The way that setuptools does it, it uses the pkg_resources.parse_version function. It should be PEP440 compliant.
Example:
#! /usr/bin/python
# -*- coding: utf-8 -*-
"""Example comparing two PEP440 formatted versions
"""
import pkg_resources
VERSION_A = pkg_resources.parse_version("1.0.1-beta.1")
VERSION_B = pkg_resources.parse_version("v2.67-rc")
VERSION_C = pkg_resources.parse_version("2.67rc")
VERSION_D = pkg_resources.parse_version("2.67rc1")
VERSION_E = pkg_resources.parse_version("1.0.0")
print(VERSION_A)
print(VERSION_B)
print(VERSION_C)
print(VERSION_D)
print(VERSION_A==VERSION_B) #FALSE
print(VERSION_B==VERSION_C) #TRUE
print(VERSION_C==VERSION_D) #FALSE
print(VERSION_A==VERSION_E) #FALSE