BioSight/python/phi/AGENTS.md

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.