feat: Phase H H4 — fail-closed adapter integration tests

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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -727,3 +727,11 @@ simulation-baseline-check:
 		--claimed-level 2 \
 		--baseline-beaten false
 	@echo "Baseline check complete."
+
+adapter-gate-check:
+	.venv/bin/openamp-foundry adapter-gate-check \
+		--module-id membrane_proxy \
+		--timeout false \
+		--schema-errors "[]" \
+		--baseline-beaten false
+	@echo "Adapter gate 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 H3 — per-module cheapest-baseline declaration — v0.5.91)
+> **Last updated:** 2026-07-09 (Phase H H4 — fail-closed adapter integration tests — v0.5.92)
+> **New in v0.5.92:** Fail-closed adapter integration tests (H4) — `FAIL_CLOSED_REASONS` dict keys (6 entries: timeout, connection_refused, invalid_response, schema_violation, module_unavailable, baseline_not_beaten). `AdapterGateResult` dataclass with module_id, passed, failure_reason, failure_detail, dry_lab_only. `evaluate_adapter_gate()` fail-closed: returns passed=False on ANY failure signal with priority ordering (timeout > connection_refused > invalid_response > schema_violation > module_unavailable > baseline_not_beaten). `run_adapter_gate_batch()` aggregates multiple adapter calls with total/passed/failed/any_failed/results/dry_lab_only. CLI (`openamp-foundry adapter-gate-check`) with `--module-id`, `--timeout`, `--connection-refused`, `--schema-errors`, `--module-unavailable`, `--baseline-beaten`, `--format text|json`. `make adapter-gate-check` target. 21 tests. **3162 total.** Avoids hidden external failures — when the adapter to an external simulation service is down or misbehaves, the pipeline must fail loudly rather than silently passing garbage through.
 > **New in v0.5.91:** Per-module cheapest-baseline declaration (H3) — `BaselineDeclaration` dataclass with module_id, module_name, baseline_description, baseline_type, evidence_level_ceiling, and notes. `BASELINE_DECLARATIONS` list (4 entries: membrane_proxy, structure_proxy, dummy_membrane_proxy, external_adapter_placeholder). `get_baseline_declaration()` and `list_baseline_declarations()` for lookup. `check_baseline_requirement()` caps effective_evidence_level to ceiling when baseline not beaten; returns dict with module_id, baseline_beaten, claimed/effective evidence levels, capped flag, message, and dry_lab_only. `validate_baseline_declarations()` checks module_id non-empty, baseline_description non-empty, baseline_type in {heuristic, random, constant, length}, evidence_level_ceiling 1-6, no duplicate module_ids. CLI (`openamp-foundry simulation-baseline-check`) with `--module-id`, `--claimed-level`, `--baseline-beaten`, `--format text|json`. `make simulation-baseline-check` target. 16 tests. **3141 total.** Forces honest enemy comparison — every simulation module must declare the simplest baseline it must beat.
 > **New in v0.5.90:** Simulation-result schema and validator (H2) — `schemas/simulation_result.schema.json` (Draft 2020-12) validates SimulationResult outputs with uncertainty 0.0–1.0 range, required fields (module, version, scope, scores, uncertainty, calibration_set, validated_against, notes), and optional `dry_lab_context` const "dry-lab-only". `validate_simulation_result()` checks module, version, scope, scores, uncertainty, validated_against, notes. Strict mode adds: module must not be "dummy" or contain "stub", uncertainty < 1.0, validated_against non-empty. `validate_simulation_result_batch()` aggregates results with counts and `any_invalid` flag. CLI (`openamp-foundry validate-simulation-result`) with `--results-json`, `--strict`, `--out-json`. `make validate-simulation-result-schema` target. 19 tests. **3125 total.** Dry-lab only.
 > **New in v0.5.89:** Simulation module registry (H1) — `SimulationModuleEntry` dataclass tracks module_id, name, description, status, evidence_level, baseline_comparison, scope, maintainer, and notes. `SIMULATION_MODULE_REGISTRY` holds 4 entries (membrane_proxy, structure_proxy, dummy_membrane_proxy, external_adapter_placeholder). Lookup functions: `get_module_entry()`, `list_module_entries()` with status/min_evidence filtering, `get_active_modules()`, `registry_summary()` with total/by_status/by_evidence_level/active_module_ids keys. `validate_registry()` checks module_id, name, baseline_comparison, evidence_level 1-6, valid status, duplicate detection. CLI (`openamp-foundry simulation-registry`) supports `--list`, `--show`, `--status`, `--min-evidence`, `--format text|json`. Schema (`schemas/simulation_module_registry.schema.json`). `make simulation-registry` target. 28 tests. 3106 total. Starts Phase H (virtual assay discipline).
@@ -82,7 +83,7 @@ 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:** v0.5.91 (H3 — per-module cheapest-baseline declaration)
+> **Pipeline version:** v0.5.92 (H4 — fail-closed adapter integration tests)
 > **Branch:** main
 
 ---
@@ -1152,7 +1153,7 @@ Decoys score low on activity. Selective AMPs score moderately on both.
 
 | Metric | Value |
 |--------|-------|
-| Total tests | 3125 |
+| Total tests | 3161 |
 | Coverage (branch) | 99% (6 CLI guard lines only) |
 | Source modules at 100% | All pipeline, QC, scoring modules |
 

docs/research/ROADMAP.md

@@ -1,5 +1,56 @@
 # Roadmap
 
+## v0.5.92 — Loop 92: Phase H H4 — Fail-Closed Adapter Integration Tests ✓ (2026-07-09)
+
+`FAIL_CLOSED_REASONS` dict (6 keys) enumerates known adapter failure reasons.
+`AdapterGateResult` dataclass with module_id, passed, failure_reason, failure_detail,
+dry_lab_only. `evaluate_adapter_gate()` fail-closed: returns passed=False on ANY
+failure signal with strict priority ordering (timeout > connection_refused >
+invalid_response > schema_violation > module_unavailable > baseline_not_beaten).
+`run_adapter_gate_batch()` aggregates multiple adapter calls with total/passed/failed/
+any_failed/results/dry_lab_only. Avoids hidden external failures — when the adapter
+to an external simulation service is down or misbehaves, the pipeline must fail
+loudly rather than silently passing garbage through.
+
+Changes:
+- `src/openamp_foundry/simulation/adapter_gate.py` (H4) — Core module with
+  `FAIL_CLOSED_REASONS` dict (6 entries), `AdapterGateResult` dataclass (5 fields:
+  module_id, passed, failure_reason, failure_detail, dry_lab_only),
+  `evaluate_adapter_gate()` with 7-path priority logic,
+  `run_adapter_gate_batch()` aggregating results with counts and any_failed flag.
+- `src/openamp_foundry/simulation/__init__.py` — Exports `AdapterGateResult`,
+  `FAIL_CLOSED_REASONS`, `evaluate_adapter_gate`, `run_adapter_gate_batch`.
+- `src/openamp_foundry/cli/main.py` — Registered `adapter-gate-check` subcommand
+  with `--module-id`, `--timeout`, `--connection-refused`, `--schema-errors`,
+  `--module-unavailable`, `--baseline-beaten`, `--format` flags. Added import
+  and dispatch.
+- `src/openamp_foundry/cli/commands/reports.py` — Added `_run_adapter_gate_check()`
+  CLI handler with text and JSON output, JSON parsing for schema errors,
+  exit code 3 on failure.
+- `Makefile` — Added `adapter-gate-check` target with default `membrane_proxy`
+  check. Added to `.PHONY`.
+- `tests/simulation/test_adapter_gate.py` — 20 tests covering: all 6 failure
+  reasons, all-clear pass, dry_lab_only always True, priority ordering (timeout
+  beats connection_refused, connection_refused beats result=None, schema_errors
+  beat module_unavailable), baseline_beaten=True passes, baseline_beaten=None
+  does not trigger, batch counts, batch any_failed, batch dry_lab_only.
+- `docs/evidence/METRICS_CURRENT.md` — v0.5.92 H4 changelog. Test count: 3161.
+- `tests/test_test_count_regression.py` — baseline updated to 3161.
+
+Honest boundaries:
+- The adapter gate checks for known failure signals only. An adapter that
+  returns plausible-looking but biologically meaningless results will pass.
+- Failure detection depends on the caller correctly setting the failure
+  flags. An adapter that silently hangs (neither timeout nor connection
+  refused) may not be caught.
+- Schema validation errors detect structural contract violations, not
+  biological correctness. A schema-valid response can still be biologically
+  meaningless.
+- The `baseline_not_beaten` check requires the caller to run the baseline
+  comparison externally; the gate does not compute it.
+- All adapter gate checks are dry-lab only and must not be presented as
+  biological proof.
+
 ## v0.5.91 — Loop 91: Phase H H3 — Per-Module Cheapest-Baseline Declaration ✓ (2026-07-09)
 
 `BaselineDeclaration` dataclass with module_id, module_name, baseline_description,

src/openamp_foundry/cli/commands/reports.py

@@ -1433,3 +1433,65 @@ def _run_simulation_baseline_check(args: argparse.Namespace) -> int:
         print("not biological proof.")
 
     return 3 if result["capped"] else 0
+
+
+def _run_adapter_gate_check(args: argparse.Namespace) -> int:
+    """Fail-closed adapter gate check for simulation adapters."""
+    from openamp_foundry.simulation.adapter_gate import (
+        evaluate_adapter_gate,
+    )
+
+    module_id = args.module_id
+    timeout_occurred = args.timeout.lower() == "true"
+    connection_refused = args.connection_refused.lower() == "true"
+    module_unavailable = args.module_unavailable.lower() == "true"
+    output_format = getattr(args, "format", "text")
+
+    schema_errors_raw = args.schema_errors
+    try:
+        schema_errors = json.loads(schema_errors_raw) if schema_errors_raw else []
+    except (json.JSONDecodeError, TypeError):
+        print(json.dumps({
+            "status": "error",
+            "error": f"Invalid JSON for --schema-errors: {schema_errors_raw!r}",
+        }))
+        return 2
+
+    if not isinstance(schema_errors, list):
+        print(json.dumps({
+            "status": "error",
+            "error": "--schema-errors must be a JSON array of strings",
+        }))
+        return 2
+
+    baseline_beaten_raw = args.baseline_beaten
+    baseline_beaten: bool | None = None
+    if baseline_beaten_raw is not None:
+        baseline_beaten = baseline_beaten_raw.lower() == "true"
+
+    gate_result = evaluate_adapter_gate(
+        module_id=module_id,
+        result=None,
+        timeout_occurred=timeout_occurred,
+        connection_refused=connection_refused,
+        schema_errors=schema_errors,
+        module_unavailable=module_unavailable,
+        baseline_beaten=baseline_beaten,
+    )
+
+    if output_format == "json":
+        print(json.dumps(gate_result.to_dict(), indent=2))
+    else:
+        status = "PASS" if gate_result.passed else "FAIL"
+        reason_info = ""
+        if gate_result.failure_reason:
+            reason_info = f"  Reason: {gate_result.failure_reason} — {gate_result.failure_detail}"
+        print(f"Adapter Gate Check: {module_id}")
+        print(f"  Status:  {status}")
+        if reason_info:
+            print(reason_info)
+        print()
+        print("Dry-lab only. Adapter gate checks are computational safeguards,")
+        print("not biological proof.")
+
+    return 0 if gate_result.passed 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
+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
 from openamp_foundry.cli.commands.gates import _run_gate_check
 
 import argparse
@@ -1430,6 +1430,45 @@ def build_parser() -> argparse.ArgumentParser:
         help="Output format (default: text).",
     )
 
+    # ── Adapter gate check (H4) ──────────────────────────────────────
+    agc = sub.add_parser(
+        "adapter-gate-check",
+        help=(
+            "Check whether a simulation adapter passes the fail-closed gate. "
+            "Dry-lab only."
+        ),
+    )
+    agc.add_argument("--module-id", type=str, required=True, help="Module ID to check.")
+    agc.add_argument(
+        "--timeout", type=str, default="false",
+        choices=["true", "false"],
+        help="Whether a timeout occurred (default: false).",
+    )
+    agc.add_argument(
+        "--connection-refused", type=str, default="false",
+        choices=["true", "false"],
+        help="Whether connection was refused (default: false).",
+    )
+    agc.add_argument(
+        "--schema-errors", type=str, default="[]",
+        help="JSON array of schema error strings (default: []).",
+    )
+    agc.add_argument(
+        "--module-unavailable", type=str, default="false",
+        choices=["true", "false"],
+        help="Whether the module is unavailable (default: false).",
+    )
+    agc.add_argument(
+        "--baseline-beaten", type=str, default=None,
+        choices=["true", "false"],
+        help="Whether the baseline was beaten (optional).",
+    )
+    agc.add_argument(
+        "--format", type=str, default="text",
+        choices=["text", "json"],
+        help="Output format (default: text).",
+    )
+
     return parser
 
 
@@ -1594,6 +1633,9 @@ def main(argv: list[str] | None = None) -> int:
     if args.command == "simulation-baseline-check":
         return _run_simulation_baseline_check(args)
 
+    if args.command == "adapter-gate-check":
+        return _run_adapter_gate_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 .adapter_gate import (
+    AdapterGateResult,
+    FAIL_CLOSED_REASONS,
+    evaluate_adapter_gate,
+    run_adapter_gate_batch,
+)
 from .baseline_registry import (
     BASELINE_DECLARATIONS,
     BaselineDeclaration,
@@ -32,6 +38,10 @@
 from .structure import StructureProxy
 
 __all__ = [
+    "AdapterGateResult",
+    "FAIL_CLOSED_REASONS",
+    "evaluate_adapter_gate",
+    "run_adapter_gate_batch",
     "SimulationResult",
     "VirtualAssayProxy",
     "ExternalSimulationAdapter",