From patchwork Sun Jan 28 23:01:54 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 59544 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 3032527BBEA; Sun, 28 Jan 2024 23:03:03 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H5,RCVD_IN_MSPIKE_WL, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham 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 8740B27BBE2 for ; Sun, 28 Jan 2024 23:02:59 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rUEAy-000627-Ak; Sun, 28 Jan 2024 18:02:56 -0500 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 ) id 1rUEAw-00061r-GD for guix-patches@gnu.org; Sun, 28 Jan 2024 18:02:54 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rUEAw-0005pl-85 for guix-patches@gnu.org; Sun, 28 Jan 2024 18:02:54 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rUEB4-0004XS-3V for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#68790] [PATCH 1/9] gnu: tinydir: Update to 1.2.6. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:03:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 68790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 68790@debbugs.gnu.org Cc: David Elsing Received: via spool by 68790-submit@debbugs.gnu.org id=B68790.170648296217340 (code B ref 68790); Sun, 28 Jan 2024 23:03:02 +0000 Received: (at 68790) by debbugs.gnu.org; 28 Jan 2024 23:02:42 +0000 Received: from localhost ([127.0.0.1]:58597 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAk-0004Va-9v for submit@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:42 -0500 Received: from mout01.posteo.de ([185.67.36.65]:40965) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAi-0004VL-OZ for 68790@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:41 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id B8F28240028 for <68790@debbugs.gnu.org>; Mon, 29 Jan 2024 00:02:26 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1706482946; bh=RKi7+9nDzwkquDbx5wY0fY8mNMim/yTpnkg6WXgB888=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: Content-Transfer-Encoding:From; b=UrCcTpDolH3t764Y1dgy8D6BjMM+BWdSUmGP5o/dfE4nEryh/viP4PSG1td6U7Iux aaTxZZfcB+Oci78M1AGcItXmJp4COJkh+Bjti9s8Uu4iKyn0sjZ4Qcoe9SKWFZgoWx Cigv8D51jy99aTD6TpWBtt6acwMPQh7qQpnlrV8ytOPvepaXLLeCQ8aHUu9Fe3ZSG0 ccJdVE5ZPhDmerF9KTmXcN2pgg2VwyXeEbbC/zeZH31O/QgJzMXxrStCVJkn0cGBiE az8MJOuslyHdjhjv3jJY2QdVhxik7Dm4G8t2/ldnFBVBlr07zdockK3i2jCqNZ3zxW 5ayMd6E0TtM5A== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TNRlk1fbTz6tx2; Mon, 29 Jan 2024 00:02:26 +0100 (CET) From: David Elsing Date: Sun, 28 Jan 2024 23:01:54 +0000 Message-ID: <20240128230215.1389-1-david.elsing@posteo.net> In-Reply-To: <20240128225919.795-2-david.elsing@posteo.net> References: <20240128225919.795-2-david.elsing@posteo.net> 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/c.scm (tinydir): Update to 1.2.6. * gnu/packages/patches/tinydir-fix-cbehave-test.patch: Adjust patch. --- gnu/packages/c.scm | 6 +++--- .../patches/tinydir-fix-cbehave-test.patch | 16 ++++++++++++++-- 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/gnu/packages/c.scm b/gnu/packages/c.scm index 1346605c71..b558145ea0 100644 --- a/gnu/packages/c.scm +++ b/gnu/packages/c.scm @@ -20,7 +20,7 @@ ;;; Copyright © 2022 Antero Mejr ;;; Copyright © 2023 zamfofex ;;; Copyright © 2023 Foundation Devices, Inc. -;;; Copyright © 2023 David Elsing +;;; Copyright © 2023, 2024 David Elsing ;;; ;;; This file is part of GNU Guix. ;;; @@ -1349,7 +1349,7 @@ (define target-machine #$(and=> (%current-target-system) (define-public tinydir (package (name "tinydir") - (version "1.2.5") + (version "1.2.6") (source (origin (method git-fetch) (uri (git-reference @@ -1358,7 +1358,7 @@ (define-public tinydir (file-name (git-file-name name version)) (sha256 (base32 - "1nprgdfx4i8wzc1idw6chan4fjfa75b5ll8kghdc0q2278pny259")) + "143n6yabznxk032gv5g2k8glf0kzicarg9cx0714zsbfmzj8lr07")) (patches (search-patches "tinydir-fix-cbehave-test.patch")) (modules '((guix build utils))) (snippet '(delete-file-recursively "tests/cbehave")))) diff --git a/gnu/packages/patches/tinydir-fix-cbehave-test.patch b/gnu/packages/patches/tinydir-fix-cbehave-test.patch index 84ecee12c2..1cad42c7a0 100644 --- a/gnu/packages/patches/tinydir-fix-cbehave-test.patch +++ b/gnu/packages/patches/tinydir-fix-cbehave-test.patch @@ -2,10 +2,22 @@ Make test work with upstream cbehave (tinydir bundles a modified version) diff --git a/tests/file_open_test.c b/tests/file_open_test.c -index 3e659bc..9f6f88d 100644 +index 09b856e..92b13ca 100644 --- a/tests/file_open_test.c +++ b/tests/file_open_test.c -@@ -19,4 +19,7 @@ FEATURE(file_open, "File open") +@@ -4,6 +4,11 @@ + #include "cbehave.h" + #include "util.h" + ++#define ASSERT(cond, ret) \ ++if (!(cond)) {\ ++ cbehave_feature_return(__FILE__, __LINE__, ret, _state); \ ++ goto _feature_over; \ ++}\ + + FEATURE(file_open, "File open") + SCENARIO("Open file in current directory") +@@ -34,4 +39,7 @@ FEATURE(file_open, "File open") SCENARIO_END FEATURE_END From patchwork Sun Jan 28 23:01:55 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 59548 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 8CFEA27BBEA; Sun, 28 Jan 2024 23:03:30 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H5,RCVD_IN_MSPIKE_WL, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham 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 DC71727BBE2 for ; Sun, 28 Jan 2024 23:03:29 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rUEB5-00064E-QA; Sun, 28 Jan 2024 18:03:03 -0500 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 ) id 1rUEAy-00062G-CK for guix-patches@gnu.org; Sun, 28 Jan 2024 18:02:58 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rUEAw-0005ps-SI for guix-patches@gnu.org; Sun, 28 Jan 2024 18:02:56 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rUEB4-0004XZ-Ik for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#68790] [PATCH 2/9] gnu: fast-float: Update to 6.0.0. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:03:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 68790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 68790@debbugs.gnu.org Cc: David Elsing Received: via spool by 68790-submit@debbugs.gnu.org id=B68790.170648296817368 (code B ref 68790); Sun, 28 Jan 2024 23:03:02 +0000 Received: (at 68790) by debbugs.gnu.org; 28 Jan 2024 23:02:48 +0000 Received: from localhost ([127.0.0.1]:58603 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAp-0004Vx-QS for submit@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:48 -0500 Received: from mout02.posteo.de ([185.67.36.66]:53131) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAn-0004VS-1T for 68790@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:46 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 6D6B1240104 for <68790@debbugs.gnu.org>; Mon, 29 Jan 2024 00:02:31 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1706482951; bh=B/DFGkQGo5UEY4l/gswgI5MpCO8tJdJ09+bnapBxrp8=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: Content-Transfer-Encoding:From; b=jgmQ5WbO4o7xmIRRbO9SD4Aq9xsVH1sRJCarhfkoyd5zOa4H9laVATAAu9HnkCoVw WzybLAu7S/ix2OOYqvFiPezZg/0bZ7Z6NrKM6MDIw9R34fQw+4aBjsO5/pQ3JvMJs7 eJJ6AlTyL1oirHAjavhsAqxfWhATlr5f0x2CzWiVzuUs3OT78hJl8MaxPwCQB9+Suq zKjWt9sWTH1ZslbZ6vDz7MrN8GDQ5Qm05XtnMCSOoyQSdP1wwsuS7zryxDkV5aPJ32 H3SUlO8VVRPd7KdS7jZzLzLNdNSHSO8aMRhpNdvYe2M8dRrPEyaYJN1PlfDs55I+5s tAzw7NzSrK+OA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TNRlq0GW6z6twF; Mon, 29 Jan 2024 00:02:31 +0100 (CET) From: David Elsing Date: Sun, 28 Jan 2024 23:01:55 +0000 Message-ID: <20240128230215.1389-2-david.elsing@posteo.net> In-Reply-To: <20240128225919.795-2-david.elsing@posteo.net> References: <20240128225919.795-2-david.elsing@posteo.net> 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cpp.scm (fast-float): Update to 6.0.0. [arguments]: Adjust path to test files. --- gnu/packages/cpp.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/gnu/packages/cpp.scm b/gnu/packages/cpp.scm index 44175231af..71c170a48b 100644 --- a/gnu/packages/cpp.scm +++ b/gnu/packages/cpp.scm @@ -29,7 +29,7 @@ ;;; Copyright © 2022 muradm ;;; Copyright © 2022 Attila Lendvai ;;; Copyright © 2022 Arun Isaac -;;; Copyright © 2022, 2023 David Elsing +;;; Copyright © 2022, 2023, 2024 David Elsing ;;; Copyright © 2022, 2023 Zheng Junjie <873216071@qq.com> ;;; Copyright © 2022, 2023, 2024 Maxim Cournoyer ;;; Copyright © 2022 Antero Mejr @@ -2449,7 +2449,7 @@ (define fast-float-test-files (define-public fast-float (package (name "fast-float") - (version "3.5.1") + (version "6.0.0") (source (origin (method git-fetch) (uri (git-reference @@ -2458,7 +2458,7 @@ (define-public fast-float (file-name (git-file-name name version)) (sha256 (base32 - "0z3rxxd0pwvw70dbnv63rm67biw829vdqf50y16isxm6g3sbrz8g")))) + "1xf4gbllha760cr0ri53zsja46dypj45lj070ijb5f78xavfd8f8")))) (build-system cmake-build-system) (arguments (list @@ -2474,9 +2474,7 @@ (define-public fast-float (("if\\(NOT supplemental_test_files_POPULATED.*") (string-append "set(supplemental_test_files_BINARY_DIR " - (search-input-directory (or native-inputs inputs) - "data") - ")\nif(0)\n")))))))) + #$fast-float-test-files ")\nif(0)\n")))))))) (native-inputs (list doctest fast-float-test-files)) (home-page "https://github.com/fastfloat/fast_float") (synopsis "Floating point number parser for C++") From patchwork Sun Jan 28 23:01:56 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 59545 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 4F35427BBEA; Sun, 28 Jan 2024 23:03:14 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H5,RCVD_IN_MSPIKE_WL, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham 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 AC62727BBE2 for ; Sun, 28 Jan 2024 23:03:13 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rUEB7-00064F-4y; Sun, 28 Jan 2024 18:03:05 -0500 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 ) id 1rUEAy-00062H-Ca for guix-patches@gnu.org; Sun, 28 Jan 2024 18:02:58 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rUEAx-0005py-45 for guix-patches@gnu.org; Sun, 28 Jan 2024 18:02:56 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rUEB4-0004Xh-VB for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#68790] [PATCH 3/9] gnu: gemmi: Update to 0.6.4. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:03:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 68790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 68790@debbugs.gnu.org Cc: David Elsing Received: via spool by 68790-submit@debbugs.gnu.org id=B68790.170648297517413 (code B ref 68790); Sun, 28 Jan 2024 23:03:02 +0000 Received: (at 68790) by debbugs.gnu.org; 28 Jan 2024 23:02:55 +0000 Received: from localhost ([127.0.0.1]:58613 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAv-0004WT-J2 for submit@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:54 -0500 Received: from mout02.posteo.de ([185.67.36.66]:38237) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAp-0004Vb-KR for 68790@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:48 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 14670240106 for <68790@debbugs.gnu.org>; Mon, 29 Jan 2024 00:02:34 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1706482954; bh=C1YIyT0st2coxHazmijrHjh84MsNqtSQQFTSHEjtLNw=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=NVVotSbvnOX1CudYyhMqdf8p/J9zIY1bEgDH07oHHAarJNoGCQM1X+pL3WHuGpbPl eADh5o5IhbhHo+GKi66GyUdMNz9v0aYOQQB1fwCaTFWaxtNXFRLBxMUELcH3WZcmcb FI109W8V499Xyz3CDmy+KNVldjKpNL4Dyqixb9h2Q/AvaaBmBRj8CsxLNDplIZWFUT /DsrZGeA30OMe/5NUNUqZbHErJ2tGmmSu42FsrVNTtohlGIboR+4nCq5ObmvV/uPFm Mcy2iVLHMHh709zP6c5yyQUKxKhCMbyw7F/USCgCfKvXRF0QKB1S0j1nTP1od+B+mA P14gcP8kbKoSA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TNRls5DFPz6tsb; Mon, 29 Jan 2024 00:02:33 +0100 (CET) From: David Elsing Date: Sun, 28 Jan 2024 23:01:56 +0000 Message-ID: <20240128230215.1389-3-david.elsing@posteo.net> In-Reply-To: <20240128225919.795-2-david.elsing@posteo.net> References: <20240128225919.795-2-david.elsing@posteo.net> 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/chemistry.scm (gemmi): Update to 0.6.4. [arguments]: Adjust include/gemmi/sprintf.hpp -> src/sprintf.cpp. (freesasa)[arguments]: Link to gemmi_cpp explicitly. --- gnu/packages/chemistry.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index df96a2f5c1..5129470e1e 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -589,7 +589,7 @@ (define-public python-pymol (define-public gemmi (package (name "gemmi") - (version "0.5.7") + (version "0.6.4") (source (origin (method git-fetch) (uri (git-reference @@ -598,7 +598,7 @@ (define-public gemmi (file-name (git-file-name name version)) (sha256 (base32 - "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a")) + "0wciqqswc4p4v4kglfv36gnvyyimqn4lnywdzd0pgrjn443i860y")) (patches (search-patches "gemmi-fix-sajson-types.patch" "gemmi-fix-pegtl-usage.patch")) @@ -625,7 +625,7 @@ (define-public gemmi #~(modify-phases %standard-phases (add-after 'unpack 'patch-includes (lambda _ - (substitute* (list "include/gemmi/sprintf.hpp" + (substitute* (list "src/sprintf.cpp" "include/gemmi/dirwalk.hpp" "include/gemmi/cif.hpp" "include/gemmi/json.hpp" @@ -722,7 +722,7 @@ (define-public freesasa (("libfreesasa\\.a") "libfreesasa.la") (("freesasa_LDADD \\+= libfreesasa\\.la" prev) (string-append prev "\nlibfreesasa_la_LIBADD" - " = -ljson-c ${libxml2_LIBS}\n")) + " = -ljson-c -lgemmi_cpp ${libxml2_LIBS}\n")) (("_a_SOURCES") "_la_SOURCES")) (substitute* "configure.ac" (("AC_PROG_INSTALL" inst) From patchwork Sun Jan 28 23:01:57 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 59547 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 6AA4C27BBEA; Sun, 28 Jan 2024 23:03:27 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H5,RCVD_IN_MSPIKE_WL, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham 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 EB78B27BBE2 for ; Sun, 28 Jan 2024 23:03:26 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rUEB5-00063y-2Z; Sun, 28 Jan 2024 18:03:03 -0500 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 ) id 1rUEAy-00062J-E2 for guix-patches@gnu.org; Sun, 28 Jan 2024 18:02:59 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rUEAx-0005q0-H1 for guix-patches@gnu.org; Sun, 28 Jan 2024 18:02:56 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rUEB5-0004Xq-Dk for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#68790] [PATCH 4/9] gnu: maeparser: Update to 1.3.1. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:03:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 68790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 68790@debbugs.gnu.org Cc: David Elsing Received: via spool by 68790-submit@debbugs.gnu.org id=B68790.170648297817426 (code B ref 68790); Sun, 28 Jan 2024 23:03:03 +0000 Received: (at 68790) by debbugs.gnu.org; 28 Jan 2024 23:02:58 +0000 Received: from localhost ([127.0.0.1]:58617 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAx-0004Wn-15 for submit@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:57 -0500 Received: from mout01.posteo.de ([185.67.36.65]:41033) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAr-0004Vl-4U for 68790@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:49 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 8FD30240029 for <68790@debbugs.gnu.org>; Mon, 29 Jan 2024 00:02:35 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1706482955; bh=nDl519OD/h7C9P7Ju2VnE+j0AsiaNhMqn68DImw5B08=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=UlbMW8lkk/XW/6WirWMkTwHzbTzt8u6tYfXEVa6KReRGWt90OoWjN9PN0hHvr/i0Z stRVXx2HePmyoihoJ5MCkjBk1GbvftdokNp/P9IkY88L0qKn/gnXqE9I96QtQXhVc9 nvzvXQHI50AHXBkcaC+CId/RhhcEW4ycMkiCBr0g9ugDpj6eDHMwU5K9N0jaAX0txq JWX7ZsZ7u8HQ4tlhnW4nZjkpL0xhJ6Mezwe5J1iuIpMwayXCjcBzSq7zL3HlMyqmMR OpDYnmjC2WA30uZ6YQfNMNEfPcC4W9fgdmLnWlc0V3oPmtjKeQOeRiOCvJQvcx/pIv DSAiLVPuPM0dg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TNRlv1QkSz6tyv; Mon, 29 Jan 2024 00:02:35 +0100 (CET) From: David Elsing Date: Sun, 28 Jan 2024 23:01:57 +0000 Message-ID: <20240128230215.1389-4-david.elsing@posteo.net> In-Reply-To: <20240128225919.795-2-david.elsing@posteo.net> References: <20240128225919.795-2-david.elsing@posteo.net> 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/chemistry.scm (maeparser): Update to 1.3.1. --- 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 5129470e1e..9086d659cc 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -765,7 +765,7 @@ (define-public freesasa (define-public maeparser (package (name "maeparser") - (version "1.3.0") + (version "1.3.1") (source (origin (method git-fetch) (uri (git-reference @@ -774,7 +774,7 @@ (define-public maeparser (file-name (git-file-name name version)) (sha256 (base32 - "1yv4y5hn49fhylziigsg922bb244lb57p69r7vg9q899zd3l5b7l")))) + "0mr5glg4br04ql5grby8yqni9fqq1l1cc75wyc159a1b9lwr7q7r")))) (build-system cmake-build-system) (inputs (list boost zlib)) (home-page "https://github.com/schrodinger/maeparser") From patchwork Sun Jan 28 23:01:58 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 59551 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 3D53627BBEA; Sun, 28 Jan 2024 23:04:19 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H5,RCVD_IN_MSPIKE_WL, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham 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 A575D27BBE2 for ; Sun, 28 Jan 2024 23:04:18 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rUEBw-0006jV-U7; Sun, 28 Jan 2024 18:03:56 -0500 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 ) id 1rUEBv-0006Zv-4e for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:55 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rUEBu-0005vt-SD for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:54 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rUEC2-0004aE-O0 for guix-patches@gnu.org; Sun, 28 Jan 2024 18:04:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#68790] [PATCH 5/9] gnu: coordgenlibs: Update to 3.0.2. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:04:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 68790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 68790@debbugs.gnu.org Cc: David Elsing Received: via spool by 68790-submit@debbugs.gnu.org id=B68790.170648298717516 (code B ref 68790); Sun, 28 Jan 2024 23:04:02 +0000 Received: (at 68790) by debbugs.gnu.org; 28 Jan 2024 23:03:07 +0000 Received: from localhost ([127.0.0.1]:58630 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEB8-0004YJ-Go for submit@debbugs.gnu.org; Sun, 28 Jan 2024 18:03:07 -0500 Received: from mout02.posteo.de ([185.67.36.66]:48789) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAs-0004Vn-Eo for 68790@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:54 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id DE8FB240104 for <68790@debbugs.gnu.org>; Mon, 29 Jan 2024 00:02:36 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1706482956; bh=Xp5MjPKUrBBKkaf4ZrPbpzie22Bu8161qrhRL6vuiwk=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: Content-Transfer-Encoding:From; b=m2Wq6yW5+HOypo2JL8hnTD8PmVDIJ6tlxbkNBqofRjTooUIF/uSdWmAZr9IJh/NbZ Tp0CYMv4H1DSMGHs83fmcLGaom+Q6MFc6LMxrULa0LPTjtA2mA2Rq6fYSeGFMe7EaO xMS0OMiiNKgDjdRuIl1J/gC03cMVGENBDv6AnRyw3FoQUNEvIcliK0w16T35MMHDXG D5RTdd0lOtVLwf+btnPeenjyz5iC+qFfPqH/y13NQDiMNN32vMMC8Z0JUagw9llZQN baOdZh8bapKJkeOU/WJvhENXkuozT1NQ6UXeitEhVCon4f67BykMGLC41jbZybGwGa ba6XJ+kwhzVpg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TNRlw3w7Fz6ty8; Mon, 29 Jan 2024 00:02:36 +0100 (CET) From: David Elsing Date: Sun, 28 Jan 2024 23:01:58 +0000 Message-ID: <20240128230215.1389-5-david.elsing@posteo.net> In-Reply-To: <20240128225919.795-2-david.elsing@posteo.net> References: <20240128225919.795-2-david.elsing@posteo.net> 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/chemistry.scm (coordgenlibs): Update to 3.0.2. --- gnu/packages/chemistry.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 9086d659cc..44833d9c3f 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Vincent Legoll ;;; Copyright © 2021 Ricardo Wurmus -;;; Copyright © 2022, 2023 David Elsing +;;; Copyright © 2022, 2023, 2024 David Elsing ;;; ;;; This file is part of GNU Guix. ;;; @@ -785,7 +785,7 @@ (define-public maeparser (define-public coordgenlibs (package (name "coordgenlibs") - (version "3.0.1") + (version "3.0.2") (source (origin (method git-fetch) (uri (git-reference @@ -794,7 +794,7 @@ (define-public coordgenlibs (file-name (git-file-name name version)) (sha256 (base32 - "0d09x3v38i9y184bml020bq7xizdrdwng38qmdxlplzfhqkjdidv")))) + "1wjaxwaihjy9xm5ys23f5abl50zcar1h9pww5ajdkgygsqy0bavi")))) (build-system cmake-build-system) (arguments (list From patchwork Sun Jan 28 23:01:59 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 59546 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 B482E27BBEA; 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Sun, 28 Jan 2024 18:02:56 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rUEB5-0004Xx-Pp for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#68790] [PATCH 6/9] gnu: yaehmop: Update to 2023.03.1. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:03:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 68790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 68790@debbugs.gnu.org Cc: David Elsing Received: via spool by 68790-submit@debbugs.gnu.org id=B68790.170648297817434 (code B ref 68790); Sun, 28 Jan 2024 23:03:03 +0000 Received: (at 68790) by debbugs.gnu.org; 28 Jan 2024 23:02:58 +0000 Received: from localhost ([127.0.0.1]:58621 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEB0-0004X6-0a for submit@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:58 -0500 Received: from mout02.posteo.de ([185.67.36.66]:34135) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAt-0004Vu-Lz for 68790@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:52 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 21AF4240105 for <68790@debbugs.gnu.org>; Mon, 29 Jan 2024 00:02:38 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1706482958; bh=KG9Lv1SzYMyI9Dk4G3B7tu7XB+0OB0Uy99fNP9PLa0g=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=rWyBWs7gblSWtgCsnkqPqHd6zniWAVcdUx6B/Tt7v/+pvXVrPlY0lAbjAI8Q+LQJC Ep5qnid2xrOopcloFQI2is1FZTR79S5FoAthFsv0TPfEujx5pdo75rc4THKParCSOc vLrmzAckUKtsiaed6OInZsix2WEksm01jgMtuX1qr0SXpirRIAIVE7AzTNRY0YTmAE IlsIU6b2GfA8Yac2tQfNbTRUtqnTttBP9qgTrZZVF+tKy4bOEJR+s//F1IFpljMhhd IAl1Ex6n5QdafJnRP+j4rQmijoAprfzRnm1+XRe+nUjf1ETKMFFibaQNrK/tQWDywM RRVNVRb5Wr7Dw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TNRlx5jp8z6twF; Mon, 29 Jan 2024 00:02:37 +0100 (CET) From: David Elsing Date: Sun, 28 Jan 2024 23:01:59 +0000 Message-ID: <20240128230215.1389-6-david.elsing@posteo.net> In-Reply-To: <20240128225919.795-2-david.elsing@posteo.net> References: <20240128225919.795-2-david.elsing@posteo.net> 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/chemistry.scm (yaehmop): Update to 2023.03.1. --- 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 44833d9c3f..4a9dd97c5b 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -812,7 +812,7 @@ (define-public coordgenlibs (define-public yaehmop (package (name "yaehmop") - (version "2022.09.1") + (version "2023.03.1") (source (origin (method git-fetch) (uri (git-reference @@ -821,7 +821,7 @@ (define-public yaehmop (file-name (git-file-name name version)) (sha256 (base32 - "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0")) + "18xnxqn8i7vswy3iffapfh9q2iimpnd23ps45hn4xxbs6dqgzprb")) (modules '((guix build utils))) (snippet '(begin From patchwork Sun Jan 28 23:02:00 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 59552 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 DD6A327BBEA; Sun, 28 Jan 2024 23:04:22 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H5,RCVD_IN_MSPIKE_WL, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham 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 463DE27BBE2 for ; Sun, 28 Jan 2024 23:04:21 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rUEBw-0006hM-0j; Sun, 28 Jan 2024 18:03:56 -0500 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 ) id 1rUEBu-0006WK-L9 for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:54 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rUEBu-0005vm-Cb for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:54 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rUEC2-0004a7-8R for guix-patches@gnu.org; Sun, 28 Jan 2024 18:04:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#68790] [PATCH 7/9] gnu: avalon-toolkit: Update to 2.0.5a. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:04:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 68790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 68790@debbugs.gnu.org Cc: David Elsing Received: via spool by 68790-submit@debbugs.gnu.org id=B68790.170648298617506 (code B ref 68790); Sun, 28 Jan 2024 23:04:02 +0000 Received: (at 68790) by debbugs.gnu.org; 28 Jan 2024 23:03:06 +0000 Received: from localhost ([127.0.0.1]:58628 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEB7-0004YG-CV for submit@debbugs.gnu.org; Sun, 28 Jan 2024 18:03:06 -0500 Received: from mout01.posteo.de ([185.67.36.65]:39999) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAu-0004Vw-Uy for 68790@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:54 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 65D4324002B for <68790@debbugs.gnu.org>; Mon, 29 Jan 2024 00:02:39 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1706482959; bh=qi6RoTHRuV7XGZNfGyT6A08Ks8RtNE7/4I0wCH7GAyo=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: Content-Transfer-Encoding:From; b=TdZcJZo1X6moBHmACHmu/428Vt2KZQOcnYL7JBiDGmEr/x1Ods/WfAIMv6y07Y83y TLPKbt3JJUJAuc7UMpwRKYYJCqWUkPE6V89uKlCbvmEnHUqb/mwHGNCT6SUl+cPGOw AklmL2VyupivpVl4PgbNkd8MkaCPo686xDVxHFTYcN3nBQ2zxHws5ey2r//tWlDSc0 ZiJIKchThxBSTCiFcBelettdZ2QYMX/o024FEZ2478VEPb6KYmIHVivci3YeBxUg8w NNHKV/6DP5QTNyJpJcdtHZe/WzmZvGTVvTvxpMbGQsrJgyhIb0MZ4u5QMGkGMNZ6LQ g4BeLzzwaHkuw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TNRlz0M6yz6tyh; Mon, 29 Jan 2024 00:02:39 +0100 (CET) From: David Elsing Date: Sun, 28 Jan 2024 23:02:00 +0000 Message-ID: <20240128230215.1389-7-david.elsing@posteo.net> In-Reply-To: <20240128225919.795-2-david.elsing@posteo.net> References: <20240128225919.795-2-david.elsing@posteo.net> 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches The bug freeing static memory and the makefile have been improved upstream, so we don't have to work around them anymore. Now, two static libraries are built instead. * gnu/packages/chemistry.scm (avalon-toolkit): Update to 2.0.5a. [source]: Switch to git reference from GitHub. Adjust snippet. Add patch from the RDKit fork. [arguments]: Remove 'dont-free-static-memory phase. Use provided makefile. Adjust 'install phase. * gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 2 + gnu/packages/chemistry.scm | 131 ++++++++---------- .../patches/avalon-toolkit-rdkit-fixes.patch | 110 +++++++++++++++ 3 files changed, 166 insertions(+), 77 deletions(-) create mode 100644 gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch diff --git a/gnu/local.mk b/gnu/local.mk index ab63bd5881..b5d61eb4dd 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -63,6 +63,7 @@ # Copyright © 2023 gemmaro # Copyright © 2023 Herman Rimm # Copyright © 2023 Troy Figiel +# Copyright © 2024 David Elsing # # This file is part of GNU Guix. # @@ -952,6 +953,7 @@ dist_patch_DATA = \ %D%/packages/patches/audiofile-function-signature.patch \ %D%/packages/patches/automake-skip-amhello-tests.patch \ %D%/packages/patches/avahi-localstatedir.patch \ + %D%/packages/patches/avalon-toolkit-rdkit-fixes.patch \ %D%/packages/patches/avidemux-install-to-lib.patch \ %D%/packages/patches/awesome-reproducible-png.patch \ %D%/packages/patches/awesome-4.3-fno-common.patch \ diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 4a9dd97c5b..5e19bdf182 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -917,90 +917,67 @@ (define-public yaehmop (define-public avalon-toolkit (package (name "avalon-toolkit") - (version "1.2.0") - (source - (origin - (method url-fetch) - (uri (string-append - "mirror://sourceforge/avalontoolkit/" - "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_" - version ".source.tar")) - (sha256 - (base32 - "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv")) - (modules '((guix build utils) (ice-9 ftw))) - (snippet - #~(begin - (delete-file-recursively "../SourceDistribution/java"))))) + (version "2.0.5a") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rohdebe1/ava-formake") + (commit (string-append "AvalonToolkit_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mfg40y5xc17sm59zdfc5sk22n9zm5zk0z1aw47chvl6hp465szk")) + (patches + (search-patches "avalon-toolkit-rdkit-fixes.patch")) + (modules '((guix build utils) (ice-9 ftw))) + (snippet + #~(begin + (delete-file-recursively "src/main/java") + (delete-file-recursively "src/test/target"))))) (build-system gnu-build-system) (arguments (list - ;; There are no intended tests + ;; There is only one test, which is missing a file #:tests? #f #:phases - #~(let ((programs '("canonizer" "matchtest" "sketch" "smi2mol" "struchk"))) - (modify-phases %standard-phases - (add-after 'unpack 'chdir - (lambda _ (chdir "common"))) - (delete 'configure) - (add-before 'build 'dont-free-static-memory - (lambda _ - (substitute* "reaccsio.c" - (("MyFree\\(.*tempdir\\)" m) - (string-append "/* freeing memory from getenv is bad */" - "// " m))))) - ;; The makefile has incorrect compiler flags and is missing some - ;; object files, so we build it ourselves. - (replace 'build - (lambda _ - (for-each - (lambda (part) - (format #t "Compiling ~a.c ~~> ~a.o~%" part part) - (invoke #$(cc-for-target) "-c" "-fPIC" "-O2" - (string-append part ".c") - "-o" (string-append part ".o"))) - (list "aacheck" "casutils" "denormal" "depictutil" - "didepict" "fixcharges" "forio" "geometry" - "graph" "hashcode" "layout" "local" "pattern" - "perceive" "reaccsio" "rtutils" "set" "shortcut" - "sketch" "ssmatch" "stereo" "symbol_lists" - "symboltable" "utilities")) - (display "Building libavalontoolkit.so\n") - (apply invoke "gcc" "-fPIC" "-shared" "-lm" - "-o" "libavalontoolkit.so" "canonizer.c" "smi2mol.c" - "struchk.c" "patclean.c" (find-files "." "\\.o$")) - ;; patclean is not built here as there is an undeclared - ;; variable in main(). - (for-each - (lambda (program) - (display (string-append "Building " program "\n")) - (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2" - (string-append "-Wl,-rpath=" #$output "/lib") - "-DMAIN" (string-append program ".c") "-o" program)) - programs))) - (replace 'install - (lambda _ - ;; Executables + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda* (#:key parallel-build? #:allow-other-keys) + (mkdir "build") + (mkdir-p "target/executables") + (mkdir-p "target/libraries") + (invoke "make" "programs" "-j" + (if parallel-build? + (number->string (parallel-job-count)) + "1")))) + (replace 'install + (lambda _ + ;; Executables + (let ((programs '("canonizer" "matchtest" "smi2mol" "struchk"))) (for-each (lambda (program) - (install-file program (string-append #$output "/bin"))) - programs) - (for-each - (lambda (name) - (symlink (string-append #$output "/bin/smi2mol") - (string-append #$output "/bin/" name))) - '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf")) - ;; Library - (install-file "libavalontoolkit.so" - (string-append #$output "/lib")) - (for-each - (lambda (file) - (install-file file (string-append #$output - "/include/avalontoolkit"))) - (find-files "." "\\.h$")) - (install-file "../license.txt" - (string-append #$output "/share/doc/" - #$name "-" #$version "/")))))))) + (install-file (string-append "target/executables/" program) + (string-append #$output "/bin"))) + programs)) + (for-each + (lambda (name) + (symlink (string-append #$output "/bin/smi2mol") + (string-append #$output "/bin/" name))) + '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf")) + ;; Library + (install-file "target/libraries/libavalon_tools.a" + (string-append #$output "/lib")) + (install-file "target/libraries/libavalon4rdkit.a" + (string-append #$output "/lib")) + (for-each + (lambda (file) + (install-file file (string-append #$output + "/include/avalontoolkit"))) + (find-files "src/main/C/include" "\\.h$")) + (install-file "license.txt" + (string-append #$output "/share/doc/" + #$name "-" #$version "/"))))))) (home-page "https://sourceforge.net/projects/avalontoolkit/") (synopsis "Tools for SMILES and MOL files and for structure fingerprinting") (description "This package contains a library and programs for diff --git a/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch b/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch new file mode 100644 index 0000000000..c93a9869ed --- /dev/null +++ b/gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch @@ -0,0 +1,110 @@ +Patches taken from the rdkit fork at this commit (there version +AvalonToolkit_2.0.6-pre.2): +https://github.com/rdkit/ava-formake/commit/d05bee0382b8f4696b2b4b05b0038fb7d559520a + +diff -ur a/src/main/C/common/reaccsio.c b/src/main/C/common/reaccsio.c +--- a/src/main/C/common/reaccsio.c ++++ b/src/main/C/common/reaccsio.c +@@ -322,34 +322,49 @@ + fprintf(fp,"\n"); + } + ++#define MAX_BONDLINE_FIELDS 7 ++#define BONDLINE_FIELD_LEN 3 ++ + int ReadREACCSBond(Fortran_FILE *fp, struct reaccs_bond_t *bp) + { +- int nitems, i; +- char buffer[MAX_BUFFER+1]; ++ int nitems, i, j, k; ++ int bond_line_len, n_chars, pos; ++ int *ptrarray[MAX_BONDLINE_FIELDS]; ++ char c; ++ char buffer[BONDLINE_FIELD_LEN+1]; + + if (fp->status != FORTRAN_NORMAL) return(fp->status); + +- strncpy(buffer,fp->buffer,MAX_BUFFER); +- /* zero pad only atom numbers! */ +- for (i=0; i<6; i++) if (buffer[i] == ' ') buffer[i] = '0'; +- + bp->stereo_symbol = 0; + bp->dummy = 0; + bp->topography = 0; + bp->reaction_mark = NONE; +- // make sure spaces are interpreted the Fortran-way +- for (i=9; iatoms[0]; ++ ptrarray[1] = &bp->atoms[1]; ++ ptrarray[2] = &bp->bond_type; ++ ptrarray[3] = &bp->stereo_symbol; ++ ptrarray[4] = &bp->dummy; ++ ptrarray[5] = &bp->topography; ++ ptrarray[6] = &bp->reaction_mark; ++ bond_line_len = strlen(fp->buffer); ++ nitems = bond_line_len ? (bond_line_len - 1) / BONDLINE_FIELD_LEN + 1 : 0; ++ if (nitems > MAX_BONDLINE_FIELDS) ++ nitems = MAX_BONDLINE_FIELDS; ++ for (i = 0; i < nitems; ++i) ++ { ++ pos = i * BONDLINE_FIELD_LEN; ++ memset(buffer, 0, BONDLINE_FIELD_LEN + 1); ++ n_chars = bond_line_len - pos; ++ if (n_chars > BONDLINE_FIELD_LEN) ++ n_chars = BONDLINE_FIELD_LEN; ++ for (j = 0, k = 0; j < n_chars; ++j) ++ { ++ c = fp->buffer[pos + j]; ++ if (c != ' ') ++ buffer[k++] = c; ++ } ++ sscanf(buffer, "%3d", ptrarray[i]); + } +- nitems = sscanf(buffer, +- "%3d%3d%3d%3d%3d%3d%3d", +- &bp->atoms[0], &bp->atoms[1], +- &bp->bond_type, &bp->stereo_symbol, +- &bp->dummy, +- &bp->topography, &bp->reaction_mark); +- + if (nitems >= 3) + { + GetBuffer(fp); +@@ -1582,6 +1597,8 @@ + + PrintREACCSMolecule(fp, mp,""); + ++ fputc('\0', fp); ++ fflush(fp); + rewind(fp); + + MolStr = _ReadFile(fp); +diff -ur a/src/main/C/programs/struchk.c b/src/main/C/programs/struchk.c +--- a/src/main/C/programs/struchk.c ++++ b/src/main/C/programs/struchk.c +@@ -1581,6 +1581,22 @@ + + if ((result & SIZE_CHECK_FAILED) == 0) + { ++ for (i = 0; i < mp->n_bonds; ++i) { ++ for (j = 0; j < 2; ++j) { ++ if (mp->bond_array[i].atoms[j] < 1 || mp->bond_array[i].atoms[j] > mp->n_atoms) ++ { ++ snprintf(msg_buffer, MAXMSG, ++ "%10s : illegal atom # (%d, max allowed is %d) in bond %d", ++ mp->name, mp->bond_array[i].atoms[j], mp->n_atoms, i + 1); ++ AddMsgToList(msg_buffer); ++ result |= SIZE_CHECK_FAILED; ++ } ++ } ++ } ++ } ++ ++ if ((result & SIZE_CHECK_FAILED) == 0) ++ { + if (convert_atom_texts) + { + tmp = ConvertAtomAliases(mp); From patchwork Sun Jan 28 23:02:01 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 59549 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 A7B2727BBE9; Sun, 28 Jan 2024 23:04:06 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H5,RCVD_IN_MSPIKE_WL, 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 C88C227BBE2 for ; Sun, 28 Jan 2024 23:04:05 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rUEBw-0006jF-OE; Sun, 28 Jan 2024 18:03:56 -0500 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 ) id 1rUEBv-0006eD-KG for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:55 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rUEBv-0005vz-Ad for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:55 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rUEC3-0004aM-6P for guix-patches@gnu.org; Sun, 28 Jan 2024 18:04:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#68790] [PATCH 8/9] gnu: freesasa: Fix memerr tests. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:04:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 68790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 68790@debbugs.gnu.org Cc: David Elsing Received: via spool by 68790-submit@debbugs.gnu.org id=B68790.170648298817523 (code B ref 68790); Sun, 28 Jan 2024 23:04:03 +0000 Received: (at 68790) by debbugs.gnu.org; 28 Jan 2024 23:03:08 +0000 Received: from localhost ([127.0.0.1]:58632 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEB9-0004YT-IQ for submit@debbugs.gnu.org; Sun, 28 Jan 2024 18:03:07 -0500 Received: from mout01.posteo.de ([185.67.36.65]:36857) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAw-0004WB-DZ for 68790@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:54 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id D66F9240027 for <68790@debbugs.gnu.org>; Mon, 29 Jan 2024 00:02:40 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1706482960; bh=IVAn8t0f+MsY16zKNYINU4vs8CmZXSAUuF+WEc1DxYM=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=pX4TLc8gWVOcSsjO2kaf7sbMsdEDp8sUmxCuKEBeTdlwfMn5sHpTYsoMGIgb55c8Q oc9Y0FARitTsm+GAmoBAOe7bJkC3svkUI+iS51qq5r1Z32XwoR4Ft8aqRdfsUzTpPN x5unZqrWzubAC/5fwJ9cgbb+2EQvST37xRAivjaM4a+olvppc4P2WRZUz6spJiEpt+ OexKsvIv1OctIvDT/IspvTl6gM0SqL/uF7vdVBJLSNHajz0xcjzrBGTj3+iK5kJ1Ju rW0rdjtGnAO0HqNU/m4REN1rVc83uDALfEKHJjdTQEIqy5Oamjfr/lBwbOVP3dUX+n j29+SHeYrz8JQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TNRm03KFZz6twm; Mon, 29 Jan 2024 00:02:40 +0100 (CET) From: David Elsing Date: Sun, 28 Jan 2024 23:02:01 +0000 Message-ID: <20240128230215.1389-8-david.elsing@posteo.net> In-Reply-To: <20240128225919.795-2-david.elsing@posteo.net> References: <20240128225919.795-2-david.elsing@posteo.net> 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/chemistry.scm (freesasa)[arguments]: Add "CFLAGS=-fno-builtin-malloc" to #:configure-flags. --- gnu/packages/chemistry.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 5e19bdf182..98141737ac 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -708,7 +708,12 @@ (define-public freesasa #~(list "--enable-check" "--enable-parser-generator" "CXXFLAGS=-std=c++17" - "--enable-doxygen") + "--enable-doxygen" + ;; Some tests rely on replacing malloc with a wrapper which + ;; fails in a controlled way, but this does not work if the call + ;; is replaced. This was fixed upstream, remove once there is a + ;; new release. + "CFLAGS=-fno-builtin-malloc") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'remove-libc++-linking From patchwork Sun Jan 28 23:02:02 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 59550 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 50DFE27BBEA; Sun, 28 Jan 2024 23:04:13 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H5,RCVD_IN_MSPIKE_WL, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham 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 4EFD727BBE2 for ; Sun, 28 Jan 2024 23:04:11 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1rUEBx-0006jy-AS; Sun, 28 Jan 2024 18:03:57 -0500 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 ) id 1rUEBw-0006ha-0U for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:56 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rUEBv-0005w6-OG for guix-patches@gnu.org; Sun, 28 Jan 2024 18:03:55 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1rUEC3-0004aT-KA for guix-patches@gnu.org; Sun, 28 Jan 2024 18:04:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#68790] [PATCH 9/9] gnu: rdkit: Update to 2023.09.4. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 28 Jan 2024 23:04:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 68790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 68790@debbugs.gnu.org Cc: David Elsing Received: via spool by 68790-submit@debbugs.gnu.org id=B68790.170648298917532 (code B ref 68790); Sun, 28 Jan 2024 23:04:03 +0000 Received: (at 68790) by debbugs.gnu.org; 28 Jan 2024 23:03:09 +0000 Received: from localhost ([127.0.0.1]:58634 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEBA-0004Ya-1I for submit@debbugs.gnu.org; Sun, 28 Jan 2024 18:03:08 -0500 Received: from mout02.posteo.de ([185.67.36.66]:47935) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rUEAx-0004WL-Nr for 68790@debbugs.gnu.org; Sun, 28 Jan 2024 18:02:56 -0500 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 2D51B24010A for <68790@debbugs.gnu.org>; Mon, 29 Jan 2024 00:02:42 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1706482962; bh=0oNkx1KMh3q9m2iip/okr2GuHU9xJsyHDF2OVXxYvZ8=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=TSxewV5eJD4J2+i5uBT4+Qa6AATTku4j964b0iJi/LQ+4BoiqK+mQHPvo9t4wFRgI mdcZSt9wWKQOsfVsB7iE9l8x1gFe2k7oDW2d1xRDya0kjTaJhrqZE0HaSox79hqgmg ajqT+Hucn5JWPAC0IYggsa6Cj6q017+A+KY/oJ6FFqstNY18/JrLtXDwdMAoaaPcpY /+aQLH0VV7sMP27sBxvsk6NsYt/Lmj5fKSmo2f+dU0qqPFL7Hnk51MpfjeVqxdic5e 6Do1NPSyKXuMApEdsRfFNhgmsoNgYHz4C1MGrS/mkk7ByW5MQmRklYydbfZljX5ect iJCKdWDVl4yeA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4TNRm151rwz6twr; Mon, 29 Jan 2024 00:02:41 +0100 (CET) From: David Elsing Date: Sun, 28 Jan 2024 23:02:02 +0000 Message-ID: <20240128230215.1389-9-david.elsing@posteo.net> In-Reply-To: <20240128225919.795-2-david.elsing@posteo.net> References: <20240128225919.795-2-david.elsing@posteo.net> 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/chemistry.scm (rdkit): Update to 2023.09.4. [arguments]: Skip testConrec test in check phase. [native-inputs]: Replace catch2 with catch2-3. * gnu/packages/patches/rdkit-unbundle-external-dependencies.patch: Adjust patch. [supported-systems]: New field. --- gnu/packages/chemistry.scm | 15 +- ...rdkit-unbundle-external-dependencies.patch | 208 ++++++++++-------- 2 files changed, 126 insertions(+), 97 deletions(-) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 98141737ac..bd27bfad7a 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -1073,7 +1073,7 @@ (define-public ringdecomposerlib (define-public rdkit (package (name "rdkit") - (version "2022.03.5") + (version "2023.09.4") (source (origin (method git-fetch) (uri (git-reference @@ -1084,7 +1084,7 @@ (define-public rdkit (file-name (git-file-name name version)) (sha256 (base32 - "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9")) + "1lgcgijlzzwpfxndsdlx13npdfk7hcii11zg25cvpmzhbpn6vyn8")) (patches (search-patches "rdkit-unbundle-external-dependencies.patch")) (modules '((guix build utils))) @@ -1183,7 +1183,10 @@ (define-public rdkit "substructLibraryTest" "pyFeatures" "pythonTestDirML" "pythonTestDirChem" ;; Catching Python exception fails - "pyRanker") "|") + "pyRanker" + ;; Flaky test depending on floating point rounding + "testConrec" + ) "|") ")"))))))))) (inputs (list avalon-toolkit @@ -1200,7 +1203,7 @@ (define-public rdkit (native-inputs (list bison boost - catch2 + catch2-3 eigen flex freesasa @@ -1214,4 +1217,8 @@ (define-public rdkit (description "RDKit is a C++ and Python library for cheminformatics, which includes (among other things) the analysis and modification of molecules in 2D and 3D and descriptor generation for machine learning.") + ;; For 32 bit systems, there is a bug in Boost.Python: + ;; https://github.com/boostorg/python/issues/312. Additionally, several + ;; other test fail. + (supported-systems %64bit-supported-systems) (license license:bsd-3))) diff --git a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch index 8ee0611d3b..e22ff57ee0 100644 --- a/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch +++ b/gnu/packages/patches/rdkit-unbundle-external-dependencies.patch @@ -58,99 +58,82 @@ diff --git a/External/AvalonTools/CMakeLists.txt b/External/AvalonTools/CMakeLis index 3e31195fc..314ba35b5 100644 --- a/External/AvalonTools/CMakeLists.txt +++ b/External/AvalonTools/CMakeLists.txt -@@ -2,107 +2,14 @@ if(NOT RDK_BUILD_AVALON_SUPPORT) +@@ -2,90 +2,8 @@ if(NOT RDK_BUILD_AVALON_SUPPORT) return() endif(NOT RDK_BUILD_AVALON_SUPPORT) +-set(AVALON_VERSION "2.0.5-pre.3") -if(NOT DEFINED AVALONTOOLS_DIR) -- set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution") -- set(fileToPatch "${CMAKE_CURRENT_SOURCE_DIR}/SourceDistribution/common/reaccsio.c") +- set(AVALONTOOLS_DIR "${CMAKE_CURRENT_SOURCE_DIR}/ava-formake-AvalonToolkit_${AVALON_VERSION}") +- set(fileToCheck "${AVALONTOOLS_DIR}/src/main/C/common/reaccsio.c") - set(needDownload "TRUE") -- if(EXISTS "${fileToPatch}") -- file(READ "${fileToPatch}" buffer) -- if("${buffer}" MATCHES "//MyFree\\(\\(char \\*\\)tempdir\\);") -- set(needDownload "FALSE") -- endif() +- if(EXISTS "${fileToCheck}") +- set(needDownload "FALSE") - endif() -else() - string(REGEX REPLACE "\\\\" "/" AVALONTOOLS_DIR ${AVALONTOOLS_DIR}) - set(needDownload "FALSE") -endif() - --set(AVALON_SRC_PATH ${AVALONTOOLS_DIR}/common) +-set(AVALON_SRC_PATH "${AVALONTOOLS_DIR}/src/main/C") +-set(AVALON_COMMON_PATH "${AVALON_SRC_PATH}/common") +-set(AVALON_INCLUDE_PATH "${AVALON_SRC_PATH}/include") +-set(AVALON_PROGRAMS_PATH "${AVALON_SRC_PATH}/programs") - -if(needDownload) - if(NOT DEFINED AVALONTOOLS_URL) -- set(AVALONTOOLS_URL "https://sourceforge.net/projects/avalontoolkit/files/AvalonToolkit_1.2/AvalonToolkit_1.2.0.source.tar") +- set(AVALONTOOLS_URL "https://github.com/rdkit/ava-formake/archive/refs/tags/AvalonToolkit_${AVALON_VERSION}.tar.gz") - endif() - if(NOT DEFINED AVALONTOOLS_MD5SUM) -- set(AVALONTOOLS_MD5SUM "092a94f421873f038aa67d4a6cc8cb54") +- set(AVALONTOOLS_MD5SUM "7a20c25a7e79f3344e0f9f49afa03351") - endif() - if(NOT DEFINED AVALONTOOLS_BASE) - string(REGEX REPLACE "^.*/" "" AVALONTOOLS_BASE "${AVALONTOOLS_URL}") - endif() - downloadAndCheckMD5(${AVALONTOOLS_URL} "${CMAKE_CURRENT_SOURCE_DIR}/${AVALONTOOLS_BASE}" ${AVALONTOOLS_MD5SUM}) -- execute_process(COMMAND ${CMAKE_COMMAND} -E tar xf -- ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_1.2.0.source.tar +- execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf +- ${CMAKE_CURRENT_SOURCE_DIR}/AvalonToolkit_${AVALON_VERSION}.tar.gz - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) -- # apply patch to AvalonTools -- configure_file("${fileToPatch}" "${fileToPatch}.orig" COPYONLY) -- file(READ "${fileToPatch}" buffer) -- string(REGEX REPLACE "MyFree\\(\\(char \\*\\)tempdir\\);" -- "//MyFree((char *)tempdir);" buffer "${buffer}") -- file(WRITE "${fileToPatch}" "${buffer}") --endif() - - if (MSVC) - add_definitions("/D_CRT_SECURE_NO_WARNINGS") - add_compile_options(/wd4224 /wd4101 /wd4018 /wd4996 /wd4244 /wd4305 /wd4013 /wd4146 /wd4334 /wd4715 /wd4715 /nologo) - endif(MSVC) - --set(avalon_clib_srcs ${AVALON_SRC_PATH}/layout.c -- ${AVALON_SRC_PATH}/symboltable.c -- ${AVALON_SRC_PATH}/patclean.c -- ${AVALON_SRC_PATH}/utilities.c -- ${AVALON_SRC_PATH}/symbol_lists.c -- ${AVALON_SRC_PATH}/stereo.c -- ${AVALON_SRC_PATH}/set.c -- ${AVALON_SRC_PATH}/perceive.c -- ${AVALON_SRC_PATH}/local.c -- ${AVALON_SRC_PATH}/graph.c -- ${AVALON_SRC_PATH}/geometry.c -- ${AVALON_SRC_PATH}/forio.c -- ${AVALON_SRC_PATH}/depictutil.c -- ${AVALON_SRC_PATH}/denormal.c -- ${AVALON_SRC_PATH}/casutils.c -- ${AVALON_SRC_PATH}/ssmatch.c -- ${AVALON_SRC_PATH}/rtutils.c -- ${AVALON_SRC_PATH}/smi2mol.c -- ${AVALON_SRC_PATH}/didepict.c -- ${AVALON_SRC_PATH}/pattern.c -- ${AVALON_SRC_PATH}/canonizer.c -- ${AVALON_SRC_PATH}/aacheck.c -- ${AVALON_SRC_PATH}/fixcharges.c -- ${AVALON_SRC_PATH}/struchk.c -- ${AVALON_SRC_PATH}/reaccsio.c -- ${AVALON_SRC_PATH}/hashcode.c -- ) -- --# we need this to ensure that builds continue --# to work on linux systems with older versions --# of glibc when we're building with gcc-4.1. --# Without this flag, we'll endup requiring --# glibc 2.7. --if(CMAKE_SYSTEM_NAME STREQUAL "Linux") -- add_definitions(-D_GNU_SOURCE=1) -endif() - --if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang") -- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-return-type -Wno-implicit-function-declaration -Wno-absolute-value -Wno-parentheses -Wno-logical-op-parentheses -Wno-dangling-else -Wno-format") +-if(CMAKE_C_COMPILER_ID STREQUAL "GNU") +- add_compile_options(-Wno-format-security -Wformat=0 -Wstringop-overflow=0 -Wformat-overflow=0 -Wno-unused-result ) -endif() --if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU") -- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unused-result -Wformat-overflow=0 -Wformat=0 -Wno-format-security -Wno-implicit-function-declaration") +-if(CMAKE_C_COMPILER_ID STREQUAL "Clang") +- add_compile_options(-Wno-absolute-value -Wno-return-type -Wno-tautological-overlap-compare) -endif() +-if (MSVC) +- add_definitions("/D_CRT_SECURE_NO_WARNINGS") +- add_compile_options(/wd4018 /wd4101 /wd4146 /wd4334 /wd4477 /wd4715 /wd4716 /wd4996 /nologo) +-endif(MSVC) - -- +-set(avalon_clib_srcs ${AVALON_COMMON_PATH}/layout.c +- ${AVALON_COMMON_PATH}/symboltable.c +- ${AVALON_COMMON_PATH}/patclean.c +- ${AVALON_COMMON_PATH}/utilities.c +- ${AVALON_COMMON_PATH}/symbol_lists.c +- ${AVALON_COMMON_PATH}/stereo.c +- ${AVALON_COMMON_PATH}/set.c +- ${AVALON_COMMON_PATH}/perceive.c +- ${AVALON_COMMON_PATH}/local.c +- ${AVALON_COMMON_PATH}/graph.c +- ${AVALON_COMMON_PATH}/geometry.c +- ${AVALON_COMMON_PATH}/forio.c +- ${AVALON_COMMON_PATH}/depictutil.c +- ${AVALON_COMMON_PATH}/denormal.c +- ${AVALON_COMMON_PATH}/casutils.c +- ${AVALON_COMMON_PATH}/ssmatch.c +- ${AVALON_COMMON_PATH}/rtutils.c +- ${AVALON_COMMON_PATH}/smi2mol.c +- ${AVALON_COMMON_PATH}/didepict.c +- ${AVALON_COMMON_PATH}/pattern.c +- ${AVALON_COMMON_PATH}/canonizer.c +- ${AVALON_COMMON_PATH}/aacheck.c +- ${AVALON_COMMON_PATH}/fixcharges.c +- ${AVALON_PROGRAMS_PATH}/struchk.c +- ${AVALON_COMMON_PATH}/reaccsio.c +- ${AVALON_COMMON_PATH}/hashcode.c +- ) - -rdkit_library(avalon_clib ${avalon_clib_srcs}) -target_compile_definitions(avalon_clib PRIVATE RDKIT_AVALONLIB_BUILD) @@ -159,11 +142,11 @@ index 3e31195fc..314ba35b5 100644 -endif() - -include_directories(${CMAKE_CURRENT_SOURCE_DIR}) --include_directories(${AVALON_SRC_PATH}) +-include_directories(${AVALON_INCLUDE_PATH}) - rdkit_library(AvalonLib AvalonTools.cpp SHARED - LINK_LIBRARIES avalon_clib SubstructMatch FileParsers SmilesParse GraphMol DataStructs ) -+ LINK_LIBRARIES -lavalontoolkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs ) ++ LINK_LIBRARIES -lavalon4rdkit SubstructMatch FileParsers SmilesParse GraphMol DataStructs ) target_compile_definitions(AvalonLib PRIVATE RDKIT_AVALONLIB_BUILD) rdkit_headers(AvalonTools.h DEST GraphMol) rdkit_test(testAvalonLib1 test1.cpp @@ -278,7 +261,7 @@ diff --git a/External/RingFamilies/CMakeLists.txt b/External/RingFamilies/CMakeL index 08dd1fe04..66ecd5834 100644 --- a/External/RingFamilies/CMakeLists.txt +++ b/External/RingFamilies/CMakeLists.txt -@@ -1,47 +1,6 @@ +@@ -1,47 +1,7 @@ -add_custom_target(ringdecomposerlib_support ALL) - if(NOT RDK_USE_URF) @@ -324,10 +307,9 @@ index 08dd1fe04..66ecd5834 100644 -rdkit_headers(${URFLIB_DIR}/RingDecomposerLib.h DEST "") - - --set(RDK_URF_LIBS RingDecomposerLib -- CACHE STRING "the libraries for the URF calculation" FORCE) +rdkit_library(RingDecomposerLib dummy.cpp SHARED LINK_LIBRARIES -lRingDecomposerLib) -+set(RDK_URF_LIBS RingDecomposerLib CACHE STRING "" FORCE) + set(RDK_URF_LIBS RingDecomposerLib + CACHE STRING "the libraries for the URF calculation" FORCE) diff --git a/External/RingFamilies/dummy.cpp b/External/RingFamilies/dummy.cpp new file mode 100644 index 000000000..e69de29bb @@ -335,40 +317,60 @@ diff --git a/External/YAeHMOP/CMakeLists.txt b/External/YAeHMOP/CMakeLists.txt index f1027b3bd..8bee2f910 100644 --- a/External/YAeHMOP/CMakeLists.txt +++ b/External/YAeHMOP/CMakeLists.txt -@@ -18,32 +18,8 @@ endif() +@@ -4,52 +4,7 @@ endif(NOT RDK_BUILD_YAEHMOP_SUPPORT) - include_directories( ${RDKit_ExternalDir}/YAeHMOP ) + add_definitions(-DRDK_BUILD_YAEHMOP_SUPPORT) --ExternalProject_Add(yaehmop_project -- GIT_REPOSITORY https://github.com/greglandrum/yaehmop.git -- GIT_TAG master -- UPDATE_COMMAND "" -- PATCH_COMMAND "" -- PREFIX ${CMAKE_CURRENT_SOURCE_DIR} -- SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop" -- SOURCE_SUBDIR "tightbind" -- CMAKE_ARGS -DUSE_BLAS_LAPACK=OFF -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR} -DCMAKE_C_FLAGS=${CMAKE_C_FLAGS} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -- TEST_COMMAND "") -- --include_directories(${PROJECT_BINARY_DIR}/include) --link_directories(${PROJECT_BINARY_DIR}/lib) --link_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build) +-if(NOT DEFINED YAEHMOP_DIR) +- set(YAEHMOP_DIR "${CMAKE_CURRENT_SOURCE_DIR}/yaehmop") +-endif() +- +-if(NOT EXISTS "${YAEHMOP_DIR}/tightbind/bind.h") +- set(RELEASE_NO "2023.03.1") +- set(MD5 "e6450f13e02c54d024233b993c3c7ff6") +- 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 +- ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz +- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) +- +- file(RENAME "yaehmop-${RELEASE_NO}" "${YAEHMOP_DIR}") +-else() +- message("-- Found YAeHMOP source in ${YAEHMOP_DIR}") +-endif() +- +-set(yaehmop_INCLUDE_DIRS ${YAEHMOP_DIR}/.. +- CACHE STRING "yaehmop Include File" FORCE) +-include_directories(${yaehmop_INCLUDE_DIRS}) +- +-if(CMAKE_COMPILER_IS_GNUCXX AND NOT CYGWIN) +- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC") +-endif() +-if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang") +- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC") +-endif() +- +-# bring in the eHT code, but skip the targets (we'll get yaehmop_eht anyway because it's a dependency) +-add_subdirectory(yaehmop/tightbind EXCLUDE_FROM_ALL True) +- +-# set install dir for the yaehmop library: +-INSTALL(TARGETS yaehmop_eht EXPORT rdkit-targets +- DESTINATION ${RDKit_LibDir}/${RDKLIB_DEST} +- COMPONENT runtime ) +- +- +- - -set(EHT_PARAM_FILE ${CMAKE_CURRENT_SOURCE_DIR}/yaehmop/tightbind/eht_parms.dat ) -install(FILES ${EHT_PARAM_FILE} - DESTINATION ${RDKit_ShareDir}/Data - COMPONENT data) - --message("YAeHMOP include_dirs: ${PROJECT_BINARY_DIR}/include") --message("YAeHMOP link_dirs: ${PROJECT_BINARY_DIR}/lib ${CMAKE_CURRENT_SOURCE_DIR}/src/yaehmop_project-build") -- -rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES yaehmop_eht GraphMol ) +rdkit_library(EHTLib EHTTools.cpp SHARED LINK_LIBRARIES -lyaehmop_eht GraphMol ) target_compile_definitions(EHTLib PRIVATE RDKIT_EHTLIB_BUILD) --add_dependencies(EHTLib yaehmop_project) rdkit_headers(EHTTools.h DEST GraphMol) rdkit_catch_test(testEHTLib1 test1.cpp - LINK_LIBRARIES EHTLib FileParsers SmilesParse ) diff --git a/External/YAeHMOP/EHTTools.cpp b/External/YAeHMOP/EHTTools.cpp index 7a229f51f..71033dc5c 100644 --- a/External/YAeHMOP/EHTTools.cpp @@ -382,3 +384,23 @@ index 7a229f51f..71033dc5c 100644 } namespace RDKit { +@@ -160,4 +160,4 @@ bool runMol(const ROMol &mol, EHTResults &results, int confId, + } + + } // end of namespace EHTTools +-} // end of namespace RDKit +\ No newline at end of file ++} // end of namespace RDKit +diff --git a/External/YAeHMOP/Wrap/CMakeLists.txt b/External/YAeHMOP/Wrap/CMakeLists.txt +index 759a9f360..114d24532 100644 +--- a/External/YAeHMOP/Wrap/CMakeLists.txt ++++ b/External/YAeHMOP/Wrap/CMakeLists.txt +@@ -4,6 +4,8 @@ rdkit_python_extension(rdEHTTools + DEST Chem + LINK_LIBRARIES + EHTLib ) ++ ++target_include_directories(rdEHTTools PRIVATE ${RDKit_ExternalDir}/YAeHMOP) + + add_pytest(pyEHTTools + ${CMAKE_CURRENT_SOURCE_DIR}/testEHTTools.py)