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For python development, I use https://github.com/jorgenschaefer/elpy (Elpy is an Emacs package to bring powerful Python editing to Emacs. It combines and configures a number of other packages, both written in Emacs Lisp as well as Python.)
For code navigation, I still use counsel-etags+ctags. Also see the new trick I invented in counsel-etags, M-x counsel-etags-find-tag-at-point can open the documentation of 3rd party python package API. For example, see https://github.com/redguardtoo/emacs.d/commit/18ff983aba1cb6f102abd0f95035d1a8b66af7fb how I set up for numpy.
project.el will help. A package like find-file-in-project will help you work with large projects.