Adding back externally defined constant dendritic delays and other small features and fixes for the compartmental feature. [WIP]#1241
Open
LeanderEwert wants to merge 446 commits intonest:mainfrom
Conversation
…t_versions_compat
…nt/updated-jinja-templates_fix
…plates_fix Maint/updated jinja templates fix
# Conflicts: # doc/running/running_nest_compartmental.rst # pynestml/cocos/co_co_cm_continuous_input_model.py # pynestml/cocos/co_cos_manager.py # pynestml/codegeneration/code_generator_utils.py # pynestml/codegeneration/nest_compartmental_code_generator.py # pynestml/codegeneration/printers/nest_variable_printer.py # pynestml/codegeneration/resources_nest_compartmental/cm_neuron/cm_neuroncurrents_@NEURON_NAME@.cpp.jinja2 # pynestml/codegeneration/resources_nest_compartmental/cm_neuron/cm_neuroncurrents_@NEURON_NAME@.h.jinja2 # pynestml/codegeneration/resources_nest_compartmental/cm_neuron/cm_tree_@NEURON_NAME@.cpp.jinja2 # pynestml/frontend/pynestml_frontend.py # pynestml/transformers/synapse_post_neuron_transformer.py # pynestml/utils/ast_mechanism_information_collector.py # pynestml/utils/ast_vector_parameter_setter_and_printer.py # pynestml/utils/continuous_input_processing.py # pynestml/utils/mechanism_processing.py # pynestml/utils/mechs_info_enricher.py # pynestml/utils/messages.py # tests/nest_compartmental_tests/resources/cm_default.nestml # tests/nest_compartmental_tests/resources/concmech.nestml # tests/nest_compartmental_tests/resources/continuous_test.nestml # tests/nest_compartmental_tests/test__cocos.py # tests/nest_compartmental_tests/test__concmech_model.py # tests/nest_compartmental_tests/test__continuous_input.py # tests/nest_compartmental_tests/test__interaction_with_disabled_mechanism.py
Co-authored-by: clinssen <c.linssen@fz-juelich.de>
Bencher Report
LeanderEwert
temporarily deployed
to
external
GitHub Actions
Inactive
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
5 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
In the normal nestml generation pipeline, the connection between the STDP synapse and the post-synaptic neuron has a minimum delay determined by the simulation resolution. Due to the STDP dynamics being directly integrated into the receptors in the compartmental case, we do not implicitly have such a delay and have initially not regarded it as necessary, as a delay should emerge from the presence of a compartmental dendritic structure. In a simple one-compartment model, this creates a small mismatch to the behaviour in the point neuron case due to the one-timestep delay missing.