[project]
name = "assaylens-agent"
version = "0.1.0"
description = "Assay-conditioned functional pharmacology benchmark and next-assay prototype."
readme = "README.md"
requires-python = ">=3.10"
dependencies = [
  "huggingface_hub>=0.36.0",
  "datasets>=3.0.0",
  "duckdb>=1.1.0",
  "polars>=1.0.0",
  "pyarrow>=15.0.0",
  "pandas>=2.2.0",
  "numpy>=1.26.0",
  "scikit-learn>=1.4.0",
  "scipy>=1.12.0",
  "lightgbm>=4.0.0",
  "xgboost>=2.0.0",
  "rdkit>=2023.9.0",
  "matplotlib>=3.8.0",
  "joblib>=1.3.0",
  "pydantic>=2.0.0",
  "pyyaml>=6.0.0",
  "tqdm>=4.66.0",
  "openai>=1.109.0",
]

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

[project.optional-dependencies]
torch = [
  "torch>=2.3.0",
]
ui = [
  "gradio>=5.0.0",
]
jobs = [
  "assaylens-agent[torch]",
]
dev = [
  "pytest>=8.0.0",
  "ruff>=0.6.0",
  "mypy>=1.8.0",
]

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

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

[tool.pytest.ini_options]
testpaths = ["tests"]
pythonpath = ["src"]

[tool.ruff]
line-length = 100
src = ["src", "scripts", "tests"]