New version #338

KristenManning · 2017-06-23T19:24:29Z

No description provided.

…st Script - control_signal -> control_signal_params • State - _instantiate_projection_to_state: updated to accomodate GatingProjection

- CombinationFunction: added support for mulitplicative_param and additive_param - Reduce: added scale and offset params added mulitplicative_param and additive_param - LinearCombination: added mulitplicative_param and additive_param

- _parse_gating_signal_spec moved from GatingMechanism to GatingSignal • GatingSignal, GatingMechanism, ControlSignal, ControlMechanism - docstring updates

…ator-functions adding rate array/list tests back in now that rate bug is fixed

# Conflicts: # PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/ControlMechanism.py # TODO List.py

- added modulation attribute • GatingSignal - set default value of modulation attribute to owner's value

- control_signal -> control_signal_params

modulatory_signal_params -> gating_signal_params

…o Control_modulate_paramstate_function

- _instantiate_projection() updated

- added modulation argument/attribute

- afferents -> afferents + mod_afferents

- crashing in DDM Test script

…ersity/PsyNeuLink into devel

• Multilayer Learning Test Script [WITH GATING] - reverted matrix assignment to Middle_Weights to standard one

Gating restored

* • Multilayer Learning Test Script [WITH GATING] - added cases for multiple GatingProjections per GatingSignal * • Gating Signal - _parse_gating_signal_spec(): allow NAME entry of GatingSignal specification dictionary to override use of key as name of GatingSignal (examples in Multilayer Learning Test Script [WITH GATING])

* • Project - TransmssiveProjection* -> PathwayProjection* * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections • ModulatoryProjection docstring * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections • ModulatoryProjection docstring • State docstring * • LearningMechanism - docstring * • LearningMechanism - implemented self.learned_projections property * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections WORKING ON: - move ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections - moved ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items WORKING ON: - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections - moved ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items WORKING ON: - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * - * - * - * - * • Moved all modulatory outputStates (LearningSignal, ControlSignal and GatingSignal) under ModulatoryOutputStates * • ModulatoryOutputStates -> ModulatorySignals * • ModulatorySignal - implemented - docstring • rst files; added: ModulatoryProjection ModulatorySignal, LearningSignal, ControlSignal, GatingSignal * • ModulatorySignal - implemented - docstring • rst files; added: ModulatoryProjection ModulatorySignal, LearningSignal, ControlSignal, GatingSignal * • ControlSignal - __init__(): deleted self.reference_value = reference_value * • ModulatorySignals - moved modulation to ModulatorySignal.__init__() * • ModulatorySignals - moved default assignment of _modulation to owner to ModulatorySignals * - * • ControlMechanism - subclassed to AdapativeMechanism_Base * • ControlMechanism - subclassed to AdapativeMechanism_Base * • State - update(): implemented handling of Modulation.OVERRIDE and Modulation.DISABLE * • State - docstring * • Project - afferents -> path_afferents * - * reorder tested (test_reinforcement.py) output states for learning mechanism in accordance with branch changes * • * • * • ModulatorySignals implemented deferred_init on ModulatorySignal and all subclasses * • ModulatorySignals - implemented deferred_init on ModulatorySignal and subclasses • ControlSignal - specify ControlSignal in tuple * • ModulatorySignals - implemented deferred_init on ModulatorySignal and subclasses • ControlSignal - specify ControlSignal in tuple * • ModulatorySignals - docstrings * - * • ControlMechanism - _take_over_as_default_controller -> _assign_as_controller * • ScratchPad - testing examples of ControlSignal specifications * • ScratchPad - examples under TEST Modulation now all work * -

…hecked by State's update()

…Link into feat/ignore-execution-id

…ut to a mechanism that is executed outside of a process/system goes]

…elf.variable (not self.input_state.value)

…g process hack, updating some caught errors, and indexing into zeroth element of returned value -- bug??] currently passing 111/111 pytests

…projection between them WITHOUT specifying a process

- Various typos

….input_state.path_afferents != [] --> _update_input_states(); else --> _assign_input; (allows you to execute mechanisms outside of process with default input values)

…so that if you execute a mechanism without input, it uses default input value [not sure if this is correct]

…ifying input to the first one (uses defaults) AND outside of a system or process

* • Project - TransmssiveProjection* -> PathwayProjection* * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections • ModulatoryProjection docstring * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections • ModulatoryProjection docstring • State docstring * • LearningMechanism - docstring * • LearningMechanism - implemented self.learned_projections property * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections WORKING ON: - move ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections - moved ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items WORKING ON: - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections - moved ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items WORKING ON: - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * - * - * - * - * • Moved all modulatory outputStates (LearningSignal, ControlSignal and GatingSignal) under ModulatoryOutputStates * • ModulatoryOutputStates -> ModulatorySignals * • ModulatorySignal - implemented - docstring • rst files; added: ModulatoryProjection ModulatorySignal, LearningSignal, ControlSignal, GatingSignal * • ModulatorySignal - implemented - docstring • rst files; added: ModulatoryProjection ModulatorySignal, LearningSignal, ControlSignal, GatingSignal * • ControlSignal - __init__(): deleted self.reference_value = reference_value * • ModulatorySignals - moved modulation to ModulatorySignal.__init__() * • ModulatorySignals - moved default assignment of _modulation to owner to ModulatorySignals * - * • ControlMechanism - subclassed to AdapativeMechanism_Base * • ControlMechanism - subclassed to AdapativeMechanism_Base * • State - update(): implemented handling of Modulation.OVERRIDE and Modulation.DISABLE * • State - docstring * • Project - afferents -> path_afferents * - * reorder tested (test_reinforcement.py) output states for learning mechanism in accordance with branch changes * • * • * • ModulatorySignals implemented deferred_init on ModulatorySignal and all subclasses * • ModulatorySignals - implemented deferred_init on ModulatorySignal and subclasses • ControlSignal - specify ControlSignal in tuple * • ModulatorySignals - implemented deferred_init on ModulatorySignal and subclasses • ControlSignal - specify ControlSignal in tuple * • ModulatorySignals - docstrings * - * • ControlMechanism - _take_over_as_default_controller -> _assign_as_controller * • ScratchPad - testing examples of ControlSignal specifications * • ScratchPad - examples under TEST Modulation now all work * - * • ControlMechanism / ParameterState - docstring revisions * • ControlMechanism / ParameterState - docstring revisions * - * • ModulatorySignal - added figure * • ModulatorySignal - added figure * - * • ParameterState - docstring revisions * - * - * - * - * -

* • Project - TransmssiveProjection* -> PathwayProjection* * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections • ModulatoryProjection docstring * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections • ModulatoryProjection docstring • State docstring * • LearningMechanism - docstring * • LearningMechanism - implemented self.learned_projections property * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections WORKING ON: - move ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections - moved ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items WORKING ON: - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections - moved ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items WORKING ON: - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * - * - * - * - * • Moved all modulatory outputStates (LearningSignal, ControlSignal and GatingSignal) under ModulatoryOutputStates * • ModulatoryOutputStates -> ModulatorySignals * • ModulatorySignal - implemented - docstring • rst files; added: ModulatoryProjection ModulatorySignal, LearningSignal, ControlSignal, GatingSignal * • ModulatorySignal - implemented - docstring • rst files; added: ModulatoryProjection ModulatorySignal, LearningSignal, ControlSignal, GatingSignal * • ControlSignal - __init__(): deleted self.reference_value = reference_value * • ModulatorySignals - moved modulation to ModulatorySignal.__init__() * • ModulatorySignals - moved default assignment of _modulation to owner to ModulatorySignals * - * • ControlMechanism - subclassed to AdapativeMechanism_Base * • ControlMechanism - subclassed to AdapativeMechanism_Base * • State - update(): implemented handling of Modulation.OVERRIDE and Modulation.DISABLE * • State - docstring * • Project - afferents -> path_afferents * - * reorder tested (test_reinforcement.py) output states for learning mechanism in accordance with branch changes * • * • * • ModulatorySignals implemented deferred_init on ModulatorySignal and all subclasses * • ModulatorySignals - implemented deferred_init on ModulatorySignal and subclasses • ControlSignal - specify ControlSignal in tuple * • ModulatorySignals - implemented deferred_init on ModulatorySignal and subclasses • ControlSignal - specify ControlSignal in tuple * • ModulatorySignals - docstrings * - * • ControlMechanism - _take_over_as_default_controller -> _assign_as_controller * • ScratchPad - testing examples of ControlSignal specifications * • ScratchPad - examples under TEST Modulation now all work * - * • ControlMechanism / ParameterState - docstring revisions * • ControlMechanism / ParameterState - docstring revisions * - * • ModulatorySignal - added figure * • ModulatorySignal - added figure * - * • ParameterState - docstring revisions * - * - * - * - * • LearningProjection, ControlProjection, GatingProjection - docstring revisions * - * - * • ModulatorySignal - added Modulation_Detail figure - docstring revisions * • ModulatorySignal more docstring revisions * • Component - make_property(): added assignment of attribute value to ParameterState.variable • ModulatorySignal more docstring revisions * • Component - make_property(): added assignment of attribute value to ParameterState.variable • ModulatorySignal more docstring revisions

* • Project - TransmssiveProjection* -> PathwayProjection* * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections • ModulatoryProjection docstring * • Project - TransmssiveProjection* -> PathwayProjection* - trans_projections -> pathway_projections • ModulatoryProjection docstring • State docstring * • LearningMechanism - docstring * • LearningMechanism - implemented self.learned_projections property * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections WORKING ON: - move ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections - moved ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items WORKING ON: - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * • LearningMechanism - fixed learning_signals to store LearningSignal outputStates rather than LearningProjections - moved ERROR_SIGNAL to first (i.e., primary) output_state and mention in docstring, and append learning_signals as subsequent items WORKING ON: - remove reference in docstring to LEARNING_SIGNAL as name of solo LearningSignal - fix naming of LearningSignals to reference name of MappingProjection, not just its matrix * - * - * - * - * • Moved all modulatory outputStates (LearningSignal, ControlSignal and GatingSignal) under ModulatoryOutputStates * • ModulatoryOutputStates -> ModulatorySignals * • ModulatorySignal - implemented - docstring • rst files; added: ModulatoryProjection ModulatorySignal, LearningSignal, ControlSignal, GatingSignal * • ModulatorySignal - implemented - docstring • rst files; added: ModulatoryProjection ModulatorySignal, LearningSignal, ControlSignal, GatingSignal * • ControlSignal - __init__(): deleted self.reference_value = reference_value * • ModulatorySignals - moved modulation to ModulatorySignal.__init__() * • ModulatorySignals - moved default assignment of _modulation to owner to ModulatorySignals * - * • ControlMechanism - subclassed to AdapativeMechanism_Base * • ControlMechanism - subclassed to AdapativeMechanism_Base * • State - update(): implemented handling of Modulation.OVERRIDE and Modulation.DISABLE * • State - docstring * • Project - afferents -> path_afferents * - * reorder tested (test_reinforcement.py) output states for learning mechanism in accordance with branch changes * • * • * • ModulatorySignals implemented deferred_init on ModulatorySignal and all subclasses * • ModulatorySignals - implemented deferred_init on ModulatorySignal and subclasses • ControlSignal - specify ControlSignal in tuple * • ModulatorySignals - implemented deferred_init on ModulatorySignal and subclasses • ControlSignal - specify ControlSignal in tuple * • ModulatorySignals - docstrings * - * • ControlMechanism - _take_over_as_default_controller -> _assign_as_controller * • ScratchPad - testing examples of ControlSignal specifications * • ScratchPad - examples under TEST Modulation now all work * - * • ControlMechanism / ParameterState - docstring revisions * • ControlMechanism / ParameterState - docstring revisions * - * • ModulatorySignal - added figure * • ModulatorySignal - added figure * - * • ParameterState - docstring revisions * - * - * - * - * • LearningProjection, ControlProjection, GatingProjection - docstring revisions * - * - * • ModulatorySignal - added Modulation_Detail figure - docstring revisions * • ModulatorySignal more docstring revisions * • Component - make_property(): added assignment of attribute value to ParameterState.variable • ModulatorySignal more docstring revisions * • Component - make_property(): added assignment of attribute value to ParameterState.variable • ModulatorySignal more docstring revisions * Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into feat_set_parameterState_variable_to_param_val # Conflicts: # PsyNeuLink/Components/States/ModulatorySignals/ModulatorySignal.py # PsyNeuLink/Components/States/State.py # docs/build/html/Function.html # docs/build/html/LearningProjection.html # docs/build/html/Mechanism.html # docs/build/html/OutputState.html # docs/build/html/ParameterState.html # docs/build/html/Process.html # docs/build/html/State.html # docs/build/html/System.html # docs/build/html/TransferMechanism.html # docs/build/html/genindex.html # docs/build/html/objects.inv # docs/build/html/searchindex.js * Merge branch 'devel' of https://github.com/PrincetonUniversity/PsyNeuLink into feat_set_parameterState_variable_to_param_val # Conflicts: # PsyNeuLink/Components/States/ModulatorySignals/ModulatorySignal.py # PsyNeuLink/Components/States/State.py # docs/build/html/Function.html # docs/build/html/LearningProjection.html # docs/build/html/Mechanism.html # docs/build/html/OutputState.html # docs/build/html/ParameterState.html # docs/build/html/Process.html # docs/build/html/State.html # docs/build/html/System.html # docs/build/html/TransferMechanism.html # docs/build/html/genindex.html # docs/build/html/objects.inv # docs/build/html/searchindex.js * • ModulatorySignal - docstring revs * • ModulatorySignal - docstring revs

- Various typos

…n-id Feat/ignore execution

Tutorial fixes

jdcpni and others added 30 commits May 29, 2017 14:37

• ControlProjection, ControlMechanism, EVC Sysem Laming Validation Te…

f0be717

…st Script - control_signal -> control_signal_params • State - _instantiate_projection_to_state: updated to accomodate GatingProjection

-

1e72d8b

-

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• Function

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- CombinationFunction: added support for mulitplicative_param and additive_param - Reduce: added scale and offset params added mulitplicative_param and additive_param - LinearCombination: added mulitplicative_param and additive_param

• Function

6ac8f6b

- CombinationFunction: added support for mulitplicative_param and additive_param - Reduce: added scale and offset params added mulitplicative_param and additive_param - LinearCombination: added mulitplicative_param and additive_param

-

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RUNS but NOT CORRECT

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WORKING

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-

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• GatingSignal, GatingMechanism

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- _parse_gating_signal_spec moved from GatingMechanism to GatingSignal • GatingSignal, GatingMechanism, ControlSignal, ControlMechanism - docstring updates

remove .idea from git tracking

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Merge branch 'GATING' into devel

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adding rate array/list tests back in now that rate bug is fixed

c00ac9b

Merge pull request #315 from PrincetonUniversity/feat/separate-integr…

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…ator-functions adding rate array/list tests back in now that rate bug is fixed

- interim on docstrings for GatingMechanism

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Merge branch 'GATING' into devel_upstream

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Merge branch 'GATING' into devel_upstream

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# Conflicts: # PsyNeuLink/Components/Mechanisms/AdaptiveMechanisms/ControlMechanisms/ControlMechanism.py # TODO List.py

• GatingMechanism

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- added modulation attribute • GatingSignal - set default value of modulation attribute to owner's value

• ControlProjection, ControlMechanism:

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- control_signal -> control_signal_params

-

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• GatingProjection, GatingMechanism

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modulatory_signal_params -> gating_signal_params

Merge branch 'devel' of github.com:PrincetonUniversity/PsyNeuLink int…

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…o Control_modulate_paramstate_function

-

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• State

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- _instantiate_projection() updated

• ControlSignal

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- added modulation argument/attribute

-

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-

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- EVC working but not RL

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• Process

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- afferents -> afferents + mod_afferents

- RL working;

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- crashing in DDM Test script

jdcpni and others added 28 commits June 15, 2017 16:30

Merge branch 'bug/gating/signal-mismatch' of github.com:PrincetonUniv…

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…ersity/PsyNeuLink into devel

Gating function restored

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• Multilayer Learning Test Script [WITH GATING] - reverted matrix assignment to Middle_Weights to standard one

Merge pull request #321 from jdcpni/devel

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Gating restored

updating devel to new gitignore and replacing idea folder

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adding dig prep file to top of branch so that dig works as expected.

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adding 'ignored_execution_id' option to Mechanism's execute() -- is c…

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…hecked by State's update()

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

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…Link into feat/ignore-execution-id

_assign_input method now updates self.variable [this is where the inp…

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…ut to a mechanism that is executed outside of a process/system goes]

updating transfer and ddm mechanisms to execute integrator fns with s…

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…elf.variable (not self.input_state.value)

updating mechanism pytests to match self.variable change. [eliminatin…

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…g process hack, updating some caught errors, and indexing into zeroth element of returned value -- bug??] currently passing 111/111 pytests

adding a pytest that demonstrates how to execute 2 mechanisms with a …

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…projection between them WITHOUT specifying a process

- Updated tutorial to run on devel

4ac6f58

- Various typos

adding an extra check to mechanism input state assignments -- if self…

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….input_state.path_afferents != [] --> _update_input_states(); else --> _assign_input; (allows you to execute mechanisms outside of process with default input values)

changing assignments of variableClassDefault and default_input_value …

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…so that if you execute a mechanism without input, it uses default input value [not sure if this is correct]

updating pytests to include executing a series of mechanisms w/o spec…

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…ifying input to the first one (uses defaults) AND outside of a system or process

- Updated tutorial to run on devel

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- Various typos

cleaning up tutorial

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merge conflicts

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fixing pytests for executing mechanisms

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Merge branch 'devel' into feat/ignore-execution-id

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Merge pull request #336 from PrincetonUniversity/feat/ignore-executio…

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…n-id Feat/ignore execution

Merge pull request #335 from PrincetonUniversity/tutorialFixes

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Tutorial fixes

Merge branch 'master' into temp/merge-master-into-devel

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KristenManning merged commit c7fb2f1 into master Jun 23, 2017

KristenManning deleted the temp/merge-master-into-devel branch June 23, 2017 19:26

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New version #338

New version #338

KristenManning commented Jun 23, 2017

New version #338

New version #338

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KristenManning commented Jun 23, 2017