Atom won't get out of a Git repository

I just installed GitHub Desktop and asked it to open one of my repositories in Atom. “Great it works!” I said, “I’ll come back to that later” and quit Atom. Then a little later I needed to do some Python not in the repository so I opened Atom but weird, it’s still pointing to the local Git repo. So I tried to create a new Python file but it created in the git repository, which isn’t unreasonable, I guess. So I used “Save As” to move the file to another folder and got on with it. But now if I connect to the different repository and click “Open in Atom” then I’m back to the Python file which isn’t even in the Git folder. But creating a new file creates it in the git folder. I can’t help feeling I’m trapped in some sort of loop that’s extremely easy to get out of if I only knew how.