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The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: Currently working on it, it's still broken for some reason. Content analysis details: (1.3 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 0.0 RCVD_IN_VALIDITY_CERTIFIED_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. [212.227.15.3 listed in sa-trusted.bondedsender.org] 0.0 RCVD_IN_VALIDITY_RPBL_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. 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guix-patches@HIDDEN:bug#76728; Package guix-patches.
Full text available.Received: (at 76728) by debbugs.gnu.org; 8 Apr 2025 11:09:44 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Tue Apr 08 07:09:44 2025 Received: from localhost ([127.0.0.1]:59347 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1u26ps-0003s4-40 for submit <at> debbugs.gnu.org; Tue, 08 Apr 2025 07:09:44 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:41402) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <andreas@HIDDEN>) id 1u26pp-0003rC-5v for 76728 <at> debbugs.gnu.org; Tue, 08 Apr 2025 07:09:41 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 0DA3129C; Tue, 8 Apr 2025 13:09:33 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id 3ZxtgvtLoLcz; Tue, 8 Apr 2025 13:09:32 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 905C155; Tue, 8 Apr 2025 13:09:30 +0200 (CEST) Date: Tue, 8 Apr 2025 13:09:28 +0200 From: Andreas Enge <andreas@HIDDEN> To: Jakob Kirsch <jakob.kirsch@HIDDEN> Subject: Re: PATCH v2 Message-ID: <Z_UD6A2vpK2mu-Zw@jurong> References: <Z8tK7S7oOKiC-QZY@kernelpanicroom> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <Z8tK7S7oOKiC-QZY@kernelpanicroom> X-Rspamd-Server: hera X-Spamd-Bar: +++++ X-Rspamd-Queue-Id: 0DA3129C X-Spamd-Result: default: False [5.40 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[1.000]; BAYES_HAM(-3.00)[99.99%]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; FREEMAIL_TO(0.00)[web.de]; ARC_NA(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; TO_DN_SOME(0.00)[]; FROM_HAS_DN(0.00)[]; FREEMAIL_ENVRCPT(0.00)[gmail.com,web.de]; RCPT_COUNT_THREE(0.00)[4]; FREEMAIL_CC(0.00)[debbugs.gnu.org,posteo.net,gmail.com] X-Spam-Level: ***** X-Rspamd-Action: greylist X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 76728 Cc: bavier@HIDDEN, sharlatanus@HIDDEN, 76728 <at> debbugs.gnu.org X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Hello Jakob, Am Fri, Mar 07, 2025 at 08:37:17PM +0100 schrieb Jakob Kirsch: > I changed some stuff (don't remember what tho). Still WIP. are you still progressing, or should we close this issue? Andreas
guix-patches@HIDDEN:bug#76728; Package guix-patches.
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From: Jakob Kirsch <jakob.kirsch@HIDDEN>
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--mqscGeM6pGqux1Ck
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I changed some stuff (don't remember what tho). Still WIP.
--mqscGeM6pGqux1Ck
Content-Type: text/plain; charset=iso-8859-1
Content-Disposition: attachment;
filename="v2-0001-Update-avogadro2-to-1.100.patch"
Content-Transfer-Encoding: quoted-printable
=46rom 372abf8bb087488d0453cfa0ed82837636466b0e Mon Sep 17 00:00:00 2001
Message-ID: <372abf8bb087488d0453cfa0ed82837636466b0e.1741376160.git.jakob=
.kirsch@HIDDEN>
From: Jakob Kirsch <jakob.kirsch@HIDDEN>
Date: Thu, 6 Mar 2025 15:51:33 +0100
Subject: [PATCH v2] Update avogadro2 to 1.100
Change-Id: Ia97823f9950a587b52b274b17338102cf4340e71
=2D--
gnu/packages/chemistry.scm | 211 ++++++++++++++++++++++++++++---------
1 file changed, 164 insertions(+), 47 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index bd27bfad7a..05eefd52f4 100644
=2D-- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -7,6 +7,7 @@
;;; Copyright =A9 2020 Vincent Legoll <vincent.legoll@HIDDEN>
;;; Copyright =A9 2021 Ricardo Wurmus <rekado@HIDDEN>
;;; Copyright =A9 2022, 2023, 2024 David Elsing <david.elsing@HIDDEN>
+;;; Copyright =A9 2025 Jakob Kirsch <jakob.kirsch@HIDDEN>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -67,13 +68,75 @@ (define-module (gnu packages chemistry)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (guix build-system cmake)
+ #:use-module (guix build-system copy)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python))
+(define-public avogadro-molecules
+ (package
+ (name "avogadro-molecules")
+ (version "1.100")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/openchemistry/molecules")
+ (commit "8a37883")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "00mfx0bwmqazbiklrvaijjd5n4wa5lp3z73291ihm78q0v9dzhl4")))=
)
+ (build-system copy-build-system)
+ (home-page "https://two.avogadro.cc/")
+ (synopsis "Common molecule fragments for visualization in Avogadro")
+ (description
+ "Common molecule fragments including a variety of organic functional=
groups.")
+ (license license:bsd-3)))
+
+(define-public avogadro-crystals
+ (package
+ (name "avogadro-crystals")
+ (version "1.100")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/openchemistry/crystals")
+ (commit "28404bd")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0kcz99q5nfl2v2qmm9cqnbb2c2qqzw79vsnv557i7x64bxsxrw1m")))=
)
+ (build-system copy-build-system)
+ (home-page "https://two.avogadro.cc/")
+ (synopsis
+ "Crystallographic files of common materials, elements, oxides, for v=
isualization in Avogadro")
+ (description
+ "Crystal structures of over 500 common materials, elements, oxides."=
)
+ (license license:bsd-3)))
+
+(define-public avogadro-fragments
+ (package
+ (name "avogadro-fragments")
+ (version "1.100")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/openchemistry/fragments")
+ (commit "c4943b5")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "17l6qmkc25wb0nvic708l25fxiy89b3vfs0x5d40qcnn27bid32n")))=
)
+ (build-system copy-build-system)
+ (home-page "https://two.avogadro.cc/")
+ (synopsis "Molecular fragments for Avogadro")
+ (description
+ "Molecular fragments and inorganic ligands for rapidly building stru=
ctures")
+ (license license:bsd-3)))
+
(define-public avogadrolibs
(package
(name "avogadrolibs")
- (version "1.93.0")
+ (version "1.100.0")
(source
(origin
(method git-fetch)
@@ -81,28 +144,33 @@ (define-public avogadrolibs
(url "https://github.com/OpenChemistry/avogadrolibs")
(commit version)))
(sha256
- (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39"))
+ (base32 "1l9bp3ba8yx9mk2in5v375jzi1w4y7l1xl37xqv869810drgjffc"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
- (native-inputs
- (list eigen
- mmtf-cpp
- googletest
- pkg-config
- pybind11))
- (inputs
- (list glew
- libarchive
- libmsym
- molequeue
- python
- spglib
- qtbase-5))
+ (native-inputs (list eigen mmtf-cpp googletest pkg-config pybind11))
+ (inputs (list glew
+ libarchive
+ libmsym
+ molequeue
+ python
+ spglib
+ qtbase-5
+ qtsvg-5
+ avogadro-molecules
+ avogadro-crystals
+ avogadro-fragments))
(arguments
- '(#:configure-flags (list "-DENABLE_TESTING=3DON"
- (string-append "-DSPGLIB_INCLUDE_DIR=3D"
- (assoc-ref %build-inputs "s=
pglib")
- "/include"))))
+ (list
+ #:configure-flags
+ #~(list "-DENABLE_TESTING=3DON")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'symlink
+ (lambda _
+ (begin
+ (symlink #$avogadro-molecules "../molecules")
+ (symlink #$avogadro-crystals "../crystals")
+ (symlink #$avogadro-fragments "../fragments")))))))
(home-page "https://www.openchemistry.org/projects/avogadro2/")
(synopsis "Libraries for chemistry, bioinformatics, and related areas=
")
(description
@@ -111,10 +179,30 @@ (define-public avogadrolibs
bioinformatics, materials science, and related areas.")
(license license:bsd-3)))
+(define-public avogadro-i18n
+ (package
+ (name "avogadro-i18n")
+ (version "1.100")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/openchemistry/avogadro-i18n")
+ (commit "07bee85")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1vhjh0gilmm90269isrkvyzwwh1cj3bwcxls394psadw1a89mk14")))=
)
+ (build-system copy-build-system)
+ (home-page "https://two.avogadro.cc/")
+ (synopsis "Translations for Avogadro app and libraries")
+ (description
+ "Translations for the Avogadro app and libraries. Contributions and =
edits are always welcome through Weblate.")
+ (license license:bsd-3)))
+
(define-public avogadro2
(package
(name "avogadro2")
- (version "1.93.0")
+ (version "1.100.0")
(source
(origin
(method git-fetch)
@@ -122,17 +210,28 @@ (define-public avogadro2
(url "https://github.com/OpenChemistry/avogadroapp")
(commit version)))
(sha256
- (base32
- "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
+ (base32 "19cd5aqvcw6xj0x1kmzmxl0vrnbhk5ymnl9p2p4d9504ma5k6aim"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
- (native-inputs
- (list eigen pkg-config))
- (inputs
- (list avogadrolibs hdf5 molequeue qtbase-5))
+ (native-inputs (list eigen pkg-config avogadro-i18n))
+ (inputs (list avogadrolibs hdf5 molequeue qtbase-5))
;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
(arguments
- '(#:tests? #f))
+ (list
+ #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'symlink
+ (lambda _
+ (begin
+ (symlink #$avogadro-i18n "../avogadro-i18n"))))
+
+ (add-after 'install 'wrap-program
+ (lambda _
+ (wrap-program (string-append #$output "/bin/avogadro2")
+ (list "PATH"
+ 'suffix
+ (list (string-append #$openbabel "/bin")))))))))
(home-page "https://www.openchemistry.org/projects/avogadro2/")
(synopsis "Advanced molecule editor")
(description
@@ -481,7 +580,7 @@ (define-public openbabel
(define-public spglib
(package
(name "spglib")
- (version "1.16.0")
+ (version "2.5.0")
(source
(origin
(method git-fetch)
@@ -489,26 +588,44 @@ (define-public spglib
(url "https://github.com/spglib/spglib")
(commit (string-append "v" version))))
(sha256
- (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws"))
- (file-name (git-file-name name version))))
+ (base32 "0x5igrqwx7r2shysmi9sqcjg4hpb7hba3ddlwg05z6c57a3ifbqc"))
+ (file-name (git-file-name name version))
+ (modules '((guix build utils)))
+ (snippet #~(begin
+ (substitute* "CMakeLists.txt"
+ (("include\\(cmake/DynamicVersion.cmake\\)")
+ "")
+ (("dynamic_version.*")
+ "")
+ (("PROJECT_PREFIX.*")
+ "")
+ (("FALLBACK_VERSION.*")
+ "set (PROJECT_VERSION 2.5.0")
+ (("\\$\\{PROJECT_VERSION_FULL\\}")
+ "2.5.0")
+ (("\\$\\{GIT_COMMIT\\}")
+ "\"\""))
+ (substitute* "src/CMakeLists.txt"
+ ((".*Spglib_GitHash.*")
+ ""))))))
(build-system cmake-build-system)
(arguments
- '(#:test-target "check"
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-header-install-dir
- (lambda _
- ;; As of the writing of this package, CMake and GNU build sy=
stems
- ;; install the header to two different location. This patch=
makes
- ;; the CMake build system's choice of header directory compa=
tible
- ;; with the GNU build system's choice and with what avogadro=
libs
- ;; expects.
- ;; See https://github.com/spglib/spglib/issues/75 and the re=
levant
- ;; part of https://github.com/OpenChemistry/avogadroapp/issu=
es/97.
- (substitute* "CMakeLists.txt"
- (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir)
- (string-append include-dir "/spglib")))
- #t)))))
+ '(#:tests? #f
+ #:configure-flags '("-DSPGLIB_WITH_TESTS=3DOFF")
+ #:phases (modify-phases %standard-phases
+ (add-after 'unpack 'patch-header-install-dir
+ (lambda _
+ ;; As of the writing of this package, CMake and GNU=
build systems
+ ;; install the header to two different location. T=
his patch makes
+ ;; the CMake build system's choice of header direct=
ory compatible
+ ;; with the GNU build system's choice and with what=
avogadrolibs
+ ;; expects.
+ ;; See https://github.com/spglib/spglib/issues/75 a=
nd the relevant
+ ;; part of https://github.com/OpenChemistry/avogadr=
oapp/issues/97.
+ (substitute* "CMakeLists.txt"
+ (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir=
)
+ (string-append include-dir "/spglib")))
+ #t)))))
(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
base-commit: 9bc4c9f521caab8aa8d88aa948a650945bb55838
=2D-
2.48.1
--mqscGeM6pGqux1Ck--
guix-patches@HIDDEN:bug#76728; Package guix-patches.
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The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: This is still WIP as some things are broken like: * icons don't render * openbabel optimization is broken with DNA Content analysis details: (1.3 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 0.0 RCVD_IN_VALIDITY_RPBL_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. [212.227.17.11 listed in bl.score.senderscore.com] 0.0 RCVD_IN_VALIDITY_CERTIFIED_BLOCKED RBL: ADMINISTRATOR NOTICE: The query to Validity was blocked. See https://knowledge.validity.com/hc/en-us/articles/20961730681243 for more information. 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guix-patches@HIDDEN:bug#76728; Package guix-patches.
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<76728 <at> debbugs.gnu.org>; Thu, 06 Mar 2025 15:53:28 +0100
Date: Thu, 6 Mar 2025 15:53:25 +0100
From: Jakob Kirsch <jakob.kirsch@HIDDEN>
To: 76728 <at> debbugs.gnu.org
Subject: New patch
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--Jjo27NijAr/RneYV
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Since we're rebuilding avogadro2, we might as well update it to the new version.
Btw etc/committer.scm is broken with this patch so the merger would have to properly format the commits or fix the committer.
--Jjo27NijAr/RneYV
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filename="v1-0001-Update-avogadro2-to-1.100.patch"
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=46rom 8a4aec3970b8eb31410933b77cd92937dca81309 Mon Sep 17 00:00:00 2001
Message-ID: <8a4aec3970b8eb31410933b77cd92937dca81309.1741272703.git.jakob=
.kirsch@HIDDEN>
From: Jakob Kirsch <jakob.kirsch@HIDDEN>
Date: Thu, 6 Mar 2025 15:51:33 +0100
Subject: [PATCH v1] Update avogadro2 to 1.100
Change-Id: Ia97823f9950a587b52b274b17338102cf4340e71
=2D--
gnu/packages/chemistry.scm | 217 +++++++++++++++++++++++++++++--------
1 file changed, 170 insertions(+), 47 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index bd27bfad7a..af51fc4d55 100644
=2D-- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -7,6 +7,7 @@
;;; Copyright =A9 2020 Vincent Legoll <vincent.legoll@HIDDEN>
;;; Copyright =A9 2021 Ricardo Wurmus <rekado@HIDDEN>
;;; Copyright =A9 2022, 2023, 2024 David Elsing <david.elsing@HIDDEN>
+;;; Copyright =A9 2025 Jakob Kirsch <jakob.kirsch@HIDDEN>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -67,13 +68,75 @@ (define-module (gnu packages chemistry)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (guix build-system cmake)
+ #:use-module (guix build-system copy)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python))
+(define-public avogadro-molecules
+ (package
+ (name "avogadro-molecules")
+ (version "1.100")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/openchemistry/molecules")
+ (commit "8a37883")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "00mfx0bwmqazbiklrvaijjd5n4wa5lp3z73291ihm78q0v9dzhl4")))=
)
+ (build-system copy-build-system)
+ (home-page "https://two.avogadro.cc/")
+ (synopsis "Common molecule fragments for visualization in Avogadro")
+ (description
+ "Common molecule fragments including a variety of organic functional=
groups.")
+ (license license:bsd-3)))
+
+(define-public avogadro-crystals
+ (package
+ (name "avogadro-crystals")
+ (version "1.100")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/openchemistry/crystals")
+ (commit "28404bd")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0kcz99q5nfl2v2qmm9cqnbb2c2qqzw79vsnv557i7x64bxsxrw1m")))=
)
+ (build-system copy-build-system)
+ (home-page "https://two.avogadro.cc/")
+ (synopsis
+ "Crystallographic files of common materials, elements, oxides, for v=
isualization in Avogadro")
+ (description
+ "Crystal structures of over 500 common materials, elements, oxides."=
)
+ (license license:bsd-3)))
+
+(define-public avogadro-fragments
+ (package
+ (name "avogadro-fragments")
+ (version "1.100")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/openchemistry/fragments")
+ (commit "c4943b5")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "17l6qmkc25wb0nvic708l25fxiy89b3vfs0x5d40qcnn27bid32n")))=
)
+ (build-system copy-build-system)
+ (home-page "https://two.avogadro.cc/")
+ (synopsis "Molecular fragments for Avogadro")
+ (description
+ "Molecular fragments and inorganic ligands for rapidly building stru=
ctures")
+ (license license:bsd-3)))
+
(define-public avogadrolibs
(package
(name "avogadrolibs")
- (version "1.93.0")
+ (version "1.100.0")
(source
(origin
(method git-fetch)
@@ -81,28 +144,39 @@ (define-public avogadrolibs
(url "https://github.com/OpenChemistry/avogadrolibs")
(commit version)))
(sha256
- (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39"))
+ (base32 "1l9bp3ba8yx9mk2in5v375jzi1w4y7l1xl37xqv869810drgjffc"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
- (native-inputs
- (list eigen
- mmtf-cpp
- googletest
- pkg-config
- pybind11))
- (inputs
- (list glew
- libarchive
- libmsym
- molequeue
- python
- spglib
- qtbase-5))
+ (native-inputs (list eigen
+ mmtf-cpp
+ googletest
+ pkg-config
+ pybind11
+ avogadro-molecules
+ avogadro-crystals
+ avogadro-fragments))
+ (inputs (list glew
+ libarchive
+ libmsym
+ molequeue
+ python
+ spglib
+ qtbase-5
+ qtsvg-5))
(arguments
- '(#:configure-flags (list "-DENABLE_TESTING=3DON"
- (string-append "-DSPGLIB_INCLUDE_DIR=3D"
- (assoc-ref %build-inputs "s=
pglib")
- "/include"))))
+ (list
+ #:configure-flags
+ #~(list "-DENABLE_TESTING=3DON"
+ (string-append "-DSPGLIB_INCLUDE_DIR=3D"
+ (assoc-ref %build-inputs "spglib") "/include=
"))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'symlink
+ (lambda _
+ (begin
+ (symlink #$avogadro-molecules "../molecules")
+ (symlink #$avogadro-crystals "../crystals")
+ (symlink #$avogadro-fragments "../fragments")))))))
(home-page "https://www.openchemistry.org/projects/avogadro2/")
(synopsis "Libraries for chemistry, bioinformatics, and related areas=
")
(description
@@ -111,10 +185,30 @@ (define-public avogadrolibs
bioinformatics, materials science, and related areas.")
(license license:bsd-3)))
+(define-public avogadro-i18n
+ (package
+ (name "avogadro-i18n")
+ (version "1.100")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/openchemistry/avogadro-i18n")
+ (commit "07bee85")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1vhjh0gilmm90269isrkvyzwwh1cj3bwcxls394psadw1a89mk14")))=
)
+ (build-system copy-build-system)
+ (home-page "https://two.avogadro.cc/")
+ (synopsis "Translations for Avogadro app and libraries")
+ (description
+ "Translations for the Avogadro app and libraries. Contributions and =
edits are always welcome through Weblate.")
+ (license license:bsd-3)))
+
(define-public avogadro2
(package
(name "avogadro2")
- (version "1.93.0")
+ (version "1.100.0")
(source
(origin
(method git-fetch)
@@ -122,17 +216,28 @@ (define-public avogadro2
(url "https://github.com/OpenChemistry/avogadroapp")
(commit version)))
(sha256
- (base32
- "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
+ (base32 "19cd5aqvcw6xj0x1kmzmxl0vrnbhk5ymnl9p2p4d9504ma5k6aim"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
- (native-inputs
- (list eigen pkg-config))
- (inputs
- (list avogadrolibs hdf5 molequeue qtbase-5))
+ (native-inputs (list eigen pkg-config avogadro-i18n))
+ (inputs (list avogadrolibs hdf5 molequeue qtbase-5))
;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
(arguments
- '(#:tests? #f))
+ (list
+ #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'symlink
+ (lambda _
+ (begin
+ (symlink #$avogadro-i18n "../avogadro-i18n"))))
+
+ (add-after 'install 'wrap-program
+ (lambda _
+ (wrap-program (string-append #$output "/bin/avogadro2")
+ (list "PATH"
+ 'suffix
+ (list (string-append #$openbabel "/bin")))))))))
(home-page "https://www.openchemistry.org/projects/avogadro2/")
(synopsis "Advanced molecule editor")
(description
@@ -481,7 +586,7 @@ (define-public openbabel
(define-public spglib
(package
(name "spglib")
- (version "1.16.0")
+ (version "2.5.0")
(source
(origin
(method git-fetch)
@@ -489,26 +594,44 @@ (define-public spglib
(url "https://github.com/spglib/spglib")
(commit (string-append "v" version))))
(sha256
- (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws"))
- (file-name (git-file-name name version))))
+ (base32 "0x5igrqwx7r2shysmi9sqcjg4hpb7hba3ddlwg05z6c57a3ifbqc"))
+ (file-name (git-file-name name version))
+ (modules '((guix build utils)))
+ (snippet #~(begin
+ (substitute* "CMakeLists.txt"
+ (("include\\(cmake/DynamicVersion.cmake\\)")
+ "")
+ (("dynamic_version.*")
+ "")
+ (("PROJECT_PREFIX.*")
+ "")
+ (("FALLBACK_VERSION.*")
+ "set (PROJECT_VERSION 2.5.0")
+ (("\\$\\{PROJECT_VERSION_FULL\\}")
+ "2.5.0")
+ (("\\$\\{GIT_COMMIT\\}")
+ "\"\""))
+ (substitute* "src/CMakeLists.txt"
+ ((".*Spglib_GitHash.*")
+ ""))))))
(build-system cmake-build-system)
(arguments
- '(#:test-target "check"
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-header-install-dir
- (lambda _
- ;; As of the writing of this package, CMake and GNU build sy=
stems
- ;; install the header to two different location. This patch=
makes
- ;; the CMake build system's choice of header directory compa=
tible
- ;; with the GNU build system's choice and with what avogadro=
libs
- ;; expects.
- ;; See https://github.com/spglib/spglib/issues/75 and the re=
levant
- ;; part of https://github.com/OpenChemistry/avogadroapp/issu=
es/97.
- (substitute* "CMakeLists.txt"
- (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir)
- (string-append include-dir "/spglib")))
- #t)))))
+ '(#:tests? #f
+ #:configure-flags '("-DSPGLIB_WITH_TESTS=3DOFF")
+ #:phases (modify-phases %standard-phases
+ (add-after 'unpack 'patch-header-install-dir
+ (lambda _
+ ;; As of the writing of this package, CMake and GNU=
build systems
+ ;; install the header to two different location. T=
his patch makes
+ ;; the CMake build system's choice of header direct=
ory compatible
+ ;; with the GNU build system's choice and with what=
avogadrolibs
+ ;; expects.
+ ;; See https://github.com/spglib/spglib/issues/75 a=
nd the relevant
+ ;; part of https://github.com/OpenChemistry/avogadr=
oapp/issues/97.
+ (substitute* "CMakeLists.txt"
+ (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir=
)
+ (string-append include-dir "/spglib")))
+ #t)))))
(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
base-commit: f2229c2afdb32ddba46bce6f37aba812af39eec5
=2D-
2.48.1
--Jjo27NijAr/RneYV--
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Date: Tue, 4 Mar 2025 20:16:26 +0100
From: Jakob Kirsch <jakob.kirsch@HIDDEN>
To: 76728 <at> debbugs.gnu.org
Subject: [PATCH] v2
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--Iyl16qkj3h7qFc1d
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
This is the v2 with wrap-program instead of propagated-inputs.
--Iyl16qkj3h7qFc1d
Content-Type: text/plain; charset=us-ascii
Content-Disposition: attachment;
filename="v2-0001-gnu-avogadro2-Update-to-1.93.0.patch"
Content-Transfer-Encoding: quoted-printable
=46rom 5608c37f14b7b5d46f6ac0a31b4f0c073bd186aa Mon Sep 17 00:00:00 2001
Message-ID: <5608c37f14b7b5d46f6ac0a31b4f0c073bd186aa.1741115763.git.jakob=
.kirsch@HIDDEN>
From: Jakob Kirsch <jakob.kirsch@HIDDEN>
Date: Tue, 4 Mar 2025 20:15:05 +0100
Subject: [PATCH v2] gnu: avogadro2: Update to 1.93.0.
* gnu/packages/chemistry.scm (avogadro2): Update to 1.93.0.
Change-Id: Ic133ed59aac11d9f48443c1d297d69060514d01f
=2D--
gnu/packages/chemistry.scm | 20 +++++++++++++-------
1 file changed, 13 insertions(+), 7 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index bd27bfad7a..78fedfd34f 100644
=2D-- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -122,17 +122,23 @@ (define-public avogadro2
(url "https://github.com/OpenChemistry/avogadroapp")
(commit version)))
(sha256
- (base32
- "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
+ (base32 "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
- (native-inputs
- (list eigen pkg-config))
- (inputs
- (list avogadrolibs hdf5 molequeue qtbase-5))
+ (native-inputs (list eigen pkg-config))
+ (inputs (list avogadrolibs hdf5 molequeue qtbase-5))
;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
(arguments
- '(#:tests? #f))
+ (list
+ #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'install 'wrap-program
+ (lambda _
+ (wrap-program (string-append #$output "/bin/avogadro2")
+ (list "PATH"
+ 'suffix
+ (list (string-append #$openbabel "/bin")))))))))
(home-page "https://www.openchemistry.org/projects/avogadro2/")
(synopsis "Advanced molecule editor")
(description
base-commit: c1ec9e8d53da209ba1d6f8466d03180d195d7334
=2D-
2.48.1
--Iyl16qkj3h7qFc1d--
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From: Z572 <z572@HIDDEN>
To: Jakob Kirsch via Guix-patches via <guix-patches@HIDDEN>
Subject: Re: [bug#76728] [PATCH] gnu: avogadro2: fix open babel input
In-Reply-To: <Z8ZNlSc-d6XXvY6_@kernelpanicroom> (Jakob Kirsch via Guix-patches
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Content preview: Jakob Kirsch via Guix-patches via <guix-patches@HIDDEN>
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> avogadro2 needs open babel at runtime so we should add this to the
propagated
inputs. > > [2. text/plain; v1-0001-gnu-avogadro2-Update-to-1.93.0.patch]...
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Content preview: Jakob Kirsch via Guix-patches via <guix-patches@HIDDEN> writes:
> avogadro2 needs open babel at runtime so we should add this to the propagated
inputs. > > [2. text/plain; v1-0001-gnu-avogadro2-Update-to-1.93.0.patch]...
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--=-=-=
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Jakob Kirsch via Guix-patches via <guix-patches@HIDDEN> writes:
> avogadro2 needs open babel at runtime so we should add this to the propagated inputs.
>
> [2. text/plain; v1-0001-gnu-avogadro2-Update-to-1.93.0.patch]...
I think wrapper might be better, if it's just an application.
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From: Z572 <z572@HIDDEN>
To: Jakob Kirsch via Guix-patches via <guix-patches@HIDDEN>
Subject: Re: [bug#76728] [PATCH] gnu: avogadro2: fix open babel input
In-Reply-To: <Z8ZNlSc-d6XXvY6_@kernelpanicroom> (Jakob Kirsch via Guix-patches
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Content preview: Jakob Kirsch via Guix-patches via <guix-patches@HIDDEN>
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> avogadro2 needs open babel at runtime so we should add this to the
propagated
inputs. > > [2. text/plain; v1-0001-gnu-avogadro2-Update-to-1.93.0.patch]...
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> avogadro2 needs open babel at runtime so we should add this to the propagated
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Jakob Kirsch via Guix-patches via <guix-patches@HIDDEN> writes:
> avogadro2 needs open babel at runtime so we should add this to the propagated inputs.
>
> [2. text/plain; v1-0001-gnu-avogadro2-Update-to-1.93.0.patch]...
I think wrapper might be better, if it's just an application.
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guix-patches@HIDDEN:bug#76728; Package guix-patches.
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Date: Tue, 4 Mar 2025 01:47:17 +0100
From: Jakob Kirsch <jakob.kirsch@HIDDEN>
To: guix-patches@HIDDEN
Subject: [PATCH] gnu: avogadro2: fix open babel input
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--CvqVe5i5AIjPvPUz
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avogadro2 needs open babel at runtime so we should add this to the propagated inputs.
--CvqVe5i5AIjPvPUz
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filename="v1-0001-gnu-avogadro2-Update-to-1.93.0.patch"
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=46rom b353ae32e3b160b47ae1b34fe65e79b141caf05f Mon Sep 17 00:00:00 2001
Message-ID: <b353ae32e3b160b47ae1b34fe65e79b141caf05f.1741049088.git.jakob=
.kirsch@HIDDEN>
From: Jakob Kirsch <jakob.kirsch@HIDDEN>
Date: Tue, 4 Mar 2025 01:44:43 +0100
Subject: [PATCH v1] gnu: avogadro2: Update to 1.93.0.
* gnu/packages/chemistry.scm (avogadro2): Update to 1.93.0.
[propagated-inputs]: Add openbabel.
Change-Id: Ia7f02e66d9caced61a6a206076513806bb7b29a9
=2D--
gnu/packages/chemistry.scm | 2 ++
1 file changed, 2 insertions(+)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index bd27bfad7a..46728bb407 100644
=2D-- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -130,6 +130,8 @@ (define-public avogadro2
(list eigen pkg-config))
(inputs
(list avogadrolibs hdf5 molequeue qtbase-5))
+ (propagated-inputs
+ (list openbabel))
;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
(arguments
'(#:tests? #f))
base-commit: 72923a75af53a819f2be9dc4ae3c096aa3147d3f
=2D-
2.48.1
--CvqVe5i5AIjPvPUz--
Jakob Kirsch <jakob.kirsch@HIDDEN>:guix-patches@HIDDEN.
Full text available.guix-patches@HIDDEN:bug#76728; Package guix-patches.
Full text available.
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