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Compatibility with SOA NEURON data structures#989

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olupton/fixes-for-soa-neuron
Jun 5, 2023
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Compatibility with SOA NEURON data structures#989
olupton merged 5 commits into
masterfrom
olupton/fixes-for-soa-neuron

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@olupton olupton commented Jan 9, 2023 •
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The data structure changes in neuronsimulator/nrn#2027 required additional "pdata` entries on the NEURON side (to avoid pointer arithmetic between ion variable data).

CoreNEURON assumes/enforces that its data structures are "very similar" to NEURON's, so this has to change on the CoreNEURON/mod2c/NMODL side too.

TODO:

CI_BRANCHES:NEURON_BRANCH=olupton/data-structures-including-mechanisms

@olupton olupton changed the title Olupton/fixes for soa neuron Compatibility with SOA NEURON data structures Jan 9, 2023
@olupton olupton marked this pull request as draft January 9, 2023 08:52
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from 592f9fc to caacb40 Compare January 23, 2023 19:40
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from caacb40 to 9897134 Compare January 25, 2023 22:57
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from 9897134 to 01e1e1a Compare February 7, 2023 13:19
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from 01e1e1a to c152118 Compare February 17, 2023 08:50
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from c152118 to 6211364 Compare February 22, 2023 14:49
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from eb86d96 to d51cac1 Compare February 23, 2023 20:38
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from d51cac1 to b5e375a Compare February 23, 2023 21:21
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codecov Bot commented Feb 23, 2023 •
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Codecov Report

Merging #989 (b6b7f15) into master (74d7dbe) will increase coverage by 0.13%.
The diff coverage is 100.00%.

❗ Current head b6b7f15 differs from pull request most recent head 2a2c793. Consider uploading reports for the commit 2a2c793 to get more accurate results

@@            Coverage Diff             @@
##           master     #989      +/-   ##
==========================================
+ Coverage   69.95%   70.09%   +0.13%     
==========================================
  Files         188      190       +2     
  Lines       25639    25823     +184     
==========================================
+ Hits        17937    18101     +164     
- Misses       7702     7722      +20
Impacted Files Coverage Δ
src/codegen/codegen_info.hpp 100.00% <ø> (ø)
test/unit/codegen/codegen_cpp_visitor.cpp 100.00% <ø> (ø)
src/codegen/codegen_cpp_visitor.cpp 85.82% <100.00%> (+0.11%) ⬆️

... and 20 files with indirect coverage changes

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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from b5e375a to e6279dc Compare February 24, 2023 09:07
@olupton olupton marked this pull request as ready for review February 24, 2023 09:08
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from e6279dc to 425311e Compare March 9, 2023 08:37
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pramodk
pramodk approved these changes Mar 20, 2023
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LGTM

Comment thread test/unit/visitor/sympy_solver.cpp Outdated
Comment thread src/codegen/codegen_cpp_visitor.cpp
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from 4c884b3 to b8966be Compare March 24, 2023 07:58
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from b8966be to ec9865d Compare April 20, 2023 14:46
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from ec9865d to 4657e08 Compare April 27, 2023 12:31
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from 4ab8fca to 4c90946 Compare May 2, 2023 11:00
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@olupton olupton mentioned this pull request May 2, 2023
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@olupton olupton force-pushed the olupton/fixes-for-soa-neuron branch from b6b7f15 to 2a2c793 Compare May 25, 2023 06:03
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Logfiles from GitLab pipeline #126377 (:white_check_mark:) have been uploaded here!

Status and direct links:

@olupton olupton merged commit 2ce4a2b into master Jun 5, 2023
@olupton olupton deleted the olupton/fixes-for-soa-neuron branch June 5, 2023 14:57
JCGoran pushed a commit to neuronsimulator/nrn that referenced this pull request Mar 12, 2025
@olupton
Compatibility with SoA NEURON data structures (BlueBrain/nmodl#989)
9cc7e78 
* Ion variables: be explicit to match SoA NEURON
* Added test for case of "have_ionout && !have_ionin" for coverage

Co-authored-by: Ioannis Magkanaris <iomagkanaris@gmail.com>

NMODL Repo SHA: BlueBrain/nmodl@2ce4a2b
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@pramodk pramodk pramodk approved these changes
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