Run notebook (Linux, CUDA) #2
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| name: run-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/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/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" | |
| 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: martinkim0/scvi-tools:py${{ inputs.python-version }}-cu${{ inputs.cuda-version }}-devel-${{ inputs.scvi-tools-version }} | |
| options: --user root --gpus all | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install Python kernel | |
| run: | | |
| python -m ipykernel install | |
| - 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 | |
| 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 }} |