Cleaning up API docs

[ianmkenney]

Changes made in this Pull Request:

• API docs recreated to look more like original documentation from the core library

Fixes #42
Fixes #43

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

[codecov]

Codecov Report

Merging #49 (60f151d) into main (3da55f8) will not change coverage.
Report is 1 commits behind head on main.
The diff coverage is 100.00%.

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Additional details and impacted files

[orbeckst]

Note: add link to https://userguide.mdanalysis.org/stable/examples/analysis/trajectory_similarity/clustering_ensemble_similarity.html

[orbeckst]

Looking really good, few things

1. move intro from API to landing page, put kit history into last paragraph
2. link to UG Note: add link to https://userguide.mdanalysis.org/stable/examples/analysis/trajectory_similarity/clustering_ensemble_similarity.html on landing page (might eventually be merged but not right now)
3. add quick intro paragraph to API section

[ianmkenney]

I referenced the user guide, but it's not quite 1:1 since the user guide references the core library implementation. I suppose I'll just a note that since the encore module hasn't been removed, that you need to modify the imports. Want to just state the explicitly here.

[orbeckst]

Add a page for the references. Clicking a reference does not go anywhere for me (eg on the first page "The package contains implementations of similarity measures between protein ensembles described in [1].") Something is not working with footcite.

Also move the (good!) paragraph with the link to the UG to the landing page.

[orbeckst]

I don't see the changes in the RTD build (neither see also box nor working refs). Did you check your build?

https://mdaencore--49.org.readthedocs.build/en/49/#footcite-lindorfflarsen2009

[ianmkenney]

I don't see the changes in the RTD build (neither see also box nor working refs). Did you check your build?

https://mdaencore--49.org.readthedocs.build/en/49/#footcite-lindorfflarsen2009

@orbeckst Do a hard refresh