If you want to use the python version from your system temporarily (until you close your current shell):
pyenv shell system
https://github.com/pyenv/pyenv/blob/master/COMMANDS.md#pyenv-shell
If you want by default your system’s python
pyenv global system
https://github.com/pyenv/pyenv/blob/master/COMMANDS.md#pyenv-global
Suppose your shell is currently in the ‘src’ folder and you want src and all its subfolders to use by default a specific version of python installed with pyenv, named for instance dev311:
pyenv local dev311
https://github.com/pyenv/pyenv/blob/master/COMMANDS.md#pyenv-local
Edited to take into account the comments