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4 commits

Author SHA1 Message Date
allaun
09b9f690e0 refactor(dna): optimize char classification and fix Unicode math symbol misclassification 
- Pre-defined and unified character sets (OPERATOR_CHARS, BRACKET_CHARS, PUNCT_CHARS, WHITESPACE_CHARS).
- Defined precise sets for SYMMETRY_CHARS, PERIODICITY_CHARS, CONTINUITY_CHARS, and META_MATH_CHARS.
- Re-ordered specific checks to precede c.isalpha() so Unicode/Greek math letters are not misclassified as standard lower/upper alpha.

Build: 3307 jobs, 0 errors (lake build)
 2026-06-27 22:53:16 -05:00
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.

Build: 3307 jobs, 0 errors (lake build)
 2026-06-27 22:51:03 -05:00
allaun
e0b2283972 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
 2026-06-24 03:57:50 -05:00
allaun
41fcbc3daa 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
 2026-06-23 18:27:35 -05:00