gubbins (3.4-1) unstable; urgency=medium * New upstream version 3.4 * d/copyright: document missing copyright owners. Those are Wellcome Trust Sanger Institute and Imperial College London. * d/control: declare compliance to standards version 4.7.0. * d/patches/*: normalise last-update timestamp to dep3. -- Étienne Mollier Sat, 30 Nov 2024 19:00:21 +0100 gubbins (3.3.5-1) unstable; urgency=medium * New upstream version 3.3.5 * iqtree2.patch: unfuzz. * python3-shebang.patch: new. This fixes a couple of occurrences of unversioned Python interpreter declared in the shebang of a couple of scripts. * d/control: move to pkgconf. * remove-numba-temporarily.patch: new. Remove temporarily numba-accelerated pyjar.py functions decorators. This allows decorellation of gubbins from numba until the latter is available again in trixie. The change may affect performances, but should not affect gubbins results and functionalities otherwise. * d/control: promote and comment out dependency on python3-numba. This prepares the field for when it will be possible to bring numba support back to gubbins, once numba 0.59 or later makes it to trixie. * d/t/control: autopkgtests do not depend on python3-numba anymore. (Closes: #1058474) -- Étienne Mollier Wed, 22 May 2024 22:19:47 +0200 gubbins (3.3.3-1) unstable; urgency=medium * New upstream version * iqtree2.patch: unfuzz. * autoupdate_configure.ac.patch: forwarding not needed. -- Étienne Mollier Sun, 04 Feb 2024 17:45:59 +0100 gubbins (3.3.1-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) [ Étienne Mollier ] * autoupdate_configure.ac.patch: refresh. * d/t/run-example: define HOME directory. This fixes numba caching issues with the newer test items. * d/control: suggest r-core-base. This is because gubbins ships a couple of R scripts, although they are not critical to proper gubbins operation. * gubbins_3.1.0_exe_in_usr_lib.patch: delete leftover. -- Étienne Mollier Sat, 16 Dec 2023 15:22:50 +0100 gubbins (3.3.0-3) unstable; urgency=medium * gubbins_drawer was removed upstream so do not link to it any more Closes: #986238 * Enable building twice in a row Closes: #1044465 * Set upstream metadata fields: Repository. * Fix lintian-overrides -- Andreas Tille Thu, 17 Aug 2023 09:25:33 +0200 gubbins (3.3.0-2) unstable; urgency=medium * Test-Depends: iqtree -- Andreas Tille Thu, 13 Jul 2023 09:44:07 +0200 gubbins (3.3.0-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.6.2 (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse. * Build-Depends: autoconf-archive * autoupdate to avoid warnings from configure.ac * Build-Depends: tox and do not override dh_auto_test * Test-Depends / Recommends: python3-numba -- Andreas Tille Wed, 12 Jul 2023 21:30:57 +0200 gubbins (2.4.1-5) unstable; urgency=medium * Team Upload. [ Andreas Tille ] * New upstream version * Standards-Version: 4.6.0 (routine-update) * Build-Depends: python3-scipy , python3-multiprocess , python3-wheel * Remove trailing whitespace in debian/changelog (routine-update) * Adapt test to iqtree2 Closes: #1005476 [ Étienne Mollier ] * d/control: update uploader address * d/watch: bump to uscan version 4 and fix broken link to github [ Nilesh Patra ] * Switch from nosetest -> pytest -- Andreas Tille Sun, 13 Feb 2022 15:17:59 +0100 gubbins (2.4.1-4) unstable; urgency=medium * Team upload. * Fix symlink to right place (Closes: #986238) -- Nilesh Patra Sun, 04 Apr 2021 16:11:03 +0530 gubbins (2.4.1-3) unstable; urgency=medium [ Andreas Tille ] * Remove non-working e-mail addresses * Remove Aidan Delaney from Uploaders since his e-mail is bouncing [ Étienne Mollier ] * Added src/ to PATH for build time tests. (Closes: #971111) * Fixed spelling error in gubbins binaries. * Added myself to Uploaders. * debhelper-compat 13 (routine-update) -- Étienne Mollier Mon, 02 Nov 2020 13:22:13 +0100 gubbins (2.4.1-2) unstable; urgency=medium * Versioned Build-Depends: raxml (>= 8.2.12+dfsg-5) Closes: #955006 * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) -- Andreas Tille Thu, 02 Apr 2020 17:03:51 +0200 gubbins (2.4.1-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.5.0 * Remove trailing whitespace in debian/changelog (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository. * Specified raxml version from Dockerfile - test complained on i386 -- Steffen Moeller Wed, 22 Jan 2020 12:30:58 +0100 gubbins (2.4.0-2) unstable; urgency=medium * Team upload. * Fix run_gubbins wrapper (Sascha Steinbiss) * raxml needed as default method at runtime - turned back into hard dependency (suggested by Sascha) -- Steffen Moeller Thu, 09 Jan 2020 02:31:16 +0100 gubbins (2.4.0-1) unstable; urgency=medium * Team upload. * New upstream version * Removing debian/patches/disable_test.patch which apparently upstream addressed in its new release. * Added build-time (testing) and recommended runtime dependency on iqtree * Demoted runtime-dependencies to fasttree and raxml to recommended -- Steffen Moeller Wed, 08 Jan 2020 12:59:28 +0100 gubbins (2.3.5-1) unstable; urgency=medium * Team upload. * New upstream version * debhelper-compat 12 * Standards-Version: 4.4.1 * Secure URI in copyright format * Set upstream metadata fields: Repository, Repository-Browse. * Cleaner clean * Reported autogenerated files in source tree to upstream -- Steffen Moeller Sat, 21 Dec 2019 00:00:10 +0100 gubbins (2.3.4-1) unstable; urgency=medium * New upstream version * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * debian/rules: - Respect DEB_BUILD_OPTIONS in override_dh_auto_test - Do not parse d/changelog * Remove unneeded Testsuite: autopkgtest -- Andreas Tille Wed, 26 Sep 2018 16:48:49 +0200 gubbins (2.3.1-1) unstable; urgency=medium * Team upload. * New upstream release. * Bump Standards-Version. -- Sascha Steinbiss Sun, 01 Oct 2017 11:59:00 +0100 gubbins (2.2.0-1) unstable; urgency=medium * Team upload. * New upstream release. -- Sascha Steinbiss Thu, 03 Nov 2016 15:25:15 +0100 gubbins (2.1.0-2) unstable; urgency=medium * Team upload. * Disable tests to address FTBFS caused by failed build time tests relying on external dependencies. Closes: #839320 -- Sascha Steinbiss Wed, 26 Oct 2016 14:26:18 +0200 gubbins (2.1.0-1) unstable; urgency=medium * New upstream release -- Andreas Tille Fri, 09 Sep 2016 10:02:51 +0200 gubbins (2.0.0-1) unstable; urgency=medium * Team upload. * New upstream release. * Fix Vcs-Git. * Remove dependencies on FastML. * Update manpage dates. * Bump Standards-Version. * Add autopkgtests. -- Sascha Steinbiss Wed, 20 Jul 2016 13:08:22 +0000 gubbins (1.4.9-1) unstable; urgency=medium * New upstream version * Build-Depends: fastml -- Andreas Tille Wed, 20 Apr 2016 19:55:22 +0200 gubbins (1.4.7-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control * enhance hardening -- Andreas Tille Sat, 19 Mar 2016 22:10:44 +0100 gubbins (1.4.5-1) unstable; urgency=medium * New upstream version * Secure Vcs-Git -- Andreas Tille Wed, 27 Jan 2016 19:53:33 +0100 gubbins (1.4.4-2) unstable; urgency=medium * do not build-dep on python3-all-dev Closes: #809489 -- Andreas Tille Thu, 31 Dec 2015 12:49:12 +0100 gubbins (1.4.4-1) unstable; urgency=medium * New upstream version Closes: #807150 -- Andreas Tille Wed, 09 Dec 2015 17:07:44 +0100 gubbins (1.4.3-1) unstable; urgency=medium * Initial Debian release (Closes: #764232, #806726) -- Andreas Tille Mon, 30 Nov 2015 15:10:52 +0100