setup.py

#!/usr/bin/env python

"""The setup script."""


import os
from setuptools import setup, find_packages
from setuptools.command.install import install
from setuptools.command.develop import develop
from setuptools.command.egg_info import egg_info

with open("README.md") as readme_file:
    readme = readme_file.read()


def git_submodule_update():
    ## submodule update
    os.system("git submodule update --init --recursive")


class CustomInstallCommand(install):
    def run(self):
        install.run(self)
        git_submodule_update()


class CustomDevelopCommand(develop):
    def run(self):
        develop.run(self)
        git_submodule_update()


class CustomEggInfoCommand(egg_info):
    def run(self):
        egg_info.run(self)
        git_submodule_update()


# read version.py
import sys, re

try:
    filepath = "GANDLF/version.py"
    version_file = open(filepath)
    (__version__,) = re.findall('__version__ = "(.*)"', version_file.read())

except Exception as error:
    __version__ = "0.0.1"
    sys.stderr.write("Warning: Could not open '%s' due %s\n" % (filepath, error))

requirements = [
    "black",
    "numpy==1.22.0",
    "scipy",
    "SimpleITK!=2.0.*",
    "torchvision",
    "tqdm",
    "torchio==0.18.75",
    "pandas",
    "scikit-learn>=0.23.2",
    "scikit-image>=0.19.1",
    'pickle5>=0.0.11; python_version < "3.8.0"',
    "setuptools",
    "seaborn",
    "pyyaml",
    "tiffslide",
    "matplotlib",
    "requests>=2.25.0",
    "pytest",
    "coverage",
    "pytest-cov",
    "psutil",
    "medcam",
    "opencv-python",
    "torchmetrics==0.5.1",  # newer versions have changed api for f1 invocation
    "OpenPatchMiner==0.1.8",
    "zarr==2.10.3",
    "pydicom",
    "onnx",
    "torchinfo==1.7.0",
    "segmentation-models-pytorch==0.3.0",
    "ACSConv==0.1.1",
]

# pytorch doesn't have LTS support on OSX - https://github.com/mlcommons/GaNDLF/issues/389
if sys.platform == "darwin":
    requirements.append("torch==1.11.0")
else:
    requirements.append("torch==1.11.0")

setup(
    name="GANDLF",
    version=__version__,
    author="MLCommons",
    author_email="gandlf@mlcommons.org",
    python_requires=">=3.7",
    packages=find_packages(),
    cmdclass={  # this ensures git_submodule_update is called during install
        "install": CustomInstallCommand,
        "develop": CustomDevelopCommand,
        "egg_info": CustomEggInfoCommand,
    },
    scripts=[
        "gandlf_run",
        "gandlf_constructCSV",
        "gandlf_collectStats",
        "gandlf_patchMiner",
        "gandlf_preprocess",
        "gandlf_anonymizer",
        "gandlf_verifyInstall",
    ],
    classifiers=[
        "Development Status :: 3 - Alpha",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: Apache Software License",
        "Natural Language :: English",
        "Operating System :: OS Independent",
        "Programming Language :: Python :: 3.7",
        "Programming Language :: Python :: 3.8",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
        "Topic :: Scientific/Engineering :: Medical Science Apps",
    ],
    description=(
        "PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging."
    ),
    install_requires=requirements,
    license="Apache-2.0",
    long_description=readme,
    long_description_content_type="text/markdown",
    include_package_data=True,
    keywords="semantic, segmentation, regression, classification, data-augmentation, medical-imaging, clinical-workflows, deep-learning, pytorch",
    zip_safe=False,
)