[med-svn] [Git][med-team/toil][upstream] 2 commits: New upstream version 9.2.0
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Thu Apr 16 14:15:17 BST 2026
Michael R. Crusoe pushed to branch upstream at Debian Med / toil
Commits:
a78392a7 by Michael R. Crusoe at 2026-04-16T10:12:37+02:00
New upstream version 9.2.0
- - - - -
f81ad2cc by Michael R. Crusoe at 2026-04-16T10:40:43+02:00
New upstream version 9.3.0
- - - - -
178 changed files:
- .git-blame-ignore-revs
- .github/workflows/codeql-analysis.yml
- .gitlab-ci.yml
- .readthedocs.yaml
- + BOTS.md
- + CLAUDE.md
- Makefile
- README.rst
- contrib/admin/mypy-with-ignore.py
- contrib/mypy-stubs/pubsub/core/topictreetraverser.pyi
- contrib/slurm-test/docker-compose.yml
- contrib/slurm-test/slurm.conf
- contrib/slurm-test/slurm_test.sh
- contrib/toil-ci-prebake/Dockerfile
- docker/Dockerfile.py
- docs/appendices/deploy.rst
- docs/cwl/conformance.rst
- docs/running/cliOptions.rst
- docs/running/hpcEnvironments.rst
- requirements-aws.txt
- requirements-cwl.txt
- requirements-dev.txt
- requirements-kubernetes.txt
- requirements-server.txt
- requirements-wdl.txt
- requirements.txt
- setup.py
- setup_gitlab_docker.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/contained_executor.py
- src/toil/batchSystems/gridengine.py
- src/toil/batchSystems/htcondor.py
- src/toil/batchSystems/kubernetes.py
- src/toil/batchSystems/local_support.py
- src/toil/batchSystems/lsf.py
- src/toil/batchSystems/mesos/batchSystem.py
- src/toil/batchSystems/mesos/test/__init__.py
- src/toil/batchSystems/options.py
- src/toil/batchSystems/registry.py
- src/toil/batchSystems/singleMachine.py
- src/toil/batchSystems/slurm.py
- src/toil/batchSystems/torque.py
- src/toil/bus.py
- src/toil/common.py
- + src/toil/conftest.py
- src/toil/cwl/cwltoil.py
- src/toil/cwl/utils.py
- src/toil/deferred.py
- src/toil/fileStores/__init__.py
- src/toil/fileStores/abstractFileStore.py
- src/toil/fileStores/cachingFileStore.py
- src/toil/fileStores/nonCachingFileStore.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/fileJobStore.py
- src/toil/jobStores/googleJobStore.py
- src/toil/jobStores/utils.py
- src/toil/leader.py
- src/toil/lib/accelerators.py
- src/toil/lib/aws/__init__.py
- src/toil/lib/aws/ami.py
- src/toil/lib/aws/iam.py
- src/toil/lib/aws/s3.py
- src/toil/lib/aws/session.py
- src/toil/lib/aws/utils.py
- src/toil/lib/checksum.py
- src/toil/lib/compatibility.py
- src/toil/lib/conversions.py
- src/toil/lib/directory.py
- src/toil/lib/docker.py
- src/toil/lib/dockstore.py
- src/toil/lib/ec2.py
- src/toil/lib/ec2nodes.py
- src/toil/lib/exceptions.py
- src/toil/lib/expando.py
- src/toil/lib/ftp_utils.py
- src/toil/lib/generatedEC2Lists.py
- src/toil/lib/history.py
- src/toil/lib/history_submission.py
- src/toil/lib/io.py
- src/toil/lib/memoize.py
- src/toil/lib/misc.py
- src/toil/lib/pipes.py
- src/toil/lib/plugins.py
- src/toil/lib/resources.py
- src/toil/lib/retry.py
- src/toil/lib/threading.py
- src/toil/lib/throttle.py
- src/toil/lib/trs.py
- src/toil/lib/url.py
- src/toil/lib/web.py
- src/toil/options/common.py
- src/toil/options/cwl.py
- src/toil/options/runner.py
- src/toil/options/wdl.py
- src/toil/provisioners/__init__.py
- src/toil/provisioners/abstractProvisioner.py
- src/toil/provisioners/aws/__init__.py
- src/toil/provisioners/aws/awsProvisioner.py
- src/toil/provisioners/clusterScaler.py
- src/toil/provisioners/gceProvisioner.py
- src/toil/provisioners/node.py
- src/toil/realtimeLogger.py
- src/toil/resource.py
- src/toil/server/app.py
- src/toil/server/cli/wes_cwl_runner.py
- src/toil/server/utils.py
- src/toil/server/wes/abstract_backend.py
- src/toil/server/wes/amazon_wes_utils.py
- src/toil/server/wes/tasks.py
- src/toil/server/wes/toil_backend.py
- src/toil/server/wsgi_app.py
- src/toil/serviceManager.py
- src/toil/statsAndLogging.py
- src/toil/test/__init__.py
- src/toil/test/batchSystems/batchSystemTest.py
- src/toil/test/batchSystems/batch_system_plugin_test.py
- src/toil/test/batchSystems/test_slurm.py
- src/toil/test/cwl/conftest.py
- src/toil/test/cwl/cwlTest.py
- + src/toil/test/cwl/download_file_uri.json
- + src/toil/test/cwl/download_file_uri_no_hostname.json
- + src/toil/test/cwl/echo_string_and_fail.cwl
- 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/dockerTest.py
- src/toil/test/lib/test_ec2.py
- src/toil/test/lib/test_history.py
- src/toil/test/lib/test_trs.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/clusterScalerTest.py
- src/toil/test/provisioners/clusterTest.py
- + src/toil/test/server/safeFileTest.py
- src/toil/test/server/serverTest.py
- src/toil/test/sort/restart_sort.py
- src/toil/test/sort/sort.py
- src/toil/test/src/deferredFunctionTest.py
- src/toil/test/src/environmentTest.py
- src/toil/test/src/fileStoreTest.py
- src/toil/test/src/importExportFileTest.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/src/workerTest.py
- src/toil/test/utils/toilDebugTest.py
- src/toil/test/utils/toilKillTest.py
- src/toil/test/utils/utilsTest.py
- + src/toil/test/wdl/singularity/singularity.wdl
- src/toil/test/wdl/wdltoil_test.py
- src/toil/test/wdl/wdltoil_test_kubernetes.py
- src/toil/toilState.py
- src/toil/utils/toilDebugFile.py
- src/toil/utils/toilDebugJob.py
- src/toil/utils/toilLaunchCluster.py
- src/toil/utils/toilSshCluster.py
- src/toil/utils/toilStats.py
- src/toil/utils/toilStatus.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/b02ef8912f816d019c2955a4c4a5ea962624d3c6...f81ad2cc09ff41969aeaeddd79f4e7e7f8bb3718
--
View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/b02ef8912f816d019c2955a4c4a5ea962624d3c6...f81ad2cc09ff41969aeaeddd79f4e7e7f8bb3718
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