mirror of
https://github.com/allaunthefox/BioSight.git
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allaun
e0d0f2f7fd
Added fixtures.json and test_verified_units.py. Verifies character classification classes, consistency rule maps under syntax errors, and Q16_16 parabola conjugate slopes exact outputs (large: 158217, small: -27147) and tolerance bounds matching Lean witnesses. Build: 0 failures (python3 equation_dna_encoder.py --verify)
122 lines
4.1 KiB
Python
122 lines
4.1 KiB
Python
#!/usr/bin/env python3
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"""
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equation_dna_encoder.py — SilverSight Φ Encoder CLI
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Thin CLI wrapper around the phi package modules. Reads one or more
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equations from argv or stdin, applies the Φ encoding pipeline
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(F → DNA → consistency), and prints the result as human-readable
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key-value lines plus the FASTQ entry.
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Usage:
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echo 'd_F(p,q) = 2*arccos(sum(sqrt(p_i*q_i)))' | python equation_dna_encoder.py
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python equation_dna_encoder.py 'E(x) = x^T Q x'
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python equation_dna_encoder.py --verify # run verification suite
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"""
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from __future__ import annotations
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import sys
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from phi import encode_phi, to_fastq
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def main():
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"""Encode equation(s) from argv or stdin and print Φ-encoded result.
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When called without arguments, reads equations line-by-line from
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stdin. When called with arguments, the first ``len(sys.argv) - 1``
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arguments are joined as a single equation.
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Each equation is passed to ``phi.encode_phi``; the resulting dict
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is printed as labelled key-value lines followed by the FASTQ entry.
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"""
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if len(sys.argv) > 1:
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equations = [" ".join(sys.argv[1:])]
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else:
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equations = [line.strip() for line in sys.stdin if line.strip()]
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for eq in equations:
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result = encode_phi(eq)
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if result is None:
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print(f"FAIL: could not parse: {eq!r}", file=sys.stderr)
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continue
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print(f"# Equation: {result['equation']}")
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print(f"# DNA: {result['dna_sequence']} ({result['length']} bases)")
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print(f"# PASS: {result['consistency_pass']}")
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print(f"# Hash: {result['sha256_prefix']}")
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print(f"# F: {result['F']}")
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print(f"# τ: {result['tau']}")
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print(f"# δ: {result['delta']}")
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print(f"# FASTQ: {to_fastq(result).rstrip()}")
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print()
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if __name__ == "__main__":
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if "--verify" in sys.argv:
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# ── Verification (python3 equation_dna_encoder.py --verify) ────
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import subprocess
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import os
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fail = 0
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# 1. Import from phi
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try:
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from phi import encode_phi, to_fastq, verify_pipeline_receipt
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print(" ✓ phi imports OK")
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except ImportError as e:
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print(f"FAIL: phi import failed: {e}")
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fail += 1
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# 1b. SilverSight Formalization Verification
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print(" Running SilverSight Formal Verification Checks...")
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try:
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ss_results = verify_pipeline_receipt()
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for check, passed in ss_results.items():
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if passed:
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print(f" ✓ {check} OK")
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else:
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print(f" FAIL: {check} failed")
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fail += 1
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except Exception as e:
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print(f"FAIL: SilverSight verification failed: {e}")
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fail += 1
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# 1c. Verified Test Units
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try:
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from phi.test_verified_units import run_verified_tests
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if not run_verified_tests():
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fail += 1
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except Exception as e:
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print(f"FAIL: Verified Test Units failed to run: {e}")
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fail += 1
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# 2. encode_phi
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result = encode_phi("E(x) = x^2")
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if result is None:
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fail += 1; print("FAIL: encode_phi returned None")
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else:
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print(f" ✓ encode_phi → {result['length']} bases, "
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f"PASS={result['consistency_pass']}")
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assert "dna_sequence" in result, "result missing dna_sequence"
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assert "F" in result, "result missing F"
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assert "consistency" in result, "result missing consistency"
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# 3. CLI mode with subprocess
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cp = subprocess.run(
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[sys.executable, __file__, "a = b"],
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capture_output=True, text=True, timeout=10,
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)
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if cp.returncode != 0:
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fail += 1
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print(f"FAIL: CLI subprocess exited {cp.returncode}: {cp.stderr}")
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elif "FASTQ:" not in cp.stdout:
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fail += 1
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print(f"FAIL: CLI output missing FASTQ:\n{cp.stdout}")
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else:
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print(" ✓ CLI subprocess output includes FASTQ")
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print(f"\nVerdict: {fail} failure(s)")
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sys.exit(fail)
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else:
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main()
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