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build(deps): bump the python-packages group across 1 directory with 8 updates#703

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build(deps): bump the python-packages group across 1 directory with 8 updates#703
gwaybio merged 2 commits into
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dependabot/uv/python-packages-5467961575

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Bumps the python-packages group with 8 updates in the / directory:

Package From To
sqlalchemy 2.0.49 2.0.50
csvkit 1.5.0 2.2.0
setuptools 69.5.1 82.0.1
mypy 1.20.2 2.1.0
ruff 0.15.14 0.15.16
cosmicqc 1.0.1 1.0.2
ipykernel 6.31.0 7.2.0
sphinxcontrib-mermaid 0.9.2 2.0.2

Updates sqlalchemy from 2.0.49 to 2.0.50

Release notes

Sourced from sqlalchemy's releases.

2.0.50

Released: May 24, 2026

orm

  • [orm] [bug] Fixed issue where using _orm.joinedload() with PropComparator.of_type() targeting a joined-table subclass combined with PropComparator.and_() referencing a column on that subclass would generate invalid SQL, where the subclass column was not adapted to the subquery alias. Pull request courtesy Joaquin Hui Gomez.

    References: #13203

  • [orm] [bug] Fixed issue where the presence of a SessionEvents.do_orm_execute() event hook would cause internal execution options such as yield_per and loader-specific state from the first orm_pre_session_exec pass to leak into the second pass, leading to errors when using relationship loaders such as selectinload() and immediateload(). The execution options passed to the second compilation pass are now based on the original options plus only the explicit updates made via ORMExecuteState.update_execution_options() within the event hook.

    References: #13301

  • [orm] [bug] Fixed issue where using _orm.with_polymorphic() on a leaf class (a subclass with no further descendants) or a non-inherited class would fail with an AttributeError when used in an ORM statement, due to _orm.configure_mappers() not being triggered implicitly. The fix ensures that AliasedInsp participates in the _post_inspect hook, triggering mapper configuration during ORM statement compilation.

    References: #13319

sql

  • [sql] [bug] Fixed issue where floor division (//) between a Float or Numeric numerator and an Integer denominator would omit the FLOOR() SQL wrapper on dialects where Dialect.div_is_floordiv is True (the default, including PostgreSQL and SQLite). FLOOR() is now applied if either the denominator or the numerator is a non-integer, so that expressions such as float_col // int_col render as FLOOR(float_col / int_col) instead of the incorrect float_col / int_col. Pull request courtesy r266-tech.

    References: #10528

postgresql

... (truncated)

Commits

Updates csvkit from 1.5.0 to 2.2.0

Changelog

Sourced from csvkit's changelog.

2.2.0 - December 15, 2025

  • fix: :doc:/scripts/csvstack no longer errors if a CSV file is empty.
  • Add Python 3.14 support. Drop support for end-of-life version 3.9.

2.1.0 - February 26, 2025

  • feat: Add a :code:--no-leading-zeroes option to tools that support type inference.
  • feat: Add a :code:--add-bom option to add the UTF-8 byte-order mark (BOM) to CSV output, for Excel compatibility.
  • feat: :doc:/scripts/csvsql adds a :code:--engine-option option.
  • feat: :doc:/scripts/csvsql adds a :code:--sql-delimiter option, to set a different delimiter than ; for the :code:--query, :code:--before-insert and :code:after-insert options.
  • feat: :doc:/scripts/sql2csv adds a :code:--execution-option option.
  • feat: :doc:/scripts/sql2csv uses the stream_results=True execution option, by default, to not load all data into memory at once.
  • fix: :doc:/scripts/csvcut no longer errors on unknown columns when using the :code:--not-columns (:code:-C) option.
  • fix: :doc:/scripts/csvsql uses a default value of 1 for the :code:--min-col-len and :code:--col-len-multiplier options.
  • fix: The :code:--encoding option defaults to the PYTHONIOENCODING environment variable if set.
  • fix: For type inference, number takes priority over date-time, if not using the :code:--datetime-format option.

2.0.1 - July 12, 2024

  • feat: :doc:/scripts/csvsql adds :code:--min-col-len and :code:--col-len-multiplier options.
  • feat: :doc:/scripts/sql2csv adds a :code:--engine-option option.
  • feat: Add a Docker image: docker pull ghcr.io/wireservice/csvkit:latest.
  • feat: Add man pages to the sdist and wheel distributions.
  • fix: :doc:/scripts/csvstat no longer errors when a column is a time delta and :code:--json is set.
  • fix: When taking arguments from sys.argv on Windows, glob patterns, user directories, and environment variables are expanded.

2.0.0 - May 1, 2024

This is the first major release since December 27, 2016. Thank you to all :ref:contributors<authors>, including 44 new contributors since 1.0.0!

Want to use csvkit programmatically? Check out agate <https://agate.readthedocs.io/en/latest/>__, used internally by csvkit.

BACKWARDS-INCOMPATIBLE CHANGES:

  • :doc:/scripts/csvclean now writes its output to standard output and its errors to standard error, instead of to basename_out.csv and basename_err.csv files. Consequently:

    • The :code:--dry-run option is removed. The :code:--dry-run option changed error output from the CSV format used in basename_err.csv files to a prosaic format like Line 1: Expected 2 columns, found 3 columns.
    • Summary information like No errors., 42 errors logged to basename_err.csv and 42 rows were joined/reduced to 24 rows after eliminating expected internal line breaks. is not written.

  • :doc:/scripts/csvclean no longer reports or fixes errors by default; it errors if no checks or fixes are enabled. Opt in to the original behavior using the :code:--length-mismatch and :code:--join-short-rows options. See new options below.

  • :doc:/scripts/csvclean no longer omits rows with errors from the output. Opt in to the original behavior using the :code:--omit-error-rows option.

  • :doc:/scripts/csvclean joins short rows using a newline by default, instead of a space. Restore the original behavior using the :code:--separator " " option.

In brief, to restore the original behavior for :doc:/scripts/csvclean:

... (truncated)

Commits
  • bdd6e7e build: Iterate the version number
  • 5e4340d build: Add 3.14 support. Drop 3.9 support.
  • e54cc79 re: Run pyupgrade --py310-plus **.*.py
  • 14e1920 docs: Make .readthedocs.yaml future-proof
  • ab0dac2 ci(automerge): Fix typo
  • 453953f build(deps): bump actions/download-artifact from 6 to 7
  • 80ffdc2 ci(automerge): Add "actions: write" to avoid error on gh pr merge
  • 002975c build(deps): bump actions/upload-artifact from 5 to 6 (#1319)
  • f03e750 build(deps): bump actions/checkout from 5 to 6 (#1315)
  • 48860e2 build(deps): bump actions/upload-artifact from 4 to 5
  • Additional commits viewable in compare view

Updates setuptools from 69.5.1 to 82.0.1

Changelog

Sourced from setuptools's changelog.

v82.0.1

Bugfixes

  • Fix the loading of launcher manifest.xml file. (#5047)
  • Replaced deprecated json.__version__ with fixture in tests. (#5186)

Improved Documentation

  • Add advice about how to improve predictability when installing sdists. (#5168)

Misc

v82.0.0

Deprecations and Removals

  • pkg_resources has been removed from Setuptools. Most common uses of pkg_resources have been superseded by the importlib.resources <https://docs.python.org/3/library/importlib.resources.html>_ and importlib.metadata <https://docs.python.org/3/library/importlib.metadata.html>_ projects. Projects and environments relying on pkg_resources for namespace packages or other behavior should depend on older versions of setuptools. (#3085)

v81.0.0

Deprecations and Removals

  • Removed support for the --dry-run parameter to setup.py. This one feature by its nature threads through lots of core and ancillary functionality, adding complexity and friction. Removal of this parameter will help decouple the compiler functionality from distutils and thus the eventual full integration of distutils. These changes do affect some class and function signatures, so any derivative functionality may require some compatibility shims to support their expected interface. Please report any issues to the Setuptools project for investigation. (#4872)

v80.10.2

Bugfixes

  • Update vendored dependencies. (#5159)

Misc

... (truncated)

Commits
  • 5a13876 Bump version: 82.0.0 → 82.0.1
  • 51ab8f1 Avoid using (deprecated) 'json.version' in tests (#5194)
  • f9c37b2 Docs/CI: Fix intersphinx references (#5195)
  • 8173db2 Docs: Fix intersphinx references
  • 09bafbc Fix past tense on newsfragment
  • 461ea56 Add news fragment
  • c4ffe53 Avoid using (deprecated) 'json.version' in tests
  • 749258b Cleanup pkg_resources dependencies and configuration (#5175)
  • 2019c16 Parse ext-module.define-macros from pyproject.toml as list of tuples (#5169)
  • b809c86 Sync setuptools schema with validate-pyproject (#5157)
  • Additional commits viewable in compare view

Updates mypy from 1.20.2 to 2.1.0

Changelog

Sourced from mypy's changelog.

Mypy Release Notes

Next Release

Mypy 2.1

We’ve just uploaded mypy 2.1.0 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.

librt.vecs: Fast Growable Array Type for Mypyc

The new librt.vecs module provides an efficient growable array type vec that is optimized for mypyc use. It provides fast, packed arrays with integer and floating point value types, which can be several times faster than list, and tens of times faster than array.array in code compiled using mypyc. It also supports nested vec objects and non-value-type items, such as vec[vec[str]].

Refer to the documentation for the details.

Contributed by Jukka Lehtosalo.

librt.random: Fast Pseudo-Random Number Generation

The new librt.random module provides fast pseudo-random number generation that is optimized for code compiled using mypyc. It can be 3x to 10x faster than the stdlib random module in compiled code.

Refer to the documentation for the details.

Contributed by Jukka Lehtosalo (PR 21433).

Mypyc Improvements

  • Enable incremental self-compilation (Vaggelis Danias, PR 21369)
  • Make compilation order with multiple files consistent (Piotr Sawicki, PR 21419)
  • Fix crash on accessing StopAsyncIteration (Piotr Sawicki, PR 21406)
  • Fix incremental compilation with separate flag (Vaggelis Danias, PR 21299)

Fixes to Crashes

  • Fix crash on partial type with --allow-redefinition and global declaration (Jukka Lehtosalo, PR 21428)
  • Fix broken awaitable generator patching (Ivan Levkivskyi, PR 21435)

... (truncated)

Commits

Updates ruff from 0.15.14 to 0.15.16

Release notes

Sourced from ruff's releases.

0.15.16

Release Notes

Released on 2026-06-04.

Preview features

  • [flake8-async] Implement yield-in-context-manager-in-async-generator (ASYNC119) (#24644)
  • [pylint] Narrow diagnostic range and exclude cases without exception handlers (PLW0717) (#25440)
  • [ruff] Treat yield before break from a terminal loop as terminal (RUF075) (#25447)

Bug fixes

  • [eradicate] Avoid flagging ruff:ignore comments as code (ERA001) (#25537)
  • [eradicate] Fix ERA001/RUF100 conflict when noqa is on commented-out code (#25414)
  • [pyflakes] Avoid removing the format call when it would change behavior (F523) (#25320)
  • [pylint] Avoid syntax errors in invalid character replacements in f-strings before Python 3.12 (PLE2510, PLE2512, PLE2513, PLE2514, PLE2515) (#25544)
  • [pyupgrade] Avoid converting format calls with more kinds of side effects (UP032) (#25484)

Rule changes

  • [flake8-pytest-style] Avoid fixes for ambiguous argnames and argvalues combinations (PT006) (#24776)

Performance

  • Drop excess capacity from statement suites during parsing (#25368)

Documentation

  • [pydocstyle] Improve discoverability of rules enabled for each convention (#24973)
  • [ruff] Restore example code for Python versions before 3.15 (RUF017) (#25439)
  • Fix typo bin/active → bin/activate in tutorial (#25473)

Other changes

  • Shrink additional parser AST collections (#25465)

Contributors

... (truncated)

Changelog

Sourced from ruff's changelog.

0.15.16

Released on 2026-06-04.

Preview features

  • [flake8-async] Implement yield-in-context-manager-in-async-generator (ASYNC119) (#24644)
  • [pylint] Narrow diagnostic range and exclude cases without exception handlers (PLW0717) (#25440)
  • [ruff] Treat yield before break from a terminal loop as terminal (RUF075) (#25447)

Bug fixes

  • [eradicate] Avoid flagging ruff:ignore comments as code (ERA001) (#25537)
  • [eradicate] Fix ERA001/RUF100 conflict when noqa is on commented-out code (#25414)
  • [pyflakes] Avoid removing the format call when it would change behavior (F523) (#25320)
  • [pylint] Avoid syntax errors in invalid character replacements in f-strings before Python 3.12 (PLE2510, PLE2512, PLE2513, PLE2514, PLE2515) (#25544)
  • [pyupgrade] Avoid converting format calls with more kinds of side effects (UP032) (#25484)

Rule changes

  • [flake8-pytest-style] Avoid fixes for ambiguous argnames and argvalues combinations (PT006) (#24776)

Performance

  • Drop excess capacity from statement suites during parsing (#25368)

Documentation

  • [pydocstyle] Improve discoverability of rules enabled for each convention (#24973)
  • [ruff] Restore example code for Python versions before 3.15 (RUF017) (#25439)
  • Fix typo bin/active → bin/activate in tutorial (#25473)

Other changes

  • Shrink additional parser AST collections (#25465)

Contributors

0.15.15

... (truncated)

Commits

Updates cosmicqc from 1.0.1 to 1.0.2

Release notes

Sourced from cosmicqc's releases.

v1.0.2

Changes

... (truncated)

Commits
  • 5959f74 Bump the python-packages group across 1 directory with 8 updates (#336)
  • 81c3822 Bump the python-packages group across 1 directory with 5 updates (#334)
  • 4875581 Bump cryptography from 46.0.6 to 46.0.7 (#326)
  • 9804fdc Bump the python-packages group across 1 directory with 16 updates (#332)
  • eed50b6 Show CytoDataFrame filter columns based on coSMicQC threshold sets (#331)
  • b2232fe Update functions for QC annotated output (#325)
  • 7741c7d Bump nbconvert from 7.16.6 to 7.17.0 (#322)
  • 5bbcd38 Bump cryptography from 45.0.7 to 46.0.5 (#321)
  • fa0ee5f Bump pyasn1 from 0.6.2 to 0.6.3 (#320)
  • 9e59072 Bump tornado from 6.5.2 to 6.5.5 (#319)
  • Additional commits viewable in compare view

Updates ipykernel from 6.31.0 to 7.2.0

Release notes

Sourced from ipykernel's releases.

v7.2.0

7.2.0

(Full Changelog)

New features added

Enhancements made

Bugs fixed

Maintenance and upkeep improvements

Contributors to this release

The following people contributed discussions, new ideas, code and documentation contributions, and review. See our definition of contributors.

(GitHub contributors page for this release)

@​arjxn-py (activity) | @​Carreau (activity) | @​ccordoba12 (activity) | @​ianthomas23 (activity) | @​JohanMabille (activity) | @​minrk (activity) | @​newville (activity) | @​SylvainCorlay (activity)

v7.2.0a1

7.2.0a1

(Full Changelog)

... (truncated)

Changelog

Sourced from ipykernel's changelog.

7.2.0

(Full Changelog)

New features added

Enhancements made

Bugs fixed

Maintenance and upkeep improvements

Contributors to this release

The following people contributed discussions, new ideas, code and documentation contributions, and review. See our definition of contributors.

(GitHub contributors page for this release)

@​arjxn-py (activity) | @​Carreau (activity) | @​ccordoba12 (activity) | @​ianthomas23 (activity) | @​JohanMabille (activity) | @​minrk (activity) | @​newville (activity) | @​SylvainCorlay (activity)

7.2.0a1

(Full Changelog)

New features added

Enhancements made

... (truncated)

Commits
  • 4b37e75 Publish 7.2.0
  • 1630c4f Temporarily revert "Test changing base method to async after (#1464)" (#1493)
  • 8086199 Temporarily revert "Test changing base method to async after (#1464)"
  • a2d47a2 chore: update pre-commit hooks (#1472)
  • 06c9aee Publish 7.2.0a1
  • 220a3c6 Made IOPubThread constructor backward compatible (#1492)
  • dee781d Update pytest requirement from <9,>=7.0 to >=7.0,<10 in the actions group acr...
  • 56b2e29 Update pytest requirement in the actions group across 1 directory
  • 13e17df Advertizes kernel protocol 5.5 (#1488)
  • 59f0c65 Advertizes kernel protocol 5.5
  • Additional commits viewable in compare view

Updates sphinxcontrib-mermaid from 0.9.2 to 2.0.2

Changelog

Sourced from sphinxcontrib-mermaid's changelog.

Changelog

Unreleased

  • Add mermaid_dark_theme and mermaid_light_theme config options for configurable theme switching

2.0.1 (March 5, 2026)

  • Export runMermaid to window for hot reloading frontend
  • Small fixes for docs publishing

2.0.0 (January 13, 2026)

  • Drop support for Python 3.8 and 3.9
  • Add support for dynamic theme changes

1.2.3 (November 25, 2025)

  • Fix issue with ELK charts by upgrading to ELK plugin 0.2.0

1.2.2 (November 23, 2025)

  • Hotfix for CSS/JS assets included via old MANIFEST mechanism

1.2.1 (November 23, 2025)

  • Adjust chart size defaults to closer resember previous
  • Fix issue with fullscreen classes after rebase

1.2.0 (November 23, 2025)

  • Normalize javascript across various configuration options
  • Make graph full width and avoid unused margins in graph image
  • Rename fullscreen container class from mermaid-fullscreen-content to mermaid-container-fullscreen

1.1.0 (November 19, 2025)

  • Upgrade Mermaid to 11.12.1
  • Add fullscreen graph view capabilities

1.0.0 (October 12, 2024)

  • Upgrade Mermaid to 11.2.0
  • Add support for ELK diagrams
  • Add support for name parameter
  • Add passthrough of mermaid frontmatter
  • Convert to native namespace package
  • Drop support for Python 3.7

... (truncated)

Commits

@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Jun 4, 2026
@dependabot dependabot Bot requested review from d33bs and gwaybio as code owners June 4, 2026 18:45
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Jun 4, 2026
@gwaybio

gwaybio commented Jun 12, 2026

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@dependabot rebase

@dependabot
build(deps): bump the python-packages group across 1 directory with 8…
3463e13 
… updates

Bumps the python-packages group with 8 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [sqlalchemy](https://github.com/sqlalchemy/sqlalchemy) | `2.0.49` | `2.0.50` |
| [csvkit](https://github.com/wireservice/csvkit) | `1.5.0` | `2.2.0` |
| [setuptools](https://github.com/pypa/setuptools) | `69.5.1` | `82.0.1` |
| [mypy](https://github.com/python/mypy) | `1.20.2` | `2.1.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.15.14` | `0.15.16` |
| [cosmicqc](https://github.com/cytomining/coSMicQC) | `1.0.1` | `1.0.2` |
| [ipykernel](https://github.com/ipython/ipykernel) | `6.31.0` | `7.2.0` |
| [sphinxcontrib-mermaid](https://github.com/mgaitan/sphinxcontrib-mermaid) | `0.9.2` | `2.0.2` |



Updates `sqlalchemy` from 2.0.49 to 2.0.50
- [Release notes](https://github.com/sqlalchemy/sqlalchemy/releases)
- [Changelog](https://github.com/sqlalchemy/sqlalchemy/blob/main/CHANGES.rst)
- [Commits](https://github.com/sqlalchemy/sqlalchemy/commits)

Updates `csvkit` from 1.5.0 to 2.2.0
- [Changelog](https://github.com/wireservice/csvkit/blob/master/CHANGELOG.rst)
- [Commits](wireservice/csvkit@1.5.0...2.2.0)

Updates `setuptools` from 69.5.1 to 82.0.1
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst)
- [Commits](pypa/setuptools@v69.5.1...v82.0.1)

Updates `mypy` from 1.20.2 to 2.1.0
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.20.2...v2.1.0)

Updates `ruff` from 0.15.14 to 0.15.16
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.15.14...0.15.16)

Updates `cosmicqc` from 1.0.1 to 1.0.2
- [Release notes](https://github.com/cytomining/coSMicQC/releases)
- [Commits](cytomining/coSMicQC@v1.0.1...v1.0.2)

Updates `ipykernel` from 6.31.0 to 7.2.0
- [Release notes](https://github.com/ipython/ipykernel/releases)
- [Changelog](https://github.com/ipython/ipykernel/blob/main/CHANGELOG.md)
- [Commits](ipython/ipykernel@v6.31.0...v7.2.0)

Updates `sphinxcontrib-mermaid` from 0.9.2 to 2.0.2
- [Changelog](https://github.com/mgaitan/sphinxcontrib-mermaid/blob/master/CHANGELOG.md)
- [Commits](mgaitan/sphinxcontrib-mermaid@0.9.2...2.0.2)

---
updated-dependencies:
- dependency-name: cosmicqc
  dependency-version: 1.0.2
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-packages
- dependency-name: csvkit
  dependency-version: 2.2.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: python-packages
- dependency-name: ipykernel
  dependency-version: 7.2.0
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: python-packages
- dependency-name: mypy
  dependency-version: 2.1.0
  dependency-type: direct:development
  update-type: version-update:semver-major
  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
- dependency-name: setuptools
  dependency-version: 82.0.1
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: python-packages
- dependency-name: sphinxcontrib-mermaid
  dependency-version: 2.0.2
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: python-packages
- dependency-name: sqlalchemy
  dependency-version: 2.0.50
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-packages
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot changed the title build(deps): bump the python-packages group with 8 updates build(deps): bump the python-packages group across 1 directory with 8 updates Jun 12, 2026
@dependabot dependabot Bot force-pushed the dependabot/uv/python-packages-5467961575 branch from c9becf0 to 3463e13 Compare June 12, 2026 16:33
@codecov-commenter

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.07%. Comparing base (dda58aa) to head (7bfde1d).

Additional details and impacted files 
@@           Coverage Diff           @@
##             main     #703   +/-   ##
=======================================
  Coverage   94.07%   94.07%           
=======================================
  Files          62       62           
  Lines        4524     4524           
=======================================
  Hits         4256     4256           
  Misses        268      268
Flag Coverage Δ
unittests 94.07% <ø> (ø)

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@gwaybio gwaybio merged commit 4463c73 into main Jun 12, 2026
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@gwaybio gwaybio deleted the dependabot/uv/python-packages-5467961575 branch June 12, 2026 17:02
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