setup.py

from setuptools import setup, Extension, distutils, find_packages
from setuptools.command.build_ext import build_ext
import platform
import codecs
import sys
import os


def read(rel_path):
    here = os.path.abspath(os.path.dirname(__file__))
    with codecs.open(os.path.join(here, rel_path), "r") as fp:
        return fp.read()


def get_version(rel_path):
    for line in read(rel_path).splitlines():
        if line.startswith("__version__"):
            delim = '"' if '"' in line else "'"
            return line.split(delim)[1]
    else:
        raise RuntimeError("Unable to find version string.")


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 __str__(self):
        import pybind11

        return pybind11.get_include()


ext_modules = [
    Extension(
        "FPSim2.FPSim2lib",
        sources=sorted(
            ["FPSim2/src/sim.cpp", "FPSim2/src/utils.cpp", "FPSim2/src/wraps.cpp"]
        ),
        include_dirs=[
            "FPSim2/src/include",
            # Path to pybind11 headers
            get_pybind_include(),
        ],
        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", delete=False) as f:
        f.write("int main (int argc, char **argv) { return 0; }")
        fname = f.name
    try:
        compiler.compile([fname], extra_postargs=[flagname])
    except distutils.errors.CompileError:
        return False
    finally:
        try:
            os.remove(fname)
        except OSError:
            pass
    return True


def cpp_flag(compiler):
    """Return the -std=c++[11/14/17] compiler flag.
    The newer version is prefered over c++11 (when it is available).
    """
    flags = ["-std=c++17", "-std=c++14", "-std=c++11"]

    for flag in flags:
        if has_flag(compiler, flag):
            return flag

    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", "/arch:AVX"], "unix": ["-O3"]}
    machine = platform.machine().lower()
    if os.getenv("FPSIM2_MARCH_NATIVE") == "1":
        c_opts["unix"] += ["-march=native"]
    else:
        if machine.startswith("x86"):
            c_opts["unix"] += ["-msse4.2"]

    l_opts = {"msvc": [], "unix": []}

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

    def build_extensions(self):
        ct = self.compiler.compiler_type
        opts = self.c_opts.get(ct, [])
        link_opts = self.l_opts.get(ct, [])
        if ct == "unix":
            opts.append(cpp_flag(self.compiler))
            if has_flag(self.compiler, "-fvisibility=hidden"):
                opts.append("-fvisibility=hidden")

        for ext in self.extensions:
            ext.define_macros = [
                ("VERSION_INFO", '"{}"'.format(self.distribution.get_version()))
            ]
            ext.extra_compile_args = opts
            ext.extra_link_args = link_opts
        build_ext.build_extensions(self)


setup(
    name="FPSim2",
    version=get_version("FPSim2/__init__.py"),
    author="Eloy Felix",
    author_email="eloyfelix@gmail.com",
    url="https://github.com/chembl/FPSim2",
    license="MIT",
    packages=find_packages(),
    description="Simple package for fast molecular similarity searching",
    long_description=open("README.md", encoding="utf-8").read(),
    long_description_content_type="text/markdown",
    ext_modules=ext_modules,
    install_requires=[
        "rdkit>=2022.3.3",
        "tables>=3.9.1",
        "numpy >=1.14",
        "sqlalchemy>=1.4.47",
        "scipy",
        "tqdm",
    ],
    cmdclass={"build_ext": BuildExt},
    python_requires=">=3.9",
    zip_safe=False,
    classifiers=[
        "Development Status :: 4 - Beta",
        "License :: OSI Approved :: MIT License",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
        "Programming Language :: Python :: 3.11",
        "Programming Language :: Python :: 3.12",
        "Topic :: Scientific/Engineering :: Chemistry",
    ],
)