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ViennaRNA - please review


Over the past months/weeks I have invested some energy into an overhaul
of the ViennaRNA package. It is needed as a testing-dependency of
seqcluster which in turn is needed for bcbio. Sadly, it is of a
"commercial redistribution only if not charging more than media costs"
non-free type of software. There is something in me that wants to just
not test seqcluster properly, so we do not need to install the ViennaRNA
package and then have a free RNA sequencing pipeline. But then that
sequencing pipeline would not be complete. This "freeness" vs
"completeness" problem is somewhat interesting: It was well-intended by
the developer and it is affecting only a side-application of an
otherwise completely free pipeline. I suggest to collect some thoughts
on this.

2.4.14 has done a few changes on how the documentation is built, which
had me just not building the documentation as a quick hack. The perl and
python interfaces I have not checked. Autotests are fine.

The package could use some help to get platform-specific(?)
optimisations in (simd?). And I was not really sure about the
floating-point precision.

So, anyway, please give this package a spin. And if someone finds this
to be good enough for non-free, then please just go and upload.


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