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setup.py
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setup.py
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#
# Copyright (C) 2016-2017 by Yuan Lufeng
# See license.txt for full license and copyright notice.
#
# Authors: Yuan Lufeng
#
# setup.py
#
# Created on: Dec 11th, 2016
# Author: Yuan Lufeng
#
##\brief this version can complie the code include cuda, C++, python and cython.
#
NAME="FCDLR-original"
DESCRIPTION = "Fast Cell Division and Lineage Reconstruction pipeline"
LONG_DESCRIPTION = ''
MAINTAINER = 'Yuan Lufeng'
MAINTAINER_EMAIL = '[email protected]'
URL = 'https://github.com/septicmk/lambdaimage'
LICENSE = 'BSD'
DOWNLOAR_URL = 'https://github.com/septicmk/lambdaimage'
#with open('lambdaimage/__init__.py') as f:
# for line in f:
# if line.startswith('__version__'):
# VERSION = line.strip().split()[-1][1:-1]
# break
#with open('requirements.txt') as f:
# REQUIRE = [l.strip() for l in f.readlines() if l]
if __name__ == '__main__':
import os
from os.path import join as pjoin
import subprocess
from setuptools import find_packages, setup
from setuptools.extension import Extension
from setuptools.command.build_ext import build_ext
import numpy
def find_in_path(name, path):
"Find a file in a search path"
#adapted fom http://code.activestate.com/recipes/52224-find-a-file-given-a-search-path/
for dir in path.split(os.pathsep):
binpath = pjoin(dir, name)
if os.path.exists(binpath):
return os.path.abspath(binpath)
return None
def locate_cuda():
"""Locate the CUDA environment on the system
Returns a dict with keys 'home', 'nvcc', 'include', and 'lib64'
and values giving the absolute path to each directory.
Starts by looking for the CUDAHOME env variable. If not found, everything
is based on finding 'nvcc' in the PATH.
"""
# first check if the CUDAHOME env variable is in use
if 'CUDAHOME' in os.environ:
home = os.environ['CUDAHOME']
nvcc = pjoin(home, 'bin', 'nvcc')
else:
# otherwise, search the PATH for NVCC
nvcc = find_in_path('nvcc', os.environ['PATH'])
if nvcc is None:
raise EnvironmentError('The nvcc binary could not be '
'located in your $PATH. Either add it to your path, or set $CUDAHOME')
home = os.path.dirname(os.path.dirname(nvcc))
cudaconfig = {'home':home, 'nvcc':nvcc,
'include': pjoin(home, 'include'),
'lib64': pjoin(home, 'lib64')}
for k, v in cudaconfig.iteritems():
if not os.path.exists(v):
raise EnvironmentError('The CUDA %s path could not be located in %s' % (k, v))
return cudaconfig
CUDA = locate_cuda()
def customize_compiler_for_nvcc(self):
"""inject deep into distutils to customize how the dispatch
to gcc/nvcc works.
If you subclass UnixCCompiler, it's not trivial to get your subclass
injected in, and still have the right customizations (i.e.
distutils.sysconfig.customize_compiler) run on it. So instead of going
the OO route, I have this. Note, it's kindof like a wierd functional
subclassing going on."""
# tell the compiler it can processes .cu
self.src_extensions.append('.cu')
# save references to the default compiler_so and _comple methods
default_compiler_so = self.compiler_so
super = self._compile
# now redefine the _compile method. This gets executed for each
# object but distutils doesn't have the ability to change compilers
# based on source extension: we add it.
def _compile(obj, src, ext, cc_args, extra_postargs, pp_opts):
if os.path.splitext(src)[1] == '.cu':
# use the cuda for .cu files
self.set_executable('compiler_so', CUDA['nvcc'])
# use only a subset of the extra_postargs, which are 1-1 translated
# from the extra_compile_args in the Extension class
postargs = extra_postargs['nvcc']
else:
postargs = extra_postargs['gcc']
super(obj, src, ext, cc_args, postargs, pp_opts)
# reset the default compiler_so, which we might have changed for cuda
self.compiler_so = default_compiler_so
# inject our redefined _compile method into the class
self._compile = _compile
# run the customize_compiler
class custom_build_ext(build_ext):
def build_extensions(self):
customize_compiler_for_nvcc(self.compiler)
build_ext.build_extensions(self)
extensions =[
Extension("_tracking_GMM",
sources=["_tracking_GMM.pyx","TrackingGaussianMixtureModel.cpp","GaussianMixtureModel.cpp","../Utils/parseConfigFile.cpp","responsibilities.cpp","variationalInference.cpp","../external/xmlParser2/xmlParser.cpp","../external/Nathan/tictoc.c","../UtilsCUDA/knnCuda.cu","../UtilsCUDA/GMEMupdateCUDA.cu","../constants.cpp","../temporalLogicalRules/temporalLogicalRules.cpp","../UtilsCUDA/3DEllipticalHaarFeatures/gentleBoost/gentleBoost.cpp","../temporalLogicalRules/trackletCalculation.cpp","cellDivision.cpp","supportFunctionsMain.cpp","../nucleiChSvWshedPBC/hierarchicalSegmentation.cpp","backgroundDetectionInterface.cpp","kdtree.cpp","../backgroundDetection/backgroundClassifier.cpp","../temporalLogicalRules/supervoxel.cpp","../temporalLogicalRules/localGeometricDescriptor.cpp","../Utils/WishartCDF.cpp","../Utils/MultinormalCDF.cpp","../temporalLogicalRules/nuclei.cpp","../temporalLogicalRules/lineageHyperTree.cpp","../temporalLogicalRules/lineage.cpp","../temporalLogicalRules/GaussianMixtureModel_Redux.cpp","../../build/mylib/array.c","../../build/mylib/mylib.c","../../build/mylib/image.c","../../build/mylib/histogram.c","../../build/mylib/region.c","../../build/mylib/MY_TIFF/tiff.io.c","../../build/mylib/MY_TIFF/tiff.image.c","../../build/mylib/water.shed.c","../../build/mylib/connectivity.c","../../build/mylib/cdf.c","../Utils/CSparse.c","../../build/mylib/draw.c","../../build/mylib/level.set.c","../../build/mylib/linear.algebra.c","../../build/mylib/svg.c","../../build/mylib/filters.c","../../build/mylib/paths.c","../../build/mylib/swc.c","../../build/mylib/fct.min.c","../../build/mylib/utilities.c","../../build/mylib/fct.root.c","../../build/mylib/hash.c","../../build/mylib/snake.c","../temporalLogicalRules/knnCUDA/knnCuda.cu","../external/gsl/gamma.c","../external/gsl/psi.c","../external/gsl/trig.c","../external/gsl/math.c","../external/gsl/exp.c","../external/gsl/zeta.c","../external/gsl/elementary.c","../external/gsl/log.c","../external/gsl/infnan.c","../external/gsl/error.c","../external/gsl/stream.c","../temporalLogicalRules/sparseHungarianAlgorithm/sparseHungarianAlgorithm.cpp","../temporalLogicalRules/sparseHungarianAlgorithm/external/munkres-cpp-master/src/munkres.cpp","../temporalLogicalRules/lineageWindowFeatures.cpp","../external/gsl/fdiv.c"],
#sources=["_tracking_GMM.pyx","TrackingGaussianMixtureModel.cpp","GaussianMixtureModel.cpp","../Utils/parseConfigFile.cpp","responsibilities.cpp","variationalInference.cpp","../external/xmlParser2/xmlParser.cpp","../external/Nathan/tictoc.c","../UtilsCUDA/knnCuda.cu","../UtilsCUDA/GMEMupdateCUDA.cu","../constants.cpp","../temporalLogicalRules/temporalLogicalRules.cpp","../UtilsCUDA/3DEllipticalHaarFeatures/gentleBoost/gentleBoost.cpp","../temporalLogicalRules/trackletCalculation.cpp","cellDivision.cpp","supportFunctionsMain.cpp","../nucleiChSvWshedPBC/hierarchicalSegmentation.cpp","backgroundDetectionInterface.cpp","kdtree.cpp","../backgroundDetection/backgroundClassifier.cpp","../temporalLogicalRules/supervoxel.cpp","../temporalLogicalRules/localGeometricDescriptor.cpp","../Utils/WishartCDF.cpp","../Utils/MultinormalCDF.cpp","../temporalLogicalRules/nuclei.cpp","../temporalLogicalRules/lineageHyperTree.cpp","../temporalLogicalRules/lineage.cpp","../temporalLogicalRules/GaussianMixtureModel_Redux.cpp","../../build2/mylib/array.c","../../build2/mylib/mylib.c","../../build2/mylib/image.c","../../build2/mylib/histogram.c","../../build2/mylib/region.c","../../build2/mylib/MY_TIFF/tiff.io.c","../../build2/mylib/MY_TIFF/tiff.image.c","../../build2/mylib/water.shed.c","../../build2/mylib/connectivity.c","../../build2/mylib/cdf.c","../Utils/CSparse.c","../../build2/mylib/draw.c","../../build2/mylib/level.set.c","../../build2/mylib/linear.algebra.c","../../build2/mylib/svg.c","../../build2/mylib/filters.c","../../build2/mylib/paths.c","../../build2/mylib/swc.c","../../build2/mylib/fct.min.c","../../build2/mylib/utilities.c","../../build2/mylib/fct.root.c","../../build2/mylib/hash.c","../../build2/mylib/snake.c","../temporalLogicalRules/knnCUDA/knnCuda.cu","../external/gsl/gamma.c","../external/gsl/psi.c","../external/gsl/trig.c","../external/gsl/math.c","../external/gsl/exp.c","../external/gsl/zeta.c","../external/gsl/elementary.c","../external/gsl/log.c","../external/gsl/infnan.c","../external/gsl/error.c","../external/gsl/stream.c","../temporalLogicalRules/sparseHungarianAlgorithm/sparseHungarianAlgorithm.cpp","../temporalLogicalRules/sparseHungarianAlgorithm/external/munkres-cpp-master/src/munkres.cpp","../UtilsCUDA/3DEllipticalHaarFeatures/AnnotationEllipsoid.cpp"],
#sources=["_tracking_GMM.pyx","TrackingGaussianMixtureModel.cpp","GaussianMixtureModel.cpp","../Utils/parseConfigFile.cpp","responsibilities.cpp","variationalInference.cpp","../external/xmlParser2/xmlParser.cpp","../external/Nathan/tictoc.c","../UtilsCUDA/knnCuda.cu","../UtilsCUDA/GMEMupdateCUDA.cu","../constants.cpp","../temporalLogicalRules/temporalLogicalRules.cpp","../UtilsCUDA/3DEllipticalHaarFeatures/EllipticalHaarFeatures.cpp","../UtilsCUDA/3DEllipticalHaarFeatures/EllipticalHaarFeatures.cu","../UtilsCUDA/3DEllipticalHaarFeatures/gentleBoost/gentleBoost.cpp","../temporalLogicalRules/trackletCalculation.cpp","cellDivision.cpp","supportFunctionsMain.cpp","../nucleiChSvWshedPBC/hierarchicalSegmentation.cpp","backgroundDetectionInterface.cpp","kdtree.cpp","../backgroundDetection/backgroundClassifier.cpp","../temporalLogicalRules/supervoxel.cpp","../temporalLogicalRules/localGeometricDescriptor.cpp","../Utils/WishartCDF.cpp","../Utils/MultinormalCDF.cpp","../temporalLogicalRules/nuclei.cpp","../temporalLogicalRules/lineageHyperTree.cpp","../temporalLogicalRules/lineage.cpp","../temporalLogicalRules/GaussianMixtureModel_Redux.cpp","../../build2/mylib/array.c","../../build2/mylib/mylib.c","../../build2/mylib/image.c","../../build2/mylib/histogram.c","../../build2/mylib/region.c","../../build2/mylib/MY_TIFF/tiff.io.c","../../build2/mylib/MY_TIFF/tiff.image.c","../../build2/mylib/water.shed.c","../../build2/mylib/connectivity.c","../../build2/mylib/cdf.c","../Utils/CSparse.c","../../build2/mylib/draw.c","../../build2/mylib/level.set.c","../../build2/mylib/linear.algebra.c","../../build2/mylib/svg.c","../../build2/mylib/filters.c","../../build2/mylib/paths.c","../../build2/mylib/swc.c","../../build2/mylib/fct.min.c","../../build2/mylib/utilities.c","../../build2/mylib/fct.root.c","../../build2/mylib/hash.c","../../build2/mylib/snake.c","../temporalLogicalRules/knnCUDA/knnCuda.cu","../external/gsl/gamma.c","../external/gsl/psi.c","../external/gsl/trig.c","../external/gsl/math.c","../external/gsl/exp.c","../external/gsl/zeta.c","../external/gsl/elementary.c","../external/gsl/log.c","../external/gsl/infnan.c","../external/gsl/error.c","../external/gsl/stream.c","../temporalLogicalRules/sparseHungarianAlgorithm/sparseHungarianAlgorithm.cpp","../temporalLogicalRules/sparseHungarianAlgorithm/external/munkres-cpp-master/src/munkres.cpp","../UtilsCUDA/3DEllipticalHaarFeatures/AnnotationEllipsoid.cpp"],
#sources=["_tracking_GMM.pyx","TrackingGaussianMixtureModel.cpp","GaussianMixtureModel.cpp","../Utils/parseConfigFile.cpp","responsibilities.cpp","variationalInference.cpp","../external/xmlParser2/xmlParser.cpp","../external/Nathan/tictoc.c","../UtilsCUDA/knnCuda.cu","../UtilsCUDA/GMEMupdateCUDA.cu","../constants.cpp","../temporalLogicalRules/temporalLogicalRules.cpp","../UtilsCUDA/3DEllipticalHaarFeatures/EllipticalHaarFeatures.cu","../UtilsCUDA/3DEllipticalHaarFeatures/gentleBoost/gentleBoost.cpp","../temporalLogicalRules/trackletCalculation.cpp","cellDivision.cpp","supportFunctionsMain.cpp","../nucleiChSvWshedPBC/hierarchicalSegmentation.cpp","backgroundDetectionInterface.cpp","kdtree.cpp","../backgroundDetection/backgroundClassifier.cpp","../temporalLogicalRules/supervoxel.cpp","../temporalLogicalRules/localGeometricDescriptor.cpp","../Utils/WishartCDF.cpp","../Utils/MultinormalCDF.cpp","../temporalLogicalRules/nuclei.cpp","../temporalLogicalRules/lineageHyperTree.cpp","../temporalLogicalRules/GaussianMixtureModel_Redux.cpp","../../build2/mylib/array.c","../../build2/mylib/mylib.c","../../build2/mylib/image.c","../../build2/mylib/histogram.c","../../build2/mylib/region.c","../../build2/mylib/MY_TIFF/tiff.io.c","../../build2/mylib/MY_TIFF/tiff.image.c","../../build2/mylib/water.shed.c","../../build2/mylib/connectivity.c","../../build2/mylib/cdf.c","../Utils/CSparse.c","../../build2/mylib/draw.c","../../build2/mylib/level.set.c","../../build2/mylib/fft.c","../../build2/mylib/linear.algebra.c","../../build2/mylib/svg.c","../../build2/mylib/filters.c","../../build2/mylib/paths.c","../../build2/mylib/swc.c","../../build2/mylib/fct.min.c","../../build2/mylib/utilities.c","../../build2/mylib/fct.root.c","../../build2/mylib/hash.c","../../build2/mylib/snake.c"],
#sources=["_tracking_GMM.pyx","TrackingGaussianMixtureModel.cpp","GaussianMixtureModel.cpp","../Utils/parseConfigFile.cpp","responsibilities.cpp","variationalInference.cpp","../external/xmlParser2/xmlParser.cpp","../external/Nathan/tictoc.c","../UtilsCUDA/knnCuda.cu","../UtilsCUDA/GMEMupdateCUDA.cu","../constants.cpp","../temporalLogicalRules/temporalLogicalRules.cpp","../UtilsCUDA/3DEllipticalHaarFeatures/EllipticalHaarFeatures.cu","../UtilsCUDA/3DEllipticalHaarFeatures/gentleBoost/gentleBoost.cpp","../temporalLogicalRules/trackletCalculation.cpp","cellDivision.cpp","supportFunctionsMain.cpp","../nucleiChSvWshedPBC/hierarchicalSegmentation.cpp","backgroundDetectionInterface.cpp","kdtree.cpp","../backgroundDetection/backgroundClassifier.cpp","../temporalLogicalRules/supervoxel.cpp","../temporalLogicalRules/localGeometricDescriptor.cpp","../Utils/WishartCDF.cpp","../Utils/MultinormalCDF.cpp","../temporalLogicalRules/nuclei.cpp","../temporalLogicalRules/lineageHyperTree.cpp","../temporalLogicalRules/GaussianMixtureModel_Redux.cpp","../../build2/mylib/array.c","../../build2/mylib/mylib.c","../../build2/mylib/image.c","../../build2/mylib/histogram.c","../../build2/mylib/region.c","../../build2/mylib/MY_TIFF/tiff.io.c","../../build2/mylib/MY_TIFF/tiff.image.c","../../build2/mylib/water.shed.c","../../build2/mylib/connectivity.c","../../build2/mylib/cdf.c","../Utils/CSparse.c","../../build2/mylib/draw.c","../../build2/mylib/level.set.c","../../build2/mylib/fft.c","../../build2/mylib/linear.algebra.c","../../build2/mylib/svg.c","../../build2/mylib/filters.c","../../build2/mylib/paths.c","../../build2/mylib/swc.c","../../build2/mylib/fct.min.c","../../build2/mylib/utilities.c","../../build2/mylib/fct.root.c","../../build2/mylib/hash.c","../../build2/mylib/snake.c","../temporalLogicalRules/mylib/MY_FFT/fft.D.c"],
#sources=["_tracking_GMM.pyx","TrackingGaussianMixtureModel.cpp","GaussianMixtureModel.cpp","../Utils/parseConfigFile.cpp","responsibilities.cpp","variationalInference.cpp","../external/xmlParser2/xmlParser.cpp","../external/Nathan/tictoc.c","../UtilsCUDA/knnCuda.cu","../UtilsCUDA/GMEMupdateCUDA.cu","../constants.cpp","../temporalLogicalRules/temporalLogicalRules.cpp","../UtilsCUDA/3DEllipticalHaarFeatures/EllipticalHaarFeatures.cu","../UtilsCUDA/3DEllipticalHaarFeatures/gentleBoost/gentleBoost.cpp","../temporalLogicalRules/trackletCalculation.cpp","cellDivision.cpp","supportFunctionsMain.cpp","../nucleiChSvWshedPBC/hierarchicalSegmentation.cpp","backgroundDetectionInterface.cpp","kdtree.cpp","../backgroundDetection/backgroundClassifier.cpp","../temporalLogicalRules/supervoxel.cpp","../temporalLogicalRules/localGeometricDescriptor.cpp","../Utils/WishartCDF.cpp","../Utils/MultinormalCDF.cpp","../temporalLogicalRules/nuclei.cpp","../temporalLogicalRules/lineageHyperTree.cpp","../temporalLogicalRules/GaussianMixtureModel_Redux.cpp","../../build2/mylib/array.c","../../build2/mylib/mylib.c","../../build2/mylib/image.c","../../build2/mylib/histogram.c","../../build2/mylib/region.c","../../build2/mylib/MY_TIFF/tiff.io.c","../../build2/mylib/MY_TIFF/tiff.image.c","../../build2/mylib/water.shed.c","../../build2/mylib/connectivity.c","../../build2/mylib/cdf.c","../Utils/CSparse.c","../../build2/mylib/draw.c","../../build2/mylib/level.set.c","../../build2/mylib/fft.c","../../build2/mylib/linear.algebra.c","../../build2/mylib/svg.c","../../build2/mylib/filters.c","../../build2/mylib/paths.c","../../build2/mylib/swc.c","../../build2/mylib/fct.min.c","../../build2/mylib/utilities.c","../../build2/mylib/fct.root.c","../../build2/mylib/hash.c","../../build2/mylib/snake.c","../temporalLogicalRules/mylib/MY_FFT/fft.D.c","../temporalLogicalRules/mylib/MY_FFT/fft.F.c"],
#sources=["_tracking_GMM.pyx","TrackingGaussianMixtureModel.cpp","GaussianMixtureModel.cpp","../Utils/parseConfigFile.cpp","responsibilities.cpp","variationalInference.cpp","../../build2/mylib/array.c","../../build2/mylib/mylib.c","../../build2/mylib/utilities.c","../../build2/mylib/image.c","../../build2/mylib/MY_TIFF/tiff.image.c","../../build2/mylib/MY_TIFF/tiff.io.c","../../build2/mylib/linear.algebra.c","selectForeground.cpp","watershedSegmentation.cpp","../temporalLogicalRules/supervoxel.cpp","../constants.cpp","set_union.c","hierarchicalSegmentation.cpp","../temporalLogicalRules/localGeometricDescriptor.cpp","agglomerateClustering.cpp","MedianFilter2D/medianFilter2D.cpp","CUDAmedianFilter2D/medianFilter2D.cu"],
#sources=["_process_stack.pyx","ProcessStack.cpp","IO.cpp","../Utils/parseConfigFile.cpp","../temporalLogicalRules/mylib/array.p"],
#sources=["_process_stack.pyx","ProcessStack.cpp","IO.cpp","../Utils/parseConfigFile.cpp","../temporalLogicalRules/supervoxel.cpp"],
#sources=["_process_stack.pyx","ProcessStack.cpp","IO.cpp","hierarchicalSegmentation.cpp","../Utils/parseConfigFile.cpp","watershedPersistanceAgglomeration.cpp","watershedSegmentation.cpp","agglomerateClustering.cpp"],
include_dirs=[numpy.get_include(),".","..","../temporalLogicalRules/","../nucleiChSvWshedPBC","../mylib/","../backgroundDetection","../UtilsCUDA/3DEllipticalHaarFeatures","../temporalLogicalRules/mylib/MY_TIFF","../temporalLogicalRules/knnCUDA","../external/gsl/","../temporalLogicalRules/sparseHungarianAlgorithm","../temporalLogicalRules/sparseHungarianAlgorithm/external/munkres-cpp-master/src",CUDA['include']],
#include_dirs=[numpy.get_include(),".","..","../temporalLogicalRules/","../temporalLogicalRules/mylib/","../temporalLogicalRules/mylib/MY_TIFF","MedianFilter2D",CUDA['include']],
language="c++",
#library_dirs = [CUDA['lib64']],
library_dirs = ["../../build/UtilsCUDA/3DEllipticalHaarFeatures",CUDA['lib64']],
#libraries = ['cudart'],
libraries = ['cudart','cusparse','cuda','ellipticalHaarFeatures'],
#libraries = ['cudart','cusparse','cuda'],
#libraries = ['cudart','cusparse'],
#libraries = ['cudart','cusparse','myfft'],
#libraries = ['cudart','cusparse','libmyfft.a'],
runtime_library_dirs = [CUDA['lib64']],
#extra_compile_args=["-std=c++0x","-pthread"],
#extra_link_args=["-std=c++0x","-pthread"]),
extra_compile_args={'gcc':["-std=c++0x"],
'nvcc':['-arch=sm_35', '--ptxas-options=-v', '-c', '--compiler-options', "'-fPIC'"]},
extra_link_args=["-std=c++0x"]),
#Extension("lambdatgmm.nucleiSegmentation._io",
# sources=["lambdatgmm/nucleiSegmentation/_io.pyx","lambdatgmm/nucleiSegmentation/IO.cpp"],
# #sources=["lambdatgmm/nucleiSegmentation/_io.pyx","lambdatgmm/nucleiSegmentation/IO.h"],
# include_dirs=[numpy.get_include()],
# language="c++"),
#Extension("lambdaimage.udf._trans",
# sources=["lambdaimage/udf/_trans.pyx","lambdaimage/udf/_trans_c.c"],
# include_dirs=[numpy.get_include()]),
#Extension("lambdaimage.udf._update",
# sources=["lambdaimage/udf/_update.pyx", "lambdaimage/udf/_update_c.c"],
# include_dirs=[numpy.get_include()]),
#Extension("lambdaimage.udf._moment",
# sources=["lambdaimage/udf/_moment.pyx"],
# inlcude_dirs=[numpy.get_include()]),
#Extension("lambdaimage.udf._intensity",
# sources=["lambdaimage/udf/_intensity.pyx"],
# include_dirs=[numpy.get_include()]),
#Extension("lambdaimage.udf._phansalkar",
# sources=["lambdaimage/udf/_phansalkar.pyx", "lambdaimage/udf/_phansalkar_c.c"],
# include_dirs=[numpy.get_include()]),
]
from Cython.Build import cythonize
extensions = cythonize(extensions)
setup(
name = NAME,
description = DESCRIPTION,
long_description = LONG_DESCRIPTION,
maintainer = MAINTAINER,
maintainer_email = MAINTAINER_EMAIL,
url=URL,
license = LICENSE,
download_url = DOWNLOAR_URL,
#version = VERSION,
classifiers = [
'Development Status :: 4 - Beta',
'Environment :: Console',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: BSD License',
'Programming Language :: C',
'Programming Language :: C++',
'Programming Language :: Python',
'Topic :: Software Development :: Libraries',
'Topic :: Scientific/Engineering',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Operating System :: Microsoft :: Windows',
'Operating System :: POSIX',
'Operating System :: Unix',
'Operating System :: MacOS',
],
#install_requires = REQUIRE,
packages = find_packages(),
#cmdclass = {'build_ext': build_ext},
cmdclass={'build_ext': custom_build_ext},
ext_modules = extensions
# since the package has c code, the egg cannot be zipped
#zip_safe=False
)