You can use

np.random.random((5,5))

to generate an array of random numbers from 0 to 1, with shape (5,5).

Then just multiply by 100 to get the numbers between 0 and 100:

100*np.random.random((5,5))

Your code gives an error because of this line:

if x in M == y in M:

That syntax doesn't work. And M == y is a comparison between an array and a number, which is why you get ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all().

You already defined x and y as elements of M in the for loops so just write

if x == y:

Take a look at numpy.random.rand:

Docstring: rand(d0, d1, ..., dn)

Random values in a given shape.

Create an array of the given shape and propagate it with random samples from a uniform distribution over [0, 1).

>>> import numpy as np
>>> np.random.rand(2,3)
array([[ 0.22568268,  0.0053246 ,  0.41282024],
       [ 0.68824936,  0.68086462,  0.6854153 ]])