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 -- View it on GitLab: https://salsa.debian.org/med-team/cwltool/-/commit/327585131f6e682b1163b1daa7b71b90b5c772d7 You're receiving this email because of your account on salsa.debian.org.
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