setup.py

#!/usr/bin/env python

"""``Setup.py`` for PyMIALSRTK."""

import os
import sys
import setuptools
from setuptools.command.install import install

from pymialsrtk.info import __version__


directory = os.path.dirname(os.path.abspath(__file__))

if os.path.exists('MANIFEST'):
    os.remove('MANIFEST')

packages = [
    "pymialsrtk",
    "pymialsrtk.bids",
    "pymialsrtk.cli",
    "pymialsrtk.interfaces",
    "pymialsrtk.workflows",
    "pymialsrtk.pipelines",
    "pymialsrtk.pipelines.anatomical",
    "pymialsrtk.sphinxext",
]

package_data = {
    "pymialsrtk": [
        'data/Network_checkpoints/Network_checkpoints_localization/*',
        'data/Network_checkpoints/Network_checkpoints_segmentation/*',
        'data/report/templates/*'
    ],
}

# Extract package requirements from Conda environment.yml
include_conda_pip_dependencies = False
install_requires = []
dependency_links = []
if include_conda_pip_dependencies:
    path = os.path.join(directory, 'docker', 'bidsapp', 'environment.yml')
    with open(path) as read_file:
        state = "PREAMBLE"
        for line in read_file:
            line = line.rstrip().lstrip(" -")
            if line == "dependencies:":
                state = "CONDA_DEPS"
            elif line == "pip:":
                state = "PIP_DEPS"
            elif state == "CONDA_DEPS":
                line = '=='.join(line.split('='))
                line = line.split('==')[0]
                # Python is a valid dependency for Conda but not setuptools, so skip it
                if "python" in line:
                    pass
                else:
                    # Appends to dependencies
                    install_requires.append(line)
            elif state == "PIP_DEPS":
                line = line.split('==')[0]
                # Appends to dependency links
                dependency_links.append(line)
                # Adds package name to dependencies
                install_requires.append(line)
print(f'Install requires: {install_requires}')
print(f'Dependency links: {dependency_links}')


class VerifyVersionCommand(install):
    """Custom command to verify that the git tag matches our version"""
    description = 'verify that the git tag matches our version'

    def run(self):
        tag = os.getenv('CIRCLE_TAG')
        version = f'v{__version__}'

        if tag != version:
            info = f'Git tag: {tag} does not match the version of this app: {version}'
            sys.exit(info)


def main():
    """Main function of the PyMIALSRTK ``setup.py``"""
    setuptools.setup(
            name='pymialsrtk',
            version=__version__,
            description='PyMIALSRTK: Nipype pipelines for the MIAL Super Resolution Toolkit ',
            long_description="PyMIALSRTK interfaces with MIALSRTK C++ tools and implements "
                             "a full processing pipeline using the NiPype dataflow library, "
                             "from motion-corrupted anisotropic multi-slice MRI scans "
                             "to a motion-free isotropic high-resolution image.",
            author='Sebastien Tourbier',
            author_email='sebastien.tourbier@alumni.epfl.ch',
            url='https://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit',
            entry_points={
                 "console_scripts": [
                     'mialsuperresolutiontoolkit_docker = pymialsrtk.cli.mialsuperresolutiontoolkit_docker:main',
                     'mialsuperresolutiontoolkit_singularity = pymialsrtk.cli.mialsuperresolutiontoolkit_singularity:main'
                 ]
            },
            license='BSD-3-Clause',
            classifiers=[
                'Development Status :: 5 - Production/Stable',
                'Intended Audience :: Science/Research',
                'Intended Audience :: Developers',
                'License :: OSI Approved',
                'Programming Language :: C++',
                'Programming Language :: Python',
                'Topic :: Software Development',
                'Topic :: Scientific/Engineering :: Image Processing',
                'Operating System :: Microsoft :: Windows',
                'Operating System :: POSIX',
                'Operating System :: Unix',
                'Operating System :: MacOS',
                'Programming Language :: Python :: 3.6',
                'Programming Language :: Python :: 3.7',
            ],
            maintainer='Medical Image Analysis Laboratory, University Hospital of Lausanne and the MIALSRTK developers',
            maintainer_email='sebastien.tourbier@alumni.epfl.ch',
            # package_dir={"": "."},  # tell distutils packages are under src
            packages=packages,
            include_package_data=True,
            package_data=package_data,
            # exclude_package_data={"": ["README.txt"]},
            install_requires=install_requires,
            dependency_links=dependency_links,
            python_requires='>=3.6',
            cmdclass={
                'verify': VerifyVersionCommand,
            }
            )


if __name__ == "__main__":
    main()