[bug#34354] [PATCH] gnu: python-biopython: Update to 1.73.

[Maxim Cournoyer]

Hello,

Brett Gilio <brettg@posteo.net> writes:

> Ricardo Wurmus writes:
>
>> Hi Brett,
>>
>>> Brett Gilio writes:
>>>
>>>> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001
>>>> From: Brett Gilio <brettg@posteo.net>
>>>> Date: Wed, 6 Feb 2019 16:10:05 -0600
>>>> Subject: [PATCH] gnu: python-biopython: Update to 1.73.
>>>>
>>>> * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
>>>> ---
>>>>  gnu/packages/bioinformatics.scm | 7 +++++--
>>>>  1 file changed, 5 insertions(+), 2 deletions(-)
>>>>
>>>> diff --git a/gnu/packages/bioinformatics.scm 
>>>> b/gnu/packages/bioinformatics.scm
>>>> index 516a7c1ee..99c205279 100644
>>>> --- a/gnu/packages/bioinformatics.scm
>>>> +++ b/gnu/packages/bioinformatics.scm
>>>> @@ -12,6 +12,7 @@
>>>>  ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
>>>>  ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
>>>>  ;;; Copyright © 2018 Mădălin Ionel Patrașcu 
>>>> <madalinionel.patrascu@mdc-berlin.de>
>>>> +;;; Copyright © 2019 Brett Gilio <brettg@posteo.net>
>>>>  ;;;
>>>>  ;;; This file is part of GNU Guix.
>>>>  ;;;
>>>> @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do 
>>>> computational biology.")
>>>>  (define-public python-biopython
>>>>    (package
>>>>      (name "python-biopython")
>>>> -    (version "1.70")
>>>> +    (version "1.73")
>>>>      (source (origin
>>>>                (method url-fetch)
>>>>                ;; use PyPi rather than biopython.org to ease updating
>>>>                (uri (pypi-uri "biopython" version))
>>>>                (sha256
>>>>                 (base32
>>>> -                "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
>>>> +                "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))))
>>>>      (build-system python-build-system)
>>>>      (arguments
>>>>       `(#:phases
>>>> @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and 
>>>> more.")
>>>>          (base32
>>>>           "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
>>>>      (build-system python-build-system)
>>>> +    (arguments
>>>> +     `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests
>>>>      (inputs
>>>>       `(("python-biopython" ,python-biopython)))
>>>>      (native-inputs
>>>
>>> I disabled the tests on package `seqmagick' because after updating
>>> biopython to 1.73 it was failing a test on integer iteration. I could
>>> not reproduce this failure on the 1.70 version of biopython, so it seems
>>> to be a temporary fix to that failure. I'm not sure if this was the
>>> "correct" way to fix that issue, but it works.
>>
>> If the tests are failing it is possibel that seqmagick doesn’t work
>> properly any more.  This would be serious.
>>
>> Could you report the test failures to the upstream developers please and
>> add the URL in a comment?
>>
>> Also please separate these two changes.  They should not go to the same
>> commit.
>
> Ricardo,
>
> Understood. I will do exactly that and reply again later with a revised
> patch series.
>
> Brett Gilio

Any news on this?

Thanks,

Maxim