add docs for DANDI hub

[bendichter]

Add docs for accessing DANDI Hub and for example-notebook best practices

[rly]

Would it be possible for DANDI to create environments and kernels for each DANDI example notebook such that when the notebook is opened, the notebook can be run from an existing kernel?

Currently, even if there is an environment.yml for each notebook, the notebook has to say something like the following to tell the user to set up a conda environment, create a kernel, and use the kernel:

If this is NOT the first time that you are running this notebook, make sure the kernel is set to "Python (demo_000004_upd)". If it is not, change your kernel to "Python (demo_000004_upd)".

If this is the first time that you are running this notebook, open a new Terminal tab in DANDI Hub, and run the following commands to create a new Python kernel called "Python (demo_000004_upd)":

PIP_NO_DEPS=1 mamba env create -f ~/dandi-notebooks/000004/RutishauserLab/environment_updated.yml

PYDEVD_DISABLE_FILE_VALIDATION=1 mamba run --name=demo_000004_upd python -m ipykernel install --user --name=demo_000004_upd --display-name "Python (demo_000004_upd)"

Then, restart your kernel so that the newly defined kernel "Python (demo_000004_upd)" is recognized. In the upper right corner of this notebook, click the current kernel, and change it from "Python 3 (ipykernel)" to "Python (demo_000004_upd)".

[rly]

Perhaps that request would be best implemented via Binder or BinderHub...

[satra]

@rly - 2i2c is working on such a project: https://2i2c.org/blog/2022/gesis-2i2c-collaboration-update/

[bendichter]

alternatively, we could put these instructions in the root README of the example-notebooks repo

[bendichter]

I've opened a PR on the example-notebooks repo here: dandi/example-notebooks#56

[yarikoptic]

FWIW, I am also checking out davos as a possible way to make those notebooks usable in dedicated environments "turnkey": ContextLab/davos#96

[yarikoptic]

minor changes. Let's finalize/merge this @bendichter !

[kabilar]

Thank you @bendichter. These instructions are great.

(I have a couple of minor suggestions for the Example notebooks section which I will submit in #108 to facilitate the merging of this pull request.)

[kabilar]

@bendichter Looks like there is a conflict with the mkdocs.yaml file that you will need to resolve before we can merge.

[kabilar]

Went ahead and provided my suggestions below since a conflict has to be resolved with this pull request before merging.

[yarikoptic]

IMHO here it would be very valuable to show how to reference those from within dandiset metadata/meditor

[kabilar]

Hi @yarikoptic, would it be best to reference these notebooks in the Related resources section of the Dandiset metadata?

[yarikoptic]

here we are talking about hub... hub is particularly "good" for notebooks. I think it was a right call to mention them here (and may be elsewhere too).

[kabilar]

Hi @yarikoptic, sorry, I am confused regarding this suggestion.

[bendichter]

I've incorporated most of the suggestions. I'm going to merge now as I think this is a substantial value-add as-is. We can always improve it later.