setup.py

#!/usr/bin/env python

#
# $File: setup.py $
# $LastChangedDate$
# $Rev$
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit https://github.com/BoPeng/simuPOP
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (Bo.Peng@bcm.edu)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU 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 General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#

"""
simuPOP installer:

A standard simuPOP package has boost and needed SWIG-generated wrapper files so
you should be able to run this script and install simuPOP using:
  > python setup.py install

If your copy of simuPOP is checked out from the subversion server, you will
need to download a supported version of boost (see variable boost_versions
below) and uncompress it under the simuPOP source directory.

"""
import os, sys, platform, shutil, glob, re, tempfile, subprocess
import distutils.sysconfig
from distutils.ccompiler import new_compiler
from distutils.errors import CompileError
from distutils.errors import DistutilsExecError
import distutils.log

USE_SETUPTOOLS = False
try:
    from setuptools import setup, find_packages, Extension
    USE_SETUPTOOLS = True
except ImportError:
    from distutils.core import setup, Extension
    print("fail to import distribute/setuptools, build the program with distutils")

if sys.version_info[0] <= 2 and sys.version_info[1] <= 4:
    print("simuPOP supports Python version 2.5 or higher, including Python 3.x. Please upgrade your Python installation and try again.")
    sys.exit(1)


# Change this to False if you would like to compile simuPOP without openMP support
USE_OPENMP = True

def is_maverick():
    try:
        ver = [int(x) for x in platform.mac_ver()[0].split('.')]
        return ver >= [10, 9, 0]
    except:
        return False


if os.name == 'nt':
    VS10PATH =  os.environ.get('VS100COMNTOOLS')
    if VS10PATH is None or not os.path.isfile(VS10PATH.replace('Common7\\Tools\\','VC\\lib\\vcomp.lib')):
        USE_OPENMP = False
else:
    p = subprocess.Popen('gcc -v', shell=True,
        stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
        close_fds=True)
    fin, fout, ferr = (p.stdin, p.stdout, p.stderr)
    output = ferr.readlines()[-1].decode('utf8')
    try:
        version = re.match(r'.*gcc version\s*(\d+).(\d+).(\d+).*', output).groups()
        if int(version[0]) < 4 or int(version[1]) < 2:
            print('Support for openMP is turned off because version %s.%s.%s of gcc does not support this feature' % version)
            USE_OPENMP = False
        if int(version[0]) == 4 and int(version[1]) == 2 and int(version[2]) == 1 and 'LLVM' in output:
            print('Support for openMP is turned off because of a bug in LLVM-gcc version 4.2.1.')
            USE_OPENMP = False
    except:
        print('Can not obtain version of gcc, and openMP is disable')
        USE_OPENMP = False

USE_ICC = False
if distutils.sysconfig.get_config_var('CC') is not None:
    USE_ICC = 'icc' in distutils.sysconfig.get_config_var('CC')

# simuPOP works with these boost versions. Newer versions will be used if these
# versions are not available, and will most likely work just fine.
boost_versions = ['1_35_0', '1_36_0', '1_37_0', '1_38_0', '1_39_0', '1_40_0',
    '1_42_0', '1_43_0', '1_44_0', '1_45_0', '1_46_0', '1_46_1', '1_47_0',
    '1_48_0', '1_62_0', '1_72_0', '1_74_0', '1_86_0']
invalid_boost_versions = ['1_41_0', '1_71_0']

included_version = [x for x in boost_versions if os.path.isdir('boost_' + x)]
invalid_version = [x for x in invalid_boost_versions if os.path.isdir('boost_' + x)]
unsupported_version = [x for x in glob.glob('boost_*') if os.path.isdir(x) \
    and x[6:] not in invalid_version + included_version]

boost_dir = ''
if len(included_version) > 0:
    boost_dir = 'boost_' + included_version[-1]  # use the latest version
elif len(invalid_version) > 0:
    print('This version of boost is known to cause problems to simuPOP: ' + ', '.join(invalid_version))

if boost_dir == '' and len(unsupported_version) > 0:
    print('This version of boost is not tested. It may or may not work: ' + ', '.join(unsupported_version))
    boost_dir = unsupported_version[-1]  # use the latest version

if boost_dir == '':
    def downloadProgress(count, blockSize, totalSize):
        perc = count * blockSize * 100 // totalSize
        if perc > downloadProgress.counter:
            sys.stdout.write('.' * (perc - downloadProgress.counter))
            downloadProgress.counter = perc
        sys.stdout.flush()
    from urllib.request import urlretrieve
    import tarfile
    downloadProgress.counter = 0
    try:
        boost_version = boost_versions[-1]
        dot_boost_version = boost_version.replace('_', '.')
        BOOST_URL = f'http://downloads.sourceforge.net/project/boost/boost/{dot_boost_version}/boost_{boost_version}.tar.gz?r=&ts=1440446866&use_mirror=iweb'
        sys.stdout.write(f'Downloading boost C++ library {dot_boost_version}')
        sys.stdout.flush()
        if not os.path.isfile(f'boost_{boost_version}.tar.gz'):
            urlretrieve(BOOST_URL, f'boost_{boost_version}.tar.gz', downloadProgress)
        sys.stdout.write('\n')
        # extract needed files
        with tarfile.open(f'boost_{boost_version}.tar.gz', 'r:gz') as tar:
            files = [h for h in tar.getmembers() if h.name.startswith(f'boost_{boost_version}/boost') \
                or h.name.startswith(f'boost_{boost_version}/libs/iostreams') \
                or h.name.startswith(f'boost_{boost_version}/libs/serialization') \
                or h.name.startswith(f'boost_{boost_version}/libs/regex') \
                or h.name.startswith(f'boost_{boost_version}/libs/detail') ]
            sys.stdout.write('Extracting %d files\n' % len(files))
            tar.extractall(members=files)
        EMBEDED_BOOST = True
        boost_dir = f'boost_{boost_version}'
    except Exception as e:
        print(e)
        print('The boost C++ library version 1.49.0 is not found under the current directory. Will try to use the system libraries.')
        print('Cannot find or download an useful version of boost header files.')
        print('Please download boost from http://www.boost.org and unpack it under the simuPOP directory')
        sys.exit(1)
elif len(included_version + unsupported_version) > 1:
    print('Using boost version: %s' % boost_dir)

boost_include_dir = boost_dir
boost_serialization_dir = os.path.join(boost_dir, 'libs', 'serialization', 'src')
boost_iostreams_dir = os.path.join(boost_dir, 'libs', 'iostreams', 'src')
boost_regex_dir = os.path.join(boost_dir, 'libs', 'regex', 'src')

############################################################################
#
# THE FOLLOWING IS NOT SUPPOSED TO BE MODIFIED
#
############################################################################

from distutils.sysconfig import get_config_var
from distutils.command.build_py import build_py


def simuPOP_version():
    # obtain version of simuPOP
    with open('src/_version.py') as version:
        for line in version:
            if line.startswith('__version__'):
                SIMUPOP_VER = eval(line.split('=')[1])
            elif line.startswith('__revision__'):
                SIMUPOP_REV = eval(line.split('=')[1])
    return SIMUPOP_VER, SIMUPOP_REV


def replaceIntHeader(file):
    ''' Replace "#include <stdint.h>" with "#include <inttypes.h>"
        Try to keep time stamp unchanged '''
    # save file modification time
    time = os.path.getmtime(file)
    # create a temp file
    tmp, name = tempfile.mkstemp()
    input = open(file)
    output = open(name, 'w')
    for line in input.readlines():
        if '#include <stdint.h>' in line:
            output.write('#include <inttypes.h>  /* no stdint.h is found so we use inttypes.h instead */\n')
        else:
            output.write(line)
    output.close()
    input.close()
    # replace file with temp file
    shutil.copyfile(name, file)
    os.remove(name)
    # restore old file modification time
    try:
        os.utime(file, (-1, time))
    except:
        pass

#
# SOURCE FILES
#

HEADER_FILES = [
    'mutant_vector.h',
    'simuPOP_cfg.h',
    'utility.h',
    'genoStru.h',
    'individual.h',
    'population.h',
    'simulator.h',
    'mating.h',
    'operator.h',
    'initializer.h',
    'migrator.h',
    'outputer.h',
    'selector.h',
    'penetrance.h',
    'qtrait.h',
    'stator.h',
    'mutator.h',
    'transmitter.h',
    'tagger.h',
    'pedigree.h',
    'virtualSubPop.h',
]

SOURCE_FILES = [
    'utility.cpp',
    'genoStru.cpp',
    'individual.cpp',
    'population.cpp',
    'simulator.cpp',
    'mating.cpp',
    'operator.cpp',
    'initializer.cpp',
    'migrator.cpp',
    'outputer.cpp',
    'selector.cpp',
    'penetrance.cpp',
    'qtrait.cpp',
    'stator.cpp',
    'mutator.cpp',
    'transmitter.cpp',
    'tagger.cpp',
    'pedigree.cpp',
    'virtualSubPop.cpp',
#    'main.cpp',
]

# since it is troublesome to link to external gsl library,
# I embed some GSL files with simuPOP.
LIB_FILES = [
    'gsl/sys/infnan.c',
    'gsl/sys/coerce.c',
    'gsl/sys/fdiv.c',
    'gsl/sys/pow_int.c',
    'gsl/sys/fcmp.c',
    'gsl/sys/log1p.c',
    'gsl/sys/invhyp.c',
    'gsl/complex/math.c',
    'gsl/specfunc/beta.c',
    'gsl/specfunc/psi.c',
    'gsl/specfunc/trig.c',
    'gsl/specfunc/exp.c',
    'gsl/specfunc/expint.c',
    'gsl/specfunc/log.c',
    'gsl/specfunc/erfc.c',
    'gsl/specfunc/zeta.c',
    'gsl/specfunc/elementary.c',
    'gsl/specfunc/gamma.c',
    'gsl/specfunc/gamma_inc.c',
    'gsl/rng/borosh13.c',
    'gsl/rng/fishman2x.c',
    'gsl/rng/mt.c',
    'gsl/rng/rand.c',
    'gsl/rng/ranmar.c',
    'gsl/rng/types.c',
    'gsl/rng/cmrg.c',
    'gsl/rng/gfsr4.c',
    'gsl/rng/r250.c',
    'gsl/rng/random.c',
    'gsl/rng/rng.c',
    'gsl/rng/uni32.c',
    'gsl/rng/coveyou.c',
    'gsl/rng/knuthran2.c',
    'gsl/rng/ran0.c',
    'gsl/rng/randu.c',
    'gsl/rng/slatec.c',
    'gsl/rng/uni.c',
    'gsl/rng/default.c',
    'gsl/rng/knuthran.c',
    'gsl/rng/ran1.c',
    'gsl/rng/ranf.c',
    'gsl/rng/taus113.c',
    'gsl/rng/vax.c',
    'gsl/rng/file.c',
    'gsl/rng/lecuyer21.c',
    'gsl/rng/ran2.c',
    'gsl/rng/ranlux.c',
    'gsl/rng/taus.c',
    'gsl/rng/waterman14.c',
    'gsl/rng/fishman18.c',
    'gsl/rng/minstd.c',
    'gsl/rng/ran3.c',
    'gsl/rng/ranlxd.c',
    'gsl/rng/transputer.c',
    'gsl/rng/zuf.c',
    'gsl/rng/fishman20.c',
    'gsl/rng/mrg.c',
    'gsl/rng/rand48.c',
    'gsl/rng/ranlxs.c',
    'gsl/rng/tt.c',
    'gsl/rng/knuthran2002.c',
    'gsl/randist/binomial.c',
    'gsl/randist/binomial_tpe.c',
    'gsl/randist/beta.c',
    'gsl/randist/exponential.c',
    'gsl/randist/geometric.c',
    'gsl/randist/nbinomial.c',
    'gsl/randist/poisson.c',
    'gsl/randist/multinomial.c',
    'gsl/randist/chisq.c',
    'gsl/randist/gauss.c',
    'gsl/randist/gausszig.c',
    'gsl/randist/gamma.c',
    'gsl/cdf/gammainv.c',
    'gsl/cdf/binomial.c',
    'gsl/cdf/beta.c',
    'gsl/cdf/betainv.c',
    'gsl/cdf/gauss.c',
    'gsl/cdf/gaussinv.c',
    'gsl/cdf/chisq.c',
    'gsl/cdf/chisqinv.c',
    'gsl/cdf/gamma.c',
    'gsl/cdf/poisson.c',
    'gsl/error.c'
] + [x for x in glob.glob(os.path.join(boost_serialization_dir, '*.cpp')) if 'xml' not in x and 'binary' not in x]\
  + [x for x in glob.glob(os.path.join(boost_iostreams_dir, '*.cpp')) if 'bzip' not in x and 'zstd' not in x and 'lzma' not in x]\
  + glob.glob(os.path.join(boost_regex_dir, '*.cpp'))

GSL_FILES = [
    'gsl/error.c',
    'gsl/sys/infnan.c',
    'gsl/sys/coerce.c',
    'gsl/sys/fdiv.c',
    'gsl/sys/pow_int.c',
    'gsl/sys/fcmp.c',
    'gsl/sys/log1p.c',
    'gsl/sys/invhyp.c',
    'gsl/sys/expm1.c',
    'gsl/complex/math.c',
    'gsl/specfunc/beta.c',
    'gsl/specfunc/elementary.c',
    'gsl/specfunc/erfc.c',
    'gsl/specfunc/exp.c',
    'gsl/specfunc/expint.c',
    'gsl/specfunc/log.c',
    'gsl/specfunc/psi.c',
    'gsl/specfunc/gamma.c',
    'gsl/specfunc/gamma_inc.c',
    'gsl/specfunc/trig.c',
    'gsl/specfunc/zeta.c',
    'gsl/cdf/beta.c',
    'gsl/cdf/betainv.c',
    'gsl/cdf/binomial.c',
    'gsl/cdf/gauss.c',
    'gsl/cdf/gaussinv.c',
    'gsl/cdf/exponential.c',
    'gsl/cdf/exponentialinv.c',
    # pdf functions for gamma, binomial, poisson and beta distributions are copied to gsl.i
    # to avoid subsequent inclusion of RNG related functions.
    #'gsl/randist/gamma.c',
    #'gsl/randist/binomial.c',
    #'gsl/randist/beta.c',
    #'gsl/randist/poisson.c',
    'gsl/cdf/gamma.c',
    'gsl/cdf/gammainv.c',
    'gsl/cdf/chisq.c',
    'gsl/cdf/chisqinv.c',
    'gsl/cdf/poisson.c',
]

SWIG_CPP_FLAGS = '-O -templatereduce -shadow -python -c++ -keyword -nodefaultctor -w-503,-312,-511,-362,-383,-384,-389,-315,-509,-525 -Ibuild -py3  -DSWIG_PYTHON_LEGACY_BOOL'
SWIG_CC_FLAGS = '-python -keyword -py3  -DSWIG_PYTHON_LEGACY_BOOL'

SWIG_RUNTIME_FLAGS = '-python -external-runtime'
# python setup.py reads py_modules from src so we have to produce simuPOP_std.py
# etc to this directory.
SWIG_OUTDIR = 'src'
if not os.path.isdir('build'):
    os.mkdir('build')

COMMON_MACROS = [
    ('BOOST_UBLAS_NDEBUG', None),
    ('BOOST_NO_CXX98_FUNCTION_BASE', None),
    ('BOOST_COMPUTE_USE_CPP11', None),
    ('_HAS_ITERATOR_DEBUGGING', 0),
    ('BOOST_ALL_NO_LIB', None),
    ('NO_ZLIB', 0),
    ('NO_BZIP', 1),
    ('NO_ZSTD', 1),
    ('NO_LZMA', 1)
    ]



STD_MACROS = [('_SECURE_SCL', 1)]
OPT_MACROS = [('NDEBUG', None), ('_SECURE_SCL', 0), ('OPTIMIZED', None)]

MACROS = {
    'std':    [('SIMUPOP_MODULE', 'simuPOP_std')] + STD_MACROS,
    'op':     [('SIMUPOP_MODULE', 'simuPOP_op') ] + OPT_MACROS,
    'la':     [('SIMUPOP_MODULE', 'simuPOP_la'),   ('LONGALLELE', None)] + STD_MACROS,
    'laop':   [('SIMUPOP_MODULE', 'simuPOP_laop'), ('LONGALLELE', None)] + OPT_MACROS,
    'ba':     [('SIMUPOP_MODULE', 'simuPOP_ba'),   ('BINARYALLELE', None)] + STD_MACROS,
    'baop':   [('SIMUPOP_MODULE', 'simuPOP_baop'), ('BINARYALLELE', None)] + OPT_MACROS,
    'mu':     [('SIMUPOP_MODULE', 'simuPOP_mu'),   ('MUTANTALLELE', None)] + STD_MACROS,
    'muop':   [('SIMUPOP_MODULE', 'simuPOP_muop'), ('MUTANTALLELE', None)] + OPT_MACROS,
    'lin':    [('SIMUPOP_MODULE', 'simuPOP_lin'),  ('LINEAGE', None)] + STD_MACROS,
    'linop':  [('SIMUPOP_MODULE', 'simuPOP_linop'),('LINEAGE', None)] + OPT_MACROS
}

WRAP_INFO = {
    'std':    ['src/simuPOP_std_wrap.cpp', 'src/simuPOP_std.i', ''],
    'op':     ['src/simuPOP_op_wrap.cpp', 'src/simuPOP_op.i', '-DOPTIMIZED'],
    'la':     ['src/simuPOP_la_wrap.cpp', 'src/simuPOP_la.i', '-DLONGALLELE'],
    'laop':   ['src/simuPOP_laop_wrap.cpp', 'src/simuPOP_laop.i', '-DLONGALLELE -DOPTIMIZED'],
    'ba':     ['src/simuPOP_ba_wrap.cpp', 'src/simuPOP_ba.i', '-DBINARYALLELE'],
    'baop':   ['src/simuPOP_baop_wrap.cpp', 'src/simuPOP_baop.i', '-DBINARYALLELE -DOPTIMIZED'],
    'mu':     ['src/simuPOP_mu_wrap.cpp', 'src/simuPOP_mu.i', '-DMUTANTALLELE'],
    'muop':   ['src/simuPOP_muop_wrap.cpp', 'src/simuPOP_muop.i', '-DMUTANTALLELE -DOPTIMIZED'],
    'lin':    ['src/simuPOP_lin_wrap.cpp', 'src/simuPOP_lin.i', '-DLINEAGE'],
    'linop':  ['src/simuPOP_linop_wrap.cpp', 'src/simuPOP_linop.i', '-DLINEAGE -DOPTIMIZED'],
}


DESCRIPTION = """
simuPOP is a forward-time population genetics simulation environment.
The core of simuPOP is a scripting language (Python) that provides
a large number of objects and functions to manipulate populations,
and a mechanism to evolve populations forward in time. Using this
R/Splus-like environment, users can create, manipulate and evolve
populations interactively, or write a script and run it as a batch
file. Owing to its flexible and extensible design, simuPOP can simulate
large and complex evolutionary processes with ease. At a more
user-friendly level, simuPOP provides an increasing number of built-in
scripts that perform simulations ranging from implementation of basic
population genetics models to generating datasets under complex
evolutionary scenarios.
"""

#
# starting from mac osx 10.9 (Maverick), the clang compiler uses libc++ as its default
# standard c++ library. This caused many problems, the most significant one is that
# the iterator class of vector<bool> hides its pointer and offset so that I cannot
# access the underlying array directly. This makes it impossible to implement function
# copyGenotype for binary modules. Fortunately, the compiler provides options to
# continue to use libstdc++. Hopefully this quick fix can work a little bit longer.
#

common_library_dirs = ['build']
common_extra_link_args = []
common_extra_include_dirs = []

# for conda environment under all systems
if 'CONDA_PREFIX' in os.environ:
    common_extra_include_dirs.append(os.path.join(os.environ['CONDA_PREFIX'], 'include'))
    common_library_dirs.append(os.path.join(os.environ['CONDA_PREFIX'], 'lib'))

for conda_var in ('CONDA_PREFIX', 'CONDA_PREFIX_1'):
    if conda_var in os.environ:
        conda_lib = os.path.join(os.environ[conda_var], 'Library')
        if os.path.isdir(conda_lib):
            if os.path.join(conda_lib, 'include') not in common_extra_include_dirs:
                common_extra_include_dirs.append(os.path.join(conda_lib, 'include'))
            if os.path.join(conda_lib, 'lib') not in common_library_dirs:
                common_library_dirs.append(os.path.join(conda_lib, 'lib'))

if os.name == 'nt':
    #common_library_dirs.append('development/win32')
    if 'LOCALAPPDATA' in os.environ:
        conda_lib = os.path.join(os.environ['LOCALAPPDATA'], 'Continuum', 'Anaconda3', 'Library')
        if os.path.isdir(conda_lib):
            common_extra_include_dirs.append(os.path.join(conda_lib, 'include'))
            common_library_dirs.append(os.path.join(conda_lib, 'lib'))

    # msvc does not have O3 option, /GR is to fix a C4541 warning

    # /EHsc is for VC exception handling,
    # /wd4819 disables warning messages for non-unicode character in boost/uitlity/enable_if.hpp
    # /wd4996 disables warning messages for unsafe function call in boost/serialization
    # /wd4068 disables warning messages for unknown pragma set by gcc
    common_extra_compile_args = ['/O2', '/GR', '/EHsc', '/wd4819', '/wd4996', '/wd4068']
    common_cpp_extra_compile_args = ['/std:c++17']
    # Enable openMP if USE_OPENMP = True
    if USE_OPENMP:
        if USE_ICC:
            common_extra_compile_args.append('/Qopenmp')
        else:
            common_extra_compile_args.append('/openmp')
else:
    common_extra_compile_args = ['-O3', '-Wall', '-Wno-unknown-pragmas', '-Wno-unused-parameter']
    common_cpp_extra_compile_args = []
    if is_maverick():
        #common_extra_link_args.append('-stdlib=libstdc++')
        #common_extra_include_dirs.append('/usr/include/c++/4.2.1')
        common_extra_compile_args.append('-Wno-error=unused-command-line-argument')
        common_cpp_extra_compile_args.append('-std=c++17')
    if not USE_ICC:   # for gcc, turn on extra warning message
        common_extra_compile_args.append('-Wextra')
    if USE_OPENMP:
        if USE_ICC:
            common_extra_compile_args.append('-openmp')
        else:
            common_extra_compile_args.append('-fopenmp')
    # if Intel ICC is used, turn off remark 981
    if USE_ICC:
        common_extra_compile_args.extend(['-wd981', '-wd191'])

# simplified version of distutils.ccompiler.CCompiler.try_compile
# that actually removes its temporary files.
def try_compile(body='', ext='.cpp'):
    tmpdir = tempfile.mkdtemp(prefix='simupop-install-')
    devnull = oldstderr = None
    try:
        try:
            fname = os.path.join(tmpdir, 'test_compile' + ext)
            with open(fname, 'w') as cpp:
                cpp.write(body)
            # Redirect stderr to /dev/null to hide any error messages
            # from the compiler.
            # This will have to be changed if we ever have to check
            # for a function on Windows.
            devnull = open(os.devnull, 'w')
            oldstderr = os.dup(sys.stderr.fileno())
            os.dup2(devnull.fileno(), sys.stderr.fileno())
            cc = new_compiler()
            distutils.sysconfig.customize_compiler(cc)
            objects = cc.compile([fname], output_dir=tmpdir)
        except:
            return False
        return True
    finally:
        if oldstderr is not None:
            os.dup2(oldstderr, sys.stderr.fileno())
        if devnull is not None:
            devnull.close()
        shutil.rmtree(tmpdir)

#
# TR1_SUPPORT = 0, use <nap>
# TR1_SUPPORT = 1, use <unordered_map>
# TR1_SUPPORT = 2, use <tr1/unordered_map>
if any(x.startswith('bdist') or x == 'install' for x in sys.argv):
    from distutils.core import Distribution
    from distutils.command.config import config

    if try_compile('#include <unordered_map>'):
        print('Testing tr1 support: \033[92myes\033[0m')
        COMMON_MACROS.append(('TR1_SUPPORT', 1))
    elif try_compile('$include <tr1/unordered_map>'):
        print('Testing tr1 support: \033[92mwith tr1 prefix\033[0m')
        COMMON_MACROS.append(('TR1_SUPPORT', 2))
    else:
        print('Testing tr1 support: \033[92mno\033[0m')
        COMMON_MACROS.append(('TR1_SUPPORT', 0))

    if os.name == 'nt':
        print('Testing c++ library: \033[92mvisual c++\033[0m')
    elif try_compile('''
#include <vector>
#include <iostream>
using namespace std;
int main () {
    cout << _S_word_bit;
}
'''):
        print('Testing c++ library: \033[92mlibstdc++\033[0m')
    else:
        COMMON_MACROS.append(('USE_LIBCPP', 1))
        print('Testing c++ library: \033[92mlibc++\033[0m')

else:
    support_binary_modules = True

if not USE_ICC and USE_OPENMP:
    COMMON_MACROS.append(('_GLIBCXX_PARALLEL', None))

#
def ModuInfo(modu, SIMUPOP_VER, SIMUPOP_REV):
    #
    res = {}
    res['src'] =  ['src/simuPOP_' + modu + '_wrap.cpp']
    for src in SOURCE_FILES:
        res['src'].append('build/%s/%s' % (modu, src))
    #
    # lib
    res['libraries'] = []
    res['include_dirs'] = ['.', 'gsl', boost_include_dir] + common_extra_include_dirs
    # define_macros (deep copy)
    res['define_macros'] = COMMON_MACROS + MACROS[modu]
    if 'op' in modu:
        res['libraries'].append('simuPOP_shop')
    else:
        res['libraries'].append('simuPOP_shstd')

    if os.name == 'nt':
        res['libraries'].append('z')
    else:
        res['libraries'].append('z')
        if USE_OPENMP:
            if USE_ICC:
                res['libraries'].append('iomp5')
                res['libraries'].append('tbb')
            else:
                res['libraries'].append('gomp')
    res['undef_macros'] = []
    return res


############################################################################
#
# Build extensions
#
############################################################################
import filecmp

if __name__ == '__main__':
    SIMUPOP_VER, SIMUPOP_REV = simuPOP_version()
    # create source file for each module
    if 'TRAVIS' in os.environ:
        # only build and test half of the modules to save time
        MODULES = ['std', 'ba', 'la', 'mu', 'lin']
    else:
        MODULES = ['std', 'op', 'ba', 'baop', 'la', 'laop', 'mu', 'muop', 'lin', 'linop']
    COMMON_MACROS.extend([
        ('SIMUPOP_VER', SIMUPOP_VER),
        ('SIMUPOP_REV', SIMUPOP_REV)
        ])

    #distutils.log.set_verbosity(distutils.log.FATAL)
    if os.name == 'nt':
        NO_WARNING_ARG = [] # ['/nowarn'] is for vc 2015 only
        SHLIB_ARG = []
    else:
        NO_WARNING_ARG = ['-w']
        SHLIB_ARG = ['-fPIC']

    if any(x.startswith('bdist') or x == 'install' for x in sys.argv):
        try:
            # try to get
            print('Building static libraries')
            c = new_compiler(verbose=1)
            distutils.sysconfig.customize_compiler(c)
            # -w suppress all warnings caused by the use of boost libraries
            objects = c.compile(LIB_FILES,
                include_dirs=['gsl', 'gsl/specfunc', 'build', '.', boost_include_dir] + common_extra_include_dirs,
                output_dir='build',
                extra_preargs = common_extra_compile_args + NO_WARNING_ARG + SHLIB_ARG,
                macros = COMMON_MACROS + STD_MACROS
            )
            c.create_static_lib(objects, "simuPOP_shstd", output_dir='build')
            #
            objects = c.compile(LIB_FILES,
                include_dirs=['gsl', 'gsl/specfunc', 'build', '.', boost_include_dir] + common_extra_include_dirs,
                output_dir='build',
                extra_preargs = common_extra_compile_args + NO_WARNING_ARG + SHLIB_ARG,
                macros = COMMON_MACROS + OPT_MACROS
            )
            c.create_static_lib(objects, "simuPOP_shop", output_dir='build')
        except Exception as e:
            sys.exit("Failed to build a shared supporting library: {}".format(e))

    #
    # Generate Wrapping files
    #
    # if any of the wrap files does not exist
    # or if the wrap files are older than any of the source files.
    if not os.path.isfile('src/gsl_wrap.c') or (not os.path.isfile('src/swigpyrun.h')) or \
            False in [os.path.isfile(WRAP_INFO[x][0]) for x in MODULES]:
        # generate header file
        print("Generating external runtime header file src/swigpyrun.h...")
        os.system('swig {} src/swigpyrun.h'.format(SWIG_RUNTIME_FLAGS))
        # try the first option set with the first library
        for lib in MODULES:
            print("Generating wrapper file " + WRAP_INFO[lib][0])
            if os.system('swig {} -outdir {} {} -o {} {}'.format(SWIG_CPP_FLAGS, \
                SWIG_OUTDIR, WRAP_INFO[lib][2], WRAP_INFO[lib][0], WRAP_INFO[lib][1])) != 0:
                print("Calling swig failed. Please check your swig version.")
                sys.exit(1)
        print("Generating wrapper file src/gsl_wrap.c")
        if os.system('swig {} -outdir {} {} -o {} {}'.format(SWIG_CC_FLAGS, \
            SWIG_OUTDIR, '', 'src/gsl_wrap.c', 'src/gsl.i')) != 0:
            print("Calling swig failed. Please check your swig version.")
            sys.exit(1)
        print("\nAll wrap files are generated successfully.\n")

    # under solaris, there is no stdint.h so I need to replace stdint.h
    # in the wrap files with inttypes.h
    if sys.platform == 'sunos5':
        for lib in MODULES:
            replaceIntHeader(WRAP_INFO[lib][0])
    # copy needed files
    copied_files = []
    for modu in MODULES:
        if not os.path.isdir('build/%s' % modu):
            os.mkdir('build/%s' % modu)
        for src in SOURCE_FILES:
            mod_src = 'build/%s/%s' % (modu, src)
            if not os.path.isfile(mod_src) or not filecmp.cmp(mod_src,'src/'+src):
                shutil.copy('src/'+src, mod_src)
    # build
    # For module simuPOP.gsl
    EXT_MODULES = [
        Extension('simuPOP._gsl',
            sources = GSL_FILES + ['src/gsl_wrap.c'],
            include_dirs = ['gsl', 'gsl/specfunc', 'build', '.'] + common_extra_include_dirs,
            extra_compile_args = common_extra_compile_args + NO_WARNING_ARG,
            extra_link_args = common_extra_link_args,
        )
    ]
    for modu in MODULES:
        info = ModuInfo(modu, SIMUPOP_VER=SIMUPOP_VER, SIMUPOP_REV=SIMUPOP_REV)
        EXT_MODULES.append(
            Extension('simuPOP._simuPOP_%s' % modu,
                sources = info['src'],
                extra_compile_args = common_extra_compile_args + common_cpp_extra_compile_args,
                include_dirs = info['include_dirs'] + ['src', 'build'],
                library_dirs = common_library_dirs,
                libraries = info['libraries'],
                define_macros = info['define_macros'],
                undef_macros = info['undef_macros'],
                extra_link_args = common_extra_link_args,
            )
        )
    if  USE_SETUPTOOLS :
        setup_params = dict(packages = find_packages(), include_package_data = True,
                        exclude_package_data = {'':['README.txt']}, zip_safe = False,
                        install_requires = ['setuptools'])
    else :
        setup_params = dict(packages = ['simuPOP'])

    setup(
        name = "simuPOP",
        version = SIMUPOP_VER,
        author = "Bo Peng",
        author_email = "Bo.Peng@bcm.edu",
        maintainer = "Bo Peng",
        maintainer_email = "Bo.Peng@bcm.edu",
        url = "https://github.com/BoPeng/simuPOP",
        description = "Forward-time population genetics simulation environment",
        long_description = DESCRIPTION,
        download_url = 'https://pypi.org/project/simuPOP/#files',
        classifiers = [
            'Development Status :: 5 - Production/Stable',
            'Environment :: Console',
            'Intended Audience :: Education',
            'Intended Audience :: Science/Research',
            'License :: OSI Approved :: GNU General Public License (GPL)',
            'Natural Language :: English',
            'Operating System :: OS Independent',
            'Programming Language :: C++',
            'Programming Language :: Python :: 3',
            'Topic :: Scientific/Engineering :: Bio-Informatics',
        ],
        platforms = ['all'],
        #
        package_dir = {'simuPOP': 'src'},
        py_modules = [
            'simuOpt',
            'simuPOP.__init__',
            'simuPOP.gsl',
            'simuPOP.utils',
            'simuPOP.demography',
            'simuPOP.sampling',
        ] + ['simuPOP.simuPOP_%s' % x for x in MODULES],
        ext_modules = EXT_MODULES,
        cmdclass = {'build_py': build_py},
        **setup_params
    )