run_notebook.yaml

name: run notebook

on:
  workflow_call:
    inputs:
      notebook:
        description: "Path to the notebook to run"
        required: true
        type: string
      version:
        description: "latest/stable/semver/branch"
        required: true
        type: string

jobs:
  notebook:
    runs-on: [self-hosted, Linux, X64, CUDA]

    container:
      image: ghcr.io/scverse/scvi-tools:py3.12-cu12-${{ inputs.version }}-tutorials
      options: --user root --gpus all

    timeout-minutes: 600 # lenient timeout for scbasset tutorial

    steps:
      - uses: actions/checkout@v4

      - name: Install Python kernel
        run: |
          python -m ipykernel install

      - name: Run notebook
        run: |
          python -m jupyter nbconvert --execute --inplace ${{ inputs.notebook }}

      - uses: peter-evans/create-pull-request@v5
        with:
          commit-message: run ${{ inputs.notebook }}
          title: automated update for ${{ inputs.notebook }}
          branch: update-${{ inputs.notebook }}