[med-svn] [Git][med-team/toil][upstream] New upstream version 9.0.0

[Michael R. Crusoe (@crusoe)]

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


Commits:
a33b0ec4 by Michael R. Crusoe at 2025-10-11T09:05:15+02:00
New upstream version 9.0.0
- - - - -


55 changed files:

- .gitlab-ci.yml
- Makefile
- 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/-/commit/a33b0ec4b5fe1c6b1b4d5b2c89a2df2e7702c297

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