execute-nbs.yaml

name: Execute notebooks
on:
  pull_request:
    branches: [main]
    paths:
      - ".github/workflows/execute-nbs.yaml"
      - "docs/**"
      - "environment.yml"

defaults:
  run:  # add -l to GitHub’s defaults to make conda work
    shell: bash -leo pipefail {0}

concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  runnbs:
    runs-on: ubuntu-latest
    permissions:
      contents: write # Allow GH actions to push changes to repo
    steps:
      - uses: actions/checkout@v6
        with:
          repository: ${{ github.event.pull_request.head.repo.full_name }}
          ref: ${{ github.head_ref }}
          filter: blob:none
          fetch-depth: 0
      - name: Cache conda
        uses: actions/cache@v5
        env:
          # Increase this value to reset cache if env file has not changed
          CACHE_NUMBER: 0
        with:
          path: ~/conda_pkgs_dir
          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
      - name: Cache notebooks
        uses: actions/cache@v5
        env:
          # Increase this value to reset cache if env file has not changed
          CACHE_NUMBER: 0
        with:
          path: .jupyter_cache
          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
      - uses: conda-incubator/setup-miniconda@v3
        with:
          activate-environment: tutorials
          channel-priority: flexible
          environment-file: environment.yml
          miniforge-variant: Miniforge3
          miniforge-version: latest
          use-mamba: true
          # some important packages are not available as .tar.bz2 anymore
          # use-only-tar-bz2: true # This needs to be set for caching to work properly!

      - name: execute notebooks
        run: |
          mkdir -p .jupyter_cache
          # set kernel to "python3" (just in case someone used a custom conda env kernel locally)
          for f in docs/notebooks/*.ipynb ; do
              jupytext --to notebook --set-kernel python3 $f
          done

          # First remove all notebooks from the project, then add all again.
          # This does not remove them from the cache. This step is required since a notebook could be in the cache, but not in the PR.
          jcache notebook clear --force
          jcache notebook add docs/notebooks/*.ipynb
          jcache project execute --timeout 1800

      - name: output logs
        run: |
          jcache notebook list
          for f in docs/notebooks/*.ipynb ; do
            jcache notebook info --tb $f
          done

      # write changed outputs back to the ipynb files
      # will fail if there was an execution error
      - name: merge notebooks
        run: |
          for f in docs/notebooks/*.ipynb ; do
            jcache notebook merge $f $f
          done

      - uses: stefanzweifel/git-auto-commit-action@v7
        with:
          commit_message: Render notebooks