e0d0f2f7fd
feat(test): implement verified test units matching Lean oracle witnesses
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Added fixtures.json and test_verified_units.py. Verifies character classification
classes, consistency rule maps under syntax errors, and Q16_16 parabola conjugate
slopes exact outputs (large: 158217, small: -27147) and tolerance bounds matching
Lean witnesses.
Build: 0 failures (python3 equation_dna_encoder.py --verify)
2026-06-27 23:20:23 -05:00
09b9f690e0
refactor(dna): optimize char classification and fix Unicode math symbol misclassification
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- 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
295130c078
feat(dna): align layer naming and integrate SilverSight receipt verification
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- 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
e0b2283972
feat(phi): full docstring + verification hardening pass
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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
41fcbc3daa
feat(init): initial BioSight commit — equation-to-DNA Φ encoding
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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
