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/simtk/openmm/app/internal/charmm/_charmmfile.py → wrappers/python/openmm/app/internal/charmm/_charmmfile.py

@@ -34,7 +34,7 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 from __future__ import absolute_import
-from simtk.openmm.app.internal.charmm.exceptions import CharmmFileError
+from openmm.app.internal.charmm.exceptions import CharmmFileError
 import sys
 if sys.version_info < (3, 0):
     from codecs import open

wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py → wrappers/python/openmm/app/internal/charmm/topologyobjects.py

@@ -33,10 +33,10 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 from __future__ import absolute_import
-from simtk.openmm.app.internal.charmm.exceptions import (
+from openmm.app.internal.charmm.exceptions import (
                 SplitResidueWarning, BondError, ResidueError, CmapError,
                 MissingParameter)
-import simtk.unit as u
+import openmm.unit as u
 import warnings
 
 TINY = 1e-8

wrappers/python/simtk/openmm/app/internal/customgbforces.py → wrappers/python/openmm/app/internal/customgbforces.py

@@ -34,9 +34,9 @@ from __future__ import division, absolute_import
 
 from collections import defaultdict
 import copy
-from simtk.openmm.app import element as E
-from simtk.openmm import CustomGBForce, Discrete2DFunction
-import simtk.unit as u
+from openmm.app import element as E
+from openmm import CustomGBForce, Discrete2DFunction
+import openmm.unit as u
 from math import floor
 
 _have_numpy = False
@@ -486,7 +486,7 @@ class CustomAmberGBForceBase(CustomGBForce):
 
         Parameters
         ----------
-        topology : simtk.openmm.app.Topology
+        topology : openmm.app.Topology
             Topology of the system to get parameters for
 
         Returns
@@ -558,7 +558,7 @@ class GBSAHCTForce(CustomAmberGBForceBase):
 
         Parameters
         ----------
-        topology : simtk.openmm.app.Topology
+        topology : openmm.app.Topology
             Topology of the system to get parameters for
 
         Returns
@@ -624,7 +624,7 @@ class GBSAOBC1Force(CustomAmberGBForceBase):
 
         Parameters
         ----------
-        topology : simtk.openmm.app.Topology
+        topology : openmm.app.Topology
             Topology of the system to get parameters for
 
         Returns
@@ -754,7 +754,7 @@ class GBSAGBnForce(CustomAmberGBForceBase):
 
         Parameters
         ----------
-        topology : simtk.openmm.app.Topology
+        topology : openmm.app.Topology
             Topology of the system to get parameters for
 
         Returns
@@ -892,7 +892,7 @@ class GBSAGBn2Force(GBSAGBnForce):
 
         Parameters
         ----------
-        topology : simtk.openmm.app.Topology
+        topology : openmm.app.Topology
             Topology of the system to get parameters for
 
         Returns

wrappers/python/simtk/openmm/app/internal/pdbstructure.py → wrappers/python/openmm/app/internal/pdbstructure.py

@@ -34,8 +34,8 @@ __author__ = "Christopher M. Bruns"
 __version__ = "1.0"
 
 
-from simtk.openmm.vec3 import Vec3
-import simtk.unit as unit
+from openmm.vec3 import Vec3
+import openmm.unit as unit
 from .. import element
 from .unitcell import computePeriodicBoxVectors
 import warnings
@@ -80,13 +80,13 @@ class PdbStructure(object):
     [13.768, -8.431, 11.865] A
 
     Strip the length units from an atomic position:
-    > import simtk.unit
+    > import openmm.unit
     > pos = pdb.iter_positions().next()
     > print pos
     [13.768, -8.431, 11.865] A
-    > print pos / simtk.unit.angstroms
+    > print pos / openmm.unit.angstroms
     [13.768, -8.431, 11.865]
-    > print pos / simtk.unit.nanometers
+    > print pos / openmm.unit.nanometers
     [1.3768, -0.8431, 1.1865]
 
 
@@ -967,8 +967,8 @@ class Atom(object):
             """
             Examples
 
-            >>> from simtk.openmm.vec3 import Vec3
-            >>> import simtk.unit as unit
+            >>> from openmm.vec3 import Vec3
+            >>> import openmm.unit as unit
             >>> l = Atom.Location(' ', Vec3(1,2,3)*unit.angstroms, 1.0, 20.0*unit.angstroms**2, "XXX")
             >>> for c in l:
             ...     print c

wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxParser.py → wrappers/python/openmm/app/internal/pdbx/reader/PdbxParser.py

@@ -36,7 +36,7 @@ __license__   = "Creative Commons Attribution 3.0 Unported"
 __version__   = "V0.01"
 
 import re,sys
-from simtk.openmm.app.internal.pdbx.reader.PdbxContainers import *
+from openmm.app.internal.pdbx.reader.PdbxContainers import *
 
 class PdbxError(Exception):
     """ Class for catch general errors 

wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxReadWriteTests.py → wrappers/python/openmm/app/internal/pdbx/reader/PdbxReadWriteTests.py

@@ -21,9 +21,9 @@ __version__   = "V0.01"
 import sys, unittest, traceback
 import sys, time, os, os.path, shutil
 
-from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
-from simtk.openmm.app.internal.pdbx.writer.PdbxWriter import PdbxWriter
-from simtk.openmm.app.internal.pdbx.reader.PdbxContainers import *
+from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
+from openmm.app.internal.pdbx.writer.PdbxWriter import PdbxWriter
+from openmm.app.internal.pdbx.reader.PdbxContainers import *
 
 
 class PdbxReadWriteTests(unittest.TestCase):

wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxReader.py → wrappers/python/openmm/app/internal/pdbx/reader/PdbxReader.py

@@ -25,7 +25,7 @@ Acknowledgements:
 from __future__ import absolute_import
 
 import re,sys
-from simtk.openmm.app.internal.pdbx.reader.PdbxContainers import *
+from openmm.app.internal.pdbx.reader.PdbxContainers import *
 
 class PdbxError(Exception):
     """ Class for catch general errors 

wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxReaderTests.py → wrappers/python/openmm/app/internal/pdbx/reader/PdbxReaderTests.py

@@ -16,8 +16,8 @@ from __future__ import absolute_import
 import sys, unittest, traceback
 import sys, time, os, os.path, shutil
 
-from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
-from simtk.openmm.app.internal.pdbx.reader.PdbxContainers import *
+from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
+from openmm.app.internal.pdbx.reader.PdbxContainers import *
 
 class PdbxReaderTests(unittest.TestCase):
     def setUp(self):

wrappers/python/simtk/openmm/app/internal/pdbx/writer/PdbxWriter.py → wrappers/python/openmm/app/internal/pdbx/writer/PdbxWriter.py

@@ -19,7 +19,7 @@ __license__   = "Creative Commons Attribution 3.0 Unported"
 __version__   = "V0.01"
 
 
-from simtk.openmm.app.internal.pdbx.reader.PdbxContainers import *
+from openmm.app.internal.pdbx.reader.PdbxContainers import *
 
 class PdbxError(Exception):
     """ Class for catch general errors 

wrappers/python/simtk/openmm/app/internal/pdbx/writer/PdbxWriterTests.py → wrappers/python/openmm/app/internal/pdbx/writer/PdbxWriterTests.py

@@ -24,9 +24,9 @@ __version__   = "V0.01"
 import sys, unittest, traceback
 import sys, time, os, os.path, shutil
 
-from simtk.openmm.app.internal.pdbx.reader.PdbxReader  import PdbxReader
-from simtk.openmm.app.internal.pdbx.writer.PdbxWriter  import PdbxWriter
-from simtk.openmm.app.internal.pdbx.reader.PdbxContainers import *
+from openmm.app.internal.pdbx.reader.PdbxReader  import PdbxReader
+from openmm.app.internal.pdbx.writer.PdbxWriter  import PdbxWriter
+from openmm.app.internal.pdbx.reader.PdbxContainers import *
 
 class PdbxWriterTests(unittest.TestCase):
     def setUp(self):

wrappers/python/simtk/openmm/app/internal/unitcell.py → wrappers/python/openmm/app/internal/unitcell.py

@@ -32,8 +32,8 @@ from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
-from simtk.openmm import Vec3
-from simtk.unit import nanometers, is_quantity, norm, dot, radians
+from openmm import Vec3
+from openmm.unit import nanometers, is_quantity, norm, dot, radians
 import math
 
 

wrappers/python/simtk/openmm/app/metadynamics.py → wrappers/python/openmm/app/metadynamics.py

@@ -27,8 +27,8 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
-import simtk.openmm as mm
-import simtk.unit as unit
+import openmm as mm
+import openmm.unit as unit
 from collections import namedtuple
 from functools import reduce
 import os