feat: Phase L L3 candidate summary card schema -- publication-ready per-candidate structured summaries

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 license-check artifact-compat-check contribution-check adoption-scorecard release-gate-check decision-log release-request-check coi-check rotation-plan-check security-report-check citation-check roadmap-sync-check advisory-review-check annual-review-check selection-rationale-check batch-priority-check pilot-package-check calibration-intake-check uncertainty-report-check preprint-bundle-check reproducibility-manifest-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 artifact-compat-check contribution-check adoption-scorecard release-gate-check decision-log release-request-check coi-check rotation-plan-check security-report-check citation-check roadmap-sync-check advisory-review-check annual-review-check selection-rationale-check batch-priority-check pilot-package-check calibration-intake-check uncertainty-report-check preprint-bundle-check reproducibility-manifest-check candidate-summary-card-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)
@@ -920,3 +920,8 @@ reproducibility-manifest-check:
 	.venv/bin/openamp-foundry reproducibility-manifest-check \
 		--entry-json '{"manifest_id":"RPM-001","batch_id":"BATCH-001","pipeline_version":"0.8.5","run_date":"2026-07-09","python_version":"3.11.9","package_checksums":{"openamp_foundry":"0.8.4","numpy":"1.26.4","pandas":"2.2.2","scikit-learn":"1.4.2","torch":"2.3.0"},"data_checksums":{"data/amp_sequences.fasta":"abc123def456"},"random_seeds":{"ensemble_sampling":42},"hardware_summary":"Apple M3 Pro, 36 GB RAM","reviewer":"alice","dry_lab_only":true}' \
 		--format text
+
+candidate-summary-card-check:
+	.venv/bin/openamp-foundry candidate-summary-card-check \
+		--entry-json '{"card_id":"CRD-001","candidate_id":"AMP-001","batch_id":"BATCH-001","pipeline_version":"0.8.6","sequence":"KWKLFKKIEK","sequence_length":10,"evidence_level":4,"predicted_activity":"high_activity","safety_flags":[],"selection_rationale_id":"SEL-001","reviewer":"alice","dry_lab_only":true}' \
+		--format text

docs/evidence/CANDIDATE_SUMMARY_CARD_GUIDE.md

@@ -0,0 +1,61 @@
+# Candidate Summary Card Guide
+
+A *candidate summary card* is a publication-ready, per-candidate structured record
+that consolidates the key computational properties, evidence level, safety flags,
+and selection rationale for a single candidate into a reviewable snapshot.
+
+## Purpose
+
+Summary cards allow:
+- external reviewers to quickly assess individual candidates without reading the full evidence package,
+- authors to generate structured supplementary tables for preprints, and
+- downstream tooling to render consistent candidate reports.
+
+## Required fields
+
+| Field | Type | Constraint |
+|---|---|---|
+| `card_id` | str | Must start with `"CRD-"` |
+| `candidate_id` | str | Non-empty |
+| `batch_id` | str | Non-empty |
+| `pipeline_version` | str | Non-empty |
+| `sequence` | str | Non-empty, only standard amino acid letters (A-Z, no B/J/O/U/X/Z) |
+| `sequence_length` | int | Must equal `len(sequence)` |
+| `evidence_level` | int | 1 – 6 |
+| `predicted_activity` | str | One of `VALID_ACTIVITY_LABELS` |
+| `safety_flags` | list[str] | May be empty; each entry is a named safety concern |
+| `selection_rationale_id` | str | Must start with `"SEL-"` |
+| `reviewer` | str | Non-empty |
+| `dry_lab_only` | bool | Must be `True` |
+
+## Valid activity labels
+
+`high_activity`, `moderate_activity`, `low_activity`, `inactive`, `uncertain`
+
+## Valid amino acid letters
+
+Standard one-letter codes: A C D E F G H I K L M N P Q R S T V W Y
+(B, J, O, U, X, Z are excluded)
+
+## Warnings
+
+- `evidence_level <= 2` — warning: low evidence; apply extra scrutiny.
+- `len(safety_flags) > 0` — warning: safety concerns are flagged; review before synthesis.
+- `predicted_activity == "uncertain"` — warning: activity is uncertain; prioritize candidates with clearer predictions.
+- `sequence_length > 50` — warning: long peptide; synthesis cost may be high.
+
+## How to validate
+
+```bash
+make candidate-summary-card-check
+# or
+openamp-foundry candidate-summary-card-check \
+  --entry-json '{"card_id":"CRD-001","candidate_id":"AMP-001","batch_id":"BATCH-001","pipeline_version":"0.8.6","sequence":"KWKLFKKIEKVGQNIRDGIVKAGPAVADPQGRPVPVPVDPVDPVD","sequence_length":45,"evidence_level":4,"predicted_activity":"high_activity","safety_flags":[],"selection_rationale_id":"SEL-001","reviewer":"alice","dry_lab_only":true}' \
+  --format text
+```
+
+## Honest-use boundary
+
+Candidate summary cards are dry-lab outputs. Predicted activity and safety flags are
+computational estimates, not experimental results. They must not be presented as
+experimental measurements or used to make clinical or safety decisions.

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 L L2 — reproducibility manifest schema — v0.8.5)
+> **Last updated:** 2026-07-09 (Phase L L3 — candidate summary card schema — v0.8.6)
+> **New in v0.8.6:** Candidate summary card schema (L3 — Loop 126) — docs/evidence/CANDIDATE_SUMMARY_CARD_GUIDE.md with purpose, required field table (12 fields), valid activity labels (5), valid amino acid set (20 standard), warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/candidate_summary_card.py with CandidateSummaryCardEntry dataclass (12 fields: card_id, candidate_id, batch_id, pipeline_version, sequence, sequence_length, evidence_level, predicted_activity, safety_flags, selection_rationale_id, reviewer, dry_lab_only), CandidateSummaryCardResult dataclass (5 fields: card_id, candidate_id, sequence_length, passed, errors, warnings, dry_lab_only=True), VALID_ACTIVITY_LABELS (5: high_activity, inactive, low_activity, moderate_activity, uncertain), VALID_AMINO_ACIDS (20 standard one-letter codes), LONG_PEPTIDE_THRESHOLD (50), VALID_EVIDENCE_LEVELS (6: 1-6), validate_candidate_summary_card() (11 checks: CRD- prefix, non-empty candidate_id/batch_id/pipeline_version/reviewer, non-empty sequence with valid amino acids, sequence_length==len(sequence), valid evidence_level, valid predicted_activity, SEL- prefix on selection_rationale_id, dry_lab_only must be True; evidence_level<=2 warns, safety_flags non-empty warns, uncertain activity warns, length>50 warns), validate_candidate_summary_card_dict() (11 required fields guard). CLI (openamp-foundry candidate-summary-card-check) with --entry-json, --format text|json. make candidate-summary-card-check target. Phase L L3: every candidate now has a machine-validated publication-ready summary card.
 > **New in v0.8.5:** Reproducibility manifest schema (L2 — Loop 125) — docs/evidence/REPRODUCIBILITY_MANIFEST_GUIDE.md with purpose, required field table (11 fields), package checksums format, data checksums format, warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/reproducibility_manifest.py with ReproducibilityManifestEntry dataclass (11 fields: manifest_id, batch_id, pipeline_version, run_date, python_version, package_checksums, data_checksums, random_seeds, hardware_summary, reviewer, dry_lab_only), ReproducibilityManifestResult dataclass (6 fields: manifest_id, batch_id, package_count, data_file_count, passed, errors, warnings, dry_lab_only=True), MINIMUM_PACKAGES (3), MINIMUM_DATA_FILES (1), RECOMMENDED_PACKAGES (5), validate_reproducibility_manifest() (10 checks: RPM- prefix, non-empty batch_id/pipeline_version/python_version/hardware_summary/reviewer, YYYY-MM-DD run_date, package_checksums>=3, data_checksums>=1, dry_lab_only must be True; empty random_seeds warns, package_count<5 warns, hardware_summary contains 'unknown' warns), validate_reproducibility_manifest_dict() (10 required fields guard). CLI (openamp-foundry reproducibility-manifest-check) with --entry-json, --format text|json. make reproducibility-manifest-check target. Phase L L2: every pipeline run now has a machine-validated reproducibility record.
 > **New in v0.8.4:** Preprint evidence bundle schema (L1 — Loop 124) — docs/evidence/PREPRINT_BUNDLE_GUIDE.md with purpose, required field table (11 fields), minimum artifact count (3), evidence level guide, warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/preprint_bundle.py with PreprintBundleEntry dataclass (11 fields: bundle_id, batch_id, pipeline_version, submission_date, title, artifact_ids, evidence_level, preprint_doi, contact_email, release_approved, dry_lab_only), PreprintBundleResult dataclass (5 fields: bundle_id, batch_id, artifact_count, passed, errors, warnings, dry_lab_only=True), MINIMUM_ARTIFACTS (3), RECOMMENDED_ARTIFACT_COUNT (5), MAX_TITLE_LENGTH (300), VALID_EVIDENCE_LEVELS (6: 1-6), validate_preprint_bundle() (10 checks: BND- prefix, non-empty batch_id/pipeline_version/contact_email, YYYY-MM-DD submission_date, non-empty title<=300 chars, artifact_ids>=3, valid evidence_level 1-6, release_approved must be True, dry_lab_only must be True; evidence_level<=2 warns, empty preprint_doi warns, artifact_count<5 warns), validate_preprint_bundle_dict() (10 required fields guard). CLI (openamp-foundry preprint-bundle-check) with --entry-json, --format text|json. make preprint-bundle-check target. Phase L L1: scientific preprints now have a machine-validated evidence bundle structure.
 > **New in v0.8.3:** Uncertainty quantification report schema (K5 — Loop 123) — docs/evidence/UNCERTAINTY_REPORT_GUIDE.md with purpose, required field table (12 fields), valid metric names (5), warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/uncertainty_report.py with UncertaintyReportEntry dataclass (12 fields: report_id, batch_id, candidate_id, pipeline_version, metric_name, point_estimate, lower_bound, upper_bound, confidence_level, calibration_source, reviewer, dry_lab_only), UncertaintyReportResult dataclass (6 fields: report_id, candidate_id, interval_width, passed, errors, warnings, dry_lab_only=True), VALID_METRIC_NAMES (5: cytotoxicity_score, hemolysis_fraction, mic, selectivity_index, stability_score), WIDE_INTERVAL_THRESHOLD (10.0), validate_uncertainty_report() (11 checks: UQ- prefix, non-empty batch_id/candidate_id/pipeline_version/calibration_source/reviewer, valid metric_name, lower_bound<=point_estimate, upper_bound>=point_estimate, confidence_level 0.0-1.0, dry_lab_only must be True; wide interval warns, confidence<0.80 warns, confidence>0.99 warns), validate_uncertainty_report_dict() (11 required fields guard). CLI (openamp-foundry uncertainty-report-check) with --entry-json, --format text|json. make uncertainty-report-check target. Phase K K5: prediction intervals for external reviewers are now machine-validated.

docs/research/ROADMAP.md

@@ -1,5 +1,8 @@
 # Roadmap
 
+### v0.8.6
+- Phase L L3: candidate summary card schema — validates publication-ready per-candidate structured summaries with sequence, evidence level, activity prediction, and safety flags. CandidateSummaryCardEntry dataclass, validate_candidate_summary_card(), CLI candidate-summary-card-check.
+
 ### v0.8.5
 - Phase L L2: reproducibility manifest schema — captures exact software versions, data checksums, and random seeds for a pipeline run. ReproducibilityManifestEntry dataclass, validate_reproducibility_manifest(), CLI reproducibility-manifest-check.
 

src/openamp_foundry/cli/commands/reports.py

@@ -3056,3 +3056,37 @@ def _run_reproducibility_manifest_check(args: argparse.Namespace) -> int:
             print("  Reproducibility manifest validated. Run is fully documented for third-party reproduction.")
 
     return 0 if result.passed else 3
+
+
+def _run_candidate_summary_card_check(args: argparse.Namespace) -> int:
+    """Validate a candidate summary card entry."""
+    import json as _json
+    from openamp_foundry.evidence.candidate_summary_card import validate_candidate_summary_card_dict
+
+    try:
+        d = _json.loads(args.entry_json)
+    except _json.JSONDecodeError as exc:
+        print(_json.dumps({"status": "error", "error": f"Invalid JSON: {exc}"}))
+        return 2
+
+    if not isinstance(d, dict):
+        print(_json.dumps({"status": "error", "error": "--entry-json must be a JSON object"}))
+        return 2
+
+    result = validate_candidate_summary_card_dict(d)
+    output_format = getattr(args, "format", "text")
+
+    if output_format == "json":
+        import dataclasses
+        print(_json.dumps(dataclasses.asdict(result), indent=2))
+    else:
+        status = "PASS" if result.passed else "FAIL"
+        print(f"Candidate summary card {result.card_id} (candidate {result.candidate_id}, length {result.sequence_length}): {status}")
+        for e in result.errors:
+            print(f"  ERROR: {e}")
+        for w in result.warnings:
+            print(f"  WARN:  {w}")
+        if result.passed:
+            print("  Candidate summary card validated. Ready for reviewer packet.")
+
+    return 0 if result.passed else 3

src/openamp_foundry/cli/main.py

@@ -15,7 +15,7 @@
 from openamp_foundry.cli.commands.reports import _run_security_report_check
 from openamp_foundry.cli.commands.reports import _run_citation_check
 from openamp_foundry.cli.commands.reports import _run_roadmap_sync_check
-from openamp_foundry.cli.commands.reports import _run_advisory_review_check, _run_annual_review_check, _run_selection_rationale_check, _run_batch_priority_check, _run_pilot_package_check, _run_calibration_intake_check, _run_uncertainty_report_check, _run_preprint_bundle_check, _run_reproducibility_manifest_check
+from openamp_foundry.cli.commands.reports import _run_advisory_review_check, _run_annual_review_check, _run_selection_rationale_check, _run_batch_priority_check, _run_pilot_package_check, _run_calibration_intake_check, _run_uncertainty_report_check, _run_preprint_bundle_check, _run_reproducibility_manifest_check, _run_candidate_summary_card_check
 
 import argparse
 import json
@@ -2107,6 +2107,24 @@ def build_parser() -> argparse.ArgumentParser:
         help="Output format (default: text).",
     )
 
+    # ── Candidate summary card check (Phase L L3) ─────────────────────
+    cscc = sub.add_parser(
+        "candidate-summary-card-check",
+        help=(
+            "Validate a candidate summary card. Confirms sequence, evidence level, "
+            "activity label, and safety flags. Dry-lab only."
+        ),
+    )
+    cscc.add_argument(
+        "--entry-json", type=str, required=True,
+        help="JSON string of a CandidateSummaryCardEntry dict (required).",
+    )
+    cscc.add_argument(
+        "--format", type=str, default="text",
+        choices=["text", "json"],
+        help="Output format (default: text).",
+    )
+
     # ── Selection rationale check (Phase K K1) ───────────────────────
     src2 = sub.add_parser(
         "selection-rationale-check",
@@ -2433,6 +2451,9 @@ def main(argv: list[str] | None = None) -> int:
     if args.command == "reproducibility-manifest-check":
         return _run_reproducibility_manifest_check(args)
 
+    if args.command == "candidate-summary-card-check":
+        return _run_candidate_summary_card_check(args)
+
     parser.error("unknown command")
     return 2