feat: Phase H H1 — simulation module registry

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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -713,3 +713,7 @@ calibration-rollback-plan:
 		--out-json /tmp/rollback_plan.json \
 		--out-md /tmp/rollback_plan.md
 	@echo "Rollback plan generated. See /tmp/rollback_plan.json"
+
+simulation-registry:
+	.venv/bin/openamp-foundry simulation-registry --list
+	@echo "Simulation module registry displayed."

docs/evidence/METRICS_CURRENT.md

@@ -5,8 +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 G G10 — recalibration rollback plan — v0.5.88)
-> **New in v0.5.88:** Recalibration rollback plan (G10) — `build_rollback_plan()` produces a structured `RollbackPlan` with 5 rollback triggers (RT-01 through RT-05) covering AUROC regression, calibration metric below threshold, safety filter bypass, cohort distribution shift, and unexplained weight delta. Each trigger has id, name, description, threshold, and severity. `RollbackStep` dataclass with step_number, action, responsible, detail, and dry_lab_only. `RollbackPlan` dataclass with plan_id, version, triggered_by, steps, notes, dry_lab_only, and to_dict(). 6 default rollback steps: halt, document, restore, verify, root-cause, and log. CLI (`openamp-foundry calibration-rollback-plan`) accepts `--plan-id`, `--version`, `--triggered-by`, `--notes`, `--out-json`, `--out-md`. JSON + Markdown output. Schema (`schemas/calibration_rollback_plan.schema.json`). `make calibration-rollback-plan` target. 15 tests. 3078 total. This completes Phase G (G1-G10 — calibration and active-learning rigor).
+> **Last updated:** 2026-07-09 (Phase H H1 — simulation module registry — v0.5.89)
+> **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).
 > **New in v0.5.87:** Calibration decision review checklist (G9) — `build_checklist()` produces a structured `CalibrationDecisionChecklist` with 12 checklist items (10 required) covering data quality, statistical validity, safety consistency, approval, and documentation. Each item has an id, category, question, rationale, and required flag. `CalibrationDecisionChecklist` dataclass tracks responses, notes, overall_pass, and missing_required. CLI (`openamp-foundry calibration-decision-checklist`) accepts `--checklist-id`, `--date`, `--reviewer`, `--responses-json`, `--out-json`, `--out-md`. JSON + Markdown output. Schema (`schemas/calibration_decision_checklist.schema.json`). `make calibration-decision-checklist` target. 14 tests. 3063 total. Makes human review structured and auditable.
 > **New in v0.5.86:** Synthetic-result policy enforcement (G8) — `check_synthetic_result_policy()` and `run_policy_batch()` enforce that synthetic/simulation outputs cannot raise the proof-ladder level of a candidate. Levels 4+ require wet-lab evidence; synthetic/unknown sources are rejected for such proposals. CLI (`openamp-foundry synthetic-result-policy-check`) accepts `--proposals-json`, `--out-json`, `--out-md`. Schema (`schemas/synthetic_result_policy_check.schema.json`). `make synthetic-result-policy-check` target. 27 tests. 3049 total. Anti-overclaim safeguard.
 > **New in v0.5.85:** Result-quality flag propagation (G7) — `assess_result_quality()` and `filter_results_for_calibration()` propagate result-quality flags into the calibration engine. Candidates with contamination or assay interference are excluded; candidates with 2+ quality flags are excluded; candidates with 1 flag are included with caution; clean candidates are fully included. `QUALITY_FLAGS` dictionary (8 flags). `ResultQualityReport` dataclass. CLI (`openamp-foundry result-quality-filter`) accepts `--results-json`, `--out-json`, `--out-md`. JSON + Markdown output. Schema (`schemas/result_quality_report.schema.json`). `make result-quality-filter` target. 27 tests. 3022 total.
@@ -80,7 +80,7 @@ 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:** v0.5.88 (G10 — Phase G complete)
+> **Pipeline version:** v0.5.89 (H1 — Phase H started)
 > **Branch:** main
 
 ---

docs/research/ROADMAP.md

@@ -1,5 +1,66 @@
 # Roadmap
 
+## v0.5.89 — Loop 89: Phase H H1 — Simulation Module Registry ✓ (2026-07-09)
+
+`SIMULATION_MODULE_REGISTRY` with 4 entries (membrane_proxy, structure_proxy,
+dummy_membrane_proxy, external_adapter_placeholder). `SimulationModuleEntry`
+dataclass tracks module_id, name, description, status, evidence_level,
+baseline_comparison, scope, maintainer, and notes. 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`) with `--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).
+
+Changes:
+- `src/openamp_foundry/simulation/module_registry.py` (H1) — Core module with
+  `SimulationModuleStatus` literal type, `SimulationModuleEntry` dataclass
+  (9 fields), `SIMULATION_MODULE_REGISTRY` list (4 entries),
+  `get_module_entry()`, `list_module_entries()`, `get_active_modules()`,
+  `registry_summary()` with aggregation, `validate_registry()` with 6 checks.
+  Imports `PROOF_LADDER_LEVELS` from `evidence/synthetic_result_policy.py`.
+- `schemas/simulation_module_registry.schema.json` (H1) — JSON Schema Draft
+  2020-12 for the registry_summary() output. Validates total, by_status
+  (all 4 status keys), by_evidence_level, active_module_ids.
+- `src/openamp_foundry/simulation/__init__.py` — Exports all module registry
+  symbols.
+- `src/openamp_foundry/cli/main.py` — Registered `simulation-registry`
+  subcommand with `--list`, `--show`, `--status`, `--min-evidence`,
+  `--format` flags.
+- `src/openamp_foundry/cli/commands/reports.py` — Added
+  `_run_simulation_registry()` CLI handler with text and JSON output,
+  per-module details, status/evidence filtering, and validation.
+- `Makefile` — Added `simulation-registry` target with `--list` default.
+  Added to `.PHONY`.
+- `tests/simulation/test_module_registry.py` — 28 tests covering: registry
+  size ≥ 4, all entries pass validation, required field presence, evidence
+  level range 1-6, valid status values, get_module_entry known/unknown,
+  list_module_entries no filter/status filter/min_evidence filter,
+  get_active_modules returns only active, registry_summary keys and totals,
+  validate_registry detection of empty fields, invalid level, invalid
+  status, duplicate ids, PROOF_LADDER_LEVELS completeness.
+- `docs/evidence/METRICS_CURRENT.md` — v0.5.89 H1 changelog. Test count: 3106.
+- `tests/test_test_count_regression.py` — baseline updated to 3106.
+
+Honest boundaries:
+- The registry lists module status and evidence level for informational
+  purposes only. It does not measure biological activity, safety, or
+  real-world performance.
+- Registry validation checks structural correctness, not scientific validity.
+  A valid entry may still produce biologically meaningless results.
+- The PROOF_LADDER_LEVELS mapping is a claim-level taxonomy. An evidence_level
+  of 2 ("virtual-assay support") means the module supports computational
+  exploration — it does not constitute biological proof.
+- The registry is dry-lab only. All module entries carry dry-lab caveats
+  regardless of their status or evidence_level.
+- "active" status means the module is available for use, not that it has
+  been biologically validated.
+
 ## v0.5.88 — Loop 88: Phase G G10 — Recalibration Rollback Plan ✓ (2026-07-09)
 
 `build_rollback_plan()` produces a structured `RollbackPlan` with 5 rollback

schemas/simulation_module_registry.schema.json

@@ -0,0 +1,39 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://openamp.ai/schemas/simulation_module_registry.schema.json",
+    "title": "Simulation Module Registry Summary",
+    "description": "Schema for the registry_summary() output. Dry-lab only — tracks module status and evidence level, not biological activity.",
+    "type": "object",
+    "properties": {
+        "total": {
+            "description": "Total number of registered modules",
+            "type": "integer",
+            "minimum": 0
+        },
+        "by_status": {
+            "description": "Count of modules per status level",
+            "type": "object",
+            "properties": {
+                "active": { "type": "integer", "minimum": 0 },
+                "experimental": { "type": "integer", "minimum": 0 },
+                "deprecated": { "type": "integer", "minimum": 0 },
+                "unavailable": { "type": "integer", "minimum": 0 }
+            },
+            "required": ["active", "experimental", "deprecated", "unavailable"]
+        },
+        "by_evidence_level": {
+            "description": "Count of modules per proof-ladder evidence level (1-6)",
+            "type": "object",
+            "patternProperties": {
+                "^[1-6]$": { "type": "integer", "minimum": 0 }
+            }
+        },
+        "active_module_ids": {
+            "description": "List of module IDs with status=active",
+            "type": "array",
+            "items": { "type": "string" }
+        }
+    },
+    "required": ["total", "by_status", "by_evidence_level", "active_module_ids"],
+    "additionalProperties": false
+}

src/openamp_foundry/cli/commands/reports.py

@@ -1230,3 +1230,111 @@ def _run_calibration_rollback_plan(args: argparse.Namespace) -> int:
         "out_md": args.out_md,
     }, indent=2))
     return 0
+
+
+def _run_simulation_registry(args: argparse.Namespace) -> int:
+    """Display simulation module registry information."""
+    from openamp_foundry.simulation.module_registry import (
+        SIMULATION_MODULE_REGISTRY,
+        get_module_entry,
+        list_module_entries,
+        registry_summary,
+        VALID_STATUSES,
+    )
+
+    PROOF_LADDER_LABELS = {
+        1: "computational nomination",
+        2: "virtual-assay support",
+        3: "in-silico ensemble agreement",
+        4: "ex-vivo preliminary",
+        5: "in-vivo preliminary",
+        6: "clinical evidence",
+    }
+
+    show = getattr(args, "show", None)
+    status_filter = getattr(args, "status", None)
+    min_evidence = getattr(args, "min_evidence", None)
+    output_format = getattr(args, "format", "text")
+
+    if show:
+        entry = get_module_entry(show)
+        if entry is None:
+            print(json.dumps({"status": "error", "error": f"Unknown module_id: '{show}'"}))
+            return 3
+        if output_format == "json":
+            print(json.dumps({
+                "module_id": entry.module_id,
+                "name": entry.name,
+                "description": entry.description,
+                "status": entry.status,
+                "evidence_level": entry.evidence_level,
+                "evidence_label": PROOF_LADDER_LABELS.get(entry.evidence_level, "unknown"),
+                "baseline_comparison": entry.baseline_comparison,
+                "scope": entry.scope,
+                "maintainer": entry.maintainer,
+                "notes": entry.notes,
+            }, indent=2))
+        else:
+            label = PROOF_LADDER_LABELS.get(entry.evidence_level, "unknown")
+            print(f"Module: {entry.module_id}")
+            print(f"  Name:               {entry.name}")
+            print(f"  Description:        {entry.description}")
+            print(f"  Status:             {entry.status}")
+            print(f"  Evidence Level:     {entry.evidence_level} ({label})")
+            print(f"  Baseline:           {entry.baseline_comparison}")
+            print(f"  Scope:              {', '.join(entry.scope)}")
+            print(f"  Maintainer:         {entry.maintainer}")
+            if entry.notes:
+                print(f"  Notes:              {entry.notes}")
+        return 0
+
+    if status_filter:
+        if status_filter not in VALID_STATUSES:
+            print(json.dumps({
+                "status": "error",
+                "error": f"Invalid status '{status_filter}'. Valid: {', '.join(sorted(VALID_STATUSES))}"
+            }))
+            return 3
+        entries = list_module_entries(status=status_filter)
+    elif min_evidence is not None:
+        entries = list_module_entries(min_evidence_level=min_evidence)
+    else:
+        entries = list(SIMULATION_MODULE_REGISTRY)
+
+    summary = registry_summary()
+
+    if output_format == "json":
+        print(json.dumps({
+            "modules": [
+                {
+                    "module_id": e.module_id,
+                    "name": e.name,
+                    "status": e.status,
+                    "evidence_level": e.evidence_level,
+                    "evidence_label": PROOF_LADDER_LABELS.get(e.evidence_level, "unknown"),
+                    "baseline_comparison": e.baseline_comparison,
+                    "scope": e.scope,
+                    "maintainer": e.maintainer,
+                    "notes": e.notes,
+                }
+                for e in entries
+            ],
+            "summary": summary,
+        }, indent=2))
+    else:
+        print("Simulation Module Registry")
+        print("=" * 60)
+        print(f"Total modules: {summary['total']}")
+        print(f"By status:     {dict(sorted(summary['by_status'].items()))}")
+        print(f"By evidence:   {dict(sorted(summary['by_evidence_level'].items()))}")
+        print(f"Active IDs:    {summary['active_module_ids']}")
+        print()
+        for entry in entries:
+            label = PROOF_LADDER_LABELS.get(entry.evidence_level, "unknown")
+            print(f"  [{entry.status:13}] {entry.module_id:35s} "
+                  f"L{entry.evidence_level} {label}")
+        print()
+        print("Dry-lab only. Registry status is informational — it does not")
+        print("measure biological activity, safety, or real-world performance.")
+
+    return 0