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setup.py
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setup.py
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# Copyright 2016-2021 The Van Valen Lab at the California Institute of
# Technology (Caltech), with support from the Paul Allen Family Foundation,
# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
# All rights reserved.
#
# Licensed under a modified Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.github.com/vanvalenlab/deepcell-toolbox/LICENSE
#
# The Work provided may be used for non-commercial academic purposes only.
# For any other use of the Work, including commercial use, please contact:
# vanvalenlab@gmail.com
#
# Neither the name of Caltech nor the names of its contributors may be used
# to endorse or promote products derived from this software without specific
# prior written permission.
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# ==============================================================================
import os
from codecs import open
from distutils.command.build_ext import build_ext as DistUtilsBuildExt
import setuptools
from setuptools import setup, find_packages
from setuptools.extension import Extension
here = os.path.abspath(os.path.dirname(__file__))
about = {}
with open(os.path.join(here, 'deepcell_toolbox', '__version__.py'), 'r', 'utf-8') as f:
exec(f.read(), about)
with open(os.path.join(here, 'README.md'), 'r', 'utf-8') as f:
readme = f.read()
class BuildExtension(setuptools.Command):
description = DistUtilsBuildExt.description
user_options = DistUtilsBuildExt.user_options
boolean_options = DistUtilsBuildExt.boolean_options
help_options = DistUtilsBuildExt.help_options
def __init__(self, *args, **kwargs):
from setuptools.command.build_ext import build_ext as SetupToolsBuildExt
# Bypass __setatrr__ to avoid infinite recursion.
self.__dict__['_command'] = SetupToolsBuildExt(*args, **kwargs)
def __getattr__(self, name):
return getattr(self._command, name)
def __setattr__(self, name, value):
setattr(self._command, name, value)
def initialize_options(self, *args, **kwargs):
return self._command.initialize_options(*args, **kwargs)
def finalize_options(self, *args, **kwargs):
ret = self._command.finalize_options(*args, **kwargs)
import numpy
self.include_dirs.append(numpy.get_include())
return ret
def run(self, *args, **kwargs):
return self._command.run(*args, **kwargs)
extensions = [
Extension(
'deepcell_toolbox.compute_overlap',
['deepcell_toolbox/compute_overlap.pyx']
),
Extension(
'deepcell_toolbox.compute_overlap_3D',
['deepcell_toolbox/compute_overlap_3D.pyx']
),
]
setup(name=about['__title__'],
version=about['__version__'],
description=about['__description__'],
author=about['__author__'],
author_email=about['__author_email__'],
url=about['__url__'],
license=about['__license__'],
download_url='{}/tarball/{}'.format(
about['__url__'], about['__version__']),
cmdclass={'build_ext': BuildExtension},
install_requires=['cython>=0.28.0',
'opencv-python-headless<=4.2.0.32; python_version < "3"',
'opencv-python-headless; python_version >= "3"',
'pandas',
'networkx>=2.1',
'numpy>=1.16.6,<1.20.0',
'scipy',
'scikit-image>=0.14.5',
'scikit-learn'],
extras_require={
'tests': ['pytest<6',
'pytest-pep8',
'pytest-cov',
'pytest-mock']},
long_description=readme,
long_description_content_type='text/markdown',
packages=find_packages(),
ext_modules=extensions,
setup_requires=['cython>=0.28', 'numpy>=1.16.6,<1.20.0'],
classifiers=[
'Programming Language :: Python',
'Programming Language :: Python :: 2',
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8'])