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