Pandas sum by groupby, but exclude certain columns

The agg function will do this for you. Pass the columns and function as a dict with column, output:

df.groupby(['Country', 'Item_Code']).agg({'Y1961': np.sum, 'Y1962': [np.sum, np.mean]})  # Added example for two output columns from a single input column

This will display only the group by columns, and the specified aggregate columns. In this example I included two agg functions applied to 'Y1962'.

To get exactly what you hoped to see, included the other columns in the group by, and apply sums to the Y variables in the frame:

df.groupby(['Code', 'Country', 'Item_Code', 'Item', 'Ele_Code', 'Unit']).agg({'Y1961': np.sum, 'Y1962': np.sum, 'Y1963': np.sum})

You can select the columns of a groupby:

In [11]: df.groupby(['Country', 'Item_Code'])[["Y1961", "Y1962", "Y1963"]].sum()
Out[11]:
                       Y1961  Y1962  Y1963
Country     Item_Code
Afghanistan 15            10     20     30
            25            10     20     30
Angola      15            30     40     50
            25            30     40     50

Note that the list passed must be a subset of the columns otherwise you'll see a KeyError.