rasdani/github-patches · Datasets at Hugging Face

RedHatInsights__insights-core-1641

RedhatRelease parser failed to parse minor release version in some scenarios In few cases where redhat_release content is something similar to below, RedhatRelease parser fails to get the minor version extracted from it Run: ``` >>> from insights.parsers.redhat_release import RedhatRelease >>> from insights.tests import context_wrap >>> RedhatRelease(context_wrap("Red Hat Enterprise Linux release 7.5-0.14")).major 7 >>> RedhatRelease(context_wrap("Red Hat Enterprise Linux release 7.5-0.14")).minor Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/opt/insights/insights-core/insights/parsers/redhat_release.py", line 59, in minor return int(s[1]) ValueError: invalid literal for int() with base 10: '5-0' >>> RedhatRelease(context_wrap("Red Hat Enterprise Linux release 7.5-0.14")).version '7.5-0.14' ```

[ { "content": "\"\"\"\nredhat-release - File ``/etc/redhat-release``\n=============================================\n\nThis module provides plugins access to file ``/etc/redhat-release``\n\nTypical content of file ``/etc/redhat-release`` is::\n\n Red Hat Enterprise Linux Server release 7.2 (Maipo)\n\nThis mod...

diff --git a/insights/parsers/redhat_release.py b/insights/parsers/redhat_release.py index a0eccf7e1c..5bc134c8b6 100644 --- a/insights/parsers/redhat_release.py +++ b/insights/parsers/redhat_release.py @@ -54,7 +54,7 @@ def major(self): @property def minor(self): """int: the minor version of this OS.""" - s = self.parsed["version"].split(".") + s = self.parsed["version"].split("-", 1)[0].split(".") if len(s) > 1: return int(s[1]) diff --git a/insights/parsers/tests/test_redhat_release.py b/insights/parsers/tests/test_redhat_release.py index f91ed08dde..8da2bb10c0 100644 --- a/insights/parsers/tests/test_redhat_release.py +++ b/insights/parsers/tests/test_redhat_release.py @@ -10,6 +10,10 @@ Red Hat Enterprise Linux Server release 7.2 (Maipo) """.strip() +REDHAT_RELEASE3 = """ +Red Hat Enterprise Linux release 7.5-0.14 +""".strip() + RHVH_RHV40 = """ Red Hat Enterprise Linux release 7.3 """.strip() @@ -43,6 +47,16 @@ def test_rhe7(): assert release.product == "Red Hat Enterprise Linux Server" +def test_rhe75_0_14(): + release = RedhatRelease(context_wrap(REDHAT_RELEASE3)) + assert release.raw == REDHAT_RELEASE3 + assert release.major == 7 + assert release.minor == 5 + assert release.version == "7.5-0.14" + assert release.is_rhel + assert release.product == "Red Hat Enterprise Linux" + + def test_rhevh35(): release = RedhatRelease(context_wrap(RHEVH_RHEV35)) assert release.raw == RHEVH_RHEV35

ipython__ipython-11978

7.10 breaking tests with exception in publish The new 7.10 release is breaking Bokeh unit tests with an exception coming from within ipython: ``` self = <IPython.core.displaypub.DisplayPublisher object at 0x11883d7f0> data = {'text/html': '\n <div class="bk-root">\n <a href="https://bokeh.org" target="_blank" class="bk-logo bk-logo...version \'1.0\' from Bokeh development version \'1.0-1-abc\'. This configuration is unsupported and may not work!</p>'} metadata = None, source = None, transient = None, update = False, kwargs = {} handlers = {} << omitted >> handlers = {} if self.shell is not None: > handlers = self.shell.mime_renderers E AttributeError: 'InteractiveShell' object has no attribute 'mime_renderers' ../miniconda/envs/testenv/lib/python3.6/site-packages/IPython/core/displaypub.py:108: AttributeError ``` Is this an intentional change (documented anwhere?) or a regression/bug? cc @Carreau

[ { "content": "\"\"\"An interface for publishing rich data to frontends.\n\nThere are two components of the display system:\n\n* Display formatters, which take a Python object and compute the\n representation of the object in various formats (text, HTML, SVG, etc.).\n* The display publisher that is used to send...

diff --git a/IPython/core/displaypub.py b/IPython/core/displaypub.py index d769692e969..f651a2a0cf6 100644 --- a/IPython/core/displaypub.py +++ b/IPython/core/displaypub.py @@ -105,7 +105,7 @@ def publish(self, data, metadata=None, source=None, *, transient=None, update=Fa handlers = {} if self.shell is not None: - handlers = self.shell.mime_renderers + handlers = getattr(self.shell, 'mime_renderers', {}) for mime, handler in handlers.items(): if mime in data:

pyodide__pyodide-3959

pyodide-build test suite fails locally I'm trying to run the pyodide-build test suite locally inside Docker, ``` source pyodide_env.sh pytest pyodide-build ``` and so far it has had multiple failures, ``` FAILED pyodide-build/pyodide_build/tests/test_build_env.py::TestOutOfTree::get_build_environment_vars[node] - PermissionError: [Errno 13] Permission denied: '/packages' FAILED pyodide-build/pyodide_build/tests/test_build_env.py::TestOutOfTree::get_build_flag[node] - PermissionError: [Errno 13] Permission denied: '/packages' FAILED pyodide-build/pyodide_build/tests/test_build_env.py::TestOutOfTree::init_environment[node] - PermissionError: [Errno 13] Permission denied: '/packages' FAILED pyodide-build/pyodide_build/tests/test_build_env.py::TestOutOfTree::get_pyodide_root[node] - PermissionError: [Errno 13] Permission denied: '/packages' FAILED pyodide-build/pyodide_build/tests/test_build_env.py::TestOutOfTree::in_xbuildenv[node] - PermissionError: [Errno 13] Permission denied: '/packages' FAILED pyodide-build/pyodide_build/tests/test_pypi.py::fetch_or_build_pypi[node] - AssertionError: * Creating virtualenv isolated environment... FAILED pyodide-build/pyodide_build/tests/test_pypi.py::fetch_or_build_pypi_with_deps_and_extras[node] - AssertionError: Successfully fetched: eth_hash-0.5.2-py3-none-any.whl FAILED pyodide-build/pyodide_build/tests/test_pypi.py::fake_pypi_succeed[node] - AssertionError: 127.0.0.1 - - [23/Jun/2023 14:06:56] "GET /simple/resolves-package/ HTTP/1.1" 200 - FAILED pyodide-build/pyodide_build/tests/test_pypi.py::fake_pypi_extras_build[node] - AssertionError: 127.0.0.1 - - [23/Jun/2023 14:07:02] "GET /simple/pkg-b/ HTTP/1.1" 200 - ``` Maybe I'm doing something wrong or I should spend time reading through what we are doing in the CircleCI config but IMO the above should have worked, or else we need to update [developer instructions](https://pyodide.org/en/stable/development/testing.html#testing-and-benchmarking). Anyway, I can probably figure it out by spending enough time on it, but we probably need to improve the docs as this is not very developer friendly.

[ { "content": "# This file contains functions for managing the Pyodide build environment.\n\nimport functools\nimport os\nimport re\nimport subprocess\nimport sys\nfrom collections.abc import Iterator\nfrom contextlib import nullcontext, redirect_stdout\nfrom io import StringIO\nfrom pathlib import Path\n\nif sy...

diff --git a/pyodide-build/pyodide_build/build_env.py b/pyodide-build/pyodide_build/build_env.py index d37a8473e7f..7155033678c 100644 --- a/pyodide-build/pyodide_build/build_env.py +++ b/pyodide-build/pyodide_build/build_env.py @@ -199,6 +199,7 @@ def _get_make_environment_vars(*, pyodide_root: Path | None = None) -> dict[str, ["make", "-f", str(PYODIDE_ROOT / "Makefile.envs"), ".output_vars"], capture_output=True, text=True, + env={"PYODIDE_ROOT": str(PYODIDE_ROOT)}, ) if result.returncode != 0: diff --git a/pyodide-build/pyodide_build/tests/fixture.py b/pyodide-build/pyodide_build/tests/fixture.py index ef123f33c8f..060dbdf91f4 100644 --- a/pyodide-build/pyodide_build/tests/fixture.py +++ b/pyodide-build/pyodide_build/tests/fixture.py @@ -1,11 +1,14 @@ import json +import os import shutil from pathlib import Path from typing import Any import pytest -from ..common import chdir +from conftest import ROOT_PATH +from pyodide_build import build_env +from pyodide_build.common import chdir @pytest.fixture(scope="module") @@ -89,3 +92,59 @@ def temp_xbuildenv(tmp_path_factory): archive_name = shutil.make_archive("xbuildenv", "tar") yield base, archive_name + + +@pytest.fixture(scope="function") +def reset_env_vars(): + # Will reset the environment variables to their original values after each test. + + os.environ.pop("PYODIDE_ROOT", None) + old_environ = dict(os.environ) + + try: + yield + finally: + os.environ.clear() + os.environ.update(old_environ) + + +@pytest.fixture(scope="function") +def reset_cache(): + # Will remove all caches before each test. + + build_env.get_pyodide_root.cache_clear() + build_env.get_build_environment_vars.cache_clear() + build_env.get_unisolated_packages.cache_clear() + + yield + + +@pytest.fixture(scope="function") +def xbuildenv(selenium, tmp_path, reset_env_vars, reset_cache): + import subprocess as sp + + assert "PYODIDE_ROOT" not in os.environ + + envpath = Path(tmp_path) / ".pyodide-xbuildenv" + result = sp.run( + [ + "pyodide", + "xbuildenv", + "create", + str(envpath), + "--root", + ROOT_PATH, + "--skip-missing-files", + ] + ) + + assert result.returncode == 0 + + cur_dir = os.getcwd() + + os.chdir(tmp_path) + + try: + yield tmp_path + finally: + os.chdir(cur_dir) diff --git a/pyodide-build/pyodide_build/tests/test_build_env.py b/pyodide-build/pyodide_build/tests/test_build_env.py index 73eee7f83ef..5545b0291f8 100644 --- a/pyodide-build/pyodide_build/tests/test_build_env.py +++ b/pyodide-build/pyodide_build/tests/test_build_env.py @@ -1,40 +1,15 @@ +# flake8: noqa # This file contains tests that ensure build environment is properly initialized in # both in-tree and out-of-tree builds. -# TODO: move functions that are tested here to a separate module - import os -from pathlib import Path import pytest from conftest import ROOT_PATH from pyodide_build import build_env, common - -@pytest.fixture(scope="function") -def reset_env_vars(): - # Will reset the environment variables to their original values after each test. - - os.environ.pop("PYODIDE_ROOT", None) - old_environ = dict(os.environ) - - try: - yield - finally: - os.environ.clear() - os.environ.update(old_environ) - - -@pytest.fixture(scope="function") -def reset_cache(): - # Will remove all caches before each test. - - build_env.get_pyodide_root.cache_clear() - build_env.get_build_environment_vars.cache_clear() - build_env.get_unisolated_packages.cache_clear() - - yield +from .fixture import reset_cache, reset_env_vars, xbuildenv class TestInTree: @@ -96,6 +71,13 @@ def test_get_build_environment_vars(self, reset_env_vars, reset_cache): for var in extra_vars: assert var in build_vars, f"Missing {var}" + def test_get_make_environment_vars(self, reset_env_vars, reset_cache): + make_vars = build_env._get_make_environment_vars() + assert make_vars["PYODIDE_ROOT"] == str(ROOT_PATH) + + make_vars = build_env._get_make_environment_vars(pyodide_root=ROOT_PATH) + assert make_vars["PYODIDE_ROOT"] == str(ROOT_PATH) + def test_get_build_flag(self, reset_env_vars, reset_cache): for key, val in build_env.get_build_environment_vars().items(): assert build_env.get_build_flag(key) == val @@ -141,41 +123,6 @@ def test_get_build_environment_vars_host_env( class TestOutOfTree(TestInTree): - # TODO: selenium fixture is a hack to make these tests run only after building Pyodide. - @pytest.fixture(scope="function", autouse=True) - def xbuildenv(self, selenium, tmp_path, reset_env_vars, reset_cache): - import subprocess as sp - - assert "PYODIDE_ROOT" not in os.environ - - envpath = Path(tmp_path) / ".pyodide-xbuildenv" - result = sp.run( - [ - "pyodide", - "xbuildenv", - "create", - str(envpath), - "--root", - ROOT_PATH, - "--skip-missing-files", - ] - ) - - assert result.returncode == 0 - - yield tmp_path - - @pytest.fixture(scope="function", autouse=True) - def chdir_xbuildenv(self, xbuildenv): - cur_dir = os.getcwd() - - os.chdir(xbuildenv) - - try: - yield - finally: - os.chdir(cur_dir) - # Note: other tests are inherited from TestInTree def test_init_environment(self, xbuildenv, reset_env_vars, reset_cache): @@ -196,9 +143,17 @@ def test_get_pyodide_root(self, xbuildenv, reset_env_vars, reset_cache): == xbuildenv / ".pyodide-xbuildenv/xbuildenv/pyodide-root" ) - def test_in_xbuildenv(self, reset_env_vars, reset_cache): + def test_in_xbuildenv(self, xbuildenv, reset_env_vars, reset_cache): assert build_env.in_xbuildenv() + def test_get_make_environment_vars(self, xbuildenv, reset_env_vars, reset_cache): + xbuildenv_root = xbuildenv / ".pyodide-xbuildenv/xbuildenv/pyodide-root" + make_vars = build_env._get_make_environment_vars() + assert make_vars["PYODIDE_ROOT"] == str(xbuildenv_root) + + make_vars = build_env._get_make_environment_vars(pyodide_root=xbuildenv_root) + assert make_vars["PYODIDE_ROOT"] == str(xbuildenv_root) + def test_check_emscripten_version(monkeypatch): s = None diff --git a/pyodide-build/pyodide_build/tests/test_pypi.py b/pyodide-build/pyodide_build/tests/test_pypi.py index 1ae181db4ed..559246edeef 100644 --- a/pyodide-build/pyodide_build/tests/test_pypi.py +++ b/pyodide-build/pyodide_build/tests/test_pypi.py @@ -1,4 +1,5 @@ -import os +# flake8: noqa + import re import subprocess import sys @@ -14,7 +15,7 @@ from typer.testing import CliRunner from pyodide_build.cli import build -from pyodide_build.common import chdir +from .fixture import reset_cache, reset_env_vars, xbuildenv runner = CliRunner() @@ -213,16 +214,15 @@ def fake_pypi_url(fake_pypi_server): pyodide_build.out_of_tree.pypi._PYPI_INDEX = pypi_old -def test_fetch_or_build_pypi(selenium, tmp_path): +def test_fetch_or_build_pypi(xbuildenv): # TODO: - make test run without pyodide - output_dir = tmp_path / "dist" + output_dir = xbuildenv / "dist" # one pure-python package (doesn't need building) and one sdist package (needs building) pkgs = ["pytest-pyodide", "pycryptodome==3.15.0"] app = typer.Typer() app.command()(build.main) - os.chdir(tmp_path) for p in pkgs: result = runner.invoke( app, @@ -234,16 +234,15 @@ def test_fetch_or_build_pypi(selenium, tmp_path): assert len(built_wheels) == len(pkgs) -def test_fetch_or_build_pypi_with_deps_and_extras(selenium, tmp_path): +def test_fetch_or_build_pypi_with_deps_and_extras(xbuildenv): # TODO: - make test run without pyodide - output_dir = tmp_path / "dist" + output_dir = xbuildenv / "dist" # one pure-python package (doesn't need building) which depends on one sdist package (needs building) pkgs = ["eth-hash[pycryptodome]==0.5.1", "safe-pysha3 (>=1.0.0)"] app = typer.Typer() app.command()(build.main) - os.chdir(tmp_path) for p in pkgs: result = runner.invoke( app, @@ -255,38 +254,36 @@ def test_fetch_or_build_pypi_with_deps_and_extras(selenium, tmp_path): assert len(built_wheels) == 3 -def test_fake_pypi_succeed(selenium, tmp_path, fake_pypi_url): +def test_fake_pypi_succeed(xbuildenv, fake_pypi_url): # TODO: - make test run without pyodide - output_dir = tmp_path / "dist" + output_dir = xbuildenv / "dist" # build package that resolves right app = typer.Typer() app.command()(build.main) - with chdir(tmp_path): - result = runner.invoke( - app, - ["resolves-package", "--build-dependencies"], - ) + result = runner.invoke( + app, + ["resolves-package", "--build-dependencies"], + ) - assert result.exit_code == 0, str(result.stdout) + str(result) + assert result.exit_code == 0, str(result.stdout) + str(result) built_wheels = set(output_dir.glob("*.whl")) assert len(built_wheels) == 5 -def test_fake_pypi_resolve_fail(selenium, tmp_path, fake_pypi_url): - # TODO: - make test run without pyodide - output_dir = tmp_path / "dist" +def test_fake_pypi_resolve_fail(xbuildenv, fake_pypi_url): + output_dir = xbuildenv / "dist" + # build package that resolves right app = typer.Typer() app.command()(build.main) - with chdir(tmp_path): - result = runner.invoke( - app, - ["fails-package", "--build-dependencies"], - ) + result = runner.invoke( + app, + ["fails-package", "--build-dependencies"], + ) # this should fail and should not build any wheels assert result.exit_code != 0, result.stdout @@ -294,18 +291,17 @@ def test_fake_pypi_resolve_fail(selenium, tmp_path, fake_pypi_url): assert len(built_wheels) == 0 -def test_fake_pypi_extras_build(selenium, tmp_path, fake_pypi_url): +def test_fake_pypi_extras_build(xbuildenv, fake_pypi_url): # TODO: - make test run without pyodide - output_dir = tmp_path / "dist" + output_dir = xbuildenv / "dist" # build package that resolves right app = typer.Typer() app.command()(build.main) - with chdir(tmp_path): - result = runner.invoke( - app, - ["pkg-b[docs]", "--build-dependencies"], - ) + result = runner.invoke( + app, + ["pkg-b[docs]", "--build-dependencies"], + ) # this should work assert result.exit_code == 0, result.stdout @@ -313,16 +309,16 @@ def test_fake_pypi_extras_build(selenium, tmp_path, fake_pypi_url): assert len(built_wheels) == 2 -def test_fake_pypi_repeatable_build(selenium, tmp_path, fake_pypi_url): - # TODO: - make test run without pyodide - output_dir = tmp_path / "dist" +def test_fake_pypi_repeatable_build(xbuildenv, fake_pypi_url): + output_dir = xbuildenv / "dist" + # build package that resolves right app = typer.Typer() app.command()(build.main) # override a dependency version and build # pkg-a - with open(tmp_path / "requirements.txt", "w") as req_file: + with open("requirements.txt", "w") as req_file: req_file.write( """ # Whole line comment @@ -330,17 +326,17 @@ def test_fake_pypi_repeatable_build(selenium, tmp_path, fake_pypi_url): pkg-a """ ) - with chdir(tmp_path): - result = runner.invoke( - app, - [ - "-r", - "requirements.txt", - "--build-dependencies", - "--output-lockfile", - "lockfile.txt", - ], - ) + + result = runner.invoke( + app, + [ + "-r", + "requirements.txt", + "--build-dependencies", + "--output-lockfile", + "lockfile.txt", + ], + ) # this should work assert result.exit_code == 0, result.stdout built_wheels = list(output_dir.glob("*.whl")) @@ -354,11 +350,10 @@ def test_fake_pypi_repeatable_build(selenium, tmp_path, fake_pypi_url): # rebuild from package-versions lockfile and # check it outputs the same version number - with chdir(tmp_path): - result = runner.invoke( - app, - ["-r", str(tmp_path / "lockfile.txt")], - ) + result = runner.invoke( + app, + ["-r", "lockfile.txt"], + ) # should still have built 1.0.0 of pkg-c built_wheels = list(output_dir.glob("*.whl")) @@ -369,7 +364,7 @@ def test_fake_pypi_repeatable_build(selenium, tmp_path, fake_pypi_url): assert len(built_wheels) == 2, result.stdout -def test_bad_requirements_text(selenium, tmp_path): +def test_bad_requirements_text(xbuildenv): app = typer.Typer() app.command()(build.main) # test 1 - error on URL location in requirements @@ -377,11 +372,11 @@ def test_bad_requirements_text(selenium, tmp_path): # test 3 - error on editable install of package bad_lines = [" pkg-c@http://www.pkg-c.org", " -r bob.txt", " -e pkg-c"] for line in bad_lines: - with open(tmp_path / "requirements.txt", "w") as req_file: + with open("requirements.txt", "w") as req_file: req_file.write(line + "\n") - with chdir(tmp_path): - result = runner.invoke( - app, - ["-r", "requirements.txt"], - ) - assert result.exit_code != 0 and line.strip() in str(result) + + result = runner.invoke( + app, + ["-r", "requirements.txt"], + ) + assert result.exit_code != 0 and line.strip() in str(result)

PrefectHQ__prefect-2609

Consider promoting `case` to the top level ## Current behavior *Please describe how the feature works today* Currently, the `case` context manager must be imported from `prefect.tasks.control_flow.case`. ## Proposed behavior *Please describe your proposed change to the current behavior* I think we should consider promoting `case` to being importable as `prefect.case`, since it forms a fundamental part of the Python API. Other control flow utilities have "task-like" semantics (even if they are called as functions), and it's more appropriate for them to live in a `tasks` submodule. However, like `task`, `Flow`, `tags`, and `unmapped`, I believe `case` represents a significant component of Prefect's Python syntax and warrants top-level availability. ## Example *Please give an example of how the enhancement would be useful* ``` from prefect import Flow, case with Flow("example"): with case(is_this_easy, True): do_stuff() with prefect.tasks.control_flow.case(is_this_easy, False): do_other_stuff() ```

[ { "content": "import prefect.utilities\nfrom prefect.configuration import config\n\nfrom prefect.utilities.context import context\n\nfrom prefect.client import Client\nimport prefect.schedules\nimport prefect.triggers\nimport prefect.environments\n\nfrom prefect.core import Task, Flow, Parameter\nimport prefect...

diff --git a/changes/issue2568.yaml b/changes/issue2568.yaml new file mode 100644 index 000000000000..40b94cf8076f --- /dev/null +++ b/changes/issue2568.yaml @@ -0,0 +1,2 @@ +enhancement: + - Add `case` to top-level namespace - [#2609](https://github.com/PrefectHQ/prefect/pull/2609) diff --git a/src/prefect/__init__.py b/src/prefect/__init__.py index 0ec3a15778d7..2bcc5d016d24 100644 --- a/src/prefect/__init__.py +++ b/src/prefect/__init__.py @@ -11,6 +11,7 @@ from prefect.core import Task, Flow, Parameter import prefect.engine import prefect.tasks +from prefect.tasks.control_flow import case from prefect.utilities.tasks import task, tags, unmapped import prefect.serialization

vacanza__python-holidays-754

Diwali Singapore is on 24th of October not 24th of November Holidays returns (datetime.date(2022, 11, 24), 'Deepavali') not the actual day which is this coming Monday the 24th of October. Full list here https://www.mom.gov.sg/employment-practices/public-holidays

[ { "content": "# python-holidays\n# ---------------\n# A fast, efficient Python library for generating country, province and state\n# specific sets of holidays on the fly. It aims to make determining whether a\n# specific date is a holiday as fast and flexible as possible.\n#\n# Authors: dr-prodigy <mauriz...

diff --git a/holidays/countries/singapore.py b/holidays/countries/singapore.py index b055f77d2..da1f9d2be 100644 --- a/holidays/countries/singapore.py +++ b/holidays/countries/singapore.py @@ -261,7 +261,7 @@ def _populate(self, year: int) -> None: 2019: (OCT, 27), 2020: (NOV, 14), 2021: (NOV, 4), - 2022: (NOV, 24), + 2022: (OCT, 24), 2023: (NOV, 12), } if year in dates_fixed_obs: diff --git a/test/countries/test_singapore.py b/test/countries/test_singapore.py index 3113c0c16..6e25c3465 100644 --- a/test/countries/test_singapore.py +++ b/test/countries/test_singapore.py @@ -60,7 +60,7 @@ def test_Singapore(self): self.assertIn(date(2022, 5, 16), self.holidays) self.assertIn(date(2022, 7, 9), self.holidays) self.assertIn(date(2022, 8, 9), self.holidays) - self.assertIn(date(2022, 11, 24), self.holidays) + self.assertIn(date(2022, 10, 24), self.holidays) self.assertIn(date(2022, 12, 25), self.holidays) self.assertIn(date(2022, 12, 26), self.holidays) # 2022: total holidays (11 + 3 falling on a Sunday)

automl__auto-sklearn-190

Add warning if dependencies are not met There should be a warning if one of the following dependencies is not met: - scikit-learn==0.17 - smac==0.0.1 - lockfile>=0.10 - ConfigSpace>=0.2.1 - pyrfr==0.2.1

[ { "content": "from warnings import warn\n\nimport pkg_resources\nimport re\n\nfrom distutils.version import LooseVersion\n\n\nRE_PATTERN = re.compile('^(?P<name>[\\w\\-]+)((?P<operation>==|>=|>)(?P<version>(\\d+\\.)?(\\d+\\.)?(\\d+)))?$')\n\n\ndef verify_packages(packages):\n if not packages:\n return...

diff --git a/autosklearn/util/dependencies.py b/autosklearn/util/dependencies.py index 61ed76adf5..d36ad7e5c8 100644 --- a/autosklearn/util/dependencies.py +++ b/autosklearn/util/dependencies.py @@ -33,7 +33,7 @@ def _verify_package(name, operation, version): try: module = pkg_resources.get_distribution(name) except pkg_resources.DistributionNotFound: - raise MissingPackageError(name) from None + raise MissingPackageError(name) if not operation: return

pre-commit__pre-commit-948

Support GIT_SSH_COMMAND Currently, `GIT_SSH` is supported for overriding the git command, but it is is sightly less ergonomic than `GIT_SSH_COMMAND` since it requires file. Adding support for passing `GIT_SSH_COMMAND` to git commands would obviate the need for creating a new file when you want to change the ssh command.

[ { "content": "from __future__ import unicode_literals\n\nimport logging\nimport os.path\nimport sys\n\nfrom pre_commit.util import cmd_output\n\n\nlogger = logging.getLogger(__name__)\n\n\ndef zsplit(s):\n s = s.strip('\\0')\n if s:\n return s.split('\\0')\n else:\n return []\n\n\ndef no_...

diff --git a/pre_commit/git.py b/pre_commit/git.py index f0b504043..4849d7c64 100644 --- a/pre_commit/git.py +++ b/pre_commit/git.py @@ -29,7 +29,7 @@ def no_git_env(): # GIT_INDEX_FILE: Causes 'error invalid object ...' during commit return { k: v for k, v in os.environ.items() - if not k.startswith('GIT_') or k in {'GIT_SSH'} + if not k.startswith('GIT_') or k in {'GIT_SSH', 'GIT_SSH_COMMAND'} }

uclapi__uclapi-4023

[Feature Request] Add /authorize Oauth route **Is your feature request related to a problem? Please describe.** I have been attempting to use 'auth0-react' to implement Oauth with UCL API, however, this requires a fair bit of tinkering as the defaults of this and many other auth libraries are to redirect to a "/authorize?client_id..." endpoint which the UCL API does not support. While this can be avoided through customisation, would it be possible to add a "/authorize" route, as I believe this could make it easier to use some of the "plug and play" Americanized auth libraries available? **Describe the solution you'd like** Edit uclapi/backend/uclapi/oauth/urls.py as below ``` urlpatterns = [ url(r'authorise/$', views.authorise), url(r'authorize/$', views.authorise), <===== Including views.authorise for the 'authorize/$' route. url(r'shibcallback', views.shibcallback), url(r'token$', views.token), url(r'tokens/scopes$', views.scope_map), url(r'tokens/test$', views.token_test), url(r'user/allow$', views.userallow), url(r'user/deny$', views.userdeny), url(r'user/data$', views.userdata), url(r'user/studentnumber$', views.get_student_number), url(r'deauthorise$', views.deauthorise_app), url(r'user/settings$', views.get_settings) ] ``` ![image](https://user-images.githubusercontent.com/57833957/219857932-86c371d5-c0f0-444b-a179-6c312b48c9c2.png) ![image](https://user-images.githubusercontent.com/57833957/219857962-7da7e11e-475b-4d6c-bb71-1c6eefcf0354.png)

[ { "content": "from django.conf.urls import url\n\nfrom . import views\n\nurlpatterns = [\n url(r'authorise/$', views.authorise),\n url(r'adcallback', views.adcallback),\n url(r'token$', views.token),\n url(r'tokens/scopes$', views.scope_map),\n url(r'tokens/test$', views.token_test),\n url(r'u...

[ { "content": "from django.conf.urls import url\n\nfrom . import views\n\nurlpatterns = [\n url(r'authorise/$', views.authorise),\n url(r'authorize/$', views.authorise),\n url(r'adcallback', views.adcallback),\n url(r'token$', views.token),\n url(r'tokens/scopes$', views.scope_map),\n url(r'tok...

diff --git a/backend/uclapi/oauth/urls.py b/backend/uclapi/oauth/urls.py index 0f9a33847..7564f4d21 100644 --- a/backend/uclapi/oauth/urls.py +++ b/backend/uclapi/oauth/urls.py @@ -4,6 +4,7 @@ urlpatterns = [ url(r'authorise/$', views.authorise), + url(r'authorize/$', views.authorise), url(r'adcallback', views.adcallback), url(r'token$', views.token), url(r'tokens/scopes$', views.scope_map), diff --git a/uclapi.openapi.json b/uclapi.openapi.json index eb0b13fe1..7fe18e8e8 100644 --- a/uclapi.openapi.json +++ b/uclapi.openapi.json @@ -2170,7 +2170,7 @@ }, "OAuthToken": { "type": "apiKey", - "description": "This API requires you to pass your OAuth2 token as a query parameter called 'token'. Use the /authorize and /oauth/token endpoints to authorize a user and get this token.", + "description": "This API requires you to pass your OAuth2 token as a query parameter called 'token'. Use the /authorise and /oauth/token endpoints to authorize a user and get this token.", "name": "token", "in": "query" },

googleapis__google-cloud-python-9604

Release google-cloud-storage Hi @tseaver, could you help cut a release for google-cloud-storage? cc: @JesseLovelace

[ { "content": "# Copyright 2018 Google LLC\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicabl...

diff --git a/storage/CHANGELOG.md b/storage/CHANGELOG.md index ff61b97c9cfe..55169d4ed82e 100644 --- a/storage/CHANGELOG.md +++ b/storage/CHANGELOG.md @@ -4,6 +4,14 @@ [1]: https://pypi.org/project/google-cloud-storage/#history +## 1.22.0 + +11-05-2019 10:22 PST + + +### New Features +- Add UBLA attrs to IAMConfiguration. ([#9475](https://github.com/googleapis/google-cloud-python/pull/9475)) + ## 1.21.0 10-28-2019 21:52 PDT diff --git a/storage/setup.py b/storage/setup.py index bbf6890bb7c4..5b3ddfa70f09 100644 --- a/storage/setup.py +++ b/storage/setup.py @@ -22,7 +22,7 @@ name = "google-cloud-storage" description = "Google Cloud Storage API client library" -version = "1.21.0" +version = "1.22.0" # Should be one of: # 'Development Status :: 3 - Alpha' # 'Development Status :: 4 - Beta'

wagtail__wagtail-9369

Wagtail version number in admin has an extra dot This is tagged as a [**good first issue**](https://github.com/wagtail/wagtail/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc+label%3A%22good+first+issue%22) – if you want to take it on, please leave a comment below to say so, no need to ask for permission, first come first serve! State your intent and share any questions / plans you have on how to approach the task. ### Issue Summary In the Settings menu, we display Wagtail’s version number at the bottom: <img width="409" alt="dot-menu" src="https://user-images.githubusercontent.com/877585/195653500-98c8c982-f39f-4f24-a8df-3ebbc7401af1.png"> This has been there for a while and I don’t think there is a specific reason for it. It’d be nice to display the version numbers the same as what we do in the docs. So rather than `v.2.16.1` – `v2.16.1`. ### Steps to Reproduce 1. Open the Wagtail admin 2. Open the Settings menu and look at the bottom ### Technical details - Wagtail version: tested in v.2.16.1 ### Proposed solution I believe this could be as simple as removing the "." here: https://github.com/wagtail/wagtail/blob/main/wagtail/admin/wagtail_hooks.py#L105 ```diff -footer_text="Wagtail v." + __version__, +footer_text="Wagtail v" + __version__, ``` We’d need to test that this doesn’t affect our other code relying on version numbers.

[ { "content": "from django.conf import settings\nfrom django.contrib.auth.models import Permission\nfrom django.urls import reverse\nfrom django.utils.http import urlencode\nfrom django.utils.translation import gettext\nfrom django.utils.translation import gettext_lazy as _\nfrom draftjs_exporter.dom import DOM\...

diff --git a/CHANGELOG.txt b/CHANGELOG.txt index 9c028178586a..abe90a8ad4be 100644 --- a/CHANGELOG.txt +++ b/CHANGELOG.txt @@ -72,6 +72,7 @@ Changelog * Fix: Ensure that buttons on custom chooser widgets are correctly shown on hover (Thibaud Colas) * Fix: Add missing asterisk to title field placeholder (Seremba Patrick) * Fix: Avoid creating an extra rich text block when inserting a new block at the end of the content (Matt Westcott) + * Fix: Removed the extra dot in the Wagtail version shown within the admin settings menu item (Loveth Omokaro) 4.0.3 (xx.xx.xxxx) - IN DEVELOPMENT diff --git a/CONTRIBUTORS.rst b/CONTRIBUTORS.rst index b7e7e19f38c2..040fe941b3d0 100644 --- a/CONTRIBUTORS.rst +++ b/CONTRIBUTORS.rst @@ -639,6 +639,7 @@ Contributors * Chizoba Nweke * Seremba Patrick * Ruqouyyah Muhammad +* Loveth Omokaro Translators diff --git a/docs/releases/4.1.md b/docs/releases/4.1.md index 8a45664103a0..c8b5fdf4244a 100644 --- a/docs/releases/4.1.md +++ b/docs/releases/4.1.md @@ -97,6 +97,7 @@ This feature was developed by Karl Hobley and Matt Westcott. * Ensure that buttons on custom chooser widgets are correctly shown on hover (Thibaud Colas) * Add missing asterisk to title field placeholder (Seremba Patrick) * Avoid creating an extra rich text block when inserting a new block at the end of the content (Matt Westcott) + * Removed the extra dot in the Wagtail version shown within the admin settings menu item (Loveth Omokaro) ## Upgrade considerations diff --git a/wagtail/admin/wagtail_hooks.py b/wagtail/admin/wagtail_hooks.py index eb358295182a..0e2d658ad131 100644 --- a/wagtail/admin/wagtail_hooks.py +++ b/wagtail/admin/wagtail_hooks.py @@ -102,7 +102,7 @@ def render_component(self, request): self.menu.render_component(request), icon_name=self.icon_name, classnames=self.classnames, - footer_text="Wagtail v." + __version__, + footer_text="Wagtail v" + __version__, )

spack__spack-19482

Installation issue: gcc  ### Steps to reproduce the issue  ```console $ spack install gcc@master ... ==> No binary for gcc found: installing from source [190/630] Reversed (or previously applied) patch detected! Assume -R? [n] Apply anyway? [n] 2 out of 2 hunks ignored -- saving rejects to file gcc/Makefile.in.rej Reversed (or previously applied) patch detected! Assume -R? [n] Apply anyway? [n] 1 out of 1 hunk ignored -- saving rejects to file gcc/configure.ac.rej ==> Patch /lustre/home/ca-tgreen/Work/git/spack/var/spack/repos/builtin/packages/gcc/zstd.patch failed. ==> Error: ProcessError: Command exited with status 1: '/usr/bin/patch' '-s' '-p' '1' '-i' '/lustre/home/ca-tgreen/Work/git/spack/var/spack/repos/builtin/packages/gcc/zstd.patch' '-d' '.' ``` ### Information on your system  * **Spack:** 0.15.4-979-ee1725828 * **Python:** 3.6.8 * **Platform:** cray-rhel8-aarch64  ### Additional information  * [spack-build-out.txt]() * [spack-build-env.txt]() Not present in staging directory.  @michaelkuhn ### General information  - [x] I have run `spack debug report` and reported the version of Spack/Python/Platform - [x] I have run `spack maintainers <name-of-the-package>` and @mentioned any maintainers - [ ] I have uploaded the build log and environment files - [x] I have searched the issues of this repo and believe this is not a duplicate

[ { "content": "# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other\n# Spack Project Developers. See the top-level COPYRIGHT file for details.\n#\n# SPDX-License-Identifier: (Apache-2.0 OR MIT)\nimport glob\nimport itertools\nimport os\nimport re\nimport sys\n\nimport llnl.util.tty as tty\ni...

diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 991f0fadb01bc1..6677961af68a01 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -270,7 +270,7 @@ class Gcc(AutotoolsPackage, GNUMirrorPackage): patch('sys_ustat-4.9.patch', when='@4.9') # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=95005 - patch('zstd.patch', when='@10:') + patch('zstd.patch', when='@10.0:10.2') build_directory = 'spack-build'

psf__black-1892

s390x: test_python2/test_python2_unicode_literals can't assign to () INTERNAL ERROR During the build of 19.10b0 in Fedora, the following test failure occurs on s390x (Big Endian) architecture: ``` ====================================================================== FAIL: test_python2 (tests.test_black.BlackTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/builddir/build/BUILD/black-19.10b0/black.py", line 3754, in assert_equivalent src_ast = parse_ast(src) File "/builddir/build/BUILD/black-19.10b0/black.py", line 3686, in parse_ast return ast27.parse(src) File "/usr/lib64/python3.8/site-packages/typed_ast/ast27.py", line 50, in parse return _ast27.parse(source, filename, mode) File "<unknown>", line 10 SyntaxError: can't assign to () During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib64/python3.8/unittest/mock.py", line 1342, in patched return func(*newargs, **newkeywargs) File "/builddir/build/BUILD/black-19.10b0/tests/test_black.py", line 543, in test_python2 black.assert_equivalent(source, actual) File "/builddir/build/BUILD/black-19.10b0/black.py", line 3756, in assert_equivalent raise AssertionError( AssertionError: cannot use --safe with this file; failed to parse source file. AST error message: can't assign to () (<unknown>, line 10) ====================================================================== FAIL: test_python2_unicode_literals (tests.test_black.BlackTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib64/python3.8/unittest/mock.py", line 1342, in patched return func(*newargs, **newkeywargs) File "/builddir/build/BUILD/black-19.10b0/tests/test_black.py", line 560, in test_python2_unicode_literals black.assert_equivalent(source, actual) File "/builddir/build/BUILD/black-19.10b0/black.py", line 3775, in assert_equivalent raise AssertionError( AssertionError: INTERNAL ERROR: Black produced code that is not equivalent to the source. Please report a bug on https://github.com/psf/black/issues. This diff might be helpful: --- src +++ dst @@ -1,4 +1,70 @@ Module( body= + ImportFrom( + level= + 0, # int + module= + '__future__', # str + names= + alias( + asname= + '_unicode_literals', # str + name= + 'unicode_literals', # str + ) # /alias + ) # /ImportFrom + ImportFrom( + level= + 0, # int + module= + '__future__', # str + names= + alias( + asname= + None, # NoneType + name= + 'absolute_import', # str + ) # /alias + ) # /ImportFrom + ImportFrom( + level= + 0, # int + module= + '__future__', # str + names= + alias( + asname= + 'lol', # str + name= + 'print_function', # str + ) # /alias + alias( + asname= + None, # NoneType + name= + 'with_function', # str + ) # /alias + ) # /ImportFrom + Expr( + value= + Constant( + value= + 'hello', # str + ) # /Constant + ) # /Expr + Expr( + value= + Constant( + value= + 'hello', # str + ) # /Constant + ) # /Expr + Expr( + value= + Constant( + value= + 'hello', # str + ) # /Constant + ) # /Expr type_ignores= ) # /Module ---------------------------------------------------------------------- Ran 119 tests in 18.012s FAILED (failures=2) ``` **To Reproduce**, run the test suite on s390x. Here is the build log with all the commands: [build.log](https://github.com/psf/black/files/3782557/build.log) Here is the root log with all the package versions: [root.log](https://github.com/psf/black/files/3782561/root.log) **Expected behavior** Test succeed an all architectures. **Environment:** - Version: 19.10b0 - OS and Python version: Linux, Fedora 32 on s390x, Python 3.8.0 **Does this bug also happen on master?** yes, on 6bedb5c58a7d8c25aa9509f8217bc24e9797e90d **Additional context** The problem does not happen on the same build system with armv7hl or ppc64le.

[ { "content": "# Copyright (C) 2020 Łukasz Langa\nfrom setuptools import setup\nimport sys\nimport os\n\nassert sys.version_info >= (3, 6, 0), \"black requires Python 3.6+\"\nfrom pathlib import Path # noqa E402\n\nCURRENT_DIR = Path(__file__).parent\nsys.path.insert(0, str(CURRENT_DIR)) # for setuptools.build...

diff --git a/Pipfile b/Pipfile index ba596b3d738..9a4d5bd7c1b 100644 --- a/Pipfile +++ b/Pipfile @@ -28,7 +28,7 @@ mypy_extensions = ">=0.4.3" pathspec = ">=0.6" regex = ">=2020.1.8" toml = ">=0.10.1" -typed-ast = "==1.4.1" +typed-ast = "==1.4.2" typing_extensions = ">=3.7.4" black = {editable = true,extras = ["d"],path = "."} dataclasses = {"python_version <" = "3.7","version >" = "0.6"} diff --git a/Pipfile.lock b/Pipfile.lock index a5c38aa0777..dd78a3c3178 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "21836c0a63b6e3e1eacd0adec7dea61d2d5989e38225edd976ff144e499f0426" + "sha256": "3c4e23d0b6e49bac5ff2347dcb07bb4dd084d39b78c93a32359842dda401e7bf" }, "pipfile-spec": 6, "requires": {}, @@ -259,39 +259,39 @@ }, "typed-ast": { "hashes": [ - "sha256:0666aa36131496aed8f7be0410ff974562ab7eeac11ef351def9ea6fa28f6355", - "sha256:0c2c07682d61a629b68433afb159376e24e5b2fd4641d35424e462169c0a7919", - "sha256:0d8110d78a5736e16e26213114a38ca35cb15b6515d535413b090bd50951556d", - "sha256:249862707802d40f7f29f6e1aad8d84b5aa9e44552d2cc17384b209f091276aa", - "sha256:24995c843eb0ad11a4527b026b4dde3da70e1f2d8806c99b7b4a7cf491612652", - "sha256:269151951236b0f9a6f04015a9004084a5ab0d5f19b57de779f908621e7d8b75", - "sha256:3742b32cf1c6ef124d57f95be609c473d7ec4c14d0090e5a5e05a15269fb4d0c", - "sha256:4083861b0aa07990b619bd7ddc365eb7fa4b817e99cf5f8d9cf21a42780f6e01", - "sha256:498b0f36cc7054c1fead3d7fc59d2150f4d5c6c56ba7fb150c013fbc683a8d2d", - "sha256:4e3e5da80ccbebfff202a67bf900d081906c358ccc3d5e3c8aea42fdfdfd51c1", - "sha256:6daac9731f172c2a22ade6ed0c00197ee7cc1221aa84cfdf9c31defeb059a907", - "sha256:715ff2f2df46121071622063fc7543d9b1fd19ebfc4f5c8895af64a77a8c852c", - "sha256:73d785a950fc82dd2a25897d525d003f6378d1cb23ab305578394694202a58c3", - "sha256:7e4c9d7658aaa1fc80018593abdf8598bf91325af6af5cce4ce7c73bc45ea53d", - "sha256:8c8aaad94455178e3187ab22c8b01a3837f8ee50e09cf31f1ba129eb293ec30b", - "sha256:8ce678dbaf790dbdb3eba24056d5364fb45944f33553dd5869b7580cdbb83614", - 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"sha256:73d785a950fc82dd2a25897d525d003f6378d1cb23ab305578394694202a58c3", - "sha256:7e4c9d7658aaa1fc80018593abdf8598bf91325af6af5cce4ce7c73bc45ea53d", - "sha256:8c8aaad94455178e3187ab22c8b01a3837f8ee50e09cf31f1ba129eb293ec30b", - "sha256:8ce678dbaf790dbdb3eba24056d5364fb45944f33553dd5869b7580cdbb83614", - "sha256:92c325624e304ebf0e025d1224b77dd4e6393f18aab8d829b5b7e04afe9b7a2c", - "sha256:aaee9905aee35ba5905cfb3c62f3e83b3bec7b39413f0a7f19be4e547ea01ebb", - "sha256:b52ccf7cfe4ce2a1064b18594381bccf4179c2ecf7f513134ec2f993dd4ab395", - "sha256:bcd3b13b56ea479b3650b82cabd6b5343a625b0ced5429e4ccad28a8973f301b", - "sha256:c9e348e02e4d2b4a8b2eedb48210430658df6951fa484e59de33ff773fbd4b41", - "sha256:d205b1b46085271b4e15f670058ce182bd1199e56b317bf2ec004b6a44f911f6", - "sha256:d43943ef777f9a1c42bf4e552ba23ac77a6351de620aa9acf64ad54933ad4d34", - "sha256:d5d33e9e7af3b34a40dc05f498939f0ebf187f07c385fd58d591c533ad8562fe", - "sha256:d648b8e3bf2fe648745c8ffcee3db3ff903d0817a01a12dd6a6ea7a8f4889072", - "sha256:f208eb7aff048f6bea9586e61af041ddf7f9ade7caed625742af423f6bae3298", - "sha256:fac11badff8313e23717f3dada86a15389d0708275bddf766cca67a84ead3e91", - "sha256:fc0fea399acb12edbf8a628ba8d2312f583bdbdb3335635db062fa98cf71fca4", - "sha256:fcf135e17cc74dbfbc05894ebca928ffeb23d9790b3167a674921db19082401f", - "sha256:fe460b922ec15dd205595c9b5b99e2f056fd98ae8f9f56b888e7a17dc2b757e7" + "sha256:07d49388d5bf7e863f7fa2f124b1b1d89d8aa0e2f7812faff0a5658c01c59aa1", + "sha256:14bf1522cdee369e8f5581238edac09150c765ec1cb33615855889cf33dcb92d", + "sha256:240296b27397e4e37874abb1df2a608a92df85cf3e2a04d0d4d61055c8305ba6", + "sha256:36d829b31ab67d6fcb30e185ec996e1f72b892255a745d3a82138c97d21ed1cd", + "sha256:37f48d46d733d57cc70fd5f30572d11ab8ed92da6e6b28e024e4a3edfb456e37", + "sha256:4c790331247081ea7c632a76d5b2a265e6d325ecd3179d06e9cf8d46d90dd151", + "sha256:5dcfc2e264bd8a1db8b11a892bd1647154ce03eeba94b461effe68790d8b8e07", + "sha256:7147e2a76c75f0f64c4319886e7639e490fee87c9d25cb1d4faef1d8cf83a440", + "sha256:7703620125e4fb79b64aa52427ec192822e9f45d37d4b6625ab37ef403e1df70", + "sha256:8368f83e93c7156ccd40e49a783a6a6850ca25b556c0fa0240ed0f659d2fe496", + "sha256:84aa6223d71012c68d577c83f4e7db50d11d6b1399a9c779046d75e24bed74ea", + "sha256:85f95aa97a35bdb2f2f7d10ec5bbdac0aeb9dafdaf88e17492da0504de2e6400", + "sha256:8db0e856712f79c45956da0c9a40ca4246abc3485ae0d7ecc86a20f5e4c09abc", + "sha256:9044ef2df88d7f33692ae3f18d3be63dec69c4fb1b5a4a9ac950f9b4ba571606", + "sha256:963c80b583b0661918718b095e02303d8078950b26cc00b5e5ea9ababe0de1fc", + "sha256:987f15737aba2ab5f3928c617ccf1ce412e2e321c77ab16ca5a293e7bbffd581", + "sha256:9ec45db0c766f196ae629e509f059ff05fc3148f9ffd28f3cfe75d4afb485412", + "sha256:9fc0b3cb5d1720e7141d103cf4819aea239f7d136acf9ee4a69b047b7986175a", + "sha256:a2c927c49f2029291fbabd673d51a2180038f8cd5a5b2f290f78c4516be48be2", + "sha256:a38878a223bdd37c9709d07cd357bb79f4c760b29210e14ad0fb395294583787", + "sha256:b4fcdcfa302538f70929eb7b392f536a237cbe2ed9cba88e3bf5027b39f5f77f", + "sha256:c0c74e5579af4b977c8b932f40a5464764b2f86681327410aa028a22d2f54937", + "sha256:c1c876fd795b36126f773db9cbb393f19808edd2637e00fd6caba0e25f2c7b64", + "sha256:c9aadc4924d4b5799112837b226160428524a9a45f830e0d0f184b19e4090487", + "sha256:cc7b98bf58167b7f2db91a4327da24fb93368838eb84a44c472283778fc2446b", + "sha256:cf54cfa843f297991b7388c281cb3855d911137223c6b6d2dd82a47ae5125a41", + "sha256:d003156bb6a59cda9050e983441b7fa2487f7800d76bdc065566b7d728b4581a", + "sha256:d175297e9533d8d37437abc14e8a83cbc68af93cc9c1c59c2c292ec59a0697a3", + "sha256:d746a437cdbca200622385305aedd9aef68e8a645e385cc483bdc5e488f07166", + "sha256:e683e409e5c45d5c9082dc1daf13f6374300806240719f95dc783d1fc942af10" ], "index": "pypi", - "version": "==1.4.1" + "version": "==1.4.2" }, "typing-extensions": { "hashes": [ diff --git a/setup.py b/setup.py index 14bc1ef586a..c97dd35fe28 100644 --- a/setup.py +++ b/setup.py @@ -71,7 +71,7 @@ def get_long_description() -> str: "click>=7.1.2", "appdirs", "toml>=0.10.1", - "typed-ast>=1.4.0", + "typed-ast>=1.4.2", "regex>=2020.1.8", "pathspec>=0.6, <1", "dataclasses>=0.6; python_version < '3.7'",

googleapis__google-cloud-python-5683

Release 'datastore 1.7.0' Major changes are: - Add support for Python 3.7. - Drop support for Python 3.4. - Bugfix: query offsets (#4675).

[ { "content": "# Copyright 2018 Google LLC\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicabl...

diff --git a/datastore/CHANGELOG.md b/datastore/CHANGELOG.md index 4c47905a4a53..2ad75b1ff3b5 100644 --- a/datastore/CHANGELOG.md +++ b/datastore/CHANGELOG.md @@ -4,6 +4,25 @@ [1]: https://pypi.org/project/google-cloud-datastore/#history +## 1.7.0 + +### Implementation Changes + +- Do not pass 'offset' once the query iterator has a cursor (#5503) +- Add test runs for Python 3.7 and remove run for 3.4 (#5295) + +### Documentation + +- minor fix to datastore example (#5452) +- Add example showing explicit unicode for text values in entities. (#5263) + +### Internal / Testing Changes + +- Modify system tests to use prerelease versions of grpcio (#5304) +- Avoid overwriting '__module__' of messages from shared modules. (#5364) +- Attempt again to reproduce #4264. (#5403) +- Fix bad trove classifier + ## 1.6.0 ### Implementation changes diff --git a/datastore/setup.py b/datastore/setup.py index 139aae2e6852..d53e4fbdc4ad 100644 --- a/datastore/setup.py +++ b/datastore/setup.py @@ -22,7 +22,7 @@ name = 'google-cloud-datastore' description = 'Google Cloud Datastore API client library' -version = '1.6.0' +version = '1.7.0' # Should be one of: # 'Development Status :: 3 - Alpha' # 'Development Status :: 4 - Beta'

dynaconf__dynaconf-809

How to use dynaconf in pytest when declared custom settings object Hi. I need to override the environment for settings in conftest.py. As I found I can do it by adding: ```python from dynaconf import settings @pytest.fixture(scope="session", autouse=True) def set_test_settings(): settings.configure(FORCE_ENV_FOR_DYNACONF="testing") ``` but in my case I' ve got my own settings object under in the `confg.py` module and it looks like this: ```python settings = Dynaconf( envvar_prefix='MY_PREFIX', settings_files=['settings.toml', '.secrets.toml'], environments=True, env_switcher='ENVIRONMENT_NAME', ) ``` and when I'm trying to do ```python from config import settings @pytest.fixture(scope="session", autouse=True) def set_test_settings(): settings.configure(FORCE_ENV_FOR_DYNACONF="testing") ``` it does not work. It only overrides settings imported directly from dynaconf module. This is a problem because in my app I'm using settings from my `config.py` and my tests are failing when I override settings from `dynaconf` and use `from dynaconf import settings` in tests - because in app I'm using `from config import settings`

[ { "content": "from __future__ import annotations\n\nimport copy\nimport glob\nimport importlib\nimport inspect\nimport os\nimport warnings\nfrom collections import defaultdict\nfrom contextlib import contextmanager\nfrom contextlib import suppress\nfrom pathlib import Path\n\nfrom dynaconf import default_settin...

diff --git a/dynaconf/base.py b/dynaconf/base.py index 51e09a404..2858b5492 100644 --- a/dynaconf/base.py +++ b/dynaconf/base.py @@ -694,6 +694,7 @@ def current_env(self): return self.MAIN_ENV_FOR_DYNACONF.lower() if self.FORCE_ENV_FOR_DYNACONF is not None: + self.ENV_FOR_DYNACONF = self.FORCE_ENV_FOR_DYNACONF return self.FORCE_ENV_FOR_DYNACONF try: diff --git a/tests_functional/issues/728_pytest/Makefile b/tests_functional/issues/728_pytest/Makefile new file mode 100644 index 000000000..ebe3e7056 --- /dev/null +++ b/tests_functional/issues/728_pytest/Makefile @@ -0,0 +1,4 @@ +.PHONY: test + +test: + pytest -sv tests.py diff --git a/tests_functional/issues/728_pytest/config.py b/tests_functional/issues/728_pytest/config.py new file mode 100644 index 000000000..14435a787 --- /dev/null +++ b/tests_functional/issues/728_pytest/config.py @@ -0,0 +1,9 @@ +from __future__ import annotations + +from dynaconf import Dynaconf + +settings = Dynaconf( + envvar_prefix="ISSUE728", + settings_files=["settings.toml", ".secrets.toml"], + environments=True, +) diff --git a/tests_functional/issues/728_pytest/settings.toml b/tests_functional/issues/728_pytest/settings.toml new file mode 100644 index 000000000..21cd18f8c --- /dev/null +++ b/tests_functional/issues/728_pytest/settings.toml @@ -0,0 +1,8 @@ +[default] +name = "default name" + +[development] +name = "development name" + +[testing] +name = "testing name" diff --git a/tests_functional/issues/728_pytest/tests.py b/tests_functional/issues/728_pytest/tests.py new file mode 100644 index 000000000..a2cad668e --- /dev/null +++ b/tests_functional/issues/728_pytest/tests.py @@ -0,0 +1,16 @@ +from __future__ import annotations + +import pytest +from config import settings + + +@pytest.fixture(scope="session", autouse=True) +def set_test_settings(): + settings.configure(FORCE_ENV_FOR_DYNACONF="testing") + assert settings.current_env == "testing" + + +def test_running_on_testing_environment(): + assert settings.current_env == "testing" + assert settings.ENV_FOR_DYNACONF == "testing" + assert settings.NAME == "testing name"

internetarchive__openlibrary-6898

Sorting buttons in Reading log don't work as intended When you press sort by "Date Added (oldest)" page refreshes and sorting is applied but "Date Added (oldest)" button doesn't turn green and doesn't become unclickable, and "Date Added (newest)" button doesn't become clickable ### Evidence / Screenshot (if possible) On this scrrencshot books are sorted by oldest ![image](https://user-images.githubusercontent.com/58372007/185414834-58610de2-e5f4-43a3-8b91-238b5195f81d.png) ### Relevant url?  ### Steps to Reproduce  1. Go to ... Reading log 2. Do ... press sort by "Date Added (oldest)"  * Actual: * Expected: ### Details - **Logged in (Y/N)?** Y - **Browser type/version?** Firefox 103 (64-bit) - **Operating system?** Linux Mint and Windows 8.1 - **Environment (prod/dev/local)?** prod  ### Proposal & Constraints  ### Related files  ### Stakeholders

[ { "content": "import json\nimport web\n\nfrom infogami.utils import delegate\nfrom infogami.utils.view import public, safeint, render\n\nfrom openlibrary import accounts\nfrom openlibrary.utils import extract_numeric_id_from_olid\nfrom openlibrary.core.booknotes import Booknotes\nfrom openlibrary.core.bookshelv...

diff --git a/openlibrary/plugins/upstream/mybooks.py b/openlibrary/plugins/upstream/mybooks.py index 23710527bd4..22772bcd013 100644 --- a/openlibrary/plugins/upstream/mybooks.py +++ b/openlibrary/plugins/upstream/mybooks.py @@ -248,6 +248,7 @@ def render(self, page=1, sort='desc', list=None): lists=self.lists, public=is_public, owners_page=is_logged_in_user, + sort_order=sort, ) raise web.seeother(self.user.key)

scikit-hep__awkward-1977

ak.from_parquet for multiple files uses wrong number of arguments to concatenate ### Version of Awkward Array 2.0.0rc6 ### Description and code to reproduce If passing a directory with more than one file to `ak.from_parquet` the following exception is raised: (the `outputs` directory in this example contains 50 files) ```python In [4]: ak.from_parquet("outputs") --------------------------------------------------------------------------- TypeError Traceback (most recent call last) Cell In [4], line 1 ----> 1 ak.from_parquet("outputs") File ~/.pyenv/versions/3.10.8/envs/dev/lib/python3.10/site-packages/awkward/operations/ak_from_parquet.py:75, in from_parquet(path, columns, row_groups, storage_options, max_gap, max_block, footer_sample_size, generate_bitmasks, highlevel, behavior) 67 import awkward._connect.pyarrow # noqa: F401 69 parquet_columns, subform, actual_paths, fs, subrg, row_counts, meta = metadata( 70 path, 71 storage_options, 72 row_groups, 73 columns, 74 ) ---> 75 return _load( 76 actual_paths, 77 parquet_columns if columns is not None else None, 78 subrg, 79 max_gap, 80 max_block, 81 footer_sample_size, 82 generate_bitmasks, 83 subform, 84 highlevel, 85 behavior, 86 fs, 87 ) File ~/.pyenv/versions/3.10.8/envs/dev/lib/python3.10/site-packages/awkward/operations/ak_from_parquet.py:246, in _load(actual_paths, parquet_columns, subrg, max_gap, max_block, footer_sample_size, generate_bitmasks, subform, highlevel, behavior, fs, metadata) 243 return ak.Array(arrays[0]) 244 else: 245 # TODO: if each array is a record? --> 246 return ak.operations.ak_concatenate._impl( 247 arrays, 0, True, True, highlevel, behavior 248 ) TypeError: _impl() takes 5 positional arguments but 6 were given ```

[ { "content": "# BSD 3-Clause License; see https://github.com/scikit-hep/awkward-1.0/blob/main/LICENSE\n\nimport awkward as ak\n\n\ndef from_parquet(\n path,\n *,\n columns=None,\n row_groups=None,\n storage_options=None,\n max_gap=64_000,\n max_block=256_000_000,\n footer_sample_size=1_0...

diff --git a/src/awkward/operations/ak_from_parquet.py b/src/awkward/operations/ak_from_parquet.py index 1f8526beb1..490790a829 100644 --- a/src/awkward/operations/ak_from_parquet.py +++ b/src/awkward/operations/ak_from_parquet.py @@ -244,7 +244,7 @@ def _load( else: # TODO: if each array is a record? return ak.operations.ak_concatenate._impl( - arrays, 0, True, True, highlevel, behavior + arrays, axis=0, mergebool=True, highlevel=highlevel, behavior=behavior )

meltano__meltano-6078

Adjust logging level for requests/urllib With the hub changes and especially snowplow changes, when running with debug mode enabled we're littering the logs with some giant http requests (scroll the code block to get an idea of how large these look in the console when line wrapped): ``` (melty-3.8) ➜ rundev MELTANO_DISABLE_TRACKING=False MELTANO_SNOWPLOW_COLLECTOR_ENDPOINTS='["http://localhost:9090"]' meltano --log-level=debug invoke tap-gitlab 2022-06-04T23:19:04.941335Z [debug ] Creating engine <meltano.core.project.Project object at 0x109533a60>@sqlite:////Users/syn/projects/meltano-projects/rundev/.meltano/meltano.db 2022-06-04T23:19:04.996207Z [debug ] Starting new HTTP connection (1): localhost:9090 2022-06-04T23:19:05.030353Z [debug ] http://localhost:9090 "GET /i?e=ue&ue_px=eyJzY2hlbWEiOiAiaWdsdTpjb20uc25vd3Bsb3dhbmFseXRpY3Muc25vd3Bsb3cvdW5zdHJ1Y3RfZXZlbnQvanNvbnNjaGVtYS8xLTAtMCIsICJkYXRhIjogeyJzY2hlbWEiOiAiaWdsdTpjb20ubWVsdGFuby9jbGlfZXZlbnQvanNvbnNjaGVtYS8xLTAtMCIsICJkYXRhIjogeyJldmVudCI6ICJzdGFydGVkIn19fQ%3D%3D&eid=ee086532-f9be-4819-9b66-3dc04049096a&dtm=1654384744990&cx=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&tv=py-0.10.0&p=pc&lang=en_US&tz=America%2FChicago&stm=1654384744000 HTTP/1.1" 200 43 2022-06-04T23:19:05.060016Z [debug ] Lockfile is feature-flagged status=False 2022-06-04T23:19:05.103509Z [debug ] Starting new HTTPS connection (1): discovery.meltano.com:443 2022-06-04T23:19:05.266283Z [debug ] https://discovery.meltano.com:443 "GET /discovery.yml?project_id=1a7d9989-f704-485b-ba7a-a7478703ca7b HTTP/1.1" 200 23607 2022-06-04T23:19:05.693139Z [debug ] Found plugin plugin=tap-gitlab source=discovery 2022-06-04T23:16:48.221553Z [debug ] http://localhost:9090 "GET /i?e=se&se_ca=meltano+invoke&se_ac=meltano+invoke+tap-gitlab+&se_la=1a7d9989-f704-485b-ba7a-a7478703ca7b&eid=ca88b1c2-551a-4334-8a25-f793f68b8a96&dtm=1654384608194&tv=py-0.10.0&p=pc&lang=en_US&tz=America%2FChicago&stm=1654384608000 HTTP/1.1" 200 43 2022-06-04T23:16:48.225794Z [debug ] Starting new HTTP connection (1): localhost:9090 2022-06-04T23:16:48.240215Z [debug ] http://localhost:9090 "GET /i?e=ue&ue_px=eyJzY2hlbWEiOiAiaWdsdTpjb20uc25vd3Bsb3dhbmFseXRpY3Muc25vd3Bsb3cvdW5zdHJ1Y3RfZXZlbnQvanNvbnNjaGVtYS8xLTAtMCIsICJkYXRhIjogeyJzY2hlbWEiOiAiaWdsdTpjb20ubWVsdGFuby9jbGlfZXZlbnQvanNvbnNjaGVtYS8xLTAtMCIsICJkYXRhIjogeyJldmVudCI6ICJjb21wbGV0ZWQifX19&eid=b42bfc91-8a1f-4dde-924f-9d7d5c634a49&dtm=1654384608222&cx=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&tv=py-0.10.0&p=pc&lang=en_US&tz=America%2FChicago&stm=1654384608000 HTTP/1.1" 200 43 ``` We should proactively set the logging level of urllib3 to only print info or higher, e.g: ```python logging.getLogger("urllib3").setLevel(logging.INFO) ```

[ { "content": "\"\"\"Various utilities for configuring logging in a meltano project.\"\"\"\nimport asyncio\nimport logging\nimport os\nfrom contextlib import suppress\nfrom logging import config as logging_config\nfrom typing import Dict, Optional\n\nimport structlog\nimport yaml\n\nfrom meltano.core.logging.for...

diff --git a/src/meltano/core/logging/utils.py b/src/meltano/core/logging/utils.py index 823aac8f5a..f483d7e182 100644 --- a/src/meltano/core/logging/utils.py +++ b/src/meltano/core/logging/utils.py @@ -95,6 +95,11 @@ def default_config(log_level: str) -> dict: "handlers": ["console"], "level": logging.ERROR, }, + "urllib3": { + "handlers": ["console"], + "level": logging.INFO, + "propagate": False, + }, }, }

pallets__click-1825

resolve_path differs on Windows depending on Python version    Hi. There was an issue filed under [Typer](https://github.com/tiangolo/typer/issues/244#issuecomment-792455309) that gives a full explanation, but basically the use of `os.path.realpath` in the `resolve_path` logic for click.Path differs between Python 3.7 and 3.8 on Windows. Prior to 3.8, `os.path.realpath` did not resolve symlinks. Therefore Click users on Windows using Python 3.7 or lower are getting the wrong results for resolve_path. More info: https://docs.python.org/3/library/os.path.html#os.path.realpath

[ { "content": "import os\nimport stat\nimport typing as t\nfrom datetime import datetime\n\nfrom ._compat import _get_argv_encoding\nfrom ._compat import filename_to_ui\nfrom ._compat import get_filesystem_encoding\nfrom ._compat import get_strerror\nfrom ._compat import open_stream\nfrom .exceptions import BadP...

diff --git a/CHANGES.rst b/CHANGES.rst index 406088e07..4f0dfb94e 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -187,6 +187,8 @@ Unreleased - Add a ``pass_meta_key`` decorator for passing a key from ``Context.meta``. This is useful for extensions using ``meta`` to store information. :issue:`1739` +- ``Path`` ``resolve_path`` resolves symlinks on Windows Python < 3.8. + :issue:`1813` Version 7.1.2 diff --git a/src/click/types.py b/src/click/types.py index 0ed73c099..6cf611fa7 100644 --- a/src/click/types.py +++ b/src/click/types.py @@ -734,6 +734,10 @@ def convert(self, value, param, ctx): if not is_dash: if self.resolve_path: + # realpath on Windows Python < 3.8 doesn't resolve symlinks + if os.path.islink(rv): + rv = os.readlink(rv) + rv = os.path.realpath(rv) try:

pyinstaller__pyinstaller-8555

with setuptools v70.0.0: `ModuleNotFoundError: No module named 'pkg_resources.extern'`   ## Description of the issue I have added some TODO notes below but wanted to submit this sooner than later for any other users running into this issue today to be able to find it. This morning I noticed an error in my tests that exercise PyInstaller generated Windows .exe's in CI. https://github.com/Chia-Network/chia-blockchain/actions/runs/9175546125/job/25229722015?pr=16898 ``` Traceback (most recent call last): File "Lib\site-packages\PyInstaller\hooks\rthooks\pyi_rth_pkgres.py", line 158, in <module> File "Lib\site-packages\PyInstaller\hooks\rthooks\pyi_rth_pkgres.py", line 36, in _pyi_rthook File "PyInstaller\loader\pyimod02_importers.py", line 419, in exec_module File "pkg_resources\__init__.py", line [7](https://github.com/Chia-Network/chia-blockchain/actions/runs/9175546125/job/25229722015?pr=16898#step:6:8)7, in <module> ModuleNotFoundError: No module named 'pkg_resources.extern' [2148] Failed to execute script 'pyi_rth_pkgres' due to unhandled exception! ``` First I correlated this with [the release of setuptools v70.0.0](https://pypi.org/project/setuptools/70.0.0/#history) a few hours earlier (and not a new PyInstaller release `:]`). After looking here and finding no issues reported I checked over at setuptools and found https://github.com/pypa/setuptools/issues/4374. In that discussion I noted that the issue appears with https://github.com/pypa/setuptools/commit/e9995828311c5e0c843622ca2be85e7f09f1ff0d and not its parent commit. That commit does indeed change how some of the `pkg_resources.extern` imports are handled inside `pkg_resources`. Another developer provided an example, though that example has not yet resulted in recreation of the issue. ### Context information (for bug reports) * Output of `pyinstaller --version`: ```(paste here)``` (TODO: add this to my CI run) * Version of Python: 3.10 * Platform: Windows (GitHub Actions runner) * How you installed Python: in-house action https://github.com/chia-network/actions/setup-python that should, in this case, pass through to upstream https://github.com/actions/setup-python * Did you also try this on another platform? Does it work there? ~Similar Linux (Rocky and Ubuntu) builds as well as macOS (Intel and ARM) builds and tests seem to continue to work fine. I could afford to review these runs in more detail for other relevant changes, but have not quite yet.~ When forcing the setuptools to be installed, this does happen on all of the platforms we build executables for (Rocky, Ubuntu (Intel and ARM), macOS (Intel and ARM), Windows) * try the latest development version, using the following command: https://github.com/Chia-Network/chia-blockchain/actions/runs/9179289212/job/25241848658?pr=18051 shows the failure using `develop`, specifically 676584885f2dfa1f885ab6155a5eda9150892c03. * follow *all* the instructions in our "If Things Go Wrong" Guide (https://github.com/pyinstaller/pyinstaller/wiki/If-Things-Go-Wrong) and ### Make sure [everything is packaged correctly](https://github.com/pyinstaller/pyinstaller/wiki/How-to-Report-Bugs#make-sure-everything-is-packaged-correctly) * [x] start with clean installation * [ ] use the latest development version * [x] Run your frozen program **from a command window (shell)** — instead of double-clicking on it * [ ] Package your program in **--onedir mode** * [ ] Package **without UPX**, say: use the option `--noupx` or set `upx=False` in your .spec-file * [ ] Repackage you application in **verbose/debug mode**. For this, pass the option `--debug` to `pyi-makespec` or `pyinstaller` or use `EXE(..., debug=1, ...)` in your .spec file. ### A minimal example program which shows the error TODO: I will try to create this ``` (paste text here) “Minimal“ means: remove everything from your code which is not relevant for this bug, esp. don't use external programs, remote requests, etc. A very good example is https://gist.github.com/ronen/024cdae9ff2d50488438. This one helped us reproducing and fixing a quite complex problem within approx 1 hour. ``` ### Stacktrace / full error message ``` (paste text here) ``` Please also see <https://github.com/pyinstaller/pyinstaller/wiki/How-to-Report-Bugs> for more about what would use to solve the issue.

[ { "content": "#-----------------------------------------------------------------------------\n# Copyright (c) 2005-2023, PyInstaller Development Team.\n#\n# Distributed under the terms of the GNU General Public License (version 2\n# or later) with exception for distributing the bootloader.\n#\n# The full licens...

diff --git a/PyInstaller/hooks/hook-pkg_resources.py b/PyInstaller/hooks/hook-pkg_resources.py index b3817f8c65..dfcf382356 100644 --- a/PyInstaller/hooks/hook-pkg_resources.py +++ b/PyInstaller/hooks/hook-pkg_resources.py @@ -55,3 +55,9 @@ 'pkg_resources._vendor.jaraco.context', 'pkg_resources._vendor.jaraco.text', ] + +# As of setuptools 70.0.0, we need pkg_resources.extern added to hidden imports. +if check_requirement("setuptools >= 70.0.0"): + hiddenimports += [ + 'pkg_resources.extern', + ] diff --git a/news/8554.hooks.rst b/news/8554.hooks.rst new file mode 100644 index 0000000000..2720218797 --- /dev/null +++ b/news/8554.hooks.rst @@ -0,0 +1,2 @@ +Update ``pkg_resources`` hook for compatibility with ``setuptools`` v70.0.0 +and later (fix ``ModuleNotFoundError: No module named 'pkg_resources.extern'``).

pandas-dev__pandas-7007

Matplotlib cursor position wrong after using asfreq method to change freq of DateTimeIndex from None to something After using the `asfreq` method to change the frequency of a time-series DataFrame from `None` to something e.g. `15Min` the cursor position in matplotlib graphs of that DataFrame is no longer correct (usually shows a datetime just after the unix epoch). The following demonstrates this (NB dt in df1 is not a constant): ``` df1 = pandas.read_csv('tseries1.csv', names=['tstamp', 'Q'], parse_dates=True, index_col='tstamp').clip_lower(0).fillna(0) df1['T'] = pandas.read_csv('tseries2.csv', names=['tstamp', 'T'], parse_dates=True, index_col='tstamp', squeeze=True).clip_lower(0).fillna(0) df2 = df1.asfreq(freq='15Min', method='ffill') # NB df1.index.freq is None # NB df2.index.freq is <15 * Minutes> df1.plot() df2.plot() plt.show() ``` I find the Matplotlib cursor position to be invaluable when looking for features in very long time-series. Versions: - pandas master (commit ID 764b444) - numpy 1.8 - matplotlib 1.3.0 Matplotlib cursor position wrong after using asfreq method to change freq of DateTimeIndex from None to something After using the `asfreq` method to change the frequency of a time-series DataFrame from `None` to something e.g. `15Min` the cursor position in matplotlib graphs of that DataFrame is no longer correct (usually shows a datetime just after the unix epoch). The following demonstrates this (NB dt in df1 is not a constant): ``` df1 = pandas.read_csv('tseries1.csv', names=['tstamp', 'Q'], parse_dates=True, index_col='tstamp').clip_lower(0).fillna(0) df1['T'] = pandas.read_csv('tseries2.csv', names=['tstamp', 'T'], parse_dates=True, index_col='tstamp', squeeze=True).clip_lower(0).fillna(0) df2 = df1.asfreq(freq='15Min', method='ffill') # NB df1.index.freq is None # NB df2.index.freq is <15 * Minutes> df1.plot() df2.plot() plt.show() ``` I find the Matplotlib cursor position to be invaluable when looking for features in very long time-series. Versions: - pandas master (commit ID 764b444) - numpy 1.8 - matplotlib 1.3.0

[ { "content": "\"\"\"\nPeriod formatters and locators adapted from scikits.timeseries by\nPierre GF Gerard-Marchant & Matt Knox\n\"\"\"\n\n#!!! TODO: Use the fact that axis can have units to simplify the process\nimport datetime as pydt\nfrom datetime import datetime\n\nfrom matplotlib import pylab\nimport matpl...

diff --git a/doc/source/release.rst b/doc/source/release.rst index 91bf6084e0faa..975d92cc215c4 100644 --- a/doc/source/release.rst +++ b/doc/source/release.rst @@ -450,8 +450,9 @@ Bug Fixes - Bug in enabling ``subplots=True`` in ``DataFrame.plot`` only has single column raises ``TypeError``, and ``Series.plot`` raises ``AttributeError`` (:issue:`6951`) - Bug in ``DataFrame.plot`` draws unnecessary axes when enabling ``subplots`` and ``kind=scatter`` (:issue:`6951`) - Bug in ``read_csv`` from a filesystem with non-utf-8 encoding (:issue:`6807`) -- Bug in ``iloc`` when setting / aligning (:issue:``6766`) +- Bug in ``iloc`` when setting / aligning (:issue:`6766`) - Bug causing UnicodeEncodeError when get_dummies called with unicode values and a prefix (:issue:`6885`) +- Bug in timeseries-with-frequency plot cursor display (:issue:`5453`) pandas 0.13.1 ------------- diff --git a/pandas/tseries/plotting.py b/pandas/tseries/plotting.py index ae32367a57cd3..abec1d469114f 100644 --- a/pandas/tseries/plotting.py +++ b/pandas/tseries/plotting.py @@ -83,8 +83,7 @@ def tsplot(series, plotf, **kwargs): ax.set_xlim(left, right) # x and y coord info - tz = series.index.to_datetime().tz - ax.format_coord = lambda t, y : "t = {} y = {:8f}".format(datetime.fromtimestamp(t, tz), y) + ax.format_coord = lambda t, y: "t = {} y = {:8f}".format(Period(ordinal=int(t), freq=ax.freq), y) return lines diff --git a/pandas/tseries/tests/test_plotting.py b/pandas/tseries/tests/test_plotting.py index 118c09ddf826f..5d1e4b67041f7 100644 --- a/pandas/tseries/tests/test_plotting.py +++ b/pandas/tseries/tests/test_plotting.py @@ -131,6 +131,21 @@ def test_get_datevalue(self): self.assertEqual(get_datevalue('1/1/1987', 'D'), Period('1987-1-1', 'D').ordinal) + @slow + def test_ts_plot_format_coord(self): + def check_format_of_first_point(ax, expected_string): + first_line = ax.get_lines()[0] + first_x = first_line.get_xdata()[0].ordinal + first_y = first_line.get_ydata()[0] + self.assertEqual(expected_string, ax.format_coord(first_x, first_y)) + + annual = Series(1, index=date_range('2014-01-01', periods=3, freq='A-DEC')) + check_format_of_first_point(annual.plot(), 't = 2014 y = 1.000000') + + # note this is added to the annual plot already in existence, and changes its freq field + daily = Series(1, index=date_range('2014-01-01', periods=3, freq='D')) + check_format_of_first_point(daily.plot(), 't = 2014-01-01 y = 1.000000') + @slow def test_line_plot_period_series(self): for s in self.period_ser:

ipython__ipython-9109

Cannot inspect callable that raise in __bool__ The following should not raise. ``` python class NoBoolCall: def __call__(self): pass def __bool__(self): raise NotImplementedError('Must be implemented') b = NoBoolCall() b? ``` Likely in `oinspect.py`: ``` 835: if callable_obj: ``` Should be `if callable_obj is not None`, though i'm not sure.

[ { "content": "# -*- coding: utf-8 -*-\n\"\"\"Tools for inspecting Python objects.\n\nUses syntax highlighting for presenting the various information elements.\n\nSimilar in spirit to the inspect module, but all calls take a name argument to\nreference the name under which an object is being read.\n\"\"\"\n\n# C...

diff --git a/IPython/core/oinspect.py b/IPython/core/oinspect.py index e7be78b6541..f819990fc26 100644 --- a/IPython/core/oinspect.py +++ b/IPython/core/oinspect.py @@ -832,7 +832,7 @@ def info(self, obj, oname='', formatter=None, info=None, detail_level=0): else: callable_obj = None - if callable_obj: + if callable_obj is not None: try: argspec = getargspec(callable_obj) except (TypeError, AttributeError): diff --git a/IPython/core/tests/test_oinspect.py b/IPython/core/tests/test_oinspect.py index 0c71f0091d9..e868730b23f 100644 --- a/IPython/core/tests/test_oinspect.py +++ b/IPython/core/tests/test_oinspect.py @@ -172,6 +172,19 @@ class Awkward(object): def __getattr__(self, name): raise Exception(name) +class NoBoolCall: + """ + callable with `__bool__` raising should still be inspect-able. + """ + + def __call__(self): + """does nothing""" + pass + + def __bool__(self): + """just raise NotImplemented""" + raise NotImplementedError('Must be implemented') + def check_calltip(obj, name, call, docstring): """Generic check pattern all calltip tests will use""" @@ -281,6 +294,9 @@ def test_info_awkward(): # Just test that this doesn't throw an error. i = inspector.info(Awkward()) +def test_bool_raise(): + inspector.info(NoBoolCall()) + def test_calldef_none(): # We should ignore __call__ for all of these. for obj in [f, SimpleClass().method, any, str.upper]:

mitmproxy__mitmproxy-3070

[mitmweb] asyncio has no attribute call_soon ##### Steps to reproduce the problem: 1.Launch mitmweb 2.Save some flow 3.Load those flows ![asyncio_attribute_error](https://user-images.githubusercontent.com/15815157/38856635-48c7130c-4227-11e8-9019-0caf8f22038c.JPG) ##### Any other comments? What have you tried so far? https://github.com/mitmproxy/mitmproxy/blob/0fa1280daa94729defa8411d86266bd2b52ad0b6/mitmproxy/tools/web/app.py#L238-L239 I replaced this line with `asyncio.ensure_future(self.master.load_flows(i))` to make the loading works. ##### System information  ![mitmdump_version](https://user-images.githubusercontent.com/15815157/38857072-93f56a8a-4228-11e8-8fbb-fed4e11c2745.JPG)

[ { "content": "import hashlib\nimport json\nimport logging\nimport os.path\nimport re\nfrom io import BytesIO\nimport asyncio\n\nimport mitmproxy.flow\nimport tornado.escape\nimport tornado.web\nimport tornado.websocket\nfrom mitmproxy import contentviews\nfrom mitmproxy import exceptions\nfrom mitmproxy import ...

diff --git a/mitmproxy/tools/web/app.py b/mitmproxy/tools/web/app.py index 61e30a2138..184778b084 100644 --- a/mitmproxy/tools/web/app.py +++ b/mitmproxy/tools/web/app.py @@ -235,7 +235,7 @@ def post(self): self.view.clear() bio = BytesIO(self.filecontents) for i in io.FlowReader(bio).stream(): - asyncio.call_soon(self.master.load_flow, i) + asyncio.ensure_future(self.master.load_flow(i)) bio.close()

ansible__molecule-1615

CMD in pre-built docker image replaced with `while true; do sleep 10000; done` # Issue Type - Bug report Was kind of reported in #1441 # Molecule and Ansible details ``` ansible 2.7.2 config file = /etc/ansible/ansible.cfg configured module search path = [u'/home/fabian/.ansible/plugins/modules', u'/usr/share/ansible/plugins/modules'] ansible python module location = /home/fabian/.local/lib/python2.7/site-packages/ansible executable location = /home/fabian/.local/bin/ansible python version = 2.7.15 (default, May 15 2018, 15:37:31) [GCC 7.3.1 20180303 (Red Hat 7.3.1-5)] molecule, version 2.19.1.dev54 ``` Molecule installation method (one of): - source Ansible installation method (one of): - pip # Desired Behavior If I don't specify a `command` or specify `null` as the value for `command`, the existing `CMD` on the image should be used. # Actual Behaviour When consuming an image with the docker driver, the existing `CMD` on the image is overwritten, even if `command` is unspecified or null. In order to get the behavior I desire from molecule, I currently need to copy-paste the content of the `CMD` directive into the `command` section of the `molecule.yml`, but this is inherently fragile as every time the container used changes its `CMD` I would need to reflect that in every related molecule specification.

[ { "content": "# Copyright (c) 2015-2018 Cisco Systems, Inc.\n#\n# Permission is hereby granted, free of charge, to any person obtaining a copy\n# of this software and associated documentation files (the \"Software\"), to\n# deal in the Software without restriction, including without limitation the\n# right...

diff --git a/molecule/cookiecutter/scenario/driver/docker/{{cookiecutter.molecule_directory}}/{{cookiecutter.scenario_name}}/Dockerfile.j2 b/molecule/cookiecutter/scenario/driver/docker/{{cookiecutter.molecule_directory}}/{{cookiecutter.scenario_name}}/Dockerfile.j2 index c727a0564b..88feb252c3 100644 --- a/molecule/cookiecutter/scenario/driver/docker/{{cookiecutter.molecule_directory}}/{{cookiecutter.scenario_name}}/Dockerfile.j2 +++ b/molecule/cookiecutter/scenario/driver/docker/{{cookiecutter.molecule_directory}}/{{cookiecutter.scenario_name}}/Dockerfile.j2 @@ -14,3 +14,5 @@ RUN if [ $(command -v apt-get) ]; then apt-get update && apt-get install -y pyth elif [ $(command -v apk) ]; then apk update && apk add --no-cache python sudo bash ca-certificates; \ elif [ $(command -v xbps-install) ]; then xbps-install -Syu && xbps-install -y python sudo bash ca-certificates && xbps-remove -O; fi {%- endraw %} + +CMD ["sh", "-c", "while true; do sleep 10000; done"] diff --git a/molecule/model/schema_v2.py b/molecule/model/schema_v2.py index db7498e6aa..bc66682286 100644 --- a/molecule/model/schema_v2.py +++ b/molecule/model/schema_v2.py @@ -638,6 +638,7 @@ def pre_validate_base_schema(env, keep_string): }, 'command': { 'type': 'string', + 'nullable': True, }, 'privileged': { 'type': 'boolean', diff --git a/molecule/provisioner/ansible/playbooks/docker/create.yml b/molecule/provisioner/ansible/playbooks/docker/create.yml index fa88eca5dd..343c22c40c 100644 --- a/molecule/provisioner/ansible/playbooks/docker/create.yml +++ b/molecule/provisioner/ansible/playbooks/docker/create.yml @@ -63,7 +63,7 @@ state: started recreate: false log_driver: json-file - command: "{{ item.command | default('bash -c \"while true; do sleep 10000; done\"') }}" + command: "{{ item.command | default(omit) }}" privileged: "{{ item.privileged | default(omit) }}" security_opts: "{{ item.security_opts | default(omit) }}" volumes: "{{ item.volumes | default(omit) }}" diff --git a/test/resources/playbooks/docker/Dockerfile.j2 b/test/resources/playbooks/docker/Dockerfile.j2 index 0a605536a2..7605e1bcb3 100644 --- a/test/resources/playbooks/docker/Dockerfile.j2 +++ b/test/resources/playbooks/docker/Dockerfile.j2 @@ -12,3 +12,5 @@ RUN if [ $(command -v apt-get) ]; then apt-get update && apt-get install -y pyth elif [ $(command -v zypper) ]; then zypper refresh && zypper install -y python sudo bash python-xml && zypper clean -a; \ elif [ $(command -v apk) ]; then apk update && apk add --no-cache python sudo bash ca-certificates; \ elif [ $(command -v xbps-install) ]; then xbps-install -Syu && xbps-install -y python sudo bash ca-certificates && xbps-remove -O; fi + +CMD ["sh", "-c", "while true; do sleep 10000; done"]

pyca__cryptography-1237

0.5 fails to compile on OS X 10.8 Full traceback: http://pastebin.com/raw.php?i=M9N6Fgzi @reaperhulk has diagnosed, but this will require an 0.5.2 release to fix for supported platform.

[ { "content": "# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicable law or agreed to in writing, so...

diff --git a/cryptography/hazmat/bindings/commoncrypto/secitem.py b/cryptography/hazmat/bindings/commoncrypto/secitem.py index 4d7710bdf893..ac3dad3ffadb 100644 --- a/cryptography/hazmat/bindings/commoncrypto/secitem.py +++ b/cryptography/hazmat/bindings/commoncrypto/secitem.py @@ -23,8 +23,6 @@ const CFTypeRef kSecAttrIsPermanent; const CFTypeRef kSecAttrKeyTypeRSA; const CFTypeRef kSecAttrKeyTypeDSA; -const CFTypeRef kSecAttrKeyTypeEC; -const CFTypeRef kSecAttrKeyTypeEC; const CFTypeRef kSecUseKeychain; """

litestar-org__litestar-1005

Bug: openapi render for multiple tags isn't consistent **Describe the bug** When the openapi renders tags from both a controller and a route it is not deterministic. This may not be a bug? But it surprised me so thought I'd raise it. I'm unsure if I'm doing something crazy but for a project, we check in the generated json openapi schema so we can browse the API live in gitlab. I've recently added a tag to both a controller and a route in it. But because the order of the tags isn't consistent they are going to keep flip flopping as we have a pre-commit that generates the json to make sure it's up to date. I hope that ramble makes sense... **To Reproduce** ```python from typing import Dict from starlite import Starlite, Controller, get class TestController(Controller): tags = ["a"] @get("/", tags=["b"]) def hello_world(self) -> Dict[str, str]: """Handler function that returns a greeting dictionary.""" return {"hello": "world"} app = Starlite(route_handlers=[TestController]) print(app.openapi_schema.paths["/"].get.tags) ``` If you run that multiple times, you will see you get either: ```python ['a', 'b'] ``` or ```python ['b', 'a'] ``` **Additional context** I believe the problem is [here](https://github.com/starlite-api/starlite/blob/835749112e8364c1516f45973c924774aca22ca9/starlite/openapi/path_item.py#L59) as it forces construction of a new set. Sorting them before returning would be viable as there shouldn't be _too many_ tags and it's a one time thing I believe? But as I said, it may not be a problem you care about as I could be doing something silly.

[ { "content": "from inspect import cleandoc\nfrom typing import TYPE_CHECKING, Dict, List, Optional, Tuple, cast\n\nfrom pydantic_openapi_schema.v3_1_0.operation import Operation\nfrom pydantic_openapi_schema.v3_1_0.path_item import PathItem\n\nfrom starlite.openapi.parameters import create_parameter_for_handler...

diff --git a/starlite/openapi/path_item.py b/starlite/openapi/path_item.py index 7c1ca54aba..af24207f26 100644 --- a/starlite/openapi/path_item.py +++ b/starlite/openapi/path_item.py @@ -56,7 +56,7 @@ def extract_layered_values( tags.extend(layer.tags) if layer.security: security.extend(layer.security) - return list(set(tags)) if tags else None, security or None + return sorted(set(tags)) if tags else None, security or None def create_path_item( diff --git a/tests/openapi/test_tags.py b/tests/openapi/test_tags.py index 542c8136cc..344e2c13af 100644 --- a/tests/openapi/test_tags.py +++ b/tests/openapi/test_tags.py @@ -23,7 +23,7 @@ class _Controller(Controller): path = "/controller" tags = ["controller"] - @get(tags=["handler"]) + @get(tags=["handler", "a"]) def _handler(self) -> Any: ... @@ -50,8 +50,8 @@ def test_openapi_schema_handler_tags(openapi_schema: "OpenAPI") -> None: def test_openapi_schema_controller_tags(openapi_schema: "OpenAPI") -> None: - assert set(openapi_schema.paths["/controller"].get.tags) == {"handler", "controller"} # type: ignore + assert openapi_schema.paths["/controller"].get.tags == ["a", "controller", "handler"] # type: ignore def test_openapi_schema_router_tags(openapi_schema: "OpenAPI") -> None: - assert set(openapi_schema.paths["/router/controller"].get.tags) == {"handler", "controller", "router"} # type: ignore + assert openapi_schema.paths["/router/controller"].get.tags == ["a", "controller", "handler", "router"] # type: ignore

pwndbg__pwndbg-1627

Heap heuristic will fail on big-endian architectures This can be reproduced by: ```console $ cat test.c #include <stdlib.h> int main(){ free(malloc(0x20)); return 0; } $ mips-linux-gnu-gcc test.c -ggdb $ qemu-mips -g 1234 -L /usr/mips-linux-gnu ./a.out ``` The libc I used is from: http://kr.archive.ubuntu.com/ubuntu/pool/universe/c/cross-toolchain-base-mipsen/libc6-mips-cross_2.30-0ubuntu2cross2_all.deb ``` console $ file /usr/mips-linux-gnu/lib/libc-2.30.so /usr/mips-linux-gnu/lib/libc-2.30.so: ELF 32-bit MSB shared object, MIPS, MIPS32 rel2 version 1 (SYSV), dynamically linked, interpreter /lib/ld.so.1, BuildID[sha1]=fff2eaa960489be0b3b109d4e52230c8fe34b2a1, for GNU/Linux 3.2.0, stripped ``` Then: ```console $ gdb -q ./a.out -ex 'set exception-verbose on' -ex 'set solib-absolute-prefix /usr/mips-linux-gnu/lib' -ex 'set solib-search-path /usr/mips-linux-gnu/lib' -ex 'target remote :1234' -ex 'break main' -ex 'continue' -ex 'next' -ex 'heap' ``` We will get: `KeyError: <class 'pwndbg.heap.structs.c_pvoid'>`. That’s because the keys in the dict are little-endian, but we try to access the dict with a big-endian type. We should use the correct endian for the keys in the dict. ---- Btw, I’m not sure if we really need to support heap heuristic for this architecture in the future, but the heuristic seems will also work for the single-threaded program for this architecture after we resolve this issue, which is good news :)

[ { "content": "import ctypes\n\nimport gdb\n\nimport pwndbg.gdblib.arch\nimport pwndbg.gdblib.memory\nimport pwndbg.gdblib.typeinfo\nimport pwndbg.glibc\nfrom pwndbg.gdblib.ctypes import Structure\n\n\ndef request2size(req):\n if req + SIZE_SZ + MALLOC_ALIGN_MASK < MINSIZE:\n return MINSIZE\n return...

diff --git a/pwndbg/heap/structs.py b/pwndbg/heap/structs.py index 0e7913f48e4..72d40f5b40d 100644 --- a/pwndbg/heap/structs.py +++ b/pwndbg/heap/structs.py @@ -78,6 +78,12 @@ class c_size_t(SIZE_T): c_size_t: pwndbg.gdblib.typeinfo.size_t, } +# Use correct endian for the dictionary keys +if pwndbg.gdblib.arch.endian == "little": + C2GDB_MAPPING = {k.__ctype_le__: v for k, v in C2GDB_MAPPING.items()} +else: + C2GDB_MAPPING = {k.__ctype_be__: v for k, v in C2GDB_MAPPING.items()} + class FakeGDBField: """

zigpy__zha-device-handlers-112

Ikea group support bind method doesn't return status as expected https://github.com/dmulcahey/zha-device-handlers/blob/b5b383939944ff541ee38a94c7f4d6cf3edc611f/zhaquirks/ikea/__init__.py#L25 https://github.com/home-assistant/home-assistant/blob/a30c37017b7782473294d7999e85d7a369a0539a/homeassistant/components/zha/core/helpers.py#L56 reported by @Adminiuga we should return the status in [ ] so the bind helper in HA is happy.

[ { "content": "\"\"\"Ikea module.\"\"\"\nimport logging\nfrom zigpy.zcl.clusters.lightlink import LightLink\nfrom zigpy.quirks import CustomCluster\n\n_LOGGER = logging.getLogger(__name__)\n\n\nclass LightLinkCluster(CustomCluster, LightLink):\n \"\"\"Ikea LightLink cluster.\"\"\"\n\n async def bind(self):...

diff --git a/zhaquirks/ikea/__init__.py b/zhaquirks/ikea/__init__.py index 8742d38808..d1f643fbfb 100644 --- a/zhaquirks/ikea/__init__.py +++ b/zhaquirks/ikea/__init__.py @@ -22,4 +22,5 @@ async def bind(self): group_list = await self.get_group_identifiers(0) group_record = group_list[2] group_id = group_record[0].group_id - await coordinator.add_to_group(group_id) + status = await coordinator.add_to_group(group_id) + return [status]

scikit-hep__awkward-2266

`NotImplementedError` from `TypeTracerArray.nan_to_num` ### Description of new feature I'm trying to use `dask-awkward` and `vector` to do vector addition. It works fine for Cartesian coordinates but not spherical: ```python >>> import awkward as ak, dask_awkward as dak, vector >>> vector.register_awkward() >>> a = ak.Array([1.0]) >>> da = dak.from_awkward(a, 1) >>> dv1 = dak.with_name(dak.zip({'x': da, 'y': da, 'z': da}), 'Vector3D') >>> (dv1 + dv1).compute() <VectorArray3D [{x: 2, y: 2, z: 2}] type='1 * Vector3D[x: float64, y: float...'> >>> dv2 = dak.with_name(dak.zip({'rho': da, 'phi': da, 'theta': da}), 'Vector3D') >>> (dv2 + dv2).compute() Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/user/miniconda3/envs/func_adl_uproot_rc/lib/python3.10/site-packages/numpy/lib/mixins.py", line 21, in func return ufunc(self, other) File "/home/user/iris-hep/src/dask-awkward/src/dask_awkward/lib/core.py", line 1027, in __array_ufunc__ new_meta = ufunc(*inputs_meta) File "/home/user/iris-hep/src/awkward-1.0/src/awkward/highlevel.py", line 1373, in __array_ufunc__ return ak._connect.numpy.array_ufunc(ufunc, method, inputs, kwargs) File "/home/user/iris-hep/src/awkward-1.0/src/awkward/_connect/numpy.py", line 291, in array_ufunc out = ak._broadcasting.broadcast_and_apply( File "/home/user/iris-hep/src/awkward-1.0/src/awkward/_broadcasting.py", line 1063, in broadcast_and_apply out = apply_step( File "/home/user/iris-hep/src/awkward-1.0/src/awkward/_broadcasting.py", line 1042, in apply_step return continuation() File "/home/user/iris-hep/src/awkward-1.0/src/awkward/_broadcasting.py", line 759, in continuation outcontent = apply_step( File "/home/user/iris-hep/src/awkward-1.0/src/awkward/_broadcasting.py", line 1028, in apply_step result = action( File "/home/user/iris-hep/src/awkward-1.0/src/awkward/_connect/numpy.py", line 193, in action return _array_ufunc_adjust(custom, inputs, kwargs, behavior) File "/home/user/iris-hep/src/awkward-1.0/src/awkward/_connect/numpy.py", line 130, in _array_ufunc_adjust out = custom(*args, **kwargs) File "/home/user/miniconda3/envs/func_adl_uproot_rc/lib/python3.10/site-packages/vector/backends/awkward.py", line 1514, in <lambda> behavior[numpy.add, left, right] = lambda v1, v2: v1.add(v2) File "/home/user/miniconda3/envs/func_adl_uproot_rc/lib/python3.10/site-packages/vector/_methods.py", line 2068, in add return module.add.dispatch(self, other) File "/home/user/miniconda3/envs/func_adl_uproot_rc/lib/python3.10/site-packages/vector/_compute/spatial/add.py", line 593, in dispatch function( File "/home/user/miniconda3/envs/func_adl_uproot_rc/lib/python3.10/site-packages/vector/_compute/spatial/add.py", line 310, in rhophi_theta_rhophi_theta z1 = z.rhophi_theta(lib, rho1, phi1, theta1) File "/home/user/miniconda3/envs/func_adl_uproot_rc/lib/python3.10/site-packages/vector/_compute/spatial/z.py", line 52, in rhophi_theta return lib.nan_to_num(rho / lib.tan(theta), nan=0.0, posinf=inf, neginf=-inf) File "<__array_function__ internals>", line 200, in nan_to_num File "/home/user/iris-hep/src/awkward-1.0/src/awkward/highlevel.py", line 1392, in __array_function__ return ak._connect.numpy.array_function( File "/home/user/iris-hep/src/awkward-1.0/src/awkward/_connect/numpy.py", line 75, in array_function return function(*args, **kwargs) File "/home/user/iris-hep/src/awkward-1.0/src/awkward/_connect/numpy.py", line 96, in ensure_valid_args return function(*args, **kwargs) File "/home/user/iris-hep/src/awkward-1.0/src/awkward/operations/ak_nan_to_num.py", line 136, in _nep_18_impl return nan_to_num(x, copy=copy, nan=nan, posinf=posinf, neginf=neginf) File "/home/user/iris-hep/src/awkward-1.0/src/awkward/operations/ak_nan_to_num.py", line 51, in nan_to_num return _impl(array, copy, nan, posinf, neginf, highlevel, behavior) File "/home/user/iris-hep/src/awkward-1.0/src/awkward/operations/ak_nan_to_num.py", line 95, in _impl out = ak._do.recursively_apply(layout, action, behavior) File "/home/user/iris-hep/src/awkward-1.0/src/awkward/_do.py", line 34, in recursively_apply return layout._recursively_apply( File "/home/user/iris-hep/src/awkward-1.0/src/awkward/contents/numpyarray.py", line 1301, in _recursively_apply result = action( File "/home/user/iris-hep/src/awkward-1.0/src/awkward/operations/ak_nan_to_num.py", line 85, in action nplike.nan_to_num( File "/home/user/iris-hep/src/awkward-1.0/src/awkward/_nplikes/typetracer.py", line 1190, in nan_to_num raise ak._errors.wrap_error(NotImplementedError) NotImplementedError: See if this has been reported at https://github.com/scikit-hep/awkward-1.0/issues ```

[ { "content": "# BSD 3-Clause License; see https://github.com/scikit-hep/awkward-1.0/blob/main/LICENSE\nfrom __future__ import annotations\n\nfrom numbers import Number\n\nimport numpy\n\nimport awkward as ak\nfrom awkward._errors import wrap_error\nfrom awkward._nplikes.numpylike import ArrayLike, IndexType, Nu...

diff --git a/src/awkward/_nplikes/typetracer.py b/src/awkward/_nplikes/typetracer.py index 62f77e3dbf..b00ed99a28 100644 --- a/src/awkward/_nplikes/typetracer.py +++ b/src/awkward/_nplikes/typetracer.py @@ -1187,7 +1187,7 @@ def nan_to_num( neginf: int | float | None = None, ) -> TypeTracerArray: try_touch_data(x) - raise ak._errors.wrap_error(NotImplementedError) + return TypeTracerArray._new(x.dtype, shape=x.shape) def isclose( self, diff --git a/tests/test_2266_fix_nan_to_num.py b/tests/test_2266_fix_nan_to_num.py new file mode 100644 index 0000000000..7f91497aa5 --- /dev/null +++ b/tests/test_2266_fix_nan_to_num.py @@ -0,0 +1,26 @@ +# BSD 3-Clause License; see https://github.com/scikit-hep/awkward-1.0/blob/main/LICENSE + +import pytest + +import awkward as ak + +dak = pytest.importorskip("dask_awkward") +vector = pytest.importorskip("vector") +vector.register_awkward() + + +def test(): + a = ak.Array([1.0]) + da = dak.from_awkward(a, 1) + dv1 = dak.with_name(dak.zip({"x": da, "y": da, "z": da}), "Vector3D") + + result1 = (dv1 + dv1).compute() + assert result1.tolist() == [{"x": 2, "y": 2, "z": 2}] + assert str(result1.type).startswith("1 * Vector3D[") + assert type(result1).__name__ == "VectorArray3D" + + dv2 = dak.with_name(dak.zip({"rho": da, "phi": da, "theta": da}), "Vector3D") + result2 = (dv2 + dv2).compute() + assert result2.tolist() == [{"rho": 2, "phi": 1, "theta": 1}] + assert str(result2.type).startswith("1 * Vector3D[") + assert type(result2).__name__ == "VectorArray3D"

Gallopsled__pwntools-470

History search crashes if item isn't found and enter is pressed The history search in term.readline crashes when an item is searched for, but not found and then enter is pressed. ``` Traceback (most recent call last): File "./t.py", line 58, in <module> code.interact(local=locals()) File "/usr/lib/python2.7/code.py", line 306, in interact console.interact(banner) File "/usr/lib/python2.7/code.py", line 234, in interact line = self.raw_input(prompt) File "./t.py", line 48, in _raw_input_wrapper ret = raw_input(prompt) File "./pwntools/pwnlib/term/readline.py", line 426, in raw_input return readline(None, prompt, float) File "./pwntools/pwnlib/term/readline.py", line 374, in readline keymap.handle_input() File "./pwntools/pwnlib/term/keymap.py", line 19, in handle_input self.send(key.get()) File "./pwntools/pwnlib/term/keymap.py", line 47, in send cb(self.trace) File "./pwntools/pwnlib/term/readline.py", line 228, in submit commit_search() File "./pwntools/pwnlib/term/readline.py", line 140, in commit_search set_buffer(history[search_results[search_idx][0]], u'') IndexError: list index out of range ``` It appears to be related to search_results being empty, but search_idx is set to 0.

[ { "content": "from . import term, text\nfrom . import keymap as km\nfrom . import keyconsts as kc\ncursor = text.reverse\n\nbuffer_left, buffer_right = u'', u''\nsaved_buffer = None\nhistory = []\nhistory_idx = None\nprompt_handle = None\nbuffer_handle = None\nsuggest_handle = None\nsearch_idx = None\nsearch_re...

diff --git a/pwnlib/term/readline.py b/pwnlib/term/readline.py index 8e435d2bd..5ebb26bb0 100644 --- a/pwnlib/term/readline.py +++ b/pwnlib/term/readline.py @@ -136,7 +136,7 @@ def cancel_search(*_): def commit_search(): global search_idx - if search_idx is not None: + if search_idx is not None and search_results: set_buffer(history[search_results[search_idx][0]], u'') search_idx = None redisplay()

facebookresearch__fairseq-214

Size Mismatch in AdaptiveSoftmax when targets are not specified Following up on #212 , I'm updating `sequence_generator.py` to generate text from a pre-trained language model (initially trained with adaptive softmax). When computing log probabilities, and the targets are set to none, I receive a size mismatch exception in the line below, possibly because the dictionary size is smaller than the adaptive softmax cut-off: https://github.com/pytorch/fairseq/blob/388c520be21752cacb9fe3b1712038f32e0e9a5f/fairseq/modules/adaptive_softmax.py#L126 I imagine this could be solved by some sort of truncation to the output of tail[i].input

[ { "content": "# Copyright (c) 2017-present, Facebook, Inc.\n# All rights reserved.\n#\n# This source code is licensed under the license found in the LICENSE file in\n# the root directory of this source tree. An additional grant of patent rights\n# can be found in the PATENTS file in the same directory.\n\n\nimp...

diff --git a/fairseq/modules/adaptive_softmax.py b/fairseq/modules/adaptive_softmax.py index 307861b6c8..aeceb486df 100644 --- a/fairseq/modules/adaptive_softmax.py +++ b/fairseq/modules/adaptive_softmax.py @@ -22,6 +22,9 @@ def __init__(self, vocab_size, input_dim, cutoff, dropout): if vocab_size > cutoff[-1]: cutoff = cutoff + [vocab_size] + else: + assert vocab_size == cutoff[ + -1], 'cannot specify cutoff smaller than vocab size' output_dim = cutoff[0] + len(cutoff) - 1

pre-commit__pre-commit-2836

Alternative to stashing files for testing Are there any plans to implement alternatives to stashing the worktree? Ideally this would be hook/scriptable, like some 'prepare-worktree' and 'restore-worktree' options (which default to the current stash behavior) but can also yield some new directory where the tests are run. The rationale here is that my editor reverts files changed on disk and I'd like to add notes to source files while the commit is in progress. In my own pre-commit hooks I use something like: git archive "$(git write-tree)" --prefix="$test_dir/" | tar xf - To create a pristine source tree (actually, I also prime it with `cp -rl` with build artifacts from the previous build to speed up incremental builds). 'git-worktree' and other tools could be used as well... Eventually I have the idea to run some (more expensive) pre-commit checks in the background while one types the commit message. Then in the commit-msg hook wait for the background results and abort the commit there. This should reduce the turn around times significantly.

[ { "content": "from __future__ import annotations\n\nimport contextlib\nimport os\nfrom typing import Generator\nfrom typing import Sequence\n\nfrom pre_commit import lang_base\nfrom pre_commit.envcontext import envcontext\nfrom pre_commit.envcontext import PatchesT\nfrom pre_commit.envcontext import Var\nfrom p...

diff --git a/pre_commit/languages/swift.py b/pre_commit/languages/swift.py index 8250ab703..f16bb0451 100644 --- a/pre_commit/languages/swift.py +++ b/pre_commit/languages/swift.py @@ -44,7 +44,7 @@ def install_environment( os.mkdir(envdir) cmd_output_b( 'swift', 'build', - '-C', prefix.prefix_dir, + '--package-path', prefix.prefix_dir, '-c', BUILD_CONFIG, '--build-path', os.path.join(envdir, BUILD_DIR), )

biopython__biopython-2059

Duplicate files in Tests/Motif and Tests/motifs The files in Test/motifs seem to be a copy of those in Test/Motif plus some more. Has the Motif directory been deprecated since renaming Bio.Motif to Bio.motifs?

[ { "content": "# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.\n# Copyright 2012-2013 by Michiel JL de Hoon. All rights reserved.\n# This code is part of the Biopython distribution and governed by its\n# license. Please see the LICENSE file that should have been included\n# as part of this pa...

diff --git a/Bio/motifs/__init__.py b/Bio/motifs/__init__.py index 982279765df..682cff9e25c 100644 --- a/Bio/motifs/__init__.py +++ b/Bio/motifs/__init__.py @@ -44,7 +44,7 @@ def parse(handle, format, strict=True): For example: >>> from Bio import motifs - >>> with open("Motif/alignace.out") as handle: + >>> with open("motifs/alignace.out") as handle: ... for m in motifs.parse(handle, "AlignAce"): ... print(m.consensus) ... diff --git a/Doc/Tutorial/chapter_motifs.tex b/Doc/Tutorial/chapter_motifs.tex index 70d9e84b1dc..dfaadc0e1de 100644 --- a/Doc/Tutorial/chapter_motifs.tex +++ b/Doc/Tutorial/chapter_motifs.tex @@ -25,7 +25,7 @@ \section{Motif objects} Since we are interested in motif analysis, we need to take a look at \verb|Motif| objects in the first place. For that we need to import the Bio.motifs library: -%doctest ../Tests/Motif +%doctest ../Tests/motifs \begin{verbatim} >>> from Bio import motifs \end{verbatim} @@ -1452,7 +1452,7 @@ \subsection{MEME} \verb|meme.out|. You can retrieve the motifs reported by MEME by running the following piece of code: -%doctest ../Tests/Motif +%doctest ../Tests/motifs \begin{verbatim} >>> from Bio import motifs >>> with open("meme.out") as handle: diff --git a/Tests/Motif/Arnt.sites b/Tests/Motif/Arnt.sites deleted file mode 100644 index c460a8efde0..00000000000 --- a/Tests/Motif/Arnt.sites +++ /dev/null @@ -1,40 +0,0 @@ ->MA0004 ARNT 1 -CACGTGatgtcctc ->MA0004 ARNT 2 -CACGTGggaggtac ->MA0004 ARNT 3 -CACGTGccgcgcgc ->MA0004 ARNT 4 -CACGTGaagttgtc ->MA0004 ARNT 5 -taaatgcCACGTG ->MA0004 ARNT 6 -aggtataCACGTG ->MA0004 ARNT 7 -agtCACGTGttcc ->MA0004 ARNT 8 -gggatCACGTGgt ->MA0004 ARNT 9 -gggtCACGTGttc ->MA0004 ARNT 10 -catgtCACGTGcc ->MA0004 ARNT 11 -agttcgCACGTGc ->MA0004 ARNT 12 -taagCACGTGgtc ->MA0004 ARNT 13 -tgaatacCACGTG ->MA0004 ARNT 14 -tgaCACGTGtccg ->MA0004 ARNT 15 -attgtgCACGTGg ->MA0004 ARNT 16 -AACGTGacttcgtacc ->MA0004 ARNT 17 -AACGTGcgtgatgtcc ->MA0004 ARNT 18 -AACGTGacagccctcc ->MA0004 ARNT 19 -AACGTGcacatcgtcc ->MA0004 ARNT 20 -aggaatCGCGTGc diff --git a/Tests/Motif/REB1.pfm b/Tests/Motif/REB1.pfm deleted file mode 100644 index 8a6b4923967..00000000000 --- a/Tests/Motif/REB1.pfm +++ /dev/null @@ -1,5 +0,0 @@ -30 0 0 100 0 0 0 0 15 -10 0 0 0 100 100 100 0 15 -50 0 0 0 0 0 0 60 55 -10 100 100 0 0 0 0 40 15 - diff --git a/Tests/Motif/SRF.pfm b/Tests/Motif/SRF.pfm deleted file mode 100644 index 09134483a47..00000000000 --- a/Tests/Motif/SRF.pfm +++ /dev/null @@ -1,4 +0,0 @@ - 2 9 0 1 32 3 46 1 43 15 2 2 - 1 33 45 45 1 1 0 0 0 1 0 1 -39 2 1 0 0 0 0 0 0 0 44 43 - 4 2 0 0 13 42 0 45 3 30 0 0 diff --git a/Tests/Motif/alignace.out b/Tests/Motif/alignace.out deleted file mode 100644 index a577bc480ba..00000000000 --- a/Tests/Motif/alignace.out +++ /dev/null @@ -1,354 +0,0 @@ -AlignACE 4.0 05/13/04 -./AlignACE -i test.fa -Parameter values: - expect = 10 - gcback = 0.38 - minpass = 200 - seed = 1227623309 - numcols = 10 - undersample = 1 - oversample = 1 - -Input sequences: -#0 SEQ1; M: CTCAATCGTAGA at 52 -#1 SEQ2; M: CTCAATCGTAGA at 172 -#2 SEQ3; M: CTCAATCGTAGA at 112 -#3 SEQ4; M: CTCAATCGTAGA at 173 -#4 SEQ5; M: CTCAATCGTAGA at 185 -#5 SEQ6; M: CTCAATCGTAGA at 105 -#6 SEQ7; M: CTCAATCGTAGA at 177 -#7 SEQ8; M: CTCAATCGTAGA at 172 -#8 SEQ9; M: CTCAATCGTAGA at 93 -#9 SEQ10; M: CTCAATCGTAGA at 3 - -Motif 1 -TCTACGATTGAG 0 51 0 -TCTACGATTGAG 1 171 0 -TCTACGATTGAG 2 111 0 -TCTACGATTGAG 3 172 0 -TCTACGATTGAG 4 184 0 -TCTACGATTGAG 5 104 0 -TCTACGATTGAG 6 176 0 -TCTACGATTGAG 7 171 0 -TCTACGATTGAG 8 92 0 -TCAAAGATAGAG 8 155 1 -TCTACGATTGAG 9 2 0 -** ***** *** -MAP Score: 57.9079 - -Motif 2 -GCGAAGGAAGCAGCGCGTGTG 0 7 1 -GGCACCGCCTCTACGATTGAG 0 51 0 -CAGAGCTTAGCATTGAACGCG 0 93 0 -CTAATGAAAGCAATGAGAGTG 0 154 1 -CTTGTGCCCTCTAAGCGTCCG 1 73 1 -GAGCACGACGCTTTGTACCTG 1 153 0 -CGGCACTTAGCAGCGTATCGT 2 36 0 -CTGGTTTCATCTACGATTGAG 2 111 0 -GGGCCAATAGCGGCGCCGGAG 2 133 0 -GTGGAGTTATCTTAGTGCGCG 2 158 0 -GAGAGGTTATCTACGATTGAG 3 172 0 -CTGCTCCCCGCATACAGCGCG 4 62 0 -CAGAACCGAGGTCCGGTACGG 4 157 1 -GTGCCCCAAGCTTACCCAGGG 5 40 1 -CGCCTCTGATCTACGATTGAG 5 104 0 -GTGCTCATAGGGACGTCGCGG 6 2 1 -CTGCCCCCCGCATAGTAGGGG 6 45 1 -GTAAAGAAATCGATGTGCCAG 6 72 0 -CACCTGCAATTGCTGGCAGCG 6 128 0 -GGCGGGCCATCCCTGTATGAA 8 65 0 -CTCCAGGTCGCATGGAGAGAG 9 89 1 -CCTCGGATCGCTTGGGAAGAG 9 134 0 -* ** * *** * * * -MAP Score: 19.6235 - -Motif 3 -GTGCGCGAAGGAAGCAGCGCG 0 3 1 -CAGAGCTTAGCATTGAACGCG 0 93 0 -GTGCCCGATGACCACCCGTCG 0 117 0 -GCCCTCTAAGCGTCCGCGGAT 1 78 1 -GAGCACGACGCTTTGTACCTG 1 153 0 -CGGCACTTAGCAGCGTATCGT 2 36 0 -GGGCCAATAGCGGCGCCGGAG 2 133 0 -GCGCACTAAGATAACTCCACG 2 159 1 -CGGCCCGTTGTCCAGCAGACG 3 2 0 -CTGCTCCCCGCATACAGCGCG 4 62 0 -GTGCCCCAAGCTTACCCAGGG 5 40 1 -GTGCTCATAGGGACGTCGCGG 6 2 1 -CTGCCCCCCGCATAGTAGGGG 6 45 1 -CGCCGCCATGCGACGCAGAGG 8 39 0 -AACCTCTAAGCATACTCTACG 9 8 0 -GACCTGGAGGCTTAGACTTGG 9 77 0 -GCGCTCTTCCCAAGCGATCCG 9 131 1 -GGGCCGTCAGCTCTCAAGTCT 9 153 1 -* ** * ** * * ** -MAP Score: 19.1804 - -Motif 4 -GCCCCAAGCTTACCCAGGGAC 5 42 1 -GCCGTCTGCTGGACAACGGGC 3 0 1 -GCCGACGGGTGGTCATCGGGC 0 115 1 -GCCAATAGCGGCGCCGGAGTC 2 131 0 -GCCCCCCGCATAGTAGGGGGA 6 47 1 -GCCCGTACCGGACCTCGGTTC 4 159 0 -GCCTCATGTACCGGAAGGGAC 3 24 1 -GACACGCGCCTGGGAGGGTTC 2 11 1 -GCCTTTGGCCTTGGATGAGAA 7 76 0 -GGCCCTCGGATCGCTTGGGAA 9 137 0 -GCATGTTGGGAATCCGCGGAC 1 89 0 -GACACGCGCTGTATGCGGGGA 4 58 1 -GCCAGGTACAAAGCGTCGTGC 1 151 1 -GCGATCAGCTTGTGGGCGTGC 4 82 1 -GACAAATCGGATACTGGGGCA 3 75 0 -GCACTTAGCAGCGTATCGTTA 2 34 0 -*** ** * *** * -MAP Score: 18.0097 - -Motif 5 -CGGCACAGAGCTT 0 106 0 -ATCCGCGGACGCT 1 86 0 -CGCCTGGGAGGGT 2 17 1 -CGGAAGGGACGTT 3 35 1 -ACACACAGACGGT 3 122 0 -TGCCAGAGAGGTT 3 185 0 -AGACTGAGACGTT 4 114 1 -AATCGTAGAGGAT 4 187 1 -CGTCTCGTAGGGT 5 61 0 -CGTCGCGGAGGAT 6 15 1 -CTTCTTAGACGCT 6 119 1 -CGACGCAGAGGAT 8 37 0 -ATGCTTAGAGGTT 9 16 1 -AGACTTGGGCGAT 9 72 0 -CGACCTGGAGGCT 9 86 0 -** * ****** * -MAP Score: 16.8287 - -Motif 6 -GTGCGCGAAGGAAGCAGCGCGTG 0 3 1 -TTGAGCCGAGTAAAGGGCTGGTG 0 33 0 -CAATGCTAAGCTCTGTGCCGACG 0 99 1 -CAACTCTCTATGTAGTGCCCGAG 1 28 0 -CGACGCTTTGTACCTGGCTTGCG 1 146 0 -CGAGTCAATGACACGCGCCTGGG 2 2 1 -CGATACGCTGCTAAGTGCCGTCC 2 37 1 -CCGGGCCAATAGCGGCGCCGGAG 2 133 0 -CCACGCTTCGACACGTGGTATAG 2 175 1 -CCGAGCCTCATGTACCGGAAGGG 3 20 1 -CTGCTCCCCGCATACAGCGCGTG 4 60 0 -CCGAGGTCCGGTACGGGCAAGCC 4 162 1 -GTGCTCATAGGGACGTCGCGGAG 6 2 1 -CCCTACTATGCGGGGGGCAGGTC 6 42 0 -GCCAGCAATTGCAGGTGGTCGTG 6 132 1 -CTCTGCGTCGCATGGCGGCGTGG 8 40 1 -GGAGGCTTAGACTTGGGCGATAC 9 70 0 -GCATGGAGAGAGATCCGGAGGAG 9 98 1 -* * ** * * ** * * -MAP Score: 15.0441 - -Motif 7 -GCGCGTGTGTGTAAC 0 19 1 -GCACAGAGCTTAGCA 0 102 0 -GGTGGTCATCGGGCA 0 122 1 -GCGCGTGTCATTGAC 2 5 0 -GGACGGCACTTAGCA 2 45 0 -GCGCGTCCCGGGCCA 2 148 0 -GCTCGGCCCGTTGTC 3 11 0 -GCGCGTGTCCTTTAA 4 52 0 -GCTGATCGCTGCTCC 4 76 0 -GCCCGTACCGGACCT 4 165 0 -GGACGTCGCGGAGGA 6 12 1 -GCGGGGGGCAGGTCA 6 41 0 -GGACGTACTGGCACA 6 65 1 -GCAGGTGGTCGTGCA 6 142 1 -GCGCATACCTTAACA 7 21 0 -GCACGGGACTTCAAC 7 38 0 -GCACGTAGCTGGTAA 7 116 0 -GCTCGTCTATGGTCA 8 139 0 -GCGCATGCTGGATCC 9 120 0 -GGCCGTCAGCTCTCA 9 154 1 -** **** * * ** -MAP Score: 13.3145 - -Motif 8 -GAACCGAGGTCCGGTACGGGC 4 159 1 -GCCCCCCGCATAGTAGGGGGA 6 47 1 -GTCCCTGGGTAAGCTTGGGGC 5 42 0 -ACTCCACGCTTCGACACGTGG 2 172 1 -ATCCTCTGCGTCGCATGGCGG 8 37 1 -GTTCAATGCTAAGCTCTGTGC 0 96 1 -GCTCATAGGGACGTCGCGGAG 6 4 1 -GTCCCGGGCCAATAGCGGCGC 2 138 0 -GCACTTAGCAGCGTATCGTTA 2 34 0 -GGCCCTCGGATCGCTTGGGAA 9 137 0 -CTGCTGGACAACGGGCCGAGC 3 5 1 -GGGCACTACATAGAGAGTTGC 1 31 1 -AGCCTCCAGGTCGCATGGAGA 9 86 1 -AATCGTAGATCAGAGGCGAGA 5 107 1 -GAACTCCACTAAGACTTGAGA 9 164 0 -GAGCAGCGATCAGCTTGTGGG 4 77 1 -GCCAGGTACAAAGCGTCGTGC 1 151 1 -AGTCAATGACACGCGCCTGGG 2 4 1 -GGTCATGGAATCTTATGTAGC 4 5 1 -GTAGATAACAGAGGTCGGGGG 1 178 1 -* * ** ** ** ** -MAP Score: 11.6098 - -Motif 9 -CCGAGTAAAGGGCTG 0 36 0 -GTGGTCATCGGGCAC 0 123 1 -GATAACAGAGGTCGG 1 181 1 -CGGCGCCGGAGTCTG 2 129 0 -GCGCGTCCCGGGCCA 2 148 0 -CTGGACAACGGGCCG 3 8 1 -CGGATACTGGGGCAG 3 74 0 -GGGAGCAGCGATCAG 4 75 1 -CAGAACCGAGGTCCG 4 157 1 -GGGTCCCTGGGTAAG 5 50 0 -GTGCTCATAGGGACG 6 2 1 -GAGATCCGGAGGAGG 9 107 1 -GCGATCCGAGGGCCG 9 144 1 -GAGTTCACATGGCTG 9 179 1 -* * ** ***** * -MAP Score: 11.2943 - -Motif 10 -TAGAGGCGGTG 0 59 1 -GCTAAGCTCTG 0 103 1 -TGGAAGCAGTG 1 121 1 -GCGAGGCTGTG 1 138 0 -ACGACGCTTTG 1 159 0 -GGGACGCGCAC 2 154 1 -TCGAAGCGTGG 2 175 0 -TGTATGCGGGG 4 67 1 -GGTAAGCTTGG 5 45 0 -TGTACGCTGGG 5 148 1 -ACTATGCGGGG 6 50 0 -GGTATGCGCTG 7 27 1 -GGTACCCGGAG 7 157 1 -GCGACGCAGAG 8 40 0 -TGGCGGCGTGG 8 52 1 -TCTAGGCGGGC 8 79 0 -AGTATGCTTAG 9 13 1 -TGGAGGCTTAG 9 83 0 -**** ****** -MAP Score: 9.7924 - -Motif 11 -GCACAGAGCTTAGCATTGAAC 0 96 0 -GTCCGCGGATTCCCAACATGC 1 89 1 -ATACACAGCCTCGCAAGCCAG 1 135 1 -GGCCCGGGACGCGCACTAAGA 2 149 1 -GCCCGTTGTCCAGCAGACGGC 3 0 0 -GAGCAGCGATCAGCTTGTGGG 4 77 1 -GAACCGAGGTCCGGTACGGGC 4 159 1 -GTCCCTGGGTAAGCTTGGGGC 5 42 0 -GACCTGCCCCCCGCATAGTAG 6 42 1 -AACCAGCGCATACCTTAACAG 7 20 0 -ATCCTCTGCGTCGCATGGCGG 8 37 1 -GACCATAGACGAGCATCAAAG 8 140 1 -GGCCCTCGGATCGCTTGGGAA 9 137 0 -* ** * **** ** -MAP Score: 9.01393 - -Motif 12 -GCCGTCCGTC 2 53 1 -GGCGTGCGCG 0 0 1 -GGCGCGTGTC 2 11 0 -AGCGCGTGTG 0 18 1 -GCGGTGCGTG 8 108 0 -AGCGCGTGTC 4 58 0 -AGCGTCCGCG 1 86 1 -ACCGTCTGTG 3 122 1 -GCCATGCGAC 8 46 0 -ACCACCCGTC 0 118 0 -GGCGCCGGAG 2 133 0 -ACCACGTGTC 2 184 0 -GGCTTGCGAG 1 144 0 -GCGATCCGAG 9 144 1 -AGTGCGCGTC 2 156 0 -AGTGCCCGAG 1 28 0 -********** -MAP Score: 7.51121 - -Motif 13 -GCCGACGGGTGGTCATCGGG 0 115 1 -GCACGACGCTTTGTACCTGG 1 152 0 -CCTGGGAGGGTTCAATAACG 2 19 1 -GCGCGTCCCGGGCCAATAGC 2 143 0 -GCCGTCTGCTGGACAACGGG 3 0 1 -GTCCCTTCCGGTACATGAGG 3 25 0 -GCTGCTCCCCGCATACAGCG 4 64 0 -GCCCCAAGCTTACCCAGGGA 5 42 1 -ACCGGCTGACGCTAATACGG 5 84 0 -GCGGGGGGCAGGTCATTACA 6 36 0 -GCTGGCAGCGTCTAAGAAGG 6 118 0 -GCAGGTGGTCGTGCAATACG 6 142 1 -GCTGGTTGAAGTCCCGTGCG 7 34 1 -GCACGTAGCTGGTAAATAGG 7 111 0 -GCGGCGTGGATTTCATACAG 8 54 1 -CCTGGAGGCTTAGACTTGGG 9 76 0 -** ** ** * * ** -MAP Score: 5.63667 - -Motif 14 -GCCGACGGGTGGTCATCGGG 0 115 1 -ATCCGCGGACGCTTAGAGGG 1 79 0 -ACGCTTTGTACCTGGCTTGC 1 147 0 -ACGGACGGCACTTAGCAGCG 2 42 0 -GCCGTCTGCTGGACAACGGG 3 0 1 -ACACACAGACGGTTGAAAGG 3 115 0 -GCCGATAGTGCTTAAGTTCG 3 147 1 -CTTGCCCGTACCGGACCTCG 4 163 0 -ACCGGCTGACGCTAATACGG 5 84 0 -GCCCCCCGCATAGTAGGGGG 6 47 1 -GCTGGCAGCGTCTAAGAAGG 6 118 0 -GCAGGTGGTCGTGCAATACG 6 142 1 -ACGCACGGGACTTCAACCAG 7 35 0 -GCACGTAGCTGGTAAATAGG 7 111 0 -ATCCTCTGCGTCGCATGGCG 8 37 1 -** * * * * * * ** -MAP Score: 3.89842 - -Motif 15 -GAGGCTGTGTAT 1 135 0 -GAGGTCGGGGGT 1 188 1 -GACGGACGGCAC 2 51 0 -TTGGCCCGGGAC 2 147 1 -GAGGCTCGGCCC 3 17 0 -CACGCGCTGTAT 4 60 1 -TAGGCCAGGTAT 4 127 0 -GAGGTCCGGTAC 4 164 1 -TACGCTGGGGAT 5 150 1 -GTCGCGGAGGAT 6 16 1 -TACGCACGGGAC 7 44 0 -TACTCCGGGTAC 7 158 0 -GACGCAGAGGAT 8 37 0 -TAGGCGGGCCAT 8 76 0 -***** *** ** -MAP Score: 3.33444 - -Motif 16 -CGGCTCAATCGTAGAGGC 0 48 1 -CGACGGGTGGTCATCGGG 0 117 1 -CGCTTAGAGGGCACAAGC 1 72 0 -TGACACGCGCCTGGGAGG 2 10 1 -CGATACGCTGCTAAGTGC 2 37 1 -CGTCCCGGGCCAATAGCG 2 142 0 -CCACGCTTCGACACGTGG 2 175 1 -CGTCTGCTGGACAACGGG 3 2 1 -ACACAGACGGTTGAAAGG 3 115 0 -TGCTCCCCGCATACAGCG 4 64 0 -TGAGGCTTGCCCGTACCG 4 170 0 -TGCCCCAAGCTTACCCAG 5 41 1 -CGGCTGACGCTAATACGG 5 84 0 -CGCGACGTCCCTATGAGC 6 4 0 -TGCCCCCCGCATAGTAGG 6 46 1 -CGTTGCCTTCTTAGACGC 6 113 1 -TGACTCAATCGTAGACCC 6 173 1 -AGTCCCGTGCGTATGTGG 7 43 1 -AGGCTCGCACGTAGCTGG 7 119 0 -CCACGCCGCCATGCGACG 8 45 0 -AGCCTCCAGGTCGCATGG 9 86 1 -** * * ** ** ** -MAP Score: 1.0395 - diff --git a/Tests/Motif/mast.dna.oops.txt b/Tests/Motif/mast.dna.oops.txt deleted file mode 100644 index 250c40f026e..00000000000 --- a/Tests/Motif/mast.dna.oops.txt +++ /dev/null @@ -1,301 +0,0 @@ -******************************************************************************** -MAST - Motif Alignment and Search Tool -******************************************************************************** - MAST version 3.0 (Release date: 2004/08/18 09:07:01) - - For further information on how to interpret these results or to get - a copy of the MAST software please access http://meme.sdsc.edu. -******************************************************************************** - - -******************************************************************************** -REFERENCE -******************************************************************************** - If you use this program in your research, please cite: - - Timothy L. Bailey and Michael Gribskov, - "Combining evidence using p-values: application to sequence homology - searches", Bioinformatics, 14(48-54), 1998. -******************************************************************************** - - -******************************************************************************** -DATABASE AND MOTIFS -******************************************************************************** - DATABASE INO_up800.s (nucleotide) - Last updated on Mon Aug 16 21:19:59 2004 - Database contains 7 sequences, 5600 residues - - Scores for positive and reverse complement strands are combined. - - MOTIFS meme.INO_up800.oops.txt (nucleotide) - MOTIF WIDTH BEST POSSIBLE MATCH - ----- ----- ------------------- - 1 12 TTCACATGCCGC - 2 10 TCTGGCACAG - - PAIRWISE MOTIF CORRELATIONS: - MOTIF 1 - ----- ----- - 2 0.32 - No overly similar pairs (correlation > 0.60) found. - - Random model letter frequencies (from non-redundant database): - A 0.281 C 0.222 G 0.229 T 0.267 -******************************************************************************** - - -******************************************************************************** -SECTION I: HIGH-SCORING SEQUENCES -******************************************************************************** - - Each of the following 7 sequences has E-value less than 10. - - The E-value of a sequence is the expected number of sequences - in a random database of the same size that would match the motifs as - well as the sequence does and is equal to the combined p-value of the - sequence times the number of sequences in the database. - - The combined p-value of a sequence measures the strength of the - match of the sequence to all the motifs and is calculated by - o finding the score of the single best match of each motif - to the sequence (best matches may overlap), - o calculating the sequence p-value of each score, - o forming the product of the p-values, - o taking the p-value of the product. - - The sequence p-value of a score is defined as the - probability of a random sequence of the same length containing - some match with as good or better a score. - - The score for the match of a position in a sequence to a motif - is computed by by summing the appropriate entry from each column of - the position-dependent scoring matrix that represents the motif. - - Sequences shorter than one or more of the motifs are skipped. - - The table is sorted by increasing E-value. -******************************************************************************** - -SEQUENCE NAME DESCRIPTION E-VALUE LENGTH -------------- ----------- -------- ------ -ACC1 sequence of the region up... 6.1e-05 800 -CHO1 sequence of the region up... 0.00016 800 -INO1 sequence of the region up... 0.00019 800 -FAS1 sequence of the region up... 0.00022 800 -OPI3 sequence of the region up... 0.00092 800 -CHO2 sequence of the region up... 0.0029 800 -FAS2 sequence of the region up... 0.0093 800 - -******************************************************************************** - - - -******************************************************************************** -SECTION II: MOTIF DIAGRAMS -******************************************************************************** - - The ordering and spacing of all non-overlapping motif occurrences - are shown for each high-scoring sequence listed in Section I. - - A motif occurrence is defined as a position in the sequence whose - match to the motif has POSITION p-value less than 0.0001. - - The POSITION p-value of a match is the probability of - a single random subsequence of the length of the motif - scoring at least as well as the observed match. - - For each sequence, all motif occurrences are shown unless there - are overlaps. In that case, a motif occurrence is shown only if its - p-value is less than the product of the p-values of the other - (lower-numbered) motif occurrences that it overlaps. - - The table also shows the E-value of each sequence. - - Spacers and motif occurences are indicated by - o -d- `d' residues separate the end of the preceding motif - occurrence and the start of the following motif occurrence - o [sn] occurrence of motif `n' with p-value less than 0.0001. - A minus sign indicates that the occurrence is on the - reverse complement strand. -******************************************************************************** - -SEQUENCE NAME E-VALUE MOTIF DIAGRAM -------------- -------- ------------- -ACC1 6.1e-05 82_[+1]_137_[+2]_559 -CHO1 0.00016 152_[+2]_396_[-2]_42_[+1]_17_ - [+1]_149 -INO1 0.00019 282_[-2]_327_[-1]_55_[+1]_102 -FAS1 0.00022 43_[+2]_41_[+1]_694 -OPI3 0.00092 185_[-2]_144_[+1]_449 -CHO2 0.0029 353_[+1]_47_[-2]_378 -FAS2 0.0093 184_[-2]_372_[+1]_222 - -******************************************************************************** - - - -******************************************************************************** -SECTION III: ANNOTATED SEQUENCES -******************************************************************************** - - The positions and p-values of the non-overlapping motif occurrences - are shown above the actual sequence for each of the high-scoring - sequences from Section I. - - A motif occurrence is defined as a position in the sequence whose - match to the motif has POSITION p-value less than 0.0001 as - defined in Section II. - - For each sequence, the first line specifies the name of the sequence. - - The second (and possibly more) lines give a description of the - sequence. - - Following the description line(s) is a line giving the length, - combined p-value, and E-value of the sequence as defined in Section I. - - The next line reproduces the motif diagram from Section II. - - The entire sequence is printed on the following lines. - - Motif occurrences are indicated directly above their positions in the - sequence on lines showing - o the motif number of the occurrence (a minus sign indicates that - the occurrence is on the reverse complement strand), - o the position p-value of the occurrence, - o the best possible match to the motif (or its reverse complement), and - o columns whose match to the motif has a positive score (indicated - by a plus sign). -******************************************************************************** - - -ACC1 - sequence of the region upstream from YNR016C - LENGTH = 800 COMBINED P-VALUE = 8.78e-06 E-VALUE = 6.1e-05 - DIAGRAM: 82_[+1]_137_[+2]_559 - - - [+1] - 3.1e-07 - TTCACATGCCGC - ++++++++++ + -76 TAAAATCTTCACATGGCCCGGCCGCGCGCGCGTTGTGCCAACAAGTCGCAGTCGAAATTCAACCGCTCATTGCCA - - [+2] - 7.4e-07 - TCTGGCACAG - ++++++++++ -226 TCGTATTCTGGCACAGTATAGCCTAGCACAATCACTGTCACAATTGTTATCGGTTCTACAATTGTTCTGCTCTCT - - -CHO1 - sequence of the region upstream from YER026C - LENGTH = 800 COMBINED P-VALUE = 2.30e-05 E-VALUE = 0.00016 - DIAGRAM: 152_[+2]_396_[-2]_42_[+1]_17_[+1]_149 - - - [+2] - 3.9e-05 - TCTGGCACAG - ++++++ + -151 CGTCTGGCGCCCTTCCCATTCCGAACCATGTTATATTGAACCATCTGGCGACAAGCAGTATTAAGCATAATACAT - - [-2] - 7.4e-07 - CTGTGCCAGA - ++++++++++ -526 CAATCCCCACTCCTTCTCAATGTGTGCAGACTTCTGTGCCAGACACTGAATATATATCAGTAATTGGTCAAAATC - - [+1] [+1] - 8.7e-07 2.2e-05 - TTCACATGCCGC TTCACATGCCGC - ++++++ +++ + +++++++++ + -601 ACTTTGAACGTTCACACGGCACCCTCACGCCTTTGAGCTTTCACATGGACCCATCTAAAGATGAAGATCCGTATT - - -INO1 - sequence of the region upstream from YJL153C - LENGTH = 800 COMBINED P-VALUE = 2.71e-05 E-VALUE = 0.00019 - DIAGRAM: 282_[-2]_327_[-1]_55_[+1]_102 - - - [-2] - 1.8e-05 - CTGTGCCAGA - +++ +++ ++ -226 ACGTTGTATATGAAACGAGTAGTGAACGTTCGTACGATCTTTCACGCAGACATGCGACTGCGCCCGCCGTAGACC - - [-1] - 4.2e-08 - GCGGCATGTGAA - ++++++++++++ -601 TGCGCTTCGGCGGCTAAATGCGGCATGTGAAAAGTATTGTCTATTTTATCTTCATCCTTCTTTCCCAGAATATTG - - [+1] - 1.3e-05 - TTCACATGCCGC - +++++++++ ++ -676 AACTTATTTAATTCACATGGAGCAGAGAAAGCGCACCTCTGCGTTGGCGGCAATGTTAATTTGAGACGTATATAA - - -FAS1 - sequence of the region upstream from YKL182W - LENGTH = 800 COMBINED P-VALUE = 3.19e-05 E-VALUE = 0.00022 - DIAGRAM: 43_[+2]_41_[+1]_694 - - [+2] - 2.2e-05 - TCTGGCACAG - ++ +++++ + -1 CCGGGTTATAGCAGCGTCTGCTCCGCATCACGATACACGAGGTGCAGGCACGGTTCACTACTCCCCTGGCCTCCA - - [+1] - 4.2e-08 - TTCACATGCCGC - ++++++++++++ -76 ACAAACGACGGCCAAAAACTTCACATGCCGCCCAGCCAAGCATAATTACGCAACAGCGATCTTTCCGTCGCACAA - - -OPI3 - sequence of the region upstream from YJR073C - LENGTH = 800 COMBINED P-VALUE = 1.32e-04 E-VALUE = 0.00092 - DIAGRAM: 185_[-2]_144_[+1]_449 - - - [-2] - 7.4e-07 - CTGTGCCAGA - ++++++++++ -151 GTTAATCTGATCAACGCTACGCCGATGACAACGGTCTGTGCCAGATCTGGTTTTCCCCACTTATTTGCTACTTCC - - [+1] - 5.8e-06 - TTCACATGCCGC - ++++ ++ ++ + -301 AACTCCGTCAGGTCTTCCACGTGGAACTGCCAAGCCTCCTTCAGATCGCTCTTGTCGACCGTCTCCAAGAGATCC - - -CHO2 - sequence of the region upstream from YGR157W - LENGTH = 800 COMBINED P-VALUE = 4.18e-04 E-VALUE = 0.0029 - DIAGRAM: 353_[+1]_47_[-2]_378 - - - [+1] - 5.2e-07 - TTCACATGCCGC - +++ ++++++++ -301 ATATATATTTTTGCCTTGGTTTAAATTGGTCAAGACAGTCAATTGCCACACTTTTCTCATGCCGCATTCATTATT - - [-2] - 2.9e-05 - CTGTGCCAGA - + +++++++ -376 CGCGAAGTTTTCCACACAAAACTGTGAAAATGAACGGCGATGCCAGAAACGGCAAAACCTCAAATGTTAGATAAC - - -FAS2 - sequence of the region upstream from YPL231W - LENGTH = 800 COMBINED P-VALUE = 1.33e-03 E-VALUE = 0.0093 - DIAGRAM: 184_[-2]_372_[+1]_222 - - - [-2] - 2.9e-05 - CTGTGCCAGA - ++++++++ -151 AACAGGGTGTCGGTCATACCGATAAAGCCGTCAAGAGTGCCAGAAAAGCAAGAAAGAACAAGATTAGATGTTGGT - - [+1] - 1.9e-06 - TTCACATGCCGC - +++++++++ + -526 GCTTAGCAAAATCCAACCATTTTTTTTTTATCTCCCGCGTTTTCACATGCTACCTCATTCGCCTCGTAACGTTAC - -******************************************************************************** - - -CPU: pmgm2 -Time 0.030000 secs. - -mast meme.INO_up800.oops.txt -text -stdout diff --git a/Tests/Motif/mast.protein.oops.txt b/Tests/Motif/mast.protein.oops.txt deleted file mode 100644 index 3fefee4db25..00000000000 --- a/Tests/Motif/mast.protein.oops.txt +++ /dev/null @@ -1,885 +0,0 @@ -******************************************************************************** -MAST - Motif Alignment and Search Tool -******************************************************************************** - MAST version 3.0 (Release date: 2004/08/18 09:07:01) - - For further information on how to interpret these results or to get - a copy of the MAST software please access http://meme.sdsc.edu. -******************************************************************************** - - -******************************************************************************** -REFERENCE -******************************************************************************** - If you use this program in your research, please cite: - - Timothy L. Bailey and Michael Gribskov, - "Combining evidence using p-values: application to sequence homology - searches", Bioinformatics, 14(48-54), 1998. -******************************************************************************** - - -******************************************************************************** -DATABASE AND MOTIFS -******************************************************************************** - DATABASE adh.s (peptide) - Last updated on Mon Aug 16 21:19:59 2004 - Database contains 33 sequences, 9996 residues - - MOTIFS meme.adh.oops.txt (peptide) - MOTIF WIDTH BEST POSSIBLE MATCH - ----- ----- ------------------- - 1 29 YSASKFAVRMLTRSMAHEYAPHGIRVNCI - 2 29 KVVLITGCSSGIGKATAKHLHKEGAKVVL - - PAIRWISE MOTIF CORRELATIONS: - MOTIF 1 - ----- ----- - 2 0.30 - No overly similar pairs (correlation > 0.60) found. - - Random model letter frequencies (from non-redundant database): - A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 - L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 - W 0.013 Y 0.033 -******************************************************************************** - - -******************************************************************************** -SECTION I: HIGH-SCORING SEQUENCES -******************************************************************************** - - Each of the following 33 sequences has E-value less than 10. - - The E-value of a sequence is the expected number of sequences - in a random database of the same size that would match the motifs as - well as the sequence does and is equal to the combined p-value of the - sequence times the number of sequences in the database. - - The combined p-value of a sequence measures the strength of the - match of the sequence to all the motifs and is calculated by - o finding the score of the single best match of each motif - to the sequence (best matches may overlap), - o calculating the sequence p-value of each score, - o forming the product of the p-values, - o taking the p-value of the product. - - The sequence p-value of a score is defined as the - probability of a random sequence of the same length containing - some match with as good or better a score. - - The score for the match of a position in a sequence to a motif - is computed by by summing the appropriate entry from each column of - the position-dependent scoring matrix that represents the motif. - - Sequences shorter than one or more of the motifs are skipped. - - The table is sorted by increasing E-value. -******************************************************************************** - -SEQUENCE NAME DESCRIPTION E-VALUE LENGTH -------------- ----------- -------- ------ -BUDC_KLETE ACETOIN(DIACETYL) REDUCTA... 2.6e-33 241 -YRTP_BACSU HYPOTHETICAL 25.3 KD PROT... 4.3e-33 238 -AP27_MOUSE ADIPOCYTE P27 PROTEIN (AP... 4.5e-33 244 -HDE_CANTR HYDRATASE-DEHYDROGENASE-E... 1.6e-32 906 -HDHA_ECOLI 7-ALPHA-HYDROXYSTEROID DE... 4.9e-31 255 -DHII_HUMAN CORTICOSTEROID 11-BETA-DE... 8.2e-31 292 -FIXR_BRAJA FIXR PROTEIN 2.6e-30 278 -DHGB_BACME GLUCOSE 1-DEHYDROGENASE B... 3.2e-30 262 -NODG_RHIME NODULATION PROTEIN G (HOS... 3.4e-29 245 -RIDH_KLEAE RIBITOL 2-DEHYDROGENASE (... 6.2e-29 249 -YINL_LISMO HYPOTHETICAL 26.8 KD PROT... 6.6e-29 248 -DHMA_FLAS1 N-ACYLMANNOSAMINE 1-DEHYD... 1.2e-28 270 -HMTR_LEIMA no comment 5.1e-28 287 -2BHD_STREX 20-BETA-HYDROXYSTEROID DE... 5.9e-28 255 -ENTA_ECOLI 2,3-DIHYDRO-2,3-DIHYDROXY... 4.8e-27 248 -DHB2_HUMAN no comment 1.7e-26 387 -BDH_HUMAN D-BETA-HYDROXYBUTYRATE DE... 2.8e-26 343 -BA72_EUBSP 7-ALPHA-HYDROXYSTEROID DE... 4.2e-26 249 -FVT1_HUMAN no comment 8.9e-26 332 -GUTD_ECOLI SORBITOL-6-PHOSPHATE 2-DE... 5.1e-25 259 -DHB3_HUMAN no comment 8.3e-25 310 -3BHD_COMTE 3-BETA-HYDROXYSTEROID DEH... 1.4e-24 253 -LIGD_PSEPA C ALPHA-DEHYDROGENASE (EC... 8.1e-24 305 -DHES_HUMAN ESTRADIOL 17 BETA-DEHYDRO... 2.4e-22 327 -RFBB_NEIGO no comment 3.2e-19 346 -BPHB_PSEPS BIPHENYL-CIS-DIOL DEHYDRO... 1e-18 275 -YURA_MYXXA no comment 1.9e-18 258 -PCR_PEA no comment 7.2e-18 399 -DHCA_HUMAN no comment 1.1e-17 276 -ADH_DROME ALCOHOL DEHYDROGENASE (EC... 2.7e-14 255 -MAS1_AGRRA no comment 3e-14 476 -FABI_ECOLI no comment 9.7e-14 262 -CSGA_MYXXA no comment 2.5e-12 166 - -******************************************************************************** - - - -******************************************************************************** -SECTION II: MOTIF DIAGRAMS -******************************************************************************** - - The ordering and spacing of all non-overlapping motif occurrences - are shown for each high-scoring sequence listed in Section I. - - A motif occurrence is defined as a position in the sequence whose - match to the motif has POSITION p-value less than 0.0001. - - The POSITION p-value of a match is the probability of - a single random subsequence of the length of the motif - scoring at least as well as the observed match. - - For each sequence, all motif occurrences are shown unless there - are overlaps. In that case, a motif occurrence is shown only if its - p-value is less than the product of the p-values of the other - (lower-numbered) motif occurrences that it overlaps. - - The table also shows the E-value of each sequence. - - Spacers and motif occurences are indicated by - o -d- `d' residues separate the end of the preceding motif - occurrence and the start of the following motif occurrence - o [n] occurrence of motif `n' with p-value less than 0.0001. -******************************************************************************** - -SEQUENCE NAME E-VALUE MOTIF DIAGRAM -------------- -------- ------------- -BUDC_KLETE 2.6e-33 2_[2]_120_[1]_61 -YRTP_BACSU 4.3e-33 6_[2]_119_[1]_55 -AP27_MOUSE 4.5e-33 7_[2]_112_[1]_67 -HDE_CANTR 1.6e-32 8_[2]_125_[1]_131_[2]_115_[1]_411 -HDHA_ECOLI 4.9e-31 11_[2]_74_[1]_15_[1]_68 -DHII_HUMAN 8.2e-31 34_[2]_119_[1]_81 -FIXR_BRAJA 2.6e-30 36_[2]_123_[1]_61 -DHGB_BACME 3.2e-30 7_[2]_123_[1]_74 -NODG_RHIME 3.4e-29 6_[2]_116_[1]_65 -RIDH_KLEAE 6.2e-29 14_[2]_116_[1]_61 -YINL_LISMO 6.6e-29 5_[2]_75_[2]_15_[1]_66 -DHMA_FLAS1 1.2e-28 14_[2]_121_[1]_77 -HMTR_LEIMA 5.1e-28 6_[2]_157_[1]_66 -2BHD_STREX 5.9e-28 6_[2]_116_[1]_75 -ENTA_ECOLI 4.8e-27 5_[2]_109_[1]_76 -DHB2_HUMAN 1.7e-26 82_[2]_120_[1]_127 -BDH_HUMAN 2.8e-26 55_[2]_123_[1]_107 -BA72_EUBSP 4.2e-26 6_[2]_121_[1]_64 -FVT1_HUMAN 8.9e-26 32_[2]_124_[1]_118 -GUTD_ECOLI 5.1e-25 2_[2]_122_[1]_77 -DHB3_HUMAN 8.3e-25 48_[2]_120_[1]_84 -3BHD_COMTE 1.4e-24 6_[2]_115_[1]_74 -LIGD_PSEPA 8.1e-24 6_[2]_121_[1]_120 -DHES_HUMAN 2.4e-22 2_[2]_50_[2]_44_[1]_144 -RFBB_NEIGO 3.2e-19 6_[2]_129_[1]_153 -BPHB_PSEPS 1e-18 5_[2]_118_[1]_94 -YURA_MYXXA 1.9e-18 65_[2]_22_[2]_14_[1]_70 -PCR_PEA 7.2e-18 25_[1]_32_[2]_284 -DHCA_HUMAN 1.1e-17 4_[2]_159_[1]_55 -ADH_DROME 2.7e-14 6_[2]_116_[1]_75 -MAS1_AGRRA 3e-14 245_[2]_74_[1]_14_[1]_56 -FABI_ECOLI 9.7e-14 6_[2]_123_[1]_75 -CSGA_MYXXA 2.5e-12 51_[2]_7_[1]_50 - -******************************************************************************** - - - -******************************************************************************** -SECTION III: ANNOTATED SEQUENCES -******************************************************************************** - - The positions and p-values of the non-overlapping motif occurrences - are shown above the actual sequence for each of the high-scoring - sequences from Section I. - - A motif occurrence is defined as a position in the sequence whose - match to the motif has POSITION p-value less than 0.0001 as - defined in Section II. - - For each sequence, the first line specifies the name of the sequence. - - The second (and possibly more) lines give a description of the - sequence. - - Following the description line(s) is a line giving the length, - combined p-value, and E-value of the sequence as defined in Section I. - - The next line reproduces the motif diagram from Section II. - - The entire sequence is printed on the following lines. - - Motif occurrences are indicated directly above their positions in the - sequence on lines showing - o the motif number of the occurrence, - o the position p-value of the occurrence, - o the best possible match to the motif, and - o columns whose match to the motif has a positive score (indicated - by a plus sign). -******************************************************************************** - - -BUDC_KLETE - ACETOIN(DIACETYL) REDUCTASE (EC 1.1.1.5) (ACETOIN DEHYDROGENASE) - LENGTH = 241 COMBINED P-VALUE = 7.82e-35 E-VALUE = 2.6e-33 - DIAGRAM: 2_[2]_120_[1]_61 - - [2] - 7.9e-21 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++++++++++++++++++ + + -1 MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATATAVAAEINQAGGRAVAIKVDVSRRDQVFAAVEQARK - - [1] - 2.6e-21 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++++++++++++++++ ++++++ -151 VYSSSKFAVRGLTQTAARDLAPLGITVNGFCPGIVKTPMWAEIDRQCRKRRANRWATARLNLPNASPLAACRSLK - - -YRTP_BACSU - HYPOTHETICAL 25.3 KD PROTEIN IN RTP 5'REGION (ORF238) - LENGTH = 238 COMBINED P-VALUE = 1.31e-34 E-VALUE = 4.3e-33 - DIAGRAM: 6_[2]_119_[1]_55 - - [2] - 2.8e-19 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - ++++++++++++++++++++++++ ++ + -1 MQSLQHKTALITGGGRGIGRATALALAKEGVNIGLIGRTSANVEKVAEEVKALGVKAAFAAADVKDADQVNQAVA - - [1] - 1.3e-22 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - ++++++++ ++++++++++++++++++++ -151 VTSAYSASKFAVLGLTESLMQEVRKHNIRVSALTPSTVASDMSIELNLTDGNPEKVMQPEDLAEYMVAQLKLDPR - - -AP27_MOUSE - ADIPOCYTE P27 PROTEIN (AP27) - LENGTH = 244 COMBINED P-VALUE = 1.37e-34 E-VALUE = 4.5e-33 - DIAGRAM: 7_[2]_112_[1]_67 - - [2] - 7.4e-20 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++++++ ++++++++++++++ -1 MKLNFSGLRALVTGAGKGIGRDTVKALHASGAKVVAVTRTNSDLVSLAKECPGIEPVCVDLGDWDATEKALGGIG - - [1 - 4. - YS - ++ -76 PVDLLVNNAALVIMQPFLEVTKEAFDRSFSVNLRSVFQVSQMVARDMINRGVPGSIVNVSSMVAHVTFPNLITYS - - ] - 8e-22 - ASKFAVRMLTRSMAHEYAPHGIRVNCI - ++++++++++++++++++++ ++++++ -151 STKGAMTMLTKAMAMELGPHKIRVNSVNPTVVLTDMGKKVSADPEFARKLKERHPLRKFAEVEDVVNSILFLLSD - - -HDE_CANTR - HYDRATASE-DEHYDROGENASE-EPIMERASE (HDE) - LENGTH = 906 COMBINED P-VALUE = 4.94e-34 E-VALUE = 1.6e-32 - DIAGRAM: 8_[2]_125_[1]_131_[2]_115_[1]_411 - - [2] - 2.5e-19 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - ++++++++++++++ + +++++ ++++++ -1 MSPVDFKDKVVIITGAGGGLGKYYSLEFAKLGAKVVVNDLGGALNGQGGNSKAADVVVDEIVKNGGVAVADYNNV - - [1] - 2.8e-13 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - + +++ ++ ++ ++++++ ++++++ +++ -151 PAGLYGNFGQANYASAKSALLGFAETLAKEGAKYNIKANAIAPLARSRMTESILPPPMLEKLGPEKVAPLVLYLS - - [2] - 1.5e-24 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++ +++++++++++++++++++ -301 TNEARKLPANDASGAPTVSLKDKVVLITGAGAGLGKEYAKWFAKYGAKVVVNDFKDATKTVDEIKAAGGEAWPDQ - - [1] - 5.2e-18 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - ++++++++ +++++++ + ++ +++++++ -451 NITSTSGIYGNFGQANYSSSKAGILGLSKTMAIEGAKNNIKVNIVAPHAETAMTLTIFREQDKNLYHADQVAPLL - - -HDHA_ECOLI - 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE (EC 1.1.1.159) (HSDH) - LENGTH = 255 COMBINED P-VALUE = 1.49e-32 E-VALUE = 4.9e-31 - DIAGRAM: 11_[2]_74_[1]_15_[1]_68 - - [2] - 4.3e-21 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++ +++++++++++++++++++ -1 MFNSDNLRLDGKCAIITGAGAGIGKEIAITFATAGASVVVSDINADAANHVVDEIQQLGGQAFACRCDITSEQEL - - [1] - 2.9e-05 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - + ++ ++++ + ++++ + + -76 SALADFAISKLGKVDILVNNAGGGGPKPFDMPMADFRRAYELNVFSFFHLSQLVAPEMEKNGGGVILTITSMAAE - - [1] - 8.6e-19 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - + +++++ +++++ +++++++++++++++ -151 NKNINMTSYASSKAAASHLVRNMAFDLGEKNIRVNGIAPGAILTDALKSVITPEIEQKMLQHTPIRRLGQPQDIA - - -DHII_HUMAN - CORTICOSTEROID 11-BETA-DEHYDROGENASE (EC 1.1.1.146) (11-DH) (11-BETA- - HYDROXYSTEROID DEHYDROGENASE) (11-BETA-HSD) - LENGTH = 292 COMBINED P-VALUE = 2.49e-32 E-VALUE = 8.2e-31 - DIAGRAM: 34_[2]_119_[1]_81 - - [2] - 3.9e-24 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++++++++++++++++++++++ -1 MAFMKKYLLPILGLFMAYYYYSANEEFRPEMLQGKKVIVTGASKGIGREMAYHLAKMGAHVVVTARSKETLQKVV - - [1] - 1.2e-15 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++++++ ++ +++++ +++++++ -151 TVAALPMLKQSNGSIVVVSSLAGKVAYPMVAAYSASKFALDGFFSSIRKEYSVSRVNVSITLCVLGLIDTETAMK - - -FIXR_BRAJA - FIXR PROTEIN - LENGTH = 278 COMBINED P-VALUE = 7.83e-32 E-VALUE = 2.6e-30 - DIAGRAM: 36_[2]_123_[1]_61 - - [2] - 3.2e-18 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - ++++ +++++++++++++ + ++++++ -1 MGLDLPNDNLIRGPLPEAHLDRLVDAVNARVDRGEPKVMLLTGASRGIGHATAKLFSEAGWRIISCARQPFDGER - - [1] - 5.1e-21 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - + +++++ ++++++++++++++++++++ -151 APILLAQGLFDELRAASGSIVNVTSIAGSRVHPFAGSAYATSKAALASLTRELAHDYAPHGIRVNAIAPGEIRTD - - -DHGB_BACME - GLUCOSE 1-DEHYDROGENASE B (EC 1.1.1.47) - LENGTH = 262 COMBINED P-VALUE = 9.77e-32 E-VALUE = 3.2e-30 - DIAGRAM: 7_[2]_123_[1]_74 - - [2] - 4.4e-19 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++ + +++++++++++++ +++++ -1 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEANSVLEEEIKKVGGEAIAVKGDVTVESDVIN - - [1] - 5.3e-20 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - + +++++++ +++++++++++++++++++ -151 KIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTPINAEKFADPEQRADVESMIPMGYIGEPEE - - -NODG_RHIME - NODULATION PROTEIN G (HOST-SPECIFICITY OF NODULATION PROTEIN C) - LENGTH = 245 COMBINED P-VALUE = 1.03e-30 E-VALUE = 3.4e-29 - DIAGRAM: 6_[2]_116_[1]_65 - - [2] - 4.0e-16 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++ ++ ++++ ++++++ + + -1 MFELTGRKALVTGASGAIGGAIARVLHAQGAIVGLHGTQIEKLETLATELGDRVKLFPANLANRDEVKALGQRAE - - [1] - 7.3e-22 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++++++++++++++++ +++++++ -151 NYCASKAGMIGFSKSLAQEIATRNITVNCVAPGFIESAMTDKLNHKQKEKIMVAIPIHRMGTGTEVASAVAYLAS - - -RIDH_KLEAE - RIBITOL 2-DEHYDROGENASE (EC 1.1.1.56) (RDH) - LENGTH = 249 COMBINED P-VALUE = 1.88e-30 E-VALUE = 6.2e-29 - DIAGRAM: 14_[2]_116_[1]_61 - - [2] - 7.0e-21 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++ +++++++++++++++++ +++++++ -1 MKHSVSSMNTSLSGKVAAITGAASGIGLECARTLLGAGAKVVLIDREGEKLNKLVAELGENAFALQVDLMQADQV - - [1] - 7.4e-17 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - ++++++++++++++ +++++++++++ ++ -151 VVPVIWEPVYTASKFAVQAFVHTTRRQVAQYGVRVGAVLPGPVVTALLDDWPKAKMDEALANGSLMQPIEVAESV - - -YINL_LISMO - HYPOTHETICAL 26.8 KD PROTEIN IN INLA 5'REGION (ORFA) - LENGTH = 248 COMBINED P-VALUE = 1.99e-30 E-VALUE = 6.6e-29 - DIAGRAM: 5_[2]_75_[2]_15_[1]_66 - - [2] - 2.9e-23 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - ++++++++++++++++++ +++++++ ++ -1 MTIKNKVIIITGASSGIGKATALLLAEKGAKLVLAARRVEKLEKIVQIIKANSGEAIFAKTDVTKREDNKKLVEL - - [2] - 3.8e-05 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - + + + ++ + +++ ++ + -76 AIERYGKVDAIFLNAGIMPNSPLSALKEDEWEQMIDINIKGVLNGIAAVLPSFIAQKSGHIIATSSVAGLKAYPG - - [1] - 1.9e-14 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++++ +++ ++++ ++++ ++++ -151 GAVYGATKWAVRDLMEVLRMESAQEGTNIRTATIYPAAINTELLETITDKETEQGMTSLYKQYGITPDRIASIVA - - -DHMA_FLAS1 - N-ACYLMANNOSAMINE 1-DEHYDROGENASE (EC 1.1.1.233) (NAM-DH) - LENGTH = 270 COMBINED P-VALUE = 3.65e-30 E-VALUE = 1.2e-28 - DIAGRAM: 14_[2]_121_[1]_77 - - [2] - 2.0e-19 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - + +++++++++++++++++ +++++++++ -1 TTAGVSRRPGRLAGKAAIVTGAAGGIGRATVEAYLREGASVVAMDLAPRLAATRYEEPGAIPIACDLADRAAIDA - - [1] - 4.2e-18 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - + ++++++ +++++++++++++++ ++++ -151 GSVNSFMAEPEAAAYVAAKGGVAMLTRAMAVDLARHGILVNMIAPGPVDVTGNNTGYSEPRLAEQVLDEVALGRP - - -HMTR_LEIMA - no comment - LENGTH = 287 COMBINED P-VALUE = 1.55e-29 E-VALUE = 5.1e-28 - DIAGRAM: 6_[2]_157_[1]_66 - - [2] - 1.6e-17 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - ++++++++++ +++++++ ++++++ +++ -1 MTAPTVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAPVS - - [1] - 2.1e-19 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++++++++++++++++ +++++++ -151 PYFLIKAFAHRSRHPSQASRTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGL - - -2BHD_STREX - 20-BETA-HYDROXYSTEROID DEHYDROGENASE (EC 1.1.1.53) - LENGTH = 255 COMBINED P-VALUE = 1.78e-29 E-VALUE = 5.9e-28 - DIAGRAM: 6_[2]_116_[1]_75 - - [2] - 7.1e-18 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++++++ + +++ +++++++++ -1 MNDLSGKTVIITGGARGLGAEAARQAVAAGARVVLADVLDEEGAATARELGDAARYQHLDVTIEEDWQRVVAYAR - - [1] - 6.8e-19 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++++++++ +++++++ +++++++ -151 SYGASKWGVRGLSKLAAVELGTDRIRVNSVHPGMTYTPMTAETGIRQGEGNYPNTPMGRVGNEPGEIAGAVVKLL - - -ENTA_ECOLI - 2,3-DIHYDRO-2,3-DIHYDROXYBENZOATE DEHYDROGENASE (EC 1.3.1.28) - LENGTH = 248 COMBINED P-VALUE = 1.45e-28 E-VALUE = 4.8e-27 - DIAGRAM: 5_[2]_109_[1]_76 - - [2] - 3.7e-20 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++++++++++++++++++++ -1 MDFSGKNVWVTGAGKGIGYATALAFVEAGAKVTGFDQAFTQEQYPFATEVMDVADAAQVAQVCQRLLAETERLDA - - [1] - 1.2e-15 - YSASKFA - +++++++ -76 LVNAAGILRMGATDQLSKEDWQQTFAVNVGGAFNLFQQTMNQFRRQRGGAIVTVASDAAHTPRIGMSAYGASKAA - - - - VRMLTRSMAHEYAPHGIRVNCI - ++++ + ++++ ++++++++ -151 LKSLALSVGLELAGSGVRCNVVSPGSTDTDMQRTLWVSDDAEEQRIRGFGEQFKLGIPLGKIARPQEIANTILFL - - -DHB2_HUMAN - no comment - LENGTH = 387 COMBINED P-VALUE = 5.05e-28 E-VALUE = 1.7e-26 - DIAGRAM: 82_[2]_120_[1]_127 - - - [2] - 3.4e-17 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - + ++++++++++++++++++ + ++ +++ -76 ELLPVDQKAVLVTGGDCGLGHALCKYLDELGFTVFAGVLNENGPGAEELRRTCSPRLSVLQMDITKPVQIKDAYS - - [1] - 1.7e-18 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++++++++ ++++++++++++ ++ -226 MERLASYGSSKAAVTMFSSVMRLELSKWGIKVASIQPGGFLTNIAGTSDKWEKLEKDILDHLPAEVQEDYGQDYI - - -BDH_HUMAN - D-BETA-HYDROXYBUTYRATE DEHYDROGENASE PRECURSOR (EC 1.1.1.30) (BDH) - (3-HYDROXYBUTYRATE DEHYDROGENASE) (FRAGMENT) - LENGTH = 343 COMBINED P-VALUE = 8.57e-28 E-VALUE = 2.8e-26 - DIAGRAM: 55_[2]_123_[1]_107 - - [2] - 2.3e-18 - KVVLITGCSSGIGKATAKHL - + +++++++++ ++++++++ -1 GLRPPPPGRFSRLPGKTLSACDRENGARRPLLLGSTSFIPIGRRTYASAAEPVGSKAVLVTGCDSGFGFSLAKHL - - - - HKEGAKVVL - +++++ +++ -76 HSKGFLVFAGCLMKDKGHDGVKELDSLNSDRLRTVQLNVFRSEEVEKVVGDCPFEPEGPEKGMWGLVNNAGISTF - - [1] - 5.5e-17 - YSASKFAVRMLTRSMAHE - ++ +++++++++++++++ -151 GEVEFTSLETYKQVAEVNLWGTVRMTKSFLPLIRRAKGRVVNISSMLGRMANPARSPYCITKFGVEAFSDCLRYE - - - - YAPHGIRVNCI - +++ +++++++ -226 MYPLGVKVSVVEPGNFIAATSLYNPESIQAIAKKMWEELPEVVRKDYGKKYFDEKIAKMETYCSSGSTDTSPVID - - -BA72_EUBSP - 7-ALPHA-HYDROXYSTEROID DEHYDROGENASE (EC 1.1.1.159) (BILE ACID - 7-DEHYDROXYLASE) (BILE ACID-INDUCIBLE PROTEIN) - LENGTH = 249 COMBINED P-VALUE = 1.28e-27 E-VALUE = 4.2e-26 - DIAGRAM: 6_[2]_121_[1]_64 - - [2] - 2.6e-18 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - ++++++++ ++++++ ++ ++ +++++ + -1 MNLVQDKVTIITGGTRGIGFAAAKIFIDNGAKVSIFGETQEEVDTALAQLKELYPEEEVLGFAPDLTSRDAVMAA - - [1] - 1.5e-16 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - + +++++++++++ + +++ +++++++++ -151 SLSGVGYPASKASVIGLTHGLGREIIRKNIRVVGVAPGVVNTDMTNGNPPEIMEGYLKALPMKRMLEPEEIANVY - - -FVT1_HUMAN - no comment - LENGTH = 332 COMBINED P-VALUE = 2.70e-27 E-VALUE = 8.9e-26 - DIAGRAM: 32_[2]_124_[1]_118 - - [2] - 2.3e-17 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - ++++++++++++++++++++++++ + + -1 MLLLAAAFLVAFVLLLYMVSPLISPKPLALPGAHVVVTGGSSGIGKCIAIECYKQGAFITLVARNEDKLLQAKKE - - [1] - 1.9e-17 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++++++ ++++++++++++++++ -151 YPSRAVITTMKERRVGRIVFVSSQAGQLGLFGFTAYSASKFAIRGLAEALQMEVKPYNVYITVAYPPDTDTPGFA - - -GUTD_ECOLI - SORBITOL-6-PHOSPHATE 2-DEHYDROGENASE (EC 1.1.1.140) (GLUCITOL-6- PHOSPHATE - DEHYDROGENASE) (KETOSEPHOSPHATE REDUCTASE) - LENGTH = 259 COMBINED P-VALUE = 1.54e-26 E-VALUE = 5.1e-25 - DIAGRAM: 2_[2]_122_[1]_77 - - [2] - 1.5e-14 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++ ++++ ++ +++ ++++++++ + -1 MNQVAVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQSDKAANVAQEINAEYGESMAYGFGADATSEQSCLALSRGV - - [1] - 3.0e-19 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++ +++++++++++++++++++++ -151 NSGYSAAKFGGVGLTQSLALDLAEYGITVHSLMLGNLLKSPMFQSLLPQYATKLGIKPDQVEQYYIDKVPLKRGC - - -DHB3_HUMAN - no comment - LENGTH = 310 COMBINED P-VALUE = 2.53e-26 E-VALUE = 8.3e-25 - DIAGRAM: 48_[2]_120_[1]_84 - - [2] - 7.4e-19 - KVVLITGCSSGIGKATAKHLHKEGAKV - +++++++++ ++++++ ++++++ ++ -1 MGDVLEQFFILTGLLVCLACLAKCVRFSRCVLLNYYKVLPKSFLRSMGQWAVITGAGDGIGKAYSFELAKRGLNV - - - - VL - ++ -76 VLISRTLEKLEAIATEIERTTGRSVKIIQADFTKDDIYEHIKEKLAGLEIGILVNNVGMLPNLLPSHFLNAPDEI - - [1] - 6.7e-15 - YSASKFAVRMLTRSMAHEYAPHGIRVNC - ++++++++++++++++ +++ + + +++ -151 QSLIHCNITSVVKMTQLILKHMESRQKGLILNISSGIALFPWPLYSMYSASKAFVCAFSKALQEEYKAKEVIIQV - - - - I - + -226 LTPYAVSTAMTKYLNTNVITKTADEFVKESLNYVTIGGETCGCLAHEILAGFLSLIPAWAFYSGAFQRLLLTHYV - - -3BHD_COMTE - 3-BETA-HYDROXYSTEROID DEHYDROGENASE (EC 1.1.1.51) - LENGTH = 253 COMBINED P-VALUE = 4.25e-26 E-VALUE = 1.4e-24 - DIAGRAM: 6_[2]_115_[1]_74 - - [2] - 2.6e-18 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++++ ++++++ ++ +++++ -1 TNRLQGKVALVTGGASGVGLEVVKLLLGEGAKVAFSDINEAAGQQLAAELGERSMFVRHDVSSEADWTLVMAAVQ - - [1] - 5.1e-15 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++++++++++++ +++++ +++ -151 YSASKAAVSALTRAAALSCRKQGYAIRVNSIHPDGIYTPMMQASLPKGVSKEMVLHDPKLNRAGRAYMPERIAQL - - -LIGD_PSEPA - C ALPHA-DEHYDROGENASE (EC -.-.-.-) - LENGTH = 305 COMBINED P-VALUE = 2.45e-25 E-VALUE = 8.1e-24 - DIAGRAM: 6_[2]_121_[1]_120 - - [2] - 6.5e-17 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++ +++++++ ++ ++ + ++++++++ -1 MKDFQDQVAFITGGASGAGFGQAKVFGQAGAKIVVADVRAEAVEKAVAELEGLGITAHGIVLDIMDREAYARAAD - - [1] - 7.9e-16 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++ +++++ +++ ++++++ ++++ -151 SALAGPYSAAKAASINLMEGYRQGLEKYGIGVSVCTPANIKSNIAEASRLRPAKYGTSGYVENEESIASLHSIHQ - - -DHES_HUMAN - ESTRADIOL 17 BETA-DEHYDROGENASE (EC 1.1.1.62) (20 ALPHA-HYDROXYSTEROID - DEHYDROGENASE) (E2DH) (17-BETA-HSD) (PLACENTAL 17-BETA-HYDROXYSTEROID - DEHYDROGENASE) - LENGTH = 327 COMBINED P-VALUE = 7.31e-24 E-VALUE = 2.4e-22 - DIAGRAM: 2_[2]_50_[2]_44_[1]_144 - - [2] - 1.4e-14 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++++++++++ +++++ ++ + -1 ARTVVLITGCSSGIGLHLAVRLASDPSQSFKVYATLRDLKTQGRLWEAARALACPPGSLETLQLDVRDSKSVAAA - - [2] - 9.3e-05 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - ++ + ++ ++++ ++ + + + + -76 RERVTEGRVDVLVCNAGLGLLGPLEALGEDAVASVLDVNVVGTVRMLQAFLPDMKRRGSGRVLVTGSVGGLMGLP - - [1] - 1.0e-16 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++++++++++++ + + +++ + + -151 FNDVYCASKFALEGLCESLAVLLLPFGVHLSLIECGPVHTAFMEKVLGSPEEVLDRTDIHTFHRFYQYLAHSKQV - - -RFBB_NEIGO - no comment - LENGTH = 346 COMBINED P-VALUE = 9.68e-21 E-VALUE = 3.2e-19 - DIAGRAM: 6_[2]_129_[1]_153 - - [2] - 1.8e-13 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - ++++++++++ ++ +++++ +++ ++ -1 MQTEGKKNILVTGGAGFIGSAVVRHIIQNTRDSVVNLDKLTYAGNLESLTDIADNPRYAFEQVDICDRAELDRVF - - [1] - 1.0e-14 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++ +++++++++ ++ ++ ++ -151 DLFTETTPYAPSSPYSASKAAADHLVRAWQRTYRLPSIVSNCSNNYGPRQFPEKLIPLMILNALSGKPLPVYGDG - - -BPHB_PSEPS - BIPHENYL-CIS-DIOL DEHYDROGENASE (EC 1.3.1.-) - LENGTH = 275 COMBINED P-VALUE = 3.02e-20 E-VALUE = 1e-18 - DIAGRAM: 5_[2]_118_[1]_94 - - [2] - 8.6e-15 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++++++++ +++++ ++ -1 MKLKGEAVLITGGASGLGRALVDRFVAEAKVAVLDKSAERLAELETDLGDNVLGIVGDVRSLEDQKQAASRCVAR - - [1] - 1.2e-12 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - ++++++++++++++++++++++ + + -151 PLYTAAKQAIVGLVRELAFELAPYVRVNGVGPGGMNSDMRGPSSLGMGSKAISTVPLADMLKSVLPIGRMPEVEE - - -YURA_MYXXA - no comment - LENGTH = 258 COMBINED P-VALUE = 5.64e-20 E-VALUE = 1.9e-18 - DIAGRAM: 65_[2]_22_[2]_14_[1]_70 - - [2] - 5.6e-05 - KVVLITGCSS - + ++ ++ -1 RQHTGGLHGGDELPDGVGDGCLQRPGTRAGAVARQAGVRVFAAGRRLPQLQAADEAPGGRRHRGARGVDVTKADA - - [2] - 5.7e-08 - GIGKATAKHLHKEGAKVVL KVVLITGCSSGIGKATAKHLHKEGAKVVL - + + +++ + + ++ + +++++ + + ++ ++ + + -76 TLERIRALDAEAGGLDLVVANAGVGGTTNAKRLPWERVRGIIDTNVTGAAATLSAVLPQMVERKRGHLVGVSSLA - - [1] - 3.8e-19 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - +++++++++ ++++++++++ ++++++++ -151 GFRGLPATRYSASKAFLSTFMESLRVDLRGTGVRVTCIYPGFVKSELTATNNFPMPFLMETHDAVELMGKGIVRG - - -PCR_PEA - no comment - LENGTH = 399 COMBINED P-VALUE = 2.17e-19 E-VALUE = 7.2e-18 - DIAGRAM: 25_[1]_32_[2]_284 - - [1] - 1.7e-08 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - ++ ++++++++++ + + +++ + -1 MALQTASMLPASFSIPKEGKIGASLKDSTLFGVSSLSDSLKGDFTSSALRCKELRQKVGAVRAETAAPATPAVNK - - [2] - 1.9e-18 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++++++++++++++++++ + ++ -76 SSSEGKKTLRKGNVVITGASSGLGLATAKALAESGKWHVIMACRDYLKAARAAKSAGLAKENYTIMHLDLASLDS - - -DHCA_HUMAN - no comment - LENGTH = 276 COMBINED P-VALUE = 3.43e-19 E-VALUE = 1.1e-17 - DIAGRAM: 4_[2]_159_[1]_55 - - [2] - 4.0e-16 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - ++++++++++++++++++++++ + ++ -1 SSGIHVALVTGGNKGIGLAIVRDLCRLFSGDVVLTARDVTRGQAAVQQLQAEGLSPRFHQLDIDDLQSIRALRDF - - [1] - 2.9e-10 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - ++ ++ +++ +++ +++ +++++ +++ -151 PELQQKFRSETITEEELVGLMNKFVEDTKKGVHQKEGWPSSAYGVTKIGVTVLSRIHARKLSEQRKGDKILLNAC - - -ADH_DROME - ALCOHOL DEHYDROGENASE (EC 1.1.1.1) - LENGTH = 255 COMBINED P-VALUE = 8.17e-16 E-VALUE = 2.7e-14 - DIAGRAM: 6_[2]_116_[1]_75 - - [2] - 1.1e-10 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - ++++ + +++++ + ++++++ + + -1 SFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENPAAIAELKAINPKVTVTFYPYDVTVPIAETTKL - - [1] - 3.6e-12 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - ++ ++++++++++++++ ++++ +++ -151 VYSGTKAAVVNFTSSLAKLAPITGVTAYTVNPGITRTTLVHKFNSWLDVEPQVAEKLLAHPTQPSLACAENFVKA - - -MAS1_AGRRA - no comment - LENGTH = 476 COMBINED P-VALUE = 9.22e-16 E-VALUE = 3e-14 - DIAGRAM: 245_[2]_74_[1]_14_[1]_56 - - - [2] - 2.9e-15 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++ + +++ ++++++++++++++ + -226 GRVLHFRRGFSHWTVEIHQSPVILVSGSNRGVGKAIAEDLIAHGYRLSLGARKVKDLEVAFGPQDEWLHYARFDA - - [1] - 4.0e-08 - YSASKFAVRMLTRSMAHEYAPHGIRVN - + + + +++ ++ + +++ +++ -301 EDHGTMAAWVTAAVEKFGRIDGLVNNAGYGEPVNLDKHVDYQRFHLQWYINCVAPLRMTELCLPHLYETGSGRIV - - [1] - 8.7e-05 - CI YSASKFAVRMLTRSMAHEYAPHGIRVNCI - ++ + +++ ++ +++++ ++ + + -376 NINSMSGQRVLNPLVGYNMTKHALGGLTKTTQHVGWDRRCAAIDICLGFVATDMSAWTDLIASKDMIQPEDIAKL - - -FABI_ECOLI - no comment - LENGTH = 262 COMBINED P-VALUE = 2.94e-15 E-VALUE = 9.7e-14 - DIAGRAM: 6_[2]_123_[1]_75 - - [2] - 4.5e-10 - KVVLITGCSSGIGKATAKHLHKEGAKVVL - +++++++ ++ + ++ ++ +++ + -1 MGFLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKGRVEEFAAQLGSDIVLQCDVAEDASIDTMF - - [1] - 3.1e-12 - YSASKFAVRMLTRSMAHEYAPHGIRVNCI - ++ +++++++ +++++ +++++++++++ -151 RAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTLAASGIKDFRKMLAHCEAVTPIRRTVTIEDV - - -CSGA_MYXXA - no comment - LENGTH = 166 COMBINED P-VALUE = 7.50e-14 E-VALUE = 2.5e-12 - DIAGRAM: 51_[2]_7_[1]_50 - - [2] - 9.0e-08 - KVVLITGCSSGIGKATAKHLHKEG - + ++ + ++ + +++ +++ -1 MRAFATNVCTGPVDVLINNAGVSGLWCALGDVDYADMARTFTINALGPLRVTSAMLPGLRQGALRRVAHVTSRMG - - [1] - 1.3e-12 - AKVVL YSASKFAVRMLTRSMAHEYAPHGIRVNCI - + + ++++++ + ++++ ++++++ + + + -76 SLAANTDGGAYAYRMSKAALNMAVRSMSTDLRPEGFVTVLLHPGWVQTDMGGPDATLPAPDSVRGMLRVIDGLNP - -******************************************************************************** - - -CPU: pmgm2 -Time 0.250000 secs. - -mast meme.adh.oops.txt -text -stdout diff --git a/Tests/Motif/mast.protein.tcm.txt b/Tests/Motif/mast.protein.tcm.txt deleted file mode 100644 index 15340c5c837..00000000000 --- a/Tests/Motif/mast.protein.tcm.txt +++ /dev/null @@ -1,332 +0,0 @@ -******************************************************************************** -MAST - Motif Alignment and Search Tool -******************************************************************************** - MAST version 3.0 (Release date: 2004/08/18 09:07:01) - - For further information on how to interpret these results or to get - a copy of the MAST software please access http://meme.sdsc.edu. -******************************************************************************** - - -******************************************************************************** -REFERENCE -******************************************************************************** - If you use this program in your research, please cite: - - Timothy L. Bailey and Michael Gribskov, - "Combining evidence using p-values: application to sequence homology - searches", Bioinformatics, 14(48-54), 1998. -******************************************************************************** - - -******************************************************************************** -DATABASE AND MOTIFS -******************************************************************************** - DATABASE farntrans5.s (peptide) - Last updated on Mon Aug 16 21:19:59 2004 - Database contains 5 sequences, 1900 residues - - MOTIFS meme.farntrans5.tcm.txt (peptide) - MOTIF WIDTH BEST POSSIBLE MATCH - ----- ----- ------------------- - 1 30 GGFQGRPNKEVHTCYTYWALAALAILNKLH - 2 14 INKEKLIQWIKSCQ - - PAIRWISE MOTIF CORRELATIONS: - MOTIF 1 - ----- ----- - 2 0.22 - No overly similar pairs (correlation > 0.60) found. - - Random model letter frequencies (from non-redundant database): - A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 - L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 - W 0.013 Y 0.033 -******************************************************************************** - - -******************************************************************************** -SECTION I: HIGH-SCORING SEQUENCES -******************************************************************************** - - Each of the following 5 sequences has E-value less than 10. - - The E-value of a sequence is the expected number of sequences - in a random database of the same size that would match the motifs as - well as the sequence does and is equal to the combined p-value of the - sequence times the number of sequences in the database. - - The combined p-value of a sequence measures the strength of the - match of the sequence to all the motifs and is calculated by - o finding the score of the single best match of each motif - to the sequence (best matches may overlap), - o calculating the sequence p-value of each score, - o forming the product of the p-values, - o taking the p-value of the product. - - The sequence p-value of a score is defined as the - probability of a random sequence of the same length containing - some match with as good or better a score. - - The score for the match of a position in a sequence to a motif - is computed by by summing the appropriate entry from each column of - the position-dependent scoring matrix that represents the motif. - - Sequences shorter than one or more of the motifs are skipped. - - The table is sorted by increasing E-value. -******************************************************************************** - -SEQUENCE NAME DESCRIPTION E-VALUE LENGTH -------------- ----------- -------- ------ -BET2_YEAST YPT1/SEC4 PROTEINS GERANY... 2.9e-27 325 -RATRABGERB Rat rab geranylgeranyl tr... 1.4e-25 331 -CAL1_YEAST RAS PROTEINS GERANYLGERAN... 9.7e-22 376 -PFTB_RAT PROTEIN FARNESYLTRANSFERA... 7.6e-21 437 -RAM1_YEAST PROTEIN FARNESYLTRANSFERA... 6.2e-20 431 - -******************************************************************************** - - - -******************************************************************************** -SECTION II: MOTIF DIAGRAMS -******************************************************************************** - - The ordering and spacing of all non-overlapping motif occurrences - are shown for each high-scoring sequence listed in Section I. - - A motif occurrence is defined as a position in the sequence whose - match to the motif has POSITION p-value less than 0.0001. - - The POSITION p-value of a match is the probability of - a single random subsequence of the length of the motif - scoring at least as well as the observed match. - - For each sequence, all motif occurrences are shown unless there - are overlaps. In that case, a motif occurrence is shown only if its - p-value is less than the product of the p-values of the other - (lower-numbered) motif occurrences that it overlaps. - - The table also shows the E-value of each sequence. - - Spacers and motif occurences are indicated by - o -d- `d' residues separate the end of the preceding motif - occurrence and the start of the following motif occurrence - o [n] occurrence of motif `n' with p-value less than 0.0001. -******************************************************************************** - -SEQUENCE NAME E-VALUE MOTIF DIAGRAM -------------- -------- ------------- -BET2_YEAST 2.9e-27 6_[2]_3_[1]_1_[2]_4_[1]_4_[2]_ - 3_[1]_1_[2]_3_[1]_21_[1]_1_[2]_ - 4_[1]_24 -RATRABGERB 1.4e-25 65_[2]_3_[1]_1_[2]_3_[1]_1_[2]_ - 3_[1]_18_[1]_1_[2]_4_[1]_26 -CAL1_YEAST 9.7e-22 125_[2]_50_[2]_1_[1]_4_[2]_22_ - [1]_22_[1]_5_[2]_1 -PFTB_RAT 7.6e-21 120_[2]_3_[1]_4_[2]_3_[1]_1_[2]_ - 3_[1]_1_[2]_4_[1]_14_[2]_4_[1]_60 -RAM1_YEAST 6.2e-20 144_[1]_5_[2]_4_[1]_1_[2]_4_[1]_ - 1_[2]_4_[1]_4_[2]_5_[1]_35_[2]_4 - -******************************************************************************** - - - -******************************************************************************** -SECTION III: ANNOTATED SEQUENCES -******************************************************************************** - - The positions and p-values of the non-overlapping motif occurrences - are shown above the actual sequence for each of the high-scoring - sequences from Section I. - - A motif occurrence is defined as a position in the sequence whose - match to the motif has POSITION p-value less than 0.0001 as - defined in Section II. - - For each sequence, the first line specifies the name of the sequence. - - The second (and possibly more) lines give a description of the - sequence. - - Following the description line(s) is a line giving the length, - combined p-value, and E-value of the sequence as defined in Section I. - - The next line reproduces the motif diagram from Section II. - - The entire sequence is printed on the following lines. - - Motif occurrences are indicated directly above their positions in the - sequence on lines showing - o the motif number of the occurrence, - o the position p-value of the occurrence, - o the best possible match to the motif, and - o columns whose match to the motif has a positive score (indicated - by a plus sign). -******************************************************************************** - - -BET2_YEAST - YPT1/SEC4 PROTEINS GERANYLGERANYLTRANSFERASE BETA SUBUNIT (EC 2. - LENGTH = 325 COMBINED P-VALUE = 5.77e-28 E-VALUE = 2.9e-27 - DIAGRAM: 6_[2]_3_[1]_1_[2]_4_[1]_4_[2]_3_[1]_1_[2]_3_[1]_21_[1]_1_[2]_4_[1]_24 - - [2] [1] [2] [1] - 5.2e-05 2.7e-10 6.6e-10 5.9 - INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGF - +++ +++++++ ++ + +++ +++ +++++ +++++++ + ++++++++++++++ + + -1 MSGSLTLLKEKHIRYIESLDTNKHNFEYWLTEHLRLNGIYWGLTALCVLDSPETFVKEEVISFVLSCWDDKYGAF - - [2] [1] - e-14 4.8e-07 2.3e-17 - QGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILN - + +++++++ + ++++++ +++++ +++ +++++++ ++ + ++++ +++++++ +++++++++++ -76 APFPRHDAHLLTTLSAVQILATYDALDVLGKDRKVRLISFIRGNQLEDGSFQGDRFGEVDTRFVYTALSALSILG - - [2] [1] [1] - 5.1e-07 1.4e-18 4.6 - KLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH GGF - +++ ++++ ++++++++ ++++ ++++++++++++++++++++++++ +++ -151 ELTSEVVDPAVDFVLKCYNFDGGFGLCPNAESHAAQAFTCLGALAIANKLDMLSDDQLEEIGWWLCERQLPEGGL - - [2] [1] - e-22 2.0e-13 3.8e-17 - QGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKL - ++++ ++++++++++++++++++++++ ++ +++++++++++ ++++++++++++++++ ++++++++++ + -226 NGRPSKLPDVCYSWWVLSSLAIIGRLDWINYEKLTEFILKCQDEKKGGISDRPENEVDVFHTVFGVAGLSLMGYD - - - - H - + -301 NLVPIDPIYCMPKSVTSKFKKYPYK - - -RATRABGERB - Rat rab geranylgeranyl transferase beta-subunit - LENGTH = 331 COMBINED P-VALUE = 2.83e-26 E-VALUE = 1.4e-25 - DIAGRAM: 65_[2]_3_[1]_1_[2]_3_[1]_1_[2]_3_[1]_18_[1]_1_[2]_4_[1]_26 - - [2] - 1.0e-11 - INKEKLIQWI - +++++++ ++ -1 MGTQQKDVTIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFI - - [1] [2] [1] - 1.6e-14 1.4e-09 5.4e-19 - KSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWAL - ++++ ++ + +++++++ ++ ++++++++++++ +++++++ ++++++ + ++++++++++++++++++ -76 KSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAV - - [2] [1] - 3.8e-12 4.8e-19 - AALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH - ++++++++++ ++++++++++++++ ++++++++ ++++++++++++ ++++++++ -151 ATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLP - - [1] [2] [1] - 3.9e-21 1.2e-12 9.6e-18 - GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAI - +++++++++++++++++++++++ ++++++ ++++++++++++++ ++++++++++++ +++ ++++++++ -226 SGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSL - - - - LNKLH - +++++ -301 LGEEQIKPVSPVFCMPEEVLQRVNVQPELVS - - -CAL1_YEAST - RAS PROTEINS GERANYLGERANYLTRANSFERASE (EC 2.5.1.-) (PROTEIN GER - LENGTH = 376 COMBINED P-VALUE = 1.94e-22 E-VALUE = 9.7e-22 - DIAGRAM: 125_[2]_50_[2]_1_[1]_4_[2]_22_[1]_22_[1]_5_[2]_1 - - - [2] - 1.8e-08 - INKEKLIQWIKSCQ - +++++++++++++ -76 LDDTENTVISGFVGSLVMNIPHATTINLPNTLFALLSMIMLRDYEYFETILDKRSLARFVSKCQRPDRGSFVSCL - - [2] [1] - 4.8e-10 8.7e-14 - INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALA - +++++++ ++++++ + + + +++++ +++ ++++ -151 DYKTNCGSSVDSDDLRFCYIAVAILYICGCRSKEDFDEYIDTEKLLGYIMSQQCYNGAFGAHNEPHSGYTSCALS - - [2] [1] - 5.9e-08 5.9e-20 - ALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAIL - +++++++++ ++++++++++++ +++++++++ +++++++++++++ ++ -226 TLALLSSLEKLSDKFKEDTITWLLHRQVSSHGCMKFESELNASYDQSDDGGFQGRENKFADTCYAFWCLNSLHLL - - [1] [2] - 4.0e-13 2.1e-07 - NKLH GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ - ++++ ++++ + ++++++++++ + +++++++ + ++ +++++++++ -301 TKDWKMLCQTELVTNYLLDRTQKTLTGGFSKNDEEDADLYHSCLGSAALALIEGKFNGELCIPQEIFNDFSKRCC - - -PFTB_RAT - PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARNES - LENGTH = 437 COMBINED P-VALUE = 1.53e-21 E-VALUE = 7.6e-21 - DIAGRAM: 120_[2]_3_[1]_4_[2]_3_[1]_1_[2]_3_[1]_1_[2]_4_[1]_14_[2]_4_[1]_60 - - - [2] [1] - 1.3e-07 2.8e-19 - INKEKLIQWIKSCQ GGFQGRPNKEVHT - ++ ++++++++ ++ +++++++++ +++ -76 EKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIVATDVCQFLELCQSPDGGFGGGPGQYPHL - - [2] [1] [2] - 2.3e-09 2.1e-14 1.8e-0 - CYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKL - + +++++++++++++++ ++++++++++ +++ + + ++ +++++++ +++++++++++++++ + +++ -151 APTYAAVNALCIIGTEEAYNVINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGT - - [1] [2] [1] - 8 7.4e-20 1.8e-08 2.2e-16 - IQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCY - ++++ +++ +++++ +++++++++++++++++ ++++++ + +++++++++++ ++++++ ++++++++ -226 AEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCY - - [2] [1] - 5.0e-08 3.1e-15 - TYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNK - ++++++ + ++++ ++++++++++++++ +++ +++++ +++++++++++++++++ -301 SFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQH - - - - LH - + -376 FGSGAMLHDVVMGVPENVLQPTHPVYNIGPDKVIQATTHFLQKPVPGFEECEDAVTSDPATD - - -RAM1_YEAST - PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARN - LENGTH = 431 COMBINED P-VALUE = 1.24e-20 E-VALUE = 6.2e-20 - DIAGRAM: 144_[1]_5_[2]_4_[1]_1_[2]_4_[1]_1_[2]_4_[1]_4_[2]_5_[1]_35_[2]_4 - - - [1] - 8.8e-1 - GGFQGR - + ++++ -76 PALTKEFHKMYLDVAFEISLPPQMTALDASQPWMLYWIANSLKVMDRDWLSDDTKRKIVVKLFTISPSGGPFGGG - - [2] [1] - 7 6.4e-07 1.0e-13 - PNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNK - ++++++++ ++++++++++ ++++ ++++++++++ +++ + ++ ++++++++ +++++++++++++ -151 PGQLSHLASTYAAINALSLCDNIDGCWDRIDRKGIYQWLISLKEPNGGFKTCLEVGEVDTRGIYCALSIATLLNI - - [2] [1] [2] [1] - 2.5e-08 3.1e-17 4.7e-11 2.4e- - LH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQG - ++ + ++++++++++++ + ++ +++++++++++++++++++++++ ++++++++++++++ ++ + -226 LTEELTEGVLNYLKNCQNYEGGFGSCPHVDEAHGGYTFCATASLAILRSMDQINVEKLLEWSSARQLQEERGFCG - - [2] [1] - 16 4.9e-09 2.7e-13 - RPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILN - + ++++++++++++ +++++++++ +++++++++++ ++ +++++++++++++++ +++ ++++++ -301 RSNKLVDGCYSFWVGGSAAILEAFGYGQCFNKHALRDYILYCCQEKEQPGLRDKPGAHSDFYHTNYCLLGLAVAE - - [2] - 9.8e-05 - KLH INKEKLIQWIKSCQ - + +++++++ + +++ -376 SSYSCTPNDSPHNIKCTPDRLIGSSKLTDVNPVYGLPIENVRKIIHYFKSNLSSPS - -******************************************************************************** - - -CPU: pmgm2 -Time 0.130000 secs. - -mast meme.farntrans5.tcm.txt -text -stdout diff --git a/Tests/Motif/meme.dna.oops.txt b/Tests/Motif/meme.dna.oops.txt deleted file mode 100644 index d2f53feedad..00000000000 --- a/Tests/Motif/meme.dna.oops.txt +++ /dev/null @@ -1,324 +0,0 @@ -******************************************************************************** -MEME - Motif discovery tool -******************************************************************************** -MEME version 3.0 (Release date: 2004/08/18 09:07:01) - -For further information on how to interpret these results or to get -a copy of the MEME software please access http://meme.sdsc.edu. - -This file may be used as input to the MAST algorithm for searching -sequence databases for matches to groups of motifs. MAST is available -for interactive use and downloading at http://meme.sdsc.edu. -******************************************************************************** - - -******************************************************************************** -REFERENCE -******************************************************************************** -If you use this program in your research, please cite: - -Timothy L. Bailey and Charles Elkan, -"Fitting a mixture model by expectation maximization to discover -motifs in biopolymers", Proceedings of the Second International -Conference on Intelligent Systems for Molecular Biology, pp. 28-36, -AAAI Press, Menlo Park, California, 1994. -******************************************************************************** - - -******************************************************************************** -TRAINING SET -******************************************************************************** -DATAFILE= INO_up800.s -ALPHABET= ACGT -Sequence name Weight Length Sequence name Weight Length -------------- ------ ------ ------------- ------ ------ -CHO1 1.0000 800 CHO2 1.0000 800 -FAS1 1.0000 800 FAS2 1.0000 800 -ACC1 1.0000 800 INO1 1.0000 800 -OPI3 1.0000 800 -******************************************************************************** - -******************************************************************************** -COMMAND LINE SUMMARY -******************************************************************************** -This information can also be useful in the event you wish to report a -problem with the MEME software. - -command: meme -mod oops -dna -revcomp -nmotifs 2 -bfile yeast.nc.6.freq INO_up800.s - -model: mod= oops nmotifs= 2 evt= inf -object function= E-value of product of p-values -width: minw= 8 maxw= 50 minic= 0.00 -width: wg= 11 ws= 1 endgaps= yes -nsites: minsites= 7 maxsites= 7 wnsites= 0.8 -theta: prob= 1 spmap= uni spfuzz= 0.5 -em: prior= dirichlet b= 0.01 maxiter= 50 - distance= 1e-05 -data: n= 5600 N= 7 -strands: + - -sample: seed= 0 seqfrac= 1 -Letter frequencies in dataset: -A 0.304 C 0.196 G 0.196 T 0.304 -Background letter frequencies (from yeast.nc.6.freq): -A 0.324 C 0.176 G 0.176 T 0.324 -******************************************************************************** - - -******************************************************************************** -MOTIF 1 width = 12 sites = 7 llr = 95 E-value = 2.0e-001 -******************************************************************************** --------------------------------------------------------------------------------- - Motif 1 Description --------------------------------------------------------------------------------- -Simplified A :::9:a::::3: -pos.-specific C ::a:9:11691a -probability G ::::1::94:4: -matrix T aa:1::9::11: - - bits 2.5 * * - 2.3 * * - 2.0 * * * * - 1.8 * * * * * -Information 1.5 *** ** *** * -content 1.3 *** ****** * -(19.5 bits) 1.0 ********** * - 0.8 ********** * - 0.5 ********** * - 0.3 ************ - 0.0 ------------ - -Multilevel TTCACATGCCGC -consensus G A -sequence - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 sites sorted by position p-value --------------------------------------------------------------------------------- -Sequence name Strand Start P-value Site -------------- ------ ----- --------- ------------ -INO1 - 620 1.85e-08 GACAATACTT TTCACATGCCGC ATTTAGCCGC -FAS1 + 95 1.85e-08 GGCCAAAAAC TTCACATGCCGC CCAGCCAAGC -ACC1 + 83 1.52e-07 CGTTAAAATC TTCACATGGCCC GGCCGCGCGC -CHO2 + 354 2.52e-07 TGCCACACTT TTCTCATGCCGC ATTCATTATT -CHO1 + 611 4.23e-07 ACTTTGAACG TTCACACGGCAC CCTCACGCCT -FAS2 + 567 9.43e-07 CTCCCGCGTT TTCACATGCTAC CTCATTCGCC -OPI3 + 340 3.32e-06 CCAAGCCTCC TTCAGATCGCTC TTGTCGACCG --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 block diagrams --------------------------------------------------------------------------------- -SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -INO1 1.8e-08 619_[-1]_169 -FAS1 1.8e-08 94_[+1]_694 -ACC1 1.5e-07 82_[+1]_706 -CHO2 2.5e-07 353_[+1]_435 -CHO1 4.2e-07 610_[+1]_178 -FAS2 9.4e-07 566_[+1]_222 -OPI3 3.3e-06 339_[+1]_449 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 in BLOCKS format --------------------------------------------------------------------------------- -BL MOTIF 1 width=12 seqs=7 -INO1 ( 620) TTCACATGCCGC 1 -FAS1 ( 95) TTCACATGCCGC 1 -ACC1 ( 83) TTCACATGGCCC 1 -CHO2 ( 354) TTCTCATGCCGC 1 -CHO1 ( 611) TTCACACGGCAC 1 -FAS2 ( 567) TTCACATGCTAC 1 -OPI3 ( 340) TTCAGATCGCTC 1 -// - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific scoring matrix --------------------------------------------------------------------------------- -log-odds matrix: alength= 4 w= 12 n= 5523 bayes= 9.62205 E= 2.0e-001 - -945 -945 -945 162 - -945 -945 -945 162 - -945 251 -945 -945 - 140 -945 -945 -118 - -945 229 -30 -945 - 162 -945 -945 -945 - -945 -30 -945 140 - -945 -30 229 -945 - -945 170 129 -945 - -945 229 -945 -118 - -18 -30 129 -118 - -945 251 -945 -945 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific probability matrix --------------------------------------------------------------------------------- -letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 2.0e-001 - 0.000000 0.000000 0.000000 1.000000 - 0.000000 0.000000 0.000000 1.000000 - 0.000000 1.000000 0.000000 0.000000 - 0.857143 0.000000 0.000000 0.142857 - 0.000000 0.857143 0.142857 0.000000 - 1.000000 0.000000 0.000000 0.000000 - 0.000000 0.142857 0.000000 0.857143 - 0.000000 0.142857 0.857143 0.000000 - 0.000000 0.571429 0.428571 0.000000 - 0.000000 0.857143 0.000000 0.142857 - 0.285714 0.142857 0.428571 0.142857 - 0.000000 1.000000 0.000000 0.000000 --------------------------------------------------------------------------------- - - - - - -Time 20.91 secs. - -******************************************************************************** - - -******************************************************************************** -MOTIF 2 width = 10 sites = 7 llr = 81 E-value = 1.1e+002 -******************************************************************************** --------------------------------------------------------------------------------- - Motif 2 Description --------------------------------------------------------------------------------- -Simplified A ::1:::9:6: -pos.-specific C :a:::a:911 -probability G 3:1aa:1:19 -matrix T 7:7::::11: - - bits 2.5 * *** - 2.3 * *** - 2.0 * *** * - 1.8 * *** * * -Information 1.5 * *** * * -content 1.3 * ***** * -(16.7 bits) 1.0 ** ***** * - 0.8 ** ***** * - 0.5 ******** * - 0.3 ********** - 0.0 ---------- - -Multilevel TCTGGCACAG -consensus G -sequence - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 sites sorted by position p-value --------------------------------------------------------------------------------- -Sequence name Strand Start P-value Site -------------- ------ ----- --------- ---------- -OPI3 - 186 3.24e-07 GAAAACCAGA TCTGGCACAG ACCGTTGTCA -ACC1 + 232 3.24e-07 CCAGTCGTAT TCTGGCACAG TATAGCCTAG -CHO1 - 559 3.24e-07 ATATTCAGTG TCTGGCACAG AAGTCTGCAC -INO1 - 283 5.29e-06 ACGGTCTACG GCGGGCGCAG TCGCATGTCT -FAS1 + 44 6.25e-06 TACACGAGGT GCAGGCACGG TTCACTACTC -FAS2 - 185 8.48e-06 TTCTTGCTTT TCTGGCACTC TTGACGGCTT -CHO2 - 413 8.48e-06 TTTTGCCGTT TCTGGCATCG CCGTTCATTT --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 block diagrams --------------------------------------------------------------------------------- -SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -OPI3 3.2e-07 185_[-2]_605 -ACC1 3.2e-07 231_[+2]_559 -CHO1 3.2e-07 558_[-2]_232 -INO1 5.3e-06 282_[-2]_508 -FAS1 6.3e-06 43_[+2]_747 -FAS2 8.5e-06 184_[-2]_606 -CHO2 8.5e-06 412_[-2]_378 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 in BLOCKS format --------------------------------------------------------------------------------- -BL MOTIF 2 width=10 seqs=7 -OPI3 ( 186) TCTGGCACAG 1 -ACC1 ( 232) TCTGGCACAG 1 -CHO1 ( 559) TCTGGCACAG 1 -INO1 ( 283) GCGGGCGCAG 1 -FAS1 ( 44) GCAGGCACGG 1 -FAS2 ( 185) TCTGGCACTC 1 -CHO2 ( 413) TCTGGCATCG 1 -// - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 position-specific scoring matrix --------------------------------------------------------------------------------- -log-odds matrix: alength= 4 w= 10 n= 5537 bayes= 9.62571 E= 1.1e+002 - -945 -945 70 114 - -945 251 -945 -945 - -118 -945 -30 114 - -945 -945 251 -945 - -945 -945 251 -945 - -945 251 -945 -945 - 140 -945 -30 -945 - -945 229 -945 -118 - 82 -30 -30 -118 - -945 -30 229 -945 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 position-specific probability matrix --------------------------------------------------------------------------------- -letter-probability matrix: alength= 4 w= 10 nsites= 7 E= 1.1e+002 - 0.000000 0.000000 0.285714 0.714286 - 0.000000 1.000000 0.000000 0.000000 - 0.142857 0.000000 0.142857 0.714286 - 0.000000 0.000000 1.000000 0.000000 - 0.000000 0.000000 1.000000 0.000000 - 0.000000 1.000000 0.000000 0.000000 - 0.857143 0.000000 0.142857 0.000000 - 0.000000 0.857143 0.000000 0.142857 - 0.571429 0.142857 0.142857 0.142857 - 0.000000 0.142857 0.857143 0.000000 --------------------------------------------------------------------------------- - - - - - -Time 41.19 secs. - -******************************************************************************** - - -******************************************************************************** -SUMMARY OF MOTIFS -******************************************************************************** - --------------------------------------------------------------------------------- - Combined block diagrams: non-overlapping sites with p-value < 0.0001 --------------------------------------------------------------------------------- -SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -CHO1 5.44e-06 152_[+2(1.10e-05)]_396_[-2(3.24e-07)]_42_[+1(4.23e-07)]_17_[+1(1.23e-05)]_149 -CHO2 6.96e-05 353_[+1(2.52e-07)]_47_[-2(8.48e-06)]_378 -FAS1 4.61e-06 43_[+2(6.25e-06)]_41_[+1(1.85e-08)]_694 -FAS2 2.34e-04 184_[-2(8.48e-06)]_372_[+1(9.43e-07)]_222 -ACC1 2.09e-06 82_[+1(1.52e-07)]_137_[+2(3.24e-07)]_559 -INO1 3.95e-06 282_[-2(5.29e-06)]_327_[-1(1.85e-08)]_55_[+1(7.55e-06)]_102 -OPI3 3.70e-05 185_[-2(3.24e-07)]_144_[+1(3.32e-06)]_449 --------------------------------------------------------------------------------- - -******************************************************************************** - - -******************************************************************************** -Stopped because nmotifs = 2 reached. -******************************************************************************** - -CPU: pmgm2 - -******************************************************************************** diff --git a/Tests/Motif/meme.out b/Tests/Motif/meme.out deleted file mode 100644 index 7c9ec1cf5aa..00000000000 --- a/Tests/Motif/meme.out +++ /dev/null @@ -1,225 +0,0 @@ -******************************************************************************** -MEME - Motif discovery tool -******************************************************************************** -MEME version 3.5.7 (Release date: 2007-12-17 16:56:19 -0800 (Mon, 17 Dec 2007)) - -For further information on how to interpret these results or to get -a copy of the MEME software please access http://meme.nbcr.net. - -This file may be used as input to the MAST algorithm for searching -sequence databases for matches to groups of motifs. MAST is available -for interactive use and downloading at http://meme.nbcr.net. -******************************************************************************** - - -******************************************************************************** -REFERENCE -******************************************************************************** -If you use this program in your research, please cite: - -Timothy L. Bailey and Charles Elkan, -"Fitting a mixture model by expectation maximization to discover -motifs in biopolymers", Proceedings of the Second International -Conference on Intelligent Systems for Molecular Biology, pp. 28-36, -AAAI Press, Menlo Park, California, 1994. -******************************************************************************** - - -******************************************************************************** -TRAINING SET -******************************************************************************** -DATAFILE= test.fa -ALPHABET= ACGT -Sequence name Weight Length Sequence name Weight Length -------------- ------ ------ ------------- ------ ------ -SEQ1; 1.0000 200 SEQ2; 1.0000 200 -SEQ3; 1.0000 200 SEQ4; 1.0000 200 -SEQ5; 1.0000 200 SEQ6; 1.0000 200 -SEQ7; 1.0000 200 SEQ8; 1.0000 200 -SEQ9; 1.0000 200 SEQ10; 1.0000 200 -******************************************************************************** - -******************************************************************************** -COMMAND LINE SUMMARY -******************************************************************************** -This information can also be useful in the event you wish to report a -problem with the MEME software. - -command: meme test.fa -dna -w 10 -dir /home/bartek/MetaMotif/meme - -model: mod= zoops nmotifs= 1 evt= inf -object function= E-value of product of p-values -width: minw= 10 maxw= 10 minic= 0.00 -width: wg= 11 ws= 1 endgaps= yes -nsites: minsites= 2 maxsites= 10 wnsites= 0.8 -theta: prob= 1 spmap= uni spfuzz= 0.5 -em: prior= dirichlet b= 0.01 maxiter= 50 - distance= 1e-05 -data: n= 2000 N= 10 -strands: + -sample: seed= 0 seqfrac= 1 -Letter frequencies in dataset: -A 0.255 C 0.235 G 0.261 T 0.249 -Background letter frequencies (from dataset with add-one prior applied): -A 0.255 C 0.236 G 0.260 T 0.249 -******************************************************************************** - - -******************************************************************************** -MOTIF 1 width = 10 sites = 10 llr = 140 E-value = 1.1e-022 -******************************************************************************** --------------------------------------------------------------------------------- - Motif 1 Description --------------------------------------------------------------------------------- -Simplified A :::aa::::a -pos.-specific C a:a:::a::: -probability G :::::::a:: -matrix T :a:::a::a: - - bits 2.1 *** ** * - 1.9 ********** - 1.7 ********** - 1.5 ********** -Information 1.3 ********** -content 1.0 ********** -(20.1 bits) 0.8 ********** - 0.6 ********** - 0.4 ********** - 0.2 ********** - 0.0 ---------- - -Multilevel CTCAATCGTA -consensus -sequence - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 sites sorted by position p-value --------------------------------------------------------------------------------- -Sequence name Start P-value Site -------------- ----- --------- ---------- -SEQ10; 3 8.71e-07 TT CTCAATCGTA GAGTATGCTT -SEQ9; 93 8.71e-07 CGCCTAGAAA CTCAATCGTA GAGTATCACG -SEQ8; 172 8.71e-07 CCCGGAGTAT CTCAATCGTA GATGAATACC -SEQ7; 177 8.71e-07 AAGTCTTTGA CTCAATCGTA GACCCAACAC -SEQ6; 105 8.71e-07 GTCAGCCGGT CTCAATCGTA GATCAGAGGC -SEQ5; 185 8.71e-07 ACGGGCAAGC CTCAATCGTA GAGGAT -SEQ4; 173 8.71e-07 GTTCGAGAGC CTCAATCGTA GATAACCTCT -SEQ3; 112 8.71e-07 GTTATATTGG CTCAATCGTA GATGAAACCA -SEQ2; 172 8.71e-07 AAGCGTCGTG CTCAATCGTA GATAACAGAG -SEQ1; 52 8.71e-07 CTTTACTCGG CTCAATCGTA GAGGCGGTGC --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 block diagrams --------------------------------------------------------------------------------- -SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -SEQ10; 8.7e-07 2_[1]_188 -SEQ9; 8.7e-07 92_[1]_98 -SEQ8; 8.7e-07 171_[1]_19 -SEQ7; 8.7e-07 176_[1]_14 -SEQ6; 8.7e-07 104_[1]_86 -SEQ5; 8.7e-07 184_[1]_6 -SEQ4; 8.7e-07 172_[1]_18 -SEQ3; 8.7e-07 111_[1]_79 -SEQ2; 8.7e-07 171_[1]_19 -SEQ1; 8.7e-07 51_[1]_139 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 in BLOCKS format --------------------------------------------------------------------------------- -BL MOTIF 1 width=10 seqs=10 -SEQ10; ( 3) CTCAATCGTA 1 -SEQ9; ( 93) CTCAATCGTA 1 -SEQ8; ( 172) CTCAATCGTA 1 -SEQ7; ( 177) CTCAATCGTA 1 -SEQ6; ( 105) CTCAATCGTA 1 -SEQ5; ( 185) CTCAATCGTA 1 -SEQ4; ( 173) CTCAATCGTA 1 -SEQ3; ( 112) CTCAATCGTA 1 -SEQ2; ( 172) CTCAATCGTA 1 -SEQ1; ( 52) CTCAATCGTA 1 -// - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific scoring matrix --------------------------------------------------------------------------------- -log-odds matrix: alength= 4 w= 10 n= 1910 bayes= 8.51691 E= 1.1e-022 - -997 208 -997 -997 - -997 -997 -997 200 - -997 208 -997 -997 - 197 -997 -997 -997 - 197 -997 -997 -997 - -997 -997 -997 200 - -997 208 -997 -997 - -997 -997 194 -997 - -997 -997 -997 200 - 197 -997 -997 -997 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific probability matrix --------------------------------------------------------------------------------- -letter-probability matrix: alength= 4 w= 10 nsites= 10 E= 1.1e-022 - 0.000000 1.000000 0.000000 0.000000 - 0.000000 0.000000 0.000000 1.000000 - 0.000000 1.000000 0.000000 0.000000 - 1.000000 0.000000 0.000000 0.000000 - 1.000000 0.000000 0.000000 0.000000 - 0.000000 0.000000 0.000000 1.000000 - 0.000000 1.000000 0.000000 0.000000 - 0.000000 0.000000 1.000000 0.000000 - 0.000000 0.000000 0.000000 1.000000 - 1.000000 0.000000 0.000000 0.000000 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 regular expression --------------------------------------------------------------------------------- -CTCAATCGTA --------------------------------------------------------------------------------- - - - - -Time 0.26 secs. - -******************************************************************************** - - -******************************************************************************** -SUMMARY OF MOTIFS -******************************************************************************** - --------------------------------------------------------------------------------- - Combined block diagrams: non-overlapping sites with p-value < 0.0001 --------------------------------------------------------------------------------- -SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -SEQ1; 1.66e-04 51_[1(8.71e-07)]_139 -SEQ2; 1.66e-04 171_[1(8.71e-07)]_19 -SEQ3; 1.66e-04 111_[1(8.71e-07)]_79 -SEQ4; 1.66e-04 172_[1(8.71e-07)]_18 -SEQ5; 1.66e-04 184_[1(8.71e-07)]_6 -SEQ6; 1.66e-04 104_[1(8.71e-07)]_86 -SEQ7; 1.66e-04 176_[1(8.71e-07)]_14 -SEQ8; 1.66e-04 171_[1(8.71e-07)]_19 -SEQ9; 1.66e-04 92_[1(8.71e-07)]_98 -SEQ10; 1.66e-04 2_[1(8.71e-07)]_188 --------------------------------------------------------------------------------- - -******************************************************************************** - - -******************************************************************************** -Stopped because nmotifs = 1 reached. -******************************************************************************** - -CPU: pc-arendt9 - -******************************************************************************** diff --git a/Tests/Motif/meme.protein.oops.txt b/Tests/Motif/meme.protein.oops.txt deleted file mode 100644 index 1d72fe2e16e..00000000000 --- a/Tests/Motif/meme.protein.oops.txt +++ /dev/null @@ -1,630 +0,0 @@ -******************************************************************************** -MEME - Motif discovery tool -******************************************************************************** -MEME version 3.0 (Release date: 2004/08/18 09:07:01) - -For further information on how to interpret these results or to get -a copy of the MEME software please access http://meme.sdsc.edu. - -This file may be used as input to the MAST algorithm for searching -sequence databases for matches to groups of motifs. MAST is available -for interactive use and downloading at http://meme.sdsc.edu. -******************************************************************************** - - -******************************************************************************** -REFERENCE -******************************************************************************** -If you use this program in your research, please cite: - -Timothy L. Bailey and Charles Elkan, -"Fitting a mixture model by expectation maximization to discover -motifs in biopolymers", Proceedings of the Second International -Conference on Intelligent Systems for Molecular Biology, pp. 28-36, -AAAI Press, Menlo Park, California, 1994. -******************************************************************************** - - -******************************************************************************** -TRAINING SET -******************************************************************************** -DATAFILE= adh.s -ALPHABET= ACDEFGHIKLMNPQRSTVWY -Sequence name Weight Length Sequence name Weight Length -------------- ------ ------ ------------- ------ ------ -2BHD_STREX 1.0000 255 3BHD_COMTE 1.0000 253 -ADH_DROME 1.0000 255 AP27_MOUSE 1.0000 244 -BA72_EUBSP 1.0000 249 BDH_HUMAN 1.0000 343 -BPHB_PSEPS 1.0000 275 BUDC_KLETE 1.0000 241 -DHES_HUMAN 1.0000 327 DHGB_BACME 1.0000 262 -DHII_HUMAN 1.0000 292 DHMA_FLAS1 1.0000 270 -ENTA_ECOLI 1.0000 248 FIXR_BRAJA 1.0000 278 -GUTD_ECOLI 1.0000 259 HDE_CANTR 1.0000 906 -HDHA_ECOLI 1.0000 255 LIGD_PSEPA 1.0000 305 -NODG_RHIME 1.0000 245 RIDH_KLEAE 1.0000 249 -YINL_LISMO 1.0000 248 YRTP_BACSU 1.0000 238 -CSGA_MYXXA 1.0000 166 DHB2_HUMAN 1.0000 387 -DHB3_HUMAN 1.0000 310 DHCA_HUMAN 1.0000 276 -FABI_ECOLI 1.0000 262 FVT1_HUMAN 1.0000 332 -HMTR_LEIMA 1.0000 287 MAS1_AGRRA 1.0000 476 -PCR_PEA 1.0000 399 RFBB_NEIGO 1.0000 346 -YURA_MYXXA 1.0000 258 -******************************************************************************** - -******************************************************************************** -COMMAND LINE SUMMARY -******************************************************************************** -This information can also be useful in the event you wish to report a -problem with the MEME software. - -command: meme adh.s -mod oops -protein -nmotifs 2 - -model: mod= oops nmotifs= 2 evt= inf -object function= E-value of product of p-values -width: minw= 8 maxw= 50 minic= 0.00 -width: wg= 11 ws= 1 endgaps= yes -nsites: minsites= 33 maxsites= 33 wnsites= 0.8 -theta: prob= 1 spmap= pam spfuzz= 120 -em: prior= dmix b= 0 maxiter= 50 - distance= 1e-05 -data: n= 9996 N= 33 - -sample: seed= 0 seqfrac= 1 -Dirichlet mixture priors file: prior30.plib -Letter frequencies in dataset: -A 0.111 C 0.012 D 0.050 E 0.055 F 0.036 G 0.090 H 0.018 I 0.057 K 0.052 -L 0.092 M 0.027 N 0.041 P 0.041 Q 0.029 R 0.049 S 0.064 T 0.057 V 0.083 -W 0.010 Y 0.027 -Background letter frequencies (from dataset with add-one prior applied): -A 0.111 C 0.012 D 0.050 E 0.055 F 0.036 G 0.090 H 0.018 I 0.057 K 0.052 -L 0.092 M 0.027 N 0.041 P 0.041 Q 0.029 R 0.049 S 0.064 T 0.057 V 0.083 -W 0.010 Y 0.027 -******************************************************************************** - - -******************************************************************************** -MOTIF 1 width = 29 sites = 33 llr = 1118 E-value = 3.6e-165 -******************************************************************************** --------------------------------------------------------------------------------- - Motif 1 Description --------------------------------------------------------------------------------- -Simplified A :162:56112:1:215:::4:::::::11 -pos.-specific C :1:::::::::::1:::::::::::1:1: -probability D ::::::::1:::1::::2::::::::::: -matrix E ::::::::1:::21:::5:111::::::: - F :::::31:::2:::::1:::::::::::: - G :2:::13::4:::1:1:::11:5:1:11: - H :::::::::1::1:::1::::1::::::: - I :::::::11:::::::::1::::5:2:13 - K ::::9:::1:::2:::1::121::1:1:: - L :::::::31:6:1:5:215::1:::::12 - M ::1::::1:2:1::2:1:1:::::::::: - N :::::::::1::::::::::::2:1:41: - P ::::::::::::::::::::3:::::::: - Q ::::::::::::1::11:::11::::::: - R ::::::::2:::3::22::21:1:4:1:: - S :426::1:11:213:::::1:11:::21: - T :1:2::::1::3:1::::::11::1:11: - V :::::::41::2:1::1:1::::316123 - W :::::1::::::::::::::::::::::: - Y 9:::::::::::::::::2::2::::::: - - bits 6.7 - 6.0 - 5.4 - 4.7 * -Information 4.0 * * -content 3.4 * * -(48.9 bits) 2.7 * ** * - 2.0 * **** * * * * * - 1.3 ******** ******* ** * ***** * - 0.7 ***************************** - 0.0 ----------------------------- - -Multilevel YSASKAAVxGLTRSLAxELAPxGIRVNVV -consensus FGL FSE MR D V I -sequence - - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 sites sorted by position p-value --------------------------------------------------------------------------------- -Sequence name Start P-value Site -------------- ----- --------- ----------------------------- -YRTP_BACSU 155 1.64e-22 GQRGAAVTSA YSASKFAVLGLTESLMQEVRKHNIRVSAL TPSTVASDMS -AP27_MOUSE 149 6.32e-22 AHVTFPNLIT YSSTKGAMTMLTKAMAMELGPHKIRVNSV NPTVVLTDMG -NODG_RHIME 152 1.13e-21 GAIGNPGQTN YCASKAGMIGFSKSLAQEIATRNITVNCV APGFIESAMT -BUDC_KLETE 152 4.04e-21 GHVGNPELAV YSSSKFAVRGLTQTAARDLAPLGITVNGF CPGIVKTPMW -FIXR_BRAJA 189 6.12e-21 SRVHPFAGSA YATSKAALASLTRELAHDYAPHGIRVNAI APGEIRTDML -DHGB_BACME 160 7.52e-20 WKIPWPLFVH YAASKGGMKLMTETLALEYAPKGIRVNNI GPGAINTPIN -HMTR_LEIMA 193 3.35e-19 TNQPLLGYTI YTMAKGALEGLTRSAALELAPLQIRVNGV GPGLSVLVDD -YURA_MYXXA 160 4.82e-19 AGFRGLPATR YSASKAFLSTFMESLRVDLRGTGVRVTCI YPGFVKSELT -GUTD_ECOLI 154 4.82e-19 GKVGSKHNSG YSAAKFGGVGLTQSLALDLAEYGITVHSL MLGNLLKSPM -2BHD_STREX 152 1.11e-18 GLMGLALTSS YGASKWGVRGLSKLAAVELGTDRIRVNSV HPGMTYTPMT -HDHA_ECOLI 159 1.25e-18 AENKNINMTS YASSKAAASHLVRNMAFDLGEKNIRVNGI APGAILTDAL -DHB2_HUMAN 232 2.23e-18 GGAPMERLAS YGSSKAAVTMFSSVMRLELSKWGIKVASI QPGGFLTNIA -DHMA_FLAS1 165 5.53e-18 SFMAEPEAAA YVAAKGGVAMLTRAMAVDLARHGILVNMI APGPVDVTGN -HDE_CANTR 467 9.65e-18 GIYGNFGQAN YSSSKAGILGLSKTMAIEGAKNNIKVNIV APHAETAMTL -FVT1_HUMAN 186 2.86e-17 GQLGLFGFTA YSASKFAIRGLAEALQMEVKPYNVYITVA YPPDTDTPGF -BDH_HUMAN 208 8.20e-17 GRMANPARSP YCITKFGVEAFSDCLRYEMYPLGVKVSVV EPGNFIAATS -RIDH_KLEAE 160 9.09e-17 GVVPVIWEPV YTASKFAVQAFVHTTRRQVAQYGVRVGAV LPGPVVTALL -DHES_HUMAN 155 1.37e-16 GLMGLPFNDV YCASKFALEGLCESLAVLLLPFGVHLSLI ECGPVHTAFM -BA72_EUBSP 157 2.52e-16 GIFGSLSGVG YPASKASVIGLTHGLGREIIRKNIRVVGV APGVVNTDMT -LIGD_PSEPA 157 1.21e-15 GFMGSALAGP YSAAKAASINLMEGYRQGLEKYGIGVSVC TPANIKSNIA -DHII_HUMAN 183 1.61e-15 GKVAYPMVAA YSASKFALDGFFSSIRKEYSVSRVNVSIT LCVLGLIDTE -ENTA_ECOLI 144 1.77e-15 AHTPRIGMSA YGASKAALKSLALSVGLELAGSGVRCNVV SPGSTDTDMQ -3BHD_COMTE 151 7.81e-15 SWLPIEQYAG YSASKAAVSALTRAAALSCRKQGYAIRVN SIHPDGIYTP -DHB3_HUMAN 198 8.55e-15 ALFPWPLYSM YSASKAFVCAFSKALQEEYKAKEVIIQVL TPYAVSTAMT -RFBB_NEIGO 165 1.47e-14 ETTPYAPSSP YSASKAAADHLVRAWQRTYRLPSIVSNCS NNYGPRQFPE -YINL_LISMO 154 3.24e-14 GLKAYPGGAV YGATKWAVRDLMEVLRMESAQEGTNIRTA TIYPAAINTE -BPHB_PSEPS 153 1.80e-12 GFYPNGGGPL YTAAKQAIVGLVRELAFELAPYVRVNGVG PGGMNSDMRG -CSGA_MYXXA 88 2.10e-12 AANTDGGAYA YRMSKAALNMAVRSMSTDLRPEGFVTVLL HPGWVQTDMG -FABI_ECOLI 159 4.15e-12 AERAIPNYNV MGLAKASLEANVRYMANAMGPEGVRVNAI SAGPIRTLAA -ADH_DROME 152 5.20e-12 GFNAIYQVPV YSGTKAAVVNFTSSLAKLAPITGVTAYTV NPGITRTTLV -DHCA_HUMAN 193 4.80e-10 HQKEGWPSSA YGVTKIGVTVLSRIHARKLSEQRKGDKIL LNACCPGWVR -PCR_PEA 26 2.77e-08 PKEGKIGASL KDSTLFGVSSLSDSLKGDFTSSALRCKEL RQKVGAVRAE -MAS1_AGRRA 349 5.72e-08 VDYQRFHLQW YINCVAPLRMTELCLPHLYETGSGRIVNI NSMSGQRVLN --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 block diagrams --------------------------------------------------------------------------------- -SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -YRTP_BACSU 1.6e-22 154_[1]_55 -AP27_MOUSE 6.3e-22 148_[1]_67 -NODG_RHIME 1.1e-21 151_[1]_65 -BUDC_KLETE 4e-21 151_[1]_61 -FIXR_BRAJA 6.1e-21 188_[1]_61 -DHGB_BACME 7.5e-20 159_[1]_74 -HMTR_LEIMA 3.4e-19 192_[1]_66 -YURA_MYXXA 4.8e-19 159_[1]_70 -GUTD_ECOLI 4.8e-19 153_[1]_77 -2BHD_STREX 1.1e-18 151_[1]_75 -HDHA_ECOLI 1.2e-18 158_[1]_68 -DHB2_HUMAN 2.2e-18 231_[1]_127 -DHMA_FLAS1 5.5e-18 164_[1]_77 -HDE_CANTR 9.7e-18 466_[1]_411 -FVT1_HUMAN 2.9e-17 185_[1]_118 -BDH_HUMAN 8.2e-17 207_[1]_107 -RIDH_KLEAE 9.1e-17 159_[1]_61 -DHES_HUMAN 1.4e-16 154_[1]_144 -BA72_EUBSP 2.5e-16 156_[1]_64 -LIGD_PSEPA 1.2e-15 156_[1]_120 -DHII_HUMAN 1.6e-15 182_[1]_81 -ENTA_ECOLI 1.8e-15 143_[1]_76 -3BHD_COMTE 7.8e-15 150_[1]_74 -DHB3_HUMAN 8.6e-15 197_[1]_84 -RFBB_NEIGO 1.5e-14 164_[1]_153 -YINL_LISMO 3.2e-14 153_[1]_66 -BPHB_PSEPS 1.8e-12 152_[1]_94 -CSGA_MYXXA 2.1e-12 87_[1]_50 -FABI_ECOLI 4.2e-12 158_[1]_75 -ADH_DROME 5.2e-12 151_[1]_75 -DHCA_HUMAN 4.8e-10 192_[1]_55 -PCR_PEA 2.8e-08 25_[1]_345 -MAS1_AGRRA 5.7e-08 348_[1]_99 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 in BLOCKS format --------------------------------------------------------------------------------- -BL MOTIF 1 width=29 seqs=33 -YRTP_BACSU ( 155) YSASKFAVLGLTESLMQEVRKHNIRVSAL 1 -AP27_MOUSE ( 149) YSSTKGAMTMLTKAMAMELGPHKIRVNSV 1 -NODG_RHIME ( 152) YCASKAGMIGFSKSLAQEIATRNITVNCV 1 -BUDC_KLETE ( 152) YSSSKFAVRGLTQTAARDLAPLGITVNGF 1 -FIXR_BRAJA ( 189) YATSKAALASLTRELAHDYAPHGIRVNAI 1 -DHGB_BACME ( 160) YAASKGGMKLMTETLALEYAPKGIRVNNI 1 -HMTR_LEIMA ( 193) YTMAKGALEGLTRSAALELAPLQIRVNGV 1 -YURA_MYXXA ( 160) YSASKAFLSTFMESLRVDLRGTGVRVTCI 1 -GUTD_ECOLI ( 154) YSAAKFGGVGLTQSLALDLAEYGITVHSL 1 -2BHD_STREX ( 152) YGASKWGVRGLSKLAAVELGTDRIRVNSV 1 -HDHA_ECOLI ( 159) YASSKAAASHLVRNMAFDLGEKNIRVNGI 1 -DHB2_HUMAN ( 232) YGSSKAAVTMFSSVMRLELSKWGIKVASI 1 -DHMA_FLAS1 ( 165) YVAAKGGVAMLTRAMAVDLARHGILVNMI 1 -HDE_CANTR ( 467) YSSSKAGILGLSKTMAIEGAKNNIKVNIV 1 -FVT1_HUMAN ( 186) YSASKFAIRGLAEALQMEVKPYNVYITVA 1 -BDH_HUMAN ( 208) YCITKFGVEAFSDCLRYEMYPLGVKVSVV 1 -RIDH_KLEAE ( 160) YTASKFAVQAFVHTTRRQVAQYGVRVGAV 1 -DHES_HUMAN ( 155) YCASKFALEGLCESLAVLLLPFGVHLSLI 1 -BA72_EUBSP ( 157) YPASKASVIGLTHGLGREIIRKNIRVVGV 1 -LIGD_PSEPA ( 157) YSAAKAASINLMEGYRQGLEKYGIGVSVC 1 -DHII_HUMAN ( 183) YSASKFALDGFFSSIRKEYSVSRVNVSIT 1 -ENTA_ECOLI ( 144) YGASKAALKSLALSVGLELAGSGVRCNVV 1 -3BHD_COMTE ( 151) YSASKAAVSALTRAAALSCRKQGYAIRVN 1 -DHB3_HUMAN ( 198) YSASKAFVCAFSKALQEEYKAKEVIIQVL 1 -RFBB_NEIGO ( 165) YSASKAAADHLVRAWQRTYRLPSIVSNCS 1 -YINL_LISMO ( 154) YGATKWAVRDLMEVLRMESAQEGTNIRTA 1 -BPHB_PSEPS ( 153) YTAAKQAIVGLVRELAFELAPYVRVNGVG 1 -CSGA_MYXXA ( 88) YRMSKAALNMAVRSMSTDLRPEGFVTVLL 1 -FABI_ECOLI ( 159) MGLAKASLEANVRYMANAMGPEGVRVNAI 1 -ADH_DROME ( 152) YSGTKAAVVNFTSSLAKLAPITGVTAYTV 1 -DHCA_HUMAN ( 193) YGVTKIGVTVLSRIHARKLSEQRKGDKIL 1 -PCR_PEA ( 26) KDSTLFGVSSLSDSLKGDFTSSALRCKEL 1 -MAS1_AGRRA ( 349) YINCVAPLRMTELCLPHLYETGSGRIVNI 1 -// - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific scoring matrix --------------------------------------------------------------------------------- -log-odds matrix: alength= 20 w= 29 n= 9072 bayes= 8.09755 E= 3.6e-165 - -716 -497 -698 -691 -172 -730 -304 -562 -80 -507 12 -550 -661 -513 -563 -605 -625 -609 -217 508 - -51 240 -90 -249 -334 53 -232 -106 -219 -337 -278 -209 -72 -192 -79 276 81 -153 -332 -306 - 257 -64 -390 -343 -320 -160 -326 -144 -343 -193 26 -120 -436 -313 -349 86 -117 -123 -309 -358 - 57 116 -511 -541 -504 -420 -453 -532 -481 -549 -470 -353 -434 -438 -470 325 161 -493 -485 -492 - -433 -317 -482 -429 -524 -520 -342 -409 413 -326 -416 -349 -435 -343 -57 -433 -392 -321 -375 -453 - 205 -259 -559 -505 282 34 -356 -70 -475 -333 -299 -445 -475 -1 -468 -326 -334 -312 255 -226 - 235 -273 -630 -622 68 154 -557 -603 -636 -616 -544 -517 -44 -518 -595 5 -371 -482 -571 -615 - -80 -195 -498 -421 -234 -161 -307 78 -389 146 165 -378 -410 -325 -384 -96 -250 223 -275 -265 - -75 107 27 110 -355 -358 -150 45 46 -69 -279 -14 -296 44 145 85 61 -5 -331 -279 - 33 -283 -54 -168 -321 176 159 -291 -150 -137 223 56 -315 -120 -208 49 -61 -125 -319 -277 - -215 -277 -532 -447 217 -558 -360 -167 -423 288 23 -95 -427 -325 -396 -413 -122 -250 -311 -327 - -89 117 -466 -101 -26 -476 -318 -198 -376 -255 156 -325 -415 -315 -380 173 259 99 -304 -300 - -295 -344 26 181 -386 -383 160 -385 151 -69 -304 -196 -322 112 242 49 -236 -378 -354 -305 - 56 211 -348 6 -258 -72 -244 -52 -256 -112 -197 -40 -364 -217 -294 224 101 -30 -286 10 - -3 -202 -498 -419 -224 -471 54 -37 -388 234 272 -382 -407 -317 -379 -325 -74 -85 143 8 - 204 -306 -264 -189 -396 -69 -189 -390 -14 -378 3 -217 -51 156 193 -72 -251 -369 -361 -322 - -277 -280 -236 -39 57 -152 158 -80 39 79 153 -21 -313 156 145 -204 -60 39 -315 8 - -164 -464 216 305 -496 -158 -268 -472 -47 -16 -396 -277 -379 31 -306 -90 -81 -452 -469 -411 - -157 123 -496 -418 -13 -163 -303 31 -385 220 113 -376 -406 -318 -379 -98 -251 25 -270 253 - 149 -311 -209 33 -354 22 -151 -97 45 -149 -278 -172 -46 -92 145 50 -59 -348 -330 5 - -142 -318 -208 76 -356 -68 -151 -97 147 -150 -280 -172 276 112 34 -61 60 -140 -332 -280 - -268 -317 -47 77 -38 -150 250 -359 121 -18 -279 -15 -46 112 -37 50 13 -352 139 222 - -156 -338 -229 -48 -391 239 -183 -396 -30 -386 -318 190 -329 27 74 -6 -247 -151 -356 -313 - -372 -253 -410 -399 -123 -293 -366 345 -197 -52 -102 -354 -429 -337 -203 -342 -171 118 -313 -110 - -144 -290 -233 -162 -327 -68 73 -84 85 -139 -256 56 -312 -113 285 -203 97 1 -321 8 - -146 94 -193 -329 -285 -443 -265 73 -337 -177 -228 -168 -320 -310 -312 -198 -113 308 -344 -389 - -142 -319 -207 -138 -356 -68 75 -360 46 -347 -280 302 -296 44 34 113 13 -5 -332 6 - 6 273 -480 -92 -230 26 -297 77 -371 -32 33 44 -403 -310 -372 80 13 130 -270 -259 - -80 123 -491 -416 -13 -162 -302 217 -383 93 -169 -51 -405 -320 -379 -96 -66 178 -270 -260 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific probability matrix --------------------------------------------------------------------------------- -letter-probability matrix: alength= 20 w= 29 nsites= 33 E= 3.6e-165 - 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.939394 - 0.090909 0.090909 0.030303 0.000000 0.000000 0.181818 0.000000 0.030303 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.030303 0.393939 0.090909 0.030303 0.000000 0.000000 - 0.575758 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.030303 0.000000 0.030303 0.060606 0.030303 0.000000 0.000000 0.000000 0.181818 0.030303 0.030303 0.000000 0.000000 - 0.181818 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.606061 0.181818 0.000000 0.000000 0.000000 - 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.939394 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 - 0.484848 0.000000 0.000000 0.000000 0.272727 0.121212 0.000000 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.000000 0.000000 0.060606 0.000000 - 0.575758 0.000000 0.000000 0.000000 0.060606 0.272727 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.060606 0.000000 0.000000 0.000000 0.000000 - 0.060606 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.090909 0.000000 0.272727 0.090909 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.424242 0.000000 0.000000 - 0.060606 0.030303 0.060606 0.121212 0.000000 0.000000 0.000000 0.090909 0.060606 0.060606 0.000000 0.030303 0.000000 0.030303 0.151515 0.121212 0.090909 0.090909 0.000000 0.000000 - 0.151515 0.000000 0.030303 0.000000 0.000000 0.363636 0.060606 0.000000 0.000000 0.030303 0.151515 0.060606 0.000000 0.000000 0.000000 0.090909 0.030303 0.030303 0.000000 0.000000 - 0.030303 0.000000 0.000000 0.000000 0.242424 0.000000 0.000000 0.000000 0.000000 0.636364 0.030303 0.030303 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.000000 - 0.060606 0.030303 0.000000 0.030303 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.242424 0.333333 0.181818 0.000000 0.000000 - 0.000000 0.000000 0.060606 0.212121 0.000000 0.000000 0.060606 0.000000 0.151515 0.060606 0.000000 0.000000 0.000000 0.060606 0.303030 0.090909 0.000000 0.000000 0.000000 0.000000 - 0.181818 0.060606 0.000000 0.060606 0.000000 0.060606 0.000000 0.030303 0.000000 0.030303 0.000000 0.030303 0.000000 0.000000 0.000000 0.333333 0.121212 0.060606 0.000000 0.030303 - 0.121212 0.000000 0.000000 0.000000 0.000000 0.000000 0.030303 0.030303 0.000000 0.484848 0.212121 0.000000 0.000000 0.000000 0.000000 0.000000 0.030303 0.030303 0.030303 0.030303 - 0.515152 0.000000 0.000000 0.000000 0.000000 0.060606 0.000000 0.000000 0.030303 0.000000 0.030303 0.000000 0.030303 0.090909 0.212121 0.030303 0.000000 0.000000 0.000000 0.000000 - 0.000000 0.000000 0.000000 0.030303 0.060606 0.030303 0.060606 0.030303 0.060606 0.181818 0.090909 0.030303 0.000000 0.090909 0.151515 0.000000 0.030303 0.121212 0.000000 0.030303 - 0.030303 0.000000 0.242424 0.484848 0.000000 0.030303 0.000000 0.000000 0.030303 0.090909 0.000000 0.000000 0.000000 0.030303 0.000000 0.030303 0.030303 0.000000 0.000000 0.000000 - 0.030303 0.030303 0.000000 0.000000 0.030303 0.030303 0.000000 0.060606 0.000000 0.454545 0.060606 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.090909 0.000000 0.181818 - 0.363636 0.000000 0.000000 0.060606 0.000000 0.121212 0.000000 0.030303 0.060606 0.030303 0.000000 0.000000 0.030303 0.000000 0.151515 0.090909 0.030303 0.000000 0.000000 0.030303 - 0.030303 0.000000 0.000000 0.090909 0.000000 0.060606 0.000000 0.030303 0.151515 0.030303 0.000000 0.000000 0.333333 0.060606 0.060606 0.030303 0.090909 0.030303 0.000000 0.000000 - 0.000000 0.000000 0.030303 0.090909 0.030303 0.030303 0.121212 0.000000 0.121212 0.090909 0.000000 0.030303 0.030303 0.060606 0.030303 0.090909 0.060606 0.000000 0.030303 0.151515 - 0.030303 0.000000 0.000000 0.030303 0.000000 0.515152 0.000000 0.000000 0.030303 0.000000 0.000000 0.181818 0.000000 0.030303 0.090909 0.060606 0.000000 0.030303 0.000000 0.000000 - 0.000000 0.000000 0.000000 0.000000 0.030303 0.030303 0.000000 0.484848 0.030303 0.030303 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.030303 0.303030 0.000000 0.030303 - 0.030303 0.000000 0.000000 0.000000 0.000000 0.060606 0.030303 0.030303 0.090909 0.030303 0.000000 0.060606 0.000000 0.000000 0.424242 0.000000 0.121212 0.090909 0.000000 0.030303 - 0.030303 0.060606 0.030303 0.000000 0.000000 0.000000 0.000000 0.151515 0.000000 0.030303 0.000000 0.030303 0.000000 0.000000 0.000000 0.030303 0.030303 0.606061 0.000000 0.000000 - 0.030303 0.000000 0.000000 0.000000 0.000000 0.060606 0.030303 0.000000 0.060606 0.000000 0.000000 0.393939 0.000000 0.030303 0.060606 0.151515 0.060606 0.090909 0.000000 0.030303 - 0.121212 0.090909 0.000000 0.030303 0.000000 0.121212 0.000000 0.090909 0.000000 0.060606 0.030303 0.060606 0.000000 0.000000 0.000000 0.121212 0.060606 0.212121 0.000000 0.000000 - 0.060606 0.030303 0.000000 0.000000 0.030303 0.030303 0.000000 0.272727 0.000000 0.181818 0.000000 0.030303 0.000000 0.000000 0.000000 0.030303 0.030303 0.303030 0.000000 0.000000 --------------------------------------------------------------------------------- - - - - - -Time 36.66 secs. - -******************************************************************************** - - -******************************************************************************** -MOTIF 2 width = 29 sites = 33 llr = 1106 E-value = 2.3e-159 -******************************************************************************** --------------------------------------------------------------------------------- - Motif 2 Description --------------------------------------------------------------------------------- -Simplified A :14::::531:1:1516:2:322:51111 -pos.-specific C :::::::1::::::::1:::::::::::: -probability D ::::::::1:::::1:::1:::1:::::: -matrix E ::::::::::::::2::11::22:::::: - F :::::::::::::1:::::2::::1::1: - G ::::::a4218:9:::::1::1:8:1:11 - H :::::::::::::1:::11:1:1::1::: - I ::124::::::5:::2:1::1:::::1:1 - K 61:::::::2:::2:::3:::21:13::: - L :::51::::::3:2:2:1151:1:111:3 - M :::::::::::::::1::::::1:::::: - N :1::::::1:::::::::::::1::1::: - P 1:::::::::::::::::::::::::::: - Q 1::::::::1:::::::::::11:::::: - R :1:::::::2:::2:::21::111:1::: - S :::::::123::1:1:1:::111:1111: - T 111::9::::1::::2::1::1:::::1: - V :4425::::::1:::12:1:1:::::553 - W ::::::::::::::::::::::::::::: - Y :::::::::::::::1::::::::1:::: - - bits 6.7 - 6.0 - 5.4 - 4.7 -Information 4.0 -content 3.4 ** -(48.4 bits) 2.7 *** * * - 2.0 * ****** *** * * * - 1.3 ****************** * * ** *** - 0.7 ***************************** - 0.0 ----------------------------- - -Multilevel KVALVTGAASGIGKATAKxLAAEGAKVVL -consensus VII GG L R I F K V -sequence S - - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 sites sorted by position p-value --------------------------------------------------------------------------------- -Sequence name Start P-value Site -------------- ----- --------- ----------------------------- -HDE_CANTR 323 2.44e-23 SGAPTVSLKD KVVLITGAGAGLGKEYAKWFAKYGAKVVV NDFKDATKTV -DHII_HUMAN 35 5.50e-23 EEFRPEMLQG KKVIVTGASKGIGREMAYHLAKMGAHVVV TARSKETLQK -YINL_LISMO 6 5.38e-22 MTIKN KVIIITGASSGIGKATALLLAEKGAKLVL AARRVEKLEK -HDHA_ECOLI 12 5.65e-20 FNSDNLRLDG KCAIITGAGAGIGKEIAITFATAGASVVV SDINADAANH -RIDH_KLEAE 15 1.17e-19 VSSMNTSLSG KVAAITGAASGIGLECARTLLGAGAKVVL IDREGEKLNK -BUDC_KLETE 3 1.17e-19 MQ KVALVTGAGQGIGKAIALRLVKDGFAVAI ADYNDATATA -ENTA_ECOLI 6 4.74e-19 MDFSG KNVWVTGAGKGIGYATALAFVEAGAKVTG FDQAFTQEQY -AP27_MOUSE 8 9.31e-19 MKLNFSG LRALVTGAGKGIGRDTVKALHASGAKVVA VTRTNSDLVS -DHMA_FLAS1 15 2.50e-18 VSRRPGRLAG KAAIVTGAAGGIGRATVEAYLREGASVVA MDLAPRLAAT -YRTP_BACSU 7 3.45e-18 MQSLQH KTALITGGGRGIGRATALALAKEGVNIGL IGRTSANVEK -DHGB_BACME 8 5.86e-18 MYKDLEG KVVVITGSSTGLGKSMAIRFATEKAKVVV NYRSKEDEAN -DHB3_HUMAN 49 9.86e-18 LPKSFLRSMG QWAVITGAGDGIGKAYSFELAKRGLNVVL ISRTLEKLEA -PCR_PEA 87 2.47e-17 SSEGKKTLRK GNVVITGASSGLGLATAKALAESGKWHVI MACRDYLKAA -BDH_HUMAN 56 3.01e-17 YASAAEPVGS KAVLVTGCDSGFGFSLAKHLHSKGFLVFA GCLMKDKGHD -BA72_EUBSP 7 3.33e-17 MNLVQD KVTIITGGTRGIGFAAAKIFIDNGAKVSI FGETQEEVDT -FIXR_BRAJA 37 4.06e-17 VNARVDRGEP KVMLLTGASRGIGHATAKLFSEAGWRIIS CARQPFDGER -3BHD_COMTE 7 4.06e-17 TNRLQG KVALVTGGASGVGLEVVKLLLGEGAKVAF SDINEAAGQQ -2BHD_STREX 7 8.05e-17 MNDLSG KTVIITGGARGLGAEAARQAVAAGARVVL ADVLDEEGAA -HMTR_LEIMA 7 1.90e-16 MTAPTV PVALVTGAAKRLGRSIAEGLHAEGYAVCL HYHRSAAEAN -FVT1_HUMAN 33 2.77e-16 ISPKPLALPG AHVVVTGGSSGIGKCIAIECYKQGAFITL VARNEDKLLQ -DHB2_HUMAN 83 3.65e-16 SGQELLPVDQ KAVLVTGGDCGLGHALCKYLDELGFTVFA GVLNENGPGA -LIGD_PSEPA 7 8.31e-16 MKDFQD QVAFITGGASGAGFGQAKVFGQAGAKIVV ADVRAEAVEK -NODG_RHIME 7 4.05e-15 MFELTG RKALVTGASGAIGGAIARVLHAQGAIVGL HGTQIEKLET -DHCA_HUMAN 5 5.24e-15 SSGI HVALVTGGNKGIGLAIVRDLCRLFSGDVV LTARDVTRGQ -MAS1_AGRRA 246 3.00e-14 SHWTVEIHQS PVILVSGSNRGVGKAIAEDLIAHGYRLSL GARKVKDLEV -BPHB_PSEPS 6 8.47e-14 MKLKG EAVLITGGASGLGRALVDRFVAEAKVAVL DKSAERLAEL -GUTD_ECOLI 3 1.46e-13 MN QVAVVIGGGQTLGAFLCHGLAAEGYRVAV VDIQSDKAAN -DHES_HUMAN 3 1.46e-13 AR TVVLITGCSSGIGLHLAVRLASDPSQSFK VYATLRDLKT -RFBB_NEIGO 7 1.59e-12 MQTEGK KNILVTGGAGFIGSAVVRHIIQNTRDSVV NLDKLTYAGN -ADH_DROME 7 6.97e-10 SFTLTN KNVIFVAGLGGIGLDTSKELLKRDLKNLV ILDRIENPAA -FABI_ECOLI 7 3.15e-09 MGFLSG KRILVTGVASKLSIAYGIAQAMHREGAEL AFTYQNDKLK -YURA_MYXXA 117 2.77e-07 RLPWERVRGI IDTNVTGAAATLSAVLPQMVERKRGHLVG VSSLAGFRGL -CSGA_MYXXA 52 4.24e-07 TINALGPLRV TSAMLPGLRQGALRRVAHVTSRMGSLAAN TDGGAYAYRM --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 block diagrams --------------------------------------------------------------------------------- -SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -HDE_CANTR 2.4e-23 322_[2]_555 -DHII_HUMAN 5.5e-23 34_[2]_229 -YINL_LISMO 5.4e-22 5_[2]_214 -HDHA_ECOLI 5.7e-20 11_[2]_215 -RIDH_KLEAE 1.2e-19 14_[2]_206 -BUDC_KLETE 1.2e-19 2_[2]_210 -ENTA_ECOLI 4.7e-19 5_[2]_214 -AP27_MOUSE 9.3e-19 7_[2]_208 -DHMA_FLAS1 2.5e-18 14_[2]_227 -YRTP_BACSU 3.4e-18 6_[2]_203 -DHGB_BACME 5.9e-18 7_[2]_226 -DHB3_HUMAN 9.9e-18 48_[2]_233 -PCR_PEA 2.5e-17 86_[2]_284 -BDH_HUMAN 3e-17 55_[2]_259 -BA72_EUBSP 3.3e-17 6_[2]_214 -FIXR_BRAJA 4.1e-17 36_[2]_213 -3BHD_COMTE 4.1e-17 6_[2]_218 -2BHD_STREX 8e-17 6_[2]_220 -HMTR_LEIMA 1.9e-16 6_[2]_252 -FVT1_HUMAN 2.8e-16 32_[2]_271 -DHB2_HUMAN 3.7e-16 82_[2]_276 -LIGD_PSEPA 8.3e-16 6_[2]_270 -NODG_RHIME 4.1e-15 6_[2]_210 -DHCA_HUMAN 5.2e-15 4_[2]_243 -MAS1_AGRRA 3e-14 245_[2]_202 -BPHB_PSEPS 8.5e-14 5_[2]_241 -GUTD_ECOLI 1.5e-13 2_[2]_228 -DHES_HUMAN 1.5e-13 2_[2]_296 -RFBB_NEIGO 1.6e-12 6_[2]_311 -ADH_DROME 7e-10 6_[2]_220 -FABI_ECOLI 3.1e-09 6_[2]_227 -YURA_MYXXA 2.8e-07 116_[2]_113 -CSGA_MYXXA 4.2e-07 51_[2]_86 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 in BLOCKS format --------------------------------------------------------------------------------- -BL MOTIF 2 width=29 seqs=33 -HDE_CANTR ( 323) KVVLITGAGAGLGKEYAKWFAKYGAKVVV 1 -DHII_HUMAN ( 35) KKVIVTGASKGIGREMAYHLAKMGAHVVV 1 -YINL_LISMO ( 6) KVIIITGASSGIGKATALLLAEKGAKLVL 1 -HDHA_ECOLI ( 12) KCAIITGAGAGIGKEIAITFATAGASVVV 1 -RIDH_KLEAE ( 15) KVAAITGAASGIGLECARTLLGAGAKVVL 1 -BUDC_KLETE ( 3) KVALVTGAGQGIGKAIALRLVKDGFAVAI 1 -ENTA_ECOLI ( 6) KNVWVTGAGKGIGYATALAFVEAGAKVTG 1 -AP27_MOUSE ( 8) LRALVTGAGKGIGRDTVKALHASGAKVVA 1 -DHMA_FLAS1 ( 15) KAAIVTGAAGGIGRATVEAYLREGASVVA 1 -YRTP_BACSU ( 7) KTALITGGGRGIGRATALALAKEGVNIGL 1 -DHGB_BACME ( 8) KVVVITGSSTGLGKSMAIRFATEKAKVVV 1 -DHB3_HUMAN ( 49) QWAVITGAGDGIGKAYSFELAKRGLNVVL 1 -PCR_PEA ( 87) GNVVITGASSGLGLATAKALAESGKWHVI 1 -BDH_HUMAN ( 56) KAVLVTGCDSGFGFSLAKHLHSKGFLVFA 1 -BA72_EUBSP ( 7) KVTIITGGTRGIGFAAAKIFIDNGAKVSI 1 -FIXR_BRAJA ( 37) KVMLLTGASRGIGHATAKLFSEAGWRIIS 1 -3BHD_COMTE ( 7) KVALVTGGASGVGLEVVKLLLGEGAKVAF 1 -2BHD_STREX ( 7) KTVIITGGARGLGAEAARQAVAAGARVVL 1 -HMTR_LEIMA ( 7) PVALVTGAAKRLGRSIAEGLHAEGYAVCL 1 -FVT1_HUMAN ( 33) AHVVVTGGSSGIGKCIAIECYKQGAFITL 1 -DHB2_HUMAN ( 83) KAVLVTGGDCGLGHALCKYLDELGFTVFA 1 -LIGD_PSEPA ( 7) QVAFITGGASGAGFGQAKVFGQAGAKIVV 1 -NODG_RHIME ( 7) RKALVTGASGAIGGAIARVLHAQGAIVGL 1 -DHCA_HUMAN ( 5) HVALVTGGNKGIGLAIVRDLCRLFSGDVV 1 -MAS1_AGRRA ( 246) PVILVSGSNRGVGKAIAEDLIAHGYRLSL 1 -BPHB_PSEPS ( 6) EAVLITGGASGLGRALVDRFVAEAKVAVL 1 -GUTD_ECOLI ( 3) QVAVVIGGGQTLGAFLCHGLAAEGYRVAV 1 -DHES_HUMAN ( 3) TVVLITGCSSGIGLHLAVRLASDPSQSFK 1 -RFBB_NEIGO ( 7) KNILVTGGAGFIGSAVVRHIIQNTRDSVV 1 -ADH_DROME ( 7) KNVIFVAGLGGIGLDTSKELLKRDLKNLV 1 -FABI_ECOLI ( 7) KRILVTGVASKLSIAYGIAQAMHREGAEL 1 -YURA_MYXXA ( 117) IDTNVTGAAATLSAVLPQMVERKRGHLVG 1 -CSGA_MYXXA ( 52) TSAMLPGLRQGALRRVAHVTSRMGSLAAN 1 -// - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 position-specific scoring matrix --------------------------------------------------------------------------------- -log-odds matrix: alength= 20 w= 29 n= 9072 bayes= 8.09755 E= 2.3e-159 - -143 -322 -212 -29 -360 -150 75 -97 323 -150 -283 -174 41 159 -35 -190 13 -356 -334 -283 - 0 103 -55 -150 -343 -365 68 -277 37 -328 -270 137 -300 -104 27 -68 8 216 134 -284 - 184 -328 -685 -628 -415 -668 -559 121 -607 -334 17 -587 -610 -559 -621 -535 7 212 -519 -487 - -171 -214 -506 -425 -20 -485 -317 170 -395 240 30 -63 -412 -320 -383 -339 -272 73 137 -278 - -548 -378 -767 -727 -25 -789 -710 277 -719 -45 -344 -695 -699 -669 -749 -678 -480 260 -602 -574 - -390 -251 -433 -462 -434 -534 -365 -109 -376 -462 -320 -258 -80 -318 -390 -26 386 -153 -406 -454 - -198 -345 -337 -398 -504 336 -361 -523 -381 -566 -470 -293 -442 -394 -385 -308 -423 -506 -397 -449 - 205 225 -616 -594 -556 193 -536 -552 -603 -163 -504 -510 -489 -501 -571 4 -361 -139 -540 -583 - 131 -370 35 -219 -442 128 -213 -456 -212 -158 -382 70 -370 -181 -55 181 -71 -445 -421 -359 - -30 108 -48 -141 -360 23 -153 -364 148 -351 -284 -173 -299 159 146 204 -60 -357 -335 -283 - -204 -337 -316 -378 -112 323 -341 -505 -141 -549 -452 -272 -427 -375 -136 -296 -74 -492 -378 -430 - -95 -361 -677 -632 -23 -695 -554 323 -604 166 -255 -593 -615 -536 -614 -563 -440 -15 -461 -462 - -326 -337 -324 -385 -492 331 -348 -511 -368 -235 -458 -280 -431 -381 -372 -66 -413 -495 -385 -437 - -30 -269 -258 -187 114 -153 158 -74 206 82 -239 -214 -326 -135 191 -71 -224 -281 -312 9 - 237 89 -43 92 -86 -158 5 -315 -262 -325 -263 -289 -394 -232 -114 27 -229 -127 -314 -338 - -79 126 -496 -418 -229 -460 -302 183 -384 95 114 -373 -406 -2 -380 -314 194 28 -269 160 - 260 176 -422 -376 -354 -156 -358 -340 -378 -355 -293 -375 -107 -342 -381 -6 -258 55 -342 -392 - -270 -314 -48 76 -39 -361 159 86 236 21 -276 -175 -299 43 146 -189 -211 -138 -330 6 - 56 -301 25 75 -338 -68 212 -90 -130 -15 8 -180 -302 41 116 -193 13 -2 141 7 - -177 105 -501 -421 238 -487 -316 -44 -391 257 -134 -393 -406 -19 -377 -340 -87 -96 -279 -4 - 151 122 -87 -90 -241 -159 248 70 -331 38 -181 -340 -395 -280 -347 -10 -242 54 -276 11 - 75 -319 -47 137 -356 -68 -150 -361 189 -347 5 -170 -296 112 117 5 13 -353 -332 -279 - 55 -318 27 179 -355 -357 159 -360 88 -69 94 59 -295 112 34 6 -209 -352 -331 6 - -204 -337 -127 -377 -112 318 -341 -505 -141 -549 -452 -272 -122 -374 -52 -296 -161 -492 -378 -430 - 225 -109 -325 -105 68 -158 -257 -288 -22 -98 -250 -283 -385 -221 -102 31 -229 -121 98 106 - -75 -318 -47 -137 -40 -68 159 -97 236 -69 -279 59 -295 44 117 6 -59 -140 140 -279 - -91 -125 -192 -330 -284 -443 -59 58 -338 -101 -228 -167 -320 -310 -312 -132 -175 304 -343 -387 - -59 39 -374 -175 10 -177 -269 -2 -342 -164 -220 -355 -327 -311 -318 -112 -56 295 -333 -366 - 6 -192 -493 -415 -11 -69 -301 78 -81 174 -170 -49 -406 -318 -378 -94 -246 162 -269 -259 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 position-specific probability matrix --------------------------------------------------------------------------------- -letter-probability matrix: alength= 20 w= 29 nsites= 33 E= 2.3e-159 - 0.030303 0.000000 0.000000 0.030303 0.000000 0.030303 0.030303 0.030303 0.575758 0.030303 0.000000 0.000000 0.060606 0.090909 0.030303 0.000000 0.060606 0.000000 0.000000 0.000000 - 0.121212 0.030303 0.030303 0.000000 0.000000 0.000000 0.030303 0.000000 0.060606 0.000000 0.000000 0.121212 0.000000 0.000000 0.060606 0.030303 0.060606 0.424242 0.030303 0.000000 - 0.424242 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.121212 0.000000 0.000000 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.060606 0.363636 0.000000 0.000000 - 0.030303 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.212121 0.000000 0.484848 0.030303 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.151515 0.030303 0.000000 - 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.393939 0.000000 0.060606 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.515152 0.000000 0.000000 - 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.030303 0.878788 0.030303 0.000000 0.000000 - 0.030303 0.000000 0.000000 0.000000 0.000000 0.969697 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 0.454545 0.060606 0.000000 0.000000 0.000000 0.363636 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.060606 0.000000 0.030303 0.000000 0.000000 - 0.303030 0.000000 0.060606 0.000000 0.000000 0.242424 0.000000 0.000000 0.000000 0.030303 0.000000 0.060606 0.000000 0.000000 0.030303 0.242424 0.030303 0.000000 0.000000 0.000000 - 0.090909 0.030303 0.030303 0.000000 0.000000 0.121212 0.000000 0.000000 0.151515 0.000000 0.000000 0.000000 0.000000 0.090909 0.151515 0.303030 0.030303 0.000000 0.000000 0.000000 - 0.030303 0.000000 0.000000 0.000000 0.030303 0.818182 0.000000 0.000000 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.060606 0.000000 0.000000 0.000000 - 0.060606 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.545455 0.000000 0.303030 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.060606 0.000000 0.000000 - 0.000000 0.000000 0.000000 0.000000 0.000000 0.909091 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.060606 0.000000 0.000000 0.000000 0.000000 - 0.090909 0.000000 0.000000 0.000000 0.090909 0.030303 0.060606 0.030303 0.242424 0.181818 0.000000 0.000000 0.000000 0.000000 0.212121 0.030303 0.000000 0.000000 0.000000 0.030303 - 0.484848 0.030303 0.060606 0.181818 0.030303 0.030303 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.030303 0.090909 0.000000 0.030303 0.000000 0.000000 - 0.060606 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.212121 0.000000 0.181818 0.060606 0.000000 0.000000 0.030303 0.000000 0.000000 0.242424 0.090909 0.000000 0.090909 - 0.636364 0.060606 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.060606 0.000000 0.181818 0.000000 0.000000 - 0.000000 0.000000 0.030303 0.090909 0.030303 0.000000 0.060606 0.121212 0.303030 0.121212 0.000000 0.000000 0.000000 0.030303 0.151515 0.000000 0.000000 0.030303 0.000000 0.030303 - 0.181818 0.000000 0.060606 0.090909 0.000000 0.060606 0.090909 0.030303 0.000000 0.090909 0.030303 0.000000 0.000000 0.030303 0.121212 0.000000 0.060606 0.090909 0.030303 0.030303 - 0.030303 0.030303 0.000000 0.000000 0.242424 0.000000 0.000000 0.030303 0.000000 0.545455 0.000000 0.000000 0.000000 0.030303 0.000000 0.000000 0.030303 0.030303 0.000000 0.030303 - 0.333333 0.030303 0.030303 0.030303 0.000000 0.030303 0.121212 0.090909 0.000000 0.121212 0.000000 0.000000 0.000000 0.000000 0.000000 0.060606 0.000000 0.121212 0.000000 0.030303 - 0.212121 0.000000 0.030303 0.151515 0.000000 0.060606 0.000000 0.000000 0.212121 0.000000 0.030303 0.000000 0.000000 0.060606 0.121212 0.060606 0.060606 0.000000 0.000000 0.000000 - 0.181818 0.000000 0.060606 0.212121 0.000000 0.000000 0.060606 0.000000 0.090909 0.060606 0.060606 0.060606 0.000000 0.060606 0.060606 0.060606 0.000000 0.000000 0.000000 0.030303 - 0.030303 0.000000 0.030303 0.000000 0.030303 0.757576 0.000000 0.000000 0.030303 0.000000 0.000000 0.000000 0.030303 0.000000 0.060606 0.000000 0.030303 0.000000 0.000000 0.000000 - 0.454545 0.000000 0.000000 0.030303 0.090909 0.030303 0.000000 0.000000 0.060606 0.060606 0.000000 0.000000 0.000000 0.000000 0.030303 0.090909 0.000000 0.030303 0.030303 0.090909 - 0.060606 0.000000 0.030303 0.000000 0.030303 0.060606 0.060606 0.030303 0.303030 0.060606 0.000000 0.060606 0.000000 0.030303 0.121212 0.060606 0.030303 0.030303 0.030303 0.000000 - 0.090909 0.000000 0.030303 0.000000 0.000000 0.000000 0.030303 0.121212 0.000000 0.090909 0.000000 0.030303 0.000000 0.000000 0.000000 0.060606 0.000000 0.545455 0.000000 0.000000 - 0.121212 0.030303 0.000000 0.030303 0.090909 0.060606 0.000000 0.030303 0.000000 0.030303 0.000000 0.000000 0.000000 0.000000 0.000000 0.060606 0.060606 0.484848 0.000000 0.000000 - 0.121212 0.000000 0.000000 0.000000 0.030303 0.060606 0.000000 0.090909 0.030303 0.333333 0.000000 0.030303 0.000000 0.000000 0.000000 0.030303 0.000000 0.272727 0.000000 0.000000 --------------------------------------------------------------------------------- - - - - - -Time 67.32 secs. - -******************************************************************************** - - -******************************************************************************** -SUMMARY OF MOTIFS -******************************************************************************** - --------------------------------------------------------------------------------- - Combined block diagrams: non-overlapping sites with p-value < 0.0001 --------------------------------------------------------------------------------- -SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -2BHD_STREX 3.15e-28 6_[2(8.05e-17)]_116_[1(1.11e-18)]_75 -3BHD_COMTE 9.69e-25 6_[2(4.06e-17)]_115_[1(7.81e-15)]_74 -ADH_DROME 6.95e-15 6_[2(6.97e-10)]_116_[1(5.20e-12)]_75 -AP27_MOUSE 2.21e-33 7_[2(9.31e-19)]_112_[1(6.32e-22)]_67 -BA72_EUBSP 2.62e-26 6_[2(3.33e-17)]_121_[1(2.52e-16)]_64 -BDH_HUMAN 1.58e-26 55_[2(3.01e-17)]_123_[1(8.20e-17)]_107 -BPHB_PSEPS 4.38e-19 5_[2(8.47e-14)]_118_[1(1.80e-12)]_94 -BUDC_KLETE 1.73e-33 2_[2(1.17e-19)]_120_[1(4.04e-21)]_61 -DHES_HUMAN 9.98e-23 2_[2(1.46e-13)]_123_[1(1.37e-16)]_144 -DHGB_BACME 1.78e-30 7_[2(5.86e-18)]_123_[1(7.52e-20)]_74 -DHII_HUMAN 4.64e-31 34_[2(5.50e-23)]_119_[1(1.61e-15)]_81 -DHMA_FLAS1 5.69e-29 14_[2(2.50e-18)]_121_[1(5.53e-18)]_77 -ENTA_ECOLI 2.69e-27 5_[2(4.74e-19)]_109_[1(1.77e-15)]_76 -FIXR_BRAJA 1.15e-30 36_[2(4.06e-17)]_123_[1(6.12e-21)]_61 -GUTD_ECOLI 2.33e-25 2_[2(1.46e-13)]_122_[1(4.82e-19)]_77 -HDE_CANTR 1.43e-32 8_[2(3.45e-18)]_125_[1(4.01e-13)]_131_[2(2.44e-23)]_115_[1(9.65e-18)]_411 -HDHA_ECOLI 2.75e-31 11_[2(5.65e-20)]_74_[1(4.42e-05)]_15_[1(1.25e-18)]_68 -LIGD_PSEPA 4.54e-24 6_[2(8.31e-16)]_121_[1(1.21e-15)]_120 -NODG_RHIME 1.55e-29 6_[2(4.05e-15)]_116_[1(1.13e-21)]_65 -RIDH_KLEAE 3.67e-29 14_[2(1.17e-19)]_116_[1(9.09e-17)]_61 -YINL_LISMO 5.92e-29 5_[2(5.38e-22)]_119_[1(3.24e-14)]_66 -YRTP_BACSU 2.01e-33 6_[2(3.45e-18)]_119_[1(1.64e-22)]_55 -CSGA_MYXXA 5.53e-13 51_[2(4.24e-07)]_7_[1(2.10e-12)]_50 -DHB2_HUMAN 6.87e-27 82_[2(3.65e-16)]_120_[1(2.23e-18)]_127 -DHB3_HUMAN 4.11e-25 48_[2(9.86e-18)]_120_[1(8.55e-15)]_84 -DHCA_HUMAN 6.86e-18 4_[2(5.24e-15)]_159_[1(4.80e-10)]_55 -FABI_ECOLI 2.57e-14 6_[2(3.15e-09)]_123_[1(4.15e-12)]_75 -FVT1_HUMAN 4.64e-26 32_[2(2.77e-16)]_124_[1(2.86e-17)]_118 -HMTR_LEIMA 2.93e-28 6_[2(1.90e-16)]_157_[1(3.35e-19)]_66 -MAS1_AGRRA 1.26e-14 245_[2(3.00e-14)]_74_[1(5.72e-08)]_99 -PCR_PEA 4.22e-18 25_[1(2.77e-08)]_32_[2(2.47e-17)]_284 -RFBB_NEIGO 1.14e-19 6_[2(1.59e-12)]_129_[1(1.47e-14)]_153 -YURA_MYXXA 3.34e-19 116_[2(2.77e-07)]_14_[1(4.82e-19)]_70 --------------------------------------------------------------------------------- - -******************************************************************************** - - -******************************************************************************** -Stopped because nmotifs = 2 reached. -******************************************************************************** - -CPU: pmgm2 - -******************************************************************************** diff --git a/Tests/Motif/meme.protein.tcm.txt b/Tests/Motif/meme.protein.tcm.txt deleted file mode 100644 index 0356bc1bc03..00000000000 --- a/Tests/Motif/meme.protein.tcm.txt +++ /dev/null @@ -1,466 +0,0 @@ -******************************************************************************** -MEME - Motif discovery tool -******************************************************************************** -MEME version 3.0 (Release date: 2004/08/18 09:07:01) - -For further information on how to interpret these results or to get -a copy of the MEME software please access http://meme.sdsc.edu. - -This file may be used as input to the MAST algorithm for searching -sequence databases for matches to groups of motifs. MAST is available -for interactive use and downloading at http://meme.sdsc.edu. -******************************************************************************** - - -******************************************************************************** -REFERENCE -******************************************************************************** -If you use this program in your research, please cite: - -Timothy L. Bailey and Charles Elkan, -"Fitting a mixture model by expectation maximization to discover -motifs in biopolymers", Proceedings of the Second International -Conference on Intelligent Systems for Molecular Biology, pp. 28-36, -AAAI Press, Menlo Park, California, 1994. -******************************************************************************** - - -******************************************************************************** -TRAINING SET -******************************************************************************** -DATAFILE= farntrans5.s -ALPHABET= ACDEFGHIKLMNPQRSTVWY -Sequence name Weight Length Sequence name Weight Length -------------- ------ ------ ------------- ------ ------ -RAM1_YEAST 1.0000 431 PFTB_RAT 1.0000 437 -BET2_YEAST 1.0000 325 RATRABGERB 1.0000 331 -CAL1_YEAST 1.0000 376 -******************************************************************************** - -******************************************************************************** -COMMAND LINE SUMMARY -******************************************************************************** -This information can also be useful in the event you wish to report a -problem with the MEME software. - -command: meme farntrans5.s -mod tcm -protein -nmotifs 2 - -model: mod= tcm nmotifs= 2 evt= inf -object function= E-value of product of p-values -width: minw= 8 maxw= 50 minic= 0.00 -width: wg= 11 ws= 1 endgaps= yes -nsites: minsites= 2 maxsites= 25 wnsites= 0.8 -theta: prob= 1 spmap= pam spfuzz= 120 -em: prior= megap b= 9500 maxiter= 50 - distance= 1e-05 -data: n= 1900 N= 5 - -sample: seed= 0 seqfrac= 1 -Dirichlet mixture priors file: prior30.plib -Letter frequencies in dataset: -A 0.061 C 0.037 D 0.062 E 0.061 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051 -L 0.114 M 0.021 N 0.034 P 0.041 Q 0.038 R 0.041 S 0.078 T 0.046 V 0.057 -W 0.018 Y 0.041 -Background letter frequencies (from dataset with add-one prior applied): -A 0.061 C 0.037 D 0.061 E 0.060 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051 -L 0.113 M 0.021 N 0.034 P 0.041 Q 0.039 R 0.041 S 0.078 T 0.046 V 0.057 -W 0.018 Y 0.041 -******************************************************************************** - - -******************************************************************************** -MOTIF 1 width = 30 sites = 24 llr = 854 E-value = 2.2e-094 -******************************************************************************** --------------------------------------------------------------------------------- - Motif 1 Description --------------------------------------------------------------------------------- -Simplified A :::2::::1:2:11:1:1413314:1:1:: -pos.-specific C ::::1::::::::2::132::::1:::::: -probability D ::::21::11:6::::::::::::::2:13 -matrix E ::::::1114::::::::::::::::1111 - F :16:::::::::111:31::::::::::1: - G 861241:42:::221:::2:22::::3::1 - H ::::::::11:4::2::::::::::::::1 - I ::1:::1::::::::1:::1:1::42:11: - K :::::1::3::::::::::::::::::2:: - L ::21:::::2::31::1::5::9:55::4: - M :::::::::::::::::::::::::::::: - N :1:1:::21:::::::::::1:::::1::: - P ::::::5:::2::::::::::::::::::: - Q :::1::::1:::::1:::::1::::::::: - R :::::3:::::::2:::::::::::::1:: - S :1:2::::::2:::13:1::32:3::12:: - T ::::::::::::2::5:1:1:1:1:1:::1 - V :::::::1::3:2:::::12::::1::::: - W ::::::::::::::::13:::::::::::: - Y :::::::::::::14:31:::::::1:::: - - bits 5.8 - 5.2 - 4.6 - 4.0 -Information 3.5 * -content 2.9 * * * -(51.4 bits) 2.3 *** * * ** * * - 1.7 *** ** *** ***** * **** - 1.2 ****************************** - 0.6 ****************************** - 0.0 ------------------------------ - -Multilevel GGFGGRPGKEVDLCYTFCALAALALLGSLD -consensus LAH HSYWCVSS SI -sequence P G - - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 sites sorted by position p-value --------------------------------------------------------------------------------- -Sequence name Start P-value Site -------------- ----- --------- ------------------------------ -BET2_YEAST 223 7.28e-22 WWLCERQLPE GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD WINYEKLTEF -RATRABGERB 227 6.18e-21 WWLCERQLPS GGLNGRPEKLPDVCYSWWVLASLKIIGRLH WIDREKLRSF -CAL1_YEAST 275 9.17e-20 LNASYDQSDD GGFQGRENKFADTCYAFWCLNSLHLLTKDW KMLCQTELVT -PFTB_RAT 237 1.15e-19 EWIARCQNWE GGIGGVPGMEAHGGYTFCGLAALVILKKER SLNLKSLLQW -PFTB_RAT 138 4.30e-19 QFLELCQSPD GGFGGGPGQYPHLAPTYAAVNALCIIGTEE AYNVINREKL -RATRABGERB 179 7.36e-19 EFVLSCMNFD GGFGCRPGSESHAGQIYCCTGFLAITSQLH QVNSDLLGWW -RATRABGERB 131 8.19e-19 AYVQSLQKED GSFAGDIWGEIDTRFSFCAVATLALLGKLD AINVEKAIEF -BET2_YEAST 172 2.10e-18 DFVLKCYNFD GGFGLCPNAESHAAQAFTCLGALAIANKLD MLSDDQLEEI -RATRABGERB 276 1.43e-17 FILACQDEET GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ IKPVSPVFCM -BET2_YEAST 124 3.41e-17 SFIRGNQLED GSFQGDRFGEVDTRFVYTALSALSILGELT SEVVDPAVDF -RAM1_YEAST 247 5.00e-17 YLKNCQNYEG GFGSCPHVDEAHGGYTFCATASLAILRSMD QINVEKLLEW -BET2_YEAST 272 6.64e-17 FILKCQDEKK GGISDRPENEVDVFHTVFGVAGLSLMGYDN LVPIDPIYCM -RAM1_YEAST 145 1.27e-16 VKLFTISPSG GPFGGGPGQLSHLASTYAAINALSLCDNID GCWDRIDRKG -PFTB_RAT 286 3.17e-16 WVTSRQMRFE GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL HAQGDPALSM -RAM1_YEAST 296 3.47e-16 WSSARQLQEE RGFCGRSNKLVDGCYSFWVGGSAAILEAFG YGQCFNKHAL -PFTB_RAT 348 4.30e-15 YILMCCQCPA GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG SGAMLHDVVM -RATRABGERB 83 2.40e-14 VFIKSCQHEC GGVSASIGHDPHLLYTLSAVQILTLYDSIH VINVDKVVAY -PFTB_RAT 189 2.81e-14 QYLYSLKQPD GSFLMHVGGEVDVRSAYCAASVASLTNIIT PDLFEGTAEW -BET2_YEAST 73 7.78e-14 FVLSCWDDKY GAFAPFPRHDAHLLTTLSAVQILATYDALD VLGKDRKVRL -CAL1_YEAST 205 1.14e-13 LLGYIMSQQC YNGAFGAHNEPHSGYTSCALSTLALLSSLE KLSDKFKEDT -RAM1_YEAST 198 1.33e-13 WLISLKEPNG GFKTCLEVGEVDTRGIYCALSIATLLNILT EELTEGVLNY -RAM1_YEAST 349 3.52e-13 ILYCCQEKEQ PGLRDKPGAHSDFYHTNYCLLGLAVAESSY SCTPNDSPHN -CAL1_YEAST 327 5.47e-13 LLDRTQKTLT GGFSKNDEEDADLYHSCLGSAALALIEGKF NGELCIPQEI -BET2_YEAST 24 3.11e-10 RYIESLDTNK HNFEYWLTEHLRLNGIYWGLTALCVLDSPE TFVKEEVISF --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 block diagrams --------------------------------------------------------------------------------- -SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -BET2_YEAST 3.1e-10 23_[1]_19_[1]_21_[1]_18_[1]_21_ - [1]_19_[1]_24 -RATRABGERB 2.4e-14 82_[1]_18_[1]_18_[1]_18_[1]_19_[1]_26 -CAL1_YEAST 1.1e-13 204_[1]_40_[1]_22_[1]_20 -PFTB_RAT 4.3e-15 137_[1]_21_[1]_18_[1]_19_[1]_32_ - [1]_60 -RAM1_YEAST 1.3e-13 144_[1]_23_[1]_19_[1]_19_[1]_23_ - [1]_53 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 in BLOCKS format --------------------------------------------------------------------------------- -BL MOTIF 1 width=30 seqs=24 -BET2_YEAST ( 223) GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD 1 -RATRABGERB ( 227) GGLNGRPEKLPDVCYSWWVLASLKIIGRLH 1 -CAL1_YEAST ( 275) GGFQGRENKFADTCYAFWCLNSLHLLTKDW 1 -PFTB_RAT ( 237) GGIGGVPGMEAHGGYTFCGLAALVILKKER 1 -PFTB_RAT ( 138) GGFGGGPGQYPHLAPTYAAVNALCIIGTEE 1 -RATRABGERB ( 179) GGFGCRPGSESHAGQIYCCTGFLAITSQLH 1 -RATRABGERB ( 131) GSFAGDIWGEIDTRFSFCAVATLALLGKLD 1 -BET2_YEAST ( 172) GGFGLCPNAESHAAQAFTCLGALAIANKLD 1 -RATRABGERB ( 276) GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ 1 -BET2_YEAST ( 124) GSFQGDRFGEVDTRFVYTALSALSILGELT 1 -RAM1_YEAST ( 247) GFGSCPHVDEAHGGYTFCATASLAILRSMD 1 -BET2_YEAST ( 272) GGISDRPENEVDVFHTVFGVAGLSLMGYDN 1 -RAM1_YEAST ( 145) GPFGGGPGQLSHLASTYAAINALSLCDNID 1 -PFTB_RAT ( 286) GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL 1 -RAM1_YEAST ( 296) RGFCGRSNKLVDGCYSFWVGGSAAILEAFG 1 -PFTB_RAT ( 348) GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG 1 -RATRABGERB ( 83) GGVSASIGHDPHLLYTLSAVQILTLYDSIH 1 -PFTB_RAT ( 189) GSFLMHVGGEVDVRSAYCAASVASLTNIIT 1 -BET2_YEAST ( 73) GAFAPFPRHDAHLLTTLSAVQILATYDALD 1 -CAL1_YEAST ( 205) YNGAFGAHNEPHSGYTSCALSTLALLSSLE 1 -RAM1_YEAST ( 198) GFKTCLEVGEVDTRGIYCALSIATLLNILT 1 -RAM1_YEAST ( 349) PGLRDKPGAHSDFYHTNYCLLGLAVAESSY 1 -CAL1_YEAST ( 327) GGFSKNDEEDADLYHSCLGSAALALIEGKF 1 -BET2_YEAST ( 24) HNFEYWLTEHLRLNGIYWGLTALCVLDSPE 1 -// - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific scoring matrix --------------------------------------------------------------------------------- -log-odds matrix: alength= 20 w= 30 n= 1755 bayes= 6.12445 E= 2.2e-094 - -218 -476 -324 -369 -492 351 -61 -474 -334 -558 -392 -225 -103 -392 -86 -303 -361 -418 -449 -109 - -81 -470 -327 -377 -1 330 -398 -485 -347 -566 -404 54 -81 -396 -330 -9 -350 -421 -467 -482 - -244 -349 -513 -434 367 -26 -384 59 -61 38 -123 -357 -404 -371 -364 -348 -238 -14 -322 -240 - 127 -17 -201 -5 -348 114 -187 -312 -81 -63 -205 120 -263 155 27 92 7 -262 -388 -304 - -26 143 115 -207 -17 219 -252 -171 -9 -112 95 -186 -16 -179 -195 -235 -164 -152 -351 -13 - -146 -17 33 -115 -32 45 38 -310 85 -143 -204 47 -13 -95 271 -53 -143 -50 83 -303 - -47 -38 -90 6 -396 -374 0 15 -233 -169 -288 -259 375 -235 -26 -97 -231 -75 -473 -424 - -148 -438 -204 99 -31 196 38 -302 -85 -335 -202 205 -266 -99 26 -54 6 33 83 -304 - 47 -444 33 57 -349 84 122 -315 209 -342 79 121 -263 109 -118 -53 -144 -265 -389 -305 - -160 -416 82 250 -25 -316 123 -254 -111 61 85 -136 -283 -122 -146 -60 -156 -221 -375 -14 - 161 -320 -465 -373 -228 -392 -333 13 -325 -90 -101 -301 208 -309 -7 90 -181 221 -331 -288 - -438 -650 318 -350 -594 -396 355 -672 -341 -686 -596 -158 -495 -373 4 -357 -386 -623 -637 -514 - 47 -316 -480 -387 82 91 -337 -111 -338 103 -98 -307 -15 -318 -312 -83 170 152 -328 -285 - 94 221 -398 -311 80 90 -301 -129 -266 -30 -111 21 -354 -263 179 -282 -178 -115 -329 139 - -167 -305 -309 -259 149 -77 196 -221 -241 -249 -153 -216 -75 19 -217 -54 -68 -205 -133 341 - 71 -383 -460 -463 -428 -445 -427 86 -370 -442 -260 -234 -417 -351 -356 143 348 -55 -479 -484 - -170 21 -317 -268 232 -354 -39 -217 -250 -54 -152 -36 -288 -261 -224 -116 -223 -78 132 328 - 46 272 -489 -397 84 -402 -334 -118 -347 -90 -105 -314 -378 -325 -320 -1 82 -106 351 88 - 277 240 -625 -594 -564 141 -583 -514 -585 -580 -446 -452 -451 4 -521 -277 -297 107 -614 -619 - 45 -317 -489 -395 -222 -96 -340 81 -346 184 -95 -313 -373 -323 -316 -85 81 179 -327 -285 - 211 -440 -247 -196 -412 97 -258 -374 -166 -146 -278 178 -325 106 -202 153 0 -314 -457 -377 - 213 -308 -476 -384 -5 88 -337 123 -337 -91 -99 -307 -372 -318 -311 118 79 12 -328 -287 - 87 -518 -675 -601 -320 -554 -562 -243 -564 290 -164 -543 -528 -491 -503 -489 -418 -296 -502 -500 - 317 38 -358 -284 -334 -229 -37 -276 -81 -332 -204 -260 -82 -270 -263 99 23 -47 -389 -383 - -408 -489 -735 -670 -387 -688 -678 294 -638 194 -240 -597 -632 -619 -631 -623 -16 84 -602 -556 - 91 0 -492 -398 -220 -404 -343 158 -348 187 109 -317 -375 -324 -318 -313 78 -100 -329 80 - -159 -454 121 100 -362 163 39 -329 20 -356 -221 172 -274 38 24 13 5 -279 -402 -316 - 47 -443 -200 57 -348 -88 38 37 160 -341 -205 47 -262 41 145 120 7 -264 -388 -19 - -28 -364 22 86 69 -344 -250 108 -9 153 95 -185 -17 -174 -192 -72 -165 -153 -352 -294 - -146 -443 171 100 -32 -6 175 -314 -80 -144 -205 47 -262 41 27 -178 126 -263 82 -19 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 1 position-specific probability matrix --------------------------------------------------------------------------------- -letter-probability matrix: alength= 20 w= 30 nsites= 24 E= 2.2e-094 - 0.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.041667 - 0.041667 0.000000 0.000000 0.000000 0.083333 0.625000 0.000000 0.000000 0.000000 0.000000 0.000000 0.083333 0.041667 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 - 0.000000 0.000000 0.000000 0.000000 0.583333 0.083333 0.000000 0.083333 0.041667 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 - 0.166667 0.041667 0.000000 0.041667 0.000000 0.208333 0.000000 0.000000 0.000000 0.083333 0.000000 0.083333 0.000000 0.125000 0.041667 0.166667 0.041667 0.000000 0.000000 0.000000 - 0.041667 0.125000 0.166667 0.000000 0.041667 0.416667 0.000000 0.000000 0.041667 0.041667 0.041667 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 - 0.000000 0.041667 0.083333 0.000000 0.041667 0.125000 0.041667 0.000000 0.083333 0.041667 0.000000 0.041667 0.041667 0.000000 0.333333 0.041667 0.000000 0.041667 0.041667 0.000000 - 0.041667 0.041667 0.041667 0.083333 0.000000 0.000000 0.041667 0.083333 0.000000 0.041667 0.000000 0.000000 0.500000 0.000000 0.041667 0.041667 0.000000 0.041667 0.000000 0.000000 - 0.000000 0.000000 0.000000 0.125000 0.041667 0.375000 0.041667 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.041667 0.041667 0.041667 0.083333 0.041667 0.000000 - 0.083333 0.000000 0.083333 0.083333 0.000000 0.166667 0.083333 0.000000 0.250000 0.000000 0.041667 0.083333 0.000000 0.083333 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 - 0.000000 0.000000 0.125000 0.416667 0.041667 0.000000 0.083333 0.000000 0.000000 0.208333 0.041667 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.041667 - 0.208333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.000000 0.208333 0.000000 0.041667 0.166667 0.000000 0.291667 0.000000 0.000000 - 0.000000 0.000000 0.583333 0.000000 0.000000 0.000000 0.375000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 - 0.083333 0.000000 0.000000 0.000000 0.083333 0.166667 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.041667 0.000000 0.000000 0.041667 0.166667 0.166667 0.000000 0.000000 - 0.125000 0.208333 0.000000 0.000000 0.083333 0.166667 0.000000 0.000000 0.000000 0.083333 0.000000 0.041667 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.125000 - 0.000000 0.000000 0.000000 0.000000 0.083333 0.083333 0.208333 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.083333 0.000000 0.083333 0.041667 0.000000 0.000000 0.375000 - 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.458333 0.041667 0.000000 0.000000 - 0.000000 0.083333 0.000000 0.000000 0.291667 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.041667 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.083333 0.291667 - 0.083333 0.291667 0.000000 0.000000 0.083333 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.083333 0.083333 0.000000 0.250000 0.083333 - 0.416667 0.208333 0.000000 0.000000 0.000000 0.208333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 - 0.083333 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.083333 0.000000 0.458333 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.083333 0.208333 0.000000 0.000000 - 0.291667 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.041667 0.000000 0.125000 0.000000 0.083333 0.000000 0.250000 0.041667 0.000000 0.000000 0.000000 - 0.291667 0.000000 0.000000 0.000000 0.041667 0.166667 0.000000 0.125000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.208333 0.083333 0.041667 0.000000 0.000000 - 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 0.416667 0.083333 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.250000 0.083333 0.041667 0.000000 0.000000 - 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.416667 0.000000 0.458333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.083333 0.000000 0.000000 - 0.125000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.458333 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.083333 0.000000 0.000000 0.083333 - 0.000000 0.000000 0.166667 0.125000 0.000000 0.291667 0.041667 0.000000 0.041667 0.000000 0.000000 0.125000 0.000000 0.041667 0.041667 0.083333 0.041667 0.000000 0.000000 0.000000 - 0.083333 0.000000 0.000000 0.083333 0.000000 0.041667 0.041667 0.083333 0.166667 0.000000 0.000000 0.041667 0.000000 0.041667 0.125000 0.208333 0.041667 0.000000 0.000000 0.041667 - 0.041667 0.000000 0.083333 0.125000 0.083333 0.000000 0.000000 0.125000 0.041667 0.375000 0.041667 0.000000 0.041667 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 - 0.000000 0.000000 0.250000 0.125000 0.041667 0.083333 0.125000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.041667 0.041667 0.000000 0.125000 0.000000 0.041667 0.041667 --------------------------------------------------------------------------------- - - - - - -Time 32.68 secs. - -******************************************************************************** - - -******************************************************************************** -MOTIF 2 width = 14 sites = 21 llr = 376 E-value = 3.1e-019 -******************************************************************************** --------------------------------------------------------------------------------- - Motif 2 Description --------------------------------------------------------------------------------- -Simplified A ::::111::::1:: -pos.-specific C ::::::::::::61 -probability D 12:11::1:::::: -matrix E 1::61::2:::::: - F 1:::::::5::::: - G ::::1::::::::: - H :::::::::::::: - I 5::::12::4:::: - K ::313:::::11:1 - L 11:::53::24:1: - M :::::::::::::: - N :4:::::::::::: - P :::::::::::::: - Q ::1::::2:::::6 - R ::1:::1::::11: - S ::::1::1:114:: - T ::1::1:::::::: - V :12::21::3:::: - W ::::::::2::::: - Y ::::::::3::::: - - bits 5.8 - 5.2 - 4.6 - 4.0 -Information 3.5 * -content 2.9 * ** -(25.8 bits) 2.3 * ** ** - 1.7 **** * ** ** - 1.2 ************** - 0.6 ************** - 0.0 -------------- - -Multilevel INKEKLLEFILSCQ -consensus YV -sequence WL - - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 sites sorted by position p-value --------------------------------------------------------------------------------- -Sequence name Start P-value Site -------------- ----- --------- -------------- -BET2_YEAST 254 2.24e-13 SLAIIGRLDW INYEKLTEFILKCQ DEKKGGISDR -RATRABGERB 258 1.30e-12 SLKIIGRLHW IDREKLRSFILACQ DEETGGFADR -RATRABGERB 162 4.20e-12 TLALLGKLDA INVEKAIEFVLSCM NFDGGFGCRP -RATRABGERB 66 9.60e-12 VMDLMGQLHR MNKEEILVFIKSCQ HECGGVSASI -RAM1_YEAST 278 5.08e-11 SLAILRSMDQ INVEKLLEWSSARQ LQEERGFCGR -CAL1_YEAST 190 5.01e-10 CRSKEDFDEY IDTEKLLGYIMSQQ CYNGAFGAHN -BET2_YEAST 55 6.90e-10 ALCVLDSPET FVKEEVISFVLSCW DDKYGAFAPF -RATRABGERB 114 1.57e-09 ILTLYDSIHV INVDKVVAYVQSLQ KEDGSFAGDI -PFTB_RAT 172 2.34e-09 IIGTEEAYNV INREKLLQYLYSLK QPDGSFLMHV -RAM1_YEAST 330 4.59e-09 ILEAFGYGQC FNKHALRDYILYCC QEKEQPGLRD -CAL1_YEAST 126 1.65e-08 LRDYEYFETI LDKRSLARFVSKCQ RPDRGSFVSC -PFTB_RAT 268 1.65e-08 ALVILKKERS LNLKSLLQWVTSRQ MRFEGGFQGR -PFTB_RAT 220 1.65e-08 VASLTNIITP DLFEGTAEWIARCQ NWEGGIGGVP -RAM1_YEAST 229 2.54e-08 IATLLNILTE ELTEGVLNYLKNCQ NYEGGFGSCP -PFTB_RAT 330 4.58e-08 DPALSMSHWM FHQQALQEYILMCC QCPAGGLLDK -CAL1_YEAST 239 5.86e-08 LLSSLEKLSD KFKEDTITWLLHRQ VSSHGCMKFE -PFTB_RAT 121 1.52e-07 LELLDEPIPQ IVATDVCQFLELCQ SPDGGFGGGP -CAL1_YEAST 362 1.91e-07 IEGKFNGELC IPQEIFNDFSKRCC F -BET2_YEAST 107 4.34e-07 TYDALDVLGK DRKVRLISFIRGNQ LEDGSFQGDR -BET2_YEAST 155 5.01e-07 ALSILGELTS EVVDPAVDFVLKCY NFDGGFGLCP -RAM1_YEAST 180 5.78e-07 CDNIDGCWDR IDRKGIYQWLISLK EPNGGFKTCL --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 block diagrams --------------------------------------------------------------------------------- -SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -BET2_YEAST 4.3e-07 54_[2]_38_[2]_34_[2]_85_[2]_58 -RATRABGERB 1.6e-09 65_[2]_34_[2]_34_[2]_82_[2]_60 -RAM1_YEAST 5.8e-07 179_[2]_35_[2]_35_[2]_38_[2]_88 -CAL1_YEAST 5.9e-08 125_[2]_50_[2]_35_[2]_109_[2]_1 -PFTB_RAT 2.3e-09 120_[2]_37_[2]_34_[2]_34_[2]_48_ - [2]_94 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 in BLOCKS format --------------------------------------------------------------------------------- -BL MOTIF 2 width=14 seqs=21 -BET2_YEAST ( 254) INYEKLTEFILKCQ 1 -RATRABGERB ( 258) IDREKLRSFILACQ 1 -RATRABGERB ( 162) INVEKAIEFVLSCM 1 -RATRABGERB ( 66) MNKEEILVFIKSCQ 1 -RAM1_YEAST ( 278) INVEKLLEWSSARQ 1 -CAL1_YEAST ( 190) IDTEKLLGYIMSQQ 1 -BET2_YEAST ( 55) FVKEEVISFVLSCW 1 -RATRABGERB ( 114) INVDKVVAYVQSLQ 1 -PFTB_RAT ( 172) INREKLLQYLYSLK 1 -RAM1_YEAST ( 330) FNKHALRDYILYCC 1 -CAL1_YEAST ( 126) LDKRSLARFVSKCQ 1 -PFTB_RAT ( 268) LNLKSLLQWVTSRQ 1 -PFTB_RAT ( 220) DLFEGTAEWIARCQ 1 -RAM1_YEAST ( 229) ELTEGVLNYLKNCQ 1 -PFTB_RAT ( 330) FHQQALQEYILMCC 1 -CAL1_YEAST ( 239) KFKEDTITWLLHRQ 1 -PFTB_RAT ( 121) IVATDVCQFLELCQ 1 -CAL1_YEAST ( 362) IPQEIFNDFSKRCC 1 -BET2_YEAST ( 107) DRKVRLISFIRGNQ 1 -BET2_YEAST ( 155) EVVDPAVDFVLKCY 1 -RAM1_YEAST ( 180) IDRKGIYQWLISLK 1 -// - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 position-specific scoring matrix --------------------------------------------------------------------------------- -log-odds matrix: alength= 20 w= 14 n= 1835 bayes= 7.42721 E= 3.1e-019 - -180 -316 28 36 140 -376 -308 299 -24 -14 117 -265 -348 -268 -271 -280 -167 -65 -321 -275 - -149 -393 133 -139 -11 -301 50 -227 -104 -40 -165 317 0 -117 32 -189 -143 106 -363 -290 - -9 -383 -234 -146 -8 -309 -205 -210 224 -111 -154 -135 -277 119 160 -196 94 147 -356 0 - -174 -491 57 300 -396 -328 51 -351 95 -378 -243 -145 -289 50 33 -217 12 -38 -433 -348 - 61 -430 48 71 -335 60 -173 -37 243 -328 -192 -95 2 -80 41 27 -130 -250 -375 -291 - 55 -332 -507 -413 10 -422 -361 96 -365 194 -94 -334 -390 -340 -334 -331 92 167 -344 -304 - 61 19 -456 -363 -205 -378 -316 176 -315 118 -79 32 -352 14 98 -285 19 91 -309 10 - -6 -431 96 174 -336 -74 -174 -302 -67 -329 -193 61 -249 205 41 72 21 -37 -376 -291 - -585 -591 -675 -658 339 -654 -303 -494 -585 -478 -424 -461 -604 -498 -508 -576 -538 -496 362 282 - -333 -431 -610 -551 -351 -574 -548 290 -506 94 -192 -471 -535 -506 -502 6 -316 227 -516 -458 - -7 -410 -200 4 -314 -290 -182 -28 139 137 97 -106 -256 51 38 25 20 -221 -366 -4 - 61 -428 -188 -102 -334 -74 52 -298 141 -130 93 61 -249 -81 112 195 -129 -248 -374 -5 - -318 386 -431 -324 -470 -438 -297 -372 -61 20 -304 47 -439 41 186 -360 -300 -347 -474 -424 - -264 97 -402 -180 -325 -446 -118 -335 29 -335 49 -229 -343 411 -155 -328 -274 -317 47 -50 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- - Motif 2 position-specific probability matrix --------------------------------------------------------------------------------- -letter-probability matrix: alength= 20 w= 14 nsites= 21 E= 3.1e-019 - 0.000000 0.000000 0.095238 0.095238 0.142857 0.000000 0.000000 0.476190 0.047619 0.095238 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 - 0.000000 0.000000 0.190476 0.000000 0.047619 0.000000 0.047619 0.000000 0.000000 0.095238 0.000000 0.380952 0.047619 0.000000 0.047619 0.000000 0.000000 0.142857 0.000000 0.000000 - 0.047619 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.285714 0.047619 0.000000 0.000000 0.000000 0.095238 0.142857 0.000000 0.095238 0.190476 0.000000 0.047619 - 0.000000 0.000000 0.095238 0.571429 0.000000 0.000000 0.047619 0.000000 0.095238 0.000000 0.000000 0.000000 0.000000 0.047619 0.047619 0.000000 0.047619 0.047619 0.000000 0.000000 - 0.095238 0.000000 0.095238 0.095238 0.000000 0.142857 0.000000 0.047619 0.333333 0.000000 0.000000 0.000000 0.047619 0.000000 0.047619 0.095238 0.000000 0.000000 0.000000 0.000000 - 0.095238 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.095238 0.000000 0.476190 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.095238 0.190476 0.000000 0.000000 - 0.095238 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.190476 0.000000 0.285714 0.000000 0.047619 0.000000 0.047619 0.095238 0.000000 0.047619 0.095238 0.000000 0.047619 - 0.047619 0.000000 0.142857 0.238095 0.000000 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.047619 0.000000 0.190476 0.047619 0.142857 0.047619 0.047619 0.000000 0.000000 - 0.000000 0.000000 0.000000 0.000000 0.476190 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.238095 0.285714 - 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.380952 0.000000 0.238095 0.000000 0.000000 0.000000 0.000000 0.000000 0.095238 0.000000 0.285714 0.000000 0.000000 - 0.047619 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.047619 0.142857 0.380952 0.047619 0.000000 0.000000 0.047619 0.047619 0.095238 0.047619 0.000000 0.000000 0.047619 - 0.095238 0.000000 0.000000 0.000000 0.000000 0.047619 0.047619 0.000000 0.142857 0.047619 0.047619 0.047619 0.000000 0.000000 0.095238 0.380952 0.000000 0.000000 0.000000 0.047619 - 0.000000 0.619048 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.047619 0.000000 0.047619 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 - 0.000000 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.095238 0.000000 0.047619 0.000000 0.000000 0.619048 0.000000 0.000000 0.000000 0.000000 0.047619 0.047619 --------------------------------------------------------------------------------- - - - - - -Time 51.86 secs. - -******************************************************************************** - - -******************************************************************************** -SUMMARY OF MOTIFS -******************************************************************************** - --------------------------------------------------------------------------------- - Combined block diagrams: non-overlapping sites with p-value < 0.0001 --------------------------------------------------------------------------------- -SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM -------------- ---------------- ------------- -RAM1_YEAST 2.14e-20 144_[1(1.27e-16)]_5_[2(5.78e-07)]_4_[1(1.33e-13)]_1_[2(2.54e-08)]_4_[1(5.00e-17)]_1_[2(5.08e-11)]_4_[1(3.47e-16)]_4_[2(4.59e-09)]_5_[1(3.52e-13)]_35_[2(9.16e-05)]_4 -PFTB_RAT 2.44e-21 120_[2(1.52e-07)]_3_[1(4.30e-19)]_4_[2(2.34e-09)]_3_[1(2.81e-14)]_1_[2(1.65e-08)]_3_[1(1.15e-19)]_1_[2(1.65e-08)]_4_[1(3.17e-16)]_14_[2(4.58e-08)]_4_[1(4.30e-15)]_60 -BET2_YEAST 1.02e-27 6_[2(5.17e-05)]_3_[1(3.11e-10)]_1_[2(6.90e-10)]_4_[1(7.78e-14)]_4_[2(4.34e-07)]_3_[1(3.41e-17)]_1_[2(5.01e-07)]_3_[1(2.10e-18)]_21_[1(7.28e-22)]_1_[2(2.24e-13)]_4_[1(6.64e-17)]_24 -RATRABGERB 4.90e-26 65_[2(9.60e-12)]_3_[1(2.40e-14)]_1_[2(1.57e-09)]_3_[1(8.19e-19)]_1_[2(4.20e-12)]_3_[1(7.36e-19)]_18_[1(6.18e-21)]_1_[2(1.30e-12)]_4_[1(1.43e-17)]_26 -CAL1_YEAST 3.16e-22 125_[2(1.65e-08)]_50_[2(5.01e-10)]_1_[1(1.14e-13)]_4_[2(5.86e-08)]_22_[1(9.17e-20)]_22_[1(5.47e-13)]_5_[2(1.91e-07)]_1 --------------------------------------------------------------------------------- - -******************************************************************************** - - -******************************************************************************** -Stopped because nmotifs = 2 reached. -******************************************************************************** - -CPU: pmgm2 - -******************************************************************************** diff --git a/Tests/Motif/transfac.dat b/Tests/Motif/transfac.dat deleted file mode 100644 index 9287f8622e5..00000000000 --- a/Tests/Motif/transfac.dat +++ /dev/null @@ -1,31 +0,0 @@ -VV EXAMPLE January 15, 2013 -XX -// -ID motif1 -P0 A C G T -01 1 2 2 0 S -02 2 1 2 0 R -03 3 0 1 1 A -04 0 5 0 0 C -05 5 0 0 0 A -06 0 0 4 1 G -07 0 1 4 0 G -08 0 0 0 5 T -09 0 0 5 0 G -10 0 1 2 2 K -11 0 2 0 3 Y -12 1 0 3 1 G -// -ID motif2 -P0 A C G T -01 2 1 2 0 R -02 1 2 2 0 S -03 0 5 0 0 C -04 3 0 1 1 A -05 0 0 4 1 G -06 5 0 0 0 A -07 0 1 4 0 G -08 0 0 5 0 G -09 0 0 0 5 T -10 0 2 0 3 Y -//

fidals__shopelectro-422

helpers.py:58-59: Move selenium timeout to env var. stb2... The puzzle `371-6673a075` from #371 has to be resolved: https://github.com/fidals/shopelectro/blob/7d319f81942692c16105a8f8703e483a7067f1ef/shopelectro/tests/helpers.py#L58-L59 The puzzle was created by duker33 on 19-Jun-18. Estimate: 15 minutes, If you have any technical questions, don't ask me, submit new tickets instead. The task will be "done" when the problem is fixed and the text of the puzzle is _removed_ from the source code. Here is more about [PDD](http://www.yegor256.com/2009/03/04/pdd.html) and [about me](http://www.yegor256.com/2017/04/05/pdd-in-action.html).

[ { "content": "\"\"\"\nDjango settings for shopelectro project.\n\nGenerated by 'django-admin startproject' using Django 1.9.5.\n\nFor more information on this file, see\nhttps://docs.djangoproject.com/en/1.9/topics/settings/\n\nFor the full list of settings and their values, see\nhttps://docs.djangoproject.com/...

diff --git a/.drone.yml b/.drone.yml index c484de09..4c4cde5e 100644 --- a/.drone.yml +++ b/.drone.yml @@ -173,10 +173,13 @@ services: selenium: image: selenium/standalone-chrome-debug:3.10.0 - environment: # https://github.com/SeleniumHQ/docker-selenium/issues/392 + environment: + # https://github.com/SeleniumHQ/docker-selenium/issues/392 - DBUS_SESSION_BUS_ADDRESS=/dev/null - SCREEN_WIDTH=1366 - SCREEN_HEIGHT=768 + - SELENIUM_WAIT_SECONDS=${SELENIUM_WAIT_SECONDS} + - SELENIUM_TIMEOUT_SECONDS=${SELENIUM_TIMEOUT_SECONDS} shm_size: 4G volumes: # https://github.com/SeleniumHQ/docker-selenium#running-the-images - /dev/shm:/dev/shm diff --git a/docker/env_files/app.dist b/docker/env_files/app.dist index c957a6d2..7cb27a0a 100644 --- a/docker/env_files/app.dist +++ b/docker/env_files/app.dist @@ -16,3 +16,6 @@ REDIS_URL=redis REDIS_PORT=6379 RABBITMQ_URL=rabbitmq RABBITMQ_PORT=5672 + +SELENIUM_WAIT_SECONDS=60 +SELENIUM_TIMEOUT_SECONDS=30 diff --git a/shopelectro/settings/base.py b/shopelectro/settings/base.py index 9c9b4d31..11b21f27 100644 --- a/shopelectro/settings/base.py +++ b/shopelectro/settings/base.py @@ -217,6 +217,8 @@ } SELENIUM_URL = os.environ.get('SELENIUM_URL', 'http://selenium:4444/wd/hub') +SELENIUM_WAIT_SECONDS = int(os.environ.get('SELENIUM_WAIT_SECONDS', 60)) +SELENIUM_TIMEOUT_SECONDS = int(os.environ.get('SELENIUM_TIMEOUT_SECONDS', 30)) SITE_CREATED = datetime(2013, 1, 1) diff --git a/shopelectro/tests/helpers.py b/shopelectro/tests/helpers.py index 30b37f6c..4bf99770 100644 --- a/shopelectro/tests/helpers.py +++ b/shopelectro/tests/helpers.py @@ -58,9 +58,9 @@ def setUpClass(cls): ) # @todo #371:15m Move selenium timeout to env var. stb2 # To be able to change it from drone without touching code. - cls.wait = WebDriverWait(cls.browser, 60) + cls.wait = WebDriverWait(cls.browser, settings.SELENIUM_WAIT_SECONDS) cls.browser.implicitly_wait(30) - cls.browser.set_page_load_timeout(30) + cls.browser.set_page_load_timeout(settings.SELENIUM_TIMEOUT_SECONDS) # Fresh created browser failures on maximizing window. # This bug is won't fixed by selenium guys https://goo.gl/6Ttguf # Ohh, so selenium is so selenium ...

feast-dev__feast-3904

Table in Postgres OnlineStore is not populated after calling `materialize` ## Expected Behavior When calling the `materialize` functionality to materialize data from a `SnowflakeSource` offline store to a local `PostgreSQLOnlineStore`, the table is not populated with the data. ## Current Behavior The feature table in the local Postgres instance is not populated, while no exception is raised, and from the logs it seems like the data should be pushed to Postgres. ## Steps to reproduce 1) Use this feature_store.yaml file: ``` project: my_project provider: local registry: registry_type: sql path: postgresql://postgres:test@0.0.0.0:5432/feature_store cache_ttl_seconds: 60 online_store: type: postgres host: 0.0.0.0 port: 5432 database: feature_store db_schema: public user: postgres password: test offline_store: <SNOWFLAKE_INFORMATION> entity_key_serialization_version: 2 ``` 2) Spin up this docker-compose file: ``` --- version: "3" services: db: restart: always image: postgres:15-alpine container_name: feast_db ports: - "5432:5432" volumes: - ~/feast_postgres_data:/var/lib/postgresql/data environment: - POSTGRES_DB=feature_store - POSTGRES_USER=postgres - POSTGRES_PASSWORD=test volumes: feast_postgres_data: null ``` 3) Initialize the Entities, SnowflakeSource (or another source), FeatureView, and FeatureService, and apply these. All using the Python SDK. ``` from datetime import timedelta from feast import ( Entity, FeatureService, FeatureView, Field, SnowflakeSource, ValueType, FeatureStore, ) from feast.types import Float32 feature_store = FeatureStore() entity = Entity( name="entity", join_keys=["entity_ID"], value_type=ValueType.STRING, ) source = SnowflakeSource( name="snowflake_source_name", timestamp_field="EVENT_TIMESTAMP", schema="TEMP", table="TABLE" ) feature_view = FeatureView( name="feature_view_name", entities=[entity], ttl=timedelta(days=0), schema=[ Field(name="feature_1", dtype=Float32), Field(name="feature_2", dtype=Float32), ], online=True, source=source, tags={"team": "team"}, ) feature_service = FeatureService( name="feature_service", features=[feature_view], ) feature_store.apply( [ entity, source, feature_view, feature_service, ] ) ``` 4) Run materialize commands using the Python SDK ``` feature_store = FeatureStore() feature_store.materialize( start_date=datetime.utcnow() - timedelta(weeks=52), end_date=datetime.utcnow(), feature_views=["feature_view_name"], ) ``` ### Specifications - Version: 0.35.0 - Platform: Local MacBook M1 ## Possible Solution It seems like a `conn.commit()` statement is missing in the `online_write_batch` method of the `PostgreSQLOnlineStore`. Specifically, on [this line](https://github.com/feast-dev/feast/blob/master/sdk/python/feast/infra/online_stores/contrib/postgres.py#L102). After adding this, the table is populated. The PR implementing this proposed fix can be found [here](https://github.com/feast-dev/feast/pull/3904). ## Additional notes When replacing the the postgres online store with the following sqlite online store in the config file, everything works without any code changes ``` online_store: type: sqlite path: data/online_store.db ```

[ { "content": "import contextlib\nimport logging\nfrom collections import defaultdict\nfrom datetime import datetime\nfrom typing import Any, Callable, Dict, List, Optional, Sequence, Tuple\n\nimport psycopg2\nimport pytz\nfrom psycopg2 import sql\nfrom psycopg2.extras import execute_values\nfrom psycopg2.pool i...

diff --git a/sdk/python/feast/infra/online_stores/contrib/postgres.py b/sdk/python/feast/infra/online_stores/contrib/postgres.py index a12e66f1090..49f87ddb0ae 100644 --- a/sdk/python/feast/infra/online_stores/contrib/postgres.py +++ b/sdk/python/feast/infra/online_stores/contrib/postgres.py @@ -99,6 +99,7 @@ def online_write_batch( cur_batch, page_size=batch_size, ) + conn.commit() if progress: progress(len(cur_batch))

netbox-community__netbox-15568

Typo in Tag model ### Deployment Type Self-hosted ### NetBox Version v3.7.4 ### Python Version 3.8 ### Steps to Reproduce Typo in help_text where "this" is mistakenly repeated. https://github.com/netbox-community/netbox/blob/69c0aac1051015660133b2ae3c86607dabd8084b/netbox/extras/models/tags.py#L40 ### Expected Behavior The object type(s) to which this tag can be applied. ### Observed Behavior The object type(s) to which this this tag can be applied.

[ { "content": "from django.conf import settings\nfrom django.db import models\nfrom django.urls import reverse\nfrom django.utils.text import slugify\nfrom django.utils.translation import gettext_lazy as _\nfrom taggit.models import TagBase, GenericTaggedItemBase\n\nfrom netbox.models import ChangeLoggedModel\nf...

diff --git a/netbox/extras/models/tags.py b/netbox/extras/models/tags.py index 3aba6df60ab..97b9087c593 100644 --- a/netbox/extras/models/tags.py +++ b/netbox/extras/models/tags.py @@ -37,7 +37,7 @@ class Tag(CloningMixin, ExportTemplatesMixin, ChangeLoggedModel, TagBase): to='contenttypes.ContentType', related_name='+', blank=True, - help_text=_("The object type(s) to which this this tag can be applied.") + help_text=_("The object type(s) to which this tag can be applied.") ) clone_fields = (

cisagov__manage.get.gov-726

Create a Staging Environment in Cloud.gov ### User Story Developers and Reviewers require a Staging environment in cloud.gov to support using stable as prod. ### Acceptance Criteria Update the environment creation script to produce and maintain a cloud.gov staging environment. ### Additional Context (optional) _No response_ ### Issue Links (optional) _No response_

[ { "content": "\"\"\"\nDjango settings for .gov registrar project.\n\nFor more information on this file, see\nhttps://docs.djangoproject.com/en/4.0/topics/settings/\n\nFor the full list of settings and their values, see\nhttps://docs.djangoproject.com/en/4.0/ref/settings/\n\nIF you'd like to see all of these set...

diff --git a/.github/ISSUE_TEMPLATE/developer-onboarding.md b/.github/ISSUE_TEMPLATE/developer-onboarding.md index 74af9ef60..92ae9e3a1 100644 --- a/.github/ISSUE_TEMPLATE/developer-onboarding.md +++ b/.github/ISSUE_TEMPLATE/developer-onboarding.md @@ -83,6 +83,6 @@ export GPG_TTY ## Setting up developer sandbox -We have two types of environments: stable, and sandbox. Stable gets deployed via tagged release every sprint, and developer sandboxes are given to get.gov developers to mess around in a production-like environment without disrupting stable. Each sandbox is namespaced and will automatically be deployed too when the appropriate branch syntax is used for that space in an open pull request. There are several things you need to setup to make the sandbox work for a developer. +We have three types of environments: stable, staging, and sandbox. Stable (production)and staging (pre-prod) get deployed via tagged release, and developer sandboxes are given to get.gov developers to mess around in a production-like environment without disrupting stable or staging. Each sandbox is namespaced and will automatically be deployed too when the appropriate branch syntax is used for that space in an open pull request. There are several things you need to setup to make the sandbox work for a developer. All automation for setting up a developer sandbox is documented in the scripts for [creating a developer sandbox](../../ops/scripts/create_dev_sandbox.sh) and [removing a developer sandbox](../../ops/scripts/destroy_dev_sandbox.sh). A Cloud.gov organization administrator will have to perform the script in order to create the sandbox. diff --git a/.github/workflows/deploy-staging.yaml b/.github/workflows/deploy-staging.yaml new file mode 100644 index 000000000..068751c30 --- /dev/null +++ b/.github/workflows/deploy-staging.yaml @@ -0,0 +1,41 @@ +# This workflow runs on pushes of tagged commits. +# "Releases" of tagged commits will deploy selected branch to staging. + +name: Build and deploy staging for tagged release + +on: + push: + paths-ignore: + - 'docs/**' + - '**.md' + - '.gitignore' + + tags: + - staging-* + +jobs: + deploy-staging: + if: ${{ github.ref_type == 'tag' }} + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + + - name: Compile USWDS assets + working-directory: ./src + run: | + docker compose run node npm install && + docker compose run node npx gulp copyAssets && + docker compose run node npx gulp compile + - name: Collect static assets + working-directory: ./src + run: docker compose run app python manage.py collectstatic --no-input + - name: Deploy to cloud.gov sandbox + uses: 18f/cg-deploy-action@main + env: + DEPLOY_NOW: thanks + with: + cf_username: ${{ secrets.CF_STAGING_USERNAME }} + cf_password: ${{ secrets.CF_STAGING_PASSWORD }} + cf_org: cisa-getgov-prototyping + cf_space: staging + push_arguments: "-f ops/manifests/manifest-staging.yaml" diff --git a/.github/workflows/migrate.yaml b/.github/workflows/migrate.yaml index 574ec9fa0..28447a605 100644 --- a/.github/workflows/migrate.yaml +++ b/.github/workflows/migrate.yaml @@ -14,6 +14,7 @@ on: description: Which environment should we run migrations for? options: - stable + - staging - gd - rb - ko diff --git a/.github/workflows/reset-db.yaml b/.github/workflows/reset-db.yaml index 4b9a9eafb..0d3ed4934 100644 --- a/.github/workflows/reset-db.yaml +++ b/.github/workflows/reset-db.yaml @@ -15,6 +15,7 @@ on: description: Which environment should we flush and re-load data for? options: - stable + - staging - gd - rb - ko diff --git a/docs/developer/database-access.md b/docs/developer/database-access.md index 9d615c477..859ef2fd6 100644 --- a/docs/developer/database-access.md +++ b/docs/developer/database-access.md @@ -42,10 +42,9 @@ Optionally, load data from fixtures as well cf run-task getgov-ENVIRONMENT --wait --command 'python manage.py load' --name loaddata ``` -For the `stable` environment, developers don't have credentials so we need to -run that command using Github Actions. Go to +For the `stable` or `staging` environments, developers don't have credentials so we need to run that command using Github Actions. Go to <https://github.com/cisagov/getgov/actions/workflows/migrate.yaml> and select -the "Run workflow" button, making sure that `stable` is selected. +the "Run workflow" button, making sure that `stable` or `staging` depending on which envirornment you desire to update. ## Getting data for fixtures diff --git a/docs/operations/README.md b/docs/operations/README.md index e9d67a5af..e4ab64135 100644 --- a/docs/operations/README.md +++ b/docs/operations/README.md @@ -35,7 +35,9 @@ Binding the database in `manifest-<ENVIRONMENT>.json` automatically inserts the # Deploy -We have two types of environments: developer "sandboxes" and `stable`. Developers can deploy locally to their sandbox whenever they want. However, only our CD service can deploy to `stable`, and it does so when we make tagged releases of `main`. This is to ensure that we have a "golden" environment to point to, and can still test things out in a sandbox space. You should make sure all of the USWDS assets are compiled and collected before deploying to your sandbox. To deploy locally to `sandbox`: +We have three types of environments: developer "sandboxes", `staging` and `stable`. Developers can deploy locally to their sandbox whenever they want. However, only our CD service can deploy to `staging` and `stable`, and it does so when we make tagged releases of `main`. For `staging`, this is done to ensure there is a non-production level test envirornment that can be used for user testing or for testing code before it is pushed to `stable`. `Staging` can be especially helpful when testing database changes or migrations that could have adververse affects in `stable`. On the other hand, `stable` is used to ensure that we have a "golden" environment to point to. We can refer to `stable` as our production environment and `staging` as our pre-production (pre-prod) environment. As such, code on main should always be tagged for `staging` before it is tagged for `stable`. + +You should make sure all of the USWDS assets are compiled and collected before deploying to your sandbox. To deploy locally to `sandbox`: For ease of use, you can run the `deploy.sh <sandbox name>` script in the `/src` directory to build the assets and deploy to your sandbox. Similarly, you could run `build.sh <sandbox name>` script to just compile and collect the assets without deploying. diff --git a/ops/manifests/manifest-staging.yaml b/ops/manifests/manifest-staging.yaml new file mode 100644 index 000000000..93c44071c --- /dev/null +++ b/ops/manifests/manifest-staging.yaml @@ -0,0 +1,29 @@ +--- +applications: +- name: getgov-staging + buildpacks: + - python_buildpack + path: ../../src + instances: 1 + memory: 512M + stack: cflinuxfs4 + timeout: 180 + command: ./run.sh + health-check-type: http + health-check-http-endpoint: /health + env: + # Send stdout and stderr straight to the terminal without buffering + PYTHONUNBUFFERED: yup + # Tell Django where to find its configuration + DJANGO_SETTINGS_MODULE: registrar.config.settings + # Tell Django where it is being hosted + DJANGO_BASE_URL: https://getgov-staging.app.cloud.gov + # Tell Django how much stuff to log + DJANGO_LOG_LEVEL: INFO + # default public site location + GETGOV_PUBLIC_SITE_URL: https://beta.get.gov + routes: + - route: getgov-staging.app.cloud.gov + services: + - getgov-credentials + - getgov-staging-database diff --git a/ops/scripts/create_dev_sandbox.sh b/ops/scripts/create_dev_sandbox.sh index df10d8d90..f180ada8d 100755 --- a/ops/scripts/create_dev_sandbox.sh +++ b/ops/scripts/create_dev_sandbox.sh @@ -43,7 +43,7 @@ cp ops/scripts/manifest-sandbox-template.yaml ops/manifests/manifest-$1.yaml sed -i '' "s/ENVIRONMENT/$1/" "ops/manifests/manifest-$1.yaml" echo "Adding new environment to settings.py..." -sed -i '' '/getgov-stable.app.cloud.gov/ {a\ +sed -i '' '/getgov-staging.app.cloud.gov/ {a\ '\"getgov-$1.app.cloud.gov\"', }' src/registrar/config/settings.py @@ -65,7 +65,7 @@ done echo "Creating new cloud.gov credentials for $1..." django_key=$(python3 -c 'from django.core.management.utils import get_random_secret_key; print(get_random_secret_key())') openssl req -nodes -x509 -days 365 -newkey rsa:2048 -keyout private-$1.pem -out public-$1.crt -login_key=$(base64 private-$1.pem) +login_key=$(base64 -i private-$1.pem) jq -n --arg django_key "$django_key" --arg login_key "$login_key" '{"DJANGO_SECRET_KEY":$django_key,"DJANGO_SECRET_LOGIN_KEY":$login_key}' > credentials-$1.json cf cups getgov-credentials -p credentials-$1.json @@ -105,11 +105,11 @@ echo echo "Moving on to setup Github automation..." echo "Adding new environment to Github Actions..." -sed -i '' '/ - stable/ {a\ +sed -i '' '/ - staging/ {a\ - '"$1"' }' .github/workflows/reset-db.yaml -sed -i '' '/ - stable/ {a\ +sed -i '' '/ - staging/ {a\ - '"$1"' }' .github/workflows/migrate.yaml diff --git a/src/registrar/config/settings.py b/src/registrar/config/settings.py index 15f8b45a9..4710b0c65 100644 --- a/src/registrar/config/settings.py +++ b/src/registrar/config/settings.py @@ -564,6 +564,7 @@ # web server configurations. ALLOWED_HOSTS = [ "getgov-stable.app.cloud.gov", + "getgov-staging.app.cloud.gov", "getgov-gd.app.cloud.gov", "getgov-rb.app.cloud.gov", "getgov-ko.app.cloud.gov",

yt-project__yt-2226

get_yt_version not working in Python 3 ### Bug report Running `yt.get_yt_version` shows the following behavior. ``` >>> import yt >>> yt.get_yt_version() Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/britton/Documents/work/yt/yt/yt/funcs.py", line 652, in get_yt_version return version[:12].strip().decode('utf-8') AttributeError: 'str' object has no attribute 'decode' ``` This is on the yt dev tip with Python 3.7.1. I can take care of this, but not at the moment. I'm making this issue so I don't forget.

[ { "content": "\"\"\"\nUseful functions. If non-original, see function for citation.\n\n\n\n\"\"\"\nfrom __future__ import print_function\n\n#-----------------------------------------------------------------------------\n# Copyright (c) 2013, yt Development Team.\n#\n# Distributed under the terms of the Modifie...

diff --git a/yt/funcs.py b/yt/funcs.py index eefe83cd1b2..b8b1d6e7f68 100644 --- a/yt/funcs.py +++ b/yt/funcs.py @@ -649,7 +649,10 @@ def get_yt_version(): if version is None: return version else: - return version[:12].strip().decode('utf-8') + v_str = version[:12].strip() + if hasattr(v_str, 'decode'): + v_str = v_str.decode('utf-8') + return v_str def get_version_stack(): version_info = {}

ansible-collections__community.general-7875

community.general.incus connection not working as inventory_hostname treated as litteral ### Summary In my environment I am connecting to an incus server via a remote client on OSX. Ansible, running on the OSX machine is utilizing roles, and gets the inventory_hostname from the filename under the host_vars directory. I suspect this environment is causing inventory_hostname to be treated as a litteral. A very similar bug was fixed community.general.lxd and be found here: https://github.com/ansible-collections/community.general/pull/4912 I have already implemented the solution and will submit a pull request. ### Issue Type Bug Report ### Component Name incus.py connection plugin ### Ansible Version ```console (paste below) ansible [core 2.16.2] config file = /Users/travis/workspace/IZUMANETWORKS/siteinfra/Ansible/work/ansible.cfg configured module search path = ['/Users/travis/.ansible/plugins/modules', '/usr/share/ansible/plugins/modules'] ansible python module location = /opt/homebrew/lib/python3.11/site-packages/ansible ansible collection location = /Users/travis/.ansible/collections:/usr/share/ansible/collections executable location = /opt/homebrew/bin/ansible python version = 3.11.7 (main, Dec 4 2023, 18:10:11) [Clang 15.0.0 (clang-1500.1.0.2.5)] (/opt/homebrew/opt/python@3.11/bin/python3.11) jinja version = 3.1.2 libyaml = True ``` ### Community.general Version ```console (paste below) $ ansible-galaxy collection list community.general # /Users/travis/.ansible/collections/ansible_collections Collection Version ----------------- ------- community.general 8.2.0 ``` ### Configuration ```console (paste below) $ ansible-config dump --only-changed CONFIG_FILE() = /Users/travis/workspace/IZUMANETWORKS/siteinfra/Ansible/work/ansible.cfg DEFAULT_HASH_BEHAVIOUR(/Users/travis/workspace/IZUMANETWORKS/siteinfra/Ansible/work/ansible.cfg) = merge DEFAULT_HOST_LIST(/Users/travis/workspace//IZUMANETWORKS/siteinfra/Ansible/work/ansible.cfg) = ['/Users/travis/workspace/IZUMANETWORKS/siteinfra/Ansible/work/ansible.cfg) = ['/Users/travis/workspace/IZUMANETWORKS/siteinfra/Ansible/work/inventory.ini'] EDITOR(env: EDITOR) = emacs HOST_KEY_CHECKING(/Users/travis/workspace/IZUMANETWORKS/siteinfra/Ansible/work/ansible.cfg) = False ``` ### OS / Environment client: OSX server: Ubuntu 22.04 ### Steps to Reproduce  ```yaml (paste below) # host_var file named IzumaMercury.yaml ansible_connection: community.general.incus ansible_user: root ansible_become: no ansible_incus_remote: IzumaExplorer ``` ### Expected Results ansible-playbook -i inventories/tests/moffett.yaml setup_izuma_networks_vm_controllers_workers.yml PLAY [vm_controllers] **************************************************************************************************** TASK [Gathering Facts] *************************************************************************************************** ok: [IzumaMercury] ### Actual Results ```console (paste below) ansible-playbook -i inventories/tests/moffett.yaml setup_izuma_networks_vm_controllers_workers.yml PLAY [vm_controllers] **************************************************************************************************** TASK [Gathering Facts] *************************************************************************************************** [WARNING]: The "community.general.incus" connection plugin has an improperly configured remote target value, forcing "inventory_hostname" templated value instead of the string fatal: [IzumaMercury]: UNREACHABLE! => {"changed": false, "msg": "instance not found: inventory_hostname", "unreachable": true} ``` ### Code of Conduct - [X] I agree to follow the Ansible Code of Conduct

[ { "content": "# -*- coding: utf-8 -*-\n# Based on lxd.py (c) 2016, Matt Clay <matt@mystile.com>\n# (c) 2023, Stephane Graber <stgraber@stgraber.org>\n# Copyright (c) 2023 Ansible Project\n# GNU General Public License v3.0+ (see LICENSES/GPL-3.0-or-later.txt or https://www.gnu.org/licenses/gpl-3.0.txt)\n# SPDX-L...

diff --git a/changelogs/fragments/7874-incus_connection_treats_inventory_hostname_as_literal_in_remotes.yml b/changelogs/fragments/7874-incus_connection_treats_inventory_hostname_as_literal_in_remotes.yml new file mode 100644 index 00000000000..83d302e9b9a --- /dev/null +++ b/changelogs/fragments/7874-incus_connection_treats_inventory_hostname_as_literal_in_remotes.yml @@ -0,0 +1,2 @@ +bugfixes: + - "incus connection plugin - treats ``inventory_hostname`` as a variable instead of a literal in remote connections (https://github.com/ansible-collections/community.general/issues/7874)." diff --git a/plugins/connection/incus.py b/plugins/connection/incus.py index f346d06170f..81d6f971c70 100644 --- a/plugins/connection/incus.py +++ b/plugins/connection/incus.py @@ -21,6 +21,7 @@ - The instance identifier. default: inventory_hostname vars: + - name: inventory_hostname - name: ansible_host - name: ansible_incus_host executable:

pennersr__django-allauth-2987

Update Facebook complete login Users may want to create custom provider which extends FacebookProvider and set custom provider_id. For example ``` from allauth.socialaccount.providers.facebook.provider import FacebookProvider class FacebookGroupProvider(FacebookProvider): id = "facebook_group" name = "Facebook Group" provider_classes = [FacebookGroupProvider] ``` The problem is in this case social account will be created with FacebookProvider.id instead of custom provider_id. https://github.com/pennersr/django-allauth/blob/master/allauth/socialaccount/providers/facebook/views.py#L66 https://github.com/pennersr/django-allauth/blob/master/allauth/socialaccount/providers/facebook/views.py#L38 https://github.com/pennersr/django-allauth/blob/master/allauth/socialaccount/providers/facebook/views.py#L49 https://github.com/pennersr/django-allauth/blob/master/allauth/socialaccount/providers/base.py#L63 https://github.com/pennersr/django-allauth/blob/master/allauth/socialaccount/providers/base.py#L86 I think we don't need to update [login_by_token](https://github.com/pennersr/django-allauth/blob/master/allauth/socialaccount/providers/facebook/views.py#L73) function for custom provider. Because we use this function for Facebook login purpose.

[ { "content": "import hashlib\nimport hmac\nimport logging\nimport requests\nfrom datetime import timedelta\n\nfrom django.utils import timezone\n\nfrom allauth.socialaccount import app_settings, providers\nfrom allauth.socialaccount.helpers import (\n complete_social_login,\n render_authentication_error,\...

diff --git a/allauth/socialaccount/providers/facebook/views.py b/allauth/socialaccount/providers/facebook/views.py index d74bd36f78..002fd3cdc4 100644 --- a/allauth/socialaccount/providers/facebook/views.py +++ b/allauth/socialaccount/providers/facebook/views.py @@ -35,7 +35,7 @@ def compute_appsecret_proof(app, token): def fb_complete_login(request, app, token): - provider = providers.registry.by_id(FacebookProvider.id, request) + provider = providers.registry.by_id(app.provider, request) resp = requests.get( GRAPH_API_URL + "/me", params={

googleapis__python-bigquery-802

ChunkedEncodingError is not retried when fetching data with list_rows() Original issue: https://github.com/googleapis/python-bigquery-storage/issues/242 A user reported that they saw an error in production when fetching table data with `Client.list_rows()`. That method uses the [default retry object](https://github.com/googleapis/python-bigquery/blob/7e0e2bafc4c3f98a4246100f504fd78a01a28e7d/google/cloud/bigquery/retry.py#L49), which currently does not consider `requests.exceptions.ChunkedEncodingError` retryable. (it does retry `requests.exceptions.ConnectionError`, but `ChunkedEncodingError` is not a subclass of that.

[ { "content": "# Copyright 2018 Google LLC\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by applicabl...

diff --git a/google/cloud/bigquery/retry.py b/google/cloud/bigquery/retry.py index 5e9075fe1..2df4de08b 100644 --- a/google/cloud/bigquery/retry.py +++ b/google/cloud/bigquery/retry.py @@ -27,6 +27,7 @@ exceptions.TooManyRequests, exceptions.InternalServerError, exceptions.BadGateway, + requests.exceptions.ChunkedEncodingError, requests.exceptions.ConnectionError, auth_exceptions.TransportError, ) diff --git a/tests/unit/test_retry.py b/tests/unit/test_retry.py index 0bef1e5e1..6fb7f93fd 100644 --- a/tests/unit/test_retry.py +++ b/tests/unit/test_retry.py @@ -51,6 +51,10 @@ def test_w_unstructured_requests_connectionerror(self): exc = requests.exceptions.ConnectionError() self.assertTrue(self._call_fut(exc)) + def test_w_unstructured_requests_chunked_encoding_error(self): + exc = requests.exceptions.ChunkedEncodingError() + self.assertTrue(self._call_fut(exc)) + def test_w_auth_transporterror(self): from google.auth.exceptions import TransportError

hylang__hy-320

hy raises ImportError out of the box This is on Python 2.6. May be related to #37 I think `hy` should probably install the `importlib` dependency at installation time, or the docs should state clearly that `importlib` needs to be installed ahead of time. Or, (worst case) state that Python 2.6 is not supported. ``` (env)09:52:13 Python (master) > hy Traceback (most recent call last): File "/Users/jacobsen/env/bin/hy", line 9, in <module> load_entry_point('hy==0.9.10', 'console_scripts', 'hy')() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pkg_resources.py", line 343, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pkg_resources.py", line 2354, in load_entry_point return ep.load() File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pkg_resources.py", line 2060, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/jacobsen/Programming/Python/hy/hy/__init__.py", line 37, in <module> import hy.importer # NOQA File "/Users/jacobsen/Programming/Python/hy/hy/importer.py", line 22, in <module> from hy.compiler import hy_compile File "/Users/jacobsen/Programming/Python/hy/hy/compiler.py", line 44, in <module> import importlib ImportError: No module named importlib (env)09:52:13 Python (master) > pip install importlib Downloading/unpacking importlib Downloading importlib-1.0.2.tar.bz2 Running setup.py egg_info for package importlib Installing collected packages: importlib Running setup.py install for importlib Successfully installed importlib Cleaning up... (env)09:52:21 Python (master) > hy hy 0.9.10 => ```

[ { "content": "#!/usr/bin/env python\n# Copyright (c) 2012, 2013 Paul Tagliamonte <paultag@debian.org>\n#\n# Permission is hereby granted, free of charge, to any person obtaining a\n# copy of this software and associated documentation files (the \"Software\"),\n# to deal in the Software without restriction, incl...

diff --git a/setup.py b/setup.py index f3e181456..24621eed5 100755 --- a/setup.py +++ b/setup.py @@ -48,6 +48,7 @@ install_requires = ['rply>=0.6.2'] if sys.version_info[:2] < (2, 7): install_requires.append('argparse>=1.2.1') + install_requires.append('importlib>=1.0.2') if os.name == 'nt': install_requires.append('pyreadline==2.0')

DDMAL__CantusDB-566

On Chant Detail page, in the Source Navigation sidebar, indicate current chant Currently, on the chant detail page, there is a sidebar that lists the chants on the current folio as well as on nearby folios. In the sidebar, there is no indication of which chant is currently being displayed: ![Screen Shot 2022-12-15 at 1 19 53 PM](https://user-images.githubusercontent.com/58090591/207939496-fdcb9a9a-1fa2-4dc3-a447-7c0d89b771bf.png) It might be helpful if we visually indicated somehow the chant that is currently being displayed. Possible options: 1. Bold it 2. make it not be a link 3. add a little arrow pointing to the chant 4. a combination of 2. and 3., or maybe all three of the options above. For example, here's a quick mockup of option 4: ![Screen Shot 2022-12-15 at 1 34 09 PM](https://user-images.githubusercontent.com/58090591/207940198-55b1d25e-f5f8-4bb7-af0a-9299d4d6c081.png)

[ { "content": "from latin_syllabification import syllabify_word\nfrom itertools import zip_longest\n\n\"\"\"\nsome useful info taken from the text entry guideline:\nthe symbols are present only in the MS spelling, not std spelling\nvertical stroke | identifies sections within a chant, it's meant to help align te...

diff --git a/django/cantusdb_project/align_text_mel.py b/django/cantusdb_project/align_text_mel.py index b7e1e1db6..fcac31f7e 100644 --- a/django/cantusdb_project/align_text_mel.py +++ b/django/cantusdb_project/align_text_mel.py @@ -155,7 +155,6 @@ def syllabize_melody(volpiano): # remove the trailing "--" (added in previous line) from the last syllable syls[-1] = syls[-1][:-2] syls_melody.append(syls) - # print(syls_melody) return syls_melody diff --git a/django/cantusdb_project/articles/templates/article_detail.html b/django/cantusdb_project/articles/templates/article_detail.html index 1966b801d..d2da28206 100644 --- a/django/cantusdb_project/articles/templates/article_detail.html +++ b/django/cantusdb_project/articles/templates/article_detail.html @@ -1,17 +1,18 @@ {% extends "base.html" %} {% block content %} +<title>{{ article.title }} | Cantus Manuscript Database</title> <div class="mr-3 p-3 col-md-12 bg-white rounded"> <object align="right" class="search-bar"> {% include "global_search_bar.html" %} </object> <h3> - {{article.title}} + {{ article.title }} </h3> <div class="row"> <div class="col"> <div class="container"> <div class="container text-wrap"> - <small>Submitted by <a href="{{ article.author.get_absolute_url }}">{{ article.author }}</a> on {{ article.date_created|date:"D, m/d/Y - H:i" }}</small> + <small>Submitted by <a href="{% url 'user-detail' article.author.id %}">{{ article.author }}</a> on {{ article.date_created|date:"D, m/d/Y - H:i" }}</small> <div style="padding-top: 1em;"> {{ article.body.html|safe }} </div> diff --git a/django/cantusdb_project/articles/templates/article_list.html b/django/cantusdb_project/articles/templates/article_list.html index 3c6aa2eec..ad2120c6b 100644 --- a/django/cantusdb_project/articles/templates/article_list.html +++ b/django/cantusdb_project/articles/templates/article_list.html @@ -1,5 +1,6 @@ {% extends "base.html" %} {% block content %} +<title>What's New | Cantus Manuscript Database</title> <div class="mr-3 p-3 col-md-10 mx-auto bg-white rounded"> <object align="right" class="search-bar"> {% include "global_search_bar.html" %} @@ -10,7 +11,7 @@ <h3>What's New</h3> <div class="col"> <small>{{ article.date_created|date:"D, m/d/Y - H:i" }}</small> <h4> - <a href="{{ article.get_absolute_url }}">{{ article.title }}</a> + <a href="{% url 'article-detail' article.id %}">{{ article.title }}</a> </h4> <div class="container"> {{ article.body|safe|truncatechars_html:3000 }} diff --git a/django/cantusdb_project/main_app/templates/century_detail.html b/django/cantusdb_project/main_app/templates/century_detail.html index 2e17c511d..57a33dcec 100644 --- a/django/cantusdb_project/main_app/templates/century_detail.html +++ b/django/cantusdb_project/main_app/templates/century_detail.html @@ -9,7 +9,7 @@ <h3>{{ century.name }}</h3> <ul> {% for source in century.sources.all|dictsort:"title" %} <li> - <a href="{{ source.get_absolute_url }}"> + <a href="{% url 'source-detail' source.id %}"> {{ source.title }} </a> </li> diff --git a/django/cantusdb_project/main_app/templates/chant_create.html b/django/cantusdb_project/main_app/templates/chant_create.html index b7b7713c8..c8770693d 100644 --- a/django/cantusdb_project/main_app/templates/chant_create.html +++ b/django/cantusdb_project/main_app/templates/chant_create.html @@ -11,7 +11,7 @@ <h3>Create Chant</h3> <div class="alert alert-success alert-dismissible"> {% for message in messages %} <a href="#" class="close" data-dismiss="alert" aria-label="close">×</a> - <a href="{{ previous_chant.get_absolute_url }}" style="color:#155724" target="_blank">{{ message }}</a> + <a href="{% url 'chant-detail' previous_chant.id %}" style="color:#155724" target="_blank">{{ message }}</a> {% endfor %} </div> {% endif %} @@ -232,12 +232,12 @@ <h3>Create Chant</h3> <div class="card mb-3 w-100"> <div class="card-header"> - <h5><a id="source" href="{{ source.get_absolute_url }}">{{ source.title }}</a></h5> + <h5><a id="source" href="{% url 'source-detail' source.id %}">{{ source.title }}</a></h5> </div> <div class="card-body" style="font-size: 15px"> <b>Suggestions based on the previous chant:</b><br> {% if previous_chant %} - {{ previous_chant.folio }} {{ previous_chant.c_sequence}} <a href="{{ previous_chant.get_absolute_url }}" target="_blank">{{ previous_chant.incipit }}</a><br> + {{ previous_chant.folio }} {{ previous_chant.c_sequence}} <a href="{% url 'chant-detail' previous_chant.id %}" target="_blank">{{ previous_chant.incipit }}</a><br> Cantus ID: <a href="http://cantusindex.org/id/{{ previous_chant.cantus_id }}" target="_blank">{{ previous_chant.cantus_id }}</a><br> {% if suggested_chants %} {% for chant in suggested_chants %} diff --git a/django/cantusdb_project/main_app/templates/chant_detail.html b/django/cantusdb_project/main_app/templates/chant_detail.html index bd8cc0564..3592c0642 100644 --- a/django/cantusdb_project/main_app/templates/chant_detail.html +++ b/django/cantusdb_project/main_app/templates/chant_detail.html @@ -30,7 +30,7 @@ <h3>{{ chant.incipit }}</h3> <div class="col"> <dt>Source</dt> <dd> - <a href="{{ chant.source.get_absolute_url }}">{{ chant.source.title }}</a> + <a href="{% url 'source-detail' chant.source.id %}">{{ chant.source.title }}</a> </dd> </div> {% endif %} @@ -64,7 +64,7 @@ <h3>{{ chant.incipit }}</h3> <div class="col-2"> <dt>Feast</dt> <dd> - <a href="{{ chant.feast.get_absolute_url }}">{{ chant.feast.name }}</a> + <a href="{% url 'feast-detail' chant.feast.id %}" title="{{ chant.feast.description }}">{{ chant.feast.name }}</a> </dd> </div> {% endif %} @@ -73,7 +73,7 @@ <h3>{{ chant.incipit }}</h3> <div class="col-2"> <dt>Office/Mass</dt> <dd> - <a href="{{ chant.office.get_absolute_url }}" title="{{ chant.office.description }}">{{ chant.office.name }}</a> + <a href="{% url 'office-detail' chant.office.id %}" title="{{ chant.office.description }}">{{ chant.office.name }}</a> </dd> </div> {% endif %} @@ -82,7 +82,7 @@ <h3>{{ chant.incipit }}</h3> <div class="col-2"> <dt>Genre</dt> <dd> - <a href="{{ chant.genre.get_absolute_url }}" title="{{ chant.genre.description }}">{{ chant.genre.name }}</a> + <a href="{% url 'genre-detail' chant.genre.id %}" title="{{ chant.genre.description }}">{{ chant.genre.name }}</a> </dd> </div> {% endif %} @@ -285,7 +285,7 @@ <h4>List of melodies</h4> <b>Source navigation</b> <br> {% if source %} - <a href="{{ source.get_absolute_url }}"> <b>{{ source.siglum }}</b> </a> + <a href="{% url 'source-detail' source.id %}" title="{{ source.title }}"> <b>{{ source.siglum }}</b> </a> {% else %} This chant is not associated with any source. {% endif %} @@ -325,10 +325,26 @@ <h4>List of melodies</h4> <table class="table table-sm small table-bordered"> {% for chant in chants %} <tr> - <td>{{ chant.c_sequence }}</td> - <td>{{ chant.office.name|default_if_none:"" }} <b>{{ chant.genre.name|default_if_none:"" }}</b> {{ chant.position|default_if_none:"" }} </td> - <td><a href="{{ chant.get_absolute_url }}">{{ chant.incipit|default_if_none:"" }}</a></td> - <td><a href="{{ chant.get_ci_url }}" target="_blank">{{ chant.cantus_id|default_if_none:"" }}</a></td> + <td> + {{ chant.c_sequence }} + </td> + <td> + <span title="{{ chant.office.description }}"> + {{ chant.office.name|default_if_none:"" }} + </span> + <b title="{{ chant.genre.description }}">{{ chant.genre.name|default_if_none:"" }}</b> + {{ chant.position|default_if_none:"" }} + </td> + <td> + <a href="{% url 'chant-detail' chant.id %}"> + {{ chant.incipit|default_if_none:"" }} + </a> + </td> + <td> + <a href="{{ chant.get_ci_url }}" target="_blank"> + {{ chant.cantus_id|default_if_none:"" }} + </a> + </td> </tr> {% endfor %} </table> @@ -337,34 +353,71 @@ <h4>List of melodies</h4> <a id="previousToggle" href="#" onclick="togglePrevious(); return false;">Display previous chants ▾</a> {% endif %} <br> - - {% for feast, chants in feasts_current_folio %} - Folio: <b>{{ chant.folio }}</b> - Feast: <b>{{ feast.name }}</b> - <table class="table table-sm small table-bordered"> - {% for chant in chants %} - <tr> - <td>{{ chant.c_sequence }}</td> - <td>{{ chant.office.name|default_if_none:"" }} <b>{{ chant.genre.name|default_if_none:"" }}</b> {{ chant.position|default_if_none:"" }} </td> - <td><a href="{{ chant.get_absolute_url }}">{{ chant.incipit|default_if_none:"" }}</a></td> - <td><a href="{{ chant.get_ci_url }}" target="_blank">{{ chant.cantus_id|default_if_none:"" }}</a></td> - </tr> - {% endfor %} - </table> - {% endfor %} + {% with chant.c_sequence as current_seq %} + {% for feast, chants in feasts_current_folio %} + Folio: <b>{{ chant.folio }}</b> - Feast: <b title="{{ feast.description }}">{{ feast.name }}</b> + <table class="table table-sm small table-bordered"> + {% for chant in chants %} + <tr> + <td> + {{ chant.c_sequence }} + </td> + <td> + <span title="{{ chant.office.description }}"> + {{ chant.office.name|default_if_none:"" }} + </span> + <b title="{{ chant.genre.description }}">{{ chant.genre.name|default_if_none:"" }}</b> + {{ chant.position|default_if_none:"" }} + </td> + <td> + <a href="{% url 'chant-detail' chant.id %}"> + {% if chant.c_sequence == current_seq %} + <b>{{ chant.incipit|default_if_none:"" }}</b> + {% else %} + {{ chant.incipit|default_if_none:"" }} + {% endif %} + </a> + </td> + <td> + <a href="{{ chant.get_ci_url }}" target="_blank"> + {{ chant.cantus_id|default_if_none:"" }} + </a> + </td> + </tr> + {% endfor %} + </table> + {% endfor %} + {% endwith %} {% if next_folio %} <a id="nextToggle" href="#" onclick="toggleNext(); return false;">Display next chants ▾</a> <br> <div id="nextDiv" style="display:none"> {% for feast, chants in feasts_next_folio %} - Folio: <b>{{ next_folio }}</b> - Feast: <b>{{ feast.name }}</b> + Folio: <b>{{ next_folio }}</b> - Feast: <b title="{{ feast.description }}">{{ feast.name }}</b> <table class="table table-sm small table-bordered"> {% for chant in chants %} <tr> - <td>{{ chant.c_sequence }}</td> - <td>{{ chant.office.name|default_if_none:"" }} <b>{{ chant.genre.name|default_if_none:"" }}</b> {{ chant.position|default_if_none:"" }} </td> - <td><a href="{{ chant.get_absolute_url }}">{{ chant.incipit|default_if_none:"" }}</a></td> - <td><a href="{{ chant.get_ci_url }}" target="_blank">{{ chant.cantus_id|default_if_none:"" }}</a></td> + <td> + {{ chant.c_sequence }} + </td> + <td> + <span title="{{ chant.office.description }}"> + {{ chant.office.name|default_if_none:"" }} + </span> + <b title="{{ chant.genre.description }}">{{ chant.genre.name|default_if_none:"" }}</b> + {{ chant.position|default_if_none:"" }} + </td> + <td> + <a href="{% url 'chant-detail' chant.id %}"> + {{ chant.incipit|default_if_none:"" }} + </a> + </td> + <td> + <a href="{{ chant.get_ci_url }}" target="_blank"> + {{ chant.cantus_id|default_if_none:"" }} + </a> + </td> </tr> {% endfor %} </table> @@ -381,12 +434,12 @@ <h4>List of melodies</h4> <div class="card-header"> <small><a href="/sources?segment={{ source.segment.id }}">{{ source.segment.name }}</a></small> <br> - {{ source.siglum }} + <span title="{{ source.title }}">{{ source.siglum }}</span> </div> <div class=" card-body"> <small> {% if source.provenance.name %} - Provenance: <b><a href="{{ source.provenance.get_absolute_url }}">{{source.provenance.name}}</a></b> + Provenance: <b><a href="{% url 'provenance-detail' source.provenance.id %}">{{source.provenance.name}}</a></b> <br> {% endif %} @@ -394,7 +447,7 @@ <h4>List of melodies</h4> Date: {% for century in source.century.all %} <b> - <a href="{{ century.get_absolute_url }}">{{ century.name }}</a> + <a href="{% url 'century-detail' century.id %}">{{ century.name }}</a> </b> {% endfor %} | @@ -409,7 +462,7 @@ <h4>List of melodies</h4> {% if source.notation.all %} <b> - <a href="{{ source.notation.all.first.get_absolute_url }}">{{ source.notation.all.first.name }}</a> + <a href="{% url 'notation-detail' source.notation.all.first.id %}">{{ source.notation.all.first.name }}</a> </b> <br> {% endif %} @@ -419,7 +472,7 @@ <h4>List of melodies</h4> <ul> {% for editor in source.inventoried_by.all %} <li> - <a href={{ editor.get_absolute_url }}><b>{{ editor.full_name }}</b></a> + <a href="{% url 'user-detail' editor.id %}"><b>{{ editor.full_name }}</b></a> <br> {{ editor.institution|default_if_none:"" }} </li> @@ -433,7 +486,7 @@ <h4>List of melodies</h4> <ul> {% for editor in source.proofreaders.all %} <li> - <a href={{ editor.get_absolute_url }}><b>{{ editor.full_name }}</b></a> + <a href="{% url 'user-detail' editor.id %}"><b>{{ editor.full_name }}</b></a> <br> </li> {% endfor %} diff --git a/django/cantusdb_project/main_app/templates/chant_edit.html b/django/cantusdb_project/main_app/templates/chant_edit.html index 1e3247a18..9b0dafbaf 100644 --- a/django/cantusdb_project/main_app/templates/chant_edit.html +++ b/django/cantusdb_project/main_app/templates/chant_edit.html @@ -227,7 +227,7 @@ <h3>Full text & Volpiano edit form</h3> <small><b>+ Add new source</b></small> </a> <br> - <a href="{{ source.get_absolute_url }}" style="display: inline-block; margin-top:5px;"> + <a href="{% url 'source-detail' source.id %}" title="{{ source.title }}" style="display: inline-block; margin-top:5px;"> {{ source.siglum }} </a> {% endif %} @@ -240,7 +240,7 @@ <h3>Full text & Volpiano edit form</h3> <div class="card mb-3 w-100"> <div class="card-header"> - <h4><a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a></h4> + <h4><a href="{% url 'source-detail' source.id %}" title="{{ source.title }}">{{ source.siglum }}</a></h4> </div> <div class="card-body"> <small> @@ -276,17 +276,40 @@ <h4><a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a></h4> {% comment %} render if the user has selected a specific folio {% endcomment %} {% if feasts_current_folio %} {% for feast, chants in feasts_current_folio %} - <small>Folio: <b>{{ chant.folio }}</b> - Feast: <b>{{ feast.name }}</b></small> + <small>Folio: <b>{{ chant.folio }}</b> - Feast: <b title="{{ chant.feast.description }}">{{ feast.name }}</b></small> <table class="table table-sm small table-bordered"> {% for chant in chants %} <tr> - <td class="h-25" style="width: 5%">{{ chant.c_sequence }}</td> - <td class="h-25" style="width: 20%">{{ chant.office.name|default_if_none:"" }} <b>{{ chant.genre.name|default_if_none:"" }}</b> {{ chant.position|default_if_none:"" }} </td> - <td class="h-25" style="width: 40%; overflow: hidden; white-space: nowrap; text-overflow: ellipsis; max-width: 0"><a href="{{ chant.get_absolute_url }}" target="_blank">{{ chant.incipit|default_if_none:"" }}</a></td> - <td class="h-25" style="width: 20%"><a href="{{ chant.get_ci_url }}" target="_blank">{{ chant.cantus_id|default_if_none:"" }}</a></td> - <td class="h-25" style="width: 5%">{{ chant.mode|default:"" }}</td> + <td class="h-25" style="width: 5%"> + {{ chant.c_sequence }} + </td> + <td class="h-25" style="width: 20%"> + <span title="{{ chant.office.description }}"> + {{ chant.office.name|default_if_none:"" }} + </span> + <b title="{{ chant.genre.description }}"> + {{ chant.genre.name|default_if_none:"" }} + </b> + {{ chant.position|default_if_none:"" }} + </td> + <td class="h-25" style="width: 40%; overflow: hidden; white-space: nowrap; text-overflow: ellipsis; max-width: 0"> + <a href="{% url 'chant-detail' chant.id %}" target="_blank"> + {{ chant.incipit|default_if_none:"" }} + </a> + </td> + <td class="h-25" style="width: 20%"> + <a href="{{ chant.get_ci_url }}" target="_blank"> + {{ chant.cantus_id|default_if_none:"" }} + </a> + </td> + <td class="h-25" style="width: 5%"> + {{ chant.mode|default:"" }} + </td> <td class="h-25" style="width: 10%"> - <a href="{% url 'source-edit-chants' source.id %}?pk={{ chant.pk }}&folio={{ chant.folio }}">EDIT</button></td> + <a href="{% url 'source-edit-chants' source.id %}?pk={{ chant.pk }}&folio={{ chant.folio }}"> + EDIT + </a> + </td> </tr> {% endfor %} </table> @@ -294,17 +317,39 @@ <h4><a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a></h4> {% comment %} render if the user has selected a specific feast {% endcomment %} {% elif folios_current_feast %} {% for folio, chants in folios_current_feast %} - <small>Folio: <b>{{ folio }}</b> - Feast: <b>{{ chant.feast }}</b></small> + <small>Folio: <b>{{ folio }}</b> - Feast: <b title="{{ chant.feast.description }}">{{ chant.feast }}</b></small> <table class="table table-sm small table-bordered"> {% for chant in chants %} <tr> - <td class="h-25" style="width: 5%">{{ chant.c_sequence }}</td> - <td class="h-25" style="width: 20%">{{ chant.office.name|default_if_none:"" }} <b>{{ chant.genre.name|default_if_none:"" }}</b> {{ chant.position|default_if_none:"" }} </td> - <td class="h-25" style="width: 40%; overflow: hidden; white-space: nowrap; text-overflow: ellipsis; max-width: 0"><a href="{{ chant.get_absolute_url }}" target="_blank">{{ chant.incipit|default_if_none:"" }}</a></td> - <td class="h-25" style="width: 20%"><a href="{{ chant.get_ci_url }}" target="_blank">{{ chant.cantus_id|default_if_none:"" }}</a></td> - <td class="h-25" style="width: 5%">{{ chant.mode|default:"" }}</td> + <td class="h-25" style="width: 5%"> + {{ chant.c_sequence }} + </td> + <td class="h-25" style="width: 20%"> + <span title="{{ chant.office.description }}"> + {{ chant.office.name|default_if_none:"" }} + </span> + <b title="{{ chant.genre.description }}"> + {{ chant.genre.name|default_if_none:"" }} + </b> + {{ chant.position|default_if_none:"" }} + </td> + <td class="h-25" style="width: 40%; overflow: hidden; white-space: nowrap; text-overflow: ellipsis; max-width: 0"> + <a href="{% url 'chant-detail' chant.id %}" target="_blank"> + {{ chant.incipit|default_if_none:"" }} + </a> + </td> + <td class="h-25" style="width: 20%"> + <a href="{{ chant.get_ci_url }}" target="_blank"> + {{ chant.cantus_id|default_if_none:"" }} + </a> + </td> + <td class="h-25" style="width: 5%"> + {{ chant.mode|default:"" }} + </td> <td class="h-25" style="width: 10%"> - <a href="{% url 'source-edit-chants' source.id %}?pk={{ chant.pk }}&feast={{ chant.feast.id }}">EDIT</button> + <a href="{% url 'source-edit-chants' source.id %}?pk={{ chant.pk }}&feast={{ chant.feast.id }}"> + EDIT + </a> </td> </tr> {% endfor %} diff --git a/django/cantusdb_project/main_app/templates/chant_list.html b/django/cantusdb_project/main_app/templates/chant_list.html index 0345ada3c..9eb75782a 100644 --- a/django/cantusdb_project/main_app/templates/chant_list.html +++ b/django/cantusdb_project/main_app/templates/chant_list.html @@ -72,11 +72,11 @@ <h3>Browse Chants</h3> <tbody> {% for chant in chants %} <tr> - <td class="text-wrap" style="text-align:center">{{ chant.siglum|default:"" }}</td> + <td class="text-wrap" style="text-align:center" title="{{ chant.source.title }}">{{ chant.source.siglum|default:"" }}</td> <td class="text-wrap" style="text-align:center"><b>{{ chant.folio|default:"" }}</b></td> <td class="text-wrap" style="text-align:center">{{ chant.c_sequence|default_if_none:"" }}</td> {# default_if_none: sometimes, c_sequence is 0, and should still be displayed #} <td class="text-wrap"> - <a href="{{ chant.get_absolute_url }}"><b>{{ chant.incipit|default:"" }}</b></a> + <a href="{% url 'chant-detail' chant.id %}"><b>{{ chant.incipit|default:"" }}</b></a> <p>{{ chant.manuscript_full_text_std_spelling|default:"" }}<br> {% if chant.volpiano %} <span style="font-family: volpiano; font-size:25px">{{ chant.volpiano|default:"" }}</span> @@ -84,13 +84,19 @@ <h3>Browse Chants</h3> </p> </td> <td class="text-wrap" style="text-align:center"> - <a href="{{ chant.feast.get_absolute_url }}">{{ chant.feast.name|default:"" }}</a> + {% if chant.feast %} + <a href="{% url 'feast-detail' chant.feast.id %}" title="{{ chant.feast.description }}">{{ chant.feast.name|default:"" }}</a> + {% endif %} </td> <td class="text-wrap" style="text-align:center"> - <a href="{{ chant.office.get_absolute_url }}" title="{{ chant.office.description }}">{{ chant.office.name|default:"" }}</a> + {% if chant.office %} + <a href="{% url 'office-detail' chant.office.id %}" title="{{ chant.office.description }}">{{ chant.office.name|default:"" }}</a> + {% endif %} </td> <td class="text-wrap" style="text-align:center"> - <a href="{{ chant.genre.get_absolute_url }}" title="{{ chant.genre.description }}">{{ chant.genre.name|default:"" }}</a> + {% if chant.genre %} + <a href="{% url 'genre-detail' chant.genre.id %}" title="{{ chant.genre.description }}">{{ chant.genre.name|default:"" }}</a> + {% endif %} </td> <td class="text-wrap" style="text-align:center">{{ chant.position|default:"" }}</td> <td class="text-wrap" style="text-align:center"> @@ -117,7 +123,7 @@ <h3>Browse Chants</h3> <div class="card mb-3 w-100"> <div class="card-header"> - <h4><a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a></h4> + <h4><a href="{% url 'source-detail' source.id %}" title="{{ source.title }}">{{ source.siglum }}</a></h4> </div> <div class="card-body"> diff --git a/django/cantusdb_project/main_app/templates/chant_proofread.html b/django/cantusdb_project/main_app/templates/chant_proofread.html index ee8c25df5..baf6a9a68 100644 --- a/django/cantusdb_project/main_app/templates/chant_proofread.html +++ b/django/cantusdb_project/main_app/templates/chant_proofread.html @@ -260,7 +260,7 @@ <h3>Proofreading tool</h3> <div class="card mb-3 w-100"> <div class="card-header"> - <h4><a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a></h4> + <h4><a href="{% url 'source-detail' source.id %}" title="{{ source.title }}">{{ source.siglum }}</a></h4> </div> <div class="card-body"> <small> @@ -296,13 +296,34 @@ <h4><a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a></h4> <table class="table table-sm small table-bordered"> {% for chant in chants %} <tr> - <td class="h-25" style="width: 5%">{{ chant.c_sequence }}</td> - <td class="h-25" style="width: 20%">{{ chant.office.name|default_if_none:"" }} <b>{{ chant.genre.name|default_if_none:"" }}</b> {{ chant.position|default_if_none:"" }} </td> - <td class="h-25" style="width: 40%; overflow: hidden; white-space: nowrap; text-overflow: ellipsis; max-width: 0"><a href="{{ chant.get_absolute_url }}">{{ chant.incipit|default_if_none:"" }}</a></td> - <td class="h-25" style="width: 20%"><a href="{{ chant.get_ci_url }}" target="_blank">{{ chant.cantus_id|default_if_none:"" }}</a></td> - <td class="h-25" style="width: 5%">{{ chant.mode|default:"" }}</td> + <td class="h-25" style="width: 5%"> + {{ chant.c_sequence }} + </td> + <td class="h-25" style="width: 20%"> + <span title="{{ chant.office.description }}">{{ chant.office.name|default_if_none:"" }}</span> + <b title="{{ chant.genre.description }}"> + {{ chant.genre.name|default_if_none:"" }} + </b> + {{ chant.position|default_if_none:"" }} + </td> + <td class="h-25" style="width: 40%; overflow: hidden; white-space: nowrap; text-overflow: ellipsis; max-width: 0"> + <a href="{% url 'chant-detail' chant.id %}"> + {{ chant.incipit|default_if_none:"" }} + </a> + </td> + <td class="h-25" style="width: 20%"> + <a href="{{ chant.get_ci_url }}" target="_blank"> + {{ chant.cantus_id|default_if_none:"" }} + </a> + </td> + <td class="h-25" style="width: 5%"> + {{ chant.mode|default:"" }} + </td> <td class="h-25" style="width: 10%"> - <a href="{% url 'chant-proofread' source.id %}?pk={{ chant.pk }}&folio={{ chant.folio }}">EDIT</button></td> + <a href="{% url 'chant-proofread' source.id %}?pk={{ chant.pk }}&folio={{ chant.folio }}"> + EDIT + </a> + </td> </tr> {% endfor %} </table> @@ -314,13 +335,33 @@ <h4><a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a></h4> <table class="table table-sm small table-bordered"> {% for chant in chants %} <tr> - <td class="h-25" style="width: 5%">{{ chant.c_sequence }}</td> - <td class="h-25" style="width: 20%">{{ chant.office.name|default_if_none:"" }} <b>{{ chant.genre.name|default_if_none:"" }}</b> {{ chant.position|default_if_none:"" }} </td> - <td class="h-25" style="width: 40%; overflow: hidden; white-space: nowrap; text-overflow: ellipsis; max-width: 0"><a href="{{ chant.get_absolute_url }}">{{ chant.incipit|default_if_none:"" }}</a></td> - <td class="h-25" style="width: 20%"><a href="{{ chant.get_ci_url }}" target="_blank">{{ chant.cantus_id|default_if_none:"" }}</a></td> - <td class="h-25" style="width: 5%">{{ chant.mode|default:"" }}</td> + <td class="h-25" style="width: 5%"> + {{ chant.c_sequence }} + </td> + <td class="h-25" style="width: 20%"> + <span title="{{ chant.office.description }}">{{ chant.office.name|default_if_none:"" }}</span> + <b title="{{ chant.genre.description }}"> + {{ chant.genre.name|default_if_none:"" }} + </b> + {{ chant.position|default_if_none:"" }} + </td> + <td class="h-25" style="width: 40%; overflow: hidden; white-space: nowrap; text-overflow: ellipsis; max-width: 0"> + <a href="{% url 'chant-detail' chant.id %}"> + {{ chant.incipit|default_if_none:"" }} + </a> + </td> + <td class="h-25" style="width: 20%"> + <a href="{{ chant.get_ci_url }}" target="_blank"> + {{ chant.cantus_id|default_if_none:"" }} + </a> + </td> + <td class="h-25" style="width: 5%"> + {{ chant.mode|default:"" }} + </td> <td class="h-25" style="width: 10%"> - <a href="{% url 'chant-proofread' source.id %}?pk={{ chant.pk }}&feast={{ chant.feast.id }}">EDIT</button> + <a href="{% url 'chant-proofread' source.id %}?pk={{ chant.pk }}&feast={{ chant.feast.id }}"> + EDIT + </a> </td> </tr> {% endfor %} diff --git a/django/cantusdb_project/main_app/templates/chant_search.html b/django/cantusdb_project/main_app/templates/chant_search.html index 980bd0472..04caba705 100644 --- a/django/cantusdb_project/main_app/templates/chant_search.html +++ b/django/cantusdb_project/main_app/templates/chant_search.html @@ -10,7 +10,7 @@ <h3>Search Chants</h3> {% if source %} <p> - <b>Searching in source: <a href="{{ source.get_absolute_url }}" target="_blank">{{ source.title }}</a></b> + <b>Searching in source: <a href="{% url 'source-detail' source.id %}" target="_blank">{{ source.title }}</a></b> </p> {% elif keyword %} <p> @@ -209,7 +209,9 @@ <h3>Search Chants</h3> {% for chant in chants %} <tr> <td class="text-wrap" style="text-align:left"> - <a href="{{ chant.source.get_absolute_url }}">{{ chant.source.siglum }}</a> + {% if chant.source %} + <a href="{% url 'source-detail' chant.source.id %}" title="{{ chant.source.title }}">{{ chant.source.siglum }}</a> + {% endif %} </td> <td class="text-wrap" style="text-align:center"> {{ chant.folio|default:""|truncatechars_html:140 }} @@ -217,12 +219,12 @@ <h3>Search Chants</h3> <td class="text-wrap" style="text-align:left"> {% comment %} this is used for distinguishing chants from sequences, - if the object is chant, use chant.get_absolute_url, - otherwise, use sequence.get_absolute_url + if the object is chant, use chant-detail view, + otherwise, use sequence-detail view. the combined queryset turned all objects into chants so this is the only way to make the distinction {% endcomment %} {% if chant.search_vector %} - <b><a href="{{ chant.get_absolute_url }}">{{ chant.incipit|default:"" }}</a></b> + <b><a href="{% url 'chant-detail' chant.id %}">{{ chant.incipit|default:"" }}</a></b> {% else %} <b><a href="{% url 'sequence-detail' chant.id %}">{{ chant.incipit|default:"" }}</a></b> {% endif %} @@ -231,13 +233,19 @@ <h3>Search Chants</h3> </p> </td> <td class="text-wrap" style="text-align:center"> - <a href="{{ chant.feast.get_absolute_url }}">{{ chant.feast.name|default:"" }}</a> + {% if chant.feast %} + <a href="{% url 'feast-detail' chant.feast.id %}" title="{{ chant.feast.description }}">{{ chant.feast.name|default:"" }}</a> + {% endif %} </td> <td class="text-wrap" style="text-align:center"> - <a href="{{ chant.office.get_absolute_url }}" title="{{ chant.office.description }}">{{ chant.office.name|default:"" }}</a> + {% if chant.office %} + <a href="{% url 'office-detail' chant.office.id %}" title="{{ chant.office.description }}">{{ chant.office.name|default:"" }}</a> + {% endif %} </td> <td class="text-wrap" style="text-align:center"> - <a href="{{ chant.genre.get_absolute_url }}" title="{{ chant.genre.description }}">{{ chant.genre.name|default:"" }}</a> + {% if chant.genre %} + <a href="{% url 'genre-detail' chant.genre.id %}" title="{{ chant.genre.description }}">{{ chant.genre.name|default:"" }}</a> + {% endif %} </td> <td class="text-wrap" style="text-align:center"> {{ chant.position|default:"" }} diff --git a/django/cantusdb_project/main_app/templates/chant_seq_by_cantus_id.html b/django/cantusdb_project/main_app/templates/chant_seq_by_cantus_id.html index d893edb19..9a407786d 100644 --- a/django/cantusdb_project/main_app/templates/chant_seq_by_cantus_id.html +++ b/django/cantusdb_project/main_app/templates/chant_seq_by_cantus_id.html @@ -31,26 +31,58 @@ <h3> {% for chant in chants %} <tr> <td class="text-wrap"> - <a href="{{ chant.source.get_absolute_url }}">{{ chant.source.siglum }}</a> + {% if chant.source %} + <a href="{% url 'source-detail' chant.source.id %}" title="{{ chant.source.title }}">{{ chant.source.siglum }}</a> + {% endif %} </td> <td class="text-wrap">{{ chant.folio }}</td> {% comment %} this is used for distinguishing chants from sequences, - if the object is chant, use chant.get_absolute_url, - otherwise, use sequence.get_absolute_url + if the object is chant, use chant-detail view, + otherwise, use sequence-detail view. the combined queryset turned all objects into chants so this is the only way to make the distinction {% endcomment %} {% if chant.search_vector %} - <td class="text-wrap"><a href="{{ chant.get_absolute_url }}">{{ chant.incipit }}</a></td> + <td class="text-wrap"><a href="{% url 'chant-detail' chant.id %}">{{ chant.incipit }}</a></td> {% else %} <td class="text-wrap"><a href="{% url 'sequence-detail' chant.id %}">{{ chant.incipit }}</a></td> {% endif %} - <td class="text-wrap" title="{{ chant.office.description }}">{{ chant.office.name|default:"" }} </td> - <td class="text-wrap" title="{{ chant.genre.description }}">{{ chant.genre.name|default:"" }} </td> - <td class="text-wrap">{{ chant.position|default:"" }}</td> - <td class="text-wrap"><a href="{{ chant.feast.get_absolute_url }}">{{ chant.feast.name|default:"" }}</a></td> - <td class="text-wrap">{{ chant.mode|default:"" }}</td> - <td class="text-wrap" style="font-family: volpiano; font-size:30px">{% if chant.volpiano %}<a href="{{ chant.get_absolute_url }}" style="text-decoration: none" title="Chant has volpiano melody">1</a>{% endif %}</td> - <td class="text-wrap">{% if chant.image_link %}<a href="{{ chant.image_link }}" target="_blank">Image</a>{% endif %}</td> + <td class="text-wrap"> + {% if chant.office %} + <a href="{% url 'office-detail' chant.office.id %}" title="{{ chant.office.description }}"> + {{ chant.office.name }} + </a> + {% endif %} + </td> + <td class="text-wrap"> + {% if chant.genre %} + <a href="{% url 'genre-detail' chant.genre.id %}" title="{{ chant.genre.description }}"> + {{ chant.genre.name }} + </a> + {% endif %} + </td> + <td class="text-wrap"> + {{ chant.position|default:"" }} + </td> + <td class="text-wrap"> + {% if chant.feast %} + <a href="{% url 'feast-detail' chant.feast.id %}" title="{{ chant.feast.description }}"> + {{ chant.feast.name }} + </a> + {% endif %} + </td> + <td class="text-wrap"> + {{ chant.mode|default:"" }} + </td> + <td class="text-wrap" style="font-family: volpiano; font-size:30px"> + {% if chant.volpiano %} + <a href="{% url 'chant-detail' chant.id %}" style="text-decoration: none" title="Chant has volpiano melody">1</a> + {% endif %} + </td> + <td class="text-wrap"> + {% if chant.image_link %} + <a href="{{ chant.image_link }}" target="_blank">Image</a> + {% endif %} + </td> </tr> {% endfor %} </tbody> diff --git a/django/cantusdb_project/main_app/templates/feast_detail.html b/django/cantusdb_project/main_app/templates/feast_detail.html index c3609112e..af363b7f5 100644 --- a/django/cantusdb_project/main_app/templates/feast_detail.html +++ b/django/cantusdb_project/main_app/templates/feast_detail.html @@ -57,7 +57,11 @@ <h4>The most frequent chants</h4> {% comment %} use `urlencode` filter because 1 chant and 2 sequences have forward slash in their cantus_id (data error) {% endcomment %} <td><a href="{% url 'chant-by-cantus-id' cantus_id|urlencode:"" %}">{{ cantus_id|default:"" }}</a></td> <td>{{ incipit }}</td> - <td><a href="{{ genre.get_absolute_url }}" title="{{ genre.description }}">{{ genre.name }}</a></td> + <td> + {% if genre %} + <a href="{% url 'genre-detail' genre.id %}" title="{{ genre.description }}">{{ genre.name }}</a> + {% endif %} + </td> <td>{{ count }}</td> </tr> {% endfor %} @@ -78,7 +82,7 @@ <h4>Sources containing the feast</h4> <tbody> {% for source, count in sources_zip %} <tr> - <td><a href="{% url 'chant-list' %}?source={{ source.id }}">{{ source.siglum }}</a></td> + <td><a href="{% url 'chant-list' %}?source={{ source.id }}" title="{{ source.title }}">{{ source.siglum }}</a></td> <td><a href="{% url 'chant-list' %}?source={{ source.id }}&feast={{ feast.id }}">{{ count }}</a></td> </tr> {% endfor %} diff --git a/django/cantusdb_project/main_app/templates/feast_list.html b/django/cantusdb_project/main_app/templates/feast_list.html index 46529b85f..2dd3f3ec0 100644 --- a/django/cantusdb_project/main_app/templates/feast_list.html +++ b/django/cantusdb_project/main_app/templates/feast_list.html @@ -69,7 +69,9 @@ <h3>List of Feasts</h3> {% for feast in feasts %} <tr> <td class="text-wrap"> - <a href="{{ feast.get_absolute_url }}"><b>{{ feast.name }}</b></a> + <a href="{% url 'feast-detail' feast.id %}" title="{{ feast.description }}"> + <b>{{ feast.name }}</b> + </a> </td> <td class="text-wrap">{{ feast.description|default:"" }}</td> <td class="text-wrap"> diff --git a/django/cantusdb_project/main_app/templates/full_index.html b/django/cantusdb_project/main_app/templates/full_index.html index d59519585..4a43434e8 100644 --- a/django/cantusdb_project/main_app/templates/full_index.html +++ b/django/cantusdb_project/main_app/templates/full_index.html @@ -22,7 +22,7 @@ <body> <title>Inventory | Cantus Manuscript Database</title> <h3>CANTUS Manuscript Inventory: - <a href="{{ source.get_absolute_url }}" target="_href">{{ source.title }}</a> + <a href="{% url 'source-detail' source.id %}" target="_href">{{ source.title }}</a> </h3> This source inventory contains {{ chants.count }} chants. <table class="table table-sm small table-bordered table-striped table-hover"> @@ -50,7 +50,7 @@ <h3>CANTUS Manuscript Inventory: `default`: use the given default if the value evaluates to False `default_if_none`: use the given default only if the value is None {% endcomment %} - <td>{{ chant.source.siglum|default_if_none:"" }}</td> + <td title="{{ chant.source.title }}">{{ chant.source.siglum|default_if_none:"" }}</td> <td>{{ chant.marginalia|default_if_none:"" }}</td> <td>{{ chant.folio|default_if_none:"" }}</td> <td> @@ -60,11 +60,23 @@ <h3>CANTUS Manuscript Inventory: {{ chant.s_sequence|default_if_none:"" }} {% endif %} </td> - <td>{{ chant.feast.name|default_if_none:"" }}</td> - <td><span title="{{ chant.office.description }}">{{ chant.office.name|default_if_none:"" }}</span></td> - <td><span title="{{ chant.genre.description }}">{{ chant.genre.name|default_if_none:"" }}</span></td> + <td> + <span title="{{ chant.feast.description }}"> + {{ chant.feast.name|default_if_none:"" }} + </span> + </td> + <td> + <span title="{{ chant.office.description }}"> + {{ chant.office.name|default_if_none:"" }} + </span> + </td> + <td> + <span title="{{ chant.genre.description }}"> + {{ chant.genre.name|default_if_none:"" }} + </span> + </td> <td>{{ chant.position|default_if_none:"" }}</td> - <td><a href="{{ chant.get_absolute_url }}" target="_blank">{{ chant.incipit|default_if_none:"" }}</a></td> + <td><a href="{% url 'chant-detail' chant.id %}" target="_blank">{{ chant.incipit|default_if_none:"" }}</a></td> <td>{{ chant.cantus_id|default_if_none:"" }}</td> <td>{{ chant.mode|default_if_none:"" }}</td> <td>{{ chant.differentia|default_if_none:"" }}</td> diff --git a/django/cantusdb_project/main_app/templates/genre_list.html b/django/cantusdb_project/main_app/templates/genre_list.html index ea9041425..5ed47b2bd 100644 --- a/django/cantusdb_project/main_app/templates/genre_list.html +++ b/django/cantusdb_project/main_app/templates/genre_list.html @@ -43,7 +43,7 @@ <h3>List of Genres</h3> {% for genre in genres %} <tr> <td style="text-align:center"> - <a href="{{ genre.get_absolute_url }}"><b>{{ genre.name }}</b></a> + <a href="{% url 'genre-detail' genre.id %}"><b>{{ genre.name }}</b></a> </td> <td style="text-align:center"> {{ genre.description|default:"" }} diff --git a/django/cantusdb_project/main_app/templates/indexer_list.html b/django/cantusdb_project/main_app/templates/indexer_list.html index 7d1eda1f3..6545f2116 100644 --- a/django/cantusdb_project/main_app/templates/indexer_list.html +++ b/django/cantusdb_project/main_app/templates/indexer_list.html @@ -31,13 +31,13 @@ <h3>List of Indexers</h3> {% for indexer in indexers %} <tr> <td class="text-center text-wrap"> - <a href="{{ indexer.get_absolute_url }}">{{ indexer.full_name }}</a> + <a href="{% url 'user-detail' indexer.id %}">{{ indexer.full_name }}</a> </td> <td class="text-center text-wrap">{{ indexer.institution|default:"" }}</td> <td class="text-center text-wrap">{{ indexer.city|default:"" }}</td> <td class="text-center text-wrap">{{ indexer.country|default:"" }}</td> <td class="text-center text-wrap"> - <a href="{{ indexer.get_absolute_url }}#sources">{{ indexer.source_count }} source{{ indexer.source_count|pluralize }}</a> + <a href="{% url 'user-detail' indexer.id %}#sources">{{ indexer.source_count }} source{{ indexer.source_count|pluralize }}</a> </td> </tr> {% endfor %} diff --git a/django/cantusdb_project/main_app/templates/melody_search.html b/django/cantusdb_project/main_app/templates/melody_search.html index d71d127c8..74fed1cc6 100644 --- a/django/cantusdb_project/main_app/templates/melody_search.html +++ b/django/cantusdb_project/main_app/templates/melody_search.html @@ -82,7 +82,7 @@ <h3>Search by melody</h3> </form> {% if source %} - <b>Searching in source: <a href="{{ source.get_absolute_url }}" target="_blank">{{ source.title }}</a></b> + <b>Searching in source: <a href="{% url 'source-detail' source.id %}" target="_blank">{{ source.title }}</a></b> {% endif %} <div id="resultsDiv"></div> diff --git a/django/cantusdb_project/main_app/templates/notation_detail.html b/django/cantusdb_project/main_app/templates/notation_detail.html index b07210d79..173ad9176 100644 --- a/django/cantusdb_project/main_app/templates/notation_detail.html +++ b/django/cantusdb_project/main_app/templates/notation_detail.html @@ -9,7 +9,7 @@ <h3>{{ notation.name }}</h3> <ul> {% for source in notation.sources.all|dictsort:"title" %} <li> - <a href="{{ source.get_absolute_url }}"> + <a href="{% url 'source-detail' source.id %}"> {{ source.title }} </a> </li> diff --git a/django/cantusdb_project/main_app/templates/office_list.html b/django/cantusdb_project/main_app/templates/office_list.html index 499ccaf86..67f6a3cc1 100644 --- a/django/cantusdb_project/main_app/templates/office_list.html +++ b/django/cantusdb_project/main_app/templates/office_list.html @@ -18,7 +18,7 @@ <h3>Office/Mass abbreviations</h3> {% for office in offices %} <tr> <td class="text-wrap"> - <a href="{{ office.get_absolute_url }}"><b>{{ office.name }}</b></a> + <a href="{% url 'office-detail' office.id %}"><b>{{ office.name }}</b></a> </td> <td class="text-wrap">{{ office.description }}</td> </tr> diff --git a/django/cantusdb_project/main_app/templates/provenance_detail.html b/django/cantusdb_project/main_app/templates/provenance_detail.html index 5df454afd..a539135b0 100644 --- a/django/cantusdb_project/main_app/templates/provenance_detail.html +++ b/django/cantusdb_project/main_app/templates/provenance_detail.html @@ -9,7 +9,7 @@ <h3>{{ provenance.name }}</h3> <ul> {% for source in provenance.sources.all|dictsort:"title" %} <li> - <a href="{{ source.get_absolute_url }}"> + <a href="{% url 'source-detail' source.id %}"> {{ source.title }} </a> </li> diff --git a/django/cantusdb_project/main_app/templates/sequence_detail.html b/django/cantusdb_project/main_app/templates/sequence_detail.html index 838732dbc..5f5c0f25a 100644 --- a/django/cantusdb_project/main_app/templates/sequence_detail.html +++ b/django/cantusdb_project/main_app/templates/sequence_detail.html @@ -26,14 +26,16 @@ <h3>{{ sequence.title }}</h3> <dd> {{ sequence.siglum }} </dd> - <dt> - Source - </dt> - <dd> - <a href="{{ sequence.source.get_absolute_url }}"> - {{ sequence.source.title }} - </a> - </dd> + {% if sequence.source %} + <dt> + Source + </dt> + <dd> + <a href="{% url 'source-detail' sequence.source.id %}"> + {{ sequence.source.title }} + </a> + </dd> + {% endif %} <div class="row"> <div class="col"> {% if sequence.folio %} @@ -80,7 +82,7 @@ <h3>{{ sequence.title }}</h3> Genre </dt> <dd> - <a href="{{ sequence.genre.get_absolute_url }}" title="{{ sequence.genre.description }}">{{ sequence.genre.name }}</a> + <a href="{% url 'genre-detail' sequence.genre.id %}" title="{{ sequence.genre.description }}">{{ sequence.genre.name }}</a> </dd> </div> {% endif %} @@ -185,12 +187,14 @@ <h4>Concordances</h4> {% for sequence in concordances %} <tr> <td class="text-wrap" style="text-align:center"> - <a href="{{ sequence.source.get_absolute_url }}"><b>{{ sequence.siglum }}</b></a> - <br> - <b>{{ sequence.folio }}</b> {{ sequence.s_sequence }} + {% if sequence.source %} + <a href="{% url 'source-detail' sequence.source.id %}" title="{{ sequence.source.title }}"><b>{{ sequence.siglum }}</b></a> + <br> + <b>{{ sequence.folio }}</b> {{ sequence.s_sequence }} + {% endif %} </td> <td class="text-wrap" style="text-align:center"> - <a href={{ sequence.get_absolute_url}} >{{ sequence.incipit|default:"" }}</a> + <a href="{% url 'sequence-detail' sequence.id %}">{{ sequence.incipit|default:"" }}</a> </td> <td class="text-wrap" style="text-align:center"> {{ sequence.rubrics|default:"" }} diff --git a/django/cantusdb_project/main_app/templates/sequence_list.html b/django/cantusdb_project/main_app/templates/sequence_list.html index 2980aae86..0427cdc1d 100644 --- a/django/cantusdb_project/main_app/templates/sequence_list.html +++ b/django/cantusdb_project/main_app/templates/sequence_list.html @@ -45,13 +45,15 @@ <h3>Clavis Sequentiarum (Calvin Bower)</h3> {% for sequence in sequences %} <tr style="text-align:center"> <td class="text-wrap"> - <a href={{ sequence.source.get_absolute_url }}> - <b>{{ sequence.source.siglum|default:"" }}</b><br> - </a> + {% if sequence.source %} + <a href="{% url 'source-detail' sequence.source.id %}" title="{{ sequence.source.title }}"> + <b>{{ sequence.source.siglum }}</b><br> + </a> + {% endif %} <b>{{ sequence.folio|default:"" }}</b> {{ sequence.s_sequence|default:"" }} </td> <td class="text-wrap"> - <a href="{{ sequence.get_absolute_url }}"> + <a href="{% url 'sequence-detail' sequence.id %}"> {{ sequence.incipit|default:"" }} </a> </td> diff --git a/django/cantusdb_project/main_app/templates/source_detail.html b/django/cantusdb_project/main_app/templates/source_detail.html index 6fd28d1a3..f657c0001 100644 --- a/django/cantusdb_project/main_app/templates/source_detail.html +++ b/django/cantusdb_project/main_app/templates/source_detail.html @@ -49,7 +49,7 @@ <h3>{{ source.title }}</h3> <dt>Other Editors</dt> <dd> {% for editor in source.other_editors.all %} - <a href={{ editor.get_absolute_url }}>{{ editor.full_name }}</a><br> + <a href="{% url 'user-detail' editor.id %}">{{ editor.full_name }}</a><br> {% endfor %} </dd> {% endif %} @@ -58,7 +58,7 @@ <h3>{{ source.title }}</h3> <dt>Full Text Entered by</dt> <dd> {% for editor in source.full_text_entered_by.all %} - <a href={{ editor.get_absolute_url }}>{{ editor.full_name }}</a><br> + <a href="{% url 'user-detail' editor.id %}">{{ editor.full_name }}</a><br> {% endfor %} </dd> {% endif %} @@ -67,7 +67,7 @@ <h3>{{ source.title }}</h3> <dt>Melodies Entered by</dt> <dd> {% for editor in source.melodies_entered_by.all %} - <a href={{ editor.get_absolute_url }}>{{ editor.full_name }}</a><br> + <a href="{% url 'user-detail' editor.id %}">{{ editor.full_name }}</a><br> {% endfor %} </dd> {% endif %} @@ -110,12 +110,12 @@ <h4>Sequences in this source</h4> {% for sequence in sequences %} <tr> <td class="text-wrap" style="text-align:center"> - <a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a> + <a href="{% url 'source-detail' source.id %}" title="{{ source.title }}">{{ source.siglum }}</a> <br> <b>{{ sequence.folio }}</b> {{ sequence.s_sequence }} </td> <td class="text-wrap" style="text-align:center"> - <a href={{ sequence.get_absolute_url }} >{{ sequence.incipit|default:"" }}</a> + <a href="{% url 'sequence-detail' sequence.id %}" >{{ sequence.incipit|default:"" }}</a> </td> <td class="text-wrap" style="text-align:center"> {{ sequence.rubrics|default:"" }} @@ -185,13 +185,13 @@ <h4>{{ source.siglum }}</h4> <div class=" card-body"> <small> {% if source.provenance.name %} - Provenance: <b><a href="{{ source.provenance.get_absolute_url }}">{{source.provenance.name}}</a></b> + Provenance: <b><a href="{% url 'provenance-detail' source.provenance.id %}">{{source.provenance.name}}</a></b> <br> {% endif %} {% if source.date %} Date: {% for century in source.century.all %} - <b><a href="{{ century.get_absolute_url }}"> + <b><a href="{% url 'century-detail' century.id %}"> {{ century.name }} </a></b> {% endfor %} @@ -204,7 +204,7 @@ <h4>{{ source.siglum }}</h4> <br> {% endif %} {% if source.notation.all %} - Notation: <b><a href="{{ source.notation.all.first.get_absolute_url }}"> + Notation: <b><a href="{% url 'notation-detail' source.notation.all.first.id %}"> {{ source.notation.all.first.name }} </a></b> <br> @@ -214,7 +214,7 @@ <h4>{{ source.siglum }}</h4> <ul> {% for editor in source.inventoried_by.all %} <li> - <a href={{ editor.get_absolute_url }}><b>{{ editor.full_name }}</b></a><br> + <a href={% url 'user-detail' editor.id %}><b>{{ editor.full_name }}</b></a><br> {{ editor.institution|default_if_none:"" }} </li> {% endfor %} @@ -226,7 +226,7 @@ <h4>{{ source.siglum }}</h4> <ul> {% for editor in source.proofreaders.all %} <li> - <a href={{ editor.get_absolute_url }}><b>{{ editor.full_name }}</b></a><br> + <a href={% url 'user-detail' editor.id %}><b>{{ editor.full_name }}</b></a><br> </li> {% endfor %} </ul> diff --git a/django/cantusdb_project/main_app/templates/source_list.html b/django/cantusdb_project/main_app/templates/source_list.html index 409fa96cd..a3ed3a580 100644 --- a/django/cantusdb_project/main_app/templates/source_list.html +++ b/django/cantusdb_project/main_app/templates/source_list.html @@ -81,14 +81,18 @@ <h3>Browse Sources</h3> {% for source in sources %} <tr> <td class="text-wrap" style="text-align:center"> - <a href="{{ source.get_absolute_url }}"><b>{{ source.siglum }}</b></a> + <a href="{% url 'source-detail' source.id %}" title="{{ source.title }}"><b>{{ source.siglum }}</b></a> </td> <td class="text-wrap" style="text-align:center"> {{ source.summary|default:""|truncatechars_html:140 }} </td> <td class="text-wrap" style="text-align:center"> - <b><a href="{{ source.century.first.get_absolute_url }}">{{ source.century.first.name }}</a></b><br> - <a href="{{ source.provenance.get_absolute_url }}">{{ source.provenance.name|default:"" }}</a> + {% if source.century.all %} + <b><a href="{% url 'century-detail' source.century.first.id %}">{{ source.century.first.name }}</a></b><br> + {% endif %} + {% if source.provenance %} + <a href="{% url 'provenance-detail' source.provenance.id %}">{{ source.provenance.name }}</a> + {% endif %} </td> <td class="text-wrap" style="text-align:center"> {% if source.image_link %} diff --git a/django/cantusdb_project/main_app/templates/user_detail.html b/django/cantusdb_project/main_app/templates/user_detail.html index 765f19533..eb326d170 100644 --- a/django/cantusdb_project/main_app/templates/user_detail.html +++ b/django/cantusdb_project/main_app/templates/user_detail.html @@ -34,7 +34,7 @@ <h5>Inventoried</h5> <ul> {% for source in inventoried_sources %} <li> - <a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a> ({{ source.title }}) + <a href="{% url 'source-detail' source.id %}" title="{{ source.title }}">{{ source.siglum }}</a> ({{ source.title }}) </li> {% endfor %} </ul> @@ -44,7 +44,7 @@ <h5>Entered Full Text</h5> <ul> {% for source in full_text_sources %} <li> - <a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a> ({{ source.title }}) + <a href="{% url 'source-detail' source.id %}" title="{{ source.title }}">{{ source.siglum }}</a> ({{ source.title }}) </li> {% endfor %} </ul> @@ -54,7 +54,7 @@ <h5>Entered Melodies</h5> <ul> {% for source in melody_sources %} <li> - <a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a> ({{ source.title }}) + <a href="{% url 'source-detail' source.id %}" title="{{ source.title }}">{{ source.siglum }}</a> ({{ source.title }}) </li> {% endfor %} </ul> @@ -64,7 +64,7 @@ <h5>Proofread</h5> <ul> {% for source in proofread_sources %} <li> - <a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a> ({{ source.title }}) + <a href="{% url 'source-detail' source.id %}" title="{{ source.title }}">{{ source.siglum }}</a> ({{ source.title }}) </li> {% endfor %} </ul> @@ -74,7 +74,7 @@ <h5>Edited</h5> <ul> {% for source in edited_sources %} <li> - <a href="{{ source.get_absolute_url }}">{{ source.siglum }}</a> ({{ source.title }}) + <a href="{% url 'source-detail' source.id %}" title="{{ source.title }}">{{ source.siglum }}</a> ({{ source.title }}) </li> {% endfor %} </ul> diff --git a/django/cantusdb_project/main_app/templates/user_list.html b/django/cantusdb_project/main_app/templates/user_list.html index 36023958b..408556e36 100644 --- a/django/cantusdb_project/main_app/templates/user_list.html +++ b/django/cantusdb_project/main_app/templates/user_list.html @@ -30,7 +30,7 @@ <h3>All Users</h3> {% for user in users %} <tr> <td class="text-center text-wrap"> - <a href="{{ user.get_absolute_url }}">{{ user.full_name|default:"" }}</a> + <a href="{% url 'user-detail' user.id %}">{{ user.full_name|default:"" }}</a> </td> <td>{{ user.institution|default:"" }}</td> <td>{{ user.city|default:"" }}</td> diff --git a/django/cantusdb_project/main_app/tests/make_fakes.py b/django/cantusdb_project/main_app/tests/make_fakes.py index d35e37eb0..189f398f6 100644 --- a/django/cantusdb_project/main_app/tests/make_fakes.py +++ b/django/cantusdb_project/main_app/tests/make_fakes.py @@ -266,7 +266,7 @@ def make_fake_source(published=None, title=None, segment=None, segment_name=None # tuples and we only need the first element of each tuple if title is None: - title = make_fake_text(LONG_CHAR_FIELD_MAX) + title = faker.sentence() if siglum is None: siglum = make_fake_text(SHORT_CHAR_FIELD_MAX) if description is None: diff --git a/django/cantusdb_project/main_app/tests/test_views.py b/django/cantusdb_project/main_app/tests/test_views.py index 4ee7583ad..e1b3732ce 100644 --- a/django/cantusdb_project/main_app/tests/test_views.py +++ b/django/cantusdb_project/main_app/tests/test_views.py @@ -752,6 +752,7 @@ def test_keyword_search_contains(self): def test_source_link_column(self): siglum = "Sigl-01" source = make_fake_source(published=True, siglum=siglum) + source_title = source.title url = source.get_absolute_url() fulltext = "manuscript full text" search_term = "full" @@ -764,8 +765,9 @@ def test_source_link_column(self): ) html = str(response.content) self.assertIn(siglum, html) + self.assertIn(source_title, html) self.assertIn(url, html) - self.assertIn(f'<a href="{url}">{siglum}</a>', html) + self.assertIn(f'<a href="{url}" title="{source_title}">{siglum}</a>', html) def test_folio_column(self): source = make_fake_source(published=True) @@ -786,6 +788,7 @@ def test_feast_column(self): source = make_fake_source(published=True) feast = make_fake_feast() feast_name = feast.name + feast_description = feast.description url = feast.get_absolute_url() fulltext = "manuscript full text" search_term = "full" @@ -799,8 +802,9 @@ def test_feast_column(self): ) html = str(response.content) self.assertIn(feast_name, html) + self.assertIn(feast_description, html) self.assertIn(url, html) - self.assertIn(f'<a href="{url}">{feast_name}</a>', html) + self.assertIn(f'<a href="{url}" title="{feast_description}">{feast_name}</a>', html) def test_office_column(self): source = make_fake_source(published=True) diff --git a/django/cantusdb_project/requirements.txt b/django/cantusdb_project/requirements.txt index 981588198..5b4d3ba28 100644 --- a/django/cantusdb_project/requirements.txt +++ b/django/cantusdb_project/requirements.txt @@ -13,6 +13,7 @@ Django==4.1.7 django-autocomplete-light==3.5.1 django-extra-views==0.13.0 django-quill-editor==0.1.40 +django_debug_toolbar==3.8.1 Faker==4.1.0 gunicorn==20.0.4 idna==2.10

matrix-org__synapse-6682

http requests for uris with non-ascii characters cause CRITICAL errors ``` 2019-11-22 13:15:59,276 - twisted - 172 - CRITICAL - - Capture point (most recent call last): File "/usr/lib/python3.5/runpy.py", line 184, in _run_module_as_main "__main__", mod_spec) File "/usr/lib/python3.5/runpy.py", line 85, in _run_code exec(code, run_globals) File "/opt/synapse/synapse/synapse/app/homeserver.py", line 659, in <module> main() File "/opt/synapse/synapse/synapse/app/homeserver.py", line 655, in main run(hs) File "/opt/synapse/synapse/synapse/app/homeserver.py", line 646, in run logger=logger, File "/opt/synapse/synapse/synapse/app/_base.py", line 139, in start_reactor run() File "/opt/synapse/synapse/synapse/app/_base.py", line 114, in run run_command() File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/internet/base.py", line 1267, in run self.mainLoop() File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/internet/base.py", line 1279, in mainLoop self.doIteration(t) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/internet/epollreactor.py", line 235, in doPoll log.callWithLogger(selectable, _drdw, selectable, fd, event) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/python/log.py", line 103, in callWithLogger return callWithContext({"system": lp}, func, *args, **kw) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/python/log.py", line 86, in callWithContext return context.call({ILogContext: newCtx}, func, *args, **kw) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/python/context.py", line 122, in callWithContext return self.currentContext().callWithContext(ctx, func, *args, **kw) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/python/context.py", line 85, in callWithContext return func(*args,**kw) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/internet/posixbase.py", line 614, in _doReadOrWrite why = selectable.doRead() File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/internet/tcp.py", line 243, in doRead return self._dataReceived(data) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/internet/tcp.py", line 249, in _dataReceived rval = self.protocol.dataReceived(data) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/web/http.py", line 2912, in dataReceived return self._channel.dataReceived(data) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/web/http.py", line 2211, in dataReceived return basic.LineReceiver.dataReceived(self, data) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/protocols/basic.py", line 579, in dataReceived why = self.rawDataReceived(data) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/web/http.py", line 2218, in rawDataReceived self._transferDecoder.dataReceived(data) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/web/http.py", line 1699, in dataReceived finishCallback(data[contentLength:]) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/web/http.py", line 2115, in _finishRequestBody self.allContentReceived() File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/web/http.py", line 2190, in allContentReceived req.requestReceived(command, path, version) File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/web/http.py", line 917, in requestReceived self.process() Traceback (most recent call last): File "/opt/synapse/env3/lib/python3.5/site-packages/twisted/web/server.py", line 199, in process self.render(resrc) File "/opt/synapse/synapse/synapse/http/site.py", line 130, in render self._started_processing(servlet_name) File "/opt/synapse/synapse/synapse/http/site.py", line 233, in _started_processing self.get_redacted_uri(), File "/opt/synapse/synapse/synapse/http/site.py", line 91, in get_redacted_uri uri = self.uri.decode("ascii") UnicodeDecodeError: 'ascii' codec can't decode byte 0xc8 in position 25: ordinal not in range(128) ```

[ { "content": "# Copyright 2016 OpenMarket Ltd\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by appli...

diff --git a/changelog.d/6682.bugfix b/changelog.d/6682.bugfix new file mode 100644 index 000000000000..d48ea31477f5 --- /dev/null +++ b/changelog.d/6682.bugfix @@ -0,0 +1,2 @@ +Fix "CRITICAL" errors being logged when a request is received for a uri containing non-ascii characters. + diff --git a/synapse/http/site.py b/synapse/http/site.py index 9f2d035fa0e5..911251c0bcff 100644 --- a/synapse/http/site.py +++ b/synapse/http/site.py @@ -88,7 +88,7 @@ def get_request_id(self): def get_redacted_uri(self): uri = self.uri if isinstance(uri, bytes): - uri = self.uri.decode("ascii") + uri = self.uri.decode("ascii", errors="replace") return redact_uri(uri) def get_method(self):

Lightning-AI__torchmetrics-2346

High memory usage of Perplexity metric ## 🐛 Bug I ran out of memory (GPU) when computing the perplexity metric and would like to propose a small optimization to decrease its memory utilization. ### To Reproduce For instance, when running the following code PyTorch tries to allocate 1024 GB of GPU memory on my system. ```py from torchmetrics.text import Perplexity import torch gen = torch.manual_seed(42) preds = torch.rand(512, 1024, 12, generator=gen).cuda() target = torch.randint(12, (512, 1024), generator=gen).cuda() perp = Perplexity().cuda() print(perp(preds, target)) ``` ### Memory Inefficiency I think the inefficiency is in this line: https://github.com/Lightning-AI/torchmetrics/blob/a68455afb9041d1d32c1d6546897fee416abdc41/src/torchmetrics/functional/text/perplexity.py#L94 `probs[:, target]` results in a large temporary tensor with `(512*1024)^2` elements. Afterwards only the diagonal values are used. ### Potential Solution In contrast ``` probs = probs[torch.arange(target.numel()), target][mask] ``` would only require memory of the size of target. Would you consider accepting a pull request with this optimization? Or was the previous implementation chosen for another reason? ### Environment - TorchMetrics v1.2.1 (installed with pip) and Master branch. - Python 3.10.12 - Pytorch 2.2.0 - CUDA 12.1

[ { "content": "# Copyright The Lightning team.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by appli...

diff --git a/CHANGELOG.md b/CHANGELOG.md index ad35113a0f6..b7d3e419e16 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +- Fixed high memory consumption in `Perplexity` metric ([#2346](https://github.com/Lightning-AI/torchmetrics/pull/2346)) + + - Fixed cached network in `FeatureShare` not being moved to the correct device ([#2348](https://github.com/Lightning-AI/torchmetrics/pull/2348)) diff --git a/src/torchmetrics/functional/text/perplexity.py b/src/torchmetrics/functional/text/perplexity.py index cb0bafd5082..39f832905cf 100644 --- a/src/torchmetrics/functional/text/perplexity.py +++ b/src/torchmetrics/functional/text/perplexity.py @@ -91,7 +91,7 @@ def _perplexity_update(preds: Tensor, target: Tensor, ignore_index: Optional[int else: mask = torch.ones_like(target, dtype=torch.bool) - probs = probs[:, target].diagonal()[mask] + probs = probs[torch.arange(target.numel()), target][mask] total_log_probs = -probs.log().sum() count = mask.sum()

RedHatInsights__insights-core-1112

hostname parser doesn't handle sos_commands/general/hostname sos_commands/general/hostname contains the hostname with a newline at the end, which results in a file with two lines. The hostname parser specifically checks for one line but doesn't gracefully handle the problem. We can update the parser to handle this case and/or investigate whether proc/sys/kernel/hostname is a valid substitute to put in sos_archive.py instead.

[ { "content": "\"\"\"\nhostname - command ``/bin/hostname``\n====================================\n\nThis parser simply reads the output of ``/bin/hostname``, which is the\nconfigured fully qualified domain name of the client system. It then\nsplits it into ``hostname`` and ``domain`` and stores these as attrib...

diff --git a/insights/parsers/hostname.py b/insights/parsers/hostname.py index 1af7ed8e60..ecb3658983 100644 --- a/insights/parsers/hostname.py +++ b/insights/parsers/hostname.py @@ -34,6 +34,7 @@ class Hostname(Parser): domain: The domain get from the fqdn. """ def parse_content(self, content): + content = filter(None, content) raw = None if len(content) == 1: raw = content[0].strip() diff --git a/insights/parsers/tests/test_hostname.py b/insights/parsers/tests/test_hostname.py index 8b25de81c9..7b3bade535 100644 --- a/insights/parsers/tests/test_hostname.py +++ b/insights/parsers/tests/test_hostname.py @@ -2,7 +2,14 @@ from insights.tests import context_wrap HOSTNAME = "rhel7.example.com" +HOSTNAME_MULTILINE = """ +rhel7.example.com +""" + HOSTNAME_SHORT = "rhel7" +HOSTNAME_SHORT_MULTILINE = """ +rhel7 +""" def test_hostname(): @@ -12,11 +19,22 @@ def test_hostname(): assert data.domain == "example.com" assert "{0}".format(data) == "<hostname: rhel7, domain: example.com>" + data = Hostname(context_wrap(HOSTNAME_MULTILINE, strip=False)) + assert data.fqdn == "rhel7.example.com" + assert data.hostname == "rhel7" + assert data.domain == "example.com" + assert "{0}".format(data) == "<hostname: rhel7, domain: example.com>" + data = Hostname(context_wrap(HOSTNAME_SHORT)) assert data.fqdn == "rhel7" assert data.hostname == "rhel7" assert data.domain == "" + data = Hostname(context_wrap(HOSTNAME_SHORT_MULTILINE, strip=False)) + assert data.fqdn == "rhel7" + assert data.hostname == "rhel7" + assert data.domain == "" + data = Hostname(context_wrap("")) assert data.fqdn is None assert data.hostname is None diff --git a/insights/tests/__init__.py b/insights/tests/__init__.py index 3d220710c4..186cfe2d42 100644 --- a/insights/tests/__init__.py +++ b/insights/tests/__init__.py @@ -77,9 +77,12 @@ def context_wrap(lines, release=DEFAULT_RELEASE, version="-1.-1", machine_id="machine_id", + strip=True, **kwargs): if isinstance(lines, basestring): - lines = lines.strip().splitlines() + if strip: + lines = lines.strip() + lines = lines.splitlines() return Context(content=lines, path=path, hostname=hostname, release=release, version=version.split("."),

beetbox__beets-2631

Broken pipe on piping `list` output on Python 3 ### Problem I'm trying to write a quick dirty script to play the first result of a search, looking much like you'd expect: ```sh mpv --no-audio-display "$(beet ls -p $@ | head -n 1)" ``` However, there's something in the formatting of the output that `head` doesn't like: ```sh $ beet ls -p home /media/beets/5 Seconds of Summer/5 Seconds of Summer/09 Long Way Home.mp3 /media/beets/5 Seconds of Summer/LIVESOS/07 Long Way Home.mp3 /media/beets/5 Seconds of Summer/Sounds Good Feels Good/12 Broken Home.mp3 /media/beets/American Authors/What We Live For/07 Go Big or Go Home.mp3 /media/beets/Boys Like Girls/Crazy World/09 Take Me Home.mp3 ... ``` However ```sh beet -vv ls -p home | head -n 1 user configuration: /home/shagaru/.config/beets/config.yaml data directory: /home/shagaru/.config/beets plugin paths: Sending event: pluginload library database: /media/Music/library.db library directory: /media/Music Sending event: library_opened /media/beets/5 Seconds of Summer/5 Seconds of Summer/09 Long Way Home.mp3 Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'> BrokenPipeError: [Errno 32] Broken pipe ``` Trying to cheat and run it through `echo` instead produces the following: ```sh $ echo -e $(beet ls -p home) | head -n 1 /media/beets/5 Seconds of Summer/5 Seconds of Summer/09 Long Way Home.mp3 /media/beets/5 Seconds of Summer/LIVESOS/07 Long Way Home.mp3 /media/beets/5 Seconds of Summer/Sounds Good Feels Good/12 Broken Home.mp3 /media/beets/American Authors/What We Live For/07 Go Big or Go Home.mp3 /media/beets/Boys Like Girls/Crazy World/09 Take Me Home.mp3 ... ``` as one string, so it seems like the proper line-ending characters aren't being properly generated. This may be expected of Python output, I don't know; I haven't written using it. End question I suppose is there any way around how Python handles printing lines short of rewriting that entire part of the program? ### Setup * OS: GNU/Linux * Python version: 3.5.2 * beets version: 1.4.4 * Turning off plugins made problem go away (yes/no): no My configuration (output of `beet config`) shouldn't matter, because it's a question of how the program functions inherently. Broken pipe on piping `list` output on Python 3 ### Problem I'm trying to write a quick dirty script to play the first result of a search, looking much like you'd expect: ```sh mpv --no-audio-display "$(beet ls -p $@ | head -n 1)" ``` However, there's something in the formatting of the output that `head` doesn't like: ```sh $ beet ls -p home /media/beets/5 Seconds of Summer/5 Seconds of Summer/09 Long Way Home.mp3 /media/beets/5 Seconds of Summer/LIVESOS/07 Long Way Home.mp3 /media/beets/5 Seconds of Summer/Sounds Good Feels Good/12 Broken Home.mp3 /media/beets/American Authors/What We Live For/07 Go Big or Go Home.mp3 /media/beets/Boys Like Girls/Crazy World/09 Take Me Home.mp3 ... ``` However ```sh beet -vv ls -p home | head -n 1 user configuration: /home/shagaru/.config/beets/config.yaml data directory: /home/shagaru/.config/beets plugin paths: Sending event: pluginload library database: /media/Music/library.db library directory: /media/Music Sending event: library_opened /media/beets/5 Seconds of Summer/5 Seconds of Summer/09 Long Way Home.mp3 Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'> BrokenPipeError: [Errno 32] Broken pipe ``` Trying to cheat and run it through `echo` instead produces the following: ```sh $ echo -e $(beet ls -p home) | head -n 1 /media/beets/5 Seconds of Summer/5 Seconds of Summer/09 Long Way Home.mp3 /media/beets/5 Seconds of Summer/LIVESOS/07 Long Way Home.mp3 /media/beets/5 Seconds of Summer/Sounds Good Feels Good/12 Broken Home.mp3 /media/beets/American Authors/What We Live For/07 Go Big or Go Home.mp3 /media/beets/Boys Like Girls/Crazy World/09 Take Me Home.mp3 ... ``` as one string, so it seems like the proper line-ending characters aren't being properly generated. This may be expected of Python output, I don't know; I haven't written using it. End question I suppose is there any way around how Python handles printing lines short of rewriting that entire part of the program? ### Setup * OS: GNU/Linux * Python version: 3.5.2 * beets version: 1.4.4 * Turning off plugins made problem go away (yes/no): no My configuration (output of `beet config`) shouldn't matter, because it's a question of how the program functions inherently. Broken pipe on piping `list` output on Python 3 ### Problem I'm trying to write a quick dirty script to play the first result of a search, looking much like you'd expect: ```sh mpv --no-audio-display "$(beet ls -p $@ | head -n 1)" ``` However, there's something in the formatting of the output that `head` doesn't like: ```sh $ beet ls -p home /media/beets/5 Seconds of Summer/5 Seconds of Summer/09 Long Way Home.mp3 /media/beets/5 Seconds of Summer/LIVESOS/07 Long Way Home.mp3 /media/beets/5 Seconds of Summer/Sounds Good Feels Good/12 Broken Home.mp3 /media/beets/American Authors/What We Live For/07 Go Big or Go Home.mp3 /media/beets/Boys Like Girls/Crazy World/09 Take Me Home.mp3 ... ``` However ```sh beet -vv ls -p home | head -n 1 user configuration: /home/shagaru/.config/beets/config.yaml data directory: /home/shagaru/.config/beets plugin paths: Sending event: pluginload library database: /media/Music/library.db library directory: /media/Music Sending event: library_opened /media/beets/5 Seconds of Summer/5 Seconds of Summer/09 Long Way Home.mp3 Exception ignored in: <_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'> BrokenPipeError: [Errno 32] Broken pipe ``` Trying to cheat and run it through `echo` instead produces the following: ```sh $ echo -e $(beet ls -p home) | head -n 1 /media/beets/5 Seconds of Summer/5 Seconds of Summer/09 Long Way Home.mp3 /media/beets/5 Seconds of Summer/LIVESOS/07 Long Way Home.mp3 /media/beets/5 Seconds of Summer/Sounds Good Feels Good/12 Broken Home.mp3 /media/beets/American Authors/What We Live For/07 Go Big or Go Home.mp3 /media/beets/Boys Like Girls/Crazy World/09 Take Me Home.mp3 ... ``` as one string, so it seems like the proper line-ending characters aren't being properly generated. This may be expected of Python output, I don't know; I haven't written using it. End question I suppose is there any way around how Python handles printing lines short of rewriting that entire part of the program? ### Setup * OS: GNU/Linux * Python version: 3.5.2 * beets version: 1.4.4 * Turning off plugins made problem go away (yes/no): no My configuration (output of `beet config`) shouldn't matter, because it's a question of how the program functions inherently.

[ { "content": "# -*- coding: utf-8 -*-\n# This file is part of beets.\n# Copyright 2016, Adrian Sampson.\n#\n# Permission is hereby granted, free of charge, to any person obtaining\n# a copy of this software and associated documentation files (the\n# \"Software\"), to deal in the Software without restriction, in...

diff --git a/beets/ui/__init__.py b/beets/ui/__init__.py index 6ba80d22f0..af2b79a198 100644 --- a/beets/ui/__init__.py +++ b/beets/ui/__init__.py @@ -1276,7 +1276,7 @@ def main(args=None): except IOError as exc: if exc.errno == errno.EPIPE: # "Broken pipe". End silently. - pass + sys.stderr.close() else: raise except KeyboardInterrupt: diff --git a/docs/changelog.rst b/docs/changelog.rst index 35785cc3ca..281f6a32ea 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -8,6 +8,11 @@ Changelog goes here! Fixes: +* Prevent Python from warning about a ``BrokenPipeError`` being ignored even + though we do take it into account. This was an issue when using beets in + simple shell scripts. + Thanks to :user:`Azphreal`. + :bug:`2622` :bug:`2631` * :doc:`/plugins/replaygain`: Fix a regression in the previous release related to the new R128 tags. :bug:`2615` :bug:`2623`

projectmesa__mesa-2125

Fix error in failing flocking benchmark Our benchmarks are failing: https://github.com/projectmesa/mesa/actions/workflows/benchmarks.yml ```bash 08:41:17 starting benchmarks. 08:41:35 Schelling (small) timings: Init 0.00771 s; Run 0.0472 s 08:41:55 Schelling (large) timings: Init 0.05062 s; Run 0.4629 s 08:42:01 WolfSheep (small) timings: Init 0.00333 s; Run 0.0124 s 08:42:[15](https://github.com/projectmesa/mesa/actions/runs/8813652146/job/24191834761#step:7:16) WolfSheep (large) timings: Init 0.05334 s; Run 0.2206 s File "/home/runner/work/mesa/mesa/benchmarks/global_benchmark.py", line 62, in <module> results = run_experiments(model, config) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/work/mesa/mesa/benchmarks/global_benchmark.py", line 47, in run_experiments init_time, run_time = run_model(model_class, seed, config["parameters"]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/work/mesa/mesa/benchmarks/global_benchmark.py", line [21](https://github.com/projectmesa/mesa/actions/runs/8813652146/job/24191834761#step:7:22), in run_model model = model_class(simulator=simulator, seed=seed, **parameters) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/runner/work/mesa/mesa/benchmarks/Flocking/flocking.py", line 139, in __init__ boid = Boid( ^^^^^ TypeError: Boid.__init__() got an unexpected keyword argument 'pos' Error: Process completed with exit code 1. ``` Most likely something was changed in [benchmarks/Flocking/flocking.py](https://github.com/projectmesa/mesa/blob/main/benchmarks/Flocking/flocking.py) that needs to be fixed/reverted.

[ { "content": "\"\"\"\nFlockers\n=============================================================\nA Mesa implementation of Craig Reynolds's Boids flocker model.\nUses numpy arrays to represent vectors.\n\"\"\"\n\nimport numpy as np\n\nimport mesa\n\n\nclass Boid(mesa.Agent):\n \"\"\"\n A Boid-style flocker a...

diff --git a/benchmarks/Flocking/flocking.py b/benchmarks/Flocking/flocking.py index fc19c6c3820..ff9f97c0c96 100644 --- a/benchmarks/Flocking/flocking.py +++ b/benchmarks/Flocking/flocking.py @@ -139,7 +139,6 @@ def __init__( boid = Boid( unique_id=i, model=self, - pos=pos, speed=speed, direction=direction, vision=vision,

Pyomo__pyomo-2633

Fixed Vars unpickle as stale ## Summary I'm not sure if this is a bug, but it seems unexpected? Anyway, if you pickle a model that has a fixed variable (not stale), when you unpickle it, it comes back as stale. ### Steps to reproduce the issue ``` from pyomo.environ import * import pickle m = ConcreteModel() m.x = Var(domain=Binary) m.x.fix(1) unpickle = pickle.loads(pickle.dumps(m)) m.x.pprint() unpickle.x.pprint() ``` ``` x : Size=1, Index=None Key : Lower : Value : Upper : Fixed : Stale : Domain None : 0 : 1 : 1 : True : False : Binary x : Size=1, Index=None Key : Lower : Value : Upper : Fixed : Stale : Domain None : 0 : 1 : 1 : True : True : Binary ``` ### Error Message It seems like these models should be identical, even up to stale-ness, right? ### Information on your system Pyomo version: main Python version: 3.8 Operating system: linux How Pyomo was installed (PyPI, conda, source): source Solver (if applicable):

[ { "content": "# ___________________________________________________________________________\n#\n# Pyomo: Python Optimization Modeling Objects\n# Copyright (c) 2008-2022\n# National Technology and Engineering Solutions of Sandia, LLC\n# Under the terms of Contract DE-NA0003525 with National Technology and\n...

diff --git a/pyomo/core/staleflag.py b/pyomo/core/staleflag.py index 1247df2247b..01cc70406a3 100644 --- a/pyomo/core/staleflag.py +++ b/pyomo/core/staleflag.py @@ -21,7 +21,7 @@ def stale_mapper(self, encode, value): if value: return 0 else: - self.get_flag(0) + return self.get_flag(0) def _get_flag(self, current_flag): """Return the current global stale flag value""" diff --git a/pyomo/core/tests/unit/test_var.py b/pyomo/core/tests/unit/test_var.py index 65081809c74..331334ef694 100644 --- a/pyomo/core/tests/unit/test_var.py +++ b/pyomo/core/tests/unit/test_var.py @@ -1598,5 +1598,27 @@ def test_stale(self): self.assertFalse(m.x.stale) self.assertFalse(m.y.stale) + def test_stale_clone(self): + m = ConcreteModel() + m.x = Var(initialize=0) + self.assertFalse(m.x.stale) + m.y = Var() + self.assertTrue(m.y.stale) + m.z = Var(initialize=0) + self.assertFalse(m.z.stale) + + i = m.clone() + self.assertFalse(i.x.stale) + self.assertTrue(i.y.stale) + self.assertFalse(i.z.stale) + + StaleFlagManager.mark_all_as_stale(delayed=True) + m.z = 5 + i = m.clone() + self.assertTrue(i.x.stale) + self.assertTrue(i.y.stale) + self.assertFalse(i.z.stale) + + if __name__ == "__main__": unittest.main()

aws__aws-cli-357

pip install awscli fails I tried `pip install awscli` from https://github.com/aws/aws-cli/blob/develop/README.rst and failed: http://sprunge.us/NfbW /home/hendry/.pip/pip.log = http://ix.io/7SC Hilarious how bad Python packaging is. I'm running Archlinux with Python 3.3.2.

[ { "content": "#!/usr/bin/env python\nimport sys\n\nfrom setuptools import setup, find_packages\n\nimport awscli\n\n\nrequires = ['botocore>=0.16.0,<0.17.0',\n 'bcdoc>=0.9.0,<0.10.0',\n 'six>=1.1.0',\n 'colorama==0.2.5',\n 'docutils>=0.10',\n 'rsa==3.1.1']\n...

[ { "content": "#!/usr/bin/env python\nimport sys\n\nfrom setuptools import setup, find_packages\n\nimport awscli\n\n\nrequires = ['botocore>=0.16.0,<0.17.0',\n 'bcdoc>=0.9.0,<0.10.0',\n 'six>=1.1.0',\n 'colorama==0.2.5',\n 'docutils>=0.10',\n 'rsa==3.1.2']\n...

diff --git a/requirements.txt b/requirements.txt index 6b6a74447dcd..fd6551a87ad9 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,4 +11,4 @@ nose==1.3.0 colorama==0.2.5 mock==1.0.1 httpretty==0.6.1 -rsa==3.1.1 +rsa==3.1.2 diff --git a/setup.py b/setup.py index 9df11b894ad8..d0c1630346d9 100644 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ 'six>=1.1.0', 'colorama==0.2.5', 'docutils>=0.10', - 'rsa==3.1.1'] + 'rsa==3.1.2'] if sys.version_info[:2] == (2, 6): # For python2.6 we have to require argparse since it

boto__boto-215

RDS call modify_dbinstance with multi_az = True doesn't actually set an instance to MultiAZ Making a call to a non-multiaz instance with multi_az=True doesn't actually switch the parameter. I assume this is also true for creating one from scratch, but I haven't tested that yet.

[ { "content": "# Copyright (c) 2010 Spotify AB\n#\n# Permission is hereby granted, free of charge, to any person obtaining a\n# copy of this software and associated documentation files (the\n# \"Software\"), to deal in the Software without restriction, including\n# without limitation the rights to use, copy, mod...

diff --git a/boto/emr/connection.py b/boto/emr/connection.py index f0145e33de..4409d69ed8 100644 --- a/boto/emr/connection.py +++ b/boto/emr/connection.py @@ -274,7 +274,7 @@ def _build_instance_args(self, ec2_keyname, availability_zone, master_instance_t if ec2_keyname: params['Instances.Ec2KeyName'] = ec2_keyname if availability_zone: - params['Placement'] = availability_zone + params['Placement.AvailabilityZone'] = availability_zone return params

microsoft__playwright-python-625

Release-blocker: uncomment cors tests Search for this issue URL in the code.

[ { "content": "# Copyright (c) Microsoft Corporation.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by ap...

diff --git a/playwright/_impl/_page.py b/playwright/_impl/_page.py index 340a473dc..5c71a692c 100644 --- a/playwright/_impl/_page.py +++ b/playwright/_impl/_page.py @@ -779,8 +779,6 @@ async def pdf( def video( self, ) -> Optional[Video]: - if "recordVideo" not in self._browser_context._options: - return None if not self._video: self._video = Video(self) return self._video diff --git a/tests/async/test_interception.py b/tests/async/test_interception.py index fa1667cf2..9304bc544 100644 --- a/tests/async/test_interception.py +++ b/tests/async/test_interception.py @@ -580,8 +580,6 @@ async def handle_route(route, request): assert "failed" in exc.value.message -# RELEASE BLOCKER: Temporary upstream issue https://github.com/microsoft/playwright-python/issues/608 -@pytest.mark.skip_browser("chromium") async def test_page_route_should_support_cors_with_POST(page, server): await page.goto(server.EMPTY_PAGE) await page.route( @@ -609,8 +607,6 @@ async def test_page_route_should_support_cors_with_POST(page, server): assert resp == ["electric", "gas"] -# RELEASE BLOCKER: Temporary upstream issue https://github.com/microsoft/playwright-python/issues/608 -@pytest.mark.skip_browser("chromium") async def test_page_route_should_support_cors_for_different_methods(page, server): await page.goto(server.EMPTY_PAGE) await page.route( diff --git a/tests/async/test_video.py b/tests/async/test_video.py index 7d8a900e9..d55e07135 100644 --- a/tests/async/test_video.py +++ b/tests/async/test_video.py @@ -14,10 +14,6 @@ import os -import pytest - -from playwright.async_api import Error - async def test_should_expose_video_path(browser, tmpdir, server): page = await browser.new_page(record_video_dir=tmpdir) @@ -36,10 +32,8 @@ async def test_short_video_should_throw(browser, tmpdir, server): assert os.path.exists(path) -# RELEASE BLOCKER: Temporary upstream issue https://github.com/microsoft/playwright-python/issues/608 -@pytest.mark.skip() async def test_short_video_should_throw_persistent_context( - browser_type, tmpdir, launch_arguments + browser_type, tmpdir, launch_arguments, server ): context = await browser_type.launch_persistent_context( str(tmpdir), @@ -48,7 +42,8 @@ async def test_short_video_should_throw_persistent_context( record_video_dir=str(tmpdir) + "1", ) page = context.pages[0] + await page.goto(server.PREFIX + "/grid.html") await context.close() - with pytest.raises(Error) as exc_info: - await page.video.path() - assert "Page closed" in exc_info.value.message + + path = await page.video.path() + assert str(tmpdir) in str(path) diff --git a/tests/sync/test_video.py b/tests/sync/test_video.py index 2d66ae428..b1bbfa348 100644 --- a/tests/sync/test_video.py +++ b/tests/sync/test_video.py @@ -14,8 +14,6 @@ import os -import pytest - def test_should_expose_video_path(browser, tmpdir, server): page = browser.new_page( @@ -46,8 +44,6 @@ def test_record_video_to_path(browser, tmpdir, server): assert os.path.exists(path) -# RELEASE BLOCKER: Temporary upstream issue https://github.com/microsoft/playwright-python/issues/608 -@pytest.mark.skip() def test_record_video_to_path_persistent( browser_type, tmpdir, server, launch_arguments ): @@ -60,3 +56,16 @@ def test_record_video_to_path_persistent( assert str(tmpdir) in str(path) context.close() assert os.path.exists(path) + + +def test_record_video_can_get_video_path_immediately( + browser_type, tmpdir, launch_arguments +): + context = browser_type.launch_persistent_context( + tmpdir, **launch_arguments, record_video_dir=tmpdir + ) + page = context.pages[0] + path = page.video.path() + assert str(tmpdir) in str(path) + context.close() + assert os.path.exists(path)

dotkom__onlineweb4-1220

Tags with a '.' will crash Ref. http://moonshine.online.ntnu.no/article/10/online-far-ny-nettside

[ { "content": "from django.contrib import admin\nfrom apps.article.models import Article, Tag, ArticleTag\nfrom django.conf import settings\nfrom filebrowser.settings import VERSIONS, ADMIN_THUMBNAIL\n\n\nclass ArticleTagAdmin(admin.ModelAdmin):\n model = ArticleTag\n\n\nclass ArticleTagInline(admin.TabularIn...

diff --git a/apps/article/admin.py b/apps/article/admin.py index ea7facf14..205fab1f4 100755 --- a/apps/article/admin.py +++ b/apps/article/admin.py @@ -18,6 +18,7 @@ class TagAdmin(admin.ModelAdmin): def save_model(self, request, obj, form, change): obj.changed_by = request.user if not change: + obj.name = obj.name.replace('.', '') obj.created_by = request.user obj.save()

gammapy__gammapy-5146

Incorrect return type for `Geom.energy_mask` `Geom.energy_mask` returns a `Map` wit the same geometry as the parent `Geom`. This is incorrect in the currentl documentation which states the return type is `np.array`: https://github.com/gammapy/gammapy/blob/e5aecb334e7aebe304affd96b545a636019f7626/gammapy/maps/geom.py#L628

[ { "content": "# Licensed under a 3-clause BSD style license - see LICENSE.rst\nimport abc\nimport copy\nimport html\nimport inspect\nimport logging\nimport numpy as np\nfrom astropy import units as u\nfrom astropy.io import fits\nfrom .io import find_bands_hdu, find_hdu\nfrom .utils import INVALID_INDEX\n\n__al...

diff --git a/gammapy/maps/geom.py b/gammapy/maps/geom.py index 5afe261137..5d8cefde7c 100644 --- a/gammapy/maps/geom.py +++ b/gammapy/maps/geom.py @@ -625,8 +625,9 @@ def energy_mask(self, energy_min=None, energy_max=None, round_to_edge=False): Returns ------- - mask : `~numpy.ndarray` - Energy mask. + mask : `~gammapy.maps.Map` + Map containing the energy mask. The geometry of the map + is the same as the geometry of the instance which called this method. """ from . import Map

conan-io__conan-center-index-7286

[package] aws-c-event-stream/0.2.7: conflicting openssl versions ``` ERROR: Conflict in s2n/1.0.11: 's2n/1.0.11' requires 'openssl/1.1.1k' while 'aws-c-cal/0.5.11' requires 'openssl/1.1.1l'. To fix this conflict you need to override the package 'openssl' in your root package. ``` seems like it was introduced by #7260 ### Package and Environment Details (include every applicable attribute) * Package Name/Version: **aws-c-event-stream/0.2.7** * Conan version: **conan 1.39.0** ### Conan profile (output of `conan profile show default` or `conan profile show <profile>` if custom profile is in use) ``` [settings] arch=x86_64 arch_build=x86_64 build_type=Release compiler=gcc compiler.libcxx=libstdc++ compiler.version=7 os=Linux os_build=Linux [options] [build_requires] [env] ``` ### Steps to reproduce (Include if Applicable) conan install --build missing aws-c-event-stream/0.2.7@

[ { "content": "from conans import ConanFile, CMake, tools\nfrom conans.errors import ConanInvalidConfiguration\nimport os\n\nrequired_conan_version = \">=1.33.0\"\n\nclass S2n(ConanFile):\n name = \"s2n\"\n description = \"An implementation of the TLS/SSL protocols\"\n topics = (\"conan\", \"aws\", \"am...

diff --git a/recipes/s2n/all/conanfile.py b/recipes/s2n/all/conanfile.py index 12cf8ff20e2f6..dbe79bb113a09 100644 --- a/recipes/s2n/all/conanfile.py +++ b/recipes/s2n/all/conanfile.py @@ -36,7 +36,7 @@ def configure(self): del self.settings.compiler.libcxx def requirements(self): - self.requires("openssl/1.1.1k") + self.requires("openssl/1.1.1l") def source(self): tools.get(**self.conan_data["sources"][self.version],

ansible__ansible-modules-core-4989

fstab parameter of mount module won't work ##### Issue Type: - Bug Report ##### Ansible Version: ansible 2.0.0.2 config file = /etc/ansible/ansible.cfg configured module search path = /usr/share/ansible ##### Ansible Configuration: ##### Environment: Ubuntu 14.04 64Bit ##### Summary: set fstab=**/tmp/fstab** in mount module result in 'can't find mount point in **/etc/fstab**' ##### Steps To Reproduce: ``` ./test-module -m ../lib/ansible/modules/core/system/mount.py -a "src=/dev/sda9 name=/tmp/mnt fstype=ext3 state=mounted **fstab=/tmp/fstab**" ``` ##### Expected Results: ``` changed: ok ``` and a line in /tmp/fstab and 'mount -a' should show the mounted device ##### Actual Results: ``` *********************************** PARSED OUTPUT { "failed": true, "invocation": { "module_args": { "dump": null, "fstab": **"/tmp/fstab"**, "fstype": "ext3", "name": "/tmp/mnt", "opts": null, "passno": null, "src": "/dev/sda9", "state": "mounted" } }, "msg": "Error mounting /tmp/mnt: mount: /tmp/mnt konnte nicht in **/etc/fstab oder /etc/mtab** gefunden werden\n" } ```

[ { "content": "#!/usr/bin/python\n# -*- coding: utf-8 -*-\n\n# (c) 2012, Red Hat, inc\n# Written by Seth Vidal\n# based on the mount modules from salt and puppet\n#\n# This file is part of Ansible\n#\n# Ansible is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Publi...

diff --git a/system/mount.py b/system/mount.py index 38785cd9303..1033c3f80ab 100644 --- a/system/mount.py +++ b/system/mount.py @@ -375,7 +375,7 @@ def mount(module, **kwargs): if get_platform().lower() == 'freebsd': cmd += ['-F', args['fstab']] - elif get_platform().lower() == 'linux': + elif get_platform().lower() == 'linux' and args['fstab'] != '/etc/fstab': cmd += ['-T', args['fstab']] cmd += [name]

zalando__patroni-2309

Patroni fails to completely strip enclosing brackets around IPv6 addresses as part of a list when port is specified **Describe the bug** When specifying PostgreSQL listen IPv6 addresses (postgresql.listen) in the Patroni configuration, Patroni fails to strip all enclosing brackets around IPv6 addresses, leaving the leading bracket on the last IPv6 address in the list. Example: _/etc/patroni/patroni.yml_: ``` ... postgresql: config_dir: /var/lib/pgsql/14/data listen: '127.0.0.1, 2001:db8::11, [2001:db8::1:2]:5678' ... ``` Resulting _/var/lib/pgsql/14/data/postgresql.conf_: ``` ... listen_addresses = '127.0.0.1, 2001:db8::11, [2001:db8::1:2' port = '5678' ... ``` However if only a single IPv6 address is specified, it works correctly: _/etc/patroni/patroni.yml_: ``` ... postgresql: config_dir: /var/lib/pgsql/14/data listen: '[2001:db8::1:2]:5678' ... ``` Resulting _/var/lib/pgsql/14/data/postgresql.conf_: ``` ... listen_addresses = 2001:db8::1:2' port = '5678' ... ``` **To Reproduce** Steps to reproduce the behavior: Configure Patroni with postgresql.listen with a list of IPv6 addresses, with the last address in the list being a bracket-enclosed IPv6 address with a port **Expected behavior** Patroni should correctly strip all enclosing brackets from IPv6 addresses **Environment** - Patroni version: 2.1.3 - PostgreSQL version: 14.1 - DCS (and its version): etcd 3.4.18 **Patroni configuration file** ``` ... postgresql: config_dir: /var/lib/pgsql/14/data listen: '127.0.0.1, 2001:db8::11, [2001:db8::1:2]:5678' ... ``` **Have you tried to use GitHub issue search?** Yes

[ { "content": "import errno\nimport json.decoder as json_decoder\nimport logging\nimport os\nimport platform\nimport random\nimport re\nimport socket\nimport sys\nimport tempfile\nimport time\n\nfrom dateutil import tz\n\nfrom .exceptions import PatroniException\nfrom .version import __version__\n\ntzutc = tz.tz...

diff --git a/patroni/utils.py b/patroni/utils.py index 1cfad9196..01953d05d 100644 --- a/patroni/utils.py +++ b/patroni/utils.py @@ -362,7 +362,7 @@ def polling_loop(timeout, interval=1): def split_host_port(value, default_port): t = value.rsplit(':', 1) if ':' in t[0]: - t[0] = t[0].strip('[]') + t[0] = ','.join([h.strip().strip('[]') for h in t[0].split(',')]) t.append(default_port) return t[0], int(t[1])

wemake-services__wemake-python-styleguide-1261

Bump flake8-builtins New version of `flake8-builtins` is released: `1.5.2` We need to update our dependency here: https://github.com/wemake-services/wemake-python-styleguide/blob/master/pyproject.toml#L63 Here's how to do it: https://github.com/wemake-services/wemake-python-styleguide/blob/master/CONTRIBUTING.md#dependencies Bump flake8-builtins New version of `flake8-builtins` is released: `1.5.2` We need to update our dependency here: https://github.com/wemake-services/wemake-python-styleguide/blob/master/pyproject.toml#L63 Here's how to do it: https://github.com/wemake-services/wemake-python-styleguide/blob/master/CONTRIBUTING.md#dependencies

[ { "content": "\"\"\"\nProvides configuration options for ``wemake-python-styleguide``.\n\nWe do not like our linter to be highly configurable.\nSince, people may take the wrong path or make wrong decisions.\nWe try to make all defaults as reasonable as possible.\n\nHowever, you can currently adjust some complex...

diff --git a/.github/workflows/wps.yml b/.github/workflows/wps.yml index a876ea97d..e0850dbdd 100644 --- a/.github/workflows/wps.yml +++ b/.github/workflows/wps.yml @@ -17,3 +17,4 @@ jobs: reporter: 'github-pr-review' env: GITHUB_TOKEN: ${{ secrets.github_token }} + continue-on-error: true # this step is optional diff --git a/poetry.lock b/poetry.lock index cc6355a5e..978540b6e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -350,7 +350,7 @@ description = "Check for python builtins being used as variables or parameters." name = "flake8-builtins" optional = false python-versions = "*" -version = "1.4.2" +version = "1.5.2" [package.dependencies] flake8 = "*" @@ -998,7 +998,7 @@ wcwidth = "*" [[package]] category = "dev" description = "Run a subprocess in a pseudo terminal" -marker = "python_version >= \"3.4\" and sys_platform != \"win32\" or sys_platform != \"win32\"" +marker = "python_version >= \"3.4\" and sys_platform != \"win32\" or sys_platform != \"win32\" or python_version >= \"3.4\" and sys_platform != \"win32\" and (python_version >= \"3.4\" and sys_platform != \"win32\" or sys_platform != \"win32\")" name = "ptyprocess" optional = false python-versions = "*" @@ -1543,7 +1543,7 @@ docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"] testing = ["jaraco.itertools", "func-timeout"] [metadata] -content-hash = "e8deb40b077abedec266929ad9972460ab948af5e3b99a8a56e31a0a59436770" +content-hash = "57b3f310e944a44b9489424860624bccd7c8e184d287b5f90c0eccb6ac2ad3f1" python-versions = "^3.6" [metadata.files] @@ -1701,8 +1701,8 @@ flake8-bugbear = [ {file = "flake8_bugbear-19.8.0-py35.py36.py37-none-any.whl", hash = "sha256:ded4d282778969b5ab5530ceba7aa1a9f1b86fa7618fc96a19a1d512331640f8"}, ] flake8-builtins = [ - {file = "flake8-builtins-1.4.2.tar.gz", hash = "sha256:c44415fb19162ef3737056e700d5b99d48c3612a533943b4e16419a5d3de3a64"}, - {file = "flake8_builtins-1.4.2-py2.py3-none-any.whl", hash = "sha256:29bc0f7e68af481d088f5c96f8aeb02520abdfc900500484e3af969f42a38a5f"}, + {file = "flake8-builtins-1.5.2.tar.gz", hash = "sha256:fe7be13fe51bfb06bdae6096c6488e328c822c3aa080e24b91b77116a4fbb8b0"}, + {file = "flake8_builtins-1.5.2-py2.py3-none-any.whl", hash = "sha256:a0296d23da92a6f2494243b9f2039bfdb73f34aba20054c1b70b2a60c84745bb"}, ] flake8-commas = [ {file = "flake8-commas-2.0.0.tar.gz", hash = "sha256:d3005899466f51380387df7151fb59afec666a0f4f4a2c6a8995b975de0f44b7"}, diff --git a/pyproject.toml b/pyproject.toml index 5a5a5f82d..a57829844 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -60,7 +60,7 @@ astor = "^0.8" pygments = "^2.4" importlib-metadata = {version = "*", python = "<3.8"} -flake8-builtins = "^1.4.2" +flake8-builtins = "^1.5.2" flake8-commas = "^2.0" flake8-quotes = "^2.0.1" flake8-comprehensions = "^3.1.0" diff --git a/wemake_python_styleguide/options/config.py b/wemake_python_styleguide/options/config.py index 1fd2ffa86..415def7b3 100644 --- a/wemake_python_styleguide/options/config.py +++ b/wemake_python_styleguide/options/config.py @@ -155,7 +155,7 @@ class _Option(object): long_option_name: str default: ConfigValuesTypes - help: str + help: str # noqa: A003 type: Optional[str] = 'int' # noqa: A003 parse_from_config: bool = True action: str = 'store'

microsoft__playwright-python-13

[BUG]: page.getAttribute returns None Actual: ```py import asyncio from playwright_web import chromium async def run(): browser = await chromium.launch(headless=False) context = await browser.newContext(viewport=0) # 0 stands for no viewport page = await context.newPage() await page.setContent("""" <input id="kekstar"/> """) await page.fill("#kekstar", "Foobar") print(await page.getAttribute("#kekstar", 'value')) await browser.close() asyncio.get_event_loop().run_until_complete(run()) ``` Expected: Returns Foobar On Try Playwright, it works: https://try.playwright.tech/?s=dzmwi

[ { "content": "# Copyright (c) Microsoft Corporation.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apache.org/licenses/LICENSE-2.0\n#\n# Unless required by ap...

diff --git a/playwright_web/frame.py b/playwright_web/frame.py index bd0a75df7..0f7ec60e2 100644 --- a/playwright_web/frame.py +++ b/playwright_web/frame.py @@ -181,7 +181,7 @@ async def getAttribute(self, selector: str, name: str, timeout: int = None) -> str: - await self._channel.send('getAttribute', locals_to_params(locals())) + return await self._channel.send('getAttribute', locals_to_params(locals())) async def hover(self, selector: str,

ansible__molecule-649

ansible-lint called from Molecule fails when no Ansible-installed-with-pip is present # Issue Type - Bug report # Molecule and Ansible details ``` # ansible --version ansible 2.2.1.0 (stable-2.2 acad2ba246) last updated 2016/12/11 20:27:02 (GMT +900) lib/ansible/modules/core: (detached HEAD 8139278530) last updated 2016/12/11 20:30:10 (GMT +900) lib/ansible/modules/extras: (detached HEAD f5f1fc934a) last updated 2016/12/11 20:30:10 (GMT +900) config file = configured module search path = Default w/o overrides # molecule --version molecule, version 1.16.1 ``` - Molecule installation method: pip - Ansible installation method: source # Desired Behaviour ``` # molecule verify --> Executing ansible-lint... [ANSIBLE0002] Trailing whitespace playbook.yml:7 - ansible-unix-python-environment ``` # Actual Behaviour (Bug report only) ``` # pip uninstall ansible ((( cut ))) Successfully uninstalled ansible-2.2.0.0 # . /usr/local/src/ansible/hacking/env-setup ((( cut ))) PYTHONPATH=/usr/local/src/ansible/lib: ((( cut ))) # ansible --version ansible 2.2.1.0 (stable-2.2 acad2ba246) last updated 2016/12/11 20:27:02 (GMT +900) lib/ansible/modules/core: (detached HEAD 8139278530) last updated 2016/12/11 20:30:10 (GMT +900) lib/ansible/modules/extras: (detached HEAD f5f1fc934a) last updated 2016/12/11 20:30:10 (GMT +900) config file = configured module search path = Default w/o overrides # molecule --debug verify --> Executing ansible-lint... DEBUG: COMMAND /usr/local/bin/ansible-lint playbook.yml --exclude .git --exclude .vagrant --exclude .molecule Traceback (most recent call last): File "/usr/local/bin/ansible-lint", line 30, in <module> import ansiblelint File "/usr/local/lib/python2.7/site-packages/ansiblelint/__init__.py", line 26, in <module> import ansiblelint.utils File "/usr/local/lib/python2.7/site-packages/ansiblelint/utils.py", line 25, in <module> import ansible.constants as C ImportError: No module named ansible.constants # /usr/local/bin/ansible-lint playbook.yml --exclude .git --exclude .vagrant --exclude .molecule [ANSIBLE0002] Trailing whitespace playbook.yml:7 - ansible-unix-python-environment ``` # Further tests With Ansible 2.2.0 installed with `pip` (regardless if the one from source configured or not; configured in the example below): ``` # pip install ansible ((( cut ))) Successfully installed ansible-2.2.0.0 # . /usr/local/src/ansible/hacking/env-setup ((( cut ))) # ansible --version ansible 2.2.1.0 (stable-2.2 acad2ba246) last updated 2016/12/11 20:27:02 (GMT +900) lib/ansible/modules/core: (detached HEAD 8139278530) last updated 2016/12/11 20:30:10 (GMT +900) lib/ansible/modules/extras: (detached HEAD f5f1fc934a) last updated 2016/12/11 20:30:10 (GMT +900) config file = configured module search path = Default w/o overrides # molecule verify --> Executing ansible-lint... [ANSIBLE0002] Trailing whitespace playbook.yml:7 - ansible-unix-python-environment ```

[ { "content": "# Copyright (c) 2015-2016 Cisco Systems, Inc.\n#\n# Permission is hereby granted, free of charge, to any person obtaining a copy\n# of this software and associated documentation files (the \"Software\"), to\n# deal in the Software without restriction, including without limitation the\n# right...

diff --git a/molecule/verifier/ansible_lint.py b/molecule/verifier/ansible_lint.py index fc117028c6..078a03e101 100644 --- a/molecule/verifier/ansible_lint.py +++ b/molecule/verifier/ansible_lint.py @@ -49,6 +49,7 @@ def execute(self): env = { 'ANSIBLE_CONFIG': self._molecule.config.config['ansible']['config_file'], + 'PYTHONPATH': os.environ.get('PYTHONPATH'), 'HOME': os.environ.get('HOME') }

freedomofpress__securedrop-2998

securedrop-admin sdconfig erases additional values in site-specific # Bug ## Description securedrop-admin sdconfig erases values in site-specific when they are not prompted for. `securedrop-admin sdconfig` should not erase entries in site-specific, which would help testing (e.g.: releases that are in development or perhaps alpha/beta features). ## Steps to Reproduce * edit `/install_files/ansible-base/group-vars/all/site-specific` and add another value * run ./securedrop-admin sdconfig * open `/install_files/ansible-base/group-vars/all/site-specific` and observe your value has disappeared ## Expected Behavior `securedrop-admin sdconfig` should not erase entries in `/install_files/ansible-base/group-vars/all/site-specific`. ## Actual Behavior `ecuredrop-admin sdconfig` erases entries in `/install_files/ansible-base/group-vars/all/site-specific`.

[ { "content": "# -*- mode: python; coding: utf-8 -*-\n#\n# Copyright (C) 2013-2018 Freedom of the Press Foundation & al\n# Copyright (C) 2018 Loic Dachary <loic@dachary.org>\n#\n# This program is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as...

diff --git a/admin/securedrop_admin/__init__.py b/admin/securedrop_admin/__init__.py index dc6290e6ce..4f88ccca58 100755 --- a/admin/securedrop_admin/__init__.py +++ b/admin/securedrop_admin/__init__.py @@ -291,7 +291,7 @@ def load_and_update_config(self): return self.update_config() def update_config(self): - self.config = self.user_prompt_config() + self.config.update(self.user_prompt_config()) self.save() self.validate_gpg_keys() return True diff --git a/admin/tests/files/site-specific b/admin/tests/files/site-specific index 9ec6831e83..c335c14b3c 100644 --- a/admin/tests/files/site-specific +++ b/admin/tests/files/site-specific @@ -17,3 +17,4 @@ securedrop_supported_locales: smtp_relay: smtp.gmail.com smtp_relay_port: 587 ssh_users: sd +user_defined_variable: "must not be discarded" diff --git a/admin/tests/test_securedrop-admin.py b/admin/tests/test_securedrop-admin.py index 6b76cb2142..4147de11ea 100644 --- a/admin/tests/test_securedrop-admin.py +++ b/admin/tests/test_securedrop-admin.py @@ -297,6 +297,7 @@ def test_update_config(self, mock_save, mock_validate_input): site_config = securedrop_admin.SiteConfig(args) assert site_config.load_and_update_config() + assert 'user_defined_variable' in site_config.config mock_save.assert_called_once() mock_validate_input.assert_called()

carpentries__amy-770

Names show up multiple times in assignment pulldown 1. Go to an event. 2. Try to assign to assign to someone other than yourself. 3. Selection dialog with pulldown appears so that you can choose person. 4. Some names (currently Greg Wilson and Tracy Teal, possibly others) show up multiple times in that list.

[ { "content": "from functools import reduce\nimport operator\nimport re\n\nfrom django.contrib.auth.models import Group\nfrom django.db.models import Q\n\nfrom selectable.base import ModelLookup\nfrom selectable.registry import registry\nfrom selectable.decorators import login_required\n\nfrom workshops import m...

diff --git a/workshops/lookups.py b/workshops/lookups.py index 2fef53b01..8f1108d38 100644 --- a/workshops/lookups.py +++ b/workshops/lookups.py @@ -83,7 +83,7 @@ def get_query(self, request, term): admin_group = Group.objects.get(name='administrators') results = results.filter( Q(is_superuser=True) | Q(groups__in=[admin_group]) - ) + ).distinct() return results

bokeh__bokeh-1617

BokehJS unrecoverable errors in notebook It seems easy to get the notebook into an unrecoverable state when using `push_notebook` and IPython interactors. Must close the session entirely and start again to regain plots. Executing all the cells in the notebook stored in this gist: https://gist.github.com/bryevdv/b4e9eb68a6234a67a570 should reproduce the problem. To be specific, by "unrecoverable" I mean that clearing all cells and restarting the kernel from the menu does not fix the problem. It is still impossible to generate plots. I have had to close the tab and shutdown from the IPython home notebook list, then re-open a new tab to be able to plot again. @damianavila this is a pretty serious bug. We should try to fix it for 0.7.1 for sure. I will take a look and add any findings but I may need your input/assistance.

[ { "content": "from __future__ import absolute_import\n\nfrom six import iteritems\nfrom collections import OrderedDict\n\nfrom .models import glyphs, markers\nfrom .mixins import FillProps, LineProps\n\ndef _glyph_function(glyphclass, dsnames, argnames, docstring, xfields=[\"x\"], yfields=[\"y\"]):\n\n def f...

diff --git a/bokeh/_glyph_functions.py b/bokeh/_glyph_functions.py index 757e0d784c6..ce6c3e21fcd 100644 --- a/bokeh/_glyph_functions.py +++ b/bokeh/_glyph_functions.py @@ -49,8 +49,6 @@ def func(document_or_plot, *args, **kwargs): raise ValueError("expected document or plot object for first argument") name = kwargs.pop('name', None) - if name: - plot._id = name select_tool = _get_select_tool(plot)

voxel51__fiftyone-1392

[BUG] App label filter not working in Colab I ran through the [quickstart](https://colab.research.google.com/github/voxel51/fiftyone-examples/blob/master/examples/quickstart.ipynb) in Colab (using `fiftyone==0.14.0`) and found an App error when trying to use a `label` filter in the App. The error also occurred when using the same label filter from the expanded modal. However, other filters such as confidence and the alternate low-choices mode of the label filter were working as expected, so I believe this is strictly related to the autocomplete-style filter UI. I cannot reproduce this error using `fiftyone==0.14.0` outside of colab. <img width="1156" alt="Screen Shot 2021-11-03 at 10 54 54 AM" src="https://user-images.githubusercontent.com/25985824/140086403-9f2ab519-c595-47a9-a3b3-a7b772ace06e.png">

[ { "content": "\"\"\"\nFiftyOne Tornado server.\n\n| Copyright 2017-2021, Voxel51, Inc.\n| `voxel51.com <https://voxel51.com/>`_\n|\n\"\"\"\nimport asyncio\nimport argparse\nfrom collections import defaultdict\nfrom datetime import date, datetime, timedelta\nimport math\nimport os\nimport traceback\n\nimport tor...

diff --git a/fiftyone/server/main.py b/fiftyone/server/main.py index 0fd89313b25..439f83b4369 100644 --- a/fiftyone/server/main.py +++ b/fiftyone/server/main.py @@ -377,6 +377,7 @@ async def post(self): message = {"state": StateHandler.state} if event in { + "count_values", "distinct", "distributions", "get_video_data",

ansible__ansible-modules-core-3295

size parameter required set to be no when state is absent in os_volume ##### Issue Type: - Documentation Report ##### Plugin Name: os_volume ##### Ansible Version: ``` 2.4 ``` ##### Ansible Configuration:  ##### Environment: centos 6 ##### Summary: def _absent_volume(module, cloud): try: cloud.delete_volume( name_or_id=module.params['display_name'], wait=module.params['wait'], timeout=module.params['timeout']) No need to add size parameter while calling os_volume as delete_volume function does not need size parameter . http://docs.ansible.com/ansible/os_volume_module.html this document needs to be modified. size parameter required set to be 'NO' when state is absent in os_volume ##### Steps To Reproduce:  ``````  ``` - name: "Delete Volumes attached" os_volume: state: "absent" display_name: "{{ item.id }}" timeout: "360" auth: auth_url: "{{ openstack_auth_url }}" username: "{{ openstack_username }}" password: "{{ openstack_password }}" project_name: "{{ openstack_tenant }}" environment: OS_VOLUME_API_VERSION: "1" OS_IMAGE_API_VERSION: "1" security_groups: default  ##### Expected Results:  ##### Actual Results:  ``````  ``` ```

[ { "content": "#!/usr/bin/python\n\n# Copyright (c) 2014 Hewlett-Packard Development Company, L.P.\n#\n# This module is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as published by\n# the Free Software Foundation, either version 3 of the License, or...

diff --git a/cloud/openstack/os_volume.py b/cloud/openstack/os_volume.py index 5a3d0aacab0..9e7436e1a5f 100644 --- a/cloud/openstack/os_volume.py +++ b/cloud/openstack/os_volume.py @@ -35,8 +35,9 @@ options: size: description: - - Size of volume in GB - required: only when state is 'present' + - Size of volume in GB. This parameter is required when the + I(state) parameter is 'present'. + required: false default: None display_name: description:

wagtail__wagtail-6263

Missing SVG icons for optional rich text features ### Issue Summary Wagtail doesn't provide SVG icons for optional rich text features like strikethrough, superscript and subscript. It would also be a good addition to provide an SVG icon for underline as well, even though this rich feature is not implemented at the moment. ### Steps to Reproduce 1. Enable the "strikethrough" rich feature: ```python class RichTextBlock(blocks.RichTextBlock): def __init__(self, **kwargs): super().__init__( features=[ 'bold', 'italic', 'strikethrough', ], **kwargs) ``` 2. Check the rich editor menu and see the empty space where it's supposed to be an icon. ![Screenshot 2020-07-28 at 13 30 58](https://user-images.githubusercontent.com/3457859/88666048-70f6f400-d0d7-11ea-8499-36f0f7989803.png) * I have confirmed that this issue can be reproduced as described on a fresh Wagtail project: (yes / no) Yes ### Technical details * Python version: Run `python --version`. ``` Python 3.8.3 ``` * Django version: Look in your requirements.txt, or run `pip show django | grep Version`. ``` Version: 3.0.8 ``` * Wagtail version: Look at the bottom of the Settings menu in the Wagtail admin, or run `pip show wagtail | grep Version:`. ``` Version: 2.10rc1 ``` * Browser version: You can use https://www.whatsmybrowser.org/ to find this out. ``` Chrome 84 ```

[ { "content": "from django.contrib.auth.models import Permission\nfrom django.urls import reverse\nfrom django.utils.http import urlencode\nfrom django.utils.translation import gettext_lazy as _\nfrom django.utils.translation import gettext\nfrom draftjs_exporter.dom import DOM\n\nimport wagtail.admin.rich_text....

diff --git a/client/src/components/Draftail/Draftail.scss b/client/src/components/Draftail/Draftail.scss index 0ce61e81f453..d8c3d6e6650c 100644 --- a/client/src/components/Draftail/Draftail.scss +++ b/client/src/components/Draftail/Draftail.scss @@ -110,6 +110,13 @@ $draftail-editor-font-family: $font-serif; border: 1px solid $color-grey-3; } +.Draftail-ToolbarButton { + &:hover, + &:active { + border: 1px solid $color-grey-3; + } +} + .title .Draftail-Editor .public-DraftEditor-content, .title .Draftail-Editor .public-DraftEditorPlaceholder-root { font-size: 2em; diff --git a/wagtail/admin/templates/wagtailadmin/icons/strikethrough.svg b/wagtail/admin/templates/wagtailadmin/icons/strikethrough.svg new file mode 100755 index 000000000000..515ac248460f --- /dev/null +++ b/wagtail/admin/templates/wagtailadmin/icons/strikethrough.svg @@ -0,0 +1,3 @@ +<symbol id="icon-strikethrough" viewBox="0 0 512 512"> + <path d="M496 224H293.9l-87.17-26.83A43.55 43.55 0 0 1 219.55 112h66.79A49.89 49.89 0 0 1 331 139.58a16 16 0 0 0 21.46 7.15l42.94-21.47a16 16 0 0 0 7.16-21.46l-.53-1A128 128 0 0 0 287.51 32h-68a123.68 123.68 0 0 0-123 135.64c2 20.89 10.1 39.83 21.78 56.36H16a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h480a16 16 0 0 0 16-16v-32a16 16 0 0 0-16-16zm-180.24 96A43 43 0 0 1 336 356.45 43.59 43.59 0 0 1 292.45 400h-66.79A49.89 49.89 0 0 1 181 372.42a16 16 0 0 0-21.46-7.15l-42.94 21.47a16 16 0 0 0-7.16 21.46l.53 1A128 128 0 0 0 224.49 480h68a123.68 123.68 0 0 0 123-135.64 114.25 114.25 0 0 0-5.34-24.36z"></path> +</symbol> diff --git a/wagtail/admin/templates/wagtailadmin/icons/subscript.svg b/wagtail/admin/templates/wagtailadmin/icons/subscript.svg new file mode 100755 index 000000000000..1b42cd01a2e7 --- /dev/null +++ b/wagtail/admin/templates/wagtailadmin/icons/subscript.svg @@ -0,0 +1,3 @@ +<symbol id="icon-subscript" viewBox="0 0 512 512"> + <path d="M496 448h-16V304a16 16 0 0 0-16-16h-48a16 16 0 0 0-14.29 8.83l-16 32A16 16 0 0 0 400 352h16v96h-16a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h96a16 16 0 0 0 16-16v-32a16 16 0 0 0-16-16zM336 64h-67a16 16 0 0 0-13.14 6.87l-79.9 115-79.9-115A16 16 0 0 0 83 64H16A16 16 0 0 0 0 80v48a16 16 0 0 0 16 16h33.48l77.81 112-77.81 112H16a16 16 0 0 0-16 16v48a16 16 0 0 0 16 16h67a16 16 0 0 0 13.14-6.87l79.9-115 79.9 115A16 16 0 0 0 269 448h67a16 16 0 0 0 16-16v-48a16 16 0 0 0-16-16h-33.48l-77.81-112 77.81-112H336a16 16 0 0 0 16-16V80a16 16 0 0 0-16-16z"></path> +</symbol> diff --git a/wagtail/admin/templates/wagtailadmin/icons/superscript.svg b/wagtail/admin/templates/wagtailadmin/icons/superscript.svg new file mode 100755 index 000000000000..61b949d8742f --- /dev/null +++ b/wagtail/admin/templates/wagtailadmin/icons/superscript.svg @@ -0,0 +1,3 @@ +<symbol id="icon-superscript" viewBox="0 0 512 512"> + <path d="M496 160h-16V16a16 16 0 0 0-16-16h-48a16 16 0 0 0-14.29 8.83l-16 32A16 16 0 0 0 400 64h16v96h-16a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h96a16 16 0 0 0 16-16v-32a16 16 0 0 0-16-16zM336 64h-67a16 16 0 0 0-13.14 6.87l-79.9 115-79.9-115A16 16 0 0 0 83 64H16A16 16 0 0 0 0 80v48a16 16 0 0 0 16 16h33.48l77.81 112-77.81 112H16a16 16 0 0 0-16 16v48a16 16 0 0 0 16 16h67a16 16 0 0 0 13.14-6.87l79.9-115 79.9 115A16 16 0 0 0 269 448h67a16 16 0 0 0 16-16v-48a16 16 0 0 0-16-16h-33.48l-77.81-112 77.81-112H336a16 16 0 0 0 16-16V80a16 16 0 0 0-16-16z"></path> +</symbol> diff --git a/wagtail/admin/wagtail_hooks.py b/wagtail/admin/wagtail_hooks.py index 43fb7ffdce49..76de591fad75 100644 --- a/wagtail/admin/wagtail_hooks.py +++ b/wagtail/admin/wagtail_hooks.py @@ -780,7 +780,10 @@ def register_icons(icons): 'site.svg', 'snippet.svg', 'spinner.svg', + 'strikethrough.svg', 'success.svg', + 'subscript.svg', + 'superscript.svg', 'table.svg', 'tag.svg', 'tasks.svg', diff --git a/wagtail/contrib/styleguide/templates/wagtailstyleguide/base.html b/wagtail/contrib/styleguide/templates/wagtailstyleguide/base.html index ae8a7f0f342a..0a2151d88f7e 100644 --- a/wagtail/contrib/styleguide/templates/wagtailstyleguide/base.html +++ b/wagtail/contrib/styleguide/templates/wagtailstyleguide/base.html @@ -845,6 +845,9 @@ <h2>SVG Icons</h2> <li>{% icon 'list-ul' %} list-ul</li> <li>{% icon 'link' %} link</li> <li>{% icon 'link-external' %} link-external</li> + <li>{% icon 'superscript' %} superscript</li> + <li>{% icon 'subscript' %} subscript</li> + <li>{% icon 'strikethrough' %} strikethrough</li> <li>{% icon 'radio-full' %} radio-full</li> <li>{% icon 'radio-empty' %} radio-empty</li> <li>{% icon 'arrow-up-big' %} arrow-up-big</li>

comic__grand-challenge.org-1062

The schema is empty for unauthorised users. Another problem with this - the schema is empty for unauthorised users. You need to add `public=True` to `get_schema_view`. _Originally posted by @jmsmkn in https://github.com/comic/grand-challenge.org/issues/1017#issuecomment-567254400_

[ { "content": "from django.conf import settings\nfrom django.conf.urls import include, url\nfrom django.urls import path\nfrom drf_yasg import openapi\nfrom drf_yasg.views import get_schema_view\nfrom rest_framework import permissions, routers\n\nfrom grandchallenge.algorithms.views import (\n AlgorithmImageV...

diff --git a/app/grandchallenge/api/urls.py b/app/grandchallenge/api/urls.py index df1c4687dd..83ed74ac34 100644 --- a/app/grandchallenge/api/urls.py +++ b/app/grandchallenge/api/urls.py @@ -78,6 +78,7 @@ "policies:detail", kwargs={"slug": "terms-of-service"} ), ), + public=True, permission_classes=(permissions.AllowAny,), patterns=[path("api/v1/", include(router.urls))], ) diff --git a/app/tests/api_tests/test_urls.py b/app/tests/api_tests/test_urls.py index 1e3f5c45d5..6e5b91da23 100644 --- a/app/tests/api_tests/test_urls.py +++ b/app/tests/api_tests/test_urls.py @@ -17,6 +17,10 @@ def test_api_docs_generation( client, schema, schema_format, ): kwargs = dict(format=schema_format) if schema == "schema-json" else None - assert_viewname_status( - code=200, url=reverse(f"api:{schema}", kwargs=kwargs), client=client, + response = assert_viewname_status( + code=200, url=reverse(f"api:{schema}", kwargs=kwargs), client=client ) + if schema_format is not None: + assert len(response.data["paths"]) > 0 + else: + assert len(response.content) > 0

Cog-Creators__Red-DiscordBot-4453

Stop backing up lavalink logs Lavalink logs are host specific, stop backing them up.

[ { "content": "from __future__ import annotations\n\nimport asyncio\nimport collections.abc\nimport json\nimport logging\nimport os\nimport re\nimport shutil\nimport tarfile\nfrom datetime import datetime\nfrom pathlib import Path\nfrom typing import (\n AsyncIterator,\n Awaitable,\n Callable,\n Iter...

diff --git a/redbot/core/utils/_internal_utils.py b/redbot/core/utils/_internal_utils.py index e5ffb6ebb52..c91149f0f12 100644 --- a/redbot/core/utils/_internal_utils.py +++ b/redbot/core/utils/_internal_utils.py @@ -211,6 +211,7 @@ async def create_backup(dest: Path = Path.home()) -> Optional[Path]: os.path.join("Downloader", "lib"), os.path.join("CogManager", "cogs"), os.path.join("RepoManager", "repos"), + os.path.join("Audio", "logs"), ] # Avoiding circular imports

plotly__dash-565

New version of dash_renderer is not automatically installed with Dash 0.36.0 Deploying apps on Dash Deployment Server results in `dash-renderer` not being updated if it is already installed (even if that version is `0.16.x` and the Dash version is specified as `0.36.0`. This causes an `Error loading dependencies`, as `dash-renderer` attempts to attach event handlers to Dash events, which don't exist any more.

[ { "content": "import io\nfrom setuptools import setup, find_packages\n\nmain_ns = {}\nexec(open('dash/version.py').read(), main_ns) # pylint: disable=exec-used\n\nsetup(\n name='dash',\n version=main_ns['__version__'],\n author='chris p',\n author_email='chris@plot.ly',\n packages=find_packages(...

diff --git a/.circleci/requirements/dev-requirements-py37.txt b/.circleci/requirements/dev-requirements-py37.txt index f23f28d4a7..45d9a67f42 100644 --- a/.circleci/requirements/dev-requirements-py37.txt +++ b/.circleci/requirements/dev-requirements-py37.txt @@ -1,8 +1,8 @@ -dash_core_components>=0.40.2 -dash_html_components==0.12.0rc3 +dash_core_components>=0.43.0 +dash_html_components==0.13.4 dash-flow-example==0.0.3 dash-dangerously-set-inner-html -git+git://github.com/plotly/dash-renderer@master#egg=dash_renderer +dash_renderer==0.17.0 percy selenium mock diff --git a/.circleci/requirements/dev-requirements.txt b/.circleci/requirements/dev-requirements.txt index dce645d828..01fef6eca0 100644 --- a/.circleci/requirements/dev-requirements.txt +++ b/.circleci/requirements/dev-requirements.txt @@ -1,8 +1,8 @@ -dash_core_components>=0.40.2 -dash_html_components>=0.12.0rc3 +dash_core_components>=0.43.0 +dash_html_components==0.13.4 dash_flow_example==0.0.3 dash-dangerously-set-inner-html -git+git://github.com/plotly/dash-renderer@master#egg=dash_renderer +dash_renderer==0.17.0 percy selenium mock diff --git a/CHANGELOG.md b/CHANGELOG.md index 015999416a..f9e7c9a630 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,9 @@ ## Fixed - Fixed collections.abc deprecation warning for python 3.8 [#563](https://github.com/plotly/dash/pull/563) +## Changed +- Added core libraries as version locked dependencies [#565](https://github.com/plotly/dash/pull/565) + ## [0.36.0] - 2019-01-25 ## Removed - Removed support for `Event` system. Use event properties instead, for example the `n_clicks` property instead of the `click` event, see [#531](https://github.com/plotly/dash/issues/531) for details. `dash_renderer` MUST be upgraded to >=0.17.0 together with this, and it is recommended to update `dash_core_components` to >=0.43.0 and `dash_html_components` to >=0.14.0. [#550](https://github.com/plotly/dash/pull/550) diff --git a/setup.py b/setup.py index 5c27cc94ee..daf3906671 100644 --- a/setup.py +++ b/setup.py @@ -20,7 +20,10 @@ 'Flask>=0.12', 'flask-compress', 'plotly', - 'dash_renderer', + 'dash_renderer==0.17.0', + 'dash-core-components==0.43.0', + 'dash-html-components==0.13.5', + 'dash-table==3.3.0' ], entry_points={ 'console_scripts': [

lutris__lutris-3306

lutris lutris:rungameid/ does not work **Describe the bug** Using desktop shortcut does work, lutris not starting the game. **Steps to reproduce** - Install kubuntu 20.10 + lutris 0.5.8. - Install game, create a desktop shortcut from lutris. - Try to launch game using desktop shortcut **Lutris debugging output (Optional)** All log: ``` ~ ❯ lutris -d lutris:rungameid/1219 INFO 2020-11-15 15:53:55,474 [application.do_command_line:319]:Lutris 0.5.8 INFO 2020-11-15 15:53:55,474 [startup.check_driver:69]:Running X.Org Mesa driver 20.2.2 on Radeon RX 560 Series (POLARIS11, DRM 3.39.0, 5.9.8-xanmod1, LLVM 11.0.0) (0x67ff) INFO 2020-11-15 15:53:55,475 [startup.check_driver:81]:GPU: 1002:67FF 1043:04BC (amdgpu drivers) ``` **System information (Optional)** [lutris-issue-report.zip](https://github.com/lutris/lutris/files/5542468/lutris-issue-report.zip) **Screenshots (Optional)** If your issue is hard to explain with words, feel free to attach screenshots.

[ { "content": "# pylint: disable=no-member,wrong-import-position\n#\n# Copyright (C) 2020 Mathieu Comandon <strider@strycore.com>\n#\n# This program is free software: you can redistribute it and/or modify\n# it under the terms of the GNU General Public License as published by\n# the Free Software Foundation, eit...

diff --git a/lutris/gui/application.py b/lutris/gui/application.py index 46e955a2ff..71e15a8d65 100644 --- a/lutris/gui/application.py +++ b/lutris/gui/application.py @@ -462,7 +462,7 @@ def do_command_line(self, command_line): # noqa: C901 # pylint: disable=argume self.do_shutdown() return 0 game = Game(db_game["id"]) - self.on_game_start(game) + self.on_game_launch(game) return 0 def on_game_launch(self, game):

django-cms__django-cms-1372

Labels missing in admin for cms.plugins.text I'm using a model that is a subclass of cms.plugins.text.models.AbstractText but in the admin the labels for all fields have disappeared. I think there should be a ``` {{ field.label_tag }} ``` at the appropriate place in /cms/plugins/text/templates/cms/plugins/text_plugin_fieldset.html (also compare with /django/contrib/admin/templates/admin/includes/fieldset.html ). The labels indeed appear when I add that piece of code.

[ { "content": "# -*- coding: utf-8 -*-\nfrom django.conf import settings\nfrom django.http import HttpResponse\nfrom django.shortcuts import render_to_response\nfrom django.template.context import RequestContext\n\nfrom django.contrib.sites.models import Site\n\nfrom cms.models import Page\nfrom cms.utils import...

diff --git a/cms/plugins/text/templates/cms/plugins/text_plugin_change_form.html b/cms/plugins/text/templates/cms/plugins/text_plugin_change_form.html index 82b4a7036e6..162fe95fec0 100644 --- a/cms/plugins/text/templates/cms/plugins/text_plugin_change_form.html +++ b/cms/plugins/text/templates/cms/plugins/text_plugin_change_form.html @@ -5,14 +5,13 @@ {% for fieldset in adminform %} {% include "admin/includes/fieldset.html" %} {% endfor %} -<script type="text/javascript" src="{{ STATIC_URL }}cms/js/libs/classy.min.js"></script> -<script type="text/javascript" src="{{ STATIC_URL }}cms/js/plugins/cms.setup.js"></script> -<script type="text/javascript" src="{{ STATIC_URL }}cms/js/plugins/cms.base.js"></script> <script type="text/javascript"> -jQuery(document).ready(function ($) { - // initialize security patch - CMS.API.Security.csrf(); -}); +(function namespacing(jQuery) { + jQuery(document).ready(function ($) { + // initialize security patch + window.CMS.API.Security.csrf(); + }); +})(window.CMS.$) </script> <style> div.field-body label {display:none} diff --git a/cms/plugins/text/templates/cms/plugins/widgets/wymeditor.html b/cms/plugins/text/templates/cms/plugins/widgets/wymeditor.html index 113e2485894..1c88d30b3be 100644 --- a/cms/plugins/text/templates/cms/plugins/widgets/wymeditor.html +++ b/cms/plugins/text/templates/cms/plugins/widgets/wymeditor.html @@ -7,110 +7,113 @@ {% include "cms/plugins/widgets/widget_lib.js" %} -jQuery(document).ready(function ($) { - // scroll to top - scrollTo(0, 0); - - // init wysiwyg - $('#id_{{ name }}').wymeditor({ - lang: '{{ language }}', - skin: 'django', - skinPath: "{{ STATIC_URL }}cms/js/wymeditor/skins/django/", - updateSelector: 'input[type=submit],', - updateEvent: 'click', - logoHtml: '', - toolsItems: [ - {{ WYM_TOOLS }} - ], - containersItems: [ - {{ WYM_CONTAINERS }} - ], - classesItems: [ - {{ WYM_CLASSES }} - ], - editorStyles: [ - {{ WYM_STYLES }} - ], - {% if WYM_STYLESHEET %} - stylesheet: - {{ WYM_STYLESHEET }} - , - {% endif %} - postInit: function(wym) { - //wym.resizable({handles: "s", maxHeight: 600}); - //construct the insertLinkButton html - html = get_plugin_html() - //add the button to the tools box - jQuery(wym._box) - .find(wym._options.toolsSelector + wym._options.toolsListSelector) - .append(html); - // Enable the placeholderbridge plugin, to allow - // the placeholder controls to talk to editor - wym.placeholderbridge({'name': '{{ name }}'}); - init_buttons("{{ name }}"); - }, - //handle click event on dialog's submit button - postInitDialog: function( wym, wdw ) { - - } - }); - - /* onclick for 'Insert object' */ - function init_buttons(placeholder){ - $('span.insert-object').click(function(){ - var select = $(this).parent().children("select"); - var pluginvalue = select.attr('value'); - var splits = window.location.href.split("?")[0].split("/"); - var parent_id = Number(splits[splits.length - 2]); - var language = $('#id_language').attr('value'); - - if (pluginvalue == "") { - alert("{% filter escapejs %}{% trans "Please select a plugin type." %}{% endfilter %}"); - return; - } - - var texteditor = get_editor(placeholder); - if (texteditor == null || texteditor.insertText == null) { - alert("{% filter escapejs %}{% trans "Text editor does not support inserting objects." %}{% endfilter %}"); - return; - } - // First create db instance using AJAX post back - add_plugin(pluginvalue, parent_id, language) - - }).css("cursor", "pointer").css("margin", "5px"); +(function namespacing(CMS) { + CMS.$(document).ready(function () { + // scroll to top + scrollTo(0, 0); - /* onclick for 'Edit selected object' */ - $('span.edit-object').click(function(){ - var texteditor = get_editor(placeholder); - if (texteditor == null || texteditor.selectedObject == null) { - alert("{% filter escapejs %}{% trans "Text editor does not support editing objects." %}{% endfilter %}"); - return; + // init wysiwyg + $('#id_{{ name }}').wymeditor({ + lang: '{{ language }}', + skin: 'django', + skinPath: "{{ STATIC_URL }}cms/js/wymeditor/skins/django/", + updateSelector: 'input[type=submit],', + updateEvent: 'click', + logoHtml: '', + toolsItems: [ + {{ WYM_TOOLS }} + ], + containersItems: [ + {{ WYM_CONTAINERS }} + ], + classesItems: [ + {{ WYM_CLASSES }} + ], + editorStyles: [ + {{ WYM_STYLES }} + ], + {% if WYM_STYLESHEET %} + stylesheet: + {{ WYM_STYLESHEET }} + , + {% endif %} + postInit: function(wym) { + //wym.resizable({handles: "s", maxHeight: 600}); + //construct the insertLinkButton html + html = get_plugin_html() + //add the button to the tools box + $(wym._box) + .find(wym._options.toolsSelector + wym._options.toolsListSelector) + .append(html); + // Enable the placeholderbridge plugin, to allow + // the placeholder controls to talk to editor + wym.placeholderbridge({'name': '{{ name }}'}); + init_buttons("{{ name }}"); + }, + //handle click event on dialog's submit button + postInitDialog: function( wym, wdw ) { + } - var imgobj = texteditor.selectedObject(); - if (imgobj == null) { - alert("{% filter escapejs %}{% trans "No object selected." %}{% endfilter %}"); - return; - } - if (imgobj.id == null || imgobj.id.indexOf("plugin_obj_") != 0) { - alert("{% filter escapejs %}{% trans "Not a plugin object" %}{% endfilter %}"); - return; - } - var plugin_id = imgobj.id.substr("plugin_obj_".length); - edit_plugin(plugin_id); - }).css("cursor", "pointer").css("margin","5px"); + }); + + /* onclick for 'Insert object' */ + function init_buttons(placeholder){ + $('span.insert-object').click(function(){ + var select = $(this).parent().children("select"); + var pluginvalue = select.attr('value'); + var splits = window.location.href.split("?")[0].split("/"); + var parent_id = Number(splits[splits.length - 2]); + var language = $('#id_language').attr('value'); + + if (pluginvalue == "") { + alert("{% filter escapejs %}{% trans "Please select a plugin type." %}{% endfilter %}"); + return; + } + + var texteditor = get_editor(placeholder); + if (texteditor == null || texteditor.insertText == null) { + alert("{% filter escapejs %}{% trans "Text editor does not support inserting objects." %}{% endfilter %}"); + return; + } + // First create db instance using AJAX post back + add_plugin(pluginvalue, parent_id, language) + + }).css("cursor", "pointer").css("margin", "5px"); + + /* onclick for 'Edit selected object' */ + $('span.edit-object').click(function(){ + var texteditor = get_editor(placeholder); + if (texteditor == null || texteditor.selectedObject == null) { + alert("{% filter escapejs %}{% trans "Text editor does not support editing objects." %}{% endfilter %}"); + return; + } + var imgobj = texteditor.selectedObject(); + if (imgobj == null) { + alert("{% filter escapejs %}{% trans "No object selected." %}{% endfilter %}"); + return; + } + if (imgobj.id == null || imgobj.id.indexOf("plugin_obj_") != 0) { + alert("{% filter escapejs %}{% trans "Not a plugin object" %}{% endfilter %}"); + return; + } + var plugin_id = imgobj.id.substr("plugin_obj_".length); + edit_plugin(plugin_id); + }).css("cursor", "pointer").css("margin","5px"); + } + }); + + function get_plugin_html(){ + html = '<li class="wym_tools_plugins">' + + '<select name="plugins">' + + '<option value="" selected="selected">{% filter escapejs %}{% trans "Available Plugins" %}{% endfilter %}</option>'{% for p in installed_plugins %} + + '<option value="{{ p.value }}">{{ p.name }}</option>'{% endfor %} + + '</select>' + + '<span class="insert-object addlink">{% filter escapejs %}{% trans "Insert plugin" %}{% endfilter %}</span>' + + '<span class="edit-object changelink">{% filter escapejs %}{% trans "Edit selected plugin" %}{% endfilter %}</span>' + + '</li>'; + return html; } -}); +})(window.CMS); -function get_plugin_html(){ - html = '<li class="wym_tools_plugins">' - + '<select name="plugins">' - + '<option value="" selected="selected">{% filter escapejs %}{% trans "Available Plugins" %}{% endfilter %}</option>'{% for p in installed_plugins %} - + '<option value="{{ p.value }}">{{ p.name }}</option>'{% endfor %} - + '</select>' - + '<span class="insert-object addlink">{% filter escapejs %}{% trans "Insert plugin" %}{% endfilter %}</span>' - + '<span class="edit-object changelink">{% filter escapejs %}{% trans "Edit selected plugin" %}{% endfilter %}</span>' - + '</li>'; -return html; -} //]]> </script> diff --git a/cms/plugins/twitter/templates/cms/plugins/twitter_recent_entries.html b/cms/plugins/twitter/templates/cms/plugins/twitter_recent_entries.html index 71382856373..4c0e6fac742 100644 --- a/cms/plugins/twitter/templates/cms/plugins/twitter_recent_entries.html +++ b/cms/plugins/twitter/templates/cms/plugins/twitter_recent_entries.html @@ -4,22 +4,24 @@ {% addtoblock "js" %} <script type="text/javascript"> //<![CDATA[ -jQuery(document).ready(function ($) { - $('#twitter-container-{{ object.pk }}').tweet({ - username: '{{ object.twitter_user }}', - avatar_size: {% if request.is_secure %}null{% else %}32{% endif %}, - count: {{ object.count }}, - join_text: 'auto', - auto_join_text_default: '{% trans "we said," %}', - auto_join_text_ed: '{% trans "we" %}', - auto_join_text_ing: '{% trans "we were" %}', - auto_join_text_reply: '{% trans "we replied to" %}', - auto_join_text_url: '{% trans "we were checking out" %}', - loading_text: '{% trans "loading tweets..." %}' - // this replaces twitter_search.html - {% if object.query %},query: '{{ object.query }}'{% endif %} +(function namespacing(CMS) { + CMS.$(document).ready(function () { + $('#twitter-container-{{ object.pk }}').tweet({ + username: '{{ object.twitter_user }}', + avatar_size: {% if request.is_secure %}null{% else %}32{% endif %}, + count: {{ object.count }}, + join_text: 'auto', + auto_join_text_default: '{% trans "we said," %}', + auto_join_text_ed: '{% trans "we" %}', + auto_join_text_ing: '{% trans "we were" %}', + auto_join_text_reply: '{% trans "we replied to" %}', + auto_join_text_url: '{% trans "we were checking out" %}', + loading_text: '{% trans "loading tweets..." %}' + // this replaces twitter_search.html + {% if object.query %},query: '{{ object.query }}'{% endif %} + }); }); -}); +})(window.CMS); //]]> </script> {% endaddtoblock %} diff --git a/cms/static/cms/js/change_list.js b/cms/static/cms/js/change_list.js index 1747d532489..73029df8817 100644 --- a/cms/static/cms/js/change_list.js +++ b/cms/static/cms/js/change_list.js @@ -1,5 +1,5 @@ // some very small jquery extensions -(function($) { +(function namespacing($) { // very simple yellow fade plugin.. $.fn.yft = function(){ this.effect("highlight", {}, 1000); }; @@ -264,28 +264,28 @@ // of the tree = current node + descendants reloadItem(jtarget, admin_base_url + "cms/page/" + pageId + "/approve/?node=1", {}, refreshIfChildren(pageId)); e.stopPropagation(); - return false; - } - - // lazy load descendants on tree open - if(jtarget.hasClass("closed")) { - // only load them once - if(jtarget.find('ul > li').length == 0 && !jtarget.hasClass("loading")) { - // keeps this event from firing multiple times before - // the dom as changed. it still needs to propagate for - // the other click event on this element to fire - jtarget.addClass("loading"); - var pageId = $(jtarget).attr("id").split("page_")[1]; + return false; + } - $.get(admin_base_url + "cms/page/" + pageId + "/descendants/", {}, function(r, status) { - jtarget.children('ul').append(r); - // show move targets if needed - if($('span.move-target-container:visible').length > 0) { - jtarget.children('ul').find('a.move-target, span.move-target-container, span.line').show(); - } - }); - } - } + // lazy load descendants on tree open + if(jtarget.hasClass("closed")) { + // only load them once + if(jtarget.find('ul > li').length == 0 && !jtarget.hasClass("loading")) { + // keeps this event from firing multiple times before + // the dom as changed. it still needs to propagate for + // the other click event on this element to fire + jtarget.addClass("loading"); + var pageId = $(jtarget).attr("id").split("page_")[1]; + + $.get(admin_base_url + "cms/page/" + pageId + "/descendants/", {}, function(r, status) { + jtarget.children('ul').append(r); + // show move targets if needed + if($('span.move-target-container:visible').length > 0) { + jtarget.children('ul').find('a.move-target, span.move-target-container, span.line').show(); + }; + }); + } + } if(jtarget.hasClass("move-target")) { if(jtarget.hasClass("left")){ @@ -321,8 +321,8 @@ var val= $(this).width(); if(val > max){max = val;} }); - $(this).each(function() { - $(this).css("width",max + 'px'); + $(this).each(function() { + $(this).css("width",max + 'px'); }); return this; }; @@ -500,4 +500,4 @@ function addUndo(node, target, position){ undos.push({node:node, target:target, position:position}); } -})(jQuery); +})(window.CMS.$); diff --git a/cms/static/cms/js/plugins/cms.base.js b/cms/static/cms/js/plugins/cms.base.js index 98748ad6123..e520ebabf75 100644 --- a/cms/static/cms/js/plugins/cms.base.js +++ b/cms/static/cms/js/plugins/cms.base.js @@ -1,125 +1,141 @@ /*##################################################|*/ /* #CMS.BASE# */ -CMS.$(document).ready(function ($) { - // assign correct jquery to $ namespace - $ = CMS.$ || $; - - /*! - * Adds security methods to api namespace - * @public_methods: - * - CMS.API.Security.csrf(); - * @compatibility: IE >= 7, FF >= 3, Safari >= 4, Chrome > =4, Opera >= 10 - */ - CMS.API.Security = { - - csrf: function () { - $.ajaxSetup({ - beforeSend: function (xhr, settings) { - if (typeof(settings.csrfTokenSet) != undefined && settings.csrfTokenSet) { - // CSRF token has already been set elsewhere so we won't touch it. - return true; - } - // get cookies without jquery.cookie.js - function getCookie(name) { - var cookieValue = null; - if(document.cookie && (document.cookie != '')) { - var cookies = document.cookie.split(';'); - for (var i = 0; i < cookies.length; i++) { - var cookie = $.trim(cookies[i]); - // Does this cookie string begin with the name we want? - if (cookie.substring(0, name.length + 1) == (name + '=')) { - cookieValue = decodeURIComponent(cookie.substring(name.length + 1)); - break; +(function namespacing(CMS) { + CMS.$(document).ready(function ($) { + // assign correct jquery to $ namespace + $ = CMS.$ || $; + + // the following is added because IE is stupid + // $.ajax requests in IE8 fail without this hack + // ref: http://stackoverflow.com/questions/4557532/jquery-ajax-requests-failing-in-ie8-with-message-error-this-method-cannot-be-c + $.ajaxSetup({ + xhr: function() { + try{ + if(window.ActiveXObject) + return new window.ActiveXObject("Microsoft.XMLHTTP"); + } catch(e) { } + + return new window.XMLHttpRequest(); + } + }); + + /*! + * Adds security methods to api namespace + * @public_methods: + * - CMS.API.Security.csrf(); + * @compatibility: IE >= 7, FF >= 3, Safari >= 4, Chrome > =4, Opera >= 10 + */ + CMS.API.Security = { + + csrf: function () { + $.ajaxSetup({ + beforeSend: function (xhr, settings) { + if (typeof(settings.csrfTokenSet) != undefined && settings.csrfTokenSet) { + // CSRF token has already been set elsewhere so we won't touch it. + return true; + } + // get cookies without jquery.cookie.js + function getCookie(name) { + var cookieValue = null; + if(document.cookie && (document.cookie != '')) { + var cookies = document.cookie.split(';'); + for (var i = 0; i < cookies.length; i++) { + var cookie = $.trim(cookies[i]); + // Does this cookie string begin with the name we want? + if (cookie.substring(0, name.length + 1) == (name + '=')) { + cookieValue = decodeURIComponent(cookie.substring(name.length + 1)); + break; + } } } + return cookieValue; + } + // do some url checks + var base_doc_url = document.URL.match(/^http[s]{0,1}:\/\/[^\/]+\//)[0]; + var base_settings_url = settings.url.match(/^http[s]{0,1}:\/\/[^\/]+\//); + if(base_settings_url != null) { + base_settings_url = base_settings_url[0]; + } + if(!(/^http:.*/.test(settings.url) || /^https:.*/.test(settings.url)) || base_doc_url == base_settings_url) { + // Only send the token to relative URLs i.e. locally. + xhr.setRequestHeader("X-CSRFToken", getCookie('csrftoken')); + settings.csrfTokenSet = true; } - return cookieValue; - } - // do some url checks - var base_doc_url = document.URL.match(/^http[s]{0,1}:\/\/[^\/]+\//)[0]; - var base_settings_url = settings.url.match(/^http[s]{0,1}:\/\/[^\/]+\//); - if(base_settings_url != null) { - base_settings_url = base_settings_url[0]; } - if(!(/^http:.*/.test(settings.url) || /^https:.*/.test(settings.url)) || base_doc_url == base_settings_url) { - // Only send the token to relative URLs i.e. locally. - xhr.setRequestHeader("X-CSRFToken", getCookie('csrftoken')); - settings.csrfTokenSet = true; + }); + return 'ready'; + } + + }; + + /*! + * Adds helper methods to api namespace + * @public_methods: + * - CMS.API.Helpers.reloadBrowser(); + * - CMS.API.Helpers.getUrl(urlString); + * - CMS.API.Helpers.setUrl(urlString, options); + */ + CMS.API.Helpers = { + + reloadBrowser: function () { + window.location.reload(); + }, + + getUrl: function(str) { + var o = { + 'strictMode': false, + 'key': ["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"], + 'q': { 'name': 'queryKey', 'parser': /(?:^|&)([^&=]*)=?([^&]*)/g }, + 'parser': { + 'strict': /^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/, + 'loose': /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/ } - } - }); - return 'ready'; - } - - }; - - /*! - * Adds helper methods to api namespace - * @public_methods: - * - CMS.API.Helpers.reloadBrowser(); - * - CMS.API.Helpers.getUrl(urlString); - * - CMS.API.Helpers.setUrl(urlString, options); - */ - CMS.API.Helpers = { - - reloadBrowser: function () { - window.location.reload(); - }, - - getUrl: function(str) { - var o = { - 'strictMode': false, - 'key': ["source","protocol","authority","userInfo","user","password","host","port","relative","path","directory","file","query","anchor"], - 'q': { 'name': 'queryKey', 'parser': /(?:^|&)([^&=]*)=?([^&]*)/g }, - 'parser': { - 'strict': /^(?:([^:\/?#]+):)?(?:\/\/((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?))?((((?:[^?#\/]*\/)*)([^?#]*))(?:\?([^#]*))?(?:#(.*))?)/, - 'loose': /^(?:(?![^:@]+:[^:@\/]*@)([^:\/?#.]+):)?(?:\/\/)?((?:(([^:@]*)(?::([^:@]*))?)?@)?([^:\/?#]*)(?::(\d*))?)(((\/(?:[^?#](?![^?#\/]*\.[^?#\/.]+(?:[?#]|$)))*\/?)?([^?#\/]*))(?:\?([^#]*))?(?:#(.*))?)/ - } - }; - - var m = o.parser[o.strictMode ? 'strict' : 'loose'].exec(str), uri = {}, i = 14; - - while(i--) uri[o.key[i]] = m[i] || ''; - - uri[o.q.name] = {}; - uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) { - if($1) { uri[o.q.name][$1] = $2; } - }); - - return uri; - }, - - setUrl: function (str, options) { - var uri = str; - - // now we neet to get the partials of the element - var getUrlObj = this.getUrl(uri); - var query = getUrlObj.queryKey; - var serialized = ''; - var index = 0; - - // we could loop the query and replace the param at the right place - // but instead of replacing it just append it to the end of the query so its more visible - if(options && options.removeParam) delete query[options.removeParam]; - if(options && options.addParam) query[options.addParam.split('=')[0]] = options.addParam.split('=')[1]; - - $.each(query, function (key, value) { - // add & - if(index != 0) serialized += '&'; - // if a value is given attach it - serialized += (value) ? (key + '=' + value) : (key); - index++; - }); - - // check if we should add the questionmark - var addition = (serialized === '') ? '' : '?'; - var anchor = (getUrlObj.anchor) ? '#' + getUrlObj.anchor : ''; - - uri = getUrlObj.protocol + '://' + getUrlObj.authority + getUrlObj.directory + getUrlObj.file + addition + serialized + anchor; - - return uri; - } - - }; - -}); + }; + + var m = o.parser[o.strictMode ? 'strict' : 'loose'].exec(str), uri = {}, i = 14; + + while(i--) uri[o.key[i]] = m[i] || ''; + + uri[o.q.name] = {}; + uri[o.key[12]].replace(o.q.parser, function ($0, $1, $2) { + if($1) { uri[o.q.name][$1] = $2; } + }); + + return uri; + }, + + setUrl: function (str, options) { + var uri = str; + + // now we neet to get the partials of the element + var getUrlObj = this.getUrl(uri); + var query = getUrlObj.queryKey; + var serialized = ''; + var index = 0; + + // we could loop the query and replace the param at the right place + // but instead of replacing it just append it to the end of the query so its more visible + if(options && options.removeParam) delete query[options.removeParam]; + if(options && options.addParam) query[options.addParam.split('=')[0]] = options.addParam.split('=')[1]; + + $.each(query, function (key, value) { + // add & + if(index != 0) serialized += '&'; + // if a value is given attach it + serialized += (value) ? (key + '=' + value) : (key); + index++; + }); + + // check if we should add the questionmark + var addition = (serialized === '') ? '' : '?'; + var anchor = (getUrlObj.anchor) ? '#' + getUrlObj.anchor : ''; + + uri = getUrlObj.protocol + '://' + getUrlObj.authority + getUrlObj.directory + getUrlObj.file + addition + serialized + anchor; + + return uri; + } + + }; + + }); +})(window.CMS); diff --git a/cms/static/cms/js/plugins/cms.setup.js b/cms/static/cms/js/plugins/cms.setup.js index 9fe6a6dc925..28dccf99d16 100644 --- a/cms/static/cms/js/plugins/cms.setup.js +++ b/cms/static/cms/js/plugins/cms.setup.js @@ -1,15 +1,16 @@ /*##################################################|*/ /* #CMS.SETUP# */ +(function namespacing() { + // insuring django namespace is available when using on admin + django = window.django || undefined; -// insuring django namespace is available when using on admin -var django = django || undefined; + // assigning correct jquery instance to jQuery variable + var jQuery = (django) ? django.jQuery : window.jQuery || undefined; -// assigning correct jquery instance to jQuery variable -var jQuery = (django) ? django.jQuery : window.jQuery || undefined; - -// assign global namespaces -var CMS = { - '$': jQuery.noConflict(), - 'Class': Class.$noConflict(), - 'API': {} -}; \ No newline at end of file + // assign global namespaces + window.CMS = { + '$': jQuery.noConflict(), + 'Class': Class.$noConflict(), + 'API': {} + }; +})(); \ No newline at end of file diff --git a/cms/templates/admin/cms/page/change_form.html b/cms/templates/admin/cms/page/change_form.html index 68d0c7986bd..9475f3e2d97 100644 --- a/cms/templates/admin/cms/page/change_form.html +++ b/cms/templates/admin/cms/page/change_form.html @@ -25,7 +25,7 @@ } }); }); -})(jQuery); +})(window.CMS.$); //]]> </script> {% endif %} @@ -169,6 +169,7 @@ <h2 class="load_remote">{% trans 'Page states' %}</h2> {% endif %} {% if moderation_delete_request %}<script type="text/javascript"> + (function namespacing($) { $(function(){ // disable all fields function lockControls(){ @@ -179,6 +180,7 @@ <h2 class="load_remote">{% trans 'Page states' %}</h2> lockControls(); setTimeout(lockControls,200); }); + })(window.CMS.$); </script>{% endif %} {% if CMS_MODERATOR and moderation_required %} @@ -261,7 +263,7 @@ <h2 class="load_remote">{% trans 'Page states' %}</h2> } }); }); - })(jQuery); + })(window.CMS.$); //]]> </script> {% endif %} diff --git a/cms/templates/admin/cms/page/change_list.html b/cms/templates/admin/cms/page/change_list.html index 5f944ee1839..72e0b3635b3 100644 --- a/cms/templates/admin/cms/page/change_list.html +++ b/cms/templates/admin/cms/page/change_list.html @@ -45,7 +45,7 @@ {% block content %} <script type="text/javascript"> //<![CDATA[ -(function($) { +(function namespacing($) { $(document).ready(function() { {% if not cl.is_filtered %} initTree(); @@ -71,7 +71,7 @@ cmsModerator: {{ CMS_MODERATOR|js }}, debug: {{ DEBUG|js }} }; -})(jQuery); +})(window.CMS.$); //]]> </script> diff --git a/cms/templates/admin/cms/page/plugin_change_form.html b/cms/templates/admin/cms/page/plugin_change_form.html index c222225b08c..ccd808f6518 100644 --- a/cms/templates/admin/cms/page/plugin_change_form.html +++ b/cms/templates/admin/cms/page/plugin_change_form.html @@ -5,8 +5,13 @@ <script type="text/javascript" src="{% admin_static_url %}js/jquery.min.js"></script> <script type="text/javascript" src="{{ STATIC_URL }}cms/js/csrf.js"></script> <script type="text/javascript" src="{% url 'admin:jsi18n' %}"></script> + {{ media }} +<script type="text/javascript" src="{{ STATIC_URL }}cms/js/libs/classy.min.js"></script> +<script type="text/javascript" src="{{ STATIC_URL }}cms/js/plugins/cms.setup.js"></script> +<script type="text/javascript" src="{{ STATIC_URL }}cms/js/plugins/cms.base.js"></script> + <script type="text/javascript"> //<![CDATA[ (function($) { @@ -50,7 +55,7 @@ } }); }); -})(jQuery); +})(window.CMS.$); //]]> </script> diff --git a/cms/utils/admin.py b/cms/utils/admin.py index 203e2d8cd29..a5204f9092e 100644 --- a/cms/utils/admin.py +++ b/cms/utils/admin.py @@ -96,4 +96,5 @@ def render_admin_menu_item(request, page, template=None): filtered = 'filtered' in request.REQUEST context.update(get_admin_menu_item_context(request, page, filtered)) - return render_to_response(template, context) + # add mimetype to help out IE + return render_to_response(template, context, mimetype="text/html; charset=utf-8")

ethereum__web3.py-3060

Default IPC path is incorrect on Windows with Anaconda 2023.07 * Version: 6.6.1 * Python: 3.11 * OS: win I updated my Anaconda to the latest version recently, which uses Python 3.11. web3.py is no longer able to set the default IPC path for IPCProvider on Windows. The problem and fix are as follows: In [ipc.py](https://github.com/ethereum/web3.py/blob/4b509a7d5fce0b9a67dbe93151e8b8a01e83b3cc/web3/providers/ipc.py#L105), line 105 `ipc_path = os.path.join("\\\\", ".", "pipe", "geth.ipc")` makes the default IPC path ` '\\\\\\.\\pipe\\geth.ipc'`, which cannot be found with `os.path.exists(ipc_path)` in the next line ### How can it be fixed? In ipc.py, replace line 105 `ipc_path = os.path.join("\\\\", ".", "pipe", "geth.ipc")` with `ipc_path = '\\\.\pipe\geth.ipc'` as is described in the [documentation](https://web3py.readthedocs.io/en/latest/providers.html#web3.providers.ipc.IPCProvider). ```[tasklist] ### Tasks ```

[ { "content": "from json import (\n JSONDecodeError,\n)\nimport logging\nimport os\nfrom pathlib import (\n Path,\n)\nimport socket\nimport sys\nimport threading\nfrom types import (\n TracebackType,\n)\nfrom typing import (\n Any,\n Optional,\n Type,\n Union,\n)\n\nfrom web3._utils.threads ...

diff --git a/docs/providers.rst b/docs/providers.rst index b560aa51d1..d45e046eae 100644 --- a/docs/providers.rst +++ b/docs/providers.rst @@ -173,7 +173,7 @@ IPCProvider - On Linux and FreeBSD: ``~/.ethereum/geth.ipc`` - On Mac OS: ``~/Library/Ethereum/geth.ipc`` - - On Windows: ``\\\.\pipe\geth.ipc`` + - On Windows: ``\\.\pipe\geth.ipc`` WebsocketProvider diff --git a/newsfragments/3058.bugfix.rst b/newsfragments/3058.bugfix.rst new file mode 100644 index 0000000000..6dfadef108 --- /dev/null +++ b/newsfragments/3058.bugfix.rst @@ -0,0 +1 @@ +Fixed default windows IPC provider path to work with python 3.11 diff --git a/web3/providers/ipc.py b/web3/providers/ipc.py index 170499a8bc..e2731b8fe3 100644 --- a/web3/providers/ipc.py +++ b/web3/providers/ipc.py @@ -102,7 +102,7 @@ def get_default_ipc_path() -> Optional[str]: return None elif sys.platform == "win32": - ipc_path = os.path.join("\\\\", ".", "pipe", "geth.ipc") + ipc_path = r"\\.\pipe\geth.ipc" if os.path.exists(ipc_path): return ipc_path return None

pyro-ppl__numpyro-1760

random_flax_module broken First and foremost **thanks** for the great work on `numpyro`! **The utility function `random_flax_module()` from the `numpyro.contrib.module` seems to be broken.** As a minimal reproducible example for the error I take the example given in the docstring of the function ([https://github.com/pyro-ppl/numpyro/blob/master/numpyro/contrib/module.py#L285](https://github.com/pyro-ppl/numpyro/blob/master/numpyro/contrib/module.py#L285)) itself. The example with imports is given below: ``` import flax import numpyro.distributions as dist from numpyro.contrib.module import random_flax_module random_flax_module( "net", flax.linen.Dense(features=1), prior={"bias": dist.Cauchy(), "kernel": dist.Normal()}, input_shape=(4,) ) ``` This leads directly to `ValueError: First argument passed to an init function should be a `jax.PRNGKey` or a dictionary mapping strings to `jax.PRNGKey`.` Hope I just missed something obvious as the function would be very handy!

[ { "content": "# Copyright Contributors to the Pyro project.\n# SPDX-License-Identifier: Apache-2.0\n\nfrom collections import namedtuple\nfrom contextlib import ExitStack, contextmanager\nimport functools\nimport warnings\n\nimport jax\nfrom jax import lax, random\nimport jax.numpy as jnp\n\nimport numpyro\nfro...

diff --git a/numpyro/primitives.py b/numpyro/primitives.py index 99cf35902..ac02a8856 100644 --- a/numpyro/primitives.py +++ b/numpyro/primitives.py @@ -622,6 +622,10 @@ def prng_key(): :return: a PRNG key of shape (2,) and dtype unit32. """ if not _PYRO_STACK: + warnings.warn( + "Cannot generate JAX PRNG key outside of `seed` handler.", + stacklevel=find_stack_level(), + ) return initial_msg = { diff --git a/test/test_handlers.py b/test/test_handlers.py index e24e22890..518f856dc 100644 --- a/test/test_handlers.py +++ b/test/test_handlers.py @@ -778,7 +778,8 @@ def guide(): def test_prng_key(): - assert numpyro.prng_key() is None + with pytest.warns(Warning, match="outside of `seed`"): + assert numpyro.prng_key() is None with handlers.seed(rng_seed=0): rng_key = numpyro.prng_key()

chainer__chainer-1022

ChainList failed to copy its children. ``` #!/usr/bin/env python from chainer import Chain, ChainList import chainer.links as L model0 = ChainList(L.Linear(10, 10)) model1 = model0.copy() model0.to_gpu(0) model1.to_gpu(1) print(model1[0].W.data.device) # => <CUDA Device 0> model0 = Chain(c=L.Linear(10, 10)) model1 = model0.copy() model0.to_gpu(0) model1.to_gpu(1) print(model1.c.W.data.device) # => <CUDA Device 1> model0 = L.Linear(10, 10) model1 = model0.copy() model0.to_gpu(0) model1.to_gpu(1) print(model1.W.data.device) # => <CUDA Device 1> ``` This issue is reported by @snuke. Thank you!

[ { "content": "import copy\n\nimport numpy\nimport six\n\nfrom chainer import cuda\nfrom chainer import variable\n\n\nclass Link(object):\n\n \"\"\"Building block of model definitions.\n\n Link is a building block of neural network models that support various\n features like handling parameters, definin...

diff --git a/chainer/link.py b/chainer/link.py index 0ca1df1dc929..907ddf2ee38b 100644 --- a/chainer/link.py +++ b/chainer/link.py @@ -615,6 +615,7 @@ def add_link(self, link): def copy(self): ret = super(ChainList, self).copy() + ret._children = list(ret._children) # copy children = ret._children for i, child in enumerate(children): child = child.copy() diff --git a/tests/chainer_tests/test_link.py b/tests/chainer_tests/test_link.py index 689aebdb092b..cc9c4c37e218 100644 --- a/tests/chainer_tests/test_link.py +++ b/tests/chainer_tests/test_link.py @@ -463,6 +463,34 @@ def test_copy(self): self.assertIs(c2[1].x.data, self.l3.x.data) self.assertIs(c2[1].x.grad, None) + @attr.gpu + def test_copy_and_send_to_gpu(self): + c2 = self.c2.copy() + self.c2.to_gpu() + self.assertIsInstance(self.c2[0][0].x.data, cuda.cupy.ndarray) + self.assertIsInstance(self.c2[0][1].x.data, cuda.cupy.ndarray) + self.assertIsInstance(c2[0][0].x.data, numpy.ndarray) + self.assertIsInstance(c2[0][1].x.data, numpy.ndarray) + + @attr.gpu + def test_copy_and_send_to_gpu_2(self): + c2 = self.c2.copy() + c2.to_gpu() + self.assertIsInstance(self.c2[0][0].x.data, numpy.ndarray) + self.assertIsInstance(self.c2[0][1].x.data, numpy.ndarray) + self.assertIsInstance(c2[0][0].x.data, cuda.cupy.ndarray) + self.assertIsInstance(c2[0][1].x.data, cuda.cupy.ndarray) + + @attr.multi_gpu(2) + def test_copy_and_send_to_gpu_multi(self): + c2 = self.c2.copy() + self.c2.to_gpu(0) + c2.to_gpu(1) + self.assertEqual(self.c2[0][0].x.data.device.id, 0) + self.assertEqual(self.c2[0][1].x.data.device.id, 0) + self.assertEqual(c2[0][0].x.data.device.id, 1) + self.assertEqual(c2[0][1].x.data.device.id, 1) + def test_to_cpu_on_cpu(self): x1 = self.l1.x.data gx1 = self.l1.x.grad

pennersr__django-allauth-3283

`OpenIDConnectProvider` generates slug using `_server_id` and does not fallback to inherited implementation KeycloakProvider started using `openid_connect` as its base url since the `OpenIDConnectProvider` implemented `get_slug`

[ { "content": "# -*- coding: utf-8 -*-\nfrom allauth.account.models import EmailAddress\nfrom allauth.socialaccount import app_settings\nfrom allauth.socialaccount.providers.base import ProviderAccount\nfrom allauth.socialaccount.providers.oauth2.provider import OAuth2Provider\n\n\nclass OpenIDConnectProviderAcc...

diff --git a/allauth/socialaccount/providers/openid_connect/provider.py b/allauth/socialaccount/providers/openid_connect/provider.py index 455f2566e0..c94ad717be 100644 --- a/allauth/socialaccount/providers/openid_connect/provider.py +++ b/allauth/socialaccount/providers/openid_connect/provider.py @@ -32,7 +32,7 @@ def token_auth_method(self): @classmethod def get_slug(cls): - return cls._server_id if cls._server_id else "openid_connect" + return cls._server_id or super().get_slug() def get_default_scope(self): return ["openid", "profile", "email"]

scikit-image__scikit-image-3152

skimage.test does not execute the unit test ## Description `skimage.test` does not run the unit tests. ``` ~$ python -c "import skimage; print(skimage.__version__); skimage.test()" 0.14.0 ====================================================================== test session starts ====================================================================== platform linux -- Python 3.6.5, pytest-3.6.1, py-1.5.3, pluggy-0.6.0 rootdir: /home/jhelmus, inifile: ================================================================= no tests ran in 0.00 seconds ================================================================== ERROR: file not found: skimage ``` <details><summary>Environment Details</summary> ``` $ conda info active environment : sktest active env location : /home/jhelmus/anaconda3/envs/sktest shell level : 1 user config file : /home/jhelmus/.condarc populated config files : /home/jhelmus/.condarc conda version : 4.5.4 conda-build version : 3.9.1 python version : 3.6.4.final.0 base environment : /home/jhelmus/anaconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/linux-64 https://repo.anaconda.com/pkgs/pro/noarch package cache : /home/jhelmus/anaconda3/pkgs /home/jhelmus/.conda/pkgs envs directories : /home/jhelmus/anaconda3/envs /home/jhelmus/.conda/envs platform : linux-64 user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.4 Linux/4.13.0-41-generic ubuntu/16.04 glibc/2.23 UID:GID : 1000:1000 netrc file : None offline mode : False $ conda create -n sktest python=3.6 pip Solving environment: done ## Package Plan ## environment location: /home/jhelmus/anaconda3/envs/sktest added / updated specs: - pip - python=3.6 The following NEW packages will be INSTALLED: ca-certificates: 2018.03.07-0 defaults certifi: 2018.4.16-py36_0 defaults libedit: 3.1.20170329-h6b74fdf_2 defaults libffi: 3.2.1-hd88cf55_4 defaults libgcc-ng: 7.2.0-hdf63c60_3 defaults libstdcxx-ng: 7.2.0-hdf63c60_3 defaults ncurses: 6.1-hf484d3e_0 defaults openssl: 1.0.2o-h20670df_0 defaults pip: 10.0.1-py36_0 defaults python: 3.6.5-hc3d631a_2 defaults readline: 7.0-ha6073c6_4 defaults setuptools: 39.2.0-py36_0 defaults sqlite: 3.23.1-he433501_0 defaults tk: 8.6.7-hc745277_3 defaults wheel: 0.31.1-py36_0 defaults xz: 5.2.4-h14c3975_4 defaults zlib: 1.2.11-ha838bed_2 defaults Proceed ([y]/n)? y ... $ pip install scikit-image Collecting scikit-image Using cached https://files.pythonhosted.org/packages/34/79/cefff573a53ca3fb4c390739d19541b95f371e24d2990aed4cd8837971f0/scikit_image-0.14.0-cp36-cp36m-manylinux1_x86_64.whl ... Successfully installed PyWavelets-0.5.2 cloudpickle-0.5.3 cycler-0.10.0 dask-0.17.5 decorator-4.3.0 kiwisolver-1.0.1 matplotlib-2.2.2 networkx-2.1 numpy-1.14.3 pillow-5.1.0 pyparsing-2.2.0 python-dateutil-2.7.3 pytz-2018.4 scikit-image-0.14.0 scipy-1.1.0 six-1.11.0 toolz-0.9.0 $ pip install pytest Collecting pytest Using cached https://files.pythonhosted.org/packages/d3/75/e79b66c9fe6166a90004bb8fb02bab06213c3348e93f3be41d7eaf625554/pytest-3.6.1-py2.py3-none-any.whl Collecting pluggy<0.7,>=0.5 (from pytest) ... Successfully installed atomicwrites-1.1.5 attrs-18.1.0 more-itertools-4.2.0 pluggy-0.6.0 py-1.5.3 pytest-3.6.1 ``` </details> ## Way to reproduce - [x] Code example - [ ] Relevant images (if any) - [x] Operating system and version - [x] Python version - [x] scikit-image version (run `skimage.__version__`) This has been observed on conda-forge, see conda-forge/scikit-image-feedstock#23

[ { "content": "\"\"\"Image Processing SciKit (Toolbox for SciPy)\n\n``scikit-image`` (a.k.a. ``skimage``) is a collection of algorithms for image\nprocessing and computer vision.\n\nThe main package of ``skimage`` only provides a few utilities for converting\nbetween image data types; for most features, you need...

diff --git a/skimage/__init__.py b/skimage/__init__.py index ac7c24c32bc..6c88dfca090 100644 --- a/skimage/__init__.py +++ b/skimage/__init__.py @@ -102,7 +102,7 @@ def _test(doctest=False, verbose=False): """Run all unit tests.""" import pytest import warnings - args = ['skimage'] + args = ['--pyargs', 'skimage'] if verbose: args.extend(['-v', '-s']) if doctest:

elastic__apm-agent-python-1947

dbapi2 fails to extract table name when using square brackets **Describe the bug**: ... Queries made to tables which requires escaping end up with the wrong span name. The following spans are SELECTs from four different tables, but only two unique span names appear. ![Screenshot 2023-10-31 at 19 13 46](https://github.com/elastic/apm-agent-python/assets/435885/5384fd4d-df13-4828-a9f2-b7e1c309f07f) **To Reproduce** Import package and call [extract_signature](https://github.com/elastic/apm-agent-python/blob/05332cd007560615b4421b1567659ff9f9634088/elasticapm/instrumentation/packages/dbapi2.py#L153): ```python >>> from elasticapm.instrumentation.packages import dbapi2 >>> dbapi2.extract_signature("SELECT username FROM user") 'SELECT FROM user' >>> dbapi2.extract_signature("SELECT username FROM [user]") 'SELECT FROM [' ``` **Environment (please complete the following information)** - OS: [e.g. Linux] - Python version: - Framework and version [e.g. Django 2.1]: - APM Server version: - Agent version: **Additional context** Add any other context about the problem here. - Agent config options  <details> <summary>Click to expand</summary> ``` replace this line with your agent config options remember to mask any sensitive fields like tokens ``` </details> - `requirements.txt`: <details> <summary>Click to expand</summary> ``` replace this line with your `requirements.txt` ``` </details>

[ { "content": "# BSD 3-Clause License\n#\n# Copyright (c) 2019, Elasticsearch BV\n# All rights reserved.\n#\n# Redistribution and use in source and binary forms, with or without\n# modification, are permitted provided that the following conditions are met:\n#\n# * Redistributions of source code must retain...

diff --git a/elasticapm/instrumentation/packages/dbapi2.py b/elasticapm/instrumentation/packages/dbapi2.py index cbe34be59..fb49723c2 100644 --- a/elasticapm/instrumentation/packages/dbapi2.py +++ b/elasticapm/instrumentation/packages/dbapi2.py @@ -76,8 +76,8 @@ def _scan_for_table_with_tokens(tokens, keyword): def tokenize(sql): - # split on anything that is not a word character, excluding dots - return [t for t in re.split(r"([^\w.])", sql) if t != ""] + # split on anything that is not a word character or a square bracket, excluding dots + return [t for t in re.split(r"([^\w.\[\]])", sql) if t != ""] def scan(tokens): diff --git a/tests/instrumentation/dbapi2_tests.py b/tests/instrumentation/dbapi2_tests.py index d2fc84aab..3d72b6632 100644 --- a/tests/instrumentation/dbapi2_tests.py +++ b/tests/instrumentation/dbapi2_tests.py @@ -154,3 +154,18 @@ def test_extract_signature_for_procedure_call(sql, expected): def test_extract_action_from_signature(sql, expected): actual = extract_action_from_signature(sql, "query") assert actual == expected + + +@pytest.mark.parametrize( + ["sql", "expected"], + [ + ("SELECT username FROM user", "SELECT FROM user"), + ("SELECT username FROM [user]", "SELECT FROM [user]"), + ("SELECT username FROM [db].[user]", "SELECT FROM [db].[user]"), + ("SELECT username FROM db.[user]", "SELECT FROM db.[user]"), + ("SELECT username FROM [db].user", "SELECT FROM [db].user"), + ], +) +def test_extract_signature_when_using_square_brackets(sql, expected): + actual = extract_signature(sql) + assert actual == expected

sublimelsp__LSP-1417

Advertise window.showMessageRequest.messageActionItem.additionalPropertiesSupport See: https://github.com/microsoft/language-server-protocol/commit/4a29ca0725469624fc07425c3fa0fde386e7ee55

[ { "content": "from .edit import apply_workspace_edit\nfrom .edit import parse_workspace_edit\nfrom .logging import debug\nfrom .logging import exception_log\nfrom .promise import Promise\nfrom .protocol import CompletionItemTag\nfrom .protocol import Error\nfrom .protocol import ErrorCode\nfrom .protocol import...

diff --git a/README.md b/README.md index f592f8a75..b5acb47a8 100644 --- a/README.md +++ b/README.md @@ -147,3 +147,4 @@ If you have any problems, see the [troubleshooting](https://lsp.readthedocs.io/e - ✅ workDoneProgress - ✅ create - ❌ cancel +- ✅ showMessage request additionalPropertiesSupport diff --git a/plugin/core/sessions.py b/plugin/core/sessions.py index 53784f2aa..cad73f893 100644 --- a/plugin/core/sessions.py +++ b/plugin/core/sessions.py @@ -229,6 +229,11 @@ def get_initialize_params(variables: Dict[str, str], workspace_folders: List[Wor "configuration": True }, "window": { + "showMessage": { + "messageActionItem": { + "additionalPropertiesSupport": True + } + }, "workDoneProgress": True } }

getsentry__sentry-19997

Invalid List-ID header within Sentry Email notifications. ## Important Details How are you running Sentry?  Saas (sentry.io) ## Description Email notifications set invalid List-ID headers according to [RFC 2919](https://tools.ietf.org/html/rfc2919) ## Steps to Reproduce 1. Receive an email from sentry.io 1. Look at the raw headers for the email The header looks like: ``` List-Id: project.team.getsentry.com ``` ### What you expected to happen The List-ID header should be valid, for example: ``` List-Id: <project.team.getsentry.com> ``` ### Possible Solution Add `<>` around your List IDs. Ideally set a display name as well.

[ { "content": "from __future__ import absolute_import\n\nimport logging\nimport os\nimport six\nimport subprocess\nimport tempfile\nimport time\n\nfrom email.utils import parseaddr\nfrom functools import partial\nfrom operator import attrgetter\nfrom random import randrange\n\nimport lxml\nimport toronado\nfrom ...

diff --git a/src/sentry/utils/email.py b/src/sentry/utils/email.py index ddd30fc7a89cdf..42342439a51685 100644 --- a/src/sentry/utils/email.py +++ b/src/sentry/utils/email.py @@ -228,7 +228,7 @@ def __call__(self, instance): label = ".".join(map(six.text_type, handler(instance))) assert is_valid_dot_atom(label) - return u"{}.{}".format(label, self.__namespace) + return u"<{}.{}>".format(label, self.__namespace) default_list_type_handlers = { diff --git a/tests/sentry/utils/email/tests.py b/tests/sentry/utils/email/tests.py index 332da9777f10b0..c25902da8f61ab 100644 --- a/tests/sentry/utils/email/tests.py +++ b/tests/sentry/utils/email/tests.py @@ -32,7 +32,7 @@ def test_rejects_invalid_types(self): self.resolver(object()) def test_generates_list_ids(self): - expected = u"{0.project.slug}.{0.organization.slug}.namespace".format(self.event) + expected = u"<{0.project.slug}.{0.organization.slug}.namespace>".format(self.event) assert self.resolver(self.event.group) == expected assert self.resolver(self.event.project) == expected @@ -297,7 +297,7 @@ def test_generates_list_ids_for_registered_types(self): MessageBuilder, subject="Test", body="hello world", html_body="<b>hello world</b>" ) - expected = u"{event.project.slug}.{event.organization.slug}.{namespace}".format( + expected = u"<{event.project.slug}.{event.organization.slug}.{namespace}>".format( event=self.event, namespace=options.get("mail.list-namespace") )

ibis-project__ibis-2368

BigQuery Covariance operator compilation includes string representation of table instead of table ID **Failing test** https://github.com/ibis-project/ibis/blob/a70d443c7931cb8bb47c52f97999589566e03cb2/ibis/tests/all/test_aggregation.py#L165-L169 **Test output** ``` $ pytest ibis/tests/all/test_aggregation.py::test_reduction_ops[BigQuery-no_cond-covar] \ ibis/tests/all/test_aggregation.py::test_reduction_ops[BigQuery-is_in-covar] ``` Output: <details> ``` ======================================================= test session starts ======================================================= platform darwin -- Python 3.7.8, pytest-5.4.3, py-1.9.0, pluggy-0.13.1 rootdir: /Users/swast/src/ibis, inifile: setup.cfg plugins: forked-1.2.0, mock-3.1.1, cov-2.10.0, xdist-1.34.0 collected 2 items ibis/tests/all/test_aggregation.py FF [100%] ============================================================ FAILURES ============================================================= ___________________________________________ test_reduction_ops[BigQuery-no_cond-covar] ____________________________________________ backend = <ibis.tests.backends.BigQuery object at 0x7fc25b7935d0> alltypes = BigQueryTable[table] name: swast-scratch.testing.functional_alltypes schema: index : int64 Unnamed_0 : int...4 date_string_col : string string_col : string timestamp_col : timestamp year : int64 month : int64 df = index Unnamed_0 id bool_col tinyint_col ... date_string_col string_col timestamp_col year m... True 6 ... 01/31/10 6 2010-01-31 05:06:13.650 2010 1 [7300 rows x 15 columns] result_fn = <function <lambda> at 0x7fc25b7c08c0>, expected_fn = <function <lambda> at 0x7fc25b7c0950> ibis_cond = <function <lambda> at 0x7fc25b7c0e60>, pandas_cond = <function <lambda> at 0x7fc25b7c0ef0> @pytest.mark.parametrize( ('result_fn', 'expected_fn'), [ param( lambda t, where: t.bool_col.count(where=where), lambda t, where: len(t.bool_col[where].dropna()), id='count', ), param( lambda t, where: t.bool_col.any(), lambda t, where: t.bool_col.any(), id='any', ), param( lambda t, where: t.bool_col.notany(), lambda t, where: ~t.bool_col.any(), id='notany', ), param( lambda t, where: -t.bool_col.any(), lambda t, where: ~t.bool_col.any(), id='any_negate', ), param( lambda t, where: t.bool_col.all(), lambda t, where: t.bool_col.all(), id='all', ), param( lambda t, where: t.bool_col.notall(), lambda t, where: ~t.bool_col.all(), id='notall', ), param( lambda t, where: -t.bool_col.all(), lambda t, where: ~t.bool_col.all(), id='all_negate', ), param( lambda t, where: t.double_col.sum(), lambda t, where: t.double_col.sum(), id='sum', ), param( lambda t, where: t.double_col.mean(), lambda t, where: t.double_col.mean(), id='mean', ), param( lambda t, where: t.double_col.min(), lambda t, where: t.double_col.min(), id='min', ), param( lambda t, where: t.double_col.max(), lambda t, where: t.double_col.max(), id='max', ), param( lambda t, where: t.double_col.approx_median(), lambda t, where: t.double_col.median(), id='approx_median', marks=pytest.mark.xpass_backends([Clickhouse]), ), param( lambda t, where: t.double_col.std(how='sample'), lambda t, where: t.double_col.std(ddof=1), id='std', ), param( lambda t, where: t.double_col.var(how='sample'), lambda t, where: t.double_col.var(ddof=1), id='var', ), param( lambda t, where: t.double_col.std(how='pop'), lambda t, where: t.double_col.std(ddof=0), id='std_pop', ), param( lambda t, where: t.double_col.var(how='pop'), lambda t, where: t.double_col.var(ddof=0), id='var_pop', ), param( lambda t, where: t.double_col.cov(t.float_col), lambda t, where: t.double_col.cov(t.float_col), id='covar', ), param( lambda t, where: t.double_col.corr(t.float_col), lambda t, where: t.double_col.corr(t.float_col), id='corr', ), param( lambda t, where: t.string_col.approx_nunique(), lambda t, where: t.string_col.nunique(), id='approx_nunique', marks=pytest.mark.xfail_backends([MySQL, SQLite]), ), param( lambda t, where: t.double_col.arbitrary(how='first'), lambda t, where: t.double_col.iloc[0], id='arbitrary_first', ), param( lambda t, where: t.double_col.arbitrary(how='last'), lambda t, where: t.double_col.iloc[-1], id='arbitrary_last', ), ], ) @pytest.mark.parametrize( ('ibis_cond', 'pandas_cond'), [ param(lambda t: None, lambda t: slice(None), id='no_cond'), param( lambda t: t.string_col.isin(['1', '7']), lambda t: t.string_col.isin(['1', '7']), id='is_in', ), ], ) @pytest.mark.xfail_unsupported def test_reduction_ops( backend, alltypes, df, result_fn, expected_fn, ibis_cond, pandas_cond ): expr = result_fn(alltypes, ibis_cond(alltypes)) > result = expr.execute() ibis/tests/all/test_aggregation.py:209: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ibis/expr/types.py:219: in execute self, limit=limit, timecontext=timecontext, params=params, **kwargs ibis/client.py:368: in execute return backend.execute(expr, limit=limit, params=params, **kwargs) ibis/client.py:221: in execute result = self._execute_query(query, **kwargs) ibis/client.py:228: in _execute_query return query.execute() ibis/bigquery/client.py:194: in execute query_parameters=self.query_parameters, ibis/bigquery/client.py:475: in _execute query.result() # blocks until finished ../../miniconda3/envs/ibis-dev/lib/python3.7/site-packages/google/cloud/bigquery/job.py:3207: in result super(QueryJob, self).result(retry=retry, timeout=timeout) ../../miniconda3/envs/ibis-dev/lib/python3.7/site-packages/google/cloud/bigquery/job.py:812: in result return super(_AsyncJob, self).result(timeout=timeout) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <google.cloud.bigquery.job.QueryJob object at 0x7fc25b890c10>, timeout = None def result(self, timeout=None): """Get the result of the operation, blocking if necessary. Args: timeout (int): How long (in seconds) to wait for the operation to complete. If None, wait indefinitely. Returns: google.protobuf.Message: The Operation's result. Raises: google.api_core.GoogleAPICallError: If the operation errors or if the timeout is reached before the operation completes. """ self._blocking_poll(timeout=timeout) if self._exception is not None: # pylint: disable=raising-bad-type # Pylint doesn't recognize that this is valid in this case. > raise self._exception E google.api_core.exceptions.BadRequest: 400 Syntax error: Expected ")" but got identifier "BigQueryTable" at [3:3] E E (job ID: fabc9d5c-9c79-482e-9320-acffbd787de1) E E -----Query Job SQL Follows----- E E | . | . | . | . | . | E 1:SELECT E 2: COVAR_SAMP(ref_0 E 3: BigQueryTable[table] E 4: name: swast-scratch.testing.functional_alltypes E 5: schema: E 6: index : int64 E 7: Unnamed_0 : int64 E 8: id : int64 E 9: bool_col : boolean E 10: tinyint_col : int64 E 11: smallint_col : int64 E 12: int_col : int64 E 13: bigint_col : int64 E 14: float_col : float64 E 15: double_col : float64 E 16: date_string_col : string E 17: string_col : string E 18: timestamp_col : timestamp E 19: year : int64 E 20: month : int64 E 21: E 22: double_col = Column[float64*] 'double_col' from table E 23: ref_0, ref_0 E 24: BigQueryTable[table] E 25: name: swast-scratch.testing.functional_alltypes E 26: schema: E 27: index : int64 E 28: Unnamed_0 : int64 E 29: id : int64 E 30: bool_col : boolean E 31: tinyint_col : int64 E 32: smallint_col : int64 E 33: int_col : int64 E 34: bigint_col : int64 E 35: float_col : float64 E 36: double_col : float64 E 37: date_string_col : string E 38: string_col : string E 39: timestamp_col : timestamp E 40: year : int64 E 41: month : int64 E 42: E 43: float_col = Column[float64*] 'float_col' from table E 44: ref_0) AS `tmp` E 45:FROM `swast-scratch.testing.functional_alltypes` E | . | . | . | . | . | ../../miniconda3/envs/ibis-dev/lib/python3.7/site-packages/google/api_core/future/polling.py:130: BadRequest ____________________________________________ test_reduction_ops[BigQuery-is_in-covar] _____________________________________________ backend = <ibis.tests.backends.BigQuery object at 0x7fc25b7935d0> alltypes = BigQueryTable[table] name: swast-scratch.testing.functional_alltypes schema: index : int64 Unnamed_0 : int...4 date_string_col : string string_col : string timestamp_col : timestamp year : int64 month : int64 df = index Unnamed_0 id bool_col tinyint_col ... date_string_col string_col timestamp_col year m... True 6 ... 01/31/10 6 2010-01-31 05:06:13.650 2010 1 [7300 rows x 15 columns] result_fn = <function <lambda> at 0x7fc25b7c08c0>, expected_fn = <function <lambda> at 0x7fc25b7c0950> ibis_cond = <function <lambda> at 0x7fc25b7c0f80>, pandas_cond = <function <lambda> at 0x7fc25b7c3050> @pytest.mark.parametrize( ('result_fn', 'expected_fn'), [ param( lambda t, where: t.bool_col.count(where=where), lambda t, where: len(t.bool_col[where].dropna()), id='count', ), param( lambda t, where: t.bool_col.any(), lambda t, where: t.bool_col.any(), id='any', ), param( lambda t, where: t.bool_col.notany(), lambda t, where: ~t.bool_col.any(), id='notany', ), param( lambda t, where: -t.bool_col.any(), lambda t, where: ~t.bool_col.any(), id='any_negate', ), param( lambda t, where: t.bool_col.all(), lambda t, where: t.bool_col.all(), id='all', ), param( lambda t, where: t.bool_col.notall(), lambda t, where: ~t.bool_col.all(), id='notall', ), param( lambda t, where: -t.bool_col.all(), lambda t, where: ~t.bool_col.all(), id='all_negate', ), param( lambda t, where: t.double_col.sum(), lambda t, where: t.double_col.sum(), id='sum', ), param( lambda t, where: t.double_col.mean(), lambda t, where: t.double_col.mean(), id='mean', ), param( lambda t, where: t.double_col.min(), lambda t, where: t.double_col.min(), id='min', ), param( lambda t, where: t.double_col.max(), lambda t, where: t.double_col.max(), id='max', ), param( lambda t, where: t.double_col.approx_median(), lambda t, where: t.double_col.median(), id='approx_median', marks=pytest.mark.xpass_backends([Clickhouse]), ), param( lambda t, where: t.double_col.std(how='sample'), lambda t, where: t.double_col.std(ddof=1), id='std', ), param( lambda t, where: t.double_col.var(how='sample'), lambda t, where: t.double_col.var(ddof=1), id='var', ), param( lambda t, where: t.double_col.std(how='pop'), lambda t, where: t.double_col.std(ddof=0), id='std_pop', ), param( lambda t, where: t.double_col.var(how='pop'), lambda t, where: t.double_col.var(ddof=0), id='var_pop', ), param( lambda t, where: t.double_col.cov(t.float_col), lambda t, where: t.double_col.cov(t.float_col), id='covar', ), param( lambda t, where: t.double_col.corr(t.float_col), lambda t, where: t.double_col.corr(t.float_col), id='corr', ), param( lambda t, where: t.string_col.approx_nunique(), lambda t, where: t.string_col.nunique(), id='approx_nunique', marks=pytest.mark.xfail_backends([MySQL, SQLite]), ), param( lambda t, where: t.double_col.arbitrary(how='first'), lambda t, where: t.double_col.iloc[0], id='arbitrary_first', ), param( lambda t, where: t.double_col.arbitrary(how='last'), lambda t, where: t.double_col.iloc[-1], id='arbitrary_last', ), ], ) @pytest.mark.parametrize( ('ibis_cond', 'pandas_cond'), [ param(lambda t: None, lambda t: slice(None), id='no_cond'), param( lambda t: t.string_col.isin(['1', '7']), lambda t: t.string_col.isin(['1', '7']), id='is_in', ), ], ) @pytest.mark.xfail_unsupported def test_reduction_ops( backend, alltypes, df, result_fn, expected_fn, ibis_cond, pandas_cond ): expr = result_fn(alltypes, ibis_cond(alltypes)) > result = expr.execute() ibis/tests/all/test_aggregation.py:209: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ ibis/expr/types.py:219: in execute self, limit=limit, timecontext=timecontext, params=params, **kwargs ibis/client.py:368: in execute return backend.execute(expr, limit=limit, params=params, **kwargs) ibis/client.py:221: in execute result = self._execute_query(query, **kwargs) ibis/client.py:228: in _execute_query return query.execute() ibis/bigquery/client.py:194: in execute query_parameters=self.query_parameters, ibis/bigquery/client.py:475: in _execute query.result() # blocks until finished ../../miniconda3/envs/ibis-dev/lib/python3.7/site-packages/google/cloud/bigquery/job.py:3207: in result super(QueryJob, self).result(retry=retry, timeout=timeout) ../../miniconda3/envs/ibis-dev/lib/python3.7/site-packages/google/cloud/bigquery/job.py:812: in result return super(_AsyncJob, self).result(timeout=timeout) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <google.cloud.bigquery.job.QueryJob object at 0x7fc25c1aa7d0>, timeout = None def result(self, timeout=None): """Get the result of the operation, blocking if necessary. Args: timeout (int): How long (in seconds) to wait for the operation to complete. If None, wait indefinitely. Returns: google.protobuf.Message: The Operation's result. Raises: google.api_core.GoogleAPICallError: If the operation errors or if the timeout is reached before the operation completes. """ self._blocking_poll(timeout=timeout) if self._exception is not None: # pylint: disable=raising-bad-type # Pylint doesn't recognize that this is valid in this case. > raise self._exception E google.api_core.exceptions.BadRequest: 400 Syntax error: Expected ")" but got identifier "BigQueryTable" at [3:3] E E (job ID: 23caa920-3cf1-4d62-9523-e81e1d58e9a9) E E -----Query Job SQL Follows----- E E | . | . | . | . | . | E 1:SELECT E 2: COVAR_SAMP(ref_0 E 3: BigQueryTable[table] E 4: name: swast-scratch.testing.functional_alltypes E 5: schema: E 6: index : int64 E 7: Unnamed_0 : int64 E 8: id : int64 E 9: bool_col : boolean E 10: tinyint_col : int64 E 11: smallint_col : int64 E 12: int_col : int64 E 13: bigint_col : int64 E 14: float_col : float64 E 15: double_col : float64 E 16: date_string_col : string E 17: string_col : string E 18: timestamp_col : timestamp E 19: year : int64 E 20: month : int64 E 21: E 22: double_col = Column[float64*] 'double_col' from table E 23: ref_0, ref_0 E 24: BigQueryTable[table] E 25: name: swast-scratch.testing.functional_alltypes E 26: schema: E 27: index : int64 E 28: Unnamed_0 : int64 E 29: id : int64 E 30: bool_col : boolean E 31: tinyint_col : int64 E 32: smallint_col : int64 E 33: int_col : int64 E 34: bigint_col : int64 E 35: float_col : float64 E 36: double_col : float64 E 37: date_string_col : string E 38: string_col : string E 39: timestamp_col : timestamp E 40: year : int64 E 41: month : int64 E 42: E 43: float_col = Column[float64*] 'float_col' from table E 44: ref_0) AS `tmp` E 45:FROM `swast-scratch.testing.functional_alltypes` E | . | . | . | . | . | ../../miniconda3/envs/ibis-dev/lib/python3.7/site-packages/google/api_core/future/polling.py:130: BadRequest ======================================================== warnings summary ========================================================= ibis/tests/all/test_aggregation.py::test_reduction_ops[BigQuery-no_cond-covar] /Users/swast/src/ibis/ibis/bigquery/client.py:545: PendingDeprecationWarning: Client.dataset is deprecated and will be removed in a future version. Use a string like 'my_project.my_dataset' or a cloud.google.bigquery.DatasetReference object, instead. table_ref = self.client.dataset(dataset, project=project).table(name) ibis/tests/all/test_aggregation.py::test_reduction_ops[BigQuery-no_cond-covar] /Users/swast/src/ibis/ibis/bigquery/client.py:432: PendingDeprecationWarning: Client.dataset is deprecated and will be removed in a future version. Use a string like 'my_project.my_dataset' or a cloud.google.bigquery.DatasetReference object, instead. dataset_ref = self.client.dataset(dataset, project=project) -- Docs: https://docs.pytest.org/en/latest/warnings.html ===================================================== short test summary info ===================================================== FAILED ibis/tests/all/test_aggregation.py::test_reduction_ops[BigQuery-no_cond-covar] - google.api_core.exceptions.BadRequest: 4... FAILED ibis/tests/all/test_aggregation.py::test_reduction_ops[BigQuery-is_in-covar] - google.api_core.exceptions.BadRequest: 400... ================================================== 2 failed, 2 warnings in 4.17s ================================================== ``` </details> **Thoughts on fix** I believe this is the relevant source: https://github.com/ibis-project/ibis/blob/4f110e1fcfb36e5763a1ed44b1e1ceaa5b5e30b2/ibis/bigquery/compiler.py#L556-L576 Perhaps it is just missing some calls to `translator.translate`?

[ { "content": "import datetime\nfrom functools import partial\n\nimport numpy as np\nimport regex as re\nimport toolz\nfrom multipledispatch import Dispatcher\n\nimport ibis\nimport ibis.common.exceptions as com\nimport ibis.expr.datatypes as dt\nimport ibis.expr.lineage as lin\nimport ibis.expr.operations as op...

diff --git a/docs/source/release/index.rst b/docs/source/release/index.rst index 568b72d63d2d..55683ed0d581 100644 --- a/docs/source/release/index.rst +++ b/docs/source/release/index.rst @@ -12,6 +12,7 @@ Release Notes These release notes are for versions of ibis **1.0 and later**. Release notes for pre-1.0 versions of ibis can be found at :doc:`release-pre-1.0` +* :bug:`2367` Fix the covariance operator in the BigQuery backend. * :feature:`2366` Add PySpark support for ReductionVectorizedUDF * :feature:`2306` Add time context in `scope` in execution for pandas backend * :support:`2351` Simplifying tests directories structure diff --git a/ibis/bigquery/compiler.py b/ibis/bigquery/compiler.py index 55ee2cce540b..6c46148290b9 100644 --- a/ibis/bigquery/compiler.py +++ b/ibis/bigquery/compiler.py @@ -573,7 +573,9 @@ def compiles_covar(translator, expr): left = where.ifelse(left, ibis.NA) right = where.ifelse(right, ibis.NA) - return "COVAR_{}({}, {})".format(how, left, right) + return "COVAR_{}({}, {})".format( + how, translator.translate(left), translator.translate(right) + ) @rewrites(ops.Any) diff --git a/ibis/bigquery/tests/test_compiler.py b/ibis/bigquery/tests/test_compiler.py index 814ebde9e3d3..1d7d4558fb48 100644 --- a/ibis/bigquery/tests/test_compiler.py +++ b/ibis/bigquery/tests/test_compiler.py @@ -457,9 +457,8 @@ def test_cov(alltypes, project_id): FROM `{project_id}.testing.functional_alltypes`""" assert result == expected - expr = d.cov(d, how='error') with pytest.raises(ValueError): - expr.compile() + d.cov(d, how='error') @pytest.mark.parametrize(

ibis-project__ibis-7364

bug: Command drop view IF EXISTS does not exist in Oracle ### What happened? Oracle queries fail while dropping the view. IF EXISTS is not supported in Oracle: https://docs.oracle.com/en/database/oracle/oracle-database/19/sqlrf/DROP-VIEW.html ### What version of ibis are you using? 7.0.0 ### What backend(s) are you using, if any? Oracle ### Relevant log output ```sh sqlalchemy.exc.DatabaseError: (oracledb.exceptions.DatabaseError) ORA-00933: SQL command not properly ended [SQL: DROP VIEW IF EXISTS "_ibis_oracle_metadata_d4gbmh4h2fa2jnq5qo3o3rg6sa"] ``` ### Code of Conduct - [X] I agree to follow this project's Code of Conduct

[ { "content": "\"\"\"The Oracle backend.\"\"\"\n\nfrom __future__ import annotations\n\nimport atexit\nimport contextlib\nimport sys\nimport warnings\nfrom typing import TYPE_CHECKING, Any\n\nimport oracledb\n\nfrom ibis import util\n\n# Wow, this is truly horrible\n# Get out your clippers, it's time to shave a ...

diff --git a/ibis/backends/oracle/__init__.py b/ibis/backends/oracle/__init__.py index 38617b7959f1..cd236c97f9c9 100644 --- a/ibis/backends/oracle/__init__.py +++ b/ibis/backends/oracle/__init__.py @@ -181,7 +181,7 @@ def _metadata(self, query: str) -> Iterable[tuple[str, dt.DataType]]: view = sa.table(name) create_view = CreateView(view, sa.text(query)) - drop_view = DropView(view, if_exists=True) + drop_view = DropView(view, if_exists=False) t = sa.table( "all_tab_columns",

fidals__shopelectro-491

order.es6:234: Test order redirect to ya.kassa The puzzle `473-f28eab07` from #473 has to be resolved: https://github.com/fidals/shopelectro/blob/f0e50b7c3b66e1d18f3f8356c245e16167c51fc3/front/js/components/order.es6#L234-L234 The puzzle was created by duker33 on 06-Aug-18. Estimate: 30 minutes, If you have any technical questions, don't ask me, submit new tickets instead. The task will be "done" when the problem is fixed and the text of the puzzle is _removed_ from the source code. Here is more about [PDD](http://www.yegor256.com/2009/03/04/pdd.html) and [about me](http://www.yegor256.com/2017/04/05/pdd-in-action.html).

[ { "content": "\"\"\"\nDjango settings for shopelectro project.\n\nGenerated by 'django-admin startproject' using Django 1.9.5.\n\nFor more information on this file, see\nhttps://docs.djangoproject.com/en/1.9/topics/settings/\n\nFor the full list of settings and their values, see\nhttps://docs.djangoproject.com/...

diff --git a/docker/env_files/paths.dist b/docker/env_files/paths.dist index 11975f16..32e14972 100644 --- a/docker/env_files/paths.dist +++ b/docker/env_files/paths.dist @@ -1,5 +1,5 @@ # Identify the dependencies folder -DEPS_DIR=/usr/local/lib/python3.6/site-packages +DEPS_DIR=/usr/app/deps # Directory, where you cloned `refarm-site` repository REFARM_DIR=/path/to_my/refarm_site # Identify the source folder diff --git a/front/js/components/order.es6 b/front/js/components/order.es6 index 0d13d9d6..c57a4ff4 100644 --- a/front/js/components/order.es6 +++ b/front/js/components/order.es6 @@ -204,11 +204,10 @@ <input type="text" name="customerNumber" value="${formData.customerNumber}"> <input type="text" name="orderNumber" value="${formData.orderNumber}"> <input type="text" name="paymentType" value="${formData.paymentType}"> - <input type="submit"> </form> `; - DOM.$yandexFormWrapper.html(formHtml); + DOM.$yandexFormWrapper.append($(formHtml)); } /** @@ -235,9 +234,9 @@ server.sendYandexOrder(orderInfo) .then((formData) => renderYandexForm(formData)) // setTimeout to wait "onOrderSend" handling - .then(() => setTimeout(() => $(DOM.yandexForm).submit(), 100)); + .then(setTimeout(() => $(DOM.yandexForm).submit(), 100)); } else { - $(DOM.fullForm).submit(); + setTimeout(() => $(DOM.fullForm).submit(), 100) } } diff --git a/shopelectro/settings/base.py b/shopelectro/settings/base.py index 7450d2f6..24d92dca 100644 --- a/shopelectro/settings/base.py +++ b/shopelectro/settings/base.py @@ -371,3 +371,6 @@ def get_robots_content(): # Multipliers are related to prices in this order: # big/medium/small/retail. First three are wholesale prices. PRICE_MULTIPLIERS = 1.0, 1.0, 1.0, 1.0 + +# default for local tests. Prod's one may differ +YANDEX_KASSA_LINK = 'https://money.yandex.ru/eshop.xml' diff --git a/shopelectro/tests/tests_selenium.py b/shopelectro/tests/tests_selenium.py index ce1447f6..bebf5a2c 100644 --- a/shopelectro/tests/tests_selenium.py +++ b/shopelectro/tests/tests_selenium.py @@ -604,6 +604,9 @@ def test_feedback_filter(self): @helpers.disable_celery class OrderPage(helpers.SeleniumTestCase): + # Ya.Kassa's domain with card processing UI + YA_KASSA_INNER_DOMAIN = 'money.yandex.ru' + @staticmethod def get_cell(pos, col): # table columns mapping: http://prntscr.com/bsv5hp # Ignore InvalidLinkBear @@ -647,12 +650,19 @@ def buy_products(self): .format(i) ).click() - def perform_operations_on_cart(self): - self.click((By.ID, 'id_payment_type_0')) + def select_payment_type(self, payment_type='cash'): + # @todo #473:15m Move `payment_type` to dict or dataclass + input_item = self.browser.find_element_by_css_selector( + f'input[name="payment_type"][value="{payment_type}"]' + ) + input_item.click() + + def append_products_to_cart(self): + self.select_payment_type('cash') add_one_more = self.click((By.XPATH, self.add_product)) self.wait.until(EC.staleness_of(add_one_more)) - def fill_and_submit_form(self): + def fill_contacts_data(self): @helpers.try_again_on_stale_element(3) def insert_value(id, keys, expected_keys=''): def expected_conditions(browser): @@ -664,8 +674,10 @@ def expected_conditions(browser): insert_value('id_city', 'Санкт-Петербург') insert_value('id_phone', '2222222222', expected_keys='+7 (222) 222 22 22') insert_value('id_email', 'test@test.test') + + def submit_form(self): + # @todo #473:30m Hide all form processing methods to a separated class. self.click((By.ID, 'submit-order')) - self.wait.until(EC.url_to_be(self.success_order_url)) def test_table_is_presented_if_there_is_some_products(self): """If there are some products in cart, we should see them in table on OrderPage.""" @@ -736,8 +748,10 @@ def assert_count(count): def test_confirm_order(self): """After filling the form we should be able to confirm an Order.""" - self.perform_operations_on_cart() - self.fill_and_submit_form() + self.append_products_to_cart() + self.fill_contacts_data() + self.submit_form() + self.wait.until(EC.url_to_be(self.success_order_url)) self.assertEqual( self.browser.current_url, self.live_server_url + reverse(Page.CUSTOM_PAGES_URL_NAME, args=('order-success', )) @@ -749,10 +763,12 @@ def test_order_email(self): 'order-table-product-id') clean_codes = [code.text for code in codes] - self.perform_operations_on_cart() + self.append_products_to_cart() final_price = self.browser.find_element_by_id('cart-page-sum').text[:-5] - self.fill_and_submit_form() + self.fill_contacts_data() + self.submit_form() + self.wait.until(EC.url_to_be(self.success_order_url)) self.assertEqual(len(mail.outbox), 1) sent_mail_body = mail.outbox[0].body @@ -778,6 +794,32 @@ def test_order_email(self): sent_mail_body ) + def test_pay_with_yandex_kassa(self): + success_page_domain = self.YA_KASSA_INNER_DOMAIN + self.fill_contacts_data() + self.select_payment_type('AC') + self.submit_form() + self.wait.until(EC.url_contains(success_page_domain)) + self.assertIn(success_page_domain, self.browser.current_url) + + # @todo #489:60m Fix yandex.kassa payment type bug. + # See details in the test case below. + @unittest.expectedFailure + def test_change_cart_and_pay_with_yandex_kassa(self): + """ + The same as `test_pay_with_yandex_kassa`, but with the detail. + + Appending products to cart on order page + suddenly breaks yandex kassa payment type. + """ + success_page_domain = self.YA_KASSA_INNER_DOMAIN + self.append_products_to_cart() + self.fill_contacts_data() # Ignore CPDBear + self.select_payment_type('AC') + self.submit_form() + self.wait.until(EC.url_contains(success_page_domain)) + self.assertIn(success_page_domain, self.browser.current_url) + class SitePage(helpers.SeleniumTestCase):

kivy__kivy-4598

ToggleButton can get released with allow_no_selection=False Ohai buddiez, I hope you're all doing goodie ^__^ I found a new bug probably due to "always_release" on ButtonBehavior having been changed recently: `Changed in version 1.9.2: The default value is now False.` Take the following example: https://gist.github.com/42e02d13c31a6504b57d5cd3ac23a460 If you try to press a button, then release outside of it, its state will be "normal", even though it should remain "down". I have made a small change to ButtonBehavior which adds an event "on_release_outside" and makes it set the state to normal by default, and overrode it in ToggleButtonBehavior to do nothing instead. Incoming PR, so please give feedback! (EDIT: See #4594 ) Thanks for reading, see you around buddiez bliblibli ^__^

[ { "content": "'''\nButton Behavior\n===============\n\nThe :class:`~kivy.uix.behaviors.button.ButtonBehavior`\n`mixin <https://en.wikipedia.org/wiki/Mixin>`_ class provides\n:class:`~kivy.uix.button.Button` behavior. You can combine this class with\nother widgets, such as an :class:`~kivy.uix.image.Image`, to p...

diff --git a/kivy/uix/behaviors/button.py b/kivy/uix/behaviors/button.py index d4f81e2f23..f2ef3a55b1 100644 --- a/kivy/uix/behaviors/button.py +++ b/kivy/uix/behaviors/button.py @@ -167,7 +167,7 @@ def on_touch_up(self, touch): if (not self.always_release and not self.collide_point(*touch.pos)): - self.state = 'normal' + self._do_release() return touchtime = time() - self.__touch_time

django-oscar__django-oscar-3324

product-lookup not working ### Issue Summary Can't select related products ### Steps to Reproduce 1. run sandbox 2. in Dashboard->products select any product eg. The shellcoder's handbook 3. in product's upselling click text field `Recommended product:` 4. dropdown contains `The results could not be loaded.` and console throws ` Internal Server Error: /en-gb/dashboard/catalogue/product-lookup/` with traceback ending ``` django-oscar/src/oscar/apps/dashboard/catalogue/views.py", line 649, in get_queryset return self.model.browsable.all() AttributeError: type object 'Product' has no attribute 'browsable' ``` ### Technical details * Python version: 3.7.5 * Django version: 2.2.11 * Oscar version: commit 5de733e

[ { "content": "from django.conf import settings\nfrom django.contrib import messages\nfrom django.db.models import Q\nfrom django.http import HttpResponseRedirect\nfrom django.shortcuts import get_object_or_404, redirect\nfrom django.template.loader import render_to_string\nfrom django.urls import reverse\nfrom ...

diff --git a/src/oscar/apps/dashboard/catalogue/views.py b/src/oscar/apps/dashboard/catalogue/views.py index ca8fa81d3de..45bd9e50ca0 100644 --- a/src/oscar/apps/dashboard/catalogue/views.py +++ b/src/oscar/apps/dashboard/catalogue/views.py @@ -646,7 +646,7 @@ class ProductLookupView(ObjectLookupView): model = Product def get_queryset(self): - return self.model.browsable.all() + return self.model.objects.browsable().all() def lookup_filter(self, qs, term): return qs.filter(Q(title__icontains=term) diff --git a/tests/functional/dashboard/test_catalogue.py b/tests/functional/dashboard/test_catalogue.py index ff257c9ce66..4e65a787fcf 100644 --- a/tests/functional/dashboard/test_catalogue.py +++ b/tests/functional/dashboard/test_catalogue.py @@ -30,7 +30,8 @@ class TestCatalogueViews(WebTestCase): def test_exist(self): urls = [reverse('dashboard:catalogue-product-list'), reverse('dashboard:catalogue-category-list'), - reverse('dashboard:stock-alert-list')] + reverse('dashboard:stock-alert-list'), + reverse('dashboard:catalogue-product-lookup')] for url in urls: self.assertIsOk(self.get(url))

django-json-api__django-rest-framework-json-api-824

JSON output incorrectly wrapping id in quotes I've dropped DRF-JSON-API into my DRF application following all the defaults but I'm getting strange output where the model's `id` is being wrapped in quotations. This is causing issues with my Ember.js frontend as it's unable to properly parse the output. I've checked the database and the id field is defined as an integer. Every other field seems to be serialized correctly. What setting am I missing?! Sample output: ``` { "links": { "first": "http://localhost:8000/dat/?page%5Bnumber%5D=1", "last": "http://localhost:8000/dat/?page%5Bnumber%5D=1", "next": null, "prev": null }, "data": [ { "type": "Dat", "id": "1", "attributes": { "name": "Nintendo - Nintendo Switch", "description": "Nintendo - Nintendo Switch", "matched_games": 0, "missing_games": 618, "last_verified": "2020-08-05T16:43:27.041339Z" } } ], "meta": { "pagination": { "page": 1, "pages": 1, "count": 1 } } } Response code: 200 (OK); Time: 55ms; Content length: 410 bytes ```

[ { "content": "\"\"\"\nRenderers\n\"\"\"\nimport copy\nfrom collections import OrderedDict, defaultdict\nfrom collections.abc import Iterable\n\nimport inflection\nfrom django.db.models import Manager\nfrom django.utils import encoding\nfrom rest_framework import relations, renderers\nfrom rest_framework.fields ...

diff --git a/README.rst b/README.rst index b3162184..bc52bbf5 100644 --- a/README.rst +++ b/README.rst @@ -48,7 +48,7 @@ like the following:: }, "data": [{ "type": "identities", - "id": 3, + "id": "3", "attributes": { "username": "john", "full-name": "John Coltrane" diff --git a/docs/getting-started.md b/docs/getting-started.md index bef744eb..58768e39 100644 --- a/docs/getting-started.md +++ b/docs/getting-started.md @@ -32,7 +32,7 @@ like the following: }, "data": [{ "type": "identities", - "id": 3, + "id": "3", "attributes": { "username": "john", "full-name": "John Coltrane" diff --git a/docs/usage.md b/docs/usage.md index 5b7010d3..9fd46e6b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -338,7 +338,7 @@ Example - Without format conversion: { "data": [{ "type": "identities", - "id": 3, + "id": "3", "attributes": { "username": "john", "first_name": "John", @@ -359,7 +359,7 @@ Example - With format conversion set to `dasherize`: { "data": [{ "type": "identities", - "id": 3, + "id": "3", "attributes": { "username": "john", "first-name": "John", @@ -389,7 +389,7 @@ Example without format conversion: { "data": [{ "type": "blog_identity", - "id": 3, + "id": "3", "attributes": { ... }, @@ -412,7 +412,7 @@ When set to dasherize: { "data": [{ "type": "blog-identity", - "id": 3, + "id": "3", "attributes": { ... }, @@ -438,7 +438,7 @@ Example without pluralization: { "data": [{ "type": "identity", - "id": 3, + "id": "3", "attributes": { ... }, @@ -446,7 +446,7 @@ Example without pluralization: "home_towns": { "data": [{ "type": "home_town", - "id": 3 + "id": "3" }] } } @@ -461,7 +461,7 @@ When set to pluralize: { "data": [{ "type": "identities", - "id": 3, + "id": "3", "attributes": { ... }, @@ -469,7 +469,7 @@ When set to pluralize: "home_towns": { "data": [{ "type": "home_towns", - "id": 3 + "id": "3" }] } } diff --git a/rest_framework_json_api/renderers.py b/rest_framework_json_api/renderers.py index ccd71510..cfc74f1f 100644 --- a/rest_framework_json_api/renderers.py +++ b/rest_framework_json_api/renderers.py @@ -33,7 +33,7 @@ class JSONRenderer(renderers.JSONRenderer): "data": [ { "type": "companies", - "id": 1, + "id": "1", "attributes": { "name": "Mozilla", "slug": "mozilla",

qtile__qtile-4246

Tasklist Widget Icons not vertically centered ### The issue: Depending on the icon size, the placement of the icon relative to the text shifts. Here is an example with icon size = 45 and text size = 30. ![1664826413](https://user-images.githubusercontent.com/12877032/193666223-f80a1051-ecbd-45fc-894a-1c50ba4d9159.png) And here it is with icon size = 30 as well: ![1664826716](https://user-images.githubusercontent.com/12877032/193666538-9f88eb29-d0b5-4676-8dc9-c8b423b5cc8d.png) A simple fix would be to add a user-defined variable to the `y` calculation for `draw_icon`. I subclassed tasklist and manually modified the `y` value to match my icon size, and that works okay. A more flexible solution would be to modify the y value so it is always drawn such that it is centered. #1714 discussed the same issue but was never fixed. ### Required: - [X] I have searched past issues to see if this bug has already been reported.

[ { "content": "# Copyright (c) 2012-2014 roger\n# Copyright (c) 2012-2015 Tycho Andersen\n# Copyright (c) 2013 dequis\n# Copyright (c) 2013 Tao Sauvage\n# Copyright (c) 2013 Craig Barnes\n# Copyright (c) 2014 Sean Vig\n# Copyright (c) 2018 Piotr Przymus\n#\n# Permission is hereby granted, free of charge, to any ...

diff --git a/CHANGELOG b/CHANGELOG index 08904917f6..e714988635 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -59,6 +59,7 @@ Qtile x.xx.x, released XXXX-XX-XX: - Fix setting tiled position by mouse for layouts using _SimpleLayoutBase. To support this in other layouts, add a swap method taking two windows. - Fix unfullscreening bug in conjunction with Chromium based clients when auto_fullscreen is set to `False`. - Ensure `CurrentLayoutIcon` expands paths for custom folders. + - Fix vertical alignment of icons in `TaskList` widget * python version support - We have added support for python 3.11 and pypy 3.9. - python 3.7, 3.8 and pypy 3.7 are not longer supported. diff --git a/libqtile/widget/tasklist.py b/libqtile/widget/tasklist.py index 6a75f29485..14995b9ff5 100644 --- a/libqtile/widget/tasklist.py +++ b/libqtile/widget/tasklist.py @@ -531,7 +531,7 @@ def draw_icon(self, surface, offset): return x = offset + self.borderwidth + self.padding_x - y = self.padding_y + self.borderwidth + y = (self.height - self.icon_size) // 2 self.drawer.ctx.save() self.drawer.ctx.translate(x, y)

litestar-org__litestar-2433

Bug: `2.2.0` does not have `[full]` group ### Description The move from `poetry` to `pdm` in 2.2.0 has a regression for the `[full]` group. ### URL to code causing the issue _No response_ ### MCVE ```python pip install litestar[full]==2.2.0 && pip show pydantic ``` ### Steps to reproduce - `pip install litestar[full]` - Observe no `[full]` group is available, and `pip show $package` does not show expected pacakges ### Screenshots _No response_ ### Logs _No response_ ### Litestar Version 2.2.0 ### Platform - [ ] Linux - [ ] Mac - [ ] Windows - [X] Other (Please specify in the description above)  > [!NOTE] > Check out all issues funded or available for funding here: https://polar.sh/litestar-org > * If you would like to see an issue prioritized, make a pledge towards it! > * We receive the pledge once the issue is completed & verified <a href="https://polar.sh/litestar-org/litestar/issues/2434"> <picture> <source media="(prefers-color-scheme: dark)" srcset="https://polar.sh/api/github/litestar-org/litestar/issues/2434/pledge.svg?darkmode=1"> <img alt="Fund with Polar" src="https://polar.sh/api/github/litestar-org/litestar/issues/2434/pledge.svg"> </picture> </a>

[ { "content": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING, Any, Callable, Literal, NamedTuple\n\nfrom litestar.utils.deprecation import warn_deprecation\n\n__all__ = (\n \"ControllerRouterHandler\",\n \"PathParameterDefinition\",\n \"PathParameterDefinition\",\n \"Reserved...

diff --git a/.gitignore b/.gitignore index 12e59642c5..ca6f32027e 100644 --- a/.gitignore +++ b/.gitignore @@ -24,7 +24,6 @@ target/ *.iml .DS_Store .coverage -.python-version .ruff_cache /docs/_build/ coverage.* @@ -34,3 +33,9 @@ setup.py .pdm.toml .pdm-python .pdm-build/ +# pdm - PEP 582 +__pypackages__/ + +# pyenv / rtx / asdf +.tool-versions +.python-version diff --git a/litestar/types/internal_types.py b/litestar/types/internal_types.py index 1224426b85..963467424c 100644 --- a/litestar/types/internal_types.py +++ b/litestar/types/internal_types.py @@ -48,7 +48,7 @@ class PathParameterDefinition(NamedTuple): def __getattr__(name: str) -> Any: if name == "LitestarType": warn_deprecation( - "2.3.0", + "2.2.1", "LitestarType", "import", removal_in="3.0.0", diff --git a/pdm.lock b/pdm.lock index 4d45f9a940..fb216aa70f 100644 --- a/pdm.lock +++ b/pdm.lock @@ -2,11 +2,11 @@ # It is not intended for manual editing. [metadata] -groups = ["default", "annotated-types", "attrs", "brotli", "cli", "cryptography", "dev", "dev-contrib", "docs", "jinja", "jwt", "linting", "mako", "minijinja", "opentelemetry", "piccolo", "picologging", "prometheus", "pydantic", "redis", "sqlalchemy", "standard", "structlog", "test"] +groups = ["default", "annotated-types", "attrs", "brotli", "cli", "cryptography", "dev", "dev-contrib", "docs", "jinja", "jwt", "linting", "mako", "minijinja", "opentelemetry", "piccolo", "picologging", "prometheus", "pydantic", "redis", "sqlalchemy", "standard", "structlog", "test", "full"] cross_platform = true static_urls = false lock_version = "4.3" -content_hash = "sha256:fa9d278def9dc75febddad6d5bd694fa3cb3841c586aaae35d21d4ce7976bc86" +content_hash = "sha256:41b63a9ef2b44b3ac01593f1ee20d7cdb14a762e03facd36c6106fd2de32eedd" [[package]] name = "accessible-pygments" @@ -804,12 +804,12 @@ files = [ [[package]] name = "cssutils" -version = "2.7.1" -requires_python = ">=3.7" +version = "2.9.0" +requires_python = ">=3.8" summary = "A CSS Cascading Style Sheets library for Python" files = [ - {file = "cssutils-2.7.1-py3-none-any.whl", hash = "sha256:1e92e0d9dab2ec8af9f38d715393964ba533dc3beacab9b072511dfc241db775"}, - {file = "cssutils-2.7.1.tar.gz", hash = "sha256:340ecfd9835d21df8f98500f0dfcea0aee41cb4e19ecbc2cf94f0a6d36d7cb6c"}, + {file = "cssutils-2.9.0-py3-none-any.whl", hash = "sha256:f8b013169e281c0c6083207366c5005f5dd4549055f7aba840384fb06a78745c"}, + {file = "cssutils-2.9.0.tar.gz", hash = "sha256:89477b3d17d790e97b9fb4def708767061055795aae6f7c82ae32e967c9be4cd"}, ] [[package]] @@ -1256,7 +1256,7 @@ files = [ [[package]] name = "hypothesis" -version = "6.87.3" +version = "6.87.4" requires_python = ">=3.8" summary = "A library for property-based testing" dependencies = [ @@ -1265,8 +1265,8 @@ dependencies = [ "sortedcontainers<3.0.0,>=2.1.0", ] files = [ - {file = "hypothesis-6.87.3-py3-none-any.whl", hash = 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"https://litestar.dev/" -repository = "https://github.com/litestar-org/litestar" +Documentation = "https://docs.litestar.dev/" +Homepage = "https://litestar.dev/" +Repository = "https://github.com/litestar-org/litestar" [project.optional-dependencies] annotated-types = ["annotated-types"] @@ -87,6 +87,9 @@ redis = ["redis[hiredis]>=4.4.4"] sqlalchemy = ["advanced-alchemy==0.2.2"] standard = ["jinja2", "jsbeautifier", "uvicorn[standard]", "fast-query-parsers>=1.0.2"] structlog = ["structlog"] +full = [ + "litestar[annotated-types,attrs,brotli,cli,cryptography,jinja,jwt,mako,minijinja,opentelemetry,piccolo,picologging,prometheus,pydantic,redis,sqlalchemy,standard,structlog]", +] [tool.pdm.dev-dependencies] dev = [

napari__napari-2063

Console no longer working ## 🐛 Bug I think we've got a regression, from #2036 where the console is no longer visible when opened with the button in the viewer. <img width="1200" alt="Screen Shot 2021-01-01 at 3 34 47 PM" src="https://user-images.githubusercontent.com/6531703/103447936-ec407100-4c46-11eb-8487-76cf63aca2a6.png"> I just see the above. I havn't looked into fix yet, but was able to narrow to that commit. I imagine it will be pretty simple fix. cc @tlambert03

[ { "content": "import os.path\nimport warnings\nfrom pathlib import Path\nfrom typing import TYPE_CHECKING, Optional\n\nimport numpy as np\nfrom qtpy.QtCore import QCoreApplication, QObject, QSize, Qt\nfrom qtpy.QtGui import QCursor, QGuiApplication\nfrom qtpy.QtWidgets import QFileDialog, QSplitter, QVBoxLayout...

diff --git a/napari/_qt/_tests/test_qt_viewer.py b/napari/_qt/_tests/test_qt_viewer.py index 8dc9cfaae40..0d31818389a 100644 --- a/napari/_qt/_tests/test_qt_viewer.py +++ b/napari/_qt/_tests/test_qt_viewer.py @@ -39,7 +39,7 @@ def test_qt_viewer_with_console(make_test_viewer): assert view._console is None # Check console is created when requested assert view.console is not None - assert view.dockConsole.widget == view.console + assert view.dockConsole.widget() is view.console def test_qt_viewer_toggle_console(make_test_viewer): @@ -51,7 +51,7 @@ def test_qt_viewer_toggle_console(make_test_viewer): # Check console has been created when it is supposed to be shown view.toggle_console_visibility(None) assert view._console is not None - assert view.dockConsole.widget == view.console + assert view.dockConsole.widget() is view.console @pytest.mark.parametrize('layer_class, data, ndim', layer_test_data) diff --git a/napari/_qt/qt_viewer.py b/napari/_qt/qt_viewer.py index 5b3975acfa6..b6c1b9276b9 100644 --- a/napari/_qt/qt_viewer.py +++ b/napari/_qt/qt_viewer.py @@ -295,7 +295,7 @@ def console(self): @console.setter def console(self, console): self._console = console - self.dockConsole.widget = console + self.dockConsole.setWidget(console) self._update_theme() def _constrain_width(self, event):

mitmproxy__mitmproxy-2615

[requires.io] dependency update on master branch

[ { "content": "import os\nimport runpy\nfrom codecs import open\n\nfrom setuptools import setup, find_packages\n\n# Based on https://github.com/pypa/sampleproject/blob/master/setup.py\n# and https://python-packaging-user-guide.readthedocs.org/\n\nhere = os.path.abspath(os.path.dirname(__file__))\n\nwith open(os....

diff --git a/setup.cfg b/setup.cfg index b8e129ee00..eaabfa12ca 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,7 +1,7 @@ [flake8] max-line-length = 140 max-complexity = 25 -ignore = E251,C901,W503,W292 +ignore = E251,C901,W503,W292,E722,E741 exclude = mitmproxy/contrib/*,test/mitmproxy/data/*,release/build/* addons = file,open,basestring,xrange,unicode,long,cmp diff --git a/setup.py b/setup.py index 9c20cdc9f3..8e68e217c6 100644 --- a/setup.py +++ b/setup.py @@ -85,7 +85,7 @@ "pydivert>=2.0.3,<2.2", ], 'dev': [ - "flake8>=3.2.1, <3.5", + "flake8>=3.5, <3.6", "Flask>=0.10.1, <0.13", "mypy>=0.530,<0.541", "pytest-cov>=2.2.1, <3",

django-crispy-forms__django-crispy-forms-468

Remove `crispy_forms.base.from_iterable` We no longer support Python 2.5

[ { "content": "def from_iterable(iterables):\n \"\"\"\n Backport of `itertools.chain.from_iterable` compatible with Python 2.5\n \"\"\"\n for it in iterables:\n for element in it:\n if isinstance(element, dict):\n for key in element:\n yield key\n ...

[ { "content": "\n\nclass KeepContext(object):\n \"\"\"\n Context manager that receives a `django.template.Context` instance and a list of keys\n\n Once the context manager is exited, it removes `keys` from the context, to avoid\n side effects in later layout objects that may use the same context vari...

diff --git a/crispy_forms/base.py b/crispy_forms/base.py index 98297def6..82da75072 100644 --- a/crispy_forms/base.py +++ b/crispy_forms/base.py @@ -1,14 +1,3 @@ -def from_iterable(iterables): - """ - Backport of `itertools.chain.from_iterable` compatible with Python 2.5 - """ - for it in iterables: - for element in it: - if isinstance(element, dict): - for key in element: - yield key - else: - yield element class KeepContext(object):

openfun__marsha-761

Searching a playlist by text raises a 500 error ## Bug Report **Expected behavior/code** In the admin, it should be possible to search a playlist by text. **Actual Behavior** Searching a playlist by text raises a 500 error (https://sentry.io/organizations/gip-fun-mooc/issues/1856670127/?project=1298925&query=is%3Aunresolved) **Steps to Reproduce** 1. go to Marsha admin playlist list page: localhost:8070/admin/core/playlist/ 2. Type a search in the search field: <img src="https://user-images.githubusercontent.com/1427165/91073123-db4d7680-e63a-11ea-97c9-4c6c604f1d63.png" width="350"/> 3. Enjoy the 500! **Environment** - Marsha version: 3.10.0 - Platform: Docker **Possible Solution** I think the error comes from this line https://github.com/openfun/marsha/blob/master/src/backend/marsha/core/admin.py#L380 which is trying to search for a text on a foreignkey... The first solution that comes to mind is to replace it by : "portable_to__title", "portable_to__id" and "portable_to__lti_id"... However, I'm not sure we want to search a playlist by the title or ids of the playlists to which it is portable... So finally, I think we should remove this line.

[ { "content": "\"\"\"Admin of the ``core`` app of the Marsha project.\"\"\"\n\nfrom django.contrib import admin\nfrom django.contrib.auth.admin import UserAdmin as DefaultUserAdmin\nfrom django.urls import reverse\nfrom django.utils.html import format_html\nfrom django.utils.translation import gettext_lazy as _\...

diff --git a/CHANGELOG.md b/CHANGELOG.md index fc950e90cc..30db09d49e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,10 @@ Versioning](https://semver.org/spec/v2.0.0.html). - Remove usage of react-intl-po - Rework front i18n workflow +### Fixed + +- Fix admin video search + ## [3.10.2] - 2020-09-29 ### Fixed diff --git a/src/backend/marsha/core/admin.py b/src/backend/marsha/core/admin.py index 2de55d5a2e..1e10aa1d17 100644 --- a/src/backend/marsha/core/admin.py +++ b/src/backend/marsha/core/admin.py @@ -377,7 +377,9 @@ class PlaylistAdmin(admin.ModelAdmin): "consumer_site__name", "organization__name", "lti_id", - "portable_to", + "portable_to__title", + "portable_to__lti_id", + "portable_to__id", "title", ) verbose_name = _("Playlist")

docker__docker-py-3023

Not a Contribution: create_api_error_from_api_exception should "raise <exception> from <original-error>" to preserve error message Not a Contribution. APIError handling should be changed to so that it doesn't hide the original exception. https://stackoverflow.com/questions/24752395/python-raise-from-usage

[ { "content": "import requests\n\n\nclass DockerException(Exception):\n \"\"\"\n A base class from which all other exceptions inherit.\n\n If you want to catch all errors that the Docker SDK might raise,\n catch this base exception.\n \"\"\"\n\n\ndef create_api_error_from_http_exception(e):\n \...

diff --git a/docker/errors.py b/docker/errors.py index ba952562c..7725295f5 100644 --- a/docker/errors.py +++ b/docker/errors.py @@ -28,7 +28,7 @@ def create_api_error_from_http_exception(e): cls = ImageNotFound else: cls = NotFound - raise cls(e, response=response, explanation=explanation) + raise cls(e, response=response, explanation=explanation) from e class APIError(requests.exceptions.HTTPError, DockerException):

pyqtgraph__pyqtgraph-888

TreeWidget.topLevelItems is broken on Python3 As per the title. The method uses `xrange`, which obviously is not available in Python 3. I haven't tried it, but I assume the regression was introduced with 6c7e0fa, where an `from ..python2_3 import xrange` was removed from the corresponding file. I can see two possible fixes for the issue. 1. Change `xrange` to `range`, which is available in both languages. 2. Revert the removal of the `python2_3` compatibility import. @campagnola Let me know which one you prefer, and I'll submit a PR.

[ { "content": "# -*- coding: utf-8 -*-\nfrom ..Qt import QtGui, QtCore\nfrom weakref import *\n\n__all__ = ['TreeWidget', 'TreeWidgetItem']\n\n\nclass TreeWidget(QtGui.QTreeWidget):\n \"\"\"Extends QTreeWidget to allow internal drag/drop with widgets in the tree.\n Also maintains the expanded state of subt...

diff --git a/pyqtgraph/widgets/TreeWidget.py b/pyqtgraph/widgets/TreeWidget.py index b0ec54c12d..8c55ae2f9b 100644 --- a/pyqtgraph/widgets/TreeWidget.py +++ b/pyqtgraph/widgets/TreeWidget.py @@ -201,7 +201,7 @@ def takeTopLevelItem(self, index): return item def topLevelItems(self): - return map(self.topLevelItem, xrange(self.topLevelItemCount())) + return [self.topLevelItem(i) for i in range(self.topLevelItemCount())] def clear(self): items = self.topLevelItems()

PaddlePaddle__models-2261

deeplabv3+反复报warning 在paddle1.4.1下，由于deeplabv3+打开了显存优化，导致反复报如下的warning： <img width="956" alt="db83046567521a831348d8eea6f2e46a" src="https://user-images.githubusercontent.com/46314656/57190981-398cac80-6f53-11e9-9ffc-3a3c7b379d82.png">

[ { "content": "from __future__ import absolute_import\nfrom __future__ import division\nfrom __future__ import print_function\nimport os\nif 'FLAGS_fraction_of_gpu_memory_to_use' not in os.environ:\n os.environ['FLAGS_fraction_of_gpu_memory_to_use'] = '0.98'\n\nimport paddle\nimport paddle.fluid as fluid\nimp...

diff --git a/PaddleCV/deeplabv3+/train.py b/PaddleCV/deeplabv3+/train.py index 5e983ed291..2cef945de7 100755 --- a/PaddleCV/deeplabv3+/train.py +++ b/PaddleCV/deeplabv3+/train.py @@ -145,6 +145,7 @@ def loss(logit, label): fluid.layers.assign(np.array( [0.1], dtype=np.float32))) loss_mean = fluid.layers.reduce_mean(loss) / area + loss_mean.persistable = True opt = fluid.optimizer.Momentum( lr,

kivy__kivy-5366

setup.py should not depend on the existence of `git` on the system ### Versions * Python: 3.5.3 * OS: nixos * Kivy: 1.10.0 * Kivy installation method: nix ### Description I tried to package kivy for nixos, a Purely Functional Linux Distribution. ``` Traceback (most recent call last): File "nix_run_setup.py", line 8, in <module> exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\\r\\n', '\\n'), __file__, 'exec')) File "setup.py", line 934, in <module> version=get_version(), File "setup.py", line 47, in get_version ['git', 'rev-parse', 'HEAD'] File "/nix/store/kgh0z7i2n7xl6pvanmi0v8dw4qy63932-python3-3.5.3/lib/python3.5/subprocess.py", line 316, in check_output **kwargs).stdout File "/nix/store/kgh0z7i2n7xl6pvanmi0v8dw4qy63932-python3-3.5.3/lib/python3.5/subprocess.py", line 383, in run with Popen(*popenargs, **kwargs) as process: File "/nix/store/kgh0z7i2n7xl6pvanmi0v8dw4qy63932-python3-3.5.3/lib/python3.5/subprocess.py", line 676, in __init__ restore_signals, start_new_session) File "/nix/store/kgh0z7i2n7xl6pvanmi0v8dw4qy63932-python3-3.5.3/lib/python3.5/subprocess.py", line 1282, in _execute_child raise child_exception_type(errno_num, err_msg) FileNotFoundError: [Errno 2] No such file or directory: 'git' ``` This can be attributed to `setup.py` attempting to run `git`. This was introduced here: https://github.com/kivy/kivy/pull/4949/commits/ffcb437fc6d183f3e34db180c9b0f0220bf2e08b I would postulate that the install-time dependency on `git` is unnecessary and bad practice.

[ { "content": "#\n# Kivy - Cross-platform UI framework\n# https://kivy.org/\n#\nfrom __future__ import print_function\n\nimport sys\nbuild_examples = False\nif \"--build_examples\" in sys.argv:\n build_examples = True\n sys.argv.remove(\"--build_examples\")\n\nfrom copy import deepcopy\nimport os\nfrom os....

diff --git a/setup.py b/setup.py index 72c8c001af..56da910481 100644 --- a/setup.py +++ b/setup.py @@ -46,7 +46,7 @@ def get_version(filename='kivy/version.py'): GIT_REVISION = check_output( ['git', 'rev-parse', 'HEAD'] ).strip().decode('ascii') - except CalledProcessError: + except (CalledProcessError, FileNotFoundError): GIT_REVISION = "Unknown" cnt = (

litestar-org__litestar-1610

StaticFilesConfig and virtual directories I'm trying to write a ``FileSystemProtocol`` to load files from the package data using [importlib_resources](https://importlib-resources.readthedocs.io/en/latest/using.html#). But because ``directories`` is defined as ``DirectoryPath``, pydantic checks if the given directories exist in the local filesystem. This is not generally true, especially in any kind of virtual filesystem (e.g. a zipped package). I think this condition should be relaxed to support virtual filesystems. https://github.com/starlite-api/starlite/blob/9bb6dcd57c10a591377cf8e3a537e9292566d5b9/starlite/config/static_files.py#L32

[ { "content": "from __future__ import annotations\n\nfrom typing import TYPE_CHECKING, Any, Generic, TypeVar, cast\n\nfrom litestar._parsers import parse_cookie_string, parse_headers, parse_query_string\nfrom litestar.datastructures.headers import Headers\nfrom litestar.datastructures.multi_dicts import MultiDic...

diff --git a/litestar/connection/base.py b/litestar/connection/base.py index c604e3471f..161eb0f606 100644 --- a/litestar/connection/base.py +++ b/litestar/connection/base.py @@ -287,7 +287,7 @@ def clear_session(self) -> None: """ self.scope["session"] = Empty - def url_for(self, name: str, **path_parameters: dict[str, Any]) -> str: + def url_for(self, name: str, **path_parameters: Any) -> str: """Return the url for a given route handler name. Args:

liberapay__liberapay.com-844

Can't cancel a bank wire payin Users who initiate a bank wire payin can't cancel it if they change their mind or realize that their bank doesn't allow them to transfer euros abroad. It's not possible to cancel a bank wire payin on MangoPay, which is why we don't already have this feature, but we should be able to implement a fake cancellation on our side: - ~~[ ] add a `canceled` status to `exchanges` (there will be some code to modify, e.g. `git grep "'failed'"`)~~ - [x] add a "Cancel" button to the bankwire page which changes the exchange status to `failed` with "Canceled by the user" in the `note` column ~~Later, maybe:~~ - ~~[ ] identify bank wires that should have been canceled and change their status~~ - ~~[ ] send the list of all canceled bank wires to MangoPay so they can manually mark them as failed on their side~~ *Edit: no longer necessary now that bank wire payins expire automatically after a month. However we'll need something else instead:* - [ ] ~~ignore mangopay's expiration notifications for "canceled" bank wires~~ *not necessary if we use the `failed` status instead of creating a `canceled` one* Mangopay account switch can mess up the wallets table Which in turn can crash payday: <https://github.com/liberapay/salon/issues/181#issuecomment-347861123>.

[ { "content": "\"\"\"Functions for moving money into, out of, or between wallets.\n\"\"\"\nfrom __future__ import division, print_function, unicode_literals\n\nfrom decimal import Decimal\nfrom time import sleep\n\nfrom mangopay.exceptions import APIError\nfrom mangopay.resources import (\n BankAccount, BankW...

diff --git a/liberapay/billing/transactions.py b/liberapay/billing/transactions.py index d4f1065e0d..e939f30bd9 100644 --- a/liberapay/billing/transactions.py +++ b/liberapay/billing/transactions.py @@ -251,6 +251,10 @@ def payin_bank_wire(db, participant, debit_amount): return payin, e +def cancel_bank_wire_payin(db, exchange, payin, participant): + record_exchange_result(db, exchange.id, payin.Id, 'failed', "canceled", participant) + + def record_unexpected_payin(db, payin): """Record an unexpected bank wire payin. """ diff --git a/sql/branch.sql b/sql/branch.sql new file mode 100644 index 0000000000..3148547071 --- /dev/null +++ b/sql/branch.sql @@ -0,0 +1,6 @@ +UPDATE wallets + SET is_current = true + FROM participants p + WHERE p.id = owner + AND p.mangopay_user_id = remote_owner_id + AND is_current IS NULL; diff --git a/www/%username/identity.spt b/www/%username/identity.spt index 9412aa07e9..ba405465d0 100644 --- a/www/%username/identity.spt +++ b/www/%username/identity.spt @@ -157,6 +157,11 @@ if request.method == 'POST': WHERE remote_owner_id = %s RETURNING * """, (old_account.Id,)) + website.db.run(""" + UPDATE wallets + SET is_current = true + WHERE remote_owner_id = %s + """, (account.Id,)) for w in (w for w in old_wallets if w.balance): transfer( website.db, participant.id, participant.id, w.balance, diff --git a/www/%username/wallet/payin/bankwire/%back_to.spt b/www/%username/wallet/payin/bankwire/%back_to.spt index 4c661c8d83..a1d7d05bdf 100644 --- a/www/%username/wallet/payin/bankwire/%back_to.spt +++ b/www/%username/wallet/payin/bankwire/%back_to.spt @@ -6,7 +6,7 @@ from decimal import Decimal as D, InvalidOperation, ROUND_UP from mangopay.resources import BankWirePayIn from liberapay.billing.fees import upcharge_bank_wire -from liberapay.billing.transactions import payin_bank_wire +from liberapay.billing.transactions import cancel_bank_wire_payin, payin_bank_wire from liberapay.constants import EVENTS, PAYIN_BANK_WIRE_MIN from liberapay.exceptions import InvalidNumber from liberapay.utils import b64decode_s, get_participant @@ -33,19 +33,26 @@ def get_exchange_payin(participant, request): participant = get_participant(state, restrict=True, block_suspended_user=True) -if request.method == 'POST' and request.body.get('action') == 'email': +if request.method == 'POST' and 'action' in request.body: exchange, payin = get_exchange_payin(participant, request) - sent = participant.send_email( - 'payin_bankwire_created', - (participant.email or participant.get_any_email()), - exchange=exchange._asdict(), payin=payin, - ) - if not sent: - raise response.error(500, _("An unknown error occurred.")) - if request.headers.get(b'X-Requested-With') == b'XMLHttpRequest': - raise response.json({'msg': _("The email has been sent.")}) - else: + action = request.body['action'] + if action == 'email': + sent = participant.send_email( + 'payin_bankwire_created', + (participant.email or participant.get_any_email()), + exchange=exchange._asdict(), payin=payin, + ) + if not sent: + raise response.error(500, _("An unknown error occurred.")) + if request.headers.get(b'X-Requested-With') == b'XMLHttpRequest': + raise response.json({'msg': _("The email has been sent.")}) + else: + response.redirect(request.line.uri) + elif action == 'cancel': + cancel_bank_wire_payin(website.db, exchange, payin, participant) response.redirect(request.line.uri) + else: + raise response.error(400, "bad `action` value '%s' in body" % action) exchange, payin = None, None if 'exchange_id' in request.qs: @@ -121,10 +128,16 @@ title = _("Adding Money") % block thin_content % if exchange and exchange.status == 'failed' + % if exchange.note == 'canceled' + <div class="alert alert-info">{{ _("This bank wire has been canceled.") }}</div> + <a class="btn btn-default" href="{{ participant.path('wallet/payin') }}" + >{{ _("Go back") }}</a> + % else <div class="alert alert-danger">{{ _("The attempt to prepare a bank wire transfer of {0} has failed. Error message: {1}", exchange.amount + exchange.fee, exchange.note) }}</div> + % endif % endif % if not show_form and not payin @@ -150,7 +163,7 @@ title = _("Adding Money") % endif </p> - % elif payin + % elif payin and exchange.status == 'created' <p>{{ _( "We are ready to receive the funds. Please send exactly {0} to the " @@ -196,10 +209,12 @@ title = _("Adding Money") >{{ _("Change your email settings") }}</a> % endif - % if back_to - <a href="{{ response.sanitize_untrusted_url(back_to) }}" - class="btn btn-default pull-right">{{ _("Go back") }}</a> - % endif + <p>{{ _("Changed your mind? Cancel the payment to avoid receiving a failure notification next month:") }}</p> + <form action="" method="POST"> + <input type="hidden" name="csrf_token" value="{{ csrf_token }}" /> + <input type="hidden" name="action" value="cancel" /> + <button class="btn btn-danger">{{ _("Cancel") }}</button> + </form> % elif show_form <form id="payin" action="javascript:" method="POST"

mampfes__hacs_waste_collection_schedule-556

Add StadtService Brühl Add Source for StadtService Brühl Update stadtservice_bruehl_de.md

[ { "content": "import datetime\nimport logging\n\nimport requests\nfrom bs4 import BeautifulSoup\nfrom waste_collection_schedule import Collection # type: ignore[attr-defined]\nfrom waste_collection_schedule.service.ICS import ICS\n\nTITLE = \"StadtService Brühl\"\nDESCRIPTION = \"Source für Abfallkalender Stad...

diff --git a/custom_components/waste_collection_schedule/waste_collection_schedule/source/stadtservice_bruehl_de.py b/custom_components/waste_collection_schedule/waste_collection_schedule/source/stadtservice_bruehl_de.py index c000778cd..b9c2ec3c0 100644 --- a/custom_components/waste_collection_schedule/waste_collection_schedule/source/stadtservice_bruehl_de.py +++ b/custom_components/waste_collection_schedule/waste_collection_schedule/source/stadtservice_bruehl_de.py @@ -18,7 +18,7 @@ class Source: def __init__(self, strasse, hnr): self._strasse = strasse self._hnr = hnr - self._ics = ICS() + self._ics = ICS(regex="(.*?) \\- ", split_at=", ") def fetch(self):

google__timesketch-90

Importing of JSON timelines creates duplicate timelines with same name. Steps to reproduce 1) command line: echo '[ { "datetime": "2012-04-12T17:24:38-08:00", "timestamp_desc": "Test", "timestamp": 1334251478000000, "message": "Test message" } ]' > test_dupe.json tsctl json2ts --name test_dupe --file test_dupe.json tsctl json2ts --name test_dupe --file test_dupe.json 2) Create new sketch 3) Notice duplicate "test_dupe" timelines on list to select from. 4) Add both 5) Explore, using "*" as filter. 6) notice duplicate results.

[ { "content": "#!/usr/bin/env python\n# Copyright 2015 Google Inc. All rights reserved.\n#\n# Licensed under the Apache License, Version 2.0 (the \"License\");\n# you may not use this file except in compliance with the License.\n# You may obtain a copy of the License at\n#\n# http://www.apache.org/licenses/L...

diff --git a/tsctl b/tsctl index 9882d1f4fb..51750bd599 100644 --- a/tsctl +++ b/tsctl @@ -248,15 +248,16 @@ class CreateTimelineFromJson(Command): events, index_name, event_type) # Create the searchindex in the Timesketch database. - searchindex = SearchIndex( + searchindex = SearchIndex.get_or_create( name=timeline_name, description=timeline_name, user=None, index_name=index_name) searchindex.grant_permission(None, u'read') db_session.add(searchindex) db_session.commit() sys.stdout.write( - u'Search index {0:s} created\n{1:d} events inserted\n'.format( - timeline_name, counter[u'events'])) + u'Timeline name: {0:s}\nElasticsearch index: {1:s}\n' + u'Events inserted: {2:d}\n'.format( + timeline_name, index_name, counter[u'events'])) except IOError as exception: sys.stderr.write(u'Error: {0:s}\n'.format(exception)) diff --git a/wsgi.py b/wsgi.py index 996e578b35..9b7fe31685 100644 --- a/wsgi.py +++ b/wsgi.py @@ -37,7 +37,8 @@ application = create_app() -# Remove the session after every request or app shutdown. +# pylint: disable=unused-argument @application.teardown_appcontext def shutdown_session(exception=None): + """Remove the database session after every request or app shutdown.""" db_session.remove()

easybuilders__easybuild-easyblocks-2267

enhanced extension filter for Python packages causes trouble for netcdf4-python sanity check The enhanced extension filter for Python packages made in #2224 causes trouble for `netcdf4-python-1.5.3-intel-2020a-Python-3.8.2.eb`: ``` == 2020-12-03 20:44:05,145 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): Sanity check failed: command "mpirun -n 1 PYTHONNOUSERSITE=1 python -c "import netCDF4"" failed; output: [proxy:0:0@node3406.kirlia.os] HYD_spawn (../../../../../src/pm/i_hydra/libhydra/spawn/intel/hydra_spawn.c:128): execvp error on file PYTHONNOUSERSITE=1 (No such file or directory) ``` We should set `$PYTHONNOUSERSITE` to `1` some other way, and make sure its set *again* after the environment is reset in the sanity check step... cc @Flamefire

[ { "content": "##\n# Copyright 2009-2020 Ghent University\n#\n# This file is part of EasyBuild,\n# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),\n# with support of Ghent University (http://ugent.be/hpc),\n# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),\n# F...

diff --git a/easybuild/easyblocks/p/python.py b/easybuild/easyblocks/p/python.py index 64a2774642a..a167cc1b1fe 100644 --- a/easybuild/easyblocks/p/python.py +++ b/easybuild/easyblocks/p/python.py @@ -53,7 +53,7 @@ import easybuild.tools.toolchain as toolchain -EXTS_FILTER_PYTHON_PACKAGES = ('PYTHONNOUSERSITE=1 python -c "import %(ext_name)s"', "") +EXTS_FILTER_PYTHON_PACKAGES = ('python -c "import %(ext_name)s"', "") # magic value for unlimited stack size UNLIMITED = 'unlimited'

aws__aws-sdk-pandas-2799

Question regarding wr.athena.to_iceberg I am having a hard time trying to figure where the to_iceberg method tries to create and subsequently destroy the temporary table needed for the INSERT INTO … SELECT statement. `wr.athena.to_iceberg(df=data, index=True, database=os.getenv("GLUE_DATABASE"), table=os.getenv("GLUE_TABLE").lower(), merge_cols=[time_measure], workgroup=athena_workgroup, encryption="SSE-KMS", kms_key=kms_key)` This is how I am using the method. I have set up the IAM role to have necessary IAM permissions on the destination bucket, the corresponding glue db and table, as well as LakeFormation permissions on said db and table. The code still raises the following exceptions. `botocore.errorfactory.AccessDeniedException: An error occurred (AccessDeniedException) when calling the GetTable operation: Insufficient Lake Formation permission(s) on temp_table_dca47e409f4a494781e27ea08cc1f74c` `botocore.errorfactory.AccessDeniedException: An error occurred (AccessDeniedException) when calling the DeleteTable operation: Insufficient Lake Formation permission(s): Required Drop on temp_table_dca47e409f4a494781e27ea08cc1f74c` I was wondering, could it be that the temp tables are created in a different db on which I did not set enough LakeFormation permissions? I tried adding LakeFormation permissions to the relevant IAM role even on default db, but nothing changed. Any help is appreciated!

[ { "content": "\"\"\"Amazon Athena Module containing all to_* write functions.\"\"\"\n\nfrom __future__ import annotations\n\nimport logging\nimport re\nimport typing\nimport uuid\nfrom typing import Any, Dict, Literal, TypedDict, cast\n\nimport boto3\nimport pandas as pd\n\nfrom awswrangler import _data_types, ...

diff --git a/awswrangler/athena/_write_iceberg.py b/awswrangler/athena/_write_iceberg.py index 28eae686b..22fdf95c9 100644 --- a/awswrangler/athena/_write_iceberg.py +++ b/awswrangler/athena/_write_iceberg.py @@ -483,6 +483,7 @@ def to_iceberg( s3.to_parquet( df=df, path=temp_path or wg_config.s3_output, + index=index, dataset=True, database=database, table=temp_table,