# 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/
ENV/
env/

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

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

# Jupyter
.ipynb_checkpoints/
*.ipynb

# Data files (large)
*.h5ad
*.h5
*.tar.gz

# Large network files
*.graphml
*.gml

# Large binary/data formats
*.pkl
*.pickle
*.npz
*.npy
*.feather
*.parquet
*.sqlite
*.db

# Large compressed files
*.zip
*.bz2

# Large TSV/CSV files
*.tsv
*.csv
!examples/*.csv

# PDF and other documents
*.pdf

# Temporary files
*.tmp
*.log
DAPCSTP_temp.*
tests/test_scppin.py

# OS
.DS_Store
Thumbs.db

# Image files
*.png
*.jpg
*.jpeg
*.gif
*.svg

# Example outputs
examples/*.pdf
examples/*.html

# Sphinx documentation
docs/build/
docs/source/_build/
docs/source/_autosummary/
docs/source/generated/
.doctrees/

# Backup files
README.old.md

# Local search directories
pcst_fast/

