setup.py

# coding=utf-8

import os as os

from setuptools import setup, find_packages, Extension


def extract_package_info():
    """
    :return:
    """
    setup_path = os.path.dirname(os.path.abspath(__file__))
    pck_path = os.path.join(setup_path, 'src', 'scidlib', '__init__.py')
    assert os.path.isfile(pck_path), \
        'Could not detect SCIDDO-lib init under path {}'.format(os.path.dirname(pck_path))
    infos = dict()
    with open(pck_path, 'r') as init:
        for line in init:
            if line.startswith('__'):
                k, v = line.split('=')
                infos[k.strip()] = eval(v.strip())
    return infos


def read_requirements():
    """
    :return:
    """
    setup_path = os.path.dirname(os.path.abspath(__file__))
    req_path = os.path.join(setup_path, 'requirements.txt')
    req_pck = []
    with open(req_path, 'r') as req:
        for line in req:
            if line.strip():
                req_pck.append(line.strip())
    return req_pck


def locate_executable():
    """
    :return:
    """
    setup_path = os.path.dirname(os.path.abspath(__file__))
    script_path = os.path.join(setup_path, 'bin', 'sciddo.py')
    relpath_script = os.path.relpath(script_path)
    return relpath_script


def locate_karlin_source():
    """
    :return:
    """
    setup_path = os.path.dirname(os.path.abspath(__file__))
    script_path = os.path.join(setup_path, 'src', 'scidlib', 'karlinmodule.c')
    relpath_script = os.path.relpath(script_path)
    return relpath_script


def locate_numpy_include_dirs():
    """
    :return:
    """
    try:
        import numpy.distutils.misc_util as nputil
        inc_dirs = nputil.get_numpy_include_dirs()
    except ImportError:
        # current hack-around, probably breakpoint
        import site as site
        site_pck = site.getsitepackages()
        inc_dirs = []
        for p in site_pck:
            if os.path.isdir(p):
                inc_dirs.append(os.path.join(p, 'numpy', 'core', 'include'))
        inc_dirs = inc_dirs[0]
    return inc_dirs


karlin_module = Extension(name='karlin',
                          sources=[locate_karlin_source()],
                          extra_compile_args=["-Wno-deprecated"],
                          include_dirs=locate_numpy_include_dirs(),
                          optional=False)

pck_infos = extract_package_info()

setup(
    name="scidlib",
    version=pck_infos['__version__'],
    packages=find_packages('src'),
    package_dir={'': 'src'},
    scripts=[locate_executable()],
    install_requires=read_requirements(),
    # the pkgconfig requirement was added due to
    # difficulties installing the PyTables dependency;
    # according to the installation notes, recent versions
    # of PyTables should be capable of finding the appropriate
    # HDF include paths if pckconfig is available
    # applies to Debian/Ubuntu systems
    # this also causes trouble with Travis CI
    # CPPFLAGS=-I/usr/include/hdf5/serial
    # LDFLAGS=-L/usr/lib/x86_64-linux-gnu/hdf5/serial

    setup_requires=['numpy'],
    ext_modules=[karlin_module],

    author=pck_infos['__author__'],
    author_email=pck_infos['__email__'],
    description="Score-based identification of differential chromatin domains",
    license="GPLv3",
    url="https://github.com/ptrebert/sciddo"   # project home page, if any

    # could also include long_description, download_url, classifiers, etc.
)