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 decision-log release-request-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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -850,3 +850,8 @@ release-request-check:
 	.venv/bin/openamp-foundry release-request-check \
 		--request-json '{"release_id":"REL-2026-001","release_type":"schema","artifact_id":"candidate_manifest","artifact_version":"1.0.0","requestor_name":"OpenAMP Team","requestor_institution":"Open Problem Lab","request_date":"2026-07-09","evidence_level":2,"dry_lab_only":true,"safety_review_status":"approved","benchmark_summary":"Passes all schema compatibility checks","known_limitations":"Dry-lab only, not wet-lab validated","intended_use":"public","data_license":"CC-BY-4.0","human_reviewer":"maintainer","review_class":"B","approval_status":"pending"}'
 	@echo "Release request check complete."
+
+coi-check:
+	.venv/bin/openamp-foundry coi-check \
+		--disclosure-json '{"disclosure_id":"COI-2026-001","disclosure_type":"reviewer","subject":"maintainer","related_artifact":"REL-2026-001","relationship_type":"none","description":"","disclosure_date":"2026-07-09","recusal_required":false,"reviewer":"lead-maintainer","review_status":"acknowledged"}'
+	@echo "COI 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 J3 — release request template — v0.7.1)
+> **Last updated:** 2026-07-09 (Phase J J4 — COI disclosure template — v0.7.2)
+> **New in v0.7.2:** COI disclosure template (J4 — Loop 112) — `docs/governance/COI_DISCLOSURE_TEMPLATE.md` with structured COI disclosure template (purpose, fill-in-the-blank template with 10 fields: Disclosure ID, disclosure type (reviewer|contributor|maintainer|external_advisor), subject, related artifact, relationship type (financial|institutional|competitive|personal|none), description (conditional), date, recusal required, reviewer, review status (pending|acknowledged|resolved); when to disclose section covering financial/institutional/competitive/personal relationships; process with machine validation and escalation; linked policies). `src/openamp_foundry/governance/coi_disclosure.py` with `COIDisclosure` dataclass (10 fields), `COIValidationResult` dataclass (6 fields, dry_lab_only=True), `VALID_DISCLOSURE_TYPES` (4: contributor, external_advisor, maintainer, reviewer), `VALID_RELATIONSHIP_TYPES` (5: competitive, financial, institutional, none, personal), `VALID_REVIEW_STATUSES` (3: acknowledged, pending, resolved), `validate_coi_disclosure()` (10 checks including disclosure_id COI- prefix, valid disclosure_type, non-empty subject/related_artifact, valid relationship_type, description required unless none, YYYY-MM-DD date, non-empty reviewer, valid review_status, dry_lab_only must be True; financial without recusal warning), `validate_coi_dict()` (dict input with 10 required fields guard, missing fields returns passed=False early). CLI (`openamp-foundry coi-check`) with `--disclosure-json`, `--format text|json`. `make coi-check` target. 20 tests. Dry-lab only. COI disclosures now have a validated structure that builds institutional trust.
 > **New in v0.7.1:** Release request template (J3 — Loop 111) — `docs/governance/RELEASE_REQUEST_TEMPLATE.md` with structured release request template (purpose, fill-in-the-blank template with 17 fields: Release ID, release type, artifact ID/version, requestor name/institution, request date, evidence level 1-6, dry_lab_only, safety_review_status, benchmark_summary, known_limitations, intended_use, data_license, human_reviewer, review_class, approval_status; review criteria with 8 checks; process with classes A-D timelines and escalation path). `src/openamp_foundry/governance/release_request.py` with `ReleaseRequest` dataclass (17 fields), `ReleaseRequestValidationResult` dataclass (6 fields, dry_lab_only=True), `VALID_RELEASE_TYPES` (5), `VALID_SAFETY_STATUSES` (3), `VALID_INTENDED_USES` (4), `VALID_APPROVAL_STATUSES` (4), `VALID_REVIEW_CLASSES` (4), `validate_release_request()` (17 checks including dry_lab_only+evidence_level>4 error, public+safety_pending error, model+review_class warning), `validate_request_dict()` (dict input with missing-fields guard). CLI (`openamp-foundry release-request-check`) with `--request-json`, `--format text|json`. `make release-request-check` target. 25 tests. **3516 total.** Formal release requests now have a validated structure before entering human review.
 > **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.
@@ -99,7 +100,7 @@ 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:** v0.7.1 (J3 — release request template)
+> **Pipeline version:** v0.7.2 (J4 — COI disclosure template)
 > **Branch:** main
 
 ---

diff --git a/docs/governance/COI_DISCLOSURE_TEMPLATE.md b/docs/governance/COI_DISCLOSURE_TEMPLATE.md
@@ -0,0 +1,63 @@
+# Conflict-of-Interest Disclosure Template
+
+## Purpose
+
+A conflict-of-interest (COI) disclosure is filed when a contributor, reviewer, maintainer, or external advisor has a potential conflict with an artifact, decision, or review they are involved with. Filing a disclosure enables transparent governance and builds institutional trust.
+
+**File a disclosure when you have:**
+- A financial interest in an artifact or organization related to the work
+- An institutional relationship (current or former employer, funder) with a stakeholder
+- A competitive relationship with parties being evaluated
+- A personal relationship that could influence objectivity
+
+**Who reviews:** the designated `reviewer` (GitHub handle) noted in the disclosure.
+
+---
+
+## Template
+
+Fill in every field. Fields marked REQUIRED must not be empty.
+
+```yaml
+disclosure_id: ""         # e.g. COI-2026-001 (REQUIRED)
+disclosure_type: ""       # reviewer | contributor | maintainer | external_advisor (REQUIRED)
+subject: ""               # GitHub handle of person filing disclosure (REQUIRED)
+related_artifact: ""      # artifact ID or PR number (REQUIRED)
+relationship_type: ""     # financial | institutional | competitive | personal | none (REQUIRED)
+description: ""           # Required when relationship_type != "none"; leave empty only if "none"
+disclosure_date: ""       # YYYY-MM-DD (REQUIRED)
+recusal_required: false   # true | false (REQUIRED)
+reviewer: ""              # GitHub handle of designated reviewer (REQUIRED)
+review_status: ""         # pending | acknowledged | resolved (REQUIRED)
+```
+
+---
+
+## When to Disclose
+
+| Relationship type | Examples | Typical action |
+|---|---|---|
+| financial | equity, grants, consulting fees from a related org | Disclose; recusal often required |
+| institutional | current/former employer, department, funder | Disclose; recusal case-by-case |
+| competitive | org whose product competes with the artifact | Disclose; recusal recommended |
+| personal | close family, romantic partner, close friend | Disclose; recusal case-by-case |
+| none | no conflict | File with description="" to document clean slate |
+
+---
+
+## Process
+
+1. **File the disclosure** — copy the template above, fill in all fields, open a GitHub issue titled `[COI Disclosure] COI-YYYY-NNN — <subject>`.
+2. **Machine validation** — run `openamp-foundry coi-check --disclosure-json '{...}'` to pre-validate.
+3. **Human review** — the designated `reviewer` acknowledges within 3 business days.
+4. **Decision** — reviewer sets `review_status` to `acknowledged` or `resolved` with written rationale on recusal.
+5. **Escalation** — if no acknowledgment within 5 business days, escalate to project maintainers via GitHub discussion.
+
+---
+
+## Linked Policies
+
+- [GOVERNANCE.md](../../GOVERNANCE.md)
+- [RESPONSIBLE_USE.md](../../RESPONSIBLE_USE.md)
+- [RELEASE_CHECKLIST.md](RELEASE_CHECKLIST.md)
+- [DECISION_LOG.md](DECISION_LOG.md)
diff --git a/docs/research/ROADMAP.md b/docs/research/ROADMAP.md
@@ -1,5 +1,76 @@
 # Roadmap
 
+## v0.7.2 — Loop 112: Phase J J4 — COI Disclosure Template ✓ (2026-07-09)
+
+`docs/governance/COI_DISCLOSURE_TEMPLATE.md` with structured COI disclosure
+template (purpose, fill-in-the-blank format with 10 fields: Disclosure ID
+COI-YYYY-NNN, disclosure type reviewer|contributor|maintainer|external_advisor,
+subject GitHub handle, related artifact or PR, relationship type
+financial|institutional|competitive|personal|none, description (required unless
+none), date YYYY-MM-DD, recusal_required true|false, reviewer GitHub handle,
+review_status pending|acknowledged|resolved).
+
+`src/openamp_foundry/governance/coi_disclosure.py` with `COIDisclosure`
+dataclass (10 fields), `COIValidationResult` dataclass (6 fields,
+dry_lab_only=True), `VALID_DISCLOSURE_TYPES` (4: contributor, external_advisor,
+maintainer, reviewer), `VALID_RELATIONSHIP_TYPES` (5: competitive, financial,
+institutional, none, personal), `VALID_REVIEW_STATUSES` (3: acknowledged,
+pending, resolved), `validate_coi_disclosure()` (10 checks: disclosure_id
+starts with COI-, valid disclosure_type, non-empty subject/related_artifact,
+valid relationship_type, description required unless none, YYYY-MM-DD date,
+non-empty reviewer, valid review_status, dry_lab_only must be True; financial
+without recusal yields warning not error), `validate_coi_dict()` (dict input
+with 10 required fields guard).
+
+CLI (`openamp-foundry coi-check`) with `--disclosure-json` (required),
+`--format text|json`. Handler `_run_coi_check` in reports.py.
+
+`make coi-check` target. 20 tests. **3536 total.**
+
+COI disclosures now have a validated structure that builds institutional trust.
+
+Changes:
+- `docs/governance/COI_DISCLOSURE_TEMPLATE.md` (J4) — Structured COI disclosure
+  template with purpose, template (10 fields), when to disclose (financial,
+  institutional, competitive, personal), process (5 steps with escalation).
+- `src/openamp_foundry/governance/coi_disclosure.py` (J4) — Core module with
+  `COIDisclosure` (10 fields), `COIValidationResult` (6 fields,
+  dry_lab_only=True), `VALID_DISCLOSURE_TYPES` (4), `VALID_RELATIONSHIP_TYPES`
+  (5), `VALID_REVIEW_STATUSES` (3), `validate_coi_disclosure()` (10 checks),
+  `validate_coi_dict()` (dict input with 10 required fields guard).
+- `tests/governance/test_coi_disclosure.py` (J4) — 20 tests covering: valid
+  reviewer none relationship passes, valid contributor financial passes,
+  disclosure_id not starting with COI- fails, empty disclosure_id fails, invalid
+  disclosure_type fails, empty subject fails, empty related_artifact fails,
+  invalid relationship_type fails, relationship not none with empty description
+  fails, relationship none with empty description passes, invalid date format
+  fails, empty reviewer fails, invalid review_status fails, dry_lab_only=False
+  fails, financial without recusal warns, validate_coi_dict passes, validate_
+  coi_dict with missing fields fails, all results dry_lab_only=True,
+  VALID_DISCLOSURE_TYPES has 4, VALID_RELATIONSHIP_TYPES has 5.
+- `src/openamp_foundry/cli/main.py` (J4) — Registered `coi-check` subcommand
+  with `--disclosure-json`, `--format` flags. Added import and dispatch.
+- `src/openamp_foundry/cli/commands/reports.py` (J4) — Added `_run_coi_check()`
+  CLI handler with JSON parsing, validate_coi_dict call, text and JSON output,
+  exit code 3 on validation failure.
+- `Makefile` (J4) — Added `coi-check` target. Added to `.PHONY`.
+- `docs/evidence/METRICS_CURRENT.md` (J4) — v0.7.2 J4 changelog. Pipeline
+  version: v0.7.2. Test count: 3536.
+- `tests/test_test_count_regression.py` — baseline updated to 3536.
+
+Honest boundaries:
+- COI disclosure validation checks structural and policy requirements only.
+  It does not verify that the disclosed information is true, complete, or
+  accurate.
+- Financial relationship without recusal produces a warning, not an error —
+  the reviewer retains discretion to determine whether recusal is necessary.
+- The validator cannot detect undisclosed conflicts — it only checks that
+  disclosed conflicts are well-formed.
+- `dry_lab_only: true` is a const field on all dataclasses — COI disclosures
+  are governance artifacts, not legal determinations.
+- The COI template is a transparency and governance tool — it does not replace
+  the judgment of the human reviewer or governance team.
+
 ## v0.7.1 — Loop 111: Phase J J3 — Release Request Template ✓ (2026-07-09)
 
 `docs/governance/RELEASE_REQUEST_TEMPLATE.md` with structured release request