diff options
Diffstat (limited to 'gnu/packages/chemistry.scm')
| -rw-r--r-- | gnu/packages/chemistry.scm | 175 |
1 files changed, 82 insertions, 93 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index df96a2f5c1..bd27bfad7a 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net> -;;; Copyright © 2022, 2023 David Elsing <david.elsing@posteo.net> +;;; Copyright © 2022, 2023, 2024 David Elsing <david.elsing@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -589,7 +589,7 @@ your colleagues, or to generate pre-rendered animations.") (define-public gemmi (package (name "gemmi") - (version "0.5.7") + (version "0.6.4") (source (origin (method git-fetch) (uri (git-reference @@ -598,7 +598,7 @@ your colleagues, or to generate pre-rendered animations.") (file-name (git-file-name name version)) (sha256 (base32 - "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a")) + "0wciqqswc4p4v4kglfv36gnvyyimqn4lnywdzd0pgrjn443i860y")) (patches (search-patches "gemmi-fix-sajson-types.patch" "gemmi-fix-pegtl-usage.patch")) @@ -625,7 +625,7 @@ your colleagues, or to generate pre-rendered animations.") #~(modify-phases %standard-phases (add-after 'unpack 'patch-includes (lambda _ - (substitute* (list "include/gemmi/sprintf.hpp" + (substitute* (list "src/sprintf.cpp" "include/gemmi/dirwalk.hpp" "include/gemmi/cif.hpp" "include/gemmi/json.hpp" @@ -708,7 +708,12 @@ It can be used for working with #~(list "--enable-check" "--enable-parser-generator" "CXXFLAGS=-std=c++17" - "--enable-doxygen") + "--enable-doxygen" + ;; Some tests rely on replacing malloc with a wrapper which + ;; fails in a controlled way, but this does not work if the call + ;; is replaced. This was fixed upstream, remove once there is a + ;; new release. + "CFLAGS=-fno-builtin-malloc") #:phases #~(modify-phases %standard-phases (add-after 'unpack 'remove-libc++-linking @@ -722,7 +727,7 @@ It can be used for working with (("libfreesasa\\.a") "libfreesasa.la") (("freesasa_LDADD \\+= libfreesasa\\.la" prev) (string-append prev "\nlibfreesasa_la_LIBADD" - " = -ljson-c ${libxml2_LIBS}\n")) + " = -ljson-c -lgemmi_cpp ${libxml2_LIBS}\n")) (("_a_SOURCES") "_la_SOURCES")) (substitute* "configure.ac" (("AC_PROG_INSTALL" inst) @@ -765,7 +770,7 @@ of the algorithms, the calculations give identical results.") (define-public maeparser (package (name "maeparser") - (version "1.3.0") + (version "1.3.1") (source (origin (method git-fetch) (uri (git-reference @@ -774,7 +779,7 @@ of the algorithms, the calculations give identical results.") (file-name (git-file-name name version)) (sha256 (base32 - "1yv4y5hn49fhylziigsg922bb244lb57p69r7vg9q899zd3l5b7l")))) + "0mr5glg4br04ql5grby8yqni9fqq1l1cc75wyc159a1b9lwr7q7r")))) (build-system cmake-build-system) (inputs (list boost zlib)) (home-page "https://github.com/schrodinger/maeparser") @@ -785,7 +790,7 @@ of the algorithms, the calculations give identical results.") (define-public coordgenlibs (package (name "coordgenlibs") - (version "3.0.1") + (version "3.0.2") (source (origin (method git-fetch) (uri (git-reference @@ -794,7 +799,7 @@ of the algorithms, the calculations give identical results.") (file-name (git-file-name name version)) (sha256 (base32 - "0d09x3v38i9y184bml020bq7xizdrdwng38qmdxlplzfhqkjdidv")))) + "1wjaxwaihjy9xm5ys23f5abl50zcar1h9pww5ajdkgygsqy0bavi")))) (build-system cmake-build-system) (arguments (list @@ -812,7 +817,7 @@ emphasis on quality rather than speed.") (define-public yaehmop (package (name "yaehmop") - (version "2022.09.1") + (version "2023.03.1") (source (origin (method git-fetch) (uri (git-reference @@ -821,7 +826,7 @@ emphasis on quality rather than speed.") (file-name (git-file-name name version)) (sha256 (base32 - "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0")) + "18xnxqn8i7vswy3iffapfh9q2iimpnd23ps45hn4xxbs6dqgzprb")) (modules '((guix build utils))) (snippet '(begin @@ -917,90 +922,67 @@ calculations and analyzing the results.") (define-public avalon-toolkit (package (name "avalon-toolkit") - (version "1.2.0") - (source - (origin - (method url-fetch) - (uri (string-append - "mirror://sourceforge/avalontoolkit/" - "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_" - version ".source.tar")) - (sha256 - (base32 - "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv")) - (modules '((guix build utils) (ice-9 ftw))) - (snippet - #~(begin - (delete-file-recursively "../SourceDistribution/java"))))) + (version "2.0.5a") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rohdebe1/ava-formake") + (commit (string-append "AvalonToolkit_" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mfg40y5xc17sm59zdfc5sk22n9zm5zk0z1aw47chvl6hp465szk")) + (patches + (search-patches "avalon-toolkit-rdkit-fixes.patch")) + (modules '((guix build utils) (ice-9 ftw))) + (snippet + #~(begin + (delete-file-recursively "src/main/java") + (delete-file-recursively "src/test/target"))))) (build-system gnu-build-system) (arguments (list - ;; There are no intended tests + ;; There is only one test, which is missing a file #:tests? #f #:phases - #~(let ((programs '("canonizer" "matchtest" "sketch" "smi2mol" "struchk"))) - (modify-phases %standard-phases - (add-after 'unpack 'chdir - (lambda _ (chdir "common"))) - (delete 'configure) - (add-before 'build 'dont-free-static-memory - (lambda _ - (substitute* "reaccsio.c" - (("MyFree\\(.*tempdir\\)" m) - (string-append "/* freeing memory from getenv is bad */" - "// " m))))) - ;; The makefile has incorrect compiler flags and is missing some - ;; object files, so we build it ourselves. - (replace 'build - (lambda _ - (for-each - (lambda (part) - (format #t "Compiling ~a.c ~~> ~a.o~%" part part) - (invoke #$(cc-for-target) "-c" "-fPIC" "-O2" - (string-append part ".c") - "-o" (string-append part ".o"))) - (list "aacheck" "casutils" "denormal" "depictutil" - "didepict" "fixcharges" "forio" "geometry" - "graph" "hashcode" "layout" "local" "pattern" - "perceive" "reaccsio" "rtutils" "set" "shortcut" - "sketch" "ssmatch" "stereo" "symbol_lists" - "symboltable" "utilities")) - (display "Building libavalontoolkit.so\n") - (apply invoke "gcc" "-fPIC" "-shared" "-lm" - "-o" "libavalontoolkit.so" "canonizer.c" "smi2mol.c" - "struchk.c" "patclean.c" (find-files "." "\\.o$")) - ;; patclean is not built here as there is an undeclared - ;; variable in main(). - (for-each - (lambda (program) - (display (string-append "Building " program "\n")) - (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2" - (string-append "-Wl,-rpath=" #$output "/lib") - "-DMAIN" (string-append program ".c") "-o" program)) - programs))) - (replace 'install - (lambda _ - ;; Executables + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda* (#:key parallel-build? #:allow-other-keys) + (mkdir "build") + (mkdir-p "target/executables") + (mkdir-p "target/libraries") + (invoke "make" "programs" "-j" + (if parallel-build? + (number->string (parallel-job-count)) + "1")))) + (replace 'install + (lambda _ + ;; Executables + (let ((programs '("canonizer" "matchtest" "smi2mol" "struchk"))) (for-each (lambda (program) - (install-file program (string-append #$output "/bin"))) - programs) - (for-each - (lambda (name) - (symlink (string-append #$output "/bin/smi2mol") - (string-append #$output "/bin/" name))) - '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf")) - ;; Library - (install-file "libavalontoolkit.so" - (string-append #$output "/lib")) - (for-each - (lambda (file) - (install-file file (string-append #$output - "/include/avalontoolkit"))) - (find-files "." "\\.h$")) - (install-file "../license.txt" - (string-append #$output "/share/doc/" - #$name "-" #$version "/")))))))) + (install-file (string-append "target/executables/" program) + (string-append #$output "/bin"))) + programs)) + (for-each + (lambda (name) + (symlink (string-append #$output "/bin/smi2mol") + (string-append #$output "/bin/" name))) + '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf")) + ;; Library + (install-file "target/libraries/libavalon_tools.a" + (string-append #$output "/lib")) + (install-file "target/libraries/libavalon4rdkit.a" + (string-append #$output "/lib")) + (for-each + (lambda (file) + (install-file file (string-append #$output + "/include/avalontoolkit"))) + (find-files "src/main/C/include" "\\.h$")) + (install-file "license.txt" + (string-append #$output "/share/doc/" + #$name "-" #$version "/"))))))) (home-page "https://sourceforge.net/projects/avalontoolkit/") (synopsis "Tools for SMILES and MOL files and for structure fingerprinting") (description "This package contains a library and programs for @@ -1091,7 +1073,7 @@ other ring topology descriptions.") (define-public rdkit (package (name "rdkit") - (version "2022.03.5") + (version "2023.09.4") (source (origin (method git-fetch) (uri (git-reference @@ -1102,7 +1084,7 @@ other ring topology descriptions.") (file-name (git-file-name name version)) (sha256 (base32 - "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9")) + "1lgcgijlzzwpfxndsdlx13npdfk7hcii11zg25cvpmzhbpn6vyn8")) (patches (search-patches "rdkit-unbundle-external-dependencies.patch")) (modules '((guix build utils))) @@ -1201,7 +1183,10 @@ other ring topology descriptions.") "substructLibraryTest" "pyFeatures" "pythonTestDirML" "pythonTestDirChem" ;; Catching Python exception fails - "pyRanker") "|") + "pyRanker" + ;; Flaky test depending on floating point rounding + "testConrec" + ) "|") ")"))))))))) (inputs (list avalon-toolkit @@ -1218,7 +1203,7 @@ other ring topology descriptions.") (native-inputs (list bison boost - catch2 + catch2-3 eigen flex freesasa @@ -1232,4 +1217,8 @@ other ring topology descriptions.") (description "RDKit is a C++ and Python library for cheminformatics, which includes (among other things) the analysis and modification of molecules in 2D and 3D and descriptor generation for machine learning.") + ;; For 32 bit systems, there is a bug in Boost.Python: + ;; https://github.com/boostorg/python/issues/312. Additionally, several + ;; other test fail. + (supported-systems %64bit-supported-systems) (license license:bsd-3))) |