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setup.py
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setup.py
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#!/usr/bin/env python
# -*- coding: latin-1 -*-
#
# Copyright John Reid 2010, 2011, 2012, 2013
#
"""
setuptools setup script for STEME.
Adapted from http://git.tiker.net/pyublas.git/tree.
"""
import os
import sys
# is it a python debug build?
_python_debug_build = hasattr(sys, "gettotalrefcount")
_build = _python_debug_build and 'debug' or 'release'
def read(*fnames):
"""
Utility function to read the README file.
Used for the long_description. It's nice, because now 1) we have a top level
README file and 2) it's easier to type in the README file than to put a raw
string in below ...
"""
return open(os.path.join(os.path.dirname(__file__), *fnames)).read()
def get_config_schema():
from aksetup_helper import ConfigSchema, Option, \
IncludeDir, Libraries, BoostLibraries, \
Switch, StringListOption, make_boost_base_options
import sys
if 'linux' in sys.platform:
default_libs = ['rt']
return ConfigSchema(
make_boost_base_options() + [
BoostLibraries("python"),
Option("SEQAN_DIR", default=''),
StringListOption(
"CXXFLAGS", [], help="Any extra C++ compiler options to include"),
StringListOption(
"LDFLAGS", [], help="Any extra linker options to include"),
]
)
def main():
from aksetup_helper import hack_distutils, get_config, setup, NumpyExtension
from setuptools import find_packages
import sys
hack_distutils()
conf = get_config(get_config_schema())
INCLUDE_DIRS = [
'c++',
os.path.join('c++', 'include'),
os.path.join('c++', 'hmm', 'myrrh'),
os.path.join('c++', 'hmm'),
os.path.join('c++', 'indexing_suite_v2'),
os.path.join('c++', 'FAST'),
os.path.join(conf['SEQAN_DIR'], 'include'),
] + conf['BOOST_INC_DIR']
LIBRARY_DIRS = conf['BOOST_LIB_DIR']
LIBRARIES = conf['BOOST_PYTHON_LIBNAME'] + ['fftw3']
CXXFLAGS = conf['CXXFLAGS']
LDFLAGS = conf['LDFLAGS']
EXTRA_DEFINES = [
("SEQAN_ENABLE_TESTING" , "0"),
("SEQAN_ENABLE_DEBUG" , "0"),
("BOOST_DISABLE_ASSERTS" , None),
("MYRRH_DISABLE_ASSERTS" , None),
("PVAL_LOOKUP" , None),
("NDEBUG" , None),
]
# need to link against librt otherwise get an undefined aio_cancel
# error or somesuch.
if 'linux' in sys.platform:
LIBRARIES.append('rt')
# want to add these options to all GCC builds
if 'linux' in sys.platform or 'darwin' in sys.platform:
CXXFLAGS += [
"-Wno-unused",
"-Wno-deprecated",
"-Wno-long-long",
"-Wno-variadic-macros",
"-Wno-sequence-point",
"-Wno-uninitialized",
"-finline-functions",
"-ftemplate-depth-128",
]
try:
from distutils.command.build_py import build_py_2to3 as build_py
except ImportError:
# 2.x
from distutils.command.build_py import build_py
#
# C++ extensions
#
lib_srcs = [
'c++/hmm/myrrh/src/python/multi_array_to_numpy.cpp',
'c++/FAST/HS.cpp',
'c++/FAST/motif_evaluator.cpp',
'c++/FAST/theta_fns.cpp',
'c++/FAST/minimize.cpp',
'c++/FAST/convolution.cpp',
'c++/FAST/fft.cpp',
'c++/FAST/utils.cpp',
'c++/FAST/llr_score.cpp',
'c++/pvalues/parse.cpp',
'c++/pvalues/bejerano.cpp',
'c++/pvalues/fast.cpp',
'c++/pvalues/shifted_hirji.cpp',
'c++/pvalues/pval.cpp',
'c++/pvalues/pvalue_test_defs.cpp',
'c++/python/steme.cpp',
]
module_stempy_srcs = [
'c++/python/module_stempy.cpp',
'c++/python/python_bs.cpp',
'c++/python/python_llr_pvalues.cpp',
'c++/python/python_utility.cpp',
]
module_index_srcs = [
'c++/python/module_index.cpp',
'c++/python/python_descender.cpp',
'c++/python/python_bg.cpp',
'c++/python/python_data.cpp',
'c++/python/python_em.cpp',
'c++/python/python_find_best_w_mers.cpp',
'c++/python/python_find_instances.cpp',
'c++/python/python_markov.cpp',
'c++/python/python_model.cpp',
'c++/python/python_seqan.cpp',
'c++/python/python_significance.cpp',
'c++/python/python_start_finder.cpp',
]
cStempy = NumpyExtension(
'stempy._%s_build._stempy' % _build,
lib_srcs + module_stempy_srcs,
include_dirs = INCLUDE_DIRS,
library_dirs = LIBRARY_DIRS,
libraries = LIBRARIES,
define_macros = EXTRA_DEFINES,
extra_compile_args = CXXFLAGS,
extra_link_args = LDFLAGS,
)
cIndex = NumpyExtension(
'stempy._%s_build._index' % _build,
module_index_srcs,
include_dirs = INCLUDE_DIRS,
library_dirs = LIBRARY_DIRS,
libraries = LIBRARIES,
define_macros = EXTRA_DEFINES + [('STEME_INDEX_MODULE_NAME', '_index')],
extra_compile_args = CXXFLAGS,
extra_link_args = LDFLAGS,
)
cIndexGenome = NumpyExtension(
'stempy._%s_build._index_genome' % _build,
module_index_srcs,
include_dirs = INCLUDE_DIRS,
library_dirs = LIBRARY_DIRS,
libraries = LIBRARIES,
define_macros = EXTRA_DEFINES + [('STEME_INDEX_MODULE_NAME', '_index_genome'), ('STEME_INDEX_MODULE_TYPE', 1)],
extra_compile_args = CXXFLAGS,
extra_link_args = LDFLAGS,
)
setup(
name = 'STEME',
zip_safe = False,
version = read('python', 'stempy', 'VERSION').strip().split('-')[0],
description = 'STEME: an accurate efficient motif finder for large data sets.',
long_description = read('python', 'stempy', 'README'),
author ='John Reid',
author_email ='[email protected]',
license = 'BSD',
url ='http://sysbio.mrc-bsu.cam.ac.uk/johns/STEME/',
classifiers = [
'Development Status :: 5 - Production/Stable',
'Environment :: Console',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: BSD License',
'Operating System :: MacOS :: MacOS X',
'Operating System :: POSIX',
'Operating System :: Microsoft :: Windows',
'Programming Language :: Python',
'Programming Language :: C++',
'Topic :: Scientific/Engineering',
'Topic :: Scientific/Engineering :: Mathematics',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Utilities',
],
packages = find_packages(where='python'),
package_dir = { '' : 'python' },
package_data = {
'stempy': [
'README',
'LICENSE',
'VERSION',
'static/style.css',
'templates/job.html',
'templates/layout.html',
'templates/motif.html',
'templates/motifs.html',
'templates/options.html',
'templates/scan-stats.html',
'templates/spacing.html',
'templates/wide-layout.html',
],
'stemewebapp': [
'STEME.wsgi',
'INSTALL',
'VERSION',
'static/style.css',
'static/logo.png',
'static/logo.svg',
'templates/_formhelpers.html',
'templates/home.html',
'templates/layout.html',
'templates/listjobs.html',
'templates/newjob.html',
],
},
include_package_data = True,
install_requires = ['cookbook', 'numpy', 'matplotlib', 'weblogo'],
scripts = [
'python/scripts/steme',
'python/scripts/steme-em',
'python/scripts/steme-find-spacings',
'python/scripts/steme-motif-logos',
'python/scripts/steme-mutate-motifs',
'python/scripts/steme-pwm-scan',
'python/scripts/steme-scan-stats',
'python/scripts/steme-seqs-2-motif',
'python/scripts/steme-spacing-analysis',
'python/scripts/stemewebapp-create-db',
'python/scripts/stemewebapp-remove-job',
],
ext_modules = [cStempy, cIndex, cIndexGenome],
# 2to3 invocation
cmdclass = {'build_py': build_py},
)
if __name__ == '__main__':
main()