making it easier to use in simulation setup

diag family number is not unique. using element number for index instead

- _dict was unused
- adding some keys in the dictionary as attributes to the class

flake8 repo change as well

can now read both PAR_diag1 and ENV_diag1

- read header
- calculate Courant-Snyder (borrowed from lib_tw)

(maybe?)

to subprocess.run (e.g. stdout/stderr)