[med-svn] [Git][med-team/cwltool][upstream] New upstream version 3.1.20250925164626

Wed Oct 1 09:56:00 BST 2025

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

Commits:
32758513 by Michael R. Crusoe at 2025-09-30T15:03:29+02:00
New upstream version 3.1.20250925164626
- - - - -

261 changed files:

- .circleci/config.yml
- .github/workflows/ci-tests.yml
- .github/workflows/codeql-analysis.yml
- .github/workflows/quay-publish.yml
- .github/workflows/wheels.yml
- MANIFEST.in
- Makefile
- PKG-INFO
- build-cwltool-docker.sh
- cibw-requirements.txt
- cwltool.egg-info/PKG-INFO
- cwltool.egg-info/SOURCES.txt
- cwltool.egg-info/requires.txt
- cwltool/_version.py
- cwltool/argparser.py
- cwltool/checker.py
- cwltool/command_line_tool.py
- cwltool/context.py
- cwltool/cuda.py
- cwltool/cwlprov/provenance_profile.py
- cwltool/cwlprov/ro.py
- cwltool/cwlviewer.py
- cwltool/errors.py
- cwltool/executors.py
- cwltool/job.py
- cwltool/load_tool.py
- cwltool/main.py
- cwltool/mutation.py
- cwltool/pack.py
- cwltool/pathmapper.py
- cwltool/process.py
- cwltool/procgenerator.py
- cwltool/resolver.py
- cwltool/schemas/v1.1.0-dev1/cwl-runner.cwl
- cwltool/schemas/v1.1/cwl-runner.cwl
- cwltool/schemas/v1.2.0-dev1/cwl-runner.cwl
- cwltool/schemas/v1.2.0-dev2/cwl-runner.cwl
- cwltool/schemas/v1.2.0-dev3/cwl-runner.cwl
- cwltool/schemas/v1.2.0-dev4/cwl-runner.cwl
- cwltool/schemas/v1.2.0-dev5/cwl-runner.cwl
- cwltool/schemas/v1.3.0-dev1/cwl-runner.cwl
- cwltool/secrets.py
- cwltool/singularity_utils.py
- cwltool/subgraph.py
- cwltool/update.py
- cwltool/utils.py
- cwltool/validate_js.py
- cwltool/workflow.py
- cwltool/workflow_job.py
- docs/conf.py
- docs/requirements.txt
- lint-requirements.txt
- mypy-requirements.txt
- mypy-stubs/pydot.pyi
- pyproject.toml
- requirements.txt
- setup.py
- test-requirements.txt
- tests/CometAdapter.cwl
- tests/arg-empty-prefix-separate-false.cwl
- + tests/cache_environment.yml
- + tests/cache_environment2.yml
- + tests/cache_environment_tool.cwl
- tests/checker_wf/optional_array_mismatch.cwl
- tests/default_values_list.cwl
- tests/echo-badposition-expr.cwl
- tests/echo-position-expr.cwl
- tests/echo-stdout-log-dir.cwl
- tests/env.cwl
- tests/env2.cwl
- tests/env3.cwl
- tests/env4.cwl
- tests/input_deps/docker-array-secondaryfiles.cwl
- tests/iwdr_bad_expr.cwl
- tests/iwdr_dir_literal_real_file.cwl
- + tests/iwdr_writable_secfile-inputs.json
- + tests/iwdr_writable_secfile.cwl
- tests/load_contents-array.cwl
- tests/loop-ext/all-output-loop-no-iteration.cwl
- tests/loop-ext/all-output-loop.cwl
- tests/loop-ext/default-value-loop.cwl
- tests/loop-ext/invalid-loop-command-line-tool.cwl
- tests/loop-ext/invalid-loop-expression-tool.cwl
- tests/loop-ext/invalid-loop-hint.cwl
- tests/loop-ext/invalid-loop-scatter.cwl
- tests/loop-ext/invalid-loop-when-exception.cwl
- tests/loop-ext/invalid-loop-when.cwl
- tests/loop-ext/invalid-loop-workflow.cwl
- tests/loop-ext/invalid-multi-source-loop-no-requirement.cwl
- tests/loop-ext/invalid-no-loopWhen.cwl
- tests/loop-ext/invalid-non-boolean-loopWhen.cwl
- tests/loop-ext/invalid-non-boolean-loopWhen2.cwl
- tests/loop-ext/invalid-value-from-loop-no-requirement.cwl
- tests/loop-ext/loop-inside-loop-all.cwl
- tests/loop-ext/loop-inside-loop.cwl
- tests/loop-ext/loop-inside-scatter.cwl
- tests/loop-ext/multi-source-loop.cwl
- tests/loop-ext/opt-var-loop.cwl
- tests/loop-ext/scatter-inside-loop.cwl
- tests/loop-ext/single-var-loop-no-iteration.cwl
- tests/loop-ext/single-var-loop.cwl
- tests/loop-ext/two-vars-loop-2.cwl
- tests/loop-ext/two-vars-loop.cwl
- tests/loop-ext/value-from-loop.cwl
- tests/loop/all-output-loop-no-iteration.cwl
- tests/loop/all-output-loop.cwl
- tests/loop/default-value-loop.cwl
- tests/loop/invalid-loop-scatter.cwl
- tests/loop/invalid-loop-when-exception.cwl
- tests/loop/invalid-loop-when-exception2.cwl
- tests/loop/invalid-multi-source-loop-no-requirement.cwl
- tests/loop/invalid-no-loopWhen.cwl
- tests/loop/invalid-non-boolean-loopWhen.cwl
- tests/loop/invalid-non-boolean-loopWhen2.cwl
- tests/loop/invalid-value-from-loop-no-requirement.cwl
- tests/loop/loop-inside-loop-all.cwl
- tests/loop/loop-inside-loop.cwl
- tests/loop/loop-inside-scatter.cwl
- tests/loop/multi-source-loop.cwl
- tests/loop/opt-var-loop.cwl
- tests/loop/scatter-inside-loop.cwl
- tests/loop/single-var-loop-no-iteration.cwl
- tests/loop/single-var-loop.cwl
- tests/loop/two-vars-loop-2.cwl
- tests/loop/two-vars-loop.cwl
- tests/loop/value-from-loop.cwl
- tests/nested-array.cwl
- tests/non_portable.cwl
- tests/non_portable2.cwl
- tests/override/env-tool.cwl
- tests/override/env-tool_v1.1.0-dev1.cwl
- tests/override/env-tool_v1.1.cwl
- tests/portable.cwl
- tests/reloc/test.cwl
- tests/scatter_numbers.cwl
- tests/secondary-files-bad.cwl
- tests/secondary-files-required-container.cwl
- tests/secondary-files-required-missing-container.cwl
- tests/secondary-files-string-v1.cwl
- tests/secondary-files.cwl
- tests/sing_pullfolder_test.cwl
- tests/subgraph/1432.cwl
- tests/subgraph/env-tool2.cwl
- tests/subgraph/env-tool2_no_env.cwl
- tests/subgraph/env-tool2_req.cwl
- tests/subgraph/env-wf2.cwl
- tests/subgraph/env-wf2_hint_collision.cwl
- tests/subgraph/env-wf2_hint_req_collision.cwl
- tests/subgraph/env-wf2_long.cwl
- tests/subgraph/env-wf2_only_hint.cwl
- tests/subgraph/env-wf2_req_collision.cwl
- tests/subgraph/env-wf2_subwf-packed.cwl
- tests/subgraph/env-wf2_subwf.cwl
- tests/subgraph/env-wf2_subwf_b.cwl
- tests/subgraph/steplevel-resreq.cwl
- tests/subgraph/timelimit2-wf.cwl
- + tests/test_caching.py
- tests/test_context.py
- tests/test_dependencies.py
- tests/test_environment.py
- tests/test_examples.py
- tests/test_iwdr.py
- tests/test_mpi.py
- tests/test_subclass_mypyc.py
- tests/test_validate.py
- tests/trs/Dockstore.cwl
- tests/trs/md5sum-tool.cwl
- tests/trs/md5sum-workflow.cwl
- tests/utf_doc_example.cwl
- tests/util.py
- tests/wc-tool-bad-hints.cwl
- tests/wc-tool-bad-reqs.cwl
- tests/wf/1496.cwl
- tests/wf/1590.cwl
- tests/wf/1st-workflow.cwl
- tests/wf/811-12.cwl
- tests/wf/811.cwl
- tests/wf/816_tool.cwl
- tests/wf/816_wf.cwl
- tests/wf/910.cwl
- tests/wf/arguments.cwl
- tests/wf/bad-stderr-expr.cwl
- tests/wf/bad-stdin-expr.cwl
- tests/wf/bad-stdout-expr.cwl
- tests/wf/bad_networkaccess.cwl
- tests/wf/bad_timelimit.cwl
- tests/wf/cache_test_workflow.cwl
- tests/wf/cat-tool.cwl
- tests/wf/conditional_step_no_inputs.cwl
- tests/wf/conflict.cwl
- tests/wf/cores_float.cwl
- tests/wf/default-dir5.cwl
- tests/wf/default-wf5.cwl
- tests/wf/double-nested.cwl
- tests/wf/expect_trick_packed.cwl
- tests/wf/extract_region_specs.cwl
- tests/wf/floats_small_and_large.cwl
- tests/wf/generator/pytoolgen.cwl
- + tests/wf/inp-filelist.txt
- tests/wf/input_named_id.cwl
- + tests/wf/iwd-container-entryname1.cwl
- + tests/wf/iwd-container-entryname3.cwl
- tests/wf/iwd-passthrough1.cwl
- tests/wf/iwdr-empty.cwl
- tests/wf/iwdr-entry.cwl
- tests/wf/iwdr-passthrough-successive.cwl
- tests/wf/literalfile.cwl
- + tests/wf/loadContents-input.yml
- tests/wf/malformed_outputs.cwl
- tests/wf/missing-tool.cwl
- tests/wf/mpi_env.cwl
- tests/wf/mpi_expr.cwl
- tests/wf/mpi_line_count.cwl
- tests/wf/mpi_simple.cwl
- tests/wf/mpi_simple_wf.cwl
- tests/wf/nested.cwl
- tests/wf/networkaccess-fail.cwl
- tests/wf/networkaccess.cwl
- tests/wf/no-parameters-echo.cwl
- tests/wf/nvidia-smi-cc.cwl
- tests/wf/nvidia-smi-container.cwl
- tests/wf/nvidia-smi-max.cwl
- tests/wf/nvidia-smi-range.cwl
- tests/wf/nvidia-smi.cwl
- tests/wf/operation/abstract-cosifer.cwl
- tests/wf/operation/operation-single.cwl
- tests/wf/optional-numerical-output-0.cwl
- tests/wf/optional_src_mandatory_sink.cwl
- tests/wf/packed-with-loadlisting.cwl
- tests/wf/packed_no_main.cwl
- tests/wf/paramref_arguments_roundtrip.cwl
- tests/wf/paramref_arguments_self.cwl
- tests/wf/record_outputeval.cwl
- tests/wf/resreq_expr_float_v1_0.cwl
- tests/wf/resreq_expr_float_v1_2.cwl
- tests/wf/scatter2.cwl
- tests/wf/scatter2_subwf.cwl
- tests/wf/schemadef-bug-1473.cwl
- tests/wf/schemadef-tool-12.cwl
- tests/wf/schemadef-tool.cwl
- tests/wf/sec-tool.cwl
- tests/wf/sec-wf-out.cwl
- tests/wf/sec-wf.cwl
- tests/wf/secret_job.cwl
- tests/wf/secret_wf.cwl
- tests/wf/separate_without_prefix.cwl
- tests/wf/shm_size.cwl
- tests/wf/storage_float.cwl
- tests/wf/tar-param.cwl
- tests/wf/three_step_color.cwl
- tests/wf/timelimit-fail.cwl
- tests/wf/timelimit.cwl
- tests/wf/touch_tool.cwl
- tests/wf/trick_defaults.cwl
- tests/wf/trick_defaults2.cwl
- tests/wf/vf-concat.cwl
- tests/wf/workreuse-fail.cwl
- tests/wf/workreuse.cwl
- tests/with_doc.cwl
- tests/without_doc.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/327585131f6e682b1163b1daa7b71b90b5c772d7

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