setup.py

#! /usr/bin/env python
#
# Copyright 2019 Square Inc.

# Apache License
# Version 2.0, January 2004
# http://www.apache.org/licenses/

import os
import codecs
import re
import glob
from setuptools import setup, Extension, find_packages

# Checking if numpy is installed
try:
  import numpy
except:
  import subprocess
  print("numpy is not installed. So pysurvival will install it now.")
  subprocess.call("pip install numpy", shell=True)
  import numpy

# Package meta-data.
NAME = 'pysurvival'
DESCRIPTION = 'Open source package for Survival Analysis modeling'
URL = 'https://www.pysurvival.io'
EMAIL = 'stephane@squareup.com'
AUTHOR = 'steph-likes-git'
LICENSE = "Apache Software License (Apache 2.0)"

# Current Directory
try:
    CURRENT_DIR = os.path.dirname(os.path.realpath(__file__)) + '/'
except:
    CURRENT_DIR = os.path.dirname(os.path.realpath('__file__')) + '/'

# Utility functions
def read_long_description():
    with open(CURRENT_DIR + 'LONG_DESCRIPTION.txt', 'r') as f:
        return f.read()

def install_requires():
	with open(CURRENT_DIR + 'requirements.txt', 'r') as requirements_file:
	    requirements = requirements_file.readlines()
	return requirements

def read_version(*file_paths):
    with codecs.open(os.path.join(CURRENT_DIR, *file_paths), 'r') as fp:
        version_file = fp.read()

    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
                              version_file, re.M)
    if version_match:
        return version_match.group(1)
    raise RuntimeError("Unable to find version string.")

# Extensions Compilation arguments #
extra_compile_args = ['-std=c++11', "-O3"] 

# Extensions info #
ext_modules = [ 

  Extension( 
    name = "pysurvival.utils._functions",
    sources = ["pysurvival/cpp_extensions/_functions.cpp",
               "pysurvival/cpp_extensions/functions.cpp" ,
               ],
    extra_compile_args = extra_compile_args, 
    language="c++", 
  ),

  Extension( 
    name = "pysurvival.utils._metrics",
    sources = ["pysurvival/cpp_extensions/_metrics.cpp",
               "pysurvival/cpp_extensions/non_parametric.cpp",
               "pysurvival/cpp_extensions/metrics.cpp",
               "pysurvival/cpp_extensions/functions.cpp",
              ],
    extra_compile_args = extra_compile_args, 
    language="c++", 
    ),

  Extension( 
    name = "pysurvival.models._non_parametric",
    sources = ["pysurvival/cpp_extensions/_non_parametric.cpp",
               "pysurvival/cpp_extensions/non_parametric.cpp",
               "pysurvival/cpp_extensions/functions.cpp" 
               ],
    extra_compile_args = extra_compile_args, 
    language="c++", 
  ),

  Extension( 
    name = "pysurvival.models._survival_forest",
    sources = [ "pysurvival/cpp_extensions/_survival_forest.cpp",
                "pysurvival/cpp_extensions/survival_forest_data.cpp",
                "pysurvival/cpp_extensions/survival_forest_utility.cpp",
                "pysurvival/cpp_extensions/survival_forest_tree.cpp",
                "pysurvival/cpp_extensions/survival_forest.cpp", 
                ],
    extra_compile_args = extra_compile_args, 
    language="c++", 
  ),

  Extension( 
    name = "pysurvival.models._coxph",
    sources = [ "pysurvival/cpp_extensions/_coxph.cpp",
                "pysurvival/cpp_extensions/functions.cpp" 
              ],
    extra_compile_args = extra_compile_args, 
    language="c++", 
    include_dirs=[numpy.get_include()],
  ),

  Extension( 
    name = "pysurvival.models._svm",
    sources = [ "pysurvival/cpp_extensions/_svm.cpp", 
              ],
    extra_compile_args = extra_compile_args, 
    language="c++", 
    include_dirs=[numpy.get_include()],
  ),
  ]

# Setup 
setup(name=NAME,
      version=read_version("pysurvival", "__init__.py"),
      description=DESCRIPTION,
      long_description=read_long_description(),
      author=AUTHOR,
      author_email=EMAIL,
      url=URL,
      license=LICENSE,
      install_requires=install_requires(),
      include_package_data=True,
      package_data={ '': ['*.csv'], },
      extras_require={ 'tests': ['pytest', 'pytest-pep8', ] },
      classifiers=[
          'Intended Audience :: Developers',
          'Intended Audience :: Education',
          'Intended Audience :: Science/Research',
          'Operating System :: MacOS',
          'Operating System :: Unix',
          'Programming Language :: Python :: 2',
          'Programming Language :: Python :: 2.7',
          'Programming Language :: Python :: 3',
          'Programming Language :: Python :: 3.7',
          'Topic :: Scientific/Engineering',
		      'Topic :: Scientific/Engineering :: Mathematics',
          'Topic :: Scientific/Engineering :: Artificial Intelligence',
          'Topic :: Software Development',
          'Topic :: Software Development :: Libraries :: Python Modules'
      ],
      packages=find_packages(),
      ext_modules=ext_modules,
  )