The current state of our pennylane_ls plugin for ultra-cold atom experiments can be viewed in this public github repository. It provides examples from our labs and can guide you to adapting it to your own experiment and needs.
Our group uses the Labscript suite to coordinate and execute experimental sequences with cold atoms.  
 The labscript suite is a collection of programs, which work together to form a control system for autonomous, hardware timed experiments.  
On the deepest level it is very nuts and bolts with plenty of commands in the style of Fig. \ref{799186} below.