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Claudeilaflott
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Add IOOS compliance-checker pipeline
- Create compliance_check.yml workflow - Add compliance-checker to environment.yaml - Add compliance_check badge to README.md Agent-Logs-Url: https://github.com/ilaflott/fremorizer/sessions/a24e9cee-7b60-4639-8c0e-1f48f931ff49 Co-authored-by: ilaflott <6273252+ilaflott@users.noreply.github.com>
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‎.github/workflows/compliance_check.yml‎

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

‎README.md‎

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[![build_conda](https://github.com/ilaflott/fremorizer/actions/workflows/build_conda.yml/badge.svg?branch=main)](https://github.com/ilaflott/fremorizer/actions/workflows/build_conda.yml)
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[![create_test_conda_env](https://github.com/ilaflott/fremorizer/actions/workflows/create_test_conda_env.yml/badge.svg?branch=main)](https://github.com/ilaflott/fremorizer/actions/workflows/create_test_conda_env.yml)
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[![compliance_check](https://github.com/ilaflott/fremorizer/actions/workflows/compliance_check.yml/badge.svg?branch=main)](https://github.com/ilaflott/fremorizer/actions/workflows/compliance_check.yml)
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[![publish_conda](https://github.com/ilaflott/fremorizer/actions/workflows/publish_conda.yml/badge.svg?branch=main)](https://github.com/ilaflott/fremorizer/actions/workflows/publish_conda.yml)
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[![pylint](https://github.com/ilaflott/fremorizer/actions/workflows/pylint.yml/badge.svg?branch=main)](https://github.com/ilaflott/fremorizer/actions/workflows/pylint.yml)
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[![codecov](https://codecov.io/gh/ilaflott/fremorizer/branch/main/graph/badge.svg)](https://codecov.io/gh/ilaflott/fremorizer)

‎environment.yaml‎

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- conda-forge::pytest
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- conda-forge::pytest-cov
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- conda-forge::pylint
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- conda-forge::compliance-checker

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