From patchwork Mon Oct 23 08:09:43 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 55155 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 E26FB27BBE2; Mon, 23 Oct 2023 09:11:33 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,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 5D8AF27BBEC for ; Mon, 23 Oct 2023 09:11:31 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1quq1X-0004Hm-LS; Mon, 23 Oct 2023 04:10:55 -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 1quq1F-00048r-Vf for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:40 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1quq1C-000746-QM for guix-patches@gnu.org; Mon, 23 Oct 2023 04:10:37 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1quq1f-0001w2-Km; Mon, 23 Oct 2023 04:11:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH 4/7] gnu: Add python-cwlformat. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 23 Oct 2023 08:11:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 66690 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 66690@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac X-Debbugs-Original-Xcc: Arun Isaac Received: via spool by 66690-submit@debbugs.gnu.org id=B66690.16980486537369 (code B ref 66690); Mon, 23 Oct 2023 08:11:03 +0000 Received: (at 66690) by debbugs.gnu.org; 23 Oct 2023 08:10:53 +0000 Received: from localhost ([127.0.0.1]:48971 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1V-0001ug-1o for submit@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:53 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:35666) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1N-0001tu-Nb for 66690@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:46 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:MIME-Version: References:In-Reply-To:Message-ID:Date:Subject:Cc:To:From:Sender:Reply-To: Content-Type:Content-ID:Content-Description:Resent-Date:Resent-From: Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=CZzpWcZKjh43tWKwZtv1OOOtx2WZPYmu85yovXcO70Y=; b=EDxogXQAGh+/3yMcqSufx0EmLd fmYpJ1KqY0ZjPYXyJFcqgb8LmyyaPKxtK7jFexNFROHjat9yoYl3ibwS4ttYgajjyvo6eHDr413s1 Pr6REvF/5A03Pwl8ipqu4Lixff3E2oo7wYjRtX6df2FBBr362BP5DjhtG55Vcdt53U/jUgHLrjG92 MTmuVZd03X7wDaW5JAitIdrPynVVpyzIGORAWzmKk2eF+0sQJKhU1JTxnHE4+snVawFsduonzs/lB QeIxCsElMgeKS+2542WgCb/mGpDEL2S3U+HZwNaw+h1AEr7Vl6UrynwGT8taOGd9Y/pSxCdoi8R7l 4TRmxftA==; Received: from [192.168.2.1] (port=51852 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96) (envelope-from ) id 1quq0r-001gvg-1k; Mon, 23 Oct 2023 09:10:14 +0100 From: Arun Isaac Date: Mon, 23 Oct 2023 09:09:43 +0100 Message-ID: <2aa865bdab3d42feca9c17861ea2b4046d02eb2c.1698013055.git.arunisaac@systemreboot.net> X-Mailer: git-send-email 2.41.0 In-Reply-To: References: 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-cwlformat): New variable. --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c6819316ae..3b2fc8de8a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4484,6 +4484,33 @@ (define-public python-scrublet doublets in single-cell RNA-seq data.") (license license:expat))) +(define-public python-cwlformat + (package + (name "python-cwlformat") + (version "2022.02.18") + (source + ;; The PyPI tarball is missing Readme.md. Readme.md is required for the + ;; build. + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rabix/cwl-format") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0agkz2w86k91rc9m5vx5hsqi5nm6fcmzkng6j99hjapz0r9233ql")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-importlib-resources + python-ruamel.yaml)) + (home-page "https://github.com/rabix/cwl-format") + (synopsis "Prettifier for CWL code") + (description "@code{python-cwlformat} is a specification and a reference +implementation for a very opinionated @acronym{CWL, Common Workflow Language} +code formatter. It outputs CWL in a standardized YAML format.") + (license license:asl2.0))) + (define-public cwltool (package (name "cwltool")