setup.py

#
# Copyright (C) 2015-2017 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/>.
#
from __future__ import division
from __future__ import print_function

from setuptools import setup, Extension

import subprocess
import platform
import os
import os.path
from warnings import warn


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

# NOTE: sadly these warnings won't work to warn users installing with pip
# https://github.com/pypa/pip/issues/2933
HAVE_NUMPY = False
try:
    import numpy as np
    version = tuple(map(int, np.__version__.split(".")))
    if version < (1, 7, 0):
        warn("numpy version is too old: version 1.7 or newer needed")
    else:
        HAVE_NUMPY = True
except ImportError:
    warn("numpy not available. Some features will not work.")


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 = []
        if HAVE_NUMPY:
            self.include_dirs = [np.get_include()]
        try:
            self._check_hdf5_version()
        except OSError as e:
            warn("Error occured checking HDF5 version: {}".format(e))
        # On Unix systems with the correct tools installed we can detect the
        # paths for include and library files.
        try:
            self._configure_hdf5()
        except OSError as e:
            warn("Error occured getting HDF5 path config: {}".format(e))
        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 _check_hdf5_version(self):
        output = self._run_command(["h5ls", "-V"]).split()
        version_str = output[2]
        version = list(map(int, version_str.split(".")[:2]))
        if version < [1, 8]:
            # TODO is there a better exception to raise here?
            raise ValueError(
                "hdf5 version {} found; we need 1.8.0 or greater".format(
                    version_str))

    def _configure_hdf5(self):
        output = self._run_command(["h5cc", "-show"]).split()
        for token in output:
            if token.startswith("-I"):
                self.include_dirs.append(token[2:])
            elif token.startswith("-L"):
                self.library_dirs.append(token[2:])

    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:])


# Now, setup the extension module. We have to do some quirky workarounds
# here so that we can get the current version number from setuptools_scm
# and also get this version provided as a compile time parameter to the
# extension module.
class DefineMacros(object):
    def __init__(self):
        self._msprime_version = None

    def __getitem__(self, index):
        if self._msprime_version is None:
            import setuptools_scm
            version = setuptools_scm.get_version()
            if IS_WINDOWS:
                self._msprime_version = '\\"{}\\"'.format(version)
            else:
                self._msprime_version = '"{}"'.format(version)

        defines = [
            # We define this macro to ensure we're using the v18 versions of
            # the HDF5 API and not earlier deprecated versions.
            ("H5_NO_DEPRECATED_SYMBOLS", None),
            # Define the library version
            ("MSP_LIBRARY_VERSION_STR", '{}'.format(self._msprime_version)),
        ]
        if IS_WINDOWS:
            defines += [
                # These two are required for GSL to compile and link against the
                # conda-forge version.
                ("GSL_DLL", None), ("WIN32", None),
                # This is needed for HDF5 to link properly.
                ("H5_BUILT_AS_DYNAMIC_LIB", None)]
        if HAVE_NUMPY:
            defines += [("HAVE_NUMPY", None)]
        return defines[index]


configurator = PathConfigurator()
source_files = [
    "msprime.c", "fenwick.c", "avl.c", "tree_sequence.c",
    "object_heap.c", "newick.c", "hapgen.c", "recomb_map.c", "mutgen.c",
    "vargen.c", "vcf.c", "ld.c", "tables.c", "util.c"]
libdir = "lib"
_msprime_module = Extension(
    '_msprime',
    sources=["_msprimemodule.c"] + [os.path.join(libdir, f) for f in source_files],
    # Enable asserts by default.
    undef_macros=["NDEBUG"],
    extra_compile_args=["-std=c99"],
    define_macros=DefineMacros(),
    libraries=["gsl", "gslcblas", "hdf5"],
    include_dirs=[libdir] + configurator.include_dirs,
    library_dirs=configurator.library_dirs,
)

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="http://pypi.python.org/pypi/msprime",
    entry_points={
        'console_scripts': [
            'mspms=msprime.cli:mspms_main',
            'msp=msprime.cli:msp_main',
        ]
    },
    install_requires=["svgwrite", "six"],
    ext_modules=[_msprime_module],
    keywords=["Coalescent simulation", "ms"],
    license="GNU GPLv3+",
    platforms=["POSIX", "Windows", "MacOS X"],
    classifiers=[
        "Programming Language :: C",
        "Programming Language :: Python",
        "Programming Language :: Python :: 2",
        "Programming Language :: Python :: 2.7",
        "Programming Language :: Python :: 3",
        "Programming Language :: Python :: 3.3",
        "Programming Language :: Python :: 3.4",
        "Programming Language :: Python :: 3.5",
        "Programming Language :: Python :: 3.6",
        "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=['setuptools_scm'],
    use_scm_version={"write_to": "msprime/_version.py"},
)