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

 #!/bin/env python
 """
-Module simtk.unit.unit_definitions
+Module openmm.unit.unit_definitions
 
 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/unit_math.py → wrappers/python/openmm/unit/unit_math.py

 #!/bin/env python
 """
-Module simtk.unit.math
+Module openmm.unit.math
 
 Arithmetic methods on Quantities and Units
 

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

 #!/bin/env python
 """
-Module simtk.unit.unit_operators
+Module openmm.unit.unit_operators
 
 Physical quantities with units, intended to produce similar functionality
 to Boost.Units package in C++ (but with a runtime cost).
@@ -9,7 +9,7 @@ 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".
 

wrappers/python/simtk/openmm/vec3.py → wrappers/python/openmm/vec3.py

@@ -32,7 +32,7 @@ from __future__ import absolute_import, division
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
-from .. import unit
+from . import unit
 from collections import namedtuple
 
 class Vec3(namedtuple('Vec3', ['x', 'y', 'z'])):

wrappers/python/setup.py

@@ -39,12 +39,12 @@ def removePackage(mod, verbose):
         except AttributeError:
             return
         if len(pathList) > 1:
-           raise Exception("more than one item in simtk.__path__")
-        simtkInstallPath = pathList[0]
-        if os.path.exists(simtkInstallPath):
+           raise Exception("more than one item in openmm.__path__")
+        installPath = pathList[0]
+        if os.path.exists(installPath):
             if verbose:
-                sys.stdout.write('REMOVING "%s"\n' % simtkInstallPath)
-            removeRecursive(simtkInstallPath)
+                sys.stdout.write('REMOVING "%s"\n' % installPath)
+            removeRecursive(installPath)
 
 def uninstall(verbose=True):
     save_path=sys.path[:]
@@ -53,8 +53,8 @@ def uninstall(verbose=True):
         if item!='.' and item!=os.getcwd():
             sys.path.append(item)
     try:
-        import simtk.openmm as openmm
-        removePackage(openmm, verbose)
+        import simtk.openmm
+        removePackage(simtk.openmm, verbose)
     except ImportError:
         pass
 
@@ -63,10 +63,16 @@ def uninstall(verbose=True):
         removePackage(unit, verbose)
     except ImportError:
         pass
+
+    try:
+        import openmm
+        removePackage(openmm, verbose)
+    except ImportError:
+        pass
     sys.path=save_path
 
 
-def writeVersionPy(filename="simtk/openmm/version.py", major_version_num=MAJOR_VERSION_NUM,
+def writeVersionPy(filename="openmm/version.py", major_version_num=MAJOR_VERSION_NUM,
                      minor_version_num=MINOR_VERSION_NUM, build_info=BUILD_INFO):
     """Write a version.py file into the python source directory before installation.
     If a version.py file already exists, we assume that it contains only the git_revision
@@ -125,27 +131,29 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
     setupKeywords["version"]           = "%s.%s.%s" % (major_version_num,
                                                        minor_version_num,
                                                        build_info)
-    setupKeywords["author"]            = "Randall J. Radmer"
-    setupKeywords["author_email"]      = "radmer@stanford.edu"
+    setupKeywords["author"]            = "Peter Eastman"
     setupKeywords["license"]           = \
     "Python Software Foundation License (BSD-like)"
-    setupKeywords["url"]               = "https://simtk.org/home/openmm"
-    setupKeywords["download_url"]      = "https://simtk.org/home/openmm"
-    setupKeywords["packages"]          = ["simtk",
+    setupKeywords["url"]               = "https://openmm.org"
+    setupKeywords["download_url"]      = "https://openmm.org"
+    setupKeywords["packages"]          = [
+                                          "simtk",
                                           "simtk.unit",
                                           "simtk.openmm",
                                           "simtk.openmm.app",
-                                          "simtk.openmm.app.internal",
-                                          "simtk.openmm.app.internal.charmm",
-                                          "simtk.openmm.app.internal.pdbx",
-                                          "simtk.openmm.app.internal.pdbx.reader",
-                                          "simtk.openmm.app.internal.pdbx.writer"]
+                                          "openmm",
+                                          "openmm.unit",
+                                          "openmm",
+                                          "openmm.app",
+                                          "openmm.app.internal",
+                                          "openmm.app.internal.charmm",
+                                          "openmm.app.internal.pdbx",
+                                          "openmm.app.internal.pdbx.reader",
+                                          "openmm.app.internal.pdbx.writer"]
     setupKeywords["data_files"]        = []
-    setupKeywords["package_data"]      = {"simtk" : [],
-                                          "simtk.unit" : [],
-                                          "simtk.openmm" : [],
-                                          "simtk.openmm.app" : ['data/*.xml', 'data/*.pdb', 'data/amber14/*.xml', 'data/charmm36/*.xml'],
-                                          "simtk.openmm.app.internal" : []}
+    setupKeywords["package_data"]      = {"openmm" : [],
+                                          "openmm.app" : ['data/*.xml', 'data/*.pdb', 'data/amber14/*.xml', 'data/charmm36/*.xml'],
+                                          "openmm.app.internal" : []}
     setupKeywords["platforms"]         = ["Linux", "Mac OS X", "Windows"]
     setupKeywords["description"]       = \
     "Python wrapper for OpenMM (a C++ MD package)"
@@ -208,7 +216,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
     include_dirs=openmm_include_path.split(';')
     include_dirs.append(numpy.get_include())
 
-    extensionArgs = {"name": "simtk.openmm._openmm",
+    extensionArgs = {"name": "openmm._openmm",
                     "sources": ["src/swig_doxygen/OpenMMSwig.cxx"],
                     "include_dirs": include_dirs,
                     "define_macros": define_macros,
@@ -219,7 +227,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
     if platform.system() != "Windows":
         extensionArgs["runtime_library_dirs"] = library_dirs
     setupKeywords["ext_modules"] = [Extension(**extensionArgs)]
-    setupKeywords["ext_modules"] += cythonize('simtk/openmm/app/internal/*.pyx')
+    setupKeywords["ext_modules"] += cythonize('openmm/app/internal/*.pyx')
 
     outputString = ''
     firstTab     = 40

wrappers/python/simtk/__init__.py

+import openmm
+import openmm.unit as unit
\ No newline at end of file

wrappers/python/simtk/openmm/__init__.py

-"""OpenMM is a toolkit for molecular simulation. It can be used either as a
-stand-alone application for running simulations, or as a library you call
-from your own code. It provides a combination of extreme flexibility
-(through custom forces and integrators), openness, and high performance
-(especially on recent GPUs) that make it truly unique among simulation codes.
-"""
-from __future__ import absolute_import
-__author__ = "Peter Eastman"
+from openmm import *
+from . import app
 
-import os, os.path
-import sys
-from . import version
-
-if sys.platform == 'win32':
-    _path = os.environ['PATH']
-    os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % {
-        'lib': version.openmm_library_path, 'path': _path}
-
-from simtk.openmm.openmm import *
-from simtk.openmm.vec3 import Vec3
-from simtk.openmm.mtsintegrator import MTSIntegrator, MTSLangevinIntegrator
-from simtk.openmm.amd import AMDIntegrator, AMDForceGroupIntegrator, DualAMDIntegrator
-
-if os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(version.openmm_library_path):
-    pluginLoadedLibNames = Platform.loadPluginsFromDirectory(os.path.join(version.openmm_library_path, 'plugins'))
-else:
-    pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
-
-if sys.platform == 'win32':
-    os.environ['PATH'] = _path
-    del _path
-__version__ = Platform.getOpenMMVersion()
-
-class OpenMMException(Exception):
-    """This is the class used for all exceptions thrown by the C++ library."""
-    pass
+import logging
+logging.getLogger().warning("Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.")
\ No newline at end of file

wrappers/python/simtk/openmm/app/__init__.py

-"""
-OpenMM Application
-"""
-from __future__ import absolute_import
-
-__docformat__ = "epytext en"
-
-__author__ = "Peter Eastman"
-__copyright__ = "Copyright 2016-2019, Stanford University and Peter Eastman"
-__credits__ = []
-__license__ = "MIT"
-__maintainer__ = "Peter Eastman"
-__email__ = "peastman@stanford.edu"
-
-from .topology import Topology, Chain, Residue, Atom
-from .pdbfile import PDBFile
-from .pdbxfile import PDBxFile
-from .forcefield import ForceField
-from .simulation import Simulation
-from .pdbreporter import PDBReporter, PDBxReporter
-from .amberprmtopfile import AmberPrmtopFile, HCT, OBC1, OBC2, GBn, GBn2
-from .amberinpcrdfile import AmberInpcrdFile
-from .dcdfile import DCDFile
-from .gromacsgrofile import GromacsGroFile
-from .gromacstopfile import GromacsTopFile
-from .dcdreporter import DCDReporter
-from .modeller import Modeller
-from .statedatareporter import StateDataReporter
-from .element import Element
-from .desmonddmsfile import DesmondDMSFile
-from .checkpointreporter import CheckpointReporter
-from .charmmcrdfiles import CharmmCrdFile, CharmmRstFile
-from .charmmparameterset import CharmmParameterSet
-from .charmmpsffile import CharmmPsfFile, CharmmPSFWarning
-from .simulatedtempering import SimulatedTempering
-from .metadynamics import Metadynamics, BiasVariable
-
-# Enumerated values
-
-NoCutoff = forcefield.NoCutoff
-CutoffNonPeriodic = forcefield.CutoffNonPeriodic
-CutoffPeriodic = forcefield.CutoffPeriodic
-Ewald = forcefield.Ewald
-PME = forcefield.PME
-LJPME = forcefield.LJPME
-
-HBonds = forcefield.HBonds
-AllBonds = forcefield.AllBonds
-HAngles = forcefield.HAngles
-
-Single = topology.Single
-Double = topology.Double
-Triple = topology.Triple
-Aromatic = topology.Aromatic
-Amide = topology.Amide
-
+from openmm.app import *

wrappers/python/simtk/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 *
+from openmm.unit import *

wrappers/python/src/swig_doxygen/swig_lib/python/exceptions.i

@@ -3,7 +3,7 @@
     try {
         $action
     } catch (std::exception &e) {
-        PyObject* mm = PyImport_AddModule("simtk.openmm");
+        PyObject* mm = PyImport_AddModule("openmm");
         PyObject* openmm_exception = PyObject_GetAttrString(mm, "OpenMMException");
         PyErr_SetString(openmm_exception, const_cast<char*>(e.what()));
         return NULL;
@@ -16,7 +16,7 @@
         $action
     } catch (std::exception &e) {
         PyEval_RestoreThread(_savePythonThreadState);
-        PyObject* mm = PyImport_AddModule("simtk.openmm");
+        PyObject* mm = PyImport_AddModule("openmm");
         PyObject* openmm_exception = PyObject_GetAttrString(mm, "OpenMMException");
         PyErr_SetString(openmm_exception, const_cast<char*>(e.what()));
         return NULL;
@@ -30,7 +30,7 @@
         $action
     } catch (std::exception &e) {
         PyEval_RestoreThread(_savePythonThreadState);
-        PyObject* mm = PyImport_AddModule("simtk.openmm");
+        PyObject* mm = PyImport_AddModule("openmm");
         PyObject* openmm_exception = PyObject_GetAttrString(mm, "OpenMMException");
         PyErr_SetString(openmm_exception, const_cast<char*>(e.what()));
         return NULL;

wrappers/python/src/swig_doxygen/swig_lib/python/header.i

@@ -8,7 +8,7 @@ PyObject *copyVVec3ToList(std::vector<Vec3> vVec3) {
 
   n=vVec3.size(); 
   pyList=PyList_New(n);
-  PyObject* mm = PyImport_AddModule("simtk.openmm");
+  PyObject* mm = PyImport_AddModule("openmm");
   PyObject* vec3 = PyObject_GetAttrString(mm, "Vec3");
   for (i=0; i<n; i++) {
     OpenMM::Vec3& v = vVec3.at(i);

wrappers/python/src/swig_doxygen/swig_lib/python/pythoncode.i

@@ -17,8 +17,8 @@ if sys.version_info[0] == 2:
 else:
     _string_types = (bytes, str)
 
-import simtk.unit as unit
-from simtk.openmm.vec3 import Vec3
+import openmm.unit as unit
+from openmm.vec3 import Vec3
 
 
 %}

wrappers/python/src/swig_doxygen/swig_lib/python/typemaps.i

 %fragment("Vec3_to_PyVec3", "header") {
 /**
- * Convert an OpenMM::Vec3 into a Python simtk.openmm.Vec3 object
+ * Convert an OpenMM::Vec3 into a Python openmm.Vec3 object
  *
  * Returns a new reference.
  */
@@ -8,7 +8,7 @@ PyObject* Vec3_to_PyVec3(const OpenMM::Vec3& v) {
     static PyObject *__s_mm = NULL;
     static PyObject *__s_Vec3 = NULL;
     if (__s_mm == NULL) {
-        __s_mm = PyImport_AddModule("simtk.openmm");
+        __s_mm = PyImport_AddModule("openmm");
         __s_Vec3 = PyObject_GetAttrString(__s_mm, "Vec3");
     }
     PyObject* tuple = Py_BuildValue("(d,d,d)", v[0], v[1], v[2]);
@@ -25,7 +25,7 @@ PyObject* Vec3_to_PyVec3(const OpenMM::Vec3& v) {
  *
  * This is equivalent to the following Python code
  *
- * >>> from simtk import unit
+ * >>> from openmm import unit
  * >>> if isinstance(input, unit.Quantity)
  * ...     if input.is_compatible(unit.bar)
  * ...         return input.value_in_unit(unit.bar)
@@ -41,9 +41,9 @@ PyObject* Py_StripOpenMMUnits(PyObject *input) {
 
     if (__s_Quantity == NULL) {
         PyObject* module = NULL;
-        module = PyImport_ImportModule("simtk.unit");
+        module = PyImport_ImportModule("openmm.unit");
         if (!module) {
-            PyErr_SetString(PyExc_ImportError, "simtk.unit"); Py_CLEAR(module); return NULL;
+            PyErr_SetString(PyExc_ImportError, "openmm.unit"); Py_CLEAR(module); return NULL;
         }
 
         __s_Quantity = PyObject_GetAttrString(module, "Quantity");

wrappers/python/tests/TestAPIUnits.py

 from __future__ import division
 
 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 *
 import random
 import math
 

wrappers/python/tests/TestAmberInpcrdFile.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
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+import openmm.app.element as elem
 try:
     from scipy.io import netcdf
     SCIPY_IMPORT_FAILED = False

wrappers/python/tests/TestAmberPrmtopFile.py

@@ -2,10 +2,10 @@ import unittest
 import os
 import tempfile
 from validateConstraints import *
-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
 
 prmtop1 = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
 prmtop2 = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
@@ -377,7 +377,7 @@ class TestAmberPrmtopFile(unittest.TestCase):
 
     def testGBneckRadii(self):
         """ Tests that GBneck radii limits are correctly enforced """
-        from simtk.openmm.app.internal.customgbforces import GBSAGBnForce
+        from openmm.app.internal.customgbforces import GBSAGBnForce
         f = GBSAGBnForce()
         # Make sure legal parameters do not raise
         f.addParticle([0, 0.1, 0.5])

wrappers/python/tests/TestBytes.py

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

wrappers/python/tests/TestCharmmFiles.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
+from openmm.app import *
+from openmm import *
+from openmm.unit import *
+import openmm.app.element as elem
 import math
 import os
 import tempfile

wrappers/python/tests/TestCheckpointReporter.py

 import os
 import unittest
 import tempfile
-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
 
 
 class TestCheckpointReporter(unittest.TestCase):

wrappers/python/tests/TestDcdFile.py

 import unittest
 import tempfile
-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
 from random import random
 import os