Update latest main - #2073
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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>
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 4.1.0 to 4.2.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](docker/setup-buildx-action@d7f5e7f...bb05f3f) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-version: 4.2.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/checkout](https://github.com/actions/checkout) from 6.0.2 to 7.0.1. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@de0fac2...3d3c42e) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 7.2.0 to 7.3.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@f9f3042...53b7df9) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-version: 7.3.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 6.3.0 to 7.0.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@ece7cb0...5fda3b9) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
* Handle list-valued doc when rendering --tool-help The CWL spec allows the doc/label fields to be either a single string or an array of strings, but the --tool-help renderer assumed doc was always a string when building the argparse description and per-input help text. A list doc crashed rich with "Unable to get render width" (or a TypeError from rich.markup.escape for input-level doc). Normalize doc to a string (joining list entries with newlines) before it reaches argparse/rich, in both generate_parser and add_argument. Fixes #2100 * Normalize list-valued doc before add_argument, not inside it The typeguard-enabled test env type-checks arguments at the call boundary, so passing the raw ruamel CommentedSeq into add_argument() failed on its 'description: str' annotation before the normalization inside the function could run. Move the doc_to_str() call up into generate_parser(), where the value is read off the input, and restore add_argument() to escaping a plain string. * Let doc_to_str own the None case in generate_parser The caller guarded doc against None before calling doc_to_str(), which duplicated the check the helper already performs and left the helper's own None branch unreachable from the public API. Pass the raw value straight through and map the resulting empty string back to None, so a tool without doc/label still gets description=None. * fix(argparser): join list-valued doc without str() repack Per review: use plain "\n".join(doc) inside the MutableSequence branch. --------- Co-authored-by: arimu1 <19286898+arimu1@users.noreply.github.com>
An empty input object file made schema-salad's Loader.fetch() raise a bare StopIteration, which main() caught in its generic handler and rendered as "I'm sorry, I couldn't load this CWL file" followed by an empty error string, giving the user nothing to act on. load_job_order() now catches StopIteration from resolve_ref and reports that the input object file is empty, matching the existing "not formatted correctly" error for malformed input objects. Fixes #2043
#2104) Builder.tostr() converts scientific-notation floats to plain decimal so they never appear as e.g. "1E-6" on the command line. To do this it checked whether the ruamel-yaml scalar's Decimal representation used "E" notation, and if so quantized it to the nearest integer (dec_value.quantize(1)). That was fine for values like 1.23e5, which are already whole numbers, but any small fractional value that needs scientific notation to display (roughly abs(x) < 1e-6) got rounded down to 0 instead of being expanded to its full decimal form. A float input defaulting to 9.999e-7 was silently turned into "0" on the command line. Replace the integer quantize with a full-precision fixed-point format (format(dec_value, "f")), which expands scientific notation to plain decimal without discarding any digits. Whole numbers still render the same ("123000", "1230000"); a float/double default of 9.999e-7 now renders as "0.0000009999" instead of "0". Extended the existing floats_small_and_large.cwl fixture with a float and a double input defaulting to 9.999e-7 and updated test_very_small_and_large_floats to assert on the full value.
Bumps [docker/login-action](https://github.com/docker/login-action) from 4.4.0 to 4.5.1. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](docker/login-action@af1e73f...abd2ef4) --- updated-dependencies: - dependency-name: docker/login-action dependency-version: 4.5.1 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 4.1.0 to 4.1.1. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](pypa/cibuildwheel@2947353...4726cd3) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-version: 4.1.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) from 0.6.0 to 0.6.1. - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](zizmorcore/zizmor-action@6599ee8...6fc4b00) --- updated-dependencies: - dependency-name: zizmorcore/zizmor-action dependency-version: 0.6.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [docker/login-action](https://github.com/docker/login-action) from 4.5.1 to 4.6.0. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](docker/login-action@abd2ef4...dbcb813) --- updated-dependencies: - dependency-name: docker/login-action dependency-version: 4.6.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 4.1.1 to 4.2.0. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](pypa/cibuildwheel@4726cd3...1828c10) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-version: 4.2.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [zizmorcore/zizmor-action](https://github.com/zizmorcore/zizmor-action) from 0.6.1 to 0.6.2. - [Release notes](https://github.com/zizmorcore/zizmor-action/releases) - [Commits](zizmorcore/zizmor-action@6fc4b00...3dc1ecc) --- updated-dependencies: - dependency-name: zizmorcore/zizmor-action dependency-version: 0.6.2 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
do not yet build for emscripten, psutil support is missing we no longer have to explictly skip the PyPy builds, that is default from cibuildwheel version 3.0.0
Bumps [actions/cache](https://github.com/actions/cache) from 5.1.0 to 6.1.0. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@v5.1.0...55cc834) --- updated-dependencies: - dependency-name: actions/cache dependency-version: 6.1.0 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 2.1.0 to 2.3.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v2.1.0...v2.3.0) --- updated-dependencies: - dependency-name: mypy dependency-version: 2.3.0 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...v26.1.1) --- updated-dependencies: - dependency-name: galaxy-tool-util dependency-version: 26.1.1 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@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...9.1.1) --- updated-dependencies: - dependency-name: pytest dependency-version: 9.1.1 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...v26.1.1) --- updated-dependencies: - dependency-name: galaxy-util dependency-version: 26.1.1 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
until pydantic releases their support
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 4.2.0 to 4.3.0. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](docker/setup-buildx-action@bb05f3f...37fe631) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-version: 4.3.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
* Delete "dirname" also for type Directory * type fix --------- Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.com> Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
Bumps [mypy](https://github.com/python/mypy) from 2.3.0 to 2.3.1. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v2.3.0...v2.3.1) --- updated-dependencies: - dependency-name: mypy dependency-version: 2.3.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
spython was imported at module level, meaning merely importing cwltool.singularity (which cwltool.workflow/command_line_tool do unconditionally) required spython to be installed even when Singularity support is never used, e.g. for `cwltool --validate`. spython itself is only used inside SingularityCommandLineJob.get_image's Dockerfile-build branch, so move the three imports there. No behavior change for actual Singularity usage.
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