force `subprocess.run` to check return code is 0

In general, this should help to capture unintentional errors.

Where the change has created failures, they have been fixed. (Mostly because the git repository that was looked for was missing.)

mpsd-software-environment.py

@@ -54,10 +54,10 @@ class os_chdir:
 
 def run(*args, counter=[0], **kwargs):
     """
-    Call subprocess.run(*args, **kwargs) and print logging data.
+    Call subprocess.run and print logging data.
 
-    Conveniene function to call `subprocess.run` and provide some metadata
-    about the call.
+    Conveniene function to call `subprocess.run(*args, **kwargs)`
+    and provide some metadata about the call.
 
     Parameters
     ----------