# MANIFEST.in

# Include all python files from the biomni package
recursive-include biomni *.py

# Include the .pkl database files
recursive-include biomni/tool/schema_db *.pkl

# Include specific files from biomni_env, but not the biomni_tools subdirectory
recursive-include biomni_env *.py *.sh *.yml *.yaml *.txt *.md *.json *.R

# Exclude specific directories that are not part of the package
prune tutorials/data
prune biomni_env/biomni_tools

# Exclude build artifacts and caches
global-exclude *.py[co]
global-exclude __pycache__
global-exclude .ruff_cache
prune build
prune dist
prune *.egg-info

# Include other necessary files
include README.md
include LICENSE
include pyproject.toml