[med-svn] [Git][med-team/toil][upstream] New upstream version 8.2.0

[Michael R. Crusoe (@crusoe)]

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


Commits:
972c1073 by Michael R. Crusoe at 2025-05-05T09:19:19+02:00
New upstream version 8.2.0
- - - - -


117 changed files:

- .gitlab-ci.yml
- MANIFEST.in
- Makefile
- README.rst
- contrib/admin/mypy-with-ignore.py
- docs/appendices/environment_vars.rst
- + docs/cwl/conformance.rst
- docs/cwl/running.rst
- docs/index.rst
- docs/python/developing.rst
- docs/running/cliOptions.rst
- docs/running/debugging.rst
- docs/running/hpcEnvironments.rst
- docs/wdl/conformance.rst
- docs/wdl/developing.rst
- docs/wdl/running.rst
- + docs/wdl/tutorial.rst
- + pyproject.toml
- requirements-dev.txt
- requirements-server.txt
- requirements.txt
- setup.cfg
- setup.py
- src/toil/__init__.py
- src/toil/batchSystems/abstractBatchSystem.py
- src/toil/batchSystems/abstractGridEngineBatchSystem.py
- src/toil/batchSystems/awsBatch.py
- src/toil/batchSystems/cleanup_support.py
- src/toil/batchSystems/kubernetes.py
- src/toil/batchSystems/local_support.py
- src/toil/batchSystems/mesos/batchSystem.py
- src/toil/batchSystems/mesos/test/__init__.py
- src/toil/batchSystems/options.py
- src/toil/batchSystems/singleMachine.py
- src/toil/batchSystems/slurm.py
- src/toil/bus.py
- src/toil/common.py
- src/toil/cwl/cwltoil.py
- src/toil/job.py
- src/toil/jobStores/abstractJobStore.py
- src/toil/jobStores/aws/jobStore.py
- src/toil/jobStores/fileJobStore.py
- src/toil/jobStores/googleJobStore.py
- src/toil/leader.py
- src/toil/lib/accelerators.py
- src/toil/lib/aws/session.py
- src/toil/lib/aws/utils.py
- src/toil/lib/bioio.py
- src/toil/lib/docker.py
- + src/toil/lib/dockstore.py
- src/toil/lib/ec2nodes.py
- src/toil/lib/exceptions.py
- + src/toil/lib/history.py
- + src/toil/lib/history_submission.py
- src/toil/lib/io.py
- src/toil/lib/misc.py
- src/toil/lib/resources.py
- src/toil/lib/retry.py
- src/toil/lib/threading.py
- src/toil/lib/integration.py → src/toil/lib/trs.py
- + src/toil/lib/web.py
- src/toil/options/common.py
- src/toil/options/cwl.py
- src/toil/options/wdl.py
- src/toil/provisioners/gceProvisioner.py
- src/toil/server/cli/wes_cwl_runner.py
- src/toil/server/utils.py
- src/toil/statsAndLogging.py
- src/toil/test/__init__.py
- src/toil/test/batchSystems/batchSystemTest.py
- src/toil/test/batchSystems/test_slurm.py
- + src/toil/test/conftest.py
- src/toil/test/cwl/conftest.py
- src/toil/test/cwl/cwlTest.py
- src/toil/test/cwl/mock_mpi/fake_mpi_run.py
- + src/toil/test/cwl/optional-file-exists.json
- + src/toil/test/cwl/optional-file-missing.json
- + src/toil/test/cwl/optional-file.cwl
- + src/toil/test/cwl/revsort-job-missing.json
- src/toil/test/lib/aws/test_iam.py
- src/toil/test/lib/dockerTest.py
- + src/toil/test/lib/test_history.py
- src/toil/test/lib/test_integration.py → src/toil/test/lib/test_trs.py
- src/toil/test/provisioners/aws/awsProvisionerTest.py
- src/toil/test/provisioners/clusterTest.py
- src/toil/test/provisioners/gceProvisionerTest.py
- src/toil/test/sort/sort.py
- src/toil/test/src/busTest.py
- src/toil/test/src/deferredFunctionTest.py
- src/toil/test/src/importExportFileTest.py
- src/toil/test/src/jobEncapsulationTest.py
- src/toil/test/src/jobServiceTest.py
- src/toil/test/src/jobTest.py
- src/toil/test/src/miscTests.py
- src/toil/test/src/promisedRequirementTest.py
- src/toil/test/src/regularLogTest.py
- src/toil/test/src/resourceTest.py
- src/toil/test/src/restartDAGTest.py
- src/toil/test/src/resumabilityTest.py
- src/toil/test/src/retainTempDirTest.py
- src/toil/test/src/systemTest.py
- src/toil/test/src/threadingTest.py
- src/toil/test/utils/ABCWorkflowDebug/debugWorkflow.py
- src/toil/test/utils/toilDebugTest.py
- src/toil/test/utils/toilKillTest.py
- src/toil/test/utils/utilsTest.py
- + src/toil/test/wdl/lint_error.wdl
- + src/toil/test/wdl/testfiles/drop_files.wdl
- + src/toil/test/wdl/testfiles/drop_files_subworkflow.wdl
- + src/toil/test/wdl/testfiles/empty.txt
- + src/toil/test/wdl/testfiles/string_file_coercion.json
- + src/toil/test/wdl/testfiles/string_file_coercion.wdl
- src/toil/test/wdl/wdltoil_test.py
- src/toil/test/wdl/wdltoil_test_kubernetes.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/972c1073a5fa9bac5fd87d69fe0b10caa8c7f55c

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