Is what is between me and my friend considered animosity, and is it true that Allah will not accept my deeds because of it?

As long as you are bothered by the companionship of this girl, the advice is to make the relationship with her superficial, so that you are neither shunning her nor being harmed by her. Shunning ceases with greetings; if you greet her when you meet her, you are not shunning her. And as long as your heart does not hold malice towards her, there is no animosity to fear that would nullify good deeds.