def extensions():
"""How do we handle cython:
1. when on git, require cython during setup time (do not distribute
generated .c files via git)
a) cython present -> fine
b) no cython present -> install it on the fly. Extensions have to have .pyx suffix
This is solved via a lazy evaluation of the extension list. This is needed,
because build_ext is being called before cython will be available.
https://bitbucket.org/pypa/setuptools/issue/288/cannot-specify-cython-under-setup_requires
2. src dist install (have pre-converted c files and pyx files)
a) cython present -> fine
b) no cython -> use .c files
"""
USE_CYTHON = False
try:
from Cython.Build import cythonize
USE_CYTHON = True
except ImportError:
warnings.warn('Cython not found. Using pre cythonized files.')
# setup OpenMP support
from setup_util import detect_openmp
openmp_enabled, needs_gomp = detect_openmp()
import mdtraj
from numpy import get_include as _np_inc
np_inc = _np_inc()
exts = []
if sys.platform.startswith('win'):
lib_prefix = 'lib'
else:
lib_prefix = ''
regspatial_module = \
Extension('pyemma.coordinates.clustering.regspatial',
sources=[
'pyemma/coordinates/clustering/src/regspatial.c',
'pyemma/coordinates/clustering/src/clustering.c'],
include_dirs=[
mdtraj.capi()['include_dir'],
np_inc,
'pyemma/coordinates/clustering/include',
],
libraries=[lib_prefix+'theobald'],
library_dirs=[mdtraj.capi()['lib_dir']],
extra_compile_args=['-std=c99', '-g', '-O3', '-pg'])
kmeans_module = \
Extension('pyemma.coordinates.clustering.kmeans_clustering',
sources=[
'pyemma/coordinates/clustering/src/kmeans.c',
'pyemma/coordinates/clustering/src/clustering.c'],
include_dirs=[
mdtraj.capi()['include_dir'],
np_inc,
'pyemma/coordinates/clustering/include'],
libraries=[lib_prefix+'theobald'],
library_dirs=[mdtraj.capi()['lib_dir']],
extra_compile_args=['-std=c99'])
covar_module = \
Extension('pyemma.coordinates.estimators.covar.covar_c.covartools',
sources=['pyemma/coordinates/estimators/covar/covar_c/covartools.pyx',
'pyemma/coordinates/estimators/covar/covar_c/_covartools.c'],
include_dirs=['pyemma/coordinates/estimators/covar/covar_c/',
np_inc,
],
extra_compile_args=['-std=c99', '-O3'])
exts += [
regspatial_module,
kmeans_module,
covar_module,
]
if not USE_CYTHON:
# replace pyx files by their pre generated c code.
for e in exts:
new_src = []
for s in e.sources:
new_src.append(s.replace('.pyx', '.c'))
e.sources = new_src
else:
exts = cythonize(exts)
if openmp_enabled:
warnings.warn('enabled openmp')
omp_compiler_args = ['-fopenmp']
omp_libraries = ['-lgomp'] if needs_gomp else []
omp_defines = [('USE_OPENMP', None)]
for e in exts:
e.extra_compile_args += omp_compiler_args
e.extra_link_args += omp_libraries
e.define_macros += omp_defines
return exts
def extensions():
"""How do we handle cython:
1. when on git, require cython during setup time (do not distribute
generated .c files via git)
a) cython present -> fine
b) no cython present -> install it on the fly. Extensions have to have .pyx suffix
This is solved via a lazy evaluation of the extension list. This is needed,
because build_ext is being called before cython will be available.
https://bitbucket.org/pypa/setuptools/issue/288/cannot-specify-cython-under-setup_requires
2. src dist install (have pre-converted c files and pyx files)
a) cython present -> fine
b) no cython -> use .c files
"""
USE_CYTHON = False
try:
from Cython.Build import cythonize
USE_CYTHON = True
except ImportError:
warnings.warn('Cython not found. Using pre cythonized files.')
# setup OpenMP support
from setup_util import detect_openmp
openmp_enabled, needs_gomp = detect_openmp()
exts = []
mle_trev_given_pi_dense_module = \
Extension('pyemma.msm.estimation.dense.mle_trev_given_pi',
sources=['pyemma/msm/estimation/dense/mle_trev_given_pi.pyx',
'pyemma/msm/estimation/dense/_mle_trev_given_pi.c'],
include_dirs=['pyemma/msm/estimation/dense'])
mle_trev_given_pi_sparse_module = \
Extension('pyemma.msm.estimation.sparse.mle_trev_given_pi',
sources=['pyemma/msm/estimation/sparse/mle_trev_given_pi.pyx',
'pyemma/msm/estimation/sparse/_mle_trev_given_pi.c'],
include_dirs=['pyemma/msm/estimation/dense'])
mle_trev_sparse_module = \
Extension('pyemma.msm.estimation.sparse.mle_trev',
sources=['pyemma/msm/estimation/sparse/mle_trev.pyx',
'pyemma/msm/estimation/sparse/_mle_trev.c'])
exts += [mle_trev_given_pi_dense_module,
mle_trev_given_pi_sparse_module,
mle_trev_sparse_module]
# kahan_sum = Extension('pyemma.coordinates.coordinate_transformation.exts.stable_sum',
# sources=['pyemma/coordinates/coordinate_transformation/exts/stable_sum.pyx'],
# extra_compile_args = ['-g'])
#
# update_mean = Extension('pyemma.coordinates.coordinate_transformation.exts.fmath_wrapper',
# sources=['pyemma/coordinates/coordinate_transformation/exts/fmath_wrapper.pyx'],)
#
# #exts += [kahan_sum]
# exts += [update_mean]
if USE_CYTHON: # if we have cython available now, cythonize module
exts = cythonize(exts)
if openmp_enabled:
warnings.warn('enabled openmp')
omp_compiler_args = ['-fopenmp']
omp_libraries = ['-lgomp'] if needs_gomp else []
omp_defines = [('USE_OPENMP', None)]
for e in exts:
e.extra_compile_args += omp_compiler_args
e.extra_link_args += omp_libraries
e.define_macros += omp_defines
return exts
def extensions():
"""How do we handle cython:
1. when on git, require cython during setup time (do not distribute
generated .c files via git)
a) cython present -> fine
b) no cython present -> install it on the fly. Extensions have to have .pyx suffix
This is solved via a lazy evaluation of the extension list. This is needed,
because build_ext is being called before cython will be available.
https://bitbucket.org/pypa/setuptools/issue/288/cannot-specify-cython-under-setup_requires
2. src dist install (have pre-converted c files and pyx files)
a) cython present -> fine
b) no cython -> use .c files
"""
USE_CYTHON = False
try:
from Cython.Build import cythonize
USE_CYTHON = True
except ImportError:
warnings.warn('Cython not found. Using pre cythonized files.')
# setup OpenMP support
from setup_util import detect_openmp
openmp_enabled, needs_gomp = detect_openmp()
import mdtraj
exts = []
mle_trev_given_pi_dense_module = \
Extension('pyemma.msm.estimation.dense.mle_trev_given_pi',
sources=['pyemma/msm/estimation/dense/mle_trev_given_pi.pyx',
'pyemma/msm/estimation/dense/_mle_trev_given_pi.c'],
include_dirs=['pyemma/msm/estimation/dense'])
mle_trev_given_pi_sparse_module = \
Extension('pyemma.msm.estimation.sparse.mle_trev_given_pi',
sources=['pyemma/msm/estimation/sparse/mle_trev_given_pi.pyx',
'pyemma/msm/estimation/sparse/_mle_trev_given_pi.c'],
include_dirs=['pyemma/msm/estimation/dense'])
mle_trev_sparse_module = \
Extension('pyemma.msm.estimation.sparse.mle_trev',
sources=['pyemma/msm/estimation/sparse/mle_trev.pyx',
'pyemma/msm/estimation/sparse/_mle_trev.c'])
if sys.platform.startswith('win'):
lib_prefix = 'lib'
else:
lib_prefix = ''
regspatial_module = \
Extension('pyemma.coordinates.clustering.regspatial',
sources = ['pyemma/coordinates/clustering/regspatial.c'],
include_dirs = [mdtraj.capi()['include_dir']],
libraries = [lib_prefix+'theobald'],
library_dirs = [mdtraj.capi()['lib_dir']])
exts += [mle_trev_given_pi_dense_module,
mle_trev_given_pi_sparse_module,
mle_trev_sparse_module,
regspatial_module]
if USE_CYTHON: # if we have cython available now, cythonize module
exts = cythonize(exts)
if openmp_enabled:
warnings.warn('enabled openmp')
omp_compiler_args = ['-fopenmp']
omp_libraries = ['-lgomp'] if needs_gomp else []
omp_defines = [('USE_OPENMP', None)]
for e in exts:
e.extra_compile_args += omp_compiler_args
e.extra_link_args += omp_libraries
e.define_macros += omp_defines
return exts