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Bumps the python group with 12 updates in the / directory:

Package From To
mlflow 3.15.1 3.16.0
numba 0.66.0 0.67.0
numpy 2.4.6 2.5.3
pandera 0.32.1 0.33.1
pydantic 2.13.4 2.13.5
scikit-learn 1.9.0 1.9.1
shap 0.49.1 0.52.0
lefthook 2.1.10 2.1.12
ruff 0.16.2 0.16.7
ty 0.0.69 0.0.80
validate-pyproject 0.25 0.26
nbformat 5.11.0 5.11.1

Updates mlflow from 3.15.1 to 3.16.0

Release notes

Sourced from mlflow's releases.

MLflow 3.16.0 includes several major features and improvements

Major New Features

  • 🎨 Custom Trace Views: Design your own trace UI in plain English — describe the view you want and the MLflow Assistant builds it for you, laying out exactly the fields you care about with no config files or custom code. Save, name, and reuse views per experiment so your whole team shares the same lens on your traces.
  • 🔭 Redesigned Trace Experience (now default): The trace explorer has been rebuilt from the ground up and is now the default — tighter row density, cleaner navigation, and a redesigned span-tree view. Reorder columns, add configurable custom columns from any trace tag or metadata field, and find multi-turn conversations inline via session grouping.
  • 🔗 Span Links: Spans rarely stand alone. MLflow 3.16.0 adds first-class span links so relationships between spans — a retrieval step, a tool call, a downstream trace — are captured and navigable. Record links in your SDK and the trace explorer surfaces them in a dedicated Links tab to jump straight to the destination span.

Breaking changes:

Features:

... (truncated)

Changelog

Sourced from mlflow's changelog.

3.16.0 (2026-09-03)

MLflow 3.16.0 includes several major features and improvements

Breaking changes:

Features:

... (truncated)

Commits

Updates numba from 0.66.0 to 0.67.0

Release notes

Sourced from numba's releases.

0.67.0

Major Numba release, adding NumPy 2.5 support. Please view the release notes here: https://numba.readthedocs.io/en/0.67.0/release/0.67.0-notes.html

Commits
  • 3190b91 Merge pull request #10772 from swap357/release0.67
  • f68f603 add current pr on 0.67 pr list
  • 86a975c update final release date for 0.67
  • c7f14cf Merge pull request #10726 from swap357/pin_deps_0.67
  • 123fa28 update test refs and pin dependencies for release0.67
  • 0c89330 Merge pull request #10724 from swap357/changelog_0.67
  • ffaa017 Merge pull request #10723 from swap357/update_version_support_table_0.67.0rc1
  • af0d879 fix wrapping on release notes
  • a5e4654 Update docs/source/release/0.67.0-notes.rst
  • e85720e Update docs/source/release/0.67.0-notes.rst
  • Additional commits viewable in compare view

Updates numpy from 2.4.6 to 2.5.3

Release notes

Sourced from numpy's releases.

v2.5.3 (Sep 6, 2026)

NumPy 2.5.3 Release Notes

The NumPy 2.5.3 is a patch release that fixes bugs discovered after the 2.5.2 release. Apart from the usual bug and maintenance work, there are a number of StringDType related fixes for problems discovered during the ongoing string work in the main branch.

This release supports Python versions 3.12-3.15

Changes

  • Casting a fixed-width byte string array (np.bytes_) to StringDType now raises TypeError when the bytes are not valid UTF-8. Previously the invalid bytes were stored as-is and later caused undefined behavior in string operations.

    (gh-32296)

  • MaskedArray._fill_value would become stale when ufuncs that change dtype left the result holding a fill_value typed for the old dtype. The mismatch was silent until something later called _check_fill_value, such as .view(), and then a TypeError would be raised. Now, when the copied fill_value is no longer valid for the new dtype, fall back to the default fill_value for that dtype instead of propagating the stale value. This may raise a ComplexWarning if the fill_value is complex and the new dtype is real.

    (gh-32423)

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
  • Iason Krommydas
  • James Davies +
  • Joren Hammudoglu
  • Maanas Arora
  • Matti Picus
  • Nathan Goldbaum
  • Shikhar Goel +
  • Yeonho Kim +

Pull requests merged

A total of 27 pull requests were merged for this release.

  • #32235: MAINT: Prepare 2.5.x for further development

... (truncated)

Commits
  • dd88c0c Merge pull request #32511 from charris/prepare-2.5.3
  • edcac6a REL: Prepare for the NumPy 2.5.3 release
  • fd4d908 Merge pull request #32509 from charris/backport-32496
  • 65bb1da BUG: fix crash in ufunc.resolve_dtypes with a Python scalar type (#32496)
  • 294956e Merge pull request #32506 from charris/backport-32503
  • 26428d9 DOC: fix scipy docs links in intersphinx mapping (#32507)
  • 5fab1cb DOC: use static scipy doc site for intershpinx (#32503)
  • 7beed2f Merge pull request #32481 from ngoldbaum/stringdtype-backport
  • 8972f70 Merge pull request #32478 from charris/backport-32466
  • ab1b589 Merge pull request #32477 from charris/backport-32423
  • Additional commits viewable in compare view

Updates pandera from 0.32.1 to 0.33.1

Release notes

Sourced from pandera's releases.

v0.33.1

What's Changed

New Contributors

Full Changelog: unionai-oss/pandera@v0.33.0...v0.33.1

v0.33.0: Introducing pandera CLI, support pyarrow table

What's Changed

New Contributors

... (truncated)

Commits
  • 62f55e2 ci: add actionlint workflow and pre-commit hook (#2436)
  • 857a3b2 Warn when optional columns are missing via on_missing option (#2447)
  • 2e307b7 fix: restore optional-column semantics for bare T | None annotations (#2458)
  • ccdabde docs: announce Pandera CLI and PyArrow support in banner (#2456)
  • c37a5b2 fix: respect pydantic serialization aliases (#2449)
  • b6ecd53 fix(docs): only apply pyspark JDK24 security-manager opt-in flag on JDK 24 (#...
  • 384d48b fix(docs): make intersphinx fetch resilient to transient failures (#2452)
  • f1245c2 ci: only run unit tests for changed areas (#2450)
  • 46b1495 fix(decorators): support keyword-only / variadic functions in check_input (#2...
  • 9e268ac fix: handle scalar groupby keys in _format_groupby_input (#2420)
  • Additional commits viewable in compare view

Updates pydantic from 2.13.4 to 2.13.5

Release notes

Sourced from pydantic's releases.

v2.13.5 (2026-08-28)

What's Changed

Fixes

  • Allow reuse of validators when plugins are set by @​Viicos in #13535
  • Fix missing GC traversal on some pydantic-core struct fields by @​Viicos in #13624
  • Fix missing GC traversal in pydantic-core for GeneralFieldsSerializer by @​Viicos in #13629
  • Count validated model fields once in smart unions by @​tamird in #13731
Changelog

Sourced from pydantic's changelog.

v2.13.5 (2026-08-28)

GitHub release

What's Changed

Fixes

  • Allow reuse of validators when plugins are set by @​Viicos in #13535
  • Fix missing GC traversal on some pydantic-core struct fields by @​Viicos in #13624
  • Fix missing GC traversal in pydantic-core for GeneralFieldsSerializer by @​Viicos in #13629
  • Count validated model fields once in smart unions by @​tamird in #13731
Commits
  • 001dea0 Bump pypa/gh-action-pypi-publish action to v1.14.2
  • 558379f Bump twine to v7.0.0
  • 2cfd5d3 Do not check for docs build
  • a735bee Fix more Clippy lints
  • 7eed4a1 Fix Clippy 0.1.95 warnings
  • b353bbb Prepare release v2.13.5
  • 63d2ccc Count validated model fields once in smart unions
  • a53ec2e Speed up PyPy CI tests
  • d65e0f9 Workaround circular import error in Mypy
  • 47a6dbf Fix missing GC traversal in pydantic-core for GeneralFieldsSerializer
  • Additional commits viewable in compare view

Updates scikit-learn from 1.9.0 to 1.9.1

Release notes

Sourced from scikit-learn's releases.

Scikit-learn 1.9.1

We're happy to announce the 1.9.1 release.

This release contains a few bug fixes and is the first version supporting Python 3.15.

You can see the changelog here: https://scikit-learn.org/stable/whats_new/v1.9.html#version-1-9-1

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
  • 866c0f5 generate changelog
  • 12f135f update upper bounds
  • 43ff2f2 bump version
  • b851524 DOC Mark dev index as orphan (#34916)
  • 01d56d4 DOC Fix wikipedia principal eigenvector example references (#34915)
  • b86a1e2 🔒 🤖 CI Update lock files for array-api CI build(s) 🔒 🤖 ...
  • d282698 🔒 🤖 CI Update lock files for main CI build(s) 🔒 🤖 (#34897)
  • eb34279 🔒 🤖 CI Update lock files for free-threaded CI build(s) 🔒 :rob...
  • 7581303 FIX: Fix QuantileTransformer(ignore_implicit_zeros=True) sub-sampling behav...
  • ac47f4d FIX: avoid EfficiencyWarning in OPTICS with metric='precomputed' (#34692)
  • Additional commits viewable in compare view

Updates shap from 0.49.1 to 0.52.0

Release notes

Sourced from shap's releases.

v0.52.0

What's Changed

Highlights

  • Native bindings rewritten with nanobind, and the build system migrated from setup.py to scikit-build-core + CMake. The Cython _kernel_lib.pyx and the existing _cext / _cext_gpu modules are now built as nanobind extensions, and MANIFEST.in / setup.py have been removed in favor of a pyproject.toml-driven build. (#4366, by @​CloseChoice and @​daidahao and @​claude)
  • Minimum dependency versions raised to follow SPEC 0. (#4310, by @​CloseChoice)

Enhancements

Bug Fixes

  • Improve GPU TreeExplainer parity: preserve XGBoost default/missing child routing so NaN values follow the same branch as the source model, preserve vector-valued XGBoost base_score values (fixing multiclass additivity offsets), and tighten categorical handling so sklearn models with enable_categorical=True raise the existing unsupported-categorical error even when the booster does not expose feature_types. (#4997, by @​RAMitchell)
  • TreeExplainer no longer crashes with pandas nullable dtypes. (#4298, by @​tudstudent)
  • Fix NameError when with_binary=False and with_cuda=True by initializing compile_args. (#4322, by @​mohityadav8)
  • Text plot colors render correctly by converting NumPy types to float. (#4332, by @​Saloni-0465)
  • Assign the result of np.flipud so it is no longer a no-op in AdditiveForceArrayVisualizer. (#4343, by @​Mahaveerjain-18)
  • Use isinstance() instead of is for type checks. (#4373, by @​divyam-jha123)
  • Record 'sample' in Explanation.op_history instead of '__getitem__'. (#4376, by @​tarun-227)
  • Move the unreachable large-dataset warning into the interventional branch. (#4392, by @​Mahaveerjain-18)
  • Fix "structure of inputs doesn't match the expected structure". (#4410, by @​shaivimalik)
  • Fix the return value from is_color_map() in plots/_beeswarm.py. (#4421, by @​maniktyagi04)
  • Suppress the UserWarning when LGBMRegressor was fitted with feature names. (#4422, by @​shaivimalik)

... (truncated)

Commits
  • 8461059 FIX: Improve GPU TreeExplainer parity (#4997)
  • 8549e6b fix: use isinstance() instead of type() is tuple checks (#4508)
  • 3be7001 remove webpack dependency for sickness scores (#5018)
  • 6e9f9b8 build(deps): bump qs and express in /javascript (#5015)
  • 9be5435 build(deps): bump idna from 3.11 to 3.15 in /docs (#5007)
  • 52dd763 pin torch to <=2.11.0 in pyproject.toml (#5017)
  • d8f2e76 build(deps-dev): bump webpack-dev-server in /javascript (#5009)
  • ac6e677 build(deps-dev): bump @​babel/plugin-transform-modules-systemjs (#4991)
  • 679b2ee FIX: warn when covariance matrix is singular in LinearExplainer (#4471)
  • ce4abd7 build(deps): bump mistune from 3.2.0 to 3.2.1 (#4990)
  • Additional commits viewable in compare view

Updates lefthook from 2.1.10 to 2.1.12

Release notes

Sourced from lefthook's releases.

v2.1.12

Changelog

  • b8350fde604197b2422adfc4ae0af080725822b9 ci: fix npm publishing by bumping Node to 24 (#1508)
  • 9fb290d786a0e122fe113b1b49a45bbd0ffa7d28 fix: LEFTHOOK_OUTPUT precedence (#1506)
  • 2f0a9f37cef73e10d95043ba3754329a21850d57 fix: fail the hook when staging fixed files errors (#1484)

v2.1.11

Changelog

  • e5b10ac3a2645784ee2e4260620c49c31b44992a deps: bump Go to 1.26.6 (#1495)
  • d4a259f460b7c1d8c512dd75eedc7068310ee961 fix: inherit terminal size for PTY commands (#1498)
Changelog

Sourced from lefthook's changelog.

2.1.12 (2026-08-28)

2.1.11 (2026-08-21)

Commits
  • 4ad40c3 2.1.12: fix LEFTHOOK_OUTPUT env precedence
  • 2f0a9f3 fix: fail the hook when staging fixed files errors (#1484)
  • 9fb290d fix: LEFTHOOK_OUTPUT precedence (#1506)
  • b8350fd ci: fix npm publishing by bumping Node to 24 (

@dependabot
chore(deps): bump the python group across 1 directory with 12 updates
fdcb835 
Bumps the python group with 12 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [mlflow](https://github.com/mlflow/mlflow) | `3.15.1` | `3.16.0` |
| [numba](https://github.com/numba/numba) | `0.66.0` | `0.67.0` |
| [numpy](https://github.com/numpy/numpy) | `2.4.6` | `2.5.3` |
| [pandera](https://github.com/pandera-dev/pandera) | `0.32.1` | `0.33.1` |
| [pydantic](https://github.com/pydantic/pydantic) | `2.13.4` | `2.13.5` |
| [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.9.0` | `1.9.1` |
| [shap](https://github.com/shap/shap) | `0.49.1` | `0.52.0` |
| [lefthook](https://github.com/evilmartians/lefthook) | `2.1.10` | `2.1.12` |
| [ruff](https://github.com/astral-sh/ruff) | `0.16.2` | `0.16.7` |
| [ty](https://github.com/astral-sh/ty) | `0.0.69` | `0.0.80` |
| [validate-pyproject](https://github.com/abravalheri/validate-pyproject) | `0.25` | `0.26` |
| [nbformat](https://github.com/jupyter/nbformat) | `5.11.0` | `5.11.1` |



Updates `mlflow` from 3.15.1 to 3.16.0
- [Release notes](https://github.com/mlflow/mlflow/releases)
- [Changelog](https://github.com/mlflow/mlflow/blob/master/CHANGELOG.md)
- [Commits](mlflow/mlflow@v3.15.1...v3.16.0)

Updates `numba` from 0.66.0 to 0.67.0
- [Release notes](https://github.com/numba/numba/releases)
- [Commits](numba/numba@0.66.0...0.67.0)

Updates `numpy` from 2.4.6 to 2.5.3
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.4.6...v2.5.3)

Updates `pandera` from 0.32.1 to 0.33.1
- [Release notes](https://github.com/pandera-dev/pandera/releases)
- [Commits](unionai-oss/pandera@v0.32.1...v0.33.1)

Updates `pydantic` from 2.13.4 to 2.13.5
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/v2.13.5/HISTORY.md)
- [Commits](pydantic/pydantic@v2.13.4...v2.13.5)

Updates `scikit-learn` from 1.9.0 to 1.9.1
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.9.0...1.9.1)

Updates `shap` from 0.49.1 to 0.52.0
- [Release notes](https://github.com/shap/shap/releases)
- [Changelog](https://github.com/shap/shap/blob/main/docs/release_notes.rst)
- [Commits](shap/shap@v0.49.1...v0.52.0)

Updates `lefthook` from 2.1.10 to 2.1.12
- [Release notes](https://github.com/evilmartians/lefthook/releases)
- [Changelog](https://github.com/evilmartians/lefthook/blob/master/CHANGELOG.md)
- [Commits](evilmartians/lefthook@v2.1.10...v2.1.12)

Updates `ruff` from 0.16.2 to 0.16.7
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.16.2...0.16.7)

Updates `ty` from 0.0.69 to 0.0.80
- [Release notes](https://github.com/astral-sh/ty/releases)
- [Changelog](https://github.com/astral-sh/ty/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ty@0.0.69...0.0.80)

Updates `validate-pyproject` from 0.25 to 0.26
- [Release notes](https://github.com/abravalheri/validate-pyproject/releases)
- [Changelog](https://github.com/abravalheri/validate-pyproject/blob/main/CHANGELOG.rst)
- [Commits](abravalheri/validate-pyproject@v0.25...0.26)

Updates `nbformat` from 5.11.0 to 5.11.1
- [Release notes](https://github.com/jupyter/nbformat/releases)
- [Changelog](https://github.com/jupyter/nbformat/blob/main/CHANGELOG.md)
- [Commits](jupyter/nbformat@v5.11.0...v5.11.1)

---
updated-dependencies:
- dependency-name: mlflow
  dependency-version: 3.16.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python
- dependency-name: numba
  dependency-version: 0.67.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python
- dependency-name: numpy
  dependency-version: 2.5.3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python
- dependency-name: pandera
  dependency-version: 0.33.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python
- dependency-name: pydantic
  dependency-version: 2.13.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python
- dependency-name: scikit-learn
  dependency-version: 1.9.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python
- dependency-name: shap
  dependency-version: 0.52.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python
- dependency-name: lefthook
  dependency-version: 2.1.12
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python
- dependency-name: ruff
  dependency-version: 0.16.7
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python
- dependency-name: ty
  dependency-version: 0.0.80
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python
- dependency-name: validate-pyproject
  dependency-version: '0.26'
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python
- dependency-name: nbformat
  dependency-version: 5.11.1
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python
...

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@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Sep 14, 2026
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