IANAL. My understanding is that the general legal precedent in the US is that a) datamining text has no copyright implications (in the same way that reading a book has no copyright implications) and b) it is not a copyright violation to use a small amount of copyrighted material provided the context is sufficiently transformative. This might seem silly or unfair to you, but that is the current legal reality.

But even ignoring that, everybody uploading code to GitHub has given GitHub the right to analyze that code as per the GitHub ToS. This is the same mechanism by which you can't upload code to GitHub with a license that says "nobody is allowed to display this code on the internet" and then sue GitHub.