Replace os.system with subprocess

[jberkus]

Our code uses os.system() in several places. This is a deprecated approach in Python. We should go through and replace it with subprocess(), partly for the benefit in trapping errors.

Ref #72

[jberkus]

Opinions on using subprocess.call() vs. subprocess.run()? Python 3.5 is 7 years old now, requring it doesn't seem like a major issue.