setup.py

#!/usr/bin/env python
from setuptools import setup, find_packages

# get version from file
version_file = open("miracl/version.txt")
version = version_file.read().strip()

setup(
    name="MIRACL",
    version=version,
    description="General-purpose pipeline for MRI / CLARITY brain & connectivity analysis",
    author="Maged Goubran",
    author_email="maged.goubran@utoronto.ca",
    packages=find_packages(),
    include_package_data=True,
    zip_safe=False,
    license="GNU GENERAL PUBLIC LICENSE v3",
    url="https://github.com/mgoubran/MIRACL",  # change later
    download_url="https://github.com/mgoubran/MIRACL",
    long_description=open("README.md").read(),
    classifiers=[
        "Development Status :: 4 - Beta",
        "Environment :: Console",
        "Environment :: X11 Applications :: Qt",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: GNU  General Public License v3 (GPLv3)",
        "Operating System :: POSIX :: Linux",
        "Operating System :: MacOS",
        "Operating System :: Unix",
        "Programming Language :: Python",
        "Programming Language :: Python :: 2",
        "Programming Language :: Python :: 2.7",
        "Programming Language :: Unix Shell",
        "Topic :: Scientific/Engineering",
        "Topic :: Scientific/Engineering :: Medical Science Apps.",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Topic :: Scientific/Engineering :: Image Recognition",
    ],
    install_requires=[
        "numpy==1.21.6",
        "pandas==1.3.5",
        "scipy==1.6.2",
        "monai-weekly==0.9.dev2202",
        "einops==0.6.1",
        "torch==1.13.1",
        "torchaudio==0.13.1",
        "torchvision==0.14.1",
        "opencv-python==4.2.0.32",
        "tifffile==2021.11.2",
        "nibabel==4.0.2",
        "argparse==1.4.0",
        "tables==3.7.0",
        "statsmodels==0.13.0",
        "allensdk==2.15.1",
        "lightning-python==1.2.1",
        "joblib==1.2.0",
        "matplotlib==3.4.2",
        "argcomplete==2.0.0",
        "dipy==1.6.0",
        "seaborn==0.12.2",
        "SimpleITK==2.2.1",
        "pyqt5==5.15.8",
        "nipype==1.8.5",
        "nilearn==0.9.1",
        "scikit-learn==1.0.2",
        "svgwrite==1.4.3",
        "loguru==0.6.0",
        'mne==1.3.1',
        'imagecodecs==2021.11.20'
    ],
    entry_points={
        "console_scripts": ["miracl=miracl.cli:main"],
        "gui_scripts": ["miraclGUI=miracl.miraclGUI:main"],
    },
    keywords=[
        "neuroscience brain-atlas connectivity networks clarity mri neuroimaging allen-brain-atlas",
        "mouse-atlases medical-imaging mouse biomedical image-processing image-registration image-segmentation",
    ],
)