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Bump biopython from 1.87 to 1.88 - #120

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Aug 10, 2026
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Bump biopython from 1.87 to 1.88#120
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dependabot/uv/biopython-1.88

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Bumps biopython from 1.87 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
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Bumps [biopython](https://github.com/biopython/biopython) from 1.87 to 1.88.
- [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst)
- [Commits](https://github.com/biopython/biopython/commits)

---
updated-dependencies:
- dependency-name: biopython
  dependency-version: '1.88'
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Aug 10, 2026
@Donaim
Donaim merged commit 05a304a into master Aug 10, 2026
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@dependabot
dependabot Bot deleted the dependabot/uv/biopython-1.88 branch August 10, 2026 16:21
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