setup.py

"""
cellSNP - Analysis of expressed alleles in single cells
See: https://github.com/huangyh09/cellSNP
"""

# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path

from setuptools.extension import Extension
from Cython.Build import cythonize
#from numpy import get_include as np_get_include
from pysam import get_include as pysam_get_include
from sys import version_info as sys_version
from sysconfig import get_config_var as get_sysconfig_var

here = path.abspath(path.dirname(__file__))

# Set __version__ for the project.
exec(open("./cellSNP/version.py").read())

# Get the long description from the relevant file
with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
    long_description = f.read()
    
reqs = ['numpy>=1.9.0', 'pysam>=0.15.2', 'cython>=0.29.16'] #, 'h5py'

def get_py_suffix():
    """ Return the sysconfig suffix of the python extensions. e.g. .cpython-38-x86_64-linux-gnu.so """
    suffix = get_sysconfig_var('EXT_SUFFIX')
    return suffix if suffix else get_sysconfig_var('SO')

def get_ext_name(name):
    """ 
    @abstract    Return the full name, with sysconfig suffix, of python extension.
    @param name  Name of the extension. e.g. chtslib [STR]
    @return      The full name of the extension. e.g. chtslib.cpython-38-x86_64-linux-gnu [STR]
    """
    return path.splitext("%s%s" % (name, get_py_suffix()))[0]

# refer to the setup.py in pysam.
extra_compile_args = [
    "-Wno-unused",
    "-Wno-sign-compare",
]

# List cython extensions in order.
# pileup_utils and pileup_regions depend on cellsnp_utils.
ext_modules = [
    dict(name = "cellSNP.utils.cellsnp_utils",
        language = "c",
        sources = [path.join('cellSNP', 'utils', 'cellsnp_utils.pyx')],
        libraries = [get_ext_name("chtslib"), get_ext_name("calignedsegment")]),
    dict(name = "cellSNP.utils.base_utils",
        language = "c",
        sources = [path.join('cellSNP', 'utils', 'base_utils.pyx')],
        libraries = []),
    dict(name = "cellSNP.utils.pileup_utils",
        language = "c",
        sources = [path.join('cellSNP', 'utils', 'pileup_utils.pyx')],
        libraries = []),
    dict(name = "cellSNP.utils.pileup_regions",
        language = "c",
        sources = [path.join('cellSNP', 'utils', 'pileup_regions.pyx')],
        libraries = []),
    dict(name = "cellSNP.utils.vcf_utils",
        language = "c",
        sources = [path.join('cellSNP', 'utils', 'vcf_utils.pyx')],
        libraries = [])
]

_s2l = lambda x: x if type(x) == list else [x]
pysam_dir_list = _s2l(pysam_get_include())
pysam_root_dir = pysam_dir_list[0]   # Fixme, check if the root dir of pysam.
ext_module_common_options = dict(
    extra_compile_args = extra_compile_args,
    include_dirs = pysam_dir_list + 
                    [path.join(pysam_root_dir, "include", "htslib", "htslib")] + 
                    [path.abspath(x) for x in ["cellSNP", "."]],
    library_dirs = pysam_dir_list
)

for module in ext_modules:
    module.update(**ext_module_common_options)

setup(
    name='cellSNP',

    # Versions should comply with PEP440.  For a discussion on single-sourcing
    # the version across setup.py and the project code, see
    # https://packaging.python.org/en/latest/single_source_version.html
    version=__version__,

    description='cellSNP - Analysis of expressed alleles in single cells',
    long_description=long_description,

    # The project's main homepage.
    url='https://github.com/huangyh09/cellSNP',

    # Author details
    author='Yuanhua Huang',
    author_email='yuanhua@ebi.ac.uk',

    # Choose your license
    license='Apache-2.0',

    # What does your project relate to?
    keywords=['allelic expression', 'single-cell RNA-seq'],

    # You can just specify the packages manually here if your project is
    # simple. Or you can use find_packages().
    packages=find_packages(),

    entry_points={
          'console_scripts': [
              'cellSNP = cellSNP.cellSNP:main'
              ],
          }, 

    # List run-time dependencies here.  These will be installed by pip when
    # your project is installed. For an analysis of "install_requires" vs pip's
    # requirements files see:
    # https://packaging.python.org/en/latest/requirements.html
    
    install_requires=reqs,

    py_modules = ['cellSNP'],

    # Cython extensions
    ext_modules = cythonize([Extension(**opts) for opts in ext_modules], language_level = sys_version.major),

    # Setting 'use_2to3 = True' to provide a facility to invoke 2to3 on the code as a part of the build process.
    use_2to3 = True

    # buid the distribution: python setup.py sdist
    # upload to pypi: twine upload dist/...

)