From patchwork Tue Sep 10 19:33:55 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Roel Janssen X-Patchwork-Id: 67858 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 9F25627BBEA; Tue, 10 Sep 2024 21:03:38 +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=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_VALIDITY_CERTIFIED, RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE,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 AB8DA27BBE2 for ; Tue, 10 Sep 2024 21:03:37 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1so75B-0006lD-7L; Tue, 10 Sep 2024 16:03:25 -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 1so6dd-0001VL-S2 for guix-patches@gnu.org; Tue, 10 Sep 2024 15:34:58 -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 1so6dd-00084S-Ix for guix-patches@gnu.org; Tue, 10 Sep 2024 15:34:57 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:Date:From:To:Subject; bh=02+XxBCmQETsp34/ElPeGllkmDpvjIcKzFQbR92q0Nw=; b=SKzfHPFB3EWdsYct8FHRUgOIDrmR08gTgYtSj/ktPiErxpVfxvEughN+ms/eqNh7wDKaN8mKzgSNCnr2lgsIn0Bxd5S5LdiTY+6qKQvGrb6WlyZ2d8IliHiGCZ4uFDxdgB9pehpVh1iKQ4Zn09xYEljuFKonOTZI7Kfy1f3+4bGalflmockxJZEi3P1bdlI01ptIIy1XSvJez2HF8cN5d4H35/Pfc/2P4t6m/+XxjGCScqTw1BXux/MS8HFfWRHu+TdmDbnGe1+4wkNFKooJonyTOVC9wkQk82PAiArDIp2dW1w6MhrRrsVDs8/eJGgTWfWLWSN2qS3NBKRU4s9M/A==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1so6di-0006NL-BR for guix-patches@gnu.org; Tue, 10 Sep 2024 15:35:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#73173] [PATCH] gnu: Update python-rdflib to 7.0.0. Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 10 Sep 2024 19:35:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 73173 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 73173@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.172599685224438 (code B ref -1); Tue, 10 Sep 2024 19:35:02 +0000 Received: (at submit) by debbugs.gnu.org; 10 Sep 2024 19:34:12 +0000 Received: from localhost ([127.0.0.1]:37053 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1so6cu-0006M5-7F for submit@debbugs.gnu.org; Tue, 10 Sep 2024 15:34:12 -0400 Received: from lists.gnu.org ([209.51.188.17]:37016) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1so6cq-0006Lv-0r for submit@debbugs.gnu.org; Tue, 10 Sep 2024 15:34:10 -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 1so6cj-0001Ml-5E for guix-patches@gnu.org; Tue, 10 Sep 2024 15:34:01 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1so6ci-000813-Qq for guix-patches@gnu.org; Tue, 10 Sep 2024 15:34:00 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:Date:To:From:Subject:in-reply-to: references; bh=02+XxBCmQETsp34/ElPeGllkmDpvjIcKzFQbR92q0Nw=; b=Zztp/dr3gD/K6+ XDMw4jfGrjXJExQ52leesqPb0D/3R+7K3vad7ATOhEY7UrYBlO70Ka2zfzCNK7f57B0BY39eR1HPO 14q/OBmXh8DLXdJA7mIb0hnizQuraLzddkRKpv5+l/OuzxAwh7lFkM5CHbEJdBLIEgpfJ9i0V6A0h xM0vqtXGOpFp4LhlN88b2aGBdLKFrYY/LjCbfjordzuiql9ijit3igKwvO4FnSjebn8SBqExbpc5s wWadO2PeQ213ntbIYLZSNNLFmrIDNtkkLiaAI1jzq5Bjd9UbjLcL3Pg8ZdN+6/wSZfnzwFTe7nsEB 6XFFgiz1rNJiH591WROQ==; Message-ID: From: Roel Janssen Date: Tue, 10 Sep 2024 21:33:55 +0200 User-Agent: Evolution 3.52.4 (3.52.4-1.fc40) MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Mailman-Approved-At: Tue, 10 Sep 2024 16:03:20 -0400 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 Dear Guix, I'd like to update python-rdflib to 7.0.0. When building the reverse- dependent packages, I found that python-prov and cwltool don't support version 7. So the attached patch keeps 6.1.1 around but upgrades all the others. I built the following packages successful after the upgrade: - carla - ardour - zeitgeist - python-schema-salad - python-sparqlwrapper - python-cfgraph - python-pyrdfa3 - python-sparqlkernel The following package failed to build, but I believe it's unrelated to the upgrade: - python-pytorch-geometric Keeping python-prov and cwltool at python-rdflib-6 doesn't affect the successful builds of these packages. So I believe the impact is minimal. Let me know if/what I can do to improve the patch. Thank you for your time in advance. Kind regards, Roel Janssen From 5c1857e08a25c9ca00d3c3acf7fade67e523fbe3 Mon Sep 17 00:00:00 2001 Message-ID: <5c1857e08a25c9ca00d3c3acf7fade67e523fbe3.1725996315.git.roel@gnu.org> From: Roel Janssen Date: Tue, 10 Sep 2024 21:19:50 +0200 Subject: [PATCH] gnu: Update python-rdflib to 7.0.0. * gnu/packages/rdf.scm: Add updated recipe for python-rdflib; Keep python-rdflib-6 for compatibility. * gnu/packages/python-xyz.scm: Build python-prov with python-rdflib-6 because rdflib-7 is not supported. * gnu/packages/bioinformatics.scm: Build cwltool with python-rdflib-6 because it fails to build with rdflib-7. Change-Id: Ibc40c16ede20e69e702915488d6b2f0a7e70b868 --- gnu/packages/bioinformatics.scm | 2 +- gnu/packages/python-xyz.scm | 2 +- gnu/packages/rdf.scm | 43 +++++++++++++++++++++++++++++++++ 3 files changed, 45 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4653360792..db8befd144 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5786,7 +5786,7 @@ (define-public cwltool python-prov python-pydot python-psutil - python-rdflib + python-rdflib-6 python-requests python-ruamel.yaml python-schema-salad diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 21e04e75e9..2fbdd32cf3 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -24995,7 +24995,7 @@ (define-public python-prov (("\\.serialize\\(format=\"nt\"\\)") ".serialize(format=\"nt\", encoding=\"utf-8\")"))))))) (propagated-inputs - (list python-dateutil python-lxml python-networkx python-rdflib)) + (list python-dateutil python-lxml python-networkx python-rdflib-6)) (native-inputs (list graphviz python-pydot)) (home-page "https://github.com/trungdong/prov") diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm index f10b530861..9a02a71d81 100644 --- a/gnu/packages/rdf.scm +++ b/gnu/packages/rdf.scm @@ -328,6 +328,49 @@ (define-public sord (license license:isc))) (define-public python-rdflib + (package + (name "python-rdflib") + (version "7.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "rdflib" version)) + (sha256 + (base32 + "1blmx4v003afr3l9qg84ymj0sldcbsr2dzdgq6w5k022d62yp5cr")))) + (build-system pyproject-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + (for-each delete-file + '(;; The tests in this file miss a test fixture. + ;; fixture 'no_cover' not found + "test/test_misc/test_plugins.py" + ;; These tests need internet access. + "test/jsonld/test_onedotone.py" + "test/test_examples.py" + "test/test_extras/test_infixowl/test_basic.py" + "test/test_extras/test_infixowl/test_context.py" + "test/test_sparql/test_service.py")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "test/"))))))) + (native-inputs + (list python-pytest python-poetry-core)) + (propagated-inputs + (list python-html5lib python-isodate python-pyparsing)) + (home-page "https://github.com/RDFLib/rdflib") + (synopsis "Python RDF library") + (description + "RDFLib is a Python library for working with RDF, a simple yet +powerful language for representing information.") + (license (license:non-copyleft "file://LICENSE" + "See LICENSE in the distribution.")))) + +(define-public python-rdflib-6 (package (name "python-rdflib") (version "6.1.1") base-commit: b82c8ceae14d5d0f4584452f34f5103ffd0e0f8d -- 2.46.0