import glob

from setuptools import setup

from distutils.extension import Extension

import numpy

import pysam

name = 'genda'

version = '0.1'

try:

from Cython.Distutils import build_ext

except ImportError:

use_cython = False

print("Cython not found")

else:

use_cython = True

cmdclass = {}

ext_modules = []

includes = pysam.get_include()

includes.append(numpy.get_include())

if use_cython:

print('**********using cython*********')

ext_modules += [

Extension("genda.transcripts.exon_utils",

["genda/transcripts/exon_utils.pyx"],

include_dirs=includes),

Extension("genda.pysam_callbacks.allele_counter",

["genda/pysam_callbacks/allele_counter.pyx"],

include_dirs=includes,

define_macros=pysam.get_defines()),

Extension("genda.stats.aei_count_samples",

["genda/stats/aei_count_samples.pyx"],

include_dirs=includes,

define_macros=pysam.get_defines()),

]

print(ext_modules)

cmdclass.update({'build_ext': build_ext})

else:

ext_modules += [

Extension("genda.transcripts.exon_utils",

["genda/transcripts/exon_utils.c"]),

Extension("genda.pysam_callbacks.allele_counter",

["genda/pysam_callbacks/allele_counter.c"]),

Extension("genda.pysam_callbacks.gene_counter",

["genda/stats/aei_count_samples.c"]),

]

metadata = {'name': name,

}

if __name__ == '__main__':

dist = setup(**metadata)

"""

Extension("genda.pysam_callbacks.gene_counter",

["genda/pysam_callbacks/gene_counter.pyx"],

include_dirs=pysam.get_include()),

"""