Nikolaus Rath added the comment:

This will probably be too radial, but I think it should at least be mentioned 
as a possible option.
 
We could just not attempt to implicitly flush buffers in the finalizer at all. 
This means scripts relying on this will break, but in contrast to the current 
behavior they will break consistently so it's easy to find and fix the problem.

I think this is still preferable to any solution that does not guarantee 
flushing in 100% of the cases.

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Python tracker <rep...@bugs.python.org>
<http://bugs.python.org/issue17852>
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