[med-svn] [python-biopython] 02/03: Merge tag 'upstream/1.68+dfsg'
Andreas Tille
tille at debian.org
Mon Aug 29 12:16:53 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-biopython.
commit a5ef97f53b7ae4ea6422b1c8cda2d5885cb51ea4
Merge: 634b43e 9511db1
Author: Andreas Tille <tille at debian.org>
Date: Mon Aug 29 13:23:04 2016 +0200
Merge tag 'upstream/1.68+dfsg'
Upstream version 1.68+dfsg
.codecov.yml | 7 +
.gitattributes | 3 +
.travis-tox.ini | 110 +
.travis.yml | 76 +-
Bio/Align/Applications/_Muscle.py | 7 +-
Bio/Align/Applications/_TCoffee.py | 108 +-
Bio/Align/Generic.py | 12 +-
Bio/Align/__init__.py | 18 +-
Bio/AlignIO/ClustalIO.py | 42 +-
Bio/AlignIO/NexusIO.py | 4 +-
Bio/AlignIO/PhylipIO.py | 44 +-
Bio/Alphabet/Reduced.py | 3 +-
Bio/Blast/Applications.py | 14 +-
Bio/Blast/NCBIStandalone.py | 55 +-
Bio/Blast/NCBIWWW.py | 5 +-
Bio/Compass/__init__.py | 2 +-
Bio/Data/CodonTable.py | 248 +-
Bio/Emboss/Applications.py | 1801 +++----
Bio/Entrez/DTDs/NCBI_Systems.dtd | 86 +
Bio/Entrez/Parser.py | 14 +-
Bio/Entrez/__init__.py | 118 +-
Bio/File.py | 12 +-
Bio/GenBank/Scanner.py | 15 +-
Bio/GenBank/__init__.py | 70 +-
Bio/Graphics/BasicChromosome.py | 55 +-
Bio/Graphics/Comparative.py | 10 +-
Bio/Graphics/DisplayRepresentation.py | 2 +-
Bio/Graphics/__init__.py | 2 +-
Bio/HMM/DynamicProgramming.py | 6 +-
Bio/MarkovModel.py | 24 +-
Bio/Nexus/Nexus.py | 29 +-
Bio/Nexus/Trees.py | 4 +-
Bio/PDB/DSSP.py | 174 +-
Bio/PDB/HSExposure.py | 6 +-
Bio/PDB/QCPSuperimposer/__init__.py | 11 +-
Bio/PDB/mmtf/DefaultParser.py | 162 +
Bio/PDB/mmtf/__init__.py | 36 +
Bio/PDB/parse_pdb_header.py | 3 +-
Bio/Phylo/Applications/_Fasttree.py | 424 +-
Bio/Phylo/Applications/_Phyml.py | 316 +-
Bio/Phylo/Applications/_Raxml.py | 251 +-
Bio/Phylo/BaseTree.py | 66 +-
Bio/Phylo/NewickIO.py | 16 +-
Bio/Phylo/PAML/_parse_baseml.py | 32 +-
Bio/Phylo/PAML/_parse_codeml.py | 30 +-
Bio/Phylo/_cdao_owl.py | 448 +-
Bio/PopGen/Async/Local.py | 6 +-
Bio/PopGen/Async/__init__.py | 10 +-
Bio/PopGen/FDist/Async.py | 3 +-
Bio/PopGen/FDist/Controller.py | 2 +-
Bio/PopGen/FDist/Utils.py | 1 +
Bio/PopGen/FDist/__init__.py | 13 +-
Bio/PopGen/SimCoal/Async.py | 4 +-
Bio/PopGen/SimCoal/Cache.py | 2 +-
Bio/PopGen/SimCoal/Controller.py | 5 +-
Bio/PopGen/SimCoal/Template.py | 2 +
Bio/PopGen/SimCoal/__init__.py | 10 +-
Bio/Restriction/Restriction.py | 354 +-
Bio/Restriction/Restriction_Dictionary.py | 936 +++-
Bio/Seq.py | 10 +-
Bio/SeqFeature.py | 101 +-
Bio/SeqIO/InsdcIO.py | 125 +-
Bio/SeqIO/PdbIO.py | 6 +-
Bio/SeqIO/__init__.py | 9 +-
Bio/SeqRecord.py | 40 +-
Bio/SeqUtils/CodonUsage.py | 4 +-
Bio/SeqUtils/ProtParamData.py | 24 +-
Bio/SeqUtils/__init__.py | 2 +-
Bio/Sequencing/Applications/_Novoalign.py | 3 +-
Bio/Sequencing/Applications/_bwa.py | 429 +-
Bio/SubsMat/MatrixInfo.py | 5052 ++++++++++----------
Bio/UniProt/GOA.py | 31 +-
Bio/__init__.py | 2 +-
Bio/_utils.py | 7 +-
Bio/bgzf.py | 47 +-
Bio/codonalign/__init__.py | 2 +-
Bio/codonalign/codonalignment.py | 2 +-
Bio/codonalign/codonseq.py | 49 +-
Bio/cpairwise2module.c | 464 +-
Bio/motifs/__init__.py | 5 +-
Bio/motifs/_pwm.c | 4 +
Bio/motifs/jaspar/db.py | 29 +-
Bio/motifs/matrix.py | 5 +-
Bio/motifs/transfac.py | 2 +-
Bio/pairwise2.py | 937 ++--
BioSQL/BioSeq.py | 39 +-
BioSQL/BioSeqDatabase.py | 10 +-
BioSQL/Loader.py | 114 +-
CONTRIB | 145 +-
DEPRECATED | 17 +-
Doc/Tutorial.tex | 3 +-
Doc/Tutorial/chapter_align.tex | 155 +-
Doc/Tutorial/chapter_introduction.tex | 19 +-
Doc/Tutorial/chapter_pdb.tex | 32 +
Doc/Tutorial/chapter_popgen.tex | 475 --
Doc/Tutorial/chapter_seq_annot.tex | 2 +-
Doc/Tutorial/chapter_testing.tex | 84 +-
Doc/examples/ACT_example.py | 4 +-
Doc/examples/Proux_et_al_2002_Figure_6.py | 26 +-
Doc/examples/alpha.faa | 4 +
Doc/examples/beta.faa | 4 +
Doc/examples/getgene.py | 40 +-
Doc/examples/nmr/simplepredict.py | 6 +-
Doc/images/bottle.png | Bin 1589 -> 0 bytes
MANIFEST.in | 1 +
NEWS | 56 +
Scripts/GenBank/check_output.py | 4 +-
Scripts/Performance/biosql_performance_load.py | 2 +-
Scripts/Performance/biosql_performance_read.py | 2 +-
Scripts/Restriction/ranacompiler.py | 14 +-
Scripts/SeqGui/SeqGui.py | 412 +-
Scripts/scop_pdb.py | 4 +-
Scripts/update_ncbi_codon_table.py | 96 +
Scripts/xbbtools/nextorf.py | 25 +-
Scripts/xbbtools/test.fas | 2 +-
Scripts/xbbtools/testrp.fas | 2 +-
Scripts/xbbtools/xbb_blast.py | 273 +-
Scripts/xbbtools/xbb_blastbg.py | 148 +-
Scripts/xbbtools/xbb_help.py | 66 +-
Scripts/xbbtools/xbb_search.py | 92 +-
Scripts/xbbtools/xbb_translations.py | 111 +-
Scripts/xbbtools/xbb_utils.py | 50 +-
Scripts/xbbtools/xbb_widget.py | 352 +-
Scripts/xbbtools/xbbtools.py | 26 +-
Tests/EMBL/embl_with_0_line.embl | 48 +
Tests/PAML/gen_results.py | 6 +-
Tests/PDB/1A8O.mmtf | Bin 0 -> 12510 bytes
Tests/PDB/4CUP.cif | 3305 +++++++++++++
Tests/PDB/4CUP.mmtf | Bin 0 -> 19438 bytes
Tests/PDB/{4zhl.cif => 4ZHL.cif} | 0
Tests/PDB/4ZHL.mmtf | Bin 0 -> 27073 bytes
Tests/PDB/Miller_RASA.txt | 130 +
Tests/PDB/Sander_RASA.txt | 130 +
Tests/PDB/Wilke_RASA.txt | 130 +
Tests/PDB/dssp_xtra_Sander.txt | 130 +
Tests/common_BioSQL.py | 95 +-
Tests/common_BioSQL_online.py | 111 +
Tests/output/test_GenBank | 1267 +----
Tests/output/test_SeqIO | 24 +-
Tests/seq_tests_common.py | 62 +-
Tests/test_AlignIO_ClustalIO.py | 7 +-
Tests/test_AlignIO_EmbossIO.py | 6 +-
Tests/test_BioSQL_MySQLdb.py | 2 +-
...QL_MySQLdb.py => test_BioSQL_MySQLdb_online.py} | 13 +-
Tests/test_BioSQL_mysql_connector.py | 2 +-
...or.py => test_BioSQL_mysql_connector_online.py} | 13 +-
Tests/test_BioSQL_psycopg2.py | 2 +-
..._psycopg2.py => test_BioSQL_psycopg2_online.py} | 13 +-
Tests/test_BioSQL_sqlite3.py | 2 +-
...QL_MySQLdb.py => test_BioSQL_sqlite3_online.py} | 23 +-
Tests/test_CAPS.py | 49 +-
Tests/test_CelFile.py | 58 +-
Tests/test_Cluster.py | 2 +-
Tests/test_CodonTable.py | 8 +
Tests/test_Compass.py | 7 +-
Tests/test_EMBL_unittest.py | 11 +
Tests/test_EmbossPrimer.py | 36 +-
Tests/test_Entrez.py | 4306 +----------------
Tests/test_Entrez_online.py | 29 +-
Tests/{test_Entrez.py => test_Entrez_parser.py} | 185 +-
Tests/test_GAQueens.py | 6 +-
Tests/test_GenBank.py | 4 +-
Tests/test_GenBank_unittest.py | 109 +-
Tests/test_KGML_nographics.py | 30 +-
Tests/test_MMCIF.py | 2 +-
Tests/test_NCBITextParser.py | 8 +-
Tests/test_NCBIXML.py | 2 +-
Tests/test_NCBI_BLAST_tools.py | 3 +-
Tests/test_Nexus.py | 2 +-
Tests/test_PAML_codeml.py | 1 -
Tests/test_PAML_yn00.py | 8 +-
Tests/test_PDB.py | 143 +-
Tests/test_Phylo.py | 40 +-
Tests/test_PhyloXML.py | 103 +-
...st_Phylo_depend.py => test_Phylo_matplotlib.py} | 34 +-
Tests/test_Phylo_networkx.py | 40 +
Tests/test_PopGen_DFDist.py | 10 +-
Tests/test_PopGen_FDist.py | 11 +-
Tests/test_PopGen_FastSimCoal.py | 10 +-
Tests/test_PopGen_SimCoal.py | 10 +-
Tests/test_PopGen_SimCoal_nodepend.py | 8 +-
Tests/test_QCPSuperimposer.py | 6 +-
Tests/test_RCSBFormats.py | 13 +-
Tests/test_Restriction.py | 12 +-
Tests/test_SCOP_Residues.py | 24 +-
Tests/test_SearchIO_hmmer2_text_index.py | 10 +-
Tests/test_SearchIO_hmmer3_domtab.py | 4 +-
Tests/test_SearchIO_hmmer3_text_index.py | 6 +-
Tests/test_SeqIO_AbiIO.py | 2 +-
Tests/test_SeqIO_Insdc.py | 18 +
Tests/test_SeqIO_QualityIO.py | 2 +-
Tests/test_SeqIO_SeqXML.py | 7 +-
Tests/test_SeqIO_features.py | 70 +-
Tests/test_SeqIO_write.py | 9 +-
Tests/test_SeqRecord.py | 19 +-
Tests/test_SeqUtils.py | 2 +-
Tests/test_Seq_objs.py | 53 +-
Tests/test_TreeConstruction.py | 20 +-
Tests/test_Tutorial.py | 43 +-
Tests/test_Uniprot.py | 2 +-
Tests/test_mmtf.py | 100 +
Tests/test_pairwise2.py | 280 +-
Tests/test_prosite1.py | 2 +-
Tests/test_raxml_tool.py | 2 +-
setup.py | 29 +-
205 files changed, 14448 insertions(+), 13720 deletions(-)
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