pybrain/pyproject.toml at main · JO-SOARES-sea/pybrain · GitHub

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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "pybrain"
version = "0.1.0"
description = "Brain tumor MRI segmentation pipeline with uncertainty quantification"
readme = "README.md"
license = {text = "MIT"}
authors = [
    {name = "PY-BRAIN Contributors"}
]
keywords = [
    "brain-tumor-segmentation",
    "mri",
    "medical-imaging",
    "monai",
    "pytorch",
    "uncertainty-quantification",
    "deep-learning",
    "research-software",
    "brats",
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
    "Field of Study :: Neuroscience :: Medical Imaging",
]
requires-python = ">=3.9"
dependencies = [
    "torch>=2.0.0",
    "torchvision",
    "monai>=1.2.0",
    "einops",
    "pydicom",
    "nibabel",
    "SimpleITK",
    "pynrrd",
    "scikit-image",
    "scipy",
    "scikit-learn",
    "pandas",
    "numpy<2.0.0",
    "reportlab",
    "matplotlib",
    "plotly",
    "rich",
    "tqdm",
    "PyYAML",
    "python-dotenv",
]

[project.optional-dependencies]
radiomics = [
    "pyradiomics",
]
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "ruff>=0.1.0",
    "pyright>=1.1.0",
]
test = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
]

[project.urls]
Homepage = "https://github.com/3ruiruirui-sketch/pybrain"
Documentation = "https://github.com/3ruiruirui-sketch/pybrain#readme"
Repository = "https://github.com/3ruiruirui-sketch/pybrain"
"Bug Tracker" = "https://github.com/3ruiruirui-sketch/pybrain/issues"
Citation = "https://github.com/3ruiruirui-sketch/pybrain/CITATION.cff"

[tool.setuptools.packages.find]
where = ["."]
include = ["pybrain*", "scripts*"]

[tool.ruff]
line-length = 120
target-version = "py39"
src = ["pybrain", "scripts"]
lint.select = ["E", "F", "W", "I", "N", "UP", "B", "C4"]
lint.ignore = ["E501", "B028", "UP007"]

[tool.pyright]
include = ["pybrain", "scripts"]
pythonVersion = "3.9"
typeCheckingMode = "basic"
reportMissingImports = true
reportMissingTypeStubs = false

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py", "*_test.py"]
addopts = "-v --tb=short"
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "gpu: marks tests that require GPU",
    "integration: marks tests that require model weights",
]