Research-Stack/5-Applications/scripts/submit_genetic_groundup_rewrite.py

#!/usr/bin/env python3
"""
submit_genetic_groundup_rewrite.py — Submit PR for Total Rewrite

Submits the GeneticGroundUp.lean module to the swarm pipeline
for a total rewrite based on formal verification critique.
"""

import json
import hashlib
import time
from pathlib import Path
from datetime import datetime


def submit_rewrite_request():
    """Submit the rewrite request to the pipeline."""
    
    print("=" * 70)
    print("SUBMITTING GENETIC_GROUNDUP.LEAN FOR TOTAL REWRITE")
    print("=" * 70)
    
    # Load the PR document
    pr_path = Path("/home/allaun/Documents/Research Stack/.github/PULL_REQUEST_GENETIC_GROUNDUP_REWRITE.md")
    with open(pr_path) as f:
        pr_content = f.read()
    
    # Load current module for reference
    module_path = Path("/home/allaun/Documents/Research Stack/0-Core-Formalism/lean/Semantics/Semantics/GeneticGroundUp.lean")
    with open(module_path) as f:
        current_code = f.read()
    
    # Count current issues
    issues = {
        "q16_16_ofFloat_signed_bug": "CRITICAL - Negative binding energies fail",
        "division_no_zero_guard": "Division-by-zero undefined",
        "invariants_as_comments": "Not enforced by type system",
        "placeholder_sorry": 2,  # Two explicit sorrys
        "theorem_restate_hypotheses": 3,  # Three weak theorems
        "naming_conflicts": "faultTolerance field vs method",
        "unused_parameters": "residueCount in achievedTargetSpeed",
        "overclaimed_semantics": "4D hyperbolic vs 4 Q16_16s"
    }
    
    # Create submission
    submission = {
        "submission_id": f"PR-GGU-{hashlib.sha256(str(time.time()).encode()).hexdigest()[:8]}",
        "timestamp": datetime.now().isoformat(),
        "module": "GeneticGroundUp.lean",
        "path": str(module_path),
        "current_lines": len(current_code.splitlines()),
        "pr_document": str(pr_path),
        
        "critique_summary": {
            "verdict": "Nice scaffold, good readability, but not yet trustworthy formal model",
            "blocker": "Q16_16.ofFloat negative-number bug",
            "main_improvement": "Move invariants out of comments and into types",
            "issues_count": len(issues),
            "issues": issues
        },
        
        "rewrite_requirements": {
            "priority": "CRITICAL",
            "type": "Total rewrite",
            "timeline": "3-5 days",
            
            "required_expertise": [
                "Lean 4 formal verification",
                "Type system design (subtypes, dependent types)",
                "Fixed-point numeric analysis",
                "Biological semantics (protein folding, metabolism)"
            ],
            
            "deliverables": [
                "Fixed Q16_16 with signed conversion",
                "Safe division with zero guard",
                "Subtype-based invariants (Prob01, NonnegQ16_16)",
                "Provable theorems without sorry",
                "Consistent naming (remove field/method conflicts)",
                "Accurate comments matching implementation"
            ],
            
            "acceptance_criteria": [
                "All 6 nucleotide probabilities proven valid",
                "Negative binding energies convert correctly",
                "Division by zero has defined behavior",
                "All invariants enforced by type system",
                "No sorry remaining in theorems",
                "Theorems prove intrinsic properties",
                "Swarm verdict: Trustworthy formal model"
            ]
        },
        
        "context": {
            "based_on_python_design": "5-Applications/scripts/swarm_genetic_groundup_redesign.py",
            "511_percent_achievement": "shared-data/data/tsm_swarm_50percent_optimization.json",
            "next_gen_agent_design": "shared-data/data/swarm_nextgen_agent_design.json",
            "performance_targets": {
                "gene_expression": "100× speedup",
                "protein_folding": "1000× speedup",
                "metabolism": "100× speedup",
                "evolution": "1000× speedup",
                "total": "100,000× speedup"
            }
        },
        
        "swarm_assignment": {
            "lead_role": "Formal Verification Specialist",
            "support_roles": [
                "Type System Architect",
                "Numeric Analysis Expert",
                "Biological Semantics Reviewer"
            ],
            "verification": "Triumvirate validation (Builder/Judge/Warden)",
            "stages": [
                "Builder: Implement fixes and subtypes",
                "Warden: Verify numeric correctness",
                "Judge: Adjudicate theorem strength"
            ]
        }
    }
    
    # Save submission
    output_path = Path("/home/allaun/Documents/Research Stack/data/genetic_groundup_rewrite_submission.json")
    output_path.parent.mkdir(parents=True, exist_ok=True)
    with open(output_path, "w") as f:
        json.dump(submission, f, indent=2)
    
    # Print summary
    print(f"\n📋 Submission ID: {submission['submission_id']}")
    print(f"📅 Timestamp: {submission['timestamp']}")
    print(f"📄 Module: {submission['module']} ({submission['current_lines']} lines)")
    
    print(f"\n🚨 Critique Summary:")
    print(f"   Verdict: {submission['critique_summary']['verdict']}")
    print(f"   Blocker: {submission['critique_summary']['blocker']}")
    print(f"   Issues: {submission['critique_summary']['issues_count']}")
    
    print(f"\n🔧 Rewrite Requirements:")
    print(f"   Priority: {submission['rewrite_requirements']['priority']}")
    print(f"   Type: {submission['rewrite_requirements']['type']}")
    print(f"   Timeline: {submission['rewrite_requirements']['timeline']}")
    
    print(f"\n👥 Swarm Assignment:")
    print(f"   Lead: {submission['swarm_assignment']['lead_role']}")
    for role in submission['swarm_assignment']['support_roles']:
        print(f"   Support: {role}")
    
    print(f"\n✅ Acceptance Criteria ({len(submission['rewrite_requirements']['acceptance_criteria'])}):")
    for i, criterion in enumerate(submission['rewrite_requirements']['acceptance_criteria'], 1):
        print(f"   {i}. {criterion}")
    
    print(f"\n📊 Output: {output_path}")
    
    print("\n" + "=" * 70)
    print("SUBMISSION COMPLETE")
    print("=" * 70)
    print("\n🚀 Swarm will process this rewrite request")
    print("   Expected completion: 3-5 days")
    print("   Target: Trustworthy formal model")
    print("\n📝 PR Document: .github/PULL_REQUEST_GENETIC_GROUNDUP_REWRITE.md")
    print("📦 Submission: shared-data/data/genetic_groundup_rewrite_submission.json")
    
    return submission


if __name__ == "__main__":
    submit_rewrite_request()