Revision 6fc67e44625189ba4d2c82ec2a3be4d6131cf1a2 authored by Jerome Kelleher on 25 August 2018, 14:31:20 UTC, committed by GitHub on 25 August 2018, 14:31:20 UTC
CHANGELOG updates for version 0.6.1.
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
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 as _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'.
class build_ext(_build_ext):
def finalize_options(self):
super(build_ext, self).finalize_options()
# Prevent numpy from thinking it is still in its setup process:
__builtins__.__NUMPY_SETUP__ = False
import numpy
self.include_dirs.append(numpy.get_include())
# The above obscure magic doesn't seem to work on py2 and prevents the
# extension from building at all, so here's a nasty workaround:
libdir = "lib"
includes = [libdir]
try:
import numpy
includes.append(numpy.get_include())
except ImportError:
pass
kastore_dir = os.path.join("kastore", "c")
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", "uuid.c",
os.path.join(kastore_dir, "kastore.c")]
# 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 = [
# 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)]
return defines[index]
libraries = ["gsl", "gslcblas"]
if IS_WINDOWS:
# Needed for generating UUIDs
libraries.append("Advapi32")
_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"],
libraries=libraries,
define_macros=DefineMacros(),
include_dirs=includes + [
os.path.join(libdir, kastore_dir)] + 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',
]
},
include_package_data=True,
install_requires=["numpy>=1.7.0", "h5py", "svgwrite", "six", "jsonschema"],
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=['numpy', 'setuptools_scm'],
use_scm_version={"write_to": "msprime/_version.py"},
)
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