D-SCRIPT/pyproject.toml at main · schafferde/D-SCRIPT · GitHub

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[build-system]
requires = ["uv_build>=0.9.15,<0.10.0"]
build-backend = "uv_build"

[project]
name = "dscript"
version = "0.3.1"
description = "D-SCRIPT: protein-protein interaction prediction"
authors = [
    {name = "Samuel Sledzieski", email = "samsl@mit.edu"}
]
license = {text = "MIT"}
readme = "README.md"
requires-python = ">=3.10"
dependencies = [
    "numpy",
    "biotite==1.2.0",
    "scipy",
    "pandas",
    "torch>=1.13",
    "matplotlib",
    "seaborn",
    "tqdm",
    "scikit-learn",
    "h5py",
    "huggingface_hub",
    "safetensors",
    "loguru",
]

[project.optional-dependencies]
test = [
    "pytest",
    "pytest-cov",
    "ruff",
]
dev = [
    "pytest",
    "pytest-cov",
    "ruff",
]
docs = [
    "jinja2<3.1",
    "Sphinx>=5.0",
    "pydata-sphinx-theme>=0.16",
    "sphinxcontrib-jsmath",
    "sphinxcontrib-serializinghtml",
]

[project.urls]
Homepage = "http://dscript.csail.mit.edu"

[project.scripts]
dscript = "dscript.__main__:main"

[tool.uv]
package = true

[tool.uv.sources]

[tool.uv.build-backend]
module-name = "dscript"
module-root = ""

[tool.ruff]
line-length = 90
target-version = "py310"

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort
    "UP",  # pyupgrade
]
ignore = ["E501"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"

[tool.ruff.lint.isort]
known-first-party = ["dscript"]

[tool.coverage.paths]
source = ["dscript"]

[tool.coverage.run]
omit = ["dscript/tests/*"]

[tool.pytest.ini_options]
filterwarnings = [
    "ignore::UserWarning",
    "ignore::DeprecationWarning",
    "ignore::PendingDeprecationWarning",
]
python_files = "test_*.py"
testpaths = [
    "dscript/tests",
]

[dependency-groups]
docs = [
    "pydata-sphinx-theme>=0.8.0",
]