Fix/comp/build predicted input dicts #2277

jdcpni · 2022-01-06T19:29:29Z

• composition.py:
- build_predicted_inputs_dict(): fixed bug in handling inputs for doubly-nested comps

• test_control.py:
- test_nested_composition_as_agent_rep:
- updated to handle test of above (and associated errors) without a nested agent_rep
- test of nested agent_rep commented out until that is supported

docstring mod to **size**

…Link into devel

added feature_input_ports attribute and num_feature_input_ports property

added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute

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

…Link into feat/ocm/feature_input_ports

…Link into devel

…Link into feat/ocm/feature_input_ports

- _instantiate_control_signals: random_seeds -> random_seed_mod_values

- _add_controller: modifying to instantiate feature_input_ports if none are specified

- add_controller: now adds feature_input_ports for Compostion INPUT nodes if not state_features not specified

- _add_controller: modifying to instantiate feature_input_ports if none are specified

- add_controller: assign simulation_input_ports

- 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)

_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

…Link into feat/composition/probes

- add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output

- add_node(): support tuple with required_role

- _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL)

…nUniversity/PsyNeuLink into feat/composition/probes � Conflicts: � tests/composition/test_composition.py

- add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value()

…Link into feat/composition/probes

- correct path ref • compositioninterfacemechanism.py: - docstring fixes

…Link into devel � Conflicts: � psyneulink/core/components/mechanisms/processing/compositioninterfacemechanism.py

…Link into devel

- build_predicted_inputs_dict(): fixed bug in handling inputs for doubly-nested comps • test_control.py: - test_nested_composition_as_agent_rep: - updated to handle test of above (and associated errors) without a nested agent_rep - test of nested agent_rep commented out until that is supported

…Link into fix/comp/build_predicted_input_dicts

github-actions · 2022-01-06T19:41:46Z

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

diff -r docs-base/Composition.html docs-head/Composition.html
4042,4044c4042,4047
< <dd><p>Get inputs for evaluate method used to execute simulations of Composition.</p>
< <p>Get values of state_input_ports which receive projections from items providing relevant input (and any
< processing of those values specified</p>
---
> <dd><p>Format predict_inputs from controller as input to evaluate method used to execute simulations of Composition.</p>
> <dl class="simple">
> <dt>Get values of state_input_ports that receive projections from items providing relevant input (and any</dt><dd><p>processing of those values specified), and format as input_dict suitable for run() method (called in evaluate)</p>
> </dd>
> </dl>
> <p>Deal with inputs for nodes in nested Compositions</p>
diff -r docs-base/CompositionInterfaceMechanism.html docs-head/CompositionInterfaceMechanism.html
390a391,401
> <dt class="sig sig-object py" id="psyneulink.core.components.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism._get_source_node_for_input_CIM">
> <span class="sig-name descname"><span class="pre">_get_source_node_for_input_CIM</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">port</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start_comp</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">end_comp</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.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism._get_source_node_for_input_CIM" title="Permalink to this definition">¶</a></dt>
> <dd><p>Return Port, Node and Composition  for source of projection to input_CIM from (possibly nested) outer comp
> <strong>port</strong> should be an InputPort or OutputPort of the CompositionInterfaceMechanism;
> <strong>comp</strong> specifies the Composition at which to begin the search (or continue it when called recursively;</p>
> <blockquote>
> <div><p>assumes the current CompositionInterfaceMechanism’s Composition by default</p>
> </div></blockquote>
> </dd></dl>
> 
> <dl class="py method">
395c406
< <strong>comp</strong> specifies the Composition at which to begin the search;  assumes the current</p>
---
> <strong>comp</strong> specifies the Composition at which to begin the search (or continue it when called recursively;</p>
397c408
< <div><p>CompositionInterfaceMechanism’s Composition by default</p>
---
> <div><p>assumes the current CompositionInterfaceMechanism’s Composition by default</p>
406c417
< <strong>comp</strong> specifies the Composition at which to begin the search;  assumes the current</p>
---
> <strong>comp</strong> specifies the Composition at which to begin the search (or continue it when called recursively;</p>
408c419
< <div><p>CompositionInterfaceMechanism’s Composition by default</p>
---
> <div><p>assumes the current CompositionInterfaceMechanism’s Composition by default</p>
diff -r docs-base/genindex.html docs-head/genindex.html
506a507,508
>       <li><a href="CompositionInterfaceMechanism.html#psyneulink.core.components.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism._get_source_node_for_input_CIM">_get_source_node_for_input_CIM() (psyneulink.core.components.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism method)</a>
> </li>
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>   </ul></td>
>   <td style="width: 33%; vertical-align: top;"><ul>
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<   </ul></td>
<   <td style="width: 33%; vertical-align: top;"><ul>
Binary files docs-base/objects.inv and docs-head/objects.inv differ
diff -r docs-base/searchindex.js docs-head/searchindex.js
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...

See CI logs for the full diff.

github-actions · 2022-01-06T19:42:05Z

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

diff -r docs-base/Composition.html docs-head/Composition.html
4042,4044c4042,4047
< <dd><p>Get inputs for evaluate method used to execute simulations of Composition.</p>
< <p>Get values of state_input_ports which receive projections from items providing relevant input (and any
< processing of those values specified</p>
---
> <dd><p>Format predict_inputs from controller as input to evaluate method used to execute simulations of Composition.</p>
> <dl class="simple">
> <dt>Get values of state_input_ports that receive projections from items providing relevant input (and any</dt><dd><p>processing of those values specified), and format as input_dict suitable for run() method (called in evaluate)</p>
> </dd>
> </dl>
> <p>Deal with inputs for nodes in nested Compositions</p>
diff -r docs-base/CompositionInterfaceMechanism.html docs-head/CompositionInterfaceMechanism.html
390a391,401
> <dt class="sig sig-object py" id="psyneulink.core.components.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism._get_source_node_for_input_CIM">
> <span class="sig-name descname"><span class="pre">_get_source_node_for_input_CIM</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">port</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start_comp</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">end_comp</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.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism._get_source_node_for_input_CIM" title="Permalink to this definition">¶</a></dt>
> <dd><p>Return Port, Node and Composition  for source of projection to input_CIM from (possibly nested) outer comp
> <strong>port</strong> should be an InputPort or OutputPort of the CompositionInterfaceMechanism;
> <strong>comp</strong> specifies the Composition at which to begin the search (or continue it when called recursively;</p>
> <blockquote>
> <div><p>assumes the current CompositionInterfaceMechanism’s Composition by default</p>
> </div></blockquote>
> </dd></dl>
> 
> <dl class="py method">
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< <strong>comp</strong> specifies the Composition at which to begin the search;  assumes the current</p>
---
> <strong>comp</strong> specifies the Composition at which to begin the search (or continue it when called recursively;</p>
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< <div><p>CompositionInterfaceMechanism’s Composition by default</p>
---
> <div><p>assumes the current CompositionInterfaceMechanism’s Composition by default</p>
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< <strong>comp</strong> specifies the Composition at which to begin the search;  assumes the current</p>
---
> <strong>comp</strong> specifies the Composition at which to begin the search (or continue it when called recursively;</p>
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< <div><p>CompositionInterfaceMechanism’s Composition by default</p>
---
> <div><p>assumes the current CompositionInterfaceMechanism’s Composition by default</p>
diff -r docs-base/genindex.html docs-head/genindex.html
506a507,508
>       <li><a href="CompositionInterfaceMechanism.html#psyneulink.core.components.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism._get_source_node_for_input_CIM">_get_source_node_for_input_CIM() (psyneulink.core.components.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism method)</a>
> </li>
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>   </ul></td>
>   <td style="width: 33%; vertical-align: top;"><ul>
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<   </ul></td>
<   <td style="width: 33%; vertical-align: top;"><ul>
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diff -r docs-base/searchindex.js docs-head/searchindex.js
1c1
< 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...

See CI logs for the full diff.

github-actions · 2022-01-06T19:45:34Z

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

diff -r docs-base/Composition.html docs-head/Composition.html
4042,4044c4042,4047
< <dd><p>Get inputs for evaluate method used to execute simulations of Composition.</p>
< <p>Get values of state_input_ports which receive projections from items providing relevant input (and any
< processing of those values specified</p>
---
> <dd><p>Format predict_inputs from controller as input to evaluate method used to execute simulations of Composition.</p>
> <dl class="simple">
> <dt>Get values of state_input_ports that receive projections from items providing relevant input (and any</dt><dd><p>processing of those values specified), and format as input_dict suitable for run() method (called in evaluate)</p>
> </dd>
> </dl>
> <p>Deal with inputs for nodes in nested Compositions</p>
diff -r docs-base/CompositionInterfaceMechanism.html docs-head/CompositionInterfaceMechanism.html
390a391,401
> <dt class="sig sig-object py" id="psyneulink.core.components.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism._get_source_node_for_input_CIM">
> <span class="sig-name descname"><span class="pre">_get_source_node_for_input_CIM</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">port</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start_comp</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">end_comp</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.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism._get_source_node_for_input_CIM" title="Permalink to this definition">¶</a></dt>
> <dd><p>Return Port, Node and Composition  for source of projection to input_CIM from (possibly nested) outer comp
> <strong>port</strong> should be an InputPort or OutputPort of the CompositionInterfaceMechanism;
> <strong>comp</strong> specifies the Composition at which to begin the search (or continue it when called recursively;</p>
> <blockquote>
> <div><p>assumes the current CompositionInterfaceMechanism’s Composition by default</p>
> </div></blockquote>
> </dd></dl>
> 
> <dl class="py method">
395c406
< <strong>comp</strong> specifies the Composition at which to begin the search;  assumes the current</p>
---
> <strong>comp</strong> specifies the Composition at which to begin the search (or continue it when called recursively;</p>
397c408
< <div><p>CompositionInterfaceMechanism’s Composition by default</p>
---
> <div><p>assumes the current CompositionInterfaceMechanism’s Composition by default</p>
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< <strong>comp</strong> specifies the Composition at which to begin the search;  assumes the current</p>
---
> <strong>comp</strong> specifies the Composition at which to begin the search (or continue it when called recursively;</p>
408c419
< <div><p>CompositionInterfaceMechanism’s Composition by default</p>
---
> <div><p>assumes the current CompositionInterfaceMechanism’s Composition by default</p>
diff -r docs-base/genindex.html docs-head/genindex.html
506a507,508
>       <li><a href="CompositionInterfaceMechanism.html#psyneulink.core.components.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism._get_source_node_for_input_CIM">_get_source_node_for_input_CIM() (psyneulink.core.components.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism method)</a>
> </li>
652a655,656
>   </ul></td>
>   <td style="width: 33%; vertical-align: top;"><ul>
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<   </ul></td>
<   <td style="width: 33%; vertical-align: top;"><ul>
Binary files docs-base/objects.inv and docs-head/objects.inv differ
diff -r docs-base/searchindex.js docs-head/searchindex.js
1c1
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See CI logs for the full diff.

jdcpni added 30 commits April 29, 2021 21:07

• component.py

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• optimizationcontrolmechanism.py:

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added feature_input_ports attribute and num_feature_input_ports property

• optimizationcontrolmechanism.py:

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added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute

• optimizationcontrolmechanism.py:

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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

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- modified test_mode_based_num_estimates

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• optimizationcontrolmechanism.py:

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- _instantiate_control_signals: random_seeds -> random_seed_mod_values

• composition.py

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- _add_controller: modifying to instantiate feature_input_ports if none are specified

• composition.py:

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- add_controller: now adds feature_input_ports for Compostion INPUT nodes if not state_features not specified

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• composition.py

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- add_controller: assign simulation_input_ports

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• optimizationcontrolmechanism.py:

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_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

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- add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output

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- _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL)

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• composition.py:

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- add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value()

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• CompositionInterfaceMechanism.rst:

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- correct path ref • compositioninterfacemechanism.py: - docstring fixes

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jdcpni merged commit da4ecb7 into devel Jan 6, 2022

jdcpni deleted the fix/comp/build_predicted_input_dicts branch January 6, 2022 22:03

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Fix/comp/build predicted input dicts #2277

Fix/comp/build predicted input dicts #2277

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Fix/comp/build predicted input dicts #2277

Fix/comp/build predicted input dicts #2277

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