macs (3.0.2-1) unstable; urgency=medium * d/rules: document that the openmp-simd and related SIMDe build flags are already set by upstream. * New upstream version * Dropped 4 patches applied upsteram; refreshed the rest -- Michael R. Crusoe Sun, 08 Sep 2024 01:09:37 +0200 macs (3.0.1-2) unstable; urgency=medium * d/rules: make use of dh_numpy3 to add the numpy ABI dependency. * d/patches/spelling: fix typos. * d/lintian-overrides: update to match change in warnings. -- Michael R. Crusoe Wed, 28 Feb 2024 12:39:52 +0100 macs (3.0.1-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version. Closes: #1056813 * New Build-Depends: python3-cykhash, python3-hmmlearn * Fix location of simde header * No runtime dependency from cython Closes: #1057991 [ Michael R. Crusoe ] * New upstream version * Refreshed patches. * d/copyright: MACS2/khash.h→MACS3/fermi-lite/khash.h * d/clean: remove temp/ directory leftover from test execution. Closes: #1047612 * d/rules: s/MACS2/MACS3/g for new major version. * d/patches/simde: doesn't need forwarding * d/control: build dep on newer packaging version of cykhash to pick up Python 3.12 support. * d/control: build dep on newer packaging version of hmmlearn to pick up Python 3.12 support. * d/rules: choose a better path to the launch script for testing TODO: cmdline test failures: 16.18.1 checking hmmratac hmmratac_yeast500k_accessible_regions.gappedPeak 16.18.2 checking hmmratac hmmratac_yeast500k_bedpe_accessible_regions.gappedPeak 16.18.3 checking hmmratac hmmratac_yeast500k_load_hmm_model_accessible_regions.gappedPeak 16.18.4 checking hmmratac hmmratac_yeast500k_load_training_regions_accessible_regions.gappedPeak * d/patch/no_install_depends_cython.patch removed, applied upstream. * add patch to force the use of Python3. * d/control: add build-dep on bc for the tests. * d/patches/adapt_to_prelease_hmmlearn.patch: patch from the upstream author to match the prelease version of hmmlearn in the archive. * d/patches/invalid_escape_sequence: fix a SyntaxWarning. -- Michael R. Crusoe Sat, 24 Feb 2024 12:56:15 +0100 macs (2.2.9.1-1) unstable; urgency=medium * New upstream release. Closes: #1042180, #1041203 * d/patches: drop enable_python3.10.patch & no-pip.patch; they are no longer needed * d/patches: forward patches upstream as appropriate. * no longer call dh_auto_clean to avoid call to "setup.py clean" which always runs cython. * Standards-Version: 4.6.2 (routine-update) * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. -- Michael R. Crusoe Wed, 09 Aug 2023 12:18:49 +0200 macs (2.2.7.1-6) unstable; urgency=medium * Fix watch file * Standards-Version: 4.6.1 -- Andreas Tille Thu, 24 Nov 2022 12:18:59 +0100 macs (2.2.7.1-5) unstable; urgency=medium * Enable Builds with python3.10 Closes: #998440 -- Andreas Tille Mon, 08 Nov 2021 14:29:12 +0100 macs (2.2.7.1-4) unstable; urgency=medium * Fix watchfile to detect new versions on github * Standards-Version: 4.6.0 (routine-update) * watch file standard 4 (routine-update) -- Andreas Tille Fri, 01 Oct 2021 16:24:57 +0200 macs (2.2.7.1-3) unstable; urgency=medium * Link properly with libm Closes: #965073 * debhelper-compat 13 (routine-update) -- Andreas Tille Wed, 15 Jul 2020 23:27:39 +0200 macs (2.2.7.1-2) unstable; urgency=medium * Ensure that debian/rules clean always suceeds. Closes #958109 -- Michael R. Crusoe Mon, 27 Apr 2020 19:31:48 +0200 macs (2.2.7.1-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.5.0 (routine-update) * debian/patches/fix_test_signal_failures: removed, applied upstream * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * Add cython3 build-dep and force a fresh cythonizing * debian/patches/keep_debug: remove the -g0 from setup.py * fix manpages by adjusting the PYTHONPATH -- Michael R. Crusoe Mon, 13 Apr 2020 10:29:34 +0200 macs (2.2.6-3) unstable; urgency=medium * Skip command line tests on arm64 ppc64el s390x. -- Michael R. Crusoe Sat, 28 Dec 2019 12:57:18 +0100 macs (2.2.6-2) unstable; urgency=medium * Run even more tests. * Patch from upstream to fix test that fails with Python 3.8.1rc1+ -- Michael R. Crusoe Fri, 20 Dec 2019 13:24:14 -0800 macs (2.2.6-1) unstable; urgency=medium [ Andreas Tille ] * Drop cython from Build-Depends [ Michael R. Crusoe ] * New upstream version * Set upstream metadata fields: Repository. * Remove obsolete fields Name from debian/upstream/metadata. * Get sources from GitHub, so we have the tests * New upstream version -- Michael R. Crusoe Tue, 17 Dec 2019 15:35:50 +0100 macs (2.2.4-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.4.1 * Build with Python3 Closes: #936976 -- Andreas Tille Thu, 03 Oct 2019 21:18:16 +0200 macs (2.1.4-1) unstable; urgency=medium * New upstream version * Add patch to fix spelling typo -- Michael R. Crusoe Tue, 01 Oct 2019 12:35:55 +0200 macs (2.1.3.3-1) unstable; urgency=medium [ Jelmer Vernooij ] * Trim trailing whitespace. [ Michael R. Crusoe ] * New upstream version * debhelper-compat 12 * Standards-Version: 4.4.0 * Set upstream metadata fields: Name. -- Michael R. Crusoe Mon, 30 Sep 2019 13:34:12 +0200 macs (2.1.2.1-1) unstable; urgency=medium [ Jelmer Vernooij ] * Use secure URI in Homepage field. [ Michael R. Crusoe ] * New upstream release * Drop spelling patch (incorporated upstream) -- Michael R. Crusoe Mon, 22 Oct 2018 08:51:13 -0700 macs (2.1.1.20160309-2) unstable; urgency=medium * Team upload. [ Andreas Tille ] * debian/upstream/metadata: - UTF-8 notation of names rather than TeX syntax - added eprint * d/rules: Do not parse d/changelog * Remove Tim Booth and H. Soon Gweon from Uploaders * Standards-Version: 4.1.3 * hardening=+all * debhelper 11 [ Katerina Kalou ] * Add autopkgtest (Closes: #879622) -- Katerina Kalou Mon, 19 Feb 2018 20:00:45 +0200 macs (2.1.1.20160309-1) unstable; urgency=medium * New upstream release. * Bump Standards-Version to 3.9.8 * Refresh & re-submit spelling patch * enable "bindnow" linker flag hardening -- Michael R. Crusoe Fri, 13 May 2016 10:49:54 -0700 macs (2.1.1.20160226-1) unstable; urgency=medium * New upstream release -- Michael R. Crusoe Sat, 05 Mar 2016 09:53:12 -0800 macs (2.1.0.20151222-1) unstable; urgency=medium * New upstream release * A couple more spelling fixes & updated VCS URLs. -- Michael R. Crusoe Mon, 01 Feb 2016 09:49:01 -0800 macs (2.1.0.20150731-1) unstable; urgency=low * debian/watch: now released via PyPI. * debian/rules: - 2.1.0 uses a single binary with subcommands, manpages have been updated - use pybuild * debian/control: - `cme fix dpkg-control` reformating - added myself to uploaders - upgrades to standards-version 3.9.6,dropped deprecated DM-Upload-Allowed - now managed via git; VCS URLs updated * debian/upstream/metadata: added paper * debian/upstream/signing-key.asc: upstream now signs their releases * debian/copyright: - upstream is now BSD-3-clause - MACS2/khash.h is Expat licensed * debian/lintian-overrides: silence warning about line breaks * debian/manpages: install manual pages using dh_installman * debian/patches/{series,spelling}: fix two spelling errors from upstream * debian/docs: README is now README.rst -- Michael R. Crusoe Sat, 03 Oct 2015 10:37:31 -0700 macs (2.0.9.1-1) unstable; urgency=low * Initial upload to Debian (Closes: #696331) * debian/control: - Adaptations to Debian Med team maintenance - X-Python-Version: >=2.7 because build fails for Python 2.6 - Standards-Version: 3.9.4 (no changes needed) - Priority: optional * debian/watch: Removed useless comments * debian/README.*: Removed unused dh-make templates * debian/copyright: Added some missing information * debian/rules: - Removed useless dh-make comment - use dh_python2 - use help2man to create manpages * debhelper 9 (control+compat) -- Andreas Tille Wed, 19 Dec 2012 19:32:44 +0100 macs (2.0.9.1-1ubuntu3) lucid; urgency=low * Fix typo in debian/rules -- Tim Booth Thu, 05 Jan 2012 18:22:46 +0000 macs (2.0.9.1-1ubuntu2) lucid; urgency=low * Package for PPA * Packaged from version 2.0.9-1 * Changed debian/rules to override dh_auto_clean to remove *.c files -- H. Soon Gweon (Key for package building) Thu, 05 Jan 2012 13:10:02 +0000 macs (2.0.9.1-1) unstable; urgency=low * Initial packaging attempt -- H. Soon Gweon (Key for package building) Thu, 05 Jan 2012 10:52:22 +0000