This is a dumb question but please help me.
Q. How do I run Python script that is saved in my local machine?
after vagrant up and vagrant ssh, I do not see any Python file in the VM. Then what if I want to run Python scripts that are saved in my Mac? I do not want to copy and paste them manually using vim. 
How would you run Python script in Vagrant ssh?
You have two options:

You can go the classic route of using the shell provisioner using vagrant
config.vm.provision "shell", inline: $script

And in your script run the python script

All files are pushed in /tmp, you can possible use this to run your python script
Run Python script in Vagrant