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setup.py
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setup.py
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#! /usr/bin/env python
# vim: set fileencoding=utf-8
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2013-2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of the Michigan State University nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: [email protected]
"""Setup for khmer project."""
import ez_setup
import os
import sys
from os import listdir as os_listdir
from os.path import join as path_join
import shutil
import subprocess
import tempfile
from setuptools import setup
from setuptools import Extension
from setuptools.command.build_ext import build_ext as _build_ext
from distutils.spawn import spawn
from distutils.sysconfig import get_config_vars
from distutils.dist import Distribution
from distutils.errors import DistutilsPlatformError
import versioneer
ez_setup.use_setuptools(version="3.4.1")
versioneer.VCS = 'git'
versioneer.versionfile_source = 'khmer/_version.py'
versioneer.versionfile_build = 'khmer/_version.py'
versioneer.tag_prefix = 'v' # tags are like v1.2.0
versioneer.parentdir_prefix = '.'
CMDCLASS = versioneer.get_cmdclass()
# strip out -Wstrict-prototypes; a hack suggested by
# http://stackoverflow.com/a/9740721
# proper fix coming in http://bugs.python.org/issue1222585
# numpy has a "nicer" fix:
# https://github.com/numpy/numpy/blob/master/numpy/distutils/ccompiler.py
OPT = get_config_vars('OPT')[0]
os.environ['OPT'] = " ".join(
flag for flag in OPT.split() if flag != '-Wstrict-prototypes'
)
# Checking for OpenMP support. Currently clang doesn't work with OpenMP,
# so it needs to be disabled for now.
# This function comes from the yt project:
# https://bitbucket.org/yt_analysis/yt/src/f7c75759e0395861b52d16921d8ce3ad6e36f89f/yt/utilities/lib/setup.py?at=yt
def check_for_openmp():
"""Check for OpenMP support."""
# Create a temporary directory
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
exit_code = 1
if os.name == 'nt':
return False
try:
os.chdir(tmpdir)
# Get compiler invocation
compiler = os.getenv('CC', 'cc')
# Attempt to compile a test script.
# See http://openmp.org/wp/openmp-compilers/
filename = r'test.c'
file = open(filename, 'wt', 1)
file.write(
"""
#include <omp.h>
#include <stdio.h>
int main() {
#pragma omp parallel
printf("Hello from thread %d, nthreads %d",
omp_get_thread_num(), omp_get_num_threads());
}
"""
)
with open(os.devnull, 'w') as fnull:
exit_code = subprocess.call([compiler, '-fopenmp', filename],
stdout=fnull, stderr=fnull)
# Clean up
file.close()
finally:
os.chdir(curdir)
shutil.rmtree(tmpdir)
return exit_code == 0
# We bundle tested versions of zlib & bzip2. To use the system zlib and bzip2
# change setup.cfg or use the `--libraries z,bz2` parameter which will make our
# custom build_ext command strip out the bundled versions.
ZLIBDIR = 'third-party/zlib'
BZIP2DIR = 'third-party/bzip2'
BUILD_DEPENDS = []
BUILD_DEPENDS.extend(path_join("lib", bn + ".hh") for bn in [
"khmer", "kmer_hash", "hashtable", "counting", "hashbits", "labelhash",
"hllcounter", "khmer_exception", "read_aligner", "subset", "read_parsers",
"traversal"])
SOURCES = ["khmer/_khmer.cc"]
SOURCES.extend(path_join("lib", bn + ".cc") for bn in [
"read_parsers", "kmer_hash", "hashtable",
"hashbits", "labelhash", "counting", "subset", "read_aligner",
"hllcounter", "traversal"])
SOURCES.extend(path_join("third-party", "smhasher", bn + ".cc") for bn in [
"MurmurHash3"])
# Don't forget to update lib/Makefile with these flags!
EXTRA_COMPILE_ARGS = ['-O3', '-std=c++11', '-pedantic']
EXTRA_LINK_ARGS = []
if sys.platform == 'darwin':
# force 64bit only builds
EXTRA_COMPILE_ARGS.extend(['-arch', 'x86_64', '-mmacosx-version-min=10.7',
'-stdlib=libc++'])
if check_for_openmp():
EXTRA_COMPILE_ARGS.extend(['-fopenmp'])
EXTRA_LINK_ARGS.extend(['-fopenmp'])
EXTENSION_MOD_DICT = \
{
"sources": SOURCES,
"extra_compile_args": EXTRA_COMPILE_ARGS,
"extra_link_args": EXTRA_LINK_ARGS,
"depends": BUILD_DEPENDS,
"language": "c++",
"define_macros": [("VERSION", versioneer.get_version()), ],
}
EXTENSION_MOD = Extension("khmer._khmer", # pylint: disable=W0142
** EXTENSION_MOD_DICT)
SCRIPTS = []
SCRIPTS.extend([path_join("scripts", script)
for script in os_listdir("scripts")
if script.endswith(".py")])
CLASSIFIERS = [
"Environment :: Console",
"Environment :: MacOS X",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: BSD License",
"Natural Language :: English",
"Operating System :: POSIX :: Linux",
"Operating System :: MacOS :: MacOS X",
"Programming Language :: C++",
"Programming Language :: Python :: 2.7",
"Programming Language :: Python :: 3.3",
"Programming Language :: Python :: 3.4",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
if "-rc" in versioneer.get_version():
CLASSIFIERS.append("Development Status :: 4 - Beta")
else:
CLASSIFIERS.append("Development Status :: 5 - Production/Stable")
SETUP_METADATA = \
{
"name": "khmer",
"version": versioneer.get_version(),
"description": 'khmer k-mer counting library',
"long_description": open("README.rst").read(),
"author": "Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, "
"Elmar Bucher, Adam Caldwell, Reed Cartwright, "
"Amanda Charbonneau, Bede Constantinides, Greg Edvenson, "
"Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, "
"Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, "
"Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, "
"Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, "
"Luiz Irber, Rhys Kidd, David Lin, Justin Lippi, "
"Tamer Mansour, Pamela McA'Nulty, Eric McDonald, "
"Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, "
"Kaben Nanlohy, Alexander Johan Nederbragt, "
"Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, "
"Charles Pepe-Ranney, Zachary N Russ, Erich Schwarz, "
"Camille Scott, Josiah Seaman, Scott Sievert, "
"Jared Simpson, Connor T. Skennerton, James Spencer, "
"Ramakrishnan Srinivasan, Daniel Standage, "
"James A. Stapleton, Joe Stein, Susan R Steinman, "
"Benjamin Taylor, Will Trimble, Heather L. Wiencko, "
"Michael Wright, Brian Wyss, Qingpeng Zhang, en zyme, "
"C. Titus Brown",
"author_email": '[email protected]',
# "maintainer": 'Michael R. Crusoe', # this overrides the author field
# "maintainer_email": '[email protected]', # so don't include it
# http://docs.python.org/2/distutils/setupscript.html
# additional-meta-data note #3
"url": 'https://khmer.readthedocs.org/',
"packages": ['khmer', 'khmer.tests', 'oxli'],
"package_dir": {'khmer.tests': 'tests'},
"install_requires": ['screed >= 0.9', 'bz2file'],
"extras_require": {':python_version=="2.6"': ['argparse>=1.2.1'],
'docs': ['sphinx', 'sphinxcontrib-autoprogram'],
'tests': ['nose >= 1.0']},
"scripts": SCRIPTS,
# "entry_points": { # Not ready for distribution yet.
# 'console_scripts': [
# "oxli = oxli:main"
# ]
# },
"ext_modules": [EXTENSION_MOD, ],
# "platforms": '', # empty as is conveyed by the classifiers below
# "license": '', # empty as is conveyed by the classifier below
"include_package_data": True,
"zip_safe": False,
"classifiers": CLASSIFIERS
}
class KhmerBuildExt(_build_ext): # pylint: disable=R0904
"""Specialized Python extension builder for khmer project.
Only run the library setup when needed, not on every invocation.
Also strips out the bundled zlib and bzip2 libraries if
`--libraries z,bz2` is specified or the equivalent is in setup.cfg
"""
def run(self):
"""Run extension builder."""
if "%x" % sys.maxsize != '7fffffffffffffff':
raise DistutilsPlatformError("%s require 64-bit operating system" %
SETUP_METADATA["packages"])
if "z" not in self.libraries:
zcmd = ['bash', '-c', 'cd ' + ZLIBDIR + ' && ( test Makefile -nt'
' configure || bash ./configure --static ) && make -f '
'Makefile.pic PIC']
spawn(cmd=zcmd, dry_run=self.dry_run)
self.extensions[0].extra_objects.extend(
path_join("third-party", "zlib", bn + ".lo") for bn in [
"adler32", "compress", "crc32", "deflate", "gzclose",
"gzlib", "gzread", "gzwrite", "infback", "inffast",
"inflate", "inftrees", "trees", "uncompr", "zutil"])
if "bz2" not in self.libraries:
bz2cmd = ['bash', '-c', 'cd ' + BZIP2DIR + ' && make -f '
'Makefile-libbz2_so all']
spawn(cmd=bz2cmd, dry_run=self.dry_run)
self.extensions[0].extra_objects.extend(
path_join("third-party", "bzip2", bn + ".o") for bn in [
"blocksort", "huffman", "crctable", "randtable",
"compress", "decompress", "bzlib"])
_build_ext.run(self)
CMDCLASS.update({'build_ext': KhmerBuildExt})
_DISTUTILS_REINIT = Distribution.reinitialize_command
def reinitialize_command(self, command, reinit_subcommands):
"""Monkeypatch the original version from distutils.
It's supposed to match the behavior of Distribution.get_command_obj()
This fixes issues with 'pip install -e' and './setup.py nosetests' not
respecting the setup.cfg configuration directives for the build_ext
command.
"""
cmd_obj = _DISTUTILS_REINIT(self, command, reinit_subcommands)
options = self.command_options.get(command)
if options:
self._set_command_options( # pylint: disable=protected-access
cmd_obj, options)
return cmd_obj
Distribution.reinitialize_command = reinitialize_command
# pylint: disable=W0142
setup(cmdclass=CMDCLASS,
**SETUP_METADATA)