python-cogent (1.9-6) unstable; urgency=medium

  * Skip some tests that do not create reproducible results at package
    build time
    Closes: #846078

 -- Andreas Tille <tille@debian.org>  Wed, 30 Nov 2016 07:46:45 +0100

python-cogent (1.9-5) unstable; urgency=medium

  * Update d/README.Debian with todo list
  * debhelper 10
  * d/watch: version=4
  * add verbosity to unit tests to enable tracking down #846078

 -- Andreas Tille <tille@debian.org>  Tue, 29 Nov 2016 09:03:40 +0100

python-cogent (1.9-4) unstable; urgency=medium

  * Need to exclude further tests on armhf and mips

 -- Andreas Tille <tille@debian.org>  Thu, 15 Sep 2016 10:45:44 +0200

python-cogent (1.9-3) unstable; urgency=medium

  * (Build-)Depends python-matplotlib
  * Some more tests for certain architectures excluded

 -- Andreas Tille <tille@debian.org>  Thu, 15 Sep 2016 08:07:35 +0200

python-cogent (1.9-2) unstable; urgency=medium

  * Properly test fasttree
  * Exclude some tests on some architectures
  * Try to support rdp_classifier (but failed - no idea why)

 -- Andreas Tille <tille@debian.org>  Wed, 14 Sep 2016 21:49:34 +0200

python-cogent (1.9-1) unstable; urgency=medium

  * New upstream version
  * Fix watch file
  * Fix homepage
  * cme fix dpkg-control
  * Build-Depends: python-setuptools
  * revert cd-hit name change in Debian
    Closes: #835213
  * hardening=+bindnow
  * Build-Depends: cdbfasta

 -- Andreas Tille <tille@debian.org>  Wed, 14 Sep 2016 17:06:59 +0200

python-cogent (1.5.3-10) unstable; urgency=medium

  * mothur does not exist on s390x
  * exclude test failed on i386 also on kfreebsd-i386

 -- Andreas Tille <tille@debian.org>  Wed, 30 Dec 2015 17:43:34 +0100

python-cogent (1.5.3-9) unstable; urgency=medium

  * Different autobuilder seems to fail on different tests - exclude another
    two tests on i386

 -- Andreas Tille <tille@debian.org>  Sat, 26 Dec 2015 07:41:10 +0100

python-cogent (1.5.3-8) unstable; urgency=medium

  * Ignore some more test issues only on ppc64

 -- Andreas Tille <tille@debian.org>  Fri, 25 Dec 2015 13:04:33 +0100

python-cogent (1.5.3-7) unstable; urgency=medium

  * Ignore a few test failures on certain architectures to at least
    document the problem debian/README.source was created

 -- Andreas Tille <tille@debian.org>  Thu, 24 Dec 2015 07:27:11 +0100

python-cogent (1.5.3-6) unstable; urgency=medium

  * Also deal with raxml that only exists on [any-amd64 any-i386]

 -- Andreas Tille <tille@debian.org>  Wed, 23 Dec 2015 20:56:16 +0100

python-cogent (1.5.3-5) unstable; urgency=medium

  * Also deal with infernal that only exists on [any-amd64 any-i386]

 -- Andreas Tille <tille@debian.org>  Wed, 23 Dec 2015 18:16:12 +0100

python-cogent (1.5.3-4) unstable; urgency=medium

  * Build-Depends: bwa [any-amd64] and exclude bwa tests for other
    architectures
    Closes: #808799
  * Really activate tests but only those that are known to pass.  All
    failed tests excluded for the moment - more detailed investigation
    is needed
  * Drop debug package in favour of automatically generated one
  * Add hint about tests to README.Debian.

 -- Andreas Tille <tille@debian.org>  Wed, 23 Dec 2015 15:23:04 +0100

python-cogent (1.5.3-3) unstable; urgency=medium

  * cme fix dpkg-control
  * Priority: optional (except for *-dbg)
  * DEP5
  * debian/watch: Adapted to Github
  * DEP3
  * README.source removed since redundant
  * cme fix dpkg-control
  * Adapt to the naming scheme of cd-hit inside Debian
    Closes: #730515
  * Switch from python-support to pybuild
    Closes: #786073

 -- Andreas Tille <tille@debian.org>  Thu, 21 May 2015 09:29:22 +0200

python-cogent (1.5.3-2biolinux1) trusty; urgency=low

  * Allow use of newer cd-hit that doesn't leave a tmp file
    Note - the tests still fail as output is different, but
    this is a quick fix.
  * Also make the script compatible with our parsinsert package
  * Add suggests dep on both of these
  * Rebuild for Trusty

 -- Tim Booth <tbooth@ceh.ac.uk>  Fri, 25 Apr 2014 17:27:42 +0100

python-cogent (1.5.3-2) unstable; urgency=low

  * debian/rules: Add -f option to rm statements to not fail if
    files to be remove do not exist
    Closes: #710339

 -- Andreas Tille <tille@debian.org>  Thu, 30 May 2013 13:02:05 +0200

python-cogent (1.5.3-1) unstable; urgency=low

  * New upstream
  * debian/control: use dh 9
  * debian/control: set standard to 3.9.4 (no changes)
  * debian/rules: add get-orig-source target
  * debian/rules: remove some superfluous files

  [ Tim Booth ]
  * Added back python2 helper and invoked dh_numpy to sort deps
  * Split out docs into separate package
  * Added extra cleanup to dh_clean

 -- Thorsten Alteholz <debian@alteholz.de>  Sun, 16 May 2013 18:00:00 +0200

python-cogent (1.5.1-3) UNRELEASED; urgency=low

  * debian/upstream: Added citations

 -- Andreas Tille <tille@debian.org>  Mon, 07 May 2012 15:39:14 +0200

python-cogent (1.5.1-2) unstable; urgency=low

  * Explicitly added python-numpy as dependency
    to binary ... where is the dh_shlibdeps?
    Many thanks to Jakub (Closes: #640262).
  * Added build-dependency on cython after look in setup.py
  * Some further formatting in debian/control
  * Added -dbg package
  * Fiddled with debian/*.install to actually install the libraries
    and fill that -dbg package.
  * Added dependency to underscore.js

 -- Steffen Moeller <moeller@debian.org>  Sun, 04 Sep 2011 10:49:49 +0200

python-cogent (1.5.1-1) unstable; urgency=low

  * New upstream version.
  * Reformatted debian/control description

 -- Steffen Moeller <moeller@debian.org>  Sun, 21 Aug 2011 21:14:08 +0200

python-cogent (1.5-3) unstable; urgency=low

  * debian/control:
    - Remove Sri Girish Srinivasa Murthy from Uploaders
    - Standards-Version: 3.9.2 (no changes needed)
    - python-all-dev (>= 2.6) to be able to use dh_python2
  * debhelper 8 (control+compat)
  * debian/rules: dh_python2
    Finally closes: #596540

 -- Andreas Tille <tille@debian.org>  Wed, 27 Apr 2011 09:16:52 +0200

python-cogent (1.5-2) unstable; urgency=low

  * debian/copyright: Clarified license of two single non-free files
    -> package can go to main
  * debian/control:
    - Added myself to uploaders
    - python-central -> python-support
    - Build-Depends: python-sphinx to create doc in HTML format
    - Depends: libjs-jquery to enable using Debian packaged version
      of this JS library
  * debian/rules:
    - Short dh syntax to simplyfy the following tasks
    - Build html doc from rst
    - avoid compressing used files
  * Removed README.Debian because the non-free issue is solved
  * debian/links: Link against Debian's jquery.js

 -- Andreas Tille <tille@debian.org>  Tue, 01 Mar 2011 11:30:18 +0100

python-cogent (1.5-1) unstable; urgency=low

  * Bumped standard to 3.9.1, no changes required.
  * New upstream version.
    - major additions to Cookbook
    - added AlleleFreqs attribute to ensembl Variation objects.
    - added getGeneByStableId method to genome objects.
    - added Introns attribute to Transcript objects and an Intron class.
    - added Mann-Whitney test and a Monte-Carlo version
    - exploratory and confirmatory period estimation techniques (suitable for
      symbolic and continuous data)
    - Information theoretic measures (AIC and BIC) added
    - drawing of trees with collapsed nodes
    - progress display indicator support for terminal and GUI apps
    - added parser for illumina HiSeq2000 and GAiix sequence files as 
      cogent.parse.illumina_sequence.MinimalIlluminaSequenceParser.
    - added parser to FASTQ files, one of the output options for illumina's
      workflow, also added cookbook demo.
    - added functionality for parsing of SFF files without the Roche tools in
      cogent.parse.binary_sff
    - thousand fold performance improvement to nmds
    - >10-fold performance improvements to some Table operations

 -- Steffen Moeller <moeller@debian.org>  Sat, 04 Dec 2010 22:30:35 +0100

python-cogent (1.4.1-1.2) unstable; urgency=low

  * Non-maintainer upload.
  * Mark package as auto-buildable

 -- Moritz Muehlenhoff <jmm@debian.org>  Wed, 13 Oct 2010 20:56:27 +0200

python-cogent (1.4.1-1.1) unstable; urgency=low

  * Non-maintainer upload.
  * Replace build-dependency on python2.5-dev with python-all-dev. Closes: #596325.

 -- Matthias Klose <doko@debian.org>  Sun, 12 Sep 2010 15:18:44 +0200

python-cogent (1.4.1-1) unstable; urgency=low

  * Initial release (Closes: #587161)

 -- Sri Girish Srinivasa Murthy <srigirish@evolbio.mpg.de>  Sat, 24 Jul 2010 00:53:31 +0200

