Well, when I start winding my strings, I always go slow, no matter what. I have broken an E (!!!) string once just by winding it. I swear it was not even near E, as soon as it built tension... it broke. And GC refused to take the string back (since then I am a happy client of juststrings.com).
The way I stretch is gentle. [Invalid or Expired Link Removed]
I tune the strings. Then 2 fingers under, I pull the strings from the 12th about a third of an inch from the fretboard, then slide my fingers up to the 5th, then again from 12th to 16th or 17th.
They I tune up, and redo the same operation. I usually expect the strings to settle after that and go slowly flat.
I used to do the same thing as what Sheehan apparently recommends, popping the string pretty hard, but I don't anymore. I don't slap or pop, not my style. My strings last quite a while actually and I play on average 90 minutes every day.
I also use flat wounds, these ones:
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