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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.3.0] - 2026-09-02

Added

  • Backend integrity check module — python -m mrnavax.backends --check-all runs 13 checks across all five tools. Used by CI; also useful as a post-install verification.
  • codon --backend ribodecode — RiboDecode-style context-aware codon optimizer with optional --ribo-weights JSON. Reference: Fu et al. Nat Commun 16, 9957 (2025).
  • scrna --variant-filter-top-fraction — AlphaMissense-style variant pre-filter using BLOSUM62 + driver-gene boost + Δhydrophobicity.
  • scrna --embedding-model — foundation-model cell embedder (stdlib TF-IDF + truncated SVD by default; scGPT plug point when installed).
  • trial --retriever dense — MedCPT-style dense retriever with biomedical synonym expansion.
  • MRNA_AI_FORCE_MOCK=1 env var for CI / sandbox runs.

Changed

  • Bumped to v0.3.0.

[0.2.0] - 2026-09-02

Added

  • New scrna tool.
  • mhcflurry backend for neoantigen.
  • pyproject.toml with extras.
  • MkDocs Material site + GitHub Pages workflow.
  • Dual AGPL-3.0-or-later + commercial license.

[0.1.0] - 2026-09-02

Added

  • Initial release: codon, neoantigen, trial, lnp.