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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -692,3 +692,14 @@ synthetic-result-policy-check:
 		--proposals-json /tmp/srp_input.json \
 		--out-json /tmp/srp_output.json --out-md /tmp/srp_output.md
 	@echo "Synthetic result policy check done. See /tmp/srp_output.json"
+
+calibration-decision-checklist:
+	echo '{"G9-01":true,"G9-02":true,"G9-03":true,"G9-04":true,"G9-05":true,"G9-06":true,"G9-07":true,"G9-08":true,"G9-09":true,"G9-10":true}' > /tmp/checklist_responses.json
+	.venv/bin/openamp-foundry calibration-decision-checklist \
+		--checklist-id CHK-2026-001 \
+		--date 2026-07-09 \
+		--reviewer "human-reviewer" \
+		--responses-json /tmp/checklist_responses.json \
+		--out-json /tmp/checklist_output.json \
+		--out-md /tmp/checklist_output.md
+	@echo "Calibration decision checklist done. See /tmp/checklist_output.json"
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 G G8 — synthetic-result policy — v0.5.86)
+> **Last updated:** 2026-07-09 (Phase G G9 — calibration decision review checklist — v0.5.87)
+> **New in v0.5.87:** Calibration decision review checklist (G9) — `build_checklist()` produces a structured `CalibrationDecisionChecklist` with 12 checklist items (10 required) covering data quality, statistical validity, safety consistency, approval, and documentation. Each item has an id, category, question, rationale, and required flag. `CalibrationDecisionChecklist` dataclass tracks responses, notes, overall_pass, and missing_required. CLI (`openamp-foundry calibration-decision-checklist`) accepts `--checklist-id`, `--date`, `--reviewer`, `--responses-json`, `--out-json`, `--out-md`. JSON + Markdown output. Schema (`schemas/calibration_decision_checklist.schema.json`). `make calibration-decision-checklist` target. 14 tests. 3063 total. Makes human review structured and auditable.
 > **New in v0.5.86:** Synthetic-result policy enforcement (G8) — `check_synthetic_result_policy()` and `run_policy_batch()` enforce that synthetic/simulation outputs cannot raise the proof-ladder level of a candidate. Levels 4+ require wet-lab evidence; synthetic/unknown sources are rejected for such proposals. CLI (`openamp-foundry synthetic-result-policy-check`) accepts `--proposals-json`, `--out-json`, `--out-md`. Schema (`schemas/synthetic_result_policy_check.schema.json`). `make synthetic-result-policy-check` target. 27 tests. 3049 total. Anti-overclaim safeguard.
 > **New in v0.5.85:** Result-quality flag propagation (G7) — `assess_result_quality()` and `filter_results_for_calibration()` propagate result-quality flags into the calibration engine. Candidates with contamination or assay interference are excluded; candidates with 2+ quality flags are excluded; candidates with 1 flag are included with caution; clean candidates are fully included. `QUALITY_FLAGS` dictionary (8 flags). `ResultQualityReport` dataclass. CLI (`openamp-foundry result-quality-filter`) accepts `--results-json`, `--out-json`, `--out-md`. JSON + Markdown output. Schema (`schemas/result_quality_report.schema.json`). `make result-quality-filter` target. 27 tests. 3022 total.
 > **New in v0.5.84:** Calibration-overfit warning (G6) — `check_cohort_overfit_risk()` and `run_overfit_check()` flag when a calibration cohort is too small relative to model parameters. Warns at three severity levels (critical/warning/caution/none). CLI (`openamp-foundry calibration-overfit-check`) accepts comma-separated cohort sizes, model params, n features. JSON + Markdown output. Schema (`schemas/calibration_overfit_check.schema.json`). `make calibration-overfit-check` target. 21 tests. 2995 total.
@@ -78,7 +79,7 @@ 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:** v0.5.86 (G8)
+> **Pipeline version:** v0.5.87 (G9)
 > **Branch:** main
 
 ---

diff --git a/docs/research/ROADMAP.md b/docs/research/ROADMAP.md
@@ -1,5 +1,56 @@
 # Roadmap
 
+## v0.5.87 — Loop 87: Phase G G9 — Calibration Decision Review Checklist ✓ (2026-07-09)
+
+`build_checklist()` produces a structured `CalibrationDecisionChecklist` with 12
+checklist items (10 required) covering data quality, statistical validity, safety
+consistency, approval, and documentation. Each item has an id, category, question,
+rationale, and required flag. `CalibrationDecisionChecklist` dataclass tracks
+responses, notes, overall_pass, and missing_required. JSON + Markdown output.
+Schema (`schemas/calibration_decision_checklist.schema.json`).
+CLI (`openamp-foundry calibration-decision-checklist`).
+`make calibration-decision-checklist` target. 14 tests. 3063 total.
+Makes human review structured and auditable.
+
+Changes:
+- `src/openamp_foundry/calibration/decision_checklist.py` (G9) — Core module with
+  `CHECKLIST_ITEMS` list (12 items), `CalibrationDecisionChecklist` dataclass
+  (8 fields: checklist_id, date, reviewer, responses, notes, overall_pass,
+  missing_required, dry_lab_only), `build_checklist()` applying response validation
+  and missing-required analysis, `write_checklist_json()` and
+  `write_checklist_markdown()` for structured output.
+- `schemas/calibration_decision_checklist.schema.json` (G9) — JSON Schema Draft
+  2020-12 for the decision checklist. Validates all 8 required fields including
+  date pattern, responses object, and dry_lab_only const=true.
+- `src/openamp_foundry/calibration/__init__.py` — Exports all decision checklist
+  symbols.
+- `src/openamp_foundry/cli/commands/reports.py` — Added
+  `_run_calibration_decision_checklist()` CLI handler with `--checklist-id`,
+  `--date`, `--reviewer`, `--responses-json`, `--out-json`, `--out-md` flags.
+- `src/openamp_foundry/cli/main.py` — Registered `calibration-decision-checklist`
+  subcommand with all argument flags and dispatch to handler.
+- `Makefile` — Added `calibration-decision-checklist` target with default example
+  data writing to `/tmp/checklist_output.json` and `/tmp/checklist_output.md`.
+  Added to `.PHONY`.
+- `tests/calibration/test_decision_checklist.py` — 14 tests covering: all required
+  pass → overall_pass=True, missing required → overall_pass=False, missing_required
+  list correct, unknown response id raises ValueError, dry_lab_only always True,
+  notes stored correctly, checklist_id stored correctly, reviewer stored correctly,
+  date stored correctly, CHECKLIST_ITEMS minimum count, required items have
+  required=True attribute, all items have required fields, JSON writer, Markdown
+  writer with table and icons.
+- `docs/evidence/METRICS_CURRENT.md` — v0.5.87 G9 changelog. Test count: 3063.
+- `tests/test_test_count_regression.py` — baseline updated to 3063.
+
+Honest boundaries:
+- The checklist validates structured human-review completion, not biological
+  correctness. A passing checklist does not confirm biological activity or safety.
+- Required items are policy-defined. Missing or false required items block the
+  overall_pass, but a pass does not guarantee that human review was thorough.
+- All calibration decisions require qualified human review regardless of checklist
+  results.
+- The dry_lab_only=True constraint is an attestation, not a technical proof.
+
 ## v0.5.86 — Loop 86: Phase G G8 — Synthetic-Result Policy (Anti-Overclaim) ✓ (2026-07-09)
 
 `check_synthetic_result_policy()` and `run_policy_batch()` enforce that synthetic/

diff --git a/schemas/calibration_decision_checklist.schema.json b/schemas/calibration_decision_checklist.schema.json
@@ -0,0 +1,36 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "OpenAMP Calibration Decision Review Checklist",
+  "description": "Structured human-review checklist applied before any recalibration update takes effect. Dry-lab only.",
+  "type": "object",
+  "required": [
+    "checklist_id",
+    "date",
+    "reviewer",
+    "responses",
+    "notes",
+    "overall_pass",
+    "missing_required",
+    "dry_lab_only"
+  ],
+  "properties": {
+    "checklist_id": { "type": "string", "minLength": 1 },
+    "date": { "type": "string", "pattern": "^\\d{4}-\\d{2}-\\d{2}$" },
+    "reviewer": { "type": "string", "minLength": 1 },
+    "responses": {
+      "type": "object",
+      "additionalProperties": { "type": "boolean" },
+      "minProperties": 1
+    },
+    "notes": {
+      "type": "object",
+      "additionalProperties": { "type": "string" }
+    },
+    "overall_pass": { "type": "boolean" },
+    "missing_required": {
+      "type": "array",
+      "items": { "type": "string" }
+    },
+    "dry_lab_only": { "type": "boolean", "const": true }
+  }
+}
diff --git a/src/openamp_foundry/calibration/__init__.py b/src/openamp_foundry/calibration/__init__.py
@@ -83,6 +83,14 @@
     write_result_quality_markdown,
 )
 
+from openamp_foundry.calibration.decision_checklist import (
+    CHECKLIST_ITEMS,
+    CalibrationDecisionChecklist,
+    build_checklist,
+    write_checklist_json,
+    write_checklist_markdown,
+)
+
 __all__ = [
     # Constants
     "MIN_COHORT_SIZE",
@@ -136,4 +144,10 @@
     "filter_results_for_calibration",
     "write_result_quality_json",
     "write_result_quality_markdown",
+    # Decision checklist
+    "CHECKLIST_ITEMS",
+    "CalibrationDecisionChecklist",
+    "build_checklist",
+    "write_checklist_json",
+    "write_checklist_markdown",
 ]