From: Brett Gilio <brettg@posteo.net>
To: Ricardo Wurmus <rekado@elephly.net>
Cc: 34354@debbugs.gnu.org
Subject: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73.
Date: Thu, 07 Feb 2019 14:05:58 -0600 [thread overview]
Message-ID: <87mun7qs7t.fsf@posteo.net> (raw)
In-Reply-To: <878sysf3c3.fsf@elephly.net>
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
next prev parent reply other threads:[~2019-02-07 20:07 UTC|newest]
Thread overview: 11+ messages / expand[flat|nested] mbox.gz Atom feed top
2019-02-06 22:11 [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73 Brett Gilio
2019-02-06 22:19 ` Brett Gilio
2019-02-07 7:46 ` Ricardo Wurmus
2019-02-07 20:05 ` Brett Gilio [this message]
2021-07-13 13:32 ` Maxim Cournoyer
2021-10-09 15:38 ` bug#34354: " Arun Isaac
2021-10-09 16:12 ` [bug#34354] (no subject) Arun Isaac
2021-10-16 11:44 ` [bug#34354] Update python-biopython to 1.79, seqmagick to 0.8.4 Arun Isaac
2022-04-12 10:04 ` zimoun
2022-04-12 12:28 ` bug#34354: " Ricardo Wurmus
2022-04-12 19:48 ` [bug#34354] " Arun Isaac
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