From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 1/6] gnu: Add spglib. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 25 Jan 2021 21:22:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 46107@debbugs.gnu.org Cc: Kei Kebreau X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.16116096655355 (code B ref -1); Mon, 25 Jan 2021 21:22:02 +0000 Received: (at submit) by debbugs.gnu.org; 25 Jan 2021 21:21:05 +0000 Received: from localhost ([127.0.0.1]:40165 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49IH-0001OJ-GD for submit@debbugs.gnu.org; Mon, 25 Jan 2021 16:21:05 -0500 Received: from lists.gnu.org ([209.51.188.17]:43362) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49IG-0001OC-9B for submit@debbugs.gnu.org; Mon, 25 Jan 2021 16:21:04 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:44336) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1l49IG-0001V4-3R for guix-patches@gnu.org; Mon, 25 Jan 2021 16:21:04 -0500 Received: from mout01.posteo.de ([185.67.36.65]:52676) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1l49ID-0000uf-JX for guix-patches@gnu.org; Mon, 25 Jan 2021 16:21:03 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id E597916005C for ; Mon, 25 Jan 2021 22:20:55 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1611609655; bh=bitKo9bBMdzOGbL+ze5908HzRCu9HcTuRcix0ebQVYw=; h=From:To:Cc:Subject:Date:From; b=OUc+l48YtQNHPyDrZc6xOJg+j3pevCmQz4c9nm1iXKezzhGsyNZ2yR5rB/UKm8zs8 oQpDti/aWTxsIIDY9Qms597dYqJN19dx2ZaCS6IcgT5lsSv+rRX5MbH6nUN0M14PBb PgvNJ+iXi4ZM9I3k8xZn4tiwAaRPAhRlIA+Gyu4kwP0zdNkIvtc/CZCjKyiLylISpn ST7qMz1DDeYU/KTRtaWQFPDUAs6/unWSxGqdkxrYkt9NDTavJXF9gfFhfzKc/foX0c dqlT8hQMgKAFyFZPUTEnRk3BaN0CNj/AD5ksXKkoxhlQR2fW2Hcg/vgYpmaqzoH+Dx 8/Icu/7E9MiyA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4DPjTL0XPcz6tm6; Mon, 25 Jan 2021 22:20:53 +0100 (CET) From: Kei Kebreau Date: Mon, 25 Jan 2021 16:20:42 -0500 Message-Id: <20210125212042.4358-1-kkebreau@posteo.net> X-Mailer: git-send-email 2.29.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=kkebreau@posteo.net; helo=mout01.posteo.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H4=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) * gnu/packages/chemistry.scm (spglib): New variable. --- gnu/packages/chemistry.scm | 45 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index ddbf5ca098..7a9b3069fa 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -29,6 +29,7 @@ #:use-module (guix git-download) #:use-module (gnu packages) #:use-module (gnu packages algebra) + #:use-module (gnu packages autotools) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -464,3 +465,47 @@ chemical data. It's a collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.") (license license:gpl2))) + +(define-public spglib + (package + (name "spglib") + (version "1.16.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/spglib/spglib") + (commit (string-append "v" version)))) + (sha256 + (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (arguments + '(#:test-target "check" + #:phases + (modify-phases %standard-phases + (replace 'bootstrap + (lambda _ + ;; These files are required by the Makefile, but not provided by + ;; the developers. + (for-each (lambda (file) (invoke "touch" file)) + '("NEWS" "README" "AUTHORS")) + (invoke "autoreconf" "-vi")))))) + (home-page "https://spglib.github.io/spglib/index.html") + (synopsis "Library for crystal symmetry search") + (description "Spglib is a library for finding and handling crystal +symmetries written in C. Spglib can be used to: + +@enumerate +@item Find symmetry operations +@item Identify space-group type +@item Wyckoff position assignment +@item Refine crystal structure +@item Find a primitive cell +@item Search irreducible k-points +@end enumerate") + (license license:bsd-3))) -- 2.29.2 From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 2/6] gnu: Add mmtf-cpp. References: <20210125212042.4358-1-kkebreau@posteo.net> In-Reply-To: <20210125212042.4358-1-kkebreau@posteo.net> Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 25 Jan 2021 21:24:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 46107@debbugs.gnu.org Cc: Kei Kebreau Received: via spool by 46107-submit@debbugs.gnu.org id=B46107.16116097965600 (code B ref 46107); Mon, 25 Jan 2021 21:24:02 +0000 Received: (at 46107) by debbugs.gnu.org; 25 Jan 2021 21:23:16 +0000 Received: from localhost ([127.0.0.1]:40171 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49KO-0001SF-07 for submit@debbugs.gnu.org; Mon, 25 Jan 2021 16:23:16 -0500 Received: from mout01.posteo.de ([185.67.36.65]:39117) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49KL-0001Rq-7a for 46107@debbugs.gnu.org; Mon, 25 Jan 2021 16:23:14 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id D996C160065 for <46107@debbugs.gnu.org>; Mon, 25 Jan 2021 22:23:06 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1611609786; bh=WqriT4z8BSO7KY0QnCMROIW23uZMxOotJZQ/p5JZIYM=; h=From:To:Cc:Subject:Date:From; b=FNa1Yhj4DRPieFFY6jE55S4iHvovwQDLPObALclm1u2fIowbY1QHyV2IhS/wMuCt6 Q53RwAFRkY2bk6KbMI8uOy4gWR1aHrca1/dWtk+GSMqTc69/kjQoexQMViF+/MWccn +s3UQKK7fikdVq/79nfYbX3GoiAheV3wHyOdFZGVeSa1lnx7TKCh9o4jD5jnzLwoOZ rKYtoi5+wK3Sndje40cFAzvlO75VnOwoa94mRqIhepvFNIIarL37zuRGT4/4eYepLr sKH+qgnbNADfmTTlY4zrOsRJ2b0TIwTjIbD58sUGjoFKm82AV2hDVUgqBdbOgXP8by 8q7k6V8VMhVmQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4DPjWs0b7Gz6tm6; Mon, 25 Jan 2021 22:23:04 +0100 (CET) From: Kei Kebreau Date: Mon, 25 Jan 2021 16:22:44 -0500 Message-Id: <20210125212248.4749-1-kkebreau@posteo.net> X-Mailer: git-send-email 2.29.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/chemistry.scm (mmtf-cpp): New variable. --- gnu/packages/chemistry.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 7a9b3069fa..4ac7a90c87 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -242,6 +242,31 @@ analogy is that InChI is the bar-code for chemistry and chemical structures.") "file://LICENCE" "See LICENCE in the distribution.")))) +(define-public mmtf-cpp + (package + (name "mmtf-cpp") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rcsb/mmtf-cpp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "17ylramda69plf5w0v5hxbl4ggkdi5s15z55cv0pljl12yvyva8l")))) + (build-system cmake-build-system) + ;; Tests require the soon-to-be-deprecated version 1 of the catch-framework. + (arguments + '(#:tests? #f)) + (home-page "https://mmtf.rcsb.org/") + (synopsis "C++ API for the Macromolecular Transmission Format") + (description "This package is a library for the +@acronym{MMTF,macromolecular transmission format}, a binary encoding of +biological structures.") + (license license:expat))) + (define with-numpy-1.8 (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8)))) -- 2.29.2 From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 3/6] gnu: Add molequeue. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 25 Jan 2021 21:24:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 46107@debbugs.gnu.org Cc: Kei Kebreau Received: via spool by 46107-submit@debbugs.gnu.org id=B46107.16116097965613 (code B ref 46107); Mon, 25 Jan 2021 21:24:02 +0000 Received: (at 46107) by debbugs.gnu.org; 25 Jan 2021 21:23:16 +0000 Received: from localhost ([127.0.0.1]:40174 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49KO-0001SH-7E for submit@debbugs.gnu.org; Mon, 25 Jan 2021 16:23:16 -0500 Received: from mout01.posteo.de ([185.67.36.65]:41764) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49KM-0001Ru-DM for 46107@debbugs.gnu.org; Mon, 25 Jan 2021 16:23:14 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id B0DBD160060 for <46107@debbugs.gnu.org>; Mon, 25 Jan 2021 22:23:08 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1611609788; bh=uKTkfNhf3pgr0KIfDm7eM7lOafR2P6bkQSCXu0DdHJo=; h=From:To:Cc:Subject:Date:From; b=AsVS/BlsvyqTkSApsjXroGFhXy1yU8Hdajje2fjqVXSu+15NW1sIr2nVuBF53M5Zu /M10J1AyF1In/qIpHCbEvfCIBxCc+h5X6zQiwk02qWknfMz2q4rlr04Olo2IJlXPoH 7xFXNEAc+Tm6n3sULOLSIWEvqfqvbJQBWsenHMiuGnUlllWDiIsaHPbKzB2Wav3n6z 9AG9cDrGXMPbjUQzN2KAxTSr5kCoc0dL9a9OIWHcbaaLoPErA/PwIx5gn3dDMIrPSB wgcH20ERggODd6WeYvBYvmNxZMJYhZHApho02uFZ4M1s2KXWArpt4zzL3pBCEP3lYi ntPYU76dqDnyQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4DPjWv10GCz6tm6; Mon, 25 Jan 2021 22:23:06 +0100 (CET) From: Kei Kebreau Date: Mon, 25 Jan 2021 16:22:45 -0500 Message-Id: <20210125212248.4749-2-kkebreau@posteo.net> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20210125212248.4749-1-kkebreau@posteo.net> References: <20210125212248.4749-1-kkebreau@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/chemistry.scm (molequeue): New variable. --- gnu/packages/chemistry.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 4ac7a90c87..2b54df564e 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -267,6 +267,35 @@ analogy is that InChI is the bar-code for chemistry and chemical structures.") biological structures.") (license license:expat))) +(define-public molequeue + (package + (name "molequeue") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/OpenChemistry/molequeue/" + "releases/download/" version "/molequeue-" + version ".tar.bz2")) + (sha256 + (base32 + "1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998")))) + (build-system cmake-build-system) + (inputs + `(("qtbase" ,qtbase))) + ;; TODO: Enable tests. + (arguments + '(#:tests? #f)) + (home-page "https://www.openchemistry.org/projects/molequeue/") + (synopsis "Application for coordinating computational jobs") + (description "MoleQueue is a system-tray resident desktop application for +abstracting, managing, and coordinating the execution of tasks both locally and + on remote computational resources. Users can set up local and remote queues +that describe where the task will be executed. Each queue can have programs, +with templates to facilitate the execution of the program. Input files can be +staged, and output files collected using a standard interface.") + (license license:bsd-3))) + (define with-numpy-1.8 (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8)))) -- 2.29.2 From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 4/6] gnu: Add libmsym. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 25 Jan 2021 21:24:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 46107@debbugs.gnu.org Cc: Kei Kebreau Received: via spool by 46107-submit@debbugs.gnu.org id=B46107.16116098015634 (code B ref 46107); Mon, 25 Jan 2021 21:24:03 +0000 Received: (at 46107) by debbugs.gnu.org; 25 Jan 2021 21:23:21 +0000 Received: from localhost ([127.0.0.1]:40178 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49KS-0001Sn-Lk for submit@debbugs.gnu.org; Mon, 25 Jan 2021 16:23:20 -0500 Received: from mout01.posteo.de ([185.67.36.65]:33869) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49KO-0001Rw-1k for 46107@debbugs.gnu.org; Mon, 25 Jan 2021 16:23:16 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 6640216005C for <46107@debbugs.gnu.org>; Mon, 25 Jan 2021 22:23:10 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1611609790; bh=cmCeqJ4A0++XTHEkZi9sQtrw4g/ynTvaNNX7wV7qZp8=; h=From:To:Cc:Subject:Date:From; b=o3JGu8zZqsjHpowNUMduknN7IM6DktSONsTIvQSPDs17+fV2zUBms6cNQr3CKG8vg aEVsaXRzdJg+IBrLT8qNy7IyBw1DmM52tNOwxOqo0lEuxl1x7mxxe2HNdn/2PMWAkC f6mXac8R/SpaUFyWN7bZSm9uwfiSBBynytaPrkW0i4zgTkG2uVptRAmrSpsCOABRS5 AexVnx/UOtIw2KCgsJNSWWHr9B1cOfpvWYWSbNkmMPOwrgpoi8PdbIVgp0j0A2GKG+ LTvkX8QAHTcftpb8CSd36Twj9Jkty8q8xtvO4TvDZxWMcOZeKcGgknBV2bQTv4jRVS saqbnaLSVPPuQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4DPjWx1Lr5z6tm6; Mon, 25 Jan 2021 22:23:09 +0100 (CET) From: Kei Kebreau Date: Mon, 25 Jan 2021 16:22:46 -0500 Message-Id: <20210125212248.4749-3-kkebreau@posteo.net> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20210125212248.4749-1-kkebreau@posteo.net> References: <20210125212248.4749-1-kkebreau@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/chemistry.scm (libmsym): New variable. --- gnu/packages/chemistry.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 2b54df564e..73aed08d43 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -242,6 +242,30 @@ analogy is that InChI is the bar-code for chemistry and chemical structures.") "file://LICENCE" "See LICENCE in the distribution.")))) +(define-public libmsym + (package + (name "libmsym") + (version "0.2.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mcodev31/libmsym") + (commit (string-append "v" version)))) + (sha256 + (base32 + "0a9j28irdsr461qpzlc9z1yjyb9kp64fh5zw7ylspc9zn3189qwk")) + (file-name (git-file-name name version)))) + (build-system cmake-build-system) + (arguments + '(#:configure-flags '("-DBUILD_SHARED_LIBS=ON") + #:tests? #f)) ; no check target + (home-page "https://github.com/mcodev31/libmsym") + (synopsis "C library dealing with point group symmetry in molecules") + (description "libmsym is a C library dealing with point group symmetry in +molecules.") + (license license:expat))) + (define-public mmtf-cpp (package (name "mmtf-cpp") -- 2.29.2 From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 5/6] gnu: Add avogadrolibs. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 25 Jan 2021 21:24:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 46107@debbugs.gnu.org Cc: Kei Kebreau Received: via spool by 46107-submit@debbugs.gnu.org id=B46107.16116098015643 (code B ref 46107); Mon, 25 Jan 2021 21:24:03 +0000 Received: (at 46107) by debbugs.gnu.org; 25 Jan 2021 21:23:21 +0000 Received: from localhost ([127.0.0.1]:40180 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49KS-0001Sp-V3 for submit@debbugs.gnu.org; Mon, 25 Jan 2021 16:23:21 -0500 Received: from mout01.posteo.de ([185.67.36.65]:60536) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49KP-0001Rz-GM for 46107@debbugs.gnu.org; Mon, 25 Jan 2021 16:23:18 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id D5D4F16005F for <46107@debbugs.gnu.org>; Mon, 25 Jan 2021 22:23:11 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1611609791; bh=I32rfNiwQ3esxYHTyBMybQ55FNmIyq4PaGlqLXaFMps=; h=From:To:Cc:Subject:Date:From; b=NoGTTb/cPb/SNFEwgO+xPDBMx6CZRUjUMfzYqkGfGbSVwfueHGXvf8vBkfDrPqi0z Xfj7firwF7g7K1FiT1/jleVQKzTnMXa2ivlaCtRUqGHmPLmMNF/fPwAaWeGcZbuxOn ZcNN7N3nRsoFYdqegKSt7udOKb82LWjtgERoXdE418CSaMBzv1cNAIbUDTQ8CJ1XL1 TUdy8AWqVCQfgA0uk66C3WIYpiw8UFLYWMx6XNOdsjriFfQCGi9SfnU52H547QuoQ+ kmJvoLlP07sE/3lJU5uj9whJSVTsYvKwLkE1Ut/kJdur/Z+Tjxx8j+YUOVu7HAqzhp Li2aXGzLX46bg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4DPjWy50vBz6tm6; Mon, 25 Jan 2021 22:23:10 +0100 (CET) From: Kei Kebreau Date: Mon, 25 Jan 2021 16:22:47 -0500 Message-Id: <20210125212248.4749-4-kkebreau@posteo.net> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20210125212248.4749-1-kkebreau@posteo.net> References: <20210125212248.4749-1-kkebreau@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/chemistry.scm (avogadrolibs): New variable. --- gnu/packages/chemistry.scm | 44 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 73aed08d43..9d4c6f07fa 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -30,6 +30,7 @@ #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) + #:use-module (gnu packages backup) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -44,6 +45,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) + #:use-module (gnu packages serialization) #:use-module (gnu packages sphinx) #:use-module (gnu packages xml) #:use-module (guix build-system cmake) @@ -135,6 +137,48 @@ science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.") (license license:gpl2+))) +(define-public avogadrolibs + (package + (name "avogadrolibs") + (version "1.93.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/OpenChemistry/avogadrolibs") + (commit version))) + (sha256 + (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39")) + (file-name (git-file-name name version)))) + (build-system cmake-build-system) + (native-inputs + `(("eigen" ,eigen) + ("mmtf-cpp" ,mmtf-cpp) + ("msgpack" ,msgpack) + ("googletest" ,googletest) + ("pkg-config" ,pkg-config) + ("pybind11" ,pybind11))) + (inputs + `(("glew" ,glew) + ("libarchive" ,libarchive) + ("libmsym" ,libmsym) + ("molequeue" ,molequeue) + ("python" ,python) + ("spglib" ,spglib) + ("qtbase" ,qtbase))) + (arguments + '(#:configure-flags (list "-DENABLE_TESTING=ON" + (string-append "-DSPGLIB_INCLUDE_DIR=" + (assoc-ref %build-inputs "spglib") + "/include")))) + (home-page "https://www.openchemistry.org/projects/avogadro2/") + (synopsis "Libraries for chemistry, bioinformatics, and related areas") + (description + "Avogadro libraries provide 3D rendering, visualization, analysis and data +processing useful in computational chemistry, molecular modeling, +bioinformatics, materials science, and related areas.") + (license license:bsd-3))) + (define-public domainfinder (package (name "domainfinder") -- 2.29.2 From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 6/6] gnu: Add avogadro2. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 25 Jan 2021 21:24:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 46107@debbugs.gnu.org Cc: Kei Kebreau Received: via spool by 46107-submit@debbugs.gnu.org id=B46107.16116098015650 (code B ref 46107); Mon, 25 Jan 2021 21:24:03 +0000 Received: (at 46107) by debbugs.gnu.org; 25 Jan 2021 21:23:21 +0000 Received: from localhost ([127.0.0.1]:40182 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49KT-0001Sy-7w for submit@debbugs.gnu.org; Mon, 25 Jan 2021 16:23:21 -0500 Received: from mout01.posteo.de ([185.67.36.65]:42067) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49KR-0001S2-Gp for 46107@debbugs.gnu.org; Mon, 25 Jan 2021 16:23:20 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id BA13A16005F for <46107@debbugs.gnu.org>; Mon, 25 Jan 2021 22:23:13 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1611609793; bh=TGciOsk6S6nOxiv6GIDYXyb399JsXl710pwTCQbt7Lw=; h=From:To:Cc:Subject:Date:From; b=YLXr2m92J1LXwPSEGQTTo7h00Vd3EaQtfLox1TtLeP1uoLHvnmuyHOldH0sReIVW5 m158YPhsJcGKzXdDQnpERLs3fzJsmoGFLOll+Acf5Umz2Gh5G8NeuZTPpw96brfuYM JDhhu++xrXud4MRYFy+SAb6rf9Z5baD2ZFJtY62qkhfFfn2H/MWelx289+lasnGqvH jP7pLIk6Wup9Be0+CVmge0wFNqzLx6irV/7j8PkfJ7fTdyfzrfIk9Xo27lt9QC2dgt Z6Y3OzMH6NjTOr7VRhyrAOjlKNzAmnDH8MciwhfnAEirCrIT2rYtv/dNrNbee6BuO7 3kHh5HQ3k0GSw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4DPjX04FFKz6tmG; Mon, 25 Jan 2021 22:23:12 +0100 (CET) From: Kei Kebreau Date: Mon, 25 Jan 2021 16:22:48 -0500 Message-Id: <20210125212248.4749-5-kkebreau@posteo.net> X-Mailer: git-send-email 2.29.2 In-Reply-To: <20210125212248.4749-1-kkebreau@posteo.net> References: <20210125212248.4749-1-kkebreau@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/chemistry.scm (avogadro2): New variable. --- gnu/packages/chemistry.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 9d4c6f07fa..8fe51d79ee 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -179,6 +179,41 @@ processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.") (license license:bsd-3))) +(define-public avogadro2 + (package + (name "avogadro2") + (version "1.93.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/OpenChemistry/avogadroapp") + (commit version))) + (sha256 + (base32 + "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7")) + (file-name (git-file-name name version)))) + (build-system cmake-build-system) + (native-inputs + `(("eigen" ,eigen) + ("pkg-config" ,pkg-config))) + (inputs + `(("avogadrolibs" ,avogadrolibs) + ("hdf5" ,hdf5) + ("molequeue" ,molequeue) + ("qtbase" ,qtbase))) + ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag. + (arguments + '(#:tests? #f)) + (home-page "https://www.openchemistry.org/projects/avogadro2/") + (synopsis "Advanced molecule editor") + (description + "Avogadro 2 is an advanced molecule editor and visualizer designed for use +in computational chemistry, molecular modeling, bioinformatics, materials +science, and related areas. It offers flexible high quality rendering and a +powerful plugin architecture.") + (license license:bsd-3))) + (define-public domainfinder (package (name "domainfinder") -- 2.29.2 From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 1/6] gnu: Add spglib. Resent-From: Leo Famulari Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 25 Jan 2021 22:19:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Kei Kebreau Cc: 46107@debbugs.gnu.org Received: via spool by 46107-submit@debbugs.gnu.org id=B46107.161161308610774 (code B ref 46107); Mon, 25 Jan 2021 22:19:01 +0000 Received: (at 46107) by debbugs.gnu.org; 25 Jan 2021 22:18:06 +0000 Received: from localhost ([127.0.0.1]:40258 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4ABR-0002ni-RQ for submit@debbugs.gnu.org; Mon, 25 Jan 2021 17:18:06 -0500 Received: from wout2-smtp.messagingengine.com ([64.147.123.25]:51961) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4ABP-0002n7-NK for 46107@debbugs.gnu.org; Mon, 25 Jan 2021 17:18:04 -0500 Received: from compute3.internal (compute3.nyi.internal [10.202.2.43]) by mailout.west.internal (Postfix) with ESMTP id B8449EBF; Mon, 25 Jan 2021 17:17:57 -0500 (EST) Received: from mailfrontend2 ([10.202.2.163]) by compute3.internal (MEProxy); Mon, 25 Jan 2021 17:17:57 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=date:from:to:cc:subject:message-id:references:mime-version :content-type:in-reply-to; s=mesmtp; bh=apFMK852/3h0BRGkWUr63R45 hmfLhJEjajQk8K/74lM=; b=YJIR4D+D1lKs8W9TqdZ9ZXl5jmhKDUWqIATpQ3Sx Yg13gByePSWRM7VI5MV1Q/QYULuzowIN+M5TkMhqlj5vOgr2NZJ0541p6Nd+2lwh OoqE9ifWAcJ386Luy+fGrQhih88EmLeU+yYxOypDl6c7cUlDV7lVuWuRFwwHYYq7 8Xc= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:from:in-reply-to :message-id:mime-version:references:subject:to:x-me-proxy :x-me-proxy:x-me-sender:x-me-sender:x-sasl-enc; s=fm1; bh=apFMK8 52/3h0BRGkWUr63R45hmfLhJEjajQk8K/74lM=; b=nwBOgEUAWx+m57aIi9FyD1 Mv7r+T6Uqi3P1YZa2MC5UwzwIabt1C9OXPXZKk2FWg2UHebZbV44XMKPez6GJE6y uvn0N3Zv5jd+yeLtXtu6vuV1e/yEvlCP9WxRkYreip7nzPkEkytZvnJE8yWcjBWl NvEvGin07QZEkgBvzlm/A/uGI8o6p3V4Wqx3goMZ6iVg3/HPL49WEsrDnKcJcoJk 3z29FppbaQbFo0yoVaPAiSyGJLm4qwDc/Cull32rBGJnpAoPU8YR6PrSwj8U0DgX CBTK7q7hXgHkQwT8vXGyDnZgyHThFCHr4G7umV9fqQafZ1VlY4pLj2p4EeVQfD8A == X-ME-Sender: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgeduledrvdefgdduheejucetufdoteggodetrfdotf fvucfrrhhofhhilhgvmecuhfgrshhtofgrihhlpdfqfgfvpdfurfetoffkrfgpnffqhgen uceurghilhhouhhtmecufedttdenucesvcftvggtihhpihgvnhhtshculddquddttddmne cujfgurhepfffhvffukfhfgggtuggjsehttdertddttddvnecuhfhrohhmpefnvghoucfh rghmuhhlrghrihcuoehlvghosehfrghmuhhlrghrihdrnhgrmhgvqeenucggtffrrghtth gvrhhnpeeukeektdffvddtudegjeegtdevhfeufeeivdejiedtieegtdevjedvjeehffev gfenucfkphepuddttddruddurdduieelrdduudeknecuvehluhhsthgvrhfuihiivgeptd enucfrrghrrghmpehmrghilhhfrhhomheplhgvohesfhgrmhhulhgrrhhirdhnrghmvg X-ME-Proxy: Received: from localhost (pool-100-11-169-118.phlapa.fios.verizon.net [100.11.169.118]) by mail.messagingengine.com (Postfix) with ESMTPA id A6C641080057; Mon, 25 Jan 2021 17:17:56 -0500 (EST) Date: Mon, 25 Jan 2021 17:17:55 -0500 From: Leo Famulari Message-ID: References: <20210125212042.4358-1-kkebreau@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20210125212042.4358-1-kkebreau@posteo.net> X-Spam-Score: -0.7 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) On Mon, Jan 25, 2021 at 04:20:42PM -0500, Kei Kebreau wrote: > * gnu/packages/chemistry.scm (spglib): New variable. Thanks! LGTM > + #:phases > + (modify-phases %standard-phases > + (replace 'bootstrap > + (lambda _ > + ;; These files are required by the Makefile, but not provided by > + ;; the developers. > + (for-each (lambda (file) (invoke "touch" file)) > + '("NEWS" "README" "AUTHORS")) > + (invoke "autoreconf" "-vi")))))) Can you file a bug upstream about this? From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 3/6] gnu: Add molequeue. Resent-From: Leo Famulari Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 25 Jan 2021 22:19:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Kei Kebreau Cc: 46107@debbugs.gnu.org Received: via spool by 46107-submit@debbugs.gnu.org id=B46107.161161313910845 (code B ref 46107); Mon, 25 Jan 2021 22:19:02 +0000 Received: (at 46107) by debbugs.gnu.org; 25 Jan 2021 22:18:59 +0000 Received: from localhost ([127.0.0.1]:40262 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4ACJ-0002or-3w for submit@debbugs.gnu.org; Mon, 25 Jan 2021 17:18:59 -0500 Received: from wout2-smtp.messagingengine.com ([64.147.123.25]:33921) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4AC3-0002oR-5e for 46107@debbugs.gnu.org; Mon, 25 Jan 2021 17:18:57 -0500 Received: from compute1.internal (compute1.nyi.internal [10.202.2.41]) by mailout.west.internal (Postfix) with ESMTP id 4F5F63EB; Mon, 25 Jan 2021 17:18:37 -0500 (EST) Received: from mailfrontend2 ([10.202.2.163]) by compute1.internal (MEProxy); Mon, 25 Jan 2021 17:18:37 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=date:from:to:cc:subject:message-id:references:mime-version :content-type:in-reply-to; s=mesmtp; bh=n6ovCeKeXELWDYZtbJpWIdQq rC6MUyTVmxhZ9lser40=; b=0Nk6gvqfZdjxCqMf9alFqwDENl08g1eErAxDfqOP LvoyTyS9n9SAKTfIyNOjUvG5kPGezHv/Vm3EjAR6lK80oFxxdI6wyQJDFYjqKxcP nCjE2fa4cNSNB9f6bqNQ+kruLcmqvdlHAbMMqgaoYHMTmUMimo3pWcMe1uqHZirz QxU= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:from:in-reply-to :message-id:mime-version:references:subject:to:x-me-proxy :x-me-proxy:x-me-sender:x-me-sender:x-sasl-enc; s=fm1; bh=n6ovCe KeXELWDYZtbJpWIdQqrC6MUyTVmxhZ9lser40=; b=ON0D/imnkv0pRylNe2H+oW 8ZkbReKhKLHFKmtOgHLok5sUM0f9vfTb3Pi/gAv44kg7lSewvBZVVcIOrJUKDGUV RaCqrOF/pQ9e4arHHvBi6tRV0HmBcgOIGbAhFpkRwcXIbqm7EBbgJUbbYCuK+Nfu S69wiLAkLM2EMwiBKlmw4Yp+bYrhSmvh/7GT2i4SPMoW1uwb1KuvdgUGtA6EsbZf UQv21qM/BOSqoB8oHckM08RWwFXIIewO3QXukW92BpcMoij2xFRpJIFd+nfQv9dc kUMoJ1TOV6L5uicH05VvTNzrxeVGQXeOtnsl+bthSGqcRZPwEG2echTtltQT7Yog == X-ME-Sender: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgeduledrvdefgdduheejucetufdoteggodetrfdotf fvucfrrhhofhhilhgvmecuhfgrshhtofgrihhlpdfqfgfvpdfurfetoffkrfgpnffqhgen uceurghilhhouhhtmecufedttdenucesvcftvggtihhpihgvnhhtshculddquddttddmne cujfgurhepfffhvffukfhfgggtuggjsehttdertddttddvnecuhfhrohhmpefnvghoucfh rghmuhhlrghrihcuoehlvghosehfrghmuhhlrghrihdrnhgrmhgvqeenucggtffrrghtth gvrhhnpeeukeektdffvddtudegjeegtdevhfeufeeivdejiedtieegtdevjedvjeehffev gfenucfkphepuddttddruddurdduieelrdduudeknecuvehluhhsthgvrhfuihiivgeptd enucfrrghrrghmpehmrghilhhfrhhomheplhgvohesfhgrmhhulhgrrhhirdhnrghmvg X-ME-Proxy: Received: from localhost (pool-100-11-169-118.phlapa.fios.verizon.net [100.11.169.118]) by mail.messagingengine.com (Postfix) with ESMTPA id 92110108005F; Mon, 25 Jan 2021 17:18:36 -0500 (EST) Date: Mon, 25 Jan 2021 17:18:35 -0500 From: Leo Famulari Message-ID: References: <20210125212248.4749-1-kkebreau@posteo.net> <20210125212248.4749-2-kkebreau@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20210125212248.4749-2-kkebreau@posteo.net> X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) On Mon, Jan 25, 2021 at 04:22:45PM -0500, Kei Kebreau wrote: > * gnu/packages/chemistry.scm (molequeue): New variable. > + ;; TODO: Enable tests. > + (arguments > + '(#:tests? #f)) Can you clarify the comment? Even "It's too much work" would be helpful for future readers. From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 6/6] gnu: Add avogadro2. Resent-From: Leo Famulari Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 25 Jan 2021 22:20:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Kei Kebreau Cc: 46107@debbugs.gnu.org Received: via spool by 46107-submit@debbugs.gnu.org id=B46107.161161318510940 (code B ref 46107); Mon, 25 Jan 2021 22:20:01 +0000 Received: (at 46107) by debbugs.gnu.org; 25 Jan 2021 22:19:45 +0000 Received: from localhost ([127.0.0.1]:40269 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4AD3-0002qN-I7 for submit@debbugs.gnu.org; Mon, 25 Jan 2021 17:19:45 -0500 Received: from wout2-smtp.messagingengine.com ([64.147.123.25]:51119) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4AD2-0002qC-9n for 46107@debbugs.gnu.org; Mon, 25 Jan 2021 17:19:44 -0500 Received: from compute3.internal (compute3.nyi.internal [10.202.2.43]) by mailout.west.internal (Postfix) with ESMTP id 6D19DE16; Mon, 25 Jan 2021 17:19:38 -0500 (EST) Received: from mailfrontend2 ([10.202.2.163]) by compute3.internal (MEProxy); Mon, 25 Jan 2021 17:19:38 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=date:from:to:cc:subject:message-id:references:mime-version :content-type:in-reply-to; s=mesmtp; bh=CW+i2UV3drkvxrN7oExnchD2 Fpv2ufGRjHkwQttouMQ=; b=uKku77W/a4w7XcqVpvWoevsLJ0COgVDmVkZLbEyo UF3Ar/tWcNsQ3QFyscbHUQngYOoaJs/pY2eUdTMSBoFXv+YbLCVH3sBwph72EaXW AQZCcoaBNBA0eOrZu6WpK3qMfmTG5FxD5Jy/Td4oHS8DvO2i0EF4Xt7z40sDVI60 A6M= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:from:in-reply-to :message-id:mime-version:references:subject:to:x-me-proxy :x-me-proxy:x-me-sender:x-me-sender:x-sasl-enc; s=fm1; bh=CW+i2U V3drkvxrN7oExnchD2Fpv2ufGRjHkwQttouMQ=; b=eKoL4p1IWZKfqR+wRncACp /iAdncsE4CYQQKR3it738UuWMRYqa6pLxw/dPVLSYmGYmZq505DHGZrmaMKM6uT7 QFDUbEdGiLEIe3w3XHRzKejaksEDOqKWO1DP+OKATPyItSZ1V79WaBbAgpAZJxuB egGztUzWX2xLw8h2Yor+88M+ERl5RTeb+zZyP5Jh05fvKX1+PgcYxUkGaMSy3Z3g lPxyxiyn65FsMXMJZWZUim7YIREgpQd53CTXjUEfjqoGfkQwox3QxuCh1E/6yuBk 7x0qKMGN2vkAkOZxXLs7wrZaLbPePFTvvcteXJq93hte/WsqXHsQtG39dXCGE/9g == X-ME-Sender: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgeduledrvdefgdduheekucetufdoteggodetrfdotf fvucfrrhhofhhilhgvmecuhfgrshhtofgrihhlpdfqfgfvpdfurfetoffkrfgpnffqhgen uceurghilhhouhhtmecufedttdenucesvcftvggtihhpihgvnhhtshculddquddttddmne cujfgurhepfffhvffukfhfgggtuggjsehgtderredttddvnecuhfhrohhmpefnvghoucfh rghmuhhlrghrihcuoehlvghosehfrghmuhhlrghrihdrnhgrmhgvqeenucggtffrrghtth gvrhhnpedukeevgeetkeeltefgiedtjefgjeekffduteehvdfhueekudelieekjeefheff teenucfkphepuddttddruddurdduieelrdduudeknecuvehluhhsthgvrhfuihiivgeptd enucfrrghrrghmpehmrghilhhfrhhomheplhgvohesfhgrmhhulhgrrhhirdhnrghmvg X-ME-Proxy: Received: from localhost (pool-100-11-169-118.phlapa.fios.verizon.net [100.11.169.118]) by mail.messagingengine.com (Postfix) with ESMTPA id 778341080057; Mon, 25 Jan 2021 17:19:37 -0500 (EST) Date: Mon, 25 Jan 2021 17:19:36 -0500 From: Leo Famulari Message-ID: References: <20210125212248.4749-1-kkebreau@posteo.net> <20210125212248.4749-5-kkebreau@posteo.net> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="OD00gEWl1WPpjWIA" Content-Disposition: inline In-Reply-To: <20210125212248.4749-5-kkebreau@posteo.net> X-Spam-Score: -0.7 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) --OD00gEWl1WPpjWIA Content-Type: text/plain; charset=us-ascii Content-Disposition: inline On Mon, Jan 25, 2021 at 04:22:48PM -0500, Kei Kebreau wrote: > * gnu/packages/chemistry.scm (avogadro2): New variable. Thanks a lot for taking care of this! I sent some other comments, but they shouldn't block these patches. LGTM --OD00gEWl1WPpjWIA Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCAAdFiEEsFFZSPHn08G5gDigJkb6MLrKfwgFAmAPQ/gACgkQJkb6MLrK fwiiyBAApfJ8MXICKC6gftKW/9hQSIj2jHin1ndsG7p/mS0EqPwshCfvqAOpYiqL cKQYVEiJprys9bPyLYSNRts+6pLGDI7RL9UCL/8qhCvzj8z8EKvyaQXQTVr7Aq8d /aCwHM+B8DeXJivhIvi48nPPBH1HvbBDLvPSIfqfv5ZsmgSHaY/TRCBwoHnoqscZ zHsjSN4g5diRgnWFu4AyAt5dOa4JVHVYUaHQPbYDwjRzVpP2aK/uf/lFe4T4QGCQ 6ISsnCKQKwc9LKfHY4tLRKDaoy7zKxQZU2siSiJ7L6wh1WiYNbwW4fx56CG7GjdC dJbQy71AmOja8KYqr13RmbtT+dC86Yu7t5ziTbukwJIl7Lo8dyky+1gbTmgQVI4b hvPXXvrzqHVz4kWuNUKJm4Q8599GNI7CLi9PQH+oxSvX5crTci142zKzv6qL0nMD 8mTBRKgDEuexDZGot1HF1G5f2vhndK86bStOTbQVwtq1a8NwgbB2UT/93jlPax/F 2SuDBjm1V/q+qz/VG9diLVaR6SUxP6uR/ei4f2mObLmbFwraYH/guA42QFwsYgpA rPpSEwevHdx1w500CjOxWOzqYUr4n5WDUb/tzElzNS6snQMio+4JQ/JYwD6h9pK3 Mrewqcnyc8GjGyUdaIoUcP6TJszkMxwpGIoZnyAZbNcyB9uUqdo= =JvZz -----END PGP SIGNATURE----- --OD00gEWl1WPpjWIA-- From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 1/6] gnu: Add spglib. Resent-From: Kei Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Jan 2021 03:21:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Leo Famulari Cc: 46107@debbugs.gnu.org Received: via spool by 46107-submit@debbugs.gnu.org id=B46107.161163123730787 (code B ref 46107); Tue, 26 Jan 2021 03:21:01 +0000 Received: (at 46107) by debbugs.gnu.org; 26 Jan 2021 03:20:37 +0000 Received: from localhost ([127.0.0.1]:40525 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4EuC-00080V-Rl for submit@debbugs.gnu.org; Mon, 25 Jan 2021 22:20:37 -0500 Received: from mout02.posteo.de ([185.67.36.66]:32899) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4EuA-00080G-Gd for 46107@debbugs.gnu.org; Mon, 25 Jan 2021 22:20:35 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id DBD2E2400FB for <46107@debbugs.gnu.org>; Tue, 26 Jan 2021 04:20:27 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1611631227; bh=Xa97hUWlrhzO0Tp/gzo2w00RES3FMFBe0652BQF4u0E=; h=Subject:From:To:Cc:Date:From; b=fMzl84yk1cT/8Or6jiT1J54sy+eNXSmxhmsf0vGkyaML9AJm03FdxDRUEAffuNt03 6xJZ2nCdznfNFF+D317BDaDVWdTqPaNYZ0eeL1rtP4gvn9OgTBadLDp9OwMdSJwmBd QvQoCM4eVRW1H5yqKVVvKHk8p/Fl69EP7UBULV0bhEpKMxjnpQBUYHOafQDIU58OEX hsQaMGfzf3MS1watBVEbPXfpwq73Iv1525QpoO5jlggkZQztYmbcj/BBEys87ipjTN /yJQRJw99fkZUI9K5wS63eVLXlxXh2/fve1GX0ZDxbwloC4JD9SM58tPXE3SMMh+qF zJoXNVDfO1VBA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4DPsS90T2tz9rxK; Tue, 26 Jan 2021 04:20:24 +0100 (CET) Message-ID: <1368650a601118e624c5dec06f7c35214de3a453.camel@posteo.net> From: Kei Date: Mon, 25 Jan 2021 22:20:19 -0500 In-Reply-To: References: <20210125212042.4358-1-kkebreau@posteo.net> Content-Type: text/plain; charset="UTF-8" User-Agent: Evolution 3.34.2 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) On Mon, 2021-01-25 at 17:17 -0500, Leo Famulari wrote: > On Mon, Jan 25, 2021 at 04:20:42PM -0500, Kei Kebreau wrote: > > * gnu/packages/chemistry.scm (spglib): New variable. > > Thanks! LGTM > > > + #:phases > > + (modify-phases %standard-phases > > + (replace 'bootstrap > > + (lambda _ > > + ;; These files are required by the Makefile, but not provided > > by > > + ;; the developers. > > + (for-each (lambda (file) (invoke "touch" file)) > > + '("NEWS" "README" "AUTHORS")) > > + (invoke "autoreconf" "-vi")))))) > > Can you file a bug upstream about this? On closer inspection, it seems that the developer is moving to make CMake the main build system. Using the CMake build system, I ran into a known [0] inconsistency [1] between the GNU and CMake build systems used by spglib. I've patched spglib to deal with this for now, with links added in the comments. [0]: https://github.com/spglib/spglib/issues/75 [1]: https://github.com/OpenChemistry/avogadroapp/issues/97 From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 3/6] gnu: Add molequeue. Resent-From: Kei Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 26 Jan 2021 03:22:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Leo Famulari Cc: 46107@debbugs.gnu.org Received: via spool by 46107-submit@debbugs.gnu.org id=B46107.161163128130893 (code B ref 46107); Tue, 26 Jan 2021 03:22:01 +0000 Received: (at 46107) by debbugs.gnu.org; 26 Jan 2021 03:21:21 +0000 Received: from localhost ([127.0.0.1]:40529 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4Euv-00082D-5X for submit@debbugs.gnu.org; Mon, 25 Jan 2021 22:21:21 -0500 Received: from mout02.posteo.de ([185.67.36.66]:37723) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4Eut-000820-Ah for 46107@debbugs.gnu.org; Mon, 25 Jan 2021 22:21:19 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id A33082400FB for <46107@debbugs.gnu.org>; Tue, 26 Jan 2021 04:21:13 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1611631273; bh=Gef/9en9fAlYUoBQyD1LoV2yXvBr0gN1/HhqW2hBTl4=; h=Subject:From:To:Cc:Date:From; b=KRiWd6QxOR+QRxdMlhyMvhuZB50xQZLzarLvOGZ+xENmsd1Adt2KAoHY/ynVFXjqT grLJk2Qh18UpbpCsG9RjXetIlJ1jXnsLgSnfTT9KAM+5P25nhE2qqHHzV4CoSwTcXq ck2uS0LiLc62eEUfDYWQ62z7Xuhkt7K3KxltOvtkcefLEt3m683a6qUVo4g9tVrw0u YmgNtIcdCS0yzTJpmQt8Bh1crkBtbEHMXL4JnrXS6ip8oODbE+df49FTSLMWS8FuDd i0FsM8HymNjZPBdwgB4hdu+EiVCfdbiO68fh6s14jrhcJPpmPxEBEkPaFtvc+GA1QX FjgHp74dkjZxQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4DPsT40cS3z9rxG; Tue, 26 Jan 2021 04:21:11 +0100 (CET) Message-ID: From: Kei Date: Mon, 25 Jan 2021 22:21:09 -0500 In-Reply-To: References: <20210125212248.4749-1-kkebreau@posteo.net> <20210125212248.4749-2-kkebreau@posteo.net> Content-Type: text/plain; charset="UTF-8" User-Agent: Evolution 3.34.2 MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) On Mon, 2021-01-25 at 17:18 -0500, Leo Famulari wrote: > On Mon, Jan 25, 2021 at 04:22:45PM -0500, Kei Kebreau wrote: > > * gnu/packages/chemistry.scm (molequeue): New variable. > > + ;; TODO: Enable tests. > > + (arguments > > + '(#:tests? #f)) > > Can you clarify the comment? Even "It's too much work" would be helpful > for future readers. While I was doing this, I went ahead and enabled all but the failing tests. From unknown Sun Jun 22 00:46:53 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Kei Kebreau Subject: bug#46107: closed (Re: [bug#46107] [PATCH 6/6] gnu: Add avogadro2.) Message-ID: References: <20210125212042.4358-1-kkebreau@posteo.net> X-Gnu-PR-Message: they-closed 46107 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 46107@debbugs.gnu.org Date: Tue, 26 Jan 2021 03:25:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1611631502-31236-1" This is a multi-part message in MIME format... ------------=_1611631502-31236-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #46107: [PATCH 1/6] gnu: Add spglib. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 46107@debbugs.gnu.org. --=20 46107: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D46107 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1611631502-31236-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 46107-done) by debbugs.gnu.org; 26 Jan 2021 03:24:42 +0000 Received: from localhost ([127.0.0.1]:40533 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4Ey9-00087F-Mf for submit@debbugs.gnu.org; Mon, 25 Jan 2021 22:24:41 -0500 Received: from mout02.posteo.de ([185.67.36.66]:34153) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l4Ey7-000870-Rx for 46107-done@debbugs.gnu.org; Mon, 25 Jan 2021 22:24:40 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 35D222400FB for <46107-done@debbugs.gnu.org>; Tue, 26 Jan 2021 04:24:34 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1611631474; bh=Yz014zV32/pBUnYkcLEAF7wnGZuuy286cRLoOSM1pRk=; h=Subject:From:To:Cc:Date:From; b=q28FWvVKR9A3rRmADMRLhBE0dwLHXE2FWZXh5GO/YbzVPm7jLuBMu5YPiIqQsvUJf sWaJhxCpaGvjRzw+hSMbJwDuxg7dSRoFyomEXSyrngg+KQ7WfNMWelOxEhsoipxWn0 b6aRBurCH+/dTE0WBFTFzSqL9SdVuW0fAUc5HgMpIAJ2qZRBPxYoYRPL6gQxGakaL2 FtPgaojBqh9gmuimiOQK4qjafUwIoIYksQWfenXktyH4oujTQukGQQBuHYlrbSaymX O/GdWZ8L8ZuOLeH/xQhZYnc1YTK0QADThdRdJ3jE1WmNX57zb/Czzv2FXX04B5phCE A8Ks5Kxl9gJyw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4DPsXw3K2Gz9rxH; Tue, 26 Jan 2021 04:24:32 +0100 (CET) Message-ID: Subject: Re: [bug#46107] [PATCH 6/6] gnu: Add avogadro2. From: Kei To: Leo Famulari Date: Mon, 25 Jan 2021 22:24:28 -0500 In-Reply-To: References: <20210125212248.4749-1-kkebreau@posteo.net> <20210125212248.4749-5-kkebreau@posteo.net> Content-Type: multipart/signed; micalg="pgp-sha256"; protocol="application/pgp-signature"; boundary="=-E6VJU6eXYDpHoM2sG1OR" User-Agent: Evolution 3.34.2 MIME-Version: 1.0 X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46107-done Cc: 46107-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --=-E6VJU6eXYDpHoM2sG1OR Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable On Mon, 2021-01-25 at 17:19 -0500, Leo Famulari wrote: > On Mon, Jan 25, 2021 at 04:22:48PM -0500, Kei Kebreau wrote: > > * gnu/packages/chemistry.scm (avogadro2): New variable. >=20 > Thanks a lot for taking care of this! I sent some other comments, but > they shouldn't block these patches. >=20 > LGTM Done and done! Thanks for reviewing and commenting. Avogadro is clear for removal, especially since it doesn't seem to build anymore. --=-E6VJU6eXYDpHoM2sG1OR Content-Type: application/pgp-signature; name="signature.asc" Content-Description: This is a digitally signed message part Content-Transfer-Encoding: 7bit -----BEGIN PGP SIGNATURE----- iQJIBAABCAAyFiEEg7ZwOtzKO2lLzi2m5qXuPBlGeg0FAmAPi2wUHGtrZWJyZWF1 QHBvc3Rlby5uZXQACgkQ5qXuPBlGeg1N1RAAiBMgyca5APv8wXzw2MynLkzeoNpc QRkGwfwdc72JYn3DM/bd5hKjOILpXw3a2j/sPon4lUUL1t3IL79JdX9CkHZFXeEA uM5TrFDYAE0vutCEte42WegZsWkuPGDv5Z6XZkWOOHYUUPWAVSlFNj+8y2UWuKGU RCXOZriQUU1J2EoV+Hs981e85+Yq4quTjZPREyqPMlabY9r1mLozOqICT3/gF+dC d6F7ojntsji6ADTbXxdthgo837aTBhxRqUYyk+sY3XGG+Y2bAPFGvvQM+vwgaB1V d2Hn6vC6OnYFLbp6UcUpmi1vjNAtM2k6EK/DzpdILpcfMDFSbqmaA1gzw7qEB0Zy 2WKeUbJNTckRVGOYiVBYf96GosjO+6OnRksOWZfufF8SWVoQ4Wi3aW4ASTyPzL1W mX8XRls1T+sse4RTQ9NL2FnmWi1eMvxbAO5hcT8GIKYkCPANWep5RPvssXYpydFP 4aDvaG4HxH0oKGwYd9D0AnvhI2X47X2xJZjDHLOy4TcBT//gxhIwmZZYrwmqhY3z 2GcHQMTbtuzxGTFZNOApKS8eD6PAo04/N6383nZWHQmJ9T1lui/IEGrKUL0oBYHl E5PkuwNLfef/mb7aQ6bNcl+IBepoBp2bL3ApOfLrfq+F4573xNgeQ5XVkhs1QdZO y9Ab0fZJ4H1A0xE= =+FuT -----END PGP SIGNATURE----- --=-E6VJU6eXYDpHoM2sG1OR-- ------------=_1611631502-31236-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 25 Jan 2021 21:21:05 +0000 Received: from localhost ([127.0.0.1]:40165 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49IH-0001OJ-GD for submit@debbugs.gnu.org; Mon, 25 Jan 2021 16:21:05 -0500 Received: from lists.gnu.org ([209.51.188.17]:43362) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l49IG-0001OC-9B for submit@debbugs.gnu.org; Mon, 25 Jan 2021 16:21:04 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:44336) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1l49IG-0001V4-3R for guix-patches@gnu.org; Mon, 25 Jan 2021 16:21:04 -0500 Received: from mout01.posteo.de ([185.67.36.65]:52676) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1l49ID-0000uf-JX for guix-patches@gnu.org; Mon, 25 Jan 2021 16:21:03 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id E597916005C for ; Mon, 25 Jan 2021 22:20:55 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1611609655; bh=bitKo9bBMdzOGbL+ze5908HzRCu9HcTuRcix0ebQVYw=; h=From:To:Cc:Subject:Date:From; b=OUc+l48YtQNHPyDrZc6xOJg+j3pevCmQz4c9nm1iXKezzhGsyNZ2yR5rB/UKm8zs8 oQpDti/aWTxsIIDY9Qms597dYqJN19dx2ZaCS6IcgT5lsSv+rRX5MbH6nUN0M14PBb PgvNJ+iXi4ZM9I3k8xZn4tiwAaRPAhRlIA+Gyu4kwP0zdNkIvtc/CZCjKyiLylISpn ST7qMz1DDeYU/KTRtaWQFPDUAs6/unWSxGqdkxrYkt9NDTavJXF9gfFhfzKc/foX0c dqlT8hQMgKAFyFZPUTEnRk3BaN0CNj/AD5ksXKkoxhlQR2fW2Hcg/vgYpmaqzoH+Dx 8/Icu/7E9MiyA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4DPjTL0XPcz6tm6; Mon, 25 Jan 2021 22:20:53 +0100 (CET) From: Kei Kebreau To: guix-patches@gnu.org Subject: [PATCH 1/6] gnu: Add spglib. Date: Mon, 25 Jan 2021 16:20:42 -0500 Message-Id: <20210125212042.4358-1-kkebreau@posteo.net> X-Mailer: git-send-email 2.29.2 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=kkebreau@posteo.net; helo=mout01.posteo.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H4=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: Kei Kebreau X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) * gnu/packages/chemistry.scm (spglib): New variable. --- gnu/packages/chemistry.scm | 45 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index ddbf5ca098..7a9b3069fa 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -29,6 +29,7 @@ #:use-module (guix git-download) #:use-module (gnu packages) #:use-module (gnu packages algebra) + #:use-module (gnu packages autotools) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) @@ -464,3 +465,47 @@ chemical data. It's a collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.") (license license:gpl2))) + +(define-public spglib + (package + (name "spglib") + (version "1.16.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/spglib/spglib") + (commit (string-append "v" version)))) + (sha256 + (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws")) + (file-name (git-file-name name version)))) + (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) + (arguments + '(#:test-target "check" + #:phases + (modify-phases %standard-phases + (replace 'bootstrap + (lambda _ + ;; These files are required by the Makefile, but not provided by + ;; the developers. + (for-each (lambda (file) (invoke "touch" file)) + '("NEWS" "README" "AUTHORS")) + (invoke "autoreconf" "-vi")))))) + (home-page "https://spglib.github.io/spglib/index.html") + (synopsis "Library for crystal symmetry search") + (description "Spglib is a library for finding and handling crystal +symmetries written in C. Spglib can be used to: + +@enumerate +@item Find symmetry operations +@item Identify space-group type +@item Wyckoff position assignment +@item Refine crystal structure +@item Find a primitive cell +@item Search irreducible k-points +@end enumerate") + (license license:bsd-3))) -- 2.29.2 ------------=_1611631502-31236-1-- From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 6/6] gnu: Add avogadro2. Resent-From: Leo Famulari Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 29 Jan 2021 01:06:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Kei Cc: 46107-done@debbugs.gnu.org Received: via spool by 46107-done@debbugs.gnu.org id=D46107.161188234215482 (code D ref 46107); Fri, 29 Jan 2021 01:06:02 +0000 Received: (at 46107-done) by debbugs.gnu.org; 29 Jan 2021 01:05:42 +0000 Received: from localhost ([127.0.0.1]:50661 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l5IEI-00041d-6I for submit@debbugs.gnu.org; Thu, 28 Jan 2021 20:05:42 -0500 Received: from wout5-smtp.messagingengine.com ([64.147.123.21]:40035) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l5IEC-00041N-M4 for 46107-done@debbugs.gnu.org; Thu, 28 Jan 2021 20:05:41 -0500 Received: from compute6.internal (compute6.nyi.internal [10.202.2.46]) by mailout.west.internal (Postfix) with ESMTP id D3DD8138A; Thu, 28 Jan 2021 20:05:30 -0500 (EST) Received: from mailfrontend2 ([10.202.2.163]) by compute6.internal (MEProxy); Thu, 28 Jan 2021 20:05:31 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=date:from:to:cc:subject:message-id:references:mime-version :content-type:in-reply-to; s=mesmtp; bh=sh9fR3TdlwWkiX2+v6XpxCV/ 4ZUwi3Ub8/WK5raNh3g=; b=IPIPAY+uWBSm2hPBntwYziEK6w8lGMBAJk9wQ2Cy eG6l9+SEVg9dfWFMsXT03E/CvkJccKBHltkvMRGz4LJow1S4xGxY2WrldstGeftL azUQdXCVQqmw18LIbpkw8sStBYioRUew4qiDlDCchzY3vtB5eo8vR6eadeQmir2Z osk= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:from:in-reply-to :message-id:mime-version:references:subject:to:x-me-proxy :x-me-proxy:x-me-sender:x-me-sender:x-sasl-enc; s=fm1; bh=sh9fR3 TdlwWkiX2+v6XpxCV/4ZUwi3Ub8/WK5raNh3g=; b=WuWe3StSACdjVcx+LnJ5PB BFhrVop/UAFS9tCMWs/oIU4Y32G6QOJVc7I5tN3Zuvva+fGvYoV/UuWt4cgZsA9v 8ColNJCtB5we+I1Nx3oaGpf/ty18or5bUHOBWV8Cp2uQgN2CFqmnCuLTCM5Qr4Xd ivukDsOOvXvVjtb1r7p8H0VajOgqFZk7M9B0kjvOQ40dIte3SDgROryo6UK5KEaS fuKAGH6pLJdvyrhq22Y/Txa8O0ms4o6KFoIK4CjF/Dkk7QRD3VC9iZi7t0kpoYBG 0SbRpJ0GeEmbWGj3Ylno7eKttGmA8B4SDyN90x7dxAGgONKqpBegON4803BYaYZQ == X-ME-Sender: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgeduledrfedugddvhecutefuodetggdotefrodftvf curfhrohhfihhlvgemucfhrghsthforghilhdpqfgfvfdpuffrtefokffrpgfnqfghnecu uegrihhlohhuthemuceftddtnecunecujfgurhepfffhvffukfhfgggtuggjsehgtderre dttddvnecuhfhrohhmpefnvghoucfhrghmuhhlrghrihcuoehlvghosehfrghmuhhlrghr ihdrnhgrmhgvqeenucggtffrrghtthgvrhhnpedukeevgeetkeeltefgiedtjefgjeekff duteehvdfhueekudelieekjeefheffteenucfkphepuddttddruddurdduieelrdduudek necuvehluhhsthgvrhfuihiivgeptdenucfrrghrrghmpehmrghilhhfrhhomheplhgvoh esfhgrmhhulhgrrhhirdhnrghmvg X-ME-Proxy: Received: from localhost (pool-100-11-169-118.phlapa.fios.verizon.net [100.11.169.118]) by mail.messagingengine.com (Postfix) with ESMTPA id E5210108005B; Thu, 28 Jan 2021 20:05:29 -0500 (EST) Date: Thu, 28 Jan 2021 20:05:28 -0500 From: Leo Famulari Message-ID: References: <20210125212248.4749-1-kkebreau@posteo.net> <20210125212248.4749-5-kkebreau@posteo.net> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha256; protocol="application/pgp-signature"; boundary="g7UAmzzPu123n0E3" Content-Disposition: inline In-Reply-To: X-Spam-Score: -0.7 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) --g7UAmzzPu123n0E3 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline On Mon, Jan 25, 2021 at 10:24:28PM -0500, Kei wrote: > Done and done! Thanks for reviewing and commenting. Avogadro is clear for > removal, especially since it doesn't seem to build anymore. Do you know if avogradro2 is suitable as a "drop-in" replacement for avogadro? If so, we could mark it as superseded by avogadro2, and then it would be automatically updated in users' profiles when they do `guix pull && guix upgrade`. --g7UAmzzPu123n0E3 Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCAAdFiEEsFFZSPHn08G5gDigJkb6MLrKfwgFAmATX1UACgkQJkb6MLrK fwjUhRAAgMxlACswKDzlR3ph7fCgB7VCN/IWOivmIlg/x/sEU0nvoufDXPhq2eoo RKSxlLUmZkmeg3P4iznhc3Dt5/dunrL4pu/3C5rfEKEym6oqkmzUr95XQshhhtJW wuDg9OYKFvggvR2oaWklsnl+Dsm0wwFTOZheIawA0gp+OA8H9+UlZV45PRltdzG1 bOaIXZBDlM3/Hkw0aXdWLY8wW3IY2Cje2YU+eEUPwPFzhXQfZEL8vqQZI8dsWnrm i1UjN8TTB80ipCSrJleLI7QsGEvVAC02VLKa4PeAhT6/wFJNVnTtLZFoOuf2m0sN gwD8uohsl62uaWNMaHpPhMvTv8Yk1QMrTmvCu31IDhf4kzXQ3zay5FHDo7n3XfkJ pm4cgg/jLUQty/8Pd4w7gcX5lklo3SuA+9SYK3u3XkRORHGcI0cPnSDICFoWzt4t CF7fylqCywQstsm52/qKazD8sJeZshGBviNpoUL14+68Z/Afg9Q9YltwMayXFVi8 bvLzfSQUqTeNkyJZp/dor60R28wyawJ+ueif+/rhI1RnO1PDur9LQ+BviLp/N+eu Ln61GUg9rLH5FMjorX/g4Fvj11wvGeYGS2AoNAvv7D0E6ihz423UE1gnUwiaxEGR Vy3d6Y5TchTt/gbMCzX+jf340p9meOIoXBiA17JiKlSSNFZEUvg= =nmp4 -----END PGP SIGNATURE----- --g7UAmzzPu123n0E3-- From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 6/6] gnu: Add avogadro2. Resent-From: kkebreau@posteo.net Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 29 Jan 2021 16:29:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Leo Famulari Cc: 46107-done@debbugs.gnu.org Received: via spool by 46107-done@debbugs.gnu.org id=D46107.16119376981558 (code D ref 46107); Fri, 29 Jan 2021 16:29:01 +0000 Received: (at 46107-done) by debbugs.gnu.org; 29 Jan 2021 16:28:18 +0000 Received: from localhost ([127.0.0.1]:52837 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l5Wd7-0000P2-TN for submit@debbugs.gnu.org; Fri, 29 Jan 2021 11:28:18 -0500 Received: from mout01.posteo.de ([185.67.36.65]:44100) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l5Wd5-0000O6-RX for 46107-done@debbugs.gnu.org; Fri, 29 Jan 2021 11:28:17 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 39029160060 for <46107-done@debbugs.gnu.org>; Fri, 29 Jan 2021 17:28:09 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1611937689; bh=sKX8O2+xOr0HDi/7e9FlJxi0Odwv/q4ObQs3B5BHGPU=; h=Date:From:To:Cc:Subject:From; b=pXTO6PiUPuQxExlVoBP5ohL9q3glFihs0eT0ek/1ZPQXSTZkFjNBNrj3kd/nwy1gT G2g/zCOrwOcG9aqb8INpDoZk+YUqrZuBJO1jW3qwG2tjkXff5YOv6pC1sHXUX1CHht JOYkesk//2296mlM+XzqWi7kqaDjkQcnStBfPMZ5gE9HAPoTjvi6JjuSh0mK/L3kGl qtTpmzjnWjbNgAl//grfKNodsqqPT6zeuFBTGyeZh6WHP3WT6yObTB6ExznICQfsdo nmuwnuVSVUpaMtCWR0gYvPWV3ktg6/PjjXZAX9SdqcErt1VgZNwD9G5rqi4d45COfb Mx2zTpjTuQ3EA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4DS2nh49yXz9rxM; Fri, 29 Jan 2021 17:28:08 +0100 (CET) MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII; format=flowed Content-Transfer-Encoding: 7bit Date: Fri, 29 Jan 2021 11:28:08 -0500 From: kkebreau@posteo.net In-Reply-To: References: <20210125212248.4749-1-kkebreau@posteo.net> <20210125212248.4749-5-kkebreau@posteo.net> Message-ID: <5d4c2474cdc539f2792e70b0dbcf7fc4@posteo.net> X-Sender: kkebreau@posteo.net User-Agent: Posteo Webmail X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) On 2021-01-28 20:05, Leo Famulari wrote: > On Mon, Jan 25, 2021 at 10:24:28PM -0500, Kei wrote: >> Done and done! Thanks for reviewing and commenting. Avogadro is >> clear for >> removal, especially since it doesn't seem to build anymore. > > Do you know if avogradro2 is suitable as a "drop-in" replacement for > avogadro? If so, we could mark it as superseded by avogadro2, and then > it would be automatically updated in users' profiles when they do `guix > pull && guix upgrade`. I think so. Development efforts seem to have been focused on Avogadro 2 for several years now, with little or no maintenance of the original Avogadro. This 2018 community survey [0] indicates the developers' full commitment to Avogadro 2, so marking it as superseding avogadro is recommended. [0]: https://avogadro.cc/news/community-survey-results/ From unknown Sun Jun 22 00:46:53 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46107] [PATCH 6/6] gnu: Add avogadro2. Resent-From: Leo Famulari Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 29 Jan 2021 20:21:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46107 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: kkebreau@posteo.net Cc: 46107-done@debbugs.gnu.org Received: via spool by 46107-done@debbugs.gnu.org id=D46107.16119516341416 (code D ref 46107); Fri, 29 Jan 2021 20:21:01 +0000 Received: (at 46107-done) by debbugs.gnu.org; 29 Jan 2021 20:20:34 +0000 Received: from localhost ([127.0.0.1]:53023 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l5aFu-0000Mm-1m for submit@debbugs.gnu.org; Fri, 29 Jan 2021 15:20:34 -0500 Received: from out4-smtp.messagingengine.com ([66.111.4.28]:46487) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1l5aFr-0000MY-Bw for 46107-done@debbugs.gnu.org; Fri, 29 Jan 2021 15:20:32 -0500 Received: from compute3.internal (compute3.nyi.internal [10.202.2.43]) by mailout.nyi.internal (Postfix) with ESMTP id 65D0F5C036A; Fri, 29 Jan 2021 15:20:25 -0500 (EST) Received: from mailfrontend1 ([10.202.2.162]) by compute3.internal (MEProxy); Fri, 29 Jan 2021 15:20:25 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=famulari.name; h=date:from:to:cc:subject:message-id:references:mime-version :content-type:in-reply-to; s=mesmtp; bh=0ouc6+pAo4FNEPASSD+Hpl3u PY88J/bwSTu7vahADt0=; b=jKqvGmCKux/MxX2T+xNPo5oMQINdtzqxKvJAA4r1 Uei1Oq3ZJTVqLowL7e4tz9Mr+RzNi3oajByEQo1a0EpARw7Coakr/TSXNcZlXBLp Ke0NTGOiKj+qjriuOMPgR0sbuy3VUi+3HvkkZvKBbUhCRzfByuiD3dPF2YEMHyns Z2g= DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d= messagingengine.com; h=cc:content-type:date:from:in-reply-to :message-id:mime-version:references:subject:to:x-me-proxy :x-me-proxy:x-me-sender:x-me-sender:x-sasl-enc; s=fm1; bh=0ouc6+ pAo4FNEPASSD+Hpl3uPY88J/bwSTu7vahADt0=; b=KhCb4HkCdojQcnyJfiOFSc QwINDmShL2kFQD1fZo4lH1Xq/7DIc4j/rjdPgWhvCXNEdo/Wvy9Whmy8XxC7ZRgX AlZuQpARS20a4Z7EiKCaz1yx/li2LEL+i+KV/m9U752yGFHDeifV0eyR76v6eH0u rfAiLyi8rLYeyK3PQg0TQRNAy3MC52GUuUyMHhRj1MxAkYSDB8GRprbWYU+p2yBZ ZCHIEYaj4es1YtIPZ+CcLDhOqlb8Um9+AknbnYTFGgtDwmxLpRtr36QIXzbI46uB yEzhj9CyKZlfW8Vl5DGxaf6LkqSAwPj/5dEo4DwxA6M5mHvP3Z1pZEEwopZ4y5WQ == X-ME-Sender: X-ME-Proxy-Cause: gggruggvucftvghtrhhoucdtuddrgeduledrfedvgddufeejucetufdoteggodetrfdotf fvucfrrhhofhhilhgvmecuhfgrshhtofgrihhlpdfqfgfvpdfurfetoffkrfgpnffqhgen uceurghilhhouhhtmecufedttdenucenucfjughrpeffhffvuffkfhggtggujgesthdtre dttddtvdenucfhrhhomhepnfgvohcuhfgrmhhulhgrrhhiuceolhgvohesfhgrmhhulhgr rhhirdhnrghmvgeqnecuggftrfgrthhtvghrnhepueekkedtffdvtddugeejgedtvefhue efiedvjeeitdeigedtveejvdejheffvefgnecukfhppedutddtrdduuddrudeiledruddu keenucevlhhushhtvghrufhiiigvpedtnecurfgrrhgrmhepmhgrihhlfhhrohhmpehlvg hosehfrghmuhhlrghrihdrnhgrmhgv X-ME-Proxy: Received: from localhost (pool-100-11-169-118.phlapa.fios.verizon.net [100.11.169.118]) by mail.messagingengine.com (Postfix) with ESMTPA id A56C2240057; Fri, 29 Jan 2021 15:20:24 -0500 (EST) Date: Fri, 29 Jan 2021 15:20:23 -0500 From: Leo Famulari Message-ID: References: <20210125212248.4749-1-kkebreau@posteo.net> <20210125212248.4749-5-kkebreau@posteo.net> <5d4c2474cdc539f2792e70b0dbcf7fc4@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <5d4c2474cdc539f2792e70b0dbcf7fc4@posteo.net> X-Spam-Score: -0.7 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.7 (-) On Fri, Jan 29, 2021 at 11:28:08AM -0500, kkebreau@posteo.net wrote: > I think so. Development efforts seem to have been focused on Avogadro 2 for > several years now, with little or no maintenance of the original Avogadro. > This > 2018 community survey [0] indicates the developers' full commitment to > Avogadro 2, so marking it as superseding avogadro is recommended. Since avogadro doesn't build, I decided to remove it rather than mark it as superseded. Removed with commit 42008264d9fff544ee00c3c109093472b8a92bd2