Display Jupyter Notebooks

[kabilar]

• Fix Include notebooks into handbook? #142
• Using mkdocs-jupyter, display select Jupyter Notebooks from the dandi/example-notebooks repo
• Add manual trigger (i.e. workflow_dispatch) so that docs can be redeployed when example-notebooks are updated
• Fix GitHub Action: Add linux-headers package mhausenblas/mkdocs-deploy-gh-pages#256
• Preview available at: https://kabilar.github.io/handbook/
• In the future, we can add titles to all the notebooks as some just start with code blocks

[yarikoptic]

This is great, thank you @kabilar for taking care about this one!

• do you see a way to add some kind of "header" or "trailer" (or both) to each notebook so we could point to the to the original notebook location on github, and possibly state something like

This Jupyter notebook is available from GitHub repository dandi / example-notebooks / demos / NWBWidget-demo.ipynb. You can also find it available while working on DANDI Hub under ... so you could run the code.

hub seems to be down ATM so couldn't double check where it is there on the hub. Also might be worth adding a link to the corresponding dandiset DLP if it is associated with a dandiset, e.g.

This notebook accompanies dandiset 000XXX.

or alike.

• could we generate/include a page with an index of all notebooks by their filename (so not yet going deep into fixing to get the titles etc) so their all content gets rendered indexed? Crude listing/page generation script

❯ { echo "## Full list of example-notebooks"; find -iname '*.ipynb' | grep -v '\.ipynb_checkpoint' | sort | while read -r l; do echo "- [$l]($l)"; done } | head
## Full list of example-notebooks
- [./000004/RutishauserLab/000004_demo_analysis.ipynb](./000004/RutishauserLab/000004_demo_analysis.ipynb)
- [./000005/DataJoint/DJ-NWB-Yu-Gutnisky-2016/notebooks/Yu-Gutnisky-2016-examples.ipynb](./000005/DataJoint/DJ-NWB-Yu-Gutnisky-2016/notebooks/Yu-Gutnisky-2016-examples.ipynb)
- [./000006/DataJoint/DJ-NWB-Economo-2018/notebooks/Economo-2018-examples.ipynb](./000006/DataJoint/DJ-NWB-Economo-2018/notebooks/Economo-2018-examples.ipynb)
- [./000007/DataJoint/DJ-NWB-Gao-2018/notebooks/erd.ipynb](./000007/DataJoint/DJ-NWB-Gao-2018/notebooks/erd.ipynb)
- [./000007/DataJoint/DJ-NWB-Gao-2018/notebooks/Gao-2018-examples.ipynb](./000007/DataJoint/DJ-NWB-Gao-2018/notebooks/Gao-2018-examples.ipynb)
- [./000009/DataJoint/DJ-NWB-Guo-Inagaki-2017/notebooks/Guo-Inagaki-2017-examples.ipynb](./000009/DataJoint/DJ-NWB-Guo-Inagaki-2017/notebooks/Guo-Inagaki-2017-examples.ipynb)
- [./000009/DataJoint/DJ-NWB-Guo-Inagaki-2017/notebooks/Guo-Inagaki-2017-NWB-examples.ipynb](./000009/DataJoint/DJ-NWB-Guo-Inagaki-2017/notebooks/Guo-Inagaki-2017-NWB-examples.ipynb)
- [./000010/DataJoint/DJ-NWB-Li-2015b/notebooks/Li-2015b-examples.ipynb](./000010/DataJoint/DJ-NWB-Li-2015b/notebooks/Li-2015b-examples.ipynb)
- [./000010/DataJoint/DJ-NWB-Li-2015b/notebooks/Schemas.ipynb](./000010/DataJoint/DJ-NWB-Li-2015b/notebooks/Schemas.ipynb)

a better version could group them neatly under "Dandiset demos", etc

[bendichter]

I think it might make more sense to render the notebooks on the example-notebooks CI and link to them rather than cloning that repo and rendering them here.

[yarikoptic]

@kabilar pushed! works nicely locally -- thanks!

The "problem" -- it does render all notebooks but we reference only few -- we should autopopulate some page listing all of them and then reference it there in the menu.
Moreover added since then "Tutorials: Dandiset examples" is somewhat of a duplicate... Any specific ideas?

we could also do it separately in a follow up issue + PR and merge this asap to avoid future conflicts etc

[kabilar]

@kabilar pushed! works nicely locally -- thanks!

Thanks, Yarik.

The "problem" -- it does render all notebooks but we reference only few -- we should autopopulate some page listing all of them and then reference it there in the menu. Moreover added since then "Tutorials: Dandiset examples" is somewhat of a duplicate... Any specific ideas?

we could also do it separately in a follow up issue + PR and merge this asap to avoid future conflicts etc

Agree that we should proceed with the merge here and address in the future. We should also probably also integrate that page listing with https://dandi.github.io/example-notebooks/.

[satra]

whenever we merge some of these notebooks, it makes me think why are we not using a jupyterbook here? it would serve all the purposes i think and for these tutorials people could actually open them in binder/jupyterhub.

[kabilar]

whenever we merge some of these notebooks, it makes me think why are we not using a jupyterbook here? it would serve all the purposes i think and for these tutorials people could actually open them in binder/jupyterhub.

Hi @satra, I agree that jupyterbook has some nice features. I proceeded with the mkdocs-jupyter plugin here since it was an easy addition and didn't require changing frameworks. We can evaluate changing to jupterbook in the future, which I would like to compare against Hugo since the about.dandiarchive.org site is now using Hugo.

[kabilar]

Filed #189