Bump the python-dependencies group across 1 directory with 2 updates

[dependabot]

Updates the requirements on uvicorn and biopython to permit the latest version.
Updates uvicorn to 0.52.3

Release notes

Sourced from uvicorn's releases.

Version 0.52.3

Changed

• Update zttp to 0.0.24 and use its combined receive path, improving HTTP/1.1 request parsing performance (#3067)

Full Changelog: Kludex/uvicorn@0.52.2...0.52.3

Changelog

Sourced from uvicorn's changelog.

0.52.3 (August 13, 2026)

Changed

• Update zttp to 0.0.24 and use its combined receive path, improving HTTP/1.1 request parsing performance (#3067)

0.52.2 (August 13, 2026)

Fixed

• Update zttp to 0.0.22, fixing bodyless request receives and improving HTTP/1 request parsing performance (#3063)

0.52.1 (August 1, 2026)

Fixed

• Complete the closing handshake on server-initiated WebSocket closes in the websockets-sansio and wsproto implementations, waiting for the client's close reply with a 10 second timeout instead of resetting the connection (#3053)
• Add missing write flow control to the websockets-sansio implementation, preventing data truncation on server-initiated closes with large in-flight payloads (#3048)
• Handle connection loss while a WebSocket write is waiting on backpressure (#3050)
• Remove duplicate Content-Type and Content-Length headers from WebSocket denial responses on the websockets-sansio implementation, and deliver non-UTF-8 denial bodies intact (#3041)

0.52.0 (July 29, 2026)

This release adds an experimental HTTP/1.1 implementation backed by zttp, a sans-IO HTTP parser I've been developing on the side: a core written in Zig, with bindings to Python. It has been running under a fuzzer for some weeks now, and has been through multiple rounds of security auditing.

It is still experimental, so don't put it in front of production traffic yet. Try it with --http zttp, and please send any feedback to the issue tracker.

Added

• Add an experimental zttp HTTP/1.1 implementation, selectable with --http zttp (#2979)

Fixed

• Keep non-ASCII WebSocket request headers intact with websockets 17.0, which encodes them with ISO-8859-1 (#3036)

0.51.0 (July 8, 2026)

Added

• Restart workers one at a time on SIGHUP, bringing each replacement up before retiring the old worker, so reloads no longer drop requests (#3025)

Removed

• Remove colorama from the standard extra (#3027)

0.50.2 (July 6, 2026)

Fixed

• Require websockets>=13.0, which the default websockets-sansio implementation needs (#3021)

... (truncated)

Commits

• a68da60 Version 0.52.3 (#3068)
• 6e3bb4c Use zttp 0.0.24 fast receive path (#3067)
• 2a5ff18 Version 0.52.2 (#3066)
• 1920297 Update zttp to 0.0.22 (#3063)
• 5c560da chore(deps): bump pymdown-extensions from 11.0 to 11.0.1 (#3061)
• See full diff in compare view

Updates biopython to 1.88

Changelog

Sourced from biopython's changelog.

6 August 2026: Biopython 1.88

This release of Biopython supports Python 3.10, 3.11, 3.12, 3.13, 3.14 and the Python 3.15 release candidate. It has also been tested on PyPy3.10 v7.3.19. Python 3.10 is approaching end of life, our support for it is now deprecated.

The primary driver for this release is a security fix to remove the use of Python's built-in function eval following a report by email from independent security researcher Anand Patil. This demonstrated arbitrary code execution via the Bio.Nexus NEXUS parser.

Additionally, a number of small bugs and typos have been fixed with additions to the test suite and type annotations.

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

• Al Fattah Suyadi (first contribution)
• Laura Piñero Roig (first contribution)
• Marcus Campbell (first contribution)
• Michiel de Hoon
• Peter Cock

30 March 2026: Biopython 1.87

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.

Migrated from setup.py to pyproject.toml for packaging configuration.

Addressed security issue CVE-2025-68463 in Bio.Entrez.Parser if parsing untrusted files.

Additionally, a number of small bugs and typos have been fixed with additions to the test suite and type annotations.

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

• Manuel Lera-Ramirez
• Michiel de Hoon
• Peter Cock
• Sebastian Pipping
• Timothy Dennis (first contribution)
• Ziyan Rao (first contribution)

28 October 2025: Biopython 1.86

... (truncated)

Commits

• See full diff in compare view

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