[Debian-med-packaging] Bug#938677: Removing tophat (Was: Bug#938677: Please check autopkgtest of (may be failed) attempt of Python3 port (Was: Bug#938677: tophat: Python2 removal in sid/bullseye))

[Andreas Tille]

On Wed, Nov 20, 2019 at 03:33:33PM +0100, Alex Mestiashvili wrote:
> 
> It is not that trivial to fix tophat and more over there is a successor
> - HISAT2.
> It is not maintained upstream since 2016 and one of the co-authors
> asks to stop using it:
> 
> > Please stop using Tophat. Cole and I developed the
> > method in *2008*. It was greatly improved in TopHat2 then HISAT
> > & HISAT2. There is no reason to use it anymore. I have been
> > saying this for years yet it has more citations this year than last

Fine for me.
 
> In 2017 we had already a discussion about removing tophat from
> Debian[0], and now I believe the time has come.

I have no problems if you file a ROM.  What we might consider for
this case or in general:  If there is a successor of some software
would we want to

   1) Use a virtual package name in the successor
   2) Create a metapackage depending from the successor and
      delivering some docs about how to use the successor
   3) Make med-bio (or whereever the outdated package was
      advertised in) conflicting with the outdated software?

Just filing a ROM request will not remove the package from user
installations.  Its a question whether we really want to prevent that
users keep that package - but in case we want this the technical means
mentioned above came to mind (not sure whether this is a complete list
of possibilities).

So you are the expert - do whatever you feel is necessary to do.

Kind regards

       Andreas.
 
> [0] https://lists.debian.org/debian-med/2017/12/msg00089.html

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