Michael R. Crusoe pushed to branch master at Debian Med / toil


Commits:
197e6806 by Michael R. Crusoe at 2026-05-07T18:02:17+02:00
New upstream version

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b534d4bc by Michael R. Crusoe at 2026-05-07T18:02:18+02:00
New upstream version 9.4.1
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60b97924 by Michael R. Crusoe at 2026-05-07T18:02:29+02:00
Update upstream source from tag 'upstream/9.4.1'

Update to upstream version '9.4.1'
with Debian dir 94e65ca6d2f5cc39b45c3fd6dbf5635b237d8ff7
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8d7703b1 by Michael R. Crusoe at 2026-05-07T18:02:45+02:00
debputy lint --auto-fix (routine-update)

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e1a5429b by Michael R. Crusoe at 2026-05-07T18:07:45+02:00
Refreshed patches, dropping one.

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3d2ec40d by Michael R. Crusoe at 2026-05-07T17:08:10+01:00
Use GitHub template in watch file instead of explicit Source/Matching-Pattern.

Changes-By: lintian-brush

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0576ebbc by Michael R. Crusoe at 2026-05-07T17:08:10+01:00
Reorder Files paragraphs in debian/copyright by directory depth.

Changes-By: lintian-brush
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html
Fixes: lintian: globbing-patterns-out-of-order
See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html

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a101176d by Michael R. Crusoe at 2026-05-07T17:08:18+01:00
Set upstream metadata fields: Repository.

Changes-By: lintian-brush

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3e6bf694 by Michael R. Crusoe at 2026-05-07T18:30:54+02:00
Bump minimum cwltool version.

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53ee8965 by Michael R. Crusoe at 2026-05-07T18:32:16+02:00
routine-update: Ready to upload to unstable

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53 changed files:

- .gitlab-ci.yml
- BOTS.md
- contrib/admin/cleanup_aws_resources.py
- + contrib/admin/find_hanging_tests.py
- contrib/admin/test-pr
- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/0001-upgrade-typing.patch
- debian/patches/accept_debian_packaged_docker_version.patch
- debian/patches/allow_newer_requests
- debian/patches/fix_tests
- debian/patches/series
- debian/patches/setting_version.patch
- debian/patches/soften-cwltool-dep.patch
- debian/upstream/metadata
- debian/watch
- docker/Dockerfile.py
- pyproject.toml
- requirements-cwl.txt
- requirements-dev.txt
- requirements.txt
- src/toil/batchSystems/mesos/batchSystem.py
- src/toil/batchSystems/slurm.py
- src/toil/cwl/cwltoil.py
- src/toil/cwl/utils.py
- src/toil/job.py
- src/toil/jobStores/aws/jobStore.py
- src/toil/lib/aws/ami.py
- src/toil/lib/aws/s3.py
- src/toil/lib/aws/utils.py
- src/toil/lib/generatedEC2Lists.py
- src/toil/options/common.py
- src/toil/provisioners/aws/awsProvisioner.py
- src/toil/server/cli/wes_cwl_runner.py
- src/toil/server/utils.py
- src/toil/server/wes/tasks.py
- src/toil/server/wes/toil_backend.py
- src/toil/test/batchSystems/batchSystemTest.py
- src/toil/test/batchSystems/test_slurm.py
- src/toil/test/cactus/test_cactus_integration.py
- src/toil/test/cwl/cwlTest.py
- src/toil/test/jobStores/jobStoreTest.py
- src/toil/test/lib/aws/test_s3.py
- src/toil/test/server/serverTest.py
- src/toil/test/sort/sortTest.py
- src/toil/test/src/jobFileStoreTest.py
- src/toil/test/src/jobServiceTest.py
- src/toil/test/src/jobTest.py
- src/toil/test/utils/utilsTest.py
- + src/toil/test/wdl/testfiles/cromwell_pair.wdl
- src/toil/test/wdl/wdltoil_test.py
- version_template.py


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/toil/-/compare/ed292b606b88f26be27550ff122696ad73a410a7...53ee8965a2dcf479fb98a0edb29a5fcc1a11c7c1

-- 
View it on GitLab: 
https://salsa.debian.org/med-team/toil/-/compare/ed292b606b88f26be27550ff122696ad73a410a7...53ee8965a2dcf479fb98a0edb29a5fcc1a11c7c1
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