hyphy (2.5.63+dfsg-1) unstable; urgency=medium * New upstream version 2.5.63+dfsg * set-zlib-after-setting-default-libs.patch: unfuzz. * use_debian_sqlite.patch: unfuzz. * d/rules: locate all HYPHYMPI to erase DT_RUNPATH. -- Étienne Mollier Sun, 03 Nov 2024 11:54:22 +0100 hyphy (2.5.62+dfsg-1) unstable; urgency=medium * New upstream version 2.5.62+dfsg * d/control: declare compliance to standards version 4.7.0. * Unfuzz all patches. * d/copyright: delete reference to */.DS_Store: not distributed anymore. -- Étienne Mollier Sun, 02 Jun 2024 10:41:46 +0200 hyphy (2.5.60+dfsg-1) unstable; urgency=medium * New upstream version 2.5.60+dfsg * Unfuzz all patches. * d/control: migrate build-dep to pkgconf. -- Étienne Mollier Sun, 10 Mar 2024 12:37:20 +0100 hyphy (2.5.59+dfsg-1) unstable; urgency=medium * New upstream version -- Étienne Mollier Sat, 13 Jan 2024 17:00:01 +0100 hyphy (2.5.58+dfsg-1) unstable; urgency=medium * New upstream version -- Étienne Mollier Fri, 15 Dec 2023 13:22:55 +0100 hyphy (2.5.57+dfsg-1) unstable; urgency=medium * New upstream version 2.5.57+dfsg -- Étienne Mollier Fri, 24 Nov 2023 12:27:51 +0100 hyphy (2.5.56+dfsg-1) unstable; urgency=medium * New upstream version 2.5.56+dfsg * rm_arch_specific_flags.patch: refresh. * use_debian_sqlite.patch: refresh. * set-zlib-after-setting-default-libs.patch: refresh. -- Étienne Mollier Mon, 06 Nov 2023 23:01:33 +0100 hyphy (2.5.53+dfsg-1) unstable; urgency=medium * New upstream version 2.5.53+dfsg * d/{clean,rules}: fix building twice in a row. This is done by cleaning temporary test data and build results on one hand, and by fixing some national encoded files in their temporary installation location instead of within upstream source code on the other hand. (Closes: #1048874) -- Étienne Mollier Sat, 26 Aug 2023 11:05:10 +0200 hyphy (2.5.52+dfsg-1) unstable; urgency=medium * New upstream version 2.5.52+dfsg * fix-configure-failure.patch: remove: fixed upstream. * d/control: remove build dependency on swig. -- Étienne Mollier Sun, 13 Aug 2023 12:09:38 +0200 hyphy (2.5.51+dfsg-1) unstable; urgency=medium * New upstream version 2.5.51+dfsg * Remove constraints unnecessary since bullseye (oldstable) * Remove 3 maintscript entries from 3 files. Changes-By: deb-scrub-obsolete * rm_arch_specific_flags.patch: refresh. * d/control: build now depends on swig. * d/control: build now depends on python3 sdk. * fix-configure-failure.patch: add: fix a cmake error. -- Étienne Mollier Sun, 09 Jul 2023 14:29:23 +0200 hyphy (2.5.50+dfsg-1) unstable; urgency=medium * New upstream version 2.5.50+dfsg -- Nilesh Patra Mon, 12 Jun 2023 17:45:32 +0000 hyphy (2.5.47+dfsg-1) unstable; urgency=medium * New upstream version -- Andreas Tille Sun, 05 Feb 2023 20:48:53 +0100 hyphy (2.5.46+dfsg-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.6.2 (routine-update) -- Andreas Tille Tue, 24 Jan 2023 15:50:21 +0100 hyphy (2.5.42+dfsg-1) unstable; urgency=medium * New upstream version -- Andreas Tille Thu, 22 Sep 2022 09:13:46 +0200 hyphy (2.5.41+dfsg-1) unstable; urgency=medium * New upstream version -- Andreas Tille Wed, 24 Aug 2022 14:08:01 +0200 hyphy (2.5.40+dfsg-1) unstable; urgency=medium * New upstream version 2.5.40+dfsg * d/*.lintian-overrides: refresh overrides to new convention. -- Étienne Mollier Fri, 15 Jul 2022 10:08:29 +0200 hyphy (2.5.39+dfsg-1) unstable; urgency=medium [ Andreas Tille ] * Proper filename for upstream tarball [ Étienne Mollier ] * New upstream version * Standards-Version: 4.6.1 (routine-update) -- Étienne Mollier Tue, 31 May 2022 19:37:50 +0200 hyphy (2.5.38+dfsg-1) unstable; urgency=medium * New upstream version -- Andreas Tille Mon, 02 May 2022 12:18:35 +0200 hyphy (2.5.36+dfsg-1) unstable; urgency=medium * New upstream version -- Étienne Mollier Fri, 11 Feb 2022 13:35:31 +0100 hyphy (2.5.33+dfsg-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.6.0 (routine-update) -- Nilesh Patra Tue, 19 Oct 2021 10:07:52 +0000 hyphy (2.5.32+dfsg-1) unstable; urgency=medium * New upstream version 2.5.32+dfsg * Refresh d/p/use_debian_sqlite.patch, do not impose ZLIB changes on the same patch so as to avoid confusion * d/p/set-zlib-after-setting-default-libs.patch: Check for existence of ZLIB *after* DEFAULT_LIBRARIES have been set -- Nilesh Patra Wed, 25 Aug 2021 19:44:43 +0530 hyphy (2.5.31+dfsg-1) unstable; urgency=medium [ Michael R. Crusoe ] * Removed spelling patch, it was merged upstream [ Étienne Mollier ] * Remove d/*.maintscriptsL: these have been brought in the earlier release of hyphy 2.5.28+dfsg-3 * d/control: update uploader address * d/watch: fix broken link to github [ Nilesh Patra ] * d/watch: Fix watch regex * New upstream version 2.5.31+dfsg * d/p/*.patch: Refresh patches * d/p/use_debian_sqlite.patch: Check for existence of ZLIB *after* DEFAULT_LIBRARIES have been set * Fix copyright -- Nilesh Patra Sun, 15 Aug 2021 19:06:23 +0530 hyphy (2.5.28+dfsg-3) unstable; urgency=medium * d/*.maintscript: handle symbolic link removal in hyphy 2.5.18+dfsg-1. Closes: #985284 -- Étienne Mollier Tue, 16 Mar 2021 21:52:00 +0100 hyphy (2.5.28+dfsg-2) unstable; urgency=medium * Team upload. * debian/rules: set LC_ALL to fix groff warnings in the manpages * debian/patches/spelling: fix some typos * debian/rules: delete erroneous rpath for the MPI binaries * debian/rules: improve the clean target -- Michael R. Crusoe Sat, 20 Feb 2021 10:57:19 +0100 hyphy (2.5.28+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version * debian/tests/run-unit-tests: don't skip four tests that are now passing -- Michael R. Crusoe Fri, 19 Feb 2021 17:15:31 +0100 hyphy (2.5.27+dfsg-4) unstable; urgency=medium * Team upload. * Fix arch independent build issue which cause the amd64 autopkgtests to fail. * On amd64, run the build-time tests the SIMD varients that are supported by the build-time CPU. -- Michael R. Crusoe Sun, 31 Jan 2021 11:05:20 +0100 hyphy (2.5.27+dfsg-3) unstable; urgency=medium * Team upload. * Fix arch independent build. * debian/control: mark hyphy-common as Multi-Arch: foreign -- Michael R. Crusoe Sat, 30 Jan 2021 12:52:56 +0100 hyphy (2.5.27+dfsg-2) unstable; urgency=medium * Team upload. * Refresh patches. * debian/rules: build avx and sse3 version for amd64 -- Michael R. Crusoe Sat, 30 Jan 2021 10:03:12 +0100 hyphy (2.5.27+dfsg-1) unstable; urgency=medium * New upstream version -- Nilesh Patra Tue, 26 Jan 2021 16:47:41 +0530 hyphy (2.5.26+dfsg-1) unstable; urgency=medium * New upstream version 2.5.26+dfsg * Add createmanpages script to manage manpages for future versions * Update hyphy manpage -- Nilesh Patra Mon, 18 Jan 2021 13:57:49 +0000 hyphy (2.5.25+dfsg-1) unstable; urgency=medium * New upstream version -- Nilesh Patra Sun, 10 Jan 2021 11:25:52 +0530 hyphy (2.5.24+dfsg-2) unstable; urgency=medium [ Pino Toscano ] * Fix reference to the build directory Closes: #977992 -- Andreas Tille Thu, 24 Dec 2020 07:11:25 +0100 hyphy (2.5.24+dfsg-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.5.1 (routine-update) -- Nilesh Patra Mon, 21 Dec 2020 13:35:37 +0530 hyphy (2.5.23+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version -- Nilesh Patra Wed, 18 Nov 2020 20:07:16 +0000 hyphy (2.5.22+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version -- Nilesh Patra Tue, 17 Nov 2020 18:54:31 +0530 hyphy (2.5.21+dfsg-2) unstable; urgency=medium * Team Upload. * Remove failing tests on 32-bit archs -- Nilesh Patra Sat, 31 Oct 2020 23:42:17 +0530 hyphy (2.5.21+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version -- Nilesh Patra Sat, 31 Oct 2020 19:16:55 +0530 hyphy (2.5.20+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version -- Nilesh Patra Thu, 22 Oct 2020 20:14:59 +0530 hyphy (2.5.19+dfsg-1) unstable; urgency=medium * New upstream version * Refresh patches * Wrap up manual pages for hyphy-pt and hyphy-mpi -- Étienne Mollier Sat, 10 Oct 2020 15:27:47 +0200 hyphy (2.5.18+dfsg-1) unstable; urgency=medium [ Étienne Mollier ] * New upstream version * 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. * Build with NOAVX and NOSSE3 cmake switches. (Closes: #961382) * GTEST removed in favor of script run_unit_tests.sh: - updated d/copyright to remove gtest and include src/contrib; - removed note about gtest in d/rules; - removed lintian-overrides related to gtest. * Refreshed patches: - removed drop_profiling_option.patch; - removed patches related to gtest; - refreshed use_debian_sqlite.patch; - added patch to fix compilation issues with NOAVX and NOSSE3; - added patch to allow compilation on non-x86 CPU architectures. * Refreshed d/hyphy-common.install. [ Andreas Tille ] * d/rules: Remove some settings made for the former Python package -- Étienne Mollier Mon, 28 Sep 2020 21:33:54 +0200 hyphy (2.5.1+dfsg-3) unstable; urgency=medium * Versioned Depends: hyphy-common (= ${source:Version}) Closes: #948093 -- Andreas Tille Tue, 07 Jan 2020 21:23:52 +0100 hyphy (2.5.1+dfsg-2) unstable; urgency=medium * Fix installation of NEWS.Debian to enable arch all only builds * Make autopkgtest more verbose -- Andreas Tille Sat, 04 Jan 2020 21:21:58 +0100 hyphy (2.5.1+dfsg-1) unstable; urgency=medium [ Helmut Grohne ] * Add pkg-config to Build-Depends as FindMPI.cmake will need it for cross compilation. (Closes: #943311) [ Andreas Tille ] * New upstream version * debhelper-compat 12 * Secure URI in copyright format * Remove trailing whitespace in debian/changelog * New upstream version * Standards-Version: 4.4.1 * Use secure URI in Homepage field. * Remove patches msse_option_only_if_available.patch that are missing from debian/patches/series. * Skip GTEST target for the moment since this is currently in flux see https://github.com/veg/hyphy/issues/1058 * No need to rename executables any more since upstream is doing this now * Autopkgtest exists since last release - so close bug Closes: #909707 -- Andreas Tille Fri, 06 Dec 2019 22:47:47 +0100 hyphy (2.3.14+dfsg-2) unstable; urgency=medium [ Saira Hussain ] * Team upload. * Add unit test description file * Add the SimpleAnalyses suite for testing * Add control file for AUTOPKGTESTS [ Andreas Tille ] * Standards-Version: 4.3.1 -- Saira Hussain Fri, 05 Jul 2019 13:45:06 +0000 hyphy (2.3.14+dfsg-1) unstable; urgency=medium * New upstream version * debhelper 11 * Standards-Version: 4.2.1 -- Andreas Tille Wed, 26 Sep 2018 16:55:30 +0200 hyphy (2.3.13+dfsg-1) unstable; urgency=medium * Team upload. [ Steffen Moeller ] * debian/upstream/metadata: Added ref to OMICtools [ Andreas Tille ] * New upstream version * debhelper 11 * Add Build-Depends: opencl-dev * debian/rules: - Do not parse d/changelog - regard $(DEB_BUILD_OPTIONS) for override_dh_auto_test [ Liubov Chuprikova ] * Drop hyphygui as it was removed from upstream * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.5 -- Liubov Chuprikova Tue, 10 Jul 2018 08:39:13 +0200 hyphy (2.2.7+dfsg-1) unstable; urgency=medium * New upstream version * Use xz compression in d/watch * python-hyphy is now distributed in separate source archive so removing it from this package -- Andreas Tille Fri, 14 Oct 2016 08:01:08 +0200 hyphy (2.2.6+dfsg-5) unstable; urgency=medium * Fix error: narrowing conversion from 'double' to 'unsigned char' * Fix error: replacing false with nil Closes: #811866 -- Andreas Tille Mon, 15 Aug 2016 12:44:58 +0200 hyphy (2.2.6+dfsg-4) unstable; urgency=medium * Fix gcc-6 build issue by incorporating upstream patch Closes: #811866 * cme fix dpkg-control * Fix more spelling errors * hardening=+bindnow -- Andreas Tille Fri, 22 Jul 2016 15:05:54 +0200 hyphy (2.2.6+dfsg-3) unstable; urgency=medium * Change build-dep on python3-dev to python3-all-dev to enable building for all supported python3 versions (thanks to Scott Kitterman for the patch) Closes: #809452 -- Andreas Tille Wed, 30 Dec 2015 21:49:03 +0100 hyphy (2.2.6+dfsg-2) unstable; urgency=medium [ Matthias Klose ] * Hand-edit swig generated file to build with Python3.5. Closes: #802999 [ Andreas Tille ] * Remove arch specific flags Closes: #802994 -- Andreas Tille Mon, 26 Oct 2015 11:20:39 +0100 hyphy (2.2.6+dfsg-1) unstable; urgency=medium * New upstream version * Hack around a mac-ism in setup.py -- Andreas Tille Tue, 22 Sep 2015 17:50:33 +0200 hyphy (2.2.5+dfsg-2) unstable; urgency=medium * Versioned Build-Depends: cmake (>= 3.0) * Drop profiling option (Thanks for the hint to Michael Banck ) Closes: #793345 * Disable unneded test that breaks on 32 bit architectures (Thanks for the hint to Jakub Wilk ) Closes: #793346 * Make sure that also in tests the existence of SSE3 extension is done Closes: #793344 -- Andreas Tille Thu, 23 Jul 2015 17:13:45 +0200 hyphy (2.2.5+dfsg-1) unstable; urgency=low * Initial release (Closes: #792087) -- Andreas Tille Sat, 11 Jul 2015 06:57:36 +0200