Update our `subprocess.Popen` commands to use `with`

Background

Currently, we're managing the subproc created by Popen instead of using with to make controlling the sub proc simpler.

We should update anywhere we're using Popen to manage the subproc using with.

Acceptance Criteria

• Update all locations where subprocess.Popen is used and either
  • Use with to manage the subproc
  • Update from Popen to run

Definition of Done

• All Popen calls are managed using with