# Python
__pycache__/
*.py[cod]
*.so
.Python
venv/
*.egg-info/
.venv/

# Node
node_modules/
dist/

# System
.DS_Store

# Environment
.env
*.log

# Data
uploads/
results/
logs/
tests/test_data/genomes/*.fna

# IDE
.vscode/
.idea/
*.swp

# Test/Build artifacts
.pytest_cache/
.hypothesis/
htmlcov/
.coverage

# Pipeline outputs
runs/
tests/output/
tests/logs/

# Pixi (keep .pixi but ignore lock in subprojects)
.pixi/envs/

# uv lock (optional, can be committed for reproducibility)
# uv.lock

# Ralph Agent files
.ralph_session
.ralph_session_history
.circuit_breaker_state
.circuit_breaker_history
.call_count
.last_reset
.exit_signals
.response_analysis
progress.json
status.json

# Kirol
.kiro

# Claude Code
.claude/