phyml (3:3.3.20200621-2) unstable; urgency=medium

  * Fix watchfile to detect new versions on github
  * Standards-Version: 4.6.0 (routine-update)

 -- Andreas Tille <tille@debian.org>  Wed, 06 Oct 2021 17:30:05 +0200

phyml (3:3.3.20200621-1) unstable; urgency=medium

  * Team upload
  * New upstream version 3.3.20200621 (Closes: #957679)
  * Standards-Version: 4.5.0 (routine-update)
  * debhelper-compat 13 (routine-update)
  * Add salsa-ci file (routine-update)
  * Rules-Requires-Root: no (routine-update)
  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
    Repository-Browse.

 -- Shayan Doust <hello@shayandoust.me>  Wed, 22 Jul 2020 16:25:36 +0000

phyml (3:3.3.20190909-1) unstable; urgency=medium

  * Team upload.
  * New upstream version
  * Standards-Version: 4.4.1
  * Reported autogenerated files in archive to upstream
    (https://github.com/stephaneguindon/phyml/issues/113)

 -- Steffen Moeller <moeller@debian.org>  Wed, 06 Nov 2019 21:46:04 +0100

phyml (3:3.3.20190321-2) unstable; urgency=medium

  * Fix autopkgtest
    Closes: #935598
  * Secure URI in copyright format
  * Remove trailing whitespace in debian/changelog
  * Remove obsolete fields Name, Contact from debian/upstream/metadata.

 -- Andreas Tille <tille@debian.org>  Sat, 24 Aug 2019 16:08:44 +0200

phyml (3:3.3.20190321-1) unstable; urgency=medium

  * New upstream version
  * debhelper-compat 12
  * Standards-Version: 4.4.0
  * Do not run dh_dwz

 -- Andreas Tille <tille@debian.org>  Thu, 01 Aug 2019 22:05:12 +0200

phyml (3:3.3.20180621-2) unstable; urgency=medium

  * Team upload

  [ Andreas Tille ]
  * Install test script to user documentation

  [ Graham Inggs ]
  * Allow MPI oversubscription in autopkgtests

 -- Graham Inggs <ginggs@debian.org>  Wed, 27 Jun 2018 16:24:13 +0000

phyml (3:3.3.20180621-1) unstable; urgency=medium

  * New upstream version
  * d/copyright: Do not exclude non-included files any more
  * Use MPI_C to enable cross building (thanks for the patch to Helmut Grohne)
    Closes: #902433

 -- Andreas Tille <tille@debian.org>  Tue, 26 Jun 2018 18:11:00 +0200

phyml (3:3.3.20180214+dfsg-1) unstable; urgency=medium

  [ Steffen Moeller ]
  * debian/upstream/metadata: Added refs to registries

  [ Andreas Tille ]
  * New upstream version
  * Point Vcs fields to salsa.debian.org
  * Standards-Version: 4.1.4
  * debhelper 11
  * Fix file permissions of example files

 -- Andreas Tille <tille@debian.org>  Fri, 27 Apr 2018 08:09:18 +0200

phyml (3:3.3.20170530+dfsg-2) unstable; urgency=medium

  * Team upload
  * Do not emit -march=native (Closes: #866139)
  * Drop autopkgtest dependency on pocl-opencl-icd

 -- Graham Inggs <ginggs@debian.org>  Fri, 30 Jun 2017 14:01:22 +0200

phyml (3:3.3.20170530+dfsg-1) unstable; urgency=medium

  * New upstream version
  * Upstream confirmed that beagle is not supported
  * Standards-Version: 4.0.0 (no changes needed)
  * Do not disable PIE
    Closes: #865654
  * Do not build phytime since it is not supported any more

 -- Andreas Tille <tille@debian.org>  Tue, 27 Jun 2017 15:06:53 +0200

phyml (3:3.2.0+dfsg-7) unstable; urgency=medium

  * Fix bug in wrapper script which really
    Closes: #853738

 -- Andreas Tille <tille@debian.org>  Wed, 01 Feb 2017 09:36:51 +0100

phyml (3:3.2.0+dfsg-6) unstable; urgency=medium

  * Also provide version without beagle library since it causes trouble
    on machines without according graphics hardware
    Closes: #853737
  * Provide link /usr/bin/phyml-beagle
  * Enable to switch of MPI version via environment variable since there
    are circumstances when it leads to wrong results
    Closes: #853738
  * Test single processor and MPI in autopkgtest

 -- Andreas Tille <tille@debian.org>  Tue, 31 Jan 2017 15:16:45 +0100

phyml (3:3.2.0+dfsg-5) unstable; urgency=medium

  * Fix wrapper to correctly use mpirun
    Closes: #853211

 -- Andreas Tille <tille@debian.org>  Mon, 30 Jan 2017 17:34:56 +0100

phyml (3:3.2.0+dfsg-4) unstable; urgency=medium

  * Add pocl-opencl-icd to autopkgtest dependencies to emulate CPU-based ICD
  * debhelper 10
  * d/watch: version=4
  * Use chrpath to remove RPATH from binary
  * Use "OMPI_MCA_plm_rsh_agent=/bin/false" in test (see #494046)

 -- Andreas Tille <tille@debian.org>  Mon, 16 Jan 2017 10:22:34 +0100

phyml (3:3.2.0+dfsg-3) unstable; urgency=medium

  * Team upload

  [ Canberk Koç ]
  * autopkgtest added
  * fix autopkgtest

  [ Andreas Tille ]
  * Add missing Depends: openmpi-bin
  * use wrapper to select MPI version if applicable
  * Use compression options in d/watch
  * Fix missing declaration
  * hardening=+all,-pie

 -- Canberk Koç	 <canberkkoc@gmail.com>  Wed, 12 Oct 2016 23:51:39 +0300

phyml (3:3.2.0+dfsg-2) unstable; urgency=medium

  [ Kevin Murray ]
  * Fix VCS link in d/control
  * Patch for reproduible build (configure.ac date)
  * Bump standards version to 3.9.7

  [ Andreas Tille ]
  * Enable MPI version of phyml

 -- Andreas Tille <tille@debian.org>  Mon, 14 Mar 2016 12:52:14 +0100

phyml (3:3.2.0+dfsg-1) unstable; urgency=medium

  [ Kevin Murray ]
  * New upstream release
  * d/watch: Source has changed location on Github
  * Patch CPPFLAGS to allow build of phytime

  [ Andreas Tille ]
  * Upstream confirmed that the development version should be fairly stable
    and most probably suitable for Debian
  * Moved debian/upstream to debian/upstream/metadata
  * cme fix dpkg-control
  * Remove executable binary from archive (as well as LaTeX remainings once
    we are starting to remove files)
  * Move to git
  * Build-Depends: pkg-config, libhmsbeagle-dev
  * debian/rules:
     - hack around removal of PDF manual
     - enable building with libhmsbeagle-dev
  * DEP5

 -- Kevin Murray <spam@kdmurray.id.au>  Sat, 06 Feb 2016 16:06:43 +0100

phyml (2:20120412-2) unstable; urgency=low

  * debian/patches/sse_only_if_supported.patch: Check architecture before
    deciding to build using -msse
    Closes: #718747

 -- Andreas Tille <tille@debian.org>  Mon, 05 Aug 2013 09:56:27 +0200

phyml (2:20120412-1) unstable; urgency=low

  [ Charles Plessy ]
  * New upstream version.
  * Updated watch file to track stable versions only.
  * debian/rules, debian/docs, the manual is now phyml-manual.pdf.

  [ Andreas Tille ]
  * debian/control:
     - cme fix dpkg-control
     - debhelper 9
     - use anonscm in Vcs fields
  * debian/rules:
     - Use dh more consequently to work around two different configure steps
     - Propagate hardening options
  * debian/upstream: Additional (newer) publication
  * debian/phytime.1: Add manpage for phytime based on some html2man output
    and the abstract of the according publication
  * debian/README.Debian: Hint to possible phyml-mpi

 -- Charles Plessy <plessy@debian.org>  Mon, 15 Jul 2013 09:55:11 +0900

phyml (2:20110919-1) unstable; urgency=low

  * New upstream version.
  * Kept manual's old name with no date (debian/docs, debian/rules).
  * Do not compress PDFs (debian/rules).

 -- Charles Plessy <plessy@debian.org>  Mon, 05 Dec 2011 13:19:40 +0900

phyml (2:20110526-1) unstable; urgency=low

  * New upstream version.
  * debian/control:
    - Corrected VCS URLs.
    - Using debhelper 8 (debian/compat).
    - Enhances bioperl-run (that has a PhyML wrapper).
    - Standards-Version incremented to reflect compliance with Policy 3.9.2.
  * Added build-arch and build-indep targets to debian/rules.
  * Build and distribute PhyTime (debian/rules, debian/control).

 -- Charles Plessy <plessy@debian.org>  Sun, 26 Jun 2011 12:14:54 +0900

phyml (2:20100720-1) unstable; urgency=low

  * New upstream version
  * Fixed watch file
  * Standard-Version: 3.9.1 (no changes needed)
  * Source format 3.0 (quilt)
  * Wrote man page

 -- Andreas Tille <tille@debian.org>  Mon, 14 Feb 2011 15:04:52 +0100

phyml (2:20100123-1) unstable; urgency=low

  * New upstream release.

  [ Nelson A. de Oliveira ]
  * Fix watch file.
  * Increment the epoch number to fix a typo in the version number.

  [ Charles Plessy ]
  * Checked conformance with Policy 3.8.4 and incremented Standards-Version
    in debian/control to reflect this (no changes needed).
  * Moved the bibliographic reference from debian/reference to
    debian/upstream-metadata.yaml.
  * Adapted debian/rules to the new location of the auto(conf|make) files.

 -- Charles Plessy <plessy@debian.org>  Sun, 07 Mar 2010 19:55:08 +0900

phyml (1:200900706-2) unstable; urgency=low

  * Disable parallel building, that was incorrectly supported and
    induced build failures by race condition (Closes: #536967).

 -- Charles Plessy <plessy@debian.org>  Wed, 15 Jul 2009 09:35:40 +0900

phyml (1:200900706-1) unstable; urgency=low

  * New upstream release.
  * Suppressed unneeded Lintian overrides, and use ‘dh clean’ in debian/rules.
  * Checked conformance with Policy 3.8.2 and incremented Standards-Version
    in debian/control to reflect this (no changes needed).
  * Experimentation on the format of debian/copyright.

 -- Charles Plessy <plessy@debian.org>  Sat, 11 Jul 2009 14:25:23 +0900

phyml (1:20090501-1) unstable; urgency=low

  * New upstream release clarifying the license of the documentation and
    switching to a versionning system that can be sorted by numerical order.
  * Added debian/source.lintian-overrides to indicate that the
    configure-generated files are deleted at cleaning time.
  * Using ‘dh binary-arch’ to simplify debian/rules.

 -- Charles Plessy <plessy@debian.org>  Sat, 16 May 2009 14:55:14 +0900

phyml (30042009-1) unstable; urgency=low

  * Initial release (Closes: #517165)

 -- Charles Plessy <plessy@debian.org>  Fri, 01 May 2009 08:53:44 +0900
