I use beancount [1] for double-entry bookkeeping. It's similar to ledger/hledger, but it enforces correctness of your ledger a bit more, and it's written in Python which suits me well. You keep a ledger in a plain text file (easy to keep under source control), and then run various commands for analysis. Fava [2] is a web interface that gives you some stats. There's also a Vim plugin [3].

For analysis and filing taxes and stuff, I've written some custom analysis scripts that take the ledger file as input. Pretty easy to write, since the tool already gives you a large and reasonably well documented Python API.

[1] http://furius.ca/beancount/

[2] https://beancount.github.io/fava/

[3] https://github.com/nathangrigg/vim-beancount