Bump the runtime-dependencies group across 1 directory with 3 updates

[dependabot]

Bumps the runtime-dependencies group with 3 updates in the / directory: numpy, ruamel-yaml and scipy.

Updates numpy from 2.0.2 to 2.2.1

Release notes

Sourced from numpy's releases.

2.2.1 (DEC 21, 2024)

NumPy 2.2.1 Release Notes

NumPy 2.2.1 is a patch release following 2.2.0. It fixes bugs found after the 2.2.0 release and has several maintenance pins to work around upstream changes.

There was some breakage in downstream projects following the 2.2.0 release due to updates to NumPy typing. Because of problems due to MyPy defects, we recommend using basedpyright for type checking, it can be installed from PyPI. The Pylance extension for Visual Studio Code is also based on Pyright. Problems that persist when using basedpyright should be reported as issues on the NumPy github site.

This release supports Python 3.10-3.13.

Contributors

A total of 9 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• Charles Harris
• Joren Hammudoglu
• Matti Picus
• Nathan Goldbaum
• Peter Hawkins
• Simon Altrogge
• Thomas A Caswell
• Warren Weckesser
• Yang Wang +

Pull requests merged

A total of 12 pull requests were merged for this release.

• #27935: MAINT: Prepare 2.2.x for further development
• #27950: TEST: cleanups
• #27958: BUG: fix use-after-free error in npy_hashtable.cpp (#27955)
• #27959: BLD: add missing include
• #27982: BUG:fix compile error libatomic link test to meson.build
• #27990: TYP: Fix falsely rejected value types in ndarray.__setitem__
• #27991: MAINT: Don't wrap #include <Python.h> with extern "C"
• #27993: BUG: Fix segfault in stringdtype lexsort
• #28006: MAINT: random: Tweak module code in mtrand.pyx to fix a Cython...
• #28007: BUG: Cython API was missing NPY_UINTP.
• #28021: CI: pin scipy-doctest to 1.5.1
• #28044: TYP: allow None in operand sequence of nditer

Checksums

... (truncated)

Changelog

Sourced from numpy's changelog.

This is a walkthrough of the NumPy 2.1.0 release on Linux, modified for building with GitHub Actions and cibuildwheels and uploading to the anaconda.org staging repository for NumPy <https://anaconda.org/multibuild-wheels-staging/numpy>_. The commands can be copied into the command line, but be sure to replace 2.1.0 by the correct version. This should be read together with the :ref:general release guide <prepare_release>.

Facility preparation

Before beginning to make a release, use the requirements/*_requirements.txt files to ensure that you have the needed software. Most software can be installed with pip, but some will require apt-get, dnf, or whatever your system uses for software. You will also need a GitHub personal access token (PAT) to push the documentation. There are a few ways to streamline things:

• Git can be set up to use a keyring to store your GitHub personal access token. Search online for the details.
• You can use the keyring app to store the PyPI password for twine. See the online twine documentation for details.

Prior to release

Add/drop Python versions

When adding or dropping Python versions, three files need to be edited:

• .github/workflows/wheels.yml # for github cibuildwheel
• tools/ci/cirrus_wheels.yml # for cibuildwheel aarch64/arm64 builds
• pyproject.toml # for classifier and minimum version check.

Make these changes in an ordinary PR against main and backport if necessary. Add [wheel build] at the end of the title line of the commit summary so that wheel builds will be run to test the changes. We currently release wheels for new Python versions after the first Python rc once manylinux and cibuildwheel support it. For Python 3.11 we were able to release within a week of the rc1 announcement.

Backport pull requests

Changes that have been marked for this release must be backported to the maintenance/2.1.x branch.

Update 2.1.0 milestones

... (truncated)

Commits

• 7469245 Merge pull request #28047 from charris/prepare-2.2.1
• acb051e REL: Prepare for the NumPy 2.2.1 release [wheel build]
• 28a091a Merge pull request #28044 from charris/backport-28039
• 723605b TST: Add test for allowing None in operand sequence passed to nditer
• 554739e TYP: allow None in operand sequence of nditer
• 31bc4c8 Merge pull request #28021 from charris/backport-28020
• 32f52a3 CI: pin scipy-doctest to 1.5.1 (#28020)
• 6219aeb Merge pull request #28007 from charris/backport-28005
• eb7071c Merge pull request #28006 from charris/backport-28003
• 4f82c32 BUG: Cython API was missing NPY_UINTP.
• Additional commits viewable in compare view

Updates ruamel-yaml from 0.18.6 to 0.18.10

Updates scipy from 1.14.1 to 1.15.1

Release notes

Sourced from scipy's releases.

SciPy 1.15.1 Release Notes

SciPy 1.15.1 is a bug-fix release with no new features compared to 1.15.0. Importantly, an issue with the import of scipy.optimize breaking other packages has been fixed.

Authors

• Name (commits)
• Ralf Gommers (3)
• Rohit Goswami (1)
• Matt Haberland (2)
• Tyler Reddy (7)
• Daniel Schmitz (1)

A total of 5 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

SciPy 1.15.0 Release Notes

SciPy 1.15.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.15.x branch, and on adding new features on the main branch.

This release requires Python 3.10-3.13 and NumPy 1.23.5 or greater.

Highlights of this release

• Sparse arrays are now fully functional for 1-D and 2-D arrays. We recommend that all new code use sparse arrays instead of sparse matrices and that developers start to migrate their existing code from sparse matrix to sparse array: migration_to_sparray. Both sparse.linalg and sparse.csgraph work with either sparse matrix or sparse array and work internally with sparse array.
• Sparse arrays now provide basic support for n-D arrays in the COO format

... (truncated)

Commits

• df134ea REL: 1.15.1 rel commit [wheel build]
• f939c19 Merge pull request #22296 from tylerjereddy/treddy_1.15.1_backports
• 609bb3c DOC: PR 22296 revisions
• 5bfd6a2 TST: stats.Normal: bump tolerance on test of logcdf (#22276)
• f9a549c DOC: update 1.15.1 relnotes
• 6f011d8 MAINT: Update highs subproject commit
• 0ff01de TST: fix thread safety issue in interpolate.bsplines memmap test
• 21c65ab BLD: fix some issues with undeclared internal build dependencies
• 826759e MAINT: fix url for array-api-extra git submodule
• 9af1fcd Merge pull request #22235 from tylerjereddy/treddy_prep_1.15.1
• Additional commits viewable in compare view

Most Recent Ignore Conditions Applied to This Pull Request

Dependency Name	Ignore Conditions
numpy	[>= 1.25.a, < 1.26]

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Summary by Sourcery

Update NumPy to 2.2.1, ruamel-yaml to 0.18.10, and SciPy to 1.15.1.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request updates the runtime-dependencies group, bumping numpy, ruamel-yaml and scipy to newer versions. The numpy version was updated from 2.0.2 to 2.2.1, ruamel-yaml from 0.18.6 to 0.18.10 and scipy from 1.14.1 to 1.15.1. Additionally, the upper bound for the numpy dependency was updated in setup.cfg.

Class diagram showing dependency version constraints

classDiagram
    class DependencyConstraints {
        +numpy: '>=1.21.2,<2.3'
        +ruamel_yaml: '0.18.10'
        +scipy: '1.15.1'
    }
    note for DependencyConstraints "Updated version constraints"

Loading

File-Level Changes

Change	Details	Files
Update numpy dependency to 2.2.1	Updated numpy from 2.0.2 to 2.2.1. Updated the upper bound for numpy to <2.3.	setup.cfg
Update ruamel-yaml dependency to 0.18.10	Updated ruamel-yaml from 0.18.6 to 0.18.10.
Update scipy dependency to 1.15.1	Updated scipy from 1.14.1 to 1.15.1.

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We have skipped reviewing this pull request. It seems to have been created by a bot (hey, dependabot[bot]!). We assume it knows what it's doing!

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Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
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0.0% Coverage on New Code
0.0% Duplication on New Code

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