5.6.0

Changelog

Highlighted Features Added

• Integrate ARM Docker builds to make multi-arch images. (#3802)
• WES support and server mode. (#3779)
• TES batch system prototype. (#3821)
• Support for new resource syntax in PBSPro. (#3048)
• Toil now looks for lost jobs every minute instead of every hour (#3948)

Breaking Changes

• Remove --disableCaching's true/false argument. (#3869)

CWL

• CWL helper jobs: better disk & memory requirements. (#3834)
• CWL: safer test path generation for post-install testing. (#3818)
• More detailed names, which show up in job names sent to BatchSystem schedulers. #3941 (was #3893)
• If you use scatter and collect files, duplicates are correctly dealt with and renamed. (#3968)
• CWL: at the end of a job, ask cwltool to cleanup (#3965)

Kubernetes

• Assign Kubernetes jobs an explicit TTL. (#3936)
• Wait for node creation. (#3934)

Dependencies

• Enable Dependabot updates. (#3827)
• Multiple consolidated dependabot updates. (#3851)
• Update addict requirement from <2.3,>=2.2.1 to >=2.2.1,<2.5. (#3861)
• Bump cwltool to 3.1.20211107152837. (#3833 #3866 #3909)
• Bump cwltest from 2.1.20210626101542 to 2.2.20210901154959. (#3848)
• Bump flake8 from 3.8.4 to 4.0.1. (#3847)
• Allow more docker-py versions. (#3860)
• Remove pyyaml dependency. (#3858)

Misc

• Update cleanup script. (#3937)
• Remove use of sys.maxsize. (#3824)
• Spelling fixes. (#3814)
• Add codeql-analysis for Python. (#3825)
• Update jobstore function names. (#3809)
• Move AMI functions to lib. (#3810)
• Add "make pyupgrade" (py36-plus). (#3805)
• Type hints. (#3930)
• Coalesce status calls in slurm. (#3822)
• Python logging takes format values as *args. (#3852)
• Change quick test to a 10 minute timeout. (#3843)
• Add make uninstall to makefile. (#3883)
• Fix toil kill to find shared pid.log file (with unit test). #3941 (was #3932)
• Update documentation. (#3947)

• Remove remains of Travis. (#3976)

Bug Fixes

• Stop checkpoints from being reissued multiple times. (#3931)
• Don't consult LSF config when explicitly defining memory units. (#3820)
• Robustly remove state dirs. (#3836)
• Fix exception checking for exit_code. (#3830)
• Use exitStatus instead of exitReason for batch exit type comparison. (#3839)
• Update cwltest to improve K8 runs. (#3935)
• Consolidated CI Fixes. (#3887)
• Fix CWL conformance tests. (#3891)
• Toil-managed cluster scaling should work again with --metrics. (#3943)

Thank you to our contributors: @mr-c, @adamnovak, @w-gao, @jonathanxu18, @Hexotical, @tmooney, @nikhil, @kannon92, @douglowe, @mhpopescu, @Phhere, and @gmloose!