def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, get_standard_file, BlasNotFoundError
config = Configuration("glm", parent_package, top_path)
site_cfg = ConfigParser()
site_cfg.read(get_standard_file("site.cfg"))
# cd fast needs CBLAS
blas_info = get_info("blas_opt", 0)
if (not blas_info) or (("NO_ATLAS_INFO", 1) in blas_info.get("define_macros", [])):
cblas_libs = ["cblas"]
blas_info.pop("libraries", None)
else:
cblas_libs = blas_info.pop("libraries", [])
config.add_extension(
"cd_fast",
sources=[join("src", "cd_fast.c")],
libraries=cblas_libs,
include_dirs=[join("..", "src", "cblas"), numpy.get_include(), blas_info.pop("include_dirs", [])],
extra_compile_args=blas_info.pop("extra_compile_args", []),
**blas_info
)
# add other directories
config.add_subpackage("tests")
config.add_subpackage("benchmarks")
config.add_subpackage("sparse")
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, get_standard_file, BlasNotFoundError
config = Configuration('glm', parent_package, top_path)
site_cfg = ConfigParser()
site_cfg.read(get_standard_file('site.cfg'))
# cd fast needs CBLAS
blas_info = get_info('blas_opt', 0)
if (not blas_info) or (
('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])) :
cblas_libs = ['cblas']
blas_info.pop('libraries', None)
else:
cblas_libs = blas_info.pop('libraries', [])
config.add_extension('cd_fast',
sources=[join('src', 'cd_fast.c')],
libraries=cblas_libs,
include_dirs=[join('..', 'src', 'cblas'),
numpy.get_include(),
blas_info.pop('include_dirs', [])],
extra_compile_args=blas_info.pop('extra_compile_args', []),
**blas_info
)
# add other directories
config.add_subpackage('tests')
config.add_subpackage('benchmarks')
config.add_subpackage('sparse')
return config
def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_standard_file
config = Configuration("sparse", parent_package, top_path)
site_cfg = ConfigParser()
site_cfg.read(get_standard_file("site.cfg"))
# add other directories
# config.add_subpackage('tests')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, get_standard_file, BlasNotFoundError
config = Configuration('preprocessing', parent_package, top_path)
site_cfg = ConfigParser()
site_cfg.read(get_standard_file('site.cfg'))
config.add_subpackage('tests')
config.add_subpackage('sparse')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_standard_file
config = Configuration('sparse', parent_package, top_path)
site_cfg = ConfigParser()
site_cfg.read(get_standard_file('site.cfg'))
config.add_extension('sgd_fast_sparse',
sources=[join('src', 'sgd_fast_sparse.c')],
include_dirs=[numpy.get_include()]
)
# add other directories
# config.add_subpackage('tests')
return config
def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info
from numpy.distutils.system_info import get_standard_file
from numpy.distutils.system_info import BlasNotFoundError
config = Configuration("sparse", parent_package, top_path)
site_cfg = ConfigParser()
site_cfg.read(get_standard_file("site.cfg"))
config.add_extension(
"_preprocessing", sources=[join("src", "_preprocessing.c")], include_dirs=[numpy.get_include()]
)
return config
def get_nipy_info():
""" Reuse numpy's distutils to get and store information about nipy
in the site.cfg.
"""
from numpy.distutils.system_info import get_standard_file
files = get_standard_file('site.cfg')
cp = ConfigParser(NIPY_DEFAULTS)
cp.read(files)
if not cp.has_section('nipy'):
cp.add_section('nipy')
info = dict(cp.items('nipy'))
for key, value in info.items():
if value.startswith('~'):
info[key] = os.path.expanduser(value)
# Ugly fix for bug 409269
if 'libraries' in info and isinstance(info['libraries'], basestring):
info['libraries'] = [info['libraries']]
# End of ugly fix
return info
def get_nipy_info():
""" Reuse numpy's distutils to get and store information about nipy
in the site.cfg.
"""
from numpy.distutils.system_info import get_standard_file
files = get_standard_file('site.cfg')
cp = ConfigParser(NIPY_DEFAULTS)
cp.read(files)
if not cp.has_section('nipy'):
cp.add_section('nipy')
info = dict(cp.items('nipy'))
for key, value in info.items():
if value.startswith('~'):
info[key] = os.path.expanduser(value)
# Ugly fix for bug 409269
if 'libraries' in info and isinstance(info['libraries'], string_types):
info['libraries'] = [info['libraries']]
# End of ugly fix
return info
def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info
from numpy.distutils.system_info import get_standard_file
from numpy.distutils.system_info import BlasNotFoundError
config = Configuration("glm", parent_package, top_path)
site_cfg = ConfigParser()
site_cfg.read(get_standard_file("site.cfg"))
config.add_extension(
"cd_fast_sparse",
sources=[join("src", "cd_fast_sparse.c")],
include_dirs=[numpy.get_include()],
extra_compile_args=["-std=c99"],
)
# add other directories
config.add_subpackage("tests")
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, get_standard_file, \
BlasNotFoundError
config = Configuration('svm', parent_package, top_path)
config.add_subpackage('tests')
config.add_subpackage('sparse')
# we parse site.cfg file for section libsvm
site_cfg = ConfigParser()
site_cfg.read(get_standard_file('site.cfg'))
# Section LibSVM
libsvm_includes = [numpy.get_include()]
libsvm_libraries = []
libsvm_library_dirs = []
libsvm_sources = [join('src', 'libsvm', '_libsvm.c')]
libsvm_depends = [join('src', 'libsvm', 'libsvm_helper.c')]
# we try to link against system-wide libsvm
if site_cfg.has_section('libsvm'):
libsvm_includes.append(site_cfg.get('libsvm', 'include_dirs'))
libsvm_libraries.append(site_cfg.get('libsvm', 'libraries'))
libsvm_library_dirs.append(site_cfg.get('libsvm', 'library_dirs'))
else:
# if not specified, we build our own libsvm
libsvm_sources.append(join('src', 'libsvm', 'svm.cpp'))
libsvm_depends.append(join('src', 'libsvm', 'svm.h'))
config.add_extension('_libsvm',
sources=libsvm_sources,
include_dirs=libsvm_includes,
libraries=libsvm_libraries,
library_dirs=libsvm_library_dirs,
depends=libsvm_depends,
)
### liblinear module
blas_sources = [join('src', 'blas', 'daxpy.c'),
join('src', 'blas', 'ddot.c'),
join('src', 'blas', 'dnrm2.c'),
join('src', 'blas', 'dscal.c')]
liblinear_sources = [join('src', 'liblinear', '_liblinear.c'),
join('src', 'liblinear', '*.cpp')]
liblinear_depends = [join('src', 'liblinear', '*.h'),
join('src', 'liblinear', 'liblinear_helper.c')]
# we try to link agains system-wide blas
blas_info = get_info('blas_opt', 0)
if not blas_info:
config.add_library('blas', blas_sources)
warnings.warn(BlasNotFoundError.__doc__)
config.add_extension('_liblinear',
sources=liblinear_sources,
libraries = blas_info.pop('libraries', ['blas']),
include_dirs=['src',
numpy.get_include(),
blas_info.pop('include_dirs', [])],
depends=liblinear_depends,
**blas_info)
## end liblinear module
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, get_standard_file, \
BlasNotFoundError
config = Configuration('learn', parent_package, top_path)
site_cfg = ConfigParser()
site_cfg.read(get_standard_file('site.cfg'))
config.add_subpackage('datasets')
config.add_subpackage('features')
config.add_subpackage('features/tests')
config.add_subpackage('cluster')
config.add_subpackage('cluster/tests')
config.add_subpackage('covariance')
config.add_subpackage('covariance/tests')
config.add_subpackage('feature_selection')
config.add_subpackage('feature_selection/tests')
config.add_subpackage('sparse')
config.add_subpackage('sparse/tests/')
config.add_subpackage('utils')
config.add_subpackage('utils/tests')
config.add_subpackage('externals')
# Section LibSVM
libsvm_includes = [numpy.get_include()]
libsvm_libraries = []
libsvm_library_dirs = []
libsvm_sources = [join('src', 'libsvm', '_libsvm.c')]
# we try to link against system-wide libsvm
if site_cfg.has_section('libsvm'):
libsvm_includes.append(site_cfg.get('libsvm', 'include_dirs'))
libsvm_libraries.append(site_cfg.get('libsvm', 'libraries'))
libsvm_library_dirs.append(site_cfg.get('libsvm', 'library_dirs'))
else:
# if not specified, we build our own libsvm
libsvm_sources.append(join('src', 'libsvm', 'svm.cpp'))
config.add_extension('_libsvm',
sources=libsvm_sources,
include_dirs=libsvm_includes,
libraries=libsvm_libraries,
library_dirs=libsvm_library_dirs,
depends=[join('src', 'libsvm', 'svm.h'),
join('src', 'libsvm', 'libsvm_helper.c')],
# add this for gdb debug
extra_compile_args=['-O0 -fno-inline']
)
### liblinear module
blas_sources = [join('src', 'blas', 'daxpy.c'),
join('src', 'blas', 'ddot.c'),
join('src', 'blas', 'dnrm2.c'),
join('src', 'blas', 'dscal.c')]
liblinear_sources = [join('src', 'liblinear', '_liblinear.c'),
join('src', 'liblinear', '*.cpp')]
# we try to link agains system-wide blas
blas_info = get_info('blas_opt', 0)
if not blas_info:
config.add_library('blas', blas_sources)
warnings.warn(BlasNotFoundError.__doc__)
config.add_extension('_liblinear',
sources=liblinear_sources,
libraries = blas_info.pop('libraries', ['blas']),
include_dirs=['src',
numpy.get_include(),
blas_info.pop('include_dirs', [])],
depends=[join('src', 'liblinear', '*.h')],
**blas_info)
## end liblinear module
# minilear needs cblas, fortran-compiled BLAS will not be sufficient
blas_info = get_info('blas_opt', 0)
if (not blas_info) or (
('NO_ATLAS_INFO', 1) in blas_info.get('define_macros', [])) :
config.add_library('cblas',
sources=[
join('src', 'cblas', '*.c'),
]
)
cblas_libs = ['cblas']
blas_info.pop('libraries', None)
else:
cblas_libs = blas_info.pop('libraries', [])
minilearn_sources = [
join('src', 'minilearn', 'lars.c'),
join('src', 'minilearn', '_minilearn.c')]
config.add_extension('_minilearn',
sources = minilearn_sources,
libraries = cblas_libs,
include_dirs=[join('src', 'minilearn'),
join('src', 'cblas'),
numpy.get_include(),
blas_info.pop('include_dirs', [])],
extra_compile_args=['-std=c99'] + \
blas_info.pop('extra_compile_args', []),
**blas_info
)
config.add_extension('ball_tree',
sources=[join('src', 'BallTree.cpp')],
include_dirs=[numpy.get_include()]
)
# this has to be build *after* cblas
config.add_subpackage('glm')
config.add_subpackage('utils')
# add the test directory
config.add_subpackage('tests')
return config
def _get_standard_file(fname):
try:
from numpy.distutils.system_info import get_standard_file
return get_standard_file(fname)
except ImportError:
return fname
