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Feat/comp/inputs #2259

Merged
merged 366 commits into from
Dec 23, 2021
Merged

Feat/comp/inputs #2259

merged 366 commits into from
Dec 23, 2021

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jdcpni
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@jdcpni jdcpni commented Dec 23, 2021

• composition.py
  - add _check_for_unused_projections(): warns if any projections are specified for Nodes that are not used in the comp
  -  _update_shadow_projections: report error for failure to find correct_sender

jdcpni and others added 30 commits November 21, 2021 16:12
   - test_parameterestimationcomposition
   - test_composition/test_partially_overlapping_control_specs (ADDED IN THIS COMMINT)

- All relevant changes to this branch are marked as "11/21/21."
  However, most are commented out as they break other things.

- The tests above both involve local control specifications (on mechanism within a nested comp)
  and on the OCM for the outer composition, some of which are for the same nested mechs

- Both tests fail with:
   "AttributeError: 'NoneType' object has no attribute '_get_by_time_scale'" (in component.py LINE 3276)
   This may be due to a problem with context setting, since the error is because the modulation Parameter
   of the ControlProjection is returning "None" rather than "multiplicative_param" (when called with get(context)),
   whereas "multiplicative_param" is returned with a call to get() (i.e., with no context specified)

- Most of test_partially_overlapping_control_specs is passed if
   changes marked "11/21/21 NEW" in optimizationcontrolmechanism.py (LINE 1390) are implemented,
   but it does not properly route ControlProjections through parameter_CIMS (see last assert in test).
   Furthermore, test_parameterestimationcompsition fails with the mod param error, even though the
   model has similar structure (i.e., outer composition -- in this case a ParameterEstimationComposition)
   with an OCM that is given control specs that overlap with ones in a nested composition.

- There are also several other things in composition I found puzzling and tried modifying, but that cuased failures:
  - _get_control_signals_for_composition():
      - seems "if node.controller" should be "if **not** node.controller" (emphasis added just for comment)
      - "append" should be "extend"
  - _instantiate_control_projection():
      -  call to self.controller._activate_projections_for_composition (at end of method) should not be indented
  - rename _check_projection_initialization_status -> _check_controller_initialization_status
  - add _check_nodes_initialization_status(context=context)
    (and calls it with _check_controller_initialization_status)
  retore append of control_signals in _instantiate_control_projections()
  restore append of control_signals in _instantiate_control_projections()

• test_composition.py:
  add test_partially_overlapping_local_and_control_mech_control_specs_in_unnested_and_nested_comp
…unnested_and_nested_comp():

  - added clear_registry() to allow names to be reused in both runs of test
  docstring:  added projections entry to list of attributes
  - add_controller:  added call to _add_node_aux_components() for controller
  _add_node_aux_components(): added deletion of item from aux_components if instantiated
  - comment out _add_node_aux_components() (causing new failures)
  - move _instantiate_control_projections to be with _instantiate_control_projections,
       after self.add_node(self.controller.objective_mechanism (to be more orderly)
…rtially_overlapping...

  (with addition of _add_aux_components in add_controller commented out)
…y one test:

    - test_agent_rep_assignement_as_controller_and_replacement
  - add_controller:  few more minor mods;
  still passes all tests
  - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms)
jdcpni and others added 26 commits December 21, 2021 15:51
  - get_results_by_nodes: allow specification of individual nodes
  - get_results_by_nodes: allow specification of individual nodes
  - get_results_by_nodes: allow specification of individual nodes
…sity/PsyNeuLink into feat/comp/inputs

� Conflicts:
�	psyneulink/core/compositions/composition.py
  add input_labels and output_labels as args to constructor
• composition.py:  found bug with specification of shadows and probes between "parallel" compositions.
  - updates to contribtors
  - add links to CGO paper
  _update_shadow_projections: report error for failure to find correct_sender
  - add _check_for_unused_projections(): warns if any projections are specified for Nodes that are not used in the comp
…Link into feat/comp/inputs

� Conflicts:
�	README.rst
�	psyneulink/core/compositions/composition.py
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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

diff -r docs-base/Composition.html docs-head/Composition.html
3624,3625c3624,3632
< Validate that all OuputStates with require_projection_in_composition == True have an efferent Projection.
< Validate that all Projections have senders and receivers.</p>
---
> Validate that all OutputPorts with require_projection_in_composition == True have an efferent Projection.
> Validate that all Projections have senders and receivers.
> Issue warning if any Projections are to/from nodes not in Composition.projections</p>
> </dd></dl>
> 
> <dl class="py method">
> <dt class="sig sig-object py" id="psyneulink.core.compositions.composition.Composition._check_for_unused_projections">
> <span class="sig-name descname"><span class="pre">_check_for_unused_projections</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">context</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.compositions.composition.Composition._check_for_unused_projections" title="Permalink to this definition">¶</a></dt>
> <dd><p>Warn if there are any Nodes in the Composition, or any nested within it, that are not used.</p>
diff -r docs-base/_sources/index.rst.txt docs-head/_sources/index.rst.txt
5a6,10
> .. *****************************************************************************************
> .. ****** NOTE:  UPDATES TO THIS PAGE SHOULD ALSO BE MADE TO README.rst ********************
> .. *****************************************************************************************
> 
> 
diff -r docs-base/genindex.html docs-head/genindex.html
290a291,292
>       <li><a href="Composition.html#psyneulink.core.compositions.composition.Composition._check_for_unused_projections">_check_for_unused_projections() (psyneulink.core.compositions.composition.Composition method)</a>
> </li>
649,650d650
<       <li><a href="ControlMechanism.html#psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism._instantiate_objective_mechanism">_instantiate_objective_mechanism() (psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism method)</a>
< </li>
652a653,654
>       <li><a href="ControlMechanism.html#psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism._instantiate_objective_mechanism">_instantiate_objective_mechanism() (psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism method)</a>
> </li>
Binary files docs-base/objects.inv and docs-head/objects.inv differ
diff -r docs-base/searchindex.js docs-head/searchindex.js
1c1
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...

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Coverage Status

Coverage decreased (-0.009%) to 84.272% when pulling 626b601 on feat/comp/inputs into 9979c07 on devel.

@jdcpni jdcpni merged commit 436f5d9 into devel Dec 23, 2021
@jdcpni jdcpni deleted the feat/comp/inputs branch December 23, 2021 21:33
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