phyml (3:3.3.20220408-4) unstable; urgency=medium * d/p/series: disable cross.patch. The cross compilation procedure relies on mpi-c.pc to operate properly, but mpich misses it for the moment. * d/control: migrate to mpi-default-*. (Closes: #1086912) * d/control: declare compliance to standards version 4.7.0. * d/control: migrate to pkgconf. * d/patches/*: normalise header, notably Last-Update format. -- Étienne Mollier Sat, 09 Nov 2024 19:50:59 +0100 phyml (3:3.3.20220408-3) unstable; urgency=medium * d/watch: move to git tag scanning; fixes uscan following github changes. -- Étienne Mollier Wed, 26 Oct 2022 19:56:40 +0200 phyml (3:3.3.20220408-2) unstable; urgency=medium * Team upload. * Bump Standards-Version to 4.6.1 (no changes needed) * Do not run autopkgtests on armel (Closes: #1016941) -- Nilesh Patra Sat, 13 Aug 2022 01:19:11 +0530 phyml (3:3.3.20220408-1) unstable; urgency=medium * New upstream version * Refresh no-configure-ac-date.patch. * Refresh fix_declaration_of_temp.patch. * Refresh filter-sse3-intrinsics.patch. * Refresh typos.patch. -- Étienne Mollier Sun, 08 May 2022 16:41:07 +0200 phyml (3:3.3.20211231-1) unstable; urgency=medium * New upstream version * Delete nodup-am-init-automake.patch: applied upstream. * Delete no-stdc++.patch: patched code section disappeared. * typos.patch: fix new typo. * Refresh most other patches. * d/copyright: - mention doc/naturemag.bst, under LaTeX Project Public License 1 or more. - update copyright year -- Étienne Mollier Fri, 11 Feb 2022 17:08:37 +0100 phyml (3:3.3.20211021-1) unstable; urgency=medium * New upstream version. * Refresh most patches. * Add apply-cflags.patch: ensure standard Debian CFLAGS are propagated throughout the build process. * Add filter-sse3-intrinsics.patch: fixes FTBFS when built with -msse but without -msse3, as the codebase also now includes SSE3 instructions; however this means that SSE acceleration is thus now disabled on amd64. * Add apply-ldflags.patch: ensure standard Debian LDFLAGS are propagated throughout the build process for proper hardening. * d/rules: autoconfigure with --enable-phyml-mpi, replacing --enable-mpi. * d/rules: fix permissions of example files nucleic and proteic. * d/{links,phyml.1}: also provide phyml-mpi manual page. * d/control: add myself to Uploaders. * d/copyright: bump project to GPL-3 and document the file src/mxml.h * d/copyright: update copyright entry of package maintenance -- Étienne Mollier Fri, 19 Nov 2021 00:22:37 +0100 phyml (3:3.3.20200621-3) unstable; urgency=medium * Team upload. * Add nodup-am-init-automake.patch (Closes: #998477) -- Étienne Mollier Thu, 04 Nov 2021 23:15:13 +0100 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Sat, 16 May 2009 14:55:14 +0900 phyml (30042009-1) unstable; urgency=low * Initial release (Closes: #517165) -- Charles Plessy Fri, 01 May 2009 08:53:44 +0900