pyproject.toml

[build-system]
requires = ["setuptools>=61", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "polyreact"
version = "0.1.0"
description = "Reliable polyreactivity prediction pipeline for antibodies"
readme = "README.md"
requires-python = ">=3.10"
authors = [{ name = "Polyreact Team" }]
license = { file = "LICENSE" }
dependencies = [
    "torch==2.2.2",
    "transformers==4.40.1",
    "tokenizers==0.19.1",
    "scikit-learn==1.4.2",
    "pandas==2.2.2",
    "numpy==1.26.4",
    "scipy==1.13.0",
    "biopython==1.83",
    "anarcii==2.0.2",
    "huggingface_hub==0.22.2",
    "matplotlib==3.8.4",
    "tqdm==4.66.2",
    "pyyaml==6.0.1",
    "joblib==1.3.2",
    "statsmodels==0.14.2",
    "gradio==4.21.0",
    "openpyxl==3.1.5",
    "importlib-resources==6.4.5"
]

[project.optional-dependencies]
dev = [
    "black==24.4.2",
    "ruff==0.4.1",
    "mypy==1.9.0",
    "pytest==8.1.1"
]

[project.scripts]
polyreact-predict = "polyreact.predict:main"
polyreact-train = "polyreact.train:main"

[tool.setuptools.packages.find]
include = ["polyreact*"]
where = ["."]

[tool.setuptools.package-data]
"polyreact" = ["configs/*.yaml"]

[tool.black]
line-length = 88

[tool.ruff]
line-length = 88

[tool.ruff.lint]
select = ["E", "F", "I", "UP", "N"]

[tool.mypy]
python_version = "3.11"
ignore_missing_imports = true
warn_unused_ignores = true
warn_return_any = true