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 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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -910,3 +910,8 @@ uncertainty-report-check:
 	.venv/bin/openamp-foundry uncertainty-report-check \
 		--entry-json '{"report_id":"UQ-001","batch_id":"BATCH-001","candidate_id":"AMP-001","pipeline_version":"0.8.3","metric_name":"mic","point_estimate":4.0,"lower_bound":2.0,"upper_bound":8.0,"confidence_level":0.90,"calibration_source":"historical_holdout_v2","reviewer":"alice","dry_lab_only":true}' \
 		--format text
+
+preprint-bundle-check:
+	.venv/bin/openamp-foundry preprint-bundle-check \
+		--entry-json '{"bundle_id":"BND-001","batch_id":"BATCH-001","pipeline_version":"0.8.4","submission_date":"2026-07-09","title":"Computational nomination of AMP candidates from the OpenAMP Foundry","artifact_ids":["SEL-001","PRI-001","PKG-001","UQ-001","CAL-001"],"evidence_level":4,"preprint_doi":"10.1101/2026.07.09.000001","contact_email":"research@openamp.org","release_approved":true,"dry_lab_only":true}' \
+		--format text
diff --git a/docs/evidence/METRICS_CURRENT.md b/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 K K5 — uncertainty quantification report schema — v0.8.3)
+> **Last updated:** 2026-07-09 (Phase L L1 — preprint evidence bundle schema — v0.8.4)
+> **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.
 > **New in v0.8.2:** Post-experiment calibration intake schema (K4 — Loop 122) — docs/evidence/CALIBRATION_INTAKE_GUIDE.md with purpose, required field table (11 fields), note on dry_lab_only=False (real lab results), valid assay types (5), valid outcome values (4), warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/calibration_intake.py with CalibrationIntakeEntry dataclass (11 fields: intake_id, batch_id, candidate_id, pipeline_version, assay_type, predicted_outcome, observed_outcome, predicted_confidence, intake_date, reviewer, dry_lab_only=False), CalibrationIntakeResult dataclass (6 fields: intake_id, candidate_id, prediction_correct, passed, errors, warnings, dry_lab_only=False), VALID_ASSAY_TYPES (5: cytotoxicity_assay, hemolysis_assay, membrane_disruption_assay, mic_assay, stability_assay), VALID_OUTCOME_VALUES (4: active, inactive, inconclusive, not_tested), validate_calibration_intake() (11 checks: CAL- prefix, non-empty batch_id/candidate_id/pipeline_version/reviewer, valid assay_type, valid predicted_outcome, valid observed_outcome, confidence 0.0-1.0, YYYY-MM-DD date, dry_lab_only must be False; high-confidence misprediction warns, inconclusive observed warns), validate_calibration_intake_dict() (10 required fields guard). CLI (openamp-foundry calibration-intake-check) with --entry-json, --format text|json. make calibration-intake-check target. Phase K K4: prediction-vs-outcome comparisons are now machine-validated with honest dry_lab_only=False enforcement.
 > **New in v0.8.1:** Pilot package completeness checker (K3 — Loop 121) — docs/evidence/PILOT_PACKAGE_GUIDE.md with purpose, required field table (11 fields), mandatory artifact types table (3 types), valid artifact types, warnings, validation workflow, honest-use boundary. src/openamp_foundry/evidence/pilot_package.py with PilotPackageEntry dataclass (11 fields: package_id, batch_id, submission_date, pipeline_version, included_artifacts, missing_artifacts, reviewer, approver, completeness_score, ready_to_submit, dry_lab_only), PilotPackageResult dataclass (5 fields, dry_lab_only=True), MINIMUM_REQUIRED_ARTIFACTS (3), READINESS_SCORE_THRESHOLD (0.80), MANDATORY_ARTIFACT_TYPES (3: batch_priority, evidence_certificate, selection_rationale), VALID_ARTIFACT_TYPES (8 types), validate_pilot_package() (11 checks: PKG- prefix, non-empty batch_id/pipeline_version/reviewer/approver, YYYY-MM-DD submission_date, included_artifacts>=3, mandatory types covered, completeness_score 0.0-1.0, ready_to_submit must be False when score<0.80, dry_lab_only must be True; missing_artifacts non-empty warns, score<0.90 warns, same reviewer/approver warns), validate_pilot_package_dict() (10 required fields guard). CLI (openamp-foundry pilot-package-check) with --entry-json, --format text|json. make pilot-package-check target. Phase K K3: every pilot submission is now machine-validated for completeness.

diff --git a/docs/evidence/PREPRINT_BUNDLE_GUIDE.md b/docs/evidence/PREPRINT_BUNDLE_GUIDE.md
@@ -0,0 +1,71 @@
+# Preprint Evidence Bundle Guide
+
+A *preprint evidence bundle* ties together all Phase K artifacts for a specific batch
+into a single structured record that can be submitted alongside a scientific preprint.
+This guide defines what a bundle must contain, how to validate it, and the honesty
+constraints that apply.
+
+## Purpose
+
+Before submitting a preprint describing a computationally-nominated antimicrobial peptide
+family, the evidence bundle ensures that:
+- all K-phase artifacts (selection rationale, batch priority, pilot package, uncertainty reports)
+  are referenced,
+- the claimed evidence level is consistent with actual artifacts,
+- the bundle passes structural review before public release.
+
+## Required fields
+
+| Field | Type | Constraint |
+|---|---|---|
+| `bundle_id` | str | Must start with `"BND-"` |
+| `batch_id` | str | Non-empty |
+| `pipeline_version` | str | Non-empty |
+| `submission_date` | str | ISO 8601 `YYYY-MM-DD` |
+| `title` | str | Non-empty, ≤ 300 characters |
+| `artifact_ids` | list[str] | ≥ `MINIMUM_ARTIFACTS` (3) entries |
+| `evidence_level` | int | 1 – 6 (from PROOF_LADDER.md) |
+| `preprint_doi` | str | May be empty (DOI assigned after submission) |
+| `contact_email` | str | Non-empty |
+| `release_approved` | bool | Must be `True` for a valid bundle |
+| `dry_lab_only` | bool | Must be `True` |
+
+## Minimum artifact types
+
+At least 3 artifact IDs must be provided. The bundle does not enforce specific artifact
+types — it enforces count — because artifact IDs are opaque references tracked in the
+pilot package system.
+
+## Evidence level
+
+Use the same 1–6 scale as PROOF_LADDER.md:
+1. Sequence only
+2. Physicochemical
+3. Computational model
+4. Ensemble
+5. Virtual assay
+6. Cross-validated virtual assay
+
+A preprint with evidence level 1 or 2 warrants a warning.
+
+## Warnings
+
+- `evidence_level <= 2` — warning: low evidence level; reviewers should apply extra scrutiny.
+- `preprint_doi` empty — warning: DOI not yet assigned; update before final release.
+- `len(artifact_ids) < 5` — warning: fewer than 5 artifacts; consider adding uncertainty reports and calibration records.
+
+## How to validate
+
+```bash
+make preprint-bundle-check
+# or
+openamp-foundry preprint-bundle-check \
+  --entry-json '{"bundle_id":"BND-001","batch_id":"BATCH-001","pipeline_version":"0.8.4","submission_date":"2026-07-09","title":"Computational nomination of AMP candidates from the OpenAMP Foundry","artifact_ids":["SEL-001","PRI-001","PKG-001","UQ-001","CAL-001"],"evidence_level":4,"preprint_doi":"10.1101/2026.07.09.000001","contact_email":"research@openamp.org","release_approved":true,"dry_lab_only":true}' \
+  --format text
+```
+
+## Honest-use boundary
+
+Preprint evidence bundles describe computational nominations, not experimental validations.
+The bundle does not imply experimental success. Wet-lab validation results must be reported
+separately and must not be attributed to the pipeline.
diff --git a/docs/research/NEXT_100_PR_MAP.md b/docs/research/NEXT_100_PR_MAP.md
@@ -200,6 +200,18 @@ Build the evidence and accountability artifacts needed for credible external val
 | K4 | Add post-experiment calibration intake schema. | Structured result-to-prediction comparison. | B/D |
 | K5 | Add uncertainty quantification report schema (complete — Loop 123). | Honest prediction intervals for reviewers. | B |
 
+## Phase L — Scientific Communication
+
+Bridge the gap between evidence packages and published science.
+
+| PR | Task | Why it matters | Review class |
+|---:|---|---|---|
+| L1 | Add preprint evidence bundle schema (complete — Loop 124). | Ties K-phase artifacts into a submission-ready package. | B |
+| L2 | Add reproducibility manifest schema. | Captures exact versions, checksums, seeds for full reproduction. | B |
+| L3 | Add candidate summary card schema. | Publication-ready per-candidate structured summary. | B |
+| L4 | Add multi-candidate comparison schema. | Structured comparison table for ≥2 candidates. | B |
+| L5 | Add dataset release package checker. | Validates open dataset releases meet data governance. | B/D |
+
 
 ## Prioritization rule
 

diff --git a/docs/research/ROADMAP.md b/docs/research/ROADMAP.md
@@ -1,5 +1,8 @@
 # Roadmap
 
+### v0.8.4
+- Phase L L1: preprint evidence bundle schema — ties K-phase artifacts into a submission-ready record for scientific preprints. PreprintBundleEntry dataclass, validate_preprint_bundle(), CLI preprint-bundle-check.
+
 ### v0.8.3
 - Phase K K5: uncertainty quantification report schema — validates prediction intervals, confidence levels, and calibration source for dry-lab candidate recommendations. UncertaintyReportEntry dataclass, validate_uncertainty_report(), CLI uncertainty-report-check.
 

diff --git a/src/openamp_foundry/cli/commands/reports.py b/src/openamp_foundry/cli/commands/reports.py
@@ -2988,3 +2988,37 @@ def _run_uncertainty_report_check(args: argparse.Namespace) -> int:
             print("  Uncertainty report validated. Prediction intervals are documented.")
 
     return 0 if result.passed else 3
+
+
+def _run_preprint_bundle_check(args: argparse.Namespace) -> int:
+    """Validate a preprint evidence bundle entry."""
+    import json as _json
+    from openamp_foundry.evidence.preprint_bundle import validate_preprint_bundle_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_preprint_bundle_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"Preprint bundle {result.bundle_id} (batch {result.batch_id}, {result.artifact_count} artifacts): {status}")
+        for e in result.errors:
+            print(f"  ERROR: {e}")
+        for w in result.warnings:
+            print(f"  WARN:  {w}")
+        if result.passed:
+            print("  Preprint bundle validated. Evidence package is ready for submission review.")
+
+    return 0 if result.passed else 3
diff --git a/src/openamp_foundry/cli/main.py b/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
+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
 
 import argparse
 import json
@@ -2071,6 +2071,24 @@ def build_parser() -> argparse.ArgumentParser:
         help="Output format (default: text).",
     )
 
+    # ── Preprint bundle check (Phase L L1) ───────────────────────────
+    pbc = sub.add_parser(
+        "preprint-bundle-check",
+        help=(
+            "Validate a preprint evidence bundle. Confirms all K-phase artifacts "
+            "are referenced and release is approved. Dry-lab only."
+        ),
+    )
+    pbc.add_argument(
+        "--entry-json", type=str, required=True,
+        help="JSON string of a PreprintBundleEntry dict (required).",
+    )
+    pbc.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",
@@ -2391,6 +2409,9 @@ def main(argv: list[str] | None = None) -> int:
     if args.command == "uncertainty-report-check":
         return _run_uncertainty_report_check(args)
 
+    if args.command == "preprint-bundle-check":
+        return _run_preprint_bundle_check(args)
+
     parser.error("unknown command")
     return 2