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

@@ -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")

appveyor.yml

@@ -35,11 +35,13 @@ install:
 
 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

@@ -4,11 +4,18 @@ 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"""
 
@@ -24,14 +31,11 @@ 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),

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):
@@ -80,6 +85,8 @@ class TestNumpyCompatibility(unittest.TestCase):
         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):