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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
to methods on System
* 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
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* 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
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* 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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- 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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- 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
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* 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
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* 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
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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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* 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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# 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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* 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
* • 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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