def extensions():
from Cython.Build import cythonize
from numpy import get_include as np_get_include
np_inc = np_get_include()
common_cflags = [
'-O3',
]
fasthist_module = Extension(
'westpa.fasthist._fasthist',
sources=['src/westpa/fasthist/_fasthist.pyx'],
include_dirs=[np_inc],
extra_compile_args=common_cflags,
)
trajtree_module = Extension(
'westpa.trajtree._trajtree',
sources=['src/westpa/trajtree/_trajtree.pyx'],
include_dirs=[np_inc],
extra_compile_args=common_cflags,
)
mclib_module = Extension('westpa.mclib._mclib',
sources=['src/westpa/mclib/_mclib.pyx'],
include_dirs=[np_inc],
extra_compile_args=common_cflags)
binning_module = Extension(
'westpa.core.binning._assign',
sources=['src/westpa/core/binning/_assign.pyx'],
include_dirs=[np_inc],
extra_compile_args=common_cflags,
)
kinetics_module = Extension(
'westpa.core.kinetics._kinetics',
sources=['src/westpa/core/kinetics/_kinetics.pyx'],
include_dirs=[np_inc],
extra_compile_args=common_cflags,
)
reweight_module = Extension(
'westpa.core.reweight._reweight',
sources=['src/westpa/core/reweight/_reweight.pyx'],
include_dirs=[np_inc],
extra_compile_args=common_cflags,
)
exts = [
fasthist_module, trajtree_module, mclib_module, binning_module,
kinetics_module, reweight_module
]
exts = cythonize(exts, language_level=sys.version_info[0])
return exts
def extensions():
from Cython.Build import cythonize
from numpy import get_include as np_get_include
pybind_inc = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'ext', 'pybind11', 'include')
assert os.path.exists(
pybind_inc), 'pybind11 headers not found at %s' % pybind_inc
from mdtraj import capi as mdtraj_capi
mdtraj_inc = mdtraj_capi()['include_dir']
mdtraj_lib = mdtraj_capi()['lib_dir']
lib_prefix = 'lib' if sys.platform.startswith('win') else ''
common_cflags = [
'-O3',
]
clustering_module = \
Extension('pyerna.coordinates.clustering._ext',
sources=['pyerna/coordinates/clustering/src/clustering_module.cpp'],
include_dirs=[
mdtraj_inc,
pybind_inc,
'pyerna/coordinates/clustering/include',
],
language='c++',
libraries=[lib_prefix+'theobald'],
library_dirs=[mdtraj_lib],
extra_compile_args=common_cflags)
covar_module = \
Extension('pyerna._ext.variational.estimators.covar_c._covartools',
sources=['pyerna/_ext/variational/estimators/covar_c/covartools.cpp'],
include_dirs=['pyerna/_ext/variational/estimators/covar_c/',
pybind_inc,
],
language='c++',
extra_compile_args=common_cflags)
eig_qr_module = \
Extension('pyerna._ext.variational.solvers.eig_qr.eig_qr',
sources=['pyerna/_ext/variational/solvers/eig_qr/eig_qr.pyx'],
include_dirs=['pyerna/_ext/variational/solvers/eig_qr/'],
extra_compile_args=['-std=c99'] + common_cflags)
orderedset = \
Extension('pyerna._ext.orderedset._orderedset',
sources=['pyerna/_ext/orderedset/_orderedset.pyx'],
extra_compile_args=['-std=c99'] + common_cflags)
extra_compile_args = ["-O3", "-std=c99"]
ext_bar = Extension("pyerna.thermo.extensions.bar",
sources=[
"pyerna/thermo/extensions/bar/bar.pyx",
"pyerna/thermo/extensions/bar/_bar.c",
"pyerna/thermo/extensions/util/_util.c"
],
extra_compile_args=extra_compile_args)
ext_wham = Extension("pyerna.thermo.extensions.wham",
sources=[
"pyerna/thermo/extensions/wham/wham.pyx",
"pyerna/thermo/extensions/wham/_wham.c",
"pyerna/thermo/extensions/util/_util.c"
],
extra_compile_args=extra_compile_args)
ext_mbar = Extension("pyerna.thermo.extensions.mbar",
sources=[
"pyerna/thermo/extensions/mbar/mbar.pyx",
"pyerna/thermo/extensions/mbar/_mbar.c",
"pyerna/thermo/extensions/util/_util.c"
],
extra_compile_args=extra_compile_args)
ext_tram = Extension("pyerna.thermo.extensions.tram",
sources=[
"pyerna/thermo/extensions/tram/tram.pyx",
"pyerna/thermo/extensions/tram/_tram.c",
"pyerna/thermo/extensions/util/_util.c"
],
extra_compile_args=extra_compile_args)
ext_dtram = Extension("pyerna.thermo.extensions.dtram",
sources=[
"pyerna/thermo/extensions/dtram/dtram.pyx",
"pyerna/thermo/extensions/dtram/_dtram.c",
"pyerna/thermo/extensions/util/_util.c"
],
extra_compile_args=extra_compile_args)
ext_trammbar = Extension(
"pyerna.thermo.extensions.trammbar",
sources=[
"pyerna/thermo/extensions/trammbar/trammbar.pyx",
"pyerna/thermo/extensions/tram/_tram.c",
"pyerna/thermo/extensions/util/_util.c"
],
extra_compile_args=extra_compile_args + ["-DTRAMMBAR"])
ext_mbar_direct = Extension(
"pyerna.thermo.extensions.mbar_direct",
sources=[
"pyerna/thermo/extensions/mbar_direct/mbar_direct.pyx",
"pyerna/thermo/extensions/mbar_direct/_mbar_direct.c",
"pyerna/thermo/extensions/util/_util.c"
],
extra_compile_args=extra_compile_args)
ext_tram_direct = Extension(
"pyerna.thermo.extensions.tram_direct",
sources=[
"pyerna/thermo/extensions/tram_direct/tram_direct.pyx",
"pyerna/thermo/extensions/tram_direct/_tram_direct.c",
"pyerna/thermo/extensions/util/_util.c"
],
extra_compile_args=extra_compile_args)
ext_trammbar_direct = Extension(
"pyerna.thermo.extensions.trammbar_direct",
sources=[
"pyerna/thermo/extensions/trammbar_direct/trammbar_direct.pyx",
"pyerna/thermo/extensions/tram_direct/_tram_direct.c",
"pyerna/thermo/extensions/util/_util.c"
],
extra_compile_args=extra_compile_args + ["-DTRAMMBAR"])
ext_util = Extension("pyerna.thermo.extensions.util",
sources=[
"pyerna/thermo/extensions/util/util.pyx",
"pyerna/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
# Note, that we add numpy include to every extension after declaration.
np_inc = np_get_include()
for e in exts:
e.include_dirs.append(np_inc)
exts = cythonize(exts, language_level=sys.version_info[0])
return exts
dist.Distribution().fetch_build_eggs(['numpy'])
from numpy import get_include as np_get_include
import causalml
with open("README.md", "r", encoding="utf-8") as f:
long_description = f.read()
with open("requirements.txt") as f:
requirements = f.readlines()
extensions = [
Extension("causalml.inference.tree.causaltree",
["causalml/inference/tree/causaltree.pyx"],
libraries=[],
include_dirs=[np_get_include()],
extra_compile_args=["-O3"]),
Extension("causalml.inference.tree.uplift",
["causalml/inference/tree/uplift.pyx"],
libraries=[],
include_dirs=[np_get_include()],
extra_compile_args=["-O3"])
]
packages = find_packages()
setup(
name="causalml",
version=causalml.__version__,
author=
"Huigang Chen, Totte Harinen, Jeong-Yoon Lee, Yuchen Luo, Jing Pan, Mike Yung, Zhenyu Zhao",
except ImportError:
print "ERROR - please install the cython dependency manually:"
print "pip install cython"
sys_exit( 1 )
try:
from numpy import get_include as np_get_include
except ImportError:
print "ERROR - please install the numpy dependency manually:"
print "pip install numpy"
sys_exit( 1 )
ext_lse = Extension(
"pytram.lse",
sources=["ext/lse/lse.pyx", "ext/lse/_lse.c" ],
include_dirs=[np_get_include()],
extra_compile_args=["-O3"]
)
ext_dtram = Extension(
"pytram._dtram.ext",
sources=["ext/dtram/dtram.pyx", "ext/dtram/_dtram.c", "ext/lse/_lse.c" ],
include_dirs=[np_get_include()],
extra_compile_args=["-O3"]
)
ext_xtram = Extension(
"pytram._xtram.ext",
sources=["ext/xtram/xtram.pyx", "ext/xtram/_xtram.c" ],
include_dirs=[np_get_include()],
extra_compile_args=["-O3"]
)
lib_dirs = [
blas_opt['library_dirs'][0], lapack_opt['library_dirs'][0], config_path
]
# Compile resource information needed by seispy.signal.detect module
eigen_path = os.getcwd() + "/seispy/signal/src"
# Add statistics and detect extension modules from the seispy.signal
# sub-module.
kwargs['ext_modules'] = [
Extension('seispy.signal.statistics', ['seispy/signal/statistics.f90'],
libraries=libs,
library_dirs=lib_dirs,
extra_link_args=['-llapack', '-lblas']),
Extension(
'seispy.signal.detect',
sources=['seispy/signal/src/detect.cc', 'seispy/signal/src/picker.cc'],
include_dirs=[np_get_include(), eigen_path],
extra_compile_args=['-O3']),
Extension('seispy.hypocenter.accelerate',
sources=['seispy/hypocenter/accelerate.cc'])
]
kwargs['packages'] = ['seispy', 'seispy.signal', 'seispy.hypocenter']
kwargs['package_dir'] = {'seispy': 'seispy'}
# If $ANTELOPE environment variable is not initialized, install only the
# portions of the distribution that will operate independently of
# Antelope.
try:
antelope_dir = os.environ['ANTELOPE']
except KeyError:
print "INFO:: $ANTELOPE environment variable not detected."
print "INFO:: Installing Antelope independent components only."
setup(**kwargs)
return libraries,library_dirs,include_dirs
# Now use the above function to set up our extension library's needs:
ext_libraries, ext_library_dirs, ext_include_dirs = pkg_config(pkg_libraries=["lal","lalsimulation","lalinspiral"])
# Setup our swig options. We need the first two to match with how the swiglal
# wrappings are compiled, so that our module can talk to theirs. Then we must
# reassemble the include_dirs to add the "-I" so swig can find things
ext_swig_opts = ['-O','-keyword','-builtin','-outdir','pycbc']
for libpath in ext_include_dirs:
ext_swig_opts.append('-I'+str(libpath))
# Numpy include must be added separately:
ext_include_dirs += [np_get_include()]
# Define our extension module
pycbc_headers = []
lalwrap_module = Extension('_lalwrap',
sources=['include/lalwrap.i'],
depends=['include/pycbc_laltypes.i'],
swig_opts=ext_swig_opts,
include_dirs=ext_include_dirs,
library_dirs=ext_library_dirs,
libraries=ext_libraries,
extra_compile_args=['-std=c99']
)
pycbc_headers.append('include/lalwrap.i')
pycbc_headers.append('include/pycbc_laltypes.i')
testlalwrap_module = Extension('_testlalwrap',
