Bump biopython from 1.79 to 1.85

[dependabot]

Bumps biopython from 1.79 to 1.85.

Changelog

Sourced from biopython's changelog.

15 January 2025: Biopython 1.85

This release of Biopython supports Python 3.9, 3.10, 3.11, 3.12 and 3.13. It has also been tested on PyPy3.9 v7.3.13. Python 3.9 is approaching end of life, our support for it is now deprecated.

Some optimisation work was done for Bio.SeqIO including avoiding nested iterators, and speeding up both FASTA and FASTQ parsing.

Bio.motifs now supports reading PFM from Cys2His2 Zinc Finger Proteins PWM Predictor and reading motifs in pfm-four-columns format will set motif name to "" instead of None, when no motif name was found.

Tests that use assertAlmostEqual calls now use places parameter with enough presision when comparing very small numbers in scientific notation.

Bio.motifs now supports reverse complementing RNA motifs and correctly generating degenerate consensus sequences for RNA motifs.

Bio.motifs.minimal now supports parsing RNA motifs and parsing motifs for which not all statistics are provided (e.g. missing E-values or nsites).

Bio.motifs.clusterbuster now supports parsing GAP and WEIGHT parameters and can optionally write Cluster Buster motif files with floats instead of integers, by specifying the precision=<int> parameter when writing: e.g. motifs.write(motifs, "clusterbuster", precision=2)

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:

• Alan Medlar
• Carlos Peña
• Gert Hulselmans
• Peter Cock
• Michiel de Hoon

28 June 2024: Biopython 1.84

This release of Biopython supports Python 3.9, 3.10, 3.11 and 3.12. It has also been tested on PyPy3.9 v7.3.13. Python 3.9 is approaching end of life, our support for it is now deprecated.

Our main documentation, the Biopython Tutorial and Cookbook, has been converted from LaTeX to reStructuredText, and combined with the existing API documentation, into a single more modern and navigable HTML output.

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