From patchwork Sun Mar 30 22:06:54 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41041 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 BC41727BBE9; Sun, 30 Mar 2025 23:09:12 +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=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, 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 13DE427BBE2 for ; Sun, 30 Mar 2025 23:09:11 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tz0q3-0000kN-1d; Sun, 30 Mar 2025 18:09:07 -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 ) id 1tz0py-0000jU-Io for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:04 -0400 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 1tz0py-0006cP-AL for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:02 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=OMSMU891Aoh63Izi2faPBpafesuBPRnJSv1gbZDisGI=; b=oX6SKFOMa0+RgZ4K1zqJxyAADWttXPelfG4hWH49iwt66bMsQlsOm3EgZ0+cVwIhIiXqSqF8mjesr1rqb3kSsSsiZhrqdxMPs3q6SPv8JFNp/Pcblrl7YtXJki63dVBl5m8nWWP9+/5jUZ7AonX/D2Oz5eHnW0wgiAYZLujQcx0SErc407Q1hQracDW4Z1g0U4Uo1kAuENGIWH18e6+OptX5Y72cRqu/3aJjb00DAEFRJOAJsNiRJKgzwq4hzIKuB2BYbN3QCc8slJvAtTBYk0LolfvXXSZlDL96+nfeI2GaNcZLk4DksunuW3gJBwdz5LOFSkcaruJ7j7XkZTZvhA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tz0px-00019y-QX for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77394] [PATCH 1/5] gnu: inchi: Update to 1.07.3. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 30 Mar 2025 22:09:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77394 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77394@debbugs.gnu.org Cc: David Elsing Received: via spool by 77394-submit@debbugs.gnu.org id=B77394.17433725004268 (code B ref 77394); Sun, 30 Mar 2025 22:09:01 +0000 Received: (at 77394) by debbugs.gnu.org; 30 Mar 2025 22:08:20 +0000 Received: from localhost ([127.0.0.1]:38348 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tz0pH-00016j-Ur for submit@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 ) id 1tz0pE-00015z-FJ for 77394@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@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 Date: Sun, 30 Mar 2025 22:06:54 +0000 Message-ID: <20250330220745.25337-1-david.elsing@posteo.net> In-Reply-To: <20250330220421.24480-1-david.elsing@posteo.net> References: <20250330220421.24480-1-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 (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 From patchwork Sun Mar 30 22:06:55 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41044 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 BFE5527BBE9; Sun, 30 Mar 2025 23:09:43 +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=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, 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 DC90C27BBE2 for ; Sun, 30 Mar 2025 23:09:42 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tz0q4-0000l7-SE; Sun, 30 Mar 2025 18:09:08 -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 ) id 1tz0py-0000jW-Rm for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:04 -0400 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 1tz0py-0006cX-J1 for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:02 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=5lIOMquK6lDltMaq3qQCGXdfp3MXKgMThHWaAa0ywpw=; b=GAyyqpFf/1WT/v+XZel6jv3TwHpN1g87KCmnkWIEeH8st6ISh7dxh7ezuYpCH9cff0oIpmUYIrRO8DDcuZ0GLrt1N395+8DWW3lLNBq2W245bHUpF/S23vDNXIhdH2bvKGrHOKjgPo2omKbfQsie+lsGuIxH/LwYPvw6xGuDaWQz7dZAJgSLWXxBscQ9/LDEQRklf9V0vtcV4wMWn853gKFTM9GldmQ8IofhS+tEFDO81zOVE7NROpIF5IcFUWoEjfp+/jc2r8Xg/2kLMBovXwL8XZCNLYRLIZwRvWg672fNc8BwIhKX8pNCbLb2UlVCsJua220/3HSo4gD/qv++lQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tz0py-0001A6-Eb for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77394] [PATCH 2/5] gnu: yaehmop: Update to 2024.03.1. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 30 Mar 2025 22:09:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77394 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77394@debbugs.gnu.org Cc: David Elsing Received: via spool by 77394-submit@debbugs.gnu.org id=B77394.17433725104331 (code B ref 77394); Sun, 30 Mar 2025 22:09:02 +0000 Received: (at 77394) by debbugs.gnu.org; 30 Mar 2025 22:08:30 +0000 Received: from localhost ([127.0.0.1]:38356 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tz0pR-00017n-Qw for submit@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 ) id 1tz0pH-00016B-0H for 77394@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@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 Date: Sun, 30 Mar 2025 22:06:55 +0000 Message-ID: <20250330220745.25337-2-david.elsing@posteo.net> In-Reply-To: <20250330220421.24480-1-david.elsing@posteo.net> References: <20250330220421.24480-1-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 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 From patchwork Sun Mar 30 22:06:56 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41045 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 1A1EA27BBEA; Sun, 30 Mar 2025 23:09:48 +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=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, 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 CFED927BBE2 for ; Sun, 30 Mar 2025 23:09:47 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tz0q4-0000l4-HY; 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Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tz0pz-0001AI-1z for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77394] [PATCH 3/5] gnu: Add boost-with-numpy. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 30 Mar 2025 22:09:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77394 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77394@debbugs.gnu.org Cc: David Elsing Received: via spool by 77394-submit@debbugs.gnu.org id=B77394.17433725104342 (code B ref 77394); Sun, 30 Mar 2025 22:09:03 +0000 Received: (at 77394) by debbugs.gnu.org; 30 Mar 2025 22:08:30 +0000 Received: from localhost ([127.0.0.1]:38358 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tz0pS-00017t-6k for submit@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 ) id 1tz0pJ-00016J-G9 for 77394@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@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 Date: Sun, 30 Mar 2025 22:06:56 +0000 Message-ID: <20250330220745.25337-3-david.elsing@posteo.net> In-Reply-To: <20250330220421.24480-1-david.elsing@posteo.net> References: <20250330220421.24480-1-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/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") From patchwork Sun Mar 30 22:06:57 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41042 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 5C42227BBEA; Sun, 30 Mar 2025 23:09:29 +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=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, 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 8CAE227BBE2 for ; Sun, 30 Mar 2025 23:09:28 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tz0q8-0000mm-1X; Sun, 30 Mar 2025 18:09:12 -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 ) id 1tz0q1-0000k2-BW for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:05 -0400 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 1tz0pz-0006cl-Lb for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:05 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=8Z+iNX0Bh3mpB/zcY2r2R4S1jEmilCkbmUEzk5tqTQU=; b=RaGFWaqYN7597aCz7D9gLsHnBxKwbW+YRmr2kLo60HJ/Pp4QvXd6Fi+90/GQwuZks0jWbiNhxF47JdzSSSkb56rKbdKdMmP2bpsDgOn7N3Q0ZfXaTgX8sob5Cxv9W2mzVIeyX8K+IW3tPdj1FdMOkPTzGpQJ74oX5iawitkoE05q+MxY7VKQAKq25PD1MfzKPJnchdROmtrtTmmefOHN3lwdTbziPvbWzOKk6JuKx4iQ/sAlG817KjZpkrBoj4dVnmA3KsqCV2gPyQX3KC4m99DdbPJA/74OWGT6I3XOWu6iwjr9Ow3SZBBhlO7o9/FhvEsvzbCEdCXaozqispOSgA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tz0pz-0001AQ-GL for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77394] [PATCH 4/5] gnu: Add pubchem-align3d. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 30 Mar 2025 22:09:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77394 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77394@debbugs.gnu.org Cc: David Elsing Received: via spool by 77394-submit@debbugs.gnu.org id=B77394.17433725114349 (code B ref 77394); Sun, 30 Mar 2025 22:09:03 +0000 Received: (at 77394) by debbugs.gnu.org; 30 Mar 2025 22:08:31 +0000 Received: from localhost ([127.0.0.1]:38360 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tz0pS-00017y-JQ for submit@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 ) id 1tz0pI-00016L-Gi for 77394@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@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 Date: Sun, 30 Mar 2025 22:06:57 +0000 Message-ID: <20250330220745.25337-4-david.elsing@posteo.net> In-Reply-To: <20250330220421.24480-1-david.elsing@posteo.net> References: <20250330220421.24480-1-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 (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") From patchwork Sun Mar 30 22:06:58 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41043 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 2913D27BBE2; Sun, 30 Mar 2025 23:09:41 +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=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, 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 82E5627BBE9 for ; Sun, 30 Mar 2025 23:09:39 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tz0q5-0000lU-LL; Sun, 30 Mar 2025 18:09:09 -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 ) id 1tz0q1-0000k3-Bo for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:05 -0400 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 1tz0q0-0006co-9S for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:05 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=E/2FtTsPi45gWz63sNO5F1Vfs2THkflxT/4918JevlA=; b=fbaPQaSrhTAV8grxplVJR7zqXO0uW0RXb/xQ9OeIRXc5p96t5fESEKcbH+5lhUvzV8JPhm0Hi9lIVGuH2GZQJRb9elu75P0ycMtCwl+XK9z5wjzwByoHFwfIfONcC/KdVHP/ArhlN1HHgibAnilrxoysxd75v6xXeOKanbyX0+qwkn4/hOcb5rEl4IEZZ2w65b3b7x6W3XW9tKyHp2BPxwA6PD5uXfZ1b0JvSngtYEpVc9cAbxW8MSsoZPofm+FdT51/9mMaNXkFxL/fS2iJi/n56miVHWp/csIF0t2lBEBiCkrrKyDvEpqzuOYLblQdX4cPmdY/mji/eH/qMeTR5w==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tz0q0-0001Ab-3J for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77394] [PATCH 5/5] gnu: rdkit: Update to 2024.09.6. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 30 Mar 2025 22:09:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77394 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77394@debbugs.gnu.org Cc: David Elsing Received: via spool by 77394-submit@debbugs.gnu.org id=B77394.17433725124358 (code B ref 77394); Sun, 30 Mar 2025 22:09:04 +0000 Received: (at 77394) by debbugs.gnu.org; 30 Mar 2025 22:08:32 +0000 Received: from localhost ([127.0.0.1]:38362 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tz0pT-000186-23 for submit@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 ) id 1tz0pN-00016i-Eo for 77394@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@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 Date: Sun, 30 Mar 2025 22:06:58 +0000 Message-ID: <20250330220745.25337-5-david.elsing@posteo.net> In-Reply-To: <20250330220421.24480-1-david.elsing@posteo.net> References: <20250330220421.24480-1-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 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 ${freesasa_h} freesasa_h_data) --string(REGEX REPLACE "(#include )" "\\1\n#include " freesasa_h_data "${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 "${freesasa_h_data}") +-if (NOT freesasa_h_data MATCHES "RDGeneral/export") +- string(REGEX REPLACE "(#include )" "\\1\n#include " freesasa_h_data "${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 +@@ -13,7 +13,7 @@ + #include extern "C" { -#include @@ -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)