snakemake (7.32.4-6) unstable; urgency=medium * Stop using pkg_resources. (Closes: #1083775) -- Rebecca N. Palmer Fri, 04 Oct 2024 19:09:12 +0100 snakemake (7.32.4-5) unstable; urgency=medium * Tests: revert extra debug output. * Tests: make test_*_solver actually call the solver. * Tests: allow extra time to avoid failing on riscv64. -- Rebecca N. Palmer Wed, 07 Aug 2024 07:57:41 +0100 snakemake (7.32.4-4) unstable; urgency=medium * Skip tests that crash in persistent_dict because Debian's pytools is too old (workaround for #1076925). * Tests: add extra debug output to test_cluster_cancel*. * Bump Standards-Version to 4.7.0 (no changes needed). -- Rebecca N. Palmer Sat, 03 Aug 2024 13:49:07 +0100 snakemake (7.32.4-3) unstable; urgency=medium * Use platformdirs not appdirs. (Closes: #1068010) -- Rebecca N. Palmer Sun, 07 Apr 2024 11:37:02 +0100 snakemake (7.32.4-2) unstable; urgency=medium * Tests: don't mix tabs and spaces, as Python 3.12 rejects this. * Adapt to f-strings being tokenized in Python 3.12. (together, Closes: #1061761) -- Rebecca N. Palmer Fri, 09 Feb 2024 19:11:23 +0000 snakemake (7.32.4-1) unstable; urgency=medium * New upstream release. Update d/copyright and patches. * Skip newly added tests that we can't run. * Clean up after docs build. (Closes: #1045316) * Depend on python3-yte. * Fix crash in config handling. -- Rebecca N. Palmer Mon, 27 Nov 2023 20:19:37 +0000 snakemake (7.21.0-2) unstable; urgency=medium * Add timeout to tests (giving a traceback when they hang). * Docs: allow building with Sphinx 7. (Closes: #1042692) -- Rebecca N. Palmer Thu, 03 Aug 2023 22:24:25 +0100 snakemake (7.21.0-1) unstable; urgency=medium * New upstream release. Refresh patches. -- Rebecca N. Palmer Tue, 07 Feb 2023 21:19:40 +0000 snakemake (7.20.0-1) unstable; urgency=medium * New upstream release. Refresh patches, d/copyright. * Use packaged python3-retry. * Don't try to use local Javascript in GUI, as this is risky. (Closes: #1019317) -- Rebecca N. Palmer Thu, 02 Feb 2023 07:28:24 +0000 snakemake (7.19.1-1) unstable; urgency=medium * Team upload. * Fix watch file * Standards-Version: 4.6.2 (routine-update) * Skip slurm tests since slurm is not setup at build time * Suggests: slurm-client * Skip lint test that is known to fail * Skip workflow test that is known to fail -- Andreas Tille Wed, 11 Jan 2023 07:29:29 +0100 snakemake (7.12.1-1) unstable; urgency=medium * Team upload. * New upstream version -- Andreas Tille Wed, 24 Aug 2022 16:45:00 +0200 snakemake (7.12.0-1) unstable; urgency=medium * Team upload. * New upstream version 7.12.0 * Refresh, re-diff patches * Add python3-pytest-mock to B-D and test dep * Update test_from_any_directory.patch -- Nilesh Patra Fri, 29 Jul 2022 19:23:21 +0530 snakemake (7.9.0-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.6.1 (routine-update) * Drop unnecessary dependency on build-essential. * Fix lintian syntax * Use Debian packaged bootstrap and jquery for privacy reasons * Add README.Debian to give a hint about potential issues inside the replaced jquery interface. * Build-Depends: pybuild-plugin-pyproject -- Andreas Tille Tue, 26 Jul 2022 12:10:25 +0200 snakemake (7.8.5-2) unstable; urgency=medium * Team upload. * Do not run second lot of tests on s390x -- Nilesh Patra Thu, 07 Jul 2022 15:49:32 +0530 snakemake (7.8.5-1) unstable; urgency=medium * Team upload. * New upstream version 7.8.5 * Refresh patches -- Nilesh Patra Tue, 05 Jul 2022 21:51:30 +0530 snakemake (7.8.3-2) unstable; urgency=medium * Team upload. * Propagate build time test ignores in autopkgtest as well * Add python3-pygments to test-deps -- Nilesh Patra Sat, 25 Jun 2022 20:53:15 +0530 snakemake (7.8.3-1) unstable; urgency=medium * Team upload. [ Nilesh Patra] * New upstream version 7.8.3 * Refresh/Rediff patches * Mark tests offline even on timeouterror * Embed retry python mod code and modify import path until python-retry is packaged * Remove yte dep for now [ Rebecca N. Palmer ] * New upstream release. Refresh patches, d/copyright. * Skip some more unrunnable-in-Debian tests. * Update dependencies. * Update Lintian overrides. -- Nilesh Patra Sat, 25 Jun 2022 15:38:25 +0530 snakemake (6.15.5-1) unstable; urgency=medium * Upstream bugfix release. * Remove drmaa Recommends, as that package is broken (see #951704). * Tests: skip peppy tests (not in Debian), use Python 3 subprocesses. -- Rebecca N. Palmer Sun, 20 Feb 2022 14:53:05 +0000 snakemake (6.15.1-2) unstable; urgency=medium * Timeout and retry an intermittently hanging autopkgtest. * Upload to unstable. -- Rebecca N. Palmer Fri, 04 Feb 2022 22:35:19 +0000 snakemake (6.15.1-1~exp1) experimental; urgency=medium * New upstream release. Refresh patches, d/copyright. * Split up the binary package (main, -doc) to save space. * Tests: skip an FTP-using test and 2 new conda-using tests, mark as needs-internet, copy the test tree to avoid writing to it. * Don't ship the test suite, as some of it doesn't work from a non-writable directory. * Reproducibility: fix sphinx locale, skip a test that fails under faketime. * salsa-ci: ignore expected Lintian error, enable diffoscope. -- Rebecca N. Palmer Wed, 02 Feb 2022 07:36:20 +0000 snakemake (6.12.3-1) unstable; urgency=medium * New upstream release. Refresh patches. * Remove unnecessary repack. * Update d/copyright. * Use python3-connection-pool instead of an embedded copy. * Remove unsatisfiable Suggests. Update and sort build/test-Depends. * Run the tests in a copy instead of trying to clean up after them. * Update Lintian overrides. * Don't try to use local Javascript in GUI, as this is risky. * Fix possibly broken local Javascript in documentation. * Merge TODO into README.source and update. * Fix some broken tests, and document still needed test skips. -- Rebecca N. Palmer Tue, 11 Jan 2022 21:22:44 +0000 snakemake (6.10.0+dfsg1-1) unstable; urgency=medium * Team Upload. * New upstream version 6.10.0+dfsg1 * Re-diff patches -- Nilesh Patra Wed, 10 Nov 2021 01:10:16 +0530 snakemake (6.9.1+dfsg1-4) unstable; urgency=medium * Team Upload. * Add patch to make build reproducible (Closes: #997000) + Thanks to Chris Lamb! -- Nilesh Patra Sun, 24 Oct 2021 00:18:19 +0530 snakemake (6.9.1+dfsg1-3) unstable; urgency=medium * Team Upload. * d/t/control: + Comment another instance of snakemake-doc + Add python3-requests-mock and python3-jinja2 to test deps * d/t/run-unit-tests: + Exclude couple of tests (similar as build time) * d/copyright, d/rules, d/connection_pool.py: + Hack around to install connection_pool.py as file, and use the same -- Nilesh Patra Wed, 20 Oct 2021 12:31:52 +0530 snakemake (6.9.1+dfsg1-2) unstable; urgency=medium * Team upload. * Removing .snakemake folders from .deb * Separated documentation and tests into -doc package -- Steffen Moeller Tue, 19 Oct 2021 19:47:19 +0200 snakemake (6.9.1+dfsg1-1) unstable; urgency=medium * Team upload. [ Andreas Tille ] * Fix watchfile to detect new versions on github * New upstream version * Standards-Version: 4.6.0 (routine-update) * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine- update) * Remove trailing whitespace in debian/copyright (routine-update) * Build-Depends: python3-requests-mock [ Nilesh Patra ] * d/control: + Add versioned Dep on pulp (>= 2.0) + Add B-D on python3-smart-open [ Steffen Moeller ] * Unselected tests needing internet access * fixing one calling pytest -> pytest-3 * d/rules: Allowing consecutive builds with better cleaning * Added d/TODO to remind about missing "tes" Python module -- Nilesh Patra Tue, 19 Oct 2021 16:32:04 +0200 snakemake (5.24.1-2) unstable; urgency=medium * Team upload. * Skip tests accessing remote locations Closes: #986768 -- Andreas Tille Mon, 12 Apr 2021 17:17:32 +0200 snakemake (5.24.1-1) unstable; urgency=medium * New upstream release. Refresh patches. * Depend on python3-pulp << 2.0. -- Rebecca N. Palmer Sun, 13 Sep 2020 16:46:02 +0100 snakemake (5.23.0-1) unstable; urgency=medium * New upstream release. * Add new dependency python3-pulp. * Remove unnecessary test skips, and document remaining ones. -- Rebecca N. Palmer Sat, 29 Aug 2020 11:46:20 +0100 snakemake (5.22.1-1) unstable; urgency=medium * New upstream release. Refresh patches. * Update Lintian overrides. -- Rebecca N. Palmer Sun, 16 Aug 2020 14:04:24 +0100 snakemake (5.20.1-1) unstable; urgency=medium * New upstream release. Refresh patches. -- Rebecca N. Palmer Wed, 15 Jul 2020 08:32:43 +0100 snakemake (5.19.3-1) unstable; urgency=medium * New upstream release. -- Rebecca N. Palmer Sun, 28 Jun 2020 22:38:45 +0100 snakemake (5.19.2-1) unstable; urgency=medium * New upstream release. -- Rebecca N. Palmer Tue, 09 Jun 2020 18:32:35 +0100 snakemake (5.18.1-1) unstable; urgency=medium * New upstream release. Refresh patches, update override path. * Docs: work around Sphinx bug 7516. * Skip more tests with not-in-Debian dependencies. * Bump dephelper compat to 13, remove now-builtin rules. -- Rebecca N. Palmer Sun, 31 May 2020 10:54:51 +0100 snakemake (5.17.0-1) unstable; urgency=medium * Team upload. * New upstream version * d/p/security.patch: adopted upstream - removed -- Steffen Moeller Sat, 09 May 2020 17:26:55 +0200 snakemake (5.16.0-1) unstable; urgency=medium * New upstream release. Drop / refresh patches. * Stop using pytest-xdist: it sometimes starts tests from a non-main thread, which breaks snakemake. * Dockerfile: fix remote root-in-container security hole. * Skip a new conda-using test. -- Rebecca N. Palmer Mon, 04 May 2020 12:16:03 +0100 snakemake (5.14.0-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version * Remove trailing whitespace in debian/changelog (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. [ Rebecca N. Palmer ] * Use Python 3 in subprocess calls. * Fix buggy test (upstream 322). * Disable tests needing conda or docker. * Delete unused patches. * Use boto3 (like upstream) not boto. * Reproducibility: don't ship (timestamped) test logs. * Add self to Uploaders. * Update d/copyright, remove no longer needed Files-Excluded. * Enable verbose test output. * Update dependencies, add minimal-Depends test. * Privacy: use local dagre-d3, add missing Javascript dependencies, don't appear to show live status when we don't. * Use https for links where available. * Remove inconveniently licensed (CC-BY-SA) snippets. * Install examples. -- Rebecca N. Palmer Sat, 25 Apr 2020 19:10:20 +0100 snakemake (5.10.0-3) unstable; urgency=medium [ Rebecca N. Palmer ] * Exclude lazy_property to make Sphinx succeed. Closes: #955056 -- Andreas Tille Thu, 09 Apr 2020 11:09:24 +0200 snakemake (5.10.0-2) unstable; urgency=medium * Team upload. * Actually fix #943956, thanks to Chris Lamb for the quick hint -- Alexandre Mestiashvili Tue, 11 Feb 2020 11:31:06 +0100 snakemake (5.10.0-1) unstable; urgency=medium * Team upload. * New upstream version 5.10.0 Closes: #943956 * Refresh python3 patch, drop 0012-reproducible-build.patch * d/control: add python3-nbformat, python3-toposort to Build-Depends, bump Policy to 4.5.0 -- Alexandre Mestiashvili Sun, 09 Feb 2020 11:57:42 +0100 snakemake (5.9.1-1) unstable; urgency=medium * Team upload. * New upstream release. * Exclude new test 'test_env_modules' as it isn't for us. -- Michael R. Crusoe Wed, 01 Jan 2020 16:06:43 +0100 snakemake (5.8.1-1) unstable; urgency=medium * Team upload. * Quilt isn't needed for the autopkgtests, so drop it -- Michael R. Crusoe Fri, 15 Nov 2019 15:55:01 +0100 snakemake (5.7.4-1) unstable; urgency=medium * Team upload. * New upstream release. * Skip test_url_include in the autopkgtest * debian/{control,copyight,watch}: upstream is now using GitHub * Set upstream metadata fields: Repository. * Adapt some of the new tests to use python3 instead of python. -- Michael R. Crusoe Wed, 30 Oct 2019 17:22:29 +0100 snakemake (5.6.0-2) unstable; urgency=medium * Team upload. * debian/tests: Add missing dependency on python3-pandas; set $HOME * Enable parallel testing everywhere -- Michael R. Crusoe Sun, 15 Sep 2019 13:33:57 +0200 snakemake (5.6.0-1) unstable; urgency=medium * Team upload. * New upstream version * 0013-remove-duplicate-keyword-argument.patch removed, applied upstream * Add AutoPkgTests -- Michael R. Crusoe Fri, 13 Sep 2019 16:15:23 +0200 snakemake (5.5.4-2) unstable; urgency=medium * set $HOME to fix build on sbuild -- Michael R. Crusoe Fri, 06 Sep 2019 13:50:09 +0900 snakemake (5.5.4-1) unstable; urgency=medium [ Dylan Aïssi ] * Apply patch from Chris Lamb to make the build reproducible (Closes: #932116). [ Michael R. Crusoe ] * New upstream release * debian/control: Add missing build-deps (as shown in errors during the documentation building) * debian/README.source: Document missing (optional?) dependencies * debian/rules: Fix test invocation, as almost all tests were missed; Document what is known about the skipped tests * Apply patch from upstream to fix duplicated argument (Closes: #933527) [ Andreas Tille ] * debhelper-compat 12 * Standards-Version: 4.4.0 * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target * Remove obsolete fields Name, Contact from debian/upstream/metadata. -- Michael R. Crusoe Wed, 31 Jul 2019 11:24:24 +0200 snakemake (5.5.3-1) unstable; urgency=medium * Team upload. * New upstream version. -- Dylan Aïssi Sat, 13 Jul 2019 17:39:18 +0200 snakemake (5.4.0-1) unstable; urgency=medium * Team upload. * New upstream version. New Build-Dep: python3-git * Standards-Version: 4.3.0 -- Dylan Aïssi Fri, 04 Jan 2019 10:47:45 +0100 snakemake (5.3.0-1) unstable; urgency=medium * Team upload. * New upstream version New build-dep: python3-pandas and python3-jsonschema * Standards-Version: 4.2.1 -- Dylan Aïssi Wed, 24 Oct 2018 07:59:34 +0200 snakemake (5.2.1-1) unstable; urgency=medium * Team upload. * New upstream version - Fix compatibility with python 3.7 (Closes: #904350) * Remove 0012-skip_test_needing_networ_connection.patch upstream applied. -- Dylan Aïssi Fri, 27 Jul 2018 19:30:16 +0200 snakemake (5.1.5-1) unstable; urgency=medium * Team upload. * New upstream version Closes: #894213 * Standards-Version: 4.1.5 * debhelper 11 * d/rules: delete get-orig-source target * Build-Depends: r-cran-rmarkdown and disable patch that skips test using RMarkdown * Recommends: r-cran-rmarkdown * (Build-)Depends: python3-datrie, python3-networkx, python3-recommonmark, python3-pygraphviz, python3-pytest * Point Vcs-fields to Salsa * Drop X-Python-Version * Merge upstream commit to skip tests needing network access (upstream issue #902) * Lintian override for test data (false positive for source-is-missing) * Remove ancient-python-version-field X-Python3-Version -- Andreas Tille Mon, 09 Jul 2018 14:18:13 +0200 snakemake (4.3.1-1) unstable; urgency=medium * Team upload [ Dylan Aïssi ] * Add upstream/metadata [ Andreas Tille ] * Remove sphinxext which spoils doc generation * Fix build with Python 3.6 Closes: #878498 [ Christian M. Amsüss ] * New upstream version 4.3.1 - updated lintian overrides * Add build dependency on python3-ratelimiter * Patch out test cases with unsatisfied dependencies * Bump standards version to 4.1.2 [ Andreas Tille ] * Avoid privacy breach. The tradeoff is that the local static copy might become but people interested in latest information will read online anyway. * Mention remaining potential privacy breach issues in debian/README.source -- Christian M. Amsüss Mon, 11 Dec 2017 20:51:06 +0100 snakemake (3.10.0-1) unstable; urgency=medium * New upstream version 3.10.0 * Refresh patches -- Kevin Murray Thu, 19 Jan 2017 11:41:55 +1100 snakemake (3.9.1-2) unstable; urgency=medium * Future-proof patch to work-around missing snakemake binary when running tests before installation * Backport fix for crash with dynamic rules (from bitbucket PR #168). * Update my email address -- Kevin Murray Wed, 18 Jan 2017 00:20:04 +0000 snakemake (3.9.1-1) unstable; urgency=medium * Team upload * New upstream version * New Build-Depends: python3-sphinx-rtd-theme -- Andreas Tille Fri, 13 Jan 2017 15:03:15 +0100 snakemake (3.9.0+dfsg-2) unstable; urgency=medium * Team upload. * Ignore failures of test that might happpen in pbuilder Closes: #848820 -- Andreas Tille Thu, 22 Dec 2016 09:55:33 +0100 snakemake (3.9.0+dfsg-1) unstable; urgency=medium [ Kevin Murray ] * New upstream version 3.9.0 (Closes: #845737) [ Andreas Tille ] * debhelper 10 * d/watch: version=4 * Ignore failures of test that might happpen in pbuilder -- Kevin Murray Wed, 07 Dec 2016 09:02:12 +1100 snakemake (3.8.2+dfsg-1) unstable; urgency=medium * Update d/watch with bitbucket's new tag page * New upstream version 3.8.2 * Patch to avoid test failure * Add new dependencies to d/control -- Kevin Murray Fri, 02 Dec 2016 13:51:01 +1100 snakemake (3.7.1+dfsg-1) unstable; urgency=low * Imported new upstream version 3.7.1 * Bump standards version to 3.9.8 -- Kevin Murray Tue, 28 Jun 2016 14:54:17 +1000 snakemake (3.6.1+dfsg-1) unstable; urgency=low * Imported new upstream version 3.6.1 -- Kevin Murray Tue, 19 Apr 2016 12:15:15 +1000 snakemake (3.5.5+dfsg-1) unstable; urgency=low * Imported new upstream version 3.5.5 * Use filenamemangle in d/watch -- Kevin Murray Fri, 29 Jan 2016 17:18:28 +0200 snakemake (3.5.4+dfsg-1) unstable; urgency=medium * Imported Upstream version 3.5.4+dfsg -- Kevin Murray Thu, 17 Dec 2015 21:11:20 +1100 snakemake (3.4.2+dfsg-2) unstable; urgency=low * Fix watch file and d/control with new upstream URL -- Kevin Murray Thu, 19 Nov 2015 11:20:03 +1100 snakemake (3.4.2+dfsg-1) unstable; urgency=low * Initial release (Closes: #798824) -- Kevin Murray Sun, 13 Sep 2015 22:58:41 +1000