setup.py

"""
setup.py: Install PDBClean
"""

import os
import sys
import re
import subprocess
from os.path import join as pjoin
from glob import glob

import setuptools
from distutils.extension import Extension
from distutils.core import setup

from Cython.Distutils import build_ext
import numpy

# ------------------------------------------------------------------------------
# HEADER
#

VERSION      = "0.0.1"
ISRELEASED   = False
DISABLE_CUDA = True
__author__   = "Levitt Lab, Stanford"
__version__  = VERSION

metadata = {
    'name': 'PDBClean',
    'version': VERSION,
    'author': __author__,
    'author_email': 'fpoitevi@stanford.edu',
    'license': 'MIT',
    'url': 'https://github.com/csblab/PDBClean',
    'download_url': 'https://github.com/csblab/PDBClean',
    'platforms': ['Linux', 'OSX'],
    'description': "PDB curation tools",
    'long_description': """PDBClean offers curation tools for structural ensemble deposited in the Protein Data Bank."""}

# ------------------------------------------------------------------------------
# HELPER FUNCTIONS -- path finding, git, python version, readthedocs
#

class bcolors:
    HEADER = '\033[95m'
    OKBLUE = '\033[94m'
    OKGREEN = '\033[92m'
    WARNING = '\033[93m'
    FAIL = '\033[91m'
    ENDC = '\033[0m'


def print_warning(string):
    print(bcolors.WARNING + string + bcolors.ENDC)


def find_in_path(name, path):
    "Find a file in a search path"
    #adapted fom http://code.activestate.com/recipes/52224-find-a-file-given-a-search-path/
    for dir in path.split(os.pathsep):
        binpath = pjoin(dir, name)
        if os.path.exists(binpath):
            return os.path.abspath(binpath)
    return None


def get_numpy_include():
    """
    Obtain the numpy include directory. This logic works across numpy versions.
    """
    try:
        numpy_include = numpy.get_include()
    except AttributeError:
        numpy_include = numpy.get_numpy_include()
    return numpy_include


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

# -----------------------------------------------------------------------------
# INSTALL

metadata['packages']     = ['PDBClean']
metadata['package_dir']  = {'PDBClean' :         'src'}
metadata['ext_modules']  = []
metadata['scripts']      = [s for s in glob('scripts/*') if not s.endswith('__.py')]
#metadata['data_files']   = [('reference', glob('./reference/*'))]
#metadata['cmdclass']     = {'build_ext': custom_build_ext}

# ------------------------------------------------------------------------------
#
# Finally, print a warning at the *end* of the build if something fails
#

def print_warnings():
    print("\n")

if __name__ == '__main__':
    setup(**metadata) # ** will unpack dictionary 'metadata' providing the values as arguments
    print_warnings()