Scheduled weekly dependency update for week 16

[pyup-bot]

Update sphinx from 7.2.6 to 7.3.7.

Changelog

7.3.7

=====================================

Bugs fixed
----------

* 12299: Defer loading themes defined via entry points until
their explicit use by the user or a child theme.
Patch by Adam Turner.
* 12305: Return the default value for ``theme.get_config()`` with
an unsupported theme configuration section.
Patch by Adam Turner.

7.3.6

=====================================

Bugs fixed
----------

* 12295: Re-export all AST types in the C and C++ domains.
Patch by Adam Turner.
* 12295: Re-export various objects from ``sphinx.domains.python._annotations``
in ``sphinx.domains.python``.
Patch by Jacob Chesslo and Adam Turner.

7.3.5

=====================================

Bugs fixed
----------

* 12295: Re-export various objects from ``sphinx.domains.python._object``
in ``sphinx.domains.python``.
Patch by Jacob Chesslo and Adam Turner.

7.3.4

=====================================

Bugs fixed
----------

* Handle cases when ``Any`` is not an instance of ``type``.
Patch by Adam Turner.

7.3.3

=====================================

Bugs fixed
----------

* 12290: Fix a false-positive warning when setting a configuration value
with ``Any`` as the valid type to a type other than the value's default.
Patch by Adam Turner.

7.3.2

=====================================

Bugs fixed
----------

* Preload all themes defined via entry points.
Patch by Adam Turner.
* Fix a bad interaction between the ``'Furo'`` theme and the new-style for
configuration values.
Patch by Adam Turner.

7.3.1

=====================================

Dependencies
------------

* Require ``tomli`` on Python 3.10 and earlier.
Patch by Adam Turner.

7.3.0

=====================================

Dependencies
------------

* 11858: Increase the minimum supported version of Alabaster to 0.7.14.
Patch by Adam Turner.
* 11411: Support `Docutils 0.21`_. Patch by Adam Turner.

.. _Docutils 0.21: https://docutils.sourceforge.io/RELEASE-NOTES.html#release-0-21-2024-04-09
* 12012: Use ``types-docutils`` instead of ``docutils-stubs``.

Deprecated
----------

* 11693: Support for old-style :file:`Makefile` and :file:`make.bat` output
in :program:`sphinx-quickstart`, and the associated options :option:`!-M`,
:option:`!-m`, :option:`!--no-use-make-mode`, and :option:`!--use-make-mode`.
* 11285: Direct access to :attr:`!sphinx.testing.util.SphinxTestApp._status`
or :attr:`!sphinx.testing.util.SphinxTestApp._warning` is deprecated. Use
the public properties :attr:`!sphinx.testing.util.SphinxTestApp.status`
and :attr:`!sphinx.testing.util.SphinxTestApp.warning` instead.
Patch by Bénédikt Tran.
* tests: :func:`!sphinx.testing.util.strip_escseq` is deprecated in favour of
:func:`!sphinx.util.console.strip_colors`.
Patch by Bénédikt Tran.

Features added
--------------

* 12265: Support theme configuration via ``theme.toml``.
* 11701: HTML Search: Adopt the new `\<search\>`_ element.
Patch by Bénédikt Tran.

.. _`\<search\>`: https://developer.mozilla.org/en-US/docs/Web/HTML/Element/search
* 11776: Add long option names to ``sphinx-build``.
Patch by Hugo van Kemenade, Adam Turner, Bénédikt Tran, and Ezio Melotti.
* Organise the ``sphinx-build`` options into groups.
Patch by Adam Turner.
* 11855: Defer computation of configuration values.
Patch by Adam Turner.
* Add ``:no-search:`` as an alias of the ``:nosearch:`` metadata field.
Patch by Adam Turner.
* 11803: autodoc: Use an overriden ``__repr__()`` function in an enum,
if defined. Patch by Shengyu Zhang.
* 11825: Allow custom targets in the manpage role.
Patch by Nicolas Peugnet.
* 11892: Improved performance when resolving cross references in the C++ domain.
Patch by Rouslan Korneychuk.
* 11905: Add a :rst:dir:`versionremoved` directive.
Patch by Hugo van Kemenade, Adam Turner, and C.A.M. Gerlach.
* 11981: Improve rendering of signatures using ``slice`` syntax,
e.g., ``def foo(arg: np.float64[:,:]) -> None: ...``.
* The manpage builder now adds `OSC 8`_ anchors to hyperlinks, using
the `groff`_ device control command.

.. _OSC 8: https://gist.github.com/egmontkob/eb114294efbcd5adb1944c9f3cb5feda
.. _groff: https://lists.gnu.org/archive/html/groff/2021-10/msg00000.html
* 11015: Change the text of the :rst:dir:`versionadded` directive from
``New in [...]`` to ``Added in [...]``.
Patch by Bénédikt Tran.
* 12131: Added :confval:`show_warning_types` configuration option.
Patch by Chris Sewell.
* 12193: Improve ``external`` warnings for unknown roles.
In particular, suggest related role names if an object type is mistakenly used.
Patch by Chris Sewell.
* Add public type alias :class:`sphinx.util.typing.ExtensionMetadata`.
This can be used by extension developers
to annotate the return type of their ``setup`` function.
Patch by Chris Sewell.

Bugs fixed
----------

* 11668: Raise a useful error when ``theme.conf`` is missing.
Patch by Vinay Sajip.
* 11622: Ensure that the order of keys in ``searchindex.js`` is deterministic.
Patch by Pietro Albini.
* 11617: ANSI control sequences are stripped from the output when writing to
a warnings file with :option:`-w <sphinx-build -w>`.
Patch by Bénédikt Tran.
* 11666: Skip all hidden directories in ``CatalogRepository.pofiles``.
Patch by Aryaz Eghbali.
* 9686: html builder: Fix MathJax lazy loading when equations appear in titles.
Patch by Bénédikt Tran.
* 11483: singlehtml builder: Fix MathJax lazy loading when the index does not
contain any math equations.
Patch by Bénédikt Tran.
* 11697: HTML Search: add 'noindex' meta robots tag.
Patch by James Addison.
* 11678: Fix a possible ``ZeroDivisionError`` in ``sphinx.ext.coverage``.
Patch by Stephen Finucane.
* 11756: LaTeX: build error with recent TeXLive due to missing ``substitutefont``
package (triggered if using ``fontenc`` with ``T2A`` option and document
language is not a Cyrillic one).
Patch by Jean-François B.
* 11675: Fix rendering of progression bars in environments that do not support
ANSI control sequences.
Patch by Bénédikt Tran.
* 11861: Whitelist more types with an incorrect ``__module__`` attribute.
Patch by Adam Turner.
* 11715: Apply ``tls_verify`` and ``tls_cacerts`` config to
``ImageDownloader``.
Patch by Nick Touran.
* Allow hyphens in group names for :rst:dir:`productionlist` cross-references.
Patch by Adam Turner.
* 11433: Added the :confval:`linkcheck_allow_unauthorized` configuration option.
Set this option to ``False`` to report HTTP 401 (unauthorized) server
responses as broken.
Patch by James Addison.
* 11868: linkcheck: added a distinct ``timeout`` reporting status code.
This can be enabled by setting :confval:`linkcheck_report_timeouts_as_broken`
to ``False``.
Patch by James Addison.
* 11869: Refresh the documentation for the ``linkcheck_timeout`` setting.
Patch by James Addison.
* 11874: Configure a default 30-second value for ``linkcheck_timeout``.
Patch by James Addison.
* 11886: Print the Jinja2 template path chain in ``TemplateNotFound`` exceptions.
Patch by Colin Marquardt.
* 11598: Do not use query components in URLs for assets in EPUB rendering.
Patch by David Runge.
* 11904: Support unary subtraction when parsing annotations.
Patch by James Addison.
* 11925: Blacklist the ``sphinxprettysearchresults`` extension; the functionality
it provides was merged into Sphinx v2.0.0.
Patch by James Addison.
* 11917: Fix rendering of annotated inherited members for Python 3.9.
Patch by Janet Carson.
* 11935: C Domain: Fix namespace-pop context.
Patch by Frank Dana.
* 11923: Avoid zombie processes when parallel builds fail.
Patch by Felix von Drigalski.
* 11353: Support enumeration classes inheriting from mixin or data types.
Patch by Bénédikt Tran.
* 11962: Fix target resolution when using ``:paramtype:`` fields.
Patch by Bénédikt Tran.
* 11944: Use anchor in search preview.
Patch by Will Lachance.
* 12008: Fix case-sensitive lookup of ``std:label`` names in intersphinx inventory.
Patch by Michael Goerz.
* 11958: HTML Search: Fix partial matches overwriting full matches.
Patch by William Lachance.
* 11959: Fix multiple term matching when word appears in both title and document.
Patch by Will Lachance.
* 11474: Fix doctrees caching causing files not be rebuilt in some cases,
e.g., when :confval:`numfig` is ``True``.
Patch by Bénédikt Tran.
* 11278: autodoc: Fix rendering of :class:`functools.singledispatchmethod`
combined with :func:`classmethod <classmethod>`.
Patch by Bénédikt Tran.
* 11894: Do not add checksums to css files if building using the htmlhelp builder.
Patch by reduerK akiM.
* 12052: Remove ``<script>`` and ``<style>`` tags from the content of search result
summary snippets.
Patch by James Addison.
* 11578: HTML Search: Order non-main index entries after other results.
Patch by Brad King.
* 12147: autosummary: Fix a bug whereby the wrong file extension
may be used,
when multiple suffixes are specified in :confval:`source_suffix`.
Patch by Sutou Kouhei.
* 10786: improve the error message when a file to be copied (e.g., an asset)
is removed during Sphinx execution.
Patch by Bénédikt Tran.
* 12040: HTML Search: Ensure that document titles that are partially-matched by
the user search query are included in search results.
Patch by James Addison.
* 11970: singlehtml builder: make target URIs to be same-document references in
the sense of :rfc:`RFC 3986, §4.4 <3986section-4.4>`, e.g., ``index.htmlfoo``
becomes ``foo``. Patch by Eric Norige.
* 12271: Partially revert Docutils' r9562__ to fix EPUB files.
Patch by Adam Turner.

__ https://sourceforge.net/p/docutils/code/9562/
* 12253: Escape reserved path characters in the remote images post-transform
download cache.
Patch by James Addison and Adam Turner.

Testing
-------

* Reorganise tests into directories.
Patch by Adam Turner.
* Clean up global state in ``SphinxTestApp``.
Patch by Adam Turner.
* 11285: :func:`!pytest.mark.sphinx` and :class:`!sphinx.testing.util.SphinxTestApp`
accept *warningiserror*, *keep_going* and *verbosity* as keyword arguments.
Patch by Bénédikt Tran.
* 11285: :class:`!sphinx.testing.util.SphinxTestApp` *status* and *warning*
arguments are checked to be :class:`io.StringIO` objects (the public API
incorrectly assumed this without checking it).
Patch by Bénédikt Tran.
* Report the result of ``test_run_epubcheck`` as ``skipped`` instead of
``success`` when either Java or ``epubcheck`` are not available.
* Use dynamic allocation of unused port numbers for the test HTTP(S) servers.
As a side-effect, this removes the need for test server lockfiles,
meaning that any remaining ``tests/test-server.lock`` files can safely be
deleted.

Links

• PyPI: https://pypi.org/project/sphinx
• Changelog: https://data.safetycli.com/changelogs/sphinx/

Update reportlab from 4.1.0 to 4.2.0.

The bot wasn't able to find a changelog for this release. Got an idea?

Links

• PyPI: https://pypi.org/project/reportlab
• Homepage: https://www.reportlab.com/

Update black from 24.3.0 to 24.4.0.

Changelog

24.4.0

Stable style

- Fix unwanted crashes caused by AST equivalency check (4290)

Preview style

- `if` guards in `case` blocks are now wrapped in parentheses when the line is too long.
(4269)
- Stop moving multiline strings to a new line unless inside brackets (4289)

Integrations

- Add a new option `use_pyproject` to the GitHub Action `psf/black`. This will read the
Black version from `pyproject.toml`. (4294)

Links

• PyPI: https://pypi.org/project/black
• Changelog: https://data.safetycli.com/changelogs/black/

Update scipy from 1.12.0 to 1.13.0.

Changelog

1.13.0

out-of-band release aims to support NumPy ``2.0.0``, and is backwards
compatible to NumPy ``1.22.4``. The version of OpenBLAS used to build
the PyPI wheels has been increased to ``0.3.26``.

This release requires Python 3.9+ and NumPy 1.22.4 or greater.

For running on PyPy, PyPy3 6.0+ is required.


Highlights of this release
===================
- Support for NumPy ``2.0.0``.
- Interactive examples have been added to the documentation, allowing users
to run the examples locally on embedded Jupyterlite notebooks in their
browser.
- Preliminary 1D array support for the COO and DOK sparse formats.
- Several `scipy.stats` functions have gained support for additional
``axis``, ``nan_policy``, and ``keepdims`` arguments. `scipy.stats` also
has several performance and accuracy improvements.


New features
==========

`scipy.integrate` improvements
==============================
- The ``terminal`` attribute of `scipy.integrate.solve_ivp` ``events``
callables now additionally accepts integer values to specify a number
of occurrences required for termination, rather than the previous restriction
of only accepting a ``bool`` value to terminate on the first registered
event.


`scipy.io` improvements
=======================
- `scipy.io.wavfile.write` has improved ``dtype`` input validation.


`scipy.interpolate` improvements
================================
- The Modified Akima Interpolation has been added to
``interpolate.Akima1DInterpolator``, available via the new ``method``
argument.
- ``RegularGridInterpolator`` gained the functionality to compute derivatives
in place. For instance, ``RegularGridInterolator((x, y), values,
method="cubic")(xi, nu=(1, 1))`` evaluates the mixed second derivative,
:math:`\partial^2 / \partial x \partial y` at ``xi``.
- Performance characteristics of tensor-product spline methods of
``RegularGridInterpolator`` have been changed: evaluations should be
significantly faster, while construction might be slower. If you experience
issues with construction times, you may need to experiment with optional
keyword arguments ``solver`` and ``solver_args``. Previous behavior (fast
construction, slow evaluations) can be obtained via `"*_legacy"` methods:
``method="cubic_legacy"`` is exactly equivalent to ``method="cubic"`` in
previous releases. See ``gh-19633`` for details.


`scipy.signal` improvements
===========================
- Many filter design functions now have improved input validation for the
sampling frequency (``fs``).


`scipy.sparse` improvements
===========================
- ``coo_array`` now supports 1D shapes, and has additional 1D support for
``min``, ``max``, ``argmin``, and ``argmax``. The DOK format now has
preliminary 1D support as well, though only supports simple integer indices
at the time of writing.
- Experimental support has been added for ``pydata/sparse`` array inputs to
`scipy.sparse.csgraph`.
- ``dok_array`` and ``dok_matrix`` now have proper implementations of
``fromkeys``.
- ``csr`` and ``csc`` formats now have improved ``setdiag`` performance.


`scipy.spatial` improvements
============================
- ``voronoi_plot_2d`` now draws Voronoi edges to infinity more clearly
when the aspect ratio is skewed.


`scipy.special` improvements
============================
- All Fortran code, namely, ``AMOS``, ``specfun``, and ``cdflib`` libraries
that the majority of special functions depend on, is ported to Cython/C.
- The function ``factorialk`` now also supports faster, approximate
calculation using ``exact=False``.


`scipy.stats` improvements
==========================
- `scipy.stats.rankdata` and `scipy.stats.wilcoxon` have been vectorized,
improving their performance and the performance of hypothesis tests that
depend on them.
- ``stats.mannwhitneyu`` should now be faster due to a vectorized statistic
calculation, improved caching, improved exploitation of symmetry, and a
memory reduction. ``PermutationMethod`` support was also added.
- `scipy.stats.mood` now has ``nan_policy`` and ``keepdims`` support.
- `scipy.stats.brunnermunzel` now has ``axis`` and ``keepdims`` support.
- `scipy.stats.friedmanchisquare`, `scipy.stats.shapiro`,
`scipy.stats.normaltest`, `scipy.stats.skewtest`,
`scipy.stats.kurtosistest`, `scipy.stats.f_oneway`,
`scipy.stats.alexandergovern`, `scipy.stats.combine_pvalues`, and
`scipy.stats.kstest` have gained ``axis``, ``nan_policy`` and
``keepdims`` support.
- `scipy.stats.boxcox_normmax` has gained a ``ymax`` parameter to allow user
specification of the maximum value of the transformed data.
- `scipy.stats.vonmises` ``pdf`` method has been extended to support
``kappa=0``. The ``fit`` method is also more performant due to the use of
non-trivial bounds to solve for ``kappa``.
- High order ``moment`` calculations for `scipy.stats.powerlaw` are now more
accurate.
- The ``fit`` methods of  `scipy.stats.gamma` (with ``method='mm'``) and
`scipy.stats.loglaplace` are faster and more reliable.
- `scipy.stats.goodness_of_fit` now supports the use of a custom ``statistic``
provided by the user.
- `scipy.stats.wilcoxon` now supports ``PermutationMethod``, enabling
calculation of accurate p-values in the presence of ties and zeros.
- `scipy.stats.monte_carlo_test` now has improved robustness in the face of
numerical noise.
- `scipy.stats.wasserstein_distance_nd` was introduced to compute the
Wasserstein-1 distance between two N-D discrete distributions.



Deprecated features
=================
- Complex dtypes in ``PchipInterpolator`` and ``Akima1DInterpolator`` have
been deprecated and will raise an error in SciPy 1.15.0. If you are trying
to use the real components of the passed array, use ``np.real`` on ``y``.




Backwards incompatible changes
=========================


Other changes
===========
- The second argument of `scipy.stats.moment` has been renamed to ``order``
while maintaining backward compatibility.




Authors
======

* Name (commits)
* h-vetinari (50)
* acceptacross (1) +
* Petteri Aimonen (1) +
* Francis Allanah (2) +
* Jonas Kock am Brink (1) +
* anupriyakkumari (12) +
* Aman Atman (2) +
* Aaditya Bansal (1) +
* Christoph Baumgarten (2)
* Sebastian Berg (4)
* Nicolas Bloyet (2) +
* Matt Borland (1)
* Jonas Bosse (1) +
* Jake Bowhay (25)
* Matthew Brett (1)
* Dietrich Brunn (7)
* Evgeni Burovski (48)
* Matthias Bussonnier (4)
* Cale (1) +
* CJ Carey (4)
* Thomas A Caswell (1)
* Sean Cheah (44) +
* Lucas Colley (97)
* com3dian (1)
* Gianluca Detommaso (1) +
* Thomas Duvernay (1)
* DWesl (2)
* f380cedric (1) +
* fancidev (13) +
* Daniel Garcia (1) +
* Lukas Geiger (3)
* Ralf Gommers (139)
* Matt Haberland (79)
* Tessa van der Heiden (2) +
* inky (3) +
* Jannes Münchmeyer (2) +
* Aditya Vidyadhar Kamath (2) +
* Agriya Khetarpal (1) +
* Andrew Landau (1) +
* Eric Larson (7)
* Zhen-Qi Liu (1) +
* Adam Lugowski (4)
* m-maggi (6) +
* Chethin Manage (1) +
* Ben Mares (1)
* Chris Markiewicz (1) +
* Mateusz Sokół (3)
* Daniel McCloy (1) +
* Melissa Weber Mendonça (6)
* Josue Melka (1)
* Michał Górny (4)
* Juan Montesinos (1) +
* Juan F. Montesinos (1) +
* Takumasa Nakamura (1)
* Andrew Nelson (26)
* Praveer Nidamaluri (1)
* Yagiz Olmez (5) +
* Dimitri Papadopoulos Orfanos (1)
* Drew Parsons (1) +
* Tirth Patel (7)
* Matti Picus (3)
* Rambaud Pierrick (1) +
* Ilhan Polat (30)
* Quentin Barthélemy (1)
* Tyler Reddy (81)
* Pamphile Roy (10)
* Atsushi Sakai (4)
* Daniel Schmitz (10)
* Dan Schult (16)
* Eli Schwartz (4)
* Stefanie Senger (1) +
* Scott Shambaugh (2)
* Kevin Sheppard (2)
* sidsrinivasan (4) +
* Samuel St-Jean (1)
* Albert Steppi (30)
* Adam J. Stewart (4)
* Kai Striega (3)
* Ruikang Sun (1) +
* Mike Taves (1)
* Nicolas Tessore (3)
* Benedict T Thekkel (1) +
* Will Tirone (4)
* Jacob Vanderplas (2)
* Christian Veenhuis (1)
* Isaac Virshup (2)
* Ben Wallace (1) +
* Xuefeng Xu (3)
* Xiao Yuan (5)
* Irwin Zaid (6)
* Mathias Zechmeister (1) +

A total of 91 people contributed to this release.
People with a "+" by their names contributed a patch for the first time.
This list of names is automatically generated, and may not be fully complete.

Links

• PyPI: https://pypi.org/project/scipy
• Changelog: https://data.safetycli.com/changelogs/scipy/
• Homepage: https://scipy.org/

Update ufo2ft from 3.2.0 to 3.2.1.

Changelog

3.2.1

- [BaseIFilter] Fixed performance regression when decomposing composite glyphs in fonts with large number of masters and/or nested components.
We now use a cache to avoid recursing too much when gathering locations from component glyphs (829).

Links

• PyPI: https://pypi.org/project/ufo2ft
• Changelog: https://data.safetycli.com/changelogs/ufo2ft/
• Repo: https://github.com/googlefonts/ufo2ft

Update lxml from 5.2.0 to 5.2.1.

Changelog

5.2.1

==================

Bugs fixed
----------

* LP2059910: The minimum CPU architecture for the Linux x86 binary wheels was set back to
"core2", but with SSE 4.2 enabled.

* LP2059977: ``Element.iterfind("//absolute_path")`` failed with a ``SyntaxError``
where it should have issued a warning.

* GH416: The documentation build was using the non-standard ``which`` command.
Patch by Michał Górny.

Links

• PyPI: https://pypi.org/project/lxml
• Changelog: https://data.safetycli.com/changelogs/lxml/
• Homepage: https://lxml.de/

[pyup-bot]

Closing this in favor of #3493