# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg

# Virtual environments
.venv/
venv/
ENV/
env/

# uv
.uv/
uv.lock

# IDE
.idea/
.vscode/
*.swp
*.swo
*~

# OS
.DS_Store
.DS_Store?
._*
.AppleDouble
.LSOverride
.Spotlight-V100
.Trashes
Icon?
Thumbs.db

# PyMOL
*.pml

# Testing
.pytest_cache/
.coverage
htmlcov/
coverage_html_agent/
coverage_agent.xml
.tox/
.nox/

# Test reference outputs with machine-specific paths
tests/toolkit/unit/test_ipsae/dunbrack_reference/test_inputs/*.pml
tests/toolkit/unit/test_ipsae/dunbrack_reference/test_inputs/*.txt

# Gateway test outputs (generated during manual testing)
tests/cli/modal_gateway_tests/test_outputs/

# Modal tool test outputs
tests/toolkit/modal_tool_tests/test_reports/

# Jupyter
.ipynb_checkpoints/

# Local config
.env
.env.local
*.local
.claude/settings.local.json

# Logs
*.log
logs/

# Build artifacts
*.whl

# Modal
.modal/
