Draft Changelog

The following items should be added to the changelog for the next Toil release, at which point the list should be cleared. Add new items at the bottom:

Version 7.x Draft

Changelog

Highlighted Features Added

• toil debug-job now has --retrieveTaskDirectory <dir> which will set up a job's downloaded files under <dir> and try to stop the job after doing the downloads. Jobs can call self.files_downloaded_hook() to provide a stopping point for this mode. (#4815)
• toil debug-job can now reconstruct the inside-the-container environment for CWL and WDL tasks. (#4815)
• Added support for caching on Slurm and other HPC schedulers (#4775)
• Replace all instances of boto2 with boto3 for all Toil AWS code (#4718)
• Add support for Python 3.12 (#4718)
• Ceph input/output errors from file locking functions are now tolerated. (#4874)
• Toil now uses flock to enable directory locks to work properly (#4924)
• Added support to get Slurm partitions and automatically send jobs to GPUs on Slurm (#4833) (supports both CWL and WDL)

Breaking Changes

CWL

• Prevent simultaneous Singularity container pulls in toil-cwl-runner (#4990)

WDL

• Update WDL conformance tests on CI (#4875)
• Added support to run task only WDL files (#4960)
• Added support for the gpu field in WDL (#4949)
• Support passing inputs into toil-wdl-runner for task only WDLs (#4977)
• toil-wdl-runner will now carry through task exit codes (#4978)
• toil-wdl-runner will respect explicit null values for optional inputs (#4981)
• toil-wdl-runner will not immediately error on nonexistent coerced files until outputted (#4994)
• File? type for string to file coercion is now supported (will be nullified)

Kubernetes

Dependencies

Misc

• Makefile: use isolated builds, add dist target (sdist+wheel) and deprecate the sdist target. (#4820) (#4826)
• Toil will now wait --jobStoreTimeout seconds (default: 30) to see an update to/removal of a job that was run, and will not let the job succeed unless it is seen to make progress. (#3814)
• Toil job descriptions no longer have a command field, and we track the link to the job body and the command to invoke the Toil worker separately. (#4811)
• Several typos in the docs were fixed (#4889)
• Add a test to ensure batchsystem plugins are installable (#4879)
• Fix Toil utils to work without the AWS extra (#4953)
• Print commit hash with toil --version when installed from source. Before: 7.1.0a1. After: 7.1.0a1-ccf57e6071e32675daabdcbacb91988e871745a9 (#4954)
• Fixed a broken URL and an omitted variable in CI tests (#4974)
• Generate default config correctly (#5014)
• Use the latest setuptools when running cactus. (#5017)

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