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STDP synapse and IAF neuron generation for the compartmental feature [WIP] #1103
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STDP synapse and IAF neuron generation for the compartmental feature [WIP] #1103
Commits on Apr 27, 2022
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removed wrongfully added files
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replace old code resolving model name
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run NEST builder for compartmental models
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Merge remote-tracking branch 'origin/maint/updated-jinja-templates' i…
…nto maint/updated-jinja-templates_fix
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fix C++ syntax error in template
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fix C++ syntax error in template
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Commits on Apr 29, 2022
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Merge remote-tracking branch 'origin/maint/updated-jinja-templates' i…
…nto maint/updated-jinja-templates_fix
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Commits on May 3, 2022
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Merge remote-tracking branch 'pnbabu/rename_calibrate' into maint/upd…
…ated-jinja-templates_fix
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Merge remote-tracking branch 'upstream/master' into maint/updated-jin…
…ja-templates_fix
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fix code generation for compartmental models
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Commits on May 4, 2022
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Merge pull request WillemWybo#2 from clinssen/maint/updated-jinja-tem…
…plates_fix Maint/updated jinja templates fix
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fix code generation for compartmental models
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merge local_variables_reference_converter_fix and convert recordables…
… strings to nest Name
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Commits on Jun 23, 2022
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Merge remote-tracking branch 'upstream/master' into maint/updated-jin…
…ja-templates_fix
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move template files to new directory layout
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Commits on Jun 29, 2022
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Merge pull request WillemWybo#4 from clinssen/maint/updated-jinja-tem…
…plates_fix Maint/updated jinja templates fix
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Commits on Jul 8, 2022
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Commits on Jul 12, 2022
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Merge branch 'master' of https://github.com/nest/nestml into maint/up…
…dated-jinja-templates
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Commits on Jul 13, 2022
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Merge remote-tracking branch 'upstream/master' into maint/updated-jin…
…ja-templates_fix
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fix incorrect merge with upstream
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Commits on Aug 1, 2022
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add automatic NEST version detection and update CI
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Commits on Aug 4, 2022
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add NEST2 compatibility to nest_logarithmic_function_test
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fix CI and tests after adding automatic NEST version check
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move tests that use the NEST code generator to integration tests subd…
…irectory
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move tests that use the NEST code generator to integration tests subd…
…irectory
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fix NEST2/NEST3 compatibility in tests
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fix NEST2/NEST3 compatibility in tests
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Merge remote-tracking branch 'clinssen/nest_versions_compat' into nes…
…t_versions_compat
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fix NEST2/NEST3 compatibility in tests
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fix NEST2/NEST3 compatibility in tests
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Commits on Aug 8, 2022
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fix NEST2/NEST3 compatibility in tests
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fix CI and tests after adding automatic NEST version check
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fix CI and tests after adding automatic NEST version check
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run Jupyter notebooks only on master branch
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improve NEST version detection and compatibility
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improve NEST version detection and compatibility
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Merge remote-tracking branch 'origin/master' into nest_versions_compat
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Commits on Aug 10, 2022
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run NEST version detection in a separate process
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fix syntax in GitHub actions workflow file
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fix syntax in GitHub actions workflow file
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remove cron comment from GitHub Actions workflow file
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Commits on Aug 16, 2022
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Merge remote-tracking branch 'clinssen/nest_versions_compat' into mai…
…nt/updated-jinja-templates_fix
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Merge remote-tracking branch 'upstream/master' into maint/updated-jin…
…ja-templates_fix
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update compartmental model templates for NEST 3.3 and NEST-master com…
…patibility
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Merge remote-tracking branch 'upstream/master' into maint/updated-jin…
…ja-templates_fix
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Merge pull request WillemWybo#7 from clinssen/maint/updated-jinja-tem…
…plates_fix Maint/updated jinja templates fix
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remove multiprocessing version of call to _detect_nest_version from c…
…ompartmental_model_test.py as it creates issues on some systems
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Commits on Dec 22, 2022
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Merge remote-tracking branch 'upstream/master' into cm-post-printers
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fix compartmental models code generation after printers refactor
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Merge pull request WillemWybo#8 from clinssen/cm-post-printers
Fix compartmental models code generator after printers refactor
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Commits on Feb 2, 2023
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Shifted synapse ode processing from nest_code_generator.py to syns_pr…
…ocessing.py excluding explicitly formulated ODEs from syn_info. State of functionality: Succesfull codegeneration and compilation. Segfault during simulation.
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Commits on Feb 9, 2023
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Added gathering of specifically synapse related odes and functions. n…
…on synaptic functions dont break synapse models anymore. State of functionality: Almost fully working. Explicitly written ODEs for synapses not supported yet. (next up)
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Commits on Feb 14, 2023
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Added performance optimization feature, checking key parameters being…
… close to zero to skip calculation of step-function. State of functionality: Almost fully working. Explicitly written ODEs for synapses not supported yet. (next up)
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Commits on Feb 28, 2023
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Decorator syntax added to inline functions and mechanism differentiat…
…ion changed to be done by decorators. Concentration mechanism imlplementation and unification of mechanism info collection in progress.
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Decorator syntax added to inline functions and mechanism differentiat…
…ion changed to be done by decorators. Concentration mechanism imlplementation and unification of mechanism info collection in progress.
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Commits on Mar 9, 2023
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Merge remote-tracking branch 'nest-upstream/master' into origin/Leand…
…erEwert # Conflicts: # doc/fig/nestml_clip_art.png # doc/fig/synapse_conceptual.png # pynestml/codegeneration/resources_nest/point_neuron/directives/CommonPropertiesDictionaryReader.jinja2 # pynestml/frontend/frontend_configuration.py # pynestml/frontend/pynestml_frontend.py # pynestml/generated/PyNestMLLexer.py # pynestml/generated/PyNestMLParser.interp # pynestml/generated/PyNestMLParser.py # pynestml/generated/PyNestMLParserVisitor.py # pynestml/utils/messages.py # pynestml/visitors/ast_symbol_table_visitor.py # tests/cocos_test.py
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Commits on May 10, 2023
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All mechanism-types now integrated into the generalized collection sy…
…stem. ToDo: Completing commenting and removing legacy code-parts and inline debugging code.
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Commits on May 19, 2023
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-Compile warnings fixed. -v_comp nestml state excluded from becoming mechanism state.
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Commits on May 20, 2023
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-syns_info_enricher structure aligned to other mechanism enrichers. -debugging code removed -antlr4-python3-runtime set to 4.12 (from 4.10) in requirements.txt to remove missmatch warnings.
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Merge remote-tracking branch 'nest-upstream/master' into origin/Leand…
…erEwert # Conflicts: # pynestml/generated/PyNestMLParser.interp # pynestml/generated/PyNestMLParser.py # pynestml/grammars/PyNestMLParser.g4 # requirements.txt # tests/docstring_comment_test.py
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Merge remote-tracking branch 'nest-upstream/master' into origin/Leand…
…erEwert # Conflicts: # pynestml/generated/PyNestMLParser.interp # pynestml/generated/PyNestMLParser.py # pynestml/grammars/PyNestMLParser.g4 # requirements.txt # tests/docstring_comment_test.py
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Merge remote-tracking branch 'origin/origin/LeanderEwert' into origin…
…/LeanderEwert # Conflicts: # pynestml/generated/PyNestMLParser.interp # pynestml/generated/PyNestMLParser.py # pynestml/grammars/PyNestMLParser.g4 # requirements.txt # tests/docstring_comment_test.py
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reverted check_co_co parameter names in cases of renaming from node t…
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…erEwert # Conflicts: # pynestml/codegeneration/printers/nest_variable_printer.py # pynestml/codegeneration/printers/python_variable_printer.py # pynestml/codegeneration/resources_nest/point_neuron/directives/IfStatement.jinja2 # pynestml/frontend/pynestml_frontend.py # pynestml/symbols/variable_symbol.py # pynestml/utils/ast_utils.py # pynestml/utils/messages.py # tests/cocos_test.py
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add compartmental models check to separate CI stage
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Merge branch 'nest-upstream-master' into origin/LeanderEwert
# Conflicts: # setup.py
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Merge branch 'origin/LeanderEwert' into origin/LeanderEwert_vectoriza…
…tion # Conflicts: # pynestml/cocos/co_cos_manager.py # pynestml/codegeneration/printers/nest_variable_printer.py # pynestml/codegeneration/resources_nest_compartmental/cm_neuron/cm_compartmentcurrents_@[email protected] # pynestml/codegeneration/resources_nest_compartmental/cm_neuron/cm_compartmentcurrents_@[email protected] # pynestml/utils/ast_mechanism_information_collector.py # pynestml/utils/mechanism_processing.py # pynestml/utils/syns_info_enricher.py
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First working version of the continuous input mechanism. Old continuo…
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Big Performance improvements mostly due to map to vector type-change.
Also consectutive area -wise processing implemented.
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Added vectorized directives_cpp templates.
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Some cleanup pre-merge, ability to record non-existing states as perm…
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Syntax changed so that continuous inputs don't have to be provided wi…
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Merge branch 'LeanderEwert_vectorization' into implicit_euler
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increase margin in test to make it pass, a more precise version will …
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Revert "Syntax changed so that continuous inputs don't have to be pro…
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Merge pull request #1 from WillemWybo/implicit_euler
Switch integration algorithm to implicit Euler
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Merge remote-tracking branch 'nest-upstream/master' into origin/Leand…
…erEwert_vectorization # Conflicts: # models/neurons/aeif_cond_alpha_neuron.nestml # models/neurons/hh_psc_alpha_neuron.nestml # models/neurons/iaf_cond_alpha_neuron.nestml # models/neurons/iaf_cond_beta_neuron.nestml # models/neurons/iaf_cond_exp_neuron.nestml # models/neurons/iaf_psc_exp.nestml # models/neurons/terub_gpe_neuron.nestml # models/neurons/terub_stn_neuron.nestml # models/neurons/traub_psc_alpha_neuron.nestml # models/neurons/wb_cond_exp_neuron.nestml # pynestml/codegeneration/nest_compartmental_code_generator.py # pynestml/utils/mechs_info_enricher.py # pynestml/utils/messages.py # setup.py # tests/nest_compartmental_tests/compartmental_model_test.py # tests/valid/CoCoOutputPortDefinedIfEmitCall.nestml
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compartmental test fix. Adjusted tolerance for numerical comparison a…
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removed debugging output from compartmental test and fixed copyright …
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returned to the previous vector printing method >>for now<<. Fixed so…
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Merge branch 'origin/LeanderEwert_vectorization' into origin/LeanderE…
…wert_cm_stdp # Conflicts: # pynestml/codegeneration/nest_compartmental_code_generator.py # pynestml/codegeneration/printers/cpp_function_call_printer.py # tests/nest_compartmental_tests/resources/continuous_test.nestml # tests/nest_tests/stdp_triplet_synapse_test.py
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