Avoid using os.system and use subprocess interface instead

[comcon1]

          `subprocess` [should be used instead of](https://peps.python.org/pep-0324/) `os.system`

Originally posted by @pbuslaev in #201 (comment)

Now os.system is used all over the code and we want to avoid it. Here developers are wellcome to provide the example code-block of how we want all calls should be handled. Do we want to envelope these calls to some class or just agree on some style and put into developer's documentation?