5.3.0

Changelog

CWL

• Run CWL conformance tests on Kubernetes. #3323
• CWL symlinking files into work directory #3445
• set resource reqs for all CWL_INTERNAL_JOBS #3442

WDL

• Add WDL flatten() function + tests. #3485
• Add WDL collect_by_key() function + tests. #3476
• Add WDL keys() function + tests. #3460
• Add WDL as_pairs() function + tests. #3364
• Add as_map() WDL function #3448
• Add basic WDL development support #3434
• Add basic WDL 1.0 support #3421
• Update dictionary structure in AnalyzeWDL. #3416

Misc

• Add extra context for disk usage warning. #3495
• Update developing.rst #3479
• Allow text/encode options for read and write functions in file store #3428
• Type hinting and mypy checking additions #3470 # #3458 #3456
• Quality of life improvements for cactus. #3463
• Add checklists for reviewing and merging PRs #3432
• Ensure that python3 and not python (2) is used #3446
• Support Kubernetes clusters in toil launch-cluster #3357
• Additional check for predecessors. #3417
• Allow setOptions to accept an argparse group. #3426

Bug Fixes

• AWS: Handle socket timeout during AWS discovery #3503
• Use back-up flatcar AMI if not found. #3513
• Lsf command parser #3475
• Retry on s3 throttling. #3504
• Stop deleting all ASGs with tags #3474
• Only determine execute permissions on files we copy/move. #3437
• cope with an invalid HTTP_PROXY #3447
• Fix failing Google jobstore test #3420
• Update Google job store #3412

Thank you to our contributors: @mr-c, @adamnovak, @w-gao, @jonathanxu18, Arthur Rand, @mberacochea, @Jessime, @thiagogenez, @julian-klode!