mirror of
https://github.com/allaunthefox/Research-Stack.git
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115 lines
5 KiB
Python
115 lines
5 KiB
Python
#!/usr/bin/env python3
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"""
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Add PeptideMoE modules to the math_entities database
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This script adds the new PeptideMoE Lean modules to the database
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so they can be indexed and reviewed by the swarm.
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"""
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import sqlite3
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import json
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from datetime import datetime
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from pathlib import Path
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# Database path
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DB_PATH = "/home/allaun/Documents/Research Stack/data/math_entities.db"
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def add_peptide_moe_modules():
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"""Add PeptideMoE modules to the database."""
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conn = sqlite3.connect(DB_PATH)
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cursor = conn.cursor()
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# PeptideMoE modules to add
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modules = [
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{
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"entity_id": "peptide_moe_001",
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"subject": "PeptideMoE",
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"secondary_subjects": "Mixture-of-Experts,conformational,peptide,thermodynamics",
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"name": "Peptide MoE Core Specification",
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"statement": "φ_peptide = structuralCoherence / (freeEnergy + c0); freeEnergy = E_internal + k_B·T·S_conformational; moeDrift = Σ g_k·(advice_φ,k, advice_ψ,k)",
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"proof_status": "theorems",
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"formal_status": "noncomputable",
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"lean_module": "0-Core-Formalism/lean/Semantics/Semantics/PeptideMoE.lean",
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"dependencies": "Mathlib.Data.Real.Basic,Mathlib.Data.List.Basic",
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"citations": "OTOM v2.0.0-Cambrian-Bind",
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"complexity_score": 85,
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"year": 2026
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},
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{
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"entity_id": "peptide_moe_002",
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"subject": "PeptideMoE",
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"secondary_subjects": "examples,toy,instantiation",
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"name": "Peptide MoE Toy Examples",
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"statement": "Concrete toy instantiation of the abstract peptide-MoE specification with fixed thermodynamic/admissibility parameters, three toy experts, three toy candidate endpoints, and example reports.",
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"proof_status": "definitions",
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"formal_status": "noncomputable",
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"lean_module": "0-Core-Formalism/lean/Semantics/Semantics/PeptideMoEExamples.lean",
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"dependencies": "Semantics.PeptideMoE",
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"citations": "OTOM v2.0.0-Cambrian-Bind",
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"complexity_score": 60,
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"year": 2026
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},
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{
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"entity_id": "peptide_moe_003",
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"subject": "PeptideMoE",
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"secondary_subjects": "failure,injection,pathological",
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"name": "Peptide MoE Failure Scenarios",
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"statement": "Failure-injection scenarios documenting why guardrails matter: c0=0 causes denominator failure, loose steric bounds admit clashing states, negative gates break MoE control, unbounded advice causes pathological drift.",
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"proof_status": "definitions",
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"formal_status": "noncomputable",
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"lean_module": "0-Core-Formalism/lean/Semantics/Semantics/PeptideMoEFailure.lean",
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"dependencies": "Semantics.PeptideMoE,Semantics.PeptideMoEExamples",
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"citations": "OTOM v2.0.0-Cambrian-Bind",
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"complexity_score": 70,
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"year": 2026
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},
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{
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"entity_id": "peptide_moe_004",
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"subject": "PeptideMoE",
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"secondary_subjects": "repair,guardrails,safety",
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"name": "Peptide MoE Repair Theorems",
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"statement": "Repair theorems documenting guardrails that restore safety: positive c0 recovers denominator safety, strict steric bounds reject clashing states, nonnegative gates guarantee unit mass, bounded advice controls drift.",
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"proof_status": "theorems",
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"formal_status": "noncomputable",
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"lean_module": "0-Core-Formalism/lean/Semantics/Semantics/PeptideMoERepair.lean",
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"dependencies": "Semantics.PeptideMoE,Semantics.PeptideMoEExamples,Semantics.PeptideMoEFailure",
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"citations": "OTOM v2.0.0-Cambrian-Bind",
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"complexity_score": 75,
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"year": 2026
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}
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]
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# Insert each module
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for module in modules:
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try:
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cursor.execute("""
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INSERT OR REPLACE INTO math_entities
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(entity_id, subject, secondary_subjects, name, statement, proof_status,
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formal_status, lean_module, dependencies, citations, complexity_score, year)
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VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
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""", (
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module["entity_id"],
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module["subject"],
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module["secondary_subjects"],
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module["name"],
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module["statement"],
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module["proof_status"],
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module["formal_status"],
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module["lean_module"],
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module["dependencies"],
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module["citations"],
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module["complexity_score"],
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module["year"]
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))
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print(f"✓ Added: {module['name']}")
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except Exception as e:
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print(f"✗ Error adding {module['name']}: {e}")
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conn.commit()
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conn.close()
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print(f"\nAdded {len(modules)} PeptideMoE modules to database.")
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print(f"Database: {DB_PATH}")
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if __name__ == "__main__":
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add_peptide_moe_modules()
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