compliance_check.yml

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: |
          echo "Running comprehensive test suite to generate NetCDF outputs..."
          echo ""

          # Run CMIP6 basic tests
          echo "=========================================="
          echo "Running CMIP6 basic tests..."
          echo "=========================================="
          pytest fremorizer/tests/test_cmor_run_subtool.py -v || true

          echo ""
          echo "=========================================="
          echo "Running extended test examples (includes CMIP7)..."
          echo "=========================================="
          # Run extended tests which include CMIP7 examples
          # Note: Some tests may fail due to missing ncgen3 or other dependencies
          # We use continue-on-error to ensure we gather whatever outputs were generated
          pytest fremorizer/tests/test_cmor_run_subtool_further_examples.py -v || true

          echo ""
          echo "Test execution complete. Proceeding to gather outputs..."
        continue-on-error: true

      - name: Gather test outputs into centralized directory
        id: gather_outputs
        run: |
          # Use the reusable script to gather all test outputs
          # This script categorizes files by CMIP version and creates a manifest
          bash .github/scripts/gather_test_outputs.sh /tmp/qa_test_outputs

          # Store the output directory path for subsequent steps
          echo "output_dir=/tmp/qa_test_outputs" >> $GITHUB_OUTPUT

          # Count total files gathered
          total_files=$(find /tmp/qa_test_outputs -name "*.nc" -type f | wc -l)
          echo "file_count=${total_files}" >> $GITHUB_OUTPUT

          # Count by category
          cmip6_files=$(find /tmp/qa_test_outputs/cmip6 -name "*.nc" -type f 2>/dev/null | wc -l || echo "0")
          cmip7_files=$(find /tmp/qa_test_outputs/cmip7 -name "*.nc" -type f 2>/dev/null | wc -l || echo "0")
          other_files=$(find /tmp/qa_test_outputs/other -name "*.nc" -type f 2>/dev/null | wc -l || echo "0")

          echo "cmip6_count=${cmip6_files}" >> $GITHUB_OUTPUT
          echo "cmip7_count=${cmip7_files}" >> $GITHUB_OUTPUT
          echo "other_count=${other_files}" >> $GITHUB_OUTPUT

          echo ""
          echo "Gathered outputs summary:"
          echo "  Total: ${total_files}"
          echo "  CMIP6: ${cmip6_files}"
          echo "  CMIP7: ${cmip7_files}"
          echo "  Other: ${other_files}"

      - name: Run compliance-checker on outputs
        if: steps.gather_outputs.outputs.file_count != '0'
        run: |
          echo "Running IOOS Compliance Checker on gathered NetCDF files..."
          echo "Total files to check: ${{ steps.gather_outputs.outputs.file_count }}"
          echo "  CMIP6: ${{ steps.gather_outputs.outputs.cmip6_count }}"
          echo "  CMIP7: ${{ steps.gather_outputs.outputs.cmip7_count }}"
          echo "  Other: ${{ steps.gather_outputs.outputs.other_count }}"
          echo ""

          mkdir -p /tmp/compliance_reports

          # Function to check files in a category
          check_category() {
            local category=$1
            local category_dir="/tmp/qa_test_outputs/${category}"

            if [ ! -d "${category_dir}" ] || [ -z "$(ls -A ${category_dir}/*.nc 2>/dev/null)" ]; then
              echo "No files in ${category} category, skipping..."
              return
            fi

            echo ""
            echo "=========================================="
            echo "Checking ${category} files..."
            echo "=========================================="

            for ncfile in "${category_dir}"/*.nc; do
              if [ -f "$ncfile" ]; then
                basename=$(basename "$ncfile" .nc)
                echo ""
                echo "Checking: ${basename}"

                # Generate text report (for viewing in logs)
                compliance-checker \
                  --test=cf \
                  --criteria=normal \
                  --verbose \
                  --format=text \
                  --output=/tmp/compliance_reports/${category}_${basename}_report.txt \
                  "$ncfile" || true

                # Also generate HTML report (for artifact download)
                compliance-checker \
                  --test=cf \
                  --criteria=normal \
                  --format=html \
                  --output=/tmp/compliance_reports/${category}_${basename}_report.html \
                  "$ncfile" 2>&1 || true

                # Display summary from text report (first 50 lines to avoid log spam)
                echo "Summary:"
                head -50 /tmp/compliance_reports/${category}_${basename}_report.txt || true
                echo ""
              fi
            done
          }

          # Check each category
          check_category "cmip6"
          check_category "cmip7"
          check_category "other"

          echo ""
          echo "=========================================="
          echo "Compliance checking complete"
          echo "=========================================="

      - name: Generate summary report
        if: steps.gather_outputs.outputs.file_count != '0'
        run: |
          echo "# IOOS Compliance Checker Results" > /tmp/compliance_reports/SUMMARY.md
          echo "" >> /tmp/compliance_reports/SUMMARY.md
          echo "**Generated:** $(date -u +%Y-%m-%dT%H:%M:%SZ)" >> /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
          echo "- **Total:** ${{ steps.gather_outputs.outputs.file_count }} files" >> /tmp/compliance_reports/SUMMARY.md
          echo "- **CMIP6:** ${{ steps.gather_outputs.outputs.cmip6_count }} files" >> /tmp/compliance_reports/SUMMARY.md
          echo "- **CMIP7:** ${{ steps.gather_outputs.outputs.cmip7_count }} files" >> /tmp/compliance_reports/SUMMARY.md
          echo "- **Other:** ${{ steps.gather_outputs.outputs.other_count }} files" >> /tmp/compliance_reports/SUMMARY.md
          echo "" >> /tmp/compliance_reports/SUMMARY.md
          echo "## Report Files" >> /tmp/compliance_reports/SUMMARY.md
          echo "" >> /tmp/compliance_reports/SUMMARY.md
          echo "Individual compliance reports are organized by CMIP version:" >> /tmp/compliance_reports/SUMMARY.md
          echo "" >> /tmp/compliance_reports/SUMMARY.md
          echo "- \`cmip6_*_report.html\` - CMIP6 file reports" >> /tmp/compliance_reports/SUMMARY.md
          echo "- \`cmip7_*_report.html\` - CMIP7 file reports" >> /tmp/compliance_reports/SUMMARY.md
          echo "- \`other_*_report.html\` - Unclassified file reports" >> /tmp/compliance_reports/SUMMARY.md
          echo "" >> /tmp/compliance_reports/SUMMARY.md
          echo "## Test Output Manifest" >> /tmp/compliance_reports/SUMMARY.md
          echo "" >> /tmp/compliance_reports/SUMMARY.md
          echo "See \`manifest.txt\` for the complete mapping of source test files to gathered outputs." >> /tmp/compliance_reports/SUMMARY.md
          echo "" >> /tmp/compliance_reports/SUMMARY.md

          # Copy the test output summary and manifest to the reports directory
          cp /tmp/qa_test_outputs/SUMMARY.md /tmp/compliance_reports/TEST_OUTPUTS_SUMMARY.md || true
          cp /tmp/qa_test_outputs/manifest.txt /tmp/compliance_reports/manifest.txt || true

          cat /tmp/compliance_reports/SUMMARY.md

      - name: Upload test outputs
        if: always() && steps.gather_outputs.outputs.file_count != '0'
        uses: actions/upload-artifact@v4
        with:
          name: qa-test-outputs
          path: /tmp/qa_test_outputs/
          retention-days: 30

      - name: Upload compliance reports
        if: always() && steps.gather_outputs.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.gather_outputs.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"