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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
42 lines
1.2 KiB
Python
42 lines
1.2 KiB
Python
import sys
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import os
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# Add current directory to path so we can import from . (or just use module names)
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sys.path.append(os.path.dirname(__file__))
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from phi.embed import encode_phi
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from phi.output import to_fastq, design_filtering_protocol
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def test():
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equations = [
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"x + y",
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"(a * b) + (c / d)",
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"x^2 + y^2 = z^2",
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"sin(x) + cos(y)",
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"sqrt(x + y) * 2",
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"", # Empty case
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]
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print(f"{'Equation':<20} | {'DNA Sequence':<30} | {'Consistency Pass':<15}")
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print("-" * 70)
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for eq in equations:
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record = encode_phi(eq)
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if record:
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dna = record["dna_sequence"]
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pass_flag = "PASS" if record["consistency_pass"] else "FAIL"
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print(f"{eq:<20} | {dna:<30} | {pass_flag:<15}")
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else:
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print(f"{eq:<20} | {'None':<30} | {'N/A':<15}")
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# Test Output functions
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sample_record = encode_phi("(a + b) * c")
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if sample_record:
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print("\n--- FASTQ Example ---")
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print(to_fastq(sample_record))
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print("--- PCR Protocol ---")
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print(design_filtering_protocol([sample_record]))
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if __name__ == "__main__":
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test()
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