feat: Phase H H8 — simulation-module deprecation enforcer

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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -756,3 +756,8 @@ 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."
+
+simulation-deprecation-check:
+	.venv/bin/openamp-foundry simulation-deprecation-check \
+		--module-ids membrane_proxy,dummy_membrane_proxy,external_adapter_placeholder
+	@echo "Deprecation 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 H7 — simulation-result confidence interval reporter — v0.5.95)
+> **Last updated:** 2026-07-09 (Phase H H8 — simulation-module deprecation enforcer — v0.5.96)
+> **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.
 > **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.
@@ -86,7 +87,7 @@ 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:** v0.5.95 (H7 — simulation-result confidence interval reporter)
+> **Pipeline version:** v0.5.96 (H8 — simulation-module deprecation enforcer)
 > **Branch:** main
 
 ---
@@ -1156,7 +1157,7 @@ Decoys score low on activity. Selective AMPs score moderately on both.
 
 | Metric | Value |
 |--------|-------|
-| Total tests | 3201 |
+| Total tests | 3238 |
 | Coverage (branch) | 99% (6 CLI guard lines only) |
 | Source modules at 100% | All pipeline, QC, scoring modules |
 

docs/research/ROADMAP.md

@@ -51,6 +51,52 @@ 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.
 
+## v0.5.96 — Loop 96: Phase H H8 — Simulation-Module Deprecation Enforcer ✓ (2026-07-09)
+
+`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 dict with 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 with demo
+invocation. Deprecated simulation modules must not be used in production
+scoring — the enforcer prevents stale or unreliable modules from tainting
+evidence packets.
+
+Changes:
+- `src/openamp_foundry/simulation/deprecation_enforcer.py` (H8) — Core
+  module with `DeprecationCheckResult` dataclass, `check_module_deprecation()`,
+  `enforce_deprecation()`, `run_deprecation_check_batch()`.
+- `src/openamp_foundry/simulation/__init__.py` — Exports `BLOCKED_STATUSES`,
+  `DeprecationCheckResult`, `check_module_deprecation`, `enforce_deprecation`,
+  `run_deprecation_check_batch`.
+- `src/openamp_foundry/cli/main.py` — Registered `simulation-deprecation-check`
+  subcommand with `--module-ids`, `--format` flags. Added import and dispatch.
+- `src/openamp_foundry/cli/commands/reports.py` — Added
+  `_run_simulation_deprecation_check()` CLI handler.
+- `Makefile` — Added `simulation-deprecation-check` target. Added to `.PHONY`.
+- `tests/simulation/test_deprecation_enforcer.py` — 21 tests covering: active
+  module not blocked, deprecated/unavailable blocked, unknown blocked with
+  status="unknown", dry_lab_only always True, enforce_deprecation filters
+  results, passed count, blocked_modules sorted/deduplicated, dry_lab_only flag,
+  all-allowed blocked=0, batch total/any_blocked/not blocked.
+- `docs/evidence/METRICS_CURRENT.md` — v0.5.96 H8 changelog. Test count: 3238.
+- `tests/test_test_count_regression.py` — baseline updated to 3238.
+
+Honest boundaries:
+- Deprecation checks are based on registry status, not biological validity.
+  A module may be "active" in the registry but still produce unreliable scores.
+- Blocking removes results from evidence packets but does not invalidate them
+  as research data — blocked results may still be useful for internal analysis.
+- The enforcer does not evaluate whether a module's underlying science is sound;
+  it enforces the pipeline's declared module lifecycle policy.
+- All outputs 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

@@ -1704,3 +1704,40 @@ def _run_simulation_provenance(args: argparse.Namespace) -> int:
         print("not biological proof.")
 
     return 0
+
+
+def _run_simulation_deprecation_check(args: argparse.Namespace) -> int:
+    """Check whether simulation modules are deprecated or unavailable."""
+    import json
+
+    from openamp_foundry.simulation.deprecation_enforcer import (
+        run_deprecation_check_batch,
+    )
+
+    module_ids = [m.strip() for m in args.module_ids.split(",") if m.strip()]
+    if not module_ids:
+        print(json.dumps({"status": "error", "error": "No module IDs provided."}))
+        return 2
+
+    result = run_deprecation_check_batch(module_ids)
+    output_format = getattr(args, "format", "text")
+
+    if output_format == "json":
+        print(json.dumps(result, indent=2))
+    else:
+        print(f"Simulation Deprecation Check")
+        print(f"  Total modules:  {result['total']}")
+        print(f"  Blocked:        {result['blocked']}")
+        print(f"  Allowed:        {result['allowed']}")
+        print(f"  Any blocked:    {result['any_blocked']}")
+        print()
+        for check in result["results"]:
+            status = "BLOCKED" if check["is_blocked"] else "ALLOWED"
+            print(f"  [{status:7}] {check['module_id']:35s} "
+                  f"status={check['status']:15s} "
+                  f"{check['block_reason']}")
+        print()
+        print("Dry-lab only. Deprecation checks are computational safeguards,")
+        print("not biological proof.")
+
+    return 3 if result["any_blocked"] else 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, _run_simulation_provenance, _run_simulation_ensemble_check, _run_simulation_ci_report
+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.gates import _run_gate_check
 
 import argparse
@@ -1519,6 +1519,25 @@ def build_parser() -> argparse.ArgumentParser:
         help="Output format (default: text).",
     )
 
+    # ── Simulation deprecation check (H8) ────────────────────────────
+    sdc = sub.add_parser(
+        "simulation-deprecation-check",
+        help=(
+            "Check whether simulation modules are deprecated or unavailable. "
+            "Blocks deprecated modules from contributing to evidence packets. "
+            "Dry-lab only."
+        ),
+    )
+    sdc.add_argument(
+        "--module-ids", type=str, required=True,
+        help="Comma-separated module IDs (e.g. membrane_proxy,dummy_membrane_proxy).",
+    )
+    sdc.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",
@@ -1718,6 +1737,9 @@ def main(argv: list[str] | None = None) -> int:
     if args.command == "simulation-ci-report":
         return _run_simulation_ci_report(args)
 
+    if args.command == "simulation-deprecation-check":
+        return _run_simulation_deprecation_check(args)
+
     parser.error("unknown command")
     return 2
 

src/openamp_foundry/simulation/__init__.py

@@ -1,5 +1,12 @@
 """Virtual assay simulation layer for OpenAMP Foundry."""
 
+from .deprecation_enforcer import (
+    BLOCKED_STATUSES,
+    DeprecationCheckResult,
+    check_module_deprecation,
+    enforce_deprecation,
+    run_deprecation_check_batch,
+)
 from .adapter_gate import (
     AdapterGateResult,
     FAIL_CLOSED_REASONS,
@@ -56,6 +63,11 @@
 from .structure import StructureProxy
 
 __all__ = [
+    "BLOCKED_STATUSES",
+    "DeprecationCheckResult",
+    "check_module_deprecation",
+    "enforce_deprecation",
+    "run_deprecation_check_batch",
     "AdapterGateResult",
     "FAIL_CLOSED_REASONS",
     "evaluate_adapter_gate",