setup.py

#!/usr/bin/env python
#-*- coding: utf-8 -*-

import os
import sys
import subprocess
import re

from setuptools import setup
from setuptools.command.sdist import sdist as _sdist
from setuptools.command.install import install as _install

VERSION_PY = """
# This file is originally generated from Git information by running 'setup.py
# version'. Distribution tarballs contain a pre-generated copy of this file.

__version__ = '%s'
"""


def update_version_py():
    if not os.path.isdir(".git"):
        print "This does not appear to be a Git repository."
        return
    try:
        p = subprocess.Popen(["git", "describe",
                              "--tags", "--always"],
                             stdout=subprocess.PIPE)
    except EnvironmentError:
        print "unable to run git, leaving eden/_version.py alone"
        return
    stdout = p.communicate()[0]
    if p.returncode != 0:
        print "unable to run git, leaving eden/_version.py alone"
        return
    ver = stdout.strip()
    f = open("eden/_version.py", "w")
    f.write(VERSION_PY % ver)
    f.close()
    print "set eden/_version.py to '%s'" % ver


def get_version():
    try:
        f = open("eden/_version.py")
    except EnvironmentError:
        return None
    for line in f.readlines():
        mo = re.match("__version__ = '([^']+)'", line)
        if mo:
            ver = mo.group(1)
            return ver
    return None


class sdist(_sdist):
    def run(self):
        update_version_py()
        self.distribution.metadata.version = get_version()
        return _sdist.run(self)


class install(_install):
    def run(self):
        _install.run(self)

    def checkProgramIsInstalled(self, program, args, where_to_download,
                                affected_tools):
        try:
            _out = subprocess.Popen([program, args], stderr=subprocess.PIPE,
                                    stdout=subprocess.PIPE)
            return True
        except EnvironmentError:
            # handle file not found error.
            # the config file is installed in:
            msg = "\n**{0} not found. This " \
                  "program is needed for the following "\
                  "tools to work properly:\n"\
                  " {1}\n"\
                  "{0} can be downloaded from here:\n " \
                  " {2}\n".format(program, affected_tools,
                                  where_to_download)
            sys.stderr.write(msg)

        except Exception as e:
            sys.stderr.write("Error: {}".format(e))

setup(
    name='eden',
    version=get_version(),
    author='Fabrizio Costa',
    author_email='eden@googlegroups.com',
    packages=['eden',
                'eden.util', 
                'eden.converter',
                'eden.converter.graph',
                'eden.converter.molecule',
                'eden.converter.RNA',
                ],
    scripts=['bin/alignment', 'bin/annotate', 'bin/cluster_kmeans',
             'bin/cluster_DBSCAN', 'bin/convert', 'bin/dendrogram',
             'bin/fit', 'bin/features', 'bin/matrix',
             'bin/nearest_neighbor', 'bin/max_subarrays', 'bin/predict',
            ],
    include_package_data=True,
    package_data={},
    url='http://pypi.python.org/pypi/eden/',
    license='LICENSE',
    description='The Explicit Decomposition with Neighborhoods (EDeN) is a decompositional kernel based on the Neighborhood Subgraph Pairwise Distance Kernel (NSPDK) that can be used to induce an explicit feature representation for graphs. This in turn allows the adoption of machine learning algorithm to perform supervised and unsupervised learning task in a scalable way (e.g. fast stochastic gradient descent methods in classification).',
    long_description=open('README').read(),
    install_requires=[
        "numpy >= 1.8.0",
        "scipy >= 0.14.0",
        "scikit-learn",
        "dill",
        "networkx",
        "matplotlib",
        "biopython",
    ],
    cmdclass={'sdist': sdist, 'install': install}
)