pyproject.toml

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

[project]
name = "deeprank2"
version = "3.1.0"
description = "DeepRank2 is an open-source deep learning framework for data mining of protein-protein interfaces or single-residue missense variants."
readme = "README.md"
requires-python = ">=3.10"
keywords = [
    "graph neural network",
    "convolutional neural network",
    "protein-protein interfaces",
    "missense variants",
    "deep learning",
    "pytorch",
]
authors = [
    { name = "Giulia Crocioni", email = "g.crocioni@esciencecenter.nl" },
    { name = "Coos Baakman", email = "coos.baakman@radboudumc.nl" },
    { name = "Dani Bodor", email = "d.bodor@esciencecenter.nl" },
    { name = "Daniel Rademaker" },
    { name = "Gayatri Ramakrishnan" },
    { name = "Sven van der Burg" },
    { name = "Li Xue" },
    { name = "Daniil Lepikhov" },
]
license = { text = "Apache-2.0 license" }
classifiers = [
    "Intended Audience :: Developers",
    "License :: OSI Approved :: Apache Software License",
    "Natural Language :: English",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
]
dependencies = [
    "notebook >= 7.2.1, < 8.0",
    "markov-clustering >= 0.0.6.dev0, < 1.0",
    "tensorboard >= 0.9.0, < 3.0",
    "protobuf >= 3.20.1, < 6.0",
    "dill >= 0.3.8, < 1.0",
    "pyarrow >= 16.1.0, < 17.0",
    "tables >= 3.9.2, < 4.0",
    "numpy >= 1.25, < 2.0",
    "scipy >= 1.13.1, < 2.0",
    "h5py >= 3.11.0, < 4.0",
    "networkx >= 3.1, < 4.0",
    "matplotlib >= 3.9.0, < 4.0",
    "scikit-learn >= 1.5.0, < 2.0",
    "chart-studio >= 1.1.0, < 2.0",
    "pdb2sql >= 0.5.3, < 1.0",
    "python-louvain >= 0.16, < 1.0",
    "tqdm >= 4.66.4, < 5.0",
    "freesasa >= 2.1.1, < 3.0",
    "biopython >= 1.83, < 2.0",
]

[project.optional-dependencies]
test = [
    "pytest >= 7.4.0, < 8.0",
    "bump-my-version >= 0.24.2, < 1.0",
    "coverage >= 6.5.0, < 7.0",
    "pycodestyle >= 2.8.0, < 3.0",
    "pytest-cov >= 4.1.0, < 5.0",
    "pytest-runner >= 6.0.0, < 7.0",
    "coveralls >= 3.3.1, < 4.0",
    "ruff == 0.6.3",
] # development dependency groups
publishing = ["build", "twine", "wheel"]
notebooks = ["nbmake"]

[project.urls]
Documentation = "https://deeprank2.readthedocs.io/en/latest/?badge=latest"
Repository = "https://github.com/DeepRank/deeprank2"
Changelog = "https://github.com/DeepRank/deeprank2/blob/main/CHANGELOG.md"

[tool.coverage.run]
branch = true
source = ["deeprank2"]

[tool.setuptools.packages.find]
include = ["deeprank2*"]

[tool.setuptools.package-data]
"*" = ["*.xlsx", "*.param", "*.top", "*residue-classes"]

[tool.pytest.ini_options]
# pytest options: -ra: show summary info for all test outcomes
addopts = "-ra"