stacks (2.68+dfsg-2) unstable; urgency=medium

  * Team upload.

  [ Andreas Tille ]
  * Remove Tim Booth <tbooth@ceh.ac.uk> since address is bouncing
    (Thank you for your work on this package, Tim)

  [ Étienne Mollier ]
  * d/control: explicitly build-depend on automake.
  * d/rules: reinforce the fetch the TAP driver for any automake version.
    Unfortunately this change is not sufficient to put upstream's super
    secret test suite on tracks, so it is still disabled for the moment.
    (Closes: #1095396)
  * use_debian_packaged_htslib.patch: normalise Last-Update timestamp.

 -- Étienne Mollier <emollier@debian.org>  Sun, 16 Feb 2025 10:54:31 +0100

stacks (2.68+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version 2.68+dfsg
  * d/patches/*: unfuzz.

 -- Étienne Mollier <emollier@debian.org>  Sat, 31 Aug 2024 11:24:11 +0200

stacks (2.67+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * Standards-Version: 4.7.0 (routine-update)
  * d/patches: Refresh patches (change_program_exit_to_success.patch,
    fix_spelling_errors.patch, script-exe-paths)

 -- Lance Lin <lq27267@gmail.com>  Sat, 10 Aug 2024 19:38:09 +0700

stacks (2.66+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * d/patches: Refresh patches (change_program_exit_to_success.patch,
    fix_spelling_errors.patch, script-exe-paths)

 -- Lance Lin <lq27267@gmail.com>  Tue, 23 Jan 2024 19:32:21 +0700

stacks (2.65+dfsg-2) unstable; urgency=medium

  * Team upload.
  * d/bin/stacks: Fix path to be libexec for executables
  * d/control: Add python3 and bsdextrautils to Depends
               Remove python3 from Recommends
               Add gdb to Suggests
  * d/tests: Add superficial autopkgtest (needs test data)
  * d/patches/change_program_exit_to_success.patch: Fix exit codes to be
    successful and output to stdout
  * d/patches/offer_help_option_for_stacks_gdb.patch: Gives usage information
    for options -h, --help, and --version

 -- Lance Lin <lq27267@gmail.com>  Fri, 01 Sep 2023 20:40:42 +0700

stacks (2.65+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version 2.65+dfsg
  * Standards-Version: 4.6.2 (routine-update)
  * d/copyright: Update year to 2023 for debian/*
  * d/patches/RisR.patch: Add patch description
  * d/patches/script-exe-paths: Update path to be libexec, not lib
  * d/rules: Update install and links paths for libexec
  * d/patches/fix_spelling_errors.patch: Fix spelling errors in generated
    binaries

 -- Lance Lin <lq27267@gmail.com>  Tue, 29 Aug 2023 20:53:01 +0700

stacks (2.62+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.6.1 (routine-update)

 -- Andreas Tille <tille@debian.org>  Tue, 27 Sep 2022 12:38:01 +0200

stacks (2.60+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version 2.60+dfsg
  * Run cme

 -- Nilesh Patra <nilesh@debian.org>  Tue, 02 Nov 2021 00:08:37 +0530

stacks (2.59+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version 2.59+dfsg

 -- Nilesh Patra <nilesh@debian.org>  Sun, 15 Aug 2021 19:19:04 +0530

stacks (2.55+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * Standards-Version: 4.5.1 (routine-update)

 -- Nilesh Patra <npatra974@gmail.com>  Sun, 10 Jan 2021 17:37:28 +0530

stacks (2.54+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * debhelper-compat 13 (routine-update)
  * Lintian warned: d/NEWS.Debian -> d/NEWS

 -- Steffen Moeller <moeller@debian.org>  Tue, 15 Sep 2020 03:16:02 +0200

stacks (2.53+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * Updated bio.tools entry to lower-case
  * Added dependency on littler to allow execution
    of R script

 -- Steffen Moeller <moeller@debian.org>  Sun, 26 Apr 2020 01:41:49 +0200

stacks (2.52+dfsg-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * Standards-Version: 4.5.0 (routine-update)
  * debhelper-compat 12 (routine-update)
  * Add salsa-ci file (routine-update)
  * Rules-Requires-Root: no (routine-update)
  * Use secure URI in Homepage field. (routine-update)
  * Removed additional autogenerated files from upstream

 -- Steffen Moeller <moeller@debian.org>  Thu, 26 Mar 2020 02:25:20 +0100

stacks (2.41+dfsg-1) unstable; urgency=medium

  * New upstream version
  * debhelper 12
  * Standards-Version: 4.4.0
  * Secure URI in copyright format
  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
  * dh_auto_install --no-parallel
  * Removed stacks-web package since the code for the web service
    was removed from upstream source and the package has no active
    users according to popcon anyway
  * Python3 port of two simple scripts using 2to3

 -- Andreas Tille <tille@debian.org>  Fri, 12 Jul 2019 20:40:33 +0200

stacks (2.2+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Point Vcs fields to salsa.debian.org
  * Standards-Version: 4.2.1
  * Fix path for Perl interpreter

 -- Andreas Tille <tille@debian.org>  Thu, 13 Sep 2018 09:51:56 +0200

stacks (2.0Beta9+dfsg-1) unstable; urgency=medium

  * New upstream Beta release

 -- Andreas Tille <tille@debian.org>  Mon, 19 Mar 2018 12:10:23 +0100

stacks (2.0Beta8c+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Remove code copy of htslib and use Debian packaged version of htslib
    instead
  * Standards-Version: 4.1.3
  * debhelper 11

 -- Andreas Tille <tille@debian.org>  Sun, 18 Feb 2018 17:15:06 +0100

stacks (1.46-1) unstable; urgency=medium

  * New upstream version
  * Standards-Version: 4.0.0 (no changes needed)
  * do not disable PIE
    Closes: #865668
  * d/rules: use DEB_SOURCE

 -- Andreas Tille <tille@debian.org>  Sat, 24 Jun 2017 08:20:24 +0200

stacks (1.44-2) unstable; urgency=medium

  * d/watch: version=4
  * debhelper 10
  * stacks-web: Depends s/ | mysql-server/ | virtual-mysql-server/
    Closes: #848464

 -- Andreas Tille <tille@debian.org>  Sat, 17 Dec 2016 17:34:44 +0100

stacks (1.44-1) unstable; urgency=medium

  [ Kevin Murray ]
  * Fix script executable paths to reflect debian install directory

  [ Andreas Tille ]
  * New upstream version
  * stacks-web Depends: default-mysql-server | mysql-server

 -- Andreas Tille <tille@debian.org>  Sat, 22 Oct 2016 21:04:24 +0200

stacks (1.42-1) unstable; urgency=medium

  * New upstream version
  * hardening -pie

 -- Andreas Tille <tille@debian.org>  Sat, 13 Aug 2016 10:49:42 +0200

stacks (1.40-1) unstable; urgency=medium

  * New upstream version
  * cme fix dpkg-control
  * Build-Depends: samtools to ensure that package builds only on those
    architectures where samtools is available

 -- Andreas Tille <tille@debian.org>  Thu, 19 May 2016 12:55:47 +0200

stacks (1.38-1) unstable; urgency=medium

  * New upstream version
  * debian/control: s/php5/php/
    Closes: #821664
  * Better hardening

 -- Andreas Tille <tille@debian.org>  Tue, 19 Apr 2016 10:45:21 +0200

stacks (1.37-1) unstable; urgency=medium

  * New upstream version
  * Moved from SVN to Git
  * cme fix dpkg-control

 -- Andreas Tille <tille@debian.org>  Thu, 10 Mar 2016 23:31:22 +0100

stacks (1.35-1) unstable; urgency=medium

  * New upstream version

 -- Andreas Tille <tille@debian.org>  Tue, 22 Sep 2015 21:05:58 +0200

stacks (1.34-1) unstable; urgency=medium

  * New upstream version

 -- Andreas Tille <tille@debian.org>  Mon, 27 Jul 2015 17:58:43 +0200

stacks (1.32-1) unstable; urgency=medium

  * New upstream version

 -- Andreas Tille <tille@debian.org>  Mon, 13 Jul 2015 19:52:06 +0200

stacks (1.25-1) unstable; urgency=medium

  * Initial upload to Debian
    Closes: #778832

 -- Andreas Tille <tille@debian.org>  Thu, 19 Feb 2015 18:31:48 +0100

stacks (1.25-0biolinux2) trusty; urgency=medium

  * Correct silly cut-and-paste-o in control file

 -- Tim Booth <tbooth@ceh.ac.uk>  Thu, 19 Feb 2015 16:52:53 +0000

stacks (1.25-0biolinux1) trusty; urgency=medium

  * New upstream
  * Re-work stacks-setup-database to make databases named by project
  * ...and to enable database deletion
  * Improve the help you get from "stacks help"

 -- Tim Booth <tbooth@ceh.ac.uk>  Wed, 18 Feb 2015 11:34:22 +0000

stacks (1.24-0ubuntu4) trusty; urgency=medium

  * Change web path back to /stacks rather than stacks-web,
    just leaving the Apache config fragment with that name.

 -- Tim Booth <tbooth@ceh.ac.uk>  Thu, 29 Jan 2015 11:06:58 +0000

stacks (1.24-0ubuntu3) trusty; urgency=low

  * Set PATH before calling any Stacks program in the wrapper

 -- Tim Booth <tbooth@ceh.ac.uk>  Fri, 23 Jan 2015 14:10:55 +0000

stacks (1.24-0ubuntu2) trusty; urgency=medium

  * Initial release.
  * Make stacks package plus stack-web for the web stuff
  * Require sparsehash >2

 -- Tim Booth <tbooth@ceh.ac.uk>  Thu, 15 Jan 2015 18:50:45 +0000
