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.