From patchwork Fri Jan 21 08:17:38 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Vivien Kraus X-Patchwork-Id: 36713 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 D92BA27BBEA; Fri, 21 Jan 2022 08:45:51 +0000 (GMT) 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,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL, 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 DB65427BBE9 for ; Fri, 21 Jan 2022 08:45:49 +0000 (GMT) Received: from localhost ([::1]:39810 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nApYK-00059J-Ps for patchwork@mira.cbaines.net; Fri, 21 Jan 2022 03:45:48 -0500 Received: from eggs.gnu.org ([209.51.188.92]:47802) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nApFK-0007p5-JB for guix-patches@gnu.org; Fri, 21 Jan 2022 03:26:15 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:38990) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nApFC-0001J1-Ab for guix-patches@gnu.org; Fri, 21 Jan 2022 03:26:10 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nApFC-00065v-8o for guix-patches@gnu.org; Fri, 21 Jan 2022 03:26:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53402] Add python-mne: fix or disable tests Resent-From: Vivien Kraus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 Jan 2022 08:26:02 +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: To: 53402@debbugs.gnu.org Received: via spool by 53402-submit@debbugs.gnu.org id=B53402.164275354723407 (code B ref 53402); Fri, 21 Jan 2022 08:26:02 +0000 Received: (at 53402) by debbugs.gnu.org; 21 Jan 2022 08:25:47 +0000 Received: from localhost ([127.0.0.1]:60126 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nApEl-00065G-Df for submit@debbugs.gnu.org; Fri, 21 Jan 2022 03:25:47 -0500 Received: from planete-kraus.eu ([89.234.140.182]:38952) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nApEh-000654-Bb for 53402@debbugs.gnu.org; Fri, 21 Jan 2022 03:25:34 -0500 Received: from planete-kraus.eu (localhost.lan [127.0.0.1]) by planete-kraus.eu (OpenSMTPD) with ESMTP id 3bbbe11e for <53402@debbugs.gnu.org>; Fri, 21 Jan 2022 08:25:17 +0000 (UTC) DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=planete-kraus.eu; h= references:from:to:subject:date:in-reply-to:message-id :mime-version:content-type; s=dkim; bh=ggIiW58CZCUTomtMUUxNwZXvv yA=; b=jfhzV/Sf+T572CelV+p9/rY5euylrDJ7q/k2LMHNeqpBuE/bKUf8okaMw 8PyB4hbzMolQDGfxiMT1hCBfIkK4RREd2qKtFvXvoqQ5l89t34Q8eUCBSS8GI0pb 12Hbl6gCjnVqZa4AIUptoikLcJyUmYuTpC98aI224Ai5CFJnwA= Received: by planete-kraus.eu (OpenSMTPD) with ESMTPSA id 9456cd3a (TLSv1.3:AEAD-CHACHA20-POLY1305-SHA256:256:NO) for <53402@debbugs.gnu.org>; Fri, 21 Jan 2022 08:24:46 +0000 (UTC) References: User-agent: mu4e 1.6.10; emacs 27.2 Date: Fri, 21 Jan 2022 09:17:38 +0100 In-reply-to: Message-ID: <878rv9ijhv.fsf@planete-kraus.eu> 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, I could fix one test suite, but as luis-felipe told me on #guix, the test data isn’t fully distributed by pypi for mne, so I had to disable it. From dc0467eec2630fc6067a7b3d49d44869497f1f8e Mon Sep 17 00:00:00 2001 From: Vivien Kraus Date: Thu, 20 Jan 2022 23:21:25 +0100 Subject: [PATCH 18/18] gnu: Add python-mne. * gnu/packages/python-science.scm (python-mne): New variable. --- gnu/packages/python-science.scm | 53 +++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 97cca59644..85af5b42cc 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -39,6 +39,7 @@ (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) @@ -1211,3 +1212,55 @@ (define-public python-nitime to express with compact and semantically clear code.") (license license:bsd-3))) +(define-public python-mne + (package + (name "python-mne") + (version "0.24.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "mne" version)) + (sha256 + (base32 + "039h0pwcvl4ywfa4ij7w6x61czd322csqr59yhzfil3a7b8gzjrq")))) + (build-system python-build-system) + (arguments + (list #:tests? #f ;The test data are not distributed + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'set-home + (lambda _ + (setenv "HOME" + (getcwd)))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "mne"))))))) + (propagated-inputs (list python-numpy python-scipy)) + (native-inputs (list python-check-manifest + python-codespell + python-edflib + python-eeglabio + python-flake8 + python-flake8-array-spacing + python-imageio-ffmpeg + python-nbclient + python-nitime + python-numpydoc + python-pooch + python-pydocstyle + python-pytest + python-pytest-cov + python-pytest-harvest + python-pytest-timeout + python-sphinx-gallery + python-twine + python-wheel)) + (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))) + + -- 2.34.0