chore(deps): bump biopython from 1.84 to 1.87

[dependabot]

Bumps biopython from 1.84 to 1.87.

Changelog

Sourced from biopython's changelog.

30 March 2026: Biopython 1.87

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:

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

28 October 2025: Biopython 1.86

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.

Bio.SearchIO now supports parsing the tabular and plain text output of Infernal <http://eddylab.org/infernal/> (v1.0.0+) RNA search tool. The format names are infernal-tab and infernal-text.

The default value of the gap score of a PairwiseAligner object was changed in this release. Previously, for consistency with Bio.pairwise2, the default value for gap score was 0. However, this means that a mismatch, an insertion followed by a deletion, and a deletion followed by an insertion all get assigned a score of 0. The aligner then finds a large number of alignments that are logically the same, but have trivial differences between them. For example, aligning AAACAAA to AAAGAAA previously yielded the following three alignments, all with score 6::

 AAACAAA        AAAC-AAA        AAA-CAAA
 AAAGAAA        AAA-GAAA        AAAG-AAA

With the new default parameter for the gap score, only the first alignment is returned.

Bio.PDB.PDBIO now ensures that b-factor values are always at most 6 characters to ensure that we do not violate the wwPDB specification. This should not have an impact on the majority of uses, as b-factor values are generally small (less than 100). When 1000 <= b-factor < 10_000, the value is rounded to a single decimal place. When,

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