check_notebooks.yml

name: Jupyter Notebooks CI
on: [push, pull_request]
jobs:
  Check-Notebooks:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - name: check out repository code
        uses: actions/checkout@v3
      - name: set up conda environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          miniforge-version: latest
          miniforge-variant: mambaforge
          channel-priority: strict
          channels: conda-forge
          show-channel-urls: true
          use-only-tar-bz2: true
          auto-update-conda: true
          auto-activate-base: false
          activate-environment: notebook-env
      - name: Install tobac dependencies
        run: |
          mamba install -c conda-forge --yes ffmpeg gcc jupyter pytables
          mamba install -c conda-forge --yes --file example_requirements.txt
      - name: Install tobac
        run: |
          pip install .
      - name: Find all notebook files
        run: |
          find . -type f -name '*.ipynb' > nbfiles.txt
          cat nbfiles.txt
      - name: Execute all notebook files
        run: |
          while IFS= read -r nbpath; do
            jupyter nbconvert --inplace --ClearMetadataPreprocessor.enabled=True --clear-output $nbpath
            jupyter nbconvert --to notebook --inplace --execute $nbpath
          done < nbfiles.txt