nERdy/pyproject.toml at main · NanoscopyAI/nERdy · GitHub

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[build-system]
requires = ["setuptools>=65.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "nERdy"
version = "1.0.0"
description = "Network analysis of endoplasmic reticulum dynamics with image processing and deep learning methods"
readme = "README.md"
license = {text = "MIT"}
authors = [
    {name = "Ashwin Samudre", email = "asamudre@sfu.ca"},
    {name = "Guang Gao"},
    {name = "Ben Cardoen"},
    {name = "Ivan Robert Nabi"},
    {name = "Ghassan Hamarneh"}
]
maintainers = [
    {name = "Ashwin Samudre", email = "asamudre@sfu.ca"}
]
keywords = [
    "endoplasmic-reticulum",
    "deep-learning",
    "image-segmentation",
    "microscopy",
    "network-analysis",
    "equivariant-neural-networks"
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Image Processing",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
]
requires-python = ">=3.8"
dependencies = [
    "numpy>=1.23.1",
    "pandas>=2.0.0",
    "scipy>=1.10.0",
    "seaborn>=0.11.2",
    "matplotlib>=3.8.0",
    "scikit-image>=0.22.0",
    "imageio>=2.33.1",
    "pillow>=10.2.0",
    "opencv-python>=4.8.0",
    "sknw>=0.15",
    "networkx>=3.0",
    "plantcv>=4.2.1",
    "torch>=2.0.0",
    "torchvision>=0.15.0",
    "tqdm>=4.65.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "black>=23.0.0",
    "flake8>=6.0.0",
    "isort>=5.12.0",
]
matlab = [
    "matlabengine>=9.14",  # For nERdy image processing method
]

[project.urls]
Homepage = "https://github.com/NanoscopyAI/nERdy"
Documentation = "https://github.com/NanoscopyAI/nERdy#readme"
Repository = "https://github.com/NanoscopyAI/nERdy"
Issues = "https://github.com/NanoscopyAI/nERdy/issues"
Paper = "https://www.biorxiv.org/content/10.1101/2024.02.20.581259v1.abstract"

[project.scripts]
nerdy-train = "nERdyplus.train:main"

[tool.setuptools.packages.find]
where = ["."]
include = ["nERdy*", "nERdyplus*", "analysis*", "groupy*"]

[tool.setuptools.package-data]
"*" = ["*.pth", "*.ini"]

[tool.pytest.ini_options]
testpaths = ["test"]
python_files = ["test_*.py"]
python_functions = ["test_*"]
addopts = "-v --tb=short"

[tool.black]
line-length = 100
target-version = ['py38', 'py39', 'py310', 'py311']
include = '\.pyi?$'
exclude = '''
/(
    \.git
    | \.hg
    | \.mypy_cache
    | \.tox
    | \.venv
    | _build
    | buck-out
    | build
    | dist
)/
'''

[tool.isort]
profile = "black"
line_length = 100