From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1.migadu.com ([2001:41d0:403:58f0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms8.migadu.com with LMTPS id eMLIM8F4zmXcNQEA62LTzQ:P1 (envelope-from ) for ; Thu, 15 Feb 2024 21:49:05 +0100 Received: from aspmx1.migadu.com ([2001:41d0:403:58f0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1.migadu.com with LMTPS id eMLIM8F4zmXcNQEA62LTzQ (envelope-from ) for ; Thu, 15 Feb 2024 21:49:05 +0100 X-Envelope-To: larch@yhetil.org Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=systemreboot.net header.s=default header.b=nM2BZJg4; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=systemreboot.net (policy=none) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1708030145; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=LA19Sn+B07M9/c4rucJOXaRUvTFZDpz0JFGe+SY2ExU=; b=AhHIXL9RLoS9Er6BdO6Wot8HHaKsy0PRKAKTnOjI9tcwb8S3HyMUOsc9MNZYT2TdptgMT3 UnIFQLU+m7xBb6C3kTJlWUYG0M0Vn7qkwXplS7JcYFfdl4cW+kEeoNiI808e49vmbbwUOe X6eFui+d+cmrK0nXrdaKHeW7mZKON8lwDYmLI9JXzMqD4fj6sFksIzStHNnSGCH0ueeELO 8XD+kSozVaZ2z4v2eJDQHT9fgonH6lcCPpyVa1M+G+8RuY4x1Im2Y47ZkbHEbjCdcNYYwm iJ+wFhOjaLHbGOD3vpEd9PDJTdDI2jXNUo9vN6BwtQOC4k5zk9YvDgEJkOM5Sg== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=systemreboot.net header.s=default header.b=nM2BZJg4; spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=systemreboot.net (policy=none) ARC-Seal: i=1; s=key1; d=yhetil.org; t=1708030145; a=rsa-sha256; cv=none; b=I40KMxZ9HZg5Dw7YCzcua8JBGFcQZYBNnczYT18xCemvYqSp/TaYv/KjfQpy0PHP6F730r F7YnrGNC3X8CunRdQglQF5bMyCc0pGQ535zrJl0vQwryPWiqQ6XKtjLUDeafP8HQAus5xj gZ9Xg3Ya4GiMjZt43qarp7ONgoDAsHAAMprBSNUz59l6v/jBPmU+MsRiwiiW9aQPpDpV4C nPE8PFJEwLMZhlOFE8WB79O8N/SI4KplnYwPj9q7QWu2V18e3KB1lmfX9Pg8A6TBRRuA/h 2NPE8D4fdO4/ewuTdHxCM4dMSbjQThkN58CWyEIyUknYGGBio6Ql3WS5kf3Vwg== Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id BF381597A5 for ; Thu, 15 Feb 2024 21:49:05 +0100 (CET) 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 Content-Transfer-Encoding: 8bit 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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN X-Migadu-Spam-Score: -3.88 X-Spam-Score: -3.88 X-Migadu-Queue-Id: BF381597A5 X-Migadu-Scanner: mx11.migadu.com X-TUID: Yub4Vcxvmt+J 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 -- 2.41.0