9.3.0

Highlighted Features Added

• Toil now supports singularity:// and file:// protocols in container in WDL, to load SIF image files by path. (#5435)

CWL

• CWL conformance badge in the README should no longer be a broken image link (#5417)
• CWL conformance page now has working badges (#5417)
• toil-cwl-runner now has the --rm-tmpdir and --leave-tmpdir options that feed through to cwltool. (Note that when not bypassing the file store, CWL temp files in per-job directories will still be subject to Toil-level cleanup.) (#5226)

Dependencies

• Update kubernetes requirement from <34,>=12.0.1 to >=12.0.1,<36 (#5437)
• Update dill requirement from <0.4,>=0.3.2 to >=0.3.2,<0.5 (#5438)

Misc

• threading: use psutil to calculate CPU affinitity size, which adds Windows & FreeBSD support (#5416)
  • Note that Toil overall still likely does not work on Windows and is not under test on FreeBSD.
• --slurmTime now understands all time formats Slurm does, and doesn't silently mistake days for hours. (#5433)
• Python workflows can now rename Toil's --config option by passing config_option to getDefaultArgumentParser() and friends. (#5420)
• Toil no longer (repeatedly) duplicates PATH entries when applying environment variables for jobs (#5425)
• Toil server mode should no longer be able to read partially-written state data. Workflows will no longer be reported as RUNNINGIZING, as fun as that sounds for them. (#5447)
• Toil retry job logic now has an exponential backoff delay, controlled by --retryBackoffSeconds (default 2) and --retryBackoffFactor (default 3). (#5452)
• Updating files in the job store by stream is now atomic: either the stream writer succeeds and the new content is visible, or something goes wrong and the old content is visible (#5456)
• job.py now has (mostly synthetic) type hints (#5462)

Thank you to our contributors:
@mr-c, @mnijhuis-tos, and @adamnovak