Not sure what operating system you are using... If you have Windows you could try VS Code instead of Atom. If you are on Windows, you should try using Atom version 1.18 with the Pymakr plugin.
More about Atom and Pymakr plugin issues on Github HERE
More info if you are using Windows 10:
The easiest way to fix this for Windows 10 is to downgrade to Atom 1.18, you can download it from here:
https://github.com/atom/atom/releases?after=v1.19.0-beta5
half way down the page is version 1.18, I downloaded the AtomSetup.exe file for windows10.
Make sure you don't upgrade to 1.19 or above until the Pymakr plugin is fixed.
Also Atom is by default set to auto update so as soon as you open it, go to menu >>> help >>> about atom
Then un-check the "Automatically download updates"
Then install the Pymakr package. From Menu >>> Packages >>> Settings View >>> Install Packages
In the Install Packages search box, type in pymakr, it's down a couple in the search, press 'Install'
I had to remove the pymakr package manually because I had Atom previously installed. It's located something like c:\users\yourusername.atom\packages
I have it all working, now dealing with a serial port connection issue. Can't connect with all the default settings and the correct com port (com6 port etc... )