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v0.4.7.0 #776
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v0.4.7.0 #776
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- added input_states and output_states to init and assign_args_to_params_dicts • LinearMatrix - keyword: fixed bug in which assignment of rows or cols could not handle scalars
* • IntegratorMechanism - added input_states and output_states to init and assign_args_to_params_dicts • LinearMatrix - keyword: fixed bug in which assignment of rows or cols could not handle scalars * • Function Stability: - function: add PROB_INDICATOR option that assigns a value of 1 to the probabilistically chosen option - _validate_params: moved call to super() to end to allow matrix param to be evaluated before continuing validation
* - * - * - * - * - * - * - * - * - * - * - * - * - * - * • Log LogCondition - subset of ContextFlags used to specified logPref • Context ContextFlags - implemented as common set of context flags for: - initialization - execution tracking - logging ContextStatus - aliases to ContextFlags (for backward compatibility) * • Log LogCondition - subset of ContextFlags used to specified logPref • Context ContextFlags - implemented as common set of context flags for: - initialization - execution tracking - logging ContextStatus - aliases to ContextFlags (for backward compatibility) * • Log LogCondition - subset of ContextFlags used to specified logPref • Context ContextFlags - implemented as common set of context flags for: - initialization - execution tracking - logging ContextStatus - aliases to ContextFlags (for backward compatibility) * - * - * - * - * - * • Context context.status replaced with specific field assignments (.initialization_phase, .execution_phase, and .source) * • Context context.status replaced with specific field assignments (.initialization_phase, .execution_phase, and .source) * • Context context.status replaced with specific field assignments (.initialization_phase, .execution_phase, and .source) * - * - * • Context context.status replaced with specific field assignments (.initialization_phase, .execution_phase, and .source) * - * - * - * - * - * • Context context.status replaced with specific field assignments (.initialization_phase, .execution_phase, and .source)
* - * - * - * - * - * - * - * - * - * - * - * - * - * - * • Log LogCondition - subset of ContextFlags used to specified logPref • Context ContextFlags - implemented as common set of context flags for: - initialization - execution tracking - logging ContextStatus - aliases to ContextFlags (for backward compatibility) * • Log LogCondition - subset of ContextFlags used to specified logPref • Context ContextFlags - implemented as common set of context flags for: - initialization - execution tracking - logging ContextStatus - aliases to ContextFlags (for backward compatibility) * • Log LogCondition - subset of ContextFlags used to specified logPref • Context ContextFlags - implemented as common set of context flags for: - initialization - execution tracking - logging ContextStatus - aliases to ContextFlags (for backward compatibility) * - * - * - * - * - * • Context context.status replaced with specific field assignments (.initialization_phase, .execution_phase, and .source) * • Context context.status replaced with specific field assignments (.initialization_phase, .execution_phase, and .source) * • Context context.status replaced with specific field assignments (.initialization_phase, .execution_phase, and .source) * - * - * • Context context.status replaced with specific field assignments (.initialization_phase, .execution_phase, and .source) * - * - * - * - * - * - * Merge branches 'devel' and 'refactor/context/structured' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/context/structured # Conflicts: # .idea/runConfigurations/Tests.xml # Scripts/McClure.py * Merge branches 'devel' and 'refactor/context/structured' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/context/structured # Conflicts: # .idea/runConfigurations/Tests.xml # Scripts/McClure.py * - * - * • Context - consolidated init_status into context.initialization_status * • Context - consolidated init_status into context.initialization_status * • Context - consolidated init_status into context.initialization_status
- initialization_status.UNSET -> initialization_status.INITALIZING where appropriate - delete InitStatus class
Cherry-picked from devel-llvm: 1dcca60
* - * - * - * - * • Environment added _parse_input_labels() and _parse_target_labels() methods run(): modified to use _parse_input_labels and _parse_target_labels * • Environment added _parse_input_labels() and _parse_target_labels() methods run(): modified to use _parse_input_labels and _parse_target_labels * • Environment added _parse_input_labels() and _parse_target_labels() methods run(): modified to use _parse_input_labels and _parse_target_labels * - * - * - * - * - * • Mechanism added input_labels and output_labels propoerties added _get_state_value_labels() method * • Merged with devel
* - * - * - * - * • Environment added _parse_input_labels() and _parse_target_labels() methods run(): modified to use _parse_input_labels and _parse_target_labels * • Environment added _parse_input_labels() and _parse_target_labels() methods run(): modified to use _parse_input_labels and _parse_target_labels * • Environment added _parse_input_labels() and _parse_target_labels() methods run(): modified to use _parse_input_labels and _parse_target_labels * - * - * - * - * - * - * • Mechanism added input_labels and output_labels propoerties added _get_state_value_labels() method * • Merged with devel * • Environment _parse_input_labels(): added error messages * • Environment _parse_input_labels(): added error messages * • Environment Run: removed _parse_target_labels (they are just the input_labels for a TARGET Mechanism • Mechanism docstring revs for INPUT_LABELS_DICDT and OUTPUT_LABELS_DICT
…n_ids - Conditions are no longer dependent on Schedulers, instead they can be checked for satisfaction with any Scheduler and any execution_id - must now provide a Scheduler and optionally execution_id (will use the Scheduler's default execution_id if not specified) to satisfaction call (typically determined contextually - user interface should not change under conceivably normal applications)
* feat/scheduling/decouple-conditions-scheduler: scheduling: decouple Scheduler and Condition, allow multiple execution_ids utilites: get method to prune unused args from a function from composition branch
* Fix/system/learning ends before terminal (#685) * • System _instantiate_learning_graph(): fixed bug in which learning failed to be instantiated for a System in which the last Mechanism in a learning sequence was not the TERMINAL Mechanism of the System. * • System _instantiate_learning_graph(): fixed bug in which learning failed to be instantiated for a System in which the last Mechanism in a learning sequence was not the TERMINAL Mechanism of the System. * • Scripts/Examples Rumelhart Semantic Network: updated with step function * Revert "Fix/system/learning ends before terminal (#685)" This reverts commit a75aeb0. * • Environment Run: removed _parse_target_labels (they are just the input_labels for a TARGET Mechanism • Mechanism docstring revs for INPUT_LABELS_DICDT and OUTPUT_LABELS_DICT * - * - * - * - * - * • Component - _execute: added **kwargs argument, passed to call to function to accomodate LearningMechanism that uses this • AutoassociativeLearningMechanism - _execute calls super(LearningMechanism, self) to skip Learning • LearningMechanism: _ execute calls super()._execute with **kwargs * • Component - _execute: added **kwargs argument, passed to call to function to accomodate LearningMechanism that uses this • AutoassociativeLearningMechanism - _execute calls super(LearningMechanism, self) to skip Learning • LearningMechanism: _ execute calls super()._execute with **kwargs • PrecictionMechanism: _execute calls super()._execute * • Component - _execute: added **kwargs argument, passed to call to function to accomodate LearningMechanism and EVCControlMechanism, the functions for which expect additional arguments • AutoassociativeLearningMechanism - _execute calls super(LearningMechanism, self) to skip Learning • LearningMechanism: _ execute calls super()._execute with **kwargs • PrecictionMechanism: _execute calls super()._execute * • Component - _execute: added **kwargs argument, passed to call to function to accomodate LearningMechanism and EVCControlMechanism, the functions for which expect additional arguments • AutoassociativeLearningMechanism - _execute calls super(LearningMechanism, self) to skip Learning • LearningMechanism: _ execute calls super()._execute with **kwargs • PrecictionMechanism: _execute calls super()._execute
docstring: added explanation of assignment of target labels to output_labels_dict for Mechanism that projects to TARGET Mechanism
* • Context docstring: added for module and for Context class _get_context_string replaced with get_context_string (removed underscore) * • Context docstring: added for module and for Context class flags_string: added as an attribute
* • Environment Run: removed _parse_target_labels (they are just the input_labels for a TARGET Mechanism • Mechanism docstring revs for INPUT_LABELS_DICDT and OUTPUT_LABELS_DICT * - * - * - * Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into JDC_WORKING # Conflicts: # psyneulink/components/mechanisms/mechanism.py * • System - replaced self.initialization_status with self.context.initialization_status * • System - replaced self.initialization_status with self.context.initialization_status • MappingProjection - _execute: got rid of test for system * • System - replaced self.initialization_status with self.context.initialization_status • MappingProjection - _execute: got rid of test for system • Log LogCondition: removed _get_context_string * • System - replaced self.initialization_status with self.context.initialization_status • MappingProjection - _execute: got rid of test for system • Log LogCondition: _get_context_string -> _get_log_condition_string
…it crossed the negative threshold
…t does not correspond to the actual results of the mechanism
Fix/ddm/threshold
…id zero division) - also add test
…t target value to be repeated
…spec-bug fixing bug in looking up target values for learning which caused firs…
* • State, Keyword: kwStateName -> STATE_NAME * • State, Keyword: kwStateName -> STATE_NAME kwStatePrefs -> STATE_PREFS * • State, Keyword: kwStateName -> STATE_NAME kwStatePrefs -> STATE_PREFS kwStateContext -> STATE_CONTEXT * - * - * - * • Component check_args: added assignment of ContextFlag.VALIDATING during validation * - * - * - * - * - * - * • Project: - implement all assignments to and tests against context regarding initialization and execution converted to context attribute - still need to implement message passing of context.source in place of context string for COMMAND_LINE and other circumstances (such as ADD_STATES, SET_ATTRIBUTES, RUN, etc.)
- ROOD = ReadOnlyOrderedDict - if you passed in function_params as an entry in params, this dictionary would get assigned to object's function_params attribute, which could result in coupling and unintended changes
- instead of copying some attributes (like an object's owner for instance), just copy the reference during a deepcopy
…s fallback for params[FUNCTION] assignment
- don't automatically make a copy of assigned Functions if not necessary (only copies an instance of a Function when it already has an owner) - when creating a default instance of a function, pass in its ClassDefaults as arguments - make Process and System have a property for self.function that refers to self.execute instead of setting this in the constructor - refactor constructor function arguments - ensure that Component has access to the actual Function instance (if specified) used to instantiate - assign defaults at the Component level - replace call using paramsCurrent to params (paramsCurrent[FUNCTION]) doesn't exist anymore - ParamsDict no longer attempts to store and retrieve 'function' as an attribute on its owner - .function attribute is now a property when not specified as a method - add ComponentError for unsupported function type in Component._instantiate_function - ensure that Function classes get instance_defaults.value assigned by executing themselves in instantiate_value - update attributes dict to safely handle case in which it is called before function params are assigned - pass function argument to pre-function instantiation methods for the purpose of it being known when instantiating parameter states - update ParameterState creation to use passed in function to construct - OutputState: update documentation examples to proper function form - pass Function object not Function.function method to arguments - make function_params a property that refers to user_params['function_params'] instead of trying to sync them manually - add capability to increase a function's dimension to its owning Component's dimension if it's specified as such tests: - update some general formatting - update tests with now wrong/unnecessary extra variable specifications on Functions - update based on random number gen shift: differentials are based off of devel at cdce0f1, and represent how many fewer random seed calls occur before the first execute call in a test. Listed beside each test are the differentials, and the function of module numpy.random. So, at this commit, to get the numbers present on cdce0f1, if a test is listed below as test: -x, f then at the beginning of the test, run np.random.f() x times. - test_reinforcement: -1, random - test_DDM_noise_0_5: -1, normal - test_DDM_noise_2_0: -1, normal - test_integrator_simple_noise_fn: -1, normal - test_integrator_simple_noise_fn_var_list: -7, normal - test_integrator_accumulator_noise_fn: -1, normal - test_integrator_accumulator_noise_fn_var_list: -7, normal - test_integrator_constant_noise_fn_var_list: -6, normal - test_integrator_adaptive_noise_fn: -1, normal - test_integrator_adaptive_noise_fn_var_list: -7, normal - test_integrator_drift_diffusion_noise_val: -1, normal validation: - start coding for a centralized and modular validation scheme - refactor Component function validation to remove redundancy and be compatible with function argument passed up hierarchy - update DDM validation to allow function to be an instance of the required types, not just a class - refactor validation of function argument and values of Components - Integrator Functions: update rate validation - validate against Integrator instance_defaults.variable if present - otherwise set instance_defaults.variable - update some tests to reflect the new restriction where when specified, a mechanism's variable must exactly match its function's variable - update tests to reflect new handling of above errors and restriction
Refac/function/init
* • Project: - implement all assignments to and tests against context regarding initialization and execution converted to context attribute - still need to implement message passing of context.source in place of context string for COMMAND_LINE and other circumstances (such as ADD_STATES, SET_ATTRIBUTES, RUN, etc.) * • Project: - implement message passing of context.source in place of context * - context = ContextFlags.CONSTRUCTOR complete * - * - * - partway through implementing all context arguments as ContextFlags * - partway through implementing all context arguments as ContextFlags * - partway through implementing all context arguments as ContextFlags * - partway through implementing all context arguments as ContextFlags * cleaning up use of helper methods in FHNIntegratorFunction and updating context check to ContextFlags * - partway through implementing all context arguments as ContextFlags * - * - * - * - * - * - * - * - passes all tests * Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/context/source_devel # Conflicts: # psyneulink/components/component.py # psyneulink/components/functions/function.py # psyneulink/components/mechanisms/adaptive/control/controlmechanism.py # psyneulink/components/mechanisms/adaptive/control/defaultcontrolmechanism.py # psyneulink/components/mechanisms/adaptive/gating/gatingmechanism.py # psyneulink/components/mechanisms/adaptive/learning/learningauxiliary.py # psyneulink/components/mechanisms/adaptive/learning/learningmechanism.py # psyneulink/components/mechanisms/mechanism.py # psyneulink/components/mechanisms/processing/compositioninterfacemechanism.py # psyneulink/components/mechanisms/processing/defaultprocessingmechanism.py # psyneulink/components/mechanisms/processing/integratormechanism.py # psyneulink/components/mechanisms/processing/objectivemechanism.py # psyneulink/components/mechanisms/processing/processingmechanism.py # psyneulink/components/mechanisms/processing/transfermechanism.py # psyneulink/components/projections/modulatory/controlprojection.py # psyneulink/components/projections/modulatory/gatingprojection.py # psyneulink/components/projections/modulatory/learningprojection.py # psyneulink/components/projections/modulatory/modulatoryprojection.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/pathway/pathwayprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/shellclasses.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # psyneulink/globals/context.py # psyneulink/globals/environment.py # psyneulink/globals/log.py # psyneulink/library/mechanisms/adaptive/learning/autoassociativelearningmechanism.py # psyneulink/library/mechanisms/processing/integrator/ddm.py # psyneulink/library/mechanisms/processing/objective/comparatormechanism.py # psyneulink/library/mechanisms/processing/transfer/lca.py # psyneulink/library/mechanisms/processing/transfer/recurrenttransfermechanism.py # psyneulink/library/projections/pathway/autoassociativeprojection.py * Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into refactor/context/source_devel # Conflicts: # psyneulink/components/component.py # psyneulink/components/functions/function.py # psyneulink/components/mechanisms/adaptive/control/controlmechanism.py # psyneulink/components/mechanisms/adaptive/control/defaultcontrolmechanism.py # psyneulink/components/mechanisms/adaptive/gating/gatingmechanism.py # psyneulink/components/mechanisms/adaptive/learning/learningauxiliary.py # psyneulink/components/mechanisms/adaptive/learning/learningmechanism.py # psyneulink/components/mechanisms/mechanism.py # psyneulink/components/mechanisms/processing/compositioninterfacemechanism.py # psyneulink/components/mechanisms/processing/defaultprocessingmechanism.py # psyneulink/components/mechanisms/processing/integratormechanism.py # psyneulink/components/mechanisms/processing/objectivemechanism.py # psyneulink/components/mechanisms/processing/processingmechanism.py # psyneulink/components/mechanisms/processing/transfermechanism.py # psyneulink/components/projections/modulatory/controlprojection.py # psyneulink/components/projections/modulatory/gatingprojection.py # psyneulink/components/projections/modulatory/learningprojection.py # psyneulink/components/projections/modulatory/modulatoryprojection.py # psyneulink/components/projections/pathway/mappingprojection.py # psyneulink/components/projections/pathway/pathwayprojection.py # psyneulink/components/projections/projection.py # psyneulink/components/shellclasses.py # psyneulink/components/states/parameterstate.py # psyneulink/components/states/state.py # psyneulink/globals/context.py # psyneulink/globals/environment.py # psyneulink/globals/log.py # psyneulink/library/mechanisms/adaptive/learning/autoassociativelearningmechanism.py # psyneulink/library/mechanisms/processing/integrator/ddm.py # psyneulink/library/mechanisms/processing/objective/comparatormechanism.py # psyneulink/library/mechanisms/processing/transfer/lca.py # psyneulink/library/mechanisms/processing/transfer/recurrenttransfermechanism.py # psyneulink/library/projections/pathway/autoassociativeprojection.py * - * - * - * - * - * - * - * • LCA, DDM: - _execute: self.function -> super._execute() * • InputState, ParameterState: - _execute: self.function -> super._execute() * - * - * - * • Context context argument of all methods replaced with ContextFlag self.context.string used for human-readable descriptive information
* • Project ADD_STATES removed * • InputState __init__: added combine arg that allows operation argument of LinearCombination (the default functon) to be specified * • InputState __init__: added combine arg that allows operation argument of LinearCombination (the default functon) to be specified * -
* • Project ADD_STATES removed * • InputState __init__: added combine arg that allows operation argument of LinearCombination (the default functon) to be specified * • InputState __init__: added combine arg that allows operation argument of LinearCombination (the default functon) to be specified * - * - * - * • LinearCombination - function: fixed problem with shape of weights and/or exponents * • LinearCombination - function: fixed problem with shape of weights and/or exponents * - * transfer mechanism's execute method now calls its function with the entire variable unless the function is a NormalizingFunction (useful for UDFs) * - * - * - * allowing transfer mechanism to have a UDF as its function and removing references to self.variable * pytests for transfer mechanisms with user defined functions * breaking TransferMechanism's _execute method up into helper methods in order to make LCA less repetitive * removing print statement from transfer mech pytest * • LCA - _execute: eliminated (by consolidating remaining bits into helper methods
* • LCA - _execute: eliminated (by consolidating remaining bits into helper methods * • MaskMappingProjection - implemented as subclass of MappingProjection * • MaskMappingProjection - implemented as subclass of MappingProjection
…nism_param - not intended for looking up 'variable'
…ble-exception adding exceptions to get_current_function_param and get_current_mecha…
MaskedMappingProjection: added rst files
* devel: Feat/projections/masked mapping projection (#775) adding exceptions to get_current_function_param and get_current_mechanism_param - not intended for looking up 'variable' Feat/projections/masked mapping projection (#771) • LCA (#770) • LCA (#769) Refactor/mechanism/transfermechanism (#768) Fix default_variable bug (#767) Feat/inputstate/combine (#766) Refactor/context/source (#765) Defaults: ensure that function attr appears when examining Defaults Rewrite Function instantiation: Component: create fewer instances during init when function arg is a class LinearMatrix: make keyword method static to reflect how it is used refactor/rename _variable_not_specified to be more generic, using enum Defaults: add enum to denote flexibility of assignments Component: add class method to get new param class defaults Defaults: add ClassDefaults.function to several classes, and use it as fallback utilities: add function to detect if obj is an instance or a subclass of a class Component: override __deepcopy__ method to use shared items parsing: add method to parse function variable from variable imports: pycharm-optimize to avoid unnecessary circularities Params: copy dict/ROODs nested in params arguments to avoid side effects Refactor/context/set and test (#762) fixing bug in looking up target values for learning which caused first target value to be repeated LinearCombination, Reduce: handle negative exponents during init (avoid zero division) Functions: simplify noise validation adding a note to the ddm plot() documentation to clarify that the plot does not correspond to the actual results of the mechanism fixing drift diffusion integrator bug - returned threshold even when it crossed the negative threshold Fix/misc/misc (#759) PredictionErrorMechanism: correct infinite recursion in _execute Docs/context/context (#757) • Mechanism (#756) Refactor/mechanisms/ execute (#754) LearningAuxilliary: rename to LearningAuxiliary (correct double l typo) scheduling: decouple Scheduler and Condition, allow multiple execution_ids utilites: get method to prune unused args from a function from composition branch Feat/mechanism/input target lable dicts (#752) testing: Resolve leftover merge conflicts, fixes #747 testing: correct pytest setup ovewrite, losing some settings Feat/mechanism/input target label dicts (#751) Scheduling: fix bug where termination conditions persisted across calls to run tests,function/LinearCombination: Add tests with absent parameters test,function/LinearCombination: Rename second test function to prevent overwriting results • Context (#746) Refactor/context/deprecate init status (#745) Refactor/context/structured (#744) Fix/function/stability (#743) • IntegratorMechanism (#742)
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Feat/projections/masked mapping projection (Feat/projections/masked mapping projection #775)
adding exceptions to get_current_function_param and get_current_mechanism_param - not intended for looking up 'variable'
Feat/projections/masked mapping projection (Feat/projections/masked mapping projection #771)
LCA (Tests/inputstates/combine arg #770)
LCA (Refactor/inputstate/combine validation #769)
Refactor/mechanism/transfermechanism (Refactor/mechanism/transfermechanism #768)
Fix default_variable bug (Fix default_variable bug #767)
Feat/inputstate/combine (Feat/inputstate/combine #766)
Refactor/context/source (Refactor/context/source #765)
Defaults: ensure that function attr appears when examining Defaults
Rewrite Function instantiation:
Component: create fewer instances during init when function arg is a class
LinearMatrix: make keyword method static to reflect how it is used
refactor/rename _variable_not_specified to be more generic, using enum
Defaults: add enum to denote flexibility of assignments
Component: add class method to get new param class defaults
Defaults: add ClassDefaults.function to several classes, and use it as fallback
utilities: add function to detect if obj is an instance or a subclass of a class
Component: override deepcopy method to use shared items
parsing: add method to parse function variable from variable
imports: pycharm-optimize to avoid unnecessary circularities
Params: copy dict/ROODs nested in params arguments to avoid side effects
Refactor/context/set and test (Refactor/context/set and test #762)
fixing bug in looking up target values for learning which caused first target value to be repeated
LinearCombination, Reduce: handle negative exponents during init (avoid zero division)
Functions: simplify noise validation
adding a note to the ddm plot() documentation to clarify that the plot does not correspond to the actual results of the mechanism
fixing drift diffusion integrator bug - returned threshold even when it crossed the negative threshold
Fix/misc/misc (Fix/misc/misc #759)
PredictionErrorMechanism: correct infinite recursion in _execute
Docs/context/context (Docs/context/context #757)
Mechanism (docs/mechanism/targets_in_output_labels_dict #756)
Refactor/mechanisms/ execute (Refactor/mechanisms/ execute #754)
LearningAuxilliary: rename to LearningAuxiliary (correct double l typo)
scheduling: decouple Scheduler and Condition, allow multiple execution_ids
utilites: get method to prune unused args from a function from composition branch
Feat/mechanism/input target lable dicts (Feat/mechanism/input target lable dicts #752)
testing: Resolve leftover merge conflicts, fixes Solve merge conflict in test_composition.py #747
testing: correct pytest setup ovewrite, losing some settings
Feat/mechanism/input target label dicts (Feat/mechanism/input target label dicts #751)
Scheduling: fix bug where termination conditions persisted across calls to run
tests,function/LinearCombination: Add tests with absent parameters
test,function/LinearCombination: Rename second test function to prevent overwriting results
Context (Removed UNSET and InitStatus #746)
Refactor/context/deprecate init status (Refactor/context/deprecate init status #745)
Refactor/context/structured (Refactor/context/structured #744)
Fix/function/stability (Fix/function/stability #743)
IntegratorMechanism (• IntegratorMechanism #742)