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 | 19.07.2018 21:49:44 | -10,800 | 8f47532c8e03876ee722ec912673409b3cfbf5e3 | Reduce code duplication with a class decorator | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -374,16 +374,25 @@ class UniProtMixin(FlavoredMixin):\n_intify(info, ('PE', 'SV'))\nreturn info\n-class UniProt(UniProtMixin, FASTA):\n+\n+def _add_init(cls):\n+ \"\"\"Add and __init__ method t... | Python | Apache License 2.0 | levitsky/pyteomics | Reduce code duplication with a class decorator |
377,522 | 20.07.2018 00:15:10 | -10,800 | 479556878748bf0ae9a77e7321c1aabc78632c3d | Add ncbi fasta parser | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "@@ -27,6 +27,7 @@ dev\n- :py:class:`pyteomics.fasta.UniRef`;\n- :py:class:`pyteomics.fasta.UniMes`;\n- :py:class:`pyteomics.fasta.SPD`;\n+ - :py:class:`pyteomics.fasta.NCBI`;\n- :py:class:`pyteomics.fasta.IndexedFA... | Python | Apache License 2.0 | levitsky/pyteomics | Add ncbi fasta parser |
377,522 | 20.07.2018 21:53:37 | -10,800 | c931cb4eeac64b17980fffb2cc20894a9a95c460 | Unify mode checking in mgf.read and fasta.read | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/__init__.py",
"new_path": "pyteomics/auxiliary/__init__.py",
"diff": "@@ -15,7 +15,8 @@ from .constants import _nist_mass\nfrom .file_helpers import (\n_file_obj, _keepstate, _keepstate_method, IteratorContextManager,\n- FileReader, Indexed... | Python | Apache License 2.0 | levitsky/pyteomics | Unify mode checking in mgf.read and fasta.read |
377,522 | 14.08.2018 00:02:49 | -10,800 | c73644b0b8f338aded599e9473681315cc0dd05c | Draft implementation of multiprocessing
Change XML byte offset indexes (TagSpecificXMLByteIndex) to use strings; ByteCountingXMLScanner still uses bytes | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/__init__.py",
"new_path": "pyteomics/auxiliary/__init__.py",
"diff": "@@ -16,7 +16,7 @@ from .constants import _nist_mass\nfrom .file_helpers import (\n_file_obj, _keepstate, _keepstate_method, IteratorContextManager,\nFileReader, IndexedTe... | Python | Apache License 2.0 | levitsky/pyteomics | Draft implementation of multiprocessing
Change XML byte offset indexes (TagSpecificXMLByteIndex) to use strings; ByteCountingXMLScanner still uses bytes |
377,522 | 14.08.2018 00:47:26 | -10,800 | 1d4f65516a7be9f0034854b9fc8329147360a3bf | Ensure the strings are encoded again in ByteCountingXMLScanner | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/xml.py",
"new_path": "pyteomics/xml.py",
"diff": "@@ -782,10 +782,13 @@ class ByteCountingXMLScanner(_file_obj):\n\"\"\"\nif lookup_id_key_mapping is None:\nlookup_id_key_mapping = {}\n+ lookup_id_key_mapping = {ensure_bytes_single(key): ensure_bytes... | Python | Apache License 2.0 | levitsky/pyteomics | Ensure the strings are encoded again in ByteCountingXMLScanner |
377,522 | 14.08.2018 00:47:47 | -10,800 | d3bf6ab8a8e3c608f9370c370894639ae4a934d1 | Make pepxml use multiprocessing | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -444,6 +444,7 @@ try:\n_NPROC = mp.cpu_count()\nexcept NotImplementedError:\n_NPROC = 4\n+_QUEUE_TIMEOUT = 4\nclass TaskMappingMixin(object):\ndef map(self, it... | Python | Apache License 2.0 | levitsky/pyteomics | Make pepxml use multiprocessing |
377,522 | 14.08.2018 23:56:42 | -10,800 | 21b80a7ede2ee1a8a8fdfec26e3bfbdcef8ffa30 | Make IndexedMGF picklable | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -219,7 +219,7 @@ class IndexedTextReader(FileReader):\nlabel_group = 1\ndef __init__(self, source, func, pass_file, args, kwargs, encoding='utf-8', block_size=... | Python | Apache License 2.0 | levitsky/pyteomics | Make IndexedMGF picklable |
377,522 | 15.08.2018 01:01:05 | -10,800 | f7aef0a9497e98ea2e23256c32521af07fd2e9c5 | Add multiprocessing for IndexedMGF | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -509,3 +509,6 @@ class TaskMappingMixin(object):\nfeeder_thread.join()\nfor worker in workers:\nworker.join()\n+\n+ def _default_iterator(self):\n+ return iter... | Python | Apache License 2.0 | levitsky/pyteomics | Add multiprocessing for IndexedMGF |
377,522 | 15.08.2018 20:40:11 | -10,800 | 7eb748cfa90b619b51fbd2233feb36e996bdf46e | Add multiprocessing to fasta indexed classes | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": ":py:func:`pyteomics.fasta.read` now returns an instance of one of these classes,\ndepending on the arguments `use_index` and `flavor`.\n+ - Multiprocessing support: all indexed XML and text file parsers now expose ... | Python | Apache License 2.0 | levitsky/pyteomics | Add multiprocessing to fasta indexed classes |
377,522 | 15.08.2018 22:15:35 | -10,800 | e11ebe889386c670e3c855658684aeb5c7d3e3bc | Add sensible len() and membership tests for indexed classes | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -209,6 +209,7 @@ class FileReader(IteratorContextManager):\ndef remove_bom(bstr):\nreturn bstr.replace(codecs.BOM_LE, b'').lstrip(b\"\\x00\")\n+\nclass Indexed... | Python | Apache License 2.0 | levitsky/pyteomics | Add sensible len() and membership tests for indexed classes |
377,522 | 15.08.2018 23:09:50 | -10,800 | 75e56a491501f67e011ebafe9546e20e7c1e7ab5 | Move unpickling of specs to run() in FileReadingProcess | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -432,14 +432,11 @@ class FileReadingProcess(mp.Process):\nThe reader class must support the :py:meth:`__getitem__` dict-like lookup.\n\"\"\"\ndef __init__(self... | Python | Apache License 2.0 | levitsky/pyteomics | Move unpickling of specs to run() in FileReadingProcess |
377,522 | 16.08.2018 16:21:01 | -10,800 | bbab5701ae5ee0480bd076bab3a6ed2ac3e62537 | Increase queue sizes | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -486,8 +486,8 @@ class TaskMappingMixin(object):\nreader_spec, target_spec, args_spec, kwargs_spec = serialized\ndone_event = mp.Event()\n- in_queue = mp.Queue... | Python | Apache License 2.0 | levitsky/pyteomics | Increase queue sizes |
377,522 | 16.08.2018 23:10:06 | -10,800 | 1567711138f23d4dbd7bf3fc2553dc82491c3a8b | Index by spectrum titles in pepXML | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -105,7 +105,8 @@ class PepXML(xml.MultiProcessingXML):\n_default_version = '1.15'\n_default_iter_tag = 'spectrum_query'\n_indexed_tags = {'spectrum_query'}\n- _indexed_tag_keys = {'spectrum_q... | Python | Apache License 2.0 | levitsky/pyteomics | Index by spectrum titles in pepXML |
377,522 | 17.08.2018 01:29:07 | -10,800 | e3d1d077b5d9a9d8e28b7eaf0140973c7ef1b6a5 | Update conversion rules in pepXML | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -109,8 +109,9 @@ class PepXML(xml.MultiProcessingXML):\n_default_id_attr = 'spectrum'\n_structures_to_flatten = {'search_score_summary', 'modification_info'}\n# attributes which contain uncon... | Python | Apache License 2.0 | levitsky/pyteomics | Update conversion rules in pepXML |
377,522 | 23.08.2018 15:10:12 | -10,800 | fd9e67cd4d949d02ac3d83661aa6ac8348f3fecc | Fix fasta picklability for Python 2 | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -213,25 +213,10 @@ class FASTA(aux.FileReader, FASTABase):\ndef _reconstruct(cls, args, kwargs):\n- return cls(*args, **kwargs, _skip_index=True)\n+ kwargs['_skip_index'] = True\n+ return cls(*... | Python | Apache License 2.0 | levitsky/pyteomics | Fix fasta picklability for Python 2 |
377,522 | 23.08.2018 15:24:53 | -10,800 | 4faa1a339f4b1b87f14c3b31742a127c790a171c | Add test for map() in fasta | [
{
"change_type": "MODIFY",
"old_path": "tests/test_fasta.py",
"new_path": "tests/test_fasta.py",
"diff": "@@ -53,6 +53,12 @@ class FastaTest(unittest.TestCase):\nself.assertEqual(reader2.block_size, reader.block_size)\nself.assertEqual(self.fasta_entries_short[2], reader2['4'])\n+ def test_mp_map(se... | Python | Apache License 2.0 | levitsky/pyteomics | Add test for map() in fasta |
377,530 | 28.08.2018 13:37:57 | 18,000 | 9196992cb4a1aa1506dfe344ed6733a548b9dba9 | Swapping the regex for pepsin1.3 and pepsin2.0 to match the description from Expasy | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/parser.py",
"new_path": "pyteomics/parser.py",
"diff": "@@ -639,10 +639,10 @@ expasy_rules = {\n'iodosobenzoic acid': r'W',\n'lysc': r'K',\n'ntcb': r'\\w(?=C)',\n- 'pepsin ph1.3': r'((?<=[^HKR][^P])[^R](?=[FLWY][^P]))|'\n- r'((?<=[^HKR][^P])[FLWY](?=... | Python | Apache License 2.0 | levitsky/pyteomics | Swapping the regex for pepsin1.3 and pepsin2.0 to match the description from Expasy |
377,522 | 05.09.2018 02:36:04 | -10,800 | 41b8982eb599382fc62f411a1b5715cb02c4892e | Rename PEFF to IndexedPEFF | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/peff.py",
"new_path": "pyteomics/peff.py",
"diff": "@@ -18,7 +18,7 @@ building on top of the :class:`~.TwoLayerIndexedFASTA` reader.\nAvailable classes:\n- :py:class:`PEFF` - Parse a PEFF format file in binary-mode, supporting\n+ :py:class:`IndexedPE... | Python | Apache License 2.0 | levitsky/pyteomics | Rename PEFF to IndexedPEFF |
377,522 | 05.09.2018 02:49:32 | -10,800 | 9c9d2858fc1b2b02d7bc7d9103b65c3003d6d4be | Add a doc page for peff | [
{
"change_type": "MODIFY",
"old_path": "doc/source/api.rst",
"new_path": "doc/source/api.rst",
"diff": "@@ -15,6 +15,7 @@ Contents:\napi/achrom\napi/electrochem\napi/fasta\n+ api/peff\napi/mzml\napi/mzxml\napi/mgf\n"
},
{
"change_type": "MODIFY",
"old_path": "doc/source/api/fasta.rst",
... | Python | Apache License 2.0 | levitsky/pyteomics | Add a doc page for peff |
377,522 | 05.09.2018 23:15:20 | -10,800 | 5af5be1d68a626d00221442398f6b2d1e829b298 | Remove _skip_empty_cvparam_values | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "- New module :py:mod:`pyteomics.peff` implements the :py:class:`IndexedPEFF` parser for protein databases\nin the new PSI standard format, `PEFF <http://www.psidev.info/peff>`_.\n+ - Removed parameter `skip_empty_c... | Python | Apache License 2.0 | levitsky/pyteomics | Remove _skip_empty_cvparam_values |
377,522 | 18.09.2018 19:28:52 | -10,800 | 3946568029a3bcaefdb785fbad0ca10a1214ba62 | Fix in CVQueryEngine._is_empty | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/structures.py",
"new_path": "pyteomics/auxiliary/structures.py",
"diff": "@@ -289,7 +289,7 @@ class CVQueryEngine(object):\ndef _is_empty(self, value):\nif isinstance(value, basestring):\n- return value != ''\n+ return value == ''\nreturn F... | Python | Apache License 2.0 | levitsky/pyteomics | Fix in CVQueryEngine._is_empty |
377,522 | 20.09.2018 19:29:12 | -10,800 | 40a9f83eaa813239bcb2d3053a0388ec5e3f8407 | Remove unused flat index classes | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/xml.py",
"new_path": "pyteomics/xml.py",
"diff": "@@ -871,58 +871,6 @@ class TagSpecificXMLByteIndex(object):\nreturn indexer.offsets\n-class FlatOffsetIndex(HierarchicalOffsetIndex):\n- def __len__(self):\n- return len(self.mapping)\n-\n- def find(s... | Python | Apache License 2.0 | levitsky/pyteomics | Remove unused flat index classes |
377,522 | 25.09.2018 15:55:53 | -10,800 | da39914648c74ab3371d241e1a17bbe8b3e487c9 | Fix IndexedMGF for files with zero spectra | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -274,7 +274,10 @@ class IndexedMGF(aux.TaskMappingMixin, aux.IndexedTextReader, MGFBase):\n@aux._keepstate_method\ndef _read_header(self):\n+ try:\nfirst = next(v for v in self._offset_index.values... | Python | Apache License 2.0 | levitsky/pyteomics | Fix IndexedMGF for files with zero spectra |
377,522 | 01.10.2018 17:57:41 | -10,800 | bcc3e23dbdffaf92dbae4f2a228b77c28653b5fd | Add IndexedReaderMixin with common rich indexing methods | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/__init__.py",
"new_path": "pyteomics/auxiliary/__init__.py",
"diff": "@@ -15,7 +15,8 @@ from .constants import _nist_mass\nfrom .file_helpers import (\n_file_obj, _keepstate, _keepstate_method, IteratorContextManager,\n- FileReader, Indexed... | Python | Apache License 2.0 | levitsky/pyteomics | Add IndexedReaderMixin with common rich indexing methods |
377,522 | 04.10.2018 17:28:03 | -10,800 | 88f9507c3399cbba79887efaa344e27b3e891aea | Add retention time indexing | [
{
"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, Indexed... | Python | Apache License 2.0 | levitsky/pyteomics | Add retention time indexing |
377,522 | 04.10.2018 17:58:04 | -10,800 | 045d6995dee85a64ea9e82b81d9ca88a5e65d4bc | Add warning patch in auxiliary | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-4.0.dev3\n\\ No newline at end of file\n+4.0.dev4\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/__init__.py",
"new_path": "pyteomics/auxiliary/__init__... | Python | Apache License 2.0 | levitsky/pyteomics | Add warning patch in auxiliary |
377,525 | 08.10.2018 03:47:33 | 0 | ad6b512ab210f864c82dbb6443c44f167701ea60 | change default fasta delimiter and label to support '>' characters in protein description | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -216,8 +216,8 @@ def _reconstruct(cls, args, kwargs):\nclass IndexedFASTA(aux.TaskMappingMixin, aux.IndexedTextReader, FASTABase):\n\"\"\"Indexed FASTA parser. Supports direct indexing by match... | Python | Apache License 2.0 | levitsky/pyteomics | change default fasta delimiter and label to support '>' characters in protein description |
377,525 | 08.10.2018 05:09:05 | 0 | fd909ac8367e686d56061cf0509ba89e539be313 | fasta.py edited online with Bitbucket | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -217,7 +217,7 @@ def _reconstruct(cls, args, kwargs):\nclass IndexedFASTA(aux.TaskMappingMixin, aux.IndexedTextReader, FASTABase):\n\"\"\"Indexed FASTA parser. Supports direct indexing by match... | Python | Apache License 2.0 | levitsky/pyteomics | fasta.py edited online with Bitbucket |
377,522 | 08.10.2018 19:31:43 | -10,800 | b8b319f3ab77f85a4adf2d9f7c1fe4f43e29a277 | Tweak mgf and fasta label patterns to strip whitespace at the end | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -217,7 +217,7 @@ def _reconstruct(cls, args, kwargs):\nclass IndexedFASTA(aux.TaskMappingMixin, aux.IndexedTextReader, FASTABase):\n\"\"\"Indexed FASTA parser. Supports direct indexing by match... | Python | Apache License 2.0 | levitsky/pyteomics | Tweak mgf and fasta label patterns to strip whitespace at the end |
377,522 | 13.12.2018 17:29:26 | -10,800 | cbb79614296fbe729b01ee6ce3f8bd9a46a43903 | Amend IndexedMGF.__init__, fix MGF time indexing | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpers.py",
"diff": "@@ -889,13 +889,6 @@ class TaskMappingMixin(object):\n------\nobject\nThe work item returned by the target function.\n-\n- Deleted Parameters\n- -----------------... | Python | Apache License 2.0 | levitsky/pyteomics | Amend IndexedMGF.__init__, fix MGF time indexing |
377,522 | 14.12.2018 00:06:16 | -10,800 | a615604907310c02c5beafc033e294fd62c8154f | Fix and refactoring in ms1 | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -240,11 +240,14 @@ class IndexedMGF(aux.TaskMappingMixin, aux.TimeOrderedIndexedReaderMixin, aux.In\nand 'params' stores a :py:class:`dict` of parameters (keys and values are\n:py:class:`str`, keys... | Python | Apache License 2.0 | levitsky/pyteomics | Fix and refactoring in ms1 |
377,522 | 14.12.2018 01:21:55 | -10,800 | c3715b9584fd60a35e1e009f09f3a74e700fda87 | Provide IndexedMS1 | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/ms1.py",
"new_path": "pyteomics/ms1.py",
"diff": "@@ -93,6 +93,8 @@ class MS1Base():\nif self._use_header: params.update(self.header)\ndef make_out():\n+ if 'RTime' in params:\n+ params['RTime'] = float(params['RTime'])\nout = {'params': params}\nif ... | Python | Apache License 2.0 | levitsky/pyteomics | Provide IndexedMS1 |
377,522 | 14.12.2018 16:11:21 | -10,800 | 0874cbd090bc4610ec90019316014a9cce88899c | Update ms1.read and docs | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -395,7 +395,7 @@ def read(*args, **kwargs):\n:py:class:`IndexedMGF` is created. This facilitates random access by spectrum titles.\nIf an open file is passed as `source`, it needs to be open in bin... | Python | Apache License 2.0 | levitsky/pyteomics | Update ms1.read and docs |
377,522 | 14.12.2018 16:39:55 | -10,800 | f28c5e7204bf989e916d790f9ab7d61a4011cea8 | Add indexing to protxml | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/protxml.py",
"new_path": "pyteomics/protxml.py",
"diff": "@@ -75,13 +75,16 @@ This module requres :py:mod:`lxml`.\nfrom . import xml, auxiliary as aux, _schema_defaults\nimport operator as op\n-class ProtXML(xml.XML):\n+class ProtXML(xml.MultiProcess... | Python | Apache License 2.0 | levitsky/pyteomics | Add indexing to protxml |
377,522 | 21.12.2018 02:52:27 | -10,800 | 7595a839b72e842c3703d8e787a5b7bc012e8b4c | Add traml doc page | [
{
"change_type": "MODIFY",
"old_path": "doc/source/api.rst",
"new_path": "doc/source/api.rst",
"diff": "@@ -26,6 +26,7 @@ Contents:\napi/mzid\napi/featurexml\napi/trafoxml\n+ api/traml\napi/auxiliary\napi/pylab_aux\napi/xml\n"
},
{
"change_type": "ADD",
"old_path": null,
"new_path": ... | Python | Apache License 2.0 | levitsky/pyteomics | Add traml doc page |
377,522 | 21.12.2018 03:14:57 | -10,800 | 2b8d500f4a8acb3586cadc37c0469b16d697b1a2 | Fix traml spec URL | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/traml.py",
"new_path": "pyteomics/traml.py",
"diff": "@@ -6,7 +6,7 @@ Summary\n-------\nTraML is a standard rich XML-format for targeted mass spectrometry method definitions.\n-Please refer to `psidev.info <http://www.psidev.info/index.php?q=node/257... | Python | Apache License 2.0 | levitsky/pyteomics | Fix traml spec URL |
377,522 | 21.12.2018 19:38:08 | -10,800 | 90f2aec646c56d678bb375daf7ef17fc7491c34d | Tweak tandem test | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/__init__.py",
"new_path": "pyteomics/auxiliary/__init__.py",
"diff": "@@ -22,7 +22,7 @@ from .file_helpers import (\nOffsetIndex, HierarchicalOffsetIndex,\n_file_reader, _file_writer,\n_make_chain, _check_use_index, FileReadingProcess, Task... | Python | Apache License 2.0 | levitsky/pyteomics | Tweak tandem test |
377,522 | 25.12.2018 19:40:03 | -10,800 | 466427bc7b4bf64cfb9ffd4b97c914d7559bbd64 | Start documentaion on indexing | [
{
"change_type": "MODIFY",
"old_path": "doc/source/achrom.rst",
"new_path": "doc/source/achrom.rst",
"diff": "@@ -12,7 +12,7 @@ the BioLCCC model of liquid chromatography of polypeptides.\n:py:mod:`pyteomics.biolccc` is not distributed with the main package and has\nto be installed separately. :py:m... | Python | Apache License 2.0 | levitsky/pyteomics | Start documentaion on indexing |
377,522 | 26.12.2018 01:49:38 | -10,800 | 78d4c2ebaabd8bcb0360463fe6b9e35372f2cdae | Update indexing doc | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "- :py:class:`pyteomics.fasta.FASTABase` - common ancestor, suitable for type checking;\n- - :py:class:`pyteomics.fasta.FASTA` - text-mode, sequential parser. Does\n- what the old :py:func:`fasta.read` was doing;\n+... | Python | Apache License 2.0 | levitsky/pyteomics | Update indexing doc |
377,522 | 26.12.2018 16:33:35 | -10,800 | ed93bad4b31eb2aa15c747d86dfc8bb4d1a57c63 | Update xml and indexing docs | [
{
"change_type": "MODIFY",
"old_path": "doc/source/data/indexing.rst",
"new_path": "doc/source/data/indexing.rst",
"diff": "@@ -62,6 +62,14 @@ Parser objects can be used as dictionaries mapping entry IDs to entries, or as l\nIn [8]: f[1]['params']['title'] # positional indexing\nOut[8]: 'Spectrum 2'... | Python | Apache License 2.0 | levitsky/pyteomics | Update xml and indexing docs |
377,522 | 26.12.2018 17:46:49 | -10,800 | 49f613fb9268d8b03dc025978d9a671c4fb324e0 | Fall back to regular indexing in PreIndexedMzML | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzml.py",
"new_path": "pyteomics/mzml.py",
"diff": "@@ -393,8 +393,7 @@ def iterfind(source, path, **kwargs):\nversion_info = xml._make_version_info(MzML)\n-chain = aux._make_chain(read, 'read')\n-\n+# chain = aux._make_chain(read, 'read')\nchain = a... | Python | Apache License 2.0 | levitsky/pyteomics | Fall back to regular indexing in PreIndexedMzML |
377,522 | 26.12.2018 18:37:25 | -10,800 | 95aca3e39e12b255625f0a90660bb12d7b294425 | Add retrieve_refs for traml; make get_by_id raise KeyError | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzid.py",
"new_path": "pyteomics/mzid.py",
"diff": "@@ -139,8 +139,9 @@ class MzIdentML(xml.IndexSavingXML, xml.MultiProcessingXML):\nends in _ref. Removes the id attribute from `info`\"\"\"\nfor k, v in dict(info).items():\nif k.endswith('_ref'):\n+... | Python | Apache License 2.0 | levitsky/pyteomics | Add retrieve_refs for traml; make get_by_id raise KeyError |
377,522 | 26.12.2018 19:05:48 | -10,800 | bbdbedd1ed1930e5ba8b19425b05a95d1688fb66 | Tweak traml behavior | [
{
"change_type": "MODIFY",
"old_path": "doc/source/data/xml.rst",
"new_path": "doc/source/data/xml.rst",
"diff": "@@ -333,6 +333,13 @@ Reading into a pandas.DataFrame\nthat reads one or several files into a single Pandas :py:class:`DataFrame`.\nThis function requires :py:mod:`pandas`.\n+TraML\n+----... | Python | Apache License 2.0 | levitsky/pyteomics | Tweak traml behavior |
377,522 | 03.01.2019 19:38:04 | -10,800 | f054448a8b9733cd51aae50668c3c408c18ae226 | Add more handlers in traml, add test | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/traml.py",
"new_path": "pyteomics/traml.py",
"diff": "@@ -82,7 +82,9 @@ class TraML(xml.MultiProcessingXML, xml.IndexSavingXML):\n_element_handlers = xml.XML._element_handlers.copy()\n_element_handlers.update({\n- \"Modification\": xml.XML._promote_e... | Python | Apache License 2.0 | levitsky/pyteomics | Add more handlers in traml, add test |
377,522 | 03.01.2019 20:13:47 | -10,800 | a1c0de9e655112b5fb70701ce6a80c7e3dd2fada | Add retrieve_refs=False to traml test | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/traml.py",
"new_path": "pyteomics/traml.py",
"diff": "@@ -127,7 +127,7 @@ class TraML(xml.MultiProcessingXML, xml.IndexSavingXML):\n-def read(source, read_schema=False, iterative=True, use_index=False, huge_tree=False):\n+def read(source, retrieve_re... | Python | Apache License 2.0 | levitsky/pyteomics | Add retrieve_refs=False to traml test |
377,522 | 03.01.2019 20:45:02 | -10,800 | 3b33cbbdbb33649883a5d42fa07f09d21b125a09 | Fix multiprocessing for mzid and featurexml | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mzid.py",
"new_path": "pyteomics/mzid.py",
"diff": "@@ -108,7 +108,7 @@ class MzIdentML(xml.IndexSavingXML, xml.MultiProcessingXML):\n_default_version = '1.1.0'\n_default_iter_tag = 'SpectrumIdentificationResult'\n_structures_to_flatten = {'Fragmenta... | Python | Apache License 2.0 | levitsky/pyteomics | Fix multiprocessing for mzid and featurexml |
377,522 | 04.01.2019 02:32:37 | -10,800 | 44816e5d87422b24bc440d25d4901b6c4d9d68bf | Minor test brush-ups | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mzid.py",
"new_path": "tests/test_mzid.py",
"diff": "@@ -6,7 +6,6 @@ from pyteomics.mzid import MzIdentML, read, chain\nfrom pyteomics import auxiliary as aux\nfrom data import mzid_spectra\nfrom itertools import product\n-import operator as op\ncla... | Python | Apache License 2.0 | levitsky/pyteomics | Minor test brush-ups |
377,522 | 05.01.2019 20:03:53 | -10,800 | 5cbdfddf3f5a179b320bec590e7850bb7d634f85 | Fix in mzml test | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mzml.py",
"new_path": "tests/test_mzml.py",
"diff": "@@ -44,11 +44,11 @@ class MzmlTest(unittest.TestCase):\nspectrum = next(reader)\nrecord = spectrum['m/z array']\nself.assertEqual(record.compression, \"no compression\")\n- self.assertEqual(record... | Python | Apache License 2.0 | levitsky/pyteomics | Fix in mzml test |
377,522 | 05.01.2019 20:11:36 | -10,800 | 0220c6509b9da5e024ff9c14fa7ae8be69a0b17a | Get rid of warnings patching | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/__init__.py",
"new_path": "pyteomics/auxiliary/__init__.py",
"diff": "@@ -5,9 +5,6 @@ except NameError:\nfrom . import patch as __patch\n-import warnings\n-warnings.formatwarning = lambda msg, *args, **kw: str(msg) + '\\n'\n-\nfrom .structu... | Python | Apache License 2.0 | levitsky/pyteomics | Get rid of warnings patching |
377,522 | 07.01.2019 15:23:31 | -10,800 | 8435e7d23b465dbcc5d5fa036067dd6d5b5bf7a1 | Patch release 4.0.1 | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "+4.0.1\n+-----\n+\n+Fix issue `#35 <https://bitbucket.org/levitsky/pyteomics/issues/35/ordereddict-may-be-in-reversed-order-on>`_\n+(incorrect order of deserialized offset indexes on older Python versions).\n+\n4.0... | Python | Apache License 2.0 | levitsky/pyteomics | Patch release 4.0.1 |
377,522 | 30.01.2019 18:29:23 | -10,800 | b90cc511c9c44c17e85c9aec956205153bf78dff | Add plot_spectrum function | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "-4.1\n----\n+4.1.dev\n+-------\n- New module :py:mod:`pyteomics.mztab` provides a parser for `mzTab files <http://www.psidev.info/mztab>`_.\n- New module :py:mod:`pyteomics.ms2` provides a parser for **ms2** files.... | Python | Apache License 2.0 | levitsky/pyteomics | Add plot_spectrum function |
377,522 | 31.01.2019 17:30:16 | -10,800 | f7151a1eda23f591e82257cdf6e26e277c01120d | Add RefSeq parser to fasta | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/fasta.py",
"new_path": "pyteomics/fasta.py",
"diff": "@@ -549,6 +549,24 @@ class IndexedNCBI(NCBIMixin, TwoLayerIndexedFASTA):\npass\n+class RefSeqMixin(FlavoredMixin):\n+ header_pattern = r'^ref\\|([^|]+)\\|\\s*([^\\[]*\\S)\\s*\\[(.*)\\]'\n+\n+ def ... | Python | Apache License 2.0 | levitsky/pyteomics | Add RefSeq parser to fasta |
377,522 | 04.02.2019 19:11:10 | -10,800 | 82d532235230c694df636fe3bfe34b2bbea08c5d | Draft annotate_spectrum function | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -61,6 +61,7 @@ This module requires :py:mod:`matplotlib`.\nimport pylab\nimport numpy as np\nfrom .auxiliary import linear_regression, PyteomicsError\n+from . import parser, mass\ndef p... | Python | Apache License 2.0 | levitsky/pyteomics | Draft annotate_spectrum function |
377,522 | 04.02.2019 19:39:34 | -10,800 | c99c608c9a6c428973dbd56f43e7d32610dba9f0 | Allow empty index keys in XML | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/xml.py",
"new_path": "pyteomics/xml.py",
"diff": "@@ -815,7 +815,7 @@ class ByteCountingXMLScanner(_file_obj):\ni = 0\npacked = b\"|\".join(self.indexed_tags)\npattern = re.compile((r\"^\\s*<(%s)\\s\" % packed.decode()).encode())\n- attrs = re.compil... | Python | Apache License 2.0 | levitsky/pyteomics | Allow empty index keys in XML |
377,522 | 05.02.2019 17:40:29 | -10,800 | 30f43c507d843d506b1229f50cebb392f734ddce | More permissive title matching in mgf | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -251,7 +251,7 @@ class IndexedMGF(aux.TaskMappingMixin, aux.TimeOrderedIndexedReaderMixin, aux.In\n\"\"\"\ndelimiter = 'BEGIN IONS'\n- label = r'TITLE=([^\\n]*\\w)\\s*'\n+ label = r'TITLE=([^\\n]*\... | Python | Apache License 2.0 | levitsky/pyteomics | More permissive title matching in mgf |
377,522 | 06.02.2019 15:44:15 | -10,800 | c43d75ade257d966b708a7e3410afca1c7e2ce44 | Adjust annotate_spectrum | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -343,26 +343,27 @@ def annotate_spectrum(spectrum, peptide, centroided=True, *args, **kwargs):\ntol = kwargs.pop('accuracy', 1e-5)\nparsed = parser.parse(peptide, True)\nn = len(parsed)... | Python | Apache License 2.0 | levitsky/pyteomics | Adjust annotate_spectrum |
377,522 | 06.02.2019 19:05:40 | -10,800 | a1e623e4fa105e317b800488d5e3a2a38dcbdae7 | Add adjustment for text | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -340,7 +340,20 @@ def annotate_spectrum(spectrum, peptide, centroided=True, *args, **kwargs):\nstd_colors = {i: 'red' for i in 'xyz'}\nstd_colors.update({i: 'blue' for i in 'abc'})\ncol... | Python | Apache License 2.0 | levitsky/pyteomics | Add adjustment for text |
377,522 | 08.02.2019 18:50:25 | -10,800 | 5646a76ee9cdb92e544484e26e2a87cc1eb8fade | Add doc for annotate_spectrum | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "- New module :py:mod:`pyteomics.ms2` provides a parser for **ms2** files.\nThis is in fact an alias to :py:mod:`ms1`, which handles both formats.\n-- New helper function :py:func:`pyteomics.pylab_aux.plot_spectrum`... | Python | Apache License 2.0 | levitsky/pyteomics | Add doc for annotate_spectrum |
377,522 | 11.02.2019 16:58:51 | -10,800 | 5e0e2369e1ac9b96ab2aa08f50287d2487353135 | Bugfix in annotate_spectrum mass calculation | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -358,6 +358,8 @@ def annotate_spectrum(spectrum, peptide, centroided=True, *args, **kwargs):\nAdjust the overlapping text annotations using :py:mod:`adjustText`.\ntext_kw : dict, option... | Python | Apache License 2.0 | levitsky/pyteomics | Bugfix in annotate_spectrum mass calculation |
377,522 | 13.02.2019 15:02:20 | -10,800 | 47827631c4f0f5e2f72351798d4545c94028e6a8 | Bugfix in annotate_spectrum | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-4.1a2\n\\ No newline at end of file\n+4.1a3\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -3... | Python | Apache License 2.0 | levitsky/pyteomics | Bugfix in annotate_spectrum |
377,522 | 17.02.2019 01:58:33 | -10,800 | 896996c7c70b9bdfaea095d94b2465b25376e84d | Allow naming expasy rules in cleave | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "- New helper functions :py:func:`pyteomics.pylab_aux.plot_spectrum` and :py:func:`pyteomics.pylab_aux.annotate_spectrum`.\n+- The `rule` and `exception` arguments in :py:func:`pyteomics.parser.cleave` can be keys f... | Python | Apache License 2.0 | levitsky/pyteomics | Allow naming expasy rules in cleave |
377,522 | 18.02.2019 17:40:07 | -10,800 | 3358544005937aa4c14cd96927df0f0817b2827d | Add index saving to pepxml | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -97,7 +97,7 @@ This module requires :py:mod:`lxml`.\nfrom lxml import etree\nfrom . import xml, auxiliary as aux, _schema_defaults\n-class PepXML(xml.MultiProcessingXML):\n+class PepXML(xml.M... | Python | Apache License 2.0 | levitsky/pyteomics | Add index saving to pepxml |
377,522 | 22.02.2019 19:31:56 | -10,800 | 8e71ab58df089502ddaf8d22532bae7fe00cd9ba | Fix title in annotate_spectrum | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -377,6 +377,7 @@ def annotate_spectrum(spectrum, peptide, centroided=True, *args, **kwargs):\nstd_colors.update({i: 'blue' for i in 'abc'})\ncolors = kwargs.pop('colors', std_colors)\nf... | Python | Apache License 2.0 | levitsky/pyteomics | Fix title in annotate_spectrum |
377,522 | 24.02.2019 23:11:39 | -10,800 | 0aeb8fa792ae2e5b3d24c1cf150feacdb95a26ee | A more proper fix | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -377,7 +377,6 @@ def annotate_spectrum(spectrum, peptide, centroided=True, *args, **kwargs):\nstd_colors.update({i: 'blue' for i in 'abc'})\ncolors = kwargs.pop('colors', std_colors)\nf... | Python | Apache License 2.0 | levitsky/pyteomics | A more proper fix |
377,522 | 25.02.2019 00:40:21 | -10,800 | dfd7858a76724fab57fc129bedb371c3e7fc2619 | Extend pd_kwargs support | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pepxml.py",
"new_path": "pyteomics/pepxml.py",
"diff": "@@ -439,7 +439,7 @@ def filter_df(*args, **kwargs):\nelse:\ndf = args[0]\nelse:\n- read_kw = {k: kwargs.pop(k) for k in ['iterative', 'read_schema', 'sep'] if k in kwargs}\n+ read_kw = {k: kwarg... | Python | Apache License 2.0 | levitsky/pyteomics | Extend pd_kwargs support |
377,522 | 26.02.2019 17:23:26 | -10,800 | 8da4324688b5d2a3d1fe8de9024a79003c7af5ef | Another fix in annotate_spectrum | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -393,7 +393,7 @@ def annotate_spectrum(spectrum, peptide, centroided=True, *args, **kwargs):\nelse:\nif adjust is None:\nadjust = True\n- parsed = parser.parse(peptide, True)\n+ parsed ... | Python | Apache License 2.0 | levitsky/pyteomics | Another fix in annotate_spectrum |
377,522 | 28.02.2019 12:22:56 | -10,800 | b75bcbb4ef509cc8a2b05bbaf9b00e9b3168a60f | Update is_modX and is_term_mod; fix issue | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-4.1a4\n\\ No newline at end of file\n+4.1a5\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/parser.py",
"new_path": "pyteomics/parser.py",
"diff": "@@ -116,6 +... | Python | Apache License 2.0 | levitsky/pyteomics | Update is_modX and is_term_mod; fix issue #36 |
377,522 | 28.02.2019 19:26:25 | -10,800 | 443af840a27e416532c97cc4e05217e19e0de89b | Add primitive index saving for text readers | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "- New module :py:mod:`pyteomics.ms2` provides a parser for **ms2** files.\nThis is in fact an alias to :py:mod:`ms1`, which handles both formats.\n+- Added index saving functionality for :py:class:`pyteomics.mgf.In... | Python | Apache License 2.0 | levitsky/pyteomics | Add primitive index saving for text readers |
377,522 | 04.03.2019 00:22:13 | -10,800 | d546984df0826d52761ee5205e3aed47bca2335b | Add schema versioning for index saving text readers, refactor stuff | [
{
"change_type": "MODIFY",
"old_path": "VERSION",
"new_path": "VERSION",
"diff": "-4.1b1\n\\ No newline at end of file\n+4.1b2\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/file_helpers.py",
"new_path": "pyteomics/auxiliary/file_helpe... | Python | Apache License 2.0 | levitsky/pyteomics | Add schema versioning for index saving text readers, refactor stuff |
377,522 | 20.03.2019 17:31:13 | -10,800 | 01ce5a8521c44e262bffdf011cc9e32869561f84 | Update pepxml test | [
{
"change_type": "MODIFY",
"old_path": "tests/test_pepxml.py",
"new_path": "tests/test_pepxml.py",
"diff": "@@ -8,11 +8,14 @@ from data import pepxml_results\nclass PepxmlTest(unittest.TestCase):\nmaxDiff = None\n+ path = 'test.pep.xml'\n+\n_kw = {'full_output': False, 'fdr': 1,\n'key': lambda x: mi... | Python | Apache License 2.0 | levitsky/pyteomics | Update pepxml test |
377,522 | 02.04.2019 03:05:00 | -10,800 | 02e04b45e17a0e49b26a4a94496d266911b92c02 | Add proof-of-principle numpress support (issue | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/utils.py",
"new_path": "pyteomics/auxiliary/utils.py",
"diff": "@@ -2,7 +2,7 @@ from __future__ import print_function\nimport base64\nimport zlib\n-\n+import sys\nfrom functools import wraps\nfrom collections import namedtuple\n@@ -17,6 +17... | Python | Apache License 2.0 | levitsky/pyteomics | Add proof-of-principle numpress support (issue #37) |
377,522 | 02.04.2019 18:15:52 | -10,800 | 76f190246c256cf61751b52f75fb81a4fbd4850b | Use pynumpress instead of PyMSNumpress | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/utils.py",
"new_path": "pyteomics/auxiliary/utils.py",
"diff": "@@ -18,9 +18,9 @@ except ImportError:\nnp = None\ntry:\n- import PyMSNumpress\n+ import pynumpress\nexcept ImportError:\n- PyMSNumpress = None\n+ pynumpress = None\ndef print_t... | Python | Apache License 2.0 | levitsky/pyteomics | Use pynumpress instead of PyMSNumpress |
377,522 | 04.04.2019 01:56:35 | -10,800 | cf98348d2c195be404133a81a81cde61543477d2 | Add support for layered compression | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/utils.py",
"new_path": "pyteomics/auxiliary/utils.py",
"diff": "@@ -97,12 +97,20 @@ def _pynumpressDecompress(decoder):\nreturn decoder(np.frombuffer(data, dtype=np.uint8))\nreturn decode\n+def _zlibNumpress(decoder):\n+ def decode(data):\n... | Python | Apache License 2.0 | levitsky/pyteomics | Add support for layered compression |
377,522 | 08.04.2019 19:23:42 | -10,800 | c9e2e1498ca71ac8dcd55acdf99e982602b73261 | Add tests for numpress in mzml | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "+dev\n+---\n+\n+ - Add `numpress <https://dx.doi.org/10.1074%2Fmcp.O114.037879>`_ support for mzML and mzXML files.\n+ To read files compressed with Numpress, install `pynumpress`\n+ (`PyPI <https://pypi.org/projec... | Python | Apache License 2.0 | levitsky/pyteomics | Add tests for numpress in mzml |
377,522 | 08.04.2019 19:35:54 | -10,800 | 14c4f9eaf40b74ae694ae2881b9369c23034c534 | Add zlib version of tests | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mzml.py",
"new_path": "tests/test_mzml.py",
"diff": "@@ -14,6 +14,7 @@ import pickle\nimport operator as op\nimport pynumpress\nimport base64\n+import zlib\nclass MzmlTest(unittest.TestCase):\nmaxDiff = None\n@@ -170,17 +171,35 @@ class MzmlTest(uni... | Python | Apache License 2.0 | levitsky/pyteomics | Add zlib version of tests |
377,522 | 15.04.2019 01:14:44 | -10,800 | 2d6ff1ae3d5d573c6ee4316191931e329e3bccd2 | Convert decoded bytes to bytesarray so that resulting arrays are mutable (issue | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/utils.py",
"new_path": "pyteomics/auxiliary/utils.py",
"diff": "@@ -2,7 +2,6 @@ from __future__ import print_function\nimport base64\nimport zlib\n-import sys\nfrom functools import wraps\nfrom collections import namedtuple\n@@ -83,7 +82,7 ... | Python | Apache License 2.0 | levitsky/pyteomics | Convert decoded bytes to bytesarray so that resulting arrays are mutable (issue #38) |
377,522 | 25.04.2019 17:28:30 | -10,800 | 724214609ee2097b0bcebdce43d5841eb4d206e4 | Fix issue disable indexing by default in ms1 and ms2, add ms2 tests | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "@@ -5,6 +5,8 @@ dev\nTo read files compressed with Numpress, install `pynumpress`\n(`PyPI <https://pypi.org/project/pynumpress/>`_, `GitHub <https://github.com/mobiusklein/pynumpress>`_).\n+ - Bugfixes.\n+\n4.1\n--... | Python | Apache License 2.0 | levitsky/pyteomics | Fix issue #39, disable indexing by default in ms1 and ms2, add ms2 tests |
377,522 | 06.05.2019 17:05:22 | -10,800 | 7e7626e62369cfd4ee9777d45524aac614b41f3a | Try changing image reference syntax in readme | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "@@ -5,6 +5,10 @@ dev\nTo read files compressed with Numpress, install `pynumpress`\n(`PyPI <https://pypi.org/project/pynumpress/>`_, `GitHub <https://github.com/mobiusklein/pynumpress>`_).\n+ .. note:: There is a `... | Python | Apache License 2.0 | levitsky/pyteomics | Try changing image reference syntax in readme |
377,522 | 06.05.2019 17:13:09 | -10,800 | ea47ff09dcfa06abd9d4a811b66a7be8d258d9d3 | Go back to rst, try adding extension | [
{
"change_type": "RENAME",
"old_path": "README",
"new_path": "README.rst",
"diff": "-\n-[](https://pyteomics.readthedocs.io/en/latest/?badge=latest)\n-![Apache licens... | Python | Apache License 2.0 | levitsky/pyteomics | Go back to rst, try adding extension |
377,522 | 07.06.2019 17:59:43 | -10,800 | cb98b95a239b501d20ddf73b86466e28a98535ea | Add pynumpress extra in setup.py | [
{
"change_type": "MODIFY",
"old_path": "setup.py",
"new_path": "setup.py",
"diff": "@@ -36,7 +36,8 @@ setup(\n'TDA': ['numpy'],\n'graphics': ['matplotlib'],\n'DF': ['pandas'],\n- 'Unimod': ['lxml', 'sqlalchemy']},\n+ 'Unimod': ['lxml', 'sqlalchemy'],\n+ 'numpress': ['pynumpress']},\nclassifiers = ['... | Python | Apache License 2.0 | levitsky/pyteomics | Add pynumpress extra in setup.py |
377,522 | 07.06.2019 18:00:42 | -10,800 | 29832311c0165cef5f52535dcdbbe49a98062f4b | Fix incorrect std mass for pyrrolysine (issue | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mass/mass.py",
"new_path": "pyteomics/mass/mass.py",
"diff": "@@ -747,7 +747,7 @@ std_aa_mass = {\n'R': 156.10111,\n'Y': 163.06333,\n'W': 186.07931,\n- 'O': 255.15829,\n+ 'O': 237.14773,\n}\n\"\"\"A dictionary with monoisotopic masses of the twenty s... | Python | Apache License 2.0 | levitsky/pyteomics | Fix incorrect std mass for pyrrolysine (issue #42) |
377,522 | 07.06.2019 18:38:37 | -10,800 | 41e560881115e1777d4759c4ad9a628cd78c1603 | Update pynumpress notice | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "@@ -12,7 +12,8 @@ Bugfix: fix the standard mass value for pyrrolysine (issue #42).\n.. note:: There is a `known issue\n<https://bitbucket.org/levitsky/pyteomics/issues/37/add-numpress-support-in-mzml#comment-515400... | Python | Apache License 2.0 | levitsky/pyteomics | Update pynumpress notice |
377,522 | 21.06.2019 00:31:08 | -10,800 | 455188bd014d5ef26563a070cea68eaa77071ecc | Fix docstring of annotate_spectrum | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/pylab_aux.py",
"new_path": "pyteomics/pylab_aux.py",
"diff": "@@ -348,6 +348,8 @@ def annotate_spectrum(spectrum, peptide, centroided=True, *args, **kwargs):\nPassed to :py:func:`plot_spectrum`.\ntypes : Container, optional\nIon types to be considere... | Python | Apache License 2.0 | levitsky/pyteomics | Fix docstring of annotate_spectrum |
377,522 | 10.08.2019 01:26:46 | -10,800 | 155ec1b8eb2dd9e35008efac4d11e3f0159896fd | Add mass.Unimod.by_id | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "+dev\n+---\n+\n+New method :py:meth:`mass.Unimod.by_id`.\n+Also, :py:class:`mass.Unimod` now supports dict-like queries with record IDs.\n+\n4.1.2\n-----\n"
},
{
"change_type": "MODIFY",
"old_path": "VE... | Python | Apache License 2.0 | levitsky/pyteomics | Add mass.Unimod.by_id |
377,522 | 22.10.2019 18:06:01 | -10,800 | 3bbe1e388b08480e97be04a8368f9d3e65955021 | Tentative solution for Convert unicode to str on PY2 in unitstr and cvstr constructor | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/structures.py",
"new_path": "pyteomics/auxiliary/structures.py",
"diff": "-import sys\nimport re\nfrom collections import defaultdict, Counter\n@@ -291,6 +290,8 @@ class unitstr(str):\n__slots__ = (\"unit_info\", )\ndef __new__(cls, value, ... | Python | Apache License 2.0 | levitsky/pyteomics | Tentative solution for #47. Convert unicode to str on PY2 in unitstr and cvstr constructor |
377,522 | 27.10.2019 19:15:44 | -10,800 | 2310eb6c1f6bbca0ef1d5a8a06be706ff698ff93 | Fix and add all_ntt_prob to pepxml dataframe output | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "dev\n---\n-New method :py:meth:`mass.Unimod.by_id`.\n+ - New method :py:meth:`mass.Unimod.by_id`.\nAlso, :py:class:`mass.Unimod` now supports dict-like queries with record IDs.\n+ - Reduce memory footprint for unit... | Python | Apache License 2.0 | levitsky/pyteomics | Fix #48 and add all_ntt_prob to pepxml dataframe output |
377,522 | 29.11.2019 16:23:09 | -10,800 | caed461879face3e5bd2ae01cd5d4a77eee7073c | Add Python 3.8 to test runner | [
{
"change_type": "MODIFY",
"old_path": "tests/runtests.sh",
"new_path": "tests/runtests.sh",
"diff": "#!/bin/bash\nexport PYTHONPATH=\"..\"\nif [ $# -eq 0 ]; then\n- find . -name 'test_*.py' -exec bash -c 'declare -a versions=(2.7 3.3 3.4 3.5 3.6 3.7); for v in \"${versions[@]}\"; do command -v \"py... | Python | Apache License 2.0 | levitsky/pyteomics | Add Python 3.8 to test runner |
377,522 | 30.11.2019 23:10:39 | -10,800 | 9d915e4f982192603845e94d8b05edae8768fb20 | Fix by adding new keyword arguments for map-supporting readers: queue_size, queue_timeout and processes.
Make __init__ signatures more cooperative throughout the class tree.
Make sure that index is not constructed in index-saving readers even if file with offsets exists. | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "@@ -6,8 +6,7 @@ dev\n- Reduce memory footprint for unit primitives (PR #35 by Joshua Klein).\n- - Fix issues #47, #48.\n-\n+ - Fix issues #44, #46, #47, #48.\n4.1.2\n"
},
{
"change_type": "MODIFY",
"old... | Python | Apache License 2.0 | levitsky/pyteomics | Fix #44 by adding new keyword arguments for map-supporting readers: queue_size, queue_timeout and processes.
Make __init__ signatures more cooperative throughout the class tree.
Make sure that index is not constructed in index-saving readers even if file with offsets exists. |
377,522 | 02.12.2019 19:51:43 | -10,800 | ece2047158e5c4843fe734a5a27c6907a2a2d394 | Trying to configure pipelines | [
{
"change_type": "MODIFY",
"old_path": "bitbucket-pipelines.yml",
"new_path": "bitbucket-pipelines.yml",
"diff": "@@ -7,6 +7,7 @@ pipelines:\ncaches:\n- pip\nscript:\n- - pip install lxml numpy sqlalchemy pandas pynumpress\n+ - pip install lxml numpy sqlalchemy pandas\n+ - pip install pynumpress\n- ... | Python | Apache License 2.0 | levitsky/pyteomics | Trying to configure pipelines |
377,522 | 02.12.2019 19:55:10 | -10,800 | 5217a5ebcec7ce81341784d323a30025166808cf | Try testing against two versions of Python | [
{
"change_type": "MODIFY",
"old_path": "bitbucket-pipelines.yml",
"new_path": "bitbucket-pipelines.yml",
"diff": "-image: python:3.8\n-\npipelines:\ndefault:\n- step:\n+ image: python:3.8\ncaches:\n- pip\nscript:\n@@ -11,3 +10,11 @@ pipelines:\n- pip install pynumpress\n- cd tests; PYTHONPATH=.. fin... | Python | Apache License 2.0 | levitsky/pyteomics | Try testing against two versions of Python |
377,522 | 02.12.2019 19:31:45 | 0 | 8afcaf4bee711ea67586384279263a40e755678e | Add cython to the build pipeline requirements | [
{
"change_type": "MODIFY",
"old_path": "bitbucket-pipelines.yml",
"new_path": "bitbucket-pipelines.yml",
"diff": "@@ -8,7 +8,7 @@ pipelines:\ncaches:\n- pip\nscript:\n- - pip install lxml numpy sqlalchemy pandas\n+ - pip install lxml numpy sqlalchemy pandas cython\n- pip install pynumpress\n- cd tes... | Python | Apache License 2.0 | levitsky/pyteomics | Add cython to the build pipeline requirements |
377,522 | 03.12.2019 18:04:46 | -10,800 | 7e75a8849062d31f602da850727bb42441a56926 | A sloppy fix for auxiliary doc | [
{
"change_type": "MODIFY",
"old_path": "doc/source/api.rst",
"new_path": "doc/source/api.rst",
"diff": "@@ -29,6 +29,6 @@ Contents:\napi/featurexml\napi/trafoxml\napi/traml\n- api/auxiliary\napi/pylab_aux\napi/xml\n+ api/auxiliary\n\\ No newline at end of file\n"
},
{
"change_type": "MODIFY"... | Python | Apache License 2.0 | levitsky/pyteomics | A sloppy fix for auxiliary doc |
377,522 | 07.12.2019 01:12:30 | -10,800 | 399ad88977da95e7a868ec635c9b36f9031cfa96 | Add changelog entry for new TaskMappingMixin kwargs | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "@@ -24,6 +24,8 @@ dev\n:py:meth:`map` calls will also operate on the full index.\n+ - New keyword arguments `queue_size`, `queue_timeout` and `processes` for indexed parsers with support for :py:meth:`map`.\n+\n- N... | Python | Apache License 2.0 | levitsky/pyteomics | Add changelog entry for new TaskMappingMixin kwargs |
377,522 | 24.12.2019 17:14:42 | -10,800 | 5982cab147056e9c87330560d1e8bb5edf2a27e5 | Add standard error calculation for fdr | [
{
"change_type": "MODIFY",
"old_path": "CHANGELOG",
"new_path": "CHANGELOG",
"diff": "@@ -31,6 +31,8 @@ dev\n- Reduce memory footprint for unit primitives (PR #35 by Joshua Klein).\n+ - New functions :py:func:`pyteomics.auxiliary.sigma_T` and :py:func:`pyteomics.auxiliary.sigma_fdr`.\n+\n- Fix issue... | Python | Apache License 2.0 | levitsky/pyteomics | Add standard error calculation for fdr |
377,524 | 08.01.2020 16:16:00 | 0 | 2be6d53f66ba9e971e7be7b1269dd264364b60e1 | Change std_parsers key from uniprotkb to uniprot | [
{
"change_type": "MODIFY",
"old_path": "doc/source/data/text.rst",
"new_path": "doc/source/data/text.rst",
"diff": "@@ -227,7 +227,7 @@ parsers that can be used for this purpose.\n.. code-block:: python\n- >>> with fasta.read('HUMAN.fasta', parser=fasta.std_parsers['uniprotkb']) as r:\n+ >>> with fa... | Python | Apache License 2.0 | levitsky/pyteomics | Change std_parsers key from uniprotkb to uniprot |
377,522 | 14.01.2020 18:10:51 | -3,600 | 17681e50d727356c06a4291c45b6c108ff99f148 | Add mgf test that breaks after | [
{
"change_type": "MODIFY",
"old_path": "tests/test_mgf.py",
"new_path": "tests/test_mgf.py",
"diff": "@@ -124,6 +124,12 @@ 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 mgf test that breaks after de236b0 |
377,522 | 14.01.2020 18:21:13 | -3,600 | 0ea70228fa54782d9fcb7d0ca52681c8e3fd2ff5 | Fix the broken MGF behavior by moving __getitem__ override from MGFBase to MGF | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/mgf.py",
"new_path": "pyteomics/mgf.py",
"diff": "@@ -230,9 +230,6 @@ class MGFBase(object):\ndef get_spectrum(self, title):\nraise NotImplementedError()\n- def __getitem__(self, key):\n- return self.get_spectrum(key)\n-\nclass IndexedMGF(MGFBase, au... | Python | Apache License 2.0 | levitsky/pyteomics | Fix the broken MGF behavior by moving __getitem__ override from MGFBase to MGF |
377,522 | 04.02.2020 15:25:41 | -10,800 | 0a080feadba274fd5767e1574365b51f28c8b64b | Do not define BinaryDataArrayTransformer if numpy is not imported | [
{
"change_type": "MODIFY",
"old_path": "pyteomics/auxiliary/utils.py",
"new_path": "pyteomics/auxiliary/utils.py",
"diff": "@@ -112,6 +112,7 @@ if pynumpress:\n'MS-Numpress linear prediction compression followed by zlib compression': _zlibNumpress(pynumpress.decode_linear),\n})\n+if np is not None:\... | Python | Apache License 2.0 | levitsky/pyteomics | Do not define BinaryDataArrayTransformer if numpy is not imported |
377,522 | 01.03.2020 01:29:17 | -10,800 | 1b9c011a7e184ce143a6b4946c48a267e538effb | Forget bibucket pipelines | [
{
"change_type": "DELETE",
"old_path": "bitbucket-pipelines.yml",
"new_path": null,
"diff": "-\n-pipelines:\n- default:\n- - parallel:\n- - step:\n- name: Python 3.8\n- image: python:3.8\n- caches:\n- - pip\n- script:\n- - pip install lxml numpy sqlalchemy pandas cython\n- - pip install pynumpress\n... | Python | Apache License 2.0 | levitsky/pyteomics | Forget bibucket pipelines |
377,522 | 01.03.2020 01:50:39 | -10,800 | 6bba4e8f6d06191bb4a6c81d741a5d684b66fca1 | Try setting up a testing workflow | [
{
"change_type": "ADD",
"old_path": null,
"new_path": ".github/workflows/pythonpackage.yml",
"diff": "+name: Python package\n+\n+on: [push, pull_request]\n+\n+jobs:\n+ build:\n+\n+ runs-on: ubuntu-latest\n+ strategy:\n+ matrix:\n+ python-version: [2.7, 3.5, 3.6, 3.7, 3.8]\n+\n+ steps:\n+ - uses: act... | Python | Apache License 2.0 | levitsky/pyteomics | Try setting up a testing workflow |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.