[FEATURE] Move update_func up to just `BaseAdapter.compute()` call

[coltonbh]

I'm currently pushing down the update_func into low level functions like execute_subprocess and various places in the GeometricAdapter. I also have multiple ways (wrappers) to capture stdout and log files covering three cases:

1. The package uses the python logger
2. The package writes to sys.stdout
3. The package (like xtb) writes to system stdout outside of Python's access to sys.stdout (by writing directly with a C library, e.g.,)

I think I could create a single high level wrapper function that I put in BaseAdapter.compute to capture all these forms of stdout and then work with the update_func only at that level. Would be much easier and cleaner.

Something like this:

# Very lazy pseudocode
with capture_logs(...) as logs: # logs is some stream that gets written to
    # Execute the program. results will be None if FileInput                
    tread = treading.Thread(update_loop, update_func, update_interval, logs ).start()
    results, stdout = self.compute_results, args=(
                inp_obj,
                update_func,
                update_interval,
                propagate_wfn=propagate_wfn,
                **kwargs,
            )
    )
    # lazy pseudocode
    thread.kill()

Then I would run the program in a background thread, capture the logs/stdout in the main thread and can run an update_func until the thread completes execution.

This would also fix #19 and maybe #18

Maybe hae the @capture_logs decorator be a master function that uses one of the three approaches to capture logs depending on a class variable on an Adapter that declares how this program writes logs (one of logger, stdout, or nonpython)?