treewide: Don't use numpy asfarray #3158

jvesely · 2025-01-09T19:03:43Z

It is not available in Numpy 2+[0] and is mostly not necessary.

[0] https://numpy.org/devdocs/numpy_2_0_migration_guide.html#main-namespace

2^31 is out of range for signed int32. Simplify calculation of the next seed value. Signed-off-by: Jan Vesely <[email protected]>

run_stab_flex_cond explicitly call the constructed composition with execution_mode=LLVMRun Signed-off-by: Jan Vesely <[email protected]>

Creating float arrays before comparing results is not necessary. Constructors using explicit dtype should use 'asarray' instead. np.asfarray is not present in Numpy 2+. Signed-off-by: Jan Vesely <[email protected]>

psyneulink/core/globals/utilities.py

github-actions · 2025-01-09T19:10:39Z

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/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" 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>

...

See CI logs for the full diff.

Signed-off-by: Jan Vesely <[email protected]>

asfarray is not present in Numpy 2+ Signed-off-by: Jan Vesely <[email protected]>

github-actions · 2025-01-09T21:11:02Z

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>
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< <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>
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< 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/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" 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>

...

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jvesely added 3 commits January 8, 2025 12:46

utilities: Change seed type to unsigned integer

3c3cee6

2^31 is out of range for signed int32. Simplify calculation of the next seed value. Signed-off-by: Jan Vesely <[email protected]>

tests/test_stab_flex_cond_fit: Mark as llvm

39d0af7

run_stab_flex_cond explicitly call the constructed composition with execution_mode=LLVMRun Signed-off-by: Jan Vesely <[email protected]>

tests: Drop unnecessary use of np.asfarray

d00a524

Creating float arrays before comparing results is not necessary. Constructors using explicit dtype should use 'asarray' instead. np.asfarray is not present in Numpy 2+. Signed-off-by: Jan Vesely <[email protected]>

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jvesely added 2 commits January 9, 2025 16:03

llvm: Use np.asarray instead of asfarray if dtype is provided

c9fcf7a

Signed-off-by: Jan Vesely <[email protected]>

treewide: Use asarray(dtype=float) instead of asfarray

c8eb799

asfarray is not present in Numpy 2+ Signed-off-by: Jan Vesely <[email protected]>

jvesely force-pushed the devel-numpy branch from c1effb2 to c8eb799 Compare January 9, 2025 21:04

jvesely merged commit 4a5472c into PrincetonUniversity:devel Jan 10, 2025
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jvesely deleted the devel-numpy branch January 10, 2025 01:13

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treewide: Don't use numpy asfarray #3158

treewide: Don't use numpy asfarray #3158

jvesely commented Jan 9, 2025 •

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treewide: Don't use numpy asfarray #3158

treewide: Don't use numpy asfarray #3158

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jvesely commented Jan 9, 2025 •

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