Bump the pip group across 1 directory with 27 updates

[dependabot]

Bumps the pip group with 27 updates in the /src directory:

Package	From	To
beautifulsoup4	4.13.4	4.14.2
biopython	1.85	1.86
bokeh	3.6.2	3.8.0
certifi	2025.7.14	2025.10.5
cryptography	45.0.5	46.0.3
idna	3.10	3.11
jsonschema	4.25.0	4.25.1
markdown	3.8.2	3.9
markupsafe	3.0.2	3.0.3
networkx	3.4.2	3.5
numpy	2.2.3	2.3.4
pillow	11.3.0	12.0.0
plotly	6.2.0	6.3.1
pycurl	7.45.6	7.45.7
pyopenssl	25.1.0	25.3.0
scipy	1.15.2	1.16.3
ipython	8.33.0	9.6.0
pandas	2.3.1	2.3.3
pymongo	4.13.2	4.15.3
pyyaml	6.0.2	6.0.3
requests	2.32.4	2.32.5
scikit-learn	1.6.1	1.7.2
tornado	6.5.1	6.5.2
coverage	7.10.1	7.11.0
pytest	8.4.1	8.4.2
pytest-cov	6.2.1	7.0.0
ruff	0.12.7	0.14.3

Updates beautifulsoup4 from 4.13.4 to 4.14.2

Updates biopython from 1.85 to 1.86

Changelog

Sourced from biopython's changelog.

28 October 2025: Biopython 1.86

This release of Biopython supports Python 3.10, 3.11, 3.12, 3.13 and 3.14. It has also been tested on PyPy3.10 v7.3.19.

Bio.SearchIO now supports parsing the tabular and plain text output of Infernal <http://eddylab.org/infernal/> (v1.0.0+) RNA search tool. The format names are infernal-tab and infernal-text.

The default value of the gap score of a PairwiseAligner object was changed in this release. Previously, for consistency with Bio.pairwise2, the default value for gap score was 0. However, this means that a mismatch, an insertion followed by a deletion, and a deletion followed by an insertion all get assigned a score of 0. The aligner then finds a large number of alignments that are logically the same, but have trivial differences between them. For example, aligning AAACAAA to AAAGAAA previously yielded the following three alignments, all with score 6::

 AAACAAA        AAAC-AAA        AAA-CAAA
 AAAGAAA        AAA-GAAA        AAAG-AAA

With the new default parameter for the gap score, only the first alignment is returned.

Bio.PDB.PDBIO now ensures that b-factor values are always at most 6 characters to ensure that we do not violate the wwPDB specification. This should not have an impact on the majority of uses, as b-factor values are generally small (less than 100). When 1000 <= b-factor < 10_000, the value is rounded to a single decimal place. When, 10_000 <= b-factor < 999_999, the value is rounded to zero decimal places. Values above 999_999 are now clamped. The justification for this is the rise in the b-factor field being used for additional metadata, typically from computational tools.

Bio.Align now provides a method Alignment.from_alignments_with_same_reference to construct a multiple sequence alignment from a collection of alignments that share the same reference sequence.

Bio.PDB.PDBIO will now raise module specific warnings: Bio.PDB.PDBExceptions.PDBIOWarning.

Bio.PDB.SCADIO now supports object selection by color in the OpenSCAD output file. This enables generation of separate STL files for each color for printing protein structures on multi-material 3D printers.

The iplotx library is mentioned in the Tutorial as an option to visualise trees using complex style options.

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

... (truncated)

Commits

• See full diff in compare view

Updates bokeh from 3.6.2 to 3.8.0

Commits

• 2378619 Deployment updates for release 3.8.0
• b83c74d Update switcher.json for 3.8 release (#14623)
• 58b18d9 Update release notes for 3.8 release (#14615)
• d08303f Prevent session reconnect attempt during page reload (#14621)
• b5c52fe Merge deployment staging branch staging-3.8.0rc2
• 77c4070 Deployment updates for release 3.8.0rc2
• 24eb853 Add support for Document configuration (#14608)
• 7971cdb Allow to image export of non-renderers in panels (#14604)
• 96e7c7c test: Add simple home for devtools server (#14605)
• 37993a8 Add 3.7.x release notes (#14611)
• Additional commits viewable in compare view

Updates certifi from 2025.7.14 to 2025.10.5

Commits

• fb14ac4 2025.10.05 (#371)
• 2c7c7ee Add Python 3.14 classifier in setup.py
• 1a5cb7b Bump actions/setup-python from 5.6.0 to 6.0.0 (#367)
• dea5960 Bump pypa/gh-action-pypi-publish from 1.12.4 to 1.13.0 (#366)
• 83566b7 Bump actions/checkout from 4.2.2 to 5.0.0
• ca2e121 Bump actions/download-artifact from 4.3.0 to 5.0.0
• a97d9ad 2025.08.03 (#362)
• See full diff in compare view

Updates cryptography from 45.0.5 to 46.0.3

Changelog

Sourced from cryptography's changelog.

46.0.3 - 2025-10-15

* Fixed compilation when using LibreSSL 4.2.0.
.. _v46-0-2:
46.0.2 - 2025-09-30

• Updated Windows, macOS, and Linux wheels to be compiled with OpenSSL 3.5.4.

.. _v46-0-1:

46.0.1 - 2025-09-16

* Fixed an issue where users installing via ``pip`` on Python 3.14 development
  versions would not properly install a dependency.
* Fixed an issue building the free-threaded macOS 3.14 wheels.
.. _v46-0-0:
46.0.0 - 2025-09-16

• BACKWARDS INCOMPATIBLE: Support for Python 3.7 has been removed.
• Support for OpenSSL < 3.0 is deprecated and will be removed in the next release.
• Support for x86_64 macOS (including publishing wheels) is deprecated and will be removed in two releases. We will switch to publishing an arm64 only wheel for macOS.
• Support for 32-bit Windows (including publishing wheels) is deprecated and will be removed in two releases. Users should move to a 64-bit Python installation.
• Updated Windows, macOS, and Linux wheels to be compiled with OpenSSL 3.5.3.
• We now build ppc64le manylinux wheels and publish them to PyPI.
• We now build win_arm64 (Windows on Arm) wheels and publish them to PyPI.
• Added support for free-threaded Python 3.14.
• Removed the deprecated get_attribute_for_oid method on :class:~cryptography.x509.CertificateSigningRequest. Users should use :meth:~cryptography.x509.Attributes.get_attribute_for_oid instead.
• Removed the deprecated CAST5, SEED, IDEA, and Blowfish classes from the cipher module. These are still available in :doc:/hazmat/decrepit/index.
• In X.509, when performing a PSS signature with a SHA-3 hash, it is now encoded with the official NIST SHA3 OID.

.. _v45-0-7:

... (truncated)

Commits

• c0af4dd release 46.0.3 (#13681)
• 99efe5a bump version for 46.0.2 (#13531)
• e735cfc release 46.0.1 (#13450)
• 4e457ff Explicitly specify python in mac uv build invocation (#13447)
• 2726efd Depend on CFFI 2.0.0 or newer on Python > 3.8 (#13448)
• 6223062 release 46.0.0 (#13446)
• 563c491 Update comment for pyopenssl-release tag (#13445)
• d2f6f7f Bump downstream dependencies in CI (#13439)
• e7ab02b we'll ship this with 3.5.3 why not (#13442)
• 0b68a4b Another pair of bump dependencies fix (#13444)
• Additional commits viewable in compare view

Updates idna from 3.10 to 3.11

Changelog

Sourced from idna's changelog.

3.11 (2025-10-12)

• Update to Unicode 16.0.0, including significant changes to UTS46 processing. As a result of Unicode ending support for it, transitional processing no longer has an effect and returns the same result.
• Add support for Python 3.14, lowest supported version is Python 3.8.
• Various updates to packaging, including PEP 740 support.

Commits

• ad949ee Release v3.11
• cae4ba7 Second release candidate for 3.11
• 8adb305 Add space in RST link
• 74cb2b6 Release candidate for 3.11
• 05dab09 Format idna-data with ruff
• 90eac78 Apply ruff formatting
• a31ce7e Remove errant test vectors
• 81f0333 Omit vectors known to be broken in test suite
• a0f3257 Merge branch 'master' into unicode-16-uts46-changes
• 38d9886 Remove extra UTS46 test vector
• Additional commits viewable in compare view

Updates jsonschema from 4.25.0 to 4.25.1

Release notes

Sourced from jsonschema's releases.

v4.25.1

What's Changed

• Fix Validator protocol init to match runtime by @​sirosen in python-jsonschema/jsonschema#1396

Full Changelog: python-jsonschema/jsonschema@v4.25.0...v4.25.1

Changelog

Sourced from jsonschema's changelog.

v4.25.1

• Fix an incorrect required argument in the Validator protocol's type annotations (#1396).

Commits

• 331c384 Add the fix to the changelog.
• c1ec0a6 Merge pull request #1398 from python-jsonschema/dependabot/github_actions/ast...
• 8e7d594 Merge pull request #1399 from python-jsonschema/dependabot/github_actions/act...
• 460f4fa Merge pull request #1396 from sirosen/improve-protocol-init-signature
• 1e58409 [pre-commit.ci] auto fixes from pre-commit.com hooks
• 64bc217 Add a typing test for the Validator protocol
• 6c25741 Bump actions/checkout from 4 to 5
• bf603d5 Bump astral-sh/setup-uv from 6.4.3 to 6.5.0
• a916d8f Fix Validator protocol init to match runtime
• de60f18 Merge pull request #1397 from python-jsonschema/pre-commit-ci-update-config
• Additional commits viewable in compare view

Updates markdown from 3.8.2 to 3.9

Release notes

Sourced from markdown's releases.

Release 3.9.0

Changed

• Footnotes are now ordered by the occurrence of their references in the document. A new configuration option for the footnotes extension, USE_DEFINITION_ORDER, has been added to support restoring the previous behavior of ordering footnotes by the occurrence of definitions (#1367).

Fixed

• Ensure inline processing iterates through elements in document order (#1546).
• Fix handling of incomplete HTML tags in code spans in Python 3.14 (#1547).

Changelog

Sourced from markdown's changelog.

title: Changelog toc_depth: 2

Python-Markdown Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to the Python Version Specification. See the Contributing Guide for details.

[Unreleased]

Fixed

• Fix an HTML comment parsing case in some Python versions that can cause an infinite loop (#1554).

[3.9.0] - 2025-09-04

Changed

• Footnotes are now ordered by the occurrence of their references in the document. A new configuration option for the footnotes extension, USE_DEFINITION_ORDER, has been added to support restoring the previous behavior of ordering footnotes by the occurrence of definitions (#1367).

Fixed

• Ensure inline processing iterates through elements in document order (#1546).
• Fix handling of incomplete HTML tags in code spans in Python 3.14 (#1547).

Commits

• f39cf84 Bump version to 3.9
• 07bf207 Order footnotes by reference
• 23c301d Fix failing cases for Python 3.14
• 4669a09 fix typo
• See full diff in compare view

Updates markupsafe from 3.0.2 to 3.0.3

Release notes

Sourced from markupsafe's releases.

3.0.3

This is the MarkupSafe 3.0.3 fix release, which fixes bugs but does not otherwise change behavior and should not result in breaking changes compared to the latest feature release.

PyPI: https://pypi.org/project/MarkupSafe/3.0.3/ Changes: https://markupsafe.palletsprojects.com/page/changes/#version-3-0-3 Milestone: https://github.com/pallets/markupsafe/milestone/15?closed=1

• __version__ raises DeprecationWarning instead of UserWarning. #487
• Adopt multi-phase initialization PEP 489 for the C extension. #494
• Build Windows ARM64 wheels. #485
• Build Python 3.14 wheels. #503
• Build riscv64 wheels. #505

Changelog

Sourced from markupsafe's changelog.

Version 3.0.3

Released 2025-09-27

• __version__ raises DeprecationWarning instead of UserWarning. :issue:487
• Adopt multi-phase initialisation (:pep:489) for the C extension. :issue:494
• Build Windows ARM64 wheels. :issue:485
• Build Python 3.14 wheels. :issue:503
• Build riscv64 wheels. :issue:505

Commits

• 297fc8e release version 3.0.3
• 7e4e6ce Free-threading: run with pytest-run-paralell (#507)
• 6100b9c enable riscv64 wheels (#506)
• c9d5ecf enable riscv64 wheels
• 2f9b337 tox for 3.14
• 78d951a update dev dependencies
• bb6744e add entry
• 65c4134 upgrade cibuildwheel, add cp314 wheels and test on CPython 3.14 (#504)
• 3a9bd88 add cp314 wheels
• aafe44d remove slsa provenance (#501)
• Additional commits viewable in compare view

Updates networkx from 3.4.2 to 3.5

Release notes

Sourced from networkx's releases.

NetworkX 3.5

networkx 3.5

We're happy to announce the release of networkx 3.5!

API Changes

• Save Layouts on Graphs (#7571).
• Expire d_separated and minimum_d_separator functions (#7830).
• Expire all_triplets deprecation (#7828).
• Expire random_triad deprecation (#7829).
• DEP: Raise an exception for k_core functions with multigraphs (#7831).
• Deprecate graph_could_be_isomorphic (#7826).
• Expire total_spanning_tree_weight deprecation (#7843).
• Expire deprecation of create kwarg in nonisomorphic_trees (#7847).
• New draw API (#7589).

Enhancements

• perf: optimise random_k_out_graph (#7702).
• Clausets local community detection algorithm (#7691).
• find_asteroidal_triple improvement (#7736).
• Add weight to harmonic_diameter (#7636).
• Densest Subgraph Problem: Greedy Peeling and Greedy++ Implementations (#7731).
• single_source_all_shortest_paths: don't loop over all nodes (#7762).
• Error message improvement for nbunch_iter ( NetworkXError raised with specific message on TypeError with "iter" in msg ) (#7790).
• Faster computation of energy in Laplacian centrality (#7793).
• Make forceatlas2_layout dispatchable (#7794).
• Update dispatchable for forceatlas2_layout (#7798).
• Enable backend-only functions where NetworkX is just an API (#7690).
• Steinertree kou enhancement in response to issue 5889 type:Enhancements (#7767).
• Add Leiden as a backend-only algorithm (#7743).
• Bipartite layout nodes optional (#7756).
• Densest Subgraph Problem: FISTA based algorithm + Large scale tests (#7770).
• Dispatch get_node_attributes and a few more from nx.classes.function (#7824).
• Faster could_be_isomorphic and number_of_cliques (#7855).
• Add square_clustering to algorithm benchmarks (#7857).
• Faster Implementation of Structural Holes (#7249).
• Improve runtime of number_of_nonisomorphic_trees() (#7917).
• Fix write_gexf timeformat for dynamic Graphs (#7914).
• Consolidate could_be_isomorphic (#7852).
• Improving rooted_tree_isomorphism for deep trees (#7945).
• Fixing nx.diameter inconsistent results with usebounds=True (#7954).
• Faster square_clustering (#7810).
• Avoid repeated cache conversion failures for backends (#7768).
• Improve _sparse_fruchterman_reingold with L-BFGS (#7889).
• Improve Performance of Tree Isomorphism and Center Calculation (#7946).
• Add option for biadjacency_matrix to be returned as a dense NumPy array (#7973).
• Add Functions for Finding Connected Dominating Sets (#7774).
• Add feature to make storing node contraction data optional (#7902).

... (truncated)

Commits

• 4fa222d Designate 3.5 release
• 9fd0532 Fix typo in min_edge_cover docstring (#8075)
• fc67a54 Clarify subgraph node/edge order is not preserved (#8069)
• 7c97a10 Minor refactor to cleanup/improve matching test suite (#8068)
• 9e33b11 Fix edge case in ISMAGS symmetry detection (#8055)
• 5f06a49 Add note about cycles in maximum_flow() (#8058)
• 6791918 TST: Minor improvements to layout test suite (#8049)
• 2bbd7a4 STY: Rm local variable remapping of heappush and heappop. (#8051)
• dc8de3b fix bug of _sparse_fruchterman_reingold and remove try/except idiom (#8041)
• 335fe23 Add a new gallery spring layout (#8042)
• Additional commits viewable in compare view

Updates numpy from 2.2.3 to 2.3.4

Release notes

Sourced from numpy's releases.

v2.3.4 (Oct 15, 2025)

NumPy 2.3.4 Release Notes

The NumPy 2.3.4 release is a patch release split between a number of maintenance updates and bug fixes. This release supports Python versions 3.11-3.14. This release is based on Python 3.14.0 final.

Changes

The npymath and npyrandom libraries now have a .lib rather than a .a file extension on win-arm64, for compatibility for building with MSVC and setuptools. Please note that using these static libraries is discouraged and for existing projects using it, it's best to use it with a matching compiler toolchain, which is clang-cl on Windows on Arm.

(gh-29750)

Contributors

A total of 17 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• !DWesl
• Charles Harris
• Christian Barbia +
• Evgeni Burovski
• Joren Hammudoglu
• Maaz +
• Mateusz Sokół
• Matti Picus
• Nathan Goldbaum
• Ralf Gommers
• Riku Sakamoto +
• Sandeep Gupta +
• Sayed Awad
• Sebastian Berg
• Sergey Fedorov +
• Warren Weckesser
• dependabot[bot]

Pull requests merged

A total of 30 pull requests were merged for this release.

• #29725: MAINT: Prepare 2.3.x for further development
• #29781: MAINT: Pin some upstream dependences
• #29782: BLD: enable x86-simd-sort to build on KNL with -mavx512f
• #29783: BUG: Include python-including headers first (#29281)
• #29784: TYP: fix np.number and np.*integer method declaration
• #29785: TYP: mypy 1.18.1

... (truncated)

Commits

• 1458b9e REL: Prepare for the NumPy 2.3.4 release (#29955)
• 7583bed Merge pull request #29950 from charris/backport-29885
• 3186751 Merge pull request #29949 from charris/backport-29948
• 7fd2ad9 STY: rename @classmethod arg to cls
• fe8447d MAINT: Simplify string arena growth strategy (#29885)
• a90f073 Merge pull request #29940 from charris/backport-29937
• 55d91ab MAINT: Bump pypa/cibuildwheel from 3.1.4 to 3.2.1
• e2f0383 Merge pull request #29926 from charris/backport-29609
• b427e83 BUG: fix negative samples generated by Wald distribution (#29609)
• 36363d6 Merge pull request #29922 from charris/backport-29914
• Additional commits viewable in compare view

Updates pillow from 11.3.0 to 12.0.0

Release notes

Sourced from pillow's releases.

12.0.0

https://pillow.readthedocs.io/en/stable/releasenotes/12.0.0.html

Removals

• Remove support for FreeType <= 2.9.0 #9159 [@​radarhere]
• Drop support for Python 3.9 #9119 [@​hugovk]
• Remove deprecations for Pillow 12.0.0 #9053 [@​radarhere]

Deprecations

• Deprecate Image._show #9186 [@​radarhere]
• Deprecate ImageCmsProfile product_name and product_info #8995 [@​lukegb]

Documentation

• ImagingHistogramInstance can use two bands #9251 [@​radarhere]
• Update 12.0.0 release notes #9247 [@​hugovk]
• Added ImageDraw alpha channel examples #9201 [@​radarhere]
• Update Python version #9230 [@​radarhere]
• Updated macOS tested Pillow versions #9209 [@​radarhere]
• Add GitHub profile link to release notes #9197 [@​radarhere]
• Split versionadded info #9190 [@​radarhere]
• Document ImageFile.MAXBLOCK #9163 [@​radarhere]
• Updated macOS version in CI targets #9157 [@​radarhere]
• Fix typos #9135 [@​radarhere]
• Added "Colors" to concepts #9067 [@​radarhere]
• Update macOS tested Pillow versions #9068 [@​radarhere]
• Thanks, folks! #9056 [@​aclark4life]
• Setup nit: "fork" should be lowercased #9055 [@​aclark4life]

Dependencies

• Update dependency cibuildwheel to v3.2.1 #9246 [@renovate[bot]]
• [pre-commit.ci] pre-commit autoupdate #9233 [@pre-commit-ci[bot]]
• Update harfbuzz to 12.1.0 #9218 [@​radarhere]
• Update libtiff to 4.7.1 #9222 [@​radarhere]
• Update FreeType to 2.14.1 on macOS and Linux wheels #9217 [@​radarhere]
• Update dependency cibuildwheel to v3.2.0 #9219 [@renovate[bot]]
• Update Ghostscript to 10.6.0 #9202 [@​radarhere]
• Update openjpeg to 2.5.4 #9215 [@​radarhere]
• Update harfbuzz to 11.5.0 #9203 [@​radarhere]
• Update dependency mypy to v1.18.2 #9213 [@renovate[bot]]
• Update dependency mypy to v1.18.1 #9207 [@renovate[bot]]
• Update github-actions #9194 [@renovate[bot]]
• Updated harfbuzz to 11.4.5 #9150 [@​radarhere]
• Update zlib-ng to 2.2.5 #9140 [@​radarhere]
• Update raqm to 0.10.3 #9137 [@​radarhere]
• Update libjpeg-turbo to 3.1.2 #9188 [@​radarhere]
• [pre-commit.ci] pre-commit autoupdate #9180 [@pre-commit-ci[bot]]

... (truncated)

Commits

• 693df7b 12.0.0 version bump
• d175bb8 Use macos-14 for iOS arm64 simulator (#9258)
• 592b2f8 Revert "Use macos-latest for iOS arm64 simulator"
• 5dddb2c Use enums for Modes and RawModes in C (#9256)
• e7b72a3 Add ImageText (#9098)
• 864d4b6 Shift bits before making value negative (#9255)
• 994a9de Install arro3 dependencies when type checking (#9254)
• d5e1601 Improved documentation
• e533ccc Merge branch 'main' into imagetext
• 95a85dc Use snake case
• Additional commits viewable in compare view

Updates plotly from 6.2.0 to 6.3.1

Release notes

Sourced from plotly's releases.

v6.3.1

Updated

• Update Plotly.js from version 3.1.0 to version 3.1.1. See the Plotly.js release notes for more information. [#5357]. Notable changes include:
  • Fix issue preventing Scattergl plots with text elements from rendering [plotly.js#7563]
• Use native legends when converting from matplotlib [#5312], with thanks to @​robertoffmoura to the contribution!
• Allow shared_yaxes to work with secondary axes [#5180], with thanks to @​gmjw for the contribution!

Fixed

• Fix issue where width/height in plot layout were not respected during Kaleido image export [#5325]
• Fix typo in default argument to _ternary_contour.py [#5315], with thanks to @​Lexachoc for the contribution!
• Fix incorrect fig.show() behavior when ipython is installed [#5258]

Full Changelog: plotly/plotly.py@v6.3.0...v6.3.1

v6.3.0

Updated

• Updated Plotly.js from version 3.0.1 to version 3.1.0. See the plotly.js release notes for more information. [#5318]

Added

• Exposed plotly.io.get_chrome() as a function which can be called from within a Python script. [#5282]

Fixed

• Resolved issue causing extraneous engine deprecation warnings [#5287], with thanks to @​jdbeel for the contribution!

Changelog

Sourced from plotly's changelog.

[6.3.1] - 2025-10-02

Updated

• Update Plotly.js from version 3.1.0 to version 3.1.1. See the Plotly.js release notes for more information. [#5357]. Notable changes include:
  • Fix issue preventing Scattergl plots with text elements from rendering [plotly.js#7563]
• Use native legends when converting from matplotlib [#5312], with thanks to @​robertoffmoura to the contribution!
• Allow shared_yaxes to work with secondary axes [#5180], with thanks to @​gmjw for the contribution!

Fixed

• Fix issue where width/height in plot layout were not respected during Kaleido image export [#5325]
• Fix typo in default argument to _ternary_contour.py [#5315], with thanks to @​Lexachoc for the contribution!
• Fix incorrect fig.show() behavior when ipython is installed [#5258]

[6.3.0] - 2025-08-12

Updated

• Updated Plotly.js from version 3.0.1 to version 3.1.0. See the Plotly.js release notes for more information. [#5318]

Added

• Exposed plotly.io.get_chrome() as a function which can be called from within a Python script. [#5282]

Fixed

• Resolved issue causing extraneous engine deprecation warnings [#5287], with thanks to @​jdbeel for the contribution!

Commits

• ecb00fe update uv lockfile
• 4e96a43 version changes for v6.3.1
• a0de8c9 Merge pull request #5361 from plotly/matplotlib-import-fix
• 832b46c Merge branch 'main' into matplotlib-import-fix
• b258862 Merge pull request #5180 from gmjw/secondary-y-shared
• 2c5e2b6 fix matplotlib import
• 610b7ee Merge branch 'main' into secondary-y-shared
• fbbc9d6 Merge pull request #5322 from mgorny/plt-import
• d2af541 Merge pull request #5258 from plotly/fix-default-renderer-when-ipython-installed
• ead0c76 Merge branch 'main' into plt-import
• Additional commits viewable in compare view

Updates pycurl from 7.45.6 to 7.45.7

Changelog

Sourced from pycurl's changelog.

Version 7.45.7 [requires libcurl-7.19.0 or better] - 2025-09-23

    * Support unsetting all callback functions (patch by Scott Talbert)
    * Fix linking fake-curl on AIX (patch by Sumitra Dawn)
    * Support PREREQFUNCTION callback (patch by Scott Talbert)
    * Fix debug test with curl 8.16.0 (patch by Carlos Henrique Lima Melara)
    * Support setting CURLOPT_ECH (patch by Tommi Rantala)
    * Officially support Python 3.14 (patch by Scott Talbert)

Commits

• See full diff in compare view

Updates pyopenssl from 25.1.0 to 25.3.0

Changelog

Sourced from pyopenssl's changelog.

25.3.0 (2025-09-16)

Backward-incompatible changes: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Deprecations: ^^^^^^^^^^^^^

Changes: ^^^^^^^^

• Maximum supported cryptography version is now 46.x.

25.2.0 (2025-09-14)

Backward-incompatible changes: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

• The minimum cryptography version is now 45.0.7.

Deprecations: ^^^^^^^^^^^^^

Changes: ^^^^^^^^

• pyOpenSSL now sets SSL_MODE_ACCEPT_MOVING_WRITE_BUFFER on connections by default, matching CPython's behavior.
• Added OpenSSL.SSL.Context.clear_mode.
• Added OpenSSL.SSL.Context.set_tls13_ciphersuites to set the allowed TLS 1.3 ciphers.
• Added OpenSSL.SSL.Connection.set_info_callback

Commits

• 41e7788 Prepare for a 25.3.0 release (#1448)
• 53b78f5 test on supported pypys (#1449)
• fb1ebc1 Update CI workflow to use 'ubuntu-latest' and 'windows-latest' (#1447)
• 6ccf90b Prepare for a release (#1446)
• 5f46403 Added OpenSSL.SSL.Connection.set_info_callback (#1438)
• 95cf8fa Update tests to not rely on mutating contexts (#1445)
• 946f87e Remove fallback path for old OpenSSL (#1443)
• 0213311 Fix for new mypy release (#1444)
• 7fd0ab8 Bump actions/setup-python from 5 to 6 (#1440)
• 8daf0d1 Bump pypa/gh-action-pypi-publish from 1.12.4 to 1.13.0 (#1439)
• Additional commits viewable in compare view

Updates scipy from 1.15.2 to 1.16.3

Release notes

Sourced from scipy's releases.

SciPy 1.16.3 Release Notes

SciPy 1.16.3 is a bug-fix release with no new features compared to 1.16.2.

Authors

• Name (commits)
• ChrisAB (1) +
• Lucas Colley (1)
• Ralf Gommers (3)
• Matt Haberland (8)
• Nick ODell (2)
• Ilhan Polat (1)
• Tyler Reddy (28)
• Lucas Roberts (2)

A total of 8 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.

The full issue and pull request lists, and the release asset hashes are available in the associated README.txt file.

SciPy 1.16.2 Release Notes

SciPy 1.16.2 is a bug-fix release with no new features compared to 1.16.1. This is the first stable release of SciPy to provide Windows on ARM wheels on PyPI.

Authors

• Name (commits)
• Dietrich B...

  Description has been truncated

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[dependabot]

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