How to respond to difficult compliment?

I have a very good Indian girl friend (India Indian, not Native American) who compliments me sometimes on my skin and eye color. I have very pale skin and blue eyes. The way that she words it and follows it with a derogatory comment about her dark brown eyes and skin makes me very uncomfortable. For example, she'll say "you're so pale and pretty! Not like me, I'm so dark." I believe that physical beauty is not limited to one skin tone, eye color, hair texture and body shape. The compliments come off as racist (or at least colorist) to me and it makes me uncomfortable. She is a very beautiful woman and I want her to see that.
How do I respond? I really care about my friend and I want her to know that she's so lovely, inside and out.