From patchwork Mon Dec 12 14:26:59 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45207 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 463F027BBEC; Mon, 12 Dec 2022 14:29:50 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 A512327BBEB for ; Mon, 12 Dec 2022 14:29:49 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jms-0005Zj-60; Mon, 12 Dec 2022 09:28:10 -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 1p4jml-0005TF-89 for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmk-0006CK-WE for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmk-0007UO-EE for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 01/18] gnu: python-graphviz: Update to 0.20.1. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085524828640 (code B ref 60009); Mon, 12 Dec 2022 14:28:02 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:27:28 +0000 Received: from localhost ([127.0.0.1]:53259 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmC-0007Rr-0k for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:28 -0500 Received: from sender3-of-o58.zoho.com ([136.143.184.58]:21870) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jm9-0007Rj-7T for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:26 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855242; cv=none; d=zohomail.com; s=zohoarc; b=cjk/MOEtBjh/aHBs2lGXyYrh4a+tqaD9Pmjlbut3NSxgQZK/W6wn6pKmGUgJ7peQgsdwnWeFz0yKgEnBffsYj4vRbwKm7Sbe4EXb4+5E1HYoe8eWxSpE9mXViCx9LGuDE6xv8PT07XjSjXorHzQHe8QrdDvicAoDvSE2twJ2IXk= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855242; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=yfCKehxFPZ1Un8hoFSr41sQWA4LoHiLvoWgWnCIYWLo=; b=FeUQDZ+SjEwAZugI9ysAIh2E56eM85lsQNRgx7Z2cothhFCkMilkpcHvqLYZXyBO625JmjC/DC50AqSIdil3mVEQk056pmP3o4UB1sGv+Av1lsj+MqFcUIzTeegfe7OxQqvEJqGwnucFWJbbEhMSL/36pmnrfDjmdg2hNzDXcbI= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855242; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Type:Content-Transfer-Encoding:Reply-To; bh=yfCKehxFPZ1Un8hoFSr41sQWA4LoHiLvoWgWnCIYWLo=; b=fvNPIvW06+phmrysTlMDZdnNB3lb6ZtmPviDrfbYP/KqG6IThIN7lTmEsxIIiW8Z HXvDidlUmXEZsVs/5+E5JGzdkiKNvHs75qE8vf0a249At7b3zJzI5p02ADrHqY9SaVK WTdidiZ/2qO7SSRyOV4lK8iKeGLkFmKIZN6kBx3Y= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855240611673.6031872565396; Mon, 12 Dec 2022 06:27:20 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:26:59 +0100 Message-Id: <20221212142716.9460-1-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <87h6y03dkr.fsf@elephly.net> References: <87h6y03dkr.fsf@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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/graphviz.scm (python-graphviz): Update to 0.20.1. [build-system]: Use pyproject-build-system. [arguments]: Remove custom "check" phase; add "prepare-check" phase. [native-inputs]: Remove python-mock. --- gnu/packages/graphviz.scm | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm index 51c1de3932..7c2cb1eae0 100644 --- a/gnu/packages/graphviz.scm +++ b/gnu/packages/graphviz.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2013, 2015, 2021 Ludovic Courtès ;;; Copyright © 2015, 2020 Efraim Flashner ;;; Copyright © 2016 Theodoros Foradis -;;; Copyright © 2017, 2018, 2019 Ricardo Wurmus +;;; Copyright © 2017, 2018, 2019, 2022 Ricardo Wurmus ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2017 Gábor Boskovits ;;; Copyright © 2018 Mathieu Lirzin @@ -32,6 +32,7 @@ (define-module (gnu packages graphviz) #:use-module (guix packages) #:use-module (guix build-system gnu) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix download) #:use-module (guix git-download) @@ -180,27 +181,25 @@ (define-public graphviz-2.38 (define-public python-graphviz (package (name "python-graphviz") - (version "0.13.2") + (version "0.20.1") (source (origin (method url-fetch) (uri (pypi-uri "graphviz" version ".zip")) (sha256 (base32 - "009alrilzx0v7kl41khbq7k6k8b8pxyvbsi1b1ai933f6kpbxb30")))) - (build-system python-build-system) + "1y1b956r01kg7qarkkrivhn71q64k0gbq6bcybd4gfd3v95g2n4c")))) + (build-system pyproject-build-system) (arguments - '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests #:allow-other-keys) - (if tests - (invoke "pytest" "-vv") - (format #t "test suite not run~%")) - #t))))) + (list + #:phases + '(modify-phases %standard-phases + (add-before 'check 'prepare-chec + ;; Needed for fontconfig cache directories + (lambda _ (setenv "HOME" (getcwd))))))) (native-inputs (list unzip ;; For tests. graphviz - python-mock python-pytest python-pytest-cov python-pytest-mock)) From patchwork Mon Dec 12 14:27:00 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45197 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 7B15427BBF1; Mon, 12 Dec 2022 14:29:03 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 CC99727BBE9 for ; Mon, 12 Dec 2022 14:29:00 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jmw-0005jP-Uy; Mon, 12 Dec 2022 09:28:14 -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 1p4jml-0005TP-Gc for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jml-0006Cj-8y for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jml-0007UW-2f for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 02/18] gnu: python-hyperopt: Update to 0.2.7. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085525128653 (code B ref 60009); Mon, 12 Dec 2022 14:28:02 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:27:31 +0000 Received: from localhost ([127.0.0.1]:53262 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmE-0007S5-MT for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:31 -0500 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21736) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmD-0007Rs-3v for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:29 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855246; cv=none; d=zohomail.com; s=zohoarc; b=Edp0D38R4IW3mA0aKkFBBsKseV5O7a021maiNEF9bXSDkfL0vE8Whlhtz0yRJ5WjX0S2d2HSI/OmT0DvPIav6uWMwqpN7SE9yA56vnqJg34j9zsGKlljMa7s/c9EUUsisUjGqYlkKDGtZ6r5JPJs+Y1Di/PPXlxnQTH2pXqq4HM= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855246; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=KWmVAVCjSRVQaXzflRd6IXdJBNoQFS3pft6odi6wybA=; b=Wqh7H0EPh+1lFtVQrTTKR/b1VYq8di6k+IUw9cDme6isG7DjYzE4aO4fo4kkkrxyXD4Rb5MwNsXQrhZik7DhdAQcI0DCn2qj4TMDEyJFVfCX/FoiTp9Lao6U1aGyCiAq/cC9gMoWCRQFzVVk75Cl59Tk9XP9dsJFJkzWldfO23w= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855246; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=KWmVAVCjSRVQaXzflRd6IXdJBNoQFS3pft6odi6wybA=; b=G4Go2qX4fc12Gf0maE+TCa0v22aq40AO1HpBkG6p2fi4vYxY+bXrEA4rzCWyeeAS 6VCh0Wg6WMX+e6SqHS0+IG6d0Vo1zWmeVuw7aRabDWLYKNkqiRkAuhNdJ5vjMyL48Dg bgzeHSeVrD/a73NTcttjJT+PLzxijy8YdKbtxC68= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855243841677.1003526184394; Mon, 12 Dec 2022 06:27:23 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:00 +0100 Message-Id: <20221212142716.9460-2-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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/machine-learning.scm (python-hyperopt): Update to 0.2.7. [arguments]: Adjust check phase; disable test_distribution_rvs test. [build-system]: Use pyproject-build-system. [propagated-inputs]: Add python-py4j. [native-inputs]: Remove python-ipython and python-ipyparallel. --- gnu/packages/machine-learning.scm | 36 ++++++++++++++++--------------- 1 file changed, 19 insertions(+), 17 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index fc8de01066..3dbe54a24a 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1552,35 +1552,39 @@ (define-public vowpal-wabbit (define-public python-hyperopt (package (name "python-hyperopt") - (version "0.2.5") + (version "0.2.7") (source (origin (method url-fetch) (uri (pypi-uri "hyperopt" version)) (sha256 - (base32 "1k4ma8ci0bxghw7g4ms944zak1pi83yv2d6bxd7fcslm1zalfq5w")))) - (build-system python-build-system) + (base32 "0jd1ghmm423kbhjvd6pxq92y5vkz25390687fcnd7fshh3jrmy0v")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (lambda* (#:key tests? #:allow-other-keys) (when tests? - (add-installed-pythonpath inputs outputs) - (invoke "python" "-m" "pytest" "--ignore" + (invoke "python" "-m" "pytest" ;; Needs python-pyspark. - "hyperopt/tests/test_spark.py" + "--ignore" "hyperopt/tests/integration/test_spark.py" ;; Needs both python-scikit-learn and python-lightgbm. - "--ignore" "hyperopt/tests/test_atpe_basic.py" + "--ignore" "hyperopt/tests/unit/test_atpe_basic.py" ;; The tests below need python-lightgbm. - "-k" (string-append "not test_branin" - " and not test_distractor" - " and not test_q1lognormal" - " and not test_quadratic1" - " and not test_twoarms")))))))) + "-k" + (string-append "not test_branin" + " and not test_distractor" + " and not test_q1lognormal" + " and not test_quadratic1" + " and not test_twoarms" + ;; XXX Type error with this version of scipy + " and not test_distribution_rvs")))))))) (propagated-inputs (list python-cloudpickle python-future + python-py4j python-networkx python-numpy python-scipy @@ -1588,8 +1592,6 @@ (define-public python-hyperopt python-tqdm)) (native-inputs (list python-black - python-ipython - python-ipyparallel python-nose python-pymongo python-pytest)) From patchwork Mon Dec 12 14:27:01 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45212 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 4969127BBEB; Mon, 12 Dec 2022 14:30:09 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 76F5027BBE9 for ; Mon, 12 Dec 2022 14:30:08 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jms-0005b3-TJ; Mon, 12 Dec 2022 09:28:10 -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 1p4jmm-0005TQ-EB for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmm-0006Cq-5x for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:04 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmm-0007Uo-0x for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 03/18] gnu: python-biopython: Update to 1.80. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085525528667 (code B ref 60009); Mon, 12 Dec 2022 14:28:03 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:27:35 +0000 Received: from localhost ([127.0.0.1]:53266 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmJ-0007SJ-3r for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:35 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21050) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmF-0007S4-5W for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:31 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855248; cv=none; d=zohomail.com; s=zohoarc; b=Qp/gLt56jAveMef7zkxstKBiWzjqkt+6vcUtvF4eff6VIU2iHC67a5Y20VjphByDKzmfig4LXYmPtOp02qKjcQA6bjSxq5c68cU1gCS6/45n0Imm4JSvAWfXa0D5PfqLoWshU8+LkX6dIuIgzOkTPryRwGzFe1HWidL5qL0ijTI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855248; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=is25P2xY+0AxoIz6qVGUWoyIjlQbpDXmeSm9/qHfEjc=; b=GDv7agSJggbV64lo8cegGXk9kdm9OeecfxqvLSldZ+qM3IKhJNF3pX4HUJLZvKI3kI4LxtLJGkVNIdjaUPVBLPqgSk0mqFWOQP4e7ohWTeNaagDeqNH3KCf/0qWDL1ZJHUaT36PH29ZxsgrI6v173ARKqhfAUJrwQjR+C5Nxpqg= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855248; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=is25P2xY+0AxoIz6qVGUWoyIjlQbpDXmeSm9/qHfEjc=; b=GyHKX0gacXgdufKXeBCAB/4Sf379E//B4P2O+MBX7K4y+aBxe8IaxiH1XrRm2M3z O9rQH6LJAW8Nq4sxWLqRFcEpkBJb09bhybWdhLVF6Sxiwor+6hL0oGtcQjuK9EMB3gy B2+W2c24FgJmmYTIYr2cKoslJr/tV4S7k3ym6PFY= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855247087244.5819688862564; Mon, 12 Dec 2022 06:27:27 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:01 +0100 Message-Id: <20221212142716.9460-3-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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-biopython): Update to 1.80. [build-system]: Use pyproject-build-system. [arguments]: Remove trailing #T from build phase. --- gnu/packages/bioinformatics.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 207f3c3d28..52abe152ee 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1237,21 +1237,21 @@ (define-public perl-bio-db-hts (define-public python-biopython (package (name "python-biopython") - (version "1.76") + (version "1.80") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32 - "0wlch9xpa0fpgjzyxi6jsfca6iakaq9a05927xg8vqnmvaccnwrq")))) - (build-system python-build-system) + "0hqf3jsxn2sphcx81fx7x3i69sarpjsi70fzw98f8rw7z2d5x02j")))) + (build-system pyproject-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases (add-before 'check 'set-home ;; Some tests require a home directory to be set. - (lambda _ (setenv "HOME" "/tmp") #t))))) + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-numpy)) (home-page "https://biopython.org/") From patchwork Mon Dec 12 14:27:02 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45205 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 8160627BBEC; Mon, 12 Dec 2022 14:29:34 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 E842927BBE9 for ; Mon, 12 Dec 2022 14:29:33 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jms-0005aF-Js; Mon, 12 Dec 2022 09:28:10 -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 1p4jmm-0005Ta-Ub for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmm-0006Cv-Mr for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:04 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmm-0007Uv-GT for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 04/18] gnu: python-hicmatrix: Update to 16. 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[build-system]: Use pyproject-build-system. [arguments]: Shuffle the quote. --- gnu/packages/bioinformatics.scm | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 52abe152ee..82801e7eeb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13373,7 +13373,7 @@ (define-public python-cooltools (define-public python-hicmatrix (package (name "python-hicmatrix") - (version "15") + (version "16") (source (origin ;;Pypi sources do not contain any test @@ -13384,11 +13384,12 @@ (define-public python-hicmatrix (file-name (git-file-name name version)) (sha256 (base32 - "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5")))) - (build-system python-build-system) + "00b9l62j4knrsdp7l3pawi9cqcsl09diycbhmmnar850bzssmq4f")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases (replace 'check (lambda* (#:key tests? #:allow-other-keys) (when tests? From patchwork Mon Dec 12 14:27:03 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45198 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 4BFAD27BBE9; Mon, 12 Dec 2022 14:29:04 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 2825C27BBEC for ; Mon, 12 Dec 2022 14:29:01 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jmw-0005iD-BR; Mon, 12 Dec 2022 09:28:14 -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 1p4jmn-0005Vg-FM for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmn-0006D0-6V for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:05 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmn-0007V2-0i for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 05/18] gnu: python-pygenometracks: Update to 3.5. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085526228700 (code B ref 60009); Mon, 12 Dec 2022 14:28:04 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:27:42 +0000 Received: from localhost ([127.0.0.1]:53273 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmQ-0007Sq-DC for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:42 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21057) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmM-0007SX-Jf for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:39 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855254; cv=none; d=zohomail.com; s=zohoarc; b=lwZCDjTsdm+1Ng9rZURHYja9PggiBU5Tl6/ZYW9L58p6WHvv4z9WBQqEOU8ZrAWaXCTi9yweqNLtz6NIKsj9t+SQ8ywCm5h2WTYdye5qcyIxK143QtaeE9c/vtN97vk7kdu4ikHTjPj3JuBmkC64GOuc2p5PWKKgj7TnJRQoalI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855254; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=vnALGN4v5ZdreRDCUNhA7ELbO3Lg8Dw9+zlcBOE0/S4=; b=efWe3sMh+LJtnzdwZFsR0Ffta4AGyaUvfHvQ7L0fMgcPTComiPYM7wYabVHW8IZqMg5IXO+uZeXwl9djvUuzcKayLFydeH67LILGPeXa0aXVtimG76c6pnrWNe+cBhMee3YfW+1Da9JLJAcGmhG6zIFZZb0BKJEstWxp9skYuvw= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855254; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=vnALGN4v5ZdreRDCUNhA7ELbO3Lg8Dw9+zlcBOE0/S4=; b=KYN2oWQpGdF9T2pu9QQ/ZQBM1ibrXYUKhC3bCN6UjRcU/udMWl2IDGSNMkdfqKSw y6NgGgdva6RpyOuzn0aRshB2ZrapOuafdKgba0wAhdW9rIsO05D6boF2DxtHu52xIyI MtPR2Wp9jtxwbWN1j+TzLROYzxQnLyuVYy38Ii4A= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855253329861.4200994581539; Mon, 12 Dec 2022 06:27:33 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:03 +0100 Message-Id: <20221212142716.9460-5-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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-pygenometracks): Update to 3.5. [build-system]: Use pyproject-build-system. [arguments]: Quote phases instead of full list of arguments; remove trailing #T from build phase. --- gnu/packages/bioinformatics.scm | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 82801e7eeb..e6a8789ea6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13466,25 +13466,25 @@ (define-public python-hicexplorer (define-public python-pygenometracks (package (name "python-pygenometracks") - (version "3.3") + (version "3.5") (source (origin (method url-fetch) (uri (pypi-uri "pyGenomeTracks" version)) (sha256 (base32 - "16laa0wnf4qn9fb9ych4w1vqhqwjss70v0y0f6wp4gwqfrlgac0f")))) - (build-system python-build-system) + "1l7smg2gc1vm2181lzmdnywb11gp6s6z6j444dbsigv65car8z8p")))) + (build-system pyproject-build-system) (arguments - `(#:tests? #f ; there are none - #:phases - (modify-phases %standard-phases + (list + #:tests? #f ;there are none + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'relax-requirements (lambda _ (substitute* "setup.py" (("matplotlib ==3.1.1") - "matplotlib >=3.1.1")) - #t))))) + "matplotlib >=3.1.1"))))))) (propagated-inputs (list python-future python-gffutils From patchwork Mon Dec 12 14:27:04 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45196 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 E67FA27BBEB; Mon, 12 Dec 2022 14:28:59 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 F2A6E27BBE9 for ; Mon, 12 Dec 2022 14:28:57 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jmw-0005iJ-C8; Mon, 12 Dec 2022 09:28:14 -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 1p4jmn-0005Vh-RO for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmn-0006D5-K5 for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:05 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmn-0007V9-Fv for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 06/18] gnu: python-hicexplorer: Update to 3.7.2. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085526528714 (code B ref 60009); Mon, 12 Dec 2022 14:28:05 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:27:45 +0000 Received: from localhost ([127.0.0.1]:53275 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmS-0007Sy-QH for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:45 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21059) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmP-0007Sk-Ae for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:42 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855258; cv=none; d=zohomail.com; s=zohoarc; b=SEPhFlpNSSk8ASATm7kabG89WAixfvwLWk0BigLIcWVZEyNFl5uAWTEbs5vnj5y/Mfg2mbKXPwAb/8a+2PTdnoIFnns8QWREkE02rnSEadGVbEcPwX2kuyts8vbjCBJDHwLSFri3ZAZUXTjHANSV5yUFXxH0QYKrHOx1d3aHQnE= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855258; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=uSzwXnuuhz18/d01xuAGZkKjZ5VpOSJCIKTeC/wQzTg=; b=mCwtUbhaydUbwcXBe8veBHm21o5FAbyw/U/n5254a3xMxPo5qyt8eI3hL9NwO9aAVbod9pOA/5A5KvhOTEIPjiTD4JeyomZ+NB9WU9ZZdaD291k64M3iVSJoZYcv3KWCR+4XDBZtZuQ/UqIAxZdT3pBUohvCZu5dSaJ/VpZE+DY= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855258; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=uSzwXnuuhz18/d01xuAGZkKjZ5VpOSJCIKTeC/wQzTg=; b=Jolnf+Eu2+UB5PTSuzlQ/6zK+qTar0lKjorzu+/YTVgeUUamtLa61qDXtI5pBdXA qj2Zm1SYNImrsEseto3ZDfvA1mPvOBX3mJ8QL4gzWSuRCByY7+gXrV48oppC79ZN4pF 9b1m6pEVHol+wMxOfXQzcFHFlkHL0ztBJ4ajoqUA= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855256905546.081618334264; Mon, 12 Dec 2022 06:27:36 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:04 +0100 Message-Id: <20221212142716.9460-6-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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-hicexplorer): Update to 3.7.2. [build-system]: Use pyproject-build-system. [arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a dependency on an unlicensed package; add phase "fix-references"; add phase "run-only-low-mem-tests". [propagated-inputs]: Remove python-configparser and python-six; add python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz, python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn, python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks, python-scikit-learn, and python-tqdm. [native-inputs]: Add graphviz. --- gnu/packages/bioinformatics.scm | 106 ++++++++++++++++++++++++++++---- 1 file changed, 94 insertions(+), 12 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e6a8789ea6..ea33311a2c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13413,7 +13413,7 @@ (define-public python-hicmatrix (define-public python-hicexplorer (package (name "python-hicexplorer") - (version "2.1.4") + (version "3.7.2") (source (origin ;; The latest version is not available on Pypi. @@ -13424,32 +13424,114 @@ (define-public python-hicexplorer (file-name (git-file-name name version)) (sha256 (base32 - "0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08")))) - (build-system python-build-system) + "1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'loosen-up-requirements - (lambda _ - (substitute* "setup.py" - (("==") ">=")) - #t))))) + (list + #:test-flags + '(list "hicexplorer/test/general/" + "--ignore" "hicexplorer/test/general/test_hicTADClassifier.py" + "--ignore" "hicexplorer/test/general/test_hicTrainTADClassifier.py" + "-k" + (string-append + ;; Unknown chromosome: ChrX + "not test_build_matrix_restrictionCutFile_two" + ;; fixture 'keepSelfLigation' not found + " and not test_build_matrix_restrictionCutFile_six" + ;; ValueError: object dtype is not supported by sparse matrices + " and not test_hic_transfer_obs_exp_perChromosome" + + ;; No KR balancing available + " and not test_correct_matrix_KR_partial_cool" + " and not test_correct_matrix_KR_cool" + " and not test_correct_matrix_KR_H5")) + #:phases + #~(modify-phases %standard-phases + ;; See https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm/issues/23 + (add-after 'unpack 'remove-dependency-on-krbalancing + (lambda _ + (substitute* "hicexplorer/hicCorrectMatrix.py" + (("from krbalancing import.*") "") + (("( *)assert\\(args.correctionMethod == 'KR'\\)" m indent) + (string-append m "\n" + indent "log.error('krbalancing not available')\n" + indent "exit(1)"))) + (substitute* "setup.py" + (("\"krbalancing >= 0.0.5\",") "")) + (substitute* "requirements.txt" + (("krbalancing >= 0.0.5") "")))) + (add-after 'unpack 'fix-references + (lambda _ + (let ((site (string-append #$output "/lib/python" + #$(version-major+minor + (package-version python)) + "/site-packages"))) + (substitute* "hicexplorer/lib/tadClassifier.py" + (("model_location = site.getsitepackages\\(\\)\\[0\\]") + (string-append "model_location = \"" site "\"")))) + (substitute* "hicexplorer/hicFindRestSite.py" + (("subprocess.check_output\\(\\[\"cat\"") + (string-append "subprocess.check_output([\"" + (which "cat") "\"")) + (("cmd = 'sort -k1") + (string-append "cmd = '" (which "sort") " -k1"))))) + ;; The tests aim to detect available memory and run more tests when + ;; there is more available memory. Let's run them deterministically + ;; instead and don't run any tests that require more than 1GB of + ;; RAM. + (add-after 'unpack 'run-only-low-mem-tests + (lambda _ + (with-directory-excursion "hicexplorer/test" + (substitute* '("trivial_runs/test_hicBuildMatrix_trivial_runs_2.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_five.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_four.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two_1.py" + "trivial_runs/test_hicBuildMatrix_trivial_runs.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two_3.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_three.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_two_2.py" + "trivial_runs/test_hicAggregateContacts_trivial_runs_six.py" + "general/test_hicDifferentialTAD.py" + "general/test_hicDetectLoops.py" + "general/test_hicPlotMatrix.py" + "general/test_hicHyperoptDetectLoops.py" + "general/test_hicCreateThresholdFile.py" + "general/test_hicMergeDomains.py" + "general/test_hicHyperoptDetectLoopsHiCCUPS.py" + "general/test_hicAggregateContacts.py" + "general/test_hicInterIntraTAD.py") + (("^memory =.*") "memory = 1\n")))))))) (propagated-inputs (list python-biopython - python-configparser + python-cleanlab-1 python-cooler + python-fit-nbinom python-future + python-graphviz + python-hic2cool + python-hicmatrix + python-hyperopt + python-imbalanced-learn python-intervaltree + python-ipykernel python-jinja2 python-matplotlib python-numpy python-pandas + python-psutil + python-pybedtools python-pybigwig + python-pygenometracks python-pysam + python-scikit-learn python-scipy - python-six python-tables + python-tqdm python-unidecode)) + (native-inputs + (list graphviz)) ;for hicexplorer/test/test_compute_function.py (home-page "https://hicexplorer.readthedocs.io") (synopsis "Process, analyze and visualize Hi-C data") (description From patchwork Mon Dec 12 14:27:05 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45195 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 E921527BBEB; Mon, 12 Dec 2022 14:28:41 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 D320A27BBE9 for ; Mon, 12 Dec 2022 14:28:40 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jmw-0005hj-2D; Mon, 12 Dec 2022 09:28:14 -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 1p4jmo-0005Vi-7w for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmo-0006DA-0R for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:06 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmn-0007VG-SJ for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 07/18] gnu: python-dna-features-viewer: Update to 3.1.1. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085526828727 (code B ref 60009); Mon, 12 Dec 2022 14:28:05 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:27:48 +0000 Received: from localhost ([127.0.0.1]:53279 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmV-0007TH-Om for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:48 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21061) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmS-0007Sx-Ma for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:45 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855262; cv=none; d=zohomail.com; s=zohoarc; b=Oa0Pl+enUZs+tzuanF1dFDUhpQ4nitenwcLV9quve3EZuF4BYrVRLmq0NP3Wj0+ICQosthcYMtc67y9b6dZBludcUu75CxTW+Jv/yrI3b4HzqGVoiBVFAuzM8F01LmLTjUyTZy4mhoawsnOQbQWq5uKP1rEPTfNBOqckJ6C0kK8= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855262; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=YezpJW0kavrBMGPm7Q5u5/mFQQY5yAp5syxFTBxpCpw=; b=U1ADM3gWCAhSYfOJnK5mdcoMfCr/yEKNLbwh8nCqiJ16nQZHpOB1pteWTMRnu3jDcT8jNh9Cwmrj2cfZgMhnN6yQ6U+Aad1+1+j1h9bvDjm3gHQlVaS7f9LWo81QbVJU65oC8ZTk4R5VJsn3CGr6hGvHXTHQ+IYSIP+arzJUnR0= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855262; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=YezpJW0kavrBMGPm7Q5u5/mFQQY5yAp5syxFTBxpCpw=; b=N6KBl5Bc6qwsirqo+cvOqH30GoL9SbKTTCENzPmoZqO4ESYZNvZh/kxljCe1YiWc LnhDm9mMzjjgC1jyrmQTxD/UrFLIOLoZQ0M8aYARrjAQ3WZmiUyjoPy0TzUNNk23J9W PEzMZBno0rZ/Crt6aEiYNAtLTNN/thhR+A9Q/hns= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855259930256.2913112913244; Mon, 12 Dec 2022 06:27:39 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:05 +0100 Message-Id: <20221212142716.9460-7-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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-dna-features-viewer): Update to 3.1.1. [build-system]: Use pyproject-build-system. [arguments]: Add build phase to fix a compatibility problem with biopython. [propagated-inputs]: Add python-packaging. --- gnu/packages/bioinformatics.scm | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ea33311a2c..371bf1077a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16597,18 +16597,31 @@ (define-public python-pybbi (define-public python-dna-features-viewer (package (name "python-dna-features-viewer") - (version "3.0.3") + (version "3.1.1") (source (origin (method url-fetch) (uri (pypi-uri "dna_features_viewer" version)) (sha256 (base32 - "0vci6kg2id6r6rh3cifq7ccnh7j0mb8iqg3hji6rva0ayrdqzafc")))) - (build-system python-build-system) - (arguments '(#:tests? #false)) ; there are none + "10a5pmh73spdgfml88zjqg1rn2j2zdxn06ir8a5q3arspyqvyqcb")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #false ;there are none + #:phases + '(modify-phases %standard-phases + ;; See https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/issues/73 + ;; and https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/pull/74 + (add-after 'unpack 'fix-biopython-compatibility + (lambda _ + (substitute* "dna_features_viewer/biotools.py" + (("zip\\(aa1 \\+ \"\\*\", aa3 \\+ \\[\"\\*\"\\]\\)") + "zip(aa1 + ('*',), aa3 + ('*',))"))))))) (propagated-inputs - (list python-biopython python-matplotlib)) + (list python-biopython + python-matplotlib + python-packaging)) (home-page "https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer") (synopsis "Plot features from DNA sequences") From patchwork Mon Dec 12 14:27:06 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45210 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 76F3E27BBEC; Mon, 12 Dec 2022 14:30:02 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 D87BB27BBEB for ; Mon, 12 Dec 2022 14:30:01 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jms-0005a6-HJ; Mon, 12 Dec 2022 09:28:10 -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 1p4jmo-0005Vj-LQ for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmo-0006DF-Dj for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:06 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmo-0007VN-9a for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:06 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 08/18] gnu: python-bokeh: Skip failing PIL test. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085527028735 (code B ref 60009); Mon, 12 Dec 2022 14:28:06 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:27:50 +0000 Received: from localhost ([127.0.0.1]:53281 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmY-0007TO-3N for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:50 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21063) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmU-0007TB-MX for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:47 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855264; cv=none; d=zohomail.com; s=zohoarc; b=lLY8ncWE3Ap7o7fFatuG3ocFV5OvnPoDc4HLSVMlNWR1fPCp7UsdxzgUErJXkrckznRdQyU0/M8ZB2jID6pg3LjnyFwpyBfVlmYr0y9HzMYJTOTyzMomYiSQmcgpPOD4oJt8MybkT7NcnOVKG+5izCGO9ME4vAlx0K6zqY1JcTI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855264; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=Ofz9AaGW97JZ9qttCLWw6i7DQpIb0MDf2QhYZSOrAus=; b=bJ+/RIof9yS3iGIQ1HnBWngdfP2qfSKLw1IueLnrZt/vlf9rKiB01EvF9lZvF40qsfDP/YXN6Ut/SimBmofPBs5fNJcPwtjAG3fiGjvcBwT9TxtGPkyDJ9JgmaG/kSWmPftWRq6Jw/VIBd2Evj9ht38umcU9o14Rg9nCaA6HqKE= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855264; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=Ofz9AaGW97JZ9qttCLWw6i7DQpIb0MDf2QhYZSOrAus=; b=UcaBHmZ5twNwjuBgUMkzC1xZkNe+g350+31CWSjUkMB9Rg7Wd5QjDEwQVkLJGVia Q1SSlKlozq/1lTpgOZoFLIyj0ToQQYqcf4Mkyzgk7lgi6WhqlMl9vhnZGxYgrpMOxgv QNgiTVIYcvj9OV2njGT8QvD23tuEh5uPIiOz5vKY= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855263158262.50372370900914; Mon, 12 Dec 2022 06:27:43 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:06 +0100 Message-Id: <20221212142716.9460-8-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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 The result seems fine, so don't worry about it. * gnu/packages/python-xyz.scm (python-bokeh)[arguments]: Ignore failing test_transform_PIL test. --- gnu/packages/python-xyz.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8591423116..c63ba212b0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -15465,7 +15465,10 @@ (define-public python-bokeh (delete-file "tests/unit/bokeh/models/test_sources.py") (delete-file "tests/unit/bokeh/embed/test_bundle.py") - (invoke "pytest" "-v"))))))) + ;; XXX: This one test transforms a gif of a red box. It + ;; transforms it all right but the base64 doesn't look as + ;; expected, probably because of a change in pillow. + (invoke "pytest" "-v" "-k" "not test_transform_PIL"))))))) (propagated-inputs (list node-lts python-jinja2 From patchwork Mon Dec 12 14:27:07 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45202 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 754E227BBEC; Mon, 12 Dec 2022 14:29:18 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 F1ABE27BBEB for ; Mon, 12 Dec 2022 14:29:17 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jmw-0005jA-Ma; Mon, 12 Dec 2022 09:28:14 -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 1p4jmp-0005Vm-BN for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmp-0006DK-3d for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmo-0007Vb-U1 for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:06 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0. 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Copyright © 2016 Ben Woodcroft ;;; Copyright © 2016 David Craven ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke -;;; Copyright © 2017 Ricardo Wurmus +;;; Copyright © 2017, 2022 Ricardo Wurmus ;;; Copyright © 2017 Jelle Licht ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2018 Alex Vong From patchwork Mon Dec 12 14:27:08 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45199 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 5B48427BBF0; Mon, 12 Dec 2022 14:29:11 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 3127327BBE9 for ; 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Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085527728766 (code B ref 60009); Mon, 12 Dec 2022 14:28:07 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:27:57 +0000 Received: from localhost ([127.0.0.1]:53289 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmf-0007Tp-0R for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:57 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21068) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jma-0007Tb-Jo for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:53 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855270; cv=none; d=zohomail.com; s=zohoarc; b=RXr368nFi3h6dZ9PHZjKjiwXaTZfFudNUWBlwah+FXiSbgi2QGZdJEimcpgYhyJcuXrXFPT/b+Z0qgPVY/fDM+aXiHzPdhY1TuYaA993URZQlWrCSKHLJAQ6V6KpKU7bsKQ0Aj72ugjv7adGr0tcW7zT0SO6OJicK83vSBq0zsM= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855270; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=6G/FhsMs5jwK6E4PHv0inxXE9ucTF4RLK2hHJepCAxU=; b=TjU6Q0mkimnPtp1Ii91uhRJairwhh6yBnok0V7iRorfDAaynBW/3M1hRr0zviCobT/GkFe9Pb1N7pttMV7adJePn4Ag4jkcfxB3wvjXctgBa7kT1mlqWg4jWrc17uYDMmbhrsENcER1FFhPw4eghfkd8fPoxtmAGD6NM0YlrOsY= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855270; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=6G/FhsMs5jwK6E4PHv0inxXE9ucTF4RLK2hHJepCAxU=; b=Pi0H7P/JRIpW4Lf0pFSxpyVqUGOasa+LHQi3Su1W/EBBeL9AsMw0MD3EFCoATqCT avSjCHx0EEtvHioBrQzzIpbm9Duiwah5W2d0YBx+XYxeCz8115rMZybWIKXffcay+h3 A8isMPYEPzkdxNhKVheica+1aFXfaU0hyyPzwh5U= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 16708552692911002.7360848962315; Mon, 12 Dec 2022 06:27:49 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:08 +0100 Message-Id: <20221212142716.9460-10-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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/databases.scm (python-apsw): Update to 3.40.0.0. [source]: Remove obsolete patch. [build-system]: Use pyproject-build-system. [native-inputs]: Add python-cython. [arguments]: Move build-extensions phase before build phase. * gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch: Remove file. --- gnu/local.mk | 1 - gnu/packages/databases.scm | 36 +++++++++---------- .../python-apsw-3.39.2.1-test-fix.patch | 27 -------------- 3 files changed, 18 insertions(+), 46 deletions(-) delete mode 100644 gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch diff --git a/gnu/local.mk b/gnu/local.mk index 6e12f9cdb1..295be3c67c 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1719,7 +1719,6 @@ dist_patch_DATA = \ %D%/packages/patches/python-3-fix-tests.patch \ %D%/packages/patches/python-3-hurd-configure.patch \ %D%/packages/patches/python-3-no-static-lib.patch \ - %D%/packages/patches/python-apsw-3.39.2.1-test-fix.patch \ %D%/packages/patches/python-aionotify-0.2.0-py3.8.patch \ %D%/packages/patches/python-argcomplete-1.11.1-fish31.patch \ %D%/packages/patches/python-cross-compile.patch \ diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index b74762789a..9d1eec5ea0 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -173,6 +173,7 @@ (define-module (gnu packages databases) #:use-module (guix build-system go) #:use-module (guix build-system meson) #:use-module (guix build-system perl) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix build-system qt) #:use-module (guix build-system ruby) @@ -3590,7 +3591,7 @@ (define-public python-pickleshare (define-public python-apsw (package (name "python-apsw") - (version "3.39.2.1") + (version "3.40.0.0") ;; The compressed release has fetching functionality disabled. (source (origin @@ -3600,24 +3601,23 @@ (define-public python-apsw version "/apsw-" version ".zip")) (sha256 (base32 - "06x3qgg71xz8l3kz8gz04wkfp5f6zfrg476a4mm1c5hikqyw6ykj")) - ;; Cherry-picked from upstream, remove when bumping to 3.39.3. - (patches - (search-patches "python-apsw-3.39.2.1-test-fix.patch")))) - (build-system python-build-system) - (native-inputs (list unzip)) - (inputs (list sqlite-next)) ;SQLite 3.39 required. + "02sgja00azvd08wi2wm105apmhp2644s7aw9b1zdg3dkcwjnsiad")))) + (build-system pyproject-build-system) + (native-inputs + (list python-cython unzip)) + (inputs (list sqlite-next)) ;SQLite 3.40 required. (arguments - (list #:phases - #~(modify-phases %standard-phases - (replace 'build - (lambda _ - (invoke "python" "setup.py" "build" "--enable-all-extensions" - "--enable=load_extension"))) - (add-after 'build 'build-test-helper - (lambda _ - (invoke "gcc" "-fPIC" "-shared" "-o" "./testextension.sqlext" - "-I." "-Isqlite3" "src/testextension.c")))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'build-extensions + (lambda _ + (invoke "python" "setup.py" "build" "--enable-all-extensions" + "--enable=load_extension"))) + (add-after 'build 'build-test-helper + (lambda _ + (invoke "gcc" "-fPIC" "-shared" "-o" "./testextension.sqlext" + "-I." "-Isqlite3" "src/testextension.c")))))) (home-page "https://github.com/rogerbinns/apsw/") (synopsis "Another Python SQLite Wrapper") (description diff --git a/gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch b/gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch deleted file mode 100644 index cc233e3ccd..0000000000 --- a/gnu/packages/patches/python-apsw-3.39.2.1-test-fix.patch +++ /dev/null @@ -1,27 +0,0 @@ -From 1111f902075169bd0d96cdd10607ef8499f0fed5 Mon Sep 17 00:00:00 2001 -From: Roger Binns -Date: Mon, 5 Sep 2022 07:12:25 -0700 -Subject: [PATCH] Deal with mismatched SQLITE_ENABLE_COLUMN_METADATA - -Address #363 ---- - apsw/tests.py | 2 +- - 1 files changed, 1 insertions(+), 1 deletion(-) - -diff --git a/apsw/tests.py b/apsw/tests.py -index b4a94d3..256ead0 100644 ---- a/apsw/tests.py -+++ b/apsw/tests.py -@@ -772,8 +772,8 @@ class APSW(unittest.TestCase): - c.execute("drop table foo; create table foo (%s)" % (", ".join(["[%s] %s" % (n, t) for n, t in cols]), )) - c.execute("insert into foo([x a space]) values(1)") - c.execute("create temp table two(fred banana); insert into two values(7); create temp view three as select fred as [a space] from two") -- has_full=any(o=="ENABLE_COLUMN_METADATA" or o.startswith("ENABLE_COLUMN_METADATA=") for o in apsw.compile_options) -+ has_full=any(o=="ENABLE_COLUMN_METADATA" or o.startswith("ENABLE_COLUMN_METADATA=") for o in apsw.compile_options) if apsw.using_amalgamation else hasattr(c, "description_full") - for row in c.execute("select * from foo"): - self.assertEqual(cols, c.getdescription()) - self.assertEqual(has_full, hasattr(c, "description_full")) - -base-commit: f628374c5857d940067ef26c9ea4e85a08a94f76 --- -2.37.2 From patchwork Mon Dec 12 14:27:09 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45211 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 05C6427BBEC; Mon, 12 Dec 2022 14:30:08 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 1630327BBE9 for ; Mon, 12 Dec 2022 14:30:07 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jms-0005aL-Lo; Mon, 12 Dec 2022 09:28:10 -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 1p4jmq-0005WG-Lp for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmq-0006DU-Ds for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmq-0007Vv-8r for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 11/18] gnu: python-cgatcore: Update to 0.6.14. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085528028776 (code B ref 60009); Mon, 12 Dec 2022 14:28:08 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:28:00 +0000 Received: from localhost ([127.0.0.1]:53291 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmh-0007U3-Pf for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:00 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21071) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jme-0007To-Jr for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:27:57 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855274; cv=none; d=zohomail.com; s=zohoarc; b=VCY5Bnda0xOsKJTc3RGi5MvnomYzE/05e+yzT4q/U1hvJaUv5nFI0CXKC2/cKQaMv7bFV1aNKK4R0+mVz5C/2qAJYsXpagi/L9dyiekUnsa3jpzZW2D7xCJOZzn1WeiKVcKtrZz9KlLt2NbC/M/cY1Cjkk20st6bOQOYJC/Gris= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855274; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=yGyzJR8yiu3qgNcOvd1lxBD4zu4kYL9CBKAPYZtSDgs=; b=n4JbIPv3nnXLJ/wEINzAzT9cZnAMrXT0hhDNpigsen+5A1fGq2WSSKGL3S0eoK6uP8fkgKcU1WSD3v2rtvtmc+K9Szfzh1ysy1DM2MCWoNn3LZfmC4BOXwpigRdPvyA5Dhky6Snc2SPg0QhH4Nxi543v1F+WpALi4Rzb8/F667c= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855274; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=yGyzJR8yiu3qgNcOvd1lxBD4zu4kYL9CBKAPYZtSDgs=; b=CEygyv7qXXBx5MrU3QaedqTCqo7+yn3u/bJY4z8HvFPR2M1yZV288LSfJdVQlT1f sN/JRnPkqUF3HTTfny6EGDZ0QBO62vm0SGYSQAG6HJO9TJ4OnDiSziXOH7OxJBEgW/0 ZIixY1ET5b88DdRDomxGf/DXdIy5BMMNjRWW/p7U= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 167085527276494.05437037664399; Mon, 12 Dec 2022 06:27:52 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:09 +0100 Message-Id: <20221212142716.9460-11-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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-cgatcore): Update to 0.6.14. [build-system]: Use pyproject-build-system. [arguments]: Disable broken tests with #:test-flags; do not replace 'check phase; add phase 'sqlite-compatibility. [native-inputs]: Drop input labels. --- gnu/packages/bioinformatics.scm | 50 ++++++++++++++++++++------------- 1 file changed, 31 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 371bf1077a..4044ff625e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16081,7 +16081,7 @@ (define-public python-pyliftover (define-public python-cgatcore (package (name "python-cgatcore") - (version "0.6.7") + (version "0.6.14") ;; The version of pypi does not include test data. (source (origin (method git-fetch) @@ -16091,11 +16091,22 @@ (define-public python-cgatcore (file-name (git-file-name name version)) (sha256 (base32 - "17vk88v1bx7x02ibzkc9i7ir4b5p1hcjr38jpsfzyzxr68352d5k")))) - (build-system python-build-system) + "0fjjaski39j8b7v21wldmbwwsfhicngajah7n4skafi56kdck33p")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:test-flags + '(list "-k" + (string-append + ;; This test actually does what it should, but the check fails with + ;; TypeError: cannot unpack non-iterable Namespace object + "not test_start_and_stop_are_logged_with_argparse" + ;; These all attempt to connect to localhost with SSH + " and not test_job_should_use_TMPDIR_and_clean_up" + " and not test_job_should_use_TMPDIR_and_clean_up_after_fail" + " and not test_job_should_write_to_explicit_temp_and_not_clean_up")) + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'fix-references (lambda _ (substitute* "cgatcore/pipeline/execution.py" @@ -16103,21 +16114,22 @@ (define-public python-cgatcore (("executable=\"/bin/bash\"") (string-append "executable=\"" (which "bash") "\"")) (("\\\\time") (which "time"))))) - (delete 'check) - (add-after 'install 'check - (lambda* (#:key tests? inputs outputs #:allow-other-keys) - (when tests? - (add-installed-pythonpath inputs outputs) - ;; Requires network access - (delete-file "tests/test_pipeline_execution.py") - (invoke "python" "-m" "pytest" "-v"))))))) + (add-after 'unpack 'sqlite-compatibility + (lambda _ + ;; Load apsw (and thus newer sqlite3) before importing Python's + ;; older sqlite3 library. + (substitute* "cgatcore/pipeline/__init__.py" + (("import os") + (string-append "import os\nimport apsw"))) + (substitute* "tests/template_pipeline.py" + (("import sys" m) + (string-append "import apsw\n" m)))))))) (native-inputs - `(("python-pytest" ,python-pytest) - ("lsof" ,lsof) - ("hostname" ,inetutils) - ("openssl" ,openssl))) - (inputs - (list time)) + (list python-pytest + lsof + inetutils + openssl)) + (inputs (list time)) (propagated-inputs (list python-apsw python-gevent From patchwork Mon Dec 12 14:27:10 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45200 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 A8C9A27BBE9; Mon, 12 Dec 2022 14:29:12 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 32B3227BBEB for ; Mon, 12 Dec 2022 14:29:11 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jmx-0005kM-9b; Mon, 12 Dec 2022 09:28:15 -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 1p4jmr-0005Xh-5Z for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:09 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmq-0006Db-SF for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmq-0007W3-NG for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:08 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 12/18] gnu: python-flask-restful: Update to 0.3.9. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085528328809 (code B ref 60009); Mon, 12 Dec 2022 14:28:08 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:28:03 +0000 Received: from localhost ([127.0.0.1]:53294 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmk-0007UQ-Ei for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:03 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21074) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmi-0007U4-Nr for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:01 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855279; cv=none; d=zohomail.com; s=zohoarc; b=fiY0MAZQV9HDzxviw4kYnFk9jt7vAISvfaaVFCBP+795G55zmRAStEA5ECSdJBLFncMMPQfqttTCeuU1nqOt8l4YREevhRnApq7kTifrPxXP/jTb8QbBld1pxoW0EGNebUeX9ArpeiCegwNXlrftVroh28+x9EjcVCmEZdzHBKo= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855279; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=Isso4PT/bf1mBzmav1+EXkrhAbYZinCRo4d6VjfA4yE=; b=W6t1fnrRiHCL1C5P+iCQqDJhWc95Txb4UKiqqPO0jDbcb/vFQ2H9ob7ydKTigTr/LSKwOycboh6Jw/yDaYMBVa0OzHHLswvhxsf8Oo5/gIJkGm8xRNRR6HJ0vyUf7CpqTlcjnr3sbmDj81J1Zvu5xGjvuWEqNTnvoi4qKZ81Dx0= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855279; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=Isso4PT/bf1mBzmav1+EXkrhAbYZinCRo4d6VjfA4yE=; b=aqB1WKDQ3yYQpzJnMC4im8uPU15EAFS+E7p/PHNcN9f3sKE+pJHzoY9mMWppfj+T pOcF97zMH3twTgDpX035zcsqRclqO9tJwnLMQ4CyCMb0/2e23nJNm29iUzsMFdooNVC Bur21jajT6B05ZUn3g4/R6RKrpz6M1WPNs2MxvX8= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855276036211.12856040822328; Mon, 12 Dec 2022 06:27:56 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:10 +0100 Message-Id: <20221212142716.9460-12-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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/python-web.scm (python-flask-restful): Update to 0.3.9. [source]: Remove patch. [build-system]: Use pyproject-build-system. [arguments]: Disable "test_redirect" test; remove 'fix-imports phase. [native-inputs]: Replace python-nose with python-pytest. * gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/patches/python-flask-restful-werkzeug-compat.patch: Remove file. --- gnu/local.mk | 1 - ...python-flask-restful-werkzeug-compat.patch | 36 ------------------- gnu/packages/python-web.scm | 31 +++++++--------- 3 files changed, 12 insertions(+), 56 deletions(-) delete mode 100644 gnu/packages/patches/python-flask-restful-werkzeug-compat.patch diff --git a/gnu/local.mk b/gnu/local.mk index 295be3c67c..60a422fd7e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1728,7 +1728,6 @@ dist_patch_DATA = \ %D%/packages/patches/python-docopt-pytest6-compat.patch \ %D%/packages/patches/python-execnet-read-only-fix.patch \ %D%/packages/patches/python-fixtures-remove-monkeypatch-test.patch \ - %D%/packages/patches/python-flask-restful-werkzeug-compat.patch \ %D%/packages/patches/python-ipython-documentation-chars.patch \ %D%/packages/patches/python-ipython-documentation-repro.patch \ %D%/packages/patches/python-keras-integration-test.patch \ diff --git a/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch b/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch deleted file mode 100644 index 0e928ef455..0000000000 --- a/gnu/packages/patches/python-flask-restful-werkzeug-compat.patch +++ /dev/null @@ -1,36 +0,0 @@ -We need one patch on top of 0.3.8 for compatibility with Werkzeug 1.0. - -Taken from upstream: -https://github.com/flask-restful/flask-restful/commit/73376a488907af3042b52678ac4c23f8a8911e5b - -diff --git a/tests/test_api.py b/tests/test_api.py -index f7f8e661..6795d362 100644 ---- a/tests/test_api.py -+++ b/tests/test_api.py -@@ -445,7 +445,9 @@ def test_handle_non_api_error(self): - - resp = app.get("/foo") - self.assertEquals(resp.status_code, 404) -- self.assertEquals('text/html', resp.headers['Content-Type']) -+ # in newer versions of werkzeug this is `text/html; charset=utf8` -+ content_type, _, _ = resp.headers['Content-Type'].partition(';') -+ self.assertEquals('text/html', content_type) - - def test_non_api_error_404_catchall(self): - app = Flask(__name__) -diff --git a/tests/test_reqparse.py b/tests/test_reqparse.py -index 2f1fbedf..9776f17c 100644 ---- a/tests/test_reqparse.py -+++ b/tests/test_reqparse.py -@@ -2,9 +2,9 @@ - import unittest - from mock import Mock, patch - from flask import Flask --from werkzeug import exceptions, MultiDict -+from werkzeug import exceptions - from werkzeug.wrappers import Request --from werkzeug.datastructures import FileStorage -+from werkzeug.datastructures import FileStorage, MultiDict - from flask_restful.reqparse import Argument, RequestParser, Namespace - import six - import decimal diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 7543e05f47..18c0b47b67 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -3924,35 +3924,28 @@ (define-public python-flask-jwt (define-public python-flask-restful (package (name "python-flask-restful") - (version "0.3.8") + (version "0.3.9") (source (origin (method url-fetch) (uri (pypi-uri "Flask-RESTful" version)) - (patches (search-patches "python-flask-restful-werkzeug-compat.patch")) (sha256 (base32 - "05b9lzx5yc3wgml2bcq50lq35h66m8zpj6dc9advcb5z3acsbaay")))) - (build-system python-build-system) + "0gm5dz088v3d2k1dkcp9b3nnqpkk0fp2jly870hijj2xhc5nbv6c")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-imports - (lambda _ - (substitute* "flask_restful/__init__.py" - (("flask\\.helpers") "flask.scaffold"))))))) + ;; This test fails because '/' is not 'http://localhost/'. + (list #:test-flags '(list "-k" "not test_redirect"))) (propagated-inputs - (list python-aniso8601 python-flask python-pytz)) + (list python-aniso8601 python-flask python-pytz)) (native-inputs - (list ;; Optional dependency of Flask. Tests need it. - python-blinker python-mock ; For tests - python-nose)) ;for tests - (home-page - "https://www.github.com/flask-restful/flask-restful/") - (synopsis - "Flask module for creating REST APIs") + (list python-blinker + python-mock + python-pytest)) + (home-page "https://www.github.com/flask-restful/flask-restful/") + (synopsis "Flask module for creating REST APIs") (description - "This package contains a Flask module for creating REST APIs.") + "This package contains a Flask module for creating REST APIs.") (license license:bsd-3))) (define-public python-flask-basicauth From patchwork Mon Dec 12 14:27:11 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45203 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 7548027BBEB; Mon, 12 Dec 2022 14:29:23 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 1885027BBE9 for ; Mon, 12 Dec 2022 14:29:22 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jmt-0005cN-BE; Mon, 12 Dec 2022 09:28:11 -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 1p4jmr-0005Yh-Ig for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:09 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jmr-0006E0-Aq for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:09 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jmr-0007WA-60 for guix-patches@gnu.org; Mon, 12 Dec 2022 09:28:09 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 13/18] gnu: python-marshmallow: Update to 3.19.0. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:28:09 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085528728865 (code B ref 60009); Mon, 12 Dec 2022 14:28:09 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:28:07 +0000 Received: from localhost ([127.0.0.1]:53305 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmo-0007VS-CA for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:06 -0500 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21741) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmk-0007UN-NN for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:03 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855280; cv=none; d=zohomail.com; s=zohoarc; b=ik6Vo5ZEemNNg0gbS85aDBK7m6IL6aBfk8rlkGQ9VOII7eUyyTjqaSE/s4YRwDlGHW0KxvJYxWTXl3mjyiDny1Z8gIvbn83fG7EMfZq4tGhfD8Wq69bekvRCQuJwm4CaH+22zcsMX/vZ56iy2kjwGRJaPZmFZvL3KJvXVQBMNjM= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855280; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=dIkx2Yu0pjvXF9lRAoaHqd7uUdrGVg5KJmDrt1pYrp0=; b=NrqHLpe22BlkCxThGpGY7ZJ8vzdN9gc8kU9XdOUiWxi85OcWig2Dmszm2RnIsd/JiLQbbGUHdP/8qK+XGokMXl94iWyqMNCqbOro54lVvBYJQ48fj1wOSPBRcRsRSefMucX3nszHVk+dHcmIEmtdq8Ys6nirNokV9tqz7cP2kR8= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855280; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=dIkx2Yu0pjvXF9lRAoaHqd7uUdrGVg5KJmDrt1pYrp0=; b=Pfp6HiBb1EtpK417bUP3vnzsVBHmG4/O6CXEIgTN1vzOY3eC5CChDRHzNQY3N3yA mmx0o1hapgnnV2lFoDplDwuIYZyuqdYlHueaRzDRXuzQVqnQI7PSbV+FAfInr2ono/G UuwRa1gFXnFxGV6Di/47gSDFezX0iGR7QpD+aqv0= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855279081850.7566964022419; Mon, 12 Dec 2022 06:27:59 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:11 +0100 Message-Id: <20221212142716.9460-13-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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/python-xyz.scm (python-marshmallow): Update to 3.19.0. [build-system]: Use pyproject-build-system. [propagated-inputs]: Remove python-dateutil and python-simplejson; add python-packaging. [native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy, python-pre-commit, and python-simplejson. --- gnu/packages/python-xyz.scm | 31 ++++++++++++++++++------------- 1 file changed, 18 insertions(+), 13 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index c63ba212b0..7d9f420412 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -20953,24 +20953,29 @@ (define-public python-flex (define-public python-marshmallow (package (name "python-marshmallow") - (version "3.9.1") + (version "3.19.0") (source (origin - (method url-fetch) - (uri (pypi-uri "marshmallow" version)) - (sha256 - (base32 - "0kizhh3mnhpa08wfnsv1gagy22bpxzxszgbiylkhpz1d8qvwrykk")))) - (build-system python-build-system) + (method url-fetch) + (uri (pypi-uri "marshmallow" version)) + (sha256 + (base32 + "0y6vpq2p5841kcw2qil68la0rx9z1vmxzj3dxjv99kjhsq7jq0wh")))) + (build-system pyproject-build-system) (propagated-inputs - (list python-dateutil python-simplejson)) + (list python-packaging)) (native-inputs - (list python-pytest python-pytz)) + (list python-flake8 + python-flake8-bugbear + python-mypy + python-pre-commit + python-pytest + python-pytz + python-simplejson)) (home-page "https://github.com/marshmallow-code/marshmallow") - (synopsis "Convert complex datatypes to and from native - Python datatypes") - (description "@code{marshmallow} provides a library for converting - complex datatypes to and from native Python datatypes.") + (synopsis "Convert complex datatypes to and from native Python datatypes") + (description "@code{marshmallow} provides a library for converting complex +datatypes to and from native Python datatypes.") (license license:expat))) (define-public python-marshmallow-jsonapi From patchwork Mon Dec 12 14:27:12 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45204 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 22A7227BBEB; Mon, 12 Dec 2022 14:29:27 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 A9FD427BBE9 for ; Mon, 12 Dec 2022 14:29:25 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jnn-0006nD-RB; Mon, 12 Dec 2022 09:29:07 -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 1p4jni-0006jt-MG for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jni-0006Sn-Bx for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jni-0007XQ-5V for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 14/18] gnu: python-apispec: Update to 6.0.2. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:29:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085529128919 (code B ref 60009); Mon, 12 Dec 2022 14:29:02 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:28:11 +0000 Received: from localhost ([127.0.0.1]:53314 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jms-0007WM-UA for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:11 -0500 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21742) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmo-0007VT-OL for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:07 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855284; cv=none; d=zohomail.com; s=zohoarc; b=bynXvQLufmMQHdYPnso241TsyFu68v1K00SaK/4y3XKwfhM3pqD/CpXDQ1RkazkRH0I6DqdebHpT1Rp2HU6+WSrHdrNXXx+fU0a91+3OqYSI3LpEGRjFYcYMjhgz4RUqCuSc+UUtlzwsTb9d/asBtPgbkVyPRGJEAKj4uQcBXx4= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855284; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=Dq96hlKHsVa0uh0SanRbtzoAeP02AYxu5noLFWdB894=; b=nIsEsFg3tdpHR5bwe8nNOJfYOUJ5uvKdRaA54BGlUzXgfVTTlExZUGeWzeuiU3zaBJKrXkYSKAvkZmRIy08Kf1T798rPQ79KEF5vO6JOaFcZFQWZtl03MwJGrSwS/1dpf8/DZApMwGRWvcdvXoxkCza2nEE7D1MnM2QkxFQ6Fj4= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855284; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=Dq96hlKHsVa0uh0SanRbtzoAeP02AYxu5noLFWdB894=; b=HPTUV/fpjVCe/85TVxNy95U/wXQ4WMNiSKjFgSzGXFzk494roSAXS/zlvT/2c+80 2ChZmhgnfUcNqgthq2V8Uu0vMhXaZIlKzvdUU8DfXktYmfVfm4WJqjMwfp7Y1NqKFRV mOVh+Zpx+G57CbNMnozwvWPFUYXdAJVVEfOgqiP4= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855282174760.6859950109064; Mon, 12 Dec 2022 06:28:02 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:12 +0100 Message-Id: <20221212142716.9460-14-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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/python-xyz.scm (python-apispec): Update to 6.0.2. [build-system]: Use pyproject-build-system. [arguments]: Disable test through test-flags, not by replacing the 'check phase. [propagated-inputs]: Remove python-pyyaml; add python-packaging. [native-inputs]: Add python-flake8, python-flake8-bugbear, python-mypy, python-pre-commit, and python-pyyaml. --- gnu/packages/python-xyz.scm | 39 ++++++++++++++++++++----------------- 1 file changed, 21 insertions(+), 18 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7d9f420412..37c2caf400 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21011,33 +21011,36 @@ (define-public python-marshmallow-jsonapi (define-public python-apispec (package (name "python-apispec") - (version "4.0.0") + (version "6.0.2") (source (origin - (method url-fetch) - (uri (pypi-uri "apispec" version)) - (sha256 + (method url-fetch) + (uri (pypi-uri "apispec" version)) + (sha256 (base32 - "12n4w5zkn4drcn8izq68vmixmqvz6abviqkdn4ip0kaax3jjh3in")))) - (build-system python-build-system) + "11vqxwdxmm7qmyhdbxk4gnx37nbzmn266ah92gi4pvzd76vq0vg7")))) + (build-system pyproject-build-system) (arguments - '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "pytest" "-vv" - ;; Disable validation tests since they require - ;; the optional 'prance' library which is not - ;; yet in Guix. - "-k" "not openapi_tools_validate")))))) + (list + ;; Disable validation tests since they require + ;; the optional 'prance' library which is not + ;; yet in Guix. + #:test-flags '(list "-k" "not openapi_tools_validate"))) (propagated-inputs - (list python-pyyaml)) + (list python-packaging)) (native-inputs - (list python-pytest python-marshmallow)) + (list python-flake8 + python-flake8-bugbear + python-marshmallow + python-mypy + python-pre-commit + python-pytest + python-pyyaml)) (home-page "https://github.com/marshmallow-code/apispec") (synopsis "Swagger/OpenAPI specification generator") (description "@code{python-apispec} is a pluggable API specification - generator. It currently supports the OpenAPI specification, formerly known - as Swagger.") +generator. It currently supports the OpenAPI specification, formerly known as +Swagger.") (license license:expat))) (define-public python-apispec-webframeworks From patchwork Mon Dec 12 14:27:13 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45206 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 D1E8827BBEB; Mon, 12 Dec 2022 14:29:44 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 C84F227BBE9 for ; Mon, 12 Dec 2022 14:29:43 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jno-0006o1-6k; Mon, 12 Dec 2022 09:29:08 -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 1p4jni-0006kQ-W8 for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jni-0006T9-Ns for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jni-0007XX-Jb for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 15/18] gnu: python-pyjwt: Update to 2.6.0. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:29:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085529128925 (code B ref 60009); Mon, 12 Dec 2022 14:29:02 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:28:11 +0000 Received: from localhost ([127.0.0.1]:53316 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmt-0007WO-Di for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:11 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21083) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmq-0007W1-P7 for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:09 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855286; cv=none; d=zohomail.com; s=zohoarc; b=Elz/0EyNxpd/NyiX29cgvP/HrpQV1tBQ4KepWZmBya4W4TyfWRQHQHRtuv/g/HLY9in86wXh1thi1yy2/n0TA31PUPoPJygFylcA6tbV9jbgndobMqBWOS9fzt/6Fs2P43yMybbXpyNkbUiCMlThscjL5m8RbumkKNz59tyuycU= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855286; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=x5PTpIHZKpqKpg3Xr6lUVuKyldseljtA4aIJs8zJFRw=; b=VDRDtVH9oMYmkVeE6ggcwVm2ACJW4kgJsydkWLHY5bNj+HnWDgY7uqtGHmrv2qYY2L5VGaZWmD092XprmfAzA/0cUOltJfVzNKNxOl7iRVV0zmrgSH5xGodGJfr5UDay3LfjbdFEJBXvZ9FvcS+Zy2QPZY2cknghV665Oim7UvA= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855286; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=x5PTpIHZKpqKpg3Xr6lUVuKyldseljtA4aIJs8zJFRw=; b=TATee+Hsf6p943jfO+SgdjC/VTtISoriLDPo1FW271Es9y1xDUd+M1i6qFfJ9Vn+ tQV1ugA3ZNb9AG1Yo1cog57HkljWmFmJRWf6Te4wQmJtrVm/oIZOzN5fbc3xb2psM3i oyt57oD2gvPVi2XEejuWtxdpZvG5ytsVPdctF0yQ= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855285211845.4445288806024; Mon, 12 Dec 2022 06:28:05 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:13 +0100 Message-Id: <20221212142716.9460-15-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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/python-xyz.scm (python-pyjwt): Update to 2.6.0. [build-system]: Use pyproject-build-system. [arguments]: Remove. [native-inputs]: Add pytohn-coverage, python-pre-commit, python-sphinx, and python-sphinx-rtd-theme. --- gnu/packages/python-xyz.scm | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 37c2caf400..a6983e4411 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -4087,23 +4087,22 @@ (define-public python-text-unidecode (define-public python-pyjwt (package (name "python-pyjwt") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (pypi-uri "PyJWT" version)) (sha256 (base32 - "1fmbcwfw1463wjzwbcgg3s16rad6kfb1mc5y7jbkp6v9ihh0hafl")))) - (build-system python-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-vv"))))))) + "1z85kwr945rbzrn5wabrsmck5x8disa9wc7b3y5gci7w65z5qa39")))) + (build-system pyproject-build-system) (native-inputs - (list python-cryptography python-pytest)) + (list python-coverage + python-cryptography + python-pre-commit + python-pytest + python-sphinx + python-sphinx-rtd-theme)) (home-page "https://github.com/progrium/pyjwt") (synopsis "JSON Web Token implementation in Python") (description From patchwork Mon Dec 12 14:27:14 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45201 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 4128027BBEC; Mon, 12 Dec 2022 14:29:16 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 6E31027BBE9 for ; Mon, 12 Dec 2022 14:29:15 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jnr-0006vI-2g; Mon, 12 Dec 2022 09:29:11 -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 1p4jnj-0006l7-Do for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jnj-0006TK-5P for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jnj-0007Xe-0g for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 16/18] gnu: python-flasgger: Update to 0.9.5. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:29:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085529628947 (code B ref 60009); Mon, 12 Dec 2022 14:29:02 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:28:16 +0000 Received: from localhost ([127.0.0.1]:53321 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmx-0007Wp-Ry for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:16 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21089) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmu-0007Wa-PK for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:13 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855290; cv=none; d=zohomail.com; s=zohoarc; b=U3O+89nMc5o9UBHHDDTKlnObB8Zz7mTekBMsT8SdXirnrE2alrCSitQMnzNQarzk3TEQOusSP6Mp55J5GUDZf6PsZNwWYEqJXGVrShofb1+vbx+k/GGk3bDS1xUBQ6ICxsb7BbmYerXR8sIGXD4n6slay2c0tM+MmkYkIT1wUAw= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855290; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=DdzFFxl8ayvO3/B/Mgj4uBgGBlmCueMnagH0IPXVWKA=; b=BzyznHvL+gwSOsl1LtbJyWNBqeiujkWxHlXttpq2KZENduvIyB68D+Ubw959ChlPERRs740jhm5QTLqMV8ogV9ulV4JYHX4bJC4IPBIhMGRlCa7dPIpknM+yqPr+SS5bAHPpNI8vTC0jiQu7du+WfwRCo4oYHViIEo/T53//FJI= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855290; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=DdzFFxl8ayvO3/B/Mgj4uBgGBlmCueMnagH0IPXVWKA=; b=SYTFG0cWWgOPgElYdcvgO6N+rH5ScAfTtZugwsZc0+Nb1xQHxQA2QeR+eMy/GIgk wrztZ2kJQjIYEjMV7WcHLdBy9IvbFqAdDYrZRP7O8z21S8Qm4bAGLsyDaWt5jU7qplG 9tPYLU/LKGplujEw7HvMFBBUm/32Z0XyIVFp/1LQ= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855288263517.0919665395581; Mon, 12 Dec 2022 06:28:08 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:14 +0100 Message-Id: <20221212142716.9460-16-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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/python-xyz.scm (python-flasgger): Update to 0.9.5. [build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase; add 'prepare-check phase; disable "test_swag" test via #:test-flags. [native-inputs]: Add python-apispec-webframeworks and python-flask-jwt. --- gnu/packages/python-xyz.scm | 36 +++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 15 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a6983e4411..e273e71fa0 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -21073,7 +21073,7 @@ (define-public python-apispec-webframeworks (define-public python-flasgger (package (name "python-flasgger") - (version "0.6.3") + (version "0.9.5") (source (origin (method git-fetch) @@ -21082,29 +21082,35 @@ (define-public python-flasgger (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0yydxsyjnc0clbrjqb1n7587l6cdqvwdagwxk5hkx01qwdfbkvpn")))) - (build-system python-build-system) + (base32 "0a2djgfq905a4in16068qz0ikg88dm4nbckaamhaz2v9khllr0bi")))) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* "Makefile" - (("flake8 flasgger --ignore=F403") - "flake8 flasgger --ignore=E731,F403")) - (invoke "py.test")))))) + (list + ;; This test fails due to missing fixtures + #:test-flags '(list "-k" "not test_swag") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'prepare-check + (lambda _ + ;; This requires a dummy package "flasgger_package" to be installed. + (delete-file "examples/package_example.py") + ;; These fail with an internal server error + (for-each delete-file '("examples/marshmallow_apispec.py" + "examples/validation.py"))))))) (propagated-inputs (list python-flask python-pyyaml python-jsonschema python-mistune python-six)) (native-inputs - (list python-decorator + (list python-apispec + python-apispec-webframeworks + python-decorator python-flake8 + python-flask-jwt python-flask-restful python-flex - python-pytest - python-pytest-cov python-marshmallow - python-apispec)) + python-pytest + python-pytest-cov)) (home-page "https://github.com/rochacbruno/flasgger/") (synopsis "Extract Swagger specs from your Flask project") (description "@code{python-flasgger} allows extracting Swagger specs From patchwork Mon Dec 12 14:27:15 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45209 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 BD39527BBEC; Mon, 12 Dec 2022 14:29:58 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 3471927BBE9 for ; Mon, 12 Dec 2022 14:29:58 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jnp-0006ra-Ho; Mon, 12 Dec 2022 09:29:09 -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 1p4jnj-0006lO-Sg for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:07 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jnj-0006TR-J1 for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jnj-0007Xl-EL for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 17/18] gnu: seqmagick: Update to 0.8.4. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:29:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085529828955 (code B ref 60009); Mon, 12 Dec 2022 14:29:03 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:28:18 +0000 Received: from localhost ([127.0.0.1]:53323 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jn0-0007Ww-6h for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:18 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21091) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jmx-0007Wi-1j for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:15 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855292; cv=none; d=zohomail.com; s=zohoarc; b=Tl6GHNdLprtHj9Kg2g51QFnXlpQnbHERpv6/bRTC7+wXqMdpcmcsC4JIKpFNMZC3usUGT6kmQ7f0FGPSR/5uR9E0cyrHZlJihSqY60RtxhzJnBYigQEKq+oDNrX4Z5dBgEpcQ7eGg3rfxpM0tIRuvAFjPfgimfloIGW89WxY3nI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855292; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=sO2ZcN5oS+uAw9cDho6kYlxQtiMWxHMzZo++KqSUpiQ=; b=YDPELWCt6QdZk8NgcZDWnZ27cDqucxnux6ogKuAEzO9O04uISFRzEdSBcBzeitdtWsbd6S1fj+ceEVfhu3wEfz94y0BBKeCTA8ZMg2EHmmfQ0oXVDWgABb/8XsDHCqYDtFYcBulOTrKuV49/Pn4228azUXzGCO7ESYmgHGM9wzc= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855292; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=sO2ZcN5oS+uAw9cDho6kYlxQtiMWxHMzZo++KqSUpiQ=; b=WfhkfeId64zjdZwKGLDiTSYhuP+e9fxViT+w/k721+OlvMU/HvNGLZiNfO/kvXXH iW+2r6ex0cI2o9tXEJPM+IN70/OFIYahH5D88NBQ6WaKukeMkN3swI9XNAPlP7GBZm/ 6B3+c6msNxKJD95Cm7QQd1/CiIGfsVOpPjjzG4P0= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855291398117.28704174865652; Mon, 12 Dec 2022 06:28:11 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:15 +0100 Message-Id: <20221212142716.9460-17-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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 (seqmagick): Update to 0.8.4. [build-system]: Use pyproject-build-system. [inputs]: Add python-pygtrie. [native-inputs]: Replace python-nose with python-pytest. --- gnu/packages/bioinformatics.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4044ff625e..e8a8ddc361 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6945,19 +6945,19 @@ (define-public seqan-1 (define-public seqmagick (package (name "seqmagick") - (version "0.8.0") + (version "0.8.4") (source (origin (method url-fetch) (uri (pypi-uri "seqmagick" version)) (sha256 (base32 - "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b")))) - (build-system python-build-system) + "0c6skyig8fyylnbj4597pjj9h0dn36rkxrhwd34yrsc6k6f7r8a0")))) + (build-system pyproject-build-system) (inputs - (list python-biopython)) + (list python-biopython python-pygtrie)) (native-inputs - (list python-nose)) + (list python-pytest)) (home-page "https://github.com/fhcrc/seqmagick") (synopsis "Tools for converting and modifying sequence files") (description From patchwork Mon Dec 12 14:27:16 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45208 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 8403327BBEC; Mon, 12 Dec 2022 14:29:52 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,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 E643B27BBE9 for ; Mon, 12 Dec 2022 14:29:51 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jnp-0006rW-HU; Mon, 12 Dec 2022 09:29:09 -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 1p4jnk-0006lP-5n for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:07 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jnj-0006TW-U7 for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jnj-0007Xs-Pp for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 18/18] gnu: cnvkit: Update to 0.9.9. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:29:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085530228967 (code B ref 60009); Mon, 12 Dec 2022 14:29:03 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:28:22 +0000 Received: from localhost ([127.0.0.1]:53326 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jn3-0007X9-FH for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:21 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21092) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jn0-0007Wx-PY for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:19 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855296; cv=none; d=zohomail.com; s=zohoarc; b=QVBQo1u5klAa4WHw7qbzgRVS+tGwC4coDZLS1b++wDCgBTF2X4blHkBWpyE6kCiTqMoCHAGowTPD+//ylHFgT4jbaYE8KmQoscaGSet5cr7974C9JSnD1UWbKRFGGyR+DP56Tgv0WDx3fkQ/MiNVL/hxYAHaIDqyxZvE4yt8pEA= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855296; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=0jZtos+EXI10E0GMGchAproh9ZH8+5zA0Deow8ZwCWA=; b=K8Nuwso7u4El7oHSV1ROs8QyrbpKp+/LFd0FiJ++S9D4/fyzkcZKeP3qVPM2punoFDLQ5Bo6fGkqGnEt6VHNfITXslu4VM001v0Ija7hsCrDjaKb/+Jr96kEiGYqVRGbbzz64nngWvKZrmO4TmG5xrxh40nRwVfabDcuBiU7WHQ= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855296; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=0jZtos+EXI10E0GMGchAproh9ZH8+5zA0Deow8ZwCWA=; b=Ry3o/IfJXVliQw2TuKqbffzwdhpw3HwtRMLZG8Z4nvN0RIgSO0xEaPameT5yt0jh q1srGGoqb9qhqQNCWJIJao4gSQi3iqPq1bUeBfFCsRU0pvXBRGxIujP5ALL9f9hpD5i InwRyK677gJG0oq5V2+OppDVTGNasshUSTa4Gmo0= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855294432507.2421434134757; Mon, 12 Dec 2022 06:28:14 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:16 +0100 Message-Id: <20221212142716.9460-18-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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 (cnvkit): Update to 0.9.9. [build-system]: Use pyproject-build-system. [arguments]: Relax restriction on python-joblib. [propagated-inputs]: Add python-pomegranate and python-scikit-learn. --- gnu/packages/bioinformatics.scm | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e8a8ddc361..5e2e0796a0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14225,7 +14225,7 @@ (define-public nanopolish (define-public cnvkit (package (name "cnvkit") - (version "0.9.5") + (version "0.9.9") (source (origin (method git-fetch) @@ -14234,17 +14234,28 @@ (define-public cnvkit (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0g2f78k68yglmj4fsfmgs8idqv3di9aj53fg0ld0hqljg8chhh82")))) - (build-system python-build-system) + (base32 "1q4l7jhr1k135an3n9aa9wsid5lk6fwxb0hcldrr6v6y76zi4gj1")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; See upstream commit eee0f6eaec57d5c6e58142d661979f3aacc5f76a + (add-after 'unpack 'compatibility + (lambda _ + (substitute* "setup.py" + (("'joblib.*") ""))))))) (propagated-inputs (list python-biopython python-future python-matplotlib python-numpy - python-reportlab python-pandas - python-pysam + python-pomegranate python-pyfaidx + python-pysam + python-reportlab + python-scikit-learn python-scipy ;; R packages r-dnacopy))