markdown-profile.yml

name: notebook_to_md (profile)
on: pull_request
jobs:
  commit-notebooks:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - name: Checkout site
        uses: actions/checkout@v4
        with:
          submodules: recursive # Fetch Hugo themes and all extra projects
          fetch-depth: 0 # Fetch all history for .GitInfo and .Lastmod
          path: site

      - name: Checkout coast
        uses: actions/checkout@v4
        with:
          repository: British-Oceanographic-Data-Centre/COAsT
          ref: develop
          path: external

      - name: Prepare environement
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: coast
          environment-file: external/environment.yml
      - name: prep exec notebooks
        run: |
          conda info
          conda list
          conda config --show
          cd $GITHUB_WORKSPACE/external
          sudo apt install wget unzip rsync -y
          wget -q https://linkedsystems.uk/erddap/files/COAsT_example_files/COAsT_example_files.zip
          unzip COAsT_example_files.zip && mv COAsT_example_files ./example_scripts/notebook_tutorials/runnable_notebooks/profile/example_files          
          mkdir -p ./example_scripts/notebook_tutorials/markdown
          ls ./example_scripts/notebook_tutorials
          pip install .
          mv config ./example_scripts/notebook_tutorials/runnable_notebooks/profile/config
          bash notebook_to_md.sh profile