Yes, GitHub calls them repositories, but, even on its home page, also calls them projects (https://github.com: "Powerful collaboration, code review, and code management for open source and private projects.")
Before GitHub (and, to a lesser extent, SourceForge), you would not find stuff such as https://github.com/Dub4ek/Scala_Ex (one 20 line file, called Week1ExerSizes.sc (sic)) in the same places as, say, the gcc or NCSA Telnet sources.
Looking at http://www.googlefight.com/index.php?lang=en_GB&word1=GitHub..., that also seems to be common terminology.
Also, both URL and title of the article (http://www.takipiblog.com/2013/12/26/the-top-100-most-popula...) do talk of projects.
Before GitHub (and, to a lesser extent, SourceForge), you would not find stuff such as https://github.com/Dub4ek/Scala_Ex (one 20 line file, called Week1ExerSizes.sc (sic)) in the same places as, say, the gcc or NCSA Telnet sources.