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Update latest main #2073

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mr-c and others added 30 commits October 4, 2024 14:20
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] <[email protected]>
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 <[email protected]>
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] <[email protected]>
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] <[email protected]>
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] <[email protected]>
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] <[email protected]>
* 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] <[email protected]>

* Update pyproject.toml

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Michael R. Crusoe <[email protected]>
* 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] <[email protected]>

* Update pyproject.toml

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Michael R. Crusoe <[email protected]>
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] <[email protected]>
…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] <[email protected]>
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 <[email protected]>
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] <[email protected]>
GlassOfWhiskey and others added 10 commits December 12, 2024 13:19
This commit fixes one small error in the `cwltool:Loop` definition that
were breaking the Schema SALAD codegen procedure.
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...24.12.12)

---
updated-dependencies:
- dependency-name: flake8-bugbear
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.21.3 to 2.22.0.
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](pypa/cibuildwheel@v2.21.3...v2.22)

---
updated-dependencies:
- dependency-name: cibuildwheel
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 3.0.1 to 3.0.2.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](readthedocs/sphinx_rtd_theme@3.0.1...3.0.2)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.21.3 to 2.22.0.
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](pypa/cibuildwheel@v2.21.3...v2.22.0)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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