Switch to MDA rtd sphinx theme

[ojeda-e]

As we agreed with @IAlibay, I am here submitting changes to update the docs theme to the official one. This PR fixes #120 and #110 (opened by @orbeckst).

Description

Update docs mdanalysis-sphinx-theme with plus maintenance.

Status

• Ready to go

It compiles locally and seems to work as expected. I'll be fixing the issues if any once it build in the CI.
Thanks.

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Codecov Report

Merging #122 (b931fad) into main (0cf4856) will not change coverage.
Report is 2 commits behind head on main.
The diff coverage is 100.00%.

Additional details and impacted files

[orbeckst]

Thanks for link fixing and face-lifting.

Is the content from the removed notebooks available elsewhere?

[ojeda-e]

Is the content from the removed notebooks available elsewhere?

@orbeckst I just noticed the diff for the notebooks are misleading. The notebooks are still part of the documentation. I had to regenerate them to verify every cell works and the output is correct -the same as before-; the nb kernel was also updated to enable docs build in the CI.
The content is available in the reviewnb app: https://app.reviewnb.com/MDAnalysis/membrane-curvature/pull/122/

Here are the build notebooks in the tutorial section in case you want to check:

• https://membrane-curvature--122.org.readthedocs.build/en/122/source/pages/Curvature_membrane-only_systems.html
• https://membrane-curvature--122.org.readthedocs.build/en/122/source/pages/Curvature_membrane_protein_nopr_all_atom.html

[orbeckst]

LGTM, thanks for putting in the effort!

[ojeda-e]

@lilyminium, if possible, would you please help me with a quick review here before I merge?

[IAlibay]

@ojeda-e apologies I am unlikely to have much time to look at this until the weekeend - please do re-ping me if you still need my input by then.

[lilyminium]

Looks pretty good @ojeda-e, I've just left some comments largely on the notes. I also think you've put last year in the "Last executed" line of docs/source/pages/Curvature_membrane-only_systems.ipynb (ReviewNB won't let me comment directly....)

Just commenting this review to avoid blocking progress :-)

[ojeda-e]

Thanks for taking the time here @lilyminium
I addressed your comments. Hopefully I didn't miss anything. Removed the editable version part, removed Sphinx from the requirements and fixed the date on the notebook.It's a bit late here, but there if there are more comments please feel free to leave them and I'll address them tomorrow.