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NMODLanguage documentation improvements and addition of tests and examples#1996

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alexsavulescu merged 60 commits into
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magkanar/nmodl_docs_tests
Dec 14, 2022
Merged

NMODLanguage documentation improvements and addition of tests and examples#1996
alexsavulescu merged 60 commits into
masterfrom
magkanar/nmodl_docs_tests

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@iomaganaris

@iomaganaris iomaganaris commented Sep 28, 2022 •
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  • Added TODOs in current NMODL keywords documentation with keywords that were missing before and what is missing from each one
  • Added jupyter notebook with mod file examples and python scripts that showcase their usage
    • Added ability to execute it as well
  • Added tests based on the example mod files and scripts

Goals of this PR are:

  • Find out which NMODL keywords we want to keep (in documentation and functional) and which not
  • Add brief description in all of them
  • Update tests and examples based on LINEAR NONLINEAR LAG nmodl examples #2037

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✔️ 6995c9f -> Azure artifacts URL

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codecov-commenter commented Sep 28, 2022 •
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Codecov Report

Merging #1996 (1657fa6) into master (5c7cf73) will increase coverage by 0.05%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #1996      +/-   ##
==========================================
+ Coverage   50.17%   50.22%   +0.05%     
==========================================
  Files         626      626              
  Lines      125092   125093       +1     
==========================================
+ Hits        62762    62828      +66     
+ Misses      62330    62265      -65
Impacted Files Coverage Δ
src/nmodl/discrete.cpp 69.84% <100.00%> (+65.07%) ⬆️
src/oc/functabl.cpp 94.68% <100.00%> (+0.05%) ⬆️
src/nrnpython/nrnpy_nrn.cpp 75.32% <0.00%> (+0.72%) ⬆️
src/scopmath/ssimplic_thread.cpp 66.66% <0.00%> (+3.03%) ⬆️
src/nmodl/solve.cpp 76.57% <0.00%> (+5.40%) ⬆️

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@iomaganaris iomaganaris mentioned this pull request Dec 8, 2022
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alkino
alkino reviewed Dec 8, 2022
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Comment thread test/nmodl/test_function_table.py
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✔️ f576273 -> Azure artifacts URL

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@alkino alkino closed this Dec 13, 2022
@alkino alkino reopened this Dec 13, 2022
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Logfiles from GitLab pipeline #90259 (:no_entry:) have been uploaded here!

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@alkino

alkino commented Dec 13, 2022

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@iomaganaris can you remember me why we should remove CoreNeuron as REQUIREMENT for those tests?

What i don't understand is why it is compiled with nvhpc even if we didn't require gpu, @olupton ?

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Logfiles from GitLab pipeline #90429 (:white_check_mark:) have been uploaded here!

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@neuronsimulator neuronsimulator deleted a comment from bbpbuildbot Dec 14, 2022
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@iomaganaris

iomaganaris commented Dec 14, 2022

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@iomaganaris can you remember me why we should remove CoreNeuron as REQUIREMENT for those tests?

We needed to remove the coreneuron REQUIREment because this would mean that the test would run only when CoreNEURON is enabled.

What i don't understand is why it is compiled with nvhpc even if we didn't require gpu, @olupton ?

NVHPC (or nvc++ to be more accurate) can be used for compilation of CPU code as well. We just use it only in GPU builds because for CPU builds it doesn't generate more optimized code than Intel or other compilers. In the GPU builds even though it is used to compile all the CPU code of NEURON and CoreNEURON.

@alkino pretty good catch with importing numpy after neuron. I vaguely remember having this issue in the past but could you remind me what's the issue with that?

@alkino

alkino commented Dec 14, 2022

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The problem is that numpy seems to bring his own uncompatible version of MPI.

@alexsavulescu alexsavulescu merged commit dddfc0c into master Dec 14, 2022
@alexsavulescu alexsavulescu deleted the magkanar/nmodl_docs_tests branch December 14, 2022 12:06
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