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From 244dc62d6ce1787dccd45be54a17354f33ba0782 Mon Sep 17 00:00:00 2001 Message-ID: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jakob.kirsch@web.de> From: Jakob Kirsch 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: In-Reply-To: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jakob.kirsch@web.de> References: <244dc62d6ce1787dccd45be54a17354f33ba0782.1744378594.git.jakob.kirsch@web.de> From: Jakob Kirsch 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 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 #$qtsvg-5 "/lib/qt5/plugins"))))))))) (home-page "https://www.openchemistry.org/projects/avogadro2/") (synopsis "Advanced molecule editor") (description -- 2.49.0 diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index d05792c56d..9ef1f72b62 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -477,7 +477,7 @@ (define-public openbabel (define-public spglib (package (name "spglib") - (version "1.16.0") + (version "2.5.0") (source (origin (method git-fetch) @@ -485,26 +485,42 @@ (define-public spglib (url "https://github.com/spglib/spglib") (commit (string-append "v" version)))) (sha256 - (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws")) + (base32 "0x5igrqwx7r2shysmi9sqcjg4hpb7hba3ddlwg05z6c57a3ifbqc")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments - '(#:test-target "check" - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-header-install-dir - (lambda _ - ;; As of the writing of this package, CMake and GNU build systems - ;; install the header to two different location. This patch makes - ;; the CMake build system's choice of header directory compatible - ;; with the GNU build system's choice and with what avogadrolibs - ;; expects. - ;; See https://github.com/spglib/spglib/issues/75 and the relevant - ;; part of https://github.com/OpenChemistry/avogadroapp/issues/97. - (substitute* "CMakeLists.txt" - (("\\$\\{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