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Add glif_psc_double_alpha model #2925

Merged
merged 51 commits into from
Sep 14, 2023
Merged

Add glif_psc_double_alpha model #2925

merged 51 commits into from
Sep 14, 2023

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shixnya
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@shixnya shixnya commented Sep 7, 2023

Continuation of PR #2861 that was accidentally closed.
The most recent change contains rebasing to the updated upstream/master, and fixing one of the newly added test cases in the updates.

Hopefully, this version passes all of the tests.

shixnya and others added 30 commits July 18, 2023 15:50
@shixnya
Merge pull request #1 from nest/master
3c797c1 
Merging recent changes
@shixnya
Adding GLIF with double alpha psc.
eee6c1c
@shixnya
Merge branch 'master' of https://github.com/shixnya/nest-simulator
bc45617
@shixnya
Cleaning up commented out codes
cd5698a 
(They were used during development.)
@shixnya
Variable name correction and adding tests
f5010ee 
Some of the parameters that are associated with the fast synaptic
components get '_fast' added to their names.

Pytest script added to test the GLIF model with double alpha synapses.

A couple of test cases require adding extra parameters for the
new glif_psc_double_alpha model, so they are added.
@shixnya
Making double-alpha description clearer
4d1c60e
@shixnya
Making math format LaTeX compatible
4bb6edb
@shixnya @clinssen
Update models/glif_psc_double_alpha.h
5500b15 
Co-authored-by: clinssen <c.linssen@fz-juelich.de>
@shixnya @clinssen
Update models/glif_psc_double_alpha.h
7222dd8 
Co-authored-by: clinssen <c.linssen@fz-juelich.de>
@shixnya @clinssen
Update models/glif_psc_double_alpha.h
e2a3aac 
Co-authored-by: clinssen <c.linssen@fz-juelich.de>
@shixnya @clinssen
Update models/glif_psc_double_alpha.h
c71e76c 
Co-authored-by: clinssen <c.linssen@fz-juelich.de>
@shixnya
black applied to a modified file
851f072
@shixnya
Merge branch 'master' of https://github.com/shixnya/nest-simulator
086f446
@shixnya
clang-format -i applied to committed files
222a617
@shixnya @nicolossus
Update models/glif_psc_double_alpha.h
b2940b5 
Co-authored-by: Nicolai Haug <39106781+nicolossus@users.noreply.github.com>
@shixnya @nicolossus
Update models/glif_psc_double_alpha.h
ecd4522 
Co-authored-by: Nicolai Haug <39106781+nicolossus@users.noreply.github.com>
@shixnya @nicolossus
Update models/glif_psc_double_alpha.h
097ecf6 
Co-authored-by: Nicolai Haug <39106781+nicolossus@users.noreply.github.com>
@shixnya @nicolossus
Update models/glif_psc_double_alpha.h
58b489d 
Co-authored-by: Nicolai Haug <39106781+nicolossus@users.noreply.github.com>
@shixnya @nicolossus
Update models/glif_psc_double_alpha.h
5084585 
Co-authored-by: Nicolai Haug <39106781+nicolossus@users.noreply.github.com>
@shixnya @nicolossus
Update models/glif_psc_double_alpha.h
0d752cd 
Co-authored-by: Nicolai Haug <39106781+nicolossus@users.noreply.github.com>
@shixnya
Adding double_alpha reference to glif_psc.h
56397f3
@shixnya
Merge branch 'master' of https://github.com/shixnya/nest-simulator
febfa9c
@shixnya
One more change for math notation
35dbf5e
@shixnya
Adding example, and reapplying clang-format
2dc50d8
@terhorstd @nicolossus
Apply suggestions from code review
f24d0de 
Co-authored-by: Nicolai Haug <39106781+nicolossus@users.noreply.github.com>
@shixnya
Adding GLIF with double alpha psc.
bf91769
@shixnya
Cleaning up commented out codes
b09fdda 
(They were used during development.)
@shixnya
Variable name correction and adding tests
ae50872 
Some of the parameters that are associated with the fast synaptic
components get '_fast' added to their names.

Pytest script added to test the GLIF model with double alpha synapses.

A couple of test cases require adding extra parameters for the
new glif_psc_double_alpha model, so they are added.
@shixnya
Making double-alpha description clearer
571dbc3
@shixnya
Making math format LaTeX compatible
2edb448
shixnya and others added 9 commits September 6, 2023 12:26
@shixnya @nicolossus
Update models/glif_psc_double_alpha.h
75b3ccb 
Co-authored-by: Nicolai Haug <39106781+nicolossus@users.noreply.github.com>
@shixnya @nicolossus
Update models/glif_psc_double_alpha.h
7ed402d 
Co-authored-by: Nicolai Haug <39106781+nicolossus@users.noreply.github.com>
@shixnya @nicolossus
Update models/glif_psc_double_alpha.h
e9232a9 
Co-authored-by: Nicolai Haug <39106781+nicolossus@users.noreply.github.com>
@shixnya
One more change for math notation
4f7ee9b
@shixnya
Adding example, and reapplying clang-format
6d6e9bd
@terhorstd @nicolossus @shixnya
Apply suggestions from code review
2152cbd 
Co-authored-by: Nicolai Haug <39106781+nicolossus@users.noreply.github.com>
@shixnya
Making the new test code compatible with
8500f3e 
glif_psc_double_alpha.
@shixnya
Merge branch 'master' of https://github.com/shixnya/nest-simulator
131a0bd
@shixnya
Merge branch 'nest:master' into master
10e8bb9
@heplesser heplesser added T: Enhancement New functionality, model or documentation S: Normal Handle this with default priority I: No breaking change Previously written code will work as before, no one should note anything changing (aside the fix) labels Sep 8, 2023
@heplesser heplesser added this to To do in Models via automation Sep 8, 2023
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@shixnya @nicolossus No problem to proceed here.
@clinssen @janskaar Could you re-review here quickly?

nicolossus
nicolossus approved these changes Sep 8, 2023
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LGTM!

janskaar
janskaar approved these changes Sep 8, 2023
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Everything looks good to me.

@clinssen clinssen changed the title Adding glif_psc_double_alpha model (2nd attempt) Adding glif_psc_double_alpha model Sep 12, 2023
@clinssen clinssen changed the title Adding glif_psc_double_alpha model Add glif_psc_double_alpha model Sep 12, 2023
jessica-mitchell
jessica-mitchell requested changes Sep 12, 2023
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Thanks @shixnya , I just a have couple of minor changes for the docs

pynest/examples/glif_psc_double_alpha_neuron.py Outdated Show resolved Hide resolved
pynest/examples/glif_psc_double_alpha_neuron.py Outdated Show resolved Hide resolved
Models automation moved this from To do to Review Sep 12, 2023
shixnya and others added 2 commits September 13, 2023 17:43
@shixnya @jessica-mitchell
Update pynest/examples/glif_psc_double_alpha_neuron.py
5df9403 
Co-authored-by: jessica-mitchell <mitchell20j@gmail.com>
@shixnya @jessica-mitchell
Update pynest/examples/glif_psc_double_alpha_neuron.py
1e9e65e 
Co-authored-by: jessica-mitchell <mitchell20j@gmail.com>
jessica-mitchell
jessica-mitchell approved these changes Sep 14, 2023
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thanks!

@heplesser heplesser merged commit 8c33673 into nest:master Sep 14, 2023
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Models automation moved this from Review to Done Sep 14, 2023
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shixnya commented Sep 15, 2023

Thank you so much, all, for your help!

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@jessica-mitchell jessica-mitchell jessica-mitchell approved these changes

@janskaar janskaar janskaar approved these changes

@nicolossus nicolossus nicolossus approved these changes

@clinssen clinssen clinssen approved these changes

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I: No breaking change Previously written code will work as before, no one should note anything changing (aside the fix) S: Normal Handle this with default priority T: Enhancement New functionality, model or documentation
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@shixnya @heplesser @jessica-mitchell @janskaar @nicolossus @clinssen @terhorstd