tm-align (20190822+dfsg-3ubuntu1) questing; urgency=medium

  * d/t/control: add allow-stderr to Restrictions (LP: #2115575)

 -- Ural Tunaboyu <ural.tunaboyu@canonical.com>  Sat, 28 Jun 2025 12:09:27 -0700

tm-align (20190822+dfsg-3) unstable; urgency=medium

  * Remove Tim Booth <tbooth@ceh.ac.uk> since address is bouncing
    (Thank you for your work on this package, Tim)
  * Standards-Version: 4.7.0 (routine-update)
  * debhelper-compat 13 (routine-update)
  * Rules-Requires-Root: no (routine-update)
  * Secure URI in watch file

 -- Andreas Tille <tille@debian.org>  Mon, 16 Sep 2024 13:01:07 +0200

tm-align (20190822+dfsg-2) unstable; urgency=medium

  [ Chris Lamb ]
  * make the build reproducible
    Closes: #943954

  [ Andreas Tille ]
  * Rename autopkgtest script to run-unit-test as in other Debian Med
    packages
  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g

 -- Andreas Tille <tille@debian.org>  Tue, 24 Dec 2019 08:07:50 +0100

tm-align (20190822+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.4.1
  * Use secure URI in Homepage field.
  * Remove obsolete fields Contact, Name from debian/upstream/metadata.

 -- Steffen Moeller <moeller@debian.org>  Tue, 17 Dec 2019 17:23:09 +0100

tm-align (20190708+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Packaged with routine-update script
  * debhelper-compat 12
  * Standards-Version: 4.4.0

 -- Steffen Moeller <moeller@debian.org>  Mon, 29 Jul 2019 23:00:47 +0200

tm-align (20170708+dfsg-2) unstable; urgency=medium

  * Point Vcs fields to salsa.debian.org
  * Standards-Version: 4.2.1
  * Secure URI in copyright format
  * Remove trailing whitespace in debian/changelog
  * Remove trailing whitespace in debian/copyright

 -- Andreas Tille <tille@debian.org>  Tue, 30 Oct 2018 11:56:31 +0100

tm-align (20170708+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.1.3
  * debhelper 11
  * d/watch: version=4 (despite upstream page supports https, watch file
    fails if using https there)

 -- Andreas Tille <tille@debian.org>  Sun, 18 Feb 2018 17:32:48 +0100

tm-align (20160521+dfsg-2) unstable; urgency=medium

  * Team upload.
  * fix typo in package's description in d/control
  * add example gzipped protein structures+mention them in d/source/binaries
  * add testsuite
  * add README.test for testsuite
  * add example files to d/copyright, add tm-align.examples file

 -- Tatiana Malygina <merlettaia@gmail.com>  Fri, 10 Jun 2016 22:12:31 +0000

tm-align (20160521+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Moved packaging from SVN to Git
  * Use xz compression in watch file
  * cme fix dpkg-control
  * Better hardening

 -- Andreas Tille <tille@debian.org>  Mon, 30 May 2016 09:35:45 +0200

tm-align (20150914+dfsg-1) unstable; urgency=medium

  * New homepage
  * New upstream version
  * cme fix dpkg-control
  * dversionmangle in d/watch

 -- Andreas Tille <tille@debian.org>  Wed, 23 Sep 2015 10:01:59 +0200

tm-align (20140601+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Use Files-Excluded consequently (in rules:get-orig-source, drop
    d/get-orig-source, adapt d/watch from dversionmangle to uversionmangle)

 -- Andreas Tille <tille@debian.org>  Thu, 07 Aug 2014 16:21:35 +0200

tm-align (20130511+dfsg-2) unstable; urgency=medium

  * Fix Vcs location
  * move debian/upstream to debian/upstream/metadata
  * cme fix dpkg-control

 -- Andreas Tille <tille@debian.org>  Thu, 13 Feb 2014 17:03:43 +0100

tm-align (20130511+dfsg-1) unstable; urgency=low

  * New upstream version
  * debian/copyright:
     - Add Files-Excluded to document what was removed from original source
  * debian/watch: enable handling of +dfsg suffix
  * debian/get-orig-source: use new uscan of available
  * debian/upstream: more detailed information
  * debian/control:
     - cme fix dpkg-control
     - use anonscm in Vcs fields

 -- Andreas Tille <tille@debian.org>  Fri, 02 Aug 2013 14:55:58 +0200

tm-align (20120507-1) unstable; urgency=low

  * New upstream version
  * debian/rules: Add hardening options

 -- Andreas Tille <tille@debian.org>  Fri, 29 Jun 2012 18:30:36 +0200

tm-align (20120124-1) unstable; urgency=low

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

  [ Andreas Tille ]
  * New upstream version
  * debian/upstream:
     - Fixed typo (s/TITILE/TITLE/)
     - Moved DOI+PMID to references
  * debian/control: Standards-Version: 3.9.3 (no changes needed)
  * debhelper 9 (control+compat)
  * debian/changelog: DEP5 verified using
      cme fix dpkg-copyright

 -- Andreas Tille <tille@debian.org>  Thu, 08 Mar 2012 15:35:07 +0100

tm-align (20111012-1) unstable; urgency=low

  * New upstream release
  * Enhances t-coffee
  * Standards-Version: 3.9.2 (no changes needed)
  * Debhelper 8 (control + compat)
  * Fixed Vcs fields

 -- Andreas Tille <tille@debian.org>  Fri, 21 Oct 2011 10:00:04 +0200

tm-align (20110130-2) unstable; urgency=low

  * New upstream version (Closes: #447505)
    - 2011/01/30: An open source license is attached to the program
  * Reverting changelog to keep the history.

 -- Steffen Moeller <moeller@debian.org>  Sat, 05 Feb 2011 12:43:32 +0100

tm-align (20110130-1) UNRELEASED; urgency=low

  * Initial release.

 -- Andreas Tille <tille@debian.org>  Sun, 30 Jan 2011 22:49:21 +0100

tm-align (20110124-1) UNRELEASED; urgency=low

  * New upstream version
    - 2005/06/01: A small bug of two-point superposition was fixed.
    - 2005/10/19: the program was reformed so that the alignment results
                  are not dependent on the specific compilers.
    - 2006/06/20: select 'A' if there is altLoc when reading PDB file.
    - 2007/02/27: rotation matrix from Chain-1 to Chain-2 was added.
    - 2007/04/18: added options with TM-score normalized by average
                  length, shorter length, or longer length of two
                  structures.
    - 2007/05/23: added additional output file 'TM.sup_all' for showing
                  all atoms while 'TM.sup' is only for aligned atoms
    - 2007/09/19: added a new feature alignment to deal with the problem
                  of aligning fractional structures (e.g. protein
                  interfaces).
    - 2007/10/16: A bug for irregular bond-length models was fixed.
    - 2009/03/14: A new initial alignment was added and previous initial
                  alignments are further enhanced. This change increased
                  accuracy by 4% but increases CPU cost by 40%.
    - 2009/08/20: A bug for asymmetry alignment result was fixed.
    - 2010/08/02: A new RMSD matrix was used to remove obsolete
                  statements. Staled subroutines were deleted.
    - 2011/01/03: The length of pdb file names were extended to 500
    - 2011/01/24: Fixed a bug on output file name created on 2011/01/03
  * Tweaked get-orig-source in rules to spot version in upstream file

  * New standards version 3.9.4

 -- Tim Booth <tbooth@ceh.ac.uk>  Sun, 30 Jan 2011 13:34:53 +0000

tm-align (20050601-2) UNRELEASED; urgency=low

  * Updated to Standards-Version 3.7.3 (no changes needed)

 -- David Paleino <d.paleino@gmail.com>  Wed, 06 Feb 2008 13:11:58 +0100

tm-align (20050601-1) UNRELEASED; urgency=low

  * Initial packaging.

 -- Steffen Moeller <moeller@debian.org>  Sun, 21 Oct 2007 17:11:53 +0200
