# 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/
ENV/
env/
.venv

# Jupyter Notebook
.ipynb_checkpoints

# PyCharm
.idea/

# VSCode
.vscode/

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

# Data + analysis outputs (project-root-anchored so nested packages aren't ignored)
/data/
/results/
*.h5ad
*.csv
figures/
*.png
*.jpg
*.pdf

# OS
.DS_Store
Thumbs.db

# Misc
*.log
.cache/

# copilot 
.github/copilot-instructions.md

# Sphinx documentation build
docs/_build/
docs/_static/
docs/_templates/

# setuptools-scm generated version file (see [tool.setuptools_scm] in pyproject.toml)
src/sonic/_version.py

# claude code
CLAUDE.md
.claude/
