From patchwork Sat Mar 6 00:57:02 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: 27465 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 183F327BC46; Sat, 6 Mar 2021 00:58:26 +0000 (GMT) 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_H3,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 3B7FA27BC50 for ; Sat, 6 Mar 2021 00:58:25 +0000 (GMT) Received: from localhost ([::1]:57524 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lILGy-0006la-Fm for patchwork@mira.cbaines.net; Fri, 05 Mar 2021 19:58:24 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:46400) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lILGd-0006jy-0A for guix-patches@gnu.org; Fri, 05 Mar 2021 19:58:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:52430) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lILGb-0007ku-MN for guix-patches@gnu.org; Fri, 05 Mar 2021 19:58:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lILGb-0001aY-KB for guix-patches@gnu.org; Fri, 05 Mar 2021 19:58:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#46955] [PATCH 1/2] 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: Sat, 06 Mar 2021 00:58:01 +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=B46955.16149922606070 (code B ref 46955); Sat, 06 Mar 2021 00:58:01 +0000 Received: (at 46955) by debbugs.gnu.org; 6 Mar 2021 00:57:40 +0000 Received: from localhost ([127.0.0.1]:35740 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lILGA-0001Ze-8p for submit@debbugs.gnu.org; Fri, 05 Mar 2021 19:57:40 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:34603) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lILG5-0001ZN-Fv for 46955@debbugs.gnu.org; Fri, 05 Mar 2021 19:57:33 -0500 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 1488F16012B; Sat, 6 Mar 2021 01:57:23 +0100 (CET) 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=1614992242; x=1616806643; bh=tulqpNiVy4P5FQDA4wI7NaUj7QfgFIQVzLR5oYvja6o=; b=h2/lgetSpXLE y8KdVea6t/dbskPKh/L+/oISWNmmyME9etV7aiInNNwjTGSE1cFA45duhdq7Dd1Q 4JtMcPWvx+5VS5l5vlHhXyytScNnUnjZeLp82wLZSJL9km41R/u7MhNuowszrtx1 1UN9lUUsjQX61uEsgqpNl+Pi8bwdAvQ= 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 RtFq4BUYj4dC; Sat, 6 Mar 2021 01:57:22 +0100 (CET) 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; Sat, 6 Mar 2021 01:57:22 +0100 (CET) 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 15.1.2176.2; Sat, 6 Mar 2021 01:57:22 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 6 Mar 2021 01:57:02 +0100 Message-ID: <20210306005703.25479-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 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-14.0.0.3080-8.6.1012-26012.003 X-TM-AS-Result: No-10--3.042000-8.000000 X-TMASE-MatchedRID: gnUNXwFR0uP/R1NSMc2qCXycvC6I0dJIS1zwNuiBtITfUZT83lbkEJwl bZPQQ0yzb1TGnuLRfUkctkosP3yazCq+GZ9ZHxIhUYXhMajr0x53G1bsm5zfjMZygq/CPmrol8w sFD5lRSvmsKqMEsXxJy2+lyx46iL0+5T6zKmlZhdV1zhVw8duYkPIlAqA4/DEvAe75exuTNFErs sMQdxI5OdccNzwjJTWNx3sWO1UiHFnDmHdcAECAMn9tWHiLD2GW1eClGWYNyjnCThanP/ghGJlH 05V7NzjkysQhBKB3lqXwGaqxb4UjqMOL4ljfmzc9FQh3flUIh4Q5L9qu3flQ5cFdomgH0lngxsf zkNRlfLdB/CxWTRRu3aDLLDbFMGF/tsmPRGXdaiD+EnTB7mS6eikSSNrgo8AgJ8EP/L19sL0xVt oJb5gks/YiEgTarFDgTu0lGnM4Bj+Bp7E1Bftcrvpvs9iIwUk1+xhfuuIbsi45jSrrr4GpqGCNX qyLhLFvoNkWY9hSsutAp7vUZi6bw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.042000-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26012.003 X-TM-SNTS-SMTP: 53C155232D36112CF637479049976B7F6D97BD6823FF8BA1EEE9700E04BF6E442000: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 | 41 ++++++++++++++++++++++++++++++++++++- 1 file changed, 40 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index fbc9ad688d..b5274c39a9 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 @@ -4719,6 +4719,45 @@ objects.") (define-public python2-colormath (package-with-python2 python-colormath)) +(define-public python-sparse + (package + (name "python-sparse") + (version "0.11.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sparse" version)) + (sha256 + (base32 + "0kw6ha83gk0dymayrxhh16xxk7aykiyiz3ksxdzj6hhjr3dkap5w")))) + (build-system python-build-system) + (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.") + ;;https://github.com/pydata/sparse/blob/master/LICENSE + (license license:bsd-3))) + (define-public python-spectra (package (name "python-spectra") From patchwork Sat Mar 6 00:57:03 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: 27466 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 83E7327BC50; Sat, 6 Mar 2021 00:58:35 +0000 (GMT) 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_H3,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 F033227BC46 for ; Sat, 6 Mar 2021 00:58:34 +0000 (GMT) Received: from localhost ([::1]:58006 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lILH6-0006xs-ID for patchwork@mira.cbaines.net; Fri, 05 Mar 2021 19:58:34 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:46396) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lILGc-0006jw-Vh for guix-patches@gnu.org; Fri, 05 Mar 2021 19:58:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:52431) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lILGc-0007kv-13 for guix-patches@gnu.org; Fri, 05 Mar 2021 19:58:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lILGc-0001af-0F for guix-patches@gnu.org; Fri, 05 Mar 2021 19:58:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#46955] [PATCH 2/2] gnu: python-cooler: Update to 0.8.10. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 06 Mar 2021 00:58:01 +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=B46955.16149922606076 (code B ref 46955); Sat, 06 Mar 2021 00:58:01 +0000 Received: (at 46955) by debbugs.gnu.org; 6 Mar 2021 00:57:40 +0000 Received: from localhost ([127.0.0.1]:35743 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lILGG-0001Zr-Gi for submit@debbugs.gnu.org; Fri, 05 Mar 2021 19:57:40 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:51133) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lILGE-0001ZX-Cv for 46955@debbugs.gnu.org; Fri, 05 Mar 2021 19:57:39 -0500 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 0CCD2300119; Sat, 6 Mar 2021 01:57:32 +0100 (CET) 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= 1614992251; x=1616806652; bh=hDB9R2F95y0mv2J2r96bJzlFd06PhbuiU5P figQ3B70=; b=Ai21/ZrZ7pG361k+9np/7+VeLMait5og+JIDRCEs4Yh7qC5Jh71 bIzEdms+VSx69T+evjR39kBxfM1jFrbAzXJ3GEEEdb81BaiitHA4joLtd5P4iPcv yIEeKwNqu2450Qf9ieRL2O16jXoRU4JOL3SM1AZdy6vPuWatApNbJfYM= 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 nLQ27qW1Vkqr; Sat, 6 Mar 2021 01:57:31 +0100 (CET) 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; Sat, 6 Mar 2021 01:57:31 +0100 (CET) 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 15.1.2176.2; Sat, 6 Mar 2021 01:57:31 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Sat, 6 Mar 2021 01:57:03 +0100 Message-ID: <20210306005703.25479-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210306005703.25479-1-madalinionel.patrascu@mdc-berlin.de> References: <20210306005703.25479-1-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-14.0.0.3080-8.6.1012-26012.003 X-TM-AS-Result: No-10--1.901600-8.000000 X-TMASE-MatchedRID: IajoWEPWtmK6/eEqqZaZmj8Ckw9b/GFeTJDl9FKHbrn7fZJfDdCIXISC l3uvYUiSC6+Zjvylmgt6n3hIvN5dLetbninbl/qrvr7oQh2H9etKhpFNiC3g3hHfiujuTbedu95 6BjcJKyQZDJ72K11ChJNb5HQLbebH7Tqch0zEtNGL6q5RsNhv5PLfqX4QTDm8xaBBt5x+Tc6YDT IhMw3OOX0tCKdnhB589yM15V5aWpj6C0ePs7A07ba607moR85R7if6eFicpJ+/L/l0xOrOcSPbi /Gx1mOfBm/2yD38/KaEQxghebWIdCJm20qIrbV/czCm0bU8FunF7/pJf0EW2mswzhJnyVc0b8fs uEgqM7bRtaXwfRDZE7Qwvjsqb5f0Rg4BBcJumqA+kK598Yf3Mg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.901600-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26012.003 X-TM-SNTS-SMTP: 17748E8121FA99A6118D2D72552E4E3E06BF5E29D72A3B461C050DD834DB8A102000: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 0.8.10/ --- gnu/packages/bioinformatics.scm | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6d21e14360..bc31d50e54 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13636,35 +13636,38 @@ fasta subsequences.") (define-public python-cooler (package (name "python-cooler") - (version "0.8.7") + (version "0.8.10") (source (origin (method url-fetch) (uri (pypi-uri "cooler" version)) (sha256 (base32 - "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp")))) + "1hi9anwz8b9p9wigzc5hypnwm6a4ikvlv69ixy3ki8939ngb1sj3")))) (build-system python-build-system) (propagated-inputs `(("python-asciitree" ,python-asciitree) - ("python-biopython" ,python-biopython) ("python-click" ,python-click) ("python-cytoolz" ,python-cytoolz) - ("python-dask" ,python-dask) ("python-h5py" ,python-h5py) ("python-multiprocess" ,python-multiprocess) ("python-numpy" ,python-numpy) ("python-pandas" ,python-pandas) ("python-pyfaidx" ,python-pyfaidx) ("python-pypairix" ,python-pypairix) - ("python-pysam" ,python-pysam) ("python-pyyaml" ,python-pyyaml) ("python-scipy" ,python-scipy) - ("python-simplejson" ,python-simplejson))) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six))) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) - (home-page "https://github.com/mirnylab/cooler") + `(("python-codecov" ,python-codecov) + ("python-dask" ,python-dask) ;;unittest.runner.TextTestResult + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-flake8" ,python-pytest-flake8) + ("python-sparse" ,python-sparse))) ;;unittest.runner.TextTestResult + (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