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 9.3 Draft

Changelog

Highlighted Features Added

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

Breaking Changes

CWL

WDL

Kubernetes

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)
• --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)

Thank you to our contributors: