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")