feat: Phase I I2 — candidate manifest schema (Loop 100)

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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -780,3 +780,15 @@ simulation-evidence-packet:
 artifact-version:
 	.venv/bin/openamp-foundry artifact-version --list
 	@echo "Artifact version list complete."
+
+candidate-manifest:
+	.venv/bin/openamp-foundry candidate-manifest \
+		--candidate-id AMP-001 \
+		--sequence AKLWKR \
+		--evidence-level 2 \
+		--scopes bacterial_binding \
+		--scores-json '{"binding_energy": 0.75}' \
+		--uncertainty 0.1 \
+		--source-modules membrane_proxy \
+		--validate
+	@echo "Candidate manifest complete."

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 I I1 — artifact versioning policy — v0.5.99)
+> **Last updated:** 2026-07-09 (Phase I I2 — candidate manifest schema — v0.6.0)
+> **New in v0.6.0:** Candidate manifest schema (I2 — Loop 100) — `schemas/candidate_manifest.schema.json` (Draft 2020-12, 14 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). `$schema`, `$id`, `title`, `description`, `additionalProperties: false`. `src/openamp_foundry/manifests/` module with `CandidateManifest` dataclass (14 fields), `make_candidate_manifest()`, `validate_candidate_manifest()` (8 checks: non-empty candidate_id, non-empty sequence, evidence_level 1-6, non-empty scopes, uncertainty 0.0-1.0, non-empty source_modules, dry_lab_only must be True, version MAJOR.MINOR.PATCH), `manifest_to_dict()`, `manifest_summary()` (total, by_evidence_level, with_safety_flags, dry_lab_only). CLI (`openamp-foundry candidate-manifest`) with `--candidate-id`, `--sequence`, `--evidence-level`, `--scopes`, `--scores-json`, `--uncertainty`, `--source-modules`, `--validate`, `--format text|json`. `make candidate-manifest` target. 19 tests. **3310 total.** A candidate manifest is the core interoperable artifact — it describes a dry-lab candidate (sequence, scores, evidence level, scopes, safety flags, provenance) in a machine-readable format that external tools can consume without the full OpenAMP stack.
 > **New in v0.5.99:** Artifact versioning policy (I1 — starts Phase I) — `docs/engineering/ARTIFACT_VERSIONING_POLICY.md` with structured versioning policy covering scope, SemVer format, breaking/non-breaking change definitions, deprecation timeline (at least one minor version warning), schema `$id` policy, changelog requirement, and three stability tiers (stable/experimental/internal). `src/openamp_foundry/versioning/` module with `ArtifactVersionInfo` dataclass (7 fields), `STABILITY_TIERS` dict, `VERSIONED_ARTIFACTS` list (6 entries covering candidate, lab_result, run_manifest, external_review_packet, safety_release_decision, simulation_result at v1.0.0), `get_artifact_version()`, `list_versioned_artifacts()`, `validate_version_format()`, `artifact_version_summary()`. CLI (`openamp-foundry artifact-version`) with `--list`, `--show`, `--tier`, `--format text|json`. `make artifact-version` target. 19 tests. **3291 total.** Starts Phase I (interoperability) — external users now have stability guarantees for schemas, evidence certificates, and candidate manifests.
 > **New in v0.5.97:** Simulation-scope coverage checker (H9) — `ScopeCoverageResult` dataclass (8 fields: module_id, requested_scopes, module_scopes, covered, uncovered, coverage_fraction, is_fully_covered, dry_lab_only). `check_scope_coverage()` looks up module in registry, computes covered (intersection) and uncovered (requested scopes not in module scopes), coverage_fraction = len(covered)/len(requested_scopes) if requested else 1.0. `check_result_scope()` uses conservative intersection of registry scopes and result.scope as effective module_scopes. `scope_coverage_report()` returns full dict. CLI (`openamp-foundry simulation-scope-check`) with `--module-id`, `--requested-scopes`, `--format text|json`. `make simulation-scope-check` target. 17 tests. **3255 total.** A simulation module may cover only some biological scopes. If a candidate is evaluated for a scope the module doesn't cover, that result must be flagged as out-of-scope rather than silently trusted.
 > **New in v0.5.96:** Simulation-module deprecation enforcer (H8) — `DeprecationCheckResult` dataclass (5 fields: module_id, status, is_blocked, block_reason, dry_lab_only). `BLOCKED_STATUSES = {"deprecated", "unavailable"}`. `check_module_deprecation()` looks up module in registry: not-found returns is_blocked=True status="unknown"; deprecated/unavailable returns is_blocked=True with reason; active/experimental returns is_blocked=False. `enforce_deprecation()` filters list[SimulationResult] to only non-blocked modules, returns total_input/passed/blocked/blocked_modules/passed_results/checks/dry_lab_only. `run_deprecation_check_batch()` bulk-checks module_ids with total/blocked/allowed/any_blocked/results/dry_lab_only. CLI (`openamp-foundry simulation-deprecation-check`) with `--module-ids`, `--format text|json`. `make simulation-deprecation-check` target. 21 tests. **3238 total.** Deprecated simulation modules must not be used in production scoring — the enforcer prevents stale or unreliable modules from tainting evidence packets.
@@ -89,7 +90,7 @@ 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:** v0.5.99 (I1 — artifact versioning policy)
+> **Pipeline version:** v0.6.0 (I2 — candidate manifest schema)
 > **Branch:** main
 
 ---

docs/research/ROADMAP.md

@@ -1,5 +1,72 @@
 # Roadmap
 
+## v0.6.0 — Loop 100: Phase I I2 — Candidate Manifest Schema ✓ (2026-07-09)
+
+`schemas/candidate_manifest.schema.json` (Draft 2020-12, 14 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). `$schema`, `$id`, `title`, `description`,
+`additionalProperties: false`.
+
+`src/openamp_foundry/manifests/` module with `CandidateManifest` dataclass
+(14 fields), `make_candidate_manifest()`, `validate_candidate_manifest()`
+(8 checks: non-empty candidate_id, non-empty sequence, evidence_level 1-6,
+non-empty scopes, uncertainty 0.0-1.0, non-empty source_modules,
+dry_lab_only must be True, version MAJOR.MINOR.PATCH), `manifest_to_dict()`,
+`manifest_summary()` (total, by_evidence_level, with_safety_flags, dry_lab_only).
+
+CLI (`openamp-foundry candidate-manifest`) with `--candidate-id`, `--sequence`,
+`--evidence-level`, `--scopes`, `--scores-json`, `--uncertainty`,
+`--source-modules`, `--validate`, `--format text|json`.
+`make candidate-manifest` target.
+
+19 tests. **3310 total.** A candidate manifest is the core interoperable
+artifact — it describes a dry-lab candidate (sequence, scores, evidence level,
+scopes, safety flags, provenance) in a machine-readable format that external
+tools can consume without the full OpenAMP stack. This is Loop 100 — the
+100th PR in the NEXT_100_PR_MAP series.
+
+Changes:
+- `schemas/candidate_manifest.schema.json` (I2) — Draft 2020-12 schema with
+  14 required fields, `$id`, `title`, `description`, `additionalProperties: false`.
+- `src/openamp_foundry/manifests/__init__.py` (I2) — Package init, exports
+  `CandidateManifest`, `make_candidate_manifest`, `validate_candidate_manifest`,
+  `manifest_to_dict`, `manifest_summary`.
+- `src/openamp_foundry/manifests/candidate_manifest.py` (I2) — Core module
+  with `CandidateManifest` dataclass (14 fields), `make_candidate_manifest()`,
+  `validate_candidate_manifest()`, `manifest_to_dict()`, `manifest_summary()`.
+- `src/openamp_foundry/cli/main.py` (I2) — Registered `candidate-manifest`
+  subcommand with `--candidate-id`, `--sequence`, `--evidence-level`,
+  `--scopes`, `--scores-json`, `--uncertainty`, `--source-modules`,
+  `--validate`, `--format` flags. Added import and dispatch.
+- `src/openamp_foundry/cli/commands/reports.py` (I2) — Added
+  `_run_candidate_manifest()` CLI handler with JSON and text output,
+  manifest creation, optional validation, and error handling.
+- `Makefile` (I2) — Added `candidate-manifest` target with demo invocation
+  using AMP-001. Added to `.PHONY`.
+- `tests/manifests/__init__.py` (I2) — Empty package init.
+- `tests/manifests/test_candidate_manifest.py` (I2) — 19 tests covering:
+  make_candidate_manifest returns CandidateManifest, dry_lab_only always True,
+  valid manifest passes validation, empty candidate_id fails, empty sequence
+  fails, evidence_level 0 or 7 fails, empty scopes fails, uncertainty out of
+  range fails, empty source_modules fails, dry_lab_only=False fails,
+  invalid version fails, manifest_to_dict returns all fields, manifest_summary
+  total correct, with_safety_flags correct, dry_lab_only=True, by_evidence_level
+  correct, schema file exists.
+- `docs/evidence/METRICS_CURRENT.md` — v0.6.0 I2 changelog. Test count: 3310.
+- `tests/test_test_count_regression.py` — baseline updated to 3310.
+
+Honest boundaries:
+- Candidate manifests describe dry-lab candidates only — they are computational
+  artifacts, not biological proof.
+- Scores and uncertainty are pipeline outputs, not measured biological properties.
+- The manifest schema is versioned (currently 1.0.0) and should be updated when
+  fields are added or changed.
+- Validation checks structural correctness only — it does not verify biological
+  plausibility, safety, or efficacy.
+- `dry_lab_only: true` is a const field — all manifests are inherently dry-lab
+  and must never be presented as validated wet-lab candidates.
+
 ## v0.5.95 — Loop 95: Phase H H7 — Simulation-Result Confidence Interval Reporter ✓ (2026-07-09)
 
 `ScoreCI` dataclass (9 fields: module_id, score_key, point_estimate, uncertainty,

schemas/candidate_manifest.schema.json

@@ -0,0 +1,100 @@
+{
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://openamp-foundry.org/schemas/candidate_manifest.schema.json",
+    "title": "CandidateManifest",
+    "description": "Schema for a dry-lab candidate manifest — a machine-readable artifact describing a candidate AMP sequence, its scores, evidence level, scopes, safety flags, and provenance. Dry-lab only — does not measure biological activity.",
+    "type": "object",
+    "properties": {
+        "candidate_id": {
+            "description": "Unique identifier for the candidate",
+            "type": "string",
+            "minLength": 1
+        },
+        "sequence": {
+            "description": "Amino acid sequence of the candidate AMP",
+            "type": "string",
+            "minLength": 1
+        },
+        "evidence_level": {
+            "description": "Proof-ladder evidence level (1=computational nomination, 2=virtual-assay support, 3=in-silico ensemble agreement, 4=ex-vivo preliminary, 5=in-vivo preliminary, 6=clinical evidence)",
+            "type": "integer",
+            "minimum": 1,
+            "maximum": 6
+        },
+        "scopes": {
+            "description": "List of biological scopes this candidate is assessed for (e.g. bacterial_binding, anti_fungal)",
+            "type": "array",
+            "items": { "type": "string" },
+            "minItems": 1
+        },
+        "scores": {
+            "description": "Dictionary of named score values from pipeline modules",
+            "type": "object",
+            "patternProperties": {
+                "^.*$": { "type": "number" }
+            }
+        },
+        "uncertainty": {
+            "description": "Overall uncertainty estimate (0.0 = fully certain, 1.0 = fully uncertain)",
+            "type": "number",
+            "minimum": 0.0,
+            "maximum": 1.0
+        },
+        "source_modules": {
+            "description": "List of pipeline modules or scorers that produced this manifest",
+            "type": "array",
+            "items": { "type": "string" },
+            "minItems": 1
+        },
+        "calibration_set": {
+            "description": "Optional identifier for the calibration dataset used",
+            "type": ["string", "null"]
+        },
+        "safety_flags": {
+            "description": "List of safety flags (empty array = no flags raised)",
+            "type": "array",
+            "items": { "type": "string" }
+        },
+        "provenance_run_id": {
+            "description": "Optional run ID linking this manifest to a specific pipeline execution",
+            "type": ["string", "null"]
+        },
+        "dry_lab_only": {
+            "description": "Must be true — this is a dry-lab computational artifact",
+            "type": "boolean",
+            "const": true
+        },
+        "version": {
+            "description": "Manifest schema version (MAJOR.MINOR.PATCH)",
+            "type": "string",
+            "pattern": "^\\d+\\.\\d+\\.\\d+$"
+        },
+        "created_at": {
+            "description": "ISO 8601 UTC timestamp of manifest creation",
+            "type": "string",
+            "format": "date-time"
+        },
+        "notes": {
+            "description": "Free-text notes about this candidate",
+            "type": "array",
+            "items": { "type": "string" }
+        }
+    },
+    "required": [
+        "candidate_id",
+        "sequence",
+        "evidence_level",
+        "scopes",
+        "scores",
+        "uncertainty",
+        "source_modules",
+        "calibration_set",
+        "safety_flags",
+        "provenance_run_id",
+        "dry_lab_only",
+        "version",
+        "created_at",
+        "notes"
+    ],
+    "additionalProperties": false
+}