From patchwork Mon Oct 23 08:09:45 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 55151 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 E7AAF27BBEA; Mon, 23 Oct 2023 09:11:18 +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 2D01627BBE9 for ; Mon, 23 Oct 2023 09:11:18 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1quq1X-0004Hn-M5; 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 1quq1G-00048v-0H 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 1quq1D-000748-Ja 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 1quq1g-0001wJ-EO; Mon, 23 Oct 2023 04:11:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH 6/7] gnu: Add python-cwl-utils. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 23 Oct 2023 08:11:04 +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 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=B66690.16980486627416 (code B ref 66690); Mon, 23 Oct 2023 08:11:04 +0000 Received: (at 66690) by debbugs.gnu.org; 23 Oct 2023 08:11:02 +0000 Received: from localhost ([127.0.0.1]:48976 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1d-0001vP-P1 for submit@debbugs.gnu.org; Mon, 23 Oct 2023 04:11:02 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:35692) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1T-0001uW-MZ for 66690@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:52 -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=S6z1YNrjdMoaMkVg/04HuYL56uFb2So+TXkmKGrgAto=; b=X6uJ2PEpJ+9chwFLpQeaL0hnUS o3fK7OnoVKcWNWI/TB/QlvHhZ2kcgBDNr1etKMXCeM6tTXs7F1WifFCK8OIPJXbkkQpQpH3RABbja pUYCnmexdQFtV68+06jEZoNhFqcE0F3SiQ0BfnT6lXUaSiPISL8Xcawus2RfFdoU/KKFkUHMQqBLa R1aev1NLqWTEpLoMynW6Ho3HmsdWxZhTNs+YWwBiYR1H5+wM+hNQv/j5J2HCJ+ZAsXhUHk186u1JO jhwle6yad9FWksbvNFVYVdNVp3xz13/ZarpzvDYTk5ACEFj2Q3TgJ/9epeAYba0HoJvkcHnnYdBSP ldufn7Nw==; 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 1quq0x-001gvg-2V; Mon, 23 Oct 2023 09:10:20 +0100 From: Arun Isaac Date: Mon, 23 Oct 2023 09:09:45 +0100 Message-ID: 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-utils): New variable. --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 79dbf0f2e6..2deec5368e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4537,6 +4537,49 @@ (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 "0.29") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cwl-utils" version)) + (sha256 + (base32 + "0rfm49wwnn4bcalkfrhvlmn7bhdf6nnwcr8fvx5gqxqyd4b5izf5")))) + (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")