[dependabot]

Bumps the python-minor-patch group with 5 updates in the / directory:

Package	From	To
mypy	2.3.1	2.4.0
pre-commit	4.6.2	4.7.0
ruff	0.16.5	0.17.0
numpy	2.5.3	2.5.4
alphagenome	0.9.0	0.10.0

Updates mypy from 2.3.1 to 2.4.0

Changelog

Sourced from mypy's changelog.

Mypy Release Notes

Next Release

Mypy 2.4

We've just uploaded mypy 2.4.0 to the Python Package Index (PyPI). Mypy is a static type checker for Python. This release includes new features, performance improvements and bug fixes. You can install it as follows:

python3 -m pip install -U mypy

You can read the full documentation for this release on Read the Docs.

Python 3.15 Support

Mypy 2.4 supports running on Python 3.15 and type checking most Python 3.15 features. This includes the new builtin sentinel type for sentinel values (PEP 661), which mypy now supports (see below for details). Lazy imports (PEP 810) and unpacking in comprehensions (PEP 798) are also supported. Closed TypedDicts (PEP 728) have been supported since mypy 2.2, but the extra_items TypedDict argument, also introduced in PEP 728, is still unsupported. Support for extra_items will be added in a future mypy release.

Native Parser Enabled by Default

Mypy now uses the new native parser by default. It's based on the Ruff parser, and it's significantly faster than the legacy parser, which uses the stdlib ast module. The native parser also has other benefits:

• You can target newer Python versions and use recent Python syntax even when running mypy on an older Python version. For example, you can use --python-version 3.15 when running mypy on Python 3.14.
• Stub files can use syntax that is newer than the target Python version. For example, stubs can use the PEP 695 generic class syntax (class Box[T]: ...) when running on or targeting Python 3.10.
• Parallel type checking requires the native parser.

The legacy parser is still available through --no-native-parser, or native_parser = False in the config file (native_parser = false under [tool.mypy] in pyproject.toml). We are planning to remove the legacy parser in early 2027. If you run into a problem with the native parser, please report it on the issue tracker.

Unlike the legacy parser, the native parser doesn't support type comments for variables defined by for and with statements. These type comments are silently ignored, and the types of the variables are

... (truncated)

Commits

• 935ba8a Bump version to 2.4.0
• 334a678 Add link for PR 22066 in mypy 2.4 changelog (#22082)
• fe69660 Finalize mypy 2.4 changelog (#22080)
• 541fd87 Various mypy 2.4 changelog updates (#22077)
• b231182 Update native parser docs (#22078)
• 04fe42c Initial Changelog for Mypy 2.4 (#22071)
• 0617494 Quick fix for non UTF-8 encodings with new parser (#22066)
• b2f9b60 Bump librt to 0.16.0 (#22067)
• 9d798dc Sync typeshed (#22054)
• 0861bb6 Reduce max protocol stack size to 20 (#22053)
• 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 ruff from 0.16.5 to 0.17.0

Release notes

Sourced from ruff's releases.

0.17.0

Release Notes

Released on 2026-10-09.

The executables in our macOS and Windows release archives and ruff wheels are now code-signed. macOS executables are signed with an Apple Developer ID certificate and notarized by Apple. Windows executables have timestamped Authenticode signatures from Azure Artifact Signing. This enables verification of the release publisher and binary integrity, supports publisher-based allowlisting, and should reduce security warnings and antivirus false positives.

Breaking changes

• Update the default and latest Python versions for 3.15 (#28792)

  Ruff now defaults to Python 3.11 instead of 3.10 when no Python version is configured through target-version or requires-python. When checking for syntax errors without a configured Python version, Ruff now defaults to Python 3.15 instead of 3.14.

• Update the default rule set (#28786)

  Several of the flake8-datetimez rules (DTZ001, DTZ005, DTZ006, DTZ007, DTZ011, DTZ012, and DTZ901) are no longer enabled by default, while undefined-local-with-nested-import-star-usage (F406), which corresponds to a syntax error, is now enabled by default.

• Update Rust crate quick-junit to 0.8.0 (#27295)

  JUnit output now uses a skipped attribute instead of disabled on <testsuite> elements and includes a skipped attribute on the root <testsuites> element.

• [flake8-import-conventions] Add datetime as dt as a conventional alias (ICN001) (#28790)

• Support Unicode dummy variable names (#28722)

  The default lint.dummy-variable-rgx now recognizes underscore-prefixed Unicode names, such as _次, as dummy variables.

• Update to Unicode 17 (#21229, #28784)

  Ruff now uses Unicode 17 data for identifier normalization and named character escapes ("\N{...}").

• Always show unsafe and display-only fixes in the CLI (#27810)

  The default full output format now shows unsafe fixes and suggestions requiring manual review, regardless of the unsafe-fixes setting. Actually applying unsafe fixes still requires explicit opt-in.

• Remove the Python dependency from conda-forge builds (conda-forge/ruff-feedstock#361)

  The conda-forge build no longer depends on Python, now supports linux-riscv64, win-arm64, and linux-ppc64le platforms, and now includes shell completions. However, no longer depending on Python means that python -m ruff and import ruff will no longer work. Use ruff directly from PATH instead. PyPI installations and those from the standalone installer are unaffected.

• Remove support for ruff-lsp (#28750)

  Support for ruff-lsp, the legacy Python language server deprecated in Ruff v0.9.5, has been removed. The Ruff VS Code extension now always uses the native language server; ruff.nativeServer is deprecated and ignored. See the migration guide.

Stabilization

The following rules have been stabilized and are no longer in preview:

• lazy-import-mismatch (TID254)
• lazy-import-immediately-resolved (TID255)
• os-path-commonprefix (RUF071)

... (truncated)

Changelog

Sourced from ruff's changelog.

0.17.0

Released on 2026-10-09.

The executables in our macOS and Windows release archives and ruff wheels are now code-signed. macOS executables are signed with an Apple Developer ID certificate and notarized by Apple. Windows executables have timestamped Authenticode signatures from Azure Artifact Signing. This enables verification of the release publisher and binary integrity, supports publisher-based allowlisting, and should reduce security warnings and antivirus false positives.

Breaking changes

• Update the default and latest Python versions for 3.15 (#28792)

  Ruff now defaults to Python 3.11 instead of 3.10 when no Python version is configured through target-version or requires-python. When checking for syntax errors without a configured Python version, Ruff now defaults to Python 3.15 instead of 3.14.

• Update the default rule set (#28786)

  Several of the flake8-datetimez rules (DTZ001, DTZ005, DTZ006, DTZ007, DTZ011, DTZ012, and DTZ901) are no longer enabled by default, while undefined-local-with-nested-import-star-usage (F406), which corresponds to a syntax error, is now enabled by default.

• Update Rust crate quick-junit to 0.8.0 (#27295)

  JUnit output now uses a skipped attribute instead of disabled on <testsuite> elements and includes a skipped attribute on the root <testsuites> element.

• [flake8-import-conventions] Add datetime as dt as a conventional alias (ICN001) (#28790)

• Support Unicode dummy variable names (#28722)

  The default lint.dummy-variable-rgx now recognizes underscore-prefixed Unicode names, such as _次, as dummy variables.

• Update to Unicode 17 (#21229, #28784)

  Ruff now uses Unicode 17 data for identifier normalization and named character escapes ("\N{...}").

• Always show unsafe and display-only fixes in the CLI (#27810)

... (truncated)

Commits

• 5b27c1c Bump version to 0.17.0 (#29259)
• 8f362bf Integrate vendored Unicode names into Ruff
• 88a50d6 Revert upstream Unicode loose matching
• 276832a Revert upstream Unicode alias normalization
• 26911ca Vendor unicode_names2 from upstream
• 27e3797 [ruff] Stabilize os-path-commonprefix (RUF071) (#28764)
• bbb52c1 [flake8-tidy-imports] Stabilize lazy-import-immediately-resolved (`TID255...
• 5aa9cbd [flake8-tidy-imports] Stabilize lazy-import-mismatch (TID254) (#28760)
• dba1bc8 [flake8-import-conventions] Add datetime as dt as a conventional alias (`...
• ef23c9c Update default and latest Python versions for 3.15 (#28792)
• Additional commits viewable in compare view

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 alphagenome from 0.9.0 to 0.10.0

Release notes

Sourced from alphagenome's releases.

v0.10.0

Added

• Feature contribution and score bar plot components, to be able to plot Atlas AVI scores.
• Support for with_name_suffix and with_metadata_column for JunctionData.

Changed

• Moved AlphaGenome model API, colabs and protos to stable v1 directory. The current locations will be removed in a future release.
• Updated documentation to reflect new v1 directory structure.
• Updated Atlas citation to medRxiv pre-print.
• Fixed bug with round-tripping scalar values.

Changelog

Sourced from alphagenome's changelog.

[0.10.0]

Added

• Feature contribution and score bar plot components, to be able to plot Atlas AVI scores.
• Support for with_name_suffix and with_metadata_column for JunctionData.

Changed

• Moved AlphaGenome model API, colabs and protos to stable v1 directory. The current locations will be removed in a future release.
• Updated documentation to reflect new v1 directory structure.
• Updated Atlas citation to medRxiv pre-print.
• Fixed bug with round-tripping scalar values.

Commits

• 9d9885c Update version to 0.10.0
• 7bd1e0a Add variant scorer info to uns and interval to obs.
• 935d2d5 Defer complementation to pyfaidx implementation.
• 9051bce Replace # pytype: disable suppressions with # pyrefly: ignore
• 9145012 Add ScoreBar component that creates a bar chart for each variant in the plot ...
• e621885 Create FeatureContribution plot component for plotting AVI feature contributi...
• 038d253 Correctly roundtrip scalar values when using tensor_utils.pack_tensor.
• edf0afd Move alphagenome colab notebooks into stable folder
• ec0e9ae Move alphagenome models into stable folder
• a8d070a Switch alphagenome's proto imports to stable location
• Additional commits viewable in compare view

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[dependabot]

Looks like these dependencies are updatable in another way, so this is no longer needed.