[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))

[Alex Mestiashvili]

Hi Andreas,

On 11/20/19 4:34 PM, Andreas Tille wrote:
> 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     3) Make med-bio (or whereever the outdated package was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        advertised in) conflicting with the outdated software?

I think 1 and 2 don't really feet for this case.
med-bio should exclude tophat from the list of recommended packages.

> 
> 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).

I guess I'll leave it to the user. However once python2 is removed the 
package will be broken, but I don't see a good way to prevent that and 
notifying the user is too much effort IMO.

So I'll take the easy way and file ROM.

Thanks,
Alex