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 | 16.09.2021 19:36:44 | -10,800 | 47a72b4c450b22ac3b4c5478cf9c0acc66b92285 | Add draft of new example | [
{
"change_type": "ADD",
"old_path": null,
"new_path": "doc/source/_static/example_annotation.py",
"diff": "+from pyteomics import pylab_aux as pa, usi\n+spectrum = usi.proxi('mzspec:PXD004732:01650b_BC2-TUM_first_pool_53_01_01-3xHCD-1h-R2:scan:41840', 'massive')\n+peptide = 'WNQLQAFWGTGK'\n+\n+pa.an... | Python | Apache License 2.0 | levitsky/pyteomics | Add draft of new example |
377,522 | 20.09.2021 16:43:45 | -10,800 | 448af682dac7a3fcc75c421c4dce3ceed710dbd0 | Finish draft of Example 4 | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "(`#35 <https://github.com/levitsky/pyteomics/pull/35>`_\nand `#38 <https://github.com/levitsky/pyteomics/pull/38>`_ by Joshua Klein)\nwith new module :py:mod:`pyteomics.mzmlb`.\n+\n- Add ProteomeExchange backend fo... | Python | Apache License 2.0 | levitsky/pyteomics | Finish draft of Example 4 |
377,522 | 20.09.2021 17:37:19 | -10,800 | 243830b024f50f4d682267de0dae1941a2167558 | Fix for interactive annotation plots | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -644,7 +644,7 @@ def _spectrum_utils_annotate_iplot(spectrum, peptide, *args, **kwargs):\nimport spectrum_utils.iplot as supi\nwith SpectrumUtilsColorScheme(kwargs.pop('colors', None)):... | Python | Apache License 2.0 | levitsky/pyteomics | Fix for interactive annotation plots |
377,522 | 15.10.2021 17:10:09 | -10,800 | c4fd36615ebedce5ff5ced0ee7072e3e8c1ec54a | Implement `charge_carrier` and `absolute` arguments for m/z calculation | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/structures.py",
"new_path": "pyteomics/auxiliary/structures.py",
"diff": "@@ -192,14 +192,15 @@ class BasicComposition(defaultdict, Counter):\ndef __mul__(self, other):\nif not isinstance(other, int):\n- raise PyteomicsError('Cannot multipl... | Python | Apache License 2.0 | levitsky/pyteomics | Implement `charge_carrier` and `absolute` arguments for m/z calculation |
377,522 | 15.10.2021 17:16:29 | -10,800 | ca3e1d8b8d37f6f1e3d9e6c42b152541d68d684d | Fix syntax error on Python 2.7 | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -569,7 +569,7 @@ def calculate_mass(*args, **kwargs):\ncharge = kwargs.pop('charge', 0)\ncharge_carrier = kwargs.pop('charge_carrier', None)\ncomposition = Composition(*args, **kwargs)\... | Python | Apache License 2.0 | levitsky/pyteomics | Fix syntax error on Python 2.7 |
377,522 | 27.10.2021 18:46:36 | -10,800 | d585e930e107da00baf0c60004bfcc911f98f4e6 | Fix charge state extraction from mzML | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/_schema_defaults.py",
"new_path": "pyteomics/_schema_defaults.py",
"diff": "@@ -397,7 +397,8 @@ _mzml_schema_defaults = {'ints': {\n('softwareList', 'count'),\n('binaryDataArrayList', 'count'),\n('spectrumList', 'count'),\n- ('chromatogramList', 'cou... | Python | Apache License 2.0 | levitsky/pyteomics | Fix charge state extraction from mzML |
377,522 | 18.11.2021 17:58:20 | -10,800 | 165ed6217423e75b36f0d651767562a66c5eecdc | Add max_length | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "+4.5.1dev1\n+---------\n+\n+ - Add `max_length` parameter in :py:func:`pyteomics.parser.cleave`.\n+ - Bugfix in :py:func:`pyteomics.parser.cleave` for `semi=True`.\n+\n+\n4.5\n---\n"
},
{
"change_type": "MO... | Python | Apache License 2.0 | levitsky/pyteomics | Add max_length |
377,522 | 18.11.2021 18:11:28 | -10,800 | 49d3ac80041ae09c1f701946c55e8516bc45a6d8 | Add regex parameter in cleave and raise a warning on lowercase characters in cleavage rule | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5.1dev1\n+4.5.1dev2\n---------\n- Add `max_length` parameter in :py:func:`pyteomics.parser.cleave`.\n- Bugfix in :py:func:`pyteomics.parser.cleave` for `semi=True`.\n-\n+ - Add `regex` parameter in :py:func:`pyt... | Python | Apache License 2.0 | levitsky/pyteomics | Add regex parameter in cleave and raise a warning on lowercase characters in cleavage rule |
377,522 | 18.11.2021 19:00:23 | -10,800 | fb1fb6d86152ba83fe087262199bfa86b76538ec | Return peptide indices in _cleave | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5.1dev2\n+4.5.1dev3\n---------\n- Add `max_length` parameter in :py:func:`pyteomics.parser.cleave`.\n- Bugfix in :py:func:`pyteomics.parser.cleave` for `semi=True`.\n- Add `regex` parameter in :py:func:`pyteomic... | Python | Apache License 2.0 | levitsky/pyteomics | Return peptide indices in _cleave |
377,522 | 25.11.2021 15:26:21 | -10,800 | fbc09df4f7f7ee1ef66bc6e07d2538794c6e4142 | Specify rcond to silence warning in achrom.get_RCs | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/achrom.py",
"new_path": "pyteomics/achrom.py",
"diff": "@@ -436,8 +436,7 @@ def get_RCs(sequences, RTs, lcp = -0.21,\nRTs.append(0.0)\n# Use least square linear regression.\n- RCs, res, rank, s = np.linalg.lstsq(np.array(composition_array),\n- np.arr... | Python | Apache License 2.0 | levitsky/pyteomics | Specify rcond to silence warning in achrom.get_RCs |
377,522 | 26.11.2021 17:41:57 | -10,800 | 23edf600e6ead8f6ccc00f39a1e4e21202bb5c9c | Expose parser.xcleave and icleave as part of API | [
{
"change_type": "MODIFY",
"old_path": "doc/source/parser.rst",
"new_path": "doc/source/parser.rst",
"diff": "@@ -18,6 +18,9 @@ either 0 or 2 terminal groups in a *modX* sequence.\nSequence operations\n-------------------\n+Parsing\n+.......\n+\nThere are two helper functions to check if a label is ... | Python | Apache License 2.0 | levitsky/pyteomics | Expose parser.xcleave and icleave as part of API |
377,522 | 26.11.2021 17:47:10 | -10,800 | c758a7a563a394ece858c4a845cb44f52c92f9ab | Changelog and dev version bump | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5.1dev3\n+4.5.1dev4\n---------\n- Add `max_length` parameter in :py:func:`pyteomics.parser.cleave`.\n- Bugfix in :py:func:`pyteomics.parser.cleave` for `semi=True`.\n- Add `regex` parameter in :py:func:`pyteomic... | Python | Apache License 2.0 | levitsky/pyteomics | Changelog and dev version bump |
377,522 | 13.12.2021 19:05:28 | -10,800 | 59d030f6dc16a2d1d212a1a347d6a9eecead3a23 | Fix collections.abc ImportError on Python 3.10 | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/electrochem.py",
"new_path": "pyteomics/electrochem.py",
"diff": "@@ -114,7 +114,11 @@ References\nfrom __future__ import division\nfrom . import parser\nfrom .auxiliary import PyteomicsError\n-from collections import Iterable, Counter\n+from collect... | Python | Apache License 2.0 | levitsky/pyteomics | Fix collections.abc ImportError on Python 3.10 |
377,522 | 13.12.2021 19:08:32 | -10,800 | 596bb3a661352874ab7e4f6524b0d25d862769de | Run GA on Python 3.10 | [
{
"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, 3.6, 3.7, 3.8, 3.9]\n+ python-version: [2.7, 3.6, 3.7, 3.8, 3.9, 3.10... | Python | Apache License 2.0 | levitsky/pyteomics | Run GA on Python 3.10 |
377,522 | 13.12.2021 19:10:47 | -10,800 | 54e7d4ea605122d236065493105305218b39bbd8 | Add 3.10 to helper test script | [
{
"change_type": "MODIFY",
"old_path": "tests/runtests.sh",
"new_path": "tests/runtests.sh",
"diff": "#!/bin/bash\nexport PYTHONPATH=\"..\"\nif [ $# -eq 0 ]; then\n- find . -name 'test_*.py' -exec bash -c 'declare -a versions=(2.7 3.3 3.4 3.5 3.6 3.7 3.8 3.9); for v in \"${versions[@]}\"; do command... | Python | Apache License 2.0 | levitsky/pyteomics | Add 3.10 to helper test script |
377,522 | 13.12.2021 19:19:16 | -10,800 | 2ac92cb30c51ee6d87da348fa3b867bede771212 | Fix 3.10 -> 3.1 error in GA | [
{
"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, 3.6, 3.7, 3.8, 3.9, 3.10]\n+ python-version: ['2.7', '3.6', '3.7', '3... | Python | Apache License 2.0 | levitsky/pyteomics | Fix 3.10 -> 3.1 error in GA |
377,522 | 16.12.2021 18:57:44 | -10,800 | fb4991b12675d58417bdc1bd73aace493e283ff2 | Bump version (Python 3.10 support) | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5.2.dev1\n-----------\n+4.5.2\n+-----\n- - Fix ImportError on Python 3.10 in :py:mod:`pyteomics.electrochem`.\n+ - Support Python 3.10.\n4.5.1\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/... | Python | Apache License 2.0 | levitsky/pyteomics | Bump version (Python 3.10 support) |
377,522 | 17.12.2021 19:33:55 | -10,800 | bf4feb193b79980b00814556d0a914f1374ecdfb | Update changelog, increment dev version | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "+4.5.3dev1\n+---------\n+\n+ - Fix ThreadPool shutdown and add new parameter `ephemeral_pool` in :py:class:`pyteomics.usi.PROXIAggregator`\n+ (`#67 <https://github.com/levitsky/pyteomics/pull/67>`_ by Joshua Klein)... | Python | Apache License 2.0 | levitsky/pyteomics | Update changelog, increment dev version |
377,522 | 27.01.2022 20:58:53 | -10,800 | 28405940d088087862d9e6f22cd380a005d0b6e1 | Add fasta.decoy_entries | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5.3dev2\n+4.5.3dev3\n---------\n- Fix ThreadPool shutdown and add new parameter `ephemeral_pool` in :py:class:`pyteomics.usi.PROXIAggregator`\n(`#67 <https://github.com/levitsky/pyteomics/pull/67>`_ by Joshua Kl... | Python | Apache License 2.0 | levitsky/pyteomics | Add fasta.decoy_entries |
377,522 | 29.01.2022 23:32:04 | -10,800 | 4b05f53fb08f883b20b3aa6daf5c6fac21adf969 | Do not take mass_data in Composition.__init__ | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -203,12 +203,10 @@ class Composition(BasicComposition):\nshow_unmodified_termini=True)\nself._from_parsed_sequence(parsed_sequence, aa_comp)\n- def _from_formula(self, formula, mass_dat... | Python | Apache License 2.0 | levitsky/pyteomics | Do not take mass_data in Composition.__init__ |
377,522 | 01.02.2022 01:27:25 | -10,800 | b72e87c08f716492453fe57fc508b1fd2b9cbd46 | Be more strict about charge | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -93,6 +93,7 @@ except ImportError:\nfrom datetime import datetime\nimport re\nimport operator\n+import warnings\nnist_mass = _nist_mass\n\"\"\"\n@@ -265,14 +266,12 @@ class Composition(... | Python | Apache License 2.0 | levitsky/pyteomics | Be more strict about charge |
377,522 | 11.02.2022 17:24:12 | -10,800 | 5644b56e120f1468ffbf4c8b45ccc76b9ce06a65 | Add charge_carrier string spec | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -104,6 +104,7 @@ abundant isotopes and a separate entry for undefined isotope with zero\nkey, mass of the most abundant isotope and 1.0 abundance.\n\"\"\"\n+PROTON = 'H+'\ndef _make_iso... | Python | Apache License 2.0 | levitsky/pyteomics | Add charge_carrier string spec |
377,522 | 11.02.2022 18:15:58 | -10,800 | 1d17f378d095890fe4cd731ca749e7b2c2c9cf3b | Support charge_carrier as composition, add carrier_charge, fix function-style calls | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -359,7 +359,7 @@ class Composition(BasicComposition):\nif sign is None:\n# only formula is given\nif PROTON not in comp:\n- raise PyteomicsError('Charge of the charge carrier group not ... | Python | Apache License 2.0 | levitsky/pyteomics | Support charge_carrier as composition, add carrier_charge, fix function-style calls |
377,522 | 11.02.2022 18:29:22 | -10,800 | c7fcb0000f7745ba90bcc9ba71610a257c0ad794 | Add absolute kwarg | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -406,6 +406,12 @@ class Composition(BasicComposition):\nion_type : str, optional\nIf specified, then the polypeptide is considered to be in the form\nof the corresponding ion. Do not fo... | Python | Apache License 2.0 | levitsky/pyteomics | Add absolute kwarg |
377,522 | 11.02.2022 18:30:40 | -10,800 | b8efe10c3aea997f0cad08b6b38ef2c476480be8 | Copy the new doc to calculate_mass() | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -581,6 +581,25 @@ def calculate_mass(*args, **kwargs):\nIf not 0 then m/z is calculated: the mass is increased\nby the corresponding number of proton masses and divided\nby `charge`.\n+... | Python | Apache License 2.0 | levitsky/pyteomics | Copy the new doc to calculate_mass() |
377,522 | 14.02.2022 13:31:11 | -10,800 | 2ac9e6d501e4f165e72dcb0e9b1e5b24e6092cdf | Future-proof protxml test | [
{
"change_type": "MODIFY",
"old_path": "tests/test_protxml.py",
"new_path": "tests/test_protxml.py",
"diff": "@@ -62,7 +62,7 @@ class ProtXMLTest(unittest.TestCase):\ndel kw['key']\nkw['remove_decoy'] = True\ndf = protxml.DataFrame(self.path)\n- df['protein_name'] = df.protein_name.str.replace(r'DEC... | Python | Apache License 2.0 | levitsky/pyteomics | Future-proof protxml test |
377,522 | 18.02.2022 15:54:58 | -10,800 | a889f0b48c714d7d9c9bb7115d66b7f8f780d5f1 | Improve exception message in Composition._from_parsed_sequence | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -164,19 +164,19 @@ class Composition(BasicComposition):\ndef _from_parsed_sequence(self, parsed_sequence, aa_comp):\nself.clear()\ncomp = defaultdict(int)\n- for aa in parsed_sequence:\... | Python | Apache License 2.0 | levitsky/pyteomics | Improve exception message in Composition._from_parsed_sequence |
377,522 | 17.05.2022 18:58:30 | -10,800 | 4ddd7ad2dccb401090bca34c183754370a4a62a5 | Start rewriting the test runner using pyenv | [
{
"change_type": "ADD",
"old_path": null,
"new_path": "tests/python-versions.txt",
"diff": "+2.7.18\n+3.6.15\n+3.7.13\n+3.8.13\n+3.9.12\n+3.10.4\n"
},
{
"change_type": "MODIFY",
"old_path": "tests/runtests.sh",
"new_path": "tests/runtests.sh",
"diff": "#!/bin/bash\n-export PYTHON... | Python | Apache License 2.0 | levitsky/pyteomics | Start rewriting the test runner using pyenv |
377,522 | 18.05.2022 17:44:47 | -10,800 | de57dff70331b05df97135e4ba278b55555ba660 | Save exit codes | [
{
"change_type": "MODIFY",
"old_path": "tests/runtests.sh",
"new_path": "tests/runtests.sh",
"diff": "@@ -5,6 +5,8 @@ NODEPS=0\nPREFIX_ALL=\"test_pyteomics_\"\nPREFIX_SINGLE=\"test_pyteomics_single_\"\nCLEAN=0\n+declare -A exitcodes\n+\nfor i in \"$@\" ; do\nif [[ \"$i\" == \"--all\" ]] ; then\nMODE... | Python | Apache License 2.0 | levitsky/pyteomics | Save exit codes |
377,522 | 18.05.2022 18:16:37 | -10,800 | c8db8982a33f9a2340a2ad2c3ac471ff3a7693ad | Do not delete envs after tests; upgrade deps | [
{
"change_type": "MODIFY",
"old_path": "tests/runtests.sh",
"new_path": "tests/runtests.sh",
"diff": "@@ -22,9 +22,15 @@ done\nif [[ $MODE == \"all\" ]] ; then\necho \"Installing Python versions...\"\nxargs -a python-versions.txt -I{} pyenv install -s {}\n- echo \"Creating environments...\"\n+ if [[... | Python | Apache License 2.0 | levitsky/pyteomics | Do not delete envs after tests; upgrade deps |
377,522 | 18.05.2022 19:13:12 | -10,800 | 224097676e6cf58e2797d7950fbf7b04fade5ec5 | Add --no-run, try to fix counting for --all | [
{
"change_type": "MODIFY",
"old_path": "tests/runtests.sh",
"new_path": "tests/runtests.sh",
"diff": "@@ -10,6 +10,8 @@ declare -A exitcodes\nfor i in \"$@\" ; do\nif [[ \"$i\" == \"--all\" ]] ; then\nMODE=\"all\"\n+ elif [[ \"$i\" == \"--no-run\" ]] ; then\n+ MODE=\"no-op\"\nfi\nif [[ \"$i\" == \"-... | Python | Apache License 2.0 | levitsky/pyteomics | Add --no-run, try to fix counting for --all |
377,522 | 19.05.2022 04:23:19 | -10,800 | 8a0e7e258497f9cdd3b2045d85df0e914b5927bd | Rewrite with GNU parallel and exceptions | [
{
"change_type": "MODIFY",
"old_path": "tests/runtests.sh",
"new_path": "tests/runtests.sh",
"diff": "#!/bin/bash\n-ROOT=\"$(pyenv root)\"\n-MODE=\"single\"\n-NODEPS=0\n-PREFIX_ALL=\"test_pyteomics_\"\n-PREFIX_SINGLE=\"test_pyteomics_single_\"\n-CLEAN=0\n+\n+export ROOT=\"$(pyenv root)\"\n+export MO... | Python | Apache License 2.0 | levitsky/pyteomics | Rewrite with GNU parallel and exceptions |
377,522 | 19.05.2022 04:50:13 | -10,800 | 0a49c98316d92763b630ed371aa3e53d1ce5fec0 | Install pyteomics consecutively | [
{
"change_type": "MODIFY",
"old_path": "tests/runtests.sh",
"new_path": "tests/runtests.sh",
"diff": "@@ -36,7 +36,6 @@ create() {\ndeps() {\neval \"${ROOT}/versions/${PREFIX}${1}/bin/pip\" install -U pip wheel\neval \"${ROOT}/versions/${PREFIX}${1}/bin/pip\" install -U -r ../test-requirements.txt\n... | Python | Apache License 2.0 | levitsky/pyteomics | Install pyteomics consecutively |
377,522 | 07.06.2022 16:11:19 | -10,800 | 32ad602bbd86deb910da93d90b281669277975f3 | Raise PyteomicsError instead of ZeroDivisionError in aux.fdr() | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5.4a1\n+4.5.4a2\n-------\n- Fix issue #74.\n+ - In :func:`pyteomics.auxiliary.fdr`, raise :exc:`PyteomicsError` instead of :exc:`ZeroDivisionError` when\n+ using formula 1 on input without any target PSMs.\n4.5.... | Python | Apache License 2.0 | levitsky/pyteomics | Raise PyteomicsError instead of ZeroDivisionError in aux.fdr() |
377,522 | 15.06.2022 14:42:33 | -10,800 | 7a20967480f211a5508bb589d0eee67a822b7932 | Improve accuracy in mass.std_aa_mass | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5.4a2\n+4.5.4a3\n-------\n- Fix issue #74.\n- In :func:`pyteomics.auxiliary.fdr`, raise :exc:`PyteomicsError` instead of :exc:`ZeroDivisionError` when\nusing formula 1 on input without any target PSMs.\n+ - Prov... | Python | Apache License 2.0 | levitsky/pyteomics | Improve accuracy in mass.std_aa_mass |
377,522 | 15.06.2022 16:23:49 | -10,800 | 6916dbe7ad9346869b01da2bbcc1af68cd0e1754 | Use Github license shield | [
{
"change_type": "MODIFY",
"old_path": "README.rst",
"new_path": "README.rst",
"diff": ":target: https://pyteomics.readthedocs.io/\n:alt: Read the Docs (latest)\n-.. image:: https://img.shields.io/aur/license/python-pyteomics.svg\n+.. image:: https://img.shields.io/github/license/levitsky/pyteomics\... | Python | Apache License 2.0 | levitsky/pyteomics | Use Github license shield |
377,522 | 17.06.2022 19:51:10 | -10,800 | b9fabac991d2da524b4700af871e56f6a255f924 | Fix SyntaxError on Python 2.7 | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5.4a3\n+4.5.4a4\n-------\n- Fix issue #74.\n- In :func:`pyteomics.auxiliary.fdr`, raise :exc:`PyteomicsError` instead of :exc:`ZeroDivisionError` when\nusing formula 1 on input without any target PSMs.\n- Provid... | Python | Apache License 2.0 | levitsky/pyteomics | Fix SyntaxError on Python 2.7 |
377,522 | 18.07.2022 16:15:00 | -10,800 | ad80a82cdab02585a6ce17097b9c781d7522cfbd | Expand docstrings in pepxml | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -247,18 +247,18 @@ def iterfind(source, path, **kwargs):\nThe path can be absolute or \"free\". Please don't specify\nnamespaces.\n- recursive : bool, optional\n+ recursive : bool, keyword on... | Python | Apache License 2.0 | levitsky/pyteomics | Expand docstrings in pepxml |
377,522 | 13.10.2022 20:44:29 | -14,400 | ece30293cd919360b1772375112c1edc2dae4ba5 | Fix fast_mass2 | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "+4.5.6a1\n+-------\n+\n+ - Prevent :func:`pyteomics.mass.fast_mass2` from changing `aa_mass`.\n+\n4.5.5\n-----\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyt... | Python | Apache License 2.0 | levitsky/pyteomics | Fix fast_mass2 |
377,529 | 24.10.2022 15:33:34 | -7,200 | b408c0c4a89386c3b73dfb465c1605852e55f6c4 | use packaging instead of distutils if available | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/patch.py",
"new_path": "pyteomics/auxiliary/patch.py",
"diff": "-from distutils.version import LooseVersion\n+try:\n+ from packaging.version import Version\n+except ImportError:\n+ from distutils.version import LooseVersion as Version\ntry:... | Python | Apache License 2.0 | levitsky/pyteomics | use packaging instead of distutils if available |
377,522 | 28.10.2022 14:16:10 | -7,200 | 96849b3227541316d9681f99551cee0d5ec037b8 | Use Proforma.mass in annotation | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -592,9 +592,10 @@ def _spectrum_utils_annotate_spectrum(spectrum, peptide, *args, **kwargs):\nprefix = kwargs.get('prefix')\ntry:\n- proforma.parse(peptide)\n+ parsed_proforma = proform... | Python | Apache License 2.0 | levitsky/pyteomics | Use Proforma.mass in annotation |
377,522 | 31.10.2022 22:20:02 | -3,600 | 3605dc58dc05e9198759900b8419c6d8987e8986 | Add spectrum_utils version check, update changelog, set version to 4.5.6 | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.5.6a3\n--------\n+4.5.6\n+-----\n- New function :py:func:`pyteomics.proforma.set_unimod_path` allowing the ProForma parsing machinery\nto work with a local Unimod copy (`#85 <https://github.com/levitsky/pyteomic... | Python | Apache License 2.0 | levitsky/pyteomics | Add spectrum_utils version check, update changelog, set version to 4.5.6 |
377,529 | 07.11.2022 20:33:48 | -3,600 | e45b309f1d710578402de4b27b55769e838b2b6c | link to https instead of http | [
{
"change_type": "MODIFY",
"old_path": "INSTALL",
"new_path": "INSTALL",
"diff": "@@ -8,13 +8,13 @@ Project dependencies\nPyteomics uses the following Python packages:\n- - `numpy <http://pypi.python.org/pypi/numpy>`_\n- - `matplotlib <http://sourceforge.net/projects/matplotlib/files/matplotlib/>`_\... | Python | Apache License 2.0 | levitsky/pyteomics | link to https instead of http |
377,529 | 07.11.2022 21:05:27 | -3,600 | f1fb0841d4f4585ddbd7b77cac5e0026626394e3 | link to official matplotlib.org website | [
{
"change_type": "MODIFY",
"old_path": "INSTALL",
"new_path": "INSTALL",
"diff": "@@ -9,7 +9,7 @@ Project dependencies\nPyteomics uses the following Python packages:\n- `numpy <https://pypi.python.org/pypi/numpy>`_\n- - `matplotlib <https://sourceforge.net/projects/matplotlib/files/matplotlib/>`_\n+... | Python | Apache License 2.0 | levitsky/pyteomics | link to official matplotlib.org website
Co-authored-by: Lev Levitsky <lev.levitsky@phystech.edu> |
377,529 | 07.11.2022 21:05:53 | -3,600 | 4a9fe89e77041f2fd5617e7749a55abfc255569b | link to official lxml.de website | [
{
"change_type": "MODIFY",
"old_path": "INSTALL",
"new_path": "INSTALL",
"diff": "@@ -11,7 +11,7 @@ Pyteomics uses the following Python packages:\n- `numpy <https://pypi.python.org/pypi/numpy>`_\n- `matplotlib <https://matplotlib.org/>`_\n(used by :py:mod:`pyteomics.pylab_aux`)\n- - `lxml <https://p... | Python | Apache License 2.0 | levitsky/pyteomics | link to official lxml.de website
Co-authored-by: Lev Levitsky <lev.levitsky@phystech.edu> |
377,529 | 07.11.2022 21:09:24 | -3,600 | 622ed3c064796847971992175275bdf821126e47 | link to official numpy.org website | [
{
"change_type": "MODIFY",
"old_path": "INSTALL",
"new_path": "INSTALL",
"diff": "@@ -8,7 +8,7 @@ Project dependencies\nPyteomics uses the following Python packages:\n- - `numpy <https://pypi.python.org/pypi/numpy>`_\n+ - `numpy <https://numpy.org/>`_\n- `matplotlib <https://matplotlib.org/>`_\n(use... | Python | Apache License 2.0 | levitsky/pyteomics | link to official numpy.org website
Co-authored-by: Lev Levitsky <lev.levitsky@phystech.edu> |
377,522 | 15.11.2022 13:02:15 | -3,600 | aa2cdb3e86356434305e862950e7de58feb29d84 | Update changelog, bump Github Actions versions | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpackage.yml",
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "@@ -17,9 +17,9 @@ jobs:\npython-version: ['2.7', '3.6', '3.7', '3.8', '3.9', '3.10']\nsteps:\n- - uses: actions/checkout@v2\n+ - uses: actions/checkout@v3\n- name... | Python | Apache License 2.0 | levitsky/pyteomics | Update changelog, bump Github Actions versions |
377,522 | 15.11.2022 16:57:10 | -3,600 | db416df7704bf9706ac0a63dadfcf446adcae4ff | Try setup-python@v4 | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpackage.yml",
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "@@ -19,7 +19,7 @@ jobs:\nsteps:\n- uses: actions/checkout@v3\n- name: Set up Python ${{ matrix.python-version }}\n- uses: actions/setup-python@v3\n+ uses: actions... | Python | Apache License 2.0 | levitsky/pyteomics | Try setup-python@v4 |
377,522 | 16.11.2022 22:33:02 | -3,600 | 7cba1aa509d214e2879a80218b9f403961e709a6 | Update INSTALL as proposed in | [
{
"change_type": "MODIFY",
"old_path": "INSTALL",
"new_path": "INSTALL",
"diff": "@@ -3,47 +3,59 @@ Supported Python versions\nPyteomics supports Python 2.7 and Python 3.3+.\n-Project dependencies\n---------------------\n-Pyteomics uses the following Python packages:\n+Install with pip\n+-----------... | Python | Apache License 2.0 | levitsky/pyteomics | Update INSTALL as proposed in #88 |
377,522 | 16.11.2022 22:40:50 | -3,600 | 3bcaf4029dadb605bda33a48dfc4a906516dbc13 | Add a conda badge | [
{
"change_type": "MODIFY",
"old_path": "README.rst",
"new_path": "README.rst",
"diff": ":target: https://pypi.org/project/pyteomics/\n:alt: PyPI\n+.. image:: https://img.shields.io/conda/vn/bioconda/pyteomics\n+ :target: http://bioconda.github.io/recipes/pyteomics/README.html\n+ :alt: conda\n+\n.. i... | Python | Apache License 2.0 | levitsky/pyteomics | Add a conda badge |
377,522 | 30.11.2022 00:00:47 | -3,600 | 995607eb0b206c88be991a388f3ebe4c0fefc6f2 | Change Uniprot header pattern to hard-code key=value keys and their order | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -402,16 +402,22 @@ class FlavoredMixin():\nclass UniProtMixin(FlavoredMixin):\n- header_pattern = r'^(\\w+)\\|([-\\w]+)\\|(\\w+)\\s+([^=]*\\S)((\\s+\\w+=[^=]+(?!\\w*=))+)\\s*$'\n- header_group ... | Python | Apache License 2.0 | levitsky/pyteomics | Change Uniprot header pattern to hard-code key=value keys and their order |
377,522 | 01.12.2022 14:24:41 | -3,600 | 16a65eb0f9ed5ede9de4557b2e040fd0d2499682 | Allow hyphen in gene names | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -402,7 +402,7 @@ class FlavoredMixin():\nclass UniProtMixin(FlavoredMixin):\n- header_pattern = r'^(?P<db>\\w+)\\|(?P<id>[-\\w]+)\\|(?P<entry>\\w+)\\s+(?P<name>.*?)(\\s+OS=(?P<OS>[^=]+))?(\\s+O... | Python | Apache License 2.0 | levitsky/pyteomics | Allow hyphen in gene names |
377,522 | 02.12.2022 15:56:13 | -3,600 | 38c3f8c318bc96367d48dcc5db28ee9c63738aea | Relax GN pattern | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -402,7 +402,7 @@ class FlavoredMixin():\nclass UniProtMixin(FlavoredMixin):\n- header_pattern = r'^(?P<db>\\w+)\\|(?P<id>[-\\w]+)\\|(?P<entry>\\w+)\\s+(?P<name>.*?)(\\s+OS=(?P<OS>[^=]+))?(\\s+O... | Python | Apache License 2.0 | levitsky/pyteomics | Relax GN pattern |
377,522 | 02.12.2022 16:03:46 | -3,600 | df236e2907cc8f34042dcf32c774d01a26667ba2 | Add get_header() for TwoLayerIndexedFASTA | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -386,6 +386,11 @@ class TwoLayerIndexedFASTA(IndexedFASTA):\nreturn super(TwoLayerIndexedFASTA, self).get_entry(header)\nraise KeyError(key)\n+ def get_header(self, key):\n+ if key in self._id2... | Python | Apache License 2.0 | levitsky/pyteomics | Add get_header() for TwoLayerIndexedFASTA |
377,522 | 14.12.2022 00:10:20 | -3,600 | 5dcfe6ffdb4d847a2145637ecba92f04c364971c | Use OR-ed groups in Uniprot pattern | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -407,7 +407,7 @@ class FlavoredMixin():\nclass UniProtMixin(FlavoredMixin):\n- header_pattern = r'^(?P<db>\\w+)\\|(?P<id>[-\\w]+)\\|(?P<entry>\\w+)\\s+(?P<name>.*?)(\\s+OS=(?P<OS>[^=]+))?(\\s+O... | Python | Apache License 2.0 | levitsky/pyteomics | Use OR-ed groups in Uniprot pattern |
377,522 | 15.12.2022 15:06:35 | -3,600 | dc313796dc4dfc8dd55963962e017d3033ddc590 | Update changelog, test on 3.11 | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpackage.yml",
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "@@ -14,7 +14,7 @@ jobs:\nruns-on: 'ubuntu-20.04'\nstrategy:\nmatrix:\n- python-version: ['2.7', '3.6', '3.7', '3.8', '3.9', '3.10']\n+ python-version: ['2.7', '3.... | Python | Apache License 2.0 | levitsky/pyteomics | Update changelog, test on 3.11 |
377,522 | 15.12.2022 15:29:08 | -3,600 | 86be7c23a4bb3e7fe57d15ced12f881c1d2d99e7 | Try to enable from-source install of h5py | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpackage.yml",
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "@@ -24,6 +24,8 @@ jobs:\npython-version: ${{ matrix.python-version }}\n- name: Install dependencies\nrun: |\n+ sudo apt-get update\n+ sudo apt-get install libhdf5... | Python | Apache License 2.0 | levitsky/pyteomics | Try to enable from-source install of h5py |
377,522 | 15.12.2022 15:44:08 | -3,600 | 600722712bc9e40a820fd6b4f9d16c07c30f4bed | Try to trigger tests on workflow file changes | [
{
"change_type": "MODIFY",
"old_path": ".github/workflows/pythonpackage.yml",
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "@@ -4,9 +4,11 @@ on:\npush:\npaths:\n- '**.py'\n+ - '.github/workflows/pythonpackage.yml'\npull_request:\npaths:\n- '**.py'\n+ - '.github/workflows/pythonpackage.... | Python | Apache License 2.0 | levitsky/pyteomics | Try to trigger tests on workflow file changes |
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