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
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 += 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')
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
config = Configuration('isolve', parent_package, top_path)
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
# iterative methods
methods = [
'BiCGREVCOM.f.src',
'BiCGSTABREVCOM.f.src',
'CGREVCOM.f.src',
'CGSREVCOM.f.src',
# 'ChebyREVCOM.f.src',
'GMRESREVCOM.f.src',
# 'JacobiREVCOM.f.src',
'QMRREVCOM.f.src',
# 'SORREVCOM.f.src'
]
Util = ['STOPTEST2.f.src', 'getbreak.f.src']
sources = Util + methods + ['_iterative.pyf.src']
sources = [join('iterative', x) for x in sources]
sources += get_g77_abi_wrappers(lapack_opt)
config.add_extension('_iterative', sources=sources, extra_info=lapack_opt)
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, NotFoundError, numpy_info
config = Configuration('lib', parent_package, top_path)
# get lapack options
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
atlas_version = ([v[3:-3] for k, v in lapack_opt.get('define_macros', [])
if k == 'ATLAS_INFO'] + [None])[0]
if atlas_version:
print(('ATLAS version: %s' % atlas_version))
# include_dirs=[os.curdir,'$MKLROOT/include']
# library_dirs=['$MKLROOT/lib/intel64']
# libraries=['mkl_intel_lp64','mkl_sequential','mkl_core', 'm', 'pthread']
# render f90 files if templates changed
render_f90s()
for extension, source in zip(extension_list, source_list):
# config.add_extension(
# extension, [os.path.join(libdir, source)], libraries=libraries,
# library_dirs=library_dirs, include_dirs=include_dirs)
config.add_extension(extension, [os.path.join(
libdir, source)], extra_info=lapack_opt)
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('pypropack', parent_package, top_path)
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
#------------------------------------------------------------
# Set up the libraries.
# We need a different python .so file for each, because they
# re-use names for functions in the LAPACK extensions. This
# could probably be remedied with some work.
type_dict = dict(s='single', d='double', c='complex8', z='complex16')
for typ in type_dict:
lapack_lib = 'sp_%slapack_util' % typ
propack_lib = '_%spropack' % typ
lapack_sources = join('PROPACK', type_dict[typ], 'Lapack_Util', '*.f')
propack_sources = join('PROPACK', type_dict[typ], '*.F')
config.add_library(lapack_lib, sources=lapack_sources)
config.add_library(propack_lib, sources=propack_sources)
config.add_extension('_%spropack' % typ,
sources='%spropack.pyf' % typ,
libraries=[lapack_lib, propack_lib],
extra_info=lapack_opt)
return config
def prediction_image(image_path, model_url, user_id):
try:
model_folder = extract_model(model_url, user_id)
model_file = model_json = ""
for i in os.listdir(model_folder):
if i.endswith(".model"):
model_file = i
if i.endswith(".json"):
model_json = i
if model_file is None:
raise NotFoundError("model not found")
if model_json is None:
raise NotFoundError("model json not found")
with open(model_folder + "/" + model_json) as f:
class_config = json.load(f)
print(class_config)
model = load_model(model_folder + "/" + model_file)
img = image.load_img(image_path, target_size=(HEIGHT, WIDTH))
x = image.img_to_array(img)
x = np.expand_dims(x, axis=0)
x = preprocess_input(x)
pred = model.predict(x)[0]
result = {}
z = 0
for i in class_config.keys():
label = class_config[i]
result[label] = str(pred[z])
z += 1
print(result)
keras.backend.clear_session()
return result
finally:
os.remove(image_path)
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('isolve', parent_package, top_path)
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
# iterative methods
methods = [
'BiCGREVCOM.f.src',
'BiCGSTABREVCOM.f.src',
'CGREVCOM.f.src',
'CGSREVCOM.f.src',
# 'ChebyREVCOM.f.src',
'GMRESREVCOM.f.src',
# 'JacobiREVCOM.f.src',
'QMRREVCOM.f.src',
# 'SORREVCOM.f.src'
]
if needs_g77_abi_wrapper(lapack_opt):
methods += [
join('FWRAPPERS', 'wrap_veclib_f.f'),
join('FWRAPPERS', 'wrap_veclib_c.c')
]
else:
methods += [join('FWRAPPERS', 'wrap_dummy.f')]
Util = ['STOPTEST2.f.src', 'getbreak.f.src']
sources = Util + methods + ['_iterative.pyf.src']
config.add_extension(
'_iterative',
sources=[join('iterative', x) for x in sources],
extra_info=lapack_opt,
depends=[
join('iterative', 'FWRAPPERS', x)
for x in ['wrap_veclib_f.f', 'wrap_veclib_c.c', 'wrap_dummy.f']
])
config.add_data_dir('tests')
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('_propack', parent_package, top_path)
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
# ------------------------------------------------------------
# Set up the libraries.
# We need a different python extension file for each, because
# names resue between functions in the LAPACK extensions. This
# could probably be remedied with some work.
# NOTES: this might not longer apply now that we build without
# LAPACK extensions
type_dict = dict(s='single', d='double', c='complex8', z='complex16')
check_propack_submodule()
for prefix, directory in type_dict.items():
propack_lib = f'_{prefix}propack'
# Need to use risc implementation for 32-bit machines
if _is_32bit:
src = list((pathlib.Path(__file__).parent / 'PROPACK' /
directory).glob('*.F'))
src = [str(p) for p in src if 'risc' not in str(p)]
else:
src = join('PROPACK', directory, '*.F')
config.add_library(propack_lib, sources=src, macros=[('_OPENMP', )])
config.add_extension(f'_{prefix}propack',
sources=f'{prefix}propack.pyf',
libraries=[propack_lib],
extra_info=lapack_opt,
undef_macros=['_OPENMP'])
# add required data files to run example matrix tests
path_list = ['PROPACK', directory, 'Examples']
config.add_data_files('.', join(*path_list, '*.coord'))
config.add_data_files('.', join(*path_list, '*.diag'))
config.add_data_files('.', join(*path_list, '*.rra'))
config.add_data_files('.', join(*path_list, '*.cua'))
config.add_data_files('.', join(*path_list, 'Output', '*.ascii'))
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 import get_include
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('_trlib', parent_package, top_path)
config.add_extension('_trlib',
sources=['_trlib.c', 'trlib_krylov.c',
'trlib_eigen_inverse.c', 'trlib_leftmost.c',
'trlib_quadratic_zero.c', 'trlib_tri_factor.c'],
include_dirs=[get_include(), 'trlib'],
extra_info=lapack_opt,
)
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, split_fortran_files
config = Configuration('linalg', parent_package, top_path)
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
atlas_version = ([
v[3:-3]
for k, v in lapack_opt.get('define_macros', []) if k == 'ATLAS_INFO'
] + [None])[0]
if atlas_version:
print(('ATLAS version: %s' % atlas_version))
# fblas:
sources = ['fblas.pyf.src']
sources += get_g77_abi_wrappers(lapack_opt)
config.add_extension('_fblas',
sources=sources,
depends=['fblas_l?.pyf.src'],
extra_info=lapack_opt)
# flapack:
sources = ['flapack.pyf.src']
sources += get_g77_abi_wrappers(lapack_opt)
config.add_extension('_flapack',
sources=sources,
depends=['flapack_user.pyf.src'],
extra_info=lapack_opt)
if atlas_version is not None:
# cblas:
config.add_extension('_cblas',
sources=['cblas.pyf.src'],
depends=['cblas.pyf.src', 'cblas_l1.pyf.src'],
extra_info=lapack_opt)
# clapack:
config.add_extension('_clapack',
sources=['clapack.pyf.src'],
depends=['clapack.pyf.src'],
extra_info=lapack_opt)
# _flinalg:
config.add_extension('_flinalg',
sources=[join('src', 'det.f'),
join('src', 'lu.f')],
extra_info=lapack_opt)
# _interpolative:
routines_to_split = [
'dfftb1',
'dfftf1',
'dffti1',
'dsint1',
'dzfft1',
'id_srand',
'idd_copyints',
'idd_id2svd0',
'idd_pairsamps',
'idd_permute',
'idd_permuter',
'idd_random_transf0',
'idd_random_transf0_inv',
'idd_random_transf_init0',
'idd_subselect',
'iddp_asvd0',
'iddp_rsvd0',
'iddr_asvd0',
'iddr_rsvd0',
'idz_estrank0',
'idz_id2svd0',
'idz_permute',
'idz_permuter',
'idz_random_transf0_inv',
'idz_random_transf_init0',
'idz_random_transf_init00',
'idz_realcomp',
'idz_realcomplex',
'idz_reco',
'idz_subselect',
'idzp_aid0',
'idzp_aid1',
'idzp_asvd0',
'idzp_rsvd0',
'idzr_asvd0',
'idzr_reco',
'idzr_rsvd0',
'zfftb1',
'zfftf1',
'zffti1',
]
print('Splitting linalg.interpolative Fortran source files')
fnames = split_fortran_files(
join(
os.path.split(os.path.abspath(__file__))[0], 'src', 'id_dist',
'src'), routines_to_split)
fnames = [join('src', 'id_dist', 'src', f) for f in fnames]
config.add_extension('_interpolative',
fnames + ["interpolative.pyf"],
extra_info=lapack_opt)
config.add_data_dir('tests')
config.add_data_dir('benchmarks')
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 (gfortran_legacy_flag_hook,
get_g77_abi_wrappers,
needs_g77_abi_wrapper)
lapack_opt = get_info('lapack_opt')
pre_build_hook = gfortran_legacy_flag_hook
f2py_options = None
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
config = Configuration('_propack', parent_package, top_path)
# ------------------------------------------------------------
# Set up the libraries.
# We need a different python extension file for each, because
# names reuse between functions in the LAPACK extensions. This
# could probably be remedied with some work.
# NOTES: this might not longer apply now that we build without
# LAPACK extensions
type_dict = dict(s='single',
d='double',
c='complex8',
z='complex16')
check_propack_submodule()
for prefix, directory in type_dict.items():
propack_lib = f'_{prefix}propack'
# Use risc msg implementation for 64-bit machines, pentium for 32-bit
src_dir = pathlib.Path(__file__).parent / 'PROPACK' / directory
src = list(src_dir.glob('*.F'))
if _is_32bit():
# don't ask me why, 32-bit blows up without second.F
src = [str(p) for p in src if 'risc' not in str(p)]
else:
src = [str(p) for p in src
if 'pentium' not in str(p) and 'second' not in str(p)]
if not _is_32bit():
# don't ask me why, 32-bit blows up with this wrapper
src += get_g77_abi_wrappers(lapack_opt)
cmacros = [('_OPENMP',)]
if needs_g77_abi_wrapper(lapack_opt):
cmacros += [('SCIPY_USE_G77_CDOTC_WRAP', 1)]
config.add_library(propack_lib,
sources=src,
macros=cmacros,
include_dirs=src_dir,
depends=['setup.py'])
ext = config.add_extension(f'_{prefix}propack',
sources=f'{prefix}propack.pyf',
libraries=[propack_lib],
extra_info=lapack_opt,
undef_macros=['_OPENMP'],
f2py_options=f2py_options,
depends=['setup.py'] + src)
ext._pre_build_hook = pre_build_hook
return config
from numpy.distutils.system_info import get_info, NotFoundError
import numpy.distutils.extension as Next
# Fortran helper files
F90ext = Next.Extension(
'Inelastica.F90helpers',
[
'package/F90/expansion_SE.f90', 'package/F90/readTSHS.f90',
'package/F90/removeUnitCellXij.f90', 'package/F90/setkpointhelper.f90'
],
)
# Retrieve the LAPACK-library...
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('No LAPACK/BLAS resources found')
F90extLapack = Next.Extension('Inelastica.F90_lapack',
['package/F90/surfaceGreen.f90'], **lapack_opt)
# Main setup of python modules
setup(
name='Inelastica',
version='1.2-rc',
# Define the requirements for Inelastica
# These probably needs to be adjusted...
requires=['python (>=2.5)', 'numpy (>=1.6)', 'netCDF4 (>=1.2.7)'],
description='Python tools for SIESTA/TranSIESTA',
long_description="""
Provides:
1: File format conversions for geometry, try: geom2geom --help
2: Phonon calculations (including e-ph coupling)
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('linalg', parent_package, top_path)
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
atlas_version = ([v[3:-3] for k,v in lapack_opt.get('define_macros',[]) \
if k=='ATLAS_INFO']+[None])[0]
if atlas_version:
print('ATLAS version: %s' % atlas_version)
target_dir = ''
skip_names = {'clapack': [], 'flapack': [], 'cblas': [], 'fblas': []}
if skip_single_routines:
target_dir = 'dbl'
skip_names['clapack'].extend(\
'sgesv cgesv sgetrf cgetrf sgetrs cgetrs sgetri cgetri'\
' sposv cposv spotrf cpotrf spotrs cpotrs spotri cpotri'\
' slauum clauum strtri ctrtri'.split())
skip_names['flapack'].extend(skip_names['clapack'])
skip_names['flapack'].extend(\
'sgesdd cgesdd sgelss cgelss sgeqrf cgeqrf sgeev cgeev'\
' sgegv cgegv ssyev cheev slaswp claswp sgees cgees'
' sggev cggev'.split())
skip_names['cblas'].extend('saxpy caxpy'.split())
skip_names['fblas'].extend(skip_names['cblas'])
skip_names['fblas'].extend(\
'srotg crotg srotmg srot csrot srotm sswap cswap sscal cscal'\
' csscal scopy ccopy sdot cdotu cdotc snrm2 scnrm2 sasum scasum'\
' isamax icamax sgemv cgemv chemv ssymv strmv ctrmv'\
' sgemm cgemm'.split())
if using_lapack_blas:
target_dir = join(target_dir, 'blas')
skip_names['fblas'].extend(\
'drotmg srotmg drotm srotm'.split())
if atlas_version == '3.2.1_pre3.3.6':
target_dir = join(target_dir, 'atlas321')
skip_names['clapack'].extend(\
'sgetri dgetri cgetri zgetri spotri dpotri cpotri zpotri'\
' slauum dlauum clauum zlauum strtri dtrtri ctrtri ztrtri'.split())
elif atlas_version and atlas_version > '3.4.0' and atlas_version <= '3.5.12':
skip_names['clapack'].extend('cpotrf zpotrf'.split())
# fblas:
if needs_cblas_wrapper(lapack_opt):
sources = ['fblas.pyf.src', join('src', 'fblaswrap_veclib_c.c')],
else:
sources = ['fblas.pyf.src', join('src', 'fblaswrap.f')]
# Note: `depends` needs to include fblaswrap(_veclib) for both files to be
# included by "python setup.py sdist"
config.add_extension('fblas',
sources=sources,
depends=[
'fblas_l?.pyf.src',
join('src', 'fblaswrap_veclib_c.c'),
join('src', 'fblaswrap.f')
],
extra_info=lapack_opt)
# flapack:
config.add_extension('flapack',
sources=['flapack.pyf.src'],
depends=['flapack_user.pyf.src'],
extra_info=lapack_opt)
if atlas_version is not None:
# cblas:
config.add_extension('cblas',
sources=['cblas.pyf.src'],
depends=['cblas.pyf.src', 'cblas_l1.pyf.src'],
f2py_options=['skip:'] + skip_names['cblas'] +
[':'],
extra_info=lapack_opt)
# clapack:
config.add_extension('clapack',
sources=['clapack.pyf.src'],
depends=['clapack.pyf.src'],
f2py_options=['skip:'] + skip_names['clapack'] +
[':'],
extra_info=lapack_opt)
# _flinalg:
config.add_extension('_flinalg',
sources=[join('src', 'det.f'),
join('src', 'lu.f')],
extra_info=lapack_opt)
# calc_lwork:
config.add_extension('calc_lwork', [join('src', 'calc_lwork.f')],
extra_info=lapack_opt)
# atlas_version:
if os.name == 'nt' and ('FPATH' in os.environ or 'MKLROOT' in os.environ):
define_macros = [('NO_ATLAS_INFO', 1)]
else:
define_macros = []
config.add_extension('atlas_version', ['atlas_version.c'],
extra_info=lapack_opt,
define_macros=define_macros)
config.add_data_dir('tests')
config.add_data_dir('benchmarks')
return config
def prediction_zip(prediction_request, user_id, worker):
worker = str(worker)
model_file_url = prediction_request.model_url
test_zip_folder = prediction_request.zip_file_url
storage_label = prediction_request.label
name = prediction_request.name
zip_path = file_download(test_zip_folder, user_id)
images_folder = extract_data(zip_path, worker)
zip_path = file_download(model_file_url, user_id)
model_folder = extract_data(zip_path, worker)
model_file = model_json = ""
for i in os.listdir(model_folder):
if i.endswith(".model"):
model_file = i
if i.endswith(".json"):
model_json = i
if model_file is None:
raise NotFoundError("model not found")
if model_json is None:
raise NotFoundError("model json not found")
with open(model_folder + "/" + model_json) as f:
class_config = json.load(f)
pred_file = name + "_" + worker + "_prediction.csv"
model = load_model(model_folder + "/" + model_file)
images = os.listdir(images_folder)
try:
labels = []
imgs = []
classes = []
for img_name in images:
if not img_name.endswith(".csv"):
path = images_folder + "/" + img_name
img = image.load_img(path, target_size=(HEIGHT, WIDTH))
x = image.img_to_array(img)
x = np.expand_dims(x, axis=0)
x = preprocess_input(x)
preds = model.predict(x)[0]
result = {}
z = 0
for i in class_config.keys():
label = class_config[i]
result[label] = preds[z]
z += 1
print(result)
cls = sorted(result.items(), key=lambda j: j[1],
reverse=True)[0][0]
imgs.append(img_name)
labels.append(result)
classes.append(cls)
df = pd.DataFrame(
list(zip(imgs, labels, classes)),
columns=["image_name", "prediction_json", "prediction_class"])
df.to_csv(pred_file, index=False)
csv_file_url = file_upload(pred_file, user_id, storage_label)
return csv_file_url
finally:
rmtree(model_folder)
os.remove(pred_file)
rmtree(images_folder)
def configuration(parent_package='', top_path=None):
from numpy.distutils.system_info import get_info, NotFoundError
from numpy.distutils.misc_util import Configuration
from interface_gen import generate_interface
config = Configuration('linalg', parent_package, top_path)
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
atlas_version = ([v[3:-3] for k,v in lapack_opt.get('define_macros',[]) \
if k=='ATLAS_INFO']+[None])[0]
if atlas_version:
print('ATLAS version: %s' % atlas_version)
target_dir = ''
skip_names = {'clapack': [], 'flapack': [], 'cblas': [], 'fblas': []}
if skip_single_routines:
target_dir = 'dbl'
skip_names['clapack'].extend(\
'sgesv cgesv sgetrf cgetrf sgetrs cgetrs sgetri cgetri'\
' sposv cposv spotrf cpotrf spotrs cpotrs spotri cpotri'\
' slauum clauum strtri ctrtri'.split())
skip_names['flapack'].extend(skip_names['clapack'])
skip_names['flapack'].extend(\
'sgesdd cgesdd sgelss cgelss sgeqrf cgeqrf sgeev cgeev'\
' sgegv cgegv ssyev cheev slaswp claswp sgees cgees'
' sggev cggev'.split())
skip_names['cblas'].extend('saxpy caxpy'.split())
skip_names['fblas'].extend(skip_names['cblas'])
skip_names['fblas'].extend(\
'srotg crotg srotmg srot csrot srotm sswap cswap sscal cscal'\
' csscal scopy ccopy sdot cdotu cdotc snrm2 scnrm2 sasum scasum'\
' isamax icamax sgemv cgemv chemv ssymv strmv ctrmv'\
' sgemm cgemm'.split())
if using_lapack_blas:
target_dir = join(target_dir, 'blas')
skip_names['fblas'].extend(\
'drotmg srotmg drotm srotm'.split())
if atlas_version == '3.2.1_pre3.3.6':
target_dir = join(target_dir, 'atlas321')
skip_names['clapack'].extend(\
'sgetri dgetri cgetri zgetri spotri dpotri cpotri zpotri'\
' slauum dlauum clauum zlauum strtri dtrtri ctrtri ztrtri'.split())
elif atlas_version and atlas_version > '3.4.0' and atlas_version <= '3.5.12':
skip_names['clapack'].extend('cpotrf zpotrf'.split())
def generate_pyf(extension, build_dir):
name = extension.name.split('.')[-1]
target = join(build_dir, target_dir, name + '.pyf')
if name[0] == 'c' and atlas_version is None and newer(
__file__, target):
f = open(target, 'w')
f.write('python module ' + name + '\n')
f.write('usercode void empty_module(void) {}\n')
f.write('interface\n')
f.write('subroutine empty_module()\n')
f.write('intent(c) empty_module\n')
f.write('end subroutine empty_module\n')
f.write('end interface\nend python module' + name + '\n')
f.close()
return target
if newer_group(extension.depends, target):
generate_interface(name, extension.depends[0], target,
skip_names[name])
return target
depends = [
'generic_fblas.pyf',
'generic_fblas1.pyf',
'generic_fblas2.pyf',
'generic_fblas3.pyf',
'interface_gen.py',
join('src', 'fblaswrap_veclib_c.c'),
join('src', 'fblaswrap.f'),
]
# fblas:
if needs_cblas_wrapper(lapack_opt):
config.add_extension(
'fblas',
sources=[generate_pyf,
join('src', 'fblaswrap_veclib_c.c')],
depends=depends,
extra_info=lapack_opt)
else:
config.add_extension(
'fblas',
sources=[generate_pyf, join('src', 'fblaswrap.f')],
depends=depends,
extra_info=lapack_opt)
# cblas:
config.add_extension('cblas',
sources=[generate_pyf],
depends=[
'generic_cblas.pyf', 'generic_cblas1.pyf',
'interface_gen.py'
],
extra_info=lapack_opt)
# flapack:
config.add_extension('flapack',
sources=[generate_pyf],
depends=[
'generic_flapack.pyf',
'flapack_user_routines.pyf', 'interface_gen.py'
],
extra_info=lapack_opt)
# clapack:
config.add_extension('clapack',
sources=[generate_pyf],
depends=['generic_clapack.pyf', 'interface_gen.py'],
extra_info=lapack_opt)
# _flinalg:
config.add_extension('_flinalg',
sources=[join('src', 'det.f'),
join('src', 'lu.f')],
extra_info=lapack_opt)
# calc_lwork:
config.add_extension('calc_lwork', [join('src', 'calc_lwork.f')],
extra_info=lapack_opt)
# atlas_version:
if os.name == 'nt' and 'FPATH' in os.environ:
define_macros = [('NO_ATLAS_INFO', 1)]
else:
define_macros = []
config.add_extension('atlas_version', ['atlas_version.c'],
extra_info=lapack_opt,
define_macros=define_macros)
config.add_data_dir('tests')
config.add_data_dir('benchmarks')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.system_info import get_info, NotFoundError, numpy_info
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from scipy._build_utils import (get_sgemv_fix, get_g77_abi_wrappers,
split_fortran_files)
config = Configuration('linalg', parent_package, top_path)
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
atlas_version = ([
v[3:-3]
for k, v in lapack_opt.get('define_macros', []) if k == 'ATLAS_INFO'
] + [None])[0]
if atlas_version:
print(('ATLAS version: %s' % atlas_version))
# fblas:
sources = ['fblas.pyf.src']
sources += get_g77_abi_wrappers(lapack_opt)
sources += get_sgemv_fix(lapack_opt)
config.add_extension('_fblas',
sources=sources,
depends=['fblas_l?.pyf.src'],
extra_info=lapack_opt)
# flapack:
sources = ['flapack.pyf.src']
sources += get_g77_abi_wrappers(lapack_opt)
config.add_extension('_flapack',
sources=sources,
depends=['flapack_user.pyf.src'],
extra_info=lapack_opt)
if atlas_version is not None:
# cblas:
config.add_extension('_cblas',
sources=['cblas.pyf.src'],
depends=['cblas.pyf.src', 'cblas_l1.pyf.src'],
extra_info=lapack_opt)
# clapack:
config.add_extension('_clapack',
sources=['clapack.pyf.src'],
depends=['clapack.pyf.src'],
extra_info=lapack_opt)
# _flinalg:
config.add_extension('_flinalg',
sources=[join('src', 'det.f'),
join('src', 'lu.f')],
extra_info=lapack_opt)
# _interpolative:
routines_to_split = [
'dfftb1',
'dfftf1',
'dffti1',
'dsint1',
'dzfft1',
'id_srand',
'idd_copyints',
'idd_id2svd0',
'idd_pairsamps',
'idd_permute',
'idd_permuter',
'idd_random_transf0',
'idd_random_transf0_inv',
'idd_random_transf_init0',
'idd_subselect',
'iddp_asvd0',
'iddp_rsvd0',
'iddr_asvd0',
'iddr_rsvd0',
'idz_estrank0',
'idz_id2svd0',
'idz_permute',
'idz_permuter',
'idz_random_transf0_inv',
'idz_random_transf_init0',
'idz_random_transf_init00',
'idz_realcomp',
'idz_realcomplex',
'idz_reco',
'idz_subselect',
'idzp_aid0',
'idzp_aid1',
'idzp_asvd0',
'idzp_rsvd0',
'idzr_asvd0',
'idzr_reco',
'idzr_rsvd0',
'zfftb1',
'zfftf1',
'zffti1',
]
print('Splitting linalg.interpolative Fortran source files')
dirname = os.path.split(os.path.abspath(__file__))[0]
fnames = split_fortran_files(join(dirname, 'src', 'id_dist', 'src'),
routines_to_split)
fnames = [join('src', 'id_dist', 'src', f) for f in fnames]
config.add_extension('_interpolative',
fnames + ["interpolative.pyf"],
extra_info=lapack_opt)
# _calc_lwork:
config.add_extension('_calc_lwork', [join('src', 'calc_lwork.f')],
extra_info=lapack_opt)
# _solve_toeplitz:
config.add_extension('_solve_toeplitz',
sources=[('_solve_toeplitz.c')],
include_dirs=[get_numpy_include_dirs()])
config.add_data_dir('tests')
# Cython BLAS/LAPACK
config.add_data_files('cython_blas.pxd')
config.add_data_files('cython_lapack.pxd')
sources = ['_blas_subroutine_wrappers.f', '_lapack_subroutine_wrappers.f']
sources += get_g77_abi_wrappers(lapack_opt)
sources += get_sgemv_fix(lapack_opt)
includes = numpy_info().get_include_dirs()
config.add_library('fwrappers', sources=sources, include_dirs=includes)
config.add_extension('cython_blas',
sources=['cython_blas.c'],
depends=[
'cython_blas.pyx', 'cython_blas.pxd',
'fortran_defs.h', '_blas_subroutines.h'
],
include_dirs=['.'],
libraries=['fwrappers'],
extra_info=lapack_opt)
config.add_extension('cython_lapack',
sources=['cython_lapack.c'],
depends=[
'cython_lapack.pyx', 'cython_lapack.pxd',
'fortran_defs.h', '_lapack_subroutines.h'
],
include_dirs=['.'],
libraries=['fwrappers'],
extra_info=lapack_opt)
config.add_extension('_decomp_update', sources=['_decomp_update.c'])
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('linalg',parent_package,top_path)
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
atlas_version = ([v[3:-3] for k,v in lapack_opt.get('define_macros',[]) \
if k=='ATLAS_INFO']+[None])[0]
if atlas_version:
print(('ATLAS version: %s' % atlas_version))
target_dir = ''
# fblas:
if needs_g77_abi_wrapper(lapack_opt):
sources = ['fblas.pyf.src', join('src', 'fblaswrap_veclib_c.c')],
else:
sources = ['fblas.pyf.src', join('src', 'fblaswrap.f')]
# Note: `depends` needs to include fblaswrap(_veclib) for both files to be
# included by "python setup.py sdist"
config.add_extension('_fblas',
sources = sources,
depends = ['fblas_l?.pyf.src',
join('src', 'fblaswrap_veclib_c.c'),
join('src', 'fblaswrap.f')],
extra_info = lapack_opt
)
# flapack:
config.add_extension('_flapack',
sources = ['flapack.pyf.src'],
depends = ['flapack_user.pyf.src'],
extra_info = lapack_opt
)
if atlas_version is not None:
# cblas:
config.add_extension('_cblas',
sources = ['cblas.pyf.src'],
depends = ['cblas.pyf.src', 'cblas_l1.pyf.src'],
extra_info = lapack_opt
)
# clapack:
config.add_extension('_clapack',
sources = ['clapack.pyf.src'],
depends = ['clapack.pyf.src'],
extra_info = lapack_opt
)
# _flinalg:
config.add_extension('_flinalg',
sources = [join('src','det.f'),join('src','lu.f')],
extra_info = lapack_opt
)
# calc_lwork:
config.add_extension('calc_lwork',
[join('src','calc_lwork.f')],
extra_info = lapack_opt
)
config.add_data_dir('tests')
config.add_data_dir('benchmarks')
return config
def configuration(parent_package='', top_path=None):
config = Configuration('mathlink', parent_package, top_path)
#Compile the amos library
config.add_library(
'famos', sources=[join('amos', '*f'),
join('amos', 'mach', '*f')])
#Add the g2c or gfortran libraries to the source, is there a better way?
def generate_fortran_library(ext, build_dir):
config_cmd = config.get_config_cmd()
config_cmd._check_compiler()
fc_type = config_cmd.fcompiler.compiler_type
config_cmd._clean()
if fc_type == 'gnu95':
ext.libraries.append('gfortran')
elif fc_type == 'gnu':
ext.libraries.append('g2c')
print("Compiler: %s, Extend libraries: %s" % (fc_type, ext.libraries))
return None
config.add_extension(
'bessel_ratios',
sources=['bessel_ratios.cpp', generate_fortran_library],
depends=['bessel_function_ratios.h'],
libraries=['famos'])
#C++ tridiagonal block solver
#Get blas/lapack resources from numpy
lapack_opt = config.get_info('lapack_opt')
#Get boost SOURCE resources from numpy
boost_src = config.get_info('boost_python')
if not lapack_opt:
from numpy.distutils.system_info import NotFoundError
raise NotFoundError('no lapack/blas resources found')
ublock_sources = [
'ublas_block_lu/ublocklu.cpp', 'ublas_block_lu/numimport.cpp'
]
ublock_depends = [
'ublas_block_lu/ublocklu.hpp', 'ublas_block_lu/numimport.hpp'
]
ublock_compile_flags = []
ublock_link_flags = []
ublock_library_dirs = []
ublock_include_dirs = ['ublas_block_lu']
ublock_libraries = []
#If boost_src is found, use that, otherwise use default directories
if boost_src:
print("Compiling boost-python from source")
ublock_include_dirs += boost_src['include_dirs']
ublock_libraries += boost_src['libraries']
elif _ublock_boost_prefix:
print("Using user configured boost-python")
boost_include_dir = join(_ublock_boost_prefix, 'include')
boost_library_dir = join(_ublock_boost_prefix, 'lib')
ublock_library_dirs = [boost_library_dir]
ublock_include_dirs = ['ublas_block_lu', boost_include_dir]
ublock_libraries = [_ublock_boost_lib]
else:
print("Using system boost-python")
boost_include_dir = "/usr/include"
boost_library_dir = "/usr/lib"
ublock_library_dirs = [boost_library_dir]
ublock_include_dirs = ['ublas_block_lu', boost_include_dir]
ublock_libraries = ['boost_python-mt']
if _ublock_compile_with_openmp:
ublock_compile_flags += ['-fopenmp', '-ftree-vectorize']
ublock_link_flags += ['-lgomp']
if _ublock_compile:
config.add_extension('ublocklu',
sources=ublock_sources,
depends=ublock_depends,
library_dirs=ublock_library_dirs,
include_dirs=ublock_include_dirs,
libraries=ublock_libraries,
extra_compile_args=ublock_compile_flags,
extra_link_args=ublock_link_flags,
extra_info=lapack_opt)
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('linalg', parent_package, top_path)
lapack_opt = get_info('lapack_opt')
if not lapack_opt:
raise NotFoundError('no lapack/blas resources found')
atlas_version = ([
v[3:-3]
for k, v in lapack_opt.get('define_macros', []) if k == 'ATLAS_INFO'
] + [None])[0]
if atlas_version:
print(('ATLAS version: %s' % atlas_version))
# fblas:
if needs_g77_abi_wrapper(lapack_opt):
sources = ['fblas.pyf.src', join('src', 'fblaswrap_veclib_c.c')],
else:
sources = ['fblas.pyf.src', join('src', 'fblaswrap_dummy.f')]
# Note: `depends` needs to include fblaswrap(_veclib) for both files to be
# included by "python setup.py sdist"
config.add_extension('_fblas',
sources=sources,
depends=[
'fblas_l?.pyf.src',
join('src', 'fblaswrap_veclib_c.c'),
join('src', 'fblaswrap_dummy.f')
],
extra_info=lapack_opt)
# flapack:
if needs_g77_abi_wrapper(lapack_opt):
sources = ['flapack.pyf.src', join('src', 'flapackwrap_veclib.f')],
else:
sources = ['flapack.pyf.src', join('src', 'flapackwrap_dummy.f')]
config.add_extension('_flapack',
sources=sources,
depends=[
'flapack_user.pyf.src',
join('src', 'flapackwrap_veclib.f'),
join('src', 'flapackwrap_dummy.f')
],
extra_info=lapack_opt)
if atlas_version is not None:
# cblas:
config.add_extension('_cblas',
sources=['cblas.pyf.src'],
depends=['cblas.pyf.src', 'cblas_l1.pyf.src'],
extra_info=lapack_opt)
# clapack:
config.add_extension('_clapack',
sources=['clapack.pyf.src'],
depends=['clapack.pyf.src'],
extra_info=lapack_opt)
# _flinalg:
config.add_extension('_flinalg',
sources=[join('src', 'det.f'),
join('src', 'lu.f')],
extra_info=lapack_opt)
# calc_lwork:
config.add_extension('calc_lwork', [join('src', 'calc_lwork.f')],
extra_info=lapack_opt)
# _interpolative:
config.add_extension('_interpolative',
[
join('src', 'id_dist', 'src', fn) for fn in [
'dfft.f',
'idd_frm.f',
'idd_house.f',
'idd_id2svd.f',
'idd_id.f',
'iddp_aid.f',
'iddp_asvd.f',
'iddp_rid.f',
'iddp_rsvd.f',
'idd_qrpiv.f',
'iddr_aid.f',
'iddr_asvd.f',
'iddr_rid.f',
'iddr_rsvd.f',
'idd_sfft.f',
'idd_snorm.f',
'idd_svd.f',
'id_rand.f',
'id_rtrans.f',
'idz_frm.f',
'idz_house.f',
'idz_id2svd.f',
'idz_id.f',
'idzp_aid.f',
'idzp_asvd.f',
'idzp_rid.f',
'idzp_rsvd.f',
'idz_qrpiv.f',
'idzr_aid.f',
'idzr_asvd.f',
'idzr_rid.f',
'idzr_rsvd.f',
'idz_sfft.f',
'idz_snorm.f',
'idz_svd.f',
]
] + ["interpolative.pyf"],
extra_info=lapack_opt)
config.add_data_dir('tests')
config.add_data_dir('benchmarks')
return config
