Update latest main by ElderMedic · Pull Request #2073 · common-workflow-language/cwltool

ElderMedic · 2024-11-21T22:24:48Z

No description provided.

Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 2.0.0 to 3.0.0. - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](readthedocs/sphinx_rtd_theme@2.0.0...3.0.0) --- updated-dependencies: - dependency-name: sphinx-rtd-theme dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>

This commit fixes #2003 by handling spurious, repeated callbacks of the `receive_scatter_output` method of the `ReceiveScatterOutput` class. The reason of multiple awakenings has not been investigated deeply, though. In the future, a thorough examination of the `MultithreadedJobExecutor` logic may be necessary. --------- Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>

Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 3.0.0 to 3.0.1. - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](readthedocs/sphinx_rtd_theme@3.0.0...3.0.1) --- updated-dependencies: - dependency-name: sphinx-rtd-theme dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

Updates the requirements on [black](https://github.com/psf/black) to permit the latest version. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@24.8.0...24.10.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [mypy](https://github.com/python/mypy) from 1.11.2 to 1.12.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.11.2...v1.12.0) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Updates the requirements on [rdflib](https://github.com/RDFLib/rdflib) to permit the latest version. - [Release notes](https://github.com/RDFLib/rdflib/releases) - [Changelog](https://github.com/RDFLib/rdflib/blob/main/CHANGELOG.md) - [Commits](RDFLib/rdflib@4.2.2...7.1.0) --- updated-dependencies: - dependency-name: rdflib dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>

* Bump mypy from 1.12.0 to 1.12.1 Bumps [mypy](https://github.com/python/mypy) from 1.12.0 to 1.12.1. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.12.0...v1.12.1) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Update pyproject.toml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>

* Bump mypy from 1.12.1 to 1.13.0 Bumps [mypy](https://github.com/python/mypy) from 1.12.1 to 1.13.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.12.1...v1.13.0) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Update pyproject.toml --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>

But don't publish them yet

- cibuildwheel: adjust pytest parallel execution - cicircle: upgrade to ubuntu 24.04 - Stop building for musllinux_1_1 pypa/manylinux#1629 > musl libc 1.1 is EOL and Alpine Linux 3.12 also (support ended 2 years ago, May 1st, 2022).

Updates the requirements on [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) to permit the latest version. - [Release notes](https://github.com/PyCQA/flake8-bugbear/releases) - [Commits](PyCQA/flake8-bugbear@16.4.1...24.10.31) --- updated-dependencies: - dependency-name: flake8-bugbear dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>

…2066) Updates the requirements on [ruamel-yaml]() to permit the latest version. --- updated-dependencies: - dependency-name: ruamel-yaml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

The class TascQueue accepts an argument `thread_count` that is used for the max size of a queue. In the `MultithreadedJobExecutor `class there is a variable defined (`max_cores`) that is getting its value from the available cores of the machine. Further down in the same class when TaskQueue is called instead of using the `max_cores` it is using `psutil.cpu_count()`. I suggest to use the self.max_cores in the call of TaskQueue in the file executor.py instead of psutil.cpu_count() Use case: when a job executor is setup as MultithreadedJobExecutor one can override the max_cores after the initialization of the object and limit the use to the specified cores. Additional enhancement would be to include an argument to allow the use to provide the number of cores available for use Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>

Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>

…dout

Updates the requirements on [setuptools-scm](https://github.com/pypa/setuptools-scm) to permit the latest version. - [Release notes](https://github.com/pypa/setuptools-scm/releases) - [Changelog](https://github.com/pypa/setuptools-scm/blob/main/RELEASE_SYSTEM.md) - [Commits](pypa/setuptools-scm@v8.0.4...setuptools-scm-v10.0.2) --- updated-dependencies: - dependency-name: setuptools-scm dependency-version: 10.0.2 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com>

…_having_namespace_location_steps

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 5 to 6. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v5...v6) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [mypy](https://github.com/python/mypy) from 1.19.1 to 1.20.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.19.1...v1.20.0) --- updated-dependencies: - dependency-name: mypy dependency-version: 1.20.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Updates the requirements on [galaxy-tool-util](https://github.com/galaxyproject/galaxy) to permit the latest version. - [Release notes](https://github.com/galaxyproject/galaxy/releases) - [Commits](galaxyproject/galaxy@galaxy-tool-util-22.1.3...v26.0.0) --- updated-dependencies: - dependency-name: galaxy-tool-util dependency-version: 26.0.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>

Updates the requirements on [galaxy-util](https://github.com/galaxyproject/galaxy) to permit the latest version. - [Release notes](https://github.com/galaxyproject/galaxy/releases) - [Commits](galaxyproject/galaxy@galaxy-util-19.9.0...v26.0.0) --- updated-dependencies: - dependency-name: galaxy-util dependency-version: 26.0.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>

The following vulnerabilities are fixed by pinning transitive dependencies: - https://snyk.io/vuln/SNYK-PYTHON-PYGMENTS-15746419 - https://snyk.io/vuln/SNYK-PYTHON-REQUESTS-6928867 - https://snyk.io/vuln/SNYK-PYTHON-URLLIB3-7267250 - https://snyk.io/vuln/SNYK-PYTHON-ZIPP-7430899

Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.com>

Bumps [mypy](https://github.com/python/mypy) from 1.20.0 to 1.20.1. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.20.0...v1.20.1) --- updated-dependencies: - dependency-name: mypy dependency-version: 1.20.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [mypy](https://github.com/python/mypy) from 1.20.1 to 1.20.2. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.20.1...v1.20.2) --- updated-dependencies: - dependency-name: mypy dependency-version: 1.20.2 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [github/codeql-action](https://github.com/github/codeql-action) from 4.35.2 to 4.35.3. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@95e58e9...e46ed2c) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 4.35.3 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

    # Initializes the CodeQL tools for scanning.
    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@e46ed2cbd01164d986452f91f178727624ae40d7 # v4



    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@e46ed2cbd01164d986452f91f178727624ae40d7 # v4


Bumps [mypy](https://github.com/python/mypy) from 1.20.2 to 2.0.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.20.2...v2.0.0) --- updated-dependencies: - dependency-name: mypy dependency-version: 2.0.0 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [mypy](https://github.com/python/mypy) from 2.0.0 to 2.1.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v2.0.0...v2.1.0) --- updated-dependencies: - dependency-name: mypy dependency-version: 2.1.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 6.0.0 to 6.0.1. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@57e3a13...e79a696) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>

+        uses: docker/setup-qemu-action@ce360397dd3f832beb865e1373c09c0e9f86d70a # v4
      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@4d04d5d9486b7bd6fa91e7baf45bbb4f8b9deedd # v4


+          lookup-only: true
      - name: Login to Quay.io
-        uses: docker/login-action@v3
+        uses: docker/login-action@4907a6ddec9925e35a0a9e82d7399ccc52663121 # v4


          password: ${{ secrets.REGISTRY_PASSWORD }}
      - name: Build and publish cwltool_module image to Quay
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@bcafcacb16a39f128d818304e6c9c0c18556b85f # v7


          cache-to: type=gha,mode=max
      - name: Build and publish cwltool image to Quay
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@bcafcacb16a39f128d818304e6c9c0c18556b85f # v7


The three Codecov upload steps use fail_ci_if_error: true with a token-gated upload (CODECOV_TOKEN). GitHub Actions withholds secrets from pull requests opened from forks, so the upload step fails and turns the whole CI run red for external contributors, regardless of whether their actual changes pass. This restores the behaviour intentionally set in #1857 ("keep running even if codecov upload fails"), which was reverted by fe1e8a9 ("Fix codecov v4 configuration"). Coverage uploads from trusted (non-fork) runs still happen; they just no longer hard-fail CI.

github-advanced-security

zizmor found more than 20 potential problems in the proposed changes. Check the Files changed tab for more details.

A CommandLineTool with no baseCommand, arguments, or input bindings produces an empty command list. This was passed straight to subprocess.Popen([]), which crashed with a raw "IndexError: list index out of range" deep inside subprocess. Guard the empty case in JobBase._execute and raise a WorkflowException with an actionable message instead. The existing handler turns this into a clean permanentFail rather than an unhandled traceback. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

mr-c and others added 30 commits October 4, 2024 14:20

prepare for mypy 1.12

48cea18

remove usage of ancient shellescape backport of Stdlib's shlex (#2041)

75e073c

setuptools is not a install requirement

04fd426

gh-actions: fail-fast false

0056ca5

prepare for future mypy release and enable --local-partial-types now

83000ae

Update lint-requirements.txt

1a2c939

Update lint-requirements.txt

83def6a

Drop Python 3.8

05af6c1

add more docs

a956766

build binary wheels

e3f6cf7

But don't publish them yet

cpu_count can be None, so fallback to 1

9cda157

add note on docker platform issue (#2064)

ee30368

Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>

Use "run" with singularity/apptainer instead of "exec", when possible

1557c8d

Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>

conformances testing: no longer skip tests for singularity/apptainer

c3c92eb

make-template: fix type error

6c86caa

--no-warnings includes schema-salad; --validate should complain to st…

7fa57dd

…dout

Append "_latest" to image id if no tag is present (#2085)

604fd12

dependabot Bot and others added 18 commits March 26, 2026 11:57

improve error reporting for test_issue_1765_print_deps_with_workflows…

a7d965b

…_having_namespace_location_steps

upgrade to cwl_utils 0.41 and use the new types

ff0e409

pin minimum pygments version to avoid CVE-2026-4539

47a6006

tox: match the python version used by GitHub Actions

ca173ba

shellcheck cleanup

45e660e

Fix all_non_null single source element (#2220)

55223a6

use the new TypeDict types from cwl-utils 0.41 more (#2192)

5377758

Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.com>

add strongly-typed visit_* functions

10cabef

tighten github actions with zizmor

8b78b90

dependabot: only widen Python deps

a43cf89

github-advanced-security AI found potential problems May 5, 2026

View reviewed changes

Comment thread .github/workflows/codeql-analysis.yml Fixed

Comment thread .github/workflows/codeql-analysis.yml Fixed

github-advanced-security AI found potential problems May 8, 2026

View reviewed changes

dependabot Bot added 2 commits May 14, 2026 10:48

github-advanced-security AI found potential problems May 21, 2026

View reviewed changes

Comment thread .github/workflows/ci-tests.yml Fixed

Comment thread .github/workflows/ci-tests.yml Fixed

Comment thread .github/workflows/ci-tests.yml Fixed

github-advanced-security AI found potential problems May 27, 2026

View reviewed changes

github-advanced-security AI found potential problems Jun 25, 2026

View reviewed changes

ryuwd and others added 2 commits July 10, 2026 12:04

Make make_path_mapper extensible like make_fs_access

5634342

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Update latest main #2073

Update latest main #2073
ElderMedic wants to merge 200 commits into
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ElderMedic commented Nov 21, 2024

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ElderMedic commented Nov 21, 2024

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