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You can't use $.fn.transition() as drop-in replacement for $.fn.animate(). It was not a design goal of this project, as far as I know.
True for .stop() but you can stop transition easily with saving transitioning property in at-the-moment state and, in same time setting $(element).css({ transition: 'all 0ms' }) which cuts off transition immediately.
You're absolutely right for not being able to use this lib for scrollTop - scrollTop is document property and not node style value.
The details of it make it sound like a drop in replacement for .animate() but there are a number of issues I found that make it not.
with .animate() if you call .stop(true) it will drop all current animations on the element.
scrollTop: and some other properties also aren't valid for .transition()
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