From debbugs-submit-bounces@debbugs.gnu.org Mon Mar 02 14:29:52 2020 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. From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 04 08:27:28 2020 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> Subject: Re: bug#39872: python-anndata fails to build From: Roel Janssen To: Maxim Cournoyer , 39872@debbugs.gnu.org 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-Debbugs-Envelope-To: 39872 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? Kind regards, Roel Janssen --=-YPSo1wMfUwcY01Bn/HzX Content-Disposition: attachment; filename="0004-gnu-Update-python-anndata-to-0.7.1.patch" Content-Transfer-Encoding: base64 Content-Type: text/x-patch; name="0004-gnu-Update-python-anndata-to-0.7.1.patch"; charset="UTF-8" RnJvbSAwOGUyNWUxMjdiN2MxOWIzMzljNTI1N2Q2MWI2ZDJjMWI5ZDlhMmM5IE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiBSb2VsIEphbnNzZW4gPHJvZWxAZ251Lm9yZz4KRGF0ZTogV2Vk LCA0IE1hciAyMDIwIDExOjEzOjIxICswMTAwClN1YmplY3Q6IFtQQVRDSCA0LzRdIGdudTogVXBk YXRlIHB5dGhvbi1hbm5kYXRhIHRvIDAuNy4xLgoKKiBnbnUvcGFja2FnZXMvcHl0aG9uLXh5ei5z Y20gKHB5dGhvbi1hbm5kYXRhKTogVXBkYXRlIHRvIDAuNy4xOyBBZGQKICBkZXBlbmRlbmNpZXMg dG8gcnVuIHRoZSB0ZXN0IHN1aXRlLgotLS0KIGdudS9wYWNrYWdlcy9weXRob24teHl6LnNjbSB8 IDExICsrKysrKysrKy0tCiAxIGZpbGUgY2hhbmdlZCwgOSBpbnNlcnRpb25zKCspLCAyIGRlbGV0 aW9ucygtKQoKZGlmZiAtLWdpdCBhL2dudS9wYWNrYWdlcy9weXRob24teHl6LnNjbSBiL2dudS9w YWNrYWdlcy9weXRob24teHl6LnNjbQppbmRleCAzZWFiYzllM2ZhLi4yZWM3OTQwNGYyIDEwMDY0 NAotLS0gYS9nbnUvcGFja2FnZXMvcHl0aG9uLXh5ei5zY20KKysrIGIvZ251L3BhY2thZ2VzL3B5 dGhvbi14eXouc2NtCkBAIC0xNTgwMCwxNSArMTU4MDAsMjIgQEAgY29tcHJlc3NlZCwgTi1kaW1l bnNpb25hbCBhcnJheXMgZm9yIFB5dGhvbi4iKQogKGRlZmluZS1wdWJsaWMgcHl0aG9uLWFubmRh dGEKICAgKHBhY2thZ2UKICAgICAobmFtZSAicHl0aG9uLWFubmRhdGEiKQotICAgICh2ZXJzaW9u ICIwLjYuMTgiKQorICAgICh2ZXJzaW9uICIwLjcuMSIpCiAgICAgKHNvdXJjZQogICAgICAob3Jp Z2luCiAgICAgICAgKG1ldGhvZCB1cmwtZmV0Y2gpCiAgICAgICAgKHVyaSAocHlwaS11cmkgImFu bmRhdGEiIHZlcnNpb24pKQogICAgICAgIChzaGEyNTYKICAgICAgICAgKGJhc2UzMgotICAgICAg ICAgIjAzeDgzeWphY2NicXN6ajd4NGZ3d21waWwwYWk1OXl4NjRkMXptZjI2OTF6YTNqMDN3NzMi KSkpKQorICAgICAgICAgIjBybmZicHI1NWoxYTFiaTJrZDRtejQ0NDc0MWhybjc0a3o5MGg1cm5q cjU5am1wZm5oMDkiKSkpKQogICAgIChidWlsZC1zeXN0ZW0gcHl0aG9uLWJ1aWxkLXN5c3RlbSkK KyAgICA7OyBUaGUgZm9sbG93aW5nIGlucHV0cyBhcmUgbmVlZGVkIGZvciB0aGUgdGVzdCBzdWl0 ZS4KKyAgICAobmF0aXZlLWlucHV0cworICAgICBgKCgicHl0aG9uLXNldHVwdG9vbHMtc2NtIiAs cHl0aG9uLXNldHVwdG9vbHMtc2NtKQorICAgICAgICgicHl0aG9uLXBhY2thZ2luZyIgLHB5dGhv bi1wYWNrYWdpbmcpCisgICAgICAgKCJweXRob24taW1wb3J0bGliLW1ldGFkYXRhIiAscHl0aG9u LWltcG9ydGxpYi1tZXRhZGF0YSkKKyAgICAgICAoInB5dGhvbi1udW1jb2RlY3MiICxweXRob24t bnVtY29kZWNzKQorICAgICAgICgicHl0aG9uLXphcnIiICxweXRob24temFycikpKQogICAgIChw cm9wYWdhdGVkLWlucHV0cwogICAgICBgKCgicHl0aG9uLWg1cHkiICxweXRob24taDVweSkKICAg ICAgICAoInB5dGhvbi1uYXRzb3J0IiAscHl0aG9uLW5hdHNvcnQpCi0tIAoyLjI1LjEKCg== --=-YPSo1wMfUwcY01Bn/HzX Content-Disposition: attachment; filename="0003-gnu-Add-python-zarr.patch" Content-Transfer-Encoding: base64 Content-Type: text/x-patch; name="0003-gnu-Add-python-zarr.patch"; charset="UTF-8" RnJvbSA4YTAxY2M4Yzc5N2RkZTQ3ZDZlNDk4MmY3Yjg3MTBmYzliZjEwNmUxIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiBSb2VsIEphbnNzZW4gPHJvZWxAZ251Lm9yZz4KRGF0ZTogV2Vk LCA0IE1hciAyMDIwIDExOjEyOjQxICswMTAwClN1YmplY3Q6IFtQQVRDSCAzLzRdIGdudTogQWRk IHB5dGhvbi16YXJyLgoKKiBnbnUvcGFja2FnZXMvcHl0aG9uLXh5ei5zY20gKHB5dGhvbi16YXJy KTogTmV3IHZhcmlhYmxlLgotLS0KIGdudS9wYWNrYWdlcy9weXRob24teHl6LnNjbSB8IDI2ICsr KysrKysrKysrKysrKysrKysrKysrKysrCiAxIGZpbGUgY2hhbmdlZCwgMjYgaW5zZXJ0aW9ucygr KQoKZGlmZiAtLWdpdCBhL2dudS9wYWNrYWdlcy9weXRob24teHl6LnNjbSBiL2dudS9wYWNrYWdl cy9weXRob24teHl6LnNjbQppbmRleCAwNjc3NTZjYWU4Li4zZWFiYzllM2ZhIDEwMDY0NAotLS0g YS9nbnUvcGFja2FnZXMvcHl0aG9uLXh5ei5zY20KKysrIGIvZ251L3BhY2thZ2VzL3B5dGhvbi14 eXouc2NtCkBAIC0xNTc3MSw2ICsxNTc3MSwzMiBAQCBjb2RlY3MgZm9yIHVzZSBpbiBkYXRhIHN0 b3JhZ2UgYW5kIGNvbW11bmljYXRpb24gYXBwbGljYXRpb25zLiIpCiAgICAgKGRlc2NyaXB0aW9u ICJEcmF3cyBBU0NJSSB0cmVlcy4iKQogICAgIChsaWNlbnNlIGxpY2Vuc2U6ZXhwYXQpKSkKIAor KGRlZmluZS1wdWJsaWMgcHl0aG9uLXphcnIKKyAgKHBhY2thZ2UKKyAgICAobmFtZSAicHl0aG9u LXphcnIiKQorICAgICh2ZXJzaW9uICIyLjQuMCIpCisgICAgKHNvdXJjZSAob3JpZ2luCisgICAg ICAgICAgICAgIChtZXRob2QgdXJsLWZldGNoKQorICAgICAgICAgICAgICAodXJpIChweXBpLXVy aSAiemFyciIgdmVyc2lvbikpCisgICAgICAgICAgICAgIChzaGEyNTYKKyAgICAgICAgICAgICAg IChiYXNlMzIKKyAgICAgICAgICAgICAgICAiMDI2bjNzanpqdjJnbXd4Nnk3MmI4aWowaGs0MmJj OHpkYnZmajVnZHF6ZDRpNndqM2FqayIpKSkpCisgICAgKGJ1aWxkLXN5c3RlbSBweXRob24tYnVp bGQtc3lzdGVtKQorICAgIChhcmd1bWVudHMKKyAgICAgOzsgVGhlIHRlc3RzIGltcG9ydCBoNXB5 LCBsbWRiLCBweW1vbmdvLCBic2RkYjMsIGFuZCBhenVyZS5zdG9yYWdlLmJsb2IgZnJvbQorICAg ICA7OyB0aGUgQXp1cmUgU0RLIGZvciBweXRob24uCisgICAgIGAoIzp0ZXN0cz8gI2YpKQorICAg IChwcm9wYWdhdGVkLWlucHV0cworICAgICBgKCgicHl0aG9uLWFzY2lpdHJlZSIgLHB5dGhvbi1h c2NpaXRyZWUpCisgICAgICAgKCJweXRob24tZmFzdGVuZXJzIiAscHl0aG9uLWZhc3RlbmVycykK KyAgICAgICAoInB5dGhvbi1udW1jb2RlY3MiICxweXRob24tbnVtY29kZWNzKQorICAgICAgICgi cHl0aG9uLW51bXB5IiAscHl0aG9uLW51bXB5KSkpCisgICAgKGhvbWUtcGFnZSAiaHR0cHM6Ly9n aXRodWIuY29tL3phcnItZGV2ZWxvcGVycy96YXJyLXB5dGhvbiIpCisgICAgKHN5bm9wc2lzICJJ bXBsZW1lbnRhdGlvbiBvZiBjaHVua2VkLCBjb21wcmVzc2VkLCBOLWRpbWVuc2lvbmFsIGFycmF5 cyBmb3IgUHl0aG9uLiIpCisgICAgKGRlc2NyaXB0aW9uICJUaGlzIHBhY2thZ2UgcHJvdmlkZXMg YW4gaW1wbGVtZW50YXRpb24gb2YgY2h1bmtlZCwKK2NvbXByZXNzZWQsIE4tZGltZW5zaW9uYWwg YXJyYXlzIGZvciBQeXRob24uIikKKyAgICAobGljZW5zZSBsaWNlbnNlOmV4cGF0KSkpCisKIChk ZWZpbmUtcHVibGljIHB5dGhvbi1hbm5kYXRhCiAgIChwYWNrYWdlCiAgICAgKG5hbWUgInB5dGhv bi1hbm5kYXRhIikKLS0gCjIuMjUuMQoK --=-YPSo1wMfUwcY01Bn/HzX Content-Disposition: attachment; filename="0002-gnu-Add-python-asciitree.patch" Content-Transfer-Encoding: base64 Content-Type: text/x-patch; name="0002-gnu-Add-python-asciitree.patch"; charset="UTF-8" RnJvbSBmNDg5MDMwNjZhNjk4N2MzYWYyYjQxMzBkZGUwM2VlMmM4YzliNzBlIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiBSb2VsIEphbnNzZW4gPHJvZWxAZ251Lm9yZz4KRGF0ZTogV2Vk LCA0IE1hciAyMDIwIDExOjEyOjA5ICswMTAwClN1YmplY3Q6IFtQQVRDSCAyLzRdIGdudTogQWRk IHB5dGhvbi1hc2NpaXRyZWUuCgoqIGdudS9wYWNrYWdlcy9weXRob24teHl6LnNjbSAocHl0aG9u LWFzY2lpdHJlZSk6IE5ldyB2YXJpYWJsZS4KLS0tCiBnbnUvcGFja2FnZXMvcHl0aG9uLXh5ei5z Y20gfCAxNiArKysrKysrKysrKysrKysrCiAxIGZpbGUgY2hhbmdlZCwgMTYgaW5zZXJ0aW9ucygr KQoKZGlmZiAtLWdpdCBhL2dudS9wYWNrYWdlcy9weXRob24teHl6LnNjbSBiL2dudS9wYWNrYWdl cy9weXRob24teHl6LnNjbQppbmRleCBkZWM0MWE4YzVlLi4wNjc3NTZjYWU4IDEwMDY0NAotLS0g YS9nbnUvcGFja2FnZXMvcHl0aG9uLXh5ei5zY20KKysrIGIvZ251L3BhY2thZ2VzL3B5dGhvbi14 eXouc2NtCkBAIC0xNTc1NSw2ICsxNTc1NSwyMiBAQCB0b29sKS4iKQogY29kZWNzIGZvciB1c2Ug aW4gZGF0YSBzdG9yYWdlIGFuZCBjb21tdW5pY2F0aW9uIGFwcGxpY2F0aW9ucy4iKQogICAgIChs aWNlbnNlIGxpY2Vuc2U6ZXhwYXQpKSkKIAorKGRlZmluZS1wdWJsaWMgcHl0aG9uLWFzY2lpdHJl ZQorICAocGFja2FnZQorICAgIChuYW1lICJweXRob24tYXNjaWl0cmVlIikKKyAgICAodmVyc2lv biAiMC4zLjMiKQorICAgIChzb3VyY2UgKG9yaWdpbgorICAgICAgICAgICAgICAobWV0aG9kIHVy bC1mZXRjaCkKKyAgICAgICAgICAgICAgKHVyaSAocHlwaS11cmkgImFzY2lpdHJlZSIgdmVyc2lv bikpCisgICAgICAgICAgICAgIChzaGEyNTYKKyAgICAgICAgICAgICAgIChiYXNlMzIKKyAgICAg ICAgICAgICAgICAiMHZoZ3JpMm0yeGxuaWJoejR4d240aHBiYzd4YWNpc3hqcXJrNms1a3lwcHE5 NnZiazkyYSIpKSkpCisgICAgKGJ1aWxkLXN5c3RlbSBweXRob24tYnVpbGQtc3lzdGVtKQorICAg IChob21lLXBhZ2UgImh0dHA6Ly9naXRodWIuY29tL21ici9hc2NpaXRyZWUiKQorICAgIChzeW5v cHNpcyAiRHJhd3MgQVNDSUkgdHJlZXMuIikKKyAgICAoZGVzY3JpcHRpb24gIkRyYXdzIEFTQ0lJ IHRyZWVzLiIpCisgICAgKGxpY2Vuc2UgbGljZW5zZTpleHBhdCkpKQorCiAoZGVmaW5lLXB1Ymxp YyBweXRob24tYW5uZGF0YQogICAocGFja2FnZQogICAgIChuYW1lICJweXRob24tYW5uZGF0YSIp Ci0tIAoyLjI1LjEKCg== --=-YPSo1wMfUwcY01Bn/HzX Content-Disposition: attachment; filename="0001-gnu-Add-python-numcodecs.patch" Content-Transfer-Encoding: base64 Content-Type: text/x-patch; name="0001-gnu-Add-python-numcodecs.patch"; charset="UTF-8" RnJvbSAwZmMzYjc3NDg2Mjg5ODM1ZjI4ZjE2YTYzODBjMTVmZDEyOGNhYjZiIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQpGcm9tOiBSb2VsIEphbnNzZW4gPHJvZWxAZ251Lm9yZz4KRGF0ZTogV2Vk LCA0IE1hciAyMDIwIDExOjExOjE3ICswMTAwClN1YmplY3Q6IFtQQVRDSCAxLzRdIGdudTogQWRk IHB5dGhvbi1udW1jb2RlY3MuCgoqIGdudS9wYWNrYWdlcy9weXRob24teHl6LnNjbSAocHl0aG9u LW51bWNvZGVjcyk6IE5ldyB2YXJpYWJsZS4KLS0tCiBnbnUvcGFja2FnZXMvcHl0aG9uLXh5ei5z Y20gfCAyNCArKysrKysrKysrKysrKysrKysrKysrKy0KIDEgZmlsZSBjaGFuZ2VkLCAyMyBpbnNl cnRpb25zKCspLCAxIGRlbGV0aW9uKC0pCgpkaWZmIC0tZ2l0IGEvZ251L3BhY2thZ2VzL3B5dGhv bi14eXouc2NtIGIvZ251L3BhY2thZ2VzL3B5dGhvbi14eXouc2NtCmluZGV4IGYzNTE5Yjc1ZjYu LmRlYzQxYThjNWUgMTAwNjQ0Ci0tLSBhL2dudS9wYWNrYWdlcy9weXRob24teHl6LnNjbQorKysg Yi9nbnUvcGFja2FnZXMvcHl0aG9uLXh5ei5zY20KQEAgLTQwLDcgKzQwLDcgQEAKIDs7OyBDb3B5 cmlnaHQgwqkgMjAxNyBCZW4gU3R1cm1mZWxzIDxiZW5Ac3R1cm0uY29tLmF1PgogOzs7IENvcHly aWdodCDCqSAyMDE3LCAyMDE4LCAyMDE5IE1hdGhpZXUgT3RoYWNlaGUgPG0ub3RoYWNlaGVAZ21h aWwuY29tPgogOzs7IENvcHlyaWdodCDCqSAyMDE3IEpvc8OpIE1pZ3VlbCBTw6FuY2hleiBHYXJj w61hIDxqbWkya0BvcGVubWFpbGJveC5vcmc+Ci07OzsgQ29weXJpZ2h0IMKpIDIwMTcgUm9lbCBK YW5zc2VuIDxyb2VsQGdudS5vcmc+Cis7OzsgQ29weXJpZ2h0IMKpIDIwMTcgMjAyMCBSb2VsIEph bnNzZW4gPHJvZWxAZ251Lm9yZz4KIDs7OyBDb3B5cmlnaHQgwqkgMjAxNywgMjAxOCwgMjAxOSBL ZWkgS2VicmVhdSA8a2tlYnJlYXVAcG9zdGVvLm5ldD4KIDs7OyBDb3B5cmlnaHQgwqkgMjAxNyBS dXRnZXIgSGVsbGluZyA8cmhlbGxpbmdAbXlrb2xhYi5jb20+CiA7OzsgQ29weXJpZ2h0IMKpIDIw MTcgTXVyaWl0aGkgRnJlZGVyaWNrIE11cml1a2kgPGZyZWRtYW5nbGlzQGdtYWlsLmNvbT4KQEAg LTE1NzMzLDYgKzE1NzMzLDI4IEBAIGluZnJhc3RydWN0dXJlIGF0IGltcG9ydCB0aW1lLCBydW50 aW1lLCBvciBzdGF0aWNhbGx5ICh1c2luZyB0aGUgaW5jbHVkZWQgcHljYwogdG9vbCkuIikKICAg ICAobGljZW5zZSBsaWNlbnNlOmJzZC0zKSkpCiAKKyhkZWZpbmUtcHVibGljIHB5dGhvbi1udW1j b2RlY3MKKyAgKHBhY2thZ2UKKyAgICAobmFtZSAicHl0aG9uLW51bWNvZGVjcyIpCisgICAgKHZl cnNpb24gIjAuNi40IikKKyAgICAoc291cmNlIChvcmlnaW4KKyAgICAgICAgICAgICAgKG1ldGhv ZCB1cmwtZmV0Y2gpCisgICAgICAgICAgICAgICh1cmkgKHB5cGktdXJpICJudW1jb2RlY3MiIHZl cnNpb24pKQorICAgICAgICAgICAgICAoc2hhMjU2CisgICAgICAgICAgICAgICAoYmFzZTMyCisg ICAgICAgICAgICAgICAgIjBrYmZyOHBsM3g5Z2xzeXBicThoemltMDAzZjE2bWwxYjFjdmdyaDR3 MXNkdmdhbDZqN2ciKSkpKQorICAgIChidWlsZC1zeXN0ZW0gcHl0aG9uLWJ1aWxkLXN5c3RlbSkK KyAgICAocHJvcGFnYXRlZC1pbnB1dHMKKyAgICAgYCgoInB5dGhvbi1udW1weSIgLHB5dGhvbi1u dW1weSkKKyAgICAgICAoInB5dGhvbi1zZXR1cHRvb2xzLXNjbSIgLHB5dGhvbi1zZXR1cHRvb2xz LXNjbSkKKyAgICAgICAoInB5dGhvbi1tc2dwYWNrIiAscHl0aG9uLW1zZ3BhY2spCisgICAgICAg KCJweXRob24tcHl0ZXN0IiAscHl0aG9uLXB5dGVzdCkpKQorICAgIChob21lLXBhZ2UgImh0dHBz Oi8vZ2l0aHViLmNvbS96YXJyLWRldmVsb3BlcnMvbnVtY29kZWNzIikKKyAgICAoc3lub3BzaXMg IkJ1ZmZlciBjb21wcmVzc2lvbiBhbmQgdHJhbnNmb3JtYXRpb24gY29kZWNzIikKKyAgICAoZGVz Y3JpcHRpb24gIlRoaXMgcGFja2FnZSBwcm92aWRlcyBidWZmZXIgY29tcHJlc3Npb24gYW5kIHRy YW5zZm9ybWF0aW9uCitjb2RlY3MgZm9yIHVzZSBpbiBkYXRhIHN0b3JhZ2UgYW5kIGNvbW11bmlj YXRpb24gYXBwbGljYXRpb25zLiIpCisgICAgKGxpY2Vuc2UgbGljZW5zZTpleHBhdCkpKQorCiAo ZGVmaW5lLXB1YmxpYyBweXRob24tYW5uZGF0YQogICAocGFja2FnZQogICAgIChuYW1lICJweXRo b24tYW5uZGF0YSIpCi0tIAoyLjI1LjEKCg== --=-YPSo1wMfUwcY01Bn/HzX-- From debbugs-submit-bounces@debbugs.gnu.org Sat Mar 07 21:54:21 2020 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 From unknown Sun Jun 22 07:51:13 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sun, 05 Apr 2020 11:24:07 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator