Weir worked with Stubbs at Everton last season.
"It's a great opportunity for him," Stubbs told evertonfc.com. "It's not going to be an easy job but it's a fantastic chance to go and we'll see what he makes of it now.
"Davey's target this season will be promotion and the fans there will demand that because it's a big club in League One and they want to be back in the Championship and then the Premier League.
"It will be tough but it's a challenge that he will really relish."