From patchwork Sat Oct 22 22:20:45 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Marius Bakke X-Patchwork-Id: 43830 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 D35FB27BBEA; Mon, 24 Oct 2022 01:34:15 +0100 (BST) 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=ham 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 4E70B27BBE9 for ; Mon, 24 Oct 2022 01:34:15 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1omjrb-00019r-Cf for patchwork@mira.cbaines.net; Sun, 23 Oct 2022 18:54:39 -0400 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 1omMsZ-0004gk-3y for guix-patches@gnu.org; Sat, 22 Oct 2022 18:22:07 -0400 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 1omMsX-0005Tx-W1 for guix-patches@gnu.org; Sat, 22 Oct 2022 18:22:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1omMsX-0001zM-Ra for guix-patches@gnu.org; Sat, 22 Oct 2022 18:22:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#58587] [PATCH v3 07/22] gnu: flair: Switch to pyproject-build-system. Resent-From: Marius Bakke Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 22 Oct 2022 22:22:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 58587 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 58587@debbugs.gnu.org Received: via spool by 58587-submit@debbugs.gnu.org id=B58587.16664773237598 (code B ref 58587); Sat, 22 Oct 2022 22:22:05 +0000 Received: (at 58587) by debbugs.gnu.org; 22 Oct 2022 22:22:03 +0000 Received: from localhost ([127.0.0.1]:42558 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1omMsV-0001yN-CX for submit@debbugs.gnu.org; Sat, 22 Oct 2022 18:22:03 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34038) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1omMsF-0001wR-Lt for 58587@debbugs.gnu.org; Sat, 22 Oct 2022 18:21:48 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1omMsA-00056Z-Gf for 58587@debbugs.gnu.org; Sat, 22 Oct 2022 18:21:42 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:References:In-Reply-To:Date:Subject:To: From; bh=GJEyjFVjDOSDLaNg7FYY8NKuh0hVe3tcRl8rQQG5NtQ=; b=KNTlgVbHs8SBdQSi6pKf 7Yl3Fk9jNCkmlKsYYDFbUJ1cq45qnQu/mSan3bixiwc7peBj2QYJyGRtrswG7oM+VTPd/B/yy678s vyUCzQKXyK4u9VWrZfP2vthbv3bFdOonyxaiEULtg+vkjZp5kZ0JLnybb5LNBEEJnoeqmoAMo4k+B 8madAez0jShH+XjRxTyW4EoZfzINRNi9yPkQcyXWfrg2aFcg/Zz5ZpyebizMPNOPoWPFWOHGcMsYd Fis2aauytana7xrsFMNZMQ2OWEYj15fYQqoewGI1l2qSmeADJwR2XTL0BE/OOus0mUzlZ624Zihra FvIRDuxczHXyJw==; Received: from [84.214.173.6] (helo=localhost) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1omMsA-0001RR-2g for 58587@debbugs.gnu.org; Sat, 22 Oct 2022 18:21:42 -0400 From: Marius Bakke Date: Sun, 23 Oct 2022 00:20:45 +0200 Message-Id: <20221022222100.18103-7-marius@gnu.org> X-Mailer: git-send-email 2.38.0 In-Reply-To: <20221022222100.18103-1-marius@gnu.org> References: <87eduzu18u.fsf@gnu.org> <20221022222100.18103-1-marius@gnu.org> MIME-Version: 1.0 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (flair)[build-system]: Switch to PYPROJECT-BUILD-SYSTEM. [arguments]: Remove #:phases. [native-inputs]: Remove. --- gnu/packages/bioinformatics.scm | 23 +++-------------------- 1 file changed, 3 insertions(+), 20 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f2de09aa32..3588f4e3fd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -56,6 +56,7 @@ (define-module (gnu packages bioinformatics) #:use-module (guix build-system meson) #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix build-system qt) #:use-module (guix build-system r) @@ -16928,33 +16929,15 @@ (define-public flair (sha256 (base32 "106swb2q7l20ki58fca1hg95q5f79bgp9gjb0clr2243ycrzyxf8")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - (list - #:tests? #false ;there are none - #:phases - #~(modify-phases %standard-phases - ;; TODO: implement as a feature of python-build-system (PEP-621, - ;; PEP-631, PEP-660) - (replace 'build - (lambda _ - (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) - ;; ZIP does not support timestamps before 1980. - (setenv "SOURCE_DATE_EPOCH" "315532800") - (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) - (replace 'install - (lambda _ - (apply invoke "pip" "--no-cache-dir" "--no-input" - "install" "--no-deps" "--prefix" #$output - (find-files "dist" "\\.whl$"))))))) + (list #:tests? #false)) ;there are none (propagated-inputs (list python-mappy python-ncls python-pybedtools python-pysam python-tqdm)) - (native-inputs - (list python-pypa-build python-setuptools)) (home-page "https://flair.readthedocs.io/en/latest/") (synopsis "Full-length alternative isoform analysis of RNA") (description "This package implements FLAIR (Full-Length Alternative