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Feat/log/nparray executions #2844

Merged
merged 62 commits into from
Nov 15, 2023
Merged

Feat/log/nparray executions #2844

merged 62 commits into from
Nov 15, 2023

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@jdcpni jdcpni commented Nov 15, 2023

  • log.py
    nparray(), nparray_dictionary(), _assemble_entry_data():
    add report_all_executions option that reports all executions for a given TIME_STEP

jdcpni added 30 commits October 11, 2023 08:06
@jdcpni
-
ce1268c
@jdcpni
• composition.py
5e65f27 
  - _add_error_projection_to_dependent_learning_mechs,
    _create_non_terminal_backprop_learning_components:
    separate error_sources for parallel InputPort/OutputPort "streams" in a single Mechanism that use TransferFunctions
@jdcpni
[skip ci]
92119b5
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[skip ci]
11f0216 
• autodiffcomposition.py, pytorchcomponents.py:
  standardize on value of PytorchMechanismWrapper as 2d
  to accomodate >1 output_ports
@jdcpni
[skip ci]
b16d9c3 
• composition.py
  _create_backpropagation_learning_pathway():
    determine dependent_learning_mechanisms locally
• learningmechanism.py
    remove dependent_learning_mechanisms property
@jdcpni
[skip ci]
1914f74
@jdcpni
[skip ci]
af81952 
• composition.py
  refactor learning pathways to be specific to input_port and output_ports (to accomodate parallel pathways through Mechanisms with TransferFunction:
   - add _get_ports_for_input_output_sources()
   - _create_terminal_backprop_learning_components()
     _create_learning_related_mechanisms()
     _create_learning_related_projections():
     all take input_source_output_port and output_source_input_port as args
@jdcpni
[skip ci]
a8e5811 
• composition.py
  - _add_error_projection_to_dependent_learning_mechs():
    if mechanism uses TransferFunction, only consider dependent_learning_projections
    for projections to input_port with same index as output_port of error_source
@jdcpni
[skip ci]
b4be7c9 
• composition.py
  refactor learning pathways to be specific to input_port and output_ports (to accomodate parallel pathways through Mechanisms with TransferFunction:
   - add _get_ports_for_input_output_sources()
   - _create_terminal_backprop_learning_components()
     _create_learning_related_mechanisms()
     _create_learning_related_projections():
     all take input_source_output_port and output_source_input_port as args
@jdcpni
[skip ci]
2ce523b
@jdcpni
[skip ci]
5f03d11 
• processingmechanism.py:
  - _instantiate_output_ports():
     if no OutputPorts are specified, and variable has more than one item, assign one OutputPort to each
@jdcpni
[skip ci]
9c958e3
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0df152e
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b4467f2 
• Passes all pytests
• Tests for multiple output_ports with learning need to be added
@jdcpni
[skip ci]
c2a1610 
• test_learning.py
  - TestAutodiffMultipleOutput_port:
    - add test_parallel_inputs_to_output_ports_converge_internal
    - add test_single_input_to_multiple_output_ports_converge_internal
@jdcpni
[skip ci]
bcb4dd1
@jdcpni
[skip ci]
499f4bb 
• test_learning.py
  - TestAutodiffMultipleOutput_ports
    - add test_single_input_to_multiple_output_ports_converge_on_OUTPUT_Node
@jdcpni
[skip ci]
4c84c36 
• composition.py
  - _create_backpropagation_learning_pathway():
    - raise error for terminal node with > 1 output_ports
@jdcpni
[skip ci]
ede9b33
@jdcpni
[skip ci]
6b72ef2 
• composition.py
  - _create_backpropagation_learning_pathway():
    - raise error for terminal node with > 1 output_ports
@jdcpni
[skip ci]
251d124
@jdcpni
[skip ci]
81444d0 
• composition.py
  _instantiate_input_dict():
  refactor to format user-specified inputs
@jdcpni
[skip ci]
ac2abf4 
• composition.py
  - _create_backpropagation_learning_pathway():
    - raise error for terminal node with > 1 output_ports
@jdcpni
Merge branch 'refactor/learning_pathways_using_ports' of https://gith…
a143219 
…ub.com/PrincetonUniversity/PsyNeuLink into refactor/learning_pathways_using_ports
@jdcpni
[skip ci]
7039cef 
• composition.py
  _instantiate_input_dict():
  refactor to format user-specified inputs
@jdcpni
Merge remote-tracking branch 'origin/refactor/learning_pathways_using…
4d02125 
…_ports' into refactor/learning_pathways_using_ports
@jdcpni
[skip ci]
8c7abf3
@jdcpni
[skip ci]
be64272
jdcpni added 25 commits November 3, 2023 08:59
@jdcpni
[skip ci]
ce6ba8d
@jdcpni
[skip ci]
079eace
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8a516ce
@jdcpni
[skip ci]
f9e4973 
PASSES ALL TESTS
@jdcpni
[skip ci]
71821f9 
PASSES ALL TESTS
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
60bbf36 
…Link into refactor/learning_pathways_using_ports
@jdcpni
[skip ci]
b3193c5 
• test_composition.py
  add test_input_shape_errors
@jdcpni
[skip ci]
f0b3787 
• processingmechanism.py
  docstring description of configuration
@jdcpni
[skip ci]
81e48a2
@jdcpni
[skip ci]
80add34 
• test_processing_mechanism.py
  - test_processing_mechanism_multiple_input_ports: add tests for specifying names and/or variables for output_ports
@jdcpni
- ready for merge to devel
8e8f986
@jdcpni
-
498cc73
@jdcpni
• test_autodiffcomposition.py
fc7b12a 
  add test_two_output_ports_on_OUTPUT_Node
@jdcpni
• test_learning.py
531d818 
  add test_two_output_ports_on_OUTPUT_Node
@jdcpni
-
1e7f9d2
@jdcpni
• emcomposition.py
5f9391e 
  - rename nodes

• autodiffcomposition.py
  infer_backpropagation_learning_pathways():
  - only exclude ModulatoryProjections or ones that don't have a 'learnable' attribute
@jdcpni
Merge branch 'refactor/learning_pathways_using_ports' into devel
131bdf0 
# Conflicts:
#	psyneulink/library/compositions/emcomposition.py
@jdcpni
- minor changes
1967f5c
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
23aa79a 
…Link into devel
@jdcpni
Merge branch 'fix/emcomposition_learnable_projections' into devel
9e4c537
@jdcpni
[skip ci]
8713422 
• emcomposition.py
  execute(): autodiff execution commented out
@jdcpni
[skip ci]
e91d494 
• emcomposition.py
  execute(): use autodiff
@jdcpni
Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…
775cc72 
…Link into devel

# Conflicts:
#	psyneulink/library/compositions/emcomposition.py
@jdcpni
- log.py
778b14a 
  nparray(), nparray_dictionary(), _assemble_entry_data():
   add report_all_executions option that reports all executions for a given TIME_STEP
@jdcpni
- log.py
5944980 
  nparray(), nparray_dictionary(), _assemble_entry_data():
   add report_all_executions option that reports all executions for a given TIME_STEP
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This PR causes the following changes to the html docs (ubuntu-latest-3.11-x64):

diff -r docs-base/AutoAssociativeProjection.html docs-head/AutoAssociativeProjection.html
246,247c246,247
< <p>Due to its specialized nature, most parameters of the AutoAssociativeProjection are not configurable: the <a class="reference internal" href="LeabraMechanism.html#psyneulink.library.components.mechanisms.processing.leabramechanism.LeabraFunction.variable" title="psyneulink.library.components.mechanisms.processing.leabramechanism.LeabraFunction.variable"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">variable</span></code></a> is
< determined by the format of the output of the RecurrentTransferMechanism, the <a class="reference internal" href="LCControlMechanism.html#psyneulink.library.components.mechanisms.modulatory.control.agt.lccontrolmechanism.LCControlMechanism.function" title="psyneulink.library.components.mechanisms.modulatory.control.agt.lccontrolmechanism.LCControlMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> is always LinearMatrix, and so
---
> <p>Due to its specialized nature, most parameters of the AutoAssociativeProjection are not configurable: the <a class="reference internal" href="ControlProjection.html#psyneulink.core.components.projections.modulatory.controlprojection.ControlProjection.variable" title="psyneulink.core.components.projections.modulatory.controlprojection.ControlProjection.variable"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">variable</span></code></a> is
> determined by the format of the output of the RecurrentTransferMechanism, the <a class="reference internal" href="ControlSignal.html#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal.function" title="psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> is always LinearMatrix, and so
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
391,392c391,392
< <li><p>the <a class="reference internal" href="KohonenMechanism.html#psyneulink.library.components.mechanisms.processing.transfer.kohonenmechanism.KohonenMechanism.matrix" title="psyneulink.library.components.mechanisms.processing.transfer.kohonenmechanism.KohonenMechanism.matrix"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">matrix</span></code></a> parameter of Projections</p></li>
< <li><p>the <a class="reference internal" href="LCControlMechanism.html#psyneulink.library.components.mechanisms.modulatory.control.agt.lccontrolmechanism.LCControlMechanism.value" title="psyneulink.library.components.mechanisms.modulatory.control.agt.lccontrolmechanism.LCControlMechanism.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> parameter of its inner components</p></li>
---
> <li><p>the <a class="reference internal" href="AutoAssociativeProjection.html#psyneulink.library.components.projections.pathway.autoassociativeprojection.AutoAssociativeProjection.matrix" title="psyneulink.library.components.projections.pathway.autoassociativeprojection.AutoAssociativeProjection.matrix"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">matrix</span></code></a> parameter of Projections</p></li>
> <li><p>the <a class="reference internal" href="ControlProjection.html#psyneulink.core.components.projections.modulatory.controlprojection.ControlProjection.value" title="psyneulink.core.components.projections.modulatory.controlprojection.ControlProjection.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> parameter of its inner components</p></li>
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
269c269
< <a class="reference internal" href="index_logo_with_text.html#tutorial"><span class="std std-ref">tutorial</span></a> provides additional introductory material for those who are newer to computational modeling,
---
> <a class="reference internal" href="index.html#tutorial"><span class="std std-ref">tutorial</span></a> provides additional introductory material for those who are newer to computational modeling,
1128c1128
< <a class="reference internal" href="index_logo_with_text.html#tutorial"><span class="std std-ref">Tutorial</span></a> provides a more thorough, interactive introduction to its use, and the <a class="reference internal" href="UserGuide.html"><span class="doc">User's Guide</span></a> provides
---
> <a class="reference internal" href="index.html#tutorial"><span class="std std-ref">Tutorial</span></a> provides a more thorough, interactive introduction to its use, and the <a class="reference internal" href="UserGuide.html"><span class="doc">User's Guide</span></a> provides
diff -r docs-base/BeukersNBackModel.html docs-head/BeukersNBackModel.html
211c211
< <p>(Instructions for running the actual notebook can be found <a class="reference internal" href="index_logo_with_text.html#tutorial"><span class="std std-ref">here</span></a>, replacing <code class="docutils literal notranslate"><span class="pre">nback_nb</span></code> for <code class="docutils literal notranslate"><span class="pre">tutorial</span></code>)</p>
---
> <p>(Instructions for running the actual notebook can be found <a class="reference internal" href="index.html#tutorial"><span class="std std-ref">here</span></a>, replacing <code class="docutils literal notranslate"><span class="pre">nback_nb</span></code> for <code class="docutils literal notranslate"><span class="pre">tutorial</span></code>)</p>
diff -r docs-base/BotvinickConflictMonitoringModel.html docs-head/BotvinickConflictMonitoringModel.html
273c273
< The <a class="reference internal" href="Log.html#module-psyneulink.core.globals.log" title="psyneulink.core.globals.log"><code class="xref any py py-mod docutils literal notranslate"><span class="pre">log</span></code></a> function is used to record the output values of <em>RESPONSE LAYER</em>. These values are used to produce
---
> The <a class="reference internal" href="Component.html#psyneulink.core.components.component.Component.log" title="psyneulink.core.components.component.Component.log"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">log</span></code></a> function is used to record the output values of <em>RESPONSE LAYER</em>. These values are used to produce
diff -r docs-base/Cohen_HustonModel.html docs-head/Cohen_HustonModel.html
292c292
< <p>The <a class="reference internal" href="Log.html#module-psyneulink.core.globals.log" title="psyneulink.core.globals.log"><code class="xref any py py-mod docutils literal notranslate"><span class="pre">log</span></code></a> function is used to record the output values of the <em>RESPONSE LAYER</em>. The cyles until a threshold is reached
---
> <p>The <a class="reference internal" href="Component.html#psyneulink.core.components.component.Component.log" title="psyneulink.core.components.component.Component.log"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">log</span></code></a> function is used to record the output values of the <em>RESPONSE LAYER</em>. The cyles until a threshold is reached
diff -r docs-base/CombinationFunctions.html docs-head/CombinationFunctions.html
588c588
< <p><code class="xref any docutils literal notranslate"><span class="pre">function</span></code> returns a 2d array with the items of <a class="reference internal" href="LeabraMechanism.html#psyneulink.library.components.mechanisms.processing.leabramechanism.LeabraFunction.variable" title="psyneulink.library.components.mechanisms.processing.leabramechanism.LeabraFunction.variable"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">variable</span></code></a> rearranged
---
> <p><code class="xref any docutils literal notranslate"><span class="pre">function</span></code> returns a 2d array with the items of <a class="reference internal" href="ControlProjection.html#psyneulink.core.components.projections.modulatory.controlprojection.ControlProjection.variable" title="psyneulink.core.components.projections.modulatory.controlprojection.ControlProjection.variable"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">variable</span></code></a> rearranged
diff -r docs-base/Component.html docs-head/Component.html
362c362
< <a class="reference internal" href="LCControlMechanism.html#psyneulink.library.components.mechanisms.modulatory.control.agt.lccontrolmechanism.LCControlMechanism.function" title="psyneulink.library.components.mechanisms.modulatory.control.agt.lccontrolmechanism.LCControlMechanism.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> attribute of the Component.</p>
---
> <a class="reference internal" href="ControlSignal.html#psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal.function" title="psyneulink.core.components.ports.modulatorysignals.controlsignal.ControlSignal.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a> attribute of the Component.</p>
390c390
< <p>In general, Components that have an execute() method may use this to assign the <a class="reference internal" href="LCControlMechanism.html#psyneulink.library.components.mechanisms.modulatory.control.agt.lccontrolmechanism.LCControlMechanism.value" title="psyneulink.library.components.mechanisms.modulatory.control.agt.lccontrolmechanism.LCControlMechanism.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> of the Component
---
> <p>In general, Components that have an execute() method may use this to assign the <a class="reference internal" href="ControlProjection.html#psyneulink.core.components.projections.modulatory.controlprojection.ControlProjection.value" title="psyneulink.core.components.projections.modulatory.controlprojection.ControlProjection.value"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">value</span></code></a> of the Component
428c428
< <a class="reference internal" href="KohonenMechanism.html#psyneulink.library.components.mechanisms.processing.transfer.kohonenmechanism.KohonenMechanism.output_ports" title="psyneulink.library.components.mechanisms.processing.transfer.kohonenmechanism.KohonenMechanism.output_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_ports</span></code></a>, and <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.function" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>, are all listed in parameters, and are user-modifiable,
---
> <a class="reference internal" href="DDM.html#psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.output_ports" title="psyneulink.library.components.mechanisms.processing.integrator.ddm.DDM.output_ports"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">output_ports</span></code></a>, and <a class="reference internal" href="Mechanism.html#psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.function" title="psyneulink.core.components.mechanisms.mechanism.Mechanism_Base.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>, are all listed in parameters, and are user-modifiable,
755c755
< <dd class="field-odd"><p><a class="reference internal" href="CompositionInterfaceMechanism.html#psyneulink.core.components.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism.Parameters" title="psyneulink.core.components.mechanisms.processing.compositioninterfacemechanism.CompositionInterfaceMechanism.Parameters">Parameters</a></p>
---
> <dd class="field-odd"><p><a class="reference internal" href="AutodiffComposition.html#psyneulink.library.compositions.autodiffcomposition.AutodiffComposition.Parameters" title="psyneulink.library.compositions.autodiffcomposition.AutodiffComposition.Parameters">Parameters</a></p>
diff -r docs-base/Composition.html docs-head/Composition.html
974c974
< the <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">NodeRoles</span></code></a> <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.TARGET" title="psyneulink.core.compositions.composition.NodeRole.TARGET"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">TARGET</span></code></a> and <a class="reference internal" href="Log.html#psyneulink.core.globals.log.LogCondition.LEARNING" title="psyneulink.core.globals.log.LogCondition.LEARNING"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">LEARNING</span></code></a> in the Composition.</p></li>
---
> the <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">NodeRoles</span></code></a> <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.TARGET" title="psyneulink.core.compositions.composition.NodeRole.TARGET"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">TARGET</span></code></a> and <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.LEARNING" title="psyneulink.core.compositions.composition.NodeRole.LEARNING"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">LEARNING</span></code></a> in the Composition.</p></li>
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< – see below); this is assigned the <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">NodeRole</span></code></a> <a class="reference internal" href="Log.html#psyneulink.core.globals.log.LogCondition.LEARNING" title="psyneulink.core.globals.log.LogCondition.LEARNING"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">LEARNING</span></code></a> in the Composition.</p></li>
---
> – see below); this is assigned the <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">NodeRole</span></code></a> <a class="reference internal" href="#psyneulink.core.compositions.composition.NodeRole.LEARNING" title="psyneulink.core.compositions.composition.NodeRole.LEARNING"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">LEARNING</span></code></a> in the Composition.</p></li>
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< <a class="reference internal" href="LearningMechanism.html#learningmechanism-learning-configurations"><span class="std std-ref">Learning Configurations</span></a> for details); these are assigned the <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">NodeRole</span></code></a> <a class="reference internal" href="Log.html#psyneulink.core.globals.log.LogCondition.LEARNING" title="psyneulink.core.globals.log.LogCondition.LEARNING"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">LEARNING</span></code></a> in
---
> <a class="reference internal" href="LearningMechanism.html#learningmechanism-learning-configurations"><span class="std std-ref">Learning Configurations</span></a> for details); these are assigned the <a class="reference internal" hre
...

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Coverage Status

coverage: 84.651% (-0.03%) from 84.681%
when pulling 5944980 on feat/log/nparray_executions
into b61f894 on devel.

@jdcpni jdcpni merged commit a947643 into devel Nov 15, 2023
63 checks passed
@jdcpni jdcpni deleted the feat/log/nparray_executions branch November 15, 2023 11:02
@kmantel kmantel mentioned this pull request Dec 16, 2023
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