Update latest main #2073
Open
Update latest main #2073
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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>
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...v25.0.0) --- updated-dependencies: - dependency-name: galaxy-util dependency-version: 25.0.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [mypy](https://github.com/python/mypy) from 1.16.1 to 1.17.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.16.1...v1.17.0) --- updated-dependencies: - dependency-name: mypy dependency-version: 1.17.0 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 3.0.0 to 3.0.1. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](pypa/cibuildwheel@v3.0.0...v3.0.1) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-version: 3.0.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
Example: `tox -e py311-unit -- --lf --pdb`
Especially with regards to overrides and
`--preserve{-entire,}-environement`
Added more tests for environment variable caching
Co-authored-by: Michael R. Crusoe <mrc@commonwl.org>
…iled, (E)rror; 'fE' is the default
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 3.0.1 to 3.1.0. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](pypa/cibuildwheel@v3.0.1...v3.1.0) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-version: 3.1.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
…ed fully by mypyc
Bumps [mypy](https://github.com/python/mypy) from 1.17.0 to 1.17.1. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.17.0...v1.17.1) --- updated-dependencies: - dependency-name: mypy dependency-version: 1.17.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v4...v5) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com>
This reverts commit 8e9d7fe.
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/CHANGELOG.md) - [Commits](pypa/setuptools-scm@v8.0.4...v9.2.0) --- updated-dependencies: - dependency-name: setuptools-scm dependency-version: 9.2.0 dependency-type: direct:development ... Signed-off-by: dependabot[bot] <support@github.com>
Updates the requirements on [setuptools-scm[toml]](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/CHANGELOG.md) - [Commits](pypa/setuptools-scm@v8.0.4...v9.2.0) --- updated-dependencies: - dependency-name: setuptools-scm[toml] dependency-version: 9.2.0 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v5...v6) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... 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...7.2.1) --- updated-dependencies: - dependency-name: rdflib dependency-version: 7.2.1 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
Bumps [mypy](https://github.com/python/mypy) from 1.17.1 to 1.18.2. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.17.1...v1.18.2) --- updated-dependencies: - dependency-name: mypy dependency-version: 1.18.2 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 3.1 to 3.2. - [Release notes](https://github.com/pypa/cibuildwheel/releases) - [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md) - [Commits](pypa/cibuildwheel@v3.1...v3.2) --- updated-dependencies: - dependency-name: pypa/cibuildwheel dependency-version: '3.2' dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com>
From 1.84user 0.18system 0:02.03elapsed to 0.71user 0.11system 0:00.83elapsed
* Bump pydantic from 2.12.0a1 to 2.12.0b1 Bumps [pydantic](https://github.com/pydantic/pydantic) from 2.12.0a1 to 2.12.0b1. - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md) - [Commits](pydantic/pydantic@v2.12.0a1...v2.12.0b1) --- updated-dependencies: - dependency-name: pydantic dependency-version: 2.12.0b1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Update mypy-requirements.txt --------- 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>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.