setup.py

import distutils
from distutils.core import setup, Extension

import sys
import os
import subprocess
import shlex

from numpy.distutils import system_info
import numpy as np

numpy_config_keys = [
    'atlas_blas_info',
    'atlas_blas_threads_info',
    'atlas_info',
    'atlas_threads_info',
    'blas_mkl_info',
    'blas_opt_info',
    'get_info',
    'lapack_mkl_info',
    'lapack_opt_info',
    'mkl_info',
    'openblas_info',
    'openblas_lapack_info'
    ]

np_define_macros = []
np_extra_compile_args = []
np_extra_link_args = []
np_libraries = []

if not 'linux' in sys.platform:
    for key in numpy_config_keys:
        try:
            np_libraries += np.__config__.get_info(key)['libraries']
        except:
            pass
        try:
            np_define_macros += np.__config__.get_info(key)['define_macros']
        except:
            pass
        try:
            np_extra_compile_args += np.__config__.get_info(key)[
                'extra_compile_args']
        except:
            pass
        try:
            np_extra_link_args += np.__config__.get_info(key)['extra_link_args']
        except:
            pass

hdf5_extra_compile_args = []
hdf5_extra_link_args = []
if 'linux' in sys.platform:
    cmd = shlex.split('pkg-config --cflags hdf5')
    p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    p.wait()
    pkg_config_out = p.stdout.read().decode("utf-8")[:-1]
    pkg_config_err = p.stderr.read().decode("utf-8")[:-1]
    if "No package" in pkg_config_err:
        hdf5_extra_compile_args = ["-I/usr/include/hdf5/serial"]
    else:
        hdf5_extra_compile_args = [pkg_config_out]

    cmd = shlex.split('pkg-config --libs hdf5')
    p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    p.wait()
    pkg_config_out = p.stdout.read().decode("utf-8")[:-1]
    pkg_config_err = p.stderr.read().decode("utf-8")[:-1]
    if "No package" in pkg_config_err:
        hdf5_extra_link_args = [
            "-L/usr/lib/x86_64-linux-gnu/",
            "-L/usr/lib/x86_64-linux-gnu/hdf5/serial"]
    else:
        hdf5_extra_link_args = [pkg_config_out]


if os.name == "nt":
    biosig_define_macros = [('WITH_BIOSIG2', None)]
    biosig_libraries = ['libbiosig2']
    biosig_lite_sources = []
else:
    biosig_define_macros = [('WITH_BIOSIG2', None), ('WITH_BIOSIGLITE', None), ('WITHOUT_NETWORK', None)]
    biosig_libraries = ['iconv']
    biosig_lite_sources = [
        'src/libbiosiglite/biosig4c++/t210/sopen_abf_read.c',
        'src/libbiosiglite/biosig4c++/t210/sopen_alpha_read.c',
        'src/libbiosiglite/biosig4c++/t210/sopen_axg_read.c',
        'src/libbiosiglite/biosig4c++/t210/sopen_cfs_read.c',
        'src/libbiosiglite/biosig4c++/t210/sopen_heka_read.c',
        'src/libbiosiglite/biosig4c++/t210/sopen_igor.c',
        'src/libbiosiglite/biosig4c++/t210/sopen_scp_read.c',
        'src/libbiosiglite/biosig4c++/t210/scp-decode.cpp',
        'src/libbiosiglite/biosig4c++/t220/crc4scp.c',
        'src/libbiosiglite/biosig4c++/t220/sopen_scp_write.c',
        'src/libbiosiglite/biosig4c++/test0/sandbox.c',
        'src/libbiosiglite/biosig4c++/biosig.c',
        'src/libbiosiglite/biosig4c++/biosig2.c',
        'src/libbiosiglite/biosig4c++/biosig-network.c',
        'src/libbiosiglite/biosig4c++/gdftime.c',
        'src/libbiosiglite/biosig4c++/mdc_ecg_codes.c',
        'src/libbiosiglite/biosig4c++/physicalunits.c'
    ]

fftw3_libraries = ['fftw3']
if 'libraries' in system_info.get_info('fftw3').keys():
    fftw3_libraries = system_info.get_info('fftw3')['libraries']

if os.name == "nt":
    win_define_macros = [("_WINDOWS", None),
                         ("__STF__", None),
                         ("STFIODLL", None),
                         ("_WIN64", None),
                         ("_WINDLL", None),
                         ("H5_USE_16_API", None),
                         ("_HDF5USEDLL_", None),
                         ("_CRT_SECURE_NO_WARNINGS", None),
                         ("UNICODE", None),
                         ("_UNICODE", None)]
    win_compile_args = ["/EHsc"]
    home_dir = os.path.expanduser("~")
    win_include_dirs = [
        os.path.join(home_dir, 'boost'),
        os.path.join(home_dir, 'biosig', 'include'),
        os.path.join(home_dir, 'hdf5', 'include'),
        os.path.join(home_dir, 'fftw'),
    ]
    win_library_dirs = [
        os.path.join(home_dir, 'hdf5', 'lib'),
        os.path.join(home_dir, 'biosig', 'lib'),
        os.path.join(home_dir, 'stimfit', 'dist', 'windows', 'libs'),
        os.path.join(home_dir, 'fftw'),
    ]
    fftw3_libraries = ['libfftw3-3']
    np_libraries = ['BLAS', 'clapack', 'libf2c']
    win_libraries = ['user32']
    win_link_args = ["/SUBSYSTEM:WINDOWS",
                     "/LARGEADDRESSAWARE",
                     "/OPT:REF",
                     "/OPT:ICF",
                     "/DYNAMICBASE",
                     "/NXCOMPAT",
                     "/MACHINE:X64",
                     "/NODEFAULTLIB:\"libc.lib\"",
                     "/NODEFAULTLIB:\"libcmt.lib\""]
    win_data_files = [(
        distutils.sysconfig.get_python_lib(), [
            os.path.join(home_dir, 'biosig', 'lib', 'libbiosig2.dll'),
            os.path.join(home_dir, 'fftw', 'libfftw3-3.dll'), ]
    )]
else:
    win_define_macros = []
    win_include_dirs = []
    win_compile_args = []
    win_library_dirs = []
    win_libraries = []
    win_link_args = []
    win_data_files = []

stfio_module = Extension(
    '_stfio',
    swig_opts=['-c++'],
    library_dirs=win_library_dirs,
    libraries=['hdf5', 'hdf5_hl'] + fftw3_libraries + np_libraries +
    biosig_libraries + win_libraries,
    define_macros=np_define_macros + biosig_define_macros +
    win_define_macros,
    extra_compile_args=np_extra_compile_args + hdf5_extra_compile_args +
    win_compile_args,
    extra_link_args=np_extra_link_args + hdf5_extra_link_args +
    win_link_args,
    include_dirs=win_include_dirs,
    sources=[
        'src/libstfio/abf/abflib.cpp',
        'src/libstfio/abf/axon/AxAbfFio32/Oldheadr.cpp',
        'src/libstfio/abf/axon/AxAbfFio32/abferror.cpp',
        'src/libstfio/abf/axon/AxAbfFio32/abffiles.cpp',
        'src/libstfio/abf/axon/AxAbfFio32/abfheadr.cpp',
        'src/libstfio/abf/axon/AxAbfFio32/abfhwave.cpp',
        'src/libstfio/abf/axon/AxAbfFio32/abfutil.cpp',
        'src/libstfio/abf/axon/AxAbfFio32/csynch.cpp',
        'src/libstfio/abf/axon/AxAbfFio32/filedesc.cpp',
        'src/libstfio/abf/axon/AxAbfFio32/msbincvt.cpp',
        'src/libstfio/abf/axon/AxAtfFio32/axatffio32.cpp',
        'src/libstfio/abf/axon/AxAtfFio32/fileio2.cpp',
        'src/libstfio/abf/axon/Common/FileIO.cpp',
        'src/libstfio/abf/axon/Common/FileReadCache.cpp',
        'src/libstfio/abf/axon/Common/unix.cpp',
        'src/libstfio/abf/axon2/ProtocolReaderABF2.cpp',
        'src/libstfio/abf/axon2/SimpleStringCache.cpp',
        'src/libstfio/abf/axon2/abf2headr.cpp',
        'src/libstfio/atf/atflib.cpp',
        'src/libstfio/axg/AxoGraph_ReadWrite.cpp',
        'src/libstfio/axg/axglib.cpp',
        'src/libstfio/axg/byteswap.cpp',
        'src/libstfio/axg/fileUtils.cpp',
        'src/libstfio/axg/stringUtils.cpp',
        'src/libstfio/biosig/biosiglib.cpp',
        'src/libstfio/cfs/cfs.c',
        'src/libstfio/cfs/cfslib.cpp',
        'src/libstfio/channel.cpp',
        'src/libstfio/hdf5/hdf5lib.cpp',
        'src/libstfio/igor/CrossPlatformFileIO.c',
        'src/libstfio/igor/WriteWave.c',
        'src/libstfio/igor/igorlib.cpp',
	'src/libstfio/intan/common.cpp',
	'src/libstfio/intan/intanlib.cpp',
	'src/libstfio/intan/streams.cpp',
        'src/libstfio/recording.cpp',
        'src/libstfio/section.cpp',
        'src/libstfio/stfio.cpp',
        'src/libstfnum/fit.cpp',
        'src/libstfnum/funclib.cpp',
        'src/libstfnum/levmar/Axb.c',
        'src/libstfnum/levmar/lm.c',
        'src/libstfnum/levmar/lmbc.c',
        'src/libstfnum/levmar/misc.c',
        'src/libstfnum/measure.cpp',
        'src/libstfnum/stfnum.cpp',
        'src/pystfio/pystfio.cxx',
        'src/pystfio/pystfio.i',
    ] + biosig_lite_sources)


setup(name='stfio',
      version='0.16.2',
      description='stfio module',
      include_dirs=system_info.default_include_dirs + [
          np.get_include()],
      scripts=[],
      package_dir={'stfio': 'src/pystfio'},
      packages=['stfio'],
      data_files=win_data_files,
      ext_modules=[stfio_module])