From patchwork Mon Dec 12 14:27:05 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45195 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 E921527BBEB; Mon, 12 Dec 2022 14:28:41 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id D320A27BBE9 for ; Mon, 12 Dec 2022 14:28:40 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jmw-0005hj-2D; Mon, 12 Dec 2022 09:28:14 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p4jmo-0005Vi-7w for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmo-0006DA-0R for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:06 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmn-0007VG-SJ for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 07/18] gnu: python-dna-features-viewer: Update to 3.1.1. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085526828727 (code B ref 60009); Mon, 12 Dec 2022 14:28:05 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:27:48 +0000 Received: from localhost ([127.0.0.1]:53279 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmV-0007TH-Om for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:48 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21061) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmS-0007Sx-Ma for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:45 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855262; cv=none; d=zohomail.com; s=zohoarc; b=Oa0Pl+enUZs+tzuanF1dFDUhpQ4nitenwcLV9quve3EZuF4BYrVRLmq0NP3Wj0+ICQosthcYMtc67y9b6dZBludcUu75CxTW+Jv/yrI3b4HzqGVoiBVFAuzM8F01LmLTjUyTZy4mhoawsnOQbQWq5uKP1rEPTfNBOqckJ6C0kK8= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855262; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=YezpJW0kavrBMGPm7Q5u5/mFQQY5yAp5syxFTBxpCpw=; b=U1ADM3gWCAhSYfOJnK5mdcoMfCr/yEKNLbwh8nCqiJ16nQZHpOB1pteWTMRnu3jDcT8jNh9Cwmrj2cfZgMhnN6yQ6U+Aad1+1+j1h9bvDjm3gHQlVaS7f9LWo81QbVJU65oC8ZTk4R5VJsn3CGr6hGvHXTHQ+IYSIP+arzJUnR0= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855262; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=YezpJW0kavrBMGPm7Q5u5/mFQQY5yAp5syxFTBxpCpw=; b=N6KBl5Bc6qwsirqo+cvOqH30GoL9SbKTTCENzPmoZqO4ESYZNvZh/kxljCe1YiWc LnhDm9mMzjjgC1jyrmQTxD/UrFLIOLoZQ0M8aYARrjAQ3WZmiUyjoPy0TzUNNk23J9W PEzMZBno0rZ/Crt6aEiYNAtLTNN/thhR+A9Q/hns= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855259930256.2913112913244; Mon, 12 Dec 2022 06:27:39 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:05 +0100 Message-Id: <20221212142716.9460-7-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-dna-features-viewer): Update to 3.1.1. [build-system]: Use pyproject-build-system. [arguments]: Add build phase to fix a compatibility problem with biopython. [propagated-inputs]: Add python-packaging. --- gnu/packages/bioinformatics.scm | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ea33311a2c..371bf1077a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16597,18 +16597,31 @@ (define-public python-pybbi (define-public python-dna-features-viewer (package (name "python-dna-features-viewer") - (version "3.0.3") + (version "3.1.1") (source (origin (method url-fetch) (uri (pypi-uri "dna_features_viewer" version)) (sha256 (base32 - "0vci6kg2id6r6rh3cifq7ccnh7j0mb8iqg3hji6rva0ayrdqzafc")))) - (build-system python-build-system) - (arguments '(#:tests? #false)) ; there are none + "10a5pmh73spdgfml88zjqg1rn2j2zdxn06ir8a5q3arspyqvyqcb")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #false ;there are none + #:phases + '(modify-phases %standard-phases + ;; See https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/issues/73 + ;; and https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/pull/74 + (add-after 'unpack 'fix-biopython-compatibility + (lambda _ + (substitute* "dna_features_viewer/biotools.py" + (("zip\\(aa1 \\+ \"\\*\", aa3 \\+ \\[\"\\*\"\\]\\)") + "zip(aa1 + ('*',), aa3 + ('*',))"))))))) (propagated-inputs - (list python-biopython python-matplotlib)) + (list python-biopython + python-matplotlib + python-packaging)) (home-page "https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer") (synopsis "Plot features from DNA sequences")