Using Python To Automate External Program
Solution 1:
I haven't done such thing. So I do not have proof of concept. But You have at least 2 options, more or less complicated:
install virtualbox/vmware, and create virtual operating system (windows or Linux) on it. Then run your pyautogui script in this virtual operating system. You operating system is available in window-like container - so you can minimize this window with running script, and you system where you can interact as a user. (long tutorial: https://www.virtualbox.org/manual/ch01.html)
If you are Linux user, then you may be familiar with virtual screen. I think many people are using this virtual screen with automating web testing in sellenium (How do I run Selenium in Xvfb?). So probably, I say probably, there is chance to run pyautogui in virtual screen: How to attach pyautogui to the virtual display? - this is similar, but not answered question.
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