Bump biopython from 1.79 to 1.88

[dependabot]

Bumps biopython from 1.79 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)

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