import subprocess

try:

cmd = cc_name + ' -E -dM -std=c++11 -x c++ /dev/null > /dev/null'

subprocess.check_call(cmd, shell=True)

except subprocess.CalledProcessError:

return False

def build_extensions(self):

import platform

from distutils import sysconfig

if (hasattr(self.compiler, 'compiler') and

len(self.compiler.compiler) > 0):

cc_name = self.compiler.compiler[0]

stdcpp = '-std=c++11'

if 'gcc' in cc_name and not _check_gcc_cpp11(cc_name):

stdcpp = '-std=c++0x'

for e in self.extensions:

e.extra_compile_args.append(stdcpp)

e.extra_compile_args.append('-Wno-deprecated-declarations')

e.extra_compile_args.append('-Wno-unused-local-typedefs')

e.extra_compile_args.append('-Wno-sign-compare')

e.extra_compile_args.append('-Wno-self-assign')

e.extra_compile_args.append('-Wno-macro-redefined')

e.extra_compile_args.append('-Wno-unused-const-variable')

conf_vars = sysconfig.get_config_vars()

if 'MACOSX_DEPLOYMENT_TARGET' in conf_vars and len(conf_vars[

'MACOSX_DEPLOYMENT_TARGET']) > 0:

_v1, _v2 = conf_vars['MACOSX_DEPLOYMENT_TARGET'].split('.')

if int(_v1) == 10 and int(_v2) < 9:

stdcpp = '--stdlib=libc++'

for e in self.extensions:

e.extra_compile_args.append(stdcpp)

import platform

from distutils import sysconfig

conf_vars = sysconfig.get_config_vars()

if compatible:

conf_vars['MACOSX_DEPLOYMENT_TARGET'] = '10.9'

return

vers = platform.mac_ver()[0].split('.')

if len(vers) == 3:

conf_vars['MACOSX_DEPLOYMENT_TARGET'] =\

vers[0] + '.' + vers[1]

else:

if sys.platform.startswith('win'):

return []

return [

'-Wno-comment', '-Wno-unused-const-variable',

'-Wno-overloaded-virtual', '-Wno-uninitialized',

'-Wno-delete-non-virtual-dtor', '-Wunused-variable'

import numpy as np

def globr(root, pattern):

import fnmatch

matches = []

for root, _, filenames in os.walk(root):

for filename in fnmatch.filter(filenames, pattern):

matches.append(os.path.join(root, filename))

return matches

def swig_opts():

return [

'-c++', '-outdir', join('limix', 'deprecated'), '-I' + join('src')

]

def nlopt_files():

src = open(join('External', 'nlopt_src.files')).readlines()

src = [join('External', 'nlopt', s).strip() for s in src]

hdr = globr(join('External', 'nlopt'), '*/*.h')

return (src, hdr)

(src, hdr) = nlopt_files()

src.extend(globr(join('src', 'limix'), '*.cpp'))

hdr.extend(globr(join('src', 'limix'), '*.h'))

incl = ['src', 'External', join('External', 'nlopt')]

incl = [join(i) for i in incl]

folder = join('External', 'nlopt')

incl += [join(folder, f) for f in os.listdir(folder)]

incl = [i for i in incl if os.path.isdir(i)]

incl.extend([np.get_include()])

wrap_file = join('src', 'interfaces', 'python', 'limix_wrap.cpp')

i_file = join('src', 'interfaces', 'python', 'limix.i')

if os.path.exists(wrap_file):

src.append(wrap_file)

else:

src.append(i_file)

depends = src + hdr

ext = Extension(

'limix.deprecated._core',

src,

include_dirs=incl,

extra_compile_args=extra_compile_args(),

swig_opts=swig_opts(),

depends=depends)

import numpy as np

src = [join('cython', 'lmm_forest', 'SplittingCore.pyx')]

incl = [join('External'), np.get_include()]

depends = src

ext = Extension(

'limix.ensemble.SplittingCore',

src,

language='c++',

include_dirs=incl,

extra_compile_args=extra_compile_args(),

depends=depends)

from Cython.Build import cythonize

src_path = os.path.dirname(os.path.abspath(sys.argv[0]))

old_path = os.getcwd()

os.chdir(src_path)

sys.path.insert(0, src_path)

if sys.platform == 'darwin':

mac_workaround(compatible)

needs_pytest = {'pytest', 'test', 'ptr'}.intersection(sys.argv)

pytest_runner = ['pytest-runner>=2.9'] if needs_pytest else []

install_requires = [

"scikit-learn", "pandas", "scipy", "h5py", "matplotlib"

]

setup_requires = ['cython'] + pytest_runner

tests_require = ['pytest']

metadata = dict(

name="limix",

version="0.8.6",

description="A flexible and fast mixed model toolbox.",

long_description=long_description,

keywords='linear mixed models, GWAS, QTL, ' +

'Variance component modelling',

maintainer="Limix Developers",

author="Danilo Horta, Christoph Lippert, Paolo Casale, Oliver Stegle",

author_email="stegle@ebi.ac.uk",

maintainer_email="stegle@ebi.ac.uk",

packages=find_packages(),

include_package_data=True,

url='http://pmbio.github.io/limix/',

install_requires=install_requires,

setup_requires=setup_requires,

tests_require=tests_require,

zip_safe=False,

license='Apache License 2.0',

ext_modules=[core_extension(reswig)] + ensemble_extension(),

cmdclass=dict(build_ext=build_ext_subclass),

entry_points={

'console_scripts': [

'limix_runner=limix.scripts.limix_runner:entry_point',

'mtSet_postprocess=limix.scripts.mtSet_postprocess:entry_point',

'mtSet_preprocess=limix.scripts.mtSet_preprocess:entry_point',

'mtSet_simPheno=limix.scripts.mtSet_simPheno:entry_point',

'mtSet_analyze=limix.scripts.mtSet_analyze:entry_point',

'limix_converter=limix.scripts.limix_converter:entry_point',

'iSet_analyze=limix.scripts.iSet_analyze:entry_point',

'iSet_postprocess=limix.scripts.iSet_postprocess:entry_point',

]

},

classifiers=[

'Development Status :: 5 - Production/Stable',

'Environment :: Console',

'Intended Audience :: Science/Research',

'License :: OSI Approved :: Apache Software License',

'Natural Language :: English',

'Programming Language :: Python :: 2.7',

'Topic :: Scientific/Engineering :: Bio-Informatics',

], )

# http://stackoverflow.com/a/29634231

import distutils.sysconfig

cfg_vars = distutils.sysconfig.get_config_vars()

for key, value in list(cfg_vars.items()):

if type(value) == str:

cfg_vars[key] = value.replace("-Wstrict-prototypes", "")

try:

setup(**metadata)

finally:

del sys.path[0]