From patchwork Mon Oct 23 08:09:42 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Arun Isaac X-Patchwork-Id: 55156 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 87CAC27BBE2; Mon, 23 Oct 2023 09:11:34 +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 4E5C327BBEA for ; Mon, 23 Oct 2023 09:11:31 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1quq1Z-0004Ji-RH; Mon, 23 Oct 2023 04:10:57 -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 1quq1F-00048t-Vh 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 1quq1C-000745-Jc 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 1quq1f-0001vo-6r; Mon, 23 Oct 2023 04:11:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66690] [PATCH 3/7] gnu: python-schema-salad: Update to 8.4.20230927144413. Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: arunisaac@systemreboot.net, guix-patches@gnu.org Resent-Date: Mon, 23 Oct 2023 08:11:03 +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 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=B66690.16980486537361 (code B ref 66690); Mon, 23 Oct 2023 08:11:03 +0000 Received: (at 66690) by debbugs.gnu.org; 23 Oct 2023 08:10:53 +0000 Received: from localhost ([127.0.0.1]:48969 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1U-0001uY-G6 for submit@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:53 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:33986) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1quq1K-0001tf-69 for 66690@debbugs.gnu.org; Mon, 23 Oct 2023 04:10:45 -0400 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=6/we5UeOjRPbsT+2Qv7NyJ5MTGG248IHrWt79vhKj6E=; b=MQmAAYBHPz2OgOs0bJYs5Sjnhd M3Dg0StP7Ar+vyl9jkARK6lg5sAli5O6ZiFhci7QjU2IGQ47BrBzTLlcESX5bDcoIAF41ukOWVZDe URtbBH7n+lJ3pnLB5Rtmr5YovET6ibDpGcxYpvF54dhQReKXaRdi+RfIBkxRJlLLeuGzVx92QCIgj Wxu0Z5SRt617okFIUQX837aesElROpO5bty0tU3gsPy6DLDoS6eVZWYRPWw8HoVhuWaqJbAKnW6v0 xElFOWtwMhdRY0q8cFlpOZgTOtaCFYl1H6oloVKdjE08lX7LFi1Zikm7H4feubMcUBlBgnoJcvspL n78R8QEg==; 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 1quq0o-001gvg-1P; Mon, 23 Oct 2023 09:10:11 +0100 From: Arun Isaac Date: Mon, 23 Oct 2023 09:09:42 +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-schema-salad): Update to 8.4.20230927144413. [propagated-inputs]: Add python-importlib-resources. Replace python-mistune with python-mistune-next. [arguments]: Use G-expressions. Set exact version number. Remove arguments that pytest does not recognize. Skip more tests that require network access. Skip tests using #:test-flags. --- gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++---------- 1 file changed, 34 insertions(+), 14 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a1eac184ad..c6819316ae 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2016, 2020, 2022 Marius Bakke ;;; Copyright © 2016, 2018 Raoul Bonnal ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice -;;; Copyright © 2017, 2021, 2022 Arun Isaac +;;; Copyright © 2017, 2021, 2022, 2023 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits ;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu @@ -4327,30 +4327,50 @@ (define-public python-pybigwig (define-public python-schema-salad (package (name "python-schema-salad") - (version "8.2.20211116214159") + (version "8.4.20230927144413") (source (origin (method url-fetch) (uri (pypi-uri "schema-salad" version)) (sha256 (base32 - "005dh2y45x92zl8sf2sqjmfvcqr4hrz8dfckgkckv87003v7lwqc")))) + "0d0mm1cwrdmz2yplfi7vgqjsfaz4z3rdm2gx2103176jdsiwq610")))) (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 + #:test-flags + ;; Skip tests that require network access. + #~(list "-k" + (string-append "not test_secondaryFiles" + " and not test_outputBinding" + " and not test_yaml_tab_error" + " and not test_idmap" + " and not test_idmap2" + " and not test_include" + " and not test_load" + " and not test_load_cwlschema" + " and not test_load_by_yaml_metaschema" + " and not test_load_metaschema" + " and not test_bad_schemas")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-version + (lambda _ + (substitute* "setup.py" + ;; Set exact version number. + (("version=\"[[:digit:].]*\"") + (string-append "version=\"" #$version "\""))))) + (add-after 'unpack 'fix-pytest-arguments + (lambda _ + (substitute* "tox.ini" + ;; pytest does not recognize the -n auto arguments. Remove + ;; them. + (("addopts=-n auto") ""))))))) (propagated-inputs (list python-cachecontrol + python-importlib-resources python-lockfile - python-mistune + python-mistune-next python-rdflib python-rdflib-jsonld python-requests