GNU bug report logs - #34354
Update python-biopython to 1.79, seqmagick to 0.8.4

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From: Brett Gilio <brettg <at> posteo.net>
To: Brett Gilio <brettg <at> posteo.net>
Cc: 34354 <at> debbugs.gnu.org
Subject: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73.
Date: Wed, 06 Feb 2019 16:19:28 -0600

Brett Gilio writes:

> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001
> From: Brett Gilio <brettg <at> 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 <at> nextjournal.com>
>  ;;; Copyright © 2018 Gábor Boskovits <boskovits <at> gmail.com>
>  ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
> +;;; Copyright © 2019 Brett Gilio <brettg <at> 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 not, please let me know so I can send a differently modified patch.

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