theseus (2.0.6-1) unstable; urgency=low

  * New upstream version
     - Adapt patches
     - debian/patches/30_fix_gcc_options.patch: Enable build on Linux
    Closes: #713461
  * debian/control:
     - Remove DM-Upload-Allowed
     - cme fix dpkg-control
  * debian/rules: use xz compression

 -- Andreas Tille <tille@debian.org>  Wed, 26 Jun 2013 16:34:53 +0200

theseus (2.0.1-1) experimental; urgency=low

  * New upstream version (most patches applied)
  * debian/control:
     - Fix typo: s/clustlaw/clustalw/
       Closes: #682994
     - Standards-Version: 3.9.4 (no changes needed)
  * removed debian/citation.bib because the very same information
    is now in debian/upstream

 -- Andreas Tille <tille@debian.org>  Thu, 11 Oct 2012 18:15:43 +0200

theseus (1.6.2-2) unstable; urgency=low

  * debian/upstream: Added missing space, fixed Name
  * debian/patches: Two patches from Simon Ruderich
    <simon@ruderich.org> to enable hardening (thanks to Simon)
    Closes: #668120

 -- Andreas Tille <tille@debian.org>  Fri, 08 Jun 2012 08:45:38 +0200

theseus (1.6.2-1) unstable; urgency=low

  * New upstream version (adapted patch)
  * debian/control:
    - Standards-Version: 3.9.3 (no changes needed)
    - Fixed Vcs fields
  * debian/{control,rules}: Do not mention quilt explicitly
    which is not needed with source version 3.0 (quilt)
  * debian/upstream: Use information from debian/citation.bib
    for References in upstream yaml format
  * debian/upstream: Use information from debian/citation.bib
    for References in upstream yaml format
  * debian/{control,compat}: debhelper 9 to enable hardening
    flags
  * debian/patches/20_hardening.patch: Enable building with hardening
    options
  * debian/patches/20_exclude_apple_options.patch: Prevent trying
    to link with Apple specific linker option and enable linking
    pthread
  * debian/copyright: Rewritten to match DEP5 and verified using
      cme fix dpkg-copyright

 -- Andreas Tille <tille@debian.org>  Sat, 24 Mar 2012 07:48:57 +0100

theseus (1.6.1-1) unstable; urgency=low

  * New upstream version
  * debian/patches:
    - 99-theseus_align.sh.patch:
      Replaced by sed script in debian/rules which works (hopefully)
      for future versions as well without manually changing the patch
    - use_muscle_instead_of_clustalw.patch:
      Removed because clustalw is no in main and we do not need
      to actively replace it by muscle
    - 00-makefile.patch:
      Removed because applied upstream
    - 200-make.inc.patch:
      Removed
      + One purpose was to replace not working libtool call by ar
        which was applied upstream
      + Other purpose was to enable liblapack (patch by Morten
        Kjeldgaard) which was discussed with upstream and seems to
        cause problems.  So it was deactivated for now and might be
        tested later for enabling higher performance if needed.

 -- Andreas Tille <tille@debian.org>  Wed, 26 Jan 2011 11:39:36 +0100

theseus (1.5.5-1) unstable; urgency=low

  * New upstream version
  * Standards-Version: 3.9.1 (no changes needed)
  * Adapt debian/patches to new upstream version
  * Source format 3.0 (quilt)
  * debian/patches/use_muscle_instead_of_clustalw.patch:
    The script thesaus_align says it would use muscle as align program
    but it actually uses clustalw which is in non-free and thus we can
    not recommend it.  The patch makes muscle really the default
  * Depends: muscle (instead of Suggests)
  * debian/theseus_align.1: Better wording for muscle preference

 -- Andreas Tille <tille@debian.org>  Wed, 24 Nov 2010 17:46:49 +0100

theseus (1.4.3-2) unstable; urgency=low

  * debian/patches/10_kbsd.patch: Correctly applied patch from
    Cyril (sorry for mixing this up)
    Closes: #542879

 -- Andreas Tille <tille@debian.org>  Thu, 03 Sep 2009 08:49:22 +0200

theseus (1.4.3-1) unstable; urgency=low

  [Andreas Tille]
  * New upstream version
    Closes: #534630
  * debian/control
    - Added myself to uploaders
    - debhelper 7
    - Build-Depends: libtool
    - Standards-Version: 3.8.3 (no changes needed)
  * Switched to quilt (affects debian/patches/*, debian/control,
    debian/rules)
  * Added Suggests: clustlaw, mafft, t-coffee, kalign, dialign
    because these are called in theseus_align
  * Use debian/{docs,manpages, examples} instead of arguments of
    the debhelper installers to enable short rules file
  * Re-enabled patch for theseus_align and do not tweak upstream
    tarball just to s?usr/local/bin?usr/bin?
  * debian/patches/200-make.inc.patch: Use ar directly to to avoid
    problems with libtool, drop -arch command line options to gcc
    which let compilation fail
  * debian/README.Debian: Removed paragraph about theseus_align
    because this is now shipped in upstream tarball
  * debian/patches/10_kbsd.patch: fix the FTBFS problem reported by
    Cyril Brulebois <kibi@debian.org> (thanks to Cyril for the patch)
    Closes: #542879

  [Morten Kjeldgaard]
  * Fix FTBFS on certain platforms that lack the Atlas libraries
    by using lapack-dev in Build-Depends. This will pull in Atlas
    on the relevant platforms, otherwise not.

 -- Andreas Tille <tille@debian.org>  Mon, 31 Aug 2009 14:50:19 +0200

theseus (1.3.9-1) unstable; urgency=low

  * New upstream release, first upload to Debian.

 -- Morten Kjeldgaard <mok0@ubuntu.com>  Sun, 16 Nov 2008 22:36:36 +0100

theseus (1.1.5-0ubuntu3) intrepid; urgency=low

  * gfortran transition for intrepid, atlas3-base -> libatlas3-base.

 -- Morten Kjeldgaard <mok0@ubuntu.com>  Thu, 04 Sep 2008 23:20:52 +0200

theseus (1.1.5-0ubuntu2) hardy; urgency=low

  * debian/rules: FTBFS on all archs but i386, due to missing
    binary-arch target (LP: #181359)
  * Removed redundant libraries.
  
 -- Morten Kjeldgaard <mok@bioxray.dk>  Tue, 08 Jan 2008 22:35:42 +0100

theseus (1.1.5-0ubuntu1) hardy; urgency=low

  * Initial release (LP: #173506)
  * The upstream tarball has been versioned as 1.1.5 (not versioned upstream)
    The get-orig-source target in debian/rules can be used for this purpose
    once the changelog has been edited to contain the right version
  * Patch to theseus.1 and theseus_align.1
    - fix incorrect .TH line in theseus.1
    - fix multiple instances of hyphen (-) to minus (\-)
  * Patch on thesus_align.sh. The script is patched to find
    programs in /usr/bin. The script makes use of the
    multiple sequence alignment program muscle, which is available
    from universe.
  * Patch make.inc to provide correct compiler switches.
  * A script (getexamples) is provided to show the user how (s)he can
    download the data in examples/

 -- Morten Kjeldgaard <mok@bioxray.dk>  Sun, 02 Dec 2007 15:53:15 +0100
