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Component: rework size argument to accept and validate numpy shapes #3056

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Component: rework size argument to accept and validate numpy shapes #3056

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@kmantel kmantel commented Oct 2, 2024

  • size=int - single input item, with numpy shape (x,)
  • size=iterable - one or more input items, each with respective numpy
    shapes
  • size containing float - no longer supported, because numpy rejects as
    shape (prior behavior casted to int, because size as float isn't
    defined)

ComponentError thrown if default_variable and size arguments are
both provided and conflict

Rename size -> input_shapes

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tests/composition/test_learning.py
input_B = pnl.ProcessingMechanism(name='INPUT_B', size=2)
output = pnl.ProcessingMechanism(name='OUTPUT', size=(2,3))
input_A = pnl.ProcessingMechanism(name='INPUT_A', input_shapes=2)
input_B = pnl.ProcessingMechanism(name='INPUT_B', input_shapes=2)

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Code scanning / CodeQL

Unused local variable Note test

Variable input_B is not used.
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This PR causes the following changes to the html docs (ubuntu-latest-3.11):

diff -r docs-base/AutoAssociativeLearningMechanism.html docs-head/AutoAssociativeLearningMechanism.html
281c281
< <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.library.components.mechanisms.modulatory.learning.autoassociativelearningmechanism.</span></span><span class="sig-name descname"><span class="pre">AutoAssociativeLearningMechanism</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_variable</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</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">function</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">learning_signals</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">modulation</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">learning_rate</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">params</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">name</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">prefs</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.library.components.mechanisms.modulatory.learning.autoassociativelearningmechanism.AutoAssociativeLearningMechanism" 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.library.components.mechanisms.modulatory.learning.autoassociativelearningmechanism.</span></span><span class="sig-name descname"><span class="pre">AutoAssociativeLearningMechanism</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_variable</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_shapes</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">function</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">learning_signals</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">modulation</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">learning_rate</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">params</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">name</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">prefs</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.library.components.mechanisms.modulatory.learning.autoassociativelearningmechanism.AutoAssociativeLearningMechanism" title="Permalink to this definition">¶</a></dt>
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
411,412c411,412
< <span class="gp">&gt;&gt;&gt; </span><span class="n">my_mech_1</span> <span class="o">=</span> <span class="n">pnl</span><span class="o">.</span><span class="n">TransferMechanism</span><span class="p">(</span><span class="n">function</span><span class="o">=</span><span class="n">pnl</span><span class="o">.</span><span class="n">Linear</span><span class="p">,</span> <span class="n">size</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
< <span class="gp">&gt;&gt;&gt; </span><span class="n">my_mech_2</span> <span class="o">=</span> <span class="n">pnl</span><span class="o">.</span><span class="n">TransferMechanism</span><span class="p">(</span><span class="n">function</span><span class="o">=</span><span class="n">pnl</span><span class="o">.</span><span class="n">Linear</span><span class="p">,</span> <span class="n">size</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
---
> <span class="gp">&gt;&gt;&gt; </span><span class="n">my_mech_1</span> <span class="o">=</span> <span class="n">pnl</span><span class="o">.</span><span class="n">TransferMechanism</span><span class="p">(</span><span class="n">function</span><span class="o">=</span><span class="n">pnl</span><span class="o">.</span><span class="n">Linear</span><span class="p">,</span> <span class="n">input_shapes</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
> <span class="gp">&gt;&gt;&gt; </span><span class="n">my_mech_2</span> <span class="o">=</span> <span class="n">pnl</span><span class="o">.</span><span class="n">TransferMechanism</span><span class="p">(</span><span class="n">function</span><span class="o">=</span><span class="n">pnl</span><span class="o">.</span><span class="n">Linear</span><span class="p">,</span> <span class="n">input_shapes</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
282,284c282,284
< <span class="n">input_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;Input&#39;</span><span class="p">)</span>
< <span class="n">hidden_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;hidden&#39;</span><span class="p">)</span>
< <span class="n">output_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;output&#39;</span><span class="p">)</span>
---
> <span class="n">input_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">input_shapes</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;Input&#39;</span><span class="p">)</span>
> <span class="n">hidden_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;hidden&#39;</span><span class="p">)</span>
> <span class="n">output_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">input_shapes</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;output&#39;</span><span class="p">)</span>
363c363
< <span class="n">color_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;COLOR INPUT&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span> <span class="c1"># note: default function is Linear</span>
---
> <span class="n">color_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;COLOR INPUT&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span> <span class="c1"># note: default function is Linear</span>
365c365
< <span class="n">color_hidden</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;COLOR HIDDEN&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">(</span><span class="n">bias</span><span class="o">=-</span><span class="mi">4</span><span class="p">))</span>
---
> <span class="n">color_hidden</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;COLOR HIDDEN&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">(</span><span class="n">bias</span><span class="o">=-</span><span class="mi">4</span><span class="p">))</span>
367c367
< <span class="n">output</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;OUTPUT&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span> <span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">)</span>
---
> <span class="n">output</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;OUTPUT&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span> <span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">)</span>
371c371
< <span class="n">word_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;WORD INPUT&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
---
> <span class="n">word_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;WORD INPUT&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
373c373
< <span class="n">word_hidden</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;WORD HIDDEN&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">(</span><span class="n">bias</span><span class="o">=-</span><span class="mi">4</span><span class="p">))</span>
---
> <span class="n">word_hidden</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;WORD HIDDEN&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">(</span><span class="n">bias</span><span class="o">=-</span><span class="mi">4</span><span class="p">))</span>
378c378
< <span class="n">task_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;TASK INPUT&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
---
> <span class="n">task_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;TASK INPUT&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
478c478
< <span class="n">task</span> <span class="o">=</span> <span class="n">LCAMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;TASK&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
---
> <span class="n">task</span> <span class="o">=</span> <span class="n">LCAMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;TASK&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
524c524
<                                                                   <span class="n">function</span><span class="o">=</span><span class="n">Energy</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
---
>                                                                   <span class="n">function</span><span class="o">=</span><span class="n">Energy</span><span class="p">(</span><span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
1049,1056c1049,1056
< <span class="n">rep_in</span> <span class="o">=</span> <sp
...

See CI logs for the full diff.

@kmantel
Component: rework size argument to accept and validate numpy shapes
d60d535 
- size=int - single input item, with numpy shape (x,)
- size=iterable - one or more input items, each with respective numpy
shapes
- size containing float - no longer supported, because numpy rejects as
shape (prior behavior casted to int, because size as float isn't
defined)

ComponentError thrown if default_variable and size arguments are
both provided and conflict
@kmantel
treewide: rename Component arg size -> input_shapes
938e7b6
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github-actions bot commented Oct 3, 2024

This PR causes the following changes to the html docs (ubuntu-latest-3.11):

diff -r docs-base/AutoAssociativeLearningMechanism.html docs-head/AutoAssociativeLearningMechanism.html
281c281
< <em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">psyneulink.library.components.mechanisms.modulatory.learning.autoassociativelearningmechanism.</span></span><span class="sig-name descname"><span class="pre">AutoAssociativeLearningMechanism</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_variable</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</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">function</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">learning_signals</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">modulation</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">learning_rate</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">params</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">name</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">prefs</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.library.components.mechanisms.modulatory.learning.autoassociativelearningmechanism.AutoAssociativeLearningMechanism" 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.library.components.mechanisms.modulatory.learning.autoassociativelearningmechanism.</span></span><span class="sig-name descname"><span class="pre">AutoAssociativeLearningMechanism</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">default_variable</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">input_shapes</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">function</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">learning_signals</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">modulation</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">learning_rate</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">params</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">name</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">prefs</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#psyneulink.library.components.mechanisms.modulatory.learning.autoassociativelearningmechanism.AutoAssociativeLearningMechanism" title="Permalink to this definition">¶</a></dt>
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
411,412c411,412
< <span class="gp">&gt;&gt;&gt; </span><span class="n">my_mech_1</span> <span class="o">=</span> <span class="n">pnl</span><span class="o">.</span><span class="n">TransferMechanism</span><span class="p">(</span><span class="n">function</span><span class="o">=</span><span class="n">pnl</span><span class="o">.</span><span class="n">Linear</span><span class="p">,</span> <span class="n">size</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
< <span class="gp">&gt;&gt;&gt; </span><span class="n">my_mech_2</span> <span class="o">=</span> <span class="n">pnl</span><span class="o">.</span><span class="n">TransferMechanism</span><span class="p">(</span><span class="n">function</span><span class="o">=</span><span class="n">pnl</span><span class="o">.</span><span class="n">Linear</span><span class="p">,</span> <span class="n">size</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
---
> <span class="gp">&gt;&gt;&gt; </span><span class="n">my_mech_1</span> <span class="o">=</span> <span class="n">pnl</span><span class="o">.</span><span class="n">TransferMechanism</span><span class="p">(</span><span class="n">function</span><span class="o">=</span><span class="n">pnl</span><span class="o">.</span><span class="n">Linear</span><span class="p">,</span> <span class="n">input_shapes</span> <span class="o">=</span> <span class="mi">3</span><span class="p">)</span>
> <span class="gp">&gt;&gt;&gt; </span><span class="n">my_mech_2</span> <span class="o">=</span> <span class="n">pnl</span><span class="o">.</span><span class="n">TransferMechanism</span><span class="p">(</span><span class="n">function</span><span class="o">=</span><span class="n">pnl</span><span class="o">.</span><span class="n">Linear</span><span class="p">,</span> <span class="n">input_shapes</span> <span class="o">=</span> <span class="mi">2</span><span class="p">)</span>
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
282,284c282,284
< <span class="n">input_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;Input&#39;</span><span class="p">)</span>
< <span class="n">hidden_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;hidden&#39;</span><span class="p">)</span>
< <span class="n">output_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;output&#39;</span><span class="p">)</span>
---
> <span class="n">input_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">input_shapes</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;Input&#39;</span><span class="p">)</span>
> <span class="n">hidden_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;hidden&#39;</span><span class="p">)</span>
> <span class="n">output_layer</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">input_shapes</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s1">&#39;output&#39;</span><span class="p">)</span>
363c363
< <span class="n">color_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;COLOR INPUT&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span> <span class="c1"># note: default function is Linear</span>
---
> <span class="n">color_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;COLOR INPUT&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span> <span class="c1"># note: default function is Linear</span>
365c365
< <span class="n">color_hidden</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;COLOR HIDDEN&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">(</span><span class="n">bias</span><span class="o">=-</span><span class="mi">4</span><span class="p">))</span>
---
> <span class="n">color_hidden</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;COLOR HIDDEN&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">(</span><span class="n">bias</span><span class="o">=-</span><span class="mi">4</span><span class="p">))</span>
367c367
< <span class="n">output</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;OUTPUT&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span> <span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">)</span>
---
> <span class="n">output</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;OUTPUT&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span> <span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">)</span>
371c371
< <span class="n">word_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;WORD INPUT&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
---
> <span class="n">word_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;WORD INPUT&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
373c373
< <span class="n">word_hidden</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;WORD HIDDEN&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">(</span><span class="n">bias</span><span class="o">=-</span><span class="mi">4</span><span class="p">))</span>
---
> <span class="n">word_hidden</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;WORD HIDDEN&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">function</span><span class="o">=</span><span class="n">Logistic</span><span class="p">(</span><span class="n">bias</span><span class="o">=-</span><span class="mi">4</span><span class="p">))</span>
378c378
< <span class="n">task_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;TASK INPUT&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
---
> <span class="n">task_input</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;TASK INPUT&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
478c478
< <span class="n">task</span> <span class="o">=</span> <span class="n">LCAMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;TASK&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
---
> <span class="n">task</span> <span class="o">=</span> <span class="n">LCAMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;TASK&#39;</span><span class="p">,</span> <span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
524c524
<                                                                   <span class="n">function</span><span class="o">=</span><span class="n">Energy</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
---
>                                                                   <span class="n">function</span><span class="o">=</span><span class="n">Energy</span><span class="p">(</span><span class="n">input_shapes</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span>
1049,1056c1049,1056
< <span class="n">rep_in</span> <span class="o">=</span> <sp
...

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@kmantel