run_linux_cuda_branch.yml

name: Run notebook (Linux, CUDA, branch)

on:
  workflow_dispatch:
    inputs:
      notebook-path:
        description: Path to the notebook to run
        required: true
        type: choice
        options: # not including R tutorials currently
          - atac/PeakVI.ipynb
          - atac/PoissonVI.ipynb
          - atac/scbasset_batch.ipynb
          - atac/scbasset.ipynb
          - dev/data_tutorial.ipynb
          - dev/model_user_guide.ipynb
          - dev/module_user_guide.ipynb
          - hub/minification.ipynb
          - hub/scvi_hub_intro_and_download.ipynb
          - hub/scvi_hub_upload_and_large_files.ipynb
          - multimodal/cite_scrna_integration_w_totalVI.ipynb
          - multimodal/MultiVI_tutorial.ipynb
          - multimodal/totalVI_reference_mapping.ipynb
          - multimodal/totalVI.ipynb
          - quick_start/api_overview.ipynb
          - quick_start/data_loading.ipynb
          - scrna/amortized_lda.ipynb
          - scrna/AutoZI_tutorial.ipynb
          - scrna/cellassign_tutorial.ipynb
          - scrna/contrastiveVI_tutorial.ipynb
          - scrna/harmonization.ipynb
          - scrna/linear_decoder.ipynb
          - scrna/query_hlca_knn.ipynb
          - scrna/scarches_scvi_tools.ipynb
          - scrna/scVI_DE_worm.ipynb
          - scrna/seed_labeling.ipynb
          - scrna/tabula_muris.ipynb
          - spatial/cell2location_lymph_node_spatial_tutorial.ipynb
          - spatial/DestVI_tutorial.ipynb
          - spatial/gimvi_tutorial.ipynb
          - spatial/stereoscope_heart_LV_tutorial.ipynb
          - spatial/tangram_scvi_tools.ipynb
          - tuning/autotune_new_model.ipynb
          - tuning/autotune_scvi.ipynb

      python-version:
        description: Python version
        required: true
        default: "3.11"
        type: choice
        options:
          - "3.11"
          - "3.10"
          - "3.9"

      cuda-version:
        description: CUDA version
        required: true
        default: "11"
        type: choice
        options:
          - "11"

      branch-name:
        description: scvi-tools branch to run on
        required: true
        default: "main"
        type: string

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

    container:
      image: scverse/scvi-tools:py${{ inputs.python-version }}-cu${{ inputs.cuda-version }}-tutorials-${{ inputs.branch-name}}
      options: --user root --gpus all

    timeout-minutes: 600 # lenient timeout for scbasset tutorial

    steps:
      - name: Checkout
        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-path }}

      - name: Submit PR with changes
        uses: peter-evans/create-pull-request@v5
        with:
          commit-message: Execute ${{ inputs.notebook-path }}
          title: Automated update for ${{ inputs.notebook-path }}
          branch: update-${{ inputs.notebook-path }}
          body: |
            Update ${{ inputs.notebook-path }}:
            - Python version: ${{ inputs.python-version }}
            - CUDA version: ${{ inputs.cuda-version }}
            - scvi-tools branch: ${{ inputs.branch-name }}