STDP synapse and IAF neuron generation for the compartmental feature [WIP]#1103

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LeanderEwert wants to merge 412 commits intonest:masterfrom LeanderEwert:origin/LeanderEwert_cm_stdp

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Commits on May 4, 2022

cleanup compartmental model test
WillemWybo
committed

Commits on Jun 23, 2022

Merge remote-tracking branch 'upstream/master' into maint/updated-jinja-templates_fix
C.A.P. Linssen
committed
fix file permissions
C.A.P. Linssen
committed
fix file permissions
C.A.P. Linssen
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move template files to new directory layout
C.A.P. Linssen
committed

Commits on Jul 8, 2022

fix pycodestyle
C.A.P. Linssen
committed

Commits on Jul 12, 2022

Merge branch 'master' of https://github.com/nest/nestml into maint/updated-jinja-templates
WillemWybo
committed

Commits on Jul 13, 2022

Merge remote-tracking branch 'upstream/master' into maint/updated-jinja-templates_fix
C.A.P. Linssen
committed
fix incorrect merge with upstream
C.A.P. Linssen
committed
Merge branch 'maint/updated-jinja-templates_fix' into maint/updated-jinja-templates
WillemWybo
committed

Commits on Jul 14, 2022

Commits on Aug 1, 2022

add automatic NEST version detection and update CI
C.A.P. Linssen
committed

Commits on Aug 4, 2022

add NEST2 compatibility to nest_logarithmic_function_test
C.A.P. Linssen
committed

Commits on Aug 5, 2022

fix CI and tests after adding automatic NEST version check
C.A.P. Linssen
committed

Commits on Aug 6, 2022

move tests that use the NEST code generator to integration tests subdirectory
C.A.P. Linssen
committed

Commits on Aug 7, 2022

move tests that use the NEST code generator to integration tests subdirectory
C.A.P. Linssen
committed
fix NEST2/NEST3 compatibility in tests
C.A.P. Linssen
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add LD_LIBRARY_PATH for NEST2
C.A.P. Linssen
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fix NEST2/NEST3 compatibility in tests
C.A.P. Linssen
committed
Merge remote-tracking branch 'clinssen/nest_versions_compat' into nest_versions_compat
C.A.P. Linssen
committed
fix NEST2/NEST3 compatibility in tests
C.A.P. Linssen
committed
fix NEST2/NEST3 compatibility in tests
C.A.P. Linssen
committed

Commits on Aug 8, 2022

fix NEST2/NEST3 compatibility in tests
C.A.P. Linssen
committed
fix CI and tests after adding automatic NEST version check
C.A.P. Linssen
committed
fix CI and tests after adding automatic NEST version check
C.A.P. Linssen
committed

Commits on Aug 9, 2022

run Jupyter notebooks only on master branch
C.A.P. Linssen
committed
add NEST 3.3 to CI
C.A.P. Linssen
committed
improve NEST version detection and compatibility
C.A.P. Linssen
committed
improve NEST version detection and compatibility
C.A.P. Linssen
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Merge remote-tracking branch 'origin/master' into nest_versions_compat
C.A.P. Linssen
committed
do not use bare except
C.A.P. Linssen
committed

Commits on Aug 10, 2022

run NEST version detection in a separate process
C.A.P. Linssen
committed
fix syntax in GitHub actions workflow file
C.A.P. Linssen
committed
fix syntax in GitHub actions workflow file
C.A.P. Linssen
committed

Commits on Aug 15, 2022

remove cron comment from GitHub Actions workflow file
C.A.P. Linssen
committed

Commits on Aug 16, 2022

Merge remote-tracking branch 'clinssen/nest_versions_compat' into maint/updated-jinja-templates_fix
C.A.P. Linssen
committed
Merge remote-tracking branch 'upstream/master' into maint/updated-jinja-templates_fix
C.A.P. Linssen
committed
update compartmental model templates for NEST 3.3 and NEST-master compatibility
C.A.P. Linssen
committed

Commits on Sep 15, 2022

Commits on Dec 22, 2022

Merge remote-tracking branch 'upstream/master' into cm-post-printers
C.A.P. Linssen
committed

Commits on Dec 29, 2022

fix compartmental models code generation after printers refactor
C.A.P. Linssen
committed

Commits on Jan 3, 2023

Merge pull request WillemWybo#8 from clinssen/cm-post-printers
WillemWybo
authored

Commits on Jan 4, 2023

std
ScipioAI
committed

Commits on Jan 12, 2023

std
ScipioAI
committed

Commits on Jan 16, 2023

Commits on Feb 2, 2023

Shifted synapse ode processing from nest_code_generator.py to syns_processing.py excluding explicitly formulated ODEs from syn_info.
LeanderEwert
committed

Commits on Feb 9, 2023

Added gathering of specifically synapse related odes and functions. non synaptic functions dont break synapse models anymore.
LeanderEwert
committed

Commits on Feb 14, 2023

Added performance optimization feature, checking key parameters being close to zero to skip calculation of step-function.
LeanderEwert
committed

Commits on Feb 28, 2023

Decorator syntax added to inline functions and mechanism differentiation changed to be done by decorators.
LeanderEwert
committed

Commits on Mar 7, 2023

Decorator syntax added to inline functions and mechanism differentiation changed to be done by decorators.
LeanderEwert
committed

Commits on Mar 9, 2023

Commits on Mar 15, 2023

changed filepermissions and some fixed post merge problems.
LeanderEwert
committed

Commits on Apr 11, 2023

some fixes on concentration mechanism info collection.
LeanderEwert
committed

Commits on Apr 12, 2023

fixed mechanism processing inheritance concept.
LeanderEwert
committed

Commits on Apr 18, 2023

First working state of concentration mechanism.
LeanderEwert
committed

Commits on May 10, 2023

Commits on May 12, 2023

Issue fixed: No longer multiple identical dependency entries collected and rendered.
LeanderEwert
committed

Commits on May 19, 2023

-Jinja Templates cleaned up.
LeanderEwert
committed

Commits on May 20, 2023

-legacy code removed
LeanderEwert
committed

Commits on Jun 13, 2023

Commits on Jun 14, 2023

cd_default.nestml fixed and gitignore changes reverted
LeanderEwert
committed

Commits on Jun 15, 2023

reverted check_co_co parameter names in cases of renaming from node to neuron if parameter is not of type ASTNeuron
LeanderEwert
committed

Commits on Jun 21, 2023

Commits on Jul 7, 2023

Started to implement the vectorisation of the step function inner loop and the required modification of the datastructure.
LeanderEwert
committed

Commits on Aug 23, 2023

Implementation of NeuronCurrents ongoing.
LeanderEwert
committed

Commits on Aug 27, 2023

Fixed codestyle errors.
LeanderEwert
committed

Commits on Aug 28, 2023

Commits on Aug 30, 2023

Review comment adjustments.
LeanderEwert
committed

Commits on Sep 6, 2023

First full vector implementation. ( untested )
LeanderEwert
committed

Commits on Sep 18, 2023

First full vector implementation. (generated code not compiling yet)
LeanderEwert
committed

Commits on Sep 19, 2023

Style fixes
LeanderEwert
committed
Merge remote-tracking branch 'upstream/master' into origin/LeanderEwert
C.A.P. Linssen
committed
add compartmental models check to separate CI stage
C.A.P. Linssen
committed
add compartmental models feature
C.A.P. Linssen
committed
Update pynestml/cocos/co_co_cm_channel_model.py

clinssen
and
pnbabu
authored
Update pynestml/cocos/co_co_cm_synapse_model.py

clinssen
and
pnbabu
authored
Update pynestml/cocos/co_co_cm_concentration_model.py

clinssen
and
pnbabu
authored
add compartmental models check to separate CI stage
C.A.P. Linssen
committed
Merge remote-tracking branch 'LeanderEwert/origin/LeanderEwert' into origin/LeanderEwert
C.A.P. Linssen
committed
Fix nest typedefs
pnbabu
committed
Merge remote-tracking branch 'LeanderEwert/origin/LeanderEwert' into comp_models
pnbabu
committed
Small description for collect_additional_base_infos function
LeanderEwert
committed
Merge remote-tracking branch 'origin/origin/LeanderEwert' into origin/LeanderEwert
LeanderEwert
committed
add compartmental models feature
C.A.P. Linssen
committed
Merge remote-tracking branch 'LeanderEwert/origin/LeanderEwert' into origin/LeanderEwert
C.A.P. Linssen
committed
add compartmental models feature
C.A.P. Linssen
committed
add compartmental models feature
C.A.P. Linssen
committed
add compartmental models feature
C.A.P. Linssen
committed
add compartmental models feature
C.A.P. Linssen
committed
Clean up templates
pnbabu
committed
Fix filename in copyright header
pnbabu
committed
add compartmental models feature
C.A.P. Linssen
committed
Merge remote-tracking branch 'origin/origin/LeanderEwert' into origin/LeanderEwert
C.A.P. Linssen
committed

Commits on Sep 21, 2023

add compartmental models feature
C.A.P. Linssen
committed
Merge remote-tracking branch 'origin/origin/LeanderEwert' into origin/LeanderEwert
C.A.P. Linssen
committed

Commits on Sep 26, 2023

Merge remote-tracking branch 'upstream/master' into origin/LeanderEwert
C.A.P. Linssen
committed
Merge remote-tracking branch 'LeanderEwert/origin/LeanderEwert' into origin/LeanderEwert
C.A.P. Linssen
committed
fix templates path
C.A.P. Linssen
committed
fix templates path
C.A.P. Linssen
committed

Commits on Sep 27, 2023

Merge remote-tracking branch 'upstream/master' into origin/LeanderEwert
C.A.P. Linssen
committed
update Python version on CI
C.A.P. Linssen
committed
add compartmental models feature
C.A.P. Linssen
committed
fixing compile errors
LeanderEwert
committed
add compartmental models feature
C.A.P. Linssen
committed

Commits on Oct 4, 2023

compiling without warnings. error: undefined symbol.
LeanderEwert
committed

Commits on Oct 10, 2023

Commits on Oct 11, 2023

Commits on Oct 12, 2023

corrected directives path.
LeanderEwert
committed

Commits on Oct 17, 2023

fixed public syntax.
LeanderEwert
committed

Commits on Oct 18, 2023

undefined symbol resolved
LeanderEwert
committed

Commits on Oct 19, 2023

current fail
LeanderEwert
committed

Commits on Oct 23, 2023

running simulation but no channel activity
LeanderEwert
committed

Commits on Oct 25, 2023

Commits on Nov 6, 2023

buffer size bug on spike receive
LeanderEwert
committed

Commits on Nov 7, 2023

multiple synapses working.
LeanderEwert
committed

Commits on Jan 15, 2024

First working general vectorization.
LeanderEwert
committed

Commits on Jan 24, 2024

First working version of the continuous input mechanism. Old continuous input handler hijacked for testing. No extensive testing done.
LeanderEwert
committed

Commits on Feb 7, 2024

Big Performance improvements mostly due to map to vector type-change.
LeanderEwert
committed

Commits on Feb 19, 2024

Added vectorized directives_cpp templates.
LeanderEwert
committed

Commits on Mar 22, 2024

Syntax changed so that continuous inputs don't have to be provided with a unit anymore.
LeanderEwert
committed

Commits on Apr 2, 2024

Passive vectorization and unittest implemented.
LeanderEwert
committed

Commits on Apr 4, 2024

Commits on Apr 11, 2024

Commits on Apr 18, 2024

common subexpression elimination implemented. Sadly no change in model performance.
LeanderEwert
committed

Commits on Apr 23, 2024

SIMD loops merged
LeanderEwert
committed

Commits on Apr 29, 2024

disabled common subexpression elimination.
LeanderEwert
committed

Commits on Apr 30, 2024

Commits on May 29, 2024

Commits on Jun 13, 2024

Commits on Jun 19, 2024

Commits on Jun 24, 2024

Commits on Jul 2, 2024

point synapse and cm neuron generation pipeline combined
LeanderEwert
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Commits on Jul 5, 2024

test experiments.
LeanderEwert
committed

Commits on Jul 8, 2024

concmech model test fix. (disabled fastexp)
LeanderEwert
committed

Commits on Jul 11, 2024

fastexp removed and vectorized cpp_directive jinja templates removed.
LeanderEwert
committed

Commits on Jul 15, 2024

Commits on Jul 17, 2024

new vector printing [WIP]
LeanderEwert
committed

Commits on Jul 18, 2024

new vector printing [WIP], and documentation
LeanderEwert
committed

Commits on Jul 19, 2024

returned to the previous vector printing method >>for now<<. Fixed some codestyle issues.
LeanderEwert
committed

Commits on Jul 31, 2024

Commits on Aug 7, 2024

Commits on Aug 13, 2024

Commits on Aug 15, 2024

code compiling test WIP
LeanderEwert
committed
change compartmental vector-based printers into a factory pattern
C.A.P. Linssen
committed

Commits on Aug 19, 2024

working on prototype for purely compartmental stdp.
LeanderEwert
committed

Commits on Aug 21, 2024

Commits on Aug 26, 2024

Merge branch 'nest-upstream-master' into origin/LeanderEwert_vectorization
LeanderEwert
committed

Commits on Aug 27, 2024

Commits on Aug 28, 2024

codestyle fixes.
LeanderEwert
committed

Commits on Sep 24, 2024

Information collection pipeline WIP
LeanderEwert
committed

Commits on Oct 14, 2024

Commits on Oct 23, 2024

completing some glanced over components of the synapse receptor cogeneration.
LeanderEwert
committed

Commits on Oct 28, 2024

First working STDP and IAF implementation (crude!).
LeanderEwert
committed

Commits on Oct 29, 2024

Adex compiling.
LeanderEwert
committed

Commits on Dec 13, 2024

convolutions for synapses.
LeanderEwert
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Commits on Dec 23, 2024

Commits on Jan 10, 2025

Commits on Jan 24, 2025

setup.py mod
LeanderEwert
committed