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References: <20210606083144.25207-1-madalinionel.patrascu@mdc-berlin.de> In-Reply-To: <20210606083144.25207-1-madalinionel.patrascu@mdc-berlin.de> Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 07 Jun 2021 11:55:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48863 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: <48863@debbugs.gnu.org> Cc: rekado@elephly.net, =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmE=?= =?utf-8?b?yJljdQ==?= Received: via spool by 48863-submit@debbugs.gnu.org id=B48863.162306689920269 (code B ref 48863); Mon, 07 Jun 2021 11:55:01 +0000 Received: (at 48863) by debbugs.gnu.org; 7 Jun 2021 11:54:59 +0000 Received: from localhost ([127.0.0.1]:54589 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lqDqN-0005Gr-JP for submit@debbugs.gnu.org; Mon, 07 Jun 2021 07:54:59 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:48113) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lqDqK-0005Gc-IB for 48863@debbugs.gnu.org; Mon, 07 Jun 2021 07:54:57 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 379BA300104; Mon, 7 Jun 2021 13:54:50 +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 :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1623066886; x=1624881287; bh=g2u9nKXtICSqM1K5qV1NkcLrjcverPWNJj6g8wthtcM=; b=byj84ObCY2R2 9LubCB1Hn6Ok50H5dVGB4wI462E691mhxnO++znZUZJYnka30WnvUv4mnSOwCrbX wdgle7EbJ9yF+MJ6ajGQ8golUbwk3hL90oszJwcbK/Qq8TuYgSF/SIIcFbL+lbUB IZVzqXiKFgUibs3Wq3k3fnd+QFYEPLo= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id N5mi4PA69sxW; Mon, 7 Jun 2021 13:54:46 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS; Mon, 7 Jun 2021 13:54:46 +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; Mon, 7 Jun 2021 13:54:46 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Mon, 7 Jun 2021 13:53:28 +0200 Message-ID: <20210607115328.28208-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.31.1 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-14.0.0.3080-8.6.1012-26204.007 X-TM-AS-Result: No-10--4.385200-8.000000 X-TMASE-MatchedRID: Wt34ZPi/yT66/eEqqZaZmmvOwg12ikVSLAnNohUyMa3GcoKvwj5q6NJS 7KSX0iF80QrM2nKquR/S1Xndr/786nY5icQIjheV2pDoO7oaT7MXivwflisSrAdkFovAReUog9x e4gtUJtr2f0BS8Vzei7K2ydSXuQZ1WqVlCx+/sImdVNZaI2n6/6QFk5omY4gNTPm/MsQarwN7i8 vAf7tRuxTjRwQRba1vJkAyRNZc6CgaPxeMMHjQbh1kSRHxj+Z5CwT2DH7iMm52ugWlXLnD6SBs0 qFMQOXvjzqLvABc+8g95p1ijjNyRdDew4wHcWTU4vM1YF6AJbbY2hczJbMEQgtuKBGekqUpOlxB O2IcOBa6aEBXtvfJeSl5T7ra+7vA4ARS7EaGVbmQdTL27gf9FzrriapAR9S7hlD4TwdxXmyVM6G /mIMlieAybHfPK8u1GCRwl9rBlAe3ShAi6P5JV4URV9DGzc3pkOCa3xB6S8HmZoJ42/8sjNUZB2 rCwOIS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.385200-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26204.007 X-TM-SNTS-SMTP: 8CF4BFFD603E6622F68E5ED7A3F6EA1526927035F4E6BFD456139D7C157ED07E2000: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-hicmatrix): Update to 15. [source]: Download via git-fetch. [arguments]: Enabled tests. Remove 'relax-requirements phase. [native-inputs]: Add python-pytest. --- gnu/packages/bioinformatics.scm | 37 ++++++++++++++++----------------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2de8a59d3c..02da131fdf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11786,29 +11786,26 @@ such as Hi-C contact matrices.") (define-public python-hicmatrix (package (name "python-hicmatrix") - (version "12") - (source - (origin - ;; Version 12 is not available on pypi. - (method git-fetch) - (uri (git-reference - (url "https://github.com/deeptools/HiCMatrix") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1xhdyx16f3brgxgxybixdi64ki8nbbkq5vk4h9ahi11pzpjfn1pj")))) + (version "15") + (source + (origin + ;;Pypi sources do not contain any test + (method git-fetch) + (uri (git-reference + (url "https://github.com/deeptools/HiCMatrix") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'relax-requirements - (lambda _ - (substitute* '("requirements.txt" - "setup.py") - (("cooler *=+ *0.8.5") - "cooler==0.8.*")) - #t))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs `(("python-cooler" ,python-cooler) ("python-intervaltree" ,python-intervaltree) @@ -11816,6 +11813,8 @@ such as Hi-C contact matrices.") ("python-pandas" ,python-pandas) ("python-scipy" ,python-scipy) ("python-tables" ,python-tables))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/deeptools/HiCMatrix/") (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks") (description