# 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)`).
- Aligned layer naming and numbering with SilverSight's 4-layer specification.
- Implemented `phi.silversight` integration module to verify rule rule ordering, N=8 necessity, and Lean compilation status.
- Integrated SilverSight verification checks into the `--verify` suite of `equation_dna_encoder.py` and the `rigour_pipeline.py`.

### In Progress
- None. Alignment and SilverSight import are complete.

## 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.
- Integrate SilverSight Lean receipt and theorem verification to prevent drift.

## Next Steps
- Implement active dry-lab to wet-lab testing workflows using the verified DNA sequences.

## Critical Context
- BioSight is a Python shim for SilverSight's Lean logic; it handles I/O and encoding while Lean handles formal admissibility. All admissibility and pipeline layout decisions are verified by the SilverSight verification module.