[med-svn] [python-biopython] 02/03: Updated version 1.70+dfsg from 'upstream/1.70+dfsg'
Steffen Möller
moeller at moszumanska.debian.org
Mon Jul 24 13:56:50 UTC 2017
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 <moeller at debian.org>
Date: Mon Jul 24 15:02:34 2017 +0200
Updated version 1.70+dfsg from 'upstream/1.70+dfsg'
with Debian dir 7c6a5fa41e2f3b60f18b3ca711ce5d54b86752de
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Tests/output/test_KEGG | 857 -
Tests/output/test_QCPSuperimposer | 12 -
Tests/output/test_SVDSuperimposer | 12 -
Tests/output/test_SeqIO | 398 +
Tests/run_tests.py | 111 +-
Tests/search_tests_common.py | 10 +-
Tests/seq_tests_common.py | 11 +-
Tests/test_Affy.py | 192 +
Tests/test_AlignIO.py | 71 +-
Tests/test_AlignIO_ClustalIO.py | 7 +-
Tests/test_AlignIO_EmbossIO.py | 6 +-
Tests/test_AlignIO_MauveIO.py | 111 +
Tests/test_AlignIO_convert.py | 1 +
Tests/test_AlignInfo.py | 36 +-
Tests/test_BWA_tool.py | 4 +-
Tests/test_BioSQL_MySQLdb.py | 6 +-
Tests/test_BioSQL_MySQLdb_online.py | 6 +-
Tests/test_BioSQL_mysql_connector.py | 6 +-
Tests/test_BioSQL_mysql_connector_online.py | 6 +-
Tests/test_BioSQL_psycopg2.py | 6 +-
Tests/test_BioSQL_psycopg2_online.py | 6 +-
Tests/test_BioSQL_sqlite3.py | 9 +-
Tests/test_BioSQL_sqlite3_online.py | 5 +-
Tests/test_CelFile.py | 6 +-
Tests/test_Chi2.py | 1 +
Tests/test_ClustalOmega_tool.py | 4 +-
Tests/test_Clustalw_tool.py | 2 +-
Tests/test_Cluster.py | 15 +-
Tests/test_ColorSpiral.py | 4 +-
Tests/test_Compass.py | 1 +
Tests/test_Consensus.py | 9 +-
Tests/test_Crystal.py | 12 +-
Tests/test_DSSP_tool.py | 39 +-
Tests/test_DocSQL.py | 6 +-
Tests/test_Emboss.py | 4 +-
Tests/test_EmbossPhylipNew.py | 1 +
Tests/test_EmbossPrimer.py | 10 +-
Tests/test_Entrez.py | 30 +-
Tests/test_Entrez_online.py | 83 +-
Tests/test_Entrez_parser.py | 19 +-
Tests/test_Enzyme.py | 29 +
Tests/test_ExPASy.py | 58 +
Tests/test_GACrossover.py | 19 +-
Tests/test_GAMutation.py | 13 +-
Tests/test_GAOrganism.py | 11 +-
Tests/test_GAQueens.py | 79 +-
Tests/test_GARepair.py | 11 +-
Tests/test_GASelection.py | 12 +-
Tests/test_GenBank.py | 82 +-
Tests/test_GenBank_unittest.py | 156 +-
Tests/test_GenomeDiagram.py | 20 +-
Tests/test_GraphicsBitmaps.py | 9 +-
Tests/test_GraphicsChromosome.py | 4 +-
Tests/test_GraphicsDistribution.py | 5 +-
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(-)
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