gromacs (5.1.2-1ubuntu1) xenial; urgency=medium

  * Limit parallel build to 2 jobs for amd64 to avoid FTBFS while building
    doxygen documentation on Ubuntu buildds.

 -- Graham Inggs <ginggs@ubuntu.com>  Tue, 05 Apr 2016 22:41:20 +0200

gromacs (5.1.2-1) unstable; urgency=medium

  * New upstream release.
  * Add hppa, s390x, x32 to list of architectures for gromacs-openmpi.
    In turn, increase required version of libopenmpi-dev to >= 1.10.2-7.
  * Add new patches/reproducible-builds.patch for... reproducible builds.
    This is preliminary work and may not be complete.
  * doxygen.patch: work around FTBFS with doxygen >= 1.8.11 (no problems
    with previous 1.8.9).  (Closes: #815678)
  * spelling.patch: Additional fixes.
  * Update Standards-Version to 3.9.7, no changes required.

 -- Nicholas Breen <nbreen@debian.org>  Sun, 28 Feb 2016 13:31:21 -0800

gromacs (5.1.1-2) unstable; urgency=medium

  * Replace compiler calls to "mpic++" with "mpicxx".  MPICH >= 3.2 no
    longer ships mpic++ links.  (Closes: #808659)
  * Remove obsolete build dependency on libgsl0-dev.

 -- Nicholas Breen <nbreen@debian.org>  Tue, 22 Dec 2015 17:18:40 -0800

gromacs (5.1.1-1) unstable; urgency=medium

  * New upstream release.

 -- Nicholas Breen <nbreen@debian.org>  Mon, 09 Nov 2015 17:24:02 -0800

gromacs (5.1-1) unstable; urgency=low

  * New upstream release.  This release completes the transition to "gmx"
    as the sole binary to replace all the former g_* commands, and the
    compatibility symlinks have been removed.  Standalone mdrun_mpi
    programs in gromacs-mpich and gromacs-openmpi are unaffected.
    - gmx anadock no longer crashes on invalid input.  (Closes: #715934)
  * Some package reshuffling: gromacs-dev becomes libgromacs-dev, and the
    shared library gets split out into libgromacs1.  (Closes: #797744)
    Upload priority set to "low" due to the unusually extensive restructure.
  * Remove gromacs-dev.preinst, only needed for upgrades from well before
    the version in squeeze.
  * Lots more documentation!  PDF manual is built once again, and doxygen
    output for developer use is included.  Several Build-Depends-Indep
    entries added to support this.
    - patches/manpage-hyphenation.patch removed, no longer needed.
    - mdrun_mpi.{mpich,openmpi}.1 updated.
  * debian/control: apply wrap-and-sort.

 -- Nicholas Breen <nbreen@debian.org>  Thu, 01 Oct 2015 17:38:08 -0700

gromacs (5.0.6-1) unstable; urgency=medium

  * New upstream release.

 -- Nicholas Breen <nbreen@debian.org>  Sun, 26 Jul 2015 13:58:11 -0700

gromacs (5.0.5-1) unstable; urgency=medium

  * New upstream release.

 -- Nicholas Breen <nbreen@debian.org>  Sat, 16 May 2015 11:30:11 -0700

gromacs (5.0.4-2) unstable; urgency=medium

  * Post-Jessie upload to unstable, no other changes.

 -- Nicholas Breen <nbreen@debian.org>  Mon, 27 Apr 2015 10:00:09 -0700

gromacs (5.0.4-1) experimental; urgency=medium

  * New upstream release.  Uploaded to experimental during the freeze.
    Minor patch rebasing only.

 -- Nicholas Breen <nbreen@debian.org>  Sun, 21 Dec 2014 12:54:35 -0800

gromacs (5.0.2-1) unstable; urgency=medium

  * New upstream release.
  * Update Standards-Version to 3.9.6, no changes required.
  * Update rules to build GPU-accelerated packages, with thanks to
    Steffen Möller.

 -- Nicholas Breen <nbreen@debian.org>  Sun, 05 Oct 2014 10:29:34 -0700

gromacs (5.0.1-1) unstable; urgency=medium

  * New upstream release.
  * Rebase patches involving man pages (moved from share/man to doc/man in
    tarball), drop 20_random123_platforms.patch (incorporated upstream),
    and remove the leading numbers from all patch filenames (a leftover from
    dpatch).
  * man/mdrun_mpi.*: Update .TH line.
  * rules: Set CMAKE_RULE_MESSAGES=OFF to work around blhc false positives
    for "W-compiler-flags-hidden".
  * Move debian/upstream to debian/upstream/metadata.

 -- Nicholas Breen <nbreen@debian.org>  Sat, 06 Sep 2014 11:20:17 -0700

gromacs (5.0-3) unstable; urgency=medium

  * Upload to unstable.

 -- Nicholas Breen <nbreen@debian.org>  Sun, 24 Aug 2014 20:02:24 -0700

gromacs (5.0-2) experimental; urgency=low

  * Add 20_random123_platforms.patch to disable architecture check from
    external Random123 code.
  * Drop discussion of shared libraries from README.Debian for
    gromacs-{mpich,openmpi}.

 -- Nicholas Breen <nbreen@debian.org>  Wed, 02 Jul 2014 20:13:01 -0700

gromacs (5.0-1) experimental; urgency=low

  * New upstream release, experimental upload.
    - g_sigeps / gmx sigeps command line handling no longer crashes on
      invalid input (Closes: #715935).
  * Rebase existing patches.  Add new patches:
    - 31_manpage_hyphenation.patch: Some parts of the man page generation
      get the hyphen/dash separation right, some don't.  A temporary fix
      pending significant overhaul of the man page system.
      <http://redmine.gromacs.org/issues/1437>
    - 32_spelling.patch: Correction of minor spelling errors.
  * man/g_{dos,kinetics,luck}.1: Incorporated upstream, removed.
  * man/gmx.1: Rudimentary man page written and added.
  * man/mdrun_mpi.*.1: Updated with text from upstream gmx-mpich.1.
  * rules: Updates for MPI builds and assorted upstream changes.
  * gromacs-data.lintian-overrides, source/lintian-overrides: Removed.
  * Add Build-Depends on external libboost-dev.
  * Switch away from hardening-wrapper in favor of dpkg-buildflags.
  * Update copyright file.

 -- Nicholas Breen <nbreen@debian.org>  Wed, 02 Jul 2014 17:35:18 -0700

gromacs (4.6.5-2) unstable; urgency=medium

  * Update list of OpenMPI architectures to include mips*, arm64. 
  * patches/21_hurd.patch: Cherry-pick upstream commit 2c81d3ab to build
    shared libraries on GNU/Hurd.
  * watch: Extend regex to detect -beta, -pre, _pre, *and* -rc suffixes.
  * Remove chrpath workaround, no longer needed as of mpich 3.0.4-6.

 -- Nicholas Breen <nbreen@debian.org>  Mon, 16 Jun 2014 18:48:37 -0700

gromacs (4.6.5-1) unstable; urgency=low

  * New upstream release.
  * rules: Override autodetection of CPU extensions on amd64 and i386; 
    force to SSE2 only, and provide new DEB_BUILD_OPTIONS=cpuopt flag to
    re-enable autodetection for local builds.  (Closes: #725013)
  * rules: Fix misplaced COPYING symlink in gromacs-data.
  * source/lintian-overrides: Add overrides for outstanding lintian bugs
    #729096 (newer policy version), #724866 (libmpich-dev not virtual).
  * patches/20_manpages.patch: Fix formatting errors in the NAME line of
    several man pages.
  * gromacs-data.doc-base: Change root to getting_started.html.  The
    shipped HTML documentation is slowly being eliminated in favor of a
    wiki on gromacs.org.

 -- Nicholas Breen <nbreen@debian.org>  Mon, 09 Dec 2013 10:40:36 -0800

gromacs (4.6.3-4) unstable; urgency=low

  * control: Add versioned Build-Depends on libmpich-dev (>= 3), to prevent
    build failures on architectures where that still represents the old 
    MPICH version 1. 
  * rules: More mpich2 -> mpich replacements.

 -- Nicholas Breen <nbreen@debian.org>  Sun, 29 Sep 2013 21:39:46 -0700

gromacs (4.6.3-3) unstable; urgency=low

  * control: 
    - Move Replaces/Breaks to MPI packages instead.  (Closes: #718001)
    - Move all mpich2 dependencies to new mpich (v3) package names.
  * control, rules:
    - Add ppc64 to list of supported architectures for gromacs-openmpi.
    - Temporarily add use of "chrpath -d" on gromacs-mpich binaries, due
      to mpicc.mpich setting RPATH unconditionally (see #724864).

 -- Nicholas Breen <nbreen@debian.org>  Sun, 29 Sep 2013 16:30:43 -0700

gromacs (4.6.3-2) unstable; urgency=low

  * control: 
    - Add B-Ds for external BLAS/LAPACK libraries.
    - Have -dev Replaces/Breaks earlier versions of -openmpi/-mpich
      to handle file move.  (Closes: #718001) 
    - For gromacs, remove Conflicts with a long-obsolete (before squeeze)
      version of radiance, and add Suggests on pymol for visualization.
  * rules: Specify verbose output from CMake.

 -- Nicholas Breen <nbreen@debian.org>  Sun, 11 Aug 2013 13:05:19 -0700

gromacs (4.6.3-1) unstable; urgency=low

  * New upstream release; post-freeze, uploading to unstable.
  * rules, control: Remove special provisions for FORTRAN on Alpha.
  * rules: Update configuration parameters.
  * rules, patches/12_copyright-file.patch: Avoid duplication of copyright
    information into two files, but provide a link to keep both filenames.
  * control: Drop obsolete B-D on lesstif2-dev.  (Closes: #714753)
  * rules: Move .so symlinks for MPI libraries from -dev to their respective
    packages, to ensure that they can't be installed without their targets.
  * control: Update SCM links.

 -- Nicholas Breen <nbreen@debian.org>  Fri, 05 Jul 2013 13:57:44 -0700

gromacs (4.6-1) experimental; urgency=low

  * New upstream release, targeted at experimental during freeze.
    - Remove patches/10_release-4-5-patches.patch (obsolete), 
      31_manpages.patch (incorporated upstream).
    - Update lintian overrides.

 -- Nicholas Breen <nbreen@debian.org>  Mon, 25 Feb 2013 10:47:14 -0800

gromacs (4.5.5-2) unstable; urgency=low

  [ Andreas Tille ]
  * debian/upstream:
     - copied citations from tasks/bio to debian/upstream
     - make last citation conform to BibTeX syntax

  [ Nicholas Breen ]
  * Update to current release-4.5-patches git (f361fa9c) via addition of
    patches/10_release-4.5-patches.patch.
  * source/format: Move to 3.0 (quilt).  Adjust patches accordingly.
  * control: Remove specific listing of MPI packages from description of
    gromacs-dev.  (Closes: #644820)  Update maintainer address and drop
    DMUA stanza.  Drop Build-Depends on dpatch, add on hardening-wrapper.
    Update to S-V 3.9.3, no packaging changes required.
  * rules, README.source: Remove dpatch cruft.
  * rules: Apply compiler hardening flags with hardening-wrapper.
  * patches/*: Tidy up with DEP-3 headers.
  * control, rules: Update list of architectures for gromacs-openmpi,
    adding armel, armhf, powerpcspe, and sparc64.

 -- Nicholas Breen <nbreen@debian.org>  Sat, 09 Jun 2012 11:42:56 -0700

gromacs (4.5.5-1) unstable; urgency=low

  * New upstream release.
    - Remove patches/30_git_release-4.5-patches.dpatch.
    - man/g_dos.1: Create man page for new binary.
  * rules: Add build-arch/build-indep targets.  Add preliminary support for
    building GPU-accelerated binaries: set DEB_BUILD_OPTIONS=gpu to try it.
  * patches/31_manpages.dpatch: Update.

 -- Nicholas Breen <nbreen@ofb.net>  Wed, 21 Sep 2011 19:10:08 -0700

gromacs (4.5.4-2) unstable; urgency=low

  * control: remove obsolete Build-Depends and Suggests on libice-dev,
    libsm-dev, libxext-dev, libxp-dev, libxt-dev.  Update Standards-Version
    to 3.9.2.
  * patches/30_git_release-4.5-patches.dpatch: Routine update from upstream
    git, to commit 873563ef of 22 April 2011.
  * patches/31_manpages.dpatch: Various minor spelling and header fixes.
  * lintian-overrides.gromacs: Remove checks no longer needed, per #120323.
  * rules: Switch to using dh_lintian.

 -- Nicholas Breen <nbreen@ofb.net>  Mon, 25 Apr 2011 13:47:00 -0700

gromacs (4.5.4-1) unstable; urgency=low

  * New upstream release.
  * Remove gromacs-lam transitional package.
  * man/g_options.1: Create man page for new binary.
  * lintian-overrides.gromacs-data: Override script-not-executable for demo
    scripts not in $PATH.

 -- Nicholas Breen <nbreen@ofb.net>  Mon, 21 Mar 2011 19:59:54 -0700

gromacs (4.5.3-1) unstable; urgency=low

  * New upstream release.
  * Force -DGMX_X11=ON to build ngmx.  (Closes: #603327)

 -- Nicholas Breen <nbreen@ofb.net>  Sat, 13 Nov 2010 12:02:17 -0800

gromacs (4.5.2-1) unstable; urgency=low

  * Major new upstream release.
  * All patches incorporated upstream and removed, except the Debian-
    specific bug reporting portion of 11_readme.dpatch.
  * man/gromacs.7: incorporated upstream, removed from Debian patch.
  * man/luck.1: Rename to g_luck.1 and edit to reflect new name.
  * man/mdrun_mpi.*.1: Resynchronize with upstream mdrun.1.
  * watch: Update to recognize -betaX tarballs and ignore -GPU builds.
  * rules: Convert from autotools to new CMake build system.
  * control:
    - Add Build-Depends on libxml2-dev.
    - Update Standards-Version to 3.9.1.
    - Replace Conflicts: with Breaks:.

 -- Nicholas Breen <nbreen@ofb.net>  Wed, 03 Nov 2010 17:39:52 -0700

gromacs (4.0.7-3) unstable; urgency=low

  * New patch 03_autoconf_bashisms.dpatch: Eliminate two bashisms (test ==
    instead of =) in configure.ac, permitting use with dash instead.
  * patches/30_git_release-4.0-patches.dpatch: Update to commit
    36df279783944c11d1ba43936ea820f8e6003ffd.

 -- Nicholas Breen <nbreen@ofb.net>  Tue, 25 May 2010 19:30:48 -0700

gromacs (4.0.7-2) unstable; urgency=low

  * rules: 
    - Drop chrpath workaround, underlying bug solved with mpich2 
      1.2.1.1-2.
    - Add sparc to list of architectures for -openmpi.
  * control:
    - Per above.
    - Set DM-Upload-Allowed: yes.
    - Update Standards-Version to 3.8.4.
    - Add ${misc:Depends} for Lintian, except for -data and -lam which
      receive overrides instead.
  * gromacs-parallel.README.Debian.in: Remove reference to LAM-MPI.
  * patches/30_git_release-4.0-patches.dpatch: Update to commit
    444432a51f87f003fc6e7098f9e07a2a2d142c64.
  * source/format: Create and set explicitly to 1.0.
  * source/lintian-overrides: Override debhelper-but-no-misc-depends for
    gromacs-data and gromacs-lam.

 -- Nicholas Breen <nbreen@ofb.net>  Tue, 13 Apr 2010 23:33:27 -0700

gromacs (4.0.7-1) unstable; urgency=low

  * New upstream release.
  * patches/30_git_release-4.0-patches.dpatch: Empty out, replace with
    fresh pull starting at the 4.0.7 release; current to git commit
    665dce86638df8ac1062b0b022d7827ea0f11788.

 -- Nicholas Breen <nbreen@ofb.net>  Thu, 31 Dec 2009 16:43:03 -0800

gromacs (4.0.5-5) unstable; urgency=low

  * Transition to only the two supported MPI implementations:
    - gromacs-mpich now builds against MPICH2, not MPICH1.
    - gromacs-lam replaced with a dummy package installing gromacs-
      openmpi on all supported architectures, -mpich on the holdouts.
    - Update documentation accordingly.
  * patches/30_git_release-4.0-patches.dpatch: Pull from upstream git
    repository, release-4.0-patches branch.  Current to git commit
    37a4dd35fec7579ca7faca25c62c71cf1d8e1621, 29 Nov. 2009.
  * patches/21_makefile_dups.dpatch: Delete, incorporated above
    (commit c93db8511af09c144fe4b2b8f57b14a5ad1e6cc7).
  * compat: Update to debhelper v7 mode.
    - rules: Replace dh_clean -k with dh_prep.
    - control: Adjust Build-Depends to debhelper (>= 7.0.0).
  * copyright: Increment year.
  * rules: Use chrpath to eliminate RPATH from MPICH2-compiled binaries.
    This is a workaround for a libmpich2-dev bug, #558960.
    - control: Add chrpath to Build-Depends.
  * rules: Add -Wl,--as-needed to LDFLAGS.

 -- Nicholas Breen <nbreen@ofb.net>  Mon, 30 Nov 2009 16:18:34 -0800

gromacs (4.0.5-4) unstable; urgency=low

  * patches/21_makefile_dups.dpatch: Eliminate duplicated files in the
    installation list of include/Makefile.am.  Automake 1.11 now passes
    multiple files to `install' at once, causing failures when one name
    is given twice.  (Closes: #543059)
  * control: Increment S-V to 3.8.3.  No changes required.
  * rules: Remove obsolete --disable-nice option from *_CONFIG_PARAMS.
  * man/gromacs.7: Update macros for lintian cleanliness.

 -- Nicholas Breen <nbreen@ofb.net>  Tue, 25 Aug 2009 12:30:15 -0700

gromacs (4.0.5-3) unstable; urgency=low

  * patches/20_altivec_kernel.dpatch: Extend patch to cover
    nb_kernel_ppc_altivec.c, which does not include the same headers.
  * control: Increment Standards-Version to 3.8.2.  No packaging changes
    required.

 -- Nicholas Breen <nbreen@ofb.net>  Wed, 24 Jun 2009 17:21:26 -0700

gromacs (4.0.5-2) unstable; urgency=low

  * patches/20_altivec_kernel.dpatch: Resolve FTBFS on AltiVec-enabled
    PPC builds caused by use of "restrict" keyword, which GCC does not
    normally accept unless in C99 mode.  Reported upstream at
    http://bugzilla.gromacs.org/show_bug.cgi?id=324

 -- Nicholas Breen <nbreen@ofb.net>  Sun, 17 May 2009 15:52:53 -0700

gromacs (4.0.5-1) unstable; urgency=low

  * New upstream release.
  * debian/control: Bump Standards-Version to 3.8.1.  No packaging
    changes required.
  * debian/control: Replace svn+ssh:// URI with svn:// .
  * debian/copyright: Replace "(C)" with "Copyright", update dates.
  * debian/rules: #452047 rears its ugly head again!  Add LDFLAGS to -lam
    and -openmpi builds with -L arguments to their respective library
    directories, exclusive of update-alternatives trickery, in order to
    prevent accidental cross-linking.  Thanks again to Manuel Prinz.
    (Closes: #526266)

 -- Nicholas Breen <nbreen@ofb.net>  Mon, 11 May 2009 18:15:11 -0700

gromacs (4.0.4-1) unstable; urgency=low

  * New upstream release.
  * patches/05_lt_init.dpatch: Add LT_INIT to configure.ac so that the
    libtool script can find its version.  Necessary for current Ubuntu
    build environment.  Patch courtesy of James Westby.

 -- Nicholas Breen <nbreen@ofb.net>  Sat, 28 Feb 2009 16:45:25 -0800

gromacs (4.0.3-1) unstable; urgency=low

  * New upstream release.
  * Remove obsoleted patches 40, 41, 50, 51, 52.

 -- Nicholas Breen <nbreen@ofb.net>  Mon, 19 Jan 2009 13:35:23 -0800

gromacs (4.0.2-2) unstable; urgency=low

  * debian/*.postinst: Resort update-alternatives priorities for the MPI
    packages to follow the newly proposed priorities of the individual
    MPI implementations themselves, OpenMPI > MPICH > LAM.
  * New patches:
    - 40_hppa_asm.dpatch: Attempt to correct FTBFS on HPPA
      inline ASM code by replacing an undefined variable.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=260)
    - 41_sprintf.dpatch: Replace sprintf calls relying on undefined
      behavior with proper, portable code.  Problem identified by Kees
      Cook: http://lists.debian.org/debian-devel/2008/12/msg01079.html
    - 50_type2bonds.dpatch: Fix grompp freeze when using type 2 bonds
      (G96) and all-angle constraints.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=261)
    - 51_mshift.dpatch: When running mdrun on multiple processors, it
      will crash under certain circumstances when an error is generated
      but there is no log file attached to that specific process.  This
      was triggered by some incorrect "inconsistent shift" warning
      messages.  Both problems are corrected by this patch.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=267)
    - 52_ia64_single_pointer.dpatch: Test for non-zero pointer in IA64
      single-precision kernel when writing to log file.  Pointer is
      zero on non-master MPI processes, and would previously segfault.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=262)
  * debian/rules: Use autoreconf in lieu of automake&&autoconf&&... to
    avoid version skew.  Thanks to James Westby for the patch.

 -- Nicholas Breen <nbreen@ofb.net>  Mon, 19 Jan 2009 10:42:26 -0800

gromacs (4.0.2-1) unstable; urgency=low

  * New upstream release.
    - Remove obsoleted debian/patches/50_confio.dpatch (fixed),
      10_manpages.dpatch (merged upstream).
  * debian/gromacs.README.Debian: suggest OpenMPI for new installations.

 -- Nicholas Breen <nbreen@ofb.net>  Mon, 10 Nov 2008 12:36:15 -0800

gromacs (4.0-1) unstable; urgency=low

  * New upstream release.
    - debian/man: Remove g_nmtraj.1, g_sdf.1, g_spatial.1 (incorporated
      upstream). Remove average.1 (no longer shipped). Update gromacs.7
      with changed commands and reference to new J. Chem. Theory Comput.
      paper.  Update mdrun_mpi.*.1 based on upstream mdrun.1.  Write new
      man pages xplor2gmx.1 and demux.1.
    - debian/lintian-overrides.gromacs: Update against new list of man
      pages.
    - debian/patches: Remove 05_autoconf_gsl.dpatch (fixed upstream) and
      40_missing_cpp.dpatch (preprocessor functionality now built in).
      Resynchronize 10_manpages.dpatch.  Add GROMACS 4 reference to
      11_readme.dpatch.
    - debian/rules: Remove g_ffscan renaming (no longer shipped).
  * debian/control: Drop versioned dependency on base-files.  Add Build-
    Depends on libtool.
  * debian/rules: Don't link MPI binaries to GSL, eliminating a spurious
    dependency.
  * patches/50_confio.dpatch: Avoid segfault when using make_ndx on .tpr
    files.  (cf.
    http://www.gromacs.org/pipermail/gmx-developers/2008-October/002775.html)

 -- Nicholas Breen <nbreen@ofb.net>  Wed, 29 Oct 2008 15:44:28 -0700

gromacs (3.3.3-3) unstable; urgency=low

  [ Daniel Leidert ]
  * debian/gromacs-data.doc-base (Section): Fixed accordingly to latest
    doc-base policy 0.8.10.

  [ Nicholas Breen ]
  * debian/README.source: add reference to dpatch system, as required by
    latest policy (sec. 4.14).  Having done so:
  * debian/control: Update Standards-Version to 3.8.0.
  * debian/rules: Remove obsolete and now-inaccurate comment about
    parallel builds.  Remove duplicated dh_installdeb call.
  * debian/man/g_kinetics.1: Update documentation.
  * debian/patches/05_autoconf_gsl.dpatch: libgsl was not properly
    detected by autoconf when the test didn't also link libgslcblas,
    rendering the g_kinetics program unusable.  This changes the test
    to pass along LIBS appropriately.

 -- Nicholas Breen <nbreen@ofb.net>  Wed, 20 Aug 2008 11:55:39 -0700

gromacs (3.3.3-2) unstable; urgency=low

  * debian/control: Eliminate unneeded Build-Depends on libxml-dev.
    Spotted by Pierre Habouzit.  (Closes: #470000)
  * debian/rules: Force --with-gsl in configuration.

 -- Nicholas Breen <nbreen@ofb.net>  Sat, 08 Mar 2008 12:34:36 -0800

gromacs (3.3.3-1) unstable; urgency=low

  [ Nicholas Breen ]
  * New upstream release.
  * debian/rules, debian/control: Reconfigure gromacs-doc as gromacs-data.
    This moves all architecture independent files into a single package,
    including many topology files formerly shipped in gromacs instead.
    - Rename debian/*gromacs-doc* to debian/*gromacs-data* .
    - debian/gromacs-doc.preinst: no longer necessary, removed.
  * Remove PDF manual for the time being, as modifiable sources are not
    currently available.
    - debian/gromacs.README.Debian, debian/man/gromacs.7: Provide pointers
      to its location online instead.
    - debian/control: Drop build dependency on sharutils, which was used
      only to provide the manual.
    - debian/gromacs-data.doc-base: Remove reference to PDF.
  * debian/control: Add Build-Depends on libgsl0-dev to support addition
    of /usr/bin/g_kinetics.
  * debian/gromacs.README.Debian: Update suggested MPI implementations.
  * debian/man: write preliminary man pages for undocumented new commands,
    g_kinetics.1 g_spatial.1 g_sdf.1
  * debian/patches/10_manpages: Update with ROFF fixes to 18 files; fix a 
    few minor typos; resync patch against upstream CVS.
  * debian/man/mdrun_mpi.{mpich,lam,openmpi}.1: Propagate those fixes.
  * debian/lintian-overrides.gromacs: Drop binary-without-manpage override.
  * debian/linda-overrides.gromacs, debian/rules: Remove linda override.

  [ Daniel Leidert ]
  * debian/man/average.1: Minor ROFF improvements, hyphen/minus and typo
    fixes.
  * debian/man/g_nmtraj.1: Ditto.
  * debian/man/luck.1: Ditto.

 -- Nicholas Breen <nbreen@ofb.net>  Mon, 03 Mar 2008 21:23:01 -0800

gromacs (3.3.3~pre1-1) unstable; urgency=low

  [ Nicholas Breen ]
  * New upstream release.
    - Remove obsolete patches now incorporated upstream:
      50_xtcio_double_range_checking, 51_180_degree_angle,
      52_pme_spline, 53_pbc_compiler.
  * debian/rules: 
    - Clean up patch syntax to prevent double compilations.
    - Add .NOTPARALLEL target to prevent the various MPI builds from
      compiling on the same source tree simultaneously, while still
      allowing -j options to be passed to sublevel targets.
    - Improve DEB_BUILD_OPTIONS=parallel=X handling, now in line with
      the example proposed for policy.
    - Disable FORTRAN inner loops for gromacs-openmpi on alpha.  This
      is a temporary workaround to avoid lingering linking problems
      regarding libmpi.so and the update-alternatives system.
    - Add support for DEB_BUILD_OPTIONS=noopt.
    - Additional rewrite work (see below): use new format for build
      commands, but split for individual MPI implementations.
    - Run autotools between patch and configuration steps.
    - New format for MPI library suffix configuration.
  * debian/control:
    - Add versioned Build-Depends on libmpich1.0-dev for its 
      g77 -> gfortran transition.
    - Add Build-Depends on autoconf and automake, and Build-Conflicts
      on autoconf2.13, to support updated mpisuffix patch.
    - Downgrade gromacs-doc Depends: on gromacs to a Recommends:, as -doc
      now ships its own copyright file.
  * debian/patches/04_autoconf_mpisuffix.dpatch: Apply dleidert's improved
    patch to allow arbitrary overrides of LIBSUFFIX; reduce patch to only
    the directly changed code in configure.ac, and add an invocation of
    autotools during the build process rather than patching configure
    itself directly.
  * debian/gromacs-{doc,dev}.preinst: Remove symlinks for package doc
    directories on upgrade, in order to replace them with actual directories.

  [ Daniel Leidert ]
  * debian/control (Suggests): Fixed a debcheck issue - gromacs-openmpi should
    only be suggested on supported architectures.
  * debian/copyright: Added copyright information to satisfy lintian.
  * debian/gromacs-doc.doc-base (Section): Fixed accordingly to menu policy.
    (Format): Fixed path to HTML files.
  * debian/rules: Major rewrite. Changes/improvements include:
    - drop dpatch target definitions in favour of dpatch.make
    - put all configure flags to the top of the file
    - moved all configure related commands into configure-stamp
    - moved all build related commands into build-stamp
    - moved all install related commands into separate install targets
    - configure and build in sub-directories to avoid $(MAKE) clean calls
    - clean target removes build/ instead to run clean/distclean
    - replaced ln with dh_link and gzip with dh_installman
    - adjusted target requirements for binary* and install*
    - install a /usr/share/doc/$package directory for gromacs-doc and -dev
      too; put the HTML into the -doc documentation directory; add links to
      the HTML directory for the gromacs and the -dev package pointing to the
      -doc directory
    - fixed .PHONY target for above
  * debian/watch: Added pre-release version handling.

 -- Nicholas Breen <nbreen@ofb.net>  Wed, 13 Feb 2008 15:01:50 -0800

gromacs (3.3.2-3) unstable; urgency=low

  * Package transferred to Debichem team maintenance.
  * debian/control:
    - Switched Maintainer to Debichem Team, moved myself to
      Uploaders.  Added Vcs-Browser, Vcs-Svn fields.
    - Increase Standards-Version to 3.7.3.  No changes required.
    - Build-Depend on libopenmpi-dev >= 1.2.4-5 (Closes: #456860).
  * debian/rules: include kfreebsd-* variants explicitly in OPENMPI_ARCH.
  * debian/patches/11_readme.dpatch: change edited README to an explicit
    patch, rather than modifying it directly in the .diff.gz.
  * Multiple bugfixes from upstream CVS:
    - 51_180_degree_angle.dpatch: apply upstream patches to avoid crashes
      crashes when operating on precisely linear 2-bond pairs.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=172,
           http://bugzilla.gromacs.org/show_bug.cgi?id=177)
    - 52_pme_spline.dpatch: calculate mesh contribution when charges
      are 0 in A state, but non-zero in B state.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=175)
    - 53_pbc_compiler: Solve regression in gmxlib/pbc.c introduced by a
      previous compiler workaround.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=179)
  * debian/gromacs-doc.doc-base: remove extraneous spaces.

 -- Nicholas Breen <nbreen@ofb.net>  Wed, 26 Dec 2007 12:26:09 -0800

gromacs (3.3.2-2) unstable; urgency=low

  * Add support for OpenMPI with new "gromacs-openmpi" binary package.
    Thanks to Manuel Prinz for assistance.  (Closes: #448635)
  * Build binaries for double-precision floating point operations, in
    addition to the existing single-precision binaries.  Double precision
    commands are denoted by a "_d" suffix.
  * debian/control: Update feature summary URL in package description,
    and add Homepage field.
  * Reformat all man page headers to work with whatis(1), apropos(1), and
    similar tools.

 -- Nicholas Breen <nbreen@ofb.net>  Tue, 13 Nov 2007 13:03:22 -0800

gromacs (3.3.2-1) unstable; urgency=low

  * New upstream release.  (Closes: #446760)
    - Incorporates fix for amd64 double-precision builds.
      (Closes: #442886)
    - Remove obsolete patches 50_gmx_order, 51_libxdrf_trajectory,
      52_genion_compiler_workaround, 60_amd64_double.
  * Add a Recommends: cpp to gromacs binary package, and improve the error
    message given by grompp when no preprocessor is installed to clarify
    the "-pp" option.  (Closes: #442139)
  * Update Build-Depends to reflect fftw3-dev -> libfftw3-dev renaming.
  * Conflict with radiance (<= 3R8+20070924.dfsg-1) due to overlapping
    /usr/bin/genbox.  Related to #446726, which will be closed by a
    future upload of radiance.
  * src/gmxlib/xtcio.c: import upstream fix for range checking failures
    when running both parallel and double-precision simulations.  (cf.
    http://www.gromacs.org/pipermail/gmx-users/2007-October/029990.html)

 -- Nicholas Breen <nbreen@ofb.net>  Mon, 15 Oct 2007 14:39:30 -0700

gromacs (3.3.1-7) unstable; urgency=low

  * debian/rules: correct typo that broke alpha builds.

 -- Nicholas Breen <nbreen@ofb.net>  Tue, 11 Sep 2007 12:23:52 -0700

gromacs (3.3.1-6) unstable; urgency=low

  * Update alpha Build-Depends from g77 to gfortran, and set F77 variable
    in debian/rules accordingly.
  * Increase update-alternatives priority of mdrun_mpi.lam to 20.
  * src/tools/gmx_xpm2ps.c: explicitly initialize 'ninp' to 0 to work
    around a peculiar compiler/shared-library/i386 bug.  (Closes: #428795)
  * debian/copyright: clarify license as GPL v2 or later.  Add Depends: on
    base-files (>=4.0.1) until the next release to ensure that the GPL v3
    license text is installed as well.  (Closes: #435208)
  * When building from source, two DEB_BUILD_OPTIONS are available:
    - "parallel" adds -j4 to the make flags.
    - "double" will compile binaries for both single-precision (the
       default) and double-precision (with _d suffix) floating point
       operations.
  * Minor packaging cleanups: set debhelper compatibility level to 5,
    clarify versioned dependencies for -doc and -dev packages, improve
    "make clean" error handling, clean up lintian overrides.

 -- Nicholas Breen <nbreen@ofb.net>  Mon, 10 Sep 2007 17:29:10 -0700

gromacs (3.3.1-5) unstable; urgency=low

  * Workaround for compiler problems on some platforms that could cause
    genion to hang in an infinite loop when using cubic boxes.
    (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=108)
  * Eliminate spurious mdrun warnings when using triclinic boxes.
    (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=121)

 -- Nicholas Breen <nbreen@ofb.net>  Tue, 10 Apr 2007 17:08:02 -0700

gromacs (3.3.1-4) unstable; urgency=medium

  * Rename /usr/bin/ffscan to g_ffscan, resolving a filename conflict with
    the 'forutil' package.  (Closes: #403879)

 -- Nicholas Breen <nbreen@ofb.net>  Sat, 23 Dec 2006 11:24:59 -0800

gromacs (3.3.1-3) unstable; urgency=low

  * Update URL to features list in package description.  (Closes: #393750)
  * Correct deuterium order parameter generation in src/tools/g_order.c.
    (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=84)
  * Patch src/gmxlib/libxdrf.c to eliminate errors when the specified time
    for a search inside a trajectory falls on a frame boundary.
    (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=106)

 -- Nicholas Breen <nbreen@ofb.net>  Wed,  6 Dec 2006 11:04:01 -0800

gromacs (3.3.1-2) unstable; urgency=low

  * _Really_ register gromacs-doc with doc-base.  (The previous attempt
    contained an error.)  Thanks again to Drew Parsons.
    (Closes: #359999)
  * Update Standards-Version to 3.7.2.  No packaging changes required.

 -- Nicholas Breen <nbreen@ofb.net>  Tue, 26 Sep 2006 15:21:48 -0700

gromacs (3.3.1-1) unstable; urgency=low

  * New upstream release.
  * Updated PDF manual to 3.3 release.
  * disco(1) is no longer shipped, so it no longer needs renaming.

 -- Nicholas Breen <nbreen@ofb.net>  Thu, 13 Apr 2006 15:53:29 -0700

gromacs (3.3-2) unstable; urgency=low

  * Adding Build-Depends on g77 for alpha only.  (No other architectures
    use FORTRAN inner loops by default.)  (Closes: #360486)
  * Recategorizing to different parts of archive: gromacs-doc to 'doc',
    gromacs-dev to 'devel'.
  * Correct implicit pointer size declaration in src/mdlib/ghat.c, which
    could lead to segfaults on 64-bit architectures.  Thanks to Dann
    Frazier for catching it.  (Closes: #360002)
  * Registered gromacs-doc with doc-base.  Patch courtesy of Drew Parsons.
    (Closes: #359999)
  * Renaming /usr/bin/disco to g_disco, to avoid filename conflict with
    mono-mcs.  (Closes: #360374)

 -- Nicholas Breen <nbreen@ofb.net>  Mon,  3 Apr 2006 09:50:44 -0700

gromacs (3.3-1) unstable; urgency=low

  * Initial Debian release.  (Closes: #228319, #252101)

 -- Nicholas Breen <nbreen@ofb.net>  Thu, 16 Mar 2006 23:00:13 -0800

