Bump cwltool from 3.1.20241217163858 to 3.1.20250110105449

[dependabot]

Bumps cwltool from 3.1.20241217163858 to 3.1.20250110105449.

Release notes

Sourced from cwltool's releases.

3.1.20250110105449

What's Changed

• docs: render the CLI groups too by @​mr-c in common-workflow-language/cwltool#2089
• Change caching pathmapper to respect the pathmapper factory by @​stxue1 in common-workflow-language/cwltool#2092

Deps

• Bump mypy from 1.13.0 to 1.14.0 by @​dependabot in common-workflow-language/cwltool#2090
• Bump mypy from 1.14.0 to 1.14.1 by @​dependabot in common-workflow-language/cwltool#2091

New Contributors

• @​stxue1 made their first contribution in common-workflow-language/cwltool#2092

Full Changelog: common-workflow-language/cwltool@3.1.20241217163858...3.1.20250110105449

Commits

• a67c898 Change caching pathmapper to respect the pathmapper factory
• baa668b Bump mypy from 1.14.0 to 1.14.1
• f453cdc Bump mypy from 1.13.0 to 1.14.0
• 6a61bed docs: render the CLI groups too
• ae5fae4 README: Python supported versions list was outdated
• See full diff in compare view

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[GlassOfWhiskey]

@dependabot rebase

[codecov]

❌ 8 Tests Failed:

Tests completed	Failed	Passed	Skipped
1996	8	1988	9

View the top 3 failed tests by shortest run time

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

Stack Traces | 3.21s 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
output:
  foo:
    location: foo
    class: File
    checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15
    size: 4
tool: 
  file:.../streamflow/streamflow/cwl-v1.2-76bdf9b55e2378432e0e6380ccedebb4a94ce483/tests/test-cwl-out3.cwl
id: 
  file:.../streamflow/streamflow/cwl-v1.2-76bdf9b55e2378432e0e6380ccedebb4a94ce483/conformance_tests.cwltest.yaml#json_output_path_relative
doc: Test support for reading cwl.output.json where 'path' is relative path in output
  dir.
tags:
- required
- command_line_tool
line: '964'

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

Stack Traces | 5.18s run time

CWL test execution failed. 
Returned non-zero but it should be zero
Test: job: 
  file:.../streamflow/streamflow/cwl-v1.2-76bdf9b55e2378432e0e6380ccedebb4a94ce483/tests/cat-job.json
output:
  output_file:
    class: File
    checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
    location: output.txt
    size: 13
tool: 
  file:.../streamflow/streamflow/cwl-v1.2-76bdf9b55e2378432e0e6380ccedebb4a94ce483/tests/cat5-tool.cwl
id: 
  file:.../streamflow/streamflow/cwl-v1.2-76bdf9b55e2378432e0e6380ccedebb4a94ce483/conformance_tests.cwltest.yaml#hints_unknown_ignored
doc: Test unknown hints are ignored.
tags:
- required
- command_line_tool
line: '500'

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

Stack Traces | 5.35s 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
output:
  foo:
    location: foo
    class: File
    checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15
    size: 4
tool: 
  file:.../streamflow/streamflow/cwl-v1.2-76bdf9b55e2378432e0e6380ccedebb4a94ce483/tests/test-cwl-out2.cwl
id: 
  file:.../streamflow/streamflow/cwl-v1.2-76bdf9b55e2378432e0e6380ccedebb4a94ce483/conformance_tests.cwltest.yaml#docker_json_output_location
doc: Test support for reading cwl.output.json when running in a Docker container and
  just 'location' is provided.
tags:
- shell_command
- command_line_tool
line: '948'

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