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Bump the all-deps group with 26 updates - #383

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Bump the all-deps group with 26 updates#383
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dependabot/uv/all-deps-2a372bd72b

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Bumps the all-deps group with 26 updates:

Package From To
numpy 2.4.6 2.5.1
scipy 1.17.1 1.18.0
docutils 0.22.4 0.23
pydata-sphinx-theme 0.19.0 0.8.0
jupyter-sphinx 0.5.3 0.4.0
sphinxcontrib-bibtex 2.7.0 2.5.0
jupytext 1.19.3 1.11.1
numpydoc 1.10.0 1.2.1
jinja2 3.1.6 3.0.3
myst-nb 1.4.0 0.8.4
pytest 9.1.0 9.1.1
pytest-memray 1.8.0 1.5.0
tox 4.55.1 4.56.2
mypy 2.1.0 2.2.0
alabaster 1.0.0 0.7.16
ast-serialize 0.5.0 0.6.0
attrs 26.1.0 20.3.0
jsonschema 4.26.0 4.17.3
jupyter-cache 1.0.1 0.2.2
librt 0.11.0 0.12.0
markdown-it-py 4.2.0 0.6.2
mdit-py-plugins 0.6.1 0.2.6
memray 1.19.3 1.10.0
myst-parser 5.1.0 0.13.6
rich 15.0.0 13.1.0
sqlalchemy 2.0.51 1.3.24

Updates numpy from 2.4.6 to 2.5.1

Release notes

Sourced from numpy's releases.

v2.5.1 (July 4, 2026)

NumPy 2.5.1 Release Notes

The NumPy 2.5.1 is a patch release that fixes bugs discovered after the 2.5.0 release. The most noticeable is the fix is to the numpy datetime cython API which should allow downstream to support NumPy versions older than 2.5. Preparation for Python 3.15 continues along with typing improvements.

This release supports Python versions 3.12-3.14

Changes

  • The minimum supported GCC version has been updated from 9.3.0 to 10.3.0

    (gh-31843)

Contributors

A total of 10 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Adhyan Gupta +
  • Ankit Ahlawat
  • Charles Harris
  • Iason Krommydas
  • Joren Hammudoglu
  • Kumar Aditya
  • Nathan Goldbaum
  • Sebastian Berg
  • Ties Jan Hefting +
  • Vineet Kumar

Pull requests merged

A total of 20 pull requests were merged for this release.

  • #31707: MAINT: Prepare 2.5.x for further development
  • #31721: CI: fix new cython-lint errors (#31711)
  • #31723: MAINT: Update meson to match main
  • #31729: TST: use setup-sde instead of curl to get SDE binaries (#31727)
  • #31829: BUG: Relax finfo to be easier accessible for all user dtypes...
  • #31831: TYP: Fix flatiter.__next__ return type for object_ and...
  • #31832: BUG: avoid deadlocks using NpyString API (#31682)
  • #31833: BUG: fix out array leak in reduceat and accumulate when dtype...
  • #31835: BUG: fix numpy datetime cython APIs to be compatible with older...
  • #31836: TYP: Fix incorrect dtype inference of asarray([]) (#31732)
  • #31837: TYP: Fix np.ma.masked_array 2.5.0 regression
  • #31838: FIX: Refactor error handling in array_setstate to prevent typecode...
  • #31839: TST: xfail multithreaded BLAS test more generously
  • #31840: MAINT: Rename subroutine for crackfortran tests

... (truncated)

Commits
  • 5e1d03f Merge pull request #31863 from charris/prepare-2.5.1
  • ad0b66b REL: Prepare for the NumPy 2.5.1 release.
  • 9df8516 Merge pull request #31858 from charris/backport-31688
  • 4dee265 Merge pull request #31857 from charris/backport-31775
  • dc8d553 Merge pull request #31856 from charris/backport-31846
  • 67cb4a8 fix:Signed integer overflow in datetime.c (#31688)
  • baa2589 TST: Clean up imports, formatting, and assertions
  • 2fe5ba4 TEST: Refactor tests to use np.testing.assert_raises_regex per review
  • bb46581 MAINT: Remove deprecated Python recursion fix
  • 8f34214 MAINT: Move SeedSequence recursion guard to C-layer and add tests
  • Additional commits viewable in compare view

Updates scipy from 1.17.1 to 1.18.0

Release notes

Sourced from scipy's releases.

SciPy 1.18.0 Release Notes

SciPy 1.18.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.18.x branch, and on adding new features on the main branch.

This release requires Python 3.12-3.14 and NumPy 2.0.0 or greater.

Highlights of this release

  • SciPy now supports three different build modes for BLAS and LAPACK LP64/ILP64 support, and machinery is provided for downstream cython_lapack consumers to gracefully handle LP64/ILP64 backend builds. ILP64 support has been substantially improved across the SciPy library.
  • Remaining Fortran to C translations have been completed---an experimental Fortran-free build option is now available to developers for testing purposes. Developer feedback is welcome on Fortran-free builds.
  • scipy.signal.whittaker_henderson now provides access to Whittaker-Henderson smoothing of a discrete signal.
  • A large number of scipy.stats functions now support lazy arrays and JAX JIT. Array API support has been improved substantially in SciPy, with at least 21 functions gaining new support in this release. 16 scipy.stats functions have also gained support for MArray input.

New features

scipy.fft improvements

  • SciPy's internal FFT backend has switched from pocketfft to its successor package ducc0.fft, which features several incremental improvements. The most significant of those from SciPy's perspective is probably that storage requirements for internally cached plans have been significantly reduced for most long 1D transforms. Plans that require more storage than 1MB will no longer be cached; this mainly affects huge 1D transforms of prime and near-prime sizes.

scipy.interpolate improvements

... (truncated)

Commits
  • 54ef542 REL: 1.18.0 release commit
  • a45e463 Merge pull request #25395 from tylerjereddy/treddy_prep_1.18.0_final
  • ee2442e TYP, MAINT, TST: PR 25395 revisions
  • 3225154 DOC: PR 25395 revisions
  • 14c7bd7 TYP: Fix mypy errors with pytest==9.1.0 (#25410)
  • 71522e9 DOC: revise SciPy 1.18.0 release notes
  • 92f8482 MAINT: fix errors from pytest 9.1 (#25378)
  • 7b27bf4 TST, MAINT: modernize spatial tests for pytest 10 (#25376)
  • d05b640 Merge pull request #25347 from tylerjereddy/treddy_version_bump_1.18.0rc3
  • e60fe8b REL: set to 1.18.0rc3 unreleased
  • Additional commits viewable in compare view

Updates docutils from 0.22.4 to 0.23

Commits

Updates pydata-sphinx-theme from 0.19.0 to 0.8.0

Commits

Updates jupyter-sphinx from 0.5.3 to 0.4.0

Commits
  • 23322c7 Merge pull request #204 from basnijholt/do-not-double-copy
  • d40b2ad add paragraph to styling section
  • d6ad4d3 add changelog entry
  • a0dcbd7 Do not overwrite files in _static if user already has custom versions of thos...
  • a74b13e Merge pull request #207 from basnijholt/fix-182
  • cfa0879 add deprecation warning
  • 75b003f add changelog entry
  • 4129ebe rename directives jupyter-download:script -> jupyter-download-script, similar...
  • d427c79 Merge pull request #206 from basnijholt/pre-commit
  • cac7aaa bump versions
  • Additional commits viewable in compare view

Updates sphinxcontrib-bibtex from 2.7.0 to 2.5.0

Changelog

Sourced from sphinxcontrib-bibtex's changelog.

2.7.0 (6 May 2026)

  • BACKWARD INCOMPATIBLE A new warning category, duplicate_local_citation, has been introduced. It is triggered when a duplicate citation appears within the same document. The existing duplicate_citation warning continues to report duplicates but now only across different documents.

    In many cases, users maintain a separate bibliography for each document (often using a docname in docnames filter). In such setups, duplicate citations across documents are usually acceptable, while duplicates within a single document are not. This distinction allows users to suppress duplicate_citation warnings while still receiving duplicate_local_citation warnings.

  • When there are duplicate citations, resolve locally first (reported by drbenvincent, see issue #385).

  • The usage section of the documentation now starts with in-depth general considerations to guide users towards best practice for the most common use cases.

  • Citation reference wrapper nodes now have a bibtex-citation CSS class, to enable Sphinx themes to style citation elements separately from other content (contributed by mmcky, see pull request #383).

  • Increase required pybtex-docutils version to 1.0.2 (reported by ego-thales).

  • Fix test suite for docutils 0.22 (fixed by mitya57, see pull request #377).

  • Dropped Python 3.9 support (EOL), added Python 3.14 support.

  • Fixed various deprecation warnings in Sphinx and docutils.

  • Improved header parsing.

  • Minimum required Sphinx version increased to 7.4.

  • Minimum required Docutils version increased to 0.20.

2.6.5 (27 June 2025)

  • Require pybtex 0.25 and remove setuptools dependency hack (fixed by flying-sheep, see pull request #372).

2.6.4 (17 June 2025)

  • Add Python 3.13 support.

... (truncated)

Commits

Updates jupytext from 1.19.3 to 1.11.1

Changelog

Sourced from jupytext's changelog.

1.19.3 (2026-05-17)

Fixed

  • The Jupytext CLI issues a warning when a notebook is not trusted. Also, trust is preserved when empty outputs are added (follow-up on #1505)

Changed

  • The dependabot config has been updated to correctly bump extension packages, now allowing only production updates and ignoring dev dependencies (#1532). Thanks to Mahendra Paipuri for this PR!
  • Removed deprecated stylelint packages (stylelint-config-prettier and stylelint-prettier) from the JupyterLab extension dependencies (#1530)
  • We have removed Python 3.9 testing from the CI (Python 3.9 reached EOL in October 2025)

1.19.2 (2026-05-10)

Fixed

  • Trusted notebooks remain trusted after jupytext --sync (#1505)
  • We have fixed the homepage link in package.json. Thanks to Michał Krassowski for making this PR (#1494)
  • Thanks to Brigitta Sipőcz for fixing a broken link in our CLI (#1428)
  • The --quiet flag now suppresses the creating missing directory warning when writing to a path that includes a prefix (#1533)

Changed

  • The CI workflow has been restructured to maximize parallelization. All test suites (pip, conda, UI) and the build step now run concurrently after pre-commit checks, instead of sequentially, reducing CI times (#1527)
  • We have skipped the tests that involve jupyterfs on Python 3.12+ as they started failing on the CI with no obvious way to fix them (#1509)
  • We have changed the configuration of Dependabot to get grouped dependency updates for our JupyterLab extension.
  • We have merged a series of Dependabot security updates: #1516, #1517, #1519, #1520, #1522, #1524

1.19.1 (2026-01-25)

Changed

  • Jupytext does not change the file icons anymore! Thanks to Michał Krassowski for finally solving this long standing issue! (#398)
  • We have bumped lodash from 4.17.21 to 4.17.23 in JupyterLab extension (#1483)
  • We require marimo<=0.19.4 in tests following a change in the location of the marimo import (#1485)

1.19.0 (2026-01-18)

Changed

  • The environment used to develop Jupytext is now maintained using Pixi (#1459)

Fixed

  • We have restored the support for .qmd documents in Jupyter (#1435)
  • We have fixed warnings about the cell ids like either Cell is missing an id field or Additional properties are not allowed ('id' was unexpected) when converting to some formats, including Pandoc (#1464)
  • We have updated the dependencies of the Jupytext extension for JupyterLab. Many thanks to Mahendra Paipuri for his PR (#1477)!

Added

... (truncated)

Commits
  • 4ae9263 Update format with format options in the notebook metadata (md:myst and md:pa...
  • 0a8b180 Normalize jupytext config options names (#754)
  • e28497a Use config in read and write functions (#753)
  • 593bcef Use non-random cell ids in tests (#751)
  • 58e8b27 Update the dependencies of the JupyterLab extension (#750)
  • 508be51 Version 1.10.2
  • c5e4bcc Rebuild the package in the Publish step
  • a3d5439 Version 1.10.2-rc0 (#745)
  • a5c4fa2 MANIFEST: Graft labextension and exclude node_modules (#741)
  • 7d45d0b Version 1.10.1 (#740)
  • Additional commits viewable in compare view

Updates numpydoc from 1.10.0 to 1.2.1

Changelog

Sourced from numpydoc's changelog.

1.2.1

Release date: 29 March 2022

Requires Python 3.7+ and Sphinx 1.8+.

Full Changelog <https://github.com/numpy/numpydoc/compare/numpydoc-1.2...HEAD>__

Implemented enhancements


-  Update year `[#370](https://github.com/numpy/numpydoc/issues/370) <https://github.com/numpy/numpydoc/pull/370>`__ (`jarrodmillman <https://github.com/jarrodmillman>`__)

Fixed bugs



-  Use consistent release tags `[#361](https://github.com/numpy/numpydoc/issues/361) &lt;https://github.com/numpy/numpydoc/pull/361&gt;`__ (`jarrodmillman &lt;https://github.com/jarrodmillman&gt;`__)
-  BUG: 1.2 raises error w.r.t. object has no attribute ‘\__name_\_’ `[#362](https://github.com/numpy/numpydoc/issues/362) &lt;https://github.com/numpy/numpydoc/issues/362&gt;`__
-  Use isgeneratorfunction to avoid false alarm YD01 validation `[#368](https://github.com/numpy/numpydoc/issues/368) &lt;https://github.com/numpy/numpydoc/pull/368&gt;`__ (`jnothman &lt;https://github.com/jnothman&gt;`__)
-  Fix AttributeError in underline length check `[#363](https://github.com/numpy/numpydoc/issues/363) &lt;https://github.com/numpy/numpydoc/pull/363&gt;`__ (`rossbar &lt;https://github.com/rossbar&gt;`__)
-  Upper bound jinja `[#369](https://github.com/numpy/numpydoc/issues/369) &lt;https://github.com/numpy/numpydoc/pull/369&gt;`__ (`jarrodmillman &lt;https://github.com/jarrodmillman&gt;`__)

Closed issues




    

  • Validation check YD01 not implemented properly [#365](https://github.com/numpy/numpydoc/issues/365) &lt;https://github.com/numpy/numpydoc/issues/365&gt;__
    • 

  • Support numpydoc validation without running sphinx [#364](https://github.com/numpy/numpydoc/issues/364) &lt;https://github.com/numpy/numpydoc/issues/364&gt;__
    • 

  • 1.2: change tagging convention? [#360](https://github.com/numpy/numpydoc/issues/360) &lt;https://github.com/numpy/numpydoc/issues/360&gt;__
    • 



1.2.0


Release date: 24 January 2022


Requires Python 3.7+ and Sphinx 1.8+.


Implemented enhancements

  • Document release process [#357](https://github.com/numpy/numpydoc/issues/357) <https://github.com/numpy/numpydoc/pull/357>__ (jarrodmillman <https://github.com/jarrodmillman>__)
  • Use setuptools [#349](https://github.com/numpy/numpydoc/issues/349) <https://github.com/numpy/numpydoc/pull/349>__ (jarrodmillman <https://github.com/jarrodmillman>__)
  • DOC: Switch docs to pydata-sphinx-theme [#313](https://github.com/numpy/numpydoc/issues/313) <https://github.com/numpy/numpydoc/pull/313>__ (rossbar <https://github.com/rossbar>__)
  • Improve error messages for see also parsing [#306](https://github.com/numpy/numpydoc/issues/306) <https://github.com/numpy/numpydoc/pull/306>__ (rossbar <https://github.com/rossbar>__)
  • ENH: Enable validation during sphinx-build process [#302](https://github.com/numpy/numpydoc/issues/302) <https://github.com/numpy/numpydoc/pull/302>__ (rossbar <https://github.com/rossbar>__)
  • Add a note to the docstring standard about long ‘See Also’ entries. [#300](https://github.com/numpy/numpydoc/issues/300) <https://github.com/numpy/numpydoc/pull/300>__ (WarrenWeckesser <https://github.com/WarrenWeckesser>__)
  • MAINT: minor refactoring in docscrape [#297](https://github.com/numpy/numpydoc/issues/297) <https://github.com/numpy/numpydoc/pull/297>__ (rossbar <https://github.com/rossbar>__)
  • ENH: Add configuration option for parameter cross-referencing [#295](https://github.com/numpy/numpydoc/issues/295) <https://github.com/numpy/numpydoc/pull/295>__ (rossbar <https://github.com/rossbar>__)
  • ENH: Better warning for sections. [#278](https://github.com/numpy/numpydoc/issues/278) <https://github.com/numpy/numpydoc/pull/278>__ (Carreau <https://github.com/Carreau>__)

... (truncated)

Commits

Updates jinja2 from 3.1.6 to 3.0.3

Changelog

Sourced from jinja2's changelog.

Version 3.1.6

Released 2025-03-05

  • The |attr filter does not bypass the environment's attribute lookup, allowing the sandbox to apply its checks. :ghsa:cpwx-vrp4-4pq7

Version 3.1.5

Released 2024-12-21

  • The sandboxed environment handles indirect calls to str.format, such as by passing a stored reference to a filter that calls its argument. :ghsa:q2x7-8rv6-6q7h
  • Escape template name before formatting it into error messages, to avoid issues with names that contain f-string syntax. :issue:1792, :ghsa:gmj6-6f8f-6699
  • Sandbox does not allow clear and pop on known mutable sequence types. :issue:2032
  • Calling sync render for an async template uses asyncio.run. :pr:1952
  • Avoid unclosed auto_aiter warnings. :pr:1960
  • Return an aclose-able AsyncGenerator from Template.generate_async. :pr:1960
  • Avoid leaving root_render_func() unclosed in Template.generate_async. :pr:1960
  • Avoid leaving async generators unclosed in blocks, includes and extends. :pr:1960
  • The runtime uses the correct concat function for the current environment when calling block references. :issue:1701
  • Make |unique async-aware, allowing it to be used after another async-aware filter. :issue:1781
  • |int filter handles OverflowError from scientific notation. :issue:1921
  • Make compiling deterministic for tuple unpacking in a {% set ... %} call. :issue:2021
  • Fix dunder protocol (copy/pickle/etc) interaction with Undefined objects. :issue:2025
  • Fix copy/pickle support for the internal missing object. :issue:2027
  • Environment.overlay(enable_async) is applied correctly. :pr:2061
  • The error message from FileSystemLoader includes the paths that were searched. :issue:1661
  • PackageLoader shows a clearer error message when the package does not contain the templates directory. :issue:1705
  • Improve annotations for methods returning copies. :pr:1880
  • urlize does not add mailto: to values like @a@b. :pr:1870

... (truncated)

Commits
  • 2a48dd8 Merge pull request #1543 from pallets/release-3.0.3
  • ce1a539 release version 3.0.3
  • 199b6d5 Merge pull request #1542 from pallets/package-loader-file
  • eec0db8 PackageLoader works with single module file
  • 46f3a68 Merge pull request #1541 from pallets/docs-pow-order
  • 0d19990 document chained pow order
  • 99daa2a Merge pull request #1540 from pallets/docs-macro-defaults
  • a6162da rewrite docs about extending template objects
  • cab5545 Merge pull request #1539 from pallets/docs-macro-defaults
  • 369ff03 remove reference to macro.defaults
  • Additional commits viewable in compare view

Updates myst-nb from 1.4.0 to 0.8.4

Changelog

Sourced from myst-nb's changelog.

Change Log

Commits

Updates pytest from 9.1.0 to 9.1.1

Release notes

Sourced from pytest's releases.

9.1.1

pytest 9.1.1 (2026-06-19)

Bug fixes

  • #14220: Fixed a logic bug in pytest.RaisesGroup which would might cause it to display incorrect "It matches FooError() which was paired with BarError" messages.
  • #14591: Fixed a regression in pytest 9.1.0 which caused overriding a parametrized fixture with an indirect @​pytest.mark.parametrize to fail with "duplicate parametrization of '<fixture name>'".
  • #14606: Fixed list-item typing errors from mypy in @pytest.mark.parametrize <pytest.mark.parametrize ref> argvalues parameter.
  • #14608: Fixed a regression in pytest 9.1.0 where conftest.py files located in <invocation dir>/test* were no longer loaded as initial conftests when invoked without arguments. This could cause certain hooks (like pytest_addoption) in these files to not fire.
Commits
  • cf470ec Prepare release version 9.1.1
  • e0c8ce6 Merge pull request #14625 from pytest-dev/patchback/backports/9.1.x/a07c31a97...
  • 1b82d16 Merge pull request #14624 from pytest-dev/patchback/backports/9.1.x/b375b79ec...
  • 501c4bc Merge pull request #14596 from bluetech/doc-classmethod
  • b61f588 Merge pull request #14622 from chrisburr/fix-14608-initial-conftest-test-subdir
  • 9a567e0 [automated] Update plugin list (#14617) (#14618)
  • ef8b299 Merge pull request #14620 from pytest-dev/patchback/backports/9.1.x/680f9f3ed...
  • 66abd07 Merge pull request #14220 from bysiber/fix-stale-iexp-raisesgroup
  • 79fbf93 Merge pull request #14612 from pytest-dev/patchback/backports/9.1.x/974ed48b6...
  • 0d312eb Merge pull request #14611 from bluetech/parametrize-argvalues-typing
  • Additional commits viewable in compare view

Updates pytest-memray from 1.8.0 to 1.5.0

Changelog

Sourced from pytest-memray's changelog.

v1.8.0 (2025-08-13)

Features - 1.8.0

- Python 3.14 is now officially supported. (:issue:`118`)

v1.7.0 (2024-07-25)


Bug Fixes - 1.7.0

  • Fix compatibility with anyio-based async test runners by using an async def wrapper when the decorated test is a coroutine function. (:issue:119)

v1.6.0 (2024-04-18)

Features - 1.6.0

- Add a new --fail-on-increase option that fails a test with the ``limit_memory`` marker if it uses more memory than its last successful run. (:issue:`91`)
- Use aggregated capture files, reducing the amount of temporary disk space required in order to run tests. (:issue:`107`)
- Add a new ``current_thread_only`` keyword argument to the ``limit_memory`` and
  ``limit_leaks`` markers to ignore all allocations made in threads other than
  the one running the test. (:issue:`117`)

Bug Fixes - 1.6.0

  • Fix the generation of histograms when the tests performed zero-byte allocations. (:issue:113)

v1.5.0 (2023-08-23)

Features - 1.5.0


- Add a new ``limit_leaks`` marker to check for memory leaks in tests. (:issue:`45`)
- Support passing ``--trace-python-allocators`` to memray to track all Python allocations. (:issue:`78` and :issue:`64`)

v1.4.1 (2023-06-06)


Bug Fixes - 1.4.1

  • Fix long test names with xdis (:issue:68)

v1.4.0 (2022-12-02)

Features - 1.4.0

... (truncated)

Commits
  • 0e33179 Add a new marker to check for memory leaks (#52)
  • b25d4b8 Bump pypa/gh-action-pypi-publish from 1.8.7 to 1.8.10
  • f889d26 docs(README.md): fix the bulleted lists
  • 78c2b07 Bump pypa/gh-action-pypi-publish from 1.8.6 to 1.8.7
  • 8fd5a43 Use ruff instead of flake8 + isort
  • ad9b759 Complete the documentation for the configuration file options
  • 9fc6c5c Support passing --trace-python-allocators to memray
  • 10a354f Relax the sizes in the 'test_limit_memory_marker_with_pytest_xdist' test
  • 6a2c733 docs: Document options --stacks and --native
  • e839fff Update usage.rst
  • Additional commits viewable in compare view

Updates tox from 4.55.1 to 4.56.2

Release notes

Sourced from tox's releases.

v4.56.2

What's Changed

Full Changelog: tox-dev/tox@4.56.1...4.56.2

v4.56.1

What's Changed

New Contributors

Full Changelog: tox-dev/tox@4.56.0...4.56.1

v4.56.0

What's Changed

New Contributors

Full Changelog: tox-dev/tox@4.55.1...4.56.0

Changelog

Sourced from tox's changelog.

Bug fixes - 4.56.2

  • Fix a batch of latent defects found in a codebase audit:

    • stop duplicating --extra-index-url when a merged requirements line repeats an already-seen index;
    • render --no-binary/--only-binary as comma-joined strings instead of leaking the internal set into the pip command line;
    • report a clear error instead of IndexError for a bare one-argument flag (-c, -r, -f, -e) in deps or constraints;
    • canonicalize optional-dependencies keys and self-referential (recursive) extra names so non-canonical spellings no longer silently drop dependencies;
    • raise a clear error instead of KeyError when dependency_groups is requested without a [dependency-groups] table;
    • stop a native TOML { replace = "env" } reference from leaking its resolution chain into sibling list entries and tripping a spurious circular chain error;
    • expand the range that actually matched in a factor expression rather than the first identical digit-range substring;
    • strip the backslash from an escaped \; in set_env values;
    • skip option values during command auto-detection so an environment named like a subcommand (e.g. tox -e list) is no longer misread;
    • treat an empty list-typed environment variable (e.g. TOX_DISCOVER=) as an empty list rather than [""];
    • report an environment whose name is an empty string as present in Config membership tests;
    • fail evaluation gracefully instead of crashing the driver thread when tox p -p all is run with an empty selection;
    • avoid rebuilding a throwaway PEP 517 frontend against the previous root when a package environment's root is reassigned before a frontend exists;
    • avoid crashing create_session_view when the package and its session copy share no common path (e.g. different Windows drives);
    • close the pseudo-terminal file descriptors that leaked on every command run under a tty and on the terminal-attribute inheritance error path;
    • honor the stop signal in the Windows overlapped-I/O reader while a read is still pending, so shutdown no longer risks hanging on a child that holds its pipe open without producing output. (:issue:3974)

v4.56.1 (2026-06-25)

Bug fixes - 4.56.1

  • Fix { replace = "if" ... extend = true } corrupting the resulting list when then or else is a scalar string (e.g. then = "-v"): a non-empty scalar string is now appended as a single element instead of being iterated character-by-character, while a false if with no else (yielding "") contributes nothing rather than an empty element, and list/set results are still spread into the parent. (:issue:3969)

v4.56.0 (2026-06-23)

Features - 4.56.0

... (truncated)

Commits
  • 5458a28 release 4.56.2
  • d3dc2d1 Fix 17 bugs found in a deep codebase sweep (#3974)
  • b55fe2f [pre-commit.ci] pre-commit autoupdate (#3973)
  • 7ba0f81 💰 Surface GitHub Sponsors + thanks.dev
  • 03c2d58 build(deps): bump actions/cache from 5.0.5 to 6.1.0 (#3972)
  • 34962f1 [pre-commit.ci] pre-commit autoupdate (#3971)
  • 0df25f4 🔧 chore(type): drop stale ty invalid-assignment ignores (#3970)
  • 4bb6421 release 4.56.1
  • ca2f561 treat scalar string then/else as a single item in if-replace extend (#3969)
  • f933bd2 build(deps): bump actions/checkout from 6.0.3 to 7.0.0 (#3968)
  • Additional commits viewable in compare view

Updates mypy from 2.1.0 to 2.2.0

Changelog

Sourced from mypy's changelog.

Mypy Release Notes

Next Release

Packaging changes

Mypy 2.3

We've just uploaded mypy 2.3.0 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.

The Upcoming Switch to the New Native Parser

We are planning to enable the new native parser (--native-parser) by default soon. We recommend that you test the native parser in your projects and report any issues in the mypy issue tracker.

Mypyc Free-threading Memory Safety

Free-threaded Python builds that don't have the GIL require additional synchronization primitives or lock-free algorithms to ensure memory safety when there are race conditions (for example, when a thread reads a list item while another thread writes the same list item concurrently). Thi...

Description has been truncated

@dependabot
Bump the all-deps group with 26 updates
2f0547e 
Bumps the all-deps group with 26 updates:

| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `2.4.6` | `2.5.1` |
| [scipy](https://github.com/scipy/scipy) | `1.17.1` | `1.18.0` |
| [docutils](https://github.com/rtfd/recommonmark) | `0.22.4` | `0.23` |
| [pydata-sphinx-theme](https://github.com/pydata/pydata-sphinx-theme) | `0.19.0` | `0.8.0` |
| [jupyter-sphinx](https://github.com/jupyter/jupyter-sphinx) | `0.5.3` | `0.4.0` |
| [sphinxcontrib-bibtex](https://github.com/mcmtroffaes/sphinxcontrib-bibtex) | `2.7.0` | `2.5.0` |
| [jupytext](https://github.com/jupytext/jupytext) | `1.19.3` | `1.11.1` |
| [numpydoc](https://github.com/numpy/numpydoc) | `1.10.0` | `1.2.1` |
| [jinja2](https://github.com/pallets/jinja) | `3.1.6` | `3.0.3` |
| [myst-nb](https://github.com/executablebooks/myst-nb) | `1.4.0` | `0.8.4` |
| [pytest](https://github.com/pytest-dev/pytest) | `9.1.0` | `9.1.1` |
| [pytest-memray](https://github.com/bloomberg/pytest-memray) | `1.8.0` | `1.5.0` |
| [tox](https://github.com/tox-dev/tox) | `4.55.1` | `4.56.2` |
| [mypy](https://github.com/python/mypy) | `2.1.0` | `2.2.0` |
| [alabaster](https://github.com/sphinx-doc/alabaster) | `1.0.0` | `0.7.16` |
| [ast-serialize](https://github.com/mypyc/ast_serialize) | `0.5.0` | `0.6.0` |
| [attrs](https://github.com/python-attrs/attrs) | `26.1.0` | `20.3.0` |
| [jsonschema](https://github.com/python-jsonschema/jsonschema) | `4.26.0` | `4.17.3` |
| [jupyter-cache](https://github.com/executablebooks/jupyter-cache) | `1.0.1` | `0.2.2` |
| [librt](https://github.com/mypyc/librt) | `0.11.0` | `0.12.0` |
| [markdown-it-py](https://github.com/executablebooks/markdown-it-py) | `4.2.0` | `0.6.2` |
| [mdit-py-plugins](https://github.com/executablebooks/mdit-py-plugins) | `0.6.1` | `0.2.6` |
| [memray](https://github.com/bloomberg/memray) | `1.19.3` | `1.10.0` |
| [myst-parser](https://github.com/executablebooks/MyST-Parser) | `5.1.0` | `0.13.6` |
| [rich](https://github.com/Textualize/rich) | `15.0.0` | `13.1.0` |
| [sqlalchemy](https://github.com/sqlalchemy/sqlalchemy) | `2.0.51` | `1.3.24` |


Updates `numpy` from 2.4.6 to 2.5.1
- [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...v2.5.1)

Updates `scipy` from 1.17.1 to 1.18.0
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.17.1...v1.18.0)

Updates `docutils` from 0.22.4 to 0.23
- [Changelog](https://github.com/readthedocs/recommonmark/blob/master/CHANGELOG.md)
- [Commits](https://github.com/rtfd/recommonmark/commits)

Updates `pydata-sphinx-theme` from 0.19.0 to 0.8.0
- [Release notes](https://github.com/pydata/pydata-sphinx-theme/releases)
- [Changelog](https://github.com/pydata/pydata-sphinx-theme/blob/main/RELEASE.md)
- [Commits](pydata/pydata-sphinx-theme@v0.19.0...v0.8.0)

Updates `jupyter-sphinx` from 0.5.3 to 0.4.0
- [Release notes](https://github.com/jupyter/jupyter-sphinx/releases)
- [Changelog](https://github.com/jupyter/jupyter-sphinx/blob/main/RELEASE.md)
- [Commits](jupyter/jupyter-sphinx@v0.5.3...v0.4.0)

Updates `sphinxcontrib-bibtex` from 2.7.0 to 2.5.0
- [Changelog](https://github.com/mcmtroffaes/sphinxcontrib-bibtex/blob/develop/CHANGELOG.rst)
- [Commits](mcmtroffaes/sphinxcontrib-bibtex@2.7.0...2.5.0)

Updates `jupytext` from 1.19.3 to 1.11.1
- [Release notes](https://github.com/jupytext/jupytext/releases)
- [Changelog](https://github.com/jupytext/jupytext/blob/main/CHANGELOG.md)
- [Commits](jupytext/jupytext@v1.19.3...v1.11.1)

Updates `numpydoc` from 1.10.0 to 1.2.1
- [Release notes](https://github.com/numpy/numpydoc/releases)
- [Changelog](https://github.com/numpy/numpydoc/blob/v1.2.1/doc/release_notes.rst)
- [Commits](numpy/numpydoc@v1.10.0...v1.2.1)

Updates `jinja2` from 3.1.6 to 3.0.3
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)
- [Commits](pallets/jinja@3.1.6...3.0.3)

Updates `myst-nb` from 1.4.0 to 0.8.4
- [Release notes](https://github.com/executablebooks/myst-nb/releases)
- [Changelog](https://github.com/executablebooks/MyST-NB/blob/main/CHANGELOG.md)
- [Commits](executablebooks/MyST-NB@v1.4.0...v0.8.4)

Updates `pytest` from 9.1.0 to 9.1.1
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@9.1.0...9.1.1)

Updates `pytest-memray` from 1.8.0 to 1.5.0
- [Release notes](https://github.com/bloomberg/pytest-memray/releases)
- [Changelog](https://github.com/bloomberg/pytest-memray/blob/main/docs/news.rst)
- [Commits](bloomberg/pytest-memray@v1.8.0...1.5.0)

Updates `tox` from 4.55.1 to 4.56.2
- [Release notes](https://github.com/tox-dev/tox/releases)
- [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst)
- [Commits](tox-dev/tox@4.55.1...4.56.2)

Updates `mypy` from 2.1.0 to 2.2.0
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v2.1.0...v2.2.0)

Updates `alabaster` from 1.0.0 to 0.7.16
- [Release notes](https://github.com/sphinx-doc/alabaster/releases)
- [Changelog](https://github.com/sphinx-doc/alabaster/blob/master/docs/changelog.rst)
- [Commits](sphinx-doc/alabaster@1.0.0...0.7.16)

Updates `ast-serialize` from 0.5.0 to 0.6.0
- [Commits](mypyc/ast_serialize@v0.5.0...v0.6.0)

Updates `attrs` from 26.1.0 to 20.3.0
- [Release notes](https://github.com/python-attrs/attrs/releases)
- [Changelog](https://github.com/python-attrs/attrs/blob/main/CHANGELOG.md)
- [Commits](python-attrs/attrs@26.1.0...20.3.0)

Updates `jsonschema` from 4.26.0 to 4.17.3
- [Release notes](https://github.com/python-jsonschema/jsonschema/releases)
- [Changelog](https://github.com/python-jsonschema/jsonschema/blob/main/CHANGELOG.rst)
- [Commits](python-jsonschema/jsonschema@v4.26.0...v4.17.3)

Updates `jupyter-cache` from 1.0.1 to 0.2.2
- [Release notes](https://github.com/executablebooks/jupyter-cache/releases)
- [Changelog](https://github.com/executablebooks/jupyter-cache/blob/main/CHANGELOG.md)
- [Commits](executablebooks/jupyter-cache@v1.0.1...v0.2.2)

Updates `librt` from 0.11.0 to 0.12.0
- [Commits](mypyc/librt@v0.11.0...v0.12.0)

Updates `markdown-it-py` from 4.2.0 to 0.6.2
- [Release notes](https://github.com/executablebooks/markdown-it-py/releases)
- [Changelog](https://github.com/executablebooks/markdown-it-py/blob/master/CHANGELOG.md)
- [Commits](executablebooks/markdown-it-py@v4.2.0...v0.6.2)

Updates `mdit-py-plugins` from 0.6.1 to 0.2.6
- [Release notes](https://github.com/executablebooks/mdit-py-plugins/releases)
- [Changelog](https://github.com/executablebooks/mdit-py-plugins/blob/master/CHANGELOG.md)
- [Commits](executablebooks/mdit-py-plugins@v0.6.1...v0.2.6)

Updates `memray` from 1.19.3 to 1.10.0
- [Release notes](https://github.com/bloomberg/memray/releases)
- [Changelog](https://github.com/bloomberg/memray/blob/main/NEWS.rst)
- [Commits](bloomberg/memray@v1.19.3...1.10.0)

Updates `myst-parser` from 5.1.0 to 0.13.6
- [Release notes](https://github.com/executablebooks/MyST-Parser/releases)
- [Changelog](https://github.com/executablebooks/MyST-Parser/blob/master/CHANGELOG.md)
- [Commits](executablebooks/MyST-Parser@v5.1.0...v0.13.6)

Updates `rich` from 15.0.0 to 13.1.0
- [Release notes](https://github.com/Textualize/rich/releases)
- [Changelog](https://github.com/Textualize/rich/blob/main/CHANGELOG.md)
- [Commits](Textualize/rich@v15.0.0...v13.1.0)

Updates `sqlalchemy` from 2.0.51 to 1.3.24
- [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)

---
updated-dependencies:
- dependency-name: numpy
  dependency-version: 2.5.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: scipy
  dependency-version: 1.18.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: docutils
  dependency-version: '0.23'
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: pydata-sphinx-theme
  dependency-version: 0.8.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: jupyter-sphinx
  dependency-version: 0.4.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: sphinxcontrib-bibtex
  dependency-version: 2.5.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: jupytext
  dependency-version: 1.11.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: numpydoc
  dependency-version: 1.2.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: jinja2
  dependency-version: 3.0.3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: myst-nb
  dependency-version: 0.8.4
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: all-deps
- dependency-name: pytest
  dependency-version: 9.1.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-deps
- dependency-name: pytest-memray
  dependency-version: 1.5.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: tox
  dependency-version: 4.56.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: mypy
  dependency-version: 2.2.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: alabaster
  dependency-version: 0.7.16
  dependency-type: indirect
  update-type: version-update:semver-major
  dependency-group: all-deps
- dependency-name: ast-serialize
  dependency-version: 0.6.0
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: attrs
  dependency-version: 20.3.0
  dependency-type: indirect
  update-type: version-update:semver-major
  dependency-group: all-deps
- dependency-name: jsonschema
  dependency-version: 4.17.3
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: jupyter-cache
  dependency-version: 0.2.2
  dependency-type: indirect
  update-type: version-update:semver-major
  dependency-group: all-deps
- dependency-name: librt
  dependency-version: 0.12.0
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: markdown-it-py
  dependency-version: 0.6.2
  dependency-type: indirect
  update-type: version-update:semver-major
  dependency-group: all-deps
- dependency-name: mdit-py-plugins
  dependency-version: 0.2.6
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: memray
  dependency-version: 1.10.0
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: all-deps
- dependency-name: myst-parser
  dependency-version: 0.13.6
  dependency-type: indirect
  update-type: version-update:semver-major
  dependency-group: all-deps
- dependency-name: rich
  dependency-version: 13.1.0
  dependency-type: indirect
  update-type: version-update:semver-major
  dependency-group: all-deps
- dependency-name: sqlalchemy
  dependency-version: 1.3.24
  dependency-type: indirect
  update-type: version-update:semver-major
  dependency-group: all-deps
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Jul 15, 2026
@dependabot @github

dependabot Bot commented on behalf of github Jul 22, 2026

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

@dependabot dependabot Bot closed this Jul 22, 2026
@dependabot
dependabot Bot deleted the dependabot/uv/all-deps-2a372bd72b branch July 22, 2026 09:43
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