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Btw etc/committer.scm is broken with this patch so the merger would have to properly format the commits or fix the committer. From 8a4aec3970b8eb31410933b77cd92937dca81309 Mon Sep 17 00:00:00 2001 Message-ID: <8a4aec3970b8eb31410933b77cd92937dca81309.1741272703.git.jakob.kirsch@web.de> From: Jakob Kirsch Date: Thu, 6 Mar 2025 15:51:33 +0100 Subject: [PATCH v1] Update avogadro2 to 1.100 Change-Id: Ia97823f9950a587b52b274b17338102cf4340e71 --- gnu/packages/chemistry.scm | 217 +++++++++++++++++++++++++++++-------- 1 file changed, 170 insertions(+), 47 deletions(-) base-commit: f2229c2afdb32ddba46bce6f37aba812af39eec5 -- 2.48.1 diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index bd27bfad7a..af51fc4d55 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2020 Vincent Legoll ;;; Copyright © 2021 Ricardo Wurmus ;;; Copyright © 2022, 2023, 2024 David Elsing +;;; Copyright © 2025 Jakob Kirsch ;;; ;;; 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 visualization 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 structures") + (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=ON" - (string-append "-DSPGLIB_INCLUDE_DIR=" - (assoc-ref %build-inputs "spglib") - "/include")))) + (list + #:configure-flags + #~(list "-DENABLE_TESTING=ON" + (string-append "-DSPGLIB_INCLUDE_DIR=" + (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 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-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