setup.py

import os
from setuptools import setup, Extension
from distutils.sysconfig import customize_compiler
import Cython.Build
from Cython.Build import cythonize


def CppExtension(name, sources):
    return Extension(
        name,
        sources=sources,
        language="c++",
        extra_compile_args=["-std=c++11", "-Werror=return-type", "-Werror=narrowing"],
        include_dirs=["src/"],
        undef_macros=["NDEBUG"],
    )


extensions = [
    CppExtension(
        "whatshap.core",
        sources=[
            "whatshap/core.pyx",
            "src/pedigree.cpp",
            "src/pedigreedptable.cpp",
            "src/pedigreecolumncostcomputer.cpp",
            "src/columnindexingiterator.cpp",
            "src/columnindexingscheme.cpp",
            "src/entry.cpp",
            "src/graycodes.cpp",
            "src/read.cpp",
            "src/readset.cpp",
            "src/columniterator.cpp",
            "src/indexset.cpp",
            "src/genotype.cpp",
            "src/binomial.cpp",
            "src/multinomial.cpp",
            "src/pedigreepartitions.cpp",
            "src/phredgenotypelikelihoods.cpp",
            "src/genotyper.cpp",
            "src/genotypedistribution.cpp",
            "src/genotypedptable.cpp",
            "src/genotypecolumncostcomputer.cpp",
            "src/backwardcolumniterator.cpp",
            "src/transitionprobabilitycomputer.cpp",
            "src/hapchat/basictypes.cpp",
            "src/hapchat/balancedcombinations.cpp",
            "src/hapchat/binomialcoefficient.cpp",
            "src/hapchat/hapchatcore.cpp",
            "src/hapchat/hapchatcolumniterator.cpp",
        ],
    ),
    CppExtension(
        "whatshap.polyphase.solver",
        sources=[
            "whatshap/polyphase/solver.pyx",
            "src/polyphase/allelematrix.cpp",
            "src/polyphase/clustereditingsolution.cpp",
            "src/polyphase/clustereditingsolver.cpp",
            "src/polyphase/edgeheap.cpp",
            "src/polyphase/inducedcostheuristic.cpp",
            "src/polyphase/progenygenotypelikelihoods.cpp",
            "src/polyphase/staticsparsegraph.cpp",
            "src/polyphase/switchflipcalculator.cpp",
            "src/polyphase/trianglesparsematrix.cpp",
            "src/polyphase/readscoring.cpp",
            "src/polyphase/haplothreader.cpp",
            "src/polyphase/tupleconverter.cpp",
        ],
    ),
    CppExtension("whatshap.readselect", sources=["whatshap/readselect.pyx"]),
    CppExtension("whatshap.priorityqueue", sources=["whatshap/priorityqueue.pyx"]),
    CppExtension("whatshap.align", sources=["whatshap/align.pyx"]),
    CppExtension("whatshap._variants", sources=["whatshap/_variants.pyx"]),
]


class BuildExt(Cython.Build.build_ext):
    def build_extensions(self):
        # Remove the warning about “-Wstrict-prototypes” not being valid for C++,
        # see http://stackoverflow.com/a/36293331/715090
        customize_compiler(self.compiler)
        if self.compiler.compiler_so[0].endswith("clang"):
            # Clang needs this option in order to find the unordered_set header
            print("detected clang, using option -stdlib=libc++")
            self.compiler.compiler_so.append("-stdlib=libc++")
        try:
            self.compiler.compiler_so.remove("-Wstrict-prototypes")
        except (AttributeError, ValueError):
            pass
        super().build_extensions()


# Avoid compilation if we are being installed within Read The Docs
if os.environ.get("READTHEDOCS") == "True":
    cmdclass = {}
    ext_modules = []
    install_requires = []
else:
    cmdclass = {"build_ext": BuildExt}
    ext_modules = extensions
    install_requires = [
        "pysam>=0.18.0",
        "pyfaidx>=0.5.5.2",
        "networkx",
        "biopython>=1.73",  # pyfaidx needs this for reading bgzipped FASTA files
        "scipy",
        "xopen>=1.2.0",
        "pulp>=2",
    ]

setup(
    use_scm_version={"write_to": "whatshap/_version.py"},
    cmdclass=cmdclass,
    ext_modules=cythonize(ext_modules),
    install_requires=install_requires,
)