Cwltool

What's Changed
* upgrade jshint to version 2.13.5 by mr-c in https://github.com/common-workflow-language/cwltool/pull/1729
* Workflow checker: ignore 'null' when comparing arrays of types by mr-c in https://github.com/common-workflow-language/cwltool/pull/1721
* Handle relative paths and locations in cwl.output.json by tetron in https://github.com/common-workflow-language/cwltool/pull/1732


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20220830195442...3.1.20220907141119

What's Changed
* fixed --beta-use-biocontainers by mr-c in https://github.com/common-workflow-language/cwltool/pull/1724
* Provenance: fix bagit structure when there are no data files by simleo in https://github.com/common-workflow-language/cwltool/pull/1727
* Fix codespell issues by kinow in https://github.com/common-workflow-language/cwltool/pull/1715

* tidy up rdflib type hints by mr-c in https://github.com/common-workflow-language/cwltool/pull/1702
* Import dependencies from cwl_utils after code refactoring by GlassOfWhiskey in https://github.com/common-workflow-language/cwltool/pull/1686
* remove some psutil type ignores by mr-c in https://github.com/common-workflow-language/cwltool/pull/1707
* Update .gitignore by jjkoehorst in https://github.com/common-workflow-language/cwltool/pull/1711
* Update CONTRIBUTING.md by jjkoehorst in https://github.com/common-workflow-language/cwltool/pull/1712
* remove old cruft by mr-c in https://github.com/common-workflow-language/cwltool/pull/1716
* tests: reduce number of software containers by mr-c in https://github.com/common-workflow-language/cwltool/pull/1718
* Import check_format from cwl-utils by GlassOfWhiskey in https://github.com/common-workflow-language/cwltool/pull/1717
* 22.x1 release of galaxy-tool-util breaks us by mr-c in https://github.com/common-workflow-language/cwltool/pull/1723
* improve test running on mac-os by mr-c in https://github.com/common-workflow-language/cwltool/pull/1710
* CONTRIBUTING.md: recommend updating pip in the dev venv by simleo in https://github.com/common-workflow-language/cwltool/pull/1726


New Contributors
* GlassOfWhiskey made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1686
* jjkoehorst made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1711

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20220802125926...3.1.20220830195442

What's Changed
* include ruamel.yaml in the mypy reqs & fix/test container build by mr-c in https://github.com/common-workflow-language/cwltool/pull/1701


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20220801180230...3.1.20220802125926

What's Changed
* Ignore flake8-bugbear false positives by mr-c in https://github.com/common-workflow-language/cwltool/pull/1691
* logging.warn is deprecated, use warning by kinow in https://github.com/common-workflow-language/cwltool/pull/1692
* Exclude children of subdirectories from symlink by jfennick in https://github.com/common-workflow-language/cwltool/pull/1690
* Set last modification date of remote file as local file timestamp by RenskeW in https://github.com/common-workflow-language/cwltool/pull/1676
* Bump mypy from 0.961 to 0.971 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1697
* Update rdflib requirement from <6.2,>=4.2.2 to >=4.2.2,<6.3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1698
* MyPy stubs rename by mr-c in https://github.com/common-workflow-language/cwltool/pull/1699

New Contributors
* jfennick made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1690

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20220628170238...3.1.20220801180230

What's Changed
* Prevent the default value from being used when values were already passed by kinow in https://github.com/common-workflow-language/cwltool/pull/1675
* Expressiontool timer by douglowe in https://github.com/common-workflow-language/cwltool/pull/1681
* Bump actions/setup-python from 3 to 4 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1679

New Contributors
* douglowe made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1681

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20220607081835...3.1.20220623174452

What's Changed
* Enhanced detection of singularity version including a distribution detection by salexan2001 in https://github.com/common-workflow-language/cwltool/pull/1654
* Fix udocker installation link by kinow in https://github.com/common-workflow-language/cwltool/pull/1667
* [fix py3.6 compat](https://github.com/common-workflow-language/cwltool/commit/2be19f3291f07653013b0a91662f518c33cf9fe4)mr-c

Deps
* Bump docker/login-action from 1 to 2 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1663
* Bump docker/setup-buildx-action from 1 to 2 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1662
* Bump docker/build-push-action from 2 to 3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1661
* Bump mypy from 0.950 to 0.960 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1670
* Bump mypy from 0.960 to 0.961 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1677

New Contributors
* salexan2001 made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1654

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20220502060230...3.1.20220607081835