From 263b22bd96a79d086f4d17667d7e4ac07d6da231 Mon Sep 17 00:00:00 2001
From: jdc <jdc@princeton.edu>
Date: Thu, 30 Nov 2017 14:56:53 -0500
Subject: [PATCH 1/9] =?UTF-8?q?=E2=80=A2=20System=20=20=20-=20show=5Fgraph?=
 =?UTF-8?q?():=20bug=20fix=20for=20ControlProjections?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .idea/runConfigurations/AGT_Test_Script.xml   |   4 +-
 .idea/runConfigurations/DDM_Learning_Test.xml |   4 +-
 .../EVC_Gratton_Script___SEBASTIAN.xml        |   4 +-
 ...aming_Validation_Test_Script_DEBUGGING.xml |   4 +-
 ..._Test_Script__SPECIFY_ControlSignals__.xml |   4 +-
 ..._Validation_Test_Script_with_Custom_Fn.xml |   4 +-
 .../EVC_System_Test_Script_with_Profiler.xml  |   4 +-
 .idea/runConfigurations/FinalProject.xml      |   4 +-
 .../Gating_Mechanism_Test_Script.xml          |   4 +-
 .idea/runConfigurations/GilzenratModel.xml    |   7 +-
 .idea/runConfigurations/Make_HTML.xml         |   4 +-
 ...ilayer_Learning_Test_Script_VARIATIONS.xml |   4 +-
 ...yer_Learning_Test_Script__WITH_GATING_.xml |   4 +-
 .../runConfigurations/NEW_Learning_Markus.xml |   4 +-
 .idea/runConfigurations/NetworkX_Examples.xml |   4 +-
 .../Profile_EVC_System_Test.xml               |   4 +-
 ...Model_Learning_and_Control_Test_Script.xml |   4 +-
 .../Stroop_Model_Test_Script_VARIATIONS.xml   |   4 +-
 .idea/runConfigurations/Tests.xml             |   4 +-
 .../Two_Layer_Test_Script.xml                 |   4 +-
 .../Xor_Script_1_process_working.xml          |   4 +-
 .../Xor_Script_2_processes.xml                |   4 +-
 .idea/runConfigurations/_DDM_Test_Script.xml  |   4 +-
 .../_DDM_scheduled_simple.xml                 |   4 +-
 .../_Documentation_Examples.xml               |   4 +-
 .../_EVC_System_DEMO_Script.xml               |   6 +-
 ...C_System_Laming_Validation_Test_Script.xml |   4 +-
 .../_Integrator_scheduled_timescales.xml      |   4 +-
 .idea/runConfigurations/_META_TEST.xml        |   4 +-
 .../_Mixed_NN___DDM_DEMO_Script.xml           |   6 +-
 .../_Mixed_Neural_Network_and_DDM.xml         |   4 +-
 .../_Multilayer_Learning_Test_Script.xml      |   4 +-
 .../_Multilayer_Learning_Test_Script_DEMO.xml |   6 +-
 .../_Reinforcement_Learning_Test_Script.xml   |   4 +-
 .idea/runConfigurations/_Scratch_Pad.xml      |   4 +-
 .../runConfigurations/_Stroop_Demo_Script.xml |   4 +-
 .../_Stroop_Model_Learning_Test_Script.xml    |   4 +-
 .../runConfigurations/_Stroop_Model_Test.xml  |   4 +-
 .../_System_Graph_and_Input_Test.xml          |   4 +-
 .../_System_Learning_Test_Script.xml          |   4 +-
 .../make_html_and_ghpages_py.xml              |   4 +-
 ...ut_and_output_states_to_gating_signals.xml |   4 +-
 ...st_for_tests_control_test_EVC_test_EVC.xml |   4 +-
 ..._mechanism_docs_test_lc_mechanism_docs.xml |   4 +-
 ...test_formats_for_control_specification.xml |   4 +-
 ..._test_formats_for_gating_specification.xml |   4 +-
 ...jection_with_mech_and_state_name_specs.xml |   4 +-
 .../py_test_in_test_lib_mechanism_docs_py.xml |   4 +-
 .idea/runConfigurations/test_system.xml       |   4 +-
 .idea/runConfigurations/topo_example.xml      |   4 +-
 Scripts/Models/GilzenratModel.py              | 192 +++++++++---------
 psyneulink/components/system.py               |  11 +-
 52 files changed, 211 insertions(+), 201 deletions(-)

diff --git a/.idea/runConfigurations/AGT_Test_Script.xml b/.idea/runConfigurations/AGT_Test_Script.xml
index e8d443a835e..3d4f6b09ec4 100644
--- a/.idea/runConfigurations/AGT_Test_Script.xml
+++ b/.idea/runConfigurations/AGT_Test_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="AGT Test Script" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="AGT Test Script" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -10,7 +10,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEBUGGING SCRIPTS/AGT Test Script.py" />
     <option name="PARAMETERS" value="" />
     <option name="SHOW_COMMAND_LINE" value="false" />
diff --git a/.idea/runConfigurations/DDM_Learning_Test.xml b/.idea/runConfigurations/DDM_Learning_Test.xml
index 1830c04f79a..f1148b39497 100644
--- a/.idea/runConfigurations/DDM_Learning_Test.xml
+++ b/.idea/runConfigurations/DDM_Learning_Test.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="DDM Learning Test" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="DDM Learning Test" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -10,7 +10,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/MISCELLANEOUS SCRIPTS/TEST SCRIPTS/DDM Learning Test Script.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/EVC_Gratton_Script___SEBASTIAN.xml b/.idea/runConfigurations/EVC_Gratton_Script___SEBASTIAN.xml
index d5ebe06c98c..5bbf0a13946 100644
--- a/.idea/runConfigurations/EVC_Gratton_Script___SEBASTIAN.xml
+++ b/.idea/runConfigurations/EVC_Gratton_Script___SEBASTIAN.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="EVC Gratton Script - SEBASTIAN" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="EVC Gratton Script - SEBASTIAN" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEBUGGING SCRIPTS/EVC Gratton Script - SEBASTIAN.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_DEBUGGING.xml b/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_DEBUGGING.xml
index 068f6e70c3c..cdd65326432 100644
--- a/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_DEBUGGING.xml
+++ b/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_DEBUGGING.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="EVC System Laming Validation Test Script DEBUGGING" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="EVC System Laming Validation Test Script DEBUGGING" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEBUGGING SCRIPTS/EVC System Laming Validation Test Script DEBUGGING.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script__SPECIFY_ControlSignals__.xml b/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script__SPECIFY_ControlSignals__.xml
index 22c4216d7c7..4b53c89b214 100644
--- a/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script__SPECIFY_ControlSignals__.xml
+++ b/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script__SPECIFY_ControlSignals__.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="EVC System Laming Validation Test Script [SPECIFY ControlSignals]]" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="EVC System Laming Validation Test Script [SPECIFY ControlSignals]]" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEBUGGING SCRIPTS/EVC System Laming Validation Test Script [SPECIFY ControlSignals]].py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_with_Custom_Fn.xml b/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_with_Custom_Fn.xml
index 29683d7ef3e..6d41f53f9c8 100644
--- a/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_with_Custom_Fn.xml
+++ b/.idea/runConfigurations/EVC_System_Laming_Validation_Test_Script_with_Custom_Fn.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="EVC System Laming Validation Test Script with Custom Fn" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="EVC System Laming Validation Test Script with Custom Fn" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -10,7 +10,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/MISCELLANEOUS SCRIPTS/EVC System Laming Validation Test Script with Custom Fn.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/EVC_System_Test_Script_with_Profiler.xml b/.idea/runConfigurations/EVC_System_Test_Script_with_Profiler.xml
index a132b8e24fa..d5d1fcaaba8 100644
--- a/.idea/runConfigurations/EVC_System_Test_Script_with_Profiler.xml
+++ b/.idea/runConfigurations/EVC_System_Test_Script_with_Profiler.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="EVC System Test Script with Profiler" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="EVC System Test Script with Profiler" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -10,7 +10,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/MISCELLANEOUS SCRIPTS/EVC System Test Script with Profiler.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/FinalProject.xml b/.idea/runConfigurations/FinalProject.xml
index e14524de681..f473fc6af86 100644
--- a/.idea/runConfigurations/FinalProject.xml
+++ b/.idea/runConfigurations/FinalProject.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="FinalProject" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="FinalProject" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/STUDENT SCRIPTS/FinalProject.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/Gating_Mechanism_Test_Script.xml b/.idea/runConfigurations/Gating_Mechanism_Test_Script.xml
index 3b434d0b03e..ad6e2aad0cc 100644
--- a/.idea/runConfigurations/Gating_Mechanism_Test_Script.xml
+++ b/.idea/runConfigurations/Gating_Mechanism_Test_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Gating Mechanism Test Script" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="Gating Mechanism Test Script" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -10,7 +10,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/Examples/Gating Mechanism Test Script.py" />
     <option name="PARAMETERS" value="" />
     <option name="SHOW_COMMAND_LINE" value="false" />
diff --git a/.idea/runConfigurations/GilzenratModel.xml b/.idea/runConfigurations/GilzenratModel.xml
index 551bfb71abb..6c9ad63fdc6 100644
--- a/.idea/runConfigurations/GilzenratModel.xml
+++ b/.idea/runConfigurations/GilzenratModel.xml
@@ -1,20 +1,21 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="GilzenratModel" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="GilzenratModel" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
       <env name="PYTHONUNBUFFERED" value="1" />
     </envs>
     <option name="SDK_HOME" value="" />
-    <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/Scripts/DEBUGGING SCRIPTS" />
+    <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$/Scripts/" />
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/Models/GilzenratModel.py" />
     <option name="PARAMETERS" value="" />
     <option name="SHOW_COMMAND_LINE" value="false" />
     <option name="EMULATE_TERMINAL" value="false" />
+    <option name="MODULE_MODE" value="false" />
     <method />
   </configuration>
 </component>
\ No newline at end of file
diff --git a/.idea/runConfigurations/Make_HTML.xml b/.idea/runConfigurations/Make_HTML.xml
index 273f929bfe6..eacc86ebae0 100644
--- a/.idea/runConfigurations/Make_HTML.xml
+++ b/.idea/runConfigurations/Make_HTML.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Make HTML" type="docs" factoryName="Sphinx task" singleton="true">
+  <configuration default="false" factoryName="Sphinx task" name="Make HTML" singleton="true" type="docs">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs />
@@ -8,7 +8,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="docutils_input_file" value="$PROJECT_DIR$/docs/source" />
     <option name="docutils_output_file" value="$PROJECT_DIR$/docs/build/html" />
diff --git a/.idea/runConfigurations/Multilayer_Learning_Test_Script_VARIATIONS.xml b/.idea/runConfigurations/Multilayer_Learning_Test_Script_VARIATIONS.xml
index 71e33c5b672..c6d8fea16c6 100644
--- a/.idea/runConfigurations/Multilayer_Learning_Test_Script_VARIATIONS.xml
+++ b/.idea/runConfigurations/Multilayer_Learning_Test_Script_VARIATIONS.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Multilayer Learning Test Script VARIATIONS" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="Multilayer Learning Test Script VARIATIONS" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEBUGGING SCRIPTS/Multilayer Learning Test Script VARIATIONS.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/Multilayer_Learning_Test_Script__WITH_GATING_.xml b/.idea/runConfigurations/Multilayer_Learning_Test_Script__WITH_GATING_.xml
index 04e08d34a15..1fda4fd49f3 100644
--- a/.idea/runConfigurations/Multilayer_Learning_Test_Script__WITH_GATING_.xml
+++ b/.idea/runConfigurations/Multilayer_Learning_Test_Script__WITH_GATING_.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Multilayer Learning Test Script [WITH GATING]" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="Multilayer Learning Test Script [WITH GATING]" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEBUGGING SCRIPTS/Multilayer Learning Test Script [WITH GATING].py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/NEW_Learning_Markus.xml b/.idea/runConfigurations/NEW_Learning_Markus.xml
index d2e7bece107..cb52aa9c21c 100644
--- a/.idea/runConfigurations/NEW_Learning_Markus.xml
+++ b/.idea/runConfigurations/NEW_Learning_Markus.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="NEW_Learning_Markus" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="NEW_Learning_Markus" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEMO SCRIPTS/NEW_Learning_Markus.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/NetworkX_Examples.xml b/.idea/runConfigurations/NetworkX_Examples.xml
index df2774f8a56..305239e043c 100644
--- a/.idea/runConfigurations/NetworkX_Examples.xml
+++ b/.idea/runConfigurations/NetworkX_Examples.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="NetworkX Examples" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="NetworkX Examples" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -10,7 +10,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/PsyNeuLink/Globals/NetworkX tesst.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/Profile_EVC_System_Test.xml b/.idea/runConfigurations/Profile_EVC_System_Test.xml
index 13365fb7733..069058f85f0 100644
--- a/.idea/runConfigurations/Profile_EVC_System_Test.xml
+++ b/.idea/runConfigurations/Profile_EVC_System_Test.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Profile EVC System Test" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="Profile EVC System Test" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -10,7 +10,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/MISCELLANEOUS SCRIPTS/Profile EVC System Test Script.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/Stroop_Model_Learning_and_Control_Test_Script.xml b/.idea/runConfigurations/Stroop_Model_Learning_and_Control_Test_Script.xml
index d110cc35e81..438bd3390ce 100644
--- a/.idea/runConfigurations/Stroop_Model_Learning_and_Control_Test_Script.xml
+++ b/.idea/runConfigurations/Stroop_Model_Learning_and_Control_Test_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Stroop Model Learning and Control Test Script" type="PythonConfigurationType" factoryName="Python" folderName="DEMO SCRIPTS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="DEMO SCRIPTS" name="Stroop Model Learning and Control Test Script" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/TEST SCRIPTS/Stroop Model Learning and Control Test Script.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/Stroop_Model_Test_Script_VARIATIONS.xml b/.idea/runConfigurations/Stroop_Model_Test_Script_VARIATIONS.xml
index d3886cc032f..a083b422b07 100644
--- a/.idea/runConfigurations/Stroop_Model_Test_Script_VARIATIONS.xml
+++ b/.idea/runConfigurations/Stroop_Model_Test_Script_VARIATIONS.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Stroop Model Test Script VARIATIONS" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="Stroop Model Test Script VARIATIONS" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEBUGGING SCRIPTS/Stroop Model Test Script VARIATIONS.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/Tests.xml b/.idea/runConfigurations/Tests.xml
index 4dba46615a7..a4b442aacdb 100644
--- a/.idea/runConfigurations/Tests.xml
+++ b/.idea/runConfigurations/Tests.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Tests" type="tests" factoryName="py.test" singleton="true">
+  <configuration default="false" factoryName="py.test" name="Tests" singleton="true" type="tests">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs />
@@ -8,7 +8,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <option name="_new_keywords" value="&quot;&quot;" />
     <option name="_new_additionalArguments" value="&quot;&quot;" />
     <option name="_new_target" value="&quot;$PROJECT_DIR$/tests&quot;" />
diff --git a/.idea/runConfigurations/Two_Layer_Test_Script.xml b/.idea/runConfigurations/Two_Layer_Test_Script.xml
index e5dd04359a9..85af3a59b79 100644
--- a/.idea/runConfigurations/Two_Layer_Test_Script.xml
+++ b/.idea/runConfigurations/Two_Layer_Test_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Two Layer Test Script" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="Two Layer Test Script" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/MISCELLANEOUS SCRIPTS/Two Layer Test Script.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/Xor_Script_1_process_working.xml b/.idea/runConfigurations/Xor_Script_1_process_working.xml
index 9c86080c6e5..ae3d7891666 100644
--- a/.idea/runConfigurations/Xor_Script_1_process_working.xml
+++ b/.idea/runConfigurations/Xor_Script_1_process_working.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Xor_Script_1_process_working" type="PythonConfigurationType" factoryName="Python" folderName="DEMO SCRIPTS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="DEMO SCRIPTS" name="Xor_Script_1_process_working" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEMO SCRIPTS/Xor_Script_Working.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/Xor_Script_2_processes.xml b/.idea/runConfigurations/Xor_Script_2_processes.xml
index a4372c37cc6..9099901b7bf 100644
--- a/.idea/runConfigurations/Xor_Script_2_processes.xml
+++ b/.idea/runConfigurations/Xor_Script_2_processes.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Xor_Script_2_processes" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="Xor_Script_2_processes" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEMO SCRIPTS/Xor_Script_2_processes.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/_DDM_Test_Script.xml b/.idea/runConfigurations/_DDM_Test_Script.xml
index a07730b20c8..48631c31cc0 100644
--- a/.idea/runConfigurations/_DDM_Test_Script.xml
+++ b/.idea/runConfigurations/_DDM_Test_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• DDM Test Script" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="&#8226; DDM Test Script" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -10,7 +10,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/TEST SCRIPTS/DDM Test Script.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/_DDM_scheduled_simple.xml b/.idea/runConfigurations/_DDM_scheduled_simple.xml
index db8dfd99dc2..76f1c7fd7a3 100644
--- a/.idea/runConfigurations/_DDM_scheduled_simple.xml
+++ b/.idea/runConfigurations/_DDM_scheduled_simple.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• DDM_scheduled_simple" type="PythonConfigurationType" factoryName="Python" folderName="DEMO SCRIPTS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="DEMO SCRIPTS" name="&#8226; DDM_scheduled_simple" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEMO SCRIPTS/DDM_scheduled_simple.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/_Documentation_Examples.xml b/.idea/runConfigurations/_Documentation_Examples.xml
index 021c739c153..e5e2da3904a 100644
--- a/.idea/runConfigurations/_Documentation_Examples.xml
+++ b/.idea/runConfigurations/_Documentation_Examples.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• Documentation Examples" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="&#8226; Documentation Examples" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -10,7 +10,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/TEST SCRIPTS/Documentation Examples Script.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/_EVC_System_DEMO_Script.xml b/.idea/runConfigurations/_EVC_System_DEMO_Script.xml
index 5d2f7244c7c..2119a4e7aa9 100644
--- a/.idea/runConfigurations/_EVC_System_DEMO_Script.xml
+++ b/.idea/runConfigurations/_EVC_System_DEMO_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• EVC System DEMO Script" type="PythonConfigurationType" factoryName="Python" folderName="DEMO SCRIPTS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="DEMO SCRIPTS" name="&#8226; EVC System DEMO Script" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,9 +11,9 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
-    <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEMO SCRIPTS/• EVC System DEMO Script.py" />
+    <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEMO SCRIPTS/&#8226; EVC System DEMO Script.py" />
     <option name="PARAMETERS" value="" />
     <option name="SHOW_COMMAND_LINE" value="false" />
     <option name="EMULATE_TERMINAL" value="false" />
diff --git a/.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml b/.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
index 8f52a8aa544..3f57422ee34 100644
--- a/.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
+++ b/.idea/runConfigurations/_EVC_System_Laming_Validation_Test_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• EVC System Laming Validation Test Script" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="&#8226; EVC System Laming Validation Test Script" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/TEST SCRIPTS/EVC System Laming Validation Test Script.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/_Integrator_scheduled_timescales.xml b/.idea/runConfigurations/_Integrator_scheduled_timescales.xml
index e8bc21786ce..59fdbefd978 100644
--- a/.idea/runConfigurations/_Integrator_scheduled_timescales.xml
+++ b/.idea/runConfigurations/_Integrator_scheduled_timescales.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• Integrator_scheduled_timescales" type="PythonConfigurationType" factoryName="Python" folderName="DEMO SCRIPTS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="DEMO SCRIPTS" name="&#8226; Integrator_scheduled_timescales" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEMO SCRIPTS/Integrator_scheduled_timescales.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/_META_TEST.xml b/.idea/runConfigurations/_META_TEST.xml
index bae196ffa6f..7d6b4e3d70d 100644
--- a/.idea/runConfigurations/_META_TEST.xml
+++ b/.idea/runConfigurations/_META_TEST.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• META TEST" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="&#8226; META TEST" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/TEST SCRIPTS/META Test Script.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/_Mixed_NN___DDM_DEMO_Script.xml b/.idea/runConfigurations/_Mixed_NN___DDM_DEMO_Script.xml
index fcc62c27e0e..5c7c7925582 100644
--- a/.idea/runConfigurations/_Mixed_NN___DDM_DEMO_Script.xml
+++ b/.idea/runConfigurations/_Mixed_NN___DDM_DEMO_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• Mixed NN &amp; DDM DEMO Script" type="PythonConfigurationType" factoryName="Python" folderName="DEMO SCRIPTS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="DEMO SCRIPTS" name="&#8226; Mixed NN &amp; DDM DEMO Script" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,9 +11,9 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
-    <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEMO SCRIPTS/• Mixed NN &amp; DDM DEMO Script.py" />
+    <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEMO SCRIPTS/&#8226; Mixed NN &amp; DDM DEMO Script.py" />
     <option name="PARAMETERS" value="" />
     <option name="SHOW_COMMAND_LINE" value="false" />
     <option name="EMULATE_TERMINAL" value="false" />
diff --git a/.idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml b/.idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml
index e349065887c..d51b15b5f0b 100644
--- a/.idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml
+++ b/.idea/runConfigurations/_Mixed_Neural_Network_and_DDM.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• Mixed Neural Network and DDM" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="&#8226; Mixed Neural Network and DDM" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -10,7 +10,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/TEST SCRIPTS/Mixed NN &amp; DDM script.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml b/.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml
index e6f3df4461a..d12ac2717e1 100644
--- a/.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml
+++ b/.idea/runConfigurations/_Multilayer_Learning_Test_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• Multilayer Learning Test Script" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="&#8226; Multilayer Learning Test Script" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,7 +11,7 @@
     <option name="IS_MODULE_SDK" value="false" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/Examples/Multilayer-Learning.py" />
     <option name="PARAMETERS" value="" />
diff --git a/.idea/runConfigurations/_Multilayer_Learning_Test_Script_DEMO.xml b/.idea/runConfigurations/_Multilayer_Learning_Test_Script_DEMO.xml
index 7664f86ca9c..14ec01694d2 100644
--- a/.idea/runConfigurations/_Multilayer_Learning_Test_Script_DEMO.xml
+++ b/.idea/runConfigurations/_Multilayer_Learning_Test_Script_DEMO.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• Multilayer Learning Test Script DEMO" type="PythonConfigurationType" factoryName="Python" folderName="DEMO SCRIPTS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="DEMO SCRIPTS" name="&#8226; Multilayer Learning Test Script DEMO" singleton="true" type="PythonConfigurationType">
     <option name="INTERPRETER_OPTIONS" value="" />
     <option name="PARENT_ENVS" value="true" />
     <envs>
@@ -11,9 +11,9 @@
     <option name="IS_MODULE_SDK" value="true" />
     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
-    <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEMO SCRIPTS/• Multilayer Learning Test Script DEMO.py" />
+    <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/DEMO SCRIPTS/&#8226; Multilayer Learning Test Script DEMO.py" />
     <option name="PARAMETERS" value="" />
     <option name="SHOW_COMMAND_LINE" value="false" />
     <option name="EMULATE_TERMINAL" value="false" />
diff --git a/.idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml b/.idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml
index 3b5775ad30b..6c9fc40dc47 100644
--- a/.idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml
+++ b/.idea/runConfigurations/_Reinforcement_Learning_Test_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• Reinforcement Learning Test Script" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="&#8226; Reinforcement Learning Test Script" singleton="true" type="PythonConfigurationType">
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     <option name="PARENT_ENVS" value="true" />
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@@ -10,7 +10,7 @@
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     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
     <EXTENSION ID="PythonCoverageRunConfigurationExtension" enabled="false" runner="coverage.py" sample_coverage="true" />
     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Scripts/TEST SCRIPTS/Reinforcement Learning Test Script.py" />
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diff --git a/.idea/runConfigurations/_Scratch_Pad.xml b/.idea/runConfigurations/_Scratch_Pad.xml
index cb1de20263c..35f487c2a27 100644
--- a/.idea/runConfigurations/_Scratch_Pad.xml
+++ b/.idea/runConfigurations/_Scratch_Pad.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• Scratch Pad" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="&#8226; Scratch Pad" singleton="true" type="PythonConfigurationType">
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@@ -10,7 +10,7 @@
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     <option name="ADD_SOURCE_ROOTS" value="true" />
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+    <module name="" />
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diff --git a/.idea/runConfigurations/_Stroop_Demo_Script.xml b/.idea/runConfigurations/_Stroop_Demo_Script.xml
index 69554f0ec22..145532dcbe7 100644
--- a/.idea/runConfigurations/_Stroop_Demo_Script.xml
+++ b/.idea/runConfigurations/_Stroop_Demo_Script.xml
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 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• Stroop Demo Script" type="PythonConfigurationType" factoryName="Python" folderName="DEMO SCRIPTS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="DEMO SCRIPTS" name="&#8226; Stroop Demo Script" singleton="true" type="PythonConfigurationType">
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@@ -11,7 +11,7 @@
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     <option name="ADD_SOURCE_ROOTS" value="true" />
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+    <module name="" />
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diff --git a/.idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml b/.idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml
index 6ad30dcbae8..5c7aed239e9 100644
--- a/.idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml
+++ b/.idea/runConfigurations/_Stroop_Model_Learning_Test_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• Stroop Model Learning Test Script" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="&#8226;&#160;Stroop Model Learning Test Script" singleton="true" type="PythonConfigurationType">
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@@ -11,7 +11,7 @@
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     <option name="ADD_SOURCE_ROOTS" value="true" />
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+    <module name="" />
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diff --git a/.idea/runConfigurations/_Stroop_Model_Test.xml b/.idea/runConfigurations/_Stroop_Model_Test.xml
index 710857aec7b..31ab27c142d 100644
--- a/.idea/runConfigurations/_Stroop_Model_Test.xml
+++ b/.idea/runConfigurations/_Stroop_Model_Test.xml
@@ -1,5 +1,5 @@
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-  <configuration default="false" name="• Stroop Model Test" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="&#8226; Stroop Model Test" singleton="true" type="PythonConfigurationType">
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@@ -11,7 +11,7 @@
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     <option name="ADD_SOURCE_ROOTS" value="true" />
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+    <module name="" />
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diff --git a/.idea/runConfigurations/_System_Graph_and_Input_Test.xml b/.idea/runConfigurations/_System_Graph_and_Input_Test.xml
index 060d51af7cc..19277f5ce09 100644
--- a/.idea/runConfigurations/_System_Graph_and_Input_Test.xml
+++ b/.idea/runConfigurations/_System_Graph_and_Input_Test.xml
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@@ -11,7 +11,7 @@
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     <option name="ADD_SOURCE_ROOTS" value="true" />
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diff --git a/.idea/runConfigurations/_System_Learning_Test_Script.xml b/.idea/runConfigurations/_System_Learning_Test_Script.xml
index f53d89841bb..9a08f0af7e6 100644
--- a/.idea/runConfigurations/_System_Learning_Test_Script.xml
+++ b/.idea/runConfigurations/_System_Learning_Test_Script.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="• System Learning Test Script" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="&#8226; System Learning Test Script" singleton="true" type="PythonConfigurationType">
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     <option name="PARENT_ENVS" value="true" />
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@@ -10,7 +10,7 @@
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     <option name="ADD_SOURCE_ROOTS" value="true" />
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+    <module name="" />
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diff --git a/.idea/runConfigurations/make_html_and_ghpages_py.xml b/.idea/runConfigurations/make_html_and_ghpages_py.xml
index bef143ce0ac..6d8ea246da1 100644
--- a/.idea/runConfigurations/make_html_and_ghpages_py.xml
+++ b/.idea/runConfigurations/make_html_and_ghpages_py.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="make_html_and_ghpages.py" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="make_html_and_ghpages.py" singleton="true" type="PythonConfigurationType">
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     <option name="ADD_SOURCE_ROOTS" value="true" />
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+    <module name="" />
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diff --git a/.idea/runConfigurations/py_test_for_test_projections_specifications_TestProjectionSpecificationFormats_test_2_item_tuple_from_input_and_output_states_to_gating_signals.xml b/.idea/runConfigurations/py_test_for_test_projections_specifications_TestProjectionSpecificationFormats_test_2_item_tuple_from_input_and_output_states_to_gating_signals.xml
index d865da7d558..7483402424d 100644
--- a/.idea/runConfigurations/py_test_for_test_projections_specifications_TestProjectionSpecificationFormats_test_2_item_tuple_from_input_and_output_states_to_gating_signals.xml
+++ b/.idea/runConfigurations/py_test_for_test_projections_specifications_TestProjectionSpecificationFormats_test_2_item_tuple_from_input_and_output_states_to_gating_signals.xml
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+  <configuration default="false" factoryName="py.test" name="py.test for test_projections_specifications.TestProjectionSpecificationFormats.test_2_item_tuple_from_input_and_output_states_to_gating_signals" nameIsGenerated="true" singleton="true" type="tests">
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@@ -8,7 +8,7 @@
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     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
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index 33319263978..449a9154266 100644
--- a/.idea/runConfigurations/py_test_for_tests_control_test_EVC_test_EVC.xml
+++ b/.idea/runConfigurations/py_test_for_tests_control_test_EVC_test_EVC.xml
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 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="py.test for tests.control.test_EVC.test_EVC" type="tests" factoryName="py.test" singleton="true" nameIsGenerated="true">
+  <configuration default="false" factoryName="py.test" name="py.test for tests.control.test_EVC.test_EVC" nameIsGenerated="true" singleton="true" type="tests">
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@@ -8,7 +8,7 @@
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     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
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+    <module name="" />
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diff --git a/.idea/runConfigurations/py_test_for_tests_documentation_library_test_lib_mechanism_docs_test_lc_mechanism_docs.xml b/.idea/runConfigurations/py_test_for_tests_documentation_library_test_lib_mechanism_docs_test_lc_mechanism_docs.xml
index 6d11c29fa19..df395bdc12d 100644
--- a/.idea/runConfigurations/py_test_for_tests_documentation_library_test_lib_mechanism_docs_test_lc_mechanism_docs.xml
+++ b/.idea/runConfigurations/py_test_for_tests_documentation_library_test_lib_mechanism_docs_test_lc_mechanism_docs.xml
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-  <configuration default="false" name="py.test for tests.documentation.library.test_lib_mechanism_docs.test_lc_mechanism_docs" type="tests" factoryName="py.test" singleton="true" nameIsGenerated="true">
+  <configuration default="false" factoryName="py.test" name="py.test for tests.documentation.library.test_lib_mechanism_docs.test_lc_mechanism_docs" nameIsGenerated="true" singleton="true" type="tests">
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@@ -8,7 +8,7 @@
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     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
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     <option name="_new_target" value="&quot;tests.documentation.library.test_lib_mechanism_docs.test_lc_mechanism_docs&quot;" />
diff --git a/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_formats_for_control_specification.xml b/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_formats_for_control_specification.xml
index a90b728db7a..dda9c26a96a 100644
--- a/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_formats_for_control_specification.xml
+++ b/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_formats_for_control_specification.xml
@@ -1,5 +1,5 @@
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+  <configuration default="false" factoryName="py.test" name="py.test for tests.projections.test_projections_specifications.TestProjectionSpecificationFormats.test_formats_for_control_specification" nameIsGenerated="true" singleton="true" type="tests">
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@@ -8,7 +8,7 @@
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     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
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     <option name="_new_target" value="&quot;tests.projections.test_projections_specifications.TestProjectionSpecificationFormats.test_formats_for_control_specification&quot;" />
diff --git a/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_formats_for_gating_specification.xml b/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_formats_for_gating_specification.xml
index e7a0c2147d6..90fc5d81e5e 100644
--- a/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_formats_for_gating_specification.xml
+++ b/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_formats_for_gating_specification.xml
@@ -1,5 +1,5 @@
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+  <configuration default="false" factoryName="py.test" name="py.test for tests.projections.test_projections_specifications.TestProjectionSpecificationFormats.test_formats_for_gating_specification" nameIsGenerated="true" singleton="true" type="tests">
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@@ -8,7 +8,7 @@
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     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
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diff --git a/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_mapping_projection_with_mech_and_state_name_specs.xml b/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_mapping_projection_with_mech_and_state_name_specs.xml
index 639ad80991a..c95bfd67e89 100644
--- a/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_mapping_projection_with_mech_and_state_name_specs.xml
+++ b/.idea/runConfigurations/py_test_for_tests_projections_test_projections_specifications_TestProjectionSpecificationFormats_test_mapping_projection_with_mech_and_state_name_specs.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
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+  <configuration default="false" factoryName="py.test" name="py.test for tests.projections.test_projections_specifications.TestProjectionSpecificationFormats.test_mapping_projection_with_mech_and_state_name_specs" nameIsGenerated="true" singleton="true" type="tests">
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@@ -8,7 +8,7 @@
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     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
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diff --git a/.idea/runConfigurations/py_test_in_test_lib_mechanism_docs_py.xml b/.idea/runConfigurations/py_test_in_test_lib_mechanism_docs_py.xml
index 6cafd894296..892f1719fa1 100644
--- a/.idea/runConfigurations/py_test_in_test_lib_mechanism_docs_py.xml
+++ b/.idea/runConfigurations/py_test_in_test_lib_mechanism_docs_py.xml
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 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="py.test in test_lib_mechanism_docs.py" type="tests" factoryName="py.test" singleton="true" nameIsGenerated="true">
+  <configuration default="false" factoryName="py.test" name="py.test in test_lib_mechanism_docs.py" nameIsGenerated="true" singleton="true" type="tests">
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     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
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diff --git a/.idea/runConfigurations/test_system.xml b/.idea/runConfigurations/test_system.xml
index 0442de18fd8..a64b85cfcb7 100644
--- a/.idea/runConfigurations/test_system.xml
+++ b/.idea/runConfigurations/test_system.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="test_system" type="PythonConfigurationType" factoryName="Python" singleton="true">
+  <configuration default="false" factoryName="Python" name="test_system" singleton="true" type="PythonConfigurationType">
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     <option name="PARENT_ENVS" value="true" />
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@@ -11,7 +11,7 @@
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     <option name="ADD_SOURCE_ROOTS" value="true" />
-    <module name="PsyNeuLink" />
+    <module name="" />
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diff --git a/.idea/runConfigurations/topo_example.xml b/.idea/runConfigurations/topo_example.xml
index 98674565da0..5f227813b7f 100644
--- a/.idea/runConfigurations/topo_example.xml
+++ b/.idea/runConfigurations/topo_example.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="topo_example" type="PythonConfigurationType" factoryName="Python" folderName="OTHER CONFIGS" singleton="true">
+  <configuration default="false" factoryName="Python" folderName="OTHER CONFIGS" name="topo_example" singleton="true" type="PythonConfigurationType">
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@@ -10,7 +10,7 @@
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     <option name="ADD_CONTENT_ROOTS" value="true" />
     <option name="ADD_SOURCE_ROOTS" value="true" />
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+    <module name="" />
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     <option name="SCRIPT_NAME" value="$PROJECT_DIR$/PsyNeuLink/Globals/toposort/topo_example.py" />
     <option name="PARAMETERS" value="" />
diff --git a/Scripts/Models/GilzenratModel.py b/Scripts/Models/GilzenratModel.py
index 9d560079f7b..d0bc3f17d89 100644
--- a/Scripts/Models/GilzenratModel.py
+++ b/Scripts/Models/GilzenratModel.py
@@ -33,7 +33,7 @@
 d = 0.50        # Baseline level of intrinsic, uncorrelated LC activity
 G = 0.50        # Base level of gain applied to decision and response units
 k = 3.00        # Scaling factor for transforming NE release (u) to gain (g) on potentiated units
-SD = 0.0        # Standard deviation of Gaussian noise distributions | NOTE: 0.22 in Gilzenrat paper
+SD = 0.1        # Standard deviation of Gaussian noise distributions | NOTE: 0.22 in Gilzenrat paper
 tau_v = 0.05    # Time constant for fast LC excitation variable v | NOTE: tau_v is misstated in the Gilzenrat paper(0.5)
 tau_u = 5.00    # Time constant for slow LC recovery variable (‘NE release’) u
 dt = 0.02       # Time step size for numerical integration
@@ -137,99 +137,103 @@
 
 task = System(processes=[decision_process])
 
-# Create Stimulus -----------------------------------------------------------------------------------------------------
-
-# number of trials
-trials = 1000
-
-# assign inputs to input_layer (Origin Mechanism) for each trial
-stimulus_dictionary = {input_layer: np.repeat(np.array([[0.0, 0.0], [1.0, 0.0]]), 500, axis=0)}
-# First 500 trials: target receives input of 0.0, distractor receives input of 0.0
-# Second 500 trials: target receives input of 1.0, distractor receives input of 0.0
-
-# Record results & run model ------------------------------------------------------------------------------------------
-
-# Function to compute h(v) from LC's v value
-def h_v(v,C,d):
-    return C*v + (1-C)*d
-
-# Initialize output arrays for plotting and storing values
-LC_results_h_of_v = [h_v(initial_v,C,d)]
-LC_results_u = [initial_u]
-decision_layer_target_values = [0.0]
-decision_layer_distractor_values = [0.0]
-response_layer_values = [0.0]
-
-def record_trial():
-    # After each trial, store all of the following values:
-    LC_results_h_of_v.append(h_v(LC.value[2][0], C, d))
-    LC_results_u.append(LC.value[3][0])
-    decision_layer_target_values.append(decision_layer.value[0][0])
-    decision_layer_distractor_values.append(decision_layer.value[0][1])
-    response_layer_values.append(response_layer.value[0][0])
-
-    # Progress bar
-    current_trial_num = len(LC_results_h_of_v)
-    if current_trial_num%50 == 0:
-        percent = int(round((float(current_trial_num) / trials)*100))
-        sys.stdout.write("\r"+ str(percent) +"% complete")
-        sys.stdout.flush()
-
-# Initialize progress bar
-sys.stdout.write("\r0% complete")
-sys.stdout.flush()
-
-# Run the model
-task.run(inputs=stimulus_dictionary,
-         num_trials=trials,
-         call_after_trial=record_trial)
-
-# Plot results of all units into one figure ---------------------------------------------------------------------------
-
-# import matplotlib
-# matplotlib.use('Agg')
-from matplotlib import pyplot as plt
-import numpy as np
+# This displays a diagram of the System
+task.show_graph(show_dimensions=True)
 
-# Create x axis "t" for plotting
-t = np.arange(0.0, 20.02, 0.02)
-
-# Plot target unit, distraction unit, response unit, h(v), and u using the values that were recorded after each trial
-plt.plot(t,
-         decision_layer_target_values,
-         label="target unit",
-         color = 'green')
-plt.plot(t,
-         decision_layer_distractor_values,
-         label="distraction unit",
-         color = 'red')
-plt.plot(t,
-         response_layer_values,
-         label="response unit",
-         color = 'magenta')
-plt.plot(t,
-         LC_results_h_of_v,
-         label="h(v)",
-         color = 'b')
-plt.plot(t,
-         LC_results_u,
-         label="u",
-         color = 'black')
-
-plt.xlabel('Time')
-plt.ylabel('Activation')
-plt.legend(loc='upper left')
-plt.xlim((0.0,20.0))
-plt.ylim((-0.2, 1.2))
-x_values = [0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20]
-plt.xticks(x_values)
-plt.title('GILZENRAT 2002 PsyNeuLink', fontweight='bold')
-
-
-plt.show()
-
-task.show()
 
-# This displays a diagram of the System
-task.show_graph()
+# Create Stimulus -----------------------------------------------------------------------------------------------------
 
+# # number of trials
+# trials = 1000
+#
+# # assign inputs to input_layer (Origin Mechanism) for each trial
+# stimulus_dictionary = {input_layer: np.repeat(np.array([[0.0, 0.0], [1.0, 0.0]]), 500, axis=0)}
+# # First 500 trials: target receives input of 0.0, distractor receives input of 0.0
+# # Second 500 trials: target receives input of 1.0, distractor receives input of 0.0
+#
+# # Record results & run model ------------------------------------------------------------------------------------------
+#
+# # Function to compute h(v) from LC's v value
+# def h_v(v,C,d):
+#     return C*v + (1-C)*d
+#
+# # Initialize output arrays for plotting and storing values
+# LC_results_h_of_v = [h_v(initial_v,C,d)]
+# LC_results_u = [initial_u]
+# decision_layer_target_values = [0.0]
+# decision_layer_distractor_values = [0.0]
+# response_layer_values = [0.0]
+#
+# def record_trial():
+#     # After each trial, store all of the following values:
+#     LC_results_h_of_v.append(h_v(LC.value[2][0], C, d))
+#     LC_results_u.append(LC.value[3][0])
+#     decision_layer_target_values.append(decision_layer.value[0][0])
+#     decision_layer_distractor_values.append(decision_layer.value[0][1])
+#     response_layer_values.append(response_layer.value[0][0])
+#
+#     # Progress bar
+#     current_trial_num = len(LC_results_h_of_v)
+#     if current_trial_num%50 == 0:
+#         percent = int(round((float(current_trial_num) / trials)*100))
+#         sys.stdout.write("\r"+ str(percent) +"% complete")
+#         sys.stdout.flush()
+#
+# # Initialize progress bar
+# sys.stdout.write("\r0% complete")
+# sys.stdout.flush()
+#
+# # Run the model
+# task.run(inputs=stimulus_dictionary,
+#          num_trials=trials,
+#          call_after_trial=record_trial)
+#
+# # Plot results of all units into one figure ---------------------------------------------------------------------------
+#
+# # import matplotlib
+# # matplotlib.use('Agg')
+# from matplotlib import pyplot as plt
+# import numpy as np
+#
+# # Create x axis "t" for plotting
+# t = np.arange(0.0, 20.02, 0.02)
+#
+# # Plot target unit, distraction unit, response unit, h(v), and u using the values that were recorded after each trial
+# plt.plot(t,
+#          decision_layer_target_values,
+#          label="target unit",
+#          color = 'green')
+# plt.plot(t,
+#          decision_layer_distractor_values,
+#          label="distraction unit",
+#          color = 'red')
+# plt.plot(t,
+#          response_layer_values,
+#          label="response unit",
+#          color = 'magenta')
+# plt.plot(t,
+#          LC_results_h_of_v,
+#          label="h(v)",
+#          color = 'b')
+# plt.plot(t,
+#          LC_results_u,
+#          label="u",
+#          color = 'black')
+#
+# plt.xlabel('Time')
+# plt.ylabel('Activation')
+# plt.legend(loc='upper left')
+# plt.xlim((0.0,20.0))
+# plt.ylim((-0.2, 1.2))
+# x_values = [0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20]
+# plt.xticks(x_values)
+# plt.title('GILZENRAT 2002 PsyNeuLink', fontweight='bold')
+#
+#
+# plt.show()
+#
+# task.show()
+#
+# # This displays a diagram of the System
+# task.show_graph()
+#
diff --git a/psyneulink/components/system.py b/psyneulink/components/system.py
index daf6eb35755..4aaab21c5a8 100644
--- a/psyneulink/components/system.py
+++ b/psyneulink/components/system.py
@@ -3319,9 +3319,14 @@ def _get_label(item):
             # For Projection, show dimensions of matrix
             elif isinstance(item, Projection):
                 if show_dimensions in {ALL, PROJECTIONS}:
-                    value = np.array(item.matrix)
-                    dim_string = "({})".format("x".join([str(i) for i in value.shape]))
-                    return "{}\n{}".format(item.name, dim_string)
+                    if isinstance(item, MappingProjection):
+                        value = np.array(item.matrix)
+                        dim_string = "({})".format("x".join([str(i) for i in value.shape]))
+                        return "{}\n{}".format(item.name, dim_string)
+                    else:
+                        value = np.array(item.value)
+                        dim_string = "({})".format(len(value))
+                        return "{}\n{}".format(item.name, dim_string)
                 else:
                     return item.name
 

From 2966f432d64188f0a8bcb9974b3eecd49ff3232a Mon Sep 17 00:00:00 2001
From: jdc <jdc@princeton.edu>
Date: Fri, 1 Dec 2017 15:24:03 -0500
Subject: [PATCH 2/9] =?UTF-8?q?=E2=80=A2=20System=20=20=20-=20show=5Fgraph?=
 =?UTF-8?q?():=20bug=20fix=20for=20ControlProjections?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 psyneulink/components/system.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/psyneulink/components/system.py b/psyneulink/components/system.py
index 4aaab21c5a8..d3cd585de4b 100644
--- a/psyneulink/components/system.py
+++ b/psyneulink/components/system.py
@@ -3334,7 +3334,6 @@ def _get_label(item):
                 raise SystemError("Unrecognized node type ({}) in graph for {}".format(item, self.name))
 
 
-
         # build graph and configure visualisation settings
         G = gv.Digraph(engine = "dot",
                        node_attr  = {

From 047cf1813592e44a8f4ff535051d2db099598880 Mon Sep 17 00:00:00 2001
From: jdc <jdc@princeton.edu>
Date: Tue, 5 Dec 2017 10:46:23 -0500
Subject: [PATCH 3/9] -

---
 psyneulink/globals/log.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/psyneulink/globals/log.py b/psyneulink/globals/log.py
index c94ec6939f5..0017f01c8ec 100644
--- a/psyneulink/globals/log.py
+++ b/psyneulink/globals/log.py
@@ -24,12 +24,12 @@
 Components that belong to it.  These are stored in `entries <Log.entries>` of the Log, that contain a sequential list
 of the recorded values, along with the time and context of the recording.  The conditions under which values are
 recorded is specified by the `logPref <Component.logPref` property of a Component.  While these can be set directly,
-they are most easily managed using three convenience methods assigned to every Component along with its `log --
-`loggable_items <Log.loggable_items>`, `log_items <Log.log_items>` and `logged_items <Log.logged_items>` -- that
-identify, specify and track items the items being logged, respectively.  This can be useful not only for observing
-the behavior of Compnents in a model, but also in debugging them during construction.  The entries of a Log can be
-displayed in a "human readable" table using its `print_entries <Log.print_entries>` method, and returned in CSV and
-numpy array formats using its `csv <Log.csv>` and `nparray <Log.nparray>` methods.
+they are most easily managed using three convenience methods assigned to every Component along with its `log
+<Component.log>` -- `loggable_items <Log.loggable_items>`, `log_items <Log.log_items>` and `logged_items
+<Log.logged_items>` -- that identify, specify and track items the items being logged, respectively.  This can be
+useful not only for observing the behavior of Compnents in a model, but also in debugging them during construction.
+The entries of a Log can be displayed in a "human readable" table using its `print_entries <Log.print_entries>`
+method, and returned in CSV and numpy array formats using its `csv <Log.csv>` and `nparray <Log.nparray>` methods.
 
 COMMENT:
 Entries can also be made by the user programmatically. Each entry contains the time at

From 2ebd78b7c13d57d612be636853b4fea08b98e4f2 Mon Sep 17 00:00:00 2001
From: "jdc@princeton.edu" <jdc@princeton.edu>
Date: Tue, 5 Dec 2017 11:40:24 -0500
Subject: [PATCH 4/9] -

---
 Scripts/Scratch Pad.py                      |  3 ++-
 psyneulink/globals/log.py                   | 28 +++++++++++++--------
 tests/documentation/global/test_log_docs.py | 12 +++++++++
 3 files changed, 31 insertions(+), 12 deletions(-)
 create mode 100644 tests/documentation/global/test_log_docs.py

diff --git a/Scripts/Scratch Pad.py b/Scripts/Scratch Pad.py
index 08f34a5a512..82db9f85a35 100644
--- a/Scripts/Scratch Pad.py	
+++ b/Scripts/Scratch Pad.py	
@@ -2299,7 +2299,8 @@ def __init__(self, error_value):
 # 0,  1.
 # 1,  1.
 
-print(my_mech_A.log.nparray(entries=['noise', 'RESULTS'], header=False, owner_name=True))
+x = my_mech_A.log.nparray(entries=['noise', 'RESULTS'], header=False, owner_name=True)
+assert True
 
 # my_mech_A = pnl.TransferMechanism(name='my_mech_1A')
 # print(my_mech_A.loggable_items)
diff --git a/psyneulink/globals/log.py b/psyneulink/globals/log.py
index 0017f01c8ec..cfa62cfac43 100644
--- a/psyneulink/globals/log.py
+++ b/psyneulink/globals/log.py
@@ -128,14 +128,15 @@
 `MappingProjection` from the first to the second::
 
     # Create a Process with two TransferMechanisms:
+    >>> import psyneulink as pnl
     >>> my_mech_A = pnl.TransferMechanism(name='mech_A')
     >>> my_mech_B = pnl.TransferMechanism(name='mech_B')
     >>> my_process = pnl.Process(pathway=[my_mech_A, my_mech_B])
 
-    # Print the loggable items for each Mechanism:
-    >>> print(my_mech_A.loggable_items)
+    # Show the loggable items for each Mechanism:
+    >>> my_mech_A.loggable_items # doctest: +SKIP
     {'Process-0_Input Projection': 'OFF', 'InputState-0': 'OFF', 'slope': 'OFF', 'RESULTS': 'OFF', 'intercept': 'OFF', 'noise': 'OFF', 'time_constant': 'OFF'}
-    >>> print(my_mech_B.loggable_items)
+    >>> my_mech_B.loggable_items # doctest: +SKIP
     {'InputState-0': 'OFF', 'slope': 'OFF', 'MappingProjection from mech_A to mech_B': 'OFF', 'RESULTS': 'OFF', 'intercept': 'OFF', 'noise': 'OFF', 'time_constant': 'OFF'}
 
 Notice that ``my_mech_B`` includes its `MappingProjection` from ``my_mech_A`` (created by the `Process`) in its list of
@@ -158,16 +159,18 @@
 
     # Execute each Process twice (to generate some values in the logs):
     >>> my_process.execute()
+    array([ 0.])
     >>> my_process.execute()
+    array([ 0.])
 
     # Print the logged items of each Mechanism:
-    >>> print(my_mech_A.logged_items)
+    >>> my_mech_A.logged_items  # doctest: +SKIP
     {'RESULTS': 'EXECUTION', 'noise': 'EXECUTION'}
-    >>> print(my_mech_B.logged_items)
+    >>> my_mech_B.logged_items  # doctest: +SKIP
     {'MappingProjection from mech_A to mech_B': 'EXECUTION'}
 
     # Print the Logs for each Mechanism:
-    >>> my_mech_A.log.print_entries()
+    >>> my_mech_A.log.print_entries() # doctest: +SKIP
     Log for mech_A:
 
     Entry     Logged Item:                                       Context                                                                 Value
@@ -179,7 +182,7 @@
     0         'noise'...........................................' EXECUTING  PROCESS Process-0'.......................................    0.0
     1         'noise'...........................................' EXECUTING  PROCESS Process-0'.......................................    0.0
 
-    >>> my_mech_B.log.print_entries()
+    >>> my_mech_B.log.print_entries() # doctest: +SKIP
     Log for mech_B:
 
     Entry     Logged Item:                                       Context                                                                 Value
@@ -187,12 +190,14 @@
     0         'MappingProjection from mech_A to mech_B'.........' EXECUTING  PROCESS Process-0'.......................................     1.
     1         'MappingProjection from mech_A to mech_B'.........' EXECUTING  PROCESS Process-0'.......................................     1.
 
-    # Display the csv formatted entries of each Log
-    >>> print(my_mech_A.log.csv(entries=['noise', 'RESULTS'], owner_name=False, quotes=None))
+    # Display the csv formatted entries of each Log (``my_mech_A`` without quotes around values, and ``my_mech_B``
+    with quotes)::
+
+    >>> my_mech_A.log.csv(entries=['noise', 'RESULTS'], owner_name=False, quotes=None) # doctest: +SKIP
     'Entry', 'noise'
     0,  0.
     1,  0.
-    >>> print(my_mech_B.log.csv(entries=proj_A_to_B.name, owner_name=False, quotes=True))
+    >>> my_mech_B.log.csv(entries=proj_A_to_B.name, owner_name=False, quotes=True) # doctest: +SKIP
     'Entry', 'MappingProjection from mech_A to mech_B'
     0, ' 1.'
     1, ' 1.'
@@ -280,6 +285,7 @@
 import typecheck as tc
 from collections import namedtuple
 from enum import IntEnum
+
 import numpy as np
 
 from psyneulink.globals.keywords import kwContext, kwTime, kwValue
@@ -514,7 +520,7 @@ def logged_items(self):
         log_level = 'LogLevel.'
         # Return LogLevel for items in log.entries
         logged_items = {key: value for (key, value) in
-                        [(l, log_level+self.owner.logPref.name)
+                        [(l, self.loggable_items[l])
                          for l in self.entries.keys()]}
         return logged_items
 
diff --git a/tests/documentation/global/test_log_docs.py b/tests/documentation/global/test_log_docs.py
new file mode 100644
index 00000000000..5ef906ddf22
--- /dev/null
+++ b/tests/documentation/global/test_log_docs.py
@@ -0,0 +1,12 @@
+import pytest
+
+import psyneulink as pnl
+import doctest
+
+
+def test_log_docs():
+    fail, total = doctest.testmod(pnl.globals.log)
+
+    if fail > 0:
+        pytest.fail("{} out of {} examples failed".format(fail, total),
+                    pytrace=False)

From f7d2b5e11025b250e92cf1b745d0240e275cf94e Mon Sep 17 00:00:00 2001
From: "jdc@princeton.edu" <jdc@princeton.edu>
Date: Tue, 5 Dec 2017 11:44:54 -0500
Subject: [PATCH 5/9] =?UTF-8?q?=E2=80=A2=20Log=20=20=20-=20logged=5Fitems:?=
 =?UTF-8?q?=20fixed=20bug=20erroneously=20reporting=20LogLevels=20as=20OFF?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

• Tests
  - added tests/global
  - added tests/global/test_log_docs
---
 Scripts/Scratch Pad.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Scripts/Scratch Pad.py b/Scripts/Scratch Pad.py
index 82db9f85a35..baffa04bd39 100644
--- a/Scripts/Scratch Pad.py	
+++ b/Scripts/Scratch Pad.py	
@@ -2300,7 +2300,6 @@ def __init__(self, error_value):
 # 1,  1.
 
 x = my_mech_A.log.nparray(entries=['noise', 'RESULTS'], header=False, owner_name=True)
-assert True
 
 # my_mech_A = pnl.TransferMechanism(name='my_mech_1A')
 # print(my_mech_A.loggable_items)

From 07b1316df6be7256dc6d5bef9494a5979bb42af2 Mon Sep 17 00:00:00 2001
From: "jdc@princeton.edu" <jdc@princeton.edu>
Date: Tue, 5 Dec 2017 11:47:05 -0500
Subject: [PATCH 6/9] -

---
 Scripts/Scratch Pad.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Scripts/Scratch Pad.py b/Scripts/Scratch Pad.py
index baffa04bd39..6ca564e1d3b 100644
--- a/Scripts/Scratch Pad.py	
+++ b/Scripts/Scratch Pad.py	
@@ -2299,7 +2299,7 @@ def __init__(self, error_value):
 # 0,  1.
 # 1,  1.
 
-x = my_mech_A.log.nparray(entries=['noise', 'RESULTS'], header=False, owner_name=True)
+my_mech_A.log.nparray(entries=['noise', 'RESULTS'], header=False, owner_name=True)
 
 # my_mech_A = pnl.TransferMechanism(name='my_mech_1A')
 # print(my_mech_A.loggable_items)

From 9bf1e8744941a91ff11f1c5702ec0debee274899 Mon Sep 17 00:00:00 2001
From: "jdc@princeton.edu" <jdc@princeton.edu>
Date: Tue, 5 Dec 2017 12:59:38 -0500
Subject: [PATCH 7/9] =?UTF-8?q?=E2=80=A2=C2=A0Log=20=20=20-=20docstring:?=
 =?UTF-8?q?=20fixed=20some=20types?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

• Component
  - docstring: added entries for Log
---
 psyneulink/components/component.py | 9 +++++++++
 psyneulink/globals/log.py          | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/psyneulink/components/component.py b/psyneulink/components/component.py
index 53e391091a4..477ee65e519 100644
--- a/psyneulink/components/component.py
+++ b/psyneulink/components/component.py
@@ -135,6 +135,12 @@
   `function <Component.function>` after the function is called.
 ..
 
+.. _Component_Log:
+
+* **log** - the `log <Component.log>` attribute contains the Component's `Log`, in which its `value <Component.value>`
+  can be recorded during initialization, validation and/or execution.
+..
+
 .. _Component_Name:
 
 * **name** - the `name <Component.name>` attribute contains the name assigned to the Component when it was created.
@@ -661,6 +667,9 @@ class Component(object):
     value : 2d np.array
         see `value <Component_Value>`
 
+    log : Log
+        see `log <Component_Log>`
+
     name : str
         see `name <Component_Name>`
 
diff --git a/psyneulink/globals/log.py b/psyneulink/globals/log.py
index cfa62cfac43..466916ae94b 100644
--- a/psyneulink/globals/log.py
+++ b/psyneulink/globals/log.py
@@ -23,7 +23,7 @@
 <Component.log>` attribute when the Component is created, that can be used to record its value and/or that of other
 Components that belong to it.  These are stored in `entries <Log.entries>` of the Log, that contain a sequential list
 of the recorded values, along with the time and context of the recording.  The conditions under which values are
-recorded is specified by the `logPref <Component.logPref` property of a Component.  While these can be set directly,
+recorded is specified by the `logPref <Component.logPref>` property of a Component.  While these can be set directly,
 they are most easily managed using three convenience methods assigned to every Component along with its `log
 <Component.log>` -- `loggable_items <Log.loggable_items>`, `log_items <Log.log_items>` and `logged_items
 <Log.logged_items>` -- that identify, specify and track items the items being logged, respectively.  This can be

From 4653b307d94911bc62071613bbe00e90c15bfb56 Mon Sep 17 00:00:00 2001
From: "jdc@princeton.edu" <jdc@princeton.edu>
Date: Tue, 5 Dec 2017 13:01:17 -0500
Subject: [PATCH 8/9] -

---
 psyneulink/globals/log.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/psyneulink/globals/log.py b/psyneulink/globals/log.py
index 466916ae94b..b62dc146d07 100644
--- a/psyneulink/globals/log.py
+++ b/psyneulink/globals/log.py
@@ -19,7 +19,7 @@
 --------
 
 A Log object is used to record the `value <Component.value>` of PsyNeuLink Components during their "life cycle" (i.e.,
-when they are created, validated, and/or executed).  Every Component has a log object, assigned to its `log
+when they are created, validated, and/or executed).  Every Component has a Log object, assigned to its `log
 <Component.log>` attribute when the Component is created, that can be used to record its value and/or that of other
 Components that belong to it.  These are stored in `entries <Log.entries>` of the Log, that contain a sequential list
 of the recorded values, along with the time and context of the recording.  The conditions under which values are

From a4b9d5d49fed660bab62c59a0da88a79ecf4bdbb Mon Sep 17 00:00:00 2001
From: "jdc@princeton.edu" <jdc@princeton.edu>
Date: Tue, 5 Dec 2017 16:32:00 -0500
Subject: [PATCH 9/9] =?UTF-8?q?=E2=80=A2=20Log=20=20=20-=20docstring=20cor?=
 =?UTF-8?q?rections?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 psyneulink/globals/log.py | 44 +++++++++++++++++++--------------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/psyneulink/globals/log.py b/psyneulink/globals/log.py
index b62dc146d07..fa84e13c7ca 100644
--- a/psyneulink/globals/log.py
+++ b/psyneulink/globals/log.py
@@ -27,7 +27,7 @@
 they are most easily managed using three convenience methods assigned to every Component along with its `log
 <Component.log>` -- `loggable_items <Log.loggable_items>`, `log_items <Log.log_items>` and `logged_items
 <Log.logged_items>` -- that identify, specify and track items the items being logged, respectively.  This can be
-useful not only for observing the behavior of Compnents in a model, but also in debugging them during construction.
+useful not only for observing the behavior of Components in a model, but also in debugging them during construction.
 The entries of a Log can be displayed in a "human readable" table using its `print_entries <Log.print_entries>`
 method, and returned in CSV and numpy array formats using its `csv <Log.csv>` and `nparray <Log.nparray>` methods.
 
@@ -42,7 +42,7 @@
 
 A log object is automatically created for and assigned to a Component's `log <Component.log>` attribute when the
 Component is created.  An entry is automatically created and added to the Log's `entries <Log.entries>` attribute
-when its `value <Component.value>` or that of a Component that belongs to it is recorded in the log.
+when its `value <Component.value>` or that of a Component that belongs to it is recorded in the Log.
 
 Structure
 ---------
@@ -72,7 +72,7 @@
       assign to that Component, or in a list with a `LogLevel` to be applied to multiple items at once.
     ..
     * `logged_items <Log.logg_items>` -- returns a list with the name of Components that currently have `entries <Log>`
-      in the log.
+      in the Log.
     ..
     * `print_entries <Log.print_entries>` -- this prints a formatted list of the `entries <Log.entries>` in the Log.
     ..
@@ -205,10 +205,10 @@
 
 COMMENT:
 
-Entries are made to the log based on the `LogLevel` specified in the
+Entries are made to the Log based on the `LogLevel` specified in the
 `logPref` item of the component's `prefs <Component.prefs>` attribute.
 
-Adding an item to prefs.logPref will validate and add an entry for that attribute to the log dict
+Adding an item to prefs.logPref will validate and add an entry for that attribute to the Log dict
 
 An attribute is logged if:
 
@@ -234,7 +234,7 @@
 Structure
 ---------
 
-Each entry of log.entries has:
+Each entry of `entries <Log.entries>` has:
     + a key that is the name of the attribute being logged
     + a value that is a list of sequentially entered LogEntry tuples since recording of the attribute began
     + each tuple has three items:
@@ -381,7 +381,7 @@ def __str__(self):
 #endregion
 
 class Log:
-    """Maintain a log for an object, which contains a dictionary of attributes being logged and their value(s).
+    """Maintain a Log for an object, which contains a dictionary of attributes being logged and their value(s).
 
     COMMENT:
     Description:
@@ -460,15 +460,15 @@ class Log:
     ALL_LOG_ENTRIES = 'all_log_entries'
 
     def __init__(self, owner, entries=None):
-        """Initialize log with list of entries
+        """Initialize Log with list of entries
 
         Each item of the entries list should be a string designating a Component to be logged;
         Initialize self.entries dict, each entry of which has a:
         - key corresponding to an attribute of the object to be logged
         - value that is a list of sequentially logged values
 
-        :parameter owner: (object in Function hierarchy) - parent object that owns the log object)
-        :parameter entries: (list) - list of keypaths used as keys for entries in the log dict
+        :parameter owner: (object in Function hierarchy) - parent object that owns the Log object)
+        :parameter entries: (list) - list of keypaths used as keys for entries in the Log dict
         """
 
         self.owner = owner
@@ -593,7 +593,7 @@ def print_entries(self, entries=None, csv=False, synch_time=False, *args):
         Print values of entries
 
         If entries is the keyword *ALL_ENTRIES*, print all entries in the self.owner.prefs.logPref list
-        Issue a warning if an entry is not in the log dict
+        Issue a warning if an entry is not in the Log dict
         """
 
         # If Log.ALL_LOG_ENTRIES, set entries to all entries in self.entries
@@ -646,7 +646,7 @@ def print_entries(self, entries=None, csv=False, synch_time=False, *args):
             try:
                 datum = self.entries[attrib_name]
             except KeyError:
-                warnings.warn("{0} is not an entry in the log for {1}".
+                warnings.warn("{0} is not an entry in the Log for {1}".
                       format(attrib_name, self.owner.name))
             else:
                 import numpy as np
@@ -750,7 +750,7 @@ def csv(self, entries=None, owner_name:bool=False, quotes:tc.optional(tc.any(boo
 
         # Currently only supports entries of the same length
         if not all(len(self.entries[e])==len(self.entries[entries[0]])for e in entries):
-            raise LogError("CSV output currently only supported for log entries of equal length")
+            raise LogError("CSV output currently only supported for Log entries of equal length")
 
         if not quotes:
             quotes = ""
@@ -854,7 +854,7 @@ def nparray(self,
 
         # Currently only supports entries of the same length
         if not all(len(self.entries[e])==len(self.entries[entries[0]])for e in entries):
-            raise LogError("CSV output currently only supported for log entries of equal length")
+            raise LogError("CSV output currently only supported for Log entries of equal length")
 
         if owner_name is True:
             owner_name_str = self.owner.name
@@ -895,7 +895,7 @@ def delete_entry(self, entries, confirm=True):
         Entries can be a single entry, a list of entries, or the keyword Log.ALL_LOG_ENTRIES;
         Notes:
         * only a single confirmation will occur for a list or Log.ALL_LOG_ENTRIES
-        * deleting entries removes them from log dict, owner.prefs.logPref, and deletes ALL data recorded in them
+        * deleting entries removes them from Log dict, owner.prefs.logPref, and deletes ALL data recorded in them
 
         :param entries: (str, list, or Log.ALL_LOG_ENTRIES)
         :param confirm: (bool)
@@ -919,7 +919,7 @@ def delete_entry(self, entries, confirm=True):
                 try:
                     self.entries[entry]
                 except KeyError:
-                    warnings.warn("Warning: {0} is not an entry in log of {1}".
+                    warnings.warn("Warning: {0} is not an entry in Log of {1}".
                                   format(entry,self.owner.name))
                     del(entries, entry)
             if len(entries) > 1:
@@ -928,10 +928,10 @@ def delete_entry(self, entries, confirm=True):
         # If any entries remain
         if entries:
             if confirm:
-                delete = input("\n{0} will be deleted (along with any recorded date) from log for {1}.  Proceed? (y/n)".
+                delete = input("\n{0} will be deleted (along with any recorded date) from Log for {1}.  Proceed? (y/n)".
                                format(msg, self.owner.name))
                 while delete != 'y' and delete != 'y':
-                    input("\nRemove entries from log for {0}? (y/n)".format(self.owner.name))
+                    input("\nRemove entries from Log for {0}? (y/n)".format(self.owner.name))
                 if delete == 'n':
                     warnings.warn("No entries deleted")
                     return
@@ -943,7 +943,7 @@ def delete_entry(self, entries, confirm=True):
                     del(self.owner.prefs.logPref, entry)
 
     def reset_entries(self, entries, confirm=True):
-        """Reset one or more entries by removing all data, but leaving entries in log dict
+        """Reset one or more entries by removing all data, but leaving entries in Log dict
 
         If verify is True, user will be asked to confirm the reset;  otherwise it will simply be done
         Entries can be a single entry, a list of entries, or the keyword Log.ALL_LOG_ENTRIES;
@@ -969,14 +969,14 @@ def reset_entries(self, entries, confirm=True):
             try:
                 self.entries[entry]
             except KeyError:
-                warnings.warn("Warning: {0} is not an entry in log of {1}".
+                warnings.warn("Warning: {0} is not an entry in Log of {1}".
                               format(entry,self.owner.name))
                 del(entries, entry)
 
         # If any entries remain
         if entries:
             if confirm:
-                delete = input("\nAll data will be deleted from {0} in the log for {1}.  Proceed? (y/n)".
+                delete = input("\nAll data will be deleted from {0} in the Log for {1}.  Proceed? (y/n)".
                                format(entries,self.owner.name))
                 while delete != 'y' and delete != 'y':
                     input("\nDelete all data from entries? (y/n)")
@@ -990,7 +990,7 @@ def reset_entries(self, entries, confirm=True):
     def suspend_entries(self, entries):
         """Suspend recording the values of attributes corresponding to entries even if logging is on
 
-        Remove entries from self.owner.prefs.logPref (but leave in log dict, i.e., self.entries)
+        Remove entries from self.owner.prefs.logPref (but leave in Log dict, i.e., self.entries)
 
         :param entries: (str or list)
         :return: