How can you iterate over all 2^(n^2) binary n by n matrices (or 2d arrays) in numpy? I would something like:
for M in ....:
Do you have to use itertools.product([0,1], repeat = n**2) and then convert to a 2d numpy array?
This code will give me a random 2d binary matrix but that isn't what I need.
np.random.randint(2, size=(n,n))
                Note that 2**(n**2) is a big number for even relatively small n, so your loop might run indefinetely long.
Being said that, one possible way to iterate matrices you need is for example
nxn = np.arange(n**2).reshape(n, -1)
for i in xrange(0, 2**(n**2)):
    arr = (i >> nxn) % 2
    # do smthng with arr
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