Feat/timermechanism (#3149)

* • recurrenttransfermechanism.py
  - _instantiate_attributes_after_function():  fix assignment of StabilityFunction, and force update of default_variable for output_port

* • recurrenttransfermechanism.py
  _instantiate_attributes_after_function:
  revise call to _update_default_variable to use energy.variable instead of value

* • recurrenttransfermechanism.py
  _instantiate_attributes_after_function:
  revise call to _update_default_variable to use energy.variable instead of value

* • composition.py
  - reset():  add clear_results arg

• timerfunctions.py
  - functions all written for python and pytorch... need llvm versions

• timerfunctions.py
  - Desmos plots updated

* Add Mechanism and Functions to support progression of integration along a trajectory

• timermechanism.py: sublass of IntegratorMechanism
• timerfunctions.py: subclass of TransferFunction
  - LinearTimer, AcceleratingTimer, DeceleratingTimer, AsymptoticTimer
• test_timer_mechanism.py

---------

Co-authored-by: jdcpni <pniintel55>

Scripts/Models (Under Development)/EGO/Using EMComposition/Coffee Shop World/DeclanParams.py

@@ -72,6 +72,7 @@ def calc_prob(em_preds, test_ys):
     normalize_field_weights = True, # whether to normalize the field weights during memory retrieval
     normalize_memories = False, # whether to normalize the memory during memory retrieval
     # normalize_memories = True, # whether to normalize the memory during memory retrieval
+    normalize_memories = False, # whether to normalize the memory vectors
     # softmax_temperature = None, # temperature of the softmax used during memory retrieval (smaller means more argmax-like
     softmax_temperature = .1, # temperature of the softmax used during memory retrieval (smaller means more argmax-like
     # softmax_temperature = ADAPTIVE, # temperature of the softmax used during memory retrieval (smaller means more argmax-like

docs/source/Core.rst

@@ -69,6 +69,8 @@ Core
 
             - `TransferFunctions`
 
+            - `TimerFunctions`
+
             - `TransformFunctions`
 
       - `StatefulFunctions`

docs/source/IntegratorMechanisms.rst

@@ -12,3 +12,4 @@ IntegratorMechanisms
 
    DDM
    EpisodicMemoryMechanism
+   TimerMechanism

docs/source/NonStatefulFunctions.rst

@@ -15,4 +15,5 @@ Functions that do *not* depend on a previous value.
    OptimizationFunctions
    SelectionFunctions
    TransferFunctions
+   TimerFunctions
    TransformFunctions

docs/source/TimerFunctions.rst

@@ -0,0 +1,10 @@
+TimerFunctions
+==============
+
+.. toctree::
+   :maxdepth: 3
+
+.. automodule:: psyneulink.core.components.functions.nonstateful.timerfunctions
+   :members: TimerFunction, LinearTimer, AcceleratingTimer, DeceleratingTimer, AsymptoticTimer
+   :private-members:
+   :exclude-members: Parameters

docs/source/TimerMechanism.rst

@@ -0,0 +1,7 @@
+TimerMechanism
+==============
+
+.. automodule:: psyneulink.library.components.mechanisms.processing.integrator.timermechanism
+   :members:
+   :private-members:
+   :exclude-members: random, Parameters

docs/source/TransferFunctions.rst

@@ -4,7 +4,8 @@ TransferFunctions
 .. toctree::
    :maxdepth: 3
 
-.. automodule:: psyneulink.core.components.functions.transferfunctions
-   :members: TransferFunction, Identity, Linear, Exponential, Logistic, Tanh, ReLU, Angle, Gaussian, GaussianDistort, BinomialDistort, Dropout, SoftMax, LinearMatrix, TransferWithCosts, CostFunctions
+.. automodule:: psyneulink.core.components.functions.nonstateful.transferfunctions
+   :members: TransferFunction, Identity, Linear, Exponential, Logistic, Tanh,ReLU, Angle, Gaussian, GaussianDistort, BinomialDistort, Dropout, SoftMax, LinearMatrix, TransferWithCosts,
+CostFunctions
    :private-members:
    :exclude-members: Parameters

psyneulink/core/components/functions/__init__.py

@@ -1,13 +1,14 @@
 from . import function
 from .nonstateful import selectionfunctions, objectivefunctions, optimizationfunctions, transformfunctions, \
-    learningfunctions, transferfunctions, distributionfunctions, fitfunctions
+    learningfunctions, timerfunctions, transferfunctions, distributionfunctions, fitfunctions
 from . import stateful
 from .stateful import integratorfunctions, memoryfunctions
 from . import userdefinedfunction
 
 from .function import *
-from psyneulink.core.components.functions.nonstateful.transformfunctions import *
 from psyneulink.core.components.functions.nonstateful.transferfunctions import *
+from psyneulink.core.components.functions.nonstateful.timerfunctions import *
+from psyneulink.core.components.functions.nonstateful.transformfunctions import *
 from psyneulink.core.components.functions.nonstateful.selectionfunctions import *
 from psyneulink.core.components.functions.nonstateful.distributionfunctions import *
 from psyneulink.core.components.functions.nonstateful.objectivefunctions import *
@@ -21,8 +22,9 @@
 
 __all__ = list(function.__all__)
 __all__.extend(userdefinedfunction.__all__)
-__all__.extend(transformfunctions.__all__)
 __all__.extend(transferfunctions.__all__)
+__all__.extend(timerfunctions.__all__)
+__all__.extend(transformfunctions.__all__)
 __all__.extend(selectionfunctions.__all__)
 __all__.extend(stateful.__all__)
 __all__.extend(distributionfunctions.__all__)

psyneulink/core/components/functions/function.py

@@ -534,13 +534,16 @@ class Function_Base(Function):
     Attributes
     ----------
 
-    variable: value
+    variable: number
         format and default value can be specified by the :keyword:`variable` argument of the constructor;  otherwise,
         they are specified by the Function's :keyword:`class_defaults.variable`.
 
     function : function
         called by the Function's `owner <Function_Base.owner>` when it is executed.
 
+    value : number
+        the result returned by calling the Function.
+
     COMMENT:
     enable_output_type_conversion : Bool : False
         specifies whether `function output type conversion <Function_Output_Type_Conversion>` is enabled.
@@ -554,7 +557,7 @@ class Function_Base(Function):
         specifies whether the return value of the function is different than the shape of either is outermost dimension
         (axis 0) of its  its `variable <Function_Base.variable>`, or any of the items in the next dimension (axis 1).
         Used to determine whether the shape of the inputs to the `Component` to which the function is assigned
-        should be based on the `variable <Function_Base.variable>` of the function or its `value <Function.value>`.
+        should be based on the `variable <Function_Base.variable>` of the function or its `value <Function_Base.value>`.
     COMMENT
 
     owner : Component