ci: refactor run notebook workflows (#295)

* ci: fix release workflow

* ci: refactor run notebook workflows

.github/workflows/run_notebook.yaml

@@ -0,0 +1,40 @@
+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:py3.11-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 }}

.github/workflows/run_notebook_all.yaml

@@ -0,0 +1,57 @@
+name: run notebook (all)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: "latest/stable/semver/branch"
+        required: true
+        type: string
+
+jobs:
+  notebook:
+    strategy:
+      matrix:
+        notebook:
+          - 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/cellxgene_census_model.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
+
+    uses: ./.github/workflows/run_notebook.yaml
+    with:
+      notebook: ${{ matrix.notebook }}
+      version: ${{ inputs.version }}

.github/workflows/run_linux_cuda_branch.yml → .github/workflows/run_notebook_individual.yaml

@@ -1,10 +1,10 @@
-name: Run notebook (Linux, CUDA, branch)
+name: run notebook (individual)
 
 on:
   workflow_dispatch:
     inputs:
-      notebook-path:
-        description: Path to the notebook to run
+      notebook:
+        description: "Path to the notebook to run"
         required: true
         type: choice
         options: # not including R tutorials currently
@@ -15,6 +15,7 @@ on:
           - dev/data_tutorial.ipynb
           - dev/model_user_guide.ipynb
           - dev/module_user_guide.ipynb
+          - hub/cellxgene_census_model.ipynb
           - hub/minification.ipynb
           - hub/scvi_hub_intro_and_download.ipynb
           - hub/scvi_hub_upload_and_large_files.ipynb
@@ -44,61 +45,14 @@ on:
           - 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
+      version:
+        description: "latest/stable/semver/branch"
         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 }}
+  notebook:
+    uses: ./.github/workflows/run_notebook.yaml
+    with:
+      notebook: ${{ inputs.notebook }}
+      version: ${{ inputs.version }}