v0.5.68 — Publication Pack Checklist (Loop 48)

docs/50_LOOP_PLAN.md

@@ -133,7 +133,7 @@ Prepare for real wet-lab partners. Make the pack reviewable, the evidence tracea
 | 45 ✅ | No chain-of-custody hashing for lab samples. Lab receives peptides but can't verify identity | `scripts/build_lab_batch_pack.py` now writes `chain_of_custody.json` + `MANIFEST.json` into the lab batch pack, including SHA-256 hashes for `panel.csv`, the ordered candidate list, each candidate sequence, and each evidence certificate. `--verify-pack` re-checks archive integrity end to end. v0.5.65 | Verification script passes on synthetic data and fails on tampered packs |
 | 46 | No pre-registered analysis plan for Wave 1 results. What analysis runs when data comes back? | `docs/WAVE1_ANALYSIS_PLAN.md`: pre-registered statistical analysis (primary: MIC ≤ 32 hit rate; secondary: selectivity index; exploratory: per-family correlation). No post-hoc changes allowed | Plan is timestamped and locked before data return |
 | 47 ✅ | No data-return validation tool. Lab sends CSV/JSON files; pipeline needs to validate them against schema | `scripts/validate_lab_data_return.py`: validates JSON files against `schemas/lab_result.schema.json`, reports per-file errors, detects control failures. v0.5.67 | 8 tests, 2008 total. Detects missing fields, invalid JSON, control failures |
-| 48 | No public-data release package. If results are publishable, what goes in the supplement? | `docs/PUBLICATION_PACK.md`: checklist for public release — benchmark data, evidence certificates, candidate scores, negative results, analysis scripts, README for reproduction | Pack is complete enough for a reviewer to reproduce all findings |
+| 48 ✅ | No public-data release package. If results are publishable, what goes in the supplement? | `docs/PUBLICATION_PACK.md`: 12-section checklist covering pipeline code, input data, scores, benchmarks, panel, wet-lab results, calibration, reproducibility, negative results, safety, README, preprint prep. v0.5.68 | Pack is complete enough for a reviewer to reproduce all findings |
 | 49 | **Culmination loop**: run the full dry-lab pipeline end-to-end, calibrate against any available wet-lab data, produce the final report. Pre-register the discovery claim | Full reproducibility report: all outputs regenerated from versioned inputs, benchmark card finalized, calibration report generated, discovery probability estimated with honest uncertainty | `make full-reproducibility-report` succeeds; all 49 gates pass; report is publishable as a preprint |
 
 **Phase 4 exit criteria:**
@@ -242,7 +242,7 @@ Phase 4: In progress — Loop 43 ✅ (Loops 40–49)
 | 28 ✅ | Policy version bump workflow for when real data arrives | `scripts/bump_recalibration_policy.py`: standalone script with `--dry-run`, decision-log guard, auto-increment + write. CI guard in `ci.yml` validates policy version changes against base branch. v0.5.49. 9 tests. | CI rejects policy PRs without valid decision log; `make bump-policy-version` and `make bump-policy-version-dry-run` available |
 | 29 ✅ | No public negative-result archive format. If Wave 1 yields all negatives, where do they go? | `docs/NEGATIVE_RESULT_ARCHIVE.md`: full template with entry schema, procedures, automation notes, and limitations. Covers pre-selection rejects, selected-untested, lab inactives, lab toxic, control failures. v0.5.50. | Template complete enough for a lab partner to fill; schema defines 18 fields with required/conditional markers |
 
-**Next loop:** Loop 48 — public-data release package.
+**Next loop:** Loop 49 — culmination reproducibility report.
 
 **Phase 2 exit criteria (all 5 met ✅):**
 - ✅ `make calibration-loop` runs from clean checkout, produces batch-2 manifest

docs/METRICS_CURRENT.md

@@ -5,7 +5,7 @@ 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:** 2026-07-06 (data-return validation — v0.5.67)
+> **Last updated:** 2026-07-06 (publication pack — v0.5.68)
 > **New in v0.5.65:** `scripts/build_lab_batch_pack.py` now writes `chain_of_custody.json` and `MANIFEST.json` into lab batch packs. The custody file includes SHA-256 hashes for `panel.csv`, the ordered candidate list, each candidate sequence, and each evidence certificate. `--verify-pack` verifies archive integrity and detects tampering. These hashes prove identity/integrity only, not biological activity, safety, or synthesis success. 5 tests.
 > **New in v0.5.64:** `schemas/decision_log.schema.json` — 12-field JSON Schema for human review decisions. Covers 9 decision types from AGENTS.md §8. Dissent conditional. 11 tests. 2000 total.
 > **New in v0.5.63:** `scripts/build_lab_batch_pack.py` — generates single zip with candidate CSV, 36 evidence certs, protocol refs, controls manifest, data return template. `make lab-batch-pack`. 10 tests. 1989 total.

docs/PUBLICATION_PACK.md

@@ -0,0 +1,156 @@
+# Publication Pack Checklist
+
+**Purpose:** What to include in a public release of OpenAMP Foundry results.
+A reviewer should be able to reproduce all findings from the contents of this pack.
+
+---
+
+## 1. Pipeline Code and Version
+
+- [ ] Git commit SHA of the pipeline version used.
+- [ ] `configs/pipeline.yaml` and `configs/phase3.yaml` used for scoring.
+- [ ] List of all Python package dependencies with versions (`pip freeze` or `pyproject.toml`).
+- [ ] Instructions to recreate the Python environment (`make install` or `pip install -e .[dev]`).
+
+---
+
+## 2. Input Data
+
+- [ ] Candidate sequences (FASTA or CSV).
+- [ ] Reference AMP database version and download instructions (APD6, DRAMP, UniProt).
+- [ ] Decoy sequences used for benchmarking.
+- [ ] Dataset cards for each dataset (source, license, date, known biases).
+- [ ] Input hashes (SHA-256) for reproducibility verification.
+
+---
+
+## 3. Scoring and Ranking Outputs
+
+- [ ] Per-candidate scores (JSONL or CSV): ensemble, activity, safety, synthesis, novelty.
+- [ ] Per-candidate simulation scores (if `--simulation-mode info` was used).
+- [ ] Selection rule used (`configs/pipeline.yaml` weights).
+- [ ] Ranked candidate list with selection reasons.
+- [ ] Evidence certificates (JSON) for all selected candidates.
+
+---
+
+## 4. Benchmark Results
+
+- [ ] Expanded benchmark (500 AMP + 500 decoy): AUROC, AUPRC, CI.
+- [ ] Cluster-split benchmark with cluster-aware CI.
+- [ ] Easy baseline comparison (charge density vs pipeline).
+- [ ] Cross-dataset generalization (DRAMP).
+- [ ] Per-family breakdown (6 structural classes).
+- [ ] Precision@k calibration.
+- [ ] Simulation ablation results (AMP-vs-decoy + within-AMP).
+- [ ] Simulation cheap-baseline comparison (0/4 signals beat baselines).
+- [ ] Benchmark gate verdict (all metrics within tolerance).
+
+---
+
+## 5. Candidate Panel
+
+- [ ] Final panel CSV with candidate IDs, sequences, scores, and selection reasons.
+- [ ] Diversity clustering report.
+- [ ] Novelty report against known AMP references (BLOSUM62 local alignment).
+- [ ] Broad novelty check results (72-AMP or 27k-sequence reference).
+- [ ] Toxicity / hemolysis risk report.
+- [ ] Synthesis feasibility report.
+- [ ] Pre-registered selection rule document.
+- [ ] Evidence certificates for all selected candidates.
+
+---
+
+## 6. Wet-Lab Results (if available)
+
+- [ ] Raw lab result JSONs (one per candidate per assay).
+- [ ] Pass/fail criteria check output (`check_wave1_pass_fail.py` verdict).
+- [ ] Primary analysis results (MIC ≤ 32 hit rate).
+- [ ] Secondary analysis (selectivity index, TI > 10).
+- [ ] Exploratory analysis (per-family, structural class, calibration).
+- [ ] Positive control results.
+- [ ] Negative results archive entries.
+- [ ] Lab batch pack zip used.
+
+---
+
+## 7. Calibration and Active Learning (if available)
+
+- [ ] Calibration intake report (`calibration-intake` output).
+- [ ] Recalibration gate verdict (`recalibration-gate` output).
+- [ ] Weight update proposal (if gate passed).
+- [ ] Decision log entries for each human review decision.
+- [ ] Batch-2 selection manifest (if applicable).
+
+---
+
+## 8. Reproducibility Evidence
+
+- [ ] Run manifest JSON for each pipeline run (input hashes, config hash, outputs).
+- [ ] `make regenerated-all` output (all derived outputs from versioned inputs).
+- [ ] Benchmark gate output (`outputs/metrics_snapshot.json`).
+- [ ] Pipeline version string (`openamp-foundry --version`).
+- [ ] Random seed documentation (all benchmark scripts use deterministic seeds).
+
+---
+
+## 9. Negative Results
+
+- [ ] Pre-selection rejects (candidates eliminated by gates).
+- [ ] Selected-but-untested candidates.
+- [ ] Lab-tested inactives (MIC > 32 µg/mL).
+- [ ] Lab-tested toxic (TI < 2).
+- [ ] Control failures.
+- [ ] Simulation ablation negative results (0/4 signals beat baselines).
+- [ ] All entries in `outputs/negative_result_archive.csv` format.
+
+---
+
+## 10. Safety and Governance
+
+- [ ] Safety review documentation (dual-use, biosecurity).
+- [ ] Decision log entries for all human review decisions.
+- [ ] Pre-registration documents (assay preregistration, analysis plan).
+- [ ] Model release policy compliance (no unscreened weights shipped).
+- [ ] Responsible use statement.
+- [ ] License information (Apache-2.0 for code, CC BY 4.0 for docs).
+
+---
+
+## 11. README for Reproduction
+
+A top-level README in the release package should include:
+
+1. One-paragraph summary of what was done.
+2. System requirements (Python 3.11+, RAM, OS).
+3. Installation instructions.
+4. Command to regenerate scoring: `make demo` or `make regenerate-all`.
+5. Command to reproduce benchmarks: `make validate-scoring`, `make bench-500`, etc.
+6. Command to build the lab batch pack: `make lab-batch-pack`.
+7. Where to find evidence certificates, scores, and manifests.
+8. How to verify data integrity (SHA-256 hashes).
+9. Citation instructions and license.
+
+---
+
+## 12. Preprint / Publication Preparation
+
+- [ ] Methods section drafted from pipeline documentation.
+- [ ] Benchmark table prepared from METRICS_CURRENT.md.
+- [ ] Honest limitations section (charge-domination, no wet-lab data, simulation modules experimental).
+- [ ] Negative result section (all negative findings from Phase 3).
+- [ ] Author contributions and acknowledgments.
+- [ ] Data and code availability statement.
+- [ ] Competing interests declaration.
+- [ ] Pre-registration DOIs or timestamps for all locked plans.
+
+---
+
+## Related Documents
+
+- `docs/RELEASE_CHECKLIST.md` — General release process.
+- `docs/CLAIM_REVIEW_CHECKLIST.md` — Claim verification before publication.
+- `docs/DATA_GOVERNANCE.md` — Data licensing and redistribution policy.
+- `docs/ARTIFACT_VERSIONING.md` — Versioning scheme for pipeline outputs.
+- `docs/MODEL_CARD_TEMPLATE.md` — Model card format for released scorers.
+- `docs/TRUST_CENTER.md` — Trust and safety documentation hub.

docs/ROADMAP.md

@@ -1,5 +1,20 @@
 # Roadmap
 
+## v0.5.68 — Publication Pack Checklist (Loop 48) ✓ (2026-07-06)
+
+Checklist for public release of OpenAMP results. A reviewer can reproduce
+all findings from the contents of this pack.
+
+Changes:
+- ``docs/PUBLICATION_PACK.md`` — 12 sections: pipeline code and version,
+  input data, scoring outputs, benchmark results, candidate panel, wet-lab
+  results, calibration, reproducibility evidence, negative results, safety
+  and governance, README for reproduction, preprint preparation. References
+  7 related governance docs.
+- ``docs/50_LOOP_PLAN.md`` — Loop 48 ✅. Next: Loop 49.
+- ``docs/METRICS_CURRENT.md`` — Changelog updated.
+- No code changes. 2013 tests still pass.
+
 ## v0.5.67 — Data-Return Validation Tool (Loop 47) ✓ (2026-07-06)
 
 CLI to validate lab result JSON files against the schema.