setup.py

#! /usr/bin/env python3

import platform
import subprocess
import sys

if sys.version_info < (3, 6):
    print('Python must be >= 3.6.0')
    raise OSError

try:
    from setuptools import setup
except ImportError as e:
    print('Please install python setuptools, '
          'https://packaging.python.org/tutorials/installing-packages/#use-pip-for-installing ')
    raise e

from setuptools.command.develop import develop
from setuptools.command.build_py import build_py

with open("README.md", "r") as fh:
    long_description = fh.read()

"""
External dependencies compiled for linux using quay.io/pypa/manylinux2010_x86_64 image:
/opt/python/cpXX-cpXX/bin/python setup.py bdist_wheel
"""


class BuildError(Exception):
    """Build error"""
    pass


def compile_dependency(compilation_command, cwd):
    comp = subprocess.Popen(compilation_command, cwd=cwd)
    comp.wait()
    if comp.returncode:
        raise BuildError


def get_platform_cmd():
    system = platform.system()
    cpu = 'x86_64'
    if system == 'Darwin':
        cpu = 'x86_64' if 'x86' in platform.platform() else 'arm64'
        return [f'--host={cpu}-apple-darwin']
    return [f'--host={cpu}-linux-gnu']


def make_external_dependencies():
    print('building bsb wgsim')
    compile_dependency(['make'], 'bsbolt/External/WGSIM')
    print('building bsb htslib')
    compile_dependency(['autoheader'], 'bsbolt/External/HTSLIB')
    compile_dependency(['autoreconf', '-i'], 'bsbolt/External/HTSLIB')
    compile_dependency(['./configure', '--disable-bz2', '--disable-lzma'] + get_platform_cmd(),
                       'bsbolt/External/HTSLIB')
    compile_dependency(['make'], 'bsbolt/External/HTSLIB')
    print('building bsb bwa')
    compile_dependency(['make'], 'bsbolt/External/BWA')


try:
    from wheel.bdist_wheel import bdist_wheel as _bdist_wheel


    class bdist_wheel(_bdist_wheel):
        def finalize_options(self):
            _bdist_wheel.finalize_options(self)
            self.root_is_pure = False
except ImportError:
    bdist_wheel = None


class DevelopCmd(develop):

    def run(self):
        make_external_dependencies()
        super().run()


class BuildCmd(build_py):

    def run(self):
        make_external_dependencies()
        self.data_files = [('bsbolt', 'bsbolt', 'build/lib/bsbolt', []),
                           ('bsbolt.Align', 'bsbolt/Align', 'build/lib/bsbolt/Align', []),
                           ('bsbolt.CallMethylation', 'bsbolt/CallMethylation', 'build/lib/bsbolt/CallMethylation', []),
                           ('bsbolt.External', 'bsbolt/External', 'build/lib/bsbolt/External',
                            ['WGSIM/wgsim', 'BWA/bwa', 'HTSLIB/stream_bam']),
                           ('bsbolt.Impute', 'bsbolt/Impute', 'build/lib/bsbolt/Impute', []),
                           ('bsbolt.Impute.Imputation', 'bsbolt/Impute/Imputation',
                            'build/lib/bsbolt/Impute/Imputation', []),
                           ('bsbolt.Impute.Impute_Utils', 'bsbolt/Impute/Impute_Utils',
                            'build/lib/bsbolt/Impute/Impute_Utils', []), (
                               'bsbolt.Impute.Validation', 'bsbolt/Impute/Validation',
                               'build/lib/bsbolt/Impute/Validation',
                               []),
                           ('bsbolt.Index', 'bsbolt/Index', 'build/lib/bsbolt/Index', []),
                           ('bsbolt.Matrix', 'bsbolt/Matrix', 'build/lib/bsbolt/Matrix', []),
                           ('bsbolt.Simulate', 'bsbolt/Simulate', 'build/lib/bsbolt/Simulate', []),
                           ('bsbolt.Utils', 'bsbolt/Utils', 'build/lib/bsbolt/Utils', []),
                           ('bsbolt.Variant', 'bsbolt/Variant', 'build/lib/bsbolt/Variant', [])]
        super().run()


setup(name='bsbolt',
      version='1.6.0',
      description='Bisulfite Sequencing Processing Platform',
      long_description=long_description,
      long_description_content_type="text/markdown",
      url='https://github.com/NuttyLogic/BSBolt',
      project_urls={'Documentation': 'https://bsbolt.readthedocs.io/en/latest/'},
      author='Colin P. Farrell',
      author_email='colinpfarrell@gmail.com',
      license='MIT',
      packages=['bsbolt',
                'bsbolt.Align',
                'bsbolt.CallMethylation',
                'bsbolt.Impute',
                'bsbolt.Impute.Imputation',
                'bsbolt.Impute.Impute_Utils',
                'bsbolt.Impute.Validation',
                'bsbolt.Index',
                'bsbolt.Matrix',
                'bsbolt.Simulate',
                'bsbolt.Utils',
                'bsbolt.Variant'],
      classifiers=['Programming Language :: Python :: 3.6',
                   'Programming Language :: Python :: 3.7',
                   'Programming Language :: Python :: 3.8'],
      platforms=["Linux", "Mac OS-X", "Unix"],
      requires=['pysam', 'numpy', 'tqdm'],
      install_requires=['pysam>=0.15.3', 'numpy>=1.16.3', 'tqdm>=4.31.1', 'setuptools>=46.0.0'],
      entry_points={'console_scripts': ['bsbolt = bsbolt.__main__:launch_bsb',
                                        'BSBolt = bsbolt.__main__:launch_bsb']},
      python_requires='>=3.6',
      test_suite='tests',
      include_package_data=True,
      cmdclass={'develop': DevelopCmd,
                'build_py': BuildCmd,
                'bdist_wheel': bdist_wheel},
      zip_safe=False
      )