feat: Phase H H9 — simulation-scope coverage checker

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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -761,3 +761,9 @@ simulation-deprecation-check:
 	.venv/bin/openamp-foundry simulation-deprecation-check \
 		--module-ids membrane_proxy,dummy_membrane_proxy,external_adapter_placeholder
 	@echo "Deprecation check complete."
+
+simulation-scope-check:
+	.venv/bin/openamp-foundry simulation-scope-check \
+		--module-id membrane_proxy \
+		--requested-scopes bacterial_binding,fungal_binding
+	@echo "Scope check complete."

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 H H8 — simulation-module deprecation enforcer — v0.5.96)
+> **Last updated:** 2026-07-09 (Phase H H9 — simulation-scope coverage checker — v0.5.97)
+> **New in v0.5.97:** Simulation-scope coverage checker (H9) — `ScopeCoverageResult` dataclass (8 fields: module_id, requested_scopes, module_scopes, covered, uncovered, coverage_fraction, is_fully_covered, dry_lab_only). `check_scope_coverage()` looks up module in registry, computes covered (intersection) and uncovered (requested scopes not in module scopes), coverage_fraction = len(covered)/len(requested_scopes) if requested else 1.0. `check_result_scope()` uses conservative intersection of registry scopes and result.scope as effective module_scopes. `scope_coverage_report()` returns full dict. CLI (`openamp-foundry simulation-scope-check`) with `--module-id`, `--requested-scopes`, `--format text|json`. `make simulation-scope-check` target. 17 tests. **3255 total.** A simulation module may cover only some biological scopes. If a candidate is evaluated for a scope the module doesn't cover, that result must be flagged as out-of-scope rather than silently trusted.
 > **New in v0.5.96:** Simulation-module deprecation enforcer (H8) — `DeprecationCheckResult` dataclass (5 fields: module_id, status, is_blocked, block_reason, dry_lab_only). `BLOCKED_STATUSES = {"deprecated", "unavailable"}`. `check_module_deprecation()` looks up module in registry: not-found returns is_blocked=True status="unknown"; deprecated/unavailable returns is_blocked=True with reason; active/experimental returns is_blocked=False. `enforce_deprecation()` filters list[SimulationResult] to only non-blocked modules, returns total_input/passed/blocked/blocked_modules/passed_results/checks/dry_lab_only. `run_deprecation_check_batch()` bulk-checks module_ids with total/blocked/allowed/any_blocked/results/dry_lab_only. CLI (`openamp-foundry simulation-deprecation-check`) with `--module-ids`, `--format text|json`. `make simulation-deprecation-check` target. 21 tests. **3238 total.** Deprecated simulation modules must not be used in production scoring — the enforcer prevents stale or unreliable modules from tainting evidence packets.
 > **New in v0.5.95:** Simulation-result confidence interval reporter (H7) — `ci_reporter.py` with `ScoreCI` dataclass (9 fields: module_id, score_key, point_estimate, uncertainty, ci_lower, ci_upper, ci_width, overlaps_with, dry_lab_only). `compute_score_ci()` builds CIs from SimulationResult.scores[score_key] ± uncertainty, returns None if score_key missing. `compare_cis()` pairwise checks overlap condition (a_lo <= b_hi and b_lo <= a_hi), returns new list with overlaps_with populated (no in-place mutation). `ci_report()` produces full report with n_results, cis list, any_overlap flag, and dry_lab_only=True. CLI (`openamp-foundry simulation-ci-report`) with `--results-json`, `--score-key`, `--format text|json`. `make simulation-ci-report` target. 16 tests. **3217 total.** Raw scores without uncertainty ranges make it impossible to judge whether two candidates are distinguishable. The CI reporter makes uncertainty explicit and auditable.
 > **New in v0.5.94:** Simulation-ensemble agreement checker (H6) — `ensemble_checker.py` with `EnsembleAgreementResult` dataclass (9 fields: sequence, modules_checked, agreement_level, agreement_description, mean_score, score_range, scores_by_module, threshold, dry_lab_only). `AGREEMENT_LEVELS` dict (5 levels: strong, moderate, weak, conflict, insufficient). `check_ensemble_agreement()` extracts score_key from each SimulationResult's scores dict, computes score_range, classifies into strong (≥3 modules within threshold), moderate (2 modules within threshold), weak (1 module), conflict (beyond threshold), or insufficient (no results). `run_ensemble_check_batch()` aggregates multiple calls with counts and any_conflict flag. CLI (`openamp-foundry simulation-ensemble-check`) with `--sequence`, `--results-json`, `--score-key`, `--threshold`, `--format text|json`. `make simulation-ensemble-check` target. 20 tests. **3201 total.** When multiple simulation modules independently agree on a candidate, that agreement is stronger evidence than a single module alone. The ensemble checker makes this agreement explicit and auditable.
@@ -87,7 +88,7 @@ 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:** v0.5.96 (H8 — simulation-module deprecation enforcer)
+> **Pipeline version:** v0.5.97 (H9 — simulation-scope coverage checker)
 > **Branch:** main
 
 ---
@@ -1157,7 +1158,7 @@ Decoys score low on activity. Selective AMPs score moderately on both.
 
 | Metric | Value |
 |--------|-------|
-| Total tests | 3238 |
+| Total tests | 3255 |
 | Coverage (branch) | 99% (6 CLI guard lines only) |
 | Source modules at 100% | All pipeline, QC, scoring modules |
 

docs/research/ROADMAP.md

@@ -51,6 +51,56 @@ Honest boundaries:
   not invalidate results; it highlights them for human review.
 - All CI reports are dry-lab only and must not be presented as biological proof.
 
+## v0.5.97 — Loop 97: Phase H H9 — Simulation-Scope Coverage Checker ✓ (2026-07-09)
+
+`ScopeCoverageResult` dataclass (8 fields: module_id, requested_scopes,
+module_scopes, covered, uncovered, coverage_fraction, is_fully_covered,
+dry_lab_only). `check_scope_coverage()` looks up module in registry, computes
+covered (intersection) and uncovered (requested scopes not in module scopes),
+coverage_fraction = len(covered)/len(requested_scopes) if requested else 1.0.
+`check_result_scope()` uses conservative intersection of registry scopes and
+result.scope as effective module_scopes. `scope_coverage_report()` returns
+full dict.
+CLI (`openamp-foundry simulation-scope-check`) with `--module-id`,
+`--requested-scopes`, `--format text|json`.
+`make simulation-scope-check` target with demo invocation.
+A simulation module may cover only some biological scopes. If a candidate is
+evaluated for a scope the module does not cover, that result must be flagged
+as out-of-scope rather than silently trusted.
+
+Changes:
+- `src/openamp_foundry/simulation/scope_checker.py` (H9) — Core module with
+  `ScopeCoverageResult` dataclass (8 fields), `check_scope_coverage()` with
+  registry lookup and set intersection, `check_result_scope()` with conservative
+  intersection of registry and result scopes, `scope_coverage_report()` dict
+  builder.
+- `src/openamp_foundry/simulation/__init__.py` — Exports `ScopeCoverageResult`,
+  `check_scope_coverage`, `check_result_scope`, `scope_coverage_report`.
+- `src/openamp_foundry/cli/main.py` — Registered `simulation-scope-check`
+  subcommand with `--module-id`, `--requested-scopes`, `--format` flags.
+  Added import and dispatch.
+- `src/openamp_foundry/cli/commands/reports.py` — Added
+  `_run_simulation_scope_check()` CLI handler with text and JSON output.
+- `Makefile` — Added `simulation-scope-check` target. Added to `.PHONY`.
+- `tests/simulation/test_scope_checker.py` — 17 tests covering: fully covered,
+  partially covered, no scopes requested, unknown module, dry_lab_only always
+  True, covered/uncovered lists correct, coverage_fraction half/full/zero,
+  check_result_scope intersection, scope_coverage_report keys and dry_lab_only,
+  membrane_proxy covers bacterial, membrane_proxy does not cover fungal, empty
+  module scopes all uncovered.
+- `docs/evidence/METRICS_CURRENT.md` — v0.5.97 H9 changelog. Test count: 3255.
+- `tests/test_test_count_regression.py` — baseline updated to 3255.
+
+Honest boundaries:
+- Scope coverage is based on the module registry's declared scopes, which may
+  be incomplete or outdated relative to a module's actual capabilities.
+- `check_result_scope` is conservative: it only trusts scopes that both the
+  registry and the result agree on. This may undercount coverage if result
+  metadata is sparse.
+- A fully covered scope does not mean the simulation is accurate or biologically
+  meaningful — only that the module claims to cover the requested scope.
+- All outputs are dry-lab only and must not be presented as biological proof.
+
 ## v0.5.96 — Loop 96: Phase H H8 — Simulation-Module Deprecation Enforcer ✓ (2026-07-09)
 
 `DeprecationCheckResult` dataclass (5 fields: module_id, status, is_blocked,

src/openamp_foundry/cli/commands/reports.py

@@ -1741,3 +1741,36 @@ def _run_simulation_deprecation_check(args: argparse.Namespace) -> int:
         print("not biological proof.")
 
     return 3 if result["any_blocked"] else 0
+
+
+def _run_simulation_scope_check(args: argparse.Namespace) -> int:
+    """Check whether a simulation module covers all requested scopes."""
+    from openamp_foundry.simulation.scope_checker import (
+        check_scope_coverage,
+    )
+
+    module_id = args.module_id
+    requested_scopes = [s.strip() for s in args.requested_scopes.split(",") if s.strip()]
+    output_format = getattr(args, "format", "text")
+
+    if not requested_scopes:
+        print({"status": "error", "error": "No scopes provided."})
+        return 2
+
+    result = check_scope_coverage(module_id, requested_scopes)
+
+    if output_format == "json":
+        print(json.dumps(result.to_dict(), indent=2))
+    else:
+        print(f"Simulation Scope Coverage Check: {module_id}")
+        print(f"  Requested scopes: {', '.join(result.requested_scopes)}")
+        print(f"  Module scopes:    {', '.join(result.module_scopes) if result.module_scopes else '(none)'}")
+        print(f"  Covered:          {', '.join(result.covered) if result.covered else '(none)'}")
+        print(f"  Uncovered:        {', '.join(result.uncovered) if result.uncovered else '(none)'}")
+        print(f"  Coverage:         {result.coverage_fraction:.1%}")
+        print(f"  Fully covered:    {result.is_fully_covered}")
+        print()
+        print("Dry-lab only. Scope coverage checks are computational safeguards,")
+        print("not biological proof.")
+
+    return 0 if result.is_fully_covered else 3

src/openamp_foundry/cli/main.py

@@ -5,7 +5,7 @@
 from openamp_foundry.cli.commands.selection import _run_pilot_panel, _run_pilot_confident, _run_diversity_check, _run_select_batch, _run_batch_rationale
 from openamp_foundry.cli.commands.external import _run_external_predict, _run_external_consensus
 from openamp_foundry.cli.commands.qc import _run_synthesis_order, _run_presynth_qc
-from openamp_foundry.cli.commands.reports import _run_reviewer_questionnaire, _run_ip_report, _run_batch_pack, _run_gold_standard, _run_novelty_check_broad, _run_lab_result_report, _run_calibration_intake, _run_recalibration_gate, _run_recalibration_engine, _run_validate_policy_version, _run_calibration_audit, _run_calibration_overfit_check, _run_result_quality_filter, _run_synthetic_result_policy_check, _run_calibration_decision_checklist, _run_calibration_rollback_plan, _run_simulation_registry, _run_validate_simulation_result, _run_simulation_baseline_check, _run_adapter_gate_check, _run_simulation_provenance, _run_simulation_ensemble_check, _run_simulation_ci_report, _run_simulation_deprecation_check
+from openamp_foundry.cli.commands.reports import _run_reviewer_questionnaire, _run_ip_report, _run_batch_pack, _run_gold_standard, _run_novelty_check_broad, _run_lab_result_report, _run_calibration_intake, _run_recalibration_gate, _run_recalibration_engine, _run_validate_policy_version, _run_calibration_audit, _run_calibration_overfit_check, _run_result_quality_filter, _run_synthetic_result_policy_check, _run_calibration_decision_checklist, _run_calibration_rollback_plan, _run_simulation_registry, _run_validate_simulation_result, _run_simulation_baseline_check, _run_adapter_gate_check, _run_simulation_provenance, _run_simulation_ensemble_check, _run_simulation_ci_report, _run_simulation_deprecation_check, _run_simulation_scope_check
 from openamp_foundry.cli.commands.gates import _run_gate_check
 
 import argparse
@@ -1538,6 +1538,29 @@ def build_parser() -> argparse.ArgumentParser:
         help="Output format (default: text).",
     )
 
+    # ── Simulation-scope coverage check (H9) ─────────────────────────
+    ssc = sub.add_parser(
+        "simulation-scope-check",
+        help=(
+            "Check whether a simulation module covers all requested biological scopes. "
+            "Flags out-of-scope results so they are not silently trusted. "
+            "Dry-lab only."
+        ),
+    )
+    ssc.add_argument(
+        "--module-id", type=str, required=True,
+        help="Module ID to check (e.g. membrane_proxy).",
+    )
+    ssc.add_argument(
+        "--requested-scopes", type=str, required=True,
+        help="Comma-separated scopes (e.g. bacterial_binding,fungal_binding).",
+    )
+    ssc.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",
@@ -1740,6 +1763,9 @@ def main(argv: list[str] | None = None) -> int:
     if args.command == "simulation-deprecation-check":
         return _run_simulation_deprecation_check(args)
 
+    if args.command == "simulation-scope-check":
+        return _run_simulation_scope_check(args)
+
     parser.error("unknown command")
     return 2
 

src/openamp_foundry/simulation/__init__.py

@@ -1,5 +1,11 @@
 """Virtual assay simulation layer for OpenAMP Foundry."""
 
+from .scope_checker import (
+    ScopeCoverageResult,
+    check_scope_coverage,
+    check_result_scope,
+    scope_coverage_report,
+)
 from .deprecation_enforcer import (
     BLOCKED_STATUSES,
     DeprecationCheckResult,
@@ -63,6 +69,10 @@
 from .structure import StructureProxy
 
 __all__ = [
+    "ScopeCoverageResult",
+    "check_scope_coverage",
+    "check_result_scope",
+    "scope_coverage_report",
     "BLOCKED_STATUSES",
     "DeprecationCheckResult",
     "check_module_deprecation",