Bump the minor_and_patch group across 1 directory with 6 updates

[dependabot]

Bumps the minor_and_patch group with 6 updates in the / directory:

Package	From	To
numpy	2.1.3	2.2.1
scipy	1.14.1	1.15.1
matplotlib	3.9.2	3.10.0
pylint	3.3.1	3.3.3
mypy	1.13.0	1.14.1
pytest	8.3.3	8.3.4

Updates numpy from 2.1.3 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)

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 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

Updates matplotlib from 3.9.2 to 3.10.0

Release notes

Sourced from matplotlib's releases.

REL: v3.10.0

Highlights of this release include:

- Preliminary support for free-threaded CPython 3.13
- New more-accessible color cycle
- Dark-mode diverging colormaps
- Exception handling control
- InsetIndicator artist
- FillBetweenPolyCollection
- Fill between 3D lines
- Data in 3D plots can now be dynamically clipped to the axes view limits
- Rotating 3d plots with the mouse
- Increased Figure limits with Agg renderer
- Subfigures no longer provisional
- Subfigures are now added in row-major order

Matplotlib v3.10.0rc1

This is the first release candidate for Matplotlib 3.10.0

REL: 3.9.4

This is the fourth bugfix release of the 3.9.x series.

This release contains two bug-fixes:

• Fix toolbar icons in GTK backend
• Fix Poly3DCollection initialization with list of lists

REL: 3.9.3

This is the third bugfix release of the 3.9.x series.

This release contains several bug-fixes and adjustments:

• Fix axline with extremely small slopes
• Fix axline with non-linear axis scales
• Fix minimumSizeHint with Qt backend
• Fix config directory usage when it's behind a symlink
• Fix draggable legend when blitting is enabled
• Fix high CPU utilization in the macosx backend
• Fix multiple hatch edgecolors passed to contourf
• Improve compatibility with pytest 8.2.0

Commits

• 8d64f03 REL: v3.10.0 release
• d9dfee8 [doc] Fix dead links
• 87a603f Update release notes for 3.10.0
• cdecf97 Update github stats for 3.10
• b8d19bd Merge pull request #29306 from meeseeksmachine/auto-backport-of-pr-29242-on-v...
• a42d0ed Backport PR #29242: DOC: Add kwdoc list to scatter() docstring
• 1900640 Merge pull request #29299 from QuLogic/merge-v39x
• 815389c Merge branch 'v3.9.x' into v3.10.x
• 73873c0 DOC: Create release notes for 3.9.4
• 9d17a2b DOC: Add Zenodo DOI for 3.9.4
• Additional commits viewable in compare view

Updates pylint from 3.3.1 to 3.3.3

Commits

• c28580b Bump pylint to 3.3.3, update changelog
• 1f9b947 Bump astroid from 3.3.5 to 3.3.8 (#10125) (#10155)
• 96d1303 Bump actions/cache from 4.1.2 to 4.2.0 (#10123) (#10154)
• a7202b1 Fix Python 3.12 generic type syntax (#10135) (#10146)
• 90cb29d [mypy] Use type-setuptools instead of types-pkg-resources (#10120)
• 9955701 Fix 'use-implicit-booleaness' wrongly emitted for generators. (#10107) (#10109)
• a5a1bc3 Bump pylint to 3.3.2, update changelog (#10088)
• 621ecf6 Fix potential-index-error false positive when iterable contains starred ele...
• 5597aae Fix source root not recognized (#10036) (#10083)
• ea8ed7e Bump astroid to 3.3.5 (#10004) (#10005)
• Additional commits viewable in compare view

Updates mypy from 1.13.0 to 1.14.1

Changelog

Sourced from mypy's changelog.

Mypy Release Notes

Next release

Performance improvements

TODO

Drop Support for Python 3.8

Mypy no longer supports running with Python 3.8, which has reached end-of-life. When running mypy with Python 3.9+, it is still possible to type check code that needs to support Python 3.8 with the --python-version 3.8 argument. Support for this will be dropped in the first half of 2025!

Contributed by Marc Mueller (PR 17492).

Mypyc accelerated mypy wheels for aarch64

Mypy can compile itself to C extension modules using mypyc. This makes mypy 3-5x faster than if mypy is interpreted with pure Python. We now build and upload mypyc accelerated mypy wheels for manylinux_aarch64 to PyPI, making it easy for users on such platforms to realise this speedup.

Contributed by Christian Bundy (PR mypy_mypyc-wheels#76)

--strict-bytes

By default, mypy treats an annotation of bytes as permitting bytearray and memoryview. PEP 688 specified the removal of this special case. Use this flag to disable this behavior. --strict-bytes will be enabled by default in mypy 2.0.

Contributed by Ali Hamdan (PR 18137) and Shantanu Jain (PR 13952).

Improvements to partial type handling in loops

This change results in mypy better modelling control flow within loops and hence detecting several issues it previously did not detect. In some cases, this change may require use of an additional explicit annotation of a variable.

Contributed by Christoph Tyralla (PR 18180).

(Speaking of partial types, another reminder that mypy plans on enabling --local-partial-types by default in mypy 2.0).

Better line numbers for decorators and slice expressions

Mypy now uses more correct line numbers for decorators and slice expressions. In some cases, this may necessitate changing the location of a # type: ignore comment.

... (truncated)

Commits

• 251d12f Remove +dev from version for release 1.14.1
• 667e5f7 Revert "Remove redundant inheritances from Iterator in builtins" (#18324)
• 67f673a Fix enum truthiness for StrEnum (#18379)
• 3755abb Fix getargs argument passing (#18350)
• b9fa8ee Update version to 1.14.1+dev for point release
• 6f37859 Remove +dev from version for release 1.14
• 5a6a754 Minor updates to 1.14 changelog (#18310)
• 9772d48 Update changelog for release 1.14 (#18301)
• 92473c8 Warn about --follow-untyped-imports (#18249)
• e6ce8be PEP 702 (@​deprecated): descriptors (#18090)
• Additional commits viewable in compare view

Updates pytest from 8.3.3 to 8.3.4

Release notes

Sourced from pytest's releases.

8.3.4

pytest 8.3.4 (2024-12-01)

Bug fixes

• #12592: Fixed KeyError{.interpreted-text role="class"} crash when using --import-mode=importlib in a directory layout where a directory contains a child directory with the same name.

• #12818: Assertion rewriting now preserves the source ranges of the original instructions, making it play well with tools that deal with the AST, like executing.

• #12849: ANSI escape codes for colored output now handled correctly in pytest.fail{.interpreted-text role="func"} with [pytrace=False]{.title-ref}.

• #9353: pytest.approx{.interpreted-text role="func"} now uses strict equality when given booleans.

Improved documentation

• #10558: Fix ambiguous docstring of pytest.Config.getoption{.interpreted-text role="func"}.

• #10829: Improve documentation on the current handling of the --basetemp option and its lack of retention functionality (temporary directory location and retention{.interpreted-text role="ref"}).

• #12866: Improved cross-references concerning the recwarn{.interpreted-text role="fixture"} fixture.

• #12966: Clarify filterwarnings{.interpreted-text role="ref"} docs on filter precedence/order when using multiple @pytest.mark.filterwarnings <pytest.mark.filterwarnings ref>{.interpreted-text role="ref"} marks.

Contributor-facing changes

• #12497: Fixed two failing pdb-related tests on Python 3.13.

Commits

• 53f8b4e Update pypa/gh-action-pypi-publish to v1.12.2
• 98dff36 Prepare release version 8.3.4
• 1b474e2 approx: use exact comparison for bool (#13013)
• b541721 docs: Fix wrong statement about sys.modules with importlib import mode (#1298...
• 16cb87b pytest.fail: fix ANSI escape codes for colored output (#12959) (#12990)
• be6bc81 Issue #12966 Clarify filterwarnings docs on precedence when using multiple ma...
• 7aeb72b Improve docs on basetemp and retention (#12912) (#12928)
• c875841 Merge pull request #12917 from pytest-dev/patchback/backports/8.3.x/ded1f44e5...
• 6502816 Merge pull request #12913 from jakkdl/dontfailonbadpath
• 52135b0 Merge pull request #12885 from The-Compiler/pdb-py311 (#12887)
• Additional commits viewable in compare view

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