[Requirement] Scheduled daily dependency update on Thursday

[pyup-bot]

Update cwltool from 3.1.20230213100550 to 3.1.20230906142556.

Changelog

3.1.20230906142556

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

3.1.20230719185429

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

3.1.20230624081518

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

3.1.20230601100705

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

3.1.20230527103121

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

3.1.20230526180938

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

3.1.20230513155734

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

3.1.20230425144158

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

3.1.20230424211314

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

3.1.20230325110543

What's Changed
* Bump mypy from 1.0.1 to 1.1.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1817
* Executor clears any saved result when execute is called. by tetron in https://github.com/common-workflow-language/cwltool/pull/1813
* CWL exprs in ResourceRequirement fields can return floats in CWL v1.2+ by mr-c in https://github.com/common-workflow-language/cwltool/pull/1818
* Update rdflib requirement from <6.3,>=4.2.2 to >=4.2.2,<6.4 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1820
* guard `import pwd` for windows by jfennick in https://github.com/common-workflow-language/cwltool/pull/1822


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230302145532...3.1.20230325110543

3.1.20230302145532

What's Changed
* Raise error is socket is **not** available by BrunoGrandePhD in https://github.com/common-workflow-language/cwltool/pull/1809
* mypyc: enable subclassing and/or pickling of popular classes by mr-c in https://github.com/common-workflow-language/cwltoo/pull/1814

Misc
* ga: cleanups from actionlint by mr-c in https://github.com/common-workflow-language/cwltool/pull/1805
* ga: colorful output by mr-c in https://github.com/common-workflow-language/cwltool/pull/1807
* Bump mypy from 1.0.0 to 1.0.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1810
* Bump actions/cache from 2 to 3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1812

New Contributors
* BrunoGrandePhD made their first contribution in https://github.com/common-workflow-language/cwltool/pull/1809

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20230213100550...3.1.20230302145532

Links

• PyPI: https://pypi.org/project/cwltool
• Changelog: https://data.safetycli.com/changelogs/cwltool/
• Repo: https://github.com/common-workflow-language/cwltool

[codecov]

Codecov Report

Merging #556 (20c1a96) into master (f7be768) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #556   +/-   ##
=======================================
  Coverage   84.43%   84.43%           
=======================================
  Files          79       79           
  Lines       17637    17637           
  Branches     2674     2674           
=======================================
  Hits        14891    14891           
  Misses       2019     2019           
  Partials      727      727           

[pyup-bot]

Closing this in favor of #557