Cwltool

What's Changed
* fix the pickling error for IO objects by ndonyapour in https://github.com/common-workflow-language/cwltool/pull/1929
* gh-actions: record version before building container to publish to quay.io by mr-c in https://github.com/common-workflow-language/cwltool/pull/1931


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20231020113452...3.1.20231020140205

What's Changed
* temporarily downgrade galaxy-tool-util to workaround issue with newer conda by mr-c in https://github.com/common-workflow-language/cwltool/pull/1930

Deps
* Bump mypy from 1.6.0 to 1.6.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1927
* Update black requirement from ~=23.9 to ~=23.10 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1926


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20231016170136...3.1.20231020113452

What's Changed

* No longer supporting Python 3.7 by mr-c in https://github.com/common-workflow-language/cwltool/pull/1901
* guard `import fcntl` for windows by jfennick in https://github.com/common-workflow-language/cwltool/pull/1914
* extend validation to the inputs of the top level proces by mr-c in https://github.com/common-workflow-language/cwltool/pull/1915
* silence spurious warning when validating some documents with "cwltool" extensions by mr-c in https://github.com/common-workflow-language/cwltool/pull/1921
* job loading: allow inputs named "id" by mr-c in https://github.com/common-workflow-language/cwltool/pull/1923

Deps
* Update galaxy-tool-util requirement from <23,>=22.1.2 to >=22.1.2,<24 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1859
* Update black requirement from ~=23.7 to ~=23.9 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1902
* Update flake8-bugbear requirement from <23.8 to <23.10 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1909
* Bump docker/build-push-action from 4 to 5 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1904
* Bump docker/setup-buildx-action from 2 to 3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1905
* Bump docker/setup-qemu-action from 2 to 3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1906
* Bump docker/login-action from 2 to 3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1907
* Bump mypy from 1.3.0 to 1.6.0 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1862
* Remove packaging requirement by dependabot in https://github.com/common-workflow-language/cwltool/pull/1917
* Update black requirement from ~=22.0 to ~=23.9 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1918
* default to testing with Python 3.12 by mr-c in https://github.com/common-workflow-language/cwltool/pull/1919

Misc
* switch to setuptools_scm by mr-c in https://github.com/common-workflow-language/cwltool/pull/1920
* release: fix target name by mr-c in https://github.com/common-workflow-language/cwltool/pull/1924
* release: set version via SCM variable by mr-c in https://github.com/common-workflow-language/cwltool/pull/1925


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230906142556...3.1.20231016170136

What's Changed

Dropped Python 3.6 support, brought back Python 3.7 support for this release only
Python 3.12 is now supported

* Fixed race condition which happens when a job runs "too fast", by jmfernandez in https://github.com/common-workflow-language/cwltool/pull/1890
* Propery locate podman images by jmfernandez in https://github.com/common-workflow-language/cwltool/pull/1891
* add cudaDeviceCount flag to the request requirements by ndonyapour in https://github.com/common-workflow-language/cwltool/pull/1895
* use nonlocal mem_tn variable by jfennick in https://github.com/common-workflow-language/cwltool/pull/1896
* start testing with Python 3.12 by mr-c in https://github.com/common-workflow-language/cwltool/pull/1882
* py version support policy, RHEL: only track full support releases by mr-c in https://github.com/common-workflow-language/cwltool/pull/1881
* Cope with narrower terminal by mr-c in https://github.com/common-workflow-language/cwltool/pull/1893
* release testing tweaks by mr-c in https://github.com/common-workflow-language/cwltool/pull/1900
* add back in Python 3.7 for one last release by mr-c in https://github.com/common-workflow-language/cwltool/pull/1898


Deps
* Update rdflib requirement from <6.4,>=4.2.2 to >=4.2.2,<7.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1880
* Bump sphinx-rtd-theme from 1.2.2 to 1.3.0 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1892
* bump minimum required schema_salad version to reflect reality. by mr-c in https://github.com/common-workflow-language/cwltool/pull/1894
* Bump actions/checkout from 3 to 4 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1897


New Contributors
* ndonyapour made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1895

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230719185429...3.1.20230906142556

What's Changed

Python 3.7 is no longer a supported version of Python (though it still likely works).

* Update Python version support document; drop Python 3.7 (EOL) by mr-c in https://github.com/common-workflow-language/cwltool/pull/1872

Fixes
* required outputs with secondaryFiles fix for containers by mr-c in https://github.com/common-workflow-language/cwltool/pull/1870
* enable pickling of cwltool.workflow.Workflow by mr-c in https://github.com/common-workflow-language/cwltool/pull/1878

Misc
* requirements.txt; remove spaces to enable re-use in other contexts by mr-c in https://github.com/common-workflow-language/cwltool/pull/1867
* confirm that enhanced TypeDSL from schema-salad 1.3 doesn't change CWL v1.2 by mr-c in https://github.com/common-workflow-language/cwltool/pull/1868
* Update flake8-bugbear requirement from <23.7 to <23.8 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1877
* Update black requirement from ~=23.3 to ~=23.7 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1876



**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230624081518...3.1.20230719185429

What's Changed
* pass through QEMU_LD_PREFIX by default by mr-c in https://github.com/common-workflow-language/cwltool/pull/1849
* dockerfile: pin graphviz to before 8.x by mr-c in https://github.com/common-workflow-language/cwltool/pull/1863

Misc
* Remove deprecated use of Pathlib.Path as a context-mananger by mr-c in https://github.com/common-workflow-language/cwltool/pull/1854
* gh-actions: keep running even if codecov upload fails by mr-c in https://github.com/common-workflow-language/cwltool/pull/1857

Deps
* Update ruamel-yaml requirement from <0.17.28,>=0.16.0 to >=0.16.0,<0.17.32 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1852
* Update flake8-bugbear requirement from <23.6 to <23.7 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1856
* Bump sphinx-rtd-theme from 1.2.1 to 1.2.2 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1858
* Update pytest requirement from <7.4,>=6.2 to >=6.2,<7.5 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1864

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230601100705...3.1.20230624081518