use a temp dir to do an atomic write for the raw file output

[jchiang87]

This addresses #517

[cwwalter]

LGTM..

One thing I don't quite understand: If it is messing up writing to the networked file, why does doing the os.replace always work? It is because everything is already flushed in this case and it happens in just one operation?

I mean I see in the documentation this is what you are supposed to do, but what causes the problem with the normal writeto()

[jchiang87]

The problem with .writeto is that it takes a relatively long time to do the write, so if we're running in batch and jobs time out during that operation, those files can be left incomplete. So as you note, os.replace just renames the file after everything has been written to disk.