# Include essential files
include README.md
include LICENSE

# Include assets and images
recursive-include assets *.png *.jpg *.svg

# Include R files
recursive-include R *.R
recursive-include R *.r
recursive-include bioneuralnet/external_tools *.R *.r
recursive-include bioneuralnet/utils *.R *.r

recursive-include bioneuralnet/datasets/monet *.csv
recursive-include bioneuralnet/datasets/example1 *.csv
include bioneuralnet/datasets/brca/clinical.csv
include bioneuralnet/datasets/brca/pam50.csv
include bioneuralnet/datasets/brca/mirna.csv

exclude bioneuralnet/datasets/brca/meth_*.csv
exclude bioneuralnet/datasets/brca/rna_*.csv


# Include documentation source files
recursive-include docs *

# Include example scripts
recursive-include examples *.py

# Exclude __pycache__ and compiled Python files
global-exclude __pycache__ *.pyc *.pyo *.pyd

# Exclude editor backup and temporary files
global-exclude *~ *.bak *.swp
