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setup.py
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setup.py
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from setuptools import setup, Extension
from setuptools.command.install import install as install_
from Cython.Distutils import build_ext
#from Cython.Build import cythonize
import numpy as np
# XXX h5py needs to be present to run setup.py. Can't be installed
# automatically?
import h5py
import os
import sys
from os import path
import shutil
import glob
VERSION_MAJOR = 0
VERSION_MINOR = 2
VERSION_POINT = 0
VERSION_DEV = 1
VERSION = "%d.%d.%d" % (VERSION_MAJOR, VERSION_MINOR, VERSION_POINT)
if VERSION_DEV:
VERSION = VERSION + ".dev%d" % VERSION_DEV
COMPILE_FLAGS = ['-Ofast', '-march=native', '-std=c99', '-fopenmp']
# Cython breaks strict aliasing rules.
COMPILE_FLAGS += ["-fno-strict-aliasing"]
#COMPILE_FLAGS = ['-Ofast', '-march=core2', '-std=c99', '-fopenmp']
MACROS = [
('BSHUF_VERSION_MAJOR', VERSION_MAJOR),
('BSHUF_VERSION_MINOR', VERSION_MINOR),
('BSHUF_VERSION_POINT', VERSION_POINT),
]
H5PLUGINS_DEFAULT = '/usr/local/hdf5/lib/plugin'
# Copied from h5py.
# TODO, figure out what the canonacal way to do this should be.
INCLUDE_DIRS = []
LIBRARY_DIRS = []
if sys.platform == 'darwin':
# putting here both macports and homebrew paths will generate
# "ld: warning: dir not found" at the linking phase
INCLUDE_DIRS += ['/opt/local/include'] # macports
LIBRARY_DIRS += ['/opt/local/lib'] # macports
INCLUDE_DIRS += ['/usr/local/include'] # homebrew
LIBRARY_DIRS += ['/usr/local/lib'] # homebrew
elif sys.platform.startswith('freebsd'):
INCLUDE_DIRS += ['/usr/local/include'] # homebrew
LIBRARY_DIRS += ['/usr/local/lib'] # homebrew
ext_bshuf = Extension("bitshuffle.ext",
["bitshuffle/ext.pyx", "src/bitshuffle.c", "lz4/lz4.c"],
include_dirs=INCLUDE_DIRS + [np.get_include(), "src/",
"lz4/"],
library_dirs = LIBRARY_DIRS,
depends=["src/bitshuffle.h", "src/iochain.h", "lz4/lz4.h"],
libraries = ['gomp'],
extra_compile_args=COMPILE_FLAGS,
define_macros=MACROS,
)
h5filter = Extension("bitshuffle.h5",
["bitshuffle/h5.pyx", "src/bshuf_h5filter.c",
"src/bitshuffle.c", "lz4/lz4.c"],
include_dirs=INCLUDE_DIRS + ["src/", "lz4/"],
library_dirs = LIBRARY_DIRS,
depends=["src/bitshuffle.h", "src/iochain.h",
'src/bshuf_h5filter.h', "lz4/lz4.h"],
libraries = ['hdf5', 'gomp'],
extra_compile_args=COMPILE_FLAGS,
define_macros=MACROS,
)
filter_plugin = Extension("plugin.libh5bshuf",
["src/bshuf_h5plugin.c", "src/bshuf_h5filter.c",
"src/bitshuffle.c", "lz4/lz4.c"],
include_dirs=INCLUDE_DIRS +["src/", "lz4/"] ,
library_dirs = LIBRARY_DIRS,
depends=["src/bitshuffle.h", "src/iochain.h",
'src/bshuf_h5filter.h', "lz4/lz4.h"],
libraries = ['hdf5', 'gomp'],
extra_compile_args=['-fPIC', '-g'] + COMPILE_FLAGS,
define_macros=MACROS,
)
lzf_plugin = Extension("plugin.libh5LZF",
["src/lzf_h5plugin.c", "lzf/lzf_filter.c",
"lzf/lzf/lzf_c.c", "lzf/lzf/lzf_d.c"],
depends=["lzf/lzf_filter.h",
"lzf/lzf/lzf.h", "lzf/lzf/lzfP.h"],
include_dirs = INCLUDE_DIRS + ["lzf/", "lzf/lzf/"],
library_dirs = LIBRARY_DIRS,
libraries = ['hdf5'],
extra_compile_args=['-fPIC', '-g'] + COMPILE_FLAGS,
)
H5VERSION = h5py.h5.get_libversion()
if (H5VERSION[0] < 1 or (H5VERSION[0] == 1
and (H5VERSION[1] < 8 or (H5VERSION[1] == 8 and H5VERSION[2] < 11)))):
H51811P = False
EXTENSIONS = [ext_bshuf, h5filter]
else:
H51811P = True
EXTENSIONS = [ext_bshuf, h5filter, filter_plugin, lzf_plugin]
#EXTENSIONS = cythonize(EXTENSIONS)
# Custom installation to include installing dynamic filters.
class install(install_):
user_options = install_.user_options + [
('h5plugin', None, 'Install HDF5 filter plugins for use outside of python.'),
('h5plugin-dir=', None,
'Where to install filter plugins. Default %s.' % H5PLUGINS_DEFAULT),
]
def initialize_options(self):
install_.initialize_options(self)
self.h5plugin = False
self.h5plugin_dir = H5PLUGINS_DEFAULT
def finalize_options(self):
install_.finalize_options(self)
assert self.h5plugin or not self.h5plugin, "Invalid h5plugin argument."
self.h5plugin_dir = path.abspath(self.h5plugin_dir)
def run(self):
install_.run(self)
if self.h5plugin:
if H51811P:
pass
else:
print "HDF5 < 1.8.11, not installing filter plugins."
return
#from h5py import h5
#h5version = h5.get_libversion()
plugin_build = path.join(self.build_lib, "plugins")
try:
os.makedirs(self.h5plugin_dir)
except OSError as e:
if e.args[0] == 17:
# Directory already exists, this is fine.
pass
else:
raise
plugin_libs = glob.glob(path.join(plugin_build, "*"))
for plugin_lib in plugin_libs:
plugin_name = path.split(plugin_lib)[1]
shutil.copy2(plugin_lib, path.join(self.h5plugin_dir, plugin_name))
print "Installed HDF5 filter plugins to %s" % self.h5plugin_dir
# TODO hdf5 support should be an "extra". Figure out how to set this up.
setup(
name = 'bitshuffle',
version = VERSION,
packages = ['bitshuffle'],
scripts=[],
ext_modules = EXTENSIONS,
cmdclass = {'build_ext': build_ext, 'install': install},
#cmdclass = {'install': install},
#install_requires = ['numpy', 'h5py', 'Cython', 'setuptools>=0.7'],
install_requires = ['numpy', 'h5py', 'Cython'],
#extras_require = {'H5': ["h5py"]},
package_data={'': ['bitshuffle/tests/data/*']},
# metadata for upload to PyPI
author = "Kiyoshi Wesley Masui",
author_email = "[email protected]",
description = "Bitshuffle filter for improving typed data compression.",
license = "MIT",
url = "http://github.com/kiyo-masui/bitshuffle"
)