[dependabot]

Bumps the pip-minor-patch group with 3 updates in the /.github directory: dnspython, onnx and requests.
Bumps the pip-minor-patch group with 1 update in the /agents/molecule-visualization/tools/molecule-visualization directory: plotly.

Updates dnspython from 2.8.0 to 2.9.0

Release notes

Sourced from dnspython's releases.

dnspython 2.9.0

This release fixes a potential excessive CPU consumption issue. Thanks to Evgenios Gkritsis, Constantinos Patsakis, and George Stergiopoulos, for discovering and reporting this issue.

See What's New for details.

The minimum supported version of Python is 3.11.

My thanks to the many people who have contributed to this release. Also thanks to my co-maintainers: Nicki Křížek, Petr Špaček, and Brian Wellington.

This release was published to PyPI using Trusted Publishing.

Changelog

Sourced from dnspython's changelog.

2.9.0

• Decompression chain length is limited to 16. Prior to this change, a maliciously crafted DNS message could cause dns.name.from_wire_parser() to use excessive CPU for DNS name decompression. Applications which processed untrusted DNS wire form messages with dnspython could be degraded or DoS'd by the extra CPU use required.

  Thanks to Evgenios Gkritsis, Constantinos Patsakis, and George Stergiopoulos for finding and reporting this issue.

  See GHSA-45c3-73f7-pv4m

• Httpx2 has replaced httpx for HTTPS TCP connections.

• The minimum supported Python version is now 3.11.

• DNSSEC now supports ML-DSA-44, a post-quantum signature algorithm.

• The NSEC3 Next Hashed Owner Name in presentation format is now decoded as base32hex (RFC 5155 Section 1.3, RFC 4648 Extended Hex Alphabet). The letters W, X, Y, and Z are not in that alphabet; they used to be accepted and silently decoded to a different owner name, so to_text of the result did not match the input. They are now rejected.

• The NID and L64 node/locator ids in presentation format are now rejected when a group contains anything other than hex digits. A sign or underscore, which int() silently accepts, produced a record whose text form did not parse back the same way (RFC 6742).

• Rdata of a known type in the generic \# syntax, such as an NS record in a zone file, no longer fails to parse when it contains a name under the origin. Its names are relativized as in the type's own text form.

• The SVCB and HTTPS ech parameter value must now be an ECHConfigList with a correct length prefix and at least 4 octets of content (RFC 9848, RFC 9849). The individual ECHConfig structures are not checked.

• SVCB and HTTPS SvcParamKeys in presentation format, including those listed in mandatory, must now be spelled as RFC 9460 requires: 1-63 lowercase letters, digits, or hyphens. Uppercase keys such as ALPN and keys with underscores such as no_default_alpn are rejected.

• SVCB and HTTPS presentation format parsing now follows the escaping rules of RFC 9460. SvcParamKeys may not contain escapes (e.g. \097lpn=h2), and in comma-separated values (alpn, docpath) only \, and \\ are valid escapes after character-string decoding (e.g. alpn="h2\\x" is rejected).

... (truncated)

Commits

• e790c8f add missing test file
• b72af67 CI release branch update
• bdd62fe release prep
• bafc963 Merge branch 'decompression-limit'
• c5fecf5 release tidying
• c7686f3 update dependencies
• 3c855c8 more type lint
• 52815c9 type lint
• f563427 lint
• b485e46 Limit decompression to a chain length of at most 16 pointers.
• Additional commits viewable in compare view

Updates onnx from 1.23.0 to 1.23.2

Release notes

Sourced from onnx's releases.

Release 1.23.2

Bug fix Release 1.23.2

What's Changed

Other Changes

• Version Miss for Opset 28 by @​sfatimar in onnx/onnx#8544

Full Changelog: onnx/onnx@v1.23.1...v1.23.2

Release 1.23.1

This patch release includes important bug fixes to ONNX build.

What's Changed

• Validate offset in save_external_data function PR Raised onnx/onnx#8260
• for Issue: onnx/onnx#8260.

Full Changelog: onnx/onnx@v1.23.0...v1.23.1

Commits

• e1ac8e7 Version Miss for Opset 28 (#8544)
• ecfb5f0 Rel 1.23.1 cherrypicks (#8483)
• See full diff in compare view

Updates requests from 2.32.5 to 2.34.2

Release notes

Sourced from requests's releases.

v2.34.2

2.34.2 (2026-05-14)

• Moved headers input type back to Mapping to avoid invariance issues with MutableMapping and inferred dict types. Users calling Request.headers.update() may need to narrow typing in their code. (#7441)

Full Changelog: https://github.com/psf/requests/blob/main/HISTORY.md#2342-2026-05-14

v2.34.1

2.34.1 (2026-05-13)

Bugfixes

• Widened json input type from dict and list to Mapping and Sequence. (#7436)
• Changed headers input type to MutableMapping and removed None from Request.headers typing to improve handling for users. (#7431)
• Response.reason moved from str | None to str to improve handling for users. (#7437)
• Fixed a bug where some bodies with custom __getattr__ implementations weren't being properly detected as Iterables. (#7433)

New Contributors

• @​k223kim made their first contribution in psf/requests#7433

Full Changelog: https://github.com/psf/requests/blob/main/HISTORY.md#2341-2026-05-13

v2.34.0

2.34.0 (2026-05-11)

Announcements

• Requests 2.34.0 introduces inline types, replacing those provided by typeshed. Public API types should be fully compatible with mypy, pyright, and ty. We believe types are comprehensive but if you find issues, please report them to the pinned tracking issue.

  Special thanks to @​bastimeyer, @​cthoyt, @​edgarrmondragon, and @​srittau for helping review and test the types ahead of the release. (#7272)

Improvements

• Digest Auth hashing algorithms have added usedforsecurity=False to clarify security considerations. (#7310)
• Requests added support for Python 3.15 based on beta1. Downstream projects should be able to start testing prior to its release in October. (#7422)
• Requests added support for Python 3.14t. (#7419)

Bugfixes

• Response.history no longer contains a reference to itself, preventing accidental looping when traversing the history list. (#7328)
• Requests no longer performs greedy matching on no_proxy domains. The

... (truncated)

Changelog

Sourced from requests's changelog.

2.34.2 (2026-05-14)

• Moved headers input type back to Mapping to avoid invariance issues with MutableMapping and inferred dict types. Users calling Request.headers.update() may need to narrow typing in their code. (#7441)

2.34.1 (2026-05-13)

Bugfixes

• Widened json input type from dict and list to Mapping and Sequence. (#7436)
• Changed headers input type to MutableMapping and removed None from Request.headers typing to improve handling for users. (#7431)
• Response.reason moved from str | None to str to improve handling for users. (#7437)
• Fixed a bug where some bodies with custom __getattr__ implementations weren't being properly detected as Iterables. (#7433)

2.34.0 (2026-05-11)

Announcements

• Requests 2.34.0 introduces inline types, replacing those provided by typeshed. Public API types should be fully compatible with mypy, pyright, and ty. We believe types are comprehensive but if you find issues, please report them to the pinned tracking issue.

  Special thanks to @​bastimeyer, @​cthoyt, @​edgarrmondragon, and @​srittau for helping review and test the types ahead of the release. (#7272)

Improvements

• Digest Auth hashing algorithms have added usedforsecurity=False to clarify security considerations. (#7310)
• Requests added support for Python 3.15 based on beta1. Downstream projects should be able to start testing prior to its release in October. (#7422)
• Requests added support for Python 3.14t. (#7419)

Bugfixes

• Response.history no longer contains a reference to itself, preventing accidental looping when traversing the history list. (#7328)
• Requests no longer performs greedy matching on no_proxy domains. The proxy_bypass implementation has been updated with CPython's fix from bpo-39057. (#7427)
• Requests no longer incorrectly strips duplicate leading slashes in URI paths. This should address user issues with specific presigned URLs. Note the full fix requires urllib3 2.7.0+. (#7315)

... (truncated)

Commits

• 6e83187 v2.34.2
• 84d10f0 Move Request.headers back to Mapping (#7441)
• b7b549b v2.34.1
• e511bc7 Fix mutability issues with headers input types (#7431)
• 5691f59 Update JsonType containers to read-based collections (#7436)
• 2144213 Constrain Response.reason to str (#7437)
• 6404f34 Fix prepare_body stream detection for __getattr__-based file wrappers (#7...
• 0b401c7 v2.34.0
• 86b378d Align Session.get parameters with requests.get (#7429)
• a4f9a59 Port bpo-39057 to Requests (#7427)
• Additional commits viewable in compare view

Updates plotly from 7.0.0 to 7.1.0

Release notes

Sourced from plotly's releases.

v7.1.0

Added

• Support marginal_x/marginal_y="heatmap" in density_heatmap, drawing a single-row/column heatmap strip in the margin colored by the same z/histfunc aggregate as the main plot and sharing its color scale [#5706], with thanks to @​lucasjamar for the contribution!
• Add support for custom tick values in mpl_to_plotly when the matplotlib tick positions don't follow an arithmetic progression, including custom tick labels and tick values on date axes [#5262], with thanks to @​robertoffmoura for the contribution!

Fixed

• Fix Plotly Express treating unsigned integer columns (uint8, uint16, uint32, uint64) in pandas DataFrames as categorical, which caused px.bar and other functions to pick the wrong orientation and render unexpected plots [#4291, #4344], with thanks to @​Belagum for the contribution!
• Fix mpl_to_plotly not setting paper_bgcolor and plot_bgcolor from the matplotlib figure and axes backgrounds, so converted figures match the source figure's background colors [#5285], with thanks to @​robertoffmoura for the contribution!
• Fix rendering issue causing a too-large div when calling Figure.show() in Google Colab [#5718]
• Fix the sphinx-gallery scraper so that it generates thumbnails for figures shown with fig.show() or displayed as the last expression of a code block [#5701], with thanks to @​larsoner for the contribution!
  • The scaper now warns once (instead of failing the build) when static image export is unavailable
• The sphinx-gallery scraper no longer scrapes files belonging to other examples during parallel builds [#5701], with thanks to @​larsoner for the contribution!

Updated

• Update plotly.js from version 4.0.0 to version 4.1.1 [#5722, #5730]. See the plotly.js release notes for v4.1.0 and v4.1.1 for details. Notable changes include:
  • Add an opt-in modebar button for downloading Plotly figures as JSON [#7990, #8022]
  • Add legend.groupdoubleclick to set the group behavior for a legend double-click [#7997]
  • Increase default double-click delay threshold to 500ms (from 300) [#8014]
  • Fix issue with per-point marker color for hover labels in scattergl, quiver traces [#8027]
  • Update maplibre-gl to v6 to address CVE-2026-85061 [#8035]
    • Note: Safari 15, Chrome 56, Firefox 51 and later are now required for map traces
• Update hex_to_rgb function to raise error for invalid-length hex codes, and emit warning for hex codes containing alpha [#5729], with thanks to @​dylanpulver for the contribution!

Changelog

Sourced from plotly's changelog.

[7.1.0] - 2026-09-15

Added

• Support marginal_x/marginal_y="heatmap" in density_heatmap, drawing a single-row/column heatmap strip in the margin colored by the same z/histfunc aggregate as the main plot and sharing its color scale [#5706], with thanks to @​lucasjamar for the contribution!
• Add support for custom tick values in mpl_to_plotly when the matplotlib tick positions don't follow an arithmetic progression, including custom tick labels and tick values on date axes [#5262], with thanks to @​robertoffmoura for the contribution!

Fixed

• Fix Plotly Express treating unsigned integer columns (uint8, uint16, uint32, uint64) in pandas DataFrames as categorical, which caused px.bar and other functions to pick the wrong orientation and render unexpected plots [#4291, #4344], with thanks to @​Belagum for the contribution!
• Fix mpl_to_plotly not setting paper_bgcolor and plot_bgcolor from the matplotlib figure and axes backgrounds, so converted figures match the source figure's background colors [#5285], with thanks to @​robertoffmoura for the contribution!
• Fix rendering issue causing a too-large div when calling Figure.show() in Google Colab [#5718]
• Fix the sphinx-gallery scraper so that it generates thumbnails for figures shown with fig.show() or displayed as the last expression of a code block [#5701], with thanks to @​larsoner for the contribution!
  • The scaper now warns once (instead of failing the build) when static image export is unavailable
• The sphinx-gallery scraper no longer scrapes files belonging to other examples during parallel builds [#5701], with thanks to @​larsoner for the contribution!

Updated

• Update plotly.js from version 4.0.0 to version 4.1.1 [#5722, #5730]. See the plotly.js release notes for v4.1.0 and v4.1.1 for details. Notable changes include:
  • Add an opt-in modebar button for downloading Plotly figures as JSON [#7990, #8022]
  • Add legend.groupdoubleclick to set the group behavior for a legend double-click [#7997]
  • Increase default double-click delay threshold to 500ms (from 300) [#8014]
  • Fix issue with per-point marker color for hover labels in scattergl, quiver traces [#8027]
  • Update maplibre-gl to v6 to address CVE-2026-85061 [#8035]
    • Note: Safari 15, Chrome 56, Firefox 51 and later are now required for map traces
• Update hex_to_rgb function to raise error for invalid-length hex codes, and emit warning for hex codes containing alpha [#5729], with thanks to @​dylanpulver for the contribution!

Commits

• 243bfd0 version changes for v7.1.0
• 9b3c4da Merge pull request #5729 from dylanpulver/hex-to-rgb-rejects-invalid-length
• 3aa898c Merge branch 'main' into hex-to-rgb-rejects-invalid-length
• a93dcc0 update changelog
• 7c85d48 add test for hex_to_rgb 4- and 8-character hex codes
• 80a94ec accept 4- and 8- character hex codes with a warning
• ac78b8b Merge pull request #5726 from Belagum/px-unsigned-int-continuous
• 1cf7756 Merge branch 'main' into px-unsigned-int-continuous
• ec79917 add attribution
• ac7bc28 edit changelog entry
• Additional commits viewable in compare view

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