setup.py

import os
import re

from setuptools import find_packages, setup

# Read the contents of your README file
with open('README.md', encoding='utf-8') as f:
    long_description = f.read()


# Read the version from the __init__.py file
def read_version():
    with open(os.path.join('qim3d', '__init__.py'), encoding='utf-8') as f:
        version_file = f.read()
    version_match = re.search(r'^__version__ = ["\']([^"\']*)["\']', version_file, re.M)
    if version_match:
        return version_match.group(1)
    raise RuntimeError('Unable to find version string.')


setup(
    name='qim3d',
    version=read_version(),
    author='Felipe Delestro',
    author_email='fima@dtu.dk',
    description='QIM tools and user interfaces for volumetric imaging',
    long_description=long_description,
    long_description_content_type='text/markdown',
    url='https://platform.qim.dk/qim3d',
    packages=find_packages(),
    include_package_data=True,
    entry_points={'console_scripts': ['qim3d=qim3d.cli:main']},
    classifiers=[
        'License :: OSI Approved :: MIT License',
        'Programming Language :: Python :: 3',
        'Development Status :: 5 - Production/Stable',
        'Intended Audience :: Education',
        'Intended Audience :: Science/Research',
        'Natural Language :: English',
        'Operating System :: OS Independent',
        'Topic :: Scientific/Engineering :: Image Processing',
        'Topic :: Scientific/Engineering :: Visualization',
        'Topic :: Software Development :: User Interfaces',
    ],
    python_requires='>=3.10',
    install_requires=[
        "gradio==4.44",
        "h5py>=3.9.0",
        "localthickness>=0.1.2",
        "matplotlib>=3.8.0",
        "pydicom==2.4.4",
        "numpy>=1.26.0",
        "outputformat>=0.1.3",
        "Pillow>=10.0.1",
        "plotly>=5.14.1",
        "scipy>=1.11.2",
        "seaborn>=0.12.2",
        "setuptools>=68.0.0",
        "tifffile>=2025.1.10",
        "imagecodecs>=2024.12.30",
        "tqdm>=4.65.0",
        "nibabel>=5.2.0",
        "ipywidgets>=8.1.2",
        "dask>=2023.6.0",
        "k3d>=2.16.1",
        "olefile>=0.46",
        "psutil>=5.9.0",
        "structure-tensor>=0.2.1",
        "noise>=1.2.2",
        "zarr>=2.18.2",
        "ome_zarr>=0.9.0",
        "dask-image>=2024.5.3",
        "scikit-image>=0.24.0",
        "trimesh>=4.4.9",
        "PyGEL3D>=0.5.2"
    ],
    extras_require={
    "deep-learning": [
        "albumentations>=1.3.1",
        "torch>=2.0.1",
        "torchvision>=0.15.2",
        "torchinfo>=1.8.0",
        "monai>=1.2.0",
    ],
    'test': [
        'testbook>=0.4.2'
    ]
}
)