def setup_extension_modules(self):
"""Sets up the C/C++/CUDA extension modules for this distribution.
Create list of extensions for Python modules within the openmoc
Python package based on the user-defined flags defined at compile time.
"""
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
# Add the NumPy include directory to the include directories
# list for each type of compiler
for cc in self.include_directories.keys():
self.include_directories[cc].append(numpy_include)
# The main openmoc extension (defaults are gcc and single precision)
self.extensions.append(
Extension(name = '_rksolver',
sources = copy.deepcopy(self.sources[self.cc]),
library_dirs = self.library_directories[self.cc],
libraries = self.shared_libraries[self.cc],
extra_link_args = self.linker_flags[self.cc],
include_dirs = self.include_directories[self.cc],
swig_opts = self.swig_flags + ['-D' + self.cc.upper()]))
def get_numpy_include():
# Obtain the numpy include directory. This logic works across numpy
# versions.
# setuptools forgets to unset numpy's setup flag and we get a crippled
# version of it unless we do it ourselves.
try:
# Python 3 renamed the ``__builin__`` module into ``builtins``.
# Here we import the python 2 or the python 3 version of the module
# with the python 3 name. This could be done with ``six`` but that
# module may not be installed at that point.
import __builtin__ as builtins
except ImportError:
import builtins
builtins.__NUMPY_SETUP__ = False
try:
import numpy as np
except ImportError:
print('*** package "numpy" not found ***')
print("MDAnalysis requires a version of NumPy (>=1.5.0), even for setup.")
print("Please get it from http://numpy.scipy.org/ or install it through " "your package manager.")
sys.exit(-1)
try:
numpy_include = np.get_include()
except AttributeError:
numpy_include = np.get_numpy_include()
return numpy_include
def get_numpy_include():
try:
# Obtain the numpy include directory. This logic works across numpy
# versions.
# setuptools forgets to unset numpy's setup flag and we get a crippled
# version of it unless we do it ourselves.
try:
import __builtin__ # py2
__builtin__.__NUMPY_SETUP__ = False
except:
import builtins # py3
builtins.__NUMPY_SETUP__ = False
import numpy as np
except ImportError as e:
print(e)
print('*** package "numpy" not found ***')
print('Simpletraj requires a version of NumPy, even for setup.')
print('Please get it from http://numpy.scipy.org/ or install it through '
'your package manager.')
sys.exit(-1)
try:
numpy_include = np.get_include()
except AttributeError:
numpy_include = np.get_numpy_include()
return numpy_include
def get_numpy_include_path():
"""
Gets the path to the numpy headers.
"""
# We need to go through this nonsense in case setuptools
# downloaded and installed Numpy for us as part of the build or
# install, since Numpy may still think it's in "setup mode", when
# in fact we're ready to use it to build astropy now.
if sys.version_info[0] >= 3:
import builtins
if hasattr(builtins, '__NUMPY_SETUP__'):
del builtins.__NUMPY_SETUP__
import imp
import numpy
imp.reload(numpy)
else:
import __builtin__
if hasattr(__builtin__, '__NUMPY_SETUP__'):
del __builtin__.__NUMPY_SETUP__
import numpy
reload(numpy)
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
return numpy_include
def main():
install_requires = ['pyparsing>=2.0.0']
#if sys.version_info[0] >= 3:
# install_requires = ['pyparsing>=2.0.0']
#else:
# pyparsing >= 2.0.0 is not compatible with Python 2
# install_requires = ['pyparsing<2.0.0']
ka = dict(name = "pyregion",
version = __version__,
description = "python parser for ds9 region files",
author = "Jae-Joon Lee",
author_email = "*****@*****.**",
url="http://leejjoon.github.com/pyregion/",
download_url="http://github.com/leejjoon/pyregion/downloads",
license = "MIT",
platforms = ["Linux","MacOS X"],
packages = ['pyregion'],
package_dir={'pyregion':'lib'},
install_requires = install_requires,
use_2to3 = False,
)
ka["classifiers"]=['Development Status :: 5 - Production/Stable',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: MIT License',
'Operating System :: MacOS :: MacOS X',
'Operating System :: POSIX :: Linux',
'Programming Language :: Cython',
'Programming Language :: Python',
'Programming Language :: Python :: 3',
'Topic :: Scientific/Engineering :: Astronomy',
]
if WITH_FILTER:
try:
import numpy
except ImportError:
warnings.warn("numpy must be installed to build the filtering module.")
sys.exit(1)
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
if cmdclass:
ka["cmdclass"] = cmdclass
ka["ext_modules"] = [ Extension("pyregion._region_filter",
[PYREX_SOURCE],
include_dirs=['./src',
numpy_include,
],
libraries=[],
)
]
setup(**ka)
def add_numpy_flags(module):
"Add the modules flags to build extensions which use numpy"
import numpy
# TODO: Remove this try statement when it is no longer needed
try:
module.include_dirs.append(numpy.get_include())
except AttributeError:
module.include_dirs.append(numpy.get_numpy_include())
def get_numpy_include():
"""
Obtain the numpy include directory. This logic works across numpy versions.
"""
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
return numpy_include
def test_include_dirs(self):
"""As a sanity check, just test that get_include and
get_numarray_include include something reasonable. Somewhat
related to ticket #1405."""
include_dirs = [np.get_include(), np.get_numarray_include(),
np.get_numpy_include()]
for path in include_dirs:
assert isinstance(path, (str, unicode))
assert path != ''
def get_numpy_include_path():
import six
if hasattr(six.moves.builtins, '__NUMPY_SETUP__'):
del six.moves.builtins.__NUMPY_SETUP__
import numpy
six.moves.reload_module(numpy)
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
return numpy_include
def get_numpy_include_path():
"""
Gets the path to the numpy headers.
"""
import numpy
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
return numpy_include
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
import numpy
config = Configuration('core', parent_package, top_path)
config.set_options(quiet=True)
config.add_subpackage('image')
config.add_subpackage('orient')
config.add_subpackage('parallel')
config.add_subpackage('learn')
try: numpy_include = numpy.get_include()
except: numpy_include = numpy.get_numpy_include() #@UndefinedVariable
config.add_include_dirs(numpy_include)
return config
def get_ext_modules(use_cython):
from numpy import get_include as get_numpy_include
cython_modules, cython_sources = get_cython_sources(use_cython)
ext_modules = [
Extension('pywt._extensions.{0}'.format(module),
sources=[make_ext_path(source)],
# Doesn't automatically rebuild if library changes
depends=c_lib[1]['sources'] + c_lib[1]['depends'],
include_dirs=[make_ext_path("c"), get_numpy_include()],
define_macros=c_macros + cython_macros,
libraries=[c_lib[0]],)
for module, source, in zip(cython_modules, cython_sources)
]
return ext_modules
def __compileDistUtils__(hash, includeDirs, lib_dirs, libraries, doOptimizeGcc = True, additonalSources = []):
'''
Compiles a inline c module with the distutils. First a swig interface is used to generated swig wrapper coder which is than compiled into a python module.
@brief Compiles a inline c module with distutils.
@param hash Name of the c, interface and module files
@param includeDirs List of directories in which distutils looks for headers needed
@param lib_dirs List of directories in which distutils looks for libs needed
@param libraries List of libraries which distutils uses for binding
@return None
'''
try:
numpy_include = np.get_include()
except AttributeError:
numpy_include = np.get_numpy_include()
includeDirs.extend([numpy_include,
os.curdir])
iFileName = hash + ".i"
cFileName = hash + "."+C_FILE_SUFFIX
cWrapFileName = hash + "_wrap."+__WRAPPER_FILE_SUFFIX__
subprocess.check_call(["swig", "-python", "-c++", iFileName])
extra_compile_args = []
if doOptimizeGcc:
extra_compile_args = ["-pthread","-O3","-march=native","-mtune=native"]
sourcesList = [cFileName, cWrapFileName]
sourcesList.extend(additonalSources)
module1 = Extension('_%s' % hash,
sources=sourcesList,
library_dirs=lib_dirs,
libraries=libraries,
include_dirs=includeDirs,
extra_compile_args = extra_compile_args)
setup (script_args=['build'],
name='_%s' % hash,
version='1.0',
description='SWICE JIT lib',
ext_modules=[module1],
include_dirs=includeDirs)
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
from numpy import get_include as get_numpy_include
config = Configuration('_extensions', parent_package, top_path)
sources = ["c/common.c", "c/convolution.c", "c/wt.c", "c/wavelets.c"]
source_templates = ["c/convolution.template.c", "c/wt.template.c"]
headers = ["c/templating.h", "c/wavelets_coeffs.h",
"c/common.h", "c/convolution.h", "c/wt.h", "c/wavelets.h"]
header_templates = ["c/convolution.template.h", "c/wt.template.h",
"c/wavelets_coeffs.template.h"]
config.add_extension(
'_pywt', sources=["_pywt.c"] + sources,
depends=source_templates + header_templates + headers,
include_dirs=["c", get_numpy_include()],
define_macros=[("PY_EXTENSION", None)],
)
config.add_extension(
'_dwt', sources=["_dwt.c"] + sources,
depends=source_templates + header_templates + headers,
include_dirs=["c", get_numpy_include()],
define_macros=[("PY_EXTENSION", None)],
)
config.add_extension(
'_swt', sources=["_swt.c"] + sources,
depends=source_templates + header_templates + headers,
include_dirs=["c", get_numpy_include()],
define_macros=[("PY_EXTENSION", None)],
)
config.make_config_py()
return config
cythonize_opts['linetrace'] = True
cython_macros.append(("CYTHON_TRACE_NOGIL", 1))
# By default C object files are rebuilt for every extension
# C files must be built once only for coverage to work
c_lib = ('c_edf',{'sources': sources,
'depends': headers,
'include_dirs': [make_ext_path("c"), get_python_inc()],
'macros': c_macros,})
ext_modules = [
Extension('pyedflib._extensions.{0}'.format(module),
sources=[make_ext_path(source)],
# Doesn't automatically rebuild if library changes
depends=c_lib[1]['sources'] + c_lib[1]['depends'],
include_dirs=[make_ext_path("c"), get_numpy_include()],
define_macros=c_macros + cython_macros,
libraries=[c_lib[0]],)
for module, source, in zip(cython_modules, cython_sources)
]
from setuptools.command.develop import develop
class develop_build_clib(develop):
"""Ugly monkeypatching to get clib to build for development installs
See coverage comment above for why we don't just let libraries be built
via extensions.
All this is a copy of the relevant part of `install_for_development`
for current master (Sep 2016) of setuptools.
Note: if you want to build in-place with ``python setup.py build_ext``,
that will only work if you first do ``python setup.py build_clib``.
"""
def add_numpy_include(module):
"Add the include path needed to build extensions which use numpy."
module.include_dirs.append(numpy.get_numpy_include())
'-fno-omit-frame-pointer',
'-funroll-loops',
'-fstrict-aliasing',
'-std=c99',
'-vec-report=0',
'-par-report=0',
'-O3',
'-xHost',
'-mtune=native',
'-Wall',
'-openmp']
try:
numpy_inc = [numpy.get_include()]
except AttributeError:
numpy_inc = [numpy.get_numpy_include()]
crwalk = Extension('glass.solvers.rwalk.csamplex',
sources = ['glass/solvers/rwalk/csamplex_omp.c', 'glass/solvers/rwalk/WELL44497a.c'],
include_dirs=numpy_inc,
undef_macros=['DEBUG'],
libraries=libraries,
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args)
setup(name = 'Glass',
author = 'Jonathan Coles',
author_email = '*****@*****.**',
version = '1.0',
description = 'Gravitational Lensing AnalysiS Software',
package_dir = {'glass': 'glass'},
import numpy
try:
print(numpy.get_include())
except AttributeError:
print(numpy.get_numpy_include())
# the generated C sources to SVN).
try:
from Pyrex.Distutils import build_ext
has_pyrex = True
except ImportError:
has_pyrex = False
import numpy
# Define a pyrex-based extension module, using the generated sources if pyrex
# is not available.
if has_pyrex:
pyx_sources = ['numpyx.pyx']
cmdclass = {'build_ext': build_ext}
else:
pyx_sources = ['numpyx.c']
cmdclass = {}
pyx_ext = Extension('numpyx',
pyx_sources,
include_dirs = [numpy.get_numpy_include()])
# Call the routine which does the real work
setup(name = 'numpyx',
description = 'Small example on using Pyrex to write a Numpy extension',
url = 'http://www.scipy.org/Cookbook/Pyrex_and_NumPy',
ext_modules = [pyx_ext],
cmdclass = cmdclass,
)
def __init__(self, *args, **kwargs):
sdist.__init__(self, *args, **kwargs)
self.unstable = False
def run(self):
if not self.unstable:
version_file = 'hyperion/version.py'
content = open(version_file, 'r').read()
open(version_file, 'w').write(content.replace('__dev__ = True', "__dev__ = False"))
try:
sdist.run(self)
finally:
if not self.unstable:
open(version_file, 'w').write(content)
numpy_includes = get_numpy_include()
cmdclass = {}
cmdclass['build_py'] = build_py
cmdclass['test'] = HyperionTest
cmdclass['sdist'] = custom_sdist
ext_modules = [Extension("hyperion.util._integrate_core",
['hyperion/util/_integrate_core.c'],
include_dirs=[numpy_includes],
extra_compile_args=['-Wno-error=declaration-after-statement']),
Extension("hyperion.util._interpolate_core",
['hyperion/util/_interpolate_core.c'],
include_dirs=[numpy_includes],
extra_compile_args=['-Wno-error=declaration-after-statement']),
Extension("hyperion.importers._discretize_sph",
def numpy_include():
try:
inc = np.get_include()
except AttributeError:
inc = np.get_numpy_include()
return inc
def setup_extension_modules(self):
"""Sets up the C/C++/CUDA extension modules for this distribution.
Create list of extensions for Python modules within the openmoc
Python package based on the user-defined flags defined at compile time.
"""
# If the user selected 'all' compilers, enumerate them
if self.cpp_compilers == ['all']:
self.cpp_compilers = ['gcc', 'icpc', 'nvcc']
# If the user selected 'all' FP precision levels, enumerate them
if self.fp_precision == ['all']:
self.fp_precision = ['double', 'single']
# If the user wishes to compile using debug mode, append the debugging
# flag to all lists of compiler flags for all distribution types
if self.debug_mode:
for k in self.compiler_flags:
self.compiler_flags[k].append('-g')
# If the user passed in the --no-numpy flag, tell SWIG not to embed
# NumPy typemaps in the source code
if not self.with_numpy:
self.swig_flags.append('-DNO_NUMPY')
# Otherwise, obtain the NumPy include directory
else:
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
# Add the NumPy include directory to the include directories
# list for each type of compiler
for cc in self.include_directories.keys():
self.include_directories[cc].append(numpy_include)
# The main openmoc extension (defaults are gcc and single precision)
self.extensions.append(
Extension(name = '_openmoc',
sources = copy.deepcopy(self.sources[self.cc]),
library_dirs = self.library_directories[self.cc],
libraries = self.shared_libraries[self.cc],
extra_link_args = self.linker_flags[self.cc],
include_dirs = self.include_directories[self.cc],
define_macros = self.macros[self.cc][self.fp],
swig_opts = self.swig_flags + ['-D' + self.cc.upper()]))
# The openmoc.cuda extension if requested by the user at compile
# time (--with-cuda)
if self.with_cuda:
self.cpp_compilers.append('nvcc')
self.extensions.append(
Extension(name = '_openmoc_cuda',
sources = copy.deepcopy(self.sources['nvcc']),
library_dirs = self.library_directories['nvcc'],
libraries = self.shared_libraries['nvcc'],
extra_link_args = self.linker_flags['nvcc'],
include_dirs = self.include_directories['nvcc'],
define_macros = self.macros['nvcc'][self.fp],
swig_opts = self.swig_flags + ['-DNVCC'],
export_symbols = ['init_openmoc']))
# Remove the main SWIG configuration file for builds of other
# extensions (ie, openmoc.cuda.single, openmoc.cuda.double)
self.sources['nvcc'].remove('openmoc/cuda/openmoc_cuda_wrap.cpp')
# Loop over the compilers and floating point precision levels to create
# extension modules for each (ie, openmoc.intel.double,
# openmoc.cuda.single, etc)
for fp in self.fp_precision:
for cc in self.cpp_compilers:
# Build the filename for the SWIG configuration file and the
# extension name depending on the compiler and floating
# point precision
# For openmoc.cuda.* modules
if cc == 'nvcc':
ext_name = '_openmoc_cuda_' + fp
swig_wrap_file = 'openmoc/cuda/' + fp
swig_wrap_file += '/openmoc_cuda_' + fp + '_wrap.cpp'
self.sources['nvcc'].append(swig_wrap_file)
# For openmoc.gnu.* modules
elif cc == 'gcc':
ext_name = '_openmoc_gnu_' + fp
swig_wrap_file = 'openmoc/gnu/' + fp
swig_wrap_file += '/openmoc_gnu_' + fp + '_wrap.cpp'
self.sources['gcc'].append(swig_wrap_file)
# For openmoc.intel.* modules
elif cc == 'icpc':
ext_name = '_openmoc_intel_' + fp
swig_wrap_file = 'openmoc/intel/' + fp
swig_wrap_file += '/openmoc_intel_' + fp + '_wrap.cpp'
self.sources['icpc'].append(swig_wrap_file)
# For openmoc.intel.* modules
elif cc == 'bgxlc':
ext_name = '_openmoc_bgq_' + fp
swig_wrap_file = 'openmoc/bgq/' + fp
swig_wrap_file += '/openmoc_bgq_' + fp + '_wrap.cpp'
self.sources['bgxlc'].append(swig_wrap_file)
# If an unsupported compiler, throw error
else:
raise NameError('Compiler ' + str(cc) + ' is not supported')
# Create the extension module and append it to the list of all
# extension modules
self.extensions.append(
Extension(name = ext_name,
sources = copy.deepcopy(self.sources[cc]),
library_dirs = self.library_directories[cc],
libraries = self.shared_libraries[cc],
extra_link_args = self.linker_flags[cc],
include_dirs = self.include_directories[cc],
define_macros = self.macros[cc][fp],
swig_opts = self.swig_flags + ['-D' + cc.upper()]))
# Clean up - remove the SWIG-generated wrap file from this
# extension for the next extension
self.sources[cc].remove(swig_wrap_file)
# setup script to compile jitter module;
# written by M. Vallisneri (2015)
#
# use python setup.py build_ext --inplace to test
import distutils.core as D
import numpy as N
from distutils.core import setup, Extension
from distutils import sysconfig
try:
numpy_include = N.get_include()
except AttributeError:
numpy_include = N.get_numpy_include()
# need to replace build_ext to build cython extension
import Cython.Distutils
extension = D.Extension('NX01_jitter',
sources = ['NX01_jitter.pyx'],
include_dirs = [numpy_include],
extra_compile_args = ['-std=c99']
)
D.setup(name = 'NX01_jitter',
ext_modules = [extension],
cmdclass = {"build_ext": Cython.Distutils.build_ext}
)
def make_cmf_core():
"""
Puts all information needed for the Python extension object together
- source files
- include dirs
- extra compiler flags
"""
libraries = None
# Include CVODE
include_dirs = [
os.path.join(
*'cmf/cmf_core_src/math/integrators/sundials_cvode/include'.split(
'/'))
]
# Include numpy
include_dirs += [get_numpy_include()]
# Platform specific stuff, alternative is to subclass build_ext command as in:
# https://stackoverflow.com/a/5192738/3032680
if sys.platform == 'win32':
# Only include boost if VS2008 compiler is used, else we use C++ 11
if sys.version_info.major == 2:
boost_path = os.environ.get('BOOSTDIR', r"..\boost_1_41_0")
include_dirs += [boost_path, boost_path + r"\boost\tr1"]
compile_args = [
"/EHsc", r'/Fd"build\vc90.pdb"', "/D_SCL_SECURE_NO_WARNINGS",
"/D_CRT_SECURE_NO_WARNINGS", "/MP"
]
if openmp:
compile_args.append("/openmp")
link_args = ["/DEBUG"]
else:
compile_args = [
'-Wno-comment', '-Wno-reorder', '-Wno-deprecated', '-Wno-unused',
'-Wno-sign-compare', '-ggdb', '-std=c++11'
]
if sys.platform == 'darwin':
compile_args += ["-stdlib=libc++"]
link_args = ['-ggdb']
libraries = []
# Disable OpenMP on Mac see https://github.com/alejandrobll/py-sphviewer/issues/3
if openmp and not sys.platform == 'darwin':
compile_args.append('-fopenmp')
link_args.append("-fopenmp")
libraries.append('gomp')
# Get the source files
cmf_files = []
for root, _dirs, files in os.walk(os.path.join('cmf', 'cmf_core_src')):
if os.path.basename(root) != 'debug_scripts':
cmf_files.extend(
os.path.join(root, f) for f in files
if is_source_file(f) and f != 'cmf_wrap.cpp')
if swig:
# Adding cmf.i when build_ext should perform the swig call
cmf_files.append("cmf/cmf_core_src/cmf.i")
swig_opts = [
'-c++', '-Wextra', '-w512', '-w511', '-O', '-keyword', '-castmode',
'-modern'
]
else:
# Else use what we have there
cmf_files.append("cmf/cmf_core_src/cmf_wrap.cpp")
swig_opts = []
cmf_core = Extension('cmf._cmf_core',
sources=cmf_files,
libraries=libraries,
include_dirs=include_dirs,
extra_compile_args=compile_args,
extra_link_args=link_args,
swig_opts=swig_opts)
return cmf_core
cudaconfig = {'home':home, 'nvcc':nvcc,
'include': pjoin(home, 'include'),
'lib64': pjoin(home, 'lib64')}
for k, v in cudaconfig.iteritems():
if not os.path.exists(v):
raise EnvironmentError('The CUDA %s path could not be located in %s' % (k, v))
return cudaconfig
CUDA = locate_cuda()
# Obtain the numpy include directory. This logic works across numpy versions.
try:
numpy_include = np.get_include()
except AttributeError:
numpy_include = np.get_numpy_include()
def customize_compiler_for_nvcc(self):
"""inject deep into distutils to customize how the dispatch
to gcc/nvcc works.
If you subclass UnixCCompiler, it's not trivial to get your subclass
injected in, and still have the right customizations (i.e.
distutils.sysconfig.customize_compiler) run on it. So instead of going
the OO route, I have this. Note, it's kindof like a wierd functional
subclassing going on."""
# tell the compiler it can processes .cu
self.src_extensions.append('.cu')
# save references to the default compiler_so and _comple methods
import versioneer
import setuptools.command.install
import setuptools.command.build_ext
from setuptools import setup
from setuptools import Extension
try:
from numpy import get_include as get_numpy_include
except ImportError:
from numpy import get_numpy_include as get_numpy_include
numpy_include = get_numpy_include()
class BuildExtFirst(setuptools.command.install.install):
def run(self):
self.run_command("build_ext")
return setuptools.command.install.install.run(self)
class BuildExtOnce(setuptools.command.build_ext.build_ext):
def __init__(self, *args, **kwargs):
# Avoiding namespace collisions...
self.setup_build_ext_already_ran = False
setuptools.command.build_ext.build_ext.__init__(self, *args, **kwargs)
def run(self):
# Only let build_ext run once
if not self.setup_build_ext_already_ran:
self.setup_build_ext_already_ran = True
return setuptools.command.build_ext.build_ext.run(self)
import os
import sys
from os.path import join
from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
# Numpy from http://www.scipy.org/Cookbook/SWIG_NumPy_examples
import numpy as np
try:
NUMPY_INCLUDE = np.get_include()
except AttributeError:
NUMPY_INCLUDE = np.get_numpy_include()
# `EIGEN_INCLUDE` and `COMMON_CPP_INCLUDE` from site.cfg.
import ConfigParser
c = ConfigParser.ConfigParser()
# Preserve case. See:
# http://stackoverflow.com/questions/1611799/preserve-case-in-configparser
c.optionxform = str
c.read('site.cfg')
EIGEN_INCLUDE = c.get('Include', 'EIGEN_INCLUDE')
COMMON_CPP_INCLUDE = c.get('Include', 'COMMON_CPP_INCLUDE')
# Setup.
qpbo_dir = 'external/QPBO-v1.32.src/'
include_dirs = [NUMPY_INCLUDE, EIGEN_INCLUDE, COMMON_CPP_INCLUDE,
'include/', qpbo_dir,
print "pyMDMix requires Python 2.5 or later. Python %d.%d detected" % \
sys.version_info[:2]
print "Please upgrade your version of Python."
sys.exit(-1)
# Make sure AMBERHOME environ variable is set
if not os.environ.get('AMBERHOME'):
print "AMBERHOME env variable not set! Please set this variable pointing to AMBER package installation directory."
#scriptlist = ['scripts/prepareMDMixProject.py','scripts/runCenteringAndRawEnergyCalculations.py','scripts/createMinotauroQueueInput.py','scripts/createPaintersQueueInput.py', 'scripts/runReplicaCentering.py','scripts/extendReplica.py', 'scripts/printReplicaInfo.py','scripts/createReplicaCenteringInput.py','scripts/runReplicaDensityAndRawCalculation.py', 'scripts/mdmix']
scriptlist = ['src/mdmix']
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
include_dirs = [numpy_include]
def getVersionFromInit():
lines = open('pyMDMix/__init__.py', 'r').readlines()
for l in lines:
if '__version__' in l: return l.split('=')[1].split('"')[1]
setup(
name='pyMDMix',
cmdclass={'install': CustomInstall},
zip_safe=False,
version=getVersionFromInit(),
def get_numpy_include():
try:
numpy_include = np.get_include()
except AttributeError:
numpy_include = np.get_numpy_include()
return numpy_include
from Cython.Build import cythonize
import numpy as np
from distutils.core import setup
try:
numpy_include = np.get_include()
except AttributeError:
numpy_include = np.get_numpy_include()
print(numpy_include)
numpy_include = r'C:/Users/Administrator/AppData/Roaming/Python/Python35/site-packages/numpy/core/include/'
#ext_modules=cythonize(["bbox.pyx","cython_nms.pyx"],include_dirs=[numpy_include]),
# include_path=[numpy_include]
setup(ext_modules=cythonize(["bbox.pyx", "cython_nms.pyx"],
include_path=[numpy_include]), )
def main():
try:
import numpy
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
except ImportError:
numpy_include = ''
assert 'NUMPY_INCLUDE' in os.environ
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
numpy_include = os.getenv('NUMPY_INCLUDE', numpy_include)
numpy_min_ver = os.getenv('NUMPY_DEP_VERSION', '')
project_name = 'deepspeech'
if '--project_name' in sys.argv:
project_name_idx = sys.argv.index('--project_name')
project_name = sys.argv[project_name_idx + 1]
sys.argv.remove('--project_name')
sys.argv.pop(project_name_idx)
with open('../../VERSION', 'r') as ver:
project_version = ver.read().strip()
class BuildExtFirst(build):
sub_commands = [('build_ext', build.has_ext_modules),
('build_py', build.has_pure_modules),
('build_clib', build.has_c_libraries),
('build_scripts', build.has_scripts)]
# Properly pass arguments for linking, setuptools will perform some checks
def lib_dirs_split(a):
if os.name == 'posix':
return a.split('-L')[1:]
if os.name == 'nt':
return []
raise AssertionError('os.name == java not expected')
def libs_split(a):
if os.name == 'posix':
return a.split('-l')[1:]
if os.name == 'nt':
return a.split('.lib')[0:1]
raise AssertionError('os.name == java not expected')
ds_ext = Extension(name='deepspeech._impl',
sources=['impl.i'],
include_dirs=[numpy_include, '../'],
library_dirs=list(map(lambda x: x.strip(), lib_dirs_split(os.getenv('MODEL_LDFLAGS', '')))),
libraries=list(map(lambda x: x.strip(), libs_split(os.getenv('MODEL_LIBS', '')))),
swig_opts=['-c++', '-keyword', '-builtin'])
setup(name=project_name,
description='A library for running inference on a DeepSpeech model',
long_description=read('../../README.md'),
long_description_content_type='text/markdown; charset=UTF-8',
author='Mozilla',
version=project_version,
package_dir={'deepspeech': '.'},
cmdclass={'build': BuildExtFirst},
license='MPL-2.0',
url='https://github.com/mozilla/DeepSpeech',
project_urls={
'Documentation': 'https://github.com/mozilla/DeepSpeech/tree/v{}#project-deepspeech'.format(project_version),
'Tracker': 'https://github.com/mozilla/DeepSpeech/issues',
'Repository': 'https://github.com/mozilla/DeepSpeech/tree/v{}'.format(project_version),
'Discussions': 'https://discourse.mozilla.org/c/deep-speech',
},
ext_modules=[ds_ext],
py_modules=['deepspeech', 'deepspeech.client', 'deepspeech.impl'],
entry_points={'console_scripts':['deepspeech=deepspeech.client:main']},
install_requires=['numpy%s' % numpy_min_ver],
include_package_data=True,
classifiers=[
'Development Status :: 3 - Alpha',
'Environment :: Console',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)',
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Programming Language :: Python :: 3.6',
'Topic :: Multimedia :: Sound/Audio :: Speech',
'Topic :: Scientific/Engineering :: Human Machine Interfaces',
'Topic :: Scientific/Engineering',
'Topic :: Utilities',
])
def setup_package():
# Rewrite the version file every time
write_version_py()
info['version'] = get_version_info()[0]
print(info['version'])
if USE_CYTHON:
# Obtain the numpy include directory. This logic works across numpy versions.
ext_modules = []
HAS_NUMPY = True
try:
import numpy as np
except:
info['setup_requires'] = ['numpy']
HAS_NUMPY = False
if HAS_NUMPY:
try:
numpy_include = np.get_include()
except AttributeError:
numpy_include = np.get_numpy_include()
# creflect extension module
_creflect = Extension(
name='refnx.analysis._creflect',
sources=['src/_creflect.pyx', 'src/refcalc.cpp'],
include_dirs=[numpy_include],
language='c',
extra_link_args=['-lpthread']
# libraries=
# extra_compile_args = "...".split(),
)
ext_modules.append(_creflect)
_cevent = Extension(
name='refnx.reduce._cevent',
sources=['src/_cevent.pyx'],
include_dirs=[numpy_include],
language='c',
# libraries=
# extra_compile_args = "...".split(),
)
ext_modules.append(_cevent)
info['cmdclass'] = {'build_ext': build_ext}
info['ext_modules'] = ext_modules
try:
setup(**info)
except ValueError:
# there probably wasn't a C-compiler (windows). Try removing extension
# compilation
print("")
print("*****WARNING*****")
print("You didn't try to build the Reflectivity calculation extension."
" Calculation will be slow, falling back to pure python."
" To compile extension install cython. If installing in windows you"
" should then install from Visual Studio command prompt (this makes"
" C compiler available")
print("*****************")
print("")
info.pop('cmdclass')
info.pop('ext_modules')
setup(**info)
This program comes with ABSOLUTELY NO WARRANTY;
This is free software, and you are welcome to redistribute it under certain
conditions; see http://www.gnu.org/licenses/gpl-3.0.html for details.
"""
# System imports
from distutils.core import *
from distutils import sysconfig
# Third-party modules - we depend on numpy for everything
import numpy
# Obtain the numpy include directory. This logic works across numpy versions.
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
# simple extension module
_sasview_vmd = Extension(
"_sasview_vmd", ["sasview_vmd.i", "sasview_vmd.c", "imd.c", "vmdsock.c"], include_dirs=[numpy_include]
)
# NumyTypemapTests setup
setup(
name="SASVIEW VMD I/O",
description="Module handles sending and receiving coordinates to VMD using numpy.i",
author="Joseph E. Curtis",
version="0.1",
ext_modules=[_sasview_vmd],
)
def __init__(self, *args, **kwargs):
sdist.__init__(self, *args, **kwargs)
self.unstable = False
def run(self):
if not self.unstable:
version_file = 'hyperion/version.py'
content = open(version_file, 'r').read()
open(version_file, 'w').write(content.replace('__dev__ = True', "__dev__ = False"))
try:
sdist.run(self)
finally:
if not self.unstable:
open(version_file, 'w').write(content)
numpy_includes = get_numpy_include()
cmdclass = {}
cmdclass['build_py'] = build_py
cmdclass['test'] = HyperionTest
cmdclass['sdist'] = custom_sdist
ext_modules = [Extension("hyperion.util._integrate_core",
['hyperion/util/_integrate_core.c'],
include_dirs=[numpy_includes],
extra_compile_args=['-Wno-error=declaration-after-statement']),
Extension("hyperion.util._interpolate_core",
['hyperion/util/_interpolate_core.c'],
include_dirs=[numpy_includes],
extra_compile_args=['-Wno-error=declaration-after-statement']),
Extension("hyperion.importers._discretize_sph",