Top level Python module is now "openmm" (#3000)

* Top level Python module is now "openmm"

* Updated module names in examples

* Updated module names in documentation

* Updated module in CI scripts

* Added deprecation warning

wrappers/python/tests/TestDesmondDMSFile.py

 import os
 import unittest
-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
-import simtk.openmm.app.element as elem
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+import openmm.app.element as elem
 
 class TestDesmondDMSFile(unittest.TestCase):
     def setUp(self):

wrappers/python/tests/TestElement.py

 import pickle
 import random
-from simtk.unit import dalton, is_quantity
-from simtk.openmm.app import element
+from openmm.unit import dalton, is_quantity
+from openmm.app import element
 import unittest
 
 class TestElement(unittest.TestCase):

wrappers/python/tests/TestForceField.py

 import unittest
 from validateConstraints import *
-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
-import simtk.openmm.app.element as elem
-import simtk.openmm.app.forcefield as forcefield
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+import openmm.app.element as elem
+import openmm.app.forcefield as forcefield
 import math
 import textwrap
 try:
@@ -404,7 +404,7 @@ class TestForceField(unittest.TestCase):
             from uuid import uuid4
             template_name = uuid4()
             # Create residue template.
-            from simtk.openmm.app.forcefield import _createResidueTemplate
+            from openmm.app.forcefield import _createResidueTemplate
             template = _createResidueTemplate(residue) # use helper function
             template.name = template_name # replace template name
             for (template_atom, residue_atom) in zip(template.atoms, residue.atoms()):

wrappers/python/tests/TestForceGroups.py

 import unittest
 import itertools
-import simtk.openmm as mm
+import openmm as mm
 
 
 class TestForceGroups(unittest.TestCase):

wrappers/python/tests/TestGenerators.py

 import unittest
 from validateConstraints import *
-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
-import simtk.openmm.app.element as elem
-import simtk.openmm.app.forcefield as forcefield
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+import openmm.app.element as elem
+import openmm.app.forcefield as forcefield
 import math
 try:
     from cStringIO import StringIO

wrappers/python/tests/TestGromacsGroFile.py

 import unittest
-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
-import simtk.openmm.app.element as elem
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+import openmm.app.element as elem
 
 class TestGromacsGroFile(unittest.TestCase):
     """Test the Gromacs GRO file parser"""

wrappers/python/tests/TestGromacsTopFile.py

 import unittest
 from validateConstraints import *
-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
-from simtk.openmm.app.gromacstopfile import _defaultGromacsIncludeDir
-import simtk.openmm.app.element as elem
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+from openmm.app.gromacstopfile import _defaultGromacsIncludeDir
+import openmm.app.element as elem
 
 GROMACS_INCLUDE = _defaultGromacsIncludeDir()
 

wrappers/python/tests/TestIntegrators.py

@@ -2,9 +2,9 @@ import unittest
 import warnings
 import tempfile
 from datetime import datetime, timedelta
-from simtk.openmm import *
-from simtk.openmm.app import *
-from simtk.unit import *
+from openmm import *
+from openmm.app import *
+from openmm.unit import *
 import math, random
 
 class TestIntegrators(unittest.TestCase):

wrappers/python/tests/TestMetadynamics.py

 import unittest
-from simtk.openmm import *
-from simtk.openmm.app import *
-from simtk.unit import *
+from openmm import *
+from openmm.app import *
+from openmm.unit import *
 
 class TestMetadynamics(unittest.TestCase):
     """Test the Metadynamics class"""

wrappers/python/tests/TestModeller.py

@@ -4,9 +4,9 @@ import math
 import sys
 
 from validateModeller import *
-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
 
 if sys.version_info >= (3, 0):
     from io import StringIO

wrappers/python/tests/TestNumpyCompatibility.py

 import unittest
-from simtk.openmm import app
-import simtk.openmm as mm
-from simtk import unit
+from openmm import app
+import openmm as mm
+from openmm import unit
 try:
     import numpy as np
     NUMPY_IMPORT_FAILED = False

wrappers/python/tests/TestPatches.py

 import unittest
-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
-import simtk.openmm.app.forcefield as forcefield
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+import openmm.app.forcefield as forcefield
 import math
 try:
     from cStringIO import StringIO

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
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+import openmm.app.element as elem
 if sys.version_info >= (3, 0):
     from io import StringIO
 else:

wrappers/python/tests/TestPdbxFile.py

 import unittest
-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
-import simtk.openmm.app.element as elem
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+import openmm.app.element as elem
 import os
 if sys.version_info >= (3, 0):
     from io import StringIO

wrappers/python/tests/TestPickle.py

 import unittest
 from validateConstraints import *
-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
-import simtk.openmm
-import simtk.openmm.app.element as elem
-import simtk.openmm.app.forcefield as forcefield
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+import openmm
+import openmm.app.element as elem
+import openmm.app.forcefield as forcefield
 import copy
 import pickle
 

wrappers/python/tests/TestSimulatedTempering.py

 import unittest
-from simtk.openmm import *
-from simtk.openmm.app import *
-from simtk.unit import *
+from openmm import *
+from openmm.app import *
+from openmm.unit import *
 
 class TestSimulatedTempering(unittest.TestCase):
     """Test the SimulatedTempering class"""

wrappers/python/tests/TestSimulation.py

 import unittest
 import tempfile
 from datetime import datetime, timedelta
-from simtk.openmm import *
-from simtk.openmm.app import *
-from simtk.unit import *
+from openmm import *
+from openmm.app import *
+from openmm.unit import *
 
 class TestSimulation(unittest.TestCase):
     """Test the Simulation class"""

wrappers/python/tests/TestSwigWrappers.py

 import unittest
-import simtk.openmm as mm
+import openmm as mm
 
 
 class TestSwigWrappers(unittest.TestCase):

wrappers/python/tests/TestTopology.py

 import pickle
 import sys
 import unittest
-from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
-import simtk.openmm.app.element as elem
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+import openmm.app.element as elem
 if sys.version_info >= (3, 0):
     from io import StringIO
 else:

wrappers/python/tests/TestUnitCell.py

 import unittest
 import math
-from simtk.openmm import Vec3
-from simtk.unit import *
-from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
-from simtk.openmm.app.internal.unitcell import computeLengthsAndAngles
-from simtk.openmm.app.internal.unitcell import reducePeriodicBoxVectors
+from openmm import Vec3
+from openmm.unit import *
+from openmm.app.internal.unitcell import computePeriodicBoxVectors
+from openmm.app.internal.unitcell import computeLengthsAndAngles
+from openmm.app.internal.unitcell import reducePeriodicBoxVectors
 
 def strip_units(x):
     if is_quantity(x): return x.value_in_unit_system(md_unit_system)