spades (3.15.5+dfsg-8) unstable; urgency=medium
* Team upload
* Fixing Python3 SyntaxWarning by using raw regex patterns (Closes: #1087093)
-- Pierre Gruet <pgt@debian.org> Sat, 14 Dec 2024 00:09:08 +0100
spades (3.15.5+dfsg-7) unstable; urgency=medium
* Replace distutils which is removed in Python3.12
Closes: #1061846
* Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
* Depends: s/python3-distutils/python3-packaging/
-- Andreas Tille <tille@debian.org> Fri, 02 Feb 2024 09:16:42 +0100
spades (3.15.5+dfsg-6) unstable; urgency=medium
* d/rules: disable lto builds.
Upstream is aware that there is a problem with lto appllied on spades,
and this seems to be caused by a lingering compiler bug. (Closes: #1015668)
-- Étienne Mollier <emollier@debian.org> Sun, 03 Dec 2023 14:52:02 +0100
spades (3.15.5+dfsg-5) unstable; urgency=medium
[ Heinrich Schuchardt ]
* Add missing libzstd-dev build dependency
Closes: #1052315 (LP: #2036726)
[ Andreas Tille ]
* Standards-Version: 4.6.2 (routine-update)
-- Andreas Tille <tille@debian.org> Thu, 21 Sep 2023 13:22:20 +0200
spades (3.15.5+dfsg-4) unstable; urgency=medium
* d/control: spades is AMD64 only, as per upstream. Closes: #976523
* d/patches: mark many as not needing forwarding
-- Michael R. Crusoe <crusoe@debian.org> Wed, 09 Aug 2023 12:45:25 +0200
spades (3.15.5+dfsg-3) unstable; urgency=medium
* Team upload.
* Add fix-gcc13.patch to fix gcc-13 build issues. (Closes: #1037863)
-- Bo YU <tsu.yubo@gmail.com> Thu, 20 Jul 2023 21:38:50 +0800
spades (3.15.5+dfsg-2) unstable; urgency=medium
* d/control: add missing build-deps following llvm reorganization.
(Closes: #1022309)
* yaml_load.patch: update to fix new pyyaml.load calls. (Closes: #1022086)
* d/copyright: bump copyright year.
-- Étienne Mollier <emollier@debian.org> Sun, 23 Oct 2022 16:59:13 +0200
spades (3.15.5+dfsg-1) unstable; urgency=medium
* New upstream version 3.15.5+dfsg
* d/patches/:
+ fix-privacy-breaches.patch: update badges list.
+ python3.patch: refresh.
+ 0003_accept-system-bwa.patch: unfuzz.
+ yaml_load.patch: unfuzz.
* d/m/coronaspades.1.adoc: add manual page for coronaspades.
* d/links: create a link for coronaspades.py manual.
* d/t/run-upstreams-tests: add self tests for plasmidspades and coronaspades.
Also, the truspades command is deprecated, so don't make it's self-test
failure critical.
* d/salsa-ci.yml: disable run for i386 architecture.
* d/NEWS: forward deprecation of truspades with notice it may not work well.
-- Étienne Mollier <emollier@debian.org> Mon, 01 Aug 2022 21:11:59 +0200
spades (3.15.4+dfsg-3) unstable; urgency=medium
* d/t/run-upstreams-tests: make tests a bit more verbose.
* Adjust 0003_accept-system-bwa.patch: import support functions.
(Closes: #1011968)
* Refresh yaml_load.patch.
* Remove patches not part of d/p/series anymore.
* Add fix-privacy-breaches.patch: remove build status badges.
* Add typos.patch: fix typos caught by lintian.
* d/copyright: reorder to match globbing properly.
* d/s/lintian-overrides: unclear why html files are missing source code.
* Standards-Version: 4.6.1 (routine-update)
-- Étienne Mollier <emollier@debian.org> Sat, 25 Jun 2022 17:41:51 +0200
spades (3.15.4+dfsg-2) unstable; urgency=medium
* Team upload.
[ Lance Lin ]
* d/patches/0003_accept-system-bwa.patch - refactored 'which'
Closes: #1010788
[ Andreas Tille ]
* Review copyright
-- Lance Lin <LQi254@protonmail.com> Tue, 10 May 2022 20:15:40 +0700
spades (3.15.4+dfsg-1) unstable; urgency=medium
[ Michael R. Crusoe ]
* New upstream version
* Refreshed patches
* debian/upstream/metadata: Added many missing papers
* remove assembler/ext/src/llvm/ConvertUTF.cpp
* Standards-Version: 4.5.1 (routine-update)
* debhelper-compat 13 (routine-update)
[ Steffen Moeller ]
* d/u/metadata
- yamllint cleanliness
- added ref to bioconda
* Add salsa-ci file (routine-update)
* Refer to common license file for Apache-2.0.
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
* Upstream addressed / -> // in generate_quality (less nice, though)
* Prepared PRs for spelling errors found by Michael
[ Andreas Tille ]
* Adjust patches
* Remove redundant gbp.conf
[ Juhani Numminen ]
* Enable parallel builds by ignoring spades_compile.sh
- Fix patches for the bypassing of spades_compile.sh
* Remove gcc7.patch: applied upstream
* python3.patch: add coronaspades.py and before_start_stage.py
* Simplify debian/rules: do not attempt to run as-installed tests before
installation
* Install scripts under FHS-compliant path /usr/libexec/spades/
- Adjust 0118_adjust_spades_home_again.patch
* Add patches to make the test suite runnable
* d/links: Add new binary coronaspades(.py)
* Remove unused adapt_to_debian_pathes.patch
* Add d/clean for test artifacts
* Add disable_local_convertutf.patch: to cover for dfsg-removed ConvertUTF.o,
link against system's LLVMSupport.a
* Build-Deps: does not build python extensions; s/python3-dev/python3-all/
* Depends: remove explicit shared libs (handled as ${shlibs:Depends})
* Use vendored boost which has local modifications to avoid include problems
during program use.
[ Étienne Mollier ]
* Add fix-sigill-on-non-popcnt-cpus.patch; fixes baseline violation.
[ Andreas Tille ]
* d/watch:
- Fix to detect new versions on github (routine-update)
- Use proper filename for download
* Standards-Version: 4.6.0 (routine-update)
* Remove constraints unnecessary since buster:
+ Build-Depends: Drop versioned constraint on asciidoctor.
[ Étienne Mollier ]
* Adjust fix-sigill-on-non-popcnt-cpus.patch to not overflow on large int.
* d/control: add myself to Uploaders.
-- Étienne Mollier <emollier@debian.org> Mon, 11 Apr 2022 21:30:33 +0200
spades (3.13.1+dfsg-2) unstable; urgency=medium
* Depends: python3-distutils
-- Andreas Tille <tille@debian.org> Fri, 22 Nov 2019 10:48:44 +0100
spades (3.13.1+dfsg-1) unstable; urgency=medium
* Fix watch file
* Moved packaging to Python3
Closes: #938521
* New upstream version
* debhelper-compat 12
* Standards-Version: 4.4.1
* Move source package lintian overrides to debian/source.
* Set upstream metadata fields: Repository.
* Make sure Python3 interpreter is used in scripts
* Specify yaml loader
* Drop webvis dir from source which has compressed JS but its not used
in the binary package
-- Andreas Tille <tille@debian.org> Mon, 18 Nov 2019 15:34:43 +0100
spades (3.13.0+dfsg2-2) unstable; urgency=medium
* Also remove jemalloc from (build-)depends.
-- Michael R. Crusoe <michael.crusoe@gmail.com> Thu, 17 Jan 2019 10:12:47 -0800
spades (3.13.0+dfsg2-1) unstable; urgency=medium
* Restore the bundled jemalloc as Debian's package is too new.
* Pull releases from GitHib.
* Standards-Version: 4.3.0 (no changes needed)
* Install README.md to /usr/share/doc/spades/
-- Michael R. Crusoe <michael.crusoe@gmail.com> Thu, 17 Jan 2019 07:54:34 -0800
spades (3.13.0+dfsg-1) unstable; urgency=medium
* New upstream version
* Upstream has removed dipspades
-- Andreas Tille <tille@debian.org> Tue, 16 Oct 2018 22:08:43 +0200
spades (3.12.0+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
Closes: #897867
* Fix watch file
* Add dh-python
[ Alexandre Mestiashvili ]
* Add tmp link for tests for spades-bwa
* Update override_dh_auto_test: implement a workaround so dh_auto_test
can access data files
* Add bwa to d/tests/control
* Remove *.pyc files
* Add patch 0118_adjust_spades_home_again.patch
replacing 0113_adjust_paths.patch
* Update d/patches/spelling
* Remove duplicated docs from /usr/share/spades
* Bump Policy to 4.2.1, add myself to uploaders
* Use https for copyright Format field, s/MIT/Expat/
* Rename overridden tag to debian-watch-does-not-check-gpg-signature
-- Alexandre Mestiashvili <mestia@debian.org> Mon, 10 Sep 2018 19:37:49 +0000
spades (3.11.1+dfsg-2) unstable; urgency=medium
* Build-Depends: libnlopt-cxx-dev
Closes: #902592
* d/rules:
+ filter nocheck,$(DEB_BUILD_OPTIONS)
+ do not parse d/changelog
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
-- Andreas Tille <tille@debian.org> Fri, 06 Jul 2018 10:54:09 +0200
spades (3.11.1+dfsg-1) unstable; urgency=medium
[ Sascha Steinbiss ]
* New upstream release.
* Bump Standards-Version.
* Remove obsolete Testsuite: entry in d/control
* Add d/copyright entry for new included BBHash headers.
[ Steffen Moeller ]
* debian/upstream/metadata:
- added references to registries
- yamllint cleanliness
-- Sascha Steinbiss <satta@debian.org> Mon, 18 Dec 2017 00:29:26 +0000
spades (3.10.1+dfsg-3) unstable; urgency=medium
* Fix FTBFS with GCC 7.
Closes: #853666
* Update homepage.
* Bump Standards-Version.
-- Sascha Steinbiss <satta@debian.org> Thu, 10 Aug 2017 16:39:50 +0200
spades (3.10.1+dfsg-2) unstable; urgency=medium
* Upload to unstable.
-- Sascha Steinbiss <satta@debian.org> Sun, 18 Jun 2017 16:31:57 +0000
spades (3.10.1+dfsg-1) experimental; urgency=medium
[ Michael R. Crusoe ]
* New upstream version 3.10.1+dfsg
[ Sascha Steinbiss ]
* Build for experimental.
-- Sascha Steinbiss <satta@debian.org> Fri, 21 Apr 2017 17:54:15 +0000
spades (3.9.1+dfsg-1) unstable; urgency=medium
* New upstream release.
-- Sascha Steinbiss <satta@debian.org> Wed, 07 Dec 2016 06:31:19 +0000
spades (3.9.0+dfsg-1) unstable; urgency=medium
* New upstream release.
* Add copyright entry for cxxopts.
* Add rnaSPAdes manpage, wrappers, tests.
-- Sascha Steinbiss <satta@debian.org> Sun, 24 Jul 2016 13:12:31 +0000
spades (3.8.2+dfsg2-1) unstable; urgency=medium
* Make sure bundled headers are not used by cleaning orig tarball.
-- Sascha Steinbiss <satta@debian.org> Tue, 19 Jul 2016 20:57:51 +0000
spades (3.8.2+dfsg-1) unstable; urgency=medium
* New upstream release.
* Adapt patches for new upstream code.
* Remove unused override.
* Build with debug symbols.
-- Sascha Steinbiss <satta@debian.org> Mon, 11 Jul 2016 08:39:53 +0000
spades (3.8.1+dfsg-2) unstable; urgency=medium
* Stop using embedded libnlopt, libssw and libhat-trie.
* Update email addresses.
-- Sascha Steinbiss <satta@debian.org> Sat, 02 Jul 2016 17:45:37 +0000
spades (3.8.1+dfsg-1) unstable; urgency=medium
* New upstream release.
-- Sascha Steinbiss <sascha@steinbiss.name> Mon, 13 Jun 2016 09:02:52 +0000
spades (3.8.0+dfsg-1) unstable; urgency=medium
* New upstream release.
* Drop patches that are no longer necessary.
* Update licenses.
* Add metaspades and plasmidspades symlinks.
* Add man page stubs for metaspades and plasmidspades.
* Bump Standards-Version.
-- Sascha Steinbiss <sascha@steinbiss.name> Sun, 05 Jun 2016 09:56:42 +0000
spades (3.7.1+dfsg-3) unstable; urgency=medium
* Force LANG and LANGUAGE to ensure reproducibility.
* Enable compiler messages.
-- Sascha Steinbiss <sascha@steinbiss.name> Thu, 21 Apr 2016 14:44:14 +0000
spades (3.7.1+dfsg-2) unstable; urgency=medium
[ Sascha Steinbiss ]
* Use asciidoctor instead of ronn for reproducible man pages
* enable full hardening
* add override for pedantic Lintian msg
* use correct YAML module
Closes: #818584
[ Afif Elghraoui ]
* Replace patch with a sed command to fix python-yaml imports
-- Sascha Steinbiss <sascha@steinbiss.name> Fri, 18 Mar 2016 14:25:06 +0000
spades (3.7.1+dfsg-1) unstable; urgency=medium
* New upstream release.
* Add gbp.conf to always use pristine-tar.
-- Sascha Steinbiss <sascha@steinbiss.name> Sat, 12 Mar 2016 07:23:31 +0000
spades (3.7.0+dfsg-1) unstable; urgency=medium
* Make changelog building reproducible.
* New upstream release.
* Update d/copyright.
-- Sascha Steinbiss <sascha@steinbiss.name> Wed, 24 Feb 2016 22:02:53 +0000
spades (3.6.2+dfsg-2) unstable; urgency=medium
* Use Debian's jemalloc.
* Fix spelling issues.
* Bump Standards-Version.
-- Sascha Steinbiss <sascha@steinbiss.name> Mon, 22 Feb 2016 09:27:51 +0000
spades (3.6.2+dfsg-1) unstable; urgency=low
* Initial release (Closes: #813988)
-- Sascha Steinbiss <sascha@steinbiss.name> Sun, 07 Feb 2016 10:21:39 +0000