Changed theme to RTD and created quick start guide

[lilyminium]

From #1 :

Story: As a molecular dynamics user, I want to set up MDAnalysis quickly and easily, so that I can move onto further analysis.

Story: As a molecular dynamics user, I want to convert my AMBER trajectory into a GROMACS format, so that I can use the GROMACS analysis tools on it.

Original plan

Sections:

1. Link to page on installation.
2. Load in a Universe.
3. Writing out coordinates.
4. Basic introduction to AtomGroups, ResidueGroups, SegmentGroups.
5. Selecting atoms.
6. Trajectories and positions.
7. Universe persistence.
8. Introduction to Analysis and modules.

Current structure:

• Overview
• Loading a structure or trajectory
• Working with groups of atoms
  • Selecting atoms
  • Getting atom information from AtomGroups
  • AtomGroup positions and methods
• Working with trajectories
  • Dynamic selection
• Writing out coordinates
  • Single frame
  • Trajectories
• Analysis
  • RMSD
• References
  • Automatic citations with duecredit

While the general gist of the original plan is here, the actual structure is somewhat out the window. I struggled to place coordinate output early on without interrupting the flow. For users that see MDAnalysis as a way to convert trajectories, a nifty command-line tool might be better. Otherwise they can use the side bar to click directly to Writing out coordinates.

Acceptance criteria:

• I know how to load in a coordinate file / simulation and write it out
  • almost immediately
• I understand the arguments necessary to create ('set up') a Universe (kind of)
• I understand basic atom selection
• I understand basic analysis
• I know how to write out coordinates.
• I know where to look for less general knowledge (e.g. complex selection).
• I have links to an index of examples, available analyses, and a tutorial for developing custom analyses.

[lilyminium]

Theme

I changed the theme from alabaster to readthedocs, modifying the CSS for sufficient orange. sphinx_rtd_theme is an additional extension. I also added nbsphinx earlier for pages that are also notebooks (the quick start guide, for example, is a notebook that users could download and work through.) Here's a screenshot of how it looks to me:

The orange links would benefit from being darker on that grey background, and suddenly the code highlighting clashes, but overall I find the collapsible menu with high contrast text/background colours to be more readable. Any thoughts?

P.S. Changing the User Guide part of the logo to the MDAnalysis font would be nice, if you know what it's called.

[orbeckst]

@beckstein what was the font that you used for the original MDAnalysis label?

[orbeckst]

The new theme looks good. I do like the menu block. It's overall appearance is quite bold – I like it.

I also agree that collapsible menus are a massive improvement in navigability (if this is a word).

[orbeckst]

I like the new theme.

I would suggest to remove a whole bunch of files from the commit (vscode, notebook checkpoints, example files, zip files, ...).

[orbeckst]

@lilyminium thanks for your patience, waiting for feedback. However, it's totally fine to ping me again if I haven't done anything for two days....

[lilyminium]

I like the new theme.

I would suggest to remove a whole bunch of files from the commit (vscode, notebook checkpoints, example files, zip files, ...).

Oops, that's what I get for early-morning commits. The files in auto_examples are generated by sphinx_gallery to create the 'Examples' page of notebooks. The zips are a collection of all of them -- this a configurable option so we can turn it off.

[lilyminium]

@lilyminium thanks for your patience, waiting for feedback. However, it's totally fine to ping me again if I haven't done anything for two days....

@orbeckst Yes, similar (sorry!) -- life has a way of getting in the way of my to-do list.

[beckstein]

@orbeckst: please find attached the original font used as basis for the logo-illustration its named „ZAG Bold“ https://www.dafont.com/de/zag.font <https://www.dafont.com/de/zag.font> Grtz Chris —————————————————————————

…

Am 22.09.2019 um 04:09 schrieb Lily Wang ***@***.*** ***@***.***>>: Merged #11 <#11> into master. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#11?email_source=notifications&email_token=AJ3URQME6DJOY4LNU2CXEHLQK3HVHA5CNFSM4IU3TRJ2YY3PNVWWK3TUL52HS4DFWZEXG43VMVCXMZLOORHG65DJMZUWGYLUNFXW5KTDN5WW2ZLOORPWSZGOTYMKKYI#event-2652415329>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJ3URQMFZCKAFZA2S7KUMELQK3HVHANCNFSM4IU3TRJQ>.

[orbeckst]

Thanks @beckstein !

[orbeckst]

@lilyminium the theme at https://www.mdanalysis.org/UserGuide/ looks really good.

I will vote for changing all our docs to your theme. I am pretty sure you'll hear similar sentiments from others, too, once they can experience the UserGuide layout and style for themselves.

We should then also to apply the altered color scheme to the webpage itself.