setup.py

from builtins import object
import sys
import setuptools

from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext

import versioneer


class get_pybind_include(object):
    """Helper class to determine the pybind11 include path

    The purpose of this class is to postpone importing pybind11
    until it is actually installed, so that the ``get_include()``
    method can be invoked. """

    def __init__(self, user=False):
        self.user = user

    def __str__(self):
        import pybind11
        return pybind11.get_include(self.user)


ext_modules = [
    Extension(
        'strainge.kmerizer',
        ['src/kmerizer/main.cpp', 'src/kmerizer/kmerizer.cpp'],
        include_dirs=[
            # Path to pybind11 headers
            get_pybind_include(),
            get_pybind_include(user=True)
        ],
        language='c++'
    ),
]


# As of Python 3.6, CCompiler has a `has_flag` method.
# cf http://bugs.python.org/issue26689
def has_flag(compiler, flagname):
    """Return a boolean indicating whether a flag name is supported on
    the specified compiler.
    """
    import tempfile
    with tempfile.NamedTemporaryFile('w', suffix='.cpp') as f:
        f.write('int main (int argc, char **argv) { return 0; }')
        try:
            compiler.compile([f.name], extra_postargs=[flagname])
        except setuptools.distutils.errors.CompileError:
            return False
    return True


def cpp_flag(compiler):
    """Return the -std=c++[11/14] compiler flag.

    The c++14 is prefered over c++11 (when it is available).
    """
    if has_flag(compiler, '-std=c++14'):
        return '-std=c++14'
    elif has_flag(compiler, '-std=c++11'):
        return '-std=c++11'
    else:
        raise RuntimeError('Unsupported compiler -- at least C++11 support '
                           'is needed!')


class BuildExt(build_ext):
    """A custom build extension for adding compiler-specific options."""
    c_opts = {
        'msvc': ['/EHsc'],
        'unix': [],
    }

    if sys.platform == 'darwin':
        c_opts['unix'] += ['-stdlib=libc++', '-mmacosx-version-min=10.9']

    def build_extensions(self):
        ct = self.compiler.compiler_type
        opts = self.c_opts.get(ct, [])
        if ct == 'unix':
            opts.append('-DVERSION_INFO="%s"' %
                        self.distribution.get_version())
            opts.append(cpp_flag(self.compiler))
            if has_flag(self.compiler, '-fvisibility=hidden'):
                opts.append('-fvisibility=hidden')
        elif ct == 'msvc':
            opts.append('/DVERSION_INFO=\\"%s\\"' %
                        self.distribution.get_version())
        for ext in self.extensions:
            ext.extra_compile_args = opts
            ext.extra_link_args = opts
        build_ext.build_extensions(self)


with open("README.md") as f:
    long_desc = f.read()

setup(
    name='strainge',
    author='Bruce Walker, Tim Straub, Lucas van Dijk',
    author_email='bruce@broadinstitute.org, tstraub@broadinstitute.org, '
                 'lvandijk@broadinstitute.org',
    description='Strain Genome Explorer: a tool suite for tracking and characterizing low-abundance strains.',
    long_description=long_desc,
    long_description_content_type="text/markdown",
    utl="https://strainge.readthedocs.io",

    classifiers=[
        "Programming Language :: Python :: 3",
        "License :: OSI Approved :: BSD License",
        "Operating System :: OS Independent",
        "Environment :: Console",
        "Topic :: Scientific/Engineering :: Bio-Informatics"
    ],

    packages=find_packages('src'),
    package_dir={'': 'src'},
    include_package_data=True,

    scripts=[
        'bin/kmerseq',
        'bin/kmercoverage',
        'bin/kmersimilarity',
        'bin/kmerspectrum',
        'bin/kmertree',
        'bin/treepath',
        'bin/pankmer',
        'bin/refseq-download',
        'bin/refseq-extract'
    ],

    # Versioneer setup
    version=versioneer.get_version(),
    cmdclass=versioneer.get_cmdclass({"build_ext": BuildExt}),

    # C++ extensions
    ext_modules=ext_modules,
    zip_safe=False,

    # Dependencies
    setup_requires=[
        'pybind11>=2.2',
        'oldest-supported-numpy',
    ],
    install_requires=[
        'numpy',
        'scipy',
        'h5py',
        'intervaltree',
        'matplotlib',
        'scikit-bio>=0.5.8',
        'scikit-learn>=0.24',
        'pysam',
    ],
    python_requires=">=3.8",

    # CLI endpoints
    entry_points={
        'console_scripts': [
            'strainge=strainge.cli.main:strainge_cli',
            'straingst=strainge.cli.main:straingst_cli',
            'straingr=strainge.cli.main:straingr_cli'
        ]
    }
)