Docs/log/log clean up (#592)

* • System
  - show_graph():
    fixed bug producing empty image for graphs with just one Mechanism
    added auto-recurrent projections

* • Log
  - added numpy_array output method

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* • Log
  - fixed bugs preventing logging during INITIALIZATION

* • Log
  - fixed bugs preventing logging during INITIALIZATION

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* • Log
  - logged_item, print_entries:  corrected to use 'value' rather than owner's name in reports

* • Log
  - logged_item, print_entries:  corrected to use 'value' rather than owner's name in reports

• Tests
  test_log:  added test_log_initialization

* • Log
  - _alias_owner_name:  added to used 'value' rather than owner's name in reports
  - nparray: bug fix to handle None values

• Tests
  test_log:  added test_log_initialization

* • Log
  - log_value: added

• Tests
  - test_multilayer: added test of log_value

* • Log
  - log_value: implemented
  - logged_item, print_entries:  corrected to use 'value' rather than owner's name in reports

• Tests
  - test_multilayer: added test of log_value

* • Log
  - log_value: implemented
  - logged_item, print_entries:  corrected to use 'value' rather than owner's name in reports

• Tests
  - test_multilayer: added test of log_value

* -

* • Log
  nparray(): fixed bug in which crashed if no log_entries

* • Log
  nparray(): fixed bug in reporting time in nparray output

* • Log
  docstring: fixed examples to reflect implementation of time field

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* • Log
  - nparray(): fixed bug in handling of duplicate of time values
  - docstrings: examples updated for print_entries, csv and nparray outputs

* • Log
  - nparray(): fixed bug in handling of duplicate of time values
  - docstrings: examples updated for print_entries, csv and nparray outputs

* • Log
  - LogCondition.CONTROL can now be used

* • Log
  - LogCondition.CONTROL can now be used

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Scripts/Examples/EVC-Gratton.py

@@ -2,16 +2,6 @@
 import psyneulink as pnl
 
 
-def test_search_function(controller=None, **kwargs):
-    result = np.array(controller.allocationPolicy).reshape(len(controller.allocationPolicy), -1)
-    return result
-
-
-def test_outcome_function(**kwargs):
-    result = np.array([0])
-    return result
-
-
 # Preferences:
 mechanism_prefs = pnl.ComponentPreferenceSet(
     prefs={
@@ -152,7 +142,7 @@ def test_outcome_function(**kwargs):
 # Show characteristics of system:
 mySystem.show()
 mySystem.controller.show()
-mySystem.show_graph(show_control=pnl.ALL, show_dimensions=pnl.ALL)
+# mySystem.show_graph(show_control=pnl.ALL, show_dimensions=pnl.ALL)
 
 # configure EVC components
 mySystem.controller.control_signals[0].intensity_cost_function = pnl.Exponential(rate=0.8046).function
@@ -199,8 +189,12 @@ def test_outcome_function(**kwargs):
 
 mySystem.controller.reportOutputPref = True
 
+Flanker_Rep.set_log_conditions((pnl.SLOPE, pnl.LogCondition.CONTROL))
 
 mySystem.run(
     num_trials=nTrials,
     inputs=stim_list_dict,
 )
+
+Flanker_Rep.log.print_entries()
+