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build(deps): bump the uv group across 2 directories with 3 updates - #30

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build(deps): bump the uv group across 2 directories with 3 updates#30
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Bumps the uv group with 1 update in the /skills/biomaster-workflows/repo directory: pillow.
Bumps the uv group with 3 updates in the /skills/biomcp-server/repo directory: pillow, cryptography and mcp.

Updates pillow from 11.1.0 to 12.3.0

Release notes

Sourced from pillow's releases.

12.3.0

https://pillow.readthedocs.io/en/stable/releasenotes/12.3.0.html

Removals

Documentation

Dependencies

Testing

... (truncated)

Changelog

Sourced from pillow's changelog.

Changelog (Pillow)

Commits
  • bb1d8e8 12.3.0 version bump
  • e63fc48 Add release notes for SBOM and performance improvements (#9747)
  • 13b701b Add release notes for #9679
  • 5564ca7 List methods
  • a0920fd Speed up ImageChops operations (#9738)
  • 07e9a6c Speed up Image.filter() (#9736)
  • a94578c Speed up Image.getchannel(), Image.merge(), Image.putalpha() and `Image...
  • 53e02c4 Speed up Image.fill(), Image.linear_gradient() and `Image.radial_gradient...
  • af03747 Speed up Image.resample() (#9739)
  • 5c9ca56 Speed up alpha_composite, matrix, negative, quantize (#9740)
  • Additional commits viewable in compare view

Updates pillow from 11.3.0 to 12.3.0

Release notes

Sourced from pillow's releases.

12.3.0

https://pillow.readthedocs.io/en/stable/releasenotes/12.3.0.html

Removals

Documentation

Dependencies

Testing

... (truncated)

Changelog

Sourced from pillow's changelog.

Changelog (Pillow)

Commits
  • bb1d8e8 12.3.0 version bump
  • e63fc48 Add release notes for SBOM and performance improvements (#9747)
  • 13b701b Add release notes for #9679
  • 5564ca7 List methods
  • a0920fd Speed up ImageChops operations (#9738)
  • 07e9a6c Speed up Image.filter() (#9736)
  • a94578c Speed up Image.getchannel(), Image.merge(), Image.putalpha() and `Image...
  • 53e02c4 Speed up Image.fill(), Image.linear_gradient() and `Image.radial_gradient...
  • af03747 Speed up Image.resample() (#9739)
  • 5c9ca56 Speed up alpha_composite, matrix, negative, quantize (#9740)
  • Additional commits viewable in compare view

Updates cryptography from 45.0.6 to 48.0.1

Changelog

Sourced from cryptography's changelog.

48.0.1 - 2026-06-09


* Updated Windows, macOS, and Linux wheels to be compiled with OpenSSL 4.0.1.

.. _v48-0-0:


48.0.0 - 2026-05-04

  • BACKWARDS INCOMPATIBLE: Support for Python 3.8 has been removed. cryptography now requires Python 3.9 or later.

  • BACKWARDS INCOMPATIBLE: Loading an X.509 CRL whose inner TBSCertList.signature algorithm does not match the outer signatureAlgorithm now raises ValueError. Previously, such CRLs were parsed successfully and only rejected during signature validation.

  • Added support for :doc:/hazmat/primitives/asymmetric/mlkem and :doc:/hazmat/primitives/asymmetric/mldsa when using OpenSSL 3.5.0 or later, in addition to the existing AWS-LC and BoringSSL support. This means post-quantum algorithms are now available to users of our wheels.

    • Note: Going forward, we do not guarantee that all functionality in cryptography will be available when building against OpenSSL. See :doc:/statements/state-of-openssl for more information.

.. _v47-0-0:

47.0.0 - 2026-04-24


* Support for Python 3.8 is deprecated and will be removed in the next
  ``cryptography`` release.
* **BACKWARDS INCOMPATIBLE:** Support for binary elliptic curves
  (``SECT*`` classes) has been removed. These curves are rarely used and
  have additional security considerations that make them undesirable.
* **BACKWARDS INCOMPATIBLE:** Support for OpenSSL 1.1.x has been removed.
  OpenSSL 3.0.0 or later is now required. LibreSSL, BoringSSL, and AWS-LC
  continue to be supported.
* **BACKWARDS INCOMPATIBLE:** Dropped support for LibreSSL < 4.1.
* **BACKWARDS INCOMPATIBLE:** Loading keys with unsupported algorithms or
  keys with unsupported explicit curve encodings now raises
  :class:`~cryptography.exceptions.UnsupportedAlgorithm` instead of
  ``ValueError``. This change affects
  :func:`~cryptography.hazmat.primitives.serialization.load_pem_private_key`,
  :func:`~cryptography.hazmat.primitives.serialization.load_der_private_key`,
  :func:`~cryptography.hazmat.primitives.serialization.load_pem_public_key`,
  :func:`~cryptography.hazmat.primitives.serialization.load_der_public_key`,
  and :meth:`~cryptography.x509.Certificate.public_key` when called on
  certificates with unsupported public key algorithms.
</tr></table>

... (truncated)

Commits

Updates mcp from 1.12.3 to 1.28.1

Release notes

Sourced from mcp's releases.

v1.28.0

Deprecations

Two API surfaces now emit DeprecationWarning ahead of their removal in v2. Nothing is removed in 1.x, and the warnings fire only when the deprecated API is called - importing the modules stays silent.

  • WebSocket transport - mcp.client.websocket.websocket_client and mcp.server.websocket.websocket_servermodelcontextprotocol/typescript-sdk#1783
  • Experimental tasks API - ClientSession.experimental, Server.experimental, ServerSession.experimental, and the experimental_task_handlers= kwarg on ClientSession. Tasks (SEP-1686) were removed from the MCP specification and are expected to return as a separate MCP extension.

If your test suite runs with filterwarnings = ["error"] and exercises these paths, add a scoped ignore such as ignore:The experimental tasks API is deprecated:DeprecationWarning or ignore:The WebSocket .* transport is deprecated:DeprecationWarning.

See #2828 for full details.

What's Changed

New Contributors

Full Changelog: modelcontextprotocol/python-sdk@v1.27.2...v1.28.0

v1.27.2

What's Changed

Full Changelog: modelcontextprotocol/python-sdk@v1.27.1...v1.27.2

v1.27.1

What's Changed

Full Changelog: modelcontextprotocol/python-sdk@v1.27.0...v1.27.1

v1.27.0

What's Changed

... (truncated)

Commits
  • 777b8d0 [v1.x] Support TransportSecuritySettings in the WebSocket server transport (#...
  • 4720467 [v1.x] Set Development Status classifier to Production/Stable (#2976)
  • 6df3d73 [v1.x] Buffer per-request StreamableHTTP streams; store priming event before ...
  • 32d3290 [v1.x] Pass a list to parametrize in test_docs_examples (pytest 9.1.0 compat)...
  • 0dca751 [v1.x] Deflake the child process cleanup tests (#2839)
  • 52258a9 [v1.x] Add a v2 status banner to the README (#2835)
  • b8f4917 [v1.x] Deprecate the WebSocket transport and the experimental tasks entry poi...
  • 2309e5e fix: omit null optional fields from task result payloads (#2809)
  • 494eb11 [v1.x] Support Python 3.14 (#2769)
  • 6213787 [v1.x] Scope experimental tasks to the session that created them (#2720)
  • Additional commits viewable in compare view

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@dependabot
build(deps): bump the uv group across 2 directories with 3 updates
95e9f96 
Bumps the uv group with 1 update in the /skills/biomaster-workflows/repo directory: [pillow](https://github.com/python-pillow/Pillow).
Bumps the uv group with 3 updates in the /skills/biomcp-server/repo directory: [pillow](https://github.com/python-pillow/Pillow), [cryptography](https://github.com/pyca/cryptography) and [mcp](https://github.com/modelcontextprotocol/python-sdk).


Updates `pillow` from 11.1.0 to 12.3.0
- [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...12.3.0)

Updates `pillow` from 11.3.0 to 12.3.0
- [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...12.3.0)

Updates `cryptography` from 45.0.6 to 48.0.1
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@45.0.6...48.0.1)

Updates `mcp` from 1.12.3 to 1.28.1
- [Release notes](https://github.com/modelcontextprotocol/python-sdk/releases)
- [Changelog](https://github.com/modelcontextprotocol/python-sdk/blob/main/RELEASE.md)
- [Commits](modelcontextprotocol/python-sdk@v1.12.3...v1.28.1)

---
updated-dependencies:
- dependency-name: pillow
  dependency-version: 12.3.0
  dependency-type: direct:production
  dependency-group: uv
- dependency-name: pillow
  dependency-version: 12.3.0
  dependency-type: indirect
  dependency-group: uv
- dependency-name: cryptography
  dependency-version: 48.0.1
  dependency-type: indirect
  dependency-group: uv
- dependency-name: mcp
  dependency-version: 1.28.1
  dependency-type: indirect
  dependency-group: uv
...

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@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Jul 21, 2026
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