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build(deps): update dnachisel requirement from >=3.2.10 to >=3.2.16#35

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build(deps): update dnachisel requirement from >=3.2.10 to >=3.2.16#35
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@dependabot dependabot Bot commented on behalf of github Apr 27, 2026

Updates the requirements on dnachisel to permit the latest version.

Release notes

Sourced from dnachisel's releases.

v3.2.16

  • Finalised TOML config (e.g. exclude unwanted folders in installations)
Changelog

Sourced from dnachisel's changelog.

Changes

v3.0.0

API-breaking changes:

  • The strand on which to look for a pattern in AvoidPattern and EnforcePatternOccurence is not given by the location (strand 1, -1, or strand 0 to look in both strands).
  • AvoidNonUniqueSegments renamed in UniquifyKmers
  • Complete rewrite of CodonOptimization, method names are now use_best_codon,

New features

  • Support for different genetic codes in EnforceTranslation.
  • Support for non-standard start codons in EnforceTranslation
  • New AvoidMatches specification based on Bowtie.
  • AvoidChanges and EnforceChanges can now tunable (EnforceChanges(60%), AvoidChanges(max_edits=2))
  • New SequencePattern MotifPssmPattern.

Misc.

  • Got rid of some tables like Genetic code, now taken from Biopython.
  • Complete code restructuring by cutting large files into smaller ones.

v2.0.0

  • problem.n_mutations became problem.mutations_per_iteration for clarity
  • 'harmonized' option in CodonOptimize() replaced by harmonized_frequencies for clarity
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Updates the requirements on [dnachisel](https://github.com/Edinburgh-Genome-Foundry/dnachisel) to permit the latest version.
- [Release notes](https://github.com/Edinburgh-Genome-Foundry/dnachisel/releases)
- [Changelog](https://github.com/Edinburgh-Genome-Foundry/DnaChisel/blob/master/changes.md)
- [Commits](Edinburgh-Genome-Foundry/DnaChisel@v3.2.10...v3.2.16)

---
updated-dependencies:
- dependency-name: dnachisel
  dependency-version: 3.2.16
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Apr 27, 2026
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