feat: Phase H H7 — simulation-result confidence interval reporter

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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -751,3 +751,8 @@ simulation-ensemble-check:
 		--sequence AKLWKR \
 		--results-json '[{"module":"membrane_proxy","version":"0.1.0","scope":["bacterial_binding"],"scores":{"binding_energy":0.75},"uncertainty":0.1,"calibration_set":null,"validated_against":["APD3"],"notes":[]},{"module":"structure_proxy","version":"0.1.0","scope":["bacterial_binding"],"scores":{"binding_energy":0.80},"uncertainty":0.1,"calibration_set":null,"validated_against":["APD3"],"notes":[]}]'
 	@echo "Ensemble check complete."
+
+simulation-ci-report:
+	.venv/bin/openamp-foundry simulation-ci-report \
+		--results-json '[{"module":"membrane_proxy","version":"0.1.0","scope":["bacterial_binding"],"scores":{"binding_energy":0.75},"uncertainty":0.1,"calibration_set":null,"validated_against":["APD3"],"notes":[]},{"module":"structure_proxy","version":"0.1.0","scope":["bacterial_binding"],"scores":{"binding_energy":0.80},"uncertainty":0.15,"calibration_set":null,"validated_against":["APD3"],"notes":[]}]'
+	@echo "CI report 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 H6 — simulation-ensemble agreement checker — v0.5.94)
+> **Last updated:** 2026-07-09 (Phase H H7 — simulation-result confidence interval reporter — v0.5.95)
+> **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.
 > **New in v0.5.93:** Simulation-result provenance chain (H5) — `SimulationProvenanceRecord` dataclass with run_id, module_id, module_version, timestamp_utc, input_hash (SHA-256 of input sequence), result_hash (SHA-256 of sorted scores dict), calibration_set, notes, and dry_lab_only. `make_provenance_record()` computes input_hash and result_hash deterministically (sort_keys=True for result_hash). `validate_provenance_record()` checks run_id, module_id, module_version non-empty; ISO 8601 timestamp contains 'T'; hashes are 64-char hex; dry_lab_only is True. `provenance_summary()` aggregates total, unique modules, run_ids, and dry_lab_only flag. CLI (`openamp-foundry simulation-provenance`) with `--run-id`, `--module-id`, `--module-version`, `--timestamp-utc`, `--input-sequence`, `--scores-json`, `--calibration-set`, `--format text|json`. `make simulation-provenance` target with demo invocation. 19 tests. **3181 total.** Every simulation result carries a traceable provenance chain so results can be audited, reproduced, or invalidated later without relying on memory.
 > **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.
@@ -85,7 +86,7 @@ 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:** v0.5.94 (H6 — simulation-ensemble agreement checker)
+> **Pipeline version:** v0.5.95 (H7 — simulation-result confidence interval reporter)
 > **Branch:** main
 
 ---

docs/research/ROADMAP.md

@@ -1,5 +1,56 @@
 # Roadmap
 
+## v0.5.95 — Loop 95: Phase H H7 — Simulation-Result Confidence Interval Reporter ✓ (2026-07-09)
+
+`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 with demo invocation.
+Raw scores without uncertainty ranges make it impossible to judge whether two
+candidates are distinguishable. The CI reporter makes uncertainty explicit and
+auditable.
+
+Changes:
+- `src/openamp_foundry/simulation/ci_reporter.py` (H7) — Core module with
+  `ScoreCI` dataclass (9 fields), `compute_score_ci()` with CI bounds from
+  score ± uncertainty, `compare_cis()` with pairwise overlap detection,
+  `ci_report()` with n_results, any_overlap, and dry_lab_only=True.
+- `src/openamp_foundry/simulation/__init__.py` — Exports `ScoreCI`,
+  `compute_score_ci`, `compare_cis`, `ci_report`.
+- `src/openamp_foundry/cli/main.py` — Registered `simulation-ci-report`
+  subcommand with `--results-json`, `--score-key`, `--format` flags.
+  Added import and dispatch.
+- `src/openamp_foundry/cli/commands/reports.py` — Added
+  `_run_simulation_ci_report()` CLI handler with JSON parsing,
+  SimulationResult deserialization, text and JSON output.
+- `Makefile` — Added `simulation-ci-report` target with demo invocation
+  using membrane_proxy + structure_proxy. Added to `.PHONY`.
+- `tests/simulation/test_ci_reporter.py` — 16 tests covering: compute_score_ci
+  returns correct bounds, ci_width = 2*uncertainty, missing key returns None,
+  dry_lab_only always True, non-overlapping CIs empty overlaps_with,
+  overlapping CIs populated overlaps_with, no in-place mutation, 0 results,
+  n_results correct, dry_lab_only=True, any_overlap false/true, overlapping
+  example, non-overlapping example.
+- `docs/evidence/METRICS_CURRENT.md` — v0.5.95 H7 changelog. Test count: 3217.
+- `tests/test_test_count_regression.py` — baseline updated to 3217.
+
+Honest boundaries:
+- Confidence intervals are computed from SimulationResult.uncertainty, which
+  is self-reported by each simulation module and not independently verified.
+- Overlap detection is a mathematical condition: two CIs overlapping means
+  the scores are not statistically distinguishable at the stated uncertainty
+  level. It does not mean the modules are biologically correct or incorrect.
+- A CI with no overlaps may still be biologically meaningless — precision
+  without accuracy is not useful.
+- The any_overlap flag is a descriptive summary, not a gate. Overlap does
+  not invalidate results; it highlights them for human review.
+- All CI reports are dry-lab only and must not be presented as biological proof.
+
 ## v0.5.94 — Loop 94: Phase H H6 — Simulation-Ensemble Agreement Checker ✓ (2026-07-09)
 
 `EnsembleAgreementResult` dataclass (9 fields: sequence, modules_checked,

src/openamp_foundry/cli/commands/reports.py

@@ -1568,6 +1568,70 @@ def _run_adapter_gate_check(args: argparse.Namespace) -> int:
     return 0 if gate_result.passed else 3
 
 
+def _run_simulation_ci_report(args: argparse.Namespace) -> int:
+    """Compute confidence intervals and overlap report for simulation results."""
+    import json
+
+    from openamp_foundry.simulation.ci_reporter import ci_report
+    from openamp_foundry.simulation.interfaces import SimulationResult
+
+    output_format = getattr(args, "format", "text")
+    score_key = args.score_key
+
+    try:
+        raw_results = json.loads(args.results_json)
+    except (json.JSONDecodeError, TypeError) as e:
+        print(json.dumps({
+            "status": "error",
+            "error": f"Invalid JSON for --results-json: {e}",
+        }))
+        return 2
+
+    if not isinstance(raw_results, list):
+        print(json.dumps({
+            "status": "error",
+            "error": "--results-json must be a JSON array of SimulationResult dicts",
+        }))
+        return 2
+
+    results = []
+    for item in raw_results:
+        results.append(SimulationResult(
+            module=item.get("module", ""),
+            version=item.get("version", ""),
+            scope=item.get("scope", []),
+            scores=item.get("scores", {}),
+            uncertainty=item.get("uncertainty", 0.0),
+            calibration_set=item.get("calibration_set"),
+            validated_against=item.get("validated_against", []),
+            notes=item.get("notes", []),
+        ))
+
+    report = ci_report(results, score_key=score_key)
+
+    if output_format == "json":
+        print(json.dumps(report, indent=2))
+    else:
+        print(f"Simulation Confidence Interval Report")
+        print(f"  Score key:      {report['score_key']}")
+        print(f"  N results:      {report['n_results']}")
+        print(f"  Any overlap:    {report['any_overlap']}")
+        print()
+        for ci_dict in report["cis"]:
+            ov = ", ".join(ci_dict["overlaps_with"]) if ci_dict["overlaps_with"] else "(none)"
+            print(f"  [{ci_dict['module_id']}]")
+            print(f"    Point estimate: {ci_dict['point_estimate']:.4f}")
+            print(f"    Uncertainty:    {ci_dict['uncertainty']:.4f}")
+            print(f"    CI:             [{ci_dict['ci_lower']:.4f}, {ci_dict['ci_upper']:.4f}]")
+            print(f"    Width:          {ci_dict['ci_width']:.4f}")
+            print(f"    Overlaps with:  {ov}")
+            print()
+        print("Dry-lab only. Confidence intervals are computational estimates,")
+        print("not biological proof.")
+
+    return 0
+
+
 def _run_simulation_provenance(args: argparse.Namespace) -> int:
     """Generate and display a simulation-result provenance record."""
     import json

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
+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
 from openamp_foundry.cli.commands.gates import _run_gate_check
 
 import argparse
@@ -1519,6 +1519,29 @@ def build_parser() -> argparse.ArgumentParser:
         help="Output format (default: text).",
     )
 
+    # ── Simulation-result confidence interval report (H7) ────────────
+    sicr = sub.add_parser(
+        "simulation-ci-report",
+        help=(
+            "Compute confidence intervals from SimulationResult uncertainty fields "
+            "and compare them for overlap. Makes uncertainty explicit and auditable. "
+            "Dry-lab only."
+        ),
+    )
+    sicr.add_argument(
+        "--results-json", type=str, required=True,
+        help="JSON array of SimulationResult dicts.",
+    )
+    sicr.add_argument(
+        "--score-key", type=str, default="binding_energy",
+        help="Score key to extract from each result's scores dict (default: binding_energy).",
+    )
+    sicr.add_argument(
+        "--format", type=str, default="text",
+        choices=["text", "json"],
+        help="Output format (default: text).",
+    )
+
     return parser
 
 
@@ -1692,6 +1715,9 @@ def main(argv: list[str] | None = None) -> int:
     if args.command == "simulation-ensemble-check":
         return _run_simulation_ensemble_check(args)
 
+    if args.command == "simulation-ci-report":
+        return _run_simulation_ci_report(args)
+
     parser.error("unknown command")
     return 2
 

src/openamp_foundry/simulation/__init__.py

@@ -26,6 +26,12 @@
     list_baseline_declarations,
     validate_baseline_declarations,
 )
+from .ci_reporter import (
+    ScoreCI,
+    ci_report,
+    compare_cis,
+    compute_score_ci,
+)
 from .gate import SimulationGateVerdict, evaluate_simulation_gate
 from .interfaces import (
     EmulatorBaseline,
@@ -58,6 +64,10 @@
     "EnsembleAgreementResult",
     "check_ensemble_agreement",
     "run_ensemble_check_batch",
+    "ScoreCI",
+    "compute_score_ci",
+    "compare_cis",
+    "ci_report",
     "SimulationResult",
     "VirtualAssayProxy",
     "ExternalSimulationAdapter",