python-biopython (1.73+dfsg-1) unstable; urgency=medium
* New upstream version
* debhelper 12
* Standards-Version: 4.3.0
-- Andreas Tille <tille@debian.org> Fri, 11 Jan 2019 23:23:52 +0100
python-biopython (1.72+dfsg-2) unstable; urgency=medium
[ Andreas Tille ]
* Remove unneeded comment about samtools - which is not found by biopython
anyway
[ Graham Inggs ]
* Team upload
* Fix compatibility with ReportLab 3.5 (Closes: #913064)
* Clean up some trailing whitespace in debian/* files
-- Graham Inggs <ginggs@debian.org> Wed, 05 Dec 2018 11:41:01 +0000
python-biopython (1.72+dfsg-1) unstable; urgency=medium
* New upstream version
Closes: #904317
* Standards-Version: 4.1.5
* debian/rules: Respect DEB_BUILD_OPTIONS in dh_auto_test
* Drop ancient Python version fields
* Deactivate exclusion of samtools_tool test and see if it works
-- Andreas Tille <tille@debian.org> Sat, 28 Jul 2018 04:45:32 +0200
python-biopython (1.71+dfsg-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.1.3
* Point Vcs fields to salsa.debian.org
* debhelper 11
* Add dh-python to Build-Depends since this will be dropped from python3's
Depends soon
* Fix Python version in Suggestes
* Make sure Doc dir ends up in python-biopython-doc package
-- Andreas Tille <tille@debian.org> Fri, 06 Apr 2018 09:03:06 +0200
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 <tille@debian.org> 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 <tille@debian.org> 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 <moeller@debian.org> 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 <moeller@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> Sun, 15 Jan 2017 14:56:26 +0100
python-biopython (1.68+dfsg-1) unstable; urgency=medium
* New upstream version
-- Andreas Tille <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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
<mjldehoon@yahoo.com>)
Closes: #751277
* Install egg metadata
Closes: #743927
* Add samtools to Build-Depends + Recommends since it is checked in test
suite
-- Andreas Tille <tille@debian.org> 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 <tille@debian.org> 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 <jwilk@debian.org>
for the patch)
Closes: #751586
-- Andreas Tille <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> Thu, 06 Mar 2014 11:51:27 +0100
python-biopython (1.63-1) unstable; urgency=low
* New upstream release
-- Philipp Benner <philipp@debian.org> 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 <philipp@debian.org> 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 <philipp@debian.org> 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 <philipp@debian.org> 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 <philipp@debian.org> 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 <philipp@debian.org> Wed, 02 Nov 2011 19:51:49 +0000
python-biopython (1.57-1) unstable; urgency=low
* New upstream release (Closes: #585282).
-- Philipp Benner <philipp@debian.org> Sun, 10 Apr 2011 17:58:01 +0000
python-biopython (1.56-1) unstable; urgency=low
* New upstream release.
-- Philipp Benner <philipp@debian.org> Thu, 02 Dec 2010 17:30:09 +0000
python-biopython (1.54-1) unstable; urgency=low
* New upstream release.
-- Philipp Benner <philipp@debian.org> Fri, 28 May 2010 00:06:43 +0200
python-biopython (1.53-1) unstable; urgency=low
* New upstream release.
-- Philipp Benner <philipp@debian.org> Mon, 21 Dec 2009 15:30:37 +0000
python-biopython (1.52-1) unstable; urgency=low
* New upstream release.
-- Philipp Benner <philipp@debian.org> 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 <philipp@debian.org> 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 <philipp@debian.org> 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 <philipp@debian.org> 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 <pbenner@uni-osnabrueck.de> 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 <plessy@debian.org> 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 <pbenner@uni-osnabrueck.de> 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 <pbenner@uni-osnabrueck.de> 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 <mok@bioxray.au.dk> Wed, 23 Apr 2008 00:01:16 +0200
python-biopython (1.45-1) unstable; urgency=low
* New upstream release.
* Added doc-base.
-- Philipp Benner <pbenner@uni-osnabrueck.de> 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 <pbenner@uni-osnabrueck.de> 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 <mail@philipp-benner.de> 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 <mail@philipp-benner.de> 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 <mail@philipp-benner.de> 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 <mail@philipp-benner.de> Tue, 27 Mar 2007 17:45:58 +0200
python-biopython (1.42-2) unstable; urgency=low
* uscan support
* package tags
-- Philipp Benner <mail@philipp-benner.de> Sat, 9 Sep 2006 14:39:18 +0200
python-biopython (1.42-1) unstable; urgency=low
* New upstream release
-- Philipp Benner <mail@philipp-benner.de> 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 <madcoder@debian.org> 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 <mail@philipp-benner.de> Mon, 20 Feb 2006 21:02:18 +0100
python-biopython (1.41-1) unstable; urgency=low
* New upstream release
-- Philipp Benner <mail@philipp-benner.de> 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 <mail@philipp-benner.de> 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 <mail@philipp-benner.de> 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 <mail@philipp-benner.de> 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 <mail@philipp-benner.de> Sun, 10 Oct 2004 19:48:04 +0200
python-biopython (1.30-1) unstable; urgency=low
* Initial Release. (closes: #157402)
-- Philipp Benner <mail@philipp-benner.de> Tue, 21 Sep 2004 20:02:00 +0200