Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Compartment Mechanism-Vectorization [WIP] #989

Open
wants to merge 359 commits into
base: master
Choose a base branch
from
Open

Compartment Mechanism-Vectorization [WIP] #989

wants to merge 359 commits into from
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jan 22, 2022

  1. adding test for existence of v_comp

    name committed Jan 22, 2022
    Configuration menu
    Copy the full SHA
    953fba7 View commit details
    Browse the repository at this point in the history

Commits on Jan 23, 2022

  1. Merge branch 'master-upstream2' into cm_structured 

    # Conflicts:
#	pynestml/cocos/co_co_parameters_assigned_only_in_parameter_block.py
#	pynestml/cocos/co_co_vector_variable_in_non_vector_declaration.py
#	pynestml/codegeneration/latex_expression_printer.py
#	pynestml/codegeneration/nest_codegenerator.py
#	pynestml/codegeneration/nest_printer.py
#	pynestml/codegeneration/nest_reference_converter.py
#	pynestml/utils/messages.py
#	pynestml/visitors/ast_builder_visitor.py
#	tests/cocos_test.py
    name committed Jan 23, 2022
    Configuration menu
    Copy the full SHA
    7fdff61 View commit details
    Browse the repository at this point in the history

  2. adding my own quick notes from what I have seen in the merge

    name committed Jan 23, 2022
    Configuration menu
    Copy the full SHA
    90120ff View commit details
    Browse the repository at this point in the history

Commits on Feb 1, 2022

  1. various fixes after the merge

    name committed Feb 1, 2022
    Configuration menu
    Copy the full SHA
    de22517 View commit details
    Browse the repository at this point in the history

Commits on Feb 24, 2022

  1. Merge remote-tracking branch 'upstream/master' into mergeJanuary

    C.A.P. Linssen committed Feb 24, 2022
    Configuration menu
    Copy the full SHA
    144b33f View commit details
    Browse the repository at this point in the history

  2. clean up after merge

    C.A.P. Linssen committed Feb 24, 2022
    Configuration menu
    Copy the full SHA
    2b0ee9e View commit details
    Browse the repository at this point in the history

Commits on Mar 9, 2022

  1. Merge remote-tracking branch 'upstream/master' into mergeJanuary

    C.A.P. Linssen committed Mar 9, 2022
    Configuration menu
    Copy the full SHA
    c532be9 View commit details
    Browse the repository at this point in the history

  2. fix

    C.A.P. Linssen committed Mar 9, 2022
    Configuration menu
    Copy the full SHA
    e30eacd View commit details
    Browse the repository at this point in the history

  3. fix

    C.A.P. Linssen committed Mar 9, 2022
    Configuration menu
    Copy the full SHA
    83ea2b3 View commit details
    Browse the repository at this point in the history

  4. fix

    C.A.P. Linssen committed Mar 9, 2022
    Configuration menu
    Copy the full SHA
    783e7cc View commit details
    Browse the repository at this point in the history

  5. fix

    C.A.P. Linssen committed Mar 9, 2022
    Configuration menu
    Copy the full SHA
    f898c3d View commit details
    Browse the repository at this point in the history

  6. fix

    C.A.P. Linssen committed Mar 9, 2022
    Configuration menu
    Copy the full SHA
    e9baa44 View commit details
    Browse the repository at this point in the history

  7. fix

    C.A.P. Linssen committed Mar 9, 2022
    Configuration menu
    Copy the full SHA
    493509a View commit details
    Browse the repository at this point in the history

Commits on Mar 23, 2022

  1. update test

    @WillemWybo
    WillemWybo committed Mar 23, 2022
    Configuration menu
    Copy the full SHA
    2a780bf View commit details
    Browse the repository at this point in the history

  2. set dt

    @WillemWybo
    WillemWybo committed Mar 23, 2022
    Configuration menu
    Copy the full SHA
    ce94405 View commit details
    Browse the repository at this point in the history

Commits on Mar 24, 2022

  1. add compartmentall target to frontend

    C.A.P. Linssen committed Mar 24, 2022
    Configuration menu
    Copy the full SHA
    9ebe9d9 View commit details
    Browse the repository at this point in the history

  2. fix compartmental target

    C.A.P. Linssen committed Mar 24, 2022
    Configuration menu
    Copy the full SHA
    7be5ebf View commit details
    Browse the repository at this point in the history

  3. Merge remote-tracking branch 'upstream/master' into maint/updated-jin… 

    …ja-templates_fix
    C.A.P. Linssen committed Mar 24, 2022
    Configuration menu
    Copy the full SHA
    acd8af8 View commit details
    Browse the repository at this point in the history

  4. fix compartmental target

    C.A.P. Linssen committed Mar 24, 2022
    Configuration menu
    Copy the full SHA
    314423a View commit details
    Browse the repository at this point in the history

  5. Merge branch 'cm_fix' into maint/updated-jinja-templates_fix

    C.A.P. Linssen committed Mar 24, 2022
    Configuration menu
    Copy the full SHA
    1a44a92 View commit details
    Browse the repository at this point in the history

Commits on Mar 29, 2022

  1. Merge remote-tracking branch 'upstream/master' into maint/updated-jin… 

    …ja-templates_fix
    C.A.P. Linssen committed Mar 29, 2022
    Configuration menu
    Copy the full SHA
    50b9118 View commit details
    Browse the repository at this point in the history

  2. clean up

    C.A.P. Linssen committed Mar 29, 2022
    Configuration menu
    Copy the full SHA
    7d39ed7 View commit details
    Browse the repository at this point in the history

  3. clean up

    C.A.P. Linssen committed Mar 29, 2022
    Configuration menu
    Copy the full SHA
    e58289f View commit details
    Browse the repository at this point in the history

Commits on Apr 5, 2022

  1. Merge pull request #1 from clinssen/maint/updated-jinja-templates_fix 

    Add compartmental target to frontend
    @WillemWybo
    WillemWybo committed Apr 5, 2022
    Configuration menu
    Copy the full SHA
    e7ee0f1 View commit details
    Browse the repository at this point in the history

  2. merge remote

    @WillemWybo
    WillemWybo committed Apr 5, 2022
    Configuration menu
    Copy the full SHA
    641eafc View commit details
    Browse the repository at this point in the history

Commits on Apr 6, 2022

  1. clean up

    C.A.P. Linssen committed Apr 6, 2022
    Configuration menu
    Copy the full SHA
    a8aedd7 View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'upstream/master' into maint/updated-jin… 

    …ja-templates_fix
    C.A.P. Linssen committed Apr 6, 2022
    Configuration menu
    Copy the full SHA
    ea098d9 View commit details
    Browse the repository at this point in the history

  3. clean up

    C.A.P. Linssen committed Apr 6, 2022
    Configuration menu
    Copy the full SHA
    6d6d60f View commit details
    Browse the repository at this point in the history

Commits on Apr 7, 2022

  1. use @NEURON_NAME@ escape sequence in template filenames

    C.A.P. Linssen committed Apr 7, 2022
    Configuration menu
    Copy the full SHA
    2f16b68 View commit details
    Browse the repository at this point in the history

  2. use @NEURON_NAME@ escape sequence in template filenames

    C.A.P. Linssen committed Apr 7, 2022
    Configuration menu
    Copy the full SHA
    697bb43 View commit details
    Browse the repository at this point in the history

  3. remove help generator

    C.A.P. Linssen committed Apr 7, 2022
    Configuration menu
    Copy the full SHA
    9653b74 View commit details
    Browse the repository at this point in the history

  4. fix template

    C.A.P. Linssen committed Apr 7, 2022
    Configuration menu
    Copy the full SHA
    dd45904 View commit details
    Browse the repository at this point in the history

Commits on Apr 8, 2022

  1. fix template

    C.A.P. Linssen committed Apr 8, 2022
    Configuration menu
    Copy the full SHA
    a9d9fe7 View commit details
    Browse the repository at this point in the history

Commits on Apr 27, 2022

  1. Merge remote-tracking branch 'upstream/master' into maint/updated-jin… 

    …ja-templates_fix
    C.A.P. Linssen committed Apr 27, 2022
    Configuration menu
    Copy the full SHA
    fc49e01 View commit details
    Browse the repository at this point in the history

  2. removed wrongfully added files

    C.A.P. Linssen committed Apr 27, 2022
    Configuration menu
    Copy the full SHA
    a969e40 View commit details
    Browse the repository at this point in the history

  3. replace old code resolving model name

    C.A.P. Linssen committed Apr 27, 2022
    Configuration menu
    Copy the full SHA
    cd4fddf View commit details
    Browse the repository at this point in the history

  4. add get_syn_idx to cm_compartmentcurrents template

    @WillemWybo
    WillemWybo committed Apr 27, 2022
    Configuration menu
    Copy the full SHA
    4d87856 View commit details
    Browse the repository at this point in the history

  5. run NEST builder for compartmental models

    C.A.P. Linssen committed Apr 27, 2022
    Configuration menu
    Copy the full SHA
    3d28553 View commit details
    Browse the repository at this point in the history

  6. Merge remote-tracking branch 'origin/maint/updated-jinja-templates' i… 

    …nto maint/updated-jinja-templates_fix
    C.A.P. Linssen committed Apr 27, 2022
    Configuration menu
    Copy the full SHA
    36848e4 View commit details
    Browse the repository at this point in the history

  7. fix C++ syntax error in template

    C.A.P. Linssen committed Apr 27, 2022
    Configuration menu
    Copy the full SHA
    4a9620e View commit details
    Browse the repository at this point in the history

  8. fix C++ syntax error in template

    C.A.P. Linssen committed Apr 27, 2022
    Configuration menu
    Copy the full SHA
    94d1572 View commit details
    Browse the repository at this point in the history

Commits on Apr 29, 2022

  1. fix cm_main and cm_tree templates, issues in cm_compartmentcurrents()

    @WillemWybo
    WillemWybo committed Apr 29, 2022
    Configuration menu
    Copy the full SHA
    1f42cee View commit details
    Browse the repository at this point in the history

Commits on Apr 30, 2022

  1. Merge remote-tracking branch 'origin/maint/updated-jinja-templates' i… 

    …nto maint/updated-jinja-templates_fix
    C.A.P. Linssen committed Apr 30, 2022
    Configuration menu
    Copy the full SHA
    5899fba View commit details
    Browse the repository at this point in the history

Commits on May 3, 2022

  1. Merge remote-tracking branch 'pnbabu/rename_calibrate' into maint/upd… 

    …ated-jinja-templates_fix
    C.A.P. Linssen committed May 3, 2022
    Configuration menu
    Copy the full SHA
    fc4729a View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'upstream/master' into maint/updated-jin… 

    …ja-templates_fix
    C.A.P. Linssen committed May 3, 2022
    Configuration menu
    Copy the full SHA
    14f2d43 View commit details
    Browse the repository at this point in the history

  3. fix code generation for compartmental models

    C.A.P. Linssen committed May 3, 2022
    Configuration menu
    Copy the full SHA
    1d56710 View commit details
    Browse the repository at this point in the history

Commits on May 4, 2022

  1. Merge pull request WillemWybo#2 from clinssen/maint/updated-jinja-tem… 

    …plates_fix

Maint/updated jinja templates fix
    @WillemWybo
    WillemWybo committed May 4, 2022
    Configuration menu
    Copy the full SHA
    b7a425d View commit details
    Browse the repository at this point in the history

  2. fix code generation for compartmental models

    C.A.P. Linssen committed May 4, 2022
    Configuration menu
    Copy the full SHA
    1c8bfd5 View commit details
    Browse the repository at this point in the history

  3. merge local_variables_reference_converter_fix and convert recordables… 

    … strings to nest Name
    @WillemWybo
    WillemWybo committed May 4, 2022
    Configuration menu
    Copy the full SHA
    c5020c1 View commit details
    Browse the repository at this point in the history

  4. working compartmental test

    @WillemWybo
    WillemWybo committed May 4, 2022
    Configuration menu
    Copy the full SHA
    eeb3de9 View commit details
    Browse the repository at this point in the history

  5. remove cm_main prefix from model name

    @WillemWybo
    WillemWybo committed May 4, 2022
    Configuration menu
    Copy the full SHA
    6695762 View commit details
    Browse the repository at this point in the history

  6. set synapse propagators in pre_run_hook, not in f_numstep

    @WillemWybo
    WillemWybo committed May 4, 2022
    Configuration menu
    Copy the full SHA
    e722e5c View commit details
    Browse the repository at this point in the history

  7. change template filename in template generation script

    @WillemWybo
    WillemWybo committed May 4, 2022
    Configuration menu
    Copy the full SHA
    b4d00ad View commit details
    Browse the repository at this point in the history

  8. cleanup compartmental model test

    @WillemWybo
    WillemWybo committed May 4, 2022
    Configuration menu
    Copy the full SHA
    32f49fc View commit details
    Browse the repository at this point in the history

Commits on Jun 16, 2022

  1. update copyright headers

    @WillemWybo
    WillemWybo committed Jun 16, 2022
    Configuration menu
    Copy the full SHA
    59e15fe View commit details
    Browse the repository at this point in the history

  2. add copyright headers second try

    @WillemWybo
    WillemWybo committed Jun 16, 2022
    Configuration menu
    Copy the full SHA
    c19390e View commit details
    Browse the repository at this point in the history

  3. codecheck copyright header try 3

    @WillemWybo
    WillemWybo committed Jun 16, 2022
    Configuration menu
    Copy the full SHA
    1815a0b View commit details
    Browse the repository at this point in the history

  4. codecheck copyright headers try 4

    @WillemWybo
    WillemWybo committed Jun 16, 2022
    Configuration menu
    Copy the full SHA
    7cb3ad8 View commit details
    Browse the repository at this point in the history

  5. correct code style issues

    @WillemWybo
    WillemWybo committed Jun 16, 2022
    Configuration menu
    Copy the full SHA
    8c59d9b View commit details
    Browse the repository at this point in the history

Commits on Jun 23, 2022

  1. Merge remote-tracking branch 'upstream/master' into maint/updated-jin… 

    …ja-templates_fix
    C.A.P. Linssen committed Jun 23, 2022
    Configuration menu
    Copy the full SHA
    750d0da View commit details
    Browse the repository at this point in the history

  2. fix file permissions

    C.A.P. Linssen committed Jun 23, 2022
    Configuration menu
    Copy the full SHA
    b14be96 View commit details
    Browse the repository at this point in the history

  3. fix file permissions

    C.A.P. Linssen committed Jun 23, 2022
    Configuration menu
    Copy the full SHA
    d89e1e2 View commit details
    Browse the repository at this point in the history

  4. move template files to new directory layout

    C.A.P. Linssen committed Jun 23, 2022
    Configuration menu
    Copy the full SHA
    c610f59 View commit details
    Browse the repository at this point in the history

Commits on Jun 29, 2022

  1. Merge pull request WillemWybo#4 from clinssen/maint/updated-jinja-tem… 

    …plates_fix

Maint/updated jinja templates fix
    @WillemWybo
    WillemWybo committed Jun 29, 2022
    Configuration menu
    Copy the full SHA
    cdd9ac5 View commit details
    Browse the repository at this point in the history

  2. fix code style issues with autopep8

    @WillemWybo
    WillemWybo committed Jun 29, 2022
    Configuration menu
    Copy the full SHA
    2252c27 View commit details
    Browse the repository at this point in the history

  3. fix code style issues with autopep8 aggressive

    @WillemWybo
    WillemWybo committed Jun 29, 2022
    Configuration menu
    Copy the full SHA
    8af8201 View commit details
    Browse the repository at this point in the history

  4. fix codestyle issues with autopep8 aggressive second round

    @WillemWybo
    WillemWybo committed Jun 29, 2022
    Configuration menu
    Copy the full SHA
    734f17b View commit details
    Browse the repository at this point in the history

  5. final code style issue, hopefully

    @WillemWybo
    WillemWybo committed Jun 29, 2022
    Configuration menu
    Copy the full SHA
    cf3a744 View commit details
    Browse the repository at this point in the history

Commits on Jul 8, 2022

  1. fix pycodestyle

    C.A.P. Linssen committed Jul 8, 2022
    Configuration menu
    Copy the full SHA
    2226954 View commit details
    Browse the repository at this point in the history

Commits on Jul 12, 2022

  1. Merge branch 'master' of https://github.com/nest/nestml into maint/up… 

    …dated-jinja-templates
    @WillemWybo
    WillemWybo committed Jul 12, 2022
    Configuration menu
    Copy the full SHA
    822db5e View commit details
    Browse the repository at this point in the history

Commits on Jul 13, 2022

  1. Merge remote-tracking branch 'upstream/master' into maint/updated-jin… 

    …ja-templates_fix
    C.A.P. Linssen committed Jul 13, 2022
    Configuration menu
    Copy the full SHA
    98c8253 View commit details
    Browse the repository at this point in the history

  2. fix incorrect merge with upstream

    C.A.P. Linssen committed Jul 13, 2022
    Configuration menu
    Copy the full SHA
    25e39e8 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'maint/updated-jinja-templates_fix' into maint/updated-j… 

    …inja-templates
    @WillemWybo
    WillemWybo committed Jul 13, 2022
    Configuration menu
    Copy the full SHA
    c86c851 View commit details
    Browse the repository at this point in the history

Commits on Jul 14, 2022

  1. print statements in compartmental_model_test.py for debugging workflo… 

    …w run
    @WillemWybo
    WillemWybo committed Jul 14, 2022
    Configuration menu
    Copy the full SHA
    a0acc38 View commit details
    Browse the repository at this point in the history

  2. print statements in compartmental_model_test.py for debugging workflo… 

    …w run
    @WillemWybo
    WillemWybo committed Jul 14, 2022
    Configuration menu
    Copy the full SHA
    ae77058 View commit details
    Browse the repository at this point in the history

Commits on Aug 1, 2022

  1. add automatic NEST version detection and update CI

    C.A.P. Linssen committed Aug 1, 2022
    Configuration menu
    Copy the full SHA
    fa5777d View commit details
    Browse the repository at this point in the history

Commits on Aug 3, 2022

  1. fix setup.py not copying compartmental model templates to install dir… 

    …ectory
    @WillemWybo
    WillemWybo committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    023cbd5 View commit details
    Browse the repository at this point in the history

  2. fix paths in compartmental model test

    @WillemWybo
    WillemWybo committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    34b7c03 View commit details
    Browse the repository at this point in the history

  3. add additional template directories to setup.py

    @WillemWybo
    WillemWybo committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    4f87f16 View commit details
    Browse the repository at this point in the history

  4. minor codestyle fixes

    @WillemWybo
    WillemWybo committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    c31cbd0 View commit details
    Browse the repository at this point in the history

  5. fix compartmental model test style issue

    @WillemWybo
    WillemWybo committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    f44eda8 View commit details
    Browse the repository at this point in the history

  6. fix compartmental model test style issue

    @WillemWybo
    WillemWybo committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    277c51e View commit details
    Browse the repository at this point in the history

  7. fix compartmental model test style issue

    @WillemWybo
    WillemWybo committed Aug 3, 2022
    Configuration menu
    Copy the full SHA
    a45359c View commit details
    Browse the repository at this point in the history

Commits on Aug 4, 2022

  1. add NEST2 compatibility to nest_logarithmic_function_test

    C.A.P. Linssen committed Aug 4, 2022
    Configuration menu
    Copy the full SHA
    92ec449 View commit details
    Browse the repository at this point in the history

Commits on Aug 5, 2022

  1. fix CI and tests after adding automatic NEST version check

    C.A.P. Linssen committed Aug 5, 2022
    Configuration menu
    Copy the full SHA
    537493e View commit details
    Browse the repository at this point in the history

Commits on Aug 6, 2022

  1. move tests that use the NEST code generator to integration tests subd… 

    …irectory
    C.A.P. Linssen committed Aug 6, 2022
    Configuration menu
    Copy the full SHA
    4936d33 View commit details
    Browse the repository at this point in the history

Commits on Aug 7, 2022

  1. move tests that use the NEST code generator to integration tests subd… 

    …irectory
    C.A.P. Linssen committed Aug 7, 2022
    Configuration menu
    Copy the full SHA
    78c8fb7 View commit details
    Browse the repository at this point in the history

  2. fix NEST2/NEST3 compatibility in tests

    C.A.P. Linssen committed Aug 7, 2022
    Configuration menu
    Copy the full SHA
    b28f4b3 View commit details
    Browse the repository at this point in the history

  3. add LD_LIBRARY_PATH for NEST2

    C.A.P. Linssen committed Aug 7, 2022
    Configuration menu
    Copy the full SHA
    9cfdaa8 View commit details
    Browse the repository at this point in the history

  4. fix NEST2/NEST3 compatibility in tests

    C.A.P. Linssen committed Aug 7, 2022
    Configuration menu
    Copy the full SHA
    e0f9559 View commit details
    Browse the repository at this point in the history

  5. Merge remote-tracking branch 'clinssen/nest_versions_compat' into nes… 

    …t_versions_compat
    C.A.P. Linssen committed Aug 7, 2022
    Configuration menu
    Copy the full SHA
    72c3678 View commit details
    Browse the repository at this point in the history

  6. fix NEST2/NEST3 compatibility in tests

    C.A.P. Linssen committed Aug 7, 2022
    Configuration menu
    Copy the full SHA
    f155e86 View commit details
    Browse the repository at this point in the history

  7. fix NEST2/NEST3 compatibility in tests

    C.A.P. Linssen committed Aug 7, 2022
    Configuration menu
    Copy the full SHA
    68c5ce6 View commit details
    Browse the repository at this point in the history

Commits on Aug 8, 2022

  1. fix NEST2/NEST3 compatibility in tests

    C.A.P. Linssen committed Aug 8, 2022
    Configuration menu
    Copy the full SHA
    3d062f3 View commit details
    Browse the repository at this point in the history

  2. fix CI and tests after adding automatic NEST version check

    C.A.P. Linssen committed Aug 8, 2022
    Configuration menu
    Copy the full SHA
    56bcca1 View commit details
    Browse the repository at this point in the history

  3. fix CI and tests after adding automatic NEST version check

    C.A.P. Linssen committed Aug 8, 2022
    Configuration menu
    Copy the full SHA
    f104621 View commit details
    Browse the repository at this point in the history

Commits on Aug 9, 2022

  1. run Jupyter notebooks only on master branch

    C.A.P. Linssen committed Aug 9, 2022
    Configuration menu
    Copy the full SHA
    79bfbe7 View commit details
    Browse the repository at this point in the history

  2. add NEST 3.3 to CI

    C.A.P. Linssen committed Aug 9, 2022
    Configuration menu
    Copy the full SHA
    fab802c View commit details
    Browse the repository at this point in the history

  3. improve NEST version detection and compatibility

    C.A.P. Linssen committed Aug 9, 2022
    Configuration menu
    Copy the full SHA
    24c0d78 View commit details
    Browse the repository at this point in the history

  4. improve NEST version detection and compatibility

    C.A.P. Linssen committed Aug 9, 2022
    Configuration menu
    Copy the full SHA
    5f783aa View commit details
    Browse the repository at this point in the history

  5. Merge remote-tracking branch 'origin/master' into nest_versions_compat

    C.A.P. Linssen committed Aug 9, 2022
    Configuration menu
    Copy the full SHA
    8e42a63 View commit details
    Browse the repository at this point in the history

  6. do not use bare except

    C.A.P. Linssen committed Aug 9, 2022
    Configuration menu
    Copy the full SHA
    891e67b View commit details
    Browse the repository at this point in the history

Commits on Aug 10, 2022

  1. run NEST version detection in a separate process

    C.A.P. Linssen committed Aug 10, 2022
    Configuration menu
    Copy the full SHA
    5f54d17 View commit details
    Browse the repository at this point in the history

  2. fix syntax in GitHub actions workflow file

    C.A.P. Linssen committed Aug 10, 2022
    Configuration menu
    Copy the full SHA
    3550eb4 View commit details
    Browse the repository at this point in the history

  3. fix syntax in GitHub actions workflow file

    C.A.P. Linssen committed Aug 10, 2022
    Configuration menu
    Copy the full SHA
    c00c6f6 View commit details
    Browse the repository at this point in the history

Commits on Aug 15, 2022

  1. remove cron comment from GitHub Actions workflow file

    C.A.P. Linssen committed Aug 15, 2022
    Configuration menu
    Copy the full SHA
    4993cf2 View commit details
    Browse the repository at this point in the history

Commits on Aug 16, 2022

  1. Merge remote-tracking branch 'clinssen/nest_versions_compat' into mai… 

    …nt/updated-jinja-templates_fix
    C.A.P. Linssen committed Aug 16, 2022
    Configuration menu
    Copy the full SHA
    0db4ef0 View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'upstream/master' into maint/updated-jin… 

    …ja-templates_fix
    C.A.P. Linssen committed Aug 16, 2022
    Configuration menu
    Copy the full SHA
    a155b33 View commit details
    Browse the repository at this point in the history

  3. update compartmental model templates for NEST 3.3 and NEST-master com… 

    …patibility
    C.A.P. Linssen committed Aug 16, 2022
    Configuration menu
    Copy the full SHA
    33c5908 View commit details
    Browse the repository at this point in the history

Commits on Sep 14, 2022

  1. Merge remote-tracking branch 'upstream/master' into maint/updated-jin… 

    …ja-templates_fix
    C.A.P. Linssen committed Sep 14, 2022
    Configuration menu
    Copy the full SHA
    9d9a98d View commit details
    Browse the repository at this point in the history

  2. Merge pull request WillemWybo#7 from clinssen/maint/updated-jinja-tem… 

    …plates_fix

Maint/updated jinja templates fix
    @WillemWybo
    WillemWybo committed Sep 14, 2022
    Configuration menu
    Copy the full SHA
    9f8d76f View commit details
    Browse the repository at this point in the history

  3. compartmental model debugging in progress

    @WillemWybo
    WillemWybo committed Sep 14, 2022
    Configuration menu
    Copy the full SHA
    3f7bae6 View commit details
    Browse the repository at this point in the history

  4. merge of upstream

    @WillemWybo
    WillemWybo committed Sep 14, 2022
    Configuration menu
    Copy the full SHA
    fe3fe3e View commit details
    Browse the repository at this point in the history

  5. attempted fix for variable-not-found error

    @WillemWybo
    WillemWybo committed Sep 14, 2022
    Configuration menu
    Copy the full SHA
    edb524f View commit details
    Browse the repository at this point in the history

  6. fix codecheck style issues

    @WillemWybo
    WillemWybo committed Sep 14, 2022
    Configuration menu
    Copy the full SHA
    c099d33 View commit details
    Browse the repository at this point in the history

  7. fix bug naming clash with nest built-in classess for ion channels and… 

    … synapses
    @WillemWybo
    WillemWybo committed Sep 14, 2022
    Configuration menu
    Copy the full SHA
    4fbecf7 View commit details
    Browse the repository at this point in the history

Commits on Sep 15, 2022

  1. fix NEST version detection

    C.A.P. Linssen committed Sep 15, 2022
    Configuration menu
    Copy the full SHA
    0301084 View commit details
    Browse the repository at this point in the history

  2. remove multiprocessing version of call to _detect_nest_version from c… 

    …ompartmental_model_test.py as it creates issues on some systems
    @WillemWybo
    WillemWybo committed Sep 15, 2022
    Configuration menu
    Copy the full SHA
    a98ace9 View commit details
    Browse the repository at this point in the history

  3. cleanup of compartmental_model_test

    @WillemWybo
    WillemWybo committed Sep 15, 2022
    Configuration menu
    Copy the full SHA
    f6d79bf View commit details
    Browse the repository at this point in the history

  4. code style issues

    @WillemWybo
    WillemWybo committed Sep 15, 2022
    Configuration menu
    Copy the full SHA
    50ebfd4 View commit details
    Browse the repository at this point in the history

Commits on Dec 22, 2022

  1. Merge remote-tracking branch 'upstream/master' into cm-post-printers

    C.A.P. Linssen committed Dec 22, 2022
    Configuration menu
    Copy the full SHA
    a3a606f View commit details
    Browse the repository at this point in the history

Commits on Dec 29, 2022

  1. fix compartmental models code generation after printers refactor

    C.A.P. Linssen committed Dec 29, 2022
    Configuration menu
    Copy the full SHA
    c7f9449 View commit details
    Browse the repository at this point in the history

Commits on Jan 3, 2023

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

    Fix compartmental models code generator after printers refactor
    @WillemWybo
    WillemWybo committed Jan 3, 2023
    Configuration menu
    Copy the full SHA
    75bd389 View commit details
    Browse the repository at this point in the history

Commits on Jan 4, 2023

  1. std

    @ScipioAI
    ScipioAI committed Jan 4, 2023
    Configuration menu
    Copy the full SHA
    9948547 View commit details
    Browse the repository at this point in the history

Commits on Jan 12, 2023

  1. std

    @ScipioAI
    ScipioAI committed Jan 12, 2023
    Configuration menu
    Copy the full SHA
    296b98f View commit details
    Browse the repository at this point in the history

Commits on Jan 16, 2023

  1. std

    @ScipioAI
    ScipioAI committed Jan 16, 2023
    Configuration menu
    Copy the full SHA
    7b420f5 View commit details
    Browse the repository at this point in the history

  2. std

    @ScipioAI
    ScipioAI committed Jan 16, 2023
    Configuration menu
    Copy the full SHA
    6dbf3a2 View commit details
    Browse the repository at this point in the history

  3. std

    @ScipioAI
    ScipioAI committed Jan 16, 2023
    Configuration menu
    Copy the full SHA
    9bc3d1a View commit details
    Browse the repository at this point in the history

Commits on Feb 2, 2023

  1. 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.
    @LeanderEwert
    LeanderEwert committed Feb 2, 2023
    Configuration menu
    Copy the full SHA
    0cccbb6 View commit details
    Browse the repository at this point in the history

Commits on Feb 9, 2023

  1. 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)
    @LeanderEwert
    LeanderEwert committed Feb 9, 2023
    Configuration menu
    Copy the full SHA
    867799b View commit details
    Browse the repository at this point in the history

Commits on Feb 14, 2023

  1. 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)
    @LeanderEwert
    LeanderEwert committed Feb 14, 2023
    Configuration menu
    Copy the full SHA
    222e83c View commit details
    Browse the repository at this point in the history

Commits on Feb 28, 2023

  1. 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.
    @LeanderEwert
    LeanderEwert committed Feb 28, 2023
    Configuration menu
    Copy the full SHA
    0d5dcee View commit details
    Browse the repository at this point in the history

Commits on Mar 7, 2023

  1. 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.
    @LeanderEwert
    LeanderEwert committed Mar 7, 2023
    Configuration menu
    Copy the full SHA
    cb3ee7a View commit details
    Browse the repository at this point in the history

Commits on Mar 9, 2023

  1. 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
    @LeanderEwert
    LeanderEwert committed Mar 9, 2023
    Configuration menu
    Copy the full SHA
    0624ec2 View commit details
    Browse the repository at this point in the history

  2. added decorators to odes in parser

    @LeanderEwert
    LeanderEwert committed Mar 9, 2023
    Configuration menu
    Copy the full SHA
    c45ac08 View commit details
    Browse the repository at this point in the history

Commits on Mar 15, 2023

  1. changed filepermissions and some fixed post merge problems.

    @LeanderEwert
    LeanderEwert committed Mar 15, 2023
    Configuration menu
    Copy the full SHA
    f9e5269 View commit details
    Browse the repository at this point in the history

Commits on Apr 11, 2023

  1. some fixes on concentration mechanism info collection.

    @LeanderEwert
    LeanderEwert committed Apr 11, 2023
    Configuration menu
    Copy the full SHA
    08e14ae View commit details
    Browse the repository at this point in the history

Commits on Apr 12, 2023

  1. fixed mechanism processing inheritance concept.

    @LeanderEwert
    LeanderEwert committed Apr 12, 2023
    Configuration menu
    Copy the full SHA
    6f8bde8 View commit details
    Browse the repository at this point in the history

Commits on Apr 18, 2023

  1. First working state of concentration mechanism.

    @LeanderEwert
    LeanderEwert committed Apr 18, 2023
    Configuration menu
    Copy the full SHA
    0767a5c View commit details
    Browse the repository at this point in the history

Commits on May 10, 2023

  1. All mechanism-types now integrated into the generalized collection sy… 

    …stem. ToDo: Completing commenting and removing legacy code-parts and inline debugging code.
    @LeanderEwert
    LeanderEwert committed May 10, 2023
    Configuration menu
    Copy the full SHA
    b9cc318 View commit details
    Browse the repository at this point in the history

  2. Some commenting

    @LeanderEwert
    LeanderEwert committed May 10, 2023
    Configuration menu
    Copy the full SHA
    089b28f View commit details
    Browse the repository at this point in the history

Commits on May 12, 2023

  1. Issue fixed: No longer multiple identical dependency entries collecte… 

    …d and rendered.
    @LeanderEwert
    LeanderEwert committed May 12, 2023
    Configuration menu
    Copy the full SHA
    99b158a View commit details
    Browse the repository at this point in the history

Commits on May 19, 2023

  1. -Jinja Templates cleaned up. 

    -Compile warnings fixed.
-v_comp nestml state excluded from becoming mechanism state.
    @LeanderEwert
    LeanderEwert committed May 19, 2023
    Configuration menu
    Copy the full SHA
    cdf6929 View commit details
    Browse the repository at this point in the history

Commits on May 20, 2023

  1. -legacy code removed 

    -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.
    @LeanderEwert
    LeanderEwert committed May 20, 2023
    Configuration menu
    Copy the full SHA
    9964898 View commit details
    Browse the repository at this point in the history

Commits on May 24, 2023

  1. - added info dictionaries to the logger.

    @LeanderEwert
    LeanderEwert committed May 24, 2023
    Configuration menu
    Copy the full SHA
    941e03c View commit details
    Browse the repository at this point in the history

  2. -some commenting added

    @LeanderEwert
    LeanderEwert committed May 24, 2023
    Configuration menu
    Copy the full SHA
    2b8c3d4 View commit details
    Browse the repository at this point in the history

  3. 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
    @LeanderEwert
    LeanderEwert committed May 24, 2023
    Configuration menu
    Copy the full SHA
    5aaf824 View commit details
    Browse the repository at this point in the history

  4. 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
    @LeanderEwert
    LeanderEwert committed May 24, 2023
    Configuration menu
    Copy the full SHA
    1bc4109 View commit details
    Browse the repository at this point in the history

  5. resolved issues after merging

    @LeanderEwert
    LeanderEwert committed May 24, 2023
    Configuration menu
    Copy the full SHA
    c8c5c12 View commit details
    Browse the repository at this point in the history

  6. 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
    @LeanderEwert
    LeanderEwert committed May 24, 2023
    Configuration menu
    Copy the full SHA
    985012e View commit details
    Browse the repository at this point in the history

Commits on Jun 13, 2023

  1. key-zero parameter search for concentrations.

    @LeanderEwert
    LeanderEwert committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    bbe041d View commit details
    Browse the repository at this point in the history

  2. copyright-headers added.

    @LeanderEwert
    LeanderEwert committed Jun 13, 2023
    Configuration menu
    Copy the full SHA
    5eddd73 View commit details
    Browse the repository at this point in the history

Commits on Jun 14, 2023

  1. cd_default.nestml fixed and gitignore changes reverted

    @LeanderEwert
    LeanderEwert committed Jun 14, 2023
    Configuration menu
    Copy the full SHA
    59a4019 View commit details
    Browse the repository at this point in the history

Commits on Jun 15, 2023

  1. reverted check_co_co parameter names in cases of renaming from node t… 

    …o neuron if parameter is not of type ASTNeuron
    @LeanderEwert
    LeanderEwert committed Jun 15, 2023
    Configuration menu
    Copy the full SHA
    49f9361 View commit details
    Browse the repository at this point in the history

Commits on Jun 21, 2023

  1. New neuroncurrent files added that will contain arrays of states, par… 

    …ameters etc. where an index in the array range points to the states/parameters that used to be contained in its own object representing a mechanism in one specific compartment.
    @LeanderEwert
    LeanderEwert committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    209d9fd View commit details
    Browse the repository at this point in the history

  2. Deleted an unneccessary outcommented code-line which the check skript… 

    … did not like the format of.
    @LeanderEwert
    LeanderEwert committed Jun 21, 2023
    Configuration menu
    Copy the full SHA
    d1ad9e7 View commit details
    Browse the repository at this point in the history

Commits on Jul 7, 2023

  1. Started to implement the vectorisation of the step function inner loo… 

    …p and the required modification of the datastructure.
    @LeanderEwert
    LeanderEwert committed Jul 7, 2023
    Configuration menu
    Copy the full SHA
    bd0f5a8 View commit details
    Browse the repository at this point in the history

Commits on Aug 23, 2023

  1. Implementation of NeuronCurrents ongoing.

    @LeanderEwert
    LeanderEwert committed Aug 23, 2023
    Configuration menu
    Copy the full SHA
    f2665d6 View commit details
    Browse the repository at this point in the history

Commits on Aug 27, 2023

  1. Fixed codestyle errors.

    @LeanderEwert
    LeanderEwert committed Aug 27, 2023
    Configuration menu
    Copy the full SHA
    4405829 View commit details
    Browse the repository at this point in the history

Commits on Aug 28, 2023

  1. Merge remote-tracking branch 'nest-upstream/master' into origin/Leand… 

    …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
    @LeanderEwert
    LeanderEwert committed Aug 28, 2023
    Configuration menu
    Copy the full SHA
    268c945 View commit details
    Browse the repository at this point in the history

  2. Merge with master.

    @LeanderEwert
    LeanderEwert committed Aug 28, 2023
    Configuration menu
    Copy the full SHA
    d9d23e0 View commit details
    Browse the repository at this point in the history

Commits on Aug 30, 2023

  1. Review comment adjustments.

    @LeanderEwert
    LeanderEwert committed Aug 30, 2023
    Configuration menu
    Copy the full SHA
    b8eeb8f View commit details
    Browse the repository at this point in the history

Commits on Sep 6, 2023

  1. First full vector implementation. ( untested )

    @LeanderEwert
    LeanderEwert committed Sep 6, 2023
    Configuration menu
    Copy the full SHA
    d77c8fc View commit details
    Browse the repository at this point in the history

Commits on Sep 18, 2023

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

    @LeanderEwert
    LeanderEwert committed Sep 18, 2023
    Configuration menu
    Copy the full SHA
    110fda5 View commit details
    Browse the repository at this point in the history

Commits on Sep 19, 2023

  1. Style fixes

    @LeanderEwert
    LeanderEwert committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    37ecc78 View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'upstream/master' into origin/LeanderEwert

    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    b596b3e View commit details
    Browse the repository at this point in the history

  3. add compartmental models check to separate CI stage

    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    c604042 View commit details
    Browse the repository at this point in the history

  4. add compartmental models feature

    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    593ca09 View commit details
    Browse the repository at this point in the history

  5. Update pynestml/cocos/co_co_cm_channel_model.py 

    Co-authored-by: Pooja Babu <75320801+pnbabu@users.noreply.github.com>
    @clinssen @pnbabu
    clinssen and pnbabu committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    bc16888 View commit details
    Browse the repository at this point in the history

  6. Update pynestml/cocos/co_co_cm_synapse_model.py 

    Co-authored-by: Pooja Babu <75320801+pnbabu@users.noreply.github.com>
    @clinssen @pnbabu
    clinssen and pnbabu committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    8d40517 View commit details
    Browse the repository at this point in the history

  7. Update pynestml/cocos/co_co_cm_concentration_model.py 

    Co-authored-by: Pooja Babu <75320801+pnbabu@users.noreply.github.com>
    @clinssen @pnbabu
    clinssen and pnbabu committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    671c81e View commit details
    Browse the repository at this point in the history

  8. add compartmental models check to separate CI stage

    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    e847153 View commit details
    Browse the repository at this point in the history

  9. Merge remote-tracking branch 'LeanderEwert/origin/LeanderEwert' into … 

    …origin/LeanderEwert
    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    6266fa2 View commit details
    Browse the repository at this point in the history

  10. Fix nest typedefs

    @pnbabu
    pnbabu committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    df41f88 View commit details
    Browse the repository at this point in the history

  11. Merge remote-tracking branch 'LeanderEwert/origin/LeanderEwert' into … 

    …comp_models
    @pnbabu
    pnbabu committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    84bd195 View commit details
    Browse the repository at this point in the history

  12. Small description for collect_additional_base_infos function

    @LeanderEwert
    LeanderEwert committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    66271bd View commit details
    Browse the repository at this point in the history

  13. Merge remote-tracking branch 'origin/origin/LeanderEwert' into origin… 

    …/LeanderEwert
    @LeanderEwert
    LeanderEwert committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    317a92a View commit details
    Browse the repository at this point in the history

  14. add compartmental models feature

    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    a4fe44f View commit details
    Browse the repository at this point in the history

  15. Merge remote-tracking branch 'LeanderEwert/origin/LeanderEwert' into … 

    …origin/LeanderEwert
    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    8f489b2 View commit details
    Browse the repository at this point in the history

  16. add compartmental models feature

    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    d79bb40 View commit details
    Browse the repository at this point in the history

  17. add compartmental models feature

    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    a3abd10 View commit details
    Browse the repository at this point in the history

  18. add compartmental models feature

    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    bb2d828 View commit details
    Browse the repository at this point in the history

  19. add compartmental models feature

    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    f4e2e02 View commit details
    Browse the repository at this point in the history

  20. Clean up templates

    @pnbabu
    pnbabu committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    130cbb5 View commit details
    Browse the repository at this point in the history

  21. Fix filename in copyright header

    @pnbabu
    pnbabu committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    c2b7611 View commit details
    Browse the repository at this point in the history

  22. add compartmental models feature

    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    a66fb42 View commit details
    Browse the repository at this point in the history

  23. Merge remote-tracking branch 'origin/origin/LeanderEwert' into origin… 

    …/LeanderEwert
    C.A.P. Linssen committed Sep 19, 2023
    Configuration menu
    Copy the full SHA
    d6d5a3b View commit details
    Browse the repository at this point in the history

Commits on Sep 20, 2023

  1. Completed compartmental doc.

    @LeanderEwert
    LeanderEwert committed Sep 20, 2023
    Configuration menu
    Copy the full SHA
    9cc9be6 View commit details
    Browse the repository at this point in the history

  2. Completed compartmental doc. (fix)

    @LeanderEwert
    LeanderEwert committed Sep 20, 2023
    Configuration menu
    Copy the full SHA
    b454bfe View commit details
    Browse the repository at this point in the history

  3. Completed compartmental doc. (fix)

    @LeanderEwert
    LeanderEwert committed Sep 20, 2023
    Configuration menu
    Copy the full SHA
    46e795a View commit details
    Browse the repository at this point in the history

  4. Completed compartmental doc. (fix)

    @LeanderEwert
    LeanderEwert committed Sep 20, 2023
    Configuration menu
    Copy the full SHA
    edc4310 View commit details
    Browse the repository at this point in the history

  5. Completed compartmental doc. (fix)

    @LeanderEwert
    LeanderEwert committed Sep 20, 2023
    Configuration menu
    Copy the full SHA
    fa813e8 View commit details
    Browse the repository at this point in the history

Commits on Sep 21, 2023

  1. add compartmental models feature

    C.A.P. Linssen committed Sep 21, 2023
    Configuration menu
    Copy the full SHA
    546420b View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'origin/origin/LeanderEwert' into origin… 

    …/LeanderEwert
    C.A.P. Linssen committed Sep 21, 2023
    Configuration menu
    Copy the full SHA
    6a1998d View commit details
    Browse the repository at this point in the history

Commits on Sep 26, 2023

  1. Merge remote-tracking branch 'upstream/master' into origin/LeanderEwert

    C.A.P. Linssen committed Sep 26, 2023
    Configuration menu
    Copy the full SHA
    bb8c343 View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'LeanderEwert/origin/LeanderEwert' into … 

    …origin/LeanderEwert
    C.A.P. Linssen committed Sep 26, 2023
    Configuration menu
    Copy the full SHA
    8f93ef1 View commit details
    Browse the repository at this point in the history

  3. fix templates path

    C.A.P. Linssen committed Sep 26, 2023
    Configuration menu
    Copy the full SHA
    be660a9 View commit details
    Browse the repository at this point in the history

  4. fix templates path

    C.A.P. Linssen committed Sep 26, 2023
    Configuration menu
    Copy the full SHA
    de0609f View commit details
    Browse the repository at this point in the history

Commits on Sep 27, 2023

  1. Merge remote-tracking branch 'upstream/master' into origin/LeanderEwert

    C.A.P. Linssen committed Sep 27, 2023
    Configuration menu
    Copy the full SHA
    15d4f10 View commit details
    Browse the repository at this point in the history

  2. update Python version on CI

    C.A.P. Linssen committed Sep 27, 2023
    Configuration menu
    Copy the full SHA
    83821b9 View commit details
    Browse the repository at this point in the history

  3. add compartmental models feature

    C.A.P. Linssen committed Sep 27, 2023
    Configuration menu
    Copy the full SHA
    45a21e8 View commit details
    Browse the repository at this point in the history

  4. fixing compile errors

    @LeanderEwert
    LeanderEwert committed Sep 27, 2023
    Configuration menu
    Copy the full SHA
    1b8c5c4 View commit details
    Browse the repository at this point in the history

  5. add compartmental models feature

    C.A.P. Linssen committed Sep 27, 2023
    Configuration menu
    Copy the full SHA
    68a310a View commit details
    Browse the repository at this point in the history

Commits on Oct 4, 2023

  1. compiling without warnings. error: undefined symbol.

    @LeanderEwert
    LeanderEwert committed Oct 4, 2023
    Configuration menu
    Copy the full SHA
    53d27cc View commit details
    Browse the repository at this point in the history

Commits on Oct 10, 2023

  1. corrected compartmental directives path in setup.py.

    @LeanderEwert
    LeanderEwert committed Oct 10, 2023
    Configuration menu
    Copy the full SHA
    6639e5a View commit details
    Browse the repository at this point in the history

  2. Merge branch 'nest-upstream-master' into origin/LeanderEwert 

    # Conflicts:
#	setup.py
    @LeanderEwert
    LeanderEwert committed Oct 10, 2023
    Configuration menu
    Copy the full SHA
    2bf108c View commit details
    Browse the repository at this point in the history

Commits on Oct 11, 2023

  1. fixed generation issue when no synapses are defined in a model.

    @LeanderEwert
    LeanderEwert committed Oct 11, 2023
    Configuration menu
    Copy the full SHA
    8c0c556 View commit details
    Browse the repository at this point in the history

  2. 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_@NEURON_NAME@.cpp.jinja2
#	pynestml/codegeneration/resources_nest_compartmental/cm_neuron/cm_compartmentcurrents_@NEURON_NAME@.h.jinja2
#	pynestml/utils/ast_mechanism_information_collector.py
#	pynestml/utils/mechanism_processing.py
#	pynestml/utils/syns_info_enricher.py
    @LeanderEwert
    LeanderEwert committed Oct 11, 2023
    Configuration menu
    Copy the full SHA
    007dd1a View commit details
    Browse the repository at this point in the history

  3. post merge with LeanderEwert

    @LeanderEwert
    LeanderEwert committed Oct 11, 2023
    Configuration menu
    Copy the full SHA
    db842ba View commit details
    Browse the repository at this point in the history

Commits on Oct 12, 2023

  1. corrected directives path.

    @LeanderEwert
    LeanderEwert committed Oct 12, 2023
    Configuration menu
    Copy the full SHA
    b2e34d2 View commit details
    Browse the repository at this point in the history

Commits on Oct 17, 2023

  1. fixed public syntax.

    @LeanderEwert
    LeanderEwert committed Oct 17, 2023
    Configuration menu
    Copy the full SHA
    42fc198 View commit details
    Browse the repository at this point in the history

Commits on Oct 18, 2023

  1. undefined symbol resolved

    @LeanderEwert
    LeanderEwert committed Oct 18, 2023
    Configuration menu
    Copy the full SHA
    4a25ec3 View commit details
    Browse the repository at this point in the history

Commits on Oct 19, 2023

  1. current fail

    @LeanderEwert
    LeanderEwert committed Oct 19, 2023
    Configuration menu
    Copy the full SHA
    4ac65f8 View commit details
    Browse the repository at this point in the history

Commits on Oct 23, 2023

  1. running simulation but no channel activity

    @LeanderEwert
    LeanderEwert committed Oct 23, 2023
    Configuration menu
    Copy the full SHA
    22b366d View commit details
    Browse the repository at this point in the history

Commits on Oct 25, 2023

  1. channels working

    @LeanderEwert
    LeanderEwert committed Oct 25, 2023
    Configuration menu
    Copy the full SHA
    386d95d View commit details
    Browse the repository at this point in the history

  2. vectorization working on all mechanisms

    @LeanderEwert
    LeanderEwert committed Oct 25, 2023
    Configuration menu
    Copy the full SHA
    5c0f23e View commit details
    Browse the repository at this point in the history

Commits on Nov 6, 2023

  1. buffer size bug on spike receive

    @LeanderEwert
    LeanderEwert committed Nov 6, 2023
    Configuration menu
    Copy the full SHA
    c210a5d View commit details
    Browse the repository at this point in the history

Commits on Nov 7, 2023

  1. multiple synapses working.

    @LeanderEwert
    LeanderEwert committed Nov 7, 2023
    Configuration menu
    Copy the full SHA
    0e39dc0 View commit details
    Browse the repository at this point in the history

Commits on Jan 15, 2024

  1. First working general vectorization.

    @LeanderEwert
    LeanderEwert committed Jan 15, 2024
    Configuration menu
    Copy the full SHA
    c2d4cdb View commit details
    Browse the repository at this point in the history

Commits on Jan 24, 2024

  1. First working version of the continuous input mechanism. Old continuo… 

    …us input handler hijacked for testing. No extensive testing done.
    @LeanderEwert
    LeanderEwert committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    b4a9f02 View commit details
    Browse the repository at this point in the history

Commits on Feb 7, 2024

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

    Also consectutive area -wise processing implemented.
    @LeanderEwert
    LeanderEwert committed Feb 7, 2024
    Configuration menu
    Copy the full SHA
    5810177 View commit details
    Browse the repository at this point in the history

Commits on Feb 19, 2024

  1. Added vectorized directives_cpp templates. 

    Modifications to main vector loop.
    @LeanderEwert
    LeanderEwert committed Feb 19, 2024
    Configuration menu
    Copy the full SHA
    032c630 View commit details
    Browse the repository at this point in the history

Commits on Mar 5, 2024

  1. Some cleanup pre-merge, ability to record non-existing states as perm… 

    …anent zero output and added error message when passing a parameter to the compartment creation that doesn't exist in the model.
    @LeanderEwert
    LeanderEwert committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    4dc48dd View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'nest-upstream/master' into origin/Leand… 

    …erEwert_vectorization
    @LeanderEwert
    LeanderEwert committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    59a2adb View commit details
    Browse the repository at this point in the history

  3. copy-right header fix.

    @LeanderEwert
    LeanderEwert committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    0a5f04c View commit details
    Browse the repository at this point in the history

  4. codestyle fix.

    @LeanderEwert
    LeanderEwert committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    74b6dda View commit details
    Browse the repository at this point in the history

  5. fixed concmech_model_test.

    @LeanderEwert
    LeanderEwert committed Mar 5, 2024
    Configuration menu
    Copy the full SHA
    1b85a61 View commit details
    Browse the repository at this point in the history

Commits on Mar 22, 2024

  1. Syntax changed so that continuous inputs don't have to be provided wi… 

    …th a unit anymore.

Bug fix by removing the consecutive area computation from pre_run_hook.
    @LeanderEwert
    LeanderEwert committed Mar 22, 2024
    Configuration menu
    Copy the full SHA
    b6cb9d8 View commit details
    Browse the repository at this point in the history

Commits on Apr 2, 2024

  1. Passive vectorization and unittest implemented.

    @LeanderEwert
    LeanderEwert committed Apr 2, 2024
    Configuration menu
    Copy the full SHA
    003fb47 View commit details
    Browse the repository at this point in the history

Commits on Apr 3, 2024

  1. fix copyright header

    @LeanderEwert
    LeanderEwert committed Apr 3, 2024
    Configuration menu
    Copy the full SHA
    e58556b View commit details
    Browse the repository at this point in the history

  2. codestyle fixes.

    @LeanderEwert
    LeanderEwert committed Apr 3, 2024
    Configuration menu
    Copy the full SHA
    2e293e8 View commit details
    Browse the repository at this point in the history

  3. codestyle fixes.

    @LeanderEwert
    LeanderEwert committed Apr 3, 2024
    Configuration menu
    Copy the full SHA
    d65eadd View commit details
    Browse the repository at this point in the history

  4. fixing I_stim continuous input syntax in test models.

    @LeanderEwert
    LeanderEwert committed Apr 3, 2024
    Configuration menu
    Copy the full SHA
    f7ccefa View commit details
    Browse the repository at this point in the history

Commits on Apr 4, 2024

  1. first step towards implicit euler, voltage recording problem

    @WillemWybo
    WillemWybo committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    0c3c9ae View commit details
    Browse the repository at this point in the history

  2. fix bug where compartment voltage readout pointers were not

    @WillemWybo
    WillemWybo committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    a9695db View commit details
    Browse the repository at this point in the history

  3. remove debug code from test

    @WillemWybo
    WillemWybo committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    e7456bb View commit details
    Browse the repository at this point in the history

  4. merge readout voltage fix 

    Merge branch 'LeanderEwert_vectorization' into implicit_euler
    @WillemWybo
    WillemWybo committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    369e849 View commit details
    Browse the repository at this point in the history

  5. cleanup of no longer used variables

    @WillemWybo
    WillemWybo committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    fd6feb0 View commit details
    Browse the repository at this point in the history

  6. increase margin in test to make it pass, a more precise version will … 

    …be in the master branch anyway
    @WillemWybo
    WillemWybo committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    f8e1766 View commit details
    Browse the repository at this point in the history

  7. additional vectorisations

    @WillemWybo
    WillemWybo committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    b897b09 View commit details
    Browse the repository at this point in the history

  8. rename construct_matrix_element() more appropriately and cleanup

    @WillemWybo
    WillemWybo committed Apr 4, 2024
    Configuration menu
    Copy the full SHA
    7bedd4a View commit details
    Browse the repository at this point in the history

Commits on Apr 11, 2024

  1. extended concentration test.

    @LeanderEwert
    LeanderEwert committed Apr 11, 2024
    Configuration menu
    Copy the full SHA
    67db6ca View commit details
    Browse the repository at this point in the history

  2. Revert "Syntax changed so that continuous inputs don't have to be pro… 

    …vided with a unit anymore."

This reverts commit b6cb9d8
    @LeanderEwert
    LeanderEwert committed Apr 11, 2024
    Configuration menu
    Copy the full SHA
    ce8b900 View commit details
    Browse the repository at this point in the history

  3. Merge pull request #1 from WillemWybo/implicit_euler 

    Switch integration algorithm to implicit Euler
    @LeanderEwert
    LeanderEwert committed Apr 11, 2024
    Configuration menu
    Copy the full SHA
    2e4634e View commit details
    Browse the repository at this point in the history

Commits on Apr 18, 2024

  1. common subexpression elimination implemented. Sadly no change in mode… 

    …l performance.
    @LeanderEwert
    LeanderEwert committed Apr 18, 2024
    Configuration menu
    Copy the full SHA
    8217d1f View commit details
    Browse the repository at this point in the history

Commits on Apr 23, 2024

  1. SIMD loops merged

    @LeanderEwert
    LeanderEwert committed Apr 23, 2024
    Configuration menu
    Copy the full SHA
    630f329 View commit details
    Browse the repository at this point in the history

Commits on Apr 29, 2024

  1. disabled common subexpression elimination.

    @LeanderEwert
    LeanderEwert committed Apr 29, 2024
    Configuration menu
    Copy the full SHA
    85670d5 View commit details
    Browse the repository at this point in the history

Commits on Apr 30, 2024

  1. python initialization extended to ODE vars.

    @LeanderEwert
    LeanderEwert committed Apr 30, 2024
    Configuration menu
    Copy the full SHA
    8320e07 View commit details
    Browse the repository at this point in the history

  2. Independent v_comp initialization added.

    @LeanderEwert
    LeanderEwert committed Apr 30, 2024
    Configuration menu
    Copy the full SHA
    ae29f05 View commit details
    Browse the repository at this point in the history

  3. new initialization test.

    @LeanderEwert
    LeanderEwert committed Apr 30, 2024
    Configuration menu
    Copy the full SHA
    06a6d52 View commit details
    Browse the repository at this point in the history