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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
30 lines
2.2 KiB
Markdown
30 lines
2.2 KiB
Markdown
# Φ Encoding Rationale: The 30-Base DNA Sequence
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This document explains the logic behind every position in the 30-base DNA sequence generated by the BioSight Φ encoding pipeline.
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## Layout Overview
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The sequence is divided into four functional blocks, each representing a different mathematical dimension of the expression $E$.
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### Block 1: Surface Identity ($F\_dna$) | Bases 0–7 (8 bases)
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**What it represents:** The primary character classification ($\Delta_{12}$).
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- **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.
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### Block 2: Topology & Connectivity ($\tau\_dna$) | Bases 8–15 (8 bases)
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**What it represents:** The structural "shape" or connectivity map.
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- **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.
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### Block 3: Depth & Weight Distribution ($\delta\_dna$) | Bases 16–23 (8 bases)
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**What it represents:** The recursive depth weight ($\omega$).
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- **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.
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### Block 4: Closure & Consistency | Bases 24–29 (6 bases)
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**What it represents:** The Rule 7 closure constraint.
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- **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.
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## Summary Table
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| Range | Component | Dimension | Key Property |
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|-------|----------|-----------|--------------|
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| 0–7 | $F\_dna$ | Surface | Identity / Type |
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| 8–15 | $\tau\_dna$| Topology | Connectivity |
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| 16–23 | $\delta\_dna$| Distribution | Depth / Weight |
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| 24–29 | Consistency| Closure | Completeness |
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