setup.py

from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext
import sys
import setuptools
from glob import glob

__version__ = '0.0.1'

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)

ext_modules = [
    Extension(
        'emeraldpy',
        [
          'src/emeraldpy/core.cpp',
          'src/emeraldpy/wrap.cpp',
          'src/calcLD.cpp',
          'src/processGenotypes.cpp'
        ] + glob("src/tabix_util/*.c") + glob("src/tabix_util/*.cpp"),
        include_dirs=[
          # Path to pybind11 headers
          get_pybind_include(),
          get_pybind_include(user=True),
          "src",
          "src/tabix_util",
          "src/emeraldpy"
        ],
        depends = [
          "src/emeraldpy/core.hpp"
        ],
        language='c++'
    ),
]

# As of Python 3.6, CCompiler has a `has_flag` method.
# cf http://bugs.python.org/issue26689
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] compiler flag.

    The c++14 is prefered over c++11 (when it is available).
    """
    if has_flag(compiler, '-std=c++14'):
        return '-std=c++14'
    elif has_flag(compiler, '-std=c++11'):
        return '-std=c++11'
    else:
        raise RuntimeError('Unsupported compiler -- at least C++11 support '
                           'is needed!')

class BuildExt(build_ext):
    """A custom build extension for adding compiler-specific options."""
    c_opts = {
        'msvc': ['/EHsc'],
        'unix': [],
    }

    if sys.platform == 'darwin':
        c_opts['unix'] += ['-stdlib=libc++', '-mmacosx-version-min=10.7']

    def build_extensions(self):
        orig_compile = self.compiler._compile

        def new_compile(obj, src, ext, cc_args, extra_postargs, pp_opts):
          """
          This hack is specifically required on MacOS, because clang will error if a .c file is compiled with -std=c++11 or similar flag. 
          We make sure to filter out those flags if C source code is given. 
          """

          if src.endswith(".c"):
            extra_postargs = list(filter(lambda x: "c++11" not in x and "c++14" not in x and "c++17" not in x, extra_postargs))

          return orig_compile(obj, src, ext, cc_args, extra_postargs, pp_opts)

        ct = self.compiler.compiler_type
        opts = self.c_opts.get(ct, [])
        if ct == 'unix':
            opts.append('-DVERSION_INFO="%s"' % self.distribution.get_version())
            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:
            if ext.language == "c++":
              opts.append(cpp_flag(self.compiler))
            ext.extra_compile_args = opts

        self.compiler._compile = new_compile
        build_ext.build_extensions(self)

setup(
    name = 'emeraldpy',
    version = __version__,
    author = 'Corbin Quick',
    author_email = 'corbinq@gmail.com',
    url = 'https://github.com/statgen/emerald',
    description = 'Python wrapper for emeraLD',
    long_description = '',
    ext_modules = ext_modules,
    install_requires = ['pybind11 >= 2.2'],
    cmdclass = {'build_ext': BuildExt},
    zip_safe = False,
)