# 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 Environment
venv/
env/
ENV/
.venv
.env

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

# Testing
.pytest_cache/
.coverage
htmlcov/
.tox/
.hypothesis/
*.cover
coverage/
coverage.xml
coverage.html

# Type checking
.mypy_cache/
.dmypy.json
dmypy.json
.pytype/

# Ruff
.ruff_cache/

# Claude
.claude/

# Environment
.env
.env.local

# Data - ignore data directory but not src/msa/data/
/data/
*.db
*.sqlite
*.parquet

# Logs
/logs/
*.log
log

# Models - ignore models directory but not src/msa/models/
/models/
*.pkl
*.joblib
*.h5
*.pt
*.pth

# Jupyter
.ipynb_checkpoints/
# Don't ignore notebooks in the project
# *.ipynb

# OS
.DS_Store
Thumbs.db

# local files
ISSUES.md
TODO.md
CLAUDE.md
site/

# log files
*.log
log.*

# registry
registry/

# reports
reports/
