[med-svn] [Git][med-team/toil][master] 12 commits: New upstream version 9.2.0

Thu Apr 16 14:15:14 BST 2026

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

Commits:
a78392a7 by Michael R. Crusoe at 2026-04-16T10:12:37+02:00
New upstream version 9.2.0
- - - - -
139ff3de by Michael R. Crusoe at 2026-04-16T10:13:05+02:00
Update upstream source from tag 'upstream/9.2.0'

Update to upstream version '9.2.0'
with Debian dir ad3d89414d917a2834cc722d51c26fe068da882d
- - - - -
62191bbb by Michael R. Crusoe at 2026-04-16T10:22:17+02:00
New upstream version.

- - - - -
80d05d91 by Michael R. Crusoe at 2026-04-16T10:22:42+02:00
Refreshed patches, removing 3 not-needed or applied upstream.

- - - - -
6ac2888b by Michael R. Crusoe at 2026-04-16T10:22:43+02:00
d/control: build-dep & recommend python3-galaxy-tool-util.

- - - - -
80ff8d89 by Michael R. Crusoe at 2026-04-16T10:40:41+02:00
New upstream version

- - - - -
f81ad2cc by Michael R. Crusoe at 2026-04-16T10:40:43+02:00
New upstream version 9.3.0
- - - - -
5fd7ea97 by Michael R. Crusoe at 2026-04-16T10:41:10+02:00
Update upstream source from tag 'upstream/9.3.0'

Update to upstream version '9.3.0'
with Debian dir 25e0b7d9dddc832ddd029957d04a900f8bc17ac7
- - - - -
1b7c634e by Michael R. Crusoe at 2026-04-16T10:41:11+02:00
Standards-Version: 4.7.4 (routine-update)

- - - - -
f56d95de by Michael R. Crusoe at 2026-04-16T10:44:22+02:00
Refreshed patches

- - - - -
a39d32ac by Michael R. Crusoe at 2026-04-16T14:55:49+02:00
Cherry-picked patch from upstream for newer cwltool & cwl-utils.

- - - - -
0d4c478d by Michael R. Crusoe at 2026-04-16T15:14:15+02:00
release to unstable

- - - - -

191 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
- debian/changelog
- debian/control
- + debian/patches/0001-upgrade-typing.patch
- debian/patches/accept_debian_packaged_docker_version.patch
- debian/patches/allow_newer_requests
- debian/patches/fix_tests
- − debian/patches/no_galaxy_lib
- − debian/patches/remove_pytest-subtests.patch
- debian/patches/series
- debian/patches/setting_version.patch
- debian/patches/soften-cwltool-dep.patch
- debian/patches/soften-mesos-deps
- − debian/patches/spelling
- 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/96b778d5aa37093e7d6e2c1e4dcae5bf968d8107...0d4c478d1b7863008f7609c1684a71c3f44102f1

-- 
View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/96b778d5aa37093e7d6e2c1e4dcae5bf968d8107...0d4c478d1b7863008f7609c1684a71c3f44102f1
You're receiving this email because of your account on salsa.debian.org.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20260416/bf3f99cc/attachment-0001.htm>