feat: Phase K K4 post-experiment calibration intake schema -- structured prediction-vs-outcome comparison

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
+.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
 
 PYTHON := $(shell [ -f .venv/bin/python ] && echo .venv/bin/python || echo python3)
 PYTEST  := $(shell [ -f .venv/bin/pytest ] && echo .venv/bin/pytest || echo pytest)
@@ -900,3 +900,8 @@ pilot-package-check:
 	.venv/bin/openamp-foundry pilot-package-check \
 		--entry-json '{"package_id":"PKG-001","batch_id":"BATCH-001","submission_date":"2026-07-09","pipeline_version":"0.8.1","included_artifacts":["selection_rationale","batch_priority","evidence_certificate"],"missing_artifacts":[],"reviewer":"alice","approver":"bob","completeness_score":1.0,"ready_to_submit":true,"dry_lab_only":true}' \
 		--format text
+
+calibration-intake-check:
+	.venv/bin/openamp-foundry calibration-intake-check \
+		--entry-json '{"intake_id":"CAL-001","batch_id":"BATCH-001","candidate_id":"AMP-001","pipeline_version":"0.8.1","assay_type":"mic_assay","predicted_outcome":"active","observed_outcome":"active","predicted_confidence":0.85,"intake_date":"2026-07-09","reviewer":"alice","dry_lab_only":false}' \
+		--format text

docs/evidence/CALIBRATION_INTAKE_GUIDE.md

@@ -0,0 +1,65 @@
+# Post-Experiment Calibration Intake Guide
+
+When an external lab returns results from a pilot batch, each experimental outcome
+must be compared against the pipeline's dry-lab predictions. This guide defines the
+structured intake format for capturing that comparison and feeding it back into the
+calibration system.
+
+## Purpose
+
+Calibration intake records exist so the pipeline can:
+- detect when prediction confidence is systematically over- or under-estimated,
+- trigger recalibration when error rates cross defined thresholds, and
+- maintain an auditable trail of prediction-vs-outcome comparisons.
+
+## Required fields
+
+| Field | Type | Constraint |
+|---|---|---|
+| `intake_id` | str | Must start with `"CAL-"` |
+| `batch_id` | str | Non-empty |
+| `candidate_id` | str | Non-empty |
+| `pipeline_version` | str | Non-empty |
+| `assay_type` | str | One of `VALID_ASSAY_TYPES` |
+| `predicted_outcome` | str | One of `VALID_OUTCOME_VALUES` |
+| `observed_outcome` | str | One of `VALID_OUTCOME_VALUES` |
+| `predicted_confidence` | float | 0.0 – 1.0 |
+| `intake_date` | str | ISO 8601 `YYYY-MM-DD` |
+| `reviewer` | str | Non-empty |
+| `dry_lab_only` | bool | Must be `False` — this record captures real lab results |
+
+## Note on dry_lab_only
+
+Unlike all other records in the pipeline, a calibration intake record **must** set
+`dry_lab_only = False` because it contains actual experimental outcome data.
+Keeping `dry_lab_only = True` on a record that contains lab results would be a
+false claim. The validator enforces this.
+
+## Valid assay types
+
+`mic_assay`, `hemolysis_assay`, `cytotoxicity_assay`, `membrane_disruption_assay`, `stability_assay`
+
+## Valid outcome values
+
+`active`, `inactive`, `inconclusive`, `not_tested`
+
+## Warnings
+
+- `predicted_outcome == observed_outcome` (correct prediction) — no warnings, just noted in PASS output.
+- `predicted_confidence >= 0.90` and prediction is wrong — warning: high-confidence misprediction.
+- `observed_outcome == "inconclusive"` — warning: result is inconclusive; do not count as calibration signal.
+
+## How to validate
+
+```bash
+make calibration-intake-check
+# or
+openamp-foundry calibration-intake-check \
+  --entry-json '{"intake_id":"CAL-001","batch_id":"BATCH-001","candidate_id":"AMP-001","pipeline_version":"0.8.1","assay_type":"mic_assay","predicted_outcome":"active","observed_outcome":"active","predicted_confidence":0.85,"intake_date":"2026-07-09","reviewer":"alice","dry_lab_only":false}' \
+  --format text
+```
+
+## Honest-use boundary
+
+Calibration intake records describe real experimental outcomes. They must never be
+confused with dry-lab predictions. `dry_lab_only` must be `False` on every intake record.

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 K3 — pilot package completeness checker — v0.8.1)
+> **Last updated:** 2026-07-09 (Phase K K4 — post-experiment calibration intake schema — v0.8.2)
+> **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.
 >
 > **New in v0.8.0:** Batch experiment priority ranker (K2 — Loop 120) — docs/evidence/BATCH_PRIORITY_GUIDE.md with purpose, required field table (11 fields), how-to-validate instructions. src/openamp_foundry/evidence/batch_priority.py with BatchPriorityEntry dataclass (12 fields: priority_id, batch_id, candidate_id, pipeline_version, priority_rank, priority_score, evidence_level, synthesis_complexity, novelty_tier, primary_rationale, disqualifying_concerns, dry_lab_only), BatchPriorityResult dataclass (6 fields, dry_lab_only=True), VALID_SYNTHESIS_COMPLEXITIES (3: high, low, medium), VALID_NOVELTY_TIERS (3: high, low, medium), VALID_EVIDENCE_LEVELS (6: 1-6), validate_batch_priority() (11 checks: PRI- prefix, non-empty batch_id/candidate_id/pipeline_version, priority_rank>=1, priority_score 0.0-1.0, valid evidence_level, valid synthesis_complexity, valid novelty_tier, non-empty primary_rationale, dry_lab_only must be True; evidence_level<=2 warns, rank==1+high-complexity warns, priority_score<0.30 warns), validate_batch_priority_dict() (10 required fields guard). CLI (openamp-foundry batch-priority-check) with --entry-json, --format text|json. make batch-priority-check target. Phase K K2: synthesis wave ranking is now machine-validated.

docs/research/ROADMAP.md

@@ -1,5 +1,8 @@
 # Roadmap
 
+### v0.8.2
+- Phase K K4: post-experiment calibration intake schema — captures structured comparison of pipeline dry-lab prediction against actual experimental outcome. CalibrationIntakeEntry dataclass (dry_lab_only=False enforced), validate_calibration_intake(), CLI calibration-intake-check.
+
 ## v0.8.1 — Loop 121: Phase K K3 — Pilot Package Completeness Checker
 
 `docs/evidence/PILOT_PACKAGE_GUIDE.md` with purpose, required field table (11

src/openamp_foundry/cli/commands/reports.py

@@ -2919,3 +2919,38 @@ def _run_pilot_package_check(args: argparse.Namespace) -> int:
             print("  Pilot package validated. All required artifacts present.")
 
     return 0 if result.passed else 3
+
+
+def _run_calibration_intake_check(args: argparse.Namespace) -> int:
+    """Validate a post-experiment calibration intake entry."""
+    import json as _json
+    from openamp_foundry.evidence.calibration_intake import validate_calibration_intake_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_calibration_intake_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"
+        correct = "correct" if result.prediction_correct else "incorrect"
+        print(f"Calibration intake {result.intake_id} (candidate {result.candidate_id}, prediction {correct}): {status}")
+        for e in result.errors:
+            print(f"  ERROR: {e}")
+        for w in result.warnings:
+            print(f"  WARN:  {w}")
+        if result.passed:
+            print("  Calibration intake validated. Prediction-vs-outcome comparison is recorded.")
+
+    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
+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
 
 import argparse
 import json
@@ -2035,6 +2035,24 @@ def build_parser() -> argparse.ArgumentParser:
         help="Output format (default: text).",
     )
 
+    # ── Calibration intake check (Phase K K4) ────────────────────────
+    cic = sub.add_parser(
+        "calibration-intake-check",
+        help=(
+            "Validate a post-experiment calibration intake entry. Compares pipeline "
+            "prediction against actual lab outcome and records the calibration signal."
+        ),
+    )
+    cic.add_argument(
+        "--entry-json", type=str, required=True,
+        help="JSON string of a CalibrationIntakeEntry dict (required).",
+    )
+    cic.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",
@@ -2349,6 +2367,9 @@ def main(argv: list[str] | None = None) -> int:
     if args.command == "pilot-package-check":
         return _run_pilot_package_check(args)
 
+    if args.command == "calibration-intake-check":
+        return _run_calibration_intake_check(args)
+
     parser.error("unknown command")
     return 2