Updating notebooks using Git pull changes owner to root

[vincentdavis]

If you use git pull to update the notebooks the changed files get the owner and group root:root. This makes the notebook unable to be saved. I tried correcting this locally(docker) by using the $chown --preserve[=ATTR_LIST] but that did not seem to work for some reason.

[vincentdavis]

I think the solution is to use switch users with $su jupyternotebook.

[tiagoantao]

I just updated the docker images at docker hub, so this problem is now mitigated. I will leave this open as this is something to be sorted out.

[vincentdavis]

Looking at this issue again, It is possible to do the git pull from a notebook. The notebook runs as the correct user "jupyteruser". If the parent biopython-notebook is owned by "jupyteruser" then from within a notebook you can execute, for example;

%%bash
git pull

What do you think of making this change?