Merge pull request #346 from scverse/detached2

docs: updated several tutorials

.github/workflows/run_linux_cuda.yml

@@ -0,0 +1,104 @@
+name: Run notebook (Linux, CUDA)
+
+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/scanvi_fix.ipynb
+          - scrna/scarches_scvi_tools.ipynb
+          - scrna/scVI_DE_worm.ipynb
+          - scrna/seed_labeling.ipynb
+          - scrna/tabula_muris.ipynb
+          - scrna/MrVI_tutorial.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: "3.12"
+        type: choice
+        options:
+          - "3.12"
+          - "3.11"
+          - "3.10"
+
+      cuda-version:
+        description: CUDA version
+        required: true
+        default: "12"
+        type: choice
+        options:
+          - "12"
+
+      scvi-tools-version:
+        description: scvi-tools version (latest, stable, or semver)
+        required: true
+        default: "latest"
+        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.scvi-tools-version }}
+      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 changes
+        uses: peter-evans/create-pull-request@v5
+        with:
+          commit-message: Rerun ${{ 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 version: ${{ inputs.scvi-tools-version }}