What are the guidelines (if any) for packaging the game? 

If I use additional packages, should I include them, leave them out as required package do be installed by user or provide full source for all external packages? 

To be more specific, I am using several scientific computing libs, do you think that would unreasonably complicate things? 

For packaging game, you should try to make a standalone bundle. This means that if a user clicks on your game, they should not have to install additional components. However if it gets complicated, feel free to list them in source and ask users to manually download libraries. At the very least, you should have the source code available, and possibly a requirements.txt or README.md with instructions on how to run your game.

You can use something like pyinstaller to make a singular game file with no other components.