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