[med-svn] [python-biopython] branch master updated (a28a896 -> 93f39f7)
Steffen Möller
moeller at moszumanska.debian.org
Mon Jul 24 13:56:44 UTC 2017
This is an automated email from the git hooks/post-receive script.
moeller pushed a change to branch master
in repository python-biopython.
from a28a896 Upload to unstable
new e6d5572 New upstream version 1.70+dfsg
new ab67306 Updated version 1.70+dfsg from 'upstream/1.70+dfsg'
new 93f39f7 Preparations for new Upstream versions
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.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 +-
Bio/AlignIO/EmbossIO.py | 22 +-
Bio/AlignIO/FastaIO.py | 21 +-
Bio/AlignIO/Interfaces.py | 49 +-
Bio/AlignIO/MafIO.py | 718 +
Bio/AlignIO/MauveIO.py | 321 +
Bio/AlignIO/NexusIO.py | 94 +-
Bio/AlignIO/PhylipIO.py | 22 +-
Bio/AlignIO/StockholmIO.py | 107 +-
Bio/AlignIO/__init__.py | 90 +-
Bio/Alphabet/IUPAC.py | 41 +-
Bio/Alphabet/Reduced.py | 12 +
Bio/Alphabet/__init__.py | 26 +-
Bio/Application/__init__.py | 95 +-
Bio/Blast/Applications.py | 31 +
Bio/Blast/NCBIStandalone.py | 24 +-
Bio/Blast/NCBIXML.py | 156 +-
Bio/Blast/ParseBlastTable.py | 1 +
Bio/Blast/Record.py | 10 +
Bio/CAPS/__init__.py | 6 +-
Bio/Cluster/__init__.py | 523 +-
Bio/Compass/__init__.py | 1 +
Bio/Crystal/__init__.py | 8 +-
Bio/Data/CodonTable.py | 4 +-
Bio/Data/IUPACData.py | 3 +
Bio/DocSQL.py | 15 +-
Bio/Emboss/Applications.py | 23 +-
Bio/Emboss/Primer3.py | 5 +-
Bio/Emboss/PrimerSearch.py | 15 +-
Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd | 280 +
Bio/Entrez/Parser.py | 20 +-
Bio/Entrez/__init__.py | 53 +-
Bio/ExPASy/Enzyme.py | 32 +-
Bio/ExPASy/Prodoc.py | 24 +-
Bio/ExPASy/Prosite.py | 141 +-
Bio/ExPASy/ScanProsite.py | 2 +-
Bio/ExPASy/__init__.py | 111 +-
Bio/ExPASy/cellosaurus.py | 164 +
Bio/FSSP/FSSPTools.py | 6 +-
Bio/FSSP/__init__.py | 15 +-
Bio/FSSP/fssp_rec.py | 1 +
Bio/File.py | 119 +-
Bio/GA/Crossover/General.py | 15 +-
Bio/GA/Crossover/GeneralPoint.py | 77 +-
Bio/GA/Crossover/Point.py | 4 +-
Bio/GA/Crossover/TwoPoint.py | 15 +-
Bio/GA/Crossover/Uniform.py | 8 +-
Bio/GA/Evolver.py | 24 +-
Bio/GA/Mutation/General.py | 20 +-
Bio/GA/Mutation/Simple.py | 30 +-
Bio/GA/Organism.py | 95 +-
Bio/GA/Repair/Stabilizing.py | 19 +-
Bio/GA/Selection/Abstract.py | 22 +-
Bio/GA/Selection/Diversity.py | 15 +-
Bio/GA/Selection/RouletteWheel.py | 34 +-
Bio/GA/Selection/Tournament.py | 18 +-
Bio/GA/__init__.py | 16 +-
Bio/GenBank/Record.py | 245 +-
Bio/GenBank/Scanner.py | 330 +-
Bio/GenBank/__init__.py | 269 +-
Bio/GenBank/utils.py | 10 +-
Bio/Geo/Record.py | 1 +
Bio/Graphics/BasicChromosome.py | 126 +-
Bio/Graphics/ColorSpiral.py | 17 +-
Bio/Graphics/Comparative.py | 8 +-
Bio/Graphics/DisplayRepresentation.py | 31 +-
Bio/Graphics/Distribution.py | 13 +-
Bio/Graphics/GenomeDiagram/_AbstractDrawer.py | 191 +-
Bio/Graphics/GenomeDiagram/_CircularDrawer.py | 318 +-
Bio/Graphics/GenomeDiagram/_Colors.py | 155 +-
Bio/Graphics/GenomeDiagram/_CrossLink.py | 19 +-
Bio/Graphics/GenomeDiagram/_Diagram.py | 130 +-
Bio/Graphics/GenomeDiagram/_Feature.py | 197 +-
Bio/Graphics/GenomeDiagram/_FeatureSet.py | 16 +-
Bio/Graphics/GenomeDiagram/_Graph.py | 180 +-
Bio/Graphics/GenomeDiagram/_GraphSet.py | 157 +-
Bio/Graphics/GenomeDiagram/_LinearDrawer.py | 428 +-
Bio/Graphics/GenomeDiagram/_Track.py | 331 +-
Bio/Graphics/KGML_vis.py | 26 +-
Bio/Graphics/__init__.py | 2 +-
Bio/HMM/DynamicProgramming.py | 78 +-
Bio/HMM/MarkovModel.py | 100 +-
Bio/HMM/Trainer.py | 139 +-
Bio/HMM/Utilities.py | 10 +-
Bio/Index.py | 7 +-
Bio/KDTree/KDTree.py | 4 +
Bio/KEGG/Compound/__init__.py | 1 +
Bio/KEGG/Enzyme/__init__.py | 4 +-
Bio/KEGG/KGML/KGML_parser.py | 87 +-
Bio/KEGG/KGML/KGML_pathway.py | 116 +-
Bio/KEGG/KGML/__init__.py | 5 +-
Bio/KEGG/Map/__init__.py | 12 +-
Bio/KEGG/REST.py | 2 +-
Bio/KEGG/__init__.py | 18 +-
Bio/LogisticRegression.py | 1 +
Bio/MarkovModel.py | 66 +-
Bio/MaxEntropy.py | 158 +-
Bio/Medline/__init__.py | 2 +
Bio/NMR/NOEtools.py | 2 +-
Bio/NMR/xpktools.py | 11 +-
Bio/NaiveBayes.py | 70 +-
Bio/NeuralNetwork/BackPropagation/Layer.py | 89 +-
Bio/NeuralNetwork/BackPropagation/Network.py | 43 +-
Bio/NeuralNetwork/Gene/Motif.py | 41 +-
Bio/NeuralNetwork/Gene/Pattern.py | 56 +-
Bio/NeuralNetwork/Gene/Schema.py | 200 +-
Bio/NeuralNetwork/Gene/Signature.py | 46 +-
Bio/NeuralNetwork/StopTraining.py | 18 +-
Bio/NeuralNetwork/Training.py | 48 +-
Bio/NeuralNetwork/__init__.py | 15 +-
Bio/Nexus/Nexus.py | 125 +-
Bio/Nexus/StandardData.py | 18 +-
Bio/Nexus/Trees.py | 45 +-
Bio/PDB/AbstractPropertyMap.py | 17 +-
Bio/PDB/Atom.py | 10 +-
Bio/PDB/Chain.py | 30 +-
Bio/PDB/DSSP.py | 151 +-
Bio/PDB/Dice.py | 22 +-
Bio/PDB/Entity.py | 126 +-
Bio/PDB/FragmentMapper.py | 95 +-
Bio/PDB/HSExposure.py | 87 +-
Bio/PDB/MMCIF2Dict.py | 38 +-
Bio/PDB/MMCIFParser.py | 47 +-
Bio/PDB/Model.py | 14 +-
Bio/PDB/NeighborSearch.py | 8 +-
Bio/PDB/PDBIO.py | 33 +-
Bio/PDB/PDBList.py | 321 +-
Bio/PDB/PDBParser.py | 27 +-
Bio/PDB/PSEA.py | 4 +-
Bio/PDB/Polypeptide.py | 40 +-
Bio/PDB/QCPSuperimposer/__init__.py | 80 +-
Bio/PDB/Residue.py | 39 +-
Bio/PDB/ResidueDepth.py | 479 +-
Bio/PDB/Selection.py | 15 +-
Bio/PDB/Structure.py | 8 +-
Bio/PDB/StructureAlignment.py | 68 +-
Bio/PDB/StructureBuilder.py | 70 +-
Bio/PDB/Superimposer.py | 39 +-
Bio/PDB/Vector.py | 169 +-
Bio/PDB/mmtf/DefaultParser.py | 38 +-
Bio/PDB/mmtf/__init__.py | 7 +-
Bio/PDB/parse_pdb_header.py | 23 +-
Bio/ParserSupport.py | 55 +-
Bio/Pathway/__init__.py | 47 +-
Bio/Phylo/Applications/__init__.py | 4 +-
Bio/Phylo/BaseTree.py | 41 +-
Bio/Phylo/CDAO.py | 2 +
Bio/Phylo/CDAOIO.py | 29 +-
Bio/Phylo/Consensus.py | 26 +-
Bio/Phylo/NeXML.py | 2 +
Bio/Phylo/NeXMLIO.py | 11 +-
Bio/Phylo/Newick.py | 2 +
Bio/Phylo/NewickIO.py | 12 +-
Bio/Phylo/NexusIO.py | 2 +-
Bio/Phylo/PAML/_paml.py | 61 +-
Bio/Phylo/PAML/_parse_baseml.py | 18 +-
Bio/Phylo/PAML/_parse_codeml.py | 53 +-
Bio/Phylo/PAML/_parse_yn00.py | 29 +-
Bio/Phylo/PAML/baseml.py | 16 +-
Bio/Phylo/PAML/codeml.py | 19 +-
Bio/Phylo/PAML/yn00.py | 12 +-
Bio/Phylo/PhyloXML.py | 79 +-
Bio/Phylo/PhyloXMLIO.py | 20 +-
Bio/Phylo/TreeConstruction.py | 116 +-
Bio/Phylo/__init__.py | 3 +-
Bio/Phylo/_cdao_owl.py | 3 +-
Bio/Phylo/_io.py | 2 +-
Bio/Phylo/_utils.py | 17 +-
Bio/PopGen/Async/Local.py | 65 -
Bio/PopGen/Async/__init__.py | 122 -
Bio/PopGen/FDist/Async.py | 180 -
Bio/PopGen/FDist/Controller.py | 297 -
Bio/PopGen/FDist/Utils.py | 214 -
Bio/PopGen/FDist/__init__.py | 93 -
Bio/PopGen/GenePop/Controller.py | 104 +-
Bio/PopGen/GenePop/EasyController.py | 45 +-
Bio/PopGen/GenePop/FileParser.py | 81 +-
Bio/PopGen/GenePop/LargeFileParser.py | 12 +-
Bio/PopGen/GenePop/__init__.py | 37 +-
Bio/PopGen/SimCoal/Async.py | 31 -
Bio/PopGen/SimCoal/Cache.py | 86 -
Bio/PopGen/SimCoal/Controller.py | 222 -
Bio/PopGen/SimCoal/Template.py | 228 -
Bio/PopGen/SimCoal/__init__.py | 26 -
Bio/PopGen/SimCoal/data/bottle.par | 14 -
Bio/PopGen/SimCoal/data/decline_lambda.par | 14 -
Bio/PopGen/SimCoal/data/decline_split.par | 23 -
Bio/PopGen/SimCoal/data/island.par | 14 -
Bio/PopGen/SimCoal/data/simple.par | 12 -
Bio/PopGen/SimCoal/data/split_island.par | 17 -
Bio/PopGen/SimCoal/data/split_ssm_1d.par | 17 -
Bio/PopGen/SimCoal/data/split_ssm_2d.par | 17 -
Bio/PopGen/SimCoal/data/ssm_1d.par | 14 -
Bio/PopGen/SimCoal/data/ssm_2d.par | 14 -
Bio/Restriction/PrintFormat.py | 38 +-
Bio/Restriction/Restriction.py | 1132 +-
Bio/Restriction/Restriction_Dictionary.py | 20115 ++++----
Bio/Restriction/__init__.py | 4 +-
Bio/SCOP/Cla.py | 10 +-
Bio/SCOP/Des.py | 6 +-
Bio/SCOP/Dom.py | 7 +-
Bio/SCOP/Hie.py | 5 +-
Bio/SCOP/Raf.py | 57 +-
Bio/SCOP/__init__.py | 160 +-
Bio/SVDSuperimposer/__init__.py | 110 +-
Bio/SearchIO/BlastIO/__init__.py | 16 +-
Bio/SearchIO/BlastIO/blast_tab.py | 14 +-
Bio/SearchIO/BlastIO/blast_text.py | 3 +-
Bio/SearchIO/BlastIO/blast_xml.py | 142 +-
Bio/SearchIO/BlatIO.py | 27 +-
Bio/SearchIO/ExonerateIO/_base.py | 128 +-
Bio/SearchIO/ExonerateIO/exonerate_cigar.py | 8 +-
Bio/SearchIO/ExonerateIO/exonerate_text.py | 21 +-
Bio/SearchIO/ExonerateIO/exonerate_vulgar.py | 4 +-
Bio/SearchIO/FastaIO.py | 17 +-
Bio/SearchIO/HmmerIO/_base.py | 6 +-
Bio/SearchIO/HmmerIO/hmmer2_text.py | 5 +-
Bio/SearchIO/HmmerIO/hmmer3_domtab.py | 29 +-
Bio/SearchIO/HmmerIO/hmmer3_tab.py | 8 +-
Bio/SearchIO/HmmerIO/hmmer3_text.py | 15 +-
Bio/SearchIO/__init__.py | 2 +-
Bio/SearchIO/_index.py | 10 +-
Bio/SearchIO/_model/__init__.py | 2 +-
Bio/SearchIO/_model/_base.py | 2 -
Bio/SearchIO/_model/hit.py | 1 -
Bio/SearchIO/_model/hsp.py | 3 +-
Bio/SearchIO/_model/query.py | 17 +-
Bio/SearchIO/_utils.py | 6 +-
Bio/Seq.py | 677 +-
Bio/SeqFeature.py | 372 +-
Bio/SeqIO/AbiIO.py | 63 +-
Bio/SeqIO/FastaIO.py | 7 +-
Bio/SeqIO/IgIO.py | 1 +
Bio/SeqIO/InsdcIO.py | 183 +-
Bio/SeqIO/Interfaces.py | 63 +-
Bio/SeqIO/PirIO.py | 21 +-
Bio/SeqIO/QualityIO.py | 40 +-
Bio/SeqIO/SeqXmlIO.py | 29 +-
Bio/SeqIO/SffIO.py | 273 +-
Bio/SeqIO/SwissIO.py | 5 +
Bio/SeqIO/TabIO.py | 3 +-
Bio/SeqIO/UniprotIO.py | 76 +-
Bio/SeqIO/__init__.py | 122 +-
Bio/SeqIO/_index.py | 172 +-
Bio/SeqRecord.py | 74 +-
Bio/SeqUtils/CheckSum.py | 1 +
Bio/SeqUtils/CodonUsage.py | 1 -
Bio/SeqUtils/MeltingTemp.py | 14 +-
Bio/SeqUtils/ProtParam.py | 3 +-
Bio/SeqUtils/ProtParamData.py | 2 +-
Bio/SeqUtils/__init__.py | 50 +-
Bio/SeqUtils/lcc.py | 3 +-
Bio/Sequencing/Ace.py | 22 +-
Bio/Sequencing/Applications/_Novoalign.py | 1 +
Bio/Sequencing/Applications/__init__.py | 12 +-
Bio/Sequencing/Applications/_bwa.py | 9 +-
Bio/Sequencing/Applications/_samtools.py | 87 +-
Bio/Sequencing/Phd.py | 5 +-
Bio/Statistics/lowess.py | 14 +-
Bio/SubsMat/FreqTable.py | 4 +-
Bio/SubsMat/MatrixInfo.py | 80 +
Bio/SubsMat/__init__.py | 116 +-
Bio/SwissProt/KeyWList.py | 18 +-
Bio/SwissProt/__init__.py | 142 +-
Bio/TogoWS/__init__.py | 72 +-
Bio/UniGene/__init__.py | 38 +-
Bio/UniProt/GOA.py | 232 +-
Bio/Wise/__init__.py | 11 +-
Bio/Wise/dnal.py | 13 +-
Bio/Wise/psw.py | 12 +-
Bio/__init__.py | 16 +-
Bio/_py3k/__init__.py | 97 +-
Bio/_py3k/_ordereddict.py | 129 -
Bio/_utils.py | 4 +-
Bio/bgzf.py | 27 +-
Bio/codonalign/__init__.py | 99 +-
Bio/codonalign/chisq.py | 256 +-
Bio/codonalign/codonalignment.py | 90 +-
Bio/codonalign/codonalphabet.py | 24 +-
Bio/codonalign/codonseq.py | 83 +-
Bio/kNN.py | 34 +-
Bio/motifs/__init__.py | 40 +-
Bio/motifs/alignace.py | 5 +-
Bio/motifs/applications/_xxmotif.py | 2 +-
Bio/motifs/jaspar/__init__.py | 5 +-
Bio/motifs/jaspar/db.py | 71 +-
Bio/motifs/mast.py | 1 +
Bio/motifs/matrix.py | 73 +-
Bio/motifs/meme.py | 20 +-
Bio/motifs/thresholds.py | 18 +-
Bio/motifs/transfac.py | 186 +-
Bio/pairwise2.py | 199 +-
Bio/phenotype/__init__.py | 1 -
Bio/phenotype/phen_micro.py | 29 +-
Bio/phenotype/pm_fitting.py | 6 +-
Bio/trie.c | 18 +-
Bio/triefind.py | 5 +-
Bio/triemodule.c | 6 +
BioSQL/.flake8 | 15 +
BioSQL/BioSeq.py | 48 +-
BioSQL/BioSeqDatabase.py | 184 +-
BioSQL/DBUtils.py | 27 +-
BioSQL/Loader.py | 154 +-
BioSQL/__init__.py | 10 +-
CONTRIB | 162 +-
CONTRIB.rst | 214 +
CONTRIBUTING.rst | 113 +
DEPRECATED | 692 +-
DEPRECATED => DEPRECATED.rst | 143 +-
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Doc/Tutorial/chapter_cookbook.tex | 184 +-
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Doc/Tutorial/chapter_introduction.tex | 38 +-
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Doc/Tutorial/chapter_motifs.tex | 18 +-
Doc/Tutorial/chapter_pdb.tex | 17 +-
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Doc/Tutorial/chapter_phylo.tex | 2 +-
Doc/Tutorial/chapter_popgen.tex | 5 +-
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README | 261 +-
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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 +-
debian/changelog | 11 +
debian/control | 2 +
debian/patches/fix_test_phyml_tool.patch | 18 -
debian/patches/series | 3 +-
debian/rules | 22 +-
debian/upstream/metadata | 7 +
setup.py | 304 +-
653 files changed, 120279 insertions(+), 86739 deletions(-)
create mode 100644 .appveyor.yml
create mode 100644 Bio/.flake8
delete mode 100644 Bio/Align/Generic.py
create mode 100644 Bio/AlignIO/MafIO.py
create mode 100644 Bio/AlignIO/MauveIO.py
create mode 100644 Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd
create mode 100644 Bio/ExPASy/cellosaurus.py
delete mode 100644 Bio/PopGen/Async/Local.py
delete mode 100644 Bio/PopGen/Async/__init__.py
delete mode 100644 Bio/PopGen/FDist/Async.py
delete mode 100644 Bio/PopGen/FDist/Controller.py
delete mode 100644 Bio/PopGen/FDist/Utils.py
delete mode 100644 Bio/PopGen/FDist/__init__.py
delete mode 100644 Bio/PopGen/SimCoal/Async.py
delete mode 100644 Bio/PopGen/SimCoal/Cache.py
delete mode 100644 Bio/PopGen/SimCoal/Controller.py
delete mode 100644 Bio/PopGen/SimCoal/Template.py
delete mode 100644 Bio/PopGen/SimCoal/__init__.py
delete mode 100644 Bio/PopGen/SimCoal/data/bottle.par
delete mode 100644 Bio/PopGen/SimCoal/data/decline_lambda.par
delete mode 100644 Bio/PopGen/SimCoal/data/decline_split.par
delete mode 100644 Bio/PopGen/SimCoal/data/island.par
delete mode 100644 Bio/PopGen/SimCoal/data/simple.par
delete mode 100644 Bio/PopGen/SimCoal/data/split_island.par
delete mode 100644 Bio/PopGen/SimCoal/data/split_ssm_1d.par
delete mode 100644 Bio/PopGen/SimCoal/data/split_ssm_2d.par
delete mode 100644 Bio/PopGen/SimCoal/data/ssm_1d.par
delete mode 100644 Bio/PopGen/SimCoal/data/ssm_2d.par
delete mode 100644 Bio/_py3k/_ordereddict.py
create mode 100644 BioSQL/.flake8
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create mode 100644 CONTRIB.rst
create mode 100644 CONTRIBUTING.rst
mode change 100644 => 120000 DEPRECATED
copy DEPRECATED => DEPRECATED.rst (87%)
create mode 100644 Doc/examples/.flake8
create mode 100644 Doc/examples/ec_5.4.2.2.txt
create mode 100644 Doc/examples/ls_orchid.gbk.bz2
create mode 100644 Doc/examples/ls_orchid.gbk.gz
create mode 100644 Doc/images/biopython_logo.pdf
create mode 100644 Doc/images/biopython_logo.svg
create mode 100644 Doc/images/biopython_logo_l.png
create mode 100644 Doc/images/biopython_logo_m.png
rename Doc/images/{biopython.jpg => biopython_logo_old.jpg} (100%)
create mode 100644 Doc/images/biopython_logo_s.png
create mode 100644 Doc/images/biopython_logo_xs.png
mode change 100644 => 120000 LICENSE
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copy NEWS => NEWS.rst (67%)
mode change 100644 => 120000 README
mode change 120000 => 100644 README.rst
create mode 100644 Scripts/.flake8
create mode 100644 Tests/.coveragerc
create mode 100644 Tests/.flake8
create mode 100644 Tests/Abi/test.fsa
create mode 100644 Tests/Affy/affy_v4_example.CEL
create mode 100644 Tests/Blat/psl_35_001.psl
create mode 100644 Tests/Blat/psl_35_002.psl
create mode 100644 Tests/Blat/pslx_35_002.pslx
create mode 100644 Tests/Cellosaurus/cell_lines_1.txt
create mode 100644 Tests/Cellosaurus/cell_lines_2.txt
create mode 100644 Tests/Cellosaurus/cell_lines_3.txt
create mode 100644 Tests/Cluster/README
create mode 100644 Tests/Cluster/cyano.txt
create mode 100644 Tests/EMBL/hla_3260_sample.imgt
create mode 100644 Tests/EMBL/kipo_prt_sample.embl
create mode 100644 Tests/GenBank/EU851978_output.gbk
create mode 100644 Tests/GenBank/HM138502_output.gbk
create mode 100644 Tests/GenBank/KF527485_output.gbk
create mode 100644 Tests/Hmmer/text_31b2_hmmsearch_001.out
create mode 100644 Tests/Hmmer/text_31b2_hmmsearch_002.out
create mode 100644 Tests/KEGG/enzyme.4letter
create mode 100644 Tests/KEGG/ko00010.xml
create mode 100644 Tests/KEGG/ko00253.xml
create mode 100644 Tests/MAF/bug2453.maf
create mode 100644 Tests/MAF/bundle_without_target.maf
create mode 100644 Tests/MAF/cnksr3.fa
create mode 100644 Tests/MAF/corrupt.idx
create mode 100644 Tests/MAF/humor.maf
create mode 100644 Tests/MAF/invalid.idx
create mode 100644 Tests/MAF/length_coords_mismatch.maf
create mode 100644 Tests/MAF/ucsc_mm9_chr10.maf
create mode 100644 Tests/MAF/ucsc_mm9_chr10.mafindex
create mode 100644 Tests/MAF/ucsc_mm9_chr10_bad.maf
create mode 100644 Tests/MAF/ucsc_mm9_chr10_bad.mafindex
create mode 100644 Tests/MAF/ucsc_mm9_chr10_big.maf
create mode 100644 Tests/MAF/ucsc_mm9_chr10_big.mafindex
create mode 100644 Tests/MAF/ucsc_test.maf
create mode 100644 Tests/MAF/unfinished.idx
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delete mode 100644 Tests/MEME/mast.dna.oops.txt
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delete mode 100644 Tests/MEME/meme.protein.oops.txt
delete mode 100644 Tests/MEME/meme.protein.tcm.txt
create mode 100644 Tests/Mauve/simple.fa
create mode 100644 Tests/Mauve/simple.xmfa
create mode 100644 Tests/Mauve/simple.xmfa.backbone
create mode 100644 Tests/Mauve/simple.xmfa.bbcols
create mode 100644 Tests/PAML/Alignments/longnames.fasta
copy Tests/PAML/Control_files/yn00/{yn00.ctl => yn00_long.ctl} (80%)
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create mode 100644 Tests/PAML/Results/yn00/yn00-4_8.out
create mode 100644 Tests/PAML/Results/yn00/yn00_long-4_8.out
create mode 100644 Tests/PDB/1A8O.xyzr
create mode 100644 Tests/PDB/1AS5.cif
create mode 100644 Tests/PDB/2BEG.cif
create mode 100644 Tests/PDB/3JQH.cif
create mode 100644 Tests/PDB/alignment_file.fa
create mode 100644 Tests/PDB/lib_10_z_5.txt
delete mode 100644 Tests/PopGen/data_dfst_outfile
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delete mode 100644 Tests/PopGen/dout.cpl
delete mode 100644 Tests/PopGen/dout.dat
delete mode 100644 Tests/PopGen/fdist1
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delete mode 100644 Tests/PopGen/simple.par
create mode 100644 Tests/SwissProt/P84001.xml
create mode 100644 Tests/SwissProt/P97881.xml
create mode 100644 Tests/SwissProt/R5HY77.xml
create mode 100644 Tests/UniProt/goa_yeast.gaf
create mode 100644 Tests/biosql.ini.appveyor
create mode 100644 Tests/motifs/meme_v_4_11_4.txt
create mode 100644 Tests/output/test_AlignIO_MauveIO
delete mode 100644 Tests/output/test_KEGG
delete mode 100644 Tests/output/test_QCPSuperimposer
delete mode 100644 Tests/output/test_SVDSuperimposer
create mode 100644 Tests/test_Affy.py
create mode 100644 Tests/test_AlignIO_MauveIO.py
create mode 100644 Tests/test_ExPASy.py
create mode 100644 Tests/test_MafIO_index.py
create mode 100644 Tests/test_PDBList.py
create mode 100644 Tests/test_PDB_FragmentMapper.py
create mode 100644 Tests/test_PDB_MMCIF2Dict.py
rename Tests/{test_MMCIF.py => test_PDB_MMCIFParser.py} (73%)
create mode 100644 Tests/test_PDB_Polypetide.py
create mode 100644 Tests/test_PDB_StructureAlignment.py
create mode 100644 Tests/test_PDB_Superimposer.py
delete mode 100644 Tests/test_PopGen_DFDist.py
delete mode 100644 Tests/test_PopGen_FDist.py
delete mode 100644 Tests/test_PopGen_FDist_nodepend.py
delete mode 100644 Tests/test_PopGen_FastSimCoal.py
delete mode 100644 Tests/test_PopGen_SimCoal.py
delete mode 100644 Tests/test_PopGen_SimCoal_nodepend.py
create mode 100644 Tests/test_cellosaurus.py
create mode 100644 Tests/test_mmtf_online.py
delete mode 100644 Tests/test_py3k.py
delete mode 100644 debian/patches/fix_test_phyml_tool.patch
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