feat: Auto-Healing System for Python Code Quality

[michaeljabbour]

Auto-Healing System for Python Code Quality

Summary

Adds an automated code quality improvement system that analyzes Python modules for complexity, type errors, and code health, then uses Claude to refactor and simplify unhealthy code. The system creates safe, trackable improvements through git branches and atomic file operations.

Features

1. Health Monitoring & Scoring

• Analyzes Python modules for:
  • Cyclomatic complexity (control flow statements)
  • Lines of code (with penalty for modules >200 lines)
  • Type errors via pyright integration
• Calculates health scores (0-100 scale)
• Configurable threshold for identifying unhealthy modules

2. Claude-Powered Code Refactoring

• Direct Claude Code SDK integration (no external dependencies)
• Generates refactored code following project philosophy:
  • Ruthless simplicity
  • Improved type safety
  • Reduced complexity
  • Better readability
• Validates improvements before committing

3. Safety Features

• Git branch creation: Each healing session gets a timestamped branch
• Clean working tree checks: Prevents accidental data loss
• Atomic file writes: Uses temp files + atomic rename to prevent corruption
• Validation: Checks syntax and imports before committing changes
• File size limit: Skips files >400 lines to prevent timeouts
• Critical file protection: Skips patterns like init, setup, config, test_

4. CLI Interface

# Check module health without making changes
amplifier heal --check-only

# Heal up to 3 unhealthy modules (with confirmation)
amplifier heal

# Heal up to 5 modules automatically
amplifier heal --max 5 --yes

# Custom health threshold (default: 70)
amplifier heal --threshold 80

5. Claude Code Integration

• Slash command: /heal for use within Claude Code sessions
• Inherits all CLI options
• Seamless integration with existing workflows
• Graceful cancellation handling (Ctrl+C)

6. Global Command Access

• make install-global installs system-wide amplifier command
• Works on any project from any directory
• Brings all Amplifier features to external codebases

Implementation Details

New Files

• amplifier/cli/ - Click-based CLI framework
  • core.py - Main CLI entry point
  • commands/heal.py - Healing command implementation
• amplifier/healing/ - Core healing logic
  • prompts/simplify.md - Healing prompt template
• amplifier/tools/ - Utility modules
  • claude_healer.py - Claude SDK integration
  • health_monitor.py - Health scoring engine
  • git_utils.py - Git operations with safety checks
  • auto_healer.py - Batch healing orchestration
• .claude/commands/heal.md - Command documentation
• .claude/slash_commands/heal.py - Slash command wrapper
• test_claude_healer.py - Integration test

Modified Files

• pyproject.toml - Added [project.scripts] entry point for global command
• Makefile - Added install-global target
• README.md - Added comprehensive auto-healing documentation (70+ lines)
• .gitignore - Added .amplifier/ runtime directory
• CLAUDE.md - Added REPOSITORY_GUIDELINES.md import
• REPOSITORY_GUIDELINES.md - Preserved custom guidelines while restoring upstream AGENTS.md

Preserved Upstream Compatibility

• ✅ Restored original AGENTS.md (707 lines) from microsoft/amplifier
• ✅ Maintained package name as "workspace"
• ✅ Created REPOSITORY_GUIDELINES.md for custom guidelines
• ✅ All changes are additive, no breaking changes

Health Score Calculation

Base score: 100
- Complexity penalty: -2 per control flow statement
- LOC penalty: -0.5 per line over 200
- Type error penalty: -10 per error

Example: A 250-line module with 15 control flow statements and 2 type errors:

• Base: 100
• Complexity: -30 (15 × 2)
• LOC: -25 (50 over × 0.5)
• Type errors: -20 (2 × 10)
• Final Score: 25 (Needs healing)

Usage Example

$ amplifier heal --check-only
[INFO] Analyzing Python modules for health issues...
[INFO] Found 3 unhealthy modules (threshold: 70):
  • amplifier/tools/complex_module.py (score: 45)
  • amplifier/healing/old_code.py (score: 52)
  • amplifier/cli/messy.py (score: 61)

$ amplifier heal --max 2 --yes
[INFO] Creating healing branch: heal/20250929_223045
[INFO] Healing amplifier/tools/complex_module.py (score: 45)...
[INFO] ✓ Improved to score: 82
[INFO] Healing amplifier/healing/old_code.py (score: 52)...
[INFO] ✓ Improved to score: 78
[INFO] Healing complete! Healed 2 modules.
[INFO] Review changes in branch: heal/20250929_223045

Limitations

• File size limit: Modules larger than 400 lines are skipped to prevent timeouts
• Critical files: Files matching patterns like __init__, setup, config, settings, or test_ are skipped for safety
• Skipped files show clear messages: ⏭️ filename.py: File too large (692 lines, limit: 400)

Testing

• ✅ All existing tests pass (make test)
• ✅ Code quality checks pass (make check)
• ✅ Integration test included (test_claude_healer.py)
• ✅ Manually tested with real unhealthy modules

Documentation

• README.md: Complete user guide with examples
• .claude/commands/heal.md: Command reference for Claude Code
• .claude/slash_commands/heal.md: Detailed slash command usage
• Code comments: Comprehensive docstrings throughout

Breaking Changes

None - This is a pure addition with no modifications to existing functionality.

Test Plan

• Run make check - All checks pass
• Run make test - All tests pass
• Test /heal --check-only - Shows health analysis
• Test /heal with cancellation - Exits gracefully
• Test file size limit - Large files skipped with warning
• Test amplifier heal --yes --max 2 - Would heal small modules (not run on repo to avoid changes)
• Verify global command installation - make install-global works
• Check documentation accuracy - All docs match implementation

Follow-up Work

Future enhancements could include:

• Watch mode for continuous monitoring
• Integration with pre-commit hooks
• Configurable healing strategies (aggressive/conservative)
• Metrics dashboard for tracking code health over time
• Support for additional languages beyond Python
• Adjustable file size limits

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🤖 Generated with Claude Code

Co-Authored-By: Claude noreply@anthropic.com