pyproject.toml

[build-system]
requires = ["setuptools>=77", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "bend2"
version = "1.0.2"
description = "BEND 2.0 — benchmark the capabilities needed to design DNA"
readme = "README-pypi.md"
requires-python = ">=3.11"
license = "MIT AND CC-BY-4.0 AND CC-BY-NC-4.0"
license-files = ["LICENSE", "docs/data.md"]
authors = [{name = "BEND 2.0 contributors"}]
keywords = ["genomics", "DNA", "benchmark", "foundation models", "sequence design", "gene regulation"]
classifiers = [
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
]
dependencies = ["numpy>=2.0", "pandas>=2.2", "pyarrow>=17", "scipy>=1.13", "scikit-learn>=1.5", "filelock>=3.16"]

[project.optional-dependencies]
genome = ["py2bit>=1.0.1"]
huggingface = ["torch>=2.7", "transformers>=4.57,<5"]
reference = ["torch>=2.7", "transformers>=4.57,<5", "einops>=0.8"]
dev = ["build>=1.2", "twine>=6", "pytest>=8", "ruff>=0.9"]

[project.urls]
Homepage = "https://machinelearninglifescience.github.io/BEND2/"
Repository = "https://github.com/MachineLearningLifeScience/BEND2"
Documentation = "https://github.com/MachineLearningLifeScience/BEND2/blob/main/README.md"
Issues = "https://github.com/MachineLearningLifeScience/BEND2/issues"
Data = "https://huggingface.co/datasets/yhsure/BEND2"
"Release notes" = "https://github.com/MachineLearningLifeScience/BEND2/releases"

[project.scripts]
bend2 = "bend2.cli:main"

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

[tool.setuptools.package-data]
bend2 = ["assets.json", "_data/*", "_examples/*.py"]

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

[tool.ruff]
line-length = 100
target-version = "py311"

[tool.ruff.lint]
select = ["E4", "E7", "E9", "F"]