feat: Phase J J9 external advisory review process -- credibility

Makefile

@@ -1,4 +1,4 @@
-.PHONY: help demo test lint ci clean bench-leakage bench-multi-negatives bench-baseline bench-hidden-active bench-cluster-split bench-expert-ablation bench-expert-ablation-500 bench-selectivity bench-feature-decomp bench-gate bench-easy-baseline bench-charge-matched bench-order-dependent bench-precision-at-k bench-per-family bench-simulation-ablation bench-simulation-ablation-within-amp simulation-gate bench-strategy-compare regenerate-all generate phase3 pilot validate-scoring validate-scoring-phase3 validate-scoring-strict external-pilot pilot-confident presynth-qc gold-standard diversity synthesis-order novelty-broad external-consensus questionnaire gate-check ip-report benchmark-card wave0-5-gate-check wave0-5-novelty-audit wave0-5-novelty-audit-v2 wave0-5-panel wave0-5-evidence wave0-5-fill-external wave0-5b-generate wave0-5b-filter recalibration-engine recalibration-engine-dry-run validate-policy-version generate-synthetic-lab-results bump-policy-version generate-review-packet failed-candidate-report safe-publication-filter classify-negative-informativeness validate-rejection-events negative-result-dashboard calibration-audit calibration-audit-example calibration-overfit-check result-quality-filter synthetic-result-policy-check calibration-decision-checklist calibration-rollback-plan simulation-registry validate-simulation-result-schema simulation-baseline-check adapter-gate-check simulation-provenance simulation-ensemble-check simulation-ci-report simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-check license-check artifact-compat-check contribution-check adoption-scorecard release-gate-check decision-log release-request-check coi-check rotation-plan-check security-report-check citation-check roadmap-sync-check
+.PHONY: help demo test lint ci clean bench-leakage bench-multi-negatives bench-baseline bench-hidden-active bench-cluster-split bench-expert-ablation bench-expert-ablation-500 bench-selectivity bench-feature-decomp bench-gate bench-easy-baseline bench-charge-matched bench-order-dependent bench-precision-at-k bench-per-family bench-simulation-ablation bench-simulation-ablation-within-amp simulation-gate bench-strategy-compare regenerate-all generate phase3 pilot validate-scoring validate-scoring-phase3 validate-scoring-strict external-pilot pilot-confident presynth-qc gold-standard diversity synthesis-order novelty-broad external-consensus questionnaire gate-check ip-report benchmark-card wave0-5-gate-check wave0-5-novelty-audit wave0-5-novelty-audit-v2 wave0-5-panel wave0-5-evidence wave0-5-fill-external wave0-5b-generate wave0-5b-filter recalibration-engine recalibration-engine-dry-run validate-policy-version generate-synthetic-lab-results bump-policy-version generate-review-packet failed-candidate-report safe-publication-filter classify-negative-informativeness validate-rejection-events negative-result-dashboard calibration-audit calibration-audit-example calibration-overfit-check result-quality-filter synthetic-result-policy-check calibration-decision-checklist calibration-rollback-plan simulation-registry validate-simulation-result-schema simulation-baseline-check adapter-gate-check simulation-provenance simulation-ensemble-check simulation-ci-report simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-check license-check artifact-compat-check contribution-check adoption-scorecard release-gate-check decision-log release-request-check coi-check rotation-plan-check security-report-check citation-check roadmap-sync-check advisory-review-check
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -875,3 +875,8 @@ roadmap-sync-check:
 	.venv/bin/openamp-foundry roadmap-sync-check \
 		--entry-json '{"item_id":"J8","phase":"J","description":"Add roadmap-to-issue sync checklist","priority":"B","sync_status":"synced","issue_number":807}'
 	@echo "Roadmap sync check complete."
+
+advisory-review-check:
+	.venv/bin/openamp-foundry advisory-review-check \
+		--review-json '{"review_id":"ADV-2026-001","review_type":"candidate_review","artifact_id":"OAMP-v0.7.6-candidates","reviewer_handle":"external-advisor-1","assigned_date":"2026-07-09","deadline_date":"2026-07-23","status":"pending"}'
+	@echo "Advisory review check complete."

docs/evidence/METRICS_CURRENT.md

@@ -5,7 +5,9 @@ Machine-readable snapshot: `outputs/metrics_snapshot.json` regenerated with `mak
 > **Purpose:** One authoritative table of current pipeline metrics. If any doc disagrees
 > with this file, this file wins. Updated whenever benchmark/benchmark config changes.
 >
-> **Last updated:** 2026-07-09 (Phase J J8 — roadmap-to-issue sync checklist — v0.7.6)
+> **Last updated:** 2026-07-09 (Phase J J9 — external advisory review process — v0.7.7)
+> **New in v0.7.7:** External advisory review process (J9 — Loop 117) — docs/governance/EXTERNAL_ADVISORY_REVIEW_PROCESS.md with reviewer eligibility criteria, review scope table (5 review types with minimum reviewer counts), 5-step review process (prepare packet, assign+disclose, receive+log, respond to findings, close), finding severity classification (critical/major/minor/informational), limitations. src/openamp_foundry/governance/advisory_review.py with AdvisoryReview dataclass (11 fields: review_id, review_type, artifact_id, reviewer_handle, assigned_date, deadline_date, status, finding_severity, finding_summary, resolved, dry_lab_only), AdvisoryReviewResult dataclass (5 fields: review_id, review_type, passed, errors, warnings, dry_lab_only=True), VALID_REVIEW_TYPES (5: benchmark_audit, candidate_review, evidence_review, governance_review, safety_policy_review), VALID_REVIEW_STATUSES (5: assigned, completed, deferred, in_progress, pending), VALID_FINDING_SEVERITIES (4: critical, informational, major, minor), MINIMUM_REVIEWER_COUNTS (5 entries: candidate_review and safety_policy_review require 2, others 1), validate_advisory_review() (9 checks: ADV- prefix, valid review_type, non-empty artifact_id, non-empty reviewer_handle, YYYY-MM-DD dates, valid status, valid finding_severity, dry_lab_only must be True; critical+unresolved warns, completed+no-summary warns, deferred warns), validate_advisory_review_dict() (7 required fields guard). CLI (openamp-foundry advisory-review-check) with --review-json, --format text|json. make advisory-review-check target. 29 tests. Credibility: external advisory reviews now have a validated structure and documented process.
+>
 > **New in v0.7.6:** Roadmap-to-issue sync checklist (J8 — Loop 116) — docs/governance/ROADMAP_ISSUE_SYNC_CHECKLIST.md with 5-section sync checklist (roadmap items → issues, issues → roadmap, completed items, priority alignment, version consistency). src/openamp_foundry/governance/roadmap_sync.py with RoadmapSyncEntry dataclass (10 fields: item_id, phase, description, priority, sync_status, issue_number, pr_number, completed, completion_date, dry_lab_only), RoadmapSyncResult dataclass (5 fields: item_id, phase, passed, errors, warnings, dry_lab_only=True), VALID_SYNC_STATUSES (5: synced, missing_issue, orphaned_issue, stale, completed), VALID_PRIORITY_LEVELS (4: A, B, C, D), VALID_PHASES (7: E, F, G, H, I, J, K), validate_roadmap_sync_entry() (8 checks: non-empty item_id, valid phase, non-empty description, valid priority, valid sync_status, dry_lab_only must be True, completed must have completion_date, completion_date must be YYYY-MM-DD; priority A + missing_issue warns, stale warns, orphaned_issue warns, no issue_number warns), validate_roadmap_sync_dict() (5 required fields guard). CLI (openamp-foundry roadmap-sync-check) with --entry-json, --format text|json. make roadmap-sync-check target. 24 tests. Keeps strategy actionable: roadmap sync entries are now machine-validated.
 >
 > **New in v0.7.5:** Citation and reuse guide (J7 — Loop 115) — docs/governance/CITATION_AND_REUSE_GUIDE.md with citation formats (inline, BibTeX), reuse table (4 artifact types, open/attribution_required/contact_required/restricted classes), attribution requirements, honest-use boundary. src/openamp_foundry/governance/citation_policy.py with CitationEntry (11 fields: artifact_id, citation_type, title, version, authors, year, license_identifier, reuse_class, url, bibtex_key, dry_lab_only), CitationValidationResult (6 fields, dry_lab_only=True), VALID_CITATION_TYPES (4: dataset, method, schema, software), VALID_REUSE_CLASSES (4: attribution_required, contact_required, open, restricted), VALID_LICENSE_IDENTIFIERS (5: Apache-2.0, CC-BY-4.0, CC-BY-NC-4.0, MIT, Proprietary), validate_citation_entry() (9 checks: non-empty artifact_id, valid citation_type, non-empty title, non-empty version, non-empty authors, 4-digit year, valid license_identifier, valid reuse_class, dry_lab_only must be True; restricted warns, contact_required+no-url warns, empty bibtex_key warns), validate_citation_dict() (8 required fields guard). CLI (openamp-foundry citation-check) with --citation-json, --format text|json. make citation-check target. 24 tests. Ecosystem clarity: citation entries are now machine-validated.
@@ -106,7 +108,7 @@ Machine-readable snapshot: `outputs/metrics_snapshot.json` regenerated with `mak
 > **New in v0.5.31:** Added dipeptide-order features for sequence-order awareness. `dipeptide_order_score` achieves AUROC 0.7861 on AMP-vs-scrambled discrimination — the strongest order-dependent feature in the pipeline. Only 7/31 features survive scrambling (amphipathicity/helix-wheel + dipeptide). All composition features are purely position-independent (exactly 0.5000 AUROC on scrambled test).
 > **New in v0.5.30:** Easy baseline benchmark added — charge density alone (AUROC 0.8166) outperforms the full pipeline ensemble (0.7792) on AMP-vs-Swiss-Prot-decoy discrimination. Honest finding documented: expected because pipeline optimizes for safety, not raw discrimination.
 > **New in v0.5.29:** Expanded benchmark to 500 AMPs + 500 composition-matched decoys (n=1000). AUROC 0.7792 (CI₉₅: 0.7505–0.8065) confirms signal generalizes. Cluster-aware CI: 0.746–0.8102. Representative AUROC: 0.778. Standard benchmark (n=191) retained for backward comparison.
-> **Pipeline version:** v0.7.6 (J8 — roadmap-to-issue sync checklist)
+> **Pipeline version:** v0.7.7 (J9 — external advisory review process)
 > **Branch:** main
 
 ---

docs/governance/EXTERNAL_ADVISORY_REVIEW_PROCESS.md

@@ -0,0 +1,96 @@
+# External Advisory Review Process
+
+This document defines the process for external advisory review of OpenAMP Foundry
+research outputs, governance decisions, and release candidates.
+
+## Purpose
+
+External review provides independent credibility for:
+- Candidate selection rationale (why these sequences, not others)
+- Benchmark honesty (do the benchmarks test what they claim?)
+- Safety policy adequacy (are the safeguards sufficient?)
+- Evidence package completeness (is the evidence ready for wet-lab partners?)
+
+External review is **advisory only** — it does not replace the internal
+governance process defined in GOVERNANCE.md.
+
+## Reviewer Eligibility
+
+External advisors must:
+1. Hold a relevant domain expertise (antimicrobial peptide biology, ML benchmarking,
+   biosafety policy, or open science governance)
+2. Have no undisclosed conflict of interest (see COI_DISCLOSURE_TEMPLATE.md)
+3. Agree in writing to the responsible use policy (RESPONSIBLE_USE.md)
+4. Not be a current contributor to the OpenAMP Foundry codebase
+
+## Review Scope
+
+| Review type          | Trigger                                   | Reviewer count |
+|----------------------|-------------------------------------------|----------------|
+| Candidate review     | Before releasing a candidate list         | ≥ 2            |
+| Benchmark audit      | Before updating a benchmark threshold     | ≥ 1            |
+| Safety policy review | Before changing dual-use or safety policy | ≥ 2            |
+| Evidence review      | Before releasing an evidence package      | ≥ 1            |
+| Governance review    | Before changing the release policy        | ≥ 1            |
+
+## Review Process
+
+### Step 1: Prepare the review packet
+
+The internal team prepares a review packet containing:
+- The artifact or decision under review
+- Relevant evidence and benchmarks
+- Known limitations and open questions
+- The specific questions the advisor is asked to answer
+
+### Step 2: Assign and disclose
+
+- Assign the review to an eligible advisor
+- Request a COI disclosure (see COI_DISCLOSURE_TEMPLATE.md)
+- Provide the advisor with the review packet and a deadline (default: 14 days)
+
+### Step 3: Receive and log the review
+
+- Receive the advisor's written review
+- Log the review outcome in the decision log (DECISION_LOG.md)
+- Note any findings that change the internal assessment
+
+### Step 4: Respond to findings
+
+For each advisory finding:
+- **Critical finding**: halt release until resolved
+- **Major finding**: resolve before release or document why not resolved
+- **Minor finding**: document and address in next release cycle
+- **Informational**: note in the evidence package
+
+### Step 5: Close the review
+
+- Record the review outcome in the governance decision log
+- Update the artifact or decision record with the advisory review reference
+- Release or defer based on the findings
+
+## Machine-Validated Review Entries
+
+Advisory review entries can be validated with:
+
+```bash
+openamp-foundry advisory-review-check --review-json '{"review_id": "ADV-2026-001", ...}'
+```
+
+See `src/openamp_foundry/governance/advisory_review.py` for the AdvisoryReview schema.
+
+## Limitations
+
+- This process validates review structure, not review quality
+- External review does not guarantee correctness of the underlying research
+- Reviewer availability may affect timelines
+- The dry-lab-only constraint applies to all reviews: external advisors cannot
+  certify wet-lab validity from computational evidence alone
+
+## Linked Policies
+
+- [GOVERNANCE.md](../../GOVERNANCE.md) — project governance structure
+- [docs/governance/COI_DISCLOSURE_TEMPLATE.md](COI_DISCLOSURE_TEMPLATE.md) — conflict of interest
+- [RESPONSIBLE_USE.md](../../RESPONSIBLE_USE.md) — responsible use
+- [docs/governance/DECISION_LOG.md](DECISION_LOG.md) — governance decision log
+- [docs/evidence/PROOF_LADDER.md](../evidence/PROOF_LADDER.md) — evidence ladder

docs/research/ROADMAP.md

@@ -1,5 +1,34 @@
 # Roadmap
 
+## v0.7.7 — Loop 117: Phase J J9 — External Advisory Review Process ✓ (2026-07-09)
+
+`docs/governance/EXTERNAL_ADVISORY_REVIEW_PROCESS.md` with reviewer eligibility
+criteria (4 requirements), review scope table (5 review types with minimum
+reviewer counts: candidate_review and safety_policy_review require ≥2 reviewers,
+others ≥1), 5-step process (prepare packet, assign+disclose COI, receive+log,
+respond to findings by severity, close and record), finding severity handling
+(critical halts release, major resolves before release, minor defers, informational
+notes), limitations section.
+
+`src/openamp_foundry/governance/advisory_review.py` with `AdvisoryReview` dataclass
+(11 fields: review_id, review_type, artifact_id, reviewer_handle, assigned_date,
+deadline_date, status, finding_severity, finding_summary, resolved, dry_lab_only),
+`AdvisoryReviewResult` dataclass (5 fields, dry_lab_only=True),
+`VALID_REVIEW_TYPES` (5: benchmark_audit, candidate_review, evidence_review,
+governance_review, safety_policy_review), `VALID_REVIEW_STATUSES` (5: assigned,
+completed, deferred, in_progress, pending), `VALID_FINDING_SEVERITIES` (4:
+critical, informational, major, minor), `MINIMUM_REVIEWER_COUNTS` (5 entries),
+`validate_advisory_review()` (9 checks + 3 warning conditions),
+`validate_advisory_review_dict()` (7 required fields guard).
+
+CLI (`openamp-foundry advisory-review-check`) with `--review-json` (required),
+`--format text|json`. Handler `_run_advisory_review_check` in reports.py.
+
+`make advisory-review-check` target. 29 tests. **3653 total.**
+
+Credibility: external advisory reviews now have a validated structure, documented
+eligibility criteria, and a clear process from assignment to closure.
+
 ## v0.7.6 — Loop 116: Phase J J8 — Roadmap-to-Issue Sync Checklist ✓ (2026-07-09)
 
 `docs/governance/ROADMAP_ISSUE_SYNC_CHECKLIST.md` with 5-section checklist:

src/openamp_foundry/cli/commands/reports.py

@@ -2717,6 +2717,40 @@ def _run_citation_check(args: argparse.Namespace) -> int:
     return 0 if result.passed else 3
 
 
+def _run_advisory_review_check(args: argparse.Namespace) -> int:
+    """Validate an advisory review entry."""
+    import json as _json
+    from openamp_foundry.governance.advisory_review import validate_advisory_review_dict
+
+    try:
+        d = _json.loads(args.review_json)
+    except _json.JSONDecodeError as exc:
+        print(_json.dumps({"status": "error", "error": f"Invalid JSON: {exc}"}))
+        return 2
+
+    if not isinstance(d, dict):
+        print(_json.dumps({"status": "error", "error": "--review-json must be a JSON object"}))
+        return 2
+
+    result = validate_advisory_review_dict(d)
+    output_format = getattr(args, "format", "text")
+
+    if output_format == "json":
+        import dataclasses
+        print(_json.dumps(dataclasses.asdict(result), indent=2))
+    else:
+        status = "PASS" if result.passed else "FAIL"
+        print(f"Advisory review {result.review_id} ({result.review_type}): {status}")
+        for e in result.errors:
+            print(f"  ERROR: {e}")
+        for w in result.warnings:
+            print(f"  WARN:  {w}")
+        if result.passed:
+            print("  Advisory review entry validated. Ready for logging.")
+
+    return 0 if result.passed else 3
+
+
 def _run_roadmap_sync_check(args: argparse.Namespace) -> int:
     """Validate a roadmap sync entry."""
     import json as _json

src/openamp_foundry/cli/main.py

@@ -15,6 +15,7 @@
 from openamp_foundry.cli.commands.reports import _run_security_report_check
 from openamp_foundry.cli.commands.reports import _run_citation_check
 from openamp_foundry.cli.commands.reports import _run_roadmap_sync_check
+from openamp_foundry.cli.commands.reports import _run_advisory_review_check
 
 import argparse
 import json
@@ -1981,6 +1982,23 @@ def build_parser() -> argparse.ArgumentParser:
         help="Output format (default: text).",
     )
 
+    # ── Advisory review check (Phase J J9) ──────────────────────────
+    arc = sub.add_parser(
+        "advisory-review-check",
+        help=(
+            "Validate an external advisory review entry. Dry-lab only."
+        ),
+    )
+    arc.add_argument(
+        "--review-json", type=str, required=True,
+        help="JSON string of an AdvisoryReview dict (required).",
+    )
+    arc.add_argument(
+        "--format", type=str, default="text",
+        choices=["text", "json"],
+        help="Output format (default: text).",
+    )
+
     # ── Simulation-result confidence interval report (H7) ────────────
     sicr = sub.add_parser(
         "simulation-ci-report",
@@ -2243,6 +2261,9 @@ def main(argv: list[str] | None = None) -> int:
     if args.command == "roadmap-sync-check":
         return _run_roadmap_sync_check(args)
 
+    if args.command == "advisory-review-check":
+        return _run_advisory_review_check(args)
+
     parser.error("unknown command")
     return 2