python-biopython (1.70+dfsg-4) unstable; urgency=medium * Symlink to mathml2.dtd of w3-dtd-mathml package Closes: #672407 * Standards-Version: 4.1.2 -- Andreas Tille Tue, 19 Dec 2017 11:07:47 +0100 python-biopython (1.70+dfsg-3) unstable; urgency=medium * Copy *.rst doc files. Closes: #872222 * Apply two upstream patches to deal with change in BWA output Closes: #880236 * Drop duplicated python*-numpy in Build-Depends * Standards-Version: 4.1.1 * Fix permission of dtd files -- Andreas Tille Tue, 07 Nov 2017 13:24:21 +0100 python-biopython (1.70+dfsg-2) unstable; urgency=medium * Team upload * Fixed build dependencies (added python-setuptools) (Closes: #869597). -- Steffen Moeller Mon, 31 Jul 2017 18:24:01 +0200 python-biopython (1.70+dfsg-1) unstable; urgency=medium * Team upload * New upstream release. * debian/upstream/metadata: Added references to OMICtools, bio.tools, RRID * debian/rules: Merged two redundant clean overrides -- Steffen Moeller Sun, 23 Jul 2017 18:08:39 +0200 python-biopython (1.68+dfsg-3) unstable; urgency=medium * (Build-)Depend: phyml only on those architectures where it is available * Relax test conditions in test_phenotype_fit to work around some rounding differences on arm64 (see https://github.com/biopython/biopython/issues/1038 ) -- Andreas Tille Fri, 20 Jan 2017 16:52:04 +0100 python-biopython (1.68+dfsg-2) unstable; urgency=medium * Add Tutorial.tex to *-doc package since its used in autopkgtest and its just an ignorable payload for this package * debhelper 10 * d/watch: version=4 * Add python-scipy since it is used in test suite -- Andreas Tille Sun, 15 Jan 2017 14:56:26 +0100 python-biopython (1.68+dfsg-1) unstable; urgency=medium * New upstream version -- Andreas Tille Mon, 29 Aug 2016 13:23:35 +0200 python-biopython (1.67+dfsg-1) unstable; urgency=medium * New upstream version * Point d/watch to github * xz compression in d/watch * Take over patch from upstream to fix detection of rpsblast * Skip test needing a network connection * Add +bindnow hardening option * Delete useless .cvsignore files from package * New Build-Depends for documentation: hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended * Makefile for Doc needs to be separately called (clean and build) * Remove doc sources from binary doc package -- Andreas Tille Thu, 09 Jun 2016 13:05:14 +0200 python-biopython (1.66+dfsg-3) unstable; urgency=medium * Apply fix from upstream for test case dealing with new blastp output format Closes: #824048 * cme fix dpkg-control -- Andreas Tille Thu, 19 May 2016 16:48:15 +0200 python-biopython (1.66+dfsg-2) unstable; urgency=medium * Packaging moved from SVN to Git * Bumped Standards-Version * Exclude phyml test for the moment Closes: #813262 -- Andreas Tille Wed, 09 Mar 2016 15:25:38 +0100 python-biopython (1.66+dfsg-1) unstable; urgency=medium * New upstream version (some patches applied upstream) -- Andreas Tille Sun, 08 Nov 2015 19:28:26 +0100 python-biopython (1.65+dfsg-3) unstable; urgency=medium * Also run Tutorial test * Prefer Github as contact point * Build-Depends: python3-mysqldb Closes: #801112 -- Andreas Tille Tue, 06 Oct 2015 16:53:06 +0200 python-biopython (1.65+dfsg-2) unstable; urgency=medium * Build-Depends & Suggests: phylip + fixed test_phyml_tool Closes: #799820 * debian/clean: Remove test results occuring now since phylip can be used * Activate more tests formerly deactivated -- Andreas Tille Wed, 23 Sep 2015 15:18:58 +0200 python-biopython (1.65+dfsg-1) unstable; urgency=medium * New upstream version * Apply fix for broken test from Upstream Git * Versioned (Build-)Depends: python-rdflib (>= 4) * Prevent privacy-breach-logo -- Andreas Tille Tue, 12 May 2015 11:08:43 +0200 python-biopython (1.64+dfsg-5) unstable; urgency=medium * Exclude samtools test from unit testing for the moment since this package is in flux and it is not clear what architectures will be supported finally * Do not suggest python3 packages in python-biopython and no python package sin python3-biopython * cme fix dpkg-control -- Andreas Tille Wed, 24 Sep 2014 10:08:12 +0200 python-biopython (1.64+dfsg-4) unstable; urgency=medium * debian/patches/fix_test_problem_on_powerpc.patch: Patch provided by upstream to run test suite on PowerPC (thanks to Michiel de Hoon ) Closes: #751277 * Install egg metadata Closes: #743927 * Add samtools to Build-Depends + Recommends since it is checked in test suite -- Andreas Tille Mon, 01 Sep 2014 15:59:30 +0200 python-biopython (1.64+dfsg-3) unstable; urgency=medium * Skip test on mips architecture which is known to fail * Versioned (Build-)Depends wise (>= 2.4.1-16) to make sure tests will pass on each architecture (problems with previous wise on powerpc, s390x) -- Andreas Tille Fri, 15 Aug 2014 11:41:23 +0200 python-biopython (1.64+dfsg-2) unstable; urgency=medium * Use HOME in build_dir for testing (thanks to Jakub Wilk for the patch) Closes: #751586 -- Andreas Tille Sat, 14 Jun 2014 20:12:02 +0200 python-biopython (1.64+dfsg-1) unstable; urgency=medium * New upstream version * Build-Depends raxml only on those architectures where it is available Closes: #750845 -- Andreas Tille Sun, 08 Jun 2014 10:25:35 +0200 python-biopython (1.63+dfsg-5) unstable; urgency=medium * Apply upstream fix to fix cpairwise2 import issue under python3 Closes: #747494 -- Andreas Tille Sat, 10 May 2014 07:52:48 +0200 python-biopython (1.63+dfsg-4) unstable; urgency=medium [ Martin Pitt ] * Depend on our own packages in the autopkgtest and add missing "allow-stderr" restriction. Closes: #747391 [ Andreas Tille ] * Move ncbi-blast+ from Suggests to Recommends due to a hint from upstream -- Andreas Tille Thu, 08 May 2014 11:33:47 +0200 python-biopython (1.63+dfsg-3) unstable; urgency=medium * Set HOME=/tmp also in autopkgtest * Do not try to create doc in arch-only builds -- Andreas Tille Sun, 04 May 2014 00:18:47 +0200 python-biopython (1.63+dfsg-2) unstable; urgency=medium * Force writable HOME to make sure t-coffee test will pass Closes: #746624 -- Andreas Tille Fri, 02 May 2014 23:14:50 +0200 python-biopython (1.63+dfsg-1) unstable; urgency=medium * Remove Bio\Entrez\DTDs\mathml2-qname-1.mod Closes: #746484 -- Andreas Tille Wed, 30 Apr 2014 14:47:53 +0200 python-biopython (1.63-2) unstable; urgency=medium * Enable Python3 * debian/copyright: - Add Upstream-Contact - DEP5 * Run (nearly) full test suite * Add autopkgtest * Add packages from Build-Depends needed for tests to Depends -- Andreas Tille Thu, 06 Mar 2014 11:51:27 +0100 python-biopython (1.63-1) unstable; urgency=low * New upstream release -- Philipp Benner Thu, 09 Jan 2014 15:38:19 +0100 python-biopython (1.62-1) unstable; urgency=low * New upstream release * Using CDBS to build the package -- Philipp Benner Sun, 15 Sep 2013 16:36:26 +0200 python-biopython (1.61-1) unstable; urgency=low [ Andreas Tille ] * debian/upstream: - Took over citation information from tasks file - Valid BibTeX authors field - Firstnames of authors * debian/control: Fixed Vcs fields [ Philipp Benner ] * New upstream release * Standards version 3.9.4 -- Philipp Benner Thu, 14 Feb 2013 22:08:04 +0100 python-biopython (1.60-1) unstable; urgency=low * New upstream release. * Removed quilt dependency. * Migrated to dh_python2. * patches/01-enable-mmCIF.patch: not required anymore. * debian/source/format: 3.0 (quilt) added. * debian/rules: added hardening flags. -- Philipp Benner Sat, 29 Sep 2012 16:43:59 +0200 python-biopython (1.59-1) unstable; urgency=low * New upstream release. * debian/control: Standards version 3.9.3. * debian/rules: added dh_numpy. -- Philipp Benner Fri, 09 Mar 2012 13:38:09 +0000 python-biopython (1.58-1) unstable; urgency=low * New upstream release. * debian/rules: added targets build-arch and build-indep. * debian/control: Standards version 3.9.2. -- Philipp Benner Wed, 02 Nov 2011 19:51:49 +0000 python-biopython (1.57-1) unstable; urgency=low * New upstream release (Closes: #585282). -- Philipp Benner Sun, 10 Apr 2011 17:58:01 +0000 python-biopython (1.56-1) unstable; urgency=low * New upstream release. -- Philipp Benner Thu, 02 Dec 2010 17:30:09 +0000 python-biopython (1.54-1) unstable; urgency=low * New upstream release. -- Philipp Benner Fri, 28 May 2010 00:06:43 +0200 python-biopython (1.53-1) unstable; urgency=low * New upstream release. -- Philipp Benner Mon, 21 Dec 2009 15:30:37 +0000 python-biopython (1.52-1) unstable; urgency=low * New upstream release. -- Philipp Benner Wed, 30 Sep 2009 10:16:03 +0000 python-biopython (1.51final-2) unstable; urgency=low * Merged patch from ubuntu to make the package ready for python2.6 (Closes: #543236). -- Philipp Benner Mon, 24 Aug 2009 09:29:27 +0000 python-biopython (1.51final-1) unstable; urgency=low * New upstream release * debian/control: suggesting muscle, clustalw, mafft, emboss, and blast2 for installation -- Philipp Benner Wed, 19 Aug 2009 10:41:19 +0000 python-biopython (1.51b-2) unstable; urgency=low * Dropped python-biopython-martel. * Dropped dependency on python-egenix-mxtexttools. * Removed DM-Upload-Allowed: yes. -- Philipp Benner Tue, 11 Aug 2009 19:47:52 +0000 python-biopython (1.51b-1) unstable; urgency=low * New upstream release * debian/control: - moved python-martel back to section python (python packages do not use section oldlibs) * debian/patches/02-fix-wise-test.patch - removed (merged with upstream) * debian/control: - Changed the description of python-biopython-sql according to Peter Cock's suggestions. [Charles Plessy] -- Philipp Benner Sat, 27 Jun 2009 15:14:52 +0000 python-biopython (1.49-1) unstable; urgency=low * New upstream release. - uses NumPy rather than its precursor Numeric (Closes: #478457) - Martel, Bio.Mindy, Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and Bio.IntelliGenetics are deprecated. - Bio.PubMed and the online code in Bio.GenBank are now considered obsolete and will be deprecated in a future release. - Bio.Fasta is also considered to be obsolete and will eventually be deprecated. * debian/control: - added myself as Uploader. - depends on python-numpy instead of python-numeric-ext. - moved python-martel to oldlibs section, priority extra as it is deprecated, and indicate this in the description. - build-depend on python-mysqldb and wise for the tests after building. * Use Debhelper 7 (debian/co{ntrol,mpat}). * debian/copyright: added myself to the Hall of Fame and updated to latest draft of the machine-readable format. * debian/watch: makes beta versions lower by prepending a tilde between numbers and letters (1.49b -> 1.49~b). * mmCIF support enabled: - debian/patches/01-enable-mmCIF.patch: as the name indicates ;) - debian/rules: patch and unpatch through /usr/share/quilt/quilt.make. - debian/control: build-depends on quilt. * debian/python-biopython-doc.doc-base: corrected index name that was changed upstream. * debian/patches/02-fix-wise-test.patch: prevents tests failing with Debian's version of Wise. * debian/rules: perform tests after build. -- Charles Plessy Fri, 23 Jan 2009 22:19:50 +0900 python-biopython (1.47-1) unstable; urgency=low * New upstream release * Standards version 3.8.0 -- Philipp Benner Sun, 03 Aug 2008 14:29:33 +0200 python-biopython (1.45-3) unstable; urgency=low * Removed dependency on python-numeric-ext since it is already in the recommends field -- Philipp Benner Sun, 01 Jun 2008 10:34:48 +0200 python-biopython (1.45-2) unstable; urgency=low * Add dependency on python-numeric-ext (Bio.PDB uses MLab from this package) -- Morten Kjeldgaard Wed, 23 Apr 2008 00:01:16 +0200 python-biopython (1.45-1) unstable; urgency=low * New upstream release. * Added doc-base. -- Philipp Benner Sat, 29 Mar 2008 12:20:41 +0100 python-biopython (1.44-3) unstable; urgency=low * New maintainer e-mail address. * debian/control: Added DM-Upload-Allowed: yes. -- Philipp Benner Mon, 14 Jan 2008 18:35:18 +0100 python-biopython (1.44-2) unstable; urgency=low * Moved suggested package python-numeric-ext to recommends field (Closes: #452379). * 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. * Removed .DS_Store.gz file from doc package. -- Philipp Benner Thu, 22 Nov 2007 13:35:00 +0100 python-biopython (1.44-1) unstable; urgency=low * New upstream release. * Machine interpretable copyright file. -- Philipp Benner Fri, 16 Nov 2007 16:49:11 +0100 python-biopython (1.43-2) unstable; urgency=low * Rebuild for python-2.5 support (Closes: #424025). -- Philipp Benner Thu, 14 Jun 2007 21:40:18 +0200 python-biopython (1.43-1) unstable; urgency=low * New upstream release * Adapted debian-med tags -- Philipp Benner Tue, 27 Mar 2007 17:45:58 +0200 python-biopython (1.42-2) unstable; urgency=low * uscan support * package tags -- Philipp Benner Sat, 9 Sep 2006 14:39:18 +0200 python-biopython (1.42-1) unstable; urgency=low * New upstream release -- Philipp Benner Sat, 22 Jul 2006 01:30:51 +0200 python-biopython (1.41-2.1) unstable; urgency=low * Non-maintainer upload. * Update package to the last python policy (Closes: #373515). -- Pierre Habouzit Fri, 30 Jun 2006 13:45:39 +0200 python-biopython (1.41-2) unstable; urgency=low * suggests python-numeric-ext * now with KDTree -- Philipp Benner Mon, 20 Feb 2006 21:02:18 +0100 python-biopython (1.41-1) unstable; urgency=low * New upstream release -- Philipp Benner Sat, 5 Nov 2005 20:15:03 +0100 python-biopython (1.40b-3) unstable; urgency=low * now using compatibility level 4 * removed obsolete dependencies (closes: #328142) -- Philipp Benner Wed, 14 Sep 2005 12:06:06 +0200 python-biopython (1.40b-2) unstable; urgency=low * Function `mmcif_get_string' implicitly converted to pointer (closes: #326403) * now standards version 3.6.2 -- Philipp Benner Wed, 7 Sep 2005 09:53:30 +0200 python-biopython (1.40b-1) unstable; urgency=low * new release * dropped support for python2.2 -- Philipp Benner Tue, 05 Apr 2005 20:55:59 +0200 python-biopython (1.30-2) unstable; urgency=low * Fixed bugs in debian/rules and debian/control which prevented porting the package. * Using -fPIC to build shared lib KDTree. (closes: #278959) -- Philipp Benner Sun, 10 Oct 2004 19:48:04 +0200 python-biopython (1.30-1) unstable; urgency=low * Initial Release. (closes: #157402) -- Philipp Benner Tue, 21 Sep 2004 20:02:00 +0200