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

Previous Next

Full log

View this message in rfc822 format

From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#34354: closed (Update python-biopython to 1.79, seqmagick to
 0.8.4)
Date: Tue, 12 Apr 2022 12:29:01 +0000

[Message part 1 (text/plain, inline)]

Your message dated Tue, 12 Apr 2022 14:28:22 +0200
with message-id <87r162xz7o.fsf <at> elephly.net>
and subject line Re: bug#34354: Update python-biopython to 1.79, seqmagick to 0.8.4
has caused the debbugs.gnu.org bug report #34354,
regarding Update python-biopython to 1.79, seqmagick to 0.8.4
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


-- 
34354: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=34354
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

[Message part 2 (message/rfc822, inline)]

From: Brett Gilio <brettg <at> posteo.net>
To: guix-patches <at> gnu.org
Subject: [PATCH] gnu: python-biopython: Update to 1.73.
Date: Wed, 06 Feb 2019 16:11:48 -0600

[0001-gnu-python-biopython-Update-to-1.73.patch (text/x-patch, inline)]

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
-- 
2.20.1

[Message part 4 (message/rfc822, inline)]

From: Ricardo Wurmus <rekado <at> elephly.net>
To: zimoun <zimon.toutoune <at> gmail.com>
Cc: 34354-done <at> debbugs.gnu.org, Arun Isaac <arunisaac <at> systemreboot.net>,
 Brett Gilio <brettg <at> posteo.net>, Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Subject: Re: bug#34354: Update python-biopython to 1.79, seqmagick to 0.8.4
Date: Tue, 12 Apr 2022 14:28:22 +0200

zimoun <zimon.toutoune <at> gmail.com> writes:

> And the update of 1.79 requires more work.  Therefore, is it worth to
> keep this submission open?  I guess the update to 1.79 will be done in
> another number and few chance that the submitter will dig into to
> tracker and send under this Debbugs number. :-)
>
> Closing?

Yes.

-- 
Ricardo

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.