From unknown Tue Jun 17 01:50:26 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#39904] Update of python-anndata Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 04 Mar 2020 15:01:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 39904 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 39904@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.15833340305736 (code B ref -1); Wed, 04 Mar 2020 15:01:01 +0000 Received: (at submit) by debbugs.gnu.org; 4 Mar 2020 15:00:30 +0000 Received: from localhost ([127.0.0.1]:41545 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j9VVd-0001UR-69 for submit@debbugs.gnu.org; Wed, 04 Mar 2020 10:00:29 -0500 Received: from lists.gnu.org ([209.51.188.17]:59373) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j9RDp-00012l-Cf for submit@debbugs.gnu.org; Wed, 04 Mar 2020 05:25:50 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:50530) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j9RDn-0006Qx-D5 for guix-patches@gnu.org; Wed, 04 Mar 2020 05:25:49 -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,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 1j9RDl-00052W-O9 for guix-patches@gnu.org; Wed, 04 Mar 2020 05:25:47 -0500 Received: from www.this-is-red.com ([164.138.25.65]:40240) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1j9RDl-0004zN-3O for guix-patches@gnu.org; Wed, 04 Mar 2020 05:25:45 -0500 Message-ID: <1eaf5ea7175f71ee190f4b3cf965608c55b5cd83.camel@roelserve.com> DKIM-Filter: OpenDKIM Filter v2.11.0 www.this-is-red.com 0AADE20449 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=roelserve.com; s=default; t=1583317727; bh=llTn3UtXvkfj/i1XbTbOAKONHdl2lQ9cTWI3iAK7Huw=; h=Subject:From:To:Date:From; b=HoUi1p3C6eeNLlpsZ32dx85shL7NEZEGViS44tOihAqO5w02gQYHYYF4aqMEPNaKy tWN8DJTkI84pKV3/NNcC/qdKKqufNa56Bnzzr0AQxi7oMjRZCGbtEkPG5zjWlSN44G GjCEpf60NaM4gXiDB4/rhLoW6sBY4GaUkxyHCx9Q= From: Roel Janssen Date: Wed, 04 Mar 2020 11:25:33 +0100 Content-Type: multipart/mixed; boundary="=-RhEqJoqqGNMwLLI8wSmv" 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] [fuzzy] X-Received-From: 164.138.25.65 X-Spam-Score: 0.2 (/) X-Mailman-Approved-At: Wed, 04 Mar 2020 10:00:27 -0500 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: -0.8 (/) --=-RhEqJoqqGNMwLLI8wSmv Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit Dear Guix, I'd like to update our package for python-anndata. For this I needed to add a few more packages that are used in the test suite of python-anndata. I attached the patches. 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? Thanks! 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boundary="----------=_1583487902-23407-1" This is a multi-part message in MIME format... ------------=_1583487902-23407-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #39904: Update of python-anndata which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 39904@debbugs.gnu.org. --=20 39904: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D39904 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1583487902-23407-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 39904-close) by debbugs.gnu.org; 6 Mar 2020 09:44:13 +0000 Received: from localhost ([127.0.0.1]:44096 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jA9We-00064F-UN for submit@debbugs.gnu.org; Fri, 06 Mar 2020 04:44:13 -0500 Received: from www.this-is-red.com ([164.138.25.65]:35428) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jA9Wc-000641-Sf for 39904-close@debbugs.gnu.org; Fri, 06 Mar 2020 04:44:11 -0500 Message-ID: DKIM-Filter: OpenDKIM Filter v2.11.0 www.this-is-red.com 3F6FB1FED7 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=roelserve.com; s=default; t=1583488039; bh=Im0lkgL/CAVxPSQT+iDMyKC4FD7pFAO9bLfvDNGs1dQ=; h=Subject:From:To:Date:In-Reply-To:References:From; b=IInp/y42mJ4gpFi/vymcX5y/tPGBbInP8yqmddNuWvaMYFDqo/InpmV0MIIunCd1/ HPgS/D/KV5yKgAwWZrU9rFdGxGd0kv7AtDwa6ephsjs1pl2EU3YSfZIXHv/OBIb2e+ MGWKaDuJ0Uk1glejUWRkNFZ3bCg7+IjqUUz5jiHg= Subject: Re: bug#39904: Acknowledgement (Update of python-anndata) From: Roel Janssen To: 39904-close@debbugs.gnu.org Date: Fri, 06 Mar 2020 10:44:05 +0100 In-Reply-To: References: <1eaf5ea7175f71ee190f4b3cf965608c55b5cd83.camel@roelserve.com> Content-Type: text/plain; charset="UTF-8" User-Agent: Evolution 3.34.4 (3.34.4-1.fc31) MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=-0.2 required=1.5 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,UNPARSEABLE_RELAY,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.4 X-Spam-Checker-Version: SpamAssassin 3.4.4 (2020-01-24) on www.this-is-red.com X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 39904-close 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 (-) On Wed, 2020-03-04 at 15:01 +0000, GNU bug Tracking System wrote: > Thank you for filing a new bug report with debbugs.gnu.org. > > This is an automatically generated reply to let you know your message > has been received. > > Your message is being forwarded to the package maintainers and other > interested parties for their attention; they will reply in due > course. > > Your message has been sent to the package maintainer(s): > guix-patches@gnu.org > > If you wish to submit further information on this problem, please > send it to 39904@debbugs.gnu.org. > > Please do not send mail to help-debbugs@gnu.org unless you wish > to report a problem with the Bug-tracking system. > So, Ricardo has pushed similar patches in the meantime. Closing this one. Kind regards, Roel Janssen ------------=_1583487902-23407-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 4 Mar 2020 15:00:30 +0000 Received: from localhost ([127.0.0.1]:41545 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j9VVd-0001UR-69 for submit@debbugs.gnu.org; Wed, 04 Mar 2020 10:00:29 -0500 Received: from lists.gnu.org ([209.51.188.17]:59373) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j9RDp-00012l-Cf for submit@debbugs.gnu.org; Wed, 04 Mar 2020 05:25:50 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:50530) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j9RDn-0006Qx-D5 for guix-patches@gnu.org; Wed, 04 Mar 2020 05:25:49 -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,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 1j9RDl-00052W-O9 for guix-patches@gnu.org; Wed, 04 Mar 2020 05:25:47 -0500 Received: from www.this-is-red.com ([164.138.25.65]:40240) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1j9RDl-0004zN-3O for guix-patches@gnu.org; Wed, 04 Mar 2020 05:25:45 -0500 Message-ID: <1eaf5ea7175f71ee190f4b3cf965608c55b5cd83.camel@roelserve.com> DKIM-Filter: OpenDKIM Filter v2.11.0 www.this-is-red.com 0AADE20449 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=roelserve.com; s=default; t=1583317727; bh=llTn3UtXvkfj/i1XbTbOAKONHdl2lQ9cTWI3iAK7Huw=; h=Subject:From:To:Date:From; b=HoUi1p3C6eeNLlpsZ32dx85shL7NEZEGViS44tOihAqO5w02gQYHYYF4aqMEPNaKy tWN8DJTkI84pKV3/NNcC/qdKKqufNa56Bnzzr0AQxi7oMjRZCGbtEkPG5zjWlSN44G GjCEpf60NaM4gXiDB4/rhLoW6sBY4GaUkxyHCx9Q= Subject: Update of python-anndata From: Roel Janssen To: guix-patches@gnu.org Date: Wed, 04 Mar 2020 11:25:33 +0100 Content-Type: multipart/mixed; boundary="=-RhEqJoqqGNMwLLI8wSmv" 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] [fuzzy] X-Received-From: 164.138.25.65 X-Spam-Score: 0.2 (/) X-Debbugs-Envelope-To: submit X-Mailman-Approved-At: Wed, 04 Mar 2020 10:00:27 -0500 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: -0.8 (/) --=-RhEqJoqqGNMwLLI8wSmv Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit Dear Guix, I'd like to update our package for python-anndata. For this I needed to add a few more packages that are used in the test suite of python-anndata. I attached the patches. 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? Thanks! 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Fri, 06 Mar 2020 22:02:01 +0000 Received: (at 39904) by debbugs.gnu.org; 6 Mar 2020 22:01:06 +0000 Received: from localhost ([127.0.0.1]:45969 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jAL1l-0004Ch-QY for submit@debbugs.gnu.org; Fri, 06 Mar 2020 17:01:06 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21110) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jAL1j-0004CY-SI for 39904@debbugs.gnu.org; Fri, 06 Mar 2020 17:01:04 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1583532060; cv=none; d=zohomail.com; s=zohoarc; b=As9C0WSSjoWr2eA4Klth/+Uo/bixiRG2Qrh2zLNqhHt3NCLuccnAZfHejpiWMs0CV3aS7cQHTWj/nFEk/KIMDUvO0GUeqI8g8E+eIGSeDa5KeQBPXvf1Gvng4UxR2RWbLdmNghjOEtStW7ZQlVxbGHJZxtuvJe50KN8QHmilQpU= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1583532060; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=arHdqZcmnB4V9933ue+7MQQo2CP6q+e/aeEDXxuqN/E=; 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emacs 26.3 From: Ricardo Wurmus In-reply-to: <1eaf5ea7175f71ee190f4b3cf965608c55b5cd83.camel@roelserve.com> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Fri, 06 Mar 2020 23:00:55 +0100 Message-ID: <878skdp2i0.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) 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 (-) Hi Roel, > I'd like to update our package for python-anndata. For this I needed to = add a > few more packages that are used in the test suite of python-anndata. I=E2=80=99m sorry I missed this patch series. I noticed that scanpy failed= to build, so I worked on upgrading it together with anndata. I must have started the work right before your patches came in. > I attached the patches. Note that for python-zarr I disabled the tests b= ecause > the majority of the tests need external packages. We could add all depen= dencies > to make the test suite work, but that requires a significant amount of wo= rk (for > example, the Azure SDK for Python is one of the external dependencies). These tests that use external services (such as Azure Storage Blob, Redis, etc) can be disabled with environment variables, which is what I did in my version of the package definition. -- Ricardo From unknown Tue Jun 17 01:50:26 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#39904] Update of python-anndata Resent-From: Roel Janssen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 07 Mar 2020 08:51:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 39904 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 39904@debbugs.gnu.org Received: via spool by 39904-submit@debbugs.gnu.org id=B39904.15835710279900 (code B ref 39904); Sat, 07 Mar 2020 08:51:02 +0000 Received: (at 39904) by debbugs.gnu.org; 7 Mar 2020 08:50:27 +0000 Received: from localhost ([127.0.0.1]:46247 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jAVAB-0002Zc-3G for submit@debbugs.gnu.org; Sat, 07 Mar 2020 03:50:27 -0500 Received: from www.this-is-red.com ([164.138.25.65]:53124) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jAVA8-0002ZT-Ni for 39904@debbugs.gnu.org; Sat, 07 Mar 2020 03:50:25 -0500 Message-ID: <8f38dc49c0e4648da46f8b240a8ff7975a8237ee.camel@roelserve.com> DKIM-Filter: OpenDKIM Filter v2.11.0 www.this-is-red.com B41ED1FED7 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=roelserve.com; s=default; t=1583571212; bh=owb8MLchCQVBflX8fcKfzfmgE/6AWVm12RZEtTWQAoo=; h=Subject:From:To:Cc:Date:In-Reply-To:References:From; b=eSXMazAJTzYmA2vcAZpSp3z2yU97t+vWpuK4UHe1HCQ03hiZQdkIwmLsY8KK8dlU1 NxgNGhVsn3tg8P6UmJ4krnIA0HHmnI+Rpf62jhDhgQopjwEA5dVzxAEfRN64h85XrS XATxpJmS1YijwwdzuinH2mDAzB82lfQJtFUwmZbc= From: Roel Janssen Date: Sat, 07 Mar 2020 09:50:19 +0100 In-Reply-To: <878skdp2i0.fsf@elephly.net> References: <1eaf5ea7175f71ee190f4b3cf965608c55b5cd83.camel@roelserve.com> <878skdp2i0.fsf@elephly.net> Content-Type: text/plain; charset="UTF-8" User-Agent: Evolution 3.34.4 (3.34.4-1.fc31) MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=-0.2 required=1.5 tests=DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,UNPARSEABLE_RELAY autolearn=ham autolearn_force=no version=3.4.4 X-Spam-Checker-Version: SpamAssassin 3.4.4 (2020-01-24) on www.this-is-red.com X-Spam-Score: 0.0 (/) 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 (-) On Fri, 2020-03-06 at 23:00 +0100, Ricardo Wurmus wrote: > Hi Roel, > > > I'd like to update our package for python-anndata. For this I > > needed to add a > > few more packages that are used in the test suite of python- > > anndata. > > I’m sorry I missed this patch series. I noticed that scanpy failed > to > build, so I worked on upgrading it together with anndata. I must > have > started the work right before your patches came in. > > > I attached the patches. 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). > > These tests that use external services (such as Azure Storage Blob, > Redis, etc) can be disabled with environment variables, which is what > I > did in my version of the package definition. Thanks.