From patchwork Sun Jun 6 00:06:49 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 29949 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 8472127BC81; Sun, 6 Jun 2021 01:08:13 +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 EDEA327BC78 for ; Sun, 6 Jun 2021 01:08:12 +0100 (BST) Received: from localhost ([::1]:35734 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lpgKq-0002cE-1t for patchwork@mira.cbaines.net; Sat, 05 Jun 2021 20:08:12 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:54458) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lpgKg-0002Zq-93 for guix-patches@gnu.org; Sat, 05 Jun 2021 20:08:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38771) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lpgKf-0004AO-Uv for guix-patches@gnu.org; Sat, 05 Jun 2021 20:08:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lpgKf-0004ov-JG for guix-patches@gnu.org; Sat, 05 Jun 2021 20:08:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#46955] [PATCH 1/3] gnu: Add python-sparse. References: <76dfa82e-53e2-c4fc-d002-df71f348cdc8@mdc-berlin.de> In-Reply-To: <76dfa82e-53e2-c4fc-d002-df71f348cdc8@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: Sun, 06 Jun 2021 00:08:01 +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=B46955.162293804118462 (code B ref 46955); Sun, 06 Jun 2021 00:08:01 +0000 Received: (at 46955) by debbugs.gnu.org; 6 Jun 2021 00:07:21 +0000 Received: from localhost ([127.0.0.1]:50311 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgJv-0004nT-G6 for submit@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:21 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:38309) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgJs-0004nD-NA for 46955@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:13 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 3C16C1600B8; Sun, 6 Jun 2021 02:07:06 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1622938025; x=1624752426; bh=z09BWfLtSeUg+iUwIuKT8U2XQgaTYM1YTjDc4ZJZTGE=; b=jjQ9AO9qu/qX i1A156klA2G/K4IstZLzjTPeoWAq+8g0dj1bOArEcdQ9FjLBJvSRVNL4loikRpzz jEXRrpHer50gIO7amto/y9xAj//u8GLH9a+H5+TeTVlMUFPnOFcn9BVlvvAHqVm6 VVPamcnVCaMUmmpO1Zdf8dLLXJzjokU= 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 NSEKTyjYoZMW; Sun, 6 Jun 2021 02:07:05 +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; Sun, 6 Jun 2021 02:07:05 +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 02:07:04 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sun, 6 Jun 2021 02:06:49 +0200 Message-ID: <20210606000651.28252-1-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-14.0.0.3080-8.6.1012-26202.003 X-TM-AS-Result: No-10--2.213100-8.000000 X-TMASE-MatchedRID: JsCi/JRnBFH/R1NSMc2qCXycvC6I0dJIS1zwNuiBtITfUZT83lbkEJwl bZPQQ0yzb1TGnuLRfUkctkosP3yazCq+GZ9ZHxIhUYXhMajr0x53G1bsm5zfjMZygq/CPmro6n1 Gl4gVhHhV9cEoYbjAXbc/ZCLk5AauxmNZL79yeAxSFqtD2wqeMV7OZ6hrwwnz/gMNehoKqTuXzC wUPmVFK+awqowSxfEnLb6XLHjqIvT7lPrMqaVmF1XXOFXDx25iF430d3dMHka8B7vl7G5M0USuy wxB3Ejk51xw3PCMlNY3HexY7VSIcWcOYd1wAQIAAD5jSg1rFtBbV4KUZZg3KOcJOFqc/+CEYmUf TlXs3OOTKxCEEoHeWpfAZqrFvhSOow4viWN+bNz0VCHd+VQiHgseQVcTRnF2lwV2iaAfSWeDGx/ OQ1GV8t0H8LFZNFG7doMssNsUwYVtH7py2mvPPfIWdF0cpec123hXtA//3sx6dbk5o2QFfNC4vf Hpz8nv70vMLL1IbJl/vFbd53rshd0wC0yCvbeT4PtO+H6AT5HX7GF+64huyLjmNKuuvgamoYI1e rIuEsW+g2RZj2FKy60Cnu9RmLpv X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.213100-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26202.003 X-TM-SNTS-SMTP: 6FC3FDB4BEA1D5D61810400AA05C087C2A3CFAF259531CB05E39F72620BF9B452000: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/python-xyz.scm(python-sparse): New variable. --- gnu/packages/python-xyz.scm | 47 ++++++++++++++++++++++++++++++++++++- 1 file changed, 46 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b63c2852d5..a4fe31a01f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -67,7 +67,7 @@ ;;; Copyright © 2019, 2020 Giacomo Leidi ;;; Copyright © 2019 Wiktor Żelazny ;;; Copyright © 2019, 2020 Tanguy Le Carrour -;;; Copyright © 2019 Mădălin Ionel Patrașcu +;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Riku Viitanen ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 sirgazil @@ -5147,6 +5147,51 @@ objects.") (define-public python2-colormath (package-with-python2 python-colormath)) +(define-public python-sparse + (package + (name "python-sparse") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sparse" version)) + (sha256 + (base32 + "05lmzckv69cvxavhdr36k803bgr5dl04cppglid1l880xswc759c")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) + (propagated-inputs + `(("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-dask" ,python-dask) + ("python-pytest" ,python-pytest) + ("python-pytest-black" ,python-pytest-black) + ("python-pytest-cov" ,python-pytest-cov))) + (home-page "https://github.com/pydata/sparse/") + (synopsis "Library for multi-dimensional sparse arrays") + (description + "This package implements sparse arrays of arbitrary dimension on top of +@code{numpy} and @code{scipy.sparse}. Sparse array is a matrix in which most +of the elements are zero. @code{python-sparse} generalizes the +@code{scipy.sparse.coo_matrix} and @code{scipy.sparse.dok_matrix} layouts, but +extends beyond just rows and columns to an arbitrary number of dimensions. +Additionally, this project maintains compatibility with the +@code{numpy.ndarray} interface rather than the @code{numpy.matrix} interface +used in @code{scipy.sparse}. These differences make this project useful in +certain situations where @code{scipy.sparse} matrices are not well suited, but +it should not be considered a full replacement. It lacks layouts that are not +easily generalized like @dfn{compressed sparse row/column}(CSR/CSC) and +depends on @code{scipy.sparse} for some computations.") + (license license:bsd-3))) + (define-public python-spectra (package (name "python-spectra") From patchwork Sun Jun 6 00:06:50 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: 29948 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 429F527BC81; Sun, 6 Jun 2021 01:08:09 +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 0BD9127BC78 for ; Sun, 6 Jun 2021 01:08:09 +0100 (BST) Received: from localhost ([::1]:35690 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lpgKm-0002aE-47 for patchwork@mira.cbaines.net; Sat, 05 Jun 2021 20:08:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:54460) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lpgKg-0002Zr-BQ for guix-patches@gnu.org; Sat, 05 Jun 2021 20:08:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38772) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lpgKg-0004AU-4e 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-0004p2-04 for guix-patches@gnu.org; Sat, 05 Jun 2021 20:08:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#46955] [PATCH 2/3] gnu: Add python-ipytree. 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 00:08:01 +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=B46955.162293804318470 (code B ref 46955); Sun, 06 Jun 2021 00:08:01 +0000 Received: (at 46955) by debbugs.gnu.org; 6 Jun 2021 00:07:23 +0000 Received: from localhost ([127.0.0.1]:50314 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgK2-0004nq-O8 for submit@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:22 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:44739) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgK0-0004nS-So for 46955@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:21 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id BB76D3000DD; Sun, 6 Jun 2021 02:07:14 +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= 1622938034; x=1624752435; bh=iotO6oFfUif/RxFJ4CtTN8iprGTNQaF4Kgp xcFFMDLg=; b=haWkUnH9Sq7RDLbdoKbdMbRUOnV8HAf/vNQFNXUwemrI5rFHeA8 hnIgqJjnffFbsUtl/cI2+dLU87mxmVcAH0hHLgJ3qi6uto5YYFDZ/M3MN/4Swt+P GYeUzw6drpd+RBBJFLqCp26+Zerk7mwhlg90Lw3KmBlWntqpVdj+xI5c= 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 r1nnZhU_m21t; Sun, 6 Jun 2021 02:07:14 +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; Sun, 6 Jun 2021 02:07:14 +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 02:07:13 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sun, 6 Jun 2021 02:06:50 +0200 Message-ID: <20210606000651.28252-2-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--1.443800-8.000000 X-TMASE-MatchedRID: R+JPWGnaB63/R1NSMc2qCT8Ckw9b/GFeTJDl9FKHbrn7fZJfDdCIXISC l3uvYUiSC6+Zjvylmgt6n3hIvN5dLetbninbl/qrTT9ZveSPAxX4qCLIu0mtIPj/xqm3b+MoAsG 1iO+HSl244n+iSEvAXL26V6COZvN4rsq/7BhdGyBkTCSz2kr7Vo5A6wTicMJ0rju6wKzzZAPHwK 23sfEl2YjQSOd69r3fmyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1GpeevGsoI5fs4kKm/I1sQ1MPM Vn7jTEmvWelgXus+6MxI9VXoBbAH4g1gQ6FVgXjCrJLK5PgSUndPK6/90qLFcnoLQoeCWIeCDWQ DDKs7yDox9rqorLqIj47jot1RqlnCuhB+Hs2Q+XFRuRzIFoKqH7cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.443800-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26202.003 X-TM-SNTS-SMTP: CCBD0360B0131F91A16BF35F325F440BBF18BF1B601D36425D27901C6214815F2000: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/python-xyz.scm (python-ipytree): New variable. --- gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a4fe31a01f..8ee43b1176 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7582,6 +7582,32 @@ away.") (define-public python2-ipython-genutils (package-with-python2 python-ipython-genutils)) +(define-public python-ipytree + (package + (name "python-ipytree") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ipytree" version)) + (sha256 + (base32 + "0ss64kxa4la50irf7vy3474f1p924pn4da5gmb02zvhn2x0pra2j")))) + (build-system python-build-system) + (native-inputs + `(("python-setuptools" ,python-setuptools))) + (propagated-inputs + `(("python-ipywidgets" ,python-ipywidgets) + ("python-jupyter-packaging" ,python-jupyter-packaging))) + (home-page "https://github.com/martinRenou/ipytree") + (synopsis "Tree widget using jsTree and Jupyter-widgets") + (description + "This package provides the possibility to create a tree using +@code{Jupyter-widgets} protocol and @code{jsTree}. @code{Jupyter-widgets} is a +way to create an interactive @dfn{graphical user interface} (GUI) for a Jupyter +notebook. @code{JsTree} is a jquery plugin, that provides interactive trees.") + (license license:expat))) + (define-public python-ipyparallel (package (name "python-ipyparallel") 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