Bundle a Python app with Pyinstaller and then sign it with Apple Developer ID

I have created a python app which includes about 12 packages as well as some images and text files. I bundled it, so it became an executable for Mac OS, but I have been getting "app is damaged" errors. Then I signed up for the Apple Developer program, so now I have a valid certificate to sign bundles. However, I cannot sign the app as it is, because I copy/pasted a lot of packages manually and not with the --add-data or --hiden-imports command.

I need you to re-bundle the app properly and the right way, and then sign it with my Apple Dev ID. I can provide you my latest .spec file to save you time.