run-linux-cuda.yml

name: run-linux-cuda

on:
  workflow_dispatch:
    inputs:
      notebook-path:
        description: Path to the notebook to run
        required: true
        type: string

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

    container:
      image: martinkim0/scvi-tools:ubuntu-latest-mamba-latest-python-3.11-cuda-11
      options: --user root --gpus all

    steps:
      - name: Checkout
        uses: actions/checkout@v3

      - name: Install dependencies
        run: |
          pip install -U scvi-tools[tutorials]

      - name: Install nbconvert
        run: |
          pip install -U nbconvert

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

      - name: Submit pull request with changes
        uses: peter-evans/create-pull-request@v5