Add separate pipeline to check output against compliance-checker #1
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| name: compliance_check | |
| on: | |
| pull_request: | |
| branches: | |
| workflow_dispatch: | |
| # cancel running jobs if theres a newer push | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| jobs: | |
| compliance-checker: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout Files | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Setup Conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: fremorizer-compliance | |
| python-version: "3.12" | |
| auto-activate-base: false | |
| miniforge-version: latest | |
| channels: conda-forge,noaa-gfdl | |
| - name: Configure Conda | |
| run: | | |
| echo "removing main and r channels from defaults" | |
| conda config --remove channels defaults || true | |
| conda config --remove channels main || true | |
| conda config --remove channels r || true | |
| echo "setting strict channel priority" | |
| conda config --set channel_priority strict | |
| echo "printing conda config just in case" | |
| conda config --show | |
| - name: Install dependencies for fremorizer | |
| run: | | |
| conda install -y \ | |
| conda-forge::cftime \ | |
| "conda-forge::click>=8.2" \ | |
| "conda-forge::cmor>=3.14" \ | |
| "conda-forge::netcdf4>=1.7" \ | |
| "conda-forge::numpy>=2" \ | |
| conda-forge::pyyaml \ | |
| conda-forge::pytest | |
| - name: Install compliance-checker | |
| run: | | |
| conda install -y conda-forge::compliance-checker | |
| - name: Install fremorizer | |
| run: | | |
| pip install . | |
| - name: Run tests to generate output files | |
| run: | | |
| pytest fremorizer/tests/test_cmor_run_subtool.py -v | |
| continue-on-error: true | |
| - name: Find generated NetCDF files | |
| id: find_files | |
| run: | | |
| echo "Searching for generated NetCDF files..." | |
| find fremorizer/tests/test_files/outdir -name "*.nc" -type f > /tmp/netcdf_files.txt || true | |
| if [ -s /tmp/netcdf_files.txt ]; then | |
| echo "Found NetCDF files:" | |
| cat /tmp/netcdf_files.txt | |
| echo "file_count=$(wc -l < /tmp/netcdf_files.txt)" >> $GITHUB_OUTPUT | |
| else | |
| echo "No NetCDF files found" | |
| echo "file_count=0" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Run compliance-checker on outputs | |
| if: steps.find_files.outputs.file_count != '0' | |
| run: | | |
| echo "Running IOOS Compliance Checker on generated NetCDF files..." | |
| mkdir -p /tmp/compliance_reports | |
| while IFS= read -r ncfile; do | |
| if [ -f "$ncfile" ]; then | |
| basename=$(basename "$ncfile" .nc) | |
| echo "" | |
| echo "==========================================" | |
| echo "Checking: $ncfile" | |
| echo "==========================================" | |
| # Run compliance checker with CF conventions | |
| # Generate text report (for viewing in logs) | |
| compliance-checker \ | |
| --test=cf \ | |
| --criteria=normal \ | |
| --verbose \ | |
| --format=text \ | |
| --output=/tmp/compliance_reports/${basename}_report.txt \ | |
| "$ncfile" || true | |
| # Also generate HTML report (for artifact download) | |
| compliance-checker \ | |
| --test=cf \ | |
| --criteria=normal \ | |
| --format=html \ | |
| --output=/tmp/compliance_reports/${basename}_report.html \ | |
| "$ncfile" 2>&1 || true | |
| # Display the text report | |
| cat /tmp/compliance_reports/${basename}_report.txt || true | |
| echo "" | |
| fi | |
| done < /tmp/netcdf_files.txt | |
| echo "" | |
| echo "==========================================" | |
| echo "Compliance checking complete" | |
| echo "==========================================" | |
| - name: Generate summary report | |
| if: steps.find_files.outputs.file_count != '0' | |
| run: | | |
| echo "# IOOS Compliance Checker Results" > /tmp/compliance_reports/SUMMARY.md | |
| echo "" >> /tmp/compliance_reports/SUMMARY.md | |
| echo "Checked ${{ steps.find_files.outputs.file_count }} NetCDF files" >> /tmp/compliance_reports/SUMMARY.md | |
| echo "" >> /tmp/compliance_reports/SUMMARY.md | |
| echo "## Files Checked" >> /tmp/compliance_reports/SUMMARY.md | |
| echo "" >> /tmp/compliance_reports/SUMMARY.md | |
| while IFS= read -r ncfile; do | |
| echo "- \`$ncfile\`" >> /tmp/compliance_reports/SUMMARY.md | |
| done < /tmp/netcdf_files.txt | |
| echo "" >> /tmp/compliance_reports/SUMMARY.md | |
| echo "See individual report files for detailed results." >> /tmp/compliance_reports/SUMMARY.md | |
| cat /tmp/compliance_reports/SUMMARY.md | |
| - name: Upload compliance reports | |
| if: always() && steps.find_files.outputs.file_count != '0' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: compliance-checker-reports | |
| path: /tmp/compliance_reports/ | |
| retention-days: 30 | |
| - name: Check if any files were tested | |
| if: steps.find_files.outputs.file_count == '0' | |
| run: | | |
| echo "::warning::No NetCDF files were found to check for compliance" | |
| echo "This may indicate that tests did not run successfully or outputs were not generated" |