Binder notebooks do not work

[srmnitc]

This is part of the review at openjournals/joss-reviews#2563

There are quite a lot of examples, which is really nice. I was trying to run the examples on mybinder, and I get the feeling that they are not really optimized to run on a binder instance. The binder instance is a good way to get started with matador, and I strongly recommend that these notebooks be made a bit more user friendly. I have summarized the issues below-

• Some of the notebooks need CASTEP to run. While this is completely fine, I think you could mark the notebooks that cannot be run on a binder instance.
• I was able to run magnes_plotting, plot_styles and pxid_plotting, however, they through a lot of warnings, often contradicting the specified example options. For example, the plot_styles often seem to fall back to the default options.
• In the notebook pymatgen_and_ase_interface, ase is not installed on binder, and hence it is not possible to run.
• phonon_results also throws an error because the folder does not exist.
• There some folders without notebooks. This is completely fine, however, some guidance to the user would be nice.
• Some notebooks lack an explanation of the example.

I completely understand that it is difficult to maintain numerous examples such as this, but since it provides a good entry point for the potential user. The notebook should be completely executable unless otherwise specified.

[ml-evs]

Thanks for this thorough review @srmnitc.

Many of these problems are related, e.g. many of the warnings on the notebooks in your second point relate to missing fonts in the Binder instance.

My suggested fix is to make another folder /interactive_examples to point the Binder link to, which will contain symlinks to the notebooks that are actually interactive without extra data.

I'll also go through and add some more clarifying descriptions to the notebooks themselves.

[srmnitc]

Thanks @ml-evs! I completely agree that separating them to a folder would be a good solution.

[ml-evs]

Hi @srmnitc, I think #125 closes this now.

I moved split the examples into interactive/non-interactive in the online documentation, added a higher level summary in the examples folder, and fixed the dependencies that were being installed under myBinder.

Unfortunately I'm struggling to get myBinder to launch the image right now (it builds fine, but runs into miscellaneous launch errors) but I'll try again in the morning.

Once again, please feel free to reopen this if you are not satisfied.

[srmnitc]

The binder instance still seems to have problems. But everything overall seems to be great!

[ml-evs]

The binder instance still seems to have problems. But everything overall seems to be great!

Yes, you're quite right, I've been trying to fix it in #130. Turns out that the Dockerfile approach is not well-supported. I just need to do a final check of every notebook to make sure they work with the new filepaths, then it should be good to go.

[ml-evs]

That seems to have done it!