ci: add notebooks yaml (#298)

* ci: fix release workflow

* ci: refactor run notebook workflows

* ci: add notebooks yaml

.github/workflows/notebooks.yaml

@@ -0,0 +1,45 @@
+# atac (missing R notebooks)
+- atac/PeakVI.ipynb
+- atac/PoissonVI.ipynb
+- atac/scbasset_batch.ipynb
+- atac/scbasset.ipynb
+# dev
+- dev/data_tutorial.ipynb
+- dev/model_user_guide.ipynb
+- dev/module_user_guide.ipynb
+# hub
+- hub/cellxgene_census_model.ipynb
+- hub/minification.ipynb
+- hub/scvi_hub_intro_and_download.ipynb
+- hub/scvi_hub_upload_and_large_files.ipynb
+# multimodal (missing R notebooks)
+- multimodal/cite_scrna_integration_w_totalVI.ipynb
+- multimodal/MultiVI_tutorial.ipynb
+- multimodal/totalVI_reference_mapping.ipynb
+- multimodal/totalVI.ipynb
+# quick_start (missing R notebooks)
+- quick_start/api_overview.ipynb
+- quick_start/data_loading.ipynb
+# scrna (missing R notebooks)
+- scrna/amortized_lda.ipynb
+- scrna/AutoZI_tutorial.ipynb
+- scrna/cellassign_tutorial.ipynb
+- scrna/contrastiveVI_tutorial.ipynb
+- scrna/harmonization.ipynb
+- scrna/linear_decoder.ipynb
+- scrna/MrVI_tutorial.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 (missing R notebooks)
+- 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
+- tuning/autotune_new_model.ipynb
+- tuning/autotune_scvi.ipynb

.github/workflows/run_notebook_all.yaml

@@ -12,44 +12,7 @@ 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
+        notebook: ${{ fromYaml(readFile('.github/workflows/notebooks.yaml')) }}
 
     uses: ./.github/workflows/run_notebook.yaml
     with:

.github/workflows/run_notebook_individual.yaml

@@ -7,44 +7,7 @@ on:
         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/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
+        options: ${{ fromYaml(readFile('.github/workflows/notebooks.yaml')) }}
       version:
         description: "latest/stable/semver/branch"
         required: true