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#pykdtree, Fast kd-tree implementation with OpenMP-enabled queries
#
#Copyright (C) 2013 - present Esben S. Nielsen
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License along
# with this program. If not, see <http://www.gnu.org/licenses/>.
import os
import sys
import re
import numpy as np
from Cython.Build import build_ext
from Cython.Distutils import Extension
from setuptools import setup
from setuptools.command.build_ext import build_ext
OMP_SETTING_TABLE = {
'1': 'probe',
'0': None,
'gcc': 'gomp',
'gomp': 'gomp',
'clang': 'omp',
'omp': 'omp',
'msvc': 'msvc',
'probe': 'probe'
}
OMP_COMPILE_ARGS = {
'gomp': ['-fopenmp'],
'omp': ['-Xpreprocessor', '-fopenmp'],
'msvc': ['/openmp']
}
OMP_LINK_ARGS = {
'gomp': ['-lgomp'],
'omp': ['-lomp'],
'msvc': []
}
class build_ext_subclass(build_ext):
"""Custom extension building to have platform and compiler specific flags."""
def build_extensions(self):
comp = self.compiler.compiler_type
omp_comp, omp_link = _omp_compile_link_args(comp)
if comp in ('unix', 'cygwin', 'mingw32'):
extra_compile_args = ['-std=c17', '-O3'] + omp_comp
extra_link_args = omp_link
elif comp == 'msvc':
extra_compile_args = ['/Ox'] + omp_comp
extra_link_args = omp_link
else:
# Add support for more compilers here
raise ValueError('Compiler flags undefined for %s. Please modify setup.py and add compiler flags'
% comp)
self.extensions[0].extra_compile_args = extra_compile_args
self.extensions[0].extra_link_args = extra_link_args
build_ext.build_extensions(self)
def _omp_compile_link_args(compiler):
# Get OpenMP setting from environment
use_omp = OMP_SETTING_TABLE[os.environ.get('USE_OMP', 'probe')]
compile_args = []
link_args = []
if use_omp == "probe":
use_omp, compile_args, link_args = _probe_omp_for_compiler_and_platform(compiler)
print(f"Will use {use_omp} for OpenMP." if use_omp else "OpenMP support not available.")
compile_args += OMP_COMPILE_ARGS.get(use_omp, [])
link_args += OMP_LINK_ARGS.get(use_omp, [])
print(f"Compiler: {compiler} / OpenMP: {use_omp} / OpenMP compile args: {compile_args} / OpenMP link args: {link_args}")
return compile_args, link_args
def _probe_omp_for_compiler_and_platform(compiler):
compile_args = []
link_args = []
if compiler == "msvc":
use_omp = "msvc"
elif _is_conda_interpreter():
# Conda provides its own compiler which does support openmp
use_omp = "gomp"
elif _is_macOS():
# OpenMP is not supported with system clang but homebrew and macports have libomp packages
compile_args, link_args = _macOS_omp_options_from_probe()
if not (compile_args or link_args):
print("Probe for libomp failed, skipping use of OpenMP with clang.")
print("It may be possible to build with OpenMP using USE_OMP=clang with CFLAGS and LDFLAGS explicit settings to use libomp.")
use_omp = None
else:
use_omp = "omp"
else:
use_omp = "gomp"
return use_omp, compile_args, link_args
def _is_conda_interpreter():
"""Is the running interpreter from Anaconda or miniconda?
See https://stackoverflow.com/a/21318941/433202
Examples::
2.7.6 |Anaconda 1.8.0 (x86_64)| (default, Jan 10 2014, 11:23:15)
2.7.6 |Continuum Analytics, Inc.| (default, Jan 10 2014, 11:23:15)
3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:55:02)
"""
return 'conda' in sys.version or 'Continuum' in sys.version
def _is_macOS():
return 'darwin' in sys.platform
def _macOS_omp_options_from_probe():
"""Get common include and library paths for libomp installation on macOS.
For example ``(['-I/opt/local/include/libomp'], ['-L/opt/local/lib/libomp'])``.
"""
for cmd in ["brew ls --verbose libomp", "port contents libomp"]:
inc, lib = _compile_link_paths_from_manifest(cmd)
if inc and lib:
return [f"-I{inc}"], [f"-L{lib}"]
return [], []
def _compile_link_paths_from_manifest(cmd):
"""Parse include and library paths from OSX package managers.
Example executions::
# Homebrew
$ brew ls --verbose libomp
/opt/homebrew/Cellar/libomp/15.0.7/INSTALL_RECEIPT.json
/opt/homebrew/Cellar/libomp/15.0.7/.brew/libomp.rb
/opt/homebrew/Cellar/libomp/15.0.7/include/ompt.h
/opt/homebrew/Cellar/libomp/15.0.7/include/omp.h
/opt/homebrew/Cellar/libomp/15.0.7/include/omp-tools.h
/opt/homebrew/Cellar/libomp/15.0.7/lib/libomp.dylib
/opt/homebrew/Cellar/libomp/15.0.7/lib/libomp.a
# MacPorts
$ port contents libomp
Port libomp contains:
/opt/local/include/libomp/omp-tools.h
/opt/local/include/libomp/omp.h
/opt/local/include/libomp/ompt.h
/opt/local/lib/libomp/libgomp.dylib
/opt/local/lib/libomp/libiomp5.dylib
/opt/local/lib/libomp/libomp.dylib
/opt/local/share/doc/libomp/LICENSE.TXT
/opt/local/share/doc/libomp/README.txt
"""
from subprocess import run
query = run(cmd, shell=True, check=False, capture_output=True)
if query.returncode != 0:
return None, None
manifest = query.stdout.decode("UTF-8")
# find all the unique directories mentioned in the manifest
dirs = set(os.path.split(filename)[0] for filename in re.findall(r'^\s*(/.*?)\s*$', manifest, re.MULTILINE))
# find a unique libdir and incdir
inc = tuple(d for d in dirs if re.search(r'/include(\W|$)', d))
lib = tuple(d for d in dirs if re.search(r'/lib(\W|$)', d))
# only return success if there's no ambiguity
return (inc + lib) if len(inc) == 1 and len(lib) == 1 else (None, None)
with open('README.rst', 'r') as readme_file:
readme = readme_file.read()
extensions = [
Extension('pykdtree.kdtree', sources=['pykdtree/kdtree.pyx', 'pykdtree/_kdtree_core.c'],
include_dirs=[np.get_include()],
define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_25_API_VERSION")],
cython_directives={"language_level": "3"},
),
]
setup(
name='pykdtree',
version='1.4.3',
url="https://github.com/storpipfugl/pykdtree",
description='Fast kd-tree implementation with OpenMP-enabled queries',
long_description=readme,
long_description_content_type="text/x-rst",
author='Esben S. Nielsen',
author_email='storpipfugl@gmail.com',
packages=['pykdtree'],
python_requires='>=3.9',
install_requires=['numpy'],
extras_require={
'test': ['pytest', 'mypy'],
},
zip_safe=False,
ext_modules=extensions,
cmdclass={'build_ext': build_ext_subclass},
license="LGPL-3.0-or-later",
license_files=["LICENSE.txt"],
classifiers=[
'Development Status :: 5 - Production/Stable',
'Programming Language :: Python',
'Operating System :: OS Independent',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering',
'Programming Language :: Python :: Free Threading :: 3 - Stable',
]
)
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