chore(deps): Bump the python-dependencies group across 1 directory with 5 updates

[dependabot]

Updates the requirements on ruff, matplotlib, numpy, mcp and cryptography to permit the latest version.
Updates ruff to 0.16.7

Release notes

Sourced from ruff's releases.

0.16.7

Release Notes

Released on 2026-09-10.

Preview features

• [ruff] Add rule for default values on method receivers (RUF077) (#26700)
• [ruff] Recognize re.prefixmatch (RUF039, RUF055) (#28311)

Bug fixes

• Alternate nested quotes inside format spec interpolations (#28259)
• [flake8-implicit-str-concat] Mark fix unsafe when it creates a docstring (ISC003) (#27981)
• [flake8-tidy-imports] Skip fixes for multi-member imports (TID254) (#26584)
• [pylint] Gate ImportCycleError on Python 3.15 (PLW0133) (#28310)

Rule changes

• Correct D211 and D203 rule conflict diagnostic (#28444)
• Recognize slice and frozendict generics (#28477)
• Stop defining __cached__ for Python 3.15 (#28476)
• [pyupgrade] Stop recommending removed typing.no_type_check_decorator (UP035) (#28475)

Performance

• Reuse parser name lookups when interning (#28399)
• Speed up inherited configuration resolution (#28299)

Documentation

• Fix line-length path in --config example (#28392)
• Remove the "Who’s Using Ruff?" list (#28455)

Other changes

• Embed archive checksums in the shell installer (#28281)

Contributors

• @​The-Compiler
• @​mdiniz97
• @​zsol
• @​gorewilliams
• @​RafaelJohn9
• @​qatcod
• @​zanieb
• @​MichaReiser
• @​ntBre
• @​charliermarsh

... (truncated)

Changelog

Sourced from ruff's changelog.

0.16.7

Released on 2026-09-10.

Preview features

• [ruff] Add rule for default values on method receivers (RUF077) (#26700)
• [ruff] Recognize re.prefixmatch (RUF039, RUF055) (#28311)

Bug fixes

• Alternate nested quotes inside format spec interpolations (#28259)
• [flake8-implicit-str-concat] Mark fix unsafe when it creates a docstring (ISC003) (#27981)
• [flake8-tidy-imports] Skip fixes for multi-member imports (TID254) (#26584)
• [pylint] Gate ImportCycleError on Python 3.15 (PLW0133) (#28310)

Rule changes

• Correct D211 and D203 rule conflict diagnostic (#28444)
• Recognize slice and frozendict generics (#28477)
• Stop defining __cached__ for Python 3.15 (#28476)
• [pyupgrade] Stop recommending removed typing.no_type_check_decorator (UP035) (#28475)

Performance

• Reuse parser name lookups when interning (#28399)
• Speed up inherited configuration resolution (#28299)

Documentation

• Fix line-length path in --config example (#28392)
• Remove the "Who’s Using Ruff?" list (#28455)

Other changes

• Embed archive checksums in the shell installer (#28281)

Contributors

• @​The-Compiler
• @​mdiniz97
• @​zsol
• @​gorewilliams
• @​RafaelJohn9
• @​qatcod
• @​zanieb
• @​MichaReiser
• @​ntBre
• @​charliermarsh
• @​nightt5879

... (truncated)

Commits

• b5dba86 Bump version to 0.16.7 (#28496)
• 5992d05 Install rustfmt before linting releases (#28495)
• 1713a1f ensure prepare release changes pass prek (#28488)
• 18cdbb4 use scoped token for release workflow (#28484)
• c3813a5 add a workflow for preparing releases (#28486)
• 00948c0 Remove the "Who’s Using Ruff?" list (#28455)
• 86a2eba [pyupgrade] Stop recommending removed typing.no_type_check_decorator (`UP...
• 609e184 Stop defining __cached__ for Python 3.15 (#28476)
• 859ff2f [ty] Track symlinked directory status in listings (#28482)
• 77f6538 Use paid GitHub-hosted runners for Linux (#28478)
• Additional commits viewable in compare view

Updates matplotlib to 3.11.2

Release notes

Sourced from matplotlib's releases.

REL: v3.11.2

This is the second bugfix release of the 3.11.x series.

This release contains several bug-fixes and adjustments:

• Speed up RGBA-stage image resampling
• Fix hexbin clipping in PDF output
• Fix \text with internal braces
• Fix some crashes and make some checks more robust to unlikely cases
• Fix frame skew when saving GIF animations with PillowWriter
• Fix HiDPI handling in Qt toolbar and WebAgg embeddings
• Fix ResizeEvent handling for TextBox
• Fix bug with PGF hatch linewidth and color
• Fix a bug with drawing an empty Collection
• Fix incorrect glyphs in Cairo backends
• Improve build system to prevent conflicts between wheels and system libraries

Commits

• d3ca917 REL: v3.11.2
• b76fea9 DOC: Set current version to 3.11.2
• 39c7f06 DOC: Prepare GitHub stats for 3.11.2
• 5dd13e3 Merge branch 'v3.11.1-doc' into release-3.11.2
• aa484be Merge branch 'v3.11.0-doc' into v3.11.1-doc
• 0e10f83 Merge pull request #32330 from meeseeksmachine/auto-backport-of-pr-32324-on-v...
• ebe947b Backport PR #32324: Don't force any diagnostics to be errors in bundled Harfbuzz
• 8f4b7c5 Merge pull request #32322 from meeseeksmachine/auto-backport-of-pr-32321-on-v...
• 93278ad Backport PR #32321: DOC: correct note about PyOS_InputHook
• b0aee78 Merge pull request #32319 from meeseeksmachine/auto-backport-of-pr-32305-on-v...
• Additional commits viewable in compare view

Updates numpy to 2.5.3

Release notes

Sourced from numpy's releases.

v2.5.3 (Sep 6, 2026)

NumPy 2.5.3 Release Notes

The NumPy 2.5.3 is a patch release that fixes bugs discovered after the 2.5.2 release. Apart from the usual bug and maintenance work, there are a number of StringDType related fixes for problems discovered during the ongoing string work in the main branch.

This release supports Python versions 3.12-3.15

Changes

• Casting a fixed-width byte string array (np.bytes_) to StringDType now raises TypeError when the bytes are not valid UTF-8. Previously the invalid bytes were stored as-is and later caused undefined behavior in string operations.

  (gh-32296)

• MaskedArray._fill_value would become stale when ufuncs that change dtype left the result holding a fill_value typed for the old dtype. The mismatch was silent until something later called _check_fill_value, such as .view(), and then a TypeError would be raised. Now, when the copied fill_value is no longer valid for the new dtype, fall back to the default fill_value for that dtype instead of propagating the stale value. This may raise a ComplexWarning if the fill_value is complex and the new dtype is real.

  (gh-32423)

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
• Iason Krommydas
• James Davies +
• Joren Hammudoglu
• Maanas Arora
• Matti Picus
• Nathan Goldbaum
• Shikhar Goel +
• Yeonho Kim +

Pull requests merged

A total of 27 pull requests were merged for this release.

• #32235: MAINT: Prepare 2.5.x for further development

... (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.

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

• dd88c0c Merge pull request #32511 from charris/prepare-2.5.3
• edcac6a REL: Prepare for the NumPy 2.5.3 release
• fd4d908 Merge pull request #32509 from charris/backport-32496
• 65bb1da BUG: fix crash in ufunc.resolve_dtypes with a Python scalar type (#32496)
• 294956e Merge pull request #32506 from charris/backport-32503
• 26428d9 DOC: fix scipy docs links in intersphinx mapping (#32507)
• 5fab1cb DOC: use static scipy doc site for intershpinx (#32503)
• 7beed2f Merge pull request #32481 from ngoldbaum/stringdtype-backport
• 8972f70 Merge pull request #32478 from charris/backport-32466
• ab1b589 Merge pull request #32477 from charris/backport-32423
• Additional commits viewable in compare view

Updates mcp to 2.2.0

Release notes

Sourced from mcp's releases.

v2.2.0

pip install -U mcp. Docs: https://py.sdk.modelcontextprotocol.io/

A few defaults changed in this release. If you run a server or client on 2.x, skim these first:

Behaviour changes

HTTP client redirects are only followed within the endpoint's origin (#3397)

• Client("https://..."), streamable_http_client and sse_client follow a redirect only if it stays on the same scheme, host and port (or upgrades http to https on the same host).
• A redirect anywhere else is not followed: the call fails with MCPError and the session stays usable (an SSE connect fails with httpx2.HTTPStatusError). If that other URL is the server you meant, use it as the endpoint URL.
• The follow_redirects setting on an httpx2.AsyncClient you pass in is no longer used for MCP requests, so you don't need it for the trailing-slash redirect any more.
• The OAuth providers apply the same rule to their own requests.

Idle Streamable HTTP sessions now expire (legacy <=2025-11-25 spec( (#3395)

• A stateful session with nothing in flight for 30 minutes is closed. The client's next request gets a 404 and it has to initialize again.
• Clients that keep the GET stream open (the SDK's Client does) are not affected. Neither are stateless servers or 2026-07-28 connections.
• A server also holds at most 10 000 sessions at once; beyond that, new sessions get a 503.
• To turn either off: mcp.run(transport="streamable-http", session_idle_timeout=None, max_sessions=None) (also on streamable_http_app() and run_streamable_http_async()).

The OAuth client checks the authorization server's issuer on the legacy path too (#3398)

• For servers without protected resource metadata, authorization server metadata whose issuer isn't the server's own origin is now rejected with OAuthFlowError: Authorization server metadata issuer mismatch. The protected-resource-metadata path has done this since 2.0.
• A 403 that isn't an insufficient_scope challenge is returned to the caller instead of retried.
• If protected resource metadata can't be fetched because of a 5xx/429, the flow now stops instead of falling back to the legacy endpoints.

Two new MCPDeprecationWarnings (#3435, #3447)

• ClientCredentialsOAuthProvider / PrivateKeyJWTOAuthProvider without issuer=. Pass your authorization server's issuer URL; 3.0 will require it.
• AuthSettings with resource_server_url set but validate_token_resource unset. Set it to True or False; 3.0 defaults it to True.
• Both keep working as before in 2.x; this mostly matters if your tests turn warnings into errors.

New

• AuthSettings.validate_token_resource: only accept tokens your TokenVerifier reports as issued for this server (#3447).
• issuer= on ClientCredentialsOAuthProvider and PrivateKeyJWTOAuthProvider (#3398).
• session_idle_timeout= and max_sessions= on the Streamable HTTP server entry points (#3395).

Fixes

• A client DELETE frees its session immediately, and a refused opening request no longer leaves a session behind (#2455, #3228, #3300).
• $refs in a tool's outputSchema resolve within that schema only; an unresolvable one surfaces as RuntimeError: Invalid schema for tool ... (#3394).

Known gaps

The tasks extension (SEP-2663), DPoP (SEP-1932) and the jwt-bearer grant are not implemented yet; https://github.com/modelcontextprotocol/python-sdk/blob/main/ROADMAP.md tracks them.

What's Changed

• Gate draft PRs too and rewrite the auto-close comment by @​maxisbey in modelcontextprotocol/python-sdk#3378
• Resolve tool output-schema references within the schema document only by @​maxisbey in modelcontextprotocol/python-sdk#3394
• Expire idle Streamable HTTP sessions by default and cap concurrent sessions by @​maxisbey in modelcontextprotocol/python-sdk#3395
• Validate the authorization server metadata issuer on every discovery path by @​maxisbey in modelcontextprotocol/python-sdk#3398

... (truncated)

Commits

• 9972c21 Replace RootModel wrappers with type aliases and TypeAdapter validation (#3470)
• fd66270 docs: refresh translations, and translate pages in parallel (#3458)
• 08a3bc8 docs: ask for AI disclosure on comments too (#3459)
• 7bb486a docs: stop presenting the in-memory client as the way to connect (#3443)
• 0c91368 Add AuthSettings.validate_token_resource to check a bearer token's resource (...
• 9771e6b Keep following a relative redirect when the endpoint URL carries userinfo (#3...
• a925e55 Bump the locked versions of eight dev and test dependencies (#3449)
• e8b9486 Bump pymdown-extensions from 11.0 to 11.0.1 (#3285)
• c6762e8 Follow redirects only within the MCP endpoint's origin (#3397)
• 5fd3abc Skip automatic docs previews for fork PRs and drop the setup-uv retry steps (...
• Additional commits viewable in compare view

Updates cryptography to 50.0.1

Changelog

Sourced from cryptography's changelog.

50.0.1 - 2026-08-25

* Updated Windows, macOS, and Linux wheels to be compiled with OpenSSL 4.0.2.
.. _v50-0-0:
50.0.0 - 2026-07-31

• SECURITY ISSUE: :func:~cryptography.hazmat.primitives.serialization.pkcs7.pkcs7_decrypt_der and its PEM and S/MIME variants no longer expose distinguishable errors or timing when unwrapping a RecipientInfo's encryptedKey, which could act as a Bleichenbacher oracle for callers that decrypt untrusted messages. A random key is now substituted on failure, as described in :rfc:3218. Credit to @​X1AOxiang for reporting the issue. CVE-2026-69247
• Deprecated Diffie-Hellman key exchange over finite fields (FFDH). Everything FFDH is deprecated, including the types in cryptography.hazmat.primitives.asymmetric.dh and loading FFDH keys or parameters with the key loading APIs. Users should migrate to a more modern key exchange algorithm.
• Added xof() class methods to :class:~cryptography.hazmat.primitives.hashes.SHAKE128 and :class:~cryptography.hazmat.primitives.hashes.SHAKE256 for constructing algorithm instances configured for use with :class:~cryptography.hazmat.primitives.hashes.XOFHash.
• The :mod:X.509 verification <cryptography.x509.verification> APIs are now considered stable and are subject to our API stability policy.
• Added the :doc:/cobblestone recipe, an implementation of the Cobblestone-128 and Cobblestone-256 instantiations of the C2SP chunked-encryption specification <https://c2sp.org/chunked-encryption>_ for streaming authenticated encryption of large messages.
• Parsing a Signed Certificate Timestamp list now rejects encodings that carry trailing bytes after the list or after an individual SCT, instead of silently ignoring them.
• Added support for using :class:~cryptography.x509.Name as a field type in the :doc:/hazmat/asn1/index module.
• Loading a public key or an EC private key now rejects DER where the subjectPublicKey (or EC publicKey) BIT STRING declares a non-zero number of unused bits, instead of silently ignoring it.
• Parsing a CRL entry's InvalidityDate extension now rejects a GeneralizedTime that carries fractional seconds or another non-DER form, matching the strict encoding already required for every other X.509 time field.
• :func:~cryptography.x509.ocsp.load_der_ocsp_request and :func:~cryptography.x509.ocsp.load_der_ocsp_response now reject a request or response whose version field is not v1, the only version defined by RFC 6960, matching the version validation already performed when loading

... (truncated)

Commits

• ffde75a bump for 50.0.1 + changelog (#15520)
• See full diff in compare view

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