[build-system]
requires = ["setuptools>=68", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "remedi-cell"
version = "0.1.0"
description = "Replicate-enabled minimax endpoint-directed inference for molecule-dose selection"
readme = "README.md"
requires-python = ">=3.11"
dependencies = ["numpy>=1.24", "scipy>=1.10", "pandas>=2.0", "scikit-learn>=1.7", "cvxpy>=1.5", "clarabel>=0.9", "joblib>=1.3", "matplotlib>=3.7", "requests>=2.31", "PyYAML>=6", "rdkit>=2023.9"]

[project.optional-dependencies]
data = ["anndata>=0.10", "h5py>=3.9", "rdkit>=2023.9", "huggingface_hub>=0.25", "pyarrow>=14", "fsspec>=2024.2", "aiohttp>=3.9"]
encoders = ["torch>=2.2", "transformers>=4.40", "rdkit>=2023.9"]
dev = ["pytest>=8", "ruff>=0.5"]

[project.scripts]
remedi = "remedi.cli:main"

[tool.setuptools.packages.find]
where = ["src"]

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "-q"

[tool.ruff]
line-length = 100


[tool.setuptools.package-data]
remedi = ["fonts/*.ttf", "fonts/UFL.txt"]