Devel #2354

kmantel · 2022-03-21T23:56:43Z

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…teger Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

…ct/_function

get_param_struct_type(): restored test on num_estimates

…ct/_function

…Link into fit

…om/PrincetonUniversity/PsyNeuLink into fit

…Link into fit

* - This branch passes all tests except: - test_parameterestimationcomposition - test_composition/test_partially_overlapping_control_specs (ADDED IN THIS COMMINT) - All relevant changes to this branch are marked as "11/21/21." However, most are commented out as they break other things. - The tests above both involve local control specifications (on mechanism within a nested comp) and on the OCM for the outer composition, some of which are for the same nested mechs - Both tests fail with: "AttributeError: 'NoneType' object has no attribute '_get_by_time_scale'" (in component.py LINE 3276) This may be due to a problem with context setting, since the error is because the modulation Parameter of the ControlProjection is returning "None" rather than "multiplicative_param" (when called with get(context)), whereas "multiplicative_param" is returned with a call to get() (i.e., with no context specified) - Most of test_partially_overlapping_control_specs is passed if changes marked "11/21/21 NEW" in optimizationcontrolmechanism.py (LINE 1390) are implemented, but it does not properly route ControlProjections through parameter_CIMS (see last assert in test). Furthermore, test_parameterestimationcompsition fails with the mod param error, even though the model has similar structure (i.e., outer composition -- in this case a ParameterEstimationComposition) with an OCM that is given control specs that overlap with ones in a nested composition. - There are also several other things in composition I found puzzling and tried modifying, but that cuased failures: - _get_control_signals_for_composition(): - seems "if node.controller" should be "if **not** node.controller" (emphasis added just for comment) - "append" should be "extend" - _instantiate_control_projection(): - call to self.controller._activate_projections_for_composition (at end of method) should not be indented * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - finished adding formatting regions to composition.py * - * • composition.py: - rename _check_projection_initialization_status -> _check_controller_initialization_status - add _check_nodes_initialization_status(context=context) (and calls it with _check_controller_initialization_status) * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * - * Composition: add_controller: set METHOD as context source early * - * • composition.py retore append of control_signals in _instantiate_control_projections() * • composition.py 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_unnested_and_nested_comp(): - added clear_registry() to allow names to be reused in both runs of test * • composition.py docstring: added projections entry to list of attributes - add_controller: added call to _add_node_aux_components() for controller * • composition.py _add_node_aux_components(): added deletion of item from aux_components if instantiated * • composition.py - 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) * - * - confirm that it passes all tests exception test_composition/test_partially_overlapping... (with addition of _add_aux_components in add_controller commented out) * • composition.py: some more fixed to add_controller that now fail only one test: - test_agent_rep_assignement_as_controller_and_replacement * • Passes *all* current tests * • composition.py: - add_controller: few more minor mods; still passes all tests * - * - * - * • controlmechanism.py: - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms) * - * • composition.py: in progress fix of bug in instantiating shadow projections for ocm.state_input_ports * • composition.py: - _get_original_senders(): added support for nested composition needs to be checked for more than one level needs to be refactored to be recursive * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: fix invalid_state_features to allow input_CIM of nested comp in agent_rep * - * • composition.py - _get_original_senders: made recursive * • test_show_graph.py: update for fixes * - * • tests: passes all in test_show_graph.py and test_report.py * Passes all tests * - comment clean-up * • composition.py - 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: allow_probes fully implemented * • show_graph.py: fixed bug causing extra projections to OCM * • composition.py: - _update_shadow_projections(): fix handling of deep nesting * • optimizationcontrolmechanism.py: add agent_rep_type property * • optimizationcontrolmechanism.py: - state_feature_function -> state_feature_functions * • optimizationcontrolmechanism.py: - _validate_params: validate state_feature_functions - _update_state_input_ports_for_controller: implement assignment of state_feature_functions * - * - * • Passes all tests except test_json with 'model_with_control' * - * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * - * • test_two_origins_two_input_ports: crashes on failure of C->B to update * - * • composition.py - added property shadowing_dict that has shadowing ports as keys and the ports they shadow as values - refactored _update_shadowing_projections to use shadowing_dict * • optimizationcontrolmechanism.py - _update_state_input_ports: modified validations for nested nodes; still failing some tests * • optimizationcontrolmechanism.py - _update_state_input_ports: more careful and informative validation that state_input_ports are in comp or nested comp and are INPUT nodes thereof; passes all tests except test_two_origins_two_input_ports as before * • composition.py _get_invalid_aux_components(): defer all shadow projections until _update_shadow_projections * • composition.py _get_invalid_aux_components(): bug fix in test for shadow projections * Port: _remove_projection_to_port: don't reduce variable below length 1 even ports with no incoming projections have variable at least length 1 * • composition.py add_node(): marked (but haven't removed) code block instantiating shadow_projections that seems now to be redundant with _update_shadow_projection * • show_graph.py - _assign_cim_components: supress showing projections not in composition * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py - add show_projections_not_in_composition option for debugging * • composition.py _update_shadow_projections(): delete unused shadow projections and corresponding ports * • composition.py _update_shadow_projections(): fix bug in deletion of unused shadow projections and ports • test_show_graph: tests failing, need mods to accomodate changes * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py fixes; now passes all show_graph tests * - * • composition.py _update_shadow_projections: raise error for attempt to shadow INTERNAL Node of nested comp * - * - * • test_composition.py implemented test_shadow_nested_nodes that tests shadowing of nested nodes * - * - * - * - * • optimizationcontrolmechanism.py: docstring mods * • composition.py: - add allow_probes and exclude_probes_from_output * • composition.py: - docstring mods re: allow_probes • optimizationcontrolmechanism.py: - allow_probes: eliminate DIRECT setting - remove _parse_monitor_for_control_input_ports (no longer needed without allow_probes=DIRECT) * • composition.py: - change "exclude_probes_from_output" -> "include_probes_in_output" * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism - add _handle_allow_probes_for_control() to reconcile setting on Composition and ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • composition.py add assignment of learning_mechanism to objective_mechanism.modulatory_mechanism for add_learning methods * • docstring mods * - * - * • optimizationcontrolmechanism.py: docstring revs * - * - * • test_composition.py: - add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output * - * • composition.py - add_node(): support tuple with required_role * - * • composition.py: - _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL) * - * • composition.py: - add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value() * - * • CompositionInterfaceMechanism.rst: - correct path ref • compositioninterfacemechanism.py: - docstring fixes * • compositioninterfacemechanism.py: - docstring edits * - * - * - * - * - * - * - * - * - * • composition.py: add_projection: _parse_projection_spec -> _instantiate_projection_from_spec * • composition.py: add_projection: _parse_projection_spec -> _instantiate_projection_from_spec * • composition.py - add_linear_processing_pathway: support one->many and many->one configurations in pathway specification (see docstring for method) * - * • composition.py _add_linear_processing_pathway, add_projection, _is_pathway_entry_spec: - support many->one and one->many projections between mech and comps in pathway spec: working - support set of Projections as legal entry in pathway spec: TBI * • composition.py _add_linear_processing_pathway, add_projection, _is_pathway_entry_spec: - support many->one and one->many projections between mech and comps in pathway spec: working - support set of Projections as legal entry in pathway spec: TBI * • show_graph.py _assign_cim_components(): fix bug in which comp1_output_cim->comp2_input_cim was skipped * • compositioninterfacemechanism.py: docstring mod * - * • composition.py: minor formatting * • composition.py add_linear_processing_pathway(): eliminate TARGET Nodes from one->many * - * • composition.py: - add_linear_processing_pathway(): add recursive search for nested INPUT and OUTPUT nodes * • composition.py: - add_linear_processing_pathway(): - exclude Target Nodes from search for INPUT nodes (handled by learning) - add recursive search for nested INPUT and OUTPUT nodes * - * - * • composition.py add_projection: working on adding support for projection sets * - * - * • composition.py - add _get_nested_nodes_with_same_roles_at_all_levels - add_linear_processing_pathway: call _get_nested_nodes_with_same_roles_at_all_levels * • composition.py - add_linear_processing_pathway: add support for inline specification of set of Projections * - * - * • composition.py add_linear_processing_pathway: refactored to support inline specification of sets of Projections * • composition.py add_linear_processing_pathway: docstring edits for Projection set specification * - * - * - * - * - * • test_composition.py: - add test_add_multiple_projections_for_nested_compositions - IN PROGRESS * • test_composition.py: - add test_add_multiple_projections_for_nested_compositions - passes * - * - * • compositioninterfacemechanism.py: add figure and example * • composition.py: - get_inputs_format(): add method - run(): allow inputs arg to take names of nodes * • composition.py: - get_inputs_format(): - implemented num_trials arg - TBI: nested and labels * - * • composition.py - get_input_format(): implement show_nested_input_nodes * • composition.py - get_input_format(): implement use_labels * - * - * - * - * - * - * - * - * - * - * - * • composition.py get_input_format() - working; TBD: tests and documentation in composition docstring * • composition.py get_results_format() - working; TBD: tests and documentation in composition docstring * - * • composition.py: add error messages to _parse_label() and _validate_single_input() * • composition.py: add error messages to _parse_label() and _validate_single_input() * - * • composition.py: docstring mods * • composition.py - reorganize docstring section on execution * - * - * - * - * • test_composition.py / test_input_labels_and_no_orphaning_of_nested_output_nodes: added tests for lables in input * • composition.py: _validate_single_input - get rid of tests (taken care of in _parse_labels) * • test_composition.py/test_input_labels_and_results_by_node_and_no_orphaning_of_nested_output_nodes: - renamed, add test for get_results_by_node * • composition.py - _parse_labels: suppress warning about targets if no learning_components in pway * - * • composition.py: further docstring updates for get_input_format() and get_results_by_node() * - * - * - * - * - * • composition.py - get_results_by_node(): add use_labels option * - * - * - * • composition.py - get_results_by_nodes: allow specification of individual nodes * • composition.py - get_results_by_nodes: allow specification of individual nodes * • composition.py - get_results_by_nodes: allow specification of individual nodes * - * - * • mechanism.py: add input_labels and output_labels as args to constructor * - * - * • project: remove scale from figures * - * - * - * • project - docstring mods • composition.py: found bug with specification of shadows and probes between "parallel" compositions. * • README.rst and composition.py: add links to CGO paper * • README.rst, index.rst and composition.py: - updates to contribtors - add links to CGO paper * • composition.py _update_shadow_projections: report error for failure to find correct_sender * • composition.py - add _check_for_unused_projections(): warns if any projections are specified for Nodes that are not used in the comp * - * - Co-authored-by: Katherine Mantel <kmantel@princeton.edu> Co-authored-by: jdcpni <pniintel55>

* - * • composition.py retore append of control_signals in _instantiate_control_projections() * • composition.py 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_unnested_and_nested_comp(): - added clear_registry() to allow names to be reused in both runs of test * • composition.py docstring: added projections entry to list of attributes - add_controller: added call to _add_node_aux_components() for controller * • composition.py _add_node_aux_components(): added deletion of item from aux_components if instantiated * • composition.py - 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) * - * - confirm that it passes all tests exception test_composition/test_partially_overlapping... (with addition of _add_aux_components in add_controller commented out) * • composition.py: some more fixed to add_controller that now fail only one test: - test_agent_rep_assignement_as_controller_and_replacement * • Passes *all* current tests * • composition.py: - add_controller: few more minor mods; still passes all tests * - * - * - * • controlmechanism.py: - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms) * - * • composition.py: in progress fix of bug in instantiating shadow projections for ocm.state_input_ports * • composition.py: - _get_original_senders(): added support for nested composition needs to be checked for more than one level needs to be refactored to be recursive * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: fix invalid_state_features to allow input_CIM of nested comp in agent_rep * - * • composition.py - _get_original_senders: made recursive * • test_show_graph.py: update for fixes * - * • tests: passes all in test_show_graph.py and test_report.py * Passes all tests * - comment clean-up * • composition.py - 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: allow_probes fully implemented * • show_graph.py: fixed bug causing extra projections to OCM * • composition.py: - _update_shadow_projections(): fix handling of deep nesting * • optimizationcontrolmechanism.py: add agent_rep_type property * • optimizationcontrolmechanism.py: - state_feature_function -> state_feature_functions * • optimizationcontrolmechanism.py: - _validate_params: validate state_feature_functions - _update_state_input_ports_for_controller: implement assignment of state_feature_functions * - * - * • Passes all tests except test_json with 'model_with_control' * - * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * - * • test_two_origins_two_input_ports: crashes on failure of C->B to update * - * • composition.py - added property shadowing_dict that has shadowing ports as keys and the ports they shadow as values - refactored _update_shadowing_projections to use shadowing_dict * • optimizationcontrolmechanism.py - _update_state_input_ports: modified validations for nested nodes; still failing some tests * • optimizationcontrolmechanism.py - _update_state_input_ports: more careful and informative validation that state_input_ports are in comp or nested comp and are INPUT nodes thereof; passes all tests except test_two_origins_two_input_ports as before * • composition.py _get_invalid_aux_components(): defer all shadow projections until _update_shadow_projections * • composition.py _get_invalid_aux_components(): bug fix in test for shadow projections * Port: _remove_projection_to_port: don't reduce variable below length 1 even ports with no incoming projections have variable at least length 1 * • composition.py add_node(): marked (but haven't removed) code block instantiating shadow_projections that seems now to be redundant with _update_shadow_projection * • show_graph.py - _assign_cim_components: supress showing projections not in composition * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py - add show_projections_not_in_composition option for debugging * • composition.py _update_shadow_projections(): delete unused shadow projections and corresponding ports * • composition.py _update_shadow_projections(): fix bug in deletion of unused shadow projections and ports • test_show_graph: tests failing, need mods to accomodate changes * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py fixes; now passes all show_graph tests * - * • composition.py _update_shadow_projections: raise error for attempt to shadow INTERNAL Node of nested comp * - * - * • test_composition.py implemented test_shadow_nested_nodes that tests shadowing of nested nodes * - * - * - * - * • optimizationcontrolmechanism.py: docstring mods * • composition.py: - add allow_probes and exclude_probes_from_output * • composition.py: - docstring mods re: allow_probes • optimizationcontrolmechanism.py: - allow_probes: eliminate DIRECT setting - remove _parse_monitor_for_control_input_ports (no longer needed without allow_probes=DIRECT) * • composition.py: - change "exclude_probes_from_output" -> "include_probes_in_output" * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism - add _handle_allow_probes_for_control() to reconcile setting on Composition and ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • composition.py add assignment of learning_mechanism to objective_mechanism.modulatory_mechanism for add_learning methods * • docstring mods * - * - * • optimizationcontrolmechanism.py: docstring revs * - * - * • test_composition.py: - add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output * - * • composition.py - add_node(): support tuple with required_role * - * • composition.py: - _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL) * - * • composition.py: - add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value() * - * • CompositionInterfaceMechanism.rst: - correct path ref • compositioninterfacemechanism.py: - docstring fixes * • compositioninterfacemechanism.py: - docstring edits * - * - * - * - * - * - * - * - * - * • composition.py: add_projection: _parse_projection_spec -> _instantiate_projection_from_spec * • composition.py: add_projection: _parse_projection_spec -> _instantiate_projection_from_spec * • composition.py - add_linear_processing_pathway: support one->many and many->one configurations in pathway specification (see docstring for method) * - * • composition.py _add_linear_processing_pathway, add_projection, _is_pathway_entry_spec: - support many->one and one->many projections between mech and comps in pathway spec: working - support set of Projections as legal entry in pathway spec: TBI * • composition.py _add_linear_processing_pathway, add_projection, _is_pathway_entry_spec: - support many->one and one->many projections between mech and comps in pathway spec: working - support set of Projections as legal entry in pathway spec: TBI * • show_graph.py _assign_cim_components(): fix bug in which comp1_output_cim->comp2_input_cim was skipped * • compositioninterfacemechanism.py: docstring mod * - * • composition.py: minor formatting * • composition.py add_linear_processing_pathway(): eliminate TARGET Nodes from one->many * - * • composition.py: - add_linear_processing_pathway(): add recursive search for nested INPUT and OUTPUT nodes * • composition.py: - add_linear_processing_pathway(): - exclude Target Nodes from search for INPUT nodes (handled by learning) - add recursive search for nested INPUT and OUTPUT nodes * - * - * • composition.py add_projection: working on adding support for projection sets * - * - * • composition.py - add _get_nested_nodes_with_same_roles_at_all_levels - add_linear_processing_pathway: call _get_nested_nodes_with_same_roles_at_all_levels * • composition.py - add_linear_processing_pathway: add support for inline specification of set of Projections * - * - * • composition.py add_linear_processing_pathway: refactored to support inline specification of sets of Projections * • composition.py add_linear_processing_pathway: docstring edits for Projection set specification * - * - * - * - * - * • test_composition.py: - add test_add_multiple_projections_for_nested_compositions - IN PROGRESS * • test_composition.py: - add test_add_multiple_projections_for_nested_compositions - passes * - * - * • compositioninterfacemechanism.py: add figure and example * • composition.py: - get_inputs_format(): add method - run(): allow inputs arg to take names of nodes * • composition.py: - get_inputs_format(): - implemented num_trials arg - TBI: nested and labels * - * • composition.py - get_input_format(): implement show_nested_input_nodes * • composition.py - get_input_format(): implement use_labels * - * - * - * - * - * - * - * - * - * - * - * • composition.py get_input_format() - working; TBD: tests and documentation in composition docstring * • composition.py get_results_format() - working; TBD: tests and documentation in composition docstring * - * • composition.py: add error messages to _parse_label() and _validate_single_input() * • composition.py: add error messages to _parse_label() and _validate_single_input() * - * • composition.py: docstring mods * • composition.py - reorganize docstring section on execution * - * - * - * - * • test_composition.py / test_input_labels_and_no_orphaning_of_nested_output_nodes: added tests for lables in input * • composition.py: _validate_single_input - get rid of tests (taken care of in _parse_labels) * • test_composition.py/test_input_labels_and_results_by_node_and_no_orphaning_of_nested_output_nodes: - renamed, add test for get_results_by_node * • composition.py - _parse_labels: suppress warning about targets if no learning_components in pway * - * • composition.py: further docstring updates for get_input_format() and get_results_by_node() * - * - * - * - * - * • composition.py - get_results_by_node(): add use_labels option * - * - * - * • composition.py - get_results_by_nodes: allow specification of individual nodes * • composition.py - get_results_by_nodes: allow specification of individual nodes * • composition.py - get_results_by_nodes: allow specification of individual nodes * - * - * • mechanism.py: add input_labels and output_labels as args to constructor * - * - * • project: remove scale from figures * - * - * - * • project - docstring mods • composition.py: found bug with specification of shadows and probes between "parallel" compositions. * • README.rst and composition.py: add links to CGO paper * • README.rst, index.rst and composition.py: - updates to contribtors - add links to CGO paper * • composition.py _update_shadow_projections: report error for failure to find correct_sender * • composition.py - add _check_for_unused_projections(): warns if any projections are specified for Nodes that are not used in the comp * - * - * - * • test_composition.py: - test_failure_to_find_node_to_shadow(self): - test_unused_projections_warning * • test_composition.py: - test_failure_to_find_node_to_shadow(self): - test_unused_projections_warning * • keywords.py: COMPOSITION: COMPOSITION -> Composition • test_composition.py: - test_failure_to_find_node_to_shadow(self): - test_unused_projections_warning * • keywords.py: COMPOSITION: COMPOSITION -> Composition * - * • show_graph.py: - RANDOMIZATION_CONTROL_PROJECTION: dashed line - docstring mods * - * - * - Co-authored-by: jdcpni <pniintel55> Co-authored-by: Katherine Mantel <kmantel@princeton.edu>

* • component.py docstring mod to **size** * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute • optimizationfunctions.py: made num_estimates a Parameter * - modified test_mode_based_num_estimates * - * - * • optimizationcontrolmechanism.py: - _instantiate_control_signals: random_seeds -> random_seed_mod_values * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: now adds feature_input_ports for Compostion INPUT nodes if not state_features not specified * - * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: assign simulation_input_ports * - * • optimizationcontrolmechanism.py: - feature_input_ports -> state_input_ports - _instantiate_input_ports(): state_features only allowed to specifying state_input_ports if agent_rep is a CompositionFunctionApproximator (i.e., model-free optimization) • composition.py: - add_controller: adds state_input_ports to shadow INPUT Nodes of Composition if controller.agent_rep is Composition (model-based optimziation) or state_features have not been specified (for model-free optimizaton) * - * • optimizationcontrolmechanism.py: _instantiate_input_ports: reinstate allowance of state_features specification if agent_rep is a Composition (i.e., model-based optimization) as long as they are all INPUT Nodes of agent_rep * - * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_estimates_per_trial * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trial_per_estimate * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trials_per_estimate * - * - * - * - * • composition.py - __init__: moved controller instantiation until after nodes, projections and pathways * • composition.py - __init__: restored add_controller position * llvm/struct generation: Make sure num_estimats per trial is always integer Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu> * - * • composition.py: - _update_controller: added - add_controller and _analyze_graph(): call _update_controller * - * • composition.py _update_controller: fixed to loop through all input_ports of comp INPUT nodes * • test_control.py - test_agent_rep_assignement_as_controller_and_replacement: updated to test that shadowing projections to state_input_ports are properly added and deleted * • optimizationfunctions.py: - _function: refactored to put use aggregation_function at end - _grid_evaluate: still needs to return all_samples * - * • composition.py - added call to _update_controller to add_node - moved test for projections to controller.state_input_ports to run() * - * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports _instantiate_controller_shadow_projections [still needs to be implemented] • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py added needs_update_controller * - * • composition.py: - implemented self.needs_update_controller - moved implementation of controlsignal projections from add_controller to _instantiate_control_projections that is called in _complete_init_of_partially_initialized_nodes Note: still need to set self.needs_update_controller to False after instantiating state_input_ports and projections to them * - * - * - * - * - * - * - * - * • Passing all test_control tests except test_mode_based_num_estimates * • Passing all test_control tests * - * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: handle nested input nodes * - * • optimizationcontrolmechanism.py _update_state_input_ports_for_controller: fixed bug with > 1 INPUT node in Composition * • test_show_graph.py: passes all tests * - * • test_report.py: passing all tests * • Passes all tests! * - * - * • composition.py: reorganize with #region and #enregions * • composition.py: reorganize with #region and #enregions * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * - * - * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * • composition.py: __init__: move controller to after add_nodes and add_linear_pathway * - * - test_control: only test_hanging_control_spec_outer_controller not passing * - * - * - * - * - * - * • composition.py: _instantiate_control_projections: weird requirement for double-call to controller._instantiate_control_signal * • test_paremtercomposition.py: restored parameter spec that causes crash ('threshold',Decision2) * ª Attempt to fix problem with partially overlapping local and ocm control specs - composition.py - _get_control_signals_for_composition: (see 11/20/21) - added (but commented out change) to "if node.controller" to "if not node.controller" - changed append to extend - _instantiation_control_projection: - got rid of try and except double-call to controller._instantiate_control_signals - outdented call to self.controller._activate_projections_for_composition at end - controlmechanism.py: - _check_for_duplicates: add warning and return duplicates - optimizationcontrolmechanism._instantiate_control_signals: - add call to self.agent_rep._get_control_signals_for_composition() to get local control specs (on mechs in comp) - eliminate duplicates with control_signal specs on OCM - instantiate local + ocm control_signals - parameterestimationcomposition.py - added context to various calls * see later commit * see later commit * see later commit * see later commit * - This branch passes all tests except: - test_parameterestimationcomposition - test_composition/test_partially_overlapping_control_specs (ADDED IN THIS COMMINT) - All relevant changes to this branch are marked as "11/21/21." However, most are commented out as they break other things. - The tests above both involve local control specifications (on mechanism within a nested comp) and on the OCM for the outer composition, some of which are for the same nested mechs - Both tests fail with: "AttributeError: 'NoneType' object has no attribute '_get_by_time_scale'" (in component.py LINE 3276) This may be due to a problem with context setting, since the error is because the modulation Parameter of the ControlProjection is returning "None" rather than "multiplicative_param" (when called with get(context)), whereas "multiplicative_param" is returned with a call to get() (i.e., with no context specified) - Most of test_partially_overlapping_control_specs is passed if changes marked "11/21/21 NEW" in optimizationcontrolmechanism.py (LINE 1390) are implemented, but it does not properly route ControlProjections through parameter_CIMS (see last assert in test). Furthermore, test_parameterestimationcompsition fails with the mod param error, even though the model has similar structure (i.e., outer composition -- in this case a ParameterEstimationComposition) with an OCM that is given control specs that overlap with ones in a nested composition. - There are also several other things in composition I found puzzling and tried modifying, but that cuased failures: - _get_control_signals_for_composition(): - seems "if node.controller" should be "if **not** node.controller" (emphasis added just for comment) - "append" should be "extend" - _instantiate_control_projection(): - call to self.controller._activate_projections_for_composition (at end of method) should not be indented * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - finished adding formatting regions to composition.py * - * • composition.py: - rename _check_projection_initialization_status -> _check_controller_initialization_status - add _check_nodes_initialization_status(context=context) (and calls it with _check_controller_initialization_status) * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * - * Composition: add_controller: set METHOD as context source early * - * • composition.py retore append of control_signals in _instantiate_control_projections() * • composition.py 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_unnested_and_nested_comp(): - added clear_registry() to allow names to be reused in both runs of test * • composition.py docstring: added projections entry to list of attributes - add_controller: added call to _add_node_aux_components() for controller * • composition.py _add_node_aux_components(): added deletion of item from aux_components if instantiated * • composition.py - 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) * - * - confirm that it passes all tests exception test_composition/test_partially_overlapping... (with addition of _add_aux_components in add_controller commented out) * • composition.py: some more fixed to add_controller that now fail only one test: - test_agent_rep_assignement_as_controller_and_replacement * • Passes *all* current tests * • composition.py: - add_controller: few more minor mods; still passes all tests * - * - * - * • controlmechanism.py: - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms) * - * • composition.py: in progress fix of bug in instantiating shadow projections for ocm.state_input_ports * • composition.py: - _get_original_senders(): added support for nested composition needs to be checked for more than one level needs to be refactored to be recursive * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: fix invalid_state_features to allow input_CIM of nested comp in agent_rep * - * • composition.py - _get_original_senders: made recursive * • test_show_graph.py: update for fixes * - * • tests: passes all in test_show_graph.py and test_report.py * Passes all tests * - comment clean-up * • composition.py - 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: allow_probes fully implemented * • show_graph.py: fixed bug causing extra projections to OCM * • composition.py: - _update_shadow_projections(): fix handling of deep nesting * • optimizationcontrolmechanism.py: add agent_rep_type property * • optimizationcontrolmechanism.py: - state_feature_function -> state_feature_functions * • optimizationcontrolmechanism.py: - _validate_params: validate state_feature_functions - _update_state_input_ports_for_controller: implement assignment of state_feature_functions * - * - * • Passes all tests except test_json with 'model_with_control' * - * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * - * • test_two_origins_two_input_ports: crashes on failure of C->B to update * - * • composition.py - added property shadowing_dict that has shadowing ports as keys and the ports they shadow as values - refactored _update_shadowing_projections to use shadowing_dict * • optimizationcontrolmechanism.py - _update_state_input_ports: modified validations for nested nodes; still failing some tests * • optimizationcontrolmechanism.py - _update_state_input_ports: more careful and informative validation that state_input_ports are in comp or nested comp and are INPUT nodes thereof; passes all tests except test_two_origins_two_input_ports as before * • composition.py _get_invalid_aux_components(): defer all shadow projections until _update_shadow_projections * • composition.py _get_invalid_aux_components(): bug fix in test for shadow projections * Port: _remove_projection_to_port: don't reduce variable below length 1 even ports with no incoming projections have variable at least length 1 * • composition.py add_node(): marked (but haven't removed) code block instantiating shadow_projections that seems now to be redundant with _update_shadow_projection * • show_graph.py - _assign_cim_components: supress showing projections not in composition * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py - add show_projections_not_in_composition option for debugging * • composition.py _update_shadow_projections(): delete unused shadow projections and corresponding ports * • composition.py _update_shadow_projections(): fix bug in deletion of unused shadow projections and ports • test_show_graph: tests failing, need mods to accomodate changes * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py fixes; now passes all show_graph tests * - * • composition.py _update_shadow_projections: raise error for attempt to shadow INTERNAL Node of nested comp * - * - * • test_composition.py implemented test_shadow_nested_nodes that tests shadowing of nested nodes * - * - * - * - * • optimizationcontrolmechanism.py: docstring mods * • composition.py: - add allow_probes and exclude_probes_from_output * • composition.py: - docstring mods re: allow_probes • optimizationcontrolmechanism.py: - allow_probes: eliminate DIRECT setting - remove _parse_monitor_for_control_input_ports (no longer needed without allow_probes=DIRECT) * • composition.py: - change "exclude_probes_from_output" -> "include_probes_in_output" * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism - add _handle_allow_probes_for_control() to reconcile setting on Composition and ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • composition.py add assignment of learning_mechanism to objective_mechanism.modulatory_mechanism for add_learning methods * • docstring mods * - * - * • optimizationcontrolmechanism.py: docstring revs * - * - * • test_composition.py: - add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output * - * • composition.py - add_node(): support tuple with required_role * - * • composition.py: - _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL) * - * • composition.py: - add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value() * - * • CompositionInterfaceMechanism.rst: - correct path ref • compositioninterfacemechanism.py: - docstring fixes * • composition.py: - _add_node_aux_components(): fix bug in which ControlProjections were getting replaced by MappingProjections in composition.projections * • show_graph.py - fix bug in check for name of RANDOMIZATION_CONTROL_SIGNAL * • optimizationcontrolmechanism.py: - _create_randomization_control_signal(): warn if num_estimates is >1 and there are no random_variables • composition.py: - add_controller: add test for num_estimates before calling _create_randomization_control_signal() • test_control - test_mode_based_num_estimates: add test for random variables (using DDM) * - * - * - Co-authored-by: jdcpni <pniintel55> Co-authored-by: Jan Vesely <jan.vesely@rutgers.edu> Co-authored-by: Katherine Mantel <kmantel@princeton.edu>

* • component.py docstring mod to **size** * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute • optimizationfunctions.py: made num_estimates a Parameter * - modified test_mode_based_num_estimates * - * - * • optimizationcontrolmechanism.py: - _instantiate_control_signals: random_seeds -> random_seed_mod_values * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: now adds feature_input_ports for Compostion INPUT nodes if not state_features not specified * - * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: assign simulation_input_ports * - * • optimizationcontrolmechanism.py: - feature_input_ports -> state_input_ports - _instantiate_input_ports(): state_features only allowed to specifying state_input_ports if agent_rep is a CompositionFunctionApproximator (i.e., model-free optimization) • composition.py: - add_controller: adds state_input_ports to shadow INPUT Nodes of Composition if controller.agent_rep is Composition (model-based optimziation) or state_features have not been specified (for model-free optimizaton) * - * • optimizationcontrolmechanism.py: _instantiate_input_ports: reinstate allowance of state_features specification if agent_rep is a Composition (i.e., model-based optimization) as long as they are all INPUT Nodes of agent_rep * - * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_estimates_per_trial * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trial_per_estimate * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trials_per_estimate * - * - * - * - * • composition.py - __init__: moved controller instantiation until after nodes, projections and pathways * • composition.py - __init__: restored add_controller position * llvm/struct generation: Make sure num_estimats per trial is always integer Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu> * - * • composition.py: - _update_controller: added - add_controller and _analyze_graph(): call _update_controller * - * • composition.py _update_controller: fixed to loop through all input_ports of comp INPUT nodes * • test_control.py - test_agent_rep_assignement_as_controller_and_replacement: updated to test that shadowing projections to state_input_ports are properly added and deleted * • optimizationfunctions.py: - _function: refactored to put use aggregation_function at end - _grid_evaluate: still needs to return all_samples * - * • composition.py - added call to _update_controller to add_node - moved test for projections to controller.state_input_ports to run() * - * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports _instantiate_controller_shadow_projections [still needs to be implemented] • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py added needs_update_controller * - * • composition.py: - implemented self.needs_update_controller - moved implementation of controlsignal projections from add_controller to _instantiate_control_projections that is called in _complete_init_of_partially_initialized_nodes Note: still need to set self.needs_update_controller to False after instantiating state_input_ports and projections to them * - * - * - * - * - * - * - * - * • Passing all test_control tests except test_mode_based_num_estimates * • Passing all test_control tests * - * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: handle nested input nodes * - * • optimizationcontrolmechanism.py _update_state_input_ports_for_controller: fixed bug with > 1 INPUT node in Composition * • test_show_graph.py: passes all tests * - * • test_report.py: passing all tests * • Passes all tests! * - * - * • composition.py: reorganize with #region and #enregions * • composition.py: reorganize with #region and #enregions * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * - * - * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * • composition.py: __init__: move controller to after add_nodes and add_linear_pathway * - * - test_control: only test_hanging_control_spec_outer_controller not passing * - * - * - * - * - * - * • composition.py: _instantiate_control_projections: weird requirement for double-call to controller._instantiate_control_signal * • test_paremtercomposition.py: restored parameter spec that causes crash ('threshold',Decision2) * ª Attempt to fix problem with partially overlapping local and ocm control specs - composition.py - _get_control_signals_for_composition: (see 11/20/21) - added (but commented out change) to "if node.controller" to "if not node.controller" - changed append to extend - _instantiation_control_projection: - got rid of try and except double-call to controller._instantiate_control_signals - outdented call to self.controller._activate_projections_for_composition at end - controlmechanism.py: - _check_for_duplicates: add warning and return duplicates - optimizationcontrolmechanism._instantiate_control_signals: - add call to self.agent_rep._get_control_signals_for_composition() to get local control specs (on mechs in comp) - eliminate duplicates with control_signal specs on OCM - instantiate local + ocm control_signals - parameterestimationcomposition.py - added context to various calls * see later commit * see later commit * see later commit * see later commit * - This branch passes all tests except: - test_parameterestimationcomposition - test_composition/test_partially_overlapping_control_specs (ADDED IN THIS COMMINT) - All relevant changes to this branch are marked as "11/21/21." However, most are commented out as they break other things. - The tests above both involve local control specifications (on mechanism within a nested comp) and on the OCM for the outer composition, some of which are for the same nested mechs - Both tests fail with: "AttributeError: 'NoneType' object has no attribute '_get_by_time_scale'" (in component.py LINE 3276) This may be due to a problem with context setting, since the error is because the modulation Parameter of the ControlProjection is returning "None" rather than "multiplicative_param" (when called with get(context)), whereas "multiplicative_param" is returned with a call to get() (i.e., with no context specified) - Most of test_partially_overlapping_control_specs is passed if changes marked "11/21/21 NEW" in optimizationcontrolmechanism.py (LINE 1390) are implemented, but it does not properly route ControlProjections through parameter_CIMS (see last assert in test). Furthermore, test_parameterestimationcompsition fails with the mod param error, even though the model has similar structure (i.e., outer composition -- in this case a ParameterEstimationComposition) with an OCM that is given control specs that overlap with ones in a nested composition. - There are also several other things in composition I found puzzling and tried modifying, but that cuased failures: - _get_control_signals_for_composition(): - seems "if node.controller" should be "if **not** node.controller" (emphasis added just for comment) - "append" should be "extend" - _instantiate_control_projection(): - call to self.controller._activate_projections_for_composition (at end of method) should not be indented * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - finished adding formatting regions to composition.py * - * • composition.py: - rename _check_projection_initialization_status -> _check_controller_initialization_status - add _check_nodes_initialization_status(context=context) (and calls it with _check_controller_initialization_status) * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * - * Composition: add_controller: set METHOD as context source early * - * • composition.py retore append of control_signals in _instantiate_control_projections() * • composition.py 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_unnested_and_nested_comp(): - added clear_registry() to allow names to be reused in both runs of test * • composition.py docstring: added projections entry to list of attributes - add_controller: added call to _add_node_aux_components() for controller * • composition.py _add_node_aux_components(): added deletion of item from aux_components if instantiated * • composition.py - 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) * - * - confirm that it passes all tests exception test_composition/test_partially_overlapping... (with addition of _add_aux_components in add_controller commented out) * • composition.py: some more fixed to add_controller that now fail only one test: - test_agent_rep_assignement_as_controller_and_replacement * • Passes *all* current tests * • composition.py: - add_controller: few more minor mods; still passes all tests * - * - * - * • controlmechanism.py: - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms) * - * • composition.py: in progress fix of bug in instantiating shadow projections for ocm.state_input_ports * • composition.py: - _get_original_senders(): added support for nested composition needs to be checked for more than one level needs to be refactored to be recursive * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: fix invalid_state_features to allow input_CIM of nested comp in agent_rep * - * • composition.py - _get_original_senders: made recursive * • test_show_graph.py: update for fixes * - * • tests: passes all in test_show_graph.py and test_report.py * Passes all tests * - comment clean-up * • composition.py - 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: allow_probes fully implemented * • show_graph.py: fixed bug causing extra projections to OCM * • composition.py: - _update_shadow_projections(): fix handling of deep nesting * • optimizationcontrolmechanism.py: add agent_rep_type property * • optimizationcontrolmechanism.py: - state_feature_function -> state_feature_functions * • optimizationcontrolmechanism.py: - _validate_params: validate state_feature_functions - _update_state_input_ports_for_controller: implement assignment of state_feature_functions * - * - * • Passes all tests except test_json with 'model_with_control' * - * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * - * • test_two_origins_two_input_ports: crashes on failure of C->B to update * - * • composition.py - added property shadowing_dict that has shadowing ports as keys and the ports they shadow as values - refactored _update_shadowing_projections to use shadowing_dict * • optimizationcontrolmechanism.py - _update_state_input_ports: modified validations for nested nodes; still failing some tests * • optimizationcontrolmechanism.py - _update_state_input_ports: more careful and informative validation that state_input_ports are in comp or nested comp and are INPUT nodes thereof; passes all tests except test_two_origins_two_input_ports as before * • composition.py _get_invalid_aux_components(): defer all shadow projections until _update_shadow_projections * • composition.py _get_invalid_aux_components(): bug fix in test for shadow projections * Port: _remove_projection_to_port: don't reduce variable below length 1 even ports with no incoming projections have variable at least length 1 * • composition.py add_node(): marked (but haven't removed) code block instantiating shadow_projections that seems now to be redundant with _update_shadow_projection * • show_graph.py - _assign_cim_components: supress showing projections not in composition * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py - add show_projections_not_in_composition option for debugging * • composition.py _update_shadow_projections(): delete unused shadow projections and corresponding ports * • composition.py _update_shadow_projections(): fix bug in deletion of unused shadow projections and ports • test_show_graph: tests failing, need mods to accomodate changes * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py fixes; now passes all show_graph tests * - * • composition.py _update_shadow_projections: raise error for attempt to shadow INTERNAL Node of nested comp * - * - * • test_composition.py implemented test_shadow_nested_nodes that tests shadowing of nested nodes * - * - * - * - * • optimizationcontrolmechanism.py: docstring mods * • composition.py: - add allow_probes and exclude_probes_from_output * • composition.py: - docstring mods re: allow_probes • optimizationcontrolmechanism.py: - allow_probes: eliminate DIRECT setting - remove _parse_monitor_for_control_input_ports (no longer needed without allow_probes=DIRECT) * • composition.py: - change "exclude_probes_from_output" -> "include_probes_in_output" * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism - add _handle_allow_probes_for_control() to reconcile setting on Composition and ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • composition.py add assignment of learning_mechanism to objective_mechanism.modulatory_mechanism for add_learning methods * • docstring mods * - * - * • optimizationcontrolmechanism.py: docstring revs * - * - * • test_composition.py: - add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output * - * • composition.py - add_node(): support tuple with required_role * - * • composition.py: - _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL) * - * • composition.py: - add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value() * - * • CompositionInterfaceMechanism.rst: - correct path ref • compositioninterfacemechanism.py: - docstring fixes * - * - * • test_control.py: - add test_warning_for_add_controller_twice() - add test_warning_for_controller_assigned_to_another_comp() * • test_control.py: - add test_warning_for_replacement_of_controller() * - * - Co-authored-by: jdcpni <pniintel55> Co-authored-by: Jan Vesely <jan.vesely@rutgers.edu> Co-authored-by: Katherine Mantel <kmantel@princeton.edu>

* • component.py docstring mod to **size** * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute • optimizationfunctions.py: made num_estimates a Parameter * - modified test_mode_based_num_estimates * - * - * • optimizationcontrolmechanism.py: - _instantiate_control_signals: random_seeds -> random_seed_mod_values * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: now adds feature_input_ports for Compostion INPUT nodes if not state_features not specified * - * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: assign simulation_input_ports * - * • optimizationcontrolmechanism.py: - feature_input_ports -> state_input_ports - _instantiate_input_ports(): state_features only allowed to specifying state_input_ports if agent_rep is a CompositionFunctionApproximator (i.e., model-free optimization) • composition.py: - add_controller: adds state_input_ports to shadow INPUT Nodes of Composition if controller.agent_rep is Composition (model-based optimziation) or state_features have not been specified (for model-free optimizaton) * - * • optimizationcontrolmechanism.py: _instantiate_input_ports: reinstate allowance of state_features specification if agent_rep is a Composition (i.e., model-based optimization) as long as they are all INPUT Nodes of agent_rep * - * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_estimates_per_trial * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trial_per_estimate * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trials_per_estimate * - * - * - * - * • composition.py - __init__: moved controller instantiation until after nodes, projections and pathways * • composition.py - __init__: restored add_controller position * llvm/struct generation: Make sure num_estimats per trial is always integer Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu> * - * • composition.py: - _update_controller: added - add_controller and _analyze_graph(): call _update_controller * - * • composition.py _update_controller: fixed to loop through all input_ports of comp INPUT nodes * • test_control.py - test_agent_rep_assignement_as_controller_and_replacement: updated to test that shadowing projections to state_input_ports are properly added and deleted * • optimizationfunctions.py: - _function: refactored to put use aggregation_function at end - _grid_evaluate: still needs to return all_samples * - * • composition.py - added call to _update_controller to add_node - moved test for projections to controller.state_input_ports to run() * - * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports _instantiate_controller_shadow_projections [still needs to be implemented] • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py added needs_update_controller * - * • composition.py: - implemented self.needs_update_controller - moved implementation of controlsignal projections from add_controller to _instantiate_control_projections that is called in _complete_init_of_partially_initialized_nodes Note: still need to set self.needs_update_controller to False after instantiating state_input_ports and projections to them * - * - * - * - * - * - * - * - * • Passing all test_control tests except test_mode_based_num_estimates * • Passing all test_control tests * - * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: handle nested input nodes * - * • optimizationcontrolmechanism.py _update_state_input_ports_for_controller: fixed bug with > 1 INPUT node in Composition * • test_show_graph.py: passes all tests * - * • test_report.py: passing all tests * • Passes all tests! * - * - * • composition.py: reorganize with #region and #enregions * • composition.py: reorganize with #region and #enregions * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * - * - * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * • composition.py: __init__: move controller to after add_nodes and add_linear_pathway * - * - test_control: only test_hanging_control_spec_outer_controller not passing * - * - * - * - * - * - * • composition.py: _instantiate_control_projections: weird requirement for double-call to controller._instantiate_control_signal * • test_paremtercomposition.py: restored parameter spec that causes crash ('threshold',Decision2) * ª Attempt to fix problem with partially overlapping local and ocm control specs - composition.py - _get_control_signals_for_composition: (see 11/20/21) - added (but commented out change) to "if node.controller" to "if not node.controller" - changed append to extend - _instantiation_control_projection: - got rid of try and except double-call to controller._instantiate_control_signals - outdented call to self.controller._activate_projections_for_composition at end - controlmechanism.py: - _check_for_duplicates: add warning and return duplicates - optimizationcontrolmechanism._instantiate_control_signals: - add call to self.agent_rep._get_control_signals_for_composition() to get local control specs (on mechs in comp) - eliminate duplicates with control_signal specs on OCM - instantiate local + ocm control_signals - parameterestimationcomposition.py - added context to various calls * see later commit * see later commit * see later commit * see later commit * - This branch passes all tests except: - test_parameterestimationcomposition - test_composition/test_partially_overlapping_control_specs (ADDED IN THIS COMMINT) - All relevant changes to this branch are marked as "11/21/21." However, most are commented out as they break other things. - The tests above both involve local control specifications (on mechanism within a nested comp) and on the OCM for the outer composition, some of which are for the same nested mechs - Both tests fail with: "AttributeError: 'NoneType' object has no attribute '_get_by_time_scale'" (in component.py LINE 3276) This may be due to a problem with context setting, since the error is because the modulation Parameter of the ControlProjection is returning "None" rather than "multiplicative_param" (when called with get(context)), whereas "multiplicative_param" is returned with a call to get() (i.e., with no context specified) - Most of test_partially_overlapping_control_specs is passed if changes marked "11/21/21 NEW" in optimizationcontrolmechanism.py (LINE 1390) are implemented, but it does not properly route ControlProjections through parameter_CIMS (see last assert in test). Furthermore, test_parameterestimationcompsition fails with the mod param error, even though the model has similar structure (i.e., outer composition -- in this case a ParameterEstimationComposition) with an OCM that is given control specs that overlap with ones in a nested composition. - There are also several other things in composition I found puzzling and tried modifying, but that cuased failures: - _get_control_signals_for_composition(): - seems "if node.controller" should be "if **not** node.controller" (emphasis added just for comment) - "append" should be "extend" - _instantiate_control_projection(): - call to self.controller._activate_projections_for_composition (at end of method) should not be indented * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - finished adding formatting regions to composition.py * - * • composition.py: - rename _check_projection_initialization_status -> _check_controller_initialization_status - add _check_nodes_initialization_status(context=context) (and calls it with _check_controller_initialization_status) * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * - * Composition: add_controller: set METHOD as context source early * - * • composition.py retore append of control_signals in _instantiate_control_projections() * • composition.py 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_unnested_and_nested_comp(): - added clear_registry() to allow names to be reused in both runs of test * • composition.py docstring: added projections entry to list of attributes - add_controller: added call to _add_node_aux_components() for controller * • composition.py _add_node_aux_components(): added deletion of item from aux_components if instantiated * • composition.py - 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) * - * - confirm that it passes all tests exception test_composition/test_partially_overlapping... (with addition of _add_aux_components in add_controller commented out) * • composition.py: some more fixed to add_controller that now fail only one test: - test_agent_rep_assignement_as_controller_and_replacement * • Passes *all* current tests * • composition.py: - add_controller: few more minor mods; still passes all tests * - * - * - * • controlmechanism.py: - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms) * - * • composition.py: in progress fix of bug in instantiating shadow projections for ocm.state_input_ports * • composition.py: - _get_original_senders(): added support for nested composition needs to be checked for more than one level needs to be refactored to be recursive * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: fix invalid_state_features to allow input_CIM of nested comp in agent_rep * - * • composition.py - _get_original_senders: made recursive * • test_show_graph.py: update for fixes * - * • tests: passes all in test_show_graph.py and test_report.py * Passes all tests * - comment clean-up * • composition.py - 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: allow_probes fully implemented * • show_graph.py: fixed bug causing extra projections to OCM * • composition.py: - _update_shadow_projections(): fix handling of deep nesting * • optimizationcontrolmechanism.py: add agent_rep_type property * • optimizationcontrolmechanism.py: - state_feature_function -> state_feature_functions * • optimizationcontrolmechanism.py: - _validate_params: validate state_feature_functions - _update_state_input_ports_for_controller: implement assignment of state_feature_functions * - * - * • Passes all tests except test_json with 'model_with_control' * - * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * - * • test_two_origins_two_input_ports: crashes on failure of C->B to update * - * • composition.py - added property shadowing_dict that has shadowing ports as keys and the ports they shadow as values - refactored _update_shadowing_projections to use shadowing_dict * • optimizationcontrolmechanism.py - _update_state_input_ports: modified validations for nested nodes; still failing some tests * • optimizationcontrolmechanism.py - _update_state_input_ports: more careful and informative validation that state_input_ports are in comp or nested comp and are INPUT nodes thereof; passes all tests except test_two_origins_two_input_ports as before * • composition.py _get_invalid_aux_components(): defer all shadow projections until _update_shadow_projections * • composition.py _get_invalid_aux_components(): bug fix in test for shadow projections * Port: _remove_projection_to_port: don't reduce variable below length 1 even ports with no incoming projections have variable at least length 1 * • composition.py add_node(): marked (but haven't removed) code block instantiating shadow_projections that seems now to be redundant with _update_shadow_projection * • show_graph.py - _assign_cim_components: supress showing projections not in composition * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py - add show_projections_not_in_composition option for debugging * • composition.py _update_shadow_projections(): delete unused shadow projections and corresponding ports * • composition.py _update_shadow_projections(): fix bug in deletion of unused shadow projections and ports • test_show_graph: tests failing, need mods to accomodate changes * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py fixes; now passes all show_graph tests * - * • composition.py _update_shadow_projections: raise error for attempt to shadow INTERNAL Node of nested comp * - * - * • test_composition.py implemented test_shadow_nested_nodes that tests shadowing of nested nodes * - * - * - * - * • optimizationcontrolmechanism.py: docstring mods * • composition.py: - add allow_probes and exclude_probes_from_output * • composition.py: - docstring mods re: allow_probes • optimizationcontrolmechanism.py: - allow_probes: eliminate DIRECT setting - remove _parse_monitor_for_control_input_ports (no longer needed without allow_probes=DIRECT) * • composition.py: - change "exclude_probes_from_output" -> "include_probes_in_output" * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism - add _handle_allow_probes_for_control() to reconcile setting on Composition and ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • composition.py add assignment of learning_mechanism to objective_mechanism.modulatory_mechanism for add_learning methods * • docstring mods * - * - * • optimizationcontrolmechanism.py: docstring revs * - * - * • test_composition.py: - add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output * - * • composition.py - add_node(): support tuple with required_role * - * • composition.py: - _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL) * - * • composition.py: - add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value() * - * • CompositionInterfaceMechanism.rst: - correct path ref • compositioninterfacemechanism.py: - docstring fixes * - * - * • test_control.py: - add test_warning_for_add_controller_twice() - add test_warning_for_controller_assigned_to_another_comp() * • test_control.py: - add test_warning_for_replacement_of_controller() * - * - * • composition.py - _check_for_unused_projections(): fix crash for projections in deferred_init - _check_controller_initialization_status(): edited warning message - _add_node_aux_components(): add projections in deferred_init to invalid_aux_components * • test_control.py: - add test_add_node_with_controller_spec_and_control_mech_but_not_a_controller() * • test_control.py: = add test_bad_objective_mechanism_spec() Co-authored-by: jdcpni <pniintel55> Co-authored-by: Jan Vesely <jan.vesely@rutgers.edu> Co-authored-by: Katherine Mantel <kmantel@princeton.edu>

* • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute • optimizationfunctions.py: made num_estimates a Parameter * - modified test_mode_based_num_estimates * - * - * • optimizationcontrolmechanism.py: - _instantiate_control_signals: random_seeds -> random_seed_mod_values * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: now adds feature_input_ports for Compostion INPUT nodes if not state_features not specified * - * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: assign simulation_input_ports * - * • optimizationcontrolmechanism.py: - feature_input_ports -> state_input_ports - _instantiate_input_ports(): state_features only allowed to specifying state_input_ports if agent_rep is a CompositionFunctionApproximator (i.e., model-free optimization) • composition.py: - add_controller: adds state_input_ports to shadow INPUT Nodes of Composition if controller.agent_rep is Composition (model-based optimziation) or state_features have not been specified (for model-free optimizaton) * - * • optimizationcontrolmechanism.py: _instantiate_input_ports: reinstate allowance of state_features specification if agent_rep is a Composition (i.e., model-based optimization) as long as they are all INPUT Nodes of agent_rep * - * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_estimates_per_trial * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trial_per_estimate * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trials_per_estimate * - * - * - * - * • composition.py - __init__: moved controller instantiation until after nodes, projections and pathways * • composition.py - __init__: restored add_controller position * llvm/struct generation: Make sure num_estimats per trial is always integer Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu> * - * • composition.py: - _update_controller: added - add_controller and _analyze_graph(): call _update_controller * - * • composition.py _update_controller: fixed to loop through all input_ports of comp INPUT nodes * • test_control.py - test_agent_rep_assignement_as_controller_and_replacement: updated to test that shadowing projections to state_input_ports are properly added and deleted * • optimizationfunctions.py: - _function: refactored to put use aggregation_function at end - _grid_evaluate: still needs to return all_samples * - * • composition.py - added call to _update_controller to add_node - moved test for projections to controller.state_input_ports to run() * - * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports _instantiate_controller_shadow_projections [still needs to be implemented] • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py added needs_update_controller * - * • composition.py: - implemented self.needs_update_controller - moved implementation of controlsignal projections from add_controller to _instantiate_control_projections that is called in _complete_init_of_partially_initialized_nodes Note: still need to set self.needs_update_controller to False after instantiating state_input_ports and projections to them * - * - * - * - * - * - * - * - * • Passing all test_control tests except test_mode_based_num_estimates * • Passing all test_control tests * - * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: handle nested input nodes * - * • optimizationcontrolmechanism.py _update_state_input_ports_for_controller: fixed bug with > 1 INPUT node in Composition * • test_show_graph.py: passes all tests * - * • test_report.py: passing all tests * • Passes all tests! * - * - * • composition.py: reorganize with #region and #enregions * • composition.py: reorganize with #region and #enregions * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * - * - * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * • composition.py: __init__: move controller to after add_nodes and add_linear_pathway * - * - test_control: only test_hanging_control_spec_outer_controller not passing * - * - * - * - * - * - * • composition.py: _instantiate_control_projections: weird requirement for double-call to controller._instantiate_control_signal * • test_paremtercomposition.py: restored parameter spec that causes crash ('threshold',Decision2) * ª Attempt to fix problem with partially overlapping local and ocm control specs - composition.py - _get_control_signals_for_composition: (see 11/20/21) - added (but commented out change) to "if node.controller" to "if not node.controller" - changed append to extend - _instantiation_control_projection: - got rid of try and except double-call to controller._instantiate_control_signals - outdented call to self.controller._activate_projections_for_composition at end - controlmechanism.py: - _check_for_duplicates: add warning and return duplicates - optimizationcontrolmechanism._instantiate_control_signals: - add call to self.agent_rep._get_control_signals_for_composition() to get local control specs (on mechs in comp) - eliminate duplicates with control_signal specs on OCM - instantiate local + ocm control_signals - parameterestimationcomposition.py - added context to various calls * see later commit * see later commit * see later commit * see later commit * - This branch passes all tests except: - test_parameterestimationcomposition - test_composition/test_partially_overlapping_control_specs (ADDED IN THIS COMMINT) - All relevant changes to this branch are marked as "11/21/21." However, most are commented out as they break other things. - The tests above both involve local control specifications (on mechanism within a nested comp) and on the OCM for the outer composition, some of which are for the same nested mechs - Both tests fail with: "AttributeError: 'NoneType' object has no attribute '_get_by_time_scale'" (in component.py LINE 3276) This may be due to a problem with context setting, since the error is because the modulation Parameter of the ControlProjection is returning "None" rather than "multiplicative_param" (when called with get(context)), whereas "multiplicative_param" is returned with a call to get() (i.e., with no context specified) - Most of test_partially_overlapping_control_specs is passed if changes marked "11/21/21 NEW" in optimizationcontrolmechanism.py (LINE 1390) are implemented, but it does not properly route ControlProjections through parameter_CIMS (see last assert in test). Furthermore, test_parameterestimationcompsition fails with the mod param error, even though the model has similar structure (i.e., outer composition -- in this case a ParameterEstimationComposition) with an OCM that is given control specs that overlap with ones in a nested composition. - There are also several other things in composition I found puzzling and tried modifying, but that cuased failures: - _get_control_signals_for_composition(): - seems "if node.controller" should be "if **not** node.controller" (emphasis added just for comment) - "append" should be "extend" - _instantiate_control_projection(): - call to self.controller._activate_projections_for_composition (at end of method) should not be indented * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - finished adding formatting regions to composition.py * - * • composition.py: - rename _check_projection_initialization_status -> _check_controller_initialization_status - add _check_nodes_initialization_status(context=context) (and calls it with _check_controller_initialization_status) * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * - * Composition: add_controller: set METHOD as context source early * - * • composition.py retore append of control_signals in _instantiate_control_projections() * • composition.py 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_unnested_and_nested_comp(): - added clear_registry() to allow names to be reused in both runs of test * • composition.py docstring: added projections entry to list of attributes - add_controller: added call to _add_node_aux_components() for controller * • composition.py _add_node_aux_components(): added deletion of item from aux_components if instantiated * • composition.py - 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) * - * - confirm that it passes all tests exception test_composition/test_partially_overlapping... (with addition of _add_aux_components in add_controller commented out) * • composition.py: some more fixed to add_controller that now fail only one test: - test_agent_rep_assignement_as_controller_and_replacement * • Passes *all* current tests * • composition.py: - add_controller: few more minor mods; still passes all tests * - * - * - * • controlmechanism.py: - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms) * - * • composition.py: in progress fix of bug in instantiating shadow projections for ocm.state_input_ports * • composition.py: - _get_original_senders(): added support for nested composition needs to be checked for more than one level needs to be refactored to be recursive * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: fix invalid_state_features to allow input_CIM of nested comp in agent_rep * - * • composition.py - _get_original_senders: made recursive * • test_show_graph.py: update for fixes * - * • tests: passes all in test_show_graph.py and test_report.py * Passes all tests * - comment clean-up * • composition.py - 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: allow_probes fully implemented * • show_graph.py: fixed bug causing extra projections to OCM * • composition.py: - _update_shadow_projections(): fix handling of deep nesting * • optimizationcontrolmechanism.py: add agent_rep_type property * • optimizationcontrolmechanism.py: - state_feature_function -> state_feature_functions * • optimizationcontrolmechanism.py: - _validate_params: validate state_feature_functions - _update_state_input_ports_for_controller: implement assignment of state_feature_functions * - * - * • Passes all tests except test_json with 'model_with_control' * - * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * - * • test_two_origins_two_input_ports: crashes on failure of C->B to update * - * • composition.py - added property shadowing_dict that has shadowing ports as keys and the ports they shadow as values - refactored _update_shadowing_projections to use shadowing_dict * • optimizationcontrolmechanism.py - _update_state_input_ports: modified validations for nested nodes; still failing some tests * • optimizationcontrolmechanism.py - _update_state_input_ports: more careful and informative validation that state_input_ports are in comp or nested comp and are INPUT nodes thereof; passes all tests except test_two_origins_two_input_ports as before * • composition.py _get_invalid_aux_components(): defer all shadow projections until _update_shadow_projections * • composition.py _get_invalid_aux_components(): bug fix in test for shadow projections * Port: _remove_projection_to_port: don't reduce variable below length 1 even ports with no incoming projections have variable at least length 1 * • composition.py add_node(): marked (but haven't removed) code block instantiating shadow_projections that seems now to be redundant with _update_shadow_projection * • show_graph.py - _assign_cim_components: supress showing projections not in composition * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py - add show_projections_not_in_composition option for debugging * • composition.py _update_shadow_projections(): delete unused shadow projections and corresponding ports * • composition.py _update_shadow_projections(): fix bug in deletion of unused shadow projections and ports • test_show_graph: tests failing, need mods to accomodate changes * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py fixes; now passes all show_graph tests * - * • composition.py _update_shadow_projections: raise error for attempt to shadow INTERNAL Node of nested comp * - * - * • test_composition.py implemented test_shadow_nested_nodes that tests shadowing of nested nodes * - * - * - * - * • optimizationcontrolmechanism.py: docstring mods * • composition.py: - add allow_probes and exclude_probes_from_output * • composition.py: - docstring mods re: allow_probes • optimizationcontrolmechanism.py: - allow_probes: eliminate DIRECT setting - remove _parse_monitor_for_control_input_ports (no longer needed without allow_probes=DIRECT) * • composition.py: - change "exclude_probes_from_output" -> "include_probes_in_output" * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism - add _handle_allow_probes_for_control() to reconcile setting on Composition and ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • composition.py add assignment of learning_mechanism to objective_mechanism.modulatory_mechanism for add_learning methods * • docstring mods * - * - * • optimizationcontrolmechanism.py: docstring revs * - * - * • test_composition.py: - add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output * - * • composition.py - add_node(): support tuple with required_role * - * • composition.py: - _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL) * - * • composition.py: - add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value() * - * • CompositionInterfaceMechanism.rst: - correct path ref • compositioninterfacemechanism.py: - docstring fixes * - * - * • test_control.py: - add test_warning_for_add_controller_twice() - add test_warning_for_controller_assigned_to_another_comp() * • test_control.py: - add test_warning_for_replacement_of_controller() * - * - * • composition.py - _check_for_unused_projections(): fix crash for projections in deferred_init - _check_controller_initialization_status(): edited warning message - _add_node_aux_components(): add projections in deferred_init to invalid_aux_components * • test_control.py: - add test_add_node_with_controller_spec_and_control_mech_but_not_a_controller() * • test_control.py: = add test_bad_objective_mechanism_spec() * • test_control.py: = add test_bad_objective_mechanism_spec() * - * • optimizationcontrolmechanism.py: update figure in docstring * • optimizationcontrolmechanism.py: document state_features attribute * • optimizationcontrolmechanism.py: - docs: - document state_feature_attribute - update figure - implement state property - _update_state_input_ports_for_controller(): fix bug in which assignment of OutputPort as state_feature caused crash * • composition.py: - _get_total_cost_of_control_allocation(): add get_controller to find controller for which self (Composition) is the agent_rep * • show_graph.py - show_graph(): add show_all option * - * - Co-authored-by: jdcpni <pniintel55> Co-authored-by: Jan Vesely <jan.vesely@rutgers.edu> Co-authored-by: Katherine Mantel <kmantel@princeton.edu>

* - * - * • optimizationcontrolmechanism.py: - _instantiate_control_signals: random_seeds -> random_seed_mod_values * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: now adds feature_input_ports for Compostion INPUT nodes if not state_features not specified * - * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: assign simulation_input_ports * - * • optimizationcontrolmechanism.py: - feature_input_ports -> state_input_ports - _instantiate_input_ports(): state_features only allowed to specifying state_input_ports if agent_rep is a CompositionFunctionApproximator (i.e., model-free optimization) • composition.py: - add_controller: adds state_input_ports to shadow INPUT Nodes of Composition if controller.agent_rep is Composition (model-based optimziation) or state_features have not been specified (for model-free optimizaton) * - * • optimizationcontrolmechanism.py: _instantiate_input_ports: reinstate allowance of state_features specification if agent_rep is a Composition (i.e., model-based optimization) as long as they are all INPUT Nodes of agent_rep * - * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_estimates_per_trial * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trial_per_estimate * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trials_per_estimate * - * - * - * - * • composition.py - __init__: moved controller instantiation until after nodes, projections and pathways * • composition.py - __init__: restored add_controller position * llvm/struct generation: Make sure num_estimats per trial is always integer Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu> * - * • composition.py: - _update_controller: added - add_controller and _analyze_graph(): call _update_controller * - * • composition.py _update_controller: fixed to loop through all input_ports of comp INPUT nodes * • test_control.py - test_agent_rep_assignement_as_controller_and_replacement: updated to test that shadowing projections to state_input_ports are properly added and deleted * • optimizationfunctions.py: - _function: refactored to put use aggregation_function at end - _grid_evaluate: still needs to return all_samples * - * • composition.py - added call to _update_controller to add_node - moved test for projections to controller.state_input_ports to run() * - * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports _instantiate_controller_shadow_projections [still needs to be implemented] • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py added needs_update_controller * - * • composition.py: - implemented self.needs_update_controller - moved implementation of controlsignal projections from add_controller to _instantiate_control_projections that is called in _complete_init_of_partially_initialized_nodes Note: still need to set self.needs_update_controller to False after instantiating state_input_ports and projections to them * - * - * - * - * - * - * - * - * • Passing all test_control tests except test_mode_based_num_estimates * • Passing all test_control tests * - * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: handle nested input nodes * - * • optimizationcontrolmechanism.py _update_state_input_ports_for_controller: fixed bug with > 1 INPUT node in Composition * • test_show_graph.py: passes all tests * - * • test_report.py: passing all tests * • Passes all tests! * - * - * • composition.py: reorganize with #region and #enregions * • composition.py: reorganize with #region and #enregions * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * - * - * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * • composition.py: __init__: move controller to after add_nodes and add_linear_pathway * - * - test_control: only test_hanging_control_spec_outer_controller not passing * - * - * - * - * - * - * • composition.py: _instantiate_control_projections: weird requirement for double-call to controller._instantiate_control_signal * • test_paremtercomposition.py: restored parameter spec that causes crash ('threshold',Decision2) * ª Attempt to fix problem with partially overlapping local and ocm control specs - composition.py - _get_control_signals_for_composition: (see 11/20/21) - added (but commented out change) to "if node.controller" to "if not node.controller" - changed append to extend - _instantiation_control_projection: - got rid of try and except double-call to controller._instantiate_control_signals - outdented call to self.controller._activate_projections_for_composition at end - controlmechanism.py: - _check_for_duplicates: add warning and return duplicates - optimizationcontrolmechanism._instantiate_control_signals: - add call to self.agent_rep._get_control_signals_for_composition() to get local control specs (on mechs in comp) - eliminate duplicates with control_signal specs on OCM - instantiate local + ocm control_signals - parameterestimationcomposition.py - added context to various calls * see later commit * see later commit * see later commit * see later commit * - This branch passes all tests except: - test_parameterestimationcomposition - test_composition/test_partially_overlapping_control_specs (ADDED IN THIS COMMINT) - All relevant changes to this branch are marked as "11/21/21." However, most are commented out as they break other things. - The tests above both involve local control specifications (on mechanism within a nested comp) and on the OCM for the outer composition, some of which are for the same nested mechs - Both tests fail with: "AttributeError: 'NoneType' object has no attribute '_get_by_time_scale'" (in component.py LINE 3276) This may be due to a problem with context setting, since the error is because the modulation Parameter of the ControlProjection is returning "None" rather than "multiplicative_param" (when called with get(context)), whereas "multiplicative_param" is returned with a call to get() (i.e., with no context specified) - Most of test_partially_overlapping_control_specs is passed if changes marked "11/21/21 NEW" in optimizationcontrolmechanism.py (LINE 1390) are implemented, but it does not properly route ControlProjections through parameter_CIMS (see last assert in test). Furthermore, test_parameterestimationcompsition fails with the mod param error, even though the model has similar structure (i.e., outer composition -- in this case a ParameterEstimationComposition) with an OCM that is given control specs that overlap with ones in a nested composition. - There are also several other things in composition I found puzzling and tried modifying, but that cuased failures: - _get_control_signals_for_composition(): - seems "if node.controller" should be "if **not** node.controller" (emphasis added just for comment) - "append" should be "extend" - _instantiate_control_projection(): - call to self.controller._activate_projections_for_composition (at end of method) should not be indented * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - finished adding formatting regions to composition.py * - * • composition.py: - rename _check_projection_initialization_status -> _check_controller_initialization_status - add _check_nodes_initialization_status(context=context) (and calls it with _check_controller_initialization_status) * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * - * Composition: add_controller: set METHOD as context source early * - * • composition.py retore append of control_signals in _instantiate_control_projections() * • composition.py 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_unnested_and_nested_comp(): - added clear_registry() to allow names to be reused in both runs of test * • composition.py docstring: added projections entry to list of attributes - add_controller: added call to _add_node_aux_components() for controller * • composition.py _add_node_aux_components(): added deletion of item from aux_components if instantiated * • composition.py - 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) * - * - confirm that it passes all tests exception test_composition/test_partially_overlapping... (with addition of _add_aux_components in add_controller commented out) * • composition.py: some more fixed to add_controller that now fail only one test: - test_agent_rep_assignement_as_controller_and_replacement * • Passes *all* current tests * • composition.py: - add_controller: few more minor mods; still passes all tests * - * - * - * • controlmechanism.py: - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms) * - * • composition.py: in progress fix of bug in instantiating shadow projections for ocm.state_input_ports * • composition.py: - _get_original_senders(): added support for nested composition needs to be checked for more than one level needs to be refactored to be recursive * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: fix invalid_state_features to allow input_CIM of nested comp in agent_rep * - * • composition.py - _get_original_senders: made recursive * • test_show_graph.py: update for fixes * - * • tests: passes all in test_show_graph.py and test_report.py * Passes all tests * - comment clean-up * • composition.py - 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: allow_probes fully implemented * • show_graph.py: fixed bug causing extra projections to OCM * • composition.py: - _update_shadow_projections(): fix handling of deep nesting * • optimizationcontrolmechanism.py: add agent_rep_type property * • optimizationcontrolmechanism.py: - state_feature_function -> state_feature_functions * • optimizationcontrolmechanism.py: - _validate_params: validate state_feature_functions - _update_state_input_ports_for_controller: implement assignment of state_feature_functions * - * - * • Passes all tests except test_json with 'model_with_control' * - * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * - * • test_two_origins_two_input_ports: crashes on failure of C->B to update * - * • composition.py - added property shadowing_dict that has shadowing ports as keys and the ports they shadow as values - refactored _update_shadowing_projections to use shadowing_dict * • optimizationcontrolmechanism.py - _update_state_input_ports: modified validations for nested nodes; still failing some tests * • optimizationcontrolmechanism.py - _update_state_input_ports: more careful and informative validation that state_input_ports are in comp or nested comp and are INPUT nodes thereof; passes all tests except test_two_origins_two_input_ports as before * • composition.py _get_invalid_aux_components(): defer all shadow projections until _update_shadow_projections * • composition.py _get_invalid_aux_components(): bug fix in test for shadow projections * Port: _remove_projection_to_port: don't reduce variable below length 1 even ports with no incoming projections have variable at least length 1 * • composition.py add_node(): marked (but haven't removed) code block instantiating shadow_projections that seems now to be redundant with _update_shadow_projection * • show_graph.py - _assign_cim_components: supress showing projections not in composition * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py - add show_projections_not_in_composition option for debugging * • composition.py _update_shadow_projections(): delete unused shadow projections and corresponding ports * • composition.py _update_shadow_projections(): fix bug in deletion of unused shadow projections and ports • test_show_graph: tests failing, need mods to accomodate changes * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py fixes; now passes all show_graph tests * - * • composition.py _update_shadow_projections: raise error for attempt to shadow INTERNAL Node of nested comp * - * - * • test_composition.py implemented test_shadow_nested_nodes that tests shadowing of nested nodes * - * - * - * - * • optimizationcontrolmechanism.py: docstring mods * • composition.py: - add allow_probes and exclude_probes_from_output * • composition.py: - docstring mods re: allow_probes • optimizationcontrolmechanism.py: - allow_probes: eliminate DIRECT setting - remove _parse_monitor_for_control_input_ports (no longer needed without allow_probes=DIRECT) * • composition.py: - change "exclude_probes_from_output" -> "include_probes_in_output" * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism - add _handle_allow_probes_for_control() to reconcile setting on Composition and ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • composition.py add assignment of learning_mechanism to objective_mechanism.modulatory_mechanism for add_learning methods * • docstring mods * - * - * • optimizationcontrolmechanism.py: docstring revs * - * - * • test_composition.py: - add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output * - * • composition.py - add_node(): support tuple with required_role * - * • composition.py: - _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL) * - * • composition.py: - add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value() * - * • CompositionInterfaceMechanism.rst: - correct path ref • compositioninterfacemechanism.py: - docstring fixes * - * - * • test_control.py: - add test_warning_for_add_controller_twice() - add test_warning_for_controller_assigned_to_another_comp() * • test_control.py: - add test_warning_for_replacement_of_controller() * - * - * • composition.py - _check_for_unused_projections(): fix crash for projections in deferred_init - _check_controller_initialization_status(): edited warning message - _add_node_aux_components(): add projections in deferred_init to invalid_aux_components * • test_control.py: - add test_add_node_with_controller_spec_and_control_mech_but_not_a_controller() * • test_control.py: = add test_bad_objective_mechanism_spec() * • test_control.py: = add test_bad_objective_mechanism_spec() * - * • optimizationcontrolmechanism.py: update figure in docstring * • optimizationcontrolmechanism.py: document state_features attribute * • optimizationcontrolmechanism.py: - docs: - document state_feature_attribute - update figure - implement state property - _update_state_input_ports_for_controller(): fix bug in which assignment of OutputPort as state_feature caused crash * • composition.py: - _get_total_cost_of_control_allocation(): add get_controller to find controller for which self (Composition) is the agent_rep * • show_graph.py - show_graph(): add show_all option * - * • show_graph: add probe_color • composition.py: docstring edits re: PROBE * - * • show_graph.py: add handling of probe_color for Projections (in progress) * - * • show_graph: supports probe_color for projections out output_CIM in outer comp if include_probes_in_output for that comp is False * • test_control.py: - add test_objective_mechanism_spec_as_monitor_for_control_error() Co-authored-by: jdcpni <pniintel55> Co-authored-by: Jan Vesely <jan.vesely@rutgers.edu> Co-authored-by: Katherine Mantel <kmantel@princeton.edu>

* • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute • optimizationfunctions.py: made num_estimates a Parameter * - modified test_mode_based_num_estimates * - * - * • optimizationcontrolmechanism.py: - _instantiate_control_signals: random_seeds -> random_seed_mod_values * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: now adds feature_input_ports for Compostion INPUT nodes if not state_features not specified * - * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: assign simulation_input_ports * - * • optimizationcontrolmechanism.py: - feature_input_ports -> state_input_ports - _instantiate_input_ports(): state_features only allowed to specifying state_input_ports if agent_rep is a CompositionFunctionApproximator (i.e., model-free optimization) • composition.py: - add_controller: adds state_input_ports to shadow INPUT Nodes of Composition if controller.agent_rep is Composition (model-based optimziation) or state_features have not been specified (for model-free optimizaton) * - * • optimizationcontrolmechanism.py: _instantiate_input_ports: reinstate allowance of state_features specification if agent_rep is a Composition (i.e., model-based optimization) as long as they are all INPUT Nodes of agent_rep * - * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_estimates_per_trial * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trial_per_estimate * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trials_per_estimate * - * - * - * - * • composition.py - __init__: moved controller instantiation until after nodes, projections and pathways * • composition.py - __init__: restored add_controller position * llvm/struct generation: Make sure num_estimats per trial is always integer Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu> * - * • composition.py: - _update_controller: added - add_controller and _analyze_graph(): call _update_controller * - * • composition.py _update_controller: fixed to loop through all input_ports of comp INPUT nodes * • test_control.py - test_agent_rep_assignement_as_controller_and_replacement: updated to test that shadowing projections to state_input_ports are properly added and deleted * • optimizationfunctions.py: - _function: refactored to put use aggregation_function at end - _grid_evaluate: still needs to return all_samples * - * • composition.py - added call to _update_controller to add_node - moved test for projections to controller.state_input_ports to run() * - * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports _instantiate_controller_shadow_projections [still needs to be implemented] • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py added needs_update_controller * - * • composition.py: - implemented self.needs_update_controller - moved implementation of controlsignal projections from add_controller to _instantiate_control_projections that is called in _complete_init_of_partially_initialized_nodes Note: still need to set self.needs_update_controller to False after instantiating state_input_ports and projections to them * - * - * - * - * - * - * - * - * • Passing all test_control tests except test_mode_based_num_estimates * • Passing all test_control tests * - * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: handle nested input nodes * - * • optimizationcontrolmechanism.py _update_state_input_ports_for_controller: fixed bug with > 1 INPUT node in Composition * • test_show_graph.py: passes all tests * - * • test_report.py: passing all tests * • Passes all tests! * - * - * • composition.py: reorganize with #region and #enregions * • composition.py: reorganize with #region and #enregions * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * - * - * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * • composition.py: __init__: move controller to after add_nodes and add_linear_pathway * - * - test_control: only test_hanging_control_spec_outer_controller not passing * - * - * - * - * - * - * • composition.py: _instantiate_control_projections: weird requirement for double-call to controller._instantiate_control_signal * • test_paremtercomposition.py: restored parameter spec that causes crash ('threshold',Decision2) * ª Attempt to fix problem with partially overlapping local and ocm control specs - composition.py - _get_control_signals_for_composition: (see 11/20/21) - added (but commented out change) to "if node.controller" to "if not node.controller" - changed append to extend - _instantiation_control_projection: - got rid of try and except double-call to controller._instantiate_control_signals - outdented call to self.controller._activate_projections_for_composition at end - controlmechanism.py: - _check_for_duplicates: add warning and return duplicates - optimizationcontrolmechanism._instantiate_control_signals: - add call to self.agent_rep._get_control_signals_for_composition() to get local control specs (on mechs in comp) - eliminate duplicates with control_signal specs on OCM - instantiate local + ocm control_signals - parameterestimationcomposition.py - added context to various calls * see later commit * see later commit * see later commit * see later commit * - This branch passes all tests except: - test_parameterestimationcomposition - test_composition/test_partially_overlapping_control_specs (ADDED IN THIS COMMINT) - All relevant changes to this branch are marked as "11/21/21." However, most are commented out as they break other things. - The tests above both involve local control specifications (on mechanism within a nested comp) and on the OCM for the outer composition, some of which are for the same nested mechs - Both tests fail with: "AttributeError: 'NoneType' object has no attribute '_get_by_time_scale'" (in component.py LINE 3276) This may be due to a problem with context setting, since the error is because the modulation Parameter of the ControlProjection is returning "None" rather than "multiplicative_param" (when called with get(context)), whereas "multiplicative_param" is returned with a call to get() (i.e., with no context specified) - Most of test_partially_overlapping_control_specs is passed if changes marked "11/21/21 NEW" in optimizationcontrolmechanism.py (LINE 1390) are implemented, but it does not properly route ControlProjections through parameter_CIMS (see last assert in test). Furthermore, test_parameterestimationcompsition fails with the mod param error, even though the model has similar structure (i.e., outer composition -- in this case a ParameterEstimationComposition) with an OCM that is given control specs that overlap with ones in a nested composition. - There are also several other things in composition I found puzzling and tried modifying, but that cuased failures: - _get_control_signals_for_composition(): - seems "if node.controller" should be "if **not** node.controller" (emphasis added just for comment) - "append" should be "extend" - _instantiate_control_projection(): - call to self.controller._activate_projections_for_composition (at end of method) should not be indented * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - finished adding formatting regions to composition.py * - * • composition.py: - rename _check_projection_initialization_status -> _check_controller_initialization_status - add _check_nodes_initialization_status(context=context) (and calls it with _check_controller_initialization_status) * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * - * Composition: add_controller: set METHOD as context source early * - * • composition.py retore append of control_signals in _instantiate_control_projections() * • composition.py 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_unnested_and_nested_comp(): - added clear_registry() to allow names to be reused in both runs of test * • composition.py docstring: added projections entry to list of attributes - add_controller: added call to _add_node_aux_components() for controller * • composition.py _add_node_aux_components(): added deletion of item from aux_components if instantiated * • composition.py - 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) * - * - confirm that it passes all tests exception test_composition/test_partially_overlapping... (with addition of _add_aux_components in add_controller commented out) * • composition.py: some more fixed to add_controller that now fail only one test: - test_agent_rep_assignement_as_controller_and_replacement * • Passes *all* current tests * • composition.py: - add_controller: few more minor mods; still passes all tests * - * - * - * • controlmechanism.py: - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms) * - * • composition.py: in progress fix of bug in instantiating shadow projections for ocm.state_input_ports * • composition.py: - _get_original_senders(): added support for nested composition needs to be checked for more than one level needs to be refactored to be recursive * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: fix invalid_state_features to allow input_CIM of nested comp in agent_rep * - * • composition.py - _get_original_senders: made recursive * • test_show_graph.py: update for fixes * - * • tests: passes all in test_show_graph.py and test_report.py * Passes all tests * - comment clean-up * • composition.py - 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: allow_probes fully implemented * • show_graph.py: fixed bug causing extra projections to OCM * • composition.py: - _update_shadow_projections(): fix handling of deep nesting * • optimizationcontrolmechanism.py: add agent_rep_type property * • optimizationcontrolmechanism.py: - state_feature_function -> state_feature_functions * • optimizationcontrolmechanism.py: - _validate_params: validate state_feature_functions - _update_state_input_ports_for_controller: implement assignment of state_feature_functions * - * - * • Passes all tests except test_json with 'model_with_control' * - * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * - * • test_two_origins_two_input_ports: crashes on failure of C->B to update * - * • composition.py - added property shadowing_dict that has shadowing ports as keys and the ports they shadow as values - refactored _update_shadowing_projections to use shadowing_dict * • optimizationcontrolmechanism.py - _update_state_input_ports: modified validations for nested nodes; still failing some tests * • optimizationcontrolmechanism.py - _update_state_input_ports: more careful and informative validation that state_input_ports are in comp or nested comp and are INPUT nodes thereof; passes all tests except test_two_origins_two_input_ports as before * • composition.py _get_invalid_aux_components(): defer all shadow projections until _update_shadow_projections * • composition.py _get_invalid_aux_components(): bug fix in test for shadow projections * Port: _remove_projection_to_port: don't reduce variable below length 1 even ports with no incoming projections have variable at least length 1 * • composition.py add_node(): marked (but haven't removed) code block instantiating shadow_projections that seems now to be redundant with _update_shadow_projection * • show_graph.py - _assign_cim_components: supress showing projections not in composition * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py - add show_projections_not_in_composition option for debugging * • composition.py _update_shadow_projections(): delete unused shadow projections and corresponding ports * • composition.py _update_shadow_projections(): fix bug in deletion of unused shadow projections and ports • test_show_graph: tests failing, need mods to accomodate changes * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py fixes; now passes all show_graph tests * - * • composition.py _update_shadow_projections: raise error for attempt to shadow INTERNAL Node of nested comp * - * - * • test_composition.py implemented test_shadow_nested_nodes that tests shadowing of nested nodes * - * - * - * - * • optimizationcontrolmechanism.py: docstring mods * • composition.py: - add allow_probes and exclude_probes_from_output * • composition.py: - docstring mods re: allow_probes • optimizationcontrolmechanism.py: - allow_probes: eliminate DIRECT setting - remove _parse_monitor_for_control_input_ports (no longer needed without allow_probes=DIRECT) * • composition.py: - change "exclude_probes_from_output" -> "include_probes_in_output" * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism - add _handle_allow_probes_for_control() to reconcile setting on Composition and ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • composition.py add assignment of learning_mechanism to objective_mechanism.modulatory_mechanism for add_learning methods * • docstring mods * - * - * • optimizationcontrolmechanism.py: docstring revs * - * - * • test_composition.py: - add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output * - * • composition.py - add_node(): support tuple with required_role * - * • composition.py: - _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL) * - * • composition.py: - add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value() * - * • CompositionInterfaceMechanism.rst: - correct path ref • compositioninterfacemechanism.py: - docstring fixes * • optimizationcontrolmechanism.py: - docstring edits * - * - * • controlmechanism.py: allow CONTROL as alias for PROJECTIONS in ControlSignal spec * • controlsignal.py: allow CONTROL as alias for PROJECTIONS in ControlSignal spec * • controlsignal.py: replaces modulates with control as arg (though still allow modulates) * • test_projection_specifications.py: - add test_control_signal_projections_arg * - * • gatingsignal.py: - __init__: replace modulates arg with gate * - * - * - * - * • CONTROL and GATE in place of PROJECTIONS Co-authored-by: jdcpni <pniintel55> Co-authored-by: Jan Vesely <jan.vesely@rutgers.edu> Co-authored-by: Katherine Mantel <kmantel@princeton.edu>

* - * • controlmechanism.py, gatingmechanism.py: - CONTROL: 'CONTROL' -> 'control' - GATING: 'GATING' -> 'gating' * • Project: - CONTROL: 'CONTROL' -> 'control' - del GATING - GATE = 'gate" Co-authored-by: jdcpni <pniintel55>

…ures Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

* - * • controlmechanism.py: - add controlType attribute • gatingmechanism.py: - remove Parameters.output_port._parse_output_ports (handled by ControlMechanism) * • controlmechanism.py: - add controlType attribute • gatingmechanism.py: - remove Parameters.output_port._parse_output_ports (handled by ControlMechanism) • gatingsignal.py: - remove _parse_port_specific_specs (handled by ControlSignal) * • controlmechanism.py: - add controlType attribute • gatingmechanism.py: - remove Parameters.output_port._parse_output_ports (handled by ControlMechanism) • gatingsignal.py: - remove _parse_port_specific_specs (handled by ControlSignal) * - * • controlmechanism.py: - Parameters._parse_output_port(): remove error for dual spec (handled by ControlSignal) * - * - * - * - Co-authored-by: jdcpni <pniintel55>

* master: Devel (#2224)

* • component.py docstring mod to **size** * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute * • optimizationcontrolmechanism.py: added feature_input_ports attribute and num_feature_input_ports property • parameterestimationcomposition.py: fixed misplacement of its Parameters() attribute • optimizationfunctions.py: made num_estimates a Parameter * - modified test_mode_based_num_estimates * - * - * • optimizationcontrolmechanism.py: - _instantiate_control_signals: random_seeds -> random_seed_mod_values * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: now adds feature_input_ports for Compostion INPUT nodes if not state_features not specified * - * • composition.py - _add_controller: modifying to instantiate feature_input_ports if none are specified * • composition.py: - add_controller: assign simulation_input_ports * - * • optimizationcontrolmechanism.py: - feature_input_ports -> state_input_ports - _instantiate_input_ports(): state_features only allowed to specifying state_input_ports if agent_rep is a CompositionFunctionApproximator (i.e., model-free optimization) • composition.py: - add_controller: adds state_input_ports to shadow INPUT Nodes of Composition if controller.agent_rep is Composition (model-based optimziation) or state_features have not been specified (for model-free optimizaton) * - * • optimizationcontrolmechanism.py: _instantiate_input_ports: reinstate allowance of state_features specification if agent_rep is a Composition (i.e., model-based optimization) as long as they are all INPUT Nodes of agent_rep * - * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_estimates_per_trial * - * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trial_per_estimate * • optimizationcontrolmechanism.py - _gen_llvm_evaluate_function: num_estimates -> num_trials_per_estimate * - * - * - * - * • composition.py - __init__: moved controller instantiation until after nodes, projections and pathways * • composition.py - __init__: restored add_controller position * llvm/struct generation: Make sure num_estimats per trial is always integer Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu> * - * • composition.py: - _update_controller: added - add_controller and _analyze_graph(): call _update_controller * - * • composition.py _update_controller: fixed to loop through all input_ports of comp INPUT nodes * • test_control.py - test_agent_rep_assignement_as_controller_and_replacement: updated to test that shadowing projections to state_input_ports are properly added and deleted * • optimizationfunctions.py: - _function: refactored to put use aggregation_function at end - _grid_evaluate: still needs to return all_samples * - * • composition.py - added call to _update_controller to add_node - moved test for projections to controller.state_input_ports to run() * - * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py: moved calls to _update_controller to _complete_init_of_partially_initialized_nodes moved _update_controller to ocm._update_state_input_ports _instantiate_controller_shadow_projections [still needs to be implemented] • optimizationcontrolmechanism.py: added _update_state_input_ports [**still needed work**] * • composition.py added needs_update_controller * - * • composition.py: - implemented self.needs_update_controller - moved implementation of controlsignal projections from add_controller to _instantiate_control_projections that is called in _complete_init_of_partially_initialized_nodes Note: still need to set self.needs_update_controller to False after instantiating state_input_ports and projections to them * - * - * - * - * - * - * - * - * • Passing all test_control tests except test_mode_based_num_estimates * • Passing all test_control tests * - * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: handle nested input nodes * - * • optimizationcontrolmechanism.py _update_state_input_ports_for_controller: fixed bug with > 1 INPUT node in Composition * • test_show_graph.py: passes all tests * - * • test_report.py: passing all tests * • Passes all tests! * - * - * • composition.py: reorganize with #region and #enregions * • composition.py: reorganize with #region and #enregions * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * - * - * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * • controlmechanism.py, optimizationcontrolmechanism.py: - _instantiate_monitor_for_control_input_ports -> _parse_monitor_control_input_ports - refactored to support allow_probes option on ocm * - * • composition.py: __init__: move controller to after add_nodes and add_linear_pathway * - * - test_control: only test_hanging_control_spec_outer_controller not passing * - * - * - * - * - * - * • composition.py: _instantiate_control_projections: weird requirement for double-call to controller._instantiate_control_signal * • test_paremtercomposition.py: restored parameter spec that causes crash ('threshold',Decision2) * ª Attempt to fix problem with partially overlapping local and ocm control specs - composition.py - _get_control_signals_for_composition: (see 11/20/21) - added (but commented out change) to "if node.controller" to "if not node.controller" - changed append to extend - _instantiation_control_projection: - got rid of try and except double-call to controller._instantiate_control_signals - outdented call to self.controller._activate_projections_for_composition at end - controlmechanism.py: - _check_for_duplicates: add warning and return duplicates - optimizationcontrolmechanism._instantiate_control_signals: - add call to self.agent_rep._get_control_signals_for_composition() to get local control specs (on mechs in comp) - eliminate duplicates with control_signal specs on OCM - instantiate local + ocm control_signals - parameterestimationcomposition.py - added context to various calls * see later commit * see later commit * see later commit * see later commit * - This branch passes all tests except: - test_parameterestimationcomposition - test_composition/test_partially_overlapping_control_specs (ADDED IN THIS COMMINT) - All relevant changes to this branch are marked as "11/21/21." However, most are commented out as they break other things. - The tests above both involve local control specifications (on mechanism within a nested comp) and on the OCM for the outer composition, some of which are for the same nested mechs - Both tests fail with: "AttributeError: 'NoneType' object has no attribute '_get_by_time_scale'" (in component.py LINE 3276) This may be due to a problem with context setting, since the error is because the modulation Parameter of the ControlProjection is returning "None" rather than "multiplicative_param" (when called with get(context)), whereas "multiplicative_param" is returned with a call to get() (i.e., with no context specified) - Most of test_partially_overlapping_control_specs is passed if changes marked "11/21/21 NEW" in optimizationcontrolmechanism.py (LINE 1390) are implemented, but it does not properly route ControlProjections through parameter_CIMS (see last assert in test). Furthermore, test_parameterestimationcompsition fails with the mod param error, even though the model has similar structure (i.e., outer composition -- in this case a ParameterEstimationComposition) with an OCM that is given control specs that overlap with ones in a nested composition. - There are also several other things in composition I found puzzling and tried modifying, but that cuased failures: - _get_control_signals_for_composition(): - seems "if node.controller" should be "if **not** node.controller" (emphasis added just for comment) - "append" should be "extend" - _instantiate_control_projection(): - call to self.controller._activate_projections_for_composition (at end of method) should not be indented * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - small mods; don't impact anything relevant to prior commit message * - finished adding formatting regions to composition.py * - * • composition.py: - rename _check_projection_initialization_status -> _check_controller_initialization_status - add _check_nodes_initialization_status(context=context) (and calls it with _check_controller_initialization_status) * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * • show_graph.py: addressed bug associated with ocm.allow_direct_probe * - * Composition: add_controller: set METHOD as context source early * - * • composition.py retore append of control_signals in _instantiate_control_projections() * • composition.py 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_unnested_and_nested_comp(): - added clear_registry() to allow names to be reused in both runs of test * • composition.py docstring: added projections entry to list of attributes - add_controller: added call to _add_node_aux_components() for controller * • composition.py _add_node_aux_components(): added deletion of item from aux_components if instantiated * • composition.py - 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) * - * - confirm that it passes all tests exception test_composition/test_partially_overlapping... (with addition of _add_aux_components in add_controller commented out) * • composition.py: some more fixed to add_controller that now fail only one test: - test_agent_rep_assignement_as_controller_and_replacement * • Passes *all* current tests * • composition.py: - add_controller: few more minor mods; still passes all tests * - * - * - * • controlmechanism.py: - __init__: resrict specification to only one of control, modulatory_signals, or control_signals (synonyms) * - * • composition.py: in progress fix of bug in instantiating shadow projections for ocm.state_input_ports * • composition.py: - _get_original_senders(): added support for nested composition needs to be checked for more than one level needs to be refactored to be recursive * • optimizationcontrolmechanism.py - _update_state_input_ports_for_controller: fix invalid_state_features to allow input_CIM of nested comp in agent_rep * - * • composition.py - _get_original_senders: made recursive * • test_show_graph.py: update for fixes * - * • tests: passes all in test_show_graph.py and test_report.py * Passes all tests * - comment clean-up * • composition.py - 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: allow_probes fully implemented * • show_graph.py: fixed bug causing extra projections to OCM * • composition.py: - _update_shadow_projections(): fix handling of deep nesting * • optimizationcontrolmechanism.py: add agent_rep_type property * • optimizationcontrolmechanism.py: - state_feature_function -> state_feature_functions * • optimizationcontrolmechanism.py: - _validate_params: validate state_feature_functions - _update_state_input_ports_for_controller: implement assignment of state_feature_functions * - * - * • Passes all tests except test_json with 'model_with_control' * - * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * • composition.py - add_projection: delete instantiation of shadow projections (handled by _update_shadow_projections) - remove calls to _update_shadows_dict * - * • test_two_origins_two_input_ports: crashes on failure of C->B to update * - * • composition.py - added property shadowing_dict that has shadowing ports as keys and the ports they shadow as values - refactored _update_shadowing_projections to use shadowing_dict * • optimizationcontrolmechanism.py - _update_state_input_ports: modified validations for nested nodes; still failing some tests * • optimizationcontrolmechanism.py - _update_state_input_ports: more careful and informative validation that state_input_ports are in comp or nested comp and are INPUT nodes thereof; passes all tests except test_two_origins_two_input_ports as before * • composition.py _get_invalid_aux_components(): defer all shadow projections until _update_shadow_projections * • composition.py _get_invalid_aux_components(): bug fix in test for shadow projections * Port: _remove_projection_to_port: don't reduce variable below length 1 even ports with no incoming projections have variable at least length 1 * • composition.py add_node(): marked (but haven't removed) code block instantiating shadow_projections that seems now to be redundant with _update_shadow_projection * • show_graph.py - _assign_cim_components: supress showing projections not in composition * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py - add show_projections_not_in_composition option for debugging * • composition.py _update_shadow_projections(): delete unused shadow projections and corresponding ports * • composition.py _update_shadow_projections(): fix bug in deletion of unused shadow projections and ports • test_show_graph: tests failing, need mods to accomodate changes * • composition.py: _analyze_graph(): add extra call to _determine_node_roles after _update_shadow_projections _run(): moved block of code at beginning initializing scheduler to after _complete_init_of_partially_initialized_nodes and _analyze_graph() • show_graph.py - add test to all loops on projections: "if proj in composition.projection" * • show_graph.py fixes; now passes all show_graph tests * - * • composition.py _update_shadow_projections: raise error for attempt to shadow INTERNAL Node of nested comp * - * - * • test_composition.py implemented test_shadow_nested_nodes that tests shadowing of nested nodes * - * - * - * - * • optimizationcontrolmechanism.py: docstring mods * • composition.py: - add allow_probes and exclude_probes_from_output * • composition.py: - docstring mods re: allow_probes • optimizationcontrolmechanism.py: - allow_probes: eliminate DIRECT setting - remove _parse_monitor_for_control_input_ports (no longer needed without allow_probes=DIRECT) * • composition.py: - change "exclude_probes_from_output" -> "include_probes_in_output" * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism - add _handle_allow_probes_for_control() to reconcile setting on Composition and ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • composition.py add assignment of learning_mechanism to objective_mechanism.modulatory_mechanism for add_learning methods * • docstring mods * - * - * • optimizationcontrolmechanism.py: docstring revs * - * - * • test_composition.py: - add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output * - * • composition.py - add_node(): support tuple with required_role * - * • composition.py: - _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL) * - * • composition.py: - add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value() * - * • CompositionInterfaceMechanism.rst: - correct path ref • compositioninterfacemechanism.py: - docstring fixes * • composition.py: - build_predicted_inputs_dict(): fixed bug in handling inputs for doubly-nested comps • test_control.py: - test_nested_composition_as_agent_rep: - updated to handle test of above (and associated errors) without a nested agent_rep - test of nested agent_rep commented out until that is supported * - Co-authored-by: jdcpni <pniintel55> Co-authored-by: Jan Vesely <jan.vesely@rutgers.edu> Co-authored-by: Katherine Mantel <kmantel@princeton.edu>

* - * - * • showgraph.py: - _assign_incoming_edges(): allow input_CIM of outermost comp to render as node * • 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 * - Co-authored-by: jdcpni <pniintel55>

* - * - * • showgraph.py: - _assign_incoming_edges(): allow input_CIM of outermost comp to render as node * • 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 * - * • optimizationcontrolmechanism.py - add state and state_dict properties • composition.py: - add _get_source() - add _get_destination() • compositioninterfacemechanism.py: - add _get_modulated_info_from_parameter_CIM() - _get_source_node_for_output_CIM -> _get_source_info_from_output_CIM - _get_destination_node_for_input_CIM -> _get_destination_info_from_input_CIM * - optimizationcontrolmechanism.py: docstring additions for state and state_dict * • optimizationcontrolmechanism.py: - state_dict: fix bug in which comp for state_feature using output_port was incorrect - _parse_state_feature_specs(): fix bug in which state_feature using output_port did not get assigned a Projection • * • optimizationcontrolmechanism.py: -_update_state_input_ports_for_controller: validate state_features that specify an output_port (vs. shadow) * - * • test_control.py: add test_ocm_state_input_ports_warnings_and_errors * - * • conf.py: restore autodoc_typehints = 'none' * • optimizationcontrolmechanism.py: _update_state_input_ports_for_controller: - add check of against format of inputs required by agent_rep.run * - * • composition.py: - add_controller(): fix bug in which state_features that receive from the outputport of a node in the same composition were not being activated * - * - * • optimizationcontrolmechanism.py: _update_state_input_ports_for_controller: modified warning message for use of state_features * - Co-authored-by: jdcpni <pniintel55>

…nition AST node This will be needed to compile lambda functions that can share source lines with other AST nodes and can't be parsed in isolation. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

_gen_llvm_function_body handles only interaction with the rest of the code framework. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

if a projection being learned is removed, disable the entire pathway because the removal will break it

Add node removal to Compositions

github-actions · 2022-03-29T18:49:01Z

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

diff -r docs-base/.buildinfo docs-head/.buildinfo
3c3
< config: 93a36d7daeeffc980fdbe13b5661e43b
---
> config: 2756124a1a258cfc1eedcf79d651812e
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
206,208c206,214
<   <section id="module-psyneulink.library.compositions.autodiffcomposition">
< <span id="autodiffcomposition"></span><h1>AutodiffComposition<a class="headerlink" href="#module-psyneulink.library.compositions.autodiffcomposition" title="Permalink to this headline">¶</a></h1>
< <section id="contents">
---
>   <section id="autodiffcomposition">
> <h1>AutodiffComposition<a class="headerlink" href="#autodiffcomposition" title="Permalink to this headline">¶</a></h1>
> <div class="related docutils container">
> <p><em>Related</em></p>
> <ul class="simple">
> <li><p><a class="reference internal" href="Composition.html#composition-learning"><span class="std std-ref">Learning in a Composition</span></a></p></li>
> </ul>
> </div>
> <span class="target" id="module-psyneulink.library.compositions.autodiffcomposition"></span><section id="contents">
438,439c444,445
< default variable. If <strong>inputs</strong> is not specified, the <a class="reference internal" href="Component.html#component-variable"><span class="std std-ref">default_variable</span></a> for
< 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> Node is used as its input (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input Formats</span></a> for
---
> default variable. If <strong>inputs</strong> is not specified, the <a class="reference internal" href="Component.html#component-variable"><span class="std std-ref">default_variable</span></a>
> for 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> Node is used as its input (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input Formats</span></a> for
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
308c308
< of computational models in neuroscience and psychology (see <a class="reference internal" href="json.html"><span class="doc">JSON</span></a>)</p>
---
> of computational models in neuroscience and psychology (see <a class="reference internal" href="mdf.html#module-psyneulink.core.globals.json" title="psyneulink.core.globals.json"><code class="xref any py py-mod docutils literal notranslate"><span class="pre">json</span></code></a>)</p>
diff -r docs-base/CombinationFunctions.html docs-head/CombinationFunctions.html
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< <dd><p>Insure that all items of list or np.ndarray in variable are of the same length</p>
---
> <dd><p>Insure that all items of list or np.array in variable are of the same length</p>
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/Component.html docs-head/Component.html
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< <p><a class="reference internal" href="Mechanisms.html"><span class="doc">Mechanisms</span></a> &lt;Mechanism&gt;` are the only type of Component that reset when the <a class="reference internal" href="#psyneulink.core.components.component.Component.reset_stateful_function_when" title="psyneulink.core.components.component.Component.reset_stateful_function_when"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">reset_stateful_function_when</span></code></a> <a class="reference internal" href="Condition.html"><span class="doc">Condition</span></a> is satisfied. Other Component types do not reset,
---
> <p><a class="reference internal" href="Mechanism.html"><span class="doc">Mechanisms</span></a> are the only type of Component that reset when the <a class="reference internal" href="#psyneulink.core.components.component.Component.reset_stateful_function_when" title="psyneulink.core.components.component.Component.reset_stateful_function_when"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">reset_stateful_function_when</span></code></a> <a class="reference internal" href="Condition.html"><span class="doc">Condition</span></a> is satisfied. Other Component types do not reset,
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< <li><p><strong>default_variable</strong> (<em>scalar</em><em>, </em><em>list</em><em> or </em><em>array : default</em><em> [</em><em>[</em><em>0</em><em>]</em><em>]</em>) – specifies template for the input to the Component’s <a class="reference internal" href="#psyneulink.core.components.component.Component.function" title="psyneulink.core.components.component.Component.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p></li>
---
> <li><p><strong>default_variable</strong> (<em>scalar</em><em>, </em><em>list</em><em> or </em><em>array : default</em><em> [</em><em>[</em><em>0</em><em>]</em><em>]</em>) – specifies template for the input to the Component’s <a class="reference internal" href="#psyneulink.core.components.component.Component.function" title="psyneulink.core.components.component.Component.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>, and the value used as the
> input to the Component if none is provided on execution (see <code class="xref any docutils literal notranslate"><span class="pre">Component_Variable</span></code> for additional information).</p></li>
diff -r docs-base/Composition.html docs-head/Composition.html
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< <ul>
---
> <ul class="current">
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> <li class="toctree-l1 current"><a class="reference internal" href="CompositionInterfaceMechanism.html">CompositionInterfaceMechanism</a></li>
> <li class="toctree-l1"><a class="reference internal" href="OptimizationControlMechanism.html">OptimizationControlMechanism</a></li>
604,607c606,609
< <li><p><em>Probes</em> – Nodes that are not <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> of a nested Composition but project to ones in an
< outer Composition are assigned <a class="reference internal" href="#id18" 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="#id18" 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
< is whether their output is included in the <a class="reference internal" href="#id0" 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 <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> attributes of the outermost Composition to which they project; this is determined by the
---
> <li><p><em>Probes</em> – Nodes that are not <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> of a nested Composition, but project to ones in an
> 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
> is whether their output is 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 <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> attributes of the <em>outermost</em> Composition to which they project; this is determined by the
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< <a class="reference internal" href="#id18" 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 in any Composition nested within it are <em>not</em> included in
< the <a class="reference internal" href="#id0" 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 Composition to which
< they project. In this respect, they can be thought of as “probing” - that is, providing access to “latent variables”
< of – the Composition to which they belong – the values of which that are not otherwise reported as part of the
< Composition’s output or results.  If <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="#id18" 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 any nested Compositions are treated the same as <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: their outputs are included in the <a class="reference internal" href="#id0" 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 <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> of that Composition.</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 <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
> in those attributes of the nested Compositions; see note below). In this respect, they can be thought of as
> “probing” - that is, providing access to “latent variables” of – the nested Composition to which they belong –
> the values of which that are not otherwise reported as part of the outermost Composition’s output or results. If
> <a class="reference internal" href="#psyneu
...

See CI logs for the full diff.

lgtm-com · 2022-03-29T19:48:48Z

This pull request introduces 47 alerts and fixes 2 when merging 3d76263 into aeddf3e - view on LGTM.com

new alerts:

22 for Unused import
6 for Unreachable code
5 for Unused local variable
5 for Variable defined multiple times
2 for Comparison using is when operands support `__eq__`
2 for Except block handles 'BaseException'
2 for Module is imported with 'import' and 'import from'
1 for Unnecessary pass
1 for Module is imported more than once
1 for `__init__` method calls overridden method

fixed alerts:

1 for Wrong name for an argument in a call
1 for Unused local variable

github-actions · 2022-03-30T00:13:15Z

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

diff -r docs-base/.buildinfo docs-head/.buildinfo
3c3
< config: 93a36d7daeeffc980fdbe13b5661e43b
---
> config: 2756124a1a258cfc1eedcf79d651812e
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
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<   <section id="module-psyneulink.library.compositions.autodiffcomposition">
< <span id="autodiffcomposition"></span><h1>AutodiffComposition<a class="headerlink" href="#module-psyneulink.library.compositions.autodiffcomposition" title="Permalink to this headline">¶</a></h1>
< <section id="contents">
---
>   <section id="autodiffcomposition">
> <h1>AutodiffComposition<a class="headerlink" href="#autodiffcomposition" title="Permalink to this headline">¶</a></h1>
> <div class="related docutils container">
> <p><em>Related</em></p>
> <ul class="simple">
> <li><p><a class="reference internal" href="Composition.html#composition-learning"><span class="std std-ref">Learning in a Composition</span></a></p></li>
> </ul>
> </div>
> <span class="target" id="module-psyneulink.library.compositions.autodiffcomposition"></span><section id="contents">
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< default variable. If <strong>inputs</strong> is not specified, the <a class="reference internal" href="Component.html#component-variable"><span class="std std-ref">default_variable</span></a> for
< 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> Node is used as its input (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input Formats</span></a> for
---
> default variable. If <strong>inputs</strong> is not specified, the <a class="reference internal" href="Component.html#component-variable"><span class="std std-ref">default_variable</span></a>
> for 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> Node is used as its input (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input Formats</span></a> for
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
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< of computational models in neuroscience and psychology (see <a class="reference internal" href="json.html"><span class="doc">JSON</span></a>)</p>
---
> of computational models in neuroscience and psychology (see <a class="reference internal" href="mdf.html#module-psyneulink.core.globals.json" title="psyneulink.core.globals.json"><code class="xref any py py-mod docutils literal notranslate"><span class="pre">json</span></code></a>)</p>
diff -r docs-base/CombinationFunctions.html docs-head/CombinationFunctions.html
1047c1047
< <dd><p>Insure that all items of list or np.ndarray in variable are of the same length</p>
---
> <dd><p>Insure that all items of list or np.array in variable are of the same length</p>
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/Component.html docs-head/Component.html
494c494
< <p><a class="reference internal" href="Mechanisms.html"><span class="doc">Mechanisms</span></a> &lt;Mechanism&gt;` are the only type of Component that reset when the <a class="reference internal" href="#psyneulink.core.components.component.Component.reset_stateful_function_when" title="psyneulink.core.components.component.Component.reset_stateful_function_when"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">reset_stateful_function_when</span></code></a> <a class="reference internal" href="Condition.html"><span class="doc">Condition</span></a> is satisfied. Other Component types do not reset,
---
> <p><a class="reference internal" href="Mechanism.html"><span class="doc">Mechanisms</span></a> are the only type of Component that reset when the <a class="reference internal" href="#psyneulink.core.components.component.Component.reset_stateful_function_when" title="psyneulink.core.components.component.Component.reset_stateful_function_when"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">reset_stateful_function_when</span></code></a> <a class="reference internal" href="Condition.html"><span class="doc">Condition</span></a> is satisfied. Other Component types do not reset,
562c562,563
< <li><p><strong>default_variable</strong> (<em>scalar</em><em>, </em><em>list</em><em> or </em><em>array : default</em><em> [</em><em>[</em><em>0</em><em>]</em><em>]</em>) – specifies template for the input to the Component’s <a class="reference internal" href="#psyneulink.core.components.component.Component.function" title="psyneulink.core.components.component.Component.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p></li>
---
> <li><p><strong>default_variable</strong> (<em>scalar</em><em>, </em><em>list</em><em> or </em><em>array : default</em><em> [</em><em>[</em><em>0</em><em>]</em><em>]</em>) – specifies template for the input to the Component’s <a class="reference internal" href="#psyneulink.core.components.component.Component.function" title="psyneulink.core.components.component.Component.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>, and the value used as the
> input to the Component if none is provided on execution (see <code class="xref any docutils literal notranslate"><span class="pre">Component_Variable</span></code> for additional information).</p></li>
diff -r docs-base/Composition.html docs-head/Composition.html
221c221
< <ul>
---
> <ul class="current">
222a223,224
> <li class="toctree-l1 current"><a class="reference internal" href="CompositionInterfaceMechanism.html">CompositionInterfaceMechanism</a></li>
> <li class="toctree-l1"><a class="reference internal" href="OptimizationControlMechanism.html">OptimizationControlMechanism</a></li>
604,607c606,609
< <li><p><em>Probes</em> – Nodes that are not <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> of a nested Composition but project to ones in an
< outer Composition are assigned <a class="reference internal" href="#id18" 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="#id18" 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
< is whether their output is included in the <a class="reference internal" href="#id0" 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 <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> attributes of the outermost Composition to which they project; this is determined by the
---
> <li><p><em>Probes</em> – Nodes that are not <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> of a nested Composition, but project to ones in an
> 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
> is whether their output is 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 <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> attributes of the <em>outermost</em> Composition to which they project; this is determined by the
610,616c612,622
< <a class="reference internal" href="#id18" 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 in any Composition nested within it are <em>not</em> included in
< the <a class="reference internal" href="#id0" 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 Composition to which
< they project. In this respect, they can be thought of as “probing” - that is, providing access to “latent variables”
< of – the Composition to which they belong – the values of which that are not otherwise reported as part of the
< Composition’s output or results.  If <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="#id18" 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 any nested Compositions are treated the same as <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: their outputs are included in the <a class="reference internal" href="#id0" 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 <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> of that Composition.</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 <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
> in those attributes of the nested Compositions; see note below). In this respect, they can be thought of as
> “probing” - that is, providing access to “latent variables” of – the nested Composition to which they belong –
> the values of which that are not otherwise reported as part of the outermost Composition’s output or results. If
> <a class="reference internal" href="#psyneu
...

See CI logs for the full diff.

lgtm-com · 2022-03-30T01:11:05Z

This pull request introduces 47 alerts and fixes 2 when merging 739a8aa into aeddf3e - view on LGTM.com

new alerts:

22 for Unused import
6 for Unreachable code
5 for Unused local variable
5 for Variable defined multiple times
2 for Comparison using is when operands support `__eq__`
2 for Except block handles 'BaseException'
2 for Module is imported with 'import' and 'import from'
1 for Unnecessary pass
1 for Module is imported more than once
1 for `__init__` method calls overridden method

fixed alerts:

1 for Wrong name for an argument in a call
1 for Unused local variable

* • optimizationcontrolmechanism.py: docstring mods * • composition.py: - add allow_probes and exclude_probes_from_output * • composition.py: - docstring mods re: allow_probes • optimizationcontrolmechanism.py: - allow_probes: eliminate DIRECT setting - remove _parse_monitor_for_control_input_ports (no longer needed without allow_probes=DIRECT) * • composition.py: - change "exclude_probes_from_output" -> "include_probes_in_output" * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • composition.py: - docstring mods re: allow_probes and include_probes_in_output * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • controlmechanism.py: - add allow_probes handling (moved from OCM) • optimizationcontrolmechanism.py: - move allow_probes to controlmechanism.py • composition.py: - refactor handling of allow_probes to permit for any ControlMechanism - add _handle_allow_probes_for_control() to reconcile setting on Composition and ControlMechanism • objectivemechanism.py: - add modulatory_mechanism attribute * • composition.py add assignment of learning_mechanism to objective_mechanism.modulatory_mechanism for add_learning methods * • docstring mods * - * - * • optimizationcontrolmechanism.py: docstring revs * - * - * • test_composition.py: - add test_unnested_PROBE - add test_nested_PROBES TBD: test include_probes_in_output * - * • composition.py - add_node(): support tuple with required_role * - * • composition.py: - _determine_node_roles: fix bug in which nested comp was prevented from being an OUTPUT Node if, in addition to Nodes that qualifed as OUTPUT, it also had nodes that projected to Nodes in an outer comp (making it look like it was INTERNAL) * - * • composition.py: - add_node(): enforce include_probes_in_output = True for nested Compositions - execute(): - replace return of output_value with get_output_value() * - * • CompositionInterfaceMechanism.rst: - correct path ref • compositioninterfacemechanism.py: - docstring fixes * • optimizationcontrolmechanism.py: - docstring edits * - * - * - * - * - * - * - * - * • composition.py, optimizationcontrolmechanism.py: _build_predicted_input_dict(): support partial specification of INPUT Nodes for nested Compositions of agent_rep * • test_control.py: - test_nested_composition_as_agent_rep(): PASSES ALL TESTS * - * • optimizationcontrolmechanism.py: - _parse_state_feature_specs: support nested composition in dict spec * • test_control.py - test_ocm_state_feature_specs_and_warnings_and_errors(): - modified to accomodate nested INPUT Node specs - PASSES ALL TESTS * • composition.py: - add _nodes_added attribute - add_nodes(): set _nodes_added attribute upon completition - _analyze_graph(): add call _determine_node_roles() if _nodes_added is True * • composition.py: - _nodes_added -> needs_determine_node_roles • optimizationcontrolmechanism.py: - _get_agent_rep_input_nodes(): call _determine_node_roles if agent_rep.needs_determine_node_roles is True * • optimizationcontrolmechanism.py: - _parse_state_feature_specs(): consolidate handling of various formats * • optimizationcontrolmechanism.py: docstring updates * • optimizationcontrolmechanism.py: _get_agent_rep_input_nodes() -> _get_agent_rep_input_receivers() _parse_state_feature_specs(): standardize on InputPorts rather than Nodes * - * - * - * - * • composition.py: - _instantiate_input_dict(): refactor to accept inputs for InputPorts of nested Nodes - add helper method _get_external_cim_input_port() - TBD: - refactor _build_predicted_inputs_dict to support above * - * • composition.py: - _instantiate_input_dict(): now generates properly formatted values in input_dict for InputPort specs * • composition.py: - _build_predicted_inputs_dict(): refactored to construct inputs_dict with InputPorts as keys * - * - * - * - * - * - * - * - * - * - * - * - * - * • optimizationcontrolmechanism.py: - refactor state_feature_values as dict that can be used as predicted_inputs / feature_values arg of evaluate() (and inputs arg of run) • composition.py: - remove _build_predicted_inputs_dict(), since state_feature_values now formatted properly as input * - * - * - * - * - * - * - * - * - * - * - * - * - * • composition.py: - _instantiate_inputs_dict(): BEFORE REFACTORING FOR MISSING PORTS OF NESTED COMP * • composition.py: - _instantiate_inputs_dict(): BEFORE REFACTORING FOR MISSING PORTS OF NESTED COMP * • composition.py: - _instantiate_inputs_dict(): BEFORE REFACTORING FOR MISSING PORTS OF NESTED COMP * • composition.py: - _instantiate_inputs_dict(): AFTER REFACTORING FOR MISSING PORTS OF NESTED COMP * - * - * - * - * • test_composition.py: - refactor test_input_type_equivalence() * - PASSES test_control * - merged from devel missing dependencies * - * - * - * • update pandas req to 1.4.1 * • composition.py: - _instantiate_inputs_dict(): refactored to consolidate treatment of nested Nodes * - * - * • composition.py - _instantiate_input_dict(): handle ports with diff numbers of trials specified * • composition.py - _instantiate_input_dict(): handle ports with diff numbers of trials specified * - * - * - * - * - * - * - * - * - * - * - * - * - * - * - * - * - * - * - * • composition.py: - _parse_names_in_inputs(): support Port.full_name as keys in inputs dict • mechanism.py: - Mechanism_Base: replaced input_labels and output_labels with labeled_input_values and labeled_output_values respectively • port.py, inputport.py, outputport.py, parameterport.py: - Port_Base: impelment labeled_value property (and value_label alias) that returns calls get_label() - deleted label attributes of InputPort and OutputPort (replaced by Port_Base.labeled_value) - added get_label() stub on ParameterPort with error message * - * - * • conf.py: comment out 'sphinx_autodoc_typehints' (crashing for sphinx_autodoc_typehints v.1.17.0) * • conf.py: restore 'sphinx_autodoc_typehints' • doc_requirements.txt: pin sphinx_autodoc_typehints < v.1.16.0; error on v1.16 and v1.17; error: https://github.com/PrincetonUniversity/PsyNeuLink/runs/5573651890?check_suite_focus=true * - * - * • composition.py: - add property: external_input_ports_of_all_input_nodes • optimizationcontrolmechanism.py: - implement state_faature_default - add SHADOW_INPUTS as individual spec for state_features * • composition.py: - add property: external_input_ports_of_all_input_nodes • optimizationcontrolmechanism.py: - implement state_faature_default - add SHADOW_INPUTS as individual spec for state_features * - * - * - * - * - * - * - * - * • inputport.py: - add figure for shadowing * - * - * • processingmechanism.py: - __init__(): modify typecheck for input_ports to allow single items * • optimizationcontrolmechanism.py - 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) * - * - * • optimizationcontrolmechanism.py: docstring mods * • optimizationcontrolmechanism.py: docstring mods * • optimizationcontrolmechanism.py: docstring mods * - * - * - * - * - * • optimizationcontrolmechanism.py: - _state_feature_values_getter(): for numeric state_feature, return state_input_port.functio(numeric_value) * • test_control.py: - test_ocm_state_feature_specs_and_warnings_and_errors() - added tests for single state_feature spec * - composition.py, inputport.py, optimizationcontrolmechanism.py: docstring mods re: "external InputPort" * - * - * - * • 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 * - * - * - * • optimizationcontrolmechanism.py: - state_features, get_state_feature_source: simplify * - * - * • optimizationcontrolmechanism.py: - state_features, get_state_feature_source: simplify * • optimizationcontrolmechanism.py: IN PROGRESS - _specified_INPUT_Node_InputPorts_in_order: use name (str) of items not yet in agent_rep rather than 'None' - state_features & state_feature_values: - use name (str) as key if INPUT Node InputPort is not yet in agent_rep - use name (str) if source (spec) is not yet in Composition * - * • optimizationcontrolmechanism.py: IMPLEMENTED - state_features: - convert all keys and values to port.full_name - if not yet in comp or agent_rep, add "DEFERRED..." * • optimizationcontrolmechanism.py: PASSES deferred_init and partial_deferred_init tests * • optimizationcontrolmechanism.py: - state_feature_values: strings for missing keys or values * • test_control.py: PASSING test_deferred and test_partial_deferred * • test_control.py: PASSING test_deferred and test_partial_deferred * • test_control.py: PASSING test_deferred and test_partial_deferred * • test_control.py: PASSING test_ocm_state_feature_specs_and_warnings_and_errors * • test_control.py: PASSING all state_feature tests * • composition.py: add _is_in_composition method * - * - * - * - * - * - * - * - * - * • optimzationcontrolmechanism.py: fix figure * • optimzationcontrolmechanism.py: fix figure * • optimizationcontrolmechanism.py: - fix bug in which state_feature_default = None was being ignored - fix bug in which deferred nodes were not being assigned state_feature_default * - * • optimizationcontrolmechanism.py: - fix bug in which state_feature_default = None was being ignored - fix bug in which deferred nodes were not being assigned state_feature_default * • test_control.py: - test_deferred_init, test_partial_deferred_init(): added tests for controller.state_input_ports path_afferents * - * - * • optimizationcontrolmechanism.py: - _parse_state_feature_specs: - fixed bug in handling of lists of numeric specs - renamed state_input_ports for numeric specs * • registry.py: - rename_instance_in_registry(): finish implementing (including **new_name** arg) • optimizationcontrolmechanism.py: - _update_state_features_dict: rename deferred state_input_ports * • registry.py: - rename_instance_in_registry(): finish implementing (including **new_name** arg) • optimizationcontrolmechanism.py: - _update_state_features_dict: rename deferred state_input_ports * - * • optimizationcontrolmechanism.py, test_control.py - standarize prefixes for state_input_ports * • optimizationcontrolmechanism.py, test_control.py - standarize prefixes for state_input_ports * - * - * • test_show_graph remaining * • mechanism.py: - _show_structure(): fix parameterport label bug * - * - * - * - * • composition.py: _validate_input_keys(): add method to validate keys of inputs to run() method * • test_composition.py: - test_inputs_key_errors() * • test_composition.py: - test_inputs_key_errors(): add test for running nested composition with inputs * - * • composition.py: - execute(): allow direct call to nested composition with inputs * - * - Co-authored-by: jdcpni <pniintel55>

github-actions · 2022-03-30T03:28:54Z

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

diff -r docs-base/.buildinfo docs-head/.buildinfo
3c3
< config: 93a36d7daeeffc980fdbe13b5661e43b
---
> config: 2756124a1a258cfc1eedcf79d651812e
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
206,208c206,214
<   <section id="module-psyneulink.library.compositions.autodiffcomposition">
< <span id="autodiffcomposition"></span><h1>AutodiffComposition<a class="headerlink" href="#module-psyneulink.library.compositions.autodiffcomposition" title="Permalink to this headline">¶</a></h1>
< <section id="contents">
---
>   <section id="autodiffcomposition">
> <h1>AutodiffComposition<a class="headerlink" href="#autodiffcomposition" title="Permalink to this headline">¶</a></h1>
> <div class="related docutils container">
> <p><em>Related</em></p>
> <ul class="simple">
> <li><p><a class="reference internal" href="Composition.html#composition-learning"><span class="std std-ref">Learning in a Composition</span></a></p></li>
> </ul>
> </div>
> <span class="target" id="module-psyneulink.library.compositions.autodiffcomposition"></span><section id="contents">
438,439c444,445
< default variable. If <strong>inputs</strong> is not specified, the <a class="reference internal" href="Component.html#component-variable"><span class="std std-ref">default_variable</span></a> for
< 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> Node is used as its input (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input Formats</span></a> for
---
> default variable. If <strong>inputs</strong> is not specified, the <a class="reference internal" href="Component.html#component-variable"><span class="std std-ref">default_variable</span></a>
> for 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> Node is used as its input (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input Formats</span></a> for
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
308c308
< of computational models in neuroscience and psychology (see <a class="reference internal" href="json.html"><span class="doc">JSON</span></a>)</p>
---
> of computational models in neuroscience and psychology (see <a class="reference internal" href="mdf.html#module-psyneulink.core.globals.json" title="psyneulink.core.globals.json"><code class="xref any py py-mod docutils literal notranslate"><span class="pre">json</span></code></a>)</p>
diff -r docs-base/CombinationFunctions.html docs-head/CombinationFunctions.html
1047c1047
< <dd><p>Insure that all items of list or np.ndarray in variable are of the same length</p>
---
> <dd><p>Insure that all items of list or np.array in variable are of the same length</p>
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/Component.html docs-head/Component.html
494c494
< <p><a class="reference internal" href="Mechanisms.html"><span class="doc">Mechanisms</span></a> &lt;Mechanism&gt;` are the only type of Component that reset when the <a class="reference internal" href="#psyneulink.core.components.component.Component.reset_stateful_function_when" title="psyneulink.core.components.component.Component.reset_stateful_function_when"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">reset_stateful_function_when</span></code></a> <a class="reference internal" href="Condition.html"><span class="doc">Condition</span></a> is satisfied. Other Component types do not reset,
---
> <p><a class="reference internal" href="Mechanism.html"><span class="doc">Mechanisms</span></a> are the only type of Component that reset when the <a class="reference internal" href="#psyneulink.core.components.component.Component.reset_stateful_function_when" title="psyneulink.core.components.component.Component.reset_stateful_function_when"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">reset_stateful_function_when</span></code></a> <a class="reference internal" href="Condition.html"><span class="doc">Condition</span></a> is satisfied. Other Component types do not reset,
562c562,563
< <li><p><strong>default_variable</strong> (<em>scalar</em><em>, </em><em>list</em><em> or </em><em>array : default</em><em> [</em><em>[</em><em>0</em><em>]</em><em>]</em>) – specifies template for the input to the Component’s <a class="reference internal" href="#psyneulink.core.components.component.Component.function" title="psyneulink.core.components.component.Component.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p></li>
---
> <li><p><strong>default_variable</strong> (<em>scalar</em><em>, </em><em>list</em><em> or </em><em>array : default</em><em> [</em><em>[</em><em>0</em><em>]</em><em>]</em>) – specifies template for the input to the Component’s <a class="reference internal" href="#psyneulink.core.components.component.Component.function" title="psyneulink.core.components.component.Component.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>, and the value used as the
> input to the Component if none is provided on execution (see <code class="xref any docutils literal notranslate"><span class="pre">Component_Variable</span></code> for additional information).</p></li>
diff -r docs-base/Composition.html docs-head/Composition.html
221c221
< <ul>
---
> <ul class="current">
222a223,224
> <li class="toctree-l1 current"><a class="reference internal" href="CompositionInterfaceMechanism.html">CompositionInterfaceMechanism</a></li>
> <li class="toctree-l1"><a class="reference internal" href="OptimizationControlMechanism.html">OptimizationControlMechanism</a></li>
604,607c606,609
< <li><p><em>Probes</em> – Nodes that are not <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> of a nested Composition but project to ones in an
< outer Composition are assigned <a class="reference internal" href="#id18" 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="#id18" 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
< is whether their output is included in the <a class="reference internal" href="#id0" 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 <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> attributes of the outermost Composition to which they project; this is determined by the
---
> <li><p><em>Probes</em> – Nodes that are not <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> of a nested Composition, but project to ones in an
> 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
> is whether their output is 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 <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> attributes of the <em>outermost</em> Composition to which they project; this is determined by the
610,616c612,622
< <a class="reference internal" href="#id18" 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 in any Composition nested within it are <em>not</em> included in
< the <a class="reference internal" href="#id0" 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 Composition to which
< they project. In this respect, they can be thought of as “probing” - that is, providing access to “latent variables”
< of – the Composition to which they belong – the values of which that are not otherwise reported as part of the
< Composition’s output or results.  If <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="#id18" 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 any nested Compositions are treated the same as <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: their outputs are included in the <a class="reference internal" href="#id0" 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 <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> of that Composition.</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 <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
> in those attributes of the nested Compositions; see note below). In this respect, they can be thought of as
> “probing” - that is, providing access to “latent variables” of – the nested Composition to which they belong –
> the values of which that are not otherwise reported as part of the outermost Composition’s output or results. If
> <a class="reference internal" href="#psyneu
...

See CI logs for the full diff.

lgtm-com · 2022-03-30T04:25:59Z

This pull request introduces 47 alerts and fixes 2 when merging 7afa437 into aeddf3e - view on LGTM.com

new alerts:

22 for Unused import
6 for Unreachable code
5 for Unused local variable
5 for Variable defined multiple times
2 for Comparison using is when operands support `__eq__`
2 for Except block handles 'BaseException'
2 for Module is imported with 'import' and 'import from'
1 for Unnecessary pass
1 for Module is imported more than once
1 for `__init__` method calls overridden method

fixed alerts:

1 for Wrong name for an argument in a call
1 for Unused local variable

Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

Not used in compiled computation. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

The mag01 array has two constant elements. These don't have to be loaded via stack location, however, since the array is dynamically indexed, the compiler won't move the constants to registers. Perform this transformation manually to reduce stack usage. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

num_runs -> num_sim_trials num_inputs -> num_sim_inputs Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

Add missing name to alloca instruction. Use more descriptive variable names when invoking simulation trials. Use conditional select instead of a stack array in the initialization of Mersenne Twister.

github-actions · 2022-03-30T17:45:05Z

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

diff -r docs-base/.buildinfo docs-head/.buildinfo
3c3
< config: 93a36d7daeeffc980fdbe13b5661e43b
---
> config: 2756124a1a258cfc1eedcf79d651812e
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
206,208c206,214
<   <section id="module-psyneulink.library.compositions.autodiffcomposition">
< <span id="autodiffcomposition"></span><h1>AutodiffComposition<a class="headerlink" href="#module-psyneulink.library.compositions.autodiffcomposition" title="Permalink to this headline">¶</a></h1>
< <section id="contents">
---
>   <section id="autodiffcomposition">
> <h1>AutodiffComposition<a class="headerlink" href="#autodiffcomposition" title="Permalink to this headline">¶</a></h1>
> <div class="related docutils container">
> <p><em>Related</em></p>
> <ul class="simple">
> <li><p><a class="reference internal" href="Composition.html#composition-learning"><span class="std std-ref">Learning in a Composition</span></a></p></li>
> </ul>
> </div>
> <span class="target" id="module-psyneulink.library.compositions.autodiffcomposition"></span><section id="contents">
438,439c444,445
< default variable. If <strong>inputs</strong> is not specified, the <a class="reference internal" href="Component.html#component-variable"><span class="std std-ref">default_variable</span></a> for
< 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> Node is used as its input (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input Formats</span></a> for
---
> default variable. If <strong>inputs</strong> is not specified, the <a class="reference internal" href="Component.html#component-variable"><span class="std std-ref">default_variable</span></a>
> for 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> Node is used as its input (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input Formats</span></a> for
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
308c308
< of computational models in neuroscience and psychology (see <a class="reference internal" href="json.html"><span class="doc">JSON</span></a>)</p>
---
> of computational models in neuroscience and psychology (see <a class="reference internal" href="mdf.html#module-psyneulink.core.globals.json" title="psyneulink.core.globals.json"><code class="xref any py py-mod docutils literal notranslate"><span class="pre">json</span></code></a>)</p>
diff -r docs-base/CombinationFunctions.html docs-head/CombinationFunctions.html
1047c1047
< <dd><p>Insure that all items of list or np.ndarray in variable are of the same length</p>
---
> <dd><p>Insure that all items of list or np.array in variable are of the same length</p>
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/Component.html docs-head/Component.html
494c494
< <p><a class="reference internal" href="Mechanisms.html"><span class="doc">Mechanisms</span></a> &lt;Mechanism&gt;` are the only type of Component that reset when the <a class="reference internal" href="#psyneulink.core.components.component.Component.reset_stateful_function_when" title="psyneulink.core.components.component.Component.reset_stateful_function_when"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">reset_stateful_function_when</span></code></a> <a class="reference internal" href="Condition.html"><span class="doc">Condition</span></a> is satisfied. Other Component types do not reset,
---
> <p><a class="reference internal" href="Mechanism.html"><span class="doc">Mechanisms</span></a> are the only type of Component that reset when the <a class="reference internal" href="#psyneulink.core.components.component.Component.reset_stateful_function_when" title="psyneulink.core.components.component.Component.reset_stateful_function_when"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">reset_stateful_function_when</span></code></a> <a class="reference internal" href="Condition.html"><span class="doc">Condition</span></a> is satisfied. Other Component types do not reset,
562c562,563
< <li><p><strong>default_variable</strong> (<em>scalar</em><em>, </em><em>list</em><em> or </em><em>array : default</em><em> [</em><em>[</em><em>0</em><em>]</em><em>]</em>) – specifies template for the input to the Component’s <a class="reference internal" href="#psyneulink.core.components.component.Component.function" title="psyneulink.core.components.component.Component.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p></li>
---
> <li><p><strong>default_variable</strong> (<em>scalar</em><em>, </em><em>list</em><em> or </em><em>array : default</em><em> [</em><em>[</em><em>0</em><em>]</em><em>]</em>) – specifies template for the input to the Component’s <a class="reference internal" href="#psyneulink.core.components.component.Component.function" title="psyneulink.core.components.component.Component.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>, and the value used as the
> input to the Component if none is provided on execution (see <code class="xref any docutils literal notranslate"><span class="pre">Component_Variable</span></code> for additional information).</p></li>
diff -r docs-base/Composition.html docs-head/Composition.html
221c221
< <ul>
---
> <ul class="current">
222a223,224
> <li class="toctree-l1 current"><a class="reference internal" href="CompositionInterfaceMechanism.html">CompositionInterfaceMechanism</a></li>
> <li class="toctree-l1"><a class="reference internal" href="OptimizationControlMechanism.html">OptimizationControlMechanism</a></li>
604,607c606,609
< <li><p><em>Probes</em> – Nodes that are not <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> of a nested Composition but project to ones in an
< outer Composition are assigned <a class="reference internal" href="#id18" 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="#id18" 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
< is whether their output is included in the <a class="reference internal" href="#id0" 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 <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> attributes of the outermost Composition to which they project; this is determined by the
---
> <li><p><em>Probes</em> – Nodes that are not <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> of a nested Composition, but project to ones in an
> 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
> is whether their output is 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 <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> attributes of the <em>outermost</em> Composition to which they project; this is determined by the
610,616c612,622
< <a class="reference internal" href="#id18" 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 in any Composition nested within it are <em>not</em> included in
< the <a class="reference internal" href="#id0" 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 Composition to which
< they project. In this respect, they can be thought of as “probing” - that is, providing access to “latent variables”
< of – the Composition to which they belong – the values of which that are not otherwise reported as part of the
< Composition’s output or results.  If <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="#id18" 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 any nested Compositions are treated the same as <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: their outputs are included in the <a class="reference internal" href="#id0" 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 <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> of that Composition.</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 <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
> in those attributes of the nested Compositions; see note below). In this respect, they can be thought of as
> “probing” - that is, providing access to “latent variables” of – the nested Composition to which they belong –
> the values of which that are not otherwise reported as part of the outermost Composition’s output or results. If
> <a class="reference internal" href="#psyneu
...

See CI logs for the full diff.

lgtm-com · 2022-03-30T18:29:18Z

This pull request introduces 47 alerts and fixes 2 when merging 41ac3a0 into aeddf3e - view on LGTM.com

new alerts:

22 for Unused import
6 for Unreachable code
5 for Unused local variable
5 for Variable defined multiple times
2 for Comparison using is when operands support `__eq__`
2 for Except block handles 'BaseException'
2 for Module is imported with 'import' and 'import from'
1 for Unnecessary pass
1 for Module is imported more than once
1 for `__init__` method calls overridden method

fixed alerts:

1 for Wrong name for an argument in a call
1 for Unused local variable

github-actions · 2022-04-01T16:55:56Z

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

diff -r docs-base/.buildinfo docs-head/.buildinfo
3c3
< config: 93a36d7daeeffc980fdbe13b5661e43b
---
> config: 2756124a1a258cfc1eedcf79d651812e
diff -r docs-base/AutodiffComposition.html docs-head/AutodiffComposition.html
206,208c206,214
<   <section id="module-psyneulink.library.compositions.autodiffcomposition">
< <span id="autodiffcomposition"></span><h1>AutodiffComposition<a class="headerlink" href="#module-psyneulink.library.compositions.autodiffcomposition" title="Permalink to this headline">¶</a></h1>
< <section id="contents">
---
>   <section id="autodiffcomposition">
> <h1>AutodiffComposition<a class="headerlink" href="#autodiffcomposition" title="Permalink to this headline">¶</a></h1>
> <div class="related docutils container">
> <p><em>Related</em></p>
> <ul class="simple">
> <li><p><a class="reference internal" href="Composition.html#composition-learning"><span class="std std-ref">Learning in a Composition</span></a></p></li>
> </ul>
> </div>
> <span class="target" id="module-psyneulink.library.compositions.autodiffcomposition"></span><section id="contents">
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< default variable. If <strong>inputs</strong> is not specified, the <a class="reference internal" href="Component.html#component-variable"><span class="std std-ref">default_variable</span></a> for
< 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> Node is used as its input (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input Formats</span></a> for
---
> default variable. If <strong>inputs</strong> is not specified, the <a class="reference internal" href="Component.html#component-variable"><span class="std std-ref">default_variable</span></a>
> for 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> Node is used as its input (see <a class="reference internal" href="Composition.html#composition-execution-inputs"><span class="std std-ref">Input Formats</span></a> for
diff -r docs-base/BasicsAndPrimer.html docs-head/BasicsAndPrimer.html
308c308
< of computational models in neuroscience and psychology (see <a class="reference internal" href="json.html"><span class="doc">JSON</span></a>)</p>
---
> of computational models in neuroscience and psychology (see <a class="reference internal" href="mdf.html#module-psyneulink.core.globals.json" title="psyneulink.core.globals.json"><code class="xref any py py-mod docutils literal notranslate"><span class="pre">json</span></code></a>)</p>
diff -r docs-base/CombinationFunctions.html docs-head/CombinationFunctions.html
1047c1047
< <dd><p>Insure that all items of list or np.ndarray in variable are of the same length</p>
---
> <dd><p>Insure that all items of list or np.array in variable are of the same length</p>
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/Component.html docs-head/Component.html
494c494
< <p><a class="reference internal" href="Mechanisms.html"><span class="doc">Mechanisms</span></a> &lt;Mechanism&gt;` are the only type of Component that reset when the <a class="reference internal" href="#psyneulink.core.components.component.Component.reset_stateful_function_when" title="psyneulink.core.components.component.Component.reset_stateful_function_when"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">reset_stateful_function_when</span></code></a> <a class="reference internal" href="Condition.html"><span class="doc">Condition</span></a> is satisfied. Other Component types do not reset,
---
> <p><a class="reference internal" href="Mechanism.html"><span class="doc">Mechanisms</span></a> are the only type of Component that reset when the <a class="reference internal" href="#psyneulink.core.components.component.Component.reset_stateful_function_when" title="psyneulink.core.components.component.Component.reset_stateful_function_when"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">reset_stateful_function_when</span></code></a> <a class="reference internal" href="Condition.html"><span class="doc">Condition</span></a> is satisfied. Other Component types do not reset,
562c562,563
< <li><p><strong>default_variable</strong> (<em>scalar</em><em>, </em><em>list</em><em> or </em><em>array : default</em><em> [</em><em>[</em><em>0</em><em>]</em><em>]</em>) – specifies template for the input to the Component’s <a class="reference internal" href="#psyneulink.core.components.component.Component.function" title="psyneulink.core.components.component.Component.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>.</p></li>
---
> <li><p><strong>default_variable</strong> (<em>scalar</em><em>, </em><em>list</em><em> or </em><em>array : default</em><em> [</em><em>[</em><em>0</em><em>]</em><em>]</em>) – specifies template for the input to the Component’s <a class="reference internal" href="#psyneulink.core.components.component.Component.function" title="psyneulink.core.components.component.Component.function"><code class="xref any py py-attr docutils literal notranslate"><span class="pre">function</span></code></a>, and the value used as the
> input to the Component if none is provided on execution (see <code class="xref any docutils literal notranslate"><span class="pre">Component_Variable</span></code> for additional information).</p></li>
diff -r docs-base/Composition.html docs-head/Composition.html
221c221
< <ul>
---
> <ul class="current">
222a223,224
> <li class="toctree-l1 current"><a class="reference internal" href="CompositionInterfaceMechanism.html">CompositionInterfaceMechanism</a></li>
> <li class="toctree-l1"><a class="reference internal" href="OptimizationControlMechanism.html">OptimizationControlMechanism</a></li>
604,607c606,609
< <li><p><em>Probes</em> – Nodes that are not <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> of a nested Composition but project to ones in an
< outer Composition are assigned <a class="reference internal" href="#id18" 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="#id18" 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
< is whether their output is included in the <a class="reference internal" href="#id0" 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 <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> attributes of the outermost Composition to which they project; this is determined by the
---
> <li><p><em>Probes</em> – Nodes that are not <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> of a nested Composition, but project to ones in an
> 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
> is whether their output is 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 <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> attributes of the <em>outermost</em> Composition to which they project; this is determined by the
610,616c612,622
< <a class="reference internal" href="#id18" 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 in any Composition nested within it are <em>not</em> included in
< the <a class="reference internal" href="#id0" 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 Composition to which
< they project. In this respect, they can be thought of as “probing” - that is, providing access to “latent variables”
< of – the Composition to which they belong – the values of which that are not otherwise reported as part of the
< Composition’s output or results.  If <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="#id18" 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 any nested Compositions are treated the same as <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: their outputs are included in the <a class="reference internal" href="#id0" 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 <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> of that Composition.</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 <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
> in those attributes of the nested Compositions; see note below). In this respect, they can be thought of as
> “probing” - that is, providing access to “latent variables” of – the nested Composition to which they belong –
> the values of which that are not otherwise reported as part of the outermost Composition’s output or results. If
> <a class="reference internal" href="#psyneu
...

See CI logs for the full diff.

lgtm-com · 2022-04-01T17:53:11Z

This pull request introduces 47 alerts and fixes 2 when merging 98f353b into aeddf3e - view on LGTM.com

new alerts:

22 for Unused import
6 for Unreachable code
5 for Unused local variable
5 for Variable defined multiple times
2 for Comparison using is when operands support `__eq__`
2 for Except block handles 'BaseException'
2 for Module is imported with 'import' and 'import from'
1 for Unnecessary pass
1 for Module is imported more than once
1 for `__init__` method calls overridden method

fixed alerts:

1 for Wrong name for an argument in a call
1 for Unused local variable

jvesely and others added 30 commits November 11, 2021 01:02

llvm/struct generation: Make sure num_estimats per trial is always in…

8edacf6

…teger Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

Merge branch 'fix/ocm/llvm_num_estimates' into refactor/optimizationf…

1c59517

…ct/_function

• builder_context.py:

c68e9d8

get_param_struct_type(): restored test on num_estimates

Merge branch 'fix/ocm/llvm_num_estimates' into refactor/optimizationf…

d256da3

…ct/_function

Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…

9d4b4c5

…Link into fit

Merge branch 'refactor/optimizationfct/_function' of https://github.c…

f61bb66

…om/PrincetonUniversity/PsyNeuLink into fit

Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeu…

525e76f

…Link into fit

refactor Optimization._function int _evaluate

1586db7

requirements: update pytest-helpers-namespace requirement (#2263)

ecaf289

Refactor/keyword control to control (#2273)

491fede

* - * • controlmechanism.py, gatingmechanism.py: - CONTROL: 'CONTROL' -> 'control' - GATING: 'GATING' -> 'gating' * • Project: - CONTROL: 'CONTROL' -> 'control' - del GATING - GATE = 'gate" Co-authored-by: jdcpni <pniintel55>

llvm, functions/UDF: Add checks that we're not trying to compile clos…

1470df4

…ures Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

llvm, functions/UDF: Fix basic block name for UDF body

a1af6f2

Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

requirements: update pillow requirement from <8.5.0 to <9.1.0 (#2274)

688f1ce

Merge branch 'master' into HEAD

b7d2db5

* master: Devel (#2224)

requirements: update sphinx-autodoc-typehints requirement (#2278)

544c1ec

llvm, functions/UDF: Search the source file to find the function defi…

b856109

…nition AST node This will be needed to compile lambda functions that can share source lines with other AST nodes and can't be parsed in isolation. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

requirements: update sphinx-autodoc-typehints requirement (#2283)

59a7c47

llvm, functions/UDF: Move Function setup code to UDF visitor

e97593d

_gen_llvm_function_body handles only interaction with the rest of the code framework. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

kmantel and others added 4 commits March 28, 2022 21:09

Composition: reconstruct scheduler with original conditions

2c09f15

Composition: fix node removal

06d4b08

Composition: remove_projection: disable learning pathway if applicable

7dd6a50

if a projection being learned is removed, disable the entire pathway because the removal will break it

Merge pull request #2364 from kmantel/removenode

3d76263

Add node removal to Compositions

kmantel temporarily deployed to github-pages March 29, 2022 18:46 Inactive

requirements: restrict modelspec to working (#2366)

739a8aa

davidt0x approved these changes Mar 30, 2022

View reviewed changes

kmantel temporarily deployed to github-pages March 30, 2022 00:10 Inactive

jdcpni temporarily deployed to github-pages March 30, 2022 03:28 Inactive

jvesely and others added 6 commits March 30, 2022 11:17

llvm, functions/DDI: Add human readable name to alloca instruction

9fd9470

Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

llvm: Drop 'competition' parameter from compiled structure

1be564c

Not used in compiled computation. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

llvm: Drop 'smoothing_factor' parameter from compiled structure

dad3c3a

Not used in compiled computation. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

llvm, mechanisms/OCM: Use more descriptive variables names

a2a267b

num_runs -> num_sim_trials num_inputs -> num_sim_inputs Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu>

llvm: More descriptive variable names less stack (#2367)

41ac3a0

Add missing name to alloca instruction. Use more descriptive variable names when invoking simulation trials. Use conditional select instead of a stack array in the initialization of Mersenne Twister.

jvesely temporarily deployed to github-pages March 30, 2022 17:45 Inactive

Refactor/ocm/state features all as input ports (#2369)

98f353b

jdcpni temporarily deployed to github-pages April 1, 2022 16:55 Inactive

kmantel merged commit 7072684 into master Apr 1, 2022

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Devel #2354

Devel #2354

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Devel #2354

Devel #2354

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kmantel commented Mar 21, 2022

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