deps: bump the python-dependencies group across 1 directory with 6 updates by dependabot[bot] · Pull Request #106 · ml4t/engineer

dependabot · 2026-10-19T10:22:43Z

Bumps the python-dependencies group with 6 updates in the / directory:

Package	From	To
numpy	`2.5.3`	`2.5.4`
shap	`0.53.0`	`0.54.1`
hypothesis	`6.169.0`	`6.170.1`
ruff	`0.17.0`	`0.17.1`
pre-commit	`4.6.2`	`4.7.0`
ty	`0.0.86`	`0.0.89`

Updates numpy from 2.5.3 to 2.5.4

Release notes

Sourced from numpy's releases.

v2.5.4 (Oct 10, 2026)

NumPy 2.5.4 Release Notes

Released on 2026-10-10.

NumPy 2.5.4 is a patch release that fixes bugs discovered after the 2.5.3 release. Highlights are:

Many typing fixes and improvements,

A workaround for the MSVC 19.51 bug, see below.

This release supports Python versions 3.12-3.15.

Improvements

numpy.linalg.svd and numpy.linalg.lstsq now raise for inputs containing infinities instead of returning garbage results.

Fixed hangs in numpy.linalg.svd and numpy.linalg.lstsq for certain inputs containing infinities for recent versions of some LAPACK implementations.

numpy.linalg.cond now handles non-finite inputs more consistently.

(gh-32593)

StringDType hashing with NaN sentinels

StringDType instances with equivalent floating-point NaN sentinels now have equal hashes. Previously, distinct NaN objects could produce equal dtype instances with different hashes, causing dictionary lookups and set deduplication to fail.

(gh-32563)

Changes

MaskedArray resets a fill_value that cannot be represented in a new dtype

A fill_value copied from a source array is now reset to the default fill_value for the new dtype when it cannot be represented in that dtype. Previously the copied value could be stale: ufuncs that change dtype left the result holding a fill_value typed for the old dtype, which raised a TypeError only when something later validated it (such as .view()), and a floating point fill_value that overflows an integer dtype was kept as an out-of-range value together with a RuntimeWarning. Both now fall back to the default, including when a masked array is passed to MaskedArray with a different dtype. A fill_value given explicitly by the user is still validated and raises as before. This can now raise a ComplexWarning if the fill_value is complex and the new dtype is real.

... (truncated)

Commits

a3d0ef1 Merge pull request #32969 from charris/prepare-2.5.4
087b536 MAINT: Make OpenBLAS version check use 2.5.x branch.
91acd87 REL: Prepare for the NumPy 2.5.4 release.
9cc555b Merge pull request #32956 from charris/backport-typing-1
e04b972 TYP: dtype[void].names: allow setting with list (#32943)
d929969 TYP: timedelta64: datetime.timedelta construction isn't deprecated (#...
839467f TYP: ma.getmaskarray: accept array-likes (#32934)
64b721b TYP: polynomial: accept scalar coef in the poly constructors (#32931)
06b7ad2 TYP: void: accept any dtype: str in constructor calls (#32928)
c7bcd2c TYP: place: widen mask (#32926)
Additional commits viewable in compare view

Updates shap from 0.53.0 to 0.54.1

Release notes

Sourced from shap's releases.

0.54.1

SHAP v0.54.1

Highlights

CUDA acceleration with shap-cuda

GPU support now lives in the separate shap-cuda package, providing the CUDA-accelerated backend for shap.GPUTreeExplainer. The GPU wheel workflow builds CUDA-enabled wheels and tests them on AWS GPU runners before publishing. By @CloseChoice in shap/shap#5140.

The GPU TreeExplainer notebook has also been refreshed by @RAMitchell in shap/shap#5220.

What's Changed

Enhancements

shap.plots.violin now accepts an ax argument and returns the axes, making it easier to customize plots and compose subplots. By @adt-kmr in shap/shap#5218.

Maintenance

Remove unused global-path-dependent Tree SHAP code. By @RAMitchell in shap/shap#5223.

Documentation

Fix typos in the "An introduction to explainable AI" notebook. By @Yaqiao-chi-helen in shap/shap#5225.

Fix typos in comments, docstrings, and an error message. By @guptaishaan in shap/shap#5213.

Fix typos and replace the deprecated API reference in the LinearExplainer correlation notebook with maskers.Impute(data). By @ojuschugh1 in shap/shap#5172.

New Contributors

@Yaqiao-chi-helen made their first contribution in shap/shap#5225.

@guptaishaan made their first contribution in shap/shap#5213.

@ojuschugh1 made their first contribution in shap/shap#5172.

Full Changelog: shap/shap@v0.53.0...v0.54.1

Full Changelog: shap/shap@v0.53.0...v0.54.1

Commits

4f8a9c9 CI: fix versioning for releases
7d48b30 ENH: add shap-cuda package and distribute via CI (#5140)
a7766a4 Fix typos and update deprecated API in LinearExplainer correlation notebook (...
62c0ca8 DOCS: fix typos in comments, docstring and error message (#5213)
c11040e DOCS: Fix typos in "An introduction to explainable AI" notebook (#5225)
c61c426 Remove unused global-path-dependent Tree SHAP code (#5223)
1b92ea0 DOCS: Refresh GPU TreeExplainer notebook (#5220)
69b04e2 ENH: accept and return ax in shap.plots.violin (#5218)
7072995 MAINT: Bump actions/cache from 4.3.0 to 6.1.0 (#5193)
833fcab add new bundle
Additional commits viewable in compare view

Updates hypothesis from 6.169.0 to 6.170.1

Commits

718686d Bump hypothesis version to 6.170.1 and update changelog
ba6c3e3 Merge pull request #4834 from Zac-HD/claude/hypothesis-4458-prototypes-nqza1f
7572cd0 Bump hypothesis version to 6.170.0 and update changelog
1ad039f Merge pull request #4871 from Zac-HD/claude/hypothesis-conformance-tests-c6877l
a03eb1b Merge pull request #4895 from TaiSakuma/add-hypothesis-awkward
7219a20 Strengthen provider conformance tests and fix BytestringProvider
e7c0eb9 Bump hypothesis version to 6.169.4 and update changelog
c3705d2 Merge pull request #4898 from Arjun-Aravind/fix/unresolved-lazy-annotations
6ec54d5 Bump hypothesis version to 6.169.3 and update changelog
37c6420 Merge pull request #4903 from MarcoGorelli/random-seed-signature
Additional commits viewable in compare view

Updates ruff from 0.17.0 to 0.17.1

Release notes

Sourced from ruff's releases.

0.17.1

Release Notes

Released on 2026-10-15.

Preview features

[pycodestyle] Don't treat None, True, or False as keywords (E271-E274) (#29322)

Bug fixes

Fix dedent with multiple leading comments (#29382)

[flake8-pyi] Detect legacy positional-only parameters in __new__ methods (PYI063) (#28502)

[flake8-pyi] Fix false positives on quoted annotations (PYI036) (#29274)

[perflint] Avoid invalid comprehension suggestions (PERF401, PERF403) (#29366)

Rule changes

Treat more collections and weakref containers as mutable (#29213)

Documentation

[flake8-import-conventions] Update default and example aliases (#29333)

Contributors

@fixfon

@mmaxjr

@joshuavetos

@nekomario28

@ntBre

@shan3520

Install ruff 0.17.1

Install prebuilt binaries via shell script
curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.17.1/ruff-installer.sh | sh
Install prebuilt binaries via powershell script
powershell -ExecutionPolicy Bypass -c "irm https://releases.astral.sh/github/ruff/releases/download/0.17.1/ruff-installer.ps1 | iex"
Download ruff 0.17.1

| File | Platform | Checksum |

... (truncated)

Changelog

Sourced from ruff's changelog.

0.17.1

Released on 2026-10-15.

Preview features

[pycodestyle] Don't treat None, True, or False as keywords (E271-E274) (#29322)

Bug fixes

Fix dedent with multiple leading comments (#29382)

[flake8-pyi] Detect legacy positional-only parameters in __new__ methods (PYI063) (#28502)

[flake8-pyi] Fix false positives on quoted annotations (PYI036) (#29274)

[perflint] Avoid invalid comprehension suggestions (PERF401, PERF403) (#29366)

Rule changes

Treat more collections and weakref containers as mutable (#29213)

Documentation

[flake8-import-conventions] Update default and example aliases (#29333)

Contributors

@fixfon

@mmaxjr

@joshuavetos

@nekomario28

@ntBre

@shan3520

Commits

4683270 Bump version to 0.17.1 (#29420)
3514027 [ty] Update typing conformance suite pin (#29417)
8294556 Update referenced PR security-review workflow (#29237)
d1e1b1f [ty] Preserve recursive aliases when rebuilding intersections (#29057)
9352615 [perflint] Avoid invalid comprehension suggestions (PERF401, PERF403) (...
83a3afc Fix dedent with multiple leading comments (#29382)
b42a873 [ty] Clarify object attribute write-contract rationale (#29384)
d01678e [ty] Clarify object attribute write-contract rationale (#29384)
355b42a [ty] Avoid writable override contracts from object (#29373)
e26e6d2 [ty] Collect intersection inference through constraint relations (#28677)
Additional commits viewable in compare view

Updates pre-commit from 4.6.2 to 4.7.0

Release notes

Sourced from pre-commit's releases.

pre-commit v4.7.0

Fixes

Fix language: node hooks during commit with -a or inside a submodule.

Regressed in 4.6.1.

#3773 issue by @cbirkhold.

#3774 PR by @cbirkhold.

Changelog

Sourced from pre-commit's changelog.

4.7.0 - 2026-10-12

Fixes

Fix language: node hooks during commit with -a or inside a submodule.

Regressed in 4.6.1.

#3773 issue by @cbirkhold.

#3774 PR by @cbirkhold.

Commits

65bb884 v4.7.0
73926c1 Merge pull request #3774 from cbirkhold/node-no-git-env-npm-install
860d07d don't leak GIT_* env into npm install for language: node
9ad8a0a Merge pull request #3775 from pre-commit/contextlib-chdir
9905e88 use contextlib.chdir
59cb792 Merge pull request #3771 from pre-commit/all-repos_autofix_py311-plus
2be1701 remove triple-nested withs for 3.14 coverage
4c8d22a py311+
c429238 Merge pull request #3770 from pre-commit/pre-commit-ci-update-config
f49e251 [pre-commit.ci] pre-commit autoupdate
Additional commits viewable in compare view

Updates ty from 0.0.86 to 0.0.89

Release notes

Sourced from ty's releases.

0.0.89

Release Notes

Released on 2026-10-16.

Core type checking
Added support for return type inference for unannotated functions and methods (#29253).

Return type inference is currently disabled by default. Enable it with the analysis.return-type-inference setting in pyproject.toml:
[tool.ty.analysis]
return-type-inference = "always"
Or in ty.toml:
[analysis]
return-type-inference = "always"
Please share your feedback, especially any problems you encounter, in the return type inference feedback issue.
Sync vendored typeshed stubs (#29402). Typeshed diff
Bug fixes

Avoid a panic when negating dynamic type aliases (#29427)

Widen tuple literal lengths when other collection elements contain nested tuple types (#29147)

Report invalid Generic and Protocol arguments containing nested variadic type variables (#29146)

Performance

Speed up generic class-pattern narrowing by skipping impossible intersection comparisons (#29240)

Contributors

@carljm

@charliermarsh

@sharkdp

Install ty 0.0.89

Install prebuilt binaries via shell script
curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ty/releases/download/0.0.89/ty-installer.sh | sh

... (truncated)

Changelog

Sourced from ty's changelog.

0.0.89

Released on 2026-10-16.

Core type checking
Added support for return type inference for unannotated functions and methods (#29253).

Return type inference is currently disabled by default. Enable it with the analysis.return-type-inference setting in pyproject.toml:
[tool.ty.analysis]
return-type-inference = "always"
Or in ty.toml:
[analysis]
return-type-inference = "always"
Please share your feedback, especially any problems you encounter, in the return type inference feedback issue.
Sync vendored typeshed stubs (#29402). Typeshed diff
Bug fixes

Avoid a panic when negating dynamic type aliases (#29427)

Widen tuple literal lengths when other collection elements contain nested tuple types (#29147)

Report invalid Generic and Protocol arguments containing nested variadic type variables (#29146)

Performance

Speed up generic class-pattern narrowing by skipping impossible intersection comparisons (#29240)

Contributors

@carljm

@charliermarsh

@sharkdp

0.0.88

Released on 2026-10-15.

Bug fixes

Avoid panics and hangs involving recursive type aliases and intersections (#29057)

Fix false invalid-mutable-override errors when overriding object attributes (#29373)

... (truncated)

Commits

82b0fd4 Bump version to 0.0.89 (#4740)
5370198 Update dependency python to 3.14 (#4721)
64e7f18 Bump version to 0.0.88 (#4732)
88c50d5 Budget the daily fuzz run based on setup time (#4706)
ec60e71 Document and lint the manually maintained release workflow (#4320)
dbc632a Update dependency prek to v0.5.3 (#4719)
7aa0f34 Update astral-sh/setup-uv action to v10.3.0 (#4720)
2eefac0 Update prek dependencies (#4722)
ea4c3d2 Bump version to 0.0.87 (#4718)
1e7a76d Require hashes for build dependencies (#4714)
Additional commits viewable in compare view

…dates Bumps the python-dependencies group with 6 updates in the / directory: | Package | From | To | | --- | --- | --- | | [numpy](https://github.com/numpy/numpy) | `2.5.3` | `2.5.4` | | [shap](https://github.com/shap/shap) | `0.53.0` | `0.54.1` | | [hypothesis](https://github.com/HypothesisWorks/hypothesis) | `6.169.0` | `6.170.1` | | [ruff](https://github.com/astral-sh/ruff) | `0.17.0` | `0.17.1` | | [pre-commit](https://github.com/pre-commit/pre-commit) | `4.6.2` | `4.7.0` | | [ty](https://github.com/astral-sh/ty) | `0.0.86` | `0.0.89` | Updates `numpy` from 2.5.3 to 2.5.4 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v2.5.3...v2.5.4) Updates `shap` from 0.53.0 to 0.54.1 - [Release notes](https://github.com/shap/shap/releases) - [Changelog](https://github.com/shap/shap/blob/main/docs/release_notes.rst) - [Commits](shap/shap@v0.53.0...v0.54.1) Updates `hypothesis` from 6.169.0 to 6.170.1 - [Release notes](https://github.com/HypothesisWorks/hypothesis/releases) - [Commits](HypothesisWorks/hypothesis@v6.169.0...v6.170.1) Updates `ruff` from 0.17.0 to 0.17.1 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@0.17.0...0.17.1) Updates `pre-commit` from 4.6.2 to 4.7.0 - [Release notes](https://github.com/pre-commit/pre-commit/releases) - [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md) - [Commits](pre-commit/pre-commit@v4.6.2...v4.7.0) Updates `ty` from 0.0.86 to 0.0.89 - [Release notes](https://github.com/astral-sh/ty/releases) - [Changelog](https://github.com/astral-sh/ty/blob/main/CHANGELOG.md) - [Commits](astral-sh/ty@0.0.86...0.0.89) --- updated-dependencies: - dependency-name: hypothesis dependency-version: 6.170.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: numpy dependency-version: 2.5.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: pre-commit dependency-version: 4.7.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: ruff dependency-version: 0.17.1 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: shap dependency-version: 0.54.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: ty dependency-version: 0.0.88 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-dependencies ... Signed-off-by: dependabot[bot] <support@github.com>

dependabot Bot added dependencies Dependency updates python Python dependencies labels Oct 19, 2026

dependabot Bot changed the title ~~deps: bump the python-dependencies group with 6 updates~~ deps: bump the python-dependencies group across 1 directory with 6 updates Oct 20, 2026

dependabot Bot force-pushed the dependabot/uv/python-dependencies-f2631800de branch 2 times, most recently from 42f47d3 to 5b929f0 Compare October 21, 2026 03:12

dependabot Bot force-pushed the dependabot/uv/python-dependencies-f2631800de branch from 5b929f0 to 15cba53 Compare October 21, 2026 05:55

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deps: bump the python-dependencies group across 1 directory with 6 updates - #106

deps: bump the python-dependencies group across 1 directory with 6 updates#106
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v2.5.4 (Oct 10, 2026)

NumPy 2.5.4 Release Notes

Improvements

StringDType hashing with NaN sentinels

Changes

MaskedArray resets a fill_value that cannot be represented in a new dtype

0.54.1

SHAP v0.54.1

Highlights

CUDA acceleration with shap-cuda

What's Changed

Enhancements

Maintenance

Documentation

New Contributors

0.17.1

Release Notes

Preview features

Bug fixes

Rule changes

Documentation

Contributors

Install ruff 0.17.1

Install prebuilt binaries via shell script

Install prebuilt binaries via powershell script

Download ruff 0.17.1

0.17.1

Preview features

Bug fixes

Rule changes

Documentation

Contributors

pre-commit v4.7.0

Fixes

4.7.0 - 2026-10-12

Fixes

0.0.89

Release Notes

Core type checking

Bug fixes

Performance

Contributors

Install ty 0.0.89

Install prebuilt binaries via shell script

0.0.89

Core type checking

Bug fixes

Performance

Contributors

0.0.88

Bug fixes

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dependabot Bot commented on behalf of github Oct 19, 2026 •

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`MaskedArray` resets a fill_value that cannot be represented in a new dtype

CUDA acceleration with `shap-cuda`