From: Brett Gilio <brettg@posteo.net>
To: Brett Gilio <brettg@posteo.net>
Cc: 34354@debbugs.gnu.org
Subject: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73.
Date: Wed, 06 Feb 2019 16:19:28 -0600 [thread overview]
Message-ID: <87zhr8y2z3.fsf@posteo.net> (raw)
In-Reply-To: <871s4kzhwb.fsf@posteo.net>
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 not, please let me know so I can send a differently modified patch.
next prev parent reply other threads:[~2019-02-06 22:20 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 [this message]
2019-02-07 7:46 ` Ricardo Wurmus
2019-02-07 20:05 ` Brett Gilio
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
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://guix.gnu.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=87zhr8y2z3.fsf@posteo.net \
--to=brettg@posteo.net \
--cc=34354@debbugs.gnu.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).