Cwltool

What's Changed
* Ensure that files with identical basenames get staged to unique paths by mr-c in https://github.com/common-workflow-language/cwltool/pull/1853


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230527103121...3.1.20230601100705

What's Changed
* synchronize setup.py & requirements.txt by mr-c in https://github.com/common-workflow-language/cwltool/pull/1848
(fixes missing dependency on `importlib_resources` and `importlib_metadata`; also drop dependency on the `bagit` library library which is only used in the tests)

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230526180938...3.1.20230527103121

What's Changed
* CWLProv snapshots: capture the workflow even if the cwl:tool trick in the input object is used by mr-c in https://github.com/common-workflow-language/cwltool/pull/1847

* Refactoring provenance.py as provenance submodule by RenskeW in https://github.com/common-workflow-language/cwltool/pull/1775
* use importlib instead of the deprecated pkg_resources by mr-c in https://github.com/common-workflow-language/cwltool/pull/1844
* Bump sphinx-rtd-theme from 1.2.0 to 1.2.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1845
* Update ruamel-yaml requirement from <0.17.27,>=0.16.0 to >=0.16.0,<0.17.28 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1846


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230513155734...3.1.20230526180938

What's Changed
* Update ruamel-yaml requirement from <0.17.22,>=0.16.0 to >=0.16.0,<0.17.27 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1838
* --leave-tmpdir includes the input staging directories by mr-c in https://github.com/common-workflow-language/cwltool/pull/1674 https://github.com/common-workflow-language/cwltool/pull/1840
* Bump mypy from 1.2.0 to 1.3.0 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1839


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230425144158...3.1.20230513155734

What's Changed
* Bump mypy from 1.1.1 to 1.2.0 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1825


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230425122939...3.1.20230425144158

What's Changed
* always print floats on the command line with decimal notation by mr-c in https://github.com/common-workflow-language/cwltool/pull/1832
* Better error message when parsing hints in the upgrader by mr-c in https://github.com/common-workflow-language/cwltool/pull/1830

Misc

* synchronize reqs. by mr-c in https://github.com/common-workflow-language/cwltool/pull/1823
* Update black requirement from ~=23.1 to ~=23.3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1824
* Update pytest requirement from <7.3,>=6.2 to >=6.2,<7.4 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1826


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230325110543...3.1.20230424211314