As part of a unit test, I need to test two DataFrames for equality. The order of the columns in the DataFrames is not important to me. However, it seems to matter to Panda
have you tried using df1.equals(df2)? i think it's more reliable that df1==df2, though i'm not sure if it will resolve your issues with column order.
http://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.equals.html