wget of .ipynb R notebooks from github do not open

[Claire Vandiedonck]

Hello @pierrepo

Some weird think we expereienced tonight with Sandrine and Clémence. Clémence had updated two notebooks on a Sandrine's repo on github. We didn't want to redeploy the corresponding environment on adenine. We used wget to download the updated notebooks. But they could not open:

We restarted the environment but no change.
However, if we redeployed the environment on adenine with a new name, the notebooks present in the repo were correctly loaded.

Any idea?

[Claire Vandiedonck]

Clémence noticed this could be a reformat in github:
jupyter/help#171

[Pierre Poulain]

When you provide a link to download a notebook, take great care to provide the link to the raw notebook not the view of the notebook through the GitHub website.
For instance, the notebook example-notebook.ipynb at the root of this repo should be downloaded with

wget https://raw.githubusercontent.com/plasmabio/template-r/master/example-notebook.ipynb

and not

wget https://github.com/plasmabio/template-r/blob/master/example-notebook.ipynb

Here's a animation to show you how to get the url of raw file:

[Claire Vandiedonck]

Fantastic! We spent more than an hour trying to sort that out today. I am relieved there is an explanation and a solution!