Bump cwltool from 3.1.20250925164626 to 3.1.20251031082601

[dependabot]

Bumps cwltool from 3.1.20250925164626 to 3.1.20251031082601.

Release notes

Sourced from cwltool's releases.

3.1.20251031082601

Python 3.9

This is the last release of cwltool with Python 3.9 support, as per our Python support version policy.

What's Changed

• 2X faster startup, defer galaxy-* imports to when needed by @​mr-c in common-workflow-language/cwltool#2155
• support Pydot versions before 3.0 by @​mr-c in common-workflow-language/cwltool#2157
• more docstrings by @​mr-c in common-workflow-language/cwltool#2158
• CUDA: if no nvidia-smi program, don't complain so loudly. by @​mr-c in common-workflow-language/cwltool#2160

Deps

• Bump pydantic from 2.12.0a1 to 2.12.0b1 by @​dependabot[bot] in common-workflow-language/cwltool#2156
• Bump github/codeql-action from 3 to 4 by @​dependabot[bot] in common-workflow-language/cwltool#2161
• Bump pydantic from 2.12.0b1 to 2.12.0 by @​dependabot[bot] in common-workflow-language/cwltool#2162
• Update rdflib requirement from <7.3,>=4.2.2 to >=4.2.2,<7.4 by @​dependabot[bot] in common-workflow-language/cwltool#2168
• Bump actions/upload-artifact from 4 to 5 by @​dependabot[bot] in common-workflow-language/cwltool#2169
• Update rdflib requirement from <7.4,>=4.2.2 to >=4.2.2,<7.5 by @​dependabot[bot] in common-workflow-language/cwltool#2172

Full Changelog: common-workflow-language/cwltool@3.1.20250925164626...3.1.20251031082601

Commits

• 0037b6d Update rdflib requirement from <7.4,>=4.2.2 to >=4.2.2,<7.5
• 72051e2 Bump actions/upload-artifact from 4 to 5
• ca47a78 Update rdflib requirement from <7.3,>=4.2.2 to >=4.2.2,<7.4
• 9781b4c Bump pydantic from 2.12.0b1 to >=2.12.0 only on Py3.14+
• ffd151f Bump github/codeql-action from 3 to 4
• 22bc7d8 CUDA: if no nvidia-smi program, don't complain so loudly.
• 8ce26ce Improve the docs
• df13e2f remove unused code
• 0a97ccd support Pydot versions before 3.0
• 2291376 Bump pydantic from 2.12.0a1 to 2.12.0b1 (#2156)
• Additional commits viewable in compare view

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[codecov]

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
1813	1	1812	10

View the top 2 failed test(s) by shortest run time

cwl-v1.2-76bdf9b55e2378432e0e6380ccedebb4a94ce483/conformance_tests.cwltest.yaml::conformance_tests::cwltest::yaml::modify_directory_content

Stack Traces | 1.39s run time

CWL test execution failed. 
Returned non-zero but it should be zero
Test: job: 
  file:.../streamflow/streamflow/cwl-v1.2-76bdf9b55e2378432e0e6380ccedebb4a94ce483/tests/empty.json
tool: 
  file:.../streamflow/streamflow/cwl-v1.2-76bdf9b55e2378432e0e6380ccedebb4a94ce483/tests/inpdir_update_wf.cwl
doc: inplace update has side effect on directory content
tags:
- inplace_update
- workflow
output:
  a:
  - basename: blurb
    class: File
    location: blurb
  b:
  - basename: blurb
    class: File
    location: blurb
id: 
  file:.../streamflow/streamflow/cwl-v1.2-76bdf9b55e2378432e0e6380ccedebb4a94ce483/conformance_tests.cwltest.yaml#modify_directory_content
line: '2834'

cwl-v1.3-2cb1dcc94e483e351528d010dc2624b8c80a2a30/conformance_tests.cwltest.yaml::conformance_tests::cwltest::yaml::modify_directory_content

Stack Traces | 6.32s run time

CWL test execution failed. 
Returned non-zero but it should be zero
Test: job: 
  file:.../streamflow/streamflow/cwl-v1.3-2cb1dcc94e483e351528d010dc2624b8c80a2a30/tests/empty.json
tool: 
  file:.../streamflow/streamflow/cwl-v1.3-2cb1dcc94e483e351528d010dc2624b8c80a2a30/tests/inpdir_update_wf.cwl
doc: inplace update has side effect on directory content
tags:
- inplace_update
- workflow
output:
  a:
  - basename: blurb
    class: File
    location: blurb
  b:
  - basename: blurb
    class: File
    location: blurb
id: 
  file:.../streamflow/streamflow/cwl-v1.3-2cb1dcc94e483e351528d010dc2624b8c80a2a30/conformance_tests.cwltest.yaml#modify_directory_content
line: '2895'

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