mirror of https://github.com/allaunthefox/BioSight.git synced 2026-07-31 03:05:22 +00:00

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

2.2 KiB

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Φ Encoding Rationale: The 30-Base DNA Sequence

This document explains the logic behind every position in the 30-base DNA sequence generated by the BioSight Φ encoding pipeline.

Layout Overview

The sequence is divided into four functional blocks, each representing a different mathematical dimension of the expression E.

Block 1: Surface Identity (`F\_dna`) | Bases 0–7 (8 bases)

What it represents: The primary character classification (\Delta_{12}).

Rationale: These bases capture the "what" of the expression. By using \Delta_{12}, we move beyond simple types to include Symmetry, Periodicity, and Continuity. It provides the immediate visual/structural signature of the components.

Block 2: Topology & Connectivity (`\tau\_dna`) | Bases 8–15 (8 bases)

What it represents: The structural "shape" or connectivity map.

Rationale: These bases capture how components are linked. It distinguishes between a linear chain, a nested structure, and a branching tree. Even for simple expressions, this ensures the relative "pathway" of operations is preserved.

Block 3: Depth & Weight Distribution (`\delta\_dna`) | Bases 16–23 (8 bases)

What it represents: The recursive depth weight (\omega).

Rationale: These bases quantify how much "weight" each sub-component carries relative to the whole. It handles the nuances of nesting—identifying which parts are deep in the tree and which are at the surface, allowing for a multi-dimensional view of complexity.

Block 4: Closure & Consistency | Bases 24–29 (6 bases)

What it represents: The Rule 7 closure constraint.

Rationale: These final bases act as the "mathematical seal." They verify that the expression is consistent within the Φ system's rules. It confirms whether the sequence of operations "closes" correctly, providing a binary or multi-state check for mathematical completeness.

Summary Table

Range	Component	Dimension	Key Property
0–7	`F\_dna`	Surface	Identity / Type
8–15	`\tau\_dna`	Topology	Connectivity
16–23	`\delta\_dna`	Distribution	Depth / Weight
24–29	Consistency	Closure	Completeness

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