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Fix/modulatory specifications (#554)
* - * 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 * - * - * • State - docstring: STATE NAME ENTRY, MECHANISM/STATE and State constructor examples * - * Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into devel # Conflicts: # Scripts/Scratch Pad.py # psyneulink/components/states/state.py * - * • LearningMechanism, ControlMechanism, GatingMechanism LearningSignal, ControlSignal, GatingSignal -> ContentAddressableList * - * • GatingSignal - implemented _parse_state_specific_params * • GatingSignal - implemented _parse_state_specific_params * • State _parse_state_spec: consolidate handling of tuples and dicts • ControlSignal, GatingSignal _parse_state_specific_params: handle (state name, mech) tuple spec * • State _parse_state_spec: consolidate handling of tuples and dicts • ControlSignal, GatingSignal _parse_state_specific_params: handle (state name, mech) tuple spec * • State _parse_state_spec: consolidate handling of tuples and dicts • ControlSignal, GatingSignal _parse_state_specific_params: handle (state name, mech) tuple spec * - * - * - * - * - * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * • State _parse_state_spec: consolidated parsing of 2-item tuples into _parse_connection_spec * - * - * • Mechanism - parse_arg_input_states: added support for 2-item State Name, Mechanism format * • InputState - parse_state_specific_specs: added support for 2-item State Name, Mechanism format * • InputState - parse_state_specific_specs: added support for 2-item State Name, Mechanism format * • OutputState - parse_state_specific_specs: added support for 2-item State Name, Mechanism format * • OutputState - parse_state_specific_specs: added support for 2-item State Name, Mechanism format * • Project - ConnectionTuple, connection_tuple -> ProjectionTuple, projection_tuple * • Project - ConnectionTuple, connection_tuple -> ProjectionTuple, projection_tuple * • Project - ConnectionTuple, connection_tuple -> ProjectionTuple, projection_tuple * • Project - ConnectionTuple, connection_tuple -> ProjectionTuple, projection_tuple * • OutputState - parse_state_specific_specs: added support for 2-item State Name, Mechanism format * - * • Projection - _parse_connection_spec: added support for list of States and/or Mechanisms in projection jspecification * - * - * - * - * • Tests - added tests for specifying input_states using list of Mechanisms and/or OutputStates • Projection _parse_connection_spec: fixed problem with specifcation of GatingProjection *FROM* GatingMechanism *TO* InputState/OutputState * • Tests - added tests for specifying input_states using list of Mechanisms and/or OutputStates • Projection _parse_connection_spec: fixed problem with specifcation of GatingProjection *FROM* GatingMechanism *TO* InputState/OutputState * - * - * - * - * - * - * - * - * - * - * - * - * • OutputState - docstring revs * • OutputState - docstring revs * • OutputState - docstring revs * • OutputState - docstring revs * • State _parse_state_spec: modified to allow State subclasses to handle value specification * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * - * Merge branch 'TEMP' of https://github.com/jdcpni/PsyNeuLink into TEMP # Conflicts: # Scripts/Scratch Pad.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/states/inputstate.py # psyneulink/components/states/modulatorysignals/controlsignal.py # psyneulink/components/states/outputstate.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # tests/mechanisms/test_input_state_spec.py # tests/projections/test_projections_specifications.py * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * Merge branch 'feat/Function/TDLearning' of https://github.com/PrincetonUniversity/PsyNeuLink into feat/Function/TDLearning # Conflicts: # .idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml # .idea/runConfigurations/_Multilayer_Learning_Test_Script.xml # .idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml # .idea/runConfigurations/_Stroop_Model_Test.xml * - * - * Merge branch 'TEMP' of https://github.com/jdcpni/PsyNeuLink into TEMP # Conflicts: # Scripts/Scratch Pad.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/states/inputstate.py # psyneulink/components/states/modulatorysignals/controlsignal.py # psyneulink/components/states/outputstate.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # tests/mechanisms/test_input_state_spec.py # tests/projections/test_projections_specifications.py * - * Merge branch 'TEMP' of https://github.com/jdcpni/PsyNeuLink into TEMP # Conflicts: # Scripts/Scratch Pad.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/states/inputstate.py # psyneulink/components/states/modulatorysignals/controlsignal.py # psyneulink/components/states/outputstate.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # tests/mechanisms/test_input_state_spec.py # tests/projections/test_projections_specifications.py * Merge branch 'TEMP' of https://github.com/jdcpni/PsyNeuLink into TEMP # Conflicts: # Scripts/Scratch Pad.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/states/inputstate.py # psyneulink/components/states/modulatorysignals/controlsignal.py # psyneulink/components/states/outputstate.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # tests/mechanisms/test_input_state_spec.py # tests/projections/test_projections_specifications.py * Merge branch 'TEMP' of https://github.com/jdcpni/PsyNeuLink into TEMP # Conflicts: # Scripts/Scratch Pad.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/states/inputstate.py # psyneulink/components/states/modulatorysignals/controlsignal.py # psyneulink/components/states/outputstate.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # tests/mechanisms/test_input_state_spec.py # tests/projections/test_projections_specifications.py * Merge branch 'TEMP' of https://github.com/jdcpni/PsyNeuLink into TEMP # Conflicts: # Scripts/Scratch Pad.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/states/inputstate.py # psyneulink/components/states/modulatorysignals/controlsignal.py # psyneulink/components/states/outputstate.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # tests/mechanisms/test_input_state_spec.py # tests/projections/test_projections_specifications.py * Merge branch 'TEMP' of https://github.com/jdcpni/PsyNeuLink into TEMP # Conflicts: # Scripts/Scratch Pad.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/states/inputstate.py # psyneulink/components/states/modulatorysignals/controlsignal.py # psyneulink/components/states/outputstate.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # tests/mechanisms/test_input_state_spec.py # tests/projections/test_projections_specifications.py * Merge branch 'TEMP' of https://github.com/jdcpni/PsyNeuLink into TEMP # Conflicts: # Scripts/Scratch Pad.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/states/inputstate.py # psyneulink/components/states/modulatorysignals/controlsignal.py # psyneulink/components/states/outputstate.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # tests/mechanisms/test_input_state_spec.py # tests/projections/test_projections_specifications.py * Merge branch 'TEMP' of https://github.com/jdcpni/PsyNeuLink into TEMP # Conflicts: # Scripts/Scratch Pad.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/states/inputstate.py # psyneulink/components/states/modulatorysignals/controlsignal.py # psyneulink/components/states/outputstate.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # tests/mechanisms/test_input_state_spec.py # tests/projections/test_projections_specifications.py * Merge branch 'TEMP' of https://github.com/jdcpni/PsyNeuLink into TEMP # Conflicts: # Scripts/Scratch Pad.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/states/inputstate.py # psyneulink/components/states/modulatorysignals/controlsignal.py # psyneulink/components/states/outputstate.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # tests/mechanisms/test_input_state_spec.py # tests/projections/test_projections_specifications.py
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