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import os
import sys
from shutil import rmtree
from subprocess import run
import platform
import setuptools
from setuptools import setup, Extension
from setuptools.command.install import install
from setuptools.command.build_ext import build_ext
LIB_SPOA = 'src/build/lib/libspoa.a'
if os.environ.get('libspoa'):
LIB_SPOA = os.environ['libspoa']
class get_pybind_include(object):
"""
Helper class to determine the pybind11 include path
The purpose of this class is to postpone importing pybind11
until it is actually installed, so that the ``get_include()``
method can be invoked.
"""
def __init__(self, user=False):
self.user = user
def __str__(self):
import pybind11
return pybind11.get_include(self.user)
def has_flag(compiler, flagname):
"""
Return a boolean indicating whether a flag name is supported on the specified compiler.
"""
import tempfile
with tempfile.NamedTemporaryFile('w', suffix='.cpp') as f:
f.write('int main (int argc, char **argv) { return 0; }')
try:
compiler.compile([f.name], extra_postargs=[flagname])
except setuptools.distutils.errors.CompileError:
return False
return True
def cpp_flag(compiler):
"""
Return the -std=c++[11/14/17] compiler flag.
The newer version is prefered over c++11 (when it is available).
"""
flags = ['-std=c++14', '-std=c++11']
for flag in flags:
if has_flag(compiler, flag):
return flag
raise RuntimeError('Unsupported compiler -- at least C++11 support is needed!')
def build_spoa():
bdir = "src/build"
rmtree(bdir, ignore_errors=True)
os.makedirs(bdir)
# x86 -- builds with -msse4.1 instead of -march=native
extra_flags = ["-D", "spoa_optimize_for_portability=ON"]
if platform.machine() in {"aarch64", "arm64"}:
extra_flags = [
"-D", "spoa_use_simde=ON",
"-D", "spoa_use_simde_nonvec=ON",
"-D", "spoa_use_simde_openmp=ON"]
run("make", cwd=bdir)
class BuildExt(build_ext):
"""
A custom build extension for adding compiler-specific options.
"""
c_opts = {
'msvc': ['/EHsc'],
'unix': [],
}
l_opts = {
'msvc': [],
'unix': [],
}
if sys.platform == 'darwin':
darwin_opts = ['-stdlib=libc++', '-mmacosx-version-min=10.7']
c_opts['unix'] += darwin_opts
l_opts['unix'] += darwin_opts
def build_extensions(self):
if not os.environ.get('libspoa'):
build_spoa()
ct = self.compiler.compiler_type
opts = self.c_opts.get(ct, [])
link_opts = self.l_opts.get(ct, [])
if ct == 'unix':
opts.append('-DVERSION_INFO="%s"' % self.distribution.get_version())
opts.append(cpp_flag(self.compiler))
if has_flag(self.compiler, '-fvisibility=hidden'):
opts.append('-fvisibility=hidden')
elif ct == 'msvc':
opts.append('/DVERSION_INFO=\\"%s\\"' % self.distribution.get_version())
for ext in self.extensions:
ext.extra_compile_args = opts
ext.extra_link_args = link_opts
build_ext.build_extensions(self)
ext_modules = [
Extension(
'spoa',
['pyspoa.cpp'],
include_dirs=[
'src/include/spoa',
'src/vendor/cereal/include',
get_pybind_include(),
get_pybind_include(user=True),
],
language='c++',
extra_objects=[
'/usr/lib/' + os.getenv('DEB_HOST_MULTIARCH') + '/libspoa.so'
],
),
]
with open('README.md', encoding='utf-8') as f:
long_description = f.read()
setup(
name='pyspoa',
version='0.2.1',
author='Oxford Nanoporetech Technologies, Ltd.',
author_email='support@nanoporetech.com',
url='https://github.com/nanoporetech/pyspoa',
description='Python bindings to spoa',
long_description=long_description,
long_description_content_type='text/markdown',
ext_modules=ext_modules,
cmdclass={
'build_ext': BuildExt,
},
zip_safe=False,
)
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