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https://github.com/allaunthefox/BioSight.git
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allaun
e0b2283972
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
34 lines
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2.2 KiB
Markdown
34 lines
No EOL
2.2 KiB
Markdown
# BioSight Agent Rules
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## Goal
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Establish an unimpeachable base layer for the BioSight project by refining its Φ encoding pipeline through mathematical audit, autonomous bug elimination, and structural upgrades.
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## Constraints & Preferences
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- Autonomous execution (agents work independently with minimal context).
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- Math-level correctness over simple syntax fixes.
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- Terse bullets preferred over prose.
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## Progress
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### Done
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- Initial directory structure exploration of the BioSight project.
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- 100-loop autonomous bug attack on `phi` modules (reached stability at loop 13).
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- Mathematical audit of Φ encoding claims (Information Density, Topology, $\Delta_7$ Sufficiency, Consistency Rules, Adleman Mapping).
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- Upgraded character classification from $\Delta_7$ to $\Delta_{12}$ in `charclass.py` to include Symmetry, Periodicity, Continuity, and Meta-math classes.
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- Implemented depth-weighted distributions ($\omega$) for both $\tau(E)$ and $\delta(E)$ in `ast_parse.py`.
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- Added Rule 7 (Closure Constraint) to `consistency.py` for mathematical completeness.
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- Integrated Depth Coefficient ($\lambda$) and Recurrence Vector ($R$) into the Φ embedding using `compute_lambda_and_r`.
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- Verified encoding logic via `test_phi.py`, confirming successful DNA mapping for arithmetic and trigonometric expressions (e.g., `sin(x) + cos(y)`).
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### In Progress
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- 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.
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## Key Decisions
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- Upgrade $F(E)$ to $\Delta_{12}$ to include Symmetry, Periodicity, Continuity, and Meta-math classes.
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- Add Depth Coefficient ($\lambda$) and Recurrence Vector ($R$) to the Φ embedding to handle structural nuances like nesting and operation flow.
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- Implement Rule 7 (Closure Constraint) in `consistency` for mathematical completeness.
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## Next Steps
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- 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).
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## Critical Context
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- BioSight is a Python shim for SilverSight's Lean logic; it handles I/O and encoding while Lean handles formal admissibility. |