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e0b2283972
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feat(phi): full docstring + verification hardening pass
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
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2026-06-24 03:57:50 -05:00 |
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41fcbc3daa
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feat(init): initial BioSight commit — equation-to-DNA Φ encoding
BioSight encodes mathematical equations as 30-base hachimoji DNA
sequences for Adleman/Lipton-style DNA computing.
4-layer Φ mapping:
Layer 1: F(E) — byte-class histogram on Δ₇
Layer 3: τ(E) + δ(E) — parse tree structure
Layer 4: 6 consistency rules → allele-specific PCR pass/fail
Independent phi/ modules:
charclass, ast_parse, consistency, embed, output
Build: python3 -m py_compile — all modules clean
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2026-06-23 18:27:35 -05:00 |
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