From patchwork Sun Jun 6 00:06:51 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 29950 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 7923D27BC81; Sun, 6 Jun 2021 01:08:19 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 08D3927BC78 for ; Sun, 6 Jun 2021 01:08:19 +0100 (BST) Received: from localhost ([::1]:36124 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lpgKw-0002t6-3t for patchwork@mira.cbaines.net; Sat, 05 Jun 2021 20:08:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:54466) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lpgKg-0002a7-OS for guix-patches@gnu.org; Sat, 05 Jun 2021 20:08:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38773) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lpgKg-0004Ag-I4 for guix-patches@gnu.org; Sat, 05 Jun 2021 20:08:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lpgKg-0004p9-DS for guix-patches@gnu.org; Sat, 05 Jun 2021 20:08:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#46955] [PATCH 3/3] gnu: python-cooler: Update to 0.8.11. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 06 Jun 2021 00:08:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46955 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <46955@debbugs.gnu.org> Cc: rekado@elephly.net, =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmE=?= =?utf-8?b?yJljdQ==?= Received: via spool by 46955-submit@debbugs.gnu.org id=B46955.162293804818489 (code B ref 46955); Sun, 06 Jun 2021 00:08:02 +0000 Received: (at 46955) by debbugs.gnu.org; 6 Jun 2021 00:07:28 +0000 Received: from localhost ([127.0.0.1]:50317 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgK8-0004o8-1r for submit@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:28 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:56081) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgK6-0004nj-TT for 46955@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:27 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 928D2A00E3; Sun, 6 Jun 2021 02:07:21 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received:received:received; s=mdc; t= 1622938041; x=1624752442; bh=Dk6uvdbfmMUP4XEWvIIrgZsuEE5DpUf1e76 IY/H9yIE=; b=gh4fNZofUfwLo/1189M/nEmrlxXmgeiXzJzOjof8f3MAIQuaUUv WFZQq3zIY29ZaUfFHZn/p7iSdhl5a6mK4Z3OEbTWqk5E9v5Ju3bd1vjg+RSlfLIK Kg83a2VFpIUKpH4exPNSdLOOT67dtp84uvlseh1jxF+EcNhuHiOjSm4g= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 4IxNbE4hBRqI; Sun, 6 Jun 2021 02:07:21 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS; Sun, 6 Jun 2021 02:07:21 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2242.10; Sun, 6 Jun 2021 02:07:20 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sun, 6 Jun 2021 02:06:51 +0200 Message-ID: <20210606000651.28252-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.31.1 In-Reply-To: <20210606000651.28252-1-madalinionel.patrascu@mdc-berlin.de> References: <20210606000651.28252-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3080-8.6.1012-26202.003 X-TM-AS-Result: No-10--2.193700-8.000000 X-TMASE-MatchedRID: b81qNyJin326/eEqqZaZmj8Ckw9b/GFeTJDl9FKHbrn7fZJfDdCIXISC l3uvYUiSC6+Zjvylmgt6n3hIvN5dLV1nLdLFTV2cB8FxO/BQHsIXivwflisSrPn6214PlHOFxVZ wHGSRvcr7bbB/MBzIMwa+LGYKVz1S64qzaFKxje/p9R8QuoVQfwoXSOLC5a44Mv8YehqjR1W2Ed aacwTXAwjQkSkt0eZ8xtgTkG+GaOc7mT8/EEC+/tqQ6Du6Gk+zSoaRTYgt4N4R34ro7k23nchyR F2A1zUTGQye9itdQoSTW+R0C23mx+06nIdMxLTR194/5X9VfCzy36l+EEw5vMWgQbecfk3OmA0y ITMNzjl9LQinZ4QefPcjNeVeWlqY+gtHj7OwNO22utO5qEfOUQagFwm5AKiUQc8ZI+qm+CvOWb5 27F6P3e5+ZKC55ULt9iVjwUzsDRMiZttKiK21f3MwptG1PBbpxe/6SX9BFtprMM4SZ8lXNG/H7L hIKjO20bWl8H0Q2RO0ML47Km+X9EYOAQXCbpqgPpCuffGH9zI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.193700-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26202.003 X-TM-SNTS-SMTP: 67D3CBE25DC29F6B807DC531479B39371E3A2A267D8CCFAAAD380A15E881181C2000:F 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11. --- gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++------ 1 file changed, 32 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dab097381a..988f663ceb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11717,15 +11717,34 @@ fasta subsequences.") (define-public python-cooler (package (name "python-cooler") - (version "0.8.7") + (version "0.8.11") (source (origin (method url-fetch) (uri (pypi-uri "cooler" version)) (sha256 (base32 - "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp")))) + "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "tests/test_create.py" + (("def test_roundtrip") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_roundtrip"))) + (substitute* "tests/test_util.py" + (("def test_fetch_chromsizes") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_fetch_chromsizes"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs `(("python-asciitree" ,python-asciitree) ("python-biopython" ,python-biopython) @@ -11741,11 +11760,18 @@ fasta subsequences.") ("python-pysam" ,python-pysam) ("python-pyyaml" ,python-pyyaml) ("python-scipy" ,python-scipy) - ("python-simplejson" ,python-simplejson))) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six) + ("python-sparse" ,python-sparse))) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) - (home-page "https://github.com/mirnylab/cooler") + `(("python-codecov" ,python-codecov) + ("python-ipytree" ,python-ipytree) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-flake8" ,python-pytest-flake8))) + ;;almost all the projects of the Mirnylab are moved under Open2C umbrella + (home-page "https://github.com/open2c/cooler") (synopsis "Sparse binary format for genomic interaction matrices") (description "Cooler is a support library for a sparse, compressed, binary persistent