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In emacs, I use ipython in the inferior python mode with config:
(setq python-shell-interpreter "ipython"
python-shell-interpreter-args "--simple-prompt -i")
When I edit my .py file, without any input to inferior python, the input number jumps occasionally.
I suspect that I send some unintentional inputs to the inferior python. But, I don't know how. It happens quite randomly.
Completion and other features of the python mode require communication between emacs and the ipython process. This communication is achieved by sending code to the interactive ipython inferior shell. These are probably the "unintentional inputs" you are sending.
