Aside: I write a lot more Python than Clojure, and I wish someone ported Datalevin/Datahike/persistent DataScript to Python. I'd try it as an alternative to SQLite. I suspect with thoughtful API design, an embedded Datalog could feel organic in Python. It might be easier to prototype with than SQLite. There are Datalog and miniKanren implementations for Python, but they are not designed as an on-disk database. PyCozo might be the closest thing that exists. (A sibling comment https://news.ycombinator.com/item?id=40995652 already mentions Cozo.)
https://github.com/cozodb/cozo
Has a dialect of Datalog + some vector support. Multiple storage engines for backend including SQLite, so if your concern is data stability that seems like a reasonable, proven option.