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Deploy Aureon OS (deploy/selfhost stack: nginx edge + fusion API x2 + console + HNC organ + redis + postgres; paper mode) (part 19)
da0ce7b verified | #!/usr/bin/env python3 | |
| """Test + benchmark the bio pipeline on the data we legitimately have. | |
| Two honest lanes, printed with ✅/❌: | |
| 1. **Bio anchor (synthetic / cited reference).** No open UPE dataset exists as a | |
| clean download (biophoton data lives in paper supplements — see | |
| ``docs/reports/UPE_DATA_AVAILABILITY.md``), so the UPE path is exercised on the | |
| cited reference profile + deterministic synthetic data: broadband/featureless | |
| UPE must score NON-separable (the honest anchor), planted emission lines must | |
| score separable, and the convergence map must run under governance. | |
| 2. **Real open molecular data.** The repo already holds genuine open-source spectra | |
| (NIST WebBook IR peaks in ``data/spectra/nist_ir_peaks.csv``). We run the | |
| falsifiable phenolic engine on them via ``connector.run_analysis`` and assert a | |
| valid, deterministic result — the "open source data + test" demonstration. | |
| Run: ``python scripts/validation/benchmark_bio_open_data.py``. | |
| """ | |
| from __future__ import annotations | |
| import sys | |
| from pathlib import Path | |
| REPO_ROOT = Path(__file__).resolve().parents[2] | |
| if str(REPO_ROOT) not in sys.path: | |
| sys.path.insert(0, str(REPO_ROOT)) | |
| DATA = REPO_ROOT / "data" / "spectra" | |
| FIXTURES = REPO_ROOT / "tests" / "fixtures" | |
| def main(argv: list[str] | None = None) -> int: | |
| """Run the bio anchor + real-open-data checks; return 0 iff all pass.""" | |
| import numpy as np | |
| from aureon.bio.convergence_map import analyze_convergence | |
| from aureon.bio.upe_signal_adapter import score_upe, synthetic_upe | |
| checks: list[tuple[bool, str]] = [] | |
| # ---- Lane 1: bio anchor (synthetic / cited reference) ------------------ | |
| broadband = score_upe(synthetic_upe("broadband"), consent=True, | |
| provenance="open-data validation (synthetic UPE)", nulls=300) | |
| structured = score_upe(synthetic_upe("structured"), consent=True, | |
| provenance="open-data validation (synthetic UPE)", nulls=300) | |
| checks.append((broadband.valid and not broadband.structure_present, | |
| "broadband UPE reference -> structure ABSENT (honest anchor)")) | |
| checks.append((structured.structure_present, | |
| "structured UPE (planted lines) -> structure PRESENT")) | |
| img = np.zeros((120, 120, 3), np.uint8) | |
| img[:60, :60] = (230, 30, 30) | |
| img[:60, 60:] = (30, 200, 30) | |
| img[60:, :60] = (30, 30, 220) | |
| img[60:, 60:] = (230, 220, 20) | |
| cmap = analyze_convergence(img, consent=True, provenance="open-data validation (synthetic image)", | |
| grid=4, nulls=200) | |
| checks.append((cmap.valid and cmap.controls_pass | |
| and all(c.converged == (c.channels_fired == 2) for c in cmap.cells), | |
| f"convergence map valid; {cmap.n_converged}/{len(cmap.cells)} both-channel cells")) | |
| # ---- Lane 2: real open molecular data (NIST IR) ------------------------ | |
| sources = [str(p) for p in ( | |
| FIXTURES / "weed_phenolic_spectral_map_codex.csv", | |
| DATA / "nist_ir_peaks.csv", | |
| DATA / "curated_open_access_peaks.csv", | |
| ) if p.exists()] | |
| nist_present = (DATA / "nist_ir_peaks.csv").exists() | |
| if sources: | |
| import connector | |
| r1 = connector.run_analysis(sources, nulls=300, seed=0) | |
| r2 = connector.run_analysis(sources, nulls=300, seed=0) | |
| d1, d2 = r1.to_dict(), r2.to_dict() | |
| checks.append((d1["valid"] and len(d1["compounds"]) > 0, | |
| f"real open data ({len(sources)} src, NIST={nist_present}) -> " | |
| f"valid, {len(d1['compounds'])} compounds")) | |
| checks.append((d1["compounds"] == d2["compounds"], | |
| "phenolic run on open data is deterministic (seed=0)")) | |
| else: | |
| checks.append((False, "no open-data sources found on disk")) | |
| print("Bio pipeline — open-source data test + benchmark") | |
| ok = True | |
| for passed, label in checks: | |
| ok = ok and passed | |
| print(f" {'✅' if passed else '❌'} {label}") | |
| print(f" broadband A_p={broadband.test_A_p} | structured A_p={structured.test_A_p} " | |
| f"B_p={structured.test_B_p}") | |
| return 0 if ok else 1 | |
| if __name__ == "__main__": | |
| raise SystemExit(main()) | |