim == 1: + y_trans = y_trans.squeeze(axis=1) + + self.regressor_ = self._get_regressor(get_clone=True) + if _routing_enabled(): + routed_params = process_routing(self, "fit", **fit_params) + else: + routed_params = Bunch(regressor=Bunch(fit=fit_params)) + + self.regressor_.fit(X, y_trans, **routed_params.regressor.fit) + + if hasattr(self.regressor_, "feature_names_in_"): + self.feature_names_in_ = self.regressor_.feature_names_in_ + + return self + + def predict(self, X, **predict_params): + """Predict using the base regressor, applying inverse. + + The regressor is used to predict and the `inverse_func` or + `inverse_transform` is applied before returning the prediction. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Samples. + + **predict_params : dict of str -> object + - If `enable_metadata_routing=False` (default): Parameters directly passed + to the `predict` method of the underlying regressor. + + - If `enable_metadata_routing=True`: Parameters safely routed to the + `predict` method of the underlying regressor. + + .. versionchanged:: 1.6 + See :ref:`Metadata Routing User Guide ` + for more details. + + Returns + ------- + y_hat : ndarray of shape (n_samples,) + Predicted values. + """ + check_is_fitted(self) + if _routing_enabled(): + routed_params = process_routing(self, "predict", **predict_params) + else: + routed_params = Bunch(regressor=Bunch(predict=predict_params)) + + pred = self.regressor_.predict(X, **routed_params.regressor.predict) + if pred.ndim == 1: + pred_trans = self.transformer_.inverse_transform(pred.reshape(-1, 1)) + else: + pred_trans = self.transformer_.inverse_transform(pred) + if ( + self._training_dim == 1 + and pred_trans.ndim == 2 + and pred_trans.shape[1] == 1 + ): + pred_trans = pred_trans.squeeze(axis=1) + + return pred_trans + + def __sklearn_tags__(self): + regressor = self._get_regressor() + tags = super().__sklearn_tags__() + tags.regressor_tags.poor_score = True + tags.input_tags.sparse = get_tags(regressor).input_tags.sparse + tags.target_tags.multi_output = get_tags(regressor).target_tags.multi_output + return tags + + @property + def n_features_in_(self): + """Number of features seen during :term:`fit`.""" + # For consistency with other estimators we raise a AttributeError so + # that hasattr() returns False the estimator isn't fitted. + try: + check_is_fitted(self) + except NotFittedError as nfe: + raise AttributeError( + "{} object has no n_features_in_ attribute.".format( + self.__class__.__name__ + ) + ) from nfe + + return self.regressor_.n_features_in_ + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + .. versionadded:: 1.6 + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + router = MetadataRouter(owner=self.__class__.__name__).add( + regressor=self._get_regressor(), + method_mapping=MethodMapping() + .add(caller="fit", callee="fit") + .add(caller="predict", callee="predict"), + ) + return router + + def _get_regressor(self, get_clone=False): + if self.regressor is None: + return LinearRegression() + + return clone(self.regressor) if get_clone else self.regressor diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/tests/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/tests/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/tests/test_column_transformer.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/tests/test_column_transformer.py new file mode 100644 index 0000000000000000000000000000000000000000..c7c69c657f2eab27e71df599d7507be8effe73cc --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/tests/test_column_transformer.py @@ -0,0 +1,2804 @@ +""" +Test the ColumnTransformer. +""" + +import pickle +import re +import warnings + +import joblib +import numpy as np +import pytest +from numpy.testing import assert_allclose +from scipy import sparse + +from sklearn import config_context +from sklearn.base import BaseEstimator, TransformerMixin +from sklearn.compose import ( + ColumnTransformer, + make_column_selector, + make_column_transformer, +) +from sklearn.exceptions import NotFittedError +from sklearn.feature_extraction import DictVectorizer +from sklearn.feature_selection import VarianceThreshold +from sklearn.preprocessing import ( + FunctionTransformer, + Normalizer, + OneHotEncoder, + StandardScaler, +) +from sklearn.tests.metadata_routing_common import ( + ConsumingTransformer, + _Registry, + check_recorded_metadata, +) +from sklearn.utils._indexing import _safe_indexing +from sklearn.utils._testing import ( + _convert_container, + assert_allclose_dense_sparse, + assert_almost_equal, + assert_array_equal, +) +from sklearn.utils.fixes import CSR_CONTAINERS, parse_version + + +class Trans(TransformerMixin, BaseEstimator): + def fit(self, X, y=None): + return self + + def transform(self, X, y=None): + # 1D Series -> 2D DataFrame + if hasattr(X, "to_frame"): + return X.to_frame() + # 1D array -> 2D array + if getattr(X, "ndim", 2) == 1: + return np.atleast_2d(X).T + return X + + +class DoubleTrans(BaseEstimator): + def fit(self, X, y=None): + return self + + def transform(self, X): + return 2 * X + + +class SparseMatrixTrans(BaseEstimator): + def __init__(self, csr_container): + self.csr_container = csr_container + + def fit(self, X, y=None): + return self + + def transform(self, X, y=None): + n_samples = len(X) + return self.csr_container(sparse.eye(n_samples, n_samples)) + + +class TransNo2D(BaseEstimator): + def fit(self, X, y=None): + return self + + def transform(self, X, y=None): + return X + + +class TransRaise(BaseEstimator): + def fit(self, X, y=None): + raise ValueError("specific message") + + def transform(self, X, y=None): + raise ValueError("specific message") + + +def test_column_transformer(): + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + + X_res_first1D = np.array([0, 1, 2]) + X_res_second1D = np.array([2, 4, 6]) + X_res_first = X_res_first1D.reshape(-1, 1) + X_res_both = X_array + + cases = [ + # single column 1D / 2D + (0, X_res_first), + ([0], X_res_first), + # list-like + ([0, 1], X_res_both), + (np.array([0, 1]), X_res_both), + # slice + (slice(0, 1), X_res_first), + (slice(0, 2), X_res_both), + # boolean mask + (np.array([True, False]), X_res_first), + ([True, False], X_res_first), + (np.array([True, True]), X_res_both), + ([True, True], X_res_both), + ] + + for selection, res in cases: + ct = ColumnTransformer([("trans", Trans(), selection)], remainder="drop") + assert_array_equal(ct.fit_transform(X_array), res) + assert_array_equal(ct.fit(X_array).transform(X_array), res) + + # callable that returns any of the allowed specifiers + ct = ColumnTransformer( + [("trans", Trans(), lambda x: selection)], remainder="drop" + ) + assert_array_equal(ct.fit_transform(X_array), res) + assert_array_equal(ct.fit(X_array).transform(X_array), res) + + ct = ColumnTransformer([("trans1", Trans(), [0]), ("trans2", Trans(), [1])]) + assert_array_equal(ct.fit_transform(X_array), X_res_both) + assert_array_equal(ct.fit(X_array).transform(X_array), X_res_both) + assert len(ct.transformers_) == 2 + + # test with transformer_weights + transformer_weights = {"trans1": 0.1, "trans2": 10} + both = ColumnTransformer( + [("trans1", Trans(), [0]), ("trans2", Trans(), [1])], + transformer_weights=transformer_weights, + ) + res = np.vstack( + [ + transformer_weights["trans1"] * X_res_first1D, + transformer_weights["trans2"] * X_res_second1D, + ] + ).T + assert_array_equal(both.fit_transform(X_array), res) + assert_array_equal(both.fit(X_array).transform(X_array), res) + assert len(both.transformers_) == 2 + + both = ColumnTransformer( + [("trans", Trans(), [0, 1])], transformer_weights={"trans": 0.1} + ) + assert_array_equal(both.fit_transform(X_array), 0.1 * X_res_both) + assert_array_equal(both.fit(X_array).transform(X_array), 0.1 * X_res_both) + assert len(both.transformers_) == 1 + + +def test_column_transformer_tuple_transformers_parameter(): + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + + transformers = [("trans1", Trans(), [0]), ("trans2", Trans(), [1])] + + ct_with_list = ColumnTransformer(transformers) + ct_with_tuple = ColumnTransformer(tuple(transformers)) + + assert_array_equal( + ct_with_list.fit_transform(X_array), ct_with_tuple.fit_transform(X_array) + ) + assert_array_equal( + ct_with_list.fit(X_array).transform(X_array), + ct_with_tuple.fit(X_array).transform(X_array), + ) + + +@pytest.mark.parametrize("constructor_name", ["dataframe", "polars"]) +def test_column_transformer_dataframe(constructor_name): + if constructor_name == "dataframe": + dataframe_lib = pytest.importorskip("pandas") + else: + dataframe_lib = pytest.importorskip(constructor_name) + + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + X_df = _convert_container( + X_array, constructor_name, columns_name=["first", "second"] + ) + + X_res_first = np.array([0, 1, 2]).reshape(-1, 1) + X_res_both = X_array + + cases = [ + # String keys: label based + # list + (["first"], X_res_first), + (["first", "second"], X_res_both), + # slice + (slice("first", "second"), X_res_both), + # int keys: positional + # list + ([0], X_res_first), + ([0, 1], X_res_both), + (np.array([0, 1]), X_res_both), + # slice + (slice(0, 1), X_res_first), + (slice(0, 2), X_res_both), + # boolean mask + (np.array([True, False]), X_res_first), + ([True, False], X_res_first), + ] + if constructor_name == "dataframe": + # Scalars are only supported for pandas dataframes. + cases.extend( + [ + # scalar + (0, X_res_first), + ("first", X_res_first), + ( + dataframe_lib.Series([True, False], index=["first", "second"]), + X_res_first, + ), + ] + ) + + for selection, res in cases: + ct = ColumnTransformer([("trans", Trans(), selection)], remainder="drop") + assert_array_equal(ct.fit_transform(X_df), res) + assert_array_equal(ct.fit(X_df).transform(X_df), res) + + # callable that returns any of the allowed specifiers + ct = ColumnTransformer( + [("trans", Trans(), lambda X: selection)], remainder="drop" + ) + assert_array_equal(ct.fit_transform(X_df), res) + assert_array_equal(ct.fit(X_df).transform(X_df), res) + + ct = ColumnTransformer( + [("trans1", Trans(), ["first"]), ("trans2", Trans(), ["second"])] + ) + assert_array_equal(ct.fit_transform(X_df), X_res_both) + assert_array_equal(ct.fit(X_df).transform(X_df), X_res_both) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] != "remainder" + + ct = ColumnTransformer([("trans1", Trans(), [0]), ("trans2", Trans(), [1])]) + assert_array_equal(ct.fit_transform(X_df), X_res_both) + assert_array_equal(ct.fit(X_df).transform(X_df), X_res_both) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] != "remainder" + + # test with transformer_weights + transformer_weights = {"trans1": 0.1, "trans2": 10} + both = ColumnTransformer( + [("trans1", Trans(), ["first"]), ("trans2", Trans(), ["second"])], + transformer_weights=transformer_weights, + ) + res = np.vstack( + [ + transformer_weights["trans1"] * X_df["first"], + transformer_weights["trans2"] * X_df["second"], + ] + ).T + assert_array_equal(both.fit_transform(X_df), res) + assert_array_equal(both.fit(X_df).transform(X_df), res) + assert len(both.transformers_) == 2 + assert both.transformers_[-1][0] != "remainder" + + # test multiple columns + both = ColumnTransformer( + [("trans", Trans(), ["first", "second"])], transformer_weights={"trans": 0.1} + ) + assert_array_equal(both.fit_transform(X_df), 0.1 * X_res_both) + assert_array_equal(both.fit(X_df).transform(X_df), 0.1 * X_res_both) + assert len(both.transformers_) == 1 + assert both.transformers_[-1][0] != "remainder" + + both = ColumnTransformer( + [("trans", Trans(), [0, 1])], transformer_weights={"trans": 0.1} + ) + assert_array_equal(both.fit_transform(X_df), 0.1 * X_res_both) + assert_array_equal(both.fit(X_df).transform(X_df), 0.1 * X_res_both) + assert len(both.transformers_) == 1 + assert both.transformers_[-1][0] != "remainder" + + # ensure pandas object is passed through + + class TransAssert(BaseEstimator): + def __init__(self, expected_type_transform): + self.expected_type_transform = expected_type_transform + + def fit(self, X, y=None): + return self + + def transform(self, X, y=None): + assert isinstance(X, self.expected_type_transform) + if isinstance(X, dataframe_lib.Series): + X = X.to_frame() + return X + + ct = ColumnTransformer( + [ + ( + "trans", + TransAssert(expected_type_transform=dataframe_lib.DataFrame), + ["first", "second"], + ) + ] + ) + ct.fit_transform(X_df) + + if constructor_name == "dataframe": + # DataFrame protocol does not have 1d columns, so we only test on Pandas + # dataframes. + ct = ColumnTransformer( + [ + ( + "trans", + TransAssert(expected_type_transform=dataframe_lib.Series), + "first", + ) + ], + remainder="drop", + ) + ct.fit_transform(X_df) + + # Only test on pandas because the dataframe protocol requires string column + # names + # integer column spec + integer column names -> still use positional + X_df2 = X_df.copy() + X_df2.columns = [1, 0] + ct = ColumnTransformer([("trans", Trans(), 0)], remainder="drop") + assert_array_equal(ct.fit_transform(X_df2), X_res_first) + assert_array_equal(ct.fit(X_df2).transform(X_df2), X_res_first) + + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] == "remainder" + assert ct.transformers_[-1][1] == "drop" + assert_array_equal(ct.transformers_[-1][2], [1]) + + +@pytest.mark.parametrize("pandas", [True, False], ids=["pandas", "numpy"]) +@pytest.mark.parametrize( + "column_selection", + [[], np.array([False, False]), [False, False]], + ids=["list", "bool", "bool_int"], +) +@pytest.mark.parametrize("callable_column", [False, True]) +def test_column_transformer_empty_columns(pandas, column_selection, callable_column): + # test case that ensures that the column transformer does also work when + # a given transformer doesn't have any columns to work on + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + X_res_both = X_array + + if pandas: + pd = pytest.importorskip("pandas") + X = pd.DataFrame(X_array, columns=["first", "second"]) + else: + X = X_array + + if callable_column: + column = lambda X: column_selection + else: + column = column_selection + + ct = ColumnTransformer( + [("trans1", Trans(), [0, 1]), ("trans2", TransRaise(), column)] + ) + assert_array_equal(ct.fit_transform(X), X_res_both) + assert_array_equal(ct.fit(X).transform(X), X_res_both) + assert len(ct.transformers_) == 2 + assert isinstance(ct.transformers_[1][1], TransRaise) + + ct = ColumnTransformer( + [("trans1", TransRaise(), column), ("trans2", Trans(), [0, 1])] + ) + assert_array_equal(ct.fit_transform(X), X_res_both) + assert_array_equal(ct.fit(X).transform(X), X_res_both) + assert len(ct.transformers_) == 2 + assert isinstance(ct.transformers_[0][1], TransRaise) + + ct = ColumnTransformer([("trans", TransRaise(), column)], remainder="passthrough") + assert_array_equal(ct.fit_transform(X), X_res_both) + assert_array_equal(ct.fit(X).transform(X), X_res_both) + assert len(ct.transformers_) == 2 # including remainder + assert isinstance(ct.transformers_[0][1], TransRaise) + + fixture = np.array([[], [], []]) + ct = ColumnTransformer([("trans", TransRaise(), column)], remainder="drop") + assert_array_equal(ct.fit_transform(X), fixture) + assert_array_equal(ct.fit(X).transform(X), fixture) + assert len(ct.transformers_) == 2 # including remainder + assert isinstance(ct.transformers_[0][1], TransRaise) + + +def test_column_transformer_output_indices(): + # Checks for the output_indices_ attribute + X_array = np.arange(6).reshape(3, 2) + + ct = ColumnTransformer([("trans1", Trans(), [0]), ("trans2", Trans(), [1])]) + X_trans = ct.fit_transform(X_array) + assert ct.output_indices_ == { + "trans1": slice(0, 1), + "trans2": slice(1, 2), + "remainder": slice(0, 0), + } + assert_array_equal(X_trans[:, [0]], X_trans[:, ct.output_indices_["trans1"]]) + assert_array_equal(X_trans[:, [1]], X_trans[:, ct.output_indices_["trans2"]]) + + # test with transformer_weights and multiple columns + ct = ColumnTransformer( + [("trans", Trans(), [0, 1])], transformer_weights={"trans": 0.1} + ) + X_trans = ct.fit_transform(X_array) + assert ct.output_indices_ == {"trans": slice(0, 2), "remainder": slice(0, 0)} + assert_array_equal(X_trans[:, [0, 1]], X_trans[:, ct.output_indices_["trans"]]) + assert_array_equal(X_trans[:, []], X_trans[:, ct.output_indices_["remainder"]]) + + # test case that ensures that the attribute does also work when + # a given transformer doesn't have any columns to work on + ct = ColumnTransformer([("trans1", Trans(), [0, 1]), ("trans2", TransRaise(), [])]) + X_trans = ct.fit_transform(X_array) + assert ct.output_indices_ == { + "trans1": slice(0, 2), + "trans2": slice(0, 0), + "remainder": slice(0, 0), + } + assert_array_equal(X_trans[:, [0, 1]], X_trans[:, ct.output_indices_["trans1"]]) + assert_array_equal(X_trans[:, []], X_trans[:, ct.output_indices_["trans2"]]) + assert_array_equal(X_trans[:, []], X_trans[:, ct.output_indices_["remainder"]]) + + ct = ColumnTransformer([("trans", TransRaise(), [])], remainder="passthrough") + X_trans = ct.fit_transform(X_array) + assert ct.output_indices_ == {"trans": slice(0, 0), "remainder": slice(0, 2)} + assert_array_equal(X_trans[:, []], X_trans[:, ct.output_indices_["trans"]]) + assert_array_equal(X_trans[:, [0, 1]], X_trans[:, ct.output_indices_["remainder"]]) + + +def test_column_transformer_output_indices_df(): + # Checks for the output_indices_ attribute with data frames + pd = pytest.importorskip("pandas") + + X_df = pd.DataFrame(np.arange(6).reshape(3, 2), columns=["first", "second"]) + + ct = ColumnTransformer( + [("trans1", Trans(), ["first"]), ("trans2", Trans(), ["second"])] + ) + X_trans = ct.fit_transform(X_df) + assert ct.output_indices_ == { + "trans1": slice(0, 1), + "trans2": slice(1, 2), + "remainder": slice(0, 0), + } + assert_array_equal(X_trans[:, [0]], X_trans[:, ct.output_indices_["trans1"]]) + assert_array_equal(X_trans[:, [1]], X_trans[:, ct.output_indices_["trans2"]]) + assert_array_equal(X_trans[:, []], X_trans[:, ct.output_indices_["remainder"]]) + + ct = ColumnTransformer([("trans1", Trans(), [0]), ("trans2", Trans(), [1])]) + X_trans = ct.fit_transform(X_df) + assert ct.output_indices_ == { + "trans1": slice(0, 1), + "trans2": slice(1, 2), + "remainder": slice(0, 0), + } + assert_array_equal(X_trans[:, [0]], X_trans[:, ct.output_indices_["trans1"]]) + assert_array_equal(X_trans[:, [1]], X_trans[:, ct.output_indices_["trans2"]]) + assert_array_equal(X_trans[:, []], X_trans[:, ct.output_indices_["remainder"]]) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_column_transformer_sparse_array(csr_container): + X_sparse = csr_container(sparse.eye(3, 2)) + + # no distinction between 1D and 2D + X_res_first = X_sparse[:, [0]] + X_res_both = X_sparse + + for col in [(0,), [0], slice(0, 1)]: + for remainder, res in [("drop", X_res_first), ("passthrough", X_res_both)]: + ct = ColumnTransformer( + [("trans", Trans(), col)], remainder=remainder, sparse_threshold=0.8 + ) + assert sparse.issparse(ct.fit_transform(X_sparse)) + assert_allclose_dense_sparse(ct.fit_transform(X_sparse), res) + assert_allclose_dense_sparse(ct.fit(X_sparse).transform(X_sparse), res) + + for col in [[0, 1], slice(0, 2)]: + ct = ColumnTransformer([("trans", Trans(), col)], sparse_threshold=0.8) + assert sparse.issparse(ct.fit_transform(X_sparse)) + assert_allclose_dense_sparse(ct.fit_transform(X_sparse), X_res_both) + assert_allclose_dense_sparse(ct.fit(X_sparse).transform(X_sparse), X_res_both) + + +def test_column_transformer_list(): + X_list = [[1, float("nan"), "a"], [0, 0, "b"]] + expected_result = np.array( + [ + [1, float("nan"), 1, 0], + [-1, 0, 0, 1], + ] + ) + + ct = ColumnTransformer( + [ + ("numerical", StandardScaler(), [0, 1]), + ("categorical", OneHotEncoder(), [2]), + ] + ) + + assert_array_equal(ct.fit_transform(X_list), expected_result) + assert_array_equal(ct.fit(X_list).transform(X_list), expected_result) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_column_transformer_sparse_stacking(csr_container): + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + col_trans = ColumnTransformer( + [("trans1", Trans(), [0]), ("trans2", SparseMatrixTrans(csr_container), 1)], + sparse_threshold=0.8, + ) + col_trans.fit(X_array) + X_trans = col_trans.transform(X_array) + assert sparse.issparse(X_trans) + assert X_trans.shape == (X_trans.shape[0], X_trans.shape[0] + 1) + assert_array_equal(X_trans.toarray()[:, 1:], np.eye(X_trans.shape[0])) + assert len(col_trans.transformers_) == 2 + assert col_trans.transformers_[-1][0] != "remainder" + + col_trans = ColumnTransformer( + [("trans1", Trans(), [0]), ("trans2", SparseMatrixTrans(csr_container), 1)], + sparse_threshold=0.1, + ) + col_trans.fit(X_array) + X_trans = col_trans.transform(X_array) + assert not sparse.issparse(X_trans) + assert X_trans.shape == (X_trans.shape[0], X_trans.shape[0] + 1) + assert_array_equal(X_trans[:, 1:], np.eye(X_trans.shape[0])) + + +def test_column_transformer_mixed_cols_sparse(): + df = np.array([["a", 1, True], ["b", 2, False]], dtype="O") + + ct = make_column_transformer( + (OneHotEncoder(), [0]), ("passthrough", [1, 2]), sparse_threshold=1.0 + ) + + # this shouldn't fail, since boolean can be coerced into a numeric + # See: https://github.com/scikit-learn/scikit-learn/issues/11912 + X_trans = ct.fit_transform(df) + assert X_trans.format == "csr" + assert_array_equal(X_trans.toarray(), np.array([[1, 0, 1, 1], [0, 1, 2, 0]])) + + ct = make_column_transformer( + (OneHotEncoder(), [0]), ("passthrough", [0]), sparse_threshold=1.0 + ) + with pytest.raises(ValueError, match="For a sparse output, all columns should"): + # this fails since strings `a` and `b` cannot be + # coerced into a numeric. + ct.fit_transform(df) + + +def test_column_transformer_sparse_threshold(): + X_array = np.array([["a", "b"], ["A", "B"]], dtype=object).T + # above data has sparsity of 4 / 8 = 0.5 + + # apply threshold even if all sparse + col_trans = ColumnTransformer( + [("trans1", OneHotEncoder(), [0]), ("trans2", OneHotEncoder(), [1])], + sparse_threshold=0.2, + ) + res = col_trans.fit_transform(X_array) + assert not sparse.issparse(res) + assert not col_trans.sparse_output_ + + # mixed -> sparsity of (4 + 2) / 8 = 0.75 + for thres in [0.75001, 1]: + col_trans = ColumnTransformer( + [ + ("trans1", OneHotEncoder(sparse_output=True), [0]), + ("trans2", OneHotEncoder(sparse_output=False), [1]), + ], + sparse_threshold=thres, + ) + res = col_trans.fit_transform(X_array) + assert sparse.issparse(res) + assert col_trans.sparse_output_ + + for thres in [0.75, 0]: + col_trans = ColumnTransformer( + [ + ("trans1", OneHotEncoder(sparse_output=True), [0]), + ("trans2", OneHotEncoder(sparse_output=False), [1]), + ], + sparse_threshold=thres, + ) + res = col_trans.fit_transform(X_array) + assert not sparse.issparse(res) + assert not col_trans.sparse_output_ + + # if nothing is sparse -> no sparse + for thres in [0.33, 0, 1]: + col_trans = ColumnTransformer( + [ + ("trans1", OneHotEncoder(sparse_output=False), [0]), + ("trans2", OneHotEncoder(sparse_output=False), [1]), + ], + sparse_threshold=thres, + ) + res = col_trans.fit_transform(X_array) + assert not sparse.issparse(res) + assert not col_trans.sparse_output_ + + +def test_column_transformer_error_msg_1D(): + X_array = np.array([[0.0, 1.0, 2.0], [2.0, 4.0, 6.0]]).T + + col_trans = ColumnTransformer([("trans", StandardScaler(), 0)]) + msg = "1D data passed to a transformer" + with pytest.raises(ValueError, match=msg): + col_trans.fit(X_array) + + with pytest.raises(ValueError, match=msg): + col_trans.fit_transform(X_array) + + col_trans = ColumnTransformer([("trans", TransRaise(), 0)]) + for func in [col_trans.fit, col_trans.fit_transform]: + with pytest.raises(ValueError, match="specific message"): + func(X_array) + + +def test_2D_transformer_output(): + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + + # if one transformer is dropped, test that name is still correct + ct = ColumnTransformer([("trans1", "drop", 0), ("trans2", TransNo2D(), 1)]) + + msg = "the 'trans2' transformer should be 2D" + with pytest.raises(ValueError, match=msg): + ct.fit_transform(X_array) + # because fit is also doing transform, this raises already on fit + with pytest.raises(ValueError, match=msg): + ct.fit(X_array) + + +def test_2D_transformer_output_pandas(): + pd = pytest.importorskip("pandas") + + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + X_df = pd.DataFrame(X_array, columns=["col1", "col2"]) + + # if one transformer is dropped, test that name is still correct + ct = ColumnTransformer([("trans1", TransNo2D(), "col1")]) + msg = "the 'trans1' transformer should be 2D" + with pytest.raises(ValueError, match=msg): + ct.fit_transform(X_df) + # because fit is also doing transform, this raises already on fit + with pytest.raises(ValueError, match=msg): + ct.fit(X_df) + + +@pytest.mark.parametrize("remainder", ["drop", "passthrough"]) +def test_column_transformer_invalid_columns(remainder): + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + + # general invalid + for col in [1.5, ["string", 1], slice(1, "s"), np.array([1.0])]: + ct = ColumnTransformer([("trans", Trans(), col)], remainder=remainder) + with pytest.raises(ValueError, match="No valid specification"): + ct.fit(X_array) + + # invalid for arrays + for col in ["string", ["string", "other"], slice("a", "b")]: + ct = ColumnTransformer([("trans", Trans(), col)], remainder=remainder) + with pytest.raises(ValueError, match="Specifying the columns"): + ct.fit(X_array) + + # transformed n_features does not match fitted n_features + col = [0, 1] + ct = ColumnTransformer([("trans", Trans(), col)], remainder=remainder) + ct.fit(X_array) + X_array_more = np.array([[0, 1, 2], [2, 4, 6], [3, 6, 9]]).T + msg = "X has 3 features, but ColumnTransformer is expecting 2 features as input." + with pytest.raises(ValueError, match=msg): + ct.transform(X_array_more) + X_array_fewer = np.array( + [ + [0, 1, 2], + ] + ).T + err_msg = ( + "X has 1 features, but ColumnTransformer is expecting 2 features as input." + ) + with pytest.raises(ValueError, match=err_msg): + ct.transform(X_array_fewer) + + +def test_column_transformer_invalid_transformer(): + class NoTrans(BaseEstimator): + def fit(self, X, y=None): + return self + + def predict(self, X): + return X + + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + ct = ColumnTransformer([("trans", NoTrans(), [0])]) + msg = "All estimators should implement fit and transform" + with pytest.raises(TypeError, match=msg): + ct.fit(X_array) + + +def test_make_column_transformer(): + scaler = StandardScaler() + norm = Normalizer() + ct = make_column_transformer((scaler, "first"), (norm, ["second"])) + names, transformers, columns = zip(*ct.transformers) + assert names == ("standardscaler", "normalizer") + assert transformers == (scaler, norm) + assert columns == ("first", ["second"]) + + +def test_make_column_transformer_pandas(): + pd = pytest.importorskip("pandas") + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + X_df = pd.DataFrame(X_array, columns=["first", "second"]) + norm = Normalizer() + ct1 = ColumnTransformer([("norm", Normalizer(), X_df.columns)]) + ct2 = make_column_transformer((norm, X_df.columns)) + assert_almost_equal(ct1.fit_transform(X_df), ct2.fit_transform(X_df)) + + +def test_make_column_transformer_kwargs(): + scaler = StandardScaler() + norm = Normalizer() + ct = make_column_transformer( + (scaler, "first"), + (norm, ["second"]), + n_jobs=3, + remainder="drop", + sparse_threshold=0.5, + ) + assert ( + ct.transformers + == make_column_transformer((scaler, "first"), (norm, ["second"])).transformers + ) + assert ct.n_jobs == 3 + assert ct.remainder == "drop" + assert ct.sparse_threshold == 0.5 + # invalid keyword parameters should raise an error message + msg = re.escape( + "make_column_transformer() got an unexpected " + "keyword argument 'transformer_weights'" + ) + with pytest.raises(TypeError, match=msg): + make_column_transformer( + (scaler, "first"), + (norm, ["second"]), + transformer_weights={"pca": 10, "Transf": 1}, + ) + + +def test_make_column_transformer_remainder_transformer(): + scaler = StandardScaler() + norm = Normalizer() + remainder = StandardScaler() + ct = make_column_transformer( + (scaler, "first"), (norm, ["second"]), remainder=remainder + ) + assert ct.remainder == remainder + + +def test_column_transformer_get_set_params(): + ct = ColumnTransformer( + [("trans1", StandardScaler(), [0]), ("trans2", StandardScaler(), [1])] + ) + + exp = { + "n_jobs": None, + "remainder": "drop", + "sparse_threshold": 0.3, + "trans1": ct.transformers[0][1], + "trans1__copy": True, + "trans1__with_mean": True, + "trans1__with_std": True, + "trans2": ct.transformers[1][1], + "trans2__copy": True, + "trans2__with_mean": True, + "trans2__with_std": True, + "transformers": ct.transformers, + "transformer_weights": None, + "verbose_feature_names_out": True, + "verbose": False, + "force_int_remainder_cols": "deprecated", + } + + assert ct.get_params() == exp + + ct.set_params(trans1__with_mean=False) + assert not ct.get_params()["trans1__with_mean"] + + ct.set_params(trans1="passthrough") + exp = { + "n_jobs": None, + "remainder": "drop", + "sparse_threshold": 0.3, + "trans1": "passthrough", + "trans2": ct.transformers[1][1], + "trans2__copy": True, + "trans2__with_mean": True, + "trans2__with_std": True, + "transformers": ct.transformers, + "transformer_weights": None, + "verbose_feature_names_out": True, + "verbose": False, + "force_int_remainder_cols": "deprecated", + } + + assert ct.get_params() == exp + + +def test_column_transformer_named_estimators(): + X_array = np.array([[0.0, 1.0, 2.0], [2.0, 4.0, 6.0]]).T + ct = ColumnTransformer( + [ + ("trans1", StandardScaler(), [0]), + ("trans2", StandardScaler(with_std=False), [1]), + ] + ) + assert not hasattr(ct, "transformers_") + ct.fit(X_array) + assert hasattr(ct, "transformers_") + assert isinstance(ct.named_transformers_["trans1"], StandardScaler) + assert isinstance(ct.named_transformers_.trans1, StandardScaler) + assert isinstance(ct.named_transformers_["trans2"], StandardScaler) + assert isinstance(ct.named_transformers_.trans2, StandardScaler) + assert not ct.named_transformers_.trans2.with_std + # check it are fitted transformers + assert ct.named_transformers_.trans1.mean_ == 1.0 + + +def test_column_transformer_cloning(): + X_array = np.array([[0.0, 1.0, 2.0], [2.0, 4.0, 6.0]]).T + + ct = ColumnTransformer([("trans", StandardScaler(), [0])]) + ct.fit(X_array) + assert not hasattr(ct.transformers[0][1], "mean_") + assert hasattr(ct.transformers_[0][1], "mean_") + + ct = ColumnTransformer([("trans", StandardScaler(), [0])]) + ct.fit_transform(X_array) + assert not hasattr(ct.transformers[0][1], "mean_") + assert hasattr(ct.transformers_[0][1], "mean_") + + +def test_column_transformer_get_feature_names(): + X_array = np.array([[0.0, 1.0, 2.0], [2.0, 4.0, 6.0]]).T + ct = ColumnTransformer([("trans", Trans(), [0, 1])]) + # raise correct error when not fitted + with pytest.raises(NotFittedError): + ct.get_feature_names_out() + # raise correct error when no feature names are available + ct.fit(X_array) + msg = re.escape( + "Transformer trans (type Trans) does not provide get_feature_names_out" + ) + with pytest.raises(AttributeError, match=msg): + ct.get_feature_names_out() + + +def test_column_transformer_special_strings(): + # one 'drop' -> ignore + X_array = np.array([[0.0, 1.0, 2.0], [2.0, 4.0, 6.0]]).T + ct = ColumnTransformer([("trans1", Trans(), [0]), ("trans2", "drop", [1])]) + exp = np.array([[0.0], [1.0], [2.0]]) + assert_array_equal(ct.fit_transform(X_array), exp) + assert_array_equal(ct.fit(X_array).transform(X_array), exp) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] != "remainder" + + # all 'drop' -> return shape 0 array + ct = ColumnTransformer([("trans1", "drop", [0]), ("trans2", "drop", [1])]) + assert_array_equal(ct.fit(X_array).transform(X_array).shape, (3, 0)) + assert_array_equal(ct.fit_transform(X_array).shape, (3, 0)) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] != "remainder" + + # 'passthrough' + X_array = np.array([[0.0, 1.0, 2.0], [2.0, 4.0, 6.0]]).T + ct = ColumnTransformer([("trans1", Trans(), [0]), ("trans2", "passthrough", [1])]) + exp = X_array + assert_array_equal(ct.fit_transform(X_array), exp) + assert_array_equal(ct.fit(X_array).transform(X_array), exp) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] != "remainder" + + +def test_column_transformer_remainder(): + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + + X_res_first = np.array([0, 1, 2]).reshape(-1, 1) + X_res_second = np.array([2, 4, 6]).reshape(-1, 1) + X_res_both = X_array + + # default drop + ct = ColumnTransformer([("trans1", Trans(), [0])]) + assert_array_equal(ct.fit_transform(X_array), X_res_first) + assert_array_equal(ct.fit(X_array).transform(X_array), X_res_first) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] == "remainder" + assert ct.transformers_[-1][1] == "drop" + assert_array_equal(ct.transformers_[-1][2], [1]) + + # specify passthrough + ct = ColumnTransformer([("trans", Trans(), [0])], remainder="passthrough") + assert_array_equal(ct.fit_transform(X_array), X_res_both) + assert_array_equal(ct.fit(X_array).transform(X_array), X_res_both) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] == "remainder" + assert isinstance(ct.transformers_[-1][1], FunctionTransformer) + assert_array_equal(ct.transformers_[-1][2], [1]) + + # column order is not preserved (passed through added to end) + ct = ColumnTransformer([("trans1", Trans(), [1])], remainder="passthrough") + assert_array_equal(ct.fit_transform(X_array), X_res_both[:, ::-1]) + assert_array_equal(ct.fit(X_array).transform(X_array), X_res_both[:, ::-1]) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] == "remainder" + assert isinstance(ct.transformers_[-1][1], FunctionTransformer) + assert_array_equal(ct.transformers_[-1][2], [0]) + + # passthrough when all actual transformers are skipped + ct = ColumnTransformer([("trans1", "drop", [0])], remainder="passthrough") + assert_array_equal(ct.fit_transform(X_array), X_res_second) + assert_array_equal(ct.fit(X_array).transform(X_array), X_res_second) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] == "remainder" + assert isinstance(ct.transformers_[-1][1], FunctionTransformer) + assert_array_equal(ct.transformers_[-1][2], [1]) + + # check default for make_column_transformer + ct = make_column_transformer((Trans(), [0])) + assert ct.remainder == "drop" + + +@pytest.mark.parametrize( + "cols1, cols2, expected_remainder_cols", + [ + ([0], [False, True, False], [2]), # mix types + ([0], [1], [2]), # ints + (lambda x: [0], lambda x: [1], [2]), # callables + (["A"], ["B"], ["C"]), # all strings + ([True, False, False], [False, True, False], [False, False, True]), # all bools + ], +) +def test_column_transformer_remainder_dtypes(cols1, cols2, expected_remainder_cols): + """Check that the remainder columns format matches the format of the other + columns when they're all strings or masks. + """ + X = np.ones((1, 3)) + + if isinstance(cols1, list) and isinstance(cols1[0], str): + pd = pytest.importorskip("pandas") + X = pd.DataFrame(X, columns=["A", "B", "C"]) + + # if inputs are column names store remainder columns as column names + ct = make_column_transformer( + (Trans(), cols1), + (Trans(), cols2), + remainder="passthrough", + ) + ct.fit_transform(X) + assert ct.transformers_[-1][-1] == expected_remainder_cols + + +# TODO(1.9): remove this test +@pytest.mark.parametrize("force_int_remainder_cols", [True, False]) +def test_force_int_remainder_cols_deprecation(force_int_remainder_cols): + """Check that ColumnTransformer raises a FutureWarning when + force_int_remainder_cols is set. + """ + X = np.ones((1, 3)) + ct = ColumnTransformer( + [("T1", Trans(), [0]), ("T2", Trans(), [1])], + remainder="passthrough", + force_int_remainder_cols=force_int_remainder_cols, + ) + + with pytest.warns(FutureWarning, match="`force_int_remainder_cols` is deprecated"): + ct.fit(X) + + +@pytest.mark.parametrize( + "key, expected_cols", + [ + ([0], [1]), + (np.array([0]), [1]), + (slice(0, 1), [1]), + (np.array([True, False]), [False, True]), + ], +) +def test_column_transformer_remainder_numpy(key, expected_cols): + # test different ways that columns are specified with passthrough + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + X_res_both = X_array + + ct = ColumnTransformer( + [("trans1", Trans(), key)], + remainder="passthrough", + ) + assert_array_equal(ct.fit_transform(X_array), X_res_both) + assert_array_equal(ct.fit(X_array).transform(X_array), X_res_both) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] == "remainder" + assert isinstance(ct.transformers_[-1][1], FunctionTransformer) + assert ct.transformers_[-1][2] == expected_cols + + +@pytest.mark.parametrize( + "key, expected_cols", + [ + ([0], [1]), + (slice(0, 1), [1]), + (np.array([True, False]), [False, True]), + (["first"], ["second"]), + ("pd-index", ["second"]), + (np.array(["first"]), ["second"]), + (np.array(["first"], dtype=object), ["second"]), + (slice(None, "first"), ["second"]), + (slice("first", "first"), ["second"]), + ], +) +def test_column_transformer_remainder_pandas(key, expected_cols): + # test different ways that columns are specified with passthrough + pd = pytest.importorskip("pandas") + if isinstance(key, str) and key == "pd-index": + key = pd.Index(["first"]) + + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + X_df = pd.DataFrame(X_array, columns=["first", "second"]) + X_res_both = X_array + + ct = ColumnTransformer( + [("trans1", Trans(), key)], + remainder="passthrough", + ) + assert_array_equal(ct.fit_transform(X_df), X_res_both) + assert_array_equal(ct.fit(X_df).transform(X_df), X_res_both) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] == "remainder" + assert isinstance(ct.transformers_[-1][1], FunctionTransformer) + assert ct.transformers_[-1][2] == expected_cols + + +@pytest.mark.parametrize( + "key, expected_cols", + [ + ([0], [1, 2]), + (np.array([0]), [1, 2]), + (slice(0, 1), [1, 2]), + (np.array([True, False, False]), [False, True, True]), + ], +) +def test_column_transformer_remainder_transformer(key, expected_cols): + X_array = np.array([[0, 1, 2], [2, 4, 6], [8, 6, 4]]).T + X_res_both = X_array.copy() + + # second and third columns are doubled when remainder = DoubleTrans + X_res_both[:, 1:3] *= 2 + + ct = ColumnTransformer( + [("trans1", Trans(), key)], + remainder=DoubleTrans(), + ) + + assert_array_equal(ct.fit_transform(X_array), X_res_both) + assert_array_equal(ct.fit(X_array).transform(X_array), X_res_both) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] == "remainder" + assert isinstance(ct.transformers_[-1][1], DoubleTrans) + assert ct.transformers_[-1][2] == expected_cols + + +def test_column_transformer_no_remaining_remainder_transformer(): + X_array = np.array([[0, 1, 2], [2, 4, 6], [8, 6, 4]]).T + + ct = ColumnTransformer([("trans1", Trans(), [0, 1, 2])], remainder=DoubleTrans()) + + assert_array_equal(ct.fit_transform(X_array), X_array) + assert_array_equal(ct.fit(X_array).transform(X_array), X_array) + assert len(ct.transformers_) == 1 + assert ct.transformers_[-1][0] != "remainder" + + +def test_column_transformer_drops_all_remainder_transformer(): + X_array = np.array([[0, 1, 2], [2, 4, 6], [8, 6, 4]]).T + + # columns are doubled when remainder = DoubleTrans + X_res_both = 2 * X_array.copy()[:, 1:3] + + ct = ColumnTransformer([("trans1", "drop", [0])], remainder=DoubleTrans()) + + assert_array_equal(ct.fit_transform(X_array), X_res_both) + assert_array_equal(ct.fit(X_array).transform(X_array), X_res_both) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] == "remainder" + assert isinstance(ct.transformers_[-1][1], DoubleTrans) + assert_array_equal(ct.transformers_[-1][2], [1, 2]) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_column_transformer_sparse_remainder_transformer(csr_container): + X_array = np.array([[0, 1, 2], [2, 4, 6], [8, 6, 4]]).T + + ct = ColumnTransformer( + [("trans1", Trans(), [0])], + remainder=SparseMatrixTrans(csr_container), + sparse_threshold=0.8, + ) + + X_trans = ct.fit_transform(X_array) + assert sparse.issparse(X_trans) + # SparseMatrixTrans creates 3 features for each column. There is + # one column in ``transformers``, thus: + assert X_trans.shape == (3, 3 + 1) + + exp_array = np.hstack((X_array[:, 0].reshape(-1, 1), np.eye(3))) + assert_array_equal(X_trans.toarray(), exp_array) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] == "remainder" + assert isinstance(ct.transformers_[-1][1], SparseMatrixTrans) + assert_array_equal(ct.transformers_[-1][2], [1, 2]) + + +@pytest.mark.parametrize("csr_container", CSR_CONTAINERS) +def test_column_transformer_drop_all_sparse_remainder_transformer(csr_container): + X_array = np.array([[0, 1, 2], [2, 4, 6], [8, 6, 4]]).T + ct = ColumnTransformer( + [("trans1", "drop", [0])], + remainder=SparseMatrixTrans(csr_container), + sparse_threshold=0.8, + ) + + X_trans = ct.fit_transform(X_array) + assert sparse.issparse(X_trans) + + # SparseMatrixTrans creates 3 features for each column, thus: + assert X_trans.shape == (3, 3) + assert_array_equal(X_trans.toarray(), np.eye(3)) + assert len(ct.transformers_) == 2 + assert ct.transformers_[-1][0] == "remainder" + assert isinstance(ct.transformers_[-1][1], SparseMatrixTrans) + assert_array_equal(ct.transformers_[-1][2], [1, 2]) + + +def test_column_transformer_get_set_params_with_remainder(): + ct = ColumnTransformer( + [("trans1", StandardScaler(), [0])], remainder=StandardScaler() + ) + + exp = { + "n_jobs": None, + "remainder": ct.remainder, + "remainder__copy": True, + "remainder__with_mean": True, + "remainder__with_std": True, + "sparse_threshold": 0.3, + "trans1": ct.transformers[0][1], + "trans1__copy": True, + "trans1__with_mean": True, + "trans1__with_std": True, + "transformers": ct.transformers, + "transformer_weights": None, + "verbose_feature_names_out": True, + "verbose": False, + "force_int_remainder_cols": "deprecated", + } + + assert ct.get_params() == exp + + ct.set_params(remainder__with_std=False) + assert not ct.get_params()["remainder__with_std"] + + ct.set_params(trans1="passthrough") + exp = { + "n_jobs": None, + "remainder": ct.remainder, + "remainder__copy": True, + "remainder__with_mean": True, + "remainder__with_std": False, + "sparse_threshold": 0.3, + "trans1": "passthrough", + "transformers": ct.transformers, + "transformer_weights": None, + "verbose_feature_names_out": True, + "verbose": False, + "force_int_remainder_cols": "deprecated", + } + assert ct.get_params() == exp + + +def test_column_transformer_no_estimators(): + X_array = np.array([[0, 1, 2], [2, 4, 6], [8, 6, 4]]).astype("float").T + ct = ColumnTransformer([], remainder=StandardScaler()) + + params = ct.get_params() + assert params["remainder__with_mean"] + + X_trans = ct.fit_transform(X_array) + assert X_trans.shape == X_array.shape + assert len(ct.transformers_) == 1 + assert ct.transformers_[-1][0] == "remainder" + assert ct.transformers_[-1][2] == [0, 1, 2] + + +@pytest.mark.parametrize( + ["est", "pattern"], + [ + ( + ColumnTransformer( + [("trans1", Trans(), [0]), ("trans2", Trans(), [1])], + remainder=DoubleTrans(), + ), + ( + r"\[ColumnTransformer\].*\(1 of 3\) Processing trans1.* total=.*\n" + r"\[ColumnTransformer\].*\(2 of 3\) Processing trans2.* total=.*\n" + r"\[ColumnTransformer\].*\(3 of 3\) Processing remainder.* total=.*\n$" + ), + ), + ( + ColumnTransformer( + [("trans1", Trans(), [0]), ("trans2", Trans(), [1])], + remainder="passthrough", + ), + ( + r"\[ColumnTransformer\].*\(1 of 3\) Processing trans1.* total=.*\n" + r"\[ColumnTransformer\].*\(2 of 3\) Processing trans2.* total=.*\n" + r"\[ColumnTransformer\].*\(3 of 3\) Processing remainder.* total=.*\n$" + ), + ), + ( + ColumnTransformer( + [("trans1", Trans(), [0]), ("trans2", "drop", [1])], + remainder="passthrough", + ), + ( + r"\[ColumnTransformer\].*\(1 of 2\) Processing trans1.* total=.*\n" + r"\[ColumnTransformer\].*\(2 of 2\) Processing remainder.* total=.*\n$" + ), + ), + ( + ColumnTransformer( + [("trans1", Trans(), [0]), ("trans2", "passthrough", [1])], + remainder="passthrough", + ), + ( + r"\[ColumnTransformer\].*\(1 of 3\) Processing trans1.* total=.*\n" + r"\[ColumnTransformer\].*\(2 of 3\) Processing trans2.* total=.*\n" + r"\[ColumnTransformer\].*\(3 of 3\) Processing remainder.* total=.*\n$" + ), + ), + ( + ColumnTransformer([("trans1", Trans(), [0])], remainder="passthrough"), + ( + r"\[ColumnTransformer\].*\(1 of 2\) Processing trans1.* total=.*\n" + r"\[ColumnTransformer\].*\(2 of 2\) Processing remainder.* total=.*\n$" + ), + ), + ( + ColumnTransformer( + [("trans1", Trans(), [0]), ("trans2", Trans(), [1])], remainder="drop" + ), + ( + r"\[ColumnTransformer\].*\(1 of 2\) Processing trans1.* total=.*\n" + r"\[ColumnTransformer\].*\(2 of 2\) Processing trans2.* total=.*\n$" + ), + ), + ( + ColumnTransformer([("trans1", Trans(), [0])], remainder="drop"), + r"\[ColumnTransformer\].*\(1 of 1\) Processing trans1.* total=.*\n$", + ), + ], +) +@pytest.mark.parametrize("method", ["fit", "fit_transform"]) +def test_column_transformer_verbose(est, pattern, method, capsys): + X_array = np.array([[0, 1, 2], [2, 4, 6], [8, 6, 4]]).T + + func = getattr(est, method) + est.set_params(verbose=False) + func(X_array) + assert not capsys.readouterr().out, "Got output for verbose=False" + + est.set_params(verbose=True) + func(X_array) + assert re.match(pattern, capsys.readouterr()[0]) + + +def test_column_transformer_no_estimators_set_params(): + ct = ColumnTransformer([]).set_params(n_jobs=2) + assert ct.n_jobs == 2 + + +def test_column_transformer_callable_specifier(): + # assert that function gets the full array + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + X_res_first = np.array([[0, 1, 2]]).T + + def func(X): + assert_array_equal(X, X_array) + return [0] + + ct = ColumnTransformer([("trans", Trans(), func)], remainder="drop") + assert_array_equal(ct.fit_transform(X_array), X_res_first) + assert_array_equal(ct.fit(X_array).transform(X_array), X_res_first) + assert callable(ct.transformers[0][2]) + assert ct.transformers_[0][2] == [0] + + +def test_column_transformer_callable_specifier_dataframe(): + # assert that function gets the full dataframe + pd = pytest.importorskip("pandas") + X_array = np.array([[0, 1, 2], [2, 4, 6]]).T + X_res_first = np.array([[0, 1, 2]]).T + + X_df = pd.DataFrame(X_array, columns=["first", "second"]) + + def func(X): + assert_array_equal(X.columns, X_df.columns) + assert_array_equal(X.values, X_df.values) + return ["first"] + + ct = ColumnTransformer([("trans", Trans(), func)], remainder="drop") + assert_array_equal(ct.fit_transform(X_df), X_res_first) + assert_array_equal(ct.fit(X_df).transform(X_df), X_res_first) + assert callable(ct.transformers[0][2]) + assert ct.transformers_[0][2] == ["first"] + + +def test_column_transformer_negative_column_indexes(): + X = np.random.randn(2, 2) + X_categories = np.array([[1], [2]]) + X = np.concatenate([X, X_categories], axis=1) + + ohe = OneHotEncoder() + + tf_1 = ColumnTransformer([("ohe", ohe, [-1])], remainder="passthrough") + tf_2 = ColumnTransformer([("ohe", ohe, [2])], remainder="passthrough") + assert_array_equal(tf_1.fit_transform(X), tf_2.fit_transform(X)) + + +@pytest.mark.parametrize("array_type", [np.asarray, *CSR_CONTAINERS]) +def test_column_transformer_mask_indexing(array_type): + # Regression test for #14510 + # Boolean array-like does not behave as boolean array with sparse matrices. + X = np.transpose([[1, 2, 3], [4, 5, 6], [5, 6, 7], [8, 9, 10]]) + X = array_type(X) + column_transformer = ColumnTransformer( + [("identity", FunctionTransformer(), [False, True, False, True])] + ) + X_trans = column_transformer.fit_transform(X) + assert X_trans.shape == (3, 2) + + +def test_n_features_in(): + # make sure n_features_in is what is passed as input to the column + # transformer. + + X = [[1, 2], [3, 4], [5, 6]] + ct = ColumnTransformer([("a", DoubleTrans(), [0]), ("b", DoubleTrans(), [1])]) + assert not hasattr(ct, "n_features_in_") + ct.fit(X) + assert ct.n_features_in_ == 2 + + +@pytest.mark.parametrize( + "cols, pattern, include, exclude", + [ + (["col_int", "col_float"], None, np.number, None), + (["col_int", "col_float"], None, None, [object, "string"]), + (["col_int", "col_float"], None, [int, float], None), + (["col_str"], None, [object, "string"], None), + (["col_float"], None, [float], None), + (["col_float"], None, float, None), + (["col_float"], "at$", [np.number], None), + (["col_int"], None, [int], None), + (["col_int"], "^col_int", [np.number], None), + (["col_float", "col_str"], "float|str", None, None), + (["col_str"], "^col_s", None, [int]), + ([], "str$", float, None), + ( + ["col_int", "col_float", "col_str"], + None, + [np.number, object, "string"], + None, + ), + ], +) +def test_make_column_selector_with_select_dtypes(cols, pattern, include, exclude): + pd = pytest.importorskip("pandas") + + X_df = pd.DataFrame( + { + "col_int": np.array([0, 1, 2], dtype=int), + "col_float": np.array([0.0, 1.0, 2.0], dtype=float), + "col_str": ["one", "two", "three"], + }, + columns=["col_int", "col_float", "col_str"], + ) + + selector = make_column_selector( + dtype_include=include, dtype_exclude=exclude, pattern=pattern + ) + + assert_array_equal(selector(X_df), cols) + + +def test_column_transformer_with_make_column_selector(): + # Functional test for column transformer + column selector + pd = pytest.importorskip("pandas") + X_df = pd.DataFrame( + { + "col_int": np.array([0, 1, 2], dtype=int), + "col_float": np.array([0.0, 1.0, 2.0], dtype=float), + "col_cat": ["one", "two", "one"], + "col_str": ["low", "middle", "high"], + }, + columns=["col_int", "col_float", "col_cat", "col_str"], + ) + X_df["col_str"] = X_df["col_str"].astype("category") + + cat_selector = make_column_selector(dtype_include=["category", object, "string"]) + num_selector = make_column_selector(dtype_include=np.number) + + ohe = OneHotEncoder() + scaler = StandardScaler() + + ct_selector = make_column_transformer((ohe, cat_selector), (scaler, num_selector)) + ct_direct = make_column_transformer( + (ohe, ["col_cat", "col_str"]), (scaler, ["col_float", "col_int"]) + ) + + X_selector = ct_selector.fit_transform(X_df) + X_direct = ct_direct.fit_transform(X_df) + + assert_allclose(X_selector, X_direct) + + +def test_make_column_selector_error(): + selector = make_column_selector(dtype_include=np.number) + X = np.array([[0.1, 0.2]]) + msg = "make_column_selector can only be applied to pandas dataframes" + with pytest.raises(ValueError, match=msg): + selector(X) + + +def test_make_column_selector_pickle(): + pd = pytest.importorskip("pandas") + + X_df = pd.DataFrame( + { + "col_int": np.array([0, 1, 2], dtype=int), + "col_float": np.array([0.0, 1.0, 2.0], dtype=float), + "col_str": ["one", "two", "three"], + }, + columns=["col_int", "col_float", "col_str"], + ) + + selector = make_column_selector(dtype_include=[object]) + selector_picked = pickle.loads(pickle.dumps(selector)) + + assert_array_equal(selector(X_df), selector_picked(X_df)) + + +@pytest.mark.parametrize( + "empty_col", + [[], np.array([], dtype=int), lambda x: []], + ids=["list", "array", "callable"], +) +def test_feature_names_empty_columns(empty_col): + pd = pytest.importorskip("pandas") + + df = pd.DataFrame({"col1": ["a", "a", "b"], "col2": ["z", "z", "z"]}) + + ct = ColumnTransformer( + transformers=[ + ("ohe", OneHotEncoder(), ["col1", "col2"]), + ("empty_features", OneHotEncoder(), empty_col), + ], + ) + + ct.fit(df) + assert_array_equal( + ct.get_feature_names_out(), ["ohe__col1_a", "ohe__col1_b", "ohe__col2_z"] + ) + + +@pytest.mark.parametrize( + "selector", + [ + [1], + lambda x: [1], + ["col2"], + lambda x: ["col2"], + [False, True], + lambda x: [False, True], + ], +) +def test_feature_names_out_pandas(selector): + """Checks name when selecting only the second column""" + pd = pytest.importorskip("pandas") + df = pd.DataFrame({"col1": ["a", "a", "b"], "col2": ["z", "z", "z"]}) + ct = ColumnTransformer([("ohe", OneHotEncoder(), selector)]) + ct.fit(df) + + assert_array_equal(ct.get_feature_names_out(), ["ohe__col2_z"]) + + +@pytest.mark.parametrize( + "selector", [[1], lambda x: [1], [False, True], lambda x: [False, True]] +) +def test_feature_names_out_non_pandas(selector): + """Checks name when selecting the second column with numpy array""" + X = [["a", "z"], ["a", "z"], ["b", "z"]] + ct = ColumnTransformer([("ohe", OneHotEncoder(), selector)]) + ct.fit(X) + + assert_array_equal(ct.get_feature_names_out(), ["ohe__x1_z"]) + + +@pytest.mark.parametrize("remainder", ["passthrough", StandardScaler()]) +def test_sk_visual_block_remainder(remainder): + # remainder='passthrough' or an estimator will be shown in repr_html + ohe = OneHotEncoder() + ct = ColumnTransformer( + transformers=[("ohe", ohe, ["col1", "col2"])], remainder=remainder + ) + visual_block = ct._sk_visual_block_() + assert visual_block.names == ("ohe", "remainder") + assert visual_block.name_details == (["col1", "col2"], "") + assert visual_block.estimators == (ohe, remainder) + + +def test_sk_visual_block_remainder_drop(): + # remainder='drop' is not shown in repr_html + ohe = OneHotEncoder() + ct = ColumnTransformer(transformers=[("ohe", ohe, ["col1", "col2"])]) + visual_block = ct._sk_visual_block_() + assert visual_block.names == ("ohe",) + assert visual_block.name_details == (["col1", "col2"],) + assert visual_block.estimators == (ohe,) + + +@pytest.mark.parametrize("remainder", ["passthrough", StandardScaler()]) +def test_sk_visual_block_remainder_fitted_pandas(remainder): + # Remainder shows the columns after fitting + pd = pytest.importorskip("pandas") + ohe = OneHotEncoder() + ct = ColumnTransformer( + transformers=[("ohe", ohe, ["col1", "col2"])], + remainder=remainder, + ) + df = pd.DataFrame( + { + "col1": ["a", "b", "c"], + "col2": ["z", "z", "z"], + "col3": [1, 2, 3], + "col4": [3, 4, 5], + } + ) + ct.fit(df) + visual_block = ct._sk_visual_block_() + assert visual_block.names == ("ohe", "remainder") + assert visual_block.name_details == (["col1", "col2"], ["col3", "col4"]) + assert visual_block.estimators == (ohe, remainder) + + +@pytest.mark.parametrize("remainder", ["passthrough", StandardScaler()]) +def test_sk_visual_block_remainder_fitted_numpy(remainder): + # Remainder shows the indices after fitting + X = np.array([[1, 2, 3], [4, 5, 6]], dtype=float) + scaler = StandardScaler() + ct = ColumnTransformer( + transformers=[("scale", scaler, [0, 2])], remainder=remainder + ) + ct.fit(X) + visual_block = ct._sk_visual_block_() + assert visual_block.names == ("scale", "remainder") + assert visual_block.name_details == ([0, 2], [1]) + assert visual_block.estimators == (scaler, remainder) + + +@pytest.mark.parametrize("explicit_colname", ["first", "second", 0, 1]) +@pytest.mark.parametrize("remainder", [Trans(), "passthrough", "drop"]) +def test_column_transformer_reordered_column_names_remainder( + explicit_colname, remainder +): + """Test the interaction between remainder and column transformer""" + pd = pytest.importorskip("pandas") + + X_fit_array = np.array([[0, 1, 2], [2, 4, 6]]).T + X_fit_df = pd.DataFrame(X_fit_array, columns=["first", "second"]) + + X_trans_array = np.array([[2, 4, 6], [0, 1, 2]]).T + X_trans_df = pd.DataFrame(X_trans_array, columns=["second", "first"]) + + tf = ColumnTransformer([("bycol", Trans(), explicit_colname)], remainder=remainder) + + tf.fit(X_fit_df) + X_fit_trans = tf.transform(X_fit_df) + + # Changing the order still works + X_trans = tf.transform(X_trans_df) + assert_allclose(X_trans, X_fit_trans) + + # extra columns are ignored + X_extended_df = X_fit_df.copy() + X_extended_df["third"] = [3, 6, 9] + X_trans = tf.transform(X_extended_df) + assert_allclose(X_trans, X_fit_trans) + + if isinstance(explicit_colname, str): + # Raise error if columns are specified by names but input only allows + # to specify by position, e.g. numpy array instead of a pandas df. + X_array = X_fit_array.copy() + err_msg = "Specifying the columns" + with pytest.raises(ValueError, match=err_msg): + tf.transform(X_array) + + +def test_feature_name_validation_missing_columns_drop_passthough(): + """Test the interaction between {'drop', 'passthrough'} and + missing column names.""" + pd = pytest.importorskip("pandas") + + X = np.ones(shape=(3, 4)) + df = pd.DataFrame(X, columns=["a", "b", "c", "d"]) + + df_dropped = df.drop("c", axis=1) + + # with remainder='passthrough', all columns seen during `fit` must be + # present + tf = ColumnTransformer([("bycol", Trans(), [1])], remainder="passthrough") + tf.fit(df) + msg = r"columns are missing: {'c'}" + with pytest.raises(ValueError, match=msg): + tf.transform(df_dropped) + + # with remainder='drop', it is allowed to have column 'c' missing + tf = ColumnTransformer([("bycol", Trans(), [1])], remainder="drop") + tf.fit(df) + + df_dropped_trans = tf.transform(df_dropped) + df_fit_trans = tf.transform(df) + assert_allclose(df_dropped_trans, df_fit_trans) + + # bycol drops 'c', thus it is allowed for 'c' to be missing + tf = ColumnTransformer([("bycol", "drop", ["c"])], remainder="passthrough") + tf.fit(df) + df_dropped_trans = tf.transform(df_dropped) + df_fit_trans = tf.transform(df) + assert_allclose(df_dropped_trans, df_fit_trans) + + +def test_feature_names_in_(): + """Feature names are stored in column transformer. + + Column transformer deliberately does not check for column name consistency. + It only checks that the non-dropped names seen in `fit` are seen + in `transform`. This behavior is already tested in + `test_feature_name_validation_missing_columns_drop_passthough`""" + + pd = pytest.importorskip("pandas") + + feature_names = ["a", "c", "d"] + df = pd.DataFrame([[1, 2, 3]], columns=feature_names) + ct = ColumnTransformer([("bycol", Trans(), ["a", "d"])], remainder="passthrough") + + ct.fit(df) + assert_array_equal(ct.feature_names_in_, feature_names) + assert isinstance(ct.feature_names_in_, np.ndarray) + assert ct.feature_names_in_.dtype == object + + +class TransWithNames(Trans): + def __init__(self, feature_names_out=None): + self.feature_names_out = feature_names_out + + def get_feature_names_out(self, input_features=None): + if self.feature_names_out is not None: + return np.asarray(self.feature_names_out, dtype=object) + return input_features + + +@pytest.mark.parametrize( + "transformers, remainder, expected_names", + [ + ( + [ + ("bycol1", TransWithNames(), ["d", "c"]), + ("bycol2", "passthrough", ["d"]), + ], + "passthrough", + ["bycol1__d", "bycol1__c", "bycol2__d", "remainder__a", "remainder__b"], + ), + ( + [ + ("bycol1", TransWithNames(), ["d", "c"]), + ("bycol2", "passthrough", ["d"]), + ], + "drop", + ["bycol1__d", "bycol1__c", "bycol2__d"], + ), + ( + [ + ("bycol1", TransWithNames(), ["b"]), + ("bycol2", "drop", ["d"]), + ], + "passthrough", + ["bycol1__b", "remainder__a", "remainder__c"], + ), + ( + [ + ("bycol1", TransWithNames(["pca1", "pca2"]), ["a", "b", "d"]), + ], + "passthrough", + ["bycol1__pca1", "bycol1__pca2", "remainder__c"], + ), + ( + [ + ("bycol1", TransWithNames(["a", "b"]), ["d"]), + ("bycol2", "passthrough", ["b"]), + ], + "drop", + ["bycol1__a", "bycol1__b", "bycol2__b"], + ), + ( + [ + ("bycol1", TransWithNames([f"pca{i}" for i in range(2)]), ["b"]), + ("bycol2", TransWithNames([f"pca{i}" for i in range(2)]), ["b"]), + ], + "passthrough", + [ + "bycol1__pca0", + "bycol1__pca1", + "bycol2__pca0", + "bycol2__pca1", + "remainder__a", + "remainder__c", + "remainder__d", + ], + ), + ( + [ + ("bycol1", "drop", ["d"]), + ], + "drop", + [], + ), + ( + [ + ("bycol1", TransWithNames(), slice(1, 3)), + ], + "drop", + ["bycol1__b", "bycol1__c"], + ), + ( + [ + ("bycol1", TransWithNames(), ["b"]), + ("bycol2", "drop", slice(3, 4)), + ], + "passthrough", + ["bycol1__b", "remainder__a", "remainder__c"], + ), + ( + [ + ("bycol1", TransWithNames(), ["d", "c"]), + ("bycol2", "passthrough", slice(3, 4)), + ], + "passthrough", + ["bycol1__d", "bycol1__c", "bycol2__d", "remainder__a", "remainder__b"], + ), + ( + [ + ("bycol1", TransWithNames(), slice("b", "c")), + ], + "drop", + ["bycol1__b", "bycol1__c"], + ), + ( + [ + ("bycol1", TransWithNames(), ["b"]), + ("bycol2", "drop", slice("c", "d")), + ], + "passthrough", + ["bycol1__b", "remainder__a"], + ), + ( + [ + ("bycol1", TransWithNames(), ["d", "c"]), + ("bycol2", "passthrough", slice("c", "d")), + ], + "passthrough", + [ + "bycol1__d", + "bycol1__c", + "bycol2__c", + "bycol2__d", + "remainder__a", + "remainder__b", + ], + ), + ], +) +def test_verbose_feature_names_out_true(transformers, remainder, expected_names): + """Check feature_names_out for verbose_feature_names_out=True (default)""" + pd = pytest.importorskip("pandas") + df = pd.DataFrame([[1, 2, 3, 4]], columns=["a", "b", "c", "d"]) + ct = ColumnTransformer( + transformers, + remainder=remainder, + ) + ct.fit(df) + + names = ct.get_feature_names_out() + assert isinstance(names, np.ndarray) + assert names.dtype == object + assert_array_equal(names, expected_names) + + +def _feature_names_out_callable_name_clash(trans_name: str, feat_name: str): + return f"{trans_name[:2]}++{feat_name}" + + +def _feature_names_out_callable_upper(trans_name: str, feat_name: str): + return f"{trans_name.upper()}={feat_name.upper()}" + + +@pytest.mark.parametrize( + "transformers, remainder, verbose_feature_names_out, expected_names", + [ + ( + [ + ("bycol1", TransWithNames(), ["d", "c"]), + ("bycol2", "passthrough", ["d"]), + ], + "passthrough", + _feature_names_out_callable_name_clash, + ["by++d", "by++c", "by++d", "re++a", "re++b"], + ), + ( + [ + ("bycol1", TransWithNames(), ["d", "c"]), + ("bycol2", "passthrough", ["d"]), + ], + "drop", + "{feature_name}-{transformer_name}", + ["d-bycol1", "c-bycol1", "d-bycol2"], + ), + ( + [ + ("bycol1", TransWithNames(), ["d", "c"]), + ("bycol2", "passthrough", slice("c", "d")), + ], + "passthrough", + _feature_names_out_callable_upper, + [ + "BYCOL1=D", + "BYCOL1=C", + "BYCOL2=C", + "BYCOL2=D", + "REMAINDER=A", + "REMAINDER=B", + ], + ), + ], +) +def test_verbose_feature_names_out_callable_or_str( + transformers, remainder, verbose_feature_names_out, expected_names +): + """Check feature_names_out for verbose_feature_names_out=True (default)""" + pd = pytest.importorskip("pandas") + df = pd.DataFrame([[1, 2, 3, 4]], columns=["a", "b", "c", "d"]) + ct = ColumnTransformer( + transformers, + remainder=remainder, + verbose_feature_names_out=verbose_feature_names_out, + ) + ct.fit(df) + + names = ct.get_feature_names_out() + assert isinstance(names, np.ndarray) + assert names.dtype == object + assert_array_equal(names, expected_names) + + +@pytest.mark.parametrize( + "transformers, remainder, expected_names", + [ + ( + [ + ("bycol1", TransWithNames(), ["d", "c"]), + ("bycol2", "passthrough", ["a"]), + ], + "passthrough", + ["d", "c", "a", "b"], + ), + ( + [ + ("bycol1", TransWithNames(["a"]), ["d", "c"]), + ("bycol2", "passthrough", ["d"]), + ], + "drop", + ["a", "d"], + ), + ( + [ + ("bycol1", TransWithNames(), ["b"]), + ("bycol2", "drop", ["d"]), + ], + "passthrough", + ["b", "a", "c"], + ), + ( + [ + ("bycol1", TransWithNames(["pca1", "pca2"]), ["a", "b", "d"]), + ], + "passthrough", + ["pca1", "pca2", "c"], + ), + ( + [ + ("bycol1", TransWithNames(["a", "c"]), ["d"]), + ("bycol2", "passthrough", ["d"]), + ], + "drop", + ["a", "c", "d"], + ), + ( + [ + ("bycol1", TransWithNames([f"pca{i}" for i in range(2)]), ["b"]), + ("bycol2", TransWithNames([f"kpca{i}" for i in range(2)]), ["b"]), + ], + "passthrough", + ["pca0", "pca1", "kpca0", "kpca1", "a", "c", "d"], + ), + ( + [ + ("bycol1", "drop", ["d"]), + ], + "drop", + [], + ), + ( + [ + ("bycol1", TransWithNames(), slice(1, 2)), + ("bycol2", "drop", ["d"]), + ], + "passthrough", + ["b", "a", "c"], + ), + ( + [ + ("bycol1", TransWithNames(), ["b"]), + ("bycol2", "drop", slice(3, 4)), + ], + "passthrough", + ["b", "a", "c"], + ), + ( + [ + ("bycol1", TransWithNames(), ["d", "c"]), + ("bycol2", "passthrough", slice(0, 2)), + ], + "drop", + ["d", "c", "a", "b"], + ), + ( + [ + ("bycol1", TransWithNames(), slice("a", "b")), + ("bycol2", "drop", ["d"]), + ], + "passthrough", + ["a", "b", "c"], + ), + ( + [ + ("bycol1", TransWithNames(), ["b"]), + ("bycol2", "drop", slice("c", "d")), + ], + "passthrough", + ["b", "a"], + ), + ( + [ + ("bycol1", TransWithNames(), ["d", "c"]), + ("bycol2", "passthrough", slice("a", "b")), + ], + "drop", + ["d", "c", "a", "b"], + ), + ( + [ + ("bycol1", TransWithNames(), ["d", "c"]), + ("bycol2", "passthrough", slice("b", "b")), + ], + "drop", + ["d", "c", "b"], + ), + ], +) +def test_verbose_feature_names_out_false(transformers, remainder, expected_names): + """Check feature_names_out for verbose_feature_names_out=False""" + pd = pytest.importorskip("pandas") + df = pd.DataFrame([[1, 2, 3, 4]], columns=["a", "b", "c", "d"]) + ct = ColumnTransformer( + transformers, + remainder=remainder, + verbose_feature_names_out=False, + ) + ct.fit(df) + + names = ct.get_feature_names_out() + assert isinstance(names, np.ndarray) + assert names.dtype == object + assert_array_equal(names, expected_names) + + +@pytest.mark.parametrize( + "transformers, remainder, colliding_columns", + [ + ( + [ + ("bycol1", TransWithNames(), ["b"]), + ("bycol2", "passthrough", ["b"]), + ], + "drop", + "['b']", + ), + ( + [ + ("bycol1", TransWithNames(["c", "d"]), ["c"]), + ("bycol2", "passthrough", ["c"]), + ], + "drop", + "['c']", + ), + ( + [ + ("bycol1", TransWithNames(["a"]), ["b"]), + ("bycol2", "passthrough", ["b"]), + ], + "passthrough", + "['a']", + ), + ( + [ + ("bycol1", TransWithNames(["a"]), ["b"]), + ("bycol2", "drop", ["b"]), + ], + "passthrough", + "['a']", + ), + ( + [ + ("bycol1", TransWithNames(["c", "b"]), ["b"]), + ("bycol2", "passthrough", ["c", "b"]), + ], + "drop", + "['b', 'c']", + ), + ( + [ + ("bycol1", TransWithNames(["a"]), ["b"]), + ("bycol2", "passthrough", ["a"]), + ("bycol3", TransWithNames(["a"]), ["b"]), + ], + "passthrough", + "['a']", + ), + ( + [ + ("bycol1", TransWithNames(["a", "b"]), ["b"]), + ("bycol2", "passthrough", ["a"]), + ("bycol3", TransWithNames(["b"]), ["c"]), + ], + "passthrough", + "['a', 'b']", + ), + ( + [ + ("bycol1", TransWithNames([f"pca{i}" for i in range(6)]), ["b"]), + ("bycol2", TransWithNames([f"pca{i}" for i in range(6)]), ["b"]), + ], + "passthrough", + "['pca0', 'pca1', 'pca2', 'pca3', 'pca4', ...]", + ), + ( + [ + ("bycol1", TransWithNames(["a", "b"]), slice(1, 2)), + ("bycol2", "passthrough", ["a"]), + ("bycol3", TransWithNames(["b"]), ["c"]), + ], + "passthrough", + "['a', 'b']", + ), + ( + [ + ("bycol1", TransWithNames(["a", "b"]), ["b"]), + ("bycol2", "passthrough", slice(0, 1)), + ("bycol3", TransWithNames(["b"]), ["c"]), + ], + "passthrough", + "['a', 'b']", + ), + ( + [ + ("bycol1", TransWithNames(["a", "b"]), slice("b", "c")), + ("bycol2", "passthrough", ["a"]), + ("bycol3", TransWithNames(["b"]), ["c"]), + ], + "passthrough", + "['a', 'b']", + ), + ( + [ + ("bycol1", TransWithNames(["a", "b"]), ["b"]), + ("bycol2", "passthrough", slice("a", "a")), + ("bycol3", TransWithNames(["b"]), ["c"]), + ], + "passthrough", + "['a', 'b']", + ), + ], +) +def test_verbose_feature_names_out_false_errors( + transformers, remainder, colliding_columns +): + """Check feature_names_out for verbose_feature_names_out=False""" + + pd = pytest.importorskip("pandas") + df = pd.DataFrame([[1, 2, 3, 4]], columns=["a", "b", "c", "d"]) + ct = ColumnTransformer( + transformers, + remainder=remainder, + verbose_feature_names_out=False, + ) + ct.fit(df) + + msg = re.escape( + f"Output feature names: {colliding_columns} are not unique. Please set " + "verbose_feature_names_out=True to add prefixes to feature names" + ) + with pytest.raises(ValueError, match=msg): + ct.get_feature_names_out() + + +@pytest.mark.parametrize("verbose_feature_names_out", [True, False]) +@pytest.mark.parametrize("remainder", ["drop", "passthrough"]) +def test_column_transformer_set_output(verbose_feature_names_out, remainder): + """Check column transformer behavior with set_output.""" + pd = pytest.importorskip("pandas") + df = pd.DataFrame([[1, 2, 3, 4]], columns=["a", "b", "c", "d"], index=[10]) + ct = ColumnTransformer( + [("first", TransWithNames(), ["a", "c"]), ("second", TransWithNames(), ["d"])], + remainder=remainder, + verbose_feature_names_out=verbose_feature_names_out, + ) + X_trans = ct.fit_transform(df) + assert isinstance(X_trans, np.ndarray) + + ct.set_output(transform="pandas") + + df_test = pd.DataFrame([[1, 2, 3, 4]], columns=df.columns, index=[20]) + X_trans = ct.transform(df_test) + assert isinstance(X_trans, pd.DataFrame) + + feature_names_out = ct.get_feature_names_out() + assert_array_equal(X_trans.columns, feature_names_out) + assert_array_equal(X_trans.index, df_test.index) + + +@pytest.mark.parametrize("remainder", ["drop", "passthrough"]) +@pytest.mark.parametrize("fit_transform", [True, False]) +def test_column_transform_set_output_mixed(remainder, fit_transform): + """Check ColumnTransformer outputs mixed types correctly.""" + pd = pytest.importorskip("pandas") + df = pd.DataFrame( + { + "pet": pd.Series(["dog", "cat", "snake"], dtype="category"), + "color": pd.Series(["green", "blue", "red"], dtype="object"), + "age": [1.4, 2.1, 4.4], + "height": [20, 40, 10], + "distance": pd.Series([20, pd.NA, 100], dtype="Int32"), + } + ) + ct = ColumnTransformer( + [ + ( + "color_encode", + OneHotEncoder(sparse_output=False, dtype="int8"), + ["color"], + ), + ("age", StandardScaler(), ["age"]), + ], + remainder=remainder, + verbose_feature_names_out=False, + ).set_output(transform="pandas") + if fit_transform: + X_trans = ct.fit_transform(df) + else: + X_trans = ct.fit(df).transform(df) + + assert isinstance(X_trans, pd.DataFrame) + assert_array_equal(X_trans.columns, ct.get_feature_names_out()) + + expected_dtypes = { + "color_blue": "int8", + "color_green": "int8", + "color_red": "int8", + "age": "float64", + "pet": "category", + "height": "int64", + "distance": "Int32", + } + for col, dtype in X_trans.dtypes.items(): + assert dtype == expected_dtypes[col] + + +@pytest.mark.parametrize("remainder", ["drop", "passthrough"]) +def test_column_transform_set_output_after_fitting(remainder): + pd = pytest.importorskip("pandas") + df = pd.DataFrame( + { + "pet": pd.Series(["dog", "cat", "snake"], dtype="category"), + "age": [1.4, 2.1, 4.4], + "height": [20, 40, 10], + } + ) + ct = ColumnTransformer( + [ + ( + "color_encode", + OneHotEncoder(sparse_output=False, dtype="int16"), + ["pet"], + ), + ("age", StandardScaler(), ["age"]), + ], + remainder=remainder, + verbose_feature_names_out=False, + ) + + # fit without calling set_output + X_trans = ct.fit_transform(df) + assert isinstance(X_trans, np.ndarray) + assert X_trans.dtype == "float64" + + ct.set_output(transform="pandas") + X_trans_df = ct.transform(df) + expected_dtypes = { + "pet_cat": "int16", + "pet_dog": "int16", + "pet_snake": "int16", + "height": "int64", + "age": "float64", + } + for col, dtype in X_trans_df.dtypes.items(): + assert dtype == expected_dtypes[col] + + +# PandasOutTransformer that does not define get_feature_names_out and always expects +# the input to be a DataFrame. +class PandasOutTransformer(BaseEstimator): + def __init__(self, offset=1.0): + self.offset = offset + + def fit(self, X, y=None): + pd = pytest.importorskip("pandas") + assert isinstance(X, pd.DataFrame) + return self + + def transform(self, X, y=None): + pd = pytest.importorskip("pandas") + assert isinstance(X, pd.DataFrame) + return X - self.offset + + def set_output(self, transform=None): + # This transformer will always output a DataFrame regardless of the + # configuration. + return self + + +@pytest.mark.parametrize( + "trans_1, expected_verbose_names, expected_non_verbose_names", + [ + ( + PandasOutTransformer(offset=2.0), + ["trans_0__feat1", "trans_1__feat0"], + ["feat1", "feat0"], + ), + ( + "drop", + ["trans_0__feat1"], + ["feat1"], + ), + ( + "passthrough", + ["trans_0__feat1", "trans_1__feat0"], + ["feat1", "feat0"], + ), + ], +) +def test_transformers_with_pandas_out_but_not_feature_names_out( + trans_1, expected_verbose_names, expected_non_verbose_names +): + """Check that set_config(transform="pandas") is compatible with more transformers. + + Specifically, if transformers returns a DataFrame, but does not define + `get_feature_names_out`. + """ + pd = pytest.importorskip("pandas") + + X_df = pd.DataFrame({"feat0": [1.0, 2.0, 3.0], "feat1": [2.0, 3.0, 4.0]}) + ct = ColumnTransformer( + [ + ("trans_0", PandasOutTransformer(offset=3.0), ["feat1"]), + ("trans_1", trans_1, ["feat0"]), + ] + ) + X_trans_np = ct.fit_transform(X_df) + assert isinstance(X_trans_np, np.ndarray) + + # `ct` does not have `get_feature_names_out` because `PandasOutTransformer` does + # not define the method. + with pytest.raises(AttributeError, match="not provide get_feature_names_out"): + ct.get_feature_names_out() + + # The feature names are prefixed because verbose_feature_names_out=True is default + ct.set_output(transform="pandas") + X_trans_df0 = ct.fit_transform(X_df) + assert_array_equal(X_trans_df0.columns, expected_verbose_names) + + ct.set_params(verbose_feature_names_out=False) + X_trans_df1 = ct.fit_transform(X_df) + assert_array_equal(X_trans_df1.columns, expected_non_verbose_names) + + +@pytest.mark.parametrize( + "empty_selection", + [[], np.array([False, False]), [False, False]], + ids=["list", "bool", "bool_int"], +) +def test_empty_selection_pandas_output(empty_selection): + """Check that pandas output works when there is an empty selection. + + Non-regression test for gh-25487 + """ + pd = pytest.importorskip("pandas") + + X = pd.DataFrame([[1.0, 2.2], [3.0, 1.0]], columns=["a", "b"]) + ct = ColumnTransformer( + [ + ("categorical", "passthrough", empty_selection), + ("numerical", StandardScaler(), ["a", "b"]), + ], + verbose_feature_names_out=True, + ) + ct.set_output(transform="pandas") + X_out = ct.fit_transform(X) + assert_array_equal(X_out.columns, ["numerical__a", "numerical__b"]) + + ct.set_params(verbose_feature_names_out=False) + X_out = ct.fit_transform(X) + assert_array_equal(X_out.columns, ["a", "b"]) + + +def test_raise_error_if_index_not_aligned(): + """Check column transformer raises error if indices are not aligned. + + Non-regression test for gh-26210. + """ + pd = pytest.importorskip("pandas") + + X = pd.DataFrame([[1.0, 2.2], [3.0, 1.0]], columns=["a", "b"], index=[8, 3]) + reset_index_transformer = FunctionTransformer( + lambda x: x.reset_index(drop=True), feature_names_out="one-to-one" + ) + + ct = ColumnTransformer( + [ + ("num1", "passthrough", ["a"]), + ("num2", reset_index_transformer, ["b"]), + ], + ) + ct.set_output(transform="pandas") + msg = ( + "Concatenating DataFrames from the transformer's output lead to" + " an inconsistent number of samples. The output may have Pandas" + " Indexes that do not match." + ) + with pytest.raises(ValueError, match=msg): + ct.fit_transform(X) + + +def test_remainder_set_output(): + """Check that the output is set for the remainder. + + Non-regression test for #26306. + """ + + pd = pytest.importorskip("pandas") + df = pd.DataFrame({"a": [True, False, True], "b": [1, 2, 3]}) + + ct = make_column_transformer( + (VarianceThreshold(), make_column_selector(dtype_include=bool)), + remainder=VarianceThreshold(), + verbose_feature_names_out=False, + ) + ct.set_output(transform="pandas") + + out = ct.fit_transform(df) + pd.testing.assert_frame_equal(out, df) + + ct.set_output(transform="default") + out = ct.fit_transform(df) + assert isinstance(out, np.ndarray) + + +def test_transform_pd_na(): + """Check behavior when a tranformer's output contains pandas.NA + + It should raise an error unless the output config is set to 'pandas'. + """ + pd = pytest.importorskip("pandas") + if not hasattr(pd, "Float64Dtype"): + pytest.skip( + "The issue with pd.NA tested here does not happen in old versions that do" + " not have the extension dtypes" + ) + df = pd.DataFrame({"a": [1.5, None]}) + ct = make_column_transformer(("passthrough", ["a"])) + # No warning with non-extension dtypes and np.nan + with warnings.catch_warnings(): + warnings.simplefilter("error") + ct.fit_transform(df) + df = df.convert_dtypes() + + # Error with extension dtype and pd.NA + with pytest.raises(ValueError, match=r"set_output\(transform='pandas'\)"): + ct.fit_transform(df) + + # No error when output is set to pandas + ct.set_output(transform="pandas") + ct.fit_transform(df) + ct.set_output(transform="default") + + # No error when there are no pd.NA + ct.fit_transform(df.fillna(-1.0)) + + +def test_dataframe_different_dataframe_libraries(): + """Check fitting and transforming on pandas and polars dataframes.""" + pd = pytest.importorskip("pandas") + pl = pytest.importorskip("polars") + X_train_np = np.array([[0, 1], [2, 4], [4, 5]]) + X_test_np = np.array([[1, 2], [1, 3], [2, 3]]) + + # Fit on pandas and transform on polars + X_train_pd = pd.DataFrame(X_train_np, columns=["a", "b"]) + X_test_pl = pl.DataFrame(X_test_np, schema=["a", "b"]) + + ct = make_column_transformer((Trans(), [0, 1])) + ct.fit(X_train_pd) + + out_pl_in = ct.transform(X_test_pl) + assert_array_equal(out_pl_in, X_test_np) + + # Fit on polars and transform on pandas + X_train_pl = pl.DataFrame(X_train_np, schema=["a", "b"]) + X_test_pd = pd.DataFrame(X_test_np, columns=["a", "b"]) + ct.fit(X_train_pl) + + out_pd_in = ct.transform(X_test_pd) + assert_array_equal(out_pd_in, X_test_np) + + +def test_column_transformer__getitem__(): + """Check __getitem__ for ColumnTransformer.""" + X = np.array([[0, 1, 2], [3, 4, 5]]) + ct = ColumnTransformer([("t1", Trans(), [0, 1]), ("t2", Trans(), [1, 2])]) + + msg = "ColumnTransformer is subscriptable after it is fitted" + with pytest.raises(TypeError, match=msg): + ct["t1"] + + ct.fit(X) + assert ct["t1"] is ct.named_transformers_["t1"] + assert ct["t2"] is ct.named_transformers_["t2"] + + msg = "'does_not_exist' is not a valid transformer name" + with pytest.raises(KeyError, match=msg): + ct["does_not_exist"] + + +@pytest.mark.parametrize("transform_output", ["default", "pandas"]) +def test_column_transformer_remainder_passthrough_naming_consistency(transform_output): + """Check that when `remainder="passthrough"`, inconsistent naming is handled + correctly by the underlying `FunctionTransformer`. + + Non-regression test for: + https://github.com/scikit-learn/scikit-learn/issues/28232 + """ + pd = pytest.importorskip("pandas") + X = pd.DataFrame(np.random.randn(10, 4)) + + preprocessor = ColumnTransformer( + transformers=[("scaler", StandardScaler(), [0, 1])], + remainder="passthrough", + ).set_output(transform=transform_output) + X_trans = preprocessor.fit_transform(X) + assert X_trans.shape == X.shape + + expected_column_names = [ + "scaler__x0", + "scaler__x1", + "remainder__x2", + "remainder__x3", + ] + if hasattr(X_trans, "columns"): + assert X_trans.columns.tolist() == expected_column_names + assert preprocessor.get_feature_names_out().tolist() == expected_column_names + + +@pytest.mark.parametrize("dataframe_lib", ["pandas", "polars"]) +def test_column_transformer_column_renaming(dataframe_lib): + """Check that we properly rename columns when using `ColumnTransformer` and + selected columns are redundant between transformers. + + Non-regression test for: + https://github.com/scikit-learn/scikit-learn/issues/28260 + """ + lib = pytest.importorskip(dataframe_lib) + + df = lib.DataFrame({"x1": [1, 2, 3], "x2": [10, 20, 30], "x3": [100, 200, 300]}) + + transformer = ColumnTransformer( + transformers=[ + ("A", "passthrough", ["x1", "x2", "x3"]), + ("B", FunctionTransformer(), ["x1", "x2"]), + ("C", StandardScaler(), ["x1", "x3"]), + # special case of a transformer returning 0-columns, e.g feature selector + ( + "D", + FunctionTransformer(lambda x: _safe_indexing(x, [], axis=1)), + ["x1", "x2", "x3"], + ), + ], + verbose_feature_names_out=True, + ).set_output(transform=dataframe_lib) + df_trans = transformer.fit_transform(df) + assert list(df_trans.columns) == [ + "A__x1", + "A__x2", + "A__x3", + "B__x1", + "B__x2", + "C__x1", + "C__x3", + ] + + +@pytest.mark.parametrize("dataframe_lib", ["pandas", "polars"]) +def test_column_transformer_error_with_duplicated_columns(dataframe_lib): + """Check that we raise an error when using `ColumnTransformer` and + the columns names are duplicated between transformers.""" + lib = pytest.importorskip(dataframe_lib) + + df = lib.DataFrame({"x1": [1, 2, 3], "x2": [10, 20, 30], "x3": [100, 200, 300]}) + + transformer = ColumnTransformer( + transformers=[ + ("A", "passthrough", ["x1", "x2", "x3"]), + ("B", FunctionTransformer(), ["x1", "x2"]), + ("C", StandardScaler(), ["x1", "x3"]), + # special case of a transformer returning 0-columns, e.g feature selector + ( + "D", + FunctionTransformer(lambda x: _safe_indexing(x, [], axis=1)), + ["x1", "x2", "x3"], + ), + ], + verbose_feature_names_out=False, + ).set_output(transform=dataframe_lib) + err_msg = re.escape( + "Duplicated feature names found before concatenating the outputs of the " + "transformers: ['x1', 'x2', 'x3'].\n" + "Transformer A has conflicting columns names: ['x1', 'x2', 'x3'].\n" + "Transformer B has conflicting columns names: ['x1', 'x2'].\n" + "Transformer C has conflicting columns names: ['x1', 'x3'].\n" + ) + with pytest.raises(ValueError, match=err_msg): + transformer.fit_transform(df) + + +@pytest.mark.skipif( + parse_version(joblib.__version__) < parse_version("1.3"), + reason="requires joblib >= 1.3", +) +def test_column_transformer_auto_memmap(): + """Check that ColumnTransformer works in parallel with joblib's auto-memmapping. + + non-regression test for issue #28781 + """ + X = np.random.RandomState(0).uniform(size=(3, 4)) + + scaler = StandardScaler(copy=False) + + transformer = ColumnTransformer( + transformers=[("scaler", scaler, [0])], + n_jobs=2, + ) + + with joblib.parallel_backend("loky", max_nbytes=1): + Xt = transformer.fit_transform(X) + + assert_allclose(Xt, StandardScaler().fit_transform(X[:, [0]])) + + +def test_column_transformer_non_default_index(): + """Check index handling when both pd.Series and pd.DataFrame slices are used in + ColumnTransformer. + + Non-regression test for issue #31546. + """ + pd = pytest.importorskip("pandas") + df = pd.DataFrame( + { + "dict_col": [{"foo": 1, "bar": 2}, {"foo": 3, "baz": 1}], + "dummy_col": [1, 2], + }, + index=[1, 2], + ) + t = make_column_transformer( + (DictVectorizer(sparse=False), "dict_col"), + (FunctionTransformer(), ["dummy_col"]), + ) + t.set_output(transform="pandas") + X = t.fit_transform(df) + assert list(X.index) == [1, 2] + + +# Metadata Routing Tests +# ====================== + + +@pytest.mark.parametrize("method", ["transform", "fit_transform", "fit"]) +def test_routing_passed_metadata_not_supported(method): + """Test that the right error message is raised when metadata is passed while + not supported when `enable_metadata_routing=False`.""" + + X = np.array([[0, 1, 2], [2, 4, 6]]).T + y = [1, 2, 3] + trs = ColumnTransformer([("trans", Trans(), [0])]).fit(X, y) + + with pytest.raises( + ValueError, match="is only supported if enable_metadata_routing=True" + ): + getattr(trs, method)([[1]], sample_weight=[1], prop="a") + + +@pytest.mark.parametrize("method", ["transform", "fit_transform", "fit"]) +@config_context(enable_metadata_routing=True) +def test_metadata_routing_for_column_transformer(method): + """Test that metadata is routed correctly for column transformer.""" + X = np.array([[0, 1, 2], [2, 4, 6]]).T + y = [1, 2, 3] + registry = _Registry() + sample_weight, metadata = [1], "a" + trs = ColumnTransformer( + [ + ( + "trans", + ConsumingTransformer(registry=registry) + .set_fit_request(sample_weight=True, metadata=True) + .set_transform_request(sample_weight=True, metadata=True), + [0], + ) + ] + ) + + if method == "transform": + trs.fit(X, y, sample_weight=sample_weight, metadata=metadata) + trs.transform(X, sample_weight=sample_weight, metadata=metadata) + else: + getattr(trs, method)(X, y, sample_weight=sample_weight, metadata=metadata) + + assert len(registry) + for _trs in registry: + check_recorded_metadata( + obj=_trs, + method=method, + parent=method, + sample_weight=sample_weight, + metadata=metadata, + ) + + +@config_context(enable_metadata_routing=True) +def test_metadata_routing_no_fit_transform(): + """Test metadata routing when the sub-estimator doesn't implement + ``fit_transform``.""" + + class NoFitTransform(BaseEstimator): + def fit(self, X, y=None, sample_weight=None, metadata=None): + assert sample_weight + assert metadata + return self + + def transform(self, X, sample_weight=None, metadata=None): + assert sample_weight + assert metadata + return X + + X = np.array([[0, 1, 2], [2, 4, 6]]).T + y = [1, 2, 3] + sample_weight, metadata = [1], "a" + trs = ColumnTransformer( + [ + ( + "trans", + NoFitTransform() + .set_fit_request(sample_weight=True, metadata=True) + .set_transform_request(sample_weight=True, metadata=True), + [0], + ) + ] + ) + + trs.fit(X, y, sample_weight=sample_weight, metadata=metadata) + trs.fit_transform(X, y, sample_weight=sample_weight, metadata=metadata) + + +@pytest.mark.parametrize("method", ["transform", "fit_transform", "fit"]) +@config_context(enable_metadata_routing=True) +def test_metadata_routing_error_for_column_transformer(method): + """Test that the right error is raised when metadata is not requested.""" + X = np.array([[0, 1, 2], [2, 4, 6]]).T + y = [1, 2, 3] + sample_weight, metadata = [1], "a" + trs = ColumnTransformer([("trans", ConsumingTransformer(), [0])]) + + error_message = ( + "[sample_weight, metadata] are passed but are not explicitly set as requested" + f" or not requested for ConsumingTransformer.{method}" + ) + with pytest.raises(ValueError, match=re.escape(error_message)): + if method == "transform": + trs.fit(X, y) + trs.transform(X, sample_weight=sample_weight, metadata=metadata) + else: + getattr(trs, method)(X, y, sample_weight=sample_weight, metadata=metadata) + + +@config_context(enable_metadata_routing=True) +def test_get_metadata_routing_works_without_fit(): + # Regression test for https://github.com/scikit-learn/scikit-learn/issues/28186 + # Make sure ct.get_metadata_routing() works w/o having called fit. + ct = ColumnTransformer([("trans", ConsumingTransformer(), [0])]) + ct.get_metadata_routing() + + +@config_context(enable_metadata_routing=True) +def test_remainder_request_always_present(): + # Test that remainder request is always present. + ct = ColumnTransformer( + [("trans", StandardScaler(), [0])], + remainder=ConsumingTransformer() + .set_fit_request(metadata=True) + .set_transform_request(metadata=True), + ) + router = ct.get_metadata_routing() + assert router.consumes("fit", ["metadata"]) == set(["metadata"]) + + +@config_context(enable_metadata_routing=True) +def test_unused_transformer_request_present(): + # Test that the request of a transformer is always present even when not + # used due to no selected columns. + ct = ColumnTransformer( + [ + ( + "trans", + ConsumingTransformer() + .set_fit_request(metadata=True) + .set_transform_request(metadata=True), + lambda X: [], + ) + ] + ) + router = ct.get_metadata_routing() + assert router.consumes("fit", ["metadata"]) == set(["metadata"]) + + +# End of Metadata Routing Tests +# ============================= diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/tests/test_target.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/tests/test_target.py new file mode 100644 index 0000000000000000000000000000000000000000..19dcfb5dc7f031f8b1a5303c84e84389fbcccc1e --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/compose/tests/test_target.py @@ -0,0 +1,439 @@ +import warnings + +import numpy as np +import pytest + +from sklearn import config_context, datasets +from sklearn.base import BaseEstimator, TransformerMixin, clone +from sklearn.compose import TransformedTargetRegressor +from sklearn.dummy import DummyRegressor +from sklearn.linear_model import LinearRegression, OrthogonalMatchingPursuit +from sklearn.pipeline import Pipeline +from sklearn.preprocessing import FunctionTransformer, StandardScaler +from sklearn.utils._testing import assert_allclose + +friedman = datasets.make_friedman1(random_state=0) + + +def test_transform_target_regressor_error(): + X, y = friedman + # provide a transformer and functions at the same time + regr = TransformedTargetRegressor( + regressor=LinearRegression(), + transformer=StandardScaler(), + func=np.exp, + inverse_func=np.log, + ) + with pytest.raises( + ValueError, + match="'transformer' and functions 'func'/'inverse_func' cannot both be set.", + ): + regr.fit(X, y) + # fit with sample_weight with a regressor which does not support it + sample_weight = np.ones((y.shape[0],)) + regr = TransformedTargetRegressor( + regressor=OrthogonalMatchingPursuit(), transformer=StandardScaler() + ) + with pytest.raises( + TypeError, + match=r"fit\(\) got an unexpected keyword argument 'sample_weight'", + ): + regr.fit(X, y, sample_weight=sample_weight) + + # one of (func, inverse_func) is given but the other one is not + regr = TransformedTargetRegressor(func=np.exp) + with pytest.raises( + ValueError, + match="When 'func' is provided, 'inverse_func' must also be provided", + ): + regr.fit(X, y) + + regr = TransformedTargetRegressor(inverse_func=np.log) + with pytest.raises( + ValueError, + match="When 'inverse_func' is provided, 'func' must also be provided", + ): + regr.fit(X, y) + + +def test_transform_target_regressor_invertible(): + X, y = friedman + regr = TransformedTargetRegressor( + regressor=LinearRegression(), + func=np.sqrt, + inverse_func=np.log, + check_inverse=True, + ) + with pytest.warns( + UserWarning, + match=(r"The provided functions.* are not strictly inverse of each other"), + ): + regr.fit(X, y) + regr = TransformedTargetRegressor( + regressor=LinearRegression(), func=np.sqrt, inverse_func=np.log + ) + regr.set_params(check_inverse=False) + + with warnings.catch_warnings(): + warnings.simplefilter("error", UserWarning) + regr.fit(X, y) + + +def _check_standard_scaled(y, y_pred): + y_mean = np.mean(y, axis=0) + y_std = np.std(y, axis=0) + assert_allclose((y - y_mean) / y_std, y_pred) + + +def _check_shifted_by_one(y, y_pred): + assert_allclose(y + 1, y_pred) + + +def test_transform_target_regressor_functions(): + X, y = friedman + regr = TransformedTargetRegressor( + regressor=LinearRegression(), func=np.log, inverse_func=np.exp + ) + y_pred = regr.fit(X, y).predict(X) + # check the transformer output + y_tran = regr.transformer_.transform(y.reshape(-1, 1)).squeeze() + assert_allclose(np.log(y), y_tran) + assert_allclose( + y, regr.transformer_.inverse_transform(y_tran.reshape(-1, 1)).squeeze() + ) + assert y.shape == y_pred.shape + assert_allclose(y_pred, regr.inverse_func(regr.regressor_.predict(X))) + # check the regressor output + lr = LinearRegression().fit(X, regr.func(y)) + assert_allclose(regr.regressor_.coef_.ravel(), lr.coef_.ravel()) + + +def test_transform_target_regressor_functions_multioutput(): + X = friedman[0] + y = np.vstack((friedman[1], friedman[1] ** 2 + 1)).T + regr = TransformedTargetRegressor( + regressor=LinearRegression(), func=np.log, inverse_func=np.exp + ) + y_pred = regr.fit(X, y).predict(X) + # check the transformer output + y_tran = regr.transformer_.transform(y) + assert_allclose(np.log(y), y_tran) + assert_allclose(y, regr.transformer_.inverse_transform(y_tran)) + assert y.shape == y_pred.shape + assert_allclose(y_pred, regr.inverse_func(regr.regressor_.predict(X))) + # check the regressor output + lr = LinearRegression().fit(X, regr.func(y)) + assert_allclose(regr.regressor_.coef_.ravel(), lr.coef_.ravel()) + + +@pytest.mark.parametrize( + "X,y", [friedman, (friedman[0], np.vstack((friedman[1], friedman[1] ** 2 + 1)).T)] +) +def test_transform_target_regressor_1d_transformer(X, y): + # All transformer in scikit-learn expect 2D data. FunctionTransformer with + # validate=False lift this constraint without checking that the input is a + # 2D vector. We check the consistency of the data shape using a 1D and 2D y + # array. + transformer = FunctionTransformer( + func=lambda x: x + 1, inverse_func=lambda x: x - 1 + ) + regr = TransformedTargetRegressor( + regressor=LinearRegression(), transformer=transformer + ) + y_pred = regr.fit(X, y).predict(X) + assert y.shape == y_pred.shape + # consistency forward transform + y_tran = regr.transformer_.transform(y) + _check_shifted_by_one(y, y_tran) + assert y.shape == y_pred.shape + # consistency inverse transform + assert_allclose(y, regr.transformer_.inverse_transform(y_tran).squeeze()) + # consistency of the regressor + lr = LinearRegression() + transformer2 = clone(transformer) + lr.fit(X, transformer2.fit_transform(y)) + y_lr_pred = lr.predict(X) + assert_allclose(y_pred, transformer2.inverse_transform(y_lr_pred)) + assert_allclose(regr.regressor_.coef_, lr.coef_) + + +@pytest.mark.parametrize( + "X,y", [friedman, (friedman[0], np.vstack((friedman[1], friedman[1] ** 2 + 1)).T)] +) +def test_transform_target_regressor_2d_transformer(X, y): + # Check consistency with transformer accepting only 2D array and a 1D/2D y + # array. + transformer = StandardScaler() + regr = TransformedTargetRegressor( + regressor=LinearRegression(), transformer=transformer + ) + y_pred = regr.fit(X, y).predict(X) + assert y.shape == y_pred.shape + # consistency forward transform + if y.ndim == 1: # create a 2D array and squeeze results + y_tran = regr.transformer_.transform(y.reshape(-1, 1)) + else: + y_tran = regr.transformer_.transform(y) + _check_standard_scaled(y, y_tran.squeeze()) + assert y.shape == y_pred.shape + # consistency inverse transform + assert_allclose(y, regr.transformer_.inverse_transform(y_tran).squeeze()) + # consistency of the regressor + lr = LinearRegression() + transformer2 = clone(transformer) + if y.ndim == 1: # create a 2D array and squeeze results + lr.fit(X, transformer2.fit_transform(y.reshape(-1, 1)).squeeze()) + y_lr_pred = lr.predict(X).reshape(-1, 1) + y_pred2 = transformer2.inverse_transform(y_lr_pred).squeeze() + else: + lr.fit(X, transformer2.fit_transform(y)) + y_lr_pred = lr.predict(X) + y_pred2 = transformer2.inverse_transform(y_lr_pred) + + assert_allclose(y_pred, y_pred2) + assert_allclose(regr.regressor_.coef_, lr.coef_) + + +def test_transform_target_regressor_2d_transformer_multioutput(): + # Check consistency with transformer accepting only 2D array and a 2D y + # array. + X = friedman[0] + y = np.vstack((friedman[1], friedman[1] ** 2 + 1)).T + transformer = StandardScaler() + regr = TransformedTargetRegressor( + regressor=LinearRegression(), transformer=transformer + ) + y_pred = regr.fit(X, y).predict(X) + assert y.shape == y_pred.shape + # consistency forward transform + y_tran = regr.transformer_.transform(y) + _check_standard_scaled(y, y_tran) + assert y.shape == y_pred.shape + # consistency inverse transform + assert_allclose(y, regr.transformer_.inverse_transform(y_tran).squeeze()) + # consistency of the regressor + lr = LinearRegression() + transformer2 = clone(transformer) + lr.fit(X, transformer2.fit_transform(y)) + y_lr_pred = lr.predict(X) + assert_allclose(y_pred, transformer2.inverse_transform(y_lr_pred)) + assert_allclose(regr.regressor_.coef_, lr.coef_) + + +def test_transform_target_regressor_3d_target(): + # Non-regression test for: + # https://github.com/scikit-learn/scikit-learn/issues/18866 + # Check with a 3D target with a transformer that reshapes the target + X = friedman[0] + y = np.tile(friedman[1].reshape(-1, 1, 1), [1, 3, 2]) + + def flatten_data(data): + return data.reshape(data.shape[0], -1) + + def unflatten_data(data): + return data.reshape(data.shape[0], -1, 2) + + transformer = FunctionTransformer(func=flatten_data, inverse_func=unflatten_data) + regr = TransformedTargetRegressor( + regressor=LinearRegression(), transformer=transformer + ) + y_pred = regr.fit(X, y).predict(X) + assert y.shape == y_pred.shape + + +def test_transform_target_regressor_multi_to_single(): + X = friedman[0] + y = np.transpose([friedman[1], (friedman[1] ** 2 + 1)]) + + def func(y): + out = np.sqrt(y[:, 0] ** 2 + y[:, 1] ** 2) + return out[:, np.newaxis] + + def inverse_func(y): + return y + + tt = TransformedTargetRegressor( + func=func, inverse_func=inverse_func, check_inverse=False + ) + tt.fit(X, y) + y_pred_2d_func = tt.predict(X) + assert y_pred_2d_func.shape == (100, 1) + + # force that the function only return a 1D array + def func(y): + return np.sqrt(y[:, 0] ** 2 + y[:, 1] ** 2) + + tt = TransformedTargetRegressor( + func=func, inverse_func=inverse_func, check_inverse=False + ) + tt.fit(X, y) + y_pred_1d_func = tt.predict(X) + assert y_pred_1d_func.shape == (100, 1) + + assert_allclose(y_pred_1d_func, y_pred_2d_func) + + +class DummyCheckerArrayTransformer(TransformerMixin, BaseEstimator): + def fit(self, X, y=None): + assert isinstance(X, np.ndarray) + return self + + def transform(self, X): + assert isinstance(X, np.ndarray) + return X + + def inverse_transform(self, X): + assert isinstance(X, np.ndarray) + return X + + +class DummyCheckerListRegressor(DummyRegressor): + def fit(self, X, y, sample_weight=None): + assert isinstance(X, list) + return super().fit(X, y, sample_weight) + + def predict(self, X): + assert isinstance(X, list) + return super().predict(X) + + +def test_transform_target_regressor_ensure_y_array(): + # check that the target ``y`` passed to the transformer will always be a + # numpy array. Similarly, if ``X`` is passed as a list, we check that the + # predictor receive as it is. + X, y = friedman + tt = TransformedTargetRegressor( + transformer=DummyCheckerArrayTransformer(), + regressor=DummyCheckerListRegressor(), + check_inverse=False, + ) + tt.fit(X.tolist(), y.tolist()) + tt.predict(X.tolist()) + with pytest.raises(AssertionError): + tt.fit(X, y.tolist()) + with pytest.raises(AssertionError): + tt.predict(X) + + +class DummyTransformer(TransformerMixin, BaseEstimator): + """Dummy transformer which count how many time fit was called.""" + + def __init__(self, fit_counter=0): + self.fit_counter = fit_counter + + def fit(self, X, y=None): + self.fit_counter += 1 + return self + + def transform(self, X): + return X + + def inverse_transform(self, X): + return X + + +@pytest.mark.parametrize("check_inverse", [False, True]) +def test_transform_target_regressor_count_fit(check_inverse): + # regression test for gh-issue #11618 + # check that we only call a single time fit for the transformer + X, y = friedman + ttr = TransformedTargetRegressor( + transformer=DummyTransformer(), check_inverse=check_inverse + ) + ttr.fit(X, y) + assert ttr.transformer_.fit_counter == 1 + + +class DummyRegressorWithExtraFitParams(DummyRegressor): + def fit(self, X, y, sample_weight=None, check_input=True): + # on the test below we force this to false, we make sure this is + # actually passed to the regressor + assert not check_input + return super().fit(X, y, sample_weight) + + +def test_transform_target_regressor_pass_fit_parameters(): + X, y = friedman + regr = TransformedTargetRegressor( + regressor=DummyRegressorWithExtraFitParams(), transformer=DummyTransformer() + ) + + regr.fit(X, y, check_input=False) + assert regr.transformer_.fit_counter == 1 + + +def test_transform_target_regressor_route_pipeline(): + X, y = friedman + + regr = TransformedTargetRegressor( + regressor=DummyRegressorWithExtraFitParams(), transformer=DummyTransformer() + ) + estimators = [("normalize", StandardScaler()), ("est", regr)] + + pip = Pipeline(estimators) + pip.fit(X, y, **{"est__check_input": False}) + + assert regr.transformer_.fit_counter == 1 + + +class DummyRegressorWithExtraPredictParams(DummyRegressor): + def predict(self, X, check_input=True): + # In the test below we make sure that the check input parameter is + # passed as false + self.predict_called = True + assert not check_input + return super().predict(X) + + +def test_transform_target_regressor_pass_extra_predict_parameters(): + # Checks that predict kwargs are passed to regressor. + X, y = friedman + regr = TransformedTargetRegressor( + regressor=DummyRegressorWithExtraPredictParams(), transformer=DummyTransformer() + ) + + regr.fit(X, y) + regr.predict(X, check_input=False) + assert regr.regressor_.predict_called + + +@pytest.mark.parametrize("output_format", ["pandas", "polars"]) +def test_transform_target_regressor_not_warns_with_global_output_set(output_format): + """Test that TransformedTargetRegressor will not raise warnings if + set_config(transform_output="pandas"/"polars") is set globally; regression test for + issue #29361.""" + X, y = datasets.make_regression() + y = np.abs(y) + 1 + with config_context(transform_output=output_format): + with warnings.catch_warnings(): + warnings.simplefilter("error") + TransformedTargetRegressor( + regressor=LinearRegression(), func=np.log, inverse_func=np.exp + ).fit(X, y) + + +class ValidateDimensionRegressor(BaseEstimator): + """A regressor that expects the target to have a specific number of dimensions.""" + + def __init__(self, ndim): + self.ndim = ndim + + def fit(self, X, y): + assert y.ndim == self.ndim + + def predict(self, X): + pass # pragma: no cover + + +@pytest.mark.parametrize("ndim", [1, 2]) +def test_transform_target_regressor_preserves_input_shape(ndim): + """Check that TransformedTargetRegressor internally preserves the shape of the input + + non-regression test for issue #26530. + """ + X, y = datasets.make_regression(n_samples=10, n_features=5, random_state=42) + if ndim == 2: + y = y.reshape(-1, 1) + + regr = TransformedTargetRegressor(regressor=ValidateDimensionRegressor(ndim)) + regr.fit(X, y) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/conftest.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/conftest.py new file mode 100644 index 0000000000000000000000000000000000000000..d5255ead1ffdceb3d825f51a24d0a531b1833ecf --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/conftest.py @@ -0,0 +1,375 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import builtins +import faulthandler +import platform +import sys +from contextlib import suppress +from functools import wraps +from os import environ +from unittest import SkipTest + +import joblib +import numpy as np +import pytest +from _pytest.doctest import DoctestItem +from threadpoolctl import threadpool_limits + +from sklearn import set_config +from sklearn._min_dependencies import PYTEST_MIN_VERSION +from sklearn.datasets import ( + fetch_20newsgroups, + fetch_20newsgroups_vectorized, + fetch_california_housing, + fetch_covtype, + fetch_kddcup99, + fetch_lfw_pairs, + fetch_lfw_people, + fetch_olivetti_faces, + fetch_rcv1, + fetch_species_distributions, +) +from sklearn.utils._testing import get_pytest_filterwarning_lines +from sklearn.utils.fixes import ( + _IS_32BIT, + np_base_version, + parse_version, + sp_version, +) + +try: + from scipy_doctest.conftest import dt_config +except ModuleNotFoundError: + dt_config = None + +if parse_version(pytest.__version__) < parse_version(PYTEST_MIN_VERSION): + raise ImportError( + f"Your version of pytest is too old. Got version {pytest.__version__}, you" + f" should have pytest >= {PYTEST_MIN_VERSION} installed." + ) + +scipy_datasets_require_network = sp_version >= parse_version("1.10") + + +def raccoon_face_or_skip(): + # SciPy >= 1.10 requires network to access to get data + if scipy_datasets_require_network: + run_network_tests = environ.get("SKLEARN_SKIP_NETWORK_TESTS", "1") == "0" + if not run_network_tests: + raise SkipTest("test is enabled when SKLEARN_SKIP_NETWORK_TESTS=0") + + try: + import pooch # noqa: F401 + except ImportError: + raise SkipTest("test requires pooch to be installed") + + from scipy.datasets import face + else: + from scipy.misc import face + + return face(gray=True) + + +dataset_fetchers = { + "fetch_20newsgroups_fxt": fetch_20newsgroups, + "fetch_20newsgroups_vectorized_fxt": fetch_20newsgroups_vectorized, + "fetch_california_housing_fxt": fetch_california_housing, + "fetch_covtype_fxt": fetch_covtype, + "fetch_kddcup99_fxt": fetch_kddcup99, + "fetch_lfw_pairs_fxt": fetch_lfw_pairs, + "fetch_lfw_people_fxt": fetch_lfw_people, + "fetch_olivetti_faces_fxt": fetch_olivetti_faces, + "fetch_rcv1_fxt": fetch_rcv1, + "fetch_species_distributions_fxt": fetch_species_distributions, +} + +if scipy_datasets_require_network: + dataset_fetchers["raccoon_face_fxt"] = raccoon_face_or_skip + +_SKIP32_MARK = pytest.mark.skipif( + environ.get("SKLEARN_RUN_FLOAT32_TESTS", "0") != "1", + reason="Set SKLEARN_RUN_FLOAT32_TESTS=1 to run float32 dtype tests", +) + + +# Global fixtures +@pytest.fixture(params=[pytest.param(np.float32, marks=_SKIP32_MARK), np.float64]) +def global_dtype(request): + yield request.param + + +def _fetch_fixture(f): + """Fetch dataset (download if missing and requested by environment).""" + download_if_missing = environ.get("SKLEARN_SKIP_NETWORK_TESTS", "1") == "0" + + @wraps(f) + def wrapped(*args, **kwargs): + kwargs["download_if_missing"] = download_if_missing + try: + return f(*args, **kwargs) + except OSError as e: + if str(e) != "Data not found and `download_if_missing` is False": + raise + pytest.skip("test is enabled when SKLEARN_SKIP_NETWORK_TESTS=0") + + return pytest.fixture(lambda: wrapped) + + +# Adds fixtures for fetching data +fetch_20newsgroups_fxt = _fetch_fixture(fetch_20newsgroups) +fetch_20newsgroups_vectorized_fxt = _fetch_fixture(fetch_20newsgroups_vectorized) +fetch_california_housing_fxt = _fetch_fixture(fetch_california_housing) +fetch_covtype_fxt = _fetch_fixture(fetch_covtype) +fetch_kddcup99_fxt = _fetch_fixture(fetch_kddcup99) +fetch_lfw_pairs_fxt = _fetch_fixture(fetch_lfw_pairs) +fetch_lfw_people_fxt = _fetch_fixture(fetch_lfw_people) +fetch_olivetti_faces_fxt = _fetch_fixture(fetch_olivetti_faces) +fetch_rcv1_fxt = _fetch_fixture(fetch_rcv1) +fetch_species_distributions_fxt = _fetch_fixture(fetch_species_distributions) +raccoon_face_fxt = pytest.fixture(raccoon_face_or_skip) + + +def pytest_collection_modifyitems(config, items): + """Called after collect is completed. + + Parameters + ---------- + config : pytest config + items : list of collected items + """ + run_network_tests = environ.get("SKLEARN_SKIP_NETWORK_TESTS", "1") == "0" + skip_network = pytest.mark.skip( + reason="test is enabled when SKLEARN_SKIP_NETWORK_TESTS=0" + ) + + # download datasets during collection to avoid thread unsafe behavior + # when running pytest in parallel with pytest-xdist + dataset_features_set = set(dataset_fetchers) + datasets_to_download = set() + + for item in items: + if isinstance(item, DoctestItem) and "fetch_" in item.name: + fetcher_function_name = item.name.split(".")[-1] + dataset_fetchers_key = f"{fetcher_function_name}_fxt" + dataset_to_fetch = set([dataset_fetchers_key]) & dataset_features_set + elif not hasattr(item, "fixturenames"): + continue + else: + item_fixtures = set(item.fixturenames) + dataset_to_fetch = item_fixtures & dataset_features_set + + if not dataset_to_fetch: + continue + + if run_network_tests: + datasets_to_download |= dataset_to_fetch + else: + # network tests are skipped + item.add_marker(skip_network) + + # Only download datasets on the first worker spawned by pytest-xdist + # to avoid thread unsafe behavior. If pytest-xdist is not used, we still + # download before tests run. + worker_id = environ.get("PYTEST_XDIST_WORKER", "gw0") + if worker_id == "gw0" and run_network_tests: + for name in datasets_to_download: + with suppress(SkipTest): + dataset_fetchers[name]() + + for item in items: + # Known failure on with GradientBoostingClassifier on ARM64 + if ( + item.name.endswith("GradientBoostingClassifier") + and platform.machine() == "aarch64" + ): + marker = pytest.mark.xfail( + reason=( + "know failure. See " + "https://github.com/scikit-learn/scikit-learn/issues/17797" + ) + ) + item.add_marker(marker) + + skip_doctests = False + try: + import matplotlib # noqa: F401 + except ImportError: + skip_doctests = True + reason = "matplotlib is required to run the doctests" + + if _IS_32BIT: + reason = "doctest are only run when the default numpy int is 64 bits." + skip_doctests = True + elif sys.platform.startswith("win32"): + reason = ( + "doctests are not run for Windows because numpy arrays " + "repr is inconsistent across platforms." + ) + skip_doctests = True + + if np_base_version < parse_version("2"): + # TODO: configure numpy to output scalar arrays as regular Python scalars + # once possible to improve readability of the tests docstrings. + # https://numpy.org/neps/nep-0051-scalar-representation.html#implementation + reason = "Due to NEP 51 numpy scalar repr has changed in numpy 2" + skip_doctests = True + + if sp_version < parse_version("1.14"): + reason = "Scipy sparse matrix repr has changed in scipy 1.14" + skip_doctests = True + + # Normally doctest has the entire module's scope. Here we set globs to an empty dict + # to remove the module's scope: + # https://docs.python.org/3/library/doctest.html#what-s-the-execution-context + for item in items: + if isinstance(item, DoctestItem): + item.dtest.globs = {} + + if skip_doctests: + skip_marker = pytest.mark.skip(reason=reason) + + for item in items: + if isinstance(item, DoctestItem): + # work-around an internal error with pytest if adding a skip + # mark to a doctest in a contextmanager, see + # https://github.com/pytest-dev/pytest/issues/8796 for more + # details. + if item.name != "sklearn._config.config_context": + item.add_marker(skip_marker) + try: + import PIL # noqa: F401 + + pillow_installed = True + except ImportError: + pillow_installed = False + + if not pillow_installed: + skip_marker = pytest.mark.skip(reason="pillow (or PIL) not installed!") + for item in items: + if item.name in [ + "sklearn.feature_extraction.image.PatchExtractor", + "sklearn.feature_extraction.image.extract_patches_2d", + ]: + item.add_marker(skip_marker) + + +@pytest.fixture(scope="function") +def pyplot(): + """Setup and teardown fixture for matplotlib. + + This fixture checks if we can import matplotlib. If not, the tests will be + skipped. Otherwise, we close the figures before and after running the + functions. + + Returns + ------- + pyplot : module + The ``matplotlib.pyplot`` module. + """ + pyplot = pytest.importorskip("matplotlib.pyplot") + pyplot.close("all") + yield pyplot + pyplot.close("all") + + +def pytest_generate_tests(metafunc): + """Parametrization of global_random_seed fixture + + based on the SKLEARN_TESTS_GLOBAL_RANDOM_SEED environment variable. + + The goal of this fixture is to prevent tests that use it to be sensitive + to a specific seed value while still being deterministic by default. + + See the documentation for the SKLEARN_TESTS_GLOBAL_RANDOM_SEED + variable for instructions on how to use this fixture. + + https://scikit-learn.org/dev/computing/parallelism.html#sklearn-tests-global-random-seed + + """ + # When using pytest-xdist this function is called in the xdist workers. + # We rely on SKLEARN_TESTS_GLOBAL_RANDOM_SEED environment variable which is + # set in before running pytest and is available in xdist workers since they + # are subprocesses. + RANDOM_SEED_RANGE = list(range(100)) # All seeds in [0, 99] should be valid. + random_seed_var = environ.get("SKLEARN_TESTS_GLOBAL_RANDOM_SEED") + + default_random_seeds = [42] + + if random_seed_var is None: + random_seeds = default_random_seeds + elif random_seed_var == "all": + random_seeds = RANDOM_SEED_RANGE + else: + if "-" in random_seed_var: + start, stop = random_seed_var.split("-") + random_seeds = list(range(int(start), int(stop) + 1)) + else: + random_seeds = [int(random_seed_var)] + + if min(random_seeds) < 0 or max(random_seeds) > 99: + raise ValueError( + "The value(s) of the environment variable " + "SKLEARN_TESTS_GLOBAL_RANDOM_SEED must be in the range [0, 99] " + f"(or 'all'), got: {random_seed_var}" + ) + + if "global_random_seed" in metafunc.fixturenames: + metafunc.parametrize("global_random_seed", random_seeds) + + +def pytest_configure(config): + # Use matplotlib agg backend during the tests including doctests + try: + import matplotlib + + matplotlib.use("agg") + except ImportError: + pass + + allowed_parallelism = joblib.cpu_count(only_physical_cores=True) + xdist_worker_count = environ.get("PYTEST_XDIST_WORKER_COUNT") + if xdist_worker_count is not None: + # Set the number of OpenMP and BLAS threads based on the number of workers + # xdist is using to prevent oversubscription. + allowed_parallelism = max(allowed_parallelism // int(xdist_worker_count), 1) + threadpool_limits(allowed_parallelism) + + if environ.get("SKLEARN_WARNINGS_AS_ERRORS", "0") != "0": + # This seems like the only way to programmatically change the config + # filterwarnings. This was suggested in + # https://github.com/pytest-dev/pytest/issues/3311#issuecomment-373177592 + for line in get_pytest_filterwarning_lines(): + config.addinivalue_line("filterwarnings", line) + + faulthandler_timeout = int(environ.get("SKLEARN_FAULTHANDLER_TIMEOUT", "0")) + if faulthandler_timeout > 0: + faulthandler.enable() + faulthandler.dump_traceback_later(faulthandler_timeout, exit=True) + + +@pytest.fixture +def hide_available_pandas(monkeypatch): + """Pretend pandas was not installed.""" + import_orig = builtins.__import__ + + def mocked_import(name, *args, **kwargs): + if name == "pandas": + raise ImportError() + return import_orig(name, *args, **kwargs) + + monkeypatch.setattr(builtins, "__import__", mocked_import) + + +@pytest.fixture +def print_changed_only_false(): + """Set `print_changed_only` to False for the duration of the test.""" + set_config(print_changed_only=False) + yield + set_config(print_changed_only=True) # reset to default + + +if dt_config is not None: + # Strict mode to differentiate between 3.14 and np.float64(3.14) + dt_config.strict_check = True + # dt_config.rtol = 0.01 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..65817ef7b977b84bcd4c8eb913866d54ce756999 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/__init__.py @@ -0,0 +1,46 @@ +"""Methods and algorithms to robustly estimate covariance. + +They estimate the covariance of features at given sets of points, as well as the +precision matrix defined as the inverse of the covariance. Covariance estimation is +closely related to the theory of Gaussian graphical models. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +from ._elliptic_envelope import EllipticEnvelope +from ._empirical_covariance import ( + EmpiricalCovariance, + empirical_covariance, + log_likelihood, +) +from ._graph_lasso import GraphicalLasso, GraphicalLassoCV, graphical_lasso +from ._robust_covariance import MinCovDet, fast_mcd +from ._shrunk_covariance import ( + OAS, + LedoitWolf, + ShrunkCovariance, + ledoit_wolf, + ledoit_wolf_shrinkage, + oas, + shrunk_covariance, +) + +__all__ = [ + "OAS", + "EllipticEnvelope", + "EmpiricalCovariance", + "GraphicalLasso", + "GraphicalLassoCV", + "LedoitWolf", + "MinCovDet", + "ShrunkCovariance", + "empirical_covariance", + "fast_mcd", + "graphical_lasso", + "ledoit_wolf", + "ledoit_wolf_shrinkage", + "log_likelihood", + "oas", + "shrunk_covariance", +] diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_elliptic_envelope.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_elliptic_envelope.py new file mode 100644 index 0000000000000000000000000000000000000000..71fb72ccd683d04a708162774487922b719cbe4c --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_elliptic_envelope.py @@ -0,0 +1,266 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +from numbers import Real + +import numpy as np + +from ..base import OutlierMixin, _fit_context +from ..metrics import accuracy_score +from ..utils._param_validation import Interval +from ..utils.validation import check_is_fitted +from ._robust_covariance import MinCovDet + + +class EllipticEnvelope(OutlierMixin, MinCovDet): + """An object for detecting outliers in a Gaussian distributed dataset. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + store_precision : bool, default=True + Specify if the estimated precision is stored. + + assume_centered : bool, default=False + If True, the support of robust location and covariance estimates + is computed, and a covariance estimate is recomputed from it, + without centering the data. + Useful to work with data whose mean is significantly equal to + zero but is not exactly zero. + If False, the robust location and covariance are directly computed + with the FastMCD algorithm without additional treatment. + + support_fraction : float, default=None + The proportion of points to be included in the support of the raw + MCD estimate. If None, the minimum value of support_fraction will + be used within the algorithm: `(n_samples + n_features + 1) / 2 * n_samples`. + Range is (0, 1). + + contamination : float, default=0.1 + The amount of contamination of the data set, i.e. the proportion + of outliers in the data set. Range is (0, 0.5]. + + random_state : int, RandomState instance or None, default=None + Determines the pseudo random number generator for shuffling + the data. Pass an int for reproducible results across multiple function + calls. See :term:`Glossary `. + + Attributes + ---------- + location_ : ndarray of shape (n_features,) + Estimated robust location. + + covariance_ : ndarray of shape (n_features, n_features) + Estimated robust covariance matrix. + + precision_ : ndarray of shape (n_features, n_features) + Estimated pseudo inverse matrix. + (stored only if store_precision is True) + + support_ : ndarray of shape (n_samples,) + A mask of the observations that have been used to compute the + robust estimates of location and shape. + + offset_ : float + Offset used to define the decision function from the raw scores. + We have the relation: ``decision_function = score_samples - offset_``. + The offset depends on the contamination parameter and is defined in + such a way we obtain the expected number of outliers (samples with + decision function < 0) in training. + + .. versionadded:: 0.20 + + raw_location_ : ndarray of shape (n_features,) + The raw robust estimated location before correction and re-weighting. + + raw_covariance_ : ndarray of shape (n_features, n_features) + The raw robust estimated covariance before correction and re-weighting. + + raw_support_ : ndarray of shape (n_samples,) + A mask of the observations that have been used to compute + the raw robust estimates of location and shape, before correction + and re-weighting. + + dist_ : ndarray of shape (n_samples,) + Mahalanobis distances of the training set (on which :meth:`fit` is + called) observations. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + EmpiricalCovariance : Maximum likelihood covariance estimator. + GraphicalLasso : Sparse inverse covariance estimation + with an l1-penalized estimator. + LedoitWolf : LedoitWolf Estimator. + MinCovDet : Minimum Covariance Determinant + (robust estimator of covariance). + OAS : Oracle Approximating Shrinkage Estimator. + ShrunkCovariance : Covariance estimator with shrinkage. + + Notes + ----- + Outlier detection from covariance estimation may break or not + perform well in high-dimensional settings. In particular, one will + always take care to work with ``n_samples > n_features ** 2``. + + References + ---------- + .. [1] Rousseeuw, P.J., Van Driessen, K. "A fast algorithm for the + minimum covariance determinant estimator" Technometrics 41(3), 212 + (1999) + + Examples + -------- + >>> import numpy as np + >>> from sklearn.covariance import EllipticEnvelope + >>> true_cov = np.array([[.8, .3], + ... [.3, .4]]) + >>> X = np.random.RandomState(0).multivariate_normal(mean=[0, 0], + ... cov=true_cov, + ... size=500) + >>> cov = EllipticEnvelope(random_state=0).fit(X) + >>> # predict returns 1 for an inlier and -1 for an outlier + >>> cov.predict([[0, 0], + ... [3, 3]]) + array([ 1, -1]) + >>> cov.covariance_ + array([[0.7411, 0.2535], + [0.2535, 0.3053]]) + >>> cov.location_ + array([0.0813 , 0.0427]) + """ + + _parameter_constraints: dict = { + **MinCovDet._parameter_constraints, + "contamination": [Interval(Real, 0, 0.5, closed="right")], + } + + def __init__( + self, + *, + store_precision=True, + assume_centered=False, + support_fraction=None, + contamination=0.1, + random_state=None, + ): + super().__init__( + store_precision=store_precision, + assume_centered=assume_centered, + support_fraction=support_fraction, + random_state=random_state, + ) + self.contamination = contamination + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the EllipticEnvelope model. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data. + + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + self : object + Returns the instance itself. + """ + super().fit(X) + self.offset_ = np.percentile(-self.dist_, 100.0 * self.contamination) + return self + + def decision_function(self, X): + """Compute the decision function of the given observations. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The data matrix. + + Returns + ------- + decision : ndarray of shape (n_samples,) + Decision function of the samples. + It is equal to the shifted Mahalanobis distances. + The threshold for being an outlier is 0, which ensures a + compatibility with other outlier detection algorithms. + """ + check_is_fitted(self) + negative_mahal_dist = self.score_samples(X) + return negative_mahal_dist - self.offset_ + + def score_samples(self, X): + """Compute the negative Mahalanobis distances. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The data matrix. + + Returns + ------- + negative_mahal_distances : array-like of shape (n_samples,) + Opposite of the Mahalanobis distances. + """ + check_is_fitted(self) + return -self.mahalanobis(X) + + def predict(self, X): + """ + Predict labels (1 inlier, -1 outlier) of X according to fitted model. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The data matrix. + + Returns + ------- + is_inlier : ndarray of shape (n_samples,) + Returns -1 for anomalies/outliers and +1 for inliers. + """ + values = self.decision_function(X) + is_inlier = np.full(values.shape[0], -1, dtype=int) + is_inlier[values >= 0] = 1 + + return is_inlier + + def score(self, X, y, sample_weight=None): + """Return the mean accuracy on the given test data and labels. + + In multi-label classification, this is the subset accuracy + which is a harsh metric since you require for each sample that + each label set be correctly predicted. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Test samples. + + y : array-like of shape (n_samples,) or (n_samples, n_outputs) + True labels for X. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. + + Returns + ------- + score : float + Mean accuracy of self.predict(X) w.r.t. y. + """ + return accuracy_score(y, self.predict(X), sample_weight=sample_weight) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_empirical_covariance.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_empirical_covariance.py new file mode 100644 index 0000000000000000000000000000000000000000..c8ee198cc477275da749de0c212c4c874937f51b --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_empirical_covariance.py @@ -0,0 +1,370 @@ +""" +Maximum likelihood covariance estimator. + +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +# avoid division truncation +import warnings + +import numpy as np +from scipy import linalg + +from sklearn.utils import metadata_routing + +from .. import config_context +from ..base import BaseEstimator, _fit_context +from ..metrics.pairwise import pairwise_distances +from ..utils import check_array +from ..utils._param_validation import validate_params +from ..utils.extmath import fast_logdet +from ..utils.validation import validate_data + + +@validate_params( + { + "emp_cov": [np.ndarray], + "precision": [np.ndarray], + }, + prefer_skip_nested_validation=True, +) +def log_likelihood(emp_cov, precision): + """Compute the sample mean of the log_likelihood under a covariance model. + + Computes the empirical expected log-likelihood, allowing for universal + comparison (beyond this software package), and accounts for normalization + terms and scaling. + + Parameters + ---------- + emp_cov : ndarray of shape (n_features, n_features) + Maximum Likelihood Estimator of covariance. + + precision : ndarray of shape (n_features, n_features) + The precision matrix of the covariance model to be tested. + + Returns + ------- + log_likelihood_ : float + Sample mean of the log-likelihood. + """ + p = precision.shape[0] + log_likelihood_ = -np.sum(emp_cov * precision) + fast_logdet(precision) + log_likelihood_ -= p * np.log(2 * np.pi) + log_likelihood_ /= 2.0 + return log_likelihood_ + + +@validate_params( + { + "X": ["array-like"], + "assume_centered": ["boolean"], + }, + prefer_skip_nested_validation=True, +) +def empirical_covariance(X, *, assume_centered=False): + """Compute the Maximum likelihood covariance estimator. + + Parameters + ---------- + X : ndarray of shape (n_samples, n_features) + Data from which to compute the covariance estimate. + + assume_centered : bool, default=False + If `True`, data will not be centered before computation. + Useful when working with data whose mean is almost, but not exactly + zero. + If `False`, data will be centered before computation. + + Returns + ------- + covariance : ndarray of shape (n_features, n_features) + Empirical covariance (Maximum Likelihood Estimator). + + Examples + -------- + >>> from sklearn.covariance import empirical_covariance + >>> X = [[1,1,1],[1,1,1],[1,1,1], + ... [0,0,0],[0,0,0],[0,0,0]] + >>> empirical_covariance(X) + array([[0.25, 0.25, 0.25], + [0.25, 0.25, 0.25], + [0.25, 0.25, 0.25]]) + """ + X = check_array(X, ensure_2d=False, ensure_all_finite=False) + + if X.ndim == 1: + X = np.reshape(X, (1, -1)) + + if X.shape[0] == 1: + warnings.warn( + "Only one sample available. You may want to reshape your data array" + ) + + if assume_centered: + covariance = np.dot(X.T, X) / X.shape[0] + else: + covariance = np.cov(X.T, bias=1) + + if covariance.ndim == 0: + covariance = np.array([[covariance]]) + return covariance + + +class EmpiricalCovariance(BaseEstimator): + """Maximum likelihood covariance estimator. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + store_precision : bool, default=True + Specifies if the estimated precision is stored. + + assume_centered : bool, default=False + If True, data are not centered before computation. + Useful when working with data whose mean is almost, but not exactly + zero. + If False (default), data are centered before computation. + + Attributes + ---------- + location_ : ndarray of shape (n_features,) + Estimated location, i.e. the estimated mean. + + covariance_ : ndarray of shape (n_features, n_features) + Estimated covariance matrix. + + precision_ : ndarray of shape (n_features, n_features) + Estimated pseudo-inverse matrix. + (stored only if store_precision is True) + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + EllipticEnvelope : An object for detecting outliers in + a Gaussian distributed dataset. + GraphicalLasso : Sparse inverse covariance estimation + with an l1-penalized estimator. + LedoitWolf : LedoitWolf Estimator. + MinCovDet : Minimum Covariance Determinant + (robust estimator of covariance). + OAS : Oracle Approximating Shrinkage Estimator. + ShrunkCovariance : Covariance estimator with shrinkage. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.covariance import EmpiricalCovariance + >>> from sklearn.datasets import make_gaussian_quantiles + >>> real_cov = np.array([[.8, .3], + ... [.3, .4]]) + >>> rng = np.random.RandomState(0) + >>> X = rng.multivariate_normal(mean=[0, 0], + ... cov=real_cov, + ... size=500) + >>> cov = EmpiricalCovariance().fit(X) + >>> cov.covariance_ + array([[0.7569, 0.2818], + [0.2818, 0.3928]]) + >>> cov.location_ + array([0.0622, 0.0193]) + """ + + # X_test should have been called X + __metadata_request__score = {"X_test": metadata_routing.UNUSED} + + _parameter_constraints: dict = { + "store_precision": ["boolean"], + "assume_centered": ["boolean"], + } + + def __init__(self, *, store_precision=True, assume_centered=False): + self.store_precision = store_precision + self.assume_centered = assume_centered + + def _set_covariance(self, covariance): + """Saves the covariance and precision estimates + + Storage is done accordingly to `self.store_precision`. + Precision stored only if invertible. + + Parameters + ---------- + covariance : array-like of shape (n_features, n_features) + Estimated covariance matrix to be stored, and from which precision + is computed. + """ + covariance = check_array(covariance) + # set covariance + self.covariance_ = covariance + # set precision + if self.store_precision: + self.precision_ = linalg.pinvh(covariance, check_finite=False) + else: + self.precision_ = None + + def get_precision(self): + """Getter for the precision matrix. + + Returns + ------- + precision_ : array-like of shape (n_features, n_features) + The precision matrix associated to the current covariance object. + """ + if self.store_precision: + precision = self.precision_ + else: + precision = linalg.pinvh(self.covariance_, check_finite=False) + return precision + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the maximum likelihood covariance estimator to X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data, where `n_samples` is the number of samples and + `n_features` is the number of features. + + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + self : object + Returns the instance itself. + """ + X = validate_data(self, X) + if self.assume_centered: + self.location_ = np.zeros(X.shape[1]) + else: + self.location_ = X.mean(0) + covariance = empirical_covariance(X, assume_centered=self.assume_centered) + self._set_covariance(covariance) + + return self + + def score(self, X_test, y=None): + """Compute the log-likelihood of `X_test` under the estimated Gaussian model. + + The Gaussian model is defined by its mean and covariance matrix which are + represented respectively by `self.location_` and `self.covariance_`. + + Parameters + ---------- + X_test : array-like of shape (n_samples, n_features) + Test data of which we compute the likelihood, where `n_samples` is + the number of samples and `n_features` is the number of features. + `X_test` is assumed to be drawn from the same distribution than + the data used in fit (including centering). + + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + res : float + The log-likelihood of `X_test` with `self.location_` and `self.covariance_` + as estimators of the Gaussian model mean and covariance matrix respectively. + """ + X_test = validate_data(self, X_test, reset=False) + # compute empirical covariance of the test set + test_cov = empirical_covariance(X_test - self.location_, assume_centered=True) + # compute log likelihood + res = log_likelihood(test_cov, self.get_precision()) + + return res + + def error_norm(self, comp_cov, norm="frobenius", scaling=True, squared=True): + """Compute the Mean Squared Error between two covariance estimators. + + Parameters + ---------- + comp_cov : array-like of shape (n_features, n_features) + The covariance to compare with. + + norm : {"frobenius", "spectral"}, default="frobenius" + The type of norm used to compute the error. Available error types: + - 'frobenius' (default): sqrt(tr(A^t.A)) + - 'spectral': sqrt(max(eigenvalues(A^t.A)) + where A is the error ``(comp_cov - self.covariance_)``. + + scaling : bool, default=True + If True (default), the squared error norm is divided by n_features. + If False, the squared error norm is not rescaled. + + squared : bool, default=True + Whether to compute the squared error norm or the error norm. + If True (default), the squared error norm is returned. + If False, the error norm is returned. + + Returns + ------- + result : float + The Mean Squared Error (in the sense of the Frobenius norm) between + `self` and `comp_cov` covariance estimators. + """ + # compute the error + error = comp_cov - self.covariance_ + # compute the error norm + if norm == "frobenius": + squared_norm = np.sum(error**2) + elif norm == "spectral": + squared_norm = np.amax(linalg.svdvals(np.dot(error.T, error))) + else: + raise NotImplementedError( + "Only spectral and frobenius norms are implemented" + ) + # optionally scale the error norm + if scaling: + squared_norm = squared_norm / error.shape[0] + # finally get either the squared norm or the norm + if squared: + result = squared_norm + else: + result = np.sqrt(squared_norm) + + return result + + def mahalanobis(self, X): + """Compute the squared Mahalanobis distances of given observations. + + For a detailed example of how outliers affects the Mahalanobis distance, + see :ref:`sphx_glr_auto_examples_covariance_plot_mahalanobis_distances.py`. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The observations, the Mahalanobis distances of the which we + compute. Observations are assumed to be drawn from the same + distribution than the data used in fit. + + Returns + ------- + dist : ndarray of shape (n_samples,) + Squared Mahalanobis distances of the observations. + """ + X = validate_data(self, X, reset=False) + + precision = self.get_precision() + with config_context(assume_finite=True): + # compute mahalanobis distances + dist = pairwise_distances( + X, self.location_[np.newaxis, :], metric="mahalanobis", VI=precision + ) + + return np.reshape(dist, (len(X),)) ** 2 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_graph_lasso.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_graph_lasso.py new file mode 100644 index 0000000000000000000000000000000000000000..e94663120216dbeab7f8edd963554b9653e58221 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_graph_lasso.py @@ -0,0 +1,1145 @@ +"""GraphicalLasso: sparse inverse covariance estimation with an l1-penalized +estimator. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import operator +import sys +import time +import warnings +from numbers import Integral, Real + +import numpy as np +from scipy import linalg + +from ..base import _fit_context +from ..exceptions import ConvergenceWarning + +# mypy error: Module 'sklearn.linear_model' has no attribute '_cd_fast' +from ..linear_model import _cd_fast as cd_fast # type: ignore[attr-defined] +from ..linear_model import lars_path_gram +from ..model_selection import check_cv, cross_val_score +from ..utils import Bunch +from ..utils._param_validation import Interval, StrOptions, validate_params +from ..utils.metadata_routing import ( + MetadataRouter, + MethodMapping, + _raise_for_params, + _routing_enabled, + process_routing, +) +from ..utils.parallel import Parallel, delayed +from ..utils.validation import ( + _is_arraylike_not_scalar, + check_random_state, + check_scalar, + validate_data, +) +from . import EmpiricalCovariance, empirical_covariance, log_likelihood + + +# Helper functions to compute the objective and dual objective functions +# of the l1-penalized estimator +def _objective(mle, precision_, alpha): + """Evaluation of the graphical-lasso objective function + + the objective function is made of a shifted scaled version of the + normalized log-likelihood (i.e. its empirical mean over the samples) and a + penalisation term to promote sparsity + """ + p = precision_.shape[0] + cost = -2.0 * log_likelihood(mle, precision_) + p * np.log(2 * np.pi) + cost += alpha * (np.abs(precision_).sum() - np.abs(np.diag(precision_)).sum()) + return cost + + +def _dual_gap(emp_cov, precision_, alpha): + """Expression of the dual gap convergence criterion + + The specific definition is given in Duchi "Projected Subgradient Methods + for Learning Sparse Gaussians". + """ + gap = np.sum(emp_cov * precision_) + gap -= precision_.shape[0] + gap += alpha * (np.abs(precision_).sum() - np.abs(np.diag(precision_)).sum()) + return gap + + +# The g-lasso algorithm +def _graphical_lasso( + emp_cov, + alpha, + *, + cov_init=None, + mode="cd", + tol=1e-4, + enet_tol=1e-4, + max_iter=100, + verbose=False, + eps=np.finfo(np.float64).eps, +): + _, n_features = emp_cov.shape + if alpha == 0: + # Early return without regularization + precision_ = linalg.inv(emp_cov) + cost = -2.0 * log_likelihood(emp_cov, precision_) + cost += n_features * np.log(2 * np.pi) + d_gap = np.sum(emp_cov * precision_) - n_features + return emp_cov, precision_, (cost, d_gap), 0 + + if cov_init is None: + covariance_ = emp_cov.copy() + else: + covariance_ = cov_init.copy() + # As a trivial regularization (Tikhonov like), we scale down the + # off-diagonal coefficients of our starting point: This is needed, as + # in the cross-validation the cov_init can easily be + # ill-conditioned, and the CV loop blows. Beside, this takes + # conservative stand-point on the initial conditions, and it tends to + # make the convergence go faster. + covariance_ *= 0.95 + diagonal = emp_cov.flat[:: n_features + 1] + covariance_.flat[:: n_features + 1] = diagonal + precision_ = linalg.pinvh(covariance_) + + indices = np.arange(n_features) + i = 0 # initialize the counter to be robust to `max_iter=0` + costs = list() + # The different l1 regression solver have different numerical errors + if mode == "cd": + errors = dict(over="raise", invalid="ignore") + else: + errors = dict(invalid="raise") + try: + # be robust to the max_iter=0 edge case, see: + # https://github.com/scikit-learn/scikit-learn/issues/4134 + d_gap = np.inf + # set a sub_covariance buffer + sub_covariance = np.copy(covariance_[1:, 1:], order="C") + for i in range(max_iter): + for idx in range(n_features): + # To keep the contiguous matrix `sub_covariance` equal to + # covariance_[indices != idx].T[indices != idx] + # we only need to update 1 column and 1 line when idx changes + if idx > 0: + di = idx - 1 + sub_covariance[di] = covariance_[di][indices != idx] + sub_covariance[:, di] = covariance_[:, di][indices != idx] + else: + sub_covariance[:] = covariance_[1:, 1:] + row = emp_cov[idx, indices != idx] + with np.errstate(**errors): + if mode == "cd": + # Use coordinate descent + coefs = -( + precision_[indices != idx, idx] + / (precision_[idx, idx] + 1000 * eps) + ) + coefs, _, _, _ = cd_fast.enet_coordinate_descent_gram( + coefs, + alpha, + 0, + sub_covariance, + row, + row, + max_iter, + enet_tol, + check_random_state(None), + False, + ) + else: # mode == "lars" + _, _, coefs = lars_path_gram( + Xy=row, + Gram=sub_covariance, + n_samples=row.size, + alpha_min=alpha / (n_features - 1), + copy_Gram=True, + eps=eps, + method="lars", + return_path=False, + ) + # Update the precision matrix + precision_[idx, idx] = 1.0 / ( + covariance_[idx, idx] + - np.dot(covariance_[indices != idx, idx], coefs) + ) + precision_[indices != idx, idx] = -precision_[idx, idx] * coefs + precision_[idx, indices != idx] = -precision_[idx, idx] * coefs + coefs = np.dot(sub_covariance, coefs) + covariance_[idx, indices != idx] = coefs + covariance_[indices != idx, idx] = coefs + if not np.isfinite(precision_.sum()): + raise FloatingPointError( + "The system is too ill-conditioned for this solver" + ) + d_gap = _dual_gap(emp_cov, precision_, alpha) + cost = _objective(emp_cov, precision_, alpha) + if verbose: + print( + "[graphical_lasso] Iteration % 3i, cost % 3.2e, dual gap %.3e" + % (i, cost, d_gap) + ) + costs.append((cost, d_gap)) + if np.abs(d_gap) < tol: + break + if not np.isfinite(cost) and i > 0: + raise FloatingPointError( + "Non SPD result: the system is too ill-conditioned for this solver" + ) + else: + warnings.warn( + "graphical_lasso: did not converge after %i iteration: dual gap: %.3e" + % (max_iter, d_gap), + ConvergenceWarning, + ) + except FloatingPointError as e: + e.args = (e.args[0] + ". The system is too ill-conditioned for this solver",) + raise e + + return covariance_, precision_, costs, i + 1 + + +def alpha_max(emp_cov): + """Find the maximum alpha for which there are some non-zeros off-diagonal. + + Parameters + ---------- + emp_cov : ndarray of shape (n_features, n_features) + The sample covariance matrix. + + Notes + ----- + This results from the bound for the all the Lasso that are solved + in GraphicalLasso: each time, the row of cov corresponds to Xy. As the + bound for alpha is given by `max(abs(Xy))`, the result follows. + """ + A = np.copy(emp_cov) + A.flat[:: A.shape[0] + 1] = 0 + return np.max(np.abs(A)) + + +@validate_params( + { + "emp_cov": ["array-like"], + "return_costs": ["boolean"], + "return_n_iter": ["boolean"], + }, + prefer_skip_nested_validation=False, +) +def graphical_lasso( + emp_cov, + alpha, + *, + mode="cd", + tol=1e-4, + enet_tol=1e-4, + max_iter=100, + verbose=False, + return_costs=False, + eps=np.finfo(np.float64).eps, + return_n_iter=False, +): + """L1-penalized covariance estimator. + + Read more in the :ref:`User Guide `. + + .. versionchanged:: v0.20 + graph_lasso has been renamed to graphical_lasso + + Parameters + ---------- + emp_cov : array-like of shape (n_features, n_features) + Empirical covariance from which to compute the covariance estimate. + + alpha : float + The regularization parameter: the higher alpha, the more + regularization, the sparser the inverse covariance. + Range is (0, inf]. + + mode : {'cd', 'lars'}, default='cd' + The Lasso solver to use: coordinate descent or LARS. Use LARS for + very sparse underlying graphs, where p > n. Elsewhere prefer cd + which is more numerically stable. + + tol : float, default=1e-4 + The tolerance to declare convergence: if the dual gap goes below + this value, iterations are stopped. Range is (0, inf]. + + enet_tol : float, default=1e-4 + The tolerance for the elastic net solver used to calculate the descent + direction. This parameter controls the accuracy of the search direction + for a given column update, not of the overall parameter estimate. Only + used for mode='cd'. Range is (0, inf]. + + max_iter : int, default=100 + The maximum number of iterations. + + verbose : bool, default=False + If verbose is True, the objective function and dual gap are + printed at each iteration. + + return_costs : bool, default=False + If return_costs is True, the objective function and dual gap + at each iteration are returned. + + eps : float, default=eps + The machine-precision regularization in the computation of the + Cholesky diagonal factors. Increase this for very ill-conditioned + systems. Default is `np.finfo(np.float64).eps`. + + return_n_iter : bool, default=False + Whether or not to return the number of iterations. + + Returns + ------- + covariance : ndarray of shape (n_features, n_features) + The estimated covariance matrix. + + precision : ndarray of shape (n_features, n_features) + The estimated (sparse) precision matrix. + + costs : list of (objective, dual_gap) pairs + The list of values of the objective function and the dual gap at + each iteration. Returned only if return_costs is True. + + n_iter : int + Number of iterations. Returned only if `return_n_iter` is set to True. + + See Also + -------- + GraphicalLasso : Sparse inverse covariance estimation + with an l1-penalized estimator. + GraphicalLassoCV : Sparse inverse covariance with + cross-validated choice of the l1 penalty. + + Notes + ----- + The algorithm employed to solve this problem is the GLasso algorithm, + from the Friedman 2008 Biostatistics paper. It is the same algorithm + as in the R `glasso` package. + + One possible difference with the `glasso` R package is that the + diagonal coefficients are not penalized. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.datasets import make_sparse_spd_matrix + >>> from sklearn.covariance import empirical_covariance, graphical_lasso + >>> true_cov = make_sparse_spd_matrix(n_dim=3,random_state=42) + >>> rng = np.random.RandomState(42) + >>> X = rng.multivariate_normal(mean=np.zeros(3), cov=true_cov, size=3) + >>> emp_cov = empirical_covariance(X, assume_centered=True) + >>> emp_cov, _ = graphical_lasso(emp_cov, alpha=0.05) + >>> emp_cov + array([[ 1.687, 0.212, -0.209], + [ 0.212, 0.221, -0.0817], + [-0.209, -0.0817, 0.232]]) + """ + model = GraphicalLasso( + alpha=alpha, + mode=mode, + covariance="precomputed", + tol=tol, + enet_tol=enet_tol, + max_iter=max_iter, + verbose=verbose, + eps=eps, + assume_centered=True, + ).fit(emp_cov) + + output = [model.covariance_, model.precision_] + if return_costs: + output.append(model.costs_) + if return_n_iter: + output.append(model.n_iter_) + return tuple(output) + + +class BaseGraphicalLasso(EmpiricalCovariance): + _parameter_constraints: dict = { + **EmpiricalCovariance._parameter_constraints, + "tol": [Interval(Real, 0, None, closed="right")], + "enet_tol": [Interval(Real, 0, None, closed="right")], + "max_iter": [Interval(Integral, 0, None, closed="left")], + "mode": [StrOptions({"cd", "lars"})], + "verbose": ["verbose"], + "eps": [Interval(Real, 0, None, closed="both")], + } + _parameter_constraints.pop("store_precision") + + def __init__( + self, + tol=1e-4, + enet_tol=1e-4, + max_iter=100, + mode="cd", + verbose=False, + eps=np.finfo(np.float64).eps, + assume_centered=False, + ): + super().__init__(assume_centered=assume_centered) + self.tol = tol + self.enet_tol = enet_tol + self.max_iter = max_iter + self.mode = mode + self.verbose = verbose + self.eps = eps + + +class GraphicalLasso(BaseGraphicalLasso): + """Sparse inverse covariance estimation with an l1-penalized estimator. + + For a usage example see + :ref:`sphx_glr_auto_examples_applications_plot_stock_market.py`. + + Read more in the :ref:`User Guide `. + + .. versionchanged:: v0.20 + GraphLasso has been renamed to GraphicalLasso + + Parameters + ---------- + alpha : float, default=0.01 + The regularization parameter: the higher alpha, the more + regularization, the sparser the inverse covariance. + Range is (0, inf]. + + mode : {'cd', 'lars'}, default='cd' + The Lasso solver to use: coordinate descent or LARS. Use LARS for + very sparse underlying graphs, where p > n. Elsewhere prefer cd + which is more numerically stable. + + covariance : "precomputed", default=None + If covariance is "precomputed", the input data in `fit` is assumed + to be the covariance matrix. If `None`, the empirical covariance + is estimated from the data `X`. + + .. versionadded:: 1.3 + + tol : float, default=1e-4 + The tolerance to declare convergence: if the dual gap goes below + this value, iterations are stopped. Range is (0, inf]. + + enet_tol : float, default=1e-4 + The tolerance for the elastic net solver used to calculate the descent + direction. This parameter controls the accuracy of the search direction + for a given column update, not of the overall parameter estimate. Only + used for mode='cd'. Range is (0, inf]. + + max_iter : int, default=100 + The maximum number of iterations. + + verbose : bool, default=False + If verbose is True, the objective function and dual gap are + plotted at each iteration. + + eps : float, default=eps + The machine-precision regularization in the computation of the + Cholesky diagonal factors. Increase this for very ill-conditioned + systems. Default is `np.finfo(np.float64).eps`. + + .. versionadded:: 1.3 + + assume_centered : bool, default=False + If True, data are not centered before computation. + Useful when working with data whose mean is almost, but not exactly + zero. + If False, data are centered before computation. + + Attributes + ---------- + location_ : ndarray of shape (n_features,) + Estimated location, i.e. the estimated mean. + + covariance_ : ndarray of shape (n_features, n_features) + Estimated covariance matrix + + precision_ : ndarray of shape (n_features, n_features) + Estimated pseudo inverse matrix. + + n_iter_ : int + Number of iterations run. + + costs_ : list of (objective, dual_gap) pairs + The list of values of the objective function and the dual gap at + each iteration. Returned only if return_costs is True. + + .. versionadded:: 1.3 + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + graphical_lasso : L1-penalized covariance estimator. + GraphicalLassoCV : Sparse inverse covariance with + cross-validated choice of the l1 penalty. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.covariance import GraphicalLasso + >>> true_cov = np.array([[0.8, 0.0, 0.2, 0.0], + ... [0.0, 0.4, 0.0, 0.0], + ... [0.2, 0.0, 0.3, 0.1], + ... [0.0, 0.0, 0.1, 0.7]]) + >>> np.random.seed(0) + >>> X = np.random.multivariate_normal(mean=[0, 0, 0, 0], + ... cov=true_cov, + ... size=200) + >>> cov = GraphicalLasso().fit(X) + >>> np.around(cov.covariance_, decimals=3) + array([[0.816, 0.049, 0.218, 0.019], + [0.049, 0.364, 0.017, 0.034], + [0.218, 0.017, 0.322, 0.093], + [0.019, 0.034, 0.093, 0.69 ]]) + >>> np.around(cov.location_, decimals=3) + array([0.073, 0.04 , 0.038, 0.143]) + """ + + _parameter_constraints: dict = { + **BaseGraphicalLasso._parameter_constraints, + "alpha": [Interval(Real, 0, None, closed="both")], + "covariance": [StrOptions({"precomputed"}), None], + } + + def __init__( + self, + alpha=0.01, + *, + mode="cd", + covariance=None, + tol=1e-4, + enet_tol=1e-4, + max_iter=100, + verbose=False, + eps=np.finfo(np.float64).eps, + assume_centered=False, + ): + super().__init__( + tol=tol, + enet_tol=enet_tol, + max_iter=max_iter, + mode=mode, + verbose=verbose, + eps=eps, + assume_centered=assume_centered, + ) + self.alpha = alpha + self.covariance = covariance + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the GraphicalLasso model to X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Data from which to compute the covariance estimate. + + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + self : object + Returns the instance itself. + """ + # Covariance does not make sense for a single feature + X = validate_data(self, X, ensure_min_features=2, ensure_min_samples=2) + + if self.covariance == "precomputed": + emp_cov = X.copy() + self.location_ = np.zeros(X.shape[1]) + else: + emp_cov = empirical_covariance(X, assume_centered=self.assume_centered) + if self.assume_centered: + self.location_ = np.zeros(X.shape[1]) + else: + self.location_ = X.mean(0) + + self.covariance_, self.precision_, self.costs_, self.n_iter_ = _graphical_lasso( + emp_cov, + alpha=self.alpha, + cov_init=None, + mode=self.mode, + tol=self.tol, + enet_tol=self.enet_tol, + max_iter=self.max_iter, + verbose=self.verbose, + eps=self.eps, + ) + return self + + +# Cross-validation with GraphicalLasso +def graphical_lasso_path( + X, + alphas, + cov_init=None, + X_test=None, + mode="cd", + tol=1e-4, + enet_tol=1e-4, + max_iter=100, + verbose=False, + eps=np.finfo(np.float64).eps, +): + """l1-penalized covariance estimator along a path of decreasing alphas + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + X : ndarray of shape (n_samples, n_features) + Data from which to compute the covariance estimate. + + alphas : array-like of shape (n_alphas,) + The list of regularization parameters, decreasing order. + + cov_init : array of shape (n_features, n_features), default=None + The initial guess for the covariance. + + X_test : array of shape (n_test_samples, n_features), default=None + Optional test matrix to measure generalisation error. + + mode : {'cd', 'lars'}, default='cd' + The Lasso solver to use: coordinate descent or LARS. Use LARS for + very sparse underlying graphs, where p > n. Elsewhere prefer cd + which is more numerically stable. + + tol : float, default=1e-4 + The tolerance to declare convergence: if the dual gap goes below + this value, iterations are stopped. The tolerance must be a positive + number. + + enet_tol : float, default=1e-4 + The tolerance for the elastic net solver used to calculate the descent + direction. This parameter controls the accuracy of the search direction + for a given column update, not of the overall parameter estimate. Only + used for mode='cd'. The tolerance must be a positive number. + + max_iter : int, default=100 + The maximum number of iterations. This parameter should be a strictly + positive integer. + + verbose : int or bool, default=False + The higher the verbosity flag, the more information is printed + during the fitting. + + eps : float, default=eps + The machine-precision regularization in the computation of the + Cholesky diagonal factors. Increase this for very ill-conditioned + systems. Default is `np.finfo(np.float64).eps`. + + .. versionadded:: 1.3 + + Returns + ------- + covariances_ : list of shape (n_alphas,) of ndarray of shape \ + (n_features, n_features) + The estimated covariance matrices. + + precisions_ : list of shape (n_alphas,) of ndarray of shape \ + (n_features, n_features) + The estimated (sparse) precision matrices. + + scores_ : list of shape (n_alphas,), dtype=float + The generalisation error (log-likelihood) on the test data. + Returned only if test data is passed. + """ + inner_verbose = max(0, verbose - 1) + emp_cov = empirical_covariance(X) + if cov_init is None: + covariance_ = emp_cov.copy() + else: + covariance_ = cov_init + covariances_ = list() + precisions_ = list() + scores_ = list() + if X_test is not None: + test_emp_cov = empirical_covariance(X_test) + + for alpha in alphas: + try: + # Capture the errors, and move on + covariance_, precision_, _, _ = _graphical_lasso( + emp_cov, + alpha=alpha, + cov_init=covariance_, + mode=mode, + tol=tol, + enet_tol=enet_tol, + max_iter=max_iter, + verbose=inner_verbose, + eps=eps, + ) + covariances_.append(covariance_) + precisions_.append(precision_) + if X_test is not None: + this_score = log_likelihood(test_emp_cov, precision_) + except FloatingPointError: + this_score = -np.inf + covariances_.append(np.nan) + precisions_.append(np.nan) + if X_test is not None: + if not np.isfinite(this_score): + this_score = -np.inf + scores_.append(this_score) + if verbose == 1: + sys.stderr.write(".") + elif verbose > 1: + if X_test is not None: + print( + "[graphical_lasso_path] alpha: %.2e, score: %.2e" + % (alpha, this_score) + ) + else: + print("[graphical_lasso_path] alpha: %.2e" % alpha) + if X_test is not None: + return covariances_, precisions_, scores_ + return covariances_, precisions_ + + +class GraphicalLassoCV(BaseGraphicalLasso): + """Sparse inverse covariance w/ cross-validated choice of the l1 penalty. + + See glossary entry for :term:`cross-validation estimator`. + + Read more in the :ref:`User Guide `. + + .. versionchanged:: v0.20 + GraphLassoCV has been renamed to GraphicalLassoCV + + Parameters + ---------- + alphas : int or array-like of shape (n_alphas,), dtype=float, default=4 + If an integer is given, it fixes the number of points on the + grids of alpha to be used. If a list is given, it gives the + grid to be used. See the notes in the class docstring for + more details. Range is [1, inf) for an integer. + Range is (0, inf] for an array-like of floats. + + n_refinements : int, default=4 + The number of times the grid is refined. Not used if explicit + values of alphas are passed. Range is [1, inf). + + cv : int, cross-validation generator or iterable, default=None + Determines the cross-validation splitting strategy. + Possible inputs for cv are: + + - None, to use the default 5-fold cross-validation, + - integer, to specify the number of folds. + - :term:`CV splitter`, + - An iterable yielding (train, test) splits as arrays of indices. + + For integer/None inputs :class:`~sklearn.model_selection.KFold` is used. + + Refer :ref:`User Guide ` for the various + cross-validation strategies that can be used here. + + .. versionchanged:: 0.20 + ``cv`` default value if None changed from 3-fold to 5-fold. + + tol : float, default=1e-4 + The tolerance to declare convergence: if the dual gap goes below + this value, iterations are stopped. Range is (0, inf]. + + enet_tol : float, default=1e-4 + The tolerance for the elastic net solver used to calculate the descent + direction. This parameter controls the accuracy of the search direction + for a given column update, not of the overall parameter estimate. Only + used for mode='cd'. Range is (0, inf]. + + max_iter : int, default=100 + Maximum number of iterations. + + mode : {'cd', 'lars'}, default='cd' + The Lasso solver to use: coordinate descent or LARS. Use LARS for + very sparse underlying graphs, where number of features is greater + than number of samples. Elsewhere prefer cd which is more numerically + stable. + + n_jobs : int, default=None + Number of jobs to run in parallel. + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + .. versionchanged:: v0.20 + `n_jobs` default changed from 1 to None + + verbose : bool, default=False + If verbose is True, the objective function and duality gap are + printed at each iteration. + + eps : float, default=eps + The machine-precision regularization in the computation of the + Cholesky diagonal factors. Increase this for very ill-conditioned + systems. Default is `np.finfo(np.float64).eps`. + + .. versionadded:: 1.3 + + assume_centered : bool, default=False + If True, data are not centered before computation. + Useful when working with data whose mean is almost, but not exactly + zero. + If False, data are centered before computation. + + Attributes + ---------- + location_ : ndarray of shape (n_features,) + Estimated location, i.e. the estimated mean. + + covariance_ : ndarray of shape (n_features, n_features) + Estimated covariance matrix. + + precision_ : ndarray of shape (n_features, n_features) + Estimated precision matrix (inverse covariance). + + costs_ : list of (objective, dual_gap) pairs + The list of values of the objective function and the dual gap at + each iteration. Returned only if return_costs is True. + + .. versionadded:: 1.3 + + alpha_ : float + Penalization parameter selected. + + cv_results_ : dict of ndarrays + A dict with keys: + + alphas : ndarray of shape (n_alphas,) + All penalization parameters explored. + + split(k)_test_score : ndarray of shape (n_alphas,) + Log-likelihood score on left-out data across (k)th fold. + + .. versionadded:: 1.0 + + mean_test_score : ndarray of shape (n_alphas,) + Mean of scores over the folds. + + .. versionadded:: 1.0 + + std_test_score : ndarray of shape (n_alphas,) + Standard deviation of scores over the folds. + + .. versionadded:: 1.0 + + n_iter_ : int + Number of iterations run for the optimal alpha. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + graphical_lasso : L1-penalized covariance estimator. + GraphicalLasso : Sparse inverse covariance estimation + with an l1-penalized estimator. + + Notes + ----- + The search for the optimal penalization parameter (`alpha`) is done on an + iteratively refined grid: first the cross-validated scores on a grid are + computed, then a new refined grid is centered around the maximum, and so + on. + + One of the challenges which is faced here is that the solvers can + fail to converge to a well-conditioned estimate. The corresponding + values of `alpha` then come out as missing values, but the optimum may + be close to these missing values. + + In `fit`, once the best parameter `alpha` is found through + cross-validation, the model is fit again using the entire training set. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.covariance import GraphicalLassoCV + >>> true_cov = np.array([[0.8, 0.0, 0.2, 0.0], + ... [0.0, 0.4, 0.0, 0.0], + ... [0.2, 0.0, 0.3, 0.1], + ... [0.0, 0.0, 0.1, 0.7]]) + >>> np.random.seed(0) + >>> X = np.random.multivariate_normal(mean=[0, 0, 0, 0], + ... cov=true_cov, + ... size=200) + >>> cov = GraphicalLassoCV().fit(X) + >>> np.around(cov.covariance_, decimals=3) + array([[0.816, 0.051, 0.22 , 0.017], + [0.051, 0.364, 0.018, 0.036], + [0.22 , 0.018, 0.322, 0.094], + [0.017, 0.036, 0.094, 0.69 ]]) + >>> np.around(cov.location_, decimals=3) + array([0.073, 0.04 , 0.038, 0.143]) + + For an example comparing :class:`sklearn.covariance.GraphicalLassoCV`, + :func:`sklearn.covariance.ledoit_wolf` shrinkage and the empirical covariance + on high-dimensional gaussian data, see + :ref:`sphx_glr_auto_examples_covariance_plot_sparse_cov.py`. + """ + + _parameter_constraints: dict = { + **BaseGraphicalLasso._parameter_constraints, + "alphas": [Interval(Integral, 0, None, closed="left"), "array-like"], + "n_refinements": [Interval(Integral, 1, None, closed="left")], + "cv": ["cv_object"], + "n_jobs": [Integral, None], + } + + def __init__( + self, + *, + alphas=4, + n_refinements=4, + cv=None, + tol=1e-4, + enet_tol=1e-4, + max_iter=100, + mode="cd", + n_jobs=None, + verbose=False, + eps=np.finfo(np.float64).eps, + assume_centered=False, + ): + super().__init__( + tol=tol, + enet_tol=enet_tol, + max_iter=max_iter, + mode=mode, + verbose=verbose, + eps=eps, + assume_centered=assume_centered, + ) + self.alphas = alphas + self.n_refinements = n_refinements + self.cv = cv + self.n_jobs = n_jobs + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None, **params): + """Fit the GraphicalLasso covariance model to X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Data from which to compute the covariance estimate. + + y : Ignored + Not used, present for API consistency by convention. + + **params : dict, default=None + Parameters to be passed to the CV splitter and the + cross_val_score function. + + .. versionadded:: 1.5 + Only available if `enable_metadata_routing=True`, + which can be set by using + ``sklearn.set_config(enable_metadata_routing=True)``. + See :ref:`Metadata Routing User Guide ` for + more details. + + Returns + ------- + self : object + Returns the instance itself. + """ + # Covariance does not make sense for a single feature + _raise_for_params(params, self, "fit") + + X = validate_data(self, X, ensure_min_features=2) + if self.assume_centered: + self.location_ = np.zeros(X.shape[1]) + else: + self.location_ = X.mean(0) + emp_cov = empirical_covariance(X, assume_centered=self.assume_centered) + + cv = check_cv(self.cv, y, classifier=False) + + # List of (alpha, scores, covs) + path = list() + n_alphas = self.alphas + inner_verbose = max(0, self.verbose - 1) + + if _is_arraylike_not_scalar(n_alphas): + for alpha in self.alphas: + check_scalar( + alpha, + "alpha", + Real, + min_val=0, + max_val=np.inf, + include_boundaries="right", + ) + alphas = self.alphas + n_refinements = 1 + else: + n_refinements = self.n_refinements + alpha_1 = alpha_max(emp_cov) + alpha_0 = 1e-2 * alpha_1 + alphas = np.logspace(np.log10(alpha_0), np.log10(alpha_1), n_alphas)[::-1] + + if _routing_enabled(): + routed_params = process_routing(self, "fit", **params) + else: + routed_params = Bunch(splitter=Bunch(split={})) + + t0 = time.time() + for i in range(n_refinements): + with warnings.catch_warnings(): + # No need to see the convergence warnings on this grid: + # they will always be points that will not converge + # during the cross-validation + warnings.simplefilter("ignore", ConvergenceWarning) + # Compute the cross-validated loss on the current grid + + # NOTE: Warm-restarting graphical_lasso_path has been tried, + # and this did not allow to gain anything + # (same execution time with or without). + this_path = Parallel(n_jobs=self.n_jobs, verbose=self.verbose)( + delayed(graphical_lasso_path)( + X[train], + alphas=alphas, + X_test=X[test], + mode=self.mode, + tol=self.tol, + enet_tol=self.enet_tol, + max_iter=int(0.1 * self.max_iter), + verbose=inner_verbose, + eps=self.eps, + ) + for train, test in cv.split(X, y, **routed_params.splitter.split) + ) + + # Little danse to transform the list in what we need + covs, _, scores = zip(*this_path) + covs = zip(*covs) + scores = zip(*scores) + path.extend(zip(alphas, scores, covs)) + path = sorted(path, key=operator.itemgetter(0), reverse=True) + + # Find the maximum (avoid using built in 'max' function to + # have a fully-reproducible selection of the smallest alpha + # in case of equality) + best_score = -np.inf + last_finite_idx = 0 + for index, (alpha, scores, _) in enumerate(path): + this_score = np.mean(scores) + if this_score >= 0.1 / np.finfo(np.float64).eps: + this_score = np.nan + if np.isfinite(this_score): + last_finite_idx = index + if this_score >= best_score: + best_score = this_score + best_index = index + + # Refine the grid + if best_index == 0: + # We do not need to go back: we have chosen + # the highest value of alpha for which there are + # non-zero coefficients + alpha_1 = path[0][0] + alpha_0 = path[1][0] + elif best_index == last_finite_idx and not best_index == len(path) - 1: + # We have non-converged models on the upper bound of the + # grid, we need to refine the grid there + alpha_1 = path[best_index][0] + alpha_0 = path[best_index + 1][0] + elif best_index == len(path) - 1: + alpha_1 = path[best_index][0] + alpha_0 = 0.01 * path[best_index][0] + else: + alpha_1 = path[best_index - 1][0] + alpha_0 = path[best_index + 1][0] + + if not _is_arraylike_not_scalar(n_alphas): + alphas = np.logspace(np.log10(alpha_1), np.log10(alpha_0), n_alphas + 2) + alphas = alphas[1:-1] + + if self.verbose and n_refinements > 1: + print( + "[GraphicalLassoCV] Done refinement % 2i out of %i: % 3is" + % (i + 1, n_refinements, time.time() - t0) + ) + + path = list(zip(*path)) + grid_scores = list(path[1]) + alphas = list(path[0]) + # Finally, compute the score with alpha = 0 + alphas.append(0) + grid_scores.append( + cross_val_score( + EmpiricalCovariance(), + X, + cv=cv, + n_jobs=self.n_jobs, + verbose=inner_verbose, + params=params, + ) + ) + grid_scores = np.array(grid_scores) + + self.cv_results_ = {"alphas": np.array(alphas)} + + for i in range(grid_scores.shape[1]): + self.cv_results_[f"split{i}_test_score"] = grid_scores[:, i] + + self.cv_results_["mean_test_score"] = np.mean(grid_scores, axis=1) + self.cv_results_["std_test_score"] = np.std(grid_scores, axis=1) + + best_alpha = alphas[best_index] + self.alpha_ = best_alpha + + # Finally fit the model with the selected alpha + self.covariance_, self.precision_, self.costs_, self.n_iter_ = _graphical_lasso( + emp_cov, + alpha=best_alpha, + mode=self.mode, + tol=self.tol, + enet_tol=self.enet_tol, + max_iter=self.max_iter, + verbose=inner_verbose, + eps=self.eps, + ) + return self + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + .. versionadded:: 1.5 + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + router = MetadataRouter(owner=self.__class__.__name__).add( + splitter=check_cv(self.cv), + method_mapping=MethodMapping().add(callee="split", caller="fit"), + ) + return router diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_robust_covariance.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_robust_covariance.py new file mode 100644 index 0000000000000000000000000000000000000000..81fc194c6e410da364db9eba432e7201e6ab44cb --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_robust_covariance.py @@ -0,0 +1,874 @@ +""" +Robust location and covariance estimators. + +Here are implemented estimators that are resistant to outliers. + +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from numbers import Integral, Real + +import numpy as np +from scipy import linalg +from scipy.stats import chi2 + +from ..base import _fit_context +from ..utils import check_array, check_random_state +from ..utils._param_validation import Interval +from ..utils.extmath import fast_logdet +from ..utils.validation import validate_data +from ._empirical_covariance import EmpiricalCovariance, empirical_covariance + + +# Minimum Covariance Determinant +# Implementing of an algorithm by Rousseeuw & Van Driessen described in +# (A Fast Algorithm for the Minimum Covariance Determinant Estimator, +# 1999, American Statistical Association and the American Society +# for Quality, TECHNOMETRICS) +# XXX Is this really a public function? It's not listed in the docs or +# exported by sklearn.covariance. Deprecate? +def c_step( + X, + n_support, + remaining_iterations=30, + initial_estimates=None, + verbose=False, + cov_computation_method=empirical_covariance, + random_state=None, +): + """C_step procedure described in [Rouseeuw1984]_ aiming at computing MCD. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Data set in which we look for the n_support observations whose + scatter matrix has minimum determinant. + + n_support : int + Number of observations to compute the robust estimates of location + and covariance from. This parameter must be greater than + `n_samples / 2`. + + remaining_iterations : int, default=30 + Number of iterations to perform. + According to [Rouseeuw1999]_, two iterations are sufficient to get + close to the minimum, and we never need more than 30 to reach + convergence. + + initial_estimates : tuple of shape (2,), default=None + Initial estimates of location and shape from which to run the c_step + procedure: + - initial_estimates[0]: an initial location estimate + - initial_estimates[1]: an initial covariance estimate + + verbose : bool, default=False + Verbose mode. + + cov_computation_method : callable, \ + default=:func:`sklearn.covariance.empirical_covariance` + The function which will be used to compute the covariance. + Must return array of shape (n_features, n_features). + + random_state : int, RandomState instance or None, default=None + Determines the pseudo random number generator for shuffling the data. + Pass an int for reproducible results across multiple function calls. + See :term:`Glossary `. + + Returns + ------- + location : ndarray of shape (n_features,) + Robust location estimates. + + covariance : ndarray of shape (n_features, n_features) + Robust covariance estimates. + + support : ndarray of shape (n_samples,) + A mask for the `n_support` observations whose scatter matrix has + minimum determinant. + + References + ---------- + .. [Rouseeuw1999] A Fast Algorithm for the Minimum Covariance Determinant + Estimator, 1999, American Statistical Association and the American + Society for Quality, TECHNOMETRICS + """ + X = np.asarray(X) + random_state = check_random_state(random_state) + return _c_step( + X, + n_support, + remaining_iterations=remaining_iterations, + initial_estimates=initial_estimates, + verbose=verbose, + cov_computation_method=cov_computation_method, + random_state=random_state, + ) + + +def _c_step( + X, + n_support, + random_state, + remaining_iterations=30, + initial_estimates=None, + verbose=False, + cov_computation_method=empirical_covariance, +): + n_samples, n_features = X.shape + dist = np.inf + + # Initialisation + if initial_estimates is None: + # compute initial robust estimates from a random subset + support_indices = random_state.permutation(n_samples)[:n_support] + else: + # get initial robust estimates from the function parameters + location = initial_estimates[0] + covariance = initial_estimates[1] + # run a special iteration for that case (to get an initial support_indices) + precision = linalg.pinvh(covariance) + X_centered = X - location + dist = (np.dot(X_centered, precision) * X_centered).sum(1) + # compute new estimates + support_indices = np.argpartition(dist, n_support - 1)[:n_support] + + X_support = X[support_indices] + location = X_support.mean(0) + covariance = cov_computation_method(X_support) + + # Iterative procedure for Minimum Covariance Determinant computation + det = fast_logdet(covariance) + # If the data already has singular covariance, calculate the precision, + # as the loop below will not be entered. + if np.isinf(det): + precision = linalg.pinvh(covariance) + + previous_det = np.inf + while det < previous_det and remaining_iterations > 0 and not np.isinf(det): + # save old estimates values + previous_location = location + previous_covariance = covariance + previous_det = det + previous_support_indices = support_indices + # compute a new support_indices from the full data set mahalanobis distances + precision = linalg.pinvh(covariance) + X_centered = X - location + dist = (np.dot(X_centered, precision) * X_centered).sum(axis=1) + # compute new estimates + support_indices = np.argpartition(dist, n_support - 1)[:n_support] + X_support = X[support_indices] + location = X_support.mean(axis=0) + covariance = cov_computation_method(X_support) + det = fast_logdet(covariance) + # update remaining iterations for early stopping + remaining_iterations -= 1 + + previous_dist = dist + dist = (np.dot(X - location, precision) * (X - location)).sum(axis=1) + # Check if best fit already found (det => 0, logdet => -inf) + if np.isinf(det): + results = location, covariance, det, support_indices, dist + # Check convergence + if np.allclose(det, previous_det): + # c_step procedure converged + if verbose: + print( + "Optimal couple (location, covariance) found before" + " ending iterations (%d left)" % (remaining_iterations) + ) + results = location, covariance, det, support_indices, dist + elif det > previous_det: + # determinant has increased (should not happen) + warnings.warn( + "Determinant has increased; this should not happen: " + "log(det) > log(previous_det) (%.15f > %.15f). " + "You may want to try with a higher value of " + "support_fraction (current value: %.3f)." + % (det, previous_det, n_support / n_samples), + RuntimeWarning, + ) + results = ( + previous_location, + previous_covariance, + previous_det, + previous_support_indices, + previous_dist, + ) + + # Check early stopping + if remaining_iterations == 0: + if verbose: + print("Maximum number of iterations reached") + results = location, covariance, det, support_indices, dist + + location, covariance, det, support_indices, dist = results + # Convert from list of indices to boolean mask. + support = np.bincount(support_indices, minlength=n_samples).astype(bool) + return location, covariance, det, support, dist + + +def select_candidates( + X, + n_support, + n_trials, + select=1, + n_iter=30, + verbose=False, + cov_computation_method=empirical_covariance, + random_state=None, +): + """Finds the best pure subset of observations to compute MCD from it. + + The purpose of this function is to find the best sets of n_support + observations with respect to a minimization of their covariance + matrix determinant. Equivalently, it removes n_samples-n_support + observations to construct what we call a pure data set (i.e. not + containing outliers). The list of the observations of the pure + data set is referred to as the `support`. + + Starting from a random support, the pure data set is found by the + c_step procedure introduced by Rousseeuw and Van Driessen in + [RV]_. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Data (sub)set in which we look for the n_support purest observations. + + n_support : int + The number of samples the pure data set must contain. + This parameter must be in the range `[(n + p + 1)/2] < n_support < n`. + + n_trials : int or tuple of shape (2,) + Number of different initial sets of observations from which to + run the algorithm. This parameter should be a strictly positive + integer. + Instead of giving a number of trials to perform, one can provide a + list of initial estimates that will be used to iteratively run + c_step procedures. In this case: + - n_trials[0]: array-like, shape (n_trials, n_features) + is the list of `n_trials` initial location estimates + - n_trials[1]: array-like, shape (n_trials, n_features, n_features) + is the list of `n_trials` initial covariances estimates + + select : int, default=1 + Number of best candidates results to return. This parameter must be + a strictly positive integer. + + n_iter : int, default=30 + Maximum number of iterations for the c_step procedure. + (2 is enough to be close to the final solution. "Never" exceeds 20). + This parameter must be a strictly positive integer. + + verbose : bool, default=False + Control the output verbosity. + + cov_computation_method : callable, \ + default=:func:`sklearn.covariance.empirical_covariance` + The function which will be used to compute the covariance. + Must return an array of shape (n_features, n_features). + + random_state : int, RandomState instance or None, default=None + Determines the pseudo random number generator for shuffling the data. + Pass an int for reproducible results across multiple function calls. + See :term:`Glossary `. + + See Also + --------- + c_step + + Returns + ------- + best_locations : ndarray of shape (select, n_features) + The `select` location estimates computed from the `select` best + supports found in the data set (`X`). + + best_covariances : ndarray of shape (select, n_features, n_features) + The `select` covariance estimates computed from the `select` + best supports found in the data set (`X`). + + best_supports : ndarray of shape (select, n_samples) + The `select` best supports found in the data set (`X`). + + References + ---------- + .. [RV] A Fast Algorithm for the Minimum Covariance Determinant + Estimator, 1999, American Statistical Association and the American + Society for Quality, TECHNOMETRICS + """ + random_state = check_random_state(random_state) + + if isinstance(n_trials, Integral): + run_from_estimates = False + elif isinstance(n_trials, tuple): + run_from_estimates = True + estimates_list = n_trials + n_trials = estimates_list[0].shape[0] + else: + raise TypeError( + "Invalid 'n_trials' parameter, expected tuple or integer, got %s (%s)" + % (n_trials, type(n_trials)) + ) + + # compute `n_trials` location and shape estimates candidates in the subset + all_estimates = [] + if not run_from_estimates: + # perform `n_trials` computations from random initial supports + for j in range(n_trials): + all_estimates.append( + _c_step( + X, + n_support, + remaining_iterations=n_iter, + verbose=verbose, + cov_computation_method=cov_computation_method, + random_state=random_state, + ) + ) + else: + # perform computations from every given initial estimates + for j in range(n_trials): + initial_estimates = (estimates_list[0][j], estimates_list[1][j]) + all_estimates.append( + _c_step( + X, + n_support, + remaining_iterations=n_iter, + initial_estimates=initial_estimates, + verbose=verbose, + cov_computation_method=cov_computation_method, + random_state=random_state, + ) + ) + all_locs_sub, all_covs_sub, all_dets_sub, all_supports_sub, all_ds_sub = zip( + *all_estimates + ) + # find the `n_best` best results among the `n_trials` ones + index_best = np.argsort(all_dets_sub)[:select] + best_locations = np.asarray(all_locs_sub)[index_best] + best_covariances = np.asarray(all_covs_sub)[index_best] + best_supports = np.asarray(all_supports_sub)[index_best] + best_ds = np.asarray(all_ds_sub)[index_best] + + return best_locations, best_covariances, best_supports, best_ds + + +def fast_mcd( + X, + support_fraction=None, + cov_computation_method=empirical_covariance, + random_state=None, +): + """Estimate the Minimum Covariance Determinant matrix. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The data matrix, with p features and n samples. + + support_fraction : float, default=None + The proportion of points to be included in the support of the raw + MCD estimate. Default is `None`, which implies that the minimum + value of `support_fraction` will be used within the algorithm: + `(n_samples + n_features + 1) / 2 * n_samples`. This parameter must be + in the range (0, 1). + + cov_computation_method : callable, \ + default=:func:`sklearn.covariance.empirical_covariance` + The function which will be used to compute the covariance. + Must return an array of shape (n_features, n_features). + + random_state : int, RandomState instance or None, default=None + Determines the pseudo random number generator for shuffling the data. + Pass an int for reproducible results across multiple function calls. + See :term:`Glossary `. + + Returns + ------- + location : ndarray of shape (n_features,) + Robust location of the data. + + covariance : ndarray of shape (n_features, n_features) + Robust covariance of the features. + + support : ndarray of shape (n_samples,), dtype=bool + A mask of the observations that have been used to compute + the robust location and covariance estimates of the data set. + + Notes + ----- + The FastMCD algorithm has been introduced by Rousseuw and Van Driessen + in "A Fast Algorithm for the Minimum Covariance Determinant Estimator, + 1999, American Statistical Association and the American Society + for Quality, TECHNOMETRICS". + The principle is to compute robust estimates and random subsets before + pooling them into a larger subsets, and finally into the full data set. + Depending on the size of the initial sample, we have one, two or three + such computation levels. + + Note that only raw estimates are returned. If one is interested in + the correction and reweighting steps described in [RouseeuwVan]_, + see the MinCovDet object. + + References + ---------- + + .. [RouseeuwVan] A Fast Algorithm for the Minimum Covariance + Determinant Estimator, 1999, American Statistical Association + and the American Society for Quality, TECHNOMETRICS + + .. [Butler1993] R. W. Butler, P. L. Davies and M. Jhun, + Asymptotics For The Minimum Covariance Determinant Estimator, + The Annals of Statistics, 1993, Vol. 21, No. 3, 1385-1400 + """ + random_state = check_random_state(random_state) + + X = check_array(X, ensure_min_samples=2, estimator="fast_mcd") + n_samples, n_features = X.shape + + # minimum breakdown value + if support_fraction is None: + n_support = min(int(np.ceil(0.5 * (n_samples + n_features + 1))), n_samples) + else: + n_support = int(support_fraction * n_samples) + + # 1-dimensional case quick computation + # (Rousseeuw, P. J. and Leroy, A. M. (2005) References, in Robust + # Regression and Outlier Detection, John Wiley & Sons, chapter 4) + if n_features == 1: + if n_support < n_samples: + # find the sample shortest halves + X_sorted = np.sort(np.ravel(X)) + diff = X_sorted[n_support:] - X_sorted[: (n_samples - n_support)] + halves_start = np.where(diff == np.min(diff))[0] + # take the middle points' mean to get the robust location estimate + location = ( + 0.5 + * (X_sorted[n_support + halves_start] + X_sorted[halves_start]).mean() + ) + support = np.zeros(n_samples, dtype=bool) + X_centered = X - location + support[np.argsort(np.abs(X_centered), 0)[:n_support]] = True + covariance = np.asarray([[np.var(X[support])]]) + location = np.array([location]) + # get precision matrix in an optimized way + precision = linalg.pinvh(covariance) + dist = (np.dot(X_centered, precision) * (X_centered)).sum(axis=1) + else: + support = np.ones(n_samples, dtype=bool) + covariance = np.asarray([[np.var(X)]]) + location = np.asarray([np.mean(X)]) + X_centered = X - location + # get precision matrix in an optimized way + precision = linalg.pinvh(covariance) + dist = (np.dot(X_centered, precision) * (X_centered)).sum(axis=1) + # Starting FastMCD algorithm for p-dimensional case + if (n_samples > 500) and (n_features > 1): + # 1. Find candidate supports on subsets + # a. split the set in subsets of size ~ 300 + n_subsets = n_samples // 300 + n_samples_subsets = n_samples // n_subsets + samples_shuffle = random_state.permutation(n_samples) + h_subset = int(np.ceil(n_samples_subsets * (n_support / float(n_samples)))) + # b. perform a total of 500 trials + n_trials_tot = 500 + # c. select 10 best (location, covariance) for each subset + n_best_sub = 10 + n_trials = max(10, n_trials_tot // n_subsets) + n_best_tot = n_subsets * n_best_sub + all_best_locations = np.zeros((n_best_tot, n_features)) + try: + all_best_covariances = np.zeros((n_best_tot, n_features, n_features)) + except MemoryError: + # The above is too big. Let's try with something much small + # (and less optimal) + n_best_tot = 10 + all_best_covariances = np.zeros((n_best_tot, n_features, n_features)) + n_best_sub = 2 + for i in range(n_subsets): + low_bound = i * n_samples_subsets + high_bound = low_bound + n_samples_subsets + current_subset = X[samples_shuffle[low_bound:high_bound]] + best_locations_sub, best_covariances_sub, _, _ = select_candidates( + current_subset, + h_subset, + n_trials, + select=n_best_sub, + n_iter=2, + cov_computation_method=cov_computation_method, + random_state=random_state, + ) + subset_slice = np.arange(i * n_best_sub, (i + 1) * n_best_sub) + all_best_locations[subset_slice] = best_locations_sub + all_best_covariances[subset_slice] = best_covariances_sub + # 2. Pool the candidate supports into a merged set + # (possibly the full dataset) + n_samples_merged = min(1500, n_samples) + h_merged = int(np.ceil(n_samples_merged * (n_support / float(n_samples)))) + if n_samples > 1500: + n_best_merged = 10 + else: + n_best_merged = 1 + # find the best couples (location, covariance) on the merged set + selection = random_state.permutation(n_samples)[:n_samples_merged] + locations_merged, covariances_merged, supports_merged, d = select_candidates( + X[selection], + h_merged, + n_trials=(all_best_locations, all_best_covariances), + select=n_best_merged, + cov_computation_method=cov_computation_method, + random_state=random_state, + ) + # 3. Finally get the overall best (locations, covariance) couple + if n_samples < 1500: + # directly get the best couple (location, covariance) + location = locations_merged[0] + covariance = covariances_merged[0] + support = np.zeros(n_samples, dtype=bool) + dist = np.zeros(n_samples) + support[selection] = supports_merged[0] + dist[selection] = d[0] + else: + # select the best couple on the full dataset + locations_full, covariances_full, supports_full, d = select_candidates( + X, + n_support, + n_trials=(locations_merged, covariances_merged), + select=1, + cov_computation_method=cov_computation_method, + random_state=random_state, + ) + location = locations_full[0] + covariance = covariances_full[0] + support = supports_full[0] + dist = d[0] + elif n_features > 1: + # 1. Find the 10 best couples (location, covariance) + # considering two iterations + n_trials = 30 + n_best = 10 + locations_best, covariances_best, _, _ = select_candidates( + X, + n_support, + n_trials=n_trials, + select=n_best, + n_iter=2, + cov_computation_method=cov_computation_method, + random_state=random_state, + ) + # 2. Select the best couple on the full dataset amongst the 10 + locations_full, covariances_full, supports_full, d = select_candidates( + X, + n_support, + n_trials=(locations_best, covariances_best), + select=1, + cov_computation_method=cov_computation_method, + random_state=random_state, + ) + location = locations_full[0] + covariance = covariances_full[0] + support = supports_full[0] + dist = d[0] + + return location, covariance, support, dist + + +class MinCovDet(EmpiricalCovariance): + """Minimum Covariance Determinant (MCD): robust estimator of covariance. + + The Minimum Covariance Determinant covariance estimator is to be applied + on Gaussian-distributed data, but could still be relevant on data + drawn from a unimodal, symmetric distribution. It is not meant to be used + with multi-modal data (the algorithm used to fit a MinCovDet object is + likely to fail in such a case). + One should consider projection pursuit methods to deal with multi-modal + datasets. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + store_precision : bool, default=True + Specify if the estimated precision is stored. + + assume_centered : bool, default=False + If True, the support of the robust location and the covariance + estimates is computed, and a covariance estimate is recomputed from + it, without centering the data. + Useful to work with data whose mean is significantly equal to + zero but is not exactly zero. + If False, the robust location and covariance are directly computed + with the FastMCD algorithm without additional treatment. + + support_fraction : float, default=None + The proportion of points to be included in the support of the raw + MCD estimate. Default is None, which implies that the minimum + value of support_fraction will be used within the algorithm: + `(n_samples + n_features + 1) / 2 * n_samples`. The parameter must be + in the range (0, 1]. + + random_state : int, RandomState instance or None, default=None + Determines the pseudo random number generator for shuffling the data. + Pass an int for reproducible results across multiple function calls. + See :term:`Glossary `. + + Attributes + ---------- + raw_location_ : ndarray of shape (n_features,) + The raw robust estimated location before correction and re-weighting. + + raw_covariance_ : ndarray of shape (n_features, n_features) + The raw robust estimated covariance before correction and re-weighting. + + raw_support_ : ndarray of shape (n_samples,) + A mask of the observations that have been used to compute + the raw robust estimates of location and shape, before correction + and re-weighting. + + location_ : ndarray of shape (n_features,) + Estimated robust location. + + For an example of comparing raw robust estimates with + the true location and covariance, refer to + :ref:`sphx_glr_auto_examples_covariance_plot_robust_vs_empirical_covariance.py`. + + covariance_ : ndarray of shape (n_features, n_features) + Estimated robust covariance matrix. + + precision_ : ndarray of shape (n_features, n_features) + Estimated pseudo inverse matrix. + (stored only if store_precision is True) + + support_ : ndarray of shape (n_samples,) + A mask of the observations that have been used to compute + the robust estimates of location and shape. + + dist_ : ndarray of shape (n_samples,) + Mahalanobis distances of the training set (on which :meth:`fit` is + called) observations. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + EllipticEnvelope : An object for detecting outliers in + a Gaussian distributed dataset. + EmpiricalCovariance : Maximum likelihood covariance estimator. + GraphicalLasso : Sparse inverse covariance estimation + with an l1-penalized estimator. + GraphicalLassoCV : Sparse inverse covariance with cross-validated + choice of the l1 penalty. + LedoitWolf : LedoitWolf Estimator. + OAS : Oracle Approximating Shrinkage Estimator. + ShrunkCovariance : Covariance estimator with shrinkage. + + References + ---------- + + .. [Rouseeuw1984] P. J. Rousseeuw. Least median of squares regression. + J. Am Stat Ass, 79:871, 1984. + .. [Rousseeuw] A Fast Algorithm for the Minimum Covariance Determinant + Estimator, 1999, American Statistical Association and the American + Society for Quality, TECHNOMETRICS + .. [ButlerDavies] R. W. Butler, P. L. Davies and M. Jhun, + Asymptotics For The Minimum Covariance Determinant Estimator, + The Annals of Statistics, 1993, Vol. 21, No. 3, 1385-1400 + + Examples + -------- + >>> import numpy as np + >>> from sklearn.covariance import MinCovDet + >>> from sklearn.datasets import make_gaussian_quantiles + >>> real_cov = np.array([[.8, .3], + ... [.3, .4]]) + >>> rng = np.random.RandomState(0) + >>> X = rng.multivariate_normal(mean=[0, 0], + ... cov=real_cov, + ... size=500) + >>> cov = MinCovDet(random_state=0).fit(X) + >>> cov.covariance_ + array([[0.7411, 0.2535], + [0.2535, 0.3053]]) + >>> cov.location_ + array([0.0813 , 0.0427]) + """ + + _parameter_constraints: dict = { + **EmpiricalCovariance._parameter_constraints, + "support_fraction": [Interval(Real, 0, 1, closed="right"), None], + "random_state": ["random_state"], + } + _nonrobust_covariance = staticmethod(empirical_covariance) + + def __init__( + self, + *, + store_precision=True, + assume_centered=False, + support_fraction=None, + random_state=None, + ): + self.store_precision = store_precision + self.assume_centered = assume_centered + self.support_fraction = support_fraction + self.random_state = random_state + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit a Minimum Covariance Determinant with the FastMCD algorithm. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data, where `n_samples` is the number of samples + and `n_features` is the number of features. + + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + self : object + Returns the instance itself. + """ + X = validate_data(self, X, ensure_min_samples=2, estimator="MinCovDet") + random_state = check_random_state(self.random_state) + n_samples, n_features = X.shape + # check that the empirical covariance is full rank + if (linalg.svdvals(np.dot(X.T, X)) > 1e-8).sum() != n_features: + warnings.warn( + "The covariance matrix associated to your dataset is not full rank" + ) + # compute and store raw estimates + raw_location, raw_covariance, raw_support, raw_dist = fast_mcd( + X, + support_fraction=self.support_fraction, + cov_computation_method=self._nonrobust_covariance, + random_state=random_state, + ) + if self.assume_centered: + raw_location = np.zeros(n_features) + raw_covariance = self._nonrobust_covariance( + X[raw_support], assume_centered=True + ) + # get precision matrix in an optimized way + precision = linalg.pinvh(raw_covariance) + raw_dist = np.sum(np.dot(X, precision) * X, 1) + self.raw_location_ = raw_location + self.raw_covariance_ = raw_covariance + self.raw_support_ = raw_support + self.location_ = raw_location + self.support_ = raw_support + self.dist_ = raw_dist + # obtain consistency at normal models + self.correct_covariance(X) + # re-weight estimator + self.reweight_covariance(X) + + return self + + def correct_covariance(self, data): + """Apply a correction to raw Minimum Covariance Determinant estimates. + + Correction using the empirical correction factor suggested + by Rousseeuw and Van Driessen in [RVD]_. + + Parameters + ---------- + data : array-like of shape (n_samples, n_features) + The data matrix, with p features and n samples. + The data set must be the one which was used to compute + the raw estimates. + + Returns + ------- + covariance_corrected : ndarray of shape (n_features, n_features) + Corrected robust covariance estimate. + + References + ---------- + + .. [RVD] A Fast Algorithm for the Minimum Covariance + Determinant Estimator, 1999, American Statistical Association + and the American Society for Quality, TECHNOMETRICS + """ + + # Check that the covariance of the support data is not equal to 0. + # Otherwise self.dist_ = 0 and thus correction = 0. + n_samples = len(self.dist_) + n_support = np.sum(self.support_) + if n_support < n_samples and np.allclose(self.raw_covariance_, 0): + raise ValueError( + "The covariance matrix of the support data " + "is equal to 0, try to increase support_fraction" + ) + correction = np.median(self.dist_) / chi2(data.shape[1]).isf(0.5) + covariance_corrected = self.raw_covariance_ * correction + self.dist_ /= correction + return covariance_corrected + + def reweight_covariance(self, data): + """Re-weight raw Minimum Covariance Determinant estimates. + + Re-weight observations using Rousseeuw's method (equivalent to + deleting outlying observations from the data set before + computing location and covariance estimates) described + in [RVDriessen]_. + + Parameters + ---------- + data : array-like of shape (n_samples, n_features) + The data matrix, with p features and n samples. + The data set must be the one which was used to compute + the raw estimates. + + Returns + ------- + location_reweighted : ndarray of shape (n_features,) + Re-weighted robust location estimate. + + covariance_reweighted : ndarray of shape (n_features, n_features) + Re-weighted robust covariance estimate. + + support_reweighted : ndarray of shape (n_samples,), dtype=bool + A mask of the observations that have been used to compute + the re-weighted robust location and covariance estimates. + + References + ---------- + + .. [RVDriessen] A Fast Algorithm for the Minimum Covariance + Determinant Estimator, 1999, American Statistical Association + and the American Society for Quality, TECHNOMETRICS + """ + n_samples, n_features = data.shape + mask = self.dist_ < chi2(n_features).isf(0.025) + if self.assume_centered: + location_reweighted = np.zeros(n_features) + else: + location_reweighted = data[mask].mean(0) + covariance_reweighted = self._nonrobust_covariance( + data[mask], assume_centered=self.assume_centered + ) + support_reweighted = np.zeros(n_samples, dtype=bool) + support_reweighted[mask] = True + self._set_covariance(covariance_reweighted) + self.location_ = location_reweighted + self.support_ = support_reweighted + X_centered = data - self.location_ + self.dist_ = np.sum(np.dot(X_centered, self.get_precision()) * X_centered, 1) + return location_reweighted, covariance_reweighted, support_reweighted diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_shrunk_covariance.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_shrunk_covariance.py new file mode 100644 index 0000000000000000000000000000000000000000..99d6f70f57d6eee24fc442bd42f496bf8ae9a9a2 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/_shrunk_covariance.py @@ -0,0 +1,822 @@ +""" +Covariance estimators using shrinkage. + +Shrinkage corresponds to regularising `cov` using a convex combination: +shrunk_cov = (1-shrinkage)*cov + shrinkage*structured_estimate. + +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +# avoid division truncation +import warnings +from numbers import Integral, Real + +import numpy as np + +from ..base import _fit_context +from ..utils import check_array +from ..utils._param_validation import Interval, validate_params +from ..utils.validation import validate_data +from . import EmpiricalCovariance, empirical_covariance + + +def _ledoit_wolf(X, *, assume_centered, block_size): + """Estimate the shrunk Ledoit-Wolf covariance matrix.""" + # for only one feature, the result is the same whatever the shrinkage + if len(X.shape) == 2 and X.shape[1] == 1: + if not assume_centered: + X = X - X.mean() + return np.atleast_2d((X**2).mean()), 0.0 + n_features = X.shape[1] + + # get Ledoit-Wolf shrinkage + shrinkage = ledoit_wolf_shrinkage( + X, assume_centered=assume_centered, block_size=block_size + ) + emp_cov = empirical_covariance(X, assume_centered=assume_centered) + mu = np.sum(np.trace(emp_cov)) / n_features + shrunk_cov = (1.0 - shrinkage) * emp_cov + shrunk_cov.flat[:: n_features + 1] += shrinkage * mu + + return shrunk_cov, shrinkage + + +def _oas(X, *, assume_centered=False): + """Estimate covariance with the Oracle Approximating Shrinkage algorithm. + + The formulation is based on [1]_. + [1] "Shrinkage algorithms for MMSE covariance estimation.", + Chen, Y., Wiesel, A., Eldar, Y. C., & Hero, A. O. + IEEE Transactions on Signal Processing, 58(10), 5016-5029, 2010. + https://arxiv.org/pdf/0907.4698.pdf + """ + if len(X.shape) == 2 and X.shape[1] == 1: + # for only one feature, the result is the same whatever the shrinkage + if not assume_centered: + X = X - X.mean() + return np.atleast_2d((X**2).mean()), 0.0 + + n_samples, n_features = X.shape + + emp_cov = empirical_covariance(X, assume_centered=assume_centered) + + # The shrinkage is defined as: + # shrinkage = min( + # trace(S @ S.T) + trace(S)**2) / ((n + 1) (trace(S @ S.T) - trace(S)**2 / p), 1 + # ) + # where n and p are n_samples and n_features, respectively (cf. Eq. 23 in [1]). + # The factor 2 / p is omitted since it does not impact the value of the estimator + # for large p. + + # Instead of computing trace(S)**2, we can compute the average of the squared + # elements of S that is equal to trace(S)**2 / p**2. + # See the definition of the Frobenius norm: + # https://en.wikipedia.org/wiki/Matrix_norm#Frobenius_norm + alpha = np.mean(emp_cov**2) + mu = np.trace(emp_cov) / n_features + mu_squared = mu**2 + + # The factor 1 / p**2 will cancel out since it is in both the numerator and + # denominator + num = alpha + mu_squared + den = (n_samples + 1) * (alpha - mu_squared / n_features) + shrinkage = 1.0 if den == 0 else min(num / den, 1.0) + + # The shrunk covariance is defined as: + # (1 - shrinkage) * S + shrinkage * F (cf. Eq. 4 in [1]) + # where S is the empirical covariance and F is the shrinkage target defined as + # F = trace(S) / n_features * np.identity(n_features) (cf. Eq. 3 in [1]) + shrunk_cov = (1.0 - shrinkage) * emp_cov + shrunk_cov.flat[:: n_features + 1] += shrinkage * mu + + return shrunk_cov, shrinkage + + +############################################################################### +# Public API +# ShrunkCovariance estimator + + +@validate_params( + { + "emp_cov": ["array-like"], + "shrinkage": [Interval(Real, 0, 1, closed="both")], + }, + prefer_skip_nested_validation=True, +) +def shrunk_covariance(emp_cov, shrinkage=0.1): + """Calculate covariance matrices shrunk on the diagonal. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + emp_cov : array-like of shape (..., n_features, n_features) + Covariance matrices to be shrunk, at least 2D ndarray. + + shrinkage : float, default=0.1 + Coefficient in the convex combination used for the computation + of the shrunk estimate. Range is [0, 1]. + + Returns + ------- + shrunk_cov : ndarray of shape (..., n_features, n_features) + Shrunk covariance matrices. + + Notes + ----- + The regularized (shrunk) covariance is given by:: + + (1 - shrinkage) * cov + shrinkage * mu * np.identity(n_features) + + where `mu = trace(cov) / n_features`. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.datasets import make_gaussian_quantiles + >>> from sklearn.covariance import empirical_covariance, shrunk_covariance + >>> real_cov = np.array([[.8, .3], [.3, .4]]) + >>> rng = np.random.RandomState(0) + >>> X = rng.multivariate_normal(mean=[0, 0], cov=real_cov, size=500) + >>> shrunk_covariance(empirical_covariance(X)) + array([[0.739, 0.254], + [0.254, 0.411]]) + """ + emp_cov = check_array(emp_cov, allow_nd=True) + n_features = emp_cov.shape[-1] + + shrunk_cov = (1.0 - shrinkage) * emp_cov + mu = np.trace(emp_cov, axis1=-2, axis2=-1) / n_features + mu = np.expand_dims(mu, axis=tuple(range(mu.ndim, emp_cov.ndim))) + shrunk_cov += shrinkage * mu * np.eye(n_features) + + return shrunk_cov + + +class ShrunkCovariance(EmpiricalCovariance): + """Covariance estimator with shrinkage. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + store_precision : bool, default=True + Specify if the estimated precision is stored. + + assume_centered : bool, default=False + If True, data will not be centered before computation. + Useful when working with data whose mean is almost, but not exactly + zero. + If False, data will be centered before computation. + + shrinkage : float, default=0.1 + Coefficient in the convex combination used for the computation + of the shrunk estimate. Range is [0, 1]. + + Attributes + ---------- + covariance_ : ndarray of shape (n_features, n_features) + Estimated covariance matrix + + location_ : ndarray of shape (n_features,) + Estimated location, i.e. the estimated mean. + + precision_ : ndarray of shape (n_features, n_features) + Estimated pseudo inverse matrix. + (stored only if store_precision is True) + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + EllipticEnvelope : An object for detecting outliers in + a Gaussian distributed dataset. + EmpiricalCovariance : Maximum likelihood covariance estimator. + GraphicalLasso : Sparse inverse covariance estimation + with an l1-penalized estimator. + GraphicalLassoCV : Sparse inverse covariance with cross-validated + choice of the l1 penalty. + LedoitWolf : LedoitWolf Estimator. + MinCovDet : Minimum Covariance Determinant + (robust estimator of covariance). + OAS : Oracle Approximating Shrinkage Estimator. + + Notes + ----- + The regularized covariance is given by: + + (1 - shrinkage) * cov + shrinkage * mu * np.identity(n_features) + + where mu = trace(cov) / n_features + + Examples + -------- + >>> import numpy as np + >>> from sklearn.covariance import ShrunkCovariance + >>> from sklearn.datasets import make_gaussian_quantiles + >>> real_cov = np.array([[.8, .3], + ... [.3, .4]]) + >>> rng = np.random.RandomState(0) + >>> X = rng.multivariate_normal(mean=[0, 0], + ... cov=real_cov, + ... size=500) + >>> cov = ShrunkCovariance().fit(X) + >>> cov.covariance_ + array([[0.7387, 0.2536], + [0.2536, 0.4110]]) + >>> cov.location_ + array([0.0622, 0.0193]) + """ + + _parameter_constraints: dict = { + **EmpiricalCovariance._parameter_constraints, + "shrinkage": [Interval(Real, 0, 1, closed="both")], + } + + def __init__(self, *, store_precision=True, assume_centered=False, shrinkage=0.1): + super().__init__( + store_precision=store_precision, assume_centered=assume_centered + ) + self.shrinkage = shrinkage + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the shrunk covariance model to X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data, where `n_samples` is the number of samples + and `n_features` is the number of features. + + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + self : object + Returns the instance itself. + """ + X = validate_data(self, X) + # Not calling the parent object to fit, to avoid a potential + # matrix inversion when setting the precision + if self.assume_centered: + self.location_ = np.zeros(X.shape[1]) + else: + self.location_ = X.mean(0) + covariance = empirical_covariance(X, assume_centered=self.assume_centered) + covariance = shrunk_covariance(covariance, self.shrinkage) + self._set_covariance(covariance) + + return self + + +# Ledoit-Wolf estimator + + +@validate_params( + { + "X": ["array-like"], + "assume_centered": ["boolean"], + "block_size": [Interval(Integral, 1, None, closed="left")], + }, + prefer_skip_nested_validation=True, +) +def ledoit_wolf_shrinkage(X, assume_centered=False, block_size=1000): + """Estimate the shrunk Ledoit-Wolf covariance matrix. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Data from which to compute the Ledoit-Wolf shrunk covariance shrinkage. + + assume_centered : bool, default=False + If True, data will not be centered before computation. + Useful to work with data whose mean is significantly equal to + zero but is not exactly zero. + If False, data will be centered before computation. + + block_size : int, default=1000 + Size of blocks into which the covariance matrix will be split. + + Returns + ------- + shrinkage : float + Coefficient in the convex combination used for the computation + of the shrunk estimate. + + Notes + ----- + The regularized (shrunk) covariance is: + + (1 - shrinkage) * cov + shrinkage * mu * np.identity(n_features) + + where mu = trace(cov) / n_features + + Examples + -------- + >>> import numpy as np + >>> from sklearn.covariance import ledoit_wolf_shrinkage + >>> real_cov = np.array([[.4, .2], [.2, .8]]) + >>> rng = np.random.RandomState(0) + >>> X = rng.multivariate_normal(mean=[0, 0], cov=real_cov, size=50) + >>> shrinkage_coefficient = ledoit_wolf_shrinkage(X) + >>> shrinkage_coefficient + np.float64(0.23) + """ + X = check_array(X) + # for only one feature, the result is the same whatever the shrinkage + if len(X.shape) == 2 and X.shape[1] == 1: + return 0.0 + if X.ndim == 1: + X = np.reshape(X, (1, -1)) + + if X.shape[0] == 1: + warnings.warn( + "Only one sample available. You may want to reshape your data array" + ) + n_samples, n_features = X.shape + + # optionally center data + if not assume_centered: + X = X - X.mean(0) + + # A non-blocked version of the computation is present in the tests + # in tests/test_covariance.py + + # number of blocks to split the covariance matrix into + n_splits = int(n_features / block_size) + X2 = X**2 + emp_cov_trace = np.sum(X2, axis=0) / n_samples + mu = np.sum(emp_cov_trace) / n_features + beta_ = 0.0 # sum of the coefficients of + delta_ = 0.0 # sum of the *squared* coefficients of + # starting block computation + for i in range(n_splits): + for j in range(n_splits): + rows = slice(block_size * i, block_size * (i + 1)) + cols = slice(block_size * j, block_size * (j + 1)) + beta_ += np.sum(np.dot(X2.T[rows], X2[:, cols])) + delta_ += np.sum(np.dot(X.T[rows], X[:, cols]) ** 2) + rows = slice(block_size * i, block_size * (i + 1)) + beta_ += np.sum(np.dot(X2.T[rows], X2[:, block_size * n_splits :])) + delta_ += np.sum(np.dot(X.T[rows], X[:, block_size * n_splits :]) ** 2) + for j in range(n_splits): + cols = slice(block_size * j, block_size * (j + 1)) + beta_ += np.sum(np.dot(X2.T[block_size * n_splits :], X2[:, cols])) + delta_ += np.sum(np.dot(X.T[block_size * n_splits :], X[:, cols]) ** 2) + delta_ += np.sum( + np.dot(X.T[block_size * n_splits :], X[:, block_size * n_splits :]) ** 2 + ) + delta_ /= n_samples**2 + beta_ += np.sum( + np.dot(X2.T[block_size * n_splits :], X2[:, block_size * n_splits :]) + ) + # use delta_ to compute beta + beta = 1.0 / (n_features * n_samples) * (beta_ / n_samples - delta_) + # delta is the sum of the squared coefficients of ( - mu*Id) / p + delta = delta_ - 2.0 * mu * emp_cov_trace.sum() + n_features * mu**2 + delta /= n_features + # get final beta as the min between beta and delta + # We do this to prevent shrinking more than "1", which would invert + # the value of covariances + beta = min(beta, delta) + # finally get shrinkage + shrinkage = 0 if beta == 0 else beta / delta + return shrinkage + + +@validate_params( + {"X": ["array-like"]}, + prefer_skip_nested_validation=False, +) +def ledoit_wolf(X, *, assume_centered=False, block_size=1000): + """Estimate the shrunk Ledoit-Wolf covariance matrix. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Data from which to compute the covariance estimate. + + assume_centered : bool, default=False + If True, data will not be centered before computation. + Useful to work with data whose mean is significantly equal to + zero but is not exactly zero. + If False, data will be centered before computation. + + block_size : int, default=1000 + Size of blocks into which the covariance matrix will be split. + This is purely a memory optimization and does not affect results. + + Returns + ------- + shrunk_cov : ndarray of shape (n_features, n_features) + Shrunk covariance. + + shrinkage : float + Coefficient in the convex combination used for the computation + of the shrunk estimate. + + Notes + ----- + The regularized (shrunk) covariance is: + + (1 - shrinkage) * cov + shrinkage * mu * np.identity(n_features) + + where mu = trace(cov) / n_features + + Examples + -------- + >>> import numpy as np + >>> from sklearn.covariance import empirical_covariance, ledoit_wolf + >>> real_cov = np.array([[.4, .2], [.2, .8]]) + >>> rng = np.random.RandomState(0) + >>> X = rng.multivariate_normal(mean=[0, 0], cov=real_cov, size=50) + >>> covariance, shrinkage = ledoit_wolf(X) + >>> covariance + array([[0.44, 0.16], + [0.16, 0.80]]) + >>> shrinkage + np.float64(0.23) + """ + estimator = LedoitWolf( + assume_centered=assume_centered, + block_size=block_size, + store_precision=False, + ).fit(X) + + return estimator.covariance_, estimator.shrinkage_ + + +class LedoitWolf(EmpiricalCovariance): + """LedoitWolf Estimator. + + Ledoit-Wolf is a particular form of shrinkage, where the shrinkage + coefficient is computed using O. Ledoit and M. Wolf's formula as + described in "A Well-Conditioned Estimator for Large-Dimensional + Covariance Matrices", Ledoit and Wolf, Journal of Multivariate + Analysis, Volume 88, Issue 2, February 2004, pages 365-411. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + store_precision : bool, default=True + Specify if the estimated precision is stored. + + assume_centered : bool, default=False + If True, data will not be centered before computation. + Useful when working with data whose mean is almost, but not exactly + zero. + If False (default), data will be centered before computation. + + block_size : int, default=1000 + Size of blocks into which the covariance matrix will be split + during its Ledoit-Wolf estimation. This is purely a memory + optimization and does not affect results. + + Attributes + ---------- + covariance_ : ndarray of shape (n_features, n_features) + Estimated covariance matrix. + + location_ : ndarray of shape (n_features,) + Estimated location, i.e. the estimated mean. + + precision_ : ndarray of shape (n_features, n_features) + Estimated pseudo inverse matrix. + (stored only if store_precision is True) + + shrinkage_ : float + Coefficient in the convex combination used for the computation + of the shrunk estimate. Range is [0, 1]. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + EllipticEnvelope : An object for detecting outliers in + a Gaussian distributed dataset. + EmpiricalCovariance : Maximum likelihood covariance estimator. + GraphicalLasso : Sparse inverse covariance estimation + with an l1-penalized estimator. + GraphicalLassoCV : Sparse inverse covariance with cross-validated + choice of the l1 penalty. + MinCovDet : Minimum Covariance Determinant + (robust estimator of covariance). + OAS : Oracle Approximating Shrinkage Estimator. + ShrunkCovariance : Covariance estimator with shrinkage. + + Notes + ----- + The regularised covariance is: + + (1 - shrinkage) * cov + shrinkage * mu * np.identity(n_features) + + where mu = trace(cov) / n_features + and shrinkage is given by the Ledoit and Wolf formula (see References) + + References + ---------- + "A Well-Conditioned Estimator for Large-Dimensional Covariance Matrices", + Ledoit and Wolf, Journal of Multivariate Analysis, Volume 88, Issue 2, + February 2004, pages 365-411. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.covariance import LedoitWolf + >>> real_cov = np.array([[.4, .2], + ... [.2, .8]]) + >>> np.random.seed(0) + >>> X = np.random.multivariate_normal(mean=[0, 0], + ... cov=real_cov, + ... size=50) + >>> cov = LedoitWolf().fit(X) + >>> cov.covariance_ + array([[0.4406, 0.1616], + [0.1616, 0.8022]]) + >>> cov.location_ + array([ 0.0595 , -0.0075]) + + See also :ref:`sphx_glr_auto_examples_covariance_plot_covariance_estimation.py` + and :ref:`sphx_glr_auto_examples_covariance_plot_lw_vs_oas.py` + for more detailed examples. + """ + + _parameter_constraints: dict = { + **EmpiricalCovariance._parameter_constraints, + "block_size": [Interval(Integral, 1, None, closed="left")], + } + + def __init__(self, *, store_precision=True, assume_centered=False, block_size=1000): + super().__init__( + store_precision=store_precision, assume_centered=assume_centered + ) + self.block_size = block_size + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the Ledoit-Wolf shrunk covariance model to X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data, where `n_samples` is the number of samples + and `n_features` is the number of features. + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + self : object + Returns the instance itself. + """ + # Not calling the parent object to fit, to avoid computing the + # covariance matrix (and potentially the precision) + X = validate_data(self, X) + if self.assume_centered: + self.location_ = np.zeros(X.shape[1]) + else: + self.location_ = X.mean(0) + covariance, shrinkage = _ledoit_wolf( + X - self.location_, assume_centered=True, block_size=self.block_size + ) + self.shrinkage_ = shrinkage + self._set_covariance(covariance) + + return self + + +# OAS estimator +@validate_params( + {"X": ["array-like"]}, + prefer_skip_nested_validation=False, +) +def oas(X, *, assume_centered=False): + """Estimate covariance with the Oracle Approximating Shrinkage. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Data from which to compute the covariance estimate. + + assume_centered : bool, default=False + If True, data will not be centered before computation. + Useful to work with data whose mean is significantly equal to + zero but is not exactly zero. + If False, data will be centered before computation. + + Returns + ------- + shrunk_cov : array-like of shape (n_features, n_features) + Shrunk covariance. + + shrinkage : float + Coefficient in the convex combination used for the computation + of the shrunk estimate. + + Notes + ----- + The regularised covariance is: + + (1 - shrinkage) * cov + shrinkage * mu * np.identity(n_features), + + where mu = trace(cov) / n_features and shrinkage is given by the OAS formula + (see [1]_). + + The shrinkage formulation implemented here differs from Eq. 23 in [1]_. In + the original article, formula (23) states that 2/p (p being the number of + features) is multiplied by Trace(cov*cov) in both the numerator and + denominator, but this operation is omitted because for a large p, the value + of 2/p is so small that it doesn't affect the value of the estimator. + + References + ---------- + .. [1] :arxiv:`"Shrinkage algorithms for MMSE covariance estimation.", + Chen, Y., Wiesel, A., Eldar, Y. C., & Hero, A. O. + IEEE Transactions on Signal Processing, 58(10), 5016-5029, 2010. + <0907.4698>` + + Examples + -------- + >>> import numpy as np + >>> from sklearn.covariance import oas + >>> rng = np.random.RandomState(0) + >>> real_cov = [[.8, .3], [.3, .4]] + >>> X = rng.multivariate_normal(mean=[0, 0], cov=real_cov, size=500) + >>> shrunk_cov, shrinkage = oas(X) + >>> shrunk_cov + array([[0.7533, 0.2763], + [0.2763, 0.3964]]) + >>> shrinkage + np.float64(0.0195) + """ + estimator = OAS( + assume_centered=assume_centered, + ).fit(X) + return estimator.covariance_, estimator.shrinkage_ + + +class OAS(EmpiricalCovariance): + """Oracle Approximating Shrinkage Estimator. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + store_precision : bool, default=True + Specify if the estimated precision is stored. + + assume_centered : bool, default=False + If True, data will not be centered before computation. + Useful when working with data whose mean is almost, but not exactly + zero. + If False (default), data will be centered before computation. + + Attributes + ---------- + covariance_ : ndarray of shape (n_features, n_features) + Estimated covariance matrix. + + location_ : ndarray of shape (n_features,) + Estimated location, i.e. the estimated mean. + + precision_ : ndarray of shape (n_features, n_features) + Estimated pseudo inverse matrix. + (stored only if store_precision is True) + + shrinkage_ : float + coefficient in the convex combination used for the computation + of the shrunk estimate. Range is [0, 1]. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + EllipticEnvelope : An object for detecting outliers in + a Gaussian distributed dataset. + EmpiricalCovariance : Maximum likelihood covariance estimator. + GraphicalLasso : Sparse inverse covariance estimation + with an l1-penalized estimator. + GraphicalLassoCV : Sparse inverse covariance with cross-validated + choice of the l1 penalty. + LedoitWolf : LedoitWolf Estimator. + MinCovDet : Minimum Covariance Determinant + (robust estimator of covariance). + ShrunkCovariance : Covariance estimator with shrinkage. + + Notes + ----- + The regularised covariance is: + + (1 - shrinkage) * cov + shrinkage * mu * np.identity(n_features), + + where mu = trace(cov) / n_features and shrinkage is given by the OAS formula + (see [1]_). + + The shrinkage formulation implemented here differs from Eq. 23 in [1]_. In + the original article, formula (23) states that 2/p (p being the number of + features) is multiplied by Trace(cov*cov) in both the numerator and + denominator, but this operation is omitted because for a large p, the value + of 2/p is so small that it doesn't affect the value of the estimator. + + References + ---------- + .. [1] :arxiv:`"Shrinkage algorithms for MMSE covariance estimation.", + Chen, Y., Wiesel, A., Eldar, Y. C., & Hero, A. O. + IEEE Transactions on Signal Processing, 58(10), 5016-5029, 2010. + <0907.4698>` + + Examples + -------- + >>> import numpy as np + >>> from sklearn.covariance import OAS + >>> from sklearn.datasets import make_gaussian_quantiles + >>> real_cov = np.array([[.8, .3], + ... [.3, .4]]) + >>> rng = np.random.RandomState(0) + >>> X = rng.multivariate_normal(mean=[0, 0], + ... cov=real_cov, + ... size=500) + >>> oas = OAS().fit(X) + >>> oas.covariance_ + array([[0.7533, 0.2763], + [0.2763, 0.3964]]) + >>> oas.precision_ + array([[ 1.7833, -1.2431 ], + [-1.2431, 3.3889]]) + >>> oas.shrinkage_ + np.float64(0.0195) + + See also :ref:`sphx_glr_auto_examples_covariance_plot_covariance_estimation.py` + and :ref:`sphx_glr_auto_examples_covariance_plot_lw_vs_oas.py` + for more detailed examples. + """ + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the Oracle Approximating Shrinkage covariance model to X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data, where `n_samples` is the number of samples + and `n_features` is the number of features. + y : Ignored + Not used, present for API consistency by convention. + + Returns + ------- + self : object + Returns the instance itself. + """ + X = validate_data(self, X) + # Not calling the parent object to fit, to avoid computing the + # covariance matrix (and potentially the precision) + if self.assume_centered: + self.location_ = np.zeros(X.shape[1]) + else: + self.location_ = X.mean(0) + + covariance, shrinkage = _oas(X - self.location_, assume_centered=True) + self.shrinkage_ = shrinkage + self._set_covariance(covariance) + + return self diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_covariance.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_covariance.py new file mode 100644 index 0000000000000000000000000000000000000000..9c55012c158e19df20e4c4770867fc19398213d0 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_covariance.py @@ -0,0 +1,374 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import numpy as np +import pytest + +from sklearn import datasets +from sklearn.covariance import ( + OAS, + EmpiricalCovariance, + LedoitWolf, + ShrunkCovariance, + empirical_covariance, + ledoit_wolf, + ledoit_wolf_shrinkage, + oas, + shrunk_covariance, +) +from sklearn.covariance._shrunk_covariance import _ledoit_wolf +from sklearn.utils._testing import ( + assert_allclose, + assert_almost_equal, + assert_array_almost_equal, + assert_array_equal, +) + +from .._shrunk_covariance import _oas + +X, _ = datasets.load_diabetes(return_X_y=True) +X_1d = X[:, 0] +n_samples, n_features = X.shape + + +def test_covariance(): + # Tests Covariance module on a simple dataset. + # test covariance fit from data + cov = EmpiricalCovariance() + cov.fit(X) + emp_cov = empirical_covariance(X) + assert_array_almost_equal(emp_cov, cov.covariance_, 4) + assert_almost_equal(cov.error_norm(emp_cov), 0) + assert_almost_equal(cov.error_norm(emp_cov, norm="spectral"), 0) + assert_almost_equal(cov.error_norm(emp_cov, norm="frobenius"), 0) + assert_almost_equal(cov.error_norm(emp_cov, scaling=False), 0) + assert_almost_equal(cov.error_norm(emp_cov, squared=False), 0) + with pytest.raises(NotImplementedError): + cov.error_norm(emp_cov, norm="foo") + # Mahalanobis distances computation test + mahal_dist = cov.mahalanobis(X) + assert np.amin(mahal_dist) > 0 + + # test with n_features = 1 + X_1d = X[:, 0].reshape((-1, 1)) + cov = EmpiricalCovariance() + cov.fit(X_1d) + assert_array_almost_equal(empirical_covariance(X_1d), cov.covariance_, 4) + assert_almost_equal(cov.error_norm(empirical_covariance(X_1d)), 0) + assert_almost_equal(cov.error_norm(empirical_covariance(X_1d), norm="spectral"), 0) + + # test with one sample + # Create X with 1 sample and 5 features + X_1sample = np.arange(5).reshape(1, 5) + cov = EmpiricalCovariance() + warn_msg = "Only one sample available. You may want to reshape your data array" + with pytest.warns(UserWarning, match=warn_msg): + cov.fit(X_1sample) + + assert_array_almost_equal(cov.covariance_, np.zeros(shape=(5, 5), dtype=np.float64)) + + # test integer type + X_integer = np.asarray([[0, 1], [1, 0]]) + result = np.asarray([[0.25, -0.25], [-0.25, 0.25]]) + assert_array_almost_equal(empirical_covariance(X_integer), result) + + # test centered case + cov = EmpiricalCovariance(assume_centered=True) + cov.fit(X) + assert_array_equal(cov.location_, np.zeros(X.shape[1])) + + +@pytest.mark.parametrize("n_matrices", [1, 3]) +def test_shrunk_covariance_func(n_matrices): + """Check `shrunk_covariance` function.""" + + n_features = 2 + cov = np.ones((n_features, n_features)) + cov_target = np.array([[1, 0.5], [0.5, 1]]) + + if n_matrices > 1: + cov = np.repeat(cov[np.newaxis, ...], n_matrices, axis=0) + cov_target = np.repeat(cov_target[np.newaxis, ...], n_matrices, axis=0) + + cov_shrunk = shrunk_covariance(cov, 0.5) + assert_allclose(cov_shrunk, cov_target) + + +def test_shrunk_covariance(): + """Check consistency between `ShrunkCovariance` and `shrunk_covariance`.""" + + # Tests ShrunkCovariance module on a simple dataset. + # compare shrunk covariance obtained from data and from MLE estimate + cov = ShrunkCovariance(shrinkage=0.5) + cov.fit(X) + assert_array_almost_equal( + shrunk_covariance(empirical_covariance(X), shrinkage=0.5), cov.covariance_, 4 + ) + + # same test with shrinkage not provided + cov = ShrunkCovariance() + cov.fit(X) + assert_array_almost_equal( + shrunk_covariance(empirical_covariance(X)), cov.covariance_, 4 + ) + + # same test with shrinkage = 0 (<==> empirical_covariance) + cov = ShrunkCovariance(shrinkage=0.0) + cov.fit(X) + assert_array_almost_equal(empirical_covariance(X), cov.covariance_, 4) + + # test with n_features = 1 + X_1d = X[:, 0].reshape((-1, 1)) + cov = ShrunkCovariance(shrinkage=0.3) + cov.fit(X_1d) + assert_array_almost_equal(empirical_covariance(X_1d), cov.covariance_, 4) + + # test shrinkage coeff on a simple data set (without saving precision) + cov = ShrunkCovariance(shrinkage=0.5, store_precision=False) + cov.fit(X) + assert cov.precision_ is None + + +def test_ledoit_wolf(): + # Tests LedoitWolf module on a simple dataset. + # test shrinkage coeff on a simple data set + X_centered = X - X.mean(axis=0) + lw = LedoitWolf(assume_centered=True) + lw.fit(X_centered) + shrinkage_ = lw.shrinkage_ + + score_ = lw.score(X_centered) + assert_almost_equal( + ledoit_wolf_shrinkage(X_centered, assume_centered=True), shrinkage_ + ) + assert_almost_equal( + ledoit_wolf_shrinkage(X_centered, assume_centered=True, block_size=6), + shrinkage_, + ) + # compare shrunk covariance obtained from data and from MLE estimate + lw_cov_from_mle, lw_shrinkage_from_mle = ledoit_wolf( + X_centered, assume_centered=True + ) + assert_array_almost_equal(lw_cov_from_mle, lw.covariance_, 4) + assert_almost_equal(lw_shrinkage_from_mle, lw.shrinkage_) + # compare estimates given by LW and ShrunkCovariance + scov = ShrunkCovariance(shrinkage=lw.shrinkage_, assume_centered=True) + scov.fit(X_centered) + assert_array_almost_equal(scov.covariance_, lw.covariance_, 4) + + # test with n_features = 1 + X_1d = X[:, 0].reshape((-1, 1)) + lw = LedoitWolf(assume_centered=True) + lw.fit(X_1d) + lw_cov_from_mle, lw_shrinkage_from_mle = ledoit_wolf(X_1d, assume_centered=True) + assert_array_almost_equal(lw_cov_from_mle, lw.covariance_, 4) + assert_almost_equal(lw_shrinkage_from_mle, lw.shrinkage_) + assert_array_almost_equal((X_1d**2).sum() / n_samples, lw.covariance_, 4) + + # test shrinkage coeff on a simple data set (without saving precision) + lw = LedoitWolf(store_precision=False, assume_centered=True) + lw.fit(X_centered) + assert_almost_equal(lw.score(X_centered), score_, 4) + assert lw.precision_ is None + + # Same tests without assuming centered data + # test shrinkage coeff on a simple data set + lw = LedoitWolf() + lw.fit(X) + assert_almost_equal(lw.shrinkage_, shrinkage_, 4) + assert_almost_equal(lw.shrinkage_, ledoit_wolf_shrinkage(X)) + assert_almost_equal(lw.shrinkage_, ledoit_wolf(X)[1]) + assert_almost_equal( + lw.shrinkage_, _ledoit_wolf(X=X, assume_centered=False, block_size=10000)[1] + ) + assert_almost_equal(lw.score(X), score_, 4) + # compare shrunk covariance obtained from data and from MLE estimate + lw_cov_from_mle, lw_shrinkage_from_mle = ledoit_wolf(X) + assert_array_almost_equal(lw_cov_from_mle, lw.covariance_, 4) + assert_almost_equal(lw_shrinkage_from_mle, lw.shrinkage_) + # compare estimates given by LW and ShrunkCovariance + scov = ShrunkCovariance(shrinkage=lw.shrinkage_) + scov.fit(X) + assert_array_almost_equal(scov.covariance_, lw.covariance_, 4) + + # test with n_features = 1 + X_1d = X[:, 0].reshape((-1, 1)) + lw = LedoitWolf() + lw.fit(X_1d) + assert_allclose( + X_1d.var(ddof=0), + _ledoit_wolf(X=X_1d, assume_centered=False, block_size=10000)[0], + ) + lw_cov_from_mle, lw_shrinkage_from_mle = ledoit_wolf(X_1d) + assert_array_almost_equal(lw_cov_from_mle, lw.covariance_, 4) + assert_almost_equal(lw_shrinkage_from_mle, lw.shrinkage_) + assert_array_almost_equal(empirical_covariance(X_1d), lw.covariance_, 4) + + # test with one sample + # warning should be raised when using only 1 sample + X_1sample = np.arange(5).reshape(1, 5) + lw = LedoitWolf() + + warn_msg = "Only one sample available. You may want to reshape your data array" + with pytest.warns(UserWarning, match=warn_msg): + lw.fit(X_1sample) + + assert_array_almost_equal(lw.covariance_, np.zeros(shape=(5, 5), dtype=np.float64)) + + # test shrinkage coeff on a simple data set (without saving precision) + lw = LedoitWolf(store_precision=False) + lw.fit(X) + assert_almost_equal(lw.score(X), score_, 4) + assert lw.precision_ is None + + +def _naive_ledoit_wolf_shrinkage(X): + # A simple implementation of the formulas from Ledoit & Wolf + + # The computation below achieves the following computations of the + # "O. Ledoit and M. Wolf, A Well-Conditioned Estimator for + # Large-Dimensional Covariance Matrices" + # beta and delta are given in the beginning of section 3.2 + n_samples, n_features = X.shape + emp_cov = empirical_covariance(X, assume_centered=False) + mu = np.trace(emp_cov) / n_features + delta_ = emp_cov.copy() + delta_.flat[:: n_features + 1] -= mu + delta = (delta_**2).sum() / n_features + X2 = X**2 + beta_ = ( + 1.0 + / (n_features * n_samples) + * np.sum(np.dot(X2.T, X2) / n_samples - emp_cov**2) + ) + + beta = min(beta_, delta) + shrinkage = beta / delta + return shrinkage + + +def test_ledoit_wolf_small(): + # Compare our blocked implementation to the naive implementation + X_small = X[:, :4] + lw = LedoitWolf() + lw.fit(X_small) + shrinkage_ = lw.shrinkage_ + + assert_almost_equal(shrinkage_, _naive_ledoit_wolf_shrinkage(X_small)) + + +def test_ledoit_wolf_large(): + # test that ledoit_wolf doesn't error on data that is wider than block_size + rng = np.random.RandomState(0) + # use a number of features that is larger than the block-size + X = rng.normal(size=(10, 20)) + lw = LedoitWolf(block_size=10).fit(X) + # check that covariance is about diagonal (random normal noise) + assert_almost_equal(lw.covariance_, np.eye(20), 0) + cov = lw.covariance_ + + # check that the result is consistent with not splitting data into blocks. + lw = LedoitWolf(block_size=25).fit(X) + assert_almost_equal(lw.covariance_, cov) + + +@pytest.mark.parametrize( + "ledoit_wolf_fitting_function", [LedoitWolf().fit, ledoit_wolf_shrinkage] +) +def test_ledoit_wolf_empty_array(ledoit_wolf_fitting_function): + """Check that we validate X and raise proper error with 0-sample array.""" + X_empty = np.zeros((0, 2)) + with pytest.raises(ValueError, match="Found array with 0 sample"): + ledoit_wolf_fitting_function(X_empty) + + +def test_oas(): + # Tests OAS module on a simple dataset. + # test shrinkage coeff on a simple data set + X_centered = X - X.mean(axis=0) + oa = OAS(assume_centered=True) + oa.fit(X_centered) + shrinkage_ = oa.shrinkage_ + score_ = oa.score(X_centered) + # compare shrunk covariance obtained from data and from MLE estimate + oa_cov_from_mle, oa_shrinkage_from_mle = oas(X_centered, assume_centered=True) + assert_array_almost_equal(oa_cov_from_mle, oa.covariance_, 4) + assert_almost_equal(oa_shrinkage_from_mle, oa.shrinkage_) + # compare estimates given by OAS and ShrunkCovariance + scov = ShrunkCovariance(shrinkage=oa.shrinkage_, assume_centered=True) + scov.fit(X_centered) + assert_array_almost_equal(scov.covariance_, oa.covariance_, 4) + + # test with n_features = 1 + X_1d = X[:, 0:1] + oa = OAS(assume_centered=True) + oa.fit(X_1d) + oa_cov_from_mle, oa_shrinkage_from_mle = oas(X_1d, assume_centered=True) + assert_array_almost_equal(oa_cov_from_mle, oa.covariance_, 4) + assert_almost_equal(oa_shrinkage_from_mle, oa.shrinkage_) + assert_array_almost_equal((X_1d**2).sum() / n_samples, oa.covariance_, 4) + + # test shrinkage coeff on a simple data set (without saving precision) + oa = OAS(store_precision=False, assume_centered=True) + oa.fit(X_centered) + assert_almost_equal(oa.score(X_centered), score_, 4) + assert oa.precision_ is None + + # Same tests without assuming centered data-------------------------------- + # test shrinkage coeff on a simple data set + oa = OAS() + oa.fit(X) + assert_almost_equal(oa.shrinkage_, shrinkage_, 4) + assert_almost_equal(oa.score(X), score_, 4) + # compare shrunk covariance obtained from data and from MLE estimate + oa_cov_from_mle, oa_shrinkage_from_mle = oas(X) + assert_array_almost_equal(oa_cov_from_mle, oa.covariance_, 4) + assert_almost_equal(oa_shrinkage_from_mle, oa.shrinkage_) + # compare estimates given by OAS and ShrunkCovariance + scov = ShrunkCovariance(shrinkage=oa.shrinkage_) + scov.fit(X) + assert_array_almost_equal(scov.covariance_, oa.covariance_, 4) + + # test with n_features = 1 + X_1d = X[:, 0].reshape((-1, 1)) + oa = OAS() + oa.fit(X_1d) + oa_cov_from_mle, oa_shrinkage_from_mle = oas(X_1d) + assert_array_almost_equal(oa_cov_from_mle, oa.covariance_, 4) + assert_almost_equal(oa_shrinkage_from_mle, oa.shrinkage_) + assert_array_almost_equal(empirical_covariance(X_1d), oa.covariance_, 4) + + # test with one sample + # warning should be raised when using only 1 sample + X_1sample = np.arange(5).reshape(1, 5) + oa = OAS() + warn_msg = "Only one sample available. You may want to reshape your data array" + with pytest.warns(UserWarning, match=warn_msg): + oa.fit(X_1sample) + + assert_array_almost_equal(oa.covariance_, np.zeros(shape=(5, 5), dtype=np.float64)) + + # test shrinkage coeff on a simple data set (without saving precision) + oa = OAS(store_precision=False) + oa.fit(X) + assert_almost_equal(oa.score(X), score_, 4) + assert oa.precision_ is None + + # test function _oas without assuming centered data + X_1f = X[:, 0:1] + oa = OAS() + oa.fit(X_1f) + # compare shrunk covariance obtained from data and from MLE estimate + _oa_cov_from_mle, _oa_shrinkage_from_mle = _oas(X_1f) + assert_array_almost_equal(_oa_cov_from_mle, oa.covariance_, 4) + assert_almost_equal(_oa_shrinkage_from_mle, oa.shrinkage_) + assert_array_almost_equal((X_1f**2).sum() / n_samples, oa.covariance_, 4) + + +def test_EmpiricalCovariance_validates_mahalanobis(): + """Checks that EmpiricalCovariance validates data with mahalanobis.""" + cov = EmpiricalCovariance().fit(X) + + msg = f"X has 2 features, but \\w+ is expecting {X.shape[1]} features as input" + with pytest.raises(ValueError, match=msg): + cov.mahalanobis(X[:, :2]) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_elliptic_envelope.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_elliptic_envelope.py new file mode 100644 index 0000000000000000000000000000000000000000..ca85717fb378243ff8dcb75db1adade9a6c50c18 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_elliptic_envelope.py @@ -0,0 +1,52 @@ +""" +Testing for Elliptic Envelope algorithm (sklearn.covariance.elliptic_envelope). +""" + +import numpy as np +import pytest + +from sklearn.covariance import EllipticEnvelope +from sklearn.exceptions import NotFittedError +from sklearn.utils._testing import ( + assert_almost_equal, + assert_array_almost_equal, + assert_array_equal, +) + + +def test_elliptic_envelope(global_random_seed): + rnd = np.random.RandomState(global_random_seed) + X = rnd.randn(100, 10) + clf = EllipticEnvelope(contamination=0.1) + with pytest.raises(NotFittedError): + clf.predict(X) + with pytest.raises(NotFittedError): + clf.decision_function(X) + clf.fit(X) + y_pred = clf.predict(X) + scores = clf.score_samples(X) + decisions = clf.decision_function(X) + + assert_array_almost_equal(scores, -clf.mahalanobis(X)) + assert_array_almost_equal(clf.mahalanobis(X), clf.dist_) + assert_almost_equal( + clf.score(X, np.ones(100)), (100 - y_pred[y_pred == -1].size) / 100.0 + ) + assert sum(y_pred == -1) == sum(decisions < 0) + + +def test_score_samples(): + X_train = [[1, 1], [1, 2], [2, 1]] + clf1 = EllipticEnvelope(contamination=0.2).fit(X_train) + clf2 = EllipticEnvelope().fit(X_train) + assert_array_equal( + clf1.score_samples([[2.0, 2.0]]), + clf1.decision_function([[2.0, 2.0]]) + clf1.offset_, + ) + assert_array_equal( + clf2.score_samples([[2.0, 2.0]]), + clf2.decision_function([[2.0, 2.0]]) + clf2.offset_, + ) + assert_array_equal( + clf1.score_samples([[2.0, 2.0]]), clf2.score_samples([[2.0, 2.0]]) + ) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_graphical_lasso.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_graphical_lasso.py new file mode 100644 index 0000000000000000000000000000000000000000..9698b64bf4407e216229b9e55fa4cd19896af823 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_graphical_lasso.py @@ -0,0 +1,318 @@ +"""Test the graphical_lasso module.""" + +import sys +from io import StringIO + +import numpy as np +import pytest +from numpy.testing import assert_allclose +from scipy import linalg + +from sklearn import config_context, datasets +from sklearn.covariance import ( + GraphicalLasso, + GraphicalLassoCV, + empirical_covariance, + graphical_lasso, +) +from sklearn.datasets import make_sparse_spd_matrix +from sklearn.model_selection import GroupKFold +from sklearn.utils import check_random_state +from sklearn.utils._testing import ( + _convert_container, + assert_array_almost_equal, + assert_array_less, +) + + +def test_graphical_lassos(random_state=1): + """Test the graphical lasso solvers. + + This checks is unstable for some random seeds where the covariance found with "cd" + and "lars" solvers are different (4 cases / 100 tries). + """ + # Sample data from a sparse multivariate normal + dim = 20 + n_samples = 100 + random_state = check_random_state(random_state) + prec = make_sparse_spd_matrix(dim, alpha=0.95, random_state=random_state) + cov = linalg.inv(prec) + X = random_state.multivariate_normal(np.zeros(dim), cov, size=n_samples) + emp_cov = empirical_covariance(X) + + for alpha in (0.0, 0.1, 0.25): + covs = dict() + icovs = dict() + for method in ("cd", "lars"): + cov_, icov_, costs = graphical_lasso( + emp_cov, return_costs=True, alpha=alpha, mode=method + ) + covs[method] = cov_ + icovs[method] = icov_ + costs, dual_gap = np.array(costs).T + # Check that the costs always decrease (doesn't hold if alpha == 0) + if not alpha == 0: + # use 1e-12 since the cost can be exactly 0 + assert_array_less(np.diff(costs), 1e-12) + # Check that the 2 approaches give similar results + assert_allclose(covs["cd"], covs["lars"], atol=5e-4) + assert_allclose(icovs["cd"], icovs["lars"], atol=5e-4) + + # Smoke test the estimator + model = GraphicalLasso(alpha=0.25).fit(X) + model.score(X) + assert_array_almost_equal(model.covariance_, covs["cd"], decimal=4) + assert_array_almost_equal(model.covariance_, covs["lars"], decimal=4) + + # For a centered matrix, assume_centered could be chosen True or False + # Check that this returns indeed the same result for centered data + Z = X - X.mean(0) + precs = list() + for assume_centered in (False, True): + prec_ = GraphicalLasso(assume_centered=assume_centered).fit(Z).precision_ + precs.append(prec_) + assert_array_almost_equal(precs[0], precs[1]) + + +def test_graphical_lasso_when_alpha_equals_0(): + """Test graphical_lasso's early return condition when alpha=0.""" + X = np.random.randn(100, 10) + emp_cov = empirical_covariance(X, assume_centered=True) + + model = GraphicalLasso(alpha=0, covariance="precomputed").fit(emp_cov) + assert_allclose(model.precision_, np.linalg.inv(emp_cov)) + + _, precision = graphical_lasso(emp_cov, alpha=0) + assert_allclose(precision, np.linalg.inv(emp_cov)) + + +@pytest.mark.parametrize("mode", ["cd", "lars"]) +def test_graphical_lasso_n_iter(mode): + X, _ = datasets.make_classification(n_samples=5_000, n_features=20, random_state=0) + emp_cov = empirical_covariance(X) + + _, _, n_iter = graphical_lasso( + emp_cov, 0.2, mode=mode, max_iter=2, return_n_iter=True + ) + assert n_iter == 2 + + +def test_graphical_lasso_iris(): + # Hard-coded solution from R glasso package for alpha=1.0 + # (need to set penalize.diagonal to FALSE) + cov_R = np.array( + [ + [0.68112222, 0.0000000, 0.265820, 0.02464314], + [0.00000000, 0.1887129, 0.000000, 0.00000000], + [0.26582000, 0.0000000, 3.095503, 0.28697200], + [0.02464314, 0.0000000, 0.286972, 0.57713289], + ] + ) + icov_R = np.array( + [ + [1.5190747, 0.000000, -0.1304475, 0.0000000], + [0.0000000, 5.299055, 0.0000000, 0.0000000], + [-0.1304475, 0.000000, 0.3498624, -0.1683946], + [0.0000000, 0.000000, -0.1683946, 1.8164353], + ] + ) + X = datasets.load_iris().data + emp_cov = empirical_covariance(X) + for method in ("cd", "lars"): + cov, icov = graphical_lasso(emp_cov, alpha=1.0, return_costs=False, mode=method) + assert_array_almost_equal(cov, cov_R) + assert_array_almost_equal(icov, icov_R) + + +def test_graph_lasso_2D(): + # Hard-coded solution from Python skggm package + # obtained by calling `quic(emp_cov, lam=.1, tol=1e-8)` + cov_skggm = np.array([[3.09550269, 1.186972], [1.186972, 0.57713289]]) + + icov_skggm = np.array([[1.52836773, -3.14334831], [-3.14334831, 8.19753385]]) + X = datasets.load_iris().data[:, 2:] + emp_cov = empirical_covariance(X) + for method in ("cd", "lars"): + cov, icov = graphical_lasso(emp_cov, alpha=0.1, return_costs=False, mode=method) + assert_array_almost_equal(cov, cov_skggm) + assert_array_almost_equal(icov, icov_skggm) + + +def test_graphical_lasso_iris_singular(): + # Small subset of rows to test the rank-deficient case + # Need to choose samples such that none of the variances are zero + indices = np.arange(10, 13) + + # Hard-coded solution from R glasso package for alpha=0.01 + cov_R = np.array( + [ + [0.08, 0.056666662595, 0.00229729713223, 0.00153153142149], + [0.056666662595, 0.082222222222, 0.00333333333333, 0.00222222222222], + [0.002297297132, 0.003333333333, 0.00666666666667, 0.00009009009009], + [0.001531531421, 0.002222222222, 0.00009009009009, 0.00222222222222], + ] + ) + icov_R = np.array( + [ + [24.42244057, -16.831679593, 0.0, 0.0], + [-16.83168201, 24.351841681, -6.206896552, -12.5], + [0.0, -6.206896171, 153.103448276, 0.0], + [0.0, -12.499999143, 0.0, 462.5], + ] + ) + X = datasets.load_iris().data[indices, :] + emp_cov = empirical_covariance(X) + for method in ("cd", "lars"): + cov, icov = graphical_lasso( + emp_cov, alpha=0.01, return_costs=False, mode=method + ) + assert_array_almost_equal(cov, cov_R, decimal=5) + assert_array_almost_equal(icov, icov_R, decimal=5) + + +def test_graphical_lasso_cv(random_state=1): + # Sample data from a sparse multivariate normal + dim = 5 + n_samples = 6 + random_state = check_random_state(random_state) + prec = make_sparse_spd_matrix(dim, alpha=0.96, random_state=random_state) + cov = linalg.inv(prec) + X = random_state.multivariate_normal(np.zeros(dim), cov, size=n_samples) + # Capture stdout, to smoke test the verbose mode + orig_stdout = sys.stdout + try: + sys.stdout = StringIO() + # We need verbose very high so that Parallel prints on stdout + GraphicalLassoCV(verbose=100, alphas=5, tol=1e-1).fit(X) + finally: + sys.stdout = orig_stdout + + +@pytest.mark.parametrize("alphas_container_type", ["list", "tuple", "array"]) +def test_graphical_lasso_cv_alphas_iterable(alphas_container_type): + """Check that we can pass an array-like to `alphas`. + + Non-regression test for: + https://github.com/scikit-learn/scikit-learn/issues/22489 + """ + true_cov = np.array( + [ + [0.8, 0.0, 0.2, 0.0], + [0.0, 0.4, 0.0, 0.0], + [0.2, 0.0, 0.3, 0.1], + [0.0, 0.0, 0.1, 0.7], + ] + ) + rng = np.random.RandomState(0) + X = rng.multivariate_normal(mean=[0, 0, 0, 0], cov=true_cov, size=200) + alphas = _convert_container([0.02, 0.03], alphas_container_type) + GraphicalLassoCV(alphas=alphas, tol=1e-1, n_jobs=1).fit(X) + + +@pytest.mark.parametrize( + "alphas,err_type,err_msg", + [ + ([-0.02, 0.03], ValueError, "must be > 0"), + ([0, 0.03], ValueError, "must be > 0"), + (["not_number", 0.03], TypeError, "must be an instance of float"), + ], +) +def test_graphical_lasso_cv_alphas_invalid_array(alphas, err_type, err_msg): + """Check that if an array-like containing a value + outside of (0, inf] is passed to `alphas`, a ValueError is raised. + Check if a string is passed, a TypeError is raised. + """ + true_cov = np.array( + [ + [0.8, 0.0, 0.2, 0.0], + [0.0, 0.4, 0.0, 0.0], + [0.2, 0.0, 0.3, 0.1], + [0.0, 0.0, 0.1, 0.7], + ] + ) + rng = np.random.RandomState(0) + X = rng.multivariate_normal(mean=[0, 0, 0, 0], cov=true_cov, size=200) + + with pytest.raises(err_type, match=err_msg): + GraphicalLassoCV(alphas=alphas, tol=1e-1, n_jobs=1).fit(X) + + +def test_graphical_lasso_cv_scores(): + splits = 4 + n_alphas = 5 + n_refinements = 3 + true_cov = np.array( + [ + [0.8, 0.0, 0.2, 0.0], + [0.0, 0.4, 0.0, 0.0], + [0.2, 0.0, 0.3, 0.1], + [0.0, 0.0, 0.1, 0.7], + ] + ) + rng = np.random.RandomState(0) + X = rng.multivariate_normal(mean=[0, 0, 0, 0], cov=true_cov, size=200) + cov = GraphicalLassoCV(cv=splits, alphas=n_alphas, n_refinements=n_refinements).fit( + X + ) + + _assert_graphical_lasso_cv_scores( + cov=cov, + n_splits=splits, + n_refinements=n_refinements, + n_alphas=n_alphas, + ) + + +@config_context(enable_metadata_routing=True) +def test_graphical_lasso_cv_scores_with_routing(global_random_seed): + """Check that `GraphicalLassoCV` internally dispatches metadata to + the splitter. + """ + splits = 5 + n_alphas = 5 + n_refinements = 3 + true_cov = np.array( + [ + [0.8, 0.0, 0.2, 0.0], + [0.0, 0.4, 0.0, 0.0], + [0.2, 0.0, 0.3, 0.1], + [0.0, 0.0, 0.1, 0.7], + ] + ) + rng = np.random.RandomState(global_random_seed) + X = rng.multivariate_normal(mean=[0, 0, 0, 0], cov=true_cov, size=300) + n_samples = X.shape[0] + groups = rng.randint(0, 5, n_samples) + params = {"groups": groups} + cv = GroupKFold(n_splits=splits) + cv.set_split_request(groups=True) + + cov = GraphicalLassoCV(cv=cv, alphas=n_alphas, n_refinements=n_refinements).fit( + X, **params + ) + + _assert_graphical_lasso_cv_scores( + cov=cov, + n_splits=splits, + n_refinements=n_refinements, + n_alphas=n_alphas, + ) + + +def _assert_graphical_lasso_cv_scores(cov, n_splits, n_refinements, n_alphas): + cv_results = cov.cv_results_ + # alpha and one for each split + + total_alphas = n_refinements * n_alphas + 1 + keys = ["alphas"] + split_keys = [f"split{i}_test_score" for i in range(n_splits)] + for key in keys + split_keys: + assert key in cv_results + assert len(cv_results[key]) == total_alphas + + cv_scores = np.asarray([cov.cv_results_[key] for key in split_keys]) + expected_mean = cv_scores.mean(axis=0) + expected_std = cv_scores.std(axis=0) + + assert_allclose(cov.cv_results_["mean_test_score"], expected_mean) + assert_allclose(cov.cv_results_["std_test_score"], expected_std) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_robust_covariance.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_robust_covariance.py new file mode 100644 index 0000000000000000000000000000000000000000..a7bd3996b9e4bdc39af0f961976eb8b727c9a130 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/covariance/tests/test_robust_covariance.py @@ -0,0 +1,171 @@ +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import itertools + +import numpy as np +import pytest + +from sklearn import datasets +from sklearn.covariance import MinCovDet, empirical_covariance, fast_mcd +from sklearn.utils._testing import assert_array_almost_equal + +X = datasets.load_iris().data +X_1d = X[:, 0] +n_samples, n_features = X.shape + + +def test_mcd(global_random_seed): + # Tests the FastMCD algorithm implementation + # Small data set + # test without outliers (random independent normal data) + launch_mcd_on_dataset(100, 5, 0, 0.02, 0.1, 75, global_random_seed) + # test with a contaminated data set (medium contamination) + launch_mcd_on_dataset(100, 5, 20, 0.3, 0.3, 65, global_random_seed) + # test with a contaminated data set (strong contamination) + launch_mcd_on_dataset(100, 5, 40, 0.1, 0.1, 50, global_random_seed) + + # Medium data set + launch_mcd_on_dataset(1000, 5, 450, 0.1, 0.1, 540, global_random_seed) + + # Large data set + launch_mcd_on_dataset(1700, 5, 800, 0.1, 0.1, 870, global_random_seed) + + # 1D data set + launch_mcd_on_dataset(500, 1, 100, 0.02, 0.02, 350, global_random_seed) + + # n_samples == n_features + launch_mcd_on_dataset(20, 20, 0, 0.1, 0.1, 15, global_random_seed) + + +def test_fast_mcd_on_invalid_input(): + X = np.arange(100) + msg = "Expected 2D array, got 1D array instead" + with pytest.raises(ValueError, match=msg): + fast_mcd(X) + + +def test_mcd_class_on_invalid_input(): + X = np.arange(100) + mcd = MinCovDet() + msg = "Expected 2D array, got 1D array instead" + with pytest.raises(ValueError, match=msg): + mcd.fit(X) + + +def launch_mcd_on_dataset( + n_samples, n_features, n_outliers, tol_loc, tol_cov, tol_support, seed +): + rand_gen = np.random.RandomState(seed) + data = rand_gen.randn(n_samples, n_features) + # add some outliers + outliers_index = rand_gen.permutation(n_samples)[:n_outliers] + outliers_offset = 10.0 * (rand_gen.randint(2, size=(n_outliers, n_features)) - 0.5) + data[outliers_index] += outliers_offset + inliers_mask = np.ones(n_samples).astype(bool) + inliers_mask[outliers_index] = False + + pure_data = data[inliers_mask] + # compute MCD by fitting an object + mcd_fit = MinCovDet(random_state=seed).fit(data) + T = mcd_fit.location_ + S = mcd_fit.covariance_ + H = mcd_fit.support_ + # compare with the estimates learnt from the inliers + error_location = np.mean((pure_data.mean(0) - T) ** 2) + assert error_location < tol_loc + error_cov = np.mean((empirical_covariance(pure_data) - S) ** 2) + assert error_cov < tol_cov + assert np.sum(H) >= tol_support + assert_array_almost_equal(mcd_fit.mahalanobis(data), mcd_fit.dist_) + + +def test_mcd_issue1127(): + # Check that the code does not break with X.shape = (3, 1) + # (i.e. n_support = n_samples) + rnd = np.random.RandomState(0) + X = rnd.normal(size=(3, 1)) + mcd = MinCovDet() + mcd.fit(X) + + +def test_mcd_issue3367(global_random_seed): + # Check that MCD completes when the covariance matrix is singular + # i.e. one of the rows and columns are all zeros + rand_gen = np.random.RandomState(global_random_seed) + + # Think of these as the values for X and Y -> 10 values between -5 and 5 + data_values = np.linspace(-5, 5, 10).tolist() + # Get the cartesian product of all possible coordinate pairs from above set + data = np.array(list(itertools.product(data_values, data_values))) + + # Add a third column that's all zeros to make our data a set of point + # within a plane, which means that the covariance matrix will be singular + data = np.hstack((data, np.zeros((data.shape[0], 1)))) + + # The below line of code should raise an exception if the covariance matrix + # is singular. As a further test, since we have points in XYZ, the + # principle components (Eigenvectors) of these directly relate to the + # geometry of the points. Since it's a plane, we should be able to test + # that the Eigenvector that corresponds to the smallest Eigenvalue is the + # plane normal, specifically [0, 0, 1], since everything is in the XY plane + # (as I've set it up above). To do this one would start by: + # + # evals, evecs = np.linalg.eigh(mcd_fit.covariance_) + # normal = evecs[:, np.argmin(evals)] + # + # After which we need to assert that our `normal` is equal to [0, 0, 1]. + # Do note that there is floating point error associated with this, so it's + # best to subtract the two and then compare some small tolerance (e.g. + # 1e-12). + MinCovDet(random_state=rand_gen).fit(data) + + +def test_mcd_support_covariance_is_zero(): + # Check that MCD returns a ValueError with informative message when the + # covariance of the support data is equal to 0. + X_1 = np.array([0.5, 0.1, 0.1, 0.1, 0.957, 0.1, 0.1, 0.1, 0.4285, 0.1]) + X_1 = X_1.reshape(-1, 1) + X_2 = np.array([0.5, 0.3, 0.3, 0.3, 0.957, 0.3, 0.3, 0.3, 0.4285, 0.3]) + X_2 = X_2.reshape(-1, 1) + msg = ( + "The covariance matrix of the support data is equal to 0, try to " + "increase support_fraction" + ) + for X in [X_1, X_2]: + with pytest.raises(ValueError, match=msg): + MinCovDet().fit(X) + + +def test_mcd_increasing_det_warning(global_random_seed): + # Check that a warning is raised if we observe increasing determinants + # during the c_step. In theory the sequence of determinants should be + # decreasing. Increasing determinants are likely due to ill-conditioned + # covariance matrices that result in poor precision matrices. + + X = [ + [5.1, 3.5, 1.4, 0.2], + [4.9, 3.0, 1.4, 0.2], + [4.7, 3.2, 1.3, 0.2], + [4.6, 3.1, 1.5, 0.2], + [5.0, 3.6, 1.4, 0.2], + [4.6, 3.4, 1.4, 0.3], + [5.0, 3.4, 1.5, 0.2], + [4.4, 2.9, 1.4, 0.2], + [4.9, 3.1, 1.5, 0.1], + [5.4, 3.7, 1.5, 0.2], + [4.8, 3.4, 1.6, 0.2], + [4.8, 3.0, 1.4, 0.1], + [4.3, 3.0, 1.1, 0.1], + [5.1, 3.5, 1.4, 0.3], + [5.7, 3.8, 1.7, 0.3], + [5.4, 3.4, 1.7, 0.2], + [4.6, 3.6, 1.0, 0.2], + [5.0, 3.0, 1.6, 0.2], + [5.2, 3.5, 1.5, 0.2], + ] + + mcd = MinCovDet(support_fraction=0.5, random_state=global_random_seed) + warn_msg = "Determinant has increased" + with pytest.warns(RuntimeWarning, match=warn_msg): + mcd.fit(X) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cross_decomposition/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cross_decomposition/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..f78f33811e5c7bfd26fac6dda83022e4d8719191 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cross_decomposition/__init__.py @@ -0,0 +1,8 @@ +"""Algorithms for cross decomposition.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +from ._pls import CCA, PLSSVD, PLSCanonical, PLSRegression + +__all__ = ["CCA", "PLSSVD", "PLSCanonical", "PLSRegression"] diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cross_decomposition/_pls.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cross_decomposition/_pls.py new file mode 100644 index 0000000000000000000000000000000000000000..0bf6ec8f01d065f7f170f278c3ba87a0b0ce9823 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cross_decomposition/_pls.py @@ -0,0 +1,1097 @@ +""" +The :mod:`sklearn.pls` module implements Partial Least Squares (PLS). +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from abc import ABCMeta, abstractmethod +from numbers import Integral, Real + +import numpy as np +from scipy.linalg import pinv, svd + +from ..base import ( + BaseEstimator, + ClassNamePrefixFeaturesOutMixin, + MultiOutputMixin, + RegressorMixin, + TransformerMixin, + _fit_context, +) +from ..exceptions import ConvergenceWarning +from ..utils import check_array, check_consistent_length +from ..utils._param_validation import Interval, StrOptions +from ..utils.extmath import svd_flip +from ..utils.validation import FLOAT_DTYPES, check_is_fitted, validate_data + +__all__ = ["PLSSVD", "PLSCanonical", "PLSRegression"] + + +def _pinv2_old(a): + # Used previous scipy pinv2 that was updated in: + # https://github.com/scipy/scipy/pull/10067 + # We can not set `cond` or `rcond` for pinv2 in scipy >= 1.3 to keep the + # same behavior of pinv2 for scipy < 1.3, because the condition used to + # determine the rank is dependent on the output of svd. + u, s, vh = svd(a, full_matrices=False, check_finite=False) + + t = u.dtype.char.lower() + factor = {"f": 1e3, "d": 1e6} + cond = np.max(s) * factor[t] * np.finfo(t).eps + rank = np.sum(s > cond) + + u = u[:, :rank] + u /= s[:rank] + return np.transpose(np.conjugate(np.dot(u, vh[:rank]))) + + +def _get_first_singular_vectors_power_method( + X, y, mode="A", max_iter=500, tol=1e-06, norm_y_weights=False +): + """Return the first left and right singular vectors of X'y. + + Provides an alternative to the svd(X'y) and uses the power method instead. + With norm_y_weights to True and in mode A, this corresponds to the + algorithm section 11.3 of the Wegelin's review, except this starts at the + "update saliences" part. + """ + + eps = np.finfo(X.dtype).eps + try: + y_score = next(col for col in y.T if np.any(np.abs(col) > eps)) + except StopIteration as e: + raise StopIteration("y residual is constant") from e + + x_weights_old = 100 # init to big value for first convergence check + + if mode == "B": + # Precompute pseudo inverse matrices + # Basically: X_pinv = (X.T X)^-1 X.T + # Which requires inverting a (n_features, n_features) matrix. + # As a result, and as detailed in the Wegelin's review, CCA (i.e. mode + # B) will be unstable if n_features > n_samples or n_targets > + # n_samples + X_pinv, y_pinv = _pinv2_old(X), _pinv2_old(y) + + for i in range(max_iter): + if mode == "B": + x_weights = np.dot(X_pinv, y_score) + else: + x_weights = np.dot(X.T, y_score) / np.dot(y_score, y_score) + + x_weights /= np.sqrt(np.dot(x_weights, x_weights)) + eps + x_score = np.dot(X, x_weights) + + if mode == "B": + y_weights = np.dot(y_pinv, x_score) + else: + y_weights = np.dot(y.T, x_score) / np.dot(x_score.T, x_score) + + if norm_y_weights: + y_weights /= np.sqrt(np.dot(y_weights, y_weights)) + eps + + y_score = np.dot(y, y_weights) / (np.dot(y_weights, y_weights) + eps) + + x_weights_diff = x_weights - x_weights_old + if np.dot(x_weights_diff, x_weights_diff) < tol or y.shape[1] == 1: + break + x_weights_old = x_weights + + n_iter = i + 1 + if n_iter == max_iter: + warnings.warn("Maximum number of iterations reached", ConvergenceWarning) + + return x_weights, y_weights, n_iter + + +def _get_first_singular_vectors_svd(X, y): + """Return the first left and right singular vectors of X'y. + + Here the whole SVD is computed. + """ + C = np.dot(X.T, y) + U, _, Vt = svd(C, full_matrices=False) + return U[:, 0], Vt[0, :] + + +def _center_scale_xy(X, y, scale=True): + """Center X, y and scale if the scale parameter==True + + Returns + ------- + X, y, x_mean, y_mean, x_std, y_std + """ + # center + x_mean = X.mean(axis=0) + X -= x_mean + y_mean = y.mean(axis=0) + y -= y_mean + # scale + if scale: + x_std = X.std(axis=0, ddof=1) + x_std[x_std == 0.0] = 1.0 + X /= x_std + y_std = y.std(axis=0, ddof=1) + y_std[y_std == 0.0] = 1.0 + y /= y_std + else: + x_std = np.ones(X.shape[1]) + y_std = np.ones(y.shape[1]) + return X, y, x_mean, y_mean, x_std, y_std + + +def _svd_flip_1d(u, v): + """Same as svd_flip but works on 1d arrays, and is inplace""" + # svd_flip would force us to convert to 2d array and would also return 2d + # arrays. We don't want that. + biggest_abs_val_idx = np.argmax(np.abs(u)) + sign = np.sign(u[biggest_abs_val_idx]) + u *= sign + v *= sign + + +class _PLS( + ClassNamePrefixFeaturesOutMixin, + TransformerMixin, + RegressorMixin, + MultiOutputMixin, + BaseEstimator, + metaclass=ABCMeta, +): + """Partial Least Squares (PLS) + + This class implements the generic PLS algorithm. + + Main ref: Wegelin, a survey of Partial Least Squares (PLS) methods, + with emphasis on the two-block case + https://stat.uw.edu/sites/default/files/files/reports/2000/tr371.pdf + """ + + _parameter_constraints: dict = { + "n_components": [Interval(Integral, 1, None, closed="left")], + "scale": ["boolean"], + "deflation_mode": [StrOptions({"regression", "canonical"})], + "mode": [StrOptions({"A", "B"})], + "algorithm": [StrOptions({"svd", "nipals"})], + "max_iter": [Interval(Integral, 1, None, closed="left")], + "tol": [Interval(Real, 0, None, closed="left")], + "copy": ["boolean"], + } + + @abstractmethod + def __init__( + self, + n_components=2, + *, + scale=True, + deflation_mode="regression", + mode="A", + algorithm="nipals", + max_iter=500, + tol=1e-06, + copy=True, + ): + self.n_components = n_components + self.deflation_mode = deflation_mode + self.mode = mode + self.scale = scale + self.algorithm = algorithm + self.max_iter = max_iter + self.tol = tol + self.copy = copy + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y): + """Fit model to data. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training vectors, where `n_samples` is the number of samples and + `n_features` is the number of predictors. + + y : array-like of shape (n_samples,) or (n_samples, n_targets) + Target vectors, where `n_samples` is the number of samples and + `n_targets` is the number of response variables. + + Returns + ------- + self : object + Fitted model. + """ + check_consistent_length(X, y) + X = validate_data( + self, + X, + dtype=np.float64, + force_writeable=True, + copy=self.copy, + ensure_min_samples=2, + ) + y = check_array( + y, + input_name="y", + dtype=np.float64, + force_writeable=True, + copy=self.copy, + ensure_2d=False, + ) + if y.ndim == 1: + self._predict_1d = True + y = y.reshape(-1, 1) + else: + self._predict_1d = False + + n = X.shape[0] + p = X.shape[1] + q = y.shape[1] + + n_components = self.n_components + # With PLSRegression n_components is bounded by the rank of (X.T X) see + # Wegelin page 25. With CCA and PLSCanonical, n_components is bounded + # by the rank of X and the rank of y: see Wegelin page 12 + rank_upper_bound = ( + min(n, p) if self.deflation_mode == "regression" else min(n, p, q) + ) + if n_components > rank_upper_bound: + raise ValueError( + f"`n_components` upper bound is {rank_upper_bound}. " + f"Got {n_components} instead. Reduce `n_components`." + ) + + self._norm_y_weights = self.deflation_mode == "canonical" # 1.1 + norm_y_weights = self._norm_y_weights + + # Scale (in place) + Xk, yk, self._x_mean, self._y_mean, self._x_std, self._y_std = _center_scale_xy( + X, y, self.scale + ) + + self.x_weights_ = np.zeros((p, n_components)) # U + self.y_weights_ = np.zeros((q, n_components)) # V + self._x_scores = np.zeros((n, n_components)) # Xi + self._y_scores = np.zeros((n, n_components)) # Omega + self.x_loadings_ = np.zeros((p, n_components)) # Gamma + self.y_loadings_ = np.zeros((q, n_components)) # Delta + self.n_iter_ = [] + + # This whole thing corresponds to the algorithm in section 4.1 of the + # review from Wegelin. See above for a notation mapping from code to + # paper. + y_eps = np.finfo(yk.dtype).eps + for k in range(n_components): + # Find first left and right singular vectors of the X.T.dot(y) + # cross-covariance matrix. + if self.algorithm == "nipals": + # Replace columns that are all close to zero with zeros + yk_mask = np.all(np.abs(yk) < 10 * y_eps, axis=0) + yk[:, yk_mask] = 0.0 + + try: + ( + x_weights, + y_weights, + n_iter_, + ) = _get_first_singular_vectors_power_method( + Xk, + yk, + mode=self.mode, + max_iter=self.max_iter, + tol=self.tol, + norm_y_weights=norm_y_weights, + ) + except StopIteration as e: + if str(e) != "y residual is constant": + raise + warnings.warn(f"y residual is constant at iteration {k}") + break + + self.n_iter_.append(n_iter_) + + elif self.algorithm == "svd": + x_weights, y_weights = _get_first_singular_vectors_svd(Xk, yk) + + # inplace sign flip for consistency across solvers and archs + _svd_flip_1d(x_weights, y_weights) + + # compute scores, i.e. the projections of X and y + x_scores = np.dot(Xk, x_weights) + if norm_y_weights: + y_ss = 1 + else: + y_ss = np.dot(y_weights, y_weights) + y_scores = np.dot(yk, y_weights) / y_ss + + # Deflation: subtract rank-one approx to obtain Xk+1 and yk+1 + x_loadings = np.dot(x_scores, Xk) / np.dot(x_scores, x_scores) + Xk -= np.outer(x_scores, x_loadings) + + if self.deflation_mode == "canonical": + # regress yk on y_score + y_loadings = np.dot(y_scores, yk) / np.dot(y_scores, y_scores) + yk -= np.outer(y_scores, y_loadings) + if self.deflation_mode == "regression": + # regress yk on x_score + y_loadings = np.dot(x_scores, yk) / np.dot(x_scores, x_scores) + yk -= np.outer(x_scores, y_loadings) + + self.x_weights_[:, k] = x_weights + self.y_weights_[:, k] = y_weights + self._x_scores[:, k] = x_scores + self._y_scores[:, k] = y_scores + self.x_loadings_[:, k] = x_loadings + self.y_loadings_[:, k] = y_loadings + + # X was approximated as Xi . Gamma.T + X_(R+1) + # Xi . Gamma.T is a sum of n_components rank-1 matrices. X_(R+1) is + # whatever is left to fully reconstruct X, and can be 0 if X is of rank + # n_components. + # Similarly, y was approximated as Omega . Delta.T + y_(R+1) + + # Compute transformation matrices (rotations_). See User Guide. + self.x_rotations_ = np.dot( + self.x_weights_, + pinv(np.dot(self.x_loadings_.T, self.x_weights_), check_finite=False), + ) + self.y_rotations_ = np.dot( + self.y_weights_, + pinv(np.dot(self.y_loadings_.T, self.y_weights_), check_finite=False), + ) + self.coef_ = np.dot(self.x_rotations_, self.y_loadings_.T) + self.coef_ = (self.coef_ * self._y_std).T / self._x_std + self.intercept_ = self._y_mean + self._n_features_out = self.x_rotations_.shape[1] + return self + + def transform(self, X, y=None, copy=True): + """Apply the dimension reduction. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Samples to transform. + + y : array-like of shape (n_samples, n_targets), default=None + Target vectors. + + copy : bool, default=True + Whether to copy `X` and `y`, or perform in-place normalization. + + Returns + ------- + x_scores, y_scores : array-like or tuple of array-like + Return `x_scores` if `y` is not given, `(x_scores, y_scores)` otherwise. + """ + check_is_fitted(self) + X = validate_data(self, X, copy=copy, dtype=FLOAT_DTYPES, reset=False) + # Normalize + X -= self._x_mean + X /= self._x_std + # Apply rotation + x_scores = np.dot(X, self.x_rotations_) + if y is not None: + y = check_array( + y, input_name="y", ensure_2d=False, copy=copy, dtype=FLOAT_DTYPES + ) + if y.ndim == 1: + y = y.reshape(-1, 1) + y -= self._y_mean + y /= self._y_std + y_scores = np.dot(y, self.y_rotations_) + return x_scores, y_scores + + return x_scores + + def inverse_transform(self, X, y=None): + """Transform data back to its original space. + + Parameters + ---------- + X : array-like of shape (n_samples, n_components) + New data, where `n_samples` is the number of samples + and `n_components` is the number of pls components. + + y : array-like of shape (n_samples,) or (n_samples, n_components) + New target, where `n_samples` is the number of samples + and `n_components` is the number of pls components. + + Returns + ------- + X_original : ndarray of shape (n_samples, n_features) + Return the reconstructed `X` data. + + y_original : ndarray of shape (n_samples, n_targets) + Return the reconstructed `X` target. Only returned when `y` is given. + + Notes + ----- + This transformation will only be exact if `n_components=n_features`. + """ + check_is_fitted(self) + X = check_array(X, input_name="X", dtype=FLOAT_DTYPES) + # From pls space to original space + X_reconstructed = np.matmul(X, self.x_loadings_.T) + # Denormalize + X_reconstructed *= self._x_std + X_reconstructed += self._x_mean + + if y is not None: + y = check_array(y, input_name="y", dtype=FLOAT_DTYPES) + # From pls space to original space + y_reconstructed = np.matmul(y, self.y_loadings_.T) + # Denormalize + y_reconstructed *= self._y_std + y_reconstructed += self._y_mean + return X_reconstructed, y_reconstructed + + return X_reconstructed + + def predict(self, X, copy=True): + """Predict targets of given samples. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Samples. + + copy : bool, default=True + Whether to copy `X` or perform in-place normalization. + + Returns + ------- + y_pred : ndarray of shape (n_samples,) or (n_samples, n_targets) + Returns predicted values. + + Notes + ----- + This call requires the estimation of a matrix of shape + `(n_features, n_targets)`, which may be an issue in high dimensional + space. + """ + check_is_fitted(self) + X = validate_data(self, X, copy=copy, dtype=FLOAT_DTYPES, reset=False) + # Only center X but do not scale it since the coefficients are already scaled + X -= self._x_mean + y_pred = X @ self.coef_.T + self.intercept_ + return y_pred.ravel() if self._predict_1d else y_pred + + def fit_transform(self, X, y=None): + """Learn and apply the dimension reduction on the train data. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training vectors, where `n_samples` is the number of samples and + `n_features` is the number of predictors. + + y : array-like of shape (n_samples, n_targets), default=None + Target vectors, where `n_samples` is the number of samples and + `n_targets` is the number of response variables. + + Returns + ------- + self : ndarray of shape (n_samples, n_components) + Return `x_scores` if `y` is not given, `(x_scores, y_scores)` otherwise. + """ + return self.fit(X, y).transform(X, y) + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.regressor_tags.poor_score = True + tags.target_tags.required = False + return tags + + +class PLSRegression(_PLS): + """PLS regression. + + PLSRegression is also known as PLS2 or PLS1, depending on the number of + targets. + + For a comparison between other cross decomposition algorithms, see + :ref:`sphx_glr_auto_examples_cross_decomposition_plot_compare_cross_decomposition.py`. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.8 + + Parameters + ---------- + n_components : int, default=2 + Number of components to keep. Should be in `[1, n_features]`. + + scale : bool, default=True + Whether to scale `X` and `y`. + + max_iter : int, default=500 + The maximum number of iterations of the power method when + `algorithm='nipals'`. Ignored otherwise. + + tol : float, default=1e-06 + The tolerance used as convergence criteria in the power method: the + algorithm stops whenever the squared norm of `u_i - u_{i-1}` is less + than `tol`, where `u` corresponds to the left singular vector. + + copy : bool, default=True + Whether to copy `X` and `y` in :term:`fit` before applying centering, + and potentially scaling. If `False`, these operations will be done + inplace, modifying both arrays. + + Attributes + ---------- + x_weights_ : ndarray of shape (n_features, n_components) + The left singular vectors of the cross-covariance matrices of each + iteration. + + y_weights_ : ndarray of shape (n_targets, n_components) + The right singular vectors of the cross-covariance matrices of each + iteration. + + x_loadings_ : ndarray of shape (n_features, n_components) + The loadings of `X`. + + y_loadings_ : ndarray of shape (n_targets, n_components) + The loadings of `y`. + + x_scores_ : ndarray of shape (n_samples, n_components) + The transformed training samples. + + y_scores_ : ndarray of shape (n_samples, n_components) + The transformed training targets. + + x_rotations_ : ndarray of shape (n_features, n_components) + The projection matrix used to transform `X`. + + y_rotations_ : ndarray of shape (n_targets, n_components) + The projection matrix used to transform `y`. + + coef_ : ndarray of shape (n_target, n_features) + The coefficients of the linear model such that `y` is approximated as + `y = X @ coef_.T + intercept_`. + + intercept_ : ndarray of shape (n_targets,) + The intercepts of the linear model such that `y` is approximated as + `y = X @ coef_.T + intercept_`. + + .. versionadded:: 1.1 + + n_iter_ : list of shape (n_components,) + Number of iterations of the power method, for each + component. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + PLSCanonical : Partial Least Squares transformer and regressor. + + Examples + -------- + >>> from sklearn.cross_decomposition import PLSRegression + >>> X = [[0., 0., 1.], [1.,0.,0.], [2.,2.,2.], [2.,5.,4.]] + >>> y = [[0.1, -0.2], [0.9, 1.1], [6.2, 5.9], [11.9, 12.3]] + >>> pls2 = PLSRegression(n_components=2) + >>> pls2.fit(X, y) + PLSRegression() + >>> y_pred = pls2.predict(X) + + For a comparison between PLS Regression and :class:`~sklearn.decomposition.PCA`, see + :ref:`sphx_glr_auto_examples_cross_decomposition_plot_pcr_vs_pls.py`. + """ + + _parameter_constraints: dict = {**_PLS._parameter_constraints} + for param in ("deflation_mode", "mode", "algorithm"): + _parameter_constraints.pop(param) + + # This implementation provides the same results that 3 PLS packages + # provided in the R language (R-project): + # - "mixOmics" with function pls(X, y, mode = "regression") + # - "plspm " with function plsreg2(X, y) + # - "pls" with function oscorespls.fit(X, y) + + def __init__( + self, n_components=2, *, scale=True, max_iter=500, tol=1e-06, copy=True + ): + super().__init__( + n_components=n_components, + scale=scale, + deflation_mode="regression", + mode="A", + algorithm="nipals", + max_iter=max_iter, + tol=tol, + copy=copy, + ) + + def fit(self, X, y): + """Fit model to data. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training vectors, where `n_samples` is the number of samples and + `n_features` is the number of predictors. + + y : array-like of shape (n_samples,) or (n_samples, n_targets) + Target vectors, where `n_samples` is the number of samples and + `n_targets` is the number of response variables. + + Returns + ------- + self : object + Fitted model. + """ + super().fit(X, y) + # expose the fitted attributes `x_scores_` and `y_scores_` + self.x_scores_ = self._x_scores + self.y_scores_ = self._y_scores + return self + + +class PLSCanonical(_PLS): + """Partial Least Squares transformer and regressor. + + For a comparison between other cross decomposition algorithms, see + :ref:`sphx_glr_auto_examples_cross_decomposition_plot_compare_cross_decomposition.py`. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.8 + + Parameters + ---------- + n_components : int, default=2 + Number of components to keep. Should be in `[1, min(n_samples, + n_features, n_targets)]`. + + scale : bool, default=True + Whether to scale `X` and `y`. + + algorithm : {'nipals', 'svd'}, default='nipals' + The algorithm used to estimate the first singular vectors of the + cross-covariance matrix. 'nipals' uses the power method while 'svd' + will compute the whole SVD. + + max_iter : int, default=500 + The maximum number of iterations of the power method when + `algorithm='nipals'`. Ignored otherwise. + + tol : float, default=1e-06 + The tolerance used as convergence criteria in the power method: the + algorithm stops whenever the squared norm of `u_i - u_{i-1}` is less + than `tol`, where `u` corresponds to the left singular vector. + + copy : bool, default=True + Whether to copy `X` and `y` in fit before applying centering, and + potentially scaling. If False, these operations will be done inplace, + modifying both arrays. + + Attributes + ---------- + x_weights_ : ndarray of shape (n_features, n_components) + The left singular vectors of the cross-covariance matrices of each + iteration. + + y_weights_ : ndarray of shape (n_targets, n_components) + The right singular vectors of the cross-covariance matrices of each + iteration. + + x_loadings_ : ndarray of shape (n_features, n_components) + The loadings of `X`. + + y_loadings_ : ndarray of shape (n_targets, n_components) + The loadings of `y`. + + x_rotations_ : ndarray of shape (n_features, n_components) + The projection matrix used to transform `X`. + + y_rotations_ : ndarray of shape (n_targets, n_components) + The projection matrix used to transform `y`. + + coef_ : ndarray of shape (n_targets, n_features) + The coefficients of the linear model such that `y` is approximated as + `y = X @ coef_.T + intercept_`. + + intercept_ : ndarray of shape (n_targets,) + The intercepts of the linear model such that `y` is approximated as + `y = X @ coef_.T + intercept_`. + + .. versionadded:: 1.1 + + n_iter_ : list of shape (n_components,) + Number of iterations of the power method, for each + component. Empty if `algorithm='svd'`. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + CCA : Canonical Correlation Analysis. + PLSSVD : Partial Least Square SVD. + + Examples + -------- + >>> from sklearn.cross_decomposition import PLSCanonical + >>> X = [[0., 0., 1.], [1.,0.,0.], [2.,2.,2.], [2.,5.,4.]] + >>> y = [[0.1, -0.2], [0.9, 1.1], [6.2, 5.9], [11.9, 12.3]] + >>> plsca = PLSCanonical(n_components=2) + >>> plsca.fit(X, y) + PLSCanonical() + >>> X_c, y_c = plsca.transform(X, y) + """ + + _parameter_constraints: dict = {**_PLS._parameter_constraints} + for param in ("deflation_mode", "mode"): + _parameter_constraints.pop(param) + + # This implementation provides the same results that the "plspm" package + # provided in the R language (R-project), using the function plsca(X, y). + # Results are equal or collinear with the function + # ``pls(..., mode = "canonical")`` of the "mixOmics" package. The + # difference relies in the fact that mixOmics implementation does not + # exactly implement the Wold algorithm since it does not normalize + # y_weights to one. + + def __init__( + self, + n_components=2, + *, + scale=True, + algorithm="nipals", + max_iter=500, + tol=1e-06, + copy=True, + ): + super().__init__( + n_components=n_components, + scale=scale, + deflation_mode="canonical", + mode="A", + algorithm=algorithm, + max_iter=max_iter, + tol=tol, + copy=copy, + ) + + +class CCA(_PLS): + """Canonical Correlation Analysis, also known as "Mode B" PLS. + + For a comparison between other cross decomposition algorithms, see + :ref:`sphx_glr_auto_examples_cross_decomposition_plot_compare_cross_decomposition.py`. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + n_components : int, default=2 + Number of components to keep. Should be in `[1, min(n_samples, + n_features, n_targets)]`. + + scale : bool, default=True + Whether to scale `X` and `y`. + + max_iter : int, default=500 + The maximum number of iterations of the power method. + + tol : float, default=1e-06 + The tolerance used as convergence criteria in the power method: the + algorithm stops whenever the squared norm of `u_i - u_{i-1}` is less + than `tol`, where `u` corresponds to the left singular vector. + + copy : bool, default=True + Whether to copy `X` and `y` in fit before applying centering, and + potentially scaling. If False, these operations will be done inplace, + modifying both arrays. + + Attributes + ---------- + x_weights_ : ndarray of shape (n_features, n_components) + The left singular vectors of the cross-covariance matrices of each + iteration. + + y_weights_ : ndarray of shape (n_targets, n_components) + The right singular vectors of the cross-covariance matrices of each + iteration. + + x_loadings_ : ndarray of shape (n_features, n_components) + The loadings of `X`. + + y_loadings_ : ndarray of shape (n_targets, n_components) + The loadings of `y`. + + x_rotations_ : ndarray of shape (n_features, n_components) + The projection matrix used to transform `X`. + + y_rotations_ : ndarray of shape (n_targets, n_components) + The projection matrix used to transform `y`. + + coef_ : ndarray of shape (n_targets, n_features) + The coefficients of the linear model such that `y` is approximated as + `y = X @ coef_.T + intercept_`. + + intercept_ : ndarray of shape (n_targets,) + The intercepts of the linear model such that `y` is approximated as + `y = X @ coef_.T + intercept_`. + + .. versionadded:: 1.1 + + n_iter_ : list of shape (n_components,) + Number of iterations of the power method, for each + component. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + PLSCanonical : Partial Least Squares transformer and regressor. + PLSSVD : Partial Least Square SVD. + + Examples + -------- + >>> from sklearn.cross_decomposition import CCA + >>> X = [[0., 0., 1.], [1.,0.,0.], [2.,2.,2.], [3.,5.,4.]] + >>> y = [[0.1, -0.2], [0.9, 1.1], [6.2, 5.9], [11.9, 12.3]] + >>> cca = CCA(n_components=1) + >>> cca.fit(X, y) + CCA(n_components=1) + >>> X_c, y_c = cca.transform(X, y) + """ + + _parameter_constraints: dict = {**_PLS._parameter_constraints} + for param in ("deflation_mode", "mode", "algorithm"): + _parameter_constraints.pop(param) + + def __init__( + self, n_components=2, *, scale=True, max_iter=500, tol=1e-06, copy=True + ): + super().__init__( + n_components=n_components, + scale=scale, + deflation_mode="canonical", + mode="B", + algorithm="nipals", + max_iter=max_iter, + tol=tol, + copy=copy, + ) + + +class PLSSVD(ClassNamePrefixFeaturesOutMixin, TransformerMixin, BaseEstimator): + """Partial Least Square SVD. + + This transformer simply performs a SVD on the cross-covariance matrix + `X'y`. It is able to project both the training data `X` and the targets + `y`. The training data `X` is projected on the left singular vectors, while + the targets are projected on the right singular vectors. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.8 + + Parameters + ---------- + n_components : int, default=2 + The number of components to keep. Should be in `[1, + min(n_samples, n_features, n_targets)]`. + + scale : bool, default=True + Whether to scale `X` and `y`. + + copy : bool, default=True + Whether to copy `X` and `y` in fit before applying centering, and + potentially scaling. If `False`, these operations will be done inplace, + modifying both arrays. + + Attributes + ---------- + x_weights_ : ndarray of shape (n_features, n_components) + The left singular vectors of the SVD of the cross-covariance matrix. + Used to project `X` in :meth:`transform`. + + y_weights_ : ndarray of (n_targets, n_components) + The right singular vectors of the SVD of the cross-covariance matrix. + Used to project `X` in :meth:`transform`. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + PLSCanonical : Partial Least Squares transformer and regressor. + CCA : Canonical Correlation Analysis. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.cross_decomposition import PLSSVD + >>> X = np.array([[0., 0., 1.], + ... [1., 0., 0.], + ... [2., 2., 2.], + ... [2., 5., 4.]]) + >>> y = np.array([[0.1, -0.2], + ... [0.9, 1.1], + ... [6.2, 5.9], + ... [11.9, 12.3]]) + >>> pls = PLSSVD(n_components=2).fit(X, y) + >>> X_c, y_c = pls.transform(X, y) + >>> X_c.shape, y_c.shape + ((4, 2), (4, 2)) + """ + + _parameter_constraints: dict = { + "n_components": [Interval(Integral, 1, None, closed="left")], + "scale": ["boolean"], + "copy": ["boolean"], + } + + def __init__(self, n_components=2, *, scale=True, copy=True): + self.n_components = n_components + self.scale = scale + self.copy = copy + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y): + """Fit model to data. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training samples. + + y : array-like of shape (n_samples,) or (n_samples, n_targets) + Targets. + + Returns + ------- + self : object + Fitted estimator. + """ + check_consistent_length(X, y) + X = validate_data( + self, + X, + dtype=np.float64, + force_writeable=True, + copy=self.copy, + ensure_min_samples=2, + ) + y = check_array( + y, + input_name="y", + dtype=np.float64, + force_writeable=True, + copy=self.copy, + ensure_2d=False, + ) + if y.ndim == 1: + y = y.reshape(-1, 1) + + # we'll compute the SVD of the cross-covariance matrix = X.T.dot(y) + # This matrix rank is at most min(n_samples, n_features, n_targets) so + # n_components cannot be bigger than that. + n_components = self.n_components + rank_upper_bound = min(X.shape[0], X.shape[1], y.shape[1]) + if n_components > rank_upper_bound: + raise ValueError( + f"`n_components` upper bound is {rank_upper_bound}. " + f"Got {n_components} instead. Reduce `n_components`." + ) + + X, y, self._x_mean, self._y_mean, self._x_std, self._y_std = _center_scale_xy( + X, y, self.scale + ) + + # Compute SVD of cross-covariance matrix + C = np.dot(X.T, y) + U, s, Vt = svd(C, full_matrices=False) + U = U[:, :n_components] + Vt = Vt[:n_components] + U, Vt = svd_flip(U, Vt) + V = Vt.T + + self.x_weights_ = U + self.y_weights_ = V + self._n_features_out = self.x_weights_.shape[1] + return self + + def transform(self, X, y=None): + """ + Apply the dimensionality reduction. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Samples to be transformed. + + y : array-like of shape (n_samples,) or (n_samples, n_targets), \ + default=None + Targets. + + Returns + ------- + x_scores : array-like or tuple of array-like + The transformed data `X_transformed` if `y is not None`, + `(X_transformed, y_transformed)` otherwise. + """ + check_is_fitted(self) + X = validate_data(self, X, dtype=np.float64, reset=False) + Xr = (X - self._x_mean) / self._x_std + x_scores = np.dot(Xr, self.x_weights_) + if y is not None: + y = check_array(y, input_name="y", ensure_2d=False, dtype=np.float64) + if y.ndim == 1: + y = y.reshape(-1, 1) + yr = (y - self._y_mean) / self._y_std + y_scores = np.dot(yr, self.y_weights_) + return x_scores, y_scores + return x_scores + + def fit_transform(self, X, y=None): + """Learn and apply the dimensionality reduction. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training samples. + + y : array-like of shape (n_samples,) or (n_samples, n_targets), \ + default=None + Targets. + + Returns + ------- + out : array-like or tuple of array-like + The transformed data `X_transformed` if `y is not None`, + `(X_transformed, y_transformed)` otherwise. + """ + return self.fit(X, y).transform(X, y) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cross_decomposition/tests/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cross_decomposition/tests/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cross_decomposition/tests/test_pls.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cross_decomposition/tests/test_pls.py new file mode 100644 index 0000000000000000000000000000000000000000..7e516d71b6f988710b71c2b8d575a80e42e87d65 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/cross_decomposition/tests/test_pls.py @@ -0,0 +1,677 @@ +import warnings + +import numpy as np +import pytest +from numpy.testing import assert_allclose, assert_array_almost_equal, assert_array_equal + +from sklearn.cross_decomposition import CCA, PLSSVD, PLSCanonical, PLSRegression +from sklearn.cross_decomposition._pls import ( + _center_scale_xy, + _get_first_singular_vectors_power_method, + _get_first_singular_vectors_svd, + _svd_flip_1d, +) +from sklearn.datasets import load_linnerud, make_regression +from sklearn.ensemble import VotingRegressor +from sklearn.exceptions import ConvergenceWarning +from sklearn.linear_model import LinearRegression +from sklearn.utils import check_random_state +from sklearn.utils.extmath import svd_flip + + +def assert_matrix_orthogonal(M): + K = np.dot(M.T, M) + assert_array_almost_equal(K, np.diag(np.diag(K))) + + +def test_pls_canonical_basics(): + # Basic checks for PLSCanonical + d = load_linnerud() + X = d.data + y = d.target + + pls = PLSCanonical(n_components=X.shape[1]) + pls.fit(X, y) + + assert_matrix_orthogonal(pls.x_weights_) + assert_matrix_orthogonal(pls.y_weights_) + assert_matrix_orthogonal(pls._x_scores) + assert_matrix_orthogonal(pls._y_scores) + + # Check X = TP' and y = UQ' + T = pls._x_scores + P = pls.x_loadings_ + U = pls._y_scores + Q = pls.y_loadings_ + # Need to scale first + Xc, yc, x_mean, y_mean, x_std, y_std = _center_scale_xy( + X.copy(), y.copy(), scale=True + ) + assert_array_almost_equal(Xc, np.dot(T, P.T)) + assert_array_almost_equal(yc, np.dot(U, Q.T)) + + # Check that rotations on training data lead to scores + Xt = pls.transform(X) + assert_array_almost_equal(Xt, pls._x_scores) + Xt, yt = pls.transform(X, y) + assert_array_almost_equal(Xt, pls._x_scores) + assert_array_almost_equal(yt, pls._y_scores) + + # Check that inverse_transform works + X_back = pls.inverse_transform(Xt) + assert_array_almost_equal(X_back, X) + _, y_back = pls.inverse_transform(Xt, yt) + assert_array_almost_equal(y_back, y) + + +def test_sanity_check_pls_regression(): + # Sanity check for PLSRegression + # The results were checked against the R-packages plspm, misOmics and pls + + d = load_linnerud() + X = d.data + y = d.target + + pls = PLSRegression(n_components=X.shape[1]) + X_trans, _ = pls.fit_transform(X, y) + + # FIXME: one would expect y_trans == pls.y_scores_ but this is not + # the case. + # xref: https://github.com/scikit-learn/scikit-learn/issues/22420 + assert_allclose(X_trans, pls.x_scores_) + + expected_x_weights = np.array( + [ + [-0.61330704, -0.00443647, 0.78983213], + [-0.74697144, -0.32172099, -0.58183269], + [-0.25668686, 0.94682413, -0.19399983], + ] + ) + + expected_x_loadings = np.array( + [ + [-0.61470416, -0.24574278, 0.78983213], + [-0.65625755, -0.14396183, -0.58183269], + [-0.51733059, 1.00609417, -0.19399983], + ] + ) + + expected_y_weights = np.array( + [ + [+0.32456184, 0.29892183, 0.20316322], + [+0.42439636, 0.61970543, 0.19320542], + [-0.13143144, -0.26348971, -0.17092916], + ] + ) + + expected_y_loadings = np.array( + [ + [+0.32456184, 0.29892183, 0.20316322], + [+0.42439636, 0.61970543, 0.19320542], + [-0.13143144, -0.26348971, -0.17092916], + ] + ) + + assert_array_almost_equal(np.abs(pls.x_loadings_), np.abs(expected_x_loadings)) + assert_array_almost_equal(np.abs(pls.x_weights_), np.abs(expected_x_weights)) + assert_array_almost_equal(np.abs(pls.y_loadings_), np.abs(expected_y_loadings)) + assert_array_almost_equal(np.abs(pls.y_weights_), np.abs(expected_y_weights)) + + # The R / Python difference in the signs should be consistent across + # loadings, weights, etc. + x_loadings_sign_flip = np.sign(pls.x_loadings_ / expected_x_loadings) + x_weights_sign_flip = np.sign(pls.x_weights_ / expected_x_weights) + y_weights_sign_flip = np.sign(pls.y_weights_ / expected_y_weights) + y_loadings_sign_flip = np.sign(pls.y_loadings_ / expected_y_loadings) + assert_array_almost_equal(x_loadings_sign_flip, x_weights_sign_flip) + assert_array_almost_equal(y_loadings_sign_flip, y_weights_sign_flip) + + +def test_sanity_check_pls_regression_constant_column_y(): + # Check behavior when the first column of y is constant + # The results are checked against a modified version of plsreg2 + # from the R-package plsdepot + d = load_linnerud() + X = d.data + y = d.target + y[:, 0] = 1 + pls = PLSRegression(n_components=X.shape[1]) + pls.fit(X, y) + + expected_x_weights = np.array( + [ + [-0.6273573, 0.007081799, 0.7786994], + [-0.7493417, -0.277612681, -0.6011807], + [-0.2119194, 0.960666981, -0.1794690], + ] + ) + + expected_x_loadings = np.array( + [ + [-0.6273512, -0.22464538, 0.7786994], + [-0.6643156, -0.09871193, -0.6011807], + [-0.5125877, 1.01407380, -0.1794690], + ] + ) + + expected_y_loadings = np.array( + [ + [0.0000000, 0.0000000, 0.0000000], + [0.4357300, 0.5828479, 0.2174802], + [-0.1353739, -0.2486423, -0.1810386], + ] + ) + + assert_array_almost_equal(np.abs(expected_x_weights), np.abs(pls.x_weights_)) + assert_array_almost_equal(np.abs(expected_x_loadings), np.abs(pls.x_loadings_)) + # For the PLSRegression with default parameters, y_loadings == y_weights + assert_array_almost_equal(np.abs(pls.y_loadings_), np.abs(expected_y_loadings)) + assert_array_almost_equal(np.abs(pls.y_weights_), np.abs(expected_y_loadings)) + + x_loadings_sign_flip = np.sign(expected_x_loadings / pls.x_loadings_) + x_weights_sign_flip = np.sign(expected_x_weights / pls.x_weights_) + # we ignore the first full-zeros row for y + y_loadings_sign_flip = np.sign(expected_y_loadings[1:] / pls.y_loadings_[1:]) + + assert_array_equal(x_loadings_sign_flip, x_weights_sign_flip) + assert_array_equal(x_loadings_sign_flip[1:], y_loadings_sign_flip) + + +def test_sanity_check_pls_canonical(): + # Sanity check for PLSCanonical + # The results were checked against the R-package plspm + + d = load_linnerud() + X = d.data + y = d.target + + pls = PLSCanonical(n_components=X.shape[1]) + pls.fit(X, y) + + expected_x_weights = np.array( + [ + [-0.61330704, 0.25616119, -0.74715187], + [-0.74697144, 0.11930791, 0.65406368], + [-0.25668686, -0.95924297, -0.11817271], + ] + ) + + expected_x_rotations = np.array( + [ + [-0.61330704, 0.41591889, -0.62297525], + [-0.74697144, 0.31388326, 0.77368233], + [-0.25668686, -0.89237972, -0.24121788], + ] + ) + + expected_y_weights = np.array( + [ + [+0.58989127, 0.7890047, 0.1717553], + [+0.77134053, -0.61351791, 0.16920272], + [-0.23887670, -0.03267062, 0.97050016], + ] + ) + + expected_y_rotations = np.array( + [ + [+0.58989127, 0.7168115, 0.30665872], + [+0.77134053, -0.70791757, 0.19786539], + [-0.23887670, -0.00343595, 0.94162826], + ] + ) + + assert_array_almost_equal(np.abs(pls.x_rotations_), np.abs(expected_x_rotations)) + assert_array_almost_equal(np.abs(pls.x_weights_), np.abs(expected_x_weights)) + assert_array_almost_equal(np.abs(pls.y_rotations_), np.abs(expected_y_rotations)) + assert_array_almost_equal(np.abs(pls.y_weights_), np.abs(expected_y_weights)) + + x_rotations_sign_flip = np.sign(pls.x_rotations_ / expected_x_rotations) + x_weights_sign_flip = np.sign(pls.x_weights_ / expected_x_weights) + y_rotations_sign_flip = np.sign(pls.y_rotations_ / expected_y_rotations) + y_weights_sign_flip = np.sign(pls.y_weights_ / expected_y_weights) + assert_array_almost_equal(x_rotations_sign_flip, x_weights_sign_flip) + assert_array_almost_equal(y_rotations_sign_flip, y_weights_sign_flip) + + assert_matrix_orthogonal(pls.x_weights_) + assert_matrix_orthogonal(pls.y_weights_) + + assert_matrix_orthogonal(pls._x_scores) + assert_matrix_orthogonal(pls._y_scores) + + +def test_sanity_check_pls_canonical_random(): + # Sanity check for PLSCanonical on random data + # The results were checked against the R-package plspm + n = 500 + p_noise = 10 + q_noise = 5 + # 2 latents vars: + rng = check_random_state(11) + l1 = rng.normal(size=n) + l2 = rng.normal(size=n) + latents = np.array([l1, l1, l2, l2]).T + X = latents + rng.normal(size=4 * n).reshape((n, 4)) + y = latents + rng.normal(size=4 * n).reshape((n, 4)) + X = np.concatenate((X, rng.normal(size=p_noise * n).reshape(n, p_noise)), axis=1) + y = np.concatenate((y, rng.normal(size=q_noise * n).reshape(n, q_noise)), axis=1) + + pls = PLSCanonical(n_components=3) + pls.fit(X, y) + + expected_x_weights = np.array( + [ + [0.65803719, 0.19197924, 0.21769083], + [0.7009113, 0.13303969, -0.15376699], + [0.13528197, -0.68636408, 0.13856546], + [0.16854574, -0.66788088, -0.12485304], + [-0.03232333, -0.04189855, 0.40690153], + [0.1148816, -0.09643158, 0.1613305], + [0.04792138, -0.02384992, 0.17175319], + [-0.06781, -0.01666137, -0.18556747], + [-0.00266945, -0.00160224, 0.11893098], + [-0.00849528, -0.07706095, 0.1570547], + [-0.00949471, -0.02964127, 0.34657036], + [-0.03572177, 0.0945091, 0.3414855], + [0.05584937, -0.02028961, -0.57682568], + [0.05744254, -0.01482333, -0.17431274], + ] + ) + + expected_x_loadings = np.array( + [ + [0.65649254, 0.1847647, 0.15270699], + [0.67554234, 0.15237508, -0.09182247], + [0.19219925, -0.67750975, 0.08673128], + [0.2133631, -0.67034809, -0.08835483], + [-0.03178912, -0.06668336, 0.43395268], + [0.15684588, -0.13350241, 0.20578984], + [0.03337736, -0.03807306, 0.09871553], + [-0.06199844, 0.01559854, -0.1881785], + [0.00406146, -0.00587025, 0.16413253], + [-0.00374239, -0.05848466, 0.19140336], + [0.00139214, -0.01033161, 0.32239136], + [-0.05292828, 0.0953533, 0.31916881], + [0.04031924, -0.01961045, -0.65174036], + [0.06172484, -0.06597366, -0.1244497], + ] + ) + + expected_y_weights = np.array( + [ + [0.66101097, 0.18672553, 0.22826092], + [0.69347861, 0.18463471, -0.23995597], + [0.14462724, -0.66504085, 0.17082434], + [0.22247955, -0.6932605, -0.09832993], + [0.07035859, 0.00714283, 0.67810124], + [0.07765351, -0.0105204, -0.44108074], + [-0.00917056, 0.04322147, 0.10062478], + [-0.01909512, 0.06182718, 0.28830475], + [0.01756709, 0.04797666, 0.32225745], + ] + ) + + expected_y_loadings = np.array( + [ + [0.68568625, 0.1674376, 0.0969508], + [0.68782064, 0.20375837, -0.1164448], + [0.11712173, -0.68046903, 0.12001505], + [0.17860457, -0.6798319, -0.05089681], + [0.06265739, -0.0277703, 0.74729584], + [0.0914178, 0.00403751, -0.5135078], + [-0.02196918, -0.01377169, 0.09564505], + [-0.03288952, 0.09039729, 0.31858973], + [0.04287624, 0.05254676, 0.27836841], + ] + ) + + assert_array_almost_equal(np.abs(pls.x_loadings_), np.abs(expected_x_loadings)) + assert_array_almost_equal(np.abs(pls.x_weights_), np.abs(expected_x_weights)) + assert_array_almost_equal(np.abs(pls.y_loadings_), np.abs(expected_y_loadings)) + assert_array_almost_equal(np.abs(pls.y_weights_), np.abs(expected_y_weights)) + + x_loadings_sign_flip = np.sign(pls.x_loadings_ / expected_x_loadings) + x_weights_sign_flip = np.sign(pls.x_weights_ / expected_x_weights) + y_weights_sign_flip = np.sign(pls.y_weights_ / expected_y_weights) + y_loadings_sign_flip = np.sign(pls.y_loadings_ / expected_y_loadings) + assert_array_almost_equal(x_loadings_sign_flip, x_weights_sign_flip) + assert_array_almost_equal(y_loadings_sign_flip, y_weights_sign_flip) + + assert_matrix_orthogonal(pls.x_weights_) + assert_matrix_orthogonal(pls.y_weights_) + + assert_matrix_orthogonal(pls._x_scores) + assert_matrix_orthogonal(pls._y_scores) + + +def test_convergence_fail(): + # Make sure ConvergenceWarning is raised if max_iter is too small + d = load_linnerud() + X = d.data + y = d.target + pls_nipals = PLSCanonical(n_components=X.shape[1], max_iter=2) + with pytest.warns(ConvergenceWarning): + pls_nipals.fit(X, y) + + +@pytest.mark.parametrize("Est", (PLSSVD, PLSRegression, PLSCanonical)) +def test_attibutes_shapes(Est): + # Make sure attributes are of the correct shape depending on n_components + d = load_linnerud() + X = d.data + y = d.target + n_components = 2 + pls = Est(n_components=n_components) + pls.fit(X, y) + assert all( + attr.shape[1] == n_components for attr in (pls.x_weights_, pls.y_weights_) + ) + + +@pytest.mark.parametrize("Est", (PLSRegression, PLSCanonical, CCA)) +def test_univariate_equivalence(Est): + # Ensure 2D y with 1 column is equivalent to 1D y + d = load_linnerud() + X = d.data + y = d.target + + est = Est(n_components=1) + one_d_coeff = est.fit(X, y[:, 0]).coef_ + two_d_coeff = est.fit(X, y[:, :1]).coef_ + + assert one_d_coeff.shape == two_d_coeff.shape + assert_array_almost_equal(one_d_coeff, two_d_coeff) + + +@pytest.mark.parametrize("Est", (PLSRegression, PLSCanonical, CCA, PLSSVD)) +def test_copy(Est): + # check that the "copy" keyword works + d = load_linnerud() + X = d.data + y = d.target + X_orig = X.copy() + + # copy=True won't modify inplace + pls = Est(copy=True).fit(X, y) + assert_array_equal(X, X_orig) + + # copy=False will modify inplace + with pytest.raises(AssertionError): + Est(copy=False).fit(X, y) + assert_array_almost_equal(X, X_orig) + + if Est is PLSSVD: + return # PLSSVD does not support copy param in predict or transform + + X_orig = X.copy() + with pytest.raises(AssertionError): + pls.transform(X, y, copy=False) + assert_array_almost_equal(X, X_orig) + + X_orig = X.copy() + with pytest.raises(AssertionError): + pls.predict(X, copy=False) + assert_array_almost_equal(X, X_orig) + + # Make sure copy=True gives same transform and predictions as predict=False + assert_array_almost_equal( + pls.transform(X, y, copy=True), pls.transform(X.copy(), y.copy(), copy=False) + ) + assert_array_almost_equal( + pls.predict(X, copy=True), pls.predict(X.copy(), copy=False) + ) + + +def _generate_test_scale_and_stability_datasets(): + """Generate dataset for test_scale_and_stability""" + # dataset for non-regression 7818 + rng = np.random.RandomState(0) + n_samples = 1000 + n_targets = 5 + n_features = 10 + Q = rng.randn(n_targets, n_features) + y = rng.randn(n_samples, n_targets) + X = np.dot(y, Q) + 2 * rng.randn(n_samples, n_features) + 1 + X *= 1000 + yield X, y + + # Data set where one of the features is constraint + X, y = load_linnerud(return_X_y=True) + # causes X[:, -1].std() to be zero + X[:, -1] = 1.0 + yield X, y + + X = np.array([[0.0, 0.0, 1.0], [1.0, 0.0, 0.0], [2.0, 2.0, 2.0], [3.0, 5.0, 4.0]]) + y = np.array([[0.1, -0.2], [0.9, 1.1], [6.2, 5.9], [11.9, 12.3]]) + yield X, y + + # Seeds that provide a non-regression test for #18746, where CCA fails + seeds = [530, 741] + for seed in seeds: + rng = np.random.RandomState(seed) + X = rng.randn(4, 3) + y = rng.randn(4, 2) + yield X, y + + +@pytest.mark.parametrize("Est", (CCA, PLSCanonical, PLSRegression, PLSSVD)) +@pytest.mark.parametrize("X, y", _generate_test_scale_and_stability_datasets()) +def test_scale_and_stability(Est, X, y): + """scale=True is equivalent to scale=False on centered/scaled data + This allows to check numerical stability over platforms as well""" + + X_s, y_s, *_ = _center_scale_xy(X, y) + + X_score, y_score = Est(scale=True).fit_transform(X, y) + X_s_score, y_s_score = Est(scale=False).fit_transform(X_s, y_s) + + assert_allclose(X_s_score, X_score, atol=1e-4) + assert_allclose(y_s_score, y_score, atol=1e-4) + + +@pytest.mark.parametrize("Estimator", (PLSSVD, PLSRegression, PLSCanonical, CCA)) +def test_n_components_upper_bounds(Estimator): + """Check the validation of `n_components` upper bounds for `PLS` regressors.""" + rng = np.random.RandomState(0) + X = rng.randn(10, 5) + y = rng.randn(10, 3) + est = Estimator(n_components=10) + err_msg = "`n_components` upper bound is .*. Got 10 instead. Reduce `n_components`." + with pytest.raises(ValueError, match=err_msg): + est.fit(X, y) + + +def test_n_components_upper_PLSRegression(): + """Check the validation of `n_components` upper bounds for PLSRegression.""" + rng = np.random.RandomState(0) + X = rng.randn(20, 64) + y = rng.randn(20, 3) + est = PLSRegression(n_components=30) + err_msg = "`n_components` upper bound is 20. Got 30 instead. Reduce `n_components`." + with pytest.raises(ValueError, match=err_msg): + est.fit(X, y) + + +@pytest.mark.parametrize("n_samples, n_features", [(100, 10), (100, 200)]) +def test_singular_value_helpers(n_samples, n_features, global_random_seed): + # Make sure SVD and power method give approximately the same results + X, y = make_regression( + n_samples, n_features, n_targets=5, random_state=global_random_seed + ) + u1, v1, _ = _get_first_singular_vectors_power_method(X, y, norm_y_weights=True) + u2, v2 = _get_first_singular_vectors_svd(X, y) + + _svd_flip_1d(u1, v1) + _svd_flip_1d(u2, v2) + + rtol = 1e-3 + # Setting atol because some coordinates are very close to zero + assert_allclose(u1, u2, atol=u2.max() * rtol) + assert_allclose(v1, v2, atol=v2.max() * rtol) + + +def test_one_component_equivalence(global_random_seed): + # PLSSVD, PLSRegression and PLSCanonical should all be equivalent when + # n_components is 1 + X, y = make_regression(100, 10, n_targets=5, random_state=global_random_seed) + svd = PLSSVD(n_components=1).fit(X, y).transform(X) + reg = PLSRegression(n_components=1).fit(X, y).transform(X) + canonical = PLSCanonical(n_components=1).fit(X, y).transform(X) + + rtol = 1e-3 + # Setting atol because some entries are very close to zero + assert_allclose(svd, reg, atol=reg.max() * rtol) + assert_allclose(svd, canonical, atol=canonical.max() * rtol) + + +def test_svd_flip_1d(): + # Make sure svd_flip_1d is equivalent to svd_flip + u = np.array([1, -4, 2]) + v = np.array([1, 2, 3]) + + u_expected, v_expected = svd_flip(u.reshape(-1, 1), v.reshape(1, -1)) + _svd_flip_1d(u, v) # inplace + + assert_allclose(u, u_expected.ravel()) + assert_allclose(u, [-1, 4, -2]) + + assert_allclose(v, v_expected.ravel()) + assert_allclose(v, [-1, -2, -3]) + + +def test_loadings_converges(global_random_seed): + """Test that CCA converges. Non-regression test for #19549.""" + X, y = make_regression( + n_samples=200, n_features=20, n_targets=20, random_state=global_random_seed + ) + + cca = CCA(n_components=10, max_iter=500) + + with warnings.catch_warnings(): + warnings.simplefilter("error", ConvergenceWarning) + + cca.fit(X, y) + + # Loadings converges to reasonable values + assert np.all(np.abs(cca.x_loadings_) < 1) + + +def test_pls_constant_y(): + """Checks warning when y is constant. Non-regression test for #19831""" + rng = np.random.RandomState(42) + x = rng.rand(100, 3) + y = np.zeros(100) + + pls = PLSRegression() + + msg = "y residual is constant at iteration" + with pytest.warns(UserWarning, match=msg): + pls.fit(x, y) + + assert_allclose(pls.x_rotations_, 0) + + +@pytest.mark.parametrize("PLSEstimator", [PLSRegression, PLSCanonical, CCA]) +def test_pls_coef_shape(PLSEstimator): + """Check the shape of `coef_` attribute. + + Non-regression test for: + https://github.com/scikit-learn/scikit-learn/issues/12410 + """ + d = load_linnerud() + X = d.data + y = d.target + + pls = PLSEstimator(copy=True).fit(X, y) + + n_targets, n_features = y.shape[1], X.shape[1] + assert pls.coef_.shape == (n_targets, n_features) + + +@pytest.mark.parametrize("scale", [True, False]) +@pytest.mark.parametrize("PLSEstimator", [PLSRegression, PLSCanonical, CCA]) +def test_pls_prediction(PLSEstimator, scale): + """Check the behaviour of the prediction function.""" + d = load_linnerud() + X = d.data + y = d.target + + pls = PLSEstimator(copy=True, scale=scale).fit(X, y) + y_pred = pls.predict(X, copy=True) + + y_mean = y.mean(axis=0) + X_trans = X - X.mean(axis=0) + + assert_allclose(pls.intercept_, y_mean) + assert_allclose(y_pred, X_trans @ pls.coef_.T + pls.intercept_) + + +@pytest.mark.parametrize("Klass", [CCA, PLSSVD, PLSRegression, PLSCanonical]) +def test_pls_feature_names_out(Klass): + """Check `get_feature_names_out` cross_decomposition module.""" + X, y = load_linnerud(return_X_y=True) + + est = Klass().fit(X, y) + names_out = est.get_feature_names_out() + + class_name_lower = Klass.__name__.lower() + expected_names_out = np.array( + [f"{class_name_lower}{i}" for i in range(est.x_weights_.shape[1])], + dtype=object, + ) + assert_array_equal(names_out, expected_names_out) + + +@pytest.mark.parametrize("Klass", [CCA, PLSSVD, PLSRegression, PLSCanonical]) +def test_pls_set_output(Klass): + """Check `set_output` in cross_decomposition module.""" + pd = pytest.importorskip("pandas") + X, y = load_linnerud(return_X_y=True, as_frame=True) + + est = Klass().set_output(transform="pandas").fit(X, y) + X_trans, y_trans = est.transform(X, y) + assert isinstance(y_trans, np.ndarray) + assert isinstance(X_trans, pd.DataFrame) + assert_array_equal(X_trans.columns, est.get_feature_names_out()) + + +def test_pls_regression_fit_1d_y(): + """Check that when fitting with 1d `y`, prediction should also be 1d. + + Non-regression test for Issue #26549. + """ + X = np.array([[1, 1], [2, 4], [3, 9], [4, 16], [5, 25], [6, 36]]) + y = np.array([2, 6, 12, 20, 30, 42]) + expected = y.copy() + + plsr = PLSRegression().fit(X, y) + y_pred = plsr.predict(X) + assert y_pred.shape == expected.shape + + # Check that it works in VotingRegressor + lr = LinearRegression().fit(X, y) + vr = VotingRegressor([("lr", lr), ("plsr", plsr)]) + y_pred = vr.fit(X, y).predict(X) + assert y_pred.shape == expected.shape + assert_allclose(y_pred, expected) + + +def test_pls_regression_scaling_coef(): + """Check that when using `scale=True`, the coefficients are using the std. dev. from + both `X` and `y`. + + Non-regression test for: + https://github.com/scikit-learn/scikit-learn/issues/27964 + """ + # handcrafted data where we can predict y from X with an additional scaling factor + rng = np.random.RandomState(0) + coef = rng.uniform(size=(3, 5)) + X = rng.normal(scale=10, size=(30, 5)) # add a std of 10 + y = X @ coef.T + + # we need to make sure that the dimension of the latent space is large enough to + # perfectly predict `y` from `X` (no information loss) + pls = PLSRegression(n_components=5, scale=True).fit(X, y) + assert_allclose(pls.coef_, coef) + + # we therefore should be able to predict `y` from `X` + assert_allclose(pls.predict(X), y) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/datasets/__init__.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/datasets/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..8863fe489f3b62740757c3801ee55d7e1e406703 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/datasets/__init__.py @@ -0,0 +1,166 @@ +"""Utilities to load popular datasets and artificial data generators.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import textwrap + +from ._base import ( + clear_data_home, + fetch_file, + get_data_home, + load_breast_cancer, + load_diabetes, + load_digits, + load_files, + load_iris, + load_linnerud, + load_sample_image, + load_sample_images, + load_wine, +) +from ._california_housing import fetch_california_housing +from ._covtype import fetch_covtype +from ._kddcup99 import fetch_kddcup99 +from ._lfw import fetch_lfw_pairs, fetch_lfw_people +from ._olivetti_faces import fetch_olivetti_faces +from ._openml import fetch_openml +from ._rcv1 import fetch_rcv1 +from ._samples_generator import ( + make_biclusters, + make_blobs, + make_checkerboard, + make_circles, + make_classification, + make_friedman1, + make_friedman2, + make_friedman3, + make_gaussian_quantiles, + make_hastie_10_2, + make_low_rank_matrix, + make_moons, + make_multilabel_classification, + make_regression, + make_s_curve, + make_sparse_coded_signal, + make_sparse_spd_matrix, + make_sparse_uncorrelated, + make_spd_matrix, + make_swiss_roll, +) +from ._species_distributions import fetch_species_distributions +from ._svmlight_format_io import ( + dump_svmlight_file, + load_svmlight_file, + load_svmlight_files, +) +from ._twenty_newsgroups import fetch_20newsgroups, fetch_20newsgroups_vectorized + +__all__ = [ + "clear_data_home", + "dump_svmlight_file", + "fetch_20newsgroups", + "fetch_20newsgroups_vectorized", + "fetch_california_housing", + "fetch_covtype", + "fetch_file", + "fetch_kddcup99", + "fetch_lfw_pairs", + "fetch_lfw_people", + "fetch_olivetti_faces", + "fetch_openml", + "fetch_rcv1", + "fetch_species_distributions", + "get_data_home", + "load_breast_cancer", + "load_diabetes", + "load_digits", + "load_files", + "load_iris", + "load_linnerud", + "load_sample_image", + "load_sample_images", + "load_svmlight_file", + "load_svmlight_files", + "load_wine", + "make_biclusters", + "make_blobs", + "make_checkerboard", + "make_circles", + "make_classification", + "make_friedman1", + "make_friedman2", + "make_friedman3", + "make_gaussian_quantiles", + "make_hastie_10_2", + "make_low_rank_matrix", + "make_moons", + "make_multilabel_classification", + "make_regression", + "make_s_curve", + "make_sparse_coded_signal", + "make_sparse_spd_matrix", + "make_sparse_uncorrelated", + "make_spd_matrix", + "make_swiss_roll", +] + + +def __getattr__(name): + if name == "load_boston": + msg = textwrap.dedent( + """ + `load_boston` has been removed from scikit-learn since version 1.2. + + The Boston housing prices dataset has an ethical problem: as + investigated in [1], the authors of this dataset engineered a + non-invertible variable "B" assuming that racial self-segregation had a + positive impact on house prices [2]. Furthermore the goal of the + research that led to the creation of this dataset was to study the + impact of air quality but it did not give adequate demonstration of the + validity of this assumption. + + The scikit-learn maintainers therefore strongly discourage the use of + this dataset unless the purpose of the code is to study and educate + about ethical issues in data science and machine learning. + + In this special case, you can fetch the dataset from the original + source:: + + import pandas as pd + import numpy as np + + data_url = "http://lib.stat.cmu.edu/datasets/boston" + raw_df = pd.read_csv(data_url, sep="\\s+", skiprows=22, header=None) + data = np.hstack([raw_df.values[::2, :], raw_df.values[1::2, :2]]) + target = raw_df.values[1::2, 2] + + Alternative datasets include the California housing dataset and the + Ames housing dataset. You can load the datasets as follows:: + + from sklearn.datasets import fetch_california_housing + housing = fetch_california_housing() + + for the California housing dataset and:: + + from sklearn.datasets import fetch_openml + housing = fetch_openml(name="house_prices", as_frame=True) + + for the Ames housing dataset. + + [1] M Carlisle. + "Racist data destruction?" + + + [2] Harrison Jr, David, and Daniel L. Rubinfeld. + "Hedonic housing prices and the demand for clean air." + Journal of environmental economics and management 5.1 (1978): 81-102. + + """ + ) + raise ImportError(msg) + try: + return globals()[name] + except KeyError: + # This is turned into the appropriate ImportError + raise AttributeError diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/discriminant_analysis.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/discriminant_analysis.py new file mode 100644 index 0000000000000000000000000000000000000000..6df26a05a87817a1c50c10c73626c1638df09ccb --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/discriminant_analysis.py @@ -0,0 +1,1129 @@ +"""Linear and quadratic discriminant analysis.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from numbers import Integral, Real + +import numpy as np +import scipy.linalg +from scipy import linalg + +from .base import ( + BaseEstimator, + ClassifierMixin, + ClassNamePrefixFeaturesOutMixin, + TransformerMixin, + _fit_context, +) +from .covariance import empirical_covariance, ledoit_wolf, shrunk_covariance +from .linear_model._base import LinearClassifierMixin +from .preprocessing import StandardScaler +from .utils._array_api import _expit, device, get_namespace, size +from .utils._param_validation import HasMethods, Interval, StrOptions +from .utils.extmath import softmax +from .utils.multiclass import check_classification_targets, unique_labels +from .utils.validation import check_is_fitted, validate_data + +__all__ = ["LinearDiscriminantAnalysis", "QuadraticDiscriminantAnalysis"] + + +def _cov(X, shrinkage=None, covariance_estimator=None): + """Estimate covariance matrix (using optional covariance_estimator). + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Input data. + + shrinkage : {'empirical', 'auto'} or float, default=None + Shrinkage parameter, possible values: + - None or 'empirical': no shrinkage (default). + - 'auto': automatic shrinkage using the Ledoit-Wolf lemma. + - float between 0 and 1: fixed shrinkage parameter. + + Shrinkage parameter is ignored if `covariance_estimator` + is not None. + + covariance_estimator : estimator, default=None + If not None, `covariance_estimator` is used to estimate + the covariance matrices instead of relying on the empirical + covariance estimator (with potential shrinkage). + The object should have a fit method and a ``covariance_`` attribute + like the estimators in :mod:`sklearn.covariance``. + if None the shrinkage parameter drives the estimate. + + .. versionadded:: 0.24 + + Returns + ------- + s : ndarray of shape (n_features, n_features) + Estimated covariance matrix. + """ + if covariance_estimator is None: + shrinkage = "empirical" if shrinkage is None else shrinkage + if isinstance(shrinkage, str): + if shrinkage == "auto": + sc = StandardScaler() # standardize features + X = sc.fit_transform(X) + s = ledoit_wolf(X)[0] + # rescale + s = sc.scale_[:, np.newaxis] * s * sc.scale_[np.newaxis, :] + elif shrinkage == "empirical": + s = empirical_covariance(X) + elif isinstance(shrinkage, Real): + s = shrunk_covariance(empirical_covariance(X), shrinkage) + else: + if shrinkage is not None and shrinkage != 0: + raise ValueError( + "covariance_estimator and shrinkage parameters " + "are not None. Only one of the two can be set." + ) + covariance_estimator.fit(X) + if not hasattr(covariance_estimator, "covariance_"): + raise ValueError( + "%s does not have a covariance_ attribute" + % covariance_estimator.__class__.__name__ + ) + s = covariance_estimator.covariance_ + return s + + +def _class_means(X, y): + """Compute class means. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Input data. + + y : array-like of shape (n_samples,) or (n_samples, n_targets) + Target values. + + Returns + ------- + means : array-like of shape (n_classes, n_features) + Class means. + """ + xp, is_array_api_compliant = get_namespace(X) + classes, y = xp.unique_inverse(y) + means = xp.zeros((classes.shape[0], X.shape[1]), device=device(X), dtype=X.dtype) + + if is_array_api_compliant: + for i in range(classes.shape[0]): + means[i, :] = xp.mean(X[y == i], axis=0) + else: + # TODO: Explore the choice of using bincount + add.at as it seems sub optimal + # from a performance-wise + cnt = np.bincount(y) + np.add.at(means, y, X) + means /= cnt[:, None] + return means + + +def _class_cov(X, y, priors, shrinkage=None, covariance_estimator=None): + """Compute weighted within-class covariance matrix. + + The per-class covariance are weighted by the class priors. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Input data. + + y : array-like of shape (n_samples,) or (n_samples, n_targets) + Target values. + + priors : array-like of shape (n_classes,) + Class priors. + + shrinkage : 'auto' or float, default=None + Shrinkage parameter, possible values: + - None: no shrinkage (default). + - 'auto': automatic shrinkage using the Ledoit-Wolf lemma. + - float between 0 and 1: fixed shrinkage parameter. + + Shrinkage parameter is ignored if `covariance_estimator` is not None. + + covariance_estimator : estimator, default=None + If not None, `covariance_estimator` is used to estimate + the covariance matrices instead of relying the empirical + covariance estimator (with potential shrinkage). + The object should have a fit method and a ``covariance_`` attribute + like the estimators in sklearn.covariance. + If None, the shrinkage parameter drives the estimate. + + .. versionadded:: 0.24 + + Returns + ------- + cov : array-like of shape (n_features, n_features) + Weighted within-class covariance matrix + """ + classes = np.unique(y) + cov = np.zeros(shape=(X.shape[1], X.shape[1])) + for idx, group in enumerate(classes): + Xg = X[y == group, :] + cov += priors[idx] * np.atleast_2d(_cov(Xg, shrinkage, covariance_estimator)) + return cov + + +class DiscriminantAnalysisPredictionMixin: + """Mixin class for QuadraticDiscriminantAnalysis and NearestCentroid.""" + + def decision_function(self, X): + """Apply decision function to an array of samples. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Array of samples (test vectors). + + Returns + ------- + y_scores : ndarray of shape (n_samples,) or (n_samples, n_classes) + Decision function values related to each class, per sample. + In the two-class case, the shape is `(n_samples,)`, giving the + log likelihood ratio of the positive class. + """ + y_scores = self._decision_function(X) + if len(self.classes_) == 2: + return y_scores[:, 1] - y_scores[:, 0] + return y_scores + + def predict(self, X): + """Perform classification on an array of vectors `X`. + + Returns the class label for each sample. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Input vectors, where `n_samples` is the number of samples and + `n_features` is the number of features. + + Returns + ------- + y_pred : ndarray of shape (n_samples,) + Class label for each sample. + """ + scores = self._decision_function(X) + return self.classes_.take(scores.argmax(axis=1)) + + def predict_proba(self, X): + """Estimate class probabilities. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Input data. + + Returns + ------- + y_proba : ndarray of shape (n_samples, n_classes) + Probability estimate of the sample for each class in the + model, where classes are ordered as they are in `self.classes_`. + """ + return np.exp(self.predict_log_proba(X)) + + def predict_log_proba(self, X): + """Estimate log class probabilities. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Input data. + + Returns + ------- + y_log_proba : ndarray of shape (n_samples, n_classes) + Estimated log probabilities. + """ + scores = self._decision_function(X) + log_likelihood = scores - scores.max(axis=1)[:, np.newaxis] + return log_likelihood - np.log( + np.exp(log_likelihood).sum(axis=1)[:, np.newaxis] + ) + + +class LinearDiscriminantAnalysis( + ClassNamePrefixFeaturesOutMixin, + LinearClassifierMixin, + TransformerMixin, + BaseEstimator, +): + """Linear Discriminant Analysis. + + A classifier with a linear decision boundary, generated by fitting class + conditional densities to the data and using Bayes' rule. + + The model fits a Gaussian density to each class, assuming that all classes + share the same covariance matrix. + + The fitted model can also be used to reduce the dimensionality of the input + by projecting it to the most discriminative directions, using the + `transform` method. + + .. versionadded:: 0.17 + + For a comparison between + :class:`~sklearn.discriminant_analysis.LinearDiscriminantAnalysis` + and :class:`~sklearn.discriminant_analysis.QuadraticDiscriminantAnalysis`, see + :ref:`sphx_glr_auto_examples_classification_plot_lda_qda.py`. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + solver : {'svd', 'lsqr', 'eigen'}, default='svd' + Solver to use, possible values: + - 'svd': Singular value decomposition (default). + Does not compute the covariance matrix, therefore this solver is + recommended for data with a large number of features. + - 'lsqr': Least squares solution. + Can be combined with shrinkage or custom covariance estimator. + - 'eigen': Eigenvalue decomposition. + Can be combined with shrinkage or custom covariance estimator. + + .. versionchanged:: 1.2 + `solver="svd"` now has experimental Array API support. See the + :ref:`Array API User Guide ` for more details. + + shrinkage : 'auto' or float, default=None + Shrinkage parameter, possible values: + - None: no shrinkage (default). + - 'auto': automatic shrinkage using the Ledoit-Wolf lemma. + - float between 0 and 1: fixed shrinkage parameter. + + This should be left to None if `covariance_estimator` is used. + Note that shrinkage works only with 'lsqr' and 'eigen' solvers. + + For a usage example, see + :ref:`sphx_glr_auto_examples_classification_plot_lda.py`. + + priors : array-like of shape (n_classes,), default=None + The class prior probabilities. By default, the class proportions are + inferred from the training data. + + n_components : int, default=None + Number of components (<= min(n_classes - 1, n_features)) for + dimensionality reduction. If None, will be set to + min(n_classes - 1, n_features). This parameter only affects the + `transform` method. + + For a usage example, see + :ref:`sphx_glr_auto_examples_decomposition_plot_pca_vs_lda.py`. + + store_covariance : bool, default=False + If True, explicitly compute the weighted within-class covariance + matrix when solver is 'svd'. The matrix is always computed + and stored for the other solvers. + + .. versionadded:: 0.17 + + tol : float, default=1.0e-4 + Absolute threshold for a singular value of X to be considered + significant, used to estimate the rank of X. Dimensions whose + singular values are non-significant are discarded. Only used if + solver is 'svd'. + + .. versionadded:: 0.17 + + covariance_estimator : covariance estimator, default=None + If not None, `covariance_estimator` is used to estimate + the covariance matrices instead of relying on the empirical + covariance estimator (with potential shrinkage). + The object should have a fit method and a ``covariance_`` attribute + like the estimators in :mod:`sklearn.covariance`. + if None the shrinkage parameter drives the estimate. + + This should be left to None if `shrinkage` is used. + Note that `covariance_estimator` works only with 'lsqr' and 'eigen' + solvers. + + .. versionadded:: 0.24 + + Attributes + ---------- + coef_ : ndarray of shape (n_features,) or (n_classes, n_features) + Weight vector(s). + + intercept_ : ndarray of shape (n_classes,) + Intercept term. + + covariance_ : array-like of shape (n_features, n_features) + Weighted within-class covariance matrix. It corresponds to + `sum_k prior_k * C_k` where `C_k` is the covariance matrix of the + samples in class `k`. The `C_k` are estimated using the (potentially + shrunk) biased estimator of covariance. If solver is 'svd', only + exists when `store_covariance` is True. + + explained_variance_ratio_ : ndarray of shape (n_components,) + Percentage of variance explained by each of the selected components. + If ``n_components`` is not set then all components are stored and the + sum of explained variances is equal to 1.0. Only available when eigen + or svd solver is used. + + means_ : array-like of shape (n_classes, n_features) + Class-wise means. + + priors_ : array-like of shape (n_classes,) + Class priors (sum to 1). + + scalings_ : array-like of shape (rank, n_classes - 1) + Scaling of the features in the space spanned by the class centroids. + Only available for 'svd' and 'eigen' solvers. + + xbar_ : array-like of shape (n_features,) + Overall mean. Only present if solver is 'svd'. + + classes_ : array-like of shape (n_classes,) + Unique class labels. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + QuadraticDiscriminantAnalysis : Quadratic Discriminant Analysis. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.discriminant_analysis import LinearDiscriminantAnalysis + >>> X = np.array([[-1, -1], [-2, -1], [-3, -2], [1, 1], [2, 1], [3, 2]]) + >>> y = np.array([1, 1, 1, 2, 2, 2]) + >>> clf = LinearDiscriminantAnalysis() + >>> clf.fit(X, y) + LinearDiscriminantAnalysis() + >>> print(clf.predict([[-0.8, -1]])) + [1] + """ + + _parameter_constraints: dict = { + "solver": [StrOptions({"svd", "lsqr", "eigen"})], + "shrinkage": [StrOptions({"auto"}), Interval(Real, 0, 1, closed="both"), None], + "n_components": [Interval(Integral, 1, None, closed="left"), None], + "priors": ["array-like", None], + "store_covariance": ["boolean"], + "tol": [Interval(Real, 0, None, closed="left")], + "covariance_estimator": [HasMethods("fit"), None], + } + + def __init__( + self, + solver="svd", + shrinkage=None, + priors=None, + n_components=None, + store_covariance=False, + tol=1e-4, + covariance_estimator=None, + ): + self.solver = solver + self.shrinkage = shrinkage + self.priors = priors + self.n_components = n_components + self.store_covariance = store_covariance # used only in svd solver + self.tol = tol # used only in svd solver + self.covariance_estimator = covariance_estimator + + def _solve_lstsq(self, X, y, shrinkage, covariance_estimator): + """Least squares solver. + + The least squares solver computes a straightforward solution of the + optimal decision rule based directly on the discriminant functions. It + can only be used for classification (with any covariance estimator), + because + estimation of eigenvectors is not performed. Therefore, dimensionality + reduction with the transform is not supported. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data. + + y : array-like of shape (n_samples,) or (n_samples, n_classes) + Target values. + + shrinkage : 'auto', float or None + Shrinkage parameter, possible values: + - None: no shrinkage. + - 'auto': automatic shrinkage using the Ledoit-Wolf lemma. + - float between 0 and 1: fixed shrinkage parameter. + + Shrinkage parameter is ignored if `covariance_estimator` i + not None + + covariance_estimator : estimator, default=None + If not None, `covariance_estimator` is used to estimate + the covariance matrices instead of relying the empirical + covariance estimator (with potential shrinkage). + The object should have a fit method and a ``covariance_`` attribute + like the estimators in sklearn.covariance. + if None the shrinkage parameter drives the estimate. + + .. versionadded:: 0.24 + + Notes + ----- + This solver is based on [1]_, section 2.6.2, pp. 39-41. + + References + ---------- + .. [1] R. O. Duda, P. E. Hart, D. G. Stork. Pattern Classification + (Second Edition). John Wiley & Sons, Inc., New York, 2001. ISBN + 0-471-05669-3. + """ + self.means_ = _class_means(X, y) + self.covariance_ = _class_cov( + X, y, self.priors_, shrinkage, covariance_estimator + ) + self.coef_ = linalg.lstsq(self.covariance_, self.means_.T)[0].T + self.intercept_ = -0.5 * np.diag(np.dot(self.means_, self.coef_.T)) + np.log( + self.priors_ + ) + + def _solve_eigen(self, X, y, shrinkage, covariance_estimator): + """Eigenvalue solver. + + The eigenvalue solver computes the optimal solution of the Rayleigh + coefficient (basically the ratio of between class scatter to within + class scatter). This solver supports both classification and + dimensionality reduction (with any covariance estimator). + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data. + + y : array-like of shape (n_samples,) or (n_samples, n_targets) + Target values. + + shrinkage : 'auto', float or None + Shrinkage parameter, possible values: + - None: no shrinkage. + - 'auto': automatic shrinkage using the Ledoit-Wolf lemma. + - float between 0 and 1: fixed shrinkage constant. + + Shrinkage parameter is ignored if `covariance_estimator` i + not None + + covariance_estimator : estimator, default=None + If not None, `covariance_estimator` is used to estimate + the covariance matrices instead of relying the empirical + covariance estimator (with potential shrinkage). + The object should have a fit method and a ``covariance_`` attribute + like the estimators in sklearn.covariance. + if None the shrinkage parameter drives the estimate. + + .. versionadded:: 0.24 + + Notes + ----- + This solver is based on [1]_, section 3.8.3, pp. 121-124. + + References + ---------- + .. [1] R. O. Duda, P. E. Hart, D. G. Stork. Pattern Classification + (Second Edition). John Wiley & Sons, Inc., New York, 2001. ISBN + 0-471-05669-3. + """ + self.means_ = _class_means(X, y) + self.covariance_ = _class_cov( + X, y, self.priors_, shrinkage, covariance_estimator + ) + + Sw = self.covariance_ # within scatter + St = _cov(X, shrinkage, covariance_estimator) # total scatter + Sb = St - Sw # between scatter + + evals, evecs = linalg.eigh(Sb, Sw) + self.explained_variance_ratio_ = np.sort(evals / np.sum(evals))[::-1][ + : self._max_components + ] + evecs = evecs[:, np.argsort(evals)[::-1]] # sort eigenvectors + + self.scalings_ = evecs + self.coef_ = np.dot(self.means_, evecs).dot(evecs.T) + self.intercept_ = -0.5 * np.diag(np.dot(self.means_, self.coef_.T)) + np.log( + self.priors_ + ) + + def _solve_svd(self, X, y): + """SVD solver. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data. + + y : array-like of shape (n_samples,) or (n_samples, n_targets) + Target values. + """ + xp, is_array_api_compliant = get_namespace(X) + + if is_array_api_compliant: + svd = xp.linalg.svd + else: + svd = scipy.linalg.svd + + n_samples, n_features = X.shape + n_classes = self.classes_.shape[0] + + self.means_ = _class_means(X, y) + if self.store_covariance: + self.covariance_ = _class_cov(X, y, self.priors_) + + Xc = [] + for idx, group in enumerate(self.classes_): + Xg = X[y == group] + Xc.append(Xg - self.means_[idx, :]) + + self.xbar_ = self.priors_ @ self.means_ + + Xc = xp.concat(Xc, axis=0) + + # 1) within (univariate) scaling by with classes std-dev + std = xp.std(Xc, axis=0) + # avoid division by zero in normalization + std[std == 0] = 1.0 + fac = xp.asarray(1.0 / (n_samples - n_classes), dtype=X.dtype, device=device(X)) + + # 2) Within variance scaling + X = xp.sqrt(fac) * (Xc / std) + # SVD of centered (within)scaled data + U, S, Vt = svd(X, full_matrices=False) + + rank = xp.sum(xp.astype(S > self.tol, xp.int32)) + # Scaling of within covariance is: V' 1/S + scalings = (Vt[:rank, :] / std).T / S[:rank] + fac = 1.0 if n_classes == 1 else 1.0 / (n_classes - 1) + + # 3) Between variance scaling + # Scale weighted centers + X = ( + (xp.sqrt((n_samples * self.priors_) * fac)) * (self.means_ - self.xbar_).T + ).T @ scalings + # Centers are living in a space with n_classes-1 dim (maximum) + # Use SVD to find projection in the space spanned by the + # (n_classes) centers + _, S, Vt = svd(X, full_matrices=False) + + if self._max_components == 0: + self.explained_variance_ratio_ = xp.empty((0,), dtype=S.dtype) + else: + self.explained_variance_ratio_ = (S**2 / xp.sum(S**2))[ + : self._max_components + ] + + rank = xp.sum(xp.astype(S > self.tol * S[0], xp.int32)) + self.scalings_ = scalings @ Vt.T[:, :rank] + coef = (self.means_ - self.xbar_) @ self.scalings_ + self.intercept_ = -0.5 * xp.sum(coef**2, axis=1) + xp.log(self.priors_) + self.coef_ = coef @ self.scalings_.T + self.intercept_ -= self.xbar_ @ self.coef_.T + + @_fit_context( + # LinearDiscriminantAnalysis.covariance_estimator is not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, y): + """Fit the Linear Discriminant Analysis model. + + .. versionchanged:: 0.19 + `store_covariance` and `tol` has been moved to main constructor. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data. + + y : array-like of shape (n_samples,) + Target values. + + Returns + ------- + self : object + Fitted estimator. + """ + xp, _ = get_namespace(X) + + X, y = validate_data( + self, X, y, ensure_min_samples=2, dtype=[xp.float64, xp.float32] + ) + self.classes_ = unique_labels(y) + n_samples, _ = X.shape + n_classes = self.classes_.shape[0] + + if n_samples == n_classes: + raise ValueError( + "The number of samples must be more than the number of classes." + ) + + if self.priors is None: # estimate priors from sample + _, cnts = xp.unique_counts(y) # non-negative ints + self.priors_ = xp.astype(cnts, X.dtype) / float(y.shape[0]) + else: + self.priors_ = xp.asarray(self.priors, dtype=X.dtype) + + if xp.any(self.priors_ < 0): + raise ValueError("priors must be non-negative") + + if xp.abs(xp.sum(self.priors_) - 1.0) > 1e-5: + warnings.warn("The priors do not sum to 1. Renormalizing", UserWarning) + self.priors_ = self.priors_ / self.priors_.sum() + + # Maximum number of components no matter what n_components is + # specified: + max_components = min(n_classes - 1, X.shape[1]) + + if self.n_components is None: + self._max_components = max_components + else: + if self.n_components > max_components: + raise ValueError( + "n_components cannot be larger than min(n_features, n_classes - 1)." + ) + self._max_components = self.n_components + + if self.solver == "svd": + if self.shrinkage is not None: + raise NotImplementedError("shrinkage not supported with 'svd' solver.") + if self.covariance_estimator is not None: + raise ValueError( + "covariance estimator " + "is not supported " + "with svd solver. Try another solver" + ) + self._solve_svd(X, y) + elif self.solver == "lsqr": + self._solve_lstsq( + X, + y, + shrinkage=self.shrinkage, + covariance_estimator=self.covariance_estimator, + ) + elif self.solver == "eigen": + self._solve_eigen( + X, + y, + shrinkage=self.shrinkage, + covariance_estimator=self.covariance_estimator, + ) + if size(self.classes_) == 2: # treat binary case as a special case + coef_ = xp.asarray(self.coef_[1, :] - self.coef_[0, :], dtype=X.dtype) + self.coef_ = xp.reshape(coef_, (1, -1)) + intercept_ = xp.asarray( + self.intercept_[1] - self.intercept_[0], dtype=X.dtype + ) + self.intercept_ = xp.reshape(intercept_, (1,)) + self._n_features_out = self._max_components + return self + + def transform(self, X): + """Project data to maximize class separation. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Input data. + + Returns + ------- + X_new : ndarray of shape (n_samples, n_components) or \ + (n_samples, min(rank, n_components)) + Transformed data. In the case of the 'svd' solver, the shape + is (n_samples, min(rank, n_components)). + """ + if self.solver == "lsqr": + raise NotImplementedError( + "transform not implemented for 'lsqr' solver (use 'svd' or 'eigen')." + ) + check_is_fitted(self) + xp, _ = get_namespace(X) + X = validate_data(self, X, reset=False) + + if self.solver == "svd": + X_new = (X - self.xbar_) @ self.scalings_ + elif self.solver == "eigen": + X_new = X @ self.scalings_ + + return X_new[:, : self._max_components] + + def predict_proba(self, X): + """Estimate probability. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Input data. + + Returns + ------- + C : ndarray of shape (n_samples, n_classes) + Estimated probabilities. + """ + check_is_fitted(self) + xp, is_array_api_compliant = get_namespace(X) + decision = self.decision_function(X) + if size(self.classes_) == 2: + proba = _expit(decision, xp) + return xp.stack([1 - proba, proba], axis=1) + else: + return softmax(decision) + + def predict_log_proba(self, X): + """Estimate log probability. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Input data. + + Returns + ------- + C : ndarray of shape (n_samples, n_classes) + Estimated log probabilities. + """ + xp, _ = get_namespace(X) + prediction = self.predict_proba(X) + + info = xp.finfo(prediction.dtype) + if hasattr(info, "smallest_normal"): + smallest_normal = info.smallest_normal + else: + # smallest_normal was introduced in NumPy 1.22 + smallest_normal = info.tiny + + prediction[prediction == 0.0] += smallest_normal + return xp.log(prediction) + + def decision_function(self, X): + """Apply decision function to an array of samples. + + The decision function is equal (up to a constant factor) to the + log-posterior of the model, i.e. `log p(y = k | x)`. In a binary + classification setting this instead corresponds to the difference + `log p(y = 1 | x) - log p(y = 0 | x)`. See :ref:`lda_qda_math`. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Array of samples (test vectors). + + Returns + ------- + y_scores : ndarray of shape (n_samples,) or (n_samples, n_classes) + Decision function values related to each class, per sample. + In the two-class case, the shape is `(n_samples,)`, giving the + log likelihood ratio of the positive class. + """ + # Only override for the doc + return super().decision_function(X) + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.array_api_support = True + return tags + + +class QuadraticDiscriminantAnalysis( + DiscriminantAnalysisPredictionMixin, ClassifierMixin, BaseEstimator +): + """Quadratic Discriminant Analysis. + + A classifier with a quadratic decision boundary, generated + by fitting class conditional densities to the data + and using Bayes' rule. + + The model fits a Gaussian density to each class. + + .. versionadded:: 0.17 + + For a comparison between + :class:`~sklearn.discriminant_analysis.QuadraticDiscriminantAnalysis` + and :class:`~sklearn.discriminant_analysis.LinearDiscriminantAnalysis`, see + :ref:`sphx_glr_auto_examples_classification_plot_lda_qda.py`. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + priors : array-like of shape (n_classes,), default=None + Class priors. By default, the class proportions are inferred from the + training data. + + reg_param : float, default=0.0 + Regularizes the per-class covariance estimates by transforming S2 as + ``S2 = (1 - reg_param) * S2 + reg_param * np.eye(n_features)``, + where S2 corresponds to the `scaling_` attribute of a given class. + + store_covariance : bool, default=False + If True, the class covariance matrices are explicitly computed and + stored in the `self.covariance_` attribute. + + .. versionadded:: 0.17 + + tol : float, default=1.0e-4 + Absolute threshold for the covariance matrix to be considered rank + deficient after applying some regularization (see `reg_param`) to each + `Sk` where `Sk` represents covariance matrix for k-th class. This + parameter does not affect the predictions. It controls when a warning + is raised if the covariance matrix is not full rank. + + .. versionadded:: 0.17 + + Attributes + ---------- + covariance_ : list of len n_classes of ndarray \ + of shape (n_features, n_features) + For each class, gives the covariance matrix estimated using the + samples of that class. The estimations are unbiased. Only present if + `store_covariance` is True. + + means_ : array-like of shape (n_classes, n_features) + Class-wise means. + + priors_ : array-like of shape (n_classes,) + Class priors (sum to 1). + + rotations_ : list of len n_classes of ndarray of shape (n_features, n_k) + For each class k an array of shape (n_features, n_k), where + ``n_k = min(n_features, number of elements in class k)`` + It is the rotation of the Gaussian distribution, i.e. its + principal axis. It corresponds to `V`, the matrix of eigenvectors + coming from the SVD of `Xk = U S Vt` where `Xk` is the centered + matrix of samples from class k. + + scalings_ : list of len n_classes of ndarray of shape (n_k,) + For each class, contains the scaling of + the Gaussian distributions along its principal axes, i.e. the + variance in the rotated coordinate system. It corresponds to `S^2 / + (n_samples - 1)`, where `S` is the diagonal matrix of singular values + from the SVD of `Xk`, where `Xk` is the centered matrix of samples + from class k. + + classes_ : ndarray of shape (n_classes,) + Unique class labels. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + LinearDiscriminantAnalysis : Linear Discriminant Analysis. + + Examples + -------- + >>> from sklearn.discriminant_analysis import QuadraticDiscriminantAnalysis + >>> import numpy as np + >>> X = np.array([[-1, -1], [-2, -1], [-3, -2], [1, 1], [2, 1], [3, 2]]) + >>> y = np.array([1, 1, 1, 2, 2, 2]) + >>> clf = QuadraticDiscriminantAnalysis() + >>> clf.fit(X, y) + QuadraticDiscriminantAnalysis() + >>> print(clf.predict([[-0.8, -1]])) + [1] + """ + + _parameter_constraints: dict = { + "priors": ["array-like", None], + "reg_param": [Interval(Real, 0, 1, closed="both")], + "store_covariance": ["boolean"], + "tol": [Interval(Real, 0, None, closed="left")], + } + + def __init__( + self, *, priors=None, reg_param=0.0, store_covariance=False, tol=1.0e-4 + ): + self.priors = priors + self.reg_param = reg_param + self.store_covariance = store_covariance + self.tol = tol + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y): + """Fit the model according to the given training data and parameters. + + .. versionchanged:: 0.19 + ``store_covariances`` has been moved to main constructor as + ``store_covariance``. + + .. versionchanged:: 0.19 + ``tol`` has been moved to main constructor. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training vector, where `n_samples` is the number of samples and + `n_features` is the number of features. + + y : array-like of shape (n_samples,) + Target values (integers). + + Returns + ------- + self : object + Fitted estimator. + """ + X, y = validate_data(self, X, y) + check_classification_targets(y) + self.classes_, y = np.unique(y, return_inverse=True) + n_samples, n_features = X.shape + n_classes = len(self.classes_) + if n_classes < 2: + raise ValueError( + "The number of classes has to be greater than one; got %d class" + % (n_classes) + ) + if self.priors is None: + self.priors_ = np.bincount(y) / float(n_samples) + else: + self.priors_ = np.array(self.priors) + + cov = None + store_covariance = self.store_covariance + if store_covariance: + cov = [] + means = [] + scalings = [] + rotations = [] + for ind in range(n_classes): + Xg = X[y == ind, :] + meang = Xg.mean(0) + means.append(meang) + if len(Xg) == 1: + raise ValueError( + "y has only 1 sample in class %s, covariance is ill defined." + % str(self.classes_[ind]) + ) + Xgc = Xg - meang + # Xgc = U * S * V.T + _, S, Vt = np.linalg.svd(Xgc, full_matrices=False) + S2 = (S**2) / (len(Xg) - 1) + S2 = ((1 - self.reg_param) * S2) + self.reg_param + rank = np.sum(S2 > self.tol) + if rank < n_features: + warnings.warn( + f"The covariance matrix of class {ind} is not full rank. " + "Increasing the value of parameter `reg_param` might help" + " reducing the collinearity.", + linalg.LinAlgWarning, + ) + if self.store_covariance or store_covariance: + # cov = V * (S^2 / (n-1)) * V.T + cov.append(np.dot(S2 * Vt.T, Vt)) + scalings.append(S2) + rotations.append(Vt.T) + if self.store_covariance or store_covariance: + self.covariance_ = cov + self.means_ = np.asarray(means) + self.scalings_ = scalings + self.rotations_ = rotations + return self + + def _decision_function(self, X): + # return log posterior, see eq (4.12) p. 110 of the ESL. + check_is_fitted(self) + + X = validate_data(self, X, reset=False) + norm2 = [] + for i in range(len(self.classes_)): + R = self.rotations_[i] + S = self.scalings_[i] + Xm = X - self.means_[i] + X2 = np.dot(Xm, R * (S ** (-0.5))) + norm2.append(np.sum(X2**2, axis=1)) + norm2 = np.array(norm2).T # shape = [len(X), n_classes] + u = np.asarray([np.sum(np.log(s)) for s in self.scalings_]) + return -0.5 * (norm2 + u) + np.log(self.priors_) + + def decision_function(self, X): + """Apply decision function to an array of samples. + + The decision function is equal (up to a constant factor) to the + log-posterior of the model, i.e. `log p(y = k | x)`. In a binary + classification setting this instead corresponds to the difference + `log p(y = 1 | x) - log p(y = 0 | x)`. See :ref:`lda_qda_math`. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Array of samples (test vectors). + + Returns + ------- + C : ndarray of shape (n_samples,) or (n_samples, n_classes) + Decision function values related to each class, per sample. + In the two-class case, the shape is `(n_samples,)`, giving the + log likelihood ratio of the positive class. + """ + return super().decision_function(X) + + def predict(self, X): + """Perform classification on an array of test vectors X. + + The predicted class C for each sample in X is returned. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Vector to be scored, where `n_samples` is the number of samples and + `n_features` is the number of features. + + Returns + ------- + C : ndarray of shape (n_samples,) + Estimated probabilities. + """ + return super().predict(X) + + def predict_proba(self, X): + """Return posterior probabilities of classification. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Array of samples/test vectors. + + Returns + ------- + C : ndarray of shape (n_samples, n_classes) + Posterior probabilities of classification per class. + """ + # compute the likelihood of the underlying gaussian models + # up to a multiplicative constant. + return super().predict_proba(X) + + def predict_log_proba(self, X): + """Return log of posterior probabilities of classification. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Array of samples/test vectors. + + Returns + ------- + C : ndarray of shape (n_samples, n_classes) + Posterior log-probabilities of classification per class. + """ + # XXX : can do better to avoid precision overflows + return super().predict_log_proba(X) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/dummy.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/dummy.py new file mode 100644 index 0000000000000000000000000000000000000000..7d44fa2e473bba9110eb2d998eb4b7eee4d2d543 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/dummy.py @@ -0,0 +1,704 @@ +"""Dummy estimators that implement simple rules of thumb.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from numbers import Integral, Real + +import numpy as np +import scipy.sparse as sp + +from .base import ( + BaseEstimator, + ClassifierMixin, + MultiOutputMixin, + RegressorMixin, + _fit_context, +) +from .utils import check_random_state +from .utils._param_validation import Interval, StrOptions +from .utils.multiclass import class_distribution +from .utils.random import _random_choice_csc +from .utils.stats import _weighted_percentile +from .utils.validation import ( + _check_sample_weight, + _num_samples, + check_array, + check_consistent_length, + check_is_fitted, + validate_data, +) + + +class DummyClassifier(MultiOutputMixin, ClassifierMixin, BaseEstimator): + """DummyClassifier makes predictions that ignore the input features. + + This classifier serves as a simple baseline to compare against other more + complex classifiers. + + The specific behavior of the baseline is selected with the `strategy` + parameter. + + All strategies make predictions that ignore the input feature values passed + as the `X` argument to `fit` and `predict`. The predictions, however, + typically depend on values observed in the `y` parameter passed to `fit`. + + Note that the "stratified" and "uniform" strategies lead to + non-deterministic predictions that can be rendered deterministic by setting + the `random_state` parameter if needed. The other strategies are naturally + deterministic and, once fit, always return the same constant prediction + for any value of `X`. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.13 + + Parameters + ---------- + strategy : {"most_frequent", "prior", "stratified", "uniform", \ + "constant"}, default="prior" + Strategy to use to generate predictions. + + * "most_frequent": the `predict` method always returns the most + frequent class label in the observed `y` argument passed to `fit`. + The `predict_proba` method returns the matching one-hot encoded + vector. + * "prior": the `predict` method always returns the most frequent + class label in the observed `y` argument passed to `fit` (like + "most_frequent"). ``predict_proba`` always returns the empirical + class distribution of `y` also known as the empirical class prior + distribution. + * "stratified": the `predict_proba` method randomly samples one-hot + vectors from a multinomial distribution parametrized by the empirical + class prior probabilities. + The `predict` method returns the class label which got probability + one in the one-hot vector of `predict_proba`. + Each sampled row of both methods is therefore independent and + identically distributed. + * "uniform": generates predictions uniformly at random from the list + of unique classes observed in `y`, i.e. each class has equal + probability. + * "constant": always predicts a constant label that is provided by + the user. This is useful for metrics that evaluate a non-majority + class. + + .. versionchanged:: 0.24 + The default value of `strategy` has changed to "prior" in version + 0.24. + + random_state : int, RandomState instance or None, default=None + Controls the randomness to generate the predictions when + ``strategy='stratified'`` or ``strategy='uniform'``. + Pass an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + constant : int or str or array-like of shape (n_outputs,), default=None + The explicit constant as predicted by the "constant" strategy. This + parameter is useful only for the "constant" strategy. + + Attributes + ---------- + classes_ : ndarray of shape (n_classes,) or list of such arrays + Unique class labels observed in `y`. For multi-output classification + problems, this attribute is a list of arrays as each output has an + independent set of possible classes. + + n_classes_ : int or list of int + Number of label for each output. + + class_prior_ : ndarray of shape (n_classes,) or list of such arrays + Frequency of each class observed in `y`. For multioutput classification + problems, this is computed independently for each output. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` has + feature names that are all strings. + + n_outputs_ : int + Number of outputs. + + sparse_output_ : bool + True if the array returned from predict is to be in sparse CSC format. + Is automatically set to True if the input `y` is passed in sparse + format. + + See Also + -------- + DummyRegressor : Regressor that makes predictions using simple rules. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.dummy import DummyClassifier + >>> X = np.array([-1, 1, 1, 1]) + >>> y = np.array([0, 1, 1, 1]) + >>> dummy_clf = DummyClassifier(strategy="most_frequent") + >>> dummy_clf.fit(X, y) + DummyClassifier(strategy='most_frequent') + >>> dummy_clf.predict(X) + array([1, 1, 1, 1]) + >>> dummy_clf.score(X, y) + 0.75 + """ + + _parameter_constraints: dict = { + "strategy": [ + StrOptions({"most_frequent", "prior", "stratified", "uniform", "constant"}) + ], + "random_state": ["random_state"], + "constant": [Integral, str, "array-like", None], + } + + def __init__(self, *, strategy="prior", random_state=None, constant=None): + self.strategy = strategy + self.random_state = random_state + self.constant = constant + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y, sample_weight=None): + """Fit the baseline classifier. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data. + + y : array-like of shape (n_samples,) or (n_samples, n_outputs) + Target values. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. + + Returns + ------- + self : object + Returns the instance itself. + """ + validate_data(self, X, skip_check_array=True) + + self._strategy = self.strategy + + if self._strategy == "uniform" and sp.issparse(y): + y = y.toarray() + warnings.warn( + ( + "A local copy of the target data has been converted " + "to a numpy array. Predicting on sparse target data " + "with the uniform strategy would not save memory " + "and would be slower." + ), + UserWarning, + ) + + self.sparse_output_ = sp.issparse(y) + + if not self.sparse_output_: + y = np.asarray(y) + y = np.atleast_1d(y) + + if y.ndim == 1: + y = np.reshape(y, (-1, 1)) + + self.n_outputs_ = y.shape[1] + + check_consistent_length(X, y) + + if sample_weight is not None: + sample_weight = _check_sample_weight(sample_weight, X) + + if self._strategy == "constant": + if self.constant is None: + raise ValueError( + "Constant target value has to be specified " + "when the constant strategy is used." + ) + else: + constant = np.reshape(np.atleast_1d(self.constant), (-1, 1)) + if constant.shape[0] != self.n_outputs_: + raise ValueError( + "Constant target value should have shape (%d, 1)." + % self.n_outputs_ + ) + + (self.classes_, self.n_classes_, self.class_prior_) = class_distribution( + y, sample_weight + ) + + if self._strategy == "constant": + for k in range(self.n_outputs_): + if not any(constant[k][0] == c for c in self.classes_[k]): + # Checking in case of constant strategy if the constant + # provided by the user is in y. + err_msg = ( + "The constant target value must be present in " + "the training data. You provided constant={}. " + "Possible values are: {}.".format( + self.constant, self.classes_[k].tolist() + ) + ) + raise ValueError(err_msg) + + if self.n_outputs_ == 1: + self.n_classes_ = self.n_classes_[0] + self.classes_ = self.classes_[0] + self.class_prior_ = self.class_prior_[0] + + return self + + def predict(self, X): + """Perform classification on test vectors X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Test data. + + Returns + ------- + y : array-like of shape (n_samples,) or (n_samples, n_outputs) + Predicted target values for X. + """ + check_is_fitted(self) + + # numpy random_state expects Python int and not long as size argument + # under Windows + n_samples = _num_samples(X) + rs = check_random_state(self.random_state) + + n_classes_ = self.n_classes_ + classes_ = self.classes_ + class_prior_ = self.class_prior_ + constant = self.constant + if self.n_outputs_ == 1: + # Get same type even for self.n_outputs_ == 1 + n_classes_ = [n_classes_] + classes_ = [classes_] + class_prior_ = [class_prior_] + constant = [constant] + # Compute probability only once + if self._strategy == "stratified": + proba = self.predict_proba(X) + if self.n_outputs_ == 1: + proba = [proba] + + if self.sparse_output_: + class_prob = None + if self._strategy in ("most_frequent", "prior"): + classes_ = [np.array([cp.argmax()]) for cp in class_prior_] + + elif self._strategy == "stratified": + class_prob = class_prior_ + + elif self._strategy == "uniform": + raise ValueError( + "Sparse target prediction is not " + "supported with the uniform strategy" + ) + + elif self._strategy == "constant": + classes_ = [np.array([c]) for c in constant] + + y = _random_choice_csc(n_samples, classes_, class_prob, self.random_state) + else: + if self._strategy in ("most_frequent", "prior"): + y = np.tile( + [ + classes_[k][class_prior_[k].argmax()] + for k in range(self.n_outputs_) + ], + [n_samples, 1], + ) + + elif self._strategy == "stratified": + y = np.vstack( + [ + classes_[k][proba[k].argmax(axis=1)] + for k in range(self.n_outputs_) + ] + ).T + + elif self._strategy == "uniform": + ret = [ + classes_[k][rs.randint(n_classes_[k], size=n_samples)] + for k in range(self.n_outputs_) + ] + y = np.vstack(ret).T + + elif self._strategy == "constant": + y = np.tile(self.constant, (n_samples, 1)) + + if self.n_outputs_ == 1: + y = np.ravel(y) + + return y + + def predict_proba(self, X): + """ + Return probability estimates for the test vectors X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Test data. + + Returns + ------- + P : ndarray of shape (n_samples, n_classes) or list of such arrays + Returns the probability of the sample for each class in + the model, where classes are ordered arithmetically, for each + output. + """ + check_is_fitted(self) + + # numpy random_state expects Python int and not long as size argument + # under Windows + n_samples = _num_samples(X) + rs = check_random_state(self.random_state) + + n_classes_ = self.n_classes_ + classes_ = self.classes_ + class_prior_ = self.class_prior_ + constant = self.constant + if self.n_outputs_ == 1: + # Get same type even for self.n_outputs_ == 1 + n_classes_ = [n_classes_] + classes_ = [classes_] + class_prior_ = [class_prior_] + constant = [constant] + + P = [] + for k in range(self.n_outputs_): + if self._strategy == "most_frequent": + ind = class_prior_[k].argmax() + out = np.zeros((n_samples, n_classes_[k]), dtype=np.float64) + out[:, ind] = 1.0 + elif self._strategy == "prior": + out = np.ones((n_samples, 1)) * class_prior_[k] + + elif self._strategy == "stratified": + out = rs.multinomial(1, class_prior_[k], size=n_samples) + out = out.astype(np.float64) + + elif self._strategy == "uniform": + out = np.ones((n_samples, n_classes_[k]), dtype=np.float64) + out /= n_classes_[k] + + elif self._strategy == "constant": + ind = np.where(classes_[k] == constant[k]) + out = np.zeros((n_samples, n_classes_[k]), dtype=np.float64) + out[:, ind] = 1.0 + + P.append(out) + + if self.n_outputs_ == 1: + P = P[0] + + return P + + def predict_log_proba(self, X): + """ + Return log probability estimates for the test vectors X. + + Parameters + ---------- + X : {array-like, object with finite length or shape} + Training data. + + Returns + ------- + P : ndarray of shape (n_samples, n_classes) or list of such arrays + Returns the log probability of the sample for each class in + the model, where classes are ordered arithmetically for each + output. + """ + proba = self.predict_proba(X) + if self.n_outputs_ == 1: + return np.log(proba) + else: + return [np.log(p) for p in proba] + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + tags.classifier_tags.poor_score = True + tags.no_validation = True + return tags + + def score(self, X, y, sample_weight=None): + """Return the mean accuracy on the given test data and labels. + + In multi-label classification, this is the subset accuracy + which is a harsh metric since you require for each sample that + each label set be correctly predicted. + + Parameters + ---------- + X : None or array-like of shape (n_samples, n_features) + Test samples. Passing None as test samples gives the same result + as passing real test samples, since DummyClassifier + operates independently of the sampled observations. + + y : array-like of shape (n_samples,) or (n_samples, n_outputs) + True labels for X. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. + + Returns + ------- + score : float + Mean accuracy of self.predict(X) w.r.t. y. + """ + if X is None: + X = np.zeros(shape=(len(y), 1)) + return super().score(X, y, sample_weight) + + +class DummyRegressor(MultiOutputMixin, RegressorMixin, BaseEstimator): + """Regressor that makes predictions using simple rules. + + This regressor is useful as a simple baseline to compare with other + (real) regressors. Do not use it for real problems. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.13 + + Parameters + ---------- + strategy : {"mean", "median", "quantile", "constant"}, default="mean" + Strategy to use to generate predictions. + + * "mean": always predicts the mean of the training set + * "median": always predicts the median of the training set + * "quantile": always predicts a specified quantile of the training set, + provided with the quantile parameter. + * "constant": always predicts a constant value that is provided by + the user. + + constant : int or float or array-like of shape (n_outputs,), default=None + The explicit constant as predicted by the "constant" strategy. This + parameter is useful only for the "constant" strategy. + + quantile : float in [0.0, 1.0], default=None + The quantile to predict using the "quantile" strategy. A quantile of + 0.5 corresponds to the median, while 0.0 to the minimum and 1.0 to the + maximum. + + Attributes + ---------- + constant_ : ndarray of shape (1, n_outputs) + Mean or median or quantile of the training targets or constant value + given by the user. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` has + feature names that are all strings. + + n_outputs_ : int + Number of outputs. + + See Also + -------- + DummyClassifier: Classifier that makes predictions using simple rules. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.dummy import DummyRegressor + >>> X = np.array([1.0, 2.0, 3.0, 4.0]) + >>> y = np.array([2.0, 3.0, 5.0, 10.0]) + >>> dummy_regr = DummyRegressor(strategy="mean") + >>> dummy_regr.fit(X, y) + DummyRegressor() + >>> dummy_regr.predict(X) + array([5., 5., 5., 5.]) + >>> dummy_regr.score(X, y) + 0.0 + """ + + _parameter_constraints: dict = { + "strategy": [StrOptions({"mean", "median", "quantile", "constant"})], + "quantile": [Interval(Real, 0.0, 1.0, closed="both"), None], + "constant": [ + Interval(Real, None, None, closed="neither"), + "array-like", + None, + ], + } + + def __init__(self, *, strategy="mean", constant=None, quantile=None): + self.strategy = strategy + self.constant = constant + self.quantile = quantile + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y, sample_weight=None): + """Fit the baseline regressor. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training data. + + y : array-like of shape (n_samples,) or (n_samples, n_outputs) + Target values. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. + + Returns + ------- + self : object + Fitted estimator. + """ + validate_data(self, X, skip_check_array=True) + + y = check_array(y, ensure_2d=False, input_name="y") + if len(y) == 0: + raise ValueError("y must not be empty.") + + if y.ndim == 1: + y = np.reshape(y, (-1, 1)) + self.n_outputs_ = y.shape[1] + + check_consistent_length(X, y, sample_weight) + + if sample_weight is not None: + sample_weight = _check_sample_weight(sample_weight, X) + + if self.strategy == "mean": + self.constant_ = np.average(y, axis=0, weights=sample_weight) + + elif self.strategy == "median": + if sample_weight is None: + self.constant_ = np.median(y, axis=0) + else: + self.constant_ = [ + _weighted_percentile(y[:, k], sample_weight, percentile_rank=50.0) + for k in range(self.n_outputs_) + ] + + elif self.strategy == "quantile": + if self.quantile is None: + raise ValueError( + "When using `strategy='quantile', you have to specify the desired " + "quantile in the range [0, 1]." + ) + percentile_rank = self.quantile * 100.0 + if sample_weight is None: + self.constant_ = np.percentile(y, axis=0, q=percentile_rank) + else: + self.constant_ = [ + _weighted_percentile( + y[:, k], sample_weight, percentile_rank=percentile_rank + ) + for k in range(self.n_outputs_) + ] + + elif self.strategy == "constant": + if self.constant is None: + raise TypeError( + "Constant target value has to be specified " + "when the constant strategy is used." + ) + + self.constant_ = check_array( + self.constant, + accept_sparse=["csr", "csc", "coo"], + ensure_2d=False, + ensure_min_samples=0, + ) + + if self.n_outputs_ != 1 and self.constant_.shape[0] != y.shape[1]: + raise ValueError( + "Constant target value should have shape (%d, 1)." % y.shape[1] + ) + + self.constant_ = np.reshape(self.constant_, (1, -1)) + return self + + def predict(self, X, return_std=False): + """Perform classification on test vectors X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Test data. + + return_std : bool, default=False + Whether to return the standard deviation of posterior prediction. + All zeros in this case. + + .. versionadded:: 0.20 + + Returns + ------- + y : array-like of shape (n_samples,) or (n_samples, n_outputs) + Predicted target values for X. + + y_std : array-like of shape (n_samples,) or (n_samples, n_outputs) + Standard deviation of predictive distribution of query points. + """ + check_is_fitted(self) + n_samples = _num_samples(X) + + y = np.full( + (n_samples, self.n_outputs_), + self.constant_, + dtype=np.array(self.constant_).dtype, + ) + y_std = np.zeros((n_samples, self.n_outputs_)) + + if self.n_outputs_ == 1: + y = np.ravel(y) + y_std = np.ravel(y_std) + + return (y, y_std) if return_std else y + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + tags.regressor_tags.poor_score = True + tags.no_validation = True + return tags + + def score(self, X, y, sample_weight=None): + """Return the coefficient of determination R^2 of the prediction. + + The coefficient R^2 is defined as `(1 - u/v)`, where `u` is the + residual sum of squares `((y_true - y_pred) ** 2).sum()` and `v` is the + total sum of squares `((y_true - y_true.mean()) ** 2).sum()`. The best + possible score is 1.0 and it can be negative (because the model can be + arbitrarily worse). A constant model that always predicts the expected + value of y, disregarding the input features, would get a R^2 score of + 0.0. + + Parameters + ---------- + X : None or array-like of shape (n_samples, n_features) + Test samples. Passing None as test samples gives the same result + as passing real test samples, since `DummyRegressor` + operates independently of the sampled observations. + + y : array-like of shape (n_samples,) or (n_samples, n_outputs) + True values for X. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. + + Returns + ------- + score : float + R^2 of `self.predict(X)` w.r.t. y. + """ + if X is None: + X = np.zeros(shape=(len(y), 1)) + return super().score(X, y, sample_weight) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/exceptions.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/exceptions.py new file mode 100644 index 0000000000000000000000000000000000000000..7db5a2ff0435f4327208860aaf0dfaa2e101a250 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/exceptions.py @@ -0,0 +1,249 @@ +"""Custom warnings and errors used across scikit-learn.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +__all__ = [ + "ConvergenceWarning", + "DataConversionWarning", + "DataDimensionalityWarning", + "EfficiencyWarning", + "EstimatorCheckFailedWarning", + "FitFailedWarning", + "NotFittedError", + "PositiveSpectrumWarning", + "SkipTestWarning", + "UndefinedMetricWarning", + "UnsetMetadataPassedError", +] + + +class UnsetMetadataPassedError(ValueError): + """Exception class to raise if a metadata is passed which is not explicitly \ + requested (metadata=True) or not requested (metadata=False). + + .. versionadded:: 1.3 + + Parameters + ---------- + message : str + The message + + unrequested_params : dict + A dictionary of parameters and their values which are provided but not + requested. + + routed_params : dict + A dictionary of routed parameters. + """ + + def __init__(self, *, message, unrequested_params, routed_params): + super().__init__(message) + self.unrequested_params = unrequested_params + self.routed_params = routed_params + + +class NotFittedError(ValueError, AttributeError): + """Exception class to raise if estimator is used before fitting. + + This class inherits from both ValueError and AttributeError to help with + exception handling and backward compatibility. + + Examples + -------- + >>> from sklearn.svm import LinearSVC + >>> from sklearn.exceptions import NotFittedError + >>> try: + ... LinearSVC().predict([[1, 2], [2, 3], [3, 4]]) + ... except NotFittedError as e: + ... print(repr(e)) + NotFittedError("This LinearSVC instance is not fitted yet. Call 'fit' with + appropriate arguments before using this estimator."...) + + .. versionchanged:: 0.18 + Moved from sklearn.utils.validation. + """ + + +class ConvergenceWarning(UserWarning): + """Custom warning to capture convergence problems + + .. versionchanged:: 0.18 + Moved from sklearn.utils. + """ + + +class DataConversionWarning(UserWarning): + """Warning used to notify implicit data conversions happening in the code. + + This warning occurs when some input data needs to be converted or + interpreted in a way that may not match the user's expectations. + + For example, this warning may occur when the user + - passes an integer array to a function which expects float input and + will convert the input + - requests a non-copying operation, but a copy is required to meet the + implementation's data-type expectations; + - passes an input whose shape can be interpreted ambiguously. + + .. versionchanged:: 0.18 + Moved from sklearn.utils.validation. + """ + + +class DataDimensionalityWarning(UserWarning): + """Custom warning to notify potential issues with data dimensionality. + + For example, in random projection, this warning is raised when the + number of components, which quantifies the dimensionality of the target + projection space, is higher than the number of features, which quantifies + the dimensionality of the original source space, to imply that the + dimensionality of the problem will not be reduced. + + .. versionchanged:: 0.18 + Moved from sklearn.utils. + """ + + +class EfficiencyWarning(UserWarning): + """Warning used to notify the user of inefficient computation. + + This warning notifies the user that the efficiency may not be optimal due + to some reason which may be included as a part of the warning message. + This may be subclassed into a more specific Warning class. + + .. versionadded:: 0.18 + """ + + +class FitFailedWarning(RuntimeWarning): + """Warning class used if there is an error while fitting the estimator. + + This Warning is used in meta estimators GridSearchCV and RandomizedSearchCV + and the cross-validation helper function cross_val_score to warn when there + is an error while fitting the estimator. + + .. versionchanged:: 0.18 + Moved from sklearn.cross_validation. + """ + + +class SkipTestWarning(UserWarning): + """Warning class used to notify the user of a test that was skipped. + + For example, one of the estimator checks requires a pandas import. + If the pandas package cannot be imported, the test will be skipped rather + than register as a failure. + """ + + +class UndefinedMetricWarning(UserWarning): + """Warning used when the metric is invalid + + .. versionchanged:: 0.18 + Moved from sklearn.base. + """ + + +class PositiveSpectrumWarning(UserWarning): + """Warning raised when the eigenvalues of a PSD matrix have issues + + This warning is typically raised by ``_check_psd_eigenvalues`` when the + eigenvalues of a positive semidefinite (PSD) matrix such as a gram matrix + (kernel) present significant negative eigenvalues, or bad conditioning i.e. + very small non-zero eigenvalues compared to the largest eigenvalue. + + .. versionadded:: 0.22 + """ + + +class InconsistentVersionWarning(UserWarning): + """Warning raised when an estimator is unpickled with an inconsistent version. + + Parameters + ---------- + estimator_name : str + Estimator name. + + current_sklearn_version : str + Current scikit-learn version. + + original_sklearn_version : str + Original scikit-learn version. + """ + + def __init__( + self, *, estimator_name, current_sklearn_version, original_sklearn_version + ): + self.estimator_name = estimator_name + self.current_sklearn_version = current_sklearn_version + self.original_sklearn_version = original_sklearn_version + + def __str__(self): + return ( + f"Trying to unpickle estimator {self.estimator_name} from version" + f" {self.original_sklearn_version} when " + f"using version {self.current_sklearn_version}. This might lead to breaking" + " code or " + "invalid results. Use at your own risk. " + "For more info please refer to:\n" + "https://scikit-learn.org/stable/model_persistence.html" + "#security-maintainability-limitations" + ) + + +class EstimatorCheckFailedWarning(UserWarning): + """Warning raised when an estimator check from the common tests fails. + + Parameters + ---------- + estimator : estimator object + Estimator instance for which the test failed. + + check_name : str + Name of the check that failed. + + exception : Exception + Exception raised by the failed check. + + status : str + Status of the check. + + expected_to_fail : bool + Whether the check was expected to fail. + + expected_to_fail_reason : str + Reason for the expected failure. + """ + + def __init__( + self, + *, + estimator, + check_name: str, + exception: Exception, + status: str, + expected_to_fail: bool, + expected_to_fail_reason: str, + ): + self.estimator = estimator + self.check_name = check_name + self.exception = exception + self.status = status + self.expected_to_fail = expected_to_fail + self.expected_to_fail_reason = expected_to_fail_reason + + def __repr__(self): + expected_to_fail_str = ( + f"Expected to fail: {self.expected_to_fail_reason}" + if self.expected_to_fail + else "Not expected to fail" + ) + return ( + f"Test {self.check_name} failed for estimator {self.estimator!r}.\n" + f"Expected to fail reason: {expected_to_fail_str}\n" + f"Exception: {self.exception}" + ) + + def __str__(self): + return self.__repr__() diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/isotonic.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/isotonic.py new file mode 100644 index 0000000000000000000000000000000000000000..2f2c56ae5d13cf51e2c165f4ab433c2abba224b7 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/isotonic.py @@ -0,0 +1,517 @@ +"""Isotonic regression for obtaining monotonic fit to data.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import math +import warnings +from numbers import Real + +import numpy as np +from scipy import interpolate, optimize +from scipy.stats import spearmanr + +from sklearn.utils import metadata_routing + +from ._isotonic import _inplace_contiguous_isotonic_regression, _make_unique +from .base import BaseEstimator, RegressorMixin, TransformerMixin, _fit_context +from .utils import check_array, check_consistent_length +from .utils._param_validation import Interval, StrOptions, validate_params +from .utils.fixes import parse_version, sp_base_version +from .utils.validation import _check_sample_weight, check_is_fitted + +__all__ = ["IsotonicRegression", "check_increasing", "isotonic_regression"] + + +@validate_params( + { + "x": ["array-like"], + "y": ["array-like"], + }, + prefer_skip_nested_validation=True, +) +def check_increasing(x, y): + """Determine whether y is monotonically correlated with x. + + y is found increasing or decreasing with respect to x based on a Spearman + correlation test. + + Parameters + ---------- + x : array-like of shape (n_samples,) + Training data. + + y : array-like of shape (n_samples,) + Training target. + + Returns + ------- + increasing_bool : boolean + Whether the relationship is increasing or decreasing. + + Notes + ----- + The Spearman correlation coefficient is estimated from the data, and the + sign of the resulting estimate is used as the result. + + In the event that the 95% confidence interval based on Fisher transform + spans zero, a warning is raised. + + References + ---------- + Fisher transformation. Wikipedia. + https://en.wikipedia.org/wiki/Fisher_transformation + + Examples + -------- + >>> from sklearn.isotonic import check_increasing + >>> x, y = [1, 2, 3, 4, 5], [2, 4, 6, 8, 10] + >>> check_increasing(x, y) + np.True_ + >>> y = [10, 8, 6, 4, 2] + >>> check_increasing(x, y) + np.False_ + """ + + # Calculate Spearman rho estimate and set return accordingly. + rho, _ = spearmanr(x, y) + increasing_bool = rho >= 0 + + # Run Fisher transform to get the rho CI, but handle rho=+/-1 + if rho not in [-1.0, 1.0] and len(x) > 3: + F = 0.5 * math.log((1.0 + rho) / (1.0 - rho)) + F_se = 1 / math.sqrt(len(x) - 3) + + # Use a 95% CI, i.e., +/-1.96 S.E. + # https://en.wikipedia.org/wiki/Fisher_transformation + rho_0 = math.tanh(F - 1.96 * F_se) + rho_1 = math.tanh(F + 1.96 * F_se) + + # Warn if the CI spans zero. + if np.sign(rho_0) != np.sign(rho_1): + warnings.warn( + "Confidence interval of the Spearman " + "correlation coefficient spans zero. " + "Determination of ``increasing`` may be " + "suspect." + ) + + return increasing_bool + + +@validate_params( + { + "y": ["array-like"], + "sample_weight": ["array-like", None], + "y_min": [Interval(Real, None, None, closed="both"), None], + "y_max": [Interval(Real, None, None, closed="both"), None], + "increasing": ["boolean"], + }, + prefer_skip_nested_validation=True, +) +def isotonic_regression( + y, *, sample_weight=None, y_min=None, y_max=None, increasing=True +): + """Solve the isotonic regression model. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + y : array-like of shape (n_samples,) + The data. + + sample_weight : array-like of shape (n_samples,), default=None + Weights on each point of the regression. + If None, weight is set to 1 (equal weights). + + y_min : float, default=None + Lower bound on the lowest predicted value (the minimum value may + still be higher). If not set, defaults to -inf. + + y_max : float, default=None + Upper bound on the highest predicted value (the maximum may still be + lower). If not set, defaults to +inf. + + increasing : bool, default=True + Whether to compute ``y_`` is increasing (if set to True) or decreasing + (if set to False). + + Returns + ------- + y_ : ndarray of shape (n_samples,) + Isotonic fit of y. + + References + ---------- + "Active set algorithms for isotonic regression; A unifying framework" + by Michael J. Best and Nilotpal Chakravarti, section 3. + + Examples + -------- + >>> from sklearn.isotonic import isotonic_regression + >>> isotonic_regression([5, 3, 1, 2, 8, 10, 7, 9, 6, 4]) + array([2.75 , 2.75 , 2.75 , 2.75 , 7.33, + 7.33, 7.33, 7.33, 7.33, 7.33]) + """ + y = check_array(y, ensure_2d=False, input_name="y", dtype=[np.float64, np.float32]) + if sp_base_version >= parse_version("1.12.0"): + res = optimize.isotonic_regression( + y=y, weights=sample_weight, increasing=increasing + ) + y = np.asarray(res.x, dtype=y.dtype) + else: + # TODO: remove this branch when Scipy 1.12 is the minimum supported version + # Also remove _inplace_contiguous_isotonic_regression. + order = np.s_[:] if increasing else np.s_[::-1] + y = np.array(y[order], dtype=y.dtype) + sample_weight = _check_sample_weight(sample_weight, y, dtype=y.dtype, copy=True) + sample_weight = np.ascontiguousarray(sample_weight[order]) + _inplace_contiguous_isotonic_regression(y, sample_weight) + y = y[order] + + if y_min is not None or y_max is not None: + # Older versions of np.clip don't accept None as a bound, so use np.inf + if y_min is None: + y_min = -np.inf + if y_max is None: + y_max = np.inf + np.clip(y, y_min, y_max, y) + return y + + +class IsotonicRegression(RegressorMixin, TransformerMixin, BaseEstimator): + """Isotonic regression model. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.13 + + Parameters + ---------- + y_min : float, default=None + Lower bound on the lowest predicted value (the minimum value may + still be higher). If not set, defaults to -inf. + + y_max : float, default=None + Upper bound on the highest predicted value (the maximum may still be + lower). If not set, defaults to +inf. + + increasing : bool or 'auto', default=True + Determines whether the predictions should be constrained to increase + or decrease with `X`. 'auto' will decide based on the Spearman + correlation estimate's sign. + + out_of_bounds : {'nan', 'clip', 'raise'}, default='nan' + Handles how `X` values outside of the training domain are handled + during prediction. + + - 'nan', predictions will be NaN. + - 'clip', predictions will be set to the value corresponding to + the nearest train interval endpoint. + - 'raise', a `ValueError` is raised. + + Attributes + ---------- + X_min_ : float + Minimum value of input array `X_` for left bound. + + X_max_ : float + Maximum value of input array `X_` for right bound. + + X_thresholds_ : ndarray of shape (n_thresholds,) + Unique ascending `X` values used to interpolate + the y = f(X) monotonic function. + + .. versionadded:: 0.24 + + y_thresholds_ : ndarray of shape (n_thresholds,) + De-duplicated `y` values suitable to interpolate the y = f(X) + monotonic function. + + .. versionadded:: 0.24 + + f_ : function + The stepwise interpolating function that covers the input domain ``X``. + + increasing_ : bool + Inferred value for ``increasing``. + + See Also + -------- + sklearn.linear_model.LinearRegression : Ordinary least squares Linear + Regression. + sklearn.ensemble.HistGradientBoostingRegressor : Gradient boosting that + is a non-parametric model accepting monotonicity constraints. + isotonic_regression : Function to solve the isotonic regression model. + + Notes + ----- + Ties are broken using the secondary method from de Leeuw, 1977. + + References + ---------- + Isotonic Median Regression: A Linear Programming Approach + Nilotpal Chakravarti + Mathematics of Operations Research + Vol. 14, No. 2 (May, 1989), pp. 303-308 + + Isotone Optimization in R : Pool-Adjacent-Violators + Algorithm (PAVA) and Active Set Methods + de Leeuw, Hornik, Mair + Journal of Statistical Software 2009 + + Correctness of Kruskal's algorithms for monotone regression with ties + de Leeuw, Psychometrica, 1977 + + Examples + -------- + >>> from sklearn.datasets import make_regression + >>> from sklearn.isotonic import IsotonicRegression + >>> X, y = make_regression(n_samples=10, n_features=1, random_state=41) + >>> iso_reg = IsotonicRegression().fit(X, y) + >>> iso_reg.predict([.1, .2]) + array([1.8628, 3.7256]) + """ + + # T should have been called X + __metadata_request__predict = {"T": metadata_routing.UNUSED} + __metadata_request__transform = {"T": metadata_routing.UNUSED} + + _parameter_constraints: dict = { + "y_min": [Interval(Real, None, None, closed="both"), None], + "y_max": [Interval(Real, None, None, closed="both"), None], + "increasing": ["boolean", StrOptions({"auto"})], + "out_of_bounds": [StrOptions({"nan", "clip", "raise"})], + } + + def __init__(self, *, y_min=None, y_max=None, increasing=True, out_of_bounds="nan"): + self.y_min = y_min + self.y_max = y_max + self.increasing = increasing + self.out_of_bounds = out_of_bounds + + def _check_input_data_shape(self, X): + if not (X.ndim == 1 or (X.ndim == 2 and X.shape[1] == 1)): + msg = ( + "Isotonic regression input X should be a 1d array or " + "2d array with 1 feature" + ) + raise ValueError(msg) + + def _build_f(self, X, y): + """Build the f_ interp1d function.""" + + bounds_error = self.out_of_bounds == "raise" + if len(y) == 1: + # single y, constant prediction + self.f_ = lambda x: y.repeat(x.shape) + else: + self.f_ = interpolate.interp1d( + X, y, kind="linear", bounds_error=bounds_error + ) + + def _build_y(self, X, y, sample_weight, trim_duplicates=True): + """Build the y_ IsotonicRegression.""" + self._check_input_data_shape(X) + X = X.reshape(-1) # use 1d view + + # Determine increasing if auto-determination requested + if self.increasing == "auto": + self.increasing_ = check_increasing(X, y) + else: + self.increasing_ = self.increasing + + # If sample_weights is passed, removed zero-weight values and clean + # order + sample_weight = _check_sample_weight(sample_weight, X, dtype=X.dtype) + mask = sample_weight > 0 + X, y, sample_weight = X[mask], y[mask], sample_weight[mask] + + order = np.lexsort((y, X)) + X, y, sample_weight = [array[order] for array in [X, y, sample_weight]] + unique_X, unique_y, unique_sample_weight = _make_unique(X, y, sample_weight) + + X = unique_X + y = isotonic_regression( + unique_y, + sample_weight=unique_sample_weight, + y_min=self.y_min, + y_max=self.y_max, + increasing=self.increasing_, + ) + + # Handle the left and right bounds on X + self.X_min_, self.X_max_ = np.min(X), np.max(X) + + if trim_duplicates: + # Remove unnecessary points for faster prediction + keep_data = np.ones((len(y),), dtype=bool) + # Aside from the 1st and last point, remove points whose y values + # are equal to both the point before and the point after it. + keep_data[1:-1] = np.logical_or( + np.not_equal(y[1:-1], y[:-2]), np.not_equal(y[1:-1], y[2:]) + ) + return X[keep_data], y[keep_data] + else: + # The ability to turn off trim_duplicates is only used to it make + # easier to unit test that removing duplicates in y does not have + # any impact the resulting interpolation function (besides + # prediction speed). + return X, y + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y, sample_weight=None): + """Fit the model using X, y as training data. + + Parameters + ---------- + X : array-like of shape (n_samples,) or (n_samples, 1) + Training data. + + .. versionchanged:: 0.24 + Also accepts 2d array with 1 feature. + + y : array-like of shape (n_samples,) + Training target. + + sample_weight : array-like of shape (n_samples,), default=None + Weights. If set to None, all weights will be set to 1 (equal + weights). + + Returns + ------- + self : object + Returns an instance of self. + + Notes + ----- + X is stored for future use, as :meth:`transform` needs X to interpolate + new input data. + """ + check_params = dict(accept_sparse=False, ensure_2d=False) + X = check_array( + X, input_name="X", dtype=[np.float64, np.float32], **check_params + ) + y = check_array(y, input_name="y", dtype=X.dtype, **check_params) + check_consistent_length(X, y, sample_weight) + + # Transform y by running the isotonic regression algorithm and + # transform X accordingly. + X, y = self._build_y(X, y, sample_weight) + + # It is necessary to store the non-redundant part of the training set + # on the model to make it possible to support model persistence via + # the pickle module as the object built by scipy.interp1d is not + # picklable directly. + self.X_thresholds_, self.y_thresholds_ = X, y + + # Build the interpolation function + self._build_f(X, y) + return self + + def _transform(self, T): + """`_transform` is called by both `transform` and `predict` methods. + + Since `transform` is wrapped to output arrays of specific types (e.g. + NumPy arrays, pandas DataFrame), we cannot make `predict` call `transform` + directly. + + The above behaviour could be changed in the future, if we decide to output + other type of arrays when calling `predict`. + """ + if hasattr(self, "X_thresholds_"): + dtype = self.X_thresholds_.dtype + else: + dtype = np.float64 + + T = check_array(T, dtype=dtype, ensure_2d=False) + + self._check_input_data_shape(T) + T = T.reshape(-1) # use 1d view + + if self.out_of_bounds == "clip": + T = np.clip(T, self.X_min_, self.X_max_) + + res = self.f_(T) + + # on scipy 0.17, interp1d up-casts to float64, so we cast back + res = res.astype(T.dtype) + + return res + + def transform(self, T): + """Transform new data by linear interpolation. + + Parameters + ---------- + T : array-like of shape (n_samples,) or (n_samples, 1) + Data to transform. + + .. versionchanged:: 0.24 + Also accepts 2d array with 1 feature. + + Returns + ------- + y_pred : ndarray of shape (n_samples,) + The transformed data. + """ + return self._transform(T) + + def predict(self, T): + """Predict new data by linear interpolation. + + Parameters + ---------- + T : array-like of shape (n_samples,) or (n_samples, 1) + Data to transform. + + Returns + ------- + y_pred : ndarray of shape (n_samples,) + Transformed data. + """ + return self._transform(T) + + # We implement get_feature_names_out here instead of using + # `ClassNamePrefixFeaturesOutMixin`` because `input_features` are ignored. + # `input_features` are ignored because `IsotonicRegression` accepts 1d + # arrays and the semantics of `feature_names_in_` are not clear for 1d arrays. + def get_feature_names_out(self, input_features=None): + """Get output feature names for transformation. + + Parameters + ---------- + input_features : array-like of str or None, default=None + Ignored. + + Returns + ------- + feature_names_out : ndarray of str objects + An ndarray with one string i.e. ["isotonicregression0"]. + """ + check_is_fitted(self, "f_") + class_name = self.__class__.__name__.lower() + return np.asarray([f"{class_name}0"], dtype=object) + + def __getstate__(self): + """Pickle-protocol - return state of the estimator.""" + state = super().__getstate__() + # remove interpolation method + state.pop("f_", None) + return state + + def __setstate__(self, state): + """Pickle-protocol - set state of the estimator. + + We need to rebuild the interpolation function. + """ + super().__setstate__(state) + if hasattr(self, "X_thresholds_") and hasattr(self, "y_thresholds_"): + self._build_f(self.X_thresholds_, self.y_thresholds_) + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.one_d_array = True + tags.input_tags.two_d_array = False + return tags diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/kernel_approximation.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/kernel_approximation.py new file mode 100644 index 0000000000000000000000000000000000000000..02c8af755baeaa53ffe13c33371167dcc2aeeb6e --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/kernel_approximation.py @@ -0,0 +1,1106 @@ +"""Approximate kernel feature maps based on Fourier transforms and count sketches.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from numbers import Integral, Real + +import numpy as np +import scipy.sparse as sp +from scipy.fft import fft, ifft +from scipy.linalg import svd + +from .base import ( + BaseEstimator, + ClassNamePrefixFeaturesOutMixin, + TransformerMixin, + _fit_context, +) +from .metrics.pairwise import KERNEL_PARAMS, PAIRWISE_KERNEL_FUNCTIONS, pairwise_kernels +from .utils import check_random_state +from .utils._param_validation import Interval, StrOptions +from .utils.extmath import safe_sparse_dot +from .utils.validation import ( + _check_feature_names_in, + check_is_fitted, + validate_data, +) + + +class PolynomialCountSketch( + ClassNamePrefixFeaturesOutMixin, TransformerMixin, BaseEstimator +): + """Polynomial kernel approximation via Tensor Sketch. + + Implements Tensor Sketch, which approximates the feature map + of the polynomial kernel:: + + K(X, Y) = (gamma * + coef0)^degree + + by efficiently computing a Count Sketch of the outer product of a + vector with itself using Fast Fourier Transforms (FFT). Read more in the + :ref:`User Guide `. + + .. versionadded:: 0.24 + + Parameters + ---------- + gamma : float, default=1.0 + Parameter of the polynomial kernel whose feature map + will be approximated. + + degree : int, default=2 + Degree of the polynomial kernel whose feature map + will be approximated. + + coef0 : int, default=0 + Constant term of the polynomial kernel whose feature map + will be approximated. + + n_components : int, default=100 + Dimensionality of the output feature space. Usually, `n_components` + should be greater than the number of features in input samples in + order to achieve good performance. The optimal score / run time + balance is typically achieved around `n_components` = 10 * `n_features`, + but this depends on the specific dataset being used. + + random_state : int, RandomState instance, default=None + Determines random number generation for indexHash and bitHash + initialization. Pass an int for reproducible results across multiple + function calls. See :term:`Glossary `. + + Attributes + ---------- + indexHash_ : ndarray of shape (degree, n_features), dtype=int64 + Array of indexes in range [0, n_components) used to represent + the 2-wise independent hash functions for Count Sketch computation. + + bitHash_ : ndarray of shape (degree, n_features), dtype=float32 + Array with random entries in {+1, -1}, used to represent + the 2-wise independent hash functions for Count Sketch computation. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + AdditiveChi2Sampler : Approximate feature map for additive chi2 kernel. + Nystroem : Approximate a kernel map using a subset of the training data. + RBFSampler : Approximate a RBF kernel feature map using random Fourier + features. + SkewedChi2Sampler : Approximate feature map for "skewed chi-squared" kernel. + sklearn.metrics.pairwise.kernel_metrics : List of built-in kernels. + + Examples + -------- + >>> from sklearn.kernel_approximation import PolynomialCountSketch + >>> from sklearn.linear_model import SGDClassifier + >>> X = [[0, 0], [1, 1], [1, 0], [0, 1]] + >>> y = [0, 0, 1, 1] + >>> ps = PolynomialCountSketch(degree=3, random_state=1) + >>> X_features = ps.fit_transform(X) + >>> clf = SGDClassifier(max_iter=10, tol=1e-3) + >>> clf.fit(X_features, y) + SGDClassifier(max_iter=10) + >>> clf.score(X_features, y) + 1.0 + + For a more detailed example of usage, see + :ref:`sphx_glr_auto_examples_kernel_approximation_plot_scalable_poly_kernels.py` + """ + + _parameter_constraints: dict = { + "gamma": [Interval(Real, 0, None, closed="left")], + "degree": [Interval(Integral, 1, None, closed="left")], + "coef0": [Interval(Real, None, None, closed="neither")], + "n_components": [Interval(Integral, 1, None, closed="left")], + "random_state": ["random_state"], + } + + def __init__( + self, *, gamma=1.0, degree=2, coef0=0, n_components=100, random_state=None + ): + self.gamma = gamma + self.degree = degree + self.coef0 = coef0 + self.n_components = n_components + self.random_state = random_state + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the model with X. + + Initializes the internal variables. The method needs no information + about the distribution of data, so we only care about n_features in X. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Training data, where `n_samples` is the number of samples + and `n_features` is the number of features. + + y : array-like of shape (n_samples,) or (n_samples, n_outputs), \ + default=None + Target values (None for unsupervised transformations). + + Returns + ------- + self : object + Returns the instance itself. + """ + X = validate_data(self, X, accept_sparse="csc") + random_state = check_random_state(self.random_state) + + n_features = X.shape[1] + if self.coef0 != 0: + n_features += 1 + + self.indexHash_ = random_state.randint( + 0, high=self.n_components, size=(self.degree, n_features) + ) + + self.bitHash_ = random_state.choice(a=[-1, 1], size=(self.degree, n_features)) + self._n_features_out = self.n_components + return self + + def transform(self, X): + """Generate the feature map approximation for X. + + Parameters + ---------- + X : {array-like}, shape (n_samples, n_features) + New data, where `n_samples` is the number of samples + and `n_features` is the number of features. + + Returns + ------- + X_new : array-like, shape (n_samples, n_components) + Returns the instance itself. + """ + + check_is_fitted(self) + X = validate_data(self, X, accept_sparse="csc", reset=False) + + X_gamma = np.sqrt(self.gamma) * X + + if sp.issparse(X_gamma) and self.coef0 != 0: + X_gamma = sp.hstack( + [X_gamma, np.sqrt(self.coef0) * np.ones((X_gamma.shape[0], 1))], + format="csc", + ) + + elif not sp.issparse(X_gamma) and self.coef0 != 0: + X_gamma = np.hstack( + [X_gamma, np.sqrt(self.coef0) * np.ones((X_gamma.shape[0], 1))] + ) + + if X_gamma.shape[1] != self.indexHash_.shape[1]: + raise ValueError( + "Number of features of test samples does not" + " match that of training samples." + ) + + count_sketches = np.zeros((X_gamma.shape[0], self.degree, self.n_components)) + + if sp.issparse(X_gamma): + for j in range(X_gamma.shape[1]): + for d in range(self.degree): + iHashIndex = self.indexHash_[d, j] + iHashBit = self.bitHash_[d, j] + count_sketches[:, d, iHashIndex] += ( + (iHashBit * X_gamma[:, [j]]).toarray().ravel() + ) + + else: + for j in range(X_gamma.shape[1]): + for d in range(self.degree): + iHashIndex = self.indexHash_[d, j] + iHashBit = self.bitHash_[d, j] + count_sketches[:, d, iHashIndex] += iHashBit * X_gamma[:, j] + + # For each same, compute a count sketch of phi(x) using the polynomial + # multiplication (via FFT) of p count sketches of x. + count_sketches_fft = fft(count_sketches, axis=2, overwrite_x=True) + count_sketches_fft_prod = np.prod(count_sketches_fft, axis=1) + data_sketch = np.real(ifft(count_sketches_fft_prod, overwrite_x=True)) + + return data_sketch + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + return tags + + +class RBFSampler(ClassNamePrefixFeaturesOutMixin, TransformerMixin, BaseEstimator): + """Approximate a RBF kernel feature map using random Fourier features. + + It implements a variant of Random Kitchen Sinks.[1] + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + gamma : 'scale' or float, default=1.0 + Parameter of RBF kernel: exp(-gamma * x^2). + If ``gamma='scale'`` is passed then it uses + 1 / (n_features * X.var()) as value of gamma. + + .. versionadded:: 1.2 + The option `"scale"` was added in 1.2. + + n_components : int, default=100 + Number of Monte Carlo samples per original feature. + Equals the dimensionality of the computed feature space. + + random_state : int, RandomState instance or None, default=None + Pseudo-random number generator to control the generation of the random + weights and random offset when fitting the training data. + Pass an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + Attributes + ---------- + random_offset_ : ndarray of shape (n_components,), dtype={np.float64, np.float32} + Random offset used to compute the projection in the `n_components` + dimensions of the feature space. + + random_weights_ : ndarray of shape (n_features, n_components),\ + dtype={np.float64, np.float32} + Random projection directions drawn from the Fourier transform + of the RBF kernel. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + AdditiveChi2Sampler : Approximate feature map for additive chi2 kernel. + Nystroem : Approximate a kernel map using a subset of the training data. + PolynomialCountSketch : Polynomial kernel approximation via Tensor Sketch. + SkewedChi2Sampler : Approximate feature map for + "skewed chi-squared" kernel. + sklearn.metrics.pairwise.kernel_metrics : List of built-in kernels. + + Notes + ----- + See "Random Features for Large-Scale Kernel Machines" by A. Rahimi and + Benjamin Recht. + + [1] "Weighted Sums of Random Kitchen Sinks: Replacing + minimization with randomization in learning" by A. Rahimi and + Benjamin Recht. + (https://people.eecs.berkeley.edu/~brecht/papers/08.rah.rec.nips.pdf) + + Examples + -------- + >>> from sklearn.kernel_approximation import RBFSampler + >>> from sklearn.linear_model import SGDClassifier + >>> X = [[0, 0], [1, 1], [1, 0], [0, 1]] + >>> y = [0, 0, 1, 1] + >>> rbf_feature = RBFSampler(gamma=1, random_state=1) + >>> X_features = rbf_feature.fit_transform(X) + >>> clf = SGDClassifier(max_iter=5, tol=1e-3) + >>> clf.fit(X_features, y) + SGDClassifier(max_iter=5) + >>> clf.score(X_features, y) + 1.0 + """ + + _parameter_constraints: dict = { + "gamma": [ + StrOptions({"scale"}), + Interval(Real, 0.0, None, closed="left"), + ], + "n_components": [Interval(Integral, 1, None, closed="left")], + "random_state": ["random_state"], + } + + def __init__(self, *, gamma=1.0, n_components=100, random_state=None): + self.gamma = gamma + self.n_components = n_components + self.random_state = random_state + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the model with X. + + Samples random projection according to n_features. + + Parameters + ---------- + X : {array-like, sparse matrix}, shape (n_samples, n_features) + Training data, where `n_samples` is the number of samples + and `n_features` is the number of features. + + y : array-like, shape (n_samples,) or (n_samples, n_outputs), \ + default=None + Target values (None for unsupervised transformations). + + Returns + ------- + self : object + Returns the instance itself. + """ + X = validate_data(self, X, accept_sparse="csr") + random_state = check_random_state(self.random_state) + n_features = X.shape[1] + sparse = sp.issparse(X) + if self.gamma == "scale": + # var = E[X^2] - E[X]^2 if sparse + X_var = (X.multiply(X)).mean() - (X.mean()) ** 2 if sparse else X.var() + self._gamma = 1.0 / (n_features * X_var) if X_var != 0 else 1.0 + else: + self._gamma = self.gamma + self.random_weights_ = (2.0 * self._gamma) ** 0.5 * random_state.normal( + size=(n_features, self.n_components) + ) + + self.random_offset_ = random_state.uniform(0, 2 * np.pi, size=self.n_components) + + if X.dtype == np.float32: + # Setting the data type of the fitted attribute will ensure the + # output data type during `transform`. + self.random_weights_ = self.random_weights_.astype(X.dtype, copy=False) + self.random_offset_ = self.random_offset_.astype(X.dtype, copy=False) + + self._n_features_out = self.n_components + return self + + def transform(self, X): + """Apply the approximate feature map to X. + + Parameters + ---------- + X : {array-like, sparse matrix}, shape (n_samples, n_features) + New data, where `n_samples` is the number of samples + and `n_features` is the number of features. + + Returns + ------- + X_new : array-like, shape (n_samples, n_components) + Returns the instance itself. + """ + check_is_fitted(self) + + X = validate_data(self, X, accept_sparse="csr", reset=False) + projection = safe_sparse_dot(X, self.random_weights_) + projection += self.random_offset_ + np.cos(projection, projection) + projection *= (2.0 / self.n_components) ** 0.5 + return projection + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + tags.transformer_tags.preserves_dtype = ["float64", "float32"] + return tags + + +class SkewedChi2Sampler( + ClassNamePrefixFeaturesOutMixin, TransformerMixin, BaseEstimator +): + """Approximate feature map for "skewed chi-squared" kernel. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + skewedness : float, default=1.0 + "skewedness" parameter of the kernel. Needs to be cross-validated. + + n_components : int, default=100 + Number of Monte Carlo samples per original feature. + Equals the dimensionality of the computed feature space. + + random_state : int, RandomState instance or None, default=None + Pseudo-random number generator to control the generation of the random + weights and random offset when fitting the training data. + Pass an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + Attributes + ---------- + random_weights_ : ndarray of shape (n_features, n_components) + Weight array, sampled from a secant hyperbolic distribution, which will + be used to linearly transform the log of the data. + + random_offset_ : ndarray of shape (n_features, n_components) + Bias term, which will be added to the data. It is uniformly distributed + between 0 and 2*pi. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + AdditiveChi2Sampler : Approximate feature map for additive chi2 kernel. + Nystroem : Approximate a kernel map using a subset of the training data. + RBFSampler : Approximate a RBF kernel feature map using random Fourier + features. + SkewedChi2Sampler : Approximate feature map for "skewed chi-squared" kernel. + sklearn.metrics.pairwise.chi2_kernel : The exact chi squared kernel. + sklearn.metrics.pairwise.kernel_metrics : List of built-in kernels. + + References + ---------- + See "Random Fourier Approximations for Skewed Multiplicative Histogram + Kernels" by Fuxin Li, Catalin Ionescu and Cristian Sminchisescu. + + Examples + -------- + >>> from sklearn.kernel_approximation import SkewedChi2Sampler + >>> from sklearn.linear_model import SGDClassifier + >>> X = [[0, 0], [1, 1], [1, 0], [0, 1]] + >>> y = [0, 0, 1, 1] + >>> chi2_feature = SkewedChi2Sampler(skewedness=.01, + ... n_components=10, + ... random_state=0) + >>> X_features = chi2_feature.fit_transform(X, y) + >>> clf = SGDClassifier(max_iter=10, tol=1e-3) + >>> clf.fit(X_features, y) + SGDClassifier(max_iter=10) + >>> clf.score(X_features, y) + 1.0 + """ + + _parameter_constraints: dict = { + "skewedness": [Interval(Real, None, None, closed="neither")], + "n_components": [Interval(Integral, 1, None, closed="left")], + "random_state": ["random_state"], + } + + def __init__(self, *, skewedness=1.0, n_components=100, random_state=None): + self.skewedness = skewedness + self.n_components = n_components + self.random_state = random_state + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit the model with X. + + Samples random projection according to n_features. + + Parameters + ---------- + X : array-like, shape (n_samples, n_features) + Training data, where `n_samples` is the number of samples + and `n_features` is the number of features. + + y : array-like, shape (n_samples,) or (n_samples, n_outputs), \ + default=None + Target values (None for unsupervised transformations). + + Returns + ------- + self : object + Returns the instance itself. + """ + X = validate_data(self, X) + random_state = check_random_state(self.random_state) + n_features = X.shape[1] + uniform = random_state.uniform(size=(n_features, self.n_components)) + # transform by inverse CDF of sech + self.random_weights_ = 1.0 / np.pi * np.log(np.tan(np.pi / 2.0 * uniform)) + self.random_offset_ = random_state.uniform(0, 2 * np.pi, size=self.n_components) + + if X.dtype == np.float32: + # Setting the data type of the fitted attribute will ensure the + # output data type during `transform`. + self.random_weights_ = self.random_weights_.astype(X.dtype, copy=False) + self.random_offset_ = self.random_offset_.astype(X.dtype, copy=False) + + self._n_features_out = self.n_components + return self + + def transform(self, X): + """Apply the approximate feature map to X. + + Parameters + ---------- + X : array-like, shape (n_samples, n_features) + New data, where `n_samples` is the number of samples + and `n_features` is the number of features. All values of X must be + strictly greater than "-skewedness". + + Returns + ------- + X_new : array-like, shape (n_samples, n_components) + Returns the instance itself. + """ + check_is_fitted(self) + X = validate_data( + self, X, copy=True, dtype=[np.float64, np.float32], reset=False + ) + if (X <= -self.skewedness).any(): + raise ValueError("X may not contain entries smaller than -skewedness.") + + X += self.skewedness + np.log(X, X) + projection = safe_sparse_dot(X, self.random_weights_) + projection += self.random_offset_ + np.cos(projection, projection) + projection *= np.sqrt(2.0) / np.sqrt(self.n_components) + return projection + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.transformer_tags.preserves_dtype = ["float64", "float32"] + return tags + + +class AdditiveChi2Sampler(TransformerMixin, BaseEstimator): + """Approximate feature map for additive chi2 kernel. + + Uses sampling the fourier transform of the kernel characteristic + at regular intervals. + + Since the kernel that is to be approximated is additive, the components of + the input vectors can be treated separately. Each entry in the original + space is transformed into 2*sample_steps-1 features, where sample_steps is + a parameter of the method. Typical values of sample_steps include 1, 2 and + 3. + + Optimal choices for the sampling interval for certain data ranges can be + computed (see the reference). The default values should be reasonable. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + sample_steps : int, default=2 + Gives the number of (complex) sampling points. + + sample_interval : float, default=None + Sampling interval. Must be specified when sample_steps not in {1,2,3}. + + Attributes + ---------- + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + SkewedChi2Sampler : A Fourier-approximation to a non-additive variant of + the chi squared kernel. + + sklearn.metrics.pairwise.chi2_kernel : The exact chi squared kernel. + + sklearn.metrics.pairwise.additive_chi2_kernel : The exact additive chi + squared kernel. + + Notes + ----- + This estimator approximates a slightly different version of the additive + chi squared kernel then ``metric.additive_chi2`` computes. + + This estimator is stateless and does not need to be fitted. However, we + recommend to call :meth:`fit_transform` instead of :meth:`transform`, as + parameter validation is only performed in :meth:`fit`. + + References + ---------- + See `"Efficient additive kernels via explicit feature maps" + `_ + A. Vedaldi and A. Zisserman, Pattern Analysis and Machine Intelligence, + 2011 + + Examples + -------- + >>> from sklearn.datasets import load_digits + >>> from sklearn.linear_model import SGDClassifier + >>> from sklearn.kernel_approximation import AdditiveChi2Sampler + >>> X, y = load_digits(return_X_y=True) + >>> chi2sampler = AdditiveChi2Sampler(sample_steps=2) + >>> X_transformed = chi2sampler.fit_transform(X, y) + >>> clf = SGDClassifier(max_iter=5, random_state=0, tol=1e-3) + >>> clf.fit(X_transformed, y) + SGDClassifier(max_iter=5, random_state=0) + >>> clf.score(X_transformed, y) + 0.9499... + """ + + _parameter_constraints: dict = { + "sample_steps": [Interval(Integral, 1, None, closed="left")], + "sample_interval": [Interval(Real, 0, None, closed="left"), None], + } + + def __init__(self, *, sample_steps=2, sample_interval=None): + self.sample_steps = sample_steps + self.sample_interval = sample_interval + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Only validates estimator's parameters. + + This method allows to: (i) validate the estimator's parameters and + (ii) be consistent with the scikit-learn transformer API. + + Parameters + ---------- + X : array-like, shape (n_samples, n_features) + Training data, where `n_samples` is the number of samples + and `n_features` is the number of features. + + y : array-like, shape (n_samples,) or (n_samples, n_outputs), \ + default=None + Target values (None for unsupervised transformations). + + Returns + ------- + self : object + Returns the transformer. + """ + X = validate_data(self, X, accept_sparse="csr", ensure_non_negative=True) + + if self.sample_interval is None and self.sample_steps not in (1, 2, 3): + raise ValueError( + "If sample_steps is not in [1, 2, 3]," + " you need to provide sample_interval" + ) + + return self + + def transform(self, X): + """Apply approximate feature map to X. + + Parameters + ---------- + X : {array-like, sparse matrix}, shape (n_samples, n_features) + Training data, where `n_samples` is the number of samples + and `n_features` is the number of features. + + Returns + ------- + X_new : {ndarray, sparse matrix}, \ + shape = (n_samples, n_features * (2*sample_steps - 1)) + Whether the return value is an array or sparse matrix depends on + the type of the input X. + """ + X = validate_data( + self, X, accept_sparse="csr", reset=False, ensure_non_negative=True + ) + sparse = sp.issparse(X) + + if self.sample_interval is None: + # See figure 2 c) of "Efficient additive kernels via explicit feature maps" + # + # A. Vedaldi and A. Zisserman, Pattern Analysis and Machine Intelligence, + # 2011 + if self.sample_steps == 1: + sample_interval = 0.8 + elif self.sample_steps == 2: + sample_interval = 0.5 + elif self.sample_steps == 3: + sample_interval = 0.4 + else: + raise ValueError( + "If sample_steps is not in [1, 2, 3]," + " you need to provide sample_interval" + ) + else: + sample_interval = self.sample_interval + + # zeroth component + # 1/cosh = sech + # cosh(0) = 1.0 + transf = self._transform_sparse if sparse else self._transform_dense + return transf(X, self.sample_steps, sample_interval) + + def get_feature_names_out(self, input_features=None): + """Get output feature names for transformation. + + Parameters + ---------- + input_features : array-like of str or None, default=None + Only used to validate feature names with the names seen in :meth:`fit`. + + Returns + ------- + feature_names_out : ndarray of str objects + Transformed feature names. + """ + # Note that passing attributes="n_features_in_" forces check_is_fitted + # to check if the attribute is present. Otherwise it will pass on this + # stateless estimator (requires_fit=False) + check_is_fitted(self, attributes="n_features_in_") + input_features = _check_feature_names_in( + self, input_features, generate_names=True + ) + est_name = self.__class__.__name__.lower() + + names_list = [f"{est_name}_{name}_sqrt" for name in input_features] + + for j in range(1, self.sample_steps): + cos_names = [f"{est_name}_{name}_cos{j}" for name in input_features] + sin_names = [f"{est_name}_{name}_sin{j}" for name in input_features] + names_list.extend(cos_names + sin_names) + + return np.asarray(names_list, dtype=object) + + @staticmethod + def _transform_dense(X, sample_steps, sample_interval): + non_zero = X != 0.0 + X_nz = X[non_zero] + + X_step = np.zeros_like(X) + X_step[non_zero] = np.sqrt(X_nz * sample_interval) + + X_new = [X_step] + + log_step_nz = sample_interval * np.log(X_nz) + step_nz = 2 * X_nz * sample_interval + + for j in range(1, sample_steps): + factor_nz = np.sqrt(step_nz / np.cosh(np.pi * j * sample_interval)) + + X_step = np.zeros_like(X) + X_step[non_zero] = factor_nz * np.cos(j * log_step_nz) + X_new.append(X_step) + + X_step = np.zeros_like(X) + X_step[non_zero] = factor_nz * np.sin(j * log_step_nz) + X_new.append(X_step) + + return np.hstack(X_new) + + @staticmethod + def _transform_sparse(X, sample_steps, sample_interval): + indices = X.indices.copy() + indptr = X.indptr.copy() + + data_step = np.sqrt(X.data * sample_interval) + X_step = sp.csr_matrix( + (data_step, indices, indptr), shape=X.shape, dtype=X.dtype, copy=False + ) + X_new = [X_step] + + log_step_nz = sample_interval * np.log(X.data) + step_nz = 2 * X.data * sample_interval + + for j in range(1, sample_steps): + factor_nz = np.sqrt(step_nz / np.cosh(np.pi * j * sample_interval)) + + data_step = factor_nz * np.cos(j * log_step_nz) + X_step = sp.csr_matrix( + (data_step, indices, indptr), shape=X.shape, dtype=X.dtype, copy=False + ) + X_new.append(X_step) + + data_step = factor_nz * np.sin(j * log_step_nz) + X_step = sp.csr_matrix( + (data_step, indices, indptr), shape=X.shape, dtype=X.dtype, copy=False + ) + X_new.append(X_step) + + return sp.hstack(X_new) + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.requires_fit = False + tags.input_tags.positive_only = True + tags.input_tags.sparse = True + return tags + + +class Nystroem(ClassNamePrefixFeaturesOutMixin, TransformerMixin, BaseEstimator): + """Approximate a kernel map using a subset of the training data. + + Constructs an approximate feature map for an arbitrary kernel + using a subset of the data as basis. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.13 + + Parameters + ---------- + kernel : str or callable, default='rbf' + Kernel map to be approximated. A callable should accept two arguments + and the keyword arguments passed to this object as `kernel_params`, and + should return a floating point number. + + gamma : float, default=None + Gamma parameter for the RBF, laplacian, polynomial, exponential chi2 + and sigmoid kernels. Interpretation of the default value is left to + the kernel; see the documentation for sklearn.metrics.pairwise. + Ignored by other kernels. + + coef0 : float, default=None + Zero coefficient for polynomial and sigmoid kernels. + Ignored by other kernels. + + degree : float, default=None + Degree of the polynomial kernel. Ignored by other kernels. + + kernel_params : dict, default=None + Additional parameters (keyword arguments) for kernel function passed + as callable object. + + n_components : int, default=100 + Number of features to construct. + How many data points will be used to construct the mapping. + + random_state : int, RandomState instance or None, default=None + Pseudo-random number generator to control the uniform sampling without + replacement of `n_components` of the training data to construct the + basis kernel. + Pass an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + n_jobs : int, default=None + The number of jobs to use for the computation. This works by breaking + down the kernel matrix into `n_jobs` even slices and computing them in + parallel. + + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + .. versionadded:: 0.24 + + Attributes + ---------- + components_ : ndarray of shape (n_components, n_features) + Subset of training points used to construct the feature map. + + component_indices_ : ndarray of shape (n_components) + Indices of ``components_`` in the training set. + + normalization_ : ndarray of shape (n_components, n_components) + Normalization matrix needed for embedding. + Square root of the kernel matrix on ``components_``. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + AdditiveChi2Sampler : Approximate feature map for additive chi2 kernel. + PolynomialCountSketch : Polynomial kernel approximation via Tensor Sketch. + RBFSampler : Approximate a RBF kernel feature map using random Fourier + features. + SkewedChi2Sampler : Approximate feature map for "skewed chi-squared" kernel. + sklearn.metrics.pairwise.kernel_metrics : List of built-in kernels. + + References + ---------- + * Williams, C.K.I. and Seeger, M. + "Using the Nystroem method to speed up kernel machines", + Advances in neural information processing systems 2001 + + * T. Yang, Y. Li, M. Mahdavi, R. Jin and Z. Zhou + "Nystroem Method vs Random Fourier Features: A Theoretical and Empirical + Comparison", + Advances in Neural Information Processing Systems 2012 + + Examples + -------- + >>> from sklearn import datasets, svm + >>> from sklearn.kernel_approximation import Nystroem + >>> X, y = datasets.load_digits(n_class=9, return_X_y=True) + >>> data = X / 16. + >>> clf = svm.LinearSVC() + >>> feature_map_nystroem = Nystroem(gamma=.2, + ... random_state=1, + ... n_components=300) + >>> data_transformed = feature_map_nystroem.fit_transform(data) + >>> clf.fit(data_transformed, y) + LinearSVC() + >>> clf.score(data_transformed, y) + 0.9987... + """ + + _parameter_constraints: dict = { + "kernel": [ + StrOptions(set(PAIRWISE_KERNEL_FUNCTIONS.keys()) | {"precomputed"}), + callable, + ], + "gamma": [Interval(Real, 0, None, closed="left"), None], + "coef0": [Interval(Real, None, None, closed="neither"), None], + "degree": [Interval(Real, 1, None, closed="left"), None], + "kernel_params": [dict, None], + "n_components": [Interval(Integral, 1, None, closed="left")], + "random_state": ["random_state"], + "n_jobs": [Integral, None], + } + + def __init__( + self, + kernel="rbf", + *, + gamma=None, + coef0=None, + degree=None, + kernel_params=None, + n_components=100, + random_state=None, + n_jobs=None, + ): + self.kernel = kernel + self.gamma = gamma + self.coef0 = coef0 + self.degree = degree + self.kernel_params = kernel_params + self.n_components = n_components + self.random_state = random_state + self.n_jobs = n_jobs + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Fit estimator to data. + + Samples a subset of training points, computes kernel + on these and computes normalization matrix. + + Parameters + ---------- + X : array-like, shape (n_samples, n_features) + Training data, where `n_samples` is the number of samples + and `n_features` is the number of features. + + y : array-like, shape (n_samples,) or (n_samples, n_outputs), \ + default=None + Target values (None for unsupervised transformations). + + Returns + ------- + self : object + Returns the instance itself. + """ + X = validate_data(self, X, accept_sparse="csr") + rnd = check_random_state(self.random_state) + n_samples = X.shape[0] + + # get basis vectors + if self.n_components > n_samples: + # XXX should we just bail? + n_components = n_samples + warnings.warn( + "n_components > n_samples. This is not possible.\n" + "n_components was set to n_samples, which results" + " in inefficient evaluation of the full kernel." + ) + + else: + n_components = self.n_components + n_components = min(n_samples, n_components) + inds = rnd.permutation(n_samples) + basis_inds = inds[:n_components] + basis = X[basis_inds] + + basis_kernel = pairwise_kernels( + basis, + metric=self.kernel, + filter_params=True, + n_jobs=self.n_jobs, + **self._get_kernel_params(), + ) + + # sqrt of kernel matrix on basis vectors + U, S, V = svd(basis_kernel) + S = np.maximum(S, 1e-12) + self.normalization_ = np.dot(U / np.sqrt(S), V) + self.components_ = basis + self.component_indices_ = basis_inds + self._n_features_out = n_components + return self + + def transform(self, X): + """Apply feature map to X. + + Computes an approximate feature map using the kernel + between some training points and X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Data to transform. + + Returns + ------- + X_transformed : ndarray of shape (n_samples, n_components) + Transformed data. + """ + check_is_fitted(self) + X = validate_data(self, X, accept_sparse="csr", reset=False) + + kernel_params = self._get_kernel_params() + embedded = pairwise_kernels( + X, + self.components_, + metric=self.kernel, + filter_params=True, + n_jobs=self.n_jobs, + **kernel_params, + ) + return np.dot(embedded, self.normalization_.T) + + def _get_kernel_params(self): + params = self.kernel_params + if params is None: + params = {} + if not callable(self.kernel) and self.kernel != "precomputed": + for param in KERNEL_PARAMS[self.kernel]: + if getattr(self, param) is not None: + params[param] = getattr(self, param) + else: + if ( + self.gamma is not None + or self.coef0 is not None + or self.degree is not None + ): + raise ValueError( + "Don't pass gamma, coef0 or degree to " + "Nystroem if using a callable " + "or precomputed kernel" + ) + + return params + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + tags.transformer_tags.preserves_dtype = ["float64", "float32"] + return tags diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/kernel_ridge.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/kernel_ridge.py new file mode 100644 index 0000000000000000000000000000000000000000..29e744647acc97d3ff7493f2cfc9af4f07ce1bdc --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/kernel_ridge.py @@ -0,0 +1,240 @@ +"""Kernel ridge regression.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +from numbers import Real + +import numpy as np + +from .base import BaseEstimator, MultiOutputMixin, RegressorMixin, _fit_context +from .linear_model._ridge import _solve_cholesky_kernel +from .metrics.pairwise import PAIRWISE_KERNEL_FUNCTIONS, pairwise_kernels +from .utils._param_validation import Interval, StrOptions +from .utils.validation import _check_sample_weight, check_is_fitted, validate_data + + +class KernelRidge(MultiOutputMixin, RegressorMixin, BaseEstimator): + """Kernel ridge regression. + + Kernel ridge regression (KRR) combines ridge regression (linear least + squares with l2-norm regularization) with the kernel trick. It thus + learns a linear function in the space induced by the respective kernel and + the data. For non-linear kernels, this corresponds to a non-linear + function in the original space. + + The form of the model learned by KRR is identical to support vector + regression (SVR). However, different loss functions are used: KRR uses + squared error loss while support vector regression uses epsilon-insensitive + loss, both combined with l2 regularization. In contrast to SVR, fitting a + KRR model can be done in closed-form and is typically faster for + medium-sized datasets. On the other hand, the learned model is non-sparse + and thus slower than SVR, which learns a sparse model for epsilon > 0, at + prediction-time. + + This estimator has built-in support for multi-variate regression + (i.e., when y is a 2d-array of shape [n_samples, n_targets]). + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + alpha : float or array-like of shape (n_targets,), default=1.0 + Regularization strength; must be a positive float. Regularization + improves the conditioning of the problem and reduces the variance of + the estimates. Larger values specify stronger regularization. + Alpha corresponds to ``1 / (2C)`` in other linear models such as + :class:`~sklearn.linear_model.LogisticRegression` or + :class:`~sklearn.svm.LinearSVC`. If an array is passed, penalties are + assumed to be specific to the targets. Hence they must correspond in + number. See :ref:`ridge_regression` for formula. + + kernel : str or callable, default="linear" + Kernel mapping used internally. This parameter is directly passed to + :class:`~sklearn.metrics.pairwise.pairwise_kernels`. + If `kernel` is a string, it must be one of the metrics + in `pairwise.PAIRWISE_KERNEL_FUNCTIONS` or "precomputed". + If `kernel` is "precomputed", X is assumed to be a kernel matrix. + Alternatively, if `kernel` is a callable function, it is called on + each pair of instances (rows) and the resulting value recorded. The + callable should take two rows from X as input and return the + corresponding kernel value as a single number. This means that + callables from :mod:`sklearn.metrics.pairwise` are not allowed, as + they operate on matrices, not single samples. Use the string + identifying the kernel instead. + + gamma : float, default=None + Gamma parameter for the RBF, laplacian, polynomial, exponential chi2 + and sigmoid kernels. Interpretation of the default value is left to + the kernel; see the documentation for sklearn.metrics.pairwise. + Ignored by other kernels. + + degree : float, default=3 + Degree of the polynomial kernel. Ignored by other kernels. + + coef0 : float, default=1 + Zero coefficient for polynomial and sigmoid kernels. + Ignored by other kernels. + + kernel_params : dict, default=None + Additional parameters (keyword arguments) for kernel function passed + as callable object. + + Attributes + ---------- + dual_coef_ : ndarray of shape (n_samples,) or (n_samples, n_targets) + Representation of weight vector(s) in kernel space + + X_fit_ : {ndarray, sparse matrix} of shape (n_samples, n_features) + Training data, which is also required for prediction. If + kernel == "precomputed" this is instead the precomputed + training matrix, of shape (n_samples, n_samples). + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + sklearn.gaussian_process.GaussianProcessRegressor : Gaussian + Process regressor providing automatic kernel hyperparameters + tuning and predictions uncertainty. + sklearn.linear_model.Ridge : Linear ridge regression. + sklearn.linear_model.RidgeCV : Ridge regression with built-in + cross-validation. + sklearn.svm.SVR : Support Vector Regression accepting a large variety + of kernels. + + References + ---------- + * Kevin P. Murphy + "Machine Learning: A Probabilistic Perspective", The MIT Press + chapter 14.4.3, pp. 492-493 + + Examples + -------- + >>> from sklearn.kernel_ridge import KernelRidge + >>> import numpy as np + >>> n_samples, n_features = 10, 5 + >>> rng = np.random.RandomState(0) + >>> y = rng.randn(n_samples) + >>> X = rng.randn(n_samples, n_features) + >>> krr = KernelRidge(alpha=1.0) + >>> krr.fit(X, y) + KernelRidge(alpha=1.0) + """ + + _parameter_constraints: dict = { + "alpha": [Interval(Real, 0, None, closed="left"), "array-like"], + "kernel": [ + StrOptions(set(PAIRWISE_KERNEL_FUNCTIONS.keys()) | {"precomputed"}), + callable, + ], + "gamma": [Interval(Real, 0, None, closed="left"), None], + "degree": [Interval(Real, 0, None, closed="left")], + "coef0": [Interval(Real, None, None, closed="neither")], + "kernel_params": [dict, None], + } + + def __init__( + self, + alpha=1, + *, + kernel="linear", + gamma=None, + degree=3, + coef0=1, + kernel_params=None, + ): + self.alpha = alpha + self.kernel = kernel + self.gamma = gamma + self.degree = degree + self.coef0 = coef0 + self.kernel_params = kernel_params + + def _get_kernel(self, X, Y=None): + if callable(self.kernel): + params = self.kernel_params or {} + else: + params = {"gamma": self.gamma, "degree": self.degree, "coef0": self.coef0} + return pairwise_kernels(X, Y, metric=self.kernel, filter_params=True, **params) + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + tags.input_tags.pairwise = self.kernel == "precomputed" + return tags + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y, sample_weight=None): + """Fit Kernel Ridge regression model. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Training data. If kernel == "precomputed" this is instead + a precomputed kernel matrix, of shape (n_samples, n_samples). + + y : array-like of shape (n_samples,) or (n_samples, n_targets) + Target values. + + sample_weight : float or array-like of shape (n_samples,), default=None + Individual weights for each sample, ignored if None is passed. + + Returns + ------- + self : object + Returns the instance itself. + """ + # Convert data + X, y = validate_data( + self, X, y, accept_sparse=("csr", "csc"), multi_output=True, y_numeric=True + ) + if sample_weight is not None and not isinstance(sample_weight, float): + sample_weight = _check_sample_weight(sample_weight, X) + + K = self._get_kernel(X) + alpha = np.atleast_1d(self.alpha) + + ravel = False + if len(y.shape) == 1: + y = y.reshape(-1, 1) + ravel = True + + copy = self.kernel == "precomputed" + self.dual_coef_ = _solve_cholesky_kernel(K, y, alpha, sample_weight, copy) + if ravel: + self.dual_coef_ = self.dual_coef_.ravel() + + self.X_fit_ = X + + return self + + def predict(self, X): + """Predict using the kernel ridge model. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Samples. If kernel == "precomputed" this is instead a + precomputed kernel matrix, shape = [n_samples, + n_samples_fitted], where n_samples_fitted is the number of + samples used in the fitting for this estimator. + + Returns + ------- + C : ndarray of shape (n_samples,) or (n_samples, n_targets) + Returns predicted values. + """ + check_is_fitted(self) + X = validate_data(self, X, accept_sparse=("csr", "csc"), reset=False) + K = self._get_kernel(X, self.X_fit_) + return np.dot(K, self.dual_coef_) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/meson.build b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/meson.build new file mode 100644 index 0000000000000000000000000000000000000000..966da14c1338b5e33cc1c2d84f26bedca35b1cde --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/meson.build @@ -0,0 +1,273 @@ +fs = import('fs') + +cython_args = [] + +# Platform detection +is_windows = host_machine.system() == 'windows' +is_mingw = is_windows and cc.get_id() == 'gcc' + +# Adapted from Scipy. mingw is untested and not officially supported. If you +# ever bump into issues when trying to compile for mingw, please open an issue +# in the scikit-learn issue tracker +if is_mingw + # For mingw-w64, link statically against the UCRT. + gcc_link_args = ['-lucrt', '-static'] + add_project_link_arguments(gcc_link_args, language: ['c', 'cpp']) + # Force gcc to float64 long doubles for compatibility with MSVC + # builds, for C only. + add_project_arguments('-mlong-double-64', language: 'c') +endif + +# Only check build dependencies version when not cross-compiling, as running +# Python interpreter can be tricky in cross-compilation settings. For more +# details, see https://docs.scipy.org/doc/scipy/building/cross_compilation.html +if not meson.is_cross_build() + if not py.version().version_compare('>=3.10') + error('scikit-learn requires Python>=3.10, got ' + py.version() + ' instead') + endif + + cython_min_version = run_command(py, ['_min_dependencies.py', 'cython'], check: true).stdout().strip() + if not cython.version().version_compare('>=' + cython_min_version) + error('scikit-learn requires Cython>=' + cython_min_version + ', got ' + cython.version() + ' instead') + endif + + numpy_version = run_command(py, + ['-c', 'import numpy; print(numpy.__version__)'], check: true).stdout().strip() + numpy_min_version = run_command(py, ['_min_dependencies.py', 'numpy'], check: true).stdout().strip() + if not numpy_version.version_compare('>=' + numpy_min_version) + error('scikit-learn requires numpy>=' + numpy_min_version + ', got ' + numpy_version + ' instead') + endif + + scipy_version = run_command(py, + ['-c', 'import scipy; print(scipy.__version__)'], check: true).stdout().strip() + scipy_min_version = run_command(py, ['_min_dependencies.py', 'scipy'], check: true).stdout().strip() + if not scipy_version.version_compare('>=' + scipy_min_version) + error('scikit-learn requires scipy>=' + scipy_min_version + ', got ' + scipy_version + ' instead') + endif + + # meson-python is required only when going through pip. Using meson directly + # should not check meson-python version. + meson_python_version_command_result = run_command(py, + ['-c', 'import importlib.metadata; print(importlib.metadata.version("meson-python"))'], check: false) + meson_python_installed = meson_python_version_command_result.returncode() == 0 + if meson_python_installed + meson_python_version = meson_python_version_command_result.stdout().strip() + meson_python_min_version = run_command(py, ['_min_dependencies.py', 'meson-python'], check: true).stdout().strip() + if not meson_python_version.version_compare('>=' + meson_python_min_version) + error('scikit-learn requires meson-python>=' + meson_python_min_version + ', got ' + meson_python_version + ' instead') + endif + endif + +endif + +# Adapted from scipy, each project seems to have its own tweaks for this. One +# day using dependency('numpy') will be a thing, see +# https://github.com/mesonbuild/meson/issues/9598. +# NumPy include directory - needed in all submodules +# Relative paths are needed when for example a virtualenv is +# placed inside the source tree; Meson rejects absolute paths to places inside +# the source tree. The try-except is needed because when things are split +# across drives on Windows, there is no relative path and an exception gets +# raised. There may be other such cases, so add a catch-all and switch to +# an absolute path. +# For cross-compilation it is often not possible to run the Python interpreter +# in order to retrieve numpy's include directory. It can be specified in the +# cross file instead: +# [properties] +# numpy-include-dir = /abspath/to/host-pythons/site-packages/numpy/core/include +# +# This uses the path as is, and avoids running the interpreter. +incdir_numpy = meson.get_external_property('numpy-include-dir', 'not-given') +if incdir_numpy == 'not-given' + incdir_numpy = run_command(py, + [ + '-c', + ''' +import os +import numpy as np +try: + incdir = os.path.relpath(np.get_include()) +except Exception: + incdir = np.get_include() +print(incdir) +''' + ], + check: true + ).stdout().strip() +endif + +inc_np = include_directories(incdir_numpy) +# Don't use the deprecated NumPy C API. Define this to a fixed version instead of +# NPY_API_VERSION in order not to break compilation for released SciPy versions +# when NumPy introduces a new deprecation. +numpy_no_deprecated_api = ['-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION'] +np_dep = declare_dependency(include_directories: inc_np, compile_args: numpy_no_deprecated_api) + +openmp_dep = dependency('OpenMP', language: 'c', required: false) + +if not openmp_dep.found() + warn_about_missing_openmp = true + # On Apple Clang avoid a misleading warning if compiler variables are set. + # See https://github.com/scikit-learn/scikit-learn/issues/28710 for more + # details. This may be removed if the OpenMP detection on Apple Clang improves, + # see https://github.com/mesonbuild/meson/issues/7435#issuecomment-2047585466. + if host_machine.system() == 'darwin' and cc.get_id() == 'clang' + compiler_env_vars_with_openmp = run_command(py, + [ + '-c', + ''' +import os + +compiler_env_vars_to_check = ["CPPFLAGS", "CFLAGS", "CXXFLAGS"] + +compiler_env_vars_with_openmp = [ + var for var in compiler_env_vars_to_check if "-fopenmp" in os.getenv(var, "")] +print(compiler_env_vars_with_openmp) +'''], check: true).stdout().strip() + warn_about_missing_openmp = compiler_env_vars_with_openmp == '[]' + endif + if warn_about_missing_openmp + warning( +''' + *********** + * WARNING * + *********** + +It seems that scikit-learn cannot be built with OpenMP. + +- Make sure you have followed the installation instructions: + + https://scikit-learn.org/dev/developers/advanced_installation.html + +- If your compiler supports OpenMP but you still see this + message, please submit a bug report at: + + https://github.com/scikit-learn/scikit-learn/issues + +- The build will continue with OpenMP-based parallelism + disabled. Note however that some estimators will run in + sequential mode instead of leveraging thread-based + parallelism. + + *** +''') + else + warning( +'''It looks like compiler environment variables were set to enable OpenMP support. +Check the output of "import sklearn; sklearn.show_versions()" after the build +to make sure that scikit-learn was actually built with OpenMP support. +''') + endif +endif + +# For now, we keep supporting SKLEARN_ENABLE_DEBUG_CYTHON_DIRECTIVES variable +# (see how it is done in sklearn/_build_utils/__init__.py when building with +# setuptools). Accessing environment variables in meson.build is discouraged, +# so once we drop setuptools this functionality should be behind a meson option +# or buildtype +boundscheck = run_command(py, + [ + '-c', + ''' +import os + +if os.environ.get("SKLEARN_ENABLE_DEBUG_CYTHON_DIRECTIVES", "0") != "0": + print(True) +else: + print(False) + ''' + ], + check: true + ).stdout().strip() + +cython_program = find_program(cython.cmd_array()[0]) + +scikit_learn_cython_args = [ + '-X language_level=3', '-X boundscheck=' + boundscheck, '-X wraparound=False', + '-X initializedcheck=False', '-X nonecheck=False', '-X cdivision=True', + '-X profile=False', + # Needed for cython imports across subpackages, e.g. cluster pyx that + # cimports metrics pxd + '--include-dir', meson.global_build_root(), +] +cython_args += scikit_learn_cython_args + +if cython.version().version_compare('>=3.1.0') + cython_shared_src = custom_target( + install: false, + output: '_cyutility.c', + command: [ + cython_program, '-3', '--fast-fail', + '--generate-shared=' + meson.current_build_dir()/'_cyutility.c' + ], + ) + + py.extension_module('_cyutility', + cython_shared_src, + subdir: 'sklearn', + cython_args: cython_args, + install: true, + ) + + cython_args += ['--shared=sklearn._cyutility'] +endif + +cython_gen = generator(cython_program, + arguments : cython_args + ['@INPUT@', '--output-file', '@OUTPUT@'], + output : '@BASENAME@.c', +) + +cython_gen_cpp = generator(cython_program, + arguments : cython_args + ['--cplus', '@INPUT@', '--output-file', '@OUTPUT@'], + output : '@BASENAME@.cpp', +) + +# Write file in Meson build dir to be able to figure out from Python code +# whether scikit-learn was built with Meson. Adapted from pandas +# _version_meson.py. +custom_target('write_built_with_meson_file', + output: '_built_with_meson.py', + command: [ + py, '-c', 'with open("sklearn/_built_with_meson.py", "w") as f: f.write("")' + ], + install: true, + install_dir: py.get_install_dir() / 'sklearn' +) + +extensions = ['_isotonic'] + +py.extension_module( + '_isotonic', + cython_gen.process('_isotonic.pyx'), + cython_args: cython_args, + install: true, + subdir: 'sklearn', +) + +# Need for Cython cimports across subpackages to work, i.e. avoid errors like +# relative cimport from non-package directory is not allowed +sklearn_root_cython_tree = [ + fs.copyfile('__init__.py') +] + +sklearn_dir = py.get_install_dir() / 'sklearn' + +# Subpackages are mostly in alphabetical order except to handle Cython +# dependencies across subpackages +subdir('__check_build') +subdir('_loss') +# utils needs to be early since plenty of other modules cimports utils .pxd +subdir('utils') +# metrics needs to be to be before cluster since cluster cimports metrics .pxd +subdir('metrics') +subdir('cluster') +subdir('datasets') +subdir('decomposition') +subdir('ensemble') +subdir('feature_extraction') +subdir('linear_model') +subdir('manifold') +subdir('neighbors') +subdir('preprocessing') +subdir('svm') +subdir('tree') diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/multiclass.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/multiclass.py new file mode 100644 index 0000000000000000000000000000000000000000..d4208e0f542c77d68c6a6d87d3b409c85e6850e6 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/multiclass.py @@ -0,0 +1,1287 @@ +"""Multiclass learning algorithms. + +- one-vs-the-rest / one-vs-all +- one-vs-one +- error correcting output codes + +The estimators provided in this module are meta-estimators: they require a base +estimator to be provided in their constructor. For example, it is possible to +use these estimators to turn a binary classifier or a regressor into a +multiclass classifier. It is also possible to use these estimators with +multiclass estimators in the hope that their accuracy or runtime performance +improves. + +All classifiers in scikit-learn implement multiclass classification; you +only need to use this module if you want to experiment with custom multiclass +strategies. + +The one-vs-the-rest meta-classifier also implements a `predict_proba` method, +so long as such a method is implemented by the base classifier. This method +returns probabilities of class membership in both the single label and +multilabel case. Note that in the multilabel case, probabilities are the +marginal probability that a given sample falls in the given class. As such, in +the multilabel case the sum of these probabilities over all possible labels +for a given sample *will not* sum to unity, as they do in the single label +case. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import array +import itertools +import warnings +from numbers import Integral, Real + +import numpy as np +import scipy.sparse as sp + +from .base import ( + BaseEstimator, + ClassifierMixin, + MetaEstimatorMixin, + MultiOutputMixin, + _fit_context, + clone, + is_classifier, + is_regressor, +) +from .metrics.pairwise import pairwise_distances_argmin +from .preprocessing import LabelBinarizer +from .utils import check_random_state +from .utils._param_validation import HasMethods, Interval +from .utils._tags import get_tags +from .utils.metadata_routing import ( + MetadataRouter, + MethodMapping, + _raise_for_params, + process_routing, +) +from .utils.metaestimators import _safe_split, available_if +from .utils.multiclass import ( + _check_partial_fit_first_call, + _ovr_decision_function, + check_classification_targets, +) +from .utils.parallel import Parallel, delayed +from .utils.validation import ( + _check_method_params, + _num_samples, + check_is_fitted, + validate_data, +) + +__all__ = [ + "OneVsOneClassifier", + "OneVsRestClassifier", + "OutputCodeClassifier", +] + + +def _fit_binary(estimator, X, y, fit_params, classes=None): + """Fit a single binary estimator.""" + unique_y = np.unique(y) + if len(unique_y) == 1: + if classes is not None: + if y[0] == -1: + c = 0 + else: + c = y[0] + warnings.warn( + "Label %s is present in all training examples." % str(classes[c]) + ) + estimator = _ConstantPredictor().fit(X, unique_y) + else: + estimator = clone(estimator) + estimator.fit(X, y, **fit_params) + return estimator + + +def _partial_fit_binary(estimator, X, y, partial_fit_params): + """Partially fit a single binary estimator.""" + estimator.partial_fit(X, y, classes=np.array((0, 1)), **partial_fit_params) + return estimator + + +def _predict_binary(estimator, X): + """Make predictions using a single binary estimator.""" + if is_regressor(estimator): + return estimator.predict(X) + try: + score = np.ravel(estimator.decision_function(X)) + except (AttributeError, NotImplementedError): + # probabilities of the positive class + score = estimator.predict_proba(X)[:, 1] + return score + + +def _threshold_for_binary_predict(estimator): + """Threshold for predictions from binary estimator.""" + if hasattr(estimator, "decision_function") and is_classifier(estimator): + return 0.0 + else: + # predict_proba threshold + return 0.5 + + +class _ConstantPredictor(BaseEstimator): + """Helper predictor to be used when only one class is present.""" + + def fit(self, X, y): + check_params = dict( + ensure_all_finite=False, dtype=None, ensure_2d=False, accept_sparse=True + ) + validate_data( + self, X, y, reset=True, validate_separately=(check_params, check_params) + ) + self.y_ = y + return self + + def predict(self, X): + check_is_fitted(self) + validate_data( + self, + X, + ensure_all_finite=False, + dtype=None, + accept_sparse=True, + ensure_2d=False, + reset=False, + ) + + return np.repeat(self.y_, _num_samples(X)) + + def decision_function(self, X): + check_is_fitted(self) + validate_data( + self, + X, + ensure_all_finite=False, + dtype=None, + accept_sparse=True, + ensure_2d=False, + reset=False, + ) + + return np.repeat(self.y_, _num_samples(X)) + + def predict_proba(self, X): + check_is_fitted(self) + validate_data( + self, + X, + ensure_all_finite=False, + dtype=None, + accept_sparse=True, + ensure_2d=False, + reset=False, + ) + y_ = self.y_.astype(np.float64) + return np.repeat([np.hstack([1 - y_, y_])], _num_samples(X), axis=0) + + +def _estimators_has(attr): + """Check if self.estimator or self.estimators_[0] has attr. + + If `self.estimators_[0]` has the attr, then its safe to assume that other + estimators have it too. We raise the original `AttributeError` if `attr` + does not exist. This function is used together with `available_if`. + """ + + def check(self): + if hasattr(self, "estimators_"): + getattr(self.estimators_[0], attr) + else: + getattr(self.estimator, attr) + + return True + + return check + + +class OneVsRestClassifier( + MultiOutputMixin, + ClassifierMixin, + MetaEstimatorMixin, + BaseEstimator, +): + """One-vs-the-rest (OvR) multiclass strategy. + + Also known as one-vs-all, this strategy consists in fitting one classifier + per class. For each classifier, the class is fitted against all the other + classes. In addition to its computational efficiency (only `n_classes` + classifiers are needed), one advantage of this approach is its + interpretability. Since each class is represented by one and one classifier + only, it is possible to gain knowledge about the class by inspecting its + corresponding classifier. This is the most commonly used strategy for + multiclass classification and is a fair default choice. + + OneVsRestClassifier can also be used for multilabel classification. To use + this feature, provide an indicator matrix for the target `y` when calling + `.fit`. In other words, the target labels should be formatted as a 2D + binary (0/1) matrix, where [i, j] == 1 indicates the presence of label j + in sample i. This estimator uses the binary relevance method to perform + multilabel classification, which involves training one binary classifier + independently for each label. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + estimator : estimator object + A regressor or a classifier that implements :term:`fit`. + When a classifier is passed, :term:`decision_function` will be used + in priority and it will fallback to :term:`predict_proba` if it is not + available. + When a regressor is passed, :term:`predict` is used. + + n_jobs : int, default=None + The number of jobs to use for the computation: the `n_classes` + one-vs-rest problems are computed in parallel. + + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + .. versionchanged:: 0.20 + `n_jobs` default changed from 1 to None + + verbose : int, default=0 + The verbosity level, if non zero, progress messages are printed. + Below 50, the output is sent to stderr. Otherwise, the output is sent + to stdout. The frequency of the messages increases with the verbosity + level, reporting all iterations at 10. See :class:`joblib.Parallel` for + more details. + + .. versionadded:: 1.1 + + Attributes + ---------- + estimators_ : list of `n_classes` estimators + Estimators used for predictions. + + classes_ : array, shape = [`n_classes`] + Class labels. + + n_classes_ : int + Number of classes. + + label_binarizer_ : LabelBinarizer object + Object used to transform multiclass labels to binary labels and + vice-versa. + + multilabel_ : boolean + Whether a OneVsRestClassifier is a multilabel classifier. + + n_features_in_ : int + Number of features seen during :term:`fit`. Only defined if the + underlying estimator exposes such an attribute when fit. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Only defined if the + underlying estimator exposes such an attribute when fit. + + .. versionadded:: 1.0 + + See Also + -------- + OneVsOneClassifier : One-vs-one multiclass strategy. + OutputCodeClassifier : (Error-Correcting) Output-Code multiclass strategy. + sklearn.multioutput.MultiOutputClassifier : Alternate way of extending an + estimator for multilabel classification. + sklearn.preprocessing.MultiLabelBinarizer : Transform iterable of iterables + to binary indicator matrix. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.multiclass import OneVsRestClassifier + >>> from sklearn.svm import SVC + >>> X = np.array([ + ... [10, 10], + ... [8, 10], + ... [-5, 5.5], + ... [-5.4, 5.5], + ... [-20, -20], + ... [-15, -20] + ... ]) + >>> y = np.array([0, 0, 1, 1, 2, 2]) + >>> clf = OneVsRestClassifier(SVC()).fit(X, y) + >>> clf.predict([[-19, -20], [9, 9], [-5, 5]]) + array([2, 0, 1]) + """ + + _parameter_constraints = { + "estimator": [HasMethods(["fit"])], + "n_jobs": [Integral, None], + "verbose": ["verbose"], + } + + def __init__(self, estimator, *, n_jobs=None, verbose=0): + self.estimator = estimator + self.n_jobs = n_jobs + self.verbose = verbose + + @_fit_context( + # OneVsRestClassifier.estimator is not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, y, **fit_params): + """Fit underlying estimators. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Data. + + y : {array-like, sparse matrix} of shape (n_samples,) or (n_samples, n_classes) + Multi-class targets. An indicator matrix turns on multilabel + classification. + + **fit_params : dict + Parameters passed to the ``estimator.fit`` method of each + sub-estimator. + + .. versionadded:: 1.4 + Only available if `enable_metadata_routing=True`. See + :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + self : object + Instance of fitted estimator. + """ + _raise_for_params(fit_params, self, "fit") + + routed_params = process_routing( + self, + "fit", + **fit_params, + ) + # A sparse LabelBinarizer, with sparse_output=True, has been shown to + # outperform or match a dense label binarizer in all cases and has also + # resulted in less or equal memory consumption in the fit_ovr function + # overall. + self.label_binarizer_ = LabelBinarizer(sparse_output=True) + Y = self.label_binarizer_.fit_transform(y) + Y = Y.tocsc() + self.classes_ = self.label_binarizer_.classes_ + columns = (col.toarray().ravel() for col in Y.T) + # In cases where individual estimators are very fast to train setting + # n_jobs > 1 in can results in slower performance due to the overhead + # of spawning threads. See joblib issue #112. + self.estimators_ = Parallel(n_jobs=self.n_jobs, verbose=self.verbose)( + delayed(_fit_binary)( + self.estimator, + X, + column, + fit_params=routed_params.estimator.fit, + classes=[ + "not %s" % self.label_binarizer_.classes_[i], + self.label_binarizer_.classes_[i], + ], + ) + for i, column in enumerate(columns) + ) + + if hasattr(self.estimators_[0], "n_features_in_"): + self.n_features_in_ = self.estimators_[0].n_features_in_ + if hasattr(self.estimators_[0], "feature_names_in_"): + self.feature_names_in_ = self.estimators_[0].feature_names_in_ + + return self + + @available_if(_estimators_has("partial_fit")) + @_fit_context( + # OneVsRestClassifier.estimator is not validated yet + prefer_skip_nested_validation=False + ) + def partial_fit(self, X, y, classes=None, **partial_fit_params): + """Partially fit underlying estimators. + + Should be used when memory is inefficient to train all data. + Chunks of data can be passed in several iterations. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Data. + + y : {array-like, sparse matrix} of shape (n_samples,) or (n_samples, n_classes) + Multi-class targets. An indicator matrix turns on multilabel + classification. + + classes : array, shape (n_classes, ) + Classes across all calls to partial_fit. + Can be obtained via `np.unique(y_all)`, where y_all is the + target vector of the entire dataset. + This argument is only required in the first call of partial_fit + and can be omitted in the subsequent calls. + + **partial_fit_params : dict + Parameters passed to the ``estimator.partial_fit`` method of each + sub-estimator. + + .. versionadded:: 1.4 + Only available if `enable_metadata_routing=True`. See + :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + self : object + Instance of partially fitted estimator. + """ + _raise_for_params(partial_fit_params, self, "partial_fit") + + routed_params = process_routing( + self, + "partial_fit", + **partial_fit_params, + ) + + if _check_partial_fit_first_call(self, classes): + self.estimators_ = [clone(self.estimator) for _ in range(self.n_classes_)] + + # A sparse LabelBinarizer, with sparse_output=True, has been + # shown to outperform or match a dense label binarizer in all + # cases and has also resulted in less or equal memory consumption + # in the fit_ovr function overall. + self.label_binarizer_ = LabelBinarizer(sparse_output=True) + self.label_binarizer_.fit(self.classes_) + + if len(np.setdiff1d(y, self.classes_)): + raise ValueError( + ( + "Mini-batch contains {0} while classes " + "must be subset of {1}" + ).format(np.unique(y), self.classes_) + ) + + Y = self.label_binarizer_.transform(y) + Y = Y.tocsc() + columns = (col.toarray().ravel() for col in Y.T) + + self.estimators_ = Parallel(n_jobs=self.n_jobs)( + delayed(_partial_fit_binary)( + estimator, + X, + column, + partial_fit_params=routed_params.estimator.partial_fit, + ) + for estimator, column in zip(self.estimators_, columns) + ) + + if hasattr(self.estimators_[0], "n_features_in_"): + self.n_features_in_ = self.estimators_[0].n_features_in_ + + return self + + def predict(self, X): + """Predict multi-class targets using underlying estimators. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Data. + + Returns + ------- + y : {array-like, sparse matrix} of shape (n_samples,) or (n_samples, n_classes) + Predicted multi-class targets. + """ + check_is_fitted(self) + + n_samples = _num_samples(X) + if self.label_binarizer_.y_type_ == "multiclass": + maxima = np.empty(n_samples, dtype=float) + maxima.fill(-np.inf) + argmaxima = np.zeros(n_samples, dtype=int) + for i, e in enumerate(self.estimators_): + pred = _predict_binary(e, X) + np.maximum(maxima, pred, out=maxima) + argmaxima[maxima == pred] = i + return self.classes_[argmaxima] + else: + thresh = _threshold_for_binary_predict(self.estimators_[0]) + indices = array.array("i") + indptr = array.array("i", [0]) + for e in self.estimators_: + indices.extend(np.where(_predict_binary(e, X) > thresh)[0]) + indptr.append(len(indices)) + data = np.ones(len(indices), dtype=int) + indicator = sp.csc_matrix( + (data, indices, indptr), shape=(n_samples, len(self.estimators_)) + ) + return self.label_binarizer_.inverse_transform(indicator) + + @available_if(_estimators_has("predict_proba")) + def predict_proba(self, X): + """Probability estimates. + + The returned estimates for all classes are ordered by label of classes. + + Note that in the multilabel case, each sample can have any number of + labels. This returns the marginal probability that the given sample has + the label in question. For example, it is entirely consistent that two + labels both have a 90% probability of applying to a given sample. + + In the single label multiclass case, the rows of the returned matrix + sum to 1. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Input data. + + Returns + ------- + T : array-like of shape (n_samples, n_classes) + Returns the probability of the sample for each class in the model, + where classes are ordered as they are in `self.classes_`. + """ + check_is_fitted(self) + # Y[i, j] gives the probability that sample i has the label j. + # In the multi-label case, these are not disjoint. + Y = np.array([e.predict_proba(X)[:, 1] for e in self.estimators_]).T + + if len(self.estimators_) == 1: + # Only one estimator, but we still want to return probabilities + # for two classes. + Y = np.concatenate(((1 - Y), Y), axis=1) + + if not self.multilabel_: + # Then, (nonzero) sample probability distributions should be normalized. + row_sums = np.sum(Y, axis=1)[:, np.newaxis] + np.divide(Y, row_sums, out=Y, where=row_sums != 0) + + return Y + + @available_if(_estimators_has("decision_function")) + def decision_function(self, X): + """Decision function for the OneVsRestClassifier. + + Return the distance of each sample from the decision boundary for each + class. This can only be used with estimators which implement the + `decision_function` method. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Input data. + + Returns + ------- + T : array-like of shape (n_samples, n_classes) or (n_samples,) for \ + binary classification. + Result of calling `decision_function` on the final estimator. + + .. versionchanged:: 0.19 + output shape changed to ``(n_samples,)`` to conform to + scikit-learn conventions for binary classification. + """ + check_is_fitted(self) + if len(self.estimators_) == 1: + return self.estimators_[0].decision_function(X) + return np.array( + [est.decision_function(X).ravel() for est in self.estimators_] + ).T + + @property + def multilabel_(self): + """Whether this is a multilabel classifier.""" + return self.label_binarizer_.y_type_.startswith("multilabel") + + @property + def n_classes_(self): + """Number of classes.""" + return len(self.classes_) + + def __sklearn_tags__(self): + """Indicate if wrapped estimator is using a precomputed Gram matrix""" + tags = super().__sklearn_tags__() + tags.input_tags.pairwise = get_tags(self.estimator).input_tags.pairwise + tags.input_tags.sparse = get_tags(self.estimator).input_tags.sparse + return tags + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + .. versionadded:: 1.4 + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + + router = ( + MetadataRouter(owner=self.__class__.__name__) + .add_self_request(self) + .add( + estimator=self.estimator, + method_mapping=MethodMapping() + .add(caller="fit", callee="fit") + .add(caller="partial_fit", callee="partial_fit"), + ) + ) + return router + + +def _fit_ovo_binary(estimator, X, y, i, j, fit_params): + """Fit a single binary estimator (one-vs-one).""" + cond = np.logical_or(y == i, y == j) + y = y[cond] + y_binary = np.empty(y.shape, int) + y_binary[y == i] = 0 + y_binary[y == j] = 1 + indcond = np.arange(_num_samples(X))[cond] + + fit_params_subset = _check_method_params(X, params=fit_params, indices=indcond) + return ( + _fit_binary( + estimator, + _safe_split(estimator, X, None, indices=indcond)[0], + y_binary, + fit_params=fit_params_subset, + classes=[i, j], + ), + indcond, + ) + + +def _partial_fit_ovo_binary(estimator, X, y, i, j, partial_fit_params): + """Partially fit a single binary estimator(one-vs-one).""" + + cond = np.logical_or(y == i, y == j) + y = y[cond] + if len(y) != 0: + y_binary = np.zeros_like(y) + y_binary[y == j] = 1 + partial_fit_params_subset = _check_method_params( + X, params=partial_fit_params, indices=cond + ) + return _partial_fit_binary( + estimator, X[cond], y_binary, partial_fit_params=partial_fit_params_subset + ) + return estimator + + +class OneVsOneClassifier(MetaEstimatorMixin, ClassifierMixin, BaseEstimator): + """One-vs-one multiclass strategy. + + This strategy consists in fitting one classifier per class pair. + At prediction time, the class which received the most votes is selected. + Since it requires to fit `n_classes * (n_classes - 1) / 2` classifiers, + this method is usually slower than one-vs-the-rest, due to its + O(n_classes^2) complexity. However, this method may be advantageous for + algorithms such as kernel algorithms which don't scale well with + `n_samples`. This is because each individual learning problem only involves + a small subset of the data whereas, with one-vs-the-rest, the complete + dataset is used `n_classes` times. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + estimator : estimator object + A regressor or a classifier that implements :term:`fit`. + When a classifier is passed, :term:`decision_function` will be used + in priority and it will fallback to :term:`predict_proba` if it is not + available. + When a regressor is passed, :term:`predict` is used. + + n_jobs : int, default=None + The number of jobs to use for the computation: the `n_classes * ( + n_classes - 1) / 2` OVO problems are computed in parallel. + + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + Attributes + ---------- + estimators_ : list of ``n_classes * (n_classes - 1) / 2`` estimators + Estimators used for predictions. + + classes_ : numpy array of shape [n_classes] + Array containing labels. + + n_classes_ : int + Number of classes. + + pairwise_indices_ : list, length = ``len(estimators_)``, or ``None`` + Indices of samples used when training the estimators. + ``None`` when ``estimator``'s `pairwise` tag is False. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + OneVsRestClassifier : One-vs-all multiclass strategy. + OutputCodeClassifier : (Error-Correcting) Output-Code multiclass strategy. + + Examples + -------- + >>> from sklearn.datasets import load_iris + >>> from sklearn.model_selection import train_test_split + >>> from sklearn.multiclass import OneVsOneClassifier + >>> from sklearn.svm import LinearSVC + >>> X, y = load_iris(return_X_y=True) + >>> X_train, X_test, y_train, y_test = train_test_split( + ... X, y, test_size=0.33, shuffle=True, random_state=0) + >>> clf = OneVsOneClassifier( + ... LinearSVC(random_state=0)).fit(X_train, y_train) + >>> clf.predict(X_test[:10]) + array([2, 1, 0, 2, 0, 2, 0, 1, 1, 1]) + """ + + _parameter_constraints: dict = { + "estimator": [HasMethods(["fit"])], + "n_jobs": [Integral, None], + } + + def __init__(self, estimator, *, n_jobs=None): + self.estimator = estimator + self.n_jobs = n_jobs + + @_fit_context( + # OneVsOneClassifier.estimator is not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, y, **fit_params): + """Fit underlying estimators. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Data. + + y : array-like of shape (n_samples,) + Multi-class targets. + + **fit_params : dict + Parameters passed to the ``estimator.fit`` method of each + sub-estimator. + + .. versionadded:: 1.4 + Only available if `enable_metadata_routing=True`. See + :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + self : object + The fitted underlying estimator. + """ + _raise_for_params(fit_params, self, "fit") + + routed_params = process_routing( + self, + "fit", + **fit_params, + ) + + # We need to validate the data because we do a safe_indexing later. + X, y = validate_data( + self, X, y, accept_sparse=["csr", "csc"], ensure_all_finite=False + ) + check_classification_targets(y) + + self.classes_ = np.unique(y) + if len(self.classes_) == 1: + raise ValueError( + "OneVsOneClassifier can not be fit when only one class is present." + ) + n_classes = self.classes_.shape[0] + estimators_indices = list( + zip( + *( + Parallel(n_jobs=self.n_jobs)( + delayed(_fit_ovo_binary)( + self.estimator, + X, + y, + self.classes_[i], + self.classes_[j], + fit_params=routed_params.estimator.fit, + ) + for i in range(n_classes) + for j in range(i + 1, n_classes) + ) + ) + ) + ) + + self.estimators_ = estimators_indices[0] + + pairwise = self.__sklearn_tags__().input_tags.pairwise + self.pairwise_indices_ = estimators_indices[1] if pairwise else None + + return self + + @available_if(_estimators_has("partial_fit")) + @_fit_context( + # OneVsOneClassifier.estimator is not validated yet + prefer_skip_nested_validation=False + ) + def partial_fit(self, X, y, classes=None, **partial_fit_params): + """Partially fit underlying estimators. + + Should be used when memory is inefficient to train all data. Chunks + of data can be passed in several iteration, where the first call + should have an array of all target variables. + + Parameters + ---------- + X : {array-like, sparse matrix) of shape (n_samples, n_features) + Data. + + y : array-like of shape (n_samples,) + Multi-class targets. + + classes : array, shape (n_classes, ) + Classes across all calls to partial_fit. + Can be obtained via `np.unique(y_all)`, where y_all is the + target vector of the entire dataset. + This argument is only required in the first call of partial_fit + and can be omitted in the subsequent calls. + + **partial_fit_params : dict + Parameters passed to the ``estimator.partial_fit`` method of each + sub-estimator. + + .. versionadded:: 1.4 + Only available if `enable_metadata_routing=True`. See + :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + self : object + The partially fitted underlying estimator. + """ + _raise_for_params(partial_fit_params, self, "partial_fit") + + routed_params = process_routing( + self, + "partial_fit", + **partial_fit_params, + ) + + first_call = _check_partial_fit_first_call(self, classes) + if first_call: + self.estimators_ = [ + clone(self.estimator) + for _ in range(self.n_classes_ * (self.n_classes_ - 1) // 2) + ] + + if len(np.setdiff1d(y, self.classes_)): + raise ValueError( + "Mini-batch contains {0} while it must be subset of {1}".format( + np.unique(y), self.classes_ + ) + ) + + X, y = validate_data( + self, + X, + y, + accept_sparse=["csr", "csc"], + ensure_all_finite=False, + reset=first_call, + ) + check_classification_targets(y) + combinations = itertools.combinations(range(self.n_classes_), 2) + self.estimators_ = Parallel(n_jobs=self.n_jobs)( + delayed(_partial_fit_ovo_binary)( + estimator, + X, + y, + self.classes_[i], + self.classes_[j], + partial_fit_params=routed_params.estimator.partial_fit, + ) + for estimator, (i, j) in zip(self.estimators_, (combinations)) + ) + + self.pairwise_indices_ = None + + if hasattr(self.estimators_[0], "n_features_in_"): + self.n_features_in_ = self.estimators_[0].n_features_in_ + + return self + + def predict(self, X): + """Estimate the best class label for each sample in X. + + This is implemented as ``argmax(decision_function(X), axis=1)`` which + will return the label of the class with most votes by estimators + predicting the outcome of a decision for each possible class pair. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Data. + + Returns + ------- + y : numpy array of shape [n_samples] + Predicted multi-class targets. + """ + Y = self.decision_function(X) + if self.n_classes_ == 2: + thresh = _threshold_for_binary_predict(self.estimators_[0]) + return self.classes_[(Y > thresh).astype(int)] + return self.classes_[Y.argmax(axis=1)] + + def decision_function(self, X): + """Decision function for the OneVsOneClassifier. + + The decision values for the samples are computed by adding the + normalized sum of pair-wise classification confidence levels to the + votes in order to disambiguate between the decision values when the + votes for all the classes are equal leading to a tie. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Input data. + + Returns + ------- + Y : array-like of shape (n_samples, n_classes) or (n_samples,) + Result of calling `decision_function` on the final estimator. + + .. versionchanged:: 0.19 + output shape changed to ``(n_samples,)`` to conform to + scikit-learn conventions for binary classification. + """ + check_is_fitted(self) + X = validate_data( + self, + X, + accept_sparse=True, + ensure_all_finite=False, + reset=False, + ) + + indices = self.pairwise_indices_ + if indices is None: + Xs = [X] * len(self.estimators_) + else: + Xs = [X[:, idx] for idx in indices] + + predictions = np.vstack( + [est.predict(Xi) for est, Xi in zip(self.estimators_, Xs)] + ).T + confidences = np.vstack( + [_predict_binary(est, Xi) for est, Xi in zip(self.estimators_, Xs)] + ).T + Y = _ovr_decision_function(predictions, confidences, len(self.classes_)) + if self.n_classes_ == 2: + return Y[:, 1] + return Y + + @property + def n_classes_(self): + """Number of classes.""" + return len(self.classes_) + + def __sklearn_tags__(self): + """Indicate if wrapped estimator is using a precomputed Gram matrix""" + tags = super().__sklearn_tags__() + tags.input_tags.pairwise = get_tags(self.estimator).input_tags.pairwise + tags.input_tags.sparse = get_tags(self.estimator).input_tags.sparse + return tags + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + .. versionadded:: 1.4 + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + + router = ( + MetadataRouter(owner=self.__class__.__name__) + .add_self_request(self) + .add( + estimator=self.estimator, + method_mapping=MethodMapping() + .add(caller="fit", callee="fit") + .add(caller="partial_fit", callee="partial_fit"), + ) + ) + return router + + +class OutputCodeClassifier(MetaEstimatorMixin, ClassifierMixin, BaseEstimator): + """(Error-Correcting) Output-Code multiclass strategy. + + Output-code based strategies consist in representing each class with a + binary code (an array of 0s and 1s). At fitting time, one binary + classifier per bit in the code book is fitted. At prediction time, the + classifiers are used to project new points in the class space and the class + closest to the points is chosen. The main advantage of these strategies is + that the number of classifiers used can be controlled by the user, either + for compressing the model (0 < `code_size` < 1) or for making the model more + robust to errors (`code_size` > 1). See the documentation for more details. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + estimator : estimator object + An estimator object implementing :term:`fit` and one of + :term:`decision_function` or :term:`predict_proba`. + + code_size : float, default=1.5 + Percentage of the number of classes to be used to create the code book. + A number between 0 and 1 will require fewer classifiers than + one-vs-the-rest. A number greater than 1 will require more classifiers + than one-vs-the-rest. + + random_state : int, RandomState instance, default=None + The generator used to initialize the codebook. + Pass an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + n_jobs : int, default=None + The number of jobs to use for the computation: the multiclass problems + are computed in parallel. + + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + Attributes + ---------- + estimators_ : list of `int(n_classes * code_size)` estimators + Estimators used for predictions. + + classes_ : ndarray of shape (n_classes,) + Array containing labels. + + code_book_ : ndarray of shape (n_classes, `len(estimators_)`) + Binary array containing the code of each class. + + n_features_in_ : int + Number of features seen during :term:`fit`. Only defined if the + underlying estimator exposes such an attribute when fit. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Only defined if the + underlying estimator exposes such an attribute when fit. + + .. versionadded:: 1.0 + + See Also + -------- + OneVsRestClassifier : One-vs-all multiclass strategy. + OneVsOneClassifier : One-vs-one multiclass strategy. + + References + ---------- + + .. [1] "Solving multiclass learning problems via error-correcting output + codes", + Dietterich T., Bakiri G., + Journal of Artificial Intelligence Research 2, + 1995. + + .. [2] "The error coding method and PICTs", + James G., Hastie T., + Journal of Computational and Graphical statistics 7, + 1998. + + .. [3] "The Elements of Statistical Learning", + Hastie T., Tibshirani R., Friedman J., page 606 (second-edition) + 2008. + + Examples + -------- + >>> from sklearn.multiclass import OutputCodeClassifier + >>> from sklearn.ensemble import RandomForestClassifier + >>> from sklearn.datasets import make_classification + >>> X, y = make_classification(n_samples=100, n_features=4, + ... n_informative=2, n_redundant=0, + ... random_state=0, shuffle=False) + >>> clf = OutputCodeClassifier( + ... estimator=RandomForestClassifier(random_state=0), + ... random_state=0).fit(X, y) + >>> clf.predict([[0, 0, 0, 0]]) + array([1]) + """ + + _parameter_constraints: dict = { + "estimator": [ + HasMethods(["fit", "decision_function"]), + HasMethods(["fit", "predict_proba"]), + ], + "code_size": [Interval(Real, 0.0, None, closed="neither")], + "random_state": ["random_state"], + "n_jobs": [Integral, None], + } + + def __init__(self, estimator, *, code_size=1.5, random_state=None, n_jobs=None): + self.estimator = estimator + self.code_size = code_size + self.random_state = random_state + self.n_jobs = n_jobs + + @_fit_context( + # OutputCodeClassifier.estimator is not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, y, **fit_params): + """Fit underlying estimators. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Data. + + y : array-like of shape (n_samples,) + Multi-class targets. + + **fit_params : dict + Parameters passed to the ``estimator.fit`` method of each + sub-estimator. + + .. versionadded:: 1.4 + Only available if `enable_metadata_routing=True`. See + :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + self : object + Returns a fitted instance of self. + """ + _raise_for_params(fit_params, self, "fit") + + routed_params = process_routing( + self, + "fit", + **fit_params, + ) + + y = validate_data(self, X="no_validation", y=y) + + random_state = check_random_state(self.random_state) + check_classification_targets(y) + + self.classes_ = np.unique(y) + n_classes = self.classes_.shape[0] + if n_classes == 0: + raise ValueError( + "OutputCodeClassifier can not be fit when no class is present." + ) + n_estimators = int(n_classes * self.code_size) + + # FIXME: there are more elaborate methods than generating the codebook + # randomly. + self.code_book_ = random_state.uniform(size=(n_classes, n_estimators)) + self.code_book_[self.code_book_ > 0.5] = 1.0 + + if hasattr(self.estimator, "decision_function"): + self.code_book_[self.code_book_ != 1] = -1.0 + else: + self.code_book_[self.code_book_ != 1] = 0.0 + + classes_index = {c: i for i, c in enumerate(self.classes_)} + + Y = np.array( + [self.code_book_[classes_index[y[i]]] for i in range(_num_samples(y))], + dtype=int, + ) + + self.estimators_ = Parallel(n_jobs=self.n_jobs)( + delayed(_fit_binary)( + self.estimator, X, Y[:, i], fit_params=routed_params.estimator.fit + ) + for i in range(Y.shape[1]) + ) + + if hasattr(self.estimators_[0], "n_features_in_"): + self.n_features_in_ = self.estimators_[0].n_features_in_ + if hasattr(self.estimators_[0], "feature_names_in_"): + self.feature_names_in_ = self.estimators_[0].feature_names_in_ + + return self + + def predict(self, X): + """Predict multi-class targets using underlying estimators. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Data. + + Returns + ------- + y : ndarray of shape (n_samples,) + Predicted multi-class targets. + """ + check_is_fitted(self) + # ArgKmin only accepts C-contiguous array. The aggregated predictions need to be + # transposed. We therefore create a F-contiguous array to avoid a copy and have + # a C-contiguous array after the transpose operation. + Y = np.array( + [_predict_binary(e, X) for e in self.estimators_], + order="F", + dtype=np.float64, + ).T + pred = pairwise_distances_argmin(Y, self.code_book_, metric="euclidean") + return self.classes_[pred] + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + .. versionadded:: 1.4 + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + + router = MetadataRouter(owner=self.__class__.__name__).add( + estimator=self.estimator, + method_mapping=MethodMapping().add(caller="fit", callee="fit"), + ) + return router + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = get_tags(self.estimator).input_tags.sparse + return tags diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/multioutput.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/multioutput.py new file mode 100644 index 0000000000000000000000000000000000000000..08b0c95c945586490ffa39e6b01c94515248cfb8 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/multioutput.py @@ -0,0 +1,1328 @@ +"""Multioutput regression and classification. + +The estimators provided in this module are meta-estimators: they require +a base estimator to be provided in their constructor. The meta-estimator +extends single output estimators to multioutput estimators. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from abc import ABCMeta, abstractmethod +from numbers import Integral + +import numpy as np +import scipy.sparse as sp + +from .base import ( + BaseEstimator, + ClassifierMixin, + MetaEstimatorMixin, + RegressorMixin, + _fit_context, + clone, + is_classifier, +) +from .model_selection import cross_val_predict +from .utils import Bunch, check_random_state, get_tags +from .utils._param_validation import ( + HasMethods, + Hidden, + StrOptions, +) +from .utils._response import _get_response_values +from .utils._user_interface import _print_elapsed_time +from .utils.metadata_routing import ( + MetadataRouter, + MethodMapping, + _raise_for_params, + _routing_enabled, + process_routing, +) +from .utils.metaestimators import available_if +from .utils.multiclass import check_classification_targets +from .utils.parallel import Parallel, delayed +from .utils.validation import ( + _check_method_params, + _check_response_method, + check_is_fitted, + has_fit_parameter, + validate_data, +) + +__all__ = [ + "ClassifierChain", + "MultiOutputClassifier", + "MultiOutputRegressor", + "RegressorChain", +] + + +def _fit_estimator(estimator, X, y, sample_weight=None, **fit_params): + estimator = clone(estimator) + if sample_weight is not None: + estimator.fit(X, y, sample_weight=sample_weight, **fit_params) + else: + estimator.fit(X, y, **fit_params) + return estimator + + +def _partial_fit_estimator( + estimator, X, y, classes=None, partial_fit_params=None, first_time=True +): + partial_fit_params = {} if partial_fit_params is None else partial_fit_params + if first_time: + estimator = clone(estimator) + + if classes is not None: + estimator.partial_fit(X, y, classes=classes, **partial_fit_params) + else: + estimator.partial_fit(X, y, **partial_fit_params) + return estimator + + +def _available_if_estimator_has(attr): + """Return a function to check if the sub-estimator(s) has(have) `attr`. + + Helper for Chain implementations. + """ + + def _check(self): + if hasattr(self, "estimators_"): + return all(hasattr(est, attr) for est in self.estimators_) + + if hasattr(self.estimator, attr): + return True + + return False + + return available_if(_check) + + +class _MultiOutputEstimator(MetaEstimatorMixin, BaseEstimator, metaclass=ABCMeta): + _parameter_constraints: dict = { + "estimator": [HasMethods(["fit", "predict"])], + "n_jobs": [Integral, None], + } + + @abstractmethod + def __init__(self, estimator, *, n_jobs=None): + self.estimator = estimator + self.n_jobs = n_jobs + + @_available_if_estimator_has("partial_fit") + @_fit_context( + # MultiOutput*.estimator is not validated yet + prefer_skip_nested_validation=False + ) + def partial_fit(self, X, y, classes=None, sample_weight=None, **partial_fit_params): + """Incrementally fit a separate model for each class output. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input data. + + y : {array-like, sparse matrix} of shape (n_samples, n_outputs) + Multi-output targets. + + classes : list of ndarray of shape (n_outputs,), default=None + Each array is unique classes for one output in str/int. + Can be obtained via + ``[np.unique(y[:, i]) for i in range(y.shape[1])]``, where `y` + is the target matrix of the entire dataset. + This argument is required for the first call to partial_fit + and can be omitted in the subsequent calls. + Note that `y` doesn't need to contain all labels in `classes`. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. If `None`, then samples are equally weighted. + Only supported if the underlying regressor supports sample + weights. + + **partial_fit_params : dict of str -> object + Parameters passed to the ``estimator.partial_fit`` method of each + sub-estimator. + + Only available if `enable_metadata_routing=True`. See the + :ref:`User Guide `. + + .. versionadded:: 1.3 + + Returns + ------- + self : object + Returns a fitted instance. + """ + _raise_for_params(partial_fit_params, self, "partial_fit") + + first_time = not hasattr(self, "estimators_") + + y = validate_data(self, X="no_validation", y=y, multi_output=True) + + if y.ndim == 1: + raise ValueError( + "y must have at least two dimensions for " + "multi-output regression but has only one." + ) + + if _routing_enabled(): + if sample_weight is not None: + partial_fit_params["sample_weight"] = sample_weight + routed_params = process_routing( + self, + "partial_fit", + **partial_fit_params, + ) + else: + if sample_weight is not None and not has_fit_parameter( + self.estimator, "sample_weight" + ): + raise ValueError( + "Underlying estimator does not support sample weights." + ) + + if sample_weight is not None: + routed_params = Bunch( + estimator=Bunch(partial_fit=Bunch(sample_weight=sample_weight)) + ) + else: + routed_params = Bunch(estimator=Bunch(partial_fit=Bunch())) + + self.estimators_ = Parallel(n_jobs=self.n_jobs)( + delayed(_partial_fit_estimator)( + self.estimators_[i] if not first_time else self.estimator, + X, + y[:, i], + classes[i] if classes is not None else None, + partial_fit_params=routed_params.estimator.partial_fit, + first_time=first_time, + ) + for i in range(y.shape[1]) + ) + + if first_time and hasattr(self.estimators_[0], "n_features_in_"): + self.n_features_in_ = self.estimators_[0].n_features_in_ + if first_time and hasattr(self.estimators_[0], "feature_names_in_"): + self.feature_names_in_ = self.estimators_[0].feature_names_in_ + + return self + + @_fit_context( + # MultiOutput*.estimator is not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, y, sample_weight=None, **fit_params): + """Fit the model to data, separately for each output variable. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input data. + + y : {array-like, sparse matrix} of shape (n_samples, n_outputs) + Multi-output targets. An indicator matrix turns on multilabel + estimation. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. If `None`, then samples are equally weighted. + Only supported if the underlying regressor supports sample + weights. + + **fit_params : dict of string -> object + Parameters passed to the ``estimator.fit`` method of each step. + + .. versionadded:: 0.23 + + Returns + ------- + self : object + Returns a fitted instance. + """ + if not hasattr(self.estimator, "fit"): + raise ValueError("The base estimator should implement a fit method") + + y = validate_data(self, X="no_validation", y=y, multi_output=True) + + if is_classifier(self): + check_classification_targets(y) + + if y.ndim == 1: + raise ValueError( + "y must have at least two dimensions for " + "multi-output regression but has only one." + ) + + if _routing_enabled(): + if sample_weight is not None: + fit_params["sample_weight"] = sample_weight + routed_params = process_routing( + self, + "fit", + **fit_params, + ) + else: + if sample_weight is not None and not has_fit_parameter( + self.estimator, "sample_weight" + ): + raise ValueError( + "Underlying estimator does not support sample weights." + ) + + fit_params_validated = _check_method_params(X, params=fit_params) + routed_params = Bunch(estimator=Bunch(fit=fit_params_validated)) + if sample_weight is not None: + routed_params.estimator.fit["sample_weight"] = sample_weight + + self.estimators_ = Parallel(n_jobs=self.n_jobs)( + delayed(_fit_estimator)( + self.estimator, X, y[:, i], **routed_params.estimator.fit + ) + for i in range(y.shape[1]) + ) + + if hasattr(self.estimators_[0], "n_features_in_"): + self.n_features_in_ = self.estimators_[0].n_features_in_ + if hasattr(self.estimators_[0], "feature_names_in_"): + self.feature_names_in_ = self.estimators_[0].feature_names_in_ + + return self + + def predict(self, X): + """Predict multi-output variable using model for each target variable. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input data. + + Returns + ------- + y : {array-like, sparse matrix} of shape (n_samples, n_outputs) + Multi-output targets predicted across multiple predictors. + Note: Separate models are generated for each predictor. + """ + check_is_fitted(self) + if not hasattr(self.estimators_[0], "predict"): + raise ValueError("The base estimator should implement a predict method") + + y = Parallel(n_jobs=self.n_jobs)( + delayed(e.predict)(X) for e in self.estimators_ + ) + + return np.asarray(y).T + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = get_tags(self.estimator).input_tags.sparse + tags.target_tags.single_output = False + tags.target_tags.multi_output = True + return tags + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + .. versionadded:: 1.3 + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + router = MetadataRouter(owner=self.__class__.__name__).add( + estimator=self.estimator, + method_mapping=MethodMapping() + .add(caller="partial_fit", callee="partial_fit") + .add(caller="fit", callee="fit"), + ) + return router + + +class MultiOutputRegressor(RegressorMixin, _MultiOutputEstimator): + """Multi target regression. + + This strategy consists of fitting one regressor per target. This is a + simple strategy for extending regressors that do not natively support + multi-target regression. + + .. versionadded:: 0.18 + + Parameters + ---------- + estimator : estimator object + An estimator object implementing :term:`fit` and :term:`predict`. + + n_jobs : int or None, optional (default=None) + The number of jobs to run in parallel. + :meth:`fit`, :meth:`predict` and :meth:`partial_fit` (if supported + by the passed estimator) will be parallelized for each target. + + When individual estimators are fast to train or predict, + using ``n_jobs > 1`` can result in slower performance due + to the parallelism overhead. + + ``None`` means `1` unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all available processes / threads. + See :term:`Glossary ` for more details. + + .. versionchanged:: 0.20 + `n_jobs` default changed from `1` to `None`. + + Attributes + ---------- + estimators_ : list of ``n_output`` estimators + Estimators used for predictions. + + n_features_in_ : int + Number of features seen during :term:`fit`. Only defined if the + underlying `estimator` exposes such an attribute when fit. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Only defined if the + underlying estimators expose such an attribute when fit. + + .. versionadded:: 1.0 + + See Also + -------- + RegressorChain : A multi-label model that arranges regressions into a + chain. + MultiOutputClassifier : Classifies each output independently rather than + chaining. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.datasets import load_linnerud + >>> from sklearn.multioutput import MultiOutputRegressor + >>> from sklearn.linear_model import Ridge + >>> X, y = load_linnerud(return_X_y=True) + >>> regr = MultiOutputRegressor(Ridge(random_state=123)).fit(X, y) + >>> regr.predict(X[[0]]) + array([[176, 35.1, 57.1]]) + """ + + def __init__(self, estimator, *, n_jobs=None): + super().__init__(estimator, n_jobs=n_jobs) + + @_available_if_estimator_has("partial_fit") + def partial_fit(self, X, y, sample_weight=None, **partial_fit_params): + """Incrementally fit the model to data, for each output variable. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input data. + + y : {array-like, sparse matrix} of shape (n_samples, n_outputs) + Multi-output targets. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. If `None`, then samples are equally weighted. + Only supported if the underlying regressor supports sample + weights. + + **partial_fit_params : dict of str -> object + Parameters passed to the ``estimator.partial_fit`` method of each + sub-estimator. + + Only available if `enable_metadata_routing=True`. See the + :ref:`User Guide `. + + .. versionadded:: 1.3 + + Returns + ------- + self : object + Returns a fitted instance. + """ + super().partial_fit(X, y, sample_weight=sample_weight, **partial_fit_params) + + +class MultiOutputClassifier(ClassifierMixin, _MultiOutputEstimator): + """Multi target classification. + + This strategy consists of fitting one classifier per target. This is a + simple strategy for extending classifiers that do not natively support + multi-target classification. + + Parameters + ---------- + estimator : estimator object + An estimator object implementing :term:`fit` and :term:`predict`. + A :term:`predict_proba` method will be exposed only if `estimator` implements + it. + + n_jobs : int or None, optional (default=None) + The number of jobs to run in parallel. + :meth:`fit`, :meth:`predict` and :meth:`partial_fit` (if supported + by the passed estimator) will be parallelized for each target. + + When individual estimators are fast to train or predict, + using ``n_jobs > 1`` can result in slower performance due + to the parallelism overhead. + + ``None`` means `1` unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all available processes / threads. + See :term:`Glossary ` for more details. + + .. versionchanged:: 0.20 + `n_jobs` default changed from `1` to `None`. + + Attributes + ---------- + classes_ : ndarray of shape (n_classes,) + Class labels. + + estimators_ : list of ``n_output`` estimators + Estimators used for predictions. + + n_features_in_ : int + Number of features seen during :term:`fit`. Only defined if the + underlying `estimator` exposes such an attribute when fit. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Only defined if the + underlying estimators expose such an attribute when fit. + + .. versionadded:: 1.0 + + See Also + -------- + ClassifierChain : A multi-label model that arranges binary classifiers + into a chain. + MultiOutputRegressor : Fits one regressor per target variable. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.datasets import make_multilabel_classification + >>> from sklearn.multioutput import MultiOutputClassifier + >>> from sklearn.linear_model import LogisticRegression + >>> X, y = make_multilabel_classification(n_classes=3, random_state=0) + >>> clf = MultiOutputClassifier(LogisticRegression()).fit(X, y) + >>> clf.predict(X[-2:]) + array([[1, 1, 1], + [1, 0, 1]]) + """ + + def __init__(self, estimator, *, n_jobs=None): + super().__init__(estimator, n_jobs=n_jobs) + + def fit(self, X, Y, sample_weight=None, **fit_params): + """Fit the model to data matrix X and targets Y. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input data. + + Y : array-like of shape (n_samples, n_classes) + The target values. + + sample_weight : array-like of shape (n_samples,), default=None + Sample weights. If `None`, then samples are equally weighted. + Only supported if the underlying classifier supports sample + weights. + + **fit_params : dict of string -> object + Parameters passed to the ``estimator.fit`` method of each step. + + .. versionadded:: 0.23 + + Returns + ------- + self : object + Returns a fitted instance. + """ + super().fit(X, Y, sample_weight=sample_weight, **fit_params) + self.classes_ = [estimator.classes_ for estimator in self.estimators_] + return self + + def _check_predict_proba(self): + if hasattr(self, "estimators_"): + # raise an AttributeError if `predict_proba` does not exist for + # each estimator + [getattr(est, "predict_proba") for est in self.estimators_] + return True + # raise an AttributeError if `predict_proba` does not exist for the + # unfitted estimator + getattr(self.estimator, "predict_proba") + return True + + @available_if(_check_predict_proba) + def predict_proba(self, X): + """Return prediction probabilities for each class of each output. + + This method will raise a ``ValueError`` if any of the + estimators do not have ``predict_proba``. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The input data. + + Returns + ------- + p : array of shape (n_samples, n_classes), or a list of n_outputs \ + such arrays if n_outputs > 1. + The class probabilities of the input samples. The order of the + classes corresponds to that in the attribute :term:`classes_`. + + .. versionchanged:: 0.19 + This function now returns a list of arrays where the length of + the list is ``n_outputs``, and each array is (``n_samples``, + ``n_classes``) for that particular output. + """ + check_is_fitted(self) + results = [estimator.predict_proba(X) for estimator in self.estimators_] + return results + + def score(self, X, y): + """Return the mean accuracy on the given test data and labels. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Test samples. + + y : array-like of shape (n_samples, n_outputs) + True values for X. + + Returns + ------- + scores : float + Mean accuracy of predicted target versus true target. + """ + check_is_fitted(self) + n_outputs_ = len(self.estimators_) + if y.ndim == 1: + raise ValueError( + "y must have at least two dimensions for " + "multi target classification but has only one" + ) + if y.shape[1] != n_outputs_: + raise ValueError( + "The number of outputs of Y for fit {0} and" + " score {1} should be same".format(n_outputs_, y.shape[1]) + ) + y_pred = self.predict(X) + return np.mean(np.all(y == y_pred, axis=1)) + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + # FIXME + tags._skip_test = True + return tags + + +def _available_if_base_estimator_has(attr): + """Return a function to check if `base_estimator` or `estimators_` has `attr`. + + Helper for Chain implementations. + """ + + def _check(self): + return hasattr(self._get_estimator(), attr) or all( + hasattr(est, attr) for est in self.estimators_ + ) + + return available_if(_check) + + +class _BaseChain(BaseEstimator, metaclass=ABCMeta): + _parameter_constraints: dict = { + "base_estimator": [ + HasMethods(["fit", "predict"]), + StrOptions({"deprecated"}), + ], + "estimator": [ + HasMethods(["fit", "predict"]), + Hidden(None), + ], + "order": ["array-like", StrOptions({"random"}), None], + "cv": ["cv_object", StrOptions({"prefit"})], + "random_state": ["random_state"], + "verbose": ["boolean"], + } + + # TODO(1.9): Remove base_estimator + def __init__( + self, + estimator=None, + *, + order=None, + cv=None, + random_state=None, + verbose=False, + base_estimator="deprecated", + ): + self.estimator = estimator + self.base_estimator = base_estimator + self.order = order + self.cv = cv + self.random_state = random_state + self.verbose = verbose + + # TODO(1.8): This is a temporary getter method to validate input wrt deprecation. + # It was only included to avoid relying on the presence of self.estimator_ + def _get_estimator(self): + """Get and validate estimator.""" + + if self.estimator is not None and (self.base_estimator != "deprecated"): + raise ValueError( + "Both `estimator` and `base_estimator` are provided. You should only" + " pass `estimator`. `base_estimator` as a parameter is deprecated in" + " version 1.7, and will be removed in version 1.9." + ) + + if self.base_estimator != "deprecated": + warning_msg = ( + "`base_estimator` as an argument was deprecated in 1.7 and will be" + " removed in 1.9. Use `estimator` instead." + ) + warnings.warn(warning_msg, FutureWarning) + return self.base_estimator + else: + return self.estimator + + def _log_message(self, *, estimator_idx, n_estimators, processing_msg): + if not self.verbose: + return None + return f"({estimator_idx} of {n_estimators}) {processing_msg}" + + def _get_predictions(self, X, *, output_method): + """Get predictions for each model in the chain.""" + check_is_fitted(self) + X = validate_data(self, X, accept_sparse=True, reset=False) + Y_output_chain = np.zeros((X.shape[0], len(self.estimators_))) + Y_feature_chain = np.zeros((X.shape[0], len(self.estimators_))) + + # `RegressorChain` does not have a `chain_method_` parameter so we + # default to "predict" + chain_method = getattr(self, "chain_method_", "predict") + hstack = sp.hstack if sp.issparse(X) else np.hstack + for chain_idx, estimator in enumerate(self.estimators_): + previous_predictions = Y_feature_chain[:, :chain_idx] + # if `X` is a scipy sparse dok_array, we convert it to a sparse + # coo_array format before hstacking, it's faster; see + # https://github.com/scipy/scipy/issues/20060#issuecomment-1937007039: + if sp.issparse(X) and not sp.isspmatrix(X) and X.format == "dok": + X = sp.coo_array(X) + X_aug = hstack((X, previous_predictions)) + + feature_predictions, _ = _get_response_values( + estimator, + X_aug, + response_method=chain_method, + ) + Y_feature_chain[:, chain_idx] = feature_predictions + + output_predictions, _ = _get_response_values( + estimator, + X_aug, + response_method=output_method, + ) + Y_output_chain[:, chain_idx] = output_predictions + + inv_order = np.empty_like(self.order_) + inv_order[self.order_] = np.arange(len(self.order_)) + Y_output = Y_output_chain[:, inv_order] + + return Y_output + + @abstractmethod + def fit(self, X, Y, **fit_params): + """Fit the model to data matrix X and targets Y. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input data. + + Y : array-like of shape (n_samples, n_classes) + The target values. + + **fit_params : dict of string -> object + Parameters passed to the `fit` method of each step. + + .. versionadded:: 0.23 + + Returns + ------- + self : object + Returns a fitted instance. + """ + X, Y = validate_data(self, X, Y, multi_output=True, accept_sparse=True) + + random_state = check_random_state(self.random_state) + self.order_ = self.order + if isinstance(self.order_, tuple): + self.order_ = np.array(self.order_) + + if self.order_ is None: + self.order_ = np.array(range(Y.shape[1])) + elif isinstance(self.order_, str): + if self.order_ == "random": + self.order_ = random_state.permutation(Y.shape[1]) + elif sorted(self.order_) != list(range(Y.shape[1])): + raise ValueError("invalid order") + + self.estimators_ = [clone(self._get_estimator()) for _ in range(Y.shape[1])] + + if self.cv is None: + Y_pred_chain = Y[:, self.order_] + if sp.issparse(X): + X_aug = sp.hstack((X, Y_pred_chain), format="lil") + X_aug = X_aug.tocsr() + else: + X_aug = np.hstack((X, Y_pred_chain)) + + elif sp.issparse(X): + # TODO: remove this condition check when the minimum supported scipy version + # doesn't support sparse matrices anymore + if not sp.isspmatrix(X): + # if `X` is a scipy sparse dok_array, we convert it to a sparse + # coo_array format before hstacking, it's faster; see + # https://github.com/scipy/scipy/issues/20060#issuecomment-1937007039: + if X.format == "dok": + X = sp.coo_array(X) + # in case that `X` is a sparse array we create `Y_pred_chain` as a + # sparse array format: + Y_pred_chain = sp.coo_array((X.shape[0], Y.shape[1])) + else: + Y_pred_chain = sp.coo_matrix((X.shape[0], Y.shape[1])) + X_aug = sp.hstack((X, Y_pred_chain), format="lil") + + else: + Y_pred_chain = np.zeros((X.shape[0], Y.shape[1])) + X_aug = np.hstack((X, Y_pred_chain)) + + del Y_pred_chain + + if _routing_enabled(): + routed_params = process_routing(self, "fit", **fit_params) + else: + routed_params = Bunch(estimator=Bunch(fit=fit_params)) + + if hasattr(self, "chain_method"): + chain_method = _check_response_method( + self._get_estimator(), + self.chain_method, + ).__name__ + self.chain_method_ = chain_method + else: + # `RegressorChain` does not have a `chain_method` parameter + chain_method = "predict" + + for chain_idx, estimator in enumerate(self.estimators_): + message = self._log_message( + estimator_idx=chain_idx + 1, + n_estimators=len(self.estimators_), + processing_msg=f"Processing order {self.order_[chain_idx]}", + ) + y = Y[:, self.order_[chain_idx]] + with _print_elapsed_time("Chain", message): + estimator.fit( + X_aug[:, : (X.shape[1] + chain_idx)], + y, + **routed_params.estimator.fit, + ) + + if self.cv is not None and chain_idx < len(self.estimators_) - 1: + col_idx = X.shape[1] + chain_idx + cv_result = cross_val_predict( + self._get_estimator(), + X_aug[:, :col_idx], + y=y, + cv=self.cv, + method=chain_method, + ) + # `predict_proba` output is 2D, we use only output for classes[-1] + if cv_result.ndim > 1: + cv_result = cv_result[:, 1] + if sp.issparse(X_aug): + X_aug[:, col_idx] = np.expand_dims(cv_result, 1) + else: + X_aug[:, col_idx] = cv_result + + return self + + def predict(self, X): + """Predict on the data matrix X using the ClassifierChain model. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input data. + + Returns + ------- + Y_pred : array-like of shape (n_samples, n_classes) + The predicted values. + """ + return self._get_predictions(X, output_method="predict") + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = get_tags(self._get_estimator()).input_tags.sparse + return tags + + +class ClassifierChain(MetaEstimatorMixin, ClassifierMixin, _BaseChain): + """A multi-label model that arranges binary classifiers into a chain. + + Each model makes a prediction in the order specified by the chain using + all of the available features provided to the model plus the predictions + of models that are earlier in the chain. + + For an example of how to use ``ClassifierChain`` and benefit from its + ensemble, see + :ref:`ClassifierChain on a yeast dataset + ` example. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.19 + + Parameters + ---------- + estimator : estimator + The base estimator from which the classifier chain is built. + + order : array-like of shape (n_outputs,) or 'random', default=None + If `None`, the order will be determined by the order of columns in + the label matrix Y.:: + + order = [0, 1, 2, ..., Y.shape[1] - 1] + + The order of the chain can be explicitly set by providing a list of + integers. For example, for a chain of length 5.:: + + order = [1, 3, 2, 4, 0] + + means that the first model in the chain will make predictions for + column 1 in the Y matrix, the second model will make predictions + for column 3, etc. + + If order is `random` a random ordering will be used. + + cv : int, cross-validation generator or an iterable, default=None + Determines whether to use cross validated predictions or true + labels for the results of previous estimators in the chain. + Possible inputs for cv are: + + - None, to use true labels when fitting, + - integer, to specify the number of folds in a (Stratified)KFold, + - :term:`CV splitter`, + - An iterable yielding (train, test) splits as arrays of indices. + + chain_method : {'predict', 'predict_proba', 'predict_log_proba', \ + 'decision_function'} or list of such str's, default='predict' + + Prediction method to be used by estimators in the chain for + the 'prediction' features of previous estimators in the chain. + + - if `str`, name of the method; + - if a list of `str`, provides the method names in order of + preference. The method used corresponds to the first method in + the list that is implemented by `base_estimator`. + + .. versionadded:: 1.5 + + random_state : int, RandomState instance or None, optional (default=None) + If ``order='random'``, determines random number generation for the + chain order. + In addition, it controls the random seed given at each `base_estimator` + at each chaining iteration. Thus, it is only used when `base_estimator` + exposes a `random_state`. + Pass an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + verbose : bool, default=False + If True, chain progress is output as each model is completed. + + .. versionadded:: 1.2 + + base_estimator : estimator, default="deprecated" + Use `estimator` instead. + + .. deprecated:: 1.7 + `base_estimator` is deprecated and will be removed in 1.9. + Use `estimator` instead. + + Attributes + ---------- + classes_ : list + A list of arrays of length ``len(estimators_)`` containing the + class labels for each estimator in the chain. + + estimators_ : list + A list of clones of base_estimator. + + order_ : list + The order of labels in the classifier chain. + + chain_method_ : str + Prediction method used by estimators in the chain for the prediction + features. + + n_features_in_ : int + Number of features seen during :term:`fit`. Only defined if the + underlying `base_estimator` exposes such an attribute when fit. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + RegressorChain : Equivalent for regression. + MultiOutputClassifier : Classifies each output independently rather than + chaining. + + References + ---------- + Jesse Read, Bernhard Pfahringer, Geoff Holmes, Eibe Frank, "Classifier + Chains for Multi-label Classification", 2009. + + Examples + -------- + >>> from sklearn.datasets import make_multilabel_classification + >>> from sklearn.linear_model import LogisticRegression + >>> from sklearn.model_selection import train_test_split + >>> from sklearn.multioutput import ClassifierChain + >>> X, Y = make_multilabel_classification( + ... n_samples=12, n_classes=3, random_state=0 + ... ) + >>> X_train, X_test, Y_train, Y_test = train_test_split( + ... X, Y, random_state=0 + ... ) + >>> base_lr = LogisticRegression(solver='lbfgs', random_state=0) + >>> chain = ClassifierChain(base_lr, order='random', random_state=0) + >>> chain.fit(X_train, Y_train).predict(X_test) + array([[1., 1., 0.], + [1., 0., 0.], + [0., 1., 0.]]) + >>> chain.predict_proba(X_test) + array([[0.8387, 0.9431, 0.4576], + [0.8878, 0.3684, 0.2640], + [0.0321, 0.9935, 0.0626]]) + """ + + _parameter_constraints: dict = { + **_BaseChain._parameter_constraints, + "chain_method": [ + list, + tuple, + StrOptions( + {"predict", "predict_proba", "predict_log_proba", "decision_function"} + ), + ], + } + + # TODO(1.9): Remove base_estimator from __init__ + def __init__( + self, + estimator=None, + *, + order=None, + cv=None, + chain_method="predict", + random_state=None, + verbose=False, + base_estimator="deprecated", + ): + super().__init__( + estimator, + order=order, + cv=cv, + random_state=random_state, + verbose=verbose, + base_estimator=base_estimator, + ) + self.chain_method = chain_method + + @_fit_context( + # ClassifierChain.base_estimator is not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, Y, **fit_params): + """Fit the model to data matrix X and targets Y. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input data. + + Y : array-like of shape (n_samples, n_classes) + The target values. + + **fit_params : dict of string -> object + Parameters passed to the `fit` method of each step. + + Only available if `enable_metadata_routing=True`. See the + :ref:`User Guide `. + + .. versionadded:: 1.3 + + Returns + ------- + self : object + Class instance. + """ + _raise_for_params(fit_params, self, "fit") + + super().fit(X, Y, **fit_params) + self.classes_ = [estimator.classes_ for estimator in self.estimators_] + return self + + @_available_if_base_estimator_has("predict_proba") + def predict_proba(self, X): + """Predict probability estimates. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input data. + + Returns + ------- + Y_prob : array-like of shape (n_samples, n_classes) + The predicted probabilities. + """ + return self._get_predictions(X, output_method="predict_proba") + + def predict_log_proba(self, X): + """Predict logarithm of probability estimates. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input data. + + Returns + ------- + Y_log_prob : array-like of shape (n_samples, n_classes) + The predicted logarithm of the probabilities. + """ + return np.log(self.predict_proba(X)) + + @_available_if_base_estimator_has("decision_function") + def decision_function(self, X): + """Evaluate the decision_function of the models in the chain. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The input data. + + Returns + ------- + Y_decision : array-like of shape (n_samples, n_classes) + Returns the decision function of the sample for each model + in the chain. + """ + return self._get_predictions(X, output_method="decision_function") + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + .. versionadded:: 1.3 + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + + router = MetadataRouter(owner=self.__class__.__name__).add( + estimator=self._get_estimator(), + method_mapping=MethodMapping().add(caller="fit", callee="fit"), + ) + return router + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + # FIXME + tags._skip_test = True + tags.target_tags.single_output = False + tags.target_tags.multi_output = True + return tags + + +class RegressorChain(MetaEstimatorMixin, RegressorMixin, _BaseChain): + """A multi-label model that arranges regressions into a chain. + + Each model makes a prediction in the order specified by the chain using + all of the available features provided to the model plus the predictions + of models that are earlier in the chain. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.20 + + Parameters + ---------- + estimator : estimator + The base estimator from which the regressor chain is built. + + order : array-like of shape (n_outputs,) or 'random', default=None + If `None`, the order will be determined by the order of columns in + the label matrix Y.:: + + order = [0, 1, 2, ..., Y.shape[1] - 1] + + The order of the chain can be explicitly set by providing a list of + integers. For example, for a chain of length 5.:: + + order = [1, 3, 2, 4, 0] + + means that the first model in the chain will make predictions for + column 1 in the Y matrix, the second model will make predictions + for column 3, etc. + + If order is 'random' a random ordering will be used. + + cv : int, cross-validation generator or an iterable, default=None + Determines whether to use cross validated predictions or true + labels for the results of previous estimators in the chain. + Possible inputs for cv are: + + - None, to use true labels when fitting, + - integer, to specify the number of folds in a (Stratified)KFold, + - :term:`CV splitter`, + - An iterable yielding (train, test) splits as arrays of indices. + + random_state : int, RandomState instance or None, optional (default=None) + If ``order='random'``, determines random number generation for the + chain order. + In addition, it controls the random seed given at each `base_estimator` + at each chaining iteration. Thus, it is only used when `base_estimator` + exposes a `random_state`. + Pass an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + verbose : bool, default=False + If True, chain progress is output as each model is completed. + + .. versionadded:: 1.2 + + base_estimator : estimator, default="deprecated" + Use `estimator` instead. + + .. deprecated:: 1.7 + `base_estimator` is deprecated and will be removed in 1.9. + Use `estimator` instead. + + Attributes + ---------- + estimators_ : list + A list of clones of base_estimator. + + order_ : list + The order of labels in the classifier chain. + + n_features_in_ : int + Number of features seen during :term:`fit`. Only defined if the + underlying `base_estimator` exposes such an attribute when fit. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + ClassifierChain : Equivalent for classification. + MultiOutputRegressor : Learns each output independently rather than + chaining. + + Examples + -------- + >>> from sklearn.multioutput import RegressorChain + >>> from sklearn.linear_model import LogisticRegression + >>> logreg = LogisticRegression(solver='lbfgs') + >>> X, Y = [[1, 0], [0, 1], [1, 1]], [[0, 2], [1, 1], [2, 0]] + >>> chain = RegressorChain(logreg, order=[0, 1]).fit(X, Y) + >>> chain.predict(X) + array([[0., 2.], + [1., 1.], + [2., 0.]]) + """ + + @_fit_context( + # RegressorChain.base_estimator is not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, Y, **fit_params): + """Fit the model to data matrix X and targets Y. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input data. + + Y : array-like of shape (n_samples, n_classes) + The target values. + + **fit_params : dict of string -> object + Parameters passed to the `fit` method at each step + of the regressor chain. + + .. versionadded:: 0.23 + + Returns + ------- + self : object + Returns a fitted instance. + """ + super().fit(X, Y, **fit_params) + return self + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + .. versionadded:: 1.3 + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + + router = MetadataRouter(owner=self.__class__.__name__).add( + estimator=self._get_estimator(), + method_mapping=MethodMapping().add(caller="fit", callee="fit"), + ) + return router + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.target_tags.single_output = False + tags.target_tags.multi_output = True + return tags diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/naive_bayes.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/naive_bayes.py new file mode 100644 index 0000000000000000000000000000000000000000..31a1b87af2916e352a55b68307ba395c9193ce70 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/naive_bayes.py @@ -0,0 +1,1540 @@ +"""Naive Bayes algorithms. + +These are supervised learning methods based on applying Bayes' theorem with strong +(naive) feature independence assumptions. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from abc import ABCMeta, abstractmethod +from numbers import Integral, Real + +import numpy as np +from scipy.special import logsumexp + +from .base import ( + BaseEstimator, + ClassifierMixin, + _fit_context, +) +from .preprocessing import LabelBinarizer, binarize, label_binarize +from .utils._param_validation import Interval +from .utils.extmath import safe_sparse_dot +from .utils.multiclass import _check_partial_fit_first_call +from .utils.validation import ( + _check_n_features, + _check_sample_weight, + check_is_fitted, + check_non_negative, + validate_data, +) + +__all__ = [ + "BernoulliNB", + "CategoricalNB", + "ComplementNB", + "GaussianNB", + "MultinomialNB", +] + + +class _BaseNB(ClassifierMixin, BaseEstimator, metaclass=ABCMeta): + """Abstract base class for naive Bayes estimators""" + + @abstractmethod + def _joint_log_likelihood(self, X): + """Compute the unnormalized posterior log probability of X + + I.e. ``log P(c) + log P(x|c)`` for all rows x of X, as an array-like of + shape (n_samples, n_classes). + + Public methods predict, predict_proba, predict_log_proba, and + predict_joint_log_proba pass the input through _check_X before handing it + over to _joint_log_likelihood. The term "joint log likelihood" is used + interchangibly with "joint log probability". + """ + + @abstractmethod + def _check_X(self, X): + """To be overridden in subclasses with the actual checks. + + Only used in predict* methods. + """ + + def predict_joint_log_proba(self, X): + """Return joint log probability estimates for the test vector X. + + For each row x of X and class y, the joint log probability is given by + ``log P(x, y) = log P(y) + log P(x|y),`` + where ``log P(y)`` is the class prior probability and ``log P(x|y)`` is + the class-conditional probability. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The input samples. + + Returns + ------- + C : ndarray of shape (n_samples, n_classes) + Returns the joint log-probability of the samples for each class in + the model. The columns correspond to the classes in sorted + order, as they appear in the attribute :term:`classes_`. + """ + check_is_fitted(self) + X = self._check_X(X) + return self._joint_log_likelihood(X) + + def predict(self, X): + """ + Perform classification on an array of test vectors X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The input samples. + + Returns + ------- + C : ndarray of shape (n_samples,) + Predicted target values for X. + """ + check_is_fitted(self) + X = self._check_X(X) + jll = self._joint_log_likelihood(X) + return self.classes_[np.argmax(jll, axis=1)] + + def predict_log_proba(self, X): + """ + Return log-probability estimates for the test vector X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The input samples. + + Returns + ------- + C : array-like of shape (n_samples, n_classes) + Returns the log-probability of the samples for each class in + the model. The columns correspond to the classes in sorted + order, as they appear in the attribute :term:`classes_`. + """ + check_is_fitted(self) + X = self._check_X(X) + jll = self._joint_log_likelihood(X) + # normalize by P(x) = P(f_1, ..., f_n) + log_prob_x = logsumexp(jll, axis=1) + return jll - np.atleast_2d(log_prob_x).T + + def predict_proba(self, X): + """ + Return probability estimates for the test vector X. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + The input samples. + + Returns + ------- + C : array-like of shape (n_samples, n_classes) + Returns the probability of the samples for each class in + the model. The columns correspond to the classes in sorted + order, as they appear in the attribute :term:`classes_`. + """ + return np.exp(self.predict_log_proba(X)) + + +class GaussianNB(_BaseNB): + """ + Gaussian Naive Bayes (GaussianNB). + + Can perform online updates to model parameters via :meth:`partial_fit`. + For details on algorithm used to update feature means and variance online, + see `Stanford CS tech report STAN-CS-79-773 by Chan, Golub, and LeVeque + `_. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + priors : array-like of shape (n_classes,), default=None + Prior probabilities of the classes. If specified, the priors are not + adjusted according to the data. + + var_smoothing : float, default=1e-9 + Portion of the largest variance of all features that is added to + variances for calculation stability. + + .. versionadded:: 0.20 + + Attributes + ---------- + class_count_ : ndarray of shape (n_classes,) + number of training samples observed in each class. + + class_prior_ : ndarray of shape (n_classes,) + probability of each class. + + classes_ : ndarray of shape (n_classes,) + class labels known to the classifier. + + epsilon_ : float + absolute additive value to variances. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + var_ : ndarray of shape (n_classes, n_features) + Variance of each feature per class. + + .. versionadded:: 1.0 + + theta_ : ndarray of shape (n_classes, n_features) + mean of each feature per class. + + See Also + -------- + BernoulliNB : Naive Bayes classifier for multivariate Bernoulli models. + CategoricalNB : Naive Bayes classifier for categorical features. + ComplementNB : Complement Naive Bayes classifier. + MultinomialNB : Naive Bayes classifier for multinomial models. + + Examples + -------- + >>> import numpy as np + >>> X = np.array([[-1, -1], [-2, -1], [-3, -2], [1, 1], [2, 1], [3, 2]]) + >>> Y = np.array([1, 1, 1, 2, 2, 2]) + >>> from sklearn.naive_bayes import GaussianNB + >>> clf = GaussianNB() + >>> clf.fit(X, Y) + GaussianNB() + >>> print(clf.predict([[-0.8, -1]])) + [1] + >>> clf_pf = GaussianNB() + >>> clf_pf.partial_fit(X, Y, np.unique(Y)) + GaussianNB() + >>> print(clf_pf.predict([[-0.8, -1]])) + [1] + """ + + _parameter_constraints: dict = { + "priors": ["array-like", None], + "var_smoothing": [Interval(Real, 0, None, closed="left")], + } + + def __init__(self, *, priors=None, var_smoothing=1e-9): + self.priors = priors + self.var_smoothing = var_smoothing + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y, sample_weight=None): + """Fit Gaussian Naive Bayes according to X, y. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training vectors, where `n_samples` is the number of samples + and `n_features` is the number of features. + + y : array-like of shape (n_samples,) + Target values. + + sample_weight : array-like of shape (n_samples,), default=None + Weights applied to individual samples (1. for unweighted). + + .. versionadded:: 0.17 + Gaussian Naive Bayes supports fitting with *sample_weight*. + + Returns + ------- + self : object + Returns the instance itself. + """ + y = validate_data(self, y=y) + return self._partial_fit( + X, y, np.unique(y), _refit=True, sample_weight=sample_weight + ) + + def _check_X(self, X): + """Validate X, used only in predict* methods.""" + return validate_data(self, X, reset=False) + + @staticmethod + def _update_mean_variance(n_past, mu, var, X, sample_weight=None): + """Compute online update of Gaussian mean and variance. + + Given starting sample count, mean, and variance, a new set of + points X, and optionally sample weights, return the updated mean and + variance. (NB - each dimension (column) in X is treated as independent + -- you get variance, not covariance). + + Can take scalar mean and variance, or vector mean and variance to + simultaneously update a number of independent Gaussians. + + See Stanford CS tech report STAN-CS-79-773 by Chan, Golub, and LeVeque: + + http://i.stanford.edu/pub/cstr/reports/cs/tr/79/773/CS-TR-79-773.pdf + + Parameters + ---------- + n_past : int + Number of samples represented in old mean and variance. If sample + weights were given, this should contain the sum of sample + weights represented in old mean and variance. + + mu : array-like of shape (number of Gaussians,) + Means for Gaussians in original set. + + var : array-like of shape (number of Gaussians,) + Variances for Gaussians in original set. + + sample_weight : array-like of shape (n_samples,), default=None + Weights applied to individual samples (1. for unweighted). + + Returns + ------- + total_mu : array-like of shape (number of Gaussians,) + Updated mean for each Gaussian over the combined set. + + total_var : array-like of shape (number of Gaussians,) + Updated variance for each Gaussian over the combined set. + """ + if X.shape[0] == 0: + return mu, var + + # Compute (potentially weighted) mean and variance of new datapoints + if sample_weight is not None: + n_new = float(sample_weight.sum()) + if np.isclose(n_new, 0.0): + return mu, var + new_mu = np.average(X, axis=0, weights=sample_weight) + new_var = np.average((X - new_mu) ** 2, axis=0, weights=sample_weight) + else: + n_new = X.shape[0] + new_var = np.var(X, axis=0) + new_mu = np.mean(X, axis=0) + + if n_past == 0: + return new_mu, new_var + + n_total = float(n_past + n_new) + + # Combine mean of old and new data, taking into consideration + # (weighted) number of observations + total_mu = (n_new * new_mu + n_past * mu) / n_total + + # Combine variance of old and new data, taking into consideration + # (weighted) number of observations. This is achieved by combining + # the sum-of-squared-differences (ssd) + old_ssd = n_past * var + new_ssd = n_new * new_var + total_ssd = old_ssd + new_ssd + (n_new * n_past / n_total) * (mu - new_mu) ** 2 + total_var = total_ssd / n_total + + return total_mu, total_var + + @_fit_context(prefer_skip_nested_validation=True) + def partial_fit(self, X, y, classes=None, sample_weight=None): + """Incremental fit on a batch of samples. + + This method is expected to be called several times consecutively + on different chunks of a dataset so as to implement out-of-core + or online learning. + + This is especially useful when the whole dataset is too big to fit in + memory at once. + + This method has some performance and numerical stability overhead, + hence it is better to call partial_fit on chunks of data that are + as large as possible (as long as fitting in the memory budget) to + hide the overhead. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training vectors, where `n_samples` is the number of samples and + `n_features` is the number of features. + + y : array-like of shape (n_samples,) + Target values. + + classes : array-like of shape (n_classes,), default=None + List of all the classes that can possibly appear in the y vector. + + Must be provided at the first call to partial_fit, can be omitted + in subsequent calls. + + sample_weight : array-like of shape (n_samples,), default=None + Weights applied to individual samples (1. for unweighted). + + .. versionadded:: 0.17 + + Returns + ------- + self : object + Returns the instance itself. + """ + return self._partial_fit( + X, y, classes, _refit=False, sample_weight=sample_weight + ) + + def _partial_fit(self, X, y, classes=None, _refit=False, sample_weight=None): + """Actual implementation of Gaussian NB fitting. + + Parameters + ---------- + X : array-like of shape (n_samples, n_features) + Training vectors, where `n_samples` is the number of samples and + `n_features` is the number of features. + + y : array-like of shape (n_samples,) + Target values. + + classes : array-like of shape (n_classes,), default=None + List of all the classes that can possibly appear in the y vector. + + Must be provided at the first call to partial_fit, can be omitted + in subsequent calls. + + _refit : bool, default=False + If true, act as though this were the first time we called + _partial_fit (ie, throw away any past fitting and start over). + + sample_weight : array-like of shape (n_samples,), default=None + Weights applied to individual samples (1. for unweighted). + + Returns + ------- + self : object + """ + if _refit: + self.classes_ = None + + first_call = _check_partial_fit_first_call(self, classes) + X, y = validate_data(self, X, y, reset=first_call) + if sample_weight is not None: + sample_weight = _check_sample_weight(sample_weight, X) + + # If the ratio of data variance between dimensions is too small, it + # will cause numerical errors. To address this, we artificially + # boost the variance by epsilon, a small fraction of the standard + # deviation of the largest dimension. + self.epsilon_ = self.var_smoothing * np.var(X, axis=0).max() + + if first_call: + # This is the first call to partial_fit: + # initialize various cumulative counters + n_features = X.shape[1] + n_classes = len(self.classes_) + self.theta_ = np.zeros((n_classes, n_features)) + self.var_ = np.zeros((n_classes, n_features)) + + self.class_count_ = np.zeros(n_classes, dtype=np.float64) + + # Initialise the class prior + # Take into account the priors + if self.priors is not None: + priors = np.asarray(self.priors) + # Check that the provided prior matches the number of classes + if len(priors) != n_classes: + raise ValueError("Number of priors must match number of classes.") + # Check that the sum is 1 + if not np.isclose(priors.sum(), 1.0): + raise ValueError("The sum of the priors should be 1.") + # Check that the priors are non-negative + if (priors < 0).any(): + raise ValueError("Priors must be non-negative.") + self.class_prior_ = priors + else: + # Initialize the priors to zeros for each class + self.class_prior_ = np.zeros(len(self.classes_), dtype=np.float64) + else: + if X.shape[1] != self.theta_.shape[1]: + msg = "Number of features %d does not match previous data %d." + raise ValueError(msg % (X.shape[1], self.theta_.shape[1])) + # Put epsilon back in each time + self.var_[:, :] -= self.epsilon_ + + classes = self.classes_ + + unique_y = np.unique(y) + unique_y_in_classes = np.isin(unique_y, classes) + + if not np.all(unique_y_in_classes): + raise ValueError( + "The target label(s) %s in y do not exist in the initial classes %s" + % (unique_y[~unique_y_in_classes], classes) + ) + + for y_i in unique_y: + i = classes.searchsorted(y_i) + X_i = X[y == y_i, :] + + if sample_weight is not None: + sw_i = sample_weight[y == y_i] + N_i = sw_i.sum() + else: + sw_i = None + N_i = X_i.shape[0] + + new_theta, new_sigma = self._update_mean_variance( + self.class_count_[i], self.theta_[i, :], self.var_[i, :], X_i, sw_i + ) + + self.theta_[i, :] = new_theta + self.var_[i, :] = new_sigma + self.class_count_[i] += N_i + + self.var_[:, :] += self.epsilon_ + + # Update if only no priors is provided + if self.priors is None: + # Empirical prior, with sample_weight taken into account + self.class_prior_ = self.class_count_ / self.class_count_.sum() + + return self + + def _joint_log_likelihood(self, X): + joint_log_likelihood = [] + for i in range(np.size(self.classes_)): + jointi = np.log(self.class_prior_[i]) + n_ij = -0.5 * np.sum(np.log(2.0 * np.pi * self.var_[i, :])) + n_ij -= 0.5 * np.sum(((X - self.theta_[i, :]) ** 2) / (self.var_[i, :]), 1) + joint_log_likelihood.append(jointi + n_ij) + + joint_log_likelihood = np.array(joint_log_likelihood).T + return joint_log_likelihood + + +class _BaseDiscreteNB(_BaseNB): + """Abstract base class for naive Bayes on discrete/categorical data + + Any estimator based on this class should provide: + + __init__ + _joint_log_likelihood(X) as per _BaseNB + _update_feature_log_prob(alpha) + _count(X, Y) + """ + + _parameter_constraints: dict = { + "alpha": [Interval(Real, 0, None, closed="left"), "array-like"], + "fit_prior": ["boolean"], + "class_prior": ["array-like", None], + "force_alpha": ["boolean"], + } + + def __init__(self, alpha=1.0, fit_prior=True, class_prior=None, force_alpha=True): + self.alpha = alpha + self.fit_prior = fit_prior + self.class_prior = class_prior + self.force_alpha = force_alpha + + @abstractmethod + def _count(self, X, Y): + """Update counts that are used to calculate probabilities. + + The counts make up a sufficient statistic extracted from the data. + Accordingly, this method is called each time `fit` or `partial_fit` + update the model. `class_count_` and `feature_count_` must be updated + here along with any model specific counts. + + Parameters + ---------- + X : {ndarray, sparse matrix} of shape (n_samples, n_features) + The input samples. + Y : ndarray of shape (n_samples, n_classes) + Binarized class labels. + """ + + @abstractmethod + def _update_feature_log_prob(self, alpha): + """Update feature log probabilities based on counts. + + This method is called each time `fit` or `partial_fit` update the + model. + + Parameters + ---------- + alpha : float + smoothing parameter. See :meth:`_check_alpha`. + """ + + def _check_X(self, X): + """Validate X, used only in predict* methods.""" + return validate_data(self, X, accept_sparse="csr", reset=False) + + def _check_X_y(self, X, y, reset=True): + """Validate X and y in fit methods.""" + return validate_data(self, X, y, accept_sparse="csr", reset=reset) + + def _update_class_log_prior(self, class_prior=None): + """Update class log priors. + + The class log priors are based on `class_prior`, class count or the + number of classes. This method is called each time `fit` or + `partial_fit` update the model. + """ + n_classes = len(self.classes_) + if class_prior is not None: + if len(class_prior) != n_classes: + raise ValueError("Number of priors must match number of classes.") + self.class_log_prior_ = np.log(class_prior) + elif self.fit_prior: + with warnings.catch_warnings(): + # silence the warning when count is 0 because class was not yet + # observed + warnings.simplefilter("ignore", RuntimeWarning) + log_class_count = np.log(self.class_count_) + + # empirical prior, with sample_weight taken into account + self.class_log_prior_ = log_class_count - np.log(self.class_count_.sum()) + else: + self.class_log_prior_ = np.full(n_classes, -np.log(n_classes)) + + def _check_alpha(self): + alpha = ( + np.asarray(self.alpha) if not isinstance(self.alpha, Real) else self.alpha + ) + alpha_min = np.min(alpha) + if isinstance(alpha, np.ndarray): + if not alpha.shape[0] == self.n_features_in_: + raise ValueError( + "When alpha is an array, it should contains `n_features`. " + f"Got {alpha.shape[0]} elements instead of {self.n_features_in_}." + ) + # check that all alpha are positive + if alpha_min < 0: + raise ValueError("All values in alpha must be greater than 0.") + alpha_lower_bound = 1e-10 + if alpha_min < alpha_lower_bound and not self.force_alpha: + warnings.warn( + "alpha too small will result in numeric errors, setting alpha =" + f" {alpha_lower_bound:.1e}. Use `force_alpha=True` to keep alpha" + " unchanged." + ) + return np.maximum(alpha, alpha_lower_bound) + return alpha + + @_fit_context(prefer_skip_nested_validation=True) + def partial_fit(self, X, y, classes=None, sample_weight=None): + """Incremental fit on a batch of samples. + + This method is expected to be called several times consecutively + on different chunks of a dataset so as to implement out-of-core + or online learning. + + This is especially useful when the whole dataset is too big to fit in + memory at once. + + This method has some performance overhead hence it is better to call + partial_fit on chunks of data that are as large as possible + (as long as fitting in the memory budget) to hide the overhead. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Training vectors, where `n_samples` is the number of samples and + `n_features` is the number of features. + + y : array-like of shape (n_samples,) + Target values. + + classes : array-like of shape (n_classes,), default=None + List of all the classes that can possibly appear in the y vector. + + Must be provided at the first call to partial_fit, can be omitted + in subsequent calls. + + sample_weight : array-like of shape (n_samples,), default=None + Weights applied to individual samples (1. for unweighted). + + Returns + ------- + self : object + Returns the instance itself. + """ + first_call = not hasattr(self, "classes_") + + X, y = self._check_X_y(X, y, reset=first_call) + _, n_features = X.shape + + if _check_partial_fit_first_call(self, classes): + # This is the first call to partial_fit: + # initialize various cumulative counters + n_classes = len(classes) + self._init_counters(n_classes, n_features) + + Y = label_binarize(y, classes=self.classes_) + if Y.shape[1] == 1: + if len(self.classes_) == 2: + Y = np.concatenate((1 - Y, Y), axis=1) + else: # degenerate case: just one class + Y = np.ones_like(Y) + + if X.shape[0] != Y.shape[0]: + msg = "X.shape[0]=%d and y.shape[0]=%d are incompatible." + raise ValueError(msg % (X.shape[0], y.shape[0])) + + # label_binarize() returns arrays with dtype=np.int64. + # We convert it to np.float64 to support sample_weight consistently + Y = Y.astype(np.float64, copy=False) + if sample_weight is not None: + sample_weight = _check_sample_weight(sample_weight, X) + sample_weight = np.atleast_2d(sample_weight) + Y *= sample_weight.T + + class_prior = self.class_prior + + # Count raw events from data before updating the class log prior + # and feature log probas + self._count(X, Y) + + # XXX: OPTIM: we could introduce a public finalization method to + # be called by the user explicitly just once after several consecutive + # calls to partial_fit and prior any call to predict[_[log_]proba] + # to avoid computing the smooth log probas at each call to partial fit + alpha = self._check_alpha() + self._update_feature_log_prob(alpha) + self._update_class_log_prior(class_prior=class_prior) + return self + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y, sample_weight=None): + """Fit Naive Bayes classifier according to X, y. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Training vectors, where `n_samples` is the number of samples and + `n_features` is the number of features. + + y : array-like of shape (n_samples,) + Target values. + + sample_weight : array-like of shape (n_samples,), default=None + Weights applied to individual samples (1. for unweighted). + + Returns + ------- + self : object + Returns the instance itself. + """ + X, y = self._check_X_y(X, y) + _, n_features = X.shape + + labelbin = LabelBinarizer() + Y = labelbin.fit_transform(y) + self.classes_ = labelbin.classes_ + if Y.shape[1] == 1: + if len(self.classes_) == 2: + Y = np.concatenate((1 - Y, Y), axis=1) + else: # degenerate case: just one class + Y = np.ones_like(Y) + + # LabelBinarizer().fit_transform() returns arrays with dtype=np.int64. + # We convert it to np.float64 to support sample_weight consistently; + # this means we also don't have to cast X to floating point + if sample_weight is not None: + Y = Y.astype(np.float64, copy=False) + sample_weight = _check_sample_weight(sample_weight, X) + sample_weight = np.atleast_2d(sample_weight) + Y *= sample_weight.T + + class_prior = self.class_prior + + # Count raw events from data before updating the class log prior + # and feature log probas + n_classes = Y.shape[1] + self._init_counters(n_classes, n_features) + self._count(X, Y) + alpha = self._check_alpha() + self._update_feature_log_prob(alpha) + self._update_class_log_prior(class_prior=class_prior) + return self + + def _init_counters(self, n_classes, n_features): + self.class_count_ = np.zeros(n_classes, dtype=np.float64) + self.feature_count_ = np.zeros((n_classes, n_features), dtype=np.float64) + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.sparse = True + tags.classifier_tags.poor_score = True + return tags + + +class MultinomialNB(_BaseDiscreteNB): + """ + Naive Bayes classifier for multinomial models. + + The multinomial Naive Bayes classifier is suitable for classification with + discrete features (e.g., word counts for text classification). The + multinomial distribution normally requires integer feature counts. However, + in practice, fractional counts such as tf-idf may also work. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + alpha : float or array-like of shape (n_features,), default=1.0 + Additive (Laplace/Lidstone) smoothing parameter + (set alpha=0 and force_alpha=True, for no smoothing). + + force_alpha : bool, default=True + If False and alpha is less than 1e-10, it will set alpha to + 1e-10. If True, alpha will remain unchanged. This may cause + numerical errors if alpha is too close to 0. + + .. versionadded:: 1.2 + .. versionchanged:: 1.4 + The default value of `force_alpha` changed to `True`. + + fit_prior : bool, default=True + Whether to learn class prior probabilities or not. + If false, a uniform prior will be used. + + class_prior : array-like of shape (n_classes,), default=None + Prior probabilities of the classes. If specified, the priors are not + adjusted according to the data. + + Attributes + ---------- + class_count_ : ndarray of shape (n_classes,) + Number of samples encountered for each class during fitting. This + value is weighted by the sample weight when provided. + + class_log_prior_ : ndarray of shape (n_classes,) + Smoothed empirical log probability for each class. + + classes_ : ndarray of shape (n_classes,) + Class labels known to the classifier + + feature_count_ : ndarray of shape (n_classes, n_features) + Number of samples encountered for each (class, feature) + during fitting. This value is weighted by the sample weight when + provided. + + feature_log_prob_ : ndarray of shape (n_classes, n_features) + Empirical log probability of features + given a class, ``P(x_i|y)``. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + BernoulliNB : Naive Bayes classifier for multivariate Bernoulli models. + CategoricalNB : Naive Bayes classifier for categorical features. + ComplementNB : Complement Naive Bayes classifier. + GaussianNB : Gaussian Naive Bayes. + + References + ---------- + C.D. Manning, P. Raghavan and H. Schuetze (2008). Introduction to + Information Retrieval. Cambridge University Press, pp. 234-265. + https://nlp.stanford.edu/IR-book/html/htmledition/naive-bayes-text-classification-1.html + + Examples + -------- + >>> import numpy as np + >>> rng = np.random.RandomState(1) + >>> X = rng.randint(5, size=(6, 100)) + >>> y = np.array([1, 2, 3, 4, 5, 6]) + >>> from sklearn.naive_bayes import MultinomialNB + >>> clf = MultinomialNB() + >>> clf.fit(X, y) + MultinomialNB() + >>> print(clf.predict(X[2:3])) + [3] + """ + + def __init__( + self, *, alpha=1.0, force_alpha=True, fit_prior=True, class_prior=None + ): + super().__init__( + alpha=alpha, + fit_prior=fit_prior, + class_prior=class_prior, + force_alpha=force_alpha, + ) + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.positive_only = True + return tags + + def _count(self, X, Y): + """Count and smooth feature occurrences.""" + check_non_negative(X, "MultinomialNB (input X)") + self.feature_count_ += safe_sparse_dot(Y.T, X) + self.class_count_ += Y.sum(axis=0) + + def _update_feature_log_prob(self, alpha): + """Apply smoothing to raw counts and recompute log probabilities""" + smoothed_fc = self.feature_count_ + alpha + smoothed_cc = smoothed_fc.sum(axis=1) + + self.feature_log_prob_ = np.log(smoothed_fc) - np.log( + smoothed_cc.reshape(-1, 1) + ) + + def _joint_log_likelihood(self, X): + """Calculate the posterior log probability of the samples X""" + return safe_sparse_dot(X, self.feature_log_prob_.T) + self.class_log_prior_ + + +class ComplementNB(_BaseDiscreteNB): + """The Complement Naive Bayes classifier described in Rennie et al. (2003). + + The Complement Naive Bayes classifier was designed to correct the "severe + assumptions" made by the standard Multinomial Naive Bayes classifier. It is + particularly suited for imbalanced data sets. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.20 + + Parameters + ---------- + alpha : float or array-like of shape (n_features,), default=1.0 + Additive (Laplace/Lidstone) smoothing parameter + (set alpha=0 and force_alpha=True, for no smoothing). + + force_alpha : bool, default=True + If False and alpha is less than 1e-10, it will set alpha to + 1e-10. If True, alpha will remain unchanged. This may cause + numerical errors if alpha is too close to 0. + + .. versionadded:: 1.2 + .. versionchanged:: 1.4 + The default value of `force_alpha` changed to `True`. + + fit_prior : bool, default=True + Only used in edge case with a single class in the training set. + + class_prior : array-like of shape (n_classes,), default=None + Prior probabilities of the classes. Not used. + + norm : bool, default=False + Whether or not a second normalization of the weights is performed. The + default behavior mirrors the implementations found in Mahout and Weka, + which do not follow the full algorithm described in Table 9 of the + paper. + + Attributes + ---------- + class_count_ : ndarray of shape (n_classes,) + Number of samples encountered for each class during fitting. This + value is weighted by the sample weight when provided. + + class_log_prior_ : ndarray of shape (n_classes,) + Smoothed empirical log probability for each class. Only used in edge + case with a single class in the training set. + + classes_ : ndarray of shape (n_classes,) + Class labels known to the classifier + + feature_all_ : ndarray of shape (n_features,) + Number of samples encountered for each feature during fitting. This + value is weighted by the sample weight when provided. + + feature_count_ : ndarray of shape (n_classes, n_features) + Number of samples encountered for each (class, feature) during fitting. + This value is weighted by the sample weight when provided. + + feature_log_prob_ : ndarray of shape (n_classes, n_features) + Empirical weights for class complements. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + BernoulliNB : Naive Bayes classifier for multivariate Bernoulli models. + CategoricalNB : Naive Bayes classifier for categorical features. + GaussianNB : Gaussian Naive Bayes. + MultinomialNB : Naive Bayes classifier for multinomial models. + + References + ---------- + Rennie, J. D., Shih, L., Teevan, J., & Karger, D. R. (2003). + Tackling the poor assumptions of naive bayes text classifiers. In ICML + (Vol. 3, pp. 616-623). + https://people.csail.mit.edu/jrennie/papers/icml03-nb.pdf + + Examples + -------- + >>> import numpy as np + >>> rng = np.random.RandomState(1) + >>> X = rng.randint(5, size=(6, 100)) + >>> y = np.array([1, 2, 3, 4, 5, 6]) + >>> from sklearn.naive_bayes import ComplementNB + >>> clf = ComplementNB() + >>> clf.fit(X, y) + ComplementNB() + >>> print(clf.predict(X[2:3])) + [3] + """ + + _parameter_constraints: dict = { + **_BaseDiscreteNB._parameter_constraints, + "norm": ["boolean"], + } + + def __init__( + self, + *, + alpha=1.0, + force_alpha=True, + fit_prior=True, + class_prior=None, + norm=False, + ): + super().__init__( + alpha=alpha, + force_alpha=force_alpha, + fit_prior=fit_prior, + class_prior=class_prior, + ) + self.norm = norm + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.positive_only = True + return tags + + def _count(self, X, Y): + """Count feature occurrences.""" + check_non_negative(X, "ComplementNB (input X)") + self.feature_count_ += safe_sparse_dot(Y.T, X) + self.class_count_ += Y.sum(axis=0) + self.feature_all_ = self.feature_count_.sum(axis=0) + + def _update_feature_log_prob(self, alpha): + """Apply smoothing to raw counts and compute the weights.""" + comp_count = self.feature_all_ + alpha - self.feature_count_ + logged = np.log(comp_count / comp_count.sum(axis=1, keepdims=True)) + # _BaseNB.predict uses argmax, but ComplementNB operates with argmin. + if self.norm: + summed = logged.sum(axis=1, keepdims=True) + feature_log_prob = logged / summed + else: + feature_log_prob = -logged + self.feature_log_prob_ = feature_log_prob + + def _joint_log_likelihood(self, X): + """Calculate the class scores for the samples in X.""" + jll = safe_sparse_dot(X, self.feature_log_prob_.T) + if len(self.classes_) == 1: + jll += self.class_log_prior_ + return jll + + +class BernoulliNB(_BaseDiscreteNB): + """Naive Bayes classifier for multivariate Bernoulli models. + + Like MultinomialNB, this classifier is suitable for discrete data. The + difference is that while MultinomialNB works with occurrence counts, + BernoulliNB is designed for binary/boolean features. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + alpha : float or array-like of shape (n_features,), default=1.0 + Additive (Laplace/Lidstone) smoothing parameter + (set alpha=0 and force_alpha=True, for no smoothing). + + force_alpha : bool, default=True + If False and alpha is less than 1e-10, it will set alpha to + 1e-10. If True, alpha will remain unchanged. This may cause + numerical errors if alpha is too close to 0. + + .. versionadded:: 1.2 + .. versionchanged:: 1.4 + The default value of `force_alpha` changed to `True`. + + binarize : float or None, default=0.0 + Threshold for binarizing (mapping to booleans) of sample features. + If None, input is presumed to already consist of binary vectors. + + fit_prior : bool, default=True + Whether to learn class prior probabilities or not. + If false, a uniform prior will be used. + + class_prior : array-like of shape (n_classes,), default=None + Prior probabilities of the classes. If specified, the priors are not + adjusted according to the data. + + Attributes + ---------- + class_count_ : ndarray of shape (n_classes,) + Number of samples encountered for each class during fitting. This + value is weighted by the sample weight when provided. + + class_log_prior_ : ndarray of shape (n_classes,) + Log probability of each class (smoothed). + + classes_ : ndarray of shape (n_classes,) + Class labels known to the classifier + + feature_count_ : ndarray of shape (n_classes, n_features) + Number of samples encountered for each (class, feature) + during fitting. This value is weighted by the sample weight when + provided. + + feature_log_prob_ : ndarray of shape (n_classes, n_features) + Empirical log probability of features given a class, P(x_i|y). + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + CategoricalNB : Naive Bayes classifier for categorical features. + ComplementNB : The Complement Naive Bayes classifier + described in Rennie et al. (2003). + GaussianNB : Gaussian Naive Bayes (GaussianNB). + MultinomialNB : Naive Bayes classifier for multinomial models. + + References + ---------- + C.D. Manning, P. Raghavan and H. Schuetze (2008). Introduction to + Information Retrieval. Cambridge University Press, pp. 234-265. + https://nlp.stanford.edu/IR-book/html/htmledition/the-bernoulli-model-1.html + + A. McCallum and K. Nigam (1998). A comparison of event models for naive + Bayes text classification. Proc. AAAI/ICML-98 Workshop on Learning for + Text Categorization, pp. 41-48. + + V. Metsis, I. Androutsopoulos and G. Paliouras (2006). Spam filtering with + naive Bayes -- Which naive Bayes? 3rd Conf. on Email and Anti-Spam (CEAS). + + Examples + -------- + >>> import numpy as np + >>> rng = np.random.RandomState(1) + >>> X = rng.randint(5, size=(6, 100)) + >>> Y = np.array([1, 2, 3, 4, 4, 5]) + >>> from sklearn.naive_bayes import BernoulliNB + >>> clf = BernoulliNB() + >>> clf.fit(X, Y) + BernoulliNB() + >>> print(clf.predict(X[2:3])) + [3] + """ + + _parameter_constraints: dict = { + **_BaseDiscreteNB._parameter_constraints, + "binarize": [None, Interval(Real, 0, None, closed="left")], + } + + def __init__( + self, + *, + alpha=1.0, + force_alpha=True, + binarize=0.0, + fit_prior=True, + class_prior=None, + ): + super().__init__( + alpha=alpha, + fit_prior=fit_prior, + class_prior=class_prior, + force_alpha=force_alpha, + ) + self.binarize = binarize + + def _check_X(self, X): + """Validate X, used only in predict* methods.""" + X = super()._check_X(X) + if self.binarize is not None: + X = binarize(X, threshold=self.binarize) + return X + + def _check_X_y(self, X, y, reset=True): + X, y = super()._check_X_y(X, y, reset=reset) + if self.binarize is not None: + X = binarize(X, threshold=self.binarize) + return X, y + + def _count(self, X, Y): + """Count and smooth feature occurrences.""" + self.feature_count_ += safe_sparse_dot(Y.T, X) + self.class_count_ += Y.sum(axis=0) + + def _update_feature_log_prob(self, alpha): + """Apply smoothing to raw counts and recompute log probabilities""" + smoothed_fc = self.feature_count_ + alpha + smoothed_cc = self.class_count_ + alpha * 2 + + self.feature_log_prob_ = np.log(smoothed_fc) - np.log( + smoothed_cc.reshape(-1, 1) + ) + + def _joint_log_likelihood(self, X): + """Calculate the posterior log probability of the samples X""" + n_features = self.feature_log_prob_.shape[1] + n_features_X = X.shape[1] + + if n_features_X != n_features: + raise ValueError( + "Expected input with %d features, got %d instead" + % (n_features, n_features_X) + ) + + neg_prob = np.log(1 - np.exp(self.feature_log_prob_)) + # Compute neg_prob · (1 - X).T as ∑neg_prob - X · neg_prob + jll = safe_sparse_dot(X, (self.feature_log_prob_ - neg_prob).T) + jll += self.class_log_prior_ + neg_prob.sum(axis=1) + + return jll + + +class CategoricalNB(_BaseDiscreteNB): + """Naive Bayes classifier for categorical features. + + The categorical Naive Bayes classifier is suitable for classification with + discrete features that are categorically distributed. The categories of + each feature are drawn from a categorical distribution. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + alpha : float, default=1.0 + Additive (Laplace/Lidstone) smoothing parameter + (set alpha=0 and force_alpha=True, for no smoothing). + + force_alpha : bool, default=True + If False and alpha is less than 1e-10, it will set alpha to + 1e-10. If True, alpha will remain unchanged. This may cause + numerical errors if alpha is too close to 0. + + .. versionadded:: 1.2 + .. versionchanged:: 1.4 + The default value of `force_alpha` changed to `True`. + + fit_prior : bool, default=True + Whether to learn class prior probabilities or not. + If false, a uniform prior will be used. + + class_prior : array-like of shape (n_classes,), default=None + Prior probabilities of the classes. If specified, the priors are not + adjusted according to the data. + + min_categories : int or array-like of shape (n_features,), default=None + Minimum number of categories per feature. + + - integer: Sets the minimum number of categories per feature to + `n_categories` for each features. + - array-like: shape (n_features,) where `n_categories[i]` holds the + minimum number of categories for the ith column of the input. + - None (default): Determines the number of categories automatically + from the training data. + + .. versionadded:: 0.24 + + Attributes + ---------- + category_count_ : list of arrays of shape (n_features,) + Holds arrays of shape (n_classes, n_categories of respective feature) + for each feature. Each array provides the number of samples + encountered for each class and category of the specific feature. + + class_count_ : ndarray of shape (n_classes,) + Number of samples encountered for each class during fitting. This + value is weighted by the sample weight when provided. + + class_log_prior_ : ndarray of shape (n_classes,) + Smoothed empirical log probability for each class. + + classes_ : ndarray of shape (n_classes,) + Class labels known to the classifier + + feature_log_prob_ : list of arrays of shape (n_features,) + Holds arrays of shape (n_classes, n_categories of respective feature) + for each feature. Each array provides the empirical log probability + of categories given the respective feature and class, ``P(x_i|y)``. + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + n_categories_ : ndarray of shape (n_features,), dtype=np.int64 + Number of categories for each feature. This value is + inferred from the data or set by the minimum number of categories. + + .. versionadded:: 0.24 + + See Also + -------- + BernoulliNB : Naive Bayes classifier for multivariate Bernoulli models. + ComplementNB : Complement Naive Bayes classifier. + GaussianNB : Gaussian Naive Bayes. + MultinomialNB : Naive Bayes classifier for multinomial models. + + Examples + -------- + >>> import numpy as np + >>> rng = np.random.RandomState(1) + >>> X = rng.randint(5, size=(6, 100)) + >>> y = np.array([1, 2, 3, 4, 5, 6]) + >>> from sklearn.naive_bayes import CategoricalNB + >>> clf = CategoricalNB() + >>> clf.fit(X, y) + CategoricalNB() + >>> print(clf.predict(X[2:3])) + [3] + """ + + _parameter_constraints: dict = { + **_BaseDiscreteNB._parameter_constraints, + "min_categories": [ + None, + "array-like", + Interval(Integral, 1, None, closed="left"), + ], + "alpha": [Interval(Real, 0, None, closed="left")], + } + + def __init__( + self, + *, + alpha=1.0, + force_alpha=True, + fit_prior=True, + class_prior=None, + min_categories=None, + ): + super().__init__( + alpha=alpha, + force_alpha=force_alpha, + fit_prior=fit_prior, + class_prior=class_prior, + ) + self.min_categories = min_categories + + def fit(self, X, y, sample_weight=None): + """Fit Naive Bayes classifier according to X, y. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Training vectors, where `n_samples` is the number of samples and + `n_features` is the number of features. Here, each feature of X is + assumed to be from a different categorical distribution. + It is further assumed that all categories of each feature are + represented by the numbers 0, ..., n - 1, where n refers to the + total number of categories for the given feature. This can, for + instance, be achieved with the help of OrdinalEncoder. + + y : array-like of shape (n_samples,) + Target values. + + sample_weight : array-like of shape (n_samples,), default=None + Weights applied to individual samples (1. for unweighted). + + Returns + ------- + self : object + Returns the instance itself. + """ + return super().fit(X, y, sample_weight=sample_weight) + + def partial_fit(self, X, y, classes=None, sample_weight=None): + """Incremental fit on a batch of samples. + + This method is expected to be called several times consecutively + on different chunks of a dataset so as to implement out-of-core + or online learning. + + This is especially useful when the whole dataset is too big to fit in + memory at once. + + This method has some performance overhead hence it is better to call + partial_fit on chunks of data that are as large as possible + (as long as fitting in the memory budget) to hide the overhead. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Training vectors, where `n_samples` is the number of samples and + `n_features` is the number of features. Here, each feature of X is + assumed to be from a different categorical distribution. + It is further assumed that all categories of each feature are + represented by the numbers 0, ..., n - 1, where n refers to the + total number of categories for the given feature. This can, for + instance, be achieved with the help of OrdinalEncoder. + + y : array-like of shape (n_samples,) + Target values. + + classes : array-like of shape (n_classes,), default=None + List of all the classes that can possibly appear in the y vector. + + Must be provided at the first call to partial_fit, can be omitted + in subsequent calls. + + sample_weight : array-like of shape (n_samples,), default=None + Weights applied to individual samples (1. for unweighted). + + Returns + ------- + self : object + Returns the instance itself. + """ + return super().partial_fit(X, y, classes, sample_weight=sample_weight) + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.input_tags.categorical = True + tags.input_tags.sparse = False + tags.input_tags.positive_only = True + return tags + + def _check_X(self, X): + """Validate X, used only in predict* methods.""" + X = validate_data( + self, + X, + dtype="int", + accept_sparse=False, + ensure_all_finite=True, + reset=False, + ) + check_non_negative(X, "CategoricalNB (input X)") + return X + + def _check_X_y(self, X, y, reset=True): + X, y = validate_data( + self, + X, + y, + dtype="int", + accept_sparse=False, + ensure_all_finite=True, + reset=reset, + ) + check_non_negative(X, "CategoricalNB (input X)") + return X, y + + def _init_counters(self, n_classes, n_features): + self.class_count_ = np.zeros(n_classes, dtype=np.float64) + self.category_count_ = [np.zeros((n_classes, 0)) for _ in range(n_features)] + + @staticmethod + def _validate_n_categories(X, min_categories): + # rely on max for n_categories categories are encoded between 0...n-1 + n_categories_X = X.max(axis=0) + 1 + min_categories_ = np.array(min_categories) + if min_categories is not None: + if not np.issubdtype(min_categories_.dtype, np.signedinteger): + raise ValueError( + "'min_categories' should have integral type. Got " + f"{min_categories_.dtype} instead." + ) + n_categories_ = np.maximum(n_categories_X, min_categories_, dtype=np.int64) + if n_categories_.shape != n_categories_X.shape: + raise ValueError( + f"'min_categories' should have shape ({X.shape[1]}," + ") when an array-like is provided. Got" + f" {min_categories_.shape} instead." + ) + return n_categories_ + else: + return n_categories_X + + def _count(self, X, Y): + def _update_cat_count_dims(cat_count, highest_feature): + diff = highest_feature + 1 - cat_count.shape[1] + if diff > 0: + # we append a column full of zeros for each new category + return np.pad(cat_count, [(0, 0), (0, diff)], "constant") + return cat_count + + def _update_cat_count(X_feature, Y, cat_count, n_classes): + for j in range(n_classes): + mask = Y[:, j].astype(bool) + if Y.dtype.type == np.int64: + weights = None + else: + weights = Y[mask, j] + counts = np.bincount(X_feature[mask], weights=weights) + indices = np.nonzero(counts)[0] + cat_count[j, indices] += counts[indices] + + self.class_count_ += Y.sum(axis=0) + self.n_categories_ = self._validate_n_categories(X, self.min_categories) + for i in range(self.n_features_in_): + X_feature = X[:, i] + self.category_count_[i] = _update_cat_count_dims( + self.category_count_[i], self.n_categories_[i] - 1 + ) + _update_cat_count( + X_feature, Y, self.category_count_[i], self.class_count_.shape[0] + ) + + def _update_feature_log_prob(self, alpha): + feature_log_prob = [] + for i in range(self.n_features_in_): + smoothed_cat_count = self.category_count_[i] + alpha + smoothed_class_count = smoothed_cat_count.sum(axis=1) + feature_log_prob.append( + np.log(smoothed_cat_count) - np.log(smoothed_class_count.reshape(-1, 1)) + ) + self.feature_log_prob_ = feature_log_prob + + def _joint_log_likelihood(self, X): + _check_n_features(self, X, reset=False) + jll = np.zeros((X.shape[0], self.class_count_.shape[0])) + for i in range(self.n_features_in_): + indices = X[:, i] + jll += self.feature_log_prob_[i][:, indices].T + total_ll = jll + self.class_log_prior_ + return total_ll diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/pipeline.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/pipeline.py new file mode 100644 index 0000000000000000000000000000000000000000..4b843563bdce395b49e9dbb9121ff6c50b9262a8 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/pipeline.py @@ -0,0 +1,2196 @@ +"""Utilities to build a composite estimator as a chain of transforms and estimators.""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from collections import Counter, defaultdict +from contextlib import contextmanager +from copy import deepcopy +from itertools import chain, islice + +import numpy as np +from scipy import sparse + +from .base import TransformerMixin, _fit_context, clone +from .exceptions import NotFittedError +from .preprocessing import FunctionTransformer +from .utils import Bunch +from .utils._metadata_requests import METHODS +from .utils._param_validation import HasMethods, Hidden +from .utils._repr_html.estimator import _VisualBlock +from .utils._set_output import ( + _get_container_adapter, + _safe_set_output, +) +from .utils._tags import get_tags +from .utils._user_interface import _print_elapsed_time +from .utils.metadata_routing import ( + MetadataRouter, + MethodMapping, + _raise_for_params, + _routing_enabled, + get_routing_for_object, + process_routing, +) +from .utils.metaestimators import _BaseComposition, available_if +from .utils.parallel import Parallel, delayed +from .utils.validation import check_is_fitted, check_memory + +__all__ = ["FeatureUnion", "Pipeline", "make_pipeline", "make_union"] + + +@contextmanager +def _raise_or_warn_if_not_fitted(estimator): + """A context manager to make sure a NotFittedError is raised, if a sub-estimator + raises the error. + + Otherwise, we raise a warning if the pipeline is not fitted, with the deprecation. + + TODO(1.8): remove this context manager and replace with check_is_fitted. + """ + try: + yield + except NotFittedError as exc: + raise NotFittedError("Pipeline is not fitted yet.") from exc + + # we only get here if the above didn't raise + try: + check_is_fitted(estimator) + except NotFittedError: + warnings.warn( + "This Pipeline instance is not fitted yet. Call 'fit' with " + "appropriate arguments before using other methods such as transform, " + "predict, etc. This will raise an error in 1.8 instead of the current " + "warning.", + FutureWarning, + ) + + +def _final_estimator_has(attr): + """Check that final_estimator has `attr`. + + Used together with `available_if` in `Pipeline`.""" + + def check(self): + # raise original `AttributeError` if `attr` does not exist + getattr(self._final_estimator, attr) + return True + + return check + + +def _cached_transform( + sub_pipeline, *, cache, param_name, param_value, transform_params +): + """Transform a parameter value using a sub-pipeline and cache the result. + + Parameters + ---------- + sub_pipeline : Pipeline + The sub-pipeline to be used for transformation. + cache : dict + The cache dictionary to store the transformed values. + param_name : str + The name of the parameter to be transformed. + param_value : object + The value of the parameter to be transformed. + transform_params : dict + The metadata to be used for transformation. This passed to the + `transform` method of the sub-pipeline. + + Returns + ------- + transformed_value : object + The transformed value of the parameter. + """ + if param_name not in cache: + # If the parameter is a tuple, transform each element of the + # tuple. This is needed to support the pattern present in + # `lightgbm` and `xgboost` where users can pass multiple + # validation sets. + if isinstance(param_value, tuple): + cache[param_name] = tuple( + sub_pipeline.transform(element, **transform_params) + for element in param_value + ) + else: + cache[param_name] = sub_pipeline.transform(param_value, **transform_params) + + return cache[param_name] + + +class Pipeline(_BaseComposition): + """ + A sequence of data transformers with an optional final predictor. + + `Pipeline` allows you to sequentially apply a list of transformers to + preprocess the data and, if desired, conclude the sequence with a final + :term:`predictor` for predictive modeling. + + Intermediate steps of the pipeline must be transformers, that is, they + must implement `fit` and `transform` methods. + The final :term:`estimator` only needs to implement `fit`. + The transformers in the pipeline can be cached using ``memory`` argument. + + The purpose of the pipeline is to assemble several steps that can be + cross-validated together while setting different parameters. For this, it + enables setting parameters of the various steps using their names and the + parameter name separated by a `'__'`, as in the example below. A step's + estimator may be replaced entirely by setting the parameter with its name + to another estimator, or a transformer removed by setting it to + `'passthrough'` or `None`. + + For an example use case of `Pipeline` combined with + :class:`~sklearn.model_selection.GridSearchCV`, refer to + :ref:`sphx_glr_auto_examples_compose_plot_compare_reduction.py`. The + example :ref:`sphx_glr_auto_examples_compose_plot_digits_pipe.py` shows how + to grid search on a pipeline using `'__'` as a separator in the parameter names. + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.5 + + Parameters + ---------- + steps : list of tuples + List of (name of step, estimator) tuples that are to be chained in + sequential order. To be compatible with the scikit-learn API, all steps + must define `fit`. All non-last steps must also define `transform`. See + :ref:`Combining Estimators ` for more details. + + transform_input : list of str, default=None + The names of the :term:`metadata` parameters that should be transformed by the + pipeline before passing it to the step consuming it. + + This enables transforming some input arguments to ``fit`` (other than ``X``) + to be transformed by the steps of the pipeline up to the step which requires + them. Requirement is defined via :ref:`metadata routing `. + For instance, this can be used to pass a validation set through the pipeline. + + You can only set this if metadata routing is enabled, which you + can enable using ``sklearn.set_config(enable_metadata_routing=True)``. + + .. versionadded:: 1.6 + + memory : str or object with the joblib.Memory interface, default=None + Used to cache the fitted transformers of the pipeline. The last step + will never be cached, even if it is a transformer. By default, no + caching is performed. If a string is given, it is the path to the + caching directory. Enabling caching triggers a clone of the transformers + before fitting. Therefore, the transformer instance given to the + pipeline cannot be inspected directly. Use the attribute ``named_steps`` + or ``steps`` to inspect estimators within the pipeline. Caching the + transformers is advantageous when fitting is time consuming. See + :ref:`sphx_glr_auto_examples_neighbors_plot_caching_nearest_neighbors.py` + for an example on how to enable caching. + + verbose : bool, default=False + If True, the time elapsed while fitting each step will be printed as it + is completed. + + Attributes + ---------- + named_steps : :class:`~sklearn.utils.Bunch` + Dictionary-like object, with the following attributes. + Read-only attribute to access any step parameter by user given name. + Keys are step names and values are steps parameters. + + classes_ : ndarray of shape (n_classes,) + The classes labels. Only exist if the last step of the pipeline is a + classifier. + + n_features_in_ : int + Number of features seen during :term:`fit`. Only defined if the + underlying first estimator in `steps` exposes such an attribute + when fit. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Only defined if the + underlying estimator exposes such an attribute when fit. + + .. versionadded:: 1.0 + + See Also + -------- + make_pipeline : Convenience function for simplified pipeline construction. + + Examples + -------- + >>> from sklearn.svm import SVC + >>> from sklearn.preprocessing import StandardScaler + >>> from sklearn.datasets import make_classification + >>> from sklearn.model_selection import train_test_split + >>> from sklearn.pipeline import Pipeline + >>> X, y = make_classification(random_state=0) + >>> X_train, X_test, y_train, y_test = train_test_split(X, y, + ... random_state=0) + >>> pipe = Pipeline([('scaler', StandardScaler()), ('svc', SVC())]) + >>> # The pipeline can be used as any other estimator + >>> # and avoids leaking the test set into the train set + >>> pipe.fit(X_train, y_train).score(X_test, y_test) + 0.88 + >>> # An estimator's parameter can be set using '__' syntax + >>> pipe.set_params(svc__C=10).fit(X_train, y_train).score(X_test, y_test) + 0.76 + """ + + # BaseEstimator interface + _parameter_constraints: dict = { + "steps": [list, Hidden(tuple)], + "transform_input": [list, None], + "memory": [None, str, HasMethods(["cache"])], + "verbose": ["boolean"], + } + + def __init__(self, steps, *, transform_input=None, memory=None, verbose=False): + self.steps = steps + self.transform_input = transform_input + self.memory = memory + self.verbose = verbose + + def set_output(self, *, transform=None): + """Set the output container when `"transform"` and `"fit_transform"` are called. + + Calling `set_output` will set the output of all estimators in `steps`. + + Parameters + ---------- + transform : {"default", "pandas", "polars"}, default=None + Configure output of `transform` and `fit_transform`. + + - `"default"`: Default output format of a transformer + - `"pandas"`: DataFrame output + - `"polars"`: Polars output + - `None`: Transform configuration is unchanged + + .. versionadded:: 1.4 + `"polars"` option was added. + + Returns + ------- + self : estimator instance + Estimator instance. + """ + for _, _, step in self._iter(): + _safe_set_output(step, transform=transform) + return self + + def get_params(self, deep=True): + """Get parameters for this estimator. + + Returns the parameters given in the constructor as well as the + estimators contained within the `steps` of the `Pipeline`. + + Parameters + ---------- + deep : bool, default=True + If True, will return the parameters for this estimator and + contained subobjects that are estimators. + + Returns + ------- + params : mapping of string to any + Parameter names mapped to their values. + """ + return self._get_params("steps", deep=deep) + + def set_params(self, **kwargs): + """Set the parameters of this estimator. + + Valid parameter keys can be listed with ``get_params()``. Note that + you can directly set the parameters of the estimators contained in + `steps`. + + Parameters + ---------- + **kwargs : dict + Parameters of this estimator or parameters of estimators contained + in `steps`. Parameters of the steps may be set using its name and + the parameter name separated by a '__'. + + Returns + ------- + self : object + Pipeline class instance. + """ + self._set_params("steps", **kwargs) + return self + + def _validate_steps(self): + if not self.steps: + raise ValueError("The pipeline is empty. Please add steps.") + names, estimators = zip(*self.steps) + + # validate names + self._validate_names(names) + + # validate estimators + transformers = estimators[:-1] + estimator = estimators[-1] + + for t in transformers: + if t is None or t == "passthrough": + continue + if not (hasattr(t, "fit") or hasattr(t, "fit_transform")) or not hasattr( + t, "transform" + ): + raise TypeError( + "All intermediate steps should be " + "transformers and implement fit and transform " + "or be the string 'passthrough' " + "'%s' (type %s) doesn't" % (t, type(t)) + ) + + # We allow last estimator to be None as an identity transformation + if ( + estimator is not None + and estimator != "passthrough" + and not hasattr(estimator, "fit") + ): + raise TypeError( + "Last step of Pipeline should implement fit " + "or be the string 'passthrough'. " + "'%s' (type %s) doesn't" % (estimator, type(estimator)) + ) + + def _iter(self, with_final=True, filter_passthrough=True): + """ + Generate (idx, (name, trans)) tuples from self.steps + + When filter_passthrough is True, 'passthrough' and None transformers + are filtered out. + """ + stop = len(self.steps) + if not with_final: + stop -= 1 + + for idx, (name, trans) in enumerate(islice(self.steps, 0, stop)): + if not filter_passthrough: + yield idx, name, trans + elif trans is not None and trans != "passthrough": + yield idx, name, trans + + def __len__(self): + """ + Returns the length of the Pipeline + """ + return len(self.steps) + + def __getitem__(self, ind): + """Returns a sub-pipeline or a single estimator in the pipeline + + Indexing with an integer will return an estimator; using a slice + returns another Pipeline instance which copies a slice of this + Pipeline. This copy is shallow: modifying (or fitting) estimators in + the sub-pipeline will affect the larger pipeline and vice-versa. + However, replacing a value in `step` will not affect a copy. + + See + :ref:`sphx_glr_auto_examples_feature_selection_plot_feature_selection_pipeline.py` + for an example of how to use slicing to inspect part of a pipeline. + """ + if isinstance(ind, slice): + if ind.step not in (1, None): + raise ValueError("Pipeline slicing only supports a step of 1") + return self.__class__( + self.steps[ind], memory=self.memory, verbose=self.verbose + ) + try: + name, est = self.steps[ind] + except TypeError: + # Not an int, try get step by name + return self.named_steps[ind] + return est + + # TODO(1.8): Remove this property + @property + def _estimator_type(self): + """Return the estimator type of the last step in the pipeline.""" + + if not self.steps: + return None + + return self.steps[-1][1]._estimator_type + + @property + def named_steps(self): + """Access the steps by name. + + Read-only attribute to access any step by given name. + Keys are steps names and values are the steps objects.""" + # Use Bunch object to improve autocomplete + return Bunch(**dict(self.steps)) + + @property + def _final_estimator(self): + try: + estimator = self.steps[-1][1] + return "passthrough" if estimator is None else estimator + except (ValueError, AttributeError, TypeError): + # This condition happens when a call to a method is first calling + # `_available_if` and `fit` did not validate `steps` yet. We + # return `None` and an `InvalidParameterError` will be raised + # right after. + return None + + def _log_message(self, step_idx): + if not self.verbose: + return None + name, _ = self.steps[step_idx] + + return "(step %d of %d) Processing %s" % (step_idx + 1, len(self.steps), name) + + def _check_method_params(self, method, props, **kwargs): + if _routing_enabled(): + routed_params = process_routing(self, method, **props, **kwargs) + return routed_params + else: + fit_params_steps = Bunch( + **{ + name: Bunch(**{method: {} for method in METHODS}) + for name, step in self.steps + if step is not None + } + ) + for pname, pval in props.items(): + if "__" not in pname: + raise ValueError( + "Pipeline.fit does not accept the {} parameter. " + "You can pass parameters to specific steps of your " + "pipeline using the stepname__parameter format, e.g. " + "`Pipeline.fit(X, y, logisticregression__sample_weight" + "=sample_weight)`.".format(pname) + ) + step, param = pname.split("__", 1) + fit_params_steps[step]["fit"][param] = pval + # without metadata routing, fit_transform and fit_predict + # get all the same params and pass it to the last fit. + fit_params_steps[step]["fit_transform"][param] = pval + fit_params_steps[step]["fit_predict"][param] = pval + return fit_params_steps + + def _get_metadata_for_step(self, *, step_idx, step_params, all_params): + """Get params (metadata) for step `name`. + + This transforms the metadata up to this step if required, which is + indicated by the `transform_input` parameter. + + If a param in `step_params` is included in the `transform_input` list, + it will be transformed. + + Parameters + ---------- + step_idx : int + Index of the step in the pipeline. + + step_params : dict + Parameters specific to the step. These are routed parameters, e.g. + `routed_params[name]`. If a parameter name here is included in the + `pipeline.transform_input`, then it will be transformed. Note that + these parameters are *after* routing, so the aliases are already + resolved. + + all_params : dict + All parameters passed by the user. Here this is used to call + `transform` on the slice of the pipeline itself. + + Returns + ------- + dict + Parameters to be passed to the step. The ones which should be + transformed are transformed. + """ + if ( + self.transform_input is None + or not all_params + or not step_params + or step_idx == 0 + ): + # we only need to process step_params if transform_input is set + # and metadata is given by the user. + return step_params + + sub_pipeline = self[:step_idx] + sub_metadata_routing = get_routing_for_object(sub_pipeline) + # here we get the metadata required by sub_pipeline.transform + transform_params = { + key: value + for key, value in all_params.items() + if key + in sub_metadata_routing.consumes( + method="transform", params=all_params.keys() + ) + } + transformed_params = dict() # this is to be returned + transformed_cache = dict() # used to transform each param once + # `step_params` is the output of `process_routing`, so it has a dict for each + # method (e.g. fit, transform, predict), which are the args to be passed to + # those methods. We need to transform the parameters which are in the + # `transform_input`, before returning these dicts. + for method, method_params in step_params.items(): + transformed_params[method] = Bunch() + for param_name, param_value in method_params.items(): + # An example of `(param_name, param_value)` is + # `('sample_weight', array([0.5, 0.5, ...]))` + if param_name in self.transform_input: + # This parameter now needs to be transformed by the sub_pipeline, to + # this step. We cache these computations to avoid repeating them. + transformed_params[method][param_name] = _cached_transform( + sub_pipeline, + cache=transformed_cache, + param_name=param_name, + param_value=param_value, + transform_params=transform_params, + ) + else: + transformed_params[method][param_name] = param_value + return transformed_params + + # Estimator interface + + def _fit(self, X, y=None, routed_params=None, raw_params=None): + """Fit the pipeline except the last step. + + routed_params is the output of `process_routing` + raw_params is the parameters passed by the user, used when `transform_input` + is set by the user, to transform metadata using a sub-pipeline. + """ + # shallow copy of steps - this should really be steps_ + self.steps = list(self.steps) + self._validate_steps() + # Setup the memory + memory = check_memory(self.memory) + + fit_transform_one_cached = memory.cache(_fit_transform_one) + + for step_idx, name, transformer in self._iter( + with_final=False, filter_passthrough=False + ): + if transformer is None or transformer == "passthrough": + with _print_elapsed_time("Pipeline", self._log_message(step_idx)): + continue + + if hasattr(memory, "location") and memory.location is None: + # we do not clone when caching is disabled to + # preserve backward compatibility + cloned_transformer = transformer + else: + cloned_transformer = clone(transformer) + # Fit or load from cache the current transformer + step_params = self._get_metadata_for_step( + step_idx=step_idx, + step_params=routed_params[name], + all_params=raw_params, + ) + + X, fitted_transformer = fit_transform_one_cached( + cloned_transformer, + X, + y, + weight=None, + message_clsname="Pipeline", + message=self._log_message(step_idx), + params=step_params, + ) + # Replace the transformer of the step with the fitted + # transformer. This is necessary when loading the transformer + # from the cache. + self.steps[step_idx] = (name, fitted_transformer) + return X + + @_fit_context( + # estimators in Pipeline.steps are not validated yet + prefer_skip_nested_validation=False + ) + def fit(self, X, y=None, **params): + """Fit the model. + + Fit all the transformers one after the other and sequentially transform the + data. Finally, fit the transformed data using the final estimator. + + Parameters + ---------- + X : iterable + Training data. Must fulfill input requirements of first step of the + pipeline. + + y : iterable, default=None + Training targets. Must fulfill label requirements for all steps of + the pipeline. + + **params : dict of str -> object + - If `enable_metadata_routing=False` (default): Parameters passed to the + ``fit`` method of each step, where each parameter name is prefixed such + that parameter ``p`` for step ``s`` has key ``s__p``. + + - If `enable_metadata_routing=True`: Parameters requested and accepted by + steps. Each step must have requested certain metadata for these parameters + to be forwarded to them. + + .. versionchanged:: 1.4 + Parameters are now passed to the ``transform`` method of the + intermediate steps as well, if requested, and if + `enable_metadata_routing=True` is set via + :func:`~sklearn.set_config`. + + See :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + self : object + Pipeline with fitted steps. + """ + if not _routing_enabled() and self.transform_input is not None: + raise ValueError( + "The `transform_input` parameter can only be set if metadata " + "routing is enabled. You can enable metadata routing using " + "`sklearn.set_config(enable_metadata_routing=True)`." + ) + + routed_params = self._check_method_params(method="fit", props=params) + Xt = self._fit(X, y, routed_params, raw_params=params) + with _print_elapsed_time("Pipeline", self._log_message(len(self.steps) - 1)): + if self._final_estimator != "passthrough": + last_step_params = self._get_metadata_for_step( + step_idx=len(self) - 1, + step_params=routed_params[self.steps[-1][0]], + all_params=params, + ) + self._final_estimator.fit(Xt, y, **last_step_params["fit"]) + + return self + + def _can_fit_transform(self): + return ( + self._final_estimator == "passthrough" + or hasattr(self._final_estimator, "transform") + or hasattr(self._final_estimator, "fit_transform") + ) + + @available_if(_can_fit_transform) + @_fit_context( + # estimators in Pipeline.steps are not validated yet + prefer_skip_nested_validation=False + ) + def fit_transform(self, X, y=None, **params): + """Fit the model and transform with the final estimator. + + Fit all the transformers one after the other and sequentially transform + the data. Only valid if the final estimator either implements + `fit_transform` or `fit` and `transform`. + + Parameters + ---------- + X : iterable + Training data. Must fulfill input requirements of first step of the + pipeline. + + y : iterable, default=None + Training targets. Must fulfill label requirements for all steps of + the pipeline. + + **params : dict of str -> object + - If `enable_metadata_routing=False` (default): Parameters passed to the + ``fit`` method of each step, where each parameter name is prefixed such + that parameter ``p`` for step ``s`` has key ``s__p``. + + - If `enable_metadata_routing=True`: Parameters requested and accepted by + steps. Each step must have requested certain metadata for these parameters + to be forwarded to them. + + .. versionchanged:: 1.4 + Parameters are now passed to the ``transform`` method of the + intermediate steps as well, if requested, and if + `enable_metadata_routing=True`. + + See :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + Xt : ndarray of shape (n_samples, n_transformed_features) + Transformed samples. + """ + routed_params = self._check_method_params(method="fit_transform", props=params) + Xt = self._fit(X, y, routed_params) + + last_step = self._final_estimator + with _print_elapsed_time("Pipeline", self._log_message(len(self.steps) - 1)): + if last_step == "passthrough": + return Xt + last_step_params = self._get_metadata_for_step( + step_idx=len(self) - 1, + step_params=routed_params[self.steps[-1][0]], + all_params=params, + ) + if hasattr(last_step, "fit_transform"): + return last_step.fit_transform( + Xt, y, **last_step_params["fit_transform"] + ) + else: + return last_step.fit(Xt, y, **last_step_params["fit"]).transform( + Xt, **last_step_params["transform"] + ) + + @available_if(_final_estimator_has("predict")) + def predict(self, X, **params): + """Transform the data, and apply `predict` with the final estimator. + + Call `transform` of each transformer in the pipeline. The transformed + data are finally passed to the final estimator that calls `predict` + method. Only valid if the final estimator implements `predict`. + + Parameters + ---------- + X : iterable + Data to predict on. Must fulfill input requirements of first step + of the pipeline. + + **params : dict of str -> object + - If `enable_metadata_routing=False` (default): Parameters to the + ``predict`` called at the end of all transformations in the pipeline. + + - If `enable_metadata_routing=True`: Parameters requested and accepted by + steps. Each step must have requested certain metadata for these parameters + to be forwarded to them. + + .. versionadded:: 0.20 + + .. versionchanged:: 1.4 + Parameters are now passed to the ``transform`` method of the + intermediate steps as well, if requested, and if + `enable_metadata_routing=True` is set via + :func:`~sklearn.set_config`. + + See :ref:`Metadata Routing User Guide ` for more + details. + + Note that while this may be used to return uncertainties from some + models with ``return_std`` or ``return_cov``, uncertainties that are + generated by the transformations in the pipeline are not propagated + to the final estimator. + + Returns + ------- + y_pred : ndarray + Result of calling `predict` on the final estimator. + """ + # TODO(1.8): Remove the context manager and use check_is_fitted(self) + with _raise_or_warn_if_not_fitted(self): + Xt = X + + if not _routing_enabled(): + for _, name, transform in self._iter(with_final=False): + Xt = transform.transform(Xt) + return self.steps[-1][1].predict(Xt, **params) + + # metadata routing enabled + routed_params = process_routing(self, "predict", **params) + for _, name, transform in self._iter(with_final=False): + Xt = transform.transform(Xt, **routed_params[name].transform) + return self.steps[-1][1].predict( + Xt, **routed_params[self.steps[-1][0]].predict + ) + + @available_if(_final_estimator_has("fit_predict")) + @_fit_context( + # estimators in Pipeline.steps are not validated yet + prefer_skip_nested_validation=False + ) + def fit_predict(self, X, y=None, **params): + """Transform the data, and apply `fit_predict` with the final estimator. + + Call `fit_transform` of each transformer in the pipeline. The + transformed data are finally passed to the final estimator that calls + `fit_predict` method. Only valid if the final estimator implements + `fit_predict`. + + Parameters + ---------- + X : iterable + Training data. Must fulfill input requirements of first step of + the pipeline. + + y : iterable, default=None + Training targets. Must fulfill label requirements for all steps + of the pipeline. + + **params : dict of str -> object + - If `enable_metadata_routing=False` (default): Parameters to the + ``predict`` called at the end of all transformations in the pipeline. + + - If `enable_metadata_routing=True`: Parameters requested and accepted by + steps. Each step must have requested certain metadata for these parameters + to be forwarded to them. + + .. versionadded:: 0.20 + + .. versionchanged:: 1.4 + Parameters are now passed to the ``transform`` method of the + intermediate steps as well, if requested, and if + `enable_metadata_routing=True`. + + See :ref:`Metadata Routing User Guide ` for more + details. + + Note that while this may be used to return uncertainties from some + models with ``return_std`` or ``return_cov``, uncertainties that are + generated by the transformations in the pipeline are not propagated + to the final estimator. + + Returns + ------- + y_pred : ndarray + Result of calling `fit_predict` on the final estimator. + """ + routed_params = self._check_method_params(method="fit_predict", props=params) + Xt = self._fit(X, y, routed_params) + + params_last_step = routed_params[self.steps[-1][0]] + with _print_elapsed_time("Pipeline", self._log_message(len(self.steps) - 1)): + y_pred = self.steps[-1][1].fit_predict( + Xt, y, **params_last_step.get("fit_predict", {}) + ) + return y_pred + + @available_if(_final_estimator_has("predict_proba")) + def predict_proba(self, X, **params): + """Transform the data, and apply `predict_proba` with the final estimator. + + Call `transform` of each transformer in the pipeline. The transformed + data are finally passed to the final estimator that calls + `predict_proba` method. Only valid if the final estimator implements + `predict_proba`. + + Parameters + ---------- + X : iterable + Data to predict on. Must fulfill input requirements of first step + of the pipeline. + + **params : dict of str -> object + - If `enable_metadata_routing=False` (default): Parameters to the + `predict_proba` called at the end of all transformations in the pipeline. + + - If `enable_metadata_routing=True`: Parameters requested and accepted by + steps. Each step must have requested certain metadata for these parameters + to be forwarded to them. + + .. versionadded:: 0.20 + + .. versionchanged:: 1.4 + Parameters are now passed to the ``transform`` method of the + intermediate steps as well, if requested, and if + `enable_metadata_routing=True`. + + See :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + y_proba : ndarray of shape (n_samples, n_classes) + Result of calling `predict_proba` on the final estimator. + """ + # TODO(1.8): Remove the context manager and use check_is_fitted(self) + with _raise_or_warn_if_not_fitted(self): + Xt = X + + if not _routing_enabled(): + for _, name, transform in self._iter(with_final=False): + Xt = transform.transform(Xt) + return self.steps[-1][1].predict_proba(Xt, **params) + + # metadata routing enabled + routed_params = process_routing(self, "predict_proba", **params) + for _, name, transform in self._iter(with_final=False): + Xt = transform.transform(Xt, **routed_params[name].transform) + return self.steps[-1][1].predict_proba( + Xt, **routed_params[self.steps[-1][0]].predict_proba + ) + + @available_if(_final_estimator_has("decision_function")) + def decision_function(self, X, **params): + """Transform the data, and apply `decision_function` with the final estimator. + + Call `transform` of each transformer in the pipeline. The transformed + data are finally passed to the final estimator that calls + `decision_function` method. Only valid if the final estimator + implements `decision_function`. + + Parameters + ---------- + X : iterable + Data to predict on. Must fulfill input requirements of first step + of the pipeline. + + **params : dict of string -> object + Parameters requested and accepted by steps. Each step must have + requested certain metadata for these parameters to be forwarded to + them. + + .. versionadded:: 1.4 + Only available if `enable_metadata_routing=True`. See + :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + y_score : ndarray of shape (n_samples, n_classes) + Result of calling `decision_function` on the final estimator. + """ + # TODO(1.8): Remove the context manager and use check_is_fitted(self) + with _raise_or_warn_if_not_fitted(self): + _raise_for_params(params, self, "decision_function") + + # not branching here since params is only available if + # enable_metadata_routing=True + routed_params = process_routing(self, "decision_function", **params) + + Xt = X + for _, name, transform in self._iter(with_final=False): + Xt = transform.transform( + Xt, **routed_params.get(name, {}).get("transform", {}) + ) + return self.steps[-1][1].decision_function( + Xt, + **routed_params.get(self.steps[-1][0], {}).get("decision_function", {}), + ) + + @available_if(_final_estimator_has("score_samples")) + def score_samples(self, X): + """Transform the data, and apply `score_samples` with the final estimator. + + Call `transform` of each transformer in the pipeline. The transformed + data are finally passed to the final estimator that calls + `score_samples` method. Only valid if the final estimator implements + `score_samples`. + + Parameters + ---------- + X : iterable + Data to predict on. Must fulfill input requirements of first step + of the pipeline. + + Returns + ------- + y_score : ndarray of shape (n_samples,) + Result of calling `score_samples` on the final estimator. + """ + # TODO(1.8): Remove the context manager and use check_is_fitted(self) + with _raise_or_warn_if_not_fitted(self): + Xt = X + for _, _, transformer in self._iter(with_final=False): + Xt = transformer.transform(Xt) + return self.steps[-1][1].score_samples(Xt) + + @available_if(_final_estimator_has("predict_log_proba")) + def predict_log_proba(self, X, **params): + """Transform the data, and apply `predict_log_proba` with the final estimator. + + Call `transform` of each transformer in the pipeline. The transformed + data are finally passed to the final estimator that calls + `predict_log_proba` method. Only valid if the final estimator + implements `predict_log_proba`. + + Parameters + ---------- + X : iterable + Data to predict on. Must fulfill input requirements of first step + of the pipeline. + + **params : dict of str -> object + - If `enable_metadata_routing=False` (default): Parameters to the + `predict_log_proba` called at the end of all transformations in the + pipeline. + + - If `enable_metadata_routing=True`: Parameters requested and accepted by + steps. Each step must have requested certain metadata for these parameters + to be forwarded to them. + + .. versionadded:: 0.20 + + .. versionchanged:: 1.4 + Parameters are now passed to the ``transform`` method of the + intermediate steps as well, if requested, and if + `enable_metadata_routing=True`. + + See :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + y_log_proba : ndarray of shape (n_samples, n_classes) + Result of calling `predict_log_proba` on the final estimator. + """ + # TODO(1.8): Remove the context manager and use check_is_fitted(self) + with _raise_or_warn_if_not_fitted(self): + Xt = X + + if not _routing_enabled(): + for _, name, transform in self._iter(with_final=False): + Xt = transform.transform(Xt) + return self.steps[-1][1].predict_log_proba(Xt, **params) + + # metadata routing enabled + routed_params = process_routing(self, "predict_log_proba", **params) + for _, name, transform in self._iter(with_final=False): + Xt = transform.transform(Xt, **routed_params[name].transform) + return self.steps[-1][1].predict_log_proba( + Xt, **routed_params[self.steps[-1][0]].predict_log_proba + ) + + def _can_transform(self): + return self._final_estimator == "passthrough" or hasattr( + self._final_estimator, "transform" + ) + + @available_if(_can_transform) + def transform(self, X, **params): + """Transform the data, and apply `transform` with the final estimator. + + Call `transform` of each transformer in the pipeline. The transformed + data are finally passed to the final estimator that calls + `transform` method. Only valid if the final estimator + implements `transform`. + + This also works where final estimator is `None` in which case all prior + transformations are applied. + + Parameters + ---------- + X : iterable + Data to transform. Must fulfill input requirements of first step + of the pipeline. + + **params : dict of str -> object + Parameters requested and accepted by steps. Each step must have + requested certain metadata for these parameters to be forwarded to + them. + + .. versionadded:: 1.4 + Only available if `enable_metadata_routing=True`. See + :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + Xt : ndarray of shape (n_samples, n_transformed_features) + Transformed data. + """ + # TODO(1.8): Remove the context manager and use check_is_fitted(self) + with _raise_or_warn_if_not_fitted(self): + _raise_for_params(params, self, "transform") + + # not branching here since params is only available if + # enable_metadata_routing=True + routed_params = process_routing(self, "transform", **params) + Xt = X + for _, name, transform in self._iter(): + Xt = transform.transform(Xt, **routed_params[name].transform) + return Xt + + def _can_inverse_transform(self): + return all(hasattr(t, "inverse_transform") for _, _, t in self._iter()) + + @available_if(_can_inverse_transform) + def inverse_transform(self, X, **params): + """Apply `inverse_transform` for each step in a reverse order. + + All estimators in the pipeline must support `inverse_transform`. + + Parameters + ---------- + X : array-like of shape (n_samples, n_transformed_features) + Data samples, where ``n_samples`` is the number of samples and + ``n_features`` is the number of features. Must fulfill + input requirements of last step of pipeline's + ``inverse_transform`` method. + + **params : dict of str -> object + Parameters requested and accepted by steps. Each step must have + requested certain metadata for these parameters to be forwarded to + them. + + .. versionadded:: 1.4 + Only available if `enable_metadata_routing=True`. See + :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + X_original : ndarray of shape (n_samples, n_features) + Inverse transformed data, that is, data in the original feature + space. + """ + # TODO(1.8): Remove the context manager and use check_is_fitted(self) + with _raise_or_warn_if_not_fitted(self): + _raise_for_params(params, self, "inverse_transform") + + # we don't have to branch here, since params is only non-empty if + # enable_metadata_routing=True. + routed_params = process_routing(self, "inverse_transform", **params) + reverse_iter = reversed(list(self._iter())) + for _, name, transform in reverse_iter: + X = transform.inverse_transform( + X, **routed_params[name].inverse_transform + ) + return X + + @available_if(_final_estimator_has("score")) + def score(self, X, y=None, sample_weight=None, **params): + """Transform the data, and apply `score` with the final estimator. + + Call `transform` of each transformer in the pipeline. The transformed + data are finally passed to the final estimator that calls + `score` method. Only valid if the final estimator implements `score`. + + Parameters + ---------- + X : iterable + Data to predict on. Must fulfill input requirements of first step + of the pipeline. + + y : iterable, default=None + Targets used for scoring. Must fulfill label requirements for all + steps of the pipeline. + + sample_weight : array-like, default=None + If not None, this argument is passed as ``sample_weight`` keyword + argument to the ``score`` method of the final estimator. + + **params : dict of str -> object + Parameters requested and accepted by steps. Each step must have + requested certain metadata for these parameters to be forwarded to + them. + + .. versionadded:: 1.4 + Only available if `enable_metadata_routing=True`. See + :ref:`Metadata Routing User Guide ` for more + details. + + Returns + ------- + score : float + Result of calling `score` on the final estimator. + """ + # TODO(1.8): Remove the context manager and use check_is_fitted(self) + with _raise_or_warn_if_not_fitted(self): + Xt = X + if not _routing_enabled(): + for _, name, transform in self._iter(with_final=False): + Xt = transform.transform(Xt) + score_params = {} + if sample_weight is not None: + score_params["sample_weight"] = sample_weight + return self.steps[-1][1].score(Xt, y, **score_params) + + # metadata routing is enabled. + routed_params = process_routing( + self, "score", sample_weight=sample_weight, **params + ) + + Xt = X + for _, name, transform in self._iter(with_final=False): + Xt = transform.transform(Xt, **routed_params[name].transform) + return self.steps[-1][1].score( + Xt, y, **routed_params[self.steps[-1][0]].score + ) + + @property + def classes_(self): + """The classes labels. Only exist if the last step is a classifier.""" + return self.steps[-1][1].classes_ + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + + if not self.steps: + return tags + + try: + if self.steps[0][1] is not None and self.steps[0][1] != "passthrough": + tags.input_tags.pairwise = get_tags( + self.steps[0][1] + ).input_tags.pairwise + # WARNING: the sparse tag can be incorrect. + # Some Pipelines accepting sparse data are wrongly tagged sparse=False. + # For example Pipeline([PCA(), estimator]) accepts sparse data + # even if the estimator doesn't as PCA outputs a dense array. + tags.input_tags.sparse = all( + get_tags(step).input_tags.sparse + for name, step in self.steps + if step is not None and step != "passthrough" + ) + except (ValueError, AttributeError, TypeError): + # This happens when the `steps` is not a list of (name, estimator) + # tuples and `fit` is not called yet to validate the steps. + pass + + try: + if self.steps[-1][1] is not None and self.steps[-1][1] != "passthrough": + last_step_tags = get_tags(self.steps[-1][1]) + tags.estimator_type = last_step_tags.estimator_type + tags.target_tags.multi_output = last_step_tags.target_tags.multi_output + tags.classifier_tags = deepcopy(last_step_tags.classifier_tags) + tags.regressor_tags = deepcopy(last_step_tags.regressor_tags) + tags.transformer_tags = deepcopy(last_step_tags.transformer_tags) + except (ValueError, AttributeError, TypeError): + # This happens when the `steps` is not a list of (name, estimator) + # tuples and `fit` is not called yet to validate the steps. + pass + + return tags + + def get_feature_names_out(self, input_features=None): + """Get output feature names for transformation. + + Transform input features using the pipeline. + + Parameters + ---------- + input_features : array-like of str or None, default=None + Input features. + + Returns + ------- + feature_names_out : ndarray of str objects + Transformed feature names. + """ + feature_names_out = input_features + for _, name, transform in self._iter(): + if not hasattr(transform, "get_feature_names_out"): + raise AttributeError( + "Estimator {} does not provide get_feature_names_out. " + "Did you mean to call pipeline[:-1].get_feature_names_out" + "()?".format(name) + ) + feature_names_out = transform.get_feature_names_out(feature_names_out) + return feature_names_out + + @property + def n_features_in_(self): + """Number of features seen during first step `fit` method.""" + # delegate to first step (which will call check_is_fitted) + return self.steps[0][1].n_features_in_ + + @property + def feature_names_in_(self): + """Names of features seen during first step `fit` method.""" + # delegate to first step (which will call check_is_fitted) + return self.steps[0][1].feature_names_in_ + + def __sklearn_is_fitted__(self): + """Indicate whether pipeline has been fit. + + This is done by checking whether the last non-`passthrough` step of the + pipeline is fitted. + + An empty pipeline is considered fitted. + """ + # First find the last step that is not 'passthrough' + last_step = None + for _, estimator in reversed(self.steps): + if estimator != "passthrough": + last_step = estimator + break + + if last_step is None: + # All steps are 'passthrough', so the pipeline is considered fitted + return True + + try: + # check if the last step of the pipeline is fitted + # we only check the last step since if the last step is fit, it + # means the previous steps should also be fit. This is faster than + # checking if every step of the pipeline is fit. + check_is_fitted(last_step) + return True + except NotFittedError: + return False + + def _sk_visual_block_(self): + _, estimators = zip(*self.steps) + + def _get_name(name, est): + if est is None or est == "passthrough": + return f"{name}: passthrough" + # Is an estimator + return f"{name}: {est.__class__.__name__}" + + names = [_get_name(name, est) for name, est in self.steps] + name_details = [str(est) for est in estimators] + return _VisualBlock( + "serial", + estimators, + names=names, + name_details=name_details, + dash_wrapped=False, + ) + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + router = MetadataRouter(owner=self.__class__.__name__) + + # first we add all steps except the last one + for _, name, trans in self._iter(with_final=False, filter_passthrough=True): + method_mapping = MethodMapping() + # fit, fit_predict, and fit_transform call fit_transform if it + # exists, or else fit and transform + if hasattr(trans, "fit_transform"): + ( + method_mapping.add(caller="fit", callee="fit_transform") + .add(caller="fit_transform", callee="fit_transform") + .add(caller="fit_predict", callee="fit_transform") + ) + else: + ( + method_mapping.add(caller="fit", callee="fit") + .add(caller="fit", callee="transform") + .add(caller="fit_transform", callee="fit") + .add(caller="fit_transform", callee="transform") + .add(caller="fit_predict", callee="fit") + .add(caller="fit_predict", callee="transform") + ) + + ( + method_mapping.add(caller="predict", callee="transform") + .add(caller="predict", callee="transform") + .add(caller="predict_proba", callee="transform") + .add(caller="decision_function", callee="transform") + .add(caller="predict_log_proba", callee="transform") + .add(caller="transform", callee="transform") + .add(caller="inverse_transform", callee="inverse_transform") + .add(caller="score", callee="transform") + ) + + router.add(method_mapping=method_mapping, **{name: trans}) + + final_name, final_est = self.steps[-1] + if final_est is None or final_est == "passthrough": + return router + + # then we add the last step + method_mapping = MethodMapping() + if hasattr(final_est, "fit_transform"): + method_mapping.add(caller="fit_transform", callee="fit_transform") + else: + method_mapping.add(caller="fit", callee="fit").add( + caller="fit", callee="transform" + ) + ( + method_mapping.add(caller="fit", callee="fit") + .add(caller="predict", callee="predict") + .add(caller="fit_predict", callee="fit_predict") + .add(caller="predict_proba", callee="predict_proba") + .add(caller="decision_function", callee="decision_function") + .add(caller="predict_log_proba", callee="predict_log_proba") + .add(caller="transform", callee="transform") + .add(caller="inverse_transform", callee="inverse_transform") + .add(caller="score", callee="score") + ) + + router.add(method_mapping=method_mapping, **{final_name: final_est}) + return router + + +def _name_estimators(estimators): + """Generate names for estimators.""" + + names = [ + estimator if isinstance(estimator, str) else type(estimator).__name__.lower() + for estimator in estimators + ] + namecount = defaultdict(int) + for est, name in zip(estimators, names): + namecount[name] += 1 + + for k, v in list(namecount.items()): + if v == 1: + del namecount[k] + + for i in reversed(range(len(estimators))): + name = names[i] + if name in namecount: + names[i] += "-%d" % namecount[name] + namecount[name] -= 1 + + return list(zip(names, estimators)) + + +def make_pipeline(*steps, memory=None, transform_input=None, verbose=False): + """Construct a :class:`Pipeline` from the given estimators. + + This is a shorthand for the :class:`Pipeline` constructor; it does not + require, and does not permit, naming the estimators. Instead, their names + will be set to the lowercase of their types automatically. + + Parameters + ---------- + *steps : list of Estimator objects + List of the scikit-learn estimators that are chained together. + + memory : str or object with the joblib.Memory interface, default=None + Used to cache the fitted transformers of the pipeline. The last step + will never be cached, even if it is a transformer. By default, no + caching is performed. If a string is given, it is the path to the + caching directory. Enabling caching triggers a clone of the transformers + before fitting. Therefore, the transformer instance given to the + pipeline cannot be inspected directly. Use the attribute ``named_steps`` + or ``steps`` to inspect estimators within the pipeline. Caching the + transformers is advantageous when fitting is time consuming. + + transform_input : list of str, default=None + This enables transforming some input arguments to ``fit`` (other than ``X``) + to be transformed by the steps of the pipeline up to the step which requires + them. Requirement is defined via :ref:`metadata routing `. + This can be used to pass a validation set through the pipeline for instance. + + You can only set this if metadata routing is enabled, which you + can enable using ``sklearn.set_config(enable_metadata_routing=True)``. + + .. versionadded:: 1.6 + + verbose : bool, default=False + If True, the time elapsed while fitting each step will be printed as it + is completed. + + Returns + ------- + p : Pipeline + Returns a scikit-learn :class:`Pipeline` object. + + See Also + -------- + Pipeline : Class for creating a pipeline of transforms with a final + estimator. + + Examples + -------- + >>> from sklearn.naive_bayes import GaussianNB + >>> from sklearn.preprocessing import StandardScaler + >>> from sklearn.pipeline import make_pipeline + >>> make_pipeline(StandardScaler(), GaussianNB(priors=None)) + Pipeline(steps=[('standardscaler', StandardScaler()), + ('gaussiannb', GaussianNB())]) + """ + return Pipeline( + _name_estimators(steps), + transform_input=transform_input, + memory=memory, + verbose=verbose, + ) + + +def _transform_one(transformer, X, y, weight, params): + """Call transform and apply weight to output. + + Parameters + ---------- + transformer : estimator + Estimator to be used for transformation. + + X : {array-like, sparse matrix} of shape (n_samples, n_features) + Input data to be transformed. + + y : ndarray of shape (n_samples,) + Ignored. + + weight : float + Weight to be applied to the output of the transformation. + + params : dict + Parameters to be passed to the transformer's ``transform`` method. + + This should be of the form ``process_routing()["step_name"]``. + """ + res = transformer.transform(X, **params.transform) + # if we have a weight for this transformer, multiply output + if weight is None: + return res + return res * weight + + +def _fit_transform_one( + transformer, X, y, weight, message_clsname="", message=None, params=None +): + """ + Fits ``transformer`` to ``X`` and ``y``. The transformed result is returned + with the fitted transformer. If ``weight`` is not ``None``, the result will + be multiplied by ``weight``. + + ``params`` needs to be of the form ``process_routing()["step_name"]``. + """ + params = params or {} + with _print_elapsed_time(message_clsname, message): + if hasattr(transformer, "fit_transform"): + res = transformer.fit_transform(X, y, **params.get("fit_transform", {})) + else: + res = transformer.fit(X, y, **params.get("fit", {})).transform( + X, **params.get("transform", {}) + ) + + if weight is None: + return res, transformer + return res * weight, transformer + + +def _fit_one(transformer, X, y, weight, message_clsname="", message=None, params=None): + """ + Fits ``transformer`` to ``X`` and ``y``. + """ + with _print_elapsed_time(message_clsname, message): + return transformer.fit(X, y, **params["fit"]) + + +class FeatureUnion(TransformerMixin, _BaseComposition): + """Concatenates results of multiple transformer objects. + + This estimator applies a list of transformer objects in parallel to the + input data, then concatenates the results. This is useful to combine + several feature extraction mechanisms into a single transformer. + + Parameters of the transformers may be set using its name and the parameter + name separated by a '__'. A transformer may be replaced entirely by + setting the parameter with its name to another transformer, removed by + setting to 'drop' or disabled by setting to 'passthrough' (features are + passed without transformation). + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.13 + + Parameters + ---------- + transformer_list : list of (str, transformer) tuples + List of transformer objects to be applied to the data. The first + half of each tuple is the name of the transformer. The transformer can + be 'drop' for it to be ignored or can be 'passthrough' for features to + be passed unchanged. + + .. versionadded:: 1.1 + Added the option `"passthrough"`. + + .. versionchanged:: 0.22 + Deprecated `None` as a transformer in favor of 'drop'. + + n_jobs : int, default=None + Number of jobs to run in parallel. + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + .. versionchanged:: v0.20 + `n_jobs` default changed from 1 to None + + transformer_weights : dict, default=None + Multiplicative weights for features per transformer. + Keys are transformer names, values the weights. + Raises ValueError if key not present in ``transformer_list``. + + verbose : bool, default=False + If True, the time elapsed while fitting each transformer will be + printed as it is completed. + + verbose_feature_names_out : bool, default=True + If True, :meth:`get_feature_names_out` will prefix all feature names + with the name of the transformer that generated that feature. + If False, :meth:`get_feature_names_out` will not prefix any feature + names and will error if feature names are not unique. + + .. versionadded:: 1.5 + + Attributes + ---------- + named_transformers : :class:`~sklearn.utils.Bunch` + Dictionary-like object, with the following attributes. + Read-only attribute to access any transformer parameter by user + given name. Keys are transformer names and values are + transformer parameters. + + .. versionadded:: 1.2 + + n_features_in_ : int + Number of features seen during :term:`fit`. Only defined if the + underlying first transformer in `transformer_list` exposes such an + attribute when fit. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when + `X` has feature names that are all strings. + + .. versionadded:: 1.3 + + See Also + -------- + make_union : Convenience function for simplified feature union + construction. + + Examples + -------- + >>> from sklearn.pipeline import FeatureUnion + >>> from sklearn.decomposition import PCA, TruncatedSVD + >>> union = FeatureUnion([("pca", PCA(n_components=1)), + ... ("svd", TruncatedSVD(n_components=2))]) + >>> X = [[0., 1., 3], [2., 2., 5]] + >>> union.fit_transform(X) + array([[-1.5 , 3.04, -0.872], + [ 1.5 , 5.72, 0.463]]) + >>> # An estimator's parameter can be set using '__' syntax + >>> union.set_params(svd__n_components=1).fit_transform(X) + array([[-1.5 , 3.04], + [ 1.5 , 5.72]]) + + For a more detailed example of usage, see + :ref:`sphx_glr_auto_examples_compose_plot_feature_union.py`. + """ + + def __init__( + self, + transformer_list, + *, + n_jobs=None, + transformer_weights=None, + verbose=False, + verbose_feature_names_out=True, + ): + self.transformer_list = transformer_list + self.n_jobs = n_jobs + self.transformer_weights = transformer_weights + self.verbose = verbose + self.verbose_feature_names_out = verbose_feature_names_out + + def set_output(self, *, transform=None): + """Set the output container when `"transform"` and `"fit_transform"` are called. + + `set_output` will set the output of all estimators in `transformer_list`. + + Parameters + ---------- + transform : {"default", "pandas", "polars"}, default=None + Configure output of `transform` and `fit_transform`. + + - `"default"`: Default output format of a transformer + - `"pandas"`: DataFrame output + - `"polars"`: Polars output + - `None`: Transform configuration is unchanged + + Returns + ------- + self : estimator instance + Estimator instance. + """ + super().set_output(transform=transform) + for _, step, _ in self._iter(): + _safe_set_output(step, transform=transform) + return self + + @property + def named_transformers(self): + # Use Bunch object to improve autocomplete + return Bunch(**dict(self.transformer_list)) + + def get_params(self, deep=True): + """Get parameters for this estimator. + + Returns the parameters given in the constructor as well as the + estimators contained within the `transformer_list` of the + `FeatureUnion`. + + Parameters + ---------- + deep : bool, default=True + If True, will return the parameters for this estimator and + contained subobjects that are estimators. + + Returns + ------- + params : mapping of string to any + Parameter names mapped to their values. + """ + return self._get_params("transformer_list", deep=deep) + + def set_params(self, **kwargs): + """Set the parameters of this estimator. + + Valid parameter keys can be listed with ``get_params()``. Note that + you can directly set the parameters of the estimators contained in + `transformer_list`. + + Parameters + ---------- + **kwargs : dict + Parameters of this estimator or parameters of estimators contained + in `transform_list`. Parameters of the transformers may be set + using its name and the parameter name separated by a '__'. + + Returns + ------- + self : object + FeatureUnion class instance. + """ + self._set_params("transformer_list", **kwargs) + return self + + def _validate_transformers(self): + names, transformers = zip(*self.transformer_list) + + # validate names + self._validate_names(names) + + # validate estimators + for t in transformers: + if t in ("drop", "passthrough"): + continue + if not (hasattr(t, "fit") or hasattr(t, "fit_transform")) or not hasattr( + t, "transform" + ): + raise TypeError( + "All estimators should implement fit and " + "transform. '%s' (type %s) doesn't" % (t, type(t)) + ) + + def _validate_transformer_weights(self): + if not self.transformer_weights: + return + + transformer_names = set(name for name, _ in self.transformer_list) + for name in self.transformer_weights: + if name not in transformer_names: + raise ValueError( + f'Attempting to weight transformer "{name}", ' + "but it is not present in transformer_list." + ) + + def _iter(self): + """ + Generate (name, trans, weight) tuples excluding None and + 'drop' transformers. + """ + + get_weight = (self.transformer_weights or {}).get + + for name, trans in self.transformer_list: + if trans == "drop": + continue + if trans == "passthrough": + trans = FunctionTransformer(feature_names_out="one-to-one") + yield (name, trans, get_weight(name)) + + def get_feature_names_out(self, input_features=None): + """Get output feature names for transformation. + + Parameters + ---------- + input_features : array-like of str or None, default=None + Input features. + + Returns + ------- + feature_names_out : ndarray of str objects + Transformed feature names. + """ + # List of tuples (name, feature_names_out) + transformer_with_feature_names_out = [] + for name, trans, _ in self._iter(): + if not hasattr(trans, "get_feature_names_out"): + raise AttributeError( + "Transformer %s (type %s) does not provide get_feature_names_out." + % (str(name), type(trans).__name__) + ) + feature_names_out = trans.get_feature_names_out(input_features) + transformer_with_feature_names_out.append((name, feature_names_out)) + + return self._add_prefix_for_feature_names_out( + transformer_with_feature_names_out + ) + + def _add_prefix_for_feature_names_out(self, transformer_with_feature_names_out): + """Add prefix for feature names out that includes the transformer names. + + Parameters + ---------- + transformer_with_feature_names_out : list of tuples of (str, array-like of str) + The tuple consistent of the transformer's name and its feature names out. + + Returns + ------- + feature_names_out : ndarray of shape (n_features,), dtype=str + Transformed feature names. + """ + if self.verbose_feature_names_out: + # Prefix the feature names out with the transformers name + names = list( + chain.from_iterable( + (f"{name}__{i}" for i in feature_names_out) + for name, feature_names_out in transformer_with_feature_names_out + ) + ) + return np.asarray(names, dtype=object) + + # verbose_feature_names_out is False + # Check that names are all unique without a prefix + feature_names_count = Counter( + chain.from_iterable(s for _, s in transformer_with_feature_names_out) + ) + top_6_overlap = [ + name for name, count in feature_names_count.most_common(6) if count > 1 + ] + top_6_overlap.sort() + if top_6_overlap: + if len(top_6_overlap) == 6: + # There are more than 5 overlapping names, we only show the 5 + # of the feature names + names_repr = str(top_6_overlap[:5])[:-1] + ", ...]" + else: + names_repr = str(top_6_overlap) + raise ValueError( + f"Output feature names: {names_repr} are not unique. Please set " + "verbose_feature_names_out=True to add prefixes to feature names" + ) + + return np.concatenate( + [name for _, name in transformer_with_feature_names_out], + ) + + def fit(self, X, y=None, **fit_params): + """Fit all transformers using X. + + Parameters + ---------- + X : iterable or array-like, depending on transformers + Input data, used to fit transformers. + + y : array-like of shape (n_samples, n_outputs), default=None + Targets for supervised learning. + + **fit_params : dict, default=None + - If `enable_metadata_routing=False` (default): + Parameters directly passed to the `fit` methods of the + sub-transformers. + + - If `enable_metadata_routing=True`: + Parameters safely routed to the `fit` methods of the + sub-transformers. See :ref:`Metadata Routing User Guide + ` for more details. + + .. versionchanged:: 1.5 + `**fit_params` can be routed via metadata routing API. + + Returns + ------- + self : object + FeatureUnion class instance. + """ + if _routing_enabled(): + routed_params = process_routing(self, "fit", **fit_params) + else: + # TODO(SLEP6): remove when metadata routing cannot be disabled. + routed_params = Bunch() + for name, _ in self.transformer_list: + routed_params[name] = Bunch(fit={}) + routed_params[name].fit = fit_params + + transformers = self._parallel_func(X, y, _fit_one, routed_params) + + if not transformers: + # All transformers are None + return self + + self._update_transformer_list(transformers) + return self + + def fit_transform(self, X, y=None, **params): + """Fit all transformers, transform the data and concatenate results. + + Parameters + ---------- + X : iterable or array-like, depending on transformers + Input data to be transformed. + + y : array-like of shape (n_samples, n_outputs), default=None + Targets for supervised learning. + + **params : dict, default=None + - If `enable_metadata_routing=False` (default): + Parameters directly passed to the `fit` methods of the + sub-transformers. + + - If `enable_metadata_routing=True`: + Parameters safely routed to the `fit` methods of the + sub-transformers. See :ref:`Metadata Routing User Guide + ` for more details. + + .. versionchanged:: 1.5 + `**params` can now be routed via metadata routing API. + + Returns + ------- + X_t : array-like or sparse matrix of \ + shape (n_samples, sum_n_components) + The `hstack` of results of transformers. `sum_n_components` is the + sum of `n_components` (output dimension) over transformers. + """ + if _routing_enabled(): + routed_params = process_routing(self, "fit_transform", **params) + else: + # TODO(SLEP6): remove when metadata routing cannot be disabled. + routed_params = Bunch() + for name, obj in self.transformer_list: + if hasattr(obj, "fit_transform"): + routed_params[name] = Bunch(fit_transform={}) + routed_params[name].fit_transform = params + else: + routed_params[name] = Bunch(fit={}) + routed_params[name] = Bunch(transform={}) + routed_params[name].fit = params + + results = self._parallel_func(X, y, _fit_transform_one, routed_params) + if not results: + # All transformers are None + return np.zeros((X.shape[0], 0)) + + Xs, transformers = zip(*results) + self._update_transformer_list(transformers) + + return self._hstack(Xs) + + def _log_message(self, name, idx, total): + if not self.verbose: + return None + return "(step %d of %d) Processing %s" % (idx, total, name) + + def _parallel_func(self, X, y, func, routed_params): + """Runs func in parallel on X and y""" + self.transformer_list = list(self.transformer_list) + self._validate_transformers() + self._validate_transformer_weights() + transformers = list(self._iter()) + + return Parallel(n_jobs=self.n_jobs)( + delayed(func)( + transformer, + X, + y, + weight, + message_clsname="FeatureUnion", + message=self._log_message(name, idx, len(transformers)), + params=routed_params[name], + ) + for idx, (name, transformer, weight) in enumerate(transformers, 1) + ) + + def transform(self, X, **params): + """Transform X separately by each transformer, concatenate results. + + Parameters + ---------- + X : iterable or array-like, depending on transformers + Input data to be transformed. + + **params : dict, default=None + + Parameters routed to the `transform` method of the sub-transformers via the + metadata routing API. See :ref:`Metadata Routing User Guide + ` for more details. + + .. versionadded:: 1.5 + + Returns + ------- + X_t : array-like or sparse matrix of shape (n_samples, sum_n_components) + The `hstack` of results of transformers. `sum_n_components` is the + sum of `n_components` (output dimension) over transformers. + """ + _raise_for_params(params, self, "transform") + + if _routing_enabled(): + routed_params = process_routing(self, "transform", **params) + else: + # TODO(SLEP6): remove when metadata routing cannot be disabled. + routed_params = Bunch() + for name, _ in self.transformer_list: + routed_params[name] = Bunch(transform={}) + + Xs = Parallel(n_jobs=self.n_jobs)( + delayed(_transform_one)(trans, X, None, weight, params=routed_params[name]) + for name, trans, weight in self._iter() + ) + if not Xs: + # All transformers are None + return np.zeros((X.shape[0], 0)) + + return self._hstack(Xs) + + def _hstack(self, Xs): + # Check if Xs dimensions are valid + for X, (name, _) in zip(Xs, self.transformer_list): + if hasattr(X, "shape") and len(X.shape) != 2: + raise ValueError( + f"Transformer '{name}' returned an array or dataframe with " + f"{len(X.shape)} dimensions, but expected 2 dimensions " + "(n_samples, n_features)." + ) + + adapter = _get_container_adapter("transform", self) + if adapter and all(adapter.is_supported_container(X) for X in Xs): + return adapter.hstack(Xs) + + if any(sparse.issparse(f) for f in Xs): + return sparse.hstack(Xs).tocsr() + + return np.hstack(Xs) + + def _update_transformer_list(self, transformers): + transformers = iter(transformers) + self.transformer_list[:] = [ + (name, old if old == "drop" else next(transformers)) + for name, old in self.transformer_list + ] + + @property + def n_features_in_(self): + """Number of features seen during :term:`fit`.""" + + # X is passed to all transformers so we just delegate to the first one + return self.transformer_list[0][1].n_features_in_ + + @property + def feature_names_in_(self): + """Names of features seen during :term:`fit`.""" + # X is passed to all transformers -- delegate to the first one + return self.transformer_list[0][1].feature_names_in_ + + def __sklearn_is_fitted__(self): + # Delegate whether feature union was fitted + for _, transformer, _ in self._iter(): + check_is_fitted(transformer) + return True + + def _sk_visual_block_(self): + names, transformers = zip(*self.transformer_list) + return _VisualBlock("parallel", transformers, names=names) + + def __getitem__(self, name): + """Return transformer with name.""" + if not isinstance(name, str): + raise KeyError("Only string keys are supported") + return self.named_transformers[name] + + def get_metadata_routing(self): + """Get metadata routing of this object. + + Please check :ref:`User Guide ` on how the routing + mechanism works. + + .. versionadded:: 1.5 + + Returns + ------- + routing : MetadataRouter + A :class:`~sklearn.utils.metadata_routing.MetadataRouter` encapsulating + routing information. + """ + router = MetadataRouter(owner=self.__class__.__name__) + + for name, transformer in self.transformer_list: + router.add( + **{name: transformer}, + method_mapping=MethodMapping() + .add(caller="fit", callee="fit") + .add(caller="fit_transform", callee="fit_transform") + .add(caller="fit_transform", callee="fit") + .add(caller="fit_transform", callee="transform") + .add(caller="transform", callee="transform"), + ) + + return router + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + try: + tags.input_tags.sparse = all( + get_tags(trans).input_tags.sparse + for name, trans in self.transformer_list + if trans not in {"passthrough", "drop"} + ) + except Exception: + # If `transformer_list` does not comply with our API (list of tuples) + # then it will fail. In this case, we assume that `sparse` is False + # but the parameter validation will raise an error during `fit`. + pass # pragma: no cover + return tags + + +def make_union( + *transformers, n_jobs=None, verbose=False, verbose_feature_names_out=True +): + """Construct a :class:`FeatureUnion` from the given transformers. + + This is a shorthand for the :class:`FeatureUnion` constructor; it does not + require, and does not permit, naming the transformers. Instead, they will + be given names automatically based on their types. It also does not allow + weighting. + + Parameters + ---------- + *transformers : list of estimators + One or more estimators. + + n_jobs : int, default=None + Number of jobs to run in parallel. + ``None`` means 1 unless in a :obj:`joblib.parallel_backend` context. + ``-1`` means using all processors. See :term:`Glossary ` + for more details. + + .. versionchanged:: v0.20 + `n_jobs` default changed from 1 to None. + + verbose : bool, default=False + If True, the time elapsed while fitting each transformer will be + printed as it is completed. + + verbose_feature_names_out : bool, default=True + If True, the feature names generated by `get_feature_names_out` will + include prefixes derived from the transformer names. + + Returns + ------- + f : FeatureUnion + A :class:`FeatureUnion` object for concatenating the results of multiple + transformer objects. + + See Also + -------- + FeatureUnion : Class for concatenating the results of multiple transformer + objects. + + Examples + -------- + >>> from sklearn.decomposition import PCA, TruncatedSVD + >>> from sklearn.pipeline import make_union + >>> make_union(PCA(), TruncatedSVD()) + FeatureUnion(transformer_list=[('pca', PCA()), + ('truncatedsvd', TruncatedSVD())]) + """ + return FeatureUnion( + _name_estimators(transformers), + n_jobs=n_jobs, + verbose=verbose, + verbose_feature_names_out=verbose_feature_names_out, + ) diff --git a/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/random_projection.py b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/random_projection.py new file mode 100644 index 0000000000000000000000000000000000000000..f98b11365dd3bcfc54eae62515e040ed5d237466 --- /dev/null +++ b/miniconda3/envs/ladir/lib/python3.10/site-packages/sklearn/random_projection.py @@ -0,0 +1,824 @@ +"""Random projection transformers. + +Random projections are a simple and computationally efficient way to +reduce the dimensionality of the data by trading a controlled amount +of accuracy (as additional variance) for faster processing times and +smaller model sizes. + +The dimensions and distribution of random projections matrices are +controlled so as to preserve the pairwise distances between any two +samples of the dataset. + +The main theoretical result behind the efficiency of random projection is the +`Johnson-Lindenstrauss lemma (quoting Wikipedia) +`_: + + In mathematics, the Johnson-Lindenstrauss lemma is a result + concerning low-distortion embeddings of points from high-dimensional + into low-dimensional Euclidean space. The lemma states that a small set + of points in a high-dimensional space can be embedded into a space of + much lower dimension in such a way that distances between the points are + nearly preserved. The map used for the embedding is at least Lipschitz, + and can even be taken to be an orthogonal projection. +""" + +# Authors: The scikit-learn developers +# SPDX-License-Identifier: BSD-3-Clause + +import warnings +from abc import ABCMeta, abstractmethod +from numbers import Integral, Real + +import numpy as np +import scipy.sparse as sp +from scipy import linalg + +from .base import ( + BaseEstimator, + ClassNamePrefixFeaturesOutMixin, + TransformerMixin, + _fit_context, +) +from .exceptions import DataDimensionalityWarning +from .utils import check_random_state +from .utils._param_validation import Interval, StrOptions, validate_params +from .utils.extmath import safe_sparse_dot +from .utils.random import sample_without_replacement +from .utils.validation import check_array, check_is_fitted, validate_data + +__all__ = [ + "GaussianRandomProjection", + "SparseRandomProjection", + "johnson_lindenstrauss_min_dim", +] + + +@validate_params( + { + "n_samples": ["array-like", Interval(Real, 1, None, closed="left")], + "eps": ["array-like", Interval(Real, 0, 1, closed="neither")], + }, + prefer_skip_nested_validation=True, +) +def johnson_lindenstrauss_min_dim(n_samples, *, eps=0.1): + """Find a 'safe' number of components to randomly project to. + + The distortion introduced by a random projection `p` only changes the + distance between two points by a factor (1 +- eps) in a euclidean space + with good probability. The projection `p` is an eps-embedding as defined + by: + + .. code-block:: text + + (1 - eps) ||u - v||^2 < ||p(u) - p(v)||^2 < (1 + eps) ||u - v||^2 + + Where u and v are any rows taken from a dataset of shape (n_samples, + n_features), eps is in ]0, 1[ and p is a projection by a random Gaussian + N(0, 1) matrix of shape (n_components, n_features) (or a sparse + Achlioptas matrix). + + The minimum number of components to guarantee the eps-embedding is + given by: + + .. code-block:: text + + n_components >= 4 log(n_samples) / (eps^2 / 2 - eps^3 / 3) + + Note that the number of dimensions is independent of the original + number of features but instead depends on the size of the dataset: + the larger the dataset, the higher is the minimal dimensionality of + an eps-embedding. + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + n_samples : int or array-like of int + Number of samples that should be an integer greater than 0. If an array + is given, it will compute a safe number of components array-wise. + + eps : float or array-like of shape (n_components,), dtype=float, \ + default=0.1 + Maximum distortion rate in the range (0, 1) as defined by the + Johnson-Lindenstrauss lemma. If an array is given, it will compute a + safe number of components array-wise. + + Returns + ------- + n_components : int or ndarray of int + The minimal number of components to guarantee with good probability + an eps-embedding with n_samples. + + References + ---------- + + .. [1] https://en.wikipedia.org/wiki/Johnson%E2%80%93Lindenstrauss_lemma + + .. [2] `Sanjoy Dasgupta and Anupam Gupta, 1999, + "An elementary proof of the Johnson-Lindenstrauss Lemma." + `_ + + Examples + -------- + >>> from sklearn.random_projection import johnson_lindenstrauss_min_dim + >>> johnson_lindenstrauss_min_dim(1e6, eps=0.5) + np.int64(663) + + >>> johnson_lindenstrauss_min_dim(1e6, eps=[0.5, 0.1, 0.01]) + array([ 663, 11841, 1112658]) + + >>> johnson_lindenstrauss_min_dim([1e4, 1e5, 1e6], eps=0.1) + array([ 7894, 9868, 11841]) + """ + eps = np.asarray(eps) + n_samples = np.asarray(n_samples) + + if np.any(eps <= 0.0) or np.any(eps >= 1): + raise ValueError("The JL bound is defined for eps in ]0, 1[, got %r" % eps) + + if np.any(n_samples <= 0): + raise ValueError( + "The JL bound is defined for n_samples greater than zero, got %r" + % n_samples + ) + + denominator = (eps**2 / 2) - (eps**3 / 3) + return (4 * np.log(n_samples) / denominator).astype(np.int64) + + +def _check_density(density, n_features): + """Factorize density check according to Li et al.""" + if density == "auto": + density = 1 / np.sqrt(n_features) + + elif density <= 0 or density > 1: + raise ValueError("Expected density in range ]0, 1], got: %r" % density) + return density + + +def _check_input_size(n_components, n_features): + """Factorize argument checking for random matrix generation.""" + if n_components <= 0: + raise ValueError( + "n_components must be strictly positive, got %d" % n_components + ) + if n_features <= 0: + raise ValueError("n_features must be strictly positive, got %d" % n_features) + + +def _gaussian_random_matrix(n_components, n_features, random_state=None): + """Generate a dense Gaussian random matrix. + + The components of the random matrix are drawn from + + N(0, 1.0 / n_components). + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + n_components : int, + Dimensionality of the target projection space. + + n_features : int, + Dimensionality of the original source space. + + random_state : int, RandomState instance or None, default=None + Controls the pseudo random number generator used to generate the matrix + at fit time. + Pass an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + Returns + ------- + components : ndarray of shape (n_components, n_features) + The generated Gaussian random matrix. + + See Also + -------- + GaussianRandomProjection + """ + _check_input_size(n_components, n_features) + rng = check_random_state(random_state) + components = rng.normal( + loc=0.0, scale=1.0 / np.sqrt(n_components), size=(n_components, n_features) + ) + return components + + +def _sparse_random_matrix(n_components, n_features, density="auto", random_state=None): + """Generalized Achlioptas random sparse matrix for random projection. + + Setting density to 1 / 3 will yield the original matrix by Dimitris + Achlioptas while setting a lower value will yield the generalization + by Ping Li et al. + + If we note :math:`s = 1 / density`, the components of the random matrix are + drawn from: + + - -sqrt(s) / sqrt(n_components) with probability 1 / 2s + - 0 with probability 1 - 1 / s + - +sqrt(s) / sqrt(n_components) with probability 1 / 2s + + Read more in the :ref:`User Guide `. + + Parameters + ---------- + n_components : int, + Dimensionality of the target projection space. + + n_features : int, + Dimensionality of the original source space. + + density : float or 'auto', default='auto' + Ratio of non-zero component in the random projection matrix in the + range `(0, 1]` + + If density = 'auto', the value is set to the minimum density + as recommended by Ping Li et al.: 1 / sqrt(n_features). + + Use density = 1 / 3.0 if you want to reproduce the results from + Achlioptas, 2001. + + random_state : int, RandomState instance or None, default=None + Controls the pseudo random number generator used to generate the matrix + at fit time. + Pass an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + Returns + ------- + components : {ndarray, sparse matrix} of shape (n_components, n_features) + The generated Gaussian random matrix. Sparse matrix will be of CSR + format. + + See Also + -------- + SparseRandomProjection + + References + ---------- + + .. [1] Ping Li, T. Hastie and K. W. Church, 2006, + "Very Sparse Random Projections". + https://web.stanford.edu/~hastie/Papers/Ping/KDD06_rp.pdf + + .. [2] D. Achlioptas, 2001, "Database-friendly random projections", + https://cgi.di.uoa.gr/~optas/papers/jl.pdf + + """ + _check_input_size(n_components, n_features) + density = _check_density(density, n_features) + rng = check_random_state(random_state) + + if density == 1: + # skip index generation if totally dense + components = rng.binomial(1, 0.5, (n_components, n_features)) * 2 - 1 + return 1 / np.sqrt(n_components) * components + + else: + # Generate location of non zero elements + indices = [] + offset = 0 + indptr = [offset] + for _ in range(n_components): + # find the indices of the non-zero components for row i + n_nonzero_i = rng.binomial(n_features, density) + indices_i = sample_without_replacement( + n_features, n_nonzero_i, random_state=rng + ) + indices.append(indices_i) + offset += n_nonzero_i + indptr.append(offset) + + indices = np.concatenate(indices) + + # Among non zero components the probability of the sign is 50%/50% + data = rng.binomial(1, 0.5, size=np.size(indices)) * 2 - 1 + + # build the CSR structure by concatenating the rows + components = sp.csr_matrix( + (data, indices, indptr), shape=(n_components, n_features) + ) + + return np.sqrt(1 / density) / np.sqrt(n_components) * components + + +class BaseRandomProjection( + ClassNamePrefixFeaturesOutMixin, TransformerMixin, BaseEstimator, metaclass=ABCMeta +): + """Base class for random projections. + + Warning: This class should not be used directly. + Use derived classes instead. + """ + + _parameter_constraints: dict = { + "n_components": [ + Interval(Integral, 1, None, closed="left"), + StrOptions({"auto"}), + ], + "eps": [Interval(Real, 0, None, closed="neither")], + "compute_inverse_components": ["boolean"], + "random_state": ["random_state"], + } + + @abstractmethod + def __init__( + self, + n_components="auto", + *, + eps=0.1, + compute_inverse_components=False, + random_state=None, + ): + self.n_components = n_components + self.eps = eps + self.compute_inverse_components = compute_inverse_components + self.random_state = random_state + + @abstractmethod + def _make_random_matrix(self, n_components, n_features): + """Generate the random projection matrix. + + Parameters + ---------- + n_components : int, + Dimensionality of the target projection space. + + n_features : int, + Dimensionality of the original source space. + + Returns + ------- + components : {ndarray, sparse matrix} of shape (n_components, n_features) + The generated random matrix. Sparse matrix will be of CSR format. + + """ + + def _compute_inverse_components(self): + """Compute the pseudo-inverse of the (densified) components.""" + components = self.components_ + if sp.issparse(components): + components = components.toarray() + return linalg.pinv(components, check_finite=False) + + @_fit_context(prefer_skip_nested_validation=True) + def fit(self, X, y=None): + """Generate a sparse random projection matrix. + + Parameters + ---------- + X : {ndarray, sparse matrix} of shape (n_samples, n_features) + Training set: only the shape is used to find optimal random + matrix dimensions based on the theory referenced in the + afore mentioned papers. + + y : Ignored + Not used, present here for API consistency by convention. + + Returns + ------- + self : object + BaseRandomProjection class instance. + """ + X = validate_data( + self, X, accept_sparse=["csr", "csc"], dtype=[np.float64, np.float32] + ) + + n_samples, n_features = X.shape + + if self.n_components == "auto": + self.n_components_ = johnson_lindenstrauss_min_dim( + n_samples=n_samples, eps=self.eps + ) + + if self.n_components_ <= 0: + raise ValueError( + "eps=%f and n_samples=%d lead to a target dimension of " + "%d which is invalid" % (self.eps, n_samples, self.n_components_) + ) + + elif self.n_components_ > n_features: + raise ValueError( + "eps=%f and n_samples=%d lead to a target dimension of " + "%d which is larger than the original space with " + "n_features=%d" + % (self.eps, n_samples, self.n_components_, n_features) + ) + else: + if self.n_components > n_features: + warnings.warn( + "The number of components is higher than the number of" + " features: n_features < n_components (%s < %s)." + "The dimensionality of the problem will not be reduced." + % (n_features, self.n_components), + DataDimensionalityWarning, + ) + + self.n_components_ = self.n_components + + # Generate a projection matrix of size [n_components, n_features] + self.components_ = self._make_random_matrix( + self.n_components_, n_features + ).astype(X.dtype, copy=False) + + if self.compute_inverse_components: + self.inverse_components_ = self._compute_inverse_components() + + # Required by ClassNamePrefixFeaturesOutMixin.get_feature_names_out. + self._n_features_out = self.n_components + + return self + + def inverse_transform(self, X): + """Project data back to its original space. + + Returns an array X_original whose transform would be X. Note that even + if X is sparse, X_original is dense: this may use a lot of RAM. + + If `compute_inverse_components` is False, the inverse of the components is + computed during each call to `inverse_transform` which can be costly. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_components) + Data to be transformed back. + + Returns + ------- + X_original : ndarray of shape (n_samples, n_features) + Reconstructed data. + """ + check_is_fitted(self) + + X = check_array(X, dtype=[np.float64, np.float32], accept_sparse=("csr", "csc")) + + if self.compute_inverse_components: + return X @ self.inverse_components_.T + + inverse_components = self._compute_inverse_components() + return X @ inverse_components.T + + def __sklearn_tags__(self): + tags = super().__sklearn_tags__() + tags.transformer_tags.preserves_dtype = ["float64", "float32"] + tags.input_tags.sparse = True + return tags + + +class GaussianRandomProjection(BaseRandomProjection): + """Reduce dimensionality through Gaussian random projection. + + The components of the random matrix are drawn from N(0, 1 / n_components). + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.13 + + Parameters + ---------- + n_components : int or 'auto', default='auto' + Dimensionality of the target projection space. + + n_components can be automatically adjusted according to the + number of samples in the dataset and the bound given by the + Johnson-Lindenstrauss lemma. In that case the quality of the + embedding is controlled by the ``eps`` parameter. + + It should be noted that Johnson-Lindenstrauss lemma can yield + very conservative estimated of the required number of components + as it makes no assumption on the structure of the dataset. + + eps : float, default=0.1 + Parameter to control the quality of the embedding according to + the Johnson-Lindenstrauss lemma when `n_components` is set to + 'auto'. The value should be strictly positive. + + Smaller values lead to better embedding and higher number of + dimensions (n_components) in the target projection space. + + compute_inverse_components : bool, default=False + Learn the inverse transform by computing the pseudo-inverse of the + components during fit. Note that computing the pseudo-inverse does not + scale well to large matrices. + + random_state : int, RandomState instance or None, default=None + Controls the pseudo random number generator used to generate the + projection matrix at fit time. + Pass an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + Attributes + ---------- + n_components_ : int + Concrete number of components computed when n_components="auto". + + components_ : ndarray of shape (n_components, n_features) + Random matrix used for the projection. + + inverse_components_ : ndarray of shape (n_features, n_components) + Pseudo-inverse of the components, only computed if + `compute_inverse_components` is True. + + .. versionadded:: 1.1 + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + SparseRandomProjection : Reduce dimensionality through sparse + random projection. + + Examples + -------- + >>> import numpy as np + >>> from sklearn.random_projection import GaussianRandomProjection + >>> rng = np.random.RandomState(42) + >>> X = rng.rand(25, 3000) + >>> transformer = GaussianRandomProjection(random_state=rng) + >>> X_new = transformer.fit_transform(X) + >>> X_new.shape + (25, 2759) + """ + + def __init__( + self, + n_components="auto", + *, + eps=0.1, + compute_inverse_components=False, + random_state=None, + ): + super().__init__( + n_components=n_components, + eps=eps, + compute_inverse_components=compute_inverse_components, + random_state=random_state, + ) + + def _make_random_matrix(self, n_components, n_features): + """Generate the random projection matrix. + + Parameters + ---------- + n_components : int, + Dimensionality of the target projection space. + + n_features : int, + Dimensionality of the original source space. + + Returns + ------- + components : ndarray of shape (n_components, n_features) + The generated random matrix. + """ + random_state = check_random_state(self.random_state) + return _gaussian_random_matrix( + n_components, n_features, random_state=random_state + ) + + def transform(self, X): + """Project the data by using matrix product with the random matrix. + + Parameters + ---------- + X : {ndarray, sparse matrix} of shape (n_samples, n_features) + The input data to project into a smaller dimensional space. + + Returns + ------- + X_new : ndarray of shape (n_samples, n_components) + Projected array. + """ + check_is_fitted(self) + X = validate_data( + self, + X, + accept_sparse=["csr", "csc"], + reset=False, + dtype=[np.float64, np.float32], + ) + + return X @ self.components_.T + + +class SparseRandomProjection(BaseRandomProjection): + """Reduce dimensionality through sparse random projection. + + Sparse random matrix is an alternative to dense random + projection matrix that guarantees similar embedding quality while being + much more memory efficient and allowing faster computation of the + projected data. + + If we note `s = 1 / density` the components of the random matrix are + drawn from: + + .. code-block:: text + + -sqrt(s) / sqrt(n_components) with probability 1 / 2s + 0 with probability 1 - 1 / s + +sqrt(s) / sqrt(n_components) with probability 1 / 2s + + Read more in the :ref:`User Guide `. + + .. versionadded:: 0.13 + + Parameters + ---------- + n_components : int or 'auto', default='auto' + Dimensionality of the target projection space. + + n_components can be automatically adjusted according to the + number of samples in the dataset and the bound given by the + Johnson-Lindenstrauss lemma. In that case the quality of the + embedding is controlled by the ``eps`` parameter. + + It should be noted that Johnson-Lindenstrauss lemma can yield + very conservative estimated of the required number of components + as it makes no assumption on the structure of the dataset. + + density : float or 'auto', default='auto' + Ratio in the range (0, 1] of non-zero component in the random + projection matrix. + + If density = 'auto', the value is set to the minimum density + as recommended by Ping Li et al.: 1 / sqrt(n_features). + + Use density = 1 / 3.0 if you want to reproduce the results from + Achlioptas, 2001. + + eps : float, default=0.1 + Parameter to control the quality of the embedding according to + the Johnson-Lindenstrauss lemma when n_components is set to + 'auto'. This value should be strictly positive. + + Smaller values lead to better embedding and higher number of + dimensions (n_components) in the target projection space. + + dense_output : bool, default=False + If True, ensure that the output of the random projection is a + dense numpy array even if the input and random projection matrix + are both sparse. In practice, if the number of components is + small the number of zero components in the projected data will + be very small and it will be more CPU and memory efficient to + use a dense representation. + + If False, the projected data uses a sparse representation if + the input is sparse. + + compute_inverse_components : bool, default=False + Learn the inverse transform by computing the pseudo-inverse of the + components during fit. Note that the pseudo-inverse is always a dense + array, even if the training data was sparse. This means that it might be + necessary to call `inverse_transform` on a small batch of samples at a + time to avoid exhausting the available memory on the host. Moreover, + computing the pseudo-inverse does not scale well to large matrices. + + random_state : int, RandomState instance or None, default=None + Controls the pseudo random number generator used to generate the + projection matrix at fit time. + Pass an int for reproducible output across multiple function calls. + See :term:`Glossary `. + + Attributes + ---------- + n_components_ : int + Concrete number of components computed when n_components="auto". + + components_ : sparse matrix of shape (n_components, n_features) + Random matrix used for the projection. Sparse matrix will be of CSR + format. + + inverse_components_ : ndarray of shape (n_features, n_components) + Pseudo-inverse of the components, only computed if + `compute_inverse_components` is True. + + .. versionadded:: 1.1 + + density_ : float in range 0.0 - 1.0 + Concrete density computed from when density = "auto". + + n_features_in_ : int + Number of features seen during :term:`fit`. + + .. versionadded:: 0.24 + + feature_names_in_ : ndarray of shape (`n_features_in_`,) + Names of features seen during :term:`fit`. Defined only when `X` + has feature names that are all strings. + + .. versionadded:: 1.0 + + See Also + -------- + GaussianRandomProjection : Reduce dimensionality through Gaussian + random projection. + + References + ---------- + + .. [1] Ping Li, T. Hastie and K. W. Church, 2006, + "Very Sparse Random Projections". + https://web.stanford.edu/~hastie/Papers/Ping/KDD06_rp.pdf + + .. [2] D. Achlioptas, 2001, "Database-friendly random projections", + https://cgi.di.uoa.gr/~optas/papers/jl.pdf + + Examples + -------- + >>> import numpy as np + >>> from sklearn.random_projection import SparseRandomProjection + >>> rng = np.random.RandomState(42) + >>> X = rng.rand(25, 3000) + >>> transformer = SparseRandomProjection(random_state=rng) + >>> X_new = transformer.fit_transform(X) + >>> X_new.shape + (25, 2759) + >>> # very few components are non-zero + >>> np.mean(transformer.components_ != 0) + np.float64(0.0182) + """ + + _parameter_constraints: dict = { + **BaseRandomProjection._parameter_constraints, + "density": [Interval(Real, 0.0, 1.0, closed="right"), StrOptions({"auto"})], + "dense_output": ["boolean"], + } + + def __init__( + self, + n_components="auto", + *, + density="auto", + eps=0.1, + dense_output=False, + compute_inverse_components=False, + random_state=None, + ): + super().__init__( + n_components=n_components, + eps=eps, + compute_inverse_components=compute_inverse_components, + random_state=random_state, + ) + + self.dense_output = dense_output + self.density = density + + def _make_random_matrix(self, n_components, n_features): + """Generate the random projection matrix + + Parameters + ---------- + n_components : int + Dimensionality of the target projection space. + + n_features : int + Dimensionality of the original source space. + + Returns + ------- + components : sparse matrix of shape (n_components, n_features) + The generated random matrix in CSR format. + + """ + random_state = check_random_state(self.random_state) + self.density_ = _check_density(self.density, n_features) + return _sparse_random_matrix( + n_components, n_features, density=self.density_, random_state=random_state + ) + + def transform(self, X): + """Project the data by using matrix product with the random matrix. + + Parameters + ---------- + X : {ndarray, sparse matrix} of shape (n_samples, n_features) + The input data to project into a smaller dimensional space. + + Returns + ------- + X_new : {ndarray, sparse matrix} of shape (n_samples, n_components) + Projected array. It is a sparse matrix only when the input is sparse and + `dense_output = False`. + """ + check_is_fitted(self) + X = validate_data( + self, + X, + accept_sparse=["csr", "csc"], + reset=False, + dtype=[np.float64, np.float32], + ) + + return safe_sparse_dot(X, self.components_.T, dense_output=self.dense_output)