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Feat/comp/inputs #2260

Merged
merged 377 commits into from
Dec 26, 2021
Merged

Feat/comp/inputs #2260

merged 377 commits into from
Dec 26, 2021

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jdcpni
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@jdcpni jdcpni commented Dec 25, 2021

• keywords.py:
COMPOSITION: COMPOSITION -> Composition

• show_graph.py:

  • RANDOMIZATION_CONTROL_PROJECTION: dashed line
  • docstring mods

• test_composition.py:
- test_failure_to_find_node_to_shadow(self):
- test_unused_projections_warning

jdcpni and others added 30 commits November 22, 2021 23:54
@jdcpni
-
7fd49c6
@jdcpni
Merge branch 'refactor/ocm/state_input_ports_PROBE_FIX' of https://gi…
35c97d3 
…thub.com/PrincetonUniversity/PsyNeuLink into refactor/ocm/state_input_ports_PROBE_FIX
@jdcpni
• composition.py
79cb012 
  retore append of control_signals in _instantiate_control_projections()
@jdcpni
• composition.py
9bc7b18 
  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
• test_partially_overlapping_local_and_control_mech_control_specs_in_…
0f93f47 
…unnested_and_nested_comp():

  - added clear_registry() to allow names to be reused in both runs of test
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
47b56b2 
…Link into devel
@jdcpni
• composition.py
81f1112 
  docstring:  added projections entry to list of attributes
  - add_controller:  added call to _add_node_aux_components() for controller
@jdcpni
• composition.py
0cd9db3 
  _add_node_aux_components(): added deletion of item from aux_components if instantiated
@jdcpni
• composition.py
c808664 
  - 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)
@jdcpni
-
0cb21ab
- confirm that it passes all tests exception test_composition/test_pa…
28289a0 
…rtially_overlapping...

  (with addition of _add_aux_components in add_controller commented out)
@jdcpni
• composition.py: some more fixed to add_controller that now fail onl…
1cf9602 
…y one test:

    - test_agent_rep_assignement_as_controller_and_replacement
@jdcpni
• Passes *all* current tests
72c4c41
• composition.py:
45b25eb 
  - add_controller:  few more minor mods;
  still passes all tests
-
a79723b
@jdcpni
-
49350a1
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
f7b9fc5 
…Link into devel
@jdcpni
-
7a6682a
@jdcpni
• controlmechanism.py:
8858ab5 
  - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms)
@jdcpni
-
d1ac2da
@jdcpni
• composition.py: in progress fix of bug in instantiating shadow proj…
dbdc2d1 
…ections for ocm.state_input_ports
@jdcpni
• composition.py:
6b00fbd 
  - _get_original_senders():  added support for nested composition
    needs to be checked for more than one level
    needs to be refactored to be recursive
@jdcpni
• optimizationcontrolmechanism.py
179e7d0 
  - _update_state_input_ports_for_controller:  fix invalid_state_features to allow input_CIM of nested comp in agent_rep
@jdcpni
-
88ce1a6
@jdcpni
• composition.py
5089cf3 
 - _get_original_senders: made recursive
• test_show_graph.py: update for fixes
97a71c4
-
3bc799e
• tests: passes all in test_show_graph.py and test_report.py
6a27e4a
Passes all tests
8cdad10
- comment clean-up
2d15f6d
jdcpni and others added 22 commits December 21, 2021 19:33
• project: remove scale from figures
e1949c4
@jdcpni
-
9ee000b
@jdcpni
-
d955ac5
@jdcpni
-
65a9fb1
@jdcpni
• project - docstring mods
46a7642 
• composition.py:  found bug with specification of shadows and probes between "parallel" compositions.
@jdcpni
• README.rst and composition.py: add links to CGO paper
755296b
@jdcpni
• README.rst, index.rst and composition.py:
edf2fc9 
  - updates to contribtors
  - add links to CGO paper
@jdcpni
Merge branch 'feat/comp/inputs' of https://github.com/PrincetonUniver…
282288a 
…sity/PsyNeuLink into feat/comp/inputs
• composition.py
b45ca49 
  _update_shadow_projections: report error for failure to find correct_sender
• composition.py
8eb7f32 
  - add _check_for_unused_projections(): warns if any projections are specified for Nodes that are not used in the comp
@jdcpni
Merge branch 'feat/comp/inputs' of https://github.com/PrincetonUniver…
28b4596 
…sity/PsyNeuLink into feat/comp/inputs
@jdcpni
-
2d443ad
@jdcpni
-
55eafa5
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
626b601 
…Link into feat/comp/inputs

� Conflicts:
�	README.rst
�	psyneulink/core/compositions/composition.py
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
5b14e03 
…Link into feat/comp/inputs
@jdcpni
-
c44ddb1
@jdcpni
• test_composition.py:
f50c38e 
    - test_failure_to_find_node_to_shadow(self):
    - test_unused_projections_warning
@jdcpni
• test_composition.py:
c3647a6 
    - test_failure_to_find_node_to_shadow(self):
    - test_unused_projections_warning
@jdcpni
• keywords.py:
7e71046 
    COMPOSITION: COMPOSITION -> Composition
• test_composition.py:
    - test_failure_to_find_node_to_shadow(self):
    - test_unused_projections_warning
@jdcpni
• keywords.py:
bb991fd 
    COMPOSITION: COMPOSITION -> Composition
@jdcpni
-
ff1021b
@jdcpni
• show_graph.py:
35f591f 
  - RANDOMIZATION_CONTROL_PROJECTION: dashed line
  - docstring mods
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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
1182,1188c1182,1189
< <p>The input specified for each <code class="xref any docutils literal notranslate"><span class="pre">Node</span></code> must be compatible with the number of <a class="reference internal" href="InputPort.html"><span class="doc">InputPorts</span></a>
< that receive external input for that Node. These are listed in its <code class="docutils literal notranslate"><span class="pre">external_input_ports</span></code> attribute (<a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_ports" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is Mechanism, or <a class="reference internal" href="#id15" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is a
< Composition).  More specifically, the shape of the input value must be compatible with the shape of the Node’s
< <a class="reference internal" href="#id16" title="psyneulink.core.compositions.composition.Composition.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">external_input_values</span></code></a> attribute (<a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_values" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is Mechanism,
< or <a class="reference internal" href="#id16" title="psyneulink.core.compositions.composition.Composition.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is a Composition). While these are always 2d arrays, the number
< and size of the items (corresponding to each InputPort) may vary; in some case shorthand notations are allowed,
< as illustrated in the <a class="reference internal" href="#composition-examples-input-dictionary"><span class="std std-ref">examples</span></a> below.</p>
---
> <p>The key for each entry of the dict can be a direct reference to the <a class="reference internal" href="#composition-nodes"><span class="std std-ref">Node</span></a>, or the name assigned
> to one (i.e., its <a class="reference internal" href="Component.html#psyneulink.core.components.component.Component.name" title="psyneulink.core.components.component.Component.name"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">name</span></code></a> attribute).  The value must an input that is compatible with the number of
> <a class="reference internal" href="InputPort.html"><span class="doc">InputPorts</span></a> that receive external input for that Node. These are listed in its <code class="docutils literal notranslate"><span class="pre">external_input_ports</span></code>
> (<a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_ports" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is Mechanism, or <a class="reference internal" href="#id15" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it
> is a Composition).  More specifically, the shape of the input value must be compatible with the shape of the Node’s
> <a class="reference internal" href="#id16" title="psyneulink.core.compositions.composition.Composition.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">external_input_values</span></code></a> attribute (<a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_values" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is Mechanism, or <a class="reference internal" href="#id16" title="psyneulink.core.compositions.composition.Composition.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is a Composition). While these are always 2d arrays, the number and size
> of the items (corresponding to each InputPort) may vary; in some case shorthand notations are allowed, as illustrated
> in the <a class="reference internal" href="#composition-examples-input-dictionary"><span class="std std-ref">examples</span></a> below.</p>
1680c1681
< <p>The <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> method generates a display of the graph structure of <a class="reference internal" href="#composition-nodes"><span class="std std-ref">Nodes</span></a> and <a class="reference internal" href="Projection.html"><span class="doc">Projections</span></a> in the Composition based on the Composition’s <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.graph" title="psyneulink.core.compositions.composition.Composition.graph"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">graph</span></code></a> (see <a class="reference internal" href="Visualization.html"><span class="doc">Visualization</span></a> for additional details).</p>
---
> <p>The <code class="xref any docutils literal notranslate"><span class="pre">show_graph</span></code> method generates a display of the graph structure of <a class="reference internal" href="#composition-nodes"><span class="std std-ref">Nodes</span></a> and <a class="reference internal" href="Projection.html"><span class="doc">Projections</span></a> in the Composition based on the Composition’s <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.graph" title="psyneulink.core.compositions.composition.Composition.graph"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">graph</span></code></a> (see <a class="reference internal" href="Visualization.html"><span class="doc">Visualization</span></a> for additional details).</p>
2488c2489
< <li><p><strong>show_graph_attributes</strong> (<em>dict : None</em>) – specifies features of how the Composition is displayed when its <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a>
---
> <li><p><strong>show_graph_attributes</strong> (<em>dict : None</em>) – specifies features of how the Composition is displayed when its <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a>
4364,4371c4365,4371
< <li><p><strong>animate</strong> (<em>dict</em><em> or </em><em>bool : default False</em>) – <p>specifies use of the <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph`show_graph</span></a> method
< to generate a gif movie showing the sequence of Components executed in a run
< (see <a class="reference internal" href="BasicsAndPrimer.html#basicsandprimer-stroop-example-animation-figure"><span class="std std-ref">example</span></a>). A dict can be specified containing
< options to pass to the <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> method; each key must be a legal
< argument for the <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> method, and its value a
< specification for that argument.  The entries listed below can also be included in the dict to specify
< parameters of the animation.  If the <strong>animate</strong> argument is specified simply as <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>, defaults are
< used for all arguments of <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> and the options below:</p>
---
> <li><p><strong>animate</strong> (<em>dict</em><em> or </em><em>bool : default False</em>) – <p>specifies use of the <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph`show_graph</span></code></a> method to generate
> a gif movie showing the sequence of Components executed in a run (see <a class="reference internal" href="BasicsAndPrimer.html#basicsandprimer-stroop-example-animation-figure"><span class="std std-ref">example</span></a>). A dict can be specified containing
> options to pass to the <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a> method; each key must be a legal
> argument for the <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a> method, and its value a specification for that
> argument.  The entries listed below can also be included in the dict to specify parameters of the
> animation.  If the <strong>animate</strong> argument is specified simply as <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>, defaults are used for all
> arguments of <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a> and the options below:</p>
4374c4374
< to treat as active in each call to <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a>. <em>COMPONENT</em> generates an
---
> to treat as active in each call to <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph()</span></code></a>. <em>COMPONENT</em> generates an
diff -r docs-base/CompositionInterfaceMechanism.html docs-head/CompositionInterfaceMechanism.html
245c245
< Composition’s <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> method (see figure below).</p>
---
> Composition’s <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a> method (see figure below).</p>
diff -r docs-base/ControlMechanism.html docs-head/ControlMechanism.html
272c272
< Components can be displayed using the Composition’s <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> method with its
---
> Components can be displayed using the Composition’s <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a> method with its
diff -r docs-base/LearningMechanism.html docs-head/LearningMechanism.html
241c241
< displayed using the Composition’s <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph`show_graph</span></a> method with its
---
> displayed using the Composition’s <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph`show_graph</span></code></a> method with its
487,488c487,488
< described below. All of the learning Components of a Composition can be displayed using its <code class="xref any docutils literal notranslate"><span class="pre">show_graph</span></code> method with
< the <strong>show_learning</strong> argument assigned <code class="xref any docutils literal notranslate"><span class="pre">True</span></code> or <em>ALL</em>.</p>
---
> described below. All of the learning Components of a Composition can be displayed using its <code class="xref any docutils literal notranslate"><span class="pre">show_graph</span>
> <span class="pre">&lt;ShowGraph.show_graph</span></code> method with the <strong>show_learning</strong> argument assigned <code class="xref any docutils literal notranslate"><span class="pre">True</span></code> or <em>ALL</em>.</p>
diff -r docs-base/Mechanism.html docs-head/Mechanism.html
832c832
< of the Composition’s <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph`show_graph</span></a> method with the keyword <strong>LABELS</strong>.</p>
---
> of the Composition’s <code class="xref any docutils literal notranslate"><span class="pre">show_graph`show_graph</span></code> method with the keyword <strong>LABELS</strong>.</p>
diff -r docs-base/Visualization.html docs-head/Visualization.html
240,243c240,297
< <p><em>Display attributes</em> – state_features (such as the colors and shapes) in which different types of nodes are displayed
< can be modified by assigning a dictionary of attribute:values pairs to the <strong>show_graph_configuration</strong> argument of the
< Composition’s constructor.  These are listed as the arguments for the ShowGraph object (used to display the graph)
< in the <a class="reference internal" href="#showgraph-class-reference"><span class="std std-ref">class reference</span></a> below.</p>
---
> <p><em>Display attributes</em> – the colors, shapes and arrow styles used in the display can be modified using the
> <strong>show_graph_attributes</strong> argument of a Composition’s constructor, as described below.</p>
> </section>
> <section id="display-attributes">
> <span id="showgraph-attributes"></span><h2><em>Display Attributes</em><a class="headerlink" href="#display-attributes" title="Permalink to this headline">¶</a></h2>
> <p>The default attributes used to display different types of <a class="reference internal" href="Component.html"><span class="doc">Components</span></a> and their <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="
...

See CI logs for the full diff.

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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
1182,1188c1182,1189
< <p>The input specified for each <code class="xref any docutils literal notranslate"><span class="pre">Node</span></code> must be compatible with the number of <a class="reference internal" href="InputPort.html"><span class="doc">InputPorts</span></a>
< that receive external input for that Node. These are listed in its <code class="docutils literal notranslate"><span class="pre">external_input_ports</span></code> attribute (<a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_ports" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is Mechanism, or <a class="reference internal" href="#id15" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is a
< Composition).  More specifically, the shape of the input value must be compatible with the shape of the Node’s
< <a class="reference internal" href="#id16" title="psyneulink.core.compositions.composition.Composition.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">external_input_values</span></code></a> attribute (<a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_values" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is Mechanism,
< or <a class="reference internal" href="#id16" title="psyneulink.core.compositions.composition.Composition.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is a Composition). While these are always 2d arrays, the number
< and size of the items (corresponding to each InputPort) may vary; in some case shorthand notations are allowed,
< as illustrated in the <a class="reference internal" href="#composition-examples-input-dictionary"><span class="std std-ref">examples</span></a> below.</p>
---
> <p>The key for each entry of the dict can be a direct reference to the <a class="reference internal" href="#composition-nodes"><span class="std std-ref">Node</span></a>, or the name assigned
> to one (i.e., its <a class="reference internal" href="Component.html#psyneulink.core.components.component.Component.name" title="psyneulink.core.components.component.Component.name"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">name</span></code></a> attribute).  The value must an input that is compatible with the number of
> <a class="reference internal" href="InputPort.html"><span class="doc">InputPorts</span></a> that receive external input for that Node. These are listed in its <code class="docutils literal notranslate"><span class="pre">external_input_ports</span></code>
> (<a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_ports" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is Mechanism, or <a class="reference internal" href="#id15" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it
> is a Composition).  More specifically, the shape of the input value must be compatible with the shape of the Node’s
> <a class="reference internal" href="#id16" title="psyneulink.core.compositions.composition.Composition.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">external_input_values</span></code></a> attribute (<a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_values" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is Mechanism, or <a class="reference internal" href="#id16" title="psyneulink.core.compositions.composition.Composition.external_input_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">here</span></code></a> if it is a Composition). While these are always 2d arrays, the number and size
> of the items (corresponding to each InputPort) may vary; in some case shorthand notations are allowed, as illustrated
> in the <a class="reference internal" href="#composition-examples-input-dictionary"><span class="std std-ref">examples</span></a> below.</p>
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< <p>The <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> method generates a display of the graph structure of <a class="reference internal" href="#composition-nodes"><span class="std std-ref">Nodes</span></a> and <a class="reference internal" href="Projection.html"><span class="doc">Projections</span></a> in the Composition based on the Composition’s <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.graph" title="psyneulink.core.compositions.composition.Composition.graph"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">graph</span></code></a> (see <a class="reference internal" href="Visualization.html"><span class="doc">Visualization</span></a> for additional details).</p>
---
> <p>The <code class="xref any docutils literal notranslate"><span class="pre">show_graph</span></code> method generates a display of the graph structure of <a class="reference internal" href="#composition-nodes"><span class="std std-ref">Nodes</span></a> and <a class="reference internal" href="Projection.html"><span class="doc">Projections</span></a> in the Composition based on the Composition’s <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.graph" title="psyneulink.core.compositions.composition.Composition.graph"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">graph</span></code></a> (see <a class="reference internal" href="Visualization.html"><span class="doc">Visualization</span></a> for additional details).</p>
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< <li><p><strong>show_graph_attributes</strong> (<em>dict : None</em>) – specifies features of how the Composition is displayed when its <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a>
---
> <li><p><strong>show_graph_attributes</strong> (<em>dict : None</em>) – specifies features of how the Composition is displayed when its <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a>
4364,4371c4365,4371
< <li><p><strong>animate</strong> (<em>dict</em><em> or </em><em>bool : default False</em>) – <p>specifies use of the <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph`show_graph</span></a> method
< to generate a gif movie showing the sequence of Components executed in a run
< (see <a class="reference internal" href="BasicsAndPrimer.html#basicsandprimer-stroop-example-animation-figure"><span class="std std-ref">example</span></a>). A dict can be specified containing
< options to pass to the <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> method; each key must be a legal
< argument for the <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> method, and its value a
< specification for that argument.  The entries listed below can also be included in the dict to specify
< parameters of the animation.  If the <strong>animate</strong> argument is specified simply as <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>, defaults are
< used for all arguments of <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> and the options below:</p>
---
> <li><p><strong>animate</strong> (<em>dict</em><em> or </em><em>bool : default False</em>) – <p>specifies use of the <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph`show_graph</span></code></a> method to generate
> a gif movie showing the sequence of Components executed in a run (see <a class="reference internal" href="BasicsAndPrimer.html#basicsandprimer-stroop-example-animation-figure"><span class="std std-ref">example</span></a>). A dict can be specified containing
> options to pass to the <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a> method; each key must be a legal
> argument for the <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a> method, and its value a specification for that
> argument.  The entries listed below can also be included in the dict to specify parameters of the
> animation.  If the <strong>animate</strong> argument is specified simply as <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>, defaults are used for all
> arguments of <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a> and the options below:</p>
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< to treat as active in each call to <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a>. <em>COMPONENT</em> generates an
---
> to treat as active in each call to <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph()</span></code></a>. <em>COMPONENT</em> generates an
diff -r docs-base/CompositionInterfaceMechanism.html docs-head/CompositionInterfaceMechanism.html
245c245
< Composition’s <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> method (see figure below).</p>
---
> Composition’s <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a> method (see figure below).</p>
diff -r docs-base/ControlMechanism.html docs-head/ControlMechanism.html
272c272
< Components can be displayed using the Composition’s <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph</span></a> method with its
---
> Components can be displayed using the Composition’s <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph</span></code></a> method with its
diff -r docs-base/LearningMechanism.html docs-head/LearningMechanism.html
241c241
< displayed using the Composition’s <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph`show_graph</span></a> method with its
---
> displayed using the Composition’s <a class="reference internal" href="Visualization.html#psyneulink.core.compositions.showgraph.ShowGraph.show_graph" title="psyneulink.core.compositions.showgraph.ShowGraph.show_graph"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">show_graph`show_graph</span></code></a> method with its
487,488c487,488
< described below. All of the learning Components of a Composition can be displayed using its <code class="xref any docutils literal notranslate"><span class="pre">show_graph</span></code> method with
< the <strong>show_learning</strong> argument assigned <code class="xref any docutils literal notranslate"><span class="pre">True</span></code> or <em>ALL</em>.</p>
---
> described below. All of the learning Components of a Composition can be displayed using its <code class="xref any docutils literal notranslate"><span class="pre">show_graph</span>
> <span class="pre">&lt;ShowGraph.show_graph</span></code> method with the <strong>show_learning</strong> argument assigned <code class="xref any docutils literal notranslate"><span class="pre">True</span></code> or <em>ALL</em>.</p>
diff -r docs-base/Mechanism.html docs-head/Mechanism.html
832c832
< of the Composition’s <a class="reference internal" href="Visualization.html#showgraph-show-graph-method"><span class="std std-ref">show_graph`show_graph</span></a> method with the keyword <strong>LABELS</strong>.</p>
---
> of the Composition’s <code class="xref any docutils literal notranslate"><span class="pre">show_graph`show_graph</span></code> method with the keyword <strong>LABELS</strong>.</p>
diff -r docs-base/Visualization.html docs-head/Visualization.html
240,243c240,297
< <p><em>Display attributes</em> – state_features (such as the colors and shapes) in which different types of nodes are displayed
< can be modified by assigning a dictionary of attribute:values pairs to the <strong>show_graph_configuration</strong> argument of the
< Composition’s constructor.  These are listed as the arguments for the ShowGraph object (used to display the graph)
< in the <a class="reference internal" href="#showgraph-class-reference"><span class="std std-ref">class reference</span></a> below.</p>
---
> <p><em>Display attributes</em> – the colors, shapes and arrow styles used in the display can be modified using the
> <strong>show_graph_attributes</strong> argument of a Composition’s constructor, as described below.</p>
> </section>
> <section id="display-attributes">
> <span id="showgraph-attributes"></span><h2><em>Display Attributes</em><a class="headerlink" href="#display-attributes" title="Permalink to this headline">¶</a></h2>
> <p>The default attributes used to display different types of <a class="reference internal" href="Component.html"><span class="doc">Components</span></a> and their <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="
...

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Coverage increased (+0.009%) to 84.281% when pulling 88b0a3f on feat/comp/inputs into 436f5d9 on devel.

@jdcpni jdcpni merged commit b383b90 into devel Dec 26, 2021
@jdcpni jdcpni deleted the feat/comp/inputs branch December 26, 2021 04:47
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@jdcpni @coveralls @kmantel