Cwltool

What's Changed
* use max_cores in taskQueue instead of system cores by kmavrommatis in https://github.com/common-workflow-language/cwltool/pull/2038
* Use "run" with singularity/apptainer instead of "exec", when possible by sameeul in https://github.com/common-workflow-language/cwltool/pull/2065
* add note on docker macOS platform issue by Brilator in https://github.com/common-workflow-language/cwltool/pull/2064

* cpu_count can be None, so fallback to 1 by mr-c in https://github.com/common-workflow-language/cwltool/pull/2063
* conformance testing: no longer skip tests for singularity/apptainer by mr-c in https://github.com/common-workflow-language/cwltool/pull/2067
* cibuildwheel: adjust pytest parallel execution ; drop musllinux_1_1 by mr-c in https://github.com/common-workflow-language/cwltool/pull/2061


Deps
* Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2066
* Update flake8-bugbear requirement from <24.9 to <24.11 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2062

New Contributors
* Brilator made their first contribution in https://github.com/common-workflow-language/cwltool/pull/2064
* kmavrommatis made their first contribution in https://github.com/common-workflow-language/cwltool/pull/2038
* sameeul made their first contribution in https://github.com/common-workflow-language/cwltool/pull/2065

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20241024121129...3.1.20241112140730

From this release onwards, `cwltool` requires Python 3.9+

What's Changed
* Remove Python 3.8 support by mr-c in https://github.com/common-workflow-language/cwltool/pull/2047
* Handle spurious `ReceiveScatterOutput` callbacks by GlassOfWhiskey in https://github.com/common-workflow-language/cwltool/pull/2051
* prepare for future mypy release and enable --local-partial-types now by mr-c in https://github.com/common-workflow-language/cwltool/pull/2052
* CI: build binary wheels by mr-c in https://github.com/common-workflow-language/cwltool/pull/2059

Deps
* Bump sphinx-rtd-theme from 3.0.0 to 3.0.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2053
* Update black requirement from ~=24.8 to ==24.* by dependabot in https://github.com/common-workflow-language/cwltool/pull/2050
* Bump mypy from 1.11.2 to 1.12.0 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2054
* Update rdflib requirement from <7.1,>=4.2.2 to >=4.2.2,<7.2 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2055
* Bump mypy from 1.12.0 to 1.12.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2057
* Bump mypy from 1.12.1 to 1.13.0 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2058

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20241007082533...3.1.20241024121129

What's Changed
* Updated `outputMethod` values by GlassOfWhiskey in https://github.com/common-workflow-language/cwltool/pull/2042
* prepare for mypy 1.12 by mr-c in https://github.com/common-workflow-language/cwltool/pull/2046

Deps
* remove usage of ancient shellescape backport of Stdlib's shlex by a-detiste in https://github.com/common-workflow-language/cwltool/pull/2041
* setuptools is not a install requirement by mr-c in https://github.com/common-workflow-language/cwltool/pull/2048
* Bump sphinx-rtd-theme from 2.0.0 to 3.0.0 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2049

New Contributors
* a-detiste made their first contribution in https://github.com/common-workflow-language/cwltool/pull/2041

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20240909164951...3.1.20241007082533

What's Changed
* cwl v1.3.0-dev1 native loop support by GlassOfWhiskey in https://github.com/common-workflow-language/cwltool/pull/1779
* Start running the draft CWL v1.3.0 conformance tests by mr-c in https://github.com/common-workflow-language/cwltool/pull/2022
* Conformance testing, skip a bad cwltest release by mr-c in https://github.com/common-workflow-language/cwltool/pull/2017
* Added new loop test by LanderOtto in https://github.com/common-workflow-language/cwltool/pull/2006
* removing duplicate "reference" by danielskatz in https://github.com/common-workflow-language/cwltool/pull/2030
* Support array of integers and floats as command argument parameters by tom-tan in https://github.com/common-workflow-language/cwltool/pull/2037
* Explicitly support Python 3.13; add to CI matrix by mr-c in https://github.com/common-workflow-language/cwltool/pul
* fix `loadContents` for `File[]` by fmigneault in https://github.com/common-workflow-language/cwltool/pull/2036

Deps
* Requires schema-salad >=8.7 for MapSchema validation by tetron in https://github.com/common-workflow-language/cwltool/pull/2024
* skip pydot 3.x+ for now by mr-c in https://github.com/common-workflow-language/cwltool/pull/2020
* Update pytest requirement from <8.3,>=6.2 to >=6.2,<8.4 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2025
* Bump mypy from 1.10.1 to 1.11.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2028
* Bump mypy from 1.11.1 to 1.11.2 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2035
* Update black requirement from ~=24.4 to ~=24.8 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2029
* Update flake8-bugbear requirement from <24.3 to <24.9 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2032
l/2040



New Contributors
* danielskatz made their first contribution in https://github.com/common-workflow-language/cwltool/pull/2030

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20240708091337...3.1.20240909164951

What's Changed
* Support Podman version 5.x which autodeletes the cidfiles by mr-c in https://github.com/common-workflow-language/cwltool/pull/2016
* Use uv compatible syntax in test-requirements.txt by hauntsaninja in https://github.com/common-workflow-language/cwltool/pull/2012
* Add docstrings to functions in `ro.py` by AGoetzee in https://github.com/common-workflow-language/cwltool/pull/2002

Deps
* Update black requirement from ~=24.3 to ~=24.4 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1992
* Bump docker/build-push-action from 5 to 6 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2008
* Update galaxy-util requirement from <24.1 to <24.2 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2015
* Bump mypy from 1.10.0 to 1.10.1 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2009
* Update galaxy-tool-util requirement from !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,<24.1,>=22.1.2 to !=23.0.1,!=23.0.2,!=23.0.3,!=23.0.4,!=23.0.5,>=24.1.1,<24.2 by dependabot in https://github.com/common-workflow-language/cwltool/pull/2014

New Contributors
* AGoetzee made their first contribution in https://github.com/common-workflow-language/cwltool/pull/2002
* hauntsaninja made their first contribution in https://github.com/common-workflow-language/cwltool/pull/2012

**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20240508115724...3.1.20240708091337

What's Changed
* Replace .decode method with str(bytes, "utf-8") by tetron in https://github.com/common-workflow-language/cwltool/pull/1998
* Update paths for the CWL v1.2 conformance tests now that 1.2.1 has been released. by mr-c in https://github.com/common-workflow-language/cwltool/pull/1993
* build now uses the module name by mr-c in https://github.com/common-workflow-language/cwltool/pull/1997
* Update pytest requirement from <8.2,>=6.2 to >=6.2,<8.3 by dependabot in https://github.com/common-workflow-language/cwltool/pull/1996
* patch dockerFile build by misterbrandonwalker in https://github.com/common-workflow-language/cwltool/pull/1979


**Full Changelog**: https://github.com/common-workflow-language/cwltool/compare/3.1.20240404144621...3.1.20240508115724