Eliminate extra warning about overriding the warning level

Clean up

Fix OpenCL platform on low-end devices

Close file before deleting in TestAmberPrmtopFile.py

Close PDBx file before deleting to fix windows test failure in TestPDbxFile.py

Fix test checkpoint reporter close file before repoening

Add bytes typemap

Update appveyor.yml

Fix exit status

Supress 4305 and 4244 warnings

Print the last failed tests output

Make numpy optional in test

Improve scipy skip too

Refactor TestCheckpointReporter.py to not require numpy

test on the proper file

Remove annoying -V

.travis.yml

@@ -41,11 +41,11 @@ script:
   - # Run the testInstallation script
   - python -m simtk.testInstallation
   - # run all of the tests, making sure failures at this stage don't cause travis failures
-  - ctest -j2 -V || true
+  - ctest -j2 || true
   - # get a list of all of the failed tests into this stupid ctest format
   - python -c 'fn = "Testing/Temporary/LastTestsFailed.log"; import os; os.path.exists(fn) or exit(0); l = [line.split(":")[0] for line in open(fn)]; triplets = zip(l, l, [","]*len(l)); print "".join(",".join(t) for t in triplets)' > FailedTests.log
   - # rerun all of the failed tests
-  - if [ -s FailedTests.log ]; then ctest -V -I FailedTests.log; fi;
+  - if [ -s Testing/Temporary/LastTestsFailed.log ]; then ctest -I FailedTests.log; fi;
   - # run the python tests too
   - cd python/tests
   - pip install nose

CMakeLists.txt

 #---------------------------------------------------
-# OpenMM 
+# OpenMM
 #
 # Creates OpenMM library.
 #
@@ -43,11 +43,11 @@ SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake_modules")
 # (cmake 2.4.7 is OK)
 if(COMMAND cmake_policy)
     if(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5)
-        cmake_policy(SET CMP0003 NEW) 
-        cmake_policy(SET CMP0005 NEW) 
+        cmake_policy(SET CMP0003 NEW)
+        cmake_policy(SET CMP0005 NEW)
     endif(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5)
     if(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2)
-        cmake_policy(SET CMP0011 NEW) 
+        cmake_policy(SET CMP0011 NEW)
     endif(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2)
 endif(COMMAND cmake_policy)
 
@@ -70,7 +70,7 @@ ENDIF (ANDROID)
 # It seems that on linux and mac, everything is trying to be installed in /usr/local/openmm
 # But if every install target is prefixed with /openmm/, on Windows the install files
 # end up in C:/Program Files/OpenMM/openmm/ which is ugly.
-# Better to set CMAKE_INSTALL_PREFIX to /usr/local/openmm and leave /openmm/ off the 
+# Better to set CMAKE_INSTALL_PREFIX to /usr/local/openmm and leave /openmm/ off the
 # install target names.  Plus, the user now has the opportunity to install into /usr/local/
 # if she so chooses.  --cmb
 IF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
@@ -122,7 +122,10 @@ ELSE (APPLE AND (NOT PNACL))
     IF (MSVC OR ANDROID OR PNACL)
         SET(EXTRA_COMPILE_FLAGS)
         IF (MSVC)
+            # Use warning level 2, not whatever warning level CMake picked.
             STRING(REGEX REPLACE "/W[0-4]" "/W2" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+            # Explicitly suppress warnings 4305 and 4244.
+            SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4305 /wd4244")
         ENDIF (MSVC)
     ELSE (MSVC OR ANDROID OR PNACL)
         SET(EXTRA_COMPILE_FLAGS "-msse2")
@@ -142,7 +145,7 @@ IF (NOT CMAKE_CXX_FLAGS_RELEASE)
         SET(CMAKE_CXX_FLAGS_RELEASE "-mfloat-abi=softfp -march=armv7-a -mfpu=neon -funsafe-math-optimizations -O3 -DNDEBUG" CACHE STRING
         "To use when CMAKE_BUILD_TYPE=Release" FORCE)
     ELSE (ANDROID)
-        SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING 
+        SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING
         "To use when CMAKE_BUILD_TYPE=Release" FORCE)
     ENDIF (ANDROID)
 ENDIF (NOT CMAKE_CXX_FLAGS_RELEASE)
@@ -205,11 +208,11 @@ SET(STATIC_TARGET ${OPENMM_LIBRARY_NAME}_static)
 ## If no one says otherwise, change the executable path to drop into the same binary
 ## location as the DLLs so that the test cases will use the just-build DLLs.
 IF(NOT EXECUTABLE_OUTPUT_PATH)
-  SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR} 
+  SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}
       CACHE INTERNAL "Single output directory for building all executables.")
 ENDIF(NOT EXECUTABLE_OUTPUT_PATH)
 IF(NOT LIBRARY_OUTPUT_PATH)
-  SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR} 
+  SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}
       CACHE INTERNAL "Single output directory for building all libraries.")
 ENDIF(NOT LIBRARY_OUTPUT_PATH)
 SET(${PROJECT_NAME}_EXECUTABLE_DIR ${EXECUTABLE_OUTPUT_PATH}/${CMAKE_CFG_INTDIR})
@@ -224,7 +227,7 @@ SET(API_INCLUDE_DIRS) # start empty
 FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
     # append
     SET(API_INCLUDE_DIRS ${API_INCLUDE_DIRS}
-                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include 
+                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include
                          ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/openmm
                          ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/openmm/internal)
 ENDFOREACH(subdir)
@@ -364,7 +367,7 @@ IF(CUDA_FOUND)
     SET(OPENMM_BUILD_CUDA_LIB ON CACHE BOOL "Build OpenMMCuda library for Nvidia GPUs")
 
     # I wish I was not hardcoding /MD here
-    # Avoid strange windows link error with cuda free energy 
+    # Avoid strange windows link error with cuda free energy
     # plugin by specifying /MD to CUDA_NVCC_FLAGS
     MARK_AS_ADVANCED(CLEAR CUDA_NVCC_FLAGS)
     IF(MSVC)
@@ -380,7 +383,7 @@ IF(CUDA_FOUND)
             if(CUDA_NVCC_FLAGS)
                 set(new_flags "${CUDA_NVCC_FLAGS};${new_flags}")
             endif(CUDA_NVCC_FLAGS)
-            SET(CUDA_NVCC_FLAGS "${new_flags}" 
+            SET(CUDA_NVCC_FLAGS "${new_flags}"
                 CACHE STRING "Semicolon delimit multiple arguments" FORCE)
         ENDIF(NOT HAS_NVCC_FLAG)
     ENDIF(MSVC)

appveyor.yml

@@ -32,14 +32,16 @@ install:
 # Run the build
   - jom install
   - jom PythonInstall
-  
+
 build: false
 test_script:
-  - ctest && exit 0
-  - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); l = [line.split(':')[0] for line in open(fn)]; triplets = zip(l, l, [',']*len(l)); print(''.join(','.join(t) for t in triplets))" > FailedTests.log
+  - ctest || exit 0
+  - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
   - ps: >
-     If (Test-Path "FailedTests.log") {
-         ctest -V -I FailedTests.log
+     If (Test-Path "Testing\\Temporary\\LastTestsFailed.log") {
+         cat Testing\\Temporary\\LastTestsFailed.log
+         cat FailedTests.log
+         ctest -I FailedTests.log
      }
   - cd python\tests
   - nosetests -vv --processes=-1 --process-timeout=200

wrappers/python/tests/TestAmberInpcrdFile.py

@@ -4,14 +4,21 @@ from simtk.openmm.app import *
 from simtk.openmm import *
 from simtk.unit import *
 import simtk.openmm.app.element as elem
+try:
+    from scipy.io import netcdf
+    SCIPY_IMPORT_FAILED = False
+except:
+    SCIPY_IMPORT_FAILED = True
+
 
 def compareByElement(array1, array2, cmp):
     for x, y in zip(array1, array2):
         cmp(x, y)
 
+
 class TestAmberInpcrdFile(unittest.TestCase):
     """Test the Amber inpcrd file parser"""
- 
+
     def test_CrdVelBox(self):
         """ Test parsing ASCII restarts with crds, vels, and box """
         cmp = self.assertAlmostEqual
@@ -24,24 +31,21 @@ class TestAmberInpcrdFile(unittest.TestCase):
         compareByElement(inpcrd.boxVectors[0].value_in_unit(angstroms),
                          [30.2642725, 0.0, 0.0], cmp)
 
+    @unittest.skipIf(SCIPY_IMPORT_FAILED, "Scipy is not installed")
     def test_NetCDF(self):
         """ Test NetCDF restart file parsing """
         cmp = self.assertAlmostEqual
-        try:
-            from scipy.io import netcdf
-        except ImportError:
-            print('Not testing NetCDF file parser... scipy cannot be found')
-        else:
-            inpcrd = AmberInpcrdFile('systems/amber.ncrst')
-            self.assertEqual(len(inpcrd.positions), 2101)
-            compareByElement(inpcrd.positions[0].value_in_unit(angstroms),
-                             [6.82122492718229, 6.6276250662042, -8.51668999892245],
-                             cmp)
-            compareByElement(inpcrd.velocities[-1].value_in_unit(angstroms/picosecond),
-                             [0.349702202733541*20.455, 0.391525333168534*20.455,
-                              0.417941679767662*20.455], cmp)
-            self.assertAlmostEqual(inpcrd.boxVectors[0][0].value_in_unit(angstroms),
-                                   30.2642725, places=6)
+
+        inpcrd = AmberInpcrdFile('systems/amber.ncrst')
+        self.assertEqual(len(inpcrd.positions), 2101)
+        compareByElement(inpcrd.positions[0].value_in_unit(angstroms),
+                         [6.82122492718229, 6.6276250662042, -8.51668999892245],
+                         cmp)
+        compareByElement(inpcrd.velocities[-1].value_in_unit(angstroms/picosecond),
+                         [0.349702202733541*20.455, 0.391525333168534*20.455,
+                          0.417941679767662*20.455], cmp)
+        self.assertAlmostEqual(inpcrd.boxVectors[0][0].value_in_unit(angstroms),
+                               30.2642725, places=6)
 
     def test_CrdBox(self):
         """ Test parsing ASCII restarts with only crds and box """

wrappers/python/tests/TestCheckpointReporter.py

 import os
 import unittest
 import tempfile
-import numpy as np
 from simtk.openmm import app
 import simtk.openmm as mm
 from simtk import unit
@@ -24,17 +23,19 @@ class TestCheckpointReporter(unittest.TestCase):
         self.simulation.step(1)
 
         # get the current positions
-        positions = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)._value
+        positions = self.simulation.context.getState(getPositions=True).getPositions()
+
         # now set the positions into junk...
-        self.simulation.context.setPositions(np.random.random(positions.shape))
+        self.simulation.context.setPositions([mm.Vec3(0, 0, 0)] * len(positions))
+
         # then reload the right positions from the checkpoint
         file.close()
         with open(file.name, 'rb') as f:
             self.simulation.context.loadCheckpoint(f.read())
         os.unlink(file.name)
 
-        newPositions = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)._value
-        np.testing.assert_array_equal(positions, newPositions)
+        newPositions = self.simulation.context.getState(getPositions=True).getPositions()
+        self.assertSequenceEqual(positions, newPositions)
 
 if __name__ == '__main__':
     unittest.main()

wrappers/python/tests/TestNumpyCompatibility.py

 import unittest
-import numpy as np
-
 from simtk.openmm import app
 import simtk.openmm as mm
 from simtk import unit
+try:
+    import numpy as np
+    NUMPY_IMPORT_FAILED = False
+except ImportError:
+    NUMPY_IMPORT_FAILED = True
+
 
+@unittest.skipIf(NUMPY_IMPORT_FAILED, 'Numpy is not installed')
 class TestNumpyCompatibility(unittest.TestCase):
-    
+
     def setUp(self):
         prmtop = app.AmberPrmtopFile('systems/water-box-216.prmtop')
-    
-        system = prmtop.createSystem(nonbondedMethod=app.PME, 
+
+        system = prmtop.createSystem(nonbondedMethod=app.PME,
                                          nonbondedCutoff=0.9*unit.nanometers,
-                                         constraints=app.HBonds, rigidWater=True, 
+                                         constraints=app.HBonds, rigidWater=True,
                                          ewaldErrorTolerance=0.0005)
-        integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picoseconds, 
+        integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picoseconds,
                                            2.0*unit.femtoseconds)
         self.simulation = app.Simulation(prmtop.topology, system, integrator,
                                     mm.Platform.getPlatformByName('Reference'))
-    
-    
+
+
     def test_setPositions(self):
         n_particles = self.simulation.context.getSystem().getNumParticles()
         input = np.random.randn(n_particles, 3)
         self.simulation.context.setPositions(input)
         output = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)
-    
+
         np.testing.assert_array_almost_equal(input, output)
-    
+
     def test_setPositions_units(self):
         n_particles = self.simulation.context.getSystem().getNumParticles()
         input = unit.Quantity(np.random.randn(n_particles, 3), unit.angstroms)
         self.simulation.context.setPositions(input)
         output = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)
-    
+
         np.testing.assert_array_almost_equal(input.value_in_unit(unit.nanometers), output.value_in_unit(unit.nanometers))
-    
-    
+
+
     def test_setVelocities(self):
         n_particles = self.simulation.context.getSystem().getNumParticles()
         input = np.random.randn(n_particles, 3)
         self.simulation.context.setVelocities(input)
         output = self.simulation.context.getState(getVelocities=True).getVelocities(asNumpy=True)
-    
+
         np.testing.assert_array_almost_equal(input, output)
-    
+
     def test_setVelocities_units(self):
         n_particles = self.simulation.context.getSystem().getNumParticles()
         input = unit.Quantity(np.random.randn(n_particles, 3), unit.angstroms / unit.femtoseconds)
         self.simulation.context.setVelocities(input)
         output = self.simulation.context.getState(getVelocities=True).getVelocities(asNumpy=True)
-    
+
         np.testing.assert_array_almost_equal(input.value_in_unit(unit.angstroms / unit.femtoseconds),
                                              output.value_in_unit(unit.angstroms / unit.femtoseconds))
-    
-    
+
+
     def test_tabulatedFunction(self):
         f = mm.CustomNonbondedForce('g(r)')
-    
+
         r = np.linspace(0,10)
         g_of_r = np.sin(r)
-    
-        indx = f.addFunction('g', g_of_r, np.min(r), np.max(r)) 
-    
+
+        indx = f.addFunction('g', g_of_r, np.min(r), np.max(r))
+
         name, g_of_r_out, min_r_out, max_r_out = f.getFunctionParameters(indx)
-    
+
         np.testing.assert_array_almost_equal(g_of_r, np.asarray(g_of_r_out))
         assert min_r_out == np.min(r)
         assert max_r_out == np.max(r)
-    
+
     def test_CMAP(self):
         f = mm.CMAPTorsionForce()
         energy = np.random.randn(10*10)
@@ -76,10 +81,12 @@ class TestNumpyCompatibility(unittest.TestCase):
         size, energy_out = f.getMapParameters(0)
         energy_out = energy_out.value_in_unit_system(unit.md_unit_system)
 
-    
+
         self.assertEqual(size, 10)
         np.testing.assert_array_almost_equal(energy, np.asarray(energy_out))
 
+
+@unittest.skipIf(NUMPY_IMPORT_FAILED, 'Numpy is not installed')
 class TestNumpyUnits(unittest.TestCase):
 
     def setUp(self):