setup.py

# ----------------------------------------------------------------------------
# Copyright (c) 2013--, BP development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import os
from setuptools import setup
from setuptools.extension import Extension
from setuptools.command.build_py import build_py
from setuptools.command.install import install
from setuptools.command.develop import develop
from setuptools.command.egg_info import egg_info
import versioneer
import subprocess

import numpy as np

classes = """
    Development Status :: 4 - Beta
    License :: OSI Approved :: BSD License
    Topic :: Scientific/Engineering
    Programming Language :: Python
    Programming Language :: Python :: 3.7
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Operating System :: Unix
    Operating System :: POSIX
    Operating System :: MacOS :: MacOS X
    Operating System :: Linux
"""
classifiers = [s.strip() for s in classes.split('\n') if s]


with open('README.md') as f:
    long_description = f.read()


curdir = os.path.abspath(__file__).rsplit('/', 1)[0]
bitarr = os.path.join(curdir, 'bp/BitArray')


class common:
    def build_bitarray(self):
        subprocess.run(['make', '-C', bitarr, 'libbitarr.a'])


class BitArrayBuild(build_py, common):
    def run(self):
        self.build_bitarray()
        build_py.run(self)


class BitArrayInstall(install, common):
    def run(self):
        self.build_bitarray()
        install.run(self)


class BitArrayDevelop(develop, common):
    def run(self):
        self.build_bitarray()
        develop.run(self)


class BitArrayEggInfo(egg_info, common):
    def run(self):
        self.build_bitarray()
        egg_info.run(self)


USE_CYTHON = os.environ.get('USE_CYTHON', True)
ext = '.pyx' if USE_CYTHON else '.c'
extensions = [Extension("bp._bp",
                        ["bp/_bp" + ext],
                        include_dirs=[bitarr],
                        library_dirs=[bitarr],
                        libraries=['bitarr']),
              Extension("bp._io",
                        ["bp/_io" + ext], ),
              Extension("bp._conv",
                        ["bp/_conv" + ext], ),
              Extension("bp._binary_tree",
                        ["bp/_binary_tree" + ext], ),
              Extension("bp._insert",
                        ["bp/_insert" + ext], ),
              Extension("bp.tests.test_bp_cy",
                        ["bp/tests/test_bp_cy" + ext],
                        include_dirs=['bp/BitArray/'],
                        library_dirs=['bp/BitArray/'],
                        libraries=['bitarr']),
              ]

extensions.extend([Extension("bp._ba",
                            ["bp/_ba" + ext],
                            include_dirs=['bp/BitArray/'],
                             library_dirs=['bp/BitArray/'],
                             libraries=['bitarr'])])


if USE_CYTHON:
    from Cython.Build import cythonize
    extensions = cythonize(extensions,
                           language_level=3)


setup(name='iow',
      version=versioneer.get_version(),
      description='Balanced parentheses',
      author='Daniel McDonald',
      author_email='damcdonald@ucsd.edu',
      maintainer='Daniel McDonald',
      maintainer_email='damcdonald@ucsd.edu',
      url='https://github.com/biocore/improved-octo-waddle',
      packages=['bp'],
      ext_modules=extensions,
      include_dirs=[np.get_include(), bitarr],
      setup_requires=['numpy >= 1.9.2'],
      package_data={'bp': ['BitArray/*', ]},
      install_requires=[
          'numpy >= 1.9.2',
          'nose >= 1.3.7',
          'cython >= 0.24.1, < 1.0.0',
          'pandas',
          'click',
          'scikit-bio >= 0.5.0'],
      long_description=long_description,
      long_description_content_type='text/markdown',
      cmdclass=versioneer.get_cmdclass({'build_py': BitArrayBuild,
                                        'install': BitArrayInstall,
                                        'develop': BitArrayDevelop,
                                        'egg_info': BitArrayEggInfo}),
      entry_points='''
          [console_scripts]
          bp=bp._cli:cli
      ''')