Run notebook (Linux, CUDA, branch) #88
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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/scanvi_fix.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 }} |