setup.py

#!/usr/bin/env python
# vim: set fileencoding=<utf-8> :

from setuptools import setup, find_packages
from codecs import open
from os import path
import os, sys
import re
import io
import platform
import subprocess

from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext
from setuptools.command.install import install
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 += ['--', '-j2']

        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='poppunk',
    version=find_version("PopPUNK/__init__.py"),
    description='PopPUNK (POPulation Partitioning Using Nucleotide Kmers)',
    long_description=long_description,
    long_description_content_type='text/markdown',
    url='https://github.com/johnlees/PopPUNK',
    author='John Lees, Nicholas Croucher, Marie Gronemeyer, Richard Fitzjohn',
    author_email='john@johnlees.me',
    license='Apache Software License',
    classifiers=[
        'Development Status :: 4 - Beta',
        'Intended Audience :: Science/Research',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'License :: OSI Approved :: Apache Software License',
        'Programming Language :: Python :: 3.8',
    ],
    python_requires='>=3.8.0',
    install_requires=['biopython',
                      'h5py',
                      'hdbscan',
                      'matplotlib',
                      # 'mandrake', #uncomment when on PyPI
                      'networkx',
                      'pandas',
                      'pp-sketchlib',
                      'requests',
                      'scikit-learn',
                      'tqdm',
                      'treeswift',
                      ],
    keywords='bacteria genomics population-genetics k-mer',
    packages=['PopPUNK'],
    entry_points={
        "console_scripts": [
            'poppunk = PopPUNK.__main__:main',
            'poppunk_assign = PopPUNK.assign:main',
            'poppunk_visualise = PopPUNK.visualise:main',
            'poppunk_mst = PopPUNK.sparse_mst:main',
            'poppunk_references = PopPUNK.reference_pick:main',
            'poppunk_mandrake = PopPUNK.mandrake:main',
            'poppunk_info = PopPUNK.info:main',
            'poppunk_lineages_from_strains = PopPUNK.lineages:main'
            ]
    },
    scripts=['scripts/poppunk_calculate_rand_indices.py',
             'scripts/poppunk_extract_components.py',
             'scripts/poppunk_calculate_silhouette.py',
             'scripts/poppunk_batch_mst.py',
             'scripts/poppunk_extract_distances.py',
             'scripts/poppunk_iterate.py',
             'scripts/poppunk_add_weights.py',
             'scripts/poppunk_easy_run.py',
             'scripts/poppunk_distribute_fit.py'],
    ext_modules=[CMakeExtension('poppunk_refine')],
    test_suite="test",
    cmdclass=dict(build_ext=CMakeBuild),
    zip_safe=False,
    include_package_data=True,
    package_data={'': ['PopPUNK/data/*.json.gz',
                       'PopPUNK/data/microreact_example.pkl']}
)