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Bump the pip group across 1 directory with 35 updates #653

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Bumps the pip group with 35 updates in the /src directory:

Package From To
beautifulsoup4 4.13.3 4.14.2
biopython 1.85 1.86
bokeh 3.6.2 3.8.0
certifi 2025.1.31 2025.10.5
cryptography 44.0.1 46.0.3
idna 3.10 3.11
jsonschema 4.23.0 4.25.1
markdown 3.7 3.9
markupsafe 3.0.2 3.0.3
networkx 3.4.2 3.5
numpy 2.2.3 2.3.4
pillow 11.1.0 12.0.0
plotly 5.24.1 6.3.1
pycurl 7.45.4 7.45.7
pygments 2.19.1 2.19.2
pyopenssl 25.0.0 25.3.0
rsa 4.9 4.9.1
scipy 1.15.2 1.16.3
setuptools 75.8.2 80.9.0
sympy 1.13.3 1.14.0
ipython 8.33.0 9.6.0
ipywidgets 8.1.5 8.1.7
jinja2 3.1.5 3.1.6
pandas 2.2.3 2.3.3
pymongo 4.11.1 4.15.3
pyyaml 6.0.2 6.0.3
requests 2.32.3 2.32.5
scikit-learn 1.6.1 1.7.2
statsmodels 0.14.4 0.14.5
tornado 6.4.2 6.5.2
coverage 7.6.12 7.11.0
pytest 8.3.4 8.4.2
pytest-cov 6.0.0 7.0.0
pytest-recording 0.13.2 0.13.4
ruff 0.9.9 0.14.3

Updates beautifulsoup4 from 4.13.3 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

Updates bokeh from 3.6.2 to 3.8.0

Commits

Updates certifi from 2025.1.31 to 2025.10.5

Commits

Updates cryptography from 44.0.1 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

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 4.23.0 to 4.25.1

Release notes

Sourced from jsonschema's releases.

v4.25.1

What's Changed

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

v4.25.0

What's Changed

New Contributors

Full Changelog: python-jsonschema/jsonschema@v4.24.1...v4.25.0

v4.24.1

What's Changed

New Contributors

Full Changelog: python-jsonschema/jsonschema@v4.24.0...v4.24.1

v4.24.0

What's Changed

New Contributors

Full Changelog: python-jsonschema/jsonschema@v4.23.0...v4.24.0

Changelog

Sourced from jsonschema's changelog.

v4.25.1

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

v4.25.0

  • Add support for the iri and iri-reference formats to the format-nongpl extra via the MIT-licensed rfc3987-syntax. They were alread supported by the format extra. (#1388).

v4.24.1

  • Properly escape segments in ValidationError.json_path (#139).

v4.24.0

  • Fix improper handling of unevaluatedProperties in the presence of additionalProperties (#1351).
  • Support for Python 3.8 has been dropped, as it is end-of-life.
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 3.7 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).

Release 3.8.2

Fixed

  • Fix codecs deprecation in Python 3.14.
  • Fix issue with unclosed comment parsing in Python 3.14.
  • Fix issue with unclosed declarations in Python 3.14.
  • Fix issue with unclosed HTML tag <foo and Python 3.14.

Release 3.8.1

Fixed

  • Ensure incomplete markup declaration in raw HTML doesn't crash parser (#1534).
  • Fixed dropped content in md_in_html (#1526).
  • Fixed HTML handling corner case that prevented some content from not being rendered (#1528).

Release 3.8

Changed

  • DRY fix in abbr extension by introducing method create_element (#1483).
  • Clean up test directory by removing some redundant tests and port non-redundant cases to the newer test framework.
  • Improved performance of the raw HTML post-processor (#1510).

Fixed

  • Backslash Unescape IDs set via attr_list on toc (#1493).
  • Ensure md_in_html processes content inside "markdown" blocks as they are parsed outside of "markdown" blocks to keep things more consistent for third-party extensions (#1503).
  • md_in_html handle tags within inline code blocks better (#1075).
  • md_in_html fix handling of one-liner block HTML handling (#1074).
  • Ensure <center> is treated like a block-level element (#1481).
  • Ensure that abbr extension respects AtomicString and does not process perceived abbreviations in these strings (#1512).
  • Ensure smarty extension correctly renders nested closing quotes (#1514).
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).

[3.8.2] - 2025-06-19

Fixed

  • Fix codecs deprecation in Python 3.14 (#1537).
  • Fix issue with unclosed comment parsing in Python 3.14 (#1537).
  • Fix issue with unclosed declarations in Python 3.14 (#1537).
  • Fix issue with unclosed HTML tag <foo and Python 3.14 (#1537).

[3.8.1] - 2025-06-18

Fixed

  • Ensure incomplete markup declaration in raw HTML doesn't crash parser (#1534).
  • Fixed dropped content in md_in_html (#1526).
  • Fixed HTML handling corner case that prevented some content from not being rendered (#1528).

[3.8.0] - 2025-04-09

... (truncated)

Commits
  • f39cf84 Bump version to 3.9
  • 07bf207 Order footnotes by reference
  • 23c301d Fix failing cases for Python 3.14
  • 4669a09 fix typo
  • d9c8431 Bump version to 3.8.2
  • 9980cb5 Fixes for Python 3.14
  • 3561310 Properly document version specification.
  • 3bb9d42 Update documentation for release process
  • 3870f20 Bump version to 3.8.1
  • 8207214 Ensure incomplete markup declaration in raw HTML doesn't crash parser.
  • Additional commits viewable 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

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 11.1.0 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

Deprecations

Documentation

Dependencies

... (truncated)

Changelog

Sourced from pillow's changelog.

Changelog (Pillow)

Commits

Updates plotly from 5.24.1 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!
<...

Description has been truncated

@dependabot
Bump the pip group across 1 directory with 35 updates
ea4b798 
Bumps the pip group with 35 updates in the /src directory:

| Package | From | To |
| --- | --- | --- |
| [beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/bs4/) | `4.13.3` | `4.14.2` |
| [biopython](https://github.com/biopython/biopython) | `1.85` | `1.86` |
| [bokeh](https://github.com/bokeh/bokeh) | `3.6.2` | `3.8.0` |
| [certifi](https://github.com/certifi/python-certifi) | `2025.1.31` | `2025.10.5` |
| [cryptography](https://github.com/pyca/cryptography) | `44.0.1` | `46.0.3` |
| [idna](https://github.com/kjd/idna) | `3.10` | `3.11` |
| [jsonschema](https://github.com/python-jsonschema/jsonschema) | `4.23.0` | `4.25.1` |
| [markdown](https://github.com/Python-Markdown/markdown) | `3.7` | `3.9` |
| [markupsafe](https://github.com/pallets/markupsafe) | `3.0.2` | `3.0.3` |
| [networkx](https://github.com/networkx/networkx) | `3.4.2` | `3.5` |
| [numpy](https://github.com/numpy/numpy) | `2.2.3` | `2.3.4` |
| [pillow](https://github.com/python-pillow/Pillow) | `11.1.0` | `12.0.0` |
| [plotly](https://github.com/plotly/plotly.py) | `5.24.1` | `6.3.1` |
| [pycurl](https://github.com/pycurl/pycurl) | `7.45.4` | `7.45.7` |
| [pygments](https://github.com/pygments/pygments) | `2.19.1` | `2.19.2` |
| [pyopenssl](https://github.com/pyca/pyopenssl) | `25.0.0` | `25.3.0` |
| [rsa](https://github.com/sybrenstuvel/python-rsa) | `4.9` | `4.9.1` |
| [scipy](https://github.com/scipy/scipy) | `1.15.2` | `1.16.3` |
| [setuptools](https://github.com/pypa/setuptools) | `75.8.2` | `80.9.0` |
| [sympy](https://github.com/sympy/sympy) | `1.13.3` | `1.14.0` |
| [ipython](https://github.com/ipython/ipython) | `8.33.0` | `9.6.0` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.5` | `8.1.7` |
| [jinja2](https://github.com/pallets/jinja) | `3.1.5` | `3.1.6` |
| [pandas](https://github.com/pandas-dev/pandas) | `2.2.3` | `2.3.3` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.11.1` | `4.15.3` |
| [pyyaml](https://github.com/yaml/pyyaml) | `6.0.2` | `6.0.3` |
| [requests](https://github.com/psf/requests) | `2.32.3` | `2.32.5` |
| [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.6.1` | `1.7.2` |
| [statsmodels](https://github.com/statsmodels/statsmodels) | `0.14.4` | `0.14.5` |
| [tornado](https://github.com/tornadoweb/tornado) | `6.4.2` | `6.5.2` |
| [coverage](https://github.com/nedbat/coveragepy) | `7.6.12` | `7.11.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.3.4` | `8.4.2` |
| [pytest-cov](https://github.com/pytest-dev/pytest-cov) | `6.0.0` | `7.0.0` |
| [pytest-recording](https://github.com/kiwicom/pytest-recording) | `0.13.2` | `0.13.4` |
| [ruff](https://github.com/astral-sh/ruff) | `0.9.9` | `0.14.3` |



Updates `beautifulsoup4` from 4.13.3 to 4.14.2

Updates `biopython` from 1.85 to 1.86
- [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst)
- [Commits](https://github.com/biopython/biopython/commits)

Updates `bokeh` from 3.6.2 to 3.8.0
- [Changelog](https://github.com/bokeh/bokeh/blob/branch-3.9/docs/CHANGELOG)
- [Commits](bokeh/bokeh@3.6.2...3.8.0)

Updates `certifi` from 2025.1.31 to 2025.10.5
- [Commits](certifi/python-certifi@2025.01.31...2025.10.05)

Updates `cryptography` from 44.0.1 to 46.0.3
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@44.0.1...46.0.3)

Updates `idna` from 3.10 to 3.11
- [Release notes](https://github.com/kjd/idna/releases)
- [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst)
- [Commits](kjd/idna@v3.10...v3.11)

Updates `jsonschema` from 4.23.0 to 4.25.1
- [Release notes](https://github.com/python-jsonschema/jsonschema/releases)
- [Changelog](https://github.com/python-jsonschema/jsonschema/blob/main/CHANGELOG.rst)
- [Commits](python-jsonschema/jsonschema@v4.23.0...v4.25.1)

Updates `markdown` from 3.7 to 3.9
- [Release notes](https://github.com/Python-Markdown/markdown/releases)
- [Changelog](https://github.com/Python-Markdown/markdown/blob/master/docs/changelog.md)
- [Commits](Python-Markdown/markdown@3.7...3.9.0)

Updates `markupsafe` from 3.0.2 to 3.0.3
- [Release notes](https://github.com/pallets/markupsafe/releases)
- [Changelog](https://github.com/pallets/markupsafe/blob/main/CHANGES.rst)
- [Commits](pallets/markupsafe@3.0.2...3.0.3)

Updates `networkx` from 3.4.2 to 3.5
- [Release notes](https://github.com/networkx/networkx/releases)
- [Commits](networkx/networkx@networkx-3.4.2...networkx-3.5)

Updates `numpy` from 2.2.3 to 2.3.4
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.2.3...v2.3.4)

Updates `pillow` from 11.1.0 to 12.0.0
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](python-pillow/Pillow@11.1.0...12.0.0)

Updates `plotly` from 5.24.1 to 6.3.1
- [Release notes](https://github.com/plotly/plotly.py/releases)
- [Changelog](https://github.com/plotly/plotly.py/blob/main/CHANGELOG.md)
- [Commits](plotly/plotly.py@v5.24.1...v6.3.1)

Updates `pycurl` from 7.45.4 to 7.45.7
- [Changelog](https://github.com/pycurl/pycurl/blob/master/ChangeLog)
- [Commits](https://github.com/pycurl/pycurl/commits)

Updates `pygments` from 2.19.1 to 2.19.2
- [Release notes](https://github.com/pygments/pygments/releases)
- [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES)
- [Commits](pygments/pygments@2.19.1...2.19.2)

Updates `pyopenssl` from 25.0.0 to 25.3.0
- [Changelog](https://github.com/pyca/pyopenssl/blob/main/CHANGELOG.rst)
- [Commits](pyca/pyopenssl@25.0.0...25.3.0)

Updates `rsa` from 4.9 to 4.9.1
- [Changelog](https://github.com/sybrenstuvel/python-rsa/blob/main/CHANGELOG.md)
- [Commits](https://github.com/sybrenstuvel/python-rsa/commits)

Updates `scipy` from 1.15.2 to 1.16.3
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.15.2...v1.16.3)

Updates `setuptools` from 75.8.2 to 80.9.0
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst)
- [Commits](pypa/setuptools@v75.8.2...v80.9.0)

Updates `sympy` from 1.13.3 to 1.14.0
- [Release notes](https://github.com/sympy/sympy/releases)
- [Commits](sympy/sympy@sympy-1.13.3...sympy-1.14.0)

Updates `ipython` from 8.33.0 to 9.6.0
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.33.0...9.6.0)

Updates `ipywidgets` from 8.1.5 to 8.1.7
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](jupyter-widgets/ipywidgets@8.1.5...8.1.7)

Updates `jinja2` from 3.1.5 to 3.1.6
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)
- [Commits](pallets/jinja@3.1.5...3.1.6)

Updates `pandas` from 2.2.3 to 2.3.3
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v2.2.3...v2.3.3)

Updates `pymongo` from 4.11.1 to 4.15.3
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](mongodb/mongo-python-driver@4.11.1...4.15.3)

Updates `pyyaml` from 6.0.2 to 6.0.3
- [Release notes](https://github.com/yaml/pyyaml/releases)
- [Changelog](https://github.com/yaml/pyyaml/blob/6.0.3/CHANGES)
- [Commits](yaml/pyyaml@6.0.2...6.0.3)

Updates `requests` from 2.32.3 to 2.32.5
- [Release notes](https://github.com/psf/requests/releases)
- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md)
- [Commits](psf/requests@v2.32.3...v2.32.5)

Updates `scikit-learn` from 1.6.1 to 1.7.2
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.6.1...1.7.2)

Updates `statsmodels` from 0.14.4 to 0.14.5
- [Release notes](https://github.com/statsmodels/statsmodels/releases)
- [Changelog](https://github.com/statsmodels/statsmodels/blob/main/CHANGES.md)
- [Commits](statsmodels/statsmodels@v0.14.4...v0.14.5)

Updates `tornado` from 6.4.2 to 6.5.2
- [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst)
- [Commits](tornadoweb/tornado@v6.4.2...v6.5.2)

Updates `coverage` from 7.6.12 to 7.11.0
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.6.12...7.11.0)

Updates `pytest` from 8.3.4 to 8.4.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.3.4...8.4.2)

Updates `pytest-cov` from 6.0.0 to 7.0.0
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v6.0.0...v7.0.0)

Updates `pytest-recording` from 0.13.2 to 0.13.4
- [Release notes](https://github.com/kiwicom/pytest-recording/releases)
- [Changelog](https://github.com/kiwicom/pytest-recording/blob/master/docs/changelog.rst)
- [Commits](kiwicom/pytest-recording@v0.13.2...v0.13.4)

Updates `ruff` from 0.9.9 to 0.14.3
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.9.9...0.14.3)

---
updated-dependencies:
- dependency-name: beautifulsoup4
  dependency-version: 4.14.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: biopython
  dependency-version: '1.86'
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  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: bokeh
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  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: certifi
  dependency-version: 2025.10.5
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  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: cryptography
  dependency-version: 46.0.3
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: idna
  dependency-version: '3.11'
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: jsonschema
  dependency-version: 4.25.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: markdown
  dependency-version: '3.9'
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  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: markupsafe
  dependency-version: 3.0.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: networkx
  dependency-version: '3.5'
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  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: numpy
  dependency-version: 2.3.4
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pillow
  dependency-version: 12.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: plotly
  dependency-version: 6.3.1
  dependency-type: direct:production
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  dependency-group: pip
- dependency-name: pycurl
  dependency-version: 7.45.7
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  dependency-group: pip
- dependency-name: pygments
  dependency-version: 2.19.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pyopenssl
  dependency-version: 25.3.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: rsa
  dependency-version: 4.9.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: scipy
  dependency-version: 1.16.3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: setuptools
  dependency-version: 80.9.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: sympy
  dependency-version: 1.14.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: ipython
  dependency-version: 9.6.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: ipywidgets
  dependency-version: 8.1.7
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: jinja2
  dependency-version: 3.1.6
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  dependency-group: pip
- dependency-name: pandas
  dependency-version: 2.3.3
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  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pymongo
  dependency-version: 4.15.3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pyyaml
  dependency-version: 6.0.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: requests
  dependency-version: 2.32.5
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  dependency-group: pip
- dependency-name: scikit-learn
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  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: statsmodels
  dependency-version: 0.14.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: tornado
  dependency-version: 6.5.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: coverage
  dependency-version: 7.11.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pytest
  dependency-version: 8.4.2
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pytest-cov
  dependency-version: 7.0.0
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: pytest-recording
  dependency-version: 0.13.4
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: ruff
  dependency-version: 0.14.3
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Nov 1, 2025
This was referenced Nov 1, 2025
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dependabot bot commented on behalf of github Jan 1, 2026

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

@dependabot dependabot bot closed this Jan 1, 2026
@dependabot dependabot bot deleted the dependabot/pip/src/pip-e53e2111ac branch January 1, 2026 09:02
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