[MNT] Bump the python-packages group across 1 directory with 3 updates

[dependabot]

Updates the requirements on numpy, scipy and scikit-learn to permit the latest version.
Updates numpy to 2.2.0

Release notes

Sourced from numpy's releases.

2.2.0 (Dec 8, 2024)

NumPy 2.2.0 Release Notes

The NumPy 2.2.0 release is quick release that brings us back into sync with the usual twice yearly release cycle. There have been an number of small cleanups, as well as work bringing the new StringDType to completion and improving support for free threaded Python. Highlights are:

• New functions matvec and vecmat, see below.
• Many improved annotations.
• Improved support for the new StringDType.
• Improved support for free threaded Python
• Fixes for f2py

This release supports Python versions 3.10-3.13.

Deprecations

• _add_newdoc_ufunc is now deprecated. ufunc.__doc__ = newdoc should be used instead.

  (gh-27735)

Expired deprecations

• bool(np.array([])) and other empty arrays will now raise an error. Use arr.size > 0 instead to check whether an array has no elements.

  (gh-27160)

Compatibility notes

• numpy.cov now properly transposes single-row (2d array) design matrices when rowvar=False. Previously, single-row design matrices would return a scalar in this scenario, which is not correct, so this is a behavior change and an array of the appropriate shape will now be returned.

  (gh-27661)

New Features

• New functions for matrix-vector and vector-matrix products

  Two new generalized ufuncs were defined:

  • numpy.matvec - matrix-vector product, treating the arguments as stacks of matrices and column vectors,

... (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

• e7a123b Merge pull request #27928 from charris/prepare-2.2.0
• d97d071 MAINT: Try fixing MacOS cirrus build failures. [wheel build]
• 1ed7b67 REL: Prepare for the NumPy 2.2.0 release [wheel build]
• fd9e7ef Merge pull request #27916 from charris/backport-27915
• 2e0941f MAINT: Bump actions/cache from 4.1.2 to 4.2.0
• 013656d Merge pull request #27912 from charris/backport-27877
• 7895ba6 Merge pull request #27913 from charris/backport-27896
• ee8d1cd PERF: improve multithreaded ufunc scaling (#27896)
• 77fff6b ENH: Refactor __qualname__ across API (#27877)
• b30a338 Merge pull request #27911 from charris/backport-27891
• Additional commits viewable in compare view

Updates scipy to 1.14.1

Release notes

Sourced from scipy's releases.

SciPy 1.14.1 Release Notes

SciPy 1.14.1 adds support for Python 3.13, including binary wheels on PyPI. Apart from that, it is a bug-fix release with no new features compared to 1.14.0.

Authors

• Name (commits)
• h-vetinari (1)
• Evgeni Burovski (1)
• CJ Carey (2)
• Lucas Colley (3)
• Ralf Gommers (3)
• Melissa Weber Mendonça (1)
• Andrew Nelson (3)
• Nick ODell (1)
• Tyler Reddy (36)
• Daniel Schmitz (1)
• Dan Schult (4)
• Albert Steppi (2)
• Ewout ter Hoeven (1)
• Tibor Völcker (2) +
• Adam Turner (1) +
• Warren Weckesser (2)
• ਗਗਨਦੀਪ ਸਿੰਘ (Gagandeep Singh) (1)

A total of 17 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.

Commits

• 92d2a85 REL: 1.14.1 rel commit [wheel build]
• 85623a1 Merge pull request #21362 from tylerjereddy/treddy_1.14.1_backports
• d924005 MAINT: PR 21362 revisions [wheel build]
• b901a4e MAINT, CI: PR 21362 revisions [wheel build]
• 2a7ec60 MAINT, BLD: PR 21362 revisions [wheel build]
• f4f084d MAINT, CI: PR 21362 revisions [wheel build]
• b712fc6 DOC: update 1.14.1 relnotes [wheel build]
• cdd5aca MAINT: special: Accommodate changed integer handling in NumPy 2.0. (#21401)
• 0f91838 BLD: cp313 wheels on manylinux_aarch64 (#21409)
• 6dd0b00 MAINT, CI: wheel build changes [wheel build]
• Additional commits viewable in compare view

Updates scikit-learn to 1.5.2

Release notes

Sourced from scikit-learn's releases.

Scikit-learn 1.5.2

We're happy to announce the 1.5.2 release.

This release contains fixes for a few regressions introduced in 1.5.

You can see the changelog here: https://scikit-learn.org/stable/whats_new/v1.5.html#version-1-5-2

You can upgrade with pip as usual:

pip install -U scikit-learn

The conda-forge builds can be installed using:

conda install -c conda-forge scikit-learn

Thanks to everyone who contributed to this release !

Commits

• 156ef14 [cd build] trigger ci/cd
• 40c7416 DOC update the list of contributors for 1.5.2 (#29819)
• c119c7e DOC add orphan option to developers/index.rst
• 4d838dc TST fix tolerance as in #29400
• 2e79f52 DOC fix entry in changelog for backport happening in 1.5.2 (#29815)
• c735641 MAINT install setuptools for debian-32bits
• c993dd2 DOC update repr for NumPy 2.0
• 8ade4f5 MAINT bump from 1.5.1 to 1.5.2
• 04b71d2 FIX solve conflict git
• b5b5017 MAINT update lock file
• Additional commits viewable in compare view

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