[Debian-med-packaging] Bug#848335: CI for filo (Was: Outreachy 2017 (Round 14))

[Andreas Tille]

retitle 848335 Filo should be removed from Debian after Stretch release since it is unmaintained and can be replaced
thanks

Hi Charles,

thanks for your explanation.

On Thu, Mar 30, 2017 at 10:54:14AM +0900, Charles Plessy wrote:
> Le Wed, Mar 29, 2017 at 08:37:28AM +0200, Andreas Tille a écrit :
> > 
> > In principle the best idea would be to convince upstream to choose less
> > generic names but I think development of filo is stalled.
> 
> Hi all,
> 
> indeed the development of filo is stalled.
> 
> Filo contains three binaires:
> 
> /usr/lib/filo/groupBy
> /usr/lib/filo/shuffle
> /usr/lib/filo/stats
> 
>  * groupBy is the main program in the filo package.  It was branched off the
>    groupBy command in bedtools, but then the author changed his mind.
>    
>    https://github.com/arq5x/bedtools2/issues/418#issuecomment-238037963

OK, it makes sense to switch to something that is actively maintained.
 
>  * shuffle has for shure many possible alternatives elsewhere.

Could you name some?  Do we need to package something?
 
>  * stats was handy, but I think that it is quite superseded by datamash.

I noticed that datamash was mentioned in med-cloud task.  I added it in
addition to filo in med-bio as well as in science-statistics.  I wished
we would care more for those metainformation to make users aware of
otherwise hidden tools.  If datamash is important for our target user
group we should also convince the current maintainer to consider team
maintenance in either Debian Med or Debian Science.

> Altogether, I am regularly tempted to request the removal of filo.  But if we
> do so, we need to update bedtools to make it ship its own groupBy command
> again.  This is not difficult, but probably not the best moment either.

Definitely not the right moment.
 
> Shall we remove filo after the Release ?

Yes.  You probably have noticed my retitle of the bug.  There is no
point in adding a test suite to a to be removed package and the bug can
serve as a reminder to make sure we will not forget to do the needed
course of action.

Büşra, I suggest to leave filo alone for the moment and pick another one
from 

   https://wiki.debian.org/SummerOfCode2017/Projects/QA_BiologyApps

I have actually remove the bug pointing to filo.  If needed I can add
new bugs with other packages to the task list of the Outreachy project.

Kind regards

      Andreas.

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