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Refactor/ocm/state features all as input ports #2350

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merged 334 commits into from
Mar 18, 2022

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@jdcpni jdcpni commented Mar 18, 2022

• optimizationcontrolmechanism.py:

  • implement state_faature_default
  • add SHADOW_INPUTS as individual spec for state_features
  • refactor _validate_state_features() around use of InputPorts rather than INPUT Node

• inputport.py:

  • add examples/figures for input shadowing

jdcpni and others added 30 commits November 21, 2021 11:20
   - 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
jdcpni and others added 23 commits March 16, 2022 10:04
  - _parse_names_in_inputs(): support Port.full_name as keys in inputs dict

• mechanism.py:
  - Mechanism_Base: replaced input_labels and output_labels with labeled_input_values and labeled_output_values respectively

• port.py, inputport.py, outputport.py, parameterport.py:
  - Port_Base: impelment labeled_value property (and value_label alias) that returns calls get_label()
  - deleted label attributes of InputPort and OutputPort (replaced by Port_Base.labeled_value)
  - added get_label() stub on ParameterPort with error message
  comment out 'sphinx_autodoc_typehints' (crashing for sphinx_autodoc_typehints v.1.17.0)
  restore 'sphinx_autodoc_typehints'

• doc_requirements.txt:
  pin sphinx_autodoc_typehints < v.1.16.0;  error on v1.16 and v1.17;  error:
  https://github.com/PrincetonUniversity/PsyNeuLink/runs/5573651890?check_suite_focus=true
  - add property: external_input_ports_of_all_input_nodes

• optimizationcontrolmechanism.py:
  - implement state_faature_default
  - add SHADOW_INPUTS as individual spec for state_features
  - add property: external_input_ports_of_all_input_nodes

• optimizationcontrolmechanism.py:
  - implement state_faature_default
  - add SHADOW_INPUTS as individual spec for state_features
  - add figure for shadowing
…Link into refactor/ocm/state_features_all_as_input_ports

� Conflicts:
�	psyneulink/core/components/mechanisms/modulatory/control/optimizationcontrolmechanism.py
�	psyneulink/core/components/ports/parameterport.py
�	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
606,608c606,608
< outer Composition, are assigned <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> in addition to their other <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="pre">roles</span></code></a> in the
< nested Composition.  The only difference between <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes
< is whether their output is included in the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the <em>outermost</em> Composition to which they project; this is determined by the
---
> outer Composition, are assigned <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> in addition to their other <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="pre">roles</span></code></a> in the
> nested Composition.  The only difference between <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes
> is whether their output is included in the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the <em>outermost</em> Composition to which they project; this is determined by the
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< <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are <em>not</em> included in the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> for the outermost Composition to which they project (although they <em>are</em> still included
---
> <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are <em>not</em> included in the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> for the outermost Composition to which they project (although they <em>are</em> still included
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< <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> is True, then any <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes
---
> <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> is True, then any <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes
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< the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition.
< <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes can be visualized, along with any Projections treated differently from those of
---
> the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition.
> <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes can be visualized, along with any Projections treated differently from those of
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< <div><p><a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are useful for <a class="reference internal" href="OptimizationControlMechanism.html#optimizationcontrolmechanism-model-based"><span class="std std-ref">model-based optimization using an</span></a>, in which the value of one or more Nodes in a nested Composition
---
> <div><p><a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are useful for <a class="reference internal" href="OptimizationControlMechanism.html#optimizationcontrolmechanism-model-based"><span class="std std-ref">model-based optimization using an</span></a>, in which the value of one or more Nodes in a nested Composition
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< include the InputPorts of the nested Composition.  These can be accessed using the Composition’s <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">exernal_input_ports</span></code></a> attribute.</p>
---
> include the InputPorts of the nested Composition.  These can be accessed using the Composition’s <a class="reference internal" href="#id20" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">exernal_input_ports</span></code></a> attribute.</p>
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< both the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the nested Composition
---
> both the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the nested Composition
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< <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition
---
> <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition
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< <a class="reference internal" href="OutputPort.html#psyneulink.core.components.ports.outputport.OutputPort.value" title="psyneulink.core.components.ports.outputport.OutputPort.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> of a corresponding OutputPort.  The latter are assigned to the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition.  If the Composition
---
> <a class="reference internal" href="OutputPort.html#psyneulink.core.components.ports.outputport.OutputPort.value" title="psyneulink.core.components.ports.outputport.OutputPort.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> of a corresponding OutputPort.  The latter are assigned to the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition.  If the Composition
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< enclosing Composition, its <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> are included in those of the enclosing
< Composition.  If the Composition has an <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes, then they too project to the Composition’s
< output_CIM.  If the Composition is nested in another, then the <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">values</span></code></a> of the <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are also included in the Composition’s <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a>;  if it
< is an outer Composition (i.e. not nested in any other), then the Compositions’ <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> attribute determines whether their values are included in its <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes (see <a class="reference interna
...

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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
606,608c606,608
< outer Composition, are assigned <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> in addition to their other <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="pre">roles</span></code></a> in the
< nested Composition.  The only difference between <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes
< is whether their output is included in the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the <em>outermost</em> Composition to which they project; this is determined by the
---
> outer Composition, are assigned <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> in addition to their other <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="pre">roles</span></code></a> in the
> nested Composition.  The only difference between <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes
> is whether their output is included in the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the <em>outermost</em> Composition to which they project; this is determined by the
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< <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are <em>not</em> included in the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> for the outermost Composition to which they project (although they <em>are</em> still included
---
> <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are <em>not</em> included in the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> for the outermost Composition to which they project (although they <em>are</em> still included
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< <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> is True, then any <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes
---
> <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> is True, then any <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes
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< the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition.
< <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes can be visualized, along with any Projections treated differently from those of
---
> the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition.
> <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes can be visualized, along with any Projections treated differently from those of
626c626
< <div><p><a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are useful for <a class="reference internal" href="OptimizationControlMechanism.html#optimizationcontrolmechanism-model-based"><span class="std std-ref">model-based optimization using an</span></a>, in which the value of one or more Nodes in a nested Composition
---
> <div><p><a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are useful for <a class="reference internal" href="OptimizationControlMechanism.html#optimizationcontrolmechanism-model-based"><span class="std std-ref">model-based optimization using an</span></a>, in which the value of one or more Nodes in a nested Composition
650c650
< include the InputPorts of the nested Composition.  These can be accessed using the Composition’s <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">exernal_input_ports</span></code></a> attribute.</p>
---
> include the InputPorts of the nested Composition.  These can be accessed using the Composition’s <a class="reference internal" href="#id20" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">exernal_input_ports</span></code></a> attribute.</p>
653c653
< both the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the nested Composition
---
> both the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the nested Composition
655c655
< <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition
---
> <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition
691c691
< <a class="reference internal" href="OutputPort.html#psyneulink.core.components.ports.outputport.OutputPort.value" title="psyneulink.core.components.ports.outputport.OutputPort.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> of a corresponding OutputPort.  The latter are assigned to the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition.  If the Composition
---
> <a class="reference internal" href="OutputPort.html#psyneulink.core.components.ports.outputport.OutputPort.value" title="psyneulink.core.components.ports.outputport.OutputPort.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> of a corresponding OutputPort.  The latter are assigned to the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition.  If the Composition
695,698c695,698
< enclosing Composition, its <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> are included in those of the enclosing
< Composition.  If the Composition has an <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes, then they too project to the Composition’s
< output_CIM.  If the Composition is nested in another, then the <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">values</span></code></a> of the <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are also included in the Composition’s <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a>;  if it
< is an outer Composition (i.e. not nested in any other), then the Compositions’ <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> attribute determines whether their values are included in its <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes (see <a class="reference interna
...

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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
606,608c606,608
< outer Composition, are assigned <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> in addition to their other <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="pre">roles</span></code></a> in the
< nested Composition.  The only difference between <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes
< is whether their output is included in the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the <em>outermost</em> Composition to which they project; this is determined by the
---
> outer Composition, are assigned <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> in addition to their other <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="pre">roles</span></code></a> in the
> nested Composition.  The only difference between <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes
> is whether their output is included in the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the <em>outermost</em> Composition to which they project; this is determined by the
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< <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are <em>not</em> included in the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> for the outermost Composition to which they project (although they <em>are</em> still included
---
> <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are <em>not</em> included in the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> for the outermost Composition to which they project (although they <em>are</em> still included
615c615
< <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> is True, then any <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes
---
> <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> is True, then any <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes
617,618c617,618
< the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition.
< <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes can be visualized, along with any Projections treated differently from those of
---
> the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition.
> <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes can be visualized, along with any Projections treated differently from those of
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< <div><p><a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are useful for <a class="reference internal" href="OptimizationControlMechanism.html#optimizationcontrolmechanism-model-based"><span class="std std-ref">model-based optimization using an</span></a>, in which the value of one or more Nodes in a nested Composition
---
> <div><p><a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are useful for <a class="reference internal" href="OptimizationControlMechanism.html#optimizationcontrolmechanism-model-based"><span class="std std-ref">model-based optimization using an</span></a>, in which the value of one or more Nodes in a nested Composition
650c650
< include the InputPorts of the nested Composition.  These can be accessed using the Composition’s <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">exernal_input_ports</span></code></a> attribute.</p>
---
> include the InputPorts of the nested Composition.  These can be accessed using the Composition’s <a class="reference internal" href="#id20" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">exernal_input_ports</span></code></a> attribute.</p>
653c653
< both the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the nested Composition
---
> both the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the nested Composition
655c655
< <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition
---
> <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> of the outermost Composition
691c691
< <a class="reference internal" href="OutputPort.html#psyneulink.core.components.ports.outputport.OutputPort.value" title="psyneulink.core.components.ports.outputport.OutputPort.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> of a corresponding OutputPort.  The latter are assigned to the <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition.  If the Composition
---
> <a class="reference internal" href="OutputPort.html#psyneulink.core.components.ports.outputport.OutputPort.value" title="psyneulink.core.components.ports.outputport.OutputPort.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> of a corresponding OutputPort.  The latter are assigned to the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition.  If the Composition
695,698c695,698
< enclosing Composition, its <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> are included in those of the enclosing
< Composition.  If the Composition has an <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes, then they too project to the Composition’s
< output_CIM.  If the Composition is nested in another, then the <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">values</span></code></a> of the <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are also included in the Composition’s <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a>;  if it
< is an outer Composition (i.e. not nested in any other), then the Compositions’ <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> attribute determines whether their values are included in its <a class="reference internal" href="#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes (see <a class="reference interna
...

See CI logs for the full diff.

@jdcpni jdcpni merged commit 8e5d581 into devel Mar 18, 2022
@jdcpni jdcpni deleted the refactor/ocm/state_features_all_as_input_ports branch March 18, 2022 21:47
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