Received: (at 77394-done) by debbugs.gnu.org; 8 Apr 2025 11:29:55 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Apr 08 07:29:55 2025 Received: from localhost ([127.0.0.1]:59420 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1u279P-00064L-Da for submit <at> debbugs.gnu.org; Tue, 08 Apr 2025 07:29:55 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:35674) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <andreas@HIDDEN>) id 1u279M-00063P-1d for 77394-done <at> debbugs.gnu.org; Tue, 08 Apr 2025 07:29:52 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 4B9472C3; Tue, 8 Apr 2025 13:29:44 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id 5WLwrjIt2eXD; Tue, 8 Apr 2025 13:29:43 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id E443D98; Tue, 8 Apr 2025 13:29:41 +0200 (CEST) Date: Tue, 8 Apr 2025 13:29:40 +0200 From: Andreas Enge <andreas@HIDDEN> To: David Elsing <david.elsing@HIDDEN> Subject: Re: [PATCH 5/5] gnu: rdkit: Update to 2024.09.6. Message-ID: <Z_UIpBGZgdqxzdHg@jurong> References: <20250330220421.24480-1-david.elsing@HIDDEN> <20250330220745.25337-5-david.elsing@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20250330220745.25337-5-david.elsing@HIDDEN> X-Rspamd-Server: hera X-Spamd-Bar: +++++ X-Rspamd-Queue-Id: 4B9472C3 X-Spamd-Result: default: False [5.42 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[1.000]; BAYES_HAM(-2.98)[99.93%]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; MIME_TRACE(0.00)[0:+]; FROM_HAS_DN(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; RCPT_COUNT_TWO(0.00)[2]; RCVD_TLS_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; TO_DN_SOME(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; ARC_NA(0.00)[] X-Spam-Level: ***** X-Rspamd-Action: greylist X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77394-done Cc: 77394-done <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: -1.0 (-) Hello David, I have just pushed with the few changes you suggested. Concerning boost-with-numpy, it also needed a "name" field, since otherwise there was a commandline collision between the two packages. In the end I opted for "boost-numpy" for the name field and the variable name, since we already have "boost-mpi" and it felt consistent. Thanks, closing! Andreas
David Elsing <david.elsing@HIDDEN>
:Andreas Enge <andreas@HIDDEN>
:Received: (at 77394) by debbugs.gnu.org; 7 Apr 2025 14:44:16 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Apr 07 10:44:16 2025 Received: from localhost ([127.0.0.1]:56177 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1u1nhw-0003wF-CS for submit <at> debbugs.gnu.org; Mon, 07 Apr 2025 10:44:16 -0400 Received: from mout01.posteo.de ([185.67.36.65]:59645) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <david.elsing@HIDDEN>) id 1u1nhs-0003vg-Qi for 77394 <at> debbugs.gnu.org; Mon, 07 Apr 2025 10:44:14 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 707A7240028 for <77394 <at> debbugs.gnu.org>; Mon, 7 Apr 2025 16:44:06 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744037046; bh=LI+Rn62GlYs38M634o7oVvIrwUEgPI0e7rem1NoVnKs=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: From; b=kmRSMIsjeGnF2+sPQJV2ZCLVMp0WOw5IIDODRabk0OvapIvQ1bvKhkRaJ5k1L7qvk icoo99+UHoCkH0SfnbOFRvp2YtLIjrYs85XOGpP/jzGp3jZSPjvBa09NqqLnd8oSww z2MEvw5t3qrVGu3lZKuu8VWgJuKnVULqYfgQ/hb6IkjRqd8sY97Ls5tZjedinEGlQp J0IpYpTkGJHdSYx+WdLrGjwWBV44lnIy6Tsa+5DHRkpWpnc5vUYfeP36dLtw/fKfwd lA8s0FZxuhqTZgkGs1gUU7a5431bF9O1I1plvz0MVuFQObgMzUqGVLJpktSIN3saQ8 3RfvVTYKPakaw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZWX5x694Mz9rxQ; Mon, 7 Apr 2025 16:44:05 +0200 (CEST) From: David Elsing <david.elsing@HIDDEN> To: Andreas Enge <andreas@HIDDEN> Subject: Re: [PATCH 1/5] gnu: inchi: Update to 1.07.3. In-Reply-To: <Z_OtYP_0fzH6ENwS@jurong> References: <20250330220421.24480-1-david.elsing@HIDDEN> <20250330220745.25337-1-david.elsing@HIDDEN> <Z_OqlJVPdh2Vd1fG@jurong> <Z_OtYP_0fzH6ENwS@jurong> Date: Mon, 07 Apr 2025 14:44:05 +0000 Message-ID: <7ytt70qbey.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77394 Cc: 77394 <at> debbugs.gnu.org, sharlatanus@HIDDEN, code@HIDDEN, bavier@HIDDEN 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 Andreas, Andreas Enge <andreas@HIDDEN> writes: > I have pushed your patches 2 and 4. Thanks! > Concerning boost with numpy, I am not sure; should we add numpy > directly to boost as an input? This might actually create a circular > dependency (I have not checked). In any case, both are monster packages, > so replacing boost by a combination of the two may be a bad idea, and > your suggestion to create a separate boost-with-numpy is preferable. I just checked and there does not seem to be a circular dependency. However, boost has *much* less transitive dependencies than python-numpy and is depended on by many packages. Its build time and compressed size (~20 MB) is also not that large, so I think a separate package is not that bad. Cheers, David
guix-patches@HIDDEN
:bug#77394
; Package guix-patches
.
Full text available.Received: (at 77394) by debbugs.gnu.org; 7 Apr 2025 14:30:16 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Apr 07 10:30:16 2025 Received: from localhost ([127.0.0.1]:56127 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1u1nUN-0000OV-M0 for submit <at> debbugs.gnu.org; Mon, 07 Apr 2025 10:30:16 -0400 Received: from mout02.posteo.de ([185.67.36.66]:55951) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <david.elsing@HIDDEN>) id 1u1nUK-0008K8-15 for 77394 <at> debbugs.gnu.org; Mon, 07 Apr 2025 10:30:13 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 78427240104 for <77394 <at> debbugs.gnu.org>; Mon, 7 Apr 2025 16:30:05 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744036205; bh=cWDKwFyFk2M8lXnHJRzKCo6V4zh6yzPm12V+IXoi5ck=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: From; b=Jv1Ui6GGBVinp9rX0FSirY4FBFulu0++myQ0wScLqo4HjjYz/xqszW12gzc4Llxgb hAhtXxu8U255fHuRjFMcQ4Ww7AG4BUdoPzW4D40wXw1hlHxE1iOA93gzA2rysc0RX+ lyDd68A+1P25P/x6+7uanW8444wRppIx9l53zdRVu9UsYjwZiohFHOmqccXG/w9zv7 Rnbmpq3a7h3qtYkegQrzdFFEr+/xX8fj9iZDxq9M94W9FPfR29zGzJNQL7wYm3nGM9 JIqlKjNLX1zOH7Ws619PwOPAuBkRW/LXYrMm8ypPFb5sp/eY1BDr6oYT3rYRFOFhGO IYUCu/AWh8niA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZWWnn0Bd5z9rxG; Mon, 7 Apr 2025 16:30:04 +0200 (CEST) From: David Elsing <david.elsing@HIDDEN> To: Andreas Enge <andreas@HIDDEN> Subject: Re: [PATCH 1/5] gnu: inchi: Update to 1.07.3. In-Reply-To: <Z_OqlJVPdh2Vd1fG@jurong> References: <20250330220421.24480-1-david.elsing@HIDDEN> <20250330220745.25337-1-david.elsing@HIDDEN> <Z_OqlJVPdh2Vd1fG@jurong> Date: Mon, 07 Apr 2025 14:30:04 +0000 Message-ID: <7ywmbwqc2b.fsf@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77394 Cc: 77394 <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, Andreas Enge <andreas@HIDDEN> writes: > You also dropped the documentation native input. Is that intended? Yes, it is included in the Git repo, but I forgot to mention it in the commit message. I also forgot to update the copyright header. :) Can you add them or should I send an updated patch? Thank you, David
guix-patches@HIDDEN
:bug#77394
; Package guix-patches
.
Full text available.Received: (at 77394) by debbugs.gnu.org; 7 Apr 2025 10:48:12 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Apr 07 06:48:11 2025 Received: from localhost ([127.0.0.1]:52932 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1u1k1T-0004DF-HI for submit <at> debbugs.gnu.org; Mon, 07 Apr 2025 06:48:11 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:42630) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <andreas@HIDDEN>) id 1u1k1R-0004Ce-3d for 77394 <at> debbugs.gnu.org; Mon, 07 Apr 2025 06:48:09 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id D8BEC5F5; Mon, 7 Apr 2025 12:48:02 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id AMo0vwo4Gakd; Mon, 7 Apr 2025 12:48:02 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id CFE3353; Mon, 7 Apr 2025 12:48:01 +0200 (CEST) Date: Mon, 7 Apr 2025 12:48:00 +0200 From: Andreas Enge <andreas@HIDDEN> To: David Elsing <david.elsing@HIDDEN> Subject: Re: [PATCH 1/5] gnu: inchi: Update to 1.07.3. Message-ID: <Z_OtYP_0fzH6ENwS@jurong> References: <20250330220421.24480-1-david.elsing@HIDDEN> <20250330220745.25337-1-david.elsing@HIDDEN> <Z_OqlJVPdh2Vd1fG@jurong> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <Z_OqlJVPdh2Vd1fG@jurong> X-Rspamd-Server: hera X-Spamd-Bar: +++++ X-Rspamd-Queue-Id: D8BEC5F5 X-Spamd-Result: default: False [5.40 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[1.000]; BAYES_HAM(-3.00)[99.99%]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCPT_COUNT_FIVE(0.00)[5]; ARC_NA(0.00)[]; FREEMAIL_ENVRCPT(0.00)[gmail.com]; RCVD_VIA_SMTP_AUTH(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_DN_SOME(0.00)[]; FREEMAIL_CC(0.00)[debbugs.gnu.org,posteo.net,gmail.com,greghogan.com] X-Spam-Level: ***** X-Rspamd-Action: greylist X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77394 Cc: 77394 <at> debbugs.gnu.org, sharlatanus@HIDDEN, code@HIDDEN, bavier@HIDDEN 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 (-) I have pushed your patches 2 and 4. Concerning boost with numpy, I am not sure; should we add numpy directly to boost as an input? This might actually create a circular dependency (I have not checked). In any case, both are monster packages, so replacing boost by a combination of the two may be a bad idea, and your suggestion to create a separate boost-with-numpy is preferable. I am cc-ing the science and C++ teams for their opinion. Andreas
guix-patches@HIDDEN
:bug#77394
; Package guix-patches
.
Full text available.Received: (at 77394) by debbugs.gnu.org; 7 Apr 2025 10:36:24 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Apr 07 06:36:24 2025 Received: from localhost ([127.0.0.1]:52896 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1u1jq4-0000NE-2G for submit <at> debbugs.gnu.org; Mon, 07 Apr 2025 06:36:24 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:57564) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <andreas@HIDDEN>) id 1u1jq0-0000Ma-D6 for 77394 <at> debbugs.gnu.org; Mon, 07 Apr 2025 06:36:21 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id B4F5F310; Mon, 7 Apr 2025 12:36:12 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id XQfPax8ekPyo; Mon, 7 Apr 2025 12:36:10 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 1B22813D; Mon, 7 Apr 2025 12:36:06 +0200 (CEST) Date: Mon, 7 Apr 2025 12:36:04 +0200 From: Andreas Enge <andreas@HIDDEN> To: David Elsing <david.elsing@HIDDEN> Subject: Re: [PATCH 1/5] gnu: inchi: Update to 1.07.3. Message-ID: <Z_OqlJVPdh2Vd1fG@jurong> References: <20250330220421.24480-1-david.elsing@HIDDEN> <20250330220745.25337-1-david.elsing@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20250330220745.25337-1-david.elsing@HIDDEN> X-Rspamd-Server: hera X-Rspamd-Queue-Id: B4F5F310 X-Spamd-Result: default: False [-5.60 / 15.00]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-3.00)[-1.000]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCPT_COUNT_TWO(0.00)[2]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_DN_SOME(0.00)[]; ARC_NA(0.00)[] X-Spamd-Bar: ----- X-Rspamd-Action: no action X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77394 Cc: 77394 <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: -1.0 (-) Hello David, thanks for the patches! Am Sun, Mar 30, 2025 at 10:06:54PM +0000 schrieb David Elsing: > [native-inputs]: Remove input label. > ;; Update the inchi-doc native input when updating inchi. > - (native-inputs > - `(("unzip" ,unzip) > - ("inchi-doc" > - ,(origin > - (method url-fetch) > - (uri (string-append "http://www.inchi-trust.org/download/" > - (string-join (string-split version #\.) "") > - "/INCHI-1-DOC.zip")) > - (sha256 > - (base32 > - "1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f")) > - (file-name (string-append name "-" version ".zip")))))) > + (native-inputs (list unzip)) You also dropped the documentation native input. Is that intended? Andreas
guix-patches@HIDDEN
:bug#77394
; Package guix-patches
.
Full text available.Received: (at 77394) by debbugs.gnu.org; 30 Mar 2025 22:08:32 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Mar 30 18:08:32 2025 Received: from localhost ([127.0.0.1]:38362 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1tz0pT-000186-23 for submit <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:08:32 -0400 Received: from mout02.posteo.de ([185.67.36.66]:57063) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <david.elsing@HIDDEN>) id 1tz0pN-00016i-Eo for 77394 <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:08:27 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id AEF26240103 for <77394 <at> debbugs.gnu.org>; Mon, 31 Mar 2025 00:08:14 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743372494; bh=akOqWmC5uQKEUWKrmpgdB37Y4qyM7jk8EB5aRCmaCgk=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=OioLkn0Oz/iqr2UdcWK9OST4ad011zs35afOnYZrOyY3po+Lv+G55Qohj+JNDCuYU 6jh1HmxVYxsYrr5J8FakNiTWIQovoAzxKQ/CFpF10z4tyUTPixuiUoJDgd9UNeX8w/ sIzBIx1Ws0SLj3hiacbVcFdtHzDLN2856/4oWxOqJUl6Wx8eYgtDEzvDxdPViIip34 ijijrDL0vvyxSd5TFfJAOM8ejlTRoTEs3OWNBZx3ETciTbNNwZcu7lTWtSdLXGPqW2 1/XkZp8B58rd4pTid942IWRMX4z56Lg4tNRsLQKKN/tiBCWw20FaIBUsVxvnW6NPsG Dxdwam/c0+laQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZQpL62jRnz6v0J; Mon, 31 Mar 2025 00:08:14 +0200 (CEST) From: David Elsing <david.elsing@HIDDEN> To: 77394 <at> debbugs.gnu.org Subject: [PATCH 5/5] gnu: rdkit: Update to 2024.09.6. Date: Sun, 30 Mar 2025 22:06:58 +0000 Message-ID: <20250330220745.25337-5-david.elsing@HIDDEN> In-Reply-To: <20250330220421.24480-1-david.elsing@HIDDEN> References: <20250330220421.24480-1-david.elsing@HIDDEN> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77394 Cc: David Elsing <david.elsing@HIDDEN> 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 (---) * gnu/packages/chemistry.scm (rdkit): Update to 2024.09.6. [arguments]: Disable more failing tests. [inputs]: Add pubchem-align3d. [native-inputs]: Replace boost with boost-with-numpy. Add python-pytest. * gnu/packages/patches/rdkit-unbundle-external-dependencies.patch: Adjust patch. --- gnu/packages/chemistry.scm | 14 +- ...rdkit-unbundle-external-dependencies.patch | 183 ++++++++++++++++-- 2 files changed, 176 insertions(+), 21 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index c1e0586534..66901a22a0 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -1115,7 +1115,7 @@ (define-public pubchem-align3d (define-public rdkit (package (name "rdkit") - (version "2023.09.4") + (version "2024.09.6") (source (origin (method git-fetch) (uri (git-reference @@ -1126,7 +1126,7 @@ (define-public rdkit (file-name (git-file-name name version)) (sha256 (base32 - "1lgcgijlzzwpfxndsdlx13npdfk7hcii11zg25cvpmzhbpn6vyn8")) + "0nagqy5c9b86ip8qr1rnvby235am1zyc4sqm0z7wphbb70cqazxg")) (patches (search-patches "rdkit-unbundle-external-dependencies.patch")) (modules '((guix build utils))) @@ -1224,10 +1224,16 @@ (define-public rdkit "graphmoltestPickler" "pyPartialCharges" "substructLibraryTest" "pyFeatures" "pythonTestDirML" "pythonTestDirChem" + "pyRealValueVect" "pyDiscreteValueVect" + "pickleTestsCatch" ;; Catching Python exception fails "pyRanker" ;; Flaky test depending on floating point rounding "testConrec" + ;; Expensive test which may time out + "pySynthonSpaceSearch" + ;; Circular import + "pythonSourceTests" ) "|") ")"))))))))) (inputs @@ -1238,18 +1244,20 @@ (define-public rdkit freetype inchi maeparser + pubchem-align3d python ringdecomposerlib sqlite yaehmop)) (native-inputs (list bison - boost + boost-with-numpy catch2-3 eigen flex freesasa pkg-config + python-pytest rapidjson tar)) (propagated-inputs diff --git a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch index e22ff57ee0..3e72f40504 100644 --- a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch +++ b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch @@ -3,10 +3,10 @@ They are packaged separately as rapidjson, avalon-toolkit, freesasa, ringdecomposerlib and yaehmop. diff --git a/Code/GraphMol/MolInterchange/CMakeLists.txt b/Code/GraphMol/MolInterchange/CMakeLists.txt -index 1673386a4..c3504e6f1 100644 +index 0c1e9a0de..c3504e6f1 100644 --- a/Code/GraphMol/MolInterchange/CMakeLists.txt +++ b/Code/GraphMol/MolInterchange/CMakeLists.txt -@@ -1,18 +1,3 @@ +@@ -1,26 +1,3 @@ - -if(NOT EXISTS "${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0") - downloadAndCheckMD5("https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz" @@ -15,8 +15,16 @@ index 1673386a4..c3504e6f1 100644 - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf - ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0.tar.gz - WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/External) +- # comment out a line which causes a compilation error on some platforms +- # (based on the change which has already been applied to the RapidJSON master branch, see +- # https://github.com/Tencent/rapidjson/blob/ab1842a2dae061284c0a62dca1cc6d5e7e37e346/include/rapidjson/document.h#L414) +- file(READ ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include/rapidjson/document.h RAPIDJSON_DOCUMENT_H) +- string(REGEX REPLACE +- "( *)(GenericStringRef& operator=\\(const GenericStringRef& rhs\\) { s = rhs\\.s. length = rhs\\.length. })" "\\1//\\2" +- RAPIDJSON_DOCUMENT_H "${RAPIDJSON_DOCUMENT_H}") +- file(WRITE ${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include/rapidjson/document.h "${RAPIDJSON_DOCUMENT_H}") -else() -- message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External") +- message("-- Found RapidJSON source in ${CMAKE_SOURCE_DIR}/External") -endif() - -include_directories(${CMAKE_SOURCE_DIR}/External/rapidjson-1.1.0/include) @@ -26,7 +34,7 @@ index 1673386a4..c3504e6f1 100644 Parser.cpp Writer.cpp LINK_LIBRARIES GraphMol) diff --git a/External/AvalonTools/AvalonTools.cpp b/External/AvalonTools/AvalonTools.cpp -index e6c382123..d83d80668 100644 +index f4b37ba5c..e1b25aed1 100644 --- a/External/AvalonTools/AvalonTools.cpp +++ b/External/AvalonTools/AvalonTools.cpp @@ -24,15 +24,15 @@ @@ -55,7 +63,7 @@ index e6c382123..d83d80668 100644 extern int RunStruchk(struct reaccs_molecule_t **mpp, struct data_line_t *data_list); diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLists.txt -index 3e31195fc..314ba35b5 100644 +index 30203ecdf..4e2661d7e 100644 --- a/External/AvalonTools/CMakeLists.txt +++ b/External/AvalonTools/CMakeLists.txt @@ -2,90 +2,8 @@ if(NOT RDK_BUILD_AVALON_SUPPORT) @@ -151,7 +159,7 @@ index 3e31195fc..314ba35b5 100644 rdkit_headers(AvalonTools.h DEST GraphMol) rdkit_test(testAvalonLib1 test1.cpp diff --git a/External/AvalonTools/Wrap/pyAvalonTools.cpp b/External/AvalonTools/Wrap/pyAvalonTools.cpp -index fb24c497e..31997bc0a 100644 +index 72c7a5ee2..e7ac609ae 100644 --- a/External/AvalonTools/Wrap/pyAvalonTools.cpp +++ b/External/AvalonTools/Wrap/pyAvalonTools.cpp @@ -12,7 +12,7 @@ @@ -164,10 +172,10 @@ index fb24c497e..31997bc0a 100644 namespace python = boost::python; diff --git a/External/FreeSASA/CMakeLists.txt b/External/FreeSASA/CMakeLists.txt -index 43dfbdc40..81165a143 100644 +index 8baadb618..81165a143 100644 --- a/External/FreeSASA/CMakeLists.txt +++ b/External/FreeSASA/CMakeLists.txt -@@ -2,88 +2,8 @@ if(NOT RDK_BUILD_FREESASA_SUPPORT) +@@ -2,174 +2,8 @@ if(NOT RDK_BUILD_FREESASA_SUPPORT) return() endif(NOT RDK_BUILD_FREESASA_SUPPORT) @@ -223,6 +231,85 @@ index 43dfbdc40..81165a143 100644 - set(freesasa_additional_exports ${CMAKE_CURRENT_SOURCE_DIR}/additional_exports.def) - file(WRITE ${freesasa_additional_exports} - "EXPORTS\n" +- "freesasa_calc_structure\n" +- "freesasa_calc_coord\n" +- "freesasa_calc_tree\n" +- "freesasa_result_classes\n" +- "freesasa_result_free\n" +- "freesasa_classifier_from_file\n" +- "freesasa_classifier_free\n" +- "freesasa_classifier_radius\n" +- "freesasa_classifier_class\n" +- "freesasa_classifier_class2str\n" +- "freesasa_classifier_name\n" +- "freesasa_selection_new\n" +- "freesasa_selection_free\n" +- "freesasa_selection_name\n" +- "freesasa_selection_command\n" +- "freesasa_selection_area\n" +- "freesasa_set_verbosity\n" +- "freesasa_get_verbosity\n" +- "freesasa_set_err_out\n" +- "freesasa_get_err_out\n" +- "freesasa_structure_new\n" +- "freesasa_structure_free\n" +- "freesasa_structure_from_pdb\n" +- "freesasa_structure_array\n" +- "freesasa_structure_add_atom\n" +- "freesasa_structure_add_atom_wopt\n" +- "freesasa_structure_get_chains\n" +- "freesasa_structure_chain_labels\n" +- "freesasa_structure_n\n" +- "freesasa_structure_n_residues\n" +- "freesasa_structure_n_chains\n" +- "freesasa_structure_radius\n" +- "freesasa_structure_set_radius\n" +- "freesasa_structure_atom_name\n" +- "freesasa_structure_atom_res_name\n" +- "freesasa_structure_atom_res_number\n" +- "freesasa_structure_atom_chain\n" +- "freesasa_structure_atom_symbol\n" +- "freesasa_structure_atom_radius\n" +- "freesasa_structure_atom_set_radius\n" +- "freesasa_structure_residue_name\n" +- "freesasa_structure_residue_number\n" +- "freesasa_structure_residue_chain\n" +- "freesasa_structure_model\n" +- "freesasa_structure_coord_array\n" +- "freesasa_structure_residue_atoms\n" +- "freesasa_structure_chain_atoms\n" +- "freesasa_structure_chain_residues\n" +- "freesasa_structure_classifier_name\n" +- "freesasa_tree_new\n" +- "freesasa_tree_init\n" +- "freesasa_tree_add_result\n" +- "freesasa_tree_join\n" +- "freesasa_tree_export\n" +- "freesasa_node_free\n" +- "freesasa_node_area\n" +- "freesasa_node_children\n" +- "freesasa_node_next\n" +- "freesasa_node_parent\n" +- "freesasa_node_type\n" +- "freesasa_node_name\n" +- "freesasa_node_classified_by\n" +- "freesasa_node_atom_is_polar\n" +- "freesasa_node_atom_is_mainchain\n" +- "freesasa_node_atom_radius\n" +- "freesasa_node_atom_pdb_line\n" +- "freesasa_node_residue_number\n" +- "freesasa_node_residue_n_atoms\n" +- "freesasa_node_residue_reference\n" +- "freesasa_node_chain_n_residues\n" +- "freesasa_node_structure_n_chains\n" +- "freesasa_node_structure_n_atoms\n" +- "freesasa_node_structure_chain_labels\n" +- "freesasa_node_structure_model\n" +- "freesasa_node_structure_result\n" +- "freesasa_node_structure_selections\n" +- "freesasa_node_structure_add_selection\n" +- "freesasa_node_result_parameters\n" +- "freesasa_select_area\n" - "freesasa_default_parameters DATA\n" - "freesasa_protor_classifier DATA\n" - "freesasa_naccess_classifier DATA\n" @@ -236,8 +323,15 @@ index 43dfbdc40..81165a143 100644 - -set (freesasa_h ${FREESASA_SRC_DIR}/src/freesasa.h) -file(READ ${freesasa_h} freesasa_h_data) --string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}") --string(REGEX REPLACE "([^R][^D][^K][^I][^T][^_][^F][^R][^E][^E][^S][^A][^S][^A][^_][^C][^L][^I][^B][^_][^E][^X][^P][^O][^R][^T][^ ])(extern const)" "\\1RDKIT_FREESASA_CLIB_EXPORT \\2" freesasa_h_data "${freesasa_h_data}") +-if (NOT freesasa_h_data MATCHES "RDGeneral/export") +- string(REGEX REPLACE "(#include <stdio.h>)" "\\1\n#include <RDGeneral/export.h>" freesasa_h_data "${freesasa_h_data}") +-endif() +-if (MSVC) +- set (RDKIT_FREESASA_CLIB_EXPORT "RDKIT_FREESASA_CLIB_EXPORT ") +-else() +- set (RDKIT_FREESASA_CLIB_EXPORT "") +-endif() +-string(REGEX REPLACE "(RDKIT_FREESASA_CLIB_EXPORT )?(extern const)" "${RDKIT_FREESASA_CLIB_EXPORT}\\2" freesasa_h_data "${freesasa_h_data}") -file(WRITE ${freesasa_h} "${freesasa_h_data}") - -add_definitions(-DUSE_THREADS=0) @@ -258,7 +352,7 @@ index 43dfbdc40..81165a143 100644 rdkit_headers(RDFreeSASA.h DEST GraphMol) diff --git a/External/RingFamilies/CMakeLists.txt b/External/RingFamilies/CMakeLists.txt -index 08dd1fe04..66ecd5834 100644 +index 08dd1fe04..068435506 100644 --- a/External/RingFamilies/CMakeLists.txt +++ b/External/RingFamilies/CMakeLists.txt @@ -1,47 +1,7 @@ @@ -314,7 +408,7 @@ diff --git a/External/RingFamilies/dummy.cpp b/External/RingFamilies/dummy.cpp new file mode 100644 index 000000000..e69de29bb diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt -index f1027b3bd..8bee2f910 100644 +index c8daef9a5..01eaddac6 100644 --- a/External/YAeHMOP/CMakeLists.txt +++ b/External/YAeHMOP/CMakeLists.txt @@ -4,52 +4,7 @@ endif(NOT RDK_BUILD_YAEHMOP_SUPPORT) @@ -326,8 +420,8 @@ index f1027b3bd..8bee2f910 100644 -endif() - -if(NOT EXISTS "${YAEHMOP_DIR}/tightbind/bind.h") -- set(RELEASE_NO "2023.03.1") -- set(MD5 "e6450f13e02c54d024233b993c3c7ff6") +- set(RELEASE_NO "2024.03.1") +- set(MD5 "ebbddca4f79ab71544cb1fef9a7eca8a") - downloadAndCheckMD5("https://github.com/greglandrum/yaehmop/archive/refs/tags/v${RELEASE_NO}.tar.gz" - "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz" ${MD5}) - execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf @@ -372,11 +466,11 @@ index f1027b3bd..8bee2f910 100644 rdkit_headers(EHTTools.h DEST GraphMol) rdkit_catch_test(testEHTLib1 test1.cpp diff --git a/External/YAeHMOP/EHTTools.cpp b/External/YAeHMOP/EHTTools.cpp -index 7a229f51f..71033dc5c 100644 +index 021c548f1..43afdca57 100644 --- a/External/YAeHMOP/EHTTools.cpp +++ b/External/YAeHMOP/EHTTools.cpp -@@ -10,7 +10,7 @@ - #include <fstream> +@@ -13,7 +13,7 @@ + #include <filesystem> extern "C" { -#include <yaehmop/tightbind/bind.h> @@ -384,7 +478,7 @@ index 7a229f51f..71033dc5c 100644 } namespace RDKit { -@@ -160,4 +160,4 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId, +@@ -211,4 +211,4 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId, } } // end of namespace EHTTools @@ -404,3 +498,56 @@ index 759a9f360..114d24532 100644 add_pytest(pyEHTTools ${CMAKE_CURRENT_SOURCE_DIR}/testEHTTools.py) +diff --git a/External/pubchem_shape/CMakeLists.txt b/External/pubchem_shape/CMakeLists.txt +index a0f16eadb..463a9e31e 100644 +--- a/External/pubchem_shape/CMakeLists.txt ++++ b/External/pubchem_shape/CMakeLists.txt +@@ -2,47 +2,8 @@ if(NOT RDK_BUILD_PUBCHEMSHAPE_SUPPORT) + return() + endif() + +-if(NOT DEFINED PUBCHEMSHAPE_DIR) +- set(PUBCHEMSHAPE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/pubchem-align3d") +- set(fileToCheck "${PUBCHEMSHAPE_DIR}/shape_functions1.cpp") +- set(needDownload "TRUE") +- if(EXISTS "${fileToCheck}") +- set(needDownload "FALSE") +- endif() +-else() +- set(needDownload "FALSE") +-endif() +- +-if(needDownload) +- set(PUBCHEM_COMMIT_SHA daefab3) +- if(NOT DEFINED PUBCHEMSHAPE_URL) +- set(PUBCHEMSHAPE_URL "https://github.com/ncbi/pubchem-align3d/archive/${PUBCHEM_COMMIT_SHA}.tar.gz") +- endif() +- if(NOT DEFINED PUBCHEMSHAPE_MD5SUM) +- set(PUBCHEMSHAPE_MD5SUM "a78a6273851709083ac3803d62cb5ae6") +- endif() +- if(NOT DEFINED PUBCHEMSHAPE_BASE) +- string(REGEX REPLACE "^.*/" "" PUBCHEMSHAPE_BASE "${PUBCHEMSHAPE_URL}") +- endif() +- downloadAndCheckMD5(${PUBCHEMSHAPE_URL} "${CMAKE_CURRENT_SOURCE_DIR}/${PUBCHEMSHAPE_BASE}" ${PUBCHEMSHAPE_MD5SUM}) +- execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf +- ${CMAKE_CURRENT_SOURCE_DIR}/${PUBCHEM_COMMIT_SHA}.tar.gz +- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +- +- file(GLOB tar_dirname ${CMAKE_CURRENT_SOURCE_DIR}/pubchem-align3d-${PUBCHEM_COMMIT_SHA}*) +- execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${tar_dirname} +- ${PUBCHEMSHAPE_DIR} +- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +-endif() +- +-rdkit_library(pubchem_align3d ./pubchem-align3d/shape_functions1.cpp +- ./pubchem-align3d/shape_functions2.cpp ./pubchem-align3d/shape_neighbor.cpp SHARED) +-if((MSVC AND RDK_INSTALL_DLLS_MSVC) OR ((NOT MSVC) AND WIN32)) +- set_target_properties(pubchem_align3d PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE) +-endif() +- + rdkit_library(PubChemShape PubChemShape.cpp SHARED +- LINK_LIBRARIES pubchem_align3d SmilesParse SubstructMatch) ++ LINK_LIBRARIES -lpubchem-align3d SmilesParse SubstructMatch) + target_compile_definitions(PubChemShape PRIVATE RDKIT_PUBCHEMSHAPE_BUILD) + + rdkit_headers(PubChemShape.hpp DEST GraphMol) -- 2.48.1
guix-patches@HIDDEN
:bug#77394
; Package guix-patches
.
Full text available.Received: (at 77394) by debbugs.gnu.org; 30 Mar 2025 22:08:31 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Mar 30 18:08:31 2025 Received: from localhost ([127.0.0.1]:38360 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1tz0pS-00017y-JQ for submit <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:08:30 -0400 Received: from mout02.posteo.de ([185.67.36.66]:49423) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <david.elsing@HIDDEN>) id 1tz0pI-00016L-Gi for 77394 <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:08:22 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id A8003240101 for <77394 <at> debbugs.gnu.org>; Mon, 31 Mar 2025 00:08:14 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743372494; bh=AIE23fd5hlRIOPxB3yqKxZgYbiLCFi7Z23XyEhZUinY=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=LPZ/kkFc0wYiSOg18IxmK/Mt3JwMTlGyCLf9clPuPn4rmsKYYOtI4ffxR1yn4x7Xc jqHov4XUS97TgTxe0W3vi4Kk4ARwcb07KZDqGVCQ/dp8iP3h018K07pOfCFjUvy5aA 2GLWPuOGfEl0zxWFHZHbTF9k7mlH3lSpmDB/9Md/LaV2l0vhL2Z5tzU82f6i5m0NOK GlxCW6Pxktb6OI0663VkvqoHmIHyB/ryzuc/oElEYHud2kE2GnPN5G6SLRhOJ0JP+R IX8CwOtsFJfpvdBfAB8Gr5TPYxoB/Syt5PuoRrCUi9HqOsiwClHQOT/d9/U6DfWPmU +aIHIn+rIhv3A== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZQpL56F7qz6v0J; Mon, 31 Mar 2025 00:08:13 +0200 (CEST) From: David Elsing <david.elsing@HIDDEN> To: 77394 <at> debbugs.gnu.org Subject: [PATCH 4/5] gnu: Add pubchem-align3d. Date: Sun, 30 Mar 2025 22:06:57 +0000 Message-ID: <20250330220745.25337-4-david.elsing@HIDDEN> In-Reply-To: <20250330220421.24480-1-david.elsing@HIDDEN> References: <20250330220421.24480-1-david.elsing@HIDDEN> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77394 Cc: David Elsing <david.elsing@HIDDEN> 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 (---) * gnu/packages/chemistry.scm (pubchem-align3d): New variable. --- gnu/packages/chemistry.scm | 46 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 36227916b6..c1e0586534 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -1066,6 +1066,52 @@ (define-public ringdecomposerlib other ring topology descriptions.") (license license:bsd-3))) +(define-public pubchem-align3d + (let ((commit "daefab3dd0c90ca56da9d3d5e375fe4d651e6be3") + (revision "0")) + (package + (name "pubchem-align3d") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ncbi/pubchem-align3d") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1nj1zz5nvn5h3dyj66zi11mmvmzpq3b8y51fld9bkxnsmk17h05m")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; circular dependency with rdkit + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "g++" + "-o" "libpubchem-align3d.so" + "-O2" "-g" "-fPIC" "-shared" + "shape_functions1.cpp" "shape_functions2.cpp" + "shape_neighbor.cpp"))) + (replace 'install + (lambda _ + (for-each + (lambda (file) + (install-file + file + (string-append #$output "/include/pubchem-align3d"))) + (find-files "." "\\.hpp")) + (install-file "libpubchem-align3d.so" + (string-append #$output "/lib"))))))) + (home-page "https://github.com/ncbi/pubchem-align3d") + (synopsis "C++ library for aligning small molecules") + (description "This is a generic C++ library that can be used to rapidly +align two small molecules in 3D space, with shape - and optionally color - +Tanimoto scoring.") + (license license:public-domain)))) + (define-public rdkit (package (name "rdkit") -- 2.48.1
guix-patches@HIDDEN
:bug#77394
; Package guix-patches
.
Full text available.Received: (at 77394) by debbugs.gnu.org; 30 Mar 2025 22:08:30 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Mar 30 18:08:30 2025 Received: from localhost ([127.0.0.1]:38358 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1tz0pS-00017t-6k for submit <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:08:30 -0400 Received: from mout01.posteo.de ([185.67.36.65]:40313) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <david.elsing@HIDDEN>) id 1tz0pJ-00016J-G9 for 77394 <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:08:21 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id D8FB0240027 for <77394 <at> debbugs.gnu.org>; Mon, 31 Mar 2025 00:08:13 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743372493; bh=TFRFJ6svFlcjhGdMqWPy3np3hh2rXMlkuPSCiDtcCx0=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=XEKhOrSLvEr8uAYj91FxxL8bMK0VAq8VVf/YwR0Fplg8tGXUI5/x5J7hmUK5JwgJe ulriQGY7f5yh3w5W2j3TjEGx0Qzt24Oq1/avfOFBIFz9xDJ2T7Ddv5eYQghLU+IlwE qmK3COvgDLfQS2tJKtdtHnoHVLnF0bewfhkJ6HZC6CaVTVALSwXQEc6X/VTcNb0zlP Q0jhpZq5TMyVeeYueyrEp5JE/0KOW5lWL0+AlaNnSKnsd4u4gM1WFzlkFHNR6fhBCj PHtN5DG1f+2Ga1xEKztyPI5GB7BJNxYhvVcU7B651ZN971YzeOxDecESiyQImDPyyr 2ok4ncIDctWhA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZQpL52Y1hz6v0J; Mon, 31 Mar 2025 00:08:13 +0200 (CEST) From: David Elsing <david.elsing@HIDDEN> To: 77394 <at> debbugs.gnu.org Subject: [PATCH 3/5] gnu: Add boost-with-numpy. Date: Sun, 30 Mar 2025 22:06:56 +0000 Message-ID: <20250330220745.25337-3-david.elsing@HIDDEN> In-Reply-To: <20250330220421.24480-1-david.elsing@HIDDEN> References: <20250330220421.24480-1-david.elsing@HIDDEN> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77394 Cc: David Elsing <david.elsing@HIDDEN> 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 (---) * gnu/packages/boost.scm (boost-with-numpy): New variable. --- gnu/packages/boost.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm index 4f54c6b578..cd625e2cbb 100644 --- a/gnu/packages/boost.scm +++ b/gnu/packages/boost.scm @@ -50,6 +50,7 @@ (define-module (gnu packages boost) #:use-module (gnu packages llvm) #:use-module (gnu packages perl) #:use-module (gnu packages python) + #:use-module (gnu packages python-xyz) #:use-module (gnu packages shells) #:use-module (gnu packages mpi)) @@ -359,6 +360,13 @@ (define-public boost-for-mysql (delete "python-minimal-wrapper"))) (properties '((hidden? . #t))))) +(define-public boost-with-numpy + (package + (inherit boost) + (native-inputs + (modify-inputs (package-native-inputs boost) + (append python-numpy))))) + (define-public boost-sync (let ((commit "e690de2d30e2f1649ff500c9a6f3539814994b1c") (version "1.55") -- 2.48.1
guix-patches@HIDDEN
:bug#77394
; Package guix-patches
.
Full text available.Received: (at 77394) by debbugs.gnu.org; 30 Mar 2025 22:08:30 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Mar 30 18:08:30 2025 Received: from localhost ([127.0.0.1]:38356 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1tz0pR-00017n-Qw for submit <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:08:30 -0400 Received: from mout02.posteo.de ([185.67.36.66]:34465) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <david.elsing@HIDDEN>) id 1tz0pH-00016B-0H for 77394 <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:08:19 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 291FE240101 for <77394 <at> debbugs.gnu.org>; Mon, 31 Mar 2025 00:08:13 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743372493; bh=7yutaNa6OMIWYtF3cbDoQ7485jcA8Ku87uAqsdnmYog=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=icDKAu0s+0plwcbymWyDluB59Ayuhn0+k9lVuezM7T9/wTu8vIpzq3gAxbWcNNijv L01Nhfm+zc3YoYiL4P+eltGLWs2uPvdGfCUNKhEjnn7TbGoe2E2uQmeMrsMD+pMILx +VeH+7Z85dORze5Lm+BTdvAcUsJlSuqg5dHFReX1NF4b5JHU8nHXcS1+ZreKm6DWD2 yL8KWwHLfR1gK7vZLIxM9Z2VD0cO4tkJWDbAeELaHSQ9eDV9ZuG2yEtsPMKz9IIG1r +W2mJMTNw71p12Xej6deLVYlUQzrOMB6Io4q7GmD2vfG1eZZSRdADPIwOvHFzdL4oR KCltjpcJ0rnXw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZQpL45vm3z6v0J; Mon, 31 Mar 2025 00:08:12 +0200 (CEST) From: David Elsing <david.elsing@HIDDEN> To: 77394 <at> debbugs.gnu.org Subject: [PATCH 2/5] gnu: yaehmop: Update to 2024.03.1. Date: Sun, 30 Mar 2025 22:06:55 +0000 Message-ID: <20250330220745.25337-2-david.elsing@HIDDEN> In-Reply-To: <20250330220421.24480-1-david.elsing@HIDDEN> References: <20250330220421.24480-1-david.elsing@HIDDEN> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77394 Cc: David Elsing <david.elsing@HIDDEN> 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 (---) * gnu/packages/chemistry.scm (yaehmop): Update to 2024.03.1. --- gnu/packages/chemistry.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index df5048d22e..36227916b6 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -813,7 +813,7 @@ (define-public coordgenlibs (define-public yaehmop (package (name "yaehmop") - (version "2023.03.1") + (version "2024.03.1") (source (origin (method git-fetch) (uri (git-reference @@ -822,7 +822,7 @@ (define-public yaehmop (file-name (git-file-name name version)) (sha256 (base32 - "18xnxqn8i7vswy3iffapfh9q2iimpnd23ps45hn4xxbs6dqgzprb")) + "1wy38cfqfs203p1k3qqsizzlpvasldjcfxmlng54y5mxzw97n55f")) (modules '((guix build utils))) (snippet '(begin -- 2.48.1
guix-patches@HIDDEN
:bug#77394
; Package guix-patches
.
Full text available.Received: (at 77394) by debbugs.gnu.org; 30 Mar 2025 22:08:20 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Mar 30 18:08:20 2025 Received: from localhost ([127.0.0.1]:38348 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1tz0pH-00016j-Ur for submit <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:08:20 -0400 Received: from mout02.posteo.de ([185.67.36.66]:41271) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <david.elsing@HIDDEN>) id 1tz0pE-00015z-FJ for 77394 <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:08:17 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 112F6240101 for <77394 <at> debbugs.gnu.org>; Mon, 31 Mar 2025 00:08:08 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743372489; bh=mJhwDmJNKORS4dC6UmFDRh5ke2e5wkDhG9D2A6rd9QE=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=Jzq14Hb2Ts9lL+e6iRfzah4mJCTQadg9q2UBk2E/nDPkKzO3Nkn4ZSNEHGIKH/mbp w7vpneLVX4C4nGnOoEtyZnRe4xncmVeykXZCWO28WtE72xQ7YRWpeb5xyIpEIq+MgO pYPTibZYubBaE6jzMubN3O9D0NE+tXRPtlwUuY8VYlmrvKx4sG2Q+6mEOmNtKko/0u rJYQXE9EqcPbdMxp7ToNwrqzBdKeQGY+y7zf1vvaeUdWsIsEA9jNgvRsa5YE+u+6Od QFc+InZh8RaOudVmfvF90h9+a3YZ3GcTqsuqdWj3ks9x08tbsVIfbKp6gXMpa+MfDz lUXtrsn/7IPYw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZQpL04MWDz6v0K; Mon, 31 Mar 2025 00:08:08 +0200 (CEST) From: David Elsing <david.elsing@HIDDEN> To: 77394 <at> debbugs.gnu.org Subject: [PATCH 1/5] gnu: inchi: Update to 1.07.3. Date: Sun, 30 Mar 2025 22:06:54 +0000 Message-ID: <20250330220745.25337-1-david.elsing@HIDDEN> In-Reply-To: <20250330220421.24480-1-david.elsing@HIDDEN> References: <20250330220421.24480-1-david.elsing@HIDDEN> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77394 Cc: David Elsing <david.elsing@HIDDEN> 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 (---) * gnu/packages/chemistry.scm (inchi): Update to 1.07.3. [source]: Switch to git-fetch. [arguments]: Use gexps. Adjust chdir-to-build-directory, build and install phases. Enable parallel building. [native-inputs]: Remove input label. [license]: Change to Expat license. --- gnu/packages/chemistry.scm | 122 ++++++++++++++++++------------------- 1 file changed, 59 insertions(+), 63 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index bd27bfad7a..df5048d22e 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -146,68 +146,66 @@ (define-public inchi (package (name "inchi") ;; Update the inchi-doc native input when updating inchi. - (version "1.06") - (source (origin - (method url-fetch) - (uri (string-append "https://www.inchi-trust.org/download/" - (string-join (string-split version #\.) "") - "/INCHI-1-SRC.zip")) - (sha256 - (base32 - "1zbygqn0443p0gxwr4kx3m1bkqaj8x9hrpch3s41py7jq08f6x28")) - (file-name (string-append name "-" version ".zip")))) + (version "1.07.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/IUPAC-InChI/InChI") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0r32f6i5d8ir96ic3nvqb5lywxrznwrkk6hnz1q0a4bgsw5pmk0n")) + (modules '((guix build utils))) + (snippet '(delete-file-recursively "INCHI-1-BIN")))) (build-system gnu-build-system) (arguments - '(#:tests? #f ; no check target - #:phases - (modify-phases %standard-phases - (delete 'configure) ; no configure script - (add-before 'build 'chdir-to-build-directory - (lambda _ (chdir "INCHI_EXE/inchi-1/gcc") #t)) - (add-after 'build 'build-library - (lambda _ - (chdir "../../../INCHI_API/libinchi/gcc") - (invoke "make"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (doc (string-append out "/share/doc/inchi")) - (include-dir (string-append out "/include/inchi")) - (lib (string-append out "/lib/inchi")) - (inchi-doc (assoc-ref inputs "inchi-doc")) - (unzip (search-input-file inputs "/bin/unzip"))) - (chdir "../../..") - ;; Install binary. - (with-directory-excursion "INCHI_EXE/bin/Linux" - (rename-file "inchi-1" "inchi") - (install-file "inchi" bin)) - ;; Install libraries. - (with-directory-excursion "INCHI_API/bin/Linux" - (for-each (lambda (file) - (install-file file lib)) - (find-files "." "libinchi\\.so\\.1\\.*"))) - ;; Install header files. - (with-directory-excursion "INCHI_BASE/src" - (for-each (lambda (file) - (install-file file include-dir)) - (find-files "." "\\.h$"))) - ;; Install documentation. - (mkdir-p doc) - (invoke unzip "-j" "-d" doc inchi-doc) - #t)))))) - (native-inputs - `(("unzip" ,unzip) - ("inchi-doc" - ,(origin - (method url-fetch) - (uri (string-append "http://www.inchi-trust.org/download/" - (string-join (string-split version #\.) "") - "/INCHI-1-DOC.zip")) - (sha256 - (base32 - "1kyda09i9p89xfq90ninwi7w13k1w3ljpl4gqdhpfhi5g8fgxx7f")) - (file-name (string-append name "-" version ".zip")))))) + (list + #:tests? #f ; no check target + #:phases + #~(modify-phases %standard-phases + (delete 'configure) ; no configure script + (add-after 'unpack 'chdir-to-build-directory + (lambda _ (chdir "INCHI-1-SRC/INCHI_EXE/inchi-1/gcc"))) + (add-after 'build 'build-library + (lambda* (#:key parallel-build? #:allow-other-keys) + (chdir "../../../INCHI_API/libinchi/gcc") + (invoke "make" "-j" (if parallel-build? + (number->string (parallel-job-count)) + "1")))) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((bin (string-append #$output "/bin")) + (doc (string-append #$output "/share/doc/inchi")) + (include-dir (string-append #$output "/include/inchi")) + (lib (string-append #$output "/lib/inchi"))) + (chdir "../../..") + ;; Install binary. + (with-directory-excursion "INCHI_EXE/bin/Linux" + (rename-file "inchi-1" "inchi") + (install-file "inchi" bin)) + ;; Install library. + (with-directory-excursion "INCHI_API/bin/Linux" + (let ((libname (basename + (car + (find-files "." "libinchi\\.so\\.1\\.*"))))) + (install-file libname lib) + (with-directory-excursion lib + (symlink libname "libinchi.so.1") + (symlink "libinchi.so.1" "libinchi.so")))) + ;; Install header files. + (with-directory-excursion "INCHI_BASE/src" + (for-each (lambda (file) + (install-file file include-dir)) + (find-files "." "\\.h$"))) + ;; Install documentation. + (with-directory-excursion "../INCHI-1-DOC" + (for-each + (lambda (file) + (install-file file doc)) + (find-files "." "\\.pdf$"))))))))) + (native-inputs (list unzip)) (home-page "https://www.inchi-trust.org") (synopsis "Utility for manipulating machine-readable chemical structures") (description @@ -216,9 +214,7 @@ (define-public inchi unique to the compound they describe and can encode absolute stereochemistry making chemicals and chemistry machine-readable and discoverable. A simple analogy is that InChI is the bar-code for chemistry and chemical structures.") - (license (license:non-copyleft - "file://LICENCE" - "See LICENCE in the distribution.")))) + (license license:expat))) (define-public libmsym (package -- 2.48.1
guix-patches@HIDDEN
:bug#77394
; Package guix-patches
.
Full text available.Received: (at submit) by debbugs.gnu.org; 30 Mar 2025 22:04:40 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Mar 30 18:04:39 2025 Received: from localhost ([127.0.0.1]:38336 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1tz0lj-0000kA-IU for submit <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:04:39 -0400 Received: from lists.gnu.org ([2001:470:142::17]:34614) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <david.elsing@HIDDEN>) id 1tz0lf-0000jQ-Sb for submit <at> debbugs.gnu.org; Sun, 30 Mar 2025 18:04:36 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <david.elsing@HIDDEN>) id 1tz0lY-00008i-59 for guix-patches@HIDDEN; Sun, 30 Mar 2025 18:04:29 -0400 Received: from mout02.posteo.de ([185.67.36.66]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <david.elsing@HIDDEN>) id 1tz0lW-0005pK-En for guix-patches@HIDDEN; Sun, 30 Mar 2025 18:04:27 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id E0AC4240101 for <guix-patches@HIDDEN>; Mon, 31 Mar 2025 00:04:23 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743372263; bh=aT+XTUTqBwLeDmsHCJzG0c9ciydz4FcLGUM00MWdMVU=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=CrBDH3r+iatq4nKOwkxVv+fFiL8JU9bvZeh88b2BDfSREaZn1ZXlzQc8q6c8/geHl sY0vOsKl14DQJAdSbULH/FyQLlZfcU7Xjzxbuyecn5VUUmXz2iYYMtglTHY/YSEs3U kGNtXeH+8rVFCinM+BdxTyl/kek5hWaPFaazUt4XiJN9wGeRsrV2JfkUN8ZzjfsYEJ MSHPvZpujBDY54jPITigO3gURfCtyEyFes0PrN+N8bQPJLc0NqYxEMldHn5tG9MvdK X3ci56VmZ7lzqtfW5mZYouSElGM6Jji5jzMNPd2zh3HGFwlX3Jq37od7kc7NuNsgeE 5gHLZJslyY1ZQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZQpFg37wBz6twH; Mon, 31 Mar 2025 00:04:23 +0200 (CEST) From: David Elsing <david.elsing@HIDDEN> To: guix-patches@HIDDEN Subject: [PATCH 0/5] Update rdkit to 2024.09.6 Date: Sun, 30 Mar 2025 22:04:10 +0000 Message-ID: <20250330220421.24480-1-david.elsing@HIDDEN> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.66; envelope-from=david.elsing@HIDDEN; helo=mout02.posteo.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.001, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit Cc: David Elsing <david.elsing@HIDDEN> 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: -0.0 (/) This patch series updates rdkit and some of its dependencies. The build now depends on the CMake files of the NumPy extension of Boost.Python and rdkit depends on python-numpy anyway, so I added a package variant of boost with it enabled. David Elsing (5): gnu: inchi: Update to 1.07.3. gnu: yaehmop: Update to 2024.03.1. gnu: Add boost-with-numpy. gnu: Add pubchem-align3d. gnu: rdkit: Update to 2024.09.6. gnu/packages/boost.scm | 8 + gnu/packages/chemistry.scm | 186 +++++++++++------- ...rdkit-unbundle-external-dependencies.patch | 183 +++++++++++++++-- 3 files changed, 291 insertions(+), 86 deletions(-) -- 2.48.1
David Elsing <david.elsing@HIDDEN>
:guix-patches@HIDDEN
.
Full text available.guix-patches@HIDDEN
:bug#77394
; Package guix-patches
.
Full text available.
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Copyright (C) 1999 Darren O. Benham,
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