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Feat/control signal/add control arg #2272

Merged
merged 252 commits into from
Jan 3, 2022
Merged

Feat/control signal/add control arg #2272

merged 252 commits into from
Jan 3, 2022

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jdcpni
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@jdcpni jdcpni commented Jan 2, 2022 •
edited

• controlsignal.py:

  • init(): replace modulates with control as arg (though still allow modulates)
  • allow CONTROL as alias for PROJECTIONS in ControlSignal spec

• gatingsignal.py:
  - init(): replace modulates with gate as arg

• gating mechanism.py:

  • add output_ports Parameter that allows GATE as alias for PROJECTIONS in specification dictionary

• test_projection_specifications.py:

  • add test_control_signal_projections_arg
  • add test_gating_signal_projections_arg
  • test_multiple_modulatory_projection_specs: add tests for gating specs

@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
a32f213 
…Link into devel
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
75cf069 
…Link into devel
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
dff1a37 
…Link into devel
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
cd5e38e 
…Link into devel
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
9361857 
…Link into devel
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
0129ff7 
…Link into devel
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
bbd20f5 
…Link into devel
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
f9aba91 
…Link into devel
@jdcpni
• optimizationcontrolmechanism.py:
a3c0f6c 
  added feature_input_ports attribute and num_feature_input_ports property
@jdcpni
• optimizationcontrolmechanism.py:
7069b3a 
  added feature_input_ports attribute and num_feature_input_ports property

• parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute
@jdcpni
• optimizationcontrolmechanism.py:
65b960e 
  added feature_input_ports attribute and num_feature_input_ports property

• parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute

• optimizationfunctions.py: made num_estimates a Parameter
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
5cc58f6 
…Link into feat/ocm/feature_input_ports
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
bc05b51 
…Link into devel
@jdcpni
- modified test_mode_based_num_estimates
a8d428b
@jdcpni
-
1218b6f
@jdcpni
-
41567bb
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
b65650f 
…Link into feat/ocm/feature_input_ports
@jdcpni
• optimizationcontrolmechanism.py:
822742f 
  - _instantiate_control_signals: random_seeds -> random_seed_mod_values
@jdcpni
• composition.py
5a3efba 
  - _add_controller:  modifying to instantiate feature_input_ports if none are specified
@jdcpni
• composition.py:
7acdebd 
  - add_controller:  now adds feature_input_ports for Compostion INPUT nodes if not state_features not specified
@jdcpni
-
f81baf5
@jdcpni
• composition.py
cc1e98e 
  - _add_controller:  modifying to instantiate feature_input_ports if none are specified
@jdcpni
• composition.py:
a00b95f 
  - add_controller:  assign simulation_input_ports
@jdcpni
-
ed0a720
@jdcpni
• optimizationcontrolmechanism.py:
cb0b930 
  - feature_input_ports -> state_input_ports
  - _instantiate_input_ports():
      state_features only allowed to specifying state_input_ports if
      agent_rep is a CompositionFunctionApproximator (i.e., model-free optimization)

• composition.py:
  - add_controller: adds state_input_ports to shadow INPUT Nodes of Composition
    if controller.agent_rep is Composition (model-based optimziation)
    or state_features have not been specified (for model-free optimizaton)
@jdcpni
-
8cadf24
@jdcpni
• optimizationcontrolmechanism.py:
1cc216e 
  _instantiate_input_ports:
     reinstate allowance of state_features specification if agent_rep is a Composition
     (i.e., model-based optimization) as long as they are all INPUT Nodes of agent_rep
@jdcpni
-
ba278c1
@jdcpni
-
b5f1c66
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
0e38f1b 
…Link into devel
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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

diff -r docs-base/ControlSignal.html docs-head/ControlSignal.html
254c254
< controlled in the <strong>projections</strong> argument or <em>PROJECTIONS</em> entry, respectively, using any of the forms below.
---
> controlled are specified in the <strong>control</strong> argument or <em>CONTROL</em> entry, respectively, using any of the forms below.
314,315c314,315
< the <strong>projections</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
< with the key <em>PROJECTIONS</em>.  These will be assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
---
> the <strong>control</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
> with the key <em>CONTROL</em>.  These are assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
317c317
< creating a Port.</p>
---
> creating a Port, including <a class="reference internal" href="Port.html#port-modulatory-projections-examples"><span class="std std-ref">examples</span></a> of ControlProjection specification.</p>
497c497
< <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">modulates</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
---
> <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">control</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
540c540
< <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">modulates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
---
> <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">control</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
561c561
< <li><p><strong>modulates</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
---
> <li><p><strong>control</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
diff -r docs-base/OptimizationControlMechanism.html docs-head/OptimizationControlMechanism.html
652a653,663
> <blockquote>
> <div><div class="admonition note">
> <p class="admonition-title">Note</p>
> <p>If a <a class="reference internal" href="Composition.html#composition-nodes"><span class="std std-ref">Node</span></a> other than an <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> of a <a class="reference internal" href="Composition.html#composition-nested"><span class="std std-ref">nested</span></a>
> Composition is <a class="reference internal" href="ControlMechanism.html#controlmechanism-monitor-for-control"><span class="std std-ref">specified to be monitored</span></a>, it is assigned as a <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> of that nested Composition. Although <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are generally treated
> like <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes (since they project out of the Composition to which they belong), their
> <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> is not included in the <a class="reference internal" href="Composition.html#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition for which the OptimizationControlMechanism is the
> <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.controller" title="psyneulink.core.compositions.composition.Composition.controller"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">controller</span></code></a>, unless that Composition’s <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> attribute is set to True (see <code class="xref any docutils literal notranslate"><span class="pre">Composition_Probes</span></code> for additional
> information).</p>
> </div>
> </div></blockquote>
diff -r docs-base/Port.html docs-head/Port.html
744c744
< <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THREHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
---
> <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THRESHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
750,752c750,754
< uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  In the example above,
< both ControlProjections are assigned to a single ControlSignal.  However, they could each be assigned to their own by
< specifying them in separate itesm of the <strong>control_signals</strong> argument:</p>
---
> uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  Note also that, for specifying Projections
> of a ControlSignal (i.e., its ControlProjections), the keyword <em>CONTROL</em> can be used in place of the more generic
> <em>PROJECTIONS</em> keyword (as shown in the example below).</p>
> <p>In the example above, both ControlProjections are assigned to a single ControlSignal.  However, they could each be
> assigned to their own by specifying them in separate items of the <strong>control_signals</strong> argument:</p>
755c757
<                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">PROJECTIONS</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">DRIFT_RATE</span><span class="p">]]},</span>
---
>                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">CONTROL</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">DRIFT_RATE</span><span class="p">]]},</span>
757c759
<                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">PROJECTIONS</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">THRESHOLD</span><span class="p">]]}])</span>
---
>                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">CONTROL</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">THRESHOLD</span><span class="p">]]}])</span>
diff -r docs-base/searchindex.js docs-head/searchindex.js
1c1
< Search.setIndex({docnames:["AGT","AGTControlMechanism","AutoAssociativeLearningMechanism","AutoAssociativeProjection","AutodiffComposition","BasicsAndPrimer","BotvinickConflictMonitoringModel","BustamanteStroopXORLVOCModel","Cohen_HustonModel","CombinationFunctions","ComparatorMechanism","Compilation","Component","Components","Composition","CompositionFunctionApproximator","CompositionInterfaceMechanism","Compositions","Condition","Context","ContrastiveHebbianMechanism","ContributorsGuide","ControlMechanism","ControlMechanisms","ControlProjection","ControlProjections","ControlSignal","ConventionsAndDefinitions","Core","DDM","DefaultControlMechanism","Defaults","DistributionFunctions","EVC","EVCAuxiliary","EVCControlMechanism","EpisodicMemoryMechanism","Function","Functions","GatingMechanism","GatingMechanisms","GatingProjection","GatingProjections","Ga
...

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This pull request introduces 3 alerts when merging 9b47e1d into 9e88ae4 - view on LGTM.com

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@jdcpni
• gatingsignal.py:
99e4007 
  - __init__: replace modulates arg with gate
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github-actions bot commented Jan 2, 2022

This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

diff -r docs-base/ControlSignal.html docs-head/ControlSignal.html
254c254
< controlled in the <strong>projections</strong> argument or <em>PROJECTIONS</em> entry, respectively, using any of the forms below.
---
> controlled are specified in the <strong>control</strong> argument or <em>CONTROL</em> entry, respectively, using any of the forms below.
314,315c314,315
< the <strong>projections</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
< with the key <em>PROJECTIONS</em>.  These will be assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
---
> the <strong>control</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
> with the key <em>CONTROL</em>.  These are assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
317c317
< creating a Port.</p>
---
> creating a Port, including <a class="reference internal" href="Port.html#port-modulatory-projections-examples"><span class="std std-ref">examples</span></a> of ControlProjection specification.</p>
497c497
< <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">modulates</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
---
> <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">control</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
540c540
< <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">modulates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
---
> <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">control</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
561c561
< <li><p><strong>modulates</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
---
> <li><p><strong>control</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
diff -r docs-base/GatingSignal.html docs-head/GatingSignal.html
437a438,440
> <li><p><strong>gate</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="GatingProjection.html"><span class="doc">GatingProjection(s)</span></a> to be assigned to the GatingSignal, and that will be
> listed in its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute (see <a class="reference internal" href="#gatingsignal-projections"><span class="std std-ref">Projections</span></a> for additional
> details).</p></li>
diff -r docs-base/OptimizationControlMechanism.html docs-head/OptimizationControlMechanism.html
652a653,663
> <blockquote>
> <div><div class="admonition note">
> <p class="admonition-title">Note</p>
> <p>If a <a class="reference internal" href="Composition.html#composition-nodes"><span class="std std-ref">Node</span></a> other than an <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> of a <a class="reference internal" href="Composition.html#composition-nested"><span class="std std-ref">nested</span></a>
> Composition is <a class="reference internal" href="ControlMechanism.html#controlmechanism-monitor-for-control"><span class="std std-ref">specified to be monitored</span></a>, it is assigned as a <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> of that nested Composition. Although <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are generally treated
> like <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes (since they project out of the Composition to which they belong), their
> <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> is not included in the <a class="reference internal" href="Composition.html#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition for which the OptimizationControlMechanism is the
> <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.controller" title="psyneulink.core.compositions.composition.Composition.controller"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">controller</span></code></a>, unless that Composition’s <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> attribute is set to True (see <code class="xref any docutils literal notranslate"><span class="pre">Composition_Probes</span></code> for additional
> information).</p>
> </div>
> </div></blockquote>
diff -r docs-base/Port.html docs-head/Port.html
744c744
< <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THREHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
---
> <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THRESHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
750,752c750,754
< uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  In the example above,
< both ControlProjections are assigned to a single ControlSignal.  However, they could each be assigned to their own by
< specifying them in separate itesm of the <strong>control_signals</strong> argument:</p>
---
> uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  Note also that, for specifying Projections
> of a ControlSignal (i.e., its ControlProjections), the keyword <em>CONTROL</em> can be used in place of the more generic
> <em>PROJECTIONS</em> keyword (as shown in the example below).</p>
> <p>In the example above, both ControlProjections are assigned to a single ControlSignal.  However, they could each be
> assigned to their own by specifying them in separate items of the <strong>control_signals</strong> argument:</p>
755c757
<                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">PROJECTIONS</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">DRIFT_RATE</span><span class="p">]]},</span>
---
>                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">CONTROL</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">DRIFT_RATE</span><span class="p">]]},</span>
757c759
<                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">PROJECTIONS</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">THRESHOLD</span><span class="p">]]}])</span>
---
>                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">CONTROL</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">THRESHOLD</span><span class="p">]]}])</span>
diff -r docs-base/searchindex.js docs-head/searchind
...

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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

diff -r docs-base/ControlSignal.html docs-head/ControlSignal.html
254c254
< controlled in the <strong>projections</strong> argument or <em>PROJECTIONS</em> entry, respectively, using any of the forms below.
---
> controlled are specified in the <strong>control</strong> argument or <em>CONTROL</em> entry, respectively, using any of the forms below.
314,315c314,315
< the <strong>projections</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
< with the key <em>PROJECTIONS</em>.  These will be assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
---
> the <strong>control</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
> with the key <em>CONTROL</em>.  These are assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
317c317
< creating a Port.</p>
---
> creating a Port, including <a class="reference internal" href="Port.html#port-modulatory-projections-examples"><span class="std std-ref">examples</span></a> of ControlProjection specification.</p>
497c497
< <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">modulates</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
---
> <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">control</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
540c540
< <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">modulates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
---
> <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">control</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
561c561
< <li><p><strong>modulates</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
---
> <li><p><strong>control</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
diff -r docs-base/GatingSignal.html docs-head/GatingSignal.html
437a438,440
> <li><p><strong>gate</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="GatingProjection.html"><span class="doc">GatingProjection(s)</span></a> to be assigned to the GatingSignal, and that will be
> listed in its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute (see <a class="reference internal" href="#gatingsignal-projections"><span class="std std-ref">Projections</span></a> for additional
> details).</p></li>
diff -r docs-base/OptimizationControlMechanism.html docs-head/OptimizationControlMechanism.html
652a653,663
> <blockquote>
> <div><div class="admonition note">
> <p class="admonition-title">Note</p>
> <p>If a <a class="reference internal" href="Composition.html#composition-nodes"><span class="std std-ref">Node</span></a> other than an <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> of a <a class="reference internal" href="Composition.html#composition-nested"><span class="std std-ref">nested</span></a>
> Composition is <a class="reference internal" href="ControlMechanism.html#controlmechanism-monitor-for-control"><span class="std std-ref">specified to be monitored</span></a>, it is assigned as a <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> of that nested Composition. Although <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are generally treated
> like <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes (since they project out of the Composition to which they belong), their
> <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> is not included in the <a class="reference internal" href="Composition.html#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition for which the OptimizationControlMechanism is the
> <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.controller" title="psyneulink.core.compositions.composition.Composition.controller"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">controller</span></code></a>, unless that Composition’s <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> attribute is set to True (see <code class="xref any docutils literal notranslate"><span class="pre">Composition_Probes</span></code> for additional
> information).</p>
> </div>
> </div></blockquote>
diff -r docs-base/Port.html docs-head/Port.html
744c744
< <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THREHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
---
> <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THRESHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
750,752c750,754
< uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  In the example above,
< both ControlProjections are assigned to a single ControlSignal.  However, they could each be assigned to their own by
< specifying them in separate itesm of the <strong>control_signals</strong> argument:</p>
---
> uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  Note also that, for specifying Projections
> of a ControlSignal (i.e., its ControlProjections), the keyword <em>CONTROL</em> can be used in place of the more generic
> <em>PROJECTIONS</em> keyword (as shown in the example below).</p>
> <p>In the example above, both ControlProjections are assigned to a single ControlSignal.  However, they could each be
> assigned to their own by specifying them in separate items of the <strong>control_signals</strong> argument:</p>
755c757
<                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">PROJECTIONS</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">DRIFT_RATE</span><span class="p">]]},</span>
---
>                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">CONTROL</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">DRIFT_RATE</span><span class="p">]]},</span>
757c759
<                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">PROJECTIONS</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">THRESHOLD</span><span class="p">]]}])</span>
---
>                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">CONTROL</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">THRESHOLD</span><span class="p">]]}])</span>
diff -r docs-base/searchindex.js docs-head/searchind
...

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Coverage increased (+0.004%) to 84.329% when pulling 2176cc1 on feat/control_signal/add_control_arg into 9e88ae4 on devel.

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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

diff -r docs-base/ControlSignal.html docs-head/ControlSignal.html
254c254
< controlled in the <strong>projections</strong> argument or <em>PROJECTIONS</em> entry, respectively, using any of the forms below.
---
> controlled are specified in the <strong>control</strong> argument or <em>CONTROL</em> entry, respectively, using any of the forms below.
314,315c314,315
< the <strong>projections</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
< with the key <em>PROJECTIONS</em>.  These will be assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
---
> the <strong>control</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
> with the key <em>CONTROL</em>.  These are assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
317c317
< creating a Port.</p>
---
> creating a Port, including <a class="reference internal" href="Port.html#port-modulatory-projections-examples"><span class="std std-ref">examples</span></a> of ControlProjection specification.</p>
497c497
< <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">modulates</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
---
> <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">control</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
540c540
< <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">modulates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
---
> <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">control</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
561c561
< <li><p><strong>modulates</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
---
> <li><p><strong>control</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
diff -r docs-base/GatingSignal.html docs-head/GatingSignal.html
437a438,440
> <li><p><strong>gate</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="GatingProjection.html"><span class="doc">GatingProjection(s)</span></a> to be assigned to the GatingSignal, and that will be
> listed in its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute (see <a class="reference internal" href="#gatingsignal-projections"><span class="std std-ref">Projections</span></a> for additional
> details).</p></li>
diff -r docs-base/OptimizationControlMechanism.html docs-head/OptimizationControlMechanism.html
652a653,663
> <blockquote>
> <div><div class="admonition note">
> <p class="admonition-title">Note</p>
> <p>If a <a class="reference internal" href="Composition.html#composition-nodes"><span class="std std-ref">Node</span></a> other than an <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> of a <a class="reference internal" href="Composition.html#composition-nested"><span class="std std-ref">nested</span></a>
> Composition is <a class="reference internal" href="ControlMechanism.html#controlmechanism-monitor-for-control"><span class="std std-ref">specified to be monitored</span></a>, it is assigned as a <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> of that nested Composition. Although <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are generally treated
> like <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes (since they project out of the Composition to which they belong), their
> <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> is not included in the <a class="reference internal" href="Composition.html#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition for which the OptimizationControlMechanism is the
> <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.controller" title="psyneulink.core.compositions.composition.Composition.controller"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">controller</span></code></a>, unless that Composition’s <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> attribute is set to True (see <code class="xref any docutils literal notranslate"><span class="pre">Composition_Probes</span></code> for additional
> information).</p>
> </div>
> </div></blockquote>
diff -r docs-base/Parameters.html docs-head/Parameters.html
285c285,286
< <li><p>as with <em>q</em>, specifying an explicit instance of the Parameter class allows you to modify the <a class="reference internal" href="#parameter-attributes-table"><span class="std std-ref">Parameter attributes</span></a></p></li>
---
> <li><p>as with <em>q</em>, specifying an explicit instance of the Parameter class allows you to modify the
> <a class="reference internal" href="#parameter-attributes-table"><span class="std std-ref">Parameter attributes</span></a></p></li>
290c291,292
< <li><p>if you want assignments to parameter <em>p</em> to be validated, add a method _validate_p(value), that returns None if value is a valid assignment, or an error string if value is not a valid assignment</p></li>
---
> <li><p>if you want assignments to parameter <em>p</em> to be validated, add a method _validate_p(value),
> that returns None if value is a valid assignment, or an error string if value is not a valid assignment</p></li>
diff -r docs-base/Port.html docs-head/Port.html
744c744
< <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THREHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
---
> <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THRESHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
750,752c750,754
< uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  In the example above,
< both ControlProjections are assigned to a single ControlSignal.  However, they could each be assigned to their own by
< specifying them in separate itesm of the <strong>control_signals</strong> argument:</p>
---
> uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  Note also that, for specifying Projections
> of a ControlSignal (i.e., its ControlProjections), the keyword <em>CONTROL</em> can be used in place of the more generic
> <em>PROJECTIONS</em> keyword (as shown in the example below).</p>
> <p>In the example above, both ControlProjections are assigned to a single ControlSignal.  However, they could each be
> assigned to their own by specifying them in separate items of the <strong>control_signals</strong> argument:</p>
755c757
<                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">PROJECTIONS</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">DRIFT_RATE</span><span class="p">]]},</span>
---
>                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">CONTROL</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span c
...

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lgtm-com bot commented Jan 3, 2022

This pull request introduces 2 alerts when merging 181ad8c into 9e88ae4 - view on LGTM.com

new alerts:

  • 2 for Unused import

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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

diff -r docs-base/ControlSignal.html docs-head/ControlSignal.html
254c254
< controlled in the <strong>projections</strong> argument or <em>PROJECTIONS</em> entry, respectively, using any of the forms below.
---
> controlled are specified in the <strong>control</strong> argument or <em>CONTROL</em> entry, respectively, using any of the forms below.
314,315c314,315
< the <strong>projections</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
< with the key <em>PROJECTIONS</em>.  These will be assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
---
> the <strong>control</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
> with the key <em>CONTROL</em>.  These are assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
317c317
< creating a Port.</p>
---
> creating a Port, including <a class="reference internal" href="Port.html#port-modulatory-projections-examples"><span class="std std-ref">examples</span></a> of ControlProjection specification.</p>
497c497
< <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">modulates</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
---
> <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">control</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
540c540
< <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">modulates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
---
> <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">control</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
561c561
< <li><p><strong>modulates</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
---
> <li><p><strong>control</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
diff -r docs-base/GatingSignal.html docs-head/GatingSignal.html
437a438,440
> <li><p><strong>gate</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="GatingProjection.html"><span class="doc">GatingProjection(s)</span></a> to be assigned to the GatingSignal, and that will be
> listed in its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute (see <a class="reference internal" href="#gatingsignal-projections"><span class="std std-ref">Projections</span></a> for additional
> details).</p></li>
diff -r docs-base/OptimizationControlMechanism.html docs-head/OptimizationControlMechanism.html
652a653,663
> <blockquote>
> <div><div class="admonition note">
> <p class="admonition-title">Note</p>
> <p>If a <a class="reference internal" href="Composition.html#composition-nodes"><span class="std std-ref">Node</span></a> other than an <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> of a <a class="reference internal" href="Composition.html#composition-nested"><span class="std std-ref">nested</span></a>
> Composition is <a class="reference internal" href="ControlMechanism.html#controlmechanism-monitor-for-control"><span class="std std-ref">specified to be monitored</span></a>, it is assigned as a <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> of that nested Composition. Although <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are generally treated
> like <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes (since they project out of the Composition to which they belong), their
> <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> is not included in the <a class="reference internal" href="Composition.html#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition for which the OptimizationControlMechanism is the
> <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.controller" title="psyneulink.core.compositions.composition.Composition.controller"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">controller</span></code></a>, unless that Composition’s <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> attribute is set to True (see <code class="xref any docutils literal notranslate"><span class="pre">Composition_Probes</span></code> for additional
> information).</p>
> </div>
> </div></blockquote>
diff -r docs-base/Parameters.html docs-head/Parameters.html
285c285,286
< <li><p>as with <em>q</em>, specifying an explicit instance of the Parameter class allows you to modify the <a class="reference internal" href="#parameter-attributes-table"><span class="std std-ref">Parameter attributes</span></a></p></li>
---
> <li><p>as with <em>q</em>, specifying an explicit instance of the Parameter class allows you to modify the
> <a class="reference internal" href="#parameter-attributes-table"><span class="std std-ref">Parameter attributes</span></a></p></li>
290c291,292
< <li><p>if you want assignments to parameter <em>p</em> to be validated, add a method _validate_p(value), that returns None if value is a valid assignment, or an error string if value is not a valid assignment</p></li>
---
> <li><p>if you want assignments to parameter <em>p</em> to be validated, add a method _validate_p(value),
> that returns None if value is a valid assignment, or an error string if value is not a valid assignment</p></li>
diff -r docs-base/Port.html docs-head/Port.html
744c744
< <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THREHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
---
> <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THRESHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
750,752c750,754
< uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  In the example above,
< both ControlProjections are assigned to a single ControlSignal.  However, they could each be assigned to their own by
< specifying them in separate itesm of the <strong>control_signals</strong> argument:</p>
---
> uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  Note also that, for specifying Projections
> of a ControlSignal (i.e., its ControlProjections), the keyword <em>CONTROL</em> can be used in place of the more generic
> <em>PROJECTIONS</em> keyword (as shown in the example below).</p>
> <p>In the example above, both ControlProjections are assigned to a single ControlSignal.  However, they could each be
> assigned to their own by specifying them in separate items of the <strong>control_signals</strong> argument:</p>
755c757
<                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">PROJECTIONS</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">DRIFT_RATE</span><span class="p">]]},</span>
---
>                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">CONTROL</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span c
...

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This pull request introduces 2 alerts when merging ecf67af into 9e88ae4 - view on LGTM.com

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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

diff -r docs-base/ControlSignal.html docs-head/ControlSignal.html
254c254
< controlled in the <strong>projections</strong> argument or <em>PROJECTIONS</em> entry, respectively, using any of the forms below.
---
> controlled are specified in the <strong>control</strong> argument or <em>CONTROL</em> entry, respectively, using any of the forms below.
314,315c314,315
< the <strong>projections</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
< with the key <em>PROJECTIONS</em>.  These will be assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
---
> the <strong>control</strong> argument of its constructor, or in an entry of a dictionary assigned to the <strong>params</strong> argument
> with the key <em>CONTROL</em>.  These are assigned to its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute.  See
317c317
< creating a Port.</p>
---
> creating a Port, including <a class="reference internal" href="Port.html#port-modulatory-projections-examples"><span class="std std-ref">examples</span></a> of ControlProjection specification.</p>
497c497
< <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">modulates</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
---
> <span class="gp">... </span>                              <span class="n">control_signals</span><span class="o">=</span><span class="n">ControlSignal</span><span class="p">(</span><span class="n">control</span><span class="o">=</span><span class="p">(</span><span class="n">INTERCEPT</span><span class="p">,</span><span class="n">mech</span><span class="p">),</span>
540c540
< <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">modulates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
---
> <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.core.components.ports.modulatorysignals.controlsignal.</span></span><span class="sig-name descname"><span class="pre">ControlSignal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_allocation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">defaultControlAllocation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">TransferWithCosts</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">costs_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">intensity_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Exponential</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adjustment_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Linear</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">duration_cost_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">IntegratorFunction</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">combine_costs_function</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Reduce(operation=SUM)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allocation_samples</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">self.class_defaults.allocation_samples</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">control</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">projections</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal" title="Permalink to this definition">¶</a></dt>
561c561
< <li><p><strong>modulates</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
---
> <li><p><strong>control</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="ControlProjection.html"><span class="doc">ControlProjection(s)</span></a> to be assigned to the ControlSignal, and that will be
diff -r docs-base/GatingSignal.html docs-head/GatingSignal.html
437a438,440
> <li><p><strong>gate</strong> (<em>list of Projection specifications</em>) – specifies the <a class="reference internal" href="GatingProjection.html"><span class="doc">GatingProjection(s)</span></a> to be assigned to the GatingSignal, and that will be
> listed in its <a class="reference internal" href="ModulatorySignal.html#psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents" title="psyneulink.core.components.ports.modulatorysignals.modulatorysignal.ModulatorySignal.efferents"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">efferents</span></code></a> attribute (see <a class="reference internal" href="#gatingsignal-projections"><span class="std std-ref">Projections</span></a> for additional
> details).</p></li>
diff -r docs-base/OptimizationControlMechanism.html docs-head/OptimizationControlMechanism.html
652a653,663
> <blockquote>
> <div><div class="admonition note">
> <p class="admonition-title">Note</p>
> <p>If a <a class="reference internal" href="Composition.html#composition-nodes"><span class="std std-ref">Node</span></a> other than an <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> of a <a class="reference internal" href="Composition.html#composition-nested"><span class="std std-ref">nested</span></a>
> Composition is <a class="reference internal" href="ControlMechanism.html#controlmechanism-monitor-for-control"><span class="std std-ref">specified to be monitored</span></a>, it is assigned as a <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> of that nested Composition. Although <a class="reference internal" href="Composition.html#id18" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are generally treated
> like <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes (since they project out of the Composition to which they belong), their
> <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> is not included in the <a class="reference internal" href="Composition.html#id0" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> attributes of the Composition for which the OptimizationControlMechanism is the
> <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.controller" title="psyneulink.core.compositions.composition.Composition.controller"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">controller</span></code></a>, unless that Composition’s <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> attribute is set to True (see <code class="xref any docutils literal notranslate"><span class="pre">Composition_Probes</span></code> for additional
> information).</p>
> </div>
> </div></blockquote>
diff -r docs-base/Parameters.html docs-head/Parameters.html
285c285,286
< <li><p>as with <em>q</em>, specifying an explicit instance of the Parameter class allows you to modify the <a class="reference internal" href="#parameter-attributes-table"><span class="std std-ref">Parameter attributes</span></a></p></li>
---
> <li><p>as with <em>q</em>, specifying an explicit instance of the Parameter class allows you to modify the
> <a class="reference internal" href="#parameter-attributes-table"><span class="std std-ref">Parameter attributes</span></a></p></li>
290c291,292
< <li><p>if you want assignments to parameter <em>p</em> to be validated, add a method _validate_p(value), that returns None if value is a valid assignment, or an error string if value is not a valid assignment</p></li>
---
> <li><p>if you want assignments to parameter <em>p</em> to be validated, add a method _validate_p(value),
> that returns None if value is a valid assignment, or an error string if value is not a valid assignment</p></li>
diff -r docs-base/Port.html docs-head/Port.html
744c744
< <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THREHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
---
> <span class="o">&gt;</span> <span class="n">MY</span> <span class="n">DDM</span> <span class="n">DRIFT</span> <span class="n">RATE</span> <span class="n">AND</span> <span class="n">THRESHOLD</span> <span class="n">CONTROL</span> <span class="n">SIGNAL</span>
750,752c750,754
< uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  In the example above,
< both ControlProjections are assigned to a single ControlSignal.  However, they could each be assigned to their own by
< specifying them in separate itesm of the <strong>control_signals</strong> argument:</p>
---
> uses <code class="xref any docutils literal notranslate"><span class="pre">ControlSignal</span></code> for its <a class="reference internal" href="OutputPort.html"><span class="doc">OutputPorts</span></a>.  Note also that, for specifying Projections
> of a ControlSignal (i.e., its ControlProjections), the keyword <em>CONTROL</em> can be used in place of the more generic
> <em>PROJECTIONS</em> keyword (as shown in the example below).</p>
> <p>In the example above, both ControlProjections are assigned to a single ControlSignal.  However, they could each be
> assigned to their own by specifying them in separate items of the <strong>control_signals</strong> argument:</p>
755c757
<                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">PROJECTIONS</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span class="p">[</span><span class="n">pnl</span><span class="o">.</span><span class="n">DRIFT_RATE</span><span class="p">]]},</span>
---
>                                                      <span class="n">pnl</span><span class="o">.</span><span class="n">CONTROL</span><span class="p">:</span> <span class="p">[</span><span class="n">my_mech</span><span class="o">.</span><span class="n">parameter_ports</span><span c
...

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lgtm-com bot commented Jan 3, 2022

This pull request introduces 2 alerts when merging 2176cc1 into 9e88ae4 - view on LGTM.com

new alerts:

  • 2 for Unused import

@jdcpni jdcpni merged commit 1fdb95d into devel Jan 3, 2022
@jdcpni jdcpni deleted the feat/control_signal/add_control_arg branch January 3, 2022 16:09
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@jdcpni @coveralls @jvesely @kmantel