I was still pitching in baseball, we would run, then do a bunch of dynamic stretching excercises like arm circles, and all sorts of other things to get the muscle warm and loose. I always did LIGHT direct stretching AFTER the muscle was warm and pliable.
If we were ever seen strching our shoulders before running, and doing all of our warm-up excercises, would get get chewed out big time because it increases injury risk 10 fold.
I still incorporate the same warm-up method in lifting, but modified for weight lifting.
Always get warm and loose before doing any direct stretching. For weight lifting, you don't want to do any direct stretching until you are finished lifting. Stretching a lot while lifting will decrease your lift potentials.