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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 <crusoe@debian.org> 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 <crusoe@debian.org> 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 <crusoe@debian.org> 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 <crusoe@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <tille@debian.org> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <aik.kalou@gmail.com> 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 <michael.crusoe@gmail.com> Fri, 13 May 2016 10:49:54 -0700
macs (2.1.1.20160226-1) unstable; urgency=medium
* New upstream release
-- Michael R. Crusoe <crusoe@ucdavis.edu> 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 <crusoe@ucdavis.edu> 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 <crusoe@ucdavis.edu> 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 <tille@debian.org> Wed, 19 Dec 2012 19:32:44 +0100
macs (2.0.9.1-1ubuntu3) lucid; urgency=low
* Fix typo in debian/rules
-- Tim Booth <tbooth@ceh.ac.uk> 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) <soonio@gmail.com> 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) <soonio@gmail.com> Thu, 05 Jan 2012 10:52:22 +0000
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