diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 313 |
1 files changed, 276 insertions, 37 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 028f0e6ef9..d7ce900682 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Eric Bavier <bavier@posteo.net> ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org> -;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com> ;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il> @@ -35,6 +35,9 @@ ;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2020 Felix Gruber <felgru@posteo.net> +;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in> +;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> +;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz> ;;; ;;; This file is part of GNU Guix. ;;; @@ -62,6 +65,7 @@ #:use-module (guix utils) #:use-module ((guix build utils) #:select (alist-replace)) #:use-module (guix build-system cmake) + #:use-module (guix build-system glib-or-gtk) #:use-module (guix build-system gnu) #:use-module (guix build-system python) #:use-module (guix build-system ruby) @@ -79,6 +83,7 @@ #:use-module (gnu packages dbm) #:use-module (gnu packages documentation) #:use-module (gnu packages elf) + #:use-module (gnu packages file) #:use-module (gnu packages flex) #:use-module (gnu packages fltk) #:use-module (gnu packages fontutils) @@ -86,8 +91,10 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages gd) #:use-module (gnu packages ghostscript) + #:use-module (gnu packages glib) #:use-module (gnu packages graphviz) #:use-module (gnu packages gtk) + #:use-module (gnu packages icu4c) #:use-module (gnu packages image) #:use-module (gnu packages java) #:use-module (gnu packages less) @@ -375,6 +382,81 @@ semiconductors.") (license license:gpl3+) (home-page "https://www.gnu.org/software/dionysus/"))) +(define-public dsfmt + (package + (name "dsfmt") + (version "2.2.3") + (source + (origin + (method url-fetch) + (uri + (string-append + "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/" + "dSFMT-src-" version ".tar.gz")) + (sha256 + (base32 + "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42")) + (modules '((guix build utils))) + ;; Don't distribute html documentation with bundled jquery. + (snippet + '(begin + (delete-file-recursively "html") #t)) + ;; Add patches borrowed from Julia. + (patches + (list + (origin + (method url-fetch) + (uri (string-append + "https://raw.githubusercontent.com/JuliaLang/julia/" + "v1.3.0/deps/patches/dSFMT.c.patch")) + (sha256 (base32 + "09mhv11bms8jsmkmdqvlcgljwhzw3b6n9nncpi2b6dla9798hw2y")) + (file-name "dSFMT.c.patch")) + (origin + (method url-fetch) + (uri (string-append + "https://raw.githubusercontent.com/JuliaLang/julia/" + "v1.3.0/deps/patches/dSFMT.h.patch")) + (sha256 (base32 + "1py5rd0yxic335lzka23f6x2dhncrpizpyrk57gi2f28c0p98y5n")) + (file-name "dSFMT.h.patch")))))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (delete 'configure) ; no configure script + (replace 'build + ;; Upstream Makefile does not build a shared library. Borrow from Julia + ;; https://github.com/JuliaLang/julia/blob/v1.3.0/deps/dsfmt.mk + (lambda _ + (invoke + "gcc" "-DNDEBUG" "-DDSFMT_MEXP=19937" + "-fPIC" "-DDSFMT_DO_NOT_USE_OLD_NAMES" + "-O3" "-finline-functions" "-fomit-frame-pointer" + "-fno-strict-aliasing" "--param" "max-inline-insns-single=1800" + "-Wmissing-prototypes" "-Wall" "-std=c99" "-shared" "dSFMT.c" + "-o" "libdSFMT.so"))) + (replace 'install ; no "install" target + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib")) + (inc (string-append out "/include")) + (doc (string-append out "/share/doc/" ,name "-" ,version))) + (install-file "libdSFMT.so" lib) + (install-file "dSFMT.h" inc) + (install-file "LICENSE.txt" doc) + #t)))))) + (synopsis "Double precision SIMD-oriented Fast Mersenne Twister") + (description + "The dSMFT package speeds up Fast Mersenne Twister generation by avoiding +the expensive conversion of integer to double (floating point). dSFMT directly +generates double precision floating point pseudorandom numbers which have the +IEEE Standard for Binary Floating-Point Arithmetic (ANSI/IEEE Std 754-1985) +format. dSFMT is only available on the CPUs which use IEEE 754 format double +precision floating point numbers.") + (home-page "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/") + (license license:bsd-3))) + (define-public gsl (package (name "gsl") @@ -1216,6 +1298,45 @@ Swath).") #t)))))) (synopsis "Management suite for data with parallel IO support"))) +(define-public hdf5-blosc + (package + (name "hdf5-blosc") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Blosc/hdf5-blosc.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1nj2bm1v6ymm3fmyvhbn6ih5fgdiapavlfghh1pvbmhw71cysyqs")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list (string-append "-DBLOSC_INSTALL_DIR=" + (assoc-ref %build-inputs "c-blosc")) + (string-append "-DPLUGIN_INSTALL_PATH=" + (assoc-ref %outputs "out") + "/hdf5/lib/plugin")) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'do-not-build-blosc + (lambda _ + (substitute* "CMakeLists.txt" + (("set\\(BLOSC_INSTALL_DIR.*") "") + (("ExternalProject_Add\\(project_blosc") "message(")) + #t))))) + (inputs + `(("c-blosc" ,c-blosc) + ("hdf5" ,hdf5-1.10))) + (home-page "https://github.com/Blosc/hdf5-blosc") + (synopsis "Filter for HDF5 using the Blosc compressor") + (description "This is a filter for HDF5 that uses the Blosc compressor; by +installing this filter, you can read and write HDF5 files with +Blosc-compressed datasets.") + (license license:expat))) + (define-public h5check (package (name "h5check") @@ -1649,9 +1770,6 @@ script files.") "qscintilla2_qt5")) #t)))))))) -(define-public qtoctave - (deprecated-package "qtoctave" octave)) - (define-public opencascade-oce (package (name "opencascade-oce") @@ -2623,8 +2741,9 @@ implemented in ANSI C, and MPI for communications.") "scotch-integer-declarations.patch")))) (build-system gnu-build-system) (inputs - `(("zlib" ,zlib) - ("flex" ,flex) + `(("zlib" ,zlib))) + (native-inputs + `(("flex" ,flex) ("bison" ,bison))) (outputs '("out" "metis")) (arguments @@ -4213,6 +4332,10 @@ as equations, scalars, vectors, and matrices.") (guix build utils)) #:phases (modify-phases %standard-phases + (add-after 'unpack 'enable-bytecode-determinism + (lambda _ + (setenv "PYTHONHASHSEED" "0") + #t)) (add-after 'unpack 'fix-compatability ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only. (lambda _ @@ -4577,7 +4700,7 @@ linear algebra primitives specifically targeting graph analytics.") (define-public dune-common (package (name "dune-common") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) @@ -4585,7 +4708,7 @@ linear algebra primitives specifically targeting graph analytics.") version "/dune-common-" version ".tar.gz")) (sha256 (base32 - "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw")))) + "140q1zh44cr5yrjwg4b5ga803rkqv55vk30l2cqm29aklj1wb0rw")))) (build-system cmake-build-system) (arguments `(#:phases @@ -4615,7 +4738,7 @@ Differences} (FD).") (define-public dune-geometry (package (name "dune-geometry") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) @@ -4623,7 +4746,7 @@ Differences} (FD).") version "/dune-geometry-" version ".tar.gz")) (sha256 (base32 - "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn")))) + "1cicvlwbyyw76npicnblxckyvhbfn3ip8isydiv3hlrlz8zcg5nr")))) (build-system cmake-build-system) (arguments `(#:phases @@ -4655,15 +4778,17 @@ This package contains the basic DUNE geometry classes.") (define-public dune-uggrid (package (name "dune-uggrid") - (version "2.6.0") + (version "2.7.0") (source (origin - (method url-fetch) - (uri (string-append "https://dune-project.org/download/" - version "/dune-uggrid-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://gitlab.dune-project.org/staging/dune-uggrid.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "05l7a1gb78mny49anyxk6rjvn66rhgm30y72v5cjg0m5kfgr1a1f")))) + "192miqgmfj6jwk969gydzpbv9ki7jg5nky3ydnrwa2nq29b5xkh0")))) (build-system cmake-build-system) (arguments `(#:phases @@ -4690,7 +4815,7 @@ This package contains the DUNE UG grid classes.") (define-public dune-grid (package (name "dune-grid") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) @@ -4698,7 +4823,7 @@ This package contains the DUNE UG grid classes.") version "/dune-grid-" version ".tar.gz")) (sha256 (base32 - "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0")))) + "17fjz30qazjgl11sryyxnw9klai4yz1ji4bs68013xcxc5hdv27s")))) (build-system cmake-build-system) (arguments `(#:phases @@ -4733,7 +4858,7 @@ This package contains the basic DUNE grid classes.") (define-public dune-istl (package (name "dune-istl") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) @@ -4741,7 +4866,8 @@ This package contains the basic DUNE grid classes.") version "/dune-istl-" version ".tar.gz")) (sha256 (base32 - "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w")))) + "0gl3wgz5rs6sb4m83440ny45sbx7z7lnbi3gx6r9nm3rvy5j33f9")) + (patches (search-patches "dune-istl-2.7-fix-non-mpi-tests.patch")))) (build-system cmake-build-system) (arguments `(#:phases @@ -4779,7 +4905,7 @@ aggregation-based algebraic multigrid.") (define-public dune-localfunctions (package (name "dune-localfunctions") - (version "2.6.0") + (version "2.7.0") (source (origin (method url-fetch) @@ -4787,7 +4913,7 @@ aggregation-based algebraic multigrid.") version "/dune-localfunctions-" version ".tar.gz")) (sha256 (base32 - "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl")))) + "1yih59h6vngii696bx1c2vil02lriij4kz0nc583mjn9kiaqxfqd")))) (build-system cmake-build-system) (arguments `(#:phases @@ -4822,15 +4948,17 @@ assemble global function spaces on finite-element grids.") (define-public dune-alugrid (package (name "dune-alugrid") - (version "2.6.0") + (version "2.7.0-git-81d35682") (source (origin - (method url-fetch) - (uri (string-append "https://dune-project.org/download/" - version "/dune-alugrid-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git") + (commit "81d356827c84454b971937db02c02b90bbcd7fe5"))) + (file-name (git-file-name name version)) (sha256 (base32 - "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj")))) + "0z54lwfp53prcrs94k8gwh047l9z642jll3l56xlyfr69z0b2zz1")))) (build-system cmake-build-system) (arguments `(#:phases @@ -4870,17 +4998,17 @@ cubes.") (define-public dune-subgrid (package (name "dune-subgrid") - (version "2.6.0") + (version "2.7.0-git-2103a363") (source (origin (method git-fetch) (uri (git-reference (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid") - (commit "releases/2.6-1"))) + (commit "2103a363f32e8d7b60e66eee7ddecf969f6cf762"))) (file-name (git-file-name name version)) (sha256 (base32 - "1gcv35rx3knqd54r4pp9rzd639db4j8w2r2ibq43w1mgwdcqhs64")))) + "1wsjlypd3835c3arqjkw836cxx5q67zy447wa65q634lf6f6v9ia")))) (build-system cmake-build-system) (arguments `(#:phases @@ -4901,7 +5029,7 @@ cubes.") ("pkg-config" ,pkg-config))) (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php") (synopsis "Distributed and Unified Numerics Environment") - (description "The dune-subgrid module allows to mark elements of + (description "The dune-subgrid module marks elements of another hierarchical dune grid. The set of marked elements can then be accessed as a hierarchical dune grid in its own right. Dune-Subgrid provides the full grid interface including adaptive mesh refinement.") @@ -4910,7 +5038,7 @@ provides the full grid interface including adaptive mesh refinement.") (define-public dune-typetree (package (name "dune-typetree") - (version "2.6.0") + (version "2.7.0") (source (origin (method git-fetch) @@ -4920,7 +5048,7 @@ provides the full grid interface including adaptive mesh refinement.") (file-name (git-file-name name version)) (sha256 (base32 - "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9")))) + "1rhv25yg0q1hw50c8wlfqhgwrjl4mh62zq9v14ilwgzbfgxmpiy7")))) (build-system cmake-build-system) (arguments `(#:phases @@ -4949,7 +5077,7 @@ operating on statically typed trees of objects.") (define-public dune-functions (package (name "dune-functions") - (version "2.6.0") + (version "2.7.0") (source (origin (method git-fetch) @@ -4959,7 +5087,7 @@ operating on statically typed trees of objects.") (file-name (git-file-name name version)) (sha256 (base32 - "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200")))) + "1na4gcih0kin37ksj2xj07ds04v7zx53pjdhm1hzy55jjfqdjk8h")))) (build-system cmake-build-system) (arguments `(#:phases @@ -4999,17 +5127,17 @@ implemented as callable objects, and bases of finite element spaces.") (define-public dune-pdelab (package (name "dune-pdelab") - (version "2.6.0-rc1") + (version "2.7.0-git-476fe437") (source (origin (method git-fetch) (uri (git-reference (url "https://gitlab.dune-project.org/pdelab/dune-pdelab") - (commit (string-append "v" version)))) + (commit "476fe43763fa6f459c5e4658e2a2b4b5582db834"))) (file-name (git-file-name name version)) (sha256 (base32 - "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v")))) + "0cs36piqzn6rq0j2ih3ab3q3q9yg199wk72k5qi86pkzh7i7fdn1")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled (inputs @@ -5319,3 +5447,114 @@ researchers and developers alike to get started on SAT.") (home-page "http://minisat.se/MiniSat.html") (license license:expat)))) + +(define-public libqalculate + (package + (name "libqalculate") + (version "3.8.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Qalculate/libqalculate/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1vbaza9c7159xf2ym90l0xkyj2mp6c3hbghhsqn29yvz08fda9df")) + (patches + (search-patches "libqalculate-3.8.0-libcurl-ssl-fix.patch")))) + (build-system gnu-build-system) + (native-inputs + `(("pkg-config" ,pkg-config) + ("gettext" ,gettext-minimal) + ("intltool" ,intltool) + ("automake" ,automake) + ("autoconf" ,autoconf) + ("libtool" ,libtool) + ("doxygen" ,doxygen) + ("file" ,file))) + (inputs + `(("gmp" ,gmp) + ("mpfr" ,mpfr) + ("libxml2" ,libxml2) + ("curl" ,curl) + ("icu4c" ,icu4c) + ("gnuplot" ,gnuplot) + ("readline" ,readline) + ("libiconv" ,libiconv))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'bootstrap 'setenv + ;; Prevent the autogen.sh script to carry out the configure + ;; script, which has not yet been patched to replace /bin/sh. + (lambda _ + (setenv "NOCONFIGURE" "TRUE") + #t))))) + (home-page "https://qalculate.github.io/") + (synopsis "Multi-purpose cli desktop calculator and library") + (description + "Libqalculate is a multi-purpose cli desktop calculator and library. +It provides basic and advanced functionality. Features include customizable +functions, unit calculations, and conversions, physical constants, symbolic +calculations (including integrals and equations), arbitrary precision, +uncertainty propagation, interval arithmetic, plotting and a user-friendly +cli.") + (license license:gpl2+))) + +(define-public qalculate-gtk + (package + (name "qalculate-gtk") + (version "3.8.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Qalculate/qalculate-gtk/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0nsg6dzg5r7rzqr671nvrf1c50rjwpz7bxv5f20i4s7agizgv840")))) + (build-system glib-or-gtk-build-system) + (native-inputs + `(("pkg-config" ,pkg-config) + ("intltool" ,intltool) + ("automake" ,automake) + ("autoconf" ,autoconf) + ("libtool" ,libtool) + ("file" ,file))) + (inputs + `(("gmp" ,gmp) + ("mpfr" ,mpfr) + ("libqalculate" ,libqalculate) + ("libxml2" ,libxml2) + ("glib" ,glib) + ("gtk+" ,gtk+))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'bootstrap 'setenv + ;; Prevent the autogen.sh script to carry out the configure + ;; script, which has not yet been patched to replace /bin/sh. + (lambda _ + (setenv "NOCONFIGURE" "TRUE") + #t)) + (add-before 'check 'add-pot-file + ;; the file contains translations and are currently not in use + ;; left out on purpose so add it to POTFILES.skip + (lambda _ + (with-output-to-file "po/POTFILES.skip" + (lambda _ + (format #t "data/shortcuts.ui~%") + #t)) + #t))))) + (home-page "https://qalculate.github.io/") + (synopsis "Multi-purpose graphical desktop calculator") + (description + "Qalculate-gtk is the GTK frontend for libqalculate. It is a +multi-purpose GUI desktop calculator. It provides basic and advanced +functionality. Features include customizable functions, unit calculations, +and conversions, physical constants, symbolic calculations (including +integrals and equations), arbitrary precision, uncertainity propagation, +interval arithmetic, plotting.") + (license license:gpl2+))) |