What does `ValueError: cannot reindex from a duplicate axis` mean?

This error usually rises when you join / assign to a column when the index has duplicate values. Since you are assigning to a row, I suspect that there is a duplicate value in affinity_matrix.columns, perhaps not shown in your question.

As others have said, you've probably got duplicate values in your original index. To find them do this:

df[df.index.duplicated()]

Indices with duplicate values often arise if you create a DataFrame by concatenating other DataFrames. IF you don't care about preserving the values of your index, and you want them to be unique values, when you concatenate the the data, set ignore_index=True.

Alternatively, to overwrite your current index with a new one, instead of using df.reindex(), set:

df.index = new_index

For people who are still struggling with this error, it can also happen if you accidentally create a duplicate column with the same name. Remove duplicate columns like so:

df = df.loc[:,~df.columns.duplicated()]