setup.py

"""
setup.py: Used for building python wrappers for Simbios' OpenMM library.
"""
import ast
import re
import os
import sys
import platform
import numpy
from distutils.core import setup

MAJOR_VERSION_NUM='@OPENMM_MAJOR_VERSION@'
MINOR_VERSION_NUM='@OPENMM_MINOR_VERSION@'
BUILD_INFO='@OPENMM_BUILD_VERSION@'
IS_RELEASED = False

__author__ = "Peter Eastman"
__version__ = "%s.%s" % (MAJOR_VERSION_NUM, MINOR_VERSION_NUM)

def reportError(message):
    sys.stdout.write("ERROR: ")
    sys.stdout.write(message)
    sys.stdout.write("\nExiting\n")
    sys.exit(1)

def removeRecursive(dir):
    for file in os.listdir(dir):
        path = os.path.join(dir, file)
        if os.path.isdir(path):
            removeRecursive(path)
        else:
            os.remove(path)
    os.rmdir(dir)

def removePackage(mod, verbose):
        try:
            pathList = mod.__path__
        except AttributeError:
            return
        if len(pathList) > 1:
           raise Exception("more than one item in simtk.__path__")
        simtkInstallPath = pathList[0]
        if os.path.exists(simtkInstallPath):
            if verbose:
                sys.stdout.write('REMOVING "%s"\n' % simtkInstallPath)
            removeRecursive(simtkInstallPath)

def uninstall(verbose=True):
    save_path=sys.path[:]
    sys.path=[]
    for item in save_path:
        if item!='.' and item!=os.getcwd():
            sys.path.append(item)
    try:
        import simtk.openmm as openmm
        removePackage(openmm, verbose)
    except ImportError:
        pass

    try:
        import simtk.unit as unit
        removePackage(unit, verbose)
    except ImportError:
        pass
    sys.path=save_path


def writeVersionPy(filename="simtk/openmm/version.py", major_version_num=MAJOR_VERSION_NUM,
                     minor_version_num=MINOR_VERSION_NUM, build_info=BUILD_INFO):
    """Write a version.py file into the python source directory before installation.
    If a version.py file already exists, we assume that it contains only the git_revision
    information, since from within this python session in the python staging directory, we're
    not in the version controlled directory hierarchy.

    When cmake is copying files into the PYTHON_STAGING_DIRECTORY, it will write the
    git revision to version.py. We read that, and then overwrite it.
    """

    cnt = """
# THIS FILE IS GENERATED FROM OPENMM SETUP.PY
short_version = '%(version)s'
version = '%(version)s'
full_version = '%(full_version)s'
git_revision = '%(git_revision)s'
release = %(isrelease)s
openmm_library_path = r'%(path)s'

if not release:
    version = full_version
"""

    if os.path.exists(filename):
        # git_revision is written to the file by cmake
        with open(filename) as f:
            text = f.read()
            match = re.search(r"git_revision\s+=\s+(.*)", text, re.MULTILINE)
        try:
            git_revision = ast.literal_eval(match.group(1))
        except:
            # except anything, including no re match or
            # literal_eval failing
            git_revision = 'Unknown'
    else:
        git_revision = 'Unknown'

    version = full_version = '%s.%s.%s' % (major_version_num, minor_version_num, build_info)
    if not IS_RELEASED:
        full_version += '.dev-' + git_revision[:7]

    a = open(filename, 'w')
    try:
        a.write(cnt % {'version': version,
                       'full_version' : full_version,
                       'git_revision' : git_revision,
                       'isrelease': str(IS_RELEASED),
                       'path': os.getenv('OPENMM_LIB_PATH')})
    finally:
        a.close()


def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                           minor_version_num=MINOR_VERSION_NUM,
                           build_info=BUILD_INFO):
    from distutils.core import Extension
    setupKeywords = {}
    setupKeywords["name"]              = "OpenMM"
    setupKeywords["version"]           = "%s.%s.%s" % (major_version_num,
                                                       minor_version_num,
                                                       build_info)
    setupKeywords["author"]            = "Randall J. Radmer"
    setupKeywords["author_email"]      = "radmer@stanford.edu"
    setupKeywords["license"]           = \
    "Python Software Foundation License (BSD-like)"
    setupKeywords["url"]               = "https://simtk.org/home/openmm"
    setupKeywords["download_url"]      = "https://simtk.org/home/openmm"
    setupKeywords["packages"]          = ["simtk",
                                          "simtk.unit",
                                          "simtk.openmm",
                                          "simtk.openmm.app",
                                          "simtk.openmm.app.internal",
                                          "simtk.openmm.app.internal.charmm",
                                          "simtk.openmm.app.internal.pdbx",
                                          "simtk.openmm.app.internal.pdbx.reader",
                                          "simtk.openmm.app.internal.pdbx.writer"]
    setupKeywords["data_files"]        = []
    setupKeywords["package_data"]      = {"simtk" : [],
                                          "simtk.unit" : [],
                                          "simtk.openmm" : [],
                                          "simtk.openmm.app" : ['data/*.xml', 'data/*.pdb'],
                                          "simtk.openmm.app.internal" : []}
    setupKeywords["platforms"]         = ["Linux", "Mac OS X", "Windows"]
    setupKeywords["description"]       = \
    "Python wrapper for OpenMM (a C++ MD package)"
    setupKeywords["long_description"]  = \
    """OpenMM is a toolkit for molecular simulation. It can be used either as a
    stand-alone application for running simulations, or as a library you call
    from your own code. It provides a combination of extreme flexibility
    (through custom forces and integrators), openness, and high performance
    (especially on recent GPUs) that make it truly unique among simulation codes.
    """

    define_macros = [('MAJOR_VERSION', major_version_num),
                     ('MINOR_VERSION', minor_version_num)]

    libraries=['OpenMM',
               'OpenMMAmoeba',
               'OpenMMRPMD',
               'OpenMMDrude',
              ]
    if 'OPENMM_USE_DEBUG_LIBS' in os.environ:
        if platform.system() == "Windows":
            raise Exception("use of OpenMM debug libs not supported on Win OS")
        else:
            sys.stdout.write("WARNING: using debug libs:\n")
            for ii in range(len(libraries)):
                libraries[ii]="%s_d" % libraries[ii]
                sys.stdout.write("%s\n" % libraries[ii])

    openmm_include_path = os.getenv('OPENMM_INCLUDE_PATH')
    if not openmm_include_path:
        reportError("Set OPENMM_INCLUDE_PATH to point to the include directory for OpenMM")
    openmm_lib_path = os.getenv('OPENMM_LIB_PATH')
    if not openmm_lib_path:
        reportError("Set OPENMM_LIB_PATH to point to the lib directory for OpenMM")

    extra_compile_args=[]
    extra_link_args=[]
    if platform.system() == "Windows":
        define_macros.append( ('WIN32', None) )
        define_macros.append( ('_WINDOWS', None) )
        define_macros.append( (' _MSC_VER', None) )
        extra_compile_args.append('/EHsc')
    else:
        if platform.system() == 'Darwin':
            extra_compile_args += ['-stdlib=libc++', '-mmacosx-version-min=10.7']
            extra_link_args += ['-stdlib=libc++', '-mmacosx-version-min=10.7', '-Wl', '-rpath', openmm_lib_path]
            # Hard-code CC and CXX to clang, since gcc/g++ will *not* work with
            # Anaconda, despite the fact that distutils will try to use them.
            # System Python, homebrew, and MacPorts on Macs will always use
            # clang, so this hack should always work and fix issues with users
            # that have GCC installed from MacPorts or homebrew *and* Anaconda
            os.environ['CC'] = 'clang'
            os.environ['CXX'] = 'clang++'

    library_dirs=[openmm_lib_path]
    include_dirs=openmm_include_path.split(';')
    include_dirs.append(numpy.get_include())

    extensionArgs = {"name": "simtk.openmm._openmm",
                    "sources": ["src/swig_doxygen/OpenMMSwig.cxx"],
                    "include_dirs": include_dirs,
                    "define_macros": define_macros,
                    "library_dirs": library_dirs,
                    "libraries": libraries,
                    "extra_compile_args": extra_compile_args,
                    "extra_link_args": extra_link_args}
    if platform.system() != "Windows":
        extensionArgs["runtime_library_dirs"] = library_dirs
    setupKeywords["ext_modules"] = [Extension(**extensionArgs)]

    outputString = ''
    firstTab     = 40
    secondTab    = 60
    for key in sorted(iter(setupKeywords)):
         value         = setupKeywords[key]
         outputString += key.rjust(firstTab) + str( value ).rjust(secondTab) + "\n"

    sys.stdout.write("%s" % outputString)

    return setupKeywords


def main():
    if sys.version_info < (2, 7):
        reportError("OpenMM requires Python 2.7 or better.")
    if platform.system() == 'Darwin':
        macVersion = [int(x) for x in platform.mac_ver()[0].split('.')]
        if tuple(macVersion) < (10, 5):
            reportError("OpenMM requires Mac OS X Leopard (10.5) or better.")
    try:
        uninstall()
    except:
        pass
    setupKeywords=buildKeywordDictionary()
    writeVersionPy()
    setup(**setupKeywords)

if __name__ == '__main__':
    main()