3.1.20230127121939

What's Changed

• Keep track of which files have already been parsed by @tetron in #1786
• Move sys.exit by @jfennick in #1772
• --write-summary to redirect final JSON output by @jfennick in #1773

misc

• Update README and other documentation cleanup by @mr-c in #1778
• Dockerfile: Security upgrade python from 3.10-alpine to 3.11-alpine by @snyk-bot in #1781
• conformance testing: switch to pytest + cwltest by @mr-c in #1783
• [doc] Add autolabels so intersphinx can link to anchors like index#install by @kinow in #1787
• flake8 cleanup by @mr-c in #1791

Full Changelog: 3.1.20221201130942...3.1.20230127121939

3.1.20221201130942

What's Changed

• support podman even when not installed as "docker" alias by @mr-c in #1769

Thanks to @sdruskat for championing the podman issue!

• trim mypy.ini by @mr-c in #1762
• Bump mypy from 0.990 to 0.991 by @dependabot in #1763
• upload to codecov using the token by @mr-c in #1764
• GA quay.io deploy: cache container layers by @mr-c in #1768

Full Changelog: 3.1.20221109155812...3.1.20221201130942

3.1.20221109155812

What's Changed

• udocker: use --nobanner as well by @mr-c in #1761

Full Changelog: 3.1.20221108205138...3.1.20221109155812

3.1.20221108205138

What's Changed

• Fix '--make-template' for union types by @tom-tan in #1760

misc

• upgrade udocker test to v1.3.5 by @mr-c in #1756
• Update pytest requirement from <7.2,>=6.2 to >=6.2,<7.3 by @dependabot in #1757
• Bump mypy from 0.982 to 0.990 by @dependabot in #1759

Full Changelog: 3.1.20221018083734...3.1.20221108205138

3.1.20221018083734

What's Changed

• link to loops docs by @mr-c in #1749
• allow mypy process type to be used as by interpreted subclasses by @fmigneault in #1746

New Contributors

• @fmigneault made their first contribution in #1746

Full Changelog: 3.1.20221008225030...3.1.20221018083734

3.1.20221008225030

What's new

• implement the loop construct extension by @GlassOfWhiskey and @mr-c in #1641

Misc

• Add QEMU step and platforms field to the publish action for Arm Docker image by @suecharo in #1736
• quay: publish ":latest" tag by @mr-c in #1737
• Bump mypy from 0.971 to 0.982 by @dependabot in #1739 #1747
• test with Python 3.11 by @mr-c in #1742

Full Changelog: 3.1.20220913185150...3.1.20221008225030

3.1.20220913185150

What's Changed

• notifyAll → notify_all: deprecated in Python 3.x; not even listed in the docs. by @mr-c in #1734
• Experimental fast validator code path, using cwl-utils by @tetron in #1720
• conformance coverage: ignore more paths by @mr-c in #1735

Full Changelog: 3.1.20220907141119...3.1.20220913185150

3.1.20220907141119

What's Changed

• upgrade jshint to version 2.13.5 by @mr-c in #1729
• Workflow checker: ignore 'null' when comparing arrays of types by @mr-c in #1721
• Handle relative paths and locations in cwl.output.json by @tetron in #1732

Full Changelog: 3.1.20220830195442...3.1.20220907141119

3.1.20220830195442

What's Changed

• fixed --beta-use-biocontainers by @mr-c in #1724

• Provenance: fix bagit structure when there are no data files by @simleo in #1727

• Fix codespell issues by @kinow in #1715

• tidy up rdflib type hints by @mr-c in #1702

• Import dependencies from cwl_utils after code refactoring by @GlassOfWhiskey in #1686

• remove some psutil type ignores by @mr-c in #1707

• Update .gitignore by @jjkoehorst in #1711

• Update CONTRIBUTING.md by @jjkoehorst in #1712

• remove old cruft by @mr-c in #1716

• tests: reduce number of software containers by @mr-c in #1718

• Import check_format from cwl-utils by @GlassOfWhiskey in #1717

• 22.x1 release of galaxy-tool-util breaks us by @mr-c in #1723

• improve test running on mac-os by @mr-c in #1710

• CONTRIBUTING.md: recommend updating pip in the dev venv by @simleo in #1726

New Contributors

• @GlassOfWhiskey made their first contribution in #1686
• @jjkoehorst made their first contribution in #1711

Full Changelog: 3.1.20220802125926...3.1.20220830195442

3.1.20220802125926

What's Changed

• include ruamel.yaml in the mypy reqs & fix/test container build by @mr-c in #1701

Full Changelog: 3.1.20220801180230...3.1.20220802125926