author int64 658 755k | date stringdate 2012-06-12 08:34:29 2024-07-22 14:51:21 | timezone int64 -46,800 43.2k | hash stringlengths 40 40 | message stringlengths 5 490 | mods listlengths 1 16 | language stringclasses 20 values | license stringclasses 3 values | repo stringlengths 5 68 | original_message stringlengths 12 491 |
|---|---|---|---|---|---|---|---|---|---|
377,522 | 01.03.2020 02:04:40 | -10,800 | 6282e21ef63465cdc76ad832708ce9041997cd7e | Try to work around error on istalling pandas with Python 2.7 | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpackage.yml",
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "@@ -19,7 +19,8 @@ jobs:\n- name: Install dependencies\nrun: |\npython -m pip install --upgrade pip\n- pip install lxml numpy sqlalchemy pandas cython\n+ pip insta... | Python | Apache License 2.0 | levitsky/pyteomics | Try to work around error on istalling pandas with Python 2.7 |
377,522 | 01.03.2020 02:07:57 | -10,800 | 599b9679adc0cc49b6249c791b6ba61f6c038e66 | Remove the linting step for now | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpackage.yml",
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "@@ -22,13 +22,6 @@ jobs:\npip install numpy\npip install lxml sqlalchemy pandas cython\npip install pynumpress\n- - name: Lint with flake8\n- run: |\n- pip instal... | Python | Apache License 2.0 | levitsky/pyteomics | Remove the linting step for now |
377,522 | 01.03.2020 18:15:36 | -10,800 | 2f1928a2054e91f59f0fb3f400f6f401cf95cc5c | Create a PyPI publishing workflow | [
{
"change_type": "ADD",
"old_path": null,
"new_path": ".github/workflows/pythonpublish.yml",
"diff": "+name: Upload Python Package\n+\n+on:\n+ release:\n+ types: [created]\n+\n+jobs:\n+ deploy:\n+ runs-on: ubuntu-latest\n+ steps:\n+ - uses: actions/checkout@v2\n+ - name: Set up Python\n+ uses: actio... | Python | Apache License 2.0 | levitsky/pyteomics | Create a PyPI publishing workflow |
377,522 | 01.03.2020 18:27:16 | -10,800 | a764d47d8929f9fc75bb44fd0bf1ddd8be8b4bae | Add a contributor from before move | [
{
"change_type": "MODIFY",
"old_path": "AUTHORS",
"new_path": "AUTHORS",
"diff": "List of contributors (in chronological order)\n---------------------------------------------\n+On Bitbucket:\n+.............\n+\nAnton Goloborodko [golobor]\nLev Levitsky [levitsky]\nMark Ivanov [markmipt]\n@@ -12,3 +1... | Python | Apache License 2.0 | levitsky/pyteomics | Add a contributor from before move |
377,522 | 20.04.2020 19:37:38 | -10,800 | d5c4013dcb316736fdc6d53d3eb804939f39e7ec | Fix broken bitbucket links | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "@@ -81,7 +81,7 @@ API changes\n4.0.1\n-----\n-Fix issue `#35 <https://bitbucket.org/levitsky/pyteomics/issues/35/ordereddict-may-be-in-reversed-order-on>`_\n+Fix issue `#35 <hhttps://levitsky.github.io/bitbucket_ba... | Python | Apache License 2.0 | levitsky/pyteomics | Fix broken bitbucket links |
377,522 | 27.04.2020 02:11:20 | -10,800 | 511655946a393f4aa214685ab7aa7450a9ab8cca | Fix error when fragment ion mass spectrum is not present in tandem xml file | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-4.3a1\n\\ No newline at end of file\n+4.3a2\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -198,6 +... | Python | Apache License 2.0 | levitsky/pyteomics | Fix error when fragment ion mass spectrum is not present in tandem xml file |
377,522 | 01.05.2020 23:09:21 | -10,800 | 46edfdc9418a9efd6f243ff08acf841fe936bd9a | Parse tandem rt as duration, convert duration to float on failure | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/_schema_defaults.py",
"new_path": "pyteomics/_schema_defaults.py",
"diff": "@@ -288,7 +288,7 @@ _tandem_schema_defaults = {'ints': {\n'a_ions', 'x_ions', 'c_ions', 'z_ions']},\n'floats': {('group', k) for k in [\n- 'fI', 'sumI', 'maxI', 'mh', 'expect... | Python | Apache License 2.0 | levitsky/pyteomics | Parse tandem rt as duration, convert duration to float on failure |
377,522 | 07.05.2020 20:57:32 | -10,800 | e697117ef449e5e4f5f2dc6cb342ab96df31d391 | Make rt None if empty in tandem | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "@@ -3,6 +3,9 @@ dev\n- New module :py:mod:`pyteomics.openms.idxml`.\n+ - Fix `#3 <https://github.com/levitsky/pyteomics/issues/3>`_, `#5 <https://github.com/levitsky/pyteomics/issues/5>`_,\n+ and some issues in :py... | Python | Apache License 2.0 | levitsky/pyteomics | Make rt None if empty in tandem |
377,522 | 18.05.2020 21:02:20 | -10,800 | 229d010151173754c45d564f8bc27b6e49b01096 | Doc fixes and version bump | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-dev\n+4.3\n---\n+First release after the move to Github. Issue and PR numbers from now on refer to the\n+`Github repo <https://github.com/levitsky/pyteomics>`_. Archive of the Bibucket issues and PRs is stored\n+`... | Python | Apache License 2.0 | levitsky/pyteomics | Doc fixes and version bump |
377,522 | 18.05.2020 22:03:04 | -10,800 | 5de0e927e01d5a59c5e3456ccf9dab7c664d419b | Update publishing workflow | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpublish.yml",
"new_path": ".github/workflows/pythonpublish.yml",
"diff": "@@ -2,7 +2,7 @@ name: Upload Python Package\non:\nrelease:\n- types: [created]\n+ types: [published]\njobs:\ndeploy:\n@@ -10,7 +10,7 @@ jobs:\nsteps:\n- uses: act... | Python | Apache License 2.0 | levitsky/pyteomics | Update publishing workflow |
377,522 | 26.05.2020 21:53:28 | -10,800 | 4a240d88c7dddbff0aa029c3d3b5d4ce645ae2c5 | Add test status badge | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpackage.yml",
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "-name: Python package\n+name: tests\non: [push, pull_request]\n"
},
{
"change_type": "MODIFY",
"old_path": "README.rst",
"new_path": "README.rst",... | Python | Apache License 2.0 | levitsky/pyteomics | Add test status badge |
377,522 | 28.05.2020 01:46:40 | -10,800 | 4425e97b67dde4a6a7ddc9cedfe4632480be4754 | Minor code brush-up, update mass.Unimod tests | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -103,6 +103,7 @@ abundant isotopes and a separate entry for undefined isotope with zero\nkey, mass of the most abundant isotope and 1.0 abundance.\n\"\"\"\n+\ndef _make_isotope_string(e... | Python | Apache License 2.0 | levitsky/pyteomics | Minor code brush-up, update mass.Unimod tests |
377,522 | 10.06.2020 17:26:12 | -10,800 | c92f9384fa34df14283bec75b9a2de9e60ffa253 | Move gravy code to electrochem with modifications | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/electrochem.py",
"new_path": "pyteomics/electrochem.py",
"diff": "@@ -8,7 +8,7 @@ Summary\nThis module is used to calculate the\nelectrochemical properties of polypeptide molecules.\n-The theory behind this module is based on the Henderson-Hasselbalc... | Python | Apache License 2.0 | levitsky/pyteomics | Move gravy code to electrochem with modifications |
377,522 | 10.06.2020 20:40:21 | -10,800 | db44a29cc8fad54d4d05bb153f3b5f4c34d4c3de | Add keepstate to xml iterfind | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/xml.py",
"new_path": "pyteomics/xml.py",
"diff": "@@ -505,6 +505,7 @@ class XML(FileReader):\n\"Do not use `retrieve_refs=True`.\").format(\nself.__class__.__name__))\n+ @_keepstate\ndef iterfind(self, path, **kwargs):\n\"\"\"Parse the XML and yield ... | Python | Apache License 2.0 | levitsky/pyteomics | Add keepstate to xml iterfind |
377,522 | 11.06.2020 18:03:18 | -10,800 | a328ca30adecb7cf207c493a7b2e9b9c81595ce6 | Update electrochem doc | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/electrochem.py",
"new_path": "pyteomics/electrochem.py",
"diff": "@@ -22,13 +22,20 @@ where the sum is taken over all ionizable groups of the polypeptide, and\n:math:`Q_i` is -1 and +1 for acidic and basic functional groups,\nrespectively.\n-Main fun... | Python | Apache License 2.0 | levitsky/pyteomics | Update electrochem doc |
377,533 | 06.07.2020 10:22:55 | -10,800 | 703b1652ee42a0c43ce684f035d61e7fe70e75d9 | Fix xpath, improve pepxml.roc_curve()
Fixes xpath bugs in pepxml.roc_curve() that caused a fatal error [XPathEvalError: Invalid predicate]; adds "charge" and "tag" keys to the output to make the function usable in real world. | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -288,26 +288,27 @@ def roc_curve(source):\nReturns\n-------\nout : list\n- A list of ROC points, sorted by ascending min prob.\n+ A list of ROC points.\n\"\"\"\nparser = etree.XMLParser(remov... | Python | Apache License 2.0 | levitsky/pyteomics | Fix xpath, improve pepxml.roc_curve()
Fixes xpath bugs in pepxml.roc_curve() that caused a fatal error [XPathEvalError: Invalid predicate]; adds "charge" and "tag" keys to the output to make the function usable in real world. |
377,523 | 16.07.2020 13:57:19 | -7,200 | 31cdefe420fe84d3c6264eebdf65e4aaa9100dc2 | Implement parsing of MGF files that contain ion names | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/__init__.py",
"new_path": "pyteomics/auxiliary/__init__.py",
"diff": "@@ -7,7 +7,7 @@ from . import patch as __patch\nfrom .structures import (\nPyteomicsError, Charge, ChargeList,\n- _parse_charge, BasicComposition,\n+ _parse_charge, _pars... | Python | Apache License 2.0 | levitsky/pyteomics | Implement parsing of MGF files that contain ion names |
377,522 | 22.07.2020 01:35:00 | -10,800 | 75ccf2ffb5dd7b9c68653a2da6a836a0cb7ec7b6 | Update example 2 for Python 3, use static folder | [
{
"change_type": "RENAME",
"old_path": "doc/source/examples/example.mgf",
"new_path": "doc/source/_static/example.mgf",
"diff": ""
},
{
"change_type": "RENAME",
"old_path": "doc/source/examples/example.pep.xml",
"new_path": "doc/source/_static/example.pep.xml",
"diff": ""
},
... | Python | Apache License 2.0 | levitsky/pyteomics | Update example 2 for Python 3, use static folder |
377,522 | 22.07.2020 16:44:03 | -10,800 | 0b7d714a8bab062c82a98ac1b05a2562a372b70b | Update filtering example script | [
{
"change_type": "MODIFY",
"old_path": "doc/source/_static/filtering.py",
"new_path": "doc/source/_static/filtering.py",
"diff": "+# place this file in the same directory as example files\nimport pylab\nfrom pyteomics import tandem, pepxml, mzid, auxiliary as aux, pylab_aux as pa\nimport pandas as p... | Python | Apache License 2.0 | levitsky/pyteomics | Update filtering example script |
377,522 | 28.07.2020 00:34:23 | -10,800 | 252bb7d68d256e51176065629381773d8ed0a26b | Fix example 1 to work with current fasta parser | [
{
"change_type": "MODIFY",
"old_path": "doc/source/_static/example_fasta.py",
"new_path": "doc/source/_static/example_fasta.py",
"diff": "@@ -15,8 +15,9 @@ if not os.path.isfile('yeast.fasta.gz'):\nprint('Cleaving the proteins with trypsin...')\nunique_peptides = set()\n-for description, sequence in... | Python | Apache License 2.0 | levitsky/pyteomics | Fix example 1 to work with current fasta parser |
377,522 | 28.07.2020 00:34:46 | -10,800 | f33b41688957ecfab400a1fb176129e1d461fdae | Fix for current Sphinx | [
{
"change_type": "MODIFY",
"old_path": "doc/source/conf.py",
"new_path": "doc/source/conf.py",
"diff": "@@ -40,6 +40,7 @@ sys.path.insert(0, pyteomics_path)\n# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.\nextensions = [\n+ 'numpydoc',\n'sphinx.ext.autodoc',\n'sphinx.ext.autosummar... | Python | Apache License 2.0 | levitsky/pyteomics | Fix for current Sphinx |
377,522 | 28.07.2020 00:36:26 | -10,800 | 1d5d70cecca64a09e0695e90e217973e04355cb2 | Add more warnings and tests for _check_use_index | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -877,21 +877,40 @@ def _make_chain(reader, readername, full_output=False):\ndef _check_use_index(source, use_index, default):\n+ try:\n+ if isinstance(source, ... | Python | Apache License 2.0 | levitsky/pyteomics | Add more warnings and tests for _check_use_index |
377,522 | 28.07.2020 01:16:04 | -10,800 | 9cd485cda16f9c6939d2d0b17833b782244002c2 | Support older Sphinx | [
{
"change_type": "MODIFY",
"old_path": "doc/source/conf.py",
"new_path": "doc/source/conf.py",
"diff": "@@ -284,7 +284,7 @@ def skip(app, what, name, obj, skip, options):\nreturn False\nreturn skip\n-autodoc_default_options = {'members': True, 'inherited-members': True, 'show-inheritance': True}\n+a... | Python | Apache License 2.0 | levitsky/pyteomics | Support older Sphinx |
377,522 | 28.07.2020 01:42:37 | -10,800 | 338612fc8afd2948b5e2922f6b32dfa7894febb2 | Use napoleon instead of numpydoc | [
{
"change_type": "MODIFY",
"old_path": "doc/build-requirements.txt",
"new_path": "doc/build-requirements.txt",
"diff": "lxml\nsqlalchemy\n-numpydoc\nmatplotlib\ngit+https://github.com/KarrLab/sphinxcontrib-googleanalytics.git\nsphinx-sitemap\n"
},
{
"change_type": "MODIFY",
"old_path": "... | Python | Apache License 2.0 | levitsky/pyteomics | Use napoleon instead of numpydoc |
377,522 | 28.07.2020 02:09:14 | -10,800 | 2cc1c91f2bda7de0824b34bfdc34692286ed4d50 | Doc fixes on args and kwargs | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -441,8 +441,10 @@ def get_spectrum(source, title, *args, **kwargs):\nFile to read from.\ntitle : str\nSpectrum title.\n-\n- The rest of the arguments are the same as for :py:func:`read`.\n+ *args\n... | Python | Apache License 2.0 | levitsky/pyteomics | Doc fixes on args and kwargs |
377,522 | 28.07.2020 02:22:09 | -10,800 | 0f57e88c419fc12f226ca9baeefd01da963aeecb | Doc fixes in pylab_aux | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -65,18 +65,23 @@ import numpy as np\nfrom .auxiliary import linear_regression, PyteomicsError\nfrom . import parser, mass\n+\ndef plot_line(a, b, xlim=None, *args, **kwargs):\n\"\"\"Plo... | Python | Apache License 2.0 | levitsky/pyteomics | Doc fixes in pylab_aux |
377,522 | 29.09.2020 15:55:59 | -10,800 | 26d2bb7432ded8e006de3716747dbdfaf6cf2244 | Fix download from Python in example 2 | [
{
"change_type": "MODIFY",
"old_path": "doc/source/_static/example_msms.py",
"new_path": "doc/source/_static/example_msms.py",
"diff": "from pyteomics import mgf, pepxml, mass\nimport os\n-from urllib.request import urlretrieve\n+from urllib.request import urlopen, Request\nimport pylab\n# get the f... | Python | Apache License 2.0 | levitsky/pyteomics | Fix download from Python in example 2 |
377,522 | 29.09.2020 18:54:21 | -10,800 | 29f41361aa75d28046ecde1924b637f89267f3c5 | Update docs, changelog, authors, bump version to 4.3.3 | [
{
"change_type": "MODIFY",
"old_path": "AUTHORS",
"new_path": "AUTHORS",
"diff": "@@ -5,6 +5,7 @@ On Github\n.........\nVladimir Gorshkov [caetera]\n+Andrey Rozenberg [alephreish]\nOn Bitbucket (before March 1, 2020)\n"
},
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path... | Python | Apache License 2.0 | levitsky/pyteomics | Update docs, changelog, authors, bump version to 4.3.3 |
377,522 | 08.10.2020 17:18:34 | -10,800 | 91cbbc227b07c09b09566b347c6c886aa5235afc | Fix URL formatting in USI doc | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/usi.py",
"new_path": "pyteomics/usi.py",
"diff": "@@ -4,12 +4,12 @@ usi - Universal Spectrum Identifier (USI) parser and minimal PROXI client\nSummary\n-------\n-`USI <http://www.psidev.info/usi>` is a standardized method of referencing a specific\n+... | Python | Apache License 2.0 | levitsky/pyteomics | Fix URL formatting in USI doc |
377,522 | 09.10.2020 19:27:06 | -10,800 | d3538dd47fe44952633179dac5d9cad879a3d2a0 | Fix mgf.write with write_ions, add a read-write mgf test with ions | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/structures.py",
"new_path": "pyteomics/auxiliary/structures.py",
"diff": "import re\nfrom collections import defaultdict, Counter\n+import warnings\ntry:\nbasestring\n@@ -82,15 +83,19 @@ class Charge(int):\ndef __str__(self):\nreturn str(ab... | Python | Apache License 2.0 | levitsky/pyteomics | Fix mgf.write with write_ions, add a read-write mgf test with ions |
377,523 | 12.10.2020 18:30:25 | -7,200 | 87897584bb85f631b5cbef306b114c2eb316dc26 | Reset changes in auxiliary/file_helpers.py | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -244,11 +244,11 @@ class IndexedReaderMixin(NoOpBaseReader):\nindex = self.default_index\nif index is None:\nraise PyteomicsError('Access by ID requires buildi... | Python | Apache License 2.0 | levitsky/pyteomics | Reset changes in auxiliary/file_helpers.py |
377,523 | 12.10.2020 18:51:16 | -7,200 | 07020e5583289ec4281293d3b46156ba7c70a8d0 | Moved read_ions parameter to end of function in mgf.py | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -275,28 +275,32 @@ class IndexedMGF(MGFBase, aux.TaskMappingMixin, aux.TimeOrderedIndexedReaderMixi\ndelimiter = 'BEGIN IONS'\ndef __init__(self, source=None, use_header=True, convert_arrays=2, rea... | Python | Apache License 2.0 | levitsky/pyteomics | Moved read_ions parameter to end of function in mgf.py |
377,522 | 13.10.2020 22:30:31 | -10,800 | b55601f86cb9ee515b88491d1eeeac20783fba06 | Undo str conversion of MGF ID | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -322,7 +322,7 @@ class IndexedMGF(MGFBase, aux.TaskMappingMixin, aux.TimeOrderedIndexedReaderMixi\nyield spectrum\ndef get_spectrum(self, key):\n- return self.get_by_id(str(key))\n+ return self.get... | Python | Apache License 2.0 | levitsky/pyteomics | Undo str conversion of MGF ID |
377,522 | 13.10.2020 23:50:35 | -10,800 | 4898a25135ad0bb6314d693bc1b41ff57d70789e | Add an extra test for index access and ions | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mgf.py",
"new_path": "tests/test_mgf.py",
"diff": "@@ -160,6 +160,10 @@ class MGFTest(unittest.TestCase):\nself.assertEqual(data.mgf_spectra_long[1], f.get_spectrum(key))\nself.assertEqual(data.mgf_spectra_long[1], mgf.get_spectrum(self.path, key))\... | Python | Apache License 2.0 | levitsky/pyteomics | Add an extra test for index access and ions |
377,522 | 14.10.2020 15:24:35 | -10,800 | 185c58d977c27b9a6eaf8b23a5271326bb22a1a7 | Add pyteomics/version, remove VERSION file | [
{
"change_type": "MODIFY",
"old_path": "MANIFEST.in",
"new_path": "MANIFEST.in",
"diff": "-include VERSION INSTALL README.rst\n+include INSTALL README.rst\n"
},
{
"change_type": "DELETE",
"old_path": "VERSION",
"new_path": null,
"diff": "-4.4.0dev1\n"
},
{
"change_type": ... | Python | Apache License 2.0 | levitsky/pyteomics | Add pyteomics/version, remove VERSION file |
377,522 | 14.10.2020 15:35:40 | -10,800 | bb4c6f9fa6d3e950026f271b720af248b66aa396 | Add tests for version parsing | [
{
"change_type": "MODIFY",
"old_path": "tests/test_auxiliary.py",
"new_path": "tests/test_auxiliary.py",
"diff": "@@ -11,6 +11,7 @@ import pyteomics\npyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]\nfrom pyteomics import auxiliary as aux\nfrom pyteomi... | Python | Apache License 2.0 | levitsky/pyteomics | Add tests for version parsing |
377,522 | 14.10.2020 22:17:45 | -10,800 | 4fb36028b7f559f2b11103b719b8fad452e9502d | Pre-compute version_info | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/version.py",
"new_path": "pyteomics/version.py",
"diff": "@@ -15,5 +15,5 @@ class _VersionInfo(namedtuple('_VersionInfo', ('major', 'minor', 'micro', 'relea\nreturn 'Pyteomics version {}'.format(self._version_str)\n-def version():\n- return _VersionI... | Python | Apache License 2.0 | levitsky/pyteomics | Pre-compute version_info |
377,522 | 15.10.2020 14:08:41 | -10,800 | 8354896f8836e1f71071367c117d83466b1cb24c | Update changelog, add minimal version doc | [
{
"change_type": "MODIFY",
"old_path": "doc/source/api.rst",
"new_path": "doc/source/api.rst",
"diff": "@@ -34,3 +34,4 @@ Contents:\napi/pylab_aux\napi/xml\napi/auxiliary\n+ api/version\n\\ No newline at end of file\n"
},
{
"change_type": "ADD",
"old_path": null,
"new_path": "doc/sou... | Python | Apache License 2.0 | levitsky/pyteomics | Update changelog, add minimal version doc |
377,522 | 22.10.2020 21:35:06 | -10,800 | 8e3a55877ea159fcb3299cab97e753ce12cf2d6d | Doc fix in pylab_aux.annotate_spectrum | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -387,9 +387,9 @@ def annotate_spectrum(spectrum, peptide, centroided=True, *args, **kwargs):\ntext_kw : dict, keyword only, optional\nKeyword arguments for :py:func:`pylab.text`.\nadjus... | Python | Apache License 2.0 | levitsky/pyteomics | Doc fix in pylab_aux.annotate_spectrum |
377,522 | 25.10.2020 01:10:03 | -10,800 | 2ed706293af3083f889827c339a7118461945f8d | Fix linter warnings in parser and test_parser | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/parser.py",
"new_path": "pyteomics/parser.py",
"diff": "@@ -119,6 +119,7 @@ std_labels = std_amino_acids + [std_nterm, std_cterm]\n_nterm_mod = r'[^-]+-$'\n_cterm_mod = r'-[^-]+$'\n+\ndef is_term_mod(label):\n\"\"\"Check if `label` corresponds to a t... | Python | Apache License 2.0 | levitsky/pyteomics | Fix linter warnings in parser and test_parser |
377,522 | 25.10.2020 03:17:30 | -10,800 | afd33e96705674389105be42e7c5ab6b2a223931 | Stabilize output ordering in parser.isoforms (issue | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/parser.py",
"new_path": "pyteomics/parser.py",
"diff": "@@ -789,11 +789,12 @@ def isoforms(sequence, **kwargs):\nreturn len(group) + i, group[i]\ndef apply_mod(label, mod):\n- # `label` is assumed to be a tuple (see split option of parse)\n+ # `label... | Python | Apache License 2.0 | levitsky/pyteomics | Stabilize output ordering in parser.isoforms (issue #15) |
377,522 | 25.10.2020 03:29:29 | -10,800 | 46305658a4a49c0c521af45cafc379d20c311bc5 | Use lists in tests to ensure order | [
{
"change_type": "MODIFY",
"old_path": "tests/test_parser.py",
"new_path": "tests/test_parser.py",
"diff": "@@ -89,17 +89,14 @@ class ParserTest(unittest.TestCase):\ndef test_isoforms_simple(self):\nself.assertEqual(\n- set(parser.isoforms('PEPTIDE', variable_mods={'xx': ['A', 'B', 'P', 'E']})),\n- ... | Python | Apache License 2.0 | levitsky/pyteomics | Use lists in tests to ensure order |
377,522 | 01.11.2020 23:21:56 | -10,800 | 0c40ead9615ca1404b7a2d52baf600638f3c7674 | Fix for fixed mods (no pun intended) | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/parser.py",
"new_path": "pyteomics/parser.py",
"diff": "@@ -832,10 +832,10 @@ def isoforms(sequence, **kwargs):\nformat_ = kwargs.get('format', 'str')\n# Apply fixed modifications\n- for cmod in fixed_mods:\n+ for cmod, res in fixed_mods.items():\nfo... | Python | Apache License 2.0 | levitsky/pyteomics | Fix for fixed mods (no pun intended) |
377,522 | 02.11.2020 19:48:06 | -10,800 | 6b32664b113b098766f401488d50e2bfec75eded | Use provided value of use_index with files passed by name. Fixes | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -49,6 +49,7 @@ except ImportError:\nfrom . import PyteomicsError\n+\ndef _keepstate(func):\n\"\"\"Decorator to help keep the position in open files passed as\n... | Python | Apache License 2.0 | levitsky/pyteomics | Use provided value of use_index with files passed by name. Fixes #16 |
377,522 | 07.11.2020 19:08:21 | -10,800 | 2e34d2cbc1fee3d9d8055026f88542ffbcfe1f8b | Rename types to ion_types in annotate_spectrum | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "- Make the order of isoforms reproducible in :py:func:`pyteomics.parser.isoforms`\n(`#15 <https://github.com/levitsky/pyteomics/issues/15>`_).\n+ - Rename `types` keyword argument to `ion_types` in :py:func:`pyteom... | Python | Apache License 2.0 | levitsky/pyteomics | Rename types to ion_types in annotate_spectrum |
377,522 | 08.12.2020 04:44:40 | -10,800 | aa0791e64038f650e554fde439e9035b02cf4279 | Add Python 3.9 to test runner | [
{
"change_type": "MODIFY",
"old_path": "tests/runtests.sh",
"new_path": "tests/runtests.sh",
"diff": "#!/bin/bash\nexport PYTHONPATH=\"..\"\nif [ $# -eq 0 ]; then\n- find . -name 'test_*.py' -exec bash -c 'declare -a versions=(2.7 3.3 3.4 3.5 3.6 3.7 3.8); for v in \"${versions[@]}\"; do command -v ... | Python | Apache License 2.0 | levitsky/pyteomics | Add Python 3.9 to test runner |
377,522 | 08.12.2020 05:54:42 | -10,800 | af098336f5489313d256121a0dd7410871ed1697 | Add Python 3.9 in Github Actions | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpackage.yml",
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "@@ -8,7 +8,7 @@ jobs:\nruns-on: ubuntu-latest\nstrategy:\nmatrix:\n- python-version: [2.7, 3.5, 3.6, 3.7, 3.8]\n+ python-version: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9]\n... | Python | Apache License 2.0 | levitsky/pyteomics | Add Python 3.9 in Github Actions |
377,522 | 08.12.2020 05:56:13 | -10,800 | e7724962febfbae60dc7e8049bb56a8339230cf4 | Rewrite _check_use_index and expand its tests | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "+dev\n+---\n+\n+Further tweaked behavior of :py:func:`pyteomics.auxiliary.file_helpers._check_use_index`, which is responsible for\n+handling of `use_index` in :py:func:`read` functions in parser modules.\n+\n4.4\n... | Python | Apache License 2.0 | levitsky/pyteomics | Rewrite _check_use_index and expand its tests |
377,522 | 11.12.2020 20:37:10 | -10,800 | 7fce8e55d6fab889498c435bfe07e040f3f82445 | Advertise Github Discussions | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "dev\n---\n-Further tweaked behavior of :py:func:`pyteomics.auxiliary.file_helpers._check_use_index`, which is responsible for\n+ - Further tweaked behavior of :py:func:`pyteomics.auxiliary.file_helpers._check_use_i... | Python | Apache License 2.0 | levitsky/pyteomics | Advertise Github Discussions |
377,522 | 14.12.2020 18:45:43 | -10,800 | 319cf52e7b1e967eac375d11d1ead2f17d12c2d0 | Use quotes in index keys in pepxml test data | [
{
"change_type": "MODIFY",
"old_path": "tests/data.py",
"new_path": "tests/data.py",
"diff": "@@ -214,7 +214,7 @@ pepxml_results = [\n{'protein': 'BL_ORD_ID:154629',\n'protein_descr': 'sp|Q99676|ZN184_HUMAN Zinc finger protein 184 OS=Homo sapiens GN=ZNF184 PE=1 SV=4:reversed'}],\n'tot_num_ions': 44}... | Python | Apache License 2.0 | levitsky/pyteomics | Use quotes in index keys in pepxml test data |
377,522 | 18.12.2020 04:50:40 | -10,800 | bff108cabd758a6a36511a2ba3e09bc127a2b19c | Refactor annotate_spectrum for possibility of external backends | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -40,7 +40,7 @@ See also\nDependencies\n------------\n-This module requires :py:mod:`matplotlib`.\n+This module requires :py:mod:`matplotlib`. Optional dependencies: :py:mod:`adjustText`... | Python | Apache License 2.0 | levitsky/pyteomics | Refactor annotate_spectrum for possibility of external backends |
377,522 | 18.12.2020 05:20:55 | -10,800 | e519afed0f9eacb44016db9b8bceee0df39146ad | Make _get_time a static method | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -377,7 +377,8 @@ class TimeOrderedIndexedReaderMixin(IndexedReaderMixin):\nsuper(TimeOrderedIndexedReaderMixin, self).__init__(*args, **kwargs)\nself._time = R... | Python | Apache License 2.0 | levitsky/pyteomics | Make _get_time a static method |
377,522 | 18.12.2020 05:31:18 | -10,800 | 63143c62bad21fe26c11f3139cc5a45fbc4db407 | Make auxiliary parsing methods on MGFBase static; move _get_time to MGFBase | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -145,13 +145,16 @@ class MGFBase(object):\nelse:\nself._header = None\n- def parse_precursor_charge(self, charge_text, list_only=False):\n+ @staticmethod\n+ def parse_precursor_charge(charge_text, ... | Python | Apache License 2.0 | levitsky/pyteomics | Make auxiliary parsing methods on MGFBase static; move _get_time to MGFBase |
377,526 | 11.01.2021 16:54:23 | -3,600 | ef75235bebf4a9ef533c84a239d284af57d4e661 | Parsing mztab 2.0 sections in `MzTab`. | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mztab.py",
"new_path": "pyteomics/mztab.py",
"diff": "@@ -276,6 +276,10 @@ class MzTab(_MzTabParserBase):\nreturn self.protein_table\nif key in ('sml', ):\nreturn self.small_molecule_table\n+ if key in ('smf', ):\n+ return self.small_molecule_feature... | Python | Apache License 2.0 | levitsky/pyteomics | Parsing mztab 2.0 sections in `MzTab`. |
377,526 | 11.01.2021 17:29:00 | -3,600 | 64e3470f6325f3dce63ca1a413e51189c4e8b153 | Fixed `test_iter`. | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mztab.py",
"new_path": "tests/test_mztab.py",
"diff": "@@ -18,7 +18,7 @@ class MzTabTest(unittest.TestCase):\ndef test_iter(self):\nreader = mztab.MzTab(self.path)\ntables = list(reader)\n- self.assertEqual(len(tables), 4)\n+ self.assertEqual(len(ta... | Python | Apache License 2.0 | levitsky/pyteomics | Fixed `test_iter`. |
377,526 | 11.01.2021 21:07:04 | -3,600 | 17f1dac4a0d314a0305dd85782cc48b1bb35fbdb | Version parser is implemented. | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mztab.py",
"new_path": "pyteomics/mztab.py",
"diff": "@@ -189,8 +189,10 @@ class MzTab(_MzTabParserBase):\nself._table_format = table_format\nself._init_tables()\nself._parse()\n+ self._determine_schema_version\nself._transform_tables()\n+\n@property... | Python | Apache License 2.0 | levitsky/pyteomics | Version parser is implemented. |
377,526 | 12.01.2021 22:17:08 | -3,600 | d699bca8b7e804330332a53413aebac28c801713 | Added test for mztab 2.0 | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mztab.py",
"new_path": "tests/test_mztab.py",
"diff": "@@ -7,23 +7,39 @@ from pyteomics import mztab\nclass MzTabTest(unittest.TestCase):\n- path = 'test.mztab'\n+ path_mztab1 = 'test.mztab'\n+ path_mztab2 = 'test_mztab2'\ndef test_metadata(self):\n... | Python | Apache License 2.0 | levitsky/pyteomics | Added test for mztab 2.0 |
377,526 | 12.01.2021 22:18:05 | -3,600 | ee9ec7ef9bfd19a79fc3d54118caccd1bd41e9d4 | Quick fix for mode and type properties | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mztab.py",
"new_path": "pyteomics/mztab.py",
"diff": "@@ -201,13 +201,14 @@ class MzTab(_MzTabParserBase):\ndef version(self):\nreturn self.metadata['mzTab-version']\n+\n@property\ndef mode(self):\n- return self.metadata['mzTab-mode']\n+ return self.... | Python | Apache License 2.0 | levitsky/pyteomics | Quick fix for mode and type properties |
377,526 | 12.01.2021 22:31:46 | -3,600 | e094cce9ab8869740978f0f54f09cf3c888aae75 | File name bug is fixed. | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mztab.py",
"new_path": "tests/test_mztab.py",
"diff": "@@ -8,7 +8,7 @@ from pyteomics import mztab\nclass MzTabTest(unittest.TestCase):\npath_mztab1 = 'test.mztab'\n- path_mztab2 = 'test_mztab2'\n+ path_mztab2 = 'test_mztab2.mztab'\ndef test_metadat... | Python | Apache License 2.0 | levitsky/pyteomics | File name bug is fixed. |
377,526 | 12.01.2021 22:43:31 | -3,600 | 14e1940696afdfa86e8abc3f7779dcab4a26c330 | Test is fixed. | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mztab.py",
"new_path": "tests/test_mztab.py",
"diff": "@@ -19,7 +19,7 @@ class MzTabTest(unittest.TestCase):\nreader_mztab2 = mztab.MzTab(self.path_mztab2)\nself.assertEqual(len(reader_mztab2.metadata), 61)\nvalue_from_mztab2 = reader_mztab2.metadat... | Python | Apache License 2.0 | levitsky/pyteomics | Test is fixed. |
377,522 | 13.01.2021 20:00:22 | -10,800 | 16d52df9b3a1607396432c0d2bbf766bc0b749d3 | Split test methods for different files | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mztab.py",
"new_path": "tests/test_mztab.py",
"diff": "@@ -10,37 +10,40 @@ class MzTabTest(unittest.TestCase):\npath_mztab1 = 'test.mztab'\npath_mztab2 = 'test_mztab2.mztab'\n- def test_metadata(self):\n+ def test_metadata_mztab1(self):\nreader_mzta... | Python | Apache License 2.0 | levitsky/pyteomics | Split test methods for different files |
377,522 | 13.01.2021 20:05:18 | -10,800 | 607581e4fc2698df12409d6a96f4a044a89f9b73 | Return None for missing metadata, add more properties | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mztab.py",
"new_path": "pyteomics/mztab.py",
"diff": "@@ -192,7 +192,6 @@ class MzTab(_MzTabParserBase):\nself._determine_schema_version()\nself._transform_tables()\n-\n@property\ndef table_format(self):\nreturn self._table_format\n@@ -201,14 +200,25... | Python | Apache License 2.0 | levitsky/pyteomics | Return None for missing metadata, add more properties |
377,522 | 14.01.2021 19:51:53 | -10,800 | a866f042a2bbc7d9f961e4cb52c39a2dc9547c27 | Add test for mztab variant property | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mztab.py",
"new_path": "tests/test_mztab.py",
"diff": "@@ -22,6 +22,14 @@ class MzTabTest(unittest.TestCase):\nvalue_from_mztab2 = reader_mztab2.metadata['sample_processing[1]']\nself.assertEqual(value_from_mztab2, 'high performance liquid chromatog... | Python | Apache License 2.0 | levitsky/pyteomics | Add test for mztab variant property |
377,522 | 14.01.2021 19:56:19 | -10,800 | f79b28acd93d7c8b92e46d05856a80f3b0aedfff | Accept partial names in test runner script | [
{
"change_type": "MODIFY",
"old_path": "tests/runtests.sh",
"new_path": "tests/runtests.sh",
"diff": "@@ -5,7 +5,14 @@ if [ $# -eq 0 ]; then\nelse\nfor f; do\nfor v in 2.7 3.3 3.4 3.5 3.6 3.7 3.8 3.9; do\n- command -v \"python${v}\" >/dev/null 2>&1 && { echo \"Executing python${v}\" \"$f\"; eval \"p... | Python | Apache License 2.0 | levitsky/pyteomics | Accept partial names in test runner script |
377,522 | 14.01.2021 20:30:05 | -10,800 | 8214b553490f3f67b452d7c9b36540c4f5503e23 | Bump version to 4.4.1 (release) | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.4.1 beta 3\n-------------\n+4.4.1\n+-----\n- Further tweaked behavior of :py:func:`pyteomics.auxiliary.file_helpers._check_use_index`, which is responsible for\nhandling of `use_index` in :py:func:`read` functio... | Python | Apache License 2.0 | levitsky/pyteomics | Bump version to 4.4.1 (release) |
377,522 | 18.01.2021 14:24:09 | -10,800 | 18be55aa7155b471c1da267486cdb3f76d58b2ce | Update Sphinx documentation, changelog and version | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "+4.4.2 beta 1\n+------------\n+\n+ - Extend the :py:mod:`pyteomics.mztab.MzTab` parser with auto-generated properties. Almost all metadata entities are\n+ now exposed as properties on the parser object (`#23 <https... | Python | Apache License 2.0 | levitsky/pyteomics | Update Sphinx documentation, changelog and version |
377,528 | 21.01.2021 21:33:28 | 25,200 | 8d3ac6c67ee0ff5c9caa71b61f2f06bf0cf63d0a | Fixed version parsing
Accepts version numbers that do not necessarily contain 3 numbers (x.x.x) - can read versions that contain 1 or 2 numbers (x) or (x.x) | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mztab.py",
"new_path": "pyteomics/mztab.py",
"diff": "@@ -744,8 +744,8 @@ class MzTab(_MzTabParserBase):\nself.small_molecule_evidence_table.add(tokens[1:])\ndef _determine_schema_version(self):\n- version_parsed, variant = re.search(r\"(?P<schema_ve... | Python | Apache License 2.0 | levitsky/pyteomics | Fixed version parsing
Accepts version numbers that do not necessarily contain 3 numbers (x.x.x) - can read versions that contain 1 or 2 numbers (x) or (x.x) |
377,528 | 22.01.2021 12:22:12 | 25,200 | 695e0e3fc7b233f318958c9d1df496bed529298c | Updated version parsing
Reverted back to a tweaked regex search for stricter parsing and added a check to ensure self.num_version is always a 3 tuple regardless of original version number. | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mztab.py",
"new_path": "pyteomics/mztab.py",
"diff": "@@ -744,10 +744,13 @@ class MzTab(_MzTabParserBase):\nself.small_molecule_evidence_table.add(tokens[1:])\ndef _determine_schema_version(self):\n- version_parsed, _, variant = str(self.version).par... | Python | Apache License 2.0 | levitsky/pyteomics | Updated version parsing
Reverted back to a tweaked regex search for stricter parsing and added a check to ensure self.num_version is always a 3 tuple regardless of original version number. |
377,522 | 24.01.2021 00:02:38 | -10,800 | 977b253efa556cedd85a6161e4190bbcd28e4eaf | Fix mztab version string pattern | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mztab.py",
"new_path": "pyteomics/mztab.py",
"diff": "@@ -744,7 +744,7 @@ class MzTab(_MzTabParserBase):\nself.small_molecule_evidence_table.add(tokens[1:])\ndef _determine_schema_version(self):\n- version_parsed, variant = re.search(r\"(?P<schema_ve... | Python | Apache License 2.0 | levitsky/pyteomics | Fix mztab version string pattern |
377,522 | 27.01.2021 17:30:17 | -10,800 | f2ab4e58c14895b2384e9740822a5ffd96f122f1 | Return unchanged value in pepxml safe_float if conversion fails | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -97,6 +97,7 @@ This module requires :py:mod:`lxml`.\nfrom lxml import etree\nfrom . import xml, auxiliary as aux, _schema_defaults\n+\nclass PepXML(xml.MultiProcessingXML, xml.IndexSavingXML)... | Python | Apache License 2.0 | levitsky/pyteomics | Return unchanged value in pepxml safe_float if conversion fails |
377,522 | 19.03.2021 23:02:01 | -10,800 | f3c813e12bd2e55cd4401c10754a3b7a151f5d75 | Add parser.psims_rules | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.4.2 beta 3\n+4.4.2 beta 4\n------------\n+ - Add cleavage rules from `MS ontology <http://purl.obolibrary.org/obo/MS_1001045>`_ as\n+ :py:data:`pyteomics.parser.psims_rules`. :py:func:`pyteomics.parser.cleave` n... | Python | Apache License 2.0 | levitsky/pyteomics | Add parser.psims_rules |
377,522 | 26.03.2021 15:44:23 | -10,800 | cbdd1c26e836b0323369778be2493110aaca26e3 | Update changelog and version - to 4.4.2 | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.4.2 beta 5\n-------------\n+4.4.2\n+-----\n- Add cleavage rules from `MS ontology <http://purl.obolibrary.org/obo/MS_1001045>`_ as\n:py:data:`pyteomics.parser.psims_rules`. :py:func:`pyteomics.parser.cleave` now... | Python | Apache License 2.0 | levitsky/pyteomics | Update changelog and version - to 4.4.2 |
377,522 | 02.04.2021 21:42:25 | -10,800 | 1a98f3d7512a73630c4bd76432c10d6a5218624f | Remove unused imports in USI test | [
{
"change_type": "MODIFY",
"old_path": "tests/test_usi.py",
"new_path": "tests/test_usi.py",
"diff": "@@ -4,8 +4,6 @@ import pyteomics\npyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]\nimport unittest\n-from itertools import product\n-import operator ... | Python | Apache License 2.0 | levitsky/pyteomics | Remove unused imports in USI test |
377,522 | 05.04.2021 16:23:38 | -10,800 | d2f9881a7ba340845defb2fc5149961831e8e168 | Raise PyteomicsError for unknown backend names | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/usi.py",
"new_path": "pyteomics/usi.py",
"diff": "@@ -52,6 +52,8 @@ except ImportError:\ndef coerce_array(array_data):\nreturn [float(v) for v in array_data]\n+from .auxiliary import PyteomicsError\n+\nclass USI(namedtuple(\"USI\", ['protocol', 'data... | Python | Apache License 2.0 | levitsky/pyteomics | Raise PyteomicsError for unknown backend names |
377,522 | 05.04.2021 16:24:11 | -10,800 | 7b8b6612cd7023ea59f7003e4a37f563c9ebed83 | Add test for proxi aggregator | [
{
"change_type": "MODIFY",
"old_path": "tests/test_usi.py",
"new_path": "tests/test_usi.py",
"diff": "@@ -5,7 +5,8 @@ pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir\nimport unittest\n-from pyteomics.usi import USI, proxi\n+from pyteomics.usi import USI, proxi, AGGRE... | Python | Apache License 2.0 | levitsky/pyteomics | Add test for proxi aggregator |
377,522 | 08.04.2021 16:40:55 | -10,800 | 295e30e15d0cf86cb0926ff824397a2a6acc8e77 | Limit paths in unit-testing Github Action | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpackage.yml",
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "name: tests\n-on: [push, pull_request]\n+on:\n+ push:\n+ paths:\n+ - '**.py'\n+ pull_request:\n+ paths:\n+ - '**.py'\njobs:\nbuild:\n@@ -13,7 +19,7 @@ jobs:\nstep... | Python | Apache License 2.0 | levitsky/pyteomics | Limit paths in unit-testing Github Action |
377,522 | 08.04.2021 17:14:28 | -10,800 | 34c87ac7198b7cff45cb46a4001345e87c6bb5a4 | Drop Python 3.5 from Github tests | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpackage.yml",
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "@@ -14,7 +14,7 @@ jobs:\nruns-on: ubuntu-latest\nstrategy:\nmatrix:\n- python-version: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9]\n+ python-version: [2.7, 3.6, 3.7, 3.8, 3.9]... | Python | Apache License 2.0 | levitsky/pyteomics | Drop Python 3.5 from Github tests |
377,522 | 18.05.2021 17:57:13 | -10,800 | d9986a677bac0354797666e5e05d31bcbf96b2a6 | Draft addition of spectrum_utils backend | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/utils.py",
"new_path": "pyteomics/auxiliary/utils.py",
"diff": "@@ -21,6 +21,7 @@ try:\nexcept ImportError:\npynumpress = None\n+\ndef print_tree(d, indent_str=' -> ', indent_count=1):\n\"\"\"Read a nested dict (with strings as keys) and pr... | Python | Apache License 2.0 | levitsky/pyteomics | Draft addition of spectrum_utils backend |
377,522 | 20.05.2021 18:13:47 | -10,800 | af182eeb4ce65c1850096b72d2f5ad4ad6bf253f | Fix numpy deprecation warnings, update changelog | [
{
"change_type": "MODIFY",
"old_path": ".gitignore",
"new_path": ".gitignore",
"diff": "@@ -4,3 +4,4 @@ __pycache__\n*.egg-info\n*.pyc\n.ipynb_checkpoints\n+*.diff\n"
},
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5dev2\n+4.5dev3\n----... | Python | Apache License 2.0 | levitsky/pyteomics | Fix numpy deprecation warnings, update changelog |
377,522 | 30.06.2021 00:32:00 | -10,800 | 0de60bc63807905584ff1bc6dd45e660e82cb5f6 | Split the spectrum_utils annotation code | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -63,7 +63,7 @@ This module requires :py:mod:`matplotlib`. Optional dependencies: :py:mod:`adjus\nimport pylab\nimport numpy as np\nfrom .auxiliary import linear_regression, PyteomicsErr... | Python | Apache License 2.0 | levitsky/pyteomics | Split the spectrum_utils annotation code |
377,522 | 11.08.2021 12:35:07 | -10,800 | 5408a430c07a34ed06da093873bdd190359c1f2a | Start work on modifications | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -504,6 +504,7 @@ def _spectrum_utils_annotate_spectrum(spectrum, peptide, *args, **kwargs):\nraise PyteomicsError('Could not extract precursor charge from spectrum. '\n'Please specify `... | Python | Apache License 2.0 | levitsky/pyteomics | Start work on modifications |
377,522 | 11.08.2021 19:44:00 | -10,800 | d47096235d15cd2a20ae44f9337f8c17a22cc6e7 | Update default featureXML schema_info and version, add overrides | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/_schema_defaults.py",
"new_path": "pyteomics/_schema_defaults.py",
"diff": "@@ -247,16 +247,22 @@ _trafoxml_schema_defaults = {'bools': set(),\n'ints': {('Pairs', 'count')},\n'lists': {'Pair', 'Param'}}\n-_featurexml_schema_defaults = {'bools': {\n- ... | Python | Apache License 2.0 | levitsky/pyteomics | Update default featureXML schema_info and version, add overrides |
377,522 | 11.08.2021 22:17:47 | -10,800 | 20e4a5bb4e5ffe0d41c8985893cffc678b17c95c | Fix superfluous use_index warning | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -914,7 +914,7 @@ def _check_use_index(source, use_index, default):\nwarnings.warn('use_index is {}, but the file mode is {}. '\n'Setting `use_index` to {}'.for... | Python | Apache License 2.0 | levitsky/pyteomics | Fix superfluous use_index warning |
377,522 | 11.08.2021 22:38:16 | -10,800 | f54469674b26d6cf7dc7ab32e4b1224584029d62 | Fix test for use_index warning | [
{
"change_type": "MODIFY",
"old_path": "tests/test_auxiliary.py",
"new_path": "tests/test_auxiliary.py",
"diff": "@@ -966,7 +966,7 @@ class UseIndexTest(unittest.TestCase):\nsource = UseIndexTest.MockFile(None, None)\nwith warnings.catch_warnings(record=True) as w:\nwarnings.simplefilter('always')\n... | Python | Apache License 2.0 | levitsky/pyteomics | Fix test for use_index warning |
377,527 | 17.08.2021 18:35:12 | -7,200 | be45ca426b5decfe87f4be6ced23af23c7546bbc | Shuffling that preserve some amino acids
incl. test | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -664,7 +664,7 @@ def reverse(sequence, keep_nterm=False, keep_cterm=False):\nreturn sequence[:start] + sequence[start:end][::-1] + sequence[end:]\n-def shuffle(sequence, keep_nterm=False, keep_... | Python | Apache License 2.0 | levitsky/pyteomics | Shuffling that preserve some amino acids
incl. test |
377,522 | 24.08.2021 00:10:34 | -10,800 | b30b03de2354c4dd6876de600c7be347c092232b | Minor fixes, rename keep_M to keep_nterm_M, extend test | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -664,7 +664,7 @@ def reverse(sequence, keep_nterm=False, keep_cterm=False):\nreturn sequence[:start] + sequence[start:end][::-1] + sequence[end:]\n-def shuffle(sequence, keep_nterm=False, keep_... | Python | Apache License 2.0 | levitsky/pyteomics | Minor fixes, rename keep_M to keep_nterm_M, extend test |
377,522 | 27.08.2021 15:39:35 | -10,800 | b179189f2fc790866024404fcf965c02b72412d8 | Increment dev version, update changelog, fix title level in doc | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5dev4\n+4.5dev5\n-------\n- Add support for `mzMLb <https://www.biorxiv.org/content/10.1101/2020.02.13.947218v3>`_\nand `#38 <https://github.com/levitsky/pyteomics/pull/38>`_ by Joshua Klein)\nwith new module :p... | Python | Apache License 2.0 | levitsky/pyteomics | Increment dev version, update changelog, fix title level in doc |
377,522 | 08.09.2021 01:58:50 | -10,800 | 4a45d4c1ac068a17f0e066bc2aa37db95ddc706b | Fixes for modifications | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -474,7 +474,7 @@ def _spectrum_utils_create_spectrum(spectrum, peptide, *args, **kwargs):\nspectrum = sus.MsmsSpectrum(\nNone, kwargs.pop('precursor_mz', None), kwargs.pop('precursor_ch... | Python | Apache License 2.0 | levitsky/pyteomics | Fixes for modifications |
377,522 | 08.09.2021 14:31:40 | -10,800 | 042e2cd8fbd4b3ac582f1a28c0f8075807e1962b | Doc fixes and cleanup | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -545,22 +545,6 @@ class SpectrumUtilsColorScheme:\nsup.colors = self.previous_colors\n-class SpectrumUtilsStaticModifications:\n- \"\"\"Context manager that temporarily changes `spectru... | Python | Apache License 2.0 | levitsky/pyteomics | Doc fixes and cleanup |
377,522 | 08.09.2021 15:22:18 | -10,800 | bcf8f9adc1c28bb94d075251de084103809f069d | Add annot_kws, start laying out plot backend structure | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -330,6 +330,34 @@ def plot_qvalue_curve(qvalues, *args, **kwargs):\nreturn pylab.plot(qvalues, 1 + np.arange(qvalues.size), *args, **kwargs)\n+def _default_plot_spectrum(spectrum, centr... | Python | Apache License 2.0 | levitsky/pyteomics | Add annot_kws, start laying out plot backend structure |
377,522 | 09.09.2021 16:42:39 | -10,800 | 08ddb4921e247438281e6c273aae74738e35a427 | Add plot_spectrum() with spectrum_utils backends | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -330,11 +330,8 @@ def plot_qvalue_curve(qvalues, *args, **kwargs):\nreturn pylab.plot(qvalues, 1 + np.arange(qvalues.size), *args, **kwargs)\n-def _default_plot_spectrum(spectrum, centr... | Python | Apache License 2.0 | levitsky/pyteomics | Add plot_spectrum() with spectrum_utils backends |
377,522 | 09.09.2021 17:46:42 | -10,800 | 8f3b1771ae44597840015c5f722a1930427a7f2e | Add a simple mirror plot function | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -24,6 +24,8 @@ Spectrum visualization\n:py:func:`annotate_spectrum` - plot and annotate peaks in MS/MS spectrum.\n+ :py:func:`mirror` - create a mirror plot of two spectra (using :py:mo... | Python | Apache License 2.0 | levitsky/pyteomics | Add a simple mirror plot function |
377,522 | 09.09.2021 17:58:36 | -10,800 | 7def94a516496d2fc9e3dd28a2f1da64c6cda322 | Add axis labels and title to mirror | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -674,6 +674,13 @@ def annotate_spectrum(spectrum, peptide, *args, **kwargs):\nA dictionary of amino acid residue masses.\ntext_kw : dict, keyword only, optional\nKeyword arguments for :... | Python | Apache License 2.0 | levitsky/pyteomics | Add axis labels and title to mirror |
377,522 | 14.09.2021 15:30:38 | -10,800 | 0a20d655d7377b37d4f4ec2ceae0d095b68abeef | Add axes arg for other functions | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -333,13 +333,14 @@ def plot_qvalue_curve(qvalues, *args, **kwargs):\ndef _default_plot_spectrum(spectrum, *args, **kwargs):\n+ ax = kwargs.pop('ax', None) or pylab.gca()\nif kwargs.pop(... | Python | Apache License 2.0 | levitsky/pyteomics | Add axes arg for other functions |
377,522 | 14.09.2021 15:47:58 | -10,800 | 6e4c8f59803a2acfe98fac71eb1a6ed770f4bb09 | Changelog update, version bump | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5dev6\n--------\n+4.5b1\n+-----\n- Add support for `mzMLb <https://www.biorxiv.org/content/10.1101/2020.02.13.947218v3>`_\n(`#35 <https://github.com/levitsky/pyteomics/pull/35>`_\n`use_index` is explicitly passe... | Python | Apache License 2.0 | levitsky/pyteomics | Changelog update, version bump |
377,522 | 14.09.2021 16:27:03 | -10,800 | 48ae335ace83d233c0b57eb73c5f7555dc245657 | Add mzmlb.chain, fix copy errors in doc | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzmlb.py",
"new_path": "pyteomics/mzmlb.py",
"diff": "@@ -15,7 +15,7 @@ about mzMLb and its features. Please refer to\n`psidev.info <https://www.psidev.info/mzML>`_ for the detailed\nspecification of the format and structure of mzML files.\n-This mod... | Python | Apache License 2.0 | levitsky/pyteomics | Add mzmlb.chain, fix copy errors in doc |
377,522 | 14.09.2021 19:28:39 | -10,800 | 11cda6e6d16866107c4abb2ebeee9c9a0df9de74 | Fix default plotting | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5b1\n+4.5b2\n-----\n- Add support for `mzMLb <https://www.biorxiv.org/content/10.1101/2020.02.13.947218v3>`_\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "py... | Python | Apache License 2.0 | levitsky/pyteomics | Fix default plotting |
377,522 | 15.09.2021 18:16:35 | -10,800 | 7ebe003e7f4373a3bc7221a5bd2650c3720be0b8 | Return Axes from plot_spectrum and annotate_spectrum | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5b2\n+4.5b3\n-----\n- Add support for `mzMLb <https://www.biorxiv.org/content/10.1101/2020.02.13.947218v3>`_\n(`#43 <https://github.com/levitsky/pyteomics/pull/43>`_).\n- New function :py:func:`pyteomics.pylab_a... | Python | Apache License 2.0 | levitsky/pyteomics | Return Axes from plot_spectrum and annotate_spectrum |
377,522 | 15.09.2021 23:33:54 | -10,800 | 170ffaf4d37766606df589e13bd203c1ca8500f6 | Update pyteomics URL in warning | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/xml.py",
"new_path": "pyteomics/xml.py",
"diff": "@@ -344,7 +344,7 @@ class XML(FileReader):\n\"`read_schema=False`.\\n\"\n\"If you think this shouldn't have happened, please \"\n\"report this to\\n\"\n- \"http://hg.theorchromo.ru/pyteomics/issues\\n... | Python | Apache License 2.0 | levitsky/pyteomics | Update pyteomics URL in warning |
377,522 | 15.09.2021 23:42:17 | -10,800 | 4f2ef41ba9e1d5282c5c696b96d81ff1bdd888b5 | Add a warning when writing to existing file in default mode | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5b2\n+4.5b3\n-----\n- Add support for `mzMLb <https://www.biorxiv.org/content/10.1101/2020.02.13.947218v3>`_\n(`#43 <https://github.com/levitsky/pyteomics/pull/43>`_).\n- New function :py:func:`pyteomics.pylab_a... | Python | Apache License 2.0 | levitsky/pyteomics | Add a warning when writing to existing file in default mode |
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