def get_distutils_extension(modname, pyxfilename, language_level=None):
# try:
# import hashlib
# except ImportError:
# import md5 as hashlib
# extra = "_" + hashlib.md5(open(pyxfilename).read()).hexdigest()
# modname = modname + extra
extension_mod,setup_args = handle_special_build(modname, pyxfilename)
if not extension_mod:
from distutils.extension import Extension
extension_mod = Extension(name = modname, sources=[pyxfilename])
if language_level is not None:
extension_mod.cython_directives = {'language_level': language_level}
return extension_mod,setup_args
def get_distutils_extension(modname, pyxfilename, language_level=None):
# try:
# import hashlib
# except ImportError:
# import md5 as hashlib
# extra = "_" + hashlib.md5(open(pyxfilename).read()).hexdigest()
# modname = modname + extra
extension_mod,setup_args = handle_special_build(modname, pyxfilename)
if not extension_mod:
if not isinstance(pyxfilename, str):
# distutils is stupid in Py2 and requires exactly 'str'
# => encode accidentally coerced unicode strings back to str
pyxfilename = pyxfilename.encode(sys.getfilesystemencoding())
from distutils.extension import Extension
extension_mod = Extension(name = modname, sources=[pyxfilename])
if language_level is not None:
extension_mod.cython_directives = {'language_level': language_level}
return extension_mod,setup_args
# Recover the CLASS version
with open(os.path.join(include_folder, 'common.h'), 'r') as v_file:
for line in v_file:
if line.find("_VERSION_") != -1:
# get rid of the " and the v
VERSION = line.split()[-1][2:-1]
break
# Define cython extension and fix Python version
classy_ext = Extension("classy", [os.path.join(classy_folder, "classy.pyx")],
include_dirs=[nm.get_include(), include_folder],
libraries=liblist,
library_dirs=[root_folder, GCCPATH],
extra_link_args=['-lgomp'])
#import six
#classy_ext.cython_directives = {'language_level': "3" if six.PY3 else "2"}
classy_ext.cython_directives = {'language_level': "2"}
setup(
name='classy',
version=VERSION,
description='Python interface to the Cosmological Boltzmann code CLASS',
url='http://www.class-code.net',
cmdclass={'build_ext': build_ext},
ext_modules=[classy_ext],
#data_files=[('bbn', ['../bbn/sBBN.dat'])]
)
if "/" in ext_name:
ext_name = ext_name.replace("/", ".")
sources = [pyxfile]
extmod = Extension(ext_name,
sources=sources,
libraries=['cpptraj'],
language='c++',
library_dirs=[libdir, ],
include_dirs=[cpptraj_include, pytraj_home],
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args)
extmod.cython_directives = {
'embedsignature': True,
'boundscheck': False,
'wraparound': False,
}
ext_modules.append(extmod)
setup_args = {}
packages = [
'pytraj',
'pytraj.utils',
'pytraj.actions',
'pytraj.analyses',
'pytraj.datasets',
'pytraj.externals',
'pytraj.trajs',
'pytraj.datafiles',
'pytraj.datafiles.Ala3',
def c_to_dll(filename, ext = None, force_rebuild = 0,
build_in_temp=False, cbuild_dir=None, setup_args={},
reload_support=False, inplace=False):
"""Compile a C file to a DLL and return the name of the generated .so
or .dll ."""
assert os.path.exists(filename), "Could not find %s" % os.path.abspath(filename)
path, name = os.path.split(os.path.abspath(filename))
if not ext:
modname, extension = os.path.splitext(name)
assert extension in (".c", ".py"), extension
if not HAS_CYTHON:
filename = filename[:-len(extension)] + '.c'
ext = Extension(name=modname, sources=[filename])
if not cbuild_dir:
cbuild_dir = os.path.join(path, "_cbld")
package_base_dir = path
for package_name in ext.name.split('.')[-2::-1]:
package_base_dir, pname = os.path.split(package_base_dir)
if pname != package_name:
# something is wrong - package path doesn't match file path
package_base_dir = None
break
script_args=setup_args.get("script_args",[])
if DEBUG or "--verbose" in script_args:
quiet = "--verbose"
else:
quiet = "--quiet"
args = [quiet, "build_ext"]
if force_rebuild:
args.append("--force")
if inplace and package_base_dir:
args.extend(['--build-lib', package_base_dir])
if ext.name == '__init__' or ext.name.endswith('.__init__'):
# package => provide __path__ early
if not hasattr(ext, 'cython_directives'):
ext.cython_directives = {'set_initial_path' : 'SOURCEFILE'}
elif 'set_initial_path' not in ext.cython_directives:
ext.cython_directives['set_initial_path'] = 'SOURCEFILE'
if HAS_CYTHON and build_in_temp:
args.append("--pyrex-c-in-temp")
sargs = setup_args.copy()
sargs.update({
"script_name": None,
"script_args": args + script_args,
})
# late import, in case setuptools replaced it
from distutils.dist import Distribution
dist = Distribution(sargs)
if not dist.ext_modules:
dist.ext_modules = []
dist.ext_modules.append(ext)
if HAS_CYTHON:
dist.cmdclass = {'build_ext': build_ext}
build = dist.get_command_obj('build')
build.build_base = cbuild_dir
cfgfiles = dist.find_config_files()
dist.parse_config_files(cfgfiles)
try:
ok = dist.parse_command_line()
except DistutilsArgError:
raise
if DEBUG:
print("options (after parsing command line):")
dist.dump_option_dicts()
assert ok
try:
obj_build_ext = dist.get_command_obj("build_ext")
dist.run_commands()
so_path = obj_build_ext.get_outputs()[0]
if obj_build_ext.inplace:
# Python distutils get_outputs()[ returns a wrong so_path
# when --inplace ; see http://bugs.python.org/issue5977
# workaround:
so_path = os.path.join(os.path.dirname(filename),
os.path.basename(so_path))
if reload_support:
org_path = so_path
timestamp = os.path.getmtime(org_path)
global _reloads
last_timestamp, last_path, count = _reloads.get(org_path, (None,None,0) )
if last_timestamp == timestamp:
so_path = last_path
else:
basename = os.path.basename(org_path)
while count < 100:
count += 1
r_path = os.path.join(obj_build_ext.build_lib,
basename + '.reload%s'%count)
try:
import shutil # late import / reload_support is: debugging
try:
# Try to unlink first --- if the .so file
# is mmapped by another process,
# overwriting its contents corrupts the
# loaded image (on Linux) and crashes the
# other process. On Windows, unlinking an
# open file just fails.
if os.path.isfile(r_path):
os.unlink(r_path)
except OSError:
continue
shutil.copy2(org_path, r_path)
so_path = r_path
except IOError:
continue
break
else:
# used up all 100 slots
raise ImportError("reload count for %s reached maximum"%org_path)
_reloads[org_path]=(timestamp, so_path, count)
return so_path
except KeyboardInterrupt:
sys.exit(1)
except (IOError, os.error):
exc = sys.exc_info()[1]
error = grok_environment_error(exc)
if DEBUG:
sys.stderr.write(error + "\n")
raise
def pyx_to_dll(filename,
ext=None,
force_rebuild=0,
build_in_temp=False,
pyxbuild_dir=None,
setup_args={},
reload_support=False,
inplace=False):
"""Compile a PYX file to a DLL and return the name of the generated .so
or .dll ."""
assert os.path.exists(
filename), "Could not find %s" % os.path.abspath(filename)
path, name = os.path.split(os.path.abspath(filename))
if not ext:
modname, extension = os.path.splitext(name)
assert extension in (".pyx", ".py"), extension
if not HAS_CYTHON:
filename = filename[:-len(extension)] + '.c'
ext = Extension(name=modname, sources=[filename])
if not pyxbuild_dir:
pyxbuild_dir = os.path.join(path, "_pyxbld")
package_base_dir = path
for package_name in ext.name.split('.')[-2::-1]:
package_base_dir, pname = os.path.split(package_base_dir)
if pname != package_name:
# something is wrong - package path doesn't match file path
package_base_dir = None
break
script_args = setup_args.get("script_args", [])
if DEBUG or "--verbose" in script_args:
quiet = "--verbose"
else:
quiet = "--quiet"
args = [quiet, "build_ext"]
if force_rebuild:
args.append("--force")
if inplace and package_base_dir:
args.extend(['--build-lib', package_base_dir])
if ext.name == '__init__' or ext.name.endswith('.__init__'):
# package => provide __path__ early
if not hasattr(ext, 'cython_directives'):
ext.cython_directives = {'set_initial_path': 'SOURCEFILE'}
elif 'set_initial_path' not in ext.cython_directives:
ext.cython_directives['set_initial_path'] = 'SOURCEFILE'
if HAS_CYTHON and build_in_temp:
args.append("--pyrex-c-in-temp")
sargs = setup_args.copy()
sargs.update({"script_name": None, "script_args": args + script_args})
dist = Distribution(sargs)
if not dist.ext_modules:
dist.ext_modules = []
dist.ext_modules.append(ext)
if HAS_CYTHON:
dist.cmdclass = {'build_ext': build_ext}
build = dist.get_command_obj('build')
build.build_base = pyxbuild_dir
cfgfiles = dist.find_config_files()
dist.parse_config_files(cfgfiles)
try:
ok = dist.parse_command_line()
except DistutilsArgError:
raise
if DEBUG:
print("options (after parsing command line):")
dist.dump_option_dicts()
assert ok
try:
obj_build_ext = dist.get_command_obj("build_ext")
dist.run_commands()
so_path = obj_build_ext.get_outputs()[0]
if obj_build_ext.inplace:
# Python distutils get_outputs()[ returns a wrong so_path
# when --inplace ; see http://bugs.python.org/issue5977
# workaround:
so_path = os.path.join(os.path.dirname(filename),
os.path.basename(so_path))
if reload_support:
org_path = so_path
timestamp = os.path.getmtime(org_path)
global _reloads
last_timestamp, last_path, count = _reloads.get(
org_path, (None, None, 0))
if last_timestamp == timestamp:
so_path = last_path
else:
basename = os.path.basename(org_path)
while count < 100:
count += 1
r_path = os.path.join(obj_build_ext.build_lib,
basename + '.reload%s' % count)
try:
import shutil # late import / reload_support is: debugging
try:
# Try to unlink first --- if the .so file
# is mmapped by another process,
# overwriting its contents corrupts the
# loaded image (on Linux) and crashes the
# other process. On Windows, unlinking an
# open file just fails.
if os.path.isfile(r_path):
os.unlink(r_path)
except OSError:
continue
shutil.copy2(org_path, r_path)
so_path = r_path
except IOError:
continue
break
else:
# used up all 100 slots
raise ImportError("reload count for %s reached maximum" %
org_path)
_reloads[org_path] = (timestamp, so_path, count)
return so_path
except KeyboardInterrupt:
sys.exit(1)
except (IOError, os.error):
exc = sys.exc_info()[1]
error = grok_environment_error(exc)
if DEBUG:
sys.stderr.write(error + "\n")
raise
# get rid of the " and the v
VERSION = line.split()[-1][2:-1]
break
classy_ext = Extension("classy", [os.path.join(classy_folder, "classy.pyx")],
include_dirs=[
nm.get_include(), include_folder,
"/Users/rmurgia/Desktop/OpenBLAS/include"
],
libraries=liblist,
library_dirs=[root_folder, GCCPATH],
extra_link_args=[
'/Users/rmurgia/Desktop/OpenBLAS/lib/libopenblas.a',
'-lgomp', '-lgsl', '-lgslcblas',
'-Wl,-rpath,/usr/local/opt/gcc/lib/gcc/9/'
])
import six
classy_ext.cython_directives = {'language_level': "3" if six.PY3 else "2"}
setup(
name='classy',
version=VERSION,
description='Python interface to the Cosmological Boltzmann code CLASS',
url='http://www.class-code.net',
cmdclass={'build_ext': build_ext},
ext_modules=[classy_ext],
#ext_modules=[classy_ext],
#data_files=[('bbn', ['../bbn/sBBN.dat'])]
)
pymilne_src = ["pyMilne.pyx"]
pymilne_inc = ["./",numpy.get_include()]
extension_kwargs = {
'sources': pymilne_src,
'include_dirs': pymilne_inc,
}
extension_kwargs = pkgconfig('eigen3', extension_kwargs)
extension_kwargs = pkgconfig('fftw3', extension_kwargs)
extension = Extension("pyMilne",
language="c++",
extra_compile_args=comp_flags,
extra_link_args=link_opts,
**extension_kwargs)
extension.cython_directives = {'language_level': "3"}
setup(
name = 'pyMilne',
version = '1.0',
author = 'J. de la Cruz Rodriguez (ISP-SU 2020)',
ext_modules=[extension],
cmdclass = {'build_ext': build_ext}
)
sources = [pyxfile]
extmod = Extension(ext_name,
sources=sources,
libraries=['cpptraj'],
language='c++',
library_dirs=[
libdir,
],
include_dirs=[cpptraj_include, pytraj_home],
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args)
extmod.cython_directives = {
'embedsignature': True,
'boundscheck': False,
'wraparound': False,
}
ext_modules.append(extmod)
setup_args = {}
packages = [
'pytraj',
'pytraj.utils',
'pytraj.actions',
'pytraj.analyses',
'pytraj.datasets',
'pytraj.externals',
'pytraj.trajs',
'pytraj.datafiles',
'pytraj.datafiles.Ala3',
#==================================================================================================
# run with:
# python setup.py build_ext --inplace
# before running Python program you will need to export the C++ shared library path:
# export LD_LIBRARY_PATH=/path/to/URT/lib:$LD_LIBRARY_PATH
from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
from Cython.Build import cythonize
from numpy import get_include
# linking to C++ libURT.so library
ext = Extension('CyURT',
sources = ['CyURT.pyx'],
include_dirs = [get_include()],
libraries = ['URT'],
extra_compile_args = ['-std=c++11','-Wall','-march=native','-DUSE_BLAZE','-DBLAZE_BLAS_INCLUDE_FILE <mkl_cblas.h>'],
extra_link_args = ['-L../lib'],
language='c++')
# NB: in extra_compile_args replace the header <mkl_cblas.h> by the one associated with the BLAS/LAPACK replacement library, for example OpenBLAS will use the header <cblas.h>
ext.cython_directives = {'boundscheck': False,'wraparound': False}
# turn off bounds-checking for entire function
# turn off negative index wrapping for entire function
setup(cmdclass = {'build_ext' : build_ext}, ext_modules = [ext])
sources=[
os.path.join(libvsc_dir, 'python', "core.pyx"),
os.path.join(libvsc_dir, 'python', 'VisitorProxy.cpp'),
os.path.join(libvsc_dir, 'python', 'py_get_vsc.cpp'),
os.path.join(libvsc_dir, 'python',
'ModelFieldDataClosure.cpp'),
os.path.join(libvsc_dir, 'python',
'ModelStructCreateHookClosure.cpp'),
os.path.join(libvsc_dir, 'python', 'VscTasks.cpp'),
],
language="c++",
include_dirs=[
os.path.join(libvsc_dir, 'src'),
os.path.join(libvsc_dir, 'src', 'include')
])
ext.cython_directives = {'language_level': '3'}
setup(name="libvsc",
packages=['libvsc'],
package_dir={'': 'python'},
author="Matthew Ballance",
author_email="*****@*****.**",
description=("Provides the core TbLink-RPC library"),
license="Apache 2.0",
keywords=["SystemVerilog", "Verilog", "RTL", "Python"],
url="https://github.com/fvutils/libvsc",
entry_points={
'console_scripts': ['tblink-rpc = tblink_rpc.__main__:main']
},
install_requires=[],
setup_requires=['setuptools_scm', 'cython'],
with open(os.path.join(include_folder, 'common.h'), 'r') as v_file:
for line in v_file:
if line.find("_VERSION_") != -1:
# get rid of the " and the v
VERSION = line.split()[-1][2:-1]
break
# Define cython extension and fix Python version
classy_ext = Extension("classy", [os.path.join(classy_folder, "classy.pyx")],
include_dirs=[
nm.get_include(), include_folder, heat_folder,
recfast_folder, hyrec_folder
],
libraries=liblist,
library_dirs=[root_folder, GCCPATH],
extra_link_args=['-lgomp'])
import sys
classy_ext.cython_directives = {
'language_level': "3" if sys.version_info.major >= 3 else "2"
}
setup(
name='classy',
version=VERSION,
description='Python interface to the Cosmological Boltzmann code CLASS',
url='http://www.class-code.net',
cmdclass={'build_ext': build_ext},
ext_modules=[classy_ext],
#data_files=[('bbn', ['../bbn/sBBN.dat'])]
)
