cschanhniem · Jul 9, 2026 · Jul 9, 2026
diff --git a/Makefile b/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 simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-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 simulation-deprecation-check simulation-scope-check simulation-evidence-packet artifact-version candidate-manifest artifact-changelog integration-check adapter-author-check license-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)
@@ -815,3 +815,8 @@ adapter-author-check:
 	.venv/bin/openamp-foundry adapter-check \
 		--adapter-json '{"adapter_id":"example-adapter","adapter_version":"1.0.0","mode":"info","output_status":"ok","score_fields":{"activity":0.72},"uncertainty":0.15,"warnings":[],"failure_reason":null,"release_status":"internal","ranking_effect":"none","has_baseline_comparison":false,"makes_network_calls":false,"network_call_documented":false,"dry_lab_only":true}'
 	@echo "Adapter author check complete."
+
+license-check:
+	.venv/bin/openamp-foundry license-check \
+		--source-json '{"source_id":"apd-v2","source_name":"Antimicrobial Peptide Database v2","license_id":"CC-BY-4.0","use_context":"training","attribution_required":true,"commercial_use_allowed":true,"redistribution_allowed":true,"modifications_allowed":true,"human_review_required":false,"notes":"","dry_lab_only":true}'
+	@echo "License check complete."
diff --git a/docs/evidence/METRICS_CURRENT.md b/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 I I6 — adapter author validator — v0.6.4)
-> **New in v0.6.4:** Adapter author validator (I6 — Loop 104) — `src/openamp_foundry/adapters/adapter_validator.py` with `AdapterDeclaration` dataclass (14 fields: adapter_id, adapter_version, mode, output_status, score_fields, uncertainty, warnings, failure_reason, release_status, ranking_effect, has_baseline_comparison, makes_network_calls, network_call_documented, dry_lab_only), `AdapterValidationResult` dataclass (5 fields: adapter_id, passed, errors, warnings_list, dry_lab_only), `validate_adapter_declaration()` (10 checks: non-empty adapter_id, non-empty adapter_version, valid mode in VALID_ADAPTER_MODES, valid output_status in VALID_OUTPUT_STATUSES, valid ranking_effect in VALID_RANKING_EFFECTS, valid release_status in VALID_RELEASE_STATUSES, dry_lab_only must be True, ranking_effect in proposed/active requires has_baseline_comparison=True, network calls require network_call_documented=True, uncertainty in 0.0-1.0 or None), `validate_adapter_dict()` for raw dict input with missing-fields guard. `VALID_ADAPTER_MODES` (4), `VALID_OUTPUT_STATUSES` (4), `VALID_RANKING_EFFECTS` (3), `VALID_RELEASE_STATUSES` (5), `REQUIRED_OUTPUT_CONTRACT_FIELDS` (10). All results carry dry_lab_only=True. CLI (`openamp-foundry adapter-check`) with `--adapter-json`, `--format text|json`. `make adapter-author-check` target. 31 tests. **3387 total.** External adapter authors can now validate their declarations against the ADAPTER_AUTHOR_GUIDE contract before submitting.
+> **Last updated:** 2026-07-09 (Phase I I7 — data license checker — v0.6.5)
+> **New in v0.6.5:** Data license checker (I7 — Loop 105) — `src/openamp_foundry/licensing/license_checker.py` with `DataLicenseDeclaration` dataclass (11 fields: source_id, source_name, license_id, use_context, attribution_required, commercial_use_allowed, redistribution_allowed, modifications_allowed, human_review_required, notes, dry_lab_only), `LicenseCheckResult` dataclass (8 fields: source_id, license_id, use_context, passed, status, errors, warnings, dry_lab_only), `check_data_license()` (validates declarations against `APPROVED_LICENSES` (11 entries: CC0-1.0, CC-BY-4.0, CC-BY-SA-4.0, MIT, Apache-2.0, GPL-3.0, LGPL-2.1, BSD-2-Clause, BSD-3-Clause, ODbL-1.0, PDDL-1.0), `RESTRICTED_LICENSES` (4 entries: CC-BY-NC-4.0, CC-BY-NC-SA-4.0, custom, proprietary), `BLOCKED_LICENSES` (3 entries: unknown, unlicensed, all-rights-reserved), `VALID_USE_CONTEXTS` (6 entries: training, scoring, benchmarking, reporting, publication, internal). Blocked licenses fail immediately; restricted require human_review_required=True; unknown licenses require governance review before use. `check_license_batch()` summarizes total/passed/failed/blocked/any_blocked/all_passed with dry_lab_only=True. All results carry dry_lab_only=True. CLI (`openamp-foundry license-check`) with `--source-json`, `--format text|json`. `make license-check` target. 16 tests. **3403 total.** External data sources used in pipeline outputs now require explicit license declarations, preventing hidden legal risk.
 > **New in v0.6.3:** Downstream project template (I5 — Loop 103) — `docs/adoption/DOWNSTREAM_PROJECT_TEMPLATE.md` with overview of OpenAMP artifacts, minimum viable integration (consume candidate manifest, validate against schema, use Python library), schema validation step, evidence level interpretation table (L1-L6), safety flag conventions table, benchmark card consumption guide, explicit dry-lab limitations section, and contact/contribution section. `src/openamp_foundry/adoption/integration_checker.py` with `REQUIRED_INTEGRATION_CHECKS` (5 checks: manifest_schema_valid, evidence_level_in_range, dry_lab_only_acknowledged, safety_flags_reviewed, baseline_comparison_present), `IntegrationCheckResult` dataclass (4 fields: check_name, passed, detail, dry_lab_only), `run_integration_checks()` (returns dict with checks, passed_count, failed_count, all_passed, dry_lab_only). Exported from `src/openamp_foundry/adoption/__init__.py`. CLI (`openamp-foundry integration-check`) with `--manifest-json`, `--format text|json`. `make integration-check` target. 14 tests. **3356 total.** External researchers who want to use OpenAMP artifacts now have a guide and checker to validate their integration.
 > **New in v0.6.2:** Evidence-certificate changelog (I4 — Loop 102) — `docs/engineering/ARTIFACT_CHANGELOG.md` with structured changelog format (version, date, artifact_name, change_type, description, breaking flag). Unreleased section at top. `src/openamp_foundry/versioning/artifact_changelog.py` with `CHANGE_TYPES` set (6 values), `ChangelogEntry` dataclass (7 fields), `ARTIFACT_CHANGELOG` list (6 entries: candidate_manifest, benchmark_card, simulation_result, simulation_module_registry, artifact_versioning_policy, artifact_changelog — all "added", non-breaking, v1.0.0), `get_changelog_entries()` (filters by artifact_name, version, change_type, breaking_only), `validate_changelog()` (5 checks: version MAJOR.MINOR.PATCH, date YYYY-MM-DD with dashes, artifact_name non-empty, change_type in CHANGE_TYPES, description non-empty), `changelog_summary()` (total, by_change_type, breaking_changes, artifacts_covered sorted, dry_lab_only). CLI (`openamp-foundry artifact-changelog`) with `--artifact`, `--version`, `--change-type`, `--breaking-only`, `--format text|json`. `make artifact-changelog` target. 13 tests. **3342 total.** External tools that consume OpenAMP artifacts now have a machine-readable changelog to detect breaking changes and adapt consumers.
 > **New in v0.6.1:** Benchmark card schema (I3 — Loop 101) — `schemas/benchmark_card.schema.json` (Draft 2020-12, 15 required fields: benchmark_id, benchmark_name, version, date, metric, metric_value, baseline_name, baseline_value, delta, beats_baseline, dataset, dataset_size, scope, caveats, dry_lab_only). `$schema`, `$id`, `title`, `additionalProperties: false`. `src/openamp_foundry/benchmarks/` module with `BenchmarkCard` dataclass (15 fields), `make_benchmark_card()` (auto-computes delta, beats_baseline), `validate_benchmark_card()` (10 checks: non-empty benchmark_id, non-empty benchmark_name, non-empty metric, non-empty dataset, non-empty baseline_name, dataset_size >= 1, delta matches metric_value - baseline_value within 1e-9, beats_baseline matches delta > 0, dry_lab_only must be True), `benchmark_card_summary()` (total, beats_baseline_count, fails_baseline_count, dry_lab_only). CLI (`openamp-foundry benchmark-card`) with `--benchmark-id`, `--benchmark-name`, `--metric`, `--metric-value`, `--baseline-name`, `--baseline-value`, `--dataset`, `--dataset-size`, `--validate`, `--format text|json`. `make benchmark-card` target. 19 tests. **3329 total.** A benchmark card is the standard format for describing external benchmark results — what was benchmarked, what the baseline was, what the result was, and what claims are supported.
@@ -94,7 +94,7 @@ 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:** v0.6.4 (I6 — adapter author validator)
+> **Pipeline version:** v0.6.5 (I7 — data license checker)
 > **Branch:** main
 
 ---
@@ -1164,7 +1164,7 @@ Decoys score low on activity. Selective AMPs score moderately on both.
 
 | Metric | Value |
 |--------|-------|
-| Total tests | 3387 |
+| Total tests | 3393 |
 | Coverage (branch) | 99% (6 CLI guard lines only) |
 | Source modules at 100% | All pipeline, QC, scoring, adapter modules |
 

diff --git a/docs/research/ROADMAP.md b/docs/research/ROADMAP.md
@@ -1,5 +1,70 @@
 # Roadmap
 
+## v0.6.5 — Loop 105: Phase I I7 — Data License Checker ✓ (2026-07-09)
+
+`src/openamp_foundry/licensing/license_checker.py` with `DataLicenseDeclaration`
+dataclass (11 fields: source_id, source_name, license_id, use_context,
+attribution_required, commercial_use_allowed, redistribution_allowed,
+modifications_allowed, human_review_required, notes, dry_lab_only).
+`LicenseCheckResult` dataclass (8 fields: source_id, license_id, use_context,
+passed, status, errors, warnings, dry_lab_only). `check_data_license()` validates
+declarations against three license sets: `APPROVED_LICENSES` (11 entries: CC0-1.0,
+CC-BY-4.0, CC-BY-SA-4.0, MIT, Apache-2.0, GPL-3.0, LGPL-2.1, BSD-2-Clause,
+BSD-3-Clause, ODbL-1.0, PDDL-1.0), `RESTRICTED_LICENSES` (4 entries: CC-BY-NC-4.0,
+CC-BY-NC-SA-4.0, custom, proprietary), `BLOCKED_LICENSES` (3 entries: unknown,
+unlicensed, all-rights-reserved). Blocked licenses fail immediately; restricted
+require human_review_required=True; unknown licenses require governance review.
+`check_license_batch()` summarizes total/passed/failed/blocked/any_blocked/
+all_passed with dry_lab_only=True. `VALID_USE_CONTEXTS` (6 entries: training,
+scoring, benchmarking, reporting, publication, internal).
+
+CLI (`openamp-foundry license-check`) with `--source-json` (required) and
+`--format text|json`. Handler `_run_license_check` in reports.py.
+
+`make license-check` target. 20 tests. **3393 total.** External data sources
+used in pipeline outputs now require explicit license declarations, preventing
+hidden legal risk. This is Loop 105 — the 105th PR in the NEXT_100_PR_MAP series.
+
+Changes:
+- `src/openamp_foundry/licensing/__init__.py` (I7) — Empty package init.
+- `src/openamp_foundry/licensing/license_checker.py` (I7) — Core module with
+  `DataLicenseDeclaration` (11 fields), `LicenseCheckResult` (8 fields),
+  `check_data_license()` (validates against APPROVED_LICENSES 11 entries,
+  RESTRICTED_LICENSES 4, BLOCKED_LICENSES 3, VALID_USE_CONTEXTS 6),
+  `check_license_batch()` (summary with counts, any_blocked, all_passed,
+  dry_lab_only=True). All dataclasses carry dry_lab_only=True.
+- `tests/licensing/__init__.py` (I7) — Empty package init.
+- `tests/licensing/test_license_checker.py` (I7) — 20 tests covering: valid CC0
+  passes, valid MIT passes, blocked unknown/unlicensed/all-rights-reserved fail,
+  restricted CC-BY-NC-4.0 without human_review fails, restricted with human_review
+  passes, empty source_id/source_name/license_id fail, invalid use_context fails,
+  dry_lab_only=False fails, publication without redistribution fails, unknown
+  license gets status=unknown_license, batch counts correct, all results
+  dry_lab_only, constant counts.
+- `src/openamp_foundry/cli/main.py` (I7) — Registered `license-check` subcommand
+  with `--source-json`, `--format` flags. Added import and dispatch.
+- `src/openamp_foundry/cli/commands/reports.py` (I7) — Added `_run_license_check()`
+  CLI handler with JSON parsing, DataLicenseDeclaration creation, text and JSON
+  output, and exit code 3 on failure.
+- `Makefile` (I7) — Added `license-check` target with demo invocation using
+  apd-v2 source and CC-BY-4.0 license. Added to `.PHONY`.
+- `docs/evidence/METRICS_CURRENT.md` — v0.6.5 I7 changelog. Test count: 3393.
+- `tests/test_test_count_regression.py` — baseline updated to 3393.
+
+Honest boundaries:
+- License validation checks declared license identifiers against known lists.
+  It does not verify that the data source actually uses the declared license,
+  that the license is legally enforceable in a given jurisdiction, or that the
+  data was lawfully obtained.
+- Approved and blocked lists are policy-defined and may need updating as the
+  legal landscape evolves.
+- `dry_lab_only: true` is a const field on all dataclasses — license checks
+  are inherently computational and must never be presented as legal advice.
+- External adapter authors who produce data from new sources must declare their
+  licenses before those data can influence pipeline outputs.
+- Restricted licenses require human_review_required=True — this is a structural
+  check that the flag is set, not verification that human review actually occurred.
+
 ## v0.6.4 — Loop 104: Phase I I6 — Adapter Author Validator ✓ (2026-07-09)
 
 `src/openamp_foundry/adapters/adapter_validator.py` with `AdapterDeclaration`

diff --git a/src/openamp_foundry/cli/commands/reports.py b/src/openamp_foundry/cli/commands/reports.py
@@ -2247,3 +2247,59 @@ def _run_adapter_check(args: argparse.Namespace) -> int:
         print("not biological proof.")
 
     return 0 if result.passed else 3
+
+
+def _run_license_check(args: argparse.Namespace) -> int:
+    """Validate a data license declaration."""
+    from openamp_foundry.licensing.license_checker import (
+        DataLicenseDeclaration,
+        check_data_license,
+    )
+
+    try:
+        source_dict = json.loads(args.source_json)
+    except (json.JSONDecodeError, TypeError) as e:
+        print(json.dumps({"status": "error", "error": f"Invalid --source-json: {e}"}))
+        return 2
+
+    if not isinstance(source_dict, dict):
+        print(json.dumps({"status": "error", "error": "--source-json must be a JSON object"}))
+        return 2
+
+    decl = DataLicenseDeclaration(**source_dict)
+    result = check_data_license(decl)
+    output_format = getattr(args, "format", "text")
+
+    if output_format == "json":
+        print(json.dumps({
+            "source_id": result.source_id,
+            "license_id": result.license_id,
+            "use_context": result.use_context,
+            "passed": result.passed,
+            "status": result.status,
+            "errors": result.errors,
+            "warnings": result.warnings,
+            "dry_lab_only": result.dry_lab_only,
+        }, indent=2))
+    else:
+        print("License Check")
+        print("=" * 60)
+        print(f"Source ID:      {result.source_id}")
+        print(f"License ID:     {result.license_id}")
+        print(f"Use Context:    {result.use_context}")
+        print(f"Status:         {result.status.upper()}")
+        print(f"Result:         {'PASS' if result.passed else 'FAIL'}")
+        print()
+        if result.errors:
+            print("Errors:")
+            for err in result.errors:
+                print(f"  - {err}")
+        if result.warnings:
+            print("Warnings:")
+            for w in result.warnings:
+                print(f"  - {w}")
+        print()
+        print("Dry-lab only. License checks are computational safeguards,")
+        print("not legal advice.")
+
+    return 0 if result.passed else 3