def __init__(self):
Extension.__init__(self, self.name, [], cython_c_in_temp=True)
self.cython_compile_time_env = { "PY_MAJOR_VERSION" : sys.version_info[0] }
self.make()
self.check_cplusplus()
self.add_optimize_flag()
self.include_dirs.append(self.dbase)
self.include_dirs = list(set(self.include_dirs))
self.libraries = list(set(self.libraries))
self.library_dirs = list(set(self.library_dirs))
self.define_macros = list(set(self.define_macros))
self.extra_link_args = list(set(self.extra_link_args))
def __init__(self):
Extension.__init__(self, self.name, [], cython_c_in_temp=True)
self.cython_compile_time_env = {
"PY_MAJOR_VERSION": sys.version_info[0]
}
self.make()
self.check_cplusplus()
self.add_optimize_flag()
self.include_dirs.append(self.dbase)
self.include_dirs = list(set(self.include_dirs))
self.libraries = list(set(self.libraries))
self.library_dirs = list(set(self.library_dirs))
self.define_macros = list(set(self.define_macros))
self.extra_link_args = list(set(self.extra_link_args))
def get_ext_modules():
if "build_ext" not in sys.argv and "bdist_wheel" not in sys.argv:
# this isn't a binary build, so we dont need to cythonize the source
return None
# cython compiles all the .py files to .so objects that are included in the .whl
# this should ONLY be run with bdist_wheel and NEVER sdist
Options.docstrings = False
Options.fast_fail = True
Options.warning_errors = True
Options.error_on_unknown_names = True
Options.error_on_uninitialized = True
compiler_directives = {
"binding": True, # default in cython 3
"language_level": "3",
"warn.unreachable": False,
}
# we need to create an Extension for each source .py file in the project
# so that cython will compile it to .so
packages = find_packages()
source_py_files = []
for pkg in packages:
for source_py in glob.glob(pkg.replace(".", os.sep) + os.sep + "*.py"):
module = source_py[:-3] # strip .py
module = module.replace(os.sep, ".")
extension = Extension(module, [source_py])
source_py_files.append(extension)
return cythonize(source_py_files, compiler_directives=compiler_directives)
def get_basic_extensions():
if MODE == 'info':
try:
from Cython.Distutils import Extension
except ImportError:
from distutils.core import Extension
try:
import numpy
except ImportError:
include_dirs = []
else:
include_dirs = [numpy.get_include()]
else:
from Cython.Distutils import Extension
import numpy
include_dirs = [numpy.get_include()]
ext_modules = [
Extension(
name="cyarray.carray",
sources=["cyarray/carray.pyx"],
include_dirs=include_dirs,
),
]
return ext_modules
def create_cython_ext_modules(cython_modules, profile_cython=False,
debug=False):
"""
Create :class:`~distutils.extension.Extension` objects from
*cython_modules*.
*cython_modules* must be a dict, as returned by :func:`parse_setup_cfg`.
If *profile_cython* is true, Cython modules are compiled to support Python
proiflers.
Debug symbols are included if *debug* is true.
"""
if profile_cython:
from Cython.Distutils import Extension
else:
from distutils.extension import Extension
ret = []
for name, mod_data in cython_modules.items():
kwargs = {'name': name}
kwargs.update(mod_data)
if profile_cython:
cython_directives = kwargs.setdefault('cython_directives', {})
cython_directives['profile'] = True
if debug:
for args_name in ('extra_compile_args', 'extra_link_args'):
args = kwargs.setdefault(args_name, [])
if '-g' not in args:
args.append('-g')
ext = Extension(**kwargs)
ret.append(ext)
return ret
def cython_module(*args, **kwargs):
from Cython.Distutils import Extension
sources = []
sources.extend(kwargs.pop('sources', []))
include_dirs = []
include_dirs.extend(kwargs.pop('include_dirs', []))
ext_package = os.path.extsep.join(args)
ext_pth = os.path.sep.join(args) + os.extsep + "pyx"
sources.insert(0, ext_pth)
language = kwargs.pop('language', 'c').lower()
extra_compile_args = ['-Wno-unused-function',
'-Wno-unneeded-internal-declaration',
'-O3',
'-fstrict-aliasing',
'-funroll-loops',
'-mtune=native']
if language in CPPLANGS:
extra_compile_args.extend(['-std=%s' % CPPVERSION,
'-stdlib=libc++',
'-Wno-sign-compare',
'-Wno-unused-private-field'])
return Extension(ext_package, sources,
language=language,
include_dirs=include_dirs,
extra_compile_args=extra_compile_args)
def def_ext_modules(self):
# Overloading compilers.
os.environ["CXX"] = "c++"
os.environ["CC"] = "gcc"
BITPIT_ENABLE_MPI = 0
include_libs = "-I" + self.PABLO_include_path
include_libs = include_libs + " -I" + self.IO_include_path
if ((not (not self.mpi_include_path)) and (ENABLE_MPI4PY)):
BITPIT_ENABLE_MPI = 1
include_libs = include_libs + " -I" + self.mpi_include_path
os.environ["CXX"] = "mpic++"
os.environ["CC"] = "mpicc"
_extra_compile_args = [
"-std=c++11", "-O3", "-fPIC", include_libs,
"-DBITPIT_ENABLE_MPI=" + str(BITPIT_ENABLE_MPI)
]
_extra_link_args = ["-fPIC"
] # Needed? We have already the same flag for
# the compiler args above.
_cython_directives = {
"boundscheck": False,
"wraparound": False,
# http://stackoverflow.com/questions/23351813/how-to-declare-an-ndarray-in-cython-with-a-general-floating-point-type
"nonecheck": False
}
_language = "c++"
_extra_objects = ["libbitpit_MPI.a" if (BITPIT_ENABLE_MPI) \
else "libbitpit.a"]
src_dir = os.path.dirname(self.IO_include_path.rstrip("/"))
common_dir = src_dir + "/common/"
operators_dir = src_dir + "/operators/"
containers_dir = src_dir + "/containers/"
_include_dirs = [
".", self.PABLO_include_path, self.IO_include_path, common_dir,
operators_dir, containers_dir,
numpy_get_include()
]
# Cython compile time environment.
_cc_time_env = {"BITPIT_ENABLE_MPI": BITPIT_ENABLE_MPI}
ext_modules = [
Extension(
os.path.splitext(self.extensions_source)[0],
[self.extensions_source],
extra_compile_args=_extra_compile_args,
extra_link_args=_extra_link_args,
cython_directives=_cython_directives,
language=_language,
extra_objects=_extra_objects,
include_dirs=_include_dirs,
cython_compile_time_env=_cc_time_env,
)
]
#return cythonize(ext_modules)
return ext_modules
def get_openmp_flags():
"""Returns any OpenMP related flags if OpenMP is avaiable on the system.
"""
omp_compile_flags, omp_link_flags = _get_openmp_flags()
from textwrap import dedent
try:
from Cython.Distutils import Extension
from pyximport import pyxbuild
except ImportError:
print("Unable to import Cython, disabling OpenMP for now.")
return [], [], False
from distutils.errors import CompileError, LinkError
import shutil
import tempfile
test_code = dedent("""
from cython.parallel import parallel, prange, threadid
cimport openmp
def n_threads():
with nogil, parallel():
openmp.omp_get_num_threads()
""")
tmp_dir = tempfile.mkdtemp()
fname = os.path.join(tmp_dir, 'check_omp.pyx')
with open(fname, 'w') as fp:
fp.write(test_code)
extension = Extension(
name='check_omp',
sources=[fname],
include_dirs=base_includes,
extra_compile_args=omp_compile_flags,
extra_link_args=omp_link_flags,
)
has_omp = True
try:
pyxbuild.pyx_to_dll(fname, extension, pyxbuild_dir=tmp_dir)
print("-" * 70)
print("Using OpenMP.")
print("-" * 70)
except CompileError:
print("*" * 70)
print("Unable to compile OpenMP code. Not using OpenMP.")
print("*" * 70)
has_omp = False
except LinkError:
print("*" * 70)
print("Unable to link OpenMP code. Not using OpenMP.")
print("*" * 70)
has_omp = False
finally:
shutil.rmtree(tmp_dir)
if has_omp:
return omp_compile_flags, omp_link_flags, True
else:
return [], [], False
def make_cy_ext(filename, inc_dirs=inc_dirs, lib_dirs=lib_dirs, libs=libs, global_compile_args=global_compile_args, debug_build=debug_build):
modname = filename.replace('.pyx', '').replace('/', '.')
if not have_cython:
filename = '%s.c' % filename[:-4]
return Extension(name=modname, sources=[filename],
include_dirs=inc_dirs, library_dirs=lib_dirs, libraries=libs,
extra_compile_args=global_compile_args + ['-fPIC'],
extra_link_args=global_compile_args + ['-fPIC'],
pyrex_gdb=debug_build,
cython_directives={'embedsignature': True})
def run(self):
if self.cythonize:
# Move py files to ext_modules except __init__.py
if not self.distribution.ext_modules:
self.distribution.ext_modules = []
for (pkg, mod, pth) in build_py.find_all_modules(self):
if self.is_to_cythonize(pkg, mod):
self.distribution.ext_modules.append(
Extension(".".join([pkg, mod]), [pth],
cython_c_in_temp=True))
return build_py.run(self)
def get_parallel_extensions():
if not HAVE_MPI:
return []
if MODE == 'info':
from distutils.core import Extension
include_dirs = []
mpi_inc_dirs, mpi_compile_args, mpi_link_args = [], [], []
zoltan_include_dirs, zoltan_library_dirs = [], []
else:
from Cython.Distutils import Extension
import numpy
include_dirs = [numpy.get_include()]
mpi_inc_dirs, mpi_compile_args, mpi_link_args = get_mpi_flags()
zoltan_include_dirs, zoltan_library_dirs = get_zoltan_args()
# We should check again here as HAVE_MPI may be set to False when we try to
# get the MPI flags and are not successful.
if not HAVE_MPI:
return []
include_dirs += base_includes
MPI4PY_V2 = False if mpi4py.__version__.startswith('1.') else True
cython_compile_time_env = {'MPI4PY_V2': MPI4PY_V2}
zoltan_lib = 'zoltan'
if 'USE_TRILINOS' in CONFIG_OPTS:
zoltan_lib = 'trilinos_zoltan'
elif os.environ.get('USE_TRILINOS', None) is not None:
zoltan_lib = 'trilinos_zoltan'
parallel_modules = [
Extension(
name="pysph.parallel.parallel_manager",
sources=["pysph/parallel/parallel_manager.pyx"],
depends=get_deps(
"pysph/base/point", "pysph/base/particle_array",
"pysph/base/nnps_base"
),
include_dirs=include_dirs + mpi_inc_dirs + zoltan_include_dirs,
library_dirs=zoltan_library_dirs,
libraries=[zoltan_lib, 'mpi'],
extra_link_args=mpi_link_args,
extra_compile_args=mpi_compile_args + extra_compile_args,
cython_compile_time_env=cython_compile_time_env,
language="c++",
define_macros=MACROS,
),
]
return parallel_modules
def run(self):
if self.cythonize:
# Move py files to ext_modules except __init__.py
if not self.distribution.ext_modules:
self.distribution.ext_modules = []
for (pkg, mod, pth) in build_py.find_all_modules(self):
if self.is_to_cythonize(pkg, mod):
self.distribution.ext_modules.append(
Extension(
".".join([pkg, mod]),
[pth],
cython_c_in_temp=True,
# Ensure cython compiles with a relevent language mode setting
cython_directives={
'language_level': sys.version[0]
}))
return build_py.run(self)
def verletCython4(self, nStr, mStr, xyStr, vStr):
global Tn, T
init = sum([list(map(float, xyStr)),
list(map(float, vStr))], [])
m = list(map(float, mStr))
n = int(nStr)
G = 6.674e-11
t = np.linspace(0, T, Tn)
dt = T / Tn
x = np.zeros(n * len(t))
y = np.zeros(n * len(t))
for i in range(n):
x[i] = init[i * 2]
y[i] = init[i * 2 + 1]
vx = np.zeros(n * len(t))
vy = np.zeros(n * len(t))
for i in range(n):
vx[i] = init[i * 2 + 2 * n]
vy[i] = init[i * 2 + 1 + 2 * n]
m1 = np.array(m)
axm = np.zeros(n * len(t))
aym = np.zeros(n * len(t))
import pyximport
pyximport.install(setup_args={'include_dirs': np.get_include(),
'ext_modules': [Extension("solver_cython4", ["solver_cython4.pyx"],
extra_compile_args=["-O3", "-fopenmp"],
extra_link_args=["-fopenmp"])]})
import solver_cython4
start_time = time.clock()
result = solver_cython4.solver(n, G, dt, m1, t, x, y, vx, vy, axm, aym)
time1 = time.clock() - start_time
# # x
# print(result[0])
# # y
# print(result[1])
# # vx
# print(result[2])
# # vy
# print(result[3])
# # axm
# print(result[4])
# # aym
# print(result[5])
# self.countError(nStr, mStr, xyStr, vStr, result[0], result[1], n)
return result[0], result[1], n, time1
def extensions():
__builtins__.__NUMPY_SETUP__ = False
from Cython.Distutils import Extension
import numpy as np
extra_compile_args = ["-O3"]
extra_link_args = []
if sys.platform == "darwin":
extra_compile_args.append("-mmacosx-version-min=10.9")
extra_compile_args.append('-stdlib=libc++')
extra_link_args.append('-stdlib=libc++')
return [
Extension('taylor_dtw.custom_dtw', ["taylor_dtw/custom_dtw.pyx"],
cython_directives={'language_level': sys.version_info[0]},
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args,
include_dirs=[np.get_include()],
language="c++")
]
project_dir = os.path.dirname(os.path.abspath(__file__))
ctp_dir = os.path.join(project_dir, "rqctp")
lib_dir = os.path.join(project_dir, "ctp")
for name in os.listdir(ctp_dir):
if name.endswith(".so") or name.endswith(".cpp"):
os.remove(os.path.join(ctp_dir, name))
for name in os.listdir(lib_dir):
if name.endswith(".so") or name.endswith(".h"):
shutil.copy(os.path.join(lib_dir, name), os.path.join(ctp_dir, name))
setup(name="rqctp",
version="0.0.1",
ext_modules=cythonize(module_list=[
Extension(
name="rqctp.TraderApi",
sources=["rqctp/TraderApi.pyx"],
libraries=["thosttraderapi_se"],
language="c++",
library_dirs=["rqctp/"],
extra_link_args=['-Wl,-rpath,$ORIGIN'],
)
],
compiler_directives={
"language_level": 3,
"binding": True
}),
requires=["Cython"])
from setuptools import setup
have_cython = False
try:
from Cython.Distutils import build_ext, Extension
have_cython = True
except ImportError:
from setuptools.command.build_ext import build_ext
from setuptools.extension import Extension
if have_cython:
packer = Extension(
"erlpack._packer",
cython_cplus=True,
extra_compile_args=['-O3'],
sources=["py/erlpack/_packer.pyx"]
)
unpacker = Extension(
"erlpack._unpacker",
cython_cplus=True,
extra_compile_args=['-O3'],
sources=["py/erlpack/_unpacker.pyx"]
)
else:
packer = Extension('erlpack._packer', sources=[
'py/erlpack/_packer.cpp'], extra_compile_args=['-O3'])
unpacker = Extension('erlpack._unpacker', sources=[
'py/erlpack/_unpacker.cpp'], extra_compile_args=['-O3'])
ext_modules = [packer, unpacker]
platforms=['Any'],
classifiers=classifiers,
url='http://github.com/fish2000/halogen',
packages=find_packages(),
package_dir={
'haldol': 'haldol',
'halogen': 'halogen'
},
package_data=dict(),
test_suite='nose.collector',
ext_modules=cythonize(
[ # type: ignore
Extension(
'halogen.api', # type: ignore
api_extension_sources + haldol_sources,
language="c++",
include_dirs=[d for d in include_dirs if os.path.isdir(d)],
define_macros=macros.to_list(),
extra_link_args=['-lHalide'],
extra_compile_args=[
'-Wno-unused-function',
'-Wno-unneeded-internal-declaration', '-O3',
'-fstrict-aliasing', '-funroll-loops', '-mtune=native',
'-std=c++17', '-stdlib=libc++'
])
],
nthreads=cpu_count(),
compiler_directives=dict(language_level=2,
infer_types=True,
embedsignature=True)))
def def_ext_modules(self):
# Define \"Extension\" being cythonized.
# Overloading compilers.
os.environ["CXX"] = "c++"
os.environ["CC"] = "gcc"
BITPIT_ENABLE_MPI = 0
include_paths = [
self.bitpit_path + "/include/bitpit/",
self.madeleine_path + "../../src/"
]
mpi_lib = ""
if ((not (not self.mpi_include_path)) and (ENABLE_MPI4PY)):
BITPIT_ENABLE_MPI = 1
include_paths.append(self.mpi_include_path)
os.environ["CXX"] = "mpic++"
os.environ["CC"] = "mpicc"
mpi_lib = "/usr/local/openmpi-1.10.5_intel/lib/libmpi.so"
mpi_lib = "/usr/lib64/openmpi-1.10/lib/libmpi.so"
_extra_compile_args = [
"-std=c++11",
"-g",
"-O0",
"-fPIC",
#include_paths,
"-DBITPIT_ENABLE_MPI=" + str(BITPIT_ENABLE_MPI)
]
_extra_link_args = ["-fPIC"
] # Needed? We have already the same flag for
# the compiler args above.
_cython_directives = {
"boundscheck": False,
"wraparound": False,
# http://stackoverflow.com/questions/23351813/how-to-declare-an-ndarray-in-cython-with-a-general-floating-point-type
"nonecheck": False
}
_language = "c++"
bitpit_lib = self.bitpit_path + "/lib/"
if (BITPIT_ENABLE_MPI):
bitpit_lib = bitpit_lib + "libbitpit_MPI_D.so"
else:
bitpit_lib = bitpit_lib + "libbitpit_D.so"
madeleine_lib = self.madeleine_path + "libmadeleine.so"
_extra_objects = [mpi_lib, bitpit_lib, madeleine_lib, "-lxml2"]
##FINO QUI!
#print(os.path.dirname(self.bitpit_include_path))
#piercedVector_subdir = os.path.dirname(self.bitpit_include_path) + "/containers/"
_include_dirs = [".", numpy_get_include()]
_include_dirs.extend(include_paths)
# Cython compile time environment.
_cc_time_env = {"BITPIT_ENABLE_MPI": BITPIT_ENABLE_MPI}
ext_modules = [
Extension(
os.path.splitext(self.extensions_source)[0],
[self.extensions_source],
extra_compile_args=_extra_compile_args,
extra_link_args=_extra_link_args,
cython_directives=_cython_directives,
language=_language,
extra_objects=_extra_objects,
include_dirs=_include_dirs,
cython_compile_time_env=_cc_time_env,
)
]
return cythonize(ext_modules, gdb_debug=True)
import pytest
errno = pytest.main(self.test_args)
sys.exit(errno)
with open('README.rst') as f:
long_description = f.read()
setup(
name="dmft-learn",
description="Educative code on DMFT",
long_description=long_description,
version=dmft.__version__,
packages=find_packages(),
author="Óscar Nájera",
author_email='*****@*****.**',
license="GNU General Public License v3 (GPLv3)",
install_requires=['numpy', 'scipy', 'matplotlib', 'slaveparticles'],
setup_requires=['Sphinx', 'cython'],
tests_require=['pytest', 'pytest-cov'],
cmdclass={
'test': PyTest,
'build_ext': build_ext
},
ext_modules=[
Extension('hffast', ['dmft/hirschfye_cy.pyx'],
include_dirs=[np.get_include()],
libraries=['blas', 'gsl']),
],
)
from distutils.core import setup
from Cython.Build import cythonize
#from distutils.extension import Extension
#from Cython.Distutils import build_ext
from Cython.Distutils import build_ext, Extension
import numpy as np
ext_modules = [
Extension(
name="bedsim.cython2.cconstraints",
sources=[
"bedsim/cython2/cconstraints.pyx", "bedsim/cython2/constraints.c"
],
# extra_objects=["fc.o"], # if you compile fc.cpp separately
include_dirs=[np.get_include()
], # .../site-packages/numpy/core/include
language="c",
extra_compile_args="-O3 -Wall".split(),
# libraries=
# extra_compile_args = "...".split(),
# extra_link_args = "...".split()
),
Extension(
name="bedsim.cython2.ccsht",
sources=["bedsim/cython2/ccsht.pyx", "bedsim/cython2/csht.c"],
include_dirs=[np.get_include()
], # .../site-packages/numpy/core/include
language="c",
extra_compile_args="-O3 -Wall".split(),
),
Extension(
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()])
])
setup(
name="dmft-learn",
description="Educative code on DMFT",
long_description=long_description,
version=dmft.__version__,
packages=find_packages(),
author="Óscar Nájera",
author_email='*****@*****.**',
license="GNU General Public License v3 (GPLv3)",
install_requires=[
'numpy', 'scipy', 'matplotlib', 'slaveparticles', 'joblib', 'pandas',
'numba', 'h5py', 'mpi4py'
],
setup_requires=['sphinx', 'cython', 'pytest-runner'],
tests_require=['pytest-cov', 'pytest'], # Somehow this order is relevant
cmdclass={'build_ext': build_ext},
ext_modules=[
Extension('dmft.hffast', ['dmft/hirschfye_cy.pyx', 'dmft/hfc.cpp'],
include_dirs=[np.get_include()],
language="c++",
extra_compile_args=["-std=c++11"],
libraries=['gsl', 'openblas']),
],
classifiers=[
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"Programming Language :: Python",
"Topic :: Scientific/Engineering",
"Topic :: Software Development",
])
"(compile/link inplace)"
# Override to keep only the stats extension.
def finalize_options(self):
# Force inplace building for ease of importation
self.inplace = True
build_ext.finalize_options(self)
ext_modules = []
ext_modules.append(
Extension(
'challenge_scoring.tractanalysis.robust_streamlines_metrics',
['challenge_scoring/tractanalysis/robust_streamlines_metrics.pyx'],
include_dirs=[
numpy.get_include(),
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'challenge_scoring/c_src')
]))
dependencies = ['dipy', 'nibabel']
setup(
name='tractometer',
version='1.0.1',
description='Scoring system used for the ISMRM 2015 Tractography Challenge',
url='https://github.com/scilus/ismrm_2015_tractography_challenge_scoring',
ext_modules=cythonize(ext_modules),
author='The challenge team',
author_email='*****@*****.**',
packages=[
])
config['include_dirs'] = [
os.path.join(pylon_dir, 'Development', 'include'),
os.path.join(pylon_cython_dir, "cython\\pxd\\cythoninterface"),
os.path.join(pylon_cython_dir, "cython\\pxd\\cinterface\\baslerpylon."),
os.path.join(pylon_cython_dir, "cython\c++"), python_dir, "cython\pxd",
"cython\c++"
]
config['language'] = 'c++'
config['include_dirs'].append(numpy.get_include())
ext_modules = [
Extension('pylonsample.sample_camera_event_handler',
sources=[
"cython/pyx/pylonsample/sample_camera_event_handler.pyx",
"cython/c++/CSampleCameraEventHandler.cpp"
],
**config),
Extension(
'pylonsample.sample_chunk_ts_image_event_handler',
sources=[
"cython/pyx/pylonsample/sample_chunk_ts_image_event_handler.pyx",
"cython/c++/CSampleChunkTSImageEventHandler.cpp"
],
**config),
Extension('pylonsample.sample_image_event_handler',
sources=[
"cython/pyx/pylonsample/sample_image_event_handler.pyx",
"cython/c++/CSampleImageEventHandler.cpp"
],
**config),
def get_basic_extensions():
if MODE == 'info':
try:
from Cython.Distutils import Extension
except ImportError:
from distutils.core import Extension
try:
import numpy
except ImportError:
include_dirs = []
else:
include_dirs = [numpy.get_include()]
else:
from Cython.Distutils import Extension
import numpy
include_dirs = [numpy.get_include()]
openmp_compile_args, openmp_link_args, openmp_env = get_openmp_flags()
ext_modules = [
Extension(
name="pyzoltan.core.carray",
sources=["pyzoltan/core/carray.pyx"],
include_dirs=include_dirs,
extra_compile_args=extra_compile_args,
language="c++"
),
Extension(
name="pysph.base.particle_array",
sources=["pysph/base/particle_array.pyx"],
depends=get_deps("pyzoltan/core/carray"),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args,
language="c++"
),
Extension(
name="pysph.base.point",
sources=["pysph/base/point.pyx"],
extra_compile_args=extra_compile_args,
include_dirs=include_dirs,
language="c++"
),
Extension(
name="pysph.base.nnps_base",
sources=["pysph/base/nnps_base.pyx"],
depends=get_deps(
"pyzoltan/core/carray", "pysph/base/point",
"pysph/base/particle_array",
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
Extension(
name="pysph.base.linked_list_nnps",
sources=["pysph/base/linked_list_nnps.pyx"],
depends=get_deps(
"pysph/base/nnps_base"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
Extension(
name="pysph.base.box_sort_nnps",
sources=["pysph/base/box_sort_nnps.pyx"],
depends=get_deps(
"pysph/base/nnps_base", "pysph/base/linked_list_nnps"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
Extension(
name="pysph.base.spatial_hash_nnps",
sources=["pysph/base/spatial_hash_nnps.pyx"],
depends=get_deps(
"pysph/base/nnps_base"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
Extension(
name="pysph.base.cell_indexing_nnps",
sources=["pysph/base/cell_indexing_nnps.pyx"],
depends=get_deps(
"pysph/base/nnps_base"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
Extension(
name="pysph.base.z_order_nnps",
sources=["pysph/base/z_order_nnps.pyx"],
depends=get_deps(
"pysph/base/nnps_base"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
Extension(
name="pysph.base.stratified_hash_nnps",
sources=["pysph/base/stratified_hash_nnps.pyx"],
depends=get_deps(
"pysph/base/nnps_base"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
Extension(
name="pysph.base.stratified_sfc_nnps",
sources=["pysph/base/stratified_sfc_nnps.pyx"],
depends=get_deps(
"pysph/base/nnps_base", "pysph/base/z_order_nnps"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
Extension(
name="pysph.base.octree",
sources=["pysph/base/octree.pyx"],
depends=get_deps(
"pysph/base/nnps_base"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
Extension(
name="pysph.base.octree_nnps",
sources=["pysph/base/octree_nnps.pyx"],
depends=get_deps(
"pysph/base/nnps_base", "pysph/base/octree"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
# kernels used for tests
Extension(
name="pysph.base.c_kernels",
sources=["pysph/base/c_kernels.pyx"],
include_dirs=include_dirs,
extra_compile_args=extra_compile_args,
language="c++"
),
# Eigen decomposition code
Extension(
name="pysph.base.linalg3",
sources=["pysph/base/linalg3.pyx"],
include_dirs=include_dirs,
extra_compile_args=extra_compile_args,
language="c++"
),
]
if HAVE_OPENCL:
ext_modules.extend((
Extension(
name="pysph.base.gpu_nnps_base",
sources=["pysph/base/gpu_nnps_base.pyx"],
depends=get_deps(
"pyzoltan/core/carray", "pysph/base/point",
"pysph/base/particle_array", "pysph/base/nnps_base"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
Extension(
name="pysph.base.z_order_gpu_nnps",
sources=["pysph/base/z_order_gpu_nnps.pyx"],
depends=get_deps(
"pysph/base/nnps_base"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
),
Extension(
name="pysph.base.stratified_sfc_gpu_nnps",
sources=["pysph/base/stratified_sfc_gpu_nnps.pyx"],
depends=get_deps(
"pysph/base/nnps_base"
),
include_dirs=include_dirs,
extra_compile_args=extra_compile_args + openmp_compile_args,
extra_link_args=openmp_link_args,
cython_compile_time_env={'OPENMP': openmp_env},
language="c++"
))
)
return ext_modules
def get_openmp_flags():
"""Returns any OpenMP related flags if OpenMP is avaiable on the system.
"""
if sys.platform == 'win32':
omp_compile_flags, omp_link_flags = ['/openmp'], []
else:
omp_compile_flags, omp_link_flags = ['-fopenmp'], ['-fopenmp']
env_var = os.environ.get('USE_OPENMP', '')
if env_var.lower() in ("0", 'false', 'n'):
print("-"*70)
print("OpenMP disabled by environment variable (USE_OPENMP).")
return [], [], False
from textwrap import dedent
try:
from Cython.Distutils import Extension
from pyximport import pyxbuild
except ImportError:
print("Unable to import Cython, disabling OpenMP for now.")
return [], [], False
from distutils.errors import CompileError, LinkError
import shutil
import tempfile
test_code = dedent("""
from cython.parallel import parallel, prange, threadid
cimport openmp
def n_threads():
with nogil, parallel():
openmp.omp_get_num_threads()
""")
tmp_dir = tempfile.mkdtemp()
fname = path.join(tmp_dir, 'check_omp.pyx')
with open(fname, 'w') as fp:
fp.write(test_code)
extension = Extension(
name='check_omp', sources=[fname],
extra_compile_args=omp_compile_flags,
extra_link_args=omp_link_flags,
)
has_omp = True
try:
pyxbuild.pyx_to_dll(fname, extension, pyxbuild_dir=tmp_dir)
print("-"*70)
print("Using OpenMP.")
print("-"*70)
except CompileError:
print("*"*70)
print("Unable to compile OpenMP code. Not using OpenMP.")
print("*"*70)
has_omp = False
except LinkError:
print("*"*70)
print("Unable to link OpenMP code. Not using OpenMP.")
print("*"*70)
has_omp = False
finally:
shutil.rmtree(tmp_dir)
if has_omp:
return omp_compile_flags, omp_link_flags, True
else:
return [], [], False
def get_omp_flags():
"""Returns openmp flags if OpenMP is available.
Implementation based on https://bitbucket.org/pysph/pysph
"""
omp_compile_flags, omp_link_flags = ['-fopenmp'], ['-fopenmp']
env_var = os.environ.get('USE_OPENMP', '')
if env_var.lower() in ['0', 'false', 'n']:
print("-" * 70)
print("OpenMP disabled. Enable using 'USE_OPENMP'")
print("-" * 70)
return [], [], False
from textwrap import dedent
try:
from Cython.Distutils import Extension
from pyximport import pyxbuild
except ImportError:
print("Unable to import Cython, disabling OpenMP for now.")
return [], [], False
from distutils.errors import CompileError, LinkError
import shutil
import tempfile
test_code = dedent("""
from cython.parallel import parallel, prange, threadid
cimport openmp
def n_threads():
with nogil, parallel():
openmp.omp_get_num_threads()
""")
tmp_dir = tempfile.mkdtemp()
fname = path.join(tmp_dir, 'check_omp.pyx')
with open(fname, 'w') as fp:
fp.write(test_code)
extension = Extension(
name='check_omp',
sources=[fname],
extra_compile_args=omp_compile_flags,
extra_link_args=omp_link_flags,
)
has_omp = True
try:
mod = pyxbuild.pyx_to_dll(fname, extension, pyxbuild_dir=tmp_dir)
print("-" * 70)
print("Using OpenMP.")
print("-" * 70)
except CompileError:
print("*" * 70)
print("Unable to compile OpenMP code. Not using OpenMP.")
print("*" * 70)
has_omp = False
except LinkError:
print("*" * 70)
print("Unable to link OpenMP code. Not using OpenMP.")
print("*" * 70)
has_omp = False
finally:
shutil.rmtree(tmp_dir)
if has_omp:
return omp_compile_flags, omp_link_flags, True
else:
return [], [], False
#from setuptools import setup, Extension
from distutils.core import setup
from numpy import get_include
from Cython.Distutils import Extension
from Cython.Distutils import build_ext
logicle_extension = Extension(
'fcm.core._logicle',
sources=[
'fcm/core/logicle_ext/%s' % i
for i in ['Logicle.cpp', 'my_logicle.cpp', 'my_logicle_wrapper.cpp']
],
include_dirs=[get_include()])
munkres_extension = Extension(
"fcm.alignment.munkres",
["fcm/alignment/munkres.pyx", "fcm/alignment/munkres_ext/Munkres.cpp"],
include_dirs=[get_include(), 'fcm/alignment/munkres_ext/'],
language='c++')
setup(
name='fcm',
version='0.9.5',
url='http://code.google.com/p/py-fcm/',
packages=[
'fcm', 'fcm.core', 'fcm.graphics', 'fcm.gui', 'fcm.io',
'fcm.statistics', 'fcm.alignment'
],
package_data={'': ['data/*']},
description='Python Flow Cytometry (FCM) Tools',
author='Jacob Frelinger',
author_email='*****@*****.**',
from distutils.core import setup
from Cython.Build import cythonize
from Cython.Distutils import Extension
import os
os.environ['LDFLAGS'] = "-framework AVFoundation -framework CoreWLAN -framework AppKit"
os.environ['CFLAGS'] = "-mmacosx-version-min=10.7 -std=c++11 --stdlib=libc++"
setup(ext_modules=cythonize(Extension(
'IAgoraRtcEngine',
['IAgoraRtcEngine_pyx.pyx'],
libraries=['AgoraRtcEngineKit'],
library_dirs=['./lib'],
include_dirs=['./include']
)))
# handle nersc-specific compiling options. This will have to be run with
# a UCS2 version of Python (the default in Ubuntu is UCS4, so a custom
# Python may have to be used.
if "--NERSC" in argv:
argv.remove("--NERSC")
extra_link_args = ["-Wl,--wrap=memcpy", "-Wl,-Bsymbolic-functions"]
sources.append("memcpy.c") # this prevents a GLIBC2.14 function
if platform == "darwin":
# paths for homebrew gmp and gmpxx
include_dirs.append("/usr/local/include")
library_dirs.append("/usr/local/lib")
elif platform == "win32":
extra_compile_args = ["-DSOPLEX_WITH_GMP", "/MT", "/EHsc"]
ext_modules = cythonize([Extension(
"soplex", sources,
include_dirs=include_dirs,
libraries=["soplex", "gmp"],
library_dirs=library_dirs,
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args,
language="c++")])
setup(
name="soplex",
cmdclass={"build_ext": build_ext},
ext_modules=ext_modules,
version="0.0.5"
)
if sys.platform == 'win32':
build_options = fake_detect_pylon_windows()
elif sys.platform == 'darwin':
build_options = fake_detect_pylon_osx()
else:
build_options = detect_pylon()
# Set build language
build_options['language'] = 'c++'
# Add numpy build options
build_options['include_dirs'].append(numpy.get_include())
pypylon_extensions = [
Extension('pypylon.cython.version', [
'cython/version.pyx',
], **build_options),
Extension('pypylon.cython.factory', [
'cython/factory.pyx',
], **build_options),
]
setup(
name='pypylon',
license="custom",
description="Cython module to provide access to Pylon's SDK.",
version='0.0.1',
author="Matthias Blaicher",
author_email="*****@*****.**",
cmdclass={'build_ext': build_ext},
ext_modules=pypylon_extensions,
