From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id KK6cMhnYu1/7YwAA0tVLHw (envelope-from ) for ; Mon, 23 Nov 2020 15:41:13 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id yKajLhnYu19seAAAB5/wlQ (envelope-from ) for ; Mon, 23 Nov 2020 15:41:13 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 72EB29404CC for ; Mon, 23 Nov 2020 15:41:13 +0000 (UTC) Received: from localhost ([::1]:52082 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1khDxo-0002i3-C5 for larch@yhetil.org; Mon, 23 Nov 2020 10:41:12 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59370) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1khDxe-0002gg-0K for guix-patches@gnu.org; Mon, 23 Nov 2020 10:41:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:39195) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1khDxd-0006sh-P1 for guix-patches@gnu.org; Mon, 23 Nov 2020 10:41:01 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1khDxd-0004Fc-KN for guix-patches@gnu.org; Mon, 23 Nov 2020 10:41:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#44819] [PATCH 2/2] gnu: Add python-opentsne. References: <20201123153813.15417-1-monego@posteo.net> In-Reply-To: <20201123153813.15417-1-monego@posteo.net> Resent-From: Vinicius Monego Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 23 Nov 2020 15:41:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 44819 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 44819@debbugs.gnu.org Cc: Vinicius Monego Received: via spool by 44819-submit@debbugs.gnu.org id=B44819.160614606016326 (code B ref 44819); Mon, 23 Nov 2020 15:41:01 +0000 Received: (at 44819) by debbugs.gnu.org; 23 Nov 2020 15:41:00 +0000 Received: from localhost ([127.0.0.1]:50741 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1khDxc-0004FG-5D for submit@debbugs.gnu.org; Mon, 23 Nov 2020 10:41:00 -0500 Received: from mout01.posteo.de ([185.67.36.65]:56675) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1khDxa-0004F3-J6 for 44819@debbugs.gnu.org; Mon, 23 Nov 2020 10:40:59 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 0AE0C16005C for <44819@debbugs.gnu.org>; Mon, 23 Nov 2020 16:40:51 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1606146052; bh=Qssgxc6xdeYajx7pIRPPBmD8hwNyfvTSwnJvxKFNyCE=; h=From:To:Cc:Subject:Date:From; b=X4k7EDwxv/KnK8gCCL/dogR0I/UJdqUJCB+hcBcPbKAwXV1boMiubl+Gl98q48mwL qkItRzlXHW2X+LeCVb16WsdKqAmRr4jagr72ujRop+AATrw9Y7sJUViMeBWudUVp3a qmIbvmxqf+rnC+vF6+W1KaKR3PCBoFA56Nk5X0fNa1OAMbCs1CKD+xbfGqAutaIIN6 7ZOwh5N6KknXy24nDtvq4JW7wY1O8x8o7jsu3tJV4Gf+naU4AvkH94xY4e/fjqo/eO VEnrooWhYsKJ8SpCV8ttWlZz5IJRTBVie3cnmcdhlPUQsueNSyKK0SwcLidbCbIMj8 XlvEG0nakx1vQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Cfrw20kF1z6tmK; Mon, 23 Nov 2020 16:40:49 +0100 (CET) From: Vinicius Monego Date: Mon, 23 Nov 2020 12:40:32 -0300 Message-Id: <20201123154032.15789-1-monego@posteo.net> X-Mailer: git-send-email 2.20.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -3.3 (---) X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Scanner: ns3122888.ip-94-23-21.eu Authentication-Results: aspmx1.migadu.com; dkim=fail (headers rsa verify failed) header.d=posteo.net header.s=2017 header.b=X4k7EDwx; dmarc=fail reason="SPF not aligned (strict)" header.from=posteo.net (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Spam-Score: 5.09 X-TUID: Gueqd8ihlUN4 * gnu/packages/machine-learning.scm (python-opentsne): New variable. --- gnu/packages/machine-learning.scm | 45 +++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 2ad148b48e..2e5af23f0f 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -896,6 +896,51 @@ data analysis.") for k-neighbor-graph construction and approximate nearest neighbor search.") (license license:bsd-2))) +(define-public python-opentsne + (package + (name "python-opentsne") + (version "0.4.4") + (source + (origin + ;; No tests in the PyPI tarball. + (method git-fetch) + (uri (git-reference + (url "https://github.com/pavlin-policar/openTSNE") + (commit (string-append "v" version)))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 "08wamsssmyf6511cbmglm67dp48i6xazs89m1cskdk219v90bc76")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; Benchmarks require the 'macosko2015' data files. + (add-after 'unpack 'delete-benchmark + (lambda _ + (delete-file-recursively "benchmarks") + #t)) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp") + #t))))) + (native-inputs + `(("python-cython" ,python-cython))) + (inputs + `(("fftw" ,fftw))) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-pynndescent" ,python-pynndescent) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy))) + (home-page "https://github.com/pavlin-policar/openTSNE") + (synopsis "Extensible, parallel implementations of t-SNE") + (description + "This is a modular Python implementation of t-Distributed Stochastic +Neighbor Embedding (t-SNE), a popular dimensionality-reduction algorithm for +visualizing high-dimensional data sets.") + (license license:bsd-3))) + (define-public python-scikit-rebate (package (name "python-scikit-rebate") -- 2.20.1