Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix/show graph/cim #2280

Merged
merged 16 commits into from
Jan 8, 2022
Merged

Fix/show graph/cim #2280

merged 16 commits into from
Jan 8, 2022

Conversation

jdcpni
Copy link
Collaborator

@jdcpni jdcpni commented Jan 7, 2022

• showgraph.py:
  - _assign_incoming_edges():  allow input_CIM of outermost comp to render as node
  - _assign_controller_components():
    allow direct projections from nested nodes to OCM or ObjectiveMechanism when show_cim=False

• test_show_graph.py:
add test_projections_from_nested_comp_to_ocm_or_obj_mech

jdcpni and others added 15 commits November 15, 2021 14:44
…Link into devel

� Conflicts:
�	psyneulink/core/components/mechanisms/modulatory/control/optimizationcontrolmechanism.py
  - _assign_incoming_edges():  allow input_CIM of outermost comp to render as node
  - _assign_incoming_edges():  allow input_CIM of outermost comp to render as node
  - _assign_controller_components():
    allow direct projections from nested nodes to OCM or ObjectiveMechanism when show_cim=False
  add test_projections_from_nested_comp_to_ocm_or_obj_mech
@github-actions
Copy link

github-actions bot commented Jan 7, 2022

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

diff -r docs-base/CompositionInterfaceMechanism.html docs-head/CompositionInterfaceMechanism.html
391,401d390
< <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">
diff -r docs-base/genindex.html docs-head/genindex.html
507,508d506
<       <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>
655,656d652
<   </ul></td>
<   <td style="width: 33%; vertical-align: top;"><ul>
672a669,670
>   </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
< Search.setIndex({docnames:["AGT","AGTControlMechanism","AutoAssociativeLearningMechanism","AutoAssociativeProjection","AutodiffComposition","BasicsAndPrimer","BotvinickConflictMonitoringModel","BustamanteStroopXORLVOCModel","Cohen_HustonModel","CombinationFunctions","ComparatorMechanism","Compilation","Component","Components","Composition","CompositionFunctionApproximator","CompositionInterfaceMechanism","Compositions","Condition","Context","ContrastiveHebbianMechanism","ContributorsGuide","ControlMechanism","ControlMechanisms","ControlProjection","ControlProjections","ControlSignal","ConventionsAndDefinitions","Core","DDM","DefaultControlMechanism","Defaults","DistributionFunctions","EVC","EVCAuxiliary","EVCControlMechanism","EpisodicMemoryMechanism","Function","Functions","GatingMechanism","GatingMechanisms","GatingProjection","GatingProjections","GatingSignal","GilzenratModel","InputPort","IntegratorFunctions","IntegratorMechanism","IntegratorMechanisms","KWTAMechanism","Keywords","KohonenMechanism","LCAMechanism","LCControlMechanism","LCMechanism","LeabraMechanism","LearningFunctions","LearningMechanism","LearningMechanisms","LearningProjection","LearningProjections","LearningSignal","Library","Log","MappingProjection","MaskedMappingProjection","Mechanism","Mechanisms","MemoryFunctions","Models","ModulatoryMechanism","ModulatoryMechanisms","ModulatoryProjection","ModulatoryProjections","ModulatorySignal","MontagueModel","NieuwenhuisModel","NonStatefulFunctions","ObjectiveFunctions","ObjectiveMechanism","ObjectiveMechanisms","OptimizationControlMechanism","OptimizationFunctions","OutputPort","PCTC_model","ParameterEstimationComposition","ParameterPort","Parameters","Pathway","PathwayProjection","PathwayProjections","Port","PredictionErrorMechanism","Preferences","ProcessingMechanism","ProcessingMechanisms","Projection","Projections","QuickReference","RecurrentTransferMechanism","RefactoredLearningGuide","Registry","RegressionCFA","Report","Scheduler","Scheduling","SelectionFunctions","Services","StatefulFunction","StatefulFunctions","Subystems","Time","TransferFunctions","TransferMechanism","TransferMechanisms","UserDefinedFunction","UserGuide","UserGuide_TBD","Visualization","globals","index","index_logo_with_text","json"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":4,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,sphinx:56},filenames:["AGT.rst","AGTControlMechanism.rst","AutoAssociativeLearningMechanism.rst","AutoAssociativeProjection.rst","AutodiffComposition.rst","BasicsAndPrimer.rst","BotvinickConflictMonitoringModel.rst","BustamanteStroopXORLVOCModel.rst","Cohen_HustonModel.rst","CombinationFunctions.rst","ComparatorMechanism.rst","Compilation.rst","Component.rst","Components.rst","Composition.rst","CompositionFunctionApproximator.rst","CompositionInterfaceMechanism.rst","Compositions.rst","Condition.rst","Context.rst","ContrastiveHebbianMechanism.rst","ContributorsGuide.rst","ControlMechanism.rst","ControlMechanisms.rst","ControlProjection.rst","ControlProjections.rst","ControlSignal.rst","ConventionsAndDefinitions.rst","Core.rst","DDM.rst","DefaultControlMechanism.rst","Defaults.rst","DistributionFunctions.rst","EVC.rst","EVCAuxiliary.rst","EVCControlMechanism.rst","EpisodicMemoryMechanism.rst","Function.rst","Functions.rst","GatingMechanism.rst","GatingMechanisms.rst","GatingProjection.rst","GatingProjections.rst","GatingSignal.rst","GilzenratModel.rst","InputPort.rst","IntegratorFunctions.rst","IntegratorMechanism.rst","IntegratorMechanisms.rst","KWTAMechanism.rst","Keywords.rst","KohonenMechanism.rst","LCAMechanism.rst","LCControlMechanism.rst","LCMechanism.rst","LeabraMechanism.rst","LearningFunctions.rst","LearningMechanism.rst","LearningMechanisms.rst","LearningProjection.rst","LearningProjections.rst","LearningSignal.rst","Library.rst","Log.rst","MappingProjection.rst","MaskedMappingProjection.rst","Mechanism.rst","Mechanisms.rst","MemoryFunctions.rst","Models.rst","ModulatoryMechanism.rst","ModulatoryMechanisms.rst","ModulatoryProjection.rst","ModulatoryProjections.rst","ModulatorySignal.rst","MontagueModel.rst","NieuwenhuisModel.rst","NonStatefulFunctions.rst","ObjectiveFunctions.rst","ObjectiveMechanism.rst","ObjectiveMechanisms.rst","OptimizationControlMechanism.rst","OptimizationFunctions.rst","OutputPort.rst","PCTC_model.rst","ParameterEstimationComposition.rst","ParameterPort.rst","Parameters.rst","Pathway.rst","PathwayProjection.rst","PathwayProjections.rst","Port.rst","PredictionErrorMechanism.rst","Preferences.rst","ProcessingMechanism.rst","ProcessingMechanisms.rst","Projection.rst","Projections.rst","QuickReference.rst","RecurrentTransferMechanism.rst","RefactoredLearningGuide.rst","Registry.rst","RegressionCFA.rst","Report.rst","Scheduler.rst","Scheduling.rst","SelectionFunctions.rst","Services.rst","StatefulFunction.rst","StatefulFunctions.rst","Subystems.rst","Time.rst","TransferFunctions.rst","TransferMechanism.rst","TransferMechanisms.rst","UserDefinedFunction.rst","UserGuide.rst","UserGuide_TBD.rst","Visualization.rst","globals.rst","index.rst","index_logo_with_text.rst","json.rst"],objects:{"psyneulink.core.components":{component:[12,0,0,"-"]},"psyneulink.core.components.component":{Component:[12,1,1,""]},"psyneulink.core.components.component.Component":{"function":[12,4,1,""],_check_args:[12,2,1,""],_check_for_composition:[12,2,1,""],_deferred_init:[12,2,1,""],_dependent_components:[12,3,1,""],_get_param_value_from_tuple:[12,2,1,""],_handle_default_variable:[12,2,1,""],_handle_size:[12,2,1,""],_instantiate_defaults:[12,2,1,""],_instantiate_function:[12,2,1,""],_instantiate_parameter_classes:[12,2,1,""],_model_spec_class_name_is_generic:[12,4,1,""],_model_spec_generic_type_name:[12,4,1,""],_model_spec_parameter_blacklist:[12,3,1,""],_parameter_components:[12,3,1,""],_parse_arg_generic:[12,2,1,""],_parse_arg_variable:[12,2,1,""],_parse_function_variable:[12,2,1,""],_set_multiple_parameter_values:[12,2,1,""],_specified_variable_shape_flexibility:[12,4,1,""],_validate:[12,2,1,""],_validate_and_assign_runtime_params:[12,2,1,""],_validate_function:[12,2,1,""],_validate_params:[12,2,1,""],_validate_variable:[12,2,1,""],all_dependent_parameters:[12,2,1,""],current_execution_time:[12,4,1,""],defaults:[12,4,1,""],execute:[12,2,1,""],execute_until_finished:[12,4,1,""],execution_count:[12,4,1,""],function_parameters:[12,3,1,""],initialization_status:[12,4,1,""],is_finished:[12,2,1,""],log:[12,4,1,""],log_values:[12,2,1,""],loggable_items:[12,3,1,""],logged_items:[12,3,1,""],max_executions_before_finished:[12,4,1,""],most_recent_context:[12,3,1,""],name:[12,4,1,""],num_executions:[12,4,1,""],num_executions_before_finished:[12,4,1,""],parameters:[12,4,1,""],prefs:[12,4,1,""],reset:[12,2,1,""],reset_params:[12,2,1,""],reset_stateful_function_when:[12,4,1,""],set_delivery_conditions:[12,2,1,""],set_log_conditions:[12,2,1,""],size:[12,4,1,""],stateful_parameters:[12,3,1,"id0"],value:[12,4,1,""],variable:[12,4,1,""]},"psyneulink.core.components.functions":{"function":[38,0,0,"-"],combinationfunctions:[9,0,0,"-"],distributionfunctions:[32,0,0,"-"],learningfunctions:[56,0,0,"-"],objectivefunctions:[78,0,0,"-"],optimizationfunctions:[82,0,0,"-"],selectionfunctions:[106,0,0,"-"],transferfunctions:[112,0,0,"-"],userdefinedfunction:[115,0,0,"-"]},"psyneulink.core.components.functions.combinationfunctions":{CombineMeans:[9,1,1,""],Concatenate:[9,1,1,""],LinearCombination:[9,1,1,""],PredictionErrorDeltaFunction:[9,1,1,""],Rearrange:[9,1,1,""],Reduce:[9,1,1,""]},"psyneulink.core.components.functions.combinationfunctions.CombineMeans":{_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""],exponents:[9,4,1,""],name:[9,4,1,""],offset:[9,4,1,""],operation:[9,4,1,""],owner:[9,4,1,""],prefs:[9,4,1,""],scale:[9,4,1,""],variable:[9,4,1,""],weights:[9,4,1,""]},"psyneulink.core.components.functions.combinationfunctions.Concatenate":{_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""],default_variable:[9,4,1,""],name:[9,4,1,""],offset:[9,4,1,""],owner:[9,4,1,""],prefs:[9,4,1,""],scale:[9,4,1,""]},"psyneulink.core.components.functions.combinationfunctions.LinearCombination":{_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""],exponents:[9,4,1,""],name:[9,4,1,""],offset:[9,4,1,""],operation:[9,4,1,""],owner:[9,4,1,""],prefs:[9,4,1,""],scale:[9,4,1,""],variable:[9,4,1,""],weights:[9,4,1,""]},"psyneulink.core.components.functions.combinationfunctions.PredictionErrorDeltaFunction":{_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""]},"psyneulink.core.components.functions.combinationfunctions.Rearrange":{_function:[9,2,1,""],_instantiate_attributes_before_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""],arrangement:[9,4,1,""],default_variable:[9,4,1,""],name:[9,4,1,""],offset:[9,4,1,""],owner:[9,4,1,""],prefs:[9,4,1,""],scale:[9,4,1,""]},"psyneulink.core.components.functions.combinationfunctions.Reduce":{_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""],default_variable:[9,4,1,""],name:[9,4,1,""],offset:[9,4,1,""],operation:[9,4,1,""],owner:[9,4,1,""],prefs:[9,4,1,""],scale:[9,4,1,""]},"psyneulink.core.components.functions.distributionfunctions":{DistributionFunction:[32,1,1,""],DriftDiffusionAnalytical:[32,1,1,""],ExponentialDist:[32,1,1,""],GammaDist:[32,1,1,""],NormalDist:[32,1,1,""],UniformDist:[32,1,1,""],UniformToNormalDist:[32,1,1,""],WaldDist:[32,1,1,""]},"psyneulink.core.components.functions.distributionfunctions.DriftDiffusionAnalytical":{_compute_conditional_rt_moments:[32,2,1,""],_function:[32,2,1,""],bias:[32,4,1,""],derivative:[32,2,1,""],drift_rate:[32,4,1,""],name:[32,4,1,""],noise:[32,4,1,""],owner:[32,4,1,""],prefs:[32,4,1,""],shenhav_et_al_compat_mode:[32,3,1,""],starting_point:[32,4,1,""],t0:[32,4,1,""],threshold:[32,4,1,""],variable:[32,4,1,""]},"psyneulink.core.components.functions.distributionfunctions.ExponentialDist":{beta:[32,4,1,""],name:[32,4,1,""],owner:[32,4,1,""],params:[32,4,1,""],prefs:[32,4,1,""],random_state:[32,4,1,""]},"psyneulink.core.components.functions.distributionfunctions.GammaDist":{dist_shape:[32,4,1,""],name:[32,4,1,""],owner:[32,4,1,""],params:[32,4,1,""],prefs:[32,4,1,""],random_state:[32,4,1,""],scale:[32,4,1,""]},"psyneulink.core.components.functions.distributionfunctions.NormalDist":{_validate_params:[32,2,1,""],mean:[32,4,1,""],name:[32,4,1,""],owner:[32,4,1,""],params:[32,4,1,""],prefs:[32,4,1,""],random_state:[32,4,1,""],standard_deviation:[32,4,1,""]},"psyneulink.core.components.functions.distributionfunctions.UniformDist":{high:[32,4,1,""],low:[32,4,1,""],name:[32,4,1,""],owner:[32,4,1,""],params:[32,4,1,""],prefs:[32,4,1,""],random_state:[32,4,1,""]},"psyneulink.core.components.functions.distributionfunctions.UniformToNormalDist":{mean:[32,4,1,""],name:[32,4,1,""],owner:[32,4,1,""],params:[32,4,1,""],prefs:[32,4,1,""],random_state:[32,4,1,""],standard_deviation:[32,4,1,""]},"psyneulink.core.components.functions.function":{ArgumentTherapy:[38,1,1,""],Function_Base:[38,1,1,""]},"psyneulink.core.components.functions.function.ArgumentTherapy":{Manner:[38,1,1,""],_function:[38,2,1,""],_validate_params:[38,2,1,""],_validate_variable:[38,2,1,""],name:[38,4,1,""],owner:[38,4,1,""],pertinacity:[38,4,1,""],prefs:[38,4,1,""],propensity:[38,4,1,""],variable:[38,4,1,""]},"psyneulink.core.components.functions.function.Function_Base":{"function":[38,4,1,""],_model_spec_parameter_blacklist:[38,3,1,""],_parse_arg_generic:[38,2,1,""],_validate_parameter_spec:[38,2,1,""],name:[38,4,1,""],owner:[38,4,1,""],prefs:[38,4,1,""],variable:[38,4,1,""]},"psyneulink.core.components.functions.learningfunctions":{BackPropagation:[56,1,1,""],BayesGLM:[56,1,1,""],ContrastiveHebbian:[56,1,1,""],Hebbian:[56,1,1,""],Kohonen:[56,1,1,""],LearningFunction:[56,1,1,""],Reinforcement:[56,1,1,""],TDLearning:[56,1,1,""]},"psyneulink.core.components.functions.learningfunctions.BackPropagation":{_function:[56,2,1,""],_validate_params:[56,2,1,""],_validate_variable:[56,2,1,""],activation_derivative_fct:[56,4,1,""],activation_input:[56,4,1,""],activation_output:[56,4,1,""],default_learning_rate:[56,4,1,""],error_matrix:[56,4,1,""],error_signal:[56,4,1,""],learning_rate:[56,4,1,""],loss_function:[56,4,1,""],owner:[56,4,1,""],prefs:[56,4,1,""],variable:[56,4,1,""]},"psyneulink.core.components.functions.learningfunctions.BayesGLM":{Lambda_n:[56,4,1,""],Lambda_prior:[56,4,1,""],_function:[56,2,1,""],_handle_default_variable:[56,2,1,""],gamma_shape_0:[56,4,1,""],gamma_shape_n:[56,4,1,""],gamma_shape_prior:[56,4,1,""],gamma_size_0:[56,4,1,""],gamma_size_n:[56,4,1,""],gamma_size_prior:[56,4,1,""],initialize_priors:[56,2,1,""],mu_0:[56,4,1,""],mu_n:[56,4,1,""],mu_prior:[56,4,1,""],owner:[56,4,1,""],prefs:[56,4,1,""],random_state:[56,4,1,""],reset:[56,2,1,""],sample_weights:[56,2,1,""],sigma_0:[56,4,1,""],variable:[56,4,1,""],weights_sample:[56,4,1,""]},"psyneulink.core.components.functions.learningfunctions.ContrastiveHebbian":{"function":[56,4,1,""],_function:[56,2,1,""],_validate_params:[56,2,1,""],_validate_variable:[56,2,1,""],default_learning_rate:[56,4,1,""],learning_rate:[56,4,1,""],owner:[56,4,1,""],prefs:[56,4,1,""],variable:[56,4,1,""]},"psyneulink.core.components.functions.learningfunctions.Hebbian":{"function":[56,4,1,""],_function:[56,2,1,""],_validate_params:[56,2,1,""],_validate_variable:[56,2,1,""],default_learning_rate:[56,4,1,""],learning_rate:[56,4,1,""],owner:[56,4,1,""],prefs:[56,4,1,""],variable:[56,4,1,""]},"psyneulink.core.components.functions.learningfunctions.Kohonen":{"function":[56,4,1,""],_function:[56,2,1,""],_validate_params:[56,2,1,""],_validate_variable:[56,2,1,""],default_learning_rate:[56,4,1,""],learning_rate:[56,4,1,""],owner:[56,4,1,""],prefs:[56,4,1,""],variable:[56,4,1,""]},"ps
...

See CI logs for the full diff.

@lgtm-com
Copy link
Contributor

lgtm-com bot commented Jan 8, 2022

This pull request introduces 1 alert when merging 67ccee1 into da4ecb7 - view on LGTM.com

new alerts:

  • 1 for Unnecessary pass

@coveralls
Copy link

Coverage Status

Coverage increased (+0.2%) to 84.494% when pulling 67ccee1 on fix/show_graph/cim into da4ecb7 on devel.

@github-actions
Copy link

github-actions bot commented Jan 8, 2022

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

diff -r docs-base/CompositionInterfaceMechanism.html docs-head/CompositionInterfaceMechanism.html
391,401d390
< <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">
diff -r docs-base/genindex.html docs-head/genindex.html
507,508d506
<       <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>
655,656d652
<   </ul></td>
<   <td style="width: 33%; vertical-align: top;"><ul>
672a669,670
>   </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
< Search.setIndex({docnames:["AGT","AGTControlMechanism","AutoAssociativeLearningMechanism","AutoAssociativeProjection","AutodiffComposition","BasicsAndPrimer","BotvinickConflictMonitoringModel","BustamanteStroopXORLVOCModel","Cohen_HustonModel","CombinationFunctions","ComparatorMechanism","Compilation","Component","Components","Composition","CompositionFunctionApproximator","CompositionInterfaceMechanism","Compositions","Condition","Context","ContrastiveHebbianMechanism","ContributorsGuide","ControlMechanism","ControlMechanisms","ControlProjection","ControlProjections","ControlSignal","ConventionsAndDefinitions","Core","DDM","DefaultControlMechanism","Defaults","DistributionFunctions","EVC","EVCAuxiliary","EVCControlMechanism","EpisodicMemoryMechanism","Function","Functions","GatingMechanism","GatingMechanisms","GatingProjection","GatingProjections","GatingSignal","GilzenratModel","InputPort","IntegratorFunctions","IntegratorMechanism","IntegratorMechanisms","KWTAMechanism","Keywords","KohonenMechanism","LCAMechanism","LCControlMechanism","LCMechanism","LeabraMechanism","LearningFunctions","LearningMechanism","LearningMechanisms","LearningProjection","LearningProjections","LearningSignal","Library","Log","MappingProjection","MaskedMappingProjection","Mechanism","Mechanisms","MemoryFunctions","Models","ModulatoryMechanism","ModulatoryMechanisms","ModulatoryProjection","ModulatoryProjections","ModulatorySignal","MontagueModel","NieuwenhuisModel","NonStatefulFunctions","ObjectiveFunctions","ObjectiveMechanism","ObjectiveMechanisms","OptimizationControlMechanism","OptimizationFunctions","OutputPort","PCTC_model","ParameterEstimationComposition","ParameterPort","Parameters","Pathway","PathwayProjection","PathwayProjections","Port","PredictionErrorMechanism","Preferences","ProcessingMechanism","ProcessingMechanisms","Projection","Projections","QuickReference","RecurrentTransferMechanism","RefactoredLearningGuide","Registry","RegressionCFA","Report","Scheduler","Scheduling","SelectionFunctions","Services","StatefulFunction","StatefulFunctions","Subystems","Time","TransferFunctions","TransferMechanism","TransferMechanisms","UserDefinedFunction","UserGuide","UserGuide_TBD","Visualization","globals","index","index_logo_with_text","json"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":4,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,sphinx:56},filenames:["AGT.rst","AGTControlMechanism.rst","AutoAssociativeLearningMechanism.rst","AutoAssociativeProjection.rst","AutodiffComposition.rst","BasicsAndPrimer.rst","BotvinickConflictMonitoringModel.rst","BustamanteStroopXORLVOCModel.rst","Cohen_HustonModel.rst","CombinationFunctions.rst","ComparatorMechanism.rst","Compilation.rst","Component.rst","Components.rst","Composition.rst","CompositionFunctionApproximator.rst","CompositionInterfaceMechanism.rst","Compositions.rst","Condition.rst","Context.rst","ContrastiveHebbianMechanism.rst","ContributorsGuide.rst","ControlMechanism.rst","ControlMechanisms.rst","ControlProjection.rst","ControlProjections.rst","ControlSignal.rst","ConventionsAndDefinitions.rst","Core.rst","DDM.rst","DefaultControlMechanism.rst","Defaults.rst","DistributionFunctions.rst","EVC.rst","EVCAuxiliary.rst","EVCControlMechanism.rst","EpisodicMemoryMechanism.rst","Function.rst","Functions.rst","GatingMechanism.rst","GatingMechanisms.rst","GatingProjection.rst","GatingProjections.rst","GatingSignal.rst","GilzenratModel.rst","InputPort.rst","IntegratorFunctions.rst","IntegratorMechanism.rst","IntegratorMechanisms.rst","KWTAMechanism.rst","Keywords.rst","KohonenMechanism.rst","LCAMechanism.rst","LCControlMechanism.rst","LCMechanism.rst","LeabraMechanism.rst","LearningFunctions.rst","LearningMechanism.rst","LearningMechanisms.rst","LearningProjection.rst","LearningProjections.rst","LearningSignal.rst","Library.rst","Log.rst","MappingProjection.rst","MaskedMappingProjection.rst","Mechanism.rst","Mechanisms.rst","MemoryFunctions.rst","Models.rst","ModulatoryMechanism.rst","ModulatoryMechanisms.rst","ModulatoryProjection.rst","ModulatoryProjections.rst","ModulatorySignal.rst","MontagueModel.rst","NieuwenhuisModel.rst","NonStatefulFunctions.rst","ObjectiveFunctions.rst","ObjectiveMechanism.rst","ObjectiveMechanisms.rst","OptimizationControlMechanism.rst","OptimizationFunctions.rst","OutputPort.rst","PCTC_model.rst","ParameterEstimationComposition.rst","ParameterPort.rst","Parameters.rst","Pathway.rst","PathwayProjection.rst","PathwayProjections.rst","Port.rst","PredictionErrorMechanism.rst","Preferences.rst","ProcessingMechanism.rst","ProcessingMechanisms.rst","Projection.rst","Projections.rst","QuickReference.rst","RecurrentTransferMechanism.rst","RefactoredLearningGuide.rst","Registry.rst","RegressionCFA.rst","Report.rst","Scheduler.rst","Scheduling.rst","SelectionFunctions.rst","Services.rst","StatefulFunction.rst","StatefulFunctions.rst","Subystems.rst","Time.rst","TransferFunctions.rst","TransferMechanism.rst","TransferMechanisms.rst","UserDefinedFunction.rst","UserGuide.rst","UserGuide_TBD.rst","Visualization.rst","globals.rst","index.rst","index_logo_with_text.rst","json.rst"],objects:{"psyneulink.core.components":{component:[12,0,0,"-"]},"psyneulink.core.components.component":{Component:[12,1,1,""]},"psyneulink.core.components.component.Component":{"function":[12,4,1,""],_check_args:[12,2,1,""],_check_for_composition:[12,2,1,""],_deferred_init:[12,2,1,""],_dependent_components:[12,3,1,""],_get_param_value_from_tuple:[12,2,1,""],_handle_default_variable:[12,2,1,""],_handle_size:[12,2,1,""],_instantiate_defaults:[12,2,1,""],_instantiate_function:[12,2,1,""],_instantiate_parameter_classes:[12,2,1,""],_model_spec_class_name_is_generic:[12,4,1,""],_model_spec_generic_type_name:[12,4,1,""],_model_spec_parameter_blacklist:[12,3,1,""],_parameter_components:[12,3,1,""],_parse_arg_generic:[12,2,1,""],_parse_arg_variable:[12,2,1,""],_parse_function_variable:[12,2,1,""],_set_multiple_parameter_values:[12,2,1,""],_specified_variable_shape_flexibility:[12,4,1,""],_validate:[12,2,1,""],_validate_and_assign_runtime_params:[12,2,1,""],_validate_function:[12,2,1,""],_validate_params:[12,2,1,""],_validate_variable:[12,2,1,""],all_dependent_parameters:[12,2,1,""],current_execution_time:[12,4,1,""],defaults:[12,4,1,""],execute:[12,2,1,""],execute_until_finished:[12,4,1,""],execution_count:[12,4,1,""],function_parameters:[12,3,1,""],initialization_status:[12,4,1,""],is_finished:[12,2,1,""],log:[12,4,1,""],log_values:[12,2,1,""],loggable_items:[12,3,1,""],logged_items:[12,3,1,""],max_executions_before_finished:[12,4,1,""],most_recent_context:[12,3,1,""],name:[12,4,1,""],num_executions:[12,4,1,""],num_executions_before_finished:[12,4,1,""],parameters:[12,4,1,""],prefs:[12,4,1,""],reset:[12,2,1,""],reset_params:[12,2,1,""],reset_stateful_function_when:[12,4,1,""],set_delivery_conditions:[12,2,1,""],set_log_conditions:[12,2,1,""],size:[12,4,1,""],stateful_parameters:[12,3,1,"id0"],value:[12,4,1,""],variable:[12,4,1,""]},"psyneulink.core.components.functions":{"function":[38,0,0,"-"],combinationfunctions:[9,0,0,"-"],distributionfunctions:[32,0,0,"-"],learningfunctions:[56,0,0,"-"],objectivefunctions:[78,0,0,"-"],optimizationfunctions:[82,0,0,"-"],selectionfunctions:[106,0,0,"-"],transferfunctions:[112,0,0,"-"],userdefinedfunction:[115,0,0,"-"]},"psyneulink.core.components.functions.combinationfunctions":{CombineMeans:[9,1,1,""],Concatenate:[9,1,1,""],LinearCombination:[9,1,1,""],PredictionErrorDeltaFunction:[9,1,1,""],Rearrange:[9,1,1,""],Reduce:[9,1,1,""]},"psyneulink.core.components.functions.combinationfunctions.CombineMeans":{_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""],exponents:[9,4,1,""],name:[9,4,1,""],offset:[9,4,1,""],operation:[9,4,1,""],owner:[9,4,1,""],prefs:[9,4,1,""],scale:[9,4,1,""],variable:[9,4,1,""],weights:[9,4,1,""]},"psyneulink.core.components.functions.combinationfunctions.Concatenate":{_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""],default_variable:[9,4,1,""],name:[9,4,1,""],offset:[9,4,1,""],owner:[9,4,1,""],prefs:[9,4,1,""],scale:[9,4,1,""]},"psyneulink.core.components.functions.combinationfunctions.LinearCombination":{_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""],exponents:[9,4,1,""],name:[9,4,1,""],offset:[9,4,1,""],operation:[9,4,1,""],owner:[9,4,1,""],prefs:[9,4,1,""],scale:[9,4,1,""],variable:[9,4,1,""],weights:[9,4,1,""]},"psyneulink.core.components.functions.combinationfunctions.PredictionErrorDeltaFunction":{_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""]},"psyneulink.core.components.functions.combinationfunctions.Rearrange":{_function:[9,2,1,""],_instantiate_attributes_before_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""],arrangement:[9,4,1,""],default_variable:[9,4,1,""],name:[9,4,1,""],offset:[9,4,1,""],owner:[9,4,1,""],prefs:[9,4,1,""],scale:[9,4,1,""]},"psyneulink.core.components.functions.combinationfunctions.Reduce":{_function:[9,2,1,""],_validate_params:[9,2,1,""],_validate_variable:[9,2,1,""],default_variable:[9,4,1,""],name:[9,4,1,""],offset:[9,4,1,""],operation:[9,4,1,""],owner:[9,4,1,""],prefs:[9,4,1,""],scale:[9,4,1,""]},"psyneulink.core.components.functions.distributionfunctions":{DistributionFunction:[32,1,1,""],DriftDiffusionAnalytical:[32,1,1,""],ExponentialDist:[32,1,1,""],GammaDist:[32,1,1,""],NormalDist:[32,1,1,""],UniformDist:[32,1,1,""],UniformToNormalDist:[32,1,1,""],WaldDist:[32,1,1,""]},"psyneulink.core.components.functions.distributionfunctions.DriftDiffusionAnalytical":{_compute_conditional_rt_moments:[32,2,1,""],_function:[32,2,1,""],bias:[32,4,1,""],derivative:[32,2,1,""],drift_rate:[32,4,1,""],name:[32,4,1,""],noise:[32,4,1,""],owner:[32,4,1,""],prefs:[32,4,1,""],shenhav_et_al_compat_mode:[32,3,1,""],starting_point:[32,4,1,""],t0:[32,4,1,""],threshold:[32,4,1,""],variable:[32,4,1,""]},"psyneulink.core.components.functions.distributionfunctions.ExponentialDist":{beta:[32,4,1,""],name:[32,4,1,""],owner:[32,4,1,""],params:[32,4,1,""],prefs:[32,4,1,""],random_state:[32,4,1,""]},"psyneulink.core.components.functions.distributionfunctions.GammaDist":{dist_shape:[32,4,1,""],name:[32,4,1,""],owner:[32,4,1,""],params:[32,4,1,""],prefs:[32,4,1,""],random_state:[32,4,1,""],scale:[32,4,1,""]},"psyneulink.core.components.functions.distributionfunctions.NormalDist":{_validate_params:[32,2,1,""],mean:[32,4,1,""],name:[32,4,1,""],owner:[32,4,1,""],params:[32,4,1,""],prefs:[32,4,1,""],random_state:[32,4,1,""],standard_deviation:[32,4,1,""]},"psyneulink.core.components.functions.distributionfunctions.UniformDist":{high:[32,4,1,""],low:[32,4,1,""],name:[32,4,1,""],owner:[32,4,1,""],params:[32,4,1,""],prefs:[32,4,1,""],random_state:[32,4,1,""]},"psyneulink.core.components.functions.distributionfunctions.UniformToNormalDist":{mean:[32,4,1,""],name:[32,4,1,""],owner:[32,4,1,""],params:[32,4,1,""],prefs:[32,4,1,""],random_state:[32,4,1,""],standard_deviation:[32,4,1,""]},"psyneulink.core.components.functions.function":{ArgumentTherapy:[38,1,1,""],Function_Base:[38,1,1,""]},"psyneulink.core.components.functions.function.ArgumentTherapy":{Manner:[38,1,1,""],_function:[38,2,1,""],_validate_params:[38,2,1,""],_validate_variable:[38,2,1,""],name:[38,4,1,""],owner:[38,4,1,""],pertinacity:[38,4,1,""],prefs:[38,4,1,""],propensity:[38,4,1,""],variable:[38,4,1,""]},"psyneulink.core.components.functions.function.Function_Base":{"function":[38,4,1,""],_model_spec_parameter_blacklist:[38,3,1,""],_parse_arg_generic:[38,2,1,""],_validate_parameter_spec:[38,2,1,""],name:[38,4,1,""],owner:[38,4,1,""],prefs:[38,4,1,""],variable:[38,4,1,""]},"psyneulink.core.components.functions.learningfunctions":{BackPropagation:[56,1,1,""],BayesGLM:[56,1,1,""],ContrastiveHebbian:[56,1,1,""],Hebbian:[56,1,1,""],Kohonen:[56,1,1,""],LearningFunction:[56,1,1,""],Reinforcement:[56,1,1,""],TDLearning:[56,1,1,""]},"psyneulink.core.components.functions.learningfunctions.BackPropagation":{_function:[56,2,1,""],_validate_params:[56,2,1,""],_validate_variable:[56,2,1,""],activation_derivative_fct:[56,4,1,""],activation_input:[56,4,1,""],activation_output:[56,4,1,""],default_learning_rate:[56,4,1,""],error_matrix:[56,4,1,""],error_signal:[56,4,1,""],learning_rate:[56,4,1,""],loss_function:[56,4,1,""],owner:[56,4,1,""],prefs:[56,4,1,""],variable:[56,4,1,""]},"psyneulink.core.components.functions.learningfunctions.BayesGLM":{Lambda_n:[56,4,1,""],Lambda_prior:[56,4,1,""],_function:[56,2,1,""],_handle_default_variable:[56,2,1,""],gamma_shape_0:[56,4,1,""],gamma_shape_n:[56,4,1,""],gamma_shape_prior:[56,4,1,""],gamma_size_0:[56,4,1,""],gamma_size_n:[56,4,1,""],gamma_size_prior:[56,4,1,""],initialize_priors:[56,2,1,""],mu_0:[56,4,1,""],mu_n:[56,4,1,""],mu_prior:[56,4,1,""],owner:[56,4,1,""],prefs:[56,4,1,""],random_state:[56,4,1,""],reset:[56,2,1,""],sample_weights:[56,2,1,""],sigma_0:[56,4,1,""],variable:[56,4,1,""],weights_sample:[56,4,1,""]},"psyneulink.core.components.functions.learningfunctions.ContrastiveHebbian":{"function":[56,4,1,""],_function:[56,2,1,""],_validate_params:[56,2,1,""],_validate_variable:[56,2,1,""],default_learning_rate:[56,4,1,""],learning_rate:[56,4,1,""],owner:[56,4,1,""],prefs:[56,4,1,""],variable:[56,4,1,""]},"psyneulink.core.components.functions.learningfunctions.Hebbian":{"function":[56,4,1,""],_function:[56,2,1,""],_validate_params:[56,2,1,""],_validate_variable:[56,2,1,""],default_learning_rate:[56,4,1,""],learning_rate:[56,4,1,""],owner:[56,4,1,""],prefs:[56,4,1,""],variable:[56,4,1,""]},"psyneulink.core.components.functions.learningfunctions.Kohonen":{"function":[56,4,1,""],_function:[56,2,1,""],_validate_params:[56,2,1,""],_validate_variable:[56,2,1,""],default_learning_rate:[56,4,1,""],learning_rate:[56,4,1,""],owner:[56,4,1,""],prefs:[56,4,1,""],variable:[56,4,1,""]},"ps
...

See CI logs for the full diff.

# The bug may be the same one as in eb61303808ad2a5ba46fdd18d0e583283397915c
raise(AssertionError,"FAILURE TO REPLICATE BUGGY SHOW_GRAPH OUTPUT -- SEE COMMENT IN TEST")
else:
raise(AssertionError)
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

thiscan be just:
raise

to forward the existing exception/assertion instead of creating a new one

@lgtm-com
Copy link
Contributor

lgtm-com bot commented Jan 8, 2022

This pull request introduces 1 alert when merging 4c3ff97 into 544c1ec - view on LGTM.com

new alerts:

  • 1 for Unnecessary pass

@jdcpni jdcpni merged commit 21e685c into devel Jan 8, 2022
@jdcpni jdcpni deleted the fix/show_graph/cim branch January 8, 2022 16:34
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

3 participants