[med-svn] [python-biopython] branch master created (now 0796da8)

[Andreas Tille]

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

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

        at  0796da8   Packaging moved from SVN to Git

This branch includes the following new commits:

       new  d15dc3d   Creating trunk directory
       new  98b62b3   [svn-inject] Applying Debian modifications to trunk
       new  e4f7a91   XS-Vcs-* tags added
       new  172b584   new release
       new  4d76148   removed .DS_Store.gz file from doc package
       new  0ae9fb1   Removing obsolete XS- prefix
       new  b457a3b   updated changelog
       new  84ce1c6     * Moved wise from recommends to suggests field.   * Removed package tags from debian/control.   * Added homepage field to debian/control.   * Changed maintainer to Debian-Med Packaging Team.
       new  99232f1   build-dep without versions as they are no longer needed
       new  efe047d   +XS-DM-Upload-Allowed: Yes
       new  a68d330   standards version 3.7.3
       new  57acb36   converted debian/copyright to utf-8
       new  1678fc6   new maintainer e-mail address
       new  5f29866   debian/{copyright,README.Debian}: changed e-mail address
       new  40009a4   Fixing case mistake
       new  faf5d03   * Using DM-Upload-Allowed instead of XS-DM-Upload-Allowed * Added ?rev=0&sc=0 to Vcs-Browser fields * Sanitized Vcs-* fields
       new  7159f4b   new upstream release
       new  ccd9bc7   changed section of doc-base tutorial
       new  acb52f6   Add dependency on python-numeric-ext (Bio.PDB use MLab from this package)
       new  e8bf531   Spelling mistake in last changelog entry fixed
       new  f03bf51   Removed dependency on python-numeric-ext
       new  4ff9d02   new upstream release
       new  caa2560   New upstream release; some issues remain to be fixed before upload.
       new  4ab3bd1   Added missing comma.
       new  bf91221   Added mmCIF support, use Debhelper 7 and quilt, fixed doc-base registration.
       new  62f8151   Described patch
       new  4e65889   Enabled tests (test_Wise fails, unfortunately).
       new  8d5be8e   Added a patch that prevents the tests from failing with Debian's version of Wise.
       new  5a439b8   Forgot to patch also the output file, that is used to compare to the local result.
       new  5c62da0   Corrected a typo and upload to unstable.
       new  b583e27   Build-depend on wise for the tests after building.
       new  4c46b84   Added python-mysqldb to the Build-Depends, again for the tests.
       new  af8b453   Changed the description of python-biopython-sql according to Peter Cock's suggestions.
       new  0ba2ed6   new upstream release
       new  b94f6ba   dropped biopython-martel
       new  ecec3b7   debian/control: added missing separator
       new  4dc3408   debian/control: added note
       new  61ebb2b   new upstream release
       new  7e6b332   merged patch from ubuntu
       new  e965e13   new upstream release
       new  03626fa   standards version 3.8.3; added README.source
       new  4fcb25f   s/Debian-Med/Debian Med
       new  224ecf7   new upstream release
       new  e810734   upstream release 1.54
       new  ed6b895   release 1.56-1
       new  2833a67   release 1.57-1
       new  9f8ef60   release 1.58-1
       new  ef6b232   release 1.59-1
       new  a99d0ff   Took over citation information from tasks file
       new  2c4c92e   Fixed Vcs fields
       new  41a4b99   Valid BibTeX authors field
       new  2482f5a   release 1.60-1
       new  d0c6bae   standards version
       new  822c597   release 1.61-1
       new  e504295   python-biopython: release 1.62-1
       new  d88d802   Move debian/upstream to debian/upstream/metadata
       new  44962d5   cme fix dpkg-control
       new  89707e7   Commit current but non-working status of packaging to ask for help on debian-python list
       new  0ed32fc   Remove comment
       new  e77c17e   Follow some hints from Debian Python team
       new  58a6d1e   More verbose testing by installing some more tools as Build-Depends to enable testing these on one hand and excluding some tests in need of online connection
       new  93cf14f   Exclude tests that need online access
       new  f0df661   Enhanced testing and documentation of the testing in README.source
       new  9a8f5bf   Enable more testing and fix Emboss test
       new  b9563a1   Clean up behind tests
       new  0a78c02   Put files in right packages
       new  4d89484   Exclude another test relying on non-free software
       new  f4d6b55   Update todo list in changelog
       new  9bf8cd5   DEP3
       new  0eda435   merged old changelog from version 1.63-1
       new  8ed1df6   removed bwa from build-dependencies
       new  1d952ba   Run bwa test on amd64 architectures
       new  770edea   *really* make test of bwa architecture dependant; fix issue with empty __pycache__ dir
       new  b0a0bf6   DSSP fix; excluded BioSQL_MySQLdb BioSQL_psycopg2 which require internet access
       new  7c1b561   Better documentation for the reasons why we exclude the database tests
       new  56fdcd3   Better documentation of the excluded database tests
       new  e60c7f4   a very first autopkgtest
       new  46747c4   Please leave the possibility to test the package at build time ... at least as long as the issue discussed on Debian Python list is open.  BTW, the test control file becomes *way* more simple if we leave it this way and as I wrote on the mainling list both tests make perfectly sense.
       new  20e2ac1   Fix test suite run
       new  8eab6b7   Make sure test suite will at least run in autopkgtest; need to check why it triggers more failures than at package build time
       new  19deb57   Enhance autopkgtest and add README.test
       new  4a352a0   More enhancements of testing
       new  eef4e88   we really need this gzipped duplicate of the example.fastq file to pass the BGZF compression test
       new  bd83438   Use offline option of run_tests.py which has the side effekt that failures are not hidden any more by setup.py.  So for the moment we need to exclude also tests that fail for unknown reasons.  Further debugging is needed - perhaps we might upload anyway and leave this for further investigation and drop an paragraph rin README.tests
       new  8feea31   Since we are running the test suite directly not via setup.py the failed tests would stop the build.  So these are separated now and left for further inspection via a script running all the tests.
       new  d4eceb1   Fixed and enhanced test script
       new  4fc1699   Further small enhancement and simplifications for the test suite
       new  04df1ba   Deal with Tutorial test
       new  876a317   Additional Build-Depends: python-imaging; We need python-rdflib (>=4) - deactivate the test until we detect that this version is available
       new  9b28da6   Add Upstream-Contact; DEP5
       new  0f1566d   add missing test_Fasttree_tool ... but this does not help for the test result
       new  06be483   Add some patches enhancing the test suite
       new  6c053cc   Upload to unstable
       new  a18a241   Remove Bio\Entrez\DTDs\mathml2-qname-1.mod
       new  04bd87e   Force writable HOME to make sure t-coffee test will pass
       new  01fdf63   Upload to unstable
       new  67ecc66   Set HOME=/tmp also in autopkgtest
       new  e3136e0   Do not try to create doc in arch-only builds
       new  85de0c2   Fix autopkgtest; move ncbi-blast+ from Suggests to Recommends
       new  8fe8328   Commit latest change: Apply upstream fix to fix cpairwise2 import issue under python3
       new  829187f   New upstream version
       new  aa2404c   Build-Depends raxml only on those architectures where it is available
       new  4539460   Updated patches to new upstream version
       new  04c6854   Upload to unstable
       new  3f20116   Use mktemp as HOME for testing
       new  400041d   Use HOME in build_dir for testing
       new  658d317   Try to get the package finally build on all architectures by skiping test on mips architecture which is known to fail and versioned (Build-)Depends wise
       new  70f3a21   Patch provided by upstream to run test suite on PowerPC
       new  e3838f9   Install egg metadata
       new  14e8ac1   Add samtools to Build-Depends + Recommends since it is checked in test suite
       new  f830df8   Several changes in one rush - main important one is not testing samtools
       new  594cd7d   2015/03/03-09:29:17 (Linux debian-med unknown)
       new  1777657   New upstream version
       new  41a881b   Refreshed patches
       new  eb82400   Add comment about fastsimcoal
       new  64b8ad1   More precise explanation for fastsimcoal
       new  ff53b3c   Provide part of doc in test dir since it is needed to run the test suite
       new  a992e8f   Apply fix for broken test from Upstream Git
       new  7e4c164   Versioned (Build-)Depends: python-rdflib (>= 4), Prevent privacy-breach-logo, Upload to unstable
       new  ed921d8   Build-Depends & Suggests: phylip + fixed test_phyml_tool
       new  c7cd288   Activate more tests formerly deactivated
       new  16e238d   Enable Fasttree_tool test
       new  004e7bd   Enable test GenomeDiagram
       new  98dacc3   Verify that samtools test is really creating problems and upload to unstable
       new  37a5218   Also run Tutorial test
       new  d3c5d7f   Prefer Github as contact point
       new  f57a51e   Fix for mafft test
       new  3b9883c   Add link to github issue
       new  8583e74   Build-Depends: python3-mysqldb
       new  7115697   Upload to unstable
       new  0b0f29a   Remove patches applied upstream
       new  8201d45   Upload to unstable
       new  80d5869   Imported Upstream version 1.66+dfsg
       new  22e5aa4   Merge tag 'upstream/1.66+dfsg'
       new  0a0022a   Re-add debian/ dir
       new  0796da8   Packaging moved from SVN to Git

The 136 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.


-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-biopython.git