toil (8.0.0-4) unstable; urgency=medium
* d/rules: skip the slow tests
* d/patches/needs_aws-proxyfix: forwarded upstream
-- Michael R. Crusoe <crusoe@debian.org> Fri, 21 Mar 2025 17:28:28 +0100
toil (8.0.0-3) unstable; urgency=medium
* d/tests/autopkgtest-pkg-pybuild.conf: fix typo
-- Michael R. Crusoe <crusoe@debian.org> Wed, 19 Mar 2025 18:39:08 +0100
toil (8.0.0-2) unstable; urgency=medium
* d/watch: mark beta releases as such
* Skip autopktests on 32-bit architectures
* d/rules: skip the testMultiplejobs tests, they are flaky during
parallel execution. Closes: #1100817
-- Michael R. Crusoe <crusoe@debian.org> Wed, 19 Mar 2025 12:41:12 +0100
toil (8.0.0-1) unstable; urgency=medium
[ Michael R. Crusoe ]
* New upstream version
* Refresh patches
* d/patches/allow_newer_requests: added
* docs: link to cwltool-doc; link to python3-doc locally
* d/patches/skip-mypy-boto3: these type hints are not packaged for
Debian yet
* d/patches/needs_aws-proxyfix: Fix build due to purposely invalid
proxy configuration.
* d/rules: skip online tests
* d/patches/setting_version.patch: update for Python 3.12
* d/rules: use DEB_BUILD_OPTION_PARALLEL instead of "auto" for setting
the amount of parallel testing.
* Refreshed patches; removed "skip-mypy-boto3" and "python3.12-
syntax.patch" as they are no longer needed.
* Added patch to remove the restrictions on the psutil Python package
version.
* Updated the fix-tests patch to fix more tests.
* d/control: cwl-utils is needed for the tests
* Added patch with a minimal PEP-517 pyproject.toml, to improve how we
run the tests.
* d/rules: simplify
* d/rules: skip manual page building in when the "nodoc" build profile
is active.
* Switch autopkgtest to autopkgtest-pkg-pybuild
* d/TODO: removed several completed items.
* d/toil.lintian-overrides: removed, no longer applicable
* d/patches/soften-configargparser-deps: removed, no longed needed
[ Andreas Tille ]
* Fix Python3.12 string syntax
Closes: #1087116
* Standards-Version: 4.7.0 (routine-update)
-- Michael R. Crusoe <crusoe@debian.org> Tue, 18 Mar 2025 17:34:39 +0100
toil (6.1.0-4) unstable; urgency=medium
* d/control: we now need an explicit dependency on python3-tz. Closes:
#1070055
-- Michael R. Crusoe <crusoe@debian.org> Mon, 29 Apr 2024 16:41:47 +0200
toil (6.1.0-3) unstable; urgency=medium
* d/README.source: make more explicit the need to follow the
instructions in debian/patch/settings_version.patch on every new
source tarball.
* d/control: drop unneeded dependency on python3-distutils.
Closes: #1065987
-- Michael R. Crusoe <crusoe@debian.org> Mon, 11 Mar 2024 12:14:38 +0100
toil (6.1.0-2) unstable; urgency=medium
* d/control: azure support is gone, don't suggest it anymore.
-- Michael R. Crusoe <crusoe@debian.org> Wed, 28 Feb 2024 15:20:36 +0100
toil (6.1.0-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
* Run test for all supported Python versions
* Do not force any specific docker version, just take the Debian
packaged one
[ Michael R. Crusoe ]
* d/patches/setting_version.patch: regenerate according to the
intructions in d/README.source.
* d/tests/run-unit-tests: two more tests need skipping.
-- Michael R. Crusoe <crusoe@debian.org> Wed, 28 Feb 2024 11:42:03 +0100
toil (6.0.0-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
Closes: #1058195
* Drop python3-future from Build-Depends
Closes: #1059945
* Drop python3-boto from (Build-/Test-)Depends since upstream considers
this module optional (see
https://github.com/DataBiosphere/toil/issues/4718#issuecomment-1904474636
)
Closes: #1058237
* Build-Depends: python3-configargparse
* Soften versioned dependency from cwltool
[ Michael R. Crusoe ]
* d/rules,d/control, d/patches/intersphinx: Fix some sphinx warnings, ignore
the rest.
* Add patch to avoid need for ruamel.yaml.string package.
* Add patch to allow for older configarparser version.
* Ignore the new test_cactus_integration
* Enhance avoid_boto patch
* d/patches: updated metatdata
* d/copyright: upstream removed wdl_functions.py
* Add patch to remove use of distutils by copying in strtobool().
* d/control: bump some minimum versions
-- Michael R. Crusoe <crusoe@debian.org> Tue, 23 Jan 2024 15:24:30 +0100
toil (5.12.0-2) unstable; urgency=medium
* d/tests/run-unit-tests: fix typo.
* Added patch to the tests: only request a single core. Closes:
#1031192
* d/clean: remove docs/autoapi and another straggler. Closes: #1047298
-- Michael R. Crusoe <crusoe@debian.org> Tue, 22 Aug 2023 15:46:37 +0200
toil (5.12.0-1) unstable; urgency=medium
* New upstream version
* Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
* refreshed patches.
* d/rules: wdltoil_test has a new path.
-- Michael R. Crusoe <crusoe@debian.org> Mon, 21 Aug 2023 19:09:01 +0200
toil (5.11.0-2) unstable; urgency=medium
* Exclude WDL from autopkgtests; as miniwdl isn't packaged yet for Debian
-- Michael R. Crusoe <crusoe@debian.org> Sat, 15 Jul 2023 09:43:56 +0200
toil (5.11.0-1) unstable; urgency=medium
[ Andreas Tille ]
* Team upload.
* New upstream version
* Build-Depends: python3-sphinx-autoapi, python3-sphinx-autodoc-typehints,
python3-sphinxcontrib.autoprogram, docker.io
[ Michael R. Crusoe ]
* d/rules: skip the WDL tests (not packaged)
* d/patches/setting_version.patch: update for Toil 5.11.0
-- Andreas Tille <tille@debian.org> Fri, 14 Jul 2023 22:43:13 +0200
toil (5.9.2-2) unstable; urgency=medium
* Add patch to handle errors when testing on ec2.
-- Michael R. Crusoe <crusoe@debian.org> Mon, 06 Feb 2023 19:24:07 +0100
toil (5.9.2-1) unstable; urgency=medium
* Team upload.
* New upstream version
* Build-Depends: s/python3-xdist/python3-pytest-xdist/
Closes: #1030558
-- Andreas Tille <tille@debian.org> Sun, 05 Feb 2023 08:38:00 +0100
toil (5.9.0-1) unstable; urgency=medium
* New upstream version
* d/control: match build-deps to upstream
* run tests in parallel
-- Michael R. Crusoe <crusoe@debian.org> Fri, 03 Feb 2023 19:05:54 +0100
toil (5.8.0-3) unstable; urgency=medium
* d/patches/setting_version.patch: really keep the python minor
version out
-- Michael R. Crusoe <crusoe@debian.org> Wed, 18 Jan 2023 15:24:50 +0100
toil (5.8.0-2) unstable; urgency=medium
* set exactPython to "python3" to always use the system version
* Recommend podman in addition to docker/singularity
-- Michael R. Crusoe <crusoe@debian.org> Sun, 15 Jan 2023 15:30:29 +0100
toil (5.8.0-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.6.2 (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse.
* refresh patches; remove test_safe_paths & typing_fix, they were
applied upstream.
* new dependency: python3-pubsub
* new patch to avoid unpackaged mypy_boto3_s3
* Skip the aws/test_iam.py tests
* python3-boto{,3} is now a hard requirement
-- Michael R. Crusoe <crusoe@debian.org> Thu, 12 Jan 2023 23:33:14 +0100
toil (5.7.1-2) unstable; urgency=medium
* d/test/control: re-enable running on arm64
-- Michael R. Crusoe <crusoe@debian.org> Mon, 26 Dec 2022 16:06:23 +0100
toil (5.7.1-1) unstable; urgency=medium
* d/watch: update for new tag structure
* New upstream version
* refresh patches
* d/patches/typing_fix: workaround for us skipping the AWS extra
during building
* d/patches/newer_cwltool: the expression module is now part of cwl-utils,
not cwltool
* d/rules: skip more tests that fail when run as root
* d/patches/test_safe_paths: fix for running tests post-installation
* d/tests/run-unit-tests: skip same tests we skip in d/rules
-- Michael R. Crusoe <crusoe@debian.org> Wed, 21 Dec 2022 11:30:22 +0100
toil (5.6.0-7) unstable; urgency=medium
* Team upload.
* Packaging update
* Standards-Version: 4.6.1 (routine-update)
* Remove trailing whitespace in debian/changelog (routine-update)
* Drop unnecessary dependency on build-essential.
* Make sure the doc applies to Debian installations with Python3
* Update lintian-overrides
* Set python3.10 instead of python3.9 in setting_version.patch
Closes: #1013275
-- Andreas Tille <tille@debian.org> Mon, 18 Jul 2022 17:39:37 +0200
toil (5.6.0-6) unstable; urgency=medium
* Team Upload.
* d/t/control: Test dep on python3-all (Closes: #1009201)
-- Nilesh Patra <nilesh@debian.org> Sat, 16 Apr 2022 00:13:39 +0530
toil (5.6.0-5) unstable; urgency=medium
* Team Upload.
* d/t/control: Do not run autopkgtests on arm64
-- Nilesh Patra <nilesh@debian.org> Sat, 12 Mar 2022 01:41:12 +0530
toil (5.6.0-4) unstable; urgency=medium
* Team Upload.
* d/salsa-ci.yml: Disable reprotest
* Apply patches before running autopkgtests
-- Nilesh Patra <nilesh@debian.org> Fri, 11 Mar 2022 03:46:49 +0530
toil (5.6.0-3) unstable; urgency=medium
* Team Upload.
* Add patch to fix FTBFS with jobStores
tests (Closes: #1005479)
-- Nilesh Patra <nilesh@debian.org> Thu, 10 Mar 2022 17:55:25 +0530
toil (5.6.0-2) unstable; urgency=medium
* {Autopkg,}tests: sync the skiped tests
-- Michael R. Crusoe <crusoe@debian.org> Mon, 24 Jan 2022 11:42:07 +0100
toil (5.6.0-1) unstable; urgency=medium
* New upstream version
* Refresh patches, retiring cwl_test_path, spelling, and
test_with_less_memory
* Skip the py-tes dependency for now.
* Skip testVirtualEnv
-- Michael R. Crusoe <crusoe@debian.org> Wed, 19 Jan 2022 14:23:52 +0100
toil (5.5.0-7) unstable; urgency=medium
* Adjust depends to match cwltool 3.1.20211104071347 or greater.
-- Michael R. Crusoe <crusoe@debian.org> Sun, 07 Nov 2021 15:44:06 +0100
toil (5.5.0-6) unstable; urgency=medium
* Support cwltool 3.1.20211104071347.
-- Michael R. Crusoe <crusoe@debian.org> Fri, 05 Nov 2021 17:24:21 +0100
toil (5.5.0-5) unstable; urgency=medium
* Another adjustment of disk/memory defaults for the autopkgtests.
* debian/patches/exit_code_exception: Fix exception checking for
exit_code
-- Michael R. Crusoe <crusoe@debian.org> Fri, 08 Oct 2021 10:57:25 +0200
toil (5.5.0-4) unstable; urgency=medium
* Adjust disk/memory defaults further downward for 32-bit systems.
-- Michael R. Crusoe <crusoe@debian.org> Wed, 06 Oct 2021 16:29:06 +0200
toil (5.5.0-3) unstable; urgency=medium
* toil binary package depedency on recent cwltool as well.
* Autopkgtests: skip collection of s3 tests
-- Michael R. Crusoe <crusoe@debian.org> Sun, 03 Oct 2021 13:20:18 +0200
toil (5.5.0-2) unstable; urgency=medium
* Correct minimum versions for cwltool, python3-boto3
-- Michael R. Crusoe <crusoe@debian.org> Thu, 30 Sep 2021 11:42:30 +0200
toil (5.5.0-1) unstable; urgency=medium
[ Steffen Moeller ]
* Fix watchfile to detect new versions on github (routine-update)
* New upstream version
* Standards-Version: 4.6.0 (routine-update)
* d/p/python3: adopted upstream
* skipped networking-based tests
* d/u/metadta: onfirmed missing registry entries
[ Michael R. Crusoe ]
* New upstream version
* Refresh patches
* Bump minimum version of cwltool needed to 3.1.20210922203925
* Testing: ignore src/toil/test/lib/aws/test_s3.py
* Add testing dependency on python3-yaml.
* debian/patches/spelling: fix some typos
* debian/toil.lintian-overrides: documented another false positive
-- Michael R. Crusoe <crusoe@debian.org> Wed, 29 Sep 2021 20:36:37 +0200
toil (5.2.0-5) unstable; urgency=high
* debian/patches/test_with_less_memory: reduce default resource reqs
for 32bit systems
-- Michael R. Crusoe <crusoe@debian.org> Wed, 10 Feb 2021 11:24:49 +0100
toil (5.2.0-4) unstable; urgency=high
* autopkgtests: skip some s3 related tests.
-- Michael R. Crusoe <crusoe@debian.org> Mon, 08 Feb 2021 08:29:12 +0100
toil (5.2.0-3) unstable; urgency=high
* autopkgtests: add missing dependency on python3-stubserver
-- Michael R. Crusoe <crusoe@debian.org> Sun, 07 Feb 2021 13:58:57 +0100
toil (5.2.0-2) unstable; urgency=high
* Enable toil-wdl-runner now that python3-wdlparse is in Debian.
* Enabled running the the tests during the build!
-- Michael R. Crusoe <crusoe@debian.org> Sun, 07 Feb 2021 13:26:16 +0100
toil (5.2.0-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.5.1 (routine-update)
* Freshen patches
* update some copyright info
* The python module "wdlparse" is not yet packaged for Debian; disable
toil-wdl-runner in this release.
* debian/control: update the minimum version of cwltool required
-- Michael R. Crusoe <crusoe@debian.org> Sun, 24 Jan 2021 12:07:21 +0100
toil (4.2.0-1) unstable; urgency=medium
* New upstream version
* Remove unneeded no_virtualenv_to_create_manpages.patch; freshen remaining
patches.
* debian/tests/control: 'superficial' is a restriction, not a feature
* Quiet a lintian false positive for repeated-path-segment
-- Michael R. Crusoe <crusoe@debian.org> Thu, 27 Aug 2020 11:26:41 +0200
toil (4.1.0-1) unstable; urgency=medium
* New upstream version
* Refreshed the patches
* debhelper-compat 13 (routine-update)
* Update patch metatdata
-- Michael R. Crusoe <crusoe@debian.org> Fri, 07 Aug 2020 17:14:01 +0200
toil (4.0.0-3) unstable; urgency=medium
* Mark the autopkgtest as superficial. (Closes: #958574)
-- Michael R. Crusoe <michael.crusoe@gmail.com> Wed, 06 May 2020 20:58:48 +0200
toil (4.0.0-2) unstable; urgency=medium
* Add python3-distutils dependency, needed for python3-docker
* debian/copyright: remove leading "./"
-- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 27 Apr 2020 15:55:22 +0200
toil (4.0.0-1) unstable; urgency=medium
* New upstream version
* Freshen our patches
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* debian/copyright: use spaces rather than tabs to start continuation
lines.
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse
* python3-chardet is no longer needed
-- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 06 Apr 2020 13:56:50 +0200
toil (3.24.0-1) unstable; urgency=medium
* New upstream version
* refresh debian/patches/settings_version.patch from pypi sdist (must be
done with every new upstream release!)
* Allow the newer schema salad package (Closes: #951139)
-- Michael R. Crusoe <michael.crusoe@gmail.com> Fri, 14 Feb 2020 13:41:12 +0100
toil (3.23.1-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.5.0 (routine-update)
* Removed patch 'debian/patches/fix_tests' which was applied upstream
-- Steffen Moeller <moeller@debian.org> Thu, 06 Feb 2020 00:15:16 +0100
toil (3.21.0-1) unstable; urgency=medium
* New upstream version
-- Michael R. Crusoe <michael.crusoe@gmail.com> Sun, 17 Nov 2019 15:13:56 +0100
toil (3.20.0-1) unstable; urgency=medium
[ Michael R. Crusoe ]
* Make the build reproducible, patch from lamby@debian.org; thanks!
(Closes: #925191)
* Update the patches.
[ Andreas Tille ]
* debhelper-compat 12
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.4.0
-- Michael R. Crusoe <michael.crusoe@gmail.com> Wed, 20 Mar 2019 21:46:34 -0500
toil (3.18.0-2) unstable; urgency=medium
* Remove errant recommend on python3-futures and depends on python3-pytest*
(Closes: #919228)
* Refined the package description, added 'Provides: cwl-runner'
* Remove the partial mesos support until python3-mesos is packaged
* Suggests: docker.io | singularity-container | docker-ce
* Added debian/TODO, updated debian/README.{debian,source}
* Add basic smoke test ( `toil* --help` ) as an AutoPkgTest
-- Michael R. Crusoe <michael.crusoe@gmail.com> Sun, 13 Jan 2019 23:25:16 -0800
toil (3.18.0-1) unstable; urgency=medium
* Initial release (Closes: #851365)
-- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 07 Jan 2019 02:04:03 -0800