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Sarbani-RoySarbani-Roy
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Merge main and restore run-benchmark.yml
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‎.github/workflows/run-benchmark.yml‎

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name: CI
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on:
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push:
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pull_request:
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branches: [ main ]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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# Runs the workflow once per day at 3:15am
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schedule:
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- cron: '3 16 * * *'
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env:
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CACHE_NUMBER: 1 # increase to reset cache manually
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SNAKEMAKE_RESULT_FILE: metadata4ing_provenance
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PROVENANACE_FILE_NAME: element_size_vs_max_mises_stress.pdf
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jobs:
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run-simulation:
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runs-on: ubuntu-latest
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steps:
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- name: checkout repo content
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uses: actions/checkout@v2
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- name: Setup Mambaforge
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-version: latest
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activate-environment: model-validation
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use-mamba: true
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- name: Set strict channel priority
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run: conda config --set channel_priority strict
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- name: Update environment
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run: mamba env update -n model-validation -f environment_benchmarks.yml
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- name: generate-config-files
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shell: bash -l {0}
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run: |
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cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
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python generate_config.py
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- name: run_linear-elastic-plate-with-hole-benchmarks_snakemake
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shell: bash -l {0}
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run: |
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cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
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snakemake --use-conda --force --cores 'all'
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snakemake --use-conda --force --cores all \
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--reporter metadata4ing \
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--report-metadata4ing-paramscript ../common/parameter_extractor.py \
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--report-metadata4ing-config metadata4ing.config \
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--report-metadata4ing-filename $SNAKEMAKE_RESULT_FILE
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- name: run_linear-elastic-plate-with-hole-benchmarks_nextflow
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shell: bash -l {0}
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run: |
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cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
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nextflow run main.nf -params-file workflow_config.json -c ../common/nextflow.config -plugins nf-prov@1.4.0
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- name: Archive Linear Elastic plate with a hole benchmark data for snakemake
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uses: actions/upload-artifact@v4
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with:
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name: snakemake_results_linear-elastic-plate-with-hole
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path: |
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benchmarks/linear-elastic-plate-with-hole/${{ env.SNAKEMAKE_RESULT_FILE }}.zip
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- name: Archive Linear Elastic plate with a hole benchmark data for nextflow
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uses: actions/upload-artifact@v4
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with:
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name: nextflow_results_linear-elastic-plate-with-hole
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path: |
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benchmarks/linear-elastic-plate-with-hole/nextflow_results/
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process-artifacts:
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runs-on: ubuntu-latest
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needs: run-simulation
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steps:
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- name: Checkout repo content
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uses: actions/checkout@v2
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- name: Download artifact
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uses: actions/download-artifact@v4
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with:
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name: snakemake_results_linear-elastic-plate-with-hole
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path: ./artifact_files
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- name: Unzip Snakemake Result File
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run: |
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mkdir -p ./$SNAKEMAKE_RESULT_FILE
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unzip -o ./artifact_files/$SNAKEMAKE_RESULT_FILE.zip -d ./$SNAKEMAKE_RESULT_FILE
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- name: Setup Mambaforge with postprocessing env
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-version: latest
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activate-environment: postprocessing
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use-mamba: true
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environment-file: benchmarks/linear-elastic-plate-with-hole/environment_postprocessing.yml
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- name: Validate Snakemake Result File
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shell: bash -l {0}
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run: |
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python benchmarks/common/validate_provenance.py \
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--provenance_folderpath "./$SNAKEMAKE_RESULT_FILE"
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- name: Run plotting script
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shell: bash -l {0}
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run: |
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python benchmarks/linear-elastic-plate-with-hole/plot_metrics.py \
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--provenance_folderpath "./$SNAKEMAKE_RESULT_FILE" \
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--output_file $PROVENANACE_FILE_NAME
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- name: Upload snakemake results file as artifact
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uses: actions/upload-artifact@v4
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with:
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name: element-size-vs-stress-plot
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path: ${{ env.PROVENANACE_FILE_NAME }}
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- name: Re-zip snakemake result folder
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run: |
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cd "./${SNAKEMAKE_RESULT_FILE}"
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zip -r "../${SNAKEMAKE_RESULT_FILE}.zip" .
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- name: Upload RoCrate Zip file onto RoHub
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id: rohub_upload
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shell: bash -l {0}
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continue-on-error: true
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run: |
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LOG_FILE=rohub_upload_error.log
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# Run Python and capture all stdout+stderr
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python benchmarks/common/upload_provenance.py \
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--provenance_folderpath "./${SNAKEMAKE_RESULT_FILE}.zip" \
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--benchmark_name "linear-elastic-plate-with-hole" \
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--username "${{ secrets.ROHUB_USERNAME }}" \
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--password "${{ secrets.ROHUB_PASSWORD }}" \
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2>&1 | tee "$LOG_FILE"
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PYTHON_EXIT_CODE=${PIPESTATUS[0]}
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# Check exit code: 0 = failure, 1 = success (per your convention)
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if [ $PYTHON_EXIT_CODE -eq 0 ]; then
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echo "=== RoHub upload failed — see log below ==="
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cat "$LOG_FILE"
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else
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echo "✅ RoHub upload succeeded"
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rm -f "$LOG_FILE"
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fi
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# Export exit code for subsequent steps if needed
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echo "python_exit_code=$PYTHON_EXIT_CODE" >> $GITHUB_ENV
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- name: Upload RoHub error log
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if: ${{ env.python_exit_code == '0' }}
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uses: actions/upload-artifact@v4
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with:
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name: rohub-upload-error-log
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path: rohub_upload_error.log
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‎.github/workflows/run-julia-benchmark.yml‎

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name: Julia-CI
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on:
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push:
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pull_request:
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branches: [ main ]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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# Runs the workflow once per day at 3:15am
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schedule:
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- cron: '3 16 * * *'
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env:
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CACHE_NUMBER: 1 # increase to reset cache manually
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jobs:
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tests:
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runs-on: ubuntu-latest
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steps:
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- name: checkout repo content
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uses: actions/checkout@v2
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- name: Setup Mambaforge
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-version: latest
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activate-environment: model-validation
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use-mamba: true
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- name: Setup Apptainer
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uses: eWaterCycle/setup-apptainer@v2
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with:
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apptainer-version: 1.4.5
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- name: Set strict channel priority
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run: conda config --set channel_priority strict
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- name: Update environment
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run: mamba env update -n model-validation -f environment_benchmarks.yml
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- name: generate-config-files
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shell: bash -l {0}
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run: |
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cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
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python generate_config.py
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- name: run_linear-elastic-plate-with-hole-benchmarks_snakemake
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shell: bash -l {0}
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run: |
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cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
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snakemake --use-conda --use-apptainer --cores=all --config tools=[extendablefem] configurations=["1","05","025","0125","00625","003125"]

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