Codeine v0.3.0

New and improved constraints:

• Added TandemRepeatConstraint
• Made Homopolymerconstraint and ForbiddenMotifConstraint public.

Codeine v0.2.2

A few minor changes:

• Update and improve docs
• Add license, keywords, classifiers, and project URLs to PyProject.toml
• Implement len with advice
• Accept negative indices in __getitem__
• Add space.count()
• Minor refactoring & tidying

Codeine v0.2.1

Minor updates:

• Remove experimental features from public API
• Code tidying.

Codeine v0.2.0

This release mainly focuses on internal refactoring of codeine.

Includes:

• Improved compiler architecture.
• Refined mutation layer implementation.
• General readability and performance improvements.

New:

• Codon weight thresholding for simplified weighted sampling.

Codeine v0.1.0

First public release of Codeine.

Includes:

• CodingSpace for exact counting, enumeration and sampling of synonymous coding sequences.
• MutationSpace for designing synonymous variants around a reference sequence.
• TranslationTable with support for custom and NCBI genetic code tables, as DNA or RNA.
• CodonWeights with custom and built-in species-specific codon usage tables.

Features:

• Built-in sequence constraints:
  • Forbidden motifs (e.g. restriction sites)
  • Maximum homopolymer length
  • Fixed codons
  • Sequence contexts
  • Mutation distances
• Exact constrained sequence generation by construction (no post-generation filtering).

Also includes full API documentation and user guide on Read the Docs.