From patchwork Sun Feb 6 14:49:44 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Vivien Kraus X-Patchwork-Id: 37024 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 6A7F227BBEA; Sun, 6 Feb 2022 14:51:52 +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,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 2B2FB27BBE9 for ; Sun, 6 Feb 2022 14:51:50 +0000 (GMT) Received: from localhost ([::1]:49698 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nGitJ-0003Xl-AX for patchwork@mira.cbaines.net; Sun, 06 Feb 2022 09:51:49 -0500 Received: from eggs.gnu.org ([209.51.188.92]:35906) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nGisY-0003RZ-9i for guix-patches@gnu.org; Sun, 06 Feb 2022 09:51:05 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:42962) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nGisX-0008RP-OM for guix-patches@gnu.org; Sun, 06 Feb 2022 09:51:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nGisX-0001B5-OA for guix-patches@gnu.org; Sun, 06 Feb 2022 09:51:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53402] Rebase it for the new python packages Resent-From: Vivien Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 06 Feb 2022 14:51:01 +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: Vinicius Monego , 53402@debbugs.gnu.org Received: via spool by 53402-submit@debbugs.gnu.org id=B53402.16441590244467 (code B ref 53402); Sun, 06 Feb 2022 14:51:01 +0000 Received: (at 53402) by debbugs.gnu.org; 6 Feb 2022 14:50:24 +0000 Received: from localhost ([127.0.0.1]:36855 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nGirj-00019h-FN for submit@debbugs.gnu.org; Sun, 06 Feb 2022 09:50:23 -0500 Received: from planete-kraus.eu ([89.234.140.182]:33730) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nGire-00019S-Rn for 53402@debbugs.gnu.org; Sun, 06 Feb 2022 09:50:09 -0500 Received: from planete-kraus.eu (localhost.lan [127.0.0.1]) by planete-kraus.eu (OpenSMTPD) with ESMTP id 1bc15849; Sun, 6 Feb 2022 14:50:03 +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=rZUCh7ug7QMAXxfcMVpf0tHIg zo=; b=dw9L4PnaV8z3+pR8jyY6u1HdMycp60aVkfYA5srQBsJYlDQDAKrnN/C/C sWm/60U/fYGY2SiI6p3RRCKUT9IUzNU/qeTc9Z+r3wqbVRdsXumb479z2VFz92+g 41AJnqvegeX7RY5kJTXzKsKjD8i+KfpDxtHjttKGUP8RuiYJ+w= Received: by planete-kraus.eu (OpenSMTPD) with ESMTPSA id fa216788 (TLSv1.3:AEAD-CHACHA20-POLY1305-SHA256:256:NO); Sun, 6 Feb 2022 14:49:55 +0000 (UTC) Message-ID: Date: Sun, 06 Feb 2022 15:49:44 +0100 In-Reply-To: <1161a7298bbbbe87ce48f4e3e4846021204ae1df.camel@posteo.net> References: <1161a7298bbbbe87ce48f4e3e4846021204ae1df.camel@posteo.net> 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 X-ACL-Warn: , Vivien via Guix-patches X-Patchwork-Original-From: Vivien via Guix-patches via From: Vivien Kraus X-getmail-retrieved-from-mailbox: Patches Hello, thank you for your review! Le jeudi 03 février 2022 à 20:49 +0000, Vinicius Monego a écrit : > To avoid future merge conflicts, please move the packages somewhere > in > the middle of the files instead of the bottom. OK. > As a rule of thumb for Python packages with tests in Pytest, the > check > phase is overriden and Pytest is called manually. When the tests are > in > a subfolder inside the module, add a --pyargs parameter to > the pytest command, see e.g. the python-cartopy package. I could run > the python-nibabel tests with this change without having to delete > anything. OK. > If the tests still can't run because of missing data, it's fine to > source from the upstream repository instead of PyPI, or skip the few > tests that need them or at all if the repository doesn't ship a > setup.py. If tests are to be disabled, they should also have a > comment > with the reason. For MNE, the test data set is a separate repository without a license, so I disabled the tests. > The 'test-less' packages shouldn't be needed AFAICS. Tests should run > by overriding the check phase as stated above (untested). The test-less packages are part of a dependency cycle; decopatch requires them for the tests to run, and they require decopatch or each other too. If I disable all tests (pytest-* and decopatch) it would work, but I’m not sure I should do that. > I also have a few comments about the patches in general: > > > +    (source (origin > > +              (method url-fetch) > > +              (uri (pypi-uri "imageio-ffmpeg" version)) > > +              (sha256 > > +               (base32 > > +               > > "0ff14079izsyxwf6ki68k9a7w5krjlal7lwqvzg2bbddl92l5spj")))) > > Could you style it as > >     (source >      (origin >        (method url-fetch) >        (uri (pypi-uri "imageio-ffmpeg" version)) >        (sha256 >         (base32 > "0ff14079izsyxwf6ki68k9a7w5krjlal7lwqvzg2bbddl92l5spj")))) > > and the other packages too? OK. > Gexps should only be used when ungexp (#$) is used. On many patches > (e.g. python-nitime) ungexp is not being used. OK, I upgraded python-pooch again and it needs gexps too now. > > When using gexp, it's better to style the arguments as: > > +    (arguments > +     (list > +       #:phases > +       #~(modify-phases %standard-phases > > to save columns (some of the packages exceeded the 78 columns limit), > instead of > > > +    (arguments > > +     (list #:phases > > +           #~(modify-phases %standard-phases > > OK. > . > > Some of the descriptions are not full sentences (e.g. in python- > pytest- > harvest-minimal). Please check that descriptions are full sentences. I’m not sure I understand. I reworked some descriptions, but didn’t find non-full sentences. Could you explain what you mean? > When sending an updated series, use patch versions with --reroll- > count=4 or -v4. I didn’t know that option. > Could you send a v4 with the requested changes? Sure! Best regards, Vivien From f1deca828dddb258791c98ef52be14a8cf6c6c22 Mon Sep 17 00:00:00 2001 From: Vivien Kraus Date: Thu, 20 Jan 2022 23:21:25 +0100 Subject: [PATCH v4 18/18] gnu: Add python-mne. * gnu/packages/python-science.scm (python-mne): New variable. --- gnu/packages/python-science.scm | 45 +++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 66c79b2e69..61ab831457 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) @@ -1194,3 +1195,47 @@ (define-public python-nitime level interface to the numerical machinery and make common analysis tasks easy 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 + ;; 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)) + (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