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 - - - - - 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 - - - - - 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. - - - - - 0291785e by Michael R. Crusoe at 2025-10-11T09:13:42+02:00 Refreshed patches. - - - - - 90699085 by Michael R. Crusoe at 2025-10-11T13:04:45+02:00 d/control: needs pytest-httpserver for a new test. - - - - - 6d065612 by Michael R. Crusoe at 2025-10-11T13:05:10+02:00 release to unstable - - - - - 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 -- View it on GitLab: https://salsa.debian.org/med-team/toil/-/compare/346681165811740b5450c223974948224532ca0e...6d065612fa14633e61ae88a37827a2864a71806c You're receiving this email because of your account on salsa.debian.org.
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