bowtie2 (2.5.4-1build1) resolute; urgency=medium

  * No-change mass rebuild for Ubuntu 26.04 (LP: #2132257)

 -- Graham Inggs <ginggs@ubuntu.com>  Wed, 14 Jan 2026 19:35:12 +0000

bowtie2 (2.5.4-1) unstable; urgency=medium

  * Remove libmath-random-perl from Test-Depends and complete patch removing
    tests needing this module
    Closes: #1078087
  * New upstream version
  * Standards-Version: 4.7.0 (routine-update)

 -- Andreas Tille <tille@debian.org>  Wed, 07 Aug 2024 13:31:40 +0200

bowtie2 (2.5.3-1) unstable; urgency=medium

  [ Michael R. Crusoe ]
  * Team upload.
  * d/control: simplify architecture specifications by using provisions
    from the architecture-properties package.

 -- Charles Plessy <plessy@debian.org>  Wed, 17 Apr 2024 08:56:57 +0900

bowtie2 (2.5.2-1) unstable; urgency=medium

  * New upstream version
  * Add build support for loongarch64
    Closes: #1059510

 -- Andreas Tille <tille@debian.org>  Wed, 10 Jan 2024 20:37:29 +0100

bowtie2 (2.5.1-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * refresh patches.
  * d/patches: update my email address, add some Forwarded hints
  * tests: remove need to build debug versions.
  * d/tests: run built-in tests as well.

 -- Michael R. Crusoe <crusoe@debian.org>  Tue, 12 Sep 2023 13:16:13 +0200

bowtie2 (2.5.0-3) unstable; urgency=medium

  * Merge all autopkgtest scripts into run-unit-test as usual in Debian Med
    packages
  * Prevent autopkgtest on s390x since the package is no built here
  * Standards-Version: 4.6.2 (routine-update)

 -- Andreas Tille <tille@debian.org>  Tue, 17 Jan 2023 16:15:35 +0100

bowtie2 (2.5.0-2) unstable; urgency=medium

  * Package does not build on s390x any more

 -- Andreas Tille <tille@debian.org>  Mon, 12 Dec 2022 15:02:31 +0100

bowtie2 (2.5.0-1) unstable; urgency=medium

  * Team upload.

  [ Andreas Tille ]
  * No salsa-ci for i386
  * Use proper download file name
  * New upstream version
  * Standards-Version: 4.6.1 (routine-update)
  * Use secure URI in Homepage field.
  * Set upstream metadata fields: Bug-Database.
  * Update patches

  [ Étienne Mollier ]
  * simde patch: adjust to introduction of AVX2 support.
  * d/control: add pandoc to build doc/manual.html.
  * d/rules: trigger refresh of the doc/manual.html.
  * d/s/lintian-overrides: override missing source on doc/manual.html.

 -- Étienne Mollier <emollier@debian.org>  Sat, 05 Nov 2022 20:25:56 +0100

bowtie2 (2.4.5-1) unstable; urgency=medium

  * New upstream version
  * Drop transition for old debug package migration.

 -- Andreas Tille <tille@debian.org>  Thu, 17 Feb 2022 16:46:58 +0100

bowtie2 (2.4.4-1) unstable; urgency=medium

  * Team upload.
  * Fix watchfile to detect new versions on github (routine-update)
  * Standards-Version: 4.6.0 (routine-update)
  * Refresh patches

 -- Michael R. Crusoe <crusoe@debian.org>  Mon, 13 Sep 2021 18:45:11 +0200

bowtie2 (2.4.2-2) unstable; urgency=medium

  [ Vagrant Cascadian ]
  * Patch Makefile to set date for BUILD_TIME using SOURCE_DATE_EPOCH.
    Closes: #977435
  * Force same hostname to enable reproducible builds
    Closes: #977436

  [ Andreas Tille ]
  * Standards-Version: 4.5.1 (routine-update)
  * debhelper-compat 13 (routine-update)
  * use binaries installed to debian/tmp

 -- Andreas Tille <tille@debian.org>  Tue, 15 Dec 2020 21:07:56 +0100

bowtie2 (2.4.2-1) unstable; urgency=medium

  * New upstream version 2.4.2
  * Refresh patches,
    drop applied by upstream gcc10_ftbfs_invalid_dquote_char.patch
  * Apply cme fix dpkg, drop version from libsimde-dev

 -- Alexandre Mestiashvili <mestia@debian.org>  Wed, 07 Oct 2020 20:06:52 +0200

bowtie2 (2.4.1-6) unstable; urgency=medium

  * Team upload.
  * Bump version requirement for libsimde-dev to grab ppc64el fixes.

 -- Michael R. Crusoe <crusoe@debian.org>  Mon, 01 Jun 2020 15:40:38 +0200

bowtie2 (2.4.1-5) unstable; urgency=medium

  * Reproducible builds: filter out -ffile-prefix-map
    Closes: #961494

 -- Andreas Tille <tille@debian.org>  Mon, 25 May 2020 14:14:23 +0200

bowtie2 (2.4.1-4) unstable; urgency=medium

  * Team upload.
  * Switch to libsimde-dev package from our code copy

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 21 Apr 2020 15:35:11 +0200

bowtie2 (2.4.1-3) UNRELEASED; urgency=medium

  * Team upload.
  * Add salsa-ci file (routine-update)

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 20 Apr 2020 17:54:38 +0200

bowtie2 (2.4.1-2) unstable; urgency=medium

  * Add patch fixing FTBFS with gcc10, thanks to Jun Aruga
    Closes: #957054

 -- Alexandre Mestiashvili <mestia@debian.org>  Sun, 19 Apr 2020 11:11:42 +0200

bowtie2 (2.4.1-1) unstable; urgency=medium

  * Team upload.
  * debian/control: not ready for 32-bit archs, and those builds often take
    2-3+ hours to fail, so lets be nice and skip them.
    Patches to fix 32-bit archs are very welcomed!
  * Standards-Version: 4.5.0 (routine-update)
  * Freshen patches
  * debian/upstream/metadata: Add Bug-{Database,Submit},Repository{,-Browse}
  * Update SIMDe version to 2a9ff6ddabfb940bdd29a0a0cd1ae3190f5fc97b 2020-04-03

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 01 Mar 2020 11:30:50 +0100

bowtie2 (2.3.5.1-6) unstable; urgency=medium

  * Team upload.
  * Remove the -m64 flag; not needed and not as universal as I thought
  * This means we build on arm64. (Closes: #925499)

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 18 Dec 2019 13:36:56 +0100

bowtie2 (2.3.5.1-5) unstable; urgency=medium

  * Team upload.
  * debian/rules: Remove -santized here as well

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Wed, 18 Dec 2019 12:15:28 +0100

bowtie2 (2.3.5.1-4) unstable; urgency=medium

  * Team upload.
  * Added patch to correct the 64bit detection logic.
  * Disable -fsanitize builds to save resources

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 16 Dec 2019 10:13:27 +0100

bowtie2 (2.3.5.1-3) unstable; urgency=medium

  * Team upload.
  * Enable all architectures via simde.
  * Unset M64_FLAG and POPCNT_CAPABILITY on non AMD64 archs.
  * debian/rules: Fix testing in with cowdancer or eatmydata by unsetting
    LD_PRELOAD (the address sanitizer must be first in the library list)
  * Added missing ${perl:Depends} for the bowtie2 binary package

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 14 Dec 2019 13:42:14 +0100

bowtie2 (2.3.5.1-2) unstable; urgency=medium

  [ Steffen Möller ]
  * Added ref to conda

  [ Andreas Tille ]
  * SEQwiki is deprecated

  [ Steffen Moeller ]
  * d/u/metadata: yamllint

  [ Alexandre Mestiashvili ]
  * Update d/patches/2to3.patch, use importlib instead of deprecated imp module
    Closes: #945422
  * Add patch silencing TBB deprecation warnings
  * d/control: bump Policy to 4.4.1, add Rules-requires-root: no

 -- Alexandre Mestiashvili <mestia@debian.org>  Fri, 06 Dec 2019 22:38:21 +0100

bowtie2 (2.3.5.1-1) unstable; urgency=medium

  [ Michael R. Crusoe ]
  * bowtie-examples: set Multi-Arch: foreign

  [ Steffen Moeller ]
  * debhelper-compat 12
  * Standards-Version: 4.4.0
  * New upstream version - yet fails to build -> crash

  [ Andreas Tille ]
  * Use 2to3 to port to Python3
    Closes: #936233
  * Remove obsolete fields Name, Contact from debian/upstream/metadata.
  * Build-Depends: libfile-which-perl
  * (Build-)Depends: s/python/python3/

 -- Alexandre Mestiashvili <mestia@debian.org>  Thu, 05 Sep 2019 15:45:04 +0200

# Older entries have been removed from this changelog.
# To read the complete changelog use `apt changelog bowtie2`.
