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Refactor/ocm/state features all as input ports #2351

Merged
merged 348 commits into from
Mar 20, 2022
Merged

Refactor/ocm/state features all as input ports #2351

merged 348 commits into from
Mar 20, 2022

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@jdcpni jdcpni commented Mar 19, 2022

• processingmechanism.py:

  • init(): modify typecheck for input_ports to allow single items

• optimizationcontrolmechanism.py

  • state_features: allow single spec (None, array, tuple, or Components)
    that is assigned to all INPUT Node InputPorts on agent_rep at time of OCM construction
  • state_feature_default is assigned to all unspecified INPUT Node InputPorts
    (i.e., for those not specified in a list, set or dict that has fewer entries
    than the number of INPUT Nodes on agent_rep when OCM is initially constructed or
    or any that are added to agent_rep afterwards)
  • update docstring for new features

kmantel and others added 30 commits November 22, 2021 23:05
@kmantel
Composition: add_controller: set METHOD as context source early
bcddef5
@jdcpni
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7fd49c6
@jdcpni
Merge branch 'refactor/ocm/state_input_ports_PROBE_FIX' of https://gi…
35c97d3 
…thub.com/PrincetonUniversity/PsyNeuLink into refactor/ocm/state_input_ports_PROBE_FIX
@jdcpni
• composition.py
79cb012 
  retore append of control_signals in _instantiate_control_projections()
@jdcpni
• composition.py
9bc7b18 
  restore append of control_signals in _instantiate_control_projections()

• test_composition.py:
  add test_partially_overlapping_local_and_control_mech_control_specs_in_unnested_and_nested_comp
• test_partially_overlapping_local_and_control_mech_control_specs_in_…
0f93f47 
…unnested_and_nested_comp():

  - added clear_registry() to allow names to be reused in both runs of test
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
47b56b2 
…Link into devel
@jdcpni
• composition.py
81f1112 
  docstring:  added projections entry to list of attributes
  - add_controller:  added call to _add_node_aux_components() for controller
@jdcpni
• composition.py
0cd9db3 
  _add_node_aux_components(): added deletion of item from aux_components if instantiated
@jdcpni
• composition.py
c808664 
  - comment out _add_node_aux_components() (causing new failures)
  - move _instantiate_control_projections to be with _instantiate_control_projections,
       after self.add_node(self.controller.objective_mechanism (to be more orderly)
@jdcpni
-
0cb21ab
- confirm that it passes all tests exception test_composition/test_pa…
28289a0 
…rtially_overlapping...

  (with addition of _add_aux_components in add_controller commented out)
@jdcpni
• composition.py: some more fixed to add_controller that now fail onl…
1cf9602 
…y one test:

    - test_agent_rep_assignement_as_controller_and_replacement
@jdcpni
• Passes *all* current tests
72c4c41
• composition.py:
45b25eb 
  - add_controller:  few more minor mods;
  still passes all tests
-
a79723b
@jdcpni
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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
@jdcpni
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0a309cb
@jdcpni
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a17e304
@jdcpni
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@jdcpni
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528f535
@jdcpni
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@jdcpni
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@jdcpni
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@jdcpni
• inputport.py:
30d1fbb 
  - add figure for shadowing
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
fcea29d 
…Link into refactor/ocm/state_features_all_as_input_ports

� Conflicts:
�	psyneulink/core/components/mechanisms/modulatory/control/optimizationcontrolmechanism.py
�	psyneulink/core/components/ports/parameterport.py
�	psyneulink/core/compositions/composition.py
@jdcpni
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f758267
@jdcpni
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7cebaa0
@jdcpni
• processingmechanism.py:
68a197a 
  - __init__(): modify typecheck for input_ports to allow single items
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
8f867c8 
…Link into refactor/ocm/state_features_all_as_input_ports

� Conflicts:
�	psyneulink/core/components/ports/inputport.py
@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
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bec6673
@jdcpni
• optimizationcontrolmechanism.py: docstring mods
f3ca261
@jdcpni
• optimizationcontrolmechanism.py: docstring mods
97a7862
@jdcpni
• optimizationcontrolmechanism.py: docstring mods
5f12880
@jdcpni
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97027c8
@jdcpni
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294df7a
@jdcpni
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9914dfa
@jdcpni
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3dda7d1
@jdcpni
-
c5a01e3
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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64):

diff -r docs-base/InputPort.html docs-head/InputPort.html
498c498
< <span class="gp">&gt;&gt;&gt; </span><span class="n">C</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;Shadowing Mech&#39;</span><span class="p">,</span> <span class="n">input_ports</span><span class="o">=</span><span class="p">[</span><span class="n">B</span><span class="o">.</span><span class="n">input_port</span><span class="p">])</span>
---
> <span class="gp">&gt;&gt;&gt; </span><span class="n">C</span> <span class="o">=</span> <span class="n">ProcessingMechanism</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s1">&#39;Shadowing Mech&#39;</span><span class="p">,</span> <span class="n">input_ports</span><span class="o">=</span><span class="n">B</span><span class="o">.</span><span class="n">input_port</span><span class="p">)</span>
518c518
< <span class="gp">... </span>                                     <span class="n">input_ports</span><span class="o">=</span><span class="p">[</span><span class="n">mech</span><span class="o">.</span><span class="n">input_port</span><span class="p">])</span>
---
> <span class="gp">... </span>                                     <span class="n">input_ports</span><span class="o">=</span><span class="n">mech</span><span class="o">.</span><span class="n">input_port</span><span class="p">)</span>
diff -r docs-base/OptimizationControlMechanism.html docs-head/OptimizationControlMechanism.html
310c310
< its <a class="reference internal" href="ControlMechanism.html#psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.net_outcome" title="psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.net_outcome"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">net_outcome</span></code></a>.  A OptimizationControlMechanism can be configured to implement
---
> its <a class="reference internal" href="ControlMechanism.html#psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.net_outcome" title="psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.net_outcome"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">net_outcome</span></code></a>.  An OptimizationControlMechanism can be configured to implement
414,423c414,423
< <li><p><strong>state_features</strong> – specifies the values provided by the OptimizationControlMechanism as the input to its
< <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">agent_rep</span></code></a>'s <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.evaluate" title="psyneulink.core.compositions.composition.Composition.evaluate"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">evaluate</span></code></a> method, together
< with a selected <a class="reference internal" href="ControlMechanism.html#psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.control_allocation" title="psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.control_allocation"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">control_allocation</span></code></a>, when that is called to estimate
< or predict the Composition’s <a class="reference internal" href="ControlMechanism.html#psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.net_outcome" title="psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.net_outcome"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">net_outcome</span></code></a>. These are used to construct the
< <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_input_ports" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">state_input_ports</span></code></a> for the OptimizationControlMechanism,
< the <a class="reference internal" href="InputPort.html#psyneulink.core.components.ports.inputport.InputPort.value" title="psyneulink.core.components.ports.inputport.InputPort.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">values</span></code></a> of which are assigned as the <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_feature_values" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_feature_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">state_feature_values</span></code></a> and provided to the <strong>predicted_inputs</strong> argument of the
< <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.evaluate" title="psyneulink.core.compositions.composition.Composition.evaluate"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">evaluate</span></code></a> method if <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">agent_rep</span></code></a> is a <a class="reference internal" href="Composition.html"><span class="doc">Composition</span></a>,
< or the <strong>feature_values</strong> argument if it is a <a class="reference internal" href="CompositionFunctionApproximator.html"><span class="doc">CompositionFunctionApproximator</span></a>.  Accordingly, the specification
< requirements for <strong>state_features</strong> depend on whether the <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">agent_rep</span></code></a> is a
< <a class="reference internal" href="Composition.html"><span class="doc">Composition</span></a> or a <a class="reference internal" href="CompositionFunctionApproximator.html"><span class="doc">CompositionFunctionApproximator</span></a>, as described in each of the two sections below.</p>
---
> <li><p><strong>state_features</strong> – specifies the sources of input to the OptimizationControlMechanism’s <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">agent_rep</span></code></a> which, together with a selected <a class="reference internal" href="ControlMechanism.html#psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.control_allocation" title="psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.control_allocation"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">control_allocation</span></code></a>, are provided as input to it’s <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.evaluate" title="psyneulink.core.compositions.composition.Composition.evaluate"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">evaluate</span></code></a> method
> when that is executed to estimate or predict the Composition’s <a class="reference internal" href="ControlMechanism.html#psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.net_outcome" title="psyneulink.core.components.mechanisms.modulatory.control.controlmechanism.ControlMechanism.net_outcome"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">net_outcome</span></code></a>.
> Those sources of input are used to construct the OptimizationControlMechanism’s <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_input_ports" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">state_input_ports</span></code></a>, one for each external <a class="reference internal" href="InputPort.html"><span class="doc">InputPort</span></a> (i.e., that is not designated
> as <a class="reference internal" href="InputPort.html#psyneulink.core.components.ports.inputport.InputPort.internal_only" title="psyneulink.core.components.ports.inputport.InputPort.internal_only"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">internal_only</span></code></a>) of each <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.INPUT" title="psyneulink.core.compositions.composition.NodeRole.INPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">INPUT</span></code></a> <a class="reference internal" href="Composition.html#composition-nodes"><span class="std std-ref">Node</span></a> of the
> <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">agent_rep</span></code></a>. The input to each <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_input_ports" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">state_input_port</span></code></a>, after being processed by it <a class="reference internal" href="InputPort.html#psyneulink.core.components.ports.inputport.InputPort.function" title="psyneulink.core.components.ports.inputport.InputPort.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>, is
> assigned as the corresponding value of <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_feature_values" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_feature_values"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">state_feature_values</span></code></a>,
> the values of which provided as the input to the corresponding InputPorts of the <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.NodeRole.INPUT" title="psyneulink.core.compositions.composition.NodeRole.INPUT"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">INPUT</span></code></a> <a class="reference internal" href="Composition.html#psyneulink.core.compositions.composition.Composition.evaluate" title="psyneulink.core.compositions.composition.Composition.evaluate"><code class="xref any py py-meth docutils literal notranslate"><span class="pre">Nodes</span>
> <span class="pre">of</span> <span class="pre">the</span> <span class="pre">agent_rep</span> <span class="pre">each</span> <span class="pre">time</span> <span class="pre">it</span> <span class="pre">is</span> <span class="pre">`evaluated</span></code></a>.  Accordingly, the specification requirements
> for <strong>state_features</strong> depend on whether the <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">agent_rep</span></code></a> is a <a class="reference internal" href="Composition.html"><span class="doc">Composition</span></a>
> or a <a class="reference internal" href="CompositionFunctionApproximator.html"><span class="doc">CompositionFunctionApproximator</span></a>, as described in each of the two sections below.</p>
431,437c431,436
< <p id="optimizationcontrolmechanism-state-features-automatic-assignment"><em>Automatic assignment.</em> The <strong>state_features</strong> specify the inputs to the Composition assigned as the <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">agent_rep</span></code></a> when it is executed by the OptimizationControlMechanism to
< <a class="reference internal" href="#optimizationcontrolmechanism-evaluation"><span class="std std-ref">evaluate</span></a> its performance.  The default is for the evaluation to use the
< same values received by the <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.agent_rep"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">agent_rep</span></code></a> as its <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">external inputs</span></a> during its last <a class="reference internal" href="Time.html#psyneulink.core.scheduling.time.TimeScale.TRIAL" title="psyneulink.core.scheduling.time.TimeScale.TRIAL"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">TRIAL</span></code></a> of execution. Accordingly, if
< <strong>state_features</strong> is not specified, a set of <a class="reference internal" href="#psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_input_ports" title="psyneulink.core.components.mechanisms.modulatory.control.optimizationcontrolmechanism.OptimizationControlMechanism.state_input_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">state_input_ports</span></code></a>
< is constructed automatically that <a class="reference internal" href="InputPort.html#inputport-shadow-inputs"><span class="std std-ref">shadow the input</span></a> to every <a class="reference internal" href="InputPort.html"><span class="doc">InputPort</span></a> of ever
...

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lgtm-com bot commented Mar 19, 2022

This pull request introduces 1 alert when merging c5a01e3 into 404030e - view on LGTM.com

new alerts:

  • 1 for Unused import

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Coverage Status

Coverage decreased (-0.008%) to 84.091% when pulling c5a01e3 on refactor/ocm/state_features_all_as_input_ports into 404030e on devel.

@jdcpni jdcpni merged commit 8fa3011 into devel Mar 20, 2022
@jdcpni jdcpni deleted the refactor/ocm/state_features_all_as_input_ports branch March 20, 2022 00:41
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@jdcpni @coveralls @kmantel