README in each folder - Githubissues

SyneRBI / SIRF-Exercises

SIRF Training and demonstration material

http://www.ccpsynerbi.ac.uk

Apache License 2.0

18 stars 21 forks source link

README in each folder #90

Closed KrisThielemans closed 3 years ago

KrisThielemans commented 3 years ago

I think it'd be nice to have a README.md in each folder, especially if jupyter display the README nicely. @ashgillman I saw it doing that for you. A plugin?

ashgillman commented 3 years ago

No, I was sharing from GitHub last meeting - which renders the README per directory. I did a quick google, but can't see how to do this.

ashgillman commented 3 years ago

Only the MR and Reg notebooks subdirectories don't currently have READMEs.

KrisThielemans commented 3 years ago

I had seen this as an abandoned PR https://github.com/jupyter/notebook/pull/5299. They recommend using https://github.com/NII-cloud-operation/Jupyter-LC_index.

JupyterLab does this though. Maybe time to switch?

ashgillman commented 3 years ago

Reading through the thread you posted, it sounds like support for Jupyter Notebooks might be fading. So it could be better to be ahead of the curve with JupyterLab. It also seems to have more features for other data formats.

JupyterLab pros:

README
If we could show the terminal/kernel output side-by-side would be very nice for STIR, since a lot of the output is hidden (not sure if this is possible though)
Continued support and coming features.
cons:
People, if they're familiar with anything, are more likely to be familiar with Notebooks
Not sure if its going to be more confusing?
More changes/testing

KrisThielemans commented 3 years ago

Turns out that @casperdcl already install jupyterlab on the docker image (of course). So, as opposed to going to http://localhost:9999/, you just go to http://localhost:9999/lab. On the VM I had to do python3 -m pip install jupyterlab; and start with jupyter lab.

If you click on a README.md, it opens it up in an editor as before, but right-clicking allows you to show it formatted. Not very smooth yet, but at least something.

However

while the keyboard shortcuts are similar between lab and notebook, for lab it seems very hard to find out what they are (in notebook, you just press h)
%matplotlib notebook results in a cryptic error. Seems we'd need to install extra stuff and use %matplotlib widget, see https://stackoverflow.com/questions/51922480/javascript-error-ipython-is-not-defined-in-jupyterlab

A bit too early days for me therefore.

ashgillman commented 3 years ago

I was hoping it would automatically preview when navigating to the folder. This still requires users to open the file - a low bar I know but one not all will navigate

KrisThielemans commented 3 years ago

yeah, doesn't help a ton.

there was a notebook extension mentioned that does the trick, but I guess it's a bit lower priority at the moment! Let's just get the READMEs in (and some other tiny bits...)

KrisThielemans commented 3 years ago

@johannesmayer @ckolbPTB can you please create a MR/README.md? Use links for the notebooks.

KrisThielemans commented 3 years ago

all done with #129