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Refactor/control signal/update to intensity #613

Merged
merged 68 commits into from
Dec 24, 2017
Merged

Refactor/control signal/update to intensity #613

merged 68 commits into from
Dec 24, 2017

Commits on Nov 30, 2017

  1. • System 

      - show_graph():
    fixed bug producing empty image for graphs with just one Mechanism
    added auto-recurrent projections
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  2. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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Commits on Dec 4, 2017

  1. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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Commits on Dec 5, 2017

  1. • Log 

      - added numpy_array output method
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  2. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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  3. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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Commits on Dec 7, 2017

  1. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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  2. -

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Commits on Dec 10, 2017

  1. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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  2. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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  3. -

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  15. Merge branch 'feat/Log/clean_up' into devel

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  16. -

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  17. • Log 

      - fixed bugs preventing logging during INITIALIZATION
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  18. • Log 

      - fixed bugs preventing logging during INITIALIZATION
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Commits on Dec 11, 2017

  1. -

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  8. • Log 

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

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

• Tests
  test_log:  added test_log_initialization
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  10. • 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
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  11. • Log 

      - log_value: added

• Tests
  - test_multilayer: added test of log_value
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  12. • 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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  13. • 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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  14. • 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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  15. Merge branch 'feat/Log/add_entry' into devel 

    # Conflicts:
#	Scripts/Scratch Pad.py
#	psyneulink/globals/log.py
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  16. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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Commits on Dec 12, 2017

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  2. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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  3. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

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  4. • Component 

      - moved value property to Component (from Mechanism, Projection and State)
    (left an override on ControlSignal that needs it for the getter)
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Commits on Dec 13, 2017

  1. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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  2. • Log 

      - docstring: added hint about using call_before_trial and call_after_trial
    to log values
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  3. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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  4. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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Commits on Dec 14, 2017

  1. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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  2. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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Commits on Dec 15, 2017

  1. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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  2. -

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  3. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel

# Conflicts:
#	Scripts/Nieuwenhuis_documented.py
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Commits on Dec 18, 2017

  1. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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  2. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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Commits on Dec 19, 2017

  1. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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Commits on Dec 21, 2017

  1. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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  2. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into devel
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Commits on Dec 23, 2017

  1. Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu… 

    …Link into names/ControlSignal/intensity_to_value
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  2. • IntegratorMechanisms 

      classPreferences:  changed reportOutputPref from True to False
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  3. • IntegratorMechanisms 

      classPreferences:  changed reportOutputPref from True to False

• ControlSignal
  update():  added notes regarding additional refactoring needed
  value.setter: now assigns value to intensity
                (though assignment of intensity still overrides
                 assignment of value in super().update)
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Commits on Dec 24, 2017

  1. • ControlSignal 

      _update(): renamed as compute_costs()
             calls super to set self.value
             uses self.value to update costs
             intensity is only used for local purposes
                 and is no longer assigned to self.value
             passes all tests except GilzenratModel
                 (which uses LCControlMechanism)
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  2. • ControlSignal 

      _update(): now just calls super() and _compute_costs()
  _compute_costs(): calls super to set self.value
                    uses self.value to update costs
                    intensity is only used for local purposes
                        and is no longer assigned to self.value
                    passes all tests except test_default_lc_control_mechanism
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  3. • ControlSignal 

      _update(): now just calls super() and _compute_costs()
  _compute_costs(): calls super to set self.value
                    uses self.value to update costs
                    intensity is only used for local purposes
                        and is no longer assigned to self.value
                    passes all tests except test_default_lc_control_mechanism
  _execute(): added (to parallel GatingSignal);
              returns float(super()._execute())
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  4. • ControlSignal 

      _update(): now just calls super() and _compute_costs()
  _compute_costs(): calls super to set self.value
                    uses self.value to update costs
                    intensity is only used for local purposes
                        and is no longer assigned to self.value
                    passes all tests except test_default_lc_control_mechanism
  _execute(): added (to parallel GatingSignal);
              returns float(super()._execute())
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  5. • ControlSignal 

      _update(): now just calls super() and _compute_costs()
  _compute_costs(): calls super to set self.value
                    uses self.value to update costs
                    intensity is only used for local purposes
                        and is no longer assigned to self.value
                    passes all tests except test_default_lc_control_mechanism
  _execute(): added (to parallel GatingSignal);
              returns float(super()._execute())
    @jdcpni
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