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 | 17.04.2017 15:38:09 | -10,800 | a565470cbc0ceace6be904b8935bcce2c8188fca | Workaround for older pandas weirdness | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-3.4.2a1\n\\ No newline at end of file\n+3.4.2a2\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary.py",
"new_path": "pyteomics/auxiliary.py",
"diff": "@... | Python | Apache License 2.0 | levitsky/pyteomics | Workaround for older pandas weirdness |
377,522 | 17.04.2017 18:42:59 | -10,800 | 212dcfeef7dda82e22844be9ead2477df5af3b08 | Draft mzid.DataFrame | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzid.py",
"new_path": "pyteomics/mzid.py",
"diff": "@@ -298,6 +298,78 @@ def is_decoy(psm):\nreturn all(pe['isDecoy'] for sii in psm['SpectrumIdentificationItem']\nfor pe in sii['PeptideEvidenceRef'])\n+\n+def DataFrame(*args, **kwargs):\n+ \"\"\"Rea... | Python | Apache License 2.0 | levitsky/pyteomics | Draft mzid.DataFrame |
377,522 | 17.04.2017 18:43:48 | -10,800 | e84d394069248ad138462d8fdde76392ae986e2c | Make pepxml and tandem read() accept (and ignore) arbitrary kwargs.
This is convenient for qvalues functions | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "3.4.2\n-----\n+ Add :py:func:`pyteomics.mzid.DataFrame` and :py:func:`pyteomics.mzid.filter_df` functions for convenience.\n+ Their behavior may be refined later on.\n+\nChanges in behavior of :py:func:`pyteomics.a... | Python | Apache License 2.0 | levitsky/pyteomics | Make pepxml and tandem read() accept (and ignore) arbitrary kwargs.
This is convenient for qvalues functions |
377,532 | 27.04.2017 17:42:41 | -10,800 | 8e527f08e682e87e33bd0f34ea6c0885c19a34bc | Speed up pepxml module | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -108,15 +108,18 @@ class PepXML(xml.XML):\ndef _get_info_smart(self, element, **kw):\n\"\"\"Extract the info in a smart way depending on the element type\"\"\"\n- name = xml._local_name(eleme... | Python | Apache License 2.0 | levitsky/pyteomics | Speed up pepxml module |
377,522 | 27.04.2017 18:01:35 | -10,800 | b8cee70c4ba906ed61e57b00186673af091428ff | Minor fixes, changelog update | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "3.4.2\n-----\n- Add :py:func:`pyteomics.mzid.DataFrame` and :py:func:`pyteomics.mzid.filter_df` functions for convenience.\n+ - Add :py:func:`pyteomics.mzid.DataFrame` and :py:func:`pyteomics.mzid.filter_df` functi... | Python | Apache License 2.0 | levitsky/pyteomics | Minor fixes, changelog update |
377,522 | 27.04.2017 18:11:55 | -10,800 | 5a7cf841b3d077fc2c20b133078e2778baaa29c0 | Remove dict duplication in pepxml _get_info_smart | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -106,9 +106,8 @@ class PepXML(xml.XML):\n_default_iter_tag = 'spectrum_query'\n_structures_to_flatten = {'search_score_summary', 'modification_info'}\n- def _get_info_smart(self, element, **k... | Python | Apache License 2.0 | levitsky/pyteomics | Remove dict duplication in pepxml _get_info_smart |
377,532 | 28.04.2017 16:54:55 | -10,800 | 888094dbdaf8eeb03bece4c3e3b625998d84fcc7 | Speed up pepxml.read() | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -105,6 +105,11 @@ class PepXML(xml.XML):\n_default_version = '1.15'\n_default_iter_tag = 'spectrum_query'\n_structures_to_flatten = {'search_score_summary', 'modification_info'}\n+ # attribut... | Python | Apache License 2.0 | levitsky/pyteomics | Speed up pepxml.read() |
377,532 | 26.05.2017 15:57:24 | -10,800 | c62b0ee762721f61d3078c9a2bd6ce8310a1ca90 | small speed up of mgf.read | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -159,7 +159,6 @@ def read(source=None, use_header=True, convert_arrays=2, read_charges=True, dtyp\nparams[l[0].lower()] = l[1].strip()\nelse: # this must be a peak list\nl = sline.split()\n- if len... | Python | Apache License 2.0 | levitsky/pyteomics | small speed up of mgf.read |
377,522 | 03.06.2017 18:04:20 | -10,800 | 9af3a48f8b141448ebffaa84c99c642cf212b340 | Add ms1 parser | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "3.4.2\n-----\n+ - New module :py:mod:`pyteomics.ms1` for parsing of MS1 files.\n+\n- Add :py:func:`pyteomics.mzid.DataFrame` and :py:func:`pyteomics.mzid.filter_df` functions for convenience.\nTheir behavior may be... | Python | Apache License 2.0 | levitsky/pyteomics | Add ms1 parser |
377,522 | 05.06.2017 19:23:03 | -10,800 | 6f1863fd626209645af153ff8d882b2378828aed | Read info from multiple PeptideEvidenceRef elements in mzid.DataFrame | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzid.py",
"new_path": "pyteomics/mzid.py",
"diff": "@@ -316,7 +316,10 @@ def DataFrame(*args, **kwargs):\n*args, **kwargs : passed to :py:func:`chain`\nsep : str or None, optional\n- Split protein descriptions by this delimiter, if given.\n+ Some val... | Python | Apache License 2.0 | levitsky/pyteomics | Read info from multiple PeptideEvidenceRef elements in mzid.DataFrame |
377,522 | 06.06.2017 17:21:06 | -10,800 | 323943ef56d852c165020d4e1536ba07bf46576e | Fix for empty dataframes | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary.py",
"new_path": "pyteomics/auxiliary.py",
"diff": "@@ -677,15 +677,22 @@ def _qvalues_df(psms, keyf, isdecoy, **kwargs):\npeps = kwargs.get('pep')\ndecoy_or_pep_label = _decoy_or_pep_label(**kwargs)\nq_label = kwargs.setdefault('q_label', ... | Python | Apache License 2.0 | levitsky/pyteomics | Fix for empty dataframes |
377,522 | 06.06.2017 17:47:21 | -10,800 | b9c4daf5a0ff6f9e64f968645df31337868a3ba1 | Another fix for empty df | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary.py",
"new_path": "pyteomics/auxiliary.py",
"diff": "@@ -695,18 +695,28 @@ def _qvalues_df(psms, keyf, isdecoy, **kwargs):\npsms[decoy_or_pep_label] = []\nisdecoy = decoy_or_pep_label\nreverse = kwargs.get('reverse', False)\n+\n+ if not full... | Python | Apache License 2.0 | levitsky/pyteomics | Another fix for empty df |
377,522 | 06.06.2017 19:22:50 | -10,800 | 4950155ce23df611ff7a66af00b4248be98dd655 | Move ion_comp and charge logic into Composition constructor | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "- New module :py:mod:`pyteomics.ms1` for parsing of MS1 files.\n- - Add :py:func:`pyteomics.mzid.DataFrame` and :py:func:`pyteomics.mzid.filter_df` functions for convenience.\n+ - :py:class:`pyteomics.mass.mass.Com... | Python | Apache License 2.0 | levitsky/pyteomics | Move ion_comp and charge logic into Composition constructor |
377,522 | 07.06.2017 22:46:32 | -10,800 | 6cc9199c9e5eeea9c27d2a2d262edd82374ad29c | Fix in pepxml.DataFrame for spectrum_queries without a search_hit | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -356,6 +356,7 @@ def DataFrame(*args, **kwargs):\nfor k, v in item.items():\nif isinstance(v, (str, int, float)):\ninfo[k] = v\n+ if 'search_hit' in item:\nsh = item['search_hit'][0]\nprotein... | Python | Apache License 2.0 | levitsky/pyteomics | Fix in pepxml.DataFrame for spectrum_queries without a search_hit |
377,522 | 09.06.2017 19:38:09 | -10,800 | ff63a10f6780eb34b099051d52371d31d4353c4a | Fixes in ms1; read_header still fails test | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/ms1.py",
"new_path": "pyteomics/ms1.py",
"diff": "@@ -99,8 +99,20 @@ def read(source=None, use_header=False, convert_arrays=2, read_charges=True, dty\nmasses = []\nintensities = []\nif use_header: params.update(header)\n+\n+ def make_out():\n+ out = ... | Python | Apache License 2.0 | levitsky/pyteomics | Fixes in ms1; read_header still fails test |
377,522 | 26.06.2017 15:51:26 | -10,800 | 7fd5a7da34bf2aa5a7d274e0612f10761a9a54e1 | Add actual test files | [
{
"change_type": "ADD",
"old_path": null,
"new_path": "tests/test.ms1",
"diff": "+H CreationDate Sat Jun 03 15:25:10 2017\n+H Extractor ProteoWizard\n+H Extractor version Xcalibur\n+H Source file Set 1. B2 at 193 nm RT.RAW\n+S 1 1\n+I RTime 0.987225\n+I BPI 585566\n+I BPM 544.2904\n+I TIC 3728760\n+... | Python | Apache License 2.0 | levitsky/pyteomics | Add actual test files |
377,522 | 27.06.2017 18:47:46 | -10,800 | 8ef13c075bcdbb344a27127876f5e1f06ae97e3c | MS1 test works | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/ms1.py",
"new_path": "pyteomics/ms1.py",
"diff": "@@ -135,8 +135,8 @@ def read(source=None, use_header=False, convert_arrays=2, read_charges=True, dty\nintensities.append(float(sline[1])) # exceptions...\\\nexcept ValueError:\nraise aux.PyteomicsErro... | Python | Apache License 2.0 | levitsky/pyteomics | MS1 test works |
377,522 | 02.07.2017 14:56:59 | -10,800 | 5b6acbd2e2872dd633e09b067bafc05da054fb6e | Change url in pkgbuild to readthedocs | [
{
"change_type": "MODIFY",
"old_path": "PKGBUILD",
"new_path": "PKGBUILD",
"diff": "@@ -4,7 +4,7 @@ pkgver=3.4.2\npkgrel=1\npkgdesc=\"A framework for proteomics data analysis.\"\narch=('any')\n-url=\"http://pythonhosted.org/pyteomics\"\n+url=\"http://pyteomics.readthedocs.io/\"\nlicense=('Apache')\n... | Python | Apache License 2.0 | levitsky/pyteomics | Change url in pkgbuild to readthedocs |
377,522 | 05.07.2017 16:09:08 | -10,800 | 5a37e2dddf955885985770fcbc58bbd7a54b5621 | Fix warning formatting problem for Python 3 | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/xml.py",
"new_path": "pyteomics/xml.py",
"diff": "@@ -29,7 +29,7 @@ This module requres :py:mod:`lxml` and :py:mod:`numpy`.\nimport re\nimport warnings\n-warnings.formatwarning = lambda msg, *args: str(msg) + '\\n'\n+warnings.formatwarning = lambda m... | Python | Apache License 2.0 | levitsky/pyteomics | Fix warning formatting problem for Python 3 |
377,522 | 05.07.2017 18:45:39 | -10,800 | a54b45ab5b08740046709e543aab638267e84330 | Remove unnecessary concat in filter_df | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -392,6 +392,7 @@ def filter_df(*args, **kwargs):\nDefault is 'expect'.\nis_decoy : str / iterable / callable, optional\nDefault is to check if all strings in the \"protein\" column start with... | Python | Apache License 2.0 | levitsky/pyteomics | Remove unnecessary concat in filter_df |
377,522 | 26.08.2017 00:47:45 | -10,800 | 56647336022f72c1e4110ca63004dfbe51b9c26b | Make _write_byte_offsets public | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/xml.py",
"new_path": "pyteomics/xml.py",
"diff": "@@ -1046,7 +1046,7 @@ class IndexSavingXML(IndexedXML):\nindex = PrebuiltOffsetIndex(self._load_byte_index_from_file(f))\nself._offset_index = index\n- def _write_byte_offsets(self):\n+ def write_byte... | Python | Apache License 2.0 | levitsky/pyteomics | Make _write_byte_offsets public |
377,522 | 29.08.2017 02:15:19 | -10,800 | 7a6258f83de5ff50d562d51232a19c956a14053a | Add decode_binary in docstring, set read_schema to False | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzml.py",
"new_path": "pyteomics/mzml.py",
"diff": "@@ -117,7 +117,7 @@ class MzML(xml.ArrayConversionMixin, xml.IndexSavingXML):\nReturns\n-------\n- str\n+ out : str\nThe name for this array entry\n\"\"\"\n# If this is a non-standard array, we hope... | Python | Apache License 2.0 | levitsky/pyteomics | Add decode_binary in docstring, set read_schema to False |
377,522 | 01.09.2017 18:27:59 | -10,800 | bc3383f143511fc55cfc8b9262302b57a558db9d | Make mzid use index saving; add try/except around type conversion in xml._get_info | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "+3.4.3\n+-----\n+\n+ - Change the default value for `read_schema` to :py:const:`False` in\n+ XML parsing modules.\n+\n+ - Add optional `decode_binary` argument in\n+ :py:class:`pyteomics.mzml.MzML` and :py:class:`p... | Python | Apache License 2.0 | levitsky/pyteomics | Make mzid use index saving; add try/except around type conversion in xml._get_info |
377,522 | 20.10.2017 17:31:26 | -10,800 | ce249fda929e5150888863f20964016dc8137e80 | Fix for multiple values lost in param tags | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/xml.py",
"new_path": "pyteomics/xml.py",
"diff": "@@ -330,6 +330,11 @@ class XML(FileReader):\nif cname in {'cvParam', 'userParam', 'UserParam'}:\nnewinfo = self._handle_param(child, **kwargs)\nif not ('name' in info and 'name' in newinfo):\n+ for ke... | Python | Apache License 2.0 | levitsky/pyteomics | Fix for multiple values lost in param tags |
377,522 | 20.10.2017 18:13:52 | -10,800 | 99d05207c0dbd2424ab0a88201e10750f869e6ed | Refactor in mgf | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-3.4.3a0\n\\ No newline at end of file\n+3.4.3a1\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -114,23 +1... | Python | Apache License 2.0 | levitsky/pyteomics | Refactor in mgf |
377,522 | 21.10.2017 16:51:39 | -10,800 | ac983a814b5de955979f3e5b9e2a3609de52df6c | Add MGF class | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary.py",
"new_path": "pyteomics/auxiliary.py",
"diff": "@@ -412,6 +412,20 @@ def _keepstate(func):\nreturn res\nreturn wrapped\n+def _keepstate_method(func):\n+ \"\"\"Decorator for :py:class:`FileReader` methods to help keep the position\n+ in ... | Python | Apache License 2.0 | levitsky/pyteomics | Add MGF class |
377,522 | 24.11.2017 16:58:56 | -10,800 | b8734610869f06b8d268c0b2d781e605949f5323 | Remove universal import in parser test | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary.py",
"new_path": "pyteomics/auxiliary.py",
"diff": "@@ -488,11 +488,11 @@ class IteratorContextManager(object):\nreturn self\ndef __next__(self):\n- try:\n+ # try:\nreturn next(self._reader)\n- except StopIteration:\n- self.__exit__(None, N... | Python | Apache License 2.0 | levitsky/pyteomics | Remove universal import in parser test |
377,522 | 05.01.2018 02:08:51 | -10,800 | 86c126aa5540aa8a88c552d185f4b73c15f77c11 | Set _default_id_attr on MzXML to "num" | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzxml.py",
"new_path": "pyteomics/mzxml.py",
"diff": "@@ -60,7 +60,6 @@ This module requires :py:mod:`lxml` and :py:mod:`numpy`.\n# See the License for the specific language governing permissions and\n# limitations under the License.\n-from collectio... | Python | Apache License 2.0 | levitsky/pyteomics | Set _default_id_attr on MzXML to "num" |
377,522 | 02.02.2018 01:37:23 | -10,800 | ce5d6a5dac4f13235e4dee4a591d28d3c62d999c | Add keep_cterm in reverse and shuffle decoy functions | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -169,7 +169,7 @@ def write(entries, output=None):\nreturn output.file\n-def reverse(sequence, keep_nterm=False):\n+def reverse(sequence, keep_nterm=False, keep_cterm=False):\n\"\"\"\nCreate a d... | Python | Apache License 2.0 | levitsky/pyteomics | Add keep_cterm in reverse and shuffle decoy functions |
377,522 | 06.02.2018 00:46:44 | -10,800 | e4d3a370c0d38cc0d7d2812554b55e8c73d30422 | Prevent some exceptions in mzid.DataFrame (fixes | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzid.py",
"new_path": "pyteomics/mzid.py",
"diff": "@@ -342,16 +342,25 @@ def DataFrame(*args, **kwargs):\nif evref:\nprot_descr, accessions, isd, starts, ends, lengths = [], [], [], [], [], []\nfor d in evref:\n- prot_descr.append(d['protein descrip... | Python | Apache License 2.0 | levitsky/pyteomics | Prevent some exceptions in mzid.DataFrame (fixes #21) |
377,522 | 09.02.2018 19:09:58 | -10,800 | 7e3ba2faac0cd2e0bbed7f96191c25aff749c8de | Update mzid schema info and move it to a separate file | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzid.py",
"new_path": "pyteomics/mzid.py",
"diff": "@@ -98,13 +98,13 @@ This module requires :py:mod:`lxml`.\nimport warnings\nwarnings.formatwarning = lambda msg, *args: str(msg) + '\\n'\nfrom . import auxiliary as aux\n-from . import xml\n+from . i... | Python | Apache License 2.0 | levitsky/pyteomics | Update mzid schema info and move it to a separate file |
377,522 | 09.02.2018 19:18:02 | -10,800 | 9ca7f0d4f7a5f494cfa510a360c9140c25d4d046 | Add new schema defaults file | [
{
"change_type": "ADD",
"old_path": null,
"new_path": "pyteomics/_schema_defaults.py",
"diff": "+_mzid_schema_defaults = {'bools': {('Enzyme', 'semiSpecific'),\n+ ('Enzymes', 'independent'),\n+ ('PeptideEvidence', 'isDecoy'),\n+ ('ProteinDetectionHypothesis', 'passThreshold'),\n+ ('SearchModificatio... | Python | Apache License 2.0 | levitsky/pyteomics | Add new schema defaults file |
377,522 | 24.02.2018 02:24:47 | -10,800 | 347e42d48f8b5951b88765211b6525273bcdedb4 | Fix (strip composition building kwargs inside mass.isotopologues) | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -152,6 +152,7 @@ class Composition(BasicComposition):\nThe main improvement over dict is that Composition objects allow\nadding and subtraction.\n\"\"\"\n+ _kw_sources = {'formula', 'se... | Python | Apache License 2.0 | levitsky/pyteomics | Fix #2 (strip composition building kwargs inside mass.isotopologues) |
377,522 | 03.03.2018 16:19:02 | -10,800 | 73824d7401857e43bdf8a881426f85f6ed659d0b | Enable huge_tree everywhere in xml and mzml | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzml.py",
"new_path": "pyteomics/mzml.py",
"diff": "@@ -384,7 +384,8 @@ class PreIndexedMzML(MzML):\nindex = {}\nself._source.seek(offset)\ntry:\n- for event, elem in etree.iterparse(self._source, events=('start', 'end'), remove_comments=True):\n+ fo... | Python | Apache License 2.0 | levitsky/pyteomics | Enable huge_tree everywhere in xml and mzml |
377,522 | 04.03.2018 00:40:08 | -10,800 | b4f26d7908d7ee01878c003f04235f9bc8b049bc | Add huge_tree to keyword arguments (fixes | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzml.py",
"new_path": "pyteomics/mzml.py",
"diff": "@@ -270,7 +270,7 @@ class MzML(xml.ArrayConversionMixin, xml.IndexSavingXML):\ninfo[k] = int(info[k])\nreturn info\n-def read(source, read_schema=False, iterative=True, use_index=False, dtype=None):... | Python | Apache License 2.0 | levitsky/pyteomics | Add huge_tree to keyword arguments (fixes #23) |
377,522 | 04.03.2018 20:22:20 | -10,800 | 18d9dda6799d80dd2b3ca6461af7a7bb27e616ba | Add `composition` to Composition._kw_sources, rename _from_dict to _from_composition | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -152,7 +152,7 @@ class Composition(BasicComposition):\nThe main improvement over dict is that Composition objects allow\nadding and subtraction.\n\"\"\"\n- _kw_sources = {'formula', 'se... | Python | Apache License 2.0 | levitsky/pyteomics | Add `composition` to Composition._kw_sources, rename _from_dict to _from_composition |
377,522 | 05.03.2018 13:44:25 | -10,800 | 71560608878b7574dfb7e9241f310146c9229329 | Add huge_tree in mzxml, update changelog | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-3.4.3\n------\n+3.5\n+---\n- - Change the default value for `read_schema` to :py:const:`False` in\n- XML parsing modules.\n+ - Preserve accession information on cvParam elements in mzML parser.\n+ Dictionaries pro... | Python | Apache License 2.0 | levitsky/pyteomics | Add huge_tree in mzxml, update changelog |
377,522 | 05.03.2018 16:41:00 | -10,800 | 3d1168a7822fb3d516c0bb1b77ecc73a1bcae982 | Remove local sphinx exts | [
{
"change_type": "MODIFY",
"old_path": "doc/source/conf.py",
"new_path": "doc/source/conf.py",
"diff": "@@ -22,7 +22,7 @@ def add_directive_header(self, sig):\nDataDocumenter.add_directive_header = add_directive_header\n-sys.path.insert(0, os.path.abspath('exts'))\n+#sys.path.insert(0, os.path.abspa... | Python | Apache License 2.0 | levitsky/pyteomics | Remove local sphinx exts |
377,522 | 05.03.2018 17:59:51 | -10,800 | 41d794cd9883145622890dd742c1646f40e73106 | Try using bitbucket version of googleanalytics in rtd requirements | [
{
"change_type": "MODIFY",
"old_path": "doc/build-requirements.txt",
"new_path": "doc/build-requirements.txt",
"diff": "numpydoc\nmatplotlib\n-sphinxcontrib-googleanalytics\n\\ No newline at end of file\n+hg+https://bitbucket.org/birkenfeld/sphinx-contrib#egg=googleanalytics&subdirectory=googleanaly... | Python | Apache License 2.0 | levitsky/pyteomics | Try using bitbucket version of googleanalytics in rtd requirements |
377,522 | 05.03.2018 18:53:18 | -10,800 | 43dbd0808bce53c9b2da5edc55613ee494912280 | Try adding badge to readme | [
{
"change_type": "MODIFY",
"old_path": "README",
"new_path": "README",
"diff": "+.. image:: http://readthedocs.org/projects/pyteomics/badge/?version=latest\n+ :target: http://pyteomics.readthedocs.io/en/latest/?badge=latest\n+ :alt: Documentation Status\n+\n+\nWhat is Pyteomics?\n------------------\... | Python | Apache License 2.0 | levitsky/pyteomics | Try adding badge to readme |
377,522 | 06.03.2018 14:05:26 | -10,800 | 90435728e634d069032da53cc0101ef59c38655b | Add cvquery to auxiliary doc page | [
{
"change_type": "MODIFY",
"old_path": "doc/source/api/auxiliary.rst",
"new_path": "doc/source/api/auxiliary.rst",
"diff": ".. automodule:: pyteomics.auxiliary\n:exclude-members: Charge, ChargeList, BasicComposition, FileReader\n+\n+ .. autofunction:: cvquery\n\\ No newline at end of file\n"
},
... | Python | Apache License 2.0 | levitsky/pyteomics | Add cvquery to auxiliary doc page |
377,522 | 10.03.2018 19:18:23 | -10,800 | 2fed6d2017d7cb0ddbd7a844bd8ec1aa32aa3e41 | Mention Controlled Vocabularies in docs | [
{
"change_type": "MODIFY",
"old_path": "doc/source/data.rst",
"new_path": "doc/source/data.rst",
"diff": "@@ -404,6 +404,7 @@ but it uses byte offset information found at the end of the file.\nUnlike the rest of the functions and classes, :py:class:`pyteomics.mzml.PreIndexedMzML`\ndoes not have a co... | Python | Apache License 2.0 | levitsky/pyteomics | Mention Controlled Vocabularies in docs |
377,522 | 14.03.2018 23:36:37 | -10,800 | 1318094ad7c14d544cf53df812571adf11b14df8 | Avoid numpy warning in cvquery | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary.py",
"new_path": "pyteomics/auxiliary.py",
"diff": "@@ -1589,7 +1589,7 @@ class CVQueryEngine(object):\ndef _query_dict(self, data, accession):\nfor key, value in data.items():\nif self._accession(key) == accession:\n- if value != '':\n+ if... | Python | Apache License 2.0 | levitsky/pyteomics | Avoid numpy warning in cvquery |
377,522 | 15.03.2018 01:19:36 | -10,800 | 43db9a8c57b9cac224e3331c1a3f039f3fb9cae8 | Add skip_empty_cvparam_values kwarg in _handle_param | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/xml.py",
"new_path": "pyteomics/xml.py",
"diff": "@@ -296,7 +296,8 @@ class XML(FileReader):\nunit_name = attribs.get(\"unitName\", unit_accesssion)\nunit_info = unit_name\naccession = attribs.get(\"accession\")\n- if 'value' in attribs:\n+ if 'value... | Python | Apache License 2.0 | levitsky/pyteomics | Add skip_empty_cvparam_values kwarg in _handle_param |
377,522 | 11.04.2018 00:08:37 | -10,800 | ce47fdd42f098892a6aaca787fe1a8b3f008c148 | Try creating df from generator in pepxml.DataFrame | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -348,8 +348,8 @@ def DataFrame(*args, **kwargs):\nout : pandas.DataFrame\n\"\"\"\nimport pandas as pd\n- data = []\nsep = kwargs.pop('sep', None)\n+ def gen_items():\nwith chain(*args, **kwar... | Python | Apache License 2.0 | levitsky/pyteomics | Try creating df from generator in pepxml.DataFrame |
377,522 | 11.04.2018 16:31:50 | -10,800 | 670568dbe583c6fa899d6432fc716652adb6ac14 | Pass kwargs to dataframe constructor in pepxml | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-3.5b0\n\\ No newline at end of file\n+3.5b1\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -343,12 ... | Python | Apache License 2.0 | levitsky/pyteomics | Pass kwargs to dataframe constructor in pepxml |
377,522 | 26.04.2018 19:26:03 | -10,800 | 9b652bed505ef7f8d8d95c552caa1ee83c23debe | Draft protxml parser | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/_schema_defaults.py",
"new_path": "pyteomics/_schema_defaults.py",
"diff": "+_protxml_schema_defaults = {'bools': set(),\n+ 'charlists': set(),\n+ 'floatlists': set(),\n+ 'floats': {('ASAPRatio', 'heavy2light_ratio_mean'),\n+ ('ASAPRatio', 'heavy2lig... | Python | Apache License 2.0 | levitsky/pyteomics | Draft protxml parser |
377,522 | 08.05.2018 16:42:17 | -10,800 | 657d55f5bba565adffc415da1a1095524338a982 | Fix modification_info flattening in protxml | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/protxml.py",
"new_path": "pyteomics/protxml.py",
"diff": "@@ -7,7 +7,7 @@ class ProtXML(xml.XML):\n_default_schema = _schema_defaults._protxml_schema_defaults\n# _default_version = None\n_default_iter_tag = 'protein_group'\n- _structures_to_flatten =... | Python | Apache License 2.0 | levitsky/pyteomics | Fix modification_info flattening in protxml |
377,522 | 09.05.2018 21:04:54 | -10,800 | 392f8ff67d49f471afda830e40e80f1ea9f8410a | Fix args[0] error in _file_reader | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -178,7 +178,10 @@ def _file_reader(_mode='r'):\n\"\"\"\n@wraps(_func)\ndef helper(*args, **kwargs):\n+ if args:\nreturn FileReader(args[0], _mode, _func, True,... | Python | Apache License 2.0 | levitsky/pyteomics | Fix args[0] error in _file_reader |
377,522 | 09.05.2018 21:14:10 | -10,800 | 6b43cb1a397efa07d5264658ae301dee2671e6c1 | Fix some consequences of auxiliary split | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/__init__.py",
"new_path": "pyteomics/auxiliary/__init__.py",
"diff": "try:\n- basestring\n+ basestring = basestring\nexcept NameError:\nbasestring = (str, bytes)\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/... | Python | Apache License 2.0 | levitsky/pyteomics | Fix some consequences of auxiliary split |
377,522 | 10.05.2018 00:07:27 | -10,800 | 74001d17e5692c4022bbe6c8a23ecd3e1171145e | Add project_urls in setup.py | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -25,6 +25,12 @@ setup(\nauthor_email = 'pyteomics@googlegroups.com',\nurl = 'http://hg.theorchromo.ru/pyteomics',\npackages = ['pyteomics', 'pyteomics.mass', 'pyteomics.openms'],\n+ project_urls = {\n+ 'Documentat... | Python | Apache License 2.0 | levitsky/pyteomics | Add project_urls in setup.py |
377,522 | 11.05.2018 19:26:58 | -10,800 | 74e1462f839bb56d4c968693969fc884cb972433 | Add auxiliary package in setup.py | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -24,7 +24,7 @@ setup(\nauthor = 'Anton Goloborodko & Lev Levitsky',\nauthor_email = 'pyteomics@googlegroups.com',\nurl = 'http://hg.theorchromo.ru/pyteomics',\n- packages = ['pyteomics', 'pyteomics.mass', 'pyteomi... | Python | Apache License 2.0 | levitsky/pyteomics | Add auxiliary package in setup.py |
377,522 | 14.05.2018 00:22:02 | -10,800 | 43f739347b7acea29ea0bdec8172f36ccc628dfd | Start protxml docs | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "This functionality will be changed in upcoming versions.\n+ - New module :py:mod:`pyteomics.protxml` for parsing of ProteinProphet output files.\n+\n- New parameter `huge_tree` in XML parser constructors and :py:fu... | Python | Apache License 2.0 | levitsky/pyteomics | Start protxml docs |
377,522 | 14.05.2018 01:48:19 | -10,800 | 8bfaf20233e13d499f5327929bc22f22acb850b4 | Make skip_empty_cvparam_values a class attr, add kwarg in mzid init | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzid.py",
"new_path": "pyteomics/mzid.py",
"diff": "@@ -112,6 +112,43 @@ class MzIdentML(xml.IndexSavingXML):\n'PeptideEvidence', 'SpectrumIdentificationItem', 'SearchDatabase',\n'DBSequence', 'SpectraData', 'Peptide'}\n+ def __init__(self, *args, **... | Python | Apache License 2.0 | levitsky/pyteomics | Make skip_empty_cvparam_values a class attr, add kwarg in mzid init |
377,522 | 14.05.2018 01:52:46 | -10,800 | e6185cebcc1eb29c64cfd8803e730b497ed9d8e3 | Move the init kwarg to xml | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzid.py",
"new_path": "pyteomics/mzid.py",
"diff": "@@ -112,43 +112,6 @@ class MzIdentML(xml.IndexSavingXML):\n'PeptideEvidence', 'SpectrumIdentificationItem', 'SearchDatabase',\n'DBSequence', 'SpectraData', 'Peptide'}\n- def __init__(self, *args, **... | Python | Apache License 2.0 | levitsky/pyteomics | Move the init kwarg to xml |
377,522 | 14.05.2018 19:06:19 | -10,800 | 9a749e46ed257a4955219367b2c97152cb80de2e | Tweak mzml for skip_empty_cvparam_values | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-3.5b1\n\\ No newline at end of file\n+3.5b2\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzml.py",
"new_path": "pyteomics/mzml.py",
"diff": "@@ -204,6 +204,... | Python | Apache License 2.0 | levitsky/pyteomics | Tweak mzml for skip_empty_cvparam_values |
377,522 | 14.05.2018 19:08:00 | -10,800 | d351c6f4f97dae94b56bd03749462cc929c7d309 | Fix dtype leak via ArrayConversionMixin | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/xml.py",
"new_path": "pyteomics/xml.py",
"diff": "@@ -1106,7 +1106,7 @@ class ArrayConversionMixin(BinaryDataArrayTransformer):\n_array_keys = ['m/z array', 'intensity array']\ndef __init__(self, *args, **kwargs):\n- self._dtype_dict.setdefault(None,... | Python | Apache License 2.0 | levitsky/pyteomics | Fix dtype leak via ArrayConversionMixin |
377,522 | 14.05.2018 19:24:10 | -10,800 | 770bf48699ad1d1e8fe59d992519cb336e6c5ad0 | Make retrieve_refs true by default in MzIdentML init | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzid.py",
"new_path": "pyteomics/mzid.py",
"diff": "@@ -112,6 +112,10 @@ class MzIdentML(xml.IndexSavingXML):\n'PeptideEvidence', 'SpectrumIdentificationItem', 'SearchDatabase',\n'DBSequence', 'SpectraData', 'Peptide'}\n+ def __init__(self, *args, **... | Python | Apache License 2.0 | levitsky/pyteomics | Make retrieve_refs true by default in MzIdentML init |
377,522 | 15.05.2018 17:48:51 | -10,800 | e11a77d3264f5b4871a9034d4714318e139e72f0 | Tweak pepxml test | [
{
"change_type": "MODIFY",
"old_path": "tests/data.py",
"new_path": "tests/data.py",
"diff": "@@ -18,7 +18,7 @@ def makeCA(arr):\narr = np.array(arr)\nreturn ComparableArray(arr.shape, arr.dtype, arr)\n-pepxml_spectra = [\n+pepxml_results = [\n{'spectrum': 'pps_sl20060731_18mix_25ul_r1_1154456409.01... | Python | Apache License 2.0 | levitsky/pyteomics | Tweak pepxml test |
377,522 | 15.05.2018 18:10:01 | -10,800 | 2f10d935522f2dfbbb2a1b7f741169dbe2e7ce64 | Start protxml test | [
{
"change_type": "MODIFY",
"old_path": "tests/data.py",
"new_path": "tests/data.py",
"diff": "@@ -1655,3 +1655,533 @@ ms1_header = {'CreationDate': 'Sat Jun 03 15:25:10 2017',\n'Extractor version': 'Xcalibur',\n'Extractor': 'ProteoWizard',\n'Source file': 'Set 1. B2 at 193 nm RT.RAW'}\n+\n+protxml_r... | Python | Apache License 2.0 | levitsky/pyteomics | Start protxml test |
377,522 | 21.05.2018 00:48:36 | -10,800 | 9dd17952e094adb28e53661507bc4d7745aea53a | Add fdr, qvalues and filter for protxml | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-3.5b2\n\\ No newline at end of file\n+3.5b3\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/protxml.py",
"new_path": "pyteomics/protxml.py",
"diff": "@@ -73,6 ... | Python | Apache License 2.0 | levitsky/pyteomics | Add fdr, qvalues and filter for protxml |
377,522 | 21.05.2018 01:53:16 | -10,800 | fe6f539b576aeaaf3abf18a5613f6bb2c5dd8606 | ProtXML doc update | [
{
"change_type": "MODIFY",
"old_path": "doc/source/api/protxml.rst",
"new_path": "doc/source/api/protxml.rst",
"diff": "----------\nfiles : iterable\nIterable of file names or file objects.\n+\n+ .. autofunction:: filter\n+\n+ .. py:function :: filter.chain(*files, **kwargs)\n+\n+ Chain :py:func:`fi... | Python | Apache License 2.0 | levitsky/pyteomics | ProtXML doc update |
377,522 | 21.05.2018 14:36:17 | -10,800 | af34b56df5caac345c1508302b705ccabcec5490 | Add prefix to is_decoy, add filter_df | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/protxml.py",
"new_path": "pyteomics/protxml.py",
"diff": "@@ -152,10 +152,11 @@ def read(source, read_schema=False, iterative=True, **kwargs):\nreturn ProtXML(source, read_schema=read_schema, iterative=iterative)\nchain = aux._make_chain(read, 'read'... | Python | Apache License 2.0 | levitsky/pyteomics | Add prefix to is_decoy, add filter_df |
377,522 | 21.05.2018 18:06:34 | -10,800 | 11702baa40b32a4eecb4ac3f116424c7b7a637dd | Use unittest assertions in new mzml test | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mzml.py",
"new_path": "tests/test_mzml.py",
"diff": "@@ -114,9 +114,9 @@ class MzmlTest(unittest.TestCase):\nderefed = list(reader.iterfind(\"instrumentConfiguration\", retrieve_refs=True))\nreader.reset()\nraw = list(reader.iterfind(\"instrumentCon... | Python | Apache License 2.0 | levitsky/pyteomics | Use unittest assertions in new mzml test |
377,522 | 21.05.2018 19:38:18 | -10,800 | bc4d819fed6c8ab0495aa7bbb4f2d2c88d19ab24 | Add XML._retrieve_refs_enabled | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/xml.py",
"new_path": "pyteomics/xml.py",
"diff": "@@ -123,6 +123,7 @@ class XML(FileReader):\n_default_id_attr = 'id'\n_huge_tree = False\n_skip_empty_cvparam_values = False\n+ _retrieve_refs_enabled = None # only some subclasses implement this\n# Co... | Python | Apache License 2.0 | levitsky/pyteomics | Add XML._retrieve_refs_enabled |
377,522 | 21.05.2018 22:28:20 | -10,800 | 888eb20eb90999996980e9fdc070fb27889f042e | Add tests for protxml.filter_df and DataFrame | [
{
"change_type": "MODIFY",
"old_path": "tests/test_protxml.py",
"new_path": "tests/test_protxml.py",
"diff": "@@ -3,7 +3,7 @@ import pyteomics\npyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]\nfrom itertools import product\nimport unittest\n-from pyte... | Python | Apache License 2.0 | levitsky/pyteomics | Add tests for protxml.filter_df and DataFrame |
377,522 | 22.05.2018 17:37:48 | -10,800 | 364792a3105cf1e57cbca62190385b5f790d5e18 | Doc update on +1 | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/target_decoy.py",
"new_path": "pyteomics/auxiliary/target_decoy.py",
"diff": "@@ -261,9 +261,16 @@ def _make_qvalues(read, is_decoy, key):\ncorrection : int or float, keyword only, optional\nPossible values are 0, 1 and 2, or floating point... | Python | Apache License 2.0 | levitsky/pyteomics | Doc update on +1 |
377,522 | 22.05.2018 18:05:48 | -10,800 | 30a0b48adf3a260b923277c7d81bd4e4b0877e18 | Add PeptideProphet support in pepxml.DataFrame | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "- New module :py:mod:`pyteomics.protxml` for parsing of ProteinProphet output files.\n+ - Add PeptideProphet analysis information to the output of :py:func:`pyteomics.pepxml.DataFrame`.\n+\n- New parameter `huge_tr... | Python | Apache License 2.0 | levitsky/pyteomics | Add PeptideProphet support in pepxml.DataFrame |
377,522 | 22.05.2018 18:25:50 | -10,800 | a70603ebb3a2a01662d7967023f2656536270cbd | Add iProphet | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "- New module :py:mod:`pyteomics.protxml` for parsing of ProteinProphet output files.\n- - Add PeptideProphet analysis information to the output of :py:func:`pyteomics.pepxml.DataFrame`.\n+ - Add PeptideProphet and ... | Python | Apache License 2.0 | levitsky/pyteomics | Add iProphet |
377,522 | 23.05.2018 19:08:11 | -10,800 | 643f683151411c0ed677eddf203cff6527377e45 | Start decoy_prefix and decoy_suffix, pepxml seems working | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "- Preserve accession information on cvParam elements in mzML parser.\nDictionaries produced by the parser can now be queried by accession using\n:py:func:`pyteomics.auxiliary.cvquery`.\n- (Contributed by J. Klein)\... | Python | Apache License 2.0 | levitsky/pyteomics | Start decoy_prefix and decoy_suffix, pepxml seems working |
377,522 | 24.05.2018 17:55:38 | -10,800 | a3c88dc49a182507b027d73b251b88a167afe6b3 | Add decoy prefix and suffix everywhere | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-3.5b5\n\\ No newline at end of file\n+3.5b6\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/target_decoy.py",
"new_path": "pyteomics/auxiliary/target_dec... | Python | Apache License 2.0 | levitsky/pyteomics | Add decoy prefix and suffix everywhere |
377,522 | 25.05.2018 17:38:47 | -10,800 | 0866b3f6f7dfb5b5569f00e276e6850df00c1420 | Add more ion_types | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "If the standard :py:func:`is_decoy` function works for your files, you can use these parameters to\nspecify either the prefix or the suffix appended to the protein names in decoy entries.\n+ - New ion types in :py:... | Python | Apache License 2.0 | levitsky/pyteomics | Add more ion_types |
377,522 | 25.05.2018 18:51:50 | -10,800 | 31dd8ddadfbbea8336c648c3a4566c7159e3cf26 | Rename FDR to TDA in setup.py extras, add zip_safe=False | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -33,7 +33,7 @@ setup(\n},\nnamespace_packages = ['pyteomics'],\nextras_require = {'XML': ['lxml', 'numpy'],\n- 'FDR': ['numpy'],\n+ 'TDA': ['numpy'],\n'graphics': ['matplotlib'],\n'DF': ['pandas'],\n'Unimod': ['lx... | Python | Apache License 2.0 | levitsky/pyteomics | Rename FDR to TDA in setup.py extras, add zip_safe=False |
377,522 | 28.05.2018 14:20:26 | -10,800 | 2747b67ad84427e73dfcc3187d06fb6ee49a88ce | Add decoy_prefix and decoy_suffix to protxml tests. Version 3.5 | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-3.5b6\n\\ No newline at end of file\n+3.5\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "tests/test_protxml.py",
"new_path": "tests/test_protxml.py",
"diff": "@@ -41,6 ... | Python | Apache License 2.0 | levitsky/pyteomics | Add decoy_prefix and decoy_suffix to protxml tests. Version 3.5 |
377,522 | 28.05.2018 14:38:17 | -10,800 | 5ba71c6bfd540d6377b360284d22c1dd6851c15c | Set homepage to documentation | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -23,10 +23,10 @@ setup(\nlong_description = long_description,\nauthor = 'Anton Goloborodko & Lev Levitsky',\nauthor_email = 'pyteomics@googlegroups.com',\n- url = 'http://hg.theorchromo.ru/pyteomics',\n+ url = 'ht... | Python | Apache License 2.0 | levitsky/pyteomics | Set homepage to documentation |
377,522 | 28.05.2018 19:07:10 | -10,800 | 4c3af7f730cdea1ee8908adb52373d2d8a67f4f0 | Remove links to pythonhosted | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-3.5\n\\ No newline at end of file\n+3.5.0\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -19,14 +19,14 @@ with open('READ... | Python | Apache License 2.0 | levitsky/pyteomics | Remove links to pythonhosted |
377,522 | 28.05.2018 19:17:08 | -10,800 | e9320992106eaa2eaa950bbdeca50d33f1b9a942 | Bump version to update doc link on PyPI | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "+3.5.1\n+-----\n+\n+Technical release to update the package metadata on PyPI.\n+Project documentation on pythonhosted.org has been deleted.\n+Latest documentation is available at: https://pyteomics.readthedocs.io/.... | Python | Apache License 2.0 | levitsky/pyteomics | Bump version to update doc link on PyPI |
377,522 | 30.05.2018 19:31:36 | -10,800 | 81c152e8fa567380819cba9ba5646dc05bee726d | Add parameter semi in parser.cleave | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "+3.5.2\n+-----\n+\n+ - Add parameter `semi` in :py:func:`pyteomics.parser.cleave`.\n+\n3.5.1\n-----\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/parser.py",
"new_path": "pyteomics/parser.... | Python | Apache License 2.0 | levitsky/pyteomics | Add parameter semi in parser.cleave |
377,522 | 31.05.2018 17:46:36 | -10,800 | b50160b158286f357e11c03f862103321c64089d | Add shields.io badges to readme | [
{
"change_type": "MODIFY",
"old_path": "README",
"new_path": "README",
"diff": ":target: http://pyteomics.readthedocs.io/en/latest/?badge=latest\n:alt: Documentation Status\n+.. image:: https://img.shields.io/pypi/v/pyteomics.svg\n+ :target: https://pypi.org/project/pyteomics/\n+ :alt: PyPI\n+\n+.. ... | Python | Apache License 2.0 | levitsky/pyteomics | Add shields.io badges to readme |
377,522 | 01.06.2018 00:38:53 | -10,800 | 6ea9288395b5af7420bfc57791b9e0243b9a8214 | Change license badge | [
{
"change_type": "MODIFY",
"old_path": "README",
"new_path": "README",
"diff": ":target: https://pyteomics.readthedocs.io/\n:alt: Read the Docs (latest)\n-.. image:: https://img.shields.io/pypi/l/pyteomics.svg\n+.. image:: https://img.shields.io/aur/license/python-pyteomics.svg\n:target: https://www... | Python | Apache License 2.0 | levitsky/pyteomics | Change license badge |
377,522 | 01.06.2018 00:45:37 | -10,800 | 84839d4137a7911fcd206016e0e349f2a5263e2f | Remove rotten link in INFO | [
{
"change_type": "MODIFY",
"old_path": "INFO",
"new_path": "INFO",
"diff": "@@ -3,10 +3,10 @@ Useful Links\nPyteomics is hosted at the following sites:\n- - Python package @ Python Package Index: https://pypi.org/project/pyteomics\n- - project documentation @ Python.org: http://pythonhosted.org/pyte... | Python | Apache License 2.0 | levitsky/pyteomics | Remove rotten link in INFO |
377,522 | 07.06.2018 19:17:11 | -10,800 | 700f71fb069e537467ca910d9c64b2570ef026eb | Add encoding parameter in file_writer | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -4,7 +4,6 @@ import codecs\nfrom functools import wraps\nfrom contextlib import contextmanager\n-\ntry:\nbasestring\nexcept NameError:\n@@ -193,11 +192,12 @@ d... | Python | Apache License 2.0 | levitsky/pyteomics | Add encoding parameter in file_writer |
377,522 | 08.06.2018 01:13:59 | -10,800 | 5b769efd23bb018d5561fc8c1ff08948c8f43d05 | Speed up mgf.write by using np.savetxt | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "- Add parameter `semi` in :py:func:`pyteomics.parser.cleave`.\n+ - Add new parameter `encoding` in file writers.\n+\n+ - Add new parameters `write_charges` and `use_numpy` in :py:func:`pyteomics.mgf.write`.\n+ Spee... | Python | Apache License 2.0 | levitsky/pyteomics | Speed up mgf.write by using np.savetxt |
377,522 | 08.06.2018 15:48:50 | -10,800 | 72f863b429f681d49a6c6473bf6dde5c5cbee5a5 | Remove pkgbuild (it is tracked in the AUR repo) | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-3.5.2\n------\n+dev\n+---\n- Add parameter `semi` in :py:func:`pyteomics.parser.cleave`.\n"
},
{
"change_type": "DELETE",
"old_path": "PKGBUILD",
"new_path": null,
"diff": "-# Maintainer: Lev L... | Python | Apache License 2.0 | levitsky/pyteomics | Remove pkgbuild (it is tracked in the AUR repo) |
377,522 | 13.06.2018 01:36:44 | -10,800 | 86f0659f4eb6a70d5264ebde0db67344afc392d4 | Start with the indexing version of mgf parser | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/__init__.py",
"new_path": "pyteomics/auxiliary/__init__.py",
"diff": "@@ -15,7 +15,7 @@ from .constants import _nist_mass\nfrom .file_helpers import (\n_file_obj, _keepstate, _keepstate_method, IteratorContextManager,\n- FileReader, _file_r... | Python | Apache License 2.0 | levitsky/pyteomics | Start with the indexing version of mgf parser |
377,522 | 20.06.2018 17:34:38 | -10,800 | 38ac856b0b41ba60e89653546e6201a934f92146 | Set default encoding to None for mgf.MGF for better performance | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -78,7 +78,7 @@ class MGFBase():\n}\n_array_keys = ['m/z array', 'intensity array', 'charge array']\n- def __init__(self, source=None, use_header=True, convert_arrays=2, read_charges=True, dtype=Non... | Python | Apache License 2.0 | levitsky/pyteomics | Set default encoding to None for mgf.MGF for better performance |
377,522 | 20.06.2018 18:49:35 | -10,800 | dc8e78013bc4250711e8894d2c3b8e12505f3172 | Add classmethod scan and fixes to IndexedTextReader | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -184,7 +184,7 @@ class IndexedTextReader(FileReader):\nif delimiter is not None:\nself.delimiter = delimiter\nif label is not None:\n- self.record_label = labe... | Python | Apache License 2.0 | levitsky/pyteomics | Add classmethod scan and fixes to IndexedTextReader |
377,522 | 21.06.2018 18:31:59 | -10,800 | 7baa0828faada104b1c98579a7b53d2042b59f05 | Fix encoding-related annoyances | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -64,6 +64,7 @@ try:\nexcept ImportError:\nnp = None\nimport itertools as it\n+import sys\nclass MGFBase():\n\"\"\"Abstract class representing an MGF file. Subclasses implement different approaches ... | Python | Apache License 2.0 | levitsky/pyteomics | Fix encoding-related annoyances |
377,522 | 21.06.2018 19:13:48 | -10,800 | 79bb488d45681422134a1784e41d2c08a31b6705 | Add a primitive get_spectrum test for mgf | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mgf.py",
"new_path": "tests/test_mgf.py",
"diff": "@@ -4,7 +4,7 @@ import pyteomics\npyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]\nimport tempfile\nimport unittest\n-from pyteomics.mgf import read,... | Python | Apache License 2.0 | levitsky/pyteomics | Add a primitive get_spectrum test for mgf |
377,522 | 02.07.2018 19:38:23 | -10,800 | 3dd0b30078ebb60eb0d8e6c8a7e0f8832fc4a9d7 | Remove IndexedTextReader.scan and use_index argument | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -177,7 +177,7 @@ class IndexedTextReader(FileReader):\nlabel = None\nblock_size = 1000000\n- def __init__(self, source, func, pass_file, args, kwargs, encoding... | Python | Apache License 2.0 | levitsky/pyteomics | Remove IndexedTextReader.scan and use_index argument |
377,522 | 03.07.2018 17:04:08 | -10,800 | de0436e6f515765a89e5d2602e29f7b8172eca38 | Add dispatching based on use_index to mgf.read, update docs | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "@@ -8,6 +8,12 @@ dev\n- Add new parameters `write_charges` and `use_numpy` in :py:func:`pyteomics.mgf.write`.\nSpeed up the writing when :py:mod:`numpy` is available.\n+ - New class :py:class:`pyteomics.mgf.Indexed... | Python | Apache License 2.0 | levitsky/pyteomics | Add dispatching based on use_index to mgf.read, update docs |
377,522 | 09.07.2018 22:31:18 | -10,800 | b1bc2d19fdfd6f940ec9bc19ce79a4dba1c0c742 | Add exception logic to parser.cleave to address issue | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "dev\n---\n- - Add parameter `semi` in :py:func:`pyteomics.parser.cleave`.\n+ - Add parameters `semi` and `exception` in :py:func:`pyteomics.parser.cleave`.\n- Add new parameter `encoding` in file writers.\n"
},
... | Python | Apache License 2.0 | levitsky/pyteomics | Add exception logic to parser.cleave to address issue #29 |
377,522 | 10.07.2018 23:24:59 | -10,800 | b6ecf6a9ab92ec93bc8874d1c216d98b361ef0af | First draft of IndexedFASTA, update fasta tests | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -249,6 +249,10 @@ class IndexedTextReader(FileReader):\nassert last_label is None\nreturn index\n+ def _read_lines_from_offsets(self, start, end):\n+ self._sou... | Python | Apache License 2.0 | levitsky/pyteomics | First draft of IndexedFASTA, update fasta tests |
377,522 | 10.07.2018 23:45:46 | -10,800 | 1bda3108ea9544b4f12768daf36a727674f851ac | Remove the use of regex in record delimiters | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -192,9 +192,8 @@ class IndexedTextReader(FileReader):\ndef _chunk_iterator(self):\nfh = self._source.file\ndelim = remove_bom(self.delimiter.encode(self.encodi... | Python | Apache License 2.0 | levitsky/pyteomics | Remove the use of regex in record delimiters |
377,522 | 11.07.2018 01:35:48 | -10,800 | 17e572bfeb1ac3f37a5b8a628ffb434147af37eb | Parametrize label group, use it as key in offset index | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -176,9 +176,12 @@ class IndexedTextReader(FileReader):\ndelimiter = None\nlabel = None\nblock_size = 1000000\n+ label_group = 1\n- def __init__(self, source, f... | Python | Apache License 2.0 | levitsky/pyteomics | Parametrize label group, use it as key in offset index |
377,522 | 11.07.2018 01:40:47 | -10,800 | 318e74d6853bc02fc2daf9b1d938d67bba5d6fd8 | Bring back parser arg in IndexedFASTA | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -144,11 +144,11 @@ class IndexedFASTA(aux.IndexedTextReader, FASTABase):\ndelimiter = '>'\nlabel = r'^>(.*)'\n- def __init__(self, source, ignore_comments=False, encoding='utf-8', block_size=No... | Python | Apache License 2.0 | levitsky/pyteomics | Bring back parser arg in IndexedFASTA |
377,522 | 11.07.2018 18:13:45 | -10,800 | 1b19872f850b9294073f040f01196de9ca25a82f | Draft TwoLayerIndexedFASTA class | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -187,6 +187,35 @@ class IndexedFASTA(aux.IndexedTextReader, FASTABase):\nreturn self._entry_from_offsets(*offsets)\n+class TwoLayerIndexedFASTA(IndexedFASTA):\n+ header_group = 1\n+ def __init_... | Python | Apache License 2.0 | levitsky/pyteomics | Draft TwoLayerIndexedFASTA class |
377,522 | 12.07.2018 00:49:59 | -10,800 | 57d099f848bd1ed1c3ad2400ff43216391c37ccb | Fill in some missing docstrings, update tests in fasta | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "@@ -13,6 +13,20 @@ dev\nThe old, sequential parser is preserved under its name, :py:class:`pyteomics.mgf.MGF`.\nThe function :py:func:`pyteomics.mgf.read` now returns an instance of one of the two classes,\nbased o... | Python | Apache License 2.0 | levitsky/pyteomics | Fill in some missing docstrings, update tests in fasta |
377,522 | 12.07.2018 19:34:37 | -10,800 | 64ea52d3ebdf6bdce83698cc5315f5dfd34263bd | Make header_pattern optional in TwoLayerIndexedFASTA | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -109,7 +109,7 @@ class FASTABase():\n\"\"\"Abstract base class for FASTA file parsers.\nCan be used for type checking.\n\"\"\"\n- parser = staticmethod(lambda x: x)\n+ parser = None\n_ignore_co... | Python | Apache License 2.0 | levitsky/pyteomics | Make header_pattern optional in TwoLayerIndexedFASTA |
377,522 | 19.07.2018 01:02:21 | -10,800 | 8102351cf14499908973d7d55d2d5410e6bd7cbf | Add format-specific fasta parser classes; change flavour to flavor in parse (sorry) | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -350,27 +350,152 @@ class TwoLayerIndexedFASTA(IndexedFASTA):\nreturn super(TwoLayerIndexedFASTA, self).get_entry(header)\n+class FlavoredMixin():\n+ \"\"\"Parser aimed at a specific FASTA flav... | Python | Apache License 2.0 | levitsky/pyteomics | Add format-specific fasta parser classes; change flavour to flavor in parse (sorry) |
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