There are several issues with this study, some of which are pointed out here in a useful summary: http://slatestarcodex.com/2016/02/12/before-you-get-too-excited-about-that-github-study/ .
Especially making the gender responsible for the difference in contrast to other attributes of the users that might be just linked to the gender (maybe the women that join GitHub are just the very best/professional women, contribute only to specific types of code, etc., etc.)