From patchwork Thu Feb 15 20:46:18 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 60419 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 87DA327BBE9; Thu, 15 Feb 2024 20:49:04 +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=unavailable 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 3EFC827BBE2 for ; Thu, 15 Feb 2024 20:49:02 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1raie7-00011K-DW; 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 1raie1-0000zW-R3 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 1raie1-0003XN-0N; 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 1raieI-0005Du-Qe; Thu, 15 Feb 2024 15:48:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH v2 1/8] gnu: python-ruamel.yaml.clib: Update to 0.2.8. 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=B66690.170803003719892 (code B ref 66690); Thu, 15 Feb 2024 20:48:02 +0000 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:17 +0000 Received: from localhost ([127.0.0.1]:57543 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidY-0005Ah-HD for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:17 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:46698) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidV-0005AQ-Qx for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:15 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:Content-Type: MIME-Version:References:In-Reply-To:Message-ID:Date:Subject:Cc:To:From:Sender :Reply-To: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=LdR1Nf/2VYqHaP23S94GIujEyxytF1iCSW0E0iwKvIQ=; b=cctmu6Y4O248T5NSXCPWOSqA+C exOHc6ErzWlEbQJ9UYItTkU7+5/zXD+E0EKEyIkYGMOOSnLGSFqA77VgtIL83rwMB1rNBG9VCtn0U oj+g7Jy/xzSHIDNaTh51nwxpcX7aUahBC2HHmJYtjCLWT0EFiQWBYz+pzjaZO5w10pDab6H+jwRKU hYBKd46v1F1F9QrcanzvvJRyWACpkGLnPXabS57teSgxN9W6xQAZDtx/EKj5Ar/wl7lesyLHap53/ egbR7hWs6KamqtVYHT/xe6TAk+b5SdfUqcvxC9clh6mEoISroI/vk4XfYEWGznpBhaqxIupfHG8hi xwqyoEBw==; 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 1raic0-0004iN-2e; Thu, 15 Feb 2024 20:45:41 +0000 From: Arun Isaac Date: Thu, 15 Feb 2024 20:46:18 +0000 Message-ID: <2509a83da5017c1ed6c16ac7687b6600d6100ab3.1708029746.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/serialization.scm (python-ruamel.yaml.clib): Update to 0.2.8. Change-Id: I18172bb4cad80b0e1a5db11fbc8fb937f46a1862 --- gnu/packages/serialization.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index ccafb8e802..963028c734 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2023 Vinicius Monego ;;; Copyright © 2023 Maxim Cournoyer ;;; Copyright © 2023 Zheng Junjie <873216071@qq.com> +;;; Copyright © 2024 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -749,7 +750,7 @@ (define-public python-ruamel.yaml (define-public python-ruamel.yaml.clib (package (name "python-ruamel.yaml.clib") - (version "0.2.6") + (version "0.2.8") (source (origin ;; pypi release code has cythonized code without corresponding source. @@ -760,7 +761,7 @@ (define-public python-ruamel.yaml.clib (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "05m3y7pjfbaarqbbgw1k6gs6cnnmxnwadjipxvw1aaaqk3s236cs")) + "0qspqnk72xrjj17b00hjibbzjk3krsrakzf08wxwz7z908cv6278")) (modules '((guix build utils))) (snippet '(begin From patchwork Thu Feb 15 20:46:19 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 60416 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 AAE8927BBEA; Thu, 15 Feb 2024 20:48:32 +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 1625127BBE2 for ; Thu, 15 Feb 2024 20:48:32 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1raie9-00012G-ED; 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 1raie1-0000za-Ry 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 1raie0-0003XJ-IC; 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 1raieJ-0005E5-BG; Thu, 15 Feb 2024 15:48:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH v2 2/8] gnu: python-ruamel-yaml: Update to 0.18.6. 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 20:48:03 +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=B66690.170803004019910 (code B ref 66690); Thu, 15 Feb 2024 20:48:03 +0000 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:20 +0000 Received: from localhost ([127.0.0.1]:57546 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidc-0005B4-2X for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:20 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:46710) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raida-0005At-8J for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:19 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:Content-Type: MIME-Version:References:In-Reply-To:Message-ID:Date:Subject:Cc:To:From:Sender :Reply-To: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=wm5Y63hBMOYBP5mp5ifDJzpvvC3Y73vgs1ljd8Wvg9A=; b=knQVQ23NOG2aaI8EdzSMYPdqFi PcJph7EGEXWq2vxrGYcQ4+NUce6UdQK5COQeAgDFPWG4qPCgoJzCMtnSAHvg1/k3mCjQU5s19H8XB OfvmOXONd8U6dOZxSKsiZqCGirLi+yWP3b+M1oLCqe9WR/KAO8LEJfblS3Hs0c2NdAhp4OXygt6N6 IPHHX5PXbhqZMIyVpCxQM+SRE04u80v6FDYVqTbQcfFvOX+XqwK9Elb7kOIfLYJbwHbk327bmjf9h ByYlQougQHT0So04Nj2jtelBahZA4H84UUugerUtfE/26E0WfZ3skxs0A8FuNVKVsI+kNIwSpYRza PNmjs+HQ==; 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 1raic4-0004iN-0E; Thu, 15 Feb 2024 20:45:44 +0000 From: Arun Isaac Date: Thu, 15 Feb 2024 20:46:19 +0000 Message-ID: <14917e292b584625ac25971a4b02cfef83101b9e.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/package/serialization.scm (python-ruamel-yaml): Update to 0.18.6. (python-ruamel.yaml-0.16): New variable. * gnu/packages/package-management.scm (conda)[inputs]: Replace python-ruamel.yaml with python-ruamel.yaml-0.16. Change-Id: Iff9eeeae043c9547d93a6c780f0c30bd760490d9 --- gnu/packages/package-management.scm | 3 ++- gnu/packages/serialization.scm | 16 ++++++++++++++-- 2 files changed, 16 insertions(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index c1ad613bee..5d6bc47b8b 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2022, 2023 Zhu Zihao ;;; Copyright © 2023 jgart ;;; Copyright © 2023 Mădălin Ionel Patrașcu +;;; Copyright © 2024 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -1251,7 +1252,7 @@ (define-public conda python-pyyaml python-requests python-responses - python-ruamel.yaml + python-ruamel.yaml-0.16 python-tqdm ;; XXX: This is dragged in by libarchive and is needed at runtime. zstd)) diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 963028c734..240646748b 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -721,14 +721,14 @@ (define-public python-msgspec (define-public python-ruamel.yaml (package (name "python-ruamel.yaml") - (version "0.16.13") + (version "0.18.6") (source (origin (method url-fetch) (uri (pypi-uri "ruamel.yaml" version)) (sha256 (base32 - "0hm9yg785f46bkrgqknd6fdvmkby9dpzjnm0b63qf0i748acaj5v")))) + "06rimidc9nb3i3r90n3a1zwf0qxw24zqykb3wpxwd1p72yifc9wb")))) (build-system python-build-system) (native-inputs (list python-pytest)) @@ -747,6 +747,18 @@ (define-public python-ruamel.yaml style and key ordering are kept, so you can diff the source.") (license license:expat))) +(define-public python-ruamel.yaml-0.16 + (package + (inherit python-ruamel.yaml) + (version "0.16.13") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ruamel.yaml" version)) + (sha256 + (base32 + "0hm9yg785f46bkrgqknd6fdvmkby9dpzjnm0b63qf0i748acaj5v")))))) + (define-public python-ruamel.yaml.clib (package (name "python-ruamel.yaml.clib") From patchwork Thu Feb 15 20:46:20 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 60417 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 EF25B27BBEA; Thu, 15 Feb 2024 20:48:42 +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 165C527BBE2 for ; Thu, 15 Feb 2024 20:48:42 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1raie9-00012j-UV; 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 1raie2-0000zb-3c 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 1raie1-0003XL-RB; 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 1raieJ-0005EF-OC; Thu, 15 Feb 2024 15:48:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH v2 3/8] gnu: python-schema-salad: Update to 8.5.20240102191335. 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 20:48:03 +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=B66690.170803004519932 (code B ref 66690); Thu, 15 Feb 2024 20:48:03 +0000 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:25 +0000 Received: from localhost ([127.0.0.1]:57550 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidg-0005BQ-JT for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:24 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:59006) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidc-0005Aw-7o for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:21 -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=xkA/mN4KuPra2RQGb4ydlRKIhh8Qq9aHppA3EsigD2o=; b=WtCyWkPiUTREkR+s7rWhz6iEL3 iaZyvnyqz/eUPLxGKhJxQMXVn8nW5jLrpA38CaR2h+/t4BU01uD+W9RCjMz9HiWgOfSPtOiFN7hWF f3M7Ar+IUpWC89KbVPRszlo1CVTTq5XS6KEU+X+eF0XUi7N1/epGukz2w2k7P0MdahMsAEX6Dvg6/ TCA89E9FTDZO+TiGnk45Y5JtDunwjhpRMpL0vkG001WK9Xyq8I1UsR6woq5hbYcllxnxGA2TZx/V8 E37iayGCNLpUl2UELFQzJSCh/mRiO3pO1UTt5DxoBOn4vymlTReHKf51Zd8GE0VikZp8dnMZm0gAC vtjFAfJQ==; 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 1raic7-0004iN-0o; Thu, 15 Feb 2024 20:45:47 +0000 From: Arun Isaac Date: Thu, 15 Feb 2024 20:46:20 +0000 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-schema-salad): Update to 8.5.20240102191335. [native-inputs]: Add python-pytest-xdist. [propagated-inputs]: Add python-importlib-resources and python-mypy-extensions. Remove python-lockfile, python-rdflib-jsonld and python-typing-extensions. Replace python-mistune with python-mistune-next. [arguments]: Use G-expressions. Set exact version number. Skip more tests that require network access. Change-Id: I4de4704f58f40fdf9bf4c02e41c2c353beaa3eb2 --- gnu/packages/bioinformatics.scm | 61 ++++++++++++++++++++------------- 1 file changed, 38 insertions(+), 23 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 84577ef760..75cfad51a6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5001,37 +5001,52 @@ (define-public python-pyfasta (define-public python-schema-salad (package (name "python-schema-salad") - (version "8.2.20211116214159") + (version "8.5.20240102191335") (source - (origin - (method url-fetch) - (uri (pypi-uri "schema-salad" version)) - (sha256 - (base32 - "005dh2y45x92zl8sf2sqjmfvcqr4hrz8dfckgkckv87003v7lwqc")))) + (origin + (method url-fetch) + (uri (pypi-uri "schema-salad" version)) + (sha256 + (base32 + "035202p696i3jylb8b3nm9qcxsqby15hhqn1dl4nrz73a17p0ckx")))) (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'skip-failing-tests - (lambda _ - ;; Skip tests that require network access. - (substitute* "schema_salad/tests/test_cwl11.py" - (("^def test_(secondaryFiles|outputBinding)" all) - (string-append "@pytest.mark.skip(reason=" - "\"test requires network access\")\n" - all)))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-version + (lambda _ + ;; Set exact version. + (substitute* "setup.py" + (("use_scm_version=True") + (string-append "version=\"" #$version "\""))))) + (add-before 'check 'skip-failing-tests + (lambda _ + ;; Skip tests that require network access. + (let ((skip-test + (lambda (test-pattern) + (string-append "@pytest.mark.skip(reason=" + "\"test requires network access\")\n" + test-pattern)))) + (substitute* "schema_salad/tests/test_cg.py" + (("^def test_(load(_by_yaml_metaschema|_metaschema|_cwlschema|)|include|idmap|idmap2)\\(" all) + (skip-test all))) + (substitute* "schema_salad/tests/test_cwl11.py" + (("^def test_(secondaryFiles|outputBinding|yaml_tab_error)\\(" all) + (skip-test all))) + (substitute* "schema_salad/tests/test_examples.py" + (("^def test_bad_schemas\\(" all) + (skip-test all))))))))) (propagated-inputs (list python-cachecontrol - python-lockfile - python-mistune + python-importlib-resources + python-mistune-next + python-mypy-extensions python-rdflib - python-rdflib-jsonld python-requests - python-ruamel.yaml - python-typing-extensions)) + python-ruamel.yaml)) (native-inputs - (list python-black python-pytest python-pytest-runner)) + (list python-black python-pytest python-pytest-runner python-pytest-xdist)) (home-page "https://github.com/common-workflow-language/schema_salad") (synopsis "Schema Annotations for Linked Avro Data (SALAD)") (description From patchwork Thu Feb 15 20:46:21 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 60413 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 A74F027BBE2; Thu, 15 Feb 2024 20:48:19 +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=unavailable 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 DDD5B27BBE9 for ; Thu, 15 Feb 2024 20:48:18 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1raie5-000116-AY; Thu, 15 Feb 2024 15:47:49 -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 1raie1-0000zY-Rf for guix-patches@gnu.org; Thu, 15 Feb 2024 15:47:45 -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 1raie1-0003XV-Cw; 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-0005ES-6Q; Thu, 15 Feb 2024 15:48:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH v2 4/8] gnu: Add python-cwlformat. 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=B66690.170803004819950 (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]:57553 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidk-0005Bg-0s for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:28 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:59008) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidf-0005BI-Cs for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:24 -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=FowdT+9noddNBLC6r97xM//2JZu6Yc37qE5PSj+dRjw=; b=U6MKTx3byOdgGRfBEBT6e6vh0C 8+YWIiFQV1HmqU189fBgLX/bxAsYppWPjCiWnUdu9Jz8ExKHOlwfhOfx+w1mWeYOLcbRu8ajzaa0r xOvg4iSPQVTHqzJpZ8cjazmzlPJAsBWOYr3SxVAI12TOmRHUIynrJWfSzw4YqG519R9L3maxwH59C i0ypiadqPZIbWrrgSrnFSvrpljxgxUoZ3Sy2x4ipW6GI43u78HdWMdl3Gz9t0AgfLfGx2etOJNW4g CVAZbvpYGTHQbpDhyPYbxeTf6jGtmxFFk7D3nbrj2pqP0AF47KtMfh4XhW2PszgSMARcM2i81Kxza aQIrtcJw==; 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 1raicA-0004iN-1I; Thu, 15 Feb 2024 20:45:51 +0000 From: Arun Isaac Date: Thu, 15 Feb 2024 20:46:21 +0000 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-cwlformat): New variable. Change-Id: Ib2d79e350ab100c61c7afe2d5d3eafc72146e493 --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 75cfad51a6..48e56945b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5138,6 +5138,33 @@ (define-public python-scrublet doublets in single-cell RNA-seq data.") (license license:expat))) +(define-public python-cwlformat + (package + (name "python-cwlformat") + (version "2022.02.18") + (source + ;; The PyPI tarball is missing Readme.md. Readme.md is required for the + ;; build. + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rabix/cwl-format") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0agkz2w86k91rc9m5vx5hsqi5nm6fcmzkng6j99hjapz0r9233ql")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-importlib-resources + python-ruamel.yaml)) + (home-page "https://github.com/rabix/cwl-format") + (synopsis "Prettifier for CWL code") + (description "@code{python-cwlformat} is a specification and a reference +implementation for a very opinionated @acronym{CWL, Common Workflow Language} +code formatter. It outputs CWL in a standardized YAML format.") + (license license:asl2.0))) + (define-public cwltool (package (name "cwltool") 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") From patchwork Thu Feb 15 20:46:23 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 60418 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 D6A4027BBE9; Thu, 15 Feb 2024 20:48:44 +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 E951E27BBE2 for ; Thu, 15 Feb 2024 20:48:43 +0000 (GMT) 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 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. 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") From patchwork Thu Feb 15 20:46:24 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 60415 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 8C01527BBEA; Thu, 15 Feb 2024 20:48:24 +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 EF3A527BBE2 for ; Thu, 15 Feb 2024 20:48:23 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1raie8-00011h-6m; Thu, 15 Feb 2024 15:47:52 -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 1raie4-00010g-7h for guix-patches@gnu.org; Thu, 15 Feb 2024 15:47:48 -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 1raie3-0003YL-Tf; Thu, 15 Feb 2024 15:47:47 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1raieL-0005Ez-HM; Thu, 15 Feb 2024 15:48:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH v2 7/8] gnu: Add python-spython. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, ludo@gnu.org, leo@famulari.name, me@tobias.gr, w@wmeyer.eu, 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?= , Leo Famulari , Tobias Geerinckx-Rice , Wilko Meyer X-Debbugs-Original-Xcc: Arun Isaac , Ludovic =?utf-8?q?Court=C3=A8s?= , Leo Famulari , Tobias Geerinckx-Rice , Wilko Meyer Received: via spool by 66690-submit@debbugs.gnu.org id=B66690.170803005719993 (code B ref 66690); Thu, 15 Feb 2024 20:48:05 +0000 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:37 +0000 Received: from localhost ([127.0.0.1]:57561 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raids-0005CP-HM for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:36 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:58864) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidp-0005C5-A9 for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:35 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Transfer-Encoding:Content-Type: MIME-Version:References:In-Reply-To:Message-ID:Date:Subject:Cc:To:From:Sender :Reply-To: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=UtEXolSSeKb+apqsP36lJdU88okgONPKGNlitHR9PdA=; b=aEEh4LyfHOfiBOS62yB+RTDbda NUmhzwLRlBKGd4W54FzXIExO9A4Sy2jRf4Kb27ZIT2OHcThqx0NGAfwrrnpYD1OpSVKqOADM//8A9 3/JnEir3/mAtarzlbEtZHG+j7BUX587zqBk3WTgi+urEZXCwdeJ/iYm8mXpkCBSvqyD0iLOQ2JDpa 65aLjn2ymi9WjmHfzryr5fhxSzpNlubx9cjOOMw6R9616oYKsrLAslJU6bwcLmW0APE5AHsNfYGO4 BLqkZPaH//VjHjajFQaiwi4Acy5qJUFOHtKlXdJHfYtxgHkEghuhB0beIo7G6fUPmVDkDtyYM5+Xo oSVjKKkg==; 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 1raicK-0004iN-0l; Thu, 15 Feb 2024 20:46:00 +0000 From: Arun Isaac Date: Thu, 15 Feb 2024 20:46:24 +0000 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/linux.scm (python-spython): New variable. Change-Id: I758f879608bc4b0c0411918b4ee0fa9cc3abc639 --- gnu/packages/linux.scm | 46 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index d798c44a8f..99bc517a96 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -80,6 +80,7 @@ ;;; Copyright © 2023 Jaeme Sifat ;;; Copyright © 2024 Gabriel Wicki ;;; Copyright © 2024 Sharlatan Hellseher +;;; Copyright © 2024 Arun Isaac ;;; ;;; This file is part of GNU Guix. ;;; @@ -5265,6 +5266,51 @@ (define-public singularity isolation or root privileges.") (license license:bsd-3))) +(define-public python-spython + (package + (name "python-spython") + (version "0.3.13") + (source + (origin + (method url-fetch) + (uri (pypi-uri "spython" version)) + (sha256 + (base32 "0kly851k6mj7xzcybciav5d0pq5q04pzg7c5a1g712bqbxkha4ck")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; Configure absolute path to singularity. + (add-after 'unpack 'configure + (lambda* (#:key inputs #:allow-other-keys) + (let ((singularity (search-input-file inputs "bin/singularity"))) + (substitute* "spython/utils/terminal.py" + (("software=\"singularity\"") + (string-append "software=\"" singularity "\""))) + (substitute* (list "spython/utils/terminal.py" + "spython/main/help.py" + "spython/main/base/command.py") + (("\\[\"singularity\"") + (string-append "[\"" singularity "\""))) + (substitute* "spython/main/execute.py" + (("shutil.which\\(\"singularity\"\\)") + (string-append "shutil.which(\"" singularity "\")")))))) + ;; Skip tests that require network access. + (add-before 'check 'skip-tests + (lambda _ + (delete-file "spython/tests/test_client.py")))))) + (inputs + (list singularity)) + (native-inputs + (list python-pytest + python-pytest-runner)) + (home-page "https://github.com/singularityhub/singularity-cli") + (synopsis "Singularity Python client") + (description "@code{python-spython} is a Python library to interact with +Singularity containers.") + (license license:mpl2.0))) + (define-public libnvme (package (name "libnvme") From patchwork Thu Feb 15 20:46:25 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 60414 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 4E02F27BBE2; Thu, 15 Feb 2024 20:48:21 +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 4417E27BBEA for ; Thu, 15 Feb 2024 20:48:19 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1raieD-00013t-8Y; Thu, 15 Feb 2024 15:47:57 -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 1raie3-00010c-MD for guix-patches@gnu.org; Thu, 15 Feb 2024 15:47:47 -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 1raie3-0003YD-Dz; Thu, 15 Feb 2024 15:47:47 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1raieL-0005F8-Vy; Thu, 15 Feb 2024 15:48:06 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH v2 8/8] gnu: cwltool: Update to 3.1.20240112164112. 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=B66690.170803006120009 (code B ref 66690); Thu, 15 Feb 2024 20:48:05 +0000 Received: (at 66690) by debbugs.gnu.org; 15 Feb 2024 20:47:41 +0000 Received: from localhost ([127.0.0.1]:57564 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raidx-0005Cf-1K for submit@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:41 -0500 Received: from mugam.systemreboot.net ([139.59.75.54]:58880) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1raids-0005CJ-IK for 66690@debbugs.gnu.org; Thu, 15 Feb 2024 15:47:37 -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=H8i66m/Dil4x3WX0TV5jjXAldcXpmVdJjOpjP/DtZCA=; b=olSi0udX71KK8EygUEbZzPqGbx SePrwa++b17LTWp2sn7OAU0XmWam3w9pgu0oAjJJsD+oUuVsCKAHyTe/H1bk7ZrOCIHiSz/PBa+vV fvdoxiiTBQiKfXg+UoqOZkmR4NHwd5iKICfUDmlLptDVBky8V/4acZRGODX22adQeXCvgbogwUBpp +gR1jX4ijU1Rn3++nEwxmki1wt1nHPDwm8JL04wWF8IUEZxmoyh9DoZqGaBgoEg3987qMgz25Q3+V 0FYrmmZZnKbz2QUKQZu7DZY465ltm7CRbMa8hTID0hsZ4NPBJUW/9FYjodya/aZRulhDGtyog13LY HMWT+cVQ==; 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 1raicN-0004iN-1Z; Thu, 15 Feb 2024 20:46:04 +0000 From: Arun Isaac Date: Thu, 15 Feb 2024 20:46:25 +0000 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 (cwltool): Update to 3.1.20240112164112. [arguments]: Use G-expressions. Set version in setup.py. Do not attempt to substitute files cwltool/schemas/v1.1/tests/env-tool1.cwl, cwltool/schemas/v1.1/tests/env-tool2.cwl and cwltool/schemas/v1.1/tests/imported-hint.cwl that have been removed in this release. Do not remove "-n auto" from pytest flags. [inputs]: Add python-cwl-utils and python-spython. [native-inputs]: Add python-pytest-xdist. Change-Id: If1be7cdf39b767c5ef2a1dbddfdc95f59ea98cb6 Change-Id: I2ba81e8569abcf43cd0fad33daab1e4f8689e77f --- gnu/packages/bioinformatics.scm | 89 ++++++++++++++++----------------- 1 file changed, 43 insertions(+), 46 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35c4d7d993..cc1a966b41 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5235,7 +5235,7 @@ (define-public python-cwl-utils (define-public cwltool (package (name "cwltool") - (version "3.1.20220119140128") + (version "3.1.20240112164112") (source (origin (method git-fetch) (uri (git-reference @@ -5244,56 +5244,51 @@ (define-public cwltool (file-name (git-file-name name version)) (sha256 (base32 - "1jmrm0qrqgka79avc1kq63fgh20gx6g07fc8p3iih4k85vhdyl3f")))) + "1fpc5kqgpbn48g5vlvy64p297x2wm3gfz8casgpk15ap593wwh33")))) (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'loosen-version-restrictions - (lambda _ - (substitute* "setup.py" - (("== 1.5.1") ">=1.5.1")))) ; prov - (add-after 'unpack 'dont-use-git - (lambda _ - (substitute* "gittaggers.py" - (("self.git_timestamp_tag\\(\\)") - (string-append "time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(" - (string-drop ,version 4) ")))"))))) - (add-after 'unpack 'modify-tests - (lambda _ - ;; Tries to connect to the internet. - (delete-file "tests/test_content_type.py") - (delete-file "tests/test_udocker.py") - (delete-file "tests/test_http_input.py") - (substitute* "tests/test_load_tool.py" - (("def test_load_graph_fragment_from_packed") - (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - "def test_load_graph_fragment_from_packed"))) - (substitute* "tests/test_examples.py" - (("def test_env_filtering") - (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - "def test_env_filtering"))) - ;; Tries to use cwl-runners. - (substitute* "tests/test_examples.py" - (("def test_v1_0_arg_empty_prefix_separate_false") - (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" - "def test_v1_0_arg_empty_prefix_separate_false"))) - - (substitute* '("cwltool/schemas/v1.1/tests/env-tool1.cwl" - "cwltool/schemas/v1.1/tests/env-tool2.cwl" - "cwltool/schemas/v1.1/tests/imported-hint.cwl" - "tests/subgraph/env-tool2.cwl" - "tests/subgraph/env-tool2_req.cwl" - "tests/subgraph/env-wf2_subwf-packed.cwl" - "tests/subgraph/env-tool2_no_env.cwl") - (("\"/bin/sh\"") (string-append "\"" (which "sh") "\""))) - ;; Pytest doesn't know what to do with "-n auto" - (substitute* "tox.ini" - (("-n auto") ""))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'loosen-version-restrictions + (lambda _ + (substitute* "setup.py" + (("== 1.5.1") "> 1.5.1")))) ; prov + (add-after 'unpack 'set-version + (lambda _ + ;; Set exact version. + (substitute* "setup.py" + (("use_scm_version=True") + (string-append "version=\"" #$version "\""))))) + (add-after 'unpack 'modify-tests + (lambda _ + ;; Tries to connect to the internet. + (delete-file "tests/test_content_type.py") + (delete-file "tests/test_udocker.py") + (delete-file "tests/test_http_input.py") + (substitute* "tests/test_load_tool.py" + (("def test_load_graph_fragment_from_packed") + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + "def test_load_graph_fragment_from_packed"))) + (substitute* "tests/test_examples.py" + (("def test_env_filtering") + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + "def test_env_filtering"))) + ;; Tries to use cwl-runners. + (substitute* "tests/test_examples.py" + (("def test_v1_0_arg_empty_prefix_separate_false") + (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n" + "def test_v1_0_arg_empty_prefix_separate_false"))) + (substitute* '("tests/subgraph/env-tool2.cwl" + "tests/subgraph/env-tool2_req.cwl" + "tests/subgraph/env-wf2_subwf-packed.cwl" + "tests/subgraph/env-tool2_no_env.cwl") + (("\"/bin/sh\"") (string-append "\"" (which "sh") "\"")))))))) (inputs (list python-argcomplete python-bagit python-coloredlogs + python-cwl-utils python-mypy-extensions python-prov python-pydot @@ -5303,6 +5298,7 @@ (define-public cwltool python-ruamel.yaml python-schema-salad python-shellescape + python-spython python-typing-extensions ;; Not listed as needed but still necessary: node)) @@ -5313,7 +5309,8 @@ (define-public cwltool python-pytest python-pytest-cov python-pytest-mock - python-pytest-runner)) + python-pytest-runner + python-pytest-xdist)) (home-page "https://github.com/common-workflow-language/common-workflow-language") (synopsis "Common Workflow Language reference implementation")