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Changelog

Full changelog: CHANGELOG.md on GitHub

FactorForge v3.0+ is the public release of an internal deterministic rule-based engine (v2) that succeeded an earlier thesis-derived prototype (v1) and a later ML prototype (v3-alpha, archived). See README for the full version lineage.

v3.1.6 — 2026-05-30

Added

  • BY-2 host (experimental) — --host by2, N. tabacum Kazusa codon table
  • Profile comparison — --compare-profiles CLI + POST /api/optimize/compare
  • Batch API — POST /api/optimize/batch (최대 20개 서열)
  • Structure links — AlphaFold DB + ESM Atlas 링크 결과 화면에 추가
  • SynCodonLM scoring — 선택적 5번째 스코어 (pip install factorforge-cds[ml])
  • GFP Tutorial — docs/tutorials/gfp-nbenthamiana.md

Fixed

  • API GC 기본값 CLI와 일치 (40-55% → 55-65%)

v3.1.5 — 2026-05-28

Fixed

  • Data file packaging — PyPI wheel에 JSON 데이터 파일 미포함 버그 수정 (pip install 후 경로 오류)
  • Path resolution — parents[N] 하드코딩 → get_data_path() 통일 (pip/Docker/Vercel 모두 정상 작동)
  • CI matrix — Python 3.13 + Windows 테스트 추가

v3.1.4 — 2026-05-27

Added

  • CITATION.cff — GitHub "Cite this repository" button; version-bumped automatically
  • SECURITY.md — vulnerability reporting policy
  • ROADMAP.md — public development direction (v3.2–v3.9, ML engine v3.7+, wet-lab scope)
  • scripts/release.py — automates version string updates across 14 files
  • Development history — v1→v2→v3-alpha→v3.x→v3.7+(ML) lineage documented across README, CHANGELOG, archive READMEs

Changed

  • Public engine naming — factorforge.engines.profile / CLI --engine profile formalized
  • Benchmark corrected — CAI 0.76, GC% 59.77%, target 55–65% (N=3,876 SGN CDS, balanced profile)

Fixed

  • Stale test version — test_design_package.py product_version 3.1.1 → 3.1.3

v3.1.3 — 2026-05-26

Fixed

  • Disabled profile cards — tooltips now accessible; "Pending wet-lab validation" notice added to 5' Ramp and Viral Delivery
  • Viral Delivery tooltip — corrected citation reference; updated to Peccoud et al. 2024 (PMC11718241)
  • Analytics notice — clarified: "Submitted sequences are not logged or stored"

v3.1.2 — 2026-05-26

Fixed

  • viral_delivery scoring — corrected citation reference; w_mfe 0.40→0.30 per PMC11718241 (Peccoud et al. 2024)
  • 5' Ramp deoptimization — N-terminal deoptimization bottom 50%→25% (mild, per PMC11718241)

v3.1.1 — 2026-05-24

Added

  • Wet-lab feedback modal — Submit result button opens embedded Google Form with version and profile pre-filled
  • JSON Copy button — one-click copy of full optimization JSON output

Changed

  • Design Objective order — reordered to match recommended wet-lab testing sequence
  • Validation fields — Issue template updated with promoter, subcellular targeting, harvest timepoint, native control

Fixed

  • Vercel deployment — resolved /api/optimize 404 caused by incorrect Root Directory setting

v3.1.0 — 2026-05-24

Added

  • Custom restriction site removal — synonymous substitution of user-specified restriction sites
  • Rare codon run detection — detects consecutive rare codons for ribosome stalling risk
  • Dinucleotide reduction — CAI-budgeted CpG/TpA reduction (aggressive / balanced / cai_preserving modes)

Fixed

  • Pipeline metric accuracy — CAI/GC/score re-measured from final sequence after dinucleotide fix
  • CAI guard weight consistency — guard now uses Sharp & Li 1987 golden set reference weights

v3.0.0 — 2026-05-23

First official release. DP Feasibility Engine, CLI, Validator, open-source under AGPL-3.0.