From patchwork Thu Feb 15 20:46:17 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 2253 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 BC8FD27BBEA; Thu, 15 Feb 2024 20:49:05 +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 E65A427BBE2 for ; Thu, 15 Feb 2024 20:49:04 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1raie7-00011M-IL; Thu, 15 Feb 2024 15:47:51 -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 1raie1-0000zX-RC 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 1raie0-0003XI-E3; Thu, 15 Feb 2024 15:47:44 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1raieI-0005Dk-Bb; Thu, 15 Feb 2024 15:48:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH v2 0/8] Upgrade cwltool References: In-Reply-To: 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 20:48:02 +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=B66690.170803003619886 (code B ref 66690); Thu, 15 Feb 2024 20:48:02 +0000 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:16 +0000 Received: from localhost ([127.0.0.1]:57541 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidY-0005Ae-6h for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:16 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:46686) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidU-0005AN-HE for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:14 -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: 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:In-Reply-To:References:List-Id:List-Help:List-Unsubscribe: List-Subscribe:List-Post:List-Owner:List-Archive; bh=LA19Sn+B07M9/c4rucJOXaRUvTFZDpz0JFGe+SY2ExU=; b=nM2BZJg46Cnm8kWYt9ldld+fho Qio8NeaSfDwfaaUs6e6JmREUOdUx7V4aJCdLE2mUuT2/XWFxDJ+HBpjkEYbatETLAQXNm+FVykG0Q eNbJCe0lkWek+Xjx7tltLTLo21vISo/Z8QCHTesWBVML24LvN1ZVr1dZx9U0XHf9kC7Tw++NVDz7M MBcg8sXZMPshM9Q95lkNhZIJWGC51GnvF8EUxfcALxs4YJeZLkqtnPLVjcl5L7q9mipOaNG+1y7sH 7QFwbxvUCc/tzrmeTR+dZND5fHd2WKUelB0JLLik+2qFGLp6kJK2a7wMANwhLUNEnLZYzrXzYsT4e TGne80UA==; 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 1raibx-0004iN-2F; Thu, 15 Feb 2024 20:45:38 +0000 From: Arun Isaac Date: Thu, 15 Feb 2024 20:46:17 +0000 Message-ID: X-Mailer: git-send-email 2.41.0 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 In this patchset, I have updated cwltool once more to the latest version. And, I have split out ruamel-yaml into two separate package variants so that conda no longer breaks. I will push this patchset if it builds successfully on QA without breaking other packages. Arun Isaac (8): gnu: python-ruamel.yaml.clib: Update to 0.2.8. gnu: python-ruamel-yaml: Update to 0.18.6. gnu: python-schema-salad: Update to 8.5.20240102191335. gnu: Add python-cwlformat. gnu: Add python-cwl-upgrader. gnu: Add python-cwl-utils. gnu: Add python-spython. gnu: cwltool: Update to 3.1.20240112164112. gnu/packages/bioinformatics.scm | 244 ++++++++++++++++++++-------- gnu/packages/linux.scm | 46 ++++++ gnu/packages/package-management.scm | 3 +- gnu/packages/serialization.scm | 21 ++- 4 files changed, 240 insertions(+), 74 deletions(-) base-commit: 5ad54df6b09b08b73453cf1071413693f053a0cc