def build_extension(self, ext):
from numpy import get_include as _np_inc
np_inc = _np_inc()
pybind_inc = 'lib/pybind11/include'
ext.include_dirs.append(np_inc)
ext.include_dirs.append(pybind_inc)
ext.extra_compile_args += ['-fopenmp' if sys.platform != 'darwin' else '-fopenmp=libiomp5']
if sys.platform.startswith('linux'):
ext.extra_link_args += ['-lgomp']
elif sys.platform == 'darwin':
ext.extra_link_args += ['-liomp5']
super(Build, self).build_extension(ext)
def build_extensions(self):
extra_compile_args = []
extra_link_args = []
define_macros = []
from numpy import get_include as _np_inc
np_inc = _np_inc()
pybind_inc = Path(pybind11.get_include())
common_inc = Path('deeptime') / 'src' / 'include'
if self.compiler.compiler_type == 'msvc':
cxx_flags = [
'/EHsc', '/std:c++latest',
'/DVERSION_INFO=\\"%s\\"' % self.distribution.get_version()
]
extra_link_args.append('/machine:X64')
else:
cxx_flags = ['-std=c++17']
extra_compile_args += ['-pthread']
extra_link_args = ['-lpthread']
has_openmp = supports_omp(self.compiler)
if has_openmp:
extra_compile_args += [
'-fopenmp' if sys.platform != 'darwin' else '-fopenmp=libiomp5'
]
if sys.platform.startswith('linux'):
extra_link_args += ['-lgomp']
elif sys.platform == 'darwin':
extra_link_args += ['-liomp5']
else:
raise ValueError("Should not happen.")
define_macros += [('USE_OPENMP', None)]
for ext in self.extensions:
ext.include_dirs.append(np_inc)
ext.include_dirs.append(pybind_inc.resolve())
ext.include_dirs.append(common_inc.resolve())
if ext.language == 'c++':
ext.extra_compile_args += cxx_flags
ext.extra_compile_args += extra_compile_args
ext.extra_link_args += extra_link_args
ext.define_macros += define_macros
super(Build, self).build_extensions()
def build_extension(self, ext):
from numpy import get_include as _np_inc
np_inc = _np_inc()
pybind_inc = 'lib/pybind11/include'
ext.include_dirs.append(np_inc)
ext.include_dirs.append(pybind_inc)
if supports_omp(self.compiler):
ext.extra_compile_args += [
'-fopenmp' if sys.platform != 'darwin' else '-fopenmp=libiomp5'
]
if sys.platform.startswith('linux'):
ext.extra_link_args += ['-lgomp']
elif sys.platform == 'darwin':
ext.extra_link_args += ['-liomp5']
else:
raise ValueError("Hmm.")
ext.define_macros += [('USE_OPENMP', None)]
super(Build, self).build_extension(ext)
def build_extensions(self):
extra_compile_args = []
extra_link_args = []
define_macros = []
from numpy import get_include as _np_inc
np_inc = _np_inc()
pybind_inc = 'lib/pybind11/include'
# TODO: this is platform dependent, e.g. win should be treated differently.
if self.compiler.compiler_type == 'msvc':
cxx_flags = [
'/EHsc', '/std:c++latest',
'/DVERSION_INFO=\\"%s\\"' % self.distribution.get_version()
]
extra_link_args.append('/machine:X64')
else:
cxx_flags = ['-std=c++14']
has_openmp = supports_omp(self.compiler)
if has_openmp:
extra_compile_args += [
'-fopenmp' if sys.platform != 'darwin' else '-fopenmp=libiomp5'
]
if sys.platform.startswith('linux'):
extra_link_args += ['-lgomp']
elif sys.platform == 'darwin':
extra_link_args += ['-liomp5']
else:
raise ValueError("Hmm.")
define_macros += [('USE_OPENMP', None)]
for ext in self.extensions:
ext.include_dirs.append(np_inc)
ext.include_dirs.append(pybind_inc)
if ext.language == 'c++':
ext.extra_compile_args += cxx_flags
ext.extra_compile_args += extra_compile_args
ext.extra_link_args += extra_link_args
ext.define_macros += define_macros
super(Build, self).build_extensions()
def build_extensions(self):
extra_compile_args = []
extra_link_args = []
define_macros = []
from numpy import get_include as _np_inc
np_inc = _np_inc()
pybind_inc = Path(pybind11.get_include())
common_inc = Path('deeptime') / 'src' / 'include'
if self.compiler.compiler_type == 'msvc':
cxx_flags = [
'/EHsc', '/std:c++17', '/bigobj',
f'/DVERSION_INFO=\\"{self.distribution.get_version()}\\"'
]
extra_link_args.append('/machine:X64')
else:
cxx_flags = [
'-std=c++17', "-fvisibility=hidden", "-g0", "-Wno-register"
]
extra_compile_args += ['-pthread']
extra_link_args = ['-lpthread']
self.setup_openmp(define_macros, extra_compile_args, extra_link_args)
for ext in self.extensions:
ext.include_dirs.append(common_inc.resolve())
ext.include_dirs.append(np_inc)
ext.include_dirs.append(pybind_inc.resolve())
if ext.language == 'c++':
ext.extra_compile_args += cxx_flags
ext.extra_compile_args += extra_compile_args
ext.extra_link_args += extra_link_args
ext.define_macros += define_macros
super(Build, self).build_extensions()
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()
from numpy import get_include as _np_inc
np_inc = _np_inc()
exts = []
mle_trev_given_pi_dense_module = \
Extension('msmtools.estimation.dense.mle_trev_given_pi',
sources=['msmtools/estimation/dense/mle_trev_given_pi.pyx',
'msmtools/estimation/dense/_mle_trev_given_pi.c'],
depends=['msmtools/util/sigint_handler.h'],
include_dirs=['msmtools/estimation/dense', np_inc])
mle_trev_given_pi_sparse_module = \
Extension('msmtools.estimation.sparse.mle_trev_given_pi',
sources=['msmtools/estimation/sparse/mle_trev_given_pi.pyx',
'msmtools/estimation/sparse/_mle_trev_given_pi.c'],
depends=['msmtools/util/sigint_handler.h'],
include_dirs=['msmtools/estimation/dense', np_inc])
mle_trev_dense_module = \
Extension('msmtools.estimation.dense.mle_trev',
sources=['msmtools/estimation/dense/mle_trev.pyx',
'msmtools/estimation/dense/_mle_trev.c'],
depends=['msmtools/util/sigint_handler.h'],
include_dirs=[np_inc])
mle_trev_sparse_module = \
Extension('msmtools.estimation.sparse.mle_trev',
sources=['msmtools/estimation/sparse/mle_trev.pyx',
'msmtools/estimation/sparse/_mle_trev.c'],
depends=['msmtools/util/sigint_handler.h'],
include_dirs=[np_inc,
])
sampler_rev = \
Extension('msmtools.estimation.dense.sampler_rev',
sources=['msmtools/estimation/dense/sampler_rev.pyx',
'msmtools/estimation/dense/sample_rev.c',
'msmtools/estimation/dense/_rnglib.c',
'msmtools/estimation/dense/_ranlib.c'],
include_dirs=[np_inc,
])
sampler_revpi = \
Extension('msmtools.estimation.dense.sampler_revpi',
sources=['msmtools/estimation/dense/sampler_revpi.pyx',
'msmtools/estimation/dense/sample_revpi.c',
'msmtools/estimation/dense/_rnglib.c',
'msmtools/estimation/dense/_ranlib.c'],
include_dirs=[np_inc,
])
kahandot_module = \
Extension('msmtools.util.kahandot',
sources = ['msmtools/util/kahandot_src/kahandot.pyx',
'msmtools/util/kahandot_src/_kahandot.c'],
depends = ['msmtools/util/kahandot_src/_kahandot.h'],
include_dirs=[np_inc,
])
exts += [
mle_trev_given_pi_dense_module, mle_trev_given_pi_sparse_module,
mle_trev_dense_module, mle_trev_sparse_module, sampler_rev,
sampler_revpi, kahandot_module
]
if USE_CYTHON: # if we have cython available now, cythonize module
exts = cythonize(exts)
else:
# 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
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.')
import mdtraj
from numpy import get_include as _np_inc
np_inc = _np_inc()
pybind_inc = os.path.join(os.path.dirname(__file__), 'pybind11', 'include')
assert os.path.exists(pybind_inc)
exts = []
lib_prefix = 'lib' if sys.platform.startswith('win') else ''
common_cflags = [
'-O3',
]
clustering_module = \
Extension('pyemma.coordinates.clustering._ext',
sources=['pyemma/coordinates/clustering/src/clustering_module.cpp'],
include_dirs=[
mdtraj.capi()['include_dir'],
np_inc,
pybind_inc,
'pyemma/coordinates/clustering/include',
],
language='c++',
libraries=[lib_prefix+'theobald'],
library_dirs=[mdtraj.capi()['lib_dir']],
extra_compile_args=common_cflags)
covar_module = \
Extension('pyemma._ext.variational.estimators.covar_c._covartools',
sources=['pyemma/_ext/variational/estimators/covar_c/covartools.cpp'],
include_dirs=['pyemma/_ext/variational/estimators/covar_c/',
np_inc,
pybind_inc,
],
language='c++',
extra_compile_args=common_cflags)
eig_qr_module = \
Extension('pyemma._ext.variational.solvers.eig_qr.eig_qr',
sources=['pyemma/_ext/variational/solvers/eig_qr/eig_qr.pyx'],
include_dirs=['pyemma/_ext/variational/solvers/eig_qr/', np_inc],
extra_compile_args=['-std=c99'] + common_cflags)
orderedset = \
Extension('pyemma._ext.orderedset._orderedset',
sources=['pyemma/_ext/orderedset/_orderedset.pyx'],
include_dirs=[np_inc],
extra_compile_args=['-std=c99'] + common_cflags)
exts += [clustering_module, covar_module, eig_qr_module, orderedset]
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)
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.')
import mdtraj
# Note, that we add numpy include to every extension after declaration.
from numpy import get_include as _np_inc
np_inc = _np_inc()
pybind_inc = get_pybind_include()
lib_prefix = 'lib' if sys.platform.startswith('win') else ''
common_cflags = ['-O3', ]
clustering_module = \
Extension('pyemma.coordinates.clustering._ext',
sources=['pyemma/coordinates/clustering/src/clustering_module.cpp'],
include_dirs=[
mdtraj.capi()['include_dir'],
pybind_inc,
'pyemma/coordinates/clustering/include',
],
language='c++',
libraries=[lib_prefix+'theobald'],
library_dirs=[mdtraj.capi()['lib_dir']],
extra_compile_args=common_cflags)
covar_module = \
Extension('pyemma._ext.variational.estimators.covar_c._covartools',
sources=['pyemma/_ext/variational/estimators/covar_c/covartools.cpp'],
include_dirs=['pyemma/_ext/variational/estimators/covar_c/',
pybind_inc,
],
language='c++',
extra_compile_args=common_cflags)
eig_qr_module = \
Extension('pyemma._ext.variational.solvers.eig_qr.eig_qr',
sources=['pyemma/_ext/variational/solvers/eig_qr/eig_qr.pyx'],
include_dirs=['pyemma/_ext/variational/solvers/eig_qr/', np_inc],
extra_compile_args=['-std=c99'] + common_cflags)
orderedset = \
Extension('pyemma._ext.orderedset._orderedset',
sources=['pyemma/_ext/orderedset/_orderedset.pyx'],
extra_compile_args=['-std=c99'] + common_cflags)
extra_compile_args = ["-O3", "-std=c99"]
ext_bar = Extension(
"pyemma.thermo.extensions.bar",
sources=["pyemma/thermo/extensions/bar/bar.pyx",
"pyemma/thermo/extensions/bar/_bar.c",
"pyemma/thermo/extensions/util/_util.c"],
extra_compile_args=extra_compile_args)
ext_wham = Extension(
"pyemma.thermo.extensions.wham",
sources=["pyemma/thermo/extensions/wham/wham.pyx",
"pyemma/thermo/extensions/wham/_wham.c",
"pyemma/thermo/extensions/util/_util.c"],
extra_compile_args=extra_compile_args)
ext_mbar = Extension(
"pyemma.thermo.extensions.mbar",
sources=["pyemma/thermo/extensions/mbar/mbar.pyx",
"pyemma/thermo/extensions/mbar/_mbar.c",
"pyemma/thermo/extensions/util/_util.c"],
extra_compile_args=extra_compile_args)
ext_tram = Extension(
"pyemma.thermo.extensions.tram",
sources=["pyemma/thermo/extensions/tram/tram.pyx",
"pyemma/thermo/extensions/tram/_tram.c",
"pyemma/thermo/extensions/util/_util.c"],
extra_compile_args=extra_compile_args)
ext_dtram = Extension(
"pyemma.thermo.extensions.dtram",
sources=["pyemma/thermo/extensions/dtram/dtram.pyx",
"pyemma/thermo/extensions/dtram/_dtram.c",
"pyemma/thermo/extensions/util/_util.c"],
extra_compile_args=extra_compile_args)
ext_trammbar = Extension(
"pyemma.thermo.extensions.trammbar",
sources=["pyemma/thermo/extensions/trammbar/trammbar.pyx",
"pyemma/thermo/extensions/tram/_tram.c",
"pyemma/thermo/extensions/util/_util.c"],
extra_compile_args=extra_compile_args + ["-DTRAMMBAR"])
ext_mbar_direct = Extension(
"pyemma.thermo.extensions.mbar_direct",
sources=["pyemma/thermo/extensions/mbar_direct/mbar_direct.pyx",
"pyemma/thermo/extensions/mbar_direct/_mbar_direct.c",
"pyemma/thermo/extensions/util/_util.c"],
extra_compile_args=extra_compile_args)
ext_tram_direct = Extension(
"pyemma.thermo.extensions.tram_direct",
sources=["pyemma/thermo/extensions/tram_direct/tram_direct.pyx",
"pyemma/thermo/extensions/tram_direct/_tram_direct.c",
"pyemma/thermo/extensions/util/_util.c"],
extra_compile_args=extra_compile_args)
ext_trammbar_direct = Extension(
"pyemma.thermo.extensions.trammbar_direct",
sources=["pyemma/thermo/extensions/trammbar_direct/trammbar_direct.pyx",
"pyemma/thermo/extensions/tram_direct/_tram_direct.c",
"pyemma/thermo/extensions/util/_util.c"],
extra_compile_args=extra_compile_args + ["-DTRAMMBAR"])
ext_util = Extension(
"pyemma.thermo.extensions.util",
sources=["pyemma/thermo/extensions/util/util.pyx",
"pyemma/thermo/extensions/util/_util.c"],
extra_compile_args=extra_compile_args)
exts_thermo = [
ext_bar,
ext_wham,
ext_mbar,
ext_tram,
ext_dtram,
ext_trammbar,
ext_mbar_direct,
ext_tram_direct,
ext_trammbar_direct,
ext_util]
exts = [clustering_module,
covar_module,
eig_qr_module,
orderedset
]
exts += exts_thermo
for e in exts:
e.include_dirs.append(np_inc)
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, language_level=sys.version_info[0])
return exts
