# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
*.so

# Build / packaging
build/
dist/
downloads/
eggs/
.eggs/
*.egg-info/
*.egg
sdist/
wheels/
pip-wheel-metadata/
share/python-wheels/
.installed.cfg

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

# Test / coverage / type-checker caches
.coverage
.coverage.*
coverage.xml
htmlcov/
.pytest_cache/
.mypy_cache/
.pyright/
.pyre/
.ruff_cache/
.tox/
.nox/
.hypothesis/

# Jupyter / IPython
.ipynb_checkpoints/
ipython_config.py

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

# OS files
.DS_Store
Thumbs.db

# Logs / temporary files
*.log
/logs/
/tmp/
/temp/
*.tmp
*.bak

# Generated figures / graph exports
*.dot
*.dot.pdf
*.gv
*.gv.pdf
*.png
*.jpg
*.jpeg

# Large local single-cell files
*.h5ad
*.h5mu
*.loom

# LaTeX artifacts
*.aux
*.bbl
*.bcf
*.blg
*.fdb_latexmk
*.fls
*.nav
*.out
*.run.xml
*.snm
*.synctex.gz
*.toc
q.log

# R
.Rhistory
.RData
.Rproj.user/

# Project-specific
*.md
!README.md
!docs/**/*.md

src/bonesistools/databases/omnipath/.cache/
/data/
/results/
!tests/
!tests/data/
!tests/data/*.h5ad
!src/bonesistools/sctools/datasets/
!src/bonesistools/sctools/datasets/*.h5ad