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setup.py
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setup.py
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#!/usr/bin/env python
# This file is part of thermotools.
#
# Copyright 2015, 2016 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# thermotools is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program 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 Lesser General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
r"""
thermotools is a lowlevel implementation toolbox for the analyis of multi-ensemble calculations.
"""
from setuptools import setup, Extension
import versioneer
def extensions():
from numpy import get_include
from Cython.Build import cythonize
extra_compile_args = ["-O3", "-std=c99"]
ext_bar = Extension(
"thermotools.bar",
sources=["ext/bar/bar.pyx", "ext/bar/_bar.c", "ext/util/_util.c"],
include_dirs=[get_include()],
extra_compile_args=extra_compile_args)
ext_wham = Extension(
"thermotools.wham",
sources=["ext/wham/wham.pyx", "ext/wham/_wham.c", "ext/util/_util.c"],
include_dirs=[get_include()],
extra_compile_args=extra_compile_args)
ext_mbar = Extension(
"thermotools.mbar",
sources=["ext/mbar/mbar.pyx", "ext/mbar/_mbar.c", "ext/util/_util.c"],
include_dirs=[get_include()],
extra_compile_args=extra_compile_args)
ext_tram = Extension(
"thermotools.tram",
sources=["ext/tram/tram.pyx", "ext/tram/_tram.c", "ext/util/_util.c"],
include_dirs=[get_include()],
extra_compile_args=extra_compile_args)
ext_dtram = Extension(
"thermotools.dtram",
sources=["ext/dtram/dtram.pyx", "ext/dtram/_dtram.c", "ext/util/_util.c"],
include_dirs=[get_include()],
extra_compile_args=extra_compile_args)
ext_trammbar = Extension(
"thermotools.trammbar",
sources=["ext/trammbar/trammbar.pyx", "ext/tram/_tram.c", "ext/util/_util.c"],
include_dirs=[get_include()],
extra_compile_args=extra_compile_args + ["-DTRAMMBAR"])
ext_mbar_direct = Extension(
"thermotools.mbar_direct",
sources=["ext/mbar_direct/mbar_direct.pyx", "ext/mbar_direct/_mbar_direct.c", "ext/util/_util.c"],
include_dirs=[get_include()],
extra_compile_args=extra_compile_args)
ext_tram_direct = Extension(
"thermotools.tram_direct",
sources=["ext/tram_direct/tram_direct.pyx", "ext/tram_direct/_tram_direct.c", "ext/util/_util.c"],
include_dirs=[get_include()],
extra_compile_args=extra_compile_args)
ext_trammbar_direct = Extension(
"thermotools.trammbar_direct",
sources=["ext/trammbar_direct/trammbar_direct.pyx", "ext/tram_direct/_tram_direct.c", "ext/util/_util.c"],
include_dirs=[get_include()],
extra_compile_args=extra_compile_args + ["-DTRAMMBAR"])
ext_util = Extension(
"thermotools.util",
sources=["ext/util/util.pyx", "ext/util/_util.c"],
include_dirs=[get_include()],
extra_compile_args=extra_compile_args)
exts = [
ext_bar,
ext_wham,
ext_mbar,
ext_tram,
ext_dtram,
ext_trammbar,
ext_mbar_direct,
ext_tram_direct,
ext_trammbar_direct,
ext_util]
return cythonize(exts)
class lazy_cythonize(list):
"""evaluates extension list lazyly.
pattern taken from http://tinyurl.com/qb8478q"""
def __init__(self, callback):
self._list, self.callback = None, callback
def c_list(self):
if self._list is None: self._list = self.callback()
return self._list
def __iter__(self):
for e in self.c_list(): yield e
def __getitem__(self, ii): return self.c_list()[ii]
def __len__(self): return len(self.c_list())
long_description = 'The thermotools package is a lowlevel implementation toolbox for the analyis \
of multi-ensemble calculations. It contains estimators for the state-continuous transition-based \
reweighting analysis method (TRAM) and its state-discrete variant (dTRAM), Bennet acceptance ratio \
(BAR) and its multi-state variant (MBAR), and the weighted histogram analysis method (WHAM). \
While you can use thermotools on its own, we recommend to use it in combination with PyEMMA.'
setup(
cmdclass=versioneer.get_cmdclass(),
ext_modules=lazy_cythonize(extensions),
name='thermotools',
version=versioneer.get_version(),
description='lowlevel implementation toolbox for the analyis of multi-ensemble calculations',
long_description=long_description,
classifiers=[
'Development Status :: 4 - Beta',
'Environment :: Console',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)',
'Natural Language :: English',
'Operating System :: MacOS :: MacOS X',
'Operating System :: POSIX',
'Operating System :: Microsoft :: Windows',
'Programming Language :: C',
'Programming Language :: Cython',
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Topic :: Scientific/Engineering :: Chemistry',
'Topic :: Scientific/Engineering :: Mathematics',
'Topic :: Scientific/Engineering :: Physics'],
keywords=[
'MEMM',
'multi ensemble',
'free energy',
'Markov state model',
'BAR',
'WHAM',
'MBAR',
'TRAM',
'dTRAM'],
url='https://github.com/markovmodel/thermotools',
maintainer='Christoph Wehmeyer',
maintainer_email='christoph.wehmeyer@fu-berlin.de',
license='LGPLv3+',
setup_requires=[
'numpy>=1.7',
'cython>=0.20',
'setuptools>=0.6'],
tests_require=[
'numpy>=1.7',
'scipy>=0.11',
'msmtools>=1.1.3',
'nose'],
install_requires=[
'numpy>=1.7',
'scipy>=0.11',
'msmtools>=1.1.3'],
packages=['thermotools'],
test_suite='nose.collector',
scripts=[]
)