Python 2/3 compatibility in single code base, plus python 3 testing on travis.

plugins/drude/platforms/reference/CMakeLists.txt

@@ -71,7 +71,7 @@ ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${AP
 
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} debug ${SHARED_DRUDE_TARGET} optimized ${SHARED_DRUDE_TARGET})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 

plugins/drude/platforms/reference/tests/CMakeLists.txt

@@ -19,6 +19,6 @@ FOREACH(TEST_PROG ${TEST_PROGS})
 
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_OPENMM_DRUDE_TARGET})
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

plugins/drude/platforms/reference/tests/TestReferenceDrudeLangevinIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -171,7 +171,7 @@ void testWater() {
     int numDrudeDof = 3*numMolecules;
     int numDof = numStandardDof+numDrudeDof;
     double expectedTemp = (numStandardDof*temperature+numDrudeDof*temperatureDrude)/numDof;
-    ASSERT_USUALLY_EQUAL_TOL(expectedTemp, ke/(0.5*numDof*BOLTZ), 0.02);
+    ASSERT_USUALLY_EQUAL_TOL(expectedTemp, ke/(0.5*numDof*BOLTZ), 0.03);
 }
 
 int main() {

plugins/drude/serialization/tests/CMakeLists.txt

@@ -12,7 +12,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     # All tests use shared libraries
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_DRUDE_TARGET})
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

plugins/rpmd/CMakeLists.txt

@@ -74,11 +74,11 @@ ENDFOREACH(subdir)
 INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 
 ADD_LIBRARY(${SHARED_RPMD_TARGET} SHARED ${SOURCE_RPMD_FILES} ${SOURCE_RPMD_INCLUDE_FILES} ${API_RPMD_ABS_INCLUDE_FILES})
-SET_TARGET_PROPERTIES(${SHARED_RPMD_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_RPMD_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_RPMD_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_RPMD_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
 
 IF(OPENMM_BUILD_STATIC_LIB)
   ADD_LIBRARY(${STATIC_RPMD_TARGET} STATIC ${SOURCE_RPMD_FILES} ${SOURCE_RPMD_INCLUDE_FILES} ${API_RPMD_ABS_INCLUDE_FILES})
-  SET_TARGET_PROPERTIES(${STATIC_RPMD_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
+  SET_TARGET_PROPERTIES(${STATIC_RPMD_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
 ENDIF(OPENMM_BUILD_STATIC_LIB)
 
 # ----------------------------------------------------------------------------

plugins/rpmd/platforms/cuda/CMakeLists.txt

@@ -93,7 +93,7 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE
 IF (APPLE)
     SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA")
 ELSE (APPLE)
-    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
 ENDIF (APPLE)
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)

plugins/rpmd/platforms/cuda/tests/CMakeLists.txt

@@ -17,7 +17,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     IF (APPLE)
         SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ELSE (APPLE)
-        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+        SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ENDIF (APPLE)
     ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
     IF (OPENMM_BUILD_CUDA_DOUBLE_PRECISION_TESTS)

plugins/rpmd/platforms/opencl/CMakeLists.txt

@@ -88,7 +88,7 @@ ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${AP
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}  ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}OpenCL)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_RPMD_TARGET})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 # Ensure that links to the main OpenCL library will be resolved.

plugins/rpmd/platforms/opencl/tests/CMakeLists.txt

@@ -14,7 +14,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     # Link with shared library
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_RPMD_TARGET} ${SHARED_TARGET})
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT}Single ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
     IF (OPENMM_BUILD_OPENCL_DOUBLE_PRECISION_TESTS)
         ADD_TEST(${TEST_ROOT}Mixed ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} mixed)

plugins/rpmd/platforms/reference/CMakeLists.txt

@@ -71,7 +71,7 @@ ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${AP
 
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_RPMD_TARGET})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 

plugins/rpmd/platforms/reference/tests/CMakeLists.txt

@@ -19,6 +19,6 @@ FOREACH(TEST_PROG ${TEST_PROGS})
 
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
     TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_OPENMM_RPMD_TARGET})
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

serialization/tests/CMakeLists.txt

@@ -15,7 +15,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     ELSE (OPENMM_BUILD_SHARED_LIB)
         TARGET_LINK_LIBRARIES(${TEST_ROOT} ${STATIC_TARGET})
     ENDIF (OPENMM_BUILD_SHARED_LIB)
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

tests/CMakeLists.txt

@@ -21,7 +21,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     IF ((${TEST_ROOT} MATCHES TestVectorize8) AND NOT (MSVC OR ANDROID OR PNACL))
         SET(EXTRA_TEST_FLAGS "${EXTRA_COMPILE_FLAGS} -mavx")
     ENDIF ((${TEST_ROOT} MATCHES TestVectorize8) AND NOT (MSVC OR ANDROID OR PNACL))
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_TEST_FLAGS}" COMPILE_FLAGS "${EXTRA_TEST_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_TEST_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 ENDFOREACH(TEST_PROG ${TEST_PROGS})
 

wrappers/python/setup.py

@@ -122,11 +122,6 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                            build_info=BUILD_INFO):
     from distutils.core import Extension
     setupKeywords = {}
-    try:
-        from distutils.command.build_py import build_py_2to3 as build_py
-    except ImportError:
-        from distutils.command.build_py import build_py
-    setupKeywords["cmdclass"]          = {'build_py': build_py}
     setupKeywords["name"]              = "OpenMM"
     setupKeywords["version"]           = "%s.%s.%s" % (major_version_num,
                                                        minor_version_num,

wrappers/python/simtk/openmm/__init__.py

@@ -4,11 +4,12 @@ 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"
 
 import os, os.path
 import sys
-from simtk.openmm import version
+from . import version
 
 if sys.platform == 'win32':
     _path = os.environ['PATH']

wrappers/python/simtk/openmm/amd.py

@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 

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

@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 

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

@@ -28,6 +28,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
 __author__ = "Peter Eastman"
 __version__ = "1.0"
 
@@ -35,8 +36,8 @@ from math import sqrt
 from simtk.openmm.app import Topology
 from simtk.openmm.app import PDBFile
 from simtk.openmm.app.internal import amber_file_parser
-import forcefield as ff
-import element as elem
+from . import forcefield as ff
+from . import element as elem
 import simtk.unit as unit
 import simtk.openmm as mm
 from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors

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

@@ -33,6 +33,8 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
+from __future__ import print_function
 
 from simtk.openmm.app.internal.charmm.exceptions import CharmmFileError
 import simtk.unit as u
@@ -117,7 +119,7 @@ class CharmmCrdFile(object):
                                        len(self.positions))
                 )
 
-        except (ValueError, IndexError), e:
+        except (ValueError, IndexError) as e:
             raise CharmmFileError('Error parsing CHARMM coordinate file')
 
         # Apply units to the positions now. Do it this way to allow for
@@ -197,7 +199,7 @@ class CharmmRstFile(object):
                         self.jhstrt = int(line[5])    # Num total steps?
                         break
                    
-                    except (ValueError, IndexError), e:
+                    except (ValueError, IndexError) as e:
                         raise CharmmFileError('Problem parsing CHARMM restart')
 
         self._scan(crdfile, '!XOLD')
@@ -255,9 +257,9 @@ class CharmmRstFile(object):
 
     def printcoords(self, crds):
         for crd in range(len(crds)):
-            print crds[crd],
+            print(crds[crd], end=' ')
             if not (crd+1) % 3:
-                print '\n',
+                print('\n', end=' ')
 
 if __name__ == '__main__':
     import doctest

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

@@ -33,6 +33,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
 OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
 USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
+from __future__ import absolute_import
 import os
 from simtk.openmm.app.internal.charmm._charmmfile import (
             CharmmFile, CharmmStreamFile)
@@ -428,7 +429,7 @@ class CharmmParameterSet(object):
                     # soldier on
                     if not read_first_nonbonded: continue
                     raise CharmmFileError('Could not parse nonbonded terms.')
-                except CharmmFileError, e:
+                except CharmmFileError as e:
                     if not read_first_nonbonded: continue
                     raise CharmmFileError(str(e))
                 else:
@@ -587,7 +588,7 @@ class CharmmParameterSet(object):
         # multiterm dihedral have to have a DIFFERENT periodicity, we don't have
         # to condense _within_ a single list of torsions assigned to the same
         # key (they're guaranteed to be different)
-        keylist = self.dihedral_types.keys()
+        keylist = list(self.dihedral_types.keys())
         for i in range(len(keylist) - 1):
             key1 = keylist[i]
             for dihedral in self.dihedral_types[key1]:
@@ -606,7 +607,7 @@ class CharmmParameterSet(object):
         Parameter:
             - typedict : Type dictionary to condense
         """
-        keylist = typedict.keys()
+        keylist = list(typedict.keys())
         for i in range(len(keylist) - 1):
             key1 = keylist[i]
             for j in range(i+1, len(keylist)):