63 benchmarking package development

.github/workflows/run-benchmark.yml

@@ -37,126 +37,18 @@ jobs:
       - name: Update environment
         run: mamba env update -n model-validation -f environment_benchmarks.yml
 
-      - name: generate-config-files
+      - name: Run Example linear-elastic-plate-with-hole_fenics using Benchmarking package
         shell: bash -l {0}
         run: |
-          cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
-          python generate_config.py
-
-      - name: run_linear-elastic-plate-with-hole-benchmarks_snakemake
-        shell: bash -l {0}
-        run: |
-          cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
-          snakemake --use-conda --force --cores 'all'
-          snakemake --use-conda --force --cores all \
-            --reporter metadata4ing \
-            --report-metadata4ing-paramscript ../common/parameter_extractor.py \
-            --report-metadata4ing-config metadata4ing.config \
-            --report-metadata4ing-filename $SNAKEMAKE_RESULT_FILE
-
-      - name: run_linear-elastic-plate-with-hole-benchmarks_nextflow
-        shell: bash -l {0}
-        run: |
-          cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
-          nextflow run main.nf -params-file workflow_config.json -c ../common/nextflow.config -plugins nf-prov@1.4.0
+          cd $GITHUB_WORKSPACE/examples/linear-elastic-plate-with-hole/fenics/
+          python run_benchmark.py
 
       - name: Archive Linear Elastic plate with a hole benchmark data for snakemake
         uses: actions/upload-artifact@v4
         with:
             name: snakemake_results_linear-elastic-plate-with-hole
             path: |
-              benchmarks/linear-elastic-plate-with-hole/${{ env.SNAKEMAKE_RESULT_FILE }}.zip
-
-      - name: Archive Linear Elastic plate with a hole benchmark data for nextflow
-        uses: actions/upload-artifact@v4
-        with:
-            name: nextflow_results_linear-elastic-plate-with-hole
-            path: |
-              benchmarks/linear-elastic-plate-with-hole/nextflow_results/
+              examples/linear-elastic-plate-with-hole/fenics/results/
 
-  process-artifacts:
-    runs-on: ubuntu-latest
-    needs: run-simulation
-    steps:
-      - name: Checkout repo content
-        uses: actions/checkout@v2
-
-      - name: Download artifact
-        uses: actions/download-artifact@v4
-        with:
-          name: snakemake_results_linear-elastic-plate-with-hole
-          path: ./artifact_files
 
-      - name: Unzip Snakemake Result File
-        run: |
-          mkdir -p ./$SNAKEMAKE_RESULT_FILE
-          unzip -o ./artifact_files/$SNAKEMAKE_RESULT_FILE.zip -d ./$SNAKEMAKE_RESULT_FILE
-
-      - name: Setup Mambaforge with postprocessing env
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-            miniforge-version: latest
-            activate-environment: postprocessing 
-            use-mamba: true
-            environment-file: benchmarks/linear-elastic-plate-with-hole/environment_postprocessing.yml
-
-      - name: Validate Snakemake Result File
-        shell: bash -l {0}
-        run: |
-          python benchmarks/common/validate_provenance.py \
-            --provenance_folderpath "./$SNAKEMAKE_RESULT_FILE" 
-
-      - name: Run plotting script
-        shell: bash -l {0}
-        run: |
-          python benchmarks/linear-elastic-plate-with-hole/plot_metrics.py \
-            --provenance_folderpath "./$SNAKEMAKE_RESULT_FILE" \
-            --output_file $PROVENANACE_FILE_NAME
-
-      - name: Upload snakemake results file as artifact
-        uses: actions/upload-artifact@v4
-        with:
-          name: element-size-vs-stress-plot
-          path: ${{ env.PROVENANACE_FILE_NAME }}
-
-      - name: Re-zip snakemake result folder
-        run: |
-          cd "./${SNAKEMAKE_RESULT_FILE}"
-          zip -r "../${SNAKEMAKE_RESULT_FILE}.zip" .
-
-      - name: Upload RoCrate Zip file onto RoHub
-        id: rohub_upload
-        shell: bash -l {0}
-        continue-on-error: true
-        run: |
-          LOG_FILE=rohub_upload_error.log
-
-          # Run Python and capture all stdout+stderr
-          python benchmarks/common/upload_provenance.py \
-            --provenance_folderpath "./${SNAKEMAKE_RESULT_FILE}.zip" \
-            --benchmark_name "linear-elastic-plate-with-hole" \
-            --username "${{ secrets.ROHUB_USERNAME }}" \
-            --password "${{ secrets.ROHUB_PASSWORD }}" \
-            2>&1 | tee "$LOG_FILE"
-
-          PYTHON_EXIT_CODE=${PIPESTATUS[0]}
-
-          # Check exit code: 0 = failure, 1 = success (per your convention)
-          if [ $PYTHON_EXIT_CODE -eq 0 ]; then
-            echo "=== RoHub upload failed — see log below ==="
-            cat "$LOG_FILE"
-          else
-            echo "✅ RoHub upload succeeded"
-            rm -f "$LOG_FILE"
-          fi
-
-          # Export exit code for subsequent steps if needed
-          echo "python_exit_code=$PYTHON_EXIT_CODE" >> $GITHUB_ENV
-
-      - name: Upload RoHub error log
-        if: ${{ env.python_exit_code == '0' }}
-        uses: actions/upload-artifact@v4
-        with:
-          name: rohub-upload-error-log
-          path: rohub_upload_error.log