import os
import unittest
import subprocess
import utils
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
test_dir = utils.set_search_paths(TOPDIR)
utils.set_search_paths(TOPDIR)

from allosmod.util import check_output

class Tests(unittest.TestCase):
    def test_bad(self):
        """Test wrong arguments to get_rest"""
        for args in ([], [''] * 2):
            out = check_output(['allosmod', 'get_rest'] + args,
                               stderr=subprocess.STDOUT, retcode=2)
            out = check_output(['python', '-m',
                                'allosmod.get_rest'] + args,
                               stderr=subprocess.STDOUT, retcode=2)

    def test_simple(self):
        """Simple complete run of get_rest"""
        with open('get_rest.in', 'w') as fh:
            pass
        out = check_output(['allosmod', 'get_rest',
                           os.path.join(test_dir, 'input',
                                        'asite_pdb1.pdb')])
        os.unlink('get_rest.in')
        # PDB file contains no sugars, so no restraints should be output
        self.assertEqual(out, '')


if __name__ == '__main__':
    unittest.main()

import os
import unittest
import subprocess
import utils
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
test_dir = utils.set_search_paths(TOPDIR)
utils.set_search_paths(TOPDIR)

from allosmod.util import check_output

class Tests(unittest.TestCase):
    def test_bad(self):
        """Test wrong arguments to get_rest"""
        for args in ([], [''] * 2):
            out = check_output(['allosmod', 'get_rest'] + args,
                               stderr=subprocess.STDOUT, retcode=2)
            out = check_output(['python', '-m',
                                'allosmod.get_rest'] + args,
                               stderr=subprocess.STDOUT, retcode=2)

    def test_simple(self):
        """Simple complete run of get_rest"""
        with open('get_rest.in', 'w') as fh:
            pass
        out = check_output(['allosmod', 'get_rest',
                           os.path.join(test_dir, 'input',
                                        'asite_pdb1.pdb')],
                           universal_newlines=True)
        os.unlink('get_rest.in')
        # PDB file contains no sugars, so no restraints should be output
        self.assertEqual(out, '')


if __name__ == '__main__':
    unittest.main()

Make sure that output is text in Python 2 & 3.
Make sure that output is text in Python 2 & 3.

  import os
  import unittest
  import subprocess
  import utils
  TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
  test_dir = utils.set_search_paths(TOPDIR)
  utils.set_search_paths(TOPDIR)
  
  from allosmod.util import check_output
  
  class Tests(unittest.TestCase):
      def test_bad(self):
          """Test wrong arguments to get_rest"""
          for args in ([], [''] * 2):
              out = check_output(['allosmod', 'get_rest'] + args,
                                 stderr=subprocess.STDOUT, retcode=2)
              out = check_output(['python', '-m',
                                  'allosmod.get_rest'] + args,
                                 stderr=subprocess.STDOUT, retcode=2)
  
      def test_simple(self):
          """Simple complete run of get_rest"""
          with open('get_rest.in', 'w') as fh:
              pass
          out = check_output(['allosmod', 'get_rest',
                             os.path.join(test_dir, 'input',
-                                         'asite_pdb1.pdb')])
+                                         'asite_pdb1.pdb')],
+                            universal_newlines=True)
          os.unlink('get_rest.in')
          # PDB file contains no sugars, so no restraints should be output
          self.assertEqual(out, '')
  
  
  if __name__ == '__main__':
      unittest.main()
  
Make sure that output is text in Python 2 & 3.
## Code Before:
import os
import unittest
import subprocess
import utils
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
test_dir = utils.set_search_paths(TOPDIR)
utils.set_search_paths(TOPDIR)

from allosmod.util import check_output

class Tests(unittest.TestCase):
    def test_bad(self):
        """Test wrong arguments to get_rest"""
        for args in ([], [''] * 2):
            out = check_output(['allosmod', 'get_rest'] + args,
                               stderr=subprocess.STDOUT, retcode=2)
            out = check_output(['python', '-m',
                                'allosmod.get_rest'] + args,
                               stderr=subprocess.STDOUT, retcode=2)

    def test_simple(self):
        """Simple complete run of get_rest"""
        with open('get_rest.in', 'w') as fh:
            pass
        out = check_output(['allosmod', 'get_rest',
                           os.path.join(test_dir, 'input',
                                        'asite_pdb1.pdb')])
        os.unlink('get_rest.in')
        # PDB file contains no sugars, so no restraints should be output
        self.assertEqual(out, '')


if __name__ == '__main__':
    unittest.main()

## Instruction:
Make sure that output is text in Python 2 & 3.
## Code After:
import os
import unittest
import subprocess
import utils
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
test_dir = utils.set_search_paths(TOPDIR)
utils.set_search_paths(TOPDIR)

from allosmod.util import check_output

class Tests(unittest.TestCase):
    def test_bad(self):
        """Test wrong arguments to get_rest"""
        for args in ([], [''] * 2):
            out = check_output(['allosmod', 'get_rest'] + args,
                               stderr=subprocess.STDOUT, retcode=2)
            out = check_output(['python', '-m',
                                'allosmod.get_rest'] + args,
                               stderr=subprocess.STDOUT, retcode=2)

    def test_simple(self):
        """Simple complete run of get_rest"""
        with open('get_rest.in', 'w') as fh:
            pass
        out = check_output(['allosmod', 'get_rest',
                           os.path.join(test_dir, 'input',
                                        'asite_pdb1.pdb')],
                           universal_newlines=True)
        os.unlink('get_rest.in')
        # PDB file contains no sugars, so no restraints should be output
        self.assertEqual(out, '')


if __name__ == '__main__':
    unittest.main()
