setup.py

#
# Copyright (C) 2015-2019 University of Oxford
#
# This file is part of msprime.
#
# msprime is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# msprime is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with msprime.  If not, see <http://www.gnu.org/licenses/>.
#
import subprocess
import platform
import os
import os.path
from warnings import warn

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


CONDA_PREFIX = os.getenv("MSP_CONDA_PREFIX", None)
IS_WINDOWS = platform.system() == "Windows"


class PathConfigurator(object):
    """
    A class to attempt configuration of the compile search paths
    on various platforms.
    """
    def __init__(self):
        self.include_dirs = []
        self.library_dirs = []
        try:
            self._configure_gsl()
        except OSError as e:
            warn("Error occured getting GSL path config: {}".format(e))
        # If the conda prefix is defined, then we are compiling in a conda
        # context. All include and lib paths should come from within this prefix.
        if CONDA_PREFIX is not None:
            prefix = CONDA_PREFIX
            if IS_WINDOWS:
                prefix = os.path.join(prefix, "Library")
            self.library_dirs.append(os.path.join(prefix, "lib"))
            self.include_dirs.append(os.path.join(prefix, "include"))

    def _run_command(self, args):
        return subprocess.check_output(args, universal_newlines=True)

    def _configure_gsl(self):
        output = self._run_command(["gsl-config", "--cflags"]).split()
        if len(output) > 0:
            token = output[0]
            self.include_dirs.append(token[2:])
        output = self._run_command(["gsl-config", "--libs"]).split()
        for token in output:
            if token.startswith("-L"):
                self.library_dirs.append(token[2:])


# Obscure magic required to allow numpy be used as an 'setup_requires'.
# Based on https://stackoverflow.com/questions/19919905
class local_build_ext(build_ext):
    def finalize_options(self):
        build_ext.finalize_options(self)
        import builtins
        # Prevent numpy from thinking it is still in its setup process:
        builtins.__NUMPY_SETUP__ = False
        import numpy
        self.include_dirs.append(numpy.get_include())


libdir = "lib"
tskroot = os.path.join(libdir, "subprojects", "tskit")
tskdir = os.path.join(tskroot, "tskit")
kasdir = os.path.join(libdir, "subprojects", "kastore")
includes = [libdir, tskroot, tskdir, kasdir]

configurator = PathConfigurator()
msp_source_files = [
    "msprime.c", "fenwick.c", "avl.c", "util.c",
    "object_heap.c", "recomb_map.c", "mutgen.c",
    "likelihood.c", "interval_map.c"
]
tsk_source_files = ["core.c", "tables.c", "trees.c"]
kas_source_files = ["kastore.c"]

sources = ["_msprimemodule.c"] + [
    os.path.join(libdir, f) for f in msp_source_files] + [
    os.path.join(tskdir, f) for f in tsk_source_files] + [
    os.path.join(kasdir, f) for f in kas_source_files]

libraries = ["gsl", "gslcblas"]
defines = []
if IS_WINDOWS:
    # Needed for generating UUIDs
    libraries.append("Advapi32")
    defines += [
        # These two are required for GSL to compile and link against the
        # conda-forge version.
        ("GSL_DLL", None), ("WIN32", None)]

_msprime_module = Extension(
    '_msprime',
    sources=sources,
    # Enable asserts by default.
    undef_macros=["NDEBUG"],
    extra_compile_args=["-std=c99"],
    libraries=libraries,
    define_macros=defines,
    include_dirs=includes + configurator.include_dirs,
    library_dirs=configurator.library_dirs,
)

numpy_ver = "numpy>=1.7"

with open("README.rst") as f:
    long_description = f.read()

setup(
    name="msprime",
    description="A fast and accurate coalescent simulator.",
    long_description=long_description,
    packages=["msprime"],
    author="Jerome Kelleher",
    author_email="jerome.kelleher@well.ox.ac.uk",
    url="https://pypi.org/project/msprime/",
    entry_points={
        'console_scripts': [
            'mspms=msprime.cli:mspms_main',
            'msp=msprime.cli:msp_main',
        ]
    },
    include_package_data=True,
    install_requires=[numpy_ver, "tskit"],
    ext_modules=[_msprime_module],
    keywords=["Coalescent simulation", "ms"],
    license="GNU GPLv3+",
    platforms=["POSIX", "Windows", "MacOS X"],
    python_requires=">=3.4",
    classifiers=[
        "Programming Language :: C",
        "Programming Language :: Python",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.4",
        "Programming Language :: Python :: 3.5",
        "Programming Language :: Python :: 3.6",
        "Programming Language :: Python :: 3.7",
        "Programming Language :: Python :: 3 :: Only",
        "Development Status :: 4 - Beta",
        "Environment :: Other Environment",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
        "Operating System :: POSIX",
        "Operating System :: MacOS :: MacOS X",
        "Operating System :: Microsoft :: Windows",
        "Topic :: Scientific/Engineering",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
    ],
    setup_requires=[numpy_ver, 'setuptools_scm'],
    use_scm_version={"write_to": "msprime/_version.py"},
    cmdclass={"build_ext": local_build_ext},
)