Skip to content

Bump the pip group across 1 directory with 28 updates #3719

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
Closed
dependabot wants to merge 1 commit into from
Closed

Bump the pip group across 1 directory with 28 updates #3719

dependabot wants to merge 1 commit into from

Conversation

@dependabot
Copy link
Contributor

@dependabot dependabot bot commented on behalf of github Dec 1, 2025 •
edited
Loading

Bumps the pip group with 28 updates in the /src directory:

Package From To
beautifulsoup4 4.13.4 4.14.3
biopython 1.85 1.86
bokeh 3.6.2 3.8.1
certifi 2025.7.14 2025.11.12
cryptography 45.0.5 46.0.3
idna 3.10 3.11
jsonschema 4.25.0 4.25.1
markdown 3.8.2 3.10
markupsafe 3.0.2 3.0.3
networkx 3.4.2 3.6
numpy 2.2.3 2.3.5
pillow 11.3.0 12.0.0
plotly 6.2.0 6.5.0
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 9.7.0
ipywidgets 8.1.7 8.1.8
pandas 2.3.1 2.3.3
pymongo 4.13.2 4.15.4
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 7.12.0
pytest 8.4.1 9.0.1
pytest-cov 6.2.1 7.0.0
ruff 0.12.7 0.14.7

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 3.8.1

Changelog

Sourced from bokeh's changelog.

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

  • features:

    • #2603 [component: bokehjs] Add a SizeBar guide to label relative scatter glyph sizes
    • #7338 Setting areas for the activation of the hover.
    • #8608 [component: bokehjs] [Feature request] automatic reconnect to server
    • #9087 [component: bokehjs] Provide hit_filter property on HoverTool and TapTool
    • #9327 [component: bokehjs] [BUG] Not possible to disable multi-select behavior for DataTable
    • #12375 [FEATURE] Set axis label at a fixed distance from the axis

... (truncated)

Commits
  • 7e37a63 Deployment updates for release 3.8.1
  • 838b7c3 Merge pull request #14704 from bokeh/mattpap/3.8.1_backports
  • 477afb3 Added release notes
  • 360d9d6 set minimal version of sphinxext-opengraph to 0.11.0 (#14625)
  • fd662c1 add copy and delete for svg icons to make.bat (#14627)
  • 9f9d602 Restore @$name support and improve replace_placeholders() (#14652)
  • b63f691 Update switcher.json
  • 6431bdf Merge deployment staging branch staging-3.8.0
  • 2378619 Deployment updates for release 3.8.0
  • b83c74d Update switcher.json for 3.8 release (#14623)
  • Additional commits viewable in compare view

Updates certifi from 2025.7.14 to 2025.11.12

Commits

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

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

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 3.10

Release notes

Sourced from markdown's releases.

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.

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.

[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

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

Release notes

Sourced from networkx's releases.

NetworkX 3.6

networkx 3.6

We're happy to announce the release of networkx 3.6!

New Features

  • ENH: add normalize option for subgraph_centrality and its _exp version (#8340).

API Changes

  • Replace random_lobster with random_lobster_graph (#8067).
  • Replace maybe_regular_expander with maybe_regular_expander_graph (#8050).
  • Rm networkx.algorithms.threshold.swap_d (#8213).
  • Expire deprecation of compute_v_structures (#8281).
  • Rm unused dissuade_hubs kwarg from forceatlas2 (#8293).
  • Expire deprecation of link kwarg in node_link fns (#8282).
  • DEP: Deprecate metric_closure (#8304).

Enhancements

  • Improve error message for removed random_tree function (#8105).
  • Update approx current_flow betweenness to use k directly (#8007).
  • Proposal: update semantics for nonisomorphic trees with order 0 or 1 (#8083).
  • SCC benchmarks and use of G._adj in Tarjan algorithm (#8064).
  • Performance improvement and tests for edges_equal (#8077).
  • optimise is_reachable() (#8112).
  • Optimise harmonic centrality (#8158).
  • feat(drawing): add missing connection styles in draw_networkx_edge_labels and display (#8108).
  • Optimizing Dijkstra's paths to target (~50x faster for graphs with multiple-hops shortest path) (#8023).
  • Add all_triangles generator yielding all unique triangles in a graph (#8135).
  • refactor: simplify k_factor (#8139).
  • feat: add directed star graph (#8151).
  • Faster intersection_array computation for checking distance-regularity (#7181).
  • enh: short-circuit in is_regular for directed graphs (#8138).
  • Avoid re-exploring nodes in Kosaraju's SCC algorithm (#8056).
  • trust rank implementation and testing (#8165).
  • Add hyper_wiener_index function (#8184).
  • Bidirectional dijkstra optimization: from 1.1x to 25x faster (#8206).
  • Implement the algorithm to find the centroid(s) of a tree (#8089).
  • Set length threshold in FR and use np.clip (#8145).
  • Add panther++ (#4400).
  • maint: use nx.circulant_graph to generate Harary graphs (#8189).
  • ENH: add directed kwarg to edges_equal (#8192).
  • Optimizing Dijkstra's path construction for all targets case (#8218).
  • ENH: adds ISMAGS support for directed and multigraph with tests and refactor (#8274).
  • Dispatch classes such as nx.Graph(backend=...) (#7760).
  • ENH: Add is_perfect_graph using SPGT (follow-up to #8111) (#8318).
  • Add benchmark suite for shortest path algorithms on weighted graphs (#8059).
  • Adding Generalized Petersen Graph (#8147).

... (truncated)

Commits
  • bb9a6de Designate 3.6 release
  • 4369736 Fix sphinx warnings 3.6rc (#8352)
  • 6dbed05 FEAT: Add a describe method for some basic info about graphs (#8338)
  • 5fa842b Pin last value to 1.0 in cumulative_distribution to address floating-point ...
  • d302ea1 Adding @​amcandio as contributor (#8345)
  • 1c64369 DOC: Add warning about special GEXF reserved keywords. (#8343)
  • f26e6bf ENH: add normalize option for subgraph_centrality and its _exp version (#...
  • 79e113b Adding Generalized Petersen Graph (#8147)
  • 8b1c5a1 Bump actions/upload-artifact from 4 to 5 in the actions group (#8335)
  • e79901a Fix formatting for release docs. (#8336)
  • Additional commits viewable in compare view

Updates numpy from 2.2.3 to 2.3.5

Release notes

Sourced from numpy's releases.

2.3.5 (Nov 16, 2025)

NumPy 2.3.5 Release Notes

The NumPy 2.3.5 release is a patch release split between a number of maintenance updates and bug fixes. This release supports Python versions 3.11-3.14.

Contributors

A total of 10 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Aaron Kollasch +
  • Charles Harris
  • Joren Hammudoglu
  • Matti Picus
  • Nathan Goldbaum
  • Rafael Laboissière +
  • Sayed Awad
  • Sebastian Berg
  • Warren Weckesser
  • Yasir Ashfaq +

Pull requests merged

A total of 16 pull requests were merged for this release.

  • #29979: MAINT: Prepare 2.3.x for further development
  • #30026: SIMD, BLD: Backport FPMATH mode on x86-32 and filter successor...
  • #30029: MAINT: Backport write_release.py
  • #30041: TYP: Various typing updates
  • #30059: BUG: Fix np.strings.slice if stop=None or start and stop >= len...
  • #30063: BUG: Fix np.strings.slice if start > stop
  • #30076: BUG: avoid negating INT_MIN in PyArray_Round implementation (#30071)
  • #30090: BUG: Fix resize when it contains references (#29970)
  • #30129: BLD: update scipy-openblas, use -Dpkg_config_path (#30049)
  • #30130: BUG: Avoid compilation error of wrapper file generated with SWIG...
  • #30157: BLD: use scipy-openblas 0.3.30.7 (#30132)
  • #30158: DOC: Remove nonexistent order parameter docs of ma.asanyarray...
  • #30185: BUG: Fix check of PyMem_Calloc return value. (#30176)
  • #30217: DOC: fix links for newly rebuilt numpy-tutorials site
  • #30218: BUG: Fix build on s390x with clang (#30214)
  • #30237: ENH: Make FPE blas check a runtime check for all apple arm systems

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.

... (truncated)

Commits
  • c3d60fc Merge pull request #30238 from charris/prepare-2.3.5
  • 11451fa REL: Prepare for the NumPy 2.3.5 release
  • eab5bd4 Merge pull request #30237 from charris/backport-30102
  • 7cea31a Fixup merge of multiarraymodule.c
  • b898173 Update numpy/_core/src/common/blas_utils.h
  • f755483 Report FPE ignoring in matmul in show_runtime()
  • c47116f Move test to Python
  • bd7b93f ooops, needs to be a calloc of course.
  • 83a1517 Guard for HAVE_CBLAS and always compile the helpers
  • ab680ef ENH: Make FPE blas check a runtime check for all arm systems
  • 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

Deprecations

Documentation

Dependencies

... (truncated)

Commits

Updates plotly from 6.2.0 to 6.5.0

Release notes

Sourced from plotly's releases.

v6.5.0

Updated

  • Update plotly.js from version 3.2.0 to version 3.3.0. See the plotly.js release notes for more information. [#5421]. Notable changes include:
    • Add hovertemplate for candlestick and ohlc traces [#7619]

Fixed

  • Fix bug where numpy datetime contained in Python list was converted to integer [#5415]

Full Changelog: plotly/plotly.py@v6.4.0...v6.5.0

v6.4.0

Updated

  • Update plotly.js from version 3.1.1 to version 3.2.0. See the plotly.js release notes for more information. [#5357]. Notable changes include:
    • Add hovertemplatefallback and texttemplatefallback attributes [#7577]
    • Add "SI extended" formatting rule for tick exponents on axis labels, allowing values to be displayed with extended SI prefixes (e.g., femto, pico, atto) [#7249]

Deprecated

  • Deprecate create_hexbin_mapbox in favor of create_hexbin_map, update related function calls [5358], with thanks to @​ajlien for the contribution!

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 [

@dependabot
Bump the pip group across 1 directory with 28 updates
b09863f 
Bumps the pip group with 28 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` | `3.8.1` |
| [certifi](https://github.com/certifi/python-certifi) | `2025.7.14` | `2025.11.12` |
| [cryptography](https://github.com/pyca/cryptography) | `45.0.5` | `46.0.3` |
| [idna](https://github.com/kjd/idna) | `3.10` | `3.11` |
| [jsonschema](https://github.com/python-jsonschema/jsonschema) | `4.25.0` | `4.25.1` |
| [markdown](https://github.com/Python-Markdown/markdown) | `3.8.2` | `3.10` |
| [markupsafe](https://github.com/pallets/markupsafe) | `3.0.2` | `3.0.3` |
| [networkx](https://github.com/networkx/networkx) | `3.4.2` | `3.6` |
| [numpy](https://github.com/numpy/numpy) | `2.2.3` | `2.3.5` |
| [pillow](https://github.com/python-pillow/Pillow) | `11.3.0` | `12.0.0` |
| [plotly](https://github.com/plotly/plotly.py) | `6.2.0` | `6.5.0` |
| [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` | `1.16.3` |
| [ipython](https://github.com/ipython/ipython) | `8.33.0` | `9.7.0` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.7` | `8.1.8` |
| [pandas](https://github.com/pandas-dev/pandas) | `2.3.1` | `2.3.3` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.13.2` | `4.15.4` |
| [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` | `1.7.2` |
| [tornado](https://github.com/tornadoweb/tornado) | `6.5.1` | `6.5.2` |
| [coverage](https://github.com/coveragepy/coveragepy) | `7.10.1` | `7.12.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.4.1` | `9.0.1` |
| [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` | `0.14.7` |



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 3.8.1
- [Changelog](https://github.com/bokeh/bokeh/blob/3.8.1/docs/CHANGELOG)
- [Commits](bokeh/bokeh@3.6.2...3.8.1)

Updates `certifi` from 2025.7.14 to 2025.11.12
- [Commits](certifi/python-certifi@2025.07.14...2025.11.12)

Updates `cryptography` from 45.0.5 to 46.0.3
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@45.0.5...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 4.25.0 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@v4.25.0...v4.25.1)

Updates `markdown` from 3.8.2 to 3.10
- [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...3.10.0)

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 3.6
- [Release notes](https://github.com/networkx/networkx/releases)
- [Commits](networkx/networkx@networkx-3.4.2...networkx-3.6)

Updates `numpy` from 2.2.3 to 2.3.5
- [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...v2.3.5)

Updates `pillow` from 11.3.0 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@11.3.0...12.0.0)

Updates `plotly` from 6.2.0 to 6.5.0
- [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...v6.5.0)

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

Updates `ipython` from 8.33.0 to 9.7.0
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](ipython/ipython@8.33.0...9.7.0)

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 2.3.3
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v2.3.1...v2.3.3)

Updates `pymongo` from 4.13.2 to 4.15.4
- [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...4.15.4)

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

Updates `tornado` from 6.5.1 to 6.5.2
- [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst)
- [Commits](tornadoweb/tornado@v6.5.1...v6.5.2)

Updates `coverage` from 7.10.1 to 7.12.0
- [Release notes](https://github.com/coveragepy/coveragepy/releases)
- [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.10.1...7.12.0)

Updates `pytest` from 8.4.1 to 9.0.1
- [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...9.0.1)

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 0.14.7
- [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...0.14.7)

---
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: 3.8.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: certifi
  dependency-version: 2025.11.12
  dependency-type: direct:production
  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-patch
  dependency-group: pip
- dependency-name: markdown
  dependency-version: '3.10'
  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'
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: numpy
  dependency-version: 2.3.5
  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: 6.5.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  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: 1.16.3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: ipython
  dependency-version: 9.7.0
  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: 2.3.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: pymongo
  dependency-version: 4.15.4
  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: 1.7.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: tornado
  dependency-version: 6.5.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: pip
- dependency-name: coverage
  dependency-version: 7.12.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: pip
- dependency-name: pytest
  dependency-version: 9.0.1
  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: 0.14.7
  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 Dec 1, 2025
@sonarqubecloud
Copy link

sonarqubecloud bot commented Dec 1, 2025

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

@dependabot @github
Copy link
Contributor Author

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-63cef11d09 branch January 1, 2026 18:01
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.

1 participant