feat: Phase I I5 -- downstream project template

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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -805,3 +805,8 @@ candidate-manifest:
 artifact-changelog:
 	.venv/bin/openamp-foundry artifact-changelog
 	@echo "Artifact changelog complete."
+
+integration-check:
+	.venv/bin/openamp-foundry integration-check \
+		--manifest-json '{"candidate_id":"AMP-001","sequence":"AKLWKR","evidence_level":2,"scopes":["bacterial_binding"],"scores":{"binding_energy":0.75},"uncertainty":0.1,"source_modules":["membrane_proxy"],"calibration_set":null,"safety_flags":[],"provenance_run_id":null,"dry_lab_only":true,"version":"1.0.0","created_at":"2026-07-09T00:00:00Z","notes":[]}'
+	@echo "Integration check complete."

docs/adoption/DOWNSTREAM_PROJECT_TEMPLATE.md

@@ -0,0 +1,274 @@
+# Downstream Project Template
+
+## Overview
+
+OpenAMP Foundry produces **computational (dry-lab) artifacts** for antimicrobial
+peptide candidate selection. These artifacts are **hypotheses and review aids
+— not biological proof**.
+
+Available artifact types:
+
+- **Candidate manifests** — structured descriptions of dry-lab candidates
+  (sequence, scores, evidence level, safety flags, provenance)
+- **Benchmark cards** — standard format for benchmark results with baseline
+  comparison
+- **Evidence certificates** — proof-ladder-level bounded claims with caveats
+- **Simulation results** — virtual-assay module outputs with uncertainty
+- **Artifact changelog** — version history for all artifact types
+
+All artifacts carry `dry_lab_only: true`. They must never be presented as
+validated biological findings without independent wet-lab confirmation.
+
+---
+
+## Minimum Viable Integration
+
+The simplest way to consume OpenAMP artifacts is to read a candidate manifest,
+validate it, and use the evidence level and scores for downstream decisions.
+
+### Step 1: Consume a Candidate Manifest
+
+Candidate manifests are produced by the OpenAMP pipeline (JSON format):
+
+```json
+{
+  "candidate_id": "AMP-001",
+  "sequence": "AKLWKR",
+  "evidence_level": 2,
+  "scopes": ["bacterial_binding"],
+  "scores": {"binding_energy": 0.75},
+  "uncertainty": 0.1,
+  "source_modules": ["membrane_proxy"],
+  "calibration_set": null,
+  "safety_flags": [],
+  "provenance_run_id": null,
+  "dry_lab_only": true,
+  "version": "1.0.0",
+  "created_at": "2026-07-09T00:00:00Z",
+  "notes": []
+}
+```
+
+Required fields: `candidate_id`, `sequence`, `evidence_level`, `scopes`,
+`scores`, `uncertainty`, `source_modules`, `calibration_set`, `safety_flags`,
+`provenance_run_id`, `dry_lab_only`, `version`, `created_at`, `notes`.
+
+### Step 2: Validate Against the Schema
+
+```python
+import json
+from openamp_foundry.evidence.schemas import validate_json_schema
+
+with open("candidate_manifest.schema.json") as f:
+    schema = json.load(f)
+
+with open("manifest.json") as f:
+    manifest = json.load(f)
+
+errors = validate_json_schema(manifest, schema)
+if errors:
+    raise ValueError(f"Manifest validation failed: {errors}")
+```
+
+The canonical schema is at `schemas/candidate_manifest.schema.json` in the
+OpenAMP repository.
+
+### Step 3: Use the Python Library (Optional)
+
+```python
+from openamp_foundry.manifests.candidate_manifest import (
+    CandidateManifest,
+    validate_candidate_manifest,
+)
+
+manifest = CandidateManifest(
+    candidate_id="AMP-001",
+    sequence="AKLWKR",
+    evidence_level=2,
+    scopes=["bacterial_binding"],
+    scores={"binding_energy": 0.75},
+    uncertainty=0.1,
+    source_modules=["membrane_proxy"],
+    calibration_set=None,
+    safety_flags=[],
+    provenance_run_id=None,
+)
+
+errors = validate_candidate_manifest(manifest)
+assert not errors, errors
+```
+
+### Step 4: Run the Integration Checker
+
+```bash
+pip install openamp-foundry
+openamp-foundry integration-check \
+  --manifest-json '{"candidate_id":"AMP-001","sequence":"AKLWKR",...}'
+```
+
+The integration checker validates all required fields, evidence level range,
+safety flag conventions, dry-lab acknowledgment, and baseline comparison.
+
+---
+
+## Schema Validation
+
+Every OpenAMP artifact type has a corresponding JSON Schema in the `schemas/`
+directory:
+
+| Artifact | Schema |
+|---|---|
+| Candidate manifest | `schemas/candidate_manifest.schema.json` |
+| Benchmark card | `schemas/benchmark_card.schema.json` |
+| Simulation result | `schemas/simulation_result.schema.json` |
+| Simulation module registry | `schemas/simulation_module_registry.schema.json` |
+
+Validate any artifact against its schema using:
+
+```python
+from openamp_foundry.evidence.schemas import validate_json_schema
+import json
+
+with open("schemas/candidate_manifest.schema.json") as f:
+    schema = json.load(f)
+with open("my_manifest.json") as f:
+    data = json.load(f)
+
+errors = validate_json_schema(data, schema)
+```
+
+All schemas use JSON Schema Draft 2020-12 with `additionalProperties: false`.
+
+---
+
+## Evidence Level Interpretation
+
+| Level | Label | Meaning | Caveat |
+|---|---|---|---|
+| **L1** | Computational nomination | ML/heuristic score above threshold | No biological testing |
+| **L2** | Virtual-assay support | Simulation or proxy-model agreement | Proxy models are not validated biology |
+| **L3** | In-silico ensemble agreement | Multiple independent scorers agree | Agreement is consistency, not proof |
+| **L4** | Ex-vivo preliminary | Preliminary non-human assay data | Small sample, non-standard assay |
+| **L5** | In-vivo preliminary | Animal model data | Not human data |
+| **L6** | Clinical evidence | Human clinical data | Requires full clinical review |
+
+**Rule:** Dry-lab scores (L1-L3) do not prove biological activity. L4-L6
+require wet-lab or clinical evidence.
+
+---
+
+## Safety Flag Conventions
+
+Safety flags are string identifiers attached to a candidate manifest:
+
+| Flag | Meaning | Suggested Action |
+|---|---|---|
+| `hemolytic_risk` | Predicted hemolytic (HC50 < 25 µg/mL) | Flag for selectivity review |
+| `cytotoxic_risk` | Predicted cytotoxic (low CC50) | Flag for counterscreen |
+| `aggregation_risk` | Predicted aggregation-prone | Flag for formulation review |
+| `oxidation_risk` | Contains oxidation-prone residues (M, W, C) | Flag for synthesis planning |
+| `proteolytic_risk` | Predicted protease-sensitive | Flag for stability review |
+| `dual_use_concern` | Sequence matches known toxins | Escalate for safety review |
+
+An empty safety flags list (`[]`) means no flags were raised by the pipeline.
+It does not guarantee biological safety — only that automated checks passed.
+
+**Downstream consumers must review safety flags before any wet-lab or
+release decision.**
+
+---
+
+## Benchmark Card Consumption
+
+Benchmark cards describe how a method performed relative to a baseline:
+
+```json
+{
+  "benchmark_id": "bench-auroc-001",
+  "benchmark_name": "AMP vs Decoy AUROC",
+  "metric": "AUROC",
+  "metric_value": 0.82,
+  "baseline_name": "random",
+  "baseline_value": 0.50,
+  "delta": 0.32,
+  "beats_baseline": true,
+  "dataset": "APD3",
+  "dataset_size": 500,
+  "scope": ["bacterial"],
+  "caveats": ["charge-inflated benchmark"],
+  "dry_lab_only": true
+}
+```
+
+### How to Compare Against Baselines
+
+1. **Check `caveats`** first — they describe known limitations.
+2. **Compare `metric_value` to `baseline_value`:** `delta > 0` and
+   `beats_baseline = true` means the method outperforms its baseline.
+3. **Check the `scope`:** benchmark results are scope-specific.
+4. **Evaluate `dataset_size`:** small benchmarks have wider confidence
+   intervals.
+
+```python
+from openamp_foundry.benchmarks.benchmark_card import BenchmarkCard
+
+card = BenchmarkCard(
+    benchmark_id="bench-auroc-001",
+    benchmark_name="AMP vs Decoy AUROC",
+    version="1.0.0",
+    date="2026-07-09",
+    metric="AUROC",
+    metric_value=0.82,
+    baseline_name="random",
+    baseline_value=0.50,
+    delta=0.32,
+    beats_baseline=True,
+    dataset="APD3",
+    dataset_size=500,
+    scope=["bacterial"],
+    caveats=["charge-inflated benchmark"],
+)
+
+print(f"Beats baseline: {card.beats_baseline} (delta={card.delta:+.4f})")
+```
+
+---
+
+## Dry-Lab Limitations
+
+**All OpenAMP artifacts are computational and dry-lab only.** They constitute:
+
+- Hypotheses for expert review
+- Computational evidence packages for candidate triage
+- Structured metadata for pipeline reproducibility
+
+They do **not** constitute:
+
+- Biological proof of antimicrobial activity
+- Safety or toxicity validation
+- Clinical efficacy evidence
+- Regulatory submission data
+- A substitute for wet-lab or clinical testing
+
+**No computational prediction, regardless of score or evidence level, should
+be treated as biological validation without independent wet-lab confirmation.**
+
+The `dry_lab_only: true` field is a safety constraint on every artifact.
+Downstream projects must preserve this field and its semantics.
+
+---
+
+## Contact and Contribution
+
+- **Repository:** https://github.com/anomalyco/openamp-foundry
+- **Issues:** Bug reports, feature requests, adoption questions
+- **Discussions:** Integration patterns, schema questions, use cases
+
+To contribute integration examples or report issues with this template,
+open a GitHub issue or pull request.
+
+---
+
+*This template is a dry-lab integration guide. It does not contain biological
+instructions, assay protocols, or safety procedures requiring qualified
+human review.*