setup.py

from codecs import open
from os import path
import os
import re
import sys
import io
import platform
import subprocess

from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext
from distutils.version import LooseVersion

def read(*names, **kwargs):
    with io.open(
        os.path.join(os.path.dirname(__file__), *names),
        encoding=kwargs.get("encoding", "utf8")
    ) as fp:
        return fp.read()

def find_version(*file_paths):
    version_file = read(*file_paths)
    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
                              version_file, re.M)
    if version_match:
        return version_match.group(1)
    raise RuntimeError("Unable to find version string.")

class CMakeExtension(Extension):
    def __init__(self, name, sourcedir=''):
        Extension.__init__(self, name, sources=[])
        self.sourcedir = os.path.abspath(sourcedir)

class CMakeBuild(build_ext):
    def run(self):
        try:
            out = subprocess.check_output(['cmake', '--version'])
        except OSError:
            raise RuntimeError("CMake must be installed to build the following extensions: " +
                               ", ".join(e.name for e in self.extensions))

        if platform.system() == "Windows":
            cmake_version = LooseVersion(re.search(r'version\s*([\d.]+)', out.decode()).group(1))
            if cmake_version < '3.1.0':
                raise RuntimeError("CMake >= 3.1.0 is required on Windows")

        for ext in self.extensions:
            self.build_extension(ext)

    def build_extension(self, ext):
        extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.name)))
        cmake_args = ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
                      '-DPYTHON_EXECUTABLE=' + sys.executable,
                      '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON']

        cfg = 'Debug' if self.debug else 'Release'
        build_args = ['--config', cfg]

        if platform.system() == "Windows":
            cmake_args += ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}'.format(cfg.upper(), extdir)]
            if sys.maxsize > 2**32:
                cmake_args += ['-A', 'x64']
            build_args += ['--', '/m']
        else:
            cmake_args += ['-DCMAKE_BUILD_TYPE=' + cfg]
            build_args += ['--', '-j1']

        env = os.environ.copy()
        env['CXXFLAGS'] = '{} -DVERSION_INFO=\\"{}\\"'.format(env.get('CXXFLAGS', ''),
                                                              self.distribution.get_version())
        if not os.path.exists(self.build_temp):
            os.makedirs(self.build_temp)
        subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
        subprocess.check_call(['cmake', '--build', '.'] + build_args, cwd=self.build_temp)

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

with open(path.join(here, 'README.md'), encoding='utf-8') as f:
    long_description = f.read()

setup(
    name='ggCaller',
    version=find_version('ggCaller/__init__.py'),
    packages=['ggCaller',
              'models',
              'panaroo_runner'],
    package_dir={'ggCaller': 'ggCaller',
                 'models': 'models',
                 'panaroo_runner': 'panaroo_runner'},
    url='https://github.com/samhorsfield96/ggCaller',
    license='MIT License',
    author='Sam Horsfield',
    author_email='s.horsfield19@imperial.ac.uk',
    description='A gene caller for Bifrost graphs; traverses Bifrost graphs constructed from bacterial genomes to identify putative protein coding sequences, known as open reading frames (ORFs).',
    entry_points={'console_scripts': ['ggcaller = ggCaller.__main__:main']},
    ext_modules=[CMakeExtension('ggCaller_cpp')],
    cmdclass=dict(build_ext=CMakeBuild),
    zip_safe=False
)