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Spinnaker new #11

Merged
merged 293 commits into from
Sep 21, 2023
Merged

Spinnaker new #11

merged 293 commits into from
Sep 21, 2023
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Mar 24, 2023

  1. Merge pull request nest#885 from clinssen/fix_sympy_predef_func 

    Fix conflict with sympy predefined/built-in functions
    @clinssen
    clinssen authored Mar 24, 2023
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  2. Fix OU noise tutorial notebook

    @pnbabu
    pnbabu committed Mar 24, 2023
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  3. Merge remote-tracking branch 'upstream/master' into fix_ou_noise_tuto… 

    …rial
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  4. Merge pull request nest#886 from pnbabu/fix_ou_noise_tutorial 

    Fix OU noise tutorial
    @clinssen
    clinssen authored Mar 24, 2023
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Commits on Mar 25, 2023

  1. spinnaker_test runs without errors

    @siirty
    siirty committed Mar 25, 2023
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Commits on Mar 29, 2023

  1. add erf() and erfc() to predefined maths functions (nest#889) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
    @clinssen
    clinssen and C.A.P. Linssen authored Mar 29, 2023
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Commits on Apr 5, 2023

  1. Remove end keyword from NESTML models (nest#866) 

    * Add lexer and parser for removing end keyword

* Remove end keyword for neuron models

* Remove end keyword for synapse models
---------

Co-authored-by: Jochen Martin Eppler <jougs@gmx.net>
    @pnbabu @jougs
    pnbabu and jougs authored Apr 5, 2023
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  2. Fix links in ipython notebooks

    @pnbabu
    pnbabu committed Apr 5, 2023
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Commits on Apr 11, 2023

  1. make sure continuous-time value buffers are properly initialized

    C.A.P. Linssen committed Apr 11, 2023
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Commits on Apr 12, 2023

  1. Merge pull request nest#890 from pnbabu/fix_ipynb_links 

    Fix links in ipython notebooks
    @clinssen
    clinssen authored Apr 12, 2023
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Commits on Apr 14, 2023

  1. Merge pull request nest#892 from clinssen/buffer_init 

    Make sure continuous-time value buffers are properly initialized
    @clinssen
    clinssen authored Apr 14, 2023
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Commits on Apr 17, 2023

  1. fix ternary operator handling

    C.A.P. Linssen committed Apr 17, 2023
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Commits on Apr 18, 2023

  1. fix ternary operator handling

    C.A.P. Linssen committed Apr 18, 2023
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Commits on Apr 19, 2023

  1. stash for laptop(example python impl)

    @siirty
    siirty committed Apr 19, 2023
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Commits on Apr 21, 2023

  1. updated template

    @siirty
    siirty committed Apr 21, 2023
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  2. improve name of GitHub Actions workflow

    @clinssen
    clinssen authored Apr 21, 2023
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  3. fix GitHub Actions status badge

    @clinssen
    clinssen authored Apr 21, 2023
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  4. Indent output block (nest#893)

    @pnbabu
    pnbabu authored Apr 21, 2023
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  5. Fix links in ipynb notebooks

    @pnbabu
    pnbabu committed Apr 21, 2023
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Commits on Apr 28, 2023

  1. Stash for laptop(Changed relevant python generation !UNDO later!)

    @siirty
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Commits on May 4, 2023

  1. Merge pull request nest#898 from pnbabu/fix_ipynb_links 

    Fix links in ipynb notebooks
    @clinssen
    clinssen authored May 4, 2023
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  2. Merge pull request nest#897 from clinssen/bail_error_strategy 

    Fix ternary operator handling
    @clinssen
    clinssen authored May 4, 2023
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  3. Fix accessing predefined time variable t in synapse event handlers (n… 

    …est#826)
    @clinssen
    clinssen authored May 4, 2023
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Commits on May 6, 2023

  1. fixed setup and bad directives

    @siirty
    siirty committed May 6, 2023
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  2. Fix numeric origin printer (nest#891)

    @clinssen
    clinssen authored May 6, 2023
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Commits on May 7, 2023

  1. Merge remote-tracking branch 'nest/master' into stash

    @le-schmidt
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Commits on May 8, 2023

  1. remove debug print statement (nest#899) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
    @clinssen
    clinssen and C.A.P. Linssen authored May 8, 2023
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  2. Fix spike buffer origin in GSL stepping function (nest#901)

    @clinssen
    clinssen authored May 8, 2023
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Commits on May 12, 2023

  1. Working iaf_psc_delta

    @le-schmidt
    le-schmidt committed May 12, 2023
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Commits on May 19, 2023

  1. Revert some unecessary changes

    @le-schmidt
    le-schmidt committed May 19, 2023
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  2. Cleanup for merge

    @le-schmidt
    le-schmidt committed May 19, 2023
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  3. Merge remote-tracking branch 'nest/master' into spinnaker-new

    @le-schmidt
    le-schmidt committed May 19, 2023
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  4. Merge branch 'merge_spinnaker' into spinnaker-new

    @le-schmidt
    le-schmidt committed May 19, 2023
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Commits on May 22, 2023

  1. forbid sympy >= 1.11 due to upstream bug (nest#906) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
    @clinssen
    clinssen and C.A.P. Linssen authored May 22, 2023
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Commits on May 24, 2023

  1. Add inputs if continous input

    @le-schmidt
    le-schmidt committed May 24, 2023
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  2. New template for constructor parameters with default values

    @le-schmidt
    le-schmidt committed May 24, 2023
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Commits on May 25, 2023

  1. stash

    @le-schmidt
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Commits on May 27, 2023

  1. Stash

    @le-schmidt
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Commits on May 28, 2023

  1. Stash

    @le-schmidt
    le-schmidt committed May 28, 2023
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Commits on Jun 7, 2023

  1. Fix links in docs (nest#913)

    @pnbabu
    pnbabu authored Jun 7, 2023
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  2. Add pandas dependency to the build workflow (nest#910) 

    * Test build

* Add pandas dependecy to Github Actions workflow
    @pnbabu
    pnbabu authored Jun 7, 2023
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  3. update version number for release

    C.A.P. Linssen committed Jun 7, 2023
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  4. add -post-dev suffix to version number to distinguish master branch v… 

    …ersion from release version
    C.A.P. Linssen committed Jun 7, 2023
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  5. update sphinx-doc version requirement

    @clinssen
    clinssen authored Jun 7, 2023
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  6. update sphinx-doc version requirement

    @clinssen
    clinssen authored Jun 7, 2023
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  7. update sphinx-doc version requirement

    @clinssen
    clinssen authored Jun 7, 2023
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  8. replace API doc link

    @clinssen
    clinssen authored Jun 7, 2023
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  9. replace API doc link

    @clinssen
    clinssen authored Jun 7, 2023
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  10. update sphinx-doc version requirement

    @clinssen
    clinssen authored Jun 7, 2023
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  11. fix formatting in docs

    @clinssen
    clinssen authored Jun 7, 2023
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  12. fix formatting in restructuredtext doc

    @clinssen
    clinssen authored Jun 7, 2023
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  13. update doc reference

    @clinssen
    clinssen authored Jun 7, 2023
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  14. update version numbers in doc requirements.txt to last known working

    @clinssen
    clinssen authored Jun 7, 2023
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Commits on Jun 8, 2023

  1. stash

    @le-schmidt
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  2. Remove and ignore reports

    @le-schmidt
    le-schmidt committed Jun 8, 2023
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  3. Removed more reports and ignored stash

    @le-schmidt
    le-schmidt committed Jun 8, 2023
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  4. Merge branch 'stash' into merge_spinnaker

    @le-schmidt
    le-schmidt committed Jun 8, 2023
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  5. Undo unnecessary changes

    @le-schmidt
    le-schmidt committed Jun 8, 2023
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  6. Clean before merge

    @le-schmidt
    le-schmidt committed Jun 8, 2023
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  7. Enable I_stim_grid_sum_

    @le-schmidt
    le-schmidt committed Jun 8, 2023
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  8. Merge branch 'merge_spinnaker' into spinnaker-new

    @le-schmidt
    le-schmidt committed Jun 8, 2023
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  9. Chnages from previous pull request

    @le-schmidt
    le-schmidt committed Jun 8, 2023
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  10. Remove :gihub from ignore

    @le-schmidt
    le-schmidt committed Jun 8, 2023
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Commits on Jun 10, 2023

  1. Changes on templates

    @le-schmidt
    le-schmidt committed Jun 10, 2023
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Commits on Jun 11, 2023

  1. stash

    @le-schmidt
    le-schmidt committed Jun 11, 2023
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Commits on Jun 12, 2023

  1. Merge remote-tracking branch 'origin/stash' into stash

    @le-schmidt
    le-schmidt committed Jun 12, 2023
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  2. stash

    @le-schmidt
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  3. Merge remote-tracking branch 'origin/stash' into stash

    @le-schmidt
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Commits on Jun 14, 2023

  1. restore neuron model from nest#403 (nest#719)

    @clinssen
    clinssen authored Jun 14, 2023
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Commits on Jun 15, 2023

  1. fix LaTeX formatting

    C.A.P. Linssen committed Jun 15, 2023
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Commits on Jun 18, 2023

  1. Integrated continuous inputs

    @le-schmidt
    le-schmidt committed Jun 18, 2023
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  2. Merge branch 'stash' of https://github.com/siirty/nestml into stash

    @le-schmidt
    le-schmidt committed Jun 18, 2023
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  3. Auto stash before merge of "stash" and "origin/stash"

    @le-schmidt
    le-schmidt committed Jun 18, 2023
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  4. Merge cleanup

    @le-schmidt
    le-schmidt committed Jun 18, 2023
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  5. Astropy units

    @le-schmidt
    le-schmidt committed Jun 18, 2023
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  6. indentation error

    @le-schmidt
    le-schmidt committed Jun 18, 2023
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  7. Integrate continuous input to python templates

    @le-schmidt
    le-schmidt committed Jun 18, 2023
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  8. Add continuous to struct

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Commits on Jun 21, 2023

  1. initialize volume transmitter pointer to null (nest#903) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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    clinssen and C.A.P. Linssen authored Jun 21, 2023
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  2. fix python_standalone code generator (nest#914) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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    clinssen and C.A.P. Linssen authored Jun 21, 2023
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Commits on Jun 22, 2023

  1. Integrate local changes

    @le-schmidt
    le-schmidt committed Jun 22, 2023
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  2. Fixed linebreak

    @le-schmidt
    le-schmidt committed Jun 22, 2023
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Commits on Jun 27, 2023

  1. Replace NEST typedefs in templates with plain C++ datatypes (nest#921) 

    * Replace NEST typedefs in templates with plain C++ datatypes

* Fix build errors

* Fix build errors
    @pnbabu
    pnbabu authored Jun 27, 2023
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Commits on Jun 28, 2023

  1. Reset continuous input on timestep update

    @le-schmidt
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  2. C and Spinnaker printer versions

    @le-schmidt
    le-schmidt committed Jun 28, 2023
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  3. Apply C and Spinnaker versions

    @le-schmidt
    le-schmidt committed Jun 28, 2023
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  4. Fixed problem with line breaks

    @le-schmidt
    le-schmidt committed Jun 28, 2023
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  5. Moved inputs init and removed unnecessary method

    @le-schmidt
    le-schmidt committed Jun 28, 2023
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  6. New line for readability

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    le-schmidt committed Jun 28, 2023
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  7. Added TODO

    @le-schmidt
    le-schmidt committed Jun 28, 2023
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  8. Switch to Spinnaker units

    @le-schmidt
    le-schmidt committed Jun 28, 2023
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Commits on Jun 29, 2023

  1. Use s1615 max instead of inf

    @le-schmidt
    le-schmidt committed Jun 29, 2023
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  2. Didn't want to call

    @le-schmidt
    le-schmidt committed Jun 29, 2023
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  3. Merge remote-tracking branch 'origin/stash' into stash

    @le-schmidt
    le-schmidt committed Jun 29, 2023
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  4. Moved recording defines

    @le-schmidt
    le-schmidt committed Jun 29, 2023
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  5. Spinnaker does not support bool literals

    @le-schmidt
    le-schmidt committed Jun 29, 2023
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  6. Merge branch 'stash' into merge_spinnaker

    @le-schmidt
    le-schmidt committed Jun 29, 2023
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  7. Merge branch 'merge_spinnaker' into spinnaker-new

    @le-schmidt
    le-schmidt committed Jun 29, 2023
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  8. Merge remote-tracking branch 'nest/master' into spinnaker-new

    @le-schmidt
    le-schmidt committed Jun 29, 2023
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  9. Undo accidental change

    @le-schmidt
    le-schmidt committed Jun 29, 2023
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  10. Merge branch 'spinnaker-new' into stash

    @le-schmidt
    le-schmidt committed Jun 29, 2023
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  11. replace == with equals

    @le-schmidt
    le-schmidt committed Jun 29, 2023
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Commits on Jun 30, 2023

  1. Missing newline in gerated code

    @le-schmidt
    le-schmidt committed Jun 30, 2023
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Commits on Jul 1, 2023

  1. Print int as unsigned int

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  2. Add printing for spinnaker datatypes

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  3. Use adaptive datatypes

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  4. generated code formatting

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  5. Using spinnaker specific datatype generation

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  6. remove TODO

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  7. Removed TODOS

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Commits on Jul 2, 2023

  1. Fixed errors

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Commits on Jul 3, 2023

  1. add funding acknowledgements to README (nest#926) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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  2. Synapse templates

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  3. Added templates to generator

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  4. Modified Model makefile (not working)

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Commits on Jul 5, 2023

  1. Add NEST code generator helper as workaround for module reloading (ne… 

    …st#791)

* add NEST code generator helper as workaround for module reloading

* add NEST code generator helper as workaround for module reloading

* add NEST code generator helper as workaround for module reloading

* add NEST code generator helper as workaround for module reloading

* use NEST code generator helper in all tutorial notebooks

---------

Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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Commits on Jul 6, 2023

  1. Removed strange null file

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  2. Run generated directly from project

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  3. Generate example

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  4. Removed old example template

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  5. include example in generation for neuron

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  6. Updated spinnaker

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  7. Symlink support

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  8. Removed null file

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  9. Merge branch 'stash' into spinnaker-new

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  10. copy generated example to example folder

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  11. Fixed errors in example

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  12. negation hack

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  13. Rename and apply hack

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  14. hack extension

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Commits on Jul 7, 2023

  1. switch to uint32

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  2. Undo extended hack

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  3. Merge branch 'stash' into spinnaker-new

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  4. Add make clean

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  5. Missed points where order is important

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  6. some more sort problems

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  7. Merge branch 'stash' into spinnaker-new

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Commits on Jul 10, 2023

  1. Printers cleanup (nest#922) 

    * printers cleanup

* printers cleanup

---------

Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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  2. Add test for string handling (nest#904) 

    * add test for string handling

* make test NEST2 compatible

---------

Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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  3. Added more templates

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  4. !! Fix cloning of AstSynapses

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Commits on Jul 12, 2023

  1. Print info instead of exception

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  2. Add line for generating synapse

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Commits on Jul 13, 2023

  1. fix LaTeX typesetting

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Commits on Jul 17, 2023

  1. Copy c files

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  2. Updated to changes in spinnaker

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  3. correct generation for makefile

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Commits on Jul 20, 2023

  1. Accidently commited change

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  2. Synapse basic API

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  3. Merge remote-tracking branch 'origin/stash' into stash

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  4. Auto stash before merge of "stash" and "origin/stash"

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  5. Changed synapse dynamics ending to c

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  6. Corrected spelling error

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  7. Full build

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  8. Updated used templates

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  9. Remove undefined

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  10. Undo change in neuron makefile

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  11. Fill API with static synapse

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  12. Remove defines not used for static

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  13. Merge branch 'stash' into spinnaker-new

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Commits on Jul 21, 2023

  1. Use "equals" instead of undefined "==" (nest#908) 

    * Moved from "==" to "equals" comparison

* fix static code check

---------

Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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Commits on Jul 26, 2023

  1. fix volume_transmitter naming after upstream change (nest/nest-simula… 

    …tor#2853) (nest#935)

Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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  2. Consistend naming

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Commits on Jul 27, 2023

  1. Test custom timing and weight

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  2. Removing logs

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  3. Fixed imports

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  4. Merge synapse_common and synapse_mad

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  5. Declare before use

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  6. Include synapse pair options

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  7. Merge branch 'stash' into spinnaker-new

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  8. refactor names in unit test

    @clinssen
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  9. fix test

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  10. Merge branch 'spinnaker-new' into stash

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  11. removed unnecessary method for copying synapses

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  12. Added TODOs for spinnaker example

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  13. Added weight in single file

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Commits on Jul 28, 2023

  1. Moving to one file, with errors

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  2. Undo changes for synapse cloning

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  3. Compile without errors

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  4. Test with static synapse

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  5. add Izhikevich model to STDP window test (nest#937) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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Commits on Aug 7, 2023

  1. independent fixes

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  2. Added transformer to allow post port in synapse

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  3. apply transformer

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  4. update to generator

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  5. updated templates

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  6. Merge branch 'stash' into spinnaker-new

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  7. split neuron to not use neuron reference

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Commits on Aug 8, 2023

  1. Trying to access post port

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  2. Add ceil, floor and round functions (nest#929)

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  3. Modify NEST version detection (nest#924)

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Commits on Aug 9, 2023

  1. change type() check to isinstance() (nest#941) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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  2. Fix NESTML printer (nest#930) 

    * fix NESTML printer

* fix NESTML printer

---------

Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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  3. run CI only on NEST 2, 3.0, 3.5, master (nest#943) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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  4. cancel in-progress CI runs (nest#942) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
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  5. Add ignore-and-fire neuron test (nest#934)

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  6. Fix and add test for second-order integration in neuromodulated synap… 

    …se (nest#905)
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  7. Add support for forward Euler integrator (nest#940)

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  8. add missing term in OU noise notebook

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Commits on Aug 10, 2023

  1. Hardcode pre and post detection

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  2. Undo changes to get_input_port_by_name

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  3. Add static synapse test (nest#933)

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  4. Fix type derivation of kernel buffers (nest#936)

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  5. Merge branch 'stash' into spinnaker-new

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  6. Merge remote-tracking branch 'upstream/master' into spinnaker-new

    C.A.P. Linssen committed Aug 10, 2023
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  7. fix merge

    C.A.P. Linssen committed Aug 10, 2023
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  8. spinnaker updates

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  9. merge test

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  10. Use pointers to reference substructs

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  11. Merge branch 'spinnaker-new' into stash

    @le-schmidt
    le-schmidt committed Aug 10, 2023
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  12. fix spinnaker builder

    @clinssen
    clinssen committed Aug 10, 2023
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  13. spinnaker updates

    @clinssen
    clinssen committed Aug 10, 2023
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  14. spinnaker updates

    @clinssen
    clinssen committed Aug 10, 2023
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  15. Add __init__.py in python_modules8

    @pnbabu
    pnbabu committed Aug 10, 2023
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Commits on Aug 16, 2023

  1. Merge remote-tracking branch 'origin/spinnaker-new' into stash

    @le-schmidt
    le-schmidt committed Aug 16, 2023
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Commits on Aug 17, 2023

  1. Updated test

    @le-schmidt
    le-schmidt committed Aug 17, 2023
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  2. Updated synapse templates

    @le-schmidt
    le-schmidt committed Aug 17, 2023
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  3. removed unnecessary test

    @le-schmidt
    le-schmidt committed Aug 17, 2023
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  4. add script

    @clinssen
    clinssen committed Aug 17, 2023
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  5. add script

    @clinssen
    clinssen committed Aug 17, 2023
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  6. Unnecessary code

    @le-schmidt
    le-schmidt committed Aug 17, 2023
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  7. Generate full state to weight state

    @le-schmidt
    le-schmidt committed Aug 17, 2023
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  8. Merge branch 'stash' into spinnaker-new

    @le-schmidt
    le-schmidt committed Aug 17, 2023
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  9. Split process function into sub-routines (nest#916)

    @med-ayssar
    med-ayssar authored Aug 17, 2023
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  10. Fixed all syntax errors

    @le-schmidt
    le-schmidt committed Aug 17, 2023
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  11. Fix type check for inline expressions (nest#945)

    @pnbabu
    pnbabu authored Aug 17, 2023
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Commits on Aug 23, 2023

  1. Don't throw exception on void

    @le-schmidt
    le-schmidt committed Aug 23, 2023
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  2. Exception on external variable

    @le-schmidt
    le-schmidt committed Aug 23, 2023
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  3. Synapse compiles

    @le-schmidt
    le-schmidt committed Aug 23, 2023
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Commits on Aug 24, 2023

  1. Added some fixed point arithmetic

    @le-schmidt
    le-schmidt committed Aug 24, 2023
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Commits on Aug 30, 2023

  1. Merge branch 'stash' into spinnaker-new

    @le-schmidt
    le-schmidt committed Aug 30, 2023
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Commits on Sep 4, 2023

  1. Remove units from spiking input ports (nest#882)

    @pnbabu
    pnbabu authored Sep 4, 2023
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Commits on Sep 13, 2023

  1. Fix input ports (nest#947)

    @pnbabu
    pnbabu authored Sep 13, 2023
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  2. Fix print function (nest#951)

    @pnbabu
    pnbabu authored Sep 13, 2023
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Commits on Sep 14, 2023

  1. Fix STDP synapse bug (nest-simulator #2443) (nest#843)

    @clinssen
    clinssen authored Sep 14, 2023
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Commits on Sep 15, 2023

  1. fix third-factor STDP test condition (nest#956) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
    @clinssen
    clinssen and C.A.P. Linssen authored Sep 15, 2023
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  2. add admonition to docs (nest#955) 

    Co-authored-by: C.A.P. Linssen <charl@turingbirds.com>
    @clinssen
    clinssen and C.A.P. Linssen authored Sep 15, 2023
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Commits on Sep 18, 2023

  1. Fix third factor STDP synapse test (nest#958)

    @clinssen
    clinssen authored Sep 18, 2023
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  2. Add/fix checks that inline expressions, parameters and internals cann… 

    …ot be assigned to (nest#953)
    @clinssen
    clinssen authored Sep 18, 2023
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  3. Fix power operator and elif functions in NESTML (nest#950)

    @pnbabu
    pnbabu authored Sep 18, 2023
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  4. Add linker flags to resolve linker errors in macOS (nest#954)

    @pnbabu
    pnbabu authored Sep 18, 2023
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Commits on Sep 21, 2023

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

    @pnbabu
    pnbabu committed Sep 21, 2023
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  2. Remove spinnaker-install directory

    @pnbabu
    pnbabu committed Sep 21, 2023
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  3. Fix pycodestyle errors

    @pnbabu
    pnbabu committed Sep 21, 2023
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  4. Fix templates

    @pnbabu
    pnbabu committed Sep 21, 2023
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  5. add support for SpiNNaker

    C.A.P. Linssen committed Sep 21, 2023
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  6. Comment out the synapses in the test

    @pnbabu
    pnbabu committed Sep 21, 2023
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  7. Fix pycodestyle errors

    @pnbabu
    pnbabu committed Sep 21, 2023
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  8. add support for SpiNNaker

    C.A.P. Linssen committed Sep 21, 2023
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  9. Merge remote-tracking branch 'le-schmidt/spinnaker-new' into spinnake… 

    …r-new
    C.A.P. Linssen committed Sep 21, 2023
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