MDA-style docs

[orbeckst]

• fix use MDA style for docs #69
• update style
• create sitemap (assuming the docs will eventually be at https://www.mdanalysis.org/mdacli)
• add the default footer with the link to the privacy (required for all MDA docs within the MDAnalysis organization)
• add preliminary logo

[orbeckst]

I used the standard MDA styles to give you a starting point . I also created a simple logo as a placeholder.

[orbeckst]

Needs

• sphinx_rtd_theme
• sphinx_sitemap

[codecov]

Codecov Report

Merging #70 (a6f42f5) into main (065ed9d) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main      #70   +/-   ##
=======================================
  Coverage   81.31%   81.31%           
=======================================
  Files           8        8           
  Lines         519      519           
  Branches       91       91           
=======================================
  Hits          422      422           
  Misses         77       77           
  Partials       20       20           

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[orbeckst]

Docs build (see https://mdacli--70.org.readthedocs.build/en/70/) but other tests fail due to some issue with bump_version. Please have a look. Thanks.

[joaomcteixeira]

Great addition. thanks! 😉

I made some changes to pass CI, but not completed yet. Need to clean some details in the documentation.

tox -e docs tells what is missing.

[orbeckst]

@joaomcteixeira I am not sure what I could do to fix the remaining issuse. Can I leave this to you?

[orbeckst]

Note that this part is necessary for analytics.

The number of page accesses is actually an important number for us to demonstrate impact so we do want to keep track of which pages are seen. This is fully anonymous, though.

[orbeckst]

in preparation for #71

[PicoCentauri]

Thanks @orbeckst!

I fixed the CI (adding a required CHANGELOG entry) and updated the AUTHORS. LGTM. @joaomcteixeira if you want to update the docs do it and merge when you think.

Just to know. For adding it to https://www.mdanalysis.org/mdacli we should update our github action for pushing it right?

[orbeckst]

Just to know. For adding it to https://www.mdanalysis.org/mdacli we should update our github action for pushing it right?

Yes. You can definitely keep your RTD as well but when we refer to the docs we refer to the ones hosted under mdanalysis.org.

Once that's up, we add your mdacli/sitemap.xml to https://www.mdanalysis.org/sitemapindex.xml so that (1) search engines can find everything and (2) the search on the website itself will eventually find the docs (although there are currently some issues with the search MDAnalysis/MDAnalysis.github.io#202).

[PicoCentauri]

Okay! Sounds like a good plan. I suggest we create another PR for displaying the docs at mdanalysis.org including a sitemap and merge this one asap.

[orbeckst]

I switched the logo to the same one that you used in PR MDAnalysis/MDAnalysis.github.io#207 ; from my end I think everything is done here. Now up to @PicoCentauri and @joaomcteixeira .