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Feat/comp/inputs #2256

Merged
merged 335 commits into from
Dec 21, 2021
Merged

Feat/comp/inputs #2256

merged 335 commits into from
Dec 21, 2021

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jdcpni
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@jdcpni jdcpni commented Dec 21, 2021

• composition.py:

  • add get_input_format()
  • add get_results_by_node()
  • _parse_labels():
    • refactor to support input_labels for nested Mechanisms
    • add error messages for no labels or wrong label

jdcpni and others added 30 commits November 18, 2021 14:04
• test_report.py: passing all tests
b6e697e
• Passes all tests!
1609acc
@jdcpni
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@jdcpni
Merge branch 'refactor/ocm/state_input_ports' of https://github.com/P…
c4b081e 
…rincetonUniversity/PsyNeuLink into refactor/ocm/state_input_ports
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@jdcpni
Merge branch 'refactor/ocm/state_input_ports' of https://github.com/P…
78f4ec6 
…rincetonUniversity/PsyNeuLink into refactor/ocm/state_input_ports
@jdcpni
• composition.py: reorganize with #region and #enregions
faaf256
@jdcpni
• composition.py: reorganize with #region and #enregions
fb9c424
@jdcpni
• controlmechanism.py, optimizationcontrolmechanism.py:
0c96840 
  - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports
  - refactored to support allow_probes option on ocm
@jdcpni
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@jdcpni
• controlmechanism.py, optimizationcontrolmechanism.py:
b1f9778 
  - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports
  - refactored to support allow_probes option on ocm
@jdcpni
• controlmechanism.py, optimizationcontrolmechanism.py:
451abb3 
  - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports
  - refactored to support allow_probes option on ocm
@jdcpni
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• composition.py:
428eed8 
  __init__: move controller to after add_nodes and add_linear_pathway
@jdcpni
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@jdcpni
- test_control: only test_hanging_control_spec_outer_controller not p…
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…assing
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@jdcpni
• composition.py:
2552f73 
  _instantiate_control_projections:
     weird requirement for double-call to controller._instantiate_control_signal
@jdcpni
• test_paremtercomposition.py:
c02735e 
  restored parameter spec that causes crash ('threshold',Decision2)
@jdcpni
ª Attempt to fix problem with partially overlapping local and ocm con…
8568b47 
…trol specs

- composition.py
  - _get_control_signals_for_composition:  (see 11/20/21)
      - added (but commented out change) to "if node.controller" to "if not node.controller"
      - changed append to extend
  - _instantiation_control_projection:
      - got rid of try and except double-call to controller._instantiate_control_signals
      -  outdented call to self.controller._activate_projections_for_composition at end

- controlmechanism.py:
    - _check_for_duplicates:  add warning and return duplicates

- optimizationcontrolmechanism._instantiate_control_signals:
    - add call to self.agent_rep._get_control_signals_for_composition() to get local control specs (on mechs in comp)
    - eliminate duplicates with control_signal specs on OCM
    - instantiate local + ocm control_signals

- parameterestimationcomposition.py
  - added context to various calls
@jdcpni
see later commit
1aadd6d
@jdcpni
see later commit
da80ad6
@jdcpni
see later commit
fa1683f
jdcpni and others added 17 commits December 20, 2021 16:22
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895d918
@jdcpni
• composition.py: docstring mods
ff1a465
@jdcpni
Merge branch 'feat/comp/inputs' of https://github.com/PrincetonUniver…
4fdef97 
…sity/PsyNeuLink into feat/comp/inputs
• composition.py - reorganize docstring section on execution
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@jdcpni
• test_composition.py / test_input_labels_and_no_orphaning_of_nested_…
654918b 
…output_nodes:

  added tests for lables in input
@jdcpni
• composition.py: _validate_single_input - get rid of tests (taken ca…
86f4c1d 
…re of in _parse_labels)
@jdcpni
• test_composition.py/test_input_labels_and_results_by_node_and_no_or…
bb0910b 
…phaning_of_nested_output_nodes:

  - renamed, add test for get_results_by_node
@jdcpni
• composition.py
7cc9a12 
  - _parse_labels:  suppress warning about targets if no learning_components in pway
@jdcpni
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@jdcpni
• composition.py: further docstring updates for get_input_format() an…
b9165bc 
…d get_results_by_node()
@jdcpni
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ca476c2
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@jdcpni
Merge branch 'devel' into feat/comp/inputs
907b334
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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

diff -r docs-base/AGTControlMechanism.html docs-head/AGTControlMechanism.html
232c232
< <p>An AGTControlMechanism is a <a class="reference internal" href="ControlMechanism.html"><span class="doc">ControlMechanism</span></a> that uses an ObjectiveMechanism with a <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code>
---
> <p>An AGTControlMechanism is a <a class="reference internal" href="ControlMechanism.html"><span class="doc">ControlMechanism</span></a> that uses an ObjectiveMechanism with a <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a>
234c234
< to regulate the <code class="xref any docutils literal notranslate"><span class="pre">mode</span></code> parameter of its <code class="xref any docutils literal notranslate"><span class="pre">FitzHughNagumoIntegrator</span></code> Function, it implements a form of the
---
> to regulate the <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator.mode" title="psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator.mode"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">mode</span></code></a> parameter of its <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">FitzHughNagumoIntegrator</span></code></a> Function, it implements a form of the
244c244
< <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code> Function as its <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
---
> <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a> Function as its <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
259c259
< ObjectiveMechanism is created automatically when the AGTControlMechanism is created, using a <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code>
---
> ObjectiveMechanism is created automatically when the AGTControlMechanism is created, using a <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a>
326c326
< <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code> as is <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
---
> <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a> as is <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
391c391
< if it is greater than there are inputs then inputs will be repeated (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a>
---
> if it is greater than there are inputs then inputs will be repeated (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a>
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
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< assigning <code class="xref any docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code> as the Mechanism’s <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> and, in the call to the Composition’s
---
> assigning <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code></a> as the Mechanism’s <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> and, in the call to the Composition’s
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< <p>The output is now the result of the <code class="xref any docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code>, which is the value of the decision variable when it
---
> <p>The output is now the result of the <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code></a>, which is the value of the decision variable when it
diff -r docs-base/Component.html docs-head/Component.html
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< arguments, so that the relevant <code class="xref any docutils literal notranslate"><span class="pre">initializer</span></code> attributes (or their equivalents
---
> arguments, so that the relevant <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction.initializer" title="psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction.initializer"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">initializer</span></code></a> attributes (or their equivalents
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< Mechanisms (see <a class="reference internal" href="Composition.html#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a>)</p>
---
> Mechanisms (see <a class="reference internal" href="Composition.html#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a>)</p>
1139c1139
< <dd><p>If the component’s execute method involves execution of an <code class="xref any docutils literal notranslate"><span class="pre">IntegratorFunction</span></code> Function, this method
---
> <dd><p>If the component’s execute method involves execution of an <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction" title="psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction"><code class="xref any py py-class docutils literal notranslate"><span class="pre">IntegratorFunction</span></code></a> Function, this method
diff -r docs-base/Composition.html docs-head/Composition.html
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< <li><p><a class="reference internal" href="#composition-execution-reporting"><span class="std std-ref">Reporting</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-execution-methods"><span class="std std-ref">Execution Methods</span></a></p></li>
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< <dt><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a></dt><dd><ul>
---
> <dt><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a></dt><dd><ul>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-input-formats"><span class="std std-ref">Input formats (including targets for learning)</span></a></dt><dd><ul>
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> </ul>
> </dd>
> </dl>
> </li>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-execution-factors"><span class="std std-ref">Execution Factors</span></a></dt><dd><ul>
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< <li><p><a class="reference internal" href="#composition-cycle"><span class="std std-ref">Cycles and synchronous execution</span></a></p></li>
< <li><p><a class="reference internal" href="#composition-feedback"><span class="std std-ref">Feedback and sequential execution</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-cycle"><span class="std std-ref">Cycles and Synchronous Execution</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-feedback"><span class="std std-ref">Feedback and Sequential Execution</span></a></p></li>
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< <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-timing"><span class="std std-ref">Timing</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a></p></li>
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> <li><p><a class="reference internal" href="#composition-execution-results-and-reporting"><span class="std std-ref">Results, Reporting and Logging</span></a></p></li>
> </ul>
> </dd>
> </dl>
> </li>
> <li><p><a class="reference internal" href="#composition-visualization"><span class="std std-ref">Visualizing a Composition</span></a></p></li>
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< <div class="admonition warning">
---
> <blockquote>
> <div><div class="admonition warning">
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> </div></blockquote>
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< <ul class="simple" id="composition-parameter-cim">
---
> <ul id="composition-parameter-cim">
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> <div class="technical-note docutils container">
> <p>The Projection from a ModulatoryMechanism to the InputPort of a parameter_CIM is the only instance in which a
> MappingProjection is used as an <a class="reference internal" href="Mechanism.html#id15" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferent</span> <span class="pre">projection</span></code></a> of a ModulatoryMechanism.</p>
> </div>
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< of a <a class="reference internal" href="UserDefinedFunction.html"><span class="doc">UserDefinedFunction</span></a>. It must be carefully coordinated with the execution of other learning-related Components in the Composition, to insure
< that each function is called at the appropriate times during execution.  Furthermore, as with an <a class="reference internal" href="AutodiffComposition.html"><span class="doc">AutodiffComposition</span></a>,
< the internal constituents of the object (e.g., intermediates layers of a neural network model) are not accessible to
< other Components in the Composition (e.g., as a source of information or for modulation).</p>
---
> of a <a class="reference internal" href="UserDefinedFunction.html"><span class="doc">UserDefinedFunction</span></a>. It must be carefully coordinated with the execution of other learning-related Components in
> the Composition, to insure that each function is called at the appropriate times during execution.  Furthermore, as
> with an <a class="reference internal" href="AutodiffComposition.html"><span class="doc">AutodiffComposition</span></a>, the internal constituents of the object (e.g., intermediates layers of a neural network
> model) are not accessible to other Components in the Composition (e.g., as a source of information or for modulation).</p>
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< <li><p><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-execution-methods"><span class="std std-ref">Execution Methods</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a></p></li>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-execution-factors"><span class="std std-ref">Execution Factors</span></a></dt><dd><ul>
1040c1064,1065
< <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-timing"><span class="std std-ref">Timing</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a></p></li>
1042a1068,1072
> </dd>
> </dl>
> </li>
> <li><p><a class="reference internal" href="#composition-execution-results-and-reporting"><span class="std std-ref">Results, Reporting and Logging</span></a></p></li>
> </ul>
1065,1088d1094
< <p id="composition-execution-reporting"><em>Results, Reporting and Logging</em>. Executing a Composition returns the results of its last <a class="reference internal" href="Time.html#psyneulink.core.scheduling.time.TimeScale.TRIAL" title="psyneulink.core.scheduling.time.TimeScale.TRIAL"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">TRIAL</span></code></a> of
< execution. If either <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.run" title="psyneulink.core.compositions.composition.Composition.run"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">run</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.learn" title="psyneulink.core.compositions.composition.Composition.learn"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">learn</span></code></a> is called, the results of all <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/AGTControlMechanism.html docs-head/AGTControlMechanism.html
232c232
< <p>An AGTControlMechanism is a <a class="reference internal" href="ControlMechanism.html"><span class="doc">ControlMechanism</span></a> that uses an ObjectiveMechanism with a <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code>
---
> <p>An AGTControlMechanism is a <a class="reference internal" href="ControlMechanism.html"><span class="doc">ControlMechanism</span></a> that uses an ObjectiveMechanism with a <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a>
234c234
< to regulate the <code class="xref any docutils literal notranslate"><span class="pre">mode</span></code> parameter of its <code class="xref any docutils literal notranslate"><span class="pre">FitzHughNagumoIntegrator</span></code> Function, it implements a form of the
---
> to regulate the <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator.mode" title="psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator.mode"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">mode</span></code></a> parameter of its <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">FitzHughNagumoIntegrator</span></code></a> Function, it implements a form of the
244c244
< <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code> Function as its <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
---
> <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a> Function as its <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
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< ObjectiveMechanism is created automatically when the AGTControlMechanism is created, using a <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code>
---
> ObjectiveMechanism is created automatically when the AGTControlMechanism is created, using a <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a>
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< <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code> as is <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
---
> <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a> as is <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
391c391
< if it is greater than there are inputs then inputs will be repeated (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a>
---
> if it is greater than there are inputs then inputs will be repeated (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a>
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
443c443
< assigning <code class="xref any docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code> as the Mechanism’s <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> and, in the call to the Composition’s
---
> assigning <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code></a> as the Mechanism’s <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> and, in the call to the Composition’s
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< <p>The output is now the result of the <code class="xref any docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code>, which is the value of the decision variable when it
---
> <p>The output is now the result of the <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code></a>, which is the value of the decision variable when it
diff -r docs-base/Component.html docs-head/Component.html
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< arguments, so that the relevant <code class="xref any docutils literal notranslate"><span class="pre">initializer</span></code> attributes (or their equivalents
---
> arguments, so that the relevant <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction.initializer" title="psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction.initializer"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">initializer</span></code></a> attributes (or their equivalents
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< Mechanisms (see <a class="reference internal" href="Composition.html#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a>)</p>
---
> Mechanisms (see <a class="reference internal" href="Composition.html#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a>)</p>
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< <dd><p>If the component’s execute method involves execution of an <code class="xref any docutils literal notranslate"><span class="pre">IntegratorFunction</span></code> Function, this method
---
> <dd><p>If the component’s execute method involves execution of an <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction" title="psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction"><code class="xref any py py-class docutils literal notranslate"><span class="pre">IntegratorFunction</span></code></a> Function, this method
diff -r docs-base/Composition.html docs-head/Composition.html
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< <li><p><a class="reference internal" href="#composition-execution-reporting"><span class="std std-ref">Reporting</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-execution-methods"><span class="std std-ref">Execution Methods</span></a></p></li>
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< <dt><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a></dt><dd><ul>
---
> <dt><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a></dt><dd><ul>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-input-formats"><span class="std std-ref">Input formats (including targets for learning)</span></a></dt><dd><ul>
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> </ul>
> </dd>
> </dl>
> </li>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-execution-factors"><span class="std std-ref">Execution Factors</span></a></dt><dd><ul>
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< <li><p><a class="reference internal" href="#composition-cycle"><span class="std std-ref">Cycles and synchronous execution</span></a></p></li>
< <li><p><a class="reference internal" href="#composition-feedback"><span class="std std-ref">Feedback and sequential execution</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-cycle"><span class="std std-ref">Cycles and Synchronous Execution</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-feedback"><span class="std std-ref">Feedback and Sequential Execution</span></a></p></li>
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< <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-timing"><span class="std std-ref">Timing</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a></p></li>
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> <li><p><a class="reference internal" href="#composition-execution-results-and-reporting"><span class="std std-ref">Results, Reporting and Logging</span></a></p></li>
> </ul>
> </dd>
> </dl>
> </li>
> <li><p><a class="reference internal" href="#composition-visualization"><span class="std std-ref">Visualizing a Composition</span></a></p></li>
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< <div class="admonition warning">
---
> <blockquote>
> <div><div class="admonition warning">
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> </div></blockquote>
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< <ul class="simple" id="composition-parameter-cim">
---
> <ul id="composition-parameter-cim">
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> <div class="technical-note docutils container">
> <p>The Projection from a ModulatoryMechanism to the InputPort of a parameter_CIM is the only instance in which a
> MappingProjection is used as an <a class="reference internal" href="Mechanism.html#id15" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferent</span> <span class="pre">projection</span></code></a> of a ModulatoryMechanism.</p>
> </div>
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< of a <a class="reference internal" href="UserDefinedFunction.html"><span class="doc">UserDefinedFunction</span></a>. It must be carefully coordinated with the execution of other learning-related Components in the Composition, to insure
< that each function is called at the appropriate times during execution.  Furthermore, as with an <a class="reference internal" href="AutodiffComposition.html"><span class="doc">AutodiffComposition</span></a>,
< the internal constituents of the object (e.g., intermediates layers of a neural network model) are not accessible to
< other Components in the Composition (e.g., as a source of information or for modulation).</p>
---
> of a <a class="reference internal" href="UserDefinedFunction.html"><span class="doc">UserDefinedFunction</span></a>. It must be carefully coordinated with the execution of other learning-related Components in
> the Composition, to insure that each function is called at the appropriate times during execution.  Furthermore, as
> with an <a class="reference internal" href="AutodiffComposition.html"><span class="doc">AutodiffComposition</span></a>, the internal constituents of the object (e.g., intermediates layers of a neural network
> model) are not accessible to other Components in the Composition (e.g., as a source of information or for modulation).</p>
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< <li><p><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-execution-methods"><span class="std std-ref">Execution Methods</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a></p></li>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-execution-factors"><span class="std std-ref">Execution Factors</span></a></dt><dd><ul>
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< <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-timing"><span class="std std-ref">Timing</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a></p></li>
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> </dd>
> </dl>
> </li>
> <li><p><a class="reference internal" href="#composition-execution-results-and-reporting"><span class="std std-ref">Results, Reporting and Logging</span></a></p></li>
> </ul>
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< <p id="composition-execution-reporting"><em>Results, Reporting and Logging</em>. Executing a Composition returns the results of its last <a class="reference internal" href="Time.html#psyneulink.core.scheduling.time.TimeScale.TRIAL" title="psyneulink.core.scheduling.time.TimeScale.TRIAL"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">TRIAL</span></code></a> of
< execution. If either <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.run" title="psyneulink.core.compositions.composition.Composition.run"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">run</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.learn" title="psyneulink.core.compositions.composition.Composition.learn"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">learn</span></code></a> is called, the results of all <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/AGTControlMechanism.html docs-head/AGTControlMechanism.html
232c232
< <p>An AGTControlMechanism is a <a class="reference internal" href="ControlMechanism.html"><span class="doc">ControlMechanism</span></a> that uses an ObjectiveMechanism with a <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code>
---
> <p>An AGTControlMechanism is a <a class="reference internal" href="ControlMechanism.html"><span class="doc">ControlMechanism</span></a> that uses an ObjectiveMechanism with a <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a>
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< to regulate the <code class="xref any docutils literal notranslate"><span class="pre">mode</span></code> parameter of its <code class="xref any docutils literal notranslate"><span class="pre">FitzHughNagumoIntegrator</span></code> Function, it implements a form of the
---
> to regulate the <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator.mode" title="psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator.mode"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">mode</span></code></a> parameter of its <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">FitzHughNagumoIntegrator</span></code></a> Function, it implements a form of the
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< <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code> Function as its <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
---
> <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a> Function as its <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
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< ObjectiveMechanism is created automatically when the AGTControlMechanism is created, using a <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code>
---
> ObjectiveMechanism is created automatically when the AGTControlMechanism is created, using a <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a>
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< <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code> as is <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
---
> <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a> as is <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
391c391
< if it is greater than there are inputs then inputs will be repeated (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a>
---
> if it is greater than there are inputs then inputs will be repeated (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a>
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
443c443
< assigning <code class="xref any docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code> as the Mechanism’s <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> and, in the call to the Composition’s
---
> assigning <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code></a> as the Mechanism’s <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> and, in the call to the Composition’s
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< <p>The output is now the result of the <code class="xref any docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code>, which is the value of the decision variable when it
---
> <p>The output is now the result of the <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code></a>, which is the value of the decision variable when it
diff -r docs-base/Component.html docs-head/Component.html
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< arguments, so that the relevant <code class="xref any docutils literal notranslate"><span class="pre">initializer</span></code> attributes (or their equivalents
---
> arguments, so that the relevant <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction.initializer" title="psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction.initializer"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">initializer</span></code></a> attributes (or their equivalents
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< Mechanisms (see <a class="reference internal" href="Composition.html#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a>)</p>
---
> Mechanisms (see <a class="reference internal" href="Composition.html#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a>)</p>
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< <dd><p>If the component’s execute method involves execution of an <code class="xref any docutils literal notranslate"><span class="pre">IntegratorFunction</span></code> Function, this method
---
> <dd><p>If the component’s execute method involves execution of an <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction" title="psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction"><code class="xref any py py-class docutils literal notranslate"><span class="pre">IntegratorFunction</span></code></a> Function, this method
diff -r docs-base/Composition.html docs-head/Composition.html
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< <li><p><a class="reference internal" href="#composition-execution-reporting"><span class="std std-ref">Reporting</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-execution-methods"><span class="std std-ref">Execution Methods</span></a></p></li>
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< <dt><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a></dt><dd><ul>
---
> <dt><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a></dt><dd><ul>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-input-formats"><span class="std std-ref">Input formats (including targets for learning)</span></a></dt><dd><ul>
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> </ul>
> </dd>
> </dl>
> </li>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-execution-factors"><span class="std std-ref">Execution Factors</span></a></dt><dd><ul>
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< <li><p><a class="reference internal" href="#composition-cycle"><span class="std std-ref">Cycles and synchronous execution</span></a></p></li>
< <li><p><a class="reference internal" href="#composition-feedback"><span class="std std-ref">Feedback and sequential execution</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-cycle"><span class="std std-ref">Cycles and Synchronous Execution</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-feedback"><span class="std std-ref">Feedback and Sequential Execution</span></a></p></li>
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< <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-timing"><span class="std std-ref">Timing</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a></p></li>
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> <li><p><a class="reference internal" href="#composition-execution-results-and-reporting"><span class="std std-ref">Results, Reporting and Logging</span></a></p></li>
> </ul>
> </dd>
> </dl>
> </li>
> <li><p><a class="reference internal" href="#composition-visualization"><span class="std std-ref">Visualizing a Composition</span></a></p></li>
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< <div class="admonition warning">
---
> <blockquote>
> <div><div class="admonition warning">
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> </div></blockquote>
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< <span id="composition-acyclic-cyclic"></span><h4>Acyclic and Cyclic Graphs<a class="headerlink" href="#acyclic-and-cyclic-graphs" title="Permalink to this headline">¶</a></h4>
---
> <span id="composition-acyclic-cyclic"></span><h4><strong>Acyclic and Cyclic Graphs</strong><a class="headerlink" href="#acyclic-and-cyclic-graphs" title="Permalink to this headline">¶</a></h4>
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< <ul class="simple" id="composition-parameter-cim">
---
> <ul id="composition-parameter-cim">
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> <div class="technical-note docutils container">
> <p>The Projection from a ModulatoryMechanism to the InputPort of a parameter_CIM is the only instance in which a
> MappingProjection is used as an <a class="reference internal" href="Mechanism.html#id15" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferent</span> <span class="pre">projection</span></code></a> of a ModulatoryMechanism.</p>
> </div>
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< of a <a class="reference internal" href="UserDefinedFunction.html"><span class="doc">UserDefinedFunction</span></a>. It must be carefully coordinated with the execution of other learning-related Components in the Composition, to insure
< that each function is called at the appropriate times during execution.  Furthermore, as with an <a class="reference internal" href="AutodiffComposition.html"><span class="doc">AutodiffComposition</span></a>,
< the internal constituents of the object (e.g., intermediates layers of a neural network model) are not accessible to
< other Components in the Composition (e.g., as a source of information or for modulation).</p>
---
> of a <a class="reference internal" href="UserDefinedFunction.html"><span class="doc">UserDefinedFunction</span></a>. It must be carefully coordinated with the execution of other learning-related Components in
> the Composition, to insure that each function is called at the appropriate times during execution.  Furthermore, as
> with an <a class="reference internal" href="AutodiffComposition.html"><span class="doc">AutodiffComposition</span></a>, the internal constituents of the object (e.g., intermediates layers of a neural network
> model) are not accessible to other Components in the Composition (e.g., as a source of information or for modulation).</p>
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< <li><p><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-execution-methods"><span class="std std-ref">Execution Methods</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a></p></li>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-execution-factors"><span class="std std-ref">Execution Factors</span></a></dt><dd><ul>
1040c1064,1065
< <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-timing"><span class="std std-ref">Timing</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a></p></li>
1042a1068,1072
> </dd>
> </dl>
> </li>
> <li><p><a class="reference internal" href="#composition-execution-results-and-reporting"><span class="std std-ref">Results, Reporting and Logging</span></a></p></li>
> </ul>
1065,1088d1094
< <p id="composition-execution-reporting"><em>Results, Reporting and Logging</em>. Executing a Composition returns the results of its last <a class="reference internal" href="Time.html#psyneulink.core.scheduling.time.TimeScale.TRIAL" title="psyneulink.core.scheduling.time.TimeScale.TRIAL"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">TRIAL</span></code></a> of
< execution. If either <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.run" title="psyneulink.core.compositions.composition.Composition.run"><code class="xref any py py-meth docutils lit
...

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coveralls commented Dec 21, 2021 •
edited

Coverage Status

Coverage increased (+0.2%) to 84.164% when pulling a082d45 on feat/comp/inputs into a2afe77 on devel.

@jdcpni
• composition.py
1e175a6 
  - get_results_by_node():  add use_labels option
@jdcpni
Merge branch 'feat/comp/inputs' of https://github.com/PrincetonUniver…
a082d45 
…sity/PsyNeuLink into feat/comp/inputs

� Conflicts:
�	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/AGTControlMechanism.html docs-head/AGTControlMechanism.html
232c232
< <p>An AGTControlMechanism is a <a class="reference internal" href="ControlMechanism.html"><span class="doc">ControlMechanism</span></a> that uses an ObjectiveMechanism with a <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code>
---
> <p>An AGTControlMechanism is a <a class="reference internal" href="ControlMechanism.html"><span class="doc">ControlMechanism</span></a> that uses an ObjectiveMechanism with a <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a>
234c234
< to regulate the <code class="xref any docutils literal notranslate"><span class="pre">mode</span></code> parameter of its <code class="xref any docutils literal notranslate"><span class="pre">FitzHughNagumoIntegrator</span></code> Function, it implements a form of the
---
> to regulate the <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator.mode" title="psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator.mode"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">mode</span></code></a> parameter of its <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.FitzHughNagumoIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">FitzHughNagumoIntegrator</span></code></a> Function, it implements a form of the
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< <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code> Function as its <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
---
> <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a> Function as its <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
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< ObjectiveMechanism is created automatically when the AGTControlMechanism is created, using a <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code>
---
> ObjectiveMechanism is created automatically when the AGTControlMechanism is created, using a <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a>
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< <code class="xref any docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code> as is <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
---
> <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DualAdaptiveIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DualAdaptiveIntegrator</span></code></a> as is <a class="reference internal" href="ObjectiveMechanism.html#psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function" title="psyneulink.core.components.mechanisms.processing.objectivemechanism.ObjectiveMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p>
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
391c391
< if it is greater than there are inputs then inputs will be repeated (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a>
---
> if it is greater than there are inputs then inputs will be repeated (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a>
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
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< assigning <code class="xref any docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code> as the Mechanism’s <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> and, in the call to the Composition’s
---
> assigning <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code></a> as the Mechanism’s <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> and, in the call to the Composition’s
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< <p>The output is now the result of the <code class="xref any docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code>, which is the value of the decision variable when it
---
> <p>The output is now the result of the <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator" title="psyneulink.core.components.functions.stateful.integratorfunctions.DriftDiffusionIntegrator"><code class="xref any py py-class docutils literal notranslate"><span class="pre">DriftDiffusionIntegrator</span></code></a>, which is the value of the decision variable when it
diff -r docs-base/Component.html docs-head/Component.html
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< arguments, so that the relevant <code class="xref any docutils literal notranslate"><span class="pre">initializer</span></code> attributes (or their equivalents
---
> arguments, so that the relevant <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction.initializer" title="psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction.initializer"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">initializer</span></code></a> attributes (or their equivalents
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< Mechanisms (see <a class="reference internal" href="Composition.html#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a>)</p>
---
> Mechanisms (see <a class="reference internal" href="Composition.html#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a>)</p>
1139c1139
< <dd><p>If the component’s execute method involves execution of an <code class="xref any docutils literal notranslate"><span class="pre">IntegratorFunction</span></code> Function, this method
---
> <dd><p>If the component’s execute method involves execution of an <a class="reference internal" href="IntegratorFunctions.html#psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction" title="psyneulink.core.components.functions.stateful.integratorfunctions.IntegratorFunction"><code class="xref any py py-class docutils literal notranslate"><span class="pre">IntegratorFunction</span></code></a> Function, this method
diff -r docs-base/Composition.html docs-head/Composition.html
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< <li><p><a class="reference internal" href="#composition-execution-reporting"><span class="std std-ref">Reporting</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-execution-methods"><span class="std std-ref">Execution Methods</span></a></p></li>
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< <dt><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a></dt><dd><ul>
---
> <dt><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a></dt><dd><ul>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-input-formats"><span class="std std-ref">Input formats (including targets for learning)</span></a></dt><dd><ul>
310a313,318
> </ul>
> </dd>
> </dl>
> </li>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-execution-factors"><span class="std std-ref">Execution Factors</span></a></dt><dd><ul>
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< <li><p><a class="reference internal" href="#composition-cycle"><span class="std std-ref">Cycles and synchronous execution</span></a></p></li>
< <li><p><a class="reference internal" href="#composition-feedback"><span class="std std-ref">Feedback and sequential execution</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-cycle"><span class="std std-ref">Cycles and Synchronous Execution</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-feedback"><span class="std std-ref">Feedback and Sequential Execution</span></a></p></li>
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< <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-timing"><span class="std std-ref">Timing</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a></p></li>
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> <li><p><a class="reference internal" href="#composition-execution-results-and-reporting"><span class="std std-ref">Results, Reporting and Logging</span></a></p></li>
> </ul>
> </dd>
> </dl>
> </li>
> <li><p><a class="reference internal" href="#composition-visualization"><span class="std std-ref">Visualizing a Composition</span></a></p></li>
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< <div class="admonition warning">
---
> <blockquote>
> <div><div class="admonition warning">
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> </div></blockquote>
536c553
< <span id="composition-acyclic-cyclic"></span><h4>Acyclic and Cyclic Graphs<a class="headerlink" href="#acyclic-and-cyclic-graphs" title="Permalink to this headline">¶</a></h4>
---
> <span id="composition-acyclic-cyclic"></span><h4><strong>Acyclic and Cyclic Graphs</strong><a class="headerlink" href="#acyclic-and-cyclic-graphs" title="Permalink to this headline">¶</a></h4>
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< <ul class="simple" id="composition-parameter-cim">
---
> <ul id="composition-parameter-cim">
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> <div class="technical-note docutils container">
> <p>The Projection from a ModulatoryMechanism to the InputPort of a parameter_CIM is the only instance in which a
> MappingProjection is used as an <a class="reference internal" href="Mechanism.html#id15" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferent</span> <span class="pre">projection</span></code></a> of a ModulatoryMechanism.</p>
> </div>
1026,1029c1047,1050
< of a <a class="reference internal" href="UserDefinedFunction.html"><span class="doc">UserDefinedFunction</span></a>. It must be carefully coordinated with the execution of other learning-related Components in the Composition, to insure
< that each function is called at the appropriate times during execution.  Furthermore, as with an <a class="reference internal" href="AutodiffComposition.html"><span class="doc">AutodiffComposition</span></a>,
< the internal constituents of the object (e.g., intermediates layers of a neural network model) are not accessible to
< other Components in the Composition (e.g., as a source of information or for modulation).</p>
---
> of a <a class="reference internal" href="UserDefinedFunction.html"><span class="doc">UserDefinedFunction</span></a>. It must be carefully coordinated with the execution of other learning-related Components in
> the Composition, to insure that each function is called at the appropriate times during execution.  Furthermore, as
> with an <a class="reference internal" href="AutodiffComposition.html"><span class="doc">AutodiffComposition</span></a>, the internal constituents of the object (e.g., intermediates layers of a neural network
> model) are not accessible to other Components in the Composition (e.g., as a source of information or for modulation).</p>
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< <li><p><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Input formats (including targets for learning)</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-execution-methods"><span class="std std-ref">Execution Methods</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-execution-inputs"><span class="std std-ref">Composition Inputs</span></a></p></li>
> <li><dl class="simple">
> <dt><a class="reference internal" href="#composition-execution-factors"><span class="std std-ref">Execution Factors</span></a></dt><dd><ul>
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< <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Parameters of stateful</span></a></p></li>
---
> <li><p><a class="reference internal" href="#composition-timing"><span class="std std-ref">Timing</span></a></p></li>
> <li><p><a class="reference internal" href="#composition-reset"><span class="std std-ref">Resetting Stateful Parameters</span></a></p></li>
1042a1068,1072
> </dd>
> </dl>
> </li>
> <li><p><a class="reference internal" href="#composition-execution-results-and-reporting"><span class="std std-ref">Results, Reporting and Logging</span></a></p></li>
> </ul>
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< <p id="composition-execution-reporting"><em>Results, Reporting and Logging</em>. Executing a Composition returns the results of its last <a class="reference internal" href="Time.html#psyneulink.core.scheduling.time.TimeScale.TRIAL" title="psyneulink.core.scheduling.time.TimeScale.TRIAL"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">TRIAL</span></code></a> of
< execution. If either <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.run" title="psyneulink.core.compositions.composition.Composition.run"><code class="xref any py py-meth docutils lit
...

See CI logs for the full diff.

@jdcpni jdcpni merged commit cc6242b into devel Dec 21, 2021
@jdcpni jdcpni deleted the feat/comp/inputs branch December 21, 2021 18:37
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