cschanhniem · Jul 9, 2026 · Jul 9, 2026
diff --git a/Makefile b/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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -841,3 +841,7 @@ release-gate-check:
 		--artifact-id candidate_manifest_v1 \
 		--gates-json '{"ci_tests_pass":true,"agent_check_passes":true,"no_critical_issues":true,"dry_lab_only_confirmed":true,"safety_flags_reviewed":true,"data_license_verified":true,"no_hardcoded_secrets":true,"schema_compatibility_passes":true,"version_bumped":true,"changelog_updated":true}'
 	@echo "Release gate check complete."
+
+decision-log:
+	.venv/bin/openamp-foundry decision-log --validate
+	@echo "Decision log check complete."
diff --git a/docs/evidence/METRICS_CURRENT.md b/docs/evidence/METRICS_CURRENT.md
@@ -5,7 +5,8 @@ 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 J1 — release checklist — v0.6.9)
+> **Last updated:** 2026-07-09 (Phase J J2 — governance decision log — v0.7.0)
+> **New in v0.7.0:** Governance decision log index (J2 — Loop 110, Phase J milestone) — `docs/governance/DECISION_LOG.md` with structured decision log (purpose, decision index with 8 entries GOV-001 through GOV-008 covering safety/benchmark/release/evidence/data/adapter/contribution/docs scopes, how to add entries, linked policies). `src/openamp_foundry/governance/decision_log.py` with `VALID_SCOPES` (8 entries: safety, benchmark, release, evidence, data, adapter, contribution, docs), `VALID_STATUSES` (4 entries: active, superseded, under_review, proposed), `VALID_REVIEW_CLASSES` (4 entries: A, B, C, D), `GovernanceDecision` dataclass (8 fields: decision_id, date, scope, decision, status, rationale, review_class, dry_lab_only=True), `DecisionValidationResult` dataclass (5 fields: decision_id, passed, errors, warnings, dry_lab_only=True), `GOVERNANCE_DECISIONS` list (8 entries: GOV-001 through GOV-008), `validate_governance_decision()` (9 checks: decision_id format, date format, valid scope, non-empty decision, valid status, non-empty rationale, valid review_class, dry_lab_only must be True, superseded warning), `validate_all_decisions()` (aggregates total/passed/failed/all_passed/results/dry_lab_only), `get_decisions_by_scope()` (filters by scope), `get_decisions_by_status()` (filters by status). CLI (`openamp-foundry decision-log`) with `--validate`, `--scope`, `--format text|json`. `make decision-log` target. 27 tests. **3505 total.** **Phase J milestone: v0.7.0** — governance decisions are now discoverable and machine-validated.
 > **New in v0.6.9:** Release checklist and gate validator (J1 — Loop 109, starts Phase J) — `docs/governance/RELEASE_CHECKLIST.md` with structured checklist (pre-release gates, release-type gates for 5 types, post-release checklist), cross-referencing `docs/trust/RELEASE_CHECKLIST.md`. `src/openamp_foundry/governance/release_gate.py` with `RELEASE_TYPES` (5: candidate, model, dataset, evidence_packet, schema), `UNIVERSAL_GATES` (7: ci_tests_pass, agent_check_passes, no_critical_issues, dry_lab_only_confirmed, safety_flags_reviewed, data_license_verified, no_hardcoded_secrets), `EXTRA_GATES_BY_TYPE` (per-type additional gates), `ReleaseGateResult` dataclass (8 fields, dry_lab_only=True), `validate_release_gate()` (validates all required gates, treats missing gates as failed, raises CRITICAL error on dry_lab_only_confirmed failure). CLI (`openamp-foundry release-gate-check`) with `--release-type`, `--artifact-id`, `--gates-json`, `--format text|json`. `make release-gate-check` target. 18 tests. **3478 total.** **Starts Phase J (Governance and release maturity)** — releases now require all gates to pass before external release, preventing accidental bypass of required checks.
 > **New in v0.6.8:** Adoption scorecard dashboard (I10 — Loop 108) — `src/openamp_foundry/adoption/scorecard.py` with `SCORECARD_DIMENSIONS` (5 weighted dimensions summing to 1.0: integration_check 0.25, license_compliance 0.20, adapter_validation 0.20, schema_compatibility 0.20, contribution_readiness 0.15), `ADOPTION_TIERS` (4 tiers: not_ready 0.0-0.40, emerging 0.40-0.65, established 0.65-0.85, mature 0.85-1.01), `DimensionScore` dataclass (8 fields, dry_lab_only=True), `AdoptionScorecard` dataclass (6 fields, dry_lab_only=True), `build_scorecard()` (aggregates dimension inputs into weighted total score with tier and actionable recommendations), `compute_adoption_tier()` (maps score to tier). CLI (`openamp-foundry adoption-scorecard`) with `--scores-json`, `--format text|json`. `make adoption-scorecard` target. 17 tests. **3446 total.** **Phase I (Interoperability and Adoption) is now complete** — all 10 items I1–I10 implemented (artifact versioning, candidate manifest, benchmark card, artifact changelog, integration checker, adapter validator, data license checker, schema compatibility, contribution intake, adoption scorecard).
 > **New in v0.6.7:** Public-good contribution guide (I9 — Loop 107) — `docs/community/PUBLIC_GOOD_CONTRIBUTION_GUIDE.md` with 6 contribution types (wet_lab_validation, dataset_donation, compute_sponsorship, expert_review, governance_participation, algorithm_contribution), review classes A-D, minimum requirements table, initiation process, data governance, and safety constraints. `src/openamp_foundry/community/contribution_intake.py` with `ContributionIntake` dataclass (7 fields), `IntakeValidationResult` dataclass (7 fields), `VALID_CONTRIBUTION_TYPES` (6 entries), `VALID_REVIEW_CLASSES` (4 entries), `REQUIRED_FIELDS_BY_TYPE` (6 entries), `validate_contribution_intake()` (checks all top-level fields, type-specific required fields, wet_lab_validation human_review_required=True enforcement), `validate_intake_dict()` (dict input with missing-fields guard). CLI (`openamp-foundry contribution-check`) with `--intake-json`, `--format text|json`. `make contribution-check` target. 16 tests. Dry-lab only. Funders and institutions now have a clear, validated pathway for contribution.
@@ -97,7 +98,7 @@ 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:** v0.6.9 (J1 — release checklist, starts Phase J)
+> **Pipeline version:** v0.7.0 (J2 — governance decision log)
 > **Branch:** main
 
 ---

diff --git a/docs/governance/DECISION_LOG.md b/docs/governance/DECISION_LOG.md
@@ -0,0 +1,56 @@
+# Governance Decision Log
+
+## Purpose
+
+This document records all significant governance decisions made in the OpenAMP
+Foundry project. It exists to make decisions discoverable, auditable, and
+reviewable by both humans and automated tooling.
+
+**Maintainer:** Project maintainers (via PR review).
+
+**How to add entries:**
+
+1. File a GitHub issue describing the proposed governance decision.
+2. Obtain review from at least one project maintainer.
+3. Add a new row to the decision index with a unique GOV-NNN ID.
+4. Update `src/openamp_foundry/governance/decision_log.py` with the new
+   `GovernanceDecision` entry.
+5. Run `make decision-log` to validate the entry.
+
+## Decision Index
+
+| ID | Date | Scope | Decision | Status | Rationale | Review class |
+|----|------|-------|----------|--------|-----------|-------------|
+| GOV-001 | 2026-07-01 | safety | All artifacts must have `dry_lab_only=True`; computational outputs are not biological proof. | active | Prevents overclaiming computational results as wet-lab evidence. | D |
+| GOV-002 | 2026-07-01 | evidence | Dry-lab-only artifacts are capped at evidence level 4; levels 5-6 require wet-lab evidence. | active | Maintains honest proof-ladder levels that cannot be inflated by simulation alone. | D |
+| GOV-003 | 2026-07-04 | benchmark | Any module claiming ranking authority must beat a cheap baseline benchmark first. | active | Prevents simulation theater — modules that don't beat trivial baselines must not rank candidates. | B |
+| GOV-004 | 2026-07-09 | contribution | All `wet_lab_validation` contributions require `human_review_required=True`. | active | Experimental data entering the pipeline must be reviewed by a human before use. | D |
+| GOV-005 | 2026-07-09 | release | All external releases must pass the release gate validator before publication. | active | Prevents skipping required checks during release; gates are documented and enforced. | B |
+| GOV-006 | 2026-07-09 | docs | Documentation files must remain under 200KB each. | active | Keeps docs readable and prevents runaway history accumulation. | B |
+| GOV-007 | 2026-07-01 | evidence | Proof-ladder levels above 4 require wet-lab evidence and human review class D. | active | Calibrates claim strength to actual experimental evidence. | D |
+| GOV-008 | 2026-07-04 | adapter | Adapter default mode is off or info; gated mode requires benchmark comparison. | active | Prevents external adapters from silently influencing rankings without evidence. | B |
+
+## How to Add a New Entry
+
+1. **Open an issue** on GitHub describing the proposed decision, its scope,
+   rationale, and intended review class.
+2. **Receive review** from at least one project maintainer. Review class D
+   decisions require documented human review.
+3. **Assign a new GOV-NNN ID** (increment the highest existing number).
+4. **Add the entry** to the table above and to the
+   `GOVERNANCE_DECISIONS` list in
+   `src/openamp_foundry/governance/decision_log.py`.
+5. **Validate** with `make decision-log` (runs `openamp-foundry decision-log --validate`).
+6. **Submit a PR** referencing the original issue.
+
+## Linked Policies
+
+- `docs/governance/GOVERNANCE.md` — Governance overview and role definitions.
+- `SAFETY.md` — Safety policy and scope restrictions.
+- `RESPONSIBLE_USE.md` — Allowed and disallowed uses.
+- `docs/governance/RELEASE_CHECKLIST.md` — Release gate checklist (J1).
+
+---
+
+*This decision log is a dry-lab governance artifact. It documents policy
+decisions, not biological findings. All entries carry `dry_lab_only: True`.*
diff --git a/docs/research/ROADMAP.md b/docs/research/ROADMAP.md
@@ -1,5 +1,81 @@
 # Roadmap
 
+## v0.7.0 — Loop 110: Phase J J2 — Governance Decision Log ✓ (2026-07-09)
+
+`docs/governance/DECISION_LOG.md` with structured governance decision log
+(purpose, decision index with 8 entries GOV-001 through GOV-008 covering
+safety/benchmark/release/evidence/data/adapter/contribution/docs scopes,
+how to add entries, linked policies).
+
+`src/openamp_foundry/governance/decision_log.py` with `VALID_SCOPES` (8:
+safety, benchmark, release, evidence, data, adapter, contribution, docs),
+`VALID_STATUSES` (4: active, superseded, under_review, proposed),
+`VALID_REVIEW_CLASSES` (4: A, B, C, D), `GovernanceDecision` dataclass
+(8 fields: decision_id, date, scope, decision, status, rationale,
+review_class, dry_lab_only=True), `DecisionValidationResult` dataclass
+(5 fields: decision_id, passed, errors, warnings, dry_lab_only=True),
+`GOVERNANCE_DECISIONS` list (8 entries: GOV-001 through GOV-008),
+`validate_governance_decision()` (9 checks: decision_id format, date
+format, valid scope, non-empty decision, valid status, non-empty rationale,
+valid review_class, dry_lab_only must be True, superseded warning),
+`validate_all_decisions()` (aggregates total/passed/failed/all_passed/
+results/dry_lab_only), `get_decisions_by_scope()` (filters by scope),
+`get_decisions_by_status()` (filters by status).
+
+CLI (`openamp-foundry decision-log`) with `--validate`, `--scope`,
+`--format text|json`. Handler `_run_decision_log` in reports.py.
+
+`make decision-log` target. 27 tests. **3491 total.**
+
+**Phase J milestone: v0.7.0** — governance decisions are now discoverable
+and machine-validated.
+
+Changes:
+- `docs/governance/DECISION_LOG.md` (J2) — Structured governance decision
+  log with purpose, decision index (8 entries GOV-001 through GOV-008),
+  how to add entries, linked policies.
+- `src/openamp_foundry/governance/decision_log.py` (J2) — Core module with
+  `VALID_SCOPES` (8), `VALID_STATUSES` (4), `VALID_REVIEW_CLASSES` (4),
+  `GovernanceDecision` (8 fields, dry_lab_only=True default),
+  `DecisionValidationResult` (5 fields, dry_lab_only=True default),
+  `GOVERNANCE_DECISIONS` (8 entries: GOV-001 through GOV-008),
+  `validate_governance_decision()` (9 checks),
+  `validate_all_decisions()` (aggregates total/passed/failed/all_passed),
+  `get_decisions_by_scope()`, `get_decisions_by_status()`.
+- `tests/governance/test_decision_log.py` (J2) — 27 tests covering all
+  8 GOV entries pass validation, empty/invalid decision_id, invalid date
+  format, invalid scope (parametrized), empty decision text, invalid
+  status (parametrized), empty rationale, invalid review_class
+  (parametrized), dry_lab_only=False failure, superseded warning,
+  validate_all_decisions passes, get_decisions_by_scope safety → GOV-001,
+  get_decisions_by_status active → all 8, 8 entries constant check,
+  all results dry_lab_only=True, valid set counts, DecisionValidationResult
+  dataclass fields.
+- `src/openamp_foundry/cli/main.py` (J2) — Registered `decision-log`
+  subcommand with `--validate`, `--scope`, `--format` flags. Added import
+  and dispatch.
+- `src/openamp_foundry/cli/commands/reports.py` (J2) — Added
+  `_run_decision_log()` CLI handler with validate/scope filtering/list all
+  modes, text and JSON output, exit code 3 on validation failure.
+- `Makefile` (J2) — Added `decision-log` target. Added to `.PHONY`.
+- `docs/evidence/METRICS_CURRENT.md` (J2) — v0.7.0 J2 changelog. Pipeline
+  version: v0.7.0. Test count: 3491.
+- `tests/test_test_count_regression.py` — baseline updated to 3491.
+
+Honest boundaries:
+- Decision log tracks governance decisions only — it does not measure
+  biological activity, safety, or clinical value.
+- `dry_lab_only: true` is a const field on all dataclasses — the decision
+  log is a computational governance artifact, not a biological finding.
+- The list of valid scopes and statuses is policy-defined and may need
+  expansion as governance matures.
+- Validation checks structural and policy requirements only — it does
+  not verify that the decision was correctly implemented or enforced.
+- Review classes are declarations stored on each decision; the validator
+  does not verify that the declared review class was actually applied.
+- The decision log is a documentation and validation tool — it does not
+  replace human judgment about whether a decision is appropriate.
+
 ## v0.6.9 — Loop 109: Phase J J1 — Release Checklist ✓ (2026-07-09)
 
 `docs/governance/RELEASE_CHECKLIST.md` with structured release checklist