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sage: import sagess
0
sage: sagess.MyFunction(1,2)
1/2

The reason for the above behavior is that in the second call, the arguments 1 and 2 are Sage Integers, not Python ints: when run interactively, Sage preparses the input, turning all integers into the type Integer. You could reproduce the effect of your original call of MyFunction(1,2) in sagess.py by this:

sage: sagess.MyFunction(int(1), int(2))

On the other hand, to get 1/2, use Sage integers: rewrite your file as

#! /usr/bin/sage -python
# -*- coding: utf8 -*-

from sage.rings.all import Integer

def MyFunction(x,y):
    print Integer(x)/Integer(y)

MyFunction(1,2)

This will give the right answer with integer arguments, but it will raise an error if you pass non-integer arguments.

sage: import sagess
0
sage: sagess.MyFunction(1,2)
1/2

The reason for the above behavior is that in the second call, the arguments 1 and 2 are Sage Integers, not Python ints: when run interactively, Sage preparses the input, turning all integers into the type Integer. You could reproduce the effect of your original call of MyFunction(1,2) in sagess.py by this:

sage: sagess.MyFunction(int(1), int(2))

On the other hand, to get 1/2, use Sage integers: rewrite your file as

#! /usr/bin/sage -python
# -*- coding: utf8 -*-

def MyFunction(x,y):
    from sage.rings.all import Integer

def MyFunction(x,y):
    print Integer(x)/Integer(y)

MyFunction(1,2)

This will give the right answer with integer arguments, but it will raise an error if you pass non-integer arguments.