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Re: ViennaRNA - please review

Hi Steffen,

I'd consider reviewing if you would contact upstream first and record
your attempt here:


Our obligation as maintainers is also to teach upstream and maintaining
non-free code is always a nuisance.  So lets do something against broken
licenses in the first place.

Thank you


On Mon, Sep 09, 2019 at 02:25:42PM +0200, Steffen Möller wrote:
> Hello,
> 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.
> Best,
> Steffen


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