From patchwork Thu Feb 15 20:46:22 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 60412 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 091AB27BBEA; Thu, 15 Feb 2024 20:48:00 +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=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL, 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 3E55927BBE2 for ; Thu, 15 Feb 2024 20:47:58 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1raie6-00011E-MA; Thu, 15 Feb 2024 15:47:50 -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 1raie2-0000zc-4O for guix-patches@gnu.org; Thu, 15 Feb 2024 15:47:46 -0500 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 1raie1-0003XZ-RU; Thu, 15 Feb 2024 15:47:45 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1raieK-0005Ed-If; Thu, 15 Feb 2024 15:48:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH v2 5/8] gnu: Add python-cwl-upgrader. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, ludo@gnu.org, guix-patches@gnu.org Resent-Date: Thu, 15 Feb 2024 20:48:04 +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 moreinfo To: 66690@debbugs.gnu.org Cc: Arun Isaac , Arun Isaac , Ludovic =?utf-8?q?Court=C3=A8s?= X-Debbugs-Original-Xcc: Arun Isaac , Ludovic =?utf-8?q?Court=C3=A8s?= Received: via spool by 66690-submit@debbugs.gnu.org id=B66690.170803004819956 (code B ref 66690); Thu, 15 Feb 2024 20:48:04 +0000 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:28 +0000 Received: from localhost ([127.0.0.1]:57555 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidk-0005Bi-Gv for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:28 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:59012) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidi-0005BY-Ki for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:27 -0500 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=31gzW5gR9nw8eO6er7l6iNDPivsKisYTp4fcJxEi0kM=; b=NEfvsp/Y2QpuG6zhoQveCPfMbg fd0NkWk1uOfi1iMLw0SvDJobZ6oYQh+4PXLelGolXfLIhB1Z//lUuKhqF7YYgo0eRBQYO3NvSJJT0 kGBSW1bonbav3p8YXb0jGJjsM13BfsDdPVQo6yA85nnI0yAX82w92TtDeePjl1XKRIrtFqjZ2HH6+ jTRCHMxu/OSygqfBNmdr4IeDSe45AVLmsWIs0DNIBxMsyj85a9zw+AcvGHdX8AjIl8uA4jR5ev33i Bcp7IPZJfu/THVMCpT/OAXmJdAI25prIVGIhiOVX9uMjt4fLLimmHjSkYqXWZKyH4g0lP2aU71jha 1rglJyuA==; Received: from [192.168.2.1] (port=57126 helo=localhost.localdomain) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.96.1) (envelope-from ) id 1raicD-0004iN-1x; Thu, 15 Feb 2024 20:45:54 +0000 From: Arun Isaac Date: Thu, 15 Feb 2024 20:46:22 +0000 Message-ID: <3c43ae3420f21566d2ee4cf6fac548db27afc8f8.1708029746.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-cwl-upgrader): New variable. Change-Id: I2022239840e9fe9e745689ef8b8bf4279be2ff9e --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 48e56945b3..438b22800c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5165,6 +5165,30 @@ (define-public python-cwlformat code formatter. It outputs CWL in a standardized YAML format.") (license license:asl2.0))) +(define-public python-cwl-upgrader + (package + (name "python-cwl-upgrader") + (version "1.2.11") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cwl-upgrader" version)) + (sha256 + (base32 + "12j6z8nvwnzjjyypz59hwj5hmrcri2r6aknw52n9dbj6lbzbdd2p")))) + (build-system pyproject-build-system) + (native-inputs + (list python-pytest)) + (propagated-inputs + (list python-ruamel.yaml + python-schema-salad)) + (home-page "https://github.com/common-workflow-language/cwl-upgrader") + (synopsis "CWL document upgrader") + (description "@code{python-cwl-upgrader} is a standalone upgrader for +@acronym{CWL, Common Workflow Language} documents from version draft-3, v1.0, +and v1.1 to v1.2.") + (license license:asl2.0))) + (define-public cwltool (package (name "cwltool")