Author here. They are very independent. In short: Cubes is OLAP framework for abstracting aggregate queries on top of a datastore, mostly through SQL. You define a so called multi-dimensional model – how the analysts see the world, and cubes knows how to project it to underlying data structures, preferably star or snowflake table schemas.

Bubbles was meant to be data integration library (also known as ETL) – get data from multiple sources, transform them and produce tables that are more suitable for further analysis or reporting.