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Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 03 Jun 2021 23:26:02 +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=B46955.16227627462352 (code B ref 46955); Thu, 03 Jun 2021 23:26:02 +0000 Received: (at 46955) by debbugs.gnu.org; 3 Jun 2021 23:25:46 +0000 Received: from localhost ([127.0.0.1]:45000 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lowif-0000bs-L6 for submit@debbugs.gnu.org; Thu, 03 Jun 2021 19:25:45 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:37427) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lowie-0000bY-Pl for 46955@debbugs.gnu.org; Thu, 03 Jun 2021 19:25:45 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 656DB1602F8; Fri, 4 Jun 2021 01:25:39 +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= 1622762738; x=1624577139; bh=A4De0ibjdllsAjWcVI7X9bSfi/Zwfp0ls+S xsWWiGRI=; b=ivurtg9Bu8xhL64IsD5lZkDAZFc/WsBbeeaAugNvq99Gvw6SV2V u9QR8kDm8ax4rRbxp7dC/WAuS4za2kivFuLlkFBFAimMp93jyacPSlJaadEBbYSy DsPo7d7ZlENqqZ2p68aP9nWWW/aJbjQ9ak500ucLvNAzeqpFiSwsKLeA= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id Jw72f-pvJfb1; Fri, 4 Jun 2021 01:25:38 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS; Fri, 4 Jun 2021 01:25:38 +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; Fri, 4 Jun 2021 01:25:38 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 4 Jun 2021 01:25:03 +0200 Message-ID: <20210603232503.29253-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.31.1 In-Reply-To: <20210603232503.29253-1-madalinionel.patrascu@mdc-berlin.de> References: <20210603232503.29253-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3080-8.6.1012-26198.003 X-TM-AS-Result: No-10--2.378700-8.000000 X-TMASE-MatchedRID: TMejBmzMW4e6/eEqqZaZmj8Ckw9b/GFeTJDl9FKHbrn7fZJfDdCIXISC l3uvYUiSC6+Zjvylmgt6n3hIvN5dLV1nLdLFTV2cB8FxO/BQHsIXivwflisSrPn6214PlHOFxVZ wHGSRvcr7bbB/MBzIMwa+LGYKVz1S64qzaFKxje/p9R8QuoVQfwoXSOLC5a44Mv8YehqjR1W2Ed aacwTXA8A5YhoszcEGg8kdcveGTlnI2RqSAXh33s6KFiylFM8l4k1wcu9E2kRpUUxjTnX0eo/j4 gKDoVqZJhu/MapJ6V4C0+r3OCivMyiFL2ygqPFl3QqJN4m15UHrixWWWJYrHx8TzIzimOwPC24o EZ6SpSk6XEE7Yhw4FjQQWtYtNU6/3IVHw3xPWBkGBazqvYGxYUYUJKPj8nOwe7VnDznzQ45COE5 0dTAZ9S9LkbgYjPPqUedhAKWTm3FiDcew7W+5ZrdKECLo/klXhRFX0MbNzemQ4JrfEHpLweZmgn jb/yyM1RkHasLA4hI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.378700-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26198.003 X-TM-SNTS-SMTP: 129F3B016466E13E36D76EC05DF58645FC3D1FA20FD491D7A2B69ACF611DD75F2000: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 | 39 ++++++++++++++++++++++++++++----- 1 file changed, 33 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 94d15cc4c0..55e25ab486 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11591,15 +11591,35 @@ 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"))) + #t)) + (replace 'check + (lambda _ + (invoke "python" "-m" "pytest" "-v") + #t))))) (propagated-inputs `(("python-asciitree" ,python-asciitree) ("python-biopython" ,python-biopython) @@ -11615,11 +11635,18 @@ 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