Make a separate logger for each file, and name the loggers to match the hierarchy of modules. For the file acert/hfesr/Runner.py, it starts with:
logger = logging.getLogger('acert.hfesr.Runner')
That's quite simple. Then you can enable and disable logging by file or by module.
The second tip is that, if you have written a library, don't use logging.basicConfig() in that library because it makes logging handlers that are difficult for subsequent client applications to quiet.