[med-svn] [python-biopython] branch master updated (634b43e -> 5009bb6)

Andreas Tille tille at debian.org
Mon Aug 29 12:16:51 UTC 2016


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tille pushed a change to branch master
in repository python-biopython.

      from  634b43e   Upload to unstable
       new  9511db1   Imported Upstream version 1.68+dfsg
       new  a5ef97f   Merge tag 'upstream/1.68+dfsg'
       new  5009bb6   New upstream version

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:
 .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_RNA.dtd => NCBI_Systems.dtd} |   14 +-
 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 +-
 debian/changelog                                   |    6 +
 debian/patches/fix_detection_of_rpsblast.patch     |   17 -
 debian/patches/series                              |    2 -
 .../skip_test_needing_network_connection.patch     |   66 -
 setup.py                                           |   29 +-
 209 files changed, 14375 insertions(+), 13812 deletions(-)
 create mode 100644 .codecov.yml
 create mode 100644 .travis-tox.ini
 copy Bio/Entrez/DTDs/{NCBI_RNA.dtd => NCBI_Systems.dtd} (91%)
 create mode 100644 Bio/PDB/mmtf/DefaultParser.py
 create mode 100644 Bio/PDB/mmtf/__init__.py
 create mode 100644 Doc/examples/alpha.faa
 create mode 100644 Doc/examples/beta.faa
 delete mode 100644 Doc/images/bottle.png
 create mode 100644 Scripts/update_ncbi_codon_table.py
 create mode 100644 Tests/EMBL/embl_with_0_line.embl
 create mode 100644 Tests/PDB/1A8O.mmtf
 create mode 100644 Tests/PDB/4CUP.cif
 create mode 100644 Tests/PDB/4CUP.mmtf
 rename Tests/PDB/{4zhl.cif => 4ZHL.cif} (100%)
 create mode 100644 Tests/PDB/4ZHL.mmtf
 create mode 100644 Tests/PDB/Miller_RASA.txt
 create mode 100644 Tests/PDB/Sander_RASA.txt
 create mode 100644 Tests/PDB/Wilke_RASA.txt
 create mode 100644 Tests/PDB/dssp_xtra_Sander.txt
 create mode 100644 Tests/common_BioSQL_online.py
 copy Tests/{test_BioSQL_MySQLdb.py => test_BioSQL_MySQLdb_online.py} (71%)
 copy Tests/{test_BioSQL_mysql_connector.py => test_BioSQL_mysql_connector_online.py} (71%)
 copy Tests/{test_BioSQL_psycopg2.py => test_BioSQL_psycopg2_online.py} (71%)
 copy Tests/{test_BioSQL_MySQLdb.py => test_BioSQL_sqlite3_online.py} (58%)
 copy Tests/{test_Entrez.py => test_Entrez_parser.py} (98%)
 rename Tests/{test_Phylo_depend.py => test_Phylo_matplotlib.py} (83%)
 create mode 100644 Tests/test_Phylo_networkx.py
 create mode 100644 Tests/test_mmtf.py
 delete mode 100644 debian/patches/fix_detection_of_rpsblast.patch
 delete mode 100644 debian/patches/skip_test_needing_network_connection.patch

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