def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from cython_gsl import get_include, get_libraries, get_library_dir
config = Configuration('growth', parent_package, top_path)
cython(['core.pyx'], working_path=base_path)
cython(['power.pyx'], working_path=base_path)
cython(['correlation.pyx'], working_path=base_path)
cython(['lensing.pyx'], working_path=base_path)
cython(['emulator.pyx'], working_path=base_path)
config.add_extension('core', sources=['core.c', 'transfer.c', 'power_tools.c'],
include_dirs=[get_numpy_include_dirs(), get_include(), ''],
libraries=get_libraries(), library_dirs=[get_library_dir()],
extra_compile_args=['-O3', '-w'],
extra_link_args=['-g'])
config.add_extension('power', sources=['power.c', 'transfer.c', 'power_tools.c'],
include_dirs=[get_numpy_include_dirs(), get_include(), ''],
libraries=get_libraries(), library_dirs=[get_library_dir()],
extra_compile_args=['-O3', '-w'],
extra_link_args=['-g'])
config.add_extension('correlation', sources=['correlation.c', 'power_tools.c', 'transfer.c'],
include_dirs=[get_numpy_include_dirs(), get_include(), ''],
libraries=get_libraries(), library_dirs=[get_library_dir()],
extra_compile_args=['-O3', '-w'],
extra_link_args=['-g'])
config.add_extension('lensing', sources=['lensing.c', 'power_tools.c', 'transfer.c'],
include_dirs=[get_numpy_include_dirs(), get_include(), ''],
libraries=get_libraries(), library_dirs=[get_library_dir()],
extra_compile_args=['-O3', '-w'],
extra_link_args=['-g'])
sources = ['emulator.c', 'emulator/core.c', 'emulator/emu.c', 'emulator/emu_noh.c', \
'emulator/hubble.c', 'hod_emulator/core.c', 'hod_emulator/emu.c']
config.add_extension('emulator', sources=sources ,
include_dirs=[get_numpy_include_dirs(), get_include(), '', 'emulator', 'hod_emulator'],
libraries=get_libraries(), library_dirs=[get_library_dir(), 'emulator', 'hod_emulator'],
extra_compile_args=['-O3', '-w'],
extra_link_args=['-g'])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from cython_gsl import get_include, get_libraries, get_library_dir
config = Configuration('halo', parent_package, top_path)
cython(['bias.pyx'], working_path=base_path)
config.add_extension('bias', sources=['bias.c', 'halo_tools.c'],
include_dirs=[get_numpy_include_dirs(), get_include(), ''],
libraries=get_libraries(), library_dirs=[get_library_dir()],
extra_compile_args=['-O3', '-w'],
extra_link_args=['-g'])
return config
Extension('ndintegration', ['ndintegration.pyx'],
include_dirs=[np.get_include()],
libraries=['cuba'] ),
Extension('mymath', ['mymath.pyx'],
include_dirs=[np.get_include()]),
Extension('mpiutil', ['mpiutil.pyx'],
include_dirs=[np.get_include(),
mpi4py_include]),
Extension("sf", ["sf.pyx"],
include_dirs= [np.get_include(), cython_gsl.get_cython_include_dir(),
'../../clib', ],
libraries=cython_gsl.get_libraries()+['mysf'],
library_dirs=[cython_gsl.get_library_dir(), '../../clib/lib'] ),
Extension("alm", ["alm.pyx"],
include_dirs= [np.get_include(), '../../clib', ],
libraries=['mysf'],
library_dirs=[ '../../clib/lib'] ),
Extension("cgalio", ["cgalio.pyx", "../c/cgalio.c"],
libraries=cython_gsl.get_libraries()+["cuba"],
include_dirs=[np.get_include(), cython_gsl.get_cython_include_dir(), "../c/"],
library_dirs=[cython_gsl.get_library_dir(), './', "../c/"] )
]
setup( name = 'cython wrapper', cmdclass = {'build_ext': build_ext},
ext_modules = ext_modules )
from __future__ import print_function
import logging
from setuptools import setup
from distutils.extension import Extension
from Cython.Build import cythonize
import numpy
import cython_gsl
extensions = [
Extension("GalDM.dm_int", ["GalDM/dm_int.pyx"],
include_dirs=[numpy.get_include(),cython_gsl.get_include()], library_dirs=[cython_gsl.get_library_dir()],libraries=["m","gsl","gslcblas"],
extra_compile_args = ["-O3", "-ffast-math", "-march=native", "-fopenmp","-lcblas","-lgslcblas","-lgsl"],
extra_link_args=['-fopenmp']),
Extension("GalDM.dm_profiles", ["GalDM/dm_profiles.pyx"],
include_dirs=[numpy.get_include(),cython_gsl.get_include()], library_dirs=[cython_gsl.get_library_dir()],libraries=["m","gsl","gslcblas"],
extra_compile_args = ["-O3", "-ffast-math", "-march=native", "-fopenmp","-lcblas","-lgslcblas","-lgsl"],
extra_link_args=['-fopenmp'])
]
setup_args = {'name':'GalDM',
'version':'0.0',
'description':'Creating galactic dark matter maps and calculated J/D factors',
'url':'https://github.com/nickrodd/GalDM',
'author':'Nicholas L Rodd',
'author_email':'*****@*****.**',
'license':'MIT',
'install_requires':[
'numpy',
'matplotlib',
'Cython',
# if len(sys.argv)>=3 and sys.argv[2][-2:]==".c":
# sources = f'"{sys.argv[1]}","{sys.argv[2]}"'
# else:
# sources = f'"{sys.argv[1]}"'
#from sysconfig import get_paths
#from pprint import pprint
#info = get_paths() # a diction
#input(info['include'])
numpy_I = np.get_include()
gls_I = cython_gsl.get_include()
lib_dir = os.getcwd()
lib_gls = cython_gsl.get_library_dir()
cython_include = cython_gsl.get_cython_include_dir()
setup = f"""
import os
import sys
from distutils.core import setup, Extension
from Cython.Build import cythonize
from Cython.Compiler import Options
import cython_gsl
##Whether or not to include docstring in the Python extension. If False, the binary size will be smaller
##but the __doc__ attribute of any class or function will be an empty string.
Options.docstrings = True
## generer un fichier html
from distutils.core import setup
from Cython.Build import cythonize
from distutils.extension import Extension
import numpy
import cython_gsl
include_gsl_dir = "/usr/include/"
lib_gsl_dir = "/usr/lib/"
extensions = [
Extension("util", ["util.pyx"],
include_dirs=[
numpy.get_include(), include_gsl_dir,
cython_gsl.get_cython_include_dir()
],
libraries=cython_gsl.get_libraries(),
library_dirs=[lib_gsl_dir,
cython_gsl.get_library_dir()]),
]
setup(ext_modules=cythonize(extensions), )
## python setup_util.py build_ext --inplace
import numpy as np
import cython_gsl
"""
"""
machine = os.environ['MACHINE']
if machine == 'mylaptop':
module = [
Extension("CGAL-IO", ["cgalio.pyx", "../c/cgalio.c"],
libraries=cython_gsl.get_libraries() + ["cuba"],
include_dirs=[
np.get_include(),
cython_gsl.get_cython_include_dir(), "../c/"
],
library_dirs=[cython_gsl.get_library_dir(), './', "../c/"]),
]
elif machine == 'gwln':
module = [
Extension(
"cgalio",
["cgalio.pyx", "../c/cgalio.c"],
libraries=cython_gsl.get_libraries() + ["cuba"],
include_dirs=[ #"/home/wangxin/workspace/lib/mylib/script/clib",
np.get_include(),
cython_gsl.get_cython_include_dir(), "../c/"
],
library_dirs=[cython_gsl.get_library_dir(), './', "../c/"]),
]
use_cython = True
ext = '.pyx' if use_cython else '.c'
# from Cython.Compiler.Options import get_directive_defaults
# directive_defaults = get_directive_defaults()
# directive_defaults['linetrace'] = True
# directive_defaults['binding'] = True
omnibus_libraries = []
omnibus_library_dirs = []
omnibus_include_dirs = ['.']
if use_cython:
omnibus_libraries.extend(cython_gsl.get_libraries())
omnibus_library_dirs.append(cython_gsl.get_library_dir())
omnibus_include_dirs.append(cython_gsl.get_cython_include_dir())
cmdclass = {}
extensions = [
Extension(
"nd.change._omnibus",
["nd/change/_omnibus" + ext],
libraries=omnibus_libraries,
library_dirs=omnibus_library_dirs,
include_dirs=omnibus_include_dirs,
extra_compile_args=['-O3', '-fopenmp'],
extra_link_args=['-fopenmp'],
),
Extension(
from Cython.Build import cythonize
except ImportError:
USE_CYTHON = False
else:
USE_CYTHON = True
if USE_CYTHON:
extensions = [
Extension(
name='beam_calc',
sources=["beam_calc.pyx"],
language="c",
extra_compile_args=['-fopenmp'],
extra_link_args=['-lomp'],
libraries=cython_gsl.get_libraries(),
library_dirs=[cython_gsl.get_library_dir(), '/usr/local/lib'],
include_dirs=[
numpy.get_include(),
cython_gsl.get_cython_include_dir()
]),
Extension(
name='st_utils',
sources=["st_utils.pyx"],
language="c",
extra_compile_args=['-fopenmp'],
extra_link_args=['-lomp'],
libraries=cython_gsl.get_libraries(),
library_dirs=[cython_gsl.get_library_dir(), '/usr/local/lib'],
include_dirs=[
numpy.get_include(),
cython_gsl.get_cython_include_dir()
Matzke, D., Dolan, C.V, Logan, G.D., Brown, S.D., & Wagenmakers, E.-J. (submitted). Bayesian parametric estimation of stop-signal reaction time distributions. Manuscript submitted for publication.""",
setup_requires=['NumPy >=1.3.0', 'kabuki >= 0.2a', 'pymc'],
include_dirs = [np.get_include(), cython_gsl.get_include(), "C:/Program Files (x86)/GnuWin32/include"],
classifiers=[
'Development Status :: 3 - Alpha',
'Environment :: Console',
'Operating System :: OS Independent',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: GNU General Public License (GPL)',
'Programming Language :: Python',
'Topic :: Scientific/Engineering',
],
ext_modules = [Extension("stop_likelihoods",
["src/stop_likelihoods.c"],
libraries=['gsl','gslcblas'],
library_dirs=[cython_gsl.get_library_dir(), "C:/Program Files (x86)/GnuWin32/lib" ])]
)
setup(
name="stopsignal_wtf",
version="0.1a",
author="Thomas V. Wiecki, Dora Matzke, Eric-Jan Wagenmakers",
author_email="*****@*****.**",
url="http://github.com/twiecki/stopsignal",
packages=["stopsignal_wtf"],
package_data={"stopsignal":["examples/*.csv"]},
description="""stopsignal implements a hierarchical Bayesian estimation of the stopsignal model presented in Matzke et al (submitted) in kabuki.
Matzke, D., Dolan, C.V, Logan, G.D., Brown, S.D., & Wagenmakers, E.-J. (submitted). Bayesian parametric estimation of stop-signal reaction time distributions. Manuscript submitted for publication.""",
setup_requires=['NumPy >=1.3.0', 'kabuki >= 0.2a', 'pymc'],
include_dirs = [np.get_include(), cython_gsl.get_include(), "C:/Program Files (x86)/GnuWin32/include"],
classifiers=[
elif machine == 'cita':
mpi4py_include = '/home/xwang/workspace/software/anaconda/lib/python2.7/site-packages/mpi4py/include'
else:
raise Exception
src_dir = './'
#src_dir= '../c/'
#src_c = ['misc.c', 'kernel.c', 'abkernel.c']
#c_lib = #'libwigner.a'
kernel_src = ['covm.pyx']
print kernel_src
module = [
Extension("covm",
sources=[kernel_src[0]],
include_dirs=[
np.get_include(), mpi4py_include, src_dir,
cython_gsl.get_cython_include_dir()
],
libraries=cython_gsl.get_libraries() + ['m'],
library_dirs=[cython_gsl.get_library_dir(), './', src_dir]),
]
setup(name='Quadratic_Estimator_Cython',
cmdclass={'build_ext': build_ext},
ext_modules=module)
# all .pyx files in a folder
import setuptools
from Cython.Build import cythonize
from Cython.Distutils import Extension
from Cython.Distutils import build_ext
import numpy
import cython_gsl
libs = {
'libraries': cython_gsl.get_libraries(),
'library_dirs': [cython_gsl.get_library_dir()],
'include_dirs': [
cython_gsl.get_cython_include_dir(),
numpy.get_include(),
]
}
extensions = [
Extension("gbnet.cchain", ["gbnet/cchain.pyx"], **libs),
Extension("gbnet.cnodes", ["gbnet/cnodes.pyx"], **libs),
]
with open("README.md", "r") as fh:
long_description = fh.read()
setuptools.setup(
name='gbnet',
version='0.1.dev1',
author="Argenis Arriojas",
author_email="*****@*****.**",
description=
from distutils.core import setup
from Cython.Build import cythonize
from distutils.extension import Extension
import numpy
import cython_gsl
include_gsl_dir = "/usr/include/"
lib_gsl_dir = "/usr/lib/"
extensions = [
Extension("util", ["util.pyx"],
include_dirs = [numpy.get_include(),
include_gsl_dir,
cython_gsl.get_cython_include_dir()],
libraries = cython_gsl.get_libraries(),
library_dirs = [lib_gsl_dir,
cython_gsl.get_library_dir()]),
]
setup(
ext_modules = cythonize(extensions),
)
## python setup_util.py build_ext --inplace
class BuildExtWithoutPlatformSuffix(build_ext):
def get_ext_filename(self, ext_name):
filename = super().get_ext_filename(ext_name)
return get_ext_filename_without_platform_suffix(filename)
cmdclass_option = {'build_ext': BuildExtWithoutPlatformSuffix}
else:
raise ValueError(
'You are not using neither Python2 nor Python3, probably you are a time traveller from the Future or from the Past'
)
#cython gsl
cy_gsl_lib = cython_gsl.get_libraries()
cy_gsl_inc = cython_gsl.get_include()
cy_gsl_lib_dic = cython_gsl.get_library_dir()
#cython
cy_gsl_inc_cy = cython_gsl.get_cython_include_dir()
#numpy
np_inc = numpy.get_include()
gh = ['galpynamics/src/pot_halo/pot_c_ext/general_halo.pyx']
gh_ext = Extension('galpynamics.src.pot_halo.pot_c_ext.general_halo',
sources=gh)
ih = ['galpynamics/src/pot_halo/pot_c_ext/isothermal_halo.pyx']
ih_ext = Extension('galpynamics.src.pot_halo.pot_c_ext.isothermal_halo',
sources=ih)
infw = ['galpynamics/src/pot_halo/pot_c_ext/nfw_halo.pyx']
infw_ext = Extension('galpynamics.src.pot_halo.pot_c_ext.nfw_halo',
from setuptools import setup
from distutils.extension import Extension
from Cython.Build import cythonize
import cython_gsl
import numpy as np
extensions = [
Extension("wigner_3j.wigner_3j",
sources=["wigner_3j/wigner_3j.pyx"],
language="c", libraries = cython_gsl.get_libraries(),
library_dirs = [cython_gsl.get_library_dir()],
include_dirs = [cython_gsl.get_cython_include_dir(), np.get_include()])
]
setup(
name='Max Help',
version='0.01',
packages=['wigner_3j'],
url='',
license='',
author='Bryan Weinstein',
author_email='*****@*****.**',
description='',
include_dirs = [cython_gsl.get_include(), np.get_include()],
ext_modules = cythonize(extensions, annotate=True, reload_support=True)
)
from setuptools import setup
from distutils.extension import Extension
from Cython.Build import cythonize
import cython_gsl
import numpy as np
extensions = [
Extension(
"rough_front_expansion.cython",
sources=["rough_front_expansion/cython.pyx"],
language="c",
libraries=cython_gsl.get_libraries(),
library_dirs=[cython_gsl.get_library_dir()],
include_dirs=[cython_gsl.get_cython_include_dir(),
np.get_include()]),
Extension(
"rough_front_expansion.cython_D2Q9",
sources=["rough_front_expansion/cython_D2Q9.pyx"],
language="c",
libraries=cython_gsl.get_libraries(),
library_dirs=[cython_gsl.get_library_dir()],
include_dirs=[cython_gsl.get_cython_include_dir(),
np.get_include()])
]
setup(name='rough_front_expansion',
version='0.1',
packages=['rough_front_expansion'],
url='',
license='',
author='btweinstein',
import numpy as np
import cython_gsl
setup(
name="stopsignal_wtf",
version="0.1a",
author="Thomas V. Wiecki, Dora Matzke, Eric-Jan Wagenmakers",
author_email="*****@*****.**",
url="http://github.com/twiecki/stopsignal",
packages=["stopsignal_wtf"],
package_data={"stopsignal":["examples/*.csv"]},
description="""stopsignal implements a hierarchical Bayesian estimation of the stopsignal model presented in Matzke et al (submitted) in kabuki.
Matzke, D., Dolan, C.V, Logan, G.D., Brown, S.D., & Wagenmakers, E.-J. (submitted). Bayesian parametric estimation of stop-signal reaction time distributions. Manuscript submitted for publication.""",
setup_requires=['NumPy >=1.3.0', 'kabuki >= 0.2a', 'pymc'],
include_dirs = [np.get_include(), cython_gsl.get_include(), "C:/Program Files (x86)/GnuWin32/include"],
classifiers=[
'Development Status :: 3 - Alpha',
'Environment :: Console',
'Operating System :: OS Independent',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: GNU General Public License (GPL)',
'Programming Language :: Python',
'Topic :: Scientific/Engineering',
],
ext_modules = [Extension("stop_likelihoods_wtf",
["src/stop_likelihoods_wtf.c"],
libraries=['gsl','gslcblas'],
library_dirs=[cython_gsl.get_library_dir(), "C:/Program Files (x86)/GnuWin32/lib"])]
)
