setup.py

#!/usr/bin/python

#from distutils.core      import setup, Extension
from setuptools import setup, Extension
from distutils.sysconfig import get_python_inc
from os                  import listdir, getcwd, path, system
from glob                import glob
import sys
import tempfile
import os
import subprocess
import shutil

from platform import architecture, mac_ver

#incdir = get_python_inc(plat_specific=1)
#print incdir

#build the list of source files
scriptPath   = path.dirname(path.realpath(__file__))
libDir       = path.split(scriptPath)[1]
hyphyPath    = path.join(scriptPath, 'hyphy-src')
srcDir       = path.join(hyphyPath, 'src')
srcPath      = srcDir
contribPath  = path.join(hyphyPath, 'contrib')
sqlitePath   = path.join(contribPath, 'SQLite-3.8.2')
linkPath     = path.join(scriptPath, 'Link')
coreSrcPath  = path.join(srcPath, 'core')
newSrcPath   = path.join(srcPath, 'new')
guiSrcPath   = path.join(srcPath, 'gui')
prefFile     = [path.join(guiSrcPath, 'preferences.cpp')]
coreSrcFiles = glob(path.join(coreSrcPath, '*.cpp'))
newSrcFiles  = glob(path.join(newSrcPath, '*.cpp'))
sqliteFiles  = glob(path.join(sqlitePath, '*.c'))
linkFiles    = glob(path.join(linkPath, '*.cpp'))
utilFiles    = glob(path.join(srcPath, 'utils', '*.cpp'))

if sys.version_info >= (3,0,0):
    swigFile = [path.join(scriptPath, 'SWIGWrappers', 'THyPhy_py3.cpp')]
else:
    swigFile = [path.join(scriptPath, 'SWIGWrappers', 'THyPhy_python.cpp')]


sourceFiles = coreSrcFiles + newSrcFiles +  sqliteFiles + prefFile + linkFiles + swigFile + utilFiles

includePaths =  [path.join(p, 'include') for p in [coreSrcPath, newSrcPath, guiSrcPath]]
includePaths += [linkPath, contribPath, sqlitePath]

# check for 64bit and define as such
define_macros = [('__HYPHY_64__', None)] if '64' in architecture()[0] else []

# see http://openmp.org/wp/openmp-compilers/
omp_test = \
r"""
#include <omp.h>
#include <stdio.h>
int main() {
#pragma omp parallel
printf("Hello from thread %d, nthreads %d\n", omp_get_thread_num(), omp_get_num_threads());
}
"""

def check_for_openmp():
    tmpdir = tempfile.mkdtemp()
    curdir = os.getcwd()
    os.chdir(tmpdir)

    filename = r'test.c'
    with open(filename, 'w') as file:
        file.write(omp_test)
    with open(os.devnull, 'w') as fnull:
        result = subprocess.call(['cc', '-fopenmp', filename],
                                 stdout=fnull, stderr=fnull)

    os.chdir(curdir)
    #clean up
    shutil.rmtree(tmpdir)

    return result

openmp = ['-fopenmp'] if check_for_openmp() == 0 else []

setup(
    name = 'hyphy-python',
    version = '0.1.12',
    description = 'HyPhy package interface library',
    author = 'Sergei L Kosakovsky Pond and Steven Weaver',
    author_email = 'spond@temple.edu',
    url = 'http://github.com/veg/hyphy',
    packages = ['HyPhy'],
    package_dir = {'HyPhy': 'HyPhy'},
    ext_modules = [Extension('_HyPhy',
            sourceFiles,
            include_dirs = includePaths,
            define_macros = [('SQLITE_PTR_SIZE','sizeof(long)'),
                             ('__UNIX__', None),
                             ('__MP__', None),
                             ('__MP2__', None),
                             ('_SLKP_LFENGINE_REWRITE_', None),
                             ('__AFYP_REWRITE_BGM__', None),
                             ('__HEADLESS__', None),
                             ('_HYPHY_LIBDIRECTORY_', '"/usr/local/lib/hyphy"')] + define_macros,
            libraries = ['pthread', 'ssl', 'crypto', 'curl'],
            library_dirs = ['/usr/local/lib/', '/usr/lib/', '/usr/local/opt/openssl/lib/'],
            extra_compile_args = [
                    '-Wno-int-to-pointer-cast',
                    '-Wno-char-subscripts',
                    '-Wno-sign-compare',
                    '-Wno-parentheses',
                    '-Wno-uninitialized',
                    '-Wno-unused-variable',
                    '-Wno-shorten-64-to-32',
                    '-Wno-c++11-narrowing',
                    '-Wno-undefined-bool-conversion',
                    '-fsigned-char',
                    '-O3',
                    '-fpermissive',
                    '-fPIC',
            ] + openmp,
            extra_link_args = [
            ] + openmp
    )]
)