From patchwork Fri Oct 7 15:21:37 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 1016 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 1F88827BBEA; Fri, 7 Oct 2022 17:15:05 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id C8B2327BBE9 for ; Fri, 7 Oct 2022 17:15:04 +0100 (BST) Received: from localhost ([::1]:42036 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ogq07-0007xE-Sk for patchwork@mira.cbaines.net; Fri, 07 Oct 2022 12:15:03 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:44080) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ogpBm-0002Ol-20 for guix-patches@gnu.org; Fri, 07 Oct 2022 11:23:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38106) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ogpBl-0005pD-P3 for guix-patches@gnu.org; Fri, 07 Oct 2022 11:23:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ogpBl-0005nl-Kf for guix-patches@gnu.org; Fri, 07 Oct 2022 11:23:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#58261] [PATCH v2 00/13] Add rdkit v2. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 07 Oct 2022 15:23:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 58261 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 58261@debbugs.gnu.org Cc: David Elsing Received: via spool by 58261-submit@debbugs.gnu.org id=B58261.166515612422060 (code B ref 58261); Fri, 07 Oct 2022 15:23:01 +0000 Received: (at 58261) by debbugs.gnu.org; 7 Oct 2022 15:22:04 +0000 Received: from localhost ([127.0.0.1]:37146 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ogpAq-0005je-0Y for submit@debbugs.gnu.org; Fri, 07 Oct 2022 11:22:04 -0400 Received: from mout02.posteo.de ([185.67.36.66]:39063) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ogpAn-0005iy-G7 for 58261@debbugs.gnu.org; Fri, 07 Oct 2022 11:22:02 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 65557240105 for <58261@debbugs.gnu.org>; Fri, 7 Oct 2022 17:21:54 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1665156115; bh=sKJS6rLCEVhnZekRcFBZ3cQi8C4GnyiOvgzu/tmGFho=; h=From:To:Cc:Subject:Date:From; b=RqLdCxWGh2mIsTNq3TahDtvqXrafUiwKpAbqWZiII5hejIg79lHcCANdQ3432tyid tUk5mO+7Fc4mASJnyRArdHBgKk3A9A9wInWMEEnS3iHDLVg+11vubJGJK/xXn/Rw56 yMWPD88uj+Qvv1ANkyTT761RhCf2S9MZka/2QX6Y+oC1qk9d9Sl/749SI89CS9ZSBM ceX4r5F/OR8Jc+i6W2vhKFebr/9L63ur9Xu+MvqT5SUZprEeMKdOKCmLRbC/jwgqMB +2OQy7dFZxVISpjfjrtXodv6R6oGLd1fbMfn5ucHBIhDRTCrXjgLV21qj6zLTA1Qxa KLtkcYiFsJ8Dw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4MkX8x5bVfz6tpj; Fri, 7 Oct 2022 17:21:51 +0200 (CEST) From: David Elsing Date: Fri, 7 Oct 2022 15:21:37 +0000 Message-Id: <20221007152148.32591-1-david.elsing@posteo.net> In-Reply-To: References: MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches Thanks a lot for your comments, they are very helpful! Sorry about the descriptions, I took them mostly from upstream. :) Are they still too short? I still have the following problems: * The tests of tinydir contain a bundled fork of cbehave which uses a (bundled) copy of rlutil, so I left them disabled for now. * Building the documentation of yaehmop with pdflatex is not reproducible even though I set FORCE_SOURCE_DATE=1. Is it even necessary to build the documentation? * Using @abbr in the description does not work (I also did not find it in any other package). Greetings, David David Elsing (13): gnu: Add fast-float. gnu: Add pocketfft. gnu: Add sajson. gnu: Add tinydir. gnu: Add optionparser. gnu: Add gemmi. gnu: Add freesasa. gnu: Add maeparser. gnu: Add coordgenlibs. gnu: Add yaehmop-tightbind. gnu: Add avalontoolkit. gnu: Add ringdecomposerlib. gnu: Add rdkit. gnu/packages/chemistry.scm | 713 ++++++++++++++++++ gnu/packages/cpp.scm | 232 ++++++ .../patches/gemmi-fix-sajson-types.patch | 11 + .../rdkit-cmake-external-dependencies.patch | 102 +++ .../patches/sajson-build-with-gcc10.patch | 45 ++ .../sajson-for-gemmi-build-with-gcc10.patch | 45 ++ .../sajson-for-gemmi-numbers-as-strings.patch | 195 +++++ 7 files changed, 1343 insertions(+) create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch create mode 100644 gnu/packages/patches/rdkit-cmake-external-dependencies.patch create mode 100644 gnu/packages/patches/sajson-build-with-gcc10.patch create mode 100644 gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch