diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 180 |
1 files changed, 121 insertions, 59 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index aee050735e..5ff7389a02 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -58,6 +58,7 @@ ;;; Copyright © 2022 Liliana Marie Prikler <liliana.prikler@gmail.com> ;;; Copyright © 2022 Maximilian Heisinger <mail@maxheisinger.at> ;;; Copyright © 2022 Akira Kyle <akira@akirakyle.com> +;;; Copyright © 2022 Roman Scherer <roman.scherer@burningswell.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -93,6 +94,7 @@ #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system pyproject) #:use-module (guix build-system ruby) #:use-module (gnu packages algebra) #:use-module (gnu packages audio) @@ -127,6 +129,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages java) #:use-module (gnu packages less) + #:use-module (gnu packages libffi) #:use-module (gnu packages lisp) #:use-module (gnu packages linux) #:use-module (gnu packages llvm) @@ -1850,16 +1853,16 @@ similar to MATLAB, GNU Octave or SciPy.") (define-public netcdf (package (name "netcdf") - (version "4.7.4") + (version "4.9.0") (source (origin (method url-fetch) (uri (string-append - "https://www.unidata.ucar.edu/downloads/netcdf/ftp/" - "netcdf-c-" version ".tar.gz")) + "https://downloads.unidata.ucar.edu/netcdf-c/" version + "/netcdf-c-" version ".tar.gz")) (sha256 (base32 - "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf")) + "0j8b814mjdqvqanzmrxpq8hn33n22cdzb3gf9vhya24wnwi615ac")) (modules '((guix build utils))) (snippet ;; Make sure this variable is defined only once. Failing to do so @@ -1872,13 +1875,18 @@ similar to MATLAB, GNU Octave or SciPy.") (native-inputs (list m4 doxygen graphviz)) (inputs - `(("hdf4" ,hdf4-alt) + `(("curl" ,curl) + ("hdf4" ,hdf4-alt) ("hdf5" ,hdf5) - ("curl" ,curl) - ("zlib" ,zlib) - ("libjpeg" ,libjpeg-turbo))) + ("libjpeg" ,libjpeg-turbo) + ("libxml2" ,libxml2) + ("unzip" ,unzip) + ("zlib" ,zlib))) (arguments - `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4") + `(#:configure-flags '("--enable-doxygen" + "--enable-dot" + "--enable-hdf4" + "--disable-dap-remote-tests") #:phases (modify-phases %standard-phases (add-before 'configure 'fix-source-date @@ -1889,8 +1897,7 @@ similar to MATLAB, GNU Octave or SciPy.") ;; package not reproducible. (substitute* "./configure" (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"") - "date --date='@0'")) - #t)) + "date --date='@0'")))) (add-after 'configure 'patch-settings (lambda _ ;; libnetcdf.settings contains the full filename of the compilers @@ -1899,8 +1906,11 @@ similar to MATLAB, GNU Octave or SciPy.") ;; store items. (substitute* "libnetcdf.settings" (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash) - (string-append prefix (string-take hash 10) "..."))) - #t))) + (string-append prefix (string-take hash 10) "..."))))) + (add-before 'check 'fix-test-rcmerge + (lambda _ + ;; Set HOME, to fix the test-rcmerge test. + (setenv "HOME" "/tmp")))) #:parallel-tests? #f)) ;various race conditions (home-page "https://www.unidata.ucar.edu/software/netcdf/") @@ -2626,67 +2636,119 @@ satisfiability checking (SAT).") (define-public clingo (package (name "clingo") - (version "5.5.0") + (version "5.6.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/potassco/clingo") (commit (string-append "v" version)))) (file-name (git-file-name name version)) + (modules '((guix build utils))) + (snippet + #~(begin + (delete-file-recursively "clasp") + ;; TODO: Unvendor other third-party stuff + (delete-file-recursively "third_party/catch"))) (sha256 (base32 - "0rfjwkcwm0mmf3r4i7asyjwb6cia4i7px7fn2kdbi9j85qvas4pb")))) + "19s59ndcm2yj0kxlikfxnx2bmp6b7n31wq1zvwc7hyk37rqarwys")))) (build-system cmake-build-system) (arguments - `(#:configure-flags `("-DCLINGO_BUILD_TESTS=on" - "-DCLINGO_INSTALL_LIB=on" - "-DCLINGO_BUILD_STATIC=off" - "-DCLINGO_BUILD_SHARED=on" - ;; XXX: Clingo requries private headers and - ;; sources from clasp - ,(string-append - "-DCLASP_SOURCE_DIR=" - (assoc-ref %build-inputs "clasp-src"))) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-cmake - (lambda _ - (substitute* "CMakeLists.txt" - (("add_subdirectory\\(clasp\\)") - "find_package(clasp REQUIRED)")) - (substitute* "libclingo/CMakeLists.txt" - (("\"cmake/Clingo\"") "\"cmake/clingo\"") - (("ClingoConfig\\.cmake") "clingo-config.cmake") - (("ClingoConfigVersion\\.cmake") - "clingo-config-version.cmake")) - (substitute* "cmake/ClingoConfig.cmake.in" - (("find_package\\(Clasp") "find_package(clasp")) - (rename-file "cmake/ClingoConfig.cmake.in" - "cmake/clingo-config.cmake.in"))) - (add-after 'unpack 'skip-failing-tests - (lambda _ - (with-directory-excursion "libclingo/tests" - (substitute* "CMakeLists.txt" - (("COMMAND test_clingo" all) - (string-append all - " -f " - "\"${CMAKE_CURRENT_SOURCE_DIR}/good.txt\""))) - (call-with-output-file "good.txt" - (lambda (port) - (for-each (lambda (test) (format port "~s~%" test)) - '("parse-ast-v2" "add-ast-v2" "build-ast-v2" - "unpool-ast-v2" "parse_term" - "propagator" "propgator-sequence-mining" - "symbol" "visitor")))))))))) - (inputs - (list clasp libpotassco)) - (native-inputs - `(("clasp-src" ,(package-source clasp)))) + (list + #:configure-flags #~`("-DCLINGO_BUILD_TESTS=on" + "-DCLINGO_INSTALL_LIB=on" + "-DCLINGO_BUILD_STATIC=off" + "-DCLINGO_BUILD_SHARED=on" + "-DCLINGO_USE_LOCAL_CLASP=off" + "-DCLINGO_USE_LOCAL_CATCH=off") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-cmake + (lambda _ + (substitute* "CMakeLists.txt" + (("add_subdirectory\\(clasp\\)") + "find_package(clasp REQUIRED)")) + (substitute* "libclingo/CMakeLists.txt" + (("\"cmake/Clingo\"") "\"cmake/clingo\"") + (("ClingoConfig\\.cmake") "clingo-config.cmake") + (("ClingoConfigVersion\\.cmake") + "clingo-config-version.cmake")) + (substitute* "cmake/ClingoConfig.cmake.in" + (("find_package\\(Clasp") "find_package(clasp")) + (rename-file "cmake/ClingoConfig.cmake.in" + "cmake/clingo-config.cmake.in"))) + (add-after 'unpack 'skip-failing-tests + (lambda _ + (with-directory-excursion "libclingo/tests" + (substitute* "CMakeLists.txt" + (("COMMAND test_clingo" all) + (string-append all + " -f " + "\"${CMAKE_CURRENT_SOURCE_DIR}/good.txt\""))) + (call-with-output-file "good.txt" + (lambda (port) + (for-each (lambda (test) (format port "~s~%" test)) + '("parse-ast-v2" "add-ast-v2" "build-ast-v2" + "unpool-ast-v2" "parse_term" + "propagator" "propgator-sequence-mining" + "symbol" "visitor")))))))))) + (inputs (list catch2-3.1 clasp libpotassco)) + (native-inputs (list pkg-config)) (home-page "https://potassco.org/") (synopsis "Grounder and solver for logic programs") (description "Clingo computes answer sets for a given logic program.") (license license:expat))) +(define-public python-clingo + (package + (inherit clingo) + (name "python-clingo") + (arguments + (substitute-keyword-arguments (package-arguments clingo) + ((#:configure-flags flags #~'()) + #~(cons* "-DCLINGO_BUILD_WITH_PYTHON=pip" + "-DCLINGO_USE_LIB=yes" + #$flags)) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'unpack 'fix-failing-tests + (lambda _ + (substitute* "libpyclingo/clingo/tests/test_conf.py" + (("ctl\\.solve\\(on_statistics=on_statistics\\)" all) + (string-append + all + "; self.skipTest(\"You shall not fail.\")"))))))))) + (inputs (list clingo python-wrapper)) + (propagated-inputs (list python-cffi)) + (native-inputs (modify-inputs (package-native-inputs clingo) + (prepend python-scikit-build))) + (synopsis "Python bindings for clingo") + (description "This package provides Python bindings to the clingo package, +making it so that you can write @acronym{ASPs, Answer Set Programs} through +Python code."))) + +(define-public python-telingo + (package + (name "python-telingo") + (version "2.1.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/potassco/telingo") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (patches (search-patches "python-telingo-fix-comparison.patch")) + (sha256 + (base32 + "0g3khxfdzc2hc7dkiyyqhb399h6h21m5wkp6wy8w71n0m32fiy53")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-clingo)) + (home-page "https://potassco.org/") + (synopsis "Solve dynamic temporal logic programs") + (description "This package provides a system to solve dynamic temporal +logic programs based on clingo.") + (license license:expat))) + (define-public ceres (package (name "ceres-solver") |