Skip to content

Bump the pip group across 1 directory with 33 updates #3728

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
dependabot wants to merge 1 commit into
base: develop
Choose a base branch
from
Open

Bump the pip group across 1 directory with 33 updates #3728

dependabot wants to merge 1 commit into from

Conversation

@dependabot
Copy link
Contributor

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

Bumps the pip group with 33 updates in the /src directory:

Package From To
beautifulsoup4 4.13.4 4.14.3
biopython 1.85 1.86
bokeh 3.6.2 3.8.2
certifi 2025.7.14 2026.1.4
cryptography 45.0.5 46.0.4
idna 3.10 3.11
jsonschema 4.25.0 4.26.0
markdown 3.8.2 3.10.1
markupsafe 3.0.2 3.0.3
networkx 3.4.2 3.6.1
numpy 2.2.3 2.4.2
pillow 11.3.0 12.1.0
plotly 6.2.0 6.5.2
pyasn1 0.6.1 0.6.2
pycurl 7.45.6 7.45.7
pyopenssl 25.1.0 25.3.0
scipy 1.15.2 1.17.0
setuptools 80.9.0 80.10.2
wordcloud 1.9.4 1.9.6
ipython 8.33.0 9.9.0
ipywidgets 8.1.7 8.1.8
pandas 2.3.1 3.0.0
pymongo 4.13.2 4.16.0
pyyaml 6.0.2 6.0.3
requests 2.32.4 2.32.5
scikit-learn 1.6.1 1.8.0
statsmodels 0.14.5 0.14.6
tornado 6.5.1 6.5.4
coverage 7.10.1 7.13.2
pytest 8.4.1 9.0.2
pytest-cov 6.2.1 7.0.0
ruff 0.12.7 0.14.14
vcrpy 7.0.0 8.1.1

Updates beautifulsoup4 from 4.13.4 to 4.14.3

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 3.8.2

Changelog

Sourced from bokeh's changelog.

2026-01-06 3.8.2:

  • bugfixes:

    • #14768 [component: server] Incomplete Origin Validation in WebSockets in Bokeh server applications

  • tasks:

2025-11-07 3.8.1:

  • bugfixes:

    • #14618 [component: docs] Local documentation build fails with Extension error (sphinxext.opengraph)
    • #14626 [component: docs] Local documentation fails on Windows because of missing svg icons
    • #14651 [component: bokehjs] HoverTool parameter @$name for stacked bar chart not working in version 3.8.0

  • tasks:

2025-08-29 3.8:

  • bugfixes:
    • #12430 [component: bokehjs] [BUG] Step glyphs do not support linked brushing
    • #12994 [component: bokehjs] [BUG] Patch does not output under certain conditions
    • #13616 [component: bokehjs] [BUG] DateRangePicker value does not reflect value in browser when selection is aborted
    • #14334 js_on_change not firing when range is updated in range tool
    • #14352 [component: bokehjs] Log Axis and Range1d < 1 failing
    • #14383 [component: bokehjs] SerializationError: circular reference When Passing List of Renderers to CustomJS Callbacks, but not when passing renderers sperately.
    • #14396 [component: examples] Remove context from time of day in span example
    • #14399 Bad typings for list_attr_splat (e.g. Plot.axis)
    • #14413 [component: bokehjs] ValueRef formatter does not handle datetime nullable well
    • #14420 [component: bokehjs] Enhance performance of WebGL multi_marker
    • #14422 [component: bokehjs] Legend renderer not correctly positioned when saved with SaveTool
    • #14424 [component: bokehjs] Patches with no data does not show plot with Bokeh 3.7+
    • #14458 [component: bokehjs] Removing and re-adding DOM nodes causes React problems
    • #14461 [component: tests] The regression test for issue #14207 is unreliable
    • #14468 [component: docs] Try on CodePen link does not work in documentation /docs/user_guide/advanced/bokehjs.html
    • #14469 [component: bokehjs] Canvas2D: Multiple readback operations using getImageData are faster with the willReadFrequently attribute set to true
    • #14476 Improve handling of pd.NA in Property.matches
    • #14497 mypy 1.15.0 fails in CI but not locally
    • #14499 [component: docs] IndexError on importing bokeh.sphinxext.bokeh_plot
    • #14520 [component: bokehjs] BokehJS complains about categorical factors for the BoxAnnotation widget
    • #14536 Flex layouts need to apply min_width and min_height selectively
    • #14540 [component: tests] Tests are failing on Windows and Python 3.10 after PR #14531
    • #14541 New SVG icons have inconsistent line widths
    • #14554 Add support for scalar uint32 color input.
    • #14565 [component: bokehjs] DataTable source update broken
    • #14574 [component: build] grammar build script failing with whitespace in path
    • #14597 [component: bokehjs] document_ready even trigger twice with Bokeh 3.4.0.dev4
    • #14602 [component: bokehjs] Layoutable components in side panels don't appear in exported images
    • #14620 Re-connect race condition on page reload

... (truncated)

Commits
  • e5ce879 Deployment updates for release 3.8.2
  • 2b3ee10 Don't validate npm credentials due to OICD limitations in npm (#14769)
  • 756e3ae Migrate from NPM tokens to trusted providers for publishing in CI (#14766)
  • 2f225a1 Update dependencies in build environment (#14758)
  • 69d197c update switcher.json
  • d915c8b update to latest ruff (#14661)
  • 5f9f7b6 update release notes
  • cedd113 handle wildcard host with port correctly
  • a961ab7 small CI fixes for advisory fork merge
  • d62939a Merge commit from fork
  • Additional commits viewable in compare view

Updates certifi from 2025.7.14 to 2026.1.4

Commits
  • c64d9f3 2026.01.04 (#389)
  • 4ac232f Bump actions/download-artifact from 6.0.0 to 7.0.0 (#387)
  • 95ae4b2 Update CI workflow to use Ubuntu 24.04 and Python 3.14 stable (#386)
  • b72a7b1 Bump dessant/lock-threads from 5.0.1 to 6.0.0 (#385)
  • ecc2672 Bump actions/upload-artifact from 5.0.0 to 6.0.0 (#384)
  • 6a897db Bump peter-evans/create-pull-request from 7.0.11 to 8.0.0 (#383)
  • 27ca98a Bump peter-evans/create-pull-request from 7.0.9 to 7.0.11 (#381)
  • 56c59a6 Bump actions/checkout from 6.0.0 to 6.0.1 (#382)
  • ae0021c Bump actions/setup-python from 6.0.0 to 6.1.0 (#380)
  • ddf5d0b Bump actions/checkout from 5.0.1 to 6.0.0 (#378)
  • Additional commits viewable in compare view

Updates cryptography from 45.0.5 to 46.0.4

Changelog

Sourced from cryptography's changelog.

46.0.4 - 2026-01-27


* `Dropped support for win_arm64 wheels`_.
* Updated Windows, macOS, and Linux wheels to be compiled with OpenSSL 3.5.5.

.. _v46-0-3:


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.
</tr></table>

... (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 4.25.0 to 4.26.0

Release notes

Sourced from jsonschema's releases.

v4.26.0

What's Changed

New Contributors

Full Changelog: python-jsonschema/jsonschema@v4.25.1...v4.26.0

v4.25.1

What's Changed

... (truncated)

Changelog

Sourced from jsonschema's changelog.

v4.26.0

  • Decrease import time by delaying importing of urllib.request (#1416).

v4.25.1

  • Fix an incorrect required argument in the Validator protocol's type annotations (#1396).
Commits
  • a727743 Add a changelog entry for 4.26.
  • 6d28c13 Update the lockfile.
  • 739499e Update pre-commit hooks.
  • cb2d779 Merge pull request #1443 from python-jsonschema/pre-commit-ci-update-config
  • e6bbbb7 [pre-commit.ci] pre-commit autoupdate
  • d56037a Merge pull request #1442 from python-jsonschema/dependabot/github_actions/ast...
  • e54ce13 Bump astral-sh/setup-uv from 7.1.4 to 7.1.6
  • 1f7c9fb Partially update docs requirements.
  • 241aec9 Merge pull request #1441 from python-jsonschema/pre-commit-ci-update-config
  • 2818efb Apache-2.0 -> nongpl
  • Additional commits viewable in compare view

Updates markdown from 3.8.2 to 3.10.1

Release notes

Sourced from markdown's releases.

Release 3.10.1

Fixed

  • Ensure nested elements inside inline comments are properly unescaped (#1571).
  • Make the docs build successfully with mkdocstrings-python 2.0 (#1575).
  • Fix infinite loop when multiple bogus or unclosed HTML comments appear in input (#1578).
  • Fix another infinite loop when handling bad comments (#1586).

Release 3.10.0

Changed

  • Officially support Python 3.14 and PyPy 3.11 and drop support for Python 3.9 and PyPy 3.9.

Fixed

  • Fix an HTML comment parsing case in some Python versions that can cause an infinite loop (#1554).
  • Revert the default behavior of USE_DEFINITION_ORDER (to True). The new behavior introduced in 3.9.0 is experimental and results are inconsistent. It should not have been made the default behavior (#1561).

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.

[3.10.1] - 2026-01-21

Fixed

  • Ensure nested elements inside inline comments are properly unescaped (#1571).
  • Make the docs build successfully with mkdocstrings-python 2.0 (#1575).
  • Fix infinite loop when multiple bogus or unclosed HTML comments appear in input (#1578).
  • Fix another infinite loop when handling bad comments (#1586).

[3.10.0] - 2025-11-03

Changed

  • Officially support Python 3.14 and PyPy 3.11 and drop support for Python 3.9 and PyPy 3.9.

Fixed

  • Fix an HTML comment parsing case in some Python versions that can cause an infinite loop (#1554).
  • Revert the default behavior of USE_DEFINITION_ORDER (to True). The new behavior introduced in 3.9.0 is experimental and results are inconsistent. It should not have been made the default behavior (#1561).

[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
  • e5fa5b8 Bump version to 3.10.1
  • f925349 More HTML fixes
  • 9933a0a Revert "Allow reference links with backticks"
  • 07dfa4e Allow reference links with backticks
  • fb6b27a Fix infinite loop when text contains multiple unclosed comments
  • 89112c2 Make the docs build successfully with mkdocstrings-python 2.0
  • 961856c Update link
  • 2b49115 Ensure nested elements inside inline comments are properly unescaped.
  • 22e89c1 Bump version to 3.10
  • c138aea + PY314 - PY39
  • 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 3.6.1

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 numpy from 2.2.3 to 2.4.2

Release notes

Sourced from numpy's releases.

2.4.2 (Feb 1, 2026)

NumPy 2.4.2 Release Notes

The NumPy 2.4.2 is a patch release that fixes bugs discovered after the 2.4.1 release. Highlights are:

  • Fixes memory leaks
  • Updates OpenBLAS to fix hangs

This release supports Python versions 3.11-3.14

Contributors

A total of 9 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Charles Harris
  • Daniel Tang +
  • Joren Hammudoglu
  • Kumar Aditya
  • Matti Picus
  • Nathan Goldbaum
  • Ralf Gommers
  • Sebastian Berg
  • Vikram Kumar +

Pull requests merged

A total of 12 pull requests were merged for this release.

  • #30629: MAINT: Prepare 2.4.x for further development
  • #30636: TYP: arange: accept datetime strings
  • #30657: MAINT: avoid possible race condition by not touching os.environ...
  • #30700: BUG: validate contraction axes in tensordot (#30521)
  • #30701: DOC: __array_namespace__info__: set_module not __module__ (#30679)
  • #30702: BUG: fix free-threaded PyObject layout in replace_scalar_type_names...
  • #30703: TST: fix limited API example in tests for latest Cython
  • #30709: BUG: Fix some bugs found via valgrind (#30680)
  • #30712: MAINT: replace ob_type access with Py_TYPE in PyArray_CheckExact
  • #30713: BUG: Fixup the quantile promotion fixup
  • #30736: BUG: fix thread safety of array_getbuffer (#30667)
  • #30737: backport scipy-openblas version change

2.4.1 (Jan 10, 2026)

NumPy 2.4.1 Release Notes

The NumPy 2.4.1 is a patch release that fixes bugs discoved after the 2.4.0 release. In particular, the typo SeedlessSequence is preserved to enable wheels using the random Cython API and built against NumPy < 2.4.0 to run without errors.

... (truncated)

Changelog

Sourced from numpy's changelog.

This is a walkthrough of the NumPy 2.4.0 release on Linux, which will be the first feature release using the numpy/numpy-release <https://github.com/numpy/numpy-release>__ repository.

The commands can be copied into the command line, but be sure to replace 2.4.0 with the correct version. This should be read together with the :ref:general release guide <prepare_release>.

Facility preparation

Before beginning to make a release, use the requirements/*_requirements.txt files to ensure that you have the needed software. Most software can be installed with pip, but some will require apt-get, dnf, or whatever your system uses for software. You will also need a GitHub personal access token (PAT) to push the documentation. There are a few ways to streamline things:

  • Git can be set up to use a keyring to store your GitHub personal access token. Search online for the details.
  • You can use the keyring app to store the PyPI password for twine. See the online twine documentation for details.

Prior to release

Add/drop Python versions

When adding or dropping Python versions, multiple config and CI files need to be edited in addition to changing the minimum version in pyproject.toml. Make these changes in an ordinary PR against main and backport if necessary. We currently release wheels for new Python versions after the first Python RC once manylinux and cibuildwheel support that new Python version.

Backport pull requests

Changes that have been marked for this release must be backported to the maintenance/2.4.x branch.

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

... (truncated)

Commits
  • c81c49f Merge pull request #30757 from charris/prepare-2.4.2
  • b3ae9c5 REL: Prepare for the NumPy 2.4.2 release
  • 9de8984 Merge pull request #30737 from mattip/scipy-openblas-backport
  • b7be329 backport scipy-openblas version change
  • 7ff9863 Merge pull request #30736 from charris/backport-30667
  • 431fffb MAINT: Skip tests that require buffer.
  • 127235f BUG: fix thread safety of array_getbuffer (#30667)
  • 18bdb2e Merge pull request #30713 from charris/backport-30710
  • 41dd751 Merge pull request #30712 from charris/backport-30705
  • 7a278da BUG: Fixup the quantile promotion fixup
  • Additional commits viewable in compare view

Updates pillow from 11.3.0 to 12.1.0

Release notes

Sourced from pillow's releases.

12.1.0

https://pillow.readthedocs.io/en/stable/releasenotes/12.1.0.html

Deprecations

Documentation

Dependencies

@dependabot
Bump the pip group across 1 directory with 33 updates
b8e9737 
Bumps the pip group with 33 updates in the /src directory:

| Package | From | To |
| --- | --- | --- |
| [beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/bs4/) | `4.13.4` | `4.14.3` |
| [biopython](https://github.com/biopython/biopython) | `1.85` | `1.86` |
| [bokeh](https://github.com/bokeh/bokeh) | `3.6.2` | `3.8.2` |
| [certifi](https://github.com/certifi/python-certifi) | `2025.7.14` | `2026.1.4` |
| [cryptography](https://github.com/pyca/cryptography) | `45.0.5` | `46.0.4` |
| [idna](https://github.com/kjd/idna) | `3.10` | `3.11` |
| [jsonschema](https://github.com/python-jsonschema/jsonschema) | `4.25.0` | `4.26.0` |
| [markdown](https://github.com/Python-Markdown/markdown) | `3.8.2` | `3.10.1` |
| [markupsafe](https://github.com/pallets/markupsafe) | `3.0.2` | `3.0.3` |
| [networkx](https://github.com/networkx/networkx) | `3.4.2` | `3.6.1` |
| [numpy](https://github.com/numpy/numpy) | `2.2.3` | `2.4.2` |
| [pillow](https://github.com/python-pillow/Pillow) | `11.3.0` | `12.1.0` |
| [plotly](https://github.com/plotly/plotly.py) | `6.2.0` | `6.5.2` |
| [pyasn1](https://github.com/pyasn1/pyasn1) | `0.6.1` | `0.6.2` |
| [pycurl](https://github.com/pycurl/pycurl) | `7.45.6` | `7.45.7` |
| [pyopenssl](https://github.com/pyca/pyopenssl) | `25.1.0` | `25.3.0` |
| [scipy](https://github.com/scipy/scipy) | `1.15.2` | `1.17.0` |
| [setuptools](https://github.com/pypa/setuptools) | `80.9.0` | `80.10.2` |
| [wordcloud](https://github.com/amueller/word_cloud) | `1.9.4` | `1.9.6` |
| [ipython](https://github.com/ipython/ipython) | `8.33.0` | `9.9.0` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.7` | `8.1.8` |
| [pandas](https://github.com/pandas-dev/pandas) | `2.3.1` | `3.0.0` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.13.2` | `4.16.0` |
| [pyyaml](https://github.com/yaml/pyyaml) | `6.0.2` | `6.0.3` |
| [requests](https://github.com/psf/requests) | `2.32.4` | `2.32.5` |
| [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.6.1` | `1.8.0` |
| [statsmodels](https://github.com/statsmodels/statsmodels) | `0.14.5` | `0.14.6` |
| [tornado](https://github.com/tornadoweb/tornado) | `6.5.1` | `6.5.4` |
| [coverage](https://github.com/coveragepy/coveragepy) | `7.10.1` | `7.13.2` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.4.1` | `9.0.2` |
| [pytest-cov](https://github.com/pytest-dev/pytest-cov) | `6.2.1` | `7.0.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.12.7` | `0.14.14` |
| [vcrpy](https://github.com/kevin1024/vcrpy) | `7.0.0` | `8.1.1` |



Updates `beautifulsoup4` from 4.13.4 to 4.14.3

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 3.8.2
- [Changelog](https://github.com/bokeh/bokeh/blob/3.8.2/docs/CHANGELOG)
- [Commits](bokeh/bokeh@3.6.2...3.8.2)

Updates `certifi` from 2025.7.14 to 2026.1.4
- [Commits](certifi/python-certifi@2025.07.14...2026.01.04)

Updates `cryptography` from 45.0.5 to 46.0.4
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@45.0.5...46.0.4)

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 4.25.0 to 4.26.0
- [Release notes](https://github.com/python-jsonschema/jsonschema/releases)
- [Changelog](https://github.com/python-jsonschema/jsonschema/blob/main/CHANGELOG.rst)
- [Commits](python-jsonschema/jsonschema@v4.25.0...v4.26.0)

Updates `markdown` from 3.8.2 to 3.10.1
- [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@3.8.2...3.10.1)

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 3.6.1
- [Release notes](https://github.com/networkx/networkx/releases)
- [Commits](networkx/networkx@networkx-3.4.2...networkx-3.6.1)

Updates `numpy` from 2.2.3 to 2.4.2
- [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...v2.4.2)

Updates `pillow` from 11.3.0 to 12.1.0
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](python-pillow/Pillow@11.3.0...12.1.0)

Updates `plotly` from 6.2.0 to 6.5.2
- [Release notes](https://github.com/plotly/plotly.py/releases)
- [Changelog](https://github.com/plotly/plotly.py/blob/main/CHANGELOG.md)
- [Commits](plotly/plotly.py@v6.2.0...v6.5.2)

Updates `pyasn1` from 0.6.1 to 0.6.2
- [Release notes](https://github.com/pyasn1/pyasn1/releases)
- [Changelog](https://github.com/pyasn1/pyasn1/blob/main/CHANGES.rst)
- [Commits](pyasn1/pyasn1@v0.6.1...v0.6.2)

Updates `pycurl` from 7.45.6 to 7.45.7
- [Changelog](https://github.com/pycurl/pycurl/blob/master/ChangeLog)
- [Commits](https://github.com/pycurl/pycurl/commits)

Updates `pyopenssl` from 25.1.0 to 25.3.0
- [Changelog](https://github.com/pyca/pyopenssl/blob/main/CHANGELOG.rst)
- [Commits](pyca/pyopenssl@25.1.0...25.3.0)

Updates `scipy` from 1.15.2 to 1.17.0
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.15.2...v1.17.0)

Updates `setuptools` from 80.9.0 to 80.10.2
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst)
- [Commits](pypa/setuptools@v80.9.0...v80.10.2)

Updates `wordcloud` from 1.9.4 to 1.9.6
- [Release notes](https://github.com/amueller/word_cloud/releases)
- [Changelog](https://github.com/amueller/word_cloud/blob/main/doc/changelog.rst)
- [Commits](amueller/word_cloud@1.9.4...1.9.6)

Updates `ipython` from 8.33.0 to 9.9.0
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.33.0...9.9.0)

Updates `ipywidgets` from 8.1.7 to 8.1.8
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](jupyter-widgets/ipywidgets@8.1.7...8.1.8)

Updates `pandas` from 2.3.1 to 3.0.0
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v2.3.1...v3.0.0)

Updates `pymongo` from 4.13.2 to 4.16.0
- [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@4.13.2...4.16.0)

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 2.32.4 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@v2.32.4...v2.32.5)

Updates `scikit-learn` from 1.6.1 to 1.8.0
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.6.1...1.8.0)

Updates `statsmodels` from 0.14.5 to 0.14.6
- [Release notes](https://github.com/statsmodels/statsmodels/releases)
- [Changelog](https://github.com/statsmodels/statsmodels/blob/main/CHANGES.md)
- [Commits](statsmodels/statsmodels@v0.14.5...v0.14.6)

Updates `tornado` from 6.5.1 to 6.5.4
- [Changelog](https://github.com/tornadoweb/tornado/blob/v6.5.4/docs/releases.rst)
- [Commits](tornadoweb/tornado@v6.5.1...v6.5.4)

Updates `coverage` from 7.10.1 to 7.13.2
- [Release notes](https://github.com/coveragepy/coveragepy/releases)
- [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.10.1...7.13.2)

Updates `pytest` from 8.4.1 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@8.4.1...9.0.2)

Updates `pytest-cov` from 6.2.1 to 7.0.0
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v6.2.1...v7.0.0)

Updates `ruff` from 0.12.7 to 0.14.14
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.12.7...0.14.14)

Updates `vcrpy` from 7.0.0 to 8.1.1
- [Release notes](https://github.com/kevin1024/vcrpy/releases)
- [Changelog](https://github.com/kevin1024/vcrpy/blob/master/docs/changelog.rst)
- [Commits](kevin1024/vcrpy@v7.0.0...v8.1.1)

---
updated-dependencies:
- dependency-name: beautifulsoup4
  dependency-version: 4.14.3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: biopython
  dependency-version: '1.86'
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: bokeh
  dependency-version: 3.8.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: certifi
  dependency-version: 2026.1.4
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: cryptography
  dependency-version: 46.0.4
  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: 4.26.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: markdown
  dependency-version: 3.10.1
  dependency-type: direct:production
  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: 3.6.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: numpy
  dependency-version: 2.4.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pillow
  dependency-version: 12.1.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: plotly
  dependency-version: 6.5.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pyasn1
  dependency-version: 0.6.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pycurl
  dependency-version: 7.45.7
  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: scipy
  dependency-version: 1.17.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: setuptools
  dependency-version: 80.10.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: wordcloud
  dependency-version: 1.9.6
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: ipython
  dependency-version: 9.9.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: ipywidgets
  dependency-version: 8.1.8
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pandas
  dependency-version: 3.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: pip
- dependency-name: pymongo
  dependency-version: 4.16.0
  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
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: scikit-learn
  dependency-version: 1.8.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: statsmodels
  dependency-version: 0.14.6
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: tornado
  dependency-version: 6.5.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: coverage
  dependency-version: 7.13.2
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pytest
  dependency-version: 9.0.2
  dependency-type: direct:development
  update-type: version-update:semver-major
  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: ruff
  dependency-version: 0.14.14
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: vcrpy
  dependency-version: 8.1.1
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Feb 1, 2026
@sonarqubecloud
Copy link

sonarqubecloud bot commented Feb 1, 2026

Quality Gate Passed 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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

dependencies Pull requests that update a dependency file python Pull requests that update Python code

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

0 participants