toil (9.1.0-1) unstable; urgency=medium * New upstream version. Toil's AWS job store now depends only on the S3 API; Amazon SimpleDB is no longer required. Toil's autoscaler should again be able to add AWS spot market nodes. Toil now checks scontrol first for Slurm jobs, and then pages through constrained time ranges of data from sacct, instead of first asking sacct about all of history. Breaking Changes Because of the new AWS job store implementation, Toil 9.1 can no longer read, delete, or resume AWS job stores created with Toil 9.0 or earlier. If you need to destroy an old job store, use toil clean from toil[aws]==9.0. In general, Toil doesn't consider losing compatibility with an older Toil's job store data on disk to be a major-version-worthy change, since it might happen any time Toil revises its internal data structures, but in this case the lack of delete support for the old format is a tripping hazard that we want to call out. * Refreshed patches * Cleaned up some lintian warnings * New typos for the spelling patch, and forwarded them upstream -- Michael R. Crusoe Fri, 17 Oct 2025 11:42:07 +0200 toil (9.0.0-1) unstable; urgency=medium * New upstream version. Added new unified plugin system. Toil now supports URL plugins. --importWorkersThreshold has been renamed to --importWorkersBatchsize. Fix a bug in Toil server mode CWL YAML parsing. CWL worker import works again. CWL: Fixed a regression with tmpdir_prefix and nonexistent diectories Added --cwl-min-ram to CWL. This specifies a minimum memory allocation for all jobs. This is different than --defaultMemory, which only applies to jobs without explicitly set memory requirements. * Refreshed patches. * d/control: needs pytest-httpserver for a new test. -- Michael R. Crusoe Sat, 11 Oct 2025 09:15:28 +0200 toil (8.2.0-1) unstable; urgency=medium * New upstream version. Fixed slurm partition selection Cleanup of unneeded files Improve Google Cloud authentication errors Caching support for CWL Add `--slurmPartition` and `--slurmGPUPartition` and support `--time` in `TOIL_SLURM_ARGS` * Standards-Version: 4.7.2 (routine-update) * Refreshed patches. Dropped 3 that are not longer needed * d/control: include cwltest, python3-pytest-timeout, python3-pytest-subtests, and python3-prompt-toolkit * Added patch to fix typos -- Michael R. Crusoe Tue, 30 Sep 2025 15:15:12 +0200 toil (8.0.0-5) unstable; urgency=medium * d/rules: skip flaky testServices. Closes: #1101085 -- Michael R. Crusoe Wed, 09 Apr 2025 13:42:27 +0200 toil (8.0.0-4) unstable; urgency=medium * d/rules: skip the slow tests * d/patches/needs_aws-proxyfix: forwarded upstream -- Michael R. Crusoe 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Sun, 07 Nov 2021 15:44:06 +0100 toil (5.5.0-6) unstable; urgency=medium * Support cwltool 3.1.20211104071347. -- Michael R. Crusoe 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Thu, 06 Feb 2020 00:15:16 +0100 toil (3.21.0-1) unstable; urgency=medium * New upstream version -- Michael R. Crusoe 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 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 Sun, 13 Jan 2019 23:25:16 -0800 toil (3.18.0-1) unstable; urgency=medium * Initial release (Closes: #851365) -- Michael R. Crusoe Mon, 07 Jan 2019 02:04:03 -0800