[med-svn] [Git][med-team/toil][master] 6 commits: New upstream version 9.0.0

[Michael R. Crusoe (@crusoe)]

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


Commits:
a33b0ec4 by Michael R. Crusoe at 2025-10-11T09:05:15+02:00
New upstream version 9.0.0
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e1f1ea99 by Michael R. Crusoe at 2025-10-11T09:05:33+02:00
Update upstream source from tag 'upstream/9.0.0'

Update to upstream version '9.0.0'
with Debian dir 91ea4d72bc047843cfda3406784a1e46e24d34a0
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49a4b57a by Michael R. Crusoe at 2025-10-11T09:09:50+02:00
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.

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0291785e by Michael R. Crusoe at 2025-10-11T09:13:42+02:00
Refreshed patches.

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90699085 by Michael R. Crusoe at 2025-10-11T13:04:45+02:00
d/control: needs pytest-httpserver for a new test.

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6d065612 by Michael R. Crusoe at 2025-10-11T13:05:10+02:00
release to unstable

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62 changed files:

- .gitlab-ci.yml
- Makefile
- debian/changelog
- debian/control
- debian/patches/atomic_copy_as_alternative.patch
- debian/patches/debianize_docs
- debian/patches/no_galaxy_lib
- debian/patches/setting_version.patch
- debian/patches/spelling
- docker/Dockerfile.py
- docs/cwl/conformance.rst
- docs/cwl/running.rst
- docs/gettingStarted/quickStart.rst
- docs/running/cliOptions.rst
- docs/wdl/running.rst
- requirements-aws.txt
- requirements-cwl.txt
- requirements-dev.txt
- requirements-server.txt
- requirements-wdl.txt
- setup.cfg
- src/toil/batchSystems/registry.py
- src/toil/common.py
- src/toil/cwl/cwltoil.py
- src/toil/cwl/utils.py
- src/toil/jobStores/abstractJobStore.py
- src/toil/jobStores/aws/jobStore.py
- src/toil/jobStores/fileJobStore.py
- src/toil/jobStores/googleJobStore.py
- src/toil/lib/accelerators.py
- src/toil/lib/generatedEC2Lists.py
- src/toil/lib/misc.py
- + src/toil/lib/plugins.py
- + src/toil/lib/url.py
- src/toil/options/cwl.py
- src/toil/options/runner.py
- src/toil/options/wdl.py
- src/toil/provisioners/aws/awsProvisioner.py
- src/toil/server/app.py
- src/toil/server/cli/wes_cwl_runner.py
- src/toil/server/wes/abstract_backend.py
- src/toil/server/wes/toil_backend.py
- src/toil/test/__init__.py
- src/toil/test/batchSystems/batchSystemTest.py
- src/toil/test/batchSystems/batch_system_plugin_test.py
- src/toil/test/cwl/cwlTest.py
- src/toil/test/docs/scriptsTest.py
- + src/toil/test/lib/test_url.py
- + src/toil/test/lib/url_plugin_test.py
- src/toil/test/provisioners/aws/awsProvisionerTest.py
- src/toil/test/provisioners/clusterTest.py
- src/toil/test/provisioners/gceProvisionerTest.py
- src/toil/test/server/serverTest.py
- src/toil/test/wdl/md5sum/md5sum-gs.json
- + src/toil/test/wdl/testfiles/read_file.wdl
- src/toil/test/wdl/testfiles/url_to_optional_file.wdl
- src/toil/test/wdl/wdltoil_test.py
- src/toil/utils/toilSshCluster.py
- src/toil/utils/toilUpdateEC2Instances.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/346681165811740b5450c223974948224532ca0e...6d065612fa14633e61ae88a37827a2864a71806c

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View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/346681165811740b5450c223974948224532ca0e...6d065612fa14633e61ae88a37827a2864a71806c
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