python 3 compatibility: removing unnecessary dict_var.keys() calls in…

… iterations; using any() to test if filter result empty; converting dict.keys() result (which has type dict_keys in python 3) to list

Sequential_WC_Simulator/core/SimulationEngine.py

@@ -107,11 +107,11 @@ def message_queues( ):
     def print_simulation_state( ):
 
         logger.debug( ' ' + '\t'.join( ['Sender', 'Message types sent'] ) )
-        for sender in MessageTypesRegistry.senders.keys():
+        for sender in MessageTypesRegistry.senders:
             logger.debug( ' ' + sender + '\t' + ', '.join( MessageTypesRegistry.senders[sender] ) )
 
         logger.debug( ' ' + '\t'.join( ['Receiver', 'Message types by priority'] ) )
-        for receiver in MessageTypesRegistry.receiver_priorities.keys():
+        for receiver in MessageTypesRegistry.receiver_priorities:
             logger.debug( ' ' + sender + '\t' + ', '.join( MessageTypesRegistry.receiver_priorities[receiver] ) )
 
     @staticmethod

Sequential_WC_Simulator/multialgorithm/CellState.py

@@ -85,7 +85,7 @@ def __init__( self, name, initial_population, initial_fluxes=None,
 
         self.population = {}
         try:
-            for specie_name in initial_population.keys():
+            for specie_name in initial_population:
                 initial_flux_given = None
                 if initial_fluxes is not None and specie_name in initial_fluxes:
                     initial_flux_given = initial_fluxes[specie_name]
@@ -112,7 +112,7 @@ def __init__( self, name, initial_population, initial_fluxes=None,
         my_level = logging.NOTSET
         if log:
             my_level = logging.DEBUG
-        for specie_name in initial_population.keys():
+        for specie_name in initial_population:
             setup_logger(specie_name, level=my_level )
             log = logging.getLogger(specie_name)
             # write log header
@@ -151,7 +151,7 @@ def handle_event( self, event_list ):
 
                 logging.getLogger( self.logger_name ).debug( 
                     "ADJUST_POPULATION_BY_DISCRETE_MODEL: {}".format( str(population_changes) ) ) 
-                for specie_name in population_changes.population_change.keys():
+                for specie_name in population_changes.population_change:
                     if not specie_name in self.population:
                         self.population[specie_name] = Specie( specie_name, 0 )
 
@@ -166,7 +166,7 @@ def handle_event( self, event_list ):
                 logging.getLogger( self.logger_name ).debug( 
                     "ADJUST_POPULATION_BY_CONTINUOUS_MODEL: {}".format( str(population_changes) ) ) 
 
-                for specie_name in population_changes.population_change.keys():
+                for specie_name in population_changes.population_change:
                     # raise exeception if an ADJUST_POPULATION_BY_CONTINUOUS_MODEL event acts on a 
                     # non-existent species because the species has no flux, and we don't want a default flux
                     if not specie_name in self.population:

Sequential_WC_Simulator/multialgorithm/shared_cell_state.py

@@ -72,10 +72,10 @@ def __init__( self, name, initial_population, initial_fluxes=None, retain_histor
 
         try:
             if initial_fluxes is not None:
-                for specie_id in initial_population.keys():
+                for specie_id in initial_population:
                     self.init_cell_state_specie( specie_id, initial_population[specie_id], initial_fluxes[specie_id] )
             else:
-                for specie_id in initial_population.keys():
+                for specie_id in initial_population:
                     self.init_cell_state_specie( specie_id, initial_population[specie_id] )
         except AssertionError as e:
             sys.stderr.write( "Cannot initialize SharedMemoryCellState: {}.\n".format( e.message ) )
@@ -100,7 +100,7 @@ def __init__( self, name, initial_population, initial_fluxes=None, retain_histor
         my_level = logging.NOTSET
         if log:
             my_level = logging.DEBUG
-            for specie_name in initial_population.keys():
+            for specie_name in initial_population:
                 setup_logger(specie_name, level=my_level )
                 log = logging.getLogger(specie_name)
                 # write log header
@@ -183,7 +183,7 @@ def history_debug(self):
             print("{}\t{}\t{}".format( len(self.history['time']), self.history['time'][0], 
                 self.history['time'][-1] ))
             print("Specie\t#values\tfirst\tlast")
-            for s in self.history['population'].keys():
+            for s in self.history['population']:
                 print("{}\t{}\t{}\t{}".format( s, len(self.history['population'][s]), 
                     self.history['population'][s][0], self.history['population'][s][-1] ))
         else:
@@ -213,7 +213,7 @@ def __check_access_time( self, time, species ):
             ValueError: if specie in species is being accessed at a time earlier than a prior access
         """
         early_accesses = filter( lambda s: time < self.last_access_time[s], species)
-        if early_accesses:
+        if any(early_accesses):
             raise ValueError( "Error: earlier access of specie(s): {}".format( early_accesses ))
 
     def __update_access_times( self, time, species ):
@@ -252,9 +252,9 @@ def adjust_discretely( self, time, adjustments ):
             ValueError: adjustment attempts to change the population of an unknown species
             ValueError: if population goes negative
         """
-        self._check_species( time, adjustments.keys() )
+        self._check_species( time, list( adjustments.keys() ) )
         self.time = time
-        for specie in adjustments.keys():
+        for specie in adjustments:
             try:
                 self.population[specie].discrete_adjustment( adjustments[specie] )
                 self.__update_access_times( time, [specie] )
@@ -274,7 +274,7 @@ def adjust_continuously( self, time, adjustments ):
             ValueError: adjustment attempts to change the population of a non-existent species
             ValueError: if population goes negative
         """
-        self._check_species( time, adjustments.keys() )
+        self._check_species( time, list( adjustments.keys() ) )
         self.time = time
 
         # record simulation state history

tests/test_CellStateMultiObj.py

@@ -141,7 +141,7 @@ def testSimulation( self ):
             )
 
         # GET_POPULATION
-        for time in pop_history_dict['get_pop'].keys():
+        for time in pop_history_dict['get_pop']:
             TestSimObj.send_event( time, cs1, GET_POPULATION, 
                 event_body=GET_POPULATION.body( set(['x']) )
             )
@@ -170,7 +170,7 @@ def testSimulationDefaultPopulation( self ):
                 event_body=ADJUST_POPULATION_BY_DISCRETE_MODEL.body( { specie:Pop_adjust } ) )
 
         # GET_POPULATION
-        for time in pop_history_dict['get_pop'].keys():
+        for time in pop_history_dict['get_pop']:
             TestSimObj.send_event( time, cs, GET_POPULATION, 
                 event_body=GET_POPULATION.body( set([ specie ]) )
             )