From unknown Tue Jun 17 03:39:32 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#44819 <44819@debbugs.gnu.org> To: bug#44819 <44819@debbugs.gnu.org> Subject: Status: [PATCH 1/2] gnu: Add python-pynndescent. Reply-To: bug#44819 <44819@debbugs.gnu.org> Date: Tue, 17 Jun 2025 10:39:32 +0000 retitle 44819 [PATCH 1/2] gnu: Add python-pynndescent. reassign 44819 guix-patches submitter 44819 Vinicius Monego severity 44819 normal tag 44819 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 23 10:38:41 2020 Received: (at submit) by debbugs.gnu.org; 23 Nov 2020 15:38:41 +0000 Received: from localhost ([127.0.0.1]:50736 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1khDvM-0004BM-N2 for submit@debbugs.gnu.org; Mon, 23 Nov 2020 10:38:40 -0500 Received: from lists.gnu.org ([209.51.188.17]:48806) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1khDvL-0004BF-D9 for submit@debbugs.gnu.org; Mon, 23 Nov 2020 10:38:40 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:58552) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1khDvK-0001MX-B8 for guix-patches@gnu.org; Mon, 23 Nov 2020 10:38:39 -0500 Received: from mout01.posteo.de ([185.67.36.65]:60172) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1khDvE-0005nH-MY for guix-patches@gnu.org; Mon, 23 Nov 2020 10:38:37 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 013DE160063 for ; Mon, 23 Nov 2020 16:38:27 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1606145908; bh=qrgIUc+GIm1SRJtd6p3D3r5Z4S9GCpmLh5Zo7lX256A=; h=From:To:Cc:Subject:Date:From; b=Re2FzKoAanlgNY1IEV1HAkANcDJQ9rfdWDM9b8JJKfvnYo//Qua9FmOTdRPHStiHa yx9RQEvfACI+MlLpQt81PxUN2Z+ZPSSgi3cQPd/sFfrJuZHX24nzG1hiDir/2llAuu phxFAcFjd4fnOnP8BSgEv9NHqgW5axaaw2vMatsi+N7ZzcmpuKm6BThAF5oVUmbXIX LqbkJ9/JrO1O3G6TZgALughQ3JHivtVW8JED6n0+Q60+b0gMucAaGvFxHpTEabUGcF 8+xigm1N8k+vvl0ZigaqtxNTyhSBKcDhvD0sBT51IZcGXYcOM+u7rcGL5+edFKf14E eLdu9d36G0fKQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4CfrsG3C0cz9rxG; Mon, 23 Nov 2020 16:38:26 +0100 (CET) From: Vinicius Monego To: guix-patches@gnu.org Subject: [PATCH 1/2] gnu: Add python-pynndescent. Date: Mon, 23 Nov 2020 12:38:13 -0300 Message-Id: <20201123153813.15417-1-monego@posteo.net> X-Mailer: git-send-email 2.20.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=monego@posteo.net; helo=mout01.posteo.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H4=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: Vinicius Monego X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) * gnu/packages/machine-learning.scm (python-pynndescent): New variable. --- Version 0.5.x was released days ago but it changes the API and breaks OpenTSNE tests. gnu/packages/machine-learning.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 34b522c99b..2ad148b48e 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -65,6 +65,7 @@ #:use-module (gnu packages gstreamer) #:use-module (gnu packages image) #:use-module (gnu packages linux) + #:use-module (gnu packages llvm) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) #:use-module (gnu packages ocaml) @@ -869,6 +870,32 @@ data analysis.") (base32 "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj"))))))) +(define-public python-pynndescent + (package + (name "python-pynndescent") + (version "0.4.8") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pynndescent" version)) + (sha256 + (base32 "0li1fclif50v6xrq7wh3lif9vv5jpj7xhrb0z6g89wwjnp9b9833")))) + (build-system python-build-system) + (native-inputs + `(("python-nose" ,python-nose))) + (propagated-inputs + `(("python-joblib" ,python-joblib) + ("python-llvmlite" ,python-llvmlite) + ("python-numba" ,python-numba) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy))) + (home-page "https://github.com/lmcinnes/pynndescent") + (synopsis "Nearest neighbor descent for approximate nearest neighbors") + (description + "PyNNDescent provides a Python implementation of Nearest Neighbor Descent +for k-neighbor-graph construction and approximate nearest neighbor search.") + (license license:bsd-2))) + (define-public python-scikit-rebate (package (name "python-scikit-rebate") -- 2.20.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 23 10:41:00 2020 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 To: 44819@debbugs.gnu.org Subject: [PATCH 2/2] gnu: Add python-opentsne. 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-Debbugs-Envelope-To: 44819 Cc: Vinicius Monego X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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 From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 25 18:38:56 2020 Received: (at 44819) by debbugs.gnu.org; 25 Nov 2020 23:38:57 +0000 Received: from localhost ([127.0.0.1]:37461 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ki4NE-0006g2-Ne for submit@debbugs.gnu.org; Wed, 25 Nov 2020 18:38:56 -0500 Received: from out5-smtp.messagingengine.com ([66.111.4.29]:57041) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ki4NC-0006fn-4T for 44819@debbugs.gnu.org; Wed, 25 Nov 2020 18:38:54 -0500 Received: from compute3.internal (compute3.nyi.internal [10.202.2.43]) by mailout.nyi.internal (Postfix) with ESMTP id A419B5C00BE; Wed, 25 Nov 2020 18:38:48 -0500 (EST) Received: from mailfrontend1 ([10.202.2.162]) by compute3.internal (MEProxy); Wed, 25 Nov 2020 18:38:48 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=date:from:to:cc:subject:message-id:references:mime-version :content-type:in-reply-to; s=mesmtp; bh=9iOsygnwjVOJg+aIcuCkTHF+ BnHYIUlwnLosM8XKZrs=; b=gfVmr7YhIJiL9JJEXan0Cjo6HKByFSjjGbzfE8/p /pXO6ToSvX7jh+3Z7cvmf9VXd6s03+M0jrpjsxqtPqbuaoWaRvJOtK2hE61RXLXk PTklVnoN0eANbr6EIdZPdcVVJgpGBoki7wE6sq4YeczhItxi709t1csrMZO/ErIU P3k= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:from:in-reply-to :message-id:mime-version:references:subject:to:x-me-proxy :x-me-proxy:x-me-sender:x-me-sender:x-sasl-enc; s=fm1; bh=9iOsyg nwjVOJg+aIcuCkTHF+BnHYIUlwnLosM8XKZrs=; b=Flou8bTqaaRgjoXA0NiPYD AvHmchdxovGs3ElPYTdhd1IpxZe4Jo2cg/2cZeyldB6er0kuLwFS5SL4+K1b9qLi qtFaMKtGVXnyYuncMmY3h0WkxDdmCozCt52uyg4sLnLVcSyCxvL99nYW2hrvq/CJ N680vFcoYNyKK+508uFtbb8Jg05DVYs8uHQzM7//96e+WVJEcO0tlyP8nmL8PqBm H3WQPcW6BfHNuTnRWEuCNHDsEAh35HyH8H4TOl2zuqANFfJD9vGQy2LDADiQHpYn mZw9kIHQnj3RtyGKPNlIuSzMghw6JvY25lfzYxaqn6FPixH5DccKRggbmF51mfHQ == X-ME-Sender: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgedujedrudehuddgudefucetufdoteggodetrfdotf fvucfrrhhofhhilhgvmecuhfgrshhtofgrihhlpdfqfgfvpdfurfetoffkrfgpnffqhgen uceurghilhhouhhtmecufedttdenucesvcftvggtihhpihgvnhhtshculddquddttddmne cujfgurhepfffhvffukfhfgggtuggjsehttdertddttddvnecuhfhrohhmpefnvghoucfh rghmuhhlrghrihcuoehlvghosehfrghmuhhlrghrihdrnhgrmhgvqeenucggtffrrghtth gvrhhnpeeukeektdffvddtudegjeegtdevhfeufeeivdejiedtieegtdevjedvjeehffev gfenucfkphepjeefrddugedurdduvdejrddugeeinecuvehluhhsthgvrhfuihiivgeptd enucfrrghrrghmpehmrghilhhfrhhomheplhgvohesfhgrmhhulhgrrhhirdhnrghmvg X-ME-Proxy: Received: from localhost (c-73-141-127-146.hsd1.pa.comcast.net [73.141.127.146]) by mail.messagingengine.com (Postfix) with ESMTPA id EDE973280059; Wed, 25 Nov 2020 18:38:47 -0500 (EST) Date: Wed, 25 Nov 2020 18:38:46 -0500 From: Leo Famulari To: Vinicius Monego Subject: Re: [bug#44819] [PATCH 1/2] gnu: Add python-pynndescent. Message-ID: <20201125233846.GA23912@jasmine.lan> References: <20201123153813.15417-1-monego@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20201123153813.15417-1-monego@posteo.net> X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 44819 Cc: 44819@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) On Mon, Nov 23, 2020 at 12:38:13PM -0300, Vinicius Monego wrote: > * gnu/packages/machine-learning.scm (python-pynndescent): New variable. Thanks! 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