From unknown Sat Aug 16 14:29:49 2025 X-Loop: help-debbugs@gnu.org Subject: bug#39872: python-anndata fails to build Resent-From: Maxim Cournoyer Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Mon, 02 Mar 2020 19:30:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 39872 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 39872@debbugs.gnu.org X-Debbugs-Original-To: bug-guix Received: via spool by submit@debbugs.gnu.org id=B.158317739223082 (code B ref -1); Mon, 02 Mar 2020 19:30:01 +0000 Received: (at submit) by debbugs.gnu.org; 2 Mar 2020 19:29:52 +0000 Received: from localhost ([127.0.0.1]:38378 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8qlE-00060D-8z for submit@debbugs.gnu.org; Mon, 02 Mar 2020 14:29:52 -0500 Received: from lists.gnu.org ([209.51.188.17]:38341) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8qlC-000606-JL for submit@debbugs.gnu.org; Mon, 02 Mar 2020 14:29:50 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:56464) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j8qlB-0000ES-Ah for bug-guix@gnu.org; Mon, 02 Mar 2020 14:29:50 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,FREEMAIL_FROM, URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1j8ql9-0005y9-US for bug-guix@gnu.org; Mon, 02 Mar 2020 14:29:49 -0500 Received: from mail-qk1-x732.google.com ([2607:f8b0:4864:20::732]:44151) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1j8ql9-0005xq-OH for bug-guix@gnu.org; Mon, 02 Mar 2020 14:29:47 -0500 Received: by mail-qk1-x732.google.com with SMTP id f198so818725qke.11 for ; Mon, 02 Mar 2020 11:29:47 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:date:message-id:mime-version; bh=nEzjyjpY9JhwhThvG4bcfUq8d0+di7C9N+UPIaGMiE8=; b=scwK6L+Sx5fKXrQ9TVpmd/JcB8UH4VeBNNESgSNW/mbjq8h3hUr5DJANcgnhVIVDUM J5PGdFUiyZMByhFKFHPQgX2afJ/ydwBmlpJKmofG5KkfJP003tRObVqAb+gf1M7Gpxfn PdOO+X9NSPQyoDsi8vEUj6/eTaebzq+PDLtQ1kuqqq1aOz0Bz4ep34x8WM/1K8kQN/tj gex5ZbcOIyrFoPEzA4fkrWyuzyXwFe8z6VB5dZryBNW84RVj4+7y0GmRdPJfay3S9rmW EBtL94fa/b2ykD6Am26Wp7oFcoVNj2W32NGrL7SG+fqGW4Re5nN0DSVAdsaxsP65f7W+ Md+Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:date:message-id:mime-version; bh=nEzjyjpY9JhwhThvG4bcfUq8d0+di7C9N+UPIaGMiE8=; b=C5JgnOmJVNtzW2/1NV30MWMcQK3C+ycXw0IkphC3E98/55bb6tNOH9KlXSlTw9W2DL oD53hacU67qAj7M/z0TzaUj737Q601yWYXsDpzGM9jJbaxet3CFGABTd8aHzUEj2nkoi Bnydi8EJV5icvXt0tLtkgjK4Ycbrd2Q0A+zZUm5+baR7YeJBBsW+PkxDFihFJamw7emh KbcOBePP1o+jghFBt7V15iSTFIyd+Gtqf85ZeUKofPLHkDUuYfQeLo02uuzmQITACMOX niN+9gBZA6inzhyFFJrcbIOBszccaThGzOunsDM4JrMYlCb+JmQp3o4Xwbdyc/hALSVf ymXw== X-Gm-Message-State: ANhLgQ2VJBFZ6qRwjcoHRrW+DYOcZGTwQkjGbt/PobWfSx192wAPxCAZ nj3DSqcjh8trcj74p0595u973Xkj X-Google-Smtp-Source: ADFU+vs0UUosCq/JIU/tYCJMal8GgfGemeN3Pf7DCLo587yhmFHDJZmnwr7DB0CgnAssvH02tt53ag== X-Received: by 2002:a05:620a:2191:: with SMTP id g17mr659061qka.427.1583177386354; Mon, 02 Mar 2020 11:29:46 -0800 (PST) Received: from raisin ([2607:fad8:4:6:235e:8579:8464:aacc]) by smtp.gmail.com with ESMTPSA id v82sm10641968qka.51.2020.03.02.11.29.45 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 02 Mar 2020 11:29:45 -0800 (PST) From: Maxim Cournoyer Date: Mon, 02 Mar 2020 14:29:44 -0500 Message-ID: <878ski5zdj.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2607:f8b0:4864:20::732 X-Spam-Score: 0.3 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.7 (/) Build log extract: --8<---------------cut here---------------start------------->8--- starting phase `check' running "python setup.py" with command "test" and parameters () running test running egg_info writing anndata.egg-info/PKG-INFO writing dependency_links to anndata.egg-info/dependency_links.txt writing requirements to anndata.egg-info/requires.txt writing top-level names to anndata.egg-info/top_level.txt reading manifest file 'anndata.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'anndata.egg-info/SOURCES.txt' running build_ext anndata (unittest.loader._FailedTest) ... ERROR ====================================================================== ERROR: anndata (unittest.loader._FailedTest) ---------------------------------------------------------------------- ImportError: Failed to import test module: anndata Traceback (most recent call last): File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-3.7.4/lib/python3.7/unittest/loader.py", line 470, in _find_test_path package = self._get_module_from_name(name) File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-3.7.4/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name __import__(name) File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-0.6.18/anndata/__init__.py", line 1, in from .base import AnnData File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-0.6.18/anndata/base.py", line 21, in from scipy.sparse.sputils import IndexMixin ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils' (/gnu/store/fd99znbw3w7k05r8xkm03w1kvpa6yl1w-python-scipy-1.3.2/lib/python3.7/site-packages/scipy/sparse/sputils.py) ---------------------------------------------------------------------- Ran 1 test in 0.000s FAILED (errors=1) Test failed: error: Test failed: command "python" "-c" "import setuptools, tokenize;__file__='setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with status 1 builder for `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv' failed with exit code 1 build of /gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv failed View build log at '/var/log/guix/drvs/ma/6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv.bz2'. guix build: error: build of `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv' failed --8<---------------cut here---------------end--------------->8--- On master c1febbbf94ee794d7a97dbde12102634f2b13529. From unknown Sat Aug 16 14:29:49 2025 X-Loop: help-debbugs@gnu.org Subject: bug#39872: python-anndata fails to build Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Wed, 04 Mar 2020 13:28:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 39872 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Maxim Cournoyer , 39872@debbugs.gnu.org Received: via spool by 39872-submit@debbugs.gnu.org id=B39872.158332844828448 (code B ref 39872); Wed, 04 Mar 2020 13:28:02 +0000 Received: (at 39872) by debbugs.gnu.org; 4 Mar 2020 13:27:28 +0000 Received: from localhost ([127.0.0.1]:40503 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j9U3U-0007Od-S7 for submit@debbugs.gnu.org; Wed, 04 Mar 2020 08:27:28 -0500 Received: from eggs.gnu.org ([209.51.188.92]:55737) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j9U3O-0007ON-Rz for 39872@debbugs.gnu.org; Wed, 04 Mar 2020 08:27:19 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:51224) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1j9U3J-0003Dc-MR; Wed, 04 Mar 2020 08:27:09 -0500 Received: from 2001-1c02-0b03-a700-f532-4553-7f2a-9b68.cable.dynamic.v6.ziggo.nl ([2001:1c02:b03:a700:f532:4553:7f2a:9b68]:54602) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1j9U3G-0004OO-FA; Wed, 04 Mar 2020 08:27:07 -0500 Message-ID: <140f49bf93cd1d27a8111b3ab588177fc379af99.camel@gnu.org> From: Roel Janssen Date: Wed, 04 Mar 2020 14:27:03 +0100 In-Reply-To: <878ski5zdj.fsf@gmail.com> References: <878ski5zdj.fsf@gmail.com> Content-Type: multipart/mixed; boundary="=-YPSo1wMfUwcY01Bn/HzX" User-Agent: Evolution 3.34.4 (3.34.4-1.fc31) MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Spam-Score: -0.7 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --=-YPSo1wMfUwcY01Bn/HzX Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit On Mon, 2020-03-02 at 14:29 -0500, Maxim Cournoyer wrote: > Build log extract: > > --8<---------------cut here---------------start------------->8--- > starting phase `check' > running "python setup.py" with command "test" and parameters () > running test > running egg_info > writing anndata.egg-info/PKG-INFO > writing dependency_links to anndata.egg-info/dependency_links.txt > writing requirements to anndata.egg-info/requires.txt > writing top-level names to anndata.egg-info/top_level.txt > reading manifest file 'anndata.egg-info/SOURCES.txt' > reading manifest template 'MANIFEST.in' > writing manifest file 'anndata.egg-info/SOURCES.txt' > running build_ext > anndata (unittest.loader._FailedTest) ... ERROR > > ====================================================================== > ERROR: anndata (unittest.loader._FailedTest) > ---------------------------------------------------------------------- > ImportError: Failed to import test module: anndata > Traceback (most recent call last): > File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python- > 3.7.4/lib/python3.7/unittest/loader.py", line 470, in _find_test_path > package = self._get_module_from_name(name) > File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python- > 3.7.4/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name > __import__(name) > File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata- > 0.6.18/anndata/__init__.py", line 1, in > from .base import AnnData > File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata- > 0.6.18/anndata/base.py", line 21, in > from scipy.sparse.sputils import IndexMixin > ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils' > (/gnu/store/fd99znbw3w7k05r8xkm03w1kvpa6yl1w-python-scipy- > 1.3.2/lib/python3.7/site-packages/scipy/sparse/sputils.py) > > > ---------------------------------------------------------------------- > Ran 1 test in 0.000s > > FAILED (errors=1) > Test failed: > error: Test failed: > command "python" "-c" "import setuptools, > tokenize;__file__='setup.py';f=getattr(tokenize, 'open', > open)(__file__);code=f.read().replace('\\r\\n', > '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with > status 1 > builder for `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata- > 0.6.18.drv' failed with exit code 1 > build of /gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv > failed > View build log at '/var/log/guix/drvs/ma/6q97h3245r7sxhqms6q1csbkss2wvq- > python-anndata-0.6.18.drv.bz2'. > guix build: error: build of > `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv' > failed > --8<---------------cut here---------------end--------------->8--- > > On master c1febbbf94ee794d7a97dbde12102634f2b13529. I sent an e-mail from another address that doesn't seem to have made the guix- patches mailing list. The attached patches updates the version of python- anndata, and fixes the build. Note that for python-zarr I disabled the tests because the majority of the tests need external packages. We could add all dependencies to make the test suite work, but that requires a significant amount of work (for example, the Azure SDK for Python is one of the external dependencies). Is it OK to move forward with the disabled test suite for python-zarr? 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boundary="----------=_1583636102-26270-1" This is a multi-part message in MIME format... ------------=_1583636102-26270-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #39872: python-anndata fails to build which was filed against the guix package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 39872@debbugs.gnu.org. --=20 39872: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D39872 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1583636102-26270-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 39872-done) by debbugs.gnu.org; 8 Mar 2020 02:54:21 +0000 Received: from localhost ([127.0.0.1]:47802 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jAm52-0006oM-DI for submit@debbugs.gnu.org; Sat, 07 Mar 2020 21:54:21 -0500 Received: from mail-qk1-f182.google.com ([209.85.222.182]:45826) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jAm4v-0006o0-IS for 39872-done@debbugs.gnu.org; Sat, 07 Mar 2020 21:54:14 -0500 Received: by mail-qk1-f182.google.com with SMTP id c145so364405qke.12 for <39872-done@debbugs.gnu.org>; Sat, 07 Mar 2020 18:54:09 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version:content-transfer-encoding; bh=Yaai4YPACweJgI/n7d/mTbcNssMkpbJ8Ga4jh5z0wEw=; b=WKZ1xlqdzNTQQ/tCuex5ubnMkxGka4N2GNrM8zweFAor29bxcJCjO/uB4xX8+Liuuk bSdVfE8YpuMjbPTf3aB/wC9xthujyCCZR6EBbrjigtW6Zh0xXo5gaJ4xmVtlzKUjPNp1 +drHEVXvLn4KsFPvcIGRI1FzfDOg+q5buqnTkhGaVdm6oK7+kyT9F7WJiCFxF4sJoAvU GvNxIm3nb+lIwlKTZHcqhhEzjimF+xOloQvuATZgSh9JuVXpyG8QejWbDZwI7JO6f9uv ZIl9QT4nWO96ECdkzqjPwQWJrj1+IOX954IcedrfzC8ew2pcVT1ZLoGlSOeHCiPFIsCk B86Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version:content-transfer-encoding; bh=Yaai4YPACweJgI/n7d/mTbcNssMkpbJ8Ga4jh5z0wEw=; b=pZVpx7l0iDbL7mI21ne88b/lrzKr/EjSRSbVorrjzmynOb5HNX6UmFTSxWjBLqJzQD Qp/N3Z/Zzbl9QjmqNZOAst+zqVcaaeKVuZDa++j5ZjWBL5lx2gqa3W12pBXasWUEn9QZ TBeHnUkZMwf/VNYxDRQxolkDz7x3ML4S7QCUcvZkkJgXaeadjoVaL5RyAPJ+7+xgshXE wxGIIMceLfs0KrYsR8OM03WyyirJxezEkriwPRmKSQMdmhn0MdfEPwksqbbxSbuj9M1G 8HCmF1peQQGOlbhcotxLRc1g0OPevD0YOwg32CSUGl6axHKOE6UntYL7nA0/TvMWcZHd M0xw== X-Gm-Message-State: ANhLgQ2vcUEosjXtD+KebmWOCfa5kOhLe4/EIuZtvUNwJmZL7WYYZVNr idoiIPLxc1YUuupApHb9fCEaO7ey X-Google-Smtp-Source: ADFU+vvAB0wjPNMuosOXnyno7uUhUvJn3Em2BVtwfE8RNBMLa/NNjW4ziMdgRchpXtMHgb8EMINwrQ== X-Received: by 2002:a05:620a:707:: with SMTP id 7mr9938711qkc.231.1583636043638; Sat, 07 Mar 2020 18:54:03 -0800 (PST) Received: from apteryx ([207.35.95.105]) by smtp.gmail.com with ESMTPSA id l20sm10090259qtu.22.2020.03.07.18.54.02 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 07 Mar 2020 18:54:03 -0800 (PST) From: Maxim Cournoyer To: Roel Janssen Subject: Re: bug#39872: python-anndata fails to build References: <878ski5zdj.fsf@gmail.com> <140f49bf93cd1d27a8111b3ab588177fc379af99.camel@gnu.org> Date: Sat, 07 Mar 2020 21:54:01 -0500 In-Reply-To: <140f49bf93cd1d27a8111b3ab588177fc379af99.camel@gnu.org> (Roel Janssen's message of "Wed, 04 Mar 2020 14:27:03 +0100") Message-ID: <87a74r7e0m.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -1.5 (-) X-Debbugs-Envelope-To: 39872-done Cc: 39872-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hello Roel, Roel Janssen writes: > On Mon, 2020-03-02 at 14:29 -0500, Maxim Cournoyer wrote: >> Build log extract: >>=20 >> --8<---------------cut here---------------start------------->8--- >> starting phase `check' >> running "python setup.py" with command "test" and parameters () >> running test >> running egg_info >> writing anndata.egg-info/PKG-INFO >> writing dependency_links to anndata.egg-info/dependency_links.txt >> writing requirements to anndata.egg-info/requires.txt >> writing top-level names to anndata.egg-info/top_level.txt >> reading manifest file 'anndata.egg-info/SOURCES.txt' >> reading manifest template 'MANIFEST.in' >> writing manifest file 'anndata.egg-info/SOURCES.txt' >> running build_ext >> anndata (unittest.loader._FailedTest) ... ERROR >>=20 >> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D >> ERROR: anndata (unittest.loader._FailedTest) >> ---------------------------------------------------------------------- >> ImportError: Failed to import test module: anndata >> Traceback (most recent call last): >> File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python- >> 3.7.4/lib/python3.7/unittest/loader.py", line 470, in _find_test_path >> package =3D self._get_module_from_name(name) >> File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python- >> 3.7.4/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_n= ame >> __import__(name) >> File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata- >> 0.6.18/anndata/__init__.py", line 1, in >> from .base import AnnData >> File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata- >> 0.6.18/anndata/base.py", line 21, in >> from scipy.sparse.sputils import IndexMixin >> ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils' >> (/gnu/store/fd99znbw3w7k05r8xkm03w1kvpa6yl1w-python-scipy- >> 1.3.2/lib/python3.7/site-packages/scipy/sparse/sputils.py) >>=20 >>=20 >> ---------------------------------------------------------------------- >> Ran 1 test in 0.000s >>=20 >> FAILED (errors=3D1) >> Test failed: >> error: Test failed: >> command "python" "-c" "import setuptools, >> tokenize;__file__=3D'setup.py';f=3Dgetattr(tokenize, 'open', >> open)(__file__);code=3Df.read().replace('\\r\\n', >> '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed wi= th >> status 1 >> builder for `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata- >> 0.6.18.drv' failed with exit code 1 >> build of /gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.= 18.drv=20 >> failed >> View build log at '/var/log/guix/drvs/ma/6q97h3245r7sxhqms6q1csbkss2wvq- >> python-anndata-0.6.18.drv.bz2'. >> guix build: error: build of >> `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv' >> failed >> --8<---------------cut here---------------end--------------->8--- >>=20 >> On master c1febbbf94ee794d7a97dbde12102634f2b13529. The problem has since been fixed on master with commits 7032c1cc6040a14e482e71b0cfbdedf957da4f8a, 8e04b233f130e01b5b6a41dfcdeb5e622d43f751, 241409cd8afe45fdecfbd7d24cdeb08aa2a43884 and a098b3498052e046c8338e0630e0166bcb12355d; Ricardo probably did not notice about this bug report and your posted patches. > I sent an e-mail from another address that doesn't seem to have made the = guix- > patches mailing list. The attached patches updates the version of python- > anndata, and fixes the build. > > Note that for python-zarr I disabled the tests because the majority of th= e tests > need external packages. We could add all dependencies to make the test s= uite > work, but that requires a significant amount of work (for example, the Az= ure SDK > for Python is one of the external dependencies). > > Is it OK to move forward with the disabled test suite for python-zarr? I think it would have been acceptable (given that anndata was broken and needed a fix); but enabling the tests that can be run ideally should be attempted. See in commit 7032c1cc6040a14e482e71b0cfbdedf957da4f8a how this was achieved. You'll find a summary review of your patches below. I've made sure that what got committed was not missing anything. > From 08e25e127b7c19b339c5257d61b6d2c1b9d9a2c9 Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Wed, 4 Mar 2020 11:13:21 +0100 > Subject: [PATCH 4/4] gnu: Update python-anndata to 0.7.1. > > * gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.1; Add > dependencies to run the test suite. > --- > gnu/packages/python-xyz.scm | 11 +++++++++-- > 1 file changed, 9 insertions(+), 2 deletions(-) > > diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm > index 3eabc9e3fa..2ec79404f2 100644 > --- a/gnu/packages/python-xyz.scm > +++ b/gnu/packages/python-xyz.scm > @@ -15800,15 +15800,22 @@ compressed, N-dimensional arrays for Python.") > (define-public python-anndata > (package > (name "python-anndata") > - (version "0.6.18") > + (version "0.7.1") > (source > (origin > (method url-fetch) > (uri (pypi-uri "anndata" version)) > (sha256 > (base32 > - "03x83yjaccbqszj7x4fwwmpil0ai59yx64d1zmf2691za3j03w73")))) > + "0rnfbpr55j1a1bi2kd4mz444741hrn74kz90h5rnjr59jmpfnh09")))) > (build-system python-build-system) > + ;; The following inputs are needed for the test suite. > + (native-inputs > + `(("python-setuptools-scm" ,python-setuptools-scm) > + ("python-packaging" ,python-packaging) > + ("python-importlib-metadata" ,python-importlib-metadata) > + ("python-numcodecs" ,python-numcodecs) > + ("python-zarr" ,python-zarr))) > (propagated-inputs > `(("python-h5py" ,python-h5py) > ("python-natsort" ,python-natsort) > --=20 > 2.25.1 Here the default check phase (which does 'python setup.py test'), was not running the test suite. It had to be overriden by a 'pytest' invocation. I find this to be very common in Python packages; I think there was something about deprecating 'python setup.py test' to; maybe we should look into making this phase of the python-build-system smarter. > From 8a01cc8c797dde47d6e4982f7b8710fc9bf106e1 Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Wed, 4 Mar 2020 11:12:41 +0100 > Subject: [PATCH 3/4] gnu: Add python-zarr. > > * gnu/packages/python-xyz.scm (python-zarr): New variable. > --- > gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++ > 1 file changed, 26 insertions(+) > > diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm > index 067756cae8..3eabc9e3fa 100644 > --- a/gnu/packages/python-xyz.scm > +++ b/gnu/packages/python-xyz.scm > @@ -15771,6 +15771,32 @@ codecs for use in data storage and communication= applications.") > (description "Draws ASCII trees.") > (license license:expat))) >=20=20 > +(define-public python-zarr > + (package > + (name "python-zarr") > + (version "2.4.0") > + (source (origin > + (method url-fetch) > + (uri (pypi-uri "zarr" version)) > + (sha256 > + (base32 > + "026n3sjzjv2gmwx6y72b8ij0hk42bc8zdbvfj5gdqzd4i6wj3ajk"))= )) > + (build-system python-build-system) > + (arguments > + ;; The tests import h5py, lmdb, pymongo, bsddb3, and azure.storage.= blob from > + ;; the Azure SDK for python. > + `(#:tests? #f)) > + (propagated-inputs > + `(("python-asciitree" ,python-asciitree) > + ("python-fasteners" ,python-fasteners) > + ("python-numcodecs" ,python-numcodecs) > + ("python-numpy" ,python-numpy))) > + (home-page "https://github.com/zarr-developers/zarr-python") > + (synopsis "Implementation of chunked, compressed, N-dimensional arra= ys for Python.") > + (description "This package provides an implementation of chunked, > +compressed, N-dimensional arrays for Python.") > + (license license:expat))) > + > (define-public python-anndata > (package > (name "python-anndata") > --=20 > 2.25.1 LGTM, but see commit for a way to partially enable the test suite: 7032c1cc6040a14e482e71b0cfbdedf957da4f8a. > From f48903066a6987c3af2b4130dde03ee2c8c9b70e Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Wed, 4 Mar 2020 11:12:09 +0100 > Subject: [PATCH 2/4] gnu: Add python-asciitree. > > * gnu/packages/python-xyz.scm (python-asciitree): New variable. > --- > gnu/packages/python-xyz.scm | 16 ++++++++++++++++ > 1 file changed, 16 insertions(+) > > diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm > index dec41a8c5e..067756cae8 100644 > --- a/gnu/packages/python-xyz.scm > +++ b/gnu/packages/python-xyz.scm > @@ -15755,6 +15755,22 @@ tool).") > codecs for use in data storage and communication applications.") > (license license:expat))) >=20=20 > +(define-public python-asciitree > + (package > + (name "python-asciitree") > + (version "0.3.3") > + (source (origin > + (method url-fetch) > + (uri (pypi-uri "asciitree" version)) > + (sha256 > + (base32 > + "0vhgri2m2xlnibhz4xwn4hpbc7xacisxjqrk6k5kyppq96vbk92a"))= )) > + (build-system python-build-system) > + (home-page "http://github.com/mbr/asciitree") The URL should use HTTPS. > + (synopsis "Draws ASCII trees.") > + (description "Draws ASCII trees.") > + (license license:expat))) The description should be expound a bit. > (define-public python-anndata > (package > (name "python-anndata") > --=20 > 2.25.1 > > > From 0fc3b77486289835f28f16a6380c15fd128cab6b Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Wed, 4 Mar 2020 11:11:17 +0100 > Subject: [PATCH 1/4] gnu: Add python-numcodecs. > > * gnu/packages/python-xyz.scm (python-numcodecs): New variable. > --- > gnu/packages/python-xyz.scm | 24 +++++++++++++++++++++++- > 1 file changed, 23 insertions(+), 1 deletion(-) > > diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm > index f3519b75f6..dec41a8c5e 100644 > --- a/gnu/packages/python-xyz.scm > +++ b/gnu/packages/python-xyz.scm > @@ -40,7 +40,7 @@ > ;;; Copyright =C2=A9 2017 Ben Sturmfels > ;;; Copyright =C2=A9 2017, 2018, 2019 Mathieu Othacehe > ;;; Copyright =C2=A9 2017 Jos=C3=A9 Miguel S=C3=A1nchez Garc=C3=ADa > -;;; Copyright =C2=A9 2017 Roel Janssen > +;;; Copyright =C2=A9 2017 2020 Roel Janssen > ;;; Copyright =C2=A9 2017, 2018, 2019 Kei Kebreau > ;;; Copyright =C2=A9 2017 Rutger Helling > ;;; Copyright =C2=A9 2017 Muriithi Frederick Muriuki > @@ -15733,6 +15733,28 @@ infrastructure at import time, runtime, or stati= cally (using the included pycc > tool).") > (license license:bsd-3))) >=20=20 > +(define-public python-numcodecs > + (package > + (name "python-numcodecs") > + (version "0.6.4") > + (source (origin > + (method url-fetch) > + (uri (pypi-uri "numcodecs" version)) > + (sha256 > + (base32 > + "0kbfr8pl3x9glsypbq8hzim003f16ml1b1cvgrh4w1sdvgal6j7g"))= )) > + (build-system python-build-system) > + (propagated-inputs > + `(("python-numpy" ,python-numpy) > + ("python-setuptools-scm" ,python-setuptools-scm) > + ("python-msgpack" ,python-msgpack) > + ("python-pytest" ,python-pytest))) Pytest and setuptools plugins are only required at build time, hence would be better found in 'native-inputs'. > + (home-page "https://github.com/zarr-developers/numcodecs") > + (synopsis "Buffer compression and transformation codecs") > + (description "This package provides buffer compression and transform= ation > +codecs for use in data storage and communication applications.") > + (license license:expat))) Otherwise LGTM! I'm sorry that this work was duplicated; I hope this small review can compensate for it a little :-). Thank you; I'm closing the issue. Maxim ------------=_1583636102-26270-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 2 Mar 2020 19:29:52 +0000 Received: from localhost ([127.0.0.1]:38378 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8qlE-00060D-8z for submit@debbugs.gnu.org; Mon, 02 Mar 2020 14:29:52 -0500 Received: from lists.gnu.org ([209.51.188.17]:38341) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8qlC-000606-JL for submit@debbugs.gnu.org; Mon, 02 Mar 2020 14:29:50 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:56464) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j8qlB-0000ES-Ah for bug-guix@gnu.org; Mon, 02 Mar 2020 14:29:50 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,FREEMAIL_FROM, URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1j8ql9-0005y9-US for bug-guix@gnu.org; Mon, 02 Mar 2020 14:29:49 -0500 Received: from mail-qk1-x732.google.com ([2607:f8b0:4864:20::732]:44151) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1j8ql9-0005xq-OH for bug-guix@gnu.org; Mon, 02 Mar 2020 14:29:47 -0500 Received: by mail-qk1-x732.google.com with SMTP id f198so818725qke.11 for ; Mon, 02 Mar 2020 11:29:47 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:date:message-id:mime-version; bh=nEzjyjpY9JhwhThvG4bcfUq8d0+di7C9N+UPIaGMiE8=; b=scwK6L+Sx5fKXrQ9TVpmd/JcB8UH4VeBNNESgSNW/mbjq8h3hUr5DJANcgnhVIVDUM J5PGdFUiyZMByhFKFHPQgX2afJ/ydwBmlpJKmofG5KkfJP003tRObVqAb+gf1M7Gpxfn PdOO+X9NSPQyoDsi8vEUj6/eTaebzq+PDLtQ1kuqqq1aOz0Bz4ep34x8WM/1K8kQN/tj gex5ZbcOIyrFoPEzA4fkrWyuzyXwFe8z6VB5dZryBNW84RVj4+7y0GmRdPJfay3S9rmW EBtL94fa/b2ykD6Am26Wp7oFcoVNj2W32NGrL7SG+fqGW4Re5nN0DSVAdsaxsP65f7W+ Md+Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:date:message-id:mime-version; bh=nEzjyjpY9JhwhThvG4bcfUq8d0+di7C9N+UPIaGMiE8=; b=C5JgnOmJVNtzW2/1NV30MWMcQK3C+ycXw0IkphC3E98/55bb6tNOH9KlXSlTw9W2DL oD53hacU67qAj7M/z0TzaUj737Q601yWYXsDpzGM9jJbaxet3CFGABTd8aHzUEj2nkoi Bnydi8EJV5icvXt0tLtkgjK4Ycbrd2Q0A+zZUm5+baR7YeJBBsW+PkxDFihFJamw7emh KbcOBePP1o+jghFBt7V15iSTFIyd+Gtqf85ZeUKofPLHkDUuYfQeLo02uuzmQITACMOX niN+9gBZA6inzhyFFJrcbIOBszccaThGzOunsDM4JrMYlCb+JmQp3o4Xwbdyc/hALSVf ymXw== X-Gm-Message-State: ANhLgQ2VJBFZ6qRwjcoHRrW+DYOcZGTwQkjGbt/PobWfSx192wAPxCAZ nj3DSqcjh8trcj74p0595u973Xkj X-Google-Smtp-Source: ADFU+vs0UUosCq/JIU/tYCJMal8GgfGemeN3Pf7DCLo587yhmFHDJZmnwr7DB0CgnAssvH02tt53ag== X-Received: by 2002:a05:620a:2191:: with SMTP id g17mr659061qka.427.1583177386354; Mon, 02 Mar 2020 11:29:46 -0800 (PST) Received: from raisin ([2607:fad8:4:6:235e:8579:8464:aacc]) by smtp.gmail.com with ESMTPSA id v82sm10641968qka.51.2020.03.02.11.29.45 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 02 Mar 2020 11:29:45 -0800 (PST) From: Maxim Cournoyer To: bug-guix Subject: python-anndata fails to build Date: Mon, 02 Mar 2020 14:29:44 -0500 Message-ID: <878ski5zdj.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2607:f8b0:4864:20::732 X-Spam-Score: 0.3 (/) X-Debbugs-Envelope-To: submit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.7 (/) Build log extract: --8<---------------cut here---------------start------------->8--- starting phase `check' running "python setup.py" with command "test" and parameters () running test running egg_info writing anndata.egg-info/PKG-INFO writing dependency_links to anndata.egg-info/dependency_links.txt writing requirements to anndata.egg-info/requires.txt writing top-level names to anndata.egg-info/top_level.txt reading manifest file 'anndata.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'anndata.egg-info/SOURCES.txt' running build_ext anndata (unittest.loader._FailedTest) ... ERROR ====================================================================== ERROR: anndata (unittest.loader._FailedTest) ---------------------------------------------------------------------- ImportError: Failed to import test module: anndata Traceback (most recent call last): File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-3.7.4/lib/python3.7/unittest/loader.py", line 470, in _find_test_path package = self._get_module_from_name(name) File "/gnu/store/78w7y0lxar70j512iqw8x3nimzj10yga-python-3.7.4/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name __import__(name) File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-0.6.18/anndata/__init__.py", line 1, in from .base import AnnData File "/tmp/guix-build-python-anndata-0.6.18.drv-0/anndata-0.6.18/anndata/base.py", line 21, in from scipy.sparse.sputils import IndexMixin ImportError: cannot import name 'IndexMixin' from 'scipy.sparse.sputils' (/gnu/store/fd99znbw3w7k05r8xkm03w1kvpa6yl1w-python-scipy-1.3.2/lib/python3.7/site-packages/scipy/sparse/sputils.py) ---------------------------------------------------------------------- Ran 1 test in 0.000s FAILED (errors=1) Test failed: error: Test failed: command "python" "-c" "import setuptools, tokenize;__file__='setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with status 1 builder for `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv' failed with exit code 1 build of /gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv failed View build log at '/var/log/guix/drvs/ma/6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv.bz2'. guix build: error: build of `/gnu/store/ma6q97h3245r7sxhqms6q1csbkss2wvq-python-anndata-0.6.18.drv' failed --8<---------------cut here---------------end--------------->8--- On master c1febbbf94ee794d7a97dbde12102634f2b13529. ------------=_1583636102-26270-1--