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Refactor/projection/connection specs #507

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merged 4 commits into from
Nov 2, 2017

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@jdcpni jdcpni commented Nov 2, 2017

• Projection
_parse_connection_spec: moved connection attributes to State subclasses

• Registry:
-register_category: added test for connection attributes on State subclasses

  _parse_connection_specs: moved connection info to states
  _parse_connection_spec:  moved connection attributes to State subclasses

• Registry:
  -register_category: added test for connection attributes on State subclasses
@jdcpni jdcpni merged commit 069e8a7 into devel Nov 2, 2017
@kmantelpton kmantelpton deleted the refactor/Projection/connection_specs branch November 3, 2017 19:17
jdcpni added a commit that referenced this pull request Nov 14, 2017
* Org/library/models (#483)

* • index.rst
  - main title changed to "Welcome to PsyNeuLink"

* • ControlMechanisms
  monitor_for_control argument and attribute changed to objective_mechanism

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	docs/source/index.rst

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	docs/source/index.rst

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

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* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

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* • ControlMechanism, EVCMechanism, ControlSignal, ObjectiveMechanism and System:
  - all refactored to make simpler and more modular:
    * most instantiation code moved from EVCMechaism to ControlMechanism
    * moved handling of monitored_output_states to ObjectiveMechanism monitored_values
    * moved parsing of ControlSignal specification from ControlMechanism to ControlSignal
    * moved identification of monitored_output_states and control_signals for System
          to methods on System
    * moved assignment of controller from ControlMechanism to System

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* • System
  - removed assignment of default controller for System, can now be None

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

# Conflicts:
#	PsyNeuLink/Components/Functions/Function.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/DefaultControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanism/LearningMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Components/States/ModulatorySignals/ControlSignal.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/ObjectiveMechanisms/ComparatorMechanism.py
#	PsyNeuLink/__init__.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py
#	tests/mechanisms/test_integrator_mechanism.py

* -

* -

* -

* -

* -

* • System, ControlMechanism, ObjectiveMechanism
  - added dictionary specification for monitored_values
  - docstring revs and examples

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/control/clean_up

# Conflicts:
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py

* -

* -

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/control/clean_up

# Conflicts:
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py

* -

* Merge branch 'devel' of https://github.com/jdcpni/PsyNeuLink into feat/ObjectiveMechanism/monitored_values_dict

# Conflicts:
#	.idea/inspectionProfiles/Project_Default.xml
#	.idea/runConfigurations/DDM_Learning_Test.xml
#	.idea/runConfigurations/EVC_Gratton_Script___SEBASTIAN.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_DEBUGGING.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script__SPECIFY_ControlSignals__.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_with_Custom_Fn.xml
#	.idea/runConfigurations/EVC_System_Test_Script_with_Profiler.xml
#	.idea/runConfigurations/FinalProject.xml
#	.idea/runConfigurations/Make_HTML.xml
#	.idea/runConfigurations/Multilayer_Learning_Test_Script_VARIATIONS.xml
#	.idea/runConfigurations/Multilayer_Learning_Test_Script__WITH_GATING_.xml
#	.idea/runConfigurations/NEW_Learning_Markus.xml
#	.idea/runConfigurations/NetworkX_Examples.xml
#	.idea/runConfigurations/Profile_EVC_System_Test.xml
#	.idea/runConfigurations/Stroop_Model_Learning_and_Control_Test_Script.xml
#	.idea/runConfigurations/Stroop_Model_Test_Script_VARIATIONS.xml
#	.idea/runConfigurations/Two_Layer_Test_Script.xml
#	.idea/runConfigurations/Xor_Script_1_process_working.xml
#	.idea/runConfigurations/Xor_Script_2_processes.xml
#	.idea/runConfigurations/_DDM_Test_Script.xml
#	.idea/runConfigurations/_DDM_scheduled_simple.xml
#	.idea/runConfigurations/_Documentation_Examples.xml
#	.idea/runConfigurations/_EVC_System_DEMO_Script.xml
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	.idea/runConfigurations/_Integrator_scheduled_timescales.xml
#	.idea/runConfigurations/_META_TEST.xml
#	.idea/runConfigurations/_Mixed_NN___DDM_DEMO_Script.xml
#	.idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script_DEMO.xml
#	.idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml
#	.idea/runConfigurations/_Scratch_Pad.xml
#	.idea/runConfigurations/_Stroop_Demo_Script.xml
#	.idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml
#	.idea/runConfigurations/_Stroop_Model_Test.xml
#	.idea/runConfigurations/_System_Graph_and_Input_Test.xml
#	.idea/runConfigurations/_System_Learning_Test_Script.xml
#	.idea/runConfigurations/make_html_and_ghpages_py.xml
#	.idea/runConfigurations/test_system.xml
#	.idea/runConfigurations/topo_example.xml
#	PsyNeuLink/Components/Component.py
#	PsyNeuLink/Components/Functions/Function.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/AdaptiveMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/ControlSignal.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/DefaultControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVCMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/GatingMechanisms/GatingMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanism/LearningAuxilliary.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanisms/LearningMechanism.py
#	PsyNeuLink/Components/Mechanisms/Mechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/DDM.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/IntegratorMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ProcessingMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/RecurrentTransferMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/TransferMechanism.py
#	PsyNeuLink/Components/Process.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/ControlProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/GatingProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/ModulatoryProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/PathwayProjection.py
#	PsyNeuLink/Components/Projections/Projection.py
#	PsyNeuLink/Components/Projections/TransmissiveProjections/MappingProjection.py
#	PsyNeuLink/Components/States/InputState.py
#	PsyNeuLink/Components/States/OutputState.py
#	PsyNeuLink/Components/States/ParameterState.py
#	PsyNeuLink/Components/States/State.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Globals/Defaults.py
#	PsyNeuLink/Globals/Keywords.py
#	PsyNeuLink/Globals/Preferences/ComponentPreferenceSet.py
#	PsyNeuLink/Globals/Preferences/MechanismPreferenceSet.py
#	PsyNeuLink/Globals/Run.py
#	PsyNeuLink/Globals/TimeScale.py
#	PsyNeuLink/Globals/Utilities.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCAuxiliary.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/LCA.py
#	PsyNeuLink/__init__.py
#	PsyNeuLink/scheduling/Scheduler.py
#	PsyNeuLink/scheduling/condition.py
#	Scripts/DEBUGGING SCRIPTS/EVC Gratton Script - SEBASTIAN.py
#	Scripts/DEBUGGING SCRIPTS/EVC System Laming Validation Test Script [SPECIFY ControlSignals]].py
#	Scripts/DEBUGGING SCRIPTS/Multilayer Learning Test Script [WITH GATING].py
#	Scripts/DEBUGGING SCRIPTS/OLD/EVC System Laming Validation Test Script DEBUGGING.py
#	Scripts/DEBUGGING SCRIPTS/OLD/EVC_Gratton_Script_Validation.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Multilayer Learning Test Script VARIATIONS.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Scripts_DEBUGGING_SCRIPTS_EVC_Gratton_Script_-_SEBASTIAN_py.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Stroop Model Test Script VARIATIONS.py
#	Scripts/DEMO SCRIPTS/EVC System DEMO Script.py
#	Scripts/MISCELLANEOUS SCRIPTS/Reinforcement Learning Test Script [SIMPLE].py
#	Scripts/MISCELLANEOUS SCRIPTS/ddm-bug.py
#	Scripts/MISCELLANEOUS SCRIPTS/rate_bug.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py
#	Scripts/TEST SCRIPTS/Multilayer Learning Test Script.py
#	Scripts/TEST SCRIPTS/Reinforcement Learning Test Script.py
#	Scripts/TEST SCRIPTS/Stroop Model Test Script.py
#	TODO List.py
#	bfg.prep
#	docs/source/index.rst
#	tests/conftest.py
#	tests/control/test_EVC.py
#	tests/learning/test_multilayer.py
#	tests/learning/test_reinforcement.py
#	tests/learning/test_stroop.py
#	tests/mechanisms/test_ddm_mechanism.py
#	tests/mechanisms/test_gating_mechanism.py
#	tests/mechanisms/test_integrator_mechanism.py
#	tests/mechanisms/test_transfer_mechanism.py
#	tests/no-learning/test_DDM.py
#	tests/no-learning/test_no-learning.py
#	tests/scheduling/test_system_newsched.py
#	tests/system/test_system.py

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* Docs/mechanism/updated states fig (#484)

* • index.rst
  - main title changed to "Welcome to PsyNeuLink"

* • ControlMechanisms
  monitor_for_control argument and attribute changed to objective_mechanism

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	docs/source/index.rst

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	docs/source/index.rst

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

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* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

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* • ControlMechanism, EVCMechanism, ControlSignal, ObjectiveMechanism and System:
  - all refactored to make simpler and more modular:
    * most instantiation code moved from EVCMechaism to ControlMechanism
    * moved handling of monitored_output_states to ObjectiveMechanism monitored_values
    * moved parsing of ControlSignal specification from ControlMechanism to ControlSignal
    * moved identification of monitored_output_states and control_signals for System
          to methods on System
    * moved assignment of controller from ControlMechanism to System

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* • System
  - removed assignment of default controller for System, can now be None

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

# Conflicts:
#	PsyNeuLink/Components/Functions/Function.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/DefaultControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanism/LearningMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Components/States/ModulatorySignals/ControlSignal.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/ObjectiveMechanisms/ComparatorMechanism.py
#	PsyNeuLink/__init__.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py
#	tests/mechanisms/test_integrator_mechanism.py

* -

* -

* -

* -

* -

* • System, ControlMechanism, ObjectiveMechanism
  - added dictionary specification for monitored_values
  - docstring revs and examples

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/control/clean_up

# Conflicts:
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py

* -

* -

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/control/clean_up

# Conflicts:
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py

* -

* Merge branch 'devel' of https://github.com/jdcpni/PsyNeuLink into feat/ObjectiveMechanism/monitored_values_dict

# Conflicts:
#	.idea/inspectionProfiles/Project_Default.xml
#	.idea/runConfigurations/DDM_Learning_Test.xml
#	.idea/runConfigurations/EVC_Gratton_Script___SEBASTIAN.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_DEBUGGING.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script__SPECIFY_ControlSignals__.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_with_Custom_Fn.xml
#	.idea/runConfigurations/EVC_System_Test_Script_with_Profiler.xml
#	.idea/runConfigurations/FinalProject.xml
#	.idea/runConfigurations/Make_HTML.xml
#	.idea/runConfigurations/Multilayer_Learning_Test_Script_VARIATIONS.xml
#	.idea/runConfigurations/Multilayer_Learning_Test_Script__WITH_GATING_.xml
#	.idea/runConfigurations/NEW_Learning_Markus.xml
#	.idea/runConfigurations/NetworkX_Examples.xml
#	.idea/runConfigurations/Profile_EVC_System_Test.xml
#	.idea/runConfigurations/Stroop_Model_Learning_and_Control_Test_Script.xml
#	.idea/runConfigurations/Stroop_Model_Test_Script_VARIATIONS.xml
#	.idea/runConfigurations/Two_Layer_Test_Script.xml
#	.idea/runConfigurations/Xor_Script_1_process_working.xml
#	.idea/runConfigurations/Xor_Script_2_processes.xml
#	.idea/runConfigurations/_DDM_Test_Script.xml
#	.idea/runConfigurations/_DDM_scheduled_simple.xml
#	.idea/runConfigurations/_Documentation_Examples.xml
#	.idea/runConfigurations/_EVC_System_DEMO_Script.xml
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	.idea/runConfigurations/_Integrator_scheduled_timescales.xml
#	.idea/runConfigurations/_META_TEST.xml
#	.idea/runConfigurations/_Mixed_NN___DDM_DEMO_Script.xml
#	.idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script_DEMO.xml
#	.idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml
#	.idea/runConfigurations/_Scratch_Pad.xml
#	.idea/runConfigurations/_Stroop_Demo_Script.xml
#	.idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml
#	.idea/runConfigurations/_Stroop_Model_Test.xml
#	.idea/runConfigurations/_System_Graph_and_Input_Test.xml
#	.idea/runConfigurations/_System_Learning_Test_Script.xml
#	.idea/runConfigurations/make_html_and_ghpages_py.xml
#	.idea/runConfigurations/test_system.xml
#	.idea/runConfigurations/topo_example.xml
#	PsyNeuLink/Components/Component.py
#	PsyNeuLink/Components/Functions/Function.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/AdaptiveMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/ControlSignal.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/DefaultControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVCMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/GatingMechanisms/GatingMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanism/LearningAuxilliary.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanisms/LearningMechanism.py
#	PsyNeuLink/Components/Mechanisms/Mechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/DDM.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/IntegratorMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ProcessingMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/RecurrentTransferMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/TransferMechanism.py
#	PsyNeuLink/Components/Process.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/ControlProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/GatingProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/ModulatoryProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/PathwayProjection.py
#	PsyNeuLink/Components/Projections/Projection.py
#	PsyNeuLink/Components/Projections/TransmissiveProjections/MappingProjection.py
#	PsyNeuLink/Components/States/InputState.py
#	PsyNeuLink/Components/States/OutputState.py
#	PsyNeuLink/Components/States/ParameterState.py
#	PsyNeuLink/Components/States/State.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Globals/Defaults.py
#	PsyNeuLink/Globals/Keywords.py
#	PsyNeuLink/Globals/Preferences/ComponentPreferenceSet.py
#	PsyNeuLink/Globals/Preferences/MechanismPreferenceSet.py
#	PsyNeuLink/Globals/Run.py
#	PsyNeuLink/Globals/TimeScale.py
#	PsyNeuLink/Globals/Utilities.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCAuxiliary.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/LCA.py
#	PsyNeuLink/__init__.py
#	PsyNeuLink/scheduling/Scheduler.py
#	PsyNeuLink/scheduling/condition.py
#	Scripts/DEBUGGING SCRIPTS/EVC Gratton Script - SEBASTIAN.py
#	Scripts/DEBUGGING SCRIPTS/EVC System Laming Validation Test Script [SPECIFY ControlSignals]].py
#	Scripts/DEBUGGING SCRIPTS/Multilayer Learning Test Script [WITH GATING].py
#	Scripts/DEBUGGING SCRIPTS/OLD/EVC System Laming Validation Test Script DEBUGGING.py
#	Scripts/DEBUGGING SCRIPTS/OLD/EVC_Gratton_Script_Validation.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Multilayer Learning Test Script VARIATIONS.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Scripts_DEBUGGING_SCRIPTS_EVC_Gratton_Script_-_SEBASTIAN_py.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Stroop Model Test Script VARIATIONS.py
#	Scripts/DEMO SCRIPTS/EVC System DEMO Script.py
#	Scripts/MISCELLANEOUS SCRIPTS/Reinforcement Learning Test Script [SIMPLE].py
#	Scripts/MISCELLANEOUS SCRIPTS/ddm-bug.py
#	Scripts/MISCELLANEOUS SCRIPTS/rate_bug.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py
#	Scripts/TEST SCRIPTS/Multilayer Learning Test Script.py
#	Scripts/TEST SCRIPTS/Reinforcement Learning Test Script.py
#	Scripts/TEST SCRIPTS/Stroop Model Test Script.py
#	TODO List.py
#	bfg.prep
#	docs/source/index.rst
#	tests/conftest.py
#	tests/control/test_EVC.py
#	tests/learning/test_multilayer.py
#	tests/learning/test_reinforcement.py
#	tests/learning/test_stroop.py
#	tests/mechanisms/test_ddm_mechanism.py
#	tests/mechanisms/test_gating_mechanism.py
#	tests/mechanisms/test_integrator_mechanism.py
#	tests/mechanisms/test_transfer_mechanism.py
#	tests/no-learning/test_DDM.py
#	tests/no-learning/test_no-learning.py
#	tests/scheduling/test_system_newsched.py
#	tests/system/test_system.py

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* • Mechanism
  - updated Mechanism_States_fig and caption

* adding all params of FHNIntegrator Function to the LCControlMechanism. Appended '_FHN' to each param name b/c Mechanism cannot have params of the same name as params of its function

* passed in all arguments to the FHNIntegrator where the LCControlMechanism specifies FHN as its function in super().__init__

* move tutorial notebook to its own dedicated folder

* change test_notebooks to only test the notebooks in the tutorial folder (if more notebooks are added in the future, add them to be run by this test

* replace Adpative with Adaptive

* import ShellClass Mechanism directly instead of implicitly importing it through the Mechanism.py module

* import ShellClass Projection directly instead of implicitly importing it through the Projection.py module

* import ShellClass State directly instead of implicitly importing it through the State.py module

* import ShellClass Process directly instead of implicitly importing it through the Process.py module

* import ShellClass System directly instead of implicitly importing it through the System.py module

* replace nonexistence ControlMechanism_Base uses with the real ControlMechanism

* optimize imports via pycharm

* make IntegratorMechanism get its paramClassDefaults from its parent ProcessingMechanism_Base rather than a more distant ancestor Mechanism_Base

* refactoring rk helper method to compute the two variables (v and w) concurrently and update their approximations of each other throughout the timestep

* adding pytest to verify FHNIntegrator function against Gilzenrat paper figure 2

* adding ipykernel>=4.6.1 to dev_requirements.txt

* fixing Project Defaults

* removing toposort from ignoredPackages

* adding Project_Default.xml to gitignore

* revising FHN integrator docs comparisons to other models (Gilzenrat, Modified FHN) to be easier to follow and have all correct signs

* Update Project_Default.xml

* ensure that MechanismPreferenceSet imports its parent class

* define undefined default values in MechanismPreferenceSet

* temporary fix: changing LCControlMechanism output to (gain(w_t), gain(w_t), v_t, w_t, t) so that both modulated mechanisms receive gain. Should be refactored so that this is handled by selecting output states/control signals

* replace calls to numpy typechecking from 64 bit to 64 or 32bit versions

* make TransferMechanism.paramClassDefaults copy its parent instead of Mechanism_Base

* cleanup test_recurrent_mechanism.py imports

* replace crude assertions with numpy assert_allclose in test_recurrent_transfer_mechanism

* test_recurrent_transfer_mechanism.py PEP8 format

* adding a new function called 'LCAIntegrator' which computes rate*previous_value + variable

* updating execute method of LCA to call LCAIntegrator and renaming time_constant --> beta to match the new function

* relaxing validation on LCAIntegrator rate param in order to create an LCA example in integrator mode with an array input

* remove mechanismGenerator

* rename packages and modules to lowercase, and handle relevant import changes

* remove old pyargs argument for pytest

* move typecheck for _get_modulated_param inside to avoid circular import

* switch name of System and System_Base

* switch name of Process and Process_Base

* remove process factory in favor of just instantiating Process class

* make LearningMechanism get its paramClassDefaults from its parent and not Projection_Base

* rework imports to avoid circularities due to packaging

* remove system factory in favor of just instantiating System class

* remove mechanism factory method

* clean up main package __init__.py

* replace paramClassDefaults PROJECTION_SENDER with OutputState class instead of keyword to prevent error due to failed conversion

* rename globals/run.py to globals/environment.py to avoid namespace conflict with run method

* add __all__ lists to modules

* update package __init__.py files for simple importing

* update tutorial to new easier import style

* update docs to handle new module/package format

* update setup.py packages

* add MANIFEST.in

* add requirements.txt mirroring setup.py requirements

* remove extraneous files

* remove SOFTWARE ARCHITECTURE and TODO List

* add docstrings to __init__.py files (for help command)

* update setup.py classifier for Apache license

* update setup.cfg for wheel creation and to include license file

* update setup.py supported Python versions to include only 3.5 and 3.6 (does not work on < 3.4 due to numpy, does not work on 3.4)

* update short description to match the title line in the long description

* reformat README into .rst format so pypi can format it nicely

* add tutorial_requirements.txt mirroring setup.py requirements

* update README and docs index.rst to new PyPI installation instructions, and tutorial section, reorganize

* adding a new Integrator function that matches the decision and response layer functions in the Gilzenrat paper, and a new transfer mechanism which calls this integrator before its primary function

* updating value of LC control mechanism output before it runs to match initial previous value (had to do this in the gilzenrat script because of other LC control mechanism hacks, but left a placeholer in ControlMechanism for how to implement this more generally for any control mechanism that accumulates)

* removing and re-adding gilzenrat transfer mechanism because name change did not seem to work

* remove DefaultProcessingMechanism from component/__init__.py because it's an instantiation of a _Base class, and doesn't get used

* make Function_Base inherit its paramClassDefaults from its parent class Function instead of Component

* improving initial conditions by making first recurrent projections to recurrent mechanisms make sense given their starting values

* Devel (#490)

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml

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* • System
  - show_graph(): allowed standard graph to show connections to ObjectiveMechanisms
                  for ControlMechanisms other than the System's controller

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* • System
  instantiate_graph:
      patched bug in which search for ORIGIN Mechanisms in Processes
      within the System fails if a Mechanisms belongs to some but not
      all Processes within the System

* correcting LCAIntegrator function to match the papers (since it represents a rate of change, we need to integrate over timesteps) and relaxing integrator rate param validation which was blocking variables of lengths > 1

* fix link to the tutorial in docs that didn't get changed when tutorial/ directory was created

* fixing bug in NormalDist() function which was shifting the mean of the distribution

* stop package-level __all__ assignments from accidentally overwriting the __all__ objects they used as bases

* skip notebook checkpoints in running notebook tests

* fold keywords into first level hierarchy, because some keywords aren't defined in Keywords.py and this is confusing

* add component module to main psyneulink package

* indexing into the first element of the transfer mechanism's integrator_function result so that the shape passed to the transfer mechanism's function is the same as if integrator_mode were false

* updating mechanism pytests to reflect integrator_function shape change and removing extraneous transfer mechanism tests which returned arrays of mixed types

* Refactored instantiation of States and Projections (#494)

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* • Mechanism
  - updated Mechanism_States_fig and caption

* • State
  - refactored _parse_state_spec to call State subclass
    for parsing of class-specific specifications

• InputState
  - added _parse_state_specific_dict_entries

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* • Projection (and subclasses)
  - added weight and exponent attributes

* -

* • Projection
  - moved _parse_connection_specs from State to here and
    renamed as _parse_projection_specs;  refactored it as a filter
    on the constructor to a projection (allowing for state-specific
    formats for the call (i.e., State specification tuples)
  - instantiates any projections that have not yet been, allowing any
    that are not yet fully specified to be assigned deferred_init status

* • Projection
  - moved _parse_connection_specs from State to here and
    renamed as _parse_projection_specs;  refactored it as a filter
    on the constructor to a projection (allowing for state-specific
    formats for the call (i.e., State specification tuples)
  - instantiates any projections that have not yet been, allowing any
    that are not yet fully specified to be assigned deferred_init status

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* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projections/_parse_connection_specs

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projections/_parse_connection_specs

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py

* • Refactor parsing of State and Projection

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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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

* 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

* 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

* 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

* 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

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

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

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* - EVC scripts working
- Gating script still failing test

* - Gating script now just failing test on Function Error

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  Added Gating Mechanism Test Script to TEST SCRIPTS

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* • Passes all tests

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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* • TEST SCRIPTS:
  Added Gating Mechanism Test Script to TEST SCRIPTS

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* • LearningMechanism, ControlMechanism, GatingMechanism:
  - _instantiate_output_states:  all now use this to instantiate ModulatorySignals
  - _instantiate_XXX_signal:  all deleted
  - all now use _parse_state_specs and _parse_connecion_specs, and _parse_projection_specs

* • LearningMechanism, ControlMechanism, GatingMechanism:
  - _instantiate_output_states:  all now use this to instantiate ModulatorySignals
  - _instantiate_XXX_signal:  all deleted
  - all now use _parse_state_specs and _parse_connecion_specs, and _parse_projection_specs

* Refactor/state and projection/specification bug fix 2 (#495)

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* • Mechanism
  - updated Mechanism_States_fig and caption

* • State
  - refactored _parse_state_spec to call State subclass
    for parsing of class-specific specifications

• InputState
  - added _parse_state_specific_dict_entries

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* • Projection (and subclasses)
  - added weight and exponent attributes

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* • Projection
  - moved _parse_connection_specs from State to here and
    renamed as _parse_projection_specs;  refactored it as a filter
    on the constructor to a projection (allowing for state-specific
    formats for the call (i.e., State specification tuples)
  - instantiates any projections that have not yet been, allowing any
    that are not yet fully specified to be assigned deferred_init status

* • Projection
  - moved _parse_connection_specs from State to here and
    renamed as _parse_projection_specs;  refactored it as a filter
    on the constructor to a projection (allowing for state-specific
    formats for the call (i.e., State specification tuples)
  - instantiates any projections that have not yet been, allowing any
    that are not yet fully specified to be assigned deferred_init status

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* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projections/_parse_connection_specs

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projections/_parse_connection_specs

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py

* • Refactor parsing of State and Projection

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# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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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

* 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

* 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

* 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

* 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

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

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

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* - EVC scripts working
- Gating script still failing test

* - Gating script now just failing test on Function Error

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  Added Gating Mechanism Test Script to TEST SCRIPTS

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* • Passes all tests

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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* • TEST SCRIPTS:
  Added Gating Mechanism Test Script to TEST SCRIPTS

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* • LearningMechanism, ControlMechanism, GatingMechanism:
  - _instantiate_output_states:  all now use this to instantiate ModulatorySignals
  - _instantiate_XXX_signal:  all deleted
  - all now use _parse_state_specs and _parse_connecion_specs, and _parse_projection_specs

* • LearningMechanism, ControlMechanism, GatingMechanism:
  - _instantiate_output_states:  all now use this to instantiate ModulatorySignals
  - _instantiate_XXX_signal:  all deleted
  - all now use _parse_state_specs and _parse_connecion_specs, and _parse_projection_specs

* • LearningMechanism, ControlMechanism, GatingMechanism:
  - _instantiate_output_states:  all now use this to instantiate ModulatorySignals
  - _instantiate_XXX_signal:  all deleted
  - all now use _parse_state_specs and _parse_connecion_specs, and _parse_projection_specs

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* updating kwta and transfer pytests with correct error message text

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* • Component
  _validate_params: fixed bug that was causing to fail to detect some params

• InputState:
  - _parse_state_specific_specs: now infers variable from projection_spec

* replacing GilzenratIntegrator with LCAIntegrator (with rate=-1) in GilzenratTransferMechanism

* implementing noise on LCAIntegrator and cleaning up unnecessary integrator function code (removing GilzenratIntegrator)

* adding progress statement ('% complete') to gilzenrat script

* Optimize registry duplicate naming

Replace inefficient renaming algorithm with faster version, that additionally provides more meaningful names (numeric suffix for duplicate names is now based on the number of duplicates per name rather than per componentType)

* fixing up a few model values in the gilzenrat model -- behavior is not quit right -- and switching number_of_trials back to 1

* adding pytests that isolate the GilzenratTransferMechanism and moving FHNIntegrator test that recreates figure 2 from gilzenrat paper from integrator mechanism tests --> gilzenrat tests

* adding full gilzenrat model to pytests -- no comparison data to assert yet, just verifying that model can run without errors

* moving imports to top of gilzenrat pytests file

* requiring version 1.4 of toposort

* 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

* Refactor/state and projections/unit tests (#501)

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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

* • tests/mechanisms/test_transfer_mechanism
  - added unit tests for specification of input_states
    COMMENTED OUT tests that need to be debugged,
    and ones that elicit bugs in the code that need attention

* Refactor/state and projection/unit tests bug fixes (#502)

* • tests/mechanisms/test_transfer_mechanism
  - added unit tests for specification of input_states
    COMMENTED OUT tests that need to be debugged,
    and ones that elicit bugs in the code that need attention

* • tests/mechanisms/test_transfer_mechanism
  - added unit tests for specification of input_states
    COMMENTED OUT tests that need to be debugged,
    and ones that elicit bugs in the code that need attention

* • tests/mechanisms/test_transfer_mechanism
  - unit tests for input_states: debugged several

* avoid using module-level Mechanisms in unit tests to avoid possible conflicts

* fix typo in ObjectiveMechanism docstring causing weird documentation formatting

* Refactor/state and projection/clean up (#503)

* • tests/mechanisms/test_transfer_mechanism
  - unit tests for input_states: debugged several

* • tests/mechanisms/test_transfer_mechanism
  - unit tests for input_states: debugged several

* • States, Projections
  - clean-up of comments/commented-out code

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* Refactor/projection/ instantiate sender (#504)

* • tests/mechanisms/test_transfer_mechanism
  - unit tests for input_states: debugged several

* • tests/mechanisms/test_transfer_mechanism
  - unit tests for input_states: debugged several

* • States, Projections
  - clean-up of comments/commented-out code

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* • Projection (#505)

_validat_params and _instantiate_sender: code simplification

* Refactor/gating mechanism/ instantiate gating signal (#506)

* • Projection
  _validat_params and _instantiate_sender: code simplification

* • Projection
  _parse_connection_spec and _parse_projection_spec

* • GatingMechanism
  _instantiate_gating_signal: reimplemented
                              refactored handling of gating_policy
• Projection
  _parse_connection_spec and _parse_projection_spec

* • GatingMechanism
  _instantiate_gating_signal: reimplemented
                              refactored handling of gating_policy
• Projection
  _parse_connection_spec and _parse_projection_spec

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* • GatingMechanism
  _instantiate_gating_signal: reimplemented
                              refactored handling of gating_policy
• Projection
  _parse_connection_spec and _parse_projection_spec

* Refactor/projection/connection specs (#507)

* • Projection
  _parse_connection_specs: moved connection info to states

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* • Projection
  _parse_connection_spec:  moved connection attributes to State subclasses

• Registry:
  -register_category: added test for connection attributes on State subclasses

* Clean up/registry/ register category (#508)

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* • Registry
  _register_category:  clean-up of connection attribute validation

* rename System and Process to add _Base suffix in shellclasses.__all__ because of abf3e7e7c and 6b9e9a4e2

* Fix/utilities/iscompatible (#511)

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml

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* • System
  - show_graph(): allowed standard graph to show connections to ObjectiveMechanisms
                  for ControlMechanisms other than the System's controller

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* • System
  instantiate_graph:
      patched bug in which search for ORIGIN Mechanisms in Processes
      within the System fail…
jdcpni added a commit that referenced this pull request Nov 16, 2017
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* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into CURRENT

# Conflicts:
#	tests/mechanisms/test_transfer_mechanism.py

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into CURRENT

# Conflicts:
#	tests/mechanisms/test_transfer_mechanism.py

* Refactor/mechanism/preprocess variable (#530)

* Org/library/models (#483)

* • index.rst
  - main title changed to "Welcome to PsyNeuLink"

* • ControlMechanisms
  monitor_for_control argument and attribute changed to objective_mechanism

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	docs/source/index.rst

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	docs/source/index.rst

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

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* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

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* • ControlMechanism, EVCMechanism, ControlSignal, ObjectiveMechanism and System:
  - all refactored to make simpler and more modular:
    * most instantiation code moved from EVCMechaism to ControlMechanism
    * moved handling of monitored_output_states to ObjectiveMechanism monitored_values
    * moved parsing of ControlSignal specification from ControlMechanism to ControlSignal
    * moved identification of monitored_output_states and control_signals for System
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    * moved assignment of controller from ControlMechanism to System

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  - removed assignment of default controller for System, can now be None

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

# Conflicts:
#	PsyNeuLink/Components/Functions/Function.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/DefaultControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanism/LearningMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Components/States/ModulatorySignals/ControlSignal.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/ObjectiveMechanisms/ComparatorMechanism.py
#	PsyNeuLink/__init__.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py
#	tests/mechanisms/test_integrator_mechanism.py

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* • System, ControlMechanism, ObjectiveMechanism
  - added dictionary specification for monitored_values
  - docstring revs and examples

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/control/clean_up

# Conflicts:
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py

* -

* -

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/control/clean_up

# Conflicts:
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py

* -

* Merge branch 'devel' of https://github.com/jdcpni/PsyNeuLink into feat/ObjectiveMechanism/monitored_values_dict

# Conflicts:
#	.idea/inspectionProfiles/Project_Default.xml
#	.idea/runConfigurations/DDM_Learning_Test.xml
#	.idea/runConfigurations/EVC_Gratton_Script___SEBASTIAN.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_DEBUGGING.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script__SPECIFY_ControlSignals__.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_with_Custom_Fn.xml
#	.idea/runConfigurations/EVC_System_Test_Script_with_Profiler.xml
#	.idea/runConfigurations/FinalProject.xml
#	.idea/runConfigurations/Make_HTML.xml
#	.idea/runConfigurations/Multilayer_Learning_Test_Script_VARIATIONS.xml
#	.idea/runConfigurations/Multilayer_Learning_Test_Script__WITH_GATING_.xml
#	.idea/runConfigurations/NEW_Learning_Markus.xml
#	.idea/runConfigurations/NetworkX_Examples.xml
#	.idea/runConfigurations/Profile_EVC_System_Test.xml
#	.idea/runConfigurations/Stroop_Model_Learning_and_Control_Test_Script.xml
#	.idea/runConfigurations/Stroop_Model_Test_Script_VARIATIONS.xml
#	.idea/runConfigurations/Two_Layer_Test_Script.xml
#	.idea/runConfigurations/Xor_Script_1_process_working.xml
#	.idea/runConfigurations/Xor_Script_2_processes.xml
#	.idea/runConfigurations/_DDM_Test_Script.xml
#	.idea/runConfigurations/_DDM_scheduled_simple.xml
#	.idea/runConfigurations/_Documentation_Examples.xml
#	.idea/runConfigurations/_EVC_System_DEMO_Script.xml
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	.idea/runConfigurations/_Integrator_scheduled_timescales.xml
#	.idea/runConfigurations/_META_TEST.xml
#	.idea/runConfigurations/_Mixed_NN___DDM_DEMO_Script.xml
#	.idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script_DEMO.xml
#	.idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml
#	.idea/runConfigurations/_Scratch_Pad.xml
#	.idea/runConfigurations/_Stroop_Demo_Script.xml
#	.idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml
#	.idea/runConfigurations/_Stroop_Model_Test.xml
#	.idea/runConfigurations/_System_Graph_and_Input_Test.xml
#	.idea/runConfigurations/_System_Learning_Test_Script.xml
#	.idea/runConfigurations/make_html_and_ghpages_py.xml
#	.idea/runConfigurations/test_system.xml
#	.idea/runConfigurations/topo_example.xml
#	PsyNeuLink/Components/Component.py
#	PsyNeuLink/Components/Functions/Function.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/AdaptiveMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/ControlSignal.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/DefaultControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVCMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/GatingMechanisms/GatingMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanism/LearningAuxilliary.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanisms/LearningMechanism.py
#	PsyNeuLink/Components/Mechanisms/Mechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/DDM.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/IntegratorMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ProcessingMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/RecurrentTransferMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/TransferMechanism.py
#	PsyNeuLink/Components/Process.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/ControlProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/GatingProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/ModulatoryProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/PathwayProjection.py
#	PsyNeuLink/Components/Projections/Projection.py
#	PsyNeuLink/Components/Projections/TransmissiveProjections/MappingProjection.py
#	PsyNeuLink/Components/States/InputState.py
#	PsyNeuLink/Components/States/OutputState.py
#	PsyNeuLink/Components/States/ParameterState.py
#	PsyNeuLink/Components/States/State.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Globals/Defaults.py
#	PsyNeuLink/Globals/Keywords.py
#	PsyNeuLink/Globals/Preferences/ComponentPreferenceSet.py
#	PsyNeuLink/Globals/Preferences/MechanismPreferenceSet.py
#	PsyNeuLink/Globals/Run.py
#	PsyNeuLink/Globals/TimeScale.py
#	PsyNeuLink/Globals/Utilities.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCAuxiliary.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/LCA.py
#	PsyNeuLink/__init__.py
#	PsyNeuLink/scheduling/Scheduler.py
#	PsyNeuLink/scheduling/condition.py
#	Scripts/DEBUGGING SCRIPTS/EVC Gratton Script - SEBASTIAN.py
#	Scripts/DEBUGGING SCRIPTS/EVC System Laming Validation Test Script [SPECIFY ControlSignals]].py
#	Scripts/DEBUGGING SCRIPTS/Multilayer Learning Test Script [WITH GATING].py
#	Scripts/DEBUGGING SCRIPTS/OLD/EVC System Laming Validation Test Script DEBUGGING.py
#	Scripts/DEBUGGING SCRIPTS/OLD/EVC_Gratton_Script_Validation.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Multilayer Learning Test Script VARIATIONS.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Scripts_DEBUGGING_SCRIPTS_EVC_Gratton_Script_-_SEBASTIAN_py.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Stroop Model Test Script VARIATIONS.py
#	Scripts/DEMO SCRIPTS/EVC System DEMO Script.py
#	Scripts/MISCELLANEOUS SCRIPTS/Reinforcement Learning Test Script [SIMPLE].py
#	Scripts/MISCELLANEOUS SCRIPTS/ddm-bug.py
#	Scripts/MISCELLANEOUS SCRIPTS/rate_bug.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py
#	Scripts/TEST SCRIPTS/Multilayer Learning Test Script.py
#	Scripts/TEST SCRIPTS/Reinforcement Learning Test Script.py
#	Scripts/TEST SCRIPTS/Stroop Model Test Script.py
#	TODO List.py
#	bfg.prep
#	docs/source/index.rst
#	tests/conftest.py
#	tests/control/test_EVC.py
#	tests/learning/test_multilayer.py
#	tests/learning/test_reinforcement.py
#	tests/learning/test_stroop.py
#	tests/mechanisms/test_ddm_mechanism.py
#	tests/mechanisms/test_gating_mechanism.py
#	tests/mechanisms/test_integrator_mechanism.py
#	tests/mechanisms/test_transfer_mechanism.py
#	tests/no-learning/test_DDM.py
#	tests/no-learning/test_no-learning.py
#	tests/scheduling/test_system_newsched.py
#	tests/system/test_system.py

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* Docs/mechanism/updated states fig (#484)

* • index.rst
  - main title changed to "Welcome to PsyNeuLink"

* • ControlMechanisms
  monitor_for_control argument and attribute changed to objective_mechanism

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	docs/source/index.rst

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	docs/source/index.rst

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

* Merge branches 'devel' and 'feat/Mechanism/LC' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Mechanism/LC

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	Scripts/DEBUGGING SCRIPTS/LCMechanism Test Script.py

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

* Merge branch 'refac/ControlMechanisms/monitor_for_control_to_objective_mechanism' of https://github.com/PrincetonUniversity/PsyNeuLink into refac/ControlMechanisms/monitor_for_control_to_objective_mechanism

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* • ControlMechanism, EVCMechanism, ControlSignal, ObjectiveMechanism and System:
  - all refactored to make simpler and more modular:
    * most instantiation code moved from EVCMechaism to ControlMechanism
    * moved handling of monitored_output_states to ObjectiveMechanism monitored_values
    * moved parsing of ControlSignal specification from ControlMechanism to ControlSignal
    * moved identification of monitored_output_states and control_signals for System
          to methods on System
    * moved assignment of controller from ControlMechanism to System

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* -

* • System
  - removed assignment of default controller for System, can now be None

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

# Conflicts:
#	PsyNeuLink/Components/Functions/Function.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/DefaultControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanism/LearningMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Components/States/ModulatorySignals/ControlSignal.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/ObjectiveMechanisms/ComparatorMechanism.py
#	PsyNeuLink/__init__.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py
#	tests/mechanisms/test_integrator_mechanism.py

* -

* -

* -

* -

* -

* • System, ControlMechanism, ObjectiveMechanism
  - added dictionary specification for monitored_values
  - docstring revs and examples

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/control/clean_up

# Conflicts:
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py

* -

* -

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/control/clean_up

# Conflicts:
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCMechanism.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py

* -

* Merge branch 'devel' of https://github.com/jdcpni/PsyNeuLink into feat/ObjectiveMechanism/monitored_values_dict

# Conflicts:
#	.idea/inspectionProfiles/Project_Default.xml
#	.idea/runConfigurations/DDM_Learning_Test.xml
#	.idea/runConfigurations/EVC_Gratton_Script___SEBASTIAN.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_DEBUGGING.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script__SPECIFY_ControlSignals__.xml
#	.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_with_Custom_Fn.xml
#	.idea/runConfigurations/EVC_System_Test_Script_with_Profiler.xml
#	.idea/runConfigurations/FinalProject.xml
#	.idea/runConfigurations/Make_HTML.xml
#	.idea/runConfigurations/Multilayer_Learning_Test_Script_VARIATIONS.xml
#	.idea/runConfigurations/Multilayer_Learning_Test_Script__WITH_GATING_.xml
#	.idea/runConfigurations/NEW_Learning_Markus.xml
#	.idea/runConfigurations/NetworkX_Examples.xml
#	.idea/runConfigurations/Profile_EVC_System_Test.xml
#	.idea/runConfigurations/Stroop_Model_Learning_and_Control_Test_Script.xml
#	.idea/runConfigurations/Stroop_Model_Test_Script_VARIATIONS.xml
#	.idea/runConfigurations/Two_Layer_Test_Script.xml
#	.idea/runConfigurations/Xor_Script_1_process_working.xml
#	.idea/runConfigurations/Xor_Script_2_processes.xml
#	.idea/runConfigurations/_DDM_Test_Script.xml
#	.idea/runConfigurations/_DDM_scheduled_simple.xml
#	.idea/runConfigurations/_Documentation_Examples.xml
#	.idea/runConfigurations/_EVC_System_DEMO_Script.xml
#	.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
#	.idea/runConfigurations/_Integrator_scheduled_timescales.xml
#	.idea/runConfigurations/_META_TEST.xml
#	.idea/runConfigurations/_Mixed_NN___DDM_DEMO_Script.xml
#	.idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script_DEMO.xml
#	.idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml
#	.idea/runConfigurations/_Scratch_Pad.xml
#	.idea/runConfigurations/_Stroop_Demo_Script.xml
#	.idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml
#	.idea/runConfigurations/_Stroop_Model_Test.xml
#	.idea/runConfigurations/_System_Graph_and_Input_Test.xml
#	.idea/runConfigurations/_System_Learning_Test_Script.xml
#	.idea/runConfigurations/make_html_and_ghpages_py.xml
#	.idea/runConfigurations/test_system.xml
#	.idea/runConfigurations/topo_example.xml
#	PsyNeuLink/Components/Component.py
#	PsyNeuLink/Components/Functions/Function.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/AdaptiveMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/ControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/ControlSignal.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/DefaultControlMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVCMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/GatingMechanisms/GatingMechanism.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanism/LearningAuxilliary.py
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/LearningMechanisms/LearningMechanism.py
#	PsyNeuLink/Components/Mechanisms/Mechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/DDM.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/IntegratorMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ObjectiveMechanisms/ObjectiveMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/ProcessingMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/RecurrentTransferMechanism.py
#	PsyNeuLink/Components/Mechanisms/ProcessingMechanisms/TransferMechanism.py
#	PsyNeuLink/Components/Process.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/ControlProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/GatingProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/ModulatoryProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/PathwayProjection.py
#	PsyNeuLink/Components/Projections/Projection.py
#	PsyNeuLink/Components/Projections/TransmissiveProjections/MappingProjection.py
#	PsyNeuLink/Components/States/InputState.py
#	PsyNeuLink/Components/States/OutputState.py
#	PsyNeuLink/Components/States/ParameterState.py
#	PsyNeuLink/Components/States/State.py
#	PsyNeuLink/Components/System.py
#	PsyNeuLink/Globals/Defaults.py
#	PsyNeuLink/Globals/Keywords.py
#	PsyNeuLink/Globals/Preferences/ComponentPreferenceSet.py
#	PsyNeuLink/Globals/Preferences/MechanismPreferenceSet.py
#	PsyNeuLink/Globals/Run.py
#	PsyNeuLink/Globals/TimeScale.py
#	PsyNeuLink/Globals/Utilities.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/EVC/EVCAuxiliary.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/LCA.py
#	PsyNeuLink/__init__.py
#	PsyNeuLink/scheduling/Scheduler.py
#	PsyNeuLink/scheduling/condition.py
#	Scripts/DEBUGGING SCRIPTS/EVC Gratton Script - SEBASTIAN.py
#	Scripts/DEBUGGING SCRIPTS/EVC System Laming Validation Test Script [SPECIFY ControlSignals]].py
#	Scripts/DEBUGGING SCRIPTS/Multilayer Learning Test Script [WITH GATING].py
#	Scripts/DEBUGGING SCRIPTS/OLD/EVC System Laming Validation Test Script DEBUGGING.py
#	Scripts/DEBUGGING SCRIPTS/OLD/EVC_Gratton_Script_Validation.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Multilayer Learning Test Script VARIATIONS.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Scripts_DEBUGGING_SCRIPTS_EVC_Gratton_Script_-_SEBASTIAN_py.py
#	Scripts/DEBUGGING SCRIPTS/OLD/Stroop Model Test Script VARIATIONS.py
#	Scripts/DEMO SCRIPTS/EVC System DEMO Script.py
#	Scripts/MISCELLANEOUS SCRIPTS/Reinforcement Learning Test Script [SIMPLE].py
#	Scripts/MISCELLANEOUS SCRIPTS/ddm-bug.py
#	Scripts/MISCELLANEOUS SCRIPTS/rate_bug.py
#	Scripts/Scratch Pad.py
#	Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py
#	Scripts/TEST SCRIPTS/Multilayer Learning Test Script.py
#	Scripts/TEST SCRIPTS/Reinforcement Learning Test Script.py
#	Scripts/TEST SCRIPTS/Stroop Model Test Script.py
#	TODO List.py
#	bfg.prep
#	docs/source/index.rst
#	tests/conftest.py
#	tests/control/test_EVC.py
#	tests/learning/test_multilayer.py
#	tests/learning/test_reinforcement.py
#	tests/learning/test_stroop.py
#	tests/mechanisms/test_ddm_mechanism.py
#	tests/mechanisms/test_gating_mechanism.py
#	tests/mechanisms/test_integrator_mechanism.py
#	tests/mechanisms/test_transfer_mechanism.py
#	tests/no-learning/test_DDM.py
#	tests/no-learning/test_no-learning.py
#	tests/scheduling/test_system_newsched.py
#	tests/system/test_system.py

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* • Mechanism
  - updated Mechanism_States_fig and caption

* adding all params of FHNIntegrator Function to the LCControlMechanism. Appended '_FHN' to each param name b/c Mechanism cannot have params of the same name as params of its function

* passed in all arguments to the FHNIntegrator where the LCControlMechanism specifies FHN as its function in super().__init__

* move tutorial notebook to its own dedicated folder

* change test_notebooks to only test the notebooks in the tutorial folder (if more notebooks are added in the future, add them to be run by this test

* replace Adpative with Adaptive

* import ShellClass Mechanism directly instead of implicitly importing it through the Mechanism.py module

* import ShellClass Projection directly instead of implicitly importing it through the Projection.py module

* import ShellClass State directly instead of implicitly importing it through the State.py module

* import ShellClass Process directly instead of implicitly importing it through the Process.py module

* import ShellClass System directly instead of implicitly importing it through the System.py module

* replace nonexistence ControlMechanism_Base uses with the real ControlMechanism

* optimize imports via pycharm

* make IntegratorMechanism get its paramClassDefaults from its parent ProcessingMechanism_Base rather than a more distant ancestor Mechanism_Base

* refactoring rk helper method to compute the two variables (v and w) concurrently and update their approximations of each other throughout the timestep

* adding pytest to verify FHNIntegrator function against Gilzenrat paper figure 2

* adding ipykernel>=4.6.1 to dev_requirements.txt

* fixing Project Defaults

* removing toposort from ignoredPackages

* adding Project_Default.xml to gitignore

* revising FHN integrator docs comparisons to other models (Gilzenrat, Modified FHN) to be easier to follow and have all correct signs

* Update Project_Default.xml

* ensure that MechanismPreferenceSet imports its parent class

* define undefined default values in MechanismPreferenceSet

* temporary fix: changing LCControlMechanism output to (gain(w_t), gain(w_t), v_t, w_t, t) so that both modulated mechanisms receive gain. Should be refactored so that this is handled by selecting output states/control signals

* replace calls to numpy typechecking from 64 bit to 64 or 32bit versions

* make TransferMechanism.paramClassDefaults copy its parent instead of Mechanism_Base

* cleanup test_recurrent_mechanism.py imports

* replace crude assertions with numpy assert_allclose in test_recurrent_transfer_mechanism

* test_recurrent_transfer_mechanism.py PEP8 format

* adding a new function called 'LCAIntegrator' which computes rate*previous_value + variable

* updating execute method of LCA to call LCAIntegrator and renaming time_constant --> beta to match the new function

* relaxing validation on LCAIntegrator rate param in order to create an LCA example in integrator mode with an array input

* remove mechanismGenerator

* rename packages and modules to lowercase, and handle relevant import changes

* remove old pyargs argument for pytest

* move typecheck for _get_modulated_param inside to avoid circular import

* switch name of System and System_Base

* switch name of Process and Process_Base

* remove process factory in favor of just instantiating Process class

* make LearningMechanism get its paramClassDefaults from its parent and not Projection_Base

* rework imports to avoid circularities due to packaging

* remove system factory in favor of just instantiating System class

* remove mechanism factory method

* clean up main package __init__.py

* replace paramClassDefaults PROJECTION_SENDER with OutputState class instead of keyword to prevent error due to failed conversion

* rename globals/run.py to globals/environment.py to avoid namespace conflict with run method

* add __all__ lists to modules

* update package __init__.py files for simple importing

* update tutorial to new easier import style

* update docs to handle new module/package format

* update setup.py packages

* add MANIFEST.in

* add requirements.txt mirroring setup.py requirements

* remove extraneous files

* remove SOFTWARE ARCHITECTURE and TODO List

* add docstrings to __init__.py files (for help command)

* update setup.py classifier for Apache license

* update setup.cfg for wheel creation and to include license file

* update setup.py supported Python versions to include only 3.5 and 3.6 (does not work on < 3.4 due to numpy, does not work on 3.4)

* update short description to match the title line in the long description

* reformat README into .rst format so pypi can format it nicely

* add tutorial_requirements.txt mirroring setup.py requirements

* update README and docs index.rst to new PyPI installation instructions, and tutorial section, reorganize

* adding a new Integrator function that matches the decision and response layer functions in the Gilzenrat paper, and a new transfer mechanism which calls this integrator before its primary function

* updating value of LC control mechanism output before it runs to match initial previous value (had to do this in the gilzenrat script because of other LC control mechanism hacks, but left a placeholer in ControlMechanism for how to implement this more generally for any control mechanism that accumulates)

* removing and re-adding gilzenrat transfer mechanism because name change did not seem to work

* remove DefaultProcessingMechanism from component/__init__.py because it's an instantiation of a _Base class, and doesn't get used

* make Function_Base inherit its paramClassDefaults from its parent class Function instead of Component

* improving initial conditions by making first recurrent projections to recurrent mechanisms make sense given their starting values

* Devel (#490)

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml

* -

* -

* • System
  - show_graph(): allowed standard graph to show connections to ObjectiveMechanisms
                  for ControlMechanisms other than the System's controller

* -

* -

* -

* • System
  instantiate_graph:
      patched bug in which search for ORIGIN Mechanisms in Processes
      within the System fails if a Mechanisms belongs to some but not
      all Processes within the System

* correcting LCAIntegrator function to match the papers (since it represents a rate of change, we need to integrate over timesteps) and relaxing integrator rate param validation which was blocking variables of lengths > 1

* fix link to the tutorial in docs that didn't get changed when tutorial/ directory was created

* fixing bug in NormalDist() function which was shifting the mean of the distribution

* stop package-level __all__ assignments from accidentally overwriting the __all__ objects they used as bases

* skip notebook checkpoints in running notebook tests

* fold keywords into first level hierarchy, because some keywords aren't defined in Keywords.py and this is confusing

* add component module to main psyneulink package

* indexing into the first element of the transfer mechanism's integrator_function result so that the shape passed to the transfer mechanism's function is the same as if integrator_mode were false

* updating mechanism pytests to reflect integrator_function shape change and removing extraneous transfer mechanism tests which returned arrays of mixed types

* Refactored instantiation of States and Projections (#494)

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • System
  - implement multiple ControlMechanism for System
  - identify Terminal Mechanism when there are control-related ObjectiveMechanisms

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* • Mechanism
  - updated Mechanism_States_fig and caption

* • State
  - refactored _parse_state_spec to call State subclass
    for parsing of class-specific specifications

• InputState
  - added _parse_state_specific_dict_entries

* -

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* • Projection (and subclasses)
  - added weight and exponent attributes

* -

* • Projection
  - moved _parse_connection_specs from State to here and
    renamed as _parse_projection_specs;  refactored it as a filter
    on the constructor to a projection (allowing for state-specific
    formats for the call (i.e., State specification tuples)
  - instantiates any projections that have not yet been, allowing any
    that are not yet fully specified to be assigned deferred_init status

* • Projection
  - moved _parse_connection_specs from State to here and
    renamed as _parse_projection_specs;  refactored it as a filter
    on the constructor to a projection (allowing for state-specific
    formats for the call (i.e., State specification tuples)
  - instantiates any projections that have not yet been, allowing any
    that are not yet fully specified to be assigned deferred_init status

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* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projections/_parse_connection_specs

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projections/_parse_connection_specs

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py

* • Refactor parsing of State and Projection

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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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

* 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

* 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

* 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

* 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

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

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

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* - EVC scripts working
- Gating script still failing test

* - Gating script now just failing test on Function Error

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  Added Gating Mechanism Test Script to TEST SCRIPTS

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* • Passes all tests

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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* • TEST SCRIPTS:
  Added Gating Mechanism Test Script to TEST SCRIPTS

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* • LearningMechanism, ControlMechanism, GatingMechanism:
  - _instantiate_output_states:  all now use this to instantiate ModulatorySignals
  - _instantiate_XXX_signal:  all deleted
  - all now use _parse_state_specs and _parse_connecion_specs, and _parse_projection_specs

* • LearningMechanism, ControlMechanism, GatingMechanism:
  - _instantiate_output_states:  all now use this to instantiate ModulatorySignals
  - _instantiate_XXX_signal:  all deleted
  - all now use _parse_state_specs and _parse_connecion_specs, and _parse_projection_specs

* Refactor/state and projection/specification bug fix 2 (#495)

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • ObjectiveMechanism, ControlMechanism
  - _instantiate_monotired_states():
        added option to include matrix specification to monitored_output_states tuple
        for projection to ObjectiveMechanism's input_state(s) from monitored_output_state(s)

* • Library
  - renamed Subystems to Compositions
  - added Models
  - added GilzenratModel as example

* • Mechanism
  - updated Mechanism_States_fig and caption

* • State
  - refactored _parse_state_spec to call State subclass
    for parsing of class-specific specifications

• InputState
  - added _parse_state_specific_dict_entries

* -

* -

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* • Projection (and subclasses)
  - added weight and exponent attributes

* -

* • Projection
  - moved _parse_connection_specs from State to here and
    renamed as _parse_projection_specs;  refactored it as a filter
    on the constructor to a projection (allowing for state-specific
    formats for the call (i.e., State specification tuples)
  - instantiates any projections that have not yet been, allowing any
    that are not yet fully specified to be assigned deferred_init status

* • Projection
  - moved _parse_connection_specs from State to here and
    renamed as _parse_projection_specs;  refactored it as a filter
    on the constructor to a projection (allowing for state-specific
    formats for the call (i.e., State specification tuples)
  - instantiates any projections that have not yet been, allowing any
    that are not yet fully specified to be assigned deferred_init status

* -

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* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projections/_parse_connection_specs

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projections/_parse_connection_specs

# Conflicts:
#	PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanism/ControlMechanism.py
#	PsyNeuLink/Components/Projections/ModulatoryProjections/LearningProjection.py
#	PsyNeuLink/Components/Projections/PathwayProjections/MappingProjection.py
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/ControlMechanisms/LCMechanism.py

* • Refactor parsing of State and Projection

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

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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

* 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

* 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

* 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

* 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

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

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

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* • System
• ControlMechanism
• ControlSignal
 - copied from old version

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* - Version diverged from merge with new devel:
  Only changes are to ControlMechanism and ControlSignal

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* - EVC scripts working
- Gating script still failing test

* - Gating script now just failing test on Function Error

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  - Added EVC System Gratton Validation Test Script

* • TEST SCRIPTS:
  Added Gating Mechanism Test Script to TEST SCRIPTS

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* • Passes all tests

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

* • GatingMechanism
  - _instantiate_gating_signal: refactoring to match _instantiate_control_signal

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* Merge branches 'devel' and 'feat/RecurrentTransferMechanism/add_learning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/RecurrentTransferMechanism/add_learning

# Conflicts:
#	PsyNeuLink/Library/Mechanisms/AdaptiveMechanisms/LearningMechanisms/AutoAssociativeLearningMechanism.py
#	PsyNeuLink/Library/Mechanisms/ProcessingMechanisms/TransferMechanisms/RecurrentTransferMechanism.py
#	Scripts/Scratch Pad.py

* -

* • TEST SCRIPTS:
  Added Gating Mechanism Test Script to TEST SCRIPTS

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* • LearningMechanism, ControlMechanism, GatingMechanism:
  - _instantiate_output_states:  all now use this to instantiate ModulatorySignals
  - _instantiate_XXX_signal:  all deleted
  - all now use _parse_state_specs and _parse_connecion_specs, and _parse_projection_specs

* • LearningMechanism, ControlMechanism, GatingMechanism:
  - _instantiate_output_states:  all now use this to instantiate ModulatorySignals
  - _instantiate_XXX_signal:  all deleted
  - all now use _parse_state_specs and _parse_connecion_specs, and _parse_projection_specs

* • LearningMechanism, ControlMechanism, GatingMechanism:
  - _instantiate_output_states:  all now use this to instantiate ModulatorySignals
  - _instantiate_XXX_signal:  all deleted
  - all now use _parse_state_specs and _parse_connecion_specs, and _parse_projection_specs

* -

* -

* -

* -

* updating kwta and transfer pytests with correct error message text

* -

* -

* • Component
  _validate_params: fixed bug that was causing to fail to detect some params

• InputState:
  - _parse_state_specific_specs: now infers variable from projection_spec

* replacing GilzenratIntegrator with LCAIntegrator (with rate=-1) in GilzenratTransferMechanism

* implementing noise on LCAIntegrator and cleaning up unnecessary integrator function code (removing GilzenratIntegrator)

* adding progress statement ('% complete') to gilzenrat script

* Optimize registry duplicate naming

Replace inefficient renaming algorithm with faster version, that additionally provides more meaningful names (numeric suffix for duplicate names is now based on the number of duplicates per name rather than per componentType)

* fixing up a few model values in the gilzenrat model -- behavior is not quit right -- and switching number_of_trials back to 1

* adding pytests that isolate the GilzenratTransferMechanism and moving FHNIntegrator test that recreates figure 2 from gilzenrat paper from integrator mechanism tests --> gilzenrat tests

* adding full gilzenrat model to pytests -- no comparison data to assert yet, just verifying that model can run without errors

* moving imports to top of gilzenrat pytests file

* requiring version 1.4 of toposort

* 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

* Refactor/state and projections/unit tests (#501)

* -

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* -

* -

* -

* -

* -

* -

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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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* -

* -

* -

* -

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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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* -

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

* • tests/mechanisms/test_transfer_mechanism
  - added unit tests for specification of input_states
    COMMENTED OUT tests that need to be debugged,
    and ones that elicit bugs in the code that need attention

* Refactor/state and projection/unit tests bug fixes (#502)

* • tests/mechanisms/test_transfer_mechanism
  - added unit tests for specification of input_states
    COMMENTED OUT tests that need to be debugged,
    and ones that elicit bugs in the code that need attention

* • tests/mechanisms/test_transfer_mechanism
  - added unit tests for specification of input_states
    COMMENTED OUT tests that need to be debugged,
    and ones that elicit bugs in the code that need attention

* • tests/mechanisms/test_transfer_mechanism
  - unit tests for input_states: debugged several

* avoid using module-level Mechanisms in unit tests to avoid possible conflicts

* fix typo in ObjectiveMechanism docstring causing weird documentation formatting

* Refactor/state and projection/clean up (#503)

* • tests/mechanisms/test_transfer_mechanism
  - unit tests for input_states: debugged several

* • tests/mechanisms/test_transfer_mechanism
  - unit tests for input_states: debugged several

* • States, Projections
  - clean-up of comments/commented-out code

* -

* -

* Refactor/projection/ instantiate sender (#504)

* • tests/mechanisms/test_transfer_mechanism
  - unit tests for input_states: debugged several

* • tests/mechanisms/test_transfer_mechanism
  - unit tests for input_states: debugged several

* • States, Projections
  - clean-up of comments/commented-out code

* -

* -

* -

* -

* • Projection (#505)

_validat_params and _instantiate_sender: code simplification

* Refactor/gating mechanism/ instantiate gating signal (#506)

* • Projection
  _validat_params and _instantiate_sender: code simplification

* • Projection
  _parse_connection_spec and _parse_projection_spec

* • GatingMechanism
  _instantiate_gating_signal: reimplemented
                              refactored handling of gating_policy
• Projection
  _parse_connection_spec and _parse_projection_spec

* • GatingMechanism
  _instantiate_gating_signal: reimplemented
                              refactored handling of gating_policy
• Projection
  _parse_connection_spec and _parse_projection_spec

* -

* • GatingMechanism
  _instantiate_gating_signal: reimplemented
                              refactored handling of gating_policy
• Projection
  _parse_connection_spec and _parse_projection_spec

* Refactor/projection/connection specs (#507)

* • Projection
  _parse_connection_specs: moved connection info to states

* -

* -

* • Projection
  _parse_connection_spec:  moved connection attributes to State subclasses

• Registry:
  -register_category: added test for connection attributes on State subclasses

* Clean up/registry/ register category (#508)

* -

* • Registry
  _register_category:  clean-up of connection attribute validation

* rename System and Process to add _Base suffix in shellclasses.__all__ because of abf3e7e7c and 6b9e9a4e2

* Fix/utilities/iscompatible (#511)

* Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel

# Conflicts:
#	.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml
…
kmantel added a commit that referenced this pull request Apr 5, 2018
* devel:
  Feat/mechanism/input target label dicts (#751)
  Scheduling: fix bug where termination conditions persisted across calls to run
  tests,function/LinearCombination: Add tests with absent parameters
  test,function/LinearCombination: Rename second test function to prevent overwriting results
  • Context (#746)
  Refactor/context/deprecate init status (#745)
  Refactor/context/structured (#744)
  Fix/function/stability (#743)
  • IntegratorMechanism (#742)
  Feat/context/time (#740)
  Feat/context/time (#739)
  Image Fix (#738)
  finally fixed image (#737)
  Image Fix (#736)
  Example Fix (#735)
  Linear combination fix (#734)
  Feat/component/execution count (#733)
  jvesely/linear_combination_function_refactor (#732)
  Refactor/project/context rev 2 (#731)
  Refactor/system/show graph structure options (#730)
  • System (#729)
  Feat/mechanism/show structure (#728)
  Feat/mechanism/show mechanism (#727)
  jvesely/linear_combination (#724)
  creating a property for TransferMechanism's integrator_mode so that the mechanism can switch integrator mode on and off
  Fix/function/udf examples (#722)
  • Function (#717)
  Refactor/function/udf (#716)
  Refactor/mechanism and output state/mech params dict added (#715)
  Docs/output state/clean up (#714)
  Clean up/function/softmax one hot (#713)
  Name/project/replace assign index calculate (#711)
  Fix/controlmechanism/assign as controller jdc (#705)
  Feat/function/one hot cleanup (#704)
  Feat/function/one hot (#703)
  adding a pytest for the clear_log method
  updating output of nparray_dictionary when there are no entries from None to an empty OrderedDict
  Tests/llvm devel sync (#684)
  removing show graph pdfs from tests folder
  revising the show_graph pytests to call '_get_label' as a proxy for whether show_graph with dimensions is working
  moving _get_label helper function outside of show_graph method, so that it can be accessed on its own
  fixing bug in show_graph(show_dimensions=True) by taking np.atleast_1d of output_state.value
  • LearningProjection   docstring rev (to include error_function)
  Feat/process/learning objective mech (#698)
  Feat/ddm/selected input array (#697)
  Feat/ddm/selected input array (#695)
  user_params and function_params now look at parameter state values (rather than param base values), and are updated whenever mechanisms update their parameter states
  adding pytests that call show graph after creating various types of systems -- may refactor these to call the individual methods of show_graph
  removing system graph pdfs
  removing show_dimensions=True from call to show_graph in GilzenratModel because it generates an error
  updating how valus are retrieved from log in Nieuwenhuis model (based on addition of Pass to log)
  Fix/system/learning ends before terminal (#692)
  Fix/system/learning ends before terminal (#691)
  Revert "Merge branch 'master' into fix/system/learning_ends_before_terminal"
  -
  • ControlMechanism   _instantiate_control_signals:  debugged OWNER_VALUE assignment
  • Scripts/Examples   Rumelhart Semantic Network: updated with step function
  • System   _instantiate_learning_graph(): fixed bug in which learning failed to     be instantiated for a System in which the last Mechanism in a     learning sequence was not the TERMINAL Mechanism of the System.
  • System   _instantiate_learning_graph(): fixed bug in which learning failed to     be instantiated for a System in which the last Mechanism in a     learning sequence was not the TERMINAL Mechanism of the System.
  • OutputState   docstring revs
  • OutputState   docstring revs
  fixing documentation formatting mistake
  continuing to add pytests and doc fixes for clip on transfer mechanism types
  allowing lca to execute function over entire variable, not just first item
  fixing documentation for clip
  continuing to add error messages to reinitialize
  allowing smoothing factor to be an integer (formerly 1.0 and 0.0 were allowed but 1 and 0 were not)
  removing typecheck on learning mechanism's default_variable
  adding exception in UDF so that function can be called without params and context
  correcting error message for initial_value validation on transfer mechanism
  fixing bug in reinitialize on arrays (needed np.atleast_2d when setting intial_value because it is compared to variable)
  -
  • OutputState   docstring revs
  Refactoring of OutputState to support flexible assignment of its variable attribute.
  Revert "-"
  Revert "-"
  Revert "-"
  -
  adding pytests for specific reinitialize cases that were not covered, and adding error messages that were missing for some of them
  -
  fixing documentation typo: integration_method was mistakenly called integration_method_FHN in docs
  -
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  Reworking Montague, Dayan, and Sejnowski model documentation.
  -
  Merge branches 'bug/parsing/input_states-use-value' and 'feat/DDM/value_based_version_input_state' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/DDM/value_based_version_input_state
  Merge branches 'bug/parsing/input_states-use-value' and 'feat/DDM/value_based_version_input_state' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/DDM/value_based_version_input_state
  -
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  -
  -
  -
  • Utilities   - recursive_update():  added non-destructive option that preserves                          any non-empty entries in destination dict
  -
  -
  -
  • OutputState   this version implements OutputState.variable as a property   that returns _parse_output_state_variable()
  • OutputState   this version implements OutputState.variable as a property   that returns _parse_output_state_variable()
  -
  -
  -
  -
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  adding pytests for invalid target specifcation to confirm that the proper error messages are generated
  • OutputState   assign function now expects dict as argument - WORKING
  adding more pytests to confirm that convenience notations and combinations of function and list target specs all run
  documenting targets and adding some checks to adjust targets: verify that num_targets = num_inputs, and ignore num_targets in the case of function specifications (because a new value is generated on each trial)
  -
  -
  -
  -
  • OutputState   - implemented assign that takes assign_params_dict as arg
  Fix/output state/assign backward compat (#676)
  • OutputState   added backward compatibility   docstring: document replacement of calcuate/CACULATE with assign/ASSIGN
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  in progress: refactoring function specification of target spec to be an option within the dictionary specification, rather than on its own
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  Feat/ddm/input state as array (#674)
  revising documentation for target specification
  cleaning up a typo in target_spec_parsing (comparator mechanism was referenced where it should have been terminal mechanism)
  moving call to _check_args in BackProp to before the error matrix is updated in order to avoid a validation bug
  adding pytests for target spec convenience notations
  adding run to rumelhart tests (previously only created systems)
  Merge branches 'clean_up/function_and_system/backprop_and_show_graph' and 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into clean_up/function_and_system/backprop_and_show_graph
  revising how target input state values are assigned in system's execute_learning
  adding a simple multilayer learning pytest
  refactor execute and _execute methods
  defaults: remove post-hoc conversion of defaults variable
  Component: don't convert defaults variable on calls to validate a variable
  parsing: add initial_value parser
  parsing: add generic argument parser used as default if none specified
  Component: add method to parse user inputted variable to useable/standard form
  utilities: handle nonuniform objects better when converting to numpy arrays
  control: refactor handling of allocation*
  projections: refactor sender instantiation to avoid directly setting instance default variable
  clean up input_states handler
  rename input_states arg parser to handler
  maint: add comments to separate handler, parsing, and validation methods
  maint: remove unused PROJECTION_SENDER_VALUE
  TransferMechanism: use standard form of setting default variable
  utilities: change number detection to accept any number, not just int and float
  OutputState: when variable not specified to constructor, pass up another value
  make self.variable read only (we should not be using it for logic)
  replace calls to self.variable to proper self.instance_defaults.variable
  validation: remove extraneous check for ClassDefaults.variable
  ClassDefaults: make RecurrentTransferMechanism default require 2d variable because it takes an AutoAssociativeProjection that uses a LinearMatrix that requires 1D
  Distance: fix validation assumption that items of passed variable are iterable
  ClassDefaults: correct and consolidate
  utilities: add method to produce a value for length calls when len() fails
  utilities: add function to determine whether something is iterable
  Integrators: handle initializer like variable in Components
  Function: standardize default_variable assignments
  ProcessingMechanism: use standard assignment of default variable
  DDM: use standard assignment of default variable
  ensure default_variable auto sets to dtype float
  combine handling of default_variable/size to create instance_defaults.variable in Component.__init__
  utilities: allow list->array element conversion to typecast internal items
  validation: fix validate_variable crashes on certain variable types
  utilities: add helper method to determine if an object contains a single value
  rename variable->default_variable
  Clean up/function and system/backprop and show graph (#671)
  Clean up/learning/misc (#670)
  Clean up/learning/misc (#669)
  Clean up/learning/misc (#668)
  Fix/transfermechanism/noise function (#667)
  Fix/transfermechanism/clip (#666)
  Refactor/modulatory signals/linear default function (#665)
  Refactor/learning/heterovergent (#664)
  in progress - refactoring adjust_target_dict method to validate all candidate targets and confirm that all mechanisms provided the same number of targets
  Tests/mechanism/hebbian learning (#663)
  Docs/function/hebbian (#662)
  Docs/function/hebbian (#661)
  updating pytest expected values based on changes to log output
  adding Pass to log output and updating pytests accordingly
  Fix/learning/hebbian (#659)
  swapping all log references to 'simple_time' with the full 'time', and removing old code which handled time stamp duplicates
  in progress - refactoring target spec/validation to work the same way as input spec/validation
  renaming object --> component in _adjust_target_dict()
  updating pytests to match RecurrentTransferMech switch from full matrix to hollow matrix; changed expected output or set auto = 1 to preserve old expected output, depending on type of test
  setting default matrix of a RecurrentTransferMechanism to a hollow matrix, and updating docs to be clearer about how auto, hetero, and matrix combine/overwrite each other when multiple arguments are specified
  renaming object --> component in _validate_targets method to avoid shadowing python built-in
  updating pytest expected results to match increment change in log
  log pytest for a mechanism that is scheduled to run many times in a row
  changing increment size on log's time_step workaround
  temporary workaround for timestep values: incrementing first decimal of timestep
  revising log tests for new time_step notation
  temporary workaround for timestep values: incrementing first decimal of timestep
  revising parse_entries_for_time_values method on log so that it edits the time values in the log items directly, rather than maintaining a separate list of modified time values
  setting axis=1 on calls to np.sum and np.product in Reduce function and adding tests for this function
  documentation typos
  documenting reinitialize on mechanism
  continuing to add tests and docs for reinitialize
  fixing bugs that prevented initialize method on system from ever executing, and adding pytests for it now that it works
  revising outdated TransferMechanism docs for reinitialize
  continuing to add tests to highlight differences between calling reinitialize on a mechanisms and on a function
  adding nparray_dictionary to docs and revising nparray to use the same helper methods as nparray_dictionary
  Time: fix bug where RUN counter would not be incremented on new runs
  fixing (temporarily) time_step bug in nparray_dictionary; reorganzing nparray_dictionary into methods that can be reused by nparray
  refactoring log to have a dictionary option and writing tests for it
  beginning to add a dictionary alternative to the options for whats returned by the log
  more calls to _dealias_owner_name required in order to create log.nparray
  fixing bug in log: needed to switch between 'value' and mechanism name in several loops in order to assemble log.nparray
  -
  Feat/rl/for mads (#652)
  Feat/rl/for mads (#651)
  adding more pytests for reinitialize and fixing reinitialize bugs; beginning to update documentation
  adding pytests for reinitializing at both function and mechanism level; cleaning up mistakes in reinitialize() methods along the way
  Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projection/Context_devel
  adding a reinitialize method on mechanisms, which calls reinitialize on its function or integrator_function, then updates the mechanism's value and output states
  beginning to refactor reinitialize as a method on integrator functions
  Removed Print Statements (#650)
  cleaning up documentation to match how LinearMatrix works in all cases
  typo in linear matrix function validation
  simplifying non-projection branch of validation on LinearMatrix function and adding more pytests
  default_variable: let argument override input_states variable spec if compatible
  adding pytests for possible combinations of variable and matrix specifications for LinearMatrix as a function of a mechanism
  adding validation comparing matrix to variable when LinearMatrix function is called by a mechanism; creating square full connectivity matrix that matches variable when matrix is not specified
  tutorial: reenable graph drawing; requires graphviz package
  tutorial: clear outputs
  Lena Program 1 Bugfix (#648)
  Hebbian learning fix (#647)
  User defined function updates (#646)
  adding working version of LinearMatrix function pytest (only works because default_variable is specified on both the mechanism and the function)
  fix input_states argparsing to not be dependent on default_variable or size args
  tests: ensure leabra tests get skipped if module is not available
  splitting linear matrix function's validation into two branches because matrix is handled differently when the function is called by a projection vs a receiver
  docstring wording change
  Docs/models/title changes (#645)
  Docs/nieuwenhuis/edits (#644)
  adding pytest for ProcessingMechanism with LinearMatrix function to begin debugging why this fn only works in Projections
  removing unrestrictedtransfermechanism file because this mechanism is now called ProcessingMechanism and does not need its own file
  adding parameter state docs examples back in with doctest SKIP
  revising proccessing mechanism docs because it is not an executable mechanism (not just an ABC)
  renaming UnrestrictedProcessingMechanism --> ProcessingMechanism and moving code into processingmechanism.py (which formerly only contained ProcessingMechanism_Base
  Leabra Update (#642)
  DDM: update is_finished to work on functions with any dimensional variable
  skipping transfer mechanism doc tests
  skipping transfer mechanism doc tests
  minor documentation changes -typos and formatting mistakes
  reorganizing integrator mechanism pytests for reinitialize
  overwriting AGTUtilityIntegrator's reinitialize property - requires custom reinitialization of short term and long term utility
  overwriting FHNIntegrator's reinitialize property - requires custom reinitialization of v, w, time, value
  overwriting reinitialize property on DriftDiffusion Integrator so that time can also be reset
  documenting reinitialize on all Integrator functions and fixing a typo in transfer mechanism docs (initial_value --> initializer)
  continuing to add docs and examples for reinitialize, and cleaning up TransferMechanism docs along the way
  fixing tutorial indexing bug
  refactoring is_finished as a property so that it is always up to date, even when values change in between executions (i.e. if threshold was crossed and then reinitialize was used)
  fixing bug in transfer mechanism documention examples (np.array typo)
  renaming reset_intializer --> reinitialize
  adding unrestricted mechanism pytests to confirm that mechanism can be constructed and executed with any function -- identified two exceptions (linear matrix and back prop)
  adding a new mechanism that has no restrictions on which functions can be used
  commenting out show graph lines in tutorial for now because graphviz is not imported on testing server
  adding updated version of tutorial from Justin
  Defaults*: fix class structure addressing bugs
  revising transfer mechanism documentation -- 'creating' section
  commenting out show_graph in EVC gratton pytest so that this line does not run on Jenkins
  adding TransferMechanism pytests to verify previous_value persists over multiple runs/executions AND previous_value resets whenever reset_initializer is used
  edited  NieuwenhuisModel docs
  tutorial: remove old version - new version is in tutorial/ dir
  tutorial: support execution on mybinder.org
  tutorial: support execution on mybinder.org
  tutorial: remove old version - new version is in tutorial/ dir
  • Niewenhuis model   - docstring edits
  -
  adding integrator_mode and integrator_function attr documentation for all transfer mechanism types
  revising outdated documentation for transfer mechanism noise
  fixed bug in plotting Nieuwenhuis Model
  updated Nieuwenhuis documentation
  adding attrs that were missing from LCA mechanism docs and revising related documentation
  Scripts: clean up
  Functions: add UniformToNormalDist to top-level psyneulink module; update docs
  revising explanation of user_params
  revising explanation of user_params
  revising parameter state documentation
  adding Markus' Nieuwenhuis documentation, plus figures and some .rst formatting
  Functions: replace internal calls to find owner's name with a property
  Component: make string version of *defaults classes be sorted
  removing parameter state example from file completely (tried commenting it out originally)
  removing parameter states example from documentation because it may be the reason parameter state tests are failing
  renaming 'Core Configurable Attributes' --> 'Core Structural Attributes' in Component documentation
  Refactor/system/controller (#627)
  Fix/controlmechanism/assign as controller (#625)
  • Log (#624)
  fixing typo in doctest (parameter state values)
  adding a docs example which walks through how a mechanism parameter and a function parameter and their mod_ versions change in value
  BogaczEtAl: use better numpy method for floating point warning handling
  utilities: update compatibility checker to terminate earlier in some cases
  updating modulation-related documentation to include mod_param and be more precise about what is updated by modulation (the parameter value used by a function changes, but the corresponding function attr does not change b/c it is the base value)
  adding documentation for mod_param
  allowing user to pass value into mod_param setter (even though setting is not allowed) in order to produce a more informative error message)
  commenting out noise and smoothing factor properties in transfer mechanism because these replace the default properties, causing unexpected behavior
  adding pytest to verify correct error message when user tries to set to mod_param_name
  adding pytest to track changes in attr, _attr, mod_param_name, and userparams[param_name] values of Transfer Mechanism's configurable params when (1) param values are updated (2) mechanism is executed
  adding an exception to make_mod_param as a temporary fix for function-specific mod_param properties that stay on mechanism class when function changes
  fixing typo in AGTUtilityIntegrator
  cleaning up function.py and verifying that self.get_current_function_param is used in all functions (skipped learning functions for now)
  Fix/controlmechanism/assign as controller (#620)
  Fix/controlmechanism/assign as controller (#619)
  cleaning up recurrent transfer mechanism pytests and fixing bugs in asserts
  updating matrix setter to also set the projection's matrix parameter state's function's previous value
  uncommenting auto and hetero properties from auto associative projection so that setting auto and hetero directly on the projections works
  adding auto and hetero properties to recurrent transfer mechanism. Auto, hetero, and matrix setters now all update recurrent_projection's matrix parameter state's function's previous_value
  Fix/controlmechanism/assign as controller (#618)
  executing projection individually in tranfer mechanism's matrix-change pytest
  adding a matrix-change pytest for a mapping projection between two transfer mechanisms in order to isolate the matrix bug from auto/hetero properties
  Defaults: clean up method organization
  fixing shape typo in gilzenrat script
  fixing overly strict rate param validation that caused bug in cases where mechanism looks up parameter state value
  refactoring transfer mechanism to use get_current_mechanism_param()
  refactoring LCA to use get_current_mechanism_param()
  refactoring kwta's _kwta_scale() to rely on get_current_mechanism_param()
  adding get_current_mechanism_param method on mechanism base to try to look up parameter state value
  remove now-unused time_scale param from many objects (not in scheduling where it's still used)
  log doctests: ignore tests with inconsistent whitespacing
  removing auto and hetero assignments from params dict in recurrent transfer mechansim
  removing unnecessary auto and hetero code in auto associative projection to clean up the relationship between the recurrent projection, its mechanism, and the auto, hetero, and  matrix, attrs
  requiring _kwta_scale method to use k_value parameter state value when available
  commenting out calssPreferences in transfer mechanism because they cause bugs in KWTA when classPreferences try to update
  removing attempt to look up recurrent projection's matrix in matrix getter (because the recurrent projection looks up its owner's matrix)
  refactoring matrix getter on auto associative projection to look up owner's matrix whenever possible
  directly updating auto and hetero attrs at the same time that their parameter states are created in the auto specified, hetero = None and hetero specified, auto = None cases
  beginning to refactor auto/hetero/matrix handling to fit with new parameter state value and make_property changes; beginning by removing obsolete code in recurrent transfer mechanism
  removed CentralClock from MontagueDayanSejnowski96.py
  fixed typo in owner attribute description
  Fix/function/validate params (#616)
  Defaults: set up structure to allow proper aliasing for *Defaults classes
  - Renamed MontagueModel.py to MontagueDayanSejnowski96.py - Correct RST formatting in PredictionErrorMechanism docs - Added Arguments and Attributes to docs for PredictionErrorMechanism
  LinearCombination: rework check for division by zero error to be more general
  default_value: refactor into instance_defaults
  Component: add metaclass for *Defaults to allow some user convenience functionality
  Refactor/control signal/update to intensity (#613)
  Fix/component/intensity and value (#612)
  Fix/gilzenrat model/prefs bug (#611)
  updating DDM mechanism to get threshold using get_current_function_param method when it uses threshold to determine decision variable
  continuing to update how parameters are accessed in pytests (should be mod_ now in many cases)
  replacing .matrix with .mod_matrix in learning pytests
  adding a call to super in projection's _instantiate_attributes_after_function so that it calls make_property_mod (on component)
  Fix/ddm/threshold validation (#610)
  calling get_current_function_param in the remaining functions and fixing small bugs along the way (missing keyword for 'gamma', np.atleast_2d(rate) in lcaintegrator)
  moving make_property_mod back to component.py (from parameterstate.py) -- it is now called for all parameter states during _instantiate_attributes_after_function rather than by individual parameter states
  Docs/td learning/doc fixes (#609)
  removed show graph call from test_reinforcement
  resetting test_multilayer from devel and removing matplotlib from test_prediction_error_delta_function
  specifying smoothing_factor=1.0 on pytests that used to use default smoothing_factor (1.0 --> 0.5)
  changing smoothing factor (formerly time_constant) default value to 0.5 -- it was confusing to users that the default param value prevented integration
  renaming 'time_constant' --> 'smoothing_factor' on TransferMechanism types that use AdaptiveIntegrator
  Fix/log/trial and run (#607)
  Feat/log/trial and run (#606)
  Refactor/project/learning vs executing (#605)
  correcting capitalization
  cleaning up documentation
  adding asserts to parameter states pytests in order to start tracking down bug where mod_noise looks up the parameter state value of the last instance created
  Refactor/mechanism/value in execute 2 (#603)
  predictionerrormechanism
  docs: move gilzenrat svg files from build dir to source dir
  Fix/log/tuple datum value (#601)
  registry: handle case where default-named projection to a duplicate named mechanism would incorrectly detect the projection name as a duplicate
  finished TD Learning documentation
  Fix/state/matrix spec and learning (#600)
  Fix/component preference set/class preferences (#598)
  Fix/log/set log conditions bug (#596)
  updating Transfer functions (Linear, Logistic, Exponential) to use get_current_params(KEYWORD) instead of paramsCurrent[KEYWORD]
  adding get_current_param method which tries to return mod_param and returns param if that doesn't exist -- will eventually be added to all functions, starting here with DriftDiffusionIntegrator
  Docs/log/hint (#595)
  updating shape inconsistencies in DriftDiffusionIntegrator / DDM Mechanism related to time and threshold
  removing special handling of DriftDiffusionIntegrator threshold in variable=array case (correct behavior is ambiguous)
  docs: add extra sub-version number in version display
  utilities: enhance method to recursively convert items to np.ndarray, handling hard cases for np.array
  remove scratch pad and ignore
  Docs/log/log clean up (#593)
  Docs/log/log clean up (#592)
  remove scratch pad
  Docs/log/log clean up (#591)
  Names/log/set log conditions (#590)
  adding pytests to verify that threshold and is_finished work as expected; commenting out tests with DriftDiffusionIntegrator and len(default_variable) > 1 because correct behavior is ambiguous (for now)
  adding 'threshold' param on DriftDiffusionIntegrator which stops accumulation at the threshold, and updated DDM's is_finished to look at this
  updating shape of time computation in FHN integrator (was list, now float)
  updating gilzenrat pytest which was checking _gain and gain to verify modulation to now use gain and mod_gain
  updating pytests and adding comments to possibly fix shape of ddm time value, which changed from a list to a float after property refactoring
  add realtime timestamps to Scheduler, for creation time and end of last RUN time
  change usages of now defunct times attribute of Schedulers to new version
  updating mod_param_name property creation to happen at the instance level in both cases (formerly created on mechanism classes)
  unindenting misplaced setting of _param_name attributes
  Bugfixes (#588)
  setting _param_name for all param_names that go through _validate_params resolves SOME of the cases where getter looks for _param_name before setter creates an _ attr
  Feat/log/add entry (#587)
  Fix/log/log initialization (#586)
  Feat/log/clean up (#585)
  Feat/log/clean up (#584)
  Feat/feat log with time (#583)
  rename psyneulink.scheduling.timescale -> psyneulink.scheduling.time
  create and integrate a new Clock class, and several new classes to keep time, used in Scheduler and Conditions
  adding _param_name to script for better output comparison with older versions (when _ stored the base value)
  solving bug where _param_name did not exist on TransferMechanism instances, but introduced new bug where last param value that was set is starting param value of next instance
  remove old Clock/CentralClock
  debugging make property execution
  main documentation for PredictionErrorMechanism done
  adding mod_slope to the current parameter state pytests
  adding make_property_mod method to parameter states -- executed at the end of _instantiate_parameter_state method and creates a property called mod_param_name on each param that has a parameter state which looks up the current parameter state value
  limiting make_property's resposibility to validation -- setter runs validation and then sets to _param_name, getter returns _param_name. mod_param_name property will handle getting parameter state value
  Feat/log/log levels (#580)
  test
  beginning to separate make property into two methods
  added PredictionErrorDeltaFunction and docs for PredictionErrorMechanism & Montague model
  Refactor/log/entry management (#579)
  montague models working!
  Docs/log/docstring update (#578)
  Add integrator function tests
  Add transfer function tests
  Add distance function tests
  function: test for both 1d and 2d noise
  setup.cfg: Use warmup if benchmarks are enabled
  setup.cfg: Disable benchmarks by default
  pytest: Add benchmarking plugin
  Fix/log/logged items bug (#577)
  using UniformToNormalDist pytest as a check of the scipy requirement error message
  adding documentation for UniformToNormalDist
  validating uniform-to-normal distribution function (matlab)
  Docs/log/docstring update (#572)
  adding gilzenrat figures in _build file
  adding pytest file for parameter states
  Name/log/numpy array to nparray (#571)
  Feat/mechanism/additional props (#570)
  Feat/log (#569)
  EVCAuxiliary: replace kwargs function signatures with explicit arguments
  add docstring explanation for processing and learning termination conditions
  Feat/log (#568)
  adding LC Control Mechanism test to verify that it is updating multiplicative param(s) of modulated mechanism(s) properly
  fix incorrect construction of Process and System in Multitasking example script
  Feat/log (#565)
  Feat/log (#564)
  almost working!
  add travis config file
  single source package requirements
  fixed error message in LinearMatrix
  adding a pytest for the new uniform --> normal distribution function
  fixed sample input
  updating recurrent transfer mechanism and transfer mechanism documentation
  • State   - _validate_variable:  removed:         if not context:             context = kwAssign + ' Base Value'         else:             context = context + kwAssign + ' Base Value'
  Fix/component/default naming (#558)
  remove Scratch Pad
  clean up DDM examples with verified parameters from matlab
  skip NavarroAndFuss doctest because build server cannot access matlab
  update NavarroAndFuss to use the correct version of the MATLAB simulation
  convert DDM return_value for NavarroAndFuss function to be floats to allow NaN assignment
  fix bug in using the matlab engine to run a script outside of the current dir
  adding validation on NormalDist function in the case where some numpy versions throw an error
  • System (#556)
  adding new UniformToNormalDist function which allows for a direct comparison of random numbers between python and matlab
  Feat/system/show graph (#555)
  adding integration_method to FHNIntegrator docs and refining error message
  Fix/modulatory specifications (#554)
  clean imports in function.py
  commenting out assertions in OU integrator pytests until its equation is validated
  fixing mistake in implementation of OUIntegrator
  adding LCAIntegrator docs to function docs page and continuing to touch up typos and incorrect info throughout function docs
  continuing to add documentation for LC Control Mechanism params
  adding matlab and psyneulink plot svgs
  adding pnl and matlab plots plus some additional notes to the Gilzenrat Model page of the documentation
  fixing typos in FHNIntegrator docs
  documenting the LCControl mechanism parameters that hand values off to the FHNIntegrator as well as scaling_factor_gain and base_value_gain
  cleaning up FHNIntegrator docs with tables for explaining parameters and latex equations
  typos in run (input spec) docs
  cleanup Scheduler doc examples
  add parsing handler for Scheduler termination_conditions
  move static .svg files from docs build directory to source dir
  update docs to show 0.0.x versions instead of just 0.x (we use the former frequently)
  fix broken package link for AutoAssociativeMechanism that caused sphinx automodule to fail
  removing references to 'inhibition' and 'decay' in LCA docs
  removing gilzenrat transfer mechanism from the repo
  updating gilzenrat unit tests to use LCA mechanism in place of GilzenratTransferMechanism
  fix bug where versioneer wasn't available at the correct time in building docs
  adding a note about the recurrent matrix to LCA docs
  rewriting gilzenrat model in terms of LCA rather than 'GilzenratTransferMechanism'
  removing LCA pytest from recurrent transfer pytests file now that LCA has its own tests
  updating LCA documentation -- removing beta & inhibition, adding leak, competition, and self_excitation.:
  setting default values for new LCA params
  adding pytest file for LCA and testing length 1 variable and length 2 variable cases
  added output_states param to call of PredictionErrorMechanism constructor
  added default variable param to call to LinearCombination in PredictionErrorMechanism
  adding 'leak' parameter and renaming 'auto'-->'self_excitation' and 'hetero'-->'competition' on LCA mechanism
  Refactor/state/doc test bugs (#551)
  fix bug where invalid escape strings in docstrings would cause failure on python 3.6.x
  fixing incorrect documentation of LCA (did not reflect new LCAIntegrator function)
  continuing to clean up Gilzenrat model and its model-specific components -- verifying that all arguments are consistent and correctly documented
  manually setting outputstate variable size
  adding params for G and k to LCControl mechanism as a temporary solution for allowing the user to modify the equation that computes gain as a function of w
  cleaning up gilzenrat script comments and labeling all params from the paper
  tried manually setting OutputState value for PEM -- didn't work
  Refactor/state/ parse state specs lots (#550)
  use versioneer for single-source versioning
  adding Gilzenrat changes from Markus
  fixed target size for PredictionErrorMechanism
  trying to fix tests
  correct W293 instances
  fix bug where intra-numpy-array list->array element conversion would fail on 0-d numpy array input
  updating logistic function and its documentation to match the more standard form, with an optional 'offset' to take the place of original 'bias' param. Updating all pytests that used what was formerly 'bias' and is now 'offset'
  trying more things to get td learning working
  clean up leabra demo script
  clean up leabramechanism
  add __all__ to leabramechanism and update relevant package
  rename certain leabra-specific functions to include "leabra" in preparation for adding to top-level namespace
  remove unnecessary (and oddly expensive) logging in scheduler
  fix bug where over/underflows in logistic functions would cause the result to be replaced with 0 (often incorrect format and destructive)
  remove forced error on warnings
  Leabra script cleaning (#547)
  cleaned up Matlab scripts & EVC Gratton example script (#546)
  Docs/project/more docstring fixes (#545)
  Docs/project/more fixes (#544)
  Docs/project/fixes (#543)
  reformat Example scripts to new import style, and clean up
  setup Scripts/Examples folder with desired scripts
  remove old/undesired scripts
  adding input spec figures to run documentation
  rename _get_matrix to get_matrix
  Revert "Fix/scripts/cleanup (#539)"
  commenting out all clip (formerly range) code because it does not work as expected
  fixing formatting typo in documentation
  continuing to clean up input specification for (1) heterogenous variables and (2) a limited version of 'sequence' specification
  Fix/scripts/cleanup (#539)
  updating documentation example pytests to verify all inpt values against specified input values
  updating documentation example typos
  Feat/transfer mechanism/add std output states (#538)
  refactoring system input state creation to create one system input state (and mapping projection) for each input state of each origin mechanism
  Feat/transfer mechanism/add std output states (#537)
  Fix/output states (#536)
  Refactor/transfer mechanism/mutiple output states (#535)
  updating transfer mech execute to check the type of its function and call it once or once per input state accordingly, plus Jon's instantiate_output_states
  reclassifying softmax as a 'NormalizingFunction' instead of a 'TransferFunction' so that we can easily identify transfer mechanism functions that should be executed separately for each input state
  use pytest fixture for registry reset in tests/naming to ensure it gets called
  renaming  -->  on TransferMechanism types in order to not overwrite Python built-in range
  Refactor/naming (#533)
  add download link for GilzenratModel.py
  updating kwta and recurrent transfer mech pytests to match new output shape
  cleaning up imports so test will run
  add values(), show(), and nice str/repr methods to InstanceDefaults
  move name assignment (in registry call) to before input_states arg handling in mechanism
  Revert "Refactor/mechanism/preprocess variable (#531)"
  updating transfer mechanism pytests to match new shape of output
  updating transfer mechanism to call its function separately for each input state (each element of variable); for now, integrator function still only executes once
  add shell classes to top-level psyneulink namespace
  correct bug that would cause specifying 3d arrays as default_variable to assign default_variable incorrectly
  add method to np.array-ify all elements within a list/array
  continuing to add pytests for input specification - stuck on verifying that the input specification worked via tools (e.g. call_after_trial) available to the user, because non primary input states are getting overwritten as None
  updating documentation for input specification -- adding tables of inputs on each trial with code snippets
  Fix/mechanism/ parse arg input states (#532)
  Increment version to 0.4.0
  add more input_state spec tests to handle currently known combinations for setting default_variable
  Refactor/mechanism/preprocess variable (#531)
  Refactor/mechanism/preprocess variable (#530)
  Docs/state and projections/docstring revs (#529)
  correct bug in _parse_arg_input_states where a non-list argument wouldn't be made into a list before processing
  change behavior of _parse_state_spec to not populate the state dict with a variable if it's a ClassDefault
  updating noise validation to compare against entire variable (possibly multiple input states) and updating error messages in pytests to reflect these changes
  updating 'try_execute_param method to expect 2d variable and return 2d param
  updating pytests for input specification documentation examples to match the new documentation examples
  continuing to update docs for inputs to system
  revising the input specification docs to describe the rules in terms of matching the mechanim's variable - also making the convenience cases clearer
  removing references to timescale in run and system docs
  Fixed/state/ parse state spec/projection spec (#528)
  Refactor/distance metrics (#526)
  Docs/latex math (#525)
  Docs/intro materials (#524)
  continuing to add pytests to test new input specification rules
  updating some reporting statements to match the new form of inputs (dict)
  continuing to clean up input specification; running inputs first through a new method called _input_matches_variable which catches some numpy mistakes specific to input validation that slip through iscompatible
  Logo (#523)
  make self.name return unnamed .__class__ in case no name was set
  Docs/input state specs (#522)
  Fix/input state specs (#521)
  continuing to add pytests for testing input specifications
  updating process and system to handle the new execution_inputs dict that they receive from run
  consolidating and revamping input processing to get rid of any references to , repetitive code. still some clean up to do -- 5 pytests failing
  Fix/input state specs (#520)
  Fix/input state specs (#519)
  beginning to consolidate input validation because we no longer have phases and don't need to handle systems and processes differently -- 22 pytests failing
  Fix/input state specs (#518)
  using new EULER option on the LCControlMechanism in GilzenratModel in order to match original model
  adding validation requiring integration_method to either be RK4 or EULER
  adding 'integration_method' to LCControlMechanism so that user can switch between euler and rk4 integration for the built-in FHN function
  fixing some params to match matlab model; made it easier to swtich between high C and low C params
  switching FHNIntegrator to use euler integration
  scaling entire noise term by sqrt(dt) rather than scaling the standard deviation of the noise term by sqrt(dt)
  Naming/registry/default name 0 (#516)
  beginning to add in an exception which will allow the case where all mechanisms specify one input which is the same shape as their variable (i.e. no outer list for trials)
  hack mechanism to be able to accept instance_defaults.variable setup via input_states argument
  still trying to fix inputs
  cleaning up sytem unit tests to match new input spec (outer set of brackets representing trials required)
  cleaning up mechanism unit tests to match new input spec (outer set of brackets representing trials required
  move input_states spec tests in test_transfer_mechanism to new file
  update current input_state spec tests
  make test_transfer_mechanism tests use instance_defaults.variable instead of incorrect .variable
  Docs/state and projection (#515)
  remove uses of self.variable. (it is vestigial and maintained only for user inspection)
  rename duplicate transfer mech test to avoid overwrite
  adding input specification pytests to test_system in order to verify which input spec formats already work and build on this
  pull from devel
  Refactor/control and gating signals (#514)
  Import leabra and run leabra tests only if leabra module is available.
  Leabra wrapper prototype (#513)
  Fix/utilities/iscompatible final rev (#512)
  Fix/utilities/iscompatible (#511)
  rename System and Process to add _Base suffix in shellclasses.__all__ because of abf3e7e and 6b9e9a4
  Clean up/registry/ register category (#508)
  Refactor/projection/connection specs (#507)
  Refactor/gating mechanism/ instantiate gating signal (#506)
  • Projection (#505)
  updating comments and error messages in _construct_stimulus_sets to reflect changes
  updating 3 recurrent transfer mech unit tests which used 'sequence format' of input specification for a process to use 'mechanism format' instead
  Refactor/projection/ instantiate sender (#504)
  Refactor/state and projection/clean up (#503)
  commenting out branch of _construct_stimulus_sets which parses inputs by the 'sequence format' rules -- seems safe to move entirely to mechanism format b/c all pytests use 'mechanism format' and new examples using 'sequence format' do not work
  weird hybrid prediction error mechanism
  fix typo in ObjectiveMechanism docstring causing weird documentation formatting
  avoid using module-level Mechanisms in unit tests to avoid possible conflicts
  Refactor/state and projection/unit tests bug fixes (#502)
  Refactor/state and projections/unit tests (#501)
  Refactor/state and projection/names and docs (#500)
  requiring version 1.4 of toposort
  moving imports to top of gilzenrat pytests file
  adding full gilzenrat model to pytests -- no comparison data to assert yet, just verifying that model can run without errors
  adding pytests that isolate the GilzenratTransferMechanism and moving FHNIntegrator test that recreates figure 2 from gilzenrat paper from integrator mechanism tests --> gilzenrat tests
  fixing up a few model values in the gilzenrat model -- behavior is not quit right -- and switching number_of_trials back to 1
  Optimize registry duplicate naming
  adding progress statement ('% complete') to gilzenrat script
  implementing noise on LCAIntegrator and cleaning up unnecessary integrator function code (removing GilzenratIntegrator)
  replacing GilzenratIntegrator with LCAIntegrator (with rate=-1) in GilzenratTransferMechanism
  Refactor/state and projection/specification bug fix 2 (#495)
  Refactored instantiation of States and Projections (#494)
  updating mechanism pytests to reflect integrator_function shape change and removing extraneous transfer mechanism tests which returned arrays of mixed types
  indexing into the first element of the transfer mechanism's integrator_function result so that the shape passed to the transfer mechanism's function is the same as if integrator_mode were false
  add component module to main psyneulink package
  fold keywords into first level hierarchy, because some keywords aren't defined in Keywords.py and this is confusing
  skip notebook checkpoints in running notebook tests
  stop package-level __all__ assignments from accidentally overwriting the __all__ objects they used as bases
  fixing bug in NormalDist() function which was shifting the mean of the distribution
  fix link to the tutorial in docs that didn't get changed when tutorial/ directory was created
  correcting LCAIntegrator function to match the papers (since it represents a rate of change, we need to integrate over timesteps) and relaxing integrator rate param validation which was blocking variables of lengths > 1
  Devel (#490)
  improving initial conditions by making first recurrent projections to recurrent mechanisms make sense given their starting values
  make Function_Base inherit its paramClassDefaults from its parent class Function instead of Component
  remove DefaultProcessingMechanism from component/__init__.py because it's an instantiation of a _Base class, and doesn't get used
  removing and re-adding gilzenrat transfer mechanism because name change did not seem to work
  updating value of LC control mechanism output before it runs to match initial previous value (had to do this in the gilzenrat script because of other LC control mechanism hacks, but left a placeholer in ControlMechanism for how to implement this more generally for any control mechanism that accumulates)
  adding a new Integrator function that matches the decision and response layer functions in the Gilzenrat paper, and a new transfer mechanism which calls this integrator before its primary function
  update README and docs index.rst to new PyPI installation instructions, and tutorial section, reorganize
  reformat README into .rst format so pypi can format it nicely
  update short description to match the title line in the long description
  update setup.cfg for wheel creation and to include license file
  update setup.py supported Python versions to include only 3.5 and 3.6 (does not work on < 3.4 due to numpy, does not work on 3.4)
  update setup.py classifier for Apache license
  add tutorial_requirements.txt mirroring setup.py requirements
  add requirements.txt mirroring setup.py requirements
  update setup.py packages
  add MANIFEST.in
  remove SOFTWARE ARCHITECTURE and TODO List
  remove extraneous files
  add docstrings to __init__.py files (for help command)
  update tutorial to new easier import style
  update docs to handle new module/package format
  update package __init__.py files for simple importing
  add __all__ lists to modules
  rename globals/run.py to globals/environment.py to avoid namespace conflict with run method
  clean up main package __init__.py
  replace paramClassDefaults PROJECTION_SENDER with OutputState class instead of keyword to prevent error due to failed conversion
  rework imports to avoid circularities due to packaging
  make LearningMechanism get its paramClassDefaults from its parent and not Projection_Base
  remove mechanism factory method
  remove system factory in favor of just instantiating System class
  remove process factory in favor of just instantiating Process class
  switch name of Process and Process_Base
  switch name of System and System_Base
  move typecheck for _get_modulated_param inside to avoid circular import
  remove old pyargs argument for pytest
  relaxing validation on LCAIntegrator rate param in order to create an LCA example in integrator mode with an array input
  cleaning up resolving merge conflicts
  fixing merge conflicts
  started mini montague model
  adding comments
  first preliminary test working
  editing testing files and minor typos
  removed unnecessary identity transform function
  updating gitignore for new version of PyCharm
  created PredictionErrorMechanism
  started mini montague model
  adding comments
  first preliminary test working
  editing testing files and minor typos
  removed unnecessary identity transform function
  updating gitignore for new version of PyCharm
  created PredictionErrorMechanism
  starting TDDelta Function -- very messy
  2 of 3 test working
  integrating td learning
  cleaning up Function.py for pull request
  tests working!
  Q-matrix initialization working; mechanism does not
  Added Q-learning and SARSA algorithm
kmantel added a commit that referenced this pull request Apr 5, 2018
* devel:
  Feat/mechanism/input target label dicts (#751)
  Scheduling: fix bug where termination conditions persisted across calls to run
  tests,function/LinearCombination: Add tests with absent parameters
  test,function/LinearCombination: Rename second test function to prevent overwriting results
  • Context (#746)
  Refactor/context/deprecate init status (#745)
  Refactor/context/structured (#744)
  Fix/function/stability (#743)
  • IntegratorMechanism (#742)
  Feat/context/time (#740)
  Feat/context/time (#739)
  Image Fix (#738)
  finally fixed image (#737)
  Image Fix (#736)
  Example Fix (#735)
  Linear combination fix (#734)
  Feat/component/execution count (#733)
  jvesely/linear_combination_function_refactor (#732)
  Refactor/project/context rev 2 (#731)
  Refactor/system/show graph structure options (#730)
  • System (#729)
  Feat/mechanism/show structure (#728)
  Feat/mechanism/show mechanism (#727)
  jvesely/linear_combination (#724)
  creating a property for TransferMechanism's integrator_mode so that the mechanism can switch integrator mode on and off
  Fix/function/udf examples (#722)
  • Function (#717)
  Refactor/function/udf (#716)
  Refactor/mechanism and output state/mech params dict added (#715)
  Docs/output state/clean up (#714)
  Clean up/function/softmax one hot (#713)
  Name/project/replace assign index calculate (#711)
  Fix/controlmechanism/assign as controller jdc (#705)
  Feat/function/one hot cleanup (#704)
  Feat/function/one hot (#703)
  adding a pytest for the clear_log method
  updating output of nparray_dictionary when there are no entries from None to an empty OrderedDict
  Tests/llvm devel sync (#684)
  removing show graph pdfs from tests folder
  revising the show_graph pytests to call '_get_label' as a proxy for whether show_graph with dimensions is working
  moving _get_label helper function outside of show_graph method, so that it can be accessed on its own
  fixing bug in show_graph(show_dimensions=True) by taking np.atleast_1d of output_state.value
  • LearningProjection   docstring rev (to include error_function)
  Feat/process/learning objective mech (#698)
  Feat/ddm/selected input array (#697)
  Feat/ddm/selected input array (#695)
  user_params and function_params now look at parameter state values (rather than param base values), and are updated whenever mechanisms update their parameter states
  adding pytests that call show graph after creating various types of systems -- may refactor these to call the individual methods of show_graph
  removing system graph pdfs
  removing show_dimensions=True from call to show_graph in GilzenratModel because it generates an error
  updating how valus are retrieved from log in Nieuwenhuis model (based on addition of Pass to log)
  Fix/system/learning ends before terminal (#692)
  Fix/system/learning ends before terminal (#691)
  Revert "Merge branch 'master' into fix/system/learning_ends_before_terminal"
  -
  • ControlMechanism   _instantiate_control_signals:  debugged OWNER_VALUE assignment
  • Scripts/Examples   Rumelhart Semantic Network: updated with step function
  • System   _instantiate_learning_graph(): fixed bug in which learning failed to     be instantiated for a System in which the last Mechanism in a     learning sequence was not the TERMINAL Mechanism of the System.
  • System   _instantiate_learning_graph(): fixed bug in which learning failed to     be instantiated for a System in which the last Mechanism in a     learning sequence was not the TERMINAL Mechanism of the System.
  • OutputState   docstring revs
  • OutputState   docstring revs
  fixing documentation formatting mistake
  continuing to add pytests and doc fixes for clip on transfer mechanism types
  allowing lca to execute function over entire variable, not just first item
  fixing documentation for clip
  continuing to add error messages to reinitialize
  allowing smoothing factor to be an integer (formerly 1.0 and 0.0 were allowed but 1 and 0 were not)
  removing typecheck on learning mechanism's default_variable
  adding exception in UDF so that function can be called without params and context
  correcting error message for initial_value validation on transfer mechanism
  fixing bug in reinitialize on arrays (needed np.atleast_2d when setting intial_value because it is compared to variable)
  -
  • OutputState   docstring revs
  Refactoring of OutputState to support flexible assignment of its variable attribute.
  Revert "-"
  Revert "-"
  Revert "-"
  -
  adding pytests for specific reinitialize cases that were not covered, and adding error messages that were missing for some of them
  -
  fixing documentation typo: integration_method was mistakenly called integration_method_FHN in docs
  -
  -
  -
  -
  -
  -
  Reworking Montague, Dayan, and Sejnowski model documentation.
  -
  Merge branches 'bug/parsing/input_states-use-value' and 'feat/DDM/value_based_version_input_state' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/DDM/value_based_version_input_state
  Merge branches 'bug/parsing/input_states-use-value' and 'feat/DDM/value_based_version_input_state' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/DDM/value_based_version_input_state
  -
  -
  -
  -
  -
  -
  • Utilities   - recursive_update():  added non-destructive option that preserves                          any non-empty entries in destination dict
  -
  -
  -
  • OutputState   this version implements OutputState.variable as a property   that returns _parse_output_state_variable()
  • OutputState   this version implements OutputState.variable as a property   that returns _parse_output_state_variable()
  -
  -
  -
  -
  -
  -
  adding pytests for invalid target specifcation to confirm that the proper error messages are generated
  • OutputState   assign function now expects dict as argument - WORKING
  adding more pytests to confirm that convenience notations and combinations of function and list target specs all run
  documenting targets and adding some checks to adjust targets: verify that num_targets = num_inputs, and ignore num_targets in the case of function specifications (because a new value is generated on each trial)
  -
  -
  -
  -
  • OutputState   - implemented assign that takes assign_params_dict as arg
  Fix/output state/assign backward compat (#676)
  • OutputState   added backward compatibility   docstring: document replacement of calcuate/CACULATE with assign/ASSIGN
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  in progress: refactoring function specification of target spec to be an option within the dictionary specification, rather than on its own
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  Feat/ddm/input state as array (#674)
  revising documentation for target specification
  cleaning up a typo in target_spec_parsing (comparator mechanism was referenced where it should have been terminal mechanism)
  moving call to _check_args in BackProp to before the error matrix is updated in order to avoid a validation bug
  adding pytests for target spec convenience notations
  adding run to rumelhart tests (previously only created systems)
  Merge branches 'clean_up/function_and_system/backprop_and_show_graph' and 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into clean_up/function_and_system/backprop_and_show_graph
  revising how target input state values are assigned in system's execute_learning
  adding a simple multilayer learning pytest
  refactor execute and _execute methods
  defaults: remove post-hoc conversion of defaults variable
  Component: don't convert defaults variable on calls to validate a variable
  parsing: add initial_value parser
  parsing: add generic argument parser used as default if none specified
  Component: add method to parse user inputted variable to useable/standard form
  utilities: handle nonuniform objects better when converting to numpy arrays
  control: refactor handling of allocation*
  projections: refactor sender instantiation to avoid directly setting instance default variable
  clean up input_states handler
  rename input_states arg parser to handler
  maint: add comments to separate handler, parsing, and validation methods
  maint: remove unused PROJECTION_SENDER_VALUE
  TransferMechanism: use standard form of setting default variable
  utilities: change number detection to accept any number, not just int and float
  OutputState: when variable not specified to constructor, pass up another value
  make self.variable read only (we should not be using it for logic)
  replace calls to self.variable to proper self.instance_defaults.variable
  validation: remove extraneous check for ClassDefaults.variable
  ClassDefaults: make RecurrentTransferMechanism default require 2d variable because it takes an AutoAssociativeProjection that uses a LinearMatrix that requires 1D
  Distance: fix validation assumption that items of passed variable are iterable
  ClassDefaults: correct and consolidate
  utilities: add method to produce a value for length calls when len() fails
  utilities: add function to determine whether something is iterable
  Integrators: handle initializer like variable in Components
  Function: standardize default_variable assignments
  ProcessingMechanism: use standard assignment of default variable
  DDM: use standard assignment of default variable
  ensure default_variable auto sets to dtype float
  combine handling of default_variable/size to create instance_defaults.variable in Component.__init__
  utilities: allow list->array element conversion to typecast internal items
  validation: fix validate_variable crashes on certain variable types
  utilities: add helper method to determine if an object contains a single value
  rename variable->default_variable
  Clean up/function and system/backprop and show graph (#671)
  Clean up/learning/misc (#670)
  Clean up/learning/misc (#669)
  Clean up/learning/misc (#668)
  Fix/transfermechanism/noise function (#667)
  Fix/transfermechanism/clip (#666)
  Refactor/modulatory signals/linear default function (#665)
  Refactor/learning/heterovergent (#664)
  in progress - refactoring adjust_target_dict method to validate all candidate targets and confirm that all mechanisms provided the same number of targets
  Tests/mechanism/hebbian learning (#663)
  Docs/function/hebbian (#662)
  Docs/function/hebbian (#661)
  updating pytest expected values based on changes to log output
  adding Pass to log output and updating pytests accordingly
  Fix/learning/hebbian (#659)
  swapping all log references to 'simple_time' with the full 'time', and removing old code which handled time stamp duplicates
  in progress - refactoring target spec/validation to work the same way as input spec/validation
  renaming object --> component in _adjust_target_dict()
  updating pytests to match RecurrentTransferMech switch from full matrix to hollow matrix; changed expected output or set auto = 1 to preserve old expected output, depending on type of test
  setting default matrix of a RecurrentTransferMechanism to a hollow matrix, and updating docs to be clearer about how auto, hetero, and matrix combine/overwrite each other when multiple arguments are specified
  renaming object --> component in _validate_targets method to avoid shadowing python built-in
  updating pytest expected results to match increment change in log
  log pytest for a mechanism that is scheduled to run many times in a row
  changing increment size on log's time_step workaround
  temporary workaround for timestep values: incrementing first decimal of timestep
  revising log tests for new time_step notation
  temporary workaround for timestep values: incrementing first decimal of timestep
  revising parse_entries_for_time_values method on log so that it edits the time values in the log items directly, rather than maintaining a separate list of modified time values
  setting axis=1 on calls to np.sum and np.product in Reduce function and adding tests for this function
  documentation typos
  documenting reinitialize on mechanism
  continuing to add tests and docs for reinitialize
  fixing bugs that prevented initialize method on system from ever executing, and adding pytests for it now that it works
  revising outdated TransferMechanism docs for reinitialize
  continuing to add tests to highlight differences between calling reinitialize on a mechanisms and on a function
  adding nparray_dictionary to docs and revising nparray to use the same helper methods as nparray_dictionary
  Time: fix bug where RUN counter would not be incremented on new runs
  fixing (temporarily) time_step bug in nparray_dictionary; reorganzing nparray_dictionary into methods that can be reused by nparray
  refactoring log to have a dictionary option and writing tests for it
  beginning to add a dictionary alternative to the options for whats returned by the log
  more calls to _dealias_owner_name required in order to create log.nparray
  fixing bug in log: needed to switch between 'value' and mechanism name in several loops in order to assemble log.nparray
  -
  Feat/rl/for mads (#652)
  Feat/rl/for mads (#651)
  adding more pytests for reinitialize and fixing reinitialize bugs; beginning to update documentation
  adding pytests for reinitializing at both function and mechanism level; cleaning up mistakes in reinitialize() methods along the way
  Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projection/Context_devel
  adding a reinitialize method on mechanisms, which calls reinitialize on its function or integrator_function, then updates the mechanism's value and output states
  beginning to refactor reinitialize as a method on integrator functions
  Removed Print Statements (#650)
  cleaning up documentation to match how LinearMatrix works in all cases
  typo in linear matrix function validation
  simplifying non-projection branch of validation on LinearMatrix function and adding more pytests
  default_variable: let argument override input_states variable spec if compatible
  adding pytests for possible combinations of variable and matrix specifications for LinearMatrix as a function of a mechanism
  adding validation comparing matrix to variable when LinearMatrix function is called by a mechanism; creating square full connectivity matrix that matches variable when matrix is not specified
  tutorial: reenable graph drawing; requires graphviz package
  tutorial: clear outputs
  Lena Program 1 Bugfix (#648)
  Hebbian learning fix (#647)
  User defined function updates (#646)
  adding working version of LinearMatrix function pytest (only works because default_variable is specified on both the mechanism and the function)
  fix input_states argparsing to not be dependent on default_variable or size args
  tests: ensure leabra tests get skipped if module is not available
  splitting linear matrix function's validation into two branches because matrix is handled differently when the function is called by a projection vs a receiver
  docstring wording change
  Docs/models/title changes (#645)
  Docs/nieuwenhuis/edits (#644)
  adding pytest for ProcessingMechanism with LinearMatrix function to begin debugging why this fn only works in Projections
  removing unrestrictedtransfermechanism file because this mechanism is now called ProcessingMechanism and does not need its own file
  adding parameter state docs examples back in with doctest SKIP
  revising proccessing mechanism docs because it is not an executable mechanism (not just an ABC)
  renaming UnrestrictedProcessingMechanism --> ProcessingMechanism and moving code into processingmechanism.py (which formerly only contained ProcessingMechanism_Base
  Leabra Update (#642)
  DDM: update is_finished to work on functions with any dimensional variable
  skipping transfer mechanism doc tests
  skipping transfer mechanism doc tests
  minor documentation changes -typos and formatting mistakes
  reorganizing integrator mechanism pytests for reinitialize
  overwriting AGTUtilityIntegrator's reinitialize property - requires custom reinitialization of short term and long term utility
  overwriting FHNIntegrator's reinitialize property - requires custom reinitialization of v, w, time, value
  overwriting reinitialize property on DriftDiffusion Integrator so that time can also be reset
  documenting reinitialize on all Integrator functions and fixing a typo in transfer mechanism docs (initial_value --> initializer)
  continuing to add docs and examples for reinitialize, and cleaning up TransferMechanism docs along the way
  fixing tutorial indexing bug
  refactoring is_finished as a property so that it is always up to date, even when values change in between executions (i.e. if threshold was crossed and then reinitialize was used)
  fixing bug in transfer mechanism documention examples (np.array typo)
  renaming reset_intializer --> reinitialize
  adding unrestricted mechanism pytests to confirm that mechanism can be constructed and executed with any function -- identified two exceptions (linear matrix and back prop)
  adding a new mechanism that has no restrictions on which functions can be used
  commenting out show graph lines in tutorial for now because graphviz is not imported on testing server
  adding updated version of tutorial from Justin
  Defaults*: fix class structure addressing bugs
  revising transfer mechanism documentation -- 'creating' section
  commenting out show_graph in EVC gratton pytest so that this line does not run on Jenkins
  adding TransferMechanism pytests to verify previous_value persists over multiple runs/executions AND previous_value resets whenever reset_initializer is used
  edited  NieuwenhuisModel docs
  tutorial: remove old version - new version is in tutorial/ dir
  tutorial: support execution on mybinder.org
  tutorial: support execution on mybinder.org
  tutorial: remove old version - new version is in tutorial/ dir
  • Niewenhuis model   - docstring edits
  -
  adding integrator_mode and integrator_function attr documentation for all transfer mechanism types
  revising outdated documentation for transfer mechanism noise
  fixed bug in plotting Nieuwenhuis Model
  updated Nieuwenhuis documentation
  adding attrs that were missing from LCA mechanism docs and revising related documentation
  Scripts: clean up
  Functions: add UniformToNormalDist to top-level psyneulink module; update docs
  revising explanation of user_params
  revising explanation of user_params
  revising parameter state documentation
  adding Markus' Nieuwenhuis documentation, plus figures and some .rst formatting
  Functions: replace internal calls to find owner's name with a property
  Component: make string version of *defaults classes be sorted
  removing parameter state example from file completely (tried commenting it out originally)
  removing parameter states example from documentation because it may be the reason parameter state tests are failing
  renaming 'Core Configurable Attributes' --> 'Core Structural Attributes' in Component documentation
  Refactor/system/controller (#627)
  Fix/controlmechanism/assign as controller (#625)
  • Log (#624)
  fixing typo in doctest (parameter state values)
  adding a docs example which walks through how a mechanism parameter and a function parameter and their mod_ versions change in value
  BogaczEtAl: use better numpy method for floating point warning handling
  utilities: update compatibility checker to terminate earlier in some cases
  updating modulation-related documentation to include mod_param and be more precise about what is updated by modulation (the parameter value used by a function changes, but the corresponding function attr does not change b/c it is the base value)
  adding documentation for mod_param
  allowing user to pass value into mod_param setter (even though setting is not allowed) in order to produce a more informative error message)
  commenting out noise and smoothing factor properties in transfer mechanism because these replace the default properties, causing unexpected behavior
  adding pytest to verify correct error message when user tries to set to mod_param_name
  adding pytest to track changes in attr, _attr, mod_param_name, and userparams[param_name] values of Transfer Mechanism's configurable params when (1) param values are updated (2) mechanism is executed
  adding an exception to make_mod_param as a temporary fix for function-specific mod_param properties that stay on mechanism class when function changes
  fixing typo in AGTUtilityIntegrator
  cleaning up function.py and verifying that self.get_current_function_param is used in all functions (skipped learning functions for now)
  Fix/controlmechanism/assign as controller (#620)
  Fix/controlmechanism/assign as controller (#619)
  cleaning up recurrent transfer mechanism pytests and fixing bugs in asserts
  updating matrix setter to also set the projection's matrix parameter state's function's previous value
  uncommenting auto and hetero properties from auto associative projection so that setting auto and hetero directly on the projections works
  adding auto and hetero properties to recurrent transfer mechanism. Auto, hetero, and matrix setters now all update recurrent_projection's matrix parameter state's function's previous_value
  Fix/controlmechanism/assign as controller (#618)
  executing projection individually in tranfer mechanism's matrix-change pytest
  adding a matrix-change pytest for a mapping projection between two transfer mechanisms in order to isolate the matrix bug from auto/hetero properties
  Defaults: clean up method organization
  fixing shape typo in gilzenrat script
  fixing overly strict rate param validation that caused bug in cases where mechanism looks up parameter state value
  refactoring transfer mechanism to use get_current_mechanism_param()
  refactoring LCA to use get_current_mechanism_param()
  refactoring kwta's _kwta_scale() to rely on get_current_mechanism_param()
  adding get_current_mechanism_param method on mechanism base to try to look up parameter state value
  remove now-unused time_scale param from many objects (not in scheduling where it's still used)
  log doctests: ignore tests with inconsistent whitespacing
  removing auto and hetero assignments from params dict in recurrent transfer mechansim
  removing unnecessary auto and hetero code in auto associative projection to clean up the relationship between the recurrent projection, its mechanism, and the auto, hetero, and  matrix, attrs
  requiring _kwta_scale method to use k_value parameter state value when available
  commenting out calssPreferences in transfer mechanism because they cause bugs in KWTA when classPreferences try to update
  removing attempt to look up recurrent projection's matrix in matrix getter (because the recurrent projection looks up its owner's matrix)
  refactoring matrix getter on auto associative projection to look up owner's matrix whenever possible
  directly updating auto and hetero attrs at the same time that their parameter states are created in the auto specified, hetero = None and hetero specified, auto = None cases
  beginning to refactor auto/hetero/matrix handling to fit with new parameter state value and make_property changes; beginning by removing obsolete code in recurrent transfer mechanism
  removed CentralClock from MontagueDayanSejnowski96.py
  fixed typo in owner attribute description
  Fix/function/validate params (#616)
  Defaults: set up structure to allow proper aliasing for *Defaults classes
  - Renamed MontagueModel.py to MontagueDayanSejnowski96.py - Correct RST formatting in PredictionErrorMechanism docs - Added Arguments and Attributes to docs for PredictionErrorMechanism
  LinearCombination: rework check for division by zero error to be more general
  default_value: refactor into instance_defaults
  Component: add metaclass for *Defaults to allow some user convenience functionality
  Refactor/control signal/update to intensity (#613)
  Fix/component/intensity and value (#612)
  Fix/gilzenrat model/prefs bug (#611)
  updating DDM mechanism to get threshold using get_current_function_param method when it uses threshold to determine decision variable
  continuing to update how parameters are accessed in pytests (should be mod_ now in many cases)
  replacing .matrix with .mod_matrix in learning pytests
  adding a call to super in projection's _instantiate_attributes_after_function so that it calls make_property_mod (on component)
  Fix/ddm/threshold validation (#610)
  calling get_current_function_param in the remaining functions and fixing small bugs along the way (missing keyword for 'gamma', np.atleast_2d(rate) in lcaintegrator)
  moving make_property_mod back to component.py (from parameterstate.py) -- it is now called for all parameter states during _instantiate_attributes_after_function rather than by individual parameter states
  Docs/td learning/doc fixes (#609)
  removed show graph call from test_reinforcement
  resetting test_multilayer from devel and removing matplotlib from test_prediction_error_delta_function
  specifying smoothing_factor=1.0 on pytests that used to use default smoothing_factor (1.0 --> 0.5)
  changing smoothing factor (formerly time_constant) default value to 0.5 -- it was confusing to users that the default param value prevented integration
  renaming 'time_constant' --> 'smoothing_factor' on TransferMechanism types that use AdaptiveIntegrator
  Fix/log/trial and run (#607)
  Feat/log/trial and run (#606)
  Refactor/project/learning vs executing (#605)
  correcting capitalization
  cleaning up documentation
  adding asserts to parameter states pytests in order to start tracking down bug where mod_noise looks up the parameter state value of the last instance created
  Refactor/mechanism/value in execute 2 (#603)
  predictionerrormechanism
  docs: move gilzenrat svg files from build dir to source dir
  Fix/log/tuple datum value (#601)
  registry: handle case where default-named projection to a duplicate named mechanism would incorrectly detect the projection name as a duplicate
  finished TD Learning documentation
  Fix/state/matrix spec and learning (#600)
  Fix/component preference set/class preferences (#598)
  Fix/log/set log conditions bug (#596)
  updating Transfer functions (Linear, Logistic, Exponential) to use get_current_params(KEYWORD) instead of paramsCurrent[KEYWORD]
  adding get_current_param method which tries to return mod_param and returns param if that doesn't exist -- will eventually be added to all functions, starting here with DriftDiffusionIntegrator
  Docs/log/hint (#595)
  updating shape inconsistencies in DriftDiffusionIntegrator / DDM Mechanism related to time and threshold
  removing special handling of DriftDiffusionIntegrator threshold in variable=array case (correct behavior is ambiguous)
  docs: add extra sub-version number in version display
  utilities: enhance method to recursively convert items to np.ndarray, handling hard cases for np.array
  remove scratch pad and ignore
  Docs/log/log clean up (#593)
  Docs/log/log clean up (#592)
  remove scratch pad
  Docs/log/log clean up (#591)
  Names/log/set log conditions (#590)
  adding pytests to verify that threshold and is_finished work as expected; commenting out tests with DriftDiffusionIntegrator and len(default_variable) > 1 because correct behavior is ambiguous (for now)
  adding 'threshold' param on DriftDiffusionIntegrator which stops accumulation at the threshold, and updated DDM's is_finished to look at this
  updating shape of time computation in FHN integrator (was list, now float)
  updating gilzenrat pytest which was checking _gain and gain to verify modulation to now use gain and mod_gain
  updating pytests and adding comments to possibly fix shape of ddm time value, which changed from a list to a float after property refactoring
  add realtime timestamps to Scheduler, for creation time and end of last RUN time
  change usages of now defunct times attribute of Schedulers to new version
  updating mod_param_name property creation to happen at the instance level in both cases (formerly created on mechanism classes)
  unindenting misplaced setting of _param_name attributes
  Bugfixes (#588)
  setting _param_name for all param_names that go through _validate_params resolves SOME of the cases where getter looks for _param_name before setter creates an _ attr
  Feat/log/add entry (#587)
  Fix/log/log initialization (#586)
  Feat/log/clean up (#585)
  Feat/log/clean up (#584)
  Feat/feat log with time (#583)
  rename psyneulink.scheduling.timescale -> psyneulink.scheduling.time
  create and integrate a new Clock class, and several new classes to keep time, used in Scheduler and Conditions
  adding _param_name to script for better output comparison with older versions (when _ stored the base value)
  solving bug where _param_name did not exist on TransferMechanism instances, but introduced new bug where last param value that was set is starting param value of next instance
  remove old Clock/CentralClock
  debugging make property execution
  main documentation for PredictionErrorMechanism done
  adding mod_slope to the current parameter state pytests
  adding make_property_mod method to parameter states -- executed at the end of _instantiate_parameter_state method and creates a property called mod_param_name on each param that has a parameter state which looks up the current parameter state value
  limiting make_property's resposibility to validation -- setter runs validation and then sets to _param_name, getter returns _param_name. mod_param_name property will handle getting parameter state value
  Feat/log/log levels (#580)
  test
  beginning to separate make property into two methods
  added PredictionErrorDeltaFunction and docs for PredictionErrorMechanism & Montague model
  Refactor/log/entry management (#579)
  montague models working!
  Docs/log/docstring update (#578)
  Add integrator function tests
  Add transfer function tests
  Add distance function tests
  function: test for both 1d and 2d noise
  setup.cfg: Use warmup if benchmarks are enabled
  setup.cfg: Disable benchmarks by default
  pytest: Add benchmarking plugin
  Fix/log/logged items bug (#577)
  using UniformToNormalDist pytest as a check of the scipy requirement error message
  adding documentation for UniformToNormalDist
  validating uniform-to-normal distribution function (matlab)
  Docs/log/docstring update (#572)
  adding gilzenrat figures in _build file
  adding pytest file for parameter states
  Name/log/numpy array to nparray (#571)
  Feat/mechanism/additional props (#570)
  Feat/log (#569)
  EVCAuxiliary: replace kwargs function signatures with explicit arguments
  add docstring explanation for processing and learning termination conditions
  Feat/log (#568)
  adding LC Control Mechanism test to verify that it is updating multiplicative param(s) of modulated mechanism(s) properly
  fix incorrect construction of Process and System in Multitasking example script
  Feat/log (#565)
  Feat/log (#564)
  almost working!
  add travis config file
  single source package requirements
  fixed error message in LinearMatrix
  adding a pytest for the new uniform --> normal distribution function
  fixed sample input
  updating recurrent transfer mechanism and transfer mechanism documentation
  • State   - _validate_variable:  removed:         if not context:             context = kwAssign + ' Base Value'         else:             context = context + kwAssign + ' Base Value'
  Fix/component/default naming (#558)
  remove Scratch Pad
  clean up DDM examples with verified parameters from matlab
  skip NavarroAndFuss doctest because build server cannot access matlab
  update NavarroAndFuss to use the correct version of the MATLAB simulation
  convert DDM return_value for NavarroAndFuss function to be floats to allow NaN assignment
  fix bug in using the matlab engine to run a script outside of the current dir
  adding validation on NormalDist function in the case where some numpy versions throw an error
  • System (#556)
  adding new UniformToNormalDist function which allows for a direct comparison of random numbers between python and matlab
  Feat/system/show graph (#555)
  adding integration_method to FHNIntegrator docs and refining error message
  Fix/modulatory specifications (#554)
  clean imports in function.py
  commenting out assertions in OU integrator pytests until its equation is validated
  fixing mistake in implementation of OUIntegrator
  adding LCAIntegrator docs to function docs page and continuing to touch up typos and incorrect info throughout function docs
  continuing to add documentation for LC Control Mechanism params
  adding matlab and psyneulink plot svgs
  adding pnl and matlab plots plus some additional notes to the Gilzenrat Model page of the documentation
  fixing typos in FHNIntegrator docs
  documenting the LCControl mechanism parameters that hand values off to the FHNIntegrator as well as scaling_factor_gain and base_value_gain
  cleaning up FHNIntegrator docs with tables for explaining parameters and latex equations
  typos in run (input spec) docs
  cleanup Scheduler doc examples
  add parsing handler for Scheduler termination_conditions
  move static .svg files from docs build directory to source dir
  update docs to show 0.0.x versions instead of just 0.x (we use the former frequently)
  fix broken package link for AutoAssociativeMechanism that caused sphinx automodule to fail
  removing references to 'inhibition' and 'decay' in LCA docs
  removing gilzenrat transfer mechanism from the repo
  updating gilzenrat unit tests to use LCA mechanism in place of GilzenratTransferMechanism
  fix bug where versioneer wasn't available at the correct time in building docs
  adding a note about the recurrent matrix to LCA docs
  rewriting gilzenrat model in terms of LCA rather than 'GilzenratTransferMechanism'
  removing LCA pytest from recurrent transfer pytests file now that LCA has its own tests
  updating LCA documentation -- removing beta & inhibition, adding leak, competition, and self_excitation.:
  setting default values for new LCA params
  adding pytest file for LCA and testing length 1 variable and length 2 variable cases
  added output_states param to call of PredictionErrorMechanism constructor
  added default variable param to call to LinearCombination in PredictionErrorMechanism
  adding 'leak' parameter and renaming 'auto'-->'self_excitation' and 'hetero'-->'competition' on LCA mechanism
  Refactor/state/doc test bugs (#551)
  fix bug where invalid escape strings in docstrings would cause failure on python 3.6.x
  fixing incorrect documentation of LCA (did not reflect new LCAIntegrator function)
  continuing to clean up Gilzenrat model and its model-specific components -- verifying that all arguments are consistent and correctly documented
  manually setting outputstate variable size
  adding params for G and k to LCControl mechanism as a temporary solution for allowing the user to modify the equation that computes gain as a function of w
  cleaning up gilzenrat script comments and labeling all params from the paper
  tried manually setting OutputState value for PEM -- didn't work
  Refactor/state/ parse state specs lots (#550)
  use versioneer for single-source versioning
  adding Gilzenrat changes from Markus
  fixed target size for PredictionErrorMechanism
  trying to fix tests
  correct W293 instances
  fix bug where intra-numpy-array list->array element conversion would fail on 0-d numpy array input
  updating logistic function and its documentation to match the more standard form, with an optional 'offset' to take the place of original 'bias' param. Updating all pytests that used what was formerly 'bias' and is now 'offset'
  trying more things to get td learning working
  clean up leabra demo script
  clean up leabramechanism
  add __all__ to leabramechanism and update relevant package
  rename certain leabra-specific functions to include "leabra" in preparation for adding to top-level namespace
  remove unnecessary (and oddly expensive) logging in scheduler
  fix bug where over/underflows in logistic functions would cause the result to be replaced with 0 (often incorrect format and destructive)
  remove forced error on warnings
  Leabra script cleaning (#547)
  cleaned up Matlab scripts & EVC Gratton example script (#546)
  Docs/project/more docstring fixes (#545)
  Docs/project/more fixes (#544)
  Docs/project/fixes (#543)
  reformat Example scripts to new import style, and clean up
  setup Scripts/Examples folder with desired scripts
  remove old/undesired scripts
  adding input spec figures to run documentation
  rename _get_matrix to get_matrix
  Revert "Fix/scripts/cleanup (#539)"
  commenting out all clip (formerly range) code because it does not work as expected
  fixing formatting typo in documentation
  continuing to clean up input specification for (1) heterogenous variables and (2) a limited version of 'sequence' specification
  Fix/scripts/cleanup (#539)
  updating documentation example pytests to verify all inpt values against specified input values
  updating documentation example typos
  Feat/transfer mechanism/add std output states (#538)
  refactoring system input state creation to create one system input state (and mapping projection) for each input state of each origin mechanism
  Feat/transfer mechanism/add std output states (#537)
  Fix/output states (#536)
  Refactor/transfer mechanism/mutiple output states (#535)
  updating transfer mech execute to check the type of its function and call it once or once per input state accordingly, plus Jon's instantiate_output_states
  reclassifying softmax as a 'NormalizingFunction' instead of a 'TransferFunction' so that we can easily identify transfer mechanism functions that should be executed separately for each input state
  use pytest fixture for registry reset in tests/naming to ensure it gets called
  renaming  -->  on TransferMechanism types in order to not overwrite Python built-in range
  Refactor/naming (#533)
  add download link for GilzenratModel.py
  updating kwta and recurrent transfer mech pytests to match new output shape
  cleaning up imports so test will run
  add values(), show(), and nice str/repr methods to InstanceDefaults
  move name assignment (in registry call) to before input_states arg handling in mechanism
  Revert "Refactor/mechanism/preprocess variable (#531)"
  updating transfer mechanism pytests to match new shape of output
  updating transfer mechanism to call its function separately for each input state (each element of variable); for now, integrator function still only executes once
  add shell classes to top-level psyneulink namespace
  correct bug that would cause specifying 3d arrays as default_variable to assign default_variable incorrectly
  add method to np.array-ify all elements within a list/array
  continuing to add pytests for input specification - stuck on verifying that the input specification worked via tools (e.g. call_after_trial) available to the user, because non primary input states are getting overwritten as None
  updating documentation for input specification -- adding tables of inputs on each trial with code snippets
  Fix/mechanism/ parse arg input states (#532)
  Increment version to 0.4.0
  add more input_state spec tests to handle currently known combinations for setting default_variable
  Refactor/mechanism/preprocess variable (#531)
  Refactor/mechanism/preprocess variable (#530)
  Docs/state and projections/docstring revs (#529)
  correct bug in _parse_arg_input_states where a non-list argument wouldn't be made into a list before processing
  change behavior of _parse_state_spec to not populate the state dict with a variable if it's a ClassDefault
  updating noise validation to compare against entire variable (possibly multiple input states) and updating error messages in pytests to reflect these changes
  updating 'try_execute_param method to expect 2d variable and return 2d param
  updating pytests for input specification documentation examples to match the new documentation examples
  continuing to update docs for inputs to system
  revising the input specification docs to describe the rules in terms of matching the mechanim's variable - also making the convenience cases clearer
  removing references to timescale in run and system docs
  Fixed/state/ parse state spec/projection spec (#528)
  Refactor/distance metrics (#526)
  Docs/latex math (#525)
  Docs/intro materials (#524)
  continuing to add pytests to test new input specification rules
  updating some reporting statements to match the new form of inputs (dict)
  continuing to clean up input specification; running inputs first through a new method called _input_matches_variable which catches some numpy mistakes specific to input validation that slip through iscompatible
  Logo (#523)
  make self.name return unnamed .__class__ in case no name was set
  Docs/input state specs (#522)
  Fix/input state specs (#521)
  continuing to add pytests for testing input specifications
  updating process and system to handle the new execution_inputs dict that they receive from run
  consolidating and revamping input processing to get rid of any references to , repetitive code. still some clean up to do -- 5 pytests failing
  Fix/input state specs (#520)
  Fix/input state specs (#519)
  beginning to consolidate input validation because we no longer have phases and don't need to handle systems and processes differently -- 22 pytests failing
  Fix/input state specs (#518)
  using new EULER option on the LCControlMechanism in GilzenratModel in order to match original model
  adding validation requiring integration_method to either be RK4 or EULER
  adding 'integration_method' to LCControlMechanism so that user can switch between euler and rk4 integration for the built-in FHN function
  fixing some params to match matlab model; made it easier to swtich between high C and low C params
  switching FHNIntegrator to use euler integration
  scaling entire noise term by sqrt(dt) rather than scaling the standard deviation of the noise term by sqrt(dt)
  Naming/registry/default name 0 (#516)
  beginning to add in an exception which will allow the case where all mechanisms specify one input which is the same shape as their variable (i.e. no outer list for trials)
  hack mechanism to be able to accept instance_defaults.variable setup via input_states argument
  still trying to fix inputs
  cleaning up sytem unit tests to match new input spec (outer set of brackets representing trials required)
  cleaning up mechanism unit tests to match new input spec (outer set of brackets representing trials required
  move input_states spec tests in test_transfer_mechanism to new file
  update current input_state spec tests
  make test_transfer_mechanism tests use instance_defaults.variable instead of incorrect .variable
  Docs/state and projection (#515)
  remove uses of self.variable. (it is vestigial and maintained only for user inspection)
  rename duplicate transfer mech test to avoid overwrite
  adding input specification pytests to test_system in order to verify which input spec formats already work and build on this
  pull from devel
  Refactor/control and gating signals (#514)
  Import leabra and run leabra tests only if leabra module is available.
  Leabra wrapper prototype (#513)
  Fix/utilities/iscompatible final rev (#512)
  Fix/utilities/iscompatible (#511)
  rename System and Process to add _Base suffix in shellclasses.__all__ because of abf3e7e and 6b9e9a4
  Clean up/registry/ register category (#508)
  Refactor/projection/connection specs (#507)
  Refactor/gating mechanism/ instantiate gating signal (#506)
  • Projection (#505)
  updating comments and error messages in _construct_stimulus_sets to reflect changes
  updating 3 recurrent transfer mech unit tests which used 'sequence format' of input specification for a process to use 'mechanism format' instead
  Refactor/projection/ instantiate sender (#504)
  Refactor/state and projection/clean up (#503)
  commenting out branch of _construct_stimulus_sets which parses inputs by the 'sequence format' rules -- seems safe to move entirely to mechanism format b/c all pytests use 'mechanism format' and new examples using 'sequence format' do not work
  weird hybrid prediction error mechanism
  fix typo in ObjectiveMechanism docstring causing weird documentation formatting
  avoid using module-level Mechanisms in unit tests to avoid possible conflicts
  Refactor/state and projection/unit tests bug fixes (#502)
  Refactor/state and projections/unit tests (#501)
  Refactor/state and projection/names and docs (#500)
  requiring version 1.4 of toposort
  moving imports to top of gilzenrat pytests file
  adding full gilzenrat model to pytests -- no comparison data to assert yet, just verifying that model can run without errors
  adding pytests that isolate the GilzenratTransferMechanism and moving FHNIntegrator test that recreates figure 2 from gilzenrat paper from integrator mechanism tests --> gilzenrat tests
  fixing up a few model values in the gilzenrat model -- behavior is not quit right -- and switching number_of_trials back to 1
  Optimize registry duplicate naming
  adding progress statement ('% complete') to gilzenrat script
  implementing noise on LCAIntegrator and cleaning up unnecessary integrator function code (removing GilzenratIntegrator)
  replacing GilzenratIntegrator with LCAIntegrator (with rate=-1) in GilzenratTransferMechanism
  Refactor/state and projection/specification bug fix 2 (#495)
  Refactored instantiation of States and Projections (#494)
  updating mechanism pytests to reflect integrator_function shape change and removing extraneous transfer mechanism tests which returned arrays of mixed types
  indexing into the first element of the transfer mechanism's integrator_function result so that the shape passed to the transfer mechanism's function is the same as if integrator_mode were false
  add component module to main psyneulink package
  fold keywords into first level hierarchy, because some keywords aren't defined in Keywords.py and this is confusing
  skip notebook checkpoints in running notebook tests
  stop package-level __all__ assignments from accidentally overwriting the __all__ objects they used as bases
  fixing bug in NormalDist() function which was shifting the mean of the distribution
  fix link to the tutorial in docs that didn't get changed when tutorial/ directory was created
  correcting LCAIntegrator function to match the papers (since it represents a rate of change, we need to integrate over timesteps) and relaxing integrator rate param validation which was blocking variables of lengths > 1
  Devel (#490)
  improving initial conditions by making first recurrent projections to recurrent mechanisms make sense given their starting values
  make Function_Base inherit its paramClassDefaults from its parent class Function instead of Component
  remove DefaultProcessingMechanism from component/__init__.py because it's an instantiation of a _Base class, and doesn't get used
  removing and re-adding gilzenrat transfer mechanism because name change did not seem to work
  updating value of LC control mechanism output before it runs to match initial previous value (had to do this in the gilzenrat script because of other LC control mechanism hacks, but left a placeholer in ControlMechanism for how to implement this more generally for any control mechanism that accumulates)
  adding a new Integrator function that matches the decision and response layer functions in the Gilzenrat paper, and a new transfer mechanism which calls this integrator before its primary function
  update README and docs index.rst to new PyPI installation instructions, and tutorial section, reorganize
  reformat README into .rst format so pypi can format it nicely
  update short description to match the title line in the long description
  update setup.cfg for wheel creation and to include license file
  update setup.py supported Python versions to include only 3.5 and 3.6 (does not work on < 3.4 due to numpy, does not work on 3.4)
  update setup.py classifier for Apache license
  add tutorial_requirements.txt mirroring setup.py requirements
  add requirements.txt mirroring setup.py requirements
  update setup.py packages
  add MANIFEST.in
  remove SOFTWARE ARCHITECTURE and TODO List
  remove extraneous files
  add docstrings to __init__.py files (for help command)
  update tutorial to new easier import style
  update docs to handle new module/package format
  update package __init__.py files for simple importing
  add __all__ lists to modules
  rename globals/run.py to globals/environment.py to avoid namespace conflict with run method
  clean up main package __init__.py
  replace paramClassDefaults PROJECTION_SENDER with OutputState class instead of keyword to prevent error due to failed conversion
  rework imports to avoid circularities due to packaging
  make LearningMechanism get its paramClassDefaults from its parent and not Projection_Base
  remove mechanism factory method
  remove system factory in favor of just instantiating System class
  remove process factory in favor of just instantiating Process class
  switch name of Process and Process_Base
  switch name of System and System_Base
  move typecheck for _get_modulated_param inside to avoid circular import
  remove old pyargs argument for pytest
  relaxing validation on LCAIntegrator rate param in order to create an LCA example in integrator mode with an array input
  cleaning up resolving merge conflicts
  fixing merge conflicts
  started mini montague model
  adding comments
  first preliminary test working
  editing testing files and minor typos
  removed unnecessary identity transform function
  updating gitignore for new version of PyCharm
  created PredictionErrorMechanism
  started mini montague model
  adding comments
  first preliminary test working
  editing testing files and minor typos
  removed unnecessary identity transform function
  updating gitignore for new version of PyCharm
  created PredictionErrorMechanism
  starting TDDelta Function -- very messy
  2 of 3 test working
  integrating td learning
  cleaning up Function.py for pull request
  tests working!
  Q-matrix initialization working; mechanism does not
  Added Q-learning and SARSA algorithm
kmantel added a commit that referenced this pull request Apr 5, 2018
* devel:
  Feat/mechanism/input target label dicts (#751)
  Scheduling: fix bug where termination conditions persisted across calls to run
  tests,function/LinearCombination: Add tests with absent parameters
  test,function/LinearCombination: Rename second test function to prevent overwriting results
  • Context (#746)
  Refactor/context/deprecate init status (#745)
  Refactor/context/structured (#744)
  Fix/function/stability (#743)
  • IntegratorMechanism (#742)
  Feat/context/time (#740)
  Feat/context/time (#739)
  Image Fix (#738)
  finally fixed image (#737)
  Image Fix (#736)
  Example Fix (#735)
  Linear combination fix (#734)
  Feat/component/execution count (#733)
  jvesely/linear_combination_function_refactor (#732)
  Refactor/project/context rev 2 (#731)
  Refactor/system/show graph structure options (#730)
  • System (#729)
  Feat/mechanism/show structure (#728)
  Feat/mechanism/show mechanism (#727)
  jvesely/linear_combination (#724)
  creating a property for TransferMechanism's integrator_mode so that the mechanism can switch integrator mode on and off
  Fix/function/udf examples (#722)
  • Function (#717)
  Refactor/function/udf (#716)
  Refactor/mechanism and output state/mech params dict added (#715)
  Docs/output state/clean up (#714)
  Clean up/function/softmax one hot (#713)
  Name/project/replace assign index calculate (#711)
  Fix/controlmechanism/assign as controller jdc (#705)
  Feat/function/one hot cleanup (#704)
  Feat/function/one hot (#703)
  adding a pytest for the clear_log method
  updating output of nparray_dictionary when there are no entries from None to an empty OrderedDict
  Tests/llvm devel sync (#684)
  removing show graph pdfs from tests folder
  revising the show_graph pytests to call '_get_label' as a proxy for whether show_graph with dimensions is working
  moving _get_label helper function outside of show_graph method, so that it can be accessed on its own
  fixing bug in show_graph(show_dimensions=True) by taking np.atleast_1d of output_state.value
  • LearningProjection   docstring rev (to include error_function)
  Feat/process/learning objective mech (#698)
  Feat/ddm/selected input array (#697)
  Feat/ddm/selected input array (#695)
  user_params and function_params now look at parameter state values (rather than param base values), and are updated whenever mechanisms update their parameter states
  adding pytests that call show graph after creating various types of systems -- may refactor these to call the individual methods of show_graph
  removing system graph pdfs
  removing show_dimensions=True from call to show_graph in GilzenratModel because it generates an error
  updating how valus are retrieved from log in Nieuwenhuis model (based on addition of Pass to log)
  Fix/system/learning ends before terminal (#692)
  Fix/system/learning ends before terminal (#691)
  Revert "Merge branch 'master' into fix/system/learning_ends_before_terminal"
  -
  • ControlMechanism   _instantiate_control_signals:  debugged OWNER_VALUE assignment
  • Scripts/Examples   Rumelhart Semantic Network: updated with step function
  • System   _instantiate_learning_graph(): fixed bug in which learning failed to     be instantiated for a System in which the last Mechanism in a     learning sequence was not the TERMINAL Mechanism of the System.
  • System   _instantiate_learning_graph(): fixed bug in which learning failed to     be instantiated for a System in which the last Mechanism in a     learning sequence was not the TERMINAL Mechanism of the System.
  • OutputState   docstring revs
  • OutputState   docstring revs
  fixing documentation formatting mistake
  continuing to add pytests and doc fixes for clip on transfer mechanism types
  allowing lca to execute function over entire variable, not just first item
  fixing documentation for clip
  continuing to add error messages to reinitialize
  allowing smoothing factor to be an integer (formerly 1.0 and 0.0 were allowed but 1 and 0 were not)
  removing typecheck on learning mechanism's default_variable
  adding exception in UDF so that function can be called without params and context
  correcting error message for initial_value validation on transfer mechanism
  fixing bug in reinitialize on arrays (needed np.atleast_2d when setting intial_value because it is compared to variable)
  -
  • OutputState   docstring revs
  Refactoring of OutputState to support flexible assignment of its variable attribute.
  Revert "-"
  Revert "-"
  Revert "-"
  -
  adding pytests for specific reinitialize cases that were not covered, and adding error messages that were missing for some of them
  -
  fixing documentation typo: integration_method was mistakenly called integration_method_FHN in docs
  -
  -
  -
  -
  -
  -
  Reworking Montague, Dayan, and Sejnowski model documentation.
  -
  Merge branches 'bug/parsing/input_states-use-value' and 'feat/DDM/value_based_version_input_state' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/DDM/value_based_version_input_state
  Merge branches 'bug/parsing/input_states-use-value' and 'feat/DDM/value_based_version_input_state' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/DDM/value_based_version_input_state
  -
  -
  -
  -
  -
  -
  • Utilities   - recursive_update():  added non-destructive option that preserves                          any non-empty entries in destination dict
  -
  -
  -
  • OutputState   this version implements OutputState.variable as a property   that returns _parse_output_state_variable()
  • OutputState   this version implements OutputState.variable as a property   that returns _parse_output_state_variable()
  -
  -
  -
  -
  -
  -
  adding pytests for invalid target specifcation to confirm that the proper error messages are generated
  • OutputState   assign function now expects dict as argument - WORKING
  adding more pytests to confirm that convenience notations and combinations of function and list target specs all run
  documenting targets and adding some checks to adjust targets: verify that num_targets = num_inputs, and ignore num_targets in the case of function specifications (because a new value is generated on each trial)
  -
  -
  -
  -
  • OutputState   - implemented assign that takes assign_params_dict as arg
  Fix/output state/assign backward compat (#676)
  • OutputState   added backward compatibility   docstring: document replacement of calcuate/CACULATE with assign/ASSIGN
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  in progress: refactoring function specification of target spec to be an option within the dictionary specification, rather than on its own
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  Feat/ddm/input state as array (#674)
  revising documentation for target specification
  cleaning up a typo in target_spec_parsing (comparator mechanism was referenced where it should have been terminal mechanism)
  moving call to _check_args in BackProp to before the error matrix is updated in order to avoid a validation bug
  adding pytests for target spec convenience notations
  adding run to rumelhart tests (previously only created systems)
  Merge branches 'clean_up/function_and_system/backprop_and_show_graph' and 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into clean_up/function_and_system/backprop_and_show_graph
  revising how target input state values are assigned in system's execute_learning
  adding a simple multilayer learning pytest
  refactor execute and _execute methods
  defaults: remove post-hoc conversion of defaults variable
  Component: don't convert defaults variable on calls to validate a variable
  parsing: add initial_value parser
  parsing: add generic argument parser used as default if none specified
  Component: add method to parse user inputted variable to useable/standard form
  utilities: handle nonuniform objects better when converting to numpy arrays
  control: refactor handling of allocation*
  projections: refactor sender instantiation to avoid directly setting instance default variable
  clean up input_states handler
  rename input_states arg parser to handler
  maint: add comments to separate handler, parsing, and validation methods
  maint: remove unused PROJECTION_SENDER_VALUE
  TransferMechanism: use standard form of setting default variable
  utilities: change number detection to accept any number, not just int and float
  OutputState: when variable not specified to constructor, pass up another value
  make self.variable read only (we should not be using it for logic)
  replace calls to self.variable to proper self.instance_defaults.variable
  validation: remove extraneous check for ClassDefaults.variable
  ClassDefaults: make RecurrentTransferMechanism default require 2d variable because it takes an AutoAssociativeProjection that uses a LinearMatrix that requires 1D
  Distance: fix validation assumption that items of passed variable are iterable
  ClassDefaults: correct and consolidate
  utilities: add method to produce a value for length calls when len() fails
  utilities: add function to determine whether something is iterable
  Integrators: handle initializer like variable in Components
  Function: standardize default_variable assignments
  ProcessingMechanism: use standard assignment of default variable
  DDM: use standard assignment of default variable
  ensure default_variable auto sets to dtype float
  combine handling of default_variable/size to create instance_defaults.variable in Component.__init__
  utilities: allow list->array element conversion to typecast internal items
  validation: fix validate_variable crashes on certain variable types
  utilities: add helper method to determine if an object contains a single value
  rename variable->default_variable
  Clean up/function and system/backprop and show graph (#671)
  Clean up/learning/misc (#670)
  Clean up/learning/misc (#669)
  Clean up/learning/misc (#668)
  Fix/transfermechanism/noise function (#667)
  Fix/transfermechanism/clip (#666)
  Refactor/modulatory signals/linear default function (#665)
  Refactor/learning/heterovergent (#664)
  in progress - refactoring adjust_target_dict method to validate all candidate targets and confirm that all mechanisms provided the same number of targets
  Tests/mechanism/hebbian learning (#663)
  Docs/function/hebbian (#662)
  Docs/function/hebbian (#661)
  updating pytest expected values based on changes to log output
  adding Pass to log output and updating pytests accordingly
  Fix/learning/hebbian (#659)
  swapping all log references to 'simple_time' with the full 'time', and removing old code which handled time stamp duplicates
  in progress - refactoring target spec/validation to work the same way as input spec/validation
  renaming object --> component in _adjust_target_dict()
  updating pytests to match RecurrentTransferMech switch from full matrix to hollow matrix; changed expected output or set auto = 1 to preserve old expected output, depending on type of test
  setting default matrix of a RecurrentTransferMechanism to a hollow matrix, and updating docs to be clearer about how auto, hetero, and matrix combine/overwrite each other when multiple arguments are specified
  renaming object --> component in _validate_targets method to avoid shadowing python built-in
  updating pytest expected results to match increment change in log
  log pytest for a mechanism that is scheduled to run many times in a row
  changing increment size on log's time_step workaround
  temporary workaround for timestep values: incrementing first decimal of timestep
  revising log tests for new time_step notation
  temporary workaround for timestep values: incrementing first decimal of timestep
  revising parse_entries_for_time_values method on log so that it edits the time values in the log items directly, rather than maintaining a separate list of modified time values
  setting axis=1 on calls to np.sum and np.product in Reduce function and adding tests for this function
  documentation typos
  documenting reinitialize on mechanism
  continuing to add tests and docs for reinitialize
  fixing bugs that prevented initialize method on system from ever executing, and adding pytests for it now that it works
  revising outdated TransferMechanism docs for reinitialize
  continuing to add tests to highlight differences between calling reinitialize on a mechanisms and on a function
  adding nparray_dictionary to docs and revising nparray to use the same helper methods as nparray_dictionary
  Time: fix bug where RUN counter would not be incremented on new runs
  fixing (temporarily) time_step bug in nparray_dictionary; reorganzing nparray_dictionary into methods that can be reused by nparray
  refactoring log to have a dictionary option and writing tests for it
  beginning to add a dictionary alternative to the options for whats returned by the log
  more calls to _dealias_owner_name required in order to create log.nparray
  fixing bug in log: needed to switch between 'value' and mechanism name in several loops in order to assemble log.nparray
  -
  Feat/rl/for mads (#652)
  Feat/rl/for mads (#651)
  adding more pytests for reinitialize and fixing reinitialize bugs; beginning to update documentation
  adding pytests for reinitializing at both function and mechanism level; cleaning up mistakes in reinitialize() methods along the way
  Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projection/Context_devel
  adding a reinitialize method on mechanisms, which calls reinitialize on its function or integrator_function, then updates the mechanism's value and output states
  beginning to refactor reinitialize as a method on integrator functions
  Removed Print Statements (#650)
  cleaning up documentation to match how LinearMatrix works in all cases
  typo in linear matrix function validation
  simplifying non-projection branch of validation on LinearMatrix function and adding more pytests
  default_variable: let argument override input_states variable spec if compatible
  adding pytests for possible combinations of variable and matrix specifications for LinearMatrix as a function of a mechanism
  adding validation comparing matrix to variable when LinearMatrix function is called by a mechanism; creating square full connectivity matrix that matches variable when matrix is not specified
  tutorial: reenable graph drawing; requires graphviz package
  tutorial: clear outputs
  Lena Program 1 Bugfix (#648)
  Hebbian learning fix (#647)
  User defined function updates (#646)
  adding working version of LinearMatrix function pytest (only works because default_variable is specified on both the mechanism and the function)
  fix input_states argparsing to not be dependent on default_variable or size args
  tests: ensure leabra tests get skipped if module is not available
  splitting linear matrix function's validation into two branches because matrix is handled differently when the function is called by a projection vs a receiver
  docstring wording change
  Docs/models/title changes (#645)
  Docs/nieuwenhuis/edits (#644)
  adding pytest for ProcessingMechanism with LinearMatrix function to begin debugging why this fn only works in Projections
  removing unrestrictedtransfermechanism file because this mechanism is now called ProcessingMechanism and does not need its own file
  adding parameter state docs examples back in with doctest SKIP
  revising proccessing mechanism docs because it is not an executable mechanism (not just an ABC)
  renaming UnrestrictedProcessingMechanism --> ProcessingMechanism and moving code into processingmechanism.py (which formerly only contained ProcessingMechanism_Base
  Leabra Update (#642)
  DDM: update is_finished to work on functions with any dimensional variable
  skipping transfer mechanism doc tests
  skipping transfer mechanism doc tests
  minor documentation changes -typos and formatting mistakes
  reorganizing integrator mechanism pytests for reinitialize
  overwriting AGTUtilityIntegrator's reinitialize property - requires custom reinitialization of short term and long term utility
  overwriting FHNIntegrator's reinitialize property - requires custom reinitialization of v, w, time, value
  overwriting reinitialize property on DriftDiffusion Integrator so that time can also be reset
  documenting reinitialize on all Integrator functions and fixing a typo in transfer mechanism docs (initial_value --> initializer)
  continuing to add docs and examples for reinitialize, and cleaning up TransferMechanism docs along the way
  fixing tutorial indexing bug
  refactoring is_finished as a property so that it is always up to date, even when values change in between executions (i.e. if threshold was crossed and then reinitialize was used)
  fixing bug in transfer mechanism documention examples (np.array typo)
  renaming reset_intializer --> reinitialize
  adding unrestricted mechanism pytests to confirm that mechanism can be constructed and executed with any function -- identified two exceptions (linear matrix and back prop)
  adding a new mechanism that has no restrictions on which functions can be used
  commenting out show graph lines in tutorial for now because graphviz is not imported on testing server
  adding updated version of tutorial from Justin
  Defaults*: fix class structure addressing bugs
  revising transfer mechanism documentation -- 'creating' section
  commenting out show_graph in EVC gratton pytest so that this line does not run on Jenkins
  adding TransferMechanism pytests to verify previous_value persists over multiple runs/executions AND previous_value resets whenever reset_initializer is used
  edited  NieuwenhuisModel docs
  tutorial: remove old version - new version is in tutorial/ dir
  tutorial: support execution on mybinder.org
  tutorial: support execution on mybinder.org
  tutorial: remove old version - new version is in tutorial/ dir
  • Niewenhuis model   - docstring edits
  -
  adding integrator_mode and integrator_function attr documentation for all transfer mechanism types
  revising outdated documentation for transfer mechanism noise
  fixed bug in plotting Nieuwenhuis Model
  updated Nieuwenhuis documentation
  adding attrs that were missing from LCA mechanism docs and revising related documentation
  Scripts: clean up
  Functions: add UniformToNormalDist to top-level psyneulink module; update docs
  revising explanation of user_params
  revising explanation of user_params
  revising parameter state documentation
  adding Markus' Nieuwenhuis documentation, plus figures and some .rst formatting
  Functions: replace internal calls to find owner's name with a property
  Component: make string version of *defaults classes be sorted
  removing parameter state example from file completely (tried commenting it out originally)
  removing parameter states example from documentation because it may be the reason parameter state tests are failing
  renaming 'Core Configurable Attributes' --> 'Core Structural Attributes' in Component documentation
  Refactor/system/controller (#627)
  Fix/controlmechanism/assign as controller (#625)
  • Log (#624)
  fixing typo in doctest (parameter state values)
  adding a docs example which walks through how a mechanism parameter and a function parameter and their mod_ versions change in value
  BogaczEtAl: use better numpy method for floating point warning handling
  utilities: update compatibility checker to terminate earlier in some cases
  updating modulation-related documentation to include mod_param and be more precise about what is updated by modulation (the parameter value used by a function changes, but the corresponding function attr does not change b/c it is the base value)
  adding documentation for mod_param
  allowing user to pass value into mod_param setter (even though setting is not allowed) in order to produce a more informative error message)
  commenting out noise and smoothing factor properties in transfer mechanism because these replace the default properties, causing unexpected behavior
  adding pytest to verify correct error message when user tries to set to mod_param_name
  adding pytest to track changes in attr, _attr, mod_param_name, and userparams[param_name] values of Transfer Mechanism's configurable params when (1) param values are updated (2) mechanism is executed
  adding an exception to make_mod_param as a temporary fix for function-specific mod_param properties that stay on mechanism class when function changes
  fixing typo in AGTUtilityIntegrator
  cleaning up function.py and verifying that self.get_current_function_param is used in all functions (skipped learning functions for now)
  Fix/controlmechanism/assign as controller (#620)
  Fix/controlmechanism/assign as controller (#619)
  cleaning up recurrent transfer mechanism pytests and fixing bugs in asserts
  updating matrix setter to also set the projection's matrix parameter state's function's previous value
  uncommenting auto and hetero properties from auto associative projection so that setting auto and hetero directly on the projections works
  adding auto and hetero properties to recurrent transfer mechanism. Auto, hetero, and matrix setters now all update recurrent_projection's matrix parameter state's function's previous_value
  Fix/controlmechanism/assign as controller (#618)
  executing projection individually in tranfer mechanism's matrix-change pytest
  adding a matrix-change pytest for a mapping projection between two transfer mechanisms in order to isolate the matrix bug from auto/hetero properties
  Defaults: clean up method organization
  fixing shape typo in gilzenrat script
  fixing overly strict rate param validation that caused bug in cases where mechanism looks up parameter state value
  refactoring transfer mechanism to use get_current_mechanism_param()
  refactoring LCA to use get_current_mechanism_param()
  refactoring kwta's _kwta_scale() to rely on get_current_mechanism_param()
  adding get_current_mechanism_param method on mechanism base to try to look up parameter state value
  remove now-unused time_scale param from many objects (not in scheduling where it's still used)
  log doctests: ignore tests with inconsistent whitespacing
  removing auto and hetero assignments from params dict in recurrent transfer mechansim
  removing unnecessary auto and hetero code in auto associative projection to clean up the relationship between the recurrent projection, its mechanism, and the auto, hetero, and  matrix, attrs
  requiring _kwta_scale method to use k_value parameter state value when available
  commenting out calssPreferences in transfer mechanism because they cause bugs in KWTA when classPreferences try to update
  removing attempt to look up recurrent projection's matrix in matrix getter (because the recurrent projection looks up its owner's matrix)
  refactoring matrix getter on auto associative projection to look up owner's matrix whenever possible
  directly updating auto and hetero attrs at the same time that their parameter states are created in the auto specified, hetero = None and hetero specified, auto = None cases
  beginning to refactor auto/hetero/matrix handling to fit with new parameter state value and make_property changes; beginning by removing obsolete code in recurrent transfer mechanism
  removed CentralClock from MontagueDayanSejnowski96.py
  fixed typo in owner attribute description
  Fix/function/validate params (#616)
  Defaults: set up structure to allow proper aliasing for *Defaults classes
  - Renamed MontagueModel.py to MontagueDayanSejnowski96.py - Correct RST formatting in PredictionErrorMechanism docs - Added Arguments and Attributes to docs for PredictionErrorMechanism
  LinearCombination: rework check for division by zero error to be more general
  default_value: refactor into instance_defaults
  Component: add metaclass for *Defaults to allow some user convenience functionality
  Refactor/control signal/update to intensity (#613)
  Fix/component/intensity and value (#612)
  Fix/gilzenrat model/prefs bug (#611)
  updating DDM mechanism to get threshold using get_current_function_param method when it uses threshold to determine decision variable
  continuing to update how parameters are accessed in pytests (should be mod_ now in many cases)
  replacing .matrix with .mod_matrix in learning pytests
  adding a call to super in projection's _instantiate_attributes_after_function so that it calls make_property_mod (on component)
  Fix/ddm/threshold validation (#610)
  calling get_current_function_param in the remaining functions and fixing small bugs along the way (missing keyword for 'gamma', np.atleast_2d(rate) in lcaintegrator)
  moving make_property_mod back to component.py (from parameterstate.py) -- it is now called for all parameter states during _instantiate_attributes_after_function rather than by individual parameter states
  Docs/td learning/doc fixes (#609)
  removed show graph call from test_reinforcement
  resetting test_multilayer from devel and removing matplotlib from test_prediction_error_delta_function
  specifying smoothing_factor=1.0 on pytests that used to use default smoothing_factor (1.0 --> 0.5)
  changing smoothing factor (formerly time_constant) default value to 0.5 -- it was confusing to users that the default param value prevented integration
  renaming 'time_constant' --> 'smoothing_factor' on TransferMechanism types that use AdaptiveIntegrator
  Fix/log/trial and run (#607)
  Feat/log/trial and run (#606)
  Refactor/project/learning vs executing (#605)
  correcting capitalization
  cleaning up documentation
  adding asserts to parameter states pytests in order to start tracking down bug where mod_noise looks up the parameter state value of the last instance created
  Refactor/mechanism/value in execute 2 (#603)
  predictionerrormechanism
  docs: move gilzenrat svg files from build dir to source dir
  Fix/log/tuple datum value (#601)
  registry: handle case where default-named projection to a duplicate named mechanism would incorrectly detect the projection name as a duplicate
  finished TD Learning documentation
  Fix/state/matrix spec and learning (#600)
  Fix/component preference set/class preferences (#598)
  Fix/log/set log conditions bug (#596)
  updating Transfer functions (Linear, Logistic, Exponential) to use get_current_params(KEYWORD) instead of paramsCurrent[KEYWORD]
  adding get_current_param method which tries to return mod_param and returns param if that doesn't exist -- will eventually be added to all functions, starting here with DriftDiffusionIntegrator
  Docs/log/hint (#595)
  updating shape inconsistencies in DriftDiffusionIntegrator / DDM Mechanism related to time and threshold
  removing special handling of DriftDiffusionIntegrator threshold in variable=array case (correct behavior is ambiguous)
  docs: add extra sub-version number in version display
  utilities: enhance method to recursively convert items to np.ndarray, handling hard cases for np.array
  remove scratch pad and ignore
  Docs/log/log clean up (#593)
  Docs/log/log clean up (#592)
  remove scratch pad
  Docs/log/log clean up (#591)
  Names/log/set log conditions (#590)
  adding pytests to verify that threshold and is_finished work as expected; commenting out tests with DriftDiffusionIntegrator and len(default_variable) > 1 because correct behavior is ambiguous (for now)
  adding 'threshold' param on DriftDiffusionIntegrator which stops accumulation at the threshold, and updated DDM's is_finished to look at this
  updating shape of time computation in FHN integrator (was list, now float)
  updating gilzenrat pytest which was checking _gain and gain to verify modulation to now use gain and mod_gain
  updating pytests and adding comments to possibly fix shape of ddm time value, which changed from a list to a float after property refactoring
  add realtime timestamps to Scheduler, for creation time and end of last RUN time
  change usages of now defunct times attribute of Schedulers to new version
  updating mod_param_name property creation to happen at the instance level in both cases (formerly created on mechanism classes)
  unindenting misplaced setting of _param_name attributes
  Bugfixes (#588)
  setting _param_name for all param_names that go through _validate_params resolves SOME of the cases where getter looks for _param_name before setter creates an _ attr
  Feat/log/add entry (#587)
  Fix/log/log initialization (#586)
  Feat/log/clean up (#585)
  Feat/log/clean up (#584)
  Feat/feat log with time (#583)
  rename psyneulink.scheduling.timescale -> psyneulink.scheduling.time
  create and integrate a new Clock class, and several new classes to keep time, used in Scheduler and Conditions
  adding _param_name to script for better output comparison with older versions (when _ stored the base value)
  solving bug where _param_name did not exist on TransferMechanism instances, but introduced new bug where last param value that was set is starting param value of next instance
  remove old Clock/CentralClock
  debugging make property execution
  main documentation for PredictionErrorMechanism done
  adding mod_slope to the current parameter state pytests
  adding make_property_mod method to parameter states -- executed at the end of _instantiate_parameter_state method and creates a property called mod_param_name on each param that has a parameter state which looks up the current parameter state value
  limiting make_property's resposibility to validation -- setter runs validation and then sets to _param_name, getter returns _param_name. mod_param_name property will handle getting parameter state value
  Feat/log/log levels (#580)
  test
  beginning to separate make property into two methods
  added PredictionErrorDeltaFunction and docs for PredictionErrorMechanism & Montague model
  Refactor/log/entry management (#579)
  montague models working!
  Docs/log/docstring update (#578)
  Add integrator function tests
  Add transfer function tests
  Add distance function tests
  function: test for both 1d and 2d noise
  setup.cfg: Use warmup if benchmarks are enabled
  setup.cfg: Disable benchmarks by default
  pytest: Add benchmarking plugin
  Fix/log/logged items bug (#577)
  using UniformToNormalDist pytest as a check of the scipy requirement error message
  adding documentation for UniformToNormalDist
  validating uniform-to-normal distribution function (matlab)
  Docs/log/docstring update (#572)
  adding gilzenrat figures in _build file
  adding pytest file for parameter states
  Name/log/numpy array to nparray (#571)
  Feat/mechanism/additional props (#570)
  Feat/log (#569)
  EVCAuxiliary: replace kwargs function signatures with explicit arguments
  add docstring explanation for processing and learning termination conditions
  Feat/log (#568)
  adding LC Control Mechanism test to verify that it is updating multiplicative param(s) of modulated mechanism(s) properly
  fix incorrect construction of Process and System in Multitasking example script
  Feat/log (#565)
  Feat/log (#564)
  almost working!
  add travis config file
  single source package requirements
  fixed error message in LinearMatrix
  adding a pytest for the new uniform --> normal distribution function
  fixed sample input
  updating recurrent transfer mechanism and transfer mechanism documentation
  • State   - _validate_variable:  removed:         if not context:             context = kwAssign + ' Base Value'         else:             context = context + kwAssign + ' Base Value'
  Fix/component/default naming (#558)
  remove Scratch Pad
  clean up DDM examples with verified parameters from matlab
  skip NavarroAndFuss doctest because build server cannot access matlab
  update NavarroAndFuss to use the correct version of the MATLAB simulation
  convert DDM return_value for NavarroAndFuss function to be floats to allow NaN assignment
  fix bug in using the matlab engine to run a script outside of the current dir
  adding validation on NormalDist function in the case where some numpy versions throw an error
  • System (#556)
  adding new UniformToNormalDist function which allows for a direct comparison of random numbers between python and matlab
  Feat/system/show graph (#555)
  adding integration_method to FHNIntegrator docs and refining error message
  Fix/modulatory specifications (#554)
  clean imports in function.py
  commenting out assertions in OU integrator pytests until its equation is validated
  fixing mistake in implementation of OUIntegrator
  adding LCAIntegrator docs to function docs page and continuing to touch up typos and incorrect info throughout function docs
  continuing to add documentation for LC Control Mechanism params
  adding matlab and psyneulink plot svgs
  adding pnl and matlab plots plus some additional notes to the Gilzenrat Model page of the documentation
  fixing typos in FHNIntegrator docs
  documenting the LCControl mechanism parameters that hand values off to the FHNIntegrator as well as scaling_factor_gain and base_value_gain
  cleaning up FHNIntegrator docs with tables for explaining parameters and latex equations
  typos in run (input spec) docs
  cleanup Scheduler doc examples
  add parsing handler for Scheduler termination_conditions
  move static .svg files from docs build directory to source dir
  update docs to show 0.0.x versions instead of just 0.x (we use the former frequently)
  fix broken package link for AutoAssociativeMechanism that caused sphinx automodule to fail
  removing references to 'inhibition' and 'decay' in LCA docs
  removing gilzenrat transfer mechanism from the repo
  updating gilzenrat unit tests to use LCA mechanism in place of GilzenratTransferMechanism
  fix bug where versioneer wasn't available at the correct time in building docs
  adding a note about the recurrent matrix to LCA docs
  rewriting gilzenrat model in terms of LCA rather than 'GilzenratTransferMechanism'
  removing LCA pytest from recurrent transfer pytests file now that LCA has its own tests
  updating LCA documentation -- removing beta & inhibition, adding leak, competition, and self_excitation.:
  setting default values for new LCA params
  adding pytest file for LCA and testing length 1 variable and length 2 variable cases
  added output_states param to call of PredictionErrorMechanism constructor
  added default variable param to call to LinearCombination in PredictionErrorMechanism
  adding 'leak' parameter and renaming 'auto'-->'self_excitation' and 'hetero'-->'competition' on LCA mechanism
  Refactor/state/doc test bugs (#551)
  fix bug where invalid escape strings in docstrings would cause failure on python 3.6.x
  fixing incorrect documentation of LCA (did not reflect new LCAIntegrator function)
  continuing to clean up Gilzenrat model and its model-specific components -- verifying that all arguments are consistent and correctly documented
  manually setting outputstate variable size
  adding params for G and k to LCControl mechanism as a temporary solution for allowing the user to modify the equation that computes gain as a function of w
  cleaning up gilzenrat script comments and labeling all params from the paper
  tried manually setting OutputState value for PEM -- didn't work
  Refactor/state/ parse state specs lots (#550)
  use versioneer for single-source versioning
  adding Gilzenrat changes from Markus
  fixed target size for PredictionErrorMechanism
  trying to fix tests
  correct W293 instances
  fix bug where intra-numpy-array list->array element conversion would fail on 0-d numpy array input
  updating logistic function and its documentation to match the more standard form, with an optional 'offset' to take the place of original 'bias' param. Updating all pytests that used what was formerly 'bias' and is now 'offset'
  trying more things to get td learning working
  clean up leabra demo script
  clean up leabramechanism
  add __all__ to leabramechanism and update relevant package
  rename certain leabra-specific functions to include "leabra" in preparation for adding to top-level namespace
  remove unnecessary (and oddly expensive) logging in scheduler
  fix bug where over/underflows in logistic functions would cause the result to be replaced with 0 (often incorrect format and destructive)
  remove forced error on warnings
  Leabra script cleaning (#547)
  cleaned up Matlab scripts & EVC Gratton example script (#546)
  Docs/project/more docstring fixes (#545)
  Docs/project/more fixes (#544)
  Docs/project/fixes (#543)
  reformat Example scripts to new import style, and clean up
  setup Scripts/Examples folder with desired scripts
  remove old/undesired scripts
  adding input spec figures to run documentation
  rename _get_matrix to get_matrix
  Revert "Fix/scripts/cleanup (#539)"
  commenting out all clip (formerly range) code because it does not work as expected
  fixing formatting typo in documentation
  continuing to clean up input specification for (1) heterogenous variables and (2) a limited version of 'sequence' specification
  Fix/scripts/cleanup (#539)
  updating documentation example pytests to verify all inpt values against specified input values
  updating documentation example typos
  Feat/transfer mechanism/add std output states (#538)
  refactoring system input state creation to create one system input state (and mapping projection) for each input state of each origin mechanism
  Feat/transfer mechanism/add std output states (#537)
  Fix/output states (#536)
  Refactor/transfer mechanism/mutiple output states (#535)
  updating transfer mech execute to check the type of its function and call it once or once per input state accordingly, plus Jon's instantiate_output_states
  reclassifying softmax as a 'NormalizingFunction' instead of a 'TransferFunction' so that we can easily identify transfer mechanism functions that should be executed separately for each input state
  use pytest fixture for registry reset in tests/naming to ensure it gets called
  renaming  -->  on TransferMechanism types in order to not overwrite Python built-in range
  Refactor/naming (#533)
  add download link for GilzenratModel.py
  updating kwta and recurrent transfer mech pytests to match new output shape
  cleaning up imports so test will run
  add values(), show(), and nice str/repr methods to InstanceDefaults
  move name assignment (in registry call) to before input_states arg handling in mechanism
  Revert "Refactor/mechanism/preprocess variable (#531)"
  updating transfer mechanism pytests to match new shape of output
  updating transfer mechanism to call its function separately for each input state (each element of variable); for now, integrator function still only executes once
  add shell classes to top-level psyneulink namespace
  correct bug that would cause specifying 3d arrays as default_variable to assign default_variable incorrectly
  add method to np.array-ify all elements within a list/array
  continuing to add pytests for input specification - stuck on verifying that the input specification worked via tools (e.g. call_after_trial) available to the user, because non primary input states are getting overwritten as None
  updating documentation for input specification -- adding tables of inputs on each trial with code snippets
  Fix/mechanism/ parse arg input states (#532)
  Increment version to 0.4.0
  add more input_state spec tests to handle currently known combinations for setting default_variable
  Refactor/mechanism/preprocess variable (#531)
  Refactor/mechanism/preprocess variable (#530)
  Docs/state and projections/docstring revs (#529)
  correct bug in _parse_arg_input_states where a non-list argument wouldn't be made into a list before processing
  change behavior of _parse_state_spec to not populate the state dict with a variable if it's a ClassDefault
  updating noise validation to compare against entire variable (possibly multiple input states) and updating error messages in pytests to reflect these changes
  updating 'try_execute_param method to expect 2d variable and return 2d param
  updating pytests for input specification documentation examples to match the new documentation examples
  continuing to update docs for inputs to system
  revising the input specification docs to describe the rules in terms of matching the mechanim's variable - also making the convenience cases clearer
  removing references to timescale in run and system docs
  Fixed/state/ parse state spec/projection spec (#528)
  Refactor/distance metrics (#526)
  Docs/latex math (#525)
  Docs/intro materials (#524)
  continuing to add pytests to test new input specification rules
  updating some reporting statements to match the new form of inputs (dict)
  continuing to clean up input specification; running inputs first through a new method called _input_matches_variable which catches some numpy mistakes specific to input validation that slip through iscompatible
  Logo (#523)
  make self.name return unnamed .__class__ in case no name was set
  Docs/input state specs (#522)
  Fix/input state specs (#521)
  continuing to add pytests for testing input specifications
  updating process and system to handle the new execution_inputs dict that they receive from run
  consolidating and revamping input processing to get rid of any references to , repetitive code. still some clean up to do -- 5 pytests failing
  Fix/input state specs (#520)
  Fix/input state specs (#519)
  beginning to consolidate input validation because we no longer have phases and don't need to handle systems and processes differently -- 22 pytests failing
  Fix/input state specs (#518)
  using new EULER option on the LCControlMechanism in GilzenratModel in order to match original model
  adding validation requiring integration_method to either be RK4 or EULER
  adding 'integration_method' to LCControlMechanism so that user can switch between euler and rk4 integration for the built-in FHN function
  fixing some params to match matlab model; made it easier to swtich between high C and low C params
  switching FHNIntegrator to use euler integration
  scaling entire noise term by sqrt(dt) rather than scaling the standard deviation of the noise term by sqrt(dt)
  Naming/registry/default name 0 (#516)
  beginning to add in an exception which will allow the case where all mechanisms specify one input which is the same shape as their variable (i.e. no outer list for trials)
  hack mechanism to be able to accept instance_defaults.variable setup via input_states argument
  still trying to fix inputs
  cleaning up sytem unit tests to match new input spec (outer set of brackets representing trials required)
  cleaning up mechanism unit tests to match new input spec (outer set of brackets representing trials required
  move input_states spec tests in test_transfer_mechanism to new file
  update current input_state spec tests
  make test_transfer_mechanism tests use instance_defaults.variable instead of incorrect .variable
  Docs/state and projection (#515)
  remove uses of self.variable. (it is vestigial and maintained only for user inspection)
  rename duplicate transfer mech test to avoid overwrite
  adding input specification pytests to test_system in order to verify which input spec formats already work and build on this
  pull from devel
  Refactor/control and gating signals (#514)
  Import leabra and run leabra tests only if leabra module is available.
  Leabra wrapper prototype (#513)
  Fix/utilities/iscompatible final rev (#512)
  Fix/utilities/iscompatible (#511)
  rename System and Process to add _Base suffix in shellclasses.__all__ because of abf3e7e and 6b9e9a4
  Clean up/registry/ register category (#508)
  Refactor/projection/connection specs (#507)
  Refactor/gating mechanism/ instantiate gating signal (#506)
  • Projection (#505)
  updating comments and error messages in _construct_stimulus_sets to reflect changes
  updating 3 recurrent transfer mech unit tests which used 'sequence format' of input specification for a process to use 'mechanism format' instead
  Refactor/projection/ instantiate sender (#504)
  Refactor/state and projection/clean up (#503)
  commenting out branch of _construct_stimulus_sets which parses inputs by the 'sequence format' rules -- seems safe to move entirely to mechanism format b/c all pytests use 'mechanism format' and new examples using 'sequence format' do not work
  weird hybrid prediction error mechanism
  fix typo in ObjectiveMechanism docstring causing weird documentation formatting
  avoid using module-level Mechanisms in unit tests to avoid possible conflicts
  Refactor/state and projection/unit tests bug fixes (#502)
  Refactor/state and projections/unit tests (#501)
  Refactor/state and projection/names and docs (#500)
  requiring version 1.4 of toposort
  moving imports to top of gilzenrat pytests file
  adding full gilzenrat model to pytests -- no comparison data to assert yet, just verifying that model can run without errors
  adding pytests that isolate the GilzenratTransferMechanism and moving FHNIntegrator test that recreates figure 2 from gilzenrat paper from integrator mechanism tests --> gilzenrat tests
  fixing up a few model values in the gilzenrat model -- behavior is not quit right -- and switching number_of_trials back to 1
  Optimize registry duplicate naming
  adding progress statement ('% complete') to gilzenrat script
  implementing noise on LCAIntegrator and cleaning up unnecessary integrator function code (removing GilzenratIntegrator)
  replacing GilzenratIntegrator with LCAIntegrator (with rate=-1) in GilzenratTransferMechanism
  Refactor/state and projection/specification bug fix 2 (#495)
  Refactored instantiation of States and Projections (#494)
  updating mechanism pytests to reflect integrator_function shape change and removing extraneous transfer mechanism tests which returned arrays of mixed types
  indexing into the first element of the transfer mechanism's integrator_function result so that the shape passed to the transfer mechanism's function is the same as if integrator_mode were false
  add component module to main psyneulink package
  fold keywords into first level hierarchy, because some keywords aren't defined in Keywords.py and this is confusing
  skip notebook checkpoints in running notebook tests
  stop package-level __all__ assignments from accidentally overwriting the __all__ objects they used as bases
  fixing bug in NormalDist() function which was shifting the mean of the distribution
  fix link to the tutorial in docs that didn't get changed when tutorial/ directory was created
  correcting LCAIntegrator function to match the papers (since it represents a rate of change, we need to integrate over timesteps) and relaxing integrator rate param validation which was blocking variables of lengths > 1
  Devel (#490)
  improving initial conditions by making first recurrent projections to recurrent mechanisms make sense given their starting values
  make Function_Base inherit its paramClassDefaults from its parent class Function instead of Component
  remove DefaultProcessingMechanism from component/__init__.py because it's an instantiation of a _Base class, and doesn't get used
  removing and re-adding gilzenrat transfer mechanism because name change did not seem to work
  updating value of LC control mechanism output before it runs to match initial previous value (had to do this in the gilzenrat script because of other LC control mechanism hacks, but left a placeholer in ControlMechanism for how to implement this more generally for any control mechanism that accumulates)
  adding a new Integrator function that matches the decision and response layer functions in the Gilzenrat paper, and a new transfer mechanism which calls this integrator before its primary function
  update README and docs index.rst to new PyPI installation instructions, and tutorial section, reorganize
  reformat README into .rst format so pypi can format it nicely
  update short description to match the title line in the long description
  update setup.cfg for wheel creation and to include license file
  update setup.py supported Python versions to include only 3.5 and 3.6 (does not work on < 3.4 due to numpy, does not work on 3.4)
  update setup.py classifier for Apache license
  add tutorial_requirements.txt mirroring setup.py requirements
  add requirements.txt mirroring setup.py requirements
  update setup.py packages
  add MANIFEST.in
  remove SOFTWARE ARCHITECTURE and TODO List
  remove extraneous files
  add docstrings to __init__.py files (for help command)
  update tutorial to new easier import style
  update docs to handle new module/package format
  update package __init__.py files for simple importing
  add __all__ lists to modules
  rename globals/run.py to globals/environment.py to avoid namespace conflict with run method
  clean up main package __init__.py
  replace paramClassDefaults PROJECTION_SENDER with OutputState class instead of keyword to prevent error due to failed conversion
  rework imports to avoid circularities due to packaging
  make LearningMechanism get its paramClassDefaults from its parent and not Projection_Base
  remove mechanism factory method
  remove system factory in favor of just instantiating System class
  remove process factory in favor of just instantiating Process class
  switch name of Process and Process_Base
  switch name of System and System_Base
  move typecheck for _get_modulated_param inside to avoid circular import
  remove old pyargs argument for pytest
  relaxing validation on LCAIntegrator rate param in order to create an LCA example in integrator mode with an array input
  cleaning up resolving merge conflicts
  fixing merge conflicts
  started mini montague model
  adding comments
  first preliminary test working
  editing testing files and minor typos
  removed unnecessary identity transform function
  updating gitignore for new version of PyCharm
  created PredictionErrorMechanism
  started mini montague model
  adding comments
  first preliminary test working
  editing testing files and minor typos
  removed unnecessary identity transform function
  updating gitignore for new version of PyCharm
  created PredictionErrorMechanism
  starting TDDelta Function -- very messy
  2 of 3 test working
  integrating td learning
  cleaning up Function.py for pull request
  tests working!
  Q-matrix initialization working; mechanism does not
  Added Q-learning and SARSA algorithm
kmantel added a commit that referenced this pull request Apr 5, 2018
* devel:
  Feat/mechanism/input target label dicts (#751)
  Scheduling: fix bug where termination conditions persisted across calls to run
  tests,function/LinearCombination: Add tests with absent parameters
  test,function/LinearCombination: Rename second test function to prevent overwriting results
  • Context (#746)
  Refactor/context/deprecate init status (#745)
  Refactor/context/structured (#744)
  Fix/function/stability (#743)
  • IntegratorMechanism (#742)
  Feat/context/time (#740)
  Feat/context/time (#739)
  Image Fix (#738)
  finally fixed image (#737)
  Image Fix (#736)
  Example Fix (#735)
  Linear combination fix (#734)
  Feat/component/execution count (#733)
  jvesely/linear_combination_function_refactor (#732)
  Refactor/project/context rev 2 (#731)
  Refactor/system/show graph structure options (#730)
  • System (#729)
  Feat/mechanism/show structure (#728)
  Feat/mechanism/show mechanism (#727)
  jvesely/linear_combination (#724)
  creating a property for TransferMechanism's integrator_mode so that the mechanism can switch integrator mode on and off
  Fix/function/udf examples (#722)
  • Function (#717)
  Refactor/function/udf (#716)
  Refactor/mechanism and output state/mech params dict added (#715)
  Docs/output state/clean up (#714)
  Clean up/function/softmax one hot (#713)
  Name/project/replace assign index calculate (#711)
  Fix/controlmechanism/assign as controller jdc (#705)
  Feat/function/one hot cleanup (#704)
  Feat/function/one hot (#703)
  adding a pytest for the clear_log method
  updating output of nparray_dictionary when there are no entries from None to an empty OrderedDict
  Tests/llvm devel sync (#684)
  removing show graph pdfs from tests folder
  revising the show_graph pytests to call '_get_label' as a proxy for whether show_graph with dimensions is working
  moving _get_label helper function outside of show_graph method, so that it can be accessed on its own
  fixing bug in show_graph(show_dimensions=True) by taking np.atleast_1d of output_state.value
  • LearningProjection   docstring rev (to include error_function)
  Feat/process/learning objective mech (#698)
  Feat/ddm/selected input array (#697)
  Feat/ddm/selected input array (#695)
  user_params and function_params now look at parameter state values (rather than param base values), and are updated whenever mechanisms update their parameter states
  adding pytests that call show graph after creating various types of systems -- may refactor these to call the individual methods of show_graph
  removing system graph pdfs
  removing show_dimensions=True from call to show_graph in GilzenratModel because it generates an error
  updating how valus are retrieved from log in Nieuwenhuis model (based on addition of Pass to log)
  Fix/system/learning ends before terminal (#692)
  Fix/system/learning ends before terminal (#691)
  Revert "Merge branch 'master' into fix/system/learning_ends_before_terminal"
  -
  • ControlMechanism   _instantiate_control_signals:  debugged OWNER_VALUE assignment
  • Scripts/Examples   Rumelhart Semantic Network: updated with step function
  • System   _instantiate_learning_graph(): fixed bug in which learning failed to     be instantiated for a System in which the last Mechanism in a     learning sequence was not the TERMINAL Mechanism of the System.
  • System   _instantiate_learning_graph(): fixed bug in which learning failed to     be instantiated for a System in which the last Mechanism in a     learning sequence was not the TERMINAL Mechanism of the System.
  • OutputState   docstring revs
  • OutputState   docstring revs
  fixing documentation formatting mistake
  continuing to add pytests and doc fixes for clip on transfer mechanism types
  allowing lca to execute function over entire variable, not just first item
  fixing documentation for clip
  continuing to add error messages to reinitialize
  allowing smoothing factor to be an integer (formerly 1.0 and 0.0 were allowed but 1 and 0 were not)
  removing typecheck on learning mechanism's default_variable
  adding exception in UDF so that function can be called without params and context
  correcting error message for initial_value validation on transfer mechanism
  fixing bug in reinitialize on arrays (needed np.atleast_2d when setting intial_value because it is compared to variable)
  -
  • OutputState   docstring revs
  Refactoring of OutputState to support flexible assignment of its variable attribute.
  Revert "-"
  Revert "-"
  Revert "-"
  -
  adding pytests for specific reinitialize cases that were not covered, and adding error messages that were missing for some of them
  -
  fixing documentation typo: integration_method was mistakenly called integration_method_FHN in docs
  -
  -
  -
  -
  -
  -
  Reworking Montague, Dayan, and Sejnowski model documentation.
  -
  Merge branches 'bug/parsing/input_states-use-value' and 'feat/DDM/value_based_version_input_state' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/DDM/value_based_version_input_state
  Merge branches 'bug/parsing/input_states-use-value' and 'feat/DDM/value_based_version_input_state' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/DDM/value_based_version_input_state
  -
  -
  -
  -
  -
  -
  • Utilities   - recursive_update():  added non-destructive option that preserves                          any non-empty entries in destination dict
  -
  -
  -
  • OutputState   this version implements OutputState.variable as a property   that returns _parse_output_state_variable()
  • OutputState   this version implements OutputState.variable as a property   that returns _parse_output_state_variable()
  -
  -
  -
  -
  -
  -
  adding pytests for invalid target specifcation to confirm that the proper error messages are generated
  • OutputState   assign function now expects dict as argument - WORKING
  adding more pytests to confirm that convenience notations and combinations of function and list target specs all run
  documenting targets and adding some checks to adjust targets: verify that num_targets = num_inputs, and ignore num_targets in the case of function specifications (because a new value is generated on each trial)
  -
  -
  -
  -
  • OutputState   - implemented assign that takes assign_params_dict as arg
  Fix/output state/assign backward compat (#676)
  • OutputState   added backward compatibility   docstring: document replacement of calcuate/CACULATE with assign/ASSIGN
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  in progress: refactoring function specification of target spec to be an option within the dictionary specification, rather than on its own
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  • Project, OutputState   replace calcuate/CACULATE with assign/ASSIGN
  Feat/ddm/input state as array (#674)
  revising documentation for target specification
  cleaning up a typo in target_spec_parsing (comparator mechanism was referenced where it should have been terminal mechanism)
  moving call to _check_args in BackProp to before the error matrix is updated in order to avoid a validation bug
  adding pytests for target spec convenience notations
  adding run to rumelhart tests (previously only created systems)
  Merge branches 'clean_up/function_and_system/backprop_and_show_graph' and 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into clean_up/function_and_system/backprop_and_show_graph
  revising how target input state values are assigned in system's execute_learning
  adding a simple multilayer learning pytest
  refactor execute and _execute methods
  defaults: remove post-hoc conversion of defaults variable
  Component: don't convert defaults variable on calls to validate a variable
  parsing: add initial_value parser
  parsing: add generic argument parser used as default if none specified
  Component: add method to parse user inputted variable to useable/standard form
  utilities: handle nonuniform objects better when converting to numpy arrays
  control: refactor handling of allocation*
  projections: refactor sender instantiation to avoid directly setting instance default variable
  clean up input_states handler
  rename input_states arg parser to handler
  maint: add comments to separate handler, parsing, and validation methods
  maint: remove unused PROJECTION_SENDER_VALUE
  TransferMechanism: use standard form of setting default variable
  utilities: change number detection to accept any number, not just int and float
  OutputState: when variable not specified to constructor, pass up another value
  make self.variable read only (we should not be using it for logic)
  replace calls to self.variable to proper self.instance_defaults.variable
  validation: remove extraneous check for ClassDefaults.variable
  ClassDefaults: make RecurrentTransferMechanism default require 2d variable because it takes an AutoAssociativeProjection that uses a LinearMatrix that requires 1D
  Distance: fix validation assumption that items of passed variable are iterable
  ClassDefaults: correct and consolidate
  utilities: add method to produce a value for length calls when len() fails
  utilities: add function to determine whether something is iterable
  Integrators: handle initializer like variable in Components
  Function: standardize default_variable assignments
  ProcessingMechanism: use standard assignment of default variable
  DDM: use standard assignment of default variable
  ensure default_variable auto sets to dtype float
  combine handling of default_variable/size to create instance_defaults.variable in Component.__init__
  utilities: allow list->array element conversion to typecast internal items
  validation: fix validate_variable crashes on certain variable types
  utilities: add helper method to determine if an object contains a single value
  rename variable->default_variable
  Clean up/function and system/backprop and show graph (#671)
  Clean up/learning/misc (#670)
  Clean up/learning/misc (#669)
  Clean up/learning/misc (#668)
  Fix/transfermechanism/noise function (#667)
  Fix/transfermechanism/clip (#666)
  Refactor/modulatory signals/linear default function (#665)
  Refactor/learning/heterovergent (#664)
  in progress - refactoring adjust_target_dict method to validate all candidate targets and confirm that all mechanisms provided the same number of targets
  Tests/mechanism/hebbian learning (#663)
  Docs/function/hebbian (#662)
  Docs/function/hebbian (#661)
  updating pytest expected values based on changes to log output
  adding Pass to log output and updating pytests accordingly
  Fix/learning/hebbian (#659)
  swapping all log references to 'simple_time' with the full 'time', and removing old code which handled time stamp duplicates
  in progress - refactoring target spec/validation to work the same way as input spec/validation
  renaming object --> component in _adjust_target_dict()
  updating pytests to match RecurrentTransferMech switch from full matrix to hollow matrix; changed expected output or set auto = 1 to preserve old expected output, depending on type of test
  setting default matrix of a RecurrentTransferMechanism to a hollow matrix, and updating docs to be clearer about how auto, hetero, and matrix combine/overwrite each other when multiple arguments are specified
  renaming object --> component in _validate_targets method to avoid shadowing python built-in
  updating pytest expected results to match increment change in log
  log pytest for a mechanism that is scheduled to run many times in a row
  changing increment size on log's time_step workaround
  temporary workaround for timestep values: incrementing first decimal of timestep
  revising log tests for new time_step notation
  temporary workaround for timestep values: incrementing first decimal of timestep
  revising parse_entries_for_time_values method on log so that it edits the time values in the log items directly, rather than maintaining a separate list of modified time values
  setting axis=1 on calls to np.sum and np.product in Reduce function and adding tests for this function
  documentation typos
  documenting reinitialize on mechanism
  continuing to add tests and docs for reinitialize
  fixing bugs that prevented initialize method on system from ever executing, and adding pytests for it now that it works
  revising outdated TransferMechanism docs for reinitialize
  continuing to add tests to highlight differences between calling reinitialize on a mechanisms and on a function
  adding nparray_dictionary to docs and revising nparray to use the same helper methods as nparray_dictionary
  Time: fix bug where RUN counter would not be incremented on new runs
  fixing (temporarily) time_step bug in nparray_dictionary; reorganzing nparray_dictionary into methods that can be reused by nparray
  refactoring log to have a dictionary option and writing tests for it
  beginning to add a dictionary alternative to the options for whats returned by the log
  more calls to _dealias_owner_name required in order to create log.nparray
  fixing bug in log: needed to switch between 'value' and mechanism name in several loops in order to assemble log.nparray
  -
  Feat/rl/for mads (#652)
  Feat/rl/for mads (#651)
  adding more pytests for reinitialize and fixing reinitialize bugs; beginning to update documentation
  adding pytests for reinitializing at both function and mechanism level; cleaning up mistakes in reinitialize() methods along the way
  Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/Projection/Context_devel
  adding a reinitialize method on mechanisms, which calls reinitialize on its function or integrator_function, then updates the mechanism's value and output states
  beginning to refactor reinitialize as a method on integrator functions
  Removed Print Statements (#650)
  cleaning up documentation to match how LinearMatrix works in all cases
  typo in linear matrix function validation
  simplifying non-projection branch of validation on LinearMatrix function and adding more pytests
  default_variable: let argument override input_states variable spec if compatible
  adding pytests for possible combinations of variable and matrix specifications for LinearMatrix as a function of a mechanism
  adding validation comparing matrix to variable when LinearMatrix function is called by a mechanism; creating square full connectivity matrix that matches variable when matrix is not specified
  tutorial: reenable graph drawing; requires graphviz package
  tutorial: clear outputs
  Lena Program 1 Bugfix (#648)
  Hebbian learning fix (#647)
  User defined function updates (#646)
  adding working version of LinearMatrix function pytest (only works because default_variable is specified on both the mechanism and the function)
  fix input_states argparsing to not be dependent on default_variable or size args
  tests: ensure leabra tests get skipped if module is not available
  splitting linear matrix function's validation into two branches because matrix is handled differently when the function is called by a projection vs a receiver
  docstring wording change
  Docs/models/title changes (#645)
  Docs/nieuwenhuis/edits (#644)
  adding pytest for ProcessingMechanism with LinearMatrix function to begin debugging why this fn only works in Projections
  removing unrestrictedtransfermechanism file because this mechanism is now called ProcessingMechanism and does not need its own file
  adding parameter state docs examples back in with doctest SKIP
  revising proccessing mechanism docs because it is not an executable mechanism (not just an ABC)
  renaming UnrestrictedProcessingMechanism --> ProcessingMechanism and moving code into processingmechanism.py (which formerly only contained ProcessingMechanism_Base
  Leabra Update (#642)
  DDM: update is_finished to work on functions with any dimensional variable
  skipping transfer mechanism doc tests
  skipping transfer mechanism doc tests
  minor documentation changes -typos and formatting mistakes
  reorganizing integrator mechanism pytests for reinitialize
  overwriting AGTUtilityIntegrator's reinitialize property - requires custom reinitialization of short term and long term utility
  overwriting FHNIntegrator's reinitialize property - requires custom reinitialization of v, w, time, value
  overwriting reinitialize property on DriftDiffusion Integrator so that time can also be reset
  documenting reinitialize on all Integrator functions and fixing a typo in transfer mechanism docs (initial_value --> initializer)
  continuing to add docs and examples for reinitialize, and cleaning up TransferMechanism docs along the way
  fixing tutorial indexing bug
  refactoring is_finished as a property so that it is always up to date, even when values change in between executions (i.e. if threshold was crossed and then reinitialize was used)
  fixing bug in transfer mechanism documention examples (np.array typo)
  renaming reset_intializer --> reinitialize
  adding unrestricted mechanism pytests to confirm that mechanism can be constructed and executed with any function -- identified two exceptions (linear matrix and back prop)
  adding a new mechanism that has no restrictions on which functions can be used
  commenting out show graph lines in tutorial for now because graphviz is not imported on testing server
  adding updated version of tutorial from Justin
  Defaults*: fix class structure addressing bugs
  revising transfer mechanism documentation -- 'creating' section
  commenting out show_graph in EVC gratton pytest so that this line does not run on Jenkins
  adding TransferMechanism pytests to verify previous_value persists over multiple runs/executions AND previous_value resets whenever reset_initializer is used
  edited  NieuwenhuisModel docs
  tutorial: remove old version - new version is in tutorial/ dir
  tutorial: support execution on mybinder.org
  tutorial: support execution on mybinder.org
  tutorial: remove old version - new version is in tutorial/ dir
  • Niewenhuis model   - docstring edits
  -
  adding integrator_mode and integrator_function attr documentation for all transfer mechanism types
  revising outdated documentation for transfer mechanism noise
  fixed bug in plotting Nieuwenhuis Model
  updated Nieuwenhuis documentation
  adding attrs that were missing from LCA mechanism docs and revising related documentation
  Scripts: clean up
  Functions: add UniformToNormalDist to top-level psyneulink module; update docs
  revising explanation of user_params
  revising explanation of user_params
  revising parameter state documentation
  adding Markus' Nieuwenhuis documentation, plus figures and some .rst formatting
  Functions: replace internal calls to find owner's name with a property
  Component: make string version of *defaults classes be sorted
  removing parameter state example from file completely (tried commenting it out originally)
  removing parameter states example from documentation because it may be the reason parameter state tests are failing
  renaming 'Core Configurable Attributes' --> 'Core Structural Attributes' in Component documentation
  Refactor/system/controller (#627)
  Fix/controlmechanism/assign as controller (#625)
  • Log (#624)
  fixing typo in doctest (parameter state values)
  adding a docs example which walks through how a mechanism parameter and a function parameter and their mod_ versions change in value
  BogaczEtAl: use better numpy method for floating point warning handling
  utilities: update compatibility checker to terminate earlier in some cases
  updating modulation-related documentation to include mod_param and be more precise about what is updated by modulation (the parameter value used by a function changes, but the corresponding function attr does not change b/c it is the base value)
  adding documentation for mod_param
  allowing user to pass value into mod_param setter (even though setting is not allowed) in order to produce a more informative error message)
  commenting out noise and smoothing factor properties in transfer mechanism because these replace the default properties, causing unexpected behavior
  adding pytest to verify correct error message when user tries to set to mod_param_name
  adding pytest to track changes in attr, _attr, mod_param_name, and userparams[param_name] values of Transfer Mechanism's configurable params when (1) param values are updated (2) mechanism is executed
  adding an exception to make_mod_param as a temporary fix for function-specific mod_param properties that stay on mechanism class when function changes
  fixing typo in AGTUtilityIntegrator
  cleaning up function.py and verifying that self.get_current_function_param is used in all functions (skipped learning functions for now)
  Fix/controlmechanism/assign as controller (#620)
  Fix/controlmechanism/assign as controller (#619)
  cleaning up recurrent transfer mechanism pytests and fixing bugs in asserts
  updating matrix setter to also set the projection's matrix parameter state's function's previous value
  uncommenting auto and hetero properties from auto associative projection so that setting auto and hetero directly on the projections works
  adding auto and hetero properties to recurrent transfer mechanism. Auto, hetero, and matrix setters now all update recurrent_projection's matrix parameter state's function's previous_value
  Fix/controlmechanism/assign as controller (#618)
  executing projection individually in tranfer mechanism's matrix-change pytest
  adding a matrix-change pytest for a mapping projection between two transfer mechanisms in order to isolate the matrix bug from auto/hetero properties
  Defaults: clean up method organization
  fixing shape typo in gilzenrat script
  fixing overly strict rate param validation that caused bug in cases where mechanism looks up parameter state value
  refactoring transfer mechanism to use get_current_mechanism_param()
  refactoring LCA to use get_current_mechanism_param()
  refactoring kwta's _kwta_scale() to rely on get_current_mechanism_param()
  adding get_current_mechanism_param method on mechanism base to try to look up parameter state value
  remove now-unused time_scale param from many objects (not in scheduling where it's still used)
  log doctests: ignore tests with inconsistent whitespacing
  removing auto and hetero assignments from params dict in recurrent transfer mechansim
  removing unnecessary auto and hetero code in auto associative projection to clean up the relationship between the recurrent projection, its mechanism, and the auto, hetero, and  matrix, attrs
  requiring _kwta_scale method to use k_value parameter state value when available
  commenting out calssPreferences in transfer mechanism because they cause bugs in KWTA when classPreferences try to update
  removing attempt to look up recurrent projection's matrix in matrix getter (because the recurrent projection looks up its owner's matrix)
  refactoring matrix getter on auto associative projection to look up owner's matrix whenever possible
  directly updating auto and hetero attrs at the same time that their parameter states are created in the auto specified, hetero = None and hetero specified, auto = None cases
  beginning to refactor auto/hetero/matrix handling to fit with new parameter state value and make_property changes; beginning by removing obsolete code in recurrent transfer mechanism
  removed CentralClock from MontagueDayanSejnowski96.py
  fixed typo in owner attribute description
  Fix/function/validate params (#616)
  Defaults: set up structure to allow proper aliasing for *Defaults classes
  - Renamed MontagueModel.py to MontagueDayanSejnowski96.py - Correct RST formatting in PredictionErrorMechanism docs - Added Arguments and Attributes to docs for PredictionErrorMechanism
  LinearCombination: rework check for division by zero error to be more general
  default_value: refactor into instance_defaults
  Component: add metaclass for *Defaults to allow some user convenience functionality
  Refactor/control signal/update to intensity (#613)
  Fix/component/intensity and value (#612)
  Fix/gilzenrat model/prefs bug (#611)
  updating DDM mechanism to get threshold using get_current_function_param method when it uses threshold to determine decision variable
  continuing to update how parameters are accessed in pytests (should be mod_ now in many cases)
  replacing .matrix with .mod_matrix in learning pytests
  adding a call to super in projection's _instantiate_attributes_after_function so that it calls make_property_mod (on component)
  Fix/ddm/threshold validation (#610)
  calling get_current_function_param in the remaining functions and fixing small bugs along the way (missing keyword for 'gamma', np.atleast_2d(rate) in lcaintegrator)
  moving make_property_mod back to component.py (from parameterstate.py) -- it is now called for all parameter states during _instantiate_attributes_after_function rather than by individual parameter states
  Docs/td learning/doc fixes (#609)
  removed show graph call from test_reinforcement
  resetting test_multilayer from devel and removing matplotlib from test_prediction_error_delta_function
  specifying smoothing_factor=1.0 on pytests that used to use default smoothing_factor (1.0 --> 0.5)
  changing smoothing factor (formerly time_constant) default value to 0.5 -- it was confusing to users that the default param value prevented integration
  renaming 'time_constant' --> 'smoothing_factor' on TransferMechanism types that use AdaptiveIntegrator
  Fix/log/trial and run (#607)
  Feat/log/trial and run (#606)
  Refactor/project/learning vs executing (#605)
  correcting capitalization
  cleaning up documentation
  adding asserts to parameter states pytests in order to start tracking down bug where mod_noise looks up the parameter state value of the last instance created
  Refactor/mechanism/value in execute 2 (#603)
  predictionerrormechanism
  docs: move gilzenrat svg files from build dir to source dir
  Fix/log/tuple datum value (#601)
  registry: handle case where default-named projection to a duplicate named mechanism would incorrectly detect the projection name as a duplicate
  finished TD Learning documentation
  Fix/state/matrix spec and learning (#600)
  Fix/component preference set/class preferences (#598)
  Fix/log/set log conditions bug (#596)
  updating Transfer functions (Linear, Logistic, Exponential) to use get_current_params(KEYWORD) instead of paramsCurrent[KEYWORD]
  adding get_current_param method which tries to return mod_param and returns param if that doesn't exist -- will eventually be added to all functions, starting here with DriftDiffusionIntegrator
  Docs/log/hint (#595)
  updating shape inconsistencies in DriftDiffusionIntegrator / DDM Mechanism related to time and threshold
  removing special handling of DriftDiffusionIntegrator threshold in variable=array case (correct behavior is ambiguous)
  docs: add extra sub-version number in version display
  utilities: enhance method to recursively convert items to np.ndarray, handling hard cases for np.array
  remove scratch pad and ignore
  Docs/log/log clean up (#593)
  Docs/log/log clean up (#592)
  remove scratch pad
  Docs/log/log clean up (#591)
  Names/log/set log conditions (#590)
  adding pytests to verify that threshold and is_finished work as expected; commenting out tests with DriftDiffusionIntegrator and len(default_variable) > 1 because correct behavior is ambiguous (for now)
  adding 'threshold' param on DriftDiffusionIntegrator which stops accumulation at the threshold, and updated DDM's is_finished to look at this
  updating shape of time computation in FHN integrator (was list, now float)
  updating gilzenrat pytest which was checking _gain and gain to verify modulation to now use gain and mod_gain
  updating pytests and adding comments to possibly fix shape of ddm time value, which changed from a list to a float after property refactoring
  add realtime timestamps to Scheduler, for creation time and end of last RUN time
  change usages of now defunct times attribute of Schedulers to new version
  updating mod_param_name property creation to happen at the instance level in both cases (formerly created on mechanism classes)
  unindenting misplaced setting of _param_name attributes
  Bugfixes (#588)
  setting _param_name for all param_names that go through _validate_params resolves SOME of the cases where getter looks for _param_name before setter creates an _ attr
  Feat/log/add entry (#587)
  Fix/log/log initialization (#586)
  Feat/log/clean up (#585)
  Feat/log/clean up (#584)
  Feat/feat log with time (#583)
  rename psyneulink.scheduling.timescale -> psyneulink.scheduling.time
  create and integrate a new Clock class, and several new classes to keep time, used in Scheduler and Conditions
  adding _param_name to script for better output comparison with older versions (when _ stored the base value)
  solving bug where _param_name did not exist on TransferMechanism instances, but introduced new bug where last param value that was set is starting param value of next instance
  remove old Clock/CentralClock
  debugging make property execution
  main documentation for PredictionErrorMechanism done
  adding mod_slope to the current parameter state pytests
  adding make_property_mod method to parameter states -- executed at the end of _instantiate_parameter_state method and creates a property called mod_param_name on each param that has a parameter state which looks up the current parameter state value
  limiting make_property's resposibility to validation -- setter runs validation and then sets to _param_name, getter returns _param_name. mod_param_name property will handle getting parameter state value
  Feat/log/log levels (#580)
  test
  beginning to separate make property into two methods
  added PredictionErrorDeltaFunction and docs for PredictionErrorMechanism & Montague model
  Refactor/log/entry management (#579)
  montague models working!
  Docs/log/docstring update (#578)
  Add integrator function tests
  Add transfer function tests
  Add distance function tests
  function: test for both 1d and 2d noise
  setup.cfg: Use warmup if benchmarks are enabled
  setup.cfg: Disable benchmarks by default
  pytest: Add benchmarking plugin
  Fix/log/logged items bug (#577)
  using UniformToNormalDist pytest as a check of the scipy requirement error message
  adding documentation for UniformToNormalDist
  validating uniform-to-normal distribution function (matlab)
  Docs/log/docstring update (#572)
  adding gilzenrat figures in _build file
  adding pytest file for parameter states
  Name/log/numpy array to nparray (#571)
  Feat/mechanism/additional props (#570)
  Feat/log (#569)
  EVCAuxiliary: replace kwargs function signatures with explicit arguments
  add docstring explanation for processing and learning termination conditions
  Feat/log (#568)
  adding LC Control Mechanism test to verify that it is updating multiplicative param(s) of modulated mechanism(s) properly
  fix incorrect construction of Process and System in Multitasking example script
  Feat/log (#565)
  Feat/log (#564)
  almost working!
  add travis config file
  single source package requirements
  fixed error message in LinearMatrix
  adding a pytest for the new uniform --> normal distribution function
  fixed sample input
  updating recurrent transfer mechanism and transfer mechanism documentation
  • State   - _validate_variable:  removed:         if not context:             context = kwAssign + ' Base Value'         else:             context = context + kwAssign + ' Base Value'
  Fix/component/default naming (#558)
  remove Scratch Pad
  clean up DDM examples with verified parameters from matlab
  skip NavarroAndFuss doctest because build server cannot access matlab
  update NavarroAndFuss to use the correct version of the MATLAB simulation
  convert DDM return_value for NavarroAndFuss function to be floats to allow NaN assignment
  fix bug in using the matlab engine to run a script outside of the current dir
  adding validation on NormalDist function in the case where some numpy versions throw an error
  • System (#556)
  adding new UniformToNormalDist function which allows for a direct comparison of random numbers between python and matlab
  Feat/system/show graph (#555)
  adding integration_method to FHNIntegrator docs and refining error message
  Fix/modulatory specifications (#554)
  clean imports in function.py
  commenting out assertions in OU integrator pytests until its equation is validated
  fixing mistake in implementation of OUIntegrator
  adding LCAIntegrator docs to function docs page and continuing to touch up typos and incorrect info throughout function docs
  continuing to add documentation for LC Control Mechanism params
  adding matlab and psyneulink plot svgs
  adding pnl and matlab plots plus some additional notes to the Gilzenrat Model page of the documentation
  fixing typos in FHNIntegrator docs
  documenting the LCControl mechanism parameters that hand values off to the FHNIntegrator as well as scaling_factor_gain and base_value_gain
  cleaning up FHNIntegrator docs with tables for explaining parameters and latex equations
  typos in run (input spec) docs
  cleanup Scheduler doc examples
  add parsing handler for Scheduler termination_conditions
  move static .svg files from docs build directory to source dir
  update docs to show 0.0.x versions instead of just 0.x (we use the former frequently)
  fix broken package link for AutoAssociativeMechanism that caused sphinx automodule to fail
  removing references to 'inhibition' and 'decay' in LCA docs
  removing gilzenrat transfer mechanism from the repo
  updating gilzenrat unit tests to use LCA mechanism in place of GilzenratTransferMechanism
  fix bug where versioneer wasn't available at the correct time in building docs
  adding a note about the recurrent matrix to LCA docs
  rewriting gilzenrat model in terms of LCA rather than 'GilzenratTransferMechanism'
  removing LCA pytest from recurrent transfer pytests file now that LCA has its own tests
  updating LCA documentation -- removing beta & inhibition, adding leak, competition, and self_excitation.:
  setting default values for new LCA params
  adding pytest file for LCA and testing length 1 variable and length 2 variable cases
  added output_states param to call of PredictionErrorMechanism constructor
  added default variable param to call to LinearCombination in PredictionErrorMechanism
  adding 'leak' parameter and renaming 'auto'-->'self_excitation' and 'hetero'-->'competition' on LCA mechanism
  Refactor/state/doc test bugs (#551)
  fix bug where invalid escape strings in docstrings would cause failure on python 3.6.x
  fixing incorrect documentation of LCA (did not reflect new LCAIntegrator function)
  continuing to clean up Gilzenrat model and its model-specific components -- verifying that all arguments are consistent and correctly documented
  manually setting outputstate variable size
  adding params for G and k to LCControl mechanism as a temporary solution for allowing the user to modify the equation that computes gain as a function of w
  cleaning up gilzenrat script comments and labeling all params from the paper
  tried manually setting OutputState value for PEM -- didn't work
  Refactor/state/ parse state specs lots (#550)
  use versioneer for single-source versioning
  adding Gilzenrat changes from Markus
  fixed target size for PredictionErrorMechanism
  trying to fix tests
  correct W293 instances
  fix bug where intra-numpy-array list->array element conversion would fail on 0-d numpy array input
  updating logistic function and its documentation to match the more standard form, with an optional 'offset' to take the place of original 'bias' param. Updating all pytests that used what was formerly 'bias' and is now 'offset'
  trying more things to get td learning working
  clean up leabra demo script
  clean up leabramechanism
  add __all__ to leabramechanism and update relevant package
  rename certain leabra-specific functions to include "leabra" in preparation for adding to top-level namespace
  remove unnecessary (and oddly expensive) logging in scheduler
  fix bug where over/underflows in logistic functions would cause the result to be replaced with 0 (often incorrect format and destructive)
  remove forced error on warnings
  Leabra script cleaning (#547)
  cleaned up Matlab scripts & EVC Gratton example script (#546)
  Docs/project/more docstring fixes (#545)
  Docs/project/more fixes (#544)
  Docs/project/fixes (#543)
  reformat Example scripts to new import style, and clean up
  setup Scripts/Examples folder with desired scripts
  remove old/undesired scripts
  adding input spec figures to run documentation
  rename _get_matrix to get_matrix
  Revert "Fix/scripts/cleanup (#539)"
  commenting out all clip (formerly range) code because it does not work as expected
  fixing formatting typo in documentation
  continuing to clean up input specification for (1) heterogenous variables and (2) a limited version of 'sequence' specification
  Fix/scripts/cleanup (#539)
  updating documentation example pytests to verify all inpt values against specified input values
  updating documentation example typos
  Feat/transfer mechanism/add std output states (#538)
  refactoring system input state creation to create one system input state (and mapping projection) for each input state of each origin mechanism
  Feat/transfer mechanism/add std output states (#537)
  Fix/output states (#536)
  Refactor/transfer mechanism/mutiple output states (#535)
  updating transfer mech execute to check the type of its function and call it once or once per input state accordingly, plus Jon's instantiate_output_states
  reclassifying softmax as a 'NormalizingFunction' instead of a 'TransferFunction' so that we can easily identify transfer mechanism functions that should be executed separately for each input state
  use pytest fixture for registry reset in tests/naming to ensure it gets called
  renaming  -->  on TransferMechanism types in order to not overwrite Python built-in range
  Refactor/naming (#533)
  add download link for GilzenratModel.py
  updating kwta and recurrent transfer mech pytests to match new output shape
  cleaning up imports so test will run
  add values(), show(), and nice str/repr methods to InstanceDefaults
  move name assignment (in registry call) to before input_states arg handling in mechanism
  Revert "Refactor/mechanism/preprocess variable (#531)"
  updating transfer mechanism pytests to match new shape of output
  updating transfer mechanism to call its function separately for each input state (each element of variable); for now, integrator function still only executes once
  add shell classes to top-level psyneulink namespace
  correct bug that would cause specifying 3d arrays as default_variable to assign default_variable incorrectly
  add method to np.array-ify all elements within a list/array
  continuing to add pytests for input specification - stuck on verifying that the input specification worked via tools (e.g. call_after_trial) available to the user, because non primary input states are getting overwritten as None
  updating documentation for input specification -- adding tables of inputs on each trial with code snippets
  Fix/mechanism/ parse arg input states (#532)
  Increment version to 0.4.0
  add more input_state spec tests to handle currently known combinations for setting default_variable
  Refactor/mechanism/preprocess variable (#531)
  Refactor/mechanism/preprocess variable (#530)
  Docs/state and projections/docstring revs (#529)
  correct bug in _parse_arg_input_states where a non-list argument wouldn't be made into a list before processing
  change behavior of _parse_state_spec to not populate the state dict with a variable if it's a ClassDefault
  updating noise validation to compare against entire variable (possibly multiple input states) and updating error messages in pytests to reflect these changes
  updating 'try_execute_param method to expect 2d variable and return 2d param
  updating pytests for input specification documentation examples to match the new documentation examples
  continuing to update docs for inputs to system
  revising the input specification docs to describe the rules in terms of matching the mechanim's variable - also making the convenience cases clearer
  removing references to timescale in run and system docs
  Fixed/state/ parse state spec/projection spec (#528)
  Refactor/distance metrics (#526)
  Docs/latex math (#525)
  Docs/intro materials (#524)
  continuing to add pytests to test new input specification rules
  updating some reporting statements to match the new form of inputs (dict)
  continuing to clean up input specification; running inputs first through a new method called _input_matches_variable which catches some numpy mistakes specific to input validation that slip through iscompatible
  Logo (#523)
  make self.name return unnamed .__class__ in case no name was set
  Docs/input state specs (#522)
  Fix/input state specs (#521)
  continuing to add pytests for testing input specifications
  updating process and system to handle the new execution_inputs dict that they receive from run
  consolidating and revamping input processing to get rid of any references to , repetitive code. still some clean up to do -- 5 pytests failing
  Fix/input state specs (#520)
  Fix/input state specs (#519)
  beginning to consolidate input validation because we no longer have phases and don't need to handle systems and processes differently -- 22 pytests failing
  Fix/input state specs (#518)
  using new EULER option on the LCControlMechanism in GilzenratModel in order to match original model
  adding validation requiring integration_method to either be RK4 or EULER
  adding 'integration_method' to LCControlMechanism so that user can switch between euler and rk4 integration for the built-in FHN function
  fixing some params to match matlab model; made it easier to swtich between high C and low C params
  switching FHNIntegrator to use euler integration
  scaling entire noise term by sqrt(dt) rather than scaling the standard deviation of the noise term by sqrt(dt)
  Naming/registry/default name 0 (#516)
  beginning to add in an exception which will allow the case where all mechanisms specify one input which is the same shape as their variable (i.e. no outer list for trials)
  hack mechanism to be able to accept instance_defaults.variable setup via input_states argument
  still trying to fix inputs
  cleaning up sytem unit tests to match new input spec (outer set of brackets representing trials required)
  cleaning up mechanism unit tests to match new input spec (outer set of brackets representing trials required
  move input_states spec tests in test_transfer_mechanism to new file
  update current input_state spec tests
  make test_transfer_mechanism tests use instance_defaults.variable instead of incorrect .variable
  Docs/state and projection (#515)
  remove uses of self.variable. (it is vestigial and maintained only for user inspection)
  rename duplicate transfer mech test to avoid overwrite
  adding input specification pytests to test_system in order to verify which input spec formats already work and build on this
  pull from devel
  Refactor/control and gating signals (#514)
  Import leabra and run leabra tests only if leabra module is available.
  Leabra wrapper prototype (#513)
  Fix/utilities/iscompatible final rev (#512)
  Fix/utilities/iscompatible (#511)
  rename System and Process to add _Base suffix in shellclasses.__all__ because of abf3e7e and 6b9e9a4
  Clean up/registry/ register category (#508)
  Refactor/projection/connection specs (#507)
  Refactor/gating mechanism/ instantiate gating signal (#506)
  • Projection (#505)
  updating comments and error messages in _construct_stimulus_sets to reflect changes
  updating 3 recurrent transfer mech unit tests which used 'sequence format' of input specification for a process to use 'mechanism format' instead
  Refactor/projection/ instantiate sender (#504)
  Refactor/state and projection/clean up (#503)
  commenting out branch of _construct_stimulus_sets which parses inputs by the 'sequence format' rules -- seems safe to move entirely to mechanism format b/c all pytests use 'mechanism format' and new examples using 'sequence format' do not work
  weird hybrid prediction error mechanism
  fix typo in ObjectiveMechanism docstring causing weird documentation formatting
  avoid using module-level Mechanisms in unit tests to avoid possible conflicts
  Refactor/state and projection/unit tests bug fixes (#502)
  Refactor/state and projections/unit tests (#501)
  Refactor/state and projection/names and docs (#500)
  requiring version 1.4 of toposort
  moving imports to top of gilzenrat pytests file
  adding full gilzenrat model to pytests -- no comparison data to assert yet, just verifying that model can run without errors
  adding pytests that isolate the GilzenratTransferMechanism and moving FHNIntegrator test that recreates figure 2 from gilzenrat paper from integrator mechanism tests --> gilzenrat tests
  fixing up a few model values in the gilzenrat model -- behavior is not quit right -- and switching number_of_trials back to 1
  Optimize registry duplicate naming
  adding progress statement ('% complete') to gilzenrat script
  implementing noise on LCAIntegrator and cleaning up unnecessary integrator function code (removing GilzenratIntegrator)
  replacing GilzenratIntegrator with LCAIntegrator (with rate=-1) in GilzenratTransferMechanism
  Refactor/state and projection/specification bug fix 2 (#495)
  Refactored instantiation of States and Projections (#494)
  updating mechanism pytests to reflect integrator_function shape change and removing extraneous transfer mechanism tests which returned arrays of mixed types
  indexing into the first element of the transfer mechanism's integrator_function result so that the shape passed to the transfer mechanism's function is the same as if integrator_mode were false
  add component module to main psyneulink package
  fold keywords into first level hierarchy, because some keywords aren't defined in Keywords.py and this is confusing
  skip notebook checkpoints in running notebook tests
  stop package-level __all__ assignments from accidentally overwriting the __all__ objects they used as bases
  fixing bug in NormalDist() function which was shifting the mean of the distribution
  fix link to the tutorial in docs that didn't get changed when tutorial/ directory was created
  correcting LCAIntegrator function to match the papers (since it represents a rate of change, we need to integrate over timesteps) and relaxing integrator rate param validation which was blocking variables of lengths > 1
  Devel (#490)
  improving initial conditions by making first recurrent projections to recurrent mechanisms make sense given their starting values
  make Function_Base inherit its paramClassDefaults from its parent class Function instead of Component
  remove DefaultProcessingMechanism from component/__init__.py because it's an instantiation of a _Base class, and doesn't get used
  removing and re-adding gilzenrat transfer mechanism because name change did not seem to work
  updating value of LC control mechanism output before it runs to match initial previous value (had to do this in the gilzenrat script because of other LC control mechanism hacks, but left a placeholer in ControlMechanism for how to implement this more generally for any control mechanism that accumulates)
  adding a new Integrator function that matches the decision and response layer functions in the Gilzenrat paper, and a new transfer mechanism which calls this integrator before its primary function
  update README and docs index.rst to new PyPI installation instructions, and tutorial section, reorganize
  reformat README into .rst format so pypi can format it nicely
  update short description to match the title line in the long description
  update setup.cfg for wheel creation and to include license file
  update setup.py supported Python versions to include only 3.5 and 3.6 (does not work on < 3.4 due to numpy, does not work on 3.4)
  update setup.py classifier for Apache license
  add tutorial_requirements.txt mirroring setup.py requirements
  add requirements.txt mirroring setup.py requirements
  update setup.py packages
  add MANIFEST.in
  remove SOFTWARE ARCHITECTURE and TODO List
  remove extraneous files
  add docstrings to __init__.py files (for help command)
  update tutorial to new easier import style
  update docs to handle new module/package format
  update package __init__.py files for simple importing
  add __all__ lists to modules
  rename globals/run.py to globals/environment.py to avoid namespace conflict with run method
  clean up main package __init__.py
  replace paramClassDefaults PROJECTION_SENDER with OutputState class instead of keyword to prevent error due to failed conversion
  rework imports to avoid circularities due to packaging
  make LearningMechanism get its paramClassDefaults from its parent and not Projection_Base
  remove mechanism factory method
  remove system factory in favor of just instantiating System class
  remove process factory in favor of just instantiating Process class
  switch name of Process and Process_Base
  switch name of System and System_Base
  move typecheck for _get_modulated_param inside to avoid circular import
  remove old pyargs argument for pytest
  relaxing validation on LCAIntegrator rate param in order to create an LCA example in integrator mode with an array input
  cleaning up resolving merge conflicts
  fixing merge conflicts
  started mini montague model
  adding comments
  first preliminary test working
  editing testing files and minor typos
  removed unnecessary identity transform function
  updating gitignore for new version of PyCharm
  created PredictionErrorMechanism
  started mini montague model
  adding comments
  first preliminary test working
  editing testing files and minor typos
  removed unnecessary identity transform function
  updating gitignore for new version of PyCharm
  created PredictionErrorMechanism
  starting TDDelta Function -- very messy
  2 of 3 test working
  integrating td learning
  cleaning up Function.py for pull request
  tests working!
  Q-matrix initialization working; mechanism does not
  Added Q-learning and SARSA algorithm

merge me
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