feat: Phase H H5 — simulation-result provenance chain

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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -735,3 +735,13 @@ adapter-gate-check:
 		--schema-errors "[]" \
 		--baseline-beaten false
 	@echo "Adapter gate check complete."
+
+simulation-provenance:
+	.venv/bin/openamp-foundry simulation-provenance \
+		--run-id test-run-001 \
+		--module-id membrane_proxy \
+		--module-version 0.1.0 \
+		--timestamp-utc 2026-07-09T12:00:00Z \
+		--input-sequence AKLWKR \
+		--scores-json '{"binding_energy": 0.75}'
+	@echo "Provenance record 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 H4 — fail-closed adapter integration tests — v0.5.92)
+> **Last updated:** 2026-07-09 (Phase H H5 — simulation-result provenance chain — v0.5.93)
+> **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.
 > **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.
@@ -83,7 +84,7 @@ 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:** v0.5.92 (H4 — fail-closed adapter integration tests)
+> **Pipeline version:** v0.5.93 (H5 — simulation-result provenance chain)
 > **Branch:** main
 
 ---

docs/research/ROADMAP.md

@@ -1,5 +1,52 @@
 # Roadmap
 
+## v0.5.93 — Loop 93: Phase H H5 — Simulation-Result Provenance Chain ✓ (2026-07-09)
+
+`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 hashes deterministically (sort_keys=True for
+result_hash). `validate_provenance_record()` checks non-empty fields, ISO 8601
+timestamp, 64-char hex hashes, and dry_lab_only=True. `provenance_summary()`
+aggregates total, unique modules, run_ids, and dry_lab_only flag. Every simulation
+result carries a traceable provenance chain so results can be audited, reproduced,
+or invalidated later without relying on memory.
+
+Changes:
+- `src/openamp_foundry/simulation/provenance.py` (H5) — Core module with
+  `SimulationProvenanceRecord` dataclass (9 fields), `make_provenance_record()`
+  computing SHA-256 input_hash and sorted result_hash, `validate_provenance_record()`
+  with 7 integrity checks, `provenance_summary()` with aggregation.
+- `src/openamp_foundry/simulation/__init__.py` — Exports `SimulationProvenanceRecord`,
+  `make_provenance_record`, `validate_provenance_record`, `provenance_summary`.
+- `src/openamp_foundry/cli/main.py` — Registered `simulation-provenance` subcommand
+  with `--run-id`, `--module-id`, `--module-version`, `--timestamp-utc`,
+  `--input-sequence`, `--scores-json`, `--calibration-set`, `--format` flags.
+  Added import and dispatch.
+- `src/openamp_foundry/cli/commands/reports.py` — Added `_run_simulation_provenance()`
+  CLI handler with JSON parsing, validation, text and JSON output, exit code 3 on
+  validation error.
+- `Makefile` — Added `simulation-provenance` target with demo invocation using
+  `test-run-001`. Added to `.PHONY`.
+- `tests/simulation/test_provenance.py` — 19 tests covering: record creation,
+  deterministic hashes, dry_lab_only always True, all validation checks
+  (empty fields, bad timestamp, wrong-length hash, dry_lab_only=False),
+  provenance_summary with 0 and N records.
+- `docs/evidence/METRICS_CURRENT.md` — v0.5.93 H5 changelog. Test count: 3181.
+- `tests/test_test_count_regression.py` — baseline updated to 3181.
+
+Honest boundaries:
+- SHA-256 hashes prove content integrity, not biological activity.
+- The provenance record attests that a simulation ran, not that the result
+  is biologically meaningful.
+- `input_hash` covers the input sequence only; other input parameters
+  (e.g., engine settings) are not hashed.
+- `result_hash` uses JSON serialisation with sort_keys=True; any future
+  change to the serialisation format will change the hash for identical data.
+- Timestamps are self-reported by the caller and not independently verified.
+- Provenance records are dry-lab only and must not be presented as
+  biological proof.
+
 ## 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.

src/openamp_foundry/cli/commands/reports.py

@@ -1495,3 +1495,77 @@ def _run_adapter_gate_check(args: argparse.Namespace) -> int:
         print("not biological proof.")
 
     return 0 if gate_result.passed else 3
+
+
+def _run_simulation_provenance(args: argparse.Namespace) -> int:
+    """Generate and display a simulation-result provenance record."""
+    import json
+
+    from openamp_foundry.simulation.provenance import (
+        make_provenance_record,
+        validate_provenance_record,
+    )
+
+    run_id = args.run_id
+    module_id = args.module_id
+    module_version = args.module_version
+    timestamp_utc = args.timestamp_utc
+    input_sequence = args.input_sequence
+    output_format = getattr(args, "format", "text")
+
+    try:
+        scores = json.loads(args.scores_json)
+    except (json.JSONDecodeError, TypeError) as e:
+        print(json.dumps({
+            "status": "error",
+            "error": f"Invalid JSON for --scores-json: {e}",
+        }))
+        return 2
+
+    if not isinstance(scores, dict):
+        print(json.dumps({
+            "status": "error",
+            "error": "--scores-json must be a JSON object (dict)",
+        }))
+        return 2
+
+    calibration_set = getattr(args, "calibration_set", None)
+
+    record = make_provenance_record(
+        run_id=run_id,
+        module_id=module_id,
+        module_version=module_version,
+        timestamp_utc=timestamp_utc,
+        input_sequence=input_sequence,
+        result_scores=scores,
+        calibration_set=calibration_set,
+    )
+
+    validation_errors = validate_provenance_record(record)
+    if validation_errors:
+        print(json.dumps({
+            "status": "validation_error",
+            "errors": validation_errors,
+        }))
+        return 3
+
+    if output_format == "json":
+        print(json.dumps(record.to_dict(), indent=2))
+    else:
+        print(f"Simulation Provenance Record")
+        print(f"  Run ID:          {record.run_id}")
+        print(f"  Module:          {record.module_id} v{record.module_version}")
+        print(f"  Timestamp (UTC): {record.timestamp_utc}")
+        print(f"  Input hash:      {record.input_hash}")
+        print(f"  Result hash:     {record.result_hash}")
+        if record.calibration_set:
+            print(f"  Calibration set: {record.calibration_set}")
+        if record.notes:
+            for note in record.notes:
+                print(f"  Note:            {note}")
+        print(f"  Dry-lab only:    {record.dry_lab_only}")
+        print()
+        print("Dry-lab only. Provenance records are computational audit trails,")
+        print("not biological proof.")
+
+    return 0

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
+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
 from openamp_foundry.cli.commands.gates import _run_gate_check
 
 import argparse
@@ -1469,6 +1469,27 @@ def build_parser() -> argparse.ArgumentParser:
         help="Output format (default: text).",
     )
 
+    # ── Simulation-result provenance (H5) ────────────────────────────────
+    sp = sub.add_parser(
+        "simulation-provenance",
+        help=(
+            "Generate a simulation-result provenance record with SHA-256 "
+            "input and result hashes. Dry-lab only."
+        ),
+    )
+    sp.add_argument("--run-id", type=str, required=True, help="Unique run ID (e.g. UUID).")
+    sp.add_argument("--module-id", type=str, required=True, help="Module ID (e.g. membrane_proxy).")
+    sp.add_argument("--module-version", type=str, required=True, help="Module version (e.g. 0.1.0).")
+    sp.add_argument("--timestamp-utc", type=str, required=True, help="ISO 8601 UTC timestamp.")
+    sp.add_argument("--input-sequence", type=str, required=True, help="Input peptide sequence.")
+    sp.add_argument("--scores-json", type=str, required=True, help="JSON object of str→float scores.")
+    sp.add_argument("--calibration-set", type=str, default=None, help="Optional calibration set identifier.")
+    sp.add_argument(
+        "--format", type=str, default="text",
+        choices=["text", "json"],
+        help="Output format (default: text).",
+    )
+
     return parser
 
 
@@ -1636,6 +1657,9 @@ def main(argv: list[str] | None = None) -> int:
     if args.command == "adapter-gate-check":
         return _run_adapter_gate_check(args)
 
+    if args.command == "simulation-provenance":
+        return _run_simulation_provenance(args)
+
     parser.error("unknown command")
     return 2
 

src/openamp_foundry/simulation/__init__.py

@@ -6,6 +6,12 @@
     evaluate_adapter_gate,
     run_adapter_gate_batch,
 )
+from .provenance import (
+    SimulationProvenanceRecord,
+    make_provenance_record,
+    provenance_summary,
+    validate_provenance_record,
+)
 from .baseline_registry import (
     BASELINE_DECLARATIONS,
     BaselineDeclaration,
@@ -57,6 +63,10 @@
     "get_active_modules",
     "registry_summary",
     "validate_registry",
+    "SimulationProvenanceRecord",
+    "make_provenance_record",
+    "validate_provenance_record",
+    "provenance_summary",
     "validate_simulation_result",
     "validate_simulation_result_batch",
     "BaselineDeclaration",