NEURON ModelDB CI #1569
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| name: NEURON ModelDB CI | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [ master ] | |
| schedule: | |
| # Run at 2am every day | |
| - cron: '0 2 * * *' | |
| workflow_call: | |
| inputs: | |
| neuron_v1: | |
| description: Last official release (neuron) / NEURON pinned version / Azure drop (artifacts) url | |
| default: 'neuron' | |
| required: true | |
| type: string | |
| neuron_v2: | |
| description: Last nightly release (neuron-nightly) / NEURON pinned version / Azure drop (artifacts) url | |
| default: 'neuron-nightly' | |
| required: true | |
| type: string | |
| models_to_run: | |
| description: 'Empty for all models, space separated accession numbers for specific models' | |
| default: '' | |
| required: false | |
| type: string | |
| repo: | |
| default: 'neuronsimulator/nrn-modeldb-ci' | |
| type: string | |
| required: false | |
| workflow_dispatch: | |
| inputs: | |
| neuron_v1: | |
| description: Last official release (neuron) / NEURON pinned version / Azure drop (artifacts) url | |
| default: 'neuron' | |
| required: true | |
| neuron_v2: | |
| description: Last nightly release (neuron-nightly) / NEURON pinned version / Azure drop (artifacts) url | |
| default: 'neuron-nightly' | |
| required: true | |
| models_to_run: | |
| description: 'Empty for all models, space separated accession numbers for specific models' | |
| default: '' | |
| required: false | |
| jobs: | |
| nrn-modeldb-ci: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| env: | |
| DISPLAY: ${{ ':0' }} | |
| NEURON_V1: ${{ github.event.inputs.neuron_v1 || inputs.neuron_v1 || 'neuron' }} | |
| NEURON_V2: ${{ github.event.inputs.neuron_v2 || inputs.neuron_v2 || 'neuron-nightly' }} | |
| MODELS_TO_RUN: ${{ github.event.inputs.models_to_run || inputs.models_to_run || '' }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: ${{ inputs.repo || github.repository }} | |
| - name: check for Azure drop NEURON_V1 -> ${{ env.NEURON_V1 }} | |
| if: startsWith(env.NEURON_V1, 'https://dev.azure.com/neuronsimulator/') | |
| run: | | |
| # check URI | |
| curl -sfSI -X GET '${{ env.NEURON_V1 }}' | |
| # Download Azure drop and unzip | |
| AZURE_DROP_URL="$NEURON_V1" | |
| rm -rf drop | |
| wget --tries=4 -LO DROP_V1.zip ${AZURE_DROP_URL} | |
| unzip DROP_V1.zip | |
| mv drop DROP_V1 | |
| # Set drop dir in the env | |
| echo "DROP_DIR_V1=`pwd`/DROP_V1" >> $GITHUB_ENV | |
| - name: check for Azure drop NEURON_V2 -> ${{ env.NEURON_V2 }} | |
| if: startsWith(env.NEURON_V2, 'https://dev.azure.com/neuronsimulator/') | |
| run: | | |
| # check URI | |
| curl -sfSI -X GET '${{ env.NEURON_V2 }}' | |
| # Download Azure drop and unzip | |
| AZURE_DROP_URL="$NEURON_V2" | |
| rm -rf drop | |
| wget --tries=4 -LO DROP_V2.zip ${AZURE_DROP_URL} | |
| unzip DROP_V2.zip | |
| mv drop DROP_V2 | |
| # Set drop dir in the env | |
| echo "DROP_DIR_V2=`pwd`/DROP_V2" >> $GITHUB_ENV | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: Set models to run for PR | |
| run: | | |
| # For PRs we only have a few models for quick sanity checking. | |
| # Once the PR is green you need to manually run the ModelDB CI workflow by simply selecting your branch in the UI. | |
| # The follwing selection aims to target different features (since we haven't worked on unit testing yet -> #38 ). | |
| # Select a few models to run CI for PRs: | |
| # 64195 -> run: null | |
| # 22203 -> skip: true | |
| # 156120 -> several model directories | |
| # 97868 -> failed nrnivmodl | |
| # 146030 -> curate_patterns | |
| # 244679 -> no entry in modeldb-run.yaml | |
| # rest: -> currently yielding differences in the pipeline | |
| echo 'MODELS_TO_RUN=64195 22203 156120 51781 97868 22203 97756 97917 105507 136803 138379 138382 146030 244679 251881' >> $GITHUB_ENV | |
| # parse PR description for models to run | |
| parse_models=$(gh pr view $PR_URL --json body -q '.body | capture("(MODELS_TO_RUN=)(?<models>\\d+( \\d+)*)")') | |
| if [ ! -z "$parse_models" ]; then | |
| echo "MODELS_TO_RUN=$(echo $parse_models | jq -r .models)" >> $GITHUB_ENV | |
| fi | |
| if: github.event_name == 'pull_request' && inputs.repo == '' | |
| env: | |
| PR_URL: ${{ github.event.pull_request.html_url }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Install dependencies and project | |
| id: install-deps | |
| run: | | |
| set | |
| # Set up Xvfb | |
| sudo apt-get install xvfb | |
| sudo /usr/bin/Xvfb $DISPLAY -screen 0 1600x1200x24 -noreset -nolock -shmem & # run in bg | |
| # Install python dependencies | |
| python -m pip install --upgrade 'pip<=24.0' | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| #Install project in editable mode | |
| python -m pip install -e . | |
| - name: Cache ModelDB models | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| cache | |
| modeldb/modeldb-meta.yaml | |
| key: dynamic-models | |
| - name: Get ModelDB models | |
| run: getmodels $MODELS_TO_RUN | |
| - name: Run Models with NEURON V1 -> ${{ env.NEURON_V1 }} | |
| run: | | |
| # Install NEURON V1 | |
| if [[ -d "${DROP_DIR_V1}" ]]; then | |
| # due to https://github.com/pypa/pip/issues/12110 we cannot rely on `--find-links` | |
| # so we use a workaround | |
| for wheel in "${DROP_DIR_V1}"/*.whl | |
| do | |
| if ! python -m pip install --user "${wheel}" | |
| then | |
| echo "Unable to install ${wheel}, trying another one" | |
| else | |
| echo "Successfully installed ${wheel}" | |
| break | |
| fi | |
| done | |
| else | |
| python -m pip install $NEURON_V1 | |
| fi | |
| nrn_ver=`python -c "from neuron import __version__ as nrn_ver; print(nrn_ver)"` | |
| runmodels --gout --workdir=$nrn_ver $MODELS_TO_RUN | |
| # Filter out the gout data before generating HTML reports. The HTML | |
| # diff uses the original gout files on disk anyway. Compress the large | |
| # JSON file including gout data for inclusion in the artifacts | |
| mv ${nrn_ver}.json ${nrn_ver}-full.json | |
| jq -r 'del(.[].gout)' ${nrn_ver}-full.json > ${nrn_ver}.json | |
| xz ${nrn_ver}-full.json | |
| report2html ${nrn_ver}.json | |
| if [[ -d "${DROP_DIR_V1}" ]]; then | |
| python -m pip uninstall --yes neuron-nightly==${nrn_ver} | |
| else | |
| python -m pip uninstall --yes $NEURON_V1 | |
| fi | |
| echo "nrn1_ver=$nrn_ver" >> $GITHUB_ENV | |
| - name: Run Models with NEURON V2 -> ${{ env.NEURON_V2 }} | |
| if: env.NEURON_V1 != env.NEURON_V2 | |
| run: | | |
| # Install NEURON V2 | |
| if [[ -d "${DROP_DIR_V2}" ]]; then | |
| # due to https://github.com/pypa/pip/issues/12110 we cannot rely on `--find-links` | |
| # so we use a workaround | |
| for wheel in "${DROP_DIR_V2}"/*.whl | |
| do | |
| if ! python -m pip install --user "${wheel}" | |
| then | |
| echo "Unable to install ${wheel}, trying another one" | |
| else | |
| echo "Successfully installed ${wheel}" | |
| break | |
| fi | |
| done | |
| else | |
| python -m pip install $NEURON_V2 | |
| fi | |
| nrn_ver=`python -c "from neuron import __version__ as nrn_ver; print(nrn_ver)"` | |
| runmodels --gout --workdir=$nrn_ver $MODELS_TO_RUN | |
| # Filter out the gout data before generating HTML reports. The HTML | |
| # diff uses the original gout files on disk anyway. Compress the large | |
| # JSON file including gout data for inclusion in the artifacts | |
| mv ${nrn_ver}.json ${nrn_ver}-full.json | |
| jq -r 'del(.[].gout)' ${nrn_ver}-full.json > ${nrn_ver}.json | |
| xz ${nrn_ver}-full.json | |
| report2html ${nrn_ver}.json | |
| if [[ -d "${DROP_DIR_V2}" ]]; then | |
| python -m pip uninstall --yes neuron-nightly==${nrn_ver} | |
| else | |
| python -m pip uninstall --yes $NEURON_V2 | |
| fi | |
| echo "nrn2_ver=$nrn_ver" >> $GITHUB_ENV | |
| - name: diffreports2html ${{ env.nrn1_ver }}.json <-> ${{ env.nrn2_ver }}.json | |
| if: env.NEURON_V1 != env.NEURON_V2 | |
| run: | | |
| diffreports2html ${nrn1_ver}.json ${nrn2_ver}.json | |
| - uses: actions/upload-artifact@v4 | |
| if: ${{ always() }} | |
| with: | |
| name: ${{ env.nrn1_ver }}-vs-${{ env.nrn2_ver }} | |
| path: | | |
| ./*.json.xz | |
| ./*.html |