Bump cwltool from 3.1.20240708091337 to 3.1.20241112140730

[dependabot]

Bumps cwltool from 3.1.20240708091337 to 3.1.20241112140730.

Release notes

Sourced from cwltool's releases.

3.1.20241112140730

What's Changed

• use max_cores in taskQueue instead of system cores by @​kmavrommatis in common-workflow-language/cwltool#2038

• Use "run" with singularity/apptainer instead of "exec", when possible by @​sameeul in common-workflow-language/cwltool#2065

• add note on docker macOS platform issue by @​Brilator in common-workflow-language/cwltool#2064

• cpu_count can be None, so fallback to 1 by @​mr-c in common-workflow-language/cwltool#2063

• conformance testing: no longer skip tests for singularity/apptainer by @​mr-c in common-workflow-language/cwltool#2067

• cibuildwheel: adjust pytest parallel execution ; drop musllinux_1_1 by @​mr-c in common-workflow-language/cwltool#2061

Deps

• Update ruamel-yaml requirement from =0.16.0,<0.19 by @​dependabot in common-workflow-language/cwltool#2066
• Update flake8-bugbear requirement from <24.9 to <24.11 by @​dependabot in common-workflow-language/cwltool#2062

New Contributors

• @​Brilator made their first contribution in common-workflow-language/cwltool#2064
• @​kmavrommatis made their first contribution in common-workflow-language/cwltool#2038
• @​sameeul made their first contribution in common-workflow-language/cwltool#2065

Full Changelog: common-workflow-language/cwltool@3.1.20241024121129...3.1.20241112140730

3.1.20241024121129

From this release onwards, cwltool requires Python 3.9+

What's Changed

• Remove Python 3.8 support by @​mr-c in common-workflow-language/cwltool#2047
• Handle spurious ReceiveScatterOutput callbacks by @​GlassOfWhiskey in common-workflow-language/cwltool#2051
• prepare for future mypy release and enable --local-partial-types now by @​mr-c in common-workflow-language/cwltool#2052
• CI: build binary wheels by @​mr-c in common-workflow-language/cwltool#2059

Deps

• Bump sphinx-rtd-theme from 3.0.0 to 3.0.1 by @​dependabot in common-workflow-language/cwltool#2053
• Update black requirement from ~=24.8 to ==24.* by @​dependabot in common-workflow-language/cwltool#2050
• Bump mypy from 1.11.2 to 1.12.0 by @​dependabot in common-workflow-language/cwltool#2054
• Update rdflib requirement from =4.2.2,<7.2 by @​dependabot in common-workflow-language/cwltool#2055
• Bump mypy from 1.12.0 to 1.12.1 by @​dependabot in common-workflow-language/cwltool#2057
• Bump mypy from 1.12.1 to 1.13.0 by @​dependabot in common-workflow-language/cwltool#2058

Full Changelog: common-workflow-language/cwltool@3.1.20241007082533...3.1.20241024121129

3.1.20241007082533

What's Changed

• Updated outputMethod values by @​GlassOfWhiskey in common-workflow-language/cwltool#2042
• prepare for mypy 1.12 by @​mr-c in common-workflow-language/cwltool#2046

Deps

• remove usage of ancient shellescape backport of Stdlib's shlex by @​a-detiste in common-workflow-language/cwltool#2041
• setuptools is not a install requirement by @​mr-c in common-workflow-language/cwltool#2048
• Bump sphinx-rtd-theme from 2.0.0 to 3.0.0 by @​dependabot in common-workflow-language/cwltool#2049

... (truncated)

Commits

• c3c92eb conformances testing: no longer skip tests for singularity/apptainer
• 1557c8d Use "run" with singularity/apptainer instead of "exec", when possible
• 048eb55 use max_cores in taskQueue instead of system cores (#2038)
• 0b64935 Update ruamel-yaml requirement from <0.18,>=0.16.0 to >=0.16.0,<0.19 (#2066)
• ee30368 add note on docker platform issue (#2064)
• 9cda157 cpu_count can be None, so fallback to 1
• d810958 Update flake8-bugbear requirement from <24.9 to <24.11
• 6cfef62 binary wheels: only build on main and other optimizations
• e3f6cf7 build binary wheels
• 8dee8e9 Bump mypy from 1.12.1 to 1.13.0 (#2058)
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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 71.11%. Comparing base (9a3ab42) to head (ad36a0d).
Report is 1 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #591      +/-   ##
==========================================
+ Coverage   71.08%   71.11%   +0.02%     
==========================================
  Files          88       88              
  Lines       11131    11131              
  Branches     1936     1936              
==========================================
+ Hits         7913     7916       +3     
+ Misses       2770     2768       -2     
+ Partials      448      447       -1     

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