@manics pointed out what is happening. One idea that you could test would be to make a sub-directory named binder in your root directory, see here, and copy the environment.yml you have to there. Then that will be used by Binder to build the image from the repo and if you environment.yml specifies everything needed, it should work. Additionally that allows you to not mess with your files in the main directory of your repo and avoids the Dockerfile use which is trickier.