[med-svn] [python-biopython] branch upstream updated (9511db1 -> d029800)

Andreas Tille tille at debian.org
Tue Dec 19 11:02:18 UTC 2017


This is an automated email from the git hooks/post-receive script.

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

      from  9511db1   Imported Upstream version 1.68+dfsg
       new  d029800   New upstream version 1.70+dfsg

The 1 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 -
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 Bio/AlignIO/ClustalIO.py                           |     8 +-
 Bio/AlignIO/EmbossIO.py                            |    22 +-
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 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 +
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 Bio/CAPS/__init__.py                               |     6 +-
 Bio/Cluster/__init__.py                            |   523 +-
 Bio/Compass/__init__.py                            |     1 +
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 Bio/Data/CodonTable.py                             |     4 +-
 Bio/Data/IUPACData.py                              |     3 +
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 Bio/Graphics/KGML_vis.py                           |    26 +-
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 Tests/test_ClustalOmega_tool.py                    |     4 +-
 Tests/test_Clustalw_tool.py                        |     2 +-
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 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 +
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 setup.py                                           |   304 +-
 647 files changed, 120244 insertions(+), 86711 deletions(-)
 create mode 100644 .appveyor.yml
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 create mode 100644 Tests/Mauve/simple.xmfa.backbone
 create mode 100644 Tests/Mauve/simple.xmfa.bbcols
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 create mode 100644 Tests/biosql.ini.appveyor
 create mode 100644 Tests/motifs/meme_v_4_11_4.txt
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 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
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 create mode 100644 Tests/test_cellosaurus.py
 create mode 100644 Tests/test_mmtf_online.py
 delete mode 100644 Tests/test_py3k.py

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