MDAnalysis / membrane-curvature

MDAnalysis tool to calculate membrane curvature.

https://membrane-curvature.readthedocs.io/

GNU General Public License v3.0

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Updated docs pages #62

Closed ojeda-e closed 3 years ago

ojeda-e commented 3 years ago

Changes in this PR fixes #58

Changes include:

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

Pending:

[x] Add real data file to the test suite.
[x] 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[bot] commented 3 years ago

Codecov Report

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

ojeda-e commented 3 years ago

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

Thanks!

pep8speaks commented 3 years ago

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! :beers:

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

ojeda-e commented 3 years ago

The most recent pushed changes include:

[x] added ipython to the Visualization page to generate the plots. (Thanks @lilyminium for the suggestion, it looks amazing!)
[x] added intersphinx_mapping to link external docs.
[x] 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 commented 3 years ago

I think this PR is ready for review.

[x] All usage cases are included.
[x] 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. :)

ojeda-e commented 3 years ago

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