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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_
from Cython.Compiler.Main import default_options
import shutil
import subprocess
import sys
import platform
VERSION_MAJOR = 0
VERSION_MINOR = 5
VERSION_POINT = 2
# Define ZSTD macro for cython compilation
default_options["compile_time_env"] = {"ZSTD_SUPPORT": False}
# Only unset in the 'release' branch and in tags.
VERSION_DEV = None
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 compiler does not support OpenMP.
if sys.platform == "darwin":
OMP_DEFAULT = False
else:
OMP_DEFAULT = True
# Build against the native architecture unless overridden by an environment variable
# This can also be overridden by a direct command line argument, or a `setup.cfg` entry
# This option is needed for the cibuildwheel action
if "BITSHUFFLE_ARCH" in os.environ:
MARCH_DEFAULT = os.environ["BITSHUFFLE_ARCH"]
else:
MARCH_DEFAULT = "native"
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
zstd_headers = ["zstd/lib/zstd.h"]
zstd_lib = ["zstd/lib/"]
zstd_sources = glob.glob("zstd/lib/common/*.c")
zstd_sources += glob.glob("zstd/lib/compress/*.c")
zstd_sources += glob.glob("zstd/lib/decompress/*.c")
ext_bshuf = Extension(
"bitshuffle.ext",
sources=[
"bitshuffle/ext.pyx",
"src/bitshuffle.c",
"src/bitshuffle_core.c",
"src/iochain.c",
],
depends=["src/bitshuffle.h", "src/bitshuffle_core.h", "src/iochain.h"],
define_macros=MACROS,
**pkgconfig("liblz4", config=dict(include_dirs=["src/"]))
)
h5filter = Extension(
"bitshuffle.h5",
sources=[
"bitshuffle/h5.pyx",
"src/bshuf_h5filter.c",
"src/bitshuffle.c",
"src/bitshuffle_core.c",
"src/iochain.c",
],
depends=[
"src/bitshuffle.h",
"src/bitshuffle_core.h",
"src/iochain.h",
"src/bshuf_h5filter.h",
],
define_macros=MACROS + [("H5_USE_18_API", None)],
**pkgconfig("hdf5", "liblz4", config=dict(include_dirs=["src/"]))
)
if not sys.platform.startswith("win"):
h5filter.sources.append("src/hdf5_dl.c")
h5filter.libraries.remove("hdf5")
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",
],
depends=[
"src/bitshuffle.h",
"src/bitshuffle_core.h",
"src/iochain.h",
"src/bshuf_h5filter.h",
],
define_macros=MACROS,
**pkgconfig("hdf5", "liblz4", config=dict(include_dirs=["src/"]))
)
lzf_plugin = Extension(
"bitshuffle.plugin.libh5LZF",
sources=[
"src/lzf_h5plugin.c",
"lzf/lzf_filter.c",
],
depends=["lzf/lzf_filter.h"],
**pkgconfig("hdf5", "liblzf", config=dict(include_dirs=["lzf/"]))
)
EXTENSIONS = [
ext_bshuf,
]
# Check for HDF5 support
HDF5_FILTER_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, "hdf5.h")):
HDF5_FILTER_SUPPORT = True
if HDF5_FILTER_SUPPORT:
EXTENSIONS.append(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])
# For enabling ZSTD support when building wheels
# This needs to be done after all Extensions have been added to EXTENSIONS
if "ENABLE_ZSTD" in os.environ:
default_options["compile_time_env"] = {"ZSTD_SUPPORT": True}
for ext in EXTENSIONS:
if ext.name in [
"bitshuffle.ext",
"bitshuffle.h5",
"bitshuffle.plugin.libh5bshuf",
]:
ext.sources += zstd_sources
ext.include_dirs += zstd_lib
ext.depends += zstd_headers
ext.libraries += ['zstd']
ext.define_macros += [("ZSTD_SUPPORT", 1)]
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,
),
("zstd", None, "Install ZSTD support."),
]
def initialize_options(self):
install_.initialize_options(self)
self.h5plugin = False
self.zstd = 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. Must be '0' or '1'.")
self.h5plugin = int(self.h5plugin)
self.h5plugin_dir = path.abspath(self.h5plugin_dir)
self.zstd = self.zstd
# Add ZSTD files and macro to extensions if ZSTD enabled
if self.zstd:
default_options["compile_time_env"] = {"ZSTD_SUPPORT": True}
for ext in EXTENSIONS:
if ext.name in [
"bitshuffle.ext",
"bitshuffle.h5",
"bitshuffle.plugin.libh5bshuf",
]:
ext.sources += zstd_sources
ext.include_dirs += zstd_lib
ext.depends += zstd_headers
ext.define_macros += [("ZSTD_SUPPORT", 1)]
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),
),
(
"march=",
None,
"Generate instructions for a specific machine type. Default is %s."
% MARCH_DEFAULT,
),
]
boolean_options = build_ext_.boolean_options + ["omp"]
def initialize_options(self):
build_ext_.initialize_options(self)
self.omp = OMP_DEFAULT
self.march = MARCH_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):
# Set compiler flags including architecture
if self.compiler.compiler_type == "msvc":
openmpflag = "/openmp"
compileflags = COMPILE_FLAGS_MSVC
else:
openmpflag = "-fopenmp"
archi = platform.machine()
if archi in ("i386", "x86_64"):
compileflags = COMPILE_FLAGS
else:
compileflags = COMPILE_FLAGS
if archi == "ppc64le":
compileflags = COMPILE_FLAGS + ["-DNO_WARN_X86_INTRINSICS"]
if self.omp not in ("0", "1", True, False):
raise ValueError("Invalid omp argument. Mut be '0' or '1'.")
self.omp = int(self.omp)
# Add the appropriate OpenMP flags if needed
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']
compileflags += [openmpflag]
linkflags = [openmpflag]
else:
linkflags = []
# Add the compile/link options to each extension
for e in self.extensions:
e.extra_compile_args = list(set(e.extra_compile_args).union(compileflags))
e.extra_link_args = list(set(e.extra_link_args).union(linkflags))
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"],
scripts=[],
ext_modules=EXTENSIONS,
cmdclass={"build_ext": build_ext, "install": install, "develop": develop},
setup_requires=setup_requires,
install_requires=requires,
python_requires=">=3.9",
# 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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