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deps(deps): bump the dependencies group with 6 updates#26

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deps(deps): bump the dependencies group with 6 updates#26
chenpeizhi merged 1 commit intomasterfrom
dependabot/uv/dependencies-1d49c30b6a

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@dependabot dependabot bot commented on behalf of github Jan 1, 2026

Bumps the dependencies group with 6 updates:

Package From To
numpy 2.3.4 2.4.0
networkx 3.5 3.6.1
ipython 9.6.0 9.8.0
sphinx 8.2.3 9.1.0
pytest 8.4.2 9.0.2
juliacall 0.9.28 0.9.31

Updates numpy from 2.3.4 to 2.4.0

Release notes

Sourced from numpy's releases.

2.4.0 (Dec 20, 2025)

NumPy 2.4.0 Release Notes

The NumPy 2.4.0 release continues the work to improve free threaded Python support, user dtypes implementation, and annotations. There are many expired deprecations and bug fixes as well.

This release supports Python versions 3.11-3.14

Highlights

Apart from annotations and same_value kwarg, the 2.4 highlights are mostly of interest to downstream developers. They should help in implementing new user dtypes.

  • Many annotation improvements. In particular, runtime signature introspection.
  • New casting kwarg 'same_value' for casting by value.
  • New PyUFunc_AddLoopsFromSpec function that can be used to add user sort loops using the ArrayMethod API.
  • New __numpy_dtype__ protocol.

Deprecations

Setting the strides attribute is deprecated

Setting the strides attribute is now deprecated since mutating an array is unsafe if an array is shared, especially by multiple threads. As an alternative, you can create a new view (no copy) via:

  • np.lib.stride_tricks.strided_window_view if applicable,
  • np.lib.stride_tricks.as_strided for the general case,
  • or the np.ndarray constructor (buffer is the original array) for a light-weight version.

(gh-28925)

Positional out argument to np.maximum, np.minimum is deprecated

Passing the output array out positionally to numpy.maximum and numpy.minimum is deprecated. For example, np.maximum(a, b, c) will emit a deprecation warning, since c is treated as the output buffer rather than a third input.

Always pass the output with the keyword form, e.g. np.maximum(a, b, out=c). This makes intent clear and simplifies type annotations.

(gh-29052)

align= must be passed as boolean to np.dtype()

... (truncated)

Changelog

Sourced from numpy's changelog.

Update 2.4.0 milestones

Look at the issues/prs with 2.4.0 milestones and either push them off to a later version, or maybe remove the milestone. You may need to add a milestone.

Check the numpy-release repo

The things to check are the cibuildwheel version in .github/workflows/wheels.yml and the openblas versions in openblas_requirements.txt.

Make a release PR

Four documents usually need to be updated or created for the release PR:

  • The changelog
  • The release notes
  • The .mailmap file
  • The pyproject.toml file

These changes should be made in an ordinary PR against the maintenance branch. Other small, miscellaneous fixes may be part of this PR. The commit message might be something like::

REL: Prepare for the NumPy 2.4.0 release

    

  • Create 2.4.0-changelog.rst.
    • 

  • Update 2.4.0-notes.rst.
    • 

  • Update .mailmap.
    • 

  • Update pyproject.toml

Set the release version

Check the pyproject.toml file and set the release version and update the classifier if needed::

$ gvim pyproject.toml

Check the doc/source/release.rst file

make sure that the release notes have an entry in the release.rst file::

... (truncated)

Commits

Updates networkx from 3.5 to 3.6.1

Release notes

Sourced from networkx's releases.

NetworkX 3.6.1

networkx 3.6.1

We're happy to announce the release of networkx 3.6.1!

API Changes

  • Add spectral bipartition community finding and greedy bipartition using node swaps (#8347).

Enhancements

  • Nodelists for from_biadjacency_matrix (#7993).
  • Add spectral bipartition community finding and greedy bipartition using node swaps (#8347).
  • Fix draw_networkx_nodes with list node_shape and add regression test (#8363).

Bug Fixes

  • Fix: allow graph subclasses to have additional arguments (#8369).

Documentation

  • DOC: Improve benchmarking readme (#8358).
  • DOC: More details re: RC releases in the release process devdocs (#8346).
  • DOC: clarify difference between G.nodes/G.nodes() and G.edges/G.edges() in tutorial (#8300).
  • DOC: Add blurb to contributor guide about drawing tests (#8370).
  • DOC: Fix underline lens in docstrings (#8371).
  • Rolling back shortest paths links (#8373).

Maintenance

  • MAINT: Replace string literal with comment (#8359).
  • Bump actions/checkout from 5 to 6 in the actions group (#8360).
  • pin python 3.14 to be version 3.14.0 until dataclasses are fixed (#8365).
  • Blocklist Python 3.14.1 (#8372).

Other

  • TST: add tests for unsupported graph types in MST algorithms (#8353).
  • TST: clean up isomorphism tests (#8364).

Contributors

10 authors added to this release (alphabetically):

... (truncated)

Commits
  • 7530809 Designate 3.6.1 release
  • 4788eb0 Rolling back shortest paths links (#8373)
  • 696edb6 Fix draw_networkx_nodes with list node_shape and add regression test (#8363)
  • c38830c Blocklist Python 3.14.1 (#8372)
  • 81d2311 DOC: Fix underline lens in docstrings. (#8371)
  • a6e2bfa DOC: Add blurb to contributor guide about drawing tests. (#8370)
  • 96b6282 DOC: clarify difference between G.nodes/G.nodes() and G.edges/G.edges() in tu...
  • 75bdd73 Fix: allow graph subclasses to have additional arguments (#8369)
  • 7663fa5 TST: clean up isomorphism tests (#8364)
  • 3dacd1b Add spectral bipartition community finding and greedy bipartition using node ...
  • Additional commits viewable in compare view

Updates ipython from 9.6.0 to 9.8.0

Commits

Updates sphinx from 8.2.3 to 9.1.0

Release notes

Sourced from sphinx's releases.

Sphinx 9.1.0

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Dependencies

  • #14153: Drop Python 3.11 support.
  • #12555: Drop Docutils 0.20 support. Patch by Adam Turner

Features added

  • Add add_static_dir() for copying static assets from extensions to the build output. Patch by Jared Dillard

Bugs fixed

  • #14189: autodoc: Fix duplicate :no-index-entry: for modules. Patch by Adam Turner
  • #13713: Fix compatibility with MyST-Parser. Patch by Adam Turner
  • Fix tests for Python 3.15. Patch by Adam Turner
  • #14089: autodoc: Fix default option parsing. Patch by Adam Turner
  • Remove incorrect static typing assertions. Patch by Adam Turner
  • #14050: LaTeXTranslator fails to build documents using the "acronym" standard role. Patch by Günter Milde
  • LaTeX: Fix rendering for grid filled merged vertical cell. Patch by Tim Nordell
  • #14228: LaTeX: Fix overrun footer for cases of merged vertical table cells. Patch by Tim Nordell
  • #14207: Fix creating HTMLThemeFactory objects in third-party extensions. Patch by Adam Turner
  • #3099: LaTeX: PDF build crashes if a code-block contains more than circa 1350 codelines (about 27 a4-sized pages at default pointsize). Patch by Jean-François B.
  • #14064: LaTeX: TABs ending up in sphinxVerbatim fail to obey tab stops. Patch by Jean-François B.
  • #14089: autodoc: Improve support for non-weakreferencable objects. Patch by Adam Turner
  • LaTeX: Fix accidental removal at 3.5.0 (#8854) of the documentation of literalblockcappos key of sphinxsetup. Patch by Jean-François B.

... (truncated)

Changelog

Sourced from sphinx's changelog.

Release 9.1.0 (released Dec 31, 2025)

Dependencies

  • #14153: Drop Python 3.11 support.
  • #12555: Drop Docutils 0.20 support. Patch by Adam Turner

Features added

  • Add :meth:~sphinx.application.Sphinx.add_static_dir for copying static assets from extensions to the build output. Patch by Jared Dillard

Bugs fixed

  • #14189: autodoc: Fix duplicate :no-index-entry: for modules. Patch by Adam Turner
  • #13713: Fix compatibility with MyST-Parser. Patch by Adam Turner
  • Fix tests for Python 3.15. Patch by Adam Turner
  • #14089: autodoc: Fix default option parsing. Patch by Adam Turner
  • Remove incorrect static typing assertions. Patch by Adam Turner
  • #14050: LaTeXTranslator fails to build documents using the "acronym" standard role. Patch by Günter Milde
  • LaTeX: Fix rendering for grid filled merged vertical cell. Patch by Tim Nordell
  • #14228: LaTeX: Fix overrun footer for cases of merged vertical table cells. Patch by Tim Nordell
  • #14207: Fix creating HTMLThemeFactory objects in third-party extensions. Patch by Adam Turner
  • #3099: LaTeX: PDF build crashes if a code-block contains more than circa 1350 codelines (about 27 a4-sized pages at default pointsize). Patch by Jean-François B.
  • #14064: LaTeX: TABs ending up in sphinxVerbatim fail to obey tab stops. Patch by Jean-François B.
  • #14089: autodoc: Improve support for non-weakreferencable objects. Patch by Adam Turner
  • LaTeX: Fix accidental removal at 3.5.0 (#8854) of the documentation of literalblockcappos key of :ref:'sphinxsetup' <latexsphinxsetup>. Patch by Jean-François B.
Commits
  • cc7c6f4 Bump to 9.1.0 final
  • b127b94 Add app.add_static_dir() for copying extension static files (#14219)
  • 20f1c46 LaTeX: Inhibit breaks for rows with merged vertical cells (#14227)
  • 3c85411 Polish CHANGES.rst (#14225)
  • 9ee5446 LaTeX: restore 1.7 documentation of literalblockcappos (#14224)
  • d75d602 LaTeX: improve (again...) some code comments in time for 9.1.0 (#14222)
  • 8dca61d Improve some LaTeX code comments (#14220)
  • 8ab9600 Bump to 9.1.0 candidate 2
  • d59b237 autodoc: Improve support for non-weakreferencable objects
  • 964424b Use the correct reference for using existing extensions (#14157)
  • Additional commits viewable in compare view

Updates pytest from 8.4.2 to 9.0.2

Release notes

Sourced from pytest's releases.

9.0.2

pytest 9.0.2 (2025-12-06)

Bug fixes

  • #13896: The terminal progress feature added in pytest 9.0.0 has been disabled by default, except on Windows, due to compatibility issues with some terminal emulators.

    You may enable it again by passing -p terminalprogress. We may enable it by default again once compatibility improves in the future.

    Additionally, when the environment variable TERM is dumb, the escape codes are no longer emitted, even if the plugin is enabled.

  • #13904: Fixed the TOML type of the tmp_path_retention_count settings in the API reference from number to string.

  • #13946: The private config.inicfg attribute was changed in a breaking manner in pytest 9.0.0. Due to its usage in the ecosystem, it is now restored to working order using a compatibility shim. It will be deprecated in pytest 9.1 and removed in pytest 10.

  • #13965: Fixed quadratic-time behavior when handling unittest subtests in Python 3.10.

Improved documentation

  • #4492: The API Reference now contains cross-reference-able documentation of pytest's command-line flags <command-line-flags>.

9.0.1

pytest 9.0.1 (2025-11-12)

Bug fixes

  • #13895: Restore support for skipping tests via raise unittest.SkipTest.
  • #13896: The terminal progress plugin added in pytest 9.0 is now automatically disabled when iTerm2 is detected, it generated desktop notifications instead of the desired functionality.
  • #13904: Fixed the TOML type of the verbosity settings in the API reference from number to string.
  • #13910: Fixed UserWarning: Do not expect file_or_dir on some earlier Python 3.12 and 3.13 point versions.

Packaging updates and notes for downstreams

  • #13933: The tox configuration has been adjusted to make sure the desired version string can be passed into its package_env through the SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYTEST environment variable as a part of the release process -- by webknjaz.

Contributor-facing changes

  • #13891, #13942: The CI/CD part of the release automation is now capable of creating GitHub Releases without having a Git checkout on disk -- by bluetech and webknjaz.
  • #13933: The tox configuration has been adjusted to make sure the desired version string can be passed into its package_env through the SETUPTOOLS_SCM_PRETEND_VERSION_FOR_PYTEST environment variable as a part of the release process -- by webknjaz.

... (truncated)

Commits
  • 3d10b51 Prepare release version 9.0.2
  • 188750b Merge pull request #14030 from pytest-dev/patchback/backports/9.0.x/1e4b01d1f...
  • b7d7bef Merge pull request #14014 from bluetech/compat-note
  • bd08e85 Merge pull request #14013 from pytest-dev/patchback/backports/9.0.x/922b60377...
  • bc78386 Add CLI options reference documentation (#13930)
  • 5a4e398 Fix docs typo (#14005) (#14008)
  • d7ae6df Merge pull request #14006 from pytest-dev/maintenance/update-plugin-list-tmpl...
  • 556f6a2 pre-commit: fix rst-lint after new release (#13999) (#14001)
  • c60fbe6 Fix quadratic-time behavior when handling unittest subtests in Python 3.10 ...
  • 73d9b01 Merge pull request #13995 from nicoddemus/patchback/backports/9.0.x/1b5200c0f...
  • Additional commits viewable in compare view

Updates juliacall from 0.9.28 to 0.9.31

Release notes

Sourced from juliacall's releases.

v0.9.31

PythonCall v0.9.31

Diff since v0.9.30

Merged pull requests:

Closed issues:

  • dtype of NumPy array created from Julia array is object on Julia nightly (#439)
  • Intermittent CI failures: Fatal Python error: _Py_CheckRecursiveCall: Unrecoverable stack overflow (#694)
  • using PythonCall in Pluto crashes Pluto Malt.TerminatedWorkerException (#711)
  • Julia crashes (Segmentation fault) when using tab completion with PythonCall (#713)
  • Make ArrayValue not callable (#728)
  • ImportError when using dolfinx in PythonCall (#729)
  • Segfault when calling Python function repeatedly. (#731)

v0.9.30

PythonCall v0.9.30

Diff since v0.9.29

Merged pull requests:

Closed issues:

  • Segfault in REPL when importing a library (#707)

v0.9.29

PythonCall v0.9.29

Diff since v0.9.28

Merged pull requests:

... (truncated)

Changelog

Sourced from juliacall's changelog.

0.9.31 (2025-12-17)

  • Restore support for Python 3.14+.

0.9.30 (2025-11-18)

  • Maximum supported Python version is now 3.13 (see the FAQ for why).

0.9.29 (2025-11-14)

  • Minimum supported Python version is now 3.10.
  • Minimum supported Julia version is now 1.10.
  • Showing Py now respects the compact option - output is limited to a single line of at most the display width.
  • Support policy now documented in the FAQ.
  • Added this changelog (was previously at docs/src/releasenotes.md).
  • Bug fixes.
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@dependabot
deps(deps): bump the dependencies group with 6 updates
aaac111 
Bumps the dependencies group with 6 updates:

| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `2.3.4` | `2.4.0` |
| [networkx](https://github.com/networkx/networkx) | `3.5` | `3.6.1` |
| [ipython](https://github.com/ipython/ipython) | `9.6.0` | `9.8.0` |
| [sphinx](https://github.com/sphinx-doc/sphinx) | `8.2.3` | `9.1.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.4.2` | `9.0.2` |
| [juliacall](https://github.com/JuliaPy/PythonCall.jl) | `0.9.28` | `0.9.31` |


Updates `numpy` from 2.3.4 to 2.4.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.3.4...v2.4.0)

Updates `networkx` from 3.5 to 3.6.1
- [Release notes](https://github.com/networkx/networkx/releases)
- [Commits](networkx/networkx@networkx-3.5...networkx-3.6.1)

Updates `ipython` from 9.6.0 to 9.8.0
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@9.6.0...9.8.0)

Updates `sphinx` from 8.2.3 to 9.1.0
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES.rst)
- [Commits](sphinx-doc/sphinx@v8.2.3...v9.1.0)

Updates `pytest` from 8.4.2 to 9.0.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.4.2...9.0.2)

Updates `juliacall` from 0.9.28 to 0.9.31
- [Release notes](https://github.com/JuliaPy/PythonCall.jl/releases)
- [Changelog](https://github.com/JuliaPy/PythonCall.jl/blob/main/CHANGELOG.md)
- [Commits](JuliaPy/PythonCall.jl@v0.9.28...v0.9.31)

---
updated-dependencies:
- dependency-name: numpy
  dependency-version: 2.4.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: dependencies
- dependency-name: networkx
  dependency-version: 3.6.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: dependencies
- dependency-name: ipython
  dependency-version: 9.8.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: dependencies
- dependency-name: sphinx
  dependency-version: 9.1.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: dependencies
- dependency-name: pytest
  dependency-version: 9.0.2
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: dependencies
- dependency-name: juliacall
  dependency-version: 0.9.31
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: dependencies
...

Signed-off-by: dependabot[bot] <support@github.com>
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coveralls commented Jan 1, 2026

Pull Request Test Coverage Report for Build 20640299120

Details

  • 0 of 0 changed or added relevant lines in 0 files are covered.
  • No unchanged relevant lines lost coverage.
  • Overall coverage remained the same at 91.198%
Totals Coverage Status
Change from base Build 19348532158: 0.0%
Covered Lines: 1782
Relevant Lines: 1954
💛 - Coveralls

@chenpeizhi chenpeizhi merged commit a4f0eb6 into master Jan 2, 2026
2 checks passed
@dependabot dependabot bot deleted the dependabot/uv/dependencies-1d49c30b6a branch January 2, 2026 23:54
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