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#!/usr/bin/env python
#
# Part of: https://github.com/mateidavid/fast5
#
# (c) 2017: Matei David, Ontario Institute for Cancer Research
# MIT License
#
import os
import sys
from setuptools import setup, Extension
use_cython = True #os.environ.get('USE_CYTHON', '') != ''
# 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('HDF5_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')
fast5_dir = os.environ.get('FAST5_DIR', '..')
fast5pack_src_dir = os.path.join(fast5_dir, 'src')
fast5_src_dir = os.path.join(fast5_dir, 'include')
fast5_version = open(os.path.join(fast5_dir, 'VERSION')).readline().strip()
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]:
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']
#if sys.platform == 'darwin':
# extra_compile_args.append('-mmacosx-version-min=10.7')
extensions = [
Extension(
'fast5',
language='c++',
sources=['fast5/fast5.' + ['cpp', 'pyx'][use_cython]],
include_dirs=[fast5_src_dir, fast5pack_src_dir],
library_dirs=[hdf5_lib_dir],
#runtime_library_dirs=[hdf5_lib_dir],
libraries=[hdf5_lib],
extra_compile_args=extra_compile_args,
extra_link_args=extra_link_args,
),
]
if use_cython:
from Cython.Build import cythonize
extensions = cythonize(extensions)
setup(
name='fast5',
description='Fast5 file interface.',
version=fast5_version,
author='Matei David, Ontario Institute for Cancer Research',
author_email='matei.david at oicr.on.ca',
license='MIT',
url='https://github.com/mateidavid/fast5',
ext_modules=extensions,
scripts=[
os.path.join('bin', 'f5ls'),
os.path.join('bin', 'f5pack'),
],
)
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