Capture warning message from notebook

Currently, we are catching a number of potential warnings in our notebooks using `warnings.catch_warnings()`. However, some of these warnings may be helpful to the user. We are discarding them primarily so that our unit tests will pass, without warnings displayed in the final HTML report.

Instead, we should think about catching these warnings and saving them to the log file, or potentially reporting them to the user some other way. Or possibly just updating our unit tests to allow certain warnings to be displayed.