create_test_conda_env.yml

name: create_test_conda_env

on: [push]

jobs:
  build-linux:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '>=3.9'
      
      - name: Add conda to system path
        run: |
          # $CONDA is an env var pointing to root of miniconda dir
          echo $CONDA/bin >> $GITHUB_PATH
      
      - name: Create fre-cli environment
        run: |
          # create environment containing all dependencies
          # the env cannot be explicitly activated in github CI/CD
          conda env create -f environment.yml --name fre-cli

          # add conda env's executables to github's PATH equiv.
          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
          
          # use *conda environment's pip* to install fre-cli
          # called w/ full path to conda's python for explicitness
          # called as a module (-m pip) for explicitness
          $CONDA/envs/fre-cli/bin/python -m pip install --prefix $CONDA/envs/fre-cli .      

      - name: Run pytest in fre-cli environment
        run: |
          # try to make sure the right things are in GITHUB_PATH
          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH
          
          # are we talking to the right python?
          which python
          python --version
          $CONDA/envs/fre-cli/bin/python --version
          
          # run pytest
          pytest --junit-xml=pytest_results.xml --config-file=fre/pytest.ini --cov-config=fre/coveragerc --cov-report=xml --cov=fre fre/
          
          # install genbadge to generate coverage badge based on xml
          pip install genbadge
          genbadge coverage -v -i coverage.xml -o docs/cov_badge.svg
          genbadge tests -v -i pytest_results.xml -o docs/pytest_badge.svg
        
      - name: Run pylint in fre-cli environment
        run: |
          # try to make sure the right things are in GITHUB_PATH
          echo $CONDA/envs/fre-cli/bin >> $GITHUB_PATH

          # are we talking to the right python?
          which python
          python --version
          $CONDA/envs/fre-cli/bin/python --version
          
          # run pylint
          pylint --ignored-modules netCDF4 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 renku-sphinx-theme sphinx-rtd-theme          
          pip install --upgrade sphinx-rtd-theme
          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