refactor/transfermech_and_fct/clip_scale_offset

[jdcpni]

• TransferFunction: standardize scale and offset Parameters to both apply to the result of the function
• TransferMechanism: issue warning if specified clip is beyond range of function (i.e., its bounds*scale+offset)

[github-actions]

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

diff -r docs-base/Component.html docs-head/Component.html
522c522
< <li><p><strong>execute_until_finished</strong> – determines whether the Component executes until its <a class="reference internal" href="#psyneulink.core.components.component.Component.is_finished" title="psyneulink.core.components.component.Component.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method returns True.
---
> <li><p><strong>execute_until_finished</strong> – determines whether the Component executes until its <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method returns True.
524,525c524,525
< irrespective of its <a class="reference internal" href="#psyneulink.core.components.component.Component.is_finished" title="psyneulink.core.components.component.Component.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method;  if it is True then, depending on how its class implements and handles its
< <a class="reference internal" href="#psyneulink.core.components.component.Component.is_finished" title="psyneulink.core.components.component.Component.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method, the Component may execute more than once per call to its <a class="reference internal" href="#psyneulink.core.components.component.Component.execute" title="psyneulink.core.components.component.Component.execute"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">execute</span></code></a> method.</p></li>
---
> irrespective of its <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method;  if it is True then, depending on how its class implements and handles its
> <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method, the Component may execute more than once per call to its <a class="reference internal" href="#psyneulink.core.components.component.Component.execute" title="psyneulink.core.components.component.Component.execute"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">execute</span></code></a> method.</p></li>
530c530
< <a class="reference internal" href="#psyneulink.core.components.component.Component.execute" title="psyneulink.core.components.component.Component.execute"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">execute</span></code></a> method, or extend over several calls.  It is set to 0 each time <a class="reference internal" href="#psyneulink.core.components.component.Component.is_finished" title="psyneulink.core.components.component.Component.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> evaluates
---
> <a class="reference internal" href="#psyneulink.core.components.component.Component.execute" title="psyneulink.core.components.component.Component.execute"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">execute</span></code></a> method, or extend over several calls.  It is set to 0 each time <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> evaluates
diff -r docs-base/Condition.html docs-head/Condition.html
463c463
< satisfied when the <a class="reference internal" href="Component.html#psyneulink.core.components.component.Component.is_finished" title="psyneulink.core.components.component.Component.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method of the specified node,       given <a class="reference internal" href="Context.html#psyneulink.core.globals.context.Context.execution_id" title="psyneulink.core.globals.context.Context.execution_id"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">execution_id</span></code></a> returns <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
---
> satisfied when the <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method of the specified node,       given <a class="reference internal" href="Context.html#psyneulink.core.globals.context.Context.execution_id" title="psyneulink.core.globals.context.Context.execution_id"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">execution_id</span></code></a> returns <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
465c465
< satisfied when the <a class="reference internal" href="Component.html#psyneulink.core.components.component.Component.is_finished" title="psyneulink.core.components.component.Component.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method of any of the specified       nodes, given <a class="reference internal" href="Context.html#psyneulink.core.globals.context.Context.execution_id" title="psyneulink.core.globals.context.Context.execution_id"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">execution_id</span></code></a> returns <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
---
> satisfied when the <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method of any of the specified       nodes, given <a class="reference internal" href="Context.html#psyneulink.core.globals.context.Context.execution_id" title="psyneulink.core.globals.context.Context.execution_id"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">execution_id</span></code></a> returns <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
467c467
< satisfied when the <a class="reference internal" href="Component.html#psyneulink.core.components.component.Component.is_finished" title="psyneulink.core.components.component.Component.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method of all of the specified       nodes, given <a class="reference internal" href="Context.html#psyneulink.core.globals.context.Context.execution_id" title="psyneulink.core.globals.context.Context.execution_id"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">execution_id</span></code></a> returns <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
---
> satisfied when the <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> method of all of the specified       nodes, given <a class="reference internal" href="Context.html#psyneulink.core.globals.context.Context.execution_id" title="psyneulink.core.globals.context.Context.execution_id"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">execution_id</span></code></a> returns <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
2154c2154
< <li><p>the <a class="reference internal" href="Component.html#psyneulink.core.components.component.Component.is_finished" title="psyneulink.core.components.component.Component.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> methods of the node specified in <strong>dependencies</strong> returns <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
---
> <li><p>the <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> methods of the node specified in <strong>dependencies</strong> returns <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
2177c2177
< <li><p>the <a class="reference internal" href="Component.html#psyneulink.core.components.component.Component.is_finished" title="psyneulink.core.components.component.Component.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> methods of all nodes specified in <strong>dependencies</strong> return <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
---
> <li><p>the <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> methods of all nodes specified in <strong>dependencies</strong> return <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
2203c2203
< <li><p>the <a class="reference internal" href="Component.html#psyneulink.core.components.component.Component.is_finished" title="psyneulink.core.components.component.Component.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> methods of any nodes specified in <strong>dependencies</strong> returns <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
---
> <li><p>the <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> methods of any nodes specified in <strong>dependencies</strong> returns <code class="xref any docutils literal notranslate"><span class="pre">True</span></code>.</p></li>
diff -r docs-base/KohonenMechanism.html docs-head/KohonenMechanism.html
405c405
< <dd><p>Determine numberr of items expected by termination_measure</p>
---
> <dd><p>Determine number of items expected by termination_measure and check clip if specified</p>
diff -r docs-base/LCAMechanism.html docs-head/LCAMechanism.html
345c345
< <li><p><strong>threshold</strong> (<em>float</em><em> or </em><em>None : default None</em>) – specifes the value at which the Mechanism’s <a class="reference internal" href="Component.html#psyneulink.core.components.component.Component.is_finished" title="psyneulink.core.components.component.Component.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> attribute is set to True
---
> <li><p><strong>threshold</strong> (<em>float</em><em> or </em><em>None : default None</em>) – specifes the value at which the Mechanism’s <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.is_finished"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">is_finished</span></code></a> attribute is set to True
diff -r docs-base/LearningFunctions.html docs-head/LearningFunctions.html
1549c1549
< error_matrix passed in the <a class="reference internal" href="AutodiffComposition.html#psyneulink.library.compositions.autodiffcomposition.AutodiffComposition.PytorchCompositionWrapper.params" title="psyneulink.library.compositions.autodiffcomposition.AutodiffComposition.PytorchCompositionWrapper.params"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">params</span></code></a> argument.</p>
---
> error_matrix passed in the <a class="reference internal" href="DistributionFunctions.html#psyneulink.core.components.functions.distributionfunctions.ExponentialDist.params" title="psyneulink.core.components.functions.distributionfunctions.ExponentialDist.params"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">params</span></code></a> argument.</p>
diff -r docs-base/RefactoredLearningGuide.html docs-head/RefactoredLearningGuide.html
282c282
< <p>Notice that we no longer have to extract the target node from the <code class="xref any docutils literal notranslate"><span class="pre">add_backpropagation_learning_pathway</span> <span class="pre">method</span></code>, and can instead pass the targets as output nodes mapped to values, in a new parameter called <code class="xref any docutils literal notranslate"><span class="pre">targets</span></code> in the <a class="reference internal" href="AutodiffComposition.html#psyneulink.library.compositions.autodiffcomposition.AutodiffComposition.learn" title="psyneulink.library.compositions.autodiffcomposition.AutodiffComposition.learn"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">learn</span></code></a> method.</p>
---
> <p>Notice that we no longer have to extract the target node from the <code class="xref any docutils literal notranslate"><span class="pre">add_backpropagation_learning_pathway</span> <span class="pre">method</span></code>, and can instead pass the targets as output nodes mapped to values, in a new parameter called <code class="xref any docutils literal notranslate"><span class="pre">targets</span></code> in the <a class="reference internal" href="EMComposition.html#psyneulink.library.compositions.emcomposition.EMComposition.learn" title="psyneulink.library.compositions.emcomposition.EMComposition.learn"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">learn</span></code></a> method.</p>
287c287
< its constructor to be runtime parameters of its <a class="reference internal" href="AutodiffComposition.html#psyneulink.library.compositions.autodiffcomposition.AutodiffComposition.learn" title="psyneulink.library.compositions.autodiffcomposition.AutodiffComposition.learn"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">learn</span></code></a> method.</p>
---
> its constructor to be runtime parameters of its <a class="reference internal" href="EMComposition.html#psyneulink.library.compositions.emcomposition.EMComposition.learn" titl
...

See CI logs for the full diff.

[coveralls]

coverage: 84.057% (+0.002%) from 84.055%
when pulling 6646a1a on refactor/transfermech_and_fct/clip_scale_offset
into d05a63a on devel.