From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2.migadu.com ([2001:41d0:303:e16b::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms8.migadu.com with LMTPS id kM3uDax4zmXAUQEAe85BDQ:P1 (envelope-from ) for ; Thu, 15 Feb 2024 21:48:44 +0100 Received: from aspmx1.migadu.com ([2001:41d0:303:e16b::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2.migadu.com with LMTPS id kM3uDax4zmXAUQEAe85BDQ (envelope-from ) for ; Thu, 15 Feb 2024 21:48:44 +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="FnxZrgt/"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=systemreboot.net (policy=none); 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" ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1708030124; 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=hXWPdNNwvH8E1a+ihn/j16c8pniTY/6Gw84kNHa9b+c=; b=aU2gXh43HiVeF0Zyf3KjTIPfRfzGglg1UwXW8L3sw41DW5QWOlx5n2gBtRKHVeHY2vr8VC ap091zX5C+au7zbetICxMfeb9ixh+fva8iRo9kBLqX1POnx6hgAul78vS+W25SlxMADhrV CKrhWbGjbC1702wFFysbC+nVbGLaIkWutzhgGJu0yqnY9U9dKW39nxDaQl3J1U0GJB6Piu C5KGPCFLd4E3Q2skjeiS+Y9SXGIeGQAoXN822wvynvk03jcg7rOUgc0Us1geo3BL7ukIRM +PtLgQgFqEpCxq9uggBFTAuVzUBve4iHfjFJCvtwnC70KUv/P/7J9aXbLl/0Hw== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=systemreboot.net header.s=default header.b="FnxZrgt/"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=systemreboot.net (policy=none); 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" ARC-Seal: i=1; s=key1; d=yhetil.org; t=1708030124; a=rsa-sha256; cv=none; b=iC51rcKZY594qxIKUV3qYZ5zCD6cWm+WQfz2O1642qEhyJ8RSnlPw9/kJPO+iXXeSBmfW8 JGSRayKQ7+0YjgmtE3AQ32W/ZXQEp6+7j07PBzx9Gdn8jq6KwY4w4osYIgySW3Su81FjtF QvcbaAO4sehYaTr88SZn6umDg9hph6UCklaYrl/wUcMmEwZ/ASnpFxf2iZmmI/UHEo3HOV 1khLDiS6dg8HUu4XcyYjw67ICt8QDxsy/pe4FtAQJh/iLC3flIcMIQSyyxWWRE5O0x+A4+ mjNcI0J3fv7e//nL7am97DCuzZJOWzCrUMlJk9hYBpmeXRUyhbH3PBZM8eFkQA== 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 1E2CE45D5C for ; Thu, 15 Feb 2024 21:48:44 +0100 (CET) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1raie9-00012g-Lo; Thu, 15 Feb 2024 15:47:53 -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 1raie2-0000zv-Hj 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 1raie2-0003Xt-96; Thu, 15 Feb 2024 15:47:46 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1raieL-0005Eo-1b; Thu, 15 Feb 2024 15:48:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH v2 6/8] gnu: Add python-cwl-utils. 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 20:48:05 +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=B66690.170803005519985 (code B ref 66690); Thu, 15 Feb 2024 20:48:05 +0000 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:35 +0000 Received: from localhost ([127.0.0.1]:57559 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidp-0005C9-So for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:35 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:58850) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidm-0005Bu-0N for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:30 -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=hXWPdNNwvH8E1a+ihn/j16c8pniTY/6Gw84kNHa9b+c=; b=FnxZrgt/wl/UAA7l1wwQPGivdI x9i98j5M2LDVpjZkiBazPjS1ky+5qpgyMYfw9AWgW0szikPRrHO4S1JztMphX/pLWtggszYNhioA1 /DpsAN4jFA1wVLVpLq7A3cbywkyL8iEm/JilpBeEYmjZFPXNwReCC+EkTFFnk46b4HPbfdBlAlcN1 H5L93BPj2WEugD/XNV1H/QH+g6tyK8BnHErzyTMYM35/Z+kMRmmPa3y+7SL9pmABEi5GpMsQ6OQJ3 yu6ZPx0eWQV8QAxqfvx1eMUqAQVQRNtX5t2vwIGhwlfz2wfmBKZOzVesMOE+ZtI/9eRJwyEthGDMq gRxF4nIQ==; 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 1raicG-0004iN-37; Thu, 15 Feb 2024 20:45:57 +0000 From: Arun Isaac Date: Thu, 15 Feb 2024 20:46:23 +0000 Message-ID: X-Mailer: git-send-email 2.41.0 In-Reply-To: References: 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-Flow: FLOW_IN X-Migadu-Country: US X-Migadu-Spam-Score: 4.02 X-Spam-Score: 4.02 X-Migadu-Queue-Id: 1E2CE45D5C X-Migadu-Scanner: mx13.migadu.com X-TUID: 1VKFor1ZNQdF * gnu/packages/bioinformatics.scm (python-cwl-utils): New variable. Change-Id: I9347c80c0e866b89a7d432091fbcf1bc009209a5 --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 438b22800c..35c4d7d993 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5189,6 +5189,49 @@ (define-public python-cwl-upgrader and v1.1 to v1.2.") (license license:asl2.0))) +(define-public python-cwl-utils + (package + (name "python-cwl-utils") + (version "0.32") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cwl-utils" version)) + (sha256 + (base32 + "06wkw8d8cqm3hnz8xwnysz874gwaym36c358cr7frw5iglhvsj98")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + #~(list "-k" + (string-append "not test_graph_split" + " and not test_load_document_with_remote_uri" + " and not test_remote_packing" + " and not test_remote_packing_github_soft_links" + " and not test_value_from_two_concatenated_expressions")))) + (inputs + (list node)) + (native-inputs + (list python-mypy-extensions + python-pytest + python-pytest-mock + python-pytest-runner)) + (propagated-inputs + (list python-cwl-upgrader + python-cwlformat + python-packaging + python-rdflib + python-requests + python-ruamel.yaml + python-schema-salad)) + (home-page "https://github.com/common-workflow-language/cwl-utils") + (synopsis "Python utilities for CWL") + (description "@code{python-cwl-utils} provides python utilities and +autogenerated classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2 +documents.") + (license license:asl2.0))) + (define-public cwltool (package (name "cwltool") -- 2.41.0