# BioSight Agent Rules

## Goal
Establish an unimpeachable base layer for the BioSight project by refining its Φ encoding pipeline through mathematical audit, autonomous bug elimination, and structural upgrades.

## Constraints & Preferences
- Autonomous execution (agents work independently with minimal context).
- Math-level correctness over simple syntax fixes.
- Terse bullets preferred over prose.

## Progress
### Done
- Initial directory structure exploration of the BioSight project.
- 100-loop autonomous bug attack on `phi` modules (reached stability at loop 13).
- Mathematical audit of Φ encoding claims (Information Density, Topology, $\Delta_7$ Sufficiency, Consistency Rules, Adleman Mapping).
- Upgraded character classification from $\Delta_7$ to $\Delta_{12}$ in `charclass.py` to include Symmetry, Periodicity, Continuity, and Meta-math classes.
- Implemented depth-weighted distributions ($\omega$) for both $\tau(E)$ and $\delta(E)$ in `ast_parse.py`.
- Added Rule 7 (Closure Constraint) to `consistency.py` for mathematical completeness.
- Integrated Depth Coefficient ($\lambda$) and Recurrence Vector ($R$) into the Φ embedding using `compute_lambda_and_r`.
- Verified encoding logic via `test_phi.py`, confirming successful DNA mapping for arithmetic and trigonometric expressions (e.g., `sin(x) + cos(y)`).

### In Progress
- Finalizing the 30-base sequence layout by slicing $\tau$ and $\delta$ vectors to exactly 8 elements each, ensuring a strict fixed length across different expressions.

## Key Decisions
- Upgrade $F(E)$ to $\Delta_{12}$ to include Symmetry, Periodicity, Continuity, and Meta-math classes.
- Add Depth Coefficient ($\lambda$) and Recurrence Vector ($R$) to the Φ embedding to handle structural nuances like nesting and operation flow.
- Implement Rule 7 (Closure Constraint) in `consistency` for mathematical completeness.

## Next Steps
- Update `embed.py` to slice $\tau$ and $\delta$ vectors to exactly 8 bases each, ensuring a consistent 30-base DNA sequence (Bases 0–7: $F\_dna$, 8–15: $\tau\_dna$, 16–23: $\delta\_dna$, 24–29: Consistency).

## Critical Context
- BioSight is a Python shim for SilverSight's Lean logic; it handles I/O and encoding while Lean handles formal admissibility.