From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([209.51.188.92]:60723) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1grpwt-00063J-D0 for guix-patches@gnu.org; Thu, 07 Feb 2019 15:07:04 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1grpws-0006gC-Hi for guix-patches@gnu.org; Thu, 07 Feb 2019 15:07:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:39367) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1grpws-0006fz-Ct for guix-patches@gnu.org; Thu, 07 Feb 2019 15:07:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1grpws-00011y-21 for guix-patches@gnu.org; Thu, 07 Feb 2019 15:07:02 -0500 Subject: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73. Resent-Message-ID: References: <871s4kzhwb.fsf@posteo.net> <87zhr8y2z3.fsf@posteo.net> <878sysf3c3.fsf@elephly.net> From: Brett Gilio In-reply-to: <878sysf3c3.fsf@elephly.net> Date: Thu, 07 Feb 2019 14:05:58 -0600 Message-ID: <87mun7qs7t.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: Ricardo Wurmus Cc: 34354@debbugs.gnu.org Ricardo Wurmus writes: > Hi Brett, > >> 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/bioinformat= ics.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= 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 t= ests >>> (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 the tests are failing it is possibel that seqmagick doesn=E2=80=99t wo= rk > properly any more. This would be serious. > > Could you report the test failures to the upstream developers please and > add the URL in a comment? > > Also please separate these two changes. They should not go to the same > commit. Ricardo, Understood. I will do exactly that and reply again later with a revised patch series. Brett Gilio