From patchwork Thu May 26 21:24:27 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Vivien Kraus X-Patchwork-Id: 39619 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 51DCF27BBEA; Thu, 26 May 2022 22:26:03 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 5150F27BBE9 for ; Thu, 26 May 2022 22:26:00 +0100 (BST) Received: from localhost ([::1]:56588 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nuKzX-000388-F7 for patchwork@mira.cbaines.net; Thu, 26 May 2022 17:25:59 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:50468) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nuKyd-00036j-3v for guix-patches@gnu.org; Thu, 26 May 2022 17:25:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38075) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nuKyc-0005vw-LO for guix-patches@gnu.org; Thu, 26 May 2022 17:25:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nuKyc-0006b4-Ek for guix-patches@gnu.org; Thu, 26 May 2022 17:25:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#53402] Update dependencies and rebase on newer work Resent-From: Vivien Kraus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 26 May 2022 21:25:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53402 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: moreinfo To: 53402@debbugs.gnu.org Received: via spool by 53402-submit@debbugs.gnu.org id=B53402.165360029625342 (code B ref 53402); Thu, 26 May 2022 21:25:02 +0000 Received: (at 53402) by debbugs.gnu.org; 26 May 2022 21:24:56 +0000 Received: from localhost ([127.0.0.1]:60205 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nuKyM-0006aX-VX for submit@debbugs.gnu.org; Thu, 26 May 2022 17:24:56 -0400 Received: from planete-kraus.eu ([89.234.140.182]:44552) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nuKyG-0006aH-O2 for 53402@debbugs.gnu.org; Thu, 26 May 2022 17:24:45 -0400 Received: from planete-kraus.eu (localhost.lan [127.0.0.1]) by planete-kraus.eu (OpenSMTPD) with ESMTP id 3344e94b for <53402@debbugs.gnu.org>; Thu, 26 May 2022 21:24:38 +0000 (UTC) DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=planete-kraus.eu; h= message-id:subject:from:to:date:in-reply-to:references :content-type:mime-version; s=dkim; bh=gCK9sMVzCsDilWd7LgI2Z5HDw c4=; b=JeTOpg156OFKqoEkvpN+Gam01T1+9YphHnYkpNrgM9nCadwayf62GG2E0 eXcIUiA0n2wUhn2fA7iy+CFHjMnfDuYz8lIb2Sd0j8x/5H+Ap4NE6+R+eATV9Og8 kGsip0EOf7shx9bekulFK1GucMsMsF+waWsCa5+GB9f8lH9R60= Received: by planete-kraus.eu (OpenSMTPD) with ESMTPSA id d0fb6bf7 (TLSv1.3:AEAD-CHACHA20-POLY1305-SHA256:256:NO) for <53402@debbugs.gnu.org>; Thu, 26 May 2022 21:24:34 +0000 (UTC) Message-ID: <3bfd0e42807f6728bbf8cd43212727eb840cdee3.camel@planete-kraus.eu> Date: Thu, 26 May 2022 23:24:27 +0200 In-Reply-To: References: User-Agent: Evolution 3.42.1 MIME-Version: 1.0 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" Reply-to: Vivien Kraus X-ACL-Warn: , Vivien Kraus via Guix-patches X-Patchwork-Original-From: Vivien Kraus via Guix-patches via From: Vivien Kraus X-getmail-retrieved-from-mailbox: Patches Dear guix, Since I made the last update to this series, someone did work in the python science packages and I had to publish a new rebase of my work, discarding duplicate packaging efforts. I also used that opportunity to update my dependencies. Could you publish the new rebase in a new branch? Previously, nckx did it to wip-python-mne. It was of great help to me because I can use the branch in gitlab CI without having to patch and rebuild guix in the pipeline. It would be wiser to use a new branch, based on master. Thank you for the time you already spent helping me. Best regards, Vivien From ed24fd862a0a9bd06ecc3a25dd4c2c6542226252 Mon Sep 17 00:00:00 2001 From: Vivien Kraus Date: Thu, 20 Jan 2022 23:21:25 +0100 Subject: [PATCH v6 28/28] gnu: Add python-mne. * gnu/packages/python-science.scm (python-mne): New variable. --- gnu/packages/python-science.scm | 65 +++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 78ef733750..ef0b7f2cd7 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -46,6 +46,7 @@ (define-module (gnu packages python-science) #:use-module (gnu packages databases) #:use-module (gnu packages gcc) #:use-module (gnu packages image-processing) + #:use-module (gnu packages jupyter) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -57,6 +58,7 @@ (define-module (gnu packages python-science) #:use-module (gnu packages python-check) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages qt) #:use-module (gnu packages simulation) #:use-module (gnu packages sphinx) #:use-module (gnu packages statistics) @@ -1636,3 +1638,66 @@ (define-public python-mffpy files are directories containing several files of mostly xml files, but also binary files.") (license license:asl2.0))) + +(define-public python-mne + (package + (name "python-mne") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "mne" version)) + (sha256 + (base32 + "1vfgqpvjq2b3x1wkw7mn7hk6gcxbvgqfknbh9qkg2r7r22cy38p5")))) + (build-system python-build-system) + (arguments + ;; The test data is distributed in a separate repository without a + ;; license, https://github.com/mne-tools/mne-testing-data + `(#:tests? #f)) + (propagated-inputs (list python-numpy python-scipy + python-matplotlib + python-tqdm + python-pooch + python-decorator + python-h5io + python-packaging + python-pymatreader + python-pyqt + python-pyqt5-sip + python-sip + python-scikit-learn + python-nibabel + python-numba + python-h5py + python-jinja2 + python-pandas + python-numexpr + jupyter + python-picard + python-statsmodels + python-joblib + python-psutil + python-dipy + vtk + python-nilearn + python-xlrd + python-imageio + python-imageio-ffmpeg + python-traitlets + python-pyvista + python-pyvistaqt + python-mffpy + python-ipywidgets + ;; FIXME: add the following dependencies: + ;; python-ipyvtklink requires NPM to build + ;; mne-qt-browser is not included, because it + ;; depends on MNE. + )) + (home-page "https://mne.tools/dev/") + (synopsis "MNE-Python project for MEG and EEG data analysis") + (description + "Open-source Python package for exploring, visualizing, and +analyzing human neurophysiological data: MEG, EEG, sEEG, ECoG, NIRS, and +more.") + (license license:bsd-3))) -- 2.36.1