{"push_id":2984366422,"size":15,"distinct_size":15,"ref":"refs/heads/master","head":"45cad0cff89d3074e50f24b6c729a815824ffa30","before":"d52fe0fb1bc52a0ebc0429229df3b8436e356929","commits":[{"sha":"27dfa6b4bfd70c5244dc067537ac8a88f64c97da","author":{"name":"mdehoon","email":"f8b19e40e3c98943ee75240dd01d43bbed5aed5b@yahoo.com"},"message":"Fix for issue1801: Add MathML, Namespace capabilities to Bio.Entrez (#1823)\n\n* all changes commented out\r\n\r\n* start on MathML\r\n\r\n* maybe not the prettiest solution, but it works\r\n\r\n* handle schemas separately\r\n\r\n* add a test with both MathML and HTML tags in text\r\n\r\n* fix flake stuff\r\n\r\n* fix unicode issues for python2","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/27dfa6b4bfd70c5244dc067537ac8a88f64c97da"},{"sha":"c04ecd81509cb8f3563e7d09ac03c6bd8d8d009a","author":{"name":"Konstantin Vdovkin","email":"dd71b534622c4a0c2f926eff639400e8da6dde27@gmail.com"},"message":"fix parsing of anisotropic B factors","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/c04ecd81509cb8f3563e7d09ac03c6bd8d8d009a"},{"sha":"4a20199a644f452121031d6c124baf8d8665d952","author":{"name":"peterjc","email":"c01a39a76d96e917f87dcda7aac0ff07d778d5c1@googlemail.com"},"message":"Access IUPACData values directly\n\nAvoid needlessly going via Bio.Alphabet classes here","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/4a20199a644f452121031d6c124baf8d8665d952"},{"sha":"e992fbab83cea20e244228f1700440801e8eedf5","author":{"name":"Peter Cock","email":"c01a39a76d96e917f87dcda7aac0ff07d778d5c1@googlemail.com"},"message":"Dual license Bio/UniGene/__init__.py (#1806)\n\nWe have not yet been able to contact Katharine Lindner\r\n(CVS username katel) who wrote the original code which\r\nwas initially in Bio/UniGene/UniGene.py\r\n\r\nHowever, the modele was completely rewritten in 2006 by\r\nSean Davis (CVS username sdavis, now on GitHub as @seandavi)\r\nand he and all the other contributors have agreed to the\r\nlicense change:\r\n\r\n - Adhemar Zerlotini (@azneto)\r\n   https://github.com/biopython/biopython/pull/1412#issue-147372599\r\n - Andrew Dalke (@adalke)\r\n   http://mailman.open-bio.org/pipermail/biopython-dev/2013-August/019941.html\r\n - Brad Chapman (@chapmanb)\r\n   http://mailman.open-bio.org/pipermail/biopython-dev/2013-July/019903.html\r\n - Christian Brueffer (@cbrueffer)\r\n   https://github.com/biopython/biopython/issues/898#issuecomment-236922857\r\n - Connor McCoy (@cmccoy)\r\n   https://github.com/biopython/biopython/issues/898#issuecomment-380478091\r\n - jchang (@jefftc)\r\n   https://github.com/biopython/biopython/issues/898#issuecomment-236968522\r\n - Michiel de Hoon (@mdehoon)\r\n   https://github.com/biopython/biopython/issues/898#issuecomment-237122630\r\n - Nick Negretti (@nimne)\r\n   https://github.com/biopython/biopython/pull/1768#issue-210631196\r\n - Peter Cock (@peterjc)\r\n   https://github.com/biopython/biopython/issues/898#issue-167420613\r\n - Sean Davis (@seandavi)\r\n   https://github.com/biopython/biopython/issues/898#issuecomment-424399275\r\n - Travis Wrightsman (@twrightsman)\r\n   https://github.com/biopython/biopython/issues/898#issuecomment-237625470","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/e992fbab83cea20e244228f1700440801e8eedf5"},{"sha":"83b6111b7b86d804a01cc33eabd770037a7598f9","author":{"name":"Stefans Mezulis","email":"07b41faf044dbd2a84b78a00ee23538b7aad0a18@imperial.ac.uk"},"message":"Add cif-seqres and cif-atom SeqIO drivers\n\nThis commit adds the 'cif-seqres' and 'cif-atom'\ndrivers to the Bio.SeqIO module. These are implemented by the\n'CifSeqresIterator' and 'CifAtomIterator' functions in the\n'Bio.SeqIO.CifIO' module.\n\nMost of the logic for the 'cif-atom' driver is identical to the\n'pdb-atom' driver, as they both read from a Bio.PDB Structure object.\nThe shared code has been refactored into the 'AtomIterator' function in\nthe 'Bio.SeqIO.structure_io' module.\n\nThe cif-seqres iterator reads three categories: '_pdbx_poly_seq_scheme',\nwhich contains the actual sequence; '_struct_ref', which contains\ndatabase cross-references; and '_struct_ref_seq', which is linked to\n_struct_ref via the ref_id field and contains the PDB and chain ID of\nthe cross-reference.\n\nSince so much of the test code is shared between the pdb-* and cif-*\nSeqIO readers, the 'test_SeqIO_PdbIO.py' file has been renamed to\n'test_SeqIO_StructureIO.py', and now contains the tests for both the\npdb-* and cif-* readers. For the sake of consistency, I have also added\n2XHE.cif and a_structure.cif to the Tests/PDB directory.\n\nShared test code is implemented in a superclass returned from a\nfunction in order to convince unittest to run the child test suites but\nnot the parent suite.","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/83b6111b7b86d804a01cc33eabd770037a7598f9"},{"sha":"3cd39a1a303a3afc0e18f975f7d8ac80b61f0d97","author":{"name":"Stefans Mezulis","email":"07b41faf044dbd2a84b78a00ee23538b7aad0a18@imperial.ac.uk"},"message":"Add StefansM to NEWS.rst","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/3cd39a1a303a3afc0e18f975f7d8ac80b61f0d97"},{"sha":"f5667ee91144ac6ae69af23cb1f51b4d1f517273","author":{"name":"Stefans Mezulis","email":"07b41faf044dbd2a84b78a00ee23538b7aad0a18@imperial.ac.uk"},"message":"Fix formatting for flake8","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/f5667ee91144ac6ae69af23cb1f51b4d1f517273"},{"sha":"88fde148af8f7b669e45f120c2cc2b99ba74d8a5","author":{"name":"Stefans Mezulis","email":"07b41faf044dbd2a84b78a00ee23538b7aad0a18@imperial.ac.uk"},"message":"Remove newlines at beginning of docstring","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/88fde148af8f7b669e45f120c2cc2b99ba74d8a5"},{"sha":"9ad3a2b6896031016341a3ff336b7403acd304ef","author":{"name":"Stefans Mezulis","email":"07b41faf044dbd2a84b78a00ee23538b7aad0a18@imperial.ac.uk"},"message":"Merge CifIO/PdbIO/structure_io\n\nMerge the Bio.SeqIO.{Cif,Pdb}IO and the Bio.SeqIO.structure_io modules\ntogether. Modules have been merged into PdbIO.py to retain backwards\ncompatibility with anyone directly using the iterators from PdbIO\ninstead of the SeqIO interface.","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/9ad3a2b6896031016341a3ff336b7403acd304ef"},{"sha":"9632e8d62c4692b6d03fab71f5a18ba3990faa04","author":{"name":"Stefans Mezulis","email":"07b41faf044dbd2a84b78a00ee23538b7aad0a18@imperial.ac.uk"},"message":"Add description to Bio.SeqIO docstring for cif-*","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/9632e8d62c4692b6d03fab71f5a18ba3990faa04"},{"sha":"1cc033d0c7628fbe563a798a083a76bea203cbd7","author":{"name":"Stefans Mezulis","email":"07b41faf044dbd2a84b78a00ee23538b7aad0a18@imperial.ac.uk"},"message":"Add {cif,pdb}-{atom,seqres} parsers to test_SeqIO\n\nAdd the pdb-atom, pdb-seqres, cif-atom and cif-seqres drivers to\ntest_SeqIO. This required the following changes:\n\n* Bio.AlignIO.PylipIO: Added a sanitize_name function for use in the\n  test_SeqIO test suite. Colons in the sequence ID were not being\n  replaced with pipes in test_SeqIO, so sequences read from the\n  structure file (1ABC:A) were being compared with the sanitised version\n  from the Phylip files (1ABC|A).\n\n* test_SeqIO.py:\n    - Added tests for the {cif,pdb}-{atom-seqres} drivers.\n\n    - Added a readlines() method to ForwardOnlyHandle, which is required\n      by the PDBParser.\n\n    - Added a condition for the Stockholm parser for sequences that have\n      a \"start\" and \"end\" annotation. The \"stockholm\" driver writes and\n      parses these like \"1ABC:A/X-Y\", but the residue range is not\n      included in the sequence ID when parsed from a structure.\n\n* output/test_SeqIO: Generated by \"run_tests.py -g\". I have taken a look\nat the additional output, and the parsed sequences are correct.","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/1cc033d0c7628fbe563a798a083a76bea203cbd7"},{"sha":"038be568d112343d34a09cb06e572825802b3769","author":{"name":"Stefans Mezulis","email":"07b41faf044dbd2a84b78a00ee23538b7aad0a18@imperial.ac.uk"},"message":"Fix typo in PhylipIO.py docstring","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/038be568d112343d34a09cb06e572825802b3769"},{"sha":"507ec91406f881c5aa8044ebfec892b32f5f16e1","author":{"name":"Stefans Mezulis","email":"07b41faf044dbd2a84b78a00ee23538b7aad0a18@imperial.ac.uk"},"message":"Replace PdbIO *Warnings → *ParserWarnings","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/507ec91406f881c5aa8044ebfec892b32f5f16e1"},{"sha":"2ceb458e076071feece69c886f5b27836ee21632","author":{"name":"peterjc","email":"c01a39a76d96e917f87dcda7aac0ff07d778d5c1@googlemail.com"},"message":"Remove Bio.ExPASy.sprot_search_ful and ..._de\n\nThis will close #253 and some of the dead URLs\nnoted on #1826.\n\nThis has not followed the letter of our deprecation\npolicy (since there was no BiopythonDeprecationWarning\nissued on attempted use, but attempted use would just\nfail), https://biopython.org/wiki/Deprecation_policy","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/2ceb458e076071feece69c886f5b27836ee21632"},{"sha":"45cad0cff89d3074e50f24b6c729a815824ffa30","author":{"name":"peterjc","email":"c01a39a76d96e917f87dcda7aac0ff07d778d5c1@googlemail.com"},"message":"fix typo and remove overlooked entry\n\nI didn't search for the escaped underscore last time.","distinct":true,"url":"https://api.github.com/repos/nimne/biopython/commits/45cad0cff89d3074e50f24b6c729a815824ffa30"}]}
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