Revert "Rolling back modifications that broke functional tests"

This reverts commit 68bcdf58.

MDANSE/Framework/Jobs/DynamicCoherentStructureFactor.py

@@ -127,10 +127,6 @@ class DynamicCoherentStructureFactor(IJob):
             traj = self.configuration['trajectory']['instance']
             
             qVectors = self.configuration["q_vectors"]["value"][shell]["q_vectors"]
-                        
-            qVectors = traj.universe._boxToRealPointArray(qVectors.T)
-    
-            qVectors = qVectors.T
                                                                         
             rho = {}
             for element in self.configuration['atom_selection']['unique_names']:
@@ -140,8 +136,6 @@ class DynamicCoherentStructureFactor(IJob):
             for i, frame in enumerate(self.configuration['frames']['value']):
                 
                 conf = traj.configuration[frame]
-                
-                conf.convertToBoxCoordinates()
 
                 for element,idxs in self._indexesPerElement.items():
                     selectedCoordinates = numpy.take(conf.array, idxs, axis=0)

MDANSE/Framework/OutputVariables/IOutputVariable.py

@@ -50,10 +50,6 @@ class OutputData(collections.OrderedDict):
         
         for fmt in formats:  
             REGISTRY["format"][fmt].write(basename, self, header)
-            
-    def __setitem__(self, item, value):
-        # Explicitely discard any changes on output data
-        pass
 
 class IOutputVariable(numpy.ndarray):
     '''