Apptainer installation in conda environment #675
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| name: CI | |
| on: | |
| push: | |
| pull_request: | |
| branches: [ main ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| # Runs the workflow once per day at 3:15am | |
| schedule: | |
| - cron: '3 16 * * *' | |
| env: | |
| CACHE_NUMBER: 1 # increase to reset cache manually | |
| SNAKEMAKE_RESULT_FILE: metadata4ing_provenance | |
| PROVENANACE_FILE_NAME: element_size_vs_max_mises_stress.pdf | |
| jobs: | |
| run-simulation: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout repo content | |
| uses: actions/checkout@v2 | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| activate-environment: model-validation | |
| use-mamba: true | |
| - name: Set strict channel priority | |
| run: conda config --set channel_priority strict | |
| - name: Update environment | |
| run: mamba env update -n model-validation -f environment_benchmarks.yml | |
| - name: generate-config-files | |
| 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 $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/ | |
| nextflow run main.nf -params-file workflow_config.json -c ../common/nextflow.config -plugins nf-prov@1.4.0 | |
| - name: Archive Linear Elastic plate with a hole benchmark data for snakemake | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: snakemake_results_linear-elastic-plate-with-hole | |
| path: | | |
| benchmarks/linear-elastic-plate-with-hole/${{ 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/ | |
| 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 | |