t-coffee (13.45.0.4846264+really13.41.0.28bdc39+dfsg-1) unstable; urgency=medium

  [ Étienne Mollier ]
  * d/t/run-unit-test: don't meddle with user's home.
  * d/rules: build with -fsigned-char.
    This fixes infinite loops on CPU architectures defaulting to the char
    type being unsigned, such as on arm*, ppc* and s390*. (Closes: #1023230)
  * d/control: add myself to uploaders.

  [ Andreas Tille ]
  * Revert version bump to latest upstream version until
     https://github.com/cbcrg/tcoffee/issues/56
    is closed.
    Closes: #1022570
  * Keep updated patches in debian/patches dir with suffix .13.45.0.4846264
    to ease upgrading to the new version once it is ready

 -- Andreas Tille <tille@debian.org>  Fri, 25 Nov 2022 11:13:19 +0100

t-coffee (13.45.0.4846264+dfsg-1) unstable; urgency=medium

  * New upstream version
  * debhelper-compat 13 (routine-update)
  * Standards-Version: 4.6.1 (routine-update)
  * Remove trailing whitespace in debian/changelog (routine-update)
  * Use secure URI in Homepage field.
  * lintian-overrides for html files
  * Force -O0 to avoid crash in test suite

 -- Andreas Tille <tille@debian.org>  Wed, 12 Oct 2022 12:12:17 +0200

t-coffee (13.41.0.28bdc39+dfsg-4) unstable; urgency=medium

  * Team upload.
  * Increase MAX_N_PID to 4194304. (Closes: #962974)
  * Updated the homepage, following permanent redirection.

 -- Etienne Mollier <etienne.mollier@mailoo.org>  Wed, 17 Jun 2020 20:34:34 +0200

t-coffee (13.41.0.28bdc39+dfsg-3) unstable; urgency=medium

  [ Aaron M. Ucko ]
  * Better way to deal with .pl extension in blast tools

  [ Andreas Tille ]
  * Breaks+Replaces: t-coffee (<< 13)
    Closes: #959850

 -- Andreas Tille <tille@debian.org>  Thu, 07 May 2020 06:37:00 +0200

t-coffee (13.41.0.28bdc39+dfsg-1) unstable; urgency=medium

  [ Michael R. Crusoe ]
  * Unhide the build flags.
  * t-coffee-examples: mark Multi-Arch: foreign

  [ Andreas Tille ]
  * New upstream version
  * debhelper-compat 12
  * Standards-Version: 4.5.0
  * Add salsa-ci file (routine-update)
  * Rules-Requires-Root: no (routine-update)
  * Trim trailing whitespace.
  * Set fields Upstream-Name, Upstream-Contact in debian/copyright.
  * Remove obsolete fields Contact, Name from debian/upstream/metadata
    (already present in machine-readable debian/copyright).
  * Do not install examples twice
  * Fix Perl interpreter
  * Remove binary executable as well as binary docs

  [ Nilesh Patra ]
  * Adapt tests with new version

 -- Andreas Tille <tille@debian.org>  Thu, 16 Apr 2020 22:16:17 +0200

t-coffee (12.00.7fb08c2-4) unstable; urgency=medium

  [ Helmut Grohne ]
  * Fix FTCBFS: Pass C++ compiler as CC.
    Closes: #922196

 -- Andreas Tille <tille@debian.org>  Fri, 15 Feb 2019 07:43:22 +0100

t-coffee (12.00.7fb08c2-3) unstable; urgency=medium

  * Do not use -i flag to ignore build failures
    Closes: #922149
  * debhelper 12
  * Secure URI in copyright format
  * Remove trailing whitespace in debian/changelog
  * Remove trailing whitespace in debian/rules

 -- Andreas Tille <tille@debian.org>  Tue, 12 Feb 2019 19:37:40 +0100

t-coffee (12.00.7fb08c2-2) unstable; urgency=medium

  * Team upload.
  * Fix "t-coffee breaks libbio-tools-run-alignment-tcoffee-perl
    autopkgtest: COREDUMP" fix_tempfile_name_sharing.patch
    (Closes: #917143)
  * Standards-Version: 4.3.0

 -- Liubov Chuprikova <chuprikovalv@gmail.com>  Mon, 04 Feb 2019 10:37:01 +0100

t-coffee (12.00.7fb08c2-1) unstable; urgency=medium

  * New upstream version

 -- Andreas Tille <tille@debian.org>  Mon, 17 Dec 2018 15:02:59 +0100

t-coffee (11.00.8cbe486-8) unstable; urgency=medium

  * Team upload.

  [ Andreas Tille ]
  * Deal with "Segmentation fault" in exit of mayhem patch
    Closes: #716373
  * Make sure autopkgtest will set HOME variable to $PWD in case HOME
    is not set

  [ Liubov Chuprikova ]
  * Fix "autopkgtest regression" add missing return in a non-void function
    Closes: #909530

 -- Liubov Chuprikova <chuprikovalv@gmail.com>  Sun, 21 Oct 2018 11:08:01 +0200

t-coffee (11.00.8cbe486-7) unstable; urgency=medium

  * debhelper 11
  * Point Vcs fields to salsa.debian.org
  * Standards-Version: 4.2.1

 -- Andreas Tille <tille@debian.org>  Mon, 24 Sep 2018 08:41:01 +0200

t-coffee (11.00.8cbe486-6) unstable; urgency=medium

  * Standards-Version: 4.1.0 (no changes needed)
  * Fix some string assignments which fail build with gcc-7
    Closes: #853677
  * d/rules: do not parse d/changelog

 -- Andreas Tille <tille@debian.org>  Mon, 28 Aug 2017 15:27:17 +0200

t-coffee (11.00.8cbe486-5) unstable; urgency=medium

  * When using bioperl-run test suite it is uncovered that t-coffee is
    wrongly seeking for a clustalw2 executable.  A patch is applied to
    rather seek for clustalw.
  * debhelper 10
  * d/watch: version=4
  * install README.test and test script as user documentation

 -- Andreas Tille <tille@debian.org>  Sat, 17 Dec 2016 18:43:04 +0100

t-coffee (11.00.8cbe486-4) unstable; urgency=medium

  * Team upload
  [ Andreas Tille ]
  * Moved packaging from SVN to Git
  * Recommend fsa since its available in Debian now

  [ Canberk Koç ]
  * Autopkgtest added

 -- Canberk Koç  <canberkkoc@gmail.com>  Sat, 25 Jun 2016 19:22:28 +0300

t-coffee (11.00.8cbe486-3) unstable; urgency=medium

  * Team upload.
  * Force stable linking order to make build reproducible.
  * Bump Standards-Version.
  * Enable full hardening.
  * Use secure Vcs-Browser.

 -- Sascha Steinbiss <sascha@steinbiss.name>  Thu, 19 May 2016 20:52:28 +0000

t-coffee (11.00.8cbe486-2) unstable; urgency=medium

  * cme fix dpkg-control
  * update debian/copyright
  * fix clean target
  * compress changelog with '-n' option
  * propagate hardening options
  * Do not build unused TMalign
  * When creating subdirectories in $HOME do not make these world
    writable but keep users umask
    Closes: #751579
  * Drop redundant debian/README.source
  * Package builds for all architectures so this
    Closes: #631249
    (feel free to reopen if tests might keep on failing on armel)

 -- Andreas Tille <tille@debian.org>  Tue, 22 Dec 2015 19:02:14 +0100

t-coffee (11.00.8cbe486-1) unstable; urgency=low

  [ Charles Plessy ]
  * Suggest ncbi-blast+.

  [ Andreas Tille ]
  * New upstream version
  * debian/patches/ncbi-blast++_has_dropped_pl_extension.patch:
    since ncbi-blast++ has renamed some perl scripts according to
    Debian policy t-coffee needs to be adapted:
      s/legacy_blast\.pl/legacy_blast/
      s/blastpgp\.pl/blastpgp/
    Closes: #730722
  * Move some suggested packages to Recommends since these are recommended
    when calling t_coffee --help
  * Suggests: fsa (will be packaged soon)

 -- Andreas Tille <tille@debian.org>  Sat, 16 Aug 2014 00:20:06 +0200

t-coffee (10.00.r1613-1) unstable; urgency=low

  * New upstream release.

 -- Charles Plessy <plessy@debian.org>  Wed, 27 Nov 2013 21:37:22 +0900

t-coffee (9.03.r1318-1) unstable; urgency=low

  * New upstream release.

  [ Tim Booth ]
  * Removed the -doc package as it is empty (Closes: #688630).
    docs are no longer in tarball but online:
     http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
  * Rejigged the rules file to use DH, not CDBS.
  * Avoid compressing files under t-coffee-examples
  * Remove TMalign binary on clean (should avoid building it at all)
  * Fix minor typo flagged by Lintian

  [ Charles Plessy ]
  * Normalised debian/control with config-model-edit.
  * Normalised VCS URLs.
  * Using Debhelper 9.
  * Complies with Policy 3.9.4.

  [Andreas Tille]
  * debian/upstream: Single Reference field instead of Reference-*

 -- Charles Plessy <plessy@debian.org>  Sun, 14 Jul 2013 19:03:20 +0900

t-coffee (9.02.r1228-2) unstable; urgency=low

  * Recommend tm-align instead of distributing local copy
    (debian/control, debian/t-coffee.install, Closes: #661516).

 -- Charles Plessy <plessy@debian.org>  Fri, 02 Mar 2012 14:04:20 +0900

t-coffee (9.02.r1228-1) unstable; urgency=low

  * New upstream release (Closes: #649263).
  * Build new Fortran tool (debian/rules debian/contol debian/t-coffee.install)
  * Corrected debian/rules as upstream test suite was removed.
  * Complies with Policy 3.9.3 (debian/control, no other changes needed).
  * Removed doc-base registrations debian/t-coffee-doc.doc-base.technical and
    debian/t-coffee-doc.doc-base.tutorial, as the files disappeared upstream.

 -- Charles Plessy <plessy@debian.org>  Mon, 27 Feb 2012 13:09:36 +0900

t-coffee (8.99-1) unstable; urgency=low

  * New upstream release in Debian.
  * Converted and validated debian/copyright to DEP 5 machine-readable format.
  * Using debhelper 8 (debian/control, debian/compat).
  * Incremented Standards-Version to reflect conformance with Policy 3.9.2.
    (debian/control, no change needed).
  * Corrected VCS URLs in debian/control.
  * Run upstream tests at build time (debian/rules, debian/README.test).

 -- Charles Plessy <plessy@debian.org>  Tue, 21 Jun 2011 14:14:10 +0900

t-coffee (8.99-0ubuntu1) lucid; urgency=low

  * Rebuild for new upstream release.
  * There is no changelog from upstream to read.

 -- Tim Booth <tbooth@ceh.ac.uk>  Sat, 29 Jan 2011 15:18:01 +0000

t-coffee (8.97-0ubuntu2) lucid; urgency=low

  * New upstream release, changed watch file and auto rebuild using uupdate
  * Cleared out old patch - apparently unneeded or else needs total re-write

 -- Tim Booth <tbooth@ceh.ac.uk>  Tue, 23 Nov 2010 14:01:22 +0000

t-coffee (8.95-1) lucid; urgency=low

  * New upstream version, rebuild by Tim for Bio-Linux/Lucid

 -- Tim Booth <tbooth@ceh.ac.uk>  Mon, 01 Nov 2010 15:05:07 +0000

t-coffee (8.84-1) unstable; urgency=low

  * New upstream version

 -- Andreas Tille <tille@debian.org>  Thu, 24 Jun 2010 14:46:16 +0200

t-coffee (8.47-1) unstable; urgency=low

  [ Charles Plessy ]
  * Collected Upstream information in debian/upstream-metadata.yaml.

  [ Andreas Tille ]
  * New upstream version
  * Source format 3.0 (quilt)
  * Standards-Version: 3.8.4 (no changes needed)

 -- Andreas Tille <tille@debian.org>  Fri, 09 Apr 2010 21:08:32 +0200

t-coffee (8.14-1) unstable; urgency=low

  * New upstream version

 -- Andreas Tille <tille@debian.org>  Tue, 03 Nov 2009 13:56:33 +0100

t-coffee (8.13-1) unstable; urgency=low

  * New upstream version

 -- Andreas Tille <tille@debian.org>  Thu, 01 Oct 2009 22:13:34 +0200

t-coffee (8.06-1) unstable; urgency=low

  [ Charles Plessy ]
  TODO:
    Identify differences and document relevant ones.
    Check that the patch can be dropped.
    Support PDB in getdata.
    Get the FORTRAN building right.
  NOTE
    The upstream install system was completely refactored, and T-Coffee
    includes new functionalities that require internet access. We have to
    understand them before updating our package.

  * New upstream release
    - say something about libsoap-lite-perl ?
  * debian/control:
    - t-coffee recommends libsoap-lite-perl.
    - Added missing comma in t-coffee Suggests field (Closes:#536956).

  [ Andreas Tille ]
  * debian/control:
    - Standards-Version: 3.8.3 (added README.source)
    - Added myself to uploaders
    - s/Debian-Med/Debian Med/
    - Bumped debhelper version to >= 7.1 to possibly enable short
      rules files.
    - Added "Depends: ${misc:Depends}" to all packages

 -- Andreas Tille <tille@debian.org>  Fri, 25 Sep 2009 14:41:41 +0200

t-coffee (5.72-1) unstable; urgency=low

  [ David Paleino ]
  * New upstream release

  [ Charles Plessy ]
  * Switched to CDBS.
  * debian/patches:
   - Upated the dm-coffee patch because dialign-t was renamed dialign-tx.
   - Dropped the unicode conversion patch.
   - Dropped the manpage patch (implements the clear rule through CDBS).
  * Updated my email address.

 -- Charles Plessy <plessy@debian.org>  Mon, 30 Jun 2008 23:34:32 +0900

t-coffee (5.31-1) unstable; urgency=low

  * New upstream version.
  * Debian menu transition: updated debian/t-coffee-doc.doc-base.
  * debian/patches/dmcoffee.patch: to make dmcoffee work
    out of the box.
  * debian/control:
    - Allowed Debian Maintainers to upload t-coffee.
    - Checked that the package conforms to Policy 3.7.3.
    - Using debhelper 5.
    - Updated homepage.
    - Moved t-coffee-doc to section doc.
  * debian/copyright: converted to machine-readable format.
  * debian/rules: builds only indep or only arch when called with
    binary-indep or binary-arch (Closes: #457921).

 -- Charles Plessy <charles-debian-nospam@plessy.org>  Sat, 29 Dec 2007 18:54:09 +0100

t-coffee (5.05-1) unstable; urgency=low

  * New upstream version.
  * Assigned maintainership to Debian-Med.
  * Moved boxshade from Recommended to Suggested.
  * Added use of quilt.
  * Homepage received its separate line.

 -- Steffen Moeller <moeller@debian.org>  Mon, 24 Sep 2007 15:05:07 +0200

t-coffee (2.50-1) unstable; urgency=low

  * Initial Release (Closes: Bug#205370).

 -- Steffen Moeller <moeller@pzr.uni-rostock.de>  Fri, 13 May 2005 10:52:14 +0200
