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
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',
author_email='*****@*****.**',
description='',
include_dirs=[cython_gsl.get_include(),
np.get_include()],
ext_modules=cythonize(extensions, annotate=True))
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)
)
import cython_gsl
except ImportError:
print("Please install numpy and cythongsl.")
# Dealing with Cython
USE_CYTHON = os.environ.get('USE_CYTHON', False)
ext = '.pyx' if USE_CYTHON else '.c'
extensions = [
Extension(
'slda._topic_models',
['slda/_topic_models' + ext],
libraries=cython_gsl.get_libraries(),
library_dirs=[cython_gsl.get_library_dir()],
include_dirs=[np.get_include(),
cython_gsl.get_include()],
),
]
if USE_CYTHON:
from Cython.Build import cythonize
extensions = cythonize(extensions)
setup(
name='slda',
version='0.1.6',
description='''Cython implementations of Gibbs sampling for latent
Dirichlet allocation and its supervised variants''',
author='Berton Earnshaw, Mimi Felicilda',
author_email='[email protected], [email protected]',
url='https://github.com/Savvysherpa/slda',
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',
sources += f'"{cf}"' + ','
sources = sources[:-1]
# 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
from distutils.core import setup
from Cython.Distutils import Extension
from Cython.Distutils import build_ext
import cython_gsl
setup(include_dirs=[cython_gsl.get_include()],
cmdclass={'build_ext': build_ext},
ext_modules=[
Extension("gslneuosc", ["src/gslneuosc.pyx"],
libraries=cython_gsl.get_libraries(),
library_dirs=[cython_gsl.get_library_dir()],
include_dirs=[cython_gsl.get_cython_include_dir()])
])
from distutils.core import setup, Extension
import numpy as np
import cython_gsl
setup(
name="stopsignal",
version="0.1a",
author="Thomas V. Wiecki, Dora Matzke, Eric-Jan Wagenmakers",
author_email="*****@*****.**",
url="http://github.com/twiecki/stopsignal",
packages=["stopsignal"],
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()],
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()])]
)
include_dirs = []
install_requires = []
if not mock_install:
install_requires.extend([
"numpy",
"scipy",
"xarray",
"dask[dataframe]",
"lxml",
"rasterio",
"pandas",
"python-dateutil",
"matplotlib",
"affine",
"opencv-python",
# "NetCDF4"
"h5py",
"h5netcdf",
"imageio"
])
include_dirs.append(numpy.get_include())
include_dirs.append(cython_gsl.get_include())
setup(cmdclass=cmdclass,
ext_modules=extensions,
include_dirs=include_dirs,
install_requires=install_requires)
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"])]
)
import numpy as np
import cython_gsl
setup(
name="stopsignal",
version="0.1a",
author="Thomas V. Wiecki, Dora Matzke, Eric-Jan Wagenmakers",
author_email="*****@*****.**",
url="http://github.com/twiecki/stopsignal",
packages=["stopsignal"],
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",
["src/stop_likelihoods.c"],
libraries=['gsl','gslcblas'],
library_dirs=[cython_gsl.get_library_dir(), "C:/Program Files (x86)/GnuWin32/lib" ])]
)
try:
import numpy as np
import cython_gsl
except ImportError:
print("Please install numpy and cythongsl.")
# Dealing with Cython
USE_CYTHON = os.environ.get('USE_CYTHON', False)
ext = '.pyx' if USE_CYTHON else '.c'
extensions = [
Extension('slda._topic_models', ['slda/_topic_models' + ext],
libraries=cython_gsl.get_libraries(),
library_dirs=[cython_gsl.get_library_dir()],
include_dirs=[np.get_include(), cython_gsl.get_include()],),
]
if USE_CYTHON:
from Cython.Build import cythonize
extensions = cythonize(extensions)
setup(
name='slda',
version='0.1.6',
description='''Cython implementations of Gibbs sampling for latent
Dirichlet allocation and its supervised variants''',
author='Berton Earnshaw, Mimi Felicilda',
author_email='[email protected], [email protected]',
url='https://github.com/Savvysherpa/slda',
license="MIT",
from setuptools import setup
from setuptools.extension import Extension
from distutils.command.build_ext import build_ext
from Cython.Build import cythonize
import numpy
import cython_gsl
ext_modules = [
Extension(
"fast_random",
["fast_random.pyx"],
libraries=cython_gsl.get_libraries(),
library_dirs=[cython_gsl.get_library_dir()],
include_dirs=[numpy.get_include(), cython_gsl.get_include()]),
Extension(
"fast_random",
["fast_random.pyx"])
]
ext_modules = cythonize(ext_modules)
setup(
name='fast_random',
ext_modules=ext_modules,
cmdclass={'build_ext': build_ext})
import cython_gsl
except ImportError:
error = 'Cannot find gsl package (required for hyp1f1), \n' + \
'try pip install cythongsl and \nsudo apt-get install libgsl0-dev libgsl0ldbl on Ubuntu and friends' + \
'\nor\n brew install gsl on mac'
raise ImportError(error)
if sys.platform.startswith('win'):
dir_path = os.path.dirname(os.path.realpath(__file__))
gsl_path = os.path.join(dir_path, 'nlsam', 'gsl_windows')
os.environ["LIB_GSL"] = gsl_path
sys.path.append(gsl_path)
from nlsam import get_setup_params
params = get_setup_params()
params['include_dirs'] = [cython_gsl.get_include()]
params['packages'] = find_packages()
params['cmdclass'] = {'build_ext': build_ext}
# Check for local version of dipy if it exists, since it would replace a locally built
# but not installed version.
try:
import dipy
print('Found local version of dipy in ' + dipy.__file__)
if LooseVersion(dipy.__version__) < LooseVersion('0.11'):
raise ValueError(
'Local dipy version is {}, but you need at least 0.11!'.format(
dipy.__version__))
except ImportError:
print('Cannot find dipy, it will be installed using pip.')
params['dependencies'].append('dipy>=0.11')
return name[:idx] + ext
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']
