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chore: mark R4 complete in NEXT_100_PR_MAP #963

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cschanhniem merged 1 commit into from
Jul 10, 2026
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chore: mark R4 complete in NEXT_100_PR_MAP #963

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2 changes: 1 addition & 1 deletion docs/research/NEXT_100_PR_MAP.md
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Expand Up @@ -221,5 +221,5 @@ Make the full pipeline auditable and reviewable by external scientists. First ph
| R1 | Add candidate family clustering evidence schema (CFC-) (complete). — src/openamp_foundry/evidence/candidate_family_clustering.py: CFC- 15-field schema; VALID_NOVELTY_EVIDENCE_TYPES (6), VALID_CLUSTERING_METHODS (5), VALID_NOVELTY_VERDICTS (4); novel_family requires hard evidence (blast/hmm/structural/charge); variant_of_known requires known_family_hits; n_candidates≥2 enforced; dry_lab_only=True enforced; 66 tests in tests/evidence/test_candidate_family_clustering.py. | Machine-verifiable grouping of related candidates into a "novel family" claim; sequence similarity threshold, family size, novelty evidence type controlled vocabulary. | B/C |
| R2 | Add family novelty report schema (FNR-) (complete). — src/openamp_foundry/evidence/family_novelty_report.py: FNR- 13-field schema; VALID_BASELINE_COMPARISON_OUTCOMES (4), VALID_NOVELTY_STRENGTH_GRADES (4), VALID_CHEAP_BASELINES_CHECKED (5); strong grade requires outside_known_space; not_supported incompatible with outside_known_space; cheap_enemy_score/family_score in [0,1]; dry_lab_only=True enforced; 64 tests in tests/evidence/test_family_novelty_report.py. | Bundles CFC- clustering with cheap-baseline comparison; prevents "novel family" overclaim when candidates are merely sequence variants of known AMPs. | B/C |
| R3 | Add full audit trail report schema (ATR-) linking BSP→WHR→PCU→HCR→PQG for a complete dry-lab→wet-lab loop trace (complete). — src/openamp_foundry/evidence/audit_trail_report.py: ATR- 15-field schema; REQUIRED_ATR_STAGES (5: BSP/WHR/PCU/HCR/PQG), VALID_TRAIL_COMPLETENESS_STATUSES (4), VALID_CHAIN_INTEGRITY_GRADES (5); complete status enforces all 5 stages; grade D incompatible with complete; build() auto-computes n_stages_complete; dry_lab_only=True enforced; 70 tests in tests/evidence/test_audit_trail_report.py. | End-to-end chain of custody from nomination to confirmed hit; required for scientific reproducibility. | B/C |
| R4 | Add scientific review readiness gate schema (SRG-). | Machine-verifiable checklist for when a candidate family has enough evidence for external scientific review; requires CFC+FNR+ATR+PQG records and no unresolved safety flags. | C |
| R4 | Add scientific review readiness gate schema (SRG-) (complete). — src/openamp_foundry/evidence/scientific_review_readiness_gate.py: SRG- 15-field schema; REQUIRED_SRG_ARTIFACT_TYPES (4: CFC/FNR/ATR/PQG), VALID_READINESS_VERDICTS (4), VALID_SAFETY_FLAG_TYPES (6), VALID_REVIEW_SCOPE_TYPES (4); ready_for_external_review blocks safety flags and failed_gates; open_preprint/peer_review blocked when not_ready/review_blocked_by_safety; dry_lab_only=True enforced; 63 tests in tests/evidence/test_scientific_review_readiness_gate.py. | Machine-verifiable checklist for when a candidate family has enough evidence for external scientific review; requires CFC+FNR+ATR+PQG records and no unresolved safety flags. PR #962. | C |
| R5 | Add preprint evidence bundle schema (PEB-) — read-only snapshot of all evidence for a run. | External reviewers can verify every claim from a single self-contained artifact; closes Phase R. | C |
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