I've got this problem with my 25.1 and Python 3.5 on Ubuntu 16.10, but I don't see it being solved anywhere. Wondering what the latest status was. Reproducing:
> emacs -Q --eval '(setq python-shell-interpreter "python3")'
then
M-x run-python gives
Warning (python): Your ‘python-shell-interpreter’ doesn’t seem to support readline, yet ‘python-shell-completion-native’ was t and "python3" is not part of the ‘python-shell-completion-native-disabled-interpreters’ list. Native completions have been disabled locally.
I saw one idea where an M-x find-function python-shell-completion-native-try would pull up the function from deep (/usr/local/share/emacs/25.1/lisp/progmodes/python.el.gz and the very last line was supposed to be nil "_"))) and not nil ""))). Another conversation here talks about changing inputrc
I switched to another user and I was able to use `run-python' without any warnings. Turns out it was my readline settings. Bash 4.3 added a new readline feature: "set colored-stats on" which I had in .inputrc Removing that line fixed my issue, I think this should be reproducible for all.
Anybody know what the latest is on this? BTW, running Python2 ((setq org-babel-python-command "python2")) doesn't have this problem.