Update and Check loadListing for input dir provenance #1986
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For systems using qemu-user-static to run foreign binaries outside of containers
…w-language#1856) 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...23.6.5) --- updated-dependencies: - dependency-name: flake8-bugbear dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
) Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.1 to 1.2.2. - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](readthedocs/sphinx_rtd_theme@1.2.1...1.2.2) --- 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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@6.2.0...7.4.0) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
Like `pip install $(grep -v mypy mypy-requirements.txt)`
…low-language#1870) * required outputs with secondaryFiles fix for containers * improve error message * leave no files behind
…w-language#1877) 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...23.7.10) --- updated-dependencies: - dependency-name: flake8-bugbear dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
…-workflow-language#1872) * refresh python version support * CI: Drop Python 3.7 from testing
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@23.3.0...23.7.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
Allow for any supported version of Python, not just the default Python version Stop tracking RHEL This would mean that we can then drop Python 3.6 support
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...7.0.0) --- updated-dependencies: - dependency-name: rdflib dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
When a podman process finishes even before reaching the monitoring method, a deadlock happens, as no one is updating `process.returncode` and spawned process is in zombie state (so, no signal is sent). This fix adds a `process.poll()` call, so it gives the chance to fill in `process.returncode`.
Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.2 to 1.3.0. - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](readthedocs/sphinx_rtd_theme@1.2.2...1.3.0) --- updated-dependencies: - dependency-name: sphinx-rtd-theme dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
This approach avoids the issue about podman using "canonical" image tags just using the "inspect" subcommand.
This udocker/podman pull command was being done even when `--disable-pull` parameter is passed to `cwltool`, and it should not be needed, as all container image pulls should have happened at this point.
Also, cosmetic changes to fix some flake8 complaints.
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@23.12.0...24.1.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
…-language/dependabot/pip/black-approx-eq-24.1 Update black requirement from ~=23.12 to ~=24.1
Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@6.2.0...8.0.0) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
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...24.1.15) --- updated-dependencies: - dependency-name: flake8-bugbear dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v3...v4) --- 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>
Co-authored-by: lihl <lihl@1123> Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.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...v23.2.1) --- updated-dependencies: - dependency-name: galaxy-tool-util dependency-type: direct:production ... 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@24.1.0...24.2.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
…1977) Also appends the program name, if not "cwltool" Should work for calrissian, reana-cwl-runner, and arvados-cwl-runner, but not toil-cwl-runner which doesn't call the cwltool.main.main() function. Probably works for streamflow, but I haven't tested that. --------- Co-authored-by: Michael R. Crusoe <1330696+mr-c@users.noreply.github.com>
Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@6.2.0...8.1.0) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
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...24.2.6) --- updated-dependencies: - dependency-name: flake8-bugbear dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
* Bump mypy from 1.8.0 to 1.9.0 Bumps [mypy](https://github.com/python/mypy) from 1.8.0 to 1.9.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.8.0...1.9.0) --- 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>
the "dist", "clean", and "release-test" targets don't need a virtualenv so as long as there is a python3 on the PATH they will work
|
Thank you @ElderMedic ; I invited you to join this repo so you can directly work on the prov_data_input_output branch |
ElderMedic
merged commit c7963b3
into
common-workflow-language:prov_data_input_output
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merged latest main in for update
fixed loadListing for provenance files copying