Outputs are mostly fine if they are larger, but for smaller outputs the close icon is blocking part of the result.

I tried a few different themes thinking that was the issue, but it doesnt seem to make any difference. I see most of the gifs on this repo show a rounded square to the upper right of the output, so im not sure if thats a Mac thing or if Im using a wrong theme?
Atom 1.1.0
Win 10 x64
So i just remembered the apm hydrogen package is an older version than whats current on Github. I assume that is probably the issue?
Exactly. Hydrogen requires atom version 1.6.0 or newer for some time now. Please update your atom installation and everything should look quite a bit different ;)
By the way the new version of Hydrogen now supports mathjax output. Try using sympy with
init_printing(use_latex='mathjax')
Yep that was it. Once I downloaded a more current version of Atom and updated Hydrogen, it worked great. Dunno why I didnt notice this sooner, but atom.io download link only downloads version 1.1 even though github is up to 1.8. Serves me right for assuming whats on atom.io is current ;-)
Thanks for the tip on using mathjax! I'll use that instead.