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allaun
6b649ad271
Critical bug fix: dna_codec.py used biological base ordering (ATGCBSPZ) instead of ASCII-ordered spec ordering (ABCGPSTZ). This violated the core monotonicity axiom (int rank = lexicographic rank) that the entire monotone LUT pipeline depends on. Changes: - python/dna_codec.py: BITS_TO_BASE, HACHIMOJI_BASES, LATIN_TO_GREEK corrected to ABCGPSTZ ordering; encode_binary_vector parameter renamed bases_per_var; module docstring updated - tests/test_dna_codec.py: hardcoded byte→DNA expectations updated for new ordering (0xFF→ZZT, 0xd1→TPC); bases_per_var parameter name updated; 31/31 tests green - formal/CoreFormalism/HachimojiLUT.lean: replace fragile canonical_phases_preserved.2.2.2.2.2.1 chains with named obtain destructuring in pythagorean_position and contradiction_position - docs/UNIFIED_THEORY.md: add ground-truth caveat to epigenetic optimizer results table (n≥24 results are local optima, not verified global minima) Note: test_dna_nn.py has 4 pre-existing failures (Ising chain correlations) unrelated to this fix — dna_qubo_nn.py has its own base encoding and does not import dna_codec.py. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> |
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| .. | ||
| BindingSite | ||
| CoreFormalism | ||
| PVGS_DQ_Bridge | ||
| RRCLib | ||
| SilverSight | ||
| UniversalEncoding | ||