pyproject.toml

[project]
name = "phage-display-bayesian-modelling"
version = "0.1.0"
description = "Add your description here"
readme = "README.md"
requires-python = ">=3.10"
dependencies = [
    "hydra-core>=1.3.2",
    "neptune>=1.14.0",
    "pyro-ppl==1.9.1",
    "shap>=0.47.2",
    "transformers>=4.51.3",
    "isort>=6.0.1",
    "pylint>=3.3.7",
    "pytest>=7.3.1,<8.0.0",
    "pytest-cov>=4.1.0",
    "pre-commit>=4.2.0",
    "matplotlib>=3.9.4",
    "ruff>=0.3.0",
    "dotenv>=0.9.9",
    "importlib>=1.0.4",
    "anarcii>=2.0.2",
    "abnumber>=0.4.4",
    "anarci-mhc>=0.0.13",
    "captum>=0.8.0",
]

[[tool.uv.index]]
name = "pytorch"
url = "https://download.pytorch.org/whl/cu118"

[[tool.uv.index]]
name = "default"
url = "https://pypi.org/simple"

[dependency-groups]
dev = [
    "ipykernel>=6.29.5",
]

[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"

[project.scripts]
train_phage_display = "scripts.train:main"
predict_phage_display = "scripts.predict:main"

[tool.setuptools.packages.find]
include=['scripts*','src*', 'tests*']