chore(deps): bump the lockfile-minor-patch group with 4 updates

[dependabot]

Bumps the lockfile-minor-patch group with 4 updates: mpi4py, numpy, snakemake and black.

Updates mpi4py from 4.1.1 to 4.1.2

Release notes

Sourced from mpi4py's releases.

4.1.2

• Fix build issues from breaking changes in setuptools 81.

• Support Windows builds with Meson and Intel MPI.

• PyPy wheels are no longer published.

Full Changelog: mpi4py/mpi4py@4.1.1...4.1.2

Changelog

Sourced from mpi4py's changelog.

Release 4.1.2 [2026-05-16]

• Fix build issues from breaking changes in setuptools 81.

• Support Windows builds with Meson and Intel MPI.

• PyPy wheels are no longer published.

Commits

• 1c40e59 Bump version number to 4.1.2
• 5ad9820 chore: Update changelog
• c9cee66 chore: Update year to 2026
• f75876c GHA: Switch to actions/attest@v4
• 70fb888 GHA: Bump actions/checkout from 5 to 6
• 582c1dd GHA: Update use of actions/setup-python to skip upgrading pip
• a0d4854 CD: PyPy wheels are no longer published
• 7a260c8 CD: Use micromamba==2.5.0-2
• c77e8a2 test: Workaround MPICH 5.0.1 issues with MPI_LONG_DOUBLE
• 7abdae3 test: Skip long-double with MPICH 5.0 on macOS arm64
• Additional commits viewable in compare view

Updates numpy from 2.4.4 to 2.4.6

Release notes

Sourced from numpy's releases.

v2.4.6 (May 18, 2026)

NumPy 2.4.6 Release Notes

NumPy 2.4.6 is a quick release that fixes a regression discovered in the 2.4.5 release.

This release supports Python versions 3.11-3.14

Contributors

A total of 4 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• !EarlMilktea
• Charles Harris
• Sebastian Berg
• Warren Weckesser

Pull requests merged

A total of 4 pull requests were merged for this release.

• #31444: MAINT: Prepare 2.4.x for further development
• #31453: BUG: Fix regression in arr.conj()
• #31459: BUG: np.linalg.svd(..., hermitian=True) returns non-unitary...
• #31460: BUG: Don't call INCREF/DECREF on descr in NpyStringAcquireAllocator...

v2.4.5 (May 15, 2026)

NumPy 2.4.5 Release Notes

NumPy 2.4.5 is a patch release that fixes bugs discovered after the 2.4.4 release, has some typing improvements, and maintains infrastructure.

This release supports Python versions 3.11-3.14

Contributors

A total of 17 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• Aleksei Nikiforov
• Anarion Zuo +
• Ankit Ahlawat
• Breno Favaretto +
• Charles Harris
• Igor Krivenko +
• Ijtihed Kilani +
• Joren Hammudoglu
• Maarten Baert +

... (truncated)

Commits

• b832a09 Merge pull request #31462 from charris/prepare-2.4.6
• 57cc147 REL: Prepare for the NumPy 2.4.6 release
• 0c72b0b Merge pull request #31459 from charris/backport-31347
• 9778d26 BUG: core: Don't call INCREF/DECREF on descr in NpyStringAcquireAllocator. (#...
• e0e3876 BUG: core: Don't call INCREF/DECREF on descr in NpyStringAcquireAllocator. (#...
• d1bffeb BUG: np.linalg.svd(..., hermitian=True) returns non-unitary vh (#31347)
• 8d8d7e5 Merge pull request #31453 from seberg/issue-31452
• bddaab7 BUG: Fix regression in arr.conj()
• 37a1ecc Merge pull request #31444 from charris/begin-2.4.6
• 3c0e043 MAINT: Prepare 2.4.x for further development
• Additional commits viewable in compare view

Updates snakemake from 9.20.0 to 9.21.0

Release notes

Sourced from snakemake's releases.

v9.21.0

9.21.0 (2026-05-13)

Features

• add a function to help with prepending arguments to filenames; close #672 (#4090) (14ccd1d)

Bug Fixes

• close plugin handlers after draining QueueListener in LoggerManager.stop() (#4137) (b2a9e69)

Performance Improvements

• adjust default sqlite PRAGMAs, auto detect network fstype (#4152) (3df2d35)

Changelog

Sourced from snakemake's changelog.

9.21.0 (2026-05-13)

Features

• add a function to help with prepending arguments to filenames; close #672 (#4090) (14ccd1d)

Bug Fixes

• close plugin handlers after draining QueueListener in LoggerManager.stop() (#4137) (b2a9e69)

Performance Improvements

• adjust default sqlite PRAGMAs, auto detect network fstype (#4152) (3df2d35)

Commits

• d853243 chore(main): release 9.21.0 (#4181)
• 3df2d35 perf: adjust default sqlite PRAGMAs, auto detect network fstype (#4152)
• 44d8976 test: docker://ubuntu too latest (#4194)
• 384b4a3 chore: restore previous environment setup as the reduced one does not work on...
• a45cc72 chore: fix envs to keep macos and win for py313
• 14ccd1d feat: add a function to help with prepending arguments to filenames; close #6...
• c0fd9a2 fix exclusion
• ae15b18 chore: exclude 311 and 312 from win and osx jobs
• 5ea77e5 fix formatting; streamline pixi envs
• b2a9e69 fix: close plugin handlers after draining QueueListener in LoggerManager.stop...
• See full diff in compare view

Updates black from 26.3.1 to 26.5.1

Release notes

Sourced from black's releases.

26.5.1

Stable style

• Fix unstable formatting of annotated assignments whose subscript annotation contains an inline comment (e.g. x: list[ # pyright: ignore[...]) (#5130)
• Preserve inline comments (including # type: ignore) immediately before a # fmt: skip line, avoiding AST equivalence failures (#5139)

Packaging

• Correct the version in the published executables (#5137)

Documentation

• Add Neovim integration guide covering conform.nvim, ALE, and simple command approaches (#5124)

26.5.0

Highlights

• Add support for unpacking in comprehensions (PEP 798) and for lazy imports (PEP 810), both new syntactic features in Python 3.15 (#5048)
• Python 3.15 is now supported. Compiled wheels are not yet provided for Python 3.15, so performance may be slower than on existing Python versions. Wheels will be provided once Python 3.15 is later in its release cycle. (#5127)

Stable style

• Fix # fmt: skip being ignored in nested if expressions with parenthesized in clauses (#4903)
• Add syntactic support for Python 3.15 (#5048)
• Fix crash when an f-string follows a # fmt: off comment inside brackets (#5097)
• Preserve multiline compound statement headers when # fmt: skip is placed on the colon line (#5117)

Preview style

• Improve heuristics around whether blank lines should appear before, within and after groups of same-name decorated functions (such as @overload groups) in .pyi stub files (#5021)
• Fix blank lines being removed between a function and a decorated class in .pyi stub files (#5092)
• Prevent string merger from creating unsplittable long lines when a pragma comment (e.g. # type: ignore) follows the closing bracket (#5096)

Packaging

• Run CI on 3.15 (#5127)

Output

... (truncated)

Changelog

Sourced from black's changelog.

Version 26.5.1

Stable style

• Fix unstable formatting of annotated assignments whose subscript annotation contains an inline comment (e.g. x: list[ # pyright: ignore[...]) (#5130)
• Preserve inline comments (including # type: ignore) immediately before a # fmt: skip line, avoiding AST equivalence failures (#5139)

Packaging

• Correct the version in the published executables (#5137)

Documentation

• Add Neovim integration guide covering conform.nvim, ALE, and simple command approaches (#5124)

Version 26.5.0

Highlights

• Add support for unpacking in comprehensions (PEP 798) and for lazy imports (PEP 810), both new syntactic features in Python 3.15 (#5048)
• Python 3.15 is now supported. Compiled wheels are not yet provided for Python 3.15, so performance may be slower than on existing Python versions. Wheels will be provided once Python 3.15 is later in its release cycle. (#5127)

Stable style

• Fix # fmt: skip being ignored in nested if expressions with parenthesized in clauses (#4903)
• Add syntactic support for Python 3.15 (#5048)
• Fix crash when an f-string follows a # fmt: off comment inside brackets (#5097)
• Preserve multiline compound statement headers when # fmt: skip is placed on the colon line (#5117)

Preview style

• Improve heuristics around whether blank lines should appear before, within and after groups of same-name decorated functions (such as @overload groups) in .pyi stub files (#5021)
• Fix blank lines being removed between a function and a decorated class in .pyi stub files (#5092)
• Prevent string merger from creating unsplittable long lines when a pragma comment (e.g. # type: ignore) follows the closing bracket (#5096)

Packaging

• Run CI on 3.15 (#5127)

... (truncated)

Commits

• 87928e6 Prepare release 26.5.1 (#5140)
• c970a49 Preserve comments before fmt: skip lines (#5139)
• 5809338 Preserve inline comments inside annotation subscripts (#5130)
• 61361b7 docs: add Neovim integration guide and fix http link (#5124)
• ebe6018 CI Hotfixes (#5136)
• 9cbd95f Fix publish binaries again on Windows (#5134)
• 3dc8e6c Add new changelog (#5132)
• 6d0fff0 Fix publish binaries workflow (#5133)
• d2490e2 Prepare release 26.5.0 (#5131)
• 2b13ea7 Preserve multiline headers with fmt skip (#5117)
• Additional commits viewable in compare view

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[cailmdaley]

Triage pass (dependabot-pr-triage convention, 2026-06-11): leaving open — this PR modifies pyproject.toml in addition to uv.lock, which puts it outside the routine lockfile-only merge path.

What changed in pyproject.toml:

• mpi4py>=4.0 → mpi4py>=4.1.2 (floor tightened to exact patch)
• numpy>=2.0 → numpy>=2.4.6 (floor tightened from major to exact patch)
• snakemake>=9.20.0 → snakemake>=9.21.0 (floor bumped one minor)

Tightening >= lower bounds narrows the installable range and is a policy decision for the maintainers (Martin/Lucie/Axel), not a mechanical lockfile update. If the intent is to track the lockfile version as the minimum, that's a deliberate call — please confirm and this can be merged; otherwise it may warrant splitting into a separate pyproject.toml PR.

CI is green (build-test-publish passes). The uv.lock changes look routine (118 add / 118 del across 2 files, all four bumps are minor/patch).

— Claude on behalf of Cail

[cailmdaley]

Merging per Cail's sign-off (2026-06-11) — lockfile-group minor/patch bumps, CI green. The held question (pyproject lower-bound bumps) was reviewed and accepted.

— Claude (Fable), on behalf of Cail