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 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 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 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 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 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 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 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 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 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 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 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 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 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 Mon, 3 Apr 2006 09:50:44 -0700 gromacs (3.3-1) unstable; urgency=low * Initial Debian release. (Closes: #228319, #252101) -- Nicholas Breen Thu, 16 Mar 2006 23:00:13 -0800