From d2edd43aa1efe0b28f5a328f3dca7f1bbae68f89 Mon Sep 17 00:00:00 2001 From: Martin Kim Date: Fri, 12 Jul 2024 16:43:11 -0700 Subject: [PATCH] ci: add notebooks yaml --- .github/workflows/notebooks.yaml | 45 +++++++++++++++++++ .github/workflows/run_notebook_all.yaml | 39 +--------------- .../workflows/run_notebook_individual.yaml | 39 +--------------- 3 files changed, 47 insertions(+), 76 deletions(-) create mode 100644 .github/workflows/notebooks.yaml diff --git a/.github/workflows/notebooks.yaml b/.github/workflows/notebooks.yaml new file mode 100644 index 0000000..765db03 --- /dev/null +++ b/.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 diff --git a/.github/workflows/run_notebook_all.yaml b/.github/workflows/run_notebook_all.yaml index 52cc8cd..d4bf3f2 100644 --- a/.github/workflows/run_notebook_all.yaml +++ b/.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: diff --git a/.github/workflows/run_notebook_individual.yaml b/.github/workflows/run_notebook_individual.yaml index 40b1c1d..1902e76 100644 --- a/.github/workflows/run_notebook_individual.yaml +++ b/.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