BioSight/python/phi/__init__.py
allaun 295130c078 feat(dna): align layer naming and integrate SilverSight receipt verification
- Aligned layer naming and numbering (1 to 4) with the formal Lean specifications in SilverSight.
- Implemented phi.silversight to verify rule ordering, N=8 necessity, and Lean compilation status.
- Integrated SilverSight validation checks into equation_dna_encoder.py and rigour_pipeline.py.

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2026-06-27 22:51:03 -05:00

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Python

"""
phi — SilverSight Equation-to-DNA Φ Encoding Pipeline
Independent modules, each reusable without the others:
charclass Layer 1: byte-class frequencies on Δ₇ (bases 0-7)
ast_parse Layer 2 & 3: AST parsing → τ (Layer 2, bases 8-15) and δ (Layer 3, bases 16-23)
consistency Layer 4: 6 consistency rules (bases 24-29) → ADMIT/QUARANTINE
embed Core Φ: (F, τ, δ) → 30-base hachimoji DNA sequence
output FASTQ, Adleman graph, PCR primer protocol
Usage:
from phi import encode_phi
result = encode_phi("d_F(p,q) = 2*arccos(sum(sqrt(p_i*q_i)))")
print(result["dna_sequence"])
"""
from .embed import encode_phi
from .output import to_fastq, to_adleman_graph, design_filtering_protocol, PRIMER_DESIGN
from .charclass import compute_F
from .ast_parse import compute_tau, compute_delta
from .consistency import check_consistency, CONSISTENCY_RULES
from .silversight import verify_pipeline_receipt