Fix/log/set log conditions bug (#596)

* • 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

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* • Component
  - moved value property to Component (from Mechanism, Projection and State)
    (left an override on ControlSignal that needs it for the getter)

* • Log
  - docstring: added hint about using call_before_trial and call_after_trial
    to log values

* • Log
  - fixed failure to call _alias_owner_name in set_log_condtion

psyneulink/globals/log.py

@@ -705,7 +705,7 @@ def assign_log_level(item, level):
                 raise LogError("\'{0}\' is not a loggable item for {1} (try using \'{1}.log.add_entries()\')".
                                format(item, self.owner.name))
             try:
-                component = next(c for c in self.loggable_components if c.name == item)
+                component = next(c for c in self.loggable_components if self._alias_owner_name(c.name) == item)
                 component.logPref=PreferenceEntry(level, PreferenceLevel.INSTANCE)
             except AttributeError:
                 raise LogError("PROGRAM ERROR: Unable to set LogCondition for {} of {}".format(item, self.owner.name))