This is an automated email from the git hooks/post-receive script. moeller pushed a commit to branch master in repository python-biopython.
commit ab673064b1dea3dddae1f59f2966c7ceaad062af Merge: a28a896 e6d5572 Author: Steffen Moeller <[email protected]> Date: Mon Jul 24 15:02:34 2017 +0200 Updated version 1.70+dfsg from 'upstream/1.70+dfsg' with Debian dir 7c6a5fa41e2f3b60f18b3ca711ce5d54b86752de .appveyor.yml | 48 + .codecov.yml | 2 +- .gitignore | 7 + .travis-tox.ini | 75 +- .travis.yml | 88 +- Bio/.flake8 | 58 + Bio/Affy/CelFile.py | 257 +- Bio/Affy/__init__.py | 3 +- Bio/Align/AlignInfo.py | 251 +- Bio/Align/Applications/_ClustalOmega.py | 6 +- Bio/Align/Applications/_Clustalw.py | 4 +- Bio/Align/Applications/_Dialign.py | 4 +- Bio/Align/Applications/_MSAProbs.py | 3 +- Bio/Align/Applications/_Mafft.py | 9 +- Bio/Align/Applications/_Muscle.py | 486 +- Bio/Align/Applications/_Prank.py | 9 +- Bio/Align/Applications/_Probcons.py | 4 +- Bio/Align/Applications/_TCoffee.py | 1 + Bio/Align/Applications/__init__.py | 4 +- Bio/Align/Generic.py | 452 - Bio/Align/__init__.py | 308 +- Bio/AlignIO/ClustalIO.py | 8 +- 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Tests/test_GraphicsGeneral.py | 60 +- Tests/test_HMMCasino.py | 6 +- Tests/test_HMMGeneral.py | 6 +- Tests/test_KDTree.py | 2 + Tests/test_KEGG.py | 170 +- Tests/test_KEGG_online.py | 11 +- Tests/test_KGML_graphics.py | 2 - Tests/test_KGML_graphics_online.py | 2 - Tests/test_KGML_nographics.py | 18 +- Tests/test_KeyWList.py | 1 + Tests/test_LogisticRegression.py | 1 + Tests/test_MafIO_index.py | 426 + Tests/test_Mafft_tool.py | 35 +- Tests/test_MarkovModel.py | 265 +- Tests/test_Muscle_tool.py | 9 +- Tests/test_NCBITextParser.py | 2 +- Tests/test_NCBI_BLAST_tools.py | 6 +- Tests/test_NCBI_qblast.py | 14 +- Tests/test_NNExclusiveOr.py | 13 +- Tests/test_NNGene.py | 23 +- Tests/test_NNGeneral.py | 11 +- Tests/test_NaiveBayes.py | 10 + Tests/test_Nexus.py | 161 +- Tests/test_PAML_baseml.py | 43 +- Tests/test_PAML_codeml.py | 149 +- Tests/test_PAML_tools.py | 16 +- Tests/test_PAML_yn00.py | 29 +- Tests/test_PDB.py | 315 +- Tests/test_PDBList.py | 117 + Tests/test_PDB_FragmentMapper.py | 40 + Tests/test_PDB_MMCIF2Dict.py | 38 + Tests/{test_MMCIF.py => test_PDB_MMCIFParser.py} | 82 + Tests/test_PDB_Polypetide.py | 69 + Tests/test_PDB_StructureAlignment.py | 49 + Tests/test_PDB_Superimposer.py | 113 + Tests/test_ParserSupport.py | 4 + Tests/test_Phd.py | 1 + Tests/test_Phylo.py | 2 + Tests/test_PhyloXML.py | 1 + Tests/test_Phylo_CDAO.py | 4 +- Tests/test_Phylo_NeXML.py | 2 + Tests/test_Phylo_matplotlib.py | 14 +- Tests/test_PopGen_DFDist.py | 133 - Tests/test_PopGen_FDist.py | 128 - Tests/test_PopGen_FDist_nodepend.py | 108 - Tests/test_PopGen_FastSimCoal.py | 63 - Tests/test_PopGen_GenePop.py | 1 + Tests/test_PopGen_GenePop_EasyController.py | 7 + Tests/test_PopGen_GenePop_nodepend.py | 82 +- Tests/test_PopGen_SimCoal.py | 65 - Tests/test_PopGen_SimCoal_nodepend.py | 52 - Tests/test_Prank_tool.py | 26 +- Tests/test_QCPSuperimposer.py | 227 +- Tests/test_RCSBFormats.py | 1 + Tests/test_Restriction.py | 486 +- Tests/test_SCOP_Astral.py | 6 +- Tests/test_SCOP_Cla.py | 2 +- Tests/test_SCOP_Residues.py | 2 +- Tests/test_SCOP_online.py | 1 + Tests/test_SVDSuperimposer.py | 142 +- Tests/test_SearchIO_blast_text.py | 2 +- Tests/test_SearchIO_blast_xml.py | 40 +- Tests/test_SearchIO_blast_xml_index.py | 1 - Tests/test_SearchIO_blat_psl.py | 107 + Tests/test_SearchIO_exonerate.py | 70 + Tests/test_SearchIO_hmmer2_text_index.py | 12 +- Tests/test_SearchIO_hmmer3_domtab.py | 1 + Tests/test_SearchIO_hmmer3_text.py | 31 + Tests/test_SearchIO_hmmer3_text_index.py | 6 +- Tests/test_SearchIO_model.py | 60 +- Tests/test_SearchIO_write.py | 12 + Tests/test_SeqFeature.py | 84 +- Tests/test_SeqIO.py | 6 +- Tests/test_SeqIO_AbiIO.py | 43 +- Tests/test_SeqIO_FastaIO.py | 3 +- Tests/test_SeqIO_Insdc.py | 12 +- Tests/test_SeqIO_PdbIO.py | 5 +- Tests/test_SeqIO_QualityIO.py | 14 +- Tests/test_SeqIO_SeqXML.py | 4 +- Tests/test_SeqIO_convert.py | 6 +- Tests/test_SeqIO_features.py | 56 +- Tests/test_SeqIO_index.py | 52 +- Tests/test_SeqIO_online.py | 14 +- Tests/test_SeqIO_write.py | 25 +- Tests/test_SeqRecord.py | 15 +- Tests/test_SeqUtils.py | 6 +- Tests/test_Seq_objs.py | 164 +- Tests/test_SffIO.py | 194 +- Tests/test_SubsMat.py | 12 +- Tests/test_SwissProt.py | 77 +- Tests/test_TCoffee_tool.py | 12 +- Tests/test_TogoWS.py | 85 +- Tests/test_TreeConstruction.py | 72 +- Tests/test_Tutorial.py | 62 +- Tests/test_Uniprot.py | 57 +- Tests/test_XXmotif_tool.py | 10 +- Tests/test_align.py | 13 +- Tests/test_bgzf.py | 16 +- Tests/test_cellosaurus.py | 135 + Tests/test_codonalign.py | 35 +- Tests/test_kNN.py | 2 + Tests/test_lowess.py | 1 + Tests/test_mmtf.py | 11 +- Tests/test_mmtf_online.py | 32 + Tests/test_motifs.py | 152 +- Tests/test_pairwise2.py | 62 +- Tests/test_phenotype.py | 1 + Tests/test_phenotype_fit.py | 5 +- Tests/test_phyml_tool.py | 16 +- Tests/test_psw.py | 1 + Tests/test_py3k.py | 24 - Tests/test_raxml_tool.py | 3 +- Tests/test_samtools_tool.py | 31 +- Tests/test_seq.py | 463 +- Tests/test_trie.py | 40 +- setup.py | 304 +- 647 files changed, 120244 insertions(+), 86711 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-biopython.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
