Refactor/state and projection/names and docs (#500)

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* Merge branch 'TEMP' into refactor/State_and_Projection/specification

# Conflicts:
#	PsyNeuLink/Components/States/State.py

* Merge branch 'TEMP' into refactor/State_and_Projection/specification

# Conflicts:
#	PsyNeuLink/Components/States/State.py

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* • GatingMechanism
  - refactor _instantiate_gating_signal to use _parse_state_spec

* • GatingMechanism
  - refactor _instantiate_gating_signal to use _parse_state_spec

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* • States and Projections
  - implemented _assign_default_name that reinstates context-sensitive naming
  - docstring revisions
  - bug fixes

Scripts/Models/GilzenratModel.py

@@ -103,7 +103,7 @@
                         threshold_FHN=0.5,        #Parameter describing shape of the FitzHugh–Nagumo cubic nullcline for the fast excitation variable v
         objective_mechanism=ObjectiveMechanism(
                                     function=Linear,
-                                    monitored_output_states=[(decision_layer, None, None, np.array([[0.3],[0.0]]))],
+                                    # monitored_output_states=[(decision_layer, None, None, np.array([[0.3],[0.0]]))],
                                     # monitored_output_states=[{PROJECTION_TYPE: MappingProjection,
                                     #                           SENDER: decision_layer,
                                     #                           MATRIX: np.array([[0.3],[0.0]])}],

Scripts/TEST SCRIPTS/Multilayer Learning Test Script.py

@@ -167,7 +167,7 @@ def show_target():
     x.reportOutputPref = True
     composition = x
 
-    x.show_graph(show_learning=ALL)
+    # x.show_graph(show_learning=ALL)
     # x.show_graph()
     results = x.run(
         num_trials=10,

psyneulink/components/mechanisms/adaptive/control/controlmechanism.py

@@ -139,7 +139,7 @@
     <ControlSignal_Specification>`;
 
   * where the `parameter is specified <ParameterState_Specification>`, by including a `ControlProjection` or
-    `ControlSignal` in a `tuple specification for the parameter.
+    `ControlSignal` in a `tuple specification <ParameterState_Tuple_Specification>` for the parameter.
 
 When a ControlMechanism is created as part of a System, a `ControlSignal` is created and assigned to the
 ControlMechanism for every parameter of any `Component <Component>` in the System that has been specified for control
@@ -848,10 +848,10 @@ def add_monitored_output_states(self, monitored_output_states, context=None):
         """Instantiate OutputStates to be monitored by ControlMechanism's `objective_mechanism
         <ControlMechanism.objective_mechanism>`.
 
-        **monitored_output_states** can be a `Mechanism`, `OutputState`, `monitored_output_states tuple
-        <ObjectiveMechanism_OutputState_Tuple>`, or list with any of these. If item is a Mechanism, its `primary
-        OutputState <OutputState_Primary>` is used. OutputStates must belong to Mechanisms in the same `System` as
-        the ControlMechanism.
+        **monitored_output_states** can be a `Mechanism`, `OutputState`, `tuple specification
+        <InputState_Tuple_Specification>`, a `State specification dicionary <InputState_Specification_Dictionary>`,
+        or list with any of these. If item is a Mechanism, its `primary OutputState <OutputState_Primary>` is used.
+        OutputStates must belong to Mechanisms in the same `System` as the ControlMechanism.
         """
         output_states = self.objective_mechanism.add_monitored_output_states(
                                                                  monitored_output_states_specs=monitored_output_states,

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

@@ -153,14 +153,14 @@
 from psyneulink.components.functions.function import ModulationParam, _is_modulation_param
 from psyneulink.components.mechanisms.adaptive.adaptivemechanism import AdaptiveMechanism_Base
 from psyneulink.components.mechanisms.mechanism import Mechanism_Base
-from psyneulink.components.shellclasses import Mechanism
 from psyneulink.components.states.modulatorysignals.gatingsignal import GatingSignal
 from psyneulink.components.states.state import State_Base, _parse_state_spec
 from psyneulink.globals.defaults import defaultGatingPolicy
-from psyneulink.globals.keywords import GATING_POLICY, GATING_PROJECTION, GATING_PROJECTIONS, GATING_SIGNAL, GATING_SIGNALS, GATING_SIGNAL_SPECS, INIT__EXECUTE__METHOD_ONLY, MAKE_DEFAULT_GATING_MECHANISM, NAME, OWNER, PARAMS, REFERENCE_VALUE, STATES
+from psyneulink.globals.keywords import \
+    GATING_POLICY, GATING_PROJECTIONS, GATING_SIGNAL, GATING_SIGNALS, GATING_SIGNAL_SPECS, \
+    INIT__EXECUTE__METHOD_ONLY, MAKE_DEFAULT_GATING_MECHANISM
 from psyneulink.globals.preferences.componentpreferenceset import is_pref_set
 from psyneulink.globals.preferences.preferenceset import PreferenceLevel
-from psyneulink.globals.utilities import ContentAddressableList
 from psyneulink.scheduling.timescale import CentralClock, TimeScale
 
 __all__ = [

psyneulink/components/mechanisms/processing/transfermechanism.py

@@ -118,9 +118,11 @@
 
 from psyneulink.components.component import Component, function_type, method_type
 from psyneulink.components.functions.function import AdaptiveIntegrator, Linear
-from psyneulink.components.mechanisms.mechanism import MechanismError
+from psyneulink.components.mechanisms.mechanism import MechanismError, Mechanism
 from psyneulink.components.mechanisms.processing.processingmechanism import ProcessingMechanism_Base
-from psyneulink.components.states.outputstate import PRIMARY_OUTPUT_STATE, StandardOutputStates, standard_output_states
+from psyneulink.components.states.inputstate import InputState
+from psyneulink.components.states.outputstate import \
+    OutputState, PRIMARY_OUTPUT_STATE, StandardOutputStates, standard_output_states
 from psyneulink.globals.keywords import FUNCTION, INITIALIZER, INITIALIZING, MEAN, MEDIAN, NOISE, RATE, RESULT, STANDARD_DEVIATION, TRANSFER_FUNCTION_TYPE, TRANSFER_MECHANISM, VARIANCE, kwPreferenceSetName
 from psyneulink.globals.preferences.componentpreferenceset import is_pref_set, kpReportOutputPref, kpRuntimeParamStickyAssignmentPref
 from psyneulink.globals.preferences.preferenceset import PreferenceEntry, PreferenceLevel
@@ -406,7 +408,7 @@ class ClassDefaults(ProcessingMechanism_Base.ClassDefaults):
     def __init__(self,
                  default_variable=None,
                  size=None,
-                 input_states:tc.optional(tc.any(list, dict))=None,
+                 input_states:tc.optional(tc.any(list, dict, Mechanism, OutputState, InputState))=None,
                  function=Linear,
                  initial_value=None,
                  noise=0.0,

psyneulink/components/projections/pathway/pathwayprojection.py

@@ -45,7 +45,7 @@
 """
 
 from psyneulink.components.projections.projection import Projection_Base
-from psyneulink.globals.keywords import PATHWAY_PROJECTION, NAME
+from psyneulink.globals.keywords import PATHWAY_PROJECTION, NAME, RECEIVER
 from psyneulink.components.component import InitStatus
 
 __all__ = []
@@ -98,6 +98,10 @@ def _assign_default_projection_name(self, state, sender_name=None, receiver_name
                               self.receiver.owner.name
 
         elif self.init_status is InitStatus.DEFERRED_INITIALIZATION:
+            if self.init_args[RECEIVER]:
+                receiver = self.init_args[RECEIVER]
+                if receiver.owner:
+                    receiver_name = "{}[{}]".format(receiver.owner.name, receiver_name)
             projection_name = self.className + " from " + sender_name + " to " + receiver_name
             self.init_args[NAME] = self.init_args[NAME] or projection_name
 

psyneulink/components/projections/projection.py

@@ -100,7 +100,9 @@
       * *MAPPING_PROJECTION* -- if the `sender <MappingProjection.sender>` and/or its `receiver
         <MappingProjection.receiver>` cannot be inferred from the context in which this specification occurs, then its
         `initialization is deferred <MappingProjection_Deferred_Initialization>` until both of those have been
-        determined (e.g., it is used in the specification of a `pathway <Process.pathway>` for a `Process`).
+        determined (e.g., it is used in the specification of a `pathway <Process.pathway>` for a `Process`). For
+        MappingProjections, a `matrix specification <Mapping_Matrix_Specification>` can also be used to specify the
+        projection.
       |
       * *LEARNING_PROJECTION*  (or *LEARNING*) -- this can only be used in the specification of a `MappingProjection`
         (see `tuple <Mapping_Matrix_Specification>` format).  If the `receiver <MappingProjection.receiver>` of the
@@ -148,7 +150,7 @@
         manner as described above for keyword specifications.
 
       COMMENT:
-          WHAT ABOUT SPECIFICATION USING OutputState/ModulatorySignal OR Mechanism?
+          WHAT ABOUT SPECIFICATION USING OutputState/ModulatorySignal OR Mechanism? OR Matrix OR Matrix keyword
       COMMENT
 
       COMMENT:  ??IMPLEMENTED FOR PROJECTION PARAMS??
@@ -170,7 +172,7 @@
 when :keyword:`learning` is specified for a `Process <Process_Learning_Sequence>` or `System
 <System_Execution_Learning>`).
 
-.. _MappingProjection_Deferred_Initialization:
+.. _Projection_Deferred_Initialization:
 
 Deferred Initialization
 ~~~~~~~~~~~~~~~~~~~~~~~