Update

Author: keller-mark

.github/workflows/docs.yml

@@ -14,5 +14,6 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install -y pandoc
-      - run: uv sync --extra docs --extra all
+      - run: uv sync --extra docs  --extra notebook --extra all
+      - run: uv run marimo export html-wasm docs/notebooks/marimo-wasm.mo.py -o docs/_static/mo/marimo-wasm.mo.html --mode edit
       - run: uv run make html

.gitignore

@@ -12,6 +12,9 @@ tests/data/*
 ./notebooks/
 docs/notebooks/data/
 docs/notebooks/data-cropped/
+docs/notebooks/kpmp-2024/
+docs/notebooks/segmentations/
+docs/notebooks/*.json
 docs/notebooks/*.html
 docs/notebooks/*.ipynb
 docs/notebooks/*.zarr/
@@ -23,6 +26,8 @@ demos/*/vitessce.local.json
 demos/*/vitessce.remote.json
 .pytest_cache/
 __marimo__/
+assets/
+docs/_static/mo/
 
 # Compiled javascript
 vitessce/static/

docs/_static/mo/.gitkeep

@@ -5,7 +5,7 @@ Data preparation examples
 .. toctree::
    :maxdepth: 2
 
-   notebooks/data_export_s3
-   notebooks/data_export_files
-   notebooks/widget_brain_with_base_dir
-   notebooks/widget_brain_h5ad
+   notebooks/__ipynb__/data_export_s3
+   notebooks/__ipynb__/data_export_files
+   notebooks/__ipynb__/widget_brain_with_base_dir
+   notebooks/__ipynb__/widget_brain_h5ad

docs/data_examples.rst

@@ -4,23 +4,23 @@ Widget examples
 .. toctree::
    :maxdepth: 1
 
-   notebooks/widget_brain
-   notebooks/widget_brain_h5ad
-   notebooks/widget_brain_with_base_dir
-   notebooks/web_app_brain
-   notebooks/widget_genomic_profiles
-   notebooks/widget_imaging
-   notebooks/widget_segmentations_beta
-   notebooks/widget_pbmc
-   notebooks/widget_pbmc_remote
-   notebooks/spatial_data
-   notebooks/spatial_data_blobs
-   notebooks/spatial_data_mouseliver
-   notebooks/spatial_data_mouseliver_remote
-   notebooks/widget_loom
-   notebooks/widget_from_dict
-   notebooks/widget_modify_config
-   notebooks/widget_plugin_demo
-   notebooks/widget_plugin_custom
-   notebooks/widget_plugin_spatial-query
-   notebooks/page_mode_example
+   notebooks/__ipynb__/widget_brain
+   notebooks/__ipynb__/widget_brain_h5ad
+   notebooks/__ipynb__/widget_brain_with_base_dir
+   notebooks/__ipynb__/web_app_brain
+   notebooks/__ipynb__/widget_genomic_profiles
+   notebooks/__ipynb__/widget_imaging
+   notebooks/__ipynb__/widget_segmentations_beta
+   notebooks/__ipynb__/widget_pbmc
+   notebooks/__ipynb__/widget_pbmc_remote
+   notebooks/__ipynb__/spatial_data
+   notebooks/__ipynb__/spatial_data_blobs
+   notebooks/__ipynb__/spatial_data_mouseliver
+   notebooks/__ipynb__/spatial_data_mouseliver_remote
+   notebooks/__ipynb__/widget_loom
+   notebooks/__ipynb__/widget_from_dict
+   notebooks/__ipynb__/widget_modify_config
+   notebooks/__ipynb__/widget_plugin_demo
+   notebooks/__ipynb__/widget_plugin_custom
+   notebooks/__ipynb__/widget_plugin_spatial-query
+   notebooks/__ipynb__/page_mode_example