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/modeller.py → wrappers/python/openmm/app/modeller.py

@@ -34,14 +34,14 @@ from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
-from simtk.openmm.app import Topology, PDBFile, ForceField
-from simtk.openmm.app.forcefield import HAngles, AllBonds, CutoffNonPeriodic, CutoffPeriodic, _createResidueSignature, DrudeGenerator
-from simtk.openmm.app.topology import Residue
-from simtk.openmm.app.internal import compiled
-from simtk.openmm.vec3 import Vec3
-from simtk.openmm import System, Context, NonbondedForce, CustomNonbondedForce, HarmonicBondForce, HarmonicAngleForce, VerletIntegrator, LangevinIntegrator, LocalEnergyMinimizer
-from simtk.unit import nanometer, molar, elementary_charge, amu, gram, liter, degree, sqrt, acos, is_quantity, dot, norm, kilojoules_per_mole
-import simtk.unit as unit
+from openmm.app import Topology, PDBFile, ForceField
+from openmm.app.forcefield import HAngles, AllBonds, CutoffNonPeriodic, CutoffPeriodic, _createResidueSignature, DrudeGenerator
+from openmm.app.topology import Residue
+from openmm.app.internal import compiled
+from openmm.vec3 import Vec3
+from openmm import System, Context, NonbondedForce, CustomNonbondedForce, HarmonicBondForce, HarmonicAngleForce, VerletIntegrator, LangevinIntegrator, LocalEnergyMinimizer
+from openmm.unit import nanometer, molar, elementary_charge, amu, gram, liter, degree, sqrt, acos, is_quantity, dot, norm, kilojoules_per_mole
+import openmm.unit as unit
 from . import element as elem
 import gc
 import os

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

@@ -38,11 +38,11 @@ import math
 import xml.etree.ElementTree as etree
 from copy import copy
 from datetime import date
-from simtk.openmm import Vec3, Platform
-from simtk.openmm.app.internal.pdbstructure import PdbStructure
-from simtk.openmm.app.internal.unitcell import computeLengthsAndAngles
-from simtk.openmm.app import Topology
-from simtk.unit import nanometers, angstroms, is_quantity, norm, Quantity, dot
+from openmm import Vec3, Platform
+from openmm.app.internal.pdbstructure import PdbStructure
+from openmm.app.internal.unitcell import computeLengthsAndAngles
+from openmm.app import Topology
+from openmm.unit import nanometers, angstroms, is_quantity, norm, Quantity, dot
 from . import element as elem
 try:
     import numpy

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

@@ -32,8 +32,8 @@ from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
-import simtk.openmm as mm
-from simtk.openmm.app import PDBFile, PDBxFile
+import openmm as mm
+from openmm.app import PDBFile, PDBxFile
 
 class PDBReporter(object):
     """PDBReporter outputs a series of frames from a Simulation to a PDB file.

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

@@ -35,12 +35,12 @@ __version__ = "2.0"
 
 import sys
 import math
-from simtk.openmm import Vec3, Platform
+from openmm import Vec3, Platform
 from datetime import date
-from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
-from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors, computeLengthsAndAngles
-from simtk.openmm.app import Topology, PDBFile
-from simtk.unit import nanometers, angstroms, is_quantity, norm, Quantity, dot
+from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
+from openmm.app.internal.unitcell import computePeriodicBoxVectors, computeLengthsAndAngles
+from openmm.app import Topology, PDBFile
+from openmm.unit import nanometers, angstroms, is_quantity, norm, Quantity, dot
 from . import element as elem
 try:
     import numpy

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

@@ -33,7 +33,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
-import simtk.unit as unit
+import openmm.unit as unit
 import math
 import random
 from sys import stdout

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

@@ -32,8 +32,8 @@ from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
-import simtk.openmm as mm
-import simtk.unit as unit
+import openmm as mm
+import openmm.unit as unit
 import sys
 from datetime import datetime, timedelta
 try:

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

@@ -43,8 +43,8 @@ try:
     have_gzip = True
 except: have_gzip = False
 
-import simtk.openmm as mm
-import simtk.unit as unit
+import openmm as mm
+import openmm.unit as unit
 import math
 import time
 

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

@@ -35,9 +35,9 @@ __version__ = "1.0"
 from collections import namedtuple
 import os
 import xml.etree.ElementTree as etree
-from simtk.openmm.vec3 import Vec3
-from simtk.openmm.app.internal.singleton import Singleton
-from simtk.unit import nanometers, sqrt, is_quantity
+from openmm.vec3 import Vec3
+from openmm.app.internal.singleton import Singleton
+from openmm.unit import nanometers, sqrt, is_quantity
 from copy import deepcopy
 
 # Enumerated values for bond type

wrappers/python/simtk/openmm/mtsintegrator.py → wrappers/python/openmm/mtsintegrator.py

@@ -32,7 +32,7 @@ from __future__ import absolute_import, division
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
-from simtk.openmm import CustomIntegrator
+from openmm import CustomIntegrator
 
 class MTSIntegrator(CustomIntegrator):
     """MTSIntegrator implements the rRESPA multiple time step integration algorithm.
@@ -169,7 +169,7 @@ class MTSLangevinIntegrator(CustomIntegrator):
         import math
         self.addGlobalVariable("a", math.exp(-friction*dt))
         self.addGlobalVariable("b", math.sqrt(1-math.exp(-2*friction*dt)))
-        from simtk.unit import MOLAR_GAS_CONSTANT_R
+        from openmm.unit import MOLAR_GAS_CONSTANT_R
         self.addGlobalVariable('kT', MOLAR_GAS_CONSTANT_R*temperature)
         self.addPerDofVariable("x1", 0)
         self.addUpdateContextState();

wrappers/python/simtk/testInstallation.py → wrappers/python/openmm/testInstallation.py

@@ -5,14 +5,14 @@ import sys
 # First make sure OpenMM is installed.
 
 try:
-    from simtk.openmm.app import *
-    from simtk.openmm import *
-    from simtk.unit import *
+    from openmm.app import *
+    from openmm import *
+    from openmm.unit import *
 except ImportError as err:
-    simtk_import_failed = True
-    simtk_import_error = str(err)
+    import_failed = True
+    import_error = str(err)
 else:
-    simtk_import_failed = False
+    import_failed = False
 
 
 def run_tests():
@@ -33,7 +33,7 @@ def run_tests():
     print()
 
     # Create a System for the tests.
-    data_dir = os.path.join(os.path.abspath(os.path.split(__file__)[0]), 'openmm', 'app', 'data')
+    data_dir = os.path.join(os.path.abspath(os.path.split(__file__)[0]), 'app', 'data')
     pdb = PDBFile(os.path.join(data_dir, 'test.pdb'))
     forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
     system = forcefield.createSystem(pdb.topology, nonbondedMethod=LJPME, nonbondedCutoff=1*nanometer, constraints=HBonds, ewaldErrorTolerance=1e-4)
@@ -96,10 +96,10 @@ def run_tests():
 
 
 def main():
-    if simtk_import_failed:
+    if import_failed:
         print('Failed to import OpenMM packages; OpenMM will not work.\n'            
               'Make sure OpenMM is installed and the library path is set correctly.'
-              '\n\nError message: %s' % simtk_import_error,
+              '\n\nError message: %s' % import_error,
               file=sys.stderr)
         sys.exit(1)
 

wrappers/python/openmm/unit/__init__.py

+"""
+Physical quantities with units for dimensional analysis and automatic unit conversion.
+"""
+from __future__ import absolute_import
+
+__docformat__ = "epytext en"
+__author__ = "Christopher M. Bruns"
+__copyright__ = "Copyright 2010, Stanford University and Christopher M. Bruns"
+__credits__ = []
+__license__ = "MIT"
+__maintainer__ = "Christopher M. Bruns"
+__email__ = "cmbruns@stanford.edu"
+
+from .unit import Unit, is_unit
+from .quantity import Quantity, is_quantity
+from .unit_math import *
+from .unit_definitions import *
+from .constants import *

wrappers/python/simtk/unit/basedimension.py → wrappers/python/openmm/unit/basedimension.py

 #!/bin/env python
 """
-Module simtk.unit.basedimension
+Module openmm.unit.basedimension
 
 BaseDimension class for use by units and quantities.
 BaseDimensions are things like "length" and "mass".
@@ -61,8 +61,7 @@ class BaseDimension(object):
         """Create a new BaseDimension.
 
         Each new BaseDimension is assumed to be independent of all other BaseDimensions.
-        Use the existing BaseDimensions in simtk.dimension instead of creating
-        new ones.
+        Use the existing BaseDimensions instead of creating new ones.
         """
         self.name = name
         if not self.name in BaseDimension._index_by_name.keys():

wrappers/python/simtk/unit/baseunit.py → wrappers/python/openmm/unit/baseunit.py

@@ -2,7 +2,7 @@
 
 
 """
-Module simtk.unit.baseunit
+Module openmm.unit.baseunit
 
 Contains BaseUnit class, which is a component of the Unit class.
 

wrappers/python/simtk/unit/constants.py → wrappers/python/openmm/unit/constants.py

 #!/bin/env python
 """
-Module simtk.unit.constants
+Module openmm.unit.constants
 
 This is part of the OpenMM molecular simulation toolkit originating from
 Simbios, the NIH National Center for Physics-Based Simulation of

wrappers/python/simtk/unit/doctests.py → wrappers/python/openmm/unit/doctests.py

 #!/bin/env python
 
 """
-Module simtk.unit.doctests
+Module openmm.unit.doctests
 
 Lots of in-place doctests would no longer work after I rearranged
 so that specific unit definitions are defined late.  So those tests
@@ -850,7 +850,7 @@ Examples
 # Thanks to Kyle Beauchamp July 2010
     >>> try:
     ...    import numpy
-    ...    from simtk.unit.quantity import _is_string
+    ...    from openmm.unit.quantity import _is_string
     ...    a = numpy.array([[1,2,3],[4,5,6]])
     ...    assert isinstance("", str)
     ...    assert _is_string("")

wrappers/python/simtk/unit/prefix.py → wrappers/python/openmm/unit/prefix.py

 #!/bin/env python
 """
-Module simtk.unit.prefix
+Module openmm.unit.prefix
 
 This is part of the OpenMM molecular simulation toolkit originating from
 Simbios, the NIH National Center for Physics-Based Simulation of
@@ -140,7 +140,7 @@ def define_prefixed_units(base_unit, module = sys.modules[__name__]):
 
     Parameters
      - base_unit (BaseUnit) existing base unit to use as a basis for prefixed units
-     - module (Module) module which will contain the new attributes.  Defaults to simtk.unit module.
+     - module (Module) module which will contain the new attributes.  Defaults to openmm.unit module.
     """
     for prefix in si_prefixes:
         new_base_unit = prefix * base_unit

wrappers/python/simtk/unit/quantity.py → wrappers/python/openmm/unit/quantity.py

 #!/bin/env python
 """
-Module simtk.unit.quantity
+Module openmm.unit.quantity
 
 Physical quantities with units, intended to produce similar functionality
 to Boost.Units package in C++ (but with a runtime cost).
@@ -9,14 +9,14 @@ but different internals to satisfy our local requirements.
 In particular, there is no underlying set of 'canonical' base
 units, whereas in Scientific.Physics.PhysicalQuantities all
 units are secretly in terms of SI units.  Also, it is easier
-to add new fundamental dimensions to simtk.dimensions.  You
+to add new fundamental dimensions to basedimension.  You
 might want to make new dimensions for, say, "currency" or
 "information".
 
 Some features of this implementation:
   * Quantities are a combination of a value and a unit.  The value
     part can be any python type, including numbers, lists, numpy
-    arrays, and anything else.  The unit part must be a simtk.unit.Unit.
+    arrays, and anything else.  The unit part must be a openmm.unit.Unit.
   * Operations like adding incompatible units raises an error.
   * Multiplying or dividing units/quantities creates new units.
   * Users can create new Units and Dimensions, but most of the useful
@@ -100,7 +100,7 @@ class Quantity(object):
 
         Parameters
          - value: (any type, usually a number) Measure of this quantity
-         - unit: (Unit) the physical unit, e.g. simtk.unit.meters.
+         - unit: (Unit) the physical unit, e.g. openmm.unit.meters.
         """
         # When no unit is specified, bend over backwards to handle all one-argument possibilities
         if unit is None: # one argument version, copied from UList

wrappers/python/simtk/unit/standard_dimensions.py → wrappers/python/openmm/unit/standard_dimensions.py

 #!/bin/env python
 """
-Module simtk.unit.standard_dimensions
+Module openmm.unit.standard_dimensions
 
 Definition of principal dimensions: mass, length, time, etc.
 

wrappers/python/simtk/unit/unit.py → wrappers/python/openmm/unit/unit.py

 #!/bin/env python
 """
-Module simtk.unit
+Module openmm.unit
 
 Contains classes Unit and ScaledUnit.