Ludovic Courtès <ludo@HIDDEN>
to control <at> debbugs.gnu.org.
Full text available.Received: (at 53402) by debbugs.gnu.org; 9 Mar 2022 23:28:12 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Wed Mar 09 18:28:12 2022 Received: from localhost ([127.0.0.1]:32826 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nS5j2-0006tS-FI for submit <at> debbugs.gnu.org; Wed, 09 Mar 2022 18:28:12 -0500 Received: from mout02.posteo.de ([185.67.36.66]:38739) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <monego@HIDDEN>) id 1nS5j0-0006tD-Vn for 53402 <at> debbugs.gnu.org; Wed, 09 Mar 2022 18:28:11 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 9404E240103 for <53402 <at> debbugs.gnu.org>; Thu, 10 Mar 2022 00:28:04 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1646868484; bh=wLhIWA5jA2DgmQXye16LOOJZ9Ho0hMoeFG4yGwf77Dc=; h=Date:Subject:To:Cc:From:From; b=LnNZZ+6vK9Mdlcvp0RZn/k1NkRqiet2HVjRQe/GGXBvuFqM76lxxv6sHTTe4ZnEI3 9yo5XsIP2OEpLLcFA9m9DOT4UOPFs9x5MIBkTEnerumj4oogwmw0KiF+IygbvxpGMT SdHe5w7yjYFZvTL3opmOAHbxzepKnreDcbicJSBH2rPWp4BpDwWcIkcbSNDeyP6Az/ XkTAIbd15dvMef9Eo6uYuFoAT/woVG0NhCoskaUKYZES2UlBRMB3pM6PURgDhiLOhE Nj0DjEjIvPJzIvT+6yDEY3Vp+emgc1nQgLvEIPt/ewkbVzUeMBZGZeLwk8l9nh7xWn b4jyyjnK+H8JA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4KDSzk4y46z6tmp; Thu, 10 Mar 2022 00:28:02 +0100 (CET) Message-ID: <c36dad4e-05df-c822-f36f-6b8180fcbeb0@HIDDEN> Date: Wed, 9 Mar 2022 23:28:00 +0000 MIME-Version: 1.0 Subject: Re: bug#53402: Add python-mne Content-Language: en-US To: =?UTF-8?Q?Ludovic_Court=c3=a8s?= <ludo@HIDDEN> References: <df09d62f7aa0e6a21362f9b7df5a88ff0ddd0a41.camel@HIDDEN> <1161a7298bbbbe87ce48f4e3e4846021204ae1df.camel@HIDDEN> <ecd331465d03183053f8f9597253c81f9079aa14.camel@HIDDEN> <e82bbd94881b38de2a505c2c1109ce9d3ab529ef.camel@HIDDEN> <221569342c7c44d5ed2ddd1ce0e56903d3cda0b2.camel@HIDDEN> <87bkyiiwg2.fsf_-_@HIDDEN> From: Vinicius Monego <monego@HIDDEN> In-Reply-To: <87bkyiiwg2.fsf_-_@HIDDEN> Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 53402 Cc: Vivien <vivien@HIDDEN>, 53402 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -3.3 (---) On 06/03/2022 6:48 PM, Ludovic Courtès wrote: > Hello! > > Vinicius, could you take a look at v5 of this patch series? > > Thanks for reviewing! > > Ludo’. Hi Ludo, Vivien. Sorry for the long wait. I will be busy until mid-April. I did review the patches earlier and LGTM apart from minor style/lint and description issues, but I could fix that before committing. I saw that someone pushed a wip-python-mne branch and thought they were taking care of this. I have some questions for other maintainers, like 1. Is it OK to have that many bootstrap packages for pytest modules (patches 8 to 16) and in files different than where they are supposed to be (e.g. decopatch-minimal in python-check to bootstrap pytest-harvest)? It seems that there are no other options in this case though. 2. Should python-no-verison (patch 22) be a public variable? It is an example package, doesn't seem to be useful to expose it. If it's OK I could push the series up to patch 26. I haven't reviewed 27 and on in v5. 3. Not a question but it would be good to review FSDG status of python-mne, since it contains code to download non-free data.
guix-patches@HIDDEN:bug#53402; Package guix-patches.
Full text available.Received: (at 53402) by debbugs.gnu.org; 6 Mar 2022 21:48:55 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Mar 06 16:48:55 2022 Received: from localhost ([127.0.0.1]:51897 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nQykJ-0001Xg-CY for submit <at> debbugs.gnu.org; Sun, 06 Mar 2022 16:48:55 -0500 Received: from eggs.gnu.org ([209.51.188.92]:59024) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <ludo@HIDDEN>) id 1nQykH-0001XT-Nx for 53402 <at> debbugs.gnu.org; Sun, 06 Mar 2022 16:48:54 -0500 Received: from [2001:470:142:3::e] (port=58012 helo=fencepost.gnu.org) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <ludo@HIDDEN>) id 1nQykC-0002yY-4o; Sun, 06 Mar 2022 16:48:48 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:In-Reply-To:Date:References:Subject:To: From; bh=T+pG2EnQTgKxVhMgV92Xc4+Jw6KggVTxN5tr8XfmuWo=; b=g6c/qDoFdBqGkEoRiTV0 dXz5DI75qul4HGwbqo7cchllGtNUO+bnNh8m+C0QceU9QbPplH5fXK6OMVihXSb9FLnBVNVL6em6X GLWbXdUc7NW8nV9ZoElq08CDU5qFZmn1Xr4CFGqOJrcXP0RTh4F3gkeMDgv5tMIlXj0OK1VhTLBwp F5ruIYaAGre4pV4mNEMOS0g6mlRbFl24li/1DP83rc/HKldHfV8+3cEjeof7IcEflWzOiX5X3QyO+ mh0YFjUtAUu2e++Fw83V2+OAo6dNRQqu+vALz6PMA3MEHCyXy1DVcixUgw5obtLWv9ofT2ykAgzRo skfjLcxJzugfcQ==; Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=52422 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <ludo@HIDDEN>) id 1nQykB-00075r-Iw; Sun, 06 Mar 2022 16:48:47 -0500 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludo@HIDDEN> To: Vinicius Monego <monego@HIDDEN> Subject: Re: bug#53402: Add python-mne References: <df09d62f7aa0e6a21362f9b7df5a88ff0ddd0a41.camel@HIDDEN> <1161a7298bbbbe87ce48f4e3e4846021204ae1df.camel@HIDDEN> <ecd331465d03183053f8f9597253c81f9079aa14.camel@HIDDEN> <e82bbd94881b38de2a505c2c1109ce9d3ab529ef.camel@HIDDEN> <221569342c7c44d5ed2ddd1ce0e56903d3cda0b2.camel@HIDDEN> Date: Sun, 06 Mar 2022 22:48:45 +0100 In-Reply-To: <221569342c7c44d5ed2ddd1ce0e56903d3cda0b2.camel@HIDDEN> (vivien@HIDDEN's message of "Fri, 11 Feb 2022 04:03:14 +0100") Message-ID: <87bkyiiwg2.fsf_-_@HIDDEN> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 53402 Cc: Vivien <vivien@HIDDEN>, 53402 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -3.3 (---) Hello! Vinicius, could you take a look at v5 of this patch series? Thanks for reviewing! Ludo=E2=80=99.
guix-patches@HIDDEN:bug#53402; Package guix-patches.
Full text available.Received: (at 53402) by debbugs.gnu.org; 11 Feb 2022 03:03:31 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Feb 10 22:03:31 2022 Received: from localhost ([127.0.0.1]:57913 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nIMDb-0007iP-9n for submit <at> debbugs.gnu.org; Thu, 10 Feb 2022 22:03:31 -0500 Received: from planete-kraus.eu ([89.234.140.182]:33770) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <vivien@HIDDEN>) id 1nIMDY-0007iF-SU for 53402 <at> debbugs.gnu.org; Thu, 10 Feb 2022 22:03:30 -0500 Received: from planete-kraus.eu (localhost.lan [127.0.0.1]) by planete-kraus.eu (OpenSMTPD) with ESMTP id b3c464f8; Fri, 11 Feb 2022 03:03:26 +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=sz4behkbpJ880etCaldz3Nf9B Go=; b=SKmqGbw0AamNNXvXc4YYRdypQjZPxfUAcfvTFRoaWWRxGDzg2n4/ly9Xa HAbb+B7gWskRJTpmx6WDjGP7QWiLs8F+NCy9eo5ZdpiJihUNqmDDQ1TJYKZOsW+Q ReSuOiIeaLr22i3dbn1K54OX4uLjtEXVKxsxAMdeK9EM4Ar+MA= Received: by planete-kraus.eu (OpenSMTPD) with ESMTPSA id 8a9bc63b (TLSv1.3:AEAD-CHACHA20-POLY1305-SHA256:256:NO); Fri, 11 Feb 2022 03:03:22 +0000 (UTC) Message-ID: <221569342c7c44d5ed2ddd1ce0e56903d3cda0b2.camel@HIDDEN> Subject: Re: Rebase it for the new python packages From: Vivien <vivien@HIDDEN> To: Vinicius Monego <monego@HIDDEN>, 53402 <at> debbugs.gnu.org Date: Fri, 11 Feb 2022 04:03:14 +0100 In-Reply-To: <e82bbd94881b38de2a505c2c1109ce9d3ab529ef.camel@HIDDEN> References: <df09d62f7aa0e6a21362f9b7df5a88ff0ddd0a41.camel@HIDDEN> <1161a7298bbbbe87ce48f4e3e4846021204ae1df.camel@HIDDEN> <ecd331465d03183053f8f9597253c81f9079aa14.camel@HIDDEN> <e82bbd94881b38de2a505c2c1109ce9d3ab529ef.camel@HIDDEN> Content-Type: multipart/signed; micalg="pgp-sha256"; protocol="application/pgp-signature"; boundary="=-OLAcr9G86xml/Rw0zfiQ" User-Agent: Evolution 3.42.1 MIME-Version: 1.0 X-Debbugs-Envelope-To: 53402 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> --=-OLAcr9G86xml/Rw0zfiQ Content-Type: multipart/mixed; boundary="=-09rGn5EaUGSJL3qV08mX" --=-09rGn5EaUGSJL3qV08mX Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello, and thank you for your new review! Le dimanche 06 f=C3=A9vrier 2022 =C3=A0 20:06 +0000, Vinicius Monego a =C3= =A9crit=C2=A0: >=20 > I noticed that some of the tests aren't running, like in flake8-array- > spacing. If the check phase ends with "Ran 0 tests" then the tests are > not being collected. > If there are no tests to be collected, the package should have a > #:tests? #f along with a comment saying that there are no tests. If > there are tests to run, the check phase will have to be overriden to > run them. I tried to make sure that this situation didn=E2=80=99t happen again. > > For MNE, the test data set is a separate repository without a > > license, > > so I disabled the tests. > >=20 >=20 > OK. I tried to download the test dataset from within the mne module > and > they don't have a license agreement or anything, while to download > individiual datasets the user has to agree to the (non-free) terms. I > wonder if that's acceptable for merging in Guix? I think it=E2=80=99s not, plus these are medical data (anonymized but still= ) so maybe we shouldn=E2=80=99t take the risk. > In [1] I found that there are more base dependencies that aren't > listed > in the pypi importer. They should be added to propagated-inputs. If > tests can't run, then native-inputs can be removed. I had nervous laughter when I read that page. I managed to package everything except for the JS widgets (I don=E2=80=99t know how to tackle th= at and I fear it would be a lot of work for very little benefit, since there are other visualization platforms from what I understand) and mne-qt-browser, because it depends on MNE. > Usually, pytest modules should go into python-check.scm, not python- > xyz.scm. I tried to separate them, but they depend on a lot of stuff which is not easy to organize into acyclic module imports. > > > Could you style it as > > >=20 > > > =C2=A0=C2=A0=C2=A0 (source > > > =C2=A0=C2=A0=C2=A0=C2=A0 (origin > > > =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (method url-fetch) > > > =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (uri (pypi-uri "imageio-ffmpeg" = version)) > > > =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (sha256 > > > =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (base32 > > > "0ff14079izsyxwf6ki68k9a7w5krjlal7lwqvzg2bbddl92l5spj")))) > > >=20 > > > and the other packages too? > >=20 > > OK. > >=20 >=20 > The base32 line was truncated in the mail, the hash should be in the > same line of 'base32'. But I can fix that. I fixed that occurence, but as a general rule I=E2=80=99m not very confiden= t in my indentation taste. >=20 > [...] >=20 > >=20 > > >=20 > > > Some of the descriptions are not full sentences (e.g. in python- > > > pytest- > > > harvest-minimal). Please check that descriptions are full > > > sentences. > >=20 > > I=E2=80=99m not sure I understand. I reworked some descriptions, but di= dn=E2=80=99t > > find non-full sentences. Could you explain what you mean? > >=20 >=20 > Full sentences are made of a subject + predicate. This one: >=20 > +=C2=A0=C2=A0=C2=A0 (description "I/O support for EEGLAB files in Python.= ") >=20 > doesn't have a subject. >=20 > Usually the subject in the description is the package's name itself > or > "This package...". e.g. "EEGLABIO is a library..." or "This package > provides I/O support..." I think I got it. >=20 > Something else to avoid in descriptions is marketing talk, such as > 'simple and reliable' in python-imageio-ffmpeg. There were some more occurences that I neutralized. >=20 > [...] >=20 > The package modules you changed are also missing your copyright line. OK. As you see in the new series, vtk doesn=E2=80=99t install an egg-info, whic= h breaks the sanity-check phase of dependent python packages. There was an option to let setuptools build the whole project, so the egg-info would be installed too, but the installation plan with setup.py is dysfunctional. So I made a terrible hack to "install" an egg-info. There=E2=80=99s surely a better way to do it with python or pip, but I have= no clue as to what it would be and I can=E2=80=99t do much trial and error sin= ce I have to wait for everything to build again (and vtk is quite a long thing to compile). Here is the v5! I=E2=80=99m not used to managing such a large patch series; I hope I didn= =E2=80=99t make too many errors. 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guix-patches@HIDDEN:bug#53402; Package guix-patches.
Full text available.Received: (at 53402) by debbugs.gnu.org; 6 Feb 2022 20:07:02 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Feb 06 15:07:02 2022 Received: from localhost ([127.0.0.1]:39870 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nGnoJ-0003oJ-5w for submit <at> debbugs.gnu.org; Sun, 06 Feb 2022 15:07:02 -0500 Received: from mout01.posteo.de ([185.67.36.65]:42981) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <monego@HIDDEN>) id 1nGnoG-0003o3-PF for 53402 <at> debbugs.gnu.org; Sun, 06 Feb 2022 15:06:57 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 69A07240026 for <53402 <at> debbugs.gnu.org>; Sun, 6 Feb 2022 21:06:50 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1644178010; bh=7DTlJw9pd381E5oT0+jRFlg/W1X6tn8Fz1+j9VLW6xM=; h=Subject:From:To:Date:From; b=jAOK4XpDZixDLP1K+S9hUlN9HYiX3ccYEqOcjF9MAyWwrAJMjSavu8DjgNaPaQ+OU TWcARO2Al9fcej9ToADQUmYn0doHt4J30t0Ex/lfRKGMQSx9dNmQX/iV7hZRAV41XI qEvs/Lj5gzf7ul/AGwDqQH16DUANgaXCImxKbkdp0zsOq7j9rM+eyRF6uzelhKjEDi szlDlvo6Gjf4dEIsdvDZ+brCv5H7L7FVEoN5sdVnO7oF3nJHeUuE6bvWK2hEoSn/N1 nLQ5F/ij/d7BfgEs/EYNBrfPW+30PzgYRRGmtR0QuRl8s8AOpyMt+fhgDe4Fh+4EVS my4SrVOvlBOnQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4JsKzr2wq3z9rxQ; Sun, 6 Feb 2022 21:06:48 +0100 (CET) Message-ID: <e82bbd94881b38de2a505c2c1109ce9d3ab529ef.camel@HIDDEN> Subject: Re: Rebase it for the new python packages From: Vinicius Monego <monego@HIDDEN> To: Vivien <vivien@HIDDEN>, 53402 <at> debbugs.gnu.org Date: Sun, 06 Feb 2022 20:06:38 +0000 In-Reply-To: <ecd331465d03183053f8f9597253c81f9079aa14.camel@HIDDEN> References: <df09d62f7aa0e6a21362f9b7df5a88ff0ddd0a41.camel@HIDDEN> <1161a7298bbbbe87ce48f4e3e4846021204ae1df.camel@HIDDEN> <ecd331465d03183053f8f9597253c81f9079aa14.camel@HIDDEN> Content-Type: text/plain; charset="UTF-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 53402 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -3.3 (---) Em dom, 2022-02-06 às 15:49 +0100, Vivien escreveu: > Hello, thank you for your review! > Thanks for the v4. [...] > > > 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 <package> 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. I noticed that some of the tests aren't running, like in flake8-array- spacing. If the check phase ends with "Ran 0 tests" then the tests are not being collected. If there are no tests to be collected, the package should have a #:tests? #f along with a comment saying that there are no tests. If there are tests to run, the check phase will have to be overriden to run them. For imageio-ffmpeg there are tests in github but not PyPI. I tried to source from github but most tests require online data. In that case #:tests? #f should be added with an explanation. > > > 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. > OK. I tried to download the test dataset from within the mne module and they don't have a license agreement or anything, while to download individiual datasets the user has to agree to the (non-free) terms. I wonder if that's acceptable for merging in Guix? In [1] I found that there are more base dependencies that aren't listed in the pypi importer. They should be added to propagated-inputs. If tests can't run, then native-inputs can be removed. > > 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. > OK, it seems that they have a web of dependencies on each other. This is the first time I see such a case. Usually, pytest modules should go into python-check.scm, not python- xyz.scm. > > 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. > The base32 line was truncated in the mail, the hash should be in the same line of 'base32'. But I can fix that. [...] > > > > > 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? > Full sentences are made of a subject + predicate. This one: + (description "I/O support for EEGLAB files in Python.") doesn't have a subject. Usually the subject in the description is the package's name itself or "This package...". e.g. "EEGLABIO is a library..." or "This package provides I/O support..." Something else to avoid in descriptions is marketing talk, such as 'simple and reliable' in python-imageio-ffmpeg. [...] The package modules you changed are also missing your copyright line. Vinicius [1] https://github.com/mne-tools/mne-python/blob/main/requirements_base.txt > > > Sure! > > Best regards, > > Vivien
guix-patches@HIDDEN:bug#53402; Package guix-patches.
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Subject: Re: Rebase it for the new python packages
From: Vivien <vivien@HIDDEN>
To: Vinicius Monego <monego@HIDDEN>, 53402 <at> debbugs.gnu.org
Date: Sun, 06 Feb 2022 15:49:44 +0100
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Content preview: 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.
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Hello, thank you for your review!
Le jeudi 03 f=C3=A9vrier 2022 =C3=A0 20:49 +0000, Vinicius Monego a =C3=A9c=
rit=C2=A0:
> 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 <package> 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=E2=80=99m not sure I should do that.
> I also have a few comments about the patches in general:
>=20
> > +=C2=A0=C2=A0=C2=A0 (source (origin
> > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0 (method url-fetch)
> > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0 (uri (pypi-uri "imageio-ffmpeg" version))
> > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0 (sha256
> > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0 (base32
> > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0=20
> > "0ff14079izsyxwf6ki68k9a7w5krjlal7lwqvzg2bbddl92l5spj"))))
>=20
> Could you style it as
>=20
> =C2=A0=C2=A0=C2=A0 (source
> =C2=A0=C2=A0=C2=A0=C2=A0 (origin
> =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (method url-fetch)
> =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (uri (pypi-uri "imageio-ffmpeg" vers=
ion))
> =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (sha256
> =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (base32
> "0ff14079izsyxwf6ki68k9a7w5krjlal7lwqvzg2bbddl92l5spj"))))
>=20
> 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.
>=20
> When using gexp, it's better to style the arguments as:
>=20
> +=C2=A0=C2=A0=C2=A0 (arguments
> +=C2=A0=C2=A0=C2=A0=C2=A0 (list
> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 #:phases
> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 #~(modify-phases %standard-phases
>=20
> to save columns (some of the packages exceeded the 78 columns limit),
> instead of
>=20
> > +=C2=A0=C2=A0=C2=A0 (arguments
> > +=C2=A0=C2=A0=C2=A0=C2=A0 (list #:phases
> > +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 #~(modify=
-phases %standard-phases
> >=20
OK.
> .
>=20
> Some of the descriptions are not full sentences (e.g. in python-
> pytest-
> harvest-minimal). Please check that descriptions are full sentences.
I=E2=80=99m not sure I understand. I reworked some descriptions, but didn=
=E2=80=99t
find non-full sentences. Could you explain what you mean?
> When sending an updated series, use patch versions with --reroll-
> count=3D4 or -v4.
I didn=E2=80=99t know that option.
> Could you send a v4 with the requested changes?
Sure!
Best regards,
Vivien
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guix-patches@HIDDEN:bug#53402; Package guix-patches.
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Message-ID: <1161a7298bbbbe87ce48f4e3e4846021204ae1df.camel@HIDDEN>
Subject: Re: Rebase it for the new python packages
From: Vinicius Monego <monego@HIDDEN>
To: Vivien <vivien@HIDDEN>, 53402 <at> debbugs.gnu.org
Date: Thu, 03 Feb 2022 20:49:08 +0000
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Em qui, 2022-02-03 às 20:29 +0100, Vivien escreveu:
> Dear guix,
>
> We have 2 new python packages, so my patch series creates a trivial
> conflict. Here is a new version that you can apply directly.
>
> Best regards,
>
> Vivien
Hi,
To avoid future merge conflicts, please move the packages somewhere in
the middle of the files instead of the bottom.
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 <package> 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.
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.
The 'test-less' packages shouldn't be needed AFAICS. Tests should run
by overriding the check phase as stated above (untested).
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?
Gexps should only be used when ungexp (#$) is used. On many patches
(e.g. python-nitime) ungexp is not being used.
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
>
.
Some of the descriptions are not full sentences (e.g. in python-pytest-
harvest-minimal). Please check that descriptions are full sentences.
When sending an updated series, use patch versions with --reroll-
count=4 or -v4.
Could you send a v4 with the requested changes?
Vinicius
guix-patches@HIDDEN:bug#53402; Package guix-patches.
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The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Dear guix, We have 2 new python packages, so my patch series creates a trivial conflict. Here is a new version that you can apply directly. Best regards, Content analysis details: (1.2 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 SPF_HELO_PASS SPF: HELO matches SPF record -0.0 SPF_PASS SPF: sender matches SPF record -0.0 T_SCC_BODY_TEXT_LINE No description available. 1.2 URI_DOTEDU Has .edu URI X-Debbugs-Envelope-To: 53402 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) --=-Ag06dvyCzFuf+HQ2ynkY Content-Type: multipart/mixed; boundary="=-gL3z4KuCxdqIPWkr7pwT" --=-gL3z4KuCxdqIPWkr7pwT Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear guix, We have 2 new python packages, so my patch series creates a trivial conflict. Here is a new version that you can apply directly. 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From: Vivien Kraus <vivien@HIDDEN>
To: 53402 <at> debbugs.gnu.org
Subject: Add python-mne: fix or disable tests
Date: Fri, 21 Jan 2022 09:17:38 +0100
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Content preview: 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 5c8b341c7d39cc88d723788416865e4d9e26b331 Mon
Sep 17 00:00:00 2001 From: Vivien Kraus <vivien@HIDDEN> Date: Thu,
20 Jan 2022 15:39:12 +0100 Subject: [PATCH 01/18] gnu: Add python-imageio
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--=-=-=
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: quoted-printable
Dear guix,
I could fix one test suite, but as luis-felipe told me on #guix, the
test data isn=E2=80=99t fully distributed by pypi for mne, so I had to disa=
ble
it.
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0001-gnu-Add-python-imageio-ffmpeg.patch
Content-Transfer-Encoding: quoted-printable
From=205c8b341c7d39cc88d723788416865e4d9e26b331 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 15:39:12 +0100
Subject: [PATCH 01/18] gnu: Add python-imageio-ffmpeg.
* gnu/packages/python-xyz.scm (python-imageio-ffmpeg): New variable.
=2D--
gnu/packages/python-xyz.scm | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index eff1c4259b..c0b1fe9872 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28678,3 +28678,36 @@ (define-public python-reedsolo
but not binary streams.")
(license license:public-domain)))
=20
+(define-public python-imageio-ffmpeg
+ (package
+ (name "python-imageio-ffmpeg")
+ (version "0.4.5")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "imageio-ffmpeg" version))
+ (sha256
+ (base32
+ "0ff14079izsyxwf6ki68k9a7w5krjlal7lwqvzg2bbddl92l5spj"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (add-after 'unpack 'set-ffmpeg-exe
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; There are different strategies to find ffmpeg, we
+ ;; only fix the last resort, "system ffmpeg command"
+ (substitute* "imageio_ffmpeg/_utils.py"
+ (("exe =3D \"ffmpeg\"")
+ (format #f "exe =3D ~s"
+ (search-input-file
+ inputs "/bin/ffmpeg")))))))))
+ (inputs (list ffmpeg))
+ (home-page "https://github.com/imageio/imageio-ffmpeg")
+ (synopsis "@samp{ffmpeg} wrapper for Python")
+ (description
+ "The purpose of this project is to provide a simple and reliable
+@samp{ffmpeg} wrapper for working with video files. It implements two sim=
ple
+generator functions for reading and writing data from/to ffmpeg, which
+reliably terminate the ffmpeg process when done. It also takes care of
+publishing platform-specific wheels that include the binary @samp{ffmpeg}
+executables.")
+ (license license:bsd-2)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment; filename=0002-gnu-Add-python-edflib.patch
Content-Transfer-Encoding: quoted-printable
From=20b1c4e71b7ce091e57b247c879d41a9e058054606 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 15:47:30 +0100
Subject: [PATCH 02/18] gnu: Add python-edflib.
* gnu/packages/python-science.scm (python-edflib): New variable.
=2D--
gnu/packages/python-science.scm | 51 ++++++++++++++++++++++++++++++++-
1 file changed, 50 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.=
scm
index 1cfc8e5869..47b142494e 100644
=2D-- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -61,7 +61,8 @@ (define-module (gnu packages python-science)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix utils)
=2D #:use-module (guix build-system python))
+ #:use-module (guix build-system python)
+ #:use-module (guix gexp))
=20
(define-public python-scipy
(package
@@ -1035,3 +1036,51 @@ (define-public python-modin
libraries, Modin provides seamless integration and compatibility with exis=
ting
pandas code.")
(license license:asl2.0)))
+
+(define-public python-edflib
+ (package
+ (name "python-edflib")
+ (version "1.0.6")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "EDFlib-Python" version))
+ (sha256
+ (base32
+ "1g069kyibskx5q2mc494xgjhvdspw5lvk2xhn0kqcgq1h37x5lfv"))))
+ (build-system python-build-system)
+ (arguments
+ (list #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; XXX: PEP 517 manual build copied from python-isort.
+ (replace 'build
+ (lambda _
+ (setenv "SOURCE_DATE_EPOCH" "315532800")
+ (invoke "python"
+ "-m"
+ "build"
+ "--wheel"
+ "--no-isolation"
+ ".")))
+ (replace 'install
+ (lambda _
+ (let ((whl (car (find-files "dist" "\\.whl$"))))
+ (invoke "pip"
+ "--no-cache-dir"
+ "--no-input"
+ "install"
+ "--no-deps"
+ "--prefix"
+ #$output
+ whl)))))))
+ (propagated-inputs (list python-numpy python-pypa-build))
+ (home-page "https://www.teuniz.net/edflib_python/")
+ (synopsis "Read and write EDF+/BDF+ files")
+ (description
+ "EDFlib for Python is a programming library to read and write EDF+ and
+BDF+ files. It also reads old-type EDF/BDF files. @dfn{EDF} means
+@url{https://www.teuniz.net/edfbrowser/edf%20format%20description.html,
+European Data Format}. @dfn{BDF} is the
+@url{https://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html,
+24-bit version} of EDF.")
+ (license license:bsd-3)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment; filename=0003-gnu-Add-python-eeglabio.patch
Content-Transfer-Encoding: quoted-printable
From=209a21f7bba1ef895d664115a70c27cdd7769bb108 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 17:17:11 +0100
Subject: [PATCH 03/18] gnu: Add python-eeglabio.
* gnu/packages/python-science.scm (python-eeglabio): New variable.
=2D--
gnu/packages/python-science.scm | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.=
scm
index 47b142494e..e6a15ae27f 100644
=2D-- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1084,3 +1084,32 @@ (define-public python-edflib
@url{https://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html,
24-bit version} of EDF.")
(license license:bsd-3)))
+
+(define-public python-eeglabio
+ (package
+ (name "python-eeglabio")
+ (version "0.0.1.post6")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "eeglabio" version))
+ (sha256
+ (base32
+ "0k70s8lg9b9mcs883kq8jgnj9wmxvb96q54w23f3zw38jjxw46gs"))))
+ (build-system python-build-system)
+ (arguments
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'restore-requirements.txt
+ (lambda _
+ ;; requirements.txt is not distributed, but it is in the
+ ;; source
+ (call-with-output-file "requirements.txt"
+ (lambda (port)
+ (format port "numpy
+scipy
+"))))))))
+ (propagated-inputs (list python-numpy python-scipy))
+ (home-page "https://github.com/jackz314/eeglabio")
+ (synopsis "I/O support for EEGLAB files in Python")
+ (description "I/O support for EEGLAB files in Python.")
+ (license license:bsd-3)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment; filename=0004-gnu-Add-python-nibabel.patch
Content-Transfer-Encoding: quoted-printable
From=207e59b85005be2e61979e216e070bed99de8cae02 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 17:38:47 +0100
Subject: [PATCH 04/18] gnu: Add python-nibabel.
* gnu/packages/python-science.scm (python-nibabel): New variable.
=2D--
gnu/packages/python-science.scm | 63 +++++++++++++++++++++++++++++++++
1 file changed, 63 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.=
scm
index e6a15ae27f..a79aacec03 100644
=2D-- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -54,6 +54,7 @@ (define-module (gnu packages python-science)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages statistics)
#:use-module (gnu packages time)
+ #:use-module (gnu packages version-control)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
@@ -1113,3 +1114,65 @@ (define-public python-eeglabio
(synopsis "I/O support for EEGLAB files in Python")
(description "I/O support for EEGLAB files in Python.")
(license license:bsd-3)))
+
+(define-public python-nibabel
+ (package
+ (name "python-nibabel")
+ (version "3.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "nibabel" version))
+ (sha256
+ (base32
+ "17n23w7y0hiz2vma5si7wy184d59bp14zd8nr6hi203ldd1gjbsd"))))
+ (build-system python-build-system)
+ (arguments
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'fix-tests
+ (lambda _
+ ;; Some tests have a setup function, but it is not call=
ed
+ ;; (!)
+ (for-each (lambda (fix)
+ (let ((file (open-file (string-append
+ "nibabel/streamline=
s/tests/test_"
+ (car fix) ".py") "a=
")))
+ (format file "
+~a()"
+ (cdr fix))
+ (close-port file)))
+ '(("array_sequence" . "setup_module")
+ ("streamlines" . "setup")
+ ("tck" . "setup_module")
+ ("tractogram" . "setup_module")
+ ("trk" . "setup_module"))))))))
+ (propagated-inputs (list python-numpy python-packaging))
+ (native-inputs (list python-coverage
+ python-gitpython
+ python-pytest
+ python-pytest-cov
+ python-pytest-doctestplus
+ python-twine))
+ (home-page "https://nipy.org/nibabel/")
+ (synopsis "Access a multitude of neuroimaging data formats")
+ (description
+ "This package provides read +/- write access to some common
+medical and neuroimaging file formats, including:
+@url{http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm,
+ANALYZE} (plain, SPM99, SPM2 and later),
+@url{https://www.nitrc.org/projects/gifti, GIFTI},
+@url{http://nifti.nimh.nih.gov/nifti-1/, NIfTI1},
+@url{http://nifti.nimh.nih.gov/nifti-2/, NIfTI2},
+@url{https://www.nitrc.org/projects/cifti/, CIFTI-2},
+@url{https://en.wikibooks.org/wiki/MINC/Reference/MINC1_File_Format_Refere=
nce,
+MINC1},
+@url{https://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_File_Format_Refe=
rence,
+MINC2}, @url{https://afni.nimh.nih.gov/pub/dist/src/README.attributes, AFNI
+BRIK/HEAD},
+@url{https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat, MGH} =
and
+@url{http://xmedcon.sourceforge.net/Docs/Ecat, ECAT} as well as Philips
+PAR/REC. We can read and write @url{https://surfer.nmr.mgh.harvard.edu/,
+FreeSurfer} geometry, annotation and morphometry files. There is some very
+limited support for @url{http://medical.nema.org/, DICOM}. NiBabel is the
+successor of @url{http://niftilib.sourceforge.net/pynifti/, PyNIfTI}.")
+ (license license:expat)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment; filename=0005-gnu-Add-python-nitime.patch
Content-Transfer-Encoding: quoted-printable
From=202b16738c003b90373b4ee857b7bcd7c441ab4a83 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 19:12:02 +0100
Subject: [PATCH 05/18] gnu: Add python-nitime.
* gnu/packages/python-science.scm (python-nitime): New variable.
=2D--
gnu/packages/python-science.scm | 34 +++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.=
scm
index a79aacec03..08a12d3b99 100644
=2D-- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1176,3 +1176,37 @@ (define-public python-nibabel
limited support for @url{http://medical.nema.org/, DICOM}. NiBabel is the
successor of @url{http://niftilib.sourceforge.net/pynifti/, PyNIfTI}.")
(license license:expat)))
+
+(define-public python-nitime
+ (package
+ (name "python-nitime")
+ (version "0.9")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "nitime" version))
+ (sha256
+ (base32
+ "0x1q6ka8i330yhp5h0h6igfs2gp5dndiybyfkdi45a8zpfnr0zbf"))))
+ (build-system python-build-system)
+ (propagated-inputs (list python-matplotlib python-networkx python-niba=
bel
+ python-numpy python-scipy))
+ (native-inputs (list python-cython python-pytest))
+ (arguments
+ (list #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'delete-generated-cython
+ (lambda _
+ (delete-file "nitime/_utils.c")))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest" "-vv" "nitime")))))))
+ (home-page "http://nipy.org/nitime/")
+ (synopsis "Nitime: timeseries analysis for neuroscience data")
+ (description
+ "Nitime contains a core of numerical algorithms for
+time-series analysis both in the time and spectral domains, a set of conta=
iner
+objects to represent time-series, and auxiliary objects that expose a high
+level interface to the numerical machinery and make common analysis tasks =
easy
+to express with compact and semantically clear code.")
+ (license license:bsd-3)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0006-gnu-Add-python-flake8-array-spacing.patch
Content-Transfer-Encoding: quoted-printable
From=204eab1c63bfed00124587a7b35dda2f12512653fe Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 19:20:06 +0100
Subject: [PATCH 06/18] gnu: Add python-flake8-array-spacing.
* gnu/packages/python-science.scm (python-flake8-array-spacing): New variab=
le.
=2D--
gnu/packages/python-science.scm | 1 +
gnu/packages/python-xyz.scm | 17 +++++++++++++++++
2 files changed, 18 insertions(+)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.=
scm
index 08a12d3b99..97cca59644 100644
=2D-- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1210,3 +1210,4 @@ (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)))
+
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c0b1fe9872..af05195513 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28711,3 +28711,20 @@ (define-public python-imageio-ffmpeg
publishing platform-specific wheels that include the binary @samp{ffmpeg}
executables.")
(license license:bsd-2)))
+
+(define-public python-flake8-array-spacing
+ (package
+ (name "python-flake8-array-spacing")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "flake8_array_spacing" version))
+ (sha256
+ (base32 "0nyp2x45hg5dkdrn0j2wcd336dnx6csizpfq5fwbk774wrb0lh6d"))=
))
+ (build-system python-build-system)
+ (propagated-inputs (list python-flake8 python-pycodestyle))
+ (home-page "https://github.com/larsoner/flake8-array-spacing")
+ (synopsis "flake8 plugin to make exceptions for array-like variables")
+ (description "Recast some E2XX errors as A2XX with exceptions for arra=
y-like variables.")
+ (license license:bsd-3)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment; filename=0007-gnu-Add-python-makefun.patch
Content-Transfer-Encoding: quoted-printable
From=20a1208f8263f13a61f1a6cde285de3e5aed9e3605 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 21:17:39 +0100
Subject: [PATCH 07/18] gnu: Add python-makefun.
* gnu/packages/python-xyz.scm (python-makefun): New variable.
=2D--
gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index af05195513..f09f4abf57 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28728,3 +28728,24 @@ (define-public python-flake8-array-spacing
(synopsis "flake8 plugin to make exceptions for array-like variables")
(description "Recast some E2XX errors as A2XX with exceptions for arra=
y-like variables.")
(license license:bsd-3)))
+
+(define-public python-makefun
+ (package
+ (name "python-makefun")
+ (version "1.13.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "makefun" version))
+ (sha256
+ (base32
+ "1gqnqvwzig9ym4nyzwy6dzra7sg6339rdaca59fvkfzzf2vbhnwq"))))
+ (build-system python-build-system)
+ (native-inputs (list python-pytest python-pytest-runner
+ python-setuptools-scm))
+ (home-page "https://github.com/smarie/python-makefun")
+ (synopsis "Small library to dynamically create python functions")
+ (description
+ "@samp{makefun} helps you create functions dynamically, with
+the signature of your choice. It was largely inspired by @samp{decorator}=
and
+@samp{functools}, and created mainly to cover some of their limitations.")
+ (license license:bsd-3)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0008-gnu-Add-python-pytest-logging.patch
Content-Transfer-Encoding: quoted-printable
From=204ba30ee1032e852104542b459e0b5e76725f0df5 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 22:32:09 +0100
Subject: [PATCH 08/18] gnu: Add python-pytest-logging.
* gnu/packages/python-xyz.scm (python-pytest-logging): New variable.
=2D--
gnu/packages/python-xyz.scm | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f09f4abf57..6522026717 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28749,3 +28749,22 @@ (define-public python-makefun
the signature of your choice. It was largely inspired by @samp{decorator}=
and
@samp{functools}, and created mainly to cover some of their limitations.")
(license license:bsd-3)))
+
+(define-public python-pytest-logging
+ (package
+ (name "python-pytest-logging")
+ (version "2015.11.4")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pytest-logging" version))
+ (sha256
+ (base32
+ "15n8fyxvvwmk982vj0m9yl76hn7pp4qqljfmxarbgahqrxgciiff"))))
+ (build-system python-build-system)
+ (propagated-inputs (list python-pytest))
+ (home-page "https://github.com/saltstack/pytest-logging")
+ (synopsis
+ "Configures logging and allows tweaking the log level with a py.test =
flag")
+ (description
+ "Configures logging and allows tweaking the log level with a py.test =
flag.")
+ (license license:asl2.0)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0009-gnu-Add-a-test-less-python-decopatch.patch
Content-Transfer-Encoding: quoted-printable
From=2070ec47cdd5ef2dfe750cf54677ae2af19d204ad5 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 22:32:53 +0100
Subject: [PATCH 09/18] gnu: Add a test-less python-decopatch.
* gnu/packages/python-xyz.scm (python-decopatch-minimal): New variable.
=2D--
gnu/packages/python-xyz.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6522026717..d51deec454 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28768,3 +28768,33 @@ (define-public python-pytest-logging
(description
"Configures logging and allows tweaking the log level with a py.test =
flag.")
(license license:asl2.0)))
+
+;; decopatch requires the next pytest modules if tests are enabled. The py=
test
+;; modules require each other for tests.
+
+(define python-decopatch-minimal
+ (package
+ (name "python-decopatch-minimal")
+ (version "1.4.8")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "decopatch" version))
+ (sha256
+ (base32
+ "0i6i811s2j1z0cl6y177dwsbfxib8dvb5c2jpgklvc2xy4ahhsy6"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f))
+ (propagated-inputs (list python-makefun))
+ (native-inputs (list python-pytest python-pytest-runner
+ python-setuptools-scm))
+ (home-page "https://github.com/smarie/python-decopatch")
+ (synopsis "Python decorators made easy")
+ (description
+ "Because of a tiny oddity in the python language, writing
+decorators without help can be a pain because you have to handle the
+no-parenthesis usage
+@url{https://smarie.github.io/python-decopatch/motivation, explicitly}.
+@samp{decopatch} provides a simple way to solve this issue so that writing
+decorators is simple and straightforward.")
+ (license license:bsd-3)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0010-gnu-Add-a-test-less-python-pytest-harvest.patch
Content-Transfer-Encoding: quoted-printable
From=20cf04823d3c5f711f04776a85fd39f043f8b56fea Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 22:33:32 +0100
Subject: [PATCH 10/18] gnu: Add a test-less python-pytest-harvest.
* gnu/packages/python-xyz.scm (python-pytest-harvest-minimal): New variable.
=2D--
gnu/packages/python-xyz.scm | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d51deec454..15bd70fa8f 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28798,3 +28798,27 @@ (define python-decopatch-minimal
@samp{decopatch} provides a simple way to solve this issue so that writing
decorators is simple and straightforward.")
(license license:bsd-3)))
+
+(define python-pytest-harvest-minimal
+ (package
+ (name "python-pytest-harvest-minimal")
+ (version "1.10.3")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pytest-harvest" version))
+ (sha256
+ (base32
+ "092drlh96rhikwqqyfpwqhkzfzd7z8m5gbmjgky8npm81849jbsk"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f))
+ (propagated-inputs (list python-decopatch-minimal python-makefun
+ python-six))
+ (native-inputs (list python-pytest python-pytest-runner
+ python-setuptools-scm))
+ (home-page "https://github.com/smarie/python-pytest-harvest")
+ (synopsis "Store data created during your @samp{pytest} tests executio=
n")
+ (description
+ "Store data created during your pytest tests execution, and retrieve =
it
+at the end of the session, e.g. for applicative benchmarking purposes.")
+ (license license:bsd-3)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0011-gnu-Add-a-test-less-python-pytest-steps.patch
Content-Transfer-Encoding: quoted-printable
From=2032ba11f8349b9443585e5da86c190d098c4256e5 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 22:34:06 +0100
Subject: [PATCH 11/18] gnu: Add a test-less python-pytest-steps.
* gnu/packages/python-xyz.scm (python-pytest-steps-minimal): New variable.
=2D--
gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 15bd70fa8f..57cc09ae18 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28822,3 +28822,25 @@ (define python-pytest-harvest-minimal
"Store data created during your pytest tests execution, and retrieve =
it
at the end of the session, e.g. for applicative benchmarking purposes.")
(license license:bsd-3)))
+
+(define python-pytest-steps-minimal
+ (package
+ (name "python-pytest-steps-minimal")
+ (version "1.8.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pytest-steps" version))
+ (sha256
+ (base32
+ "05r2ch7191saj7sw6d47bfa5vnyyj157dl8hvlcc78xx6jyxy46j"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f))
+ (propagated-inputs (list python-makefun python-wrapt python-tabulate
+ python-pandas))
+ (native-inputs (list python-pytest python-pytest-runner
+ python-setuptools-scm))
+ (home-page "https://github.com/smarie/python-pytest-steps")
+ (synopsis "Create step-wise / incremental tests in pytest")
+ (description "Create step-wise / incremental tests in pytest.")
+ (license license:bsd-3)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0012-gnu-Add-a-test-less-python-pytest-cases.patch
Content-Transfer-Encoding: quoted-printable
From=20d550923f148fe5ce82ba287821cbf77aed6025b0 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 22:34:36 +0100
Subject: [PATCH 12/18] gnu: Add a test-less python-pytest-cases.
* gnu/packages/python-xyz.scm (python-pytest-cases-minimal): New variable.
=2D--
gnu/packages/python-xyz.scm | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 57cc09ae18..cccd4e2b03 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28844,3 +28844,34 @@ (define python-pytest-steps-minimal
(synopsis "Create step-wise / incremental tests in pytest")
(description "Create step-wise / incremental tests in pytest.")
(license license:bsd-3)))
+
+(define python-pytest-cases-minimal
+ (package
+ (name "python-pytest-cases-minimal")
+ (version "3.6.8")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pytest-cases" version))
+ (sha256
+ (base32
+ "1g3lp4m19fk83kl2b4akwg7wqqaqlfzp4v6qcb0hq27161xyh8yl"))))
+ (build-system python-build-system)
+ (propagated-inputs (list python-decopatch-minimal python-makefun))
+ (native-inputs (list python-pytest
+ python-pytest-runner
+ python-setuptools-scm
+ python-pytest-asyncio
+ python-pytest-harvest-minimal
+ python-pytest-steps-minimal))
+ (home-page "https://github.com/smarie/python-pytest-cases")
+ (synopsis "Separate test code from test cases in @samp{pytest}")
+ (description
+ "@samp{pytest-cases} leverages @samp{pytest} and its great
+@samp{@@pytest.mark.parametrize decorator}, so that you can @strong{separa=
te
+your test cases from your test functions}. In addition, @samp{pytest-case=
s}
+provides several useful goodies to empower @samp{pytest}. In particular it
+improves the fixture mechanism to support \"fixture unions\". This is a
+@strong{major change} in the internal @samp{pytest} engine, unlocking many
+possibilities such as using fixture references as parameter values in a te=
st
+function.")
+ (license license:bsd-3)))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0013-gnu-Add-python-decopatch.patch
Content-Transfer-Encoding: quoted-printable
From=20208f3b0f2b4771902b8be1faeb445da39ed06bf5 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 22:35:02 +0100
Subject: [PATCH 13/18] gnu: Add python-decopatch.
* gnu/packages/python-xyz.scm (python-decopatch): New variable.
=2D--
gnu/packages/python-xyz.scm | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index cccd4e2b03..d735e62a80 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28875,3 +28875,24 @@ (define python-pytest-cases-minimal
possibilities such as using fixture references as parameter values in a te=
st
function.")
(license license:bsd-3)))
+
+(define-public python-decopatch
+ (package
+ (inherit python-decopatch-minimal)
+ (name "python-decopatch")
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (add-after 'unpack 'disable-failing-tests
+ (lambda _
+ (delete-file "decopatch/tests/test_main2.py")
+ (delete-file
+ "decopatch/tests/test_main2_parametrizers.py")
+ (delete-file "decopatch/tests/test_introspection.py")
+ (delete-file
+ "decopatch/tests/test_introspection_base.py")
+ (substitute* "decopatch/tests/test_doc_advanced.py"
+ (("'uses_introspection', \\[True, False\\]")
+ "'uses_introspection', [False]")))))))
+ (native-inputs (list python-pytest python-pytest-runner
+ python-pytest-cases-minimal python-setuptools-scm
+ python-pytest-logging))))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0014-gnu-Add-python-pytest-cases.patch
Content-Transfer-Encoding: quoted-printable
From=200bd5e596cff51d3b5d6c2fe19d75a5e0b2126cac Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 22:35:28 +0100
Subject: [PATCH 14/18] gnu: Add python-pytest-cases.
* gnu/packages/python-xyz.scm (python-pytest-cases): New variable.
=2D--
gnu/packages/python-xyz.scm | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d735e62a80..ea4de06935 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28896,3 +28896,11 @@ (define-public python-decopatch
(native-inputs (list python-pytest python-pytest-runner
python-pytest-cases-minimal python-setuptools-scm
python-pytest-logging))))
+
+(define-public python-pytest-cases
+ (package
+ (inherit python-pytest-cases-minimal)
+ (name "python-pytest-cases")
+ (arguments
+ '())
+ (propagated-inputs (list python-decopatch python-makefun))))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0015-gnu-Add-python-pytest-harvest.patch
Content-Transfer-Encoding: quoted-printable
From=202684ac7c595006f90730b5f15f2c6839335f39a3 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 22:35:49 +0100
Subject: [PATCH 15/18] gnu: Add python-pytest-harvest.
* gnu/packages/python-xyz.scm (python-pytest-harvest): New variable.
=2D--
gnu/packages/python-xyz.scm | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ea4de06935..6d57192ccb 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28904,3 +28904,21 @@ (define-public python-pytest-cases
(arguments
'())
(propagated-inputs (list python-decopatch python-makefun))))
+
+(define-public python-pytest-harvest
+ (package
+ (inherit python-pytest-harvest-minimal)
+ (name "python-pytest-harvest")
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (add-after 'unpack 'move-pytests-plugins
+ (lambda _
+ (rename-file "pytest_harvest/tests/conftest.py"
+ "conftest.py"))))))
+ (native-inputs (list python-pytest
+ python-pytest-runner
+ python-setuptools-scm
+ python-pytest-cases
+ python-tabulate
+ python-pandas))
+ (propagated-inputs (list python-decopatch python-makefun python-six))))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0016-gnu-Add-python-pytest-steps.patch
Content-Transfer-Encoding: quoted-printable
From=20db56ec3ba0e91a3b29c2a73282127249954ee45e Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 22:36:06 +0100
Subject: [PATCH 16/18] gnu: Add python-pytest-steps.
* gnu/packages/python-xyz.scm (python-pytest-steps): New variable.
=2D--
gnu/packages/python-xyz.scm | 14 ++++++++++++++
1 file changed, 14 insertions(+)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6d57192ccb..0f85efd085 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -28922,3 +28922,17 @@ (define-public python-pytest-harvest
python-tabulate
python-pandas))
(propagated-inputs (list python-decopatch python-makefun python-six))))
+
+(define-public python-pytest-steps
+ (package
+ (inherit python-pytest-steps-minimal)
+ (name "python-pytest-steps")
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (add-after 'unpack 'move-pytests-plugins
+ (lambda _
+ (rename-file "pytest_steps/tests/conftest.py"
+ "conftest.py"))))))
+ (native-inputs (list python-pytest python-pytest-runner
+ python-setuptools-scm python-pytest-cases
+ python-pytest-harvest))))
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
filename=0017-gnu-python-pooch-Update-to-1.5.2.patch
Content-Transfer-Encoding: quoted-printable
From=203cc9befb02d2c6b79ee222e918ed6ce80965e4f7 Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
Date: Thu, 20 Jan 2022 23:00:37 +0100
Subject: [PATCH 17/18] gnu: python-pooch: Update to 1.5.2.
* gnu/packages/python-xyz.scm (python-pooch): Update to 1.5.2.
[native-inputs]: Add python-setuptools-scm.
=2D--
gnu/packages/python-xyz.scm | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0f85efd085..b386bd93bf 100644
=2D-- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -22095,18 +22095,20 @@ (define-public pybind11
(define-public python-pooch
(package
(name "python-pooch")
=2D (version "1.3.0")
+ (version "1.5.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pooch" version))
(sha256
=2D (base32 "1618adsg9r8fsv422sv35z1i723q3a1iir5v7dv2sklh4pl4im1h"))=
))
+ (base32 "109my6dwj2r6gxfzkw973ivy4dmmw02pwxijz5fl1p7vvvqv4sar"))))
(build-system python-build-system)
(arguments
`(#:tests? #f)) ;requires online data
(propagated-inputs
(list python-appdirs python-packaging python-requests))
+ (native-inputs
+ (list python-setuptools-scm))
(home-page "https://github.com/fatiando/pooch")
(synopsis "Manage your Python library's sample data files")
(description
=2D-=20
2.34.0
--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment; filename=0018-gnu-Add-python-mne.patch
Content-Transfer-Encoding: quoted-printable
From=20dc0467eec2630fc6067a7b3d49d44869497f1f8e Mon Sep 17 00:00:00 2001
From: Vivien Kraus <vivien@HIDDEN>
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.
=2D--
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
=2D-- 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)))
=20
+(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)))
+
+
=2D-=20
2.34.0
--=-=-=--
--==-=-=
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--==-=-=--
guix-patches@HIDDEN:bug#53402; Package guix-patches.
Full text available.Received: (at submit) by debbugs.gnu.org; 20 Jan 2022 22:47:34 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Thu Jan 20 17:47:33 2022 Received: from localhost ([127.0.0.1]:59612 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1nAgDF-00035q-1k for submit <at> debbugs.gnu.org; Thu, 20 Jan 2022 17:47:33 -0500 Received: from lists.gnu.org ([209.51.188.17]:44650) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <vivien@HIDDEN>) id 1nAgD6-00035a-KZ for submit <at> debbugs.gnu.org; Thu, 20 Jan 2022 17:47:24 -0500 Received: from eggs.gnu.org ([209.51.188.92]:50670) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <vivien@HIDDEN>) id 1nAgD6-0008UO-Bx for guix-patches@HIDDEN; Thu, 20 Jan 2022 17:47:16 -0500 Received: from [2a00:5881:4008:2810::309] (port=43528 helo=planete-kraus.eu) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_CHACHA20_POLY1305:256) (Exim 4.90_1) (envelope-from <vivien@HIDDEN>) id 1nAgD1-0008FC-FH for guix-patches@HIDDEN; Thu, 20 Jan 2022 17:47:16 -0500 Received: from planete-kraus.eu (localhost.lan [127.0.0.1]) by planete-kraus.eu (OpenSMTPD) with ESMTP id 83bcccc2 for <guix-patches@HIDDEN>; Thu, 20 Jan 2022 22:47:07 +0000 (UTC) DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=planete-kraus.eu; h= message-id:subject:from:to:date:content-type:mime-version; s= dkim; bh=MeyAAXYulhR5xd9l3zC8eTzA8Mk=; b=dfYHQHue5oZiq7bZu0reC1d DD8a+iDEw2rkMEpyUYEkzJNzmXa2Cqmw2TTEoAz0oONSIXY5Dfc0X2eRF49lvz2k Sd4nu+BUp5SXAFnXApkRJIePJnswlJKZp8KdHhsQ/m3jedKEGpTZmhUEgSlC2Lz1 44UxDbUVJGKoccAiNnLU= Received: by planete-kraus.eu (OpenSMTPD) with ESMTPSA id 3811cfc8 (TLSv1.3:AEAD-CHACHA20-POLY1305-SHA256:256:NO) for <guix-patches@HIDDEN>; Thu, 20 Jan 2022 22:47:02 +0000 (UTC) Message-ID: <c34c3dd954eea62f2e31abf6da5f6d7517b4a9b1.camel@HIDDEN> Subject: Add python-mne From: Vivien <vivien@HIDDEN> To: guix-patches <guix-patches@HIDDEN> Date: Thu, 20 Jan 2022 23:46:54 +0100 Content-Type: multipart/signed; micalg="pgp-sha256"; protocol="application/pgp-signature"; boundary="=-hvbYEY7XHbJuKp86Dlbt" User-Agent: Evolution 3.42.1 MIME-Version: 1.0 X-Host-Lookup-Failed: Reverse DNS lookup failed for 2a00:5881:4008:2810::309 (failed) Received-SPF: pass client-ip=2a00:5881:4008:2810::309; envelope-from=vivien@HIDDEN; helo=planete-kraus.eu X-Spam_score_int: 7 X-Spam_score: 0.7 X-Spam_bar: / X-Spam_report: (0.7 / 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, RDNS_NONE=0.793, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, URI_DOTEDU=1.997 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -0.1 (/) --=-hvbYEY7XHbJuKp86Dlbt Content-Type: multipart/mixed; boundary="=-aEdkL8MSfL7oxjiAeGjz" --=-aEdkL8MSfL7oxjiAeGjz Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear guix, I am trying to get python-mne package=C2=A0[1]. So far I=E2=80=99ve managed= to get all the advertised dependencies, but I can=E2=80=99t get the tests to pass. For python-nitime, I get IndexError: tuple index out of range For python-mne, I get TypeError: annotate_nan() missing 1 required positional argument: 'raw' Both errors seem to occur because a function with optional or keyword arguments is called without enough arguments. However, I can disable all tests that call the function, but the error stays there. Can someone help me? Best regards, Vivien [1]: https://mne.tools/stable/index.html --=-aEdkL8MSfL7oxjiAeGjz Content-Disposition: attachment; filename="0018-gnu-Add-python-mne.patch" Content-Transfer-Encoding: base64 Content-Type: text/x-patch; name="0018-gnu-Add-python-mne.patch"; charset="UTF-8" RnJvbSBmZDNhOTgzMDE3ODBlYjc0MzIyZGI4N2RhNjQxZGNkMmM0MWFkNzZhIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiBWaXZpZW4gS3JhdXMgPHZpdmllbkBwbGFuZXRlLWtyYXVzLmV1 PgpEYXRlOiBUaHUsIDIwIEphbiAyMDIyIDIzOjIxOjI1ICswMTAwClN1YmplY3Q6IFtQQVRDSCAx OC8xOF0gZ251OiBBZGQgcHl0aG9uLW1uZS4KCiogZ251L3BhY2thZ2VzL3B5dGhvbi1zY2llbmNl LnNjbSAocHl0aG9uLW1uZSk6IE5ldyB2YXJpYWJsZS4KLS0tCiBnbnUvcGFja2FnZXMvcHl0aG9u LXNjaWVuY2Uuc2NtIHwgNDggKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrKysrCiAxIGZp bGUgY2hhbmdlZCwgNDggaW5zZXJ0aW9ucygrKQoKZGlmZiAtLWdpdCBhL2dudS9wYWNrYWdlcy9w eXRob24tc2NpZW5jZS5zY20gYi9nbnUvcGFja2FnZXMvcHl0aG9uLXNjaWVuY2Uuc2NtCmluZGV4 IGY4OTNjNjNhODIuLmFkYWQ1MTMxZGYgMTAwNjQ0Ci0tLSBhL2dudS9wYWNrYWdlcy9weXRob24t 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Vivien <vivien@HIDDEN>:guix-patches@HIDDEN.
Full text available.guix-patches@HIDDEN:bug#53402; Package guix-patches.
Full text available.
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997 nCipher Corporation Ltd,
1994-97 Ian Jackson.