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Refactor/ocm/state features all as input ports #2352

Merged
merged 361 commits into from
Mar 21, 2022
Merged

Refactor/ocm/state features all as input ports #2352

merged 361 commits into from
Mar 21, 2022

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jdcpni
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@jdcpni jdcpni commented Mar 21, 2022

• optimizationcontrolmechanism.py:

  • _state_feature_values_getter(): for numeric state_feature, return state_input_port.function(numeric_value)

• test_control.py:

  • test_state_features_in_nested_composition_as_agent_rep():
  • add tests for single state_feature specs
  • add tests for INPUT Node with more than on InputPort

jdcpni and others added 30 commits November 25, 2021 09:47
@jdcpni
• Passes *all* current tests
72c4c41
• composition.py:
45b25eb 
  - add_controller:  few more minor mods;
  still passes all tests
-
a79723b
@jdcpni
-
49350a1
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
f7b9fc5 
…Link into devel
@jdcpni
-
7a6682a
@jdcpni
• controlmechanism.py:
8858ab5 
  - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms)
@jdcpni
-
d1ac2da
@jdcpni
• composition.py: in progress fix of bug in instantiating shadow proj…
dbdc2d1 
…ections for ocm.state_input_ports
@jdcpni
• composition.py:
6b00fbd 
  - _get_original_senders():  added support for nested composition
    needs to be checked for more than one level
    needs to be refactored to be recursive
@jdcpni
• optimizationcontrolmechanism.py
179e7d0 
  - _update_state_input_ports_for_controller:  fix invalid_state_features to allow input_CIM of nested comp in agent_rep
@jdcpni
-
88ce1a6
@jdcpni
• composition.py
5089cf3 
 - _get_original_senders: made recursive
• test_show_graph.py: update for fixes
97a71c4
-
3bc799e
• tests: passes all in test_show_graph.py and test_report.py
6a27e4a
Passes all tests
8cdad10
- comment clean-up
2d15f6d
@jdcpni
• composition.py
787856b 
 - add_controller and _get_nested_node_CIM_port:
   added support for forced assignment of NodeRole.OUTPUT for nodes specified in OCM.monitor_for_control,
   but referenced 'allow_probes' attribute still needs to be implemented
• composition.py, optimizationcontrolmechanism.py:
3ed598e 
  allow_probes fully implemented
@jdcpni
• show_graph.py: fixed bug causing extra projections to OCM
38e5f99
@jdcpni
• composition.py:
658c161 
  - _update_shadow_projections(): fix handling of deep nesting
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
7396806 
…Link into refactor/ocm/state_input_ports_PROBE
@jdcpni
• optimizationcontrolmechanism.py: add agent_rep_type property
8b54f03
@jdcpni
• optimizationcontrolmechanism.py:
1ecf0fa 
  - state_feature_function -> state_feature_functions
@jdcpni
• optimizationcontrolmechanism.py:
24a03f3 
  - _validate_params:  validate state_feature_functions
  - _update_state_input_ports_for_controller: implement assignment of state_feature_functions
@jdcpni
-
6713df9
@jdcpni
-
8b3bdf0
@jdcpni
• Passes all tests except test_json with 'model_with_control'
d001991
@jdcpni
-
888863a
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
36ae355 
…Link into refactor/ocm/state_features_all_as_input_ports
@jdcpni
• optimizationcontrolmechanism.py
341472c 
  - allow single spec (None, array, tuple, or Components) that is assigned to all INPUT Node InputPorts
  - state_feature_default is assigned to all unspecified INPUT Node InputPorts
    (for a list that is shorter than the number, a dict or a set that has fewer,
     or any that are added to agent_rep after controller is initially constructed and added to Composition)
@jdcpni
-
626ed19
@jdcpni
-
bec6673
@jdcpni
• optimizationcontrolmechanism.py: docstring mods
f3ca261
@jdcpni
• optimizationcontrolmechanism.py: docstring mods
97a7862
@jdcpni
• optimizationcontrolmechanism.py: docstring mods
5f12880
@jdcpni
-
97027c8
@jdcpni
-
294df7a
@jdcpni
-
9914dfa
@jdcpni
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3dda7d1
@jdcpni
-
c5a01e3
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
8a9015c 
…Link into refactor/ocm/state_features_all_as_input_ports
@jdcpni
• optimizationcontrolmechanism.py:
17de2e1 
  - _state_feature_values_getter(): for numeric state_feature, return state_input_port.functio(numeric_value)
@jdcpni
• test_control.py:
0df2e81 
  - test_ocm_state_feature_specs_and_warnings_and_errors() - added tests for single state_feature spec
@jdcpni
- composition.py, inputport.py, optimizationcontrolmechanism.py: docs…
99b19c7 
…tring mods re: "external InputPort"
@jdcpni
-
050facc
@jdcpni
-
d979b1c
@jdcpni
-
0d02c12
@jdcpni
• test_control.py:
b6fe2d4 
  - test_state_features_in_nested_composition_as_agent_rep():
    - add tests for single state_feature specs
    - add tests for INPUT Node with more than on InputPort
@jdcpni
-
f5ee7d2
@jdcpni
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9907a64
@jdcpni
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ceafa93
@jdcpni
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7d9394c
@jdcpni
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42c3fca
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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

diff -r docs-base/ComparatorMechanism.html docs-head/ComparatorMechanism.html
374,376c374,376
< <dd><p>used to compare the <a class="reference internal" href="#psyneulink.library.components.mechanisms.processing.objective.comparatormechanism.ComparatorMechanism.sample" title="psyneulink.library.components.mechanisms.processing.objective.comparatormechanism.ComparatorMechanism.sample"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">sample</span></code></a> with the <a class="reference internal" href="#psyneulink.library.components.mechanisms.processing.objective.comparatormechanism.ComparatorMechanism.target" title="psyneulink.library.components.mechanisms.processing.objective.comparatormechanism.ComparatorMechanism.target"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">target</span></code></a>.  It can be any PsyNeuLink <code class="xref any docutils literal notranslate"><span class="pre">CombinationFunction</span></code>,
< or a python function that takes a 2d array with two items and returns a 1d array of the same length
< as the two input items.</p>
---
> <dd><p>used to compare the <a class="reference internal" href="#psyneulink.library.components.mechanisms.processing.objective.comparatormechanism.ComparatorMechanism.sample" title="psyneulink.library.components.mechanisms.processing.objective.comparatormechanism.ComparatorMechanism.sample"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">sample</span></code></a> with the <a class="reference internal" href="#psyneulink.library.components.mechanisms.processing.objective.comparatormechanism.ComparatorMechanism.target" title="psyneulink.library.components.mechanisms.processing.objective.comparatormechanism.ComparatorMechanism.target"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">target</span></code></a>.  It can be any <a class="reference internal" href="CombinationFunctions.html"><span class="doc">CombinationFunction</span></a>,
> or a python function that takes a 2d array with two items and returns a 1d array of the same length as the
> two input items.</p>
diff -r docs-base/Composition.html docs-head/Composition.html
606,607c606,607
< outer Composition, are assigned <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> in addition to their other <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="pre">roles</span></code></a> in the
< nested Composition.  The only difference between <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes
---
> outer Composition, are assigned <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> in addition to their other <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole" title="psyneulink.core.compositions.composition.NodeRole"><code class="xref any py py-class docutils literal notranslate"><span class="pre">roles</span></code></a> in the
> nested Composition.  The only difference between <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes
611c611
< <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are <em>not</em> included in the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> for the outermost Composition to which they project (although they <em>are</em> still included
---
> <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are <em>not</em> included in the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> or <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.results" title="psyneulink.core.compositions.composition.Composition.results"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">results</span></code></a> for the outermost Composition to which they project (although they <em>are</em> still included
615c615
< <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> is True, then any <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes
---
> <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.include_probes_in_output" title="psyneulink.core.compositions.composition.Composition.include_probes_in_output"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">include_probes_in_output</span></code></a> is True, then any <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes
618c618
< <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes can be visualized, along with any Projections treated differently from those of
---
> <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes can be visualized, along with any Projections treated differently from those of
626c626
< <div><p><a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are useful for <a class="reference internal" href="OptimizationControlMechanism.html#optimizationcontrolmechanism-model-based"><span class="std std-ref">model-based optimization using an</span></a>, in which the value of one or more Nodes in a nested Composition
---
> <div><p><a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are useful for <a class="reference internal" href="OptimizationControlMechanism.html#optimizationcontrolmechanism-model-based"><span class="std std-ref">model-based optimization using an</span></a>, in which the value of one or more Nodes in a nested Composition
650c650,651
< include the InputPorts of the nested Composition.  These can be accessed using the Composition’s <a class="reference internal" href="#id20" title="psyneulink.core.compositions.composition.Composition.external_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">exernal_input_ports</span></code></a> attribute.</p>
---
> include the InputPorts of the nested Composition.  These can be accessed using the Composition’s
> <a class="reference internal" href="#psyneulink.core.compositions.composition.Composition.external_input_ports_of_all_input_nodes" title="psyneulink.core.compositions.composition.Composition.external_input_ports_of_all_input_nodes"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">external_input_ports_of_all_input_nodes</span></code></a> attribute.</p>
696,697c697,698
< Composition.  If the Composition has an <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes, then they too project to the Composition’s
< output_CIM.  If the Composition is nested in another, then the <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">values</span></code></a> of the <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are also included in the Composition’s <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a>;  if it
---
> Composition.  If the Composition has an <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes, then they too project to the Composition’s
> output_CIM.  If the Composition is nested in another, then the <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">values</span></code></a> of the <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are also included in the Composition’s <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a>;  if it
744c745
< <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes of a nested Composition, like <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes,
---
> <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes of a nested Composition, like <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Nodes,
746c747
< The outputs of <a class="reference internal" href="#id26" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are included in the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and
---
> The outputs of <a class="reference internal" href="#id24" title="psyneulink.core.compositions.composition.NodeRole.PROBE"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">PROBE</span></code></a> Nodes are included in the <a class="reference internal" href="#id19" title="psyneulink.core.compositions.composition.Composition.output_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_values</span></code></a> and
949c950
< <li><p><em>OUTPUT_MECHANISM</em> – the final <code class="xref any docutils literal notranslate"><span class="pre">Node</span></code> in the learning Pathway, the target <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> for which is specified as input to the <code class="xref any docutils literal notranslate"><span class="pre">TARGET_MECHANISM</span></code>; the Node is assigned
---
> <li><p><em>OUTPUT_MECHANISM</em> – the final <a class="reference internal" href="#composition-nodes"><span class="std std-ref">Node</span></a> in the learning Pathway, the target <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> for which is specified as input to the <code class="xref any docutils literal notranslate"><span class="pre">TARGET_MECHANISM</span></code>; the Node is assigned
966c967
< <figure class="align-default" id="id27">
---
> <figure class="align-default" id="id25">
972c973
< and in italics, above each Mechanism).</span><a class="headerlink" href="#id27" title="Permalink to this image">¶</a></p>
---
> and in italics, above each Mechanism).</span><a class="headerlink" href="#id25" title="Permalink to this image">¶</a></p>
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< <figure class="align-default" id="id28">
---
> <figure class="align-default" id="id26">
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< one that projects to the ComparatorMechanism and assigned as the <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.OUTPUT" title="psyneulink.core.compositions.composition.NodeRole.OUTPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">OUTPUT</span></code></a> Node.</span><a class="headerlink" href="#id28" title="Permalink to this image">¶</a></p>
---
> one that projects
...

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lgtm-com bot commented Mar 21, 2022

This pull request introduces 1 alert when merging 42c3fca into 8fa3011 - view on LGTM.com

new alerts:

  • 1 for Comparison using is when operands support `__eq__`

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Coverage decreased (-0.003%) to 84.091% when pulling 42c3fca on refactor/ocm/state_features_all_as_input_ports into 8fa3011 on devel.

@jdcpni jdcpni merged commit b582287 into devel Mar 21, 2022
@jdcpni jdcpni deleted the refactor/ocm/state_features_all_as_input_ports branch March 21, 2022 16:18
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