Refactor/context/deprecate init status (#745)

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* • Log
  LogCondition - subset of ContextFlags used to specified logPref

• Context
  ContextFlags - implemented as common set of context flags for:
  - initialization
  - execution tracking
  - logging
  ContextStatus - aliases to ContextFlags (for backward compatibility)

* • Log
  LogCondition - subset of ContextFlags used to specified logPref

• Context
  ContextFlags - implemented as common set of context flags for:
  - initialization
  - execution tracking
  - logging
  ContextStatus - aliases to ContextFlags (for backward compatibility)

* • Log
  LogCondition - subset of ContextFlags used to specified logPref

• Context
  ContextFlags - implemented as common set of context flags for:
  - initialization
  - execution tracking
  - logging
  ContextStatus - aliases to ContextFlags (for backward compatibility)

* -

* -

* -

* -

* -

* • Context
  context.status replaced with specific field assignments
  (.initialization_phase, .execution_phase, and .source)

* • Context
  context.status replaced with specific field assignments
  (.initialization_phase, .execution_phase, and .source)

* • Context
  context.status replaced with specific field assignments
  (.initialization_phase, .execution_phase, and .source)

* -

* -

* • Context
  context.status replaced with specific field assignments
  (.initialization_phase, .execution_phase, and .source)

* -

* -

* -

* -

* -

* -

* Merge branches 'devel' and 'refactor/context/structured' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/context/structured

# Conflicts:
#	.idea/runConfigurations/Tests.xml
#	Scripts/McClure.py

* Merge branches 'devel' and 'refactor/context/structured' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/context/structured

# Conflicts:
#	.idea/runConfigurations/Tests.xml
#	Scripts/McClure.py

* -

* -

* • Context
  - consolidated init_status into context.initialization_status

* • Context
  - consolidated init_status into context.initialization_status

* • Context
  - consolidated init_status into context.initialization_status

psyneulink/components/component.py

@@ -862,7 +862,7 @@ def __init__(self,
         # # MODIFIED 8/14/16 NEW:
         # # PROBLEM: variable has different name for different classes;  need to standardize name across classes
         # try:
-        #     if self.init_status is InitStatus.DEFERRED_INITIALIZATION:
+        #     if self.initialization_status is ContextFlags.DEFERRED_INITIALIZATION:
         #         defer_init = True
         # except AttributeError:
         #     pass
@@ -878,8 +878,8 @@ def __init__(self,
         self.context.source = ContextFlags.COMPONENT
         self.context.string = context + INITIALIZING + ": " + COMPONENT_INIT
 
-        self.init_status = InitStatus.UNSET
-        # self.init_status = InitStatus.INITIALIZING
+        # self.context.initialization_status = ContextFlags.INITIALIZING
+        self.context.initialization_status = ContextFlags.UNSET
 
         defaults = self.ClassDefaults.values().copy()
         if param_defaults is not None:
@@ -1001,7 +1001,7 @@ def __init__(self,
         #    (e.g., instantiate_output_state in Mechanism)
         self._instantiate_attributes_after_function(context=context)
 
-        self.init_status = InitStatus.INITIALIZED
+        self.context.initialization_status = ContextFlags.INITIALIZED
 
     def __repr__(self):
         return '({0} {1})'.format(type(self).__name__, self.name)
@@ -1168,12 +1168,12 @@ def checkAndCastInt(x):
     def _deferred_init(self, context=None):
         """Use in subclasses that require deferred initialization
         """
-        if self.init_status is InitStatus.DEFERRED_INITIALIZATION:
+        if self.context.initialization_status == ContextFlags.DEFERRED_INIT:
 
             # Flag that object is now being initialized
             # Note: self.value will be resolved to the object's value as part of initialization
             #       (usually in _instantiate_function)
-            self.init_status = InitStatus.INITIALIZING
+            self.context.initialization_status = ContextFlags.INITIALIZING
 
             del self.init_args['self']
 
@@ -1206,7 +1206,7 @@ def _deferred_init(self, context=None):
             else:
                 self._assign_default_name()
 
-            self.init_status = InitStatus.INITIALIZED
+            self.context.initialization_status = ContextFlags.INITIALIZED
 
     def _assign_deferred_init_name(self, name, context):
 
@@ -2913,20 +2913,6 @@ def size(self):
             s.append(len(v[i]))
         return np.array(s)
 
-    # @property
-    # def init_status(self):
-    #     try:
-    #         return self._init_status
-    #     except AttributeError:
-    #         return InitStatus.UNSET
-    #
-    # @init_status.setter
-    # def init_status(self, value):
-    #     if not isinstance(value, InitStatus):
-    #         raise ComponentError("PROGRAM ERROR:  Attempt to assign \'init_status\' attribute of {} "
-    #                              "a value ({}) other than one of InitStatus".format(self.name, value))
-    #     self._init_status = value
-
     @property
     def prefs(self):
         # Whenever pref is accessed, use current owner as context (for level checking)
@@ -3078,7 +3064,7 @@ def log(self):
         try:
             return self._log
         except AttributeError:
-            if self.init_status is InitStatus.DEFERRED_INITIALIZATION:
+            if self.context.initialization_status == ContextFlags.DEFERRED_INIT:
                 raise ComponentError("Initialization of {} is deferred; try assigning {} after it is complete "
                                      "or appropriately configuring a system to which it belongs".
                                      format(self.name, 'log'))

psyneulink/components/mechanisms/adaptive/gating/gatingmechanism.py

@@ -171,6 +171,7 @@
 from psyneulink.components.mechanisms.mechanism import Mechanism_Base
 from psyneulink.components.states.modulatorysignals.gatingsignal import GatingSignal
 from psyneulink.components.states.state import State_Base, _parse_state_spec
+from psyneulink.globals.context import ContextFlags
 from psyneulink.globals.defaults import defaultGatingPolicy
 from psyneulink.globals.keywords import \
     GATING, GATING_POLICY, GATING_PROJECTION, GATING_PROJECTIONS, GATING_SIGNAL, GATING_SIGNALS, GATING_SIGNAL_SPECS, \
@@ -547,7 +548,7 @@ def _assign_as_gating_mechanism(self, context=None):
             for state in mech._input_states + mech._output_states:
                 for projection in state.mod_afferents:
                     # If projection was deferred for init, initialize it now and instantiate for self
-                    if (projection.init_status is InitStatus.DEFERRED_INITIALIZATION
+                    if (projection.context.initialization_status == ContextFlags.DEFERRED_INIT
                         and projection.init_args['sender'] is None):
                         # FIX 5/23/17: MODIFY THIS WHEN (param, GatingProjection) tuple
                         # FIX:         IS REPLACED WITH (param, GatingSignal) tuple

psyneulink/components/mechanisms/adaptive/learning/learningmechanism.py

@@ -930,7 +930,8 @@ def __init__(self,
         # delete self.init_args[ERROR_SOURCES]
 
         # # Flag for deferred initialization
-        # self.init_status = InitStatus.DEFERRED_INITIALIZATION
+        # self.context.initialization_status = ContextFlags.DEFERRED_INIT
+        # self.initialization_status = ContextFlags.DEFERRED_INIT
 
         self._learning_rate = learning_rate
 

psyneulink/components/mechanisms/mechanism.py

@@ -1433,7 +1433,7 @@ def _handle_arg_input_states(self, input_states):
                 except KeyError:
                     pass
             elif isinstance(parsed_spec, (Projection, Mechanism, State)):
-                if parsed_spec.init_status is InitStatus.DEFERRED_INITIALIZATION:
+                if parsed_spec.context.initialization_status == ContextFlags.DEFERRED_INIT:
                     args = parsed_spec.init_args
                     # MODIFIED 2/21/18 OLD:
                     if REFERENCE_VALUE in args and args[REFERENCE_VALUE] is not None:
@@ -1980,7 +1980,10 @@ def execute(self,
             # These need to be set for states to use as context
             self.context.string = context
             if not INITIALIZING in context: # cxt-set
-                self.context.initialization_status &= ~ContextFlags.INITIALIZING
+                # FIX: 3/31/18 - THIS SHOULD BE MOVED TO END OF __init__ METHOD(S)
+                # self.context.initialization_status &= ~ContextFlags.INITIALIZING
+                # self.context.initialization_status = ContextFlags.INITIALIZED
+
                 if EXECUTING in context:
                     self.context.execution_phase = ContextFlags.PROCESSING
                 if LEARNING in context:

psyneulink/components/mechanisms/processing/objectivemechanism.py

@@ -332,6 +332,7 @@
 from psyneulink.components.mechanisms.processing.processingmechanism import ProcessingMechanism_Base
 from psyneulink.components.states.outputstate import OutputState, PRIMARY, standard_output_states
 from psyneulink.components.states.state import _parse_state_spec
+from psyneulink.globals.context import ContextFlags
 from psyneulink.globals.keywords import PARAMS, PROJECTION, PROJECTIONS, CONTROL, DEFAULT_MATRIX, DEFAULT_VARIABLE, \
     EXPONENT, EXPONENTS, FUNCTION, \
     INPUT_STATES, LEARNING, MATRIX, NAME, OBJECTIVE_MECHANISM, SENDER, STATE_TYPE, VARIABLE, WEIGHT, WEIGHTS, \
@@ -657,7 +658,7 @@ def _instantiate_input_states(self, monitored_output_states_specs=None, referenc
         """
         from psyneulink.components.states.inputstate import InputState
         # If call is for initialization
-        if self.init_status is InitStatus.UNSET:
+        if self.context.initialization_status == ContextFlags.UNSET:
             # Use self.input_states (containing specs from **input_states** arg of constructor) or default InputState
             input_states = self.input_states or [{STATE_TYPE: InputState, VARIABLE: [0]}]
             return super()._instantiate_input_states(input_states=input_states, context=context)
@@ -858,7 +859,7 @@ def _instantiate_monitoring_projections(owner,
         if isinstance(sender, OutputState):
             # Projection has been specified for receiver and initialization begun, so call deferred_init()
             if receiver.path_afferents:
-                if not receiver.path_afferents[0].init_status is InitStatus.DEFERRED_INITIALIZATION:
+                if not receiver.path_afferents[0].context.initialization_status == ContextFlags.DEFERRED_INIT:
                     raise ObjectiveMechanismError("PROGRAM ERROR: {} of {} already has an afferent projection "
                                                   "implemented and initialized ({})".
                                                   format(receiver.name, owner.name, receiver.path_afferents[0].name))

psyneulink/components/process.py

@@ -1449,17 +1449,18 @@ def _parse_and_instantiate_projection_entries(self, pathway, context=None):
 
                         # If initialization of MappingProjection has been deferred,
                         #    check sender and receiver, assign them if they have not been assigned, and initialize it
-                        if item.init_status is InitStatus.DEFERRED_INITIALIZATION:
+                        if item.context.initialization_status == ContextFlags.DEFERRED_INIT:
                             # Check sender arg
                             try:
                                 sender_arg = item.init_args[SENDER]
                             except AttributeError:
-                                raise ProcessError("PROGRAM ERROR: init_status of {} is {} but it does not have init_args".
-                                                   format(item, InitStatus.DEFERRED_INITIALIZATION))
+                                raise ProcessError("PROGRAM ERROR: initialization_status of {} is {} "
+                                                   "but it does not have init_args".
+                                                   format(item, ContextFlags.DEFERRED_INIT.name))
                             except KeyError:
-                                raise ProcessError("PROGRAM ERROR: Value of {} is {} "
-                                                   "but init_args does not have entry for {}".
-                                                   format(item.init_args[NAME], InitStatus.DEFERRED_INITIALIZATION, SENDER))
+                                raise ProcessError("PROGRAM ERROR: Value of {} is {} but "
+                                                   "init_args does not have entry for {}".
+                                                   format(item.init_args[NAME],ContextFlags.DEFERRED_INIT.name, SENDER))
                             else:
                                 # If sender is not specified for the Projection,
                                 #    assign mechanism that precedes in pathway
@@ -1475,12 +1476,15 @@ def _parse_and_instantiate_projection_entries(self, pathway, context=None):
                             try:
                                 receiver_arg = item.init_args[kwReceiverArg]
                             except AttributeError:
-                                raise ProcessError("PROGRAM ERROR: init_status of {} is {} but it does not have init_args".
-                                                   format(item, InitStatus.DEFERRED_INITIALIZATION))
+                                raise ProcessError("PROGRAM ERROR: initialization_status of {} is {} "
+                                                   "but it does not have init_args".
+                                                   format(item, ContextFlags.DEFERRED_INIT))
                             except KeyError:
-                                raise ProcessError("PROGRAM ERROR: init_status of {} is {} "
+                                raise ProcessError("PROGRAM ERROR: initialization_status of {} is {} "
                                                    "but init_args does not have entry for {}".
-                                                   format(item.init_args[NAME], InitStatus.DEFERRED_INITIALIZATION, kwReceiverArg))
+                                                   format(item.init_args[NAME],
+                                                          ContextFlags.DEFERRED_INIT,
+                                                          kwReceiverArg))
                             else:
                                 # If receiver is not specified for the Projection,
                                 #    assign mechanism that follows it in the pathway

psyneulink/components/projections/modulatory/controlprojection.py

@@ -106,6 +106,7 @@
 from psyneulink.components.projections.modulatory.modulatoryprojection import ModulatoryProjection_Base
 from psyneulink.components.projections.projection import ProjectionError, Projection_Base, projection_keywords
 from psyneulink.components.shellclasses import Mechanism, Process_Base
+from psyneulink.globals.context import ContextFlags
 from psyneulink.globals.defaults import defaultControlAllocation
 from psyneulink.globals.keywords import CONTROL, CONTROL_PROJECTION, CONTROL_SIGNAL, PARAMETER_STATE, PROJECTION_SENDER
 from psyneulink.globals.preferences.componentpreferenceset import is_pref_set
@@ -298,10 +299,10 @@ def __init__(self,
                                                   params=params)
 
         # If receiver has not been assigned, defer init to State.instantiate_projection_to_state()
-        if (sender is None or sender.init_status is InitStatus.DEFERRED_INITIALIZATION or
+        if (sender is None or sender.context.initialization_status == ContextFlags.DEFERRED_INIT or
                 inspect.isclass(receiver) or receiver is None or
-                    receiver.init_status is InitStatus.DEFERRED_INITIALIZATION):
-            self.init_status = InitStatus.DEFERRED_INITIALIZATION
+                    receiver.context.initialization_status == ContextFlags.DEFERRED_INIT):
+            self.context.initialization_status = ContextFlags.DEFERRED_INIT
 
         # Validate sender (as variable) and params, and assign to variable and paramInstanceDefaults
         # Note: pass name of mechanism (to override assignment of componentName in super.__init__)

psyneulink/components/projections/modulatory/gatingprojection.py

@@ -95,6 +95,7 @@
 from psyneulink.components.projections.modulatory.modulatoryprojection import ModulatoryProjection_Base
 from psyneulink.components.projections.projection import ProjectionError, Projection_Base, projection_keywords
 from psyneulink.components.shellclasses import Mechanism, Process_Base
+from psyneulink.globals.context import ContextFlags
 from psyneulink.globals.defaults import defaultGatingPolicy
 from psyneulink.globals.keywords import FUNCTION_OUTPUT_TYPE, GATING, GATING_MECHANISM, GATING_PROJECTION, GATING_SIGNAL, INITIALIZING, INPUT_STATE, OUTPUT_STATE, PROJECTION_SENDER
 from psyneulink.globals.preferences.componentpreferenceset import is_pref_set
@@ -288,7 +289,7 @@ def __init__(self,
         # If receiver has not been assigned, defer init to State.instantiate_projection_to_state()
         if sender is None or receiver is None:
             # Flag for deferred initialization
-            self.init_status = InitStatus.DEFERRED_INITIALIZATION
+            self.context.initialization_status = ContextFlags.DEFERRED_INIT
 
         # Validate sender (as variable) and params, and assign to variable and paramInstanceDefaults
         # Note: pass name of mechanism (to override assignment of componentName in super.__init__)

psyneulink/components/projections/modulatory/learningprojection.py

@@ -450,7 +450,7 @@ def __init__(self,
         # If receiver has not been assigned, defer init to State.instantiate_projection_to_state()
         if sender is None or receiver is None:
             # Flag for deferred initialization
-            self.init_status = InitStatus.DEFERRED_INITIALIZATION
+            self.context.initialization_status = ContextFlags.DEFERRED_INIT
         super().__init__(sender=sender,
                          receiver=receiver,
                          weight=weight,
@@ -617,8 +617,8 @@ def _execute(self, variable, runtime_params=None, context=None):
         runtime_params = runtime_params or {}
 
         # Pass during initialization (since has not yet been fully initialized
-        if self.init_status is InitStatus.DEFERRED_INITIALIZATION:
-            return self.init_status
+        if self.context.initialization_status == ContextFlags.DEFERRED_INIT:
+            return self.context.initialization_status
 
         # if self.learning_rate:
         #     runtime_params.update({SLOPE:self.learning_rate})

psyneulink/components/projections/modulatory/modulatoryprojection.py

@@ -229,17 +229,18 @@ def _assign_default_projection_name(self, state=None, sender_name=None, receiver
 
         template = "{} for {}[{}]"
 
-        if self.init_status in {InitStatus.INITIALIZED, InitStatus.INITIALIZING, InitStatus.UNSET}:
+        if self.context.initialization_status &  \
+                (ContextFlags.INITIALIZED | ContextFlags.INITIALIZING | ContextFlags.UNSET):
             # If the name is not a default name for the class, return
             if not self.className + '-' in self.name:
                 return self.name
             self.name = template.format(self.className, self.receiver.owner.name, self.receiver.name)
 
-        elif self.init_status is InitStatus.DEFERRED_INITIALIZATION:
+        elif self.context.initialization_status == ContextFlags.DEFERRED_INIT:
             projection_name = template.format(self.className, state.owner.name, state.name)
             # self.init_args[NAME] = self.init_args[NAME] or projection_name
             self.name = self.init_args[NAME] or projection_name
 
         else:
             raise ModulatoryProjectionError("PROGRAM ERROR: {} has unrecognized InitStatus ({})".
-                                            format(self, self.init_status))
+                                            format(self, ContextFlags._get_context_string(self.context.initialization_status)))

psyneulink/components/projections/pathway/mappingprojection.py

@@ -483,7 +483,7 @@ def __init__(self,
 
         # If sender or receiver has not been assigned, defer init to State.instantiate_projection_to_state()
         if sender is None or receiver is None:
-            self.init_status = InitStatus.DEFERRED_INITIALIZATION
+            self.context.initialization_status = ContextFlags.DEFERRED_INIT
 
         # Validate sender (as variable) and params, and assign to variable and paramInstanceDefaults
         super().__init__(sender=sender,
@@ -627,7 +627,8 @@ def _execute(self, variable=None, runtime_params=None, context=None):
 
         # FIX: MOVE THIS TO SUPER
         if EXECUTING in context: # cxt-test
-            self.context.initialization_status &= ~(ContextFlags.VALIDATING | ContextFlags.INITIALIZING)
+            # self.context.initialization_status &= ~(ContextFlags.VALIDATING | ContextFlags.INITIALIZING)
+            # self.context.initialization_status = ContextFlags.INITIALIZED
             self.context.execution_phase = ContextFlags.PROCESSING
             self.context.string = context