From patchwork Mon Oct 17 20:11:53 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Marius Bakke X-Patchwork-Id: 43478 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 848C027BBEA; Mon, 17 Oct 2022 21:14:41 +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=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 414DC27BBE9 for ; Mon, 17 Oct 2022 21:14:41 +0100 (BST) Received: from localhost ([::1]:55890 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1okWVU-00079L-32 for patchwork@mira.cbaines.net; Mon, 17 Oct 2022 16:14:40 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:48352) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1okWTy-0006w8-7q for guix-patches@gnu.org; Mon, 17 Oct 2022 16:13:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51103) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1okWTx-0002HU-Ue for guix-patches@gnu.org; Mon, 17 Oct 2022 16:13:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1okWTx-0007PJ-QZ for guix-patches@gnu.org; Mon, 17 Oct 2022 16:13:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#58587] [PATCH 06/14] gnu: flair: Switch to pyproject-build-system. Resent-From: Marius Bakke Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 17 Oct 2022 20:13:05 +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=B58587.166603754528245 (code B ref 58587); Mon, 17 Oct 2022 20:13:05 +0000 Received: (at 58587) by debbugs.gnu.org; 17 Oct 2022 20:12:25 +0000 Received: from localhost ([127.0.0.1]:50135 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1okWTI-0007LO-Th for submit@debbugs.gnu.org; Mon, 17 Oct 2022 16:12:25 -0400 Received: from eggs.gnu.org ([209.51.188.92]:49518) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1okWTF-0007KS-9O for 58587@debbugs.gnu.org; Mon, 17 Oct 2022 16:12:22 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:51252) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1okWT8-0002DR-Ja for 58587@debbugs.gnu.org; Mon, 17 Oct 2022 16:12:14 -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=L3sg34qs4y8ba07LgNmB Ng0pDE2+0mBD7TVVsXyqnYYtRkRgeb1AEfCzVWi/s9cCAkSlRGif4HPYq99giJDO8+lq1EQ+TKk0Z bTPXttgZhh2xQGpvZzziHw8eUrWABESSIJTQI9gd9P6BHVUbq4GKtkj1odJwhphtmHCsLG03j7l+M oZpyGJT+sYZUmtS6fEubrySk2U2gtA8rfC7XpAKHfqlnYaRbwe4PE3jBMJslEXW7rebCu0cmYCBEw G1NFf6VlyXSuIXAvG9CwVmMA0Ko64kx30BftbkN9KVrkwIM/tAXW1ZaoZsNGhg2Um9IIfK4oKL/00 muAGSXj/1TwsOw==; Received: from [84.211.203.64] (port=33092 helo=localhost) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1okWT7-00050Q-OU for 58587@debbugs.gnu.org; Mon, 17 Oct 2022 16:12:14 -0400 From: Marius Bakke Date: Mon, 17 Oct 2022 22:11:53 +0200 Message-Id: <20221017201201.4808-6-marius@gnu.org> X-Mailer: git-send-email 2.38.0 In-Reply-To: <20221017201201.4808-1-marius@gnu.org> References: <20221017200624.4076-1-marius@gnu.org> <20221017201201.4808-1-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