execute-nbs.yaml

name: Execute notebooks
on:
    pull_request:
        branches: [main]
        paths:
            - "docs/**"
            - "environment.yml"

jobs:
    runnbs:
        runs-on: ubuntu-latest
        concurrency:
            group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
            cancel-in-progress: true
        defaults:
            run:
                shell: bash -el {0}
        steps:
            - uses: actions/checkout@v2
              with:
                  repository: ${{ github.event.pull_request.head.repo.full_name }}
                  ref: ${{ github.head_ref }}
            - name: Cache conda
              uses: actions/cache@v2
              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@v2
              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@v2
              with:
                  activate-environment: tutorials
                  channel-priority: strict
                  environment-file: environment.yml
                  miniforge-variant: Mambaforge
                  miniforge-version: latest
                  use-mamba: true
                  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@v4
              with:
                  commit_message: Render notebooks