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Bump the python-packages group with 3 updates#108

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Bump the python-packages group with 3 updates#108
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dependabot/uv/python-packages-b5042f4f73

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@dependabot dependabot Bot commented on behalf of github Jun 1, 2026

Bumps the python-packages group with 3 updates: polars, pycytominer and ruff.

Updates polars from 1.40.1 to 1.41.2

Release notes

Sourced from polars's releases.

Python Polars 1.41.2

🚀 Performance improvements

  • Update to new jemalloc (#27797)
  • Do not materialize ScalarColumn in Column split_at (#27782)
  • Avoid materializing broadcast in array.shift (#27740)
  • Avoid materializing broadcast list in list.sample(n) and list.sample(frac) (#27679)

✨ Enhancements

  • Update to new jemalloc (#27797)

🐞 Bug fixes

  • Broken link to AI Policy corrected (#27793)
  • Update to new jemalloc (#27797)

📖 Documentation

  • Update Polars On-Prem version stamp (#27799)
  • Broken link to AI Policy corrected (#27793)
  • Add release dates to the On-Prem releases page (#27787)
  • Improve on-prem docs (#27788)
  • Add query profiler video to On-Prem user guide (#27786)
  • Add EKS/AKS/GKE guides (#27774)
  • Add Polars On-Prem 0.4.2 (#27780)

🛠️ Other improvements

  • Run Pyrefly on _utils and functions (#27789)
  • Harden against async blocking deadlocks (take 2) (#27767)

Thank you to all our contributors for making this release possible! @​ButteryPaws, @​EndPositive, @​Kevin-Patyk, @​MarcoGorelli, @​TNieuwdorp, @​azimafroozeh, @​carnarez, @​kdn36, @​lun3x, @​orlp and @​ritchie46

Python Polars 1.41.1

🚀 Performance improvements

  • Adaptive size dispatch to hashset or radix sort + capacity-aware reset in agg_n_unique (#27719)

✨ Enhancements

  • Allow deeper expressions (#27768)

🐞 Bug fixes

  • Raise length mismatch in multiple sort_by in group_by (#27772)
  • Respect min_samples for rolling_by ops with nulls (#27706)
  • Fix memory usage regression affecting TPCH Q22 (#27758)
  • Add POLARS_ALLOW_NESTED_CSPE env var and make nested CSPE opt-in (#27765)

... (truncated)

Commits

Updates pycytominer from 1.4.0 to 1.5.1

Release notes

Sourced from pycytominer's releases.

v1.5.1 (2026-05-30)

What's Changed

Full Changelog: cytomining/pycytominer@v1.5.0...v1.5.1

v1.5.0 (2026-05-22)

What's Changed

... (truncated)

Changelog

Sourced from pycytominer's changelog.

v1.5.1 (2026-05-28)

Detailed release notes

Feat

  • normalize: add drop_cosmicqc_rows parameter to drop coSMicQC-flagged cells before normalization (#682)

Docs

  • add introduction to pycytominer tutorial with simulated pipeline walkthrough (#681)

Build

  • prune test data, media, and walkthroughs from PyPI sdist to reduce package size (#683)

v1.5.0 (2026-05-21)

Detailed release notes

Feat

  • blocklist: introduce Blocklist class and get_blocklist_features with named YAML registry, custom registry support, and blocklist_name parameter; deprecate blocklist_file (#674)
  • annotate: update annotate to support parquet ingest and QC workflows (#657)
  • cells: make SingleCells.count_cells() use configurable count columns (#671)
  • load: add CytoTable warehouse profile loading; ignore OME-Arrow payload columns during normalization (#643)

Refactor

  • collate: remove noqa: S603 suppression in subprocess calls (#666)
  • replace tmp path usage with tempfile.gettempdir() for cross-platform compatibility (#670)

Docs

  • expand left navigation bar to specific functions and differentiate colors for css docstrings (#680)
  • fix API docs rendering: correct code blocks in core function docs, add doc build integration, fix RTD integration (#677)
  • update docs build to use uv, parse readme, remove legacy docs, and point RTD to cytomining.github.io/pycytominer (#676)
  • clarify CellProfiler and CytoTable input guidance (#669)

Build

  • migrate from poetry to uv (#650)
  • deps: various dependency updates automated by dependabot

CI

  • add Python 3.14 CI support (#668)
  • add contribution interest checkbox to issue templates (#665)
Commits
  • ea6e97a bump: version 1.5.0 → 1.5.1 (#685)
  • 37f3728 prune files to reduce package size (#683)
  • 1a9e4a0 Add drop qc rows parameter in normalize with test (#682)
  • 67a742f Adding intro to pycytominer tutorial (#681)
  • 584a9cc bump: version 1.4.0 → 1.5.0 (#679)
  • 3444fc5 Add specific links to core functions in left navigation bar in docs, also upd...
  • 7c39633 Dynamic blocklist object implementation (#674)
  • 4162330 Update annotate ingest qc parquet (#657)
  • d30b180 build(deps): bump astral-sh/setup-uv in /.github/actions/setup-env (#678)
  • e7bc7ba Removal of noqa: S603 in collate subprocess calls (#666)
  • Additional commits viewable in compare view

Updates ruff from 0.15.12 to 0.15.15

Release notes

Sourced from ruff's releases.

0.15.15

Release Notes

Released on 2026-05-28.

Preview features

  • Fix Markdown closing fence handling (#25310)
  • [pyflakes] Report duplicate imports in typing.TYPE_CHECKING block (F811) (#22560)

Bug fixes

  • [pyflakes] Treat function-scope bare annotations as locals per PEP 526 (F821) (#21540)

Performance

  • Avoid redundant TokenValue drops in the lexer (#25300)
  • Reduce memory usage by dropping token-excess capacity and improve performance by approximating the initial tokens Vec size (#25354)
  • Use ThinVec in AST to shrink Stmt (#25361)

Documentation

  • Fix line-length example for --config option (#25389)
  • [flake8-comprehensions] Document RecursionError edge case in __len__ (C416) (#25286)
  • [mccabe] Improve example (C901) (#25287)
  • [pyupgrade] Clarify fix safety docs (UP007, UP045) (#25288)
  • [refurb] Document FURB192 exception change for empty sequences (#25317)
  • [ruff] Document false negative for user-defined types (RUF013) (#25289)

Formatter

  • Fix formatting of lambdas nested within f-strings (#25398)

Server

  • Return code action for codeAction/resolve requests that contain no or no valid URL (#25365)

Other changes

  • Expand semantic syntax errors for invalid walruses (#25415)

Contributors

... (truncated)

Changelog

Sourced from ruff's changelog.

0.15.15

Released on 2026-05-28.

Preview features

  • Fix Markdown closing fence handling (#25310)
  • [pyflakes] Report duplicate imports in typing.TYPE_CHECKING block (F811) (#22560)

Bug fixes

  • [pyflakes] Treat function-scope bare annotations as locals per PEP 526 (F821) (#21540)

Performance

  • Avoid redundant TokenValue drops in the lexer (#25300)
  • Reduce memory usage by dropping token-excess capacity and improve performance by approximating the initial tokens Vec size (#25354)
  • Use ThinVec in AST to shrink Stmt (#25361)

Documentation

  • Fix line-length example for --config option (#25389)
  • [flake8-comprehensions] Document RecursionError edge case in __len__ (C416) (#25286)
  • [mccabe] Improve example (C901) (#25287)
  • [pyupgrade] Clarify fix safety docs (UP007, UP045) (#25288)
  • [refurb] Document FURB192 exception change for empty sequences (#25317)
  • [ruff] Document false negative for user-defined types (RUF013) (#25289)

Formatter

  • Fix formatting of lambdas nested within f-strings (#25398)

Server

  • Return code action for codeAction/resolve requests that contain no or no valid URL (#25365)

Other changes

  • Expand semantic syntax errors for invalid walruses (#25415)

Contributors

... (truncated)

Commits
  • db5aa0a Bump 0.15.15 (#25431)
  • 366fe21 [ty] Improve diagnostics for syntax errors in forward annotations (#25158)
  • e2e1e64 [ty] Remove excess capacity from more Salsa cached collections (#25411)
  • 1bd77e1 [ty] Use diagnostic message as tie breaker when sorting (#25424)
  • 7e1bc1e Add agent skills for working on ty (#25422)
  • 574e107 Expand semantic syntax errors for invalid walruses (#25415)
  • 4a7ca06 [ty] Display docs for matching parameter when hovering over the name of an ar...
  • 5432709 Refine a few agents instructions (#25423)
  • 3cb09eb [ty] Support typing.TypeForm (#25334)
  • c8cd59f [ty] Infer class attributes assigned by metaclass initialization (#25342)
  • Additional commits viewable in compare view

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Bumps the python-packages group with 3 updates: [polars](https://github.com/pola-rs/polars), [pycytominer](https://github.com/cytomining/pycytominer) and [ruff](https://github.com/astral-sh/ruff).


Updates `polars` from 1.40.1 to 1.41.2
- [Release notes](https://github.com/pola-rs/polars/releases)
- [Commits](pola-rs/polars@py-1.40.1...py-1.41.2)

Updates `pycytominer` from 1.4.0 to 1.5.1
- [Release notes](https://github.com/cytomining/pycytominer/releases)
- [Changelog](https://github.com/cytomining/pycytominer/blob/main/CHANGELOG.md)
- [Commits](cytomining/pycytominer@v1.4.0...v1.5.1)

Updates `ruff` from 0.15.12 to 0.15.15
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.15.12...0.15.15)

---
updated-dependencies:
- dependency-name: polars
  dependency-version: 1.41.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: pycytominer
  dependency-version: 1.5.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-packages
- dependency-name: ruff
  dependency-version: 0.15.15
  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 Jun 1, 2026
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