From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([209.51.188.92]:39364) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1grVYF-0007if-0v for guix-patches@gnu.org; Wed, 06 Feb 2019 17:20:16 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1grVY7-0004oc-2c for guix-patches@gnu.org; Wed, 06 Feb 2019 17:20:10 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:37012) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1grVY2-0004nK-3f for guix-patches@gnu.org; Wed, 06 Feb 2019 17:20:05 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1grVY1-0001fE-PF for guix-patches@gnu.org; Wed, 06 Feb 2019 17:20:01 -0500 Subject: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73. Resent-Message-ID: References: <871s4kzhwb.fsf@posteo.net> From: Brett Gilio In-reply-to: <871s4kzhwb.fsf@posteo.net> Date: Wed, 06 Feb 2019 16:19:28 -0600 Message-ID: <87zhr8y2z3.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: Brett Gilio Cc: 34354@debbugs.gnu.org Brett Gilio writes: > From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 > From: Brett Gilio > 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/bioinformatic= s.scm > index 516a7c1ee..99c205279 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -12,6 +12,7 @@ > ;;; Copyright =C2=A9 2018 Joshua Sierles, Nextjournal > ;;; Copyright =C2=A9 2018 G=C3=A1bor Boskovits > ;;; Copyright =C2=A9 2018 M=C4=83d=C4=83lin Ionel Patra=C8=99cu > +;;; Copyright =C2=A9 2019 Brett Gilio > ;;; > ;;; This file is part of GNU Guix. > ;;; > @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to d= o 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, an= d more.") > (base32 > "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) > (build-system python-build-system) > + (arguments > + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tes= ts > (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.