Python 2/3 compatibility in single code base, plus python 3 testing on travis.

wrappers/python/tests/TestNumpyCompatibility.py

 import unittest
-import numpy as np
-
 from simtk.openmm import app
 import simtk.openmm as mm
 from simtk import unit
+try:
+    import numpy as np
+    NUMPY_IMPORT_FAILED = False
+except ImportError:
+    NUMPY_IMPORT_FAILED = True
+
 
+@unittest.skipIf(NUMPY_IMPORT_FAILED, 'Numpy is not installed')
 class TestNumpyCompatibility(unittest.TestCase):
 
     def setUp(self):
@@ -80,6 +85,8 @@ class TestNumpyCompatibility(unittest.TestCase):
         self.assertEqual(size, 10)
         np.testing.assert_array_almost_equal(energy, np.asarray(energy_out))
 
+
+@unittest.skipIf(NUMPY_IMPORT_FAILED, 'Numpy is not installed')
 class TestNumpyUnits(unittest.TestCase):
 
     def setUp(self):

wrappers/python/tests/TestPdbFile.py

+import sys
 import unittest
 from simtk.openmm.app import *
 from simtk.openmm import *
 from simtk.unit import *
 import simtk.openmm.app.element as elem
-import cStringIO
+if sys.version_info >= (3, 0):
+    from io import StringIO
+else:
+    from cStringIO import StringIO
+
 
 class TestPdbFile(unittest.TestCase):
     """Test the PDB file parser"""
@@ -43,9 +48,9 @@ class TestPdbFile(unittest.TestCase):
     def test_WriteFile(self):
         """Write a file, read it back, and make sure it matches the original."""
         pdb1 = PDBFile('systems/triclinic.pdb')
-        output = cStringIO.StringIO()
+        output = StringIO()
         PDBFile.writeFile(pdb1.topology, pdb1.positions, output)
-        input = cStringIO.StringIO(output.getvalue())
+        input = StringIO(output.getvalue())
         pdb2 = PDBFile(input)
         output.close();
         input.close();

wrappers/python/tests/TestPdbxFile.py

@@ -70,6 +70,7 @@ class TestPdbxFile(unittest.TestCase):
         # There should only be 10 frames (0 through 9)
         self.assertRaises(IndexError, lambda: pdb.getPositions(frame=10))
         self.assertIs(pdb.topology.getPeriodicBoxVectors(), None)
+        del sim
         os.unlink('test.cif')
 
     def assertAlmostEqualVec(self, vec1, vec2, *args, **kwargs):
@@ -111,6 +112,7 @@ class TestPdbxFile(unittest.TestCase):
         self.assertAlmostEqualVec(parm.topology.getPeriodicBoxVectors()[2],
                                   pdb.topology.getPeriodicBoxVectors()[2],
                                   places=5)
+        del sim
         os.unlink('test.cif')
 
 if __name__ == '__main__':