From patchwork Wed Apr 1 14:24:48 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?q?Maja_K=C4=85dzio=C5=82ka?= X-Patchwork-Id: 21034 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 0D26D27BBE4; Wed, 1 Apr 2020 15:25:12 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.9 required=5.0 tests=BAYES_00,MAILING_LIST_MULTI, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id B458A27BBE1 for ; Wed, 1 Apr 2020 15:25:11 +0100 (BST) Received: from localhost ([::1]:32808 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jJeIp-00088E-6a for patchwork@mira.cbaines.net; Wed, 01 Apr 2020 10:25:11 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53923) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jJeIh-00087r-KU for guix-patches@gnu.org; Wed, 01 Apr 2020 10:25:04 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1jJeIg-0004yN-Ef for guix-patches@gnu.org; Wed, 01 Apr 2020 10:25:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:55222) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1jJeIg-0004xy-BQ for guix-patches@gnu.org; Wed, 01 Apr 2020 10:25:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jJeIg-0006PD-5o for guix-patches@gnu.org; Wed, 01 Apr 2020 10:25:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#40265] [PATCH v2] gnu: python-intervaltree: Update to 3.0.2. References: <20200327235125.3250-1-kuba@kadziolka.net> In-Reply-To: <20200327235125.3250-1-kuba@kadziolka.net> Resent-From: Jakub =?utf-8?b?S8SFZHppb8WCa2E=?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 01 Apr 2020 14:25:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40265 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40265@debbugs.gnu.org Cc: mbakke@fastmail.com, efraim@flashner.co.il Received: via spool by 40265-submit@debbugs.gnu.org id=B40265.158575109924602 (code B ref 40265); Wed, 01 Apr 2020 14:25:02 +0000 Received: (at 40265) by debbugs.gnu.org; 1 Apr 2020 14:24:59 +0000 Received: from localhost ([127.0.0.1]:38535 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jJeIc-0006Og-IV for submit@debbugs.gnu.org; Wed, 01 Apr 2020 10:24:58 -0400 Received: from pat.zlotemysli.pl ([37.59.186.212]:60720) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jJeIa-0006ON-Vg for 40265@debbugs.gnu.org; Wed, 01 Apr 2020 10:24:57 -0400 Received: (qmail 25833 invoked by uid 1009); 1 Apr 2020 16:24:54 +0200 Received: from 188.123.215.55 (kuba@kadziolka.net@188.123.215.55) by pat (envelope-from , uid 1002) with qmail-scanner-2.08st (clamdscan: 0.98.6/25768. spamassassin: 3.4.0. perlscan: 2.08st. Clear:RC:1(188.123.215.55):. Processed in 0.00903 secs); 01 Apr 2020 14:24:54 -0000 Received: from unknown (HELO localhost.localdomain) (kuba@kadziolka.net@188.123.215.55) by pat.zlotemysli.pl with AES256-SHA encrypted SMTP; 1 Apr 2020 16:24:54 +0200 From: Jakub =?utf-8?b?S8SFZHppb8WCa2E=?= Date: Wed, 1 Apr 2020 16:24:48 +0200 Message-Id: <20200401142448.2683-1-kuba@kadziolka.net> X-Mailer: git-send-email 2.26.0 MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2. [arguments]: Don't skip the tests, work around the problematic sanity-check instead. --- Thanks for your helpful comments. I have added a comment, which, in hindsight, should've been there in the first place :D I will defer moving the package until committing the new dependent (pwntools, #40265), as this is best done in a separate commit anyway. gnu/packages/bioinformatics.scm | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d69c2aea63..943369b275 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2019 Brian Leung ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling +;;; Copyright © 2020 Jakub Kądziołka ;;; ;;; This file is part of GNU Guix. ;;; @@ -13552,17 +13553,27 @@ allowing the insertion of arbitrary types into the tree.") (define-public python-intervaltree (package (name "python-intervaltree") - (version "2.1.0") + (version "3.0.2") (source (origin (method url-fetch) (uri (pypi-uri "intervaltree" version)) (sha256 (base32 - "02w191m9zxkcjqr1kv2slxvhymwhj3jnsyy3a28b837pi15q19dc")))) + "0wz234g6irlm4hivs2qzmnywk0ss06ckagwh15nflkyb3p462kyb")))) (build-system python-build-system) - ;; FIXME: error when collecting tests - (arguments '(#:tests? #f)) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; pytest seems to have a check to make sure the user is testing + ;; their checked-out code and not an installed, potentially + ;; out-of-date copy. This is harmless here, since we just installed + ;; the package, so we disable the check to avoid skipping tests + ;; entirely. + (add-before 'check 'import-mismatch-error-workaround + (lambda _ + (setenv "PY_IGNORE_IMPORTMISMATCH" "1") + #t))))) (propagated-inputs `(("python-sortedcontainers" ,python-sortedcontainers))) (native-inputs