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

[Alex Mestiashvili]

On 10/11/19 11:11 AM, Andreas Tille wrote:
> Hi,
> 
> I tried to use 2to3 to port tophat to Python3 in Git[1].  Unfortunately
> the autopkgtest fails with:
> 
> 
> autopkgtest [09:04:13]: test run-unit-test: [-----------------------
> 
> [2019-10-11 09:04:13] Beginning TopHat run (v2.1.1)
> -----------------------------------------------
> Traceback (most recent call last):
>   File "/usr/bin/tophat", line 4106, in <module>
>     sys.exit(main())
>   File "/usr/bin/tophat", line 3898, in main
>     run_log = open(logging_dir + "run.log", "w", 0)
> ValueError: can't have unbuffered text I/O
> autopkgtest [09:04:13]: test run-unit-test: -----------------------]
> autopkgtest [09:04:14]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
> run-unit-test        FAIL non-zero exit status 1
> 
> 
> I'd applaude if in beginning of November if I'm back from beeing offline
> if this would be fixed. :-)
> 
> Kind regards
> 
>      Andreas.
> 
> [1] https://salsa.debian.org/med-team/tophat
> 

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

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

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