CodonForge v0.2.0

CodonForge v0.2.0

Adds the first research-useful beam-search optimizer and reproducibility package.

Added

• --strategy beam with CAI, GC%, U%, and adjacent-repeat objective terms.
• Beam-search CLI flags for beam width, targets, and objective weights.
• GC%, U%, and repeat penalty metrics in stdout.
• Public RP mini-benchmark for RHO, PRPF31, RPE65, and RPGR-ORF15.
• Kazusa-derived Homo sapiens codon usage table provenance.
• JOSS paper scaffold and code of conduct.

Verification

• 35 unit tests + 9 integration tests pass.
• clippy clean with -D warnings.
• cargo publish --dry-run passes.
• GitHub Actions CI passes on main.

Research preview only: not a clinical or therapeutic design tool.

CodonForge v0.1.0

CodonForge v0.1.0

Initial public research preview of CodonForge.

Included

• Greedy highest-frequency human codon optimizer
• Protein FASTA and stdin input
• Pure mRNA FASTA output via --fasta-out
• LinearDesign-style stdout for benchmark compatibility
• CAI computation
• Protein-fidelity validation by RNA translation
• Rust CI: fmt, clippy, tests, docs, and publish dry-run
• Data provenance notes, citation metadata, examples, and contribution/security docs

Limitations

• Greedy CAI optimizer only
• No LinearDesign algorithm parity
• No Turner energy model
• No internal MFE calculation
• No GPU acceleration
• Computational research software only; no clinical, diagnostic, or therapeutic claims

Verification

The release commit passed GitHub Actions CI:

• cargo fmt
• cargo clippy
• cargo test
• cargo doc
• cargo publish --dry-run