[med-svn] [Git][med-team/toil][master] 7 commits: New upstream version 9.1.0

[Michael R. Crusoe (@crusoe)]

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


Commits:
fbd8c711 by Michael R. Crusoe at 2025-10-16T13:07:10+02:00
New upstream version 9.1.0
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3c0d1336 by Michael R. Crusoe at 2025-10-16T13:07:27+02:00
Update upstream source from tag 'upstream/9.1.0'

Update to upstream version '9.1.0'
with Debian dir 2226d8b5b3c021c69812c879e67bf4021ead2e6f
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bc04f86d by Michael R. Crusoe at 2025-10-16T13:10:21+02:00
changes upstream for 9.1.0

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20f87498 by Michael R. Crusoe at 2025-10-16T13:30:46+02:00
Refreshed patches

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4bff7d5c by Michael R. Crusoe at 2025-10-16T14:56:24+02:00
Cleaned up some lintian warnings

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c6cf6b23 by Michael R. Crusoe at 2025-10-16T14:56:50+02:00
New typos for the spelling patch, and forwarded them upstream

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3d67f26d by Michael R. Crusoe at 2025-10-17T11:42:19+02:00
Upload to unstable

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80 changed files:

- .github/workflows/codeql-analysis.yml
- .gitlab-ci.yml
- Makefile
- contrib/admin/cleanup_aws_resources.py
- contrib/admin/mypy-with-ignore.py
- debian/changelog
- debian/patches/accept_debian_packaged_docker_version.patch
- debian/patches/allow_newer_requests
- debian/patches/fix_tests
- debian/patches/no_galaxy_lib
- debian/patches/soften-cwltool-dep.patch
- debian/patches/spelling
- + debian/toil.lintian-overrides
- docker/Dockerfile.py
- docs/appendices/aws_min_permissions.rst
- requirements-cwl.txt
- requirements-dev.txt
- requirements-google.txt
- requirements-kubernetes.txt
- requirements-server.txt
- requirements.txt
- src/toil/batchSystems/abstractBatchSystem.py
- src/toil/batchSystems/abstractGridEngineBatchSystem.py
- src/toil/batchSystems/kubernetes.py
- src/toil/batchSystems/mesos/batchSystem.py
- src/toil/batchSystems/slurm.py
- src/toil/cwl/cwltoil.py
- src/toil/fileStores/__init__.py
- src/toil/fileStores/abstractFileStore.py
- src/toil/fileStores/cachingFileStore.py
- src/toil/job.py
- src/toil/jobStores/abstractJobStore.py
- src/toil/jobStores/aws/jobStore.py
- src/toil/jobStores/aws/utils.py
- src/toil/jobStores/googleJobStore.py
- src/toil/jobStores/utils.py
- src/toil/leader.py
- + src/toil/lib/aws/config.py
- src/toil/lib/aws/s3.py
- src/toil/lib/aws/utils.py
- + src/toil/lib/checksum.py
- src/toil/lib/conversions.py
- + src/toil/lib/directory.py
- src/toil/lib/ec2.py
- src/toil/lib/exceptions.py
- src/toil/lib/expando.py
- src/toil/lib/generatedEC2Lists.py
- src/toil/lib/io.py
- − src/toil/lib/iterables.py
- src/toil/lib/memoize.py
- + src/toil/lib/pipes.py
- src/toil/lib/retry.py
- src/toil/lib/threading.py
- src/toil/lib/web.py
- src/toil/provisioners/__init__.py
- src/toil/provisioners/aws/__init__.py
- src/toil/provisioners/aws/awsProvisioner.py
- src/toil/provisioners/node.py
- src/toil/resource.py
- src/toil/test/__init__.py
- src/toil/test/batchSystems/test_slurm.py
- − src/toil/test/docs/scripts/stagingExampleFiles/in.txt
- src/toil/test/docs/scripts/tutorial_staging.py
- src/toil/test/jobStores/jobStoreTest.py
- src/toil/test/lib/aws/test_iam.py
- src/toil/test/lib/aws/test_s3.py
- src/toil/test/lib/aws/test_utils.py
- src/toil/test/provisioners/aws/awsProvisionerTest.py
- src/toil/test/src/autoDeploymentTest.py
- src/toil/test/src/fileStoreTest.py
- src/toil/test/utils/ABCWorkflowDebug/debugWorkflow.py
- src/toil/test/utils/toilKillTest.py
- src/toil/test/wdl/md5sum/md5sum.json
- src/toil/test/wdl/wdltoil_test.py
- src/toil/test/wdl/wdltoil_test_kubernetes.py
- src/toil/utils/toilDebugFile.py
- src/toil/utils/toilStats.py
- src/toil/wdl/wdltoil.py
- src/toil/worker.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/6d065612fa14633e61ae88a37827a2864a71806c...3d67f26d91b7a2a71e3043bfdf0918191c3d2bee

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View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/6d065612fa14633e61ae88a37827a2864a71806c...3d67f26d91b7a2a71e3043bfdf0918191c3d2bee
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