[bug#76728] New patch series
Commit Message
I've implemented the changes and split it into 3 commits (spglib, avogadrolibs, avogadro2).
From 244dc62d6ce1787dccd45be54a17354f33ba0782 Mon Sep 17 00:00:00 2001
Message-ID: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jakob.kirsch@web.de>
From: Jakob Kirsch <jakob.kirsch@web.de>
Date: Fri, 11 Apr 2025 15:33:14 +0200
Subject: [PATCH 1/3] gnu: spglib: Update to 2.5.0.
* gnu/packages/chemistry.scm (spglib): Update to 2.5.0.
Change-Id: Ia05bb8e2f012fcf4c576db8a6e5d2f8b153493ff
---
gnu/packages/chemistry.scm | 52 +++++++++++++++++++++++++-------------
1 file changed, 34 insertions(+), 18 deletions(-)
base-commit: 172e9a1aa1ee2ef3e557cf46a11e451aa7982983
--
2.49.0
From c8899e851eb85df748f1cab13de88ab2c746fc3a Mon Sep 17 00:00:00 2001
Message-ID: <c8899e851eb85df748f1cab13de88ab2c746fc3a.1744378594.git.jakob.kirsch@web.de>
In-Reply-To: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jakob.kirsch@web.de>
References: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jakob.kirsch@web.de>
From: Jakob Kirsch <jakob.kirsch@web.de>
Date: Fri, 11 Apr 2025 15:34:12 +0200
Subject: [PATCH 2/3] gnu: avogadrolibs: Update to 1.100.0.
* gnu/packages/chemistry.scm (avogadrolibs): Update to 1.100.0.
[inputs]: Add qtsvg-5, avogadro-molecules, avogadro-crystals, avogadro-fragments.
Change-Id: I16693aff5f986f062c4683ca9b64bb2f7321a9d1
---
gnu/packages/chemistry.scm | 70 +++++++++++++++++++++++++++-----------
1 file changed, 50 insertions(+), 20 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 9ef1f72b62..c597d4736a 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -73,7 +73,7 @@ (define-module (gnu packages chemistry)
(define-public avogadrolibs
(package
(name "avogadrolibs")
- (version "1.93.0")
+ (version "1.100.0")
(source
(origin
(method git-fetch)
@@ -81,28 +81,58 @@ (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 `(("glew" ,glew)
+ ("libarchive" ,libarchive)
+ ("libmsym" ,libmsym)
+ ("molequeue" ,molequeue)
+ ("python" ,python)
+ ("spglib" ,spglib)
+ ("qtbase-5" ,qtbase-5)
+ ("qtsvg-5" ,qtsvg-5)
+ ("avogadro-molecules" ,(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"))))
+ ("avogadro-crystals" ,(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"))))
+ ("avogadro-fragments" ,(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"))))))
(arguments
- '(#:configure-flags (list "-DENABLE_TESTING=ON"
- (string-append "-DSPGLIB_INCLUDE_DIR="
- (assoc-ref %build-inputs "spglib")
- "/include"))))
+
+ (list
+ #:configure-flags
+ #~(list "-DENABLE_TESTING=ON")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'symlink
+ (lambda _
+ (begin
+ (symlink (assoc-ref %build-inputs "avogadro-molecules")
+ "../molecules")
+ (symlink (assoc-ref %build-inputs "avogadro-crystals")
+ "../crystals")
+ (symlink (assoc-ref %build-inputs "avogadro-fragments")
+ "../fragments")))))))
(home-page "https://www.openchemistry.org/projects/avogadro2/")
(synopsis "Libraries for chemistry, bioinformatics, and related areas")
(description
--
2.49.0
From 585bdca7666a4cc52e32baa11cdddec04cdd9552 Mon Sep 17 00:00:00 2001
Message-ID: <585bdca7666a4cc52e32baa11cdddec04cdd9552.1744378594.git.jakob.kirsch@web.de>
In-Reply-To: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jakob.kirsch@web.de>
References: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jakob.kirsch@web.de>
From: Jakob Kirsch <jakob.kirsch@web.de>
Date: Fri, 11 Apr 2025 15:35:46 +0200
Subject: [PATCH 3/3] gnu: avogadro2: Update to 1.100.0.
* gnu/packages/chemistry.scm (avogadro2): Update to 1.100.0.
[inputs]: Add qtsvg-5.
[native-inputs]: Add avogadro-i18n.
Change-Id: I9577e27021ca449426d7506589939c050a5d0cfb
---
gnu/packages/chemistry.scm | 40 ++++++++++++++++++++++++++++++--------
1 file changed, 32 insertions(+), 8 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index c597d4736a..d44bfd2334 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -144,7 +144,7 @@ (define-public avogadrolibs
(define-public avogadro2
(package
(name "avogadro2")
- (version "1.93.0")
+ (version "1.100.0")
(source
(origin
(method git-fetch)
@@ -152,17 +152,41 @@ (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 `(("eigen" ,eigen)
+ ("pkg-config" ,pkg-config)
+ ("avogadro-i18n" ,(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"))))))
+ (inputs (list avogadrolibs hdf5 molequeue qtbase-5 qtsvg-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 (assoc-ref %build-inputs "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")))
+ (list "QT_PLUGIN_PATH"
+ 'suffix
+ (list (string-append #$qtsvg-5 "/lib/qt5/plugins")))))))))
(home-page "https://www.openchemistry.org/projects/avogadro2/")
(synopsis "Advanced molecule editor")
(description
--
2.49.0
@@ -477,7 +477,7 @@ (define-public openbabel
(define-public spglib
(package
(name "spglib")
- (version "1.16.0")
+ (version "2.5.0")
(source
(origin
(method git-fetch)
@@ -485,26 +485,42 @@ (define-public spglib
(url "https://github.com/spglib/spglib")
(commit (string-append "v" version))))
(sha256
- (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws"))
+ (base32 "0x5igrqwx7r2shysmi9sqcjg4hpb7hba3ddlwg05z6c57a3ifbqc"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
(arguments
- '(#:test-target "check"
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-header-install-dir
- (lambda _
- ;; As of the writing of this package, CMake and GNU build systems
- ;; install the header to two different location. This patch makes
- ;; the CMake build system's choice of header directory compatible
- ;; with the GNU build system's choice and with what avogadrolibs
- ;; expects.
- ;; See https://github.com/spglib/spglib/issues/75 and the relevant
- ;; part of https://github.com/OpenChemistry/avogadroapp/issues/97.
- (substitute* "CMakeLists.txt"
- (("\\$\\{CMAKE_INSTALL_INCLUDEDIR\\}" include-dir)
- (string-append include-dir "/spglib")))
- #t)))))
+ '(#:tests? #f
+ #:configure-flags '("-DSPGLIB_WITH_TESTS=OFF")
+ #:phases (modify-phases %standard-phases
+ (add-before 'configure 'patch-files (lambda _ (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.*")
+ ""))))
+ (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. This patch makes
+ ;; the CMake build system's choice of header directory compatible
+ ;; with the GNU build system's choice and with what avogadrolibs
+ ;; expects.
+ ;; See https://github.com/spglib/spglib/issues/75 and the relevant
+ ;; part of https://github.com/OpenChemistry/avogadroapp/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