def configuration(parent_package="", top_path=None):
config = Configuration("math", parent_package, top_path)
config.add_subpackage("test")
config.add_subpackage("fit")
# =====================================
# histogramnd
# =====================================
histo_dir = "histogramnd"
histo_src = [os.path.join(histo_dir, srcf) for srcf in ["chistogramnd.pyx", "src/histogramnd_c.c"]]
histo_inc = [os.path.join(histo_dir, "include"), numpy.get_include()]
config.add_extension("chistogramnd", sources=histo_src, include_dirs=histo_inc, language="c")
# =====================================
# =====================================
# =====================================
# histogramnd_lut
# =====================================
histo_dir = "histogramnd"
histo_src = [os.path.join(histo_dir, srcf) for srcf in ["chistogramnd_lut.pyx"]]
histo_inc = [os.path.join(histo_dir, "include"), numpy.get_include()]
config.add_extension("chistogramnd_lut", sources=histo_src, include_dirs=histo_inc, language="c")
# =====================================
# =====================================
# marching cubes
mc_dir = "marchingcubes"
mc_src = [os.path.join(mc_dir, srcf) for srcf in ["marchingcubes.pyx", "mc_lut.cpp"]]
config.add_extension("marchingcubes", sources=mc_src, include_dirs=[mc_dir, numpy.get_include()], language="c++")
return config
def Extension(name, source=None, can_use_openmp=False, extra_sources=None, **kwargs):
"""
Wrapper for distutils' Extension
"""
if source is None:
source = name
cython_c_ext = ".pyx" if USE_CYTHON else ".c"
sources = [os.path.join("src", source + cython_c_ext)]
if extra_sources:
sources.extend(extra_sources)
if "include_dirs" in kwargs:
include_dirs = set(kwargs.pop("include_dirs"))
include_dirs.add(numpy.get_include())
include_dirs.add("src")
include_dirs = list(include_dirs)
else:
include_dirs = ["src", numpy.get_include()]
if can_use_openmp and USE_OPENMP:
extra_compile_args = set(kwargs.pop("extra_compile_args", []))
extra_compile_args.add(USE_OPENMP)
kwargs["extra_compile_args"] = list(extra_compile_args)
extra_link_args = set(kwargs.pop("extra_link_args", []))
extra_link_args.add(USE_OPENMP)
kwargs["extra_link_args"] = list(extra_link_args)
ext = _Extension(name=name, sources=sources, include_dirs=include_dirs, **kwargs)
if USE_CYTHON:
cext = cythonize([ext], compile_time_env={"HAVE_OPENMP": bool(USE_OPENMP)})
if cext:
ext = cext[0]
return ext
def rmsd_extensions():
compiler_args = (compiler.compiler_args_openmp + compiler.compiler_args_sse2 +
compiler.compiler_args_sse3 + compiler.compiler_args_opt)
compiler_libraries = compiler.compiler_libraries_openmp
rmsd = Extension('mdtraj._rmsd',
sources=[
'MDTraj/rmsd/src/theobald_rmsd.c',
'MDTraj/rmsd/src/rotation.c',
'MDTraj/rmsd/src/center.c',
'MDTraj/rmsd/_rmsd.pyx'],
include_dirs=[
'MDTraj/rmsd/include', numpy.get_include()],
extra_compile_args=compiler_args,
libraries=compiler_libraries)
lprmsd = Extension('mdtraj._lprmsd',
sources=[
'MDTraj/rmsd/src/theobald_rmsd.c',
'MDTraj/rmsd/src/rotation.c',
'MDTraj/rmsd/src/center.c',
'MDTraj/rmsd/src/fancy_index.cpp',
'MDTraj/rmsd/src/Munkres.cpp',
'MDTraj/rmsd/src/euclidean_permutation.cpp',
'MDTraj/rmsd/_lprmsd.pyx'],
language='c++',
include_dirs=[
'MDTraj/rmsd/include', numpy.get_include()],
extra_compile_args=compiler_args,
libraries=compiler_libraries + extra_cpp_libraries)
return rmsd, lprmsd
def initialize_options(self):
from numpy import get_include
_build_ext.initialize_options(self)
if self.include_dirs is None:
self.include_dirs = get_include()
else:
self.include_dirs += get_include()
def geometry_extensions():
compiler_args = (compiler.compiler_args_sse2 + compiler.compiler_args_sse3 + compiler.compiler_args_sse41 +
compiler.compiler_args_opt + compiler.compiler_args_sse41)
define_macros = compiler.define_macros_sse41
return [
Extension('mdtraj.geometry._geometry',
sources=['MDTraj/geometry/src/geometry.c',
'MDTraj/geometry/src/sasa.c',
'MDTraj/geometry/src/dssp.cpp',
'MDTraj/geometry/src/_geometry.pyx'],
include_dirs=['MDTraj/geometry/include',
'MDTraj/geometry/src/kernels',
numpy.get_include()],
define_macros=define_macros,
extra_compile_args=compiler_args,
libraries=extra_cpp_libraries,
language='c++'),
Extension('mdtraj.geometry.drid',
sources=["MDTraj/geometry/drid.pyx",
"MDTraj/geometry/src/dridkernels.c",
"MDTraj/geometry/src/cephes/cbrt.c",
"MDTraj/geometry/src/cephes/isnan.c",
"MDTraj/geometry/src/moments.c"],
include_dirs=["MDTraj/geometry/include",
"MDTraj/geometry/include/cephes",
numpy.get_include()],
define_macros=define_macros,
extra_compile_args=compiler_args)
]
def build_sps(ext_modules):
if platform.system() == 'Linux' :
extra_compile_args = ['-pthread']
#extra_compile_args = []
elif platform.system() == 'SunOS' :
#extra_compile_args = ['-pthreads']
extra_compile_args = []
else:
extra_compile_args = []
module = Extension(name = 'PyMca5.spslut',
sources = ['PyMca5/PyMcaIO/sps/Src/sps_lut.c',
'PyMca5/PyMcaIO/sps/Src/spslut_py.c'],
define_macros = define_macros,
extra_compile_args = extra_compile_args,
include_dirs = ['PyMca5/PyMcaIO/sps/Include',
numpy.get_include()])
ext_modules.append(module)
if sys.platform != "win32":
module = (Extension(name = 'PyMca5.PyMcaIO.sps',
sources = ['PyMca5/PyMcaIO/sps/Src/sps.c',
'PyMca5/PyMcaIO/sps/Src/sps_py.c'],
define_macros = define_macros,
extra_compile_args = extra_compile_args,
include_dirs = ['PyMca5/PyMcaIO/sps/Include',
numpy.get_include()]))
ext_modules.append(module)
def configuration(parent_package='', top_path=None):
import numpy
from numpy.distutils.misc_util import Configuration
config = Configuration('neighbors', parent_package, top_path)
libraries = []
if os.name == 'posix':
libraries.append('m')
config.add_extension('ball_tree',
sources=['ball_tree.c'],
include_dirs=[numpy.get_include()],
libraries=libraries)
config.add_extension('kd_tree',
sources=['kd_tree.c'],
include_dirs=[numpy.get_include()],
libraries=libraries)
config.add_extension('dist_metrics',
sources=['dist_metrics.c'],
include_dirs=[numpy.get_include(),
os.path.join(numpy.get_include(),
'numpy')],
libraries=libraries)
config.add_extension('typedefs',
sources=['typedefs.c'],
include_dirs=[numpy.get_include()],
libraries=libraries)
config.add_subpackage('tests')
return config
def configuration(parent_package='', top_path=None):
import numpy
from numpy.distutils.misc_util import Configuration
config = Configuration('csgraph', parent_package, top_path)
config.add_data_dir('tests')
config.add_extension('_shortest_path',
sources=['_shortest_path.c'],
include_dirs=[numpy.get_include()])
config.add_extension('_traversal',
sources=['_traversal.c'],
include_dirs=[numpy.get_include()])
config.add_extension('_min_spanning_tree',
sources=['_min_spanning_tree.c'],
include_dirs=[numpy.get_include()])
config.add_extension('_tools',
sources=['_tools.c'],
include_dirs=[numpy.get_include()])
return config
def configuration(parent_package="", top_path=None):
config = Configuration("tree", parent_package, top_path)
libraries = []
if os.name == 'posix':
libraries.append('m')
# check for pre-compiled versions for the encountered sklearn version
if not os.path.isdir("{}/headers/{}".format(os.path.dirname(os.path.realpath(__file__)), sklearn.__version__)) or \
not os.path.isfile("{}/headers/{}/_tree.c".format(os.path.dirname(os.path.realpath(__file__)), sklearn.__version__)):
raise Exception(\
"""sklearnef holds no pre-compiled _tree.c for your current scikit-learn version ({version}).
Please download the corresponding header file from \
https://raw.githubusercontent.com/scikit-learn/scikit-learn/{version}/sklearn/tree/_tree.pxd,
place it in sklearnef/tree/headers/sklearn/tree/ and compile _tree.pyx with cython using \
'cython _tree.pyx -o headers/{version}/_tree.c -I headers/'. Then re-run \
the installation of sklearnef.""".format(version=sklearn.__version__))
config.add_extension("_diffentropy",
sources=["headers/_diffentropy.c"],
include_dirs=[numpy.get_include()],
libraries=libraries + ['lapack', 'blas'],
extra_compile_args=["-O3"])
config.add_extension("_tree",
sources=["headers/{version}/_tree.c".format(version=sklearn.__version__)],
include_dirs=[numpy.get_include()],
libraries=libraries,
extra_compile_args=["-O3"])
config.add_subpackage("tests")
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
libraries = []
if os.name == 'posix':
libraries.append('m')
config = Configuration('iced', parent_package, top_path)
config.add_subpackage('utils')
config.add_subpackage("io")
config.add_extension(
'_normalization_',
libraries=libraries,
sources=['_normalization_.c'],
include_dirs=[join('..', 'src', 'cblas'),
numpy.get_include()])
config.add_extension(
'_filter_',
libraries=libraries,
sources=['_filter_.c'],
include_dirs=[join('..', 'src', 'cblas'),
numpy.get_include()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
cblas_libs, blas_info = get_blas_info()
libraries = []
if os.name == 'posix':
cblas_libs.append('m')
libraries.append('m')
config = Configuration('cluster', parent_package, top_path)
config.add_extension('_hierarchical',
sources=['_hierarchical.c'],
include_dirs=[numpy.get_include()],
libraries=libraries)
config.add_extension(
'_k_means',
libraries=cblas_libs,
sources=['_k_means.c'],
include_dirs=[join('..', 'src', 'cblas'),
numpy.get_include(),
blas_info.pop('include_dirs', [])],
extra_compile_args=blas_info.pop('extra_compile_args', []),
**blas_info
)
return config
def main():
setup(name = 'glu',
version = get_version(),
author = 'Kevin Jacobs',
author_email = '*****@*****.**',
maintainer = 'Kevin Jacobs',
maintainer_email = '*****@*****.**',
platforms = ['any'],
description = 'Genotype Library and Utilities (GLU)',
long_description = ('Genotype Library and Utilities (GLU): Tools for the management of large '
'amounts of SNP genotype data and programs to check its quality and to '
'test for association between SNP markers with continuous or discrete '
'trait phenotypes.'),
classifiers = filter(None, classifiers.split('\n')),
install_requires = requires,
packages = find_packages(),
include_package_data = True,
scripts = ['bin/glu'],
zip_safe = False,
test_suite = 'nose.collector',
ext_modules = [
Extension('glu.lib.genolib.bitarrayc', sources = ['glu/lib/genolib/bitarrayc.c']),
Extension('glu.lib.genolib._genoarray', sources = ['glu/lib/genolib/_genoarray.c',
'glu/lib/genolib/bitarrayc.c',
'glu/lib/genolib/_ibs.c',
'glu/lib/genolib/_ld.c'],
include_dirs = [np.get_include()]),
Extension('glu.modules.struct._admix', sources = ['glu/modules/struct/_admix.c'],
include_dirs = [np.get_include()]),
Extension('glu.modules.ld.pqueue', sources = ['glu/modules/ld/pqueue.c']),
glmnet_config(),
] + cython_modules(),
entry_points={ 'console_scripts' : ['glu = glu.lib.glu_launcher:main'],
} )
def cython_modules():
try:
from Cython.Build import cythonize
ext = [
Extension('glu.lib._illumina', sources = ['glu/lib/_illumina.pyx']),
Extension('glu.lib.genolib.helpers', sources = ['glu/lib/genolib/helpers.pyx'],
include_dirs = [np.get_include()]),
Extension('glu.lib.seqlib._cigar', sources = ['glu/lib/seqlib/_cigar.pyx']),
Extension('glu.lib.seqlib._edits', sources = ['glu/lib/seqlib/_edits.pyx']),
Extension('glu.lib.seqlib.gc', sources = ['glu/lib/seqlib/gc.pyx']),
Extension('glu.lib.seqlib.intervaltree', sources = ['glu/lib/seqlib/intervaltree.pyx']),
]
ext = cythonize(ext)
# Fall back to using pre-generated C files
except ImportError:
ext = [
Extension('glu.lib._illumina', sources = ['glu/lib/_illumina.c']),
Extension('glu.lib.genolib.helpers', sources = ['glu/lib/genolib/helpers.c'],
include_dirs = [np.get_include()]),
Extension('glu.lib.seqlib._cigar', sources = ['glu/lib/seqlib/_cigar.c']),
Extension('glu.lib.seqlib._edits', sources = ['glu/lib/seqlib/_edits.c']),
Extension('glu.lib.seqlib.gc', sources = ['glu/lib/seqlib/gc.c']),
Extension('glu.lib.seqlib.intervaltree', sources = ['glu/lib/seqlib/intervaltree.c']),
]
return ext
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, BlasNotFoundError
config = Configuration('io', parent_package, top_path)
config.add_data_dir('tests')
# determine and verify the at RSL location
rsl_path = os.environ.get('RSL_PATH')
if rsl_path is None:
rsl_path = guess_rsl_path()
rsl_lib_path = os.path.join(rsl_path, 'lib')
rsl_include_path = os.path.join(rsl_path, 'include')
# build the RSL interface if RSL is installed
if check_rsl_path(rsl_lib_path, rsl_include_path):
config.add_extension(
'_rsl_interface',
sources=['_rsl_interface.c'],
libraries=['rsl'],
library_dirs=[rsl_lib_path],
include_dirs=[rsl_include_path] + [get_include()],
runtime_library_dirs=[rsl_lib_path])
else:
import warnings
warnings.warn(RSL_MISSING_WARNING % (rsl_path))
config.add_extension('_sigmetfile',
sources=['_sigmetfile.c'],
include_dirs=[get_include()])
config.add_extension('nexrad_interpolate',
sources=['nexrad_interpolate.c'],
include_dirs=[get_include()])
return config
def configuration(parent_package='', top_path=None):
import numpy
from numpy.distutils.misc_util import Configuration
config = Configuration('utils', parent_package, top_path)
config.add_subpackage('sparsetools')
cblas_libs, blas_info = get_blas_info()
libraries = []
if os.name == 'posix':
libraries.append('m')
cblas_libs.append('m')
config.add_extension('arraybuilder', sources=['arraybuilder.c'])
config.add_extension('sparsefuncs', sources=['sparsefuncs.c'],
libraries=libraries)
config.add_extension('arrayfuncs',
sources=['arrayfuncs.c'],
depends=[join('src', 'cholesky_delete.h')],
libraries=cblas_libs,
include_dirs=[join('..', 'src', 'cblas'),
numpy.get_include(),
blas_info.pop('include_dirs', [])],
extra_compile_args=blas_info.pop('extra_compile_args',
[]),
**blas_info
)
config.add_extension(
'murmurhash',
sources=['murmurhash.c', join('src', 'MurmurHash3.cpp')],
include_dirs=['src'])
config.add_extension('lgamma',
sources=['lgamma.cpp', join('src', 'Gamma.cpp')],
include_dirs=['src'],
libraries=libraries)
config.add_extension('graph_shortest_path',
sources=['graph_shortest_path.c'],
include_dirs=[numpy.get_include()])
config.add_extension('seq_dataset',
sources=['seq_dataset.c'],
include_dirs=[numpy.get_include()])
config.add_extension('weight_vector',
sources=['weight_vector.c'],
include_dirs=[numpy.get_include()],
libraries=libraries)
config.add_extension("random",
sources=["random.c"],
include_dirs=[numpy.get_include()],
libraries=libraries)
return config
def configuration(parent_package="", top_path=None):
config = Configuration("tree", parent_package, top_path)
libraries = []
if os.name == 'posix':
libraries.append('m')
config.add_extension("_tree",
sources=["_tree.pyx"],
include_dirs=[numpy.get_include()],
libraries=libraries,
extra_compile_args=["-O3"])
config.add_extension("_splitter",
sources=["_splitter.pyx"],
include_dirs=[numpy.get_include()],
libraries=libraries,
extra_compile_args=["-O3"])
config.add_extension("_criterion",
sources=["_criterion.pyx"],
include_dirs=[numpy.get_include()],
libraries=libraries,
extra_compile_args=["-O3"])
config.add_extension("_utils",
sources=["_utils.pyx"],
include_dirs=[numpy.get_include()],
libraries=libraries,
extra_compile_args=["-O3"])
config.add_subpackage("tests")
return config
def main():
packages = ['disvis', 'disvis.IO']
requirements = ['numpy']
ext = '.pyx' if CYTHON else '.c'
ext_modules = [Extension("disvis.libdisvis",
[join("src", "libdisvis" + ext)],
include_dirs = [numpy.get_include()],
)]
cmdclass = {}
if CYTHON:
ext_modules = cythonize(ext_modules)
cmdclass = {'build_ext' : build_ext}
package_data = {'disvis': [join('data', '*.npy'),
join('kernels', '*.cl')]}
scripts = [join('scripts', 'disvis')]
setup(name="disvis",
version='1.0.1',
description='Quantifying and visualizing the interaction space of distance-constrainted macromolecular complexes',
author='Gydo C.P. van Zundert',
author_email='*****@*****.**',
packages=packages,
cmdclass=cmdclass,
ext_modules=ext_modules,
package_data=package_data,
scripts=scripts,
requires=requirements,
include_dirs=[numpy.get_include()],
)
def configuration(parent_package='', top_path=None):
# compiles files during installation
from numpy.distutils.misc_util import Configuration
config = Configuration('cy', parent_package, top_path)
exts = ['spmatfuncs', 'stochastic', 'sparse_utils', 'graph_utils']
if os.environ['QUTIP_RELEASE'] == 'TRUE':
for ext in exts:
config.add_extension(ext,
sources=[ext + ".c"],
include_dirs=[np.get_include()],
extra_compile_args=['-w -ffast-math -O3 -march=native -mfpmath=sse'],
extra_link_args=[])
else:
for ext in exts:
config.add_extension(ext,
sources=[ext + ".pyx"],
include_dirs=[np.get_include()],
extra_compile_args=['-w -ffast-math -O3 -march=native -mfpmath=sse'],
extra_link_args=[])
config.ext_modules = cythonize(config.ext_modules)
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info
blas_info = get_info('blas_opt', 0)
if (not blas_info) or (
('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])):
cblas_libs = ['cblas']
blas_info.pop('libraries', None)
else:
cblas_libs = blas_info.pop('libraries', [])
config = Configuration('cluster', parent_package, top_path)
config.add_extension(
'_inertia',
sources=['_inertia.c'],
include_dirs=[numpy.get_include()],
)
config.add_extension(
'_k_means',
libraries=cblas_libs,
sources=['_k_means.c'],
include_dirs=[join('..', 'src', 'cblas'),
numpy.get_include(),
blas_info.pop('include_dirs', [])],
extra_compile_args=blas_info.pop('extra_compile_args', []),
**blas_info
)
return config
def configuration(parent_package='', top_path=None):
config = Configuration('ndimage', parent_package, top_path)
config.add_extension("_nd_image",
sources=["src/nd_image.c","src/ni_filters.c",
"src/ni_fourier.c","src/ni_interpolation.c",
"src/ni_measure.c",
"src/ni_morphology.c","src/ni_support.c"],
include_dirs=['src']+[get_include()])
# Cython wants the .c and .pyx to have the underscore.
config.add_extension("_ni_label",
sources=["src/_ni_label.c",],
include_dirs=['src']+[get_include()])
config.add_extension("_ctest",
sources=["src/_ctest.c"],
include_dirs=[get_include()])
config.add_extension("_ctest_oldapi",
sources=["src/_ctest.c"],
include_dirs=[get_include()],
define_macros=[("OLDAPI", 1)])
config.add_extension("_cytest",
sources=["src/_cytest.c"])
config.add_data_dir('tests')
return config
def configuration(parent_package='', top_path=None):
import numpy
from numpy.distutils.misc_util import Configuration
config = Configuration('utils', parent_package, top_path)
config.add_subpackage('sparsetools')
# cd fast needs CBLAS
blas_info = get_info('blas_opt', 0)
if (not blas_info) or (
('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])):
cblas_libs = ['cblas']
blas_info.pop('libraries', None)
else:
cblas_libs = blas_info.pop('libraries', [])
config.add_extension('arrayfuncs',
sources=['arrayfuncs.c'],
depends=[join('src', 'cholesky_delete.c')],
libraries=cblas_libs,
include_dirs=[join('..', 'src', 'cblas'),
numpy.get_include(),
blas_info.pop('include_dirs', [])],
extra_compile_args=blas_info.pop('extra_compile_args', []),
**blas_info
)
config.add_extension('graph_shortest_path',
sources=['graph_shortest_path.c'],
include_dirs=[numpy.get_include()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('impl', parent_package, top_path)
cblas_libs, blas_info = get_blas_info()
config.add_extension('dataset_fast',
sources=['dataset_fast.c'],
include_dirs=[numpy.get_include()])
config.add_extension('matrix_fact_fast',
sources=['matrix_fact_fast.c'],
include_dirs=[numpy.get_include()])
config.add_extension('preprocessing_fast',
sources=['preprocessing_fast.c'],
include_dirs=[numpy.get_include()])
config.add_extension('dict_fact_fast',
sources=['dict_fact_fast.c'],
include_dirs=[numpy.get_include()])
config.add_extension('dict_fact_fast_partial',
sources=['dict_fact_fast_partial.c'],
include_dirs=[numpy.get_include()])
config.add_subpackage('tests')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, BlasNotFoundError
config = Configuration('map', parent_package, top_path)
config.add_data_dir('tests')
libraries = []
if os.name == 'posix':
libraries.append('m')
config.add_extension('ball_tree',
sources=['ball_tree.c'],
include_dirs=[numpy.get_include()],
libraries=libraries)
config.add_extension('ckdtree',
sources=['ckdtree.c'],
include_dirs=[numpy.get_include()],
libraries=libraries)
config.add_extension('_load_nn_field_data',
sources=['_load_nn_field_data.c'],
include_dirs=[numpy.get_include()])
config.add_extension('_gate_to_grid_map',
sources=['_gate_to_grid_map.c'],
libraries=libraries)
return config
def make_extension_modules(mode="disable_threads", nfft_library_dirs=[], nfft_include_dirs=[]):
ext_icosahedron = Extension(
"condor.utils.icosahedron",
sources=["src/utils/icosahedron/icosahedronmodule.c"],
include_dirs=[numpy.get_include()],
)
_nfft_libraries = {
"disable_threads": ["nfft3"],
"enable_threads": ["nfft3_threads" ,"fftw3_threads" ,"fftw3"]
}
_nfft_macros = {
"disable_threads" : [],
"enable_threads" : [("ENABLE_THREADS", None)],
}
ext_nfft = Extension(
"condor.utils.nfft",
sources=["src/utils/nfft/nfftmodule.c"],
library_dirs=nfft_library_dirs,
libraries=_nfft_libraries[mode],
include_dirs=[numpy.get_include()] + nfft_include_dirs,
define_macros=_nfft_macros[mode],
runtime_library_dirs = nfft_library_dirs,
extra_link_args = [] if (nfft_library_dirs == []) else ['-Wl,-rpath,'+nfft_library_dirs[0]+',-L'+nfft_library_dirs[0]],
)
return [ext_icosahedron, ext_nfft]
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('lightning', parent_package, top_path)
randomdir = os.path.join(top_path, "lightning", "random")
config.add_extension('dataset_fast',
sources=['dataset_fast.cpp'],
include_dirs=[numpy.get_include(), randomdir])
config.add_extension('dual_cd_fast',
sources=['dual_cd_fast.cpp'],
include_dirs=[numpy.get_include(), randomdir])
config.add_extension('loss_fast',
sources=['loss_fast.cpp'],
include_dirs=[numpy.get_include(), randomdir])
config.add_extension('primal_cd_fast',
sources=['primal_cd_fast.cpp'],
include_dirs=[numpy.get_include(), randomdir])
config.add_extension('sgd_fast',
sources=['sgd_fast.cpp'],
include_dirs=[numpy.get_include(), randomdir])
config.add_subpackage('random')
config.add_subpackage('tests')
config.add_subpackage('datasets')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, BlasNotFoundError
config = Configuration('pyLLE', parent_package, top_path)
config.add_subpackage('python_only')
config.add_extension('ball_tree',
language='c++',
sources=[join('wrappers', 'ball_tree.cpp')],
depends=[join('include', 'BallTree.h'),
join('include', 'BallTreePoint.h')],
include_dirs=['include',numpy.get_include()])
config.add_extension('LLE',
language='c++',
sources=[join('wrappers','LLE.cpp')]\
+ MatVec_sources + LLE_sources,
libraries=['stdc++','blas','lapack','arpack'],
library_dirs = LIBS,
include_dirs=['include','lib/MatVec',
numpy.get_include()] )
return config
def extensions():
__builtins__.__NUMPY_SETUP__ = False
import numpy as np
ext_modules = [
Extension(
'pysas.world',
["pysas/world.pyx"] + glob("lib/world/*.cpp"),
include_dirs=['lib/world', np.get_include()],
extra_compile_args=["-O3"],
language="c++",
),
Extension(
'pysas.mcep',
["pysas/mcep.pyx"],
include_dirs=[np.get_include()],
extra_compile_args=["-O3"],
language="c++",
),
Extension(
'pysas.excite',
["pysas/excite.pyx"],
include_dirs=[np.get_include()],
extra_compile_args=["-O3"],
language="c++",
),
Extension(
'pysas.synthesis.mlsa',
["pysas/synthesis/mlsa.pyx"],
include_dirs=[np.get_include()],
extra_compile_args=["-O3"],
language="c++",
)
]
return ext_modules
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('linear_model', parent_package, top_path)
cblas_libs, blas_info = get_blas_info()
libraries = []
if os.name == 'posix':
cblas_libs.append('m')
libraries.append('m')
config.add_extension('cd_fast',
sources=['cd_fast.c'],
libraries=cblas_libs,
include_dirs=[join('..', 'src', 'cblas'),
numpy.get_include(),
blas_info.pop('include_dirs', [])],
extra_compile_args=blas_info.pop('extra_compile_args', []),
**blas_info
)
config.add_extension('sgd_fast',
sources=['sgd_fast.c'],
include_dirs=[numpy.get_include()],
libraries=libraries,
)
# add other directories
config.add_subpackage('tests')
return config
def main():
ext_modules = [
Extension("lz4.lz4",
sources=["lz4/lz4.pyx", os.path.join(c_src_dir, 'lz4.c')],
include_dirs=[np.get_include(), c_src_dir],
define_macros=[],
extra_link_args=[],
extra_compile_args=['-mssse3', '-std=c99']),
Extension("lz4.shuffle",
sources=["lz4/shuffle.pyx"],
include_dirs=[np.get_include()],
define_macros=[],
extra_link_args=[],
extra_compile_args=['-mssse3', '-std=c99']),
]
kwargs = dict(
name = 'lz4',
packages = ['lz4'],
cmdclass = {'build_ext': build_ext},
ext_modules = cythonize(ext_modules),
)
setup(**kwargs)
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
libraries = []
if os.name == 'posix':
libraries.append('m')
config = Configuration('cluster', parent_package, top_path)
config.add_extension('_dbscan_inner',
sources=['_dbscan_inner.pyx'],
include_dirs=[numpy.get_include()],
language="c++")
config.add_extension('_hierarchical',
sources=['_hierarchical.pyx'],
language="c++",
include_dirs=[numpy.get_include()],
libraries=libraries)
config.add_extension('_k_means_elkan',
sources=['_k_means_elkan.pyx'],
include_dirs=[numpy.get_include()],
libraries=libraries)
config.add_extension('_k_means',
sources=['_k_means.pyx'],
include_dirs=numpy.get_include(),
libraries=libraries)
config.add_subpackage('tests')
return config
cython_extension('arraydatatype'),
cython_extension('errorchecker'),
cython_extension('vbo'),
cython_extension('nones_formathandler'),
cython_extension('latebind'),
])
try:
import numpy
except ImportError:
sys.stderr.write(
"""Unable to import numpy, skipping numpy extension building\n""")
else:
if hasattr(numpy, 'get_include'):
includeDirectories = [
numpy.get_include(),
]
else:
includeDirectories = [
os.path.join(
os.path.dirname(numpy.__file__),
'core',
'include',
),
]
extensions.append(
cython_extension('numpy_formathandler', includeDirectories))
if __name__ == "__main__":
extraArguments = {
'classifiers': [
include_dirs=include_dirs,
libraries=libraries,
library_dirs=library_dirs,
))
if BUILD_HINTSVM:
print("Build HintSVM...")
extensions.append(
Extension(
"libact.query_strategies._hintsvm",
sources=[
"libact/query_strategies/_hintsvm.pyx",
"libact/query_strategies/src/hintsvm/libsvm_helper.c",
"libact/query_strategies/src/hintsvm/svm.cpp"
],
include_dirs=[
numpy.get_include(), "libact/query_strategies/src/hintsvm/"
],
extra_compile_args=['-lstdc++'],
))
extensions = cythonize(extensions)
cmdclasses = {'build_ext': build_ext}
setup_requires = []
with open('./requirements.txt') as f:
requirements = f.read().splitlines()
install_requires = requirements
tests_require = [
'coverage',
]
setup(
define_macros=[('CYTHON_TRACE', '1')]),
Extension(name='_cython._mf',
sources=["_cython/_mf.pyx"],
define_macros=[('CYTHON_TRACE', '1')]),
]
setup(name='RecPy',
version="0.2.0",
description=
'Recommender Systems framework for the 2016 Recsys Course at Polimi',
url='https://github.com/mquad/recsys-course',
author='Massimo Quadrana and Yashar Deldjoo',
author_email='Massimo Quadrana',
license='MIT',
classifiers=[
'Development Status :: 3 - Alpha',
'Natural Language :: English',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: MIT License',
'Programming Language :: Python',
'Programming Language :: Python :: 3',
'Programming Language :: Cython',
'Operating System :: OS Independent',
'Topic :: Software Development :: Libraries :: Python Modules',
],
install_requires=['numpy', 'scipy>=0.16'],
packages=['_cython'],
setup_requires=["Cython >= 0.19"],
ext_modules=cythonize(extensions),
include_dirs=[numpy.get_include()])
# requires proj4 headers
ext_modules=[
Extension(
'cartopy.trace',
['lib/cartopy/trace.pyx', 'lib/cartopy/_trace.cpp'],
include_dirs=[include_dir,
'./lib/cartopy'] + proj_includes + geos_includes,
libraries=proj_libraries + geos_libraries,
library_dirs=[library_dir] + proj_library_dirs + geos_library_dirs,
language='c++',
**extra_extension_args
),
Extension(
'cartopy._crs',
['lib/cartopy/_crs.pyx'],
include_dirs=[include_dir, np.get_include()] + proj_includes,
libraries=proj_libraries,
library_dirs=[library_dir] + proj_library_dirs,
**extra_extension_args
),
],
cmdclass={'build_ext': build_ext},
classifiers=[
'Development Status :: 4 - Beta',
'License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)',
'Operating System :: MacOS :: MacOS X',
'Operating System :: Microsoft :: Windows',
'Operating System :: POSIX',
'Operating System :: POSIX :: AIX',
'Operating System :: POSIX :: Linux',
"*",
sources=cython_files,
include_dirs=[
os.path.abspath(os.path.join(CUDF_ROOT, "../include/cudf")),
os.path.abspath(os.path.join(CUDF_ROOT, "../include")),
os.path.abspath(
os.path.join(CUDF_ROOT, "../libcudf_kafka/include/cudf_kafka")
),
os.path.join(CUDF_ROOT, "include"),
os.path.join(CUDF_ROOT, "_deps/libcudacxx-src/include"),
os.path.join(
os.path.dirname(sysconfig.get_path("include")),
"rapids/libcudacxx",
),
os.path.dirname(sysconfig.get_path("include")),
np.get_include(),
cuda_include_dir,
],
library_dirs=([get_python_lib(), os.path.join(os.sys.prefix, "lib")]),
libraries=["cudf", "cudf_kafka"],
language="c++",
extra_compile_args=["-std=c++17"],
)
]
setup(
name="cudf_kafka",
version=versioneer.get_version(),
description="cuDF Kafka Datasource",
url="https://github.com/rapidsai/cudf",
author="NVIDIA Corporation",
def __str__():
import numpy
return numpy.get_include()
def c_header_dirs(self):
return [pygpu.get_include(), numpy.get_include()]
USE_CYTHON = True
DISTNAME = 'lsh'
DESCRIPTION = 'A library for performing shingling and LSH for python.'
MAINTAINER = 'Matti Lyra'
MAINTAINER_EMAIL = '*****@*****.**'
URL = 'https://github.com/mattilyra/lsh'
DOWNLOAD_URL = 'https://github.com/mattilyra/lsh'
VERSION = '0.3.2'
ext = '.pyx' if USE_CYTHON else '.cpp'
try:
import numpy as np
includes = [np.get_include()]
except ImportError:
includes = []
extensions = [
Extension("lsh.cMinhash",
["lsh/cMinhash{}".format(ext), 'lsh/MurmurHash3.cpp'],
include_dirs=includes)
]
if USE_CYTHON:
from Cython.Build import cythonize
extensions = cythonize(extensions)
install_deps = ['numpy', 'cython>=0.24.1']
test_deps = [
def finalize_options(self):
_build_ext.finalize_options(self)
__builtins__.__NUMPY_SETUP__ = False
import numpy
self.include_dirs.append(numpy.get_include())
],
# What does your project relate to?
keywords='nefis file_format',
# You can just specify the packages manually here if your project is
# simple. Or you can use find_packages().
packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
cmdclass=cmdclass,
ext_modules=ext_modules,
# List run-time dependencies here. These will be installed by pip when your
# project is installed. For an analysis of "install_requires" vs pip's
# requirements files see:
# https://packaging.python.org/en/latest/technical.html#install-requires-vs-requirements-files
install_requires=requirements,
include_dirs=[np.get_include()], # <---- New line
# hmm, where did the data go?
# data_files=[('nefis_data', ['data/trim-f34.dat', 'data/trim-f34.def'])],
# To provide executable scripts, use entry points in preference to the
# "scripts" keyword. Entry points provide cross-platform support and allow
# pip to create the appropriate form of executable for the target platform.
entry_points={
'console_scripts': [
# TODO: check if you prefer this interface
'nefis=nefis.cli:cli'
],
},
)
from setuptools import setup, Extension
from Cython.Distutils import build_ext
import glob
import numpy as np
sources = ['pysofia/_sofia_ml.pyx'] + glob.glob('pysofia/src/*.cc')
setup(name='pysofia',
version='0.10.dev0',
description='Python bindings for sofia-ml',
long_description=open('README.rst').read(),
author='Fabian Pedregosa & Csy',
author_email='*****@*****.**',
url='http://pypi.python.org/pypi/pysofia',
packages=['pysofia'],
cmdclass={'build_ext': build_ext},
install_requires=['six'],
ext_modules=[Extension('pysofia._sofia_ml',
sources=sources,
language='c++', include_dirs=[np.get_include()])],
)
from Cython.Build import cythonize
from cython import __version__ as cython_version
min_cython_version = '0.20.1'
if LooseVersion(cython_version) < LooseVersion(min_cython_version):
raise ValueError(
'cython support requires cython>={}'.format(min_cython_version))
cython = True
except ImportError:
cython = False
clang = False
if sys.platform.lower().startswith('darwin'):
clang = True
include_dirs = ['include', 'distributions']
include_dirs.append(numpy.get_include())
if 'EXTRA_INCLUDE_PATH' in os.environ:
include_dirs.append(os.environ['EXTRA_INCLUDE_PATH'])
extra_compile_args = [
'-DDIST_DEBUG_LEVEL=3',
'-DDIST_THROW_ON_ERROR=1',
'-Wno-unused-function',
]
if clang:
extra_compile_args.extend([
'-mmacosx-version-min=10.7', # for anaconda
'-std=c++0x',
'-stdlib=libc++',
'-Wno-deprecated-register',
import time
import numpy as np
from scipy import linalg
from numba import njit, jit, float64, int64
import pyximport
pyximport.install(setup_args={"include_dirs": np.get_include()},
reload_support=True)
from lasso_ct import lasso_ct
def timeit(method):
def timed(*args, **kw):
ts = time.time()
result = method(*args, **kw)
te = time.time()
print('%r %2.2f sec' % (method.__name__, te - ts))
return result
return timed
@njit(float64(float64))
def fsign(f):
if f == 0:
return 0
elif f > 0:
return 1.0
else:
return -1.0
def finalize_options(self):
_build_ext.finalize_options(self)
# Prevent numpy from thinking it is still in its setup process:
__builtins__.__NUMPY_SETUP__ = False
import numpy
self.include_dirs.append(numpy.get_include())
import os
from setuptools import setup, find_packages
from setuptools.extension import Extension
from Cython.Build import cythonize
from Cython.Distutils import build_ext
import numpy
extensions = [
Extension("openpiv.process", ["./openpiv/process.pyx"],
include_dirs=[numpy.get_include()]),
Extension("openpiv.lib", ["./openpiv/lib.pyx"],
include_dirs=[numpy.get_include()])
]
extensions = cythonize(extensions, include_path=[numpy.get_include()])
# read the contents of your README file
from os import path
this_directory = path.abspath(path.dirname(__file__))
#with open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
with open(path.join(this_directory, 'README.md')) as f:
long_description = f.read()
setup(
name="OpenPIV",
version='0.21.8c',
cmdclass={'build_ext': build_ext},
ext_modules=extensions,
packages=find_packages(),
include_package_data=True,
'include': pjoin(home, 'include'),
'lib64': pjoin(home, 'lib64')
}
for k, v in iteritems(cudaconfig):
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()
# Obtain the numpy include directory. This logic works across numpy versions.
try:
numpy_include = np.get_include()
except AttributeError:
numpy_include = np.get_numpy_include()
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
CXX_FLAGS += '-DEGL_ADD_PYTHON_INIT '
CXX_FLAGS += '-DB3_ENABLE_FILEIO_PLUGIN '
CXX_FLAGS += '-DB3_USE_ZIPFILE_FILEIO '
CXX_FLAGS += '-DBT_THREADSAFE=1 '
CXX_FLAGS += '-DSTATIC_LINK_SPD_PLUGIN '
EGL_CXX_FLAGS = ''
# libraries += [current_python]
libraries = []
include_dirs = []
try:
import numpy
NP_DIRS = [numpy.get_include()]
except:
print("numpy is disabled. getCameraImage maybe slower.")
else:
print("numpy is enabled.")
CXX_FLAGS += '-DPYBULLET_USE_NUMPY '
for d in NP_DIRS:
print("numpy_include_dirs = %s" % d)
include_dirs += NP_DIRS
sources = ["examples/pybullet/pybullet.c"]\
+["src/btLinearMathAll.cpp"]\
+["src/btBulletCollisionAll.cpp"]\
+["src/btBulletDynamicsAll.cpp"]\
+["examples/ExampleBrowser/InProcessExampleBrowser.cpp"]\
+["examples/TinyRenderer/geometry.cpp"]\
ext = '.pyx' if USE_CYTHON else '.cpp'
extensions = [
Extension(name='cornac.models.c2pf.c2pf',
sources=[
'cornac/models/c2pf/cython/c2pf' + ext,
'cornac/models/c2pf/cpp/cpp_c2pf.cpp'],
include_dirs=[
'cornac/models/c2pf/cpp/',
'cornac/utils/external/eigen/Eigen',
'cornac/utils/external/eigen/unsupported/Eigen/'
],
language='c++'),
Extension(name='cornac.models.nmf.recom_nmf',
sources=['cornac/models/nmf/recom_nmf' + ext],
include_dirs=[np.get_include()],
language='c++'),
Extension(name='cornac.models.pmf.pmf',
sources=['cornac/models/pmf/cython/pmf' + ext],
language='c++'),
Extension(name='cornac.models.mcf.mcf',
sources=['cornac/models/mcf/cython/mcf' + ext],
language='c++'),
Extension(name='cornac.models.sorec.sorec',
sources=['cornac/models/sorec/cython/sorec' + ext],
language='c++'),
Extension('cornac.models.hpf.hpf',
sources=['cornac/models/hpf/cython/hpf' + ext,
'cornac/models/hpf/cpp/cpp_hpf.cpp'],
include_dirs=[
'cornac/models/hpf/cpp/',
from Cython.Build import cythonize
from setuptools.extension import Extension
import numpy as np
ext_modules = cythonize([
'astrid/circle.pyx',
'astrid/defaults.pyx',
'astrid/io.pyx',
'astrid/logger.pyx',
'astrid/orc.pyx',
'astrid/midi.pyx',
'astrid/names.pyx',
'astrid/sampler.pyx',
'astrid/server.pyx',
'astrid/voices.pyx',
], include_path=[np.get_include()], annotate=True)
ext_modules = [
Extension('astrid.circle', ['astrid/circle.c']),
Extension('astrid.defaults', ['astrid/defaults.c']),
Extension('astrid.io',
['astrid/io.c'],
extra_compile_args=['-fopenmp'],
extra_link_args=['-fopenmp']
),
Extension('astrid.logger', ['astrid/logger.c']),
Extension('astrid.orc', ['astrid/orc.c']),
Extension('astrid.midi', ['astrid/midi.c']),
Extension('astrid.names', ['astrid/names.c']),
Extension('astrid.sampler', ['astrid/sampler.c']),
Extension('astrid.server', ['astrid/server.c']),
'''
SASSIE Copyright (C) 2011 Joseph E. Curtis
This program comes with ABSOLUTELY NO WARRANTY;
This is free software, and you are welcome to redistribute it under certain
conditions; see http://www.gnu.org/licenses/gpl-3.0.html for details.
'''
# System imports
from distutils.core import *
from distutils import sysconfig
# Third-party modules - we depend on numpy for everything
import numpy
# Obtain the numpy include directory. This logic works across numpy versions.
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
# simple extension module
_view_vmd = Extension(
"_view_vmd",
["view_vmd.i", "view_vmd.c", "imd.c", "vmdsock.c"],
include_dirs=[numpy_include],
)
# NumyTypemapTests setup
setup(name="SASVIEW VMD I/O",
description=
"Module handles sending and receiving coordinates to VMD using numpy.i",
author="Joseph E. Curtis",
def run():
'''
Dump on stdout the config flags required to compile pythran-generated code.
'''
import argparse
import distutils.sysconfig
import pythran
import numpy
parser = argparse.ArgumentParser(
prog='pythran-config',
description='output build options for pythran-generated code',
epilog="It's a megablast!"
)
parser.add_argument('--compiler', action='store_true',
help='print default compiler')
parser.add_argument('--cflags', action='store_true',
help='print compilation flags')
parser.add_argument('--libs', action='store_true',
help='print linker flags')
parser.add_argument('--no-python', action='store_true',
help='do not include Python-related flags')
parser.add_argument('--verbose', '-v', action='count', default=0,
help=(
'verbose mode: [-v] prints warnings if pythranrc '
'has an invalid configuration; use '
'[-vv] for more information')
)
args = parser.parse_args(sys.argv[1:])
args.python = not args.no_python
output = []
extension = pythran.config.make_extension(python=args.python)
if args.verbose >= 1:
if args.verbose == 1:
logger.setLevel(logging.WARNING)
else:
logger.setLevel(logging.INFO)
lint_cfg(cfg)
if args.compiler or args.verbose >= 2:
cxx = compiler() or 'c++'
logger.info('CXX = '.rjust(10) + cxx)
if args.compiler:
output.append(cxx)
if args.cflags or args.verbose >= 2:
def fmt_define(define):
name, value = define
if value is None:
return '-D' + name
else:
return '-D' + name + '=' + value
cflags = []
cflags.extend(fmt_define(define)
for define in extension['define_macros'])
cflags.extend(('-I' + include)
for include in extension['include_dirs'])
if args.python:
cflags.append('-I' + numpy.get_include())
cflags.append('-I' + distutils.sysconfig.get_python_inc())
logger.info('CFLAGS = '.rjust(10) + ' '.join(cflags))
if args.cflags:
output.extend(cflags)
if args.libs or args.verbose >= 2:
ldflags = []
ldflags.extend(('-L' + include)
for include in extension['library_dirs'])
ldflags.extend(('-l' + include)
for include in extension['libraries'])
if args.python:
ldflags.append('-L' + distutils.sysconfig.get_config_var('LIBPL'))
ldflags.extend(distutils.sysconfig.get_config_var('LIBS').split())
ldflags.append('-lpython'
+ distutils.sysconfig.get_config_var('VERSION'))
logger.info('LDFLAGS = '.rjust(10) + ' '.join(ldflags))
if args.libs:
output.extend(ldflags)
if output:
print(' '.join(output))
from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext
import numpy as np
# Avoid a gcc warning below:
# cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid
# for C/ObjC but not for C++
class BuildExt(build_ext):
def build_extensions(self):
self.compiler.compiler_so.remove('-Wstrict-prototypes')
super(BuildExt, self).build_extensions()
module = 'HWDecode'
hwdecode_utils_module = Extension(
module,
sources=['hw_decode.cpp'],
include_dirs=[np.get_include(), '/usr/local/include/'],
extra_compile_args=['-DNDEBUG', '-O3'],
extra_link_args=[
'-lavutil', '-lavcodec', '-lavformat', '-lswscale', '-L/usr/local/lib/'
])
setup(name=module,
version='0.1',
description='Utils for hwdecode',
ext_modules=[hwdecode_utils_module],
cmdclass={'build_ext': BuildExt})
from distutils.extension import Extension
import numpy as np
import os.path as op
import sys
sys.path.insert(0, op.dirname(__file__))
try:
import methylcoder.version as V
except ImportError:
class V(object):
version = 0.0
ext_modules = [ Extension("methylcoder.cbowtie",
sources=["methylcoder/cbowtie.c"],
include_dirs=[np.get_include(), "methylcoder"]) ]
setup(
license="BSD",
name = "methylcoder",
version = V.version,
ext_modules = ext_modules,
packages=['methylcoder'],
package_dir={'methylcoder': 'methylcoder'},
zip_safe=False,
requires=['numpy', 'pyfasta'],
test_suite="nose.collector",
entry_points = {
'console_scripts': ['methylcoder = methylcoder:main']
}
)
# CC=cc LDSHARED="cc -shared" python setup.py build_ext --inplace
from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
import numpy
extensions = [
Extension(
"kernels_spectral_cy",
sources=["kernels_spectral_cy.pyx"],
#libraries=["kernels"],
#library_dirs=["lib"],
include_dirs=[numpy.get_include(), "lib"],
extra_compile_args=[
"-fopenmp",
], ## for GCC. Recommended with Python
extra_link_args=["-fopenmp"]),
]
setup(name="kernels_spectral_cy",
ext_modules=cythonize(extensions,
compiler_directives={'language_level': "3"}))
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 10 12:45:53 2016
@author: ricketsonl
"""
import numpy as np
#from numpy.linalg import norm
import pyximport
pyximport.install(setup_args={"include_dirs":np.get_include()},reload_support=True)
import InterpolationRoutines as IR
import SpectralOps as SO
#from scipy.optimize import newton_krylov
import matplotlib.pyplot as plt
from matplotlib import animation
#plt.rcParams['animation.ffmpeg_path'] = '/usr/local/bin/ffmpeg'
class PICES2DFGV:
chrge = -1.
chrgi = +1.
space_norm = 1; time_norm = np.inf # Sets the space- and time-norms for variances
imptol = 1.e-10 # Tolerance for Newton-Krylov iteration
B = 10.
def __init__(self,T_final,domx,domy,numcellsx,numcellsy,numsteps,idata,Npi,varwts=False,RHSe=0.,RHSi=0.,Efield = 0.,mSe=0.,mSi=0.):
self.T = T_final
self.ncelx = numcellsx; self.ncely = numcellsy
self.nstep = numsteps
self.dt = T_final/numsteps
self.DomLenX = domx; self.DomLenY = domy
def make_extension(python, **extra):
# load platform specific configuration then user configuration
cfg = init_cfg('pythran.cfg',
'pythran-{}.cfg'.format(sys.platform),
'.pythranrc',
extra.get('config', None))
if 'config' in extra:
extra.pop('config')
def parse_define(define):
index = define.find('=')
if index < 0:
return (define, None)
else:
return define[:index], define[index + 1:]
extension = {
"language": "c++",
# forcing str conversion to handle Unicode case (the default on MS)
"define_macros": [str(x) for x in
cfg.get('compiler', 'defines').split()],
"undef_macros": [str(x) for x in
cfg.get('compiler', 'undefs').split()],
"include_dirs": [str(x) for x in
cfg.get('compiler', 'include_dirs').split()],
"library_dirs": [str(x) for x in
cfg.get('compiler', 'library_dirs').split()],
"libraries": [str(x) for x in
cfg.get('compiler', 'libs').split()],
"extra_compile_args": [str(x) for x in
cfg.get('compiler', 'cflags').split()],
"extra_link_args": [str(x) for x in
cfg.get('compiler', 'ldflags').split()],
"extra_objects": []
}
if python:
extension['define_macros'].append('ENABLE_PYTHON_MODULE')
extension['define_macros'].append(
'__PYTHRAN__={}'.format(sys.version_info.major))
here = os.path.dirname(os.path.dirname(__file__)) or '.'
# using / as separator as advised in the distutils doc
extension["include_dirs"].append(here + '/pythran')
extra.pop('language', None) # forced to c++ anyway
cxx = extra.pop('cxx', None)
cc = extra.pop('cc', None)
if cxx is None:
cxx = compiler()
if cxx is not None:
extension['cxx'] = cxx
extension['cc'] = cc or cxx
for k, w in extra.items():
extension[k].extend(w)
if cfg.getboolean('pythran', 'complex_hook'):
# the patch is *not* portable
extension["include_dirs"].append(here + '/pythran/pythonic/patch')
# Numpy can pollute stdout with warning message which should be on stderr
old_stdout = sys.stdout
try:
sys.stdout = sys.stderr
# numpy specific
if python:
extension['include_dirs'].append(numpy.get_include())
# blas dependency
user_blas = cfg.get('compiler', 'blas')
if user_blas == 'pythran-openblas':
try:
import pythran_openblas as openblas
# required to cope with atlas missing extern "C"
extension['define_macros'].append('PYTHRAN_BLAS_OPENBLAS')
extension['include_dirs'].extend(openblas.include_dirs)
extension['extra_objects'].append(os.path.join(openblas.library_dir,
openblas.static_library))
except ImportError:
logger.warn("Failed to find 'pythran-openblas' package. "
"Please install it or change the compiler.blas setting. "
"Defaulting to 'blas'")
user_blas = 'blas'
if user_blas != 'pythran-openblas':
numpy_blas = numpy_sys.get_info(user_blas)
# required to cope with atlas missing extern "C"
extension['define_macros'].append('PYTHRAN_BLAS_{}'
.format(user_blas.upper()))
extension['libraries'].extend(numpy_blas.get('libraries', []))
extension['library_dirs'].extend(numpy_blas.get('library_dirs', []))
extension['include_dirs'].extend(numpy_blas.get('include_dirs', []))
finally:
sys.stdout = old_stdout
# final macro normalization
extension["define_macros"] = [
dm if isinstance(dm, tuple) else parse_define(dm)
for dm in extension["define_macros"]]
return extension
def finalize_options(self):
TestCommand.finalize_options(self)
if self.args:
self.args = __import__('shlex').split(self.args)
def run_tests(self):
# Run nose ensuring that argv simulates running nosetests directly
nose_args = ['nosetests']
nose_args.extend(self.args)
__import__('nose').run_exit(argv=nose_args)
commands = versioneer.get_cmdclass()
commands['test'] = NoseTestCommand
incDirs = [sysconfig.get_python_inc(), numpy.get_include()]
ext = [
Extension("radiomics._cmatrices",
["radiomics/src/_cmatrices.c", "radiomics/src/cmatrices.c"],
include_dirs=incDirs),
Extension("radiomics._cshape",
["radiomics/src/_cshape.c", "radiomics/src/cshape.c"],
include_dirs=incDirs)
]
setup(
name='pyradiomics',
url='http://github.com/Radiomics/pyradiomics#readme',
author='pyradiomics community',
author_email='*****@*****.**',
libs.append('CbcSolver')
libDirs.extend(['.', join('.', cythonFilesDir)])
try:
libDirs.append(join(CoinDir, 'lib'))
except:
pass
if operatingSystem == 'windows':
try:
libDirs.append(join(CoinDir, 'lib', 'intel'))
except:
pass
incDirs.extend([join('.', cppFilesDir), join('.', cythonFilesDir),
numpy.get_include(), '.'])
try:
incDirs.extend([join(CoinDir, 'include', 'coin')])
except:
pass
cmdclass = {}
if USECYTHON:
from Cython.Distutils import build_ext
from Cython.Distutils import extension
Extension = extension.Extension
import Cython.Compiler.Options
Cython.Compiler.Options.annotate = True
cmdclass.update({'build_ext': build_ext})
fileext = '.pyx'
else:
exit_with_usage(code=0)
for opt in opt_flags:
if opt == '--prefix':
print sysconfig.PREFIX
elif opt == '--exec-prefix':
print sysconfig.EXEC_PREFIX
elif opt in ('--includes', '--cflags'):
flags = ['-I' + sysconfig.get_python_inc(),
'-I' + sysconfig.get_python_inc(plat_specific=True)]
try:
import numpy
flags += ['-I' + numpy.get_include() + ' -DSMILEI_USE_NUMPY -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION']
except:
pass
if opt == '--cflags':
flags.extend(getvar('CFLAGS').split())
print ' '.join(flags)
elif opt in ('--libs', '--ldflags'):
libs = ['-lpython' + pyver]
libs += getvar('LIBS').split()
libs += getvar('SYSLIBS').split()
# add the prefix/lib/pythonX.Y/config dir, but only if there is no
# shared library in prefix/lib/.
if opt == '--ldflags':
if not getvar('Py_ENABLE_SHARED'):
use_setuptools = False
print("distutils is used.")
try:
from setuptools_scm import get_version
except ImportError:
git_num = None
if 'setuptools_scm' in sys.modules.keys():
try:
git_ver = get_version()
git_num = int(git_ver.split('.')[3].split('+')[0].replace("dev", ""))
except:
git_num = None
include_dirs_numpy = [numpy.get_include()]
cc = None
if 'CC' in os.environ:
if 'clang' in os.environ['CC']:
cc = 'clang'
if 'gcc' in os.environ['CC']:
cc = 'gcc'
# Workaround Python issue 21121
import sysconfig
config_var = sysconfig.get_config_var("CFLAGS")
if config_var is not None and "-Werror=declaration-after-statement" in config_var:
os.environ['CFLAGS'] = config_var.replace(
"-Werror=declaration-after-statement", "")
######################