Updated docs pages

[ojeda-e]

Changes in this PR fixes #58

Changes include:

• Updated algorithm page.
• Update Usage page for three cases
• Membrane-only
• Membrane-protein with posres.
• Membrane-protein with no posres.
• Updated visualization page.

Pending:

• Add real data file to the test suite.
• Add real plots to the Visualization page.

Question:
I left the usage page as if I were going to use a different test data file for each case.

• Is it a good idea to add a dataset for each one of the cases I have or better to reuse some MDA tests?

Happy to receive any other suggestions. Thanks!

@lilyminium @orbeckst @IAlibay @fiona-naughton

[codecov]

Codecov Report

Merging #62 (3e235e7) into main (8a52295) will not change coverage.
The diff coverage is n/a.

[ojeda-e]

Hi @lilyminium @orbeckst. I would appreciate some feedback on the pushed changes.

Thanks!

[lilyminium]

This looks amazing @ojeda-e! Lovely figures as always. I have some comments, mostly on how you can get sphinx to do the work for you.

Regarding test files, I do think it'd be a good idea to add the additional test files that you mention in the examples somewhere so users can immediately use your library, and you can also use them for tests. However, one option that you could consider (if they're small) is not adding them to MDAnalysis.tests, but rather adding them to membrane_curvature.tests. (If the files are large, they will be better off in MDAnalysis.data`.

[pep8speaks]

Hello @ojeda-e! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2021-08-08 04:05:59 UTC

[ojeda-e]

The most recent pushed changes include:

• added ipython to the Visualization page to generate the plots. (Thanks @lilyminium for the suggestion, it looks amazing!)
• added intersphinx_mapping to link external docs.
• general requested changes.

Two points to discuss:

• I couldn't fix the links of MembraneCurvature.results.avearge_z_surface and other attributes on the Algorithm page. Can I just leave it like that for now? I knwo it isn't perfect, but I tried several options and couldn't make it work as it should.

Edit: I am not sure what to do about the example for the case of protein with no posres. I can't make my systems public at this very moment. Maybe there is a system with such features in tests or MDAnalysisData? I'm open to suggestions case covered :) .

Thanks!

[ojeda-e]

I think this PR is ready for review.

• All usage cases are included.
• In visualization, plots render with iPython.

Thanks @lilyminium for all the suggestions!
@orbeckst @IAlibay @fiona-naughton I would appreciate your feedback here although I think it's ready to go. :)

[lilyminium]

Thanks for making those changes @ojeda-e!

[ojeda-e]

Thanks for taking the time to double-check the changes and approve the PR @lilyminium!
I will merge after fixing the PEP8.