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"""
fast5.setup.py
(c) 2016: Matei David, Ontario Institute for Cancer Research
MIT License
"""
import os
import re
import pkg_resources
import sys
from setuptools import setup, Extension
exec(open('fast5/version.py').read())
# check HDF5 include and lib dirs
hdf5_dir = os.environ.get('HDF5_DIR', '/usr')
hdf5_include_dir = os.environ.get('HDF5_INCLUDE_DIR', os.path.join(hdf5_dir, 'include'))
hdf5_lib_dir = os.environ.get('HDF5_LIB_DIR', os.path.join(hdf5_dir, 'lib'))
hdf5_lib = os.environ.get('HDF_LIB', 'hdf5')
if not os.path.isfile(os.path.join(hdf5_include_dir, 'H5pubconf.h')):
sys.exit(hdf5_include_dir + ': could not find HDF5 header files; use HDF5_DIR or HDF5_INCLUDE_DIR')
if (not os.path.isfile(os.path.join(hdf5_lib_dir, 'lib' + hdf5_lib + '.so'))
and not os.path.isfile(os.path.join(hdf5_lib_dir, 'lib' + hdf5_lib + '.a'))):
sys.exit(hdf5_lib_dir + ': could not find HDF5 library file; use HDF5_DIR or HDF5_LIB_DIR/HDF5_LIB')
# check Boost.Python include and lib dirs
boost_dir = os.environ.get('BOOST_DIR', '/usr')
boost_include_dir = os.environ.get('BOOST_INCLUDE_DIR', os.path.join(boost_dir, 'include'))
boost_lib_dir = os.environ.get('BOOST_LIB_DIR', os.path.join(boost_dir, 'lib'))
boost_python_lib = os.environ.get('BOOST_PYTHON_LIB', 'boost_python')
if not os.path.isfile(os.path.join(boost_include_dir, 'boost', 'python.hpp')):
sys.exit(boost_include_dir + ': could not find Boost Python header files; use BOOST_DIR or BOOST_INCLUDE_DIR')
if (not os.path.isfile(os.path.join(boost_lib_dir, 'lib' + boost_python_lib + '.so'))
and not os.path.isfile(os.path.join(boost_lib_dir, 'lib' + boost_python_lib + '.a'))):
sys.exit(boost_lib_dir + ': could not find Boost Python library file; use BOOST_DIR or BOOST_LIB_DIR/BOOST_PYTHON_LIB')
fast5_dir = os.environ.get('FAST5_DIR', os.path.join('..', 'src'))
extra_compile_args = [
'-std=c++11',
'-Wall', '-Wextra', '-Wpedantic',
]
# don't indiscriminately add /usr/include to work around bug:
# https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org/thread/Q5SWCUUMWQ4EMS7CU2CBOZHV3WZYOOTT/
for d in [hdf5_include_dir, boost_include_dir]:
if d != '/usr/include':
extra_compile_args += ['-isystem', d]
#extra_compile_args += ['-O0', '-g3', '-ggdb', '-fno-eliminate-unused-debug-types', '-v']
extra_link_args = []
#extra_link_args += ['-v']
extensions = [
Extension(
'fast5.fast5',
include_dirs=[
fast5_dir,
],
sources=[
os.path.join('fast5', 'source', 'fast5.cpp'),
],
depends=[
os.path.join(fast5_dir, fn)
for fn in ['fast5.hpp', 'hdf5_tools.hpp']
],
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args,
library_dirs=[
hdf5_lib_dir,
boost_lib_dir,
],
libraries=[
hdf5_lib,
boost_python_lib,
],
),
]
setup(
name='fast5',
description='Fast5 file interface.',
version=__version__,
#long_description=open('README').read(),
author='Matei David, Ontario Institute for Cancer Research',
author_email='matei.david at oicr.on.ca',
license='MIT',
url='https://github.com/mateidavid/fast5',
packages=['fast5'],
exclude_package_data={
'': ['*.c', '*.cpp', '*.h', '*.hpp'],
},
ext_modules=extensions,
scripts=[],
)
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