setup.py

"""
The pymbar package contains the pymbar suite of tools for the analysis of
simulated and experimental data with the multistate Bennett acceptance
ratio (MBAR) estimator.

"""
from distutils.core import setup
from setuptools import setup, Extension
import numpy
import os
import subprocess
import six

##########################
VERSION = "3.0.4"
ISRELEASED = False
__version__ = VERSION
##########################

################################################################################
# Writing version control information to the module
################################################################################

def git_version():
    # Return the git revision as a string
    # copied from numpy setup.py
    def _minimal_ext_cmd(cmd):
        # construct minimal environment
        env = {}
        for k in ['SYSTEMROOT', 'PATH']:
            v = os.environ.get(k)
            if v is not None:
                env[k] = v
        # LANGUAGE is used on win32
        env['LANGUAGE'] = 'C'
        env['LANG'] = 'C'
        env['LC_ALL'] = 'C'
        out = subprocess.Popen(
            cmd, stdout=subprocess.PIPE, env=env).communicate()[0]
        return out

    try:
        out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
        GIT_REVISION = out.strip().decode('ascii')
    except OSError:
        GIT_REVISION = 'Unknown'

    return GIT_REVISION


def write_version_py(filename='pymbar/version.py'):
    cnt = """
# This file is automatically generated by setup.py
short_version = '%(version)s'
version = '%(version)s'
full_version = '%(full_version)s'
git_revision = '%(git_revision)s'
release = %(isrelease)s

if not release:
    version = full_version
"""
    # Adding the git rev number needs to be done inside write_version_py(),
    # otherwise the import of numpy.version messes up the build under Python 3.
    FULLVERSION = VERSION
    if os.path.exists('.git'):
        GIT_REVISION = git_version()
    else:
        GIT_REVISION = 'Unknown'

    if not ISRELEASED:
        FULLVERSION += '.dev-' + GIT_REVISION[:7]

    a = open(filename, 'w')
    try:
        a.write(cnt % {'version': VERSION,
                       'full_version': FULLVERSION,
                       'git_revision': GIT_REVISION,
                       'isrelease': str(ISRELEASED)})
    finally:
        a.close()

################################################################################
# Installation
################################################################################

write_version_py()
CMBAR = Extension('_pymbar',
                  sources = ["pymbar/_pymbar.c"],
                  extra_compile_args=["-std=c99","-O2","-shared","-msse2","-msse3"],
                  include_dirs = [numpy.get_include(),numpy.get_include()+"/numpy/"]
                  )

def buildKeywordDictionary():
    from distutils.core import Extension
    setupKeywords = {}
    setupKeywords["name"]              = "pymbar"
    setupKeywords["version"]           = VERSION
    setupKeywords["author"]            = "Levi N. Naden and Michael R. Shirts and John D. Chodera"
    setupKeywords["author_email"]      = "levi.naden@choderalab.org, michael.shirts@virginia.edu, john.chodera@choderalab.org"
    setupKeywords["license"]           = "MIT"
    setupKeywords["url"]               = "http://github.com/choderalab/pymbar"
    setupKeywords["download_url"]      = "http://github.com/choderalab/pymbar"
    setupKeywords["packages"]          = ['pymbar', 'pymbar.testsystems', 'pymbar.tests']
    setupKeywords["package_dir"]       = {'pymbar' : 'pymbar', 'pymbar.tests' : 'pymbar/tests'}
    setupKeywords["zip_safe"]          = False
    #setupKeywords["py_modules"]        = ["pymbar", "timeseries", "testsystems", "confidenceintervals"]
    setupKeywords["data_files"]        = [('pymbar', ["pymbar/_pymbar.c"])]  # Ensures the _pymbar.c files are shipped regardless of Py Version
    setupKeywords["ext_modules"]       = [CMBAR] if six.PY2 else []
    # setupKeywords["test_suite"]        = "tests" # requires we migrate to setuptools
    setupKeywords["platforms"]         = ["Linux", "Mac OS X", "Windows"]
    setupKeywords["description"]       = "Python implementation of the multistate Bennett acceptance ratio (MBAR) method."
    setupKeywords["requires"]          = ["numpy", "scipy", "nose", "numexpr"]
    setupKeywords["long_description"]  = """
    Pymbar (https://simtk.org/home/pymbar) is a library
    that provides tools for optimally combining simulations
    from multiple thermodynamic states using maximum likelihood
    methods to compute free energies (normalization constants)
    and expectation values from all of the samples simultaneously.
    """
    outputString=""
    firstTab     = 40
    secondTab    = 60
    for key in sorted(setupKeywords.keys()):
         value         = setupKeywords[key]
         outputString += key.rjust(firstTab) + str( value ).rjust(secondTab) + "\n"

    print("%s" % outputString)

    #get_config_var(None)  # this line is necessary to fix the imports Mac OS X
    return setupKeywords


def main():
    setupKeywords = buildKeywordDictionary()
    setup(**setupKeywords)

if __name__ == '__main__':
    main()