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Update docs about possible MOD files compilation errors with >=9.0#3106

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Oct 3, 2024
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Update docs about possible MOD files compilation errors with >=9.0#3106
pramodk merged 4 commits into
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pramodk/mod-cpp-docs-9.0

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@pramodk

@pramodk pramodk commented Oct 1, 2024 •
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  • Add a table with all models and MOD files so that it would be easy for users to find the changed mod file.

  • Change version to >= 9.0

  • Add a link in the top-level README

  • Check if we should add a link to docs if nrnivmodl fails to compile.

Changes

With this PR, in top level README me / RTD landing page we have

image

And the table in the main docs looks like

image

fixes #1876

Script used to generate table

#!/bin/bash

repos=(
    "https://github.com/ModelDBRepository/2487/pull/1"
    "https://github.com/ModelDBRepository/2730/pull/1"
    "https://github.com/ModelDBRepository/2733/pull/1"
    "https://github.com/ModelDBRepository/3658/pull/1"
    "https://github.com/ModelDBRepository/7399/pull/1"
    "https://github.com/ModelDBRepository/7400/pull/1"
    "https://github.com/ModelDBRepository/8284/pull/1"
    "https://github.com/ModelDBRepository/9889/pull/1"
    "https://github.com/ModelDBRepository/12631/pull/2"
    "https://github.com/ModelDBRepository/26997/pull/1"
    "https://github.com/ModelDBRepository/35358/pull/2"
    "https://github.com/ModelDBRepository/37819/pull/1"
    "https://github.com/ModelDBRepository/51781/pull/1"
    "https://github.com/ModelDBRepository/52034/pull/1"
    "https://github.com/ModelDBRepository/64229/pull/1"
    "https://github.com/ModelDBRepository/64296/pull/1"
    "https://github.com/ModelDBRepository/87585/pull/1"
    "https://github.com/ModelDBRepository/93321/pull/1"
    "https://github.com/ModelDBRepository/97868/pull/2"
    "https://github.com/ModelDBRepository/97874/pull/2"
    "https://github.com/ModelDBRepository/97917/pull/2"
    "https://github.com/ModelDBRepository/105507/pull/2"
    "https://github.com/ModelDBRepository/106891/pull/3"
    "https://github.com/ModelDBRepository/113732/pull/1"
    "https://github.com/ModelDBRepository/116094/pull/1"
    "https://github.com/ModelDBRepository/116830/pull/1"
    "https://github.com/ModelDBRepository/116838/pull/1"
    "https://github.com/ModelDBRepository/116862/pull/1"
    "https://github.com/ModelDBRepository/123815/pull/1"
    "https://github.com/ModelDBRepository/136095/pull/1"
    "https://github.com/ModelDBRepository/136310/pull/1"
    "https://github.com/ModelDBRepository/137845/pull/1"
    "https://github.com/ModelDBRepository/138379/pull/1"
    "https://github.com/ModelDBRepository/139421/pull/1"
    "https://github.com/ModelDBRepository/140881/pull/1"
    "https://github.com/ModelDBRepository/141505/pull/1"
    "https://github.com/ModelDBRepository/144538/pull/1"
    "https://github.com/ModelDBRepository/144549/pull/1"
    "https://github.com/ModelDBRepository/144586/pull/1"
    "https://github.com/ModelDBRepository/146949/pull/1"
    "https://github.com/ModelDBRepository/149000/pull/1"
    "https://github.com/ModelDBRepository/149739/pull/1"
    "https://github.com/ModelDBRepository/150240/pull/1"
    "https://github.com/ModelDBRepository/150245/pull/1"
    "https://github.com/ModelDBRepository/150551/pull/1"
    "https://github.com/ModelDBRepository/150556/pull/1"
    "https://github.com/ModelDBRepository/150691/pull/1"
    "https://github.com/ModelDBRepository/151126/pull/1"
    "https://github.com/ModelDBRepository/151282/pull/1"
    "https://github.com/ModelDBRepository/153280/pull/1"
    "https://github.com/ModelDBRepository/154732/pull/1"
    "https://github.com/ModelDBRepository/155568/pull/1"
    "https://github.com/ModelDBRepository/155601/pull/1"
    "https://github.com/ModelDBRepository/155602/pull/1"
    "https://github.com/ModelDBRepository/156780/pull/1"
    "https://github.com/ModelDBRepository/157157/pull/1"
    "https://github.com/ModelDBRepository/168874/pull/4"
    "https://github.com/ModelDBRepository/181967/pull/1"
    "https://github.com/ModelDBRepository/182129/pull/1"
    "https://github.com/ModelDBRepository/183300/pull/1"
    "https://github.com/ModelDBRepository/185355/pull/2"
    "https://github.com/ModelDBRepository/185858/pull/1"
    "https://github.com/ModelDBRepository/186768/pull/1"
    "https://github.com/ModelDBRepository/187604/pull/2"
    "https://github.com/ModelDBRepository/189154/pull/1"
    "https://github.com/ModelDBRepository/194897/pull/2"
    "https://github.com/ModelDBRepository/195615/pull/1"
    "https://github.com/ModelDBRepository/223031/pull/1"
    "https://github.com/ModelDBRepository/225080/pull/1"
    "https://github.com/ModelDBRepository/231427/pull/2"
    "https://github.com/ModelDBRepository/232097/pull/1"
    "https://github.com/ModelDBRepository/239177/pull/1"
    "https://github.com/ModelDBRepository/241165/pull/1"
    "https://github.com/ModelDBRepository/241240/pull/1"
    "https://github.com/ModelDBRepository/244262/pull/1"
    "https://github.com/ModelDBRepository/244848/pull/2"
    "https://github.com/ModelDBRepository/247968/pull/1"
    "https://github.com/ModelDBRepository/249463/pull/1"
    "https://github.com/ModelDBRepository/256388/pull/1"
    "https://github.com/ModelDBRepository/259366/pull/1"
)


for repo_url in "${repos[@]}"; do
    base_repo_url=$(echo "$repo_url" | sed -E 's/(https:\/\/github\.com\/[^\/]+\/[^\/]+)\/pull\/.*/\1/')
    pull_request_id=$(echo "$repo_url" | sed -E 's/.*\/pull\/([0-9]+)$/\1/')

    json_output=$(gh repo view "$base_repo_url" --json name,url,description,homepageUrl)

    modeldb_id=$(echo "$json_output" | jq -r '.name')
    model_name=$(echo "$json_output" | jq -r '.description')

    if [ ${#model_name} -gt 50 ]; then
        model_name="${model_name:0:20}...${model_name: -30}"
    fi

    diff_output=$(gh pr diff "$pull_request_id" --name-only --repo "$base_repo_url")

    filtered_diff=$(echo "$diff_output" | grep -vE '^(README|.*\.(md|html|txt))$' | tr '\n' ' ')

    # concatenate the output
    echo -e "   * - \`$modeldb_id <https://modeldb.science/$modeldb_id>\`_\n     - $model_name\n     - \`ModelDBRepository/$modeldb_id <$base_repo_url>\`_\n     - \`pull/$pull_request_id <$repo_url/files>\`_ \n     - $filtered_diff"
done

@pramodk
Update docs about possible MOD files compilation errors with 9.0
775ec26 
- Add table with all models and MOD files so that it would be
  easy for users to find the changed mod file.
- Change version to >= 9.0
- Add link in  the top level README

fixes #1876
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azure-pipelines Bot commented Oct 1, 2024

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✔️ 775ec26 -> Azure artifacts URL

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codecov Bot commented Oct 2, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 66.89%. Comparing base (5b49b24) to head (2fcabe4).
Report is 2 commits behind head on master.

Additional details and impacted files 
@@           Coverage Diff           @@
##           master    #3106   +/-   ##
=======================================
  Coverage   66.89%   66.89%           
=======================================
  Files         572      572           
  Lines      106664   106664           
=======================================
  Hits        71348    71348           
  Misses      35316    35316

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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✔️ ac53e5c -> Azure artifacts URL

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@1uc

1uc commented Oct 2, 2024

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Is this just C->C++ or also about the new data structures? It might be nice to treat them as one topic or at least make sure that the datastructures related documentation is discoverable.

@pramodk

pramodk commented Oct 2, 2024

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Is this just C->C++ or also about the new data structures?

@1uc : this is only the user-facing parts and hence only C->C++ part for MOD files.

@pramodk

pramodk commented Oct 2, 2024 •
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@nrnhines: In issue #1876, we mentioned the following:

If compilation fails within nrnivmodl, we should provide an error message that includes a link to the C++ migration documentation.

If this seems beneficial, one potential approach would be to display a message when *.cpp compilation fails in nrnivmodl (or at the end), such as:

Note: If you are encountering compilation issues specifically with NEURON version 9.0 or later, please refer to the C++ migration guide at .

Do you think this would be helpful for users, or could it become more of a distraction than an aid?

@nrnhines

nrnhines commented Oct 2, 2024

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Do you think this would be helpful for users, or could it become more of a distraction than an aid?

Seems to me that that would be helpful.

pramodk
pramodk commented Oct 3, 2024
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Comment thread bin/nrnivmodl.in
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sonarqubecloud Bot commented Oct 3, 2024

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Please retry analysis of this Pull-Request directly on SonarCloud

nrnhines
nrnhines approved these changes Oct 3, 2024
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Great job!

Comment thread docs/guide/porting_mechanisms_to_cpp.rst
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bbpbuildbot commented Oct 3, 2024

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Logfiles from GitLab pipeline #234822 (:white_check_mark:) have been uploaded here!

Status and direct links:

@pramodk pramodk enabled auto-merge (squash) October 3, 2024 14:32
@azure-pipelines

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✔️ 2fcabe4 -> Azure artifacts URL

@pramodk pramodk merged commit 90f2ec2 into master Oct 3, 2024
@pramodk pramodk deleted the pramodk/mod-cpp-docs-9.0 branch October 3, 2024 15:14
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Improve C++ migration documentation and link to it from nrnivmodl

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