diff options
Diffstat (limited to 'gnu/packages/maths.scm')
-rw-r--r-- | gnu/packages/maths.scm | 176 |
1 files changed, 96 insertions, 80 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index d39292e825..0a9f2ab7fb 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -22,7 +22,7 @@ ;;; Copyright © 2017, 2019, 2022 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Dave Love <me@fx@gnu.org> -;;; Copyright © 2018, 2019, 2020, 2021, 2022 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> +;;; Copyright © 2018, 2019, 2020, 2021, 2022, 2024 Janneke Nieuwenhuizen <janneke@gnu.org> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com> ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com> @@ -1400,19 +1400,19 @@ in the terminal or with an external viewer.") (define-public gnuplot (package (name "gnuplot") - (version "5.4.9") + (version "6.0.1") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" version "/gnuplot-" version ".tar.gz")) (sha256 - (base32 "15vabi30s4ln4vi82csx4nvfms3ik8704rk0prcm9h1xylhs0a53")))) + (base32 "16ipf7m2c2v1cldp3kwxbjj6db6bzy0rkrpp4kzhh61a3866cnp8")))) (build-system gnu-build-system) (native-inputs (list pkg-config (texlive-updmap.cfg))) (inputs - (list cairo gd lua pango readline)) + (list cairo gd libcerf lua pango readline)) (arguments (list #:configure-flags #~(list "--with-qt=no" @@ -1459,7 +1459,7 @@ C++ with a C API. It contains a LU and LLt solver, and a few other things.") (define-public primesieve (package (name "primesieve") - (version "11.1") + (version "12.3") (source (origin (method git-fetch) (uri (git-reference @@ -1468,7 +1468,7 @@ C++ with a C API. It contains a LU and LLt solver, and a few other things.") (file-name (git-file-name name version)) (sha256 (base32 - "0ja3kxvpya7bwrib40hnyahsiiiavf65ppk7i7afvc093b7gg9bg")))) + "1lxvs1jgch0zgpa5axx6zlvgab4rmm3lqpbah75072xpj8ndhhld")))) (build-system cmake-build-system) (arguments (list #:configure-flags #~(list "-DBUILD_STATIC_LIBS=off" @@ -1486,7 +1486,7 @@ C++ with a C API. It contains a LU and LLt solver, and a few other things.") (define-public cminpack (package (name "cminpack") - (version "1.3.8") + (version "1.3.9") (source (origin (method git-fetch) (uri (git-reference @@ -1495,7 +1495,7 @@ C++ with a C API. It contains a LU and LLt solver, and a few other things.") (file-name (git-file-name name version)) (sha256 (base32 - "1bg0954mwry22izsvikpai16pkfp8srz4z34n267bhkmrvvb0zgy")))) + "05cjb54in7kks70rrnmvczwkg4nsxhwyf23abxqdj143zwbz4yyr")))) (build-system cmake-build-system) (arguments (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON"))) @@ -1814,7 +1814,7 @@ extremely large and complex data collections.") (define-public hdf5-1.14 (package (inherit hdf5-1.8) - (version "1.14.0") + (version "1.14.3") (source (origin (method url-fetch) @@ -1828,8 +1828,19 @@ extremely large and complex data collections.") (take (string-split version #\.) 2)) "/src/hdf5-" version ".tar.bz2"))) (sha256 - (base32 "181bdh8hp7v9xqwcby3lknr92lxlicc2hqscba3f5nhf8lrr9rz4")) - (patches (search-patches "hdf5-config-date.patch")))))) + (base32 "05zr11y3bivfwrbvzbky1q2gjf6r7n92cvvdnh5jilbmxljg49cl")) + (patches (search-patches "hdf5-config-date.patch")))) + (arguments + (substitute-keyword-arguments (package-arguments hdf5-1.8) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'configure 'skip-version-test + (lambda _ + ;; Skip test_check_version since the 'patch-settings' phase + ;; modifies the test reference. + (substitute* "test/test_check_version.sh.in" + (("TESTING\\(\\).*" all) + (string-append all "\nSKIP; exit 0\n"))))))))))) (define-public hdf5 ;; Default version of HDF5. @@ -2069,35 +2080,34 @@ Swath).") (license (license:non-copyleft home-page)))) (define-public hdf5-parallel-openmpi - (package/inherit hdf5-1.10 ;use the latest + (package/inherit hdf5-1.14 ;use the latest (name "hdf5-parallel-openmpi") (inputs `(("mpi" ,openmpi) ,@(package-inputs hdf5))) (arguments - (substitute-keyword-arguments (package-arguments hdf5) + (substitute-keyword-arguments (package-arguments hdf5-1.14) ((#:configure-flags flags) - ``("--enable-parallel" - ,@(delete "--enable-cxx" - (delete "--enable-threadsafe" ,flags)))) + #~(cons "--enable-parallel" + (delete "--enable-cxx" + (delete "--enable-threadsafe" #$flags)))) ((#:phases phases) - `(modify-phases ,phases - (add-after 'build 'mpi-setup - ,%openmpi-setup) - (add-before 'check 'patch-tests - (lambda _ - ;; OpenMPI's mpirun will exit with non-zero status if it - ;; detects an "abnormal termination", i.e. any process not - ;; calling MPI_Finalize(). Since the test is explicitly - ;; avoiding MPI_Finalize so as not to have at_exit and thus - ;; H5C_flush_cache from being called, mpirun will always - ;; complain, so turn this test off. - (substitute* "testpar/Makefile" - (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back) - (string-append front back "\n"))) - (substitute* "tools/test/h5diff/testph5diff.sh" - (("/bin/sh") (which "sh"))) - #t)))))) + #~(modify-phases #$phases + (add-after 'build 'mpi-setup + #$%openmpi-setup) + (add-before 'check 'patch-tests + (lambda _ + ;; OpenMPI's mpirun will exit with non-zero status if it + ;; detects an "abnormal termination", i.e. any process not + ;; calling MPI_Finalize(). Since the test is explicitly + ;; avoiding MPI_Finalize so as not to have at_exit and thus + ;; H5C_flush_cache from being called, mpirun will always + ;; complain, so turn this test off. + (substitute* "testpar/Makefile" + (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back) + (string-append front back "\n"))) + (substitute* "tools/test/h5diff/testph5diff.sh" + (("/bin/sh") (which "sh"))))))))) (synopsis "Management suite for data with parallel IO support"))) (define-public hdf5-blosc @@ -3529,7 +3539,8 @@ September 2004}") "--with-openblas=1" (string-append "--with-openblas-dir=" #$(this-package-input "openblas")) - "--with-superlu=1") + "--with-superlu=1" + "--with-debugging=0") #:make-flags ;; Honor (parallel-job-count) for build. Do not use --with-make-np, ;; whose value is dumped to $out/lib/petsc/conf/petscvariables. @@ -3544,6 +3555,11 @@ September 2004}") (let* ((prefix (assoc-ref outputs "out")) (flags `(,(string-append "--prefix=" prefix) ,@configure-flags))) + ;; Sort source files in configure (for reproducibility). + (substitute* "config/gmakegen.py" + (("join\\(srcs\\[lang\\]\\)") + "join(sorted(srcs[lang]))")) + (format #t "build directory: ~s~%" (getcwd)) (format #t "configure flags: ~s~%" flags) (apply invoke "./configure" flags) @@ -3558,8 +3574,8 @@ September 2004}") (substitute* (find-files "." "^petsc(conf|machineinfo).h$") ;; Prevent build directory from leaking into compiled code (((getcwd)) out) - ;; Scrub timestamp for reproducibility - ((".*Libraries compiled on.*") "")) + (("Machine characteristics: Linux-[0-9]+\\.[0-9]+\\.[0-9]+") + "Machine characteristics: Linux-x.x.x")) (substitute* (find-files "." "petscvariables") ;; Do not expose build machine characteristics, set to defaults. (("MAKE_NP = [:digit:]+") "MAKE_NP = 2") @@ -7066,7 +7082,7 @@ evaluates expressions using the standard order of operations.") (define-public xaos (package (name "xaos") - (version "4.2.1") + (version "4.3.2") (source (origin (method git-fetch) (uri (git-reference @@ -7075,53 +7091,53 @@ evaluates expressions using the standard order of operations.") (file-name (git-file-name name version)) (sha256 (base32 - "0maw5am6rrkyjrprfg113zjq37mqj0iaznkg4h2927ff7wrprc94")))) + "0a5n3g1xcsd8k65q5skm4xsdllr3mmkahh4vi59db1l0jv81v06q")))) (build-system gnu-build-system) (native-inputs `(("gettext" ,gettext-minimal) - ("qtbase" ,qtbase-5) - ("qttools-5" ,qttools-5))) + ("qtbase" ,qtbase) + ("qttools" ,qttools))) (inputs (list libx11 zlib libpng gsl)) ;; The upstream project file ("XaoS.pro") and the Makefile it generates are ;; not enough for this package to install properly. These phases fix that. (arguments - `(#:tests? #f ;no "check" target - #:phases - (modify-phases %standard-phases - (add-before 'configure 'make-qt-deterministic - (lambda _ - ;; Make Qt deterministic. - (setenv "QT_RCC_SOURCE_DATE_OVERRIDE" "1") - #t)) - (replace 'configure - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (substitute* "XaoS.pro" - ;; The DESTDIR is originally set to install the xaos binary to - ;; the "bin" folder inside the build directory. Setting make - ;; flags doesn't seem to change this. - (("DESTDIR.*$") - (string-append "DESTDIR=" out "/bin")) - ;; Set the correct path to the lrelease binary. - (("lrelease-qt5") "lrelease")) - (substitute* "src/include/config.h" - (("/usr/share/XaoS") - (string-append out "/share/XaoS"))) - (invoke "qmake")))) - (add-after 'install 'install-data - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (share (string-append out "/share"))) - (mkdir-p share) - (for-each - (lambda (folder) - (copy-recursively folder - (string-append share "/XaoS/" folder))) - '("catalogs" "examples" "tutorial")) - (install-file "xdg/xaos.png" - (string-append share "/pixmaps")) - (install-file "xdg/xaos.desktop" - (string-append share "/applications"))) - #t))))) + (list #:tests? #f ;no "check" target + #:phases + #~(modify-phases %standard-phases + (add-before 'configure 'make-qt-deterministic + (lambda _ + ;; Make Qt deterministic. + (setenv "QT_RCC_SOURCE_DATE_OVERRIDE" "1"))) + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* "XaoS.pro" + ;; The DESTDIR is originally set to install the xaos binary to + ;; the "bin" folder inside the build directory. Setting make + ;; flags doesn't seem to change this. + (("DESTDIR.*$") + (string-append "DESTDIR=" out "/bin")) + (("/usr/local") + out) + ;; Set the correct path to the lrelease binary. + (("lrelease-qt6") "lrelease")) + (substitute* "src/include/config.h" + (("/usr/share/XaoS") + (string-append out "/share/XaoS"))) + (invoke "qmake")))) + (add-after 'install 'install-data + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share"))) + (mkdir-p share) + (for-each + (lambda (folder) + (copy-recursively folder + (string-append share "/XaoS/" folder))) + '("catalogs" "examples" "tutorial")) + (install-file "xdg/xaos.png" + (string-append share "/pixmaps")) + (install-file "xdg/io.github.xaos_project.XaoS.desktop" + (string-append share "/applications")))))))) (synopsis "Real-time fractal zoomer") (description "GNU XaoS is a graphical program that generates fractal patterns and allows you to zoom in and out of them infinitely in a fluid, @@ -7909,7 +7925,7 @@ reduction.") (define-public mcrl2 (package (name "mcrl2") - (version "202206.1") + (version "202307.1") (source (origin (method url-fetch) (uri (string-append @@ -7917,7 +7933,7 @@ reduction.") version ".tar.gz")) (sha256 (base32 - "1rbfyw47bi31qla1sa4fd1npryb5kbdr0vijmdc2gg1zhpqfv0ia")))) + "147002dl3gq2jsk5gcmvw7hj3mfxrpgxwcfda5mfrj26rcxw48fc")))) (inputs (list boost glu mesa qtbase-5)) (build-system cmake-build-system) |