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Bump biopython from 1.84 to 1.85 #242

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@dependabot dependabot bot commented on behalf of github Jan 20, 2025

Bumps biopython from 1.84 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
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Bumps [biopython](https://github.com/biopython/biopython) from 1.84 to 1.85.
- [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst)
- [Commits](https://github.com/biopython/biopython/commits)

---
updated-dependencies:
- dependency-name: biopython
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Jan 20, 2025
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@dependabot ignore this dependency

@dependabot dependabot bot closed this Jan 21, 2025
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dependabot bot commented on behalf of github Jan 21, 2025

OK, I won't notify you about biopython again, unless you re-open this PR.

@dependabot dependabot bot deleted the dependabot/pip/biopython-1.85 branch January 21, 2025 02:57
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