I would like to ask what the following does in Python. It was taken from http://danieljlewis.org/files/2010/06/Jenks.pdf
I have entered comments telling what I think is happening there.
# Seems to be a function that returns a float vector
# dataList seems to be a vector of flat. 
# numClass seems to an int
def getJenksBreaks( dataList, numClass ):
    # dataList seems to be a vector of float. "Sort" seems to sort it ascendingly
    dataList.sort() 
    # create a 1-dimensional vector 
    mat1 = []
    # "in range" seems to be something like "for i = 0 to len(dataList)+1)
    for i in range(0,len(dataList)+1):
        # create a 1-dimensional-vector?
        temp = []
        for j in range(0,numClass+1):
            # append a zero to the vector?
            temp.append(0)
        # append the vector to a vector??
        mat1.append(temp)
(...)
I am a little confused because in the pdf there are no explicit variable declarations. However I think and hope I could guess the variables.
Yes, the method append() adds elements to the end of the list. I think your interpretation of the code is correct.
But note the following:
x =[1,2,3,4]
x.append(5)
print(x)
    [1, 2, 3, 4, 5]
while
x.append([6,7])
print(x)
    [1, 2, 3, 4, 5, [6, 7]]
If you want something like
    [1, 2, 3, 4, 5, 6, 7]
you may use extend()
x.extend([6,7])
print(x)
    [1, 2, 3, 4, 5, 6, 7]
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