#!/usr/bin/env python

from setuptools import setup, Extension, find_packages

# from distutils.core import setup, Extension # old way, replaced by setuptools

from Cython.Distutils import build_ext

import numpy

import sys

# Add include and library directories from conda envs for swig.

std_include = [sys.prefix + '/include', sys.prefix + '/Library/include']

# Obtain the numpy include directory. This logic works across numpy versions.

try:

numpy_include = numpy.get_include()

except AttributeError:

numpy_include = numpy.get_numpy_include()

cmdclass = {}

python_requires = '>=3.11'

install_requires = [

'numpy>=1.23,<2.4',

'scipy>=1.10',

'pandas>=2.0',

'h5py>=3.8',

'matplotlib>=3.7',

'ipyparallel>=8.0',

'tqdm>=4.60',

'six>=1.16',

'cooler>=0.8.11',

'pyBigWig>=0.3.22',

]

tests_require = [

'mock'

]

extras_require = {

'docs': [

'Sphinx>=1.1',

]

}

extensions = [

Extension(

"alabtools.numutils",

["alabtools/numutils.pyx"],

extra_compile_args=["-std=gnu99"],

),

Extension("alabtools._cmtools", ["alabtools/cmtools/cmtools.i", "alabtools/cmtools/cmtools.cpp"],

swig_opts=['-c++'],

language="c++",

include_dirs=[numpy_include]+std_include,

)

]

clscripts = [

'bin/triplets-compact',

'bin/triplets-compute',

'bin/triplets-extract'

]

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

setup(

name='alabtools',

version='1.1.31',

author='Nan Hua, Francesco Musella',

author_email='[email protected]',

url='https://github.com/alberlab/alabtools',

description='Alber lab toolbox',

cmdclass=cmdclass,

# packages=['alabtools'], # old way, replaced by find_packages()

packages=find_packages(),

package_data={'alabtools': ['genomes/*', 'config/*']},

python_requires=python_requires,

install_requires=install_requires,

# tests_require=tests_require,

# extras_require=extras_require,

scripts=clscripts,

ext_modules=extensions,

include_dirs=[numpy_include]+std_include

)