def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_info
# compile_args = ['-std=c99', '-Wall', '-Werror']
compile_args = ['-std=c99', '-Wall']
config = Configuration(None, parent_package, top_path)
config.add_subpackage('numtypes')
config.add_subpackage('numtypes/tests')
config.add_extension('numtypes._nint',
extra_compile_args=compile_args,
sources=[join('src', '_nint.c.src')],
**get_info("npymath"))
config.add_extension('numtypes._complex_int',
extra_compile_args=compile_args,
sources=[join('src', '_complex_int.c.src')],
**get_info("npymath"))
config.add_extension('numtypes._polarcomplex',
extra_compile_args=compile_args,
sources=[join('src', '_polarcomplex.c.src')])
config.add_extension(
'numtypes._python_logtypes',
extra_compile_args=compile_args,
sources=[join('src', 'logtypes', '_python_logtypes.c')])
config.add_extension('numtypes._logtypes',
extra_compile_args=compile_args,
sources=[join('src', 'logtypes', '_logtypes.c.src')])
return config
def test_installed_npymath_ini():
# Regression test for gh-7707. If npymath.ini wasn't installed, then this
# will give an error.
info = get_info('npymath')
assert isinstance(info, dict)
assert "define_macros" in info
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import get_info
npymath_info = get_info('npymath')
# {
# 'include_dirs': ['/usr/local/lib/python3.7/site-packages/numpy/core/include'],
# 'library_dirs': ['/usr/local/lib/python3.7/site-packages/numpy/core/lib'],
# 'libraries': ['npymath'],
# 'define_macros': []
# }
if os.name == 'posix':
npymath_info['libraries'].append('m')
from numpy.distutils.misc_util import Configuration
config = Configuration(package_name='clib',
parent_name=parent_package,
top_path=top_path)
p = Path(CLIB_ABS_PATH)
for abs_prog_path in p.glob("*.pyx"):
fn = abs_prog_path.name # hoge.pyx
*name, _ = fn.split(".")
name = ".".join(name) # hoge
config.add_extension(
name=name,
sources=[fn],
language="c++",
**npymath_info,
)
print(
f"* \033[34m{fn}\033[0m is compiled by Cython to \033[34m{name}.cpp\033[0m file."
)
# config.add_subpackage('tests')
return config
def configuration(parent_package="", top_path=None):
config = Configuration("", parent_package, top_path)
config.add_extension("hpyc", ["hpyc.cpp"],
extra_info=get_info("npymath"),
extra_compile_args=CFLAGS)
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_info
config = Configuration('ssm', parent_package, top_path)
info = get_info("npymath")
config.add_extension('_statespace',
include_dirs=['dismalpy/src'],
sources=['_statespace.c'], extra_info=info)
config.add_extension('_kalman_filter',
include_dirs=['dismalpy/src'],
sources=['_kalman_filter.c'], extra_info=info)
config.add_extension('_kalman_smoother',
include_dirs=['dismalpy/src'],
sources=['_kalman_smoother.c'], extra_info=info)
config.add_extension('_simulation_smoother',
include_dirs=['dismalpy/src'],
sources=['_simulation_smoother.c'], extra_info=info)
config.add_extension('_tools',
include_dirs=['dismalpy/src'],
sources=['_tools.c'])
config.add_subpackage('compat')
config.add_data_dir('tests')
config.add_subpackage('_filters')
config.add_subpackage('_smoothers')
config.make_config_py()
return config
def __init__(self, *args, **kwargs):
from numpy import get_include
from numpy.distutils.misc_util import get_info
kwargs.update(get_info('npymath'))
kwargs['include_dirs'] += [get_include()]
Extension.__init__(self, *args, **kwargs)
def __init__(self, *args, **kwargs):
from numpy import get_include
from numpy.distutils.misc_util import get_info
kwargs.update(get_info('npymath'))
kwargs['include_dirs'] += [get_include()]
Extension.__init__(self, *args, **kwargs)
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_info
config = Configuration('ssm', parent_package, top_path)
info = get_info("npymath")
config.add_extension('_statespace',
include_dirs=['dismalpy/src'],
sources=['_statespace.c'],
extra_info=info)
config.add_extension('_kalman_filter',
include_dirs=['dismalpy/src'],
sources=['_kalman_filter.c'],
extra_info=info)
config.add_extension('_kalman_smoother',
include_dirs=['dismalpy/src'],
sources=['_kalman_smoother.c'],
extra_info=info)
config.add_extension('_simulation_smoother',
include_dirs=['dismalpy/src'],
sources=['_simulation_smoother.c'],
extra_info=info)
config.add_extension('_tools',
include_dirs=['dismalpy/src'],
sources=['_tools.c'])
config.add_subpackage('compat')
config.add_data_dir('tests')
config.add_subpackage('_filters')
config.add_subpackage('_smoothers')
config.make_config_py()
return config
def __init__(self, *args, **kwargs):
if len(sys.argv) < 2 or not self.is_special_command():
from numpy import get_include
from numpy.distutils.misc_util import get_info
kwargs.update(get_info('npymath'))
kwargs['include_dirs'] += [get_include()]
Extension.__init__(self, *args, **kwargs)
def __init__(self):
# Need to import it here since setuptools may monkeypatch it
from distutils.dist import Distribution
self._verbose = False
self._compiler = new_compiler()
customize_compiler(self._compiler)
self._build_ext = build_ext(Distribution())
self._build_ext.finalize_options()
self._py_lib_dirs = self._build_ext.library_dirs
self._py_include_dirs = self._build_ext.include_dirs
self._math_info = np_misc.get_info('npymath')
def configuration(parent_package='', top_path=None):
import numpy
from numpy.distutils.misc_util import Configuration
from numpy.distutils.misc_util import get_info
info = get_info('npymath')
config = Configuration('sfa_utils', parent_package, top_path)
config.add_extension('npufunc', ['src/pysfa/log_erfc.c'], extra_info=info)
return config
def __init__(self):
# Need to import it here since setuptools may monkeypatch it
from distutils.dist import Distribution
self._verbose = False
self._compiler = new_compiler()
customize_compiler(self._compiler)
self._build_ext = build_ext(Distribution())
self._build_ext.finalize_options()
self._py_lib_dirs = self._build_ext.library_dirs
self._py_include_dirs = self._build_ext.include_dirs
self._math_info = np_misc.get_info('npymath')
def configuration(parent_package='', top_path=None):
import numpy
from numpy.distutils.misc_util import Configuration
from numpy.distutils.misc_util import get_info
#Necessary for the half-float d-type.
info = get_info('npymath')
config = Configuration('', parent_package, top_path)
config.add_extension('numpy_test', ['numpy_test.c'], extra_info=info)
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('special', parent_package, top_path)
define_macros = []
if sys.platform=='win32':
# define_macros.append(('NOINFINITIES',None))
# define_macros.append(('NONANS',None))
define_macros.append(('_USE_MATH_DEFINES',None))
# C libraries
config.add_library('sc_c_misc',sources=[join('c_misc','*.c')])
config.add_library('sc_cephes',sources=[join('cephes','*.c')],
include_dirs=[get_python_inc(), get_numpy_include_dirs()],
macros=define_macros)
# Fortran libraries
config.add_library('sc_mach',sources=[join('mach','*.f')],
config_fc={'noopt':(__file__,1)})
config.add_library('sc_toms',sources=[join('amos','*.f')])
config.add_library('sc_amos',sources=[join('toms','*.f')])
config.add_library('sc_cdf',sources=[join('cdflib','*.f')])
config.add_library('sc_specfun',sources=[join('specfun','*.f')])
# Extension _cephes
sources = ['_cephesmodule.c', 'amos_wrappers.c', 'specfun_wrappers.c',
'toms_wrappers.c','cdf_wrappers.c','ufunc_extras.c']
config.add_extension('_cephes', sources=sources,
libraries=['sc_amos','sc_toms','sc_c_misc','sc_cephes','sc_mach',
'sc_cdf', 'sc_specfun'],
depends=["ufunc_extras.h", "cephes.h",
"amos_wrappers.h", "toms_wrappers.h",
"cdf_wrappers.h", "specfun_wrappers.h",
"c_misc/misc.h", "cephes_doc.h",
"cephes/mconf.h", "cephes/cephes_names.h"],
define_macros = define_macros,
extra_info=get_info("npymath")
)
# Extension specfun
config.add_extension('specfun',
sources=['specfun.pyf'],
f2py_options=['--no-wrap-functions'],
define_macros=[],
libraries=['sc_specfun'])
config.add_data_files('tests/*.py')
config.add_data_files('tests/data/README')
config.add_data_files('tests/data/*.npz')
return config
def configuration(parent_package='', top_path=None):
import numpy
from numpy.distutils.misc_util import Configuration
from numpy.distutils.misc_util import get_info
info = get_info('npymath')
config = Configuration('c_faces',
parent_package,
top_path)
config.add_extension('c_faces',
['c_faces.cpp'],
extra_info=info,
extra_compile_args= ["-Wall", "-Werror", "-O3"])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_info
config = Configuration('_filters', parent_package, top_path)
info = get_info("npymath")
config.add_extension('_conventional',
include_dirs=['dismalpy/src'],
sources=['_conventional.c'], extra_info=info)
config.add_extension('_univariate',
include_dirs=['dismalpy/src'],
sources=['_univariate.c'], extra_info=info)
config.add_extension('_inversions',
include_dirs=['dismalpy/src'],
sources=['_inversions.c'], extra_info=info)
config.make_config_py()
return config
def _update_extensions(self):
import numpy
from numpy.distutils.misc_util import get_info
numpy_includes = [numpy.get_include()]
extra_incl = pkg_resources.resource_filename('numpy', 'core/include')
numpy_includes += [extra_incl]
numpy_includes = list(set(numpy_includes))
numpy_math_libs = get_info('npymath')
for extension in self.extensions:
if not hasattr(extension, 'include_dirs'):
continue
extension.include_dirs = list(set(extension.include_dirs +
numpy_includes))
if extension.name in EXT_REQUIRES_NUMPY_MATH_LIBS:
extension.include_dirs += numpy_math_libs['include_dirs']
extension.libraries += numpy_math_libs['libraries']
extension.library_dirs += numpy_math_libs['library_dirs']
def _update_extensions(self):
import numpy
from numpy.distutils.misc_util import get_info
numpy_includes = [numpy.get_include()]
extra_incl = pkg_resources.resource_filename('numpy', 'core/include')
numpy_includes += [extra_incl]
numpy_includes = list(set(numpy_includes))
numpy_math_libs = get_info('npymath')
for extension in self.extensions:
if not hasattr(extension, 'include_dirs'):
continue
extension.include_dirs = list(
set(extension.include_dirs + numpy_includes))
if extension.name in EXT_REQUIRES_NUMPY_MATH_LIBS:
extension.include_dirs += numpy_math_libs['include_dirs']
extension.libraries += numpy_math_libs['libraries']
extension.library_dirs += numpy_math_libs['library_dirs']
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.misc_util import get_info
info = get_info('npymath')
config = Configuration('', parent_package, top_path)
config.add_extension(
'cNeuralReluplex',
sources=['reluplex/Reluplex2py.cpp'],
include_dirs=[common_inc, glpk_inc, reluplex_inc, src_inc],
library_dirs=[glpk_lib],
runtime_library_dirs=[glpk_lib],
libraries=["glpk"],
extra_compile_args=['--std=c++14'],
language='c++',
extra_info=info)
return config
def update_extension(extension, requires_math=True):
import numpy # noqa: F811
from numpy.distutils.log import set_verbosity
from numpy.distutils.misc_util import get_info
set_verbosity(1)
numpy_includes = [numpy.get_include()]
extra_incl = pkg_resources.resource_filename("numpy", "core/include")
numpy_includes += [extra_incl]
numpy_includes = list(set(numpy_includes))
numpy_math_libs = get_info("npymath")
if not hasattr(extension, "include_dirs"):
return
extension.include_dirs = list(set(extension.include_dirs + numpy_includes))
if requires_math:
extension.include_dirs += numpy_math_libs["include_dirs"]
extension.libraries += numpy_math_libs["libraries"]
extension.library_dirs += numpy_math_libs["library_dirs"]
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_info
config = Configuration('_filters', parent_package, top_path)
info = get_info("npymath")
config.add_extension('_conventional',
include_dirs=['dismalpy/src'],
sources=['_conventional.c'],
extra_info=info)
config.add_extension('_univariate',
include_dirs=['dismalpy/src'],
sources=['_univariate.c'],
extra_info=info)
config.add_extension('_inversions',
include_dirs=['dismalpy/src'],
sources=['_inversions.c'],
extra_info=info)
config.make_config_py()
return config
def configuration(parent_package='', top_path=''):
'''
Function to do the configuration.
'''
from numpy.distutils.misc_util import Configuration
config = Configuration('cpython', parent_package, top_path)
numpy_nodepr_api = [('NPY_NO_DEPRECATED_API', 'NPY_1_9_API_VERSION')]
headers = glob.glob('*.h')
# Add CPYTHON extension
from numpy.distutils.misc_util import get_info
math_aux_cpy_src = ['math_aux_cpy.c']
config.add_extension('math_aux_cpy',
sources=math_aux_cpy_src,
depends=headers + math_aux_cpy_src,
extra_info=get_info('npymath'),
define_macros=numpy_nodepr_api,
)
return config
install_requires = ["numpy", "scikit-learn>=0.16"]
tests_require = install_requires + ["pytest"]
docs_require = install_requires + [
"Sphinx", "sphinx-gallery", "numpydoc", "Pillow", "matplotlib"
]
setup_options = dict(name="hmmlearn",
version=VERSION,
description=DESCRIPTION,
long_description=LONG_DESCRIPTION,
maintainer=MAINTAINER,
maintainer_email=MAINTAINER_EMAIL,
license=LICENSE,
url="https://github.com/hmmlearn/hmmlearn",
packages=["hmmlearn", "hmmlearn.tests"],
classifiers=CLASSIFIERS,
ext_modules=[
Extension("hmmlearn._hmmc", ["hmmlearn/_hmmc.c"],
extra_compile_args=["-O3"],
**get_info("npymath"))
],
install_requires=install_requires,
tests_require=tests_require,
extras_require={
"tests": tests_require,
"docs": docs_require
})
if __name__ == "__main__":
setup(**setup_options)
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('special', parent_package, top_path)
define_macros = []
if sys.platform=='win32':
# define_macros.append(('NOINFINITIES',None))
# define_macros.append(('NONANS',None))
define_macros.append(('_USE_MATH_DEFINES',None))
curdir = os.path.abspath(os.path.dirname(__file__))
# C libraries
config.add_library('sc_c_misc',sources=[join('c_misc','*.c')],
include_dirs=[curdir, get_python_inc(), get_numpy_include_dirs()],
macros=define_macros)
config.add_library('sc_cephes',sources=[join('cephes','*.c')],
include_dirs=[curdir, get_python_inc(), get_numpy_include_dirs()],
macros=define_macros)
# Fortran/C++ libraries
config.add_library('sc_mach',sources=[join('mach','*.f')],
config_fc={'noopt':(__file__,1)})
config.add_library('sc_amos',sources=[join('amos','*.f')])
config.add_library('sc_cdf',sources=[join('cdflib','*.f')])
config.add_library('sc_specfun',sources=[join('specfun','*.f')])
# Extension specfun
config.add_extension('specfun',
sources=['specfun.pyf'],
f2py_options=['--no-wrap-functions'],
define_macros=[],
libraries=['sc_specfun'])
# Extension _ufuncs
config.add_extension('_ufuncs',
libraries=['sc_amos','sc_c_misc','sc_cephes','sc_mach',
'sc_cdf', 'sc_specfun'],
depends=["_logit.h", "cephes.h",
"amos_wrappers.h",
"cdf_wrappers.h", "specfun_wrappers.h",
"c_misc/misc.h", "cephes/mconf.h", "cephes/cephes_names.h"],
sources=['_ufuncs.c', 'sf_error.c', '_logit.c.src',
"amos_wrappers.c", "cdf_wrappers.c", "specfun_wrappers.c"],
include_dirs=[curdir],
define_macros = define_macros,
extra_info=get_info("npymath"))
# Extension _ufuncs_cxx
config.add_extension('_ufuncs_cxx',
sources=['_ufuncs_cxx.cxx',
'sf_error.c',
'_faddeeva.cxx',
'Faddeeva.cc',
],
libraries=['sc_cephes'],
include_dirs=[curdir],
define_macros=define_macros,
extra_info=get_info("npymath"))
config.add_data_files('tests/*.py')
config.add_data_files('tests/data/README')
config.add_data_files('tests/data/*.npz')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info as get_system_info
config = Configuration('special', parent_package, top_path)
define_macros = []
if sys.platform == 'win32':
# define_macros.append(('NOINFINITIES',None))
# define_macros.append(('NONANS',None))
define_macros.append(('_USE_MATH_DEFINES', None))
curdir = os.path.abspath(os.path.dirname(__file__))
inc_dirs = [get_python_inc(), os.path.join(curdir, "c_misc")]
if inc_dirs[0] != get_python_inc(plat_specific=1):
inc_dirs.append(get_python_inc(plat_specific=1))
inc_dirs.insert(0, get_numpy_include_dirs())
# C libraries
c_misc_src = [join('c_misc', '*.c')]
c_misc_hdr = [join('c_misc', '*.h')]
cephes_src = [join('cephes', '*.c')]
cephes_hdr = [join('cephes', '*.h')]
config.add_library('sc_c_misc',
sources=c_misc_src,
include_dirs=[curdir] + inc_dirs,
depends=(cephes_hdr + cephes_src + c_misc_hdr +
cephes_hdr + ['*.h']),
macros=define_macros)
config.add_library('sc_cephes',
sources=cephes_src,
include_dirs=[curdir] + inc_dirs,
depends=(cephes_hdr + ['*.h']),
macros=define_macros)
# Fortran/C++ libraries
mach_src = [join('mach', '*.f')]
amos_src = [join('amos', '*.f')]
cdf_src = [join('cdflib', '*.f')]
specfun_src = [join('specfun', '*.f')]
config.add_library('sc_mach',
sources=mach_src,
config_fc={'noopt': (__file__, 1)})
config.add_library('sc_amos', sources=amos_src)
config.add_library('sc_cdf', sources=cdf_src)
config.add_library('sc_specfun', sources=specfun_src)
# Extension specfun
config.add_extension('specfun',
sources=['specfun.pyf'],
f2py_options=['--no-wrap-functions'],
depends=specfun_src,
define_macros=[],
libraries=['sc_specfun'])
# Extension _ufuncs
headers = ['*.h', join('c_misc', '*.h'), join('cephes', '*.h')]
ufuncs_src = [
'_ufuncs.c', 'sf_error.c', '_logit.c.src', "amos_wrappers.c",
"cdf_wrappers.c", "specfun_wrappers.c"
]
ufuncs_dep = (headers + ufuncs_src + amos_src + c_misc_src + cephes_src +
mach_src + cdf_src + specfun_src)
cfg = dict(get_system_info('lapack_opt'))
cfg.setdefault('include_dirs',
[]).extend([curdir] + inc_dirs + [numpy.get_include()])
cfg.setdefault('libraries', []).extend([
'sc_amos', 'sc_c_misc', 'sc_cephes', 'sc_mach', 'sc_cdf', 'sc_specfun'
])
cfg.setdefault('define_macros', []).extend(define_macros)
config.add_extension('_ufuncs',
depends=ufuncs_dep,
sources=ufuncs_src,
extra_info=get_info("npymath"),
**cfg)
# Extension _ufuncs_cxx
ufuncs_cxx_src = [
'_ufuncs_cxx.cxx', 'sf_error.c', '_faddeeva.cxx', 'Faddeeva.cc',
'_wright.cxx', 'wright.cc'
]
ufuncs_cxx_dep = (headers + ufuncs_cxx_src + cephes_src + ['*.hh'])
config.add_extension('_ufuncs_cxx',
sources=ufuncs_cxx_src,
depends=ufuncs_cxx_dep,
include_dirs=[curdir],
define_macros=define_macros,
extra_info=get_info("npymath"))
cfg = dict(get_system_info('lapack_opt'))
config.add_extension('_ellip_harm_2',
sources=[
'_ellip_harm_2.c',
'sf_error.c',
],
**cfg)
# Cython API
config.add_data_files('cython_special.pxd')
cython_special_src = [
'cython_special.c', 'sf_error.c', '_logit.c.src', "amos_wrappers.c",
"cdf_wrappers.c", "specfun_wrappers.c"
]
cython_special_dep = (headers + ufuncs_src + ufuncs_cxx_src + amos_src +
c_misc_src + cephes_src + mach_src + cdf_src +
specfun_src)
cfg.setdefault('include_dirs',
[]).extend([curdir] + inc_dirs + [numpy.get_include()])
cfg.setdefault('libraries', []).extend([
'sc_amos', 'sc_c_misc', 'sc_cephes', 'sc_mach', 'sc_cdf', 'sc_specfun'
])
cfg.setdefault('define_macros',
[]).extend(define_macros + [('CYTHON_SPECIAL', 1)])
config.add_extension('cython_special',
depends=cython_special_dep,
sources=cython_special_src,
extra_info=get_info("npymath"),
**cfg)
# combinatorics
config.add_extension('_comb', sources=['_comb.c'])
# testing for _round.h
config.add_extension('_test_round',
sources=['_test_round.c'],
depends=['_round.h', 'c_misc/double2.h'],
include_dirs=[numpy.get_include()],
extra_info=get_info('npymath'))
config.add_data_files('tests/*.py')
config.add_data_files('tests/data/README')
config.add_data_files('tests/data/*.npz')
config.add_subpackage('_precompute')
return config
foo, _ = subprocess.Popen(["curl-config", "--libs"], stdout=subprocess.PIPE).communicate()
except:
sys.exit(
"Either libcurl isn't installed, it didn't come with curl-config, or curl-config isn't in your $PATH. This must be corrected before installing pyBigWig!\n"
)
foo = foo.strip().split()
for v in foo:
if v[0:2] == "-L":
additional_libs.append(v[2:])
include_dirs = ["libBigWig", sysconfig.get_config_var("INCLUDEPY")]
defines = []
if WITHNUMPY is True:
defines.extend([("WITHNUMPY", None), ("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")])
extra_info = get_info("npymath")
include_dirs.extend(extra_info["include_dirs"])
libs.extend(extra_info["libraries"])
extra_info["library_dirs"].extend(additional_libs)
additional_libs = extra_info["library_dirs"]
module1 = Extension(
"pyBigWig",
sources=srcs,
libraries=libs,
library_dirs=additional_libs,
define_macros=defines,
include_dirs=include_dirs,
)
setup(
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info as get_system_info
config = Configuration('special', parent_package, top_path)
define_macros = []
if sys.platform == 'win32':
# define_macros.append(('NOINFINITIES',None))
# define_macros.append(('NONANS',None))
define_macros.append(('_USE_MATH_DEFINES',None))
curdir = os.path.abspath(os.path.dirname(__file__))
inc_dirs = [get_python_inc(), os.path.join(curdir, "c_misc")]
if inc_dirs[0] != get_python_inc(plat_specific=1):
inc_dirs.append(get_python_inc(plat_specific=1))
inc_dirs.insert(0, get_numpy_include_dirs())
# C libraries
c_misc_src = [join('c_misc','*.c')]
c_misc_hdr = [join('c_misc','*.h')]
cephes_src = [join('cephes','*.c')]
cephes_hdr = [join('cephes', '*.h')]
config.add_library('sc_c_misc',sources=c_misc_src,
include_dirs=[curdir] + inc_dirs,
depends=(cephes_hdr + cephes_src
+ c_misc_hdr + cephes_hdr
+ ['*.h']),
macros=define_macros)
config.add_library('sc_cephes',sources=cephes_src,
include_dirs=[curdir] + inc_dirs,
depends=(cephes_hdr + ['*.h']),
macros=define_macros)
# Fortran/C++ libraries
mach_src = [join('mach','*.f')]
amos_src = [join('amos','*.f')]
cdf_src = [join('cdflib','*.f')]
specfun_src = [join('specfun','*.f')]
config.add_library('sc_mach',sources=mach_src,
config_fc={'noopt':(__file__,1)})
config.add_library('sc_amos',sources=amos_src)
config.add_library('sc_cdf',sources=cdf_src)
config.add_library('sc_specfun',sources=specfun_src)
# Extension specfun
config.add_extension('specfun',
sources=['specfun.pyf'],
f2py_options=['--no-wrap-functions'],
depends=specfun_src,
define_macros=[],
libraries=['sc_specfun'])
# Extension _ufuncs
headers = ['*.h', join('c_misc', '*.h'), join('cephes', '*.h')]
ufuncs_src = ['_ufuncs.c', 'sf_error.c', '_logit.c.src',
"amos_wrappers.c", "cdf_wrappers.c", "specfun_wrappers.c"]
ufuncs_dep = (headers + ufuncs_src + amos_src + c_misc_src + cephes_src
+ mach_src + cdf_src + specfun_src)
cfg = dict(get_system_info('lapack_opt'))
cfg.setdefault('include_dirs', []).extend([curdir] + inc_dirs + [numpy.get_include()])
cfg.setdefault('libraries', []).extend(['sc_amos','sc_c_misc','sc_cephes','sc_mach',
'sc_cdf', 'sc_specfun'])
cfg.setdefault('define_macros', []).extend(define_macros)
config.add_extension('_ufuncs',
depends=ufuncs_dep,
sources=ufuncs_src,
extra_info=get_info("npymath"),
**cfg)
# Extension _ufuncs_cxx
ufuncs_cxx_src = ['_ufuncs_cxx.cxx', 'sf_error.c',
'_faddeeva.cxx', 'Faddeeva.cc']
ufuncs_cxx_dep = (headers + ufuncs_cxx_src + cephes_src
+ ['*.hh'])
config.add_extension('_ufuncs_cxx',
sources=ufuncs_cxx_src,
depends=ufuncs_cxx_dep,
include_dirs=[curdir],
define_macros=define_macros,
extra_info=get_info("npymath"))
cfg = dict(get_system_info('lapack_opt'))
config.add_extension('_ellip_harm_2',
sources=['_ellip_harm_2.c', 'sf_error.c',],
**cfg
)
config.add_data_files('tests/*.py')
config.add_data_files('tests/data/README')
config.add_data_files('tests/data/*.npz')
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('special', parent_package, top_path)
define_macros = []
if sys.platform == 'win32':
# define_macros.append(('NOINFINITIES',None))
# define_macros.append(('NONANS',None))
define_macros.append(('_USE_MATH_DEFINES',None))
curdir = os.path.abspath(os.path.dirname(__file__))
inc_dirs = [get_python_inc(), os.path.join(curdir, "c_misc")]
if inc_dirs[0] != get_python_inc(plat_specific=1):
inc_dirs.append(get_python_inc(plat_specific=1))
inc_dirs.insert(0, get_numpy_include_dirs())
# C libraries
c_misc_src = [join('c_misc','*.c')]
c_misc_hdr = [join('c_misc','*.h')]
cephes_src = [join('cephes','*.c')]
cephes_hdr = [join('cephes', '*.h')]
config.add_library('sc_c_misc',sources=c_misc_src,
include_dirs=[curdir] + inc_dirs,
depends=(cephes_hdr + cephes_src
+ c_misc_hdr + cephes_hdr
+ ['*.h']),
macros=define_macros)
config.add_library('sc_cephes',sources=cephes_src,
include_dirs=[curdir] + inc_dirs,
depends=(cephes_hdr + ['*.h']),
macros=define_macros)
# Fortran/C++ libraries
mach_src = [join('mach','*.f')]
amos_src = [join('amos','*.f')]
cdf_src = [join('cdflib','*.f')]
specfun_src = [join('specfun','*.f')]
config.add_library('sc_mach',sources=mach_src,
config_fc={'noopt':(__file__,1)})
config.add_library('sc_amos',sources=amos_src)
config.add_library('sc_cdf',sources=cdf_src)
config.add_library('sc_specfun',sources=specfun_src)
# Extension specfun
config.add_extension('specfun',
sources=['specfun.pyf'],
f2py_options=['--no-wrap-functions'],
depends=specfun_src,
define_macros=[],
libraries=['sc_specfun'])
# Extension _ufuncs
headers = ['*.h', join('c_misc', '*.h'), join('cephes', '*.h')]
ufuncs_src = ['_ufuncs.c', 'sf_error.c', '_logit.c.src',
"amos_wrappers.c", "cdf_wrappers.c", "specfun_wrappers.c"]
ufuncs_dep = (headers + ufuncs_src + amos_src + c_misc_src + cephes_src
+ mach_src + cdf_src + specfun_src)
config.add_extension('_ufuncs',
libraries=['sc_amos','sc_c_misc','sc_cephes','sc_mach',
'sc_cdf', 'sc_specfun'],
depends=ufuncs_dep,
sources=ufuncs_src,
include_dirs=[curdir] + inc_dirs,
define_macros=define_macros,
extra_info=get_info("npymath"))
# Extension _ufuncs_cxx
ufuncs_cxx_src = ['_ufuncs_cxx.cxx', 'sf_error.c',
'_faddeeva.cxx', 'Faddeeva.cc']
ufuncs_cxx_dep = (headers + ufuncs_cxx_src + cephes_src
+ ['*.hh'])
config.add_extension('_ufuncs_cxx',
sources=ufuncs_cxx_src,
depends=ufuncs_cxx_dep,
include_dirs=[curdir],
define_macros=define_macros,
extra_info=get_info("npymath"))
config.add_data_files('tests/*.py')
config.add_data_files('tests/data/README')
config.add_data_files('tests/data/*.npz')
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info as get_system_info
config = Configuration('special', parent_package, top_path)
define_macros = []
if sys.platform == 'win32':
# define_macros.append(('NOINFINITIES',None))
# define_macros.append(('NONANS',None))
define_macros.append(('_USE_MATH_DEFINES',None))
curdir = os.path.abspath(os.path.dirname(__file__))
inc_dirs = [get_python_inc(), os.path.join(curdir, "c_misc")]
if inc_dirs[0] != get_python_inc(plat_specific=1):
inc_dirs.append(get_python_inc(plat_specific=1))
inc_dirs.insert(0, get_numpy_include_dirs())
inc_dirs.append(join(dirname(dirname(__file__)), '_lib'))
# C libraries
c_misc_src = [join('c_misc','*.c')]
c_misc_hdr = [join('c_misc','*.h')]
cephes_src = [join('cephes','*.c')]
cephes_hdr = [join('cephes', '*.h')]
config.add_library('sc_c_misc',sources=c_misc_src,
include_dirs=[curdir] + inc_dirs,
depends=(cephes_hdr + cephes_src
+ c_misc_hdr + cephes_hdr
+ ['*.h']),
macros=define_macros)
config.add_library('sc_cephes',sources=cephes_src,
include_dirs=[curdir] + inc_dirs,
depends=(cephes_hdr + ['*.h']),
macros=define_macros)
# Fortran/C++ libraries
mach_src = [join('mach','*.f')]
amos_src = [join('amos','*.f')]
cdf_src = [join('cdflib','*.f')]
specfun_src = [join('specfun','*.f')]
config.add_library('sc_mach',sources=mach_src,
config_fc={'noopt':(__file__,1)})
config.add_library('sc_amos',sources=amos_src)
config.add_library('sc_cdf',sources=cdf_src)
config.add_library('sc_specfun',sources=specfun_src)
# Extension specfun
config.add_extension('specfun',
sources=['specfun.pyf'],
f2py_options=['--no-wrap-functions'],
depends=specfun_src,
define_macros=[],
libraries=['sc_specfun'])
# Extension _ufuncs
headers = ['*.h', join('c_misc', '*.h'), join('cephes', '*.h')]
ufuncs_src = ['_ufuncs.c', 'sf_error.c', '_logit.c.src',
"amos_wrappers.c", "cdf_wrappers.c", "specfun_wrappers.c"]
ufuncs_dep = (headers + ufuncs_src + amos_src + c_misc_src + cephes_src
+ mach_src + cdf_src + specfun_src)
cfg = dict(get_system_info('lapack_opt'))
cfg.setdefault('include_dirs', []).extend([curdir] + inc_dirs + [numpy.get_include()])
cfg.setdefault('libraries', []).extend(['sc_amos','sc_c_misc','sc_cephes','sc_mach',
'sc_cdf', 'sc_specfun'])
cfg.setdefault('define_macros', []).extend(define_macros)
config.add_extension('_ufuncs',
depends=ufuncs_dep,
sources=ufuncs_src,
extra_info=get_info("npymath"),
**cfg)
# Extension _ufuncs_cxx
ufuncs_cxx_src = ['_ufuncs_cxx.cxx', 'sf_error.c',
'_faddeeva.cxx', 'Faddeeva.cc',
'_wright.cxx', 'wright.cc']
ufuncs_cxx_dep = (headers + ufuncs_cxx_src + cephes_src
+ ['*.hh'])
config.add_extension('_ufuncs_cxx',
sources=ufuncs_cxx_src,
depends=ufuncs_cxx_dep,
include_dirs=[curdir] + inc_dirs,
define_macros=define_macros,
extra_info=get_info("npymath"))
cfg = dict(get_system_info('lapack_opt'))
config.add_extension('_ellip_harm_2',
sources=['_ellip_harm_2.c', 'sf_error.c',],
**cfg
)
# Cython API
config.add_data_files('cython_special.pxd')
cython_special_src = ['cython_special.c', 'sf_error.c', '_logit.c.src',
"amos_wrappers.c", "cdf_wrappers.c", "specfun_wrappers.c"]
cython_special_dep = (headers + ufuncs_src + ufuncs_cxx_src + amos_src
+ c_misc_src + cephes_src + mach_src + cdf_src
+ specfun_src)
cfg = dict(get_system_info('lapack_opt'))
cfg.setdefault('include_dirs', []).extend([curdir] + inc_dirs + [numpy.get_include()])
cfg.setdefault('libraries', []).extend(['sc_amos','sc_c_misc','sc_cephes','sc_mach',
'sc_cdf', 'sc_specfun'])
cfg.setdefault('define_macros', []).extend(define_macros)
config.add_extension('cython_special',
depends=cython_special_dep,
sources=cython_special_src,
extra_info=get_info("npymath"),
**cfg)
# combinatorics
config.add_extension('_comb',
sources=['_comb.c'])
# testing for _round.h
config.add_extension('_test_round',
sources=['_test_round.c'],
depends=['_round.h', 'c_misc/double2.h'],
include_dirs=[numpy.get_include()] + inc_dirs,
extra_info=get_info('npymath'))
config.add_data_files('tests/*.py')
config.add_data_files('tests/data/README')
# regenerate npz data files
makenpz = os.path.join(os.path.dirname(__file__),
'utils', 'makenpz.py')
data_dir = os.path.join(os.path.dirname(__file__),
'tests', 'data')
for name in ['boost', 'gsl', 'local']:
subprocess.check_call([sys.executable, makenpz,
'--use-timestamp',
os.path.join(data_dir, name)])
config.add_data_files('tests/data/*.npz')
config.add_subpackage('_precompute')
return config
extra_setuptools_args = {}
from distutils.command import install
# Import distutils _after_ potential setuptools import above, and after removing
# MANIFEST
from distutils.core import setup
from distutils.extension import Extension
from distutils.command import build_py, build_ext
from cythexts import cyproc_exts, get_pyx_sdist, derror_maker
from setup_helpers import install_scripts_bat, add_flag_checking, check_npymath
# Define extensions
EXTS = []
# Add flags for linking to npymath library
ext_kwargs = get_info('npymath')
ext_kwargs['include_dirs'].append('src')
for modulename, other_sources, language in (
('dipy.reconst.recspeed', [], 'c'),
('dipy.reconst.vec_val_sum', [], 'c'),
('dipy.reconst.quick_squash', [], 'c'),
('dipy.tracking.distances', [], 'c'),
('dipy.tracking.streamlinespeed', [], 'c'),
('dipy.tracking.vox2track', [], 'c'),
('dipy.tracking.propspeed', [], 'c'),
('dipy.denoise.denspeed', [], 'c'),
('dipy.align.vector_fields', [], 'c'),
('dipy.align.sumsqdiff', [], 'c'),
('dipy.align.expectmax', [], 'c'),
('dipy.align.crosscorr', [], 'c'),
('dipy.align.bundlemin', [], 'c')):
CFLAGS = []
if sys.platform == "darwin" and sys.version_info[:2] == (2, 6):
cpp_link_args = ["-lstdc++"]
else:
cpp_link_args = []
install_name_tool_fixer = []
if sys.platform == "darwin":
install_name_tool_fixer += ["-headerpad_max_install_names"]
npymath_info = np_misc.get_info("npymath")
ext_dynfunc = Extension(
name="numba._dynfunc", sources=["numba/_dynfunc.c"], extra_compile_args=CFLAGS, depends=["numba/_pymodule.h"]
)
ext_npymath_exports = Extension(
name="numba._npymath_exports",
sources=["numba/_npymath_exports.c"],
include_dirs=npymath_info["include_dirs"],
libraries=npymath_info["libraries"],
library_dirs=npymath_info["library_dirs"],
define_macros=npymath_info["define_macros"],
)
"Sphinx", "sphinx-gallery", "numpydoc", "Pillow", "matplotlib"
]
setup_options = dict(
name="hmmlearn",
version=VERSION,
description=DESCRIPTION,
long_description=LONG_DESCRIPTION,
maintainer=MAINTAINER,
maintainer_email=MAINTAINER_EMAIL,
license=LICENSE,
url="https://github.com/hmmlearn/hmmlearn",
packages=["hmmlearn", "hmmlearn.tests"],
classifiers=CLASSIFIERS,
ext_modules=[
Extension("hmmlearn._hmmc", ["hmmlearn/_hmmc.c"],
extra_compile_args=["-O3"],
**get_info("npymath"))
],
install_requires=install_requires,
tests_require=tests_require,
extras_require={
"tests": tests_require,
"docs": docs_require
}
)
if __name__ == "__main__":
setup(**setup_options)
def get_ext_modules():
"""
Return a list of Extension instances for the setup() call.
"""
# Note we don't import Numpy at the toplevel, since setup.py
# should be able to run without Numpy for pip to discover the
# build dependencies
import numpy.distutils.misc_util as np_misc
# Inject required options for extensions compiled against the Numpy
# C API (include dirs, library dirs etc.)
np_compile_args = np_misc.get_info('npymath')
ext_dynfunc = Extension(name='numba._dynfunc',
sources=['numba/_dynfuncmod.c'],
extra_compile_args=CFLAGS,
depends=['numba/_pymodule.h',
'numba/_dynfunc.c'])
ext_dispatcher = Extension(name="numba._dispatcher",
sources=['numba/_dispatcher.c',
'numba/_typeof.c',
'numba/_hashtable.c',
'numba/_dispatcherimpl.cpp',
'numba/typeconv/typeconv.cpp'],
depends=["numba/_pymodule.h",
"numba/_dispatcher.h",
"numba/_typeof.h",
"numba/_hashtable.h"],
**np_compile_args)
ext_helperlib = Extension(name="numba._helperlib",
sources=["numba/_helpermod.c",
"numba/_math_c99.c"],
extra_compile_args=CFLAGS,
extra_link_args=install_name_tool_fixer,
depends=["numba/_pymodule.h",
"numba/_math_c99.h",
"numba/_helperlib.c",
"numba/_lapack.c",
"numba/_npymath_exports.c",
"numba/_random.c",
"numba/mathnames.inc"],
**np_compile_args)
ext_typeconv = Extension(name="numba.typeconv._typeconv",
sources=["numba/typeconv/typeconv.cpp",
"numba/typeconv/_typeconv.cpp"],
depends=["numba/_pymodule.h"],
)
ext_npyufunc_ufunc = Extension(name="numba.npyufunc._internal",
sources=["numba/npyufunc/_internal.c"],
depends=["numba/npyufunc/_ufunc.c",
"numba/npyufunc/_internal.h",
"numba/_pymodule.h"],
**np_compile_args)
ext_npyufunc_workqueue_impls = []
def check_file_at_path(path2file):
"""
Takes a list as a path, a single glob (*) is permitted as an entry which
indicates that expansion at this location is required (i.e. version
might not be known).
"""
found = None
path2check = [os.path.split(os.path.split(sys.executable)[0])[0]]
path2check += [os.getenv(n, '') for n in ['CONDA_PREFIX', 'PREFIX']]
if sys.platform.startswith('win'):
path2check += [os.path.join(p, 'Library') for p in path2check]
for p in path2check:
if p:
if '*' in path2file:
globloc = path2file.index('*')
searchroot = os.path.join(*path2file[:globloc])
try:
potential_locs = os.listdir(os.path.join(p, searchroot))
except BaseException:
continue
searchfor = path2file[globloc + 1:]
for x in potential_locs:
potpath = os.path.join(p, searchroot, x, *searchfor)
if os.path.isfile(potpath):
found = p # the latest is used
elif os.path.isfile(os.path.join(p, *path2file)):
found = p # the latest is used
return found
# Search for Intel TBB, first check env var TBBROOT then conda locations
tbb_root = os.getenv('TBBROOT')
if not tbb_root:
tbb_root = check_file_at_path(['include', 'tbb', 'tbb.h'])
# Set various flags for use in TBB and openmp. On OSX, also find OpenMP!
have_openmp = True
if sys.platform.startswith('win'):
cpp11flags = []
ompcompileflags = ['-openmp']
omplinkflags = []
elif sys.platform.startswith('darwin'):
cpp11flags = ['-std=c++11']
# This is a bit unusual but necessary...
# llvm (clang) OpenMP is used for headers etc at compile time
# Intel OpenMP (libiomp5) provides the link library.
# They are binary compatible and may not safely coexist in a process, as
# libiomp5 is more prevalent and often linked in for NumPy it is used
# here!
ompcompileflags = ['-fopenmp']
omplinkflags = ['-fopenmp=libiomp5']
omppath = ['lib', 'clang', '*', 'include', 'omp.h']
have_openmp = check_file_at_path(omppath)
else:
cpp11flags = ['-std=c++11']
ompcompileflags = ['-fopenmp']
if platform.machine() == 'ppc64le':
omplinkflags = ['-fopenmp']
else:
omplinkflags = ['-fopenmp']
if tbb_root:
print("Using Intel TBB from:", tbb_root)
ext_npyufunc_tbb_workqueue = Extension(
name='numba.npyufunc.tbbpool',
sources=['numba/npyufunc/tbbpool.cpp', 'numba/npyufunc/gufunc_scheduler.cpp'],
depends=['numba/npyufunc/workqueue.h'],
include_dirs=[os.path.join(tbb_root, 'include')],
extra_compile_args=cpp11flags,
libraries =['tbb'], # TODO: if --debug or -g, use 'tbb_debug'
library_dirs=[os.path.join(tbb_root, 'lib', 'intel64', 'gcc4.4'), # for Linux
os.path.join(tbb_root, 'lib'), # for MacOS
os.path.join(tbb_root, 'lib', 'intel64', 'vc_mt'), # for Windows
],
)
ext_npyufunc_workqueue_impls.append(ext_npyufunc_tbb_workqueue)
else:
print("TBB not found")
# Disable OpenMP if we are building a wheel or
# forced by user with NUMBA_NO_OPENMP=1
if is_building_wheel() or os.getenv('NUMBA_NO_OPENMP'):
print("OpenMP disabled")
elif have_openmp:
print("Using OpenMP from:", have_openmp)
# OpenMP backed work queue
ext_npyufunc_omppool = Extension( name='numba.npyufunc.omppool',
sources=['numba/npyufunc/omppool.cpp',
'numba/npyufunc/gufunc_scheduler.cpp'],
depends=['numba/npyufunc/workqueue.h'],
extra_compile_args=ompcompileflags + cpp11flags,
extra_link_args = omplinkflags)
ext_npyufunc_workqueue_impls.append(ext_npyufunc_omppool)
else:
print("OpenMP not found")
# Build the Numba workqueue implementation irrespective of whether the TBB
# version is built. Users can select a backend via env vars.
ext_npyufunc_workqueue = Extension(
name='numba.npyufunc.workqueue',
sources=['numba/npyufunc/workqueue.c', 'numba/npyufunc/gufunc_scheduler.cpp'],
depends=['numba/npyufunc/workqueue.h'])
ext_npyufunc_workqueue_impls.append(ext_npyufunc_workqueue)
ext_mviewbuf = Extension(name='numba.mviewbuf',
extra_link_args=install_name_tool_fixer,
sources=['numba/mviewbuf.c'])
ext_nrt_python = Extension(name='numba.runtime._nrt_python',
sources=['numba/runtime/_nrt_pythonmod.c',
'numba/runtime/nrt.c'],
depends=['numba/runtime/nrt.h',
'numba/_pymodule.h',
'numba/runtime/_nrt_python.c'],
**np_compile_args)
ext_jitclass_box = Extension(name='numba.jitclass._box',
sources=['numba/jitclass/_box.c'],
depends=['numba/_pymodule.h'],
)
ext_cuda_extras = Extension(name='numba.cuda.cudadrv._extras',
sources=['numba/cuda/cudadrv/_extras.c'],
depends=['numba/_pymodule.h'],
include_dirs=["numba"])
ext_modules = [ext_dynfunc, ext_dispatcher, ext_helperlib, ext_typeconv,
ext_npyufunc_ufunc, ext_mviewbuf, ext_nrt_python,
ext_jitclass_box, ext_cuda_extras]
ext_modules += ext_npyufunc_workqueue_impls
return ext_modules
def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration("special", parent_package, top_path)
define_macros = []
if sys.platform == "win32":
# define_macros.append(('NOINFINITIES',None))
# define_macros.append(('NONANS',None))
define_macros.append(("_USE_MATH_DEFINES", None))
curdir = os.path.abspath(os.path.dirname(__file__))
inc_dirs = [get_python_inc()]
if inc_dirs[0] != get_python_inc(plat_specific=1):
inc_dirs.append(get_python_inc(plat_specific=1))
inc_dirs.append(get_numpy_include_dirs())
# C libraries
config.add_library(
"sc_c_misc", sources=[join("c_misc", "*.c")], include_dirs=[curdir] + inc_dirs, macros=define_macros
)
config.add_library(
"sc_cephes", sources=[join("cephes", "*.c")], include_dirs=[curdir] + inc_dirs, macros=define_macros
)
# Fortran/C++ libraries
config.add_library("sc_mach", sources=[join("mach", "*.f")], config_fc={"noopt": (__file__, 1)})
config.add_library("sc_amos", sources=[join("amos", "*.f")])
config.add_library("sc_cdf", sources=[join("cdflib", "*.f")])
config.add_library("sc_specfun", sources=[join("specfun", "*.f")])
# Extension specfun
config.add_extension(
"specfun",
sources=["specfun.pyf"],
f2py_options=["--no-wrap-functions"],
define_macros=[],
libraries=["sc_specfun"],
)
# Extension _ufuncs
config.add_extension(
"_ufuncs",
libraries=["sc_amos", "sc_c_misc", "sc_cephes", "sc_mach", "sc_cdf", "sc_specfun"],
depends=[
"_logit.h",
"cephes.h",
"amos_wrappers.h",
"cdf_wrappers.h",
"specfun_wrappers.h",
"c_misc/misc.h",
"cephes/mconf.h",
"cephes/cephes_names.h",
],
sources=["_ufuncs.c", "sf_error.c", "_logit.c.src", "amos_wrappers.c", "cdf_wrappers.c", "specfun_wrappers.c"],
include_dirs=[curdir],
define_macros=define_macros,
extra_info=get_info("npymath"),
)
# Extension _ufuncs_cxx
config.add_extension(
"_ufuncs_cxx",
sources=["_ufuncs_cxx.cxx", "sf_error.c", "_faddeeva.cxx", "Faddeeva.cc"],
libraries=["sc_cephes"],
include_dirs=[curdir],
define_macros=define_macros,
extra_info=get_info("npymath"),
)
config.add_data_files("tests/*.py")
config.add_data_files("tests/data/README")
config.add_data_files("tests/data/*.npz")
return config
from distutils.core import setup, Extension
import numpy.distutils.misc_util as npy_util
npy_info = npy_util.get_info('npymath')
distance_wrap = Extension('_distance_wrap', sources = ['distance_wrap.c'], **npy_info)
setup(name = 'simple-distance-cpy',
version = '0.21',
description = 'I want euclidean cdist and I want it now',
py_modules = ['distance'],
ext_modules = [distance_wrap],
url='https://github.com/tocisz/simple-distance-cpy',
author='Tomasz Cichocki',
author_email='cichymail at gmail dot com')
from distutils.core import setup, Extension
import numpy.distutils.misc_util as npy_util
npy_info = npy_util.get_info('npymath')
distance_wrap = Extension('_distance_wrap',
sources=['distance_wrap.c'],
**npy_info)
setup(name='simple-distance-cpy',
version='0.21',
description='I want euclidean cdist and I want it now',
py_modules=['distance'],
ext_modules=[distance_wrap],
url='https://github.com/tocisz/simple-distance-cpy',
author='Tomasz Cichocki',
author_email='cichymail at gmail dot com')
def test_installed_npymath_ini():
# Regression test for gh-7707. If npymath.ini wasn't installed, then this
# will give an error.
info = get_info('npymath')
if not lapack_info:
# No LAPACK in NumPy
print('### Warning: Using unoptimized blas/lapack @@@')
MODULE_SOURCES.extend(lapack_lite_files[:-1]) # all but f2c.h
MODULE_DEPENDENCIES.extend(lapack_lite_files)
else:
if sys.platform == 'win32':
print('### Warning: python.xerbla.c is disabled ###')
else:
MODULE_SOURCES.extend(lapack_lite_files[:1]) # python_xerbla.c
MODULE_DEPENDENCIES.extend(lapack_lite_files[:1])
npymath_info = np_misc_util.get_info('npymath')
extra_opts = copy.deepcopy(lapack_info)
for key, val in npymath_info.items():
if extra_opts.get(key):
extra_opts[key].extend(val)
else:
extra_opts[key] = copy.deepcopy(val)
gufunc_module = Extension('gulinalg._impl',
sources = MODULE_SOURCES,
depends = MODULE_DEPENDENCIES,
**extra_opts)
packages = [
def get_ext_modules():
"""
Return a list of Extension instances for the setup() call.
"""
# Note we don't import Numpy at the toplevel, since setup.py
# should be able to run without Numpy for pip to discover the
# build dependencies
import numpy.distutils.misc_util as np_misc
# Inject required options for extensions compiled against the Numpy
# C API (include dirs, library dirs etc.)
np_compile_args = np_misc.get_info("npymath")
ext_dynfunc = Extension(
name="numba._dynfunc",
sources=["numba/_dynfuncmod.c"],
extra_compile_args=CFLAGS,
depends=["numba/_pymodule.h", "numba/_dynfunc.c"],
)
ext_dispatcher = Extension(
name="numba._dispatcher",
sources=[
"numba/_dispatcher.c",
"numba/_typeof.c",
"numba/_hashtable.c",
"numba/_dispatcherimpl.cpp",
"numba/typeconv/typeconv.cpp",
],
depends=["numba/_pymodule.h", "numba/_dispatcher.h", "numba/_typeof.h", "numba/_hashtable.h"],
**np_compile_args
)
ext_helperlib = Extension(
name="numba._helperlib",
sources=["numba/_helpermod.c", "numba/_math_c99.c"],
extra_compile_args=CFLAGS,
extra_link_args=install_name_tool_fixer,
depends=[
"numba/_pymodule.h",
"numba/_math_c99.h",
"numba/_helperlib.c",
"numba/_lapack.c",
"numba/_npymath_exports.c",
"numba/_random.c",
"numba/mathnames.inc",
],
**np_compile_args
)
ext_typeconv = Extension(
name="numba.typeconv._typeconv",
sources=["numba/typeconv/typeconv.cpp", "numba/typeconv/_typeconv.cpp"],
depends=["numba/_pymodule.h"],
)
ext_npyufunc_ufunc = Extension(
name="numba.npyufunc._internal",
sources=["numba/npyufunc/_internal.c"],
depends=["numba/npyufunc/_ufunc.c", "numba/npyufunc/_internal.h", "numba/_pymodule.h"],
**np_compile_args
)
ext_npyufunc_workqueue = Extension(
name="numba.npyufunc.workqueue", sources=["numba/npyufunc/workqueue.c"], depends=["numba/npyufunc/workqueue.h"]
)
ext_mviewbuf = Extension(name="numba.mviewbuf", sources=["numba/mviewbuf.c"])
ext_nrt_python = Extension(
name="numba.runtime._nrt_python",
sources=["numba/runtime/_nrt_pythonmod.c", "numba/runtime/nrt.c"],
depends=["numba/runtime/nrt.h", "numba/_pymodule.h", "numba/runtime/_nrt_python.c"],
**np_compile_args
)
ext_jitclass_box = Extension(
name="numba.jitclass._box", sources=["numba/jitclass/_box.c"], depends=["numba/_pymodule.h"]
)
ext_modules = [
ext_dynfunc,
ext_dispatcher,
ext_helperlib,
ext_typeconv,
ext_npyufunc_ufunc,
ext_npyufunc_workqueue,
ext_mviewbuf,
ext_nrt_python,
ext_jitclass_box,
]
return ext_modules
def test_installed_npymath_ini():
# Regression test for gh-7707. If npymath.ini wasn't installed, then this
# will give an error.
info = get_info('npymath')
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from scipy._build_utils.compiler_helper import set_cxx_flags_hook
import numpy as np
config = Configuration('stats', parent_package, top_path)
statlib_src = [join('statlib', '*.f')]
config.add_library('statlib', sources=statlib_src)
# add statlib module
config.add_extension('statlib',
sources=['statlib.pyf'],
f2py_options=['--no-wrap-functions'],
libraries=['statlib'],
depends=statlib_src)
# add _stats module
config.add_extension('_stats', sources=['_stats.c'])
# add mvn module
config.add_extension('mvn', sources=['mvn.pyf', 'mvndst.f'])
# add _sobol module
config.add_extension('_sobol', sources=['_sobol.c'])
config.add_data_files('_sobol_direction_numbers.npz')
# add _qmc_cy module
ext = config.add_extension('_qmc_cy', sources=['_qmc_cy.cxx'])
ext._pre_build_hook = set_cxx_flags_hook
if int(os.environ.get('SCIPY_USE_PYTHRAN', 1)):
import pythran
ext = pythran.dist.PythranExtension(
'scipy.stats._hypotests_pythran',
sources=["scipy/stats/_hypotests_pythran.py"],
config=['compiler.blas=none'])
config.ext_modules.append(ext)
# add BiasedUrn module
config.add_data_files('biasedurn.pxd')
from _generate_pyx import isNPY_OLD # type: ignore[import]
NPY_OLD = isNPY_OLD()
if NPY_OLD:
biasedurn_libs = []
biasedurn_libdirs = []
else:
biasedurn_libs = ['npyrandom', 'npymath']
biasedurn_libdirs = [
join(np.get_include(), '..', '..', 'random', 'lib')
]
biasedurn_libdirs += get_info('npymath')['library_dirs']
ext = config.add_extension(
'biasedurn',
sources=[
'biasedurn.cxx', 'biasedurn/impls.cpp', 'biasedurn/fnchyppr.cpp',
'biasedurn/wnchyppr.cpp', 'biasedurn/stoc1.cpp',
'biasedurn/stoc3.cpp'
],
include_dirs=[np.get_include()],
library_dirs=biasedurn_libdirs,
libraries=biasedurn_libs,
define_macros=[('R_BUILD', None)],
language='c++',
depends=['biasedurn/stocR.h'],
)
ext._pre_build_hook = pre_build_hook
# add boost stats distributions
config.add_subpackage('_boost')
# Type stubs
config.add_data_files('*.pyi')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('special', parent_package, top_path)
define_macros = []
if sys.platform == 'win32':
# define_macros.append(('NOINFINITIES',None))
# define_macros.append(('NONANS',None))
define_macros.append(('_USE_MATH_DEFINES', None))
curdir = os.path.abspath(os.path.dirname(__file__))
inc_dirs = [get_python_inc()]
if inc_dirs[0] != get_python_inc(plat_specific=1):
inc_dirs.append(get_python_inc(plat_specific=1))
inc_dirs.append(get_numpy_include_dirs())
# C libraries
config.add_library('sc_c_misc',
sources=[join('c_misc', '*.c')],
include_dirs=[curdir] + inc_dirs,
macros=define_macros)
config.add_library('sc_cephes',
sources=[join('cephes', '*.c')],
include_dirs=[curdir] + inc_dirs,
macros=define_macros)
# Fortran/C++ libraries
config.add_library('sc_mach',
sources=[join('mach', '*.f')],
config_fc={'noopt': (__file__, 1)})
config.add_library('sc_amos', sources=[join('amos', '*.f')])
config.add_library('sc_cdf', sources=[join('cdflib', '*.f')])
config.add_library('sc_specfun', sources=[join('specfun', '*.f')])
# Extension specfun
config.add_extension('specfun',
sources=['specfun.pyf'],
f2py_options=['--no-wrap-functions'],
define_macros=[],
libraries=['sc_specfun'])
# Extension _ufuncs
config.add_extension('_ufuncs',
libraries=[
'sc_amos', 'sc_c_misc', 'sc_cephes', 'sc_mach',
'sc_cdf', 'sc_specfun'
],
depends=[
"_logit.h", "cephes.h", "amos_wrappers.h",
"cdf_wrappers.h", "specfun_wrappers.h",
"c_misc/misc.h", "cephes/mconf.h",
"cephes/cephes_names.h"
],
sources=[
'_ufuncs.c', 'sf_error.c', '_logit.c.src',
"amos_wrappers.c", "cdf_wrappers.c",
"specfun_wrappers.c"
],
include_dirs=[curdir],
define_macros=define_macros,
extra_info=get_info("npymath"))
# Extension _ufuncs_cxx
config.add_extension('_ufuncs_cxx',
sources=[
'_ufuncs_cxx.cxx',
'sf_error.c',
'_faddeeva.cxx',
'Faddeeva.cc',
],
libraries=['sc_cephes'],
include_dirs=[curdir],
define_macros=define_macros,
extra_info=get_info("npymath"))
config.add_data_files('tests/*.py')
config.add_data_files('tests/data/README')
config.add_data_files('tests/data/*.npz')
return config
versioneer.parentdir_prefix = 'numba-'
cmdclass = versioneer.get_cmdclass()
setup_args = {
'long_description': open('README.md').read(),
}
GCCFLAGS = ["-std=c89", "-Wdeclaration-after-statement", "-Werror"]
if os.environ.get("NUMBA_GCC_FLAGS"):
CFLAGS = GCCFLAGS
else:
CFLAGS = []
npymath_info = np_misc.get_info('npymath')
ext_dynfunc = Extension(name='numba._dynfunc', sources=['numba/_dynfunc.c'],
extra_compile_args=CFLAGS,
depends=["numba/_pymodule.h"])
ext_numpyadapt = Extension(name='numba._numpyadapt',
sources=['numba/_numpyadapt.c'],
include_dirs=[numpy.get_include()],
extra_compile_args=CFLAGS,
depends=["numba/_pymodule.h"])
ext_npymath_exports = Extension(name='numba._npymath_exports',
sources=['numba/_npymath_exports.c'],
include_dirs=npymath_info['include_dirs'],
libraries=npymath_info['libraries'],
def get_ext_modules():
"""
Return a list of Extension instances for the setup() call.
"""
# Note we don't import Numpy at the toplevel, since setup.py
# should be able to run without Numpy for pip to discover the
# build dependencies
import numpy.distutils.misc_util as np_misc
# Inject required options for extensions compiled against the Numpy
# C API (include dirs, library dirs etc.)
np_compile_args = np_misc.get_info('npymath')
ext_dynfunc = Extension(name='numba._dynfunc',
sources=['numba/_dynfuncmod.c'],
extra_compile_args=CFLAGS,
depends=['numba/_pymodule.h',
'numba/_dynfunc.c'])
ext_dispatcher = Extension(name="numba._dispatcher",
sources=['numba/_dispatcher.c',
'numba/_typeof.c',
'numba/_hashtable.c',
'numba/_dispatcherimpl.cpp',
'numba/typeconv/typeconv.cpp'],
depends=["numba/_pymodule.h",
"numba/_dispatcher.h",
"numba/_typeof.h",
"numba/_hashtable.h"],
**np_compile_args)
ext_helperlib = Extension(name="numba._helperlib",
sources=["numba/_helpermod.c",
"numba/_math_c99.c"],
extra_compile_args=CFLAGS,
extra_link_args=install_name_tool_fixer,
depends=["numba/_pymodule.h",
"numba/_math_c99.h",
"numba/_helperlib.c",
"numba/_lapack.c",
"numba/_npymath_exports.c",
"numba/_random.c",
"numba/mathnames.inc"],
**np_compile_args)
ext_typeconv = Extension(name="numba.typeconv._typeconv",
sources=["numba/typeconv/typeconv.cpp",
"numba/typeconv/_typeconv.cpp"],
depends=["numba/_pymodule.h"],
)
ext_npyufunc_ufunc = Extension(name="numba.npyufunc._internal",
sources=["numba/npyufunc/_internal.c"],
depends=["numba/npyufunc/_ufunc.c",
"numba/npyufunc/_internal.h",
"numba/_pymodule.h"],
**np_compile_args)
tbb_root = os.getenv('TBBROOT')
if tbb_root:
print("Using TBBROOT=", tbb_root)
ext_npyufunc_workqueue = Extension(
name='numba.npyufunc.workqueue',
sources=['numba/npyufunc/tbbpool.cpp', 'numba/npyufunc/gufunc_scheduler.cpp'],
depends=['numba/npyufunc/workqueue.h'],
include_dirs=[os.path.join(tbb_root, 'include')],
extra_compile_args=[] if sys.platform.startswith('win') else ['-std=c++11'],
libraries =['tbb'],
library_dirs=[os.path.join(tbb_root, 'lib', 'intel64', 'gcc4.4'), # for Linux
os.path.join(tbb_root, 'lib'), # for MacOS
os.path.join(tbb_root, 'lib', 'intel64', 'vc_mt'), # for Windows
],
)
else:
ext_npyufunc_workqueue = Extension(
name='numba.npyufunc.workqueue',
sources=['numba/npyufunc/workqueue.c', 'numba/npyufunc/gufunc_scheduler.cpp'],
depends=['numba/npyufunc/workqueue.h'])
ext_mviewbuf = Extension(name='numba.mviewbuf',
extra_link_args=install_name_tool_fixer,
sources=['numba/mviewbuf.c'])
ext_nrt_python = Extension(name='numba.runtime._nrt_python',
sources=['numba/runtime/_nrt_pythonmod.c',
'numba/runtime/nrt.c'],
depends=['numba/runtime/nrt.h',
'numba/_pymodule.h',
'numba/runtime/_nrt_python.c'],
**np_compile_args)
ext_jitclass_box = Extension(name='numba.jitclass._box',
sources=['numba/jitclass/_box.c'],
depends=['numba/_pymodule.h'],
)
ext_cuda_extras = Extension(name='numba.cuda.cudadrv._extras',
sources=['numba/cuda/cudadrv/_extras.c'],
depends=['numba/_pymodule.h'],
include_dirs=["numba"])
ext_modules = [ext_dynfunc, ext_dispatcher,
ext_helperlib, ext_typeconv,
ext_npyufunc_ufunc, ext_npyufunc_workqueue, ext_mviewbuf,
ext_nrt_python, ext_jitclass_box, ext_cuda_extras]
return ext_modules
cmdclass = {'clean': CleanCommand, 'build': build}
cmdclass["build_src"] = DummyBuildSrc
cmdclass["build_ext"] = CheckingBuildExt
# some linux distros require it
#NOTE: we are not currently using this but add it to Extension, if needed.
# libraries = ['m'] if 'win32' not in sys.platform else []
from numpy.distutils.misc_util import get_info
# Reset the cython exclusions file
init_cython_exclusion(CYTHON_EXCLUSION_FILE)
npymath_info = get_info("npymath")
ext_data = dict(kalman_loglike={
"name": "statsmodels/tsa/kalmanf/kalman_loglike.c",
"depends": ["statsmodels/src/capsule.h"],
"include_dirs": ["statsmodels/src"],
"sources": []
},
_hamilton_filter={
"name":
"statsmodels/tsa/regime_switching/_hamilton_filter.c",
"depends": [],
"include_dirs": [],
"sources": []
},
_kim_smoother={
"name": "statsmodels/tsa/regime_switching/_kim_smoother.c",
depends=tseries_depends + ['pandas/src/numpy_helper.h'],
sources=[srcpath('tseries', suffix=suffix),
'pandas/src/period.c',
'pandas/src/datetime/np_datetime.c',
'pandas/src/datetime/np_datetime_strings.c'],
include_dirs=[np.get_include()],
# pyrex_gdb=True,
# extra_compile_args=['-Wconversion']
)
sparse_ext = Extension('pandas._sparse',
sources=[srcpath('sparse', suffix=suffix)],
include_dirs=[np.get_include()])
npymath_info = get_info('npymath')
npymath_libdir = npymath_info['library_dirs'][0]
npymath_libdir = npymath_libdir.replace('\\\\', '\\')
ujson_ext = Extension('pandas._ujson',
sources=['pandas/src/ujson/python/ujson.c',
'pandas/src/ujson/python/objToJSON.c',
'pandas/src/ujson/python/JSONtoObj.c',
'pandas/src/ujson/lib/ultrajsonenc.c',
'pandas/src/ujson/lib/ultrajsondec.c',
'pandas/src/datetime/np_datetime.c'
],
include_dirs=['pandas/src/ujson/python',
'pandas/src/ujson/lib',
'pandas/src/datetime',
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from scipy._build_utils.compiler_helper import set_cxx_flags_hook
import numpy as np
config = Configuration('stats', parent_package, top_path)
config.add_data_dir('tests')
statlib_src = [join('statlib', '*.f')]
config.add_library('statlib', sources=statlib_src)
# add statlib module
config.add_extension('statlib',
sources=['statlib.pyf'],
f2py_options=['--no-wrap-functions'],
libraries=['statlib'],
depends=statlib_src)
# add _stats module
config.add_extension('_stats', sources=['_stats.c'])
# add mvn module
config.add_extension('mvn', sources=['mvn.pyf', 'mvndst.f'])
# add _sobol module
config.add_extension('_sobol', sources=['_sobol.c'])
config.add_data_files('_sobol_direction_numbers.npz')
# add _qmc_cy module
ext = config.add_extension('_qmc_cy', sources=['_qmc_cy.cxx'])
ext._pre_build_hook = set_cxx_flags_hook
# add BiasedUrn module
config.add_data_files('biasedurn.pxd')
from _generate_pyx import isNPY_OLD # type: ignore[import]
NPY_OLD = isNPY_OLD()
if NPY_OLD:
biasedurn_libs = []
biasedurn_libdirs = []
else:
biasedurn_libs = ['npyrandom', 'npymath']
biasedurn_libdirs = [
join(np.get_include(), '..', '..', 'random', 'lib')
]
biasedurn_libdirs += get_info('npymath')['library_dirs']
ext = config.add_extension(
'biasedurn',
sources=[
'biasedurn.cxx', 'biasedurn/impls.cpp', 'biasedurn/fnchyppr.cpp',
'biasedurn/wnchyppr.cpp', 'biasedurn/stoc1.cpp',
'biasedurn/stoc3.cpp'
],
include_dirs=[np.get_include()],
library_dirs=biasedurn_libdirs,
libraries=biasedurn_libs,
define_macros=[('R_BUILD', None)],
language='c++',
extra_compile_args=['-Wno-narrowing'] if system() == 'Darwin' else [],
depends=['biasedurn/stocR.h'],
)
ext._pre_build_hook = pre_build_hook
# add boost stats distributions
config.add_subpackage('_boost')
# Type stubs
config.add_data_files('*.pyi')
return config
cmdclass = {'clean': CleanCommand,
'build': build}
cmdclass["build_src"] = DummyBuildSrc
cmdclass["build_ext"] = CheckingBuildExt
# some linux distros require it
#NOTE: we are not currently using this but add it to Extension, if needed.
# libraries = ['m'] if 'win32' not in sys.platform else []
from numpy.distutils.misc_util import get_info
npymath_info = get_info("npymath")
ext_data = dict(
kalman_loglike = {"name" : "statsmodels/tsa/kalmanf/kalman_loglike.c",
"depends" : ["statsmodels/src/capsule.h"],
"include_dirs": ["statsmodels/src"],
"sources" : []},
_statespace = {"name" : "statsmodels/tsa/statespace/_statespace.c",
"depends" : ["statsmodels/src/capsule.h"],
"include_dirs": ["statsmodels/src"] + npymath_info['include_dirs'],
"libraries": npymath_info['libraries'],
"library_dirs": npymath_info['library_dirs'],
"sources" : []},
linbin = {"name" : "statsmodels/nonparametric/linbin.c",
"depends" : [],
"sources" : []},
_smoothers_lowess = {"name" : "statsmodels/nonparametric/_smoothers_lowess.c",
]
]
if not lapack_info:
# No LAPACK in NumPy
print('### Warning: Using unoptimized blas/lapack @@@')
MODULE_SOURCES.extend(lapack_lite_files[:-1]) # all but f2c.h
MODULE_DEPENDENCIES.extend(lapack_lite_files)
else:
if sys.platform == 'win32':
print('### Warning: python.xerbla.c is disabled ###')
else:
MODULE_SOURCES.extend(lapack_lite_files[:1]) # python_xerbla.c
MODULE_DEPENDENCIES.extend(lapack_lite_files[:1])
npymath_info = np_misc_util.get_info('npymath')
extra_opts = copy.deepcopy(lapack_info)
for key, val in npymath_info.items():
if extra_opts.get(key):
extra_opts[key].extend(val)
else:
extra_opts[key] = copy.deepcopy(val)
# make sure the compiler can find conditional_omp.h
extra_opts['include_dirs'] += [os.path.join(C_SRC_PATH)]
cmdclass = versioneer.get_cmdclass()
if "GULINALG_DISABLE_OPENMP" not in os.environ:
# OpenMP will be disabled unless omp_test_c below compiles successfully
import pyarrow as pa
from docs.source.buildscripts.sdc_build_doc import SDCBuildDoc
# Note we don't import Numpy at the toplevel, since setup.py
# should be able to run without Numpy for pip to discover the
# build dependencies
import numpy.distutils.misc_util as np_misc
import versioneer
# String constants for Intel SDC project configuration
# This name is used for wheel package build
SDC_NAME_STR = 'sdc'
# Inject required options for extensions compiled against the Numpy
# C API (include dirs, library dirs etc.)
np_compile_args = np_misc.get_info('npymath')
is_win = platform.system() == 'Windows'
is_osx = platform.system() == 'Darwin'
def readme():
with open('README.rst', encoding='utf-8') as f:
return f.read()
# package environment variable is PREFIX during build time
if 'CONDA_BUILD' in os.environ:
PREFIX_DIR = os.environ['PREFIX']
else:
PREFIX_DIR = os.environ['CONDA_PREFIX']
def get_ext_modules():
"""
Return a list of Extension instances for the setup() call.
"""
# Note we don't import Numpy at the toplevel, since setup.py
# should be able to run without Numpy for pip to discover the
# build dependencies
import numpy.distutils.misc_util as np_misc
# Inject required options for extensions compiled against the Numpy
# C API (include dirs, library dirs etc.)
np_compile_args = np_misc.get_info('npymath')
ext_dynfunc = Extension(name='numba._dynfunc',
sources=['numba/_dynfuncmod.c'],
extra_compile_args=CFLAGS,
depends=['numba/_pymodule.h',
'numba/_dynfunc.c'])
ext_dispatcher = Extension(name="numba._dispatcher",
sources=['numba/_dispatcher.c',
'numba/_typeof.c',
'numba/_hashtable.c',
'numba/_dispatcherimpl.cpp',
'numba/typeconv/typeconv.cpp'],
depends=["numba/_pymodule.h",
"numba/_dispatcher.h",
"numba/_typeof.h",
"numba/_hashtable.h"],
**np_compile_args)
ext_helperlib = Extension(name="numba._helperlib",
sources=["numba/_helpermod.c",
"numba/_math_c99.c"],
extra_compile_args=CFLAGS,
extra_link_args=install_name_tool_fixer,
depends=["numba/_pymodule.h",
"numba/_math_c99.h",
"numba/_helperlib.c",
"numba/_lapack.c",
"numba/_npymath_exports.c",
"numba/_random.c",
"numba/_dictobject.c",
"numba/mathnames.inc",],
**np_compile_args)
ext_typeconv = Extension(name="numba.typeconv._typeconv",
sources=["numba/typeconv/typeconv.cpp",
"numba/typeconv/_typeconv.cpp"],
depends=["numba/_pymodule.h"],
)
ext_npyufunc_ufunc = Extension(name="numba.npyufunc._internal",
sources=["numba/npyufunc/_internal.c"],
depends=["numba/npyufunc/_ufunc.c",
"numba/npyufunc/_internal.h",
"numba/_pymodule.h"],
**np_compile_args)
ext_npyufunc_workqueue_impls = []
def check_file_at_path(path2file):
"""
Takes a list as a path, a single glob (*) is permitted as an entry which
indicates that expansion at this location is required (i.e. version
might not be known).
"""
found = None
path2check = [os.path.split(os.path.split(sys.executable)[0])[0]]
path2check += [os.getenv(n, '') for n in ['CONDA_PREFIX', 'PREFIX']]
if sys.platform.startswith('win'):
path2check += [os.path.join(p, 'Library') for p in path2check]
for p in path2check:
if p:
if '*' in path2file:
globloc = path2file.index('*')
searchroot = os.path.join(*path2file[:globloc])
try:
potential_locs = os.listdir(os.path.join(p, searchroot))
except BaseException:
continue
searchfor = path2file[globloc + 1:]
for x in potential_locs:
potpath = os.path.join(p, searchroot, x, *searchfor)
if os.path.isfile(potpath):
found = p # the latest is used
elif os.path.isfile(os.path.join(p, *path2file)):
found = p # the latest is used
return found
# Search for Intel TBB, first check env var TBBROOT then conda locations
tbb_root = os.getenv('TBBROOT')
if not tbb_root:
tbb_root = check_file_at_path(['include', 'tbb', 'tbb.h'])
# Set various flags for use in TBB and openmp. On OSX, also find OpenMP!
have_openmp = True
if sys.platform.startswith('win'):
cpp11flags = []
ompcompileflags = ['-openmp']
omplinkflags = []
elif sys.platform.startswith('darwin'):
cpp11flags = ['-std=c++11']
# This is a bit unusual but necessary...
# llvm (clang) OpenMP is used for headers etc at compile time
# Intel OpenMP (libiomp5) provides the link library.
# They are binary compatible and may not safely coexist in a process, as
# libiomp5 is more prevalent and often linked in for NumPy it is used
# here!
ompcompileflags = ['-fopenmp']
omplinkflags = ['-fopenmp=libiomp5']
omppath = ['lib', 'clang', '*', 'include', 'omp.h']
have_openmp = check_file_at_path(omppath)
else:
cpp11flags = ['-std=c++11']
ompcompileflags = ['-fopenmp']
if platform.machine() == 'ppc64le':
omplinkflags = ['-fopenmp']
else:
omplinkflags = ['-fopenmp']
if tbb_root:
print("Using Intel TBB from:", tbb_root)
ext_npyufunc_tbb_workqueue = Extension(
name='numba.npyufunc.tbbpool',
sources=['numba/npyufunc/tbbpool.cpp', 'numba/npyufunc/gufunc_scheduler.cpp'],
depends=['numba/npyufunc/workqueue.h'],
include_dirs=[os.path.join(tbb_root, 'include')],
extra_compile_args=cpp11flags,
libraries =['tbb'], # TODO: if --debug or -g, use 'tbb_debug'
library_dirs=[os.path.join(tbb_root, 'lib', 'intel64', 'gcc4.4'), # for Linux
os.path.join(tbb_root, 'lib'), # for MacOS
os.path.join(tbb_root, 'lib', 'intel64', 'vc_mt'), # for Windows
],
)
ext_npyufunc_workqueue_impls.append(ext_npyufunc_tbb_workqueue)
else:
print("TBB not found")
# Disable OpenMP if we are building a wheel or
# forced by user with NUMBA_NO_OPENMP=1
if is_building_wheel() or os.getenv('NUMBA_NO_OPENMP'):
print("OpenMP disabled")
elif have_openmp:
print("Using OpenMP from:", have_openmp)
# OpenMP backed work queue
ext_npyufunc_omppool = Extension( name='numba.npyufunc.omppool',
sources=['numba/npyufunc/omppool.cpp',
'numba/npyufunc/gufunc_scheduler.cpp'],
depends=['numba/npyufunc/workqueue.h'],
extra_compile_args=ompcompileflags + cpp11flags,
extra_link_args = omplinkflags)
ext_npyufunc_workqueue_impls.append(ext_npyufunc_omppool)
else:
print("OpenMP not found")
# Build the Numba workqueue implementation irrespective of whether the TBB
# version is built. Users can select a backend via env vars.
ext_npyufunc_workqueue = Extension(
name='numba.npyufunc.workqueue',
sources=['numba/npyufunc/workqueue.c', 'numba/npyufunc/gufunc_scheduler.cpp'],
depends=['numba/npyufunc/workqueue.h'])
ext_npyufunc_workqueue_impls.append(ext_npyufunc_workqueue)
ext_mviewbuf = Extension(name='numba.mviewbuf',
extra_link_args=install_name_tool_fixer,
sources=['numba/mviewbuf.c'])
ext_nrt_python = Extension(name='numba.runtime._nrt_python',
sources=['numba/runtime/_nrt_pythonmod.c',
'numba/runtime/nrt.c'],
depends=['numba/runtime/nrt.h',
'numba/_pymodule.h',
'numba/runtime/_nrt_python.c'],
**np_compile_args)
ext_jitclass_box = Extension(name='numba.jitclass._box',
sources=['numba/jitclass/_box.c'],
depends=['numba/_pymodule.h'],
)
ext_cuda_extras = Extension(name='numba.cuda.cudadrv._extras',
sources=['numba/cuda/cudadrv/_extras.c'],
depends=['numba/_pymodule.h'],
include_dirs=["numba"])
ext_modules = [ext_dynfunc, ext_dispatcher, ext_helperlib, ext_typeconv,
ext_npyufunc_ufunc, ext_mviewbuf, ext_nrt_python,
ext_jitclass_box, ext_cuda_extras]
ext_modules += ext_npyufunc_workqueue_impls
return ext_modules
def get_ext_modules():
"""
Return a list of Extension instances for the setup() call.
"""
# Note we don't import Numpy at the toplevel, since setup.py
# should be able to run without Numpy for pip to discover the
# build dependencies
import numpy.distutils.misc_util as np_misc
# Inject required options for extensions compiled against the Numpy
# C API (include dirs, library dirs etc.)
np_compile_args = np_misc.get_info('npymath')
ext_dynfunc = Extension(name='numba._dynfunc',
sources=['numba/_dynfuncmod.c'],
extra_compile_args=CFLAGS,
depends=['numba/_pymodule.h',
'numba/_dynfunc.c'])
ext_dispatcher = Extension(name="numba._dispatcher",
sources=['numba/_dispatcher.c',
'numba/_typeof.c',
'numba/_hashtable.c',
'numba/_dispatcherimpl.cpp',
'numba/typeconv/typeconv.cpp'],
depends=["numba/_pymodule.h",
"numba/_dispatcher.h",
"numba/_typeof.h",
"numba/_hashtable.h"],
**np_compile_args)
ext_helperlib = Extension(name="numba._helperlib",
sources=["numba/_helpermod.c",
"numba/_math_c99.c"],
extra_compile_args=CFLAGS,
extra_link_args=install_name_tool_fixer,
depends=["numba/_pymodule.h",
"numba/_math_c99.h",
"numba/_helperlib.c",
"numba/_lapack.c",
"numba/_npymath_exports.c",
"numba/_random.c",
"numba/mathnames.inc"],
**np_compile_args)
ext_typeconv = Extension(name="numba.typeconv._typeconv",
sources=["numba/typeconv/typeconv.cpp",
"numba/typeconv/_typeconv.cpp"],
depends=["numba/_pymodule.h"],
)
ext_npyufunc_ufunc = Extension(name="numba.npyufunc._internal",
sources=["numba/npyufunc/_internal.c"],
depends=["numba/npyufunc/_ufunc.c",
"numba/npyufunc/_internal.h",
"numba/_pymodule.h"],
**np_compile_args)
tbb_root = os.getenv('TBBROOT')
if tbb_root:
print("Using TBBROOT=", tbb_root)
ext_npyufunc_workqueue = Extension(
name='numba.npyufunc.workqueue',
sources=['numba/npyufunc/tbbpool.cpp', 'numba/npyufunc/gufunc_scheduler.cpp'],
depends=['numba/npyufunc/workqueue.h'],
include_dirs=[os.path.join(tbb_root, 'include')],
extra_compile_args=[] if sys.platform.startswith('win') else ['-std=c++11'],
libraries =['tbb'],
library_dirs=[os.path.join(tbb_root, 'lib', 'intel64', 'gcc4.4'), # for Linux
os.path.join(tbb_root, 'lib'), # for MacOS
os.path.join(tbb_root, 'lib', 'intel64', 'vc_mt'), # for Windows
],
)
else:
ext_npyufunc_workqueue = Extension(
name='numba.npyufunc.workqueue',
sources=['numba/npyufunc/workqueue.c', 'numba/npyufunc/gufunc_scheduler.cpp'],
depends=['numba/npyufunc/workqueue.h'])
ext_mviewbuf = Extension(name='numba.mviewbuf',
extra_link_args=install_name_tool_fixer,
sources=['numba/mviewbuf.c'])
ext_nrt_python = Extension(name='numba.runtime._nrt_python',
sources=['numba/runtime/_nrt_pythonmod.c',
'numba/runtime/nrt.c'],
depends=['numba/runtime/nrt.h',
'numba/_pymodule.h',
'numba/runtime/_nrt_python.c'],
**np_compile_args)
ext_jitclass_box = Extension(name='numba.jitclass._box',
sources=['numba/jitclass/_box.c'],
depends=['numba/_pymodule.h'],
)
ext_cuda_extras = Extension(name='numba.cuda.cudadrv._extras',
sources=['numba/cuda/cudadrv/_extras.c'],
depends=['numba/_pymodule.h'],
include_dirs=["numba"])
ext_modules = [ext_dynfunc, ext_dispatcher,
ext_helperlib, ext_typeconv,
ext_npyufunc_ufunc, ext_npyufunc_workqueue, ext_mviewbuf,
ext_nrt_python, ext_jitclass_box, ext_cuda_extras]
return ext_modules
def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info as get_system_info
config = Configuration("special", parent_package, top_path)
define_macros = []
if sys.platform == "win32":
# define_macros.append(('NOINFINITIES',None))
# define_macros.append(('NONANS',None))
define_macros.append(("_USE_MATH_DEFINES", None))
curdir = os.path.abspath(os.path.dirname(__file__))
inc_dirs = [get_python_inc(), os.path.join(curdir, "c_misc")]
if inc_dirs[0] != get_python_inc(plat_specific=1):
inc_dirs.append(get_python_inc(plat_specific=1))
inc_dirs.insert(0, get_numpy_include_dirs())
# C libraries
c_misc_src = [join("c_misc", "*.c")]
c_misc_hdr = [join("c_misc", "*.h")]
cephes_src = [join("cephes", "*.c")]
cephes_hdr = [join("cephes", "*.h")]
config.add_library(
"sc_c_misc",
sources=c_misc_src,
include_dirs=[curdir] + inc_dirs,
depends=(cephes_hdr + cephes_src + c_misc_hdr + cephes_hdr + ["*.h"]),
macros=define_macros,
)
config.add_library(
"sc_cephes",
sources=cephes_src,
include_dirs=[curdir] + inc_dirs,
depends=(cephes_hdr + ["*.h"]),
macros=define_macros,
)
# Fortran/C++ libraries
mach_src = [join("mach", "*.f")]
amos_src = [join("amos", "*.f")]
cdf_src = [join("cdflib", "*.f")]
specfun_src = [join("specfun", "*.f")]
config.add_library("sc_mach", sources=mach_src, config_fc={"noopt": (__file__, 1)})
config.add_library("sc_amos", sources=amos_src)
config.add_library("sc_cdf", sources=cdf_src)
config.add_library("sc_specfun", sources=specfun_src)
# Extension specfun
config.add_extension(
"specfun",
sources=["specfun.pyf"],
f2py_options=["--no-wrap-functions"],
depends=specfun_src,
define_macros=[],
libraries=["sc_specfun"],
)
# Extension _ufuncs
headers = ["*.h", join("c_misc", "*.h"), join("cephes", "*.h")]
ufuncs_src = ["_ufuncs.c", "sf_error.c", "_logit.c.src", "amos_wrappers.c", "cdf_wrappers.c", "specfun_wrappers.c"]
ufuncs_dep = headers + ufuncs_src + amos_src + c_misc_src + cephes_src + mach_src + cdf_src + specfun_src
cfg = dict(get_system_info("lapack_opt"))
cfg.setdefault("include_dirs", []).extend([curdir] + inc_dirs + [numpy.get_include()])
cfg.setdefault("libraries", []).extend(["sc_amos", "sc_c_misc", "sc_cephes", "sc_mach", "sc_cdf", "sc_specfun"])
cfg.setdefault("define_macros", []).extend(define_macros)
config.add_extension("_ufuncs", depends=ufuncs_dep, sources=ufuncs_src, extra_info=get_info("npymath"), **cfg)
# Extension _ufuncs_cxx
ufuncs_cxx_src = ["_ufuncs_cxx.cxx", "sf_error.c", "_faddeeva.cxx", "Faddeeva.cc"]
ufuncs_cxx_dep = headers + ufuncs_cxx_src + cephes_src + ["*.hh"]
config.add_extension(
"_ufuncs_cxx",
sources=ufuncs_cxx_src,
depends=ufuncs_cxx_dep,
include_dirs=[curdir],
define_macros=define_macros,
extra_info=get_info("npymath"),
)
cfg = dict(get_system_info("lapack_opt"))
config.add_extension("_ellip_harm_2", sources=["_ellip_harm_2.c", "sf_error.c"], **cfg)
# combinatoris
config.add_extension("_comb", sources=["_comb.c"])
config.add_data_files("tests/*.py")
config.add_data_files("tests/data/README")
config.add_data_files("tests/data/*.npz")
return config
