I worked with large-ish Python codebases focused on “full-stack ML“ (data pipelines ending with trained models and APIs for using these models). Some of my colleagues relied on PyCharm for refactoring. I preferred to use cli tools (vim + tmux, ripgrep) and ran a linter from time to time. Ideally, we should’ve integrated the linter with CI, but it was in a deep backlog.

Pycharm seems to be great with all kinds of refactoring.