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[bug#34354] [PATCH] gnu: python-biopython: Update to 1.73.
From: |
Brett Gilio |
Subject: |
[bug#34354] [PATCH] gnu: python-biopython: Update to 1.73. |
Date: |
Wed, 06 Feb 2019 16:19:28 -0600 |
User-agent: |
mu4e 1.0; emacs 26.1 |
Brett Gilio writes:
> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001
> From: Brett Gilio <address@hidden>
> 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 <address@hidden>
> ;;; Copyright © 2018 Gábor Boskovits <address@hidden>
> ;;; Copyright © 2018 Mădălin Ionel Patrașcu <address@hidden>
> +;;; Copyright © 2019 Brett Gilio <address@hidden>
> ;;;
> ;;; 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.