mirror of
https://github.com/allaunthefox/BioSight.git
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allaun
e0b2283972
Every function in all 5 phi modules now has: - Google-style docstring with Args/Returns/Examples - Verified behavior via doctest examples (46 total) - Self-verification assertion blocks on direct execution Verification results: charclass: 10 doctests, 16 assertions — PASS ast_parse: 21 doctests, 7 assertions — PASS consistency: 6 assertions — PASS embed: multiple assertions — PASS output: 15 doctests, 16 assertions — PASS CLI wrapper: 3 checks — PASS End-to-end: 9 equation domains — PASS Also added: - .opencode/opencode.jsonc (gemma4 MCP config) - phi/AGENTS.md (module-level contract) - phi/test_phi.py (unittest test file) - phi/encoding_rationale.md (design docs) - dag/ (project dependency graph) - harness/ (Lean formalism constraints) - 7-Pipeline/ (rigour verification harness) Build: python3 -W error -m py_compile — 0 warnings
99 lines
3.3 KiB
Python
99 lines
3.3 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
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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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# 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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