setup.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import os
import platform

from setuptools import setup, Extension

def check_rna_lib_installed(**kwa):
  "Check Vienna RNA Packages"
  def check_libs(paths):
    for path in paths:
      exts = ('.so', '.la', '.a')
      libpaths = [path + '/libRNA' + ext for ext in exts]
      return any(libpaths)
    return False

  def check_includes(paths):
    for path in paths:
      foldpath = path + '/ViennaRNA/fold.h'
      if os.path.exists(foldpath):
        return True
    return False

  return check_includes(kwa['include_dirs']) and check_libs(kwa['library_dirs'])

def get_rna_lib_intallation_path():
  "Attempts to get the RNAlib Path"
  includes = [
    '/usr/include',
    '/usr/local/include',
    os.path.abspath('.build/include'),
  ]
  libs = [
    '/usr/lib',
    '/usr/local/lib',
    os.path.abspath('.build/lib'),
  ]

  if 'VIENNA_RNA_PATH' in os.environ:
    px = os.environ['VIENNA_RNA_PATH']
    includes.append(px + '/include')
    libs.append(px + '/lib')

  return {
    'include_dirs': includes[::-1],
    'library_dirs': libs[::-1]
  }

def check_sanity():
  """
  Check Sanity of the System. Since metaRNA core depends on C extension,
  only posix systems are supported at the moment.
  """

  if not os.name == 'posix':
    print("metaRNA is currently not tested on non-posix systems.")

  if sys.version_info[:2] not in [(2, 7), (3, 3), (3, 4), (3, 5), (3, 6)]:
    print("metaRNA is only supported on Python 2.7, 3.3, 3.4, 3.5, 3.6.")
    return False

  if not check_rna_lib_installed(**get_rna_lib_intallation_path()):
    print(
      "metaRNA requires Vienna RNA package. Please read the docs "
      "for installation instructions.\n"
      "If you have Vienna Package, then perhaps the installer is "
      "unable to find the location. The location may be set by "
      "setting the `VIENNA_RNA_PATH` environment variable."
    )
    return False
  return True

if not check_sanity():
  sys.exit(1)

def extension_args():
  args = get_rna_lib_intallation_path()
  args['depends'] = [
    'metarna/pymiranda/miranda.h',
  ]
  args['sources'] = [
    'metarna/pymiranda/pymiranda.c',
    'metarna/pymiranda/scan.c',
    'metarna/pymiranda/swat.c',
    'metarna/pymiranda/thermo.c',
    'metarna/pymiranda/utils.c',
    'metarna/pymiranda/output.c',
    'metarna/pymiranda/ExpString.c',
  ]
  args['libraries'] = [
    'RNA',
    'm'
  ]
  if not platform.system() == 'Darwin':
    args['extra_compile_args'] = ['-fopenmp']
    args['extra_link_args'] = ['-lgomp']
  return args

setup_args = {
  'name': 'metarna',
  'version': '4.0.5',
  'author': 'Prashant Sinha',
  'author_email': 'prashant@ducic.ac.in',
  'url': 'https://github.com/prashnts/metarna',
  'license': 'GPLv3',
  'description': 'Finds target sites for the miRNAs in genomic sequences.',
  'packages': ['metarna'],
  'ext_modules': [
    Extension('metarna.pymiranda', **extension_args()),
  ],
  'classifiers': [
    'Development Status :: 4 - Beta',
    'Intended Audience :: Developers',
    'Intended Audience :: Science/Research',
    'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
    'Programming Language :: Python',
    'Programming Language :: Python :: 2',
    'Programming Language :: Python :: 3',
    'Topic :: Scientific/Engineering :: Bio-Informatics',
  ]
}

setup(**setup_args)