qiime (1.8.0+dfsg-2) unstable; urgency=medium

  * debian/qiime.links: Fix links to new biom_format
  * debian/control:
     - New dependency: python-qcli (this should be dropped in version
       2.0 of qiime)
     - Recommends: python-mpi4py since this is used in some tests
  * debian/rules: Remove remainings from running test suite

 -- Andreas Tille <tille@debian.org>  Thu, 26 Dec 2013 07:39:57 +0100

qiime (1.8.0+dfsg-1) unstable; urgency=low

  * New upstream version
  * Fixed debian/watch
  * Suggests: torque-client
    Closes: #721902
  * debian/control:
     - cme fix dpkg-control
     - rdp-classifier can only be suggested since it is not in Debian
       and currently it seems that it can only go into non-free
     - Canonical Vcs URLs
  * debian/patches/prevent_google_addsense.patch: Remove Google Addsense
    from user documentation to save user privacy

 -- Andreas Tille <tille@debian.org>  Sat, 21 Dec 2013 08:50:20 +0100

qiime (1.7.0+dfsg-1) unstable; urgency=low

  * Upload preparations done for BioLinux to Debian

 -- Andreas Tille <tille@debian.org>  Mon, 17 Jun 2013 18:28:26 +0200

qiime (1.7.0-0biolinux1) precise; urgency=low

  * New usptream
  * Adopt new naming convention for bl releases
  * Add usearch script to match uclust warning message
  * Re-fix biom-format script aliases (as links, needed for script to see them)
  * Clean out old patches
  * Patch to fix significant typo in error message
  * Patch to stop warning for matplotlib
  * Depend on newer Pynast (Pynast now maintained along with QIIME)

 -- Tim Booth <tbooth@ceh.ac.uk>  Tue, 11 Jun 2013 16:49:19 +0100

qiime (1.6.0-0ubuntu2) precise; urgency=low

  * Add some aliases so that the python-biom-format tools can be
    called with .py extensions inside the qiime shell, because this 
    is consistent with what QIIME users expect.

 -- Tim Booth <tbooth@ceh.ac.uk>  Thu, 02 May 2013 15:05:34 +0100

qiime (1.6.0-0ubuntu1) precise; urgency=low

  * New upstream release
  * Don't bother re-packing the tarball for PPA.  Package now
    builds the same with re-packed or pristine.
  * Remove t-test bug patch as this is in upstream
  * Re-jig RDP version patch which is simplified but still needed
  * Note the upstream no longer includes an example parameters.txt

 -- Tim Booth <tbooth@ceh.ac.uk>  Fri, 04 Jan 2013 12:51:49 +0000

qiime (1.5.0+repack-2ubuntu11) precise; urgency=low

  [Tim Booth]
  * The support_files patch only solved part of the problem,
    so trying a different, and simpler, tack.
  * Changes from Debian:

  [Andreas Tille]
   * debian/rules: Use xz compression for binary packages

 -- Tim Booth <tbooth@ceh.ac.uk>  Tue, 20 Nov 2012 12:26:24 +0000

qiime (1.5.0+dfsg-1) unstable; urgency=low

  * debian/copyright: - Add Files-Excluded to document what was removed
    from original source
  * debian/watch: Enable '+dfsg' / '+repack' suffix in Debian versions
  * debian/control:
     - Remove DM-Upload-Allowed
     - Standards-Version: 3.9.4 (no changes needed)
     - Priority: optional (per Debian Med policy)
     - normalised format
     - Build-Depends: ghc (instead of ghc6)
       Closes: #710774

 -- Andreas Tille <tille@debian.org>  Wed, 29 Aug 2012 14:30:02 +0200

qiime (1.5.0+repack-2ubuntu10) precise; urgency=low

  * Made QIIME accept RDP classifier >2.2 though the patch is
    a total hack.  Solves issue reported by MJC.
  * Add patch to make QIIME look in the Debian standard location
    for king.jar and other support_files
  * Added patch to fix alpha diversity bug and tested by running
    test_compare_alpha_diversities.py
  * QIIME now needs python-cogent 1.5.3

 -- Tim Booth <tbooth@ceh.ac.uk>  Wed, 14 Nov 2012 09:59:24 +0000

qiime (1.5.0+repack-2ubuntu5) precise; urgency=low

  * Tweaked startup script to report the QIIME version

 -- Tim Booth <tbooth@ceh.ac.uk>  Thu, 11 Oct 2012 13:49:35 +0100

qiime (1.5.0+repack-2ubuntu4) precise; urgency=low

  * Remove python26_trim_sff_primers.patch as Qiime now requires 
    2.7 anyway
  * Avoid calling dh_auto_clean at all as it triggers a partial
    rebuild
  * Added various support files in /usr/share/qiime/support_files
  * Added various symlinks as Qiime wants everything in one place
  * Set python-biom-format as a hard dependency because even built-in
    self-test won't start without it
  * Added patch to self-test where it looks for default config file
  * Modified to work with new RDP-classifier package

 -- Tim Booth <tbooth@ceh.ac.uk>  Tue, 14 Aug 2012 17:53:13 +0100

qiime (1.5.0-2) unstable; urgency=low

  * debian/control:
     - Recommends: python-biom-format
       Closes: #682199
     - Depends: python >= 2.7
       Closes: #682198
  * debian/get-orig-source: For next release use xz compression of
    repackaged source
  * debian/rules: use xz compression

 -- Andreas Tille <tille@debian.org>  Mon, 06 Aug 2012 09:22:42 +0200

qiime (1.5.0-1) unstable; urgency=low

  * New upstream version (adapted patches + remove patch that was applied
    upstream)
  * debian/get-orig-source: Strip *.jar file from upstream source which
    should never have been there
  * debian/upstream:
     - more complete authors information in BibTeX conform format
     - Moved DOI+PMID to References
  * debian/qiime.links: Link to king.jar
  * debian/control: Depends: king
  * debhelper 9 (control+compat)

 -- Andreas Tille <tille@debian.org>  Tue, 08 May 2012 18:07:56 +0200

qiime (1.4.0-2) unstable; urgency=low

  * debian/qiime.install: Include *.py files
    Closes: #668999

 -- Andreas Tille <tille@debian.org>  Mon, 16 Apr 2012 15:39:02 +0200

qiime (1.4.0-1) unstable; urgency=low

  * New upstream version (updated patches)
  * debian/patches/fix_shebang_lines.patch: Removed because file
    to patch was removed upstream
  * debian/copyright: rewritten to confirm DEP5 and verified using
      cme fix dpkg-copyright

 -- Andreas Tille <tille@debian.org>  Tue, 20 Mar 2012 14:41:20 +0100

qiime (1.3.0-3) unstable; urgency=low

  [ Charles Plessy ]
  * renamed debian/upstream-metadata.yaml to debian/upstream

  [ Andreas Tille ]
  * Standards-Version: 3.9.3 (no changes needed)
  * debian/patches/ghc_7.4.2_compatibility.patch: Fix build problem based
    on illegal use of 'import System' (Thanks to Joachim Breitner
    <nomeata@debian.org>) for the patch
    Closes: #663889

 -- Andreas Tille <tille@debian.org>  Sat, 17 Mar 2012 19:19:38 +0100

qiime (1.3.0-2) unstable; urgency=low

  * debian/control:
    - Added myself to uploaders
    - moved from contrib/science to science because there are
      no non-free components used any more
    - Removed duplicated entry ${misc:Depends}
    - Extra package qiime-doc arch all to avoid
    - Provides/Replaces/Conflicts denoiser
    - Fix Vcs fields
    - DM-Upload-Allowed: yes
    - Build-Depends:
       + python-all-dev (>= 2.6) (instead of python-central)
       + python-sphinx to create python documentation
  * debian/rules:
    - short dh notation instead of cdbs
      Closes: #639389
    - allow overriding python2 by environemnt which helps backporters
      like Tim for BioLinux
    - use calculated $(pkg) variable instead of fixed string 'qiime'
  * debian/{rules,qiime.install}: Adapted to new binary package layout
  * debian/qiime.{doc,links}: Move documentation into place and use
    packaged JavaScript libraries
  * debian/qiime-doc.doc-base
  * debian/upstream-metadata.yaml

 -- Andreas Tille <tille@debian.org>  Tue, 29 Nov 2011 09:23:18 +0100

qiime (1.3.0-0ubuntu6) lucid; urgency=low

  * Attempt to fix some errors reported by print_qiime_config -t
    Fixes to environment, configuration and small patches 

 -- Tim Booth <tbooth@ceh.ac.uk>  Wed, 02 Nov 2011 18:06:37 +0000

qiime (1.3.0-1) unstable; urgency=low

  * Bringing qiime to Debian
  [Steffen]
  * Some reformatting of debian/control

 -- Tim Booth <tbooth@ceh.ac.uk>  Fri, 26 Aug 2011 17:48:30 +0200

qiime (1.3.0-0ubuntu5) lucid; urgency=low

  * Very minor fix to scripts/shell/qiime_environment

 -- Tim Booth <tbooth@ceh.ac.uk>  Tue, 16 Aug 2011 12:35:06 +0100

qiime (1.3.0-0ubuntu4) lucid; urgency=low

  * New upstream release.  Needs newer Python-Cogent
    and includes built-in denoiser, so I have now aliased
    denoiser to run the qiime wrapper.
  * As the upstream now contains a tiny compiled package I've had
    to make it arch dependent (support_files/denoiser/FlowgramAlignment
    code written in Haskell).
  * Added build dep on ghc6 for the same reson

 -- Tim Booth <tbooth@ceh.ac.uk>  Tue, 19 Jul 2011 17:38:28 +0100

qiime (1.2.1-ubuntu5) lucid; urgency=low

  * Fixed silly error in qiime wrapper script
  * Added uclust wrapper to deal with uclust being expected but missing

 -- Tim Booth <tbooth@ceh.ac.uk>  Thu, 24 Mar 2011 16:52:43 +0000

qiime (1.2.1-ubuntu4) lucid; urgency=low

  * Fixed dependency - needs python-cogent >= 1.5

 -- Tim Booth <tbooth@ceh.ac.uk>  Thu, 24 Mar 2011 15:33:03 +0000

qiime (1.2.1-ubuntu3) lucid; urgency=low

  * Moved .py scripts out of /usr/bin
  * Added /usr/bin/qiime wrapper script as per Bio-Linux
  * Added default configuration file
  * Cleaned up documentation
  * Added many dependencies (some of which are still not packaged) 

 -- Tim Booth <tbooth@ceh.ac.uk>  Thu, 24 Mar 2011 11:35:58 +0000

qiime (1.2.1-ubuntu2) lucid; urgency=low

  * Pulled 1.2.1 source and tried a rebuild.
  * Fixed Lintian changelog warning.

 -- Tim Booth <tbooth@ceh.ac.uk>  Tue, 22 Mar 2011 13:55:49 +0000

qiime (1.2.1-2) experimental; urgency=low

  * Initial release (Closes: #587275)
  * Fixed Python 2.6 incompatibility.

 -- Steffen Moeller <moeller@debian.org>  Wed, 02 Mar 2011 22:33:45 +0100

qiime (1.2.1-1) experimental; urgency=low

  * Corrected home page
  * Updated policy to 3.9.1
  * Updated debian/README.Debian

 -- Steffen Moeller <moeller@debian.org>  Wed, 02 Mar 2011 18:19:39 +0100

qiime (1.1.0-1) experimental; urgency=low

  * Initial release.

 -- Sri Girish Srinivasa Murthy <srigirish@evolbio.mpg.de>  Tue, 20 Jul 2010 00:03:02 +0200

