Top level Python module is now "openmm" (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

.travis.yml

@@ -212,7 +212,7 @@ script:
       else
           make PythonInstall;
       fi;
-      python -m simtk.testInstallation;
+      python -m openmm.testInstallation;
       (cd python/tests && py.test -v);
     fi
 

devtools/ci/jenkins/install_and_test_cpu.sh

@@ -6,5 +6,5 @@ python devtools/run-ctest.py --job-duration=120 --timeout 300 --in-order -R 'Tes
 
 # Build & test Python
 make PythonInstall
-python -m simtk.testInstallation
+python -m openmm.testInstallation
 cd python/tests && py.test -v

devtools/packaging/install.sh

@@ -54,7 +54,7 @@ then
     echo "Installation is complete.  You should now test your installation to make sure"
     echo "it is working correctly by typing the following command:"
     echo
-    echo "python -m simtk.testInstallation"
+    echo "python -m openmm.testInstallation"
 else
     echo
     echo "INSTALLATION FAILED"

docs-source/api-python/app.rst.jinja2

@@ -20,20 +20,20 @@ Representation and Manipulation
     :toctree: generated/
     :template: class.rst
 
-    ~simtk.openmm.app.topology.Topology
-    ~simtk.openmm.app.topology.Chain
-    ~simtk.openmm.app.topology.Residue
-    ~simtk.openmm.app.topology.Atom
-    ~simtk.openmm.app.modeller.Modeller
+    ~openmm.app.topology.Topology
+    ~openmm.app.topology.Chain
+    ~openmm.app.topology.Residue
+    ~openmm.app.topology.Atom
+    ~openmm.app.modeller.Modeller
 
 Simulation
 ~~~~~~~~~~
 .. autosummary::
     :toctree: generated/
     :template: class.rst
 
-    ~simtk.openmm.app.forcefield.ForceField
-    ~simtk.openmm.app.simulation.Simulation
+    ~openmm.app.forcefield.ForceField
+    ~openmm.app.simulation.Simulation
 
 
 Reporting Output

docs-source/api-python/conf.py

@@ -2,7 +2,7 @@
 
 import sys
 import os
-import simtk.openmm.version
+import openmm.version
 
 extensions = ['sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.autosummary',
               'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'process-docstring',
@@ -18,8 +18,8 @@
 project = u'OpenMM'
 copyright = u'2015, Stanford University and the Authors'
 
-version = simtk.openmm.version.short_version
-release = simtk.openmm.version.full_version
+version = openmm.version.short_version
+release = openmm.version.full_version
 
 exclude_patterns = ['_build', '_templates']
 html_static_path = ['_static']

docs-source/api-python/index.rst

@@ -1,4 +1,4 @@
-.. currentmodule:: simtk.openmm.openmm
+.. currentmodule:: openmm.openmm
 
 OpenMM Python API
 =================

docs-source/api-python/library.rst.jinja2

@@ -11,10 +11,10 @@ Core Objects
     :template: class.rst
     :nosignatures:
 
-    ~simtk.openmm.openmm.System
-    ~simtk.openmm.openmm.Context
-    ~simtk.openmm.openmm.Platform
-    ~simtk.openmm.openmm.State
+    ~openmm.openmm.System
+    ~openmm.openmm.Context
+    ~openmm.openmm.Platform
+    ~openmm.openmm.State
 
 
 Forces

docs-source/api-python/render.py

@@ -8,8 +8,8 @@
 import inspect
 
 import jinja2
-import simtk.openmm
-import simtk.openmm.app
+import openmm
+import openmm.app
 
 
 
@@ -21,7 +21,7 @@ def library_template_variables():
     """Create the data structure available to the Jinja2 renderer when
     filling in the templates.
 
-    This function extracts all of classes in ``simtk.openmm.openmm`` and returns
+    This function extracts all of classes in ``openmm.openmm`` and returns
     a dictionary with them grouped into three lists, the integrators, the forces,
     and the remainder (library_extras).
 
@@ -35,39 +35,39 @@ def library_template_variables():
         'units': [],
     }
 
-    mm_klasses = inspect.getmembers(simtk.openmm, predicate=inspect.isclass)
+    mm_klasses = inspect.getmembers(openmm, predicate=inspect.isclass)
 
 
     # gather all Force subclasses
     for name, klass in mm_klasses:
-        if issubclass(klass, simtk.openmm.openmm.Force):
+        if issubclass(klass, openmm.openmm.Force):
             data['forces'].append(fullname(klass))
 
     # gather all Integrator subclasses
     for _, klass in mm_klasses:
-        if issubclass(klass, simtk.openmm.openmm.Integrator):
+        if issubclass(klass, openmm.openmm.Integrator):
             data['integrators'].append(fullname(klass))
 
-    # gather all extra subclasses in simtk.openmm.openmm
+    # gather all extra subclasses in openmm.openmm
 
     # core classes that are already included in library.rst.jinja2
-    exclude = ['simtk.openmm.openmm.Platform', 'simtk.openmm.openmm.Context',
-              'simtk.openmm.openmm.System', 'simtk.openmm.openmm.State']
+    exclude = ['openmm.openmm.Platform', 'openmm.openmm.Context',
+              'openmm.openmm.System', 'openmm.openmm.State']
     exclude.extend(data['forces'])
     exclude.extend(data['integrators'])
 
     # these classes are useless and not worth documenting.
     exclude.extend([
-        'simtk.openmm.openmm.SwigPyIterator',
-        'simtk.openmm.openmm.OpenMMException'])
+        'openmm.openmm.SwigPyIterator',
+        'openmm.openmm.OpenMMException'])
 
     for _, klass in mm_klasses:
         full = fullname(klass)
         if full not in exclude and not klass.__name__[0].islower():
             data['library_extras'].append(full)
 
     # gather units related classes
-    unit_klasses = inspect.getmembers(simtk.unit, predicate=inspect.isclass)
+    unit_klasses = inspect.getmembers(openmm.unit, predicate=inspect.isclass)
     for name, klass in unit_klasses:
         data['units'].append(fullname(klass))
 
@@ -78,7 +78,7 @@ def app_template_variables():
     """Create the data structure available to the Jinja2 renderer when
     filling in the templates.
 
-    This function extracts all of classes in ``simtk.openmm.app`` and returns
+    This function extracts all of classes in ``openmm.app`` and returns
     a dictionary with them grouped into three lists, the reporters, the
     classes with the word "File" in the name, and the remainder.
 
@@ -90,7 +90,7 @@ def app_template_variables():
         'fileclasses': [],
         'app_extras': [],
     }
-    app_klasses = inspect.getmembers(simtk.openmm.app, predicate=inspect.isclass)
+    app_klasses = inspect.getmembers(openmm.app, predicate=inspect.isclass)
 
     # gather all Reporters
     for name, klass in app_klasses:
@@ -102,14 +102,14 @@ def app_template_variables():
         if 'File' in name or 'CharmmParameterSet' in name:
             data['fileclasses'].append(fullname(klass))
 
-    # gather all extra subclasses in simtk.openmm.app
-    exclude = ['simtk.openmm.app.topology.Topology',
-               'simtk.openmm.app.topology.Chain',
-               'simtk.openmm.app.topology.Residue',
-               'simtk.openmm.app.topology.Atom',
-               'simtk.openmm.app.modeller.Modeller',
-               'simtk.openmm.app.forcefield.ForceField',
-               'simtk.openmm.app.simulation.Simulation']
+    # gather all extra subclasses in openmm.app
+    exclude = ['openmm.app.topology.Topology',
+               'openmm.app.topology.Chain',
+               'openmm.app.topology.Residue',
+               'openmm.app.topology.Atom',
+               'openmm.app.modeller.Modeller',
+               'openmm.app.forcefield.ForceField',
+               'openmm.app.simulation.Simulation']
     exclude.extend(data['reporters'])
     exclude.extend(data['fileclasses'])
 

docs-source/licenses/Licenses.txt

@@ -126,7 +126,7 @@ freely, subject to the following restrictions:
 OpenMM uses the PDBx/mmCIF parser written by John Westbrook.  It is distributed
 under the Creative Commons Attribution 3.0 Unported license.  For details, see
 https://creativecommons.org/licenses/by/3.0.  This library was modified to move
-it inside the simtk.openmm.app.internal module.
+it inside the openmm.app.internal module.
 
 
 7. irrXML

docs-source/usersguide/application.rst

@@ -95,7 +95,7 @@ CUDA version it was compiled with.
 4. Verify your installation by typing the following command:
 ::
 
-    python -m simtk.testInstallation
+    python -m openmm.testInstallation
 
 This command confirms that OpenMM is installed, checks whether GPU acceleration
 is available (via the OpenCL and/or CUDA platforms), and verifies that all
@@ -121,9 +121,9 @@ steps.
 .. samepage::
     ::
 
-        from simtk.openmm.app import *
-        from simtk.openmm import *
-        from simtk.unit import *
+        from openmm.app import *
+        from openmm import *
+        from openmm.unit import *
         from sys import stdout
 
         pdb = PDBFile('input.pdb')
@@ -164,9 +164,9 @@ You can name your own scripts whatever you want.  Let’s go through the script
 by line and see how it works.
 ::
 
-    from simtk.openmm.app import *
-    from simtk.openmm import *
-    from simtk.unit import *
+    from openmm.app import *
+    from openmm import *
+    from openmm.unit import *
     from sys import stdout
 
 These lines are just telling the Python interpreter about some libraries we will
@@ -299,9 +299,9 @@ found in OpenMM’s :file:`examples` folder with the name :file:`simulateAmber.p
 .. samepage::
     ::
 
-        from simtk.openmm.app import *
-        from simtk.openmm import *
-        from simtk.unit import *
+        from openmm.app import *
+        from openmm import *
+        from openmm.unit import *
         from sys import stdout
 
         prmtop = AmberPrmtopFile('input.prmtop')
@@ -392,9 +392,9 @@ with the name :file:`simulateGromacs.py`.
 .. samepage::
     ::
 
-        from simtk.openmm.app import *
-        from simtk.openmm import *
-        from simtk.unit import *
+        from openmm.app import *
+        from openmm import *
+        from openmm.unit import *
         from sys import stdout
 
         gro = GromacsGroFile('input.gro')
@@ -456,9 +456,9 @@ on the :class:`CharmmPsfFile`.
 .. samepage::
     ::
 
-        from simtk.openmm.app import *
-        from simtk.openmm import *
-        from simtk.unit import *
+        from openmm.app import *
+        from openmm import *
+        from openmm.unit import *
         from sys import stdout, exit, stderr
 
         psf = CharmmPsfFile('input.psf')
@@ -824,7 +824,7 @@ Field Initiative small molecule force fields using the following example:
     from openmmforcefields.generators import SMIRNOFFTemplateGenerator
     smirnoff = SMIRNOFFTemplateGenerator(molecules=molecule)
     # Create an OpenMM ForceField object with AMBER ff14SB and TIP3P with compatible ions
-    from simtk.openmm.app import ForceField
+    from openmm.app import ForceField
     forcefield = ForceField('amber/protein.ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml')
     # Register the SMIRNOFF template generator
     forcefield.registerTemplateGenerator(smirnoff.generator)
@@ -840,14 +840,14 @@ Alternatively, you can use the older `AMBER GAFF small molecule force field <htt
     from openmmforcefields.generators import GAFFTemplateGenerator
     gaff = GAFFTemplateGenerator(molecules=molecule)
     # Create an OpenMM ForceField object with AMBER ff14SB and TIP3P with compatible ions
-    from simtk.openmm.app import ForceField
+    from openmm.app import ForceField
     forcefield = ForceField('amber/protein.ff14SB.xml', 'amber/tip3p_standard.xml', 'amber/tip3p_HFE_multivalent.xml')
     # Register the GAFF template generator
     forcefield.registerTemplateGenerator(gaff.generator)
     # You can now parameterize an OpenMM Topology object that contains the specified molecule.
     # forcefield will load the appropriate GAFF parameters when needed, and antechamber
     # will be used to generate small molecule parameters on the fly.
-    from simtk.openmm.app import PDBFile
+    from openmm.app import PDBFile
     pdbfile = PDBFile('t4-lysozyme-L99A-with-benzene.pdb')
     system = forcefield.createSystem(pdbfile.topology)
 
@@ -864,8 +864,8 @@ small molecule force field you want to use:
 ::
 
     # Define the keyword arguments to feed to ForceField
-    from simtk import unit
-    from simtk.openmm import app
+    from openmm import unit
+    from openmm import app
     forcefield_kwargs = { 'constraints' : app.HBonds, 'rigidWater' : True, 'removeCMMotion' : False, 'hydrogenMass' : 4*unit.amu }
     # Initialize a SystemGenerator using the Open Force Field Initiative 1.2.0 force field (openff-1.2.0)
     from openmmforcefields.generators import SystemGenerator
@@ -1787,9 +1787,9 @@ PDB file.
 .. samepage::
     ::
 
-        from simtk.openmm.app import *
-        from simtk.openmm import *
-        from simtk.unit import *
+        from openmm.app import *
+        from openmm import *
+        from openmm.unit import *
 
         print('Loading...')
         pdb = PDBFile('input.pdb')
@@ -3261,9 +3261,9 @@ This :code:`generator` function must conform to the following API:
         """
         Parameters
         ----------
-        forcefield : simtk.openmm.app.ForceField
+        forcefield : openmm.app.ForceField
             The ForceField object to which residue templates and/or parameters are to be added.
-        residue : simtk.openmm.app.Topology.Residue
+        residue : openmm.app.Topology.Residue
             The residue topology for which a template is to be generated.
 
         Returns