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

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

# Testing
.pytest_cache/
.coverage
.coverage.*
htmlcov/
.tox/
.nox/

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

# IDEs
.vscode/
.idea/
*.swp
*.swo
*~
.DS_Store

# uv
.python-version
uv.lock

# Ruff
.ruff_cache/

.claude/*
notebooks/downloads/*
notebooks/work/*
**/*.ipynb_checkpoints
examples/herc2/herc2_*.tsv
examples/herc2/classify_herc2_*.py

examples/**/work/*
examples/**/.nextflow*