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from __future__ import absolute_import, division, print_function
# I didn't import unicode_literals. They break setuptools or Cython in python
# 2.7, but python 3 seems to be happy with them.
import glob
import os
from os import path
from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext as build_ext_
from setuptools.command.develop import develop as develop_
from setuptools.command.install import install as install_
import shutil
import subprocess
import sys
VERSION_MAJOR = 0
VERSION_MINOR = 3
VERSION_POINT = 5
# Only unset in the 'release' branch and in tags.
VERSION_DEV = 0
VERSION = "%d.%d.%d" % (VERSION_MAJOR, VERSION_MINOR, VERSION_POINT)
if VERSION_DEV:
VERSION = VERSION + ".dev%d" % VERSION_DEV
COMPILE_FLAGS = ['-O3', '-ffast-math', '-std=c99']
# Cython breaks strict aliasing rules.
COMPILE_FLAGS += ['-fno-strict-aliasing']
COMPILE_FLAGS += ['-fPIC']
COMPILE_FLAGS_MSVC = ['/Ox', '/fp:fast']
MACROS = [
('BSHUF_VERSION_MAJOR', VERSION_MAJOR),
('BSHUF_VERSION_MINOR', VERSION_MINOR),
('BSHUF_VERSION_POINT', VERSION_POINT),
]
H5PLUGINS_DEFAULT = '/usr/local/hdf5/lib/plugin'
# OSX's clang compliler does not support OpenMP.
if sys.platform == 'darwin':
OMP_DEFAULT = False
else:
OMP_DEFAULT = True
FALLBACK_CONFIG = {
'include_dirs': [],
'library_dirs': [],
'libraries': [],
'extra_compile_args': [],
'extra_link_args': [],
}
if 'HDF5_DIR' in os.environ:
FALLBACK_CONFIG['include_dirs'] += [os.environ['HDF5_DIR'] + '/include'] # macports
FALLBACK_CONFIG['library_dirs'] += [os.environ['HDF5_DIR'] + '/lib'] # macports
elif sys.platform == 'darwin':
# putting here both macports and homebrew paths will generate
# "ld: warning: dir not found" at the linking phase
FALLBACK_CONFIG['include_dirs'] += ['/opt/local/include'] # macports
FALLBACK_CONFIG['library_dirs'] += ['/opt/local/lib'] # macports
FALLBACK_CONFIG['include_dirs'] += ['/usr/local/include'] # homebrew
FALLBACK_CONFIG['library_dirs'] += ['/usr/local/lib'] # homebrew
elif sys.platform.startswith('freebsd'):
FALLBACK_CONFIG['include_dirs'] += ['/usr/local/include'] # homebrew
FALLBACK_CONFIG['library_dirs'] += ['/usr/local/lib'] # homebrew
FALLBACK_CONFIG['include_dirs'] = [d for d in FALLBACK_CONFIG['include_dirs']
if path.isdir(d)]
FALLBACK_CONFIG['library_dirs'] = [d for d in FALLBACK_CONFIG['library_dirs']
if path.isdir(d)]
FALLBACK_CONFIG['extra_compile_args'] = ['-DH5_BUILT_AS_DYNAMIC_LIB']
def pkgconfig(*packages, **kw):
config = kw.setdefault('config', {})
optional_args = kw.setdefault('optional', '')
flag_map = {'include_dirs': ['--cflags-only-I', 2],
'library_dirs': ['--libs-only-L', 2],
'libraries': ['--libs-only-l', 2],
'extra_compile_args': ['--cflags-only-other', 0],
'extra_link_args': ['--libs-only-other', 0],
}
for package in packages:
try:
subprocess.check_output(["pkg-config", package])
except (subprocess.CalledProcessError, OSError):
print("Can't find %s with pkg-config fallback to "
"static config" % package)
for distutils_key in flag_map:
config.setdefault(distutils_key, []).extend(
FALLBACK_CONFIG[distutils_key])
config['libraries'].append(package)
else:
for distutils_key, (pkg_option, n) in flag_map.items():
items = subprocess.check_output(
['pkg-config', optional_args, pkg_option, package]
).decode('utf8').split()
opt = config.setdefault(distutils_key, [])
opt.extend([i[n:] for i in items])
return config
ext_bshuf = Extension(
"bitshuffle.ext",
sources=["bitshuffle/ext.pyx", "src/bitshuffle.c",
"src/bitshuffle_core.c", "src/iochain.c",
"lz4/lz4.c"],
include_dirs=["src/", "lz4/"],
depends=["src/bitshuffle.h", "src/bitshuffle_core.h",
"src/iochain.h", "lz4/lz4.h"],
libraries=[],
define_macros=MACROS,
)
h5filter = Extension(
"bitshuffle.h5",
sources=["bitshuffle/h5.pyx", "src/bshuf_h5filter.c",
"src/bitshuffle.c", "src/bitshuffle_core.c",
"src/iochain.c", "lz4/lz4.c"],
depends=["src/bitshuffle.h", "src/bitshuffle_core.h",
"src/iochain.h", "src/bshuf_h5filter.h",
"lz4/lz4.h"],
define_macros=MACROS,
**pkgconfig("hdf5", config=dict(
include_dirs=["src/", "lz4/"]))
)
filter_plugin = Extension(
"bitshuffle.plugin.libh5bshuf",
sources=["src/bshuf_h5plugin.c", "src/bshuf_h5filter.c",
"src/bitshuffle.c", "src/bitshuffle_core.c",
"src/iochain.c", "lz4/lz4.c"],
depends=["src/bitshuffle.h", "src/bitshuffle_core.h",
"src/iochain.h", 'src/bshuf_h5filter.h',
"lz4/lz4.h"],
define_macros=MACROS,
**pkgconfig("hdf5", config=dict(
include_dirs=["src/", "lz4/"]))
)
lzf_plugin = Extension(
"bitshuffle.plugin.libh5LZF",
sources=["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"],
**pkgconfig("hdf5", config=dict(
include_dirs=["lzf/", "lzf/lzf/"]))
)
EXTENSIONS = [ext_bshuf, h5filter]
# Check for plugin hdf5 plugin support (hdf5 >= 1.8.11)
HDF5_PLUGIN_SUPPORT = False
CPATHS = os.environ['CPATH'].split(':') if 'CPATH' in os.environ else []
for p in ["/usr/include"] + pkgconfig("hdf5")["include_dirs"] + CPATHS:
if os.path.exists(os.path.join(p, "H5PLextern.h")):
HDF5_PLUGIN_SUPPORT = True
if HDF5_PLUGIN_SUPPORT:
EXTENSIONS.extend([filter_plugin, lzf_plugin])
class develop(develop_):
def run(self):
# Dummy directory for copying build plugins.
if not path.isdir('bitshuffle/plugin'):
os.mkdir('bitshuffle/plugin')
develop_.run(self)
# 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)
if self.h5plugin not in ('0', '1', True, False):
raise ValueError("Invalid h5plugin argument. Mut be '0' or '1'.")
self.h5plugin = int(self.h5plugin)
self.h5plugin_dir = path.abspath(self.h5plugin_dir)
def run(self):
install_.run(self)
if self.h5plugin:
if not HDF5_PLUGIN_SUPPORT:
print("HDF5 < 1.8.11, not installing filter plugins.")
return
plugin_build = path.join(self.build_lib, "bitshuffle", "plugin")
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)
# Command line or site.cfg specification of OpenMP.
class build_ext(build_ext_):
user_options = build_ext_.user_options + [
('omp=', None, "Whether to compile with OpenMP threading. Default"
" on current system is %s." % str(OMP_DEFAULT))
]
boolean_options = build_ext_.boolean_options + ['omp']
def initialize_options(self):
build_ext_.initialize_options(self)
self.omp = OMP_DEFAULT
def finalize_options(self):
# For some reason this gets run twice. Careful to print messages and
# add arguments only one time.
build_ext_.finalize_options(self)
if self.omp not in ('0', '1', True, False):
raise ValueError("Invalid omp argument. Mut be '0' or '1'.")
self.omp = int(self.omp)
import numpy as np
ext_bshuf.include_dirs.append(np.get_include())
# Required only by old version of setuptools < 18.0
from Cython.Build import cythonize
self.extensions = cythonize(self.extensions)
for ext in self.extensions:
ext._needs_stub = False
def build_extensions(self):
c = self.compiler.compiler_type
if self.omp not in ('0', '1', True, False):
raise ValueError("Invalid omp argument. Mut be '0' or '1'.")
self.omp = int(self.omp)
if self.omp:
if not hasattr(self, "_printed_omp_message"):
self._printed_omp_message = True
print("\n#################################")
print("# Compiling with OpenMP support #")
print("#################################\n")
# More portable to pass -fopenmp to linker.
# self.libraries += ['gomp']
if self.compiler.compiler_type == 'msvc':
openmpflag = '/openmp'
compileflags = COMPILE_FLAGS_MSVC
else:
openmpflag = '-fopenmp'
compileflags = COMPILE_FLAGS
for e in self.extensions:
e.extra_compile_args = list(set(e.extra_compile_args).union(compileflags))
if openmpflag not in e.extra_compile_args:
e.extra_compile_args += [openmpflag]
if openmpflag not in e.extra_link_args:
e.extra_link_args += [openmpflag]
build_ext_.build_extensions(self)
# Don't install numpy/cython/hdf5 if not needed
for cmd in ["sdist", "clean",
"--help", "--help-commands", "--version"]:
if cmd in sys.argv:
setup_requires = []
break
else:
setup_requires = ["Cython>=0.19", "numpy>=1.6.1"]
with open('requirements.txt') as f:
requires = f.read().splitlines()
requires = [r.split()[0] for r in requires]
with open('README.rst') as r:
long_description = r.read()
# TODO hdf5 support should be an "extra". Figure out how to set this up.
setup(
name='bitshuffle',
version=VERSION,
packages=['bitshuffle', 'bitshuffle.tests'],
scripts=[],
ext_modules=EXTENSIONS,
cmdclass={'build_ext': build_ext, 'install': install, 'develop': develop},
setup_requires=setup_requires,
install_requires=requires,
# extras_require={'H5': ["h5py"]},
package_data={'': ['data/*']},
# metadata for upload to PyPI
author="Kiyoshi Wesley Masui",
author_email="kiyo@physics.ubc.ca",
description="Bitshuffle filter for improving typed data compression.",
long_description=long_description,
license="MIT",
url="https://github.com/kiyo-masui/bitshuffle",
download_url=("https://github.com/kiyo-masui/bitshuffle/tarball/%s"
% VERSION),
keywords=['compression', 'hdf5', 'numpy'],
)
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