[med-svn] [Git][med-team/cwltool][upstream] New upstream version 3.1.20260108082145

[Michael R. Crusoe (@crusoe)]

Michael R. Crusoe pushed to branch upstream at Debian Med / cwltool


Commits:
6b723d75 by Michael R. Crusoe at 2026-01-24T19:54:22+01:00
New upstream version 3.1.20260108082145
- - - - -


117 changed files:

- .github/workflows/ci-tests.yml
- .github/workflows/codeql-analysis.yml
- .github/workflows/quay-publish.yml
- .github/workflows/wheels.yml
- CONTRIBUTING.md
- MANIFEST.in
- Makefile
- PKG-INFO
- README.rst
- cwltool.egg-info/PKG-INFO
- cwltool.egg-info/SOURCES.txt
- cwltool.egg-info/requires.txt
- cwltool/_version.py
- cwltool/argparser.py
- cwltool/builder.py
- cwltool/checker.py
- cwltool/command_line_tool.py
- cwltool/context.py
- cwltool/cuda.py
- cwltool/cwlprov/__init__.py
- cwltool/cwlprov/provenance_profile.py
- cwltool/cwlprov/ro.py
- cwltool/cwlprov/writablebagfile.py
- cwltool/cwlrdf.py
- cwltool/docker.py
- cwltool/docker_id.py
- cwltool/executors.py
- cwltool/extensions-v1.1.yml
- cwltool/extensions-v1.2.yml
- cwltool/extensions-v1.3.yml
- cwltool/extensions.yml
- cwltool/factory.py
- cwltool/flatten.py
- cwltool/job.py
- cwltool/load_tool.py
- cwltool/main.py
- cwltool/mpi.py
- cwltool/pack.py
- cwltool/pathmapper.py
- cwltool/process.py
- cwltool/procgenerator.py
- cwltool/resolver.py
- cwltool/run_job.py
- cwltool/secrets.py
- cwltool/singularity.py
- cwltool/singularity_utils.py
- cwltool/software_requirements.py
- cwltool/stdfsaccess.py
- cwltool/subgraph.py
- cwltool/task_queue.py
- cwltool/update.py
- cwltool/utils.py
- cwltool/validate_js.py
- cwltool/workflow.py
- cwltool/workflow_job.py
- docs/Makefile
- mypy-requirements.txt
- mypy-stubs/arcp/parse.pyi
- mypy-stubs/bagit.pyi
- mypy-stubs/prov/constants.py
- mypy-stubs/prov/identifier.pyi
- mypy-stubs/prov/model.pyi
- mypy-stubs/rdflib/collection.pyi
- mypy-stubs/rdflib/graph.pyi
- mypy-stubs/rdflib/namespace/__init__.pyi
- mypy-stubs/rdflib/paths.pyi
- mypy-stubs/rdflib/plugin.pyi
- mypy-stubs/rdflib/query.pyi
- mypy-stubs/rdflib/resource.pyi
- mypy-stubs/rdflib/term.pyi
- mypy-stubs/spython/main/__init__.pyi
- mypy-stubs/spython/main/build.pyi
- mypy-stubs/spython/main/parse/recipe.pyi
- mypy-stubs/spython/main/parse/writers/singularity.pyi
- pyproject.toml
- requirements.txt
- setup.py
- test-requirements.txt
- tests/cwl-conformance/cwltool-conftest.py
- + tests/loop-ext/value-from-loop-2.cwl
- + tests/loop-ext/value-from-loop-3.cwl
- + tests/loop/value-from-loop-2.cwl
- + tests/loop/value-from-loop-3.cwl
- + tests/sing_dockerfile_named_test.cwl
- + tests/sing_dockerfile_test.cwl
- + tests/sing_local_sandbox_img_id_test.cwl
- + tests/sing_local_sandbox_test.cwl
- + tests/test-cwl-out-v1.0.cwl
- + tests/test-cwl-out-v1.1.cwl
- + tests/test-cwl-out-v1.2.cwl
- + tests/test-cwl-out-v1.3.cwl
- tests/test_cuda.py
- + tests/test_cwl_output_json.py
- tests/test_dependencies.py
- tests/test_docker.py
- tests/test_environment.py
- tests/test_examples.py
- tests/test_ext.py
- tests/test_fetch.py
- tests/test_iwdr.py
- tests/test_loop.py
- tests/test_loop_ext.py
- tests/test_mpi.py
- tests/test_parallel.py
- tests/test_procgenerator.py
- tests/test_rdfprint.py
- tests/test_secrets.py
- tests/test_singularity.py
- tests/test_singularity_versions.py
- tests/test_subgraph.py
- tests/test_tmpdir.py
- tests/test_toolargparse.py
- tests/test_trs.py
- tests/test_udocker.py
- tests/util.py
- + tests/wf/hello_gpu.cwl
- tox.ini


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/cwltool/-/commit/6b723d75fbc9f1e25d19ce3e23c7b128637440e8

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