create_test_conda_env.yml

name: create_test_conda_env

on:
  pull_request:
    branches:
      - main
  push:
    branches:
      - main

jobs:
  build-linux:
    runs-on: ubuntu-latest
    container:
      image: ghcr.io/noaa-gfdl/fre-cli:miniconda24.7.1_gcc14.2.0
    steps:
      - uses: actions/checkout@v4
        with:
          submodules: 'recursive'
      - name: Create fre-cli environment
        run: |
          # create env holding all deps, the env cant be explicitly activated in CI/CD        
          conda env create -f environment.yml --name fre-cli

          # sets CONDA to wherever it may be on the image
          source /root/.bashrc

          # add conda env's executables and mkmf to github's PATH equiv.
          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
          echo $PWD/mkmf/bin >> $GITHUB_PATH

          # use *conda environment's pip* to install fre-cli, called w/ full path as module for explicitness
          $CONDA/envs/fre-cli/bin/python -m pip install --prefix $CONDA/envs/fre-cli .

      - name: Run pytest in fre-cli environment
        run: |
          # add spack installed binaries to front of path so that conda's netcdf/hdf5 installs don't break compilation tests
          export path_save=$PATH
          export PATH="/opt/views/view/bin:$PATH"

          # run pytest
          coverage run -m pytest --junit-xml=pytest_results.xml --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov-report=xml --cov=fre fre/

          # restore original path and install genbadge to generate coverage badge based on xml
          export PATH="$path_save"

          # install genbadge to make badge from coverage/test stats
          pip install genbadge

          # genbadge coverage
          genbadge coverage -v -i coverage.xml -o docs/cov_badge.svg

          # genbadge tests
          genbadge tests -v -i pytest_results.xml -o docs/pytest_badge.svg

      - name: Archive code coverage results
        uses: actions/upload-artifact@v4
        with:
          name: code-coverage-report
          path: coverage.xml

      - name: Run pylint in fre-cli environment
        run: |
          # run pylint, ignored modules avoid warnings arising from code internal to those modules
          pylint --max-line-length 120 --max-args 6 -ry --ignored-modules netCDF4,cmor fre/ || echo "pylint returned non-zero exit code. preventing workflow from dying with this echo."

      - name: Install Sphinx and Build Documentation
        run: |
          # pip install sphinx and themes, upgrade theme
          pip install sphinx renku-sphinx-theme sphinx-rtd-theme
          pip install --upgrade sphinx-rtd-theme

          # have sphinx build the docs
          sphinx-apidoc --output-dir docs fre/ --separate
          sphinx-build docs build

      - name: Deploy to GitHub Pages
        uses: peaceiris/actions-gh-pages@v3
        if: ${{ github.ref == 'refs/heads/main' }}
        with:
          publish_branch: gh-pages
          github_token: ${{ secrets.GITHUB_TOKEN }}
          publish_dir: build/
          force_orphan: true