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setup.py
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setup.py
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from __future__ import absolute_import, print_function
from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext
from numpy.distutils.misc_util import get_numpy_include_dirs
from os import path
class build_ext_openmp(build_ext):
# https://www.openmp.org/resources/openmp-compilers-tools/
# python setup.py build_ext --help-compiler
openmp_compile_args = {
'msvc': ['/openmp'],
'intel': ['-qopenmp'],
'*': ['-fopenmp']
}
openmp_link_args = openmp_compile_args # ?
def build_extension(self, ext):
compiler = self.compiler.compiler_type.lower()
if compiler.startswith('intel'):
compiler = 'intel'
if compiler not in self.openmp_compile_args:
compiler = '*'
_extra_compile_args = list(ext.extra_compile_args)
_extra_link_args = list(ext.extra_link_args)
try:
ext.extra_compile_args += self.openmp_compile_args[compiler]
ext.extra_link_args += self.openmp_link_args[compiler]
super(build_ext_openmp, self).build_extension(ext)
except:
print('compiling with OpenMP support failed, re-trying without')
ext.extra_compile_args = _extra_compile_args
ext.extra_link_args = _extra_link_args
super(build_ext_openmp, self).build_extension(ext)
_dir = path.abspath(path.dirname(__file__))
with open(path.join(_dir,'stardist','version.py')) as f:
exec(f.read())
with open(path.join(_dir,'README.md')) as f:
long_description = f.read()
setup(
name='stardist',
version=__version__,
description='StarDist',
long_description=long_description,
long_description_content_type='text/markdown',
url='https://github.com/mpicbg-csbd/stardist',
author='Uwe Schmidt, Martin Weigert',
author_email='uschmidt@mpi-cbg.de, mweigert@mpi-cbg.de',
license='BSD 3-Clause License',
packages=find_packages(),
python_requires='>=3.5',
cmdclass={'build_ext': build_ext_openmp},
ext_modules=[
Extension(
'stardist.lib.stardist',
sources=['stardist/lib/stardist.cpp','stardist/lib/clipper.cpp'],
include_dirs=get_numpy_include_dirs(),
)
],
classifiers=[
'Development Status :: 4 - Beta',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering',
'License :: OSI Approved :: BSD License',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
],
install_requires=[
'csbdeep>=0.3.0',
'scikit-image',
],
)