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Bump the python-packages group with 12 updates - #63

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Bumps the python-packages group with 12 updates:

Package From To
beartype 0.22.9 0.23.1
bioio 3.5.1 3.6.0
pandas 3.0.6 3.1.0
pandera 0.33.1 0.35.0
pyarrow 25.0.1 26.0.0
pydantic 2.13.5 2.14.1
tomli 2.4.1 2.5.0
poethepoet 0.48.0 0.49.0
ruff 0.16.9 0.17.2
black 26.5.1 26.10.1
isort 9.0.1 9.0.2
jupytext 1.19.5 1.19.6

Updates beartype from 0.22.9 to 0.23.1

Release notes

Sourced from beartype's releases.

Beartype 0.23.1: The Ultimate QA Suplex

@​beartype 0.23.1 is the minor release that wishes it was the ultimate QA suplex. Instead, it just resolves a single regression at the intersection between @​beartype 0.23.1, Python ≤ 3.13, and PEP 557-compliant @dataclasses.dataclass-decorated dataclasses defining one or more methods annotated by one or more PEP 484-compliant forward self-references (i.e., stringified forward references referring to the dataclass currently being defined). Ordinarily, @​leycec would've uselessly sat on this issue resolution for nine months. Fortunately, he's done with ordinary – and so are you. The dog days are QA are over. The @​beartype 0.23.0 release cycle changed the nature of @​leycec. He now releases things so you don't have to:

# Via "pip", the once-great venerable master packager now fallen on hard times:
$ pip install --upgrade beartype      # <-- you go, pipe-smoking pip
Via "uv", the plucky upstart spiky-haired kid wielding a sword larger than its body:
$ uv pip install --upgrade beartype   # <-- when you no longer have the strength to care about lock files
Via "conda", the corporate scientist in casual lab attire who wants to be your buddy, pal:
$ conda config --add channels conda-forge  # <-- where did python packaging go wrong?
$ conda install conda-forge::beartype      # <-- it all seemed so simple, once.

Right: @​beartype 0.23.1. Left: Your codebase. Middle: Your CTO stares dumbfounded.

@​beartype 0.23.1 is helping @​leycec and his beautiful science wife to eat food. Thanks entirely to...

GitHub Sponsors: Befriend the Bear and Get a Bear for Life

This release comes courtesy these proud GitHub Sponsors, without whom everyone in the @​leycec family would currently be eating grasshoppers in the abandoned back lot again:

If you represent a security-conscious corporate, government, or non-profit, the best way bar none for you to support @​beartype and secure your own workflow is by subscribing to [Tidelift][] through [SonarQube Advanced Security][]. Security giant [Sonar][] recently acquired [Tidelift][], guaranteeing the economic viability of the Tidelift model for billions of future open-source projects that have yet to be born. Join the jargon-laden conversation and pay someone else to think about unreadable acronyms like SAST, SCA, and SBOM for once.

Thanks so much, masters of fintech and lifted tides.

The Masters of Fintech and Lifted Tides. That's who.

Lastly but Beastly (but not Leastly)...

we doin' this

...to financially feed @​leycec and his friendly @​beartype through either:

Cue hypnagogic rave music that encourages fiscal irresponsibility. 🎵 🎹 🎶

... (truncated)

Commits
  • f85b67d Beartype 0.23.1: The Ultimate QA Suplex
  • 9fe5727 PEP 557 dataclass annotated by forward self-reference.
  • f37deb0 Beartype 0.23.1 started.
  • ee36089 Beartype 0.23.0: The Year of the QA Fire Ho(r)se
  • 3c6fa37 @​beartype 0.23.0 pre-flight.
  • 348a8e0 PEP 484 type variable type-checking plan x 2.
  • c81d5ef Zensical header.
  • d253988 Issue template configuration file.
  • 729cee8 PEP 484 forward reference resolution in unnamed namespaces.
  • 109b277 PEP 484 stringified "None" forward references.
  • Additional commits viewable in compare view

Updates bioio from 3.5.1 to 3.6.0

Release notes

Sourced from bioio's releases.

v3.6.0

What's Changed

Full Changelog: bioio-devs/bioio@v3.5.1...v3.6.0

Commits
  • dbb372d Merge pull request #227 from bioio-devs/feature/directory-image-detection
  • 8f69772 Share directory plugin spec across plugin tests
  • fec716c Detect directory images via ReaderMetadata.supports_directory_images
  • 2a376b3 Merge pull request #221 from bioio-devs/docs/zenodo-doi
  • 20d6fba Add Zenodo concept DOI to README citation and CITATION.cff
  • See full diff in compare view

Updates pandas from 3.0.6 to 3.1.0

Release notes

Sourced from pandas's releases.

pandas 3.1.0

We are pleased to announce the release of pandas 3.1.0. This release includes some new features, bug fixes, and performance improvements. We recommend that all users upgrade to this version.

Highlights include:

See the detailed release notes for a list of all the changes.

The release can be installed from PyPI:

python -m pip install --upgrade pandas

Or from conda-forge

conda install -c conda-forge pandas

Please report any issues with the release on the pandas issue tracker.

Thanks to all the contributors who made this release possible.

pandas 3.1.0rc0

We are pleased to announce a release candidate for pandas 3.1.0.

See the whatsnew for a list of all the changes.

The release can be installed from PyPI:

python -m pip install --upgrade --pre pandas==3.1.0rc0

Or from conda-forge

conda install -c conda-forge/label/pandas_rc pandas==3.1.0rc0

Please report any issues with the release candidate on the pandas issue tracker.

Thanks to all the contributors who made this release possible.

Commits
  • c6f4676 RLS: 3.1.0
  • dd69475 Backport PR #71468 on branch 3.1.x (DOC: 3.1 whatsnew: add some structure to ...
  • 4ccc19a Backport PR #71465 on branch 3.1.x (DOC: update announce (contributor listing...
  • 24dae63 [backport 3.1.x] DOC: cleanup 3.1.0 whatsnew (#71408) (#71466)
  • 8519ca6 [backport 3.1.x] CI: temporary pin dateutil to <3 (#71461) (#71464)
  • 2126193 Backport PR #71387 on branch 3.1.x (BUG: fix string regex operations with $ e...
  • 4700f5d Backport PR #71442 on branch 3.1.x (BUG: parallel read_csv raising released m...
  • 08efb14 Backport PR #71456 on branch 3.1.x (TST: Fix test_reduce_array until reduct...
  • ee8dcb7 Backport PR #71429 on branch 3.1.x (DOC: add dedicated 3.1 whatsnew section f...
  • d93e32c Backport PR #71383 on branch 3.1.x (BUG: fix string regex operations with Pyt...
  • Additional commits viewable in compare view

Updates pandera from 0.33.1 to 0.35.0

Release notes

Sourced from pandera's releases.

v0.35.0

⭐️ Highlights

Pandera now supports DataFusion schemas

import pyarrow
from datafusion import SessionContext
import pandera.datafusion as pa
schema = pa.DataFrameSchema(
{
"state": pa.Column(str),
"city": pa.Column(str),
"price": pa.Column(int, pa.Check.in_range(5, 20)),
}
)
ctx = SessionContext()
df = ctx.from_arrow(
pyarrow.table(
{
"state": ["FL", "FL", "CA", "CA"],
"city": ["Orlando", "Miami", "Los Angeles", "San Francisco"],
"price": [8, 12, 10, 16],
}
)
)
schema.validate(df)

And of course the class-based dataframe models as well:

class Schema(pa.DataFrameModel):
    state: str
    city: str
    price: int = pa.Field(in_range={"min_value": 5, "max_value": 20})
Schema.validate(df)

What's Changed

... (truncated)

Commits
  • 02b375a docs(contributing): fix broken Dataframe schemas examples link (#2587)
  • ed3e370 chore: configure Ruff as VS Code formatter (#2588)
  • 4efb60d ci: don't run the full test matrix for non-CI files under .github/ (#2589)
  • dd6a012 fix: only patch numpy 2 aliases for pyspark < 4 (#2134) (#2590)
  • f8b0034 docs(api): drop the stray dataframe_schema param from to_json_schema (#2597)
  • 2e16e49 fix(pandas): don't repeat duplicate-label columns when adding missing columns...
  • a43a169 fix(datafusion): fix warning lint and backend test matrix (#2606)
  • b0a2ad5 Add explicit stacklevel to warnings and enforce with ruff B028 (#2500)
  • 9d82ffd docs: advertise DataFusion support in the top-level banner (#2604)
  • edb0d8b fix(polars): exclude explicit columns from regex alias selectors (#2343) (#2441)
  • Additional commits viewable in compare view

Updates pyarrow from 25.0.1 to 26.0.0

Release notes

Sourced from pyarrow's releases.

Apache Arrow 26.0.0

Release Notes URL: https://arrow.apache.org/release/26.0.0.html

Apache Arrow 26.0.0 RC0

Release Notes: Release Candidate: 26.0.0 RC0

Commits
  • 4461671 MINOR: [Release] Update versions for 26.0.0
  • 9d03a26 MINOR: [Release] Update .deb/.rpm changelogs for 26.0.0
  • 5ce3c95 MINOR: [Release] Update CHANGELOG.md for 26.0.0
  • 28e6c67 GH-51687: [C++] Skipt tests that require threads if ARROW_ENABLE_THREADING=OF...
  • 12409f8 GH-51682: [CI][C++] Add liburiparser-dev to system dependency image (#51683)
  • 1deceed GH-51675: [Python][Packaging] Apply upstream fix to UriParser from vcpkg and ...
  • cca44b5 GH-51638: [CI][C++][Parquet] Update expected JSON output in parquet-reader-te...
  • 5183e21 GH-46901: [C++][Compute] Add remainder and modulo kernels (#48914)
  • f0d043c MINOR: [Docs][C++] Fix doxygenfile path for arrow/flight/transport.h (#51677)
  • 17be9c7 GH-51652: [Python] Add NumPy StringDType to Arrow conversion (#51157)
  • Additional commits viewable in compare view

Updates pydantic from 2.13.5 to 2.14.1

Release notes

Sourced from pydantic's releases.

v2.14.1 2026-10-11

What's Changed

Performance

  • Avoid Python tuple allocation during model fields validation by @​Viicos in #13955
  • Avoid unnecessary extra dict allocation in model validation by @​Viicos in #13956

Fixes

Full Changelog: pydantic/pydantic@v2.14.0...v2.14.1

v2.14.0 2026-10-08

What's Changed

The highlights of the v2.14 release are available in the blog post. Several minor changes (considered non-breaking changes according to our versioning policy) are also included in this release. Make sure to look into them before upgrading.

This release drops support for Python 3.9 and adds support for Python 3.15.

Two security fixes are fixed by this release: GHSA-gj4f-r7mf-jjxh and GHSA-955g-x97g-8mcp.

New Features

  • Add support for multiple_of constraint in fraction and timedelta core schemas by @​Viicos in #13873
  • Add __namespace__ parameter to create_model() by @​Viicos in #13895

Changes

Fixes

... (truncated)

Changelog

Sourced from pydantic's changelog.

v2.14.0 (2026-10-08)

GitHub release

What's Changed

The highlights of the v2.14 release are available in the blog post. Several minor changes (considered non-breaking changes according to our versioning policy) are also included in this release. Make sure to look into them before upgrading.

This release drops support for Python 3.9 and adds support for Python 3.15.

New Features

  • Add support for multiple_of constraint in fraction and timedelta core schemas by @​Viicos in #13873
  • Add __namespace__ parameter to create_model() by @​Viicos in #13895

Changes

Fixes

  • Call enum constructors in both validation modes by @​Viicos in #13792
  • Fix documentation examples not raising and remove unused string_sub_type unused error code by @​Viicos in #13821
  • Catch OverflowError during ByteSize validation by @​Viicos in #13850
  • Require multiple_of constraints to be positive by @​Viicos in #13862
  • Always pop field name and model type stacks during schema generation by @​saquibjawedbit in #13859
  • Handle TypeError gracefully during docstring extraction by @​Viicos in #13874
  • Fix config propagation of stdlib dataclasses and TypedDicts in JSON Schema by @​Viicos in #13891
  • Don't apply ser_json_timedelta to all datetime types in serialization inference by @​Viicos in #13892
  • Encode JSON Schema defaults with a consistent configuration by @​Viicos in #13893
  • Propagate init and kw_only=False from Field() to stdlib dataclass fields by @​Viicos in #13898
  • Respect propagated extra config in the JSON Schema of stdlib dataclasses by @​Viicos in #13899
  • Handle OS errors during ZoneInfo validation by @​Viicos in #13912
  • Handle exceptions during Decimal validation by @​Viicos in #13940
  • Rebuild incomplete types during serialization inference by @​Viicos in #13922
  • Reject large exponents in Fraction validation by @​Viicos in #13944
  • Avoid validating URL prefix multiple times in multi host URLs by @​Viicos in #13945

New Contributors

... (truncated)

Commits
  • b2212c7 Prepare release v2.14.1
  • 968fb2b Fix docs conversion table
  • 6adc8b3 Support named tuples in Sequence validation
  • 7637fbc Reject out-of-range int inputs for timedelta
  • dfdbfcb Enforce the max_digits whole-digits limit in the Python Decimal validator
  • e2456d3 Support closed and extra_items via inheritance in TypedDict
  • 317655d Harden CI security
  • 3ba1dd4 Fix TypeError on ForwardRef on Python 3.10.0
  • 43681ab Bump samuelcolvin/check-python-version action to v5.1
  • d6bc53a Avoid unnecessary extra dict allocation in model validation
  • Additional commits viewable in compare view

Updates tomli from 2.4.1 to 2.5.0

Changelog

Sourced from tomli's changelog.

2.5.0

  • Added
    • Binary wheels for Python 3.15
  • Fixed
    • Set nested inline array/table limit to 400 to fix mypyc generated binaries crashing unrecoverably in constrained environments (e.g. worker thread in a python:3.13-alpine image)

2.3.1

  • Fixed
    • Backport: Limit number of parts of a TOML key to address quadratic time complexity
Commits
  • a2a5789 Bump version: 2.4.1 → 2.5.0
  • 94a6081 Add 2.5.0 changelog
  • 85f8748 Update README.md
  • 70fd460 Allow flit_core v4
  • 00d0610 Update pre-commit
  • eb93c12 Improve tomllib compatibility and sync docs (#299)
  • 18d8d59 Bump cibuildwheel for Python 3.15 wheels (#317)
  • 1e6e869 Set smaller MAX_INLINE_NESTING to avoid python:3.13-alpine worker thread crash
  • c329998 Use Trusted Publishing
  • ba611c5 Add zizmor security scanner to pre-commit (#301)
  • Additional commits viewable in compare view

Updates poethepoet from 0.48.0 to 0.49.0

Release notes

Sourced from poethepoet's releases.

0.49.0

Enhancements

Fixes

  • Resolve glob patterns in cmd tasks after parameter expansion, so expansions and quotes inside square bracket patterns are respected and unmatched globs are passed on unescaped by @​nat-n in nat-n/poethepoet#425
  • Handle absolute glob patterns (e.g. /etc/host*) and ** within a path component in cmd tasks instead of crashing by @​nat-n in nat-n/poethepoet#431
  • Propagate errors and exit codes from failed subtasks: errors in a switch case or a ref'd task are no longer swallowed, and poe now exits with the exit code of the first failed subtask instead of 1 by @​nat-n in nat-n/poethepoet#430
  • Resolve subtask arg defaults against the env inherited from the parent task by @​nat-n in nat-n/poethepoet#421
  • Detect and report cyclic deps/uses instead of silently running nothing or crashing by @​nat-n in nat-n/poethepoet#421
  • Report malformed, empty, and non-table config files with clear errors instead of tracebacks by @​nat-n in nat-n/poethepoet#428
  • Fix boolean flags forwarded to python tasks being inverted when their default is templated by @​nat-n in nat-n/poethepoet#420

Breaking changes

These changes may affect a small number of existing configurations:

  • Consistent sys.argv for Python tasks with declared args. Script tasks that call a function, and expr tasks, now get the same sys.argv as script tasks that run a module: declared args as parsed (with defaults applied), followed by any args given after --. Templates like ${VAR} in args given on the command line are also no longer expanded for these tasks, matching other task types. See the migration guide for an example. (nat-n/poethepoet#420)

  • Square bracket glob patterns in cmd tasks are parsed like in bash. Whitespace, backslashes, quotes, and parameter expansions inside [...] are no longer taken literally, so e.g. [ -f foo ] is now four words rather than one pattern. To match a space or backslash, escape or quote it, e.g. [a\ b]. See the migration guide for details. (nat-n/poethepoet#425)

AI Agent Skill 🤖

  • Teach the task graph (deps, uses, uses_env) and steer agents towards declarative poe features rather than bash logic by @​nat-n in nat-n/poethepoet#429

Upgrade an installed skill with:

poe _install_skill --upgrade

New Contributors

Full Changelog: nat-n/poethepoet@v0.48.0...v0.49.0

Commits
  • b8e96a9 Bump version to 0.49.0
  • 98da6fe fix(cmd): handle absolute glob patterns and misplaced ** without crashing (...
  • 5e67f11 fix: propagate errors and exit codes from failed subtasks (#430)
  • 65f2390 fix!: resolve glob patterns in cmd tasks after parameter expansion (#425)
  • 0f56a81 docs(skill): teach the task graph and steer bash logic to poe features (#429)
  • eec9c33 fix!: consistent sys.argv for Python tasks with declared args (#420)
  • ac60c37 fix(config): report malformed and non-table config files cleanly (#428)
  • af160fe feat: support both .yaml and .yml file extensions (#426)
  • 31b931e fix: resolve subtask arg defaults against the inherited env, and detect cycli...
  • ee5b9bc feat: customize boolean argument string values (#419)
  • Additional commits viewable in compare view

Updates ruff from 0.16.9 to 0.17.2

Release notes

Sourced from ruff's releases.

0.17.2

Release Notes

Released on 2026-10-22.

Preview features

  • [complexity] Add unnecessary-regular-expression-compile (#25533)

Bug fixes

  • Avoid syntax errors for type variables with starred constraints (UP040, UP046, UP047, RUF053) (#28362)
  • [pydocstyle] Treat backslash-escaped *args and **kwargs as documented (D417) (#29536)
  • [pylint] Avoid false positive on starred elements (PLE0643) (#29483)
  • [pylint] Mark fixes unsafe when deleting comments (PLR5501, PLW0120) (#29414)
  • [pyupgrade] Mark fix unsafe when deleting comments (UP035) (#29413)

Performance

  • Avoid intermediate names in lint name resolution (#29506)
  • Prefilter bidirectional Unicode checks by UTF-8 leading bytes (#29561)
  • Share postfix parsing and reduce expression copies (#29480)

Configuration

  • [pylint] Add a configurable allowlist for magic-value-comparison (PLR2004) (#18961)

Documentation

  • Clarify documentation and correct stale guidance (#29374)
  • [pyupgrade] Remove mentions of variance related to fix safety (UP040, UP047) (#29592)

Contributors

Install ruff 0.17.2

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.17.2/ruff-installer.sh | sh
</tr></table>

... (truncated)

Changelog

Sourced from ruff's changelog.

0.17.2

Released on 2026-10-22.

Preview features

  • [complexity] Add unnecessary-regular-expression-compile (#25533)

Bug fixes

  • Avoid syntax errors for type variables with starred constraints (UP040, UP046, UP047, RUF053) (#28362)
  • [pydocstyle] Treat backslash-escaped *args and **kwargs as documented (D417) (#29536)
  • [pylint] Avoid false positive on starred elements (PLE0643) (#29483)
  • [pylint] Mark fixes unsafe when deleting comments (PLR5501, PLW0120) (#29414)
  • [pyupgrade] Mark fix unsafe when deleting comments (UP035) (#29413)

Performance

  • Avoid intermediate names in lint name resolution (#29506)
  • Prefilter bidirectional Unicode checks by UTF-8 leading bytes (#29561)
  • Share postfix parsing and reduce expression copies (#29480)

Configuration

  • [pylint] Add a configurable allowlist for magic-value-comparison (PLR2004) (#18961)

Documentation

  • Clarify documentation and correct stale guidance (#29374)
  • [pyupgrade] Remove mentions of variance related to fix safety (UP040, UP047) (#29592)

Contributors

0.17.1

Released on 2026-10-15.

Preview features

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

... (truncated)

Commits
  • 30516b4 Bump version to 0.17.2 (#29637)
  • 59a9e85 [ty] Generalize nested types in inferred return types (#29488)
  • 0d562aa [ty] Check inherited attribute conflicts (#28559)
  • 48dcdd0 [ty] Restrict range implications from gradual equivalence (#29577)
  • 734d75a [ty] Check for unsatisfiable bodies before existentially quantifying (#29504)
  • b0f9526 [ty] Preserve checks for recursive descriptor setter types (#29148)
  • 32869b4 Avoid creating deployments for automation jobs (#29626)
  • ec891ba Link the commit in pull request report footers (#29621)
  • 8958748 [ty] Publish ecosystem reports from GitHub Actions (#29609)
  • 01f5394 [ty] Publish typing conformance reports from GitHub Actions (#29608)
  • Additional commits viewable in compare view

Updates black from 26.5.1 to 26.10.1

Release notes

Sourced from black's releases.

26.10.1

Highlights

This release fixes a security issue in Black's bundled GitHub Action. Repositories that use the action are encouraged to update to the latest version of Black immediately. This update is received automatically when using psf/black@stable, and is independent of the version of Black installed by the action.

When the GitHub Action reads version specifiers from tool.black.required-version, it now only accepts released versions of Black, as it already did for black requirements in dependency lists. Other values, such as URL references, are now rejected. This issue has been registered as GHSA-cg8m-r9f2-5wm2; a CVE identifier is pending.

Stable style

  • Fix a long Jupyter notebook assignment magic (for example x = !ls -la) being wrapped in parentheses, which IPython can no longer run; such cells are now left unchanged (#5481)
  • Keep repeated lines outside the selected --line-ranges unchanged (#5436)
  • Fix --line-ranges formatting lines that follow a statement when formatting joins or re-indents that statement (#5484)
  • Fix --line-ranges crashing with an internal error when an unselected statement has a # fmt: skip comment on the last line before a closing bracket (#5477)
  • Prevent moving an encoding declaration (for example # -*- coding: latin-1 -*-) onto the first two lines of a file (#5487)
  • Fix adding an extra trailing blank line inside a multi-line module docstring when its last line is near the line length limit (#5494)

Preview style

  • Do not split short expressions on delimiters (such as binary operators, comparisons, or comprehensions) inside brackets when preceded by a standalone comment (#5455)
  • Fix the unstable string_processing feature removing backslash-newline sequences from raw strings, which changed their value (#5482)
  • Avoid adding unnecessary parentheses around unbreakable right-hand side expressions in assignments (such as annotated assignments or subscript targets) (#5473)
  • Parenthesize expressions with parameter comments when they exceed the line length under --preview (#5442)
  • Fix wrap_long_dict_values_in_parens dropping the parentheses around a right-hand side that contains a dictionary, leaving a line over the length limit (#5492)
  • Fix the unstable string_processing feature adding a space after * or ** in ...

    Description has been truncated

    📚 Documentation preview 📚: https://zedprofiler--63.org.readthedocs.build/en/63/

@dependabot
Bump the python-packages group with 12 updates
409c985 
Bumps the python-packages group with 12 updates:

| Package | From | To |
| --- | --- | --- |
| [beartype](https://github.com/beartype/beartype) | `0.22.9` | `0.23.1` |
| [bioio](https://github.com/bioio-devs/bioio) | `3.5.1` | `3.6.0` |
| [pandas](https://github.com/pandas-dev/pandas) | `3.0.6` | `3.1.0` |
| [pandera](https://github.com/pandera-dev/pandera) | `0.33.1` | `0.35.0` |
| [pyarrow](https://github.com/apache/arrow) | `25.0.1` | `26.0.0` |
| [pydantic](https://github.com/pydantic/pydantic) | `2.13.5` | `2.14.1` |
| [tomli](https://github.com/hukkin/tomli) | `2.4.1` | `2.5.0` |
| [poethepoet](https://github.com/nat-n/poethepoet) | `0.48.0` | `0.49.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.16.9` | `0.17.2` |
| [black](https://github.com/psf/black) | `26.5.1` | `26.10.1` |
| [isort](https://github.com/PyCQA/isort) | `9.0.1` | `9.0.2` |
| [jupytext](https://github.com/jupytext/jupytext) | `1.19.5` | `1.19.6` |


Updates `beartype` from 0.22.9 to 0.23.1
- [Release notes](https://github.com/beartype/beartype/releases)
- [Changelog](https://github.com/beartype/beartype/blob/main/RELEASE.md)
- [Commits](beartype/beartype@v0.22.9...v0.23.1)

Updates `bioio` from 3.5.1 to 3.6.0
- [Release notes](https://github.com/bioio-devs/bioio/releases)
- [Commits](bioio-devs/bioio@v3.5.1...v3.6.0)

Updates `pandas` from 3.0.6 to 3.1.0
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v3.0.6...v3.1.0)

Updates `pandera` from 0.33.1 to 0.35.0
- [Release notes](https://github.com/pandera-dev/pandera/releases)
- [Commits](unionai-oss/pandera@v0.33.1...v0.35.0)

Updates `pyarrow` from 25.0.1 to 26.0.0
- [Release notes](https://github.com/apache/arrow/releases)
- [Commits](apache/arrow@apache-arrow-25.0.1...apache-arrow-26.0.0)

Updates `pydantic` from 2.13.5 to 2.14.1
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](pydantic/pydantic@v2.13.5...v2.14.1)

Updates `tomli` from 2.4.1 to 2.5.0
- [Changelog](https://github.com/hukkin/tomli/blob/master/CHANGELOG.md)
- [Commits](hukkin/tomli@2.4.1...2.5.0)

Updates `poethepoet` from 0.48.0 to 0.49.0
- [Release notes](https://github.com/nat-n/poethepoet/releases)
- [Commits](nat-n/poethepoet@v0.48.0...v0.49.0)

Updates `ruff` from 0.16.9 to 0.17.2
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.16.9...0.17.2)

Updates `black` from 26.5.1 to 26.10.1
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@26.5.1...26.10.1)

Updates `isort` from 9.0.1 to 9.0.2
- [Release notes](https://github.com/PyCQA/isort/releases)
- [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md)
- [Commits](PyCQA/isort@9.0.1...9.0.2)

Updates `jupytext` from 1.19.5 to 1.19.6
- [Release notes](https://github.com/jupytext/jupytext/releases)
- [Changelog](https://github.com/jupytext/jupytext/blob/main/CHANGELOG.md)
- [Commits](jupytext/jupytext@v1.19.5...v1.19.6)

---
updated-dependencies:
- dependency-name: beartype
  dependency-version: 0.23.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: bioio
  dependency-version: 3.6.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: pandas
  dependency-version: 3.1.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: pandera
  dependency-version: 0.35.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: pyarrow
  dependency-version: 26.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: python-packages
- dependency-name: pydantic
  dependency-version: 2.14.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: tomli
  dependency-version: 2.5.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: poethepoet
  dependency-version: 0.49.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: ruff
  dependency-version: 0.17.2
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: black
  dependency-version: 26.10.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: isort
  dependency-version: 9.0.2
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: jupytext
  dependency-version: 1.19.6
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-packages
...

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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 Nov 1, 2026
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