def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info
config = Configuration("dsolve", parent_package, top_path)
config.add_data_dir("tests")
lapack_opt = get_info("lapack_opt", notfound_action=2)
if sys.platform == "win32":
superlu_defs = [("NO_TIMER", 1)]
else:
superlu_defs = []
superlu_defs.append(("USE_VENDOR_BLAS", 1))
superlu_src = join(dirname(__file__), "SuperLU", "SRC")
sources = list(glob.glob(join(superlu_src, "*.c")))
headers = list(glob.glob(join(superlu_src, "*.h")))
if os.name == "nt" and ("FPATH" in os.environ or "MKLROOT" in os.environ):
# when using MSVC + MKL, lsame is already in MKL
sources.remove(join(superlu_src, "lsame.c"))
config.add_library("superlu_src", sources=sources, macros=superlu_defs, include_dirs=[superlu_src])
# Extension
config.add_extension(
"_superlu",
sources=["_superlumodule.c", "_superlu_utils.c", "_superluobject.c"],
libraries=["superlu_src"],
depends=(sources + headers),
extra_info=lapack_opt,
)
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
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'],
)
return config
def configuration(parent_package='', top_path=None):
plat_specifier = ".%s-%s" % (get_platform(), sys.version[0:3])
inc_dir = ['build/temp%s' % plat_specifier]
config = Configuration('tt', parent_package, top_path)
config.add_include_dirs(inc_dir)
config.set_options(
ignore_setup_xxx_py=True,
assume_default_configuration=True,
delegate_options_to_subpackages=True,
quiet=False,
)
config.add_library('print_lib', sources=[join(PRINT_DIR, x) for x in PRINT_SRC])
config.add_library('mytt', sources=[join(TTFORT_DIR, x) for x in TTFORT_SRC])
config.add_subpackage('core')
config.add_subpackage('amen')
config.add_subpackage('ksl')
config.add_subpackage('eigb')
config.add_subpackage('maxvol')
config.add_subpackage('cross')
config.add_subpackage('optimize')
config.add_subpackage('utils')
config.add_subpackage('riemannian')
return config
def configuration(parent_package='', top_path=None or ''):
from numpy.distutils.misc_util import Configuration
config = Configuration('',parent_package,top_path)
flibname = modulename + '_fortran_f2py'
if fortran_files:
config.add_library(flibname,
sources = fortran_files)
libraries.insert(0,flibname)
for module_info in module_infos:
name = module_info['name']
c_sources = module_info['c_sources']
f_sources = module_info['f_sources']
language = module_info['language']
if f_sources:
f_lib = '%s_f_wrappers_f2py' % (name)
config.add_library(f_lib, sources = f_sources)
libs = [f_lib] + libraries
else:
libs = libraries
config.add_extension(name,
sources=c_sources + c_files,
libraries = libs,
define_macros = define_macros,
undef_macros = undef_macros,
include_dirs = include_dirs,
extra_objects = extra_objects,
language = language,
)
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.system_info import get_info, NotFoundError
from numpy.distutils.misc_util import Configuration
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError,'no lapack/blas resources found'
config = Configuration('arpack', parent_package, top_path)
arpack_sources=[join('ARPACK','SRC', '*.f')]
arpack_sources.extend([join('ARPACK','UTIL', '*.f')])
# arpack_sources.extend([join('ARPACK','BLAS', '*.f')])
arpack_sources.extend([join('ARPACK','LAPACK', '*.f')])
config.add_library('arpack', sources=arpack_sources,
include_dirs=[join('ARPACK', 'SRC')])
config.add_extension('_arpack',
sources='arpack.pyf.src',
libraries=['arpack'],
extra_info = lapack_opt
)
config.add_data_dir('tests')
return config
def configuration(parent_package='', top_path=None):
# http://docs.scipy.org/doc/numpy/reference/distutils.html#numpy.distutils.misc_util.Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration("carmcmc", parent_package, top_path)
config.version = extension_version
config.add_data_dir((".", "carmcmc"))
config.add_library(
"carmcmc",
sources=["carmcmc.cpp", "carpack.cpp", "kfilter.cpp", "proposals.cpp", "samplers.cpp", "random.cpp",
"steps.cpp"],
include_dirs=include_dirs,
library_dirs=library_dirs,
libraries=["boost_python", "boost_filesystem", "boost_system", "armadillo"],
extra_compiler_args=compiler_args
)
config.add_extension(
"_carmcmc",
sources=["boost_python_wrapper.cpp", "carmcmc.cpp"],
include_dirs=include_dirs,
library_dirs=library_dirs,
libraries=["boost_python", "boost_filesystem", "boost_system", "armadillo", "carmcmc"],
extra_compile_args=compiler_args
)
config.add_data_dir(("../../../../include", "include"))
config.add_data_dir(("../../../../examples", "examples"))
config.test_suite = "tests/testCarmcmc"
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('fftpack',parent_package, top_path)
config.add_data_dir('tests')
config.add_data_dir('benchmarks')
config.add_library('dfftpack',
sources=[join('src/dfftpack','*.f')])
sources = ['fftpack.pyf','src/zfft.c','src/drfft.c','src/zrfft.c',
'src/zfftnd.c']
config.add_extension('_fftpack',
sources=sources,
libraries=['dfftpack'],
depends=['src/zfft_fftpack.c', 'src/drfft_fftpack.c',
'src/zfftnd_fftpack.c'])
config.add_extension('convolve',
sources=['convolve.pyf','src/convolve.c'],
libraries=['dfftpack'],
)
return config
def configuration(parent_package='', top_path=None):
expokit_src = [join(EXPM_DIR, x) for x in EXPOKIT_SRC]
ttksl_src = [join(TTFORT_DIR, x) for x in TTKSL_SRC]
ttksl_src.append('tt_ksl.pyf')
config = Configuration('ksl', parent_package, top_path)
config.add_library(
'expokit',
sources=expokit_src,
)
config.add_extension(
'dyn_tt',
sources=ttksl_src,
depends=[
'print_lib',
'expokit',
'mytt',
],
libraries=[
'print_lib',
'expokit',
'mytt',
],
)
return config
def configuration(parent_package='', top_path=None):
import warnings
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, BlasNotFoundError
config = Configuration('odr', parent_package, top_path)
libodr_files = ['d_odr.f',
'd_mprec.f',
'dlunoc.f']
blas_info = get_info('blas_opt')
if blas_info:
libodr_files.append('d_lpk.f')
else:
warnings.warn(BlasNotFoundError.__doc__)
libodr_files.append('d_lpkbls.f')
odrpack_src = [join('odrpack', x) for x in libodr_files]
config.add_library('odrpack', sources=odrpack_src)
sources = ['__odrpack.c']
libraries = ['odrpack'] + blas_info.pop('libraries', [])
include_dirs = ['.'] + blas_info.pop('include_dirs', [])
config.add_extension('__odrpack',
sources=sources,
libraries=libraries,
include_dirs=include_dirs,
depends=(['odrpack.h'] + odrpack_src),
**blas_info
)
config.add_data_dir('tests')
return config
def configuration(parent_package='',top_path=None):
sys.argv.extend ( ['config_fc', '--fcompiler=gnu95'])
config = Configuration('tt', parent_package, top_path)
config.set_options(ignore_setup_xxx_py=True,
assume_default_configuration=True,
delegate_options_to_subpackages=True,
quiet=False,
)
plat_specifier = ".%s-%s" % (get_platform(), sys.version[0:3])
inc_dir = ['build/temp%s' % plat_specifier]
tt_dir = 'tt-fort'
tt_src = ['nan.f90', 'timef.f90', 'say.f90', 'rnd.f90', 'ptype.f90', 'sort.f90', 'trans.f90', 'ort.f90',
'mat.f90', 'check.f90', 'lr.f90', 'maxvol.f90', 'svd.f90', 'matrix_util.f90', 'tt.f90', 'ttaux.f90',
'ttop.f90', 'ttio.f90', 'tts.f90', 'python_conv.f90','tt_linalg.f90']
tt_src = [tt_dir+'/'+x for x in tt_src]
print_dir = 'tt-fort/print'
print_src = ['putstrmodule.F90','dispmodule.f90']
print_src = [print_dir+'/'+x for x in print_src]
config.add_include_dirs(inc_dir)
config.add_library('print_lib',sources=print_src)
config.add_library('mytt',sources=tt_src)
config.add_subpackage('core')
config.add_subpackage('amr')
config.add_subpackage('kls')
config.add_subpackage('ksl')
config.add_subpackage('eigb')
return config
def configuration(parent_package = '', top_path = None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from numpy.distutils.system_info import get_info
config = Configuration('spatial', parent_package, top_path)
config.add_data_dir('tests')
qhull_src = ['geom.c', 'geom2.c', 'global.c', 'io.c', 'mem.c',
'merge.c', 'poly.c', 'poly2.c', 'qset.c', 'user.c',
'stat.c', 'qhull.c']
config.add_library('qhull',
sources=[join('qhull', 'src', x) for x in qhull_src],
# XXX: GCC dependency!
#extra_compiler_args=['-fno-strict-aliasing'],
)
lapack = dict(get_info('lapack_opt'))
try:
libs = ['qhull'] + lapack.pop('libraries')
except KeyError:
libs = ['qhull']
config.add_extension('qhull',
sources=['qhull.c'],
libraries=libs,
**lapack)
config.add_extension('ckdtree', sources=['ckdtree.c']) # FIXME: cython
config.add_extension('_distance_wrap',
sources=[join('src', 'distance_wrap.c'), join('src', 'distance.c')],
include_dirs = [get_numpy_include_dirs()])
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('fftpack',parent_package, top_path)
config.add_data_dir('tests')
dfftpack_src = [join('src/dfftpack','*.f')]
config.add_library('dfftpack', sources=dfftpack_src)
fftpack_src = [join('src/fftpack','*.f')]
config.add_library('fftpack', sources=fftpack_src)
sources = ['fftpack.pyf','src/zfft.c','src/drfft.c','src/zrfft.c',
'src/zfftnd.c', 'src/dct.c.src', 'src/dst.c.src']
config.add_extension('_fftpack',
sources=sources,
libraries=['dfftpack', 'fftpack'],
include_dirs=['src'],
depends=(dfftpack_src + fftpack_src))
config.add_extension('convolve',
sources=['convolve.pyf','src/convolve.c'],
libraries=['dfftpack'],
depends=dfftpack_src,
)
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('stats', parent_package, top_path)
config.add_data_dir('tests')
config.add_library('statlib',
sources=[join('statlib', '*.f')])
# add statlib module
config.add_extension('statlib',
sources=['statlib.pyf'],
f2py_options=['--no-wrap-functions'],
libraries=['statlib'],
)
# add vonmises_cython module
config.add_extension('vonmises_cython',
sources=['vonmises_cython.c'], # FIXME: use cython source
)
# add futil module
config.add_extension('futil',
sources=['futil.f'],
)
# add mvn module
config.add_extension('mvn',
sources=['mvn.pyf','mvndst.f'],
)
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.system_info import get_info, NotFoundError
from numpy.distutils.misc_util import Configuration
from scipy._build_utils import get_g77_abi_wrappers, get_sgemv_fix
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
config = Configuration('arpack', parent_package, top_path)
arpack_sources = [join('ARPACK','SRC', '*.f')]
arpack_sources.extend([join('ARPACK','UTIL', '*.f')])
arpack_sources += get_g77_abi_wrappers(lapack_opt)
config.add_library('arpack_scipy', sources=arpack_sources,
include_dirs=[join('ARPACK', 'SRC')])
ext_sources = ['arpack.pyf.src']
ext_sources += get_sgemv_fix(lapack_opt)
config.add_extension('_arpack',
sources=ext_sources,
libraries=['arpack_scipy'],
extra_info=lapack_opt,
depends=arpack_sources,
)
config.add_data_dir('tests')
# Add license files
config.add_data_files('ARPACK/COPYING')
return config
def configuration(parent_package='', top_path=None):
tteigb_src = [join(TTFORT_DIR, x) for x in TTEIGB_SRC]
tteigb_src.append('tt_eigb.pyf')
config = Configuration('eigb', parent_package, top_path)
config.add_library(
'primme',
sources=[join(PRIMME_DIR, '*.c')] + [join(PRIMME_DIR, '*.f')],
include_dirs=['.'],
)
config.add_extension(
'tt_eigb',
sources=tteigb_src,
depends=[
'primme',
'mytt',
'print_lib',
],
libraries=[
'primme',
'mytt',
'print_lib',
],
)
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from numpy.distutils.system_info import get_info, system_info
config = Configuration('labs', parent_package, top_path)
# fff library
config.add_include_dirs(os.path.join(LIBS,'fff'))
config.add_include_dirs(os.path.join(LIBS,'fff_python_wrapper'))
config.add_include_dirs(get_numpy_include_dirs())
sources = [os.path.join(LIBS,'fff','*.c')]
sources.append(os.path.join(LIBS,'fff_python_wrapper','*.c'))
config.add_library('cstat', sources=sources)
# Subpackages
config.add_subpackage('bindings')
config.add_subpackage('glm')
config.add_subpackage('group')
config.add_subpackage('spatial_models')
config.add_subpackage('utils')
config.add_subpackage('viz_tools')
config.add_subpackage('datasets')
config.add_subpackage('tests')
config.make_config_py() # installs __config__.py
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('interpolate', parent_package, top_path)
fitpack_src = [join('fitpack', '*.f')]
config.add_library('fitpack', sources=fitpack_src)
config.add_extension('interpnd',
sources=['interpnd.c'])
config.add_extension('_fitpack',
sources=['src/_fitpackmodule.c'],
libraries=['fitpack'],
depends=(['src/__fitpack.h','src/multipack.h']
+ fitpack_src)
)
config.add_extension('dfitpack',
sources=['src/fitpack.pyf'],
libraries=['fitpack'],
depends=fitpack_src,
)
config.add_extension('_interpolate',
sources=['src/_interpolate.cpp'],
include_dirs=['src'],
depends=['src/interpolate.h'])
config.add_data_dir('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
config = Configuration('dsolve',parent_package,top_path)
config.add_data_dir('tests')
lapack_opt = get_info('lapack_opt',notfound_action=2)
if sys.platform=='win32':
superlu_defs = [('NO_TIMER',1)]
else:
superlu_defs = []
superlu_defs.append(('USE_VENDOR_BLAS',1))
superlu_src = os.path.join(dirname(__file__), 'SuperLU', 'SRC')
config.add_library('superlu_src',
sources = [join(superlu_src,'*.c')],
macros = superlu_defs,
include_dirs=[superlu_src],
)
# Extension
config.add_extension('_superlu',
sources = ['_superlumodule.c',
'_superlu_utils.c',
'_superluobject.c'],
libraries = ['superlu_src'],
extra_info = lapack_opt,
)
config.add_subpackage('umfpack')
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration(pynio_pkg_name,parent_package, top_path)
files = os.listdir('libsrc')
sources = [ file for file in files if not file.startswith('._') and (file.endswith('.c') or file.endswith('.f')) ]
for file in LIB_EXCLUDE_SOURCES:
sources.remove(file)
sources = [ join('libsrc', file) for file in sources ]
config.add_library('nio',sources,
include_dirs=INC_DIRS,
macros=LIB_MACROS,
# extra_compiler_args = [ '-O0 -g', '-w' ]
extra_compiler_args = [ '-O2', '-w' ]
)
sources = ['niomodule.c']
config.add_extension('nio',
sources=sources,
libraries=LIBRARIES,
include_dirs=INC_DIRS,
define_macros = DMACROS,
library_dirs = LIB_DIRS,
extra_objects = EXTRA_OBJECTS,
language = 'c++'
)
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, NotFoundError
config = Configuration('ops',parent_package,top_path)
config.add_extension('apply_window_ext', join('src','apply_window_ext.c'))
config.add_extension('local_extrema_ext', join('src','local_extrema_ext.c'))
config.add_library('fminpack',
sources = [join ('src', 'minpack', '*.f'),
],
)
config.add_extension('regress_ext',
sources = [join('src','regress_ext.c'),
],
)
config.add_extension('acf_ext',
sources = [join('src','acf_ext.c'),
join('src','acf.c')],
libraries = ['fminpack'])
fftw3_info = get_info('fftw3')
if fftw3_info:
config.add_extension('discrete_gauss_ext',
sources = [join('src','discrete_gauss_ext.c'),
join('src','discrete_gauss.c')],
extra_info = fftw3_info)
else:
print 'FFTW3 not found: skipping discrete_gauss_ext extension'
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
print("=============================================")
print("parent package is %s" % parent_package)
print("top path is %s" % top_path)
print("=============================================")
config = Configuration('odes', parent_package,top_path)
config.add_library('daepack',
sources=[join('daepack','*.f')])
# ddaspk
config.add_extension('ddaspk',
sources=['ddaspk.pyf'],
libraries=['daepack'])
# lsodi
config.add_extension('lsodi',
sources=['lsodi.pyf'],
libraries=['daepack'])
# sundials
config.add_subpackage('sundials')
# add the test directory
config.add_subpackage('tests')
return config
def configuration(parent_package="", top_path=None):
import warnings
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, BlasNotFoundError
config = Configuration("odr", parent_package, top_path)
libodr_files = ["d_odr.f", "d_mprec.f", "dlunoc.f"]
blas_info = get_info("blas_opt")
if blas_info:
libodr_files.append("d_lpk.f")
else:
warnings.warn(BlasNotFoundError.__doc__)
libodr_files.append("d_lpkbls.f")
libodr = [join("odrpack", x) for x in libodr_files]
config.add_library("odrpack", sources=libodr)
sources = ["__odrpack.c"]
libraries = ["odrpack"] + blas_info.pop("libraries", [])
include_dirs = ["."] + blas_info.pop("include_dirs", [])
config.add_extension(
"__odrpack", sources=sources, libraries=libraries, include_dirs=include_dirs, depends=["odrpack.h"], **blas_info
)
config.add_data_dir("tests")
return config
def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, BlasNotFoundError
import numpy
config = Configuration("sklearn", parent_package, top_path)
config.add_subpackage("check_build")
config.add_subpackage("svm")
config.add_subpackage("datasets")
config.add_subpackage("datasets/tests")
config.add_subpackage("feature_extraction")
config.add_subpackage("feature_extraction/tests")
config.add_subpackage("cluster")
config.add_subpackage("cluster/tests")
config.add_subpackage("covariance")
config.add_subpackage("covariance/tests")
config.add_subpackage("decomposition")
config.add_subpackage("decomposition/tests")
config.add_subpackage("ensemble")
config.add_subpackage("ensemble/tests")
config.add_subpackage("feature_selection")
config.add_subpackage("feature_selection/tests")
config.add_subpackage("utils")
config.add_subpackage("utils/tests")
config.add_subpackage("externals")
config.add_subpackage("mixture")
config.add_subpackage("mixture/tests")
config.add_subpackage("gaussian_process")
config.add_subpackage("gaussian_process/tests")
config.add_subpackage("neighbors")
config.add_subpackage("manifold")
config.add_subpackage("metrics")
config.add_subpackage("semi_supervised")
config.add_subpackage("tree")
config.add_subpackage("tree/tests")
config.add_subpackage("metrics/tests")
config.add_subpackage("metrics/tests")
config.add_subpackage("metrics/cluster")
config.add_subpackage("metrics/cluster/tests")
# add cython extension module for hmm
config.add_extension("_hmmc", sources=["_hmmc.c"], include_dirs=[numpy.get_include()])
# some libs 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")])
warnings.warn(BlasNotFoundError.__doc__)
# the following packages depend on cblas, so they have to be build
# after the above.
config.add_subpackage("linear_model")
config.add_subpackage("utils")
# add the test directory
config.add_subpackage("tests")
return config
def configuration(parent_package='',top_path=None):
import numpy
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, NotFoundError
import os
config = Configuration('ls', parent_package, top_path)
# Get info from site.cfg
blas_info = get_info('blas_opt',0)
if not blas_info:
print 'No blas info found'
libcsrch_src = ['dcsrch.f', 'dcstep.f']
pycsrch_src = ['_pycsrch.c']
libmcsrch_src = ['mcsrch.f', 'mcstep.f']
pymcsrch_src = ['_pymcsrch.c']
config.add_library(
name='nlpy_csrch',
sources=[os.path.join('src',name) for name in libcsrch_src],
libraries=[],
library_dirs=[],
include_dirs=['src'],
extra_info=blas_info,
)
config.add_extension(
name='_pycsrch',
sources=[os.path.join('src',name) for name in pycsrch_src],
depends=[],
libraries=['nlpy_csrch'],
library_dirs=[],
include_dirs=['src'],
extra_info=blas_info,
)
config.add_library(
name='nlpy_mcsrch',
sources=[os.path.join('src',name) for name in libmcsrch_src],
libraries=[],
library_dirs=[],
include_dirs=['src'],
extra_info=blas_info,
)
config.add_extension(
name='_pymcsrch',
sources=[os.path.join('src',name) for name in pymcsrch_src],
depends=[],
libraries=['nlpy_mcsrch'],
library_dirs=[],
include_dirs=['src'],
extra_info=blas_info,
)
config.make_config_py()
return config
def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration("", parent_package, top_path)
config.add_library(name="normalize_c", sources=["normalize_c.cxx"])
config.add_extension("_norm_c", sources=["normalize_c.pyf", "normalize_c_wrap.c"], libraries=["normalize_c"])
return config
def configuration(parent_package='', top_path=None):
config = Configuration('dummy', parent_package, top_path)
config.add_library('dummy', sources=["dummy.f"])
config.add_extension('_dummy',
sources='dummy.pyf',
libraries=['dummy'])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, BlasNotFoundError
config = Configuration('sklearn', parent_package, top_path)
config.add_subpackage('check_build')
config.add_subpackage('svm')
config.add_subpackage('datasets')
config.add_subpackage('datasets/tests')
config.add_subpackage('feature_extraction')
config.add_subpackage('feature_extraction/tests')
config.add_subpackage('cluster')
config.add_subpackage('cluster/tests')
config.add_subpackage('covariance')
config.add_subpackage('covariance/tests')
config.add_subpackage('decomposition')
config.add_subpackage('decomposition/tests')
config.add_subpackage("ensemble")
config.add_subpackage("ensemble/tests")
config.add_subpackage('feature_selection')
config.add_subpackage('feature_selection/tests')
config.add_subpackage('utils')
config.add_subpackage('utils/tests')
config.add_subpackage('externals')
config.add_subpackage('mixture')
config.add_subpackage('mixture/tests')
config.add_subpackage('gaussian_process')
config.add_subpackage('gaussian_process/tests')
config.add_subpackage('neighbors')
config.add_subpackage('manifold')
config.add_subpackage('metrics')
config.add_subpackage('semi_supervised')
config.add_subpackage("tree")
config.add_subpackage("tree/tests")
config.add_subpackage('metrics/tests')
config.add_subpackage('metrics/tests')
config.add_subpackage('metrics/cluster')
config.add_subpackage('metrics/cluster/tests')
# some libs 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')])
warnings.warn(BlasNotFoundError.__doc__)
# the following packages depend on cblas, so they have to be build
# after the above.
config.add_subpackage('linear_model')
config.add_subpackage('utils')
# add the test directory
config.add_subpackage('tests')
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('bathy_smoother',parent_package,top_path,
package_path='bathy_smoother')
config.set_options(ignore_setup_xxx_py=True,
assume_default_configuration=True,
delegate_options_to_subpackages=True)
# quiet=True)
define_macros = []
define_macros.append(('YY_NEVER_INTERACTIVE', None))
define_macros.append(('PARSER_LP', None))
define_macros.append(('INVERSE_ACTIVE', 'INVERSE_LUSOL'))
define_macros.append(('RoleIsExternalInvEngine', None))
sources = ['external/lp_solve_5.5/lp_MDO.c',
'external/lp_solve_5.5/shared/*.c',
'external/lp_solve_5.5/colamd/*.c',
'external/lp_solve_5.5/bfp/bfp_LUSOL/lp_LUSOL.c',
'external/lp_solve_5.5/bfp/bfp_LUSOL/LUSOL/lusol.c',
'external/lp_solve_5.5/ini.c',
'external/lp_solve_5.5/fortify.c',
'external/lp_solve_5.5/lp_rlp.c',
'external/lp_solve_5.5/lp_crash.c',
'external/lp_solve_5.5/lp_Hash.c',
'external/lp_solve_5.5/lp_lib.c',
'external/lp_solve_5.5/lp_wlp.c',
'external/lp_solve_5.5/lp_matrix.c',
'external/lp_solve_5.5/lp_mipbb.c',
'external/lp_solve_5.5/lp_MPS.c',
'external/lp_solve_5.5/lp_params.c',
'external/lp_solve_5.5/lp_presolve.c',
'external/lp_solve_5.5/lp_price.c',
'external/lp_solve_5.5/lp_pricePSE.c',
'external/lp_solve_5.5/lp_report.c',
'external/lp_solve_5.5/lp_scale.c',
'external/lp_solve_5.5/lp_simplex.c',
'external/lp_solve_5.5/lp_SOS.c',
'external/lp_solve_5.5/lp_utils.c',
'external/lp_solve_5.5/yacc_read.c'],
inc_dirs = ['external/lp_solve_5.5',
'external/lp_solve_5.5/bfp',
'external/lp_solve_5.5/bfp/bfp_LUSOL',
'external/lp_solve_5.5/bfp/bfp_LUSOL/LUSOL',
'external/lp_solve_5.5/colamd',
'external/lp_solve_5.5/shared'],
config.add_library('lpsolve55',
sources = sources,
include_dirs = inc_dirs,
macros=define_macros)
config.add_extension('lpsolve55',
sources = sources,
include_dirs = inc_dirs,
libraries = ['lpsolve55']
)
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 arachnid.distutils.compiler import compiler_options #detect_openmp
import os
compiler_args, compiler_libraries, compiler_defs, ccompiler_args, ccompiler_lib, ccompiler_defs = compiler_options()[:6]
ccompiler_lib;
try:
fftw_opt = get_info('mkl',notfound_action=2)
except:
try:
fftw_opt = get_info('fftw',notfound_action=2)
#fftw_opt['libraries']=['fftw3f']
fftw_opt['libraries'].extend(['fftw3f'])
fftw_opt['library_dirs'].extend(['/usr/lib'])
except: fftw_opt=dict(libraries=['fftw3f'])
if 'library_dirs' not in fftw_opt: fftw_opt['library_dirs']=[]
if 'include_dirs' not in fftw_opt: fftw_opt['include_dirs']=[]
config = Configuration('spi', parent_package, top_path)
#-ftrap=common
if 1 == 0:
f2py_options = ['--debug-capi']
else: f2py_options=[]
flink_args = compiler_args
#-ffixed-form define_macros=[('SP_LIBFFTW3', 1)]+compiler_defs,
library_options=dict(macros=[('SP_LIBFFTW3', 1)]+compiler_defs, extra_f77_compile_args=compiler_args, extra_f90_compile_args=compiler_args)#extra_f77_compiler_args=['-fdefault-real-8'],, ('SP_MP', 1)
#extra_f90_compiler_args=['-fdefault-real-8'])
config.add_library('spiutil', sources=['spiutil.F90', 'spider/tfd.F90', 'spider/fq_q.F90', 'spider/fq3_p.F90', 'spider/parabl.F90', 'spider/pksr3.F90', 'spider/fftw3.F90',
'spider/ccrs.F90', 'spider/apcc.F90', 'spider/quadri.F90', 'spider/rtsq.F90', 'spider/cald.F90', 'spider/bldr.F90',
'spider/fmrs.F90', 'spider/fmrs_2.F90', 'spider/besi1.F90', 'spider/wpro_n.F90', 'spider/prepcub.F90',
'spider/fint.F90', 'spider/fint3.F90', 'spider/betai.F90', 'spider/gammln.F90', 'spider/betacf.F90', 'spider/histe.F90',
'spider/interp_fbs3.F90', 'spider/interp_fbs.F90', 'spider/fbs2.F90', 'spider/fbs3.F90'],
depends=['spider/CMBLOCK.INC', 'spider/FFTW3.INC'], **library_options) #, 'fmrs_info.mod', 'type_kinds.mod'
fftlibs = fftw_opt['libraries']+compiler_libraries
del fftw_opt['libraries']
config.add_extension('_spider_reconstruct', sources=['backproject_nn4.f90', 'backproject_bp3f.f90'], libraries=['spiutil']+fftlibs, f2py_options=f2py_options, define_macros=ccompiler_defs, extra_compile_args=ccompiler_args, extra_link_args=flink_args, library_dirs=fftw_opt['library_dirs'])
config.add_extension('_spider_reproject', sources=['reproject.F90'], libraries=['spiutil']+fftlibs, f2py_options=f2py_options, define_macros=ccompiler_defs, extra_compile_args=ccompiler_args, extra_link_args=flink_args, library_dirs=fftw_opt['library_dirs'])
config.add_extension('_spider_interpolate', sources=['interpolate.F90'], libraries=['spiutil']+fftlibs, f2py_options=f2py_options, define_macros=ccompiler_defs, extra_compile_args=ccompiler_args, extra_link_args=flink_args, library_dirs=fftw_opt['library_dirs'])
config.add_extension('_spider_ctf', sources=['ctf.F90'], libraries=['spiutil']+fftlibs, f2py_options=f2py_options, define_macros=ccompiler_defs, extra_compile_args=ccompiler_args, extra_link_args=flink_args, library_dirs=fftw_opt['library_dirs'])
#config.add_extension('_spider_interpolate', sources=['interpolate.F90'], libraries=['spiutil']+fftlibs, f2py_options=f2py_options, define_macros=ccompiler_defs, extra_compile_args=ccompiler_args, extra_link_args=compiler_args, library_dirs=fftw_opt['library_dirs'])
#-fdefault-real-8
#rot_src = 'spider_rotate_dist_wrap.cpp' if os.path.exists(os.path.join(os.path.dirname(__file__), 'spider_rotate_dist_wrap.cpp')) else 'rotate.i'
#config.add_extension('_spider_rotate_dist', sources=[rot_src], define_macros=[('__STDC_FORMAT_MACROS', 1)]+ccompiler_defs, depends=['rotate.hpp'], swig_opts=['-c++'], libraries=['spiutil']+fftlibs, extra_compile_args=ccompiler_args, extra_link_args=compiler_args, library_dirs=fftw_opt['library_dirs'])
config.add_extension('_spider_rotate', sources=['rotate.F90'], libraries=['spiutil']+fftlibs, f2py_options=f2py_options, define_macros=ccompiler_defs, extra_compile_args=ccompiler_args, extra_link_args=flink_args, library_dirs=fftw_opt['library_dirs'])
#config.add_extension('_spider_align', sources=['align.F90'], libraries=['spiutil']+fftlibs, f2py_options=f2py_options, define_macros=ccompiler_defs, extra_compile_args=ccompiler_args, extra_link_args=flink_args, library_dirs=fftw_opt['library_dirs'])
config.add_extension('_spider_filter', sources=['filter.F90'], libraries=['spiutil']+fftlibs, f2py_options=f2py_options, define_macros=ccompiler_defs, extra_compile_args=ccompiler_args, extra_link_args=flink_args, library_dirs=fftw_opt['library_dirs'])
config.add_include_dirs(os.path.dirname(__file__))
config.add_include_dirs(os.path.join(os.path.dirname(__file__), 'spider'))
config.add_include_dirs(fftw_opt['include_dirs'])
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info
config = Configuration('dsolve',parent_package,top_path)
config.add_data_dir('tests')
lapack_opt = get_info('lapack_opt',notfound_action=2)
if sys.platform=='win32':
superlu_defs = [('NO_TIMER',1)]
else:
superlu_defs = []
superlu_defs.append(('USE_VENDOR_BLAS',1))
config.add_library('superlu_src',
sources = [join('SuperLU','SRC','*.c')],
macros = superlu_defs
)
#SuperLU/SRC/util.h has been modifed to use these by default
#macs = [('USER_ABORT','superlu_python_module_abort'),
# ('USER_MALLOC','superlu_python_module_malloc'),
# ('USER_FREE','superlu_python_module_free')]
# Extension
config.add_extension('_zsuperlu',
sources = ['_zsuperlumodule.c','_superlu_utils.c',
'_superluobject.c'],
libraries = ['superlu_src'],
extra_info = lapack_opt
)
config.add_extension('_dsuperlu',
sources = ['_dsuperlumodule.c','_superlu_utils.c',
'_superluobject.c'],
libraries = ['superlu_src'],
extra_info = lapack_opt
)
config.add_extension('_csuperlu',
sources = ['_csuperlumodule.c','_superlu_utils.c',
'_superluobject.c'],
libraries = ['superlu_src'],
extra_info = lapack_opt
)
config.add_extension('_ssuperlu',
sources = ['_ssuperlumodule.c','_superlu_utils.c',
'_superluobject.c'],
libraries = ['superlu_src'],
extra_info = lapack_opt
)
config.add_subpackage('umfpack')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_info
config = Configuration('eigb', parent_package, top_path)
tt_fort = '../tt-fort/'
primme_dir = '../tt-fort/primme/'
src = ['ttals.f90', 'tt_eigb.f90']
src = [tt_fort + '/' + x for x in src]
config.add_library('primme',sources=[join(primme_dir,'*.c')] + [join(primme_dir,'*.f')], \
include_dirs = ['.'])#,macros=['F77UNDERSCORE'])
src.append('tt_eigb.pyf')
config.add_extension('tt_eigb',
sources=src,
depends=['primme', 'mytt', 'print_lib'],
libraries=['primme', 'mytt', 'print_lib'])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info, BlasNotFoundError
config = Configuration('learn', parent_package, top_path)
config.add_subpackage('svm')
config.add_subpackage('datasets')
config.add_subpackage('feature_extraction')
config.add_subpackage('feature_extraction/tests')
config.add_subpackage('feature_extraction/text')
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('preprocessing')
config.add_subpackage('utils')
config.add_subpackage('utils/tests')
config.add_subpackage('externals')
config.add_subpackage('gaussian_process')
config.add_subpackage('gaussian_process/tests')
config.add_subpackage('metrics')
config.add_subpackage('metrics/tests')
# some libs 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')])
warnings.warn(BlasNotFoundError.__doc__)
config.add_extension('ball_tree',
sources=[join('src', 'BallTree.cpp')],
include_dirs=[numpy.get_include()])
# the following packages depend on cblas, so they have to be build
# after the above.
config.add_subpackage('linear_model')
config.add_subpackage('utils')
# add the test directory
config.add_subpackage('tests')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('_levy_stable', parent_package, top_path)
config.add_library(
'_levyst',
sources=[join('c_src', 'levyst.c')],
headers=[join('c_src', 'levyst.h')]
)
config.add_extension(
'levyst',
libraries=['_levyst'],
sources=['levyst.c']
)
return config
def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration
dependencies_src = [join("dependencies", "*.f")]
config = Configuration("minpack", parent_package, top_path)
config.add_library("dependencies", sources=dependencies_src)
config.add_extension(
"_minpack",
sources=["minpack.pyf", "minpack.f"],
libraries=["dependencies"],
include_dirs=["dependencies"],
depends=dependencies_src
)
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('signal', parent_package, top_path)
CFLAGS = ['-lm', '-O2', '-lpthread', '-fPIC']
npdir = np.get_include() + '/numpy'
config.add_extension('_filter_modc',
sources=['filter_modules/filter_modc.cpp'],
libraries=[],
library_dirs=[],
include_dirs=[npdir],
extra_compile_args=CFLAGS)
config.add_library('conefiltpack',
sources=['filter_modules/conefilt.cpp'],
headers=['filter_modules/conefilt.h'],
extra_compile_args=CFLAGS)
config.add_extension('_conefilt_modc',
sources=['filter_modules/conefilt_modc.cpp'],
depends=['filter_modules/conefilt.h'],
libraries=['conefiltpack'],
library_dirs=[],
include_dirs=[npdir, 'filter_modules'],
extra_compile_args=CFLAGS)
config.add_library('medfiltpack',
sources=['filter_modules/medfilt.cpp'],
headers=['filter_modules/medfilt.h'],
extra_compile_args=CFLAGS)
config.add_extension('_medfilt_modc',
sources=['filter_modules/medfilt_modc.cpp'],
depends=['filter_modules/medfilt.h'],
libraries=['medfiltpack'],
library_dirs=[],
include_dirs=[npdir, 'filter_modules'],
extra_compile_args=CFLAGS)
config.add_extension('_xapiir_sub',
sources=['filter_modules/xapiir_sub.f'],
libraries=[],
library_dirs=[],
include_dirs=[],
extra_compile_args=['-O3'])
config.add_extension('_butter_bandpass',
sources=['filter_modules/butter_bandpass.f'],
libraries=[],
library_dirs=[],
include_dirs=[],
extra_compile_args=['-O3'])
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy.distutils.system_info import get_info
config = Configuration('optimize',parent_package, top_path)
config.add_library('minpack',sources=[join('minpack','*f')])
config.add_extension('_minpack',
sources=['_minpackmodule.c'],
libraries=['minpack'],
depends=["minpack.h","__minpack.h"])
config.add_library('rootfind',
sources=[join('Zeros','*.c')],
headers=[join('Zeros','zeros.h')])
config.add_extension('_zeros',
sources=['zeros.c'],
libraries=['rootfind'])
lapack = get_info('lapack_opt')
sources=['lbfgsb.pyf','routines.f']
config.add_extension('_lbfgsb',
sources=[join('lbfgsb',x) for x in sources],
**lapack)
sources=['moduleTNC.c','tnc.c']
config.add_extension('moduleTNC',
sources=[join('tnc',x) for x in sources],
depends=[join('tnc','tnc.h')])
config.add_extension('_cobyla',
sources=[join('cobyla',x) for x in ['cobyla.pyf',
'cobyla2.f',
'trstlp.f']])
sources = ['minpack2.pyf', 'dcsrch.f', 'dcstep.f']
config.add_extension('minpack2',
sources=[join('minpack2',x) for x in sources])
sources = ['slsqp.pyf', 'slsqp_optmz.f']
config.add_extension('_slsqp', sources=[join('slsqp', x) for x in sources])
config.add_extension('_nnls', sources=[join('nnls', x) \
for x in ["nnls.f","nnls.pyf"]])
config.add_data_dir('tests')
config.add_data_dir('benchmarks')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('polyhedron', parent_package, top_path)
cddlib_dir = 'cddlib-094d-p1'
sources = [
'cddcore.c', 'cddlp.c', 'cddmp.c', 'cddio.c', 'cddlib.c', 'cddproj.c',
'setoper.c'
]
sources = [os.path.join(cddlib_dir, 'lib-src', fn) for fn in sources]
include_dirs = [os.path.join(cddlib_dir, 'lib-src')]
config.add_library('cddlib', sources=sources, include_dirs=include_dirs)
config.add_extension('_cdd',
sources=['_cddmodule.c'],
libraries=['cddlib'],
include_dirs=include_dirs)
return config
def configuration(parent_package='',top_path=None):
config = Configuration('ram_pe', parent_package, top_path)
sources = ['src/constants.f90',
'src/cmplx_roots_sg.f90',
'src/pade_coeffs.f90',
'src/pade_coeffs_wrapper.f90',
'src/ram_io.f90',
'src/ram_v4.f90',
'src/ram_v4_wrapper.f90']
config.add_library('ram_src', sources=sources)
config.add_extension('epade',
sources=['src/epade.c',],
libraries=['ram_src'])
config.add_extension('ram_main_v4',
sources=['src/ram_main_v4.c',],
libraries=['ram_src'])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('pySNOPT', parent_package, top_path)
config.add_data_files('LICENSE', 'README')
# Since snopt has a bunch of source files, we will just check if
# snoptc.c exists. If so, we will assume all the rest of the files
# are present.
snoptc = os.path.join('pyoptsparse/pySNOPT/source', 'snoptc.f')
if os.path.exists(snoptc):
config.add_library('snopt', sources=[os.path.join('source', '*.f')])
config.add_extension('snopt',
sources=['source/f2py/snopt.pyf'],
libraries=['snopt'])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('tmat_sampling', parent_package, top_path)
config.add_library('rnglib',
sources=['src/rnglib/rnglib.c', 'src/rnglib/ranlib.c'])
config.add_extension('sampler_rev',
sources=['sampler_rev.pyx', 'src/sample_rev.c'],
include_dirs=['src/', np.get_include()],
libraries=['rnglib'])
config.add_extension('sampler_revpi',
sources=['sampler_revpi.pyx', 'src/sample_revpi.c'],
include_dirs=['src/', np.get_include()],
libraries=['rnglib'])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from os.path import join
config = Configuration('decomposition', parent_package, top_path)
# get the src file glob, make a fortran lib
dqrlib_src = [join('src/dqrlib', '*.f')]
config.add_library('dqrlib', sources=dqrlib_src)
# and now all .pyf sources:
sources = ['dqrsl.pyf']
config.add_extension('_dqrsl',
sources=sources,
libraries=['dqrlib'],
depends=dqrlib_src)
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.system_info import get_info, NotFoundError
from numpy.distutils.misc_util import Configuration
config = Configuration('arpack', parent_package, top_path)
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
config = Configuration('arpack', parent_package, top_path)
arpack_sources = [join('ARPACK', 'SRC', '*.f')]
arpack_sources.extend([join('ARPACK', 'UTIL', '*.f')])
arpack_sources.extend([join('ARPACK', 'LAPACK', '*.f')])
if needs_g77_abi_wrapper(lapack_opt):
arpack_sources += [
join('ARPACK', 'FWRAPPERS', 'wrap_veclib_f.f'),
join('ARPACK', 'FWRAPPERS', 'wrap_veclib_c.c')
]
else:
arpack_sources += [join('ARPACK', 'FWRAPPERS', 'wrap_dummy.f')]
config.add_library('arpack_scipy',
sources=arpack_sources,
include_dirs=[join('ARPACK', 'SRC')],
depends=[
join('ARPACK', 'FWRAPPERS', 'wrap_veclib_f.f'),
join('ARPACK', 'FWRAPPERS', 'wrap_veclib_c.c'),
join('ARPACK', 'FWRAPPERS', 'wrap_dummy.f')
])
config.add_extension(
'_arpack',
sources='arpack.pyf.src',
libraries=['arpack_scipy'],
extra_info=lapack_opt,
depends=arpack_sources,
)
config.add_data_dir('tests')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('pyNSGA2', parent_package, top_path)
# platform-specific settings
extra_link_args = []
if sys.platform == "darwin":
extra_link_args.append("-bundle")
config.add_library('nsga2', sources=[os.path.join('source', '*.c')])
config.add_extension('nsga2',
sources=['source/swig/nsga2.i'],
include_dirs=['source'],
libraries=['nsga2'],
extra_link_args=extra_link_args)
config.add_data_files('LICENSE', 'README')
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('polsar', parent_package, top_path)
npdir = np.get_include() + '/numpy'
CFLAGS = ['-lm','-O2','-lpthread']
config.add_library('pdpack',
sources=['src/pdpack.cpp'],
headers=['src/decomp.h'],
extra_compile_args=CFLAGS)
config.add_extension('_decomp_modc',
sources=['src/decomp_modc.cpp'],
depends=['src/decomp.h'],
libraries=['pdpack'],
library_dirs=[],
include_dirs=[npdir,'src'],
extra_compile_args=CFLAGS)
return config
