gnu/packages/maths.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020 Andreas Enge <andreas@enge.fr>
   3 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
   4 ;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
   5 ;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Eric Bavier <bavier@posteo.net>
   6 ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
   7 ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
   8 ;;; Copyright © 2015–2021 Ricardo Wurmus <rekado@elephly.net>
   9 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
  10 ;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
  11 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
  12 ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
  13 ;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
  14 ;;; Copyright © 2016, 2018, 2020, 2021 Kei Kebreau <kkebreau@posteo.net>
  15 ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
  16 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
  17 ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
  18 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
  19 ;;; Copyright © 2017 Nikita <nikita@n0.is>
  20 ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
  21 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
  22 ;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net>
  23 ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr>
  24 ;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
  25 ;;; Copyright © 2018, 2019, 2020, 2021 Jan (janneke) Nieuwenhuizen <janneke@gnu.org>
  26 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
  27 ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
  28 ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
  29 ;;; Copyright © 2018, 2020, 2021 Marius Bakke <marius@gnu.org>
  30 ;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
  31 ;;; Copyright © 2018, 2021 Julien Lepiller <julien@lepiller.eu>
  32 ;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
  33 ;;; Copyright © 2019, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
  34 ;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
  35 ;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
  36 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
  37 ;;; Copyright © 2020, 2021 Felix Gruber <felgru@posteo.net>
  38 ;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
  39 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
  40 ;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
  41 ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com>
  42 ;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
  43 ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
  44 ;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net>
  45 ;;; Copyright © 2021 Gerd Heber <gerd.heber@gmail.com>
  46 ;;; Copyright © 2021 Franck Pérignon <franck.perignon@univ-grenoble-alpes.fr>
  47 ;;; Copyright © 2021 Philip McGrath <philip@philipmcgrath.com>
  48 ;;; Copyright © 2021 Paul A. Patience <paul@apatience.com>
  49 ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
  50 ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
  51 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
  52 ;;;
  53 ;;; This file is part of GNU Guix.
  54 ;;;
  55 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  56 ;;; under the terms of the GNU General Public License as published by
  57 ;;; the Free Software Foundation; either version 3 of the License, or (at
  58 ;;; your option) any later version.
  59 ;;;
  60 ;;; GNU Guix is distributed in the hope that it will be useful, but
  61 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  62 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  63 ;;; GNU General Public License for more details.
  64 ;;;
  65 ;;; You should have received a copy of the GNU General Public License
  66 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  67
  68 (define-module (gnu packages maths)
  69   #:use-module (ice-9 regex)
  70   #:use-module (ice-9 match)
  71   #:use-module (gnu packages)
  72   #:use-module ((guix licenses) #:prefix license:)
  73   #:use-module (guix packages)
  74   #:use-module (guix download)
  75   #:use-module (guix git-download)
  76   #:use-module (guix gexp)
  77   #:use-module (guix utils)
  78   #:use-module ((guix build utils) #:select (alist-replace))
  79   #:use-module (guix build-system cmake)
  80   #:use-module (guix build-system glib-or-gtk)
  81   #:use-module (guix build-system gnu)
  82   #:use-module (guix build-system ocaml)
  83   #:use-module (guix build-system python)
  84   #:use-module (guix build-system ruby)
  85   #:use-module (gnu packages algebra)
  86   #:use-module (gnu packages audio)
  87   #:use-module (gnu packages autotools)
  88   #:use-module (gnu packages base)
  89   #:use-module (gnu packages bash)
  90   #:use-module (gnu packages bison)
  91   #:use-module (gnu packages boost)
  92   #:use-module (gnu packages check)
  93   #:use-module (gnu packages cmake)
  94   #:use-module (gnu packages compression)
  95   #:use-module (gnu packages coq)
  96   #:use-module (gnu packages curl)
  97   #:use-module (gnu packages cyrus-sasl)
  98   #:use-module (gnu packages dbm)
  99   #:use-module (gnu packages documentation)
 100   #:use-module (gnu packages elf)
 101   #:use-module (gnu packages emacs)
 102   #:use-module (gnu packages file)
 103   #:use-module (gnu packages flex)
 104   #:use-module (gnu packages fltk)
 105   #:use-module (gnu packages fontutils)
 106   #:use-module (gnu packages gettext)
 107   #:use-module (gnu packages gcc)
 108   #:use-module (gnu packages gd)
 109   #:use-module (gnu packages ghostscript)
 110   #:use-module (gnu packages glib)
 111   #:use-module (gnu packages graphviz)
 112   #:use-module (gnu packages gtk)
 113   #:use-module (gnu packages icu4c)
 114   #:use-module (gnu packages image)
 115   #:use-module (gnu packages java)
 116   #:use-module (gnu packages less)
 117   #:use-module (gnu packages lisp)
 118   #:use-module (gnu packages linux)
 119   #:use-module (gnu packages llvm)
 120   #:use-module (gnu packages logging)
 121   #:use-module (gnu packages lua)
 122   #:use-module (gnu packages gnome)
 123   #:use-module (gnu packages guile)
 124   #:use-module (gnu packages xorg)
 125   #:use-module (gnu packages gl)
 126   #:use-module (gnu packages imagemagick)
 127   #:use-module (gnu packages m4)
 128   #:use-module (gnu packages mpi)
 129   #:use-module (gnu packages multiprecision)
 130   #:use-module (gnu packages ncurses)
 131   #:use-module (gnu packages netpbm)
 132   #:use-module (gnu packages ocaml)
 133   #:use-module (gnu packages onc-rpc)
 134   #:use-module (gnu packages parallel)
 135   #:use-module (gnu packages pcre)
 136   #:use-module (gnu packages popt)
 137   #:use-module (gnu packages perl)
 138   #:use-module (gnu packages pkg-config)
 139   #:use-module (gnu packages pulseaudio)
 140   #:use-module (gnu packages python)
 141   #:use-module (gnu packages python-web)
 142   #:use-module (gnu packages python-xyz)
 143   #:use-module (gnu packages qt)
 144   #:use-module (gnu packages readline)
 145   #:use-module (gnu packages ruby)
 146   #:use-module (gnu packages tbb)
 147   #:use-module (gnu packages scheme)
 148   #:use-module (gnu packages serialization)
 149   #:use-module (gnu packages shells)
 150   #:use-module (gnu packages sphinx)
 151   #:use-module (gnu packages tcl)
 152   #:use-module (gnu packages texinfo)
 153   #:use-module (gnu packages tex)
 154   #:use-module (gnu packages tls)
 155   #:use-module (gnu packages version-control)
 156   #:use-module (gnu packages wxwidgets)
 157   #:use-module (gnu packages xml)
 158   #:use-module (srfi srfi-1)
 159   #:use-module (srfi srfi-26))
 160
 161 (define-public aris
 162   (package
 163     (name "aris")
 164     (version "2.2")
 165     (source (origin
 166               (method url-fetch)
 167               (uri (string-append "mirror://gnu/" name "/" name "-" version ".tar.gz"))
 168               (sha256 (base32
 169                        "1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
 170     (build-system gnu-build-system)
 171     (inputs (list gtk+ libxml2))
 172     (native-inputs (list pkg-config))
 173     (arguments
 174      `(#:configure-flags '("CFLAGS=-O2 -g -fcommon")))
 175     (synopsis "Natural deduction first-order logic interface")
 176     (description "Aris is a program for performing logical proofs.  It supports
 177 propositional and predicate logic, as well as Boolean algebra and
 178 arithmetical logic.  In addition to its predefined inference and equivalence
 179 rules, Aris also supports references to older proofs.  Its use of standard
 180 logical symbols and its natural deduction interface make it easy to use for
 181 beginners.")
 182     (license license:gpl3+)
 183     (home-page "https://www.gnu.org/software/aris/")))
 184
 185 (define-public bitwise
 186   (package
 187     (name "bitwise")
 188     (version "0.42")
 189     (source (origin
 190               (method url-fetch)
 191               (uri (string-append "https://github.com/mellowcandle/bitwise"
 192                                   "/releases/download/v" version
 193                                   "/bitwise-v" version ".tar.gz"))
 194               (sha256
 195                (base32 "1lniw4bsb5qs5ybf018qllf95pzixb1q3lvybzl4k3xz8zpkrm6k"))))
 196     (build-system gnu-build-system)
 197     (inputs
 198      (list ncurses readline))
 199     (native-inputs
 200      (list cunit pkg-config))
 201     (synopsis "Terminal based bit manipulator in ncurses")
 202     (description "Bitwise is a multi base interactive calculator supporting
 203 dynamic base conversion and bit manipulation.  It's a handy tool for low level
 204 hackers, kernel developers and device drivers developers.
 205
 206 Some of the features include:
 207 @itemize
 208 @item Interactive ncurses interface.
 209 @item Command line calculator supporting all bitwise operations.
 210 @item Individual bit manipulator.
 211 @item Bitwise operations such as NOT, OR, AND, XOR, and shifts.
 212 @end itemize")
 213     (license license:gpl3+)
 214     (home-page "https://github.com/mellowcandle/bitwise/")))
 215
 216 (define-public c-graph
 217   (package
 218    (name "c-graph")
 219    (version "2.0.1")
 220    (source (origin
 221             (method url-fetch)
 222             (uri (string-append "mirror://gnu/c-graph/c-graph-" version
 223                                 ".tar.gz"))
 224             (sha256 (base32
 225                      "092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id"))))
 226    (build-system gnu-build-system)
 227    (inputs
 228     (list gfortran))
 229    (synopsis "Visualizing and demonstrating convolution")
 230    (description
 231     "GNU C-Graph is a tool for demonstrating the theory of convolution.
 232 Thus, it can serve as an excellent aid to students of signal and systems
 233 theory in visualizing the convolution process.  Rather than forcing the
 234 student to write code, the program offers an intuitive interface with
 235 interactive dialogs to guide them.")
 236    (license license:gpl3+)
 237    (home-page "https://www.gnu.org/software/c-graph/")))
 238
 239 (define-public coda
 240   (package
 241     (name "coda")
 242     (version "2.19")
 243     (source
 244      (origin
 245        (method url-fetch)
 246        (uri (string-append "https://github.com/stcorp/coda/releases/download/"
 247                            version "/coda-" version ".tar.gz"))
 248        (sha256
 249         (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
 250        (patches (search-patches "coda-use-system-libs.patch"))
 251        (modules '((guix build utils)))
 252        (snippet
 253         ;; Make sure we don't use the bundled software.
 254         '(begin
 255            (for-each (lambda (d)
 256                        (delete-file-recursively (string-append "libcoda/" d)))
 257                      '("zlib" "pcre" "expat"))
 258            #t))))
 259     (native-inputs
 260      `(("fortran" ,gfortran)
 261        ("python" ,python)
 262        ("python-numpy" ,python-numpy)))
 263     (inputs
 264      `(("zlib" ,zlib)
 265        ("pcre" ,pcre)
 266        ("expat" ,expat)
 267        ("hdf4" ,hdf4-alt)
 268        ("hdf5" ,hdf5)))
 269     (build-system gnu-build-system)
 270     (arguments
 271      '(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
 272                            "LIBS= -lz -lpcre -lexpat")))
 273     (synopsis "A common interface to various earth observation data formats")
 274     (description
 275      "The Common Data Access toolbox (CODA) provides a set of interfaces for
 276 reading remote sensing data from earth observation data files.  It consists of
 277 command line applications and interfaces to the C, Fortran, Python, and Java
 278 programming languages.")
 279     (home-page "https://stcorp.nl/coda")
 280     (license license:gpl2+)))
 281
 282 (define-public qhull
 283   (package
 284     (name "qhull")
 285     (version "2020.2")
 286     (source (origin
 287               (method url-fetch)
 288               (uri (string-append "http://www.qhull.org/download/qhull-"
 289                                   (car (string-split version #\.))
 290                                   "-src-8.0.2.tgz"))
 291               (sha256
 292                (base32
 293                 "0zlbhg0lb6j60188c2xhcrvviskr079552icjldqhy1jhgmxghmm"))))
 294     (build-system cmake-build-system)
 295     (arguments
 296      `(#:configure-flags '("-DLINK_APPS_SHARED=ON"
 297                            "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")))
 298     (synopsis "Calculate convex hulls and related structures")
 299     (description
 300      "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi
 301 diagram, halfspace intersection about a point, furthest-site Delaunay
 302 triangulation, and furthest-site Voronoi diagram.  The source code runs in 2-d,
 303 3-d, 4-d, and higher dimensions.  @code{Qhull} implements the Quickhull
 304 algorithm for computing the convex hull.  It handles roundoff errors from
 305 floating point arithmetic.  It computes volumes, surface areas, and
 306 approximations to the convex hull.
 307
 308 @code{Qhull} does not support triangulation of non-convex surfaces, mesh
 309 generation of non-convex objects, medium-sized inputs in 9-D and higher, alpha
 310 shapes, weighted Voronoi diagrams, Voronoi volumes, or constrained Delaunay
 311 triangulations.")
 312     (home-page "http://qhull.org")
 313     (license (license:non-copyleft "file://COPYING.txt"
 314                                    "See COPYING in the distribution."))))
 315
 316 (define-public python-cvxopt
 317   (package
 318     (name "python-cvxopt")
 319     (version "1.2.3")
 320     (source (origin
 321               (method git-fetch)
 322               (uri (git-reference
 323                     (url "https://github.com/cvxopt/cvxopt")
 324                     (commit version)))
 325               (file-name (git-file-name name version))
 326               (sha256
 327                (base32
 328                 "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b"))))
 329     (build-system python-build-system)
 330     (arguments
 331      `(#:phases
 332        (modify-phases %standard-phases
 333          (add-after 'unpack 'find-libraries
 334            (lambda* (#:key inputs #:allow-other-keys)
 335              (setenv "CVXOPT_BLAS_LIB" "openblas")
 336              (setenv "CVXOPT_BUILD_FFTW" "1")
 337              (setenv "CVXOPT_BUILD_GLPK" "1")
 338              (setenv "CVXOPT_BUILD_GSL" "1")
 339              #t)))))
 340     (inputs
 341      (list fftw
 342            glpk
 343            gsl
 344            lapack
 345            openblas
 346            suitesparse))
 347     (home-page "https://www.cvxopt.org")
 348     (synopsis "Python library for convex optimization")
 349     (description
 350      "CVXOPT is a package for convex optimization based on the Python
 351 programming language.  Its main purpose is to make the development of software
 352 for convex optimization applications straightforward by building on Python’s
 353 extensive standard library and on the strengths of Python as a high-level
 354 programming language.")
 355     (license license:gpl3+)))
 356
 357 (define-public python2-cvxopt
 358   (package-with-python2 python-cvxopt))
 359
 360 (define-public units
 361   (package
 362    (name "units")
 363    (version "2.21")
 364    (source (origin
 365             (method url-fetch)
 366             (uri (string-append "mirror://gnu/units/units-" version
 367                                 ".tar.gz"))
 368             (sha256 (base32
 369                      "1bybhqs4yrly9myb5maz3kdmf8k4fhk2m1d5cbcryn40z6lq0gkc"))))
 370    (build-system gnu-build-system)
 371    (inputs
 372     `(("readline" ,readline)
 373       ("python" ,python-wrapper)        ;for 'units_cur' script
 374       ("python-requests" ,python-requests)))
 375    (arguments
 376     `(#:phases (modify-phases %standard-phases
 377                  (add-after 'install 'wrap-units_cur
 378                    (lambda* (#:key outputs #:allow-other-keys)
 379                      (let* ((out (assoc-ref outputs "out"))
 380                             (bin (string-append out "/bin")))
 381                        (wrap-program (string-append bin "/units_cur")
 382                          `("GUIX_PYTHONPATH" ":" prefix
 383                            ,(search-path-as-string->list (getenv "GUIX_PYTHONPATH"))))
 384                        #t))))))
 385    (synopsis "Conversion between thousands of scales")
 386    (description
 387     "GNU Units converts numeric quantities between units of measure.  It
 388 can handle scale changes through adaptive usage of standard scale
 389 prefixes (micro-, kilo-, etc.).  It can also handle nonlinear
 390 conversions such as Fahrenheit to Celsius.  Its interpreter is powerful
 391 enough to be used effectively as a scientific calculator.")
 392    (license license:gpl3+)
 393    (home-page "https://www.gnu.org/software/units/")))
 394
 395 (define-public double-conversion
 396   (package
 397     (name "double-conversion")
 398     (version "3.1.5")
 399     (home-page "https://github.com/google/double-conversion")
 400     (source (origin
 401               (method git-fetch)
 402               (uri (git-reference (url home-page)
 403                                   (commit (string-append "v" version))))
 404               (file-name (git-file-name name version))
 405               (sha256
 406                (base32
 407                 "0csy4pjw1p8rp6g5qxi2h0ychhhp1fldv7gb761627fs2mclw9gv"))))
 408     (build-system cmake-build-system)
 409     (arguments
 410      '(#:test-target "test"
 411        #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
 412                            "-DBUILD_TESTING=ON")))
 413     (synopsis "Conversion routines for IEEE doubles")
 414     (description
 415      "The double-conversion library provides binary-decimal and decimal-binary
 416 routines for IEEE doubles.  The library consists of efficient conversion
 417 routines that have been extracted from the V8 JavaScript engine.")
 418     (license license:bsd-3)))
 419
 420 (define-public dionysus
 421   (package
 422     (name "dionysus")
 423     (version "1.4.0")
 424     (source (origin
 425               (method url-fetch)
 426               (uri (string-append "mirror://gnu/dionysus/dionysus-" version
 427                                   ".tar.xz"))
 428               (sha256
 429                (base32
 430                 "194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
 431     (build-system gnu-build-system)
 432     (inputs (list tcl))                      ;for 'tclsh'
 433     (synopsis "Local search for universal constants and scientific values")
 434     (description
 435      "GNU Dionysus is a convenient system for quickly retrieving the values of
 436 mathematical constants used in science and engineering.  Values can be
 437 searched using a simple command-line tool, choosing from three databases:
 438 universal constants, atomic numbers, and constants related to
 439 semiconductors.")
 440     (license license:gpl3+)
 441     (home-page "https://www.gnu.org/software/dionysus/")))
 442
 443 (define-public dsfmt
 444   (package
 445     (name "dsfmt")
 446     (version "2.2.3")
 447     (source
 448      (origin
 449        (method url-fetch)
 450        (uri
 451          (string-append
 452            "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/"
 453            "dSFMT-src-" version ".tar.gz"))
 454        (sha256
 455         (base32
 456          "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))
 457        (modules '((guix build utils)))
 458        ;; Don't distribute html documentation with bundled jquery.
 459        (snippet
 460         '(begin
 461            (delete-file-recursively "html") #t))
 462        ;; Add patches borrowed from Julia.
 463        (patches
 464          (list
 465            (origin
 466              (method url-fetch)
 467              (uri (string-append
 468                     "https://raw.githubusercontent.com/JuliaLang/julia/"
 469                     "v1.3.0/deps/patches/dSFMT.c.patch"))
 470              (sha256 (base32
 471                       "09mhv11bms8jsmkmdqvlcgljwhzw3b6n9nncpi2b6dla9798hw2y"))
 472              (file-name "dSFMT.c.patch"))
 473            (origin
 474              (method url-fetch)
 475              (uri (string-append
 476                     "https://raw.githubusercontent.com/JuliaLang/julia/"
 477                     "v1.3.0/deps/patches/dSFMT.h.patch"))
 478              (sha256 (base32
 479                       "1py5rd0yxic335lzka23f6x2dhncrpizpyrk57gi2f28c0p98y5n"))
 480              (file-name "dSFMT.h.patch"))))))
 481     (build-system gnu-build-system)
 482     (arguments
 483      `(#:phases
 484        (modify-phases %standard-phases
 485          (delete 'configure)            ; no configure script
 486          (replace 'build
 487            ;; Upstream Makefile does not build a shared library. Borrow from Julia
 488            ;; https://github.com/JuliaLang/julia/blob/v1.3.0/deps/dsfmt.mk
 489            (lambda _
 490              (invoke
 491                "gcc" "-DNDEBUG" "-DDSFMT_MEXP=19937"
 492                "-fPIC" "-DDSFMT_DO_NOT_USE_OLD_NAMES"
 493                "-O3" "-finline-functions" "-fomit-frame-pointer"
 494                "-fno-strict-aliasing" "--param" "max-inline-insns-single=1800"
 495                "-Wmissing-prototypes" "-Wall" "-std=c99" "-shared" "dSFMT.c"
 496                "-o" "libdSFMT.so")))
 497          (replace 'install              ; no "install" target
 498            (lambda* (#:key outputs #:allow-other-keys)
 499              (let* ((out (assoc-ref outputs "out"))
 500                     (lib (string-append out "/lib"))
 501                     (inc (string-append out "/include"))
 502                     (doc (string-append out "/share/doc/" ,name "-" ,version)))
 503                (install-file "libdSFMT.so" lib)
 504                (install-file "dSFMT.h" inc)
 505                (install-file "LICENSE.txt" doc)
 506                #t))))))
 507     (synopsis "Double precision SIMD-oriented Fast Mersenne Twister")
 508     (description
 509      "The dSMFT package speeds up Fast Mersenne Twister generation by avoiding
 510 the expensive conversion of integer to double (floating point).  dSFMT directly
 511 generates double precision floating point pseudorandom numbers which have the
 512 IEEE Standard for Binary Floating-Point Arithmetic (ANSI/IEEE Std 754-1985)
 513 format.  dSFMT is only available on the CPUs which use IEEE 754 format double
 514 precision floating point numbers.")
 515     (home-page "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/")
 516     (license license:bsd-3)))
 517
 518 (define-public gsl
 519   (package
 520     (name "gsl")
 521     (version "2.7")
 522     (source (origin
 523               (method url-fetch)
 524               (uri (string-append "mirror://gnu/gsl/gsl-"
 525                                   version ".tar.gz"))
 526               (sha256
 527                (base32
 528                 "0av04cpblphvvs3kl5rwphniarml503501vrpqw31rd0bmwg7fzg"))))
 529     (build-system gnu-build-system)
 530     (arguments
 531      (let ((system (%current-system)))
 532        `(#:configure-flags (list "--disable-static") ;halves package size
 533          #:phases
 534          (modify-phases %standard-phases
 535            ,@(cond
 536               ((or (string-prefix? "aarch64" system)
 537                    (string-prefix? "powerpc" system))
 538                ;; Some sparse matrix tests are failing on AArch64 and PowerPC:
 539                ;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00001.html
 540                '((add-before 'check 'disable-failing-tests
 541                    (lambda _
 542                      (substitute* "spmatrix/test.c"
 543                        ((".*test_complex.*") "\n"))))))
 544
 545               ((string-prefix? "i686" system)
 546                ;; There are rounding issues with these tests on i686:
 547                ;; https://lists.gnu.org/archive/html/bug-gsl/2016-10/msg00000.html
 548                ;; https://lists.gnu.org/archive/html/bug-gsl/2020-04/msg00000.html
 549                '((add-before 'check 'disable-failing-tests
 550                    (lambda _
 551                      (substitute* "linalg/test.c"
 552                        ((".*gsl_test\\(test_LU_decomp.*") "\n")
 553                        ((".*gsl_test\\(test_LUc_decomp.*") "\n")
 554                        ((".*gsl_test\\(test_QR_decomp_r.*") "\n")
 555                        ((".*gsl_test\\(test_cholesky_decomp.*") "\n")
 556                        ((".*gsl_test\\(test_pcholesky_solve.*") "\n")
 557                        ((".*gsl_test\\(test_COD_lssolve2.*") "\n"))
 558                      (substitute* "spmatrix/test.c"
 559                        ((".*test_all.*") "\n")
 560                        ((".*test_float.*") "\n")
 561                        ((".*test_complex.*") "\n"))
 562
 563                      ;; XXX: These tests abort with:
 564                      ;; gsl: cholesky.c:645: ERROR: matrix is not positive definite
 565                      (substitute* '("multifit_nlinear/test.c"
 566                                     "multilarge_nlinear/test.c")
 567                        (("gsl_ieee_env_setup.*" all)
 568                         (string-append "exit (77);\n" all)))))))
 569
 570               (else '()))))))
 571     (home-page "https://www.gnu.org/software/gsl/")
 572     (synopsis "Numerical library for C and C++")
 573     (description
 574      "The GNU Scientific Library is a library for numerical analysis in C
 575 and C++.  It includes a wide range of mathematical routines, with over 1000
 576 functions in total.  Subject areas covered by the library include:
 577 differential equations, linear algebra, Fast Fourier Transforms and random
 578 numbers.")
 579     (license license:gpl3+)))
 580
 581 ;; TODO: Merge back into the gsl package as a separate output.
 582 (define-public gsl-static
 583   (package/inherit gsl
 584     (name "gsl-static")
 585     (arguments
 586      `(,@(package-arguments gsl)
 587         #:configure-flags (list "--disable-shared")
 588         #:make-flags (list "CFLAGS=-fPIC")))))
 589
 590 (define-public sleef
 591   (package
 592     (name "sleef")
 593     (version "3.5.1")
 594     (source
 595      (origin
 596        (method git-fetch)
 597        (uri (git-reference
 598              (url "https://github.com/shibatch/sleef")
 599              (commit version)))
 600        (file-name (git-file-name name version))
 601        (sha256
 602         (base32 "1jybqrl2dvjxzg30xrhh847s375n2jr1pix644wi6hb5wh5mx3f7"))))
 603     (build-system cmake-build-system)
 604     (arguments
 605      '(#:configure-flags (list "-DCMAKE_BUILD_TYPE=Release"
 606                                (string-append "-DCMAKE_INSTALL_LIBDIR="
 607                                               (assoc-ref %outputs "out")
 608                                               "/lib")
 609                                (string-append "-DCMAKE_INSTALL_PREFIX="
 610                                               (assoc-ref %outputs "out")))
 611        #:phases
 612        (modify-phases %standard-phases
 613          ;; SLEEF generates a header library during the build process and writes
 614          ;; to it via shell redirection.  Make the checkout writable so the
 615          ;; build can succeed.
 616          (add-after 'unpack 'make-git-checkout-writable
 617            (lambda _
 618              (for-each make-file-writable (find-files "."))
 619              #t)))))
 620     (inputs
 621      (list fftw gmp mpfr openssl))
 622     (home-page "https://sleef.org/")
 623     (synopsis "SIMD library for evaluating elementary functions and DFT")
 624     (description
 625      "SLEEF (SIMD Library for Evaluating Elementary Functions) is a library that
 626 implements vectorized versions of all C99 real floating point math functions.
 627 It can utilize SIMD instructions that are available on modern processors.")
 628     (license (list license:boost1.0       ;sleef
 629                    license:cc-by4.0))))   ;simplex algorithm
 630
 631 (define-public glpk
 632   (package
 633     (name "glpk")
 634     (version "5.0")
 635     (source
 636      (origin
 637       (method url-fetch)
 638       (uri (string-append "mirror://gnu/glpk/glpk-"
 639                           version ".tar.gz"))
 640       (sha256
 641        (base32
 642         "05bgxidxj8d9xdp82niy7cy36w181cxq7p8vc3y2ixshpgp1642a"))))
 643     (build-system gnu-build-system)
 644     (inputs
 645      (list gmp))
 646     (arguments
 647      `(#:configure-flags '("--with-gmp"
 648                            "--disable-static")))
 649     (home-page "https://www.gnu.org/software/glpk/")
 650     (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
 651     (description
 652      "GLPK is a C library for solving large-scale linear programming (LP),
 653 mixed integer programming (MIP), and other related problems.  It supports the
 654 GNU MathProg modeling language, a subset of the AMPL language, and features a
 655 translator for the language.  In addition to the C library, a stand-alone
 656 LP/MIP solver is included in the package.")
 657     (license license:gpl3+)))
 658
 659 (define-public glpk-4
 660   (package
 661     (inherit glpk)
 662     (name "glpk")
 663     (version "4.65")
 664     (source
 665      (origin
 666       (method url-fetch)
 667       (uri (string-append "mirror://gnu/glpk/glpk-"
 668                           version ".tar.gz"))
 669       (sha256
 670        (base32
 671         "040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))))
 672
 673 (define-public 4ti2
 674   (package
 675     (name "4ti2")
 676     (version "1.6.9")
 677     (source
 678      (origin
 679        (method url-fetch)
 680        (uri (string-append "https://github.com/4ti2/4ti2/releases/download/"
 681                            "Release_"
 682                            (string-map (lambda (c) (if (char=? c #\.) #\_ c))
 683                                        version)
 684                            "/4ti2-" version ".tar.gz"))
 685        (sha256
 686         (base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
 687     (build-system gnu-build-system)
 688     (native-inputs
 689      (list (@ (gnu packages base) which))) ; for the tests
 690     (inputs
 691      (list glpk gmp))
 692     (home-page "http://www.4ti2.de/")
 693     (synopsis "Mathematical tool suite for problems on linear spaces")
 694     (description
 695      "4ti2 implements algorithms for solving algebraic, geometric and
 696 combinatorial problems on linear spaces.  Among others, it solves systems
 697 of linear equations, computes extreme rays of polyhedral cones, solves
 698 integer programming problems and computes Markov bases for statistics.")
 699     (license license:gpl2+)))
 700
 701 (define-public cddlib
 702   (package
 703     (name "cddlib")
 704     (version "0.94i")
 705     (source
 706      (origin
 707       (method url-fetch)
 708       (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
 709                           (string-delete #\. version) ".tar.gz"))
 710       (sha256
 711        (base32
 712         "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
 713     (build-system gnu-build-system)
 714     (inputs
 715      (list gmp))
 716     (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
 717     (synopsis "Library for convex hulls and extreme rays of polyhedra")
 718     (description
 719      "The C-library cddlib implements the Double Description Method of
 720 Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
 721 rays of a general convex polyhedron given by a system of linear inequalities
 722 in arbitrary dimension.  It can also be used for the converse operation of
 723 computing convex hulls.")
 724     (license license:gpl2+)))
 725
 726 (define-public lrslib
 727   (package
 728     (name "lrslib")
 729     (version "7.1")
 730     (source
 731      (origin
 732        (method url-fetch)
 733        (uri (string-append "http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/"
 734                            "lrslib-0"
 735                            (string-delete #\. version) ".tar.gz"))
 736        (sha256
 737         (base32
 738          "05kq3hzam31dlmkccv3v358r478kpvx76mw37ka12c6ypwv5dsnk"))))
 739     (build-system gnu-build-system)
 740     (inputs
 741      (list gmp))
 742     (arguments
 743      `(#:tests? #f                      ; no check phase
 744        #:make-flags `("CC=gcc"
 745                       ,(string-append "prefix=" (assoc-ref %outputs "out"))
 746                       "all-shared")
 747        #:phases
 748        (modify-phases %standard-phases
 749          (replace 'configure
 750            (lambda _
 751              (substitute* "makefile"
 752                (("-L \\.") "-L . -Wl,-rpath='$$ORIGIN/../lib'"))
 753              #t)))))
 754     (home-page "http://cgm.cs.mcgill.ca/~avis/C/lrs.html")
 755     (synopsis "Convex hulls of polyhedra with exact arithmetic")
 756     (description
 757      "The C code of lrslib implements the reverse search algorithm for
 758 vertex enumeration and convex hull problems.  Its input file format is
 759 compatible with cddlib.  All computations are done exactly in either
 760 multiple precision or fixed integer arithmetic.  Output is not stored
 761 in memory, so even problems with very large output sizes can sometimes
 762 be solved.")
 763     (license license:gpl2+)))
 764
 765 (define-public libcerf
 766   (package
 767     (name "libcerf")
 768     (version "1.14")
 769     (source
 770      (origin
 771        (method git-fetch)
 772        (uri (git-reference
 773              (url "https://jugit.fz-juelich.de/mlz/libcerf")
 774              (commit (string-append "v" version))))
 775        (file-name (git-file-name name version))
 776        (sha256
 777         (base32 "1ic2q7kvxpqmgxlishygvx8d00i4wn51vkq4fyac44ahhf6c3kwd"))))
 778     (build-system cmake-build-system)
 779     (native-inputs
 780      (list perl))
 781     (home-page "https://jugit.fz-juelich.de/mlz/libcerf")
 782     (synopsis "Library for complex error functions")
 783     (description
 784      "@code{libcerf} is a self-contained numeric library that provides an
 785 efficient and accurate implementation of complex error functions, along with
 786 Dawson, Faddeeva, and Voigt functions.")
 787     (license license:expat)))
 788
 789 (define-public vinci
 790   (package
 791     (name "vinci")
 792     (version "1.0.5")
 793     (source
 794      (origin
 795        (method url-fetch)
 796        (uri (string-append "https://www.math.u-bordeaux.fr/~aenge/software/"
 797                            "vinci/vinci-" version ".tar.gz"))
 798        (sha256
 799         (base32
 800          "1aq0qc1y27iw9grhgnyji3290wwfznsrk3sg6ynqpxwjdda53h4m"))))
 801     (build-system gnu-build-system)
 802     (inputs
 803      (list lrslib))
 804     (arguments
 805      `(#:tests? #f                      ; no check phase
 806        #:phases
 807        (modify-phases %standard-phases
 808          (replace 'configure
 809            ;; register the lrs location in the config file
 810            (lambda* (#:key inputs #:allow-other-keys)
 811              (let* ((lrs (assoc-ref inputs "lrslib"))
 812                     (lrsexec (string-append lrs "/bin/lrs")))
 813                (substitute* "vinci.h"
 814                  (("#define LRS_EXEC      \"lrs\"")
 815                   (string-append "#define LRS_EXEC \"" lrsexec "\""))))
 816              #t))
 817          (replace 'install
 818            (lambda* (#:key outputs #:allow-other-keys)
 819              (let* ((out (assoc-ref outputs "out"))
 820                     (bin (string-append out "/bin")))
 821                (install-file "vinci" bin))
 822              #t)))))
 823     (home-page
 824      "https://www.math.u-bordeaux.fr/~aenge/?category=software&page=vinci")
 825     (synopsis "Volume computation for polytopes")
 826     (description
 827      "Vinci implements a number of volume computation algorithms for convex
 828 polytopes in arbitrary dimension.  The polytopes can be given by their
 829 V-representation (as the convex hull of a finite number of vertices), by
 830 their H-representation (as the bounded intersection of a finite number of
 831 halfspaces) or by their double description with both representations.")
 832     (license license:gpl2+)))
 833
 834 (define-public arpack-ng
 835   (package
 836     (name "arpack-ng")
 837     (version "3.8.0")
 838     (home-page "https://github.com/opencollab/arpack-ng")
 839     (source (origin
 840               (method git-fetch)
 841               (uri (git-reference (url home-page) (commit version)))
 842               (file-name (git-file-name name version))
 843               (sha256
 844                (base32
 845                 "0l7as5z6xvbxly8alam9s4kws70952qq35a6vkljzayi4b9gbklx"))))
 846     (build-system gnu-build-system)
 847     (native-inputs
 848      (list autoconf automake libtool pkg-config))
 849     (inputs
 850      (list eigen lapack gfortran))
 851     (synopsis "Fortran subroutines for solving eigenvalue problems")
 852     (description
 853      "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
 854 large scale eigenvalue problems.")
 855     (license (license:non-copyleft "file://COPYING"
 856                                 "See COPYING in the distribution."))))
 857
 858 (define-public arpack-ng-3.3.0
 859   (package
 860     (inherit arpack-ng)
 861     (version "3.3.0")
 862     (source
 863      (origin
 864        (method git-fetch)
 865        (uri (git-reference (url (package-home-page arpack-ng))
 866                            (commit version)))
 867        (file-name (git-file-name (package-name arpack-ng) version))
 868        (sha256
 869         (base32
 870          "00h6bjvxjq7bv0b8pwnc0gw33ns6brlqv00xx2rh3w9b5n205918"))))))
 871
 872 (define-public arpack-ng-openmpi
 873   (package (inherit arpack-ng)
 874     (name "arpack-ng-openmpi")
 875     (inputs
 876      `(("mpi" ,openmpi)
 877        ,@(package-inputs arpack-ng)))
 878     (arguments
 879      (substitute-keyword-arguments (package-arguments arpack-ng)
 880        ((#:configure-flags _ '())
 881         ''("--enable-mpi"))
 882        ((#:phases phases '%standard-phases)
 883         `(modify-phases ,phases
 884            (add-before 'check 'mpi-setup
 885              ,%openmpi-setup)))))
 886     (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
 887
 888 (define-public lapack
 889   (package
 890     (name "lapack")
 891     (version "3.9.0")
 892     (source
 893      (origin
 894       (method url-fetch)
 895       (uri (string-append "http://www.netlib.org/lapack/lapack-"
 896                           version ".tgz"))
 897       (sha256
 898        (base32
 899         "1155qixp26c12yrxc76z9mlfw2h3xxymxxv5znpgzh5gaykpndgj"))))
 900     (build-system cmake-build-system)
 901     (home-page "http://www.netlib.org/lapack/")
 902     (inputs `(("fortran" ,gfortran)
 903               ("python" ,python-wrapper)))
 904     (arguments
 905      `(#:configure-flags (list
 906                           "-DBUILD_SHARED_LIBS:BOOL=YES"
 907                           "-DLAPACKE=ON"
 908                           ;; Build the 'LAPACKE_clatms' functions.
 909                           "-DLAPACKE_WITH_TMG=ON"
 910                           "-DBUILD_TESTING=ON")))
 911     (synopsis "Library for numerical linear algebra")
 912     (description
 913      "LAPACK is a Fortran 90 library for solving the most commonly occurring
 914 problems in numerical linear algebra.")
 915     (license (license:non-copyleft "file://LICENSE"
 916                                 "See LICENSE in the distribution."))))
 917
 918 (define-public clapack
 919   (package
 920     (name "clapack")
 921     (version "3.2.1")
 922     (source
 923      (origin
 924       (method url-fetch)
 925       (uri (string-append "http://www.netlib.org/clapack/clapack-"
 926                           version "-CMAKE.tgz"))
 927       (sha256
 928        (base32
 929         "0nnap9q1mv14g57dl3vkvxrdr10k5w7zzyxs6rgxhia8q8mphgqb"))))
 930     (build-system cmake-build-system)
 931     (arguments
 932      `(#:configure-flags '("-DCMAKE_C_FLAGS=-fcommon -O2")
 933        #:phases
 934        (modify-phases %standard-phases
 935          ;; These tests use a lot of stack variables and segfault without
 936          ;; lifting resource limits.
 937          (add-after 'unpack 'disable-broken-tests
 938            (lambda _
 939              (substitute* "TESTING/CMakeLists.txt"
 940                (("add_lapack_test.* xeigtstz\\)") ""))))
 941          (replace 'install
 942            (lambda* (#:key outputs #:allow-other-keys)
 943              (let* ((out (assoc-ref outputs "out"))
 944                     (libdir (string-append out "/lib"))
 945                     (f2cinc (string-append out "/include/libf2c")))
 946                (mkdir-p f2cinc)
 947                (display (getcwd))
 948                (for-each (lambda (file)
 949                            (install-file file libdir))
 950                          '("SRC/liblapack.a"
 951                            "F2CLIBS/libf2c/libf2c.a"
 952                            "TESTING/MATGEN/libtmglib.a"
 953                            "BLAS/SRC/libblas.a"))
 954                (for-each (lambda (file)
 955                            (install-file file f2cinc))
 956                          (cons "F2CLIBS/libf2c/arith.h"
 957                                (find-files (string-append "../clapack-"
 958                                                           ,version "-CMAKE/F2CLIBS/libf2c")
 959                                            "\\.h$")))
 960                (copy-recursively (string-append "../clapack-"
 961                                                 ,version "-CMAKE/INCLUDE")
 962                                  (string-append out "/include"))))))))
 963     (home-page "https://www.netlib.org/clapack/")
 964     (synopsis "Numerical linear algebra library for C")
 965     (description
 966      "The CLAPACK library was built using a Fortran to C conversion utility
 967 called f2c.  The entire Fortran 77 LAPACK library is run through f2c to obtain
 968 C code, and then modified to improve readability.  CLAPACK's goal is to
 969 provide LAPACK for someone who does not have access to a Fortran compiler.")
 970     (license (license:non-copyleft "file://LICENSE"
 971                                    "See LICENSE in the distribution."))))
 972
 973 (define-public scalapack
 974   (package
 975     (name "scalapack")
 976     (version "2.1.0")
 977     (source
 978      (origin
 979        (method url-fetch)
 980        (uri (string-append "http://www.netlib.org/scalapack/scalapack-"
 981                            version ".tgz"))
 982        (sha256
 983         (base32
 984          "19i0h9vdc3zsy58r6fy1vs2kz2l7amifkz0cf926j90xz1n23nb1"))
 985        (patches (search-patches "scalapack-gcc-10-compilation.patch"))))
 986     (build-system cmake-build-system)
 987     (inputs
 988      `(("mpi" ,openmpi)
 989        ("fortran" ,gfortran)
 990        ("lapack" ,lapack)))             ;for testing only
 991     (arguments
 992      `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
 993        #:phases (modify-phases %standard-phases
 994                   (add-before 'check 'mpi-setup
 995                     ,%openmpi-setup)
 996                   (add-after 'unpack 'skip-faulty-test
 997                     (lambda _
 998                       ;; FIXME: Skip these two tests that fail to complete for
 999                       ;; unknown reasons:
1000                       ;; <https://github.com/Reference-ScaLAPACK/scalapack/issues/43>.
1001                       (substitute* "TESTING/CMakeLists.txt"
1002                         (("^add_test\\(x[sd]hseqr.*" all)
1003                          (string-append "# " all "\n"))))))))
1004     (home-page "http://www.netlib.org/scalapack/")
1005     (synopsis "Library for scalable numerical linear algebra")
1006     (description
1007      "ScaLAPACK is a Fortran 90 library of high-performance linear algebra
1008 routines on parallel distributed memory machines.  ScaLAPACK solves dense and
1009 banded linear systems, least squares problems, eigenvalue problems, and
1010 singular value problems.")
1011     (license (license:non-copyleft "file://LICENSE"
1012                                    "See LICENSE in the distribution."))))
1013
1014 (define-public gnuplot
1015   (package
1016     (name "gnuplot")
1017     (version "5.4.2")
1018     (source (origin
1019               (method url-fetch)
1020               (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
1021                                   version "/gnuplot-"
1022                                   version ".tar.gz"))
1023        (sha256
1024         (base32 "1fp7rbhjmz2w63r72kicf8lfszzimz2csfx868fracw167hpaz75"))))
1025     (build-system gnu-build-system)
1026     (inputs (list readline cairo pango gd lua))
1027     (native-inputs
1028      `(("pkg-config" ,pkg-config)
1029        ("texlive" ,texlive-tiny)))
1030     (arguments `(#:configure-flags (list (string-append
1031                                           "--with-texdir=" %output
1032                                           "/texmf-local/tex/latex/gnuplot"))
1033                  ;; Plot on a dumb terminal during tests.
1034                  #:make-flags '("GNUTERM=dumb")))
1035     (home-page "http://www.gnuplot.info")
1036     (synopsis "Command-line driven graphing utility")
1037     (description "Gnuplot is a portable command-line driven graphing
1038 utility.  It was originally created to allow scientists and students to
1039 visualize mathematical functions and data interactively, but has grown to
1040 support many non-interactive uses such as web scripting.  It is also used as a
1041 plotting engine by third-party applications like Octave.")
1042     ;;  X11 Style with the additional restriction that derived works may only be
1043     ;;  distributed as patches to the original.
1044     (license (license:fsf-free
1045               "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
1046
1047 (define-public gctp
1048   (package
1049     (name "gctp")
1050     (version "2.0.0")
1051     (source
1052      (origin
1053        (method git-fetch)
1054        (uri (git-reference
1055              (url "https://github.com/OkoSanto/GCTP")
1056              (commit (string-append "v" version))))
1057        (file-name (git-file-name name version))
1058        (sha256
1059         (base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
1060     (native-inputs
1061      (list gfortran))
1062     (build-system gnu-build-system)
1063     (synopsis "General Cartographic Transformation Package (GCTP)")
1064     (description
1065      "The General Cartographic Transformation Package (GCTP) is a system of
1066 software routines designed to permit the transformation of coordinate pairs
1067 from one map projection to another.  The GCTP is the standard computer
1068 software used by the National Mapping Division for map projection
1069 computations.")
1070     (home-page "https://github.com/OkoSanto/GCTP")
1071     (license license:public-domain))) ;https://www2.usgs.gov/laws/info_policies.html
1072
1073 (define-public hdf4
1074   (package
1075     (name "hdf4")
1076     (version "4.2.14")
1077     (source
1078      (origin
1079        (method url-fetch)
1080        (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF"
1081                            version "/src/hdf-" version ".tar.bz2"))
1082        (sha256
1083         (base32 "0n29klrrbwan9307np0d9hr128dlpc4nnlf57a140080ll3jmp8l"))
1084        (patches (search-patches "hdf4-architectures.patch"
1085                                 "hdf4-reproducibility.patch"
1086                                 "hdf4-shared-fortran.patch"
1087                                 "hdf4-tirpc.patch"))))
1088     (build-system gnu-build-system)
1089     (native-inputs
1090      (list gfortran bison flex))
1091     (inputs
1092      `(("zlib" ,zlib)
1093        ("libjpeg" ,libjpeg-turbo)
1094        ("libtirpc" ,libtirpc)))
1095     (arguments
1096      `(#:parallel-tests? #f
1097        #:configure-flags (list "--enable-shared"
1098                                "FCFLAGS=-fallow-argument-mismatch"
1099                                "FFLAGS=-fallow-argument-mismatch"
1100                                (string-append "CPPFLAGS=-I"
1101                                               (assoc-ref %build-inputs "libtirpc")
1102                                               "/include/tirpc"))
1103        #:phases
1104        (modify-phases %standard-phases
1105          ;; This is inspired by two of Debian's patches.
1106          (add-before 'configure 'add-more-aarch64-support
1107            (lambda _
1108              (substitute* '("mfhdf/ncgen/ncgen.l"
1109                             "mfhdf/ncgen/ncgenyy.c"
1110                             "mfhdf/libsrc/netcdf.h.in")
1111                (("AIX5L64") "__aarch64__"))
1112              #t))
1113          (add-before 'configure 'patchbuild
1114            (lambda _
1115              (substitute*
1116                  '("mfhdf/hdfimport/testutil.sh.in" "hdf/util/testutil.sh.in")
1117                (("/bin/rm") "rm")
1118                (("/bin/mkdir") "mkdir"))
1119              (substitute* (find-files "." "^Makefile\\.in$")
1120                (("@HDF_BUILD_XDR_TRUE@XDR_ADD = \
1121 -R\\$\\(abs_top_builddir\\)/mfhdf/xdr/\\.libs") "")
1122                (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \
1123 -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \
1124 -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") ""))
1125              #t))
1126          (add-after 'configure 'patch-settings
1127            (lambda _
1128              ;; libhdf4.settings contains the full path of the
1129              ;; compilers used, and its contents are included in
1130              ;; .so-files.  We truncate the hashes to avoid
1131              ;; unnecessary store references to those compilers:
1132              (substitute* "libhdf4.settings"
1133                (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash)
1134                 (string-append prefix (string-take hash 10) "...")))
1135              #t))
1136          (add-after 'install 'provide-absolute-libjpeg-reference
1137            (lambda* (#:key inputs outputs #:allow-other-keys)
1138              (let ((out (assoc-ref outputs "out"))
1139                    (libjpeg (assoc-ref inputs "libjpeg")))
1140                ;; libjpeg-turbo does not provide a .la file, so libtool is
1141                ;; unable to add an absolute reference for -ljpeg in the .la
1142                ;; files.  Fix it manually to avoid having to propagate it.
1143                (substitute* (find-files (string-append out "/lib") "\\.la$")
1144                  (("-ljpeg")
1145                   (string-append "-L" libjpeg "/lib -ljpeg")))
1146                #t))))))
1147     (home-page "https://www.hdfgroup.org/products/hdf4/")
1148     (synopsis
1149      "Library and multi-object file format for storing and managing data")
1150     (description "HDF4 is a library and multi-object file format for storing
1151 and managing data between machines.  HDF4 is an older hierarchical data format,
1152 incompatible with HDF5.")
1153     (license
1154      (license:non-copyleft
1155       "https://www.hdfgroup.org/ftp/HDF/HDF_Current/src/unpacked/COPYING"))))
1156
1157 (define-public hdf4-alt
1158   (package
1159     (inherit hdf4)
1160     (name "hdf4-alt")
1161     (arguments
1162      (substitute-keyword-arguments (package-arguments hdf4)
1163        ((#:configure-flags flags) `(cons* "--disable-netcdf" ,flags))))
1164     (synopsis
1165      "HDF4 without netCDF API, can be combined with the regular netCDF library")))
1166
1167 (define-public hdf5-1.8
1168   (package
1169     (name "hdf5")
1170     (version "1.8.22")
1171     (source
1172      (origin
1173       (method url-fetch)
1174       (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
1175                                 "hdf5-" (version-major+minor version)
1176                                 "/hdf5-" version "/src/hdf5-"
1177                                 version ".tar.bz2")
1178                  (string-append "https://support.hdfgroup.org/ftp/HDF5/"
1179                                 "current"
1180                                 (match (string-split version #\.)
1181                                   ((major minor _ ...)
1182                                    (string-append major minor)))
1183                                 "/src/hdf5-" version ".tar.bz2")))
1184       (sha256
1185        (base32 "194ki2s5jrgl4czkvy5nc9nwjyapah0fj72l0gb0aysplp38i6v8"))
1186       (patches (search-patches "hdf5-config-date.patch"))))
1187     (build-system gnu-build-system)
1188     (inputs
1189      (list zlib))
1190     (native-inputs
1191      (list gfortran perl))                 ;part of the test machinery needs Perl
1192     (outputs '("out"       ; core library
1193                "fortran")) ; fortran interface
1194     (arguments
1195      `(;; Some of the users, notably Flann, need the C++ interface.
1196        #:configure-flags '("--enable-cxx"
1197                            "--enable-fortran"
1198                            "--enable-fortran2003"
1199
1200                            ;; Build a thread-safe library.  Unfortunately,
1201                            ;; 'configure' invites you to either turn off C++,
1202                            ;; Fortran, and the high-level interface (HL), or
1203                            ;; to pass '--enable-unsupported'.  Debian
1204                            ;; packagers chose to pass '--enable-unsupported'
1205                            ;; and we follow their lead here.
1206                            "--enable-threadsafe"
1207                            "--with-pthread"
1208                            "--enable-unsupported")
1209        ;; Use -fPIC to allow the R bindings to link with the static libraries
1210        #:make-flags (list "CFLAGS=-fPIC"
1211                           "CXXFLAGS=-fPIC")
1212        #:phases
1213        (modify-phases %standard-phases
1214          (add-before 'configure 'patch-configure
1215            (lambda* (#:key outputs #:allow-other-keys)
1216              (substitute* "configure"
1217                (("/bin/mv") "mv"))
1218              (substitute* "fortran/src/Makefile.in"
1219                (("libhdf5_fortran_la_LDFLAGS =")
1220                 (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
1221                                (assoc-ref outputs "fortran") "/lib")))
1222              (substitute* "hl/fortran/src/Makefile.in"
1223                (("libhdf5hl_fortran_la_LDFLAGS =")
1224                 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
1225                                (assoc-ref outputs "fortran") "/lib")))
1226              #t))
1227          (add-after 'configure 'patch-settings
1228            (lambda _
1229              ;; libhdf5.settings contains the full path of the
1230              ;; compilers used, and its contents are included in
1231              ;; libhdf5.so.  We truncate the hashes to avoid
1232              ;; unnecessary store references to those compilers:
1233              (substitute* "src/libhdf5.settings"
1234               (("(/gnu/store/)([a-zA-Z0-9]*)" all prefix hash)
1235                (string-append prefix (string-take hash 10) "..."))
1236               ;; Don't record the build-time kernel version to make the
1237               ;; settings file reproducible.
1238               (("Uname information:.*")
1239                "Uname information: Linux\n"))
1240              #t))
1241          (add-after 'install 'patch-references
1242            (lambda* (#:key inputs outputs #:allow-other-keys)
1243              (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
1244                    (zlib (assoc-ref inputs "zlib")))
1245                (substitute* (find-files bin "h5p?cc")
1246                  (("-lz" lib)
1247                   (string-append "-L" zlib "/lib " lib)))
1248                #t)))
1249          (add-after 'install 'split
1250             (lambda* (#:key inputs outputs #:allow-other-keys)
1251               ;; Move all fortran-related files
1252               (let* ((out (assoc-ref outputs "out"))
1253                      (bin (string-append out "/bin"))
1254                      (lib (string-append out "/lib"))
1255                      (inc (string-append out "/include"))
1256                      (ex (string-append out "/share/hdf5_examples/fortran"))
1257                      (fort (assoc-ref outputs "fortran"))
1258                      (fbin (string-append fort "/bin"))
1259                      (flib (string-append fort "/lib"))
1260                      (finc (string-append fort "/include"))
1261                      (fex (string-append fort "/share/hdf5_examples/fortran")))
1262                 (mkdir-p fbin)
1263                 (mkdir-p flib)
1264                 (mkdir-p finc)
1265                 (mkdir-p fex)
1266                 ;; Note: When built with --enable-parallel, the 'h5fc' file
1267                 ;; doesn't exist, hence this condition.
1268                 (when (file-exists? (string-append bin "/h5fc"))
1269                   (rename-file (string-append bin "/h5fc")
1270                                (string-append fbin "/h5fc")))
1271                 (for-each (lambda (file)
1272                             (rename-file file
1273                                          (string-append flib "/" (basename file))))
1274                           (find-files lib ".*fortran.*"))
1275                 (for-each (lambda (file)
1276                             (rename-file file
1277                                          (string-append finc "/" (basename file))))
1278                           (find-files inc ".*mod"))
1279                 (for-each (lambda (file)
1280                             (rename-file file
1281                                          (string-append fex "/" (basename file))))
1282                           (find-files ex ".*"))
1283                 (delete-file-recursively ex))
1284               #t)))))
1285     (home-page "https://www.hdfgroup.org")
1286     (synopsis "Management suite for extremely large and complex data")
1287     (description "HDF5 is a suite that makes possible the management of
1288 extremely large and complex data collections.")
1289     (license (license:x11-style
1290               "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
1291
1292 (define-public hdf5-1.10
1293   (package
1294     (inherit hdf5-1.8)
1295     (version "1.10.7")
1296     (source
1297      (origin
1298        (method url-fetch)
1299        (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
1300                                  "hdf5-" (version-major+minor version)
1301                                  "/hdf5-" version "/src/hdf5-"
1302                                  version ".tar.bz2")
1303                   (string-append "https://support.hdfgroup.org/ftp/HDF5/"
1304                                  "current"
1305                                  (apply string-append
1306                                         (take (string-split version #\.) 2))
1307                                  "/src/hdf5-" version ".tar.bz2")))
1308        (sha256
1309         (base32 "0pm5xxry55i0h7wmvc7svzdaa90rnk7h78rrjmnlkz2ygsn8y082"))
1310        (patches (search-patches "hdf5-config-date.patch"))))))
1311
1312 (define-public hdf5-1.12
1313   (package
1314     (inherit hdf5-1.8)
1315     (version "1.12.1")
1316     (source
1317      (origin
1318        (method url-fetch)
1319        (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
1320                                  "hdf5-" (version-major+minor version)
1321                                  "/hdf5-" version "/src/hdf5-"
1322                                  version ".tar.bz2")
1323                   (string-append "https://support.hdfgroup.org/ftp/HDF5/"
1324                                  "current"
1325                                  (apply string-append
1326                                         (take (string-split version #\.) 2))
1327                                  "/src/hdf5-" version ".tar.bz2")))
1328        (sha256
1329         (base32 "074g3z504xf77ff38igs30i1aqxpm508p7yw78ykva7dncrgbyda"))
1330        (patches (search-patches "hdf5-config-date.patch"))))))
1331
1332 (define-public hdf5
1333   ;; Default version of HDF5.
1334   hdf5-1.10)
1335
1336 (define-public hdf-java
1337   (package
1338     (name "hdf-java")
1339     (version "3.3.2")
1340     (source
1341      (origin
1342        (method url-fetch)
1343        (uri (string-append
1344              "https://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdfjni-"
1345              version "/src/CMake-hdfjava-" version ".tar.gz"))
1346        (sha256
1347         (base32 "0m1gp2aspcblqzmpqbdpfp6giskws85ds6p5gz8sx7asyp7wznpr"))
1348        (modules '((guix build utils)))
1349        (snippet     ; Make sure we don't use the bundled sources and binaries.
1350         `(begin
1351            (for-each delete-file
1352                      (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz"
1353                            "HDF4.tar.gz" "HDF5.tar.gz"))
1354            (delete-file-recursively ,(string-append "hdfjava-" version "/lib"))
1355            #t))))
1356     (build-system gnu-build-system)
1357     (native-inputs
1358      `(("jdk" ,icedtea "jdk")
1359        ("automake" ,automake) ; For up to date 'config.guess' and 'config.sub'.
1360        ;; For tests:
1361        ("hamcrest-core" ,java-hamcrest-core)
1362        ("junit" ,java-junit)
1363        ("slf4j-simple" ,java-slf4j-simple)))
1364     (inputs
1365      `(("hdf4" ,hdf4)
1366        ("hdf5" ,hdf5-1.8)
1367        ("zlib" ,zlib)
1368        ("libjpeg" ,libjpeg-turbo)
1369        ("slf4j-api" ,java-slf4j-api)))
1370     (arguments
1371      `(#:configure-flags
1372        (list (string-append "--target=" ,(or (%current-target-system) (%current-system)))
1373              (string-append "--with-jdk=" (assoc-ref %build-inputs "jdk") "/include,"
1374                             (assoc-ref %build-inputs "jdk") "/lib" )
1375              (string-append "--with-hdf4=" (assoc-ref %build-inputs "hdf4") "/lib")
1376              (string-append "--with-hdf5=" (assoc-ref %build-inputs "hdf5") "/lib"))
1377
1378        #:make-flags
1379        (list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
1380              (string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
1381              (string-append "ZLIB=" (search-input-file %build-inputs "/lib/libz.so"))
1382              (string-append "JPEGLIB="
1383                             (search-input-file %build-inputs "/lib/libjpeg.so"))
1384              "LLEXT=so")
1385
1386        #:phases
1387        (modify-phases %standard-phases
1388          (add-before 'configure 'chdir-to-source
1389            (lambda _ (chdir ,(string-append "hdfjava-" version)) #t))
1390          (add-before 'configure 'patch-build
1391            (lambda* (#:key inputs outputs #:allow-other-keys)
1392              (substitute* "configure"
1393                (("COPT=\"") "COPT=\"-O2 ") ; CFLAGS is ignored in Makefiles
1394                (("/bin/cat") (which "cat")))
1395              ;; Set classpath for compilation
1396              (substitute* '("hdf/hdf5lib/Makefile.in"
1397                             "hdf/hdf5lib/exceptions/Makefile.in"
1398                             "hdf/hdflib/Makefile.in")
1399                (("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
1400                 ;; 'slf4j-api-X.Y.Z.jar' is installed in a Maven-style
1401                 ;; directory, so use 'find-files' to find it.
1402                 (car (find-files (assoc-ref inputs "slf4j-api")
1403                                  "^slf4j-api.*\\.jar$"))))
1404              ;; Replace outdated config.sub and config.guess:
1405              (with-directory-excursion "config"
1406                (for-each (lambda (file)
1407                            (install-file
1408                             (search-input-file inputs
1409                                                (string-append
1410                                                 "/share/automake-"
1411                                                 ,(version-major+minor (package-version automake))
1412                                                 "/" file))
1413                             "."))
1414                          '("config.sub" "config.guess")))
1415
1416              ;; Fix embedded version number
1417              (let ((hdf5version (list ,@(string-split (package-version hdf5) #\.))))
1418                (substitute* "hdf/hdf5lib/H5.java"
1419                  (("1, 8, 19")
1420                   (string-join hdf5version ", "))))
1421
1422              (mkdir-p (string-append (assoc-ref outputs "out")))
1423              ;; Set classpath for tests
1424              (let* ((build-dir (getcwd))
1425                     (lib (string-append build-dir "/lib"))
1426                     (jhdf (string-append lib "/jhdf.jar"))
1427                     (jhdf5 (string-append lib "/jhdf5.jar"))
1428                     (testjars
1429                      (append
1430                        (map (lambda (i)
1431                               (car (find-files (assoc-ref inputs i)
1432                                                (string-append "^" i
1433                                                               ".*\\.jar$"))))
1434                             '("slf4j-api" "slf4j-simple"))
1435                        (list
1436                          (car (find-files (assoc-ref inputs "junit") "jar$"))
1437                          (car (find-files (assoc-ref inputs "hamcrest-core")
1438                                           "jar$")))))
1439                     (class-path
1440                      (string-join `("." ,build-dir ,jhdf ,jhdf5 ,@testjars) ":")))
1441
1442                (substitute* '("test/hdf5lib/Makefile.in"
1443                               "test/hdf5lib/junit.sh.in"
1444                               "examples/runExample.sh.in")
1445                  (("/usr/bin/test")
1446                   (search-input-file inputs "/bin/test"))
1447                  (("/usr/bin/uname")
1448                   (search-input-file inputs "/bin/uname"))
1449                  (("CLASSPATH=[^\n]*")
1450                   (string-append "CLASSPATH=" class-path)))
1451                (setenv "CLASSPATH" class-path))
1452              #t))
1453          (add-before 'check 'build-examples
1454            (lambda _
1455              (apply invoke `("javac"
1456                              ,@(find-files "examples" ".*\\.java"))))))
1457
1458        #:parallel-build? #f
1459
1460        #:parallel-tests? #f ))
1461     (home-page "https://support.hdfgroup.org/products/java")
1462     (synopsis "Java interface for the HDF4 and HDF5 libraries")
1463     (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use
1464 the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are
1465 implemented in C.")
1466
1467     ;; BSD-style license:
1468     (license (license:x11-style
1469               "https://support.hdfgroup.org/ftp/HDF5/hdf-java\
1470 /current/src/unpacked/COPYING"))))
1471
1472 (define-public hdf-eos2
1473   (package
1474     (name "hdf-eos2")
1475     (version "19.1.0")
1476     (source
1477      (origin
1478        (method url-fetch)
1479        (uri "ftp://edhs1.gsfc.nasa.gov\
1480 /edhs/hdfeos/latest_release/HDF-EOS2.19v1.00.tar.Z")
1481        (sha256
1482         (base32 "0c9fcz25s292ldap12wxmlrvnyz99z24p63d8fwx51bf8s0s1zrz"))
1483        (patches (search-patches "hdf-eos2-remove-gctp.patch"
1484                                 "hdf-eos2-build-shared.patch"
1485                                 "hdf-eos2-fortrantests.patch"))))
1486     (build-system gnu-build-system)
1487     (native-inputs
1488      (list gfortran))
1489     (inputs
1490      `(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
1491        ;; XXX: These inputs are really dependencies of hdf4.
1492        ("zlib" ,zlib)
1493        ("libjpeg" ,libjpeg-turbo)
1494        ("libtirpc" ,libtirpc)
1495
1496        ("gctp" ,gctp)))
1497     (arguments
1498      `( #:configure-flags '("--enable-install-include" "--enable-shared"
1499                             "CC=h4cc -Df2cFortran" "LIBS=-lgctp")
1500         #:parallel-tests? #f))
1501     (home-page "https://hdfeos.org/software/library.php#HDF-EOS2")
1502     (synopsis "HDF4-based data format for NASA's Earth Observing System")
1503     (description "HDF-EOS2 is a software library built on HDF4 which supports
1504 the construction of data structures used in NASA's Earth Observing
1505 System (Grid, Point and Swath).")
1506
1507     ;; Source files carry a permissive license header.
1508     (license (license:non-copyleft home-page))))
1509
1510 (define-public hdf-eos5
1511   (package
1512     (name "hdf-eos5")
1513     (version "1.15")
1514     (source (origin
1515               (method url-fetch)
1516               (uri (string-append "ftp://edhs1.gsfc.nasa.gov\
1517 /edhs/hdfeos5/latest_release/HDF-EOS5." version ".tar.Z"))
1518               (sha256
1519                (base32
1520                 "1p83333nzzy8rn5chxlm0hrkjjnhh2w1ji8ac0f9q4xzg838i58i"))
1521               (patches (search-patches "hdf-eos5-build-shared.patch"
1522                                        "hdf-eos5-remove-gctp.patch"
1523                                        "hdf-eos5-fix-szip.patch"
1524                                        "hdf-eos5-fortrantests.patch"))))
1525     (native-inputs
1526      (list gfortran))
1527     (build-system gnu-build-system)
1528     (inputs
1529      (list hdf5-1.8 zlib gctp))
1530     (arguments
1531      `(#:configure-flags '("--enable-install-include" "--enable-shared"
1532                            "CC=h5cc -Df2cFortran" "LIBS=-lgctp")
1533        #:parallel-tests? #f))
1534     (synopsis "HDF5-based data format for NASA's Earth Observing System")
1535     (description
1536      "HDF-EOS5 is a software library built on HDF5 to support the construction
1537 of data structures used in NASA's Earth Observing System (Grid, Point and
1538 Swath).")
1539     (home-page "http://www.hdfeos.org/software/library.php#HDF-EOS5")
1540
1541     ;; Source files carry a permissive license header.
1542     (license (license:non-copyleft home-page))))
1543
1544 (define-public hdf5-parallel-openmpi
1545   (package/inherit hdf5-1.10                      ;use the latest
1546     (name "hdf5-parallel-openmpi")
1547     (inputs
1548      `(("mpi" ,openmpi)
1549        ,@(package-inputs hdf5)))
1550     (arguments
1551      (substitute-keyword-arguments (package-arguments hdf5)
1552        ((#:configure-flags flags)
1553         ``("--enable-parallel"
1554            ,@(delete "--enable-cxx"
1555                      (delete "--enable-threadsafe" ,flags))))
1556        ((#:phases phases)
1557         `(modify-phases ,phases
1558            (add-after 'build 'mpi-setup
1559              ,%openmpi-setup)
1560            (add-before 'check 'patch-tests
1561              (lambda _
1562                ;; OpenMPI's mpirun will exit with non-zero status if it
1563                ;; detects an "abnormal termination", i.e. any process not
1564                ;; calling MPI_Finalize().  Since the test is explicitly
1565                ;; avoiding MPI_Finalize so as not to have at_exit and thus
1566                ;; H5C_flush_cache from being called, mpirun will always
1567                ;; complain, so turn this test off.
1568                (substitute* "testpar/Makefile"
1569                  (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
1570                   (string-append front back "\n")))
1571                (substitute* "tools/test/h5diff/testph5diff.sh"
1572                  (("/bin/sh") (which "sh")))
1573                #t))))))
1574     (synopsis "Management suite for data with parallel IO support")))
1575
1576 (define-public hdf5-blosc
1577   (package
1578     (name "hdf5-blosc")
1579     (version "1.0.0")
1580     (source
1581      (origin
1582        (method git-fetch)
1583        (uri (git-reference
1584              (url "https://github.com/Blosc/hdf5-blosc")
1585              (commit (string-append "v" version))))
1586        (file-name (git-file-name name version))
1587        (sha256
1588         (base32 "1nj2bm1v6ymm3fmyvhbn6ih5fgdiapavlfghh1pvbmhw71cysyqs"))))
1589     (build-system cmake-build-system)
1590     (arguments
1591      `(#:configure-flags
1592        (list (string-append "-DBLOSC_INSTALL_DIR="
1593                             (assoc-ref %build-inputs "c-blosc"))
1594              (string-append "-DPLUGIN_INSTALL_PATH="
1595                             (assoc-ref %outputs "out")
1596                             "/hdf5/lib/plugin"))
1597        #:phases
1598        (modify-phases %standard-phases
1599          (add-after 'unpack 'do-not-build-blosc
1600            (lambda _
1601              (substitute* "CMakeLists.txt"
1602                (("set\\(BLOSC_INSTALL_DIR.*") "")
1603                (("ExternalProject_Add\\(project_blosc") "message("))
1604              #t)))))
1605     (inputs
1606      (list c-blosc hdf5-1.10))
1607     (home-page "https://github.com/Blosc/hdf5-blosc")
1608     (synopsis "Filter for HDF5 using the Blosc compressor")
1609     (description "This is a filter for HDF5 that uses the Blosc compressor; by
1610 installing this filter, you can read and write HDF5 files with
1611 Blosc-compressed datasets.")
1612     (license license:expat)))
1613
1614 (define-public h5check
1615   (package
1616     (name "h5check")
1617     (version "2.0.1")
1618     (source
1619      (origin
1620        (method url-fetch)
1621        (uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/"
1622                            "h5check/src/h5check-" version ".tar.gz"))
1623        (sha256
1624         (base32
1625          "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
1626     (build-system gnu-build-system)
1627     (inputs (list hdf5-1.8))                ;h5cc for tests
1628     (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
1629     (synopsis "HDF5 format checker")
1630     (description "@code{h5check} is a validation tool for verifying that an
1631 HDF5 file is encoded according to the HDF File Format Specification.")
1632     (license (license:x11-style "file://COPYING"))))
1633
1634 (define-public itpp
1635   (package
1636     (name "itpp")
1637     (version "4.3.1")
1638     (source (origin
1639               (method url-fetch)
1640               (uri (string-append "mirror://sourceforge/itpp/itpp/"
1641                                   version "/itpp-"
1642                                   version ".tar.gz"))
1643        (sha256
1644         (base32
1645          "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
1646     (build-system cmake-build-system)
1647     (arguments `(#:tests? #f)) ; Tests require googletest *sources*
1648     (inputs (list lapack fftw))
1649     ;; FIXME: Even though the fonts are available dvips complains:
1650     ;; "Font cmmi10 not found; characters will be left blank."
1651     (native-inputs
1652      `(("texlive" ,texlive-tiny)
1653        ("ghostscript" ,ghostscript)
1654        ("doxygen" ,doxygen)))
1655     (home-page "http://itpp.sourceforge.net")
1656     (synopsis "C++ library of maths, signal processing and communication classes")
1657     (description "IT++ is a C++ library of mathematical, signal processing and
1658 communication classes and functions.  Its main use is in simulation of
1659 communication systems and for performing research in the area of
1660 communications.  The kernel of the library consists of generic vector and
1661 matrix classes, and a set of accompanying routines.  Such a kernel makes IT++
1662 similar to MATLAB, GNU Octave or SciPy.")
1663     (license license:gpl3+)))
1664
1665 (define-public netcdf
1666   (package
1667     (name "netcdf")
1668     (version "4.7.4")
1669     (source
1670      (origin
1671        (method url-fetch)
1672        (uri (string-append
1673              "https://www.unidata.ucar.edu/downloads/netcdf/ftp/"
1674              "netcdf-c-" version ".tar.gz"))
1675        (sha256
1676         (base32
1677          "1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf"))
1678        (modules '((guix build utils)))
1679        (snippet
1680         ;; Make sure this variable is defined only once.  Failing to do so
1681         ;; would break builds of 'netcdf-parallel-openmpi' with a
1682         ;; multiple-definition link error with GCC 10.
1683         '(substitute* "ncdump/ocprint.c"
1684            (("^int ocdebug") "static int ocdebug")))
1685        (patches (search-patches "netcdf-date-time.patch"))))
1686     (build-system gnu-build-system)
1687     (native-inputs
1688      (list m4 doxygen graphviz))
1689     (inputs
1690      `(("hdf4" ,hdf4-alt)
1691        ("hdf5" ,hdf5)
1692        ("curl" ,curl)
1693        ("zlib" ,zlib)
1694        ("libjpeg" ,libjpeg-turbo)))
1695     (arguments
1696      `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
1697
1698        #:phases (modify-phases %standard-phases
1699          (add-before 'configure 'fix-source-date
1700            (lambda _
1701              ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
1702              ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
1703              ;; to '1st hour of the current day', and therefore makes the
1704              ;; package not reproducible.
1705              (substitute* "./configure"
1706                (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
1707                 "date --date='@0'"))
1708              #t))
1709          (add-after 'configure 'patch-settings
1710            (lambda _
1711              ;; libnetcdf.settings contains the full filename of the compilers
1712              ;; used to build the library.  We truncate the hashes of those
1713              ;; filenames to avoid unnecessary references to the corresponding
1714              ;; store items.
1715              (substitute* "libnetcdf.settings"
1716                (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash)
1717                 (string-append prefix (string-take hash 10) "...")))
1718              #t)))
1719
1720        #:parallel-tests? #f))           ;various race conditions
1721     (home-page "https://www.unidata.ucar.edu/software/netcdf/")
1722     (synopsis "Library for scientific data")
1723     (description "NetCDF is an interface for scientific data access and a
1724 software library that provides an implementation of the interface.  The netCDF
1725 library defines a machine-independent format for representing scientific data.
1726 Together, the interface, library, and format support the creation, access, and
1727 sharing of scientific data.")
1728     (license (license:x11-style "file://COPYRIGHT"))))
1729
1730 (define-public netcdf-parallel-openmpi
1731   (package (inherit netcdf)
1732     (name "netcdf-parallel-openmpi")
1733     (inputs
1734      `(("mpi" ,openmpi)
1735        ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
1736                         (package-inputs netcdf))))
1737     ;; TODO: Replace pkg-config references in nc-config with absolute references
1738     (arguments
1739      (substitute-keyword-arguments (package-arguments netcdf)
1740        ((#:configure-flags flags)
1741         `(cons* "CC=mpicc" "CXX=mpicxx"
1742                 "--enable-parallel-tests"
1743                 ;; Shared libraries not supported with parallel IO.
1744                 "--disable-shared" "--with-pic"
1745                 ,flags))
1746        ((#:phases phases '%standard-phases)
1747         `(modify-phases ,phases
1748            (add-after 'build 'mpi-setup
1749              ,%openmpi-setup)))))))
1750
1751 (define-public netcdf-fortran
1752   (package
1753     (name "netcdf-fortran")
1754     (version "4.5.3")
1755     (source (origin
1756               (method url-fetch)
1757               (uri (string-append
1758                     "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-"
1759                     version ".tar.gz"))
1760               (sha256
1761                (base32
1762                 "0x4acvfhbsx1q79dkkwrwbgfhm0w5ngnp4zj5kk92s1khihmqfhj"))))
1763     (build-system gnu-build-system)
1764     (arguments
1765      `(#:configure-flags '("FCFLAGS=-fallow-argument-mismatch"
1766                            "FFLAGS=-fallow-argument-mismatch")
1767        #:parallel-tests? #f))
1768     (inputs
1769      (list netcdf))
1770     (native-inputs
1771      (list gfortran))
1772     (synopsis "Fortran interface for the netCDF library")
1773     (description (package-description netcdf))
1774     (home-page (package-home-page netcdf))
1775     (license (package-license netcdf))))
1776
1777 (define-public nlopt
1778   (package
1779     (name "nlopt")
1780     (version "2.4.2")
1781     (source (origin
1782               (method url-fetch)
1783               (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
1784                                   version ".tar.gz"))
1785               (sha256
1786                (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
1787     (build-system gnu-build-system)
1788     (arguments
1789      `(;; Shared libraries are not built by default.  They are required to
1790        ;; build the Guile, Octave, and Python bindings.
1791        #:configure-flags '("--enable-shared")
1792
1793        #:phases
1794        (modify-phases %standard-phases
1795          (add-before 'configure 'set-libnlopt-file-name
1796            (lambda* (#:key outputs #:allow-other-keys)
1797              ;; Make sure the Scheme module refers to the library by its
1798              ;; absolute file name (we cannot do that from a snippet
1799              ;; because the expansion of @libdir@ contains
1800              ;; ${exec_prefix}.)
1801              (let ((out (assoc-ref outputs "out")))
1802                (substitute* "swig/nlopt.scm.in"
1803                  (("libnlopt")
1804                   (string-append out "/lib/libnlopt")))
1805                #t))))))
1806     (inputs (list guile-2.0))
1807     (native-inputs (list pkg-config))
1808     (home-page "http://ab-initio.mit.edu/wiki/")
1809     (synopsis "Library for nonlinear optimization")
1810     (description "NLopt is a library for nonlinear optimization, providing a
1811 common interface for a number of different free optimization routines available
1812 online as well as original implementations of various other algorithms.")
1813     (license license:lgpl2.1+)))
1814
1815 (define-public ipopt
1816   (package
1817     (name "ipopt")
1818     (version "3.13.4")
1819     (source (origin
1820               (method git-fetch)
1821               (uri (git-reference
1822                     (url "https://github.com/coin-or/Ipopt")
1823                     (commit (string-append "releases/" version))))
1824               (file-name (git-file-name name version))
1825               (sha256
1826                (base32
1827                 "08gznhwhqv1x4baksz350ih8q16r5rd0k8vals6078m3h94khr4b"))))
1828     (build-system gnu-build-system)
1829     (arguments
1830      '(#:phases (modify-phases %standard-phases
1831                   (add-after 'install 'add--L-flags-in-ipopt.pc
1832                     (lambda* (#:key inputs outputs #:allow-other-keys)
1833                       ;; The '.pc' file lists '-llapack -lblas' in "Libs";
1834                       ;; move it to "Libs.private" where it belongs, and add a
1835                       ;; '-L' flag for LAPACK.
1836                       (let ((out    (assoc-ref outputs "out"))
1837                             (lapack (assoc-ref inputs "lapack")))
1838                         (substitute* (string-append out "/lib/pkgconfig/"
1839                                                     "ipopt.pc")
1840                           (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
1841                            (string-append "Libs: " before " " after "\n"
1842                                           "Libs.private: " before
1843                                           "-L" lapack "/lib -llapack -lblas "
1844                                           after "\n")))
1845                         #t))))))
1846     (native-inputs
1847      (list gfortran pkg-config))
1848     (inputs
1849      ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
1850      (list lapack))                    ;for both libblas and liblapack
1851     (home-page "https://www.coin-or.org")
1852     (synopsis "Large-scale nonlinear optimizer")
1853     (description
1854      "The Interior Point Optimizer (IPOPT) is a software package for
1855 large-scale nonlinear optimization.  It provides C++, C, and Fortran
1856 interfaces.")
1857     (license license:epl2.0)))
1858
1859 (define-public nomad-optimizer
1860   (package
1861     (name "nomad-optimizer")
1862     (version "4.1.0")
1863     (source
1864      (origin
1865        (method git-fetch)
1866        (uri (git-reference
1867              (url "https://github.com/bbopt/nomad/")
1868              (commit (string-append "v" version))))
1869        (file-name (git-file-name name version))
1870        (sha256
1871         (base32
1872          "0w386d8r5ldbvnv0c0g7vz95pfpvwdxis26vaalk2amsa5akl775"))))
1873     (build-system cmake-build-system)
1874     (native-inputs
1875      `(("python" ,python-wrapper)
1876        ("python-cython" ,python-cython)))
1877     (arguments
1878      `(#:imported-modules ((guix build python-build-system)
1879                            ,@%cmake-build-system-modules)
1880        #:modules (((guix build python-build-system)
1881                    #:select (python-version site-packages))
1882                   (guix build cmake-build-system)
1883                   (guix build utils))
1884        #:configure-flags
1885        '("-DBUILD_INTERFACES=ON"
1886          "-DBUILD_TESTS=ON")
1887        #:phases
1888        (modify-phases %standard-phases
1889          (add-after 'unpack 'fix-sources-for-build
1890            (lambda* (#:key outputs #:allow-other-keys)
1891              (substitute* "CMakeLists.txt"
1892                ;; CMAKE_INSTALL_PREFIX is accidentally hardcoded.
1893                (("set\\(CMAKE_INSTALL_PREFIX .* FORCE\\)") "")
1894                ;; Requiring GCC version 8 or later is unwarranted.
1895                (("message\\(FATAL_ERROR \"GCC version < 8")
1896                 "message(STATUS \"GCC version < 8"))
1897
1898              (let ((out (assoc-ref outputs "out")))
1899                (substitute* "interfaces/PyNomad/CMakeLists.txt"
1900                  ;; We don't want to build in-place, and anyway the install
1901                  ;; command further below runs build_ext as a prerequisite.
1902                  (("COMMAND python setup_PyNomad\\.py .* build_ext --inplace\n")
1903                   "")
1904                  ;; Don't install locally.
1905                  (("COMMAND python (setup_PyNomad\\.py .* install) --user\n"
1906                    _ args)
1907                   (string-append "COMMAND ${CMAKE_COMMAND} -E env"
1908                                  " CC=" ,(cc-for-target)
1909                                  " CXX=" ,(cxx-for-target)
1910                                  " " (which "python")
1911                                  " " args
1912                                  " --prefix=" out
1913                                  "\n")))
1914                ;; Fix erroneous assumptions about the paths of the include and
1915                ;; library directories.
1916                (substitute* "interfaces/PyNomad/setup_PyNomad.py"
1917                  (("^( +os_include_dirs = ).*" _ prefix)
1918                   (string-append prefix "[\"../../src\"]\n"))
1919                  (("^(installed_lib_dir = ).*" _ prefix)
1920                   (string-append prefix "\"" out "/lib\"\n"))))
1921              #t))
1922
1923          ;; Fix the tests so they run in out-of-source builds.
1924          (add-after 'fix-sources-for-build 'fix-sources-for-tests
1925            (lambda _
1926              (substitute*
1927                  (map (lambda (d) (string-append "examples/" d "/CMakeLists.txt"))
1928                       (append
1929                        (map (lambda (d) (string-append "basic/library/" d))
1930                             '("example1" "example2" "example3"
1931                               "single_obj_parallel"))
1932                        (map (lambda (d) (string-append "advanced/library/" d))
1933                             '("FixedVariable" "NMonly" "PSDMads" "Restart"
1934                               "c_api/example1" "c_api/example2"
1935                               "exampleSuggestAndObserve"))))
1936                ;; The built examples are assumed to be in the source tree
1937                ;; (which isn't the case here).
1938                (("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)"
1939                  _ command test)
1940                 (string-append command "${CMAKE_CURRENT_BINARY_DIR}" test)))
1941              ;; (Unrelated to support for out-of-source testing.)
1942              (make-file-writable
1943               "examples/advanced/library/exampleSuggestAndObserve/cache0.txt")
1944
1945              (let* ((builddir (string-append (getcwd) "/../build"))
1946                     ;; The BB_EXE and SURROGATE_EXE paths are interpreted
1947                     ;; relative to the configuration file provided to NOMAD.
1948                     ;; However, the configuration files are all in the source
1949                     ;; tree rather than in the build tree (unlike the compiled
1950                     ;; executables).
1951                     (fix-exe-path (lambda* (dir #:optional
1952                                                 (file "param.txt")
1953                                                 (exe-opt "BB_EXE"))
1954                                     (substitute* (string-append dir "/" file)
1955                                       (((string-append "^" exe-opt " +"))
1956                                        ;; The $ prevents NOMAD from prefixing
1957                                        ;; the executable with the path of the
1958                                        ;; parent directory of the configuration
1959                                        ;; file NOMAD was provided with as
1960                                        ;; argument (param.txt or some such).
1961                                        (string-append exe-opt " $"
1962                                                       builddir "/" dir "/"))))))
1963                (for-each
1964                 (lambda (dir)
1965                   (let ((dir (string-append "examples/" dir)))
1966                     (substitute* (string-append dir "/CMakeLists.txt")
1967                       ;; The install phase has not yet run.
1968                       (("COMMAND \\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad ")
1969                        "COMMAND ${CMAKE_BINARY_DIR}/src/nomad "))
1970                     (fix-exe-path dir)
1971                     (when (equal? dir "examples/basic/batch/surrogate_sort")
1972                       (fix-exe-path dir "param.txt" "SURROGATE_EXE"))))
1973                 (append (map (lambda (d) (string-append "basic/batch/" d))
1974                              '("example1" "example2"
1975                                "single_obj" "single_obj_parallel"
1976                                "surrogate_sort"))
1977                         '("advanced/batch/LHonly")))
1978
1979                (let ((dir "examples/advanced/batch/FixedVariable"))
1980                  (substitute* (string-append dir "/runFixed.sh")
1981                    ;; Hardcoded path to NOMAD executable.
1982                    (("^\\.\\./\\.\\./\\.\\./\\.\\./bin/nomad ")
1983                     (string-append builddir "/src/nomad ")))
1984                  (for-each
1985                   (lambda (f) (fix-exe-path dir f))
1986                   '("param1.txt" "param2.txt" "param3.txt" "param10.txt"))))
1987              #t))
1988
1989          ;; The information in the .egg-info file is not kept up to date.
1990          (add-after 'install 'delete-superfluous-egg-info
1991            (lambda* (#:key inputs outputs #:allow-other-keys)
1992              (delete-file (string-append
1993                            (site-packages inputs outputs)
1994                            "/PyNomad-0.0.0-py"
1995                            (python-version (assoc-ref inputs "python"))
1996                            ".egg-info"))
1997              #t)))))
1998     (home-page "https://www.gerad.ca/nomad/")
1999     (synopsis "Nonlinear optimization by mesh-adaptive direct search")
2000     (description
2001      "NOMAD is a C++ implementation of the mesh-adaptive direct search (MADS)
2002 algorithm, designed for difficult blackbox optimization problems.  These
2003 problems occur when the functions defining the objective and constraints are
2004 the result of costly computer simulations.")
2005     (license license:lgpl3+)))
2006
2007 (define-public cbc
2008   (package
2009     (name "cbc")
2010     (version "2.10.5")
2011     (source (origin
2012               (method url-fetch)
2013               (uri (string-append "https://www.coin-or.org/download/source/"
2014                                   "Cbc/Cbc-" version ".tgz"))
2015               (sha256
2016                (base32
2017                 "0wk9vr6zc62gw71v7gnra5wxqlcljcgbhm5lasx236v791b986ns"))
2018               (modules '((guix build utils)))
2019               (snippet
2020                ;; Make sure we don't use the bundled software.
2021                '(delete-file-recursively "ThirdParty"))))
2022     (build-system gnu-build-system)
2023     (native-inputs
2024      (list gfortran pkg-config))
2025     (inputs
2026      (list openblas))
2027     (home-page "https://www.coin-or.org")
2028     (synopsis "Branch-and-cut solver")
2029     (description
2030      "Cbc (Coin-or branch and cut) is a mixed integer linear programming
2031 solver written in C++.  It can be used as a library or as a standalone
2032 executable.")
2033     (license license:epl1.0)))
2034
2035 (define-public clp
2036   (package
2037     (name "clp")
2038     (version "1.17.6")
2039     (source (origin
2040               (method url-fetch)
2041               (uri (string-append "https://www.coin-or.org/download/source/"
2042                                   "Clp/Clp-" version ".tgz"))
2043               (sha256
2044                (base32
2045                 "0ap1f0lxppa6pnbc4bg7ih7a96avwaki482nig8w5fr3vg9wvkzr"))
2046               (modules '((guix build utils)))
2047               (snippet
2048                ;; Make sure we don't use the bundled software.
2049                '(begin
2050                   (delete-file-recursively "ThirdParty")
2051                   #t))))
2052     (build-system gnu-build-system)
2053     (native-inputs
2054      (list gfortran pkg-config))
2055     (inputs
2056      (list openblas))
2057     (home-page "https://www.coin-or.org")
2058     (synopsis "Linear programming solver")
2059     (description
2060      "CLP is a high quality linear programming solver.  Its main strengths are
2061 its dual and primal Simplex algorithms.  It also has a barrier algorithm for
2062 linear and quadratic objectives.  There are limited facilities for nonlinear
2063 and quadratic objectives using the Simplex algorithm.")
2064     (license license:epl1.0)))
2065
2066 (define-public gecode
2067   (package
2068     (name "gecode")
2069     (version "6.2.0")
2070     (source (origin
2071               (method git-fetch)
2072               (uri (git-reference
2073                     (url "https://github.com/Gecode/gecode")
2074                     (commit (string-append "release-" version))))
2075               (file-name (git-file-name name version))
2076               (sha256
2077                (base32
2078                 "0b1cq0c810j1xr2x9y9996p894571sdxng5h74py17c6nr8c6dmk"))
2079               (modules '((guix build utils)))
2080               (snippet
2081                '(begin
2082                   ;; delete generated sources
2083                   (for-each delete-file
2084                             '("gecode/kernel/var-imp.hpp"
2085                               "gecode/kernel/var-type.hpp"))))))
2086     (outputs '("out" "examples"))
2087     (build-system gnu-build-system)
2088     (arguments
2089      `(#:configure-flags
2090        (list (string-append "GLDFLAGS=-Wl,-rpath="
2091                             (assoc-ref %outputs "out")
2092                             "/lib")
2093              "--enable-examples=no")
2094        #:modules ((guix build gnu-build-system)
2095                   (guix build utils)
2096                   (ice-9 rdelim)
2097                   (ice-9 popen))
2098        #:phases
2099        (modify-phases %standard-phases
2100          (add-after 'build 'build-examples
2101            (lambda* (#:key outputs #:allow-other-keys)
2102              (invoke "make" "compileexamples")))
2103          ;; The Makefile disrespects GLDFLAGS for some reason, so we have to
2104          ;; patch it ourselves... *sigh*
2105          (add-after 'install 'fix-rpath
2106            (lambda* (#:key outputs #:allow-other-keys)
2107              (let ((libdir (string-append (assoc-ref outputs "out") "/lib")))
2108                (for-each
2109                 (lambda (file)
2110                   (let* ((pipe (open-pipe* OPEN_READ "patchelf"
2111                                           "--print-rpath" file))
2112                          (line (read-line pipe)))
2113                     (and (zero? (close-pipe pipe))
2114                          (invoke "patchelf" "--set-rpath"
2115                                  (string-append libdir ":" line)
2116                                  file))))
2117                 (find-files libdir ".*\\.so$")))))
2118          (add-after 'install 'install-examples
2119            (lambda* (#:key outputs #:allow-other-keys)
2120              (invoke "make" "installexamples"
2121                      (string-append "bindir=" (assoc-ref outputs "examples")
2122                                     "/bin"))))
2123          ;; Tests depend on installed libraries.
2124          (delete 'check)
2125          (add-after 'fix-rpath 'check
2126            (assoc-ref %standard-phases 'check)))))
2127     (native-inputs
2128      (list patchelf perl sed))
2129     (home-page "https://www.gecode.org")
2130     (synopsis "Toolkit for developing constraint-based systems")
2131     (description "Gecode is a C++ toolkit for developing constraint-based
2132 systems and applications.  It provides a modular and extensible solver.")
2133     (license license:expat)))
2134
2135 (define-public libflame
2136   (package
2137     (name "libflame")
2138     (version "5.2.0")
2139     (outputs '("out" "static"))
2140     (source
2141       (origin
2142         (method git-fetch)
2143         (uri (git-reference
2144                (url "https://github.com/flame/libflame")
2145                (commit version)))
2146         (file-name (git-file-name name version))
2147         (sha256
2148          (base32
2149           "1n6lf0wvpp77lxqlr721h2jbfbzigphdp19wq8ajiccilcksh7ay"))))
2150     (build-system gnu-build-system)
2151     (arguments
2152      `(#:configure-flags
2153        ;; Sensible defaults: https://github.com/flame/libflame/issues/28
2154        (list "--enable-dynamic-build"
2155              "--enable-max-arg-list-hack"
2156              "--enable-lapack2flame"
2157              "--enable-verbose-make-output"
2158              "--enable-multithreading=pthreads" ; Openblas isn't built with openmp.
2159              ,@(if (any (cute string-prefix? <> (or (%current-target-system)
2160                                                     (%current-system)))
2161                         '("x86_64" "i686"))
2162                  '("--enable-vector-intrinsics=sse")
2163                  '())
2164              "--enable-supermatrix"
2165              "--enable-memory-alignment=16"
2166              "--enable-ldim-alignment")
2167        #:phases
2168        (modify-phases %standard-phases
2169          (add-after 'unpack 'patch-/usr/bin/env-bash
2170            (lambda _
2171              (substitute* "build/config.mk.in"
2172                (("/usr/bin/env bash") (which "bash")))
2173              #t))
2174          (replace 'check
2175            (lambda* (#:key tests? #:allow-other-keys)
2176              (substitute* "test/Makefile"
2177                (("LIBBLAS .*") "LIBBLAS = -lblas\n")
2178                (("LIBLAPACK .*") "LIBLAPACK = -llapack\n"))
2179              (if tests?
2180                (with-directory-excursion "test"
2181                  (mkdir "obj")
2182                  (invoke "make")
2183                  (invoke "./test_libflame.x"))
2184                #t)))
2185          (add-after 'install 'install-static
2186            (lambda* (#:key outputs #:allow-other-keys)
2187              (let ((out (assoc-ref outputs "out"))
2188                    (static (assoc-ref outputs "static")))
2189                (mkdir-p (string-append static "/lib"))
2190                (rename-file (string-append out "/lib/libflame.a")
2191                             (string-append static "/lib/libflame.a"))
2192                (install-file (string-append out "/include/FLAME.h")
2193                              (string-append static "/include"))
2194                #t))))))
2195     (inputs
2196      (list gfortran))
2197     (native-inputs
2198      `(("lapack" ,lapack)
2199        ("openblas" ,openblas)
2200        ("perl" ,perl)
2201        ("python" ,python-wrapper)))
2202     (home-page "https://github.com/flame/libflame")
2203     (synopsis "High-performance object-based library for DLA computations")
2204     (description "@code{libflame} is a portable library for dense matrix
2205 computations, providing much of the functionality present in LAPACK, developed
2206 by current and former members of the @acronym{SHPC, Science of High-Performance
2207 Computing} group in the @url{https://www.ices.utexas.edu/, Institute for
2208 Computational Engineering and Sciences} at The University of Texas at Austin.
2209 @code{libflame} includes a compatibility layer, @code{lapack2flame}, which
2210 includes a complete LAPACK implementation.")
2211     (license license:bsd-3)))
2212
2213 (define-public libpotassco
2214   ;; No public release, update together with clasp
2215   (let ((revision "1")
2216         (commit "2f9fb7ca2c202f1b47643aa414054f2f4f9c1821"))
2217     (package
2218       (name "libpotassco")
2219       (version (git-version "0.0" revision commit))
2220       (source (origin
2221                 (method git-fetch)
2222                 (uri (git-reference
2223                       (url "https://github.com/potassco/libpotassco")
2224                       (commit commit)))
2225                 (file-name (git-file-name name version))
2226                 (sha256
2227                  (base32
2228                   "1c32f9gqclf7qx07lpx8wd720vfhkjqhzc6nyy8mjmgwpmb3iyyn"))))
2229       (arguments
2230        `(#:configure-flags '("-DLIB_POTASSCO_BUILD_TESTS=on"
2231                              "-DLIB_POTASSCO_INSTALL_LIB=on"
2232                              "-DBUILD_SHARED_LIBS=on")
2233          #:phases
2234          (modify-phases %standard-phases
2235            (add-after 'unpack 'patch-cmake
2236              (lambda _
2237                (substitute* "CMakeLists.txt"
2238                  ;; clasp expects lowercase potassco and include directory is
2239                  ;; lowercase as well, so let's use that
2240                  (("\"cmake/Potassco\"") "\"cmake/potassco\"")
2241                  (("PotasscoConfig\\.cmake") "potassco-config.cmake")
2242                  (("PotasscoConfigVersion\\.cmake")
2243                   "potassco-config-version.cmake"))
2244                (rename-file "cmake/PotasscoConfig.cmake.in"
2245                             "cmake/potassco-config.cmake.in"))))))
2246       (build-system cmake-build-system)
2247       (home-page "https://potassco.org/")
2248       (synopsis "Utility library for Potassco's projects")
2249       (description "@code{libpotassco} is a utility library providing functions
2250 and datatypes for
2251 @itemize
2252 @item parsing, writing, and converting logic programs in aspif and smodels
2253 format,
2254 @item passing information between a grounder and a solver,
2255 @item and defining and parsing command-line options and for creating
2256 command-line applications.
2257 @end itemize
2258 Furthermore, it comes with the tool @command{lpconvert} that converts either
2259 between aspif and smodels format or to a human-readable text format.")
2260       (license license:expat))))
2261
2262 (define-public clasp
2263   (package
2264     (name "clasp")
2265     (version "3.3.6")
2266     (source (origin
2267               (method git-fetch)
2268               (uri (git-reference
2269                     (url "https://github.com/potassco/clasp")
2270                     (commit (string-append "v" version))))
2271               (file-name (git-file-name name version))
2272               (sha256
2273                (base32
2274                 "0rahqiq530jckvx717858h1q5p8znp1kb6sjm95p8blkr4n3pvmj"))))
2275     (build-system cmake-build-system)
2276     (arguments
2277      `(#:configure-flags '("-DCLASP_BUILD_TESTS=on"
2278                            "-DCLASP_INSTALL_LIB=on"
2279                            "-DCLASP_USE_LOCAL_LIB_POTASSCO=off"
2280                            "-DBUILD_SHARED_LIBS=on")
2281        #:phases
2282        (modify-phases %standard-phases
2283          (add-after 'unpack 'patch-cmake
2284            (lambda _
2285              (substitute* "CMakeLists.txt"
2286                ;; Use lowercase to be consistent with libpotassco
2287                (("\"cmake/Clasp\"") "\"cmake/clasp\"")
2288                (("ClaspConfig\\.cmake") "clasp-config.cmake")
2289                (("ClaspConfigVersion\\.cmake")
2290                 "clasp-config-version.cmake"))
2291              (substitute* "cmake/ClaspConfig.cmake.in"
2292                (("find_package\\(Potassco") "find_package(potassco"))
2293              (rename-file "cmake/ClaspConfig.cmake.in"
2294                           "cmake/clasp-config.cmake.in"))))))
2295     (inputs
2296      (list libpotassco))
2297     (home-page "https://potassco.org/")
2298     (synopsis "Answer set solver")
2299     (description "clasp is an answer set solver for (extended) normal and
2300 disjunctive logic programs.  The primary algorithm of clasp relies on
2301 conflict-driven nogood learning, a technique that proved very successful for
2302 satisfiability checking (SAT).")
2303     (license license:expat)))
2304
2305 (define-public clingo
2306   (package
2307     (name "clingo")
2308     (version "5.5.0")
2309     (source (origin
2310               (method git-fetch)
2311               (uri (git-reference
2312                     (url "https://github.com/potassco/clingo")
2313                     (commit (string-append "v" version))))
2314               (file-name (git-file-name name version))
2315               (sha256
2316                (base32
2317                 "0rfjwkcwm0mmf3r4i7asyjwb6cia4i7px7fn2kdbi9j85qvas4pb"))))
2318     (build-system cmake-build-system)
2319     (arguments
2320      `(#:configure-flags `("-DCLINGO_BUILD_TESTS=on"
2321                            "-DCLINGO_INSTALL_LIB=on"
2322                            "-DCLINGO_BUILD_STATIC=off"
2323                            "-DCLINGO_BUILD_SHARED=on"
2324                            ;; XXX: Clingo requries private headers and
2325                            ;;      sources from clasp
2326                            ,(string-append
2327                              "-DCLASP_SOURCE_DIR="
2328                              (assoc-ref %build-inputs "clasp-src")))
2329        #:phases
2330        (modify-phases %standard-phases
2331          (add-after 'unpack 'patch-cmake
2332            (lambda _
2333              (substitute* "CMakeLists.txt"
2334                (("add_subdirectory\\(clasp\\)")
2335                 "find_package(clasp REQUIRED)"))
2336              (substitute* "libclingo/CMakeLists.txt"
2337                (("\"cmake/Clingo\"") "\"cmake/clingo\"")
2338                (("ClingoConfig\\.cmake") "clingo-config.cmake")
2339                (("ClingoConfigVersion\\.cmake")
2340                 "clingo-config-version.cmake"))
2341              (substitute* "cmake/ClingoConfig.cmake.in"
2342                (("find_package\\(Clasp") "find_package(clasp"))
2343              (rename-file "cmake/ClingoConfig.cmake.in"
2344                           "cmake/clingo-config.cmake.in")))
2345          (add-after 'unpack 'skip-failing-tests
2346            (lambda _
2347              (with-directory-excursion "libclingo/tests"
2348                (substitute* "CMakeLists.txt"
2349                  (("COMMAND test_clingo" all)
2350                   (string-append all
2351                                  " -f "
2352                                  "\"${CMAKE_CURRENT_SOURCE_DIR}/good.txt\"")))
2353                (call-with-output-file "good.txt"
2354                  (lambda (port)
2355                    (for-each (lambda (test) (format port "~s~%" test))
2356                              '("parse-ast-v2" "add-ast-v2" "build-ast-v2"
2357                                "unpool-ast-v2" "parse_term"
2358                                "propagator" "propgator-sequence-mining"
2359                                "symbol" "visitor"))))))))))
2360     (inputs
2361      (list clasp libpotassco))
2362     (native-inputs
2363      `(("clasp-src" ,(package-source clasp))))
2364     (home-page "https://potassco.org/")
2365     (synopsis "Grounder and solver for logic programs")
2366     (description "Clingo computes answer sets for a given logic program.")
2367     (license license:expat)))
2368
2369 (define-public ceres
2370   (package
2371     (name "ceres-solver")
2372     (version "1.14.0")
2373     (home-page "http://ceres-solver.org/")
2374     (source (origin
2375               (method url-fetch)
2376               (uri (string-append home-page "ceres-solver-"
2377                                   version ".tar.gz"))
2378               (sha256
2379                (base32
2380                 "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
2381     (build-system cmake-build-system)
2382     (arguments
2383      ;; TODO: Build HTML user documentation and install separately.
2384      '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
2385                            "-DBUILD_SHARED_LIBS=ON")
2386
2387        #:phases (modify-phases %standard-phases
2388                   (add-before 'configure 'set-library-directory
2389                     (lambda _
2390                       ;; Install libraries to lib/, not lib64/.
2391                       (substitute* "CMakeLists.txt"
2392                         (("set\\(LIB_SUFFIX \"64\"\\)")
2393                          "set(LIB_SUFFIX \"\")")))))))
2394     (native-inputs
2395      (list pkg-config))
2396     (propagated-inputs
2397      (list glog))                           ;for #include <glog/glog.h>
2398     (inputs
2399      `(("eigen" ,eigen)
2400        ("blas" ,openblas)
2401        ("lapack" ,lapack)
2402        ("suitesparse" ,suitesparse)
2403        ("gflags" ,gflags)))
2404     (synopsis "C++ library for solving large optimization problems")
2405     (description
2406      "Ceres Solver is a C++ library for modeling and solving large,
2407 complicated optimization problems.  It is a feature rich, mature and
2408 performant library which has been used in production since 2010.  Ceres Solver
2409 can solve two kinds of problems:
2410 @enumerate
2411 @item non-linear least squares problems with bounds constraints;
2412 @item general unconstrained optimization problems.
2413 @end enumerate\n")
2414     (license license:bsd-3)))
2415
2416 ;; For a fully featured Octave, users are strongly recommended also to install
2417 ;; the following packages: less, ghostscript, gnuplot.
2418 (define-public octave-cli
2419   (package
2420     (name "octave-cli")
2421     (version "6.2.0")
2422     (source
2423      (origin
2424       (method url-fetch)
2425       (uri (string-append "mirror://gnu/octave/octave-"
2426                           version ".tar.xz"))
2427       (sha256
2428        (base32
2429         "06id09zspya24gshcwgp039cp35c06150mdlxysawgnbrhj16wkv"))))
2430     (build-system gnu-build-system)
2431     (inputs
2432      `(("alsa-lib" ,alsa-lib)
2433        ("arpack" ,arpack-ng)
2434        ("bdb" ,bdb)
2435        ("curl" ,curl)
2436        ("fftw" ,fftw)
2437        ("fftwf" ,fftwf)
2438        ("fltk" ,fltk)
2439        ("fontconfig" ,fontconfig)
2440        ("freetype" ,freetype)
2441        ("gl2ps" ,gl2ps)
2442        ("glpk" ,glpk)
2443        ("glu" ,glu)
2444        ("graphicsmagick" ,graphicsmagick)
2445
2446        ;; TODO: libjpeg-turbo is indirectly required through libtiff.  In
2447        ;; the next rebuild cycle, add an absolute reference for -ljpeg in
2448        ;; libtiff.la instead of having to provide it here.
2449        ("libjpeg" ,libjpeg-turbo)
2450
2451        ("hdf5" ,hdf5)
2452        ("lapack" ,lapack)
2453        ("libsndfile" ,libsndfile)
2454        ("libxft" ,libxft)
2455        ("mesa" ,mesa)
2456        ("pcre" ,pcre)
2457        ("portaudio" ,portaudio)
2458        ("qhull" ,qhull)
2459        ("readline" ,readline)
2460        ("suitesparse" ,suitesparse)
2461        ("texinfo" ,texinfo)
2462        ("zlib" ,zlib)))
2463     (native-inputs
2464      (list gfortran
2465            pkg-config
2466            perl
2467            ;; The following inputs are not actually used in the build process.
2468            ;; However, the ./configure gratuitously tests for their existence and
2469            ;; assumes that programs not present at build time are also not, and
2470            ;; can never be, available at run time!  If these inputs are therefore
2471            ;; not present, support for them will be built out.  However, Octave
2472            ;; will still run without them, albeit without the features they
2473            ;; provide.
2474            less
2475            ghostscript
2476            gnuplot))
2477     ;; Octave code uses this variable to detect directories holding multiple CA
2478     ;; certificates to verify peers with.  This is required for the networking
2479     ;; functions that require encryption to work properly.
2480     (native-search-paths
2481      (list (search-path-specification
2482             (variable "CURLOPT_CAPATH")
2483             (files '("etc/ssl/certs")))))
2484     (arguments
2485      `(#:configure-flags
2486        (list (string-append "--with-shell="
2487                             (assoc-ref %build-inputs "bash")
2488                             "/bin/sh")
2489
2490              ;; XXX: Without this flag, linking octave-cli fails with
2491              ;; undefined references to 'logf@GLIBCXX_3.4' et.al. due to
2492              ;; not pulling in liboctinterp.la for -lstdc++.
2493              "--enable-link-all-dependencies")
2494        #:phases
2495        (modify-phases %standard-phases
2496          (add-after 'configure 'configure-makeinfo
2497            (lambda* (#:key inputs #:allow-other-keys)
2498              (substitute* "libinterp/corefcn/help.h"
2499                (("\"makeinfo\"")
2500                 (string-append
2501                  "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
2502              #t)))))
2503     (home-page "https://www.gnu.org/software/octave/")
2504     (synopsis "High-level language for numerical computation (no GUI)")
2505     (description "GNU Octave is a high-level interpreted language that is
2506 specialized for numerical computations.  It can be used for both linear and
2507 non-linear applications and it provides great support for visualizing results.
2508 Work may be performed both at the interactive command-line as well as via
2509 script files.")
2510     (license license:gpl3+)))
2511
2512 (define-public octave
2513   (package (inherit octave-cli)
2514     (name "octave")
2515     (inputs
2516      `(("qscintilla" ,qscintilla)
2517        ("qt" ,qtbase-5)
2518        ,@(package-inputs octave-cli)))
2519     (native-inputs
2520      `(("qttools" , qttools) ;for lrelease
2521        ("texlive" ,(texlive-updmap.cfg (list texlive-epsf))) ; for texi2dvi
2522        ,@(package-native-inputs octave-cli)))
2523     (arguments
2524      (substitute-keyword-arguments (package-arguments octave-cli)
2525        ((#:phases phases)
2526         `(modify-phases ,phases
2527            (add-before 'configure 'patch-qscintilla-library-name
2528              (lambda* (#:key inputs #:allow-other-keys)
2529                ;; The QScintilla library that the Octave configure script tries
2530                ;; to link with should be named libqscintilla-qt5.so, but the
2531                ;; QScintilla input provides the shared library as
2532                ;; libqscintilla2_qt5.so.
2533                (substitute* "configure"
2534                  (("qscintilla2-qt5")
2535                   "qscintilla2_qt5"))
2536                #t))))))
2537     (synopsis "High-level language for numerical computation (with GUI)")))
2538
2539 (define-public opencascade-oce
2540   (package
2541     (name "opencascade-oce")
2542     (version "0.17.2")
2543     (source
2544       (origin
2545         (method git-fetch)
2546         (uri (git-reference
2547               (url "https://github.com/tpaviot/oce")
2548               (commit (string-append "OCE-" version))))
2549         (file-name (git-file-name name version))
2550         (patches (search-patches "opencascade-oce-glibc-2.26.patch"))
2551         (sha256
2552           (base32 "0rg5wzkvfmzfl6v2amyryb8dnjad0nn9kyr607wy2gch6rciah69"))))
2553     (build-system cmake-build-system)
2554     (arguments
2555      '(#:configure-flags
2556         (list "-DOCE_TESTING:BOOL=ON"
2557               "-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=ON"
2558               "-DOCE_DRAW:BOOL=ON"
2559               (string-append "-DOCE_INSTALL_PREFIX:PATH="
2560                         (assoc-ref %outputs "out"))
2561               "-UCMAKE_INSTALL_RPATH")))
2562     (inputs
2563       (list freetype
2564             glu
2565             libxmu
2566             mesa
2567             tcl
2568             tk))
2569     (native-inputs
2570       `(("python" ,python-wrapper)))
2571     (home-page "https://github.com/tpaviot/oce")
2572     (synopsis "Libraries for 3D modeling and numerical simulation")
2573     (description
2574      "Open CASCADE is a set of libraries for the development of applications
2575 dealing with 3D CAD data or requiring industrial 3D capabilities.  It includes
2576 C++ class libraries providing services for 3D surface and solid modeling, CAD
2577 data exchange, and visualization.  It is used for development of specialized
2578 software dealing with 3D models in design (CAD), manufacturing (CAM),
2579 numerical simulation (CAE), measurement equipment (CMM), and quality
2580 control (CAQ) domains.
2581
2582 This is the ``Community Edition'' (OCE) of Open CASCADE, which gathers
2583 patches, improvements, and experiments contributed by users over the official
2584 Open CASCADE library.")
2585     (license (list license:lgpl2.1; OCE libraries, with an exception for the
2586                                   ; use of header files; see
2587                                   ; OCCT_LGPL_EXCEPTION.txt
2588                    license:public-domain; files
2589                                   ; src/Standard/Standard_StdAllocator.hxx and
2590                                   ; src/NCollection/NCollection_StdAllocator.hxx
2591                    license:expat; file src/OpenGl/OpenGl_glext.h
2592                    license:bsd-3)))); test framework gtest
2593
2594 (define-public opencascade-occt
2595   (package
2596     (name "opencascade-occt")
2597     (version "7.3.0p3")
2598     (source
2599       (origin
2600         (method git-fetch)
2601         (uri (git-reference
2602               (url "https://git.dev.opencascade.org/repos/occt.git")
2603               (commit
2604                (string-append "V"
2605                               (string-map (lambda (x) (if (eq? x #\.) #\_ x))
2606                                           version)))))
2607         (file-name (git-file-name name version))
2608         (sha256
2609          (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
2610         (modules '((guix build utils)))
2611         (snippet
2612          '(begin
2613             ;; Remove files specific to non-free operating systems.
2614             (delete-file-recursively "samples/ios")
2615             (delete-file-recursively "samples/mfc")
2616             (delete-file-recursively "samples/qt/FuncDemo")
2617             (delete-file "genconf.bat")
2618             (delete-file "gendoc.bat")
2619             (delete-file "genproj.bat")
2620             (delete-file "upgrade.bat")
2621             ;; Remove references to deleted files.
2622             (substitute* "dox/FILES_HTML.txt"
2623               ((".*standard.*") "" )
2624               ((".*UIKitSample.*") ""))
2625             #t))))
2626     (build-system cmake-build-system)
2627     (arguments
2628      '(;; There is no test target for make.  OCCT provides an
2629        ;; 'Automated Testing System', which may be accessed after
2630        ;; installation via the draw.sh script.  draw.sh is located in
2631        ;; the bin directory. For details see:
2632        ;; https://www.opencascade.com/doc/occt-7.3.0/overview/html/\
2633        ;; occt_dev_guides__tests.html
2634        #:tests? #f
2635        ;; Configure without freeimage: attempting to link against the
2636        ;; freeimage version 3.17 library leads to 'undefined
2637        ;; reference' errors.
2638        #:configure-flags
2639         (list "-DUSE_FREEIMAGE:BOOL=OFF"
2640               "-DUSE_TBB:BOOL=ON"
2641               "-DUSE_VTK:BOOL=OFF"
2642               "-DBUILD_DOC_Overview:BOOL=OFF"
2643               "-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
2644               "-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
2645               "-UCMAKE_INSTALL_LIBDIR")))
2646     (inputs
2647      (list doxygen
2648            ;("freeimage" ,freeimage)
2649            freetype
2650            glu
2651            libxext
2652            libxi
2653            libxmu
2654            mesa
2655            tbb-2020
2656            tcl
2657            tk))
2658     ;; TODO: build Overview documentation and add 'doc' output.
2659     (home-page "https://www.opencascade.com")
2660     (synopsis "Libraries for 3D modeling and numerical simulation")
2661     (description
2662      "Open CASCADE is a set of libraries for the development of applications
2663 dealing with 3D CAD data or requiring industrial 3D capabilities.  It includes
2664 C++ class libraries providing services for 3D surface and solid modeling, CAD
2665 data exchange, and visualization.  It is used for development of specialized
2666 software dealing with 3D models in design (CAD), manufacturing (CAM),
2667 numerical simulation (CAE), measurement equipment (CMM), and quality
2668 control (CAQ) domains.
2669
2670 This is the certified version of the Open Cascade Technology (OCCT) library.")
2671     (license (list ;; OCCT library:
2672                    license:lgpl2.1; with an exception for the use of header
2673                                   ; files, see OCCT_LGPL_EXCEPTION.txt.
2674                    ;; Files src/OpenGl/glext.h, adm/cmake/cotire.cmake and
2675                    ;; src/OpenGl/OpenGl_HaltonSampler.hxx:
2676                    license:expat
2677                    ;; Files src/ExprIntrp/ExprIntrp.tab.* and
2678                    ;; src/StepFile/step.tab.*:
2679                    license:gpl3+  ; with Bison 2.2 exception.
2680                    ;; File src/NCollection/NCollection_UtfIterator.lxx:
2681                    (license:non-copyleft
2682                     "https://www.unicode.org/license.html")
2683                    ;; File src/NCollection/NCollection_StdAllocator.hxx:
2684                    license:public-domain))))
2685
2686 (define-public gmsh
2687   (package
2688     (name "gmsh")
2689     (version "4.8.4")
2690     (source
2691      (origin
2692       (method git-fetch)
2693       (uri (git-reference
2694             (url "https://gitlab.onelab.info/gmsh/gmsh.git")
2695             (commit
2696              (string-append "gmsh_"
2697                             (string-replace-substring version "." "_")))))
2698       (file-name (git-file-name name version))
2699       (sha256
2700        (base32 "07mi6ja3b9libgcdp2b4dwnkap1b9ha2wi2zdn9mhmwvp3g1pxhp"))
2701       (modules '((guix build utils)))
2702       (snippet
2703        '(begin
2704           (delete-file-recursively "contrib/metis")
2705           #t))))
2706     (build-system cmake-build-system)
2707     (propagated-inputs
2708      (list fltk
2709            gfortran
2710            glu
2711            gmp
2712            hdf5
2713            lapack
2714            libx11
2715            libxext
2716            mesa
2717            metis
2718            opencascade-occt))
2719     (inputs
2720      `(("fontconfig" ,fontconfig)
2721        ("libxft" ,libxft)
2722        ("python" ,python)))
2723     (arguments
2724      `(#:configure-flags `("-DENABLE_SYSTEM_CONTRIB:BOOL=ON"
2725                            "-DENABLE_BUILD_SHARED:BOOL=ON"
2726                            "-DENABLE_BUILD_DYNAMIC:BOOL=ON")
2727        #:imported-modules (,@%cmake-build-system-modules
2728                            (guix build python-build-system))
2729        #:modules (((guix build python-build-system) #:select (site-packages))
2730                   (guix build cmake-build-system)
2731                   (guix build utils))
2732        #:phases
2733        (modify-phases %standard-phases
2734          (add-after 'unpack 'patch-paths
2735            (lambda* (#:key inputs outputs #:allow-other-keys)
2736              ;; Use the standard Guix site-package path for
2737              ;; installation of the Python API.
2738              (substitute* "CMakeLists.txt"
2739                (("include\\(GNUInstallDirs\\)\n")
2740                 (string-append "include(GNUInstallDirs)\n"
2741                                "  set(GMSH_PY_LIB "
2742                                (site-packages inputs outputs) ")\n"))
2743                (("\\$\\{GMSH\\_PY\\} DESTINATION \\$\\{GMSH\\_LIB\\}")
2744                 "${GMSH_PY} DESTINATION ${GMSH_PY_LIB}"))
2745              ;; Find the shared library.
2746              (let ((libgmsh (string-append (assoc-ref outputs "out")
2747                                            "/lib/libgmsh.so")))
2748                (substitute* "api/gmsh.py"
2749                  (("find_library\\(\"gmsh\"\\)")
2750                   (simple-format #f "\"~a\"" libgmsh))))
2751              #t)))))
2752     (home-page "http://gmsh.info/")
2753     (synopsis "3D finite element grid generator")
2754     (description "Gmsh is a 3D finite element grid generator with a built-in
2755 CAD engine and post-processor.  Its design goal is to provide a fast, light
2756 and user-friendly meshing tool with parametric input and advanced
2757 visualization capabilities.  Gmsh is built around four modules: geometry,
2758 mesh, solver and post-processing.  The specification of any input to these
2759 modules is done either interactively using the graphical user interface or in
2760 ASCII text files using Gmsh's own scripting language.")
2761     (license license:gpl2+)))
2762
2763 (define-public veusz
2764   (package
2765     (name "veusz")
2766     (version "3.3.1")
2767     (source
2768      (origin
2769        (method url-fetch)
2770        (uri (pypi-uri "veusz" version))
2771        (sha256
2772         (base32 "1q7hi1qwwg4pgiz62isvv1pia85m13bspdpp1q3mrnwl11in0ag0"))))
2773     (build-system python-build-system)
2774     (arguments
2775      `(;; Tests will fail because they depend on optional packages like
2776        ;; python-astropy, which is not packaged.
2777        #:tests? #f
2778        #:phases
2779        (modify-phases %standard-phases
2780          ;; Veusz will append 'PyQt5' to sip_dir by default. That is not how
2781          ;; the path is defined in Guix, therefore we have to change it.
2782          (add-after 'unpack 'fix-sip-dir
2783            (lambda _
2784              (substitute* "pyqtdistutils.py"
2785                (("os.path.join\\(sip_dir, 'PyQt5'\\)") "sip_dir"))
2786              #t))
2787          ;; Now we have to pass the correct sip_dir to setup.py.
2788          (replace 'build
2789            (lambda* (#:key inputs #:allow-other-keys)
2790              ;; We need to tell setup.py where to locate QtCoremod.sip
2791              ((@@ (guix build python-build-system) call-setuppy)
2792               "build_ext"
2793               (list (string-append "--sip-dir="
2794                                    (assoc-ref inputs "python-pyqt")
2795                                    "/share/sip"))
2796               #t)))
2797          ;; Ensure that icons are found at runtime.
2798          (add-after 'install 'wrap-executable
2799            (lambda* (#:key inputs outputs #:allow-other-keys)
2800              (let ((out (assoc-ref outputs "out")))
2801                (wrap-program (string-append out "/bin/veusz")
2802                  `("QT_PLUGIN_PATH" prefix
2803                    ,(list (string-append (assoc-ref inputs "qtsvg")
2804                                          "/lib/qt5/plugins/"))))))))))
2805     (native-inputs
2806      (list pkg-config
2807            ;;("python-astropy" ,python-astropy) ;; FIXME: Package this.
2808            qttools python-sip-4))
2809     (inputs
2810      (list ghostscript ;optional, for EPS/PS output
2811            python-dbus
2812            python-h5py ;optional, for HDF5 data
2813            python-pyqt
2814            qtbase-5
2815            qtsvg))
2816     (propagated-inputs
2817      (list python-numpy))
2818     (home-page "https://veusz.github.io/")
2819     (synopsis "Scientific plotting package")
2820     (description
2821      "Veusz is a scientific plotting and graphing program with a graphical
2822 user interface, designed to produce publication-ready 2D and 3D plots.  In
2823 addition it can be used as a module in Python for plotting.  It supports
2824 vector and bitmap output, including PDF, Postscript, SVG and EMF.")
2825     (license license:gpl2+)))
2826
2827 (define-public maxflow
2828   (package
2829     (name "maxflow")
2830     ;; Versioning is ambiguous: the git tag matching this commit is ‘3.0.5’,
2831     ;; which matches CMakeLists.txt, but README.md and CHANGES say ‘3.04’.
2832     (version "3.0.5")
2833     (source (origin
2834               (method git-fetch)
2835               (uri (git-reference
2836                     (url "https://github.com/gerddie/maxflow")
2837                     (commit version)))
2838               (file-name (git-file-name name version))
2839               (sha256
2840                (base32
2841                 "0rll38whw55h0vcjrrwdnh9ascvxby0ph7n1l0d12z17cg215kkb"))))
2842     (build-system cmake-build-system)
2843     (home-page "https://pub.ist.ac.at/~vnk/software.html")
2844     (synopsis "Library implementing Maxflow algorithm")
2845     (description "An implementation of the maxflow algorithm described in
2846 @cite{An Experimental Comparison of Min-Cut/Max-Flow Algorithms for
2847 Energy Minimization in Computer Vision.\n
2848 Yuri Boykov and Vladimir Kolmogorov.\n
2849 In IEEE Transactions on Pattern Analysis and Machine Intelligence,\n
2850 September 2004}")
2851     (license license:gpl3+)))
2852
2853 (define-public petsc
2854   (package
2855     (name "petsc")
2856     (version "3.16.1")
2857     (source
2858      (origin
2859       (method url-fetch)
2860       ;; The *-lite-* tarball does not contain the *large* documentation
2861       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
2862                           "petsc-lite-" version ".tar.gz"))
2863       (sha256
2864        (base32 "0sm03vpg010q9icidiq587n325m0598cj6hab2rdv85nwyygg74h"))))
2865     (outputs '("out"                    ; libraries and headers
2866                "examples"))             ; ~30MiB of examples
2867     (build-system gnu-build-system)
2868     (native-inputs
2869      (list python which))
2870     (inputs
2871      (list gfortran openblas superlu
2872            ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
2873            ;; leaving out opengl, as configuration seems to only be for mac
2874            ))
2875     (arguments
2876      (list
2877       #:test-target "test"
2878       #:parallel-build? #f             ; build is parallel by default
2879       #:configure-flags
2880       #~(list "--with-mpi=0"
2881               "--with-openmp=1"
2882               "--with-openblas=1"
2883               (string-append "--with-openblas-dir="
2884                              #$(this-package-input "openblas"))
2885               "--with-superlu=1")
2886       #:make-flags
2887       ;; Honor (parallel-job-count) for build.  Do not use --with-make-np,
2888       ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
2889       #~(list (format #f "MAKE_NP=~a" (parallel-job-count)))
2890       #:phases
2891       #~(modify-phases %standard-phases
2892           (replace 'configure
2893             ;; PETSc's configure script is actually a python script, so we can't
2894             ;; run it with bash.
2895             (lambda* (#:key outputs (configure-flags '())
2896                       #:allow-other-keys)
2897               (let* ((prefix (assoc-ref outputs "out"))
2898                      (flags `(,(string-append "--prefix=" prefix)
2899                               ,@configure-flags)))
2900                 (format #t "build directory: ~s~%" (getcwd))
2901                 (format #t "configure flags: ~s~%" flags)
2902                 (apply invoke "./configure" flags)
2903
2904                 ;; Generate test scripts with the right shebang.
2905                 (substitute* "config/example_template.py"
2906                   (("#!/usr/bin/env bash")
2907                    (string-append "#!" (which "bash")))))))
2908           (add-after 'configure 'clean-local-references
2909             (lambda* (#:key outputs #:allow-other-keys)
2910               (let ((out (assoc-ref outputs "out")))
2911                 (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
2912                   ;; Prevent build directory from leaking into compiled code
2913                   (((getcwd)) out)
2914                   ;; Scrub timestamp for reproducibility
2915                   ((".*Libraries compiled on.*") ""))
2916                 (substitute* (find-files "." "petscvariables")
2917                   ;; Do not expose build machine characteristics, set to defaults.
2918                   (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
2919                   (("NPMAX = [:digit:]+") "NPMAX = 2")))))
2920           (add-after 'install 'clean-install
2921             ;; Try to keep installed files from leaking build directory names.
2922             (lambda* (#:key inputs outputs #:allow-other-keys)
2923               (let ((out (assoc-ref outputs "out")))
2924                 (substitute* (map (lambda (file)
2925                                     (string-append out "/lib/petsc/conf/" file))
2926                                   '("petscvariables"))
2927                   (((getcwd)) out))
2928                 ;; Make compiler references point to the store
2929                 (substitute* (string-append out "/lib/petsc/conf/petscvariables")
2930                   (("= (gcc|g\\+\\+|gfortran)" _ compiler)
2931                    (string-append "= " (which compiler))))
2932                 ;; PETSc installs some build logs, which aren't necessary.
2933                 (for-each (lambda (file)
2934                             (let ((f (string-append out "/lib/petsc/conf/" file)))
2935                               (when (file-exists? f)
2936                                 (delete-file f))))
2937                           '("configure.log" "make.log" "gmake.log"
2938                             "test.log" "error.log" "RDict.db"
2939                             "PETScBuildInternal.cmake"
2940                             ;; Once installed, should uninstall with Guix
2941                             "uninstall.py")))))
2942           (add-after 'install 'move-examples
2943             (lambda* (#:key outputs #:allow-other-keys)
2944               (let* ((out (assoc-ref outputs "out"))
2945                      (examples (assoc-ref outputs "examples"))
2946                      (exdir (string-append out "/share/petsc/examples"))
2947                      (exdir' (string-append examples "/share/petsc/examples")))
2948                 (copy-recursively exdir exdir')
2949                 (delete-file-recursively exdir)))))))
2950     (home-page "https://www.mcs.anl.gov/petsc")
2951     (synopsis "Library to solve PDEs")
2952     (description "PETSc, pronounced PET-see (the S is silent), is a suite of
2953 data structures and routines for the scalable (parallel) solution of
2954 scientific applications modeled by partial differential equations.")
2955     (license (license:non-copyleft
2956               "https://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
2957
2958 (define-public petsc-complex
2959   (package
2960     (inherit petsc)
2961     (name "petsc-complex")
2962     (arguments
2963      (substitute-keyword-arguments (package-arguments petsc)
2964        ((#:configure-flags cf)
2965         #~(cons "--with-scalar-type=complex" #$cf))))
2966     (synopsis "Library to solve PDEs (with complex scalars)")))
2967
2968 (define-public petsc-openmpi
2969   (package
2970     (inherit petsc)
2971     (name "petsc-openmpi")
2972     (inputs
2973      `(("hdf5" ,hdf5-parallel-openmpi)
2974        ("hypre" ,hypre-openmpi)
2975        ("metis" ,metis)
2976        ("mumps" ,mumps-openmpi)
2977        ("openmpi" ,openmpi)
2978        ("scalapack" ,scalapack)
2979        ("scotch" ,pt-scotch32)
2980        ,@(package-inputs petsc)))
2981     (arguments
2982      (substitute-keyword-arguments (package-arguments petsc)
2983        ((#:configure-flags cf)
2984         #~`("--with-hypre=1"
2985             "--with-mpiexec=mpirun"
2986             "--with-metis=1"
2987             "--with-mumps=1"
2988             "--with-scalapack=1"
2989             "--with-ptscotch=1"
2990             ,(string-append "--with-mpi-dir="
2991                             #$(this-package-input "openmpi"))
2992             ,(string-append "--with-hdf5-include="
2993                             #$(this-package-input "hdf5") "/include")
2994             ,(string-append "--with-hdf5-lib="
2995                             #$(this-package-input "hdf5") "/lib/libhdf5.a")
2996             ,@(delete "--with-mpi=0" #$cf)))
2997        ((#:phases phases)
2998         #~(modify-phases #$phases
2999             (add-before 'configure 'mpi-setup
3000               #$%openmpi-setup)))))
3001     (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
3002
3003 (define-public petsc-complex-openmpi
3004   (package
3005     (inherit petsc-complex)
3006     (name "petsc-complex-openmpi")
3007     (inputs
3008      (modify-inputs (package-inputs petsc-complex)
3009        (prepend openmpi)))
3010     (arguments
3011      (substitute-keyword-arguments (package-arguments petsc-complex)
3012        ((#:configure-flags cf)
3013         #~`("--with-mpiexec=mpirun"
3014             ,(string-append "--with-mpi-dir="
3015                             #$(this-package-input "openmpi"))
3016             ,@(delete "--with-mpi=0" #$cf)))
3017        ((#:phases phases)
3018         #~(modify-phases #$phases
3019             (add-before 'configure 'mpi-setup
3020               #$%openmpi-setup)))))
3021     (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
3022
3023 (define-public python-petsc4py
3024   (package
3025     (name "python-petsc4py")
3026     (version "3.16.1")
3027     (source
3028       (origin
3029         (method url-fetch)
3030         (uri (pypi-uri "petsc4py" version))
3031         (sha256
3032           (base32
3033            "0pxr6qa7p0pmpq0av29lx8lzlrdcfdzj87ynixzr8dn42y13a662"))
3034         (modules '((guix build utils)))
3035         (snippet
3036          '(begin
3037             ;; Ensure source file is regenerated in the build phase.
3038             (delete-file "src/petsc4py.PETSc.c")
3039             ;; Remove legacy GC code.  See
3040             ;; https://bitbucket.org/petsc/petsc4py/issues/125.
3041             (substitute* "src/PETSc/cyclicgc.pxi"
3042                          ((".*gc_refs.*") "" )
3043                          ((".*PyGC_Head.*") ""))
3044             #t))))
3045     (build-system python-build-system)
3046     (arguments
3047      `(#:phases
3048        (modify-phases %standard-phases
3049          (add-before 'build 'pre-build
3050            (lambda _
3051              ;; Define path to PETSc installation.
3052              (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
3053              #t))
3054          (add-before 'check 'mpi-setup
3055            ,%openmpi-setup))))
3056     (native-inputs
3057      (list python-cython))
3058     (inputs
3059      `(("petsc" ,petsc-openmpi)
3060        ("python-numpy" ,python-numpy)))
3061     (home-page "https://bitbucket.org/petsc/petsc4py/")
3062     (synopsis "Python bindings for PETSc")
3063     (description "PETSc, the Portable, Extensible Toolkit for
3064 Scientific Computation, is a suite of data structures and routines for
3065 the scalable (parallel) solution of scientific applications modeled by
3066 partial differential equations.  It employs the MPI standard for all
3067 message-passing communication.  @code{petsc4py} provides Python
3068 bindings to almost all functions of PETSc.")
3069     (license license:bsd-3)))
3070
3071 (define-public python-kiwisolver
3072   (package
3073     (name "python-kiwisolver")
3074     (version "1.0.1")
3075     (source (origin
3076               (method url-fetch)
3077               (uri (pypi-uri "kiwisolver" version))
3078               (sha256
3079                (base32
3080                 "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf"))))
3081     (build-system python-build-system)
3082     (home-page "https://github.com/nucleic/kiwi")
3083     (synopsis "Fast implementation of the Cassowary constraint solver")
3084     (description
3085      "Kiwi is an efficient C++ implementation of the Cassowary constraint
3086 solving algorithm.  Kiwi has been designed from the ground up to be
3087 lightweight and fast.  Kiwi ranges from 10x to 500x faster than the original
3088 Cassowary solver with typical use cases gaining a 40x improvement.  Memory
3089 savings are consistently > 5x.")
3090     (license license:bsd-3)))
3091
3092 (define-public python2-kiwisolver
3093   (package-with-python2 python-kiwisolver))
3094
3095 (define-public slepc
3096   (package
3097     (name "slepc")
3098     (version "3.16.1")
3099     (source
3100      (origin
3101        (method url-fetch)
3102        (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
3103                            version ".tar.gz"))
3104        (sha256
3105         (base32
3106          "1ysfm77s5fcissv3q0k5d65mlp93zi4anqg62q3cd25dn66sva5i"))))
3107     (build-system gnu-build-system)
3108     (native-inputs
3109      `(("python" ,python)
3110        ("which" ,which)
3111        ("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
3112     (inputs
3113      `(("arpack" ,arpack-ng)
3114        ("gfortran" ,gfortran)))
3115     (propagated-inputs
3116      (list petsc))
3117     (arguments
3118      `(#:parallel-build? #f             ;build is parallel by default
3119        #:configure-flags
3120        `(,(string-append "--with-arpack-dir="
3121                          (assoc-ref %build-inputs "arpack") "/lib"))
3122        #:make-flags                     ;honor (parallel-job-count)
3123        `(,(format #f "MAKE_NP=~a" (parallel-job-count))
3124          ,(string-append "PETSCCONFIGDIR="
3125                          (assoc-ref %build-inputs "petsc:examples")
3126                          "/share/petsc/examples/config"))
3127        #:phases
3128        (modify-phases %standard-phases
3129          (replace 'configure
3130           ;; configure is a python script, so we can't run it with bash.
3131           (lambda* (#:key inputs outputs (configure-flags '())
3132                     #:allow-other-keys)
3133             (let* ((prefix (assoc-ref outputs "out"))
3134                    (flags `(,(string-append "--prefix=" prefix)
3135                             ,@configure-flags)))
3136               (format #t "build directory: ~s~%" (getcwd))
3137               (format #t "configure flags: ~s~%" flags)
3138               (setenv "SLEPC_DIR" (getcwd))
3139               (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
3140               (apply invoke "./configure" flags))))
3141          (add-after 'install 'delete-doc
3142           ;; TODO: SLEPc installs HTML documentation alongside headers in
3143           ;; $out/include.  We'd like to move them to share/doc, but delete
3144           ;; them for now, as they are incomplete and installing the complete
3145           ;; documentation is difficult.
3146           (lambda* (#:key outputs #:allow-other-keys)
3147             (let* ((out (assoc-ref outputs "out")))
3148               (for-each delete-file (find-files out "\\.html$"))
3149               #t)))
3150          (add-after 'install 'clean-install
3151           ;; Clean up unnecessary build logs from installation.
3152           (lambda* (#:key outputs #:allow-other-keys)
3153             (let ((out (assoc-ref outputs "out")))
3154               (for-each (lambda (file)
3155                           (let ((f (string-append out "/lib/slepc/conf/" file)))
3156                             (when (file-exists? f)
3157                               (delete-file f))))
3158                         '("configure.log" "make.log" "gmake.log"
3159                           "test.log" "error.log" "RDict.db"
3160                           "uninstall.py"))
3161               #t))))))
3162     (home-page "https://slepc.upv.es")
3163     (synopsis "Scalable library for eigenproblems")
3164     (description "SLEPc is a software library for the solution of large sparse
3165 eigenproblems on parallel computers.  It can be used for the solution of
3166 linear eigenvalue problems formulated in either standard or generalized form,
3167 as well as other related problems such as the singular value decomposition.
3168 The emphasis of the software is on methods and techniques appropriate for
3169 problems in which the associated matrices are sparse, for example, those
3170 arising after the discretization of partial differential equations.")
3171     (license license:bsd-2)
3172     (properties
3173      `((release-monitoring-url . "http://slepc.upv.es/download/")))))
3174
3175 (define-public slepc-complex
3176   (package (inherit slepc)
3177     (name "slepc-complex")
3178     (propagated-inputs
3179      `(("petsc" ,petsc-complex)
3180        ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
3181     (synopsis "Scalable library for eigenproblems (with complex scalars)")))
3182
3183 (define-public slepc-openmpi
3184   (package (inherit slepc)
3185     (name "slepc-openmpi")
3186     (arguments
3187      (substitute-keyword-arguments (package-arguments slepc)
3188        ((#:phases phases '%standard-phases)
3189         `(modify-phases ,phases
3190            (add-before 'check 'mpi-setup
3191              ,%openmpi-setup)))))
3192     (inputs
3193      `(("mpi" ,openmpi)
3194        ,@(alist-delete "arpack" (package-inputs slepc))))
3195     (propagated-inputs
3196      `(("petsc" ,petsc-openmpi)
3197        ("arpack" ,arpack-ng-openmpi)
3198        ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
3199     (synopsis "Scalable library for eigenproblems (with MPI support)")))
3200
3201 (define-public slepc-complex-openmpi
3202   (package (inherit slepc-openmpi)
3203     (name "slepc-complex-openmpi")
3204     (propagated-inputs
3205      `(("petsc" ,petsc-complex-openmpi)
3206        ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
3207     (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
3208
3209 (define-public python-slepc4py
3210   (package
3211     (name "python-slepc4py")
3212     (version "3.16.1")
3213     (source
3214       (origin
3215         (method url-fetch)
3216         (uri (pypi-uri "slepc4py" version))
3217         (sha256
3218           (base32
3219             "0fq997y73ymvcvdrxycp450pxwdgnqaw62gv9rwncfgsfplkvs9w"))))
3220     (build-system python-build-system)
3221     (arguments
3222      `(#:phases
3223        (modify-phases %standard-phases
3224          (add-before 'build 'pre-build
3225            (lambda _
3226              ;; Define path to PETSc installation.
3227              (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
3228              ;; Define path to SLEPc installation.
3229              (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
3230              #t))
3231          (add-before 'check 'mpi-setup
3232            ,%openmpi-setup))))
3233     (inputs
3234      `(("python-numpy" ,python-numpy)
3235        ("python-petsc4py" ,python-petsc4py)
3236        ("slepc" ,slepc-openmpi)))
3237     (home-page "https://bitbucket.org/slepc/slepc4py/")
3238     (synopsis "Python bindings for SLEPc")
3239     (description "SLEPc, the Scalable Library for Eigenvalue Problem
3240 Computations, is based on PETSc, the Portable, Extensible Toolkit for
3241 Scientific Computation.  It employs the MPI standard for all
3242 message-passing communication.  @code{slepc4py} provides Python
3243 bindings to almost all functions of SLEPc.")
3244     (license license:bsd-3)))
3245
3246 (define-public metamath
3247   (package
3248     (name "metamath")
3249     (version "0.193")
3250     (source
3251      (origin
3252        (method git-fetch)
3253        (uri (git-reference
3254              (url "https://github.com/metamath/metamath-exe")
3255              (commit (string-append "v" version))))
3256        (file-name (git-file-name name version))
3257        (sha256
3258         (base32 "1s9hyknfvhj86g3giayyf3dxzg23iij0rs7bdvj075v9qbyhqn9b"))))
3259     (build-system gnu-build-system)
3260     (native-inputs
3261      (list autoconf automake))
3262     (home-page "http://us.metamath.org/")
3263     (synopsis "Proof verifier based on a minimalistic formalism")
3264     (description
3265      "Metamath is a tiny formal language and that can express theorems in
3266 abstract mathematics, with an accompyaning @command{metamath} executable that
3267 verifies databases of these proofs.  There is a public database,
3268 @url{https://github.com/metamath/set.mm, set.mm}, implementing first-order
3269 logic and Zermelo-Frenkel set theory with Choice, along with a large swath of
3270 associated, high-level theorems, e.g.@: the fundamental theorem of arithmetic,
3271 the Cauchy-Schwarz inequality, Stirling's formula, etc.  See the Metamath
3272 book.")
3273     (license license:gpl2+)))
3274
3275 (define-public minizinc
3276   (package
3277     (name "minizinc")
3278     (version "2.5.5")
3279     (source (origin
3280               (method git-fetch)
3281               (uri (git-reference
3282                     (url "https://github.com/MiniZinc/libminizinc")
3283                     (commit version)))
3284               (file-name (git-file-name name version))
3285               (sha256
3286                (base32
3287                 "10b2hsl1fx9psh0iagmp8ki3f60f3qg5hmvra5aczjlfmbl88ggp"))
3288               (modules '((guix build utils)
3289                          (ice-9 ftw)
3290                          (srfi srfi-1)))
3291               (snippet
3292                '(begin
3293                   ;; Do not advertise proprietary solvers
3294                   (with-directory-excursion "cmake/targets"
3295                     (let ((targets '("libminizinc_fzn.cmake"
3296                                      "libminizinc_gecode.cmake"
3297                                      "libminizinc_mip.cmake"
3298                                      "libminizinc_nl.cmake"
3299                                      "libminizinc_osicbc.cmake"
3300                                      "libminizinc_parser.cmake"
3301                                      "libmzn.cmake"
3302                                      "minizinc.cmake"
3303                                      "mzn2doc.cmake")))
3304                      (for-each delete-file
3305                               (remove
3306                                (lambda (file)
3307                                  (member file (cons* "." ".." targets)))
3308                                (scandir ".")))
3309                     (substitute* "libmzn.cmake"
3310                       (("include\\(cmake/targets/(.*)\\)" all target)
3311                        (if (member target targets) all "")))))
3312                   (with-directory-excursion "include/minizinc/solvers/MIP"
3313                     (for-each delete-file
3314                               (remove
3315                                (lambda (file)
3316                                  (member file '("." ".."
3317                                                 "MIP_osicbc_solverfactory.hh"
3318                                                 "MIP_osicbc_wrap.hh"
3319                                                 "MIP_solverinstance.hh"
3320                                                 "MIP_solverinstance.hpp"
3321                                                 "MIP_wrap.hh")))
3322                                (scandir "."))))
3323                   (with-directory-excursion "solvers/MIP"
3324                     (for-each delete-file
3325                               (remove
3326                                (lambda (file)
3327                                  (member file '("." ".."
3328                                                 "MIP_osicbc_solverfactory.cpp"
3329                                                 "MIP_osicbc_wrap.cpp"
3330                                                 "MIP_solverinstance.cpp"
3331                                                 "MIP_wrap.cpp")))
3332                                (scandir "."))))
3333                   (substitute* "CMakeLists.txt"
3334                     (("find_package\\(([^ ]*).*\\)" all pkg)
3335                      (if (member pkg '("Gecode" "OsiCBC" "Threads"))
3336                          all
3337                          "")))
3338                   ;; TODO: swap out miniz for zlib
3339                   #t))))
3340     (build-system cmake-build-system)
3341     (arguments
3342      `(#:tests? #f ; no ‘check’ target
3343        #:modules ((guix build cmake-build-system)
3344                   (guix build utils)
3345                   (srfi srfi-1))
3346        #:phases
3347        (modify-phases %standard-phases
3348          (add-after 'install 'install-solver-configs
3349            (lambda* (#:key inputs outputs #:allow-other-keys)
3350              (let ((gecode (assoc-ref inputs "gecode"))
3351                    (pkgdatadir (string-append (assoc-ref outputs "out")
3352                                                   "/share/minizinc")))
3353                (call-with-output-file (string-append pkgdatadir
3354                                                      "/Preferences.json")
3355                  (lambda (port)
3356                    (display "\
3357 {
3358   \"tagDefaults\": [
3359     [\"\", \"org.gecode.gecode\"],
3360     [\"gecode\", \"org.gecode.gecode\"]
3361   ],
3362   \"solverDefaults\": []
3363 }"
3364                             port)
3365                    (newline port)))
3366
3367                (mkdir-p (string-append pkgdatadir "/solvers"))
3368                (call-with-output-file (string-append pkgdatadir
3369                                                      "/solvers/gecode.msc")
3370                  (lambda (port)
3371                    (format port
3372                     "\
3373 {
3374   \"id\": \"org.gecode.gecode\",
3375   \"name\": \"Gecode\",
3376   \"description\": \"Gecode FlatZinc executable\",
3377   \"version\": ~s,
3378   \"mznlib\": ~s,
3379   \"executable\": ~s,
3380   \"supportsMzn\": false,
3381   \"supportsFzn\": true,
3382   \"needsSolns2Out\": true,
3383   \"needsMznExecutable\": false,
3384   \"needsStdlibDir\": false,
3385   \"isGUIApplication\": false
3386 }"
3387                     (last (string-split gecode #\-))
3388                     (string-append gecode "/share/gecode/mznlib")
3389                     (string-append gecode "/bin/fzn-gecode"))
3390                    (newline port)))))))))
3391     (native-inputs
3392      (list bison flex))
3393     (inputs
3394      (list cbc gecode zlib))
3395     (home-page "https://www.minizinc.org")
3396     (synopsis "High-level constraint modeling language")
3397     (description "MiniZinc is a high-level modeling language for constraint
3398 satisfaction and optimization problems.  Models are compiled to FlatZinc, a
3399 language understood by many solvers.")
3400     (license license:mpl2.0)))
3401
3402 (define-public mumps
3403   (package
3404     (name "mumps")
3405     (version "5.2.1")
3406     (source
3407      (origin
3408        (method url-fetch)
3409        (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
3410                            version ".tar.gz"))
3411        (sha256
3412         (base32
3413          "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
3414        (patches (search-patches "mumps-build-parallelism.patch"
3415                                 "mumps-shared-libseq.patch"
3416                                 "mumps-shared-mumps.patch"
3417                                 "mumps-shared-pord.patch"))))
3418     (build-system gnu-build-system)
3419     (inputs
3420      `(("fortran" ,gfortran)
3421        ;; These are required for linking against mumps, but we let the user
3422        ;; declare the dependency.
3423        ("blas" ,openblas)
3424        ("metis" ,metis)
3425        ("scotch" ,scotch)))
3426     (arguments
3427      `(#:modules ((ice-9 match)
3428                   (ice-9 popen)
3429                   (srfi srfi-1)
3430                   ,@%gnu-build-system-modules)
3431        #:phases
3432        (modify-phases %standard-phases
3433          (replace 'configure
3434           (lambda* (#:key inputs #:allow-other-keys)
3435             (call-with-output-file "Makefile.inc"
3436               (lambda (port)
3437                 (format port "
3438 PLAT         =
3439 LIBEXT       = .a
3440 OUTC         = -o
3441 OUTF         = -o
3442 RM           = rm -f~:[
3443 CC           = gcc
3444 FC           = gfortran
3445 FL           = gfortran
3446 INCSEQ       = -I$(topdir)/libseq
3447 LIBSEQ       = $(topdir)/libseq/libmpiseq.a
3448 LIBSEQNEEDED = libseqneeded~;
3449 CC           = mpicc
3450 FC           = mpifort
3451 FL           = mpifort~]
3452 AR           = ar vr # rules require trailing space, ugh...
3453 RANLIB       = ranlib
3454 BLASDIR      = ~a
3455 LIBBLAS      = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
3456 SCALAPDIR    = ~a
3457 SCALAP       = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
3458 LIBOTHERS    = -pthread
3459 CDEFS        = -DAdd_
3460 PIC          = -fPIC
3461 OPTF         = -O2 -DALLOW_NON_INIT -fallow-argument-mismatch $(PIC)
3462 OPTL         = -O2 $(PIC)
3463 OPTC         = -O2 $(PIC)
3464 INCS         = $(INCSEQ)
3465 LIBS         = $(SCALAP) $(LIBSEQ)
3466 LPORDDIR     = $(topdir)/PORD/lib
3467 IPORD        = -I$(topdir)/PORD/include
3468 LPORD        = $(LPORDDIR)/libpord.a
3469 ORDERINGSF   = -Dpord~@[
3470 METISDIR     = ~a
3471 IMETIS       = -I$(METISDIR)/include
3472 LMETIS       = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
3473 ORDERINGSF  += -Dmetis~]~@[~:{
3474 SCOTCHDIR    = ~a
3475 ISCOTCH      = -I$(SCOTCHDIR)/include
3476 LSCOTCH      = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
3477 ORDERINGSF  += ~a~}~]
3478 ORDERINGSC   = $(ORDERINGSF)
3479 LORDERINGS   = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
3480 IORDERINGSF  = $(ISCOTCH)
3481 IORDERINGSC  = $(IPORD) $(IMETIS) $(ISCOTCH)"
3482                         (assoc-ref inputs "mpi")
3483                         (assoc-ref inputs "blas")
3484                         (assoc-ref inputs "scalapack")
3485                         (assoc-ref inputs "metis")
3486                         (match (list (assoc-ref inputs "pt-scotch")
3487                                      (assoc-ref inputs "scotch"))
3488                           ((#f #f)
3489                            #f)
3490                           ((#f scotch)
3491                            `((,scotch "" "-Dscotch")))
3492                           ((ptscotch _)
3493                            `((,ptscotch
3494                               "-lptesmumps -lptscotch -lptscotcherr "
3495                               "-Dptscotch")))))))))
3496          (replace 'build
3497           ;; By default only the d-precision library is built.  Make with "all"
3498           ;; target so that all precision libraries and examples are built.
3499           (lambda _
3500             (invoke "make" "all"
3501                     (format #f "-j~a" (parallel-job-count)))))
3502          (replace 'check
3503           ;; Run the simple test drivers, which read test input from stdin:
3504           ;; from the "real" input for the single- and double-precision
3505           ;; testers, and from the "cmplx" input for complex-precision
3506           ;; testers.  The EXEC-PREFIX key is used by the mumps-openmpi
3507           ;; package to prefix execution with "mpirun".
3508           (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
3509             (with-directory-excursion "examples"
3510               (every
3511                (lambda (prec type)
3512                  (let ((tester (apply open-pipe*
3513                                       `(,OPEN_WRITE
3514                                         ,@exec-prefix
3515                                         ,(string-append "./" prec
3516                                                         "simpletest"))))
3517                        (input  (open-input-file
3518                                 (string-append "input_simpletest_" type))))
3519                    (begin
3520                      (dump-port input tester)
3521                      (close-port input)
3522                      (zero? (close-pipe tester)))))
3523                '("s" "d" "c" "z")
3524                '("real" "real" "cmplx" "cmplx")))))
3525          (replace 'install
3526            (lambda* (#:key outputs #:allow-other-keys)
3527              (let* ((out (assoc-ref outputs "out"))
3528                     (libdir (string-append out "/lib")))
3529                (copy-recursively "lib" libdir)
3530                (copy-recursively "include" (string-append out "/include"))
3531                (when (file-exists? "libseq/libmpiseq.a")
3532                  (install-file "libseq/libmpiseq.a" libdir))
3533                (when (file-exists? "libseq/libmpiseq.so")
3534                  (install-file "libseq/libmpiseq.so" libdir))
3535                #t))))))
3536     (home-page "http://mumps.enseeiht.fr")
3537     (synopsis "Multifrontal sparse direct solver")
3538     (description
3539      "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
3540 sparse system of linear equations A x = b using Gaussian elimination.")
3541     (license license:cecill-c)))
3542
3543 (define-public mumps-metis
3544   (package (inherit mumps)
3545     (name "mumps-metis")
3546     (inputs
3547      (alist-delete "scotch" (package-inputs mumps)))))
3548
3549 (define-public mumps-openmpi
3550   (package (inherit mumps)
3551     (name "mumps-openmpi")
3552     (inputs
3553      `(("mpi" ,openmpi)
3554        ("scalapack" ,scalapack)
3555        ("pt-scotch" ,pt-scotch)
3556        ,@(alist-delete "scotch" (package-inputs mumps))))
3557     (arguments
3558      (substitute-keyword-arguments (package-arguments mumps)
3559        ((#:phases phases)
3560         `(modify-phases ,phases
3561            (add-before 'check 'mpi-setup
3562              ,%openmpi-setup)
3563            (replace 'check
3564              (lambda _
3565                ((assoc-ref ,phases 'check)
3566                 #:exec-prefix '("mpirun" "-n" "2"))))))))
3567     (synopsis "Multifrontal sparse direct solver (with MPI)")))
3568
3569 (define-public mumps-metis-openmpi
3570   (package (inherit mumps-openmpi)
3571     (name "mumps-metis-openmpi")
3572     (inputs
3573      (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
3574
3575 (define-public ruby-asciimath
3576   (package
3577     (name "ruby-asciimath")
3578     (version "2.0.1")
3579     (source
3580      (origin
3581        (method url-fetch)
3582        (uri (rubygems-uri "asciimath" version))
3583        (sha256
3584         (base32
3585          "1aapydwwkydbwgz07n7ma3a5jy9n3v0shy6q6j8mi4wr3crhx45a"))))
3586     (build-system ruby-build-system)
3587     (native-inputs
3588      (list ruby-nokogiri ruby-rspec))
3589     (synopsis "AsciiMath parsing and conversion library")
3590     (description
3591      "A pure Ruby AsciiMath parsing and conversion library.  AsciiMath is an
3592 easy-to-write markup language for mathematics.")
3593     (home-page "https://github.com/asciidoctor/asciimath")
3594     (license license:expat)))
3595
3596 (define-public superlu
3597   (package
3598     (name "superlu")
3599     (version "5.2.2")
3600     (source
3601      (origin
3602        (method url-fetch)
3603        (uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
3604                            "superlu_" version ".tar.gz"))
3605        (sha256
3606         (base32 "13520vk6fqspyl22cq4ak2jh3rlmhja4czq56j75fdx65fkk80s7"))
3607        (modules '((guix build utils)))
3608        (snippet
3609         ;; Replace the non-free implementation of MC64 with a stub adapted
3610         ;; from Debian
3611         '(begin
3612            (use-modules (ice-9 regex)
3613                         (ice-9 rdelim))
3614            (call-with-output-file "SRC/mc64ad.c"
3615              (lambda (port)
3616                (display "
3617 #include <stdio.h>
3618 #include <stdlib.h>
3619 void mc64id_(int *a) {
3620   fprintf (stderr, \"SuperLU: non-free MC64 not available.  Aborting.\\n\");
3621   abort ();
3622 }
3623 void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
3624               int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
3625   fprintf (stderr, \"SuperLU: non-free MC64 not available.  Aborting.\\n\");
3626   abort ();
3627 }\n" port)))
3628            ;; Remove the corresponding license verbiage.  MC64 license follows
3629            ;; a "------" line separator.
3630            (with-atomic-file-replacement "License.txt"
3631              (let ((rx (make-regexp "-{8}")))
3632                (lambda (in out)
3633                  (let loop ()
3634                    (let ((line (read-line in 'concat)))
3635                     (unless (regexp-exec rx line)
3636                       (display line out)
3637                       (loop))))
3638                  #t)))))))
3639     (build-system cmake-build-system)
3640     (native-inputs
3641      (list tcsh))
3642     (inputs
3643      `(("blas" ,openblas)
3644        ("gfortran" ,gfortran)))
3645     (arguments
3646      `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
3647                            "-DTPL_BLAS_LIBRARIES=openblas"
3648                            "-DBUILD_SHARED_LIBS:BOOL=YES")))
3649     (home-page "https://portal.nersc.gov/project/sparse/superlu/")
3650     (synopsis "Supernodal direct solver for sparse linear systems")
3651     (description
3652      "SuperLU is a general purpose library for the direct solution of large,
3653 sparse, nonsymmetric systems of linear equations on high performance machines.
3654 The library is written in C and is callable from either C or Fortran.  The
3655 library routines perform an LU decomposition with partial pivoting and
3656 triangular system solves through forward and back substitution.  The library
3657 also provides threshold-based ILU factorization preconditioners.")
3658     (license (list license:bsd-3
3659                    license:gpl2+        ;EXAMPLE/*fgmr.c
3660                    (license:fsf-free "file://SRC/colamd.h")))))
3661
3662 (define-public superlu-dist
3663   (package
3664     (name "superlu-dist")
3665     (version "6.4.0")
3666     (source
3667      (origin
3668        (method git-fetch)
3669        (uri (git-reference
3670              (url "https://github.com/xiaoyeli/superlu_dist")
3671              (commit (string-append "v" version))))
3672        (file-name (git-file-name name version))
3673        (sha256
3674         (base32 "0fa29yr72p4yq5ln4rgfsawmi5935n4qcr5niz6864bjladz4lql"))
3675        (modules '((guix build utils)))
3676        (snippet
3677         ;; Replace the non-free implementation of MC64 with a stub
3678         '(begin
3679            (make-file-writable "SRC/mc64ad_dist.c")
3680            (call-with-output-file "SRC/mc64ad_dist.c"
3681              (lambda (port)
3682                (display "
3683 #include <stdio.h>
3684 #include <stdlib.h>
3685 void mc64id_dist(int *a) {
3686   fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available.  Aborting.\\n\");
3687   abort ();
3688 }
3689 void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
3690               int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
3691   fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available.  Aborting.\\n\");
3692   abort ();
3693 }\n" port)))
3694            (substitute* "SRC/util.c"    ;adjust default algorithm
3695              (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
3696               ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
3697               ;; general (i.e. non-square) processor-grid support.
3698               "RowPerm = NOROWPERM;"))
3699            #t))
3700        (patches (search-patches "superlu-dist-scotchmetis.patch"
3701                                 "superlu-dist-awpm-grid.patch"))))
3702     (build-system cmake-build-system)
3703     (native-inputs
3704      (list tcsh))
3705     (inputs
3706      `(("gfortran" ,gfortran)
3707        ("blas" ,openblas)
3708        ("lapack" ,lapack)
3709        ("combblas" ,combinatorial-blas)))
3710     (propagated-inputs
3711      `(("mpi" ,openmpi)                 ;headers include MPI heades
3712        ("parmetis" ,pt-scotch32 "metis")
3713        ("pt-scotch" ,pt-scotch32)))
3714     (arguments
3715      `(#:parallel-tests? #f             ;tests use MPI and OpenMP
3716        #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
3717                                "-DTPL_ENABLE_COMBBLASLIB=YES"
3718                                "-DTPL_BLAS_LIBRARIES=-lopenblas"
3719                                "-DTPL_LAPACK_LIBRARIES=-llapack"
3720                                (string-append "-DTPL_PARMETIS_LIBRARIES="
3721                                               (string-join
3722                                                '("ptscotchparmetis" "ptscotch" "ptscotcherr"
3723                                                  "scotchmetis" "scotch" "scotcherr")
3724                                                ";"))
3725                                (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
3726                                               (assoc-ref %build-inputs "parmetis")
3727                                               "/include")
3728                                "-DTPL_ENABLE_COMBBLASLIB=ON"
3729                                (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
3730                                               (assoc-ref %build-inputs "combblas")
3731                                               "/include/CombBLAS;"
3732                                               (assoc-ref %build-inputs "combblas")
3733                                               "/include/BipartiteMatchings")
3734                                "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
3735        #:phases
3736        (modify-phases %standard-phases
3737          (add-before 'configure 'set-c++-standard
3738            (lambda _
3739              (substitute* "CMakeLists.txt"
3740                ;; AWPM headers require C++14
3741                (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
3742          (add-before 'check 'mpi-setup
3743            ,%openmpi-setup)
3744          (add-before 'check 'omp-setup
3745            (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
3746     (home-page (package-home-page superlu))
3747     (synopsis "Parallel supernodal direct solver")
3748     (description
3749      "SuperLU_DIST is a parallel extension to the serial SuperLU library.
3750 It is targeted for distributed memory parallel machines.  SuperLU_DIST is
3751 implemented in ANSI C, and MPI for communications.")
3752     (license license:bsd-3)))
3753
3754 (define-public scotch
3755   (package
3756     (name "scotch")
3757     (version "6.1.1")
3758     (source
3759      (origin
3760       (method url-fetch)
3761       (uri (string-append "https://gforge.inria.fr/frs/download.php/"
3762                           "latestfile/298/scotch_" version ".tar.gz"))
3763       (sha256
3764        (base32 "04dkz24a2g20wq703fnyi4440ac4mwycy9gwrrllljj7zxcjy19r"))
3765       (patches (search-patches "scotch-build-parallelism.patch"
3766                                "scotch-integer-declarations.patch"))))
3767     (build-system gnu-build-system)
3768     (inputs
3769      (list zlib))
3770     (native-inputs
3771      (list flex bison gfortran))
3772     (outputs '("out" "metis"))
3773     (arguments
3774      `(#:make-flags (list (string-append "prefix=" %output))
3775        #:phases
3776        (modify-phases %standard-phases
3777          (add-after
3778           'unpack 'chdir-to-src
3779           (lambda _ (chdir "src") #t))
3780          (replace
3781           'configure
3782           (lambda _
3783             (call-with-output-file "Makefile.inc"
3784               (lambda (port)
3785                 (format port "
3786 EXE =
3787 LIB = .a
3788 OBJ = .o
3789 MAKE = make
3790 AR = ar
3791 ARFLAGS = -ruv
3792 CAT = cat
3793 CCS = gcc
3794 CCP = mpicc
3795 CCD = gcc
3796 FC = gfortran
3797 CPPFLAGS =~{ -D~a~}
3798 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
3799 LDFLAGS = -lz -lm -lrt -lpthread
3800 CP = cp
3801 LEX = flex -Pscotchyy -olex.yy.c
3802 LN = ln
3803 MKDIR = mkdir
3804 MV = mv
3805 RANLIB = ranlib
3806 YACC = bison -pscotchyy -y -b y
3807 "
3808                         '("COMMON_FILE_COMPRESS_GZ"
3809                           "COMMON_PTHREAD"
3810                           "COMMON_RANDOM_FIXED_SEED"
3811                           "INTSIZE64"             ;use 'int64_t'
3812                           ;; Prevents symbol clashes with libesmumps
3813                           "SCOTCH_RENAME"
3814                           ;; XXX: Causes invalid frees in superlu-dist tests
3815                           ;; "SCOTCH_PTHREAD"
3816                           ;; "SCOTCH_PTHREAD_NUMBER=2"
3817                           "restrict=__restrict"))))
3818             #t))
3819          (add-after 'build 'build-esmumps
3820           (lambda _
3821             (invoke "make"
3822                     (format #f "-j~a" (parallel-job-count))
3823                     "esmumps")))
3824          (add-before 'install 'make-install-dirs
3825            (lambda* (#:key outputs #:allow-other-keys)
3826              (mkdir (assoc-ref outputs "out"))))
3827          (add-after 'install 'install-metis
3828            (lambda* (#:key outputs #:allow-other-keys)
3829              (let ((out (assoc-ref outputs "metis")))
3830                (mkdir out)
3831                ;; metis files are not installed with 'make install'
3832                (for-each (lambda (f)
3833                            (install-file f (string-append out "/include")))
3834                          (find-files "../include/" ".*metis\\.h"))
3835                (for-each (lambda (f)
3836                            (install-file f (string-append out "/lib")))
3837                          (find-files "../lib/" ".*metis\\..*"))
3838                #t))))))
3839     (home-page "https://www.labri.fr/perso/pelegrin/scotch/")
3840     (properties
3841      `((release-monitoring-url . "https://gforge.inria.fr/frs/?group_id=248")))
3842     (synopsis "Programs and libraries for graph algorithms")
3843     (description "SCOTCH is a set of programs and libraries which implement
3844 the static mapping and sparse matrix reordering algorithms developed within
3845 the SCOTCH project.  Its purpose is to apply graph theory, with a divide and
3846 conquer approach, to scientific computing problems such as graph and mesh
3847 partitioning, static mapping, and sparse matrix ordering, in application
3848 domains ranging from structural mechanics to operating systems or
3849 bio-chemistry.")
3850     ;; See LICENSE_en.txt
3851     (license license:cecill-c)))
3852
3853 (define-public scotch32
3854   ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
3855   ;; some applications.
3856   (package (inherit scotch)
3857     (name "scotch32")
3858     (arguments
3859      (substitute-keyword-arguments (package-arguments scotch)
3860        ((#:phases scotch-phases)
3861         `(modify-phases ,scotch-phases
3862           (replace
3863            'configure
3864            (lambda _
3865              (call-with-output-file "Makefile.inc"
3866                (lambda (port)
3867                  (format port "
3868 EXE =
3869 LIB = .a
3870 OBJ = .o
3871 MAKE = make
3872 AR = ar
3873 ARFLAGS = -ruv
3874 CAT = cat
3875 CCS = gcc
3876 CCP = mpicc
3877 CCD = gcc
3878 FC = gfortran
3879 CPPFLAGS =~{ -D~a~}
3880 CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
3881 LDFLAGS = -lz -lm -lrt -lpthread
3882 CP = cp
3883 LEX = flex -Pscotchyy -olex.yy.c
3884 LN = ln
3885 MKDIR = mkdir
3886 MV = mv
3887 RANLIB = ranlib
3888 YACC = bison -pscotchyy -y -b y
3889 "
3890                         '("COMMON_FILE_COMPRESS_GZ"
3891                           "COMMON_PTHREAD"
3892                           "COMMON_RANDOM_FIXED_SEED"
3893                           "INTSIZE32"   ;use 32-bit integers.  See INSTALL.txt
3894                           ;; Prevents symbolc clashes with libesmumps
3895                           "SCOTCH_RENAME"
3896                           ;; XXX: Causes invalid frees in superlu-dist tests
3897                           ;; "SCOTCH_PTHREAD"
3898                           ;; "SCOTCH_PTHREAD_NUMBER=2"
3899                           "restrict=__restrict"))))))))))
3900     (synopsis
3901      "Programs and libraries for graph algorithms (32-bit integers)")))
3902
3903 (define-public scotch-shared
3904   (package (inherit scotch)
3905     (name "scotch-shared")
3906     (native-inputs
3907      (list gcc flex bison))
3908     (arguments
3909      (substitute-keyword-arguments (package-arguments scotch)
3910        ((#:phases scotch-shared-phases)
3911         `(modify-phases ,scotch-shared-phases
3912            (replace
3913             'configure
3914            (lambda _
3915              ;; Otherwise, the RUNPATH will lack the final path component.
3916              (setenv "RPATHFLAGS" (string-append "-Wl,-rpath="
3917                                               (assoc-ref %outputs "out") "/lib"))
3918             (call-with-output-file "Makefile.inc"
3919               (lambda (port)
3920                 (format port "
3921 EXE =
3922 LIB = .so
3923 OBJ = .o
3924 MAKE = make
3925 AR = gcc
3926 ARFLAGS = -shared -o
3927 CAT = cat
3928 CCS = gcc
3929 CCP = mpicc
3930 CCD = gcc
3931 FC = gfortran
3932 CPPFLAGS =~{ -D~a~}
3933 CFLAGS = -O2 -g -fPIC $(CPPFLAGS) $(RPATHFLAGS)
3934 CLIBFLAGS = -shared -fPIC
3935 LDFLAGS = -lz -lm -lrt -lpthread -Xlinker --no-as-needed
3936 CP = cp
3937 LEX = flex -Pscotchyy -olex.yy.c
3938 LN = ln
3939 MKDIR = mkdir
3940 MV = mv
3941 RANLIB = echo
3942 YACC = bison -pscotchyy -y -b y
3943 "
3944                         '("COMMON_FILE_COMPRESS_GZ"
3945                           "COMMON_PTHREAD"
3946                           "COMMON_RANDOM_FIXED_SEED"
3947                           "INTSIZE64"             ;use 'int64_t'
3948                           ;; Prevents symbolc clashes with libesmumps
3949                           "SCOTCH_RENAME"
3950                           ;; XXX: Causes invalid frees in superlu-dist tests
3951                           ;; "SCOTCH_PTHREAD"
3952                           ;; "SCOTCH_PTHREAD_NUMBER=2"
3953                           "restrict=__restrict"
3954                           ))))#t))
3955            (delete 'check)))))
3956      (synopsis
3957       "Programs and libraries for graph algorithms (shared libraries version)")))
3958
3959 (define-public pt-scotch
3960   (package (inherit scotch)
3961     (name "pt-scotch")
3962     (propagated-inputs
3963      (list openmpi))           ;Headers include MPI headers
3964     (arguments
3965      (substitute-keyword-arguments (package-arguments scotch)
3966        ((#:phases scotch-phases)
3967         `(modify-phases ,scotch-phases
3968            (replace
3969             'build
3970             (lambda _
3971               (invoke "make" (format #f "-j~a" (parallel-job-count))
3972                       "ptscotch" "ptesmumps")
3973
3974               ;; Install the serial metis compatibility library
3975               (invoke "make" "-C" "libscotchmetis" "install")))
3976            (add-before 'check 'mpi-setup
3977              ,%openmpi-setup)
3978            (replace 'check
3979              (lambda _
3980                (invoke "make" "ptcheck")))))))
3981     (synopsis "Programs and libraries for graph algorithms (with MPI)")))
3982
3983 (define-public pt-scotch32
3984   (package (inherit scotch32)
3985     (name "pt-scotch32")
3986     (propagated-inputs
3987      (list openmpi))                     ;headers include MPI headers
3988     (arguments
3989      (substitute-keyword-arguments (package-arguments scotch32)
3990        ((#:phases scotch32-phases)
3991         `(modify-phases ,scotch32-phases
3992            (replace 'build
3993              (lambda _
3994                (invoke "make" (format #f "-j~a" (parallel-job-count))
3995                        "ptscotch" "ptesmumps")
3996                ;; Install the serial metis compatibility library
3997                (invoke "make" "-C" "libscotchmetis" "install")))
3998            (add-before 'check 'mpi-setup
3999              ,%openmpi-setup)
4000            (replace 'check
4001              (lambda _
4002                (invoke "make" "ptcheck")))))))
4003     (synopsis
4004      "Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
4005
4006 (define-public pt-scotch-shared
4007   (package (inherit scotch-shared)
4008     (name "pt-scotch-shared")
4009     (propagated-inputs
4010      (list openmpi))           ;Headers include MPI headers
4011     (arguments
4012      (substitute-keyword-arguments (package-arguments scotch-shared)
4013        ((#:phases scotch-shared-phases)
4014         `(modify-phases ,scotch-shared-phases
4015            (replace
4016             'build
4017             (lambda _
4018               (invoke "make" (format #f "-j~a" (parallel-job-count))
4019                       "ptscotch" "ptesmumps")
4020
4021               ;; Install the serial metis compatibility library
4022               (invoke "make" "-C" "libscotchmetis" "install")))
4023            (add-before 'check 'mpi-setup
4024              ,%openmpi-setup)))))
4025     (synopsis "Graph algorithms (shared libraries version, with MPI)")))
4026
4027
4028 (define-public metis
4029   (package
4030     (name "metis")
4031     (version "5.1.0")
4032     (source
4033      (origin
4034        (method url-fetch)
4035        (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
4036                            "metis-" version ".tar.gz"))
4037        (sha256
4038         (base32
4039          "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
4040     (properties
4041      `((release-monitoring-url
4042         . "http://glaros.dtc.umn.edu/gkhome/metis/metis/download")))
4043     (build-system cmake-build-system)
4044     (inputs
4045      `(("blas" ,openblas)))
4046     (arguments
4047      `(#:tests? #f                      ;no tests
4048        #:configure-flags `("-DSHARED=ON"
4049                            ,(string-append "-DGKLIB_PATH=" (getcwd)
4050                                            "/metis-" ,version "/GKlib"))))
4051     (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
4052     (synopsis "Graph partitioning and fill-reducing matrix ordering library")
4053     (description
4054      "METIS is a set of serial programs for partitioning graphs, partitioning
4055 finite element meshes, and producing fill-reducing orderings for sparse
4056 matrices.  The algorithms implemented in METIS are based on the multilevel
4057 recursive-bisection, multilevel k-way, and multi-constraint partitioning
4058 schemes.")
4059     (license license:asl2.0)))          ;As of version 5.0.3
4060
4061 (define-public p4est
4062   (package
4063     (name "p4est")
4064     (version "2.0")
4065     (source
4066      (origin
4067        (method url-fetch)
4068        (uri (string-append "http://p4est.github.io/release/p4est-"
4069                            version ".tar.gz"))
4070        (sha256
4071         (base32
4072          "16h267z256kxcxfjs390qqzv19hr58vrj4x8lndb7alnk2vca8n5"))))
4073     (build-system gnu-build-system)
4074     (inputs
4075      `(("fortran" ,gfortran)
4076        ("blas" ,openblas)
4077        ("lapack" ,lapack)
4078        ("zlib" ,zlib)))
4079     (arguments
4080      `(#:configure-flags `(,(string-append "BLAS_LIBS=-L"
4081                                            (assoc-ref %build-inputs "blas")
4082                                            " -lopenblas")
4083                            ,(string-append "LAPACK_LIBS=-L"
4084                                            (assoc-ref %build-inputs "lapack")
4085                                            " -llapack"))
4086        #:phases (modify-phases %standard-phases
4087                   (add-before 'check 'mpi-setup
4088                     ,%openmpi-setup))))
4089     (home-page "http://www.p4est.org")
4090     (synopsis "Adaptive mesh refinement on forests of octrees")
4091     (description
4092      "The p4est software library enables the dynamic management of a
4093 collection of adaptive octrees, conveniently called a forest of octrees.
4094 p4est is designed to work in parallel and scales to hundreds of thousands of
4095 processor cores.")
4096     (license license:gpl2+)))
4097
4098 (define-public p4est-openmpi
4099   (package (inherit p4est)
4100     (name "p4est-openmpi")
4101     (inputs
4102      `(("mpi" ,openmpi)
4103        ,@(package-inputs p4est)))
4104     (arguments
4105      (substitute-keyword-arguments (package-arguments p4est)
4106        ((#:configure-flags cf)
4107         ``("--enable-mpi" ,@,cf))))
4108     (synopsis "Parallel adaptive mesh refinement on forests of octrees")))
4109
4110 (define-public gsegrafix
4111   ;; This is an old and equally dead "experimental fork" of the longer-dead
4112   ;; original. At least it no longer requires the even-deader libgnomeprint{,ui}
4113   ;; libraries, instead rendering plots with Pango.
4114   (package
4115     (name "gsegrafix")
4116     (version "1.0.7.2")
4117     (source
4118      (origin
4119        (method url-fetch)
4120        (uri (string-append "mirror://savannah/gsegrafix-experimental/"
4121                            "gsegrafix-experimental-" version ".tar.gz"))
4122        (sha256
4123         (base32 "0fwh6719xy2zasmqlp0vdx6kzm45hn37ga88xmw5cz0yx7xw4j6f"))))
4124     (build-system gnu-build-system)
4125     (arguments
4126      `(#:configure-flags
4127        (list "--disable-static")))
4128     (inputs
4129      (list glib gtk+))
4130     (native-inputs
4131      (list pkg-config))
4132     (home-page "https://www.gnu.org/software/gsegrafix/")
4133     (synopsis "GNOME application to create scientific and engineering plots")
4134     (description
4135      "GSEGrafix is an application which produces high-quality graphical
4136 plots for science and engineering.  Plots are specified via simple ASCII
4137 parameter files and data files and are presented in an anti-aliased GNOME
4138 canvas.  The program supports rectangular two-dimensional plots, histograms,
4139 polar-axis plots and three-dimensional plots.  Plots can be printed or saved
4140 to BMP, JPEG or PNG image formats.")
4141     (license license:gpl3+)))
4142
4143 (define-public maxima
4144   (package
4145     (name "maxima")
4146     (version "5.45.1")
4147     (source
4148      (origin
4149        (method url-fetch)
4150        (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
4151                            version "-source/" name "-" version ".tar.gz"))
4152        (sha256
4153         (base32
4154          "1p77nk5sz1qfkn5zr97szpbi8ib4b22k8i52l4ag5gkhd4kid47y"))
4155        (patches (search-patches "maxima-defsystem-mkdir.patch"))))
4156     (build-system gnu-build-system)
4157     (inputs
4158      `(("bash" ,bash-minimal)
4159        ("gnuplot" ,gnuplot)                       ;for plots
4160        ("sbcl" ,sbcl)
4161        ("sed" ,sed)
4162        ("tk" ,tk)))                               ;Tcl/Tk is used by 'xmaxima'
4163     (native-inputs
4164      (list texinfo perl python))
4165     (arguments
4166      `(#:configure-flags
4167        ,#~(list "--enable-sbcl"
4168                 (string-append "--with-sbcl=" #$sbcl "/bin/sbcl")
4169                 (string-append "--with-posix-shell=" #$bash-minimal "/bin/sh")
4170                 (string-append "--with-wish=" #$tk "/bin/wish"
4171                                #$(version-major+minor (package-version tk))))
4172        ;; By default Maxima attempts to write temporary files to
4173        ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
4174        ;; Work around that.
4175        #:make-flags (list "TMPDIR=/tmp")
4176        #:phases
4177        (modify-phases %standard-phases
4178          (add-after 'unpack 'patch-paths
4179            (lambda* (#:key inputs #:allow-other-keys)
4180              (let* ((sed (search-input-file inputs "/bin/sed"))
4181                     (coreutils (assoc-ref inputs "coreutils"))
4182                     (dirname (string-append coreutils "/bin/dirname"))
4183                     (head (string-append coreutils "/bin/head"))
4184                     (perl (search-input-file inputs "/bin/perl"))
4185                     (python (search-input-file inputs "/bin/python3")))
4186                (substitute* "src/maxima.in"
4187                  (("sed ") (string-append sed " "))
4188                  (("dirname") dirname)
4189                  (("head") head))
4190                (substitute* "doc/info/Makefile.in"
4191                  (("/usr/bin/env perl") perl))
4192                (substitute* "doc/info/build_html.sh.in"
4193                  (("python") python))
4194                #t)))
4195          (add-before 'check 'pre-check
4196            (lambda _
4197              (chmod "src/maxima" #o555)
4198              #t))
4199          (replace 'check
4200            (lambda _
4201              ;; This is derived from the testing code in the "debian/rules" file
4202              ;; of Debian's Maxima package.
4203              ;; If Maxima can successfully run this, the binary to be installed
4204              ;; should be fine.
4205              (invoke "sh" "-c"
4206                      (string-append
4207                       "./maxima-local "
4208                       "--lisp=sbcl "
4209                       "--batch-string=\"run_testsuite();\" "
4210                       "| grep -q \"No unexpected errors found\""))))
4211          ;; Make sure the doc and emacs files are found in the
4212          ;; standard location.  Also configure maxima to find gnuplot
4213          ;; without having it on the PATH.
4214          (add-after 'install 'post-install
4215            (lambda* (#:key outputs inputs #:allow-other-keys)
4216              (let* ((gnuplot (assoc-ref inputs "gnuplot"))
4217                     (out (assoc-ref outputs "out"))
4218                     (datadir (string-append out "/share/maxima/" ,version))
4219                     (binutils (dirname (search-input-file inputs "/bin/as"))))
4220                (with-directory-excursion out
4221                  (mkdir-p "share/emacs")
4222                  (mkdir-p "share/doc")
4223                  (symlink
4224                   (string-append datadir "/doc/")
4225                   (string-append out "/share/doc/maxima"))
4226                  (with-atomic-file-replacement
4227                   (string-append datadir "/share/maxima-init.lisp")
4228                   (lambda (in out)
4229                     (format out "~a ~s~a~%"
4230                             "(setf $gnuplot_command "
4231                             (string-append gnuplot "/bin/gnuplot") ")")
4232                     (dump-port in out))))
4233                ;; Ensure that Maxima will have access to the GNU binutils
4234                ;; components at runtime.
4235                (wrap-program (string-append out "/bin/maxima")
4236                  `("PATH" prefix (,binutils))))
4237              #t)))))
4238     (home-page "https://maxima.sourceforge.io")
4239     (synopsis "Numeric and symbolic expression manipulation")
4240     (description "Maxima is a system for the manipulation of symbolic and
4241 numerical expressions.  It yields high precision numeric results by using
4242 exact fractions, arbitrary precision integers, and variable precision floating
4243 point numbers.")
4244     ;; Some files are lgpl2.1+. Some are gpl2+.  Some explicitly state gpl1+.
4245     ;; Others simply say "GNU General Public License" without stating a
4246     ;; version (which implicitly means gpl1+).
4247     ;; At least one file (src/maxima.asd) says "version 2."
4248     ;; GPLv2 only is therefore the smallest subset.
4249     (license license:gpl2)))
4250
4251 (define-public wxmaxima
4252   (package
4253     (name "wxmaxima")
4254     (version "21.05.2")
4255     (source
4256      (origin
4257        (method git-fetch)
4258        (uri (git-reference
4259              (url "https://github.com/wxMaxima-developers/wxmaxima")
4260              (commit (string-append "Version-" version))))
4261        (file-name (git-file-name name version))
4262        (sha256
4263         (base32 "0h7ryykh2dapcyvpp4f1j1b3vrrz80x9k8nkci2yxifgdb29vyhw"))))
4264     (build-system cmake-build-system)
4265     (native-inputs
4266      `(("gettext" ,gettext-minimal)))
4267     (inputs
4268      (list wxwidgets
4269            maxima
4270            ;; Runtime support.
4271            adwaita-icon-theme
4272            gtk+
4273            shared-mime-info))
4274     (arguments
4275      `(#:tests? #f                      ; tests fail non-deterministically
4276        #:phases
4277        (modify-phases %standard-phases
4278          (add-after 'unpack 'patch-doc-path
4279            (lambda _
4280              ;; Don't look in share/doc/wxmaxima-xx.xx.x for the
4281              ;; documentation.  Only licensing information is placed there by
4282              ;; Guix.
4283              (substitute* "src/Dirstructure.cpp"
4284                (("/doc/wxmaxima-\\%s") "/doc/wxmaxima"))
4285              #t))
4286          (add-after 'install 'wrap-program
4287            (lambda* (#:key inputs outputs #:allow-other-keys)
4288              (wrap-program (string-append (assoc-ref outputs "out")
4289                                           "/bin/wxmaxima")
4290                `("PATH" ":" prefix
4291                  (,(string-append (assoc-ref inputs "maxima")
4292                                   "/bin")))
4293                ;; For GtkFileChooserDialog.
4294                `("GSETTINGS_SCHEMA_DIR" =
4295                  (,(string-append (assoc-ref inputs "gtk+")
4296                                   "/share/glib-2.0/schemas")))
4297                `("XDG_DATA_DIRS" ":" prefix
4298                  (;; Needed by gdk-pixbuf to know supported icon formats.
4299                   ,(string-append
4300                     (assoc-ref inputs "shared-mime-info") "/share")
4301                   ;; The default icon theme of GTK+.
4302                   ,(string-append
4303                     (assoc-ref inputs "adwaita-icon-theme") "/share"))))
4304              #t)))))
4305     (home-page "https://wxmaxima-developers.github.io/wxmaxima/")
4306     (synopsis "Graphical user interface for the Maxima computer algebra system")
4307     (description
4308      "wxMaxima is a graphical user interface for the Maxima computer algebra
4309 system.  It eases the use of Maxima by making most of its commands available
4310 through a menu system and by providing input dialogs for commands that require
4311 more than one argument.  It also implements its own display engine that
4312 outputs mathematical symbols directly instead of depicting them with ASCII
4313 characters.
4314
4315 wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
4316 text and mathematical calculations to create documents, exporting of input and
4317 output to TeX, and a browser for Maxima's manual including command index and
4318 full text searching.")
4319     (license license:gpl2+)))
4320
4321 (define-public armadillo
4322   (package
4323     (name "armadillo")
4324     (version "9.100.5")
4325     (source (origin
4326               (method url-fetch)
4327               (uri (string-append "mirror://sourceforge/arma/armadillo-"
4328                                   version ".tar.xz"))
4329               (sha256
4330                (base32
4331                 "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
4332     (build-system cmake-build-system)
4333     (arguments `(#:tests? #f))          ; no test target
4334     (inputs
4335      `(("openblas" ,openblas)
4336        ("lapack" ,lapack)
4337        ("arpack" ,arpack-ng)))
4338     (home-page "http://arma.sourceforge.net/")
4339     (synopsis "C++ linear algebra library")
4340     (description
4341      "Armadillo is a C++ linear algebra library, aiming towards a good balance
4342 between speed and ease of use.  It is useful for algorithm development
4343 directly in C++, or quick conversion of research code into production
4344 environments.  It can be used for machine learning, pattern recognition,
4345 signal processing, bioinformatics, statistics, econometrics, etc.  The library
4346 provides efficient classes for vectors, matrices and cubes, as well as 150+
4347 associated functions (e.g., contiguous and non-contiguous submatrix views).")
4348     (license license:asl2.0)))
4349
4350 (define-public muparser
4351   ;; When switching download sites, muparser re-issued a 2.2.5 release with a
4352   ;; different hash. In order to make `guix package --upgrade` work correctly,
4353   ;; we set a Guix packaging revision.
4354   ;; When the next version of muparser is released, we can remove
4355   ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
4356   (let ((upstream-version "2.2.5")
4357         (revision "2"))
4358     (package
4359       (name "muparser")
4360       (version (string-append upstream-version "-" revision))
4361       (source
4362        (origin
4363          (method git-fetch)
4364          (uri (git-reference
4365                (url "https://github.com/beltoforion/muparser")
4366                (commit (string-append "v" upstream-version))))
4367          (file-name (git-file-name name version))
4368          (sha256
4369           (base32 "0f0g4995xngf1pp3zr4p6ai2f8v6f8bxwa0k8ayjjiv1l8h44m24"))))
4370       (build-system gnu-build-system)
4371       (arguments
4372        `(#:configure-flags '("--enable-samples=no")
4373          #:tests? #f)) ;no "check" target
4374       (home-page "http://muparser.beltoforion.de/")
4375       (synopsis "Fast parser library for mathematical expressions")
4376       (description
4377        "muParser is an extensible high performance math parser library.  It is
4378 based on transforming an expression into a bytecode and precalculating constant
4379 parts of it.")
4380       (license license:expat))))
4381
4382 (define-public openblas
4383   (package
4384     (name "openblas")
4385     (version "0.3.18")
4386     (source
4387      (origin
4388        (method git-fetch)
4389        (uri (git-reference
4390              (url "https://github.com/xianyi/OpenBLAS")
4391              (commit (string-append "v" version))))
4392        (file-name (git-file-name name version))
4393        (sha256
4394         (base32
4395          "17zdd8asylz2w71hczrz5y344p6d5ds1jn4901maw7zcp3dbk63g"))))
4396     (build-system gnu-build-system)
4397     (arguments
4398      `(#:test-target "test"
4399        ;; DYNAMIC_ARCH is only supported on x86.  When it is disabled and no
4400        ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
4401        ;; we need to disable substitutions.
4402        #:substitutable?
4403         ,(let ((system (or (%current-target-system) (%current-system))))
4404            (or (string-prefix? "x86_64" system)
4405                (string-prefix? "i686" system)
4406                (string-prefix? "mips" system)
4407                (string-prefix? "aarch64" system)))
4408        #:make-flags
4409        (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
4410              "SHELL=bash"
4411              "MAKE_NB_JOBS=0"           ;use jobserver for submakes
4412              "NO_STATIC=1"              ;avoid a 67 MiB static archive
4413
4414              ;; This is the maximum number of threads OpenBLAS will ever use (that
4415              ;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
4416              ;; is used.)  If we don't set it, the makefile sets it to the number
4417              ;; of cores of the build machine, which is obviously wrong.
4418              "NUM_THREADS=128"
4419
4420              ;; Build the library for all supported CPUs.  This allows
4421              ;; switching CPU targets at runtime with the environment variable
4422              ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
4423              ;; Unfortunately, this is not supported on all architectures,
4424              ;; where it leads to failed builds.
4425              ,@(let ((system (or (%current-target-system) (%current-system))))
4426                  (cond
4427                   ((or (string-prefix? "x86_64" system)
4428                        (string-prefix? "i686" system)
4429                        (string-prefix? "powerpc64le" system)
4430                        (string-prefix? "aarch64" system))
4431                    ;; Dynamic older enables a few extra CPU architectures that
4432                    ;; were released before 2010.
4433                    '("DYNAMIC_ARCH=1" "DYNAMIC_OLDER=1" "TARGET=GENERIC"))
4434                   ;; On some of these architectures the CPU can't be detected.
4435                   ;; On MIPS we force the "SICORTEX" TARGET, as for the other
4436                   ;; two available MIPS targets special extended instructions
4437                   ;; for Loongson cores are used.
4438                   ((string-prefix? "mips" system)
4439                    '("TARGET=SICORTEX"))
4440                   ;; Failed to detect CPU.
4441                   ((string-prefix? "armhf" system)
4442                    '("TARGET=ARMV7"))
4443                   (else '()))))
4444        ;; no configure script
4445        #:phases
4446        (modify-phases %standard-phases
4447          (delete 'configure)
4448          (add-before 'build 'set-extralib
4449            (lambda* (#:key inputs #:allow-other-keys)
4450              ;; Get libgfortran found when building in utest.
4451              (setenv "FEXTRALIB"
4452                      (string-append "-L" (assoc-ref inputs "fortran-lib")
4453                                     "/lib")))))))
4454     (inputs
4455      `(("fortran-lib" ,gfortran "lib")))
4456     (native-inputs
4457      `(("cunit" ,cunit)
4458        ("fortran" ,gfortran)
4459        ("perl" ,perl)))
4460     (home-page "https://www.openblas.net/")
4461     (synopsis "Optimized BLAS library based on GotoBLAS")
4462     (description
4463      "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
4464     (license license:bsd-3)))
4465
4466 (define-public openblas-ilp64
4467   (package/inherit openblas
4468     (name "openblas-ilp64")
4469     (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
4470     (arguments
4471      (substitute-keyword-arguments (package-arguments openblas)
4472        ((#:make-flags flags '())
4473         `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
4474                  ,flags))))
4475     (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
4476     (license license:bsd-3)))
4477
4478 (define-public blis
4479   (package
4480     (name "blis")
4481     (version "0.8.1")
4482     (home-page "https://github.com/flame/blis")
4483     (source (origin
4484               (method git-fetch)
4485               (uri (git-reference (url home-page) (commit version)))
4486               (sha256
4487                (base32
4488                 "05ifil6jj9424sr8kmircl8k4bmxnl3y12a79vwj1kxxva5gz50g"))
4489               (file-name (git-file-name "blis" version))))
4490     (native-inputs
4491      (list python perl))
4492     (build-system gnu-build-system)
4493     (arguments
4494      `(#:modules
4495        ((guix build gnu-build-system)
4496         (guix build utils)
4497         (srfi srfi-1))
4498         #:test-target "test"
4499        #:phases
4500        (modify-phases %standard-phases
4501          (replace 'configure
4502            (lambda* (#:key outputs
4503                            target
4504                            system
4505                            (configure-flags '())
4506                            #:allow-other-keys)
4507              ;; This is a home-made 'configure' script.
4508              (let* ((out (assoc-ref outputs "out"))
4509                      ;; Guix-specific support for choosing the configuration
4510                      ;; via #:configure-flags: see below for details.
4511                     (config-flag-prefix "--blis-config=")
4512                     (maybe-config-flag (find
4513                                         (lambda (s)
4514                                           (string-prefix? config-flag-prefix s))
4515                                         configure-flags))
4516                     (configure-flags (if maybe-config-flag
4517                                          (delete maybe-config-flag
4518                                                  configure-flags)
4519                                          configure-flags))
4520                     ;; Select the "configuration" to build.
4521                     ;; The "generic" configuration is non-optimized but
4522                     ;; portable (no assembly).
4523                     ;; The "x86_64" configuration family includes
4524                     ;; sub-configurations for all supported
4525                     ;; x86_64 microarchitectures.
4526                     ;; BLIS currently lacks runtime hardware detection
4527                     ;; for other architectures: see
4528                     ;; <https://github.com/flame/blis/commit/c534da6>.
4529                     ;; Conservatively, we stick to "generic" on armhf,
4530                     ;; aarch64, and ppc64le for now. (But perhaps
4531                     ;; "power9", "cortexa9", and "cortexa57" might be
4532                     ;; general enough to use?)
4533                     ;; Another approach would be to use the "auto"
4534                     ;; configuration and make this package
4535                     ;; non-substitutable.
4536                     ;; The build is fairly intensive, though.
4537                     (blis-config
4538                      (cond
4539                       (maybe-config-flag
4540                        (substring maybe-config-flag
4541                                   (string-length config-flag-prefix)))
4542                       ((string-prefix? "x86_64" (or target system))
4543                        "x86_64")
4544                       (else
4545                        "generic")))
4546                     (configure-args
4547                      `("-p" ,out
4548                        "-d" "opt"
4549                        "--disable-static"
4550                        "--enable-shared"
4551                        "--enable-threading=openmp"
4552                        "--enable-verbose-make"
4553                        ,@configure-flags
4554                        ,blis-config)))
4555                (format #t "configure args: ~s~%" configure-args)
4556                (apply invoke
4557                       "./configure"
4558                       configure-args)
4559                #t)))
4560          (add-before 'check 'show-test-output
4561            (lambda _
4562              ;; By default "make check" is silent.  Make it verbose.
4563              (system "tail -F output.testsuite &")
4564              #t)))))
4565     (synopsis "High-performance basic linear algebra (BLAS) routines")
4566     (description
4567      "BLIS is a portable software framework for instantiating high-performance
4568 BLAS-like dense linear algebra libraries.  The framework was designed to
4569 isolate essential kernels of computation that, when optimized, immediately
4570 enable optimized implementations of most of its commonly used and
4571 computationally intensive operations.  While BLIS exports a new BLAS-like API,
4572 it also includes a BLAS compatibility layer which gives application developers
4573 access to BLIS implementations via traditional BLAS routine calls.")
4574     (license license:bsd-3)))
4575
4576 (define-public blis-sandybridge (deprecated-package "blis-sandybridge" blis))
4577 (define-public blis-haswell (deprecated-package "blis-haswell" blis))
4578 (define-public blis-knl (deprecated-package "blis-knl" blis))
4579
4580 (define ignorance blis)
4581
4582 (define-public openlibm
4583   (package
4584     (name "openlibm")
4585     (version "0.7.4")
4586     (source
4587      (origin
4588        (method git-fetch)
4589        (uri (git-reference
4590              (url "https://github.com/JuliaLang/openlibm")
4591              (commit (string-append "v" version))))
4592        (file-name (git-file-name name version))
4593        (sha256
4594         (base32 "1azms0lpxb7vxb3bln5lyz0wpwx6jnzbffkclclpq2v5aiw8d14i"))))
4595     (build-system gnu-build-system)
4596     (arguments
4597      `(#:make-flags
4598        (list (string-append "prefix=" (assoc-ref %outputs "out"))
4599              ,(string-append "CC=" (cc-for-target)))
4600        #:phases
4601        ;; no configure script
4602        (modify-phases %standard-phases (delete 'configure))
4603        #:tests? #f)) ;the tests are part of the default target
4604     (home-page "https://openlibm.org/")
4605     (synopsis "Portable C mathematical library (libm)")
4606     (description
4607      "OpenLibm is an effort to have a high quality, portable, standalone C
4608 mathematical library (libm).  It can be used standalone in applications and
4609 programming language implementations.  The project was born out of a need to
4610 have a good libm for the Julia programming language that worked consistently
4611 across compilers and operating systems, and in 32-bit and 64-bit
4612 environments.")
4613     ;; Each architecture has its own make target, and there is none for mips.
4614     (supported-systems (delete "mips64el-linux" %supported-systems))
4615     ;; See LICENSE.md for details.
4616     (license (list license:expat
4617                    license:isc
4618                    license:bsd-2
4619                    license:public-domain
4620                    license:lgpl2.1+))))
4621
4622 (define-public openspecfun
4623   (package
4624     (name "openspecfun")
4625     (version "0.5.3")
4626     (source
4627      (origin
4628        (method git-fetch)
4629        (uri (git-reference
4630              (url "https://github.com/JuliaLang/openspecfun")
4631              (commit (string-append "v" version))))
4632        (file-name (git-file-name name version))
4633        (sha256
4634         (base32 "0pfw6l3ch7isz403llx7inxlvavqh01jh1hb9dpidi86sjjx9kfh"))))
4635     (build-system gnu-build-system)
4636     (arguments
4637      '(#:tests? #f                      ; no "check" target
4638        #:make-flags
4639        (list (string-append "prefix=" (assoc-ref %outputs "out")))
4640        #:phases
4641        (modify-phases %standard-phases
4642          (delete 'configure))))         ; no configure script
4643     (inputs
4644      `(("fortran" ,gfortran)))
4645     (home-page "https://github.com/JuliaLang/openspecfun")
4646     (synopsis "Collection of special mathematical functions")
4647     (description
4648      "Openspecfun provides AMOS and Faddeeva.  AMOS (from Netlib) is a
4649 portable package for Bessel Functions of a Complex Argument and Nonnegative
4650 Order; it contains subroutines for computing Bessel functions and Airy
4651 functions.  Faddeeva allows computing the various error functions of arbitrary
4652 complex arguments (Faddeeva function, error function, complementary error
4653 function, scaled complementary error function, imaginary error function, and
4654 Dawson function); given these, one can also easily compute Voigt functions,
4655 Fresnel integrals, and similar related functions as well.")
4656     ;; Faddeeva is released under the Expat license; AMOS is included as
4657     ;; public domain software.
4658     (license (list license:expat license:public-domain))))
4659
4660 (define-public suitesparse
4661   (package
4662     (name "suitesparse")
4663     (version "5.10.1")
4664     (source
4665      (origin
4666        (method git-fetch)
4667        (uri (git-reference
4668              (url "https://github.com/DrTimothyAldenDavis/SuiteSparse")
4669              (commit (string-append "v" version))))
4670        (file-name (git-file-name name version))
4671        (sha256
4672         (base32
4673          "19gx5wlgqnqpgz6mvam9lalyzpbfwgqhppps8z3np9sh0mgaiyw9"))
4674        (patches (search-patches "suitesparse-mongoose-cmake.patch"))
4675        (modules '((guix build utils)))
4676        (snippet
4677         ;; Remove bundled metis source
4678         '(begin
4679            (delete-file-recursively "metis-5.1.0")
4680            #t))))
4681     (build-system gnu-build-system)
4682     (arguments
4683      `(#:tests? #f  ;no "check" target
4684        #:make-flags
4685        (list (string-append "CC=" ,(cc-for-target))
4686              "TBB=-ltbb"
4687              "MY_METIS_LIB=-lmetis"
4688
4689              ;; The default is to link against netlib lapack.  Use OpenBLAS
4690              ;; instead.
4691              "BLAS=-lopenblas" "LAPACK=-lopenblas"
4692
4693              ;; Flags for cmake (required to build GraphBLAS and Mongoose)
4694              (string-append "CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX="
4695                             (assoc-ref %outputs "out")
4696                             " -DCMAKE_VERBOSE_MAKEFILE=ON"
4697                             " -DCMAKE_C_FLAGS_RELEASE=\"$(CFLAGS) $(CPPFLAGS)\""
4698                             " -DCMAKE_CXX_FLAGS_RELEASE=\"$(CXXFLAGS) $(CPPFLAGS)\""
4699                             " -DCMAKE_SKIP_RPATH=TRUE"
4700                             " -DCMAKE_BUILD_TYPE=Release"
4701                             " -DCMAKE_INSTALL_LIBDIR=lib")
4702              (string-append "INSTALL_LIB="
4703                             (assoc-ref %outputs "out") "/lib")
4704              (string-append "INSTALL_INCLUDE="
4705                             (assoc-ref %outputs "out") "/include")
4706              "library")
4707        #:phases
4708        (modify-phases %standard-phases
4709          (delete 'configure))))         ;no configure script
4710     (inputs
4711      (list tbb openblas gmp mpfr metis))
4712     (native-inputs
4713      `(("cmake" ,cmake-minimal)
4714        ("m4" ,m4)))
4715     (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
4716     (synopsis "Suite of sparse matrix software")
4717     (description
4718      "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
4719 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
4720 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
4721 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
4722 CXSparse, a concise sparse Cholesky factorization package; and many other
4723 packages.")
4724     ;; LGPLv2.1+:
4725     ;;   AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
4726     ;; GPLv2+:
4727     ;;  GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
4728     (license (list license:gpl2+ license:lgpl2.1+))))
4729
4730 (define-public atlas
4731   (package
4732     (name "atlas")
4733     (version "3.10.3")
4734     (source (origin
4735               (method url-fetch)
4736               (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
4737                                   version "/atlas" version ".tar.bz2"))
4738               (patches (search-patches "atlas-gfortran-compat.patch"))
4739               (sha256
4740                (base32
4741                 "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216"))))
4742     (build-system gnu-build-system)
4743     (home-page "http://math-atlas.sourceforge.net/")
4744     (inputs `(("gfortran" ,gfortran)
4745               ("lapack-tar" ,(package-source lapack))))
4746     (outputs '("out" "doc"))
4747     ;; For the moment we drop support for MIPS at it fails to compile. See
4748     ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
4749     (supported-systems (delete "mips64el-linux" %supported-systems))
4750     (arguments
4751      `(#:parallel-build? #f
4752        #:parallel-tests? #f
4753
4754        ;; ATLAS tunes itself for the machine it is built on, as explained at
4755        ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
4756        ;; For this reason, we want users to build it locally instead of using
4757        ;; substitutes.
4758        #:substitutable? #f
4759
4760        #:modules ((srfi srfi-26)
4761                   (guix build gnu-build-system)
4762                   (guix build utils))
4763        #:configure-flags
4764        `(;; Generate position independent code suitable for dynamic libraries
4765          ;; and use WALL timer to get more accurate timing.
4766          "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
4767          ;; Set word width.
4768          "-b"
4769          ,,(if (string-match "64" (%current-system))
4770                "64"
4771                "32")
4772          ;; Disable parallel build as it gives errors: atlas_pthread.h is
4773          ;; needed to compile C files before it is generated.
4774          "-Ss" "pmake" "make -j 1"
4775          ;; Probe is failing for MIPS.  We therefore define the system
4776          ;; architecture explicitly by setting (-A) MACHINETYPE = 49
4777          ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
4778          ,,@(if (string-prefix? "mips" (%current-system))
4779               (list "-A" "49" "-V" "1")
4780               (list))
4781          ;; Generate shared libraries.
4782          "--shared"
4783          ;; Build a full LAPACK library.
4784          ,(string-append "--with-netlib-lapack-tarfile="
4785                          (assoc-ref %build-inputs "lapack-tar")))
4786        #:phases
4787        (modify-phases %standard-phases
4788          (add-after 'install 'install-doc
4789            (lambda* (#:key outputs inputs #:allow-other-keys)
4790              (let ((doc (string-append (assoc-ref outputs "doc")
4791                                        "/share/doc/atlas")))
4792                (mkdir-p doc)
4793                (for-each (cut install-file <> doc)
4794                          (find-files "../ATLAS/doc" ".*"))
4795                #t)))
4796          (add-after 'check 'check-pt
4797            (lambda _ (invoke "make" "ptcheck")))
4798          ;; Fix files required to run configure.
4799          (add-before 'configure 'fix-/bin/sh
4800            (lambda _
4801              ;; Use `sh', not `/bin/sh'.
4802              (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
4803                (("/bin/sh")
4804                 "sh"))
4805              #t))
4806          ;; Fix /bin/sh in generated make files.
4807          (add-after 'configure 'fix-/bin/sh-in-generated-files
4808            (lambda _
4809              (substitute* (find-files "." "^[Mm]ake\\.inc.*")
4810                (("/bin/sh")
4811                 "sh"))
4812              #t))
4813          ;; ATLAS configure program does not accepts the default flags
4814          ;; passed by the 'gnu-build-system'.
4815          (replace 'configure
4816            (lambda* (#:key native-inputs inputs outputs
4817                            (configure-flags '())
4818                            #:allow-other-keys #:rest args)
4819              (let* ((prefix     (assoc-ref outputs "out"))
4820                     (bash       (or (and=> (assoc-ref
4821                                             (or native-inputs inputs) "bash")
4822                                            (cut string-append <> "/bin/bash"))
4823                                     "/bin/sh"))
4824                     (flags      `(,(string-append "--prefix=" prefix)
4825                                   ,@configure-flags))
4826                     (abs-srcdir (getcwd))
4827                     (srcdir     (string-append "../" (basename abs-srcdir))))
4828                (format #t "source directory: ~s (relative from build: ~s)~%"
4829                        abs-srcdir srcdir)
4830                (mkdir "../build")
4831                (chdir "../build")
4832                (format #t "build directory: ~s~%" (getcwd))
4833                (format #t "configure flags: ~s~%" flags)
4834                (apply invoke bash
4835                       (string-append srcdir "/configure")
4836                       flags)))))))
4837     (synopsis "Automatically Tuned Linear Algebra Software")
4838     (description
4839      "ATLAS is an automatically tuned linear algebra software library
4840 providing C and Fortran77 interfaces to a portably efficient BLAS
4841 implementation, as well as a few routines from LAPACK.
4842
4843 Optimization occurs at build time.  For this reason, the library is built on
4844 the machine where it is installed, without resorting to pre-built substitutes.
4845
4846 Before building the library, CPU throttling should be disabled.  This can be
4847 done in the BIOS, or, on GNU/Linux, with the following command:
4848
4849 @example
4850 # cpupower --governor performance
4851 @end example
4852
4853 Failure to do so will result in a library with poor performance.")
4854     ;; The test suite is notoriously lengthy and routinely exceeds the default
4855     ;; timeout of 21600 seconds on the not unbeefy berlin build nodes.
4856     (properties '((timeout . 86400)))        ; 1 day
4857     (license license:bsd-3)))
4858
4859 (define-public cglm
4860   (package
4861     (name "cglm")
4862     (version "0.8.2")
4863     (source
4864      (origin
4865        (method git-fetch)
4866        (uri (git-reference
4867              (url "https://github.com/recp/cglm")
4868              (commit (string-append "v" version))))
4869        (file-name (git-file-name name version))
4870        (sha256
4871         (base32 "1lcfl9ph4bnl3hckpx4hzwh8r4llnw94ik75igc5qy38wk468gmk"))))
4872     (build-system cmake-build-system)
4873     (arguments
4874      `(#:configure-flags
4875        (list "-DCGLM_USE_TEST=ON")))
4876     (home-page "https://github.com/recp/cglm")
4877     (synopsis "Mathematics C library for graphics programming")
4878     (description
4879      "@acronym{CGLM, C OpenGL Mathematics} is an optimised 3D maths library
4880 for graphics software based on the @acronym{GLSL, OpenGL Shading Language}
4881 specifications.
4882
4883 It's similar to the original C++ GLM library but written in C99 and compatible
4884 with C89.")
4885     (license license:expat)))
4886
4887 (define-public glm
4888   (package
4889     (name "glm")
4890     (version "0.9.9.8")
4891     (source
4892      (origin
4893        (method url-fetch)
4894        (uri (string-append "https://github.com/g-truc/glm/releases/download/"
4895                            version  "/glm-" version ".zip"))
4896        (sha256
4897         (base32 "0k6yk9v46h690rshdx49x98y5qspkzibld1wb51jwcm35vba7qip"))))
4898     (build-system cmake-build-system)
4899     (arguments
4900      `(#:phases (modify-phases %standard-phases
4901                   (replace 'install
4902                     (lambda* (#:key outputs #:allow-other-keys)
4903                       ;; Since version 0.9.9.6, 'make install' is not supported
4904                       ;; and we have to do it "manually".  Upstream discussion:
4905                       ;; <https://github.com/g-truc/glm/pull/968>.
4906                       (let* ((source (string-append "../glm"))
4907                              (out (assoc-ref outputs "out"))
4908                              (inc (string-append out "/include"))
4909                              (lib (string-append out "/lib"))
4910                              (pkgconfig (string-append lib "/pkgconfig")))
4911                         (with-directory-excursion source
4912                           (mkdir-p inc)
4913                           (mkdir-p pkgconfig)
4914                           (copy-recursively "glm" (string-append inc "/glm"))
4915                           (copy-recursively "cmake" (string-append lib "/cmake"))
4916                           (call-with-output-file (string-append pkgconfig "/glm.pc")
4917                             (lambda (port)
4918                               (format port
4919                                       "prefix=~a
4920 includedir=${prefix}/include
4921
4922 Name: GLM
4923 Description: OpenGL Mathematics
4924 Version: ~a
4925 Cflags: -I${includedir}~%" out ,(version-prefix version 3)))))
4926                         #t))))))
4927     (native-inputs
4928      (list unzip))
4929     (home-page "https://glm.g-truc.net/")
4930     (synopsis "OpenGL Mathematics library")
4931     (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
4932 library for graphics software based on the OpenGL Shading Language (GLSL)
4933 specifications.")
4934     (license license:expat)))
4935
4936 (define-public lpsolve
4937   (package
4938     (name "lpsolve")
4939     (version "5.5.2.5")
4940     (source
4941      (origin
4942       (method url-fetch)
4943       (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
4944                           "/lp_solve_" version "_source.tar.gz"))
4945       (sha256
4946        (base32
4947         "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"))
4948       (modules '((guix build utils)))
4949       (snippet
4950        '(begin
4951           (substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
4952             (("^c=cc") "c=gcc")
4953             ;; Pretend to be on a 64 bit platform to obtain a common directory
4954             ;; name for the build results on all architectures; nothing else
4955             ;; seems to depend on it.
4956             (("^PLATFORM=.*$") "PLATFORM=ux64\n")
4957
4958             ;; The check for 'isnan' as it is written fails with
4959             ;; "non-floating-point argument in call to function
4960             ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
4961             ;; definition, which in turn leads to bad things.  Fix the feature
4962             ;; test.
4963             (("isnan\\(0\\)") "isnan(0.)"))
4964           #t))))
4965     (build-system gnu-build-system)
4966     (arguments
4967      `(#:tests? #f                      ; no check target
4968        #:phases
4969        (modify-phases %standard-phases
4970          (delete 'configure)            ; no configure script
4971          (replace 'build
4972            (lambda _
4973              (with-directory-excursion "lpsolve55"
4974                (invoke "bash" "ccc"))
4975              (with-directory-excursion "lp_solve"
4976                (invoke "bash" "ccc"))
4977              #t))
4978          (replace 'install
4979            (lambda* (#:key outputs #:allow-other-keys)
4980              (let* ((out (assoc-ref outputs "out"))
4981                     (bin (string-append out "/bin"))
4982                     (lib (string-append out "/lib"))
4983                     ;; This is where LibreOffice expects to find the header
4984                     ;; files, and where they are installed by Debian.
4985                     (include (string-append out "/include/lpsolve")))
4986                (install-file "lpsolve55/bin/ux64/liblpsolve55.a" lib)
4987                (install-file "lpsolve55/bin/ux64/liblpsolve55.so" lib)
4988                (install-file "lp_solve/bin/ux64/lp_solve" bin)
4989
4990                ;; Install a subset of the header files as on Debian
4991                ;; (plus lp_bit.h, which matches the regular expression).
4992                (for-each (lambda (name)
4993                            (install-file name include))
4994                          (find-files "." "lp_[HMSa-z].*\\.h$"))
4995                (with-directory-excursion "shared"
4996                  (for-each (lambda (name)
4997                              (install-file name include))
4998                            (find-files "." "\\.h$")))
4999                #t))))))
5000     (home-page "http://lpsolve.sourceforge.net/")
5001     (synopsis "Mixed integer linear programming (MILP) solver")
5002     (description
5003      "lp_solve is a mixed integer linear programming solver based on the
5004 revised simplex and the branch-and-bound methods.")
5005     (license license:lgpl2.1+)))
5006
5007 ;; Private Trilinos package for dealii-openmpi (similar to
5008 ;; trilinos-serial-xyce and trilinos-parallel-xyce).
5009 ;; This version is the latest known to be compatible with deal.II [1].
5010 ;; Since the latest version of Trilinos is not necessarily supported by
5011 ;; deal.II, it may be worth keeping this package even if and when Trilinos
5012 ;; gets packaged separately for Guix (unless various versions of Trilinos are
5013 ;; packaged).
5014 ;;
5015 ;; An insightful source of information for building Trilinos for deal.II lies
5016 ;; in the Trilinos package for candi [2], which is a source-based installer
5017 ;; for deal.II and its dependencies.
5018 ;;
5019 ;; [1]: https://www.dealii.org/current/external-libs/trilinos.html
5020 ;; [2]: https://github.com/dealii/candi/blob/master/deal.II-toolchain/packages/trilinos.package
5021 (define trilinos-for-dealii-openmpi
5022   (package
5023     (name "trilinos-for-dealii-openmpi")
5024     (version "12.18.1")
5025     (source
5026      (origin
5027        (method git-fetch)
5028        (uri (git-reference
5029              (url "https://github.com/trilinos/Trilinos/")
5030              (commit
5031               (string-append "trilinos-release-"
5032                              (string-replace-substring version "." "-")))))
5033        (file-name (git-file-name "trilinos" version))
5034        (sha256
5035         (base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
5036     (build-system cmake-build-system)
5037     (native-inputs
5038      `(("gfortran" ,gfortran)
5039        ;; Trilinos's repository contains several C-shell scripts, but adding
5040        ;; tcsh to the native inputs does not result in the check phase running
5041        ;; any more tests than without it (nor is tcsh required to build
5042        ;; Trilinos).
5043        ;; It seems that Trilinos has replaced its use of C-shell test scripts
5044        ;; with CMake's testing facilities.
5045        ;; For example,
5046        ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
5047        ;; states that Zoltan's C-shell test script
5048        ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now
5049        ;; performed through CMake.
5050        ;;
5051        ;; Perl is required for some Zoltan tests and Python 2 for one ML test.
5052        ;;
5053        ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
5054        ("perl" ,perl)
5055        ("python" ,python-2)))
5056     (inputs
5057      `(("blas" ,openblas)
5058        ("lapack" ,lapack)
5059        ("mumps" ,mumps-openmpi)
5060        ("scalapack" ,scalapack)))
5061     (propagated-inputs
5062      `(("mpi" ,openmpi)))
5063     (arguments
5064      `(#:build-type "Release"
5065        #:configure-flags
5066        `("-DBUILD_SHARED_LIBS=ON"
5067          ;; Obtain the equivalent of RelWithDebInfo but with -O3 (the Release
5068          ;; default) rather than -O2 (the RelWithDebInfo default), to conform
5069          ;; to candi's trilinos.package's compilation flags, which are -g -O3.
5070          "-DCMAKE_C_FLAGS=-g"
5071          "-DCMAKE_CXX_FLAGS=-g"
5072          "-DCMAKE_Fortran_FLAGS=-g"
5073
5074          ;; Trilinos libraries that deal.II can interface with.
5075          "-DTrilinos_ENABLE_Amesos=ON"
5076          "-DTrilinos_ENABLE_AztecOO=ON"
5077          "-DTrilinos_ENABLE_Epetra=ON"
5078          "-DTrilinos_ENABLE_EpetraExt=ON"
5079          "-DTrilinos_ENABLE_Ifpack=ON"
5080          "-DTrilinos_ENABLE_ML=ON"
5081          "-DTrilinos_ENABLE_MueLu=ON"
5082          "-DTrilinos_ENABLE_ROL=ON"
5083          ;; Optional; required for deal.II's GridIn::read_exodusii, but
5084          ;; depends on netcdf.
5085          ;; Enable if and when someone needs it.
5086          ;;"-DTrilinos_ENABLE_SEACAS=ON"
5087          "-DTrilinos_ENABLE_Sacado=ON"
5088          "-DTrilinos_ENABLE_Teuchos=ON"
5089          "-DTrilinos_ENABLE_Tpetra=ON"
5090          "-DTrilinos_ENABLE_Zoltan=ON"
5091
5092          ;; Third-party libraries (TPLs) that Trilinos can interface with.
5093          "-DBLAS_LIBRARY_NAMES=openblas"
5094          "-DTPL_ENABLE_MPI=ON"
5095          "-DTPL_ENABLE_MUMPS=ON"
5096          "-DTPL_ENABLE_SCALAPACK=ON"
5097
5098          ;; Enable the tests but not the examples (which are enabled by
5099          ;; default when enabling tests).
5100          ;; Although some examples are run as tests, they are otherwise
5101          ;; unnecessary since this is a private package meant for
5102          ;; dealii-openmpi.
5103          ;; Besides, some MueLu and ROL examples require a lot of memory to
5104          ;; compile.
5105          ;;
5106          ;; (For future reference, note that some ROL and SEACAS examples
5107          ;; require removing gfortran from CPLUS_INCLUDE_PATH as in the
5108          ;; dune-istl, dune-localfunctions and dune-alugrid packages.)
5109          "-DTrilinos_ENABLE_TESTS=ON"
5110          "-DTrilinos_ENABLE_EXAMPLES=OFF"
5111          ;; MueLu tests require considerably more time and memory to compile
5112          ;; than the rest of the tests.
5113          "-DMueLu_ENABLE_TESTS=OFF"
5114
5115          ;; The following options were gleaned from candi's trilinos.package.
5116          ;; (We do not enable the complex instantiations, which are anyway
5117          ;; provided only as an option in trilinos.package, because they are
5118          ;; costly in compilation time and memory usage, and disk space [1].)
5119          ;;
5120          ;; [1]: https://www.docs.trilinos.org/files/TrilinosBuildReference.html#enabling-float-and-complex-scalar-types
5121          "-DTrilinos_ENABLE_Ifpack2=OFF"
5122          "-DTeuchos_ENABLE_FLOAT=ON"
5123          "-DTpetra_INST_INT_LONG=ON"
5124          "-DTPL_ENABLE_Boost=OFF")
5125        #:phases
5126        (modify-phases %standard-phases
5127          (add-after 'configure 'fix-kokkos-config
5128            (lambda _
5129              ;; GNU Make 4.3 accidentally leaves the backslash preceding the
5130              ;; number sign in strings containing a literal backslash–number
5131              ;; sign (\#) [1, 2].
5132              ;; This is still an issue in Trilinos 13.0.1, but should be fixed
5133              ;; in the following version.
5134              ;; (The latest versions of Kokkos incorporate the fix [2].)
5135              ;;
5136              ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136
5137              ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441
5138              (substitute* "KokkosCore_config.h"
5139                (("\\\\#") "#"))
5140              #t))
5141          (add-before 'check 'mpi-setup
5142            ,%openmpi-setup))))
5143     (home-page "https://trilinos.github.io/")
5144     (synopsis "Algorithms for engineering and scientific problems")
5145     (description
5146      "The Trilinos Project is an effort to develop algorithms and enabling
5147 technologies within an object-oriented software framework for the solution of
5148 large-scale, complex multi-physics engineering and scientific problems.
5149 A unique design feature of Trilinos is its focus on packages.")
5150     ;; The packages are variously licensed under more than just BSD-3 and
5151     ;; LGPL-2.1+, but all the licenses are either BSD- or LGPL-compatible.
5152     ;; See https://trilinos.github.io/license.html.
5153     (license (list license:bsd-3 license:lgpl2.1+))))
5154
5155 (define-public dealii
5156   (package
5157     (name "dealii")
5158     (version "9.3.1")
5159     (source
5160      (origin
5161        (method url-fetch)
5162        (uri (string-append "https://github.com/dealii/dealii/releases/"
5163                            "download/v" version "/dealii-" version ".tar.gz"))
5164        (sha256
5165         (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6"))
5166        (modules '((guix build utils)))
5167        (snippet
5168         '(begin
5169            ;; Remove bundled boost, muparser, TBB and UMFPACK.
5170            (delete-file-recursively "bundled")
5171            #t))))
5172     (build-system cmake-build-system)
5173     (outputs '("out" "doc"))
5174     (native-inputs
5175      ;; Required to build the documentation.
5176      `(("dot" ,graphviz)
5177        ("doxygen" ,doxygen)
5178        ("perl" ,perl)))
5179     (inputs
5180      `(("arpack" ,arpack-ng)
5181        ("blas" ,openblas)
5182        ("gfortran" ,gfortran)
5183        ("lapack" ,lapack)
5184        ("muparser" ,muparser)
5185        ("zlib" ,zlib)))
5186     (propagated-inputs
5187      ;; Some scripts are installed into share/deal.II/scripts that require
5188      ;; perl and python, but they are not executable (and some are missing the
5189      ;; shebang line) and therefore must be explicitly passed to the
5190      ;; interpreter.
5191      ;; Anyway, they are meant to be used at build time, so rather than adding
5192      ;; the interpreters here, any package depending on them should just add
5193      ;; the requisite interpreter to its native inputs.
5194      (list boost hdf5 suitesparse ; For UMFPACK.
5195            tbb))
5196     (arguments
5197      `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
5198        ;; The tests take too long and must be explicitly enabled with "make
5199        ;; setup_tests".
5200        ;; See https://www.dealii.org/developer/developers/testsuite.html.
5201        ;; (They can also be run for an already installed deal.II.)
5202        #:tests? #f
5203        #:configure-flags
5204        (let ((doc (string-append (assoc-ref %outputs "doc")
5205                                  "/share/doc/" ,name "-" ,version)))
5206          `("-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
5207            ,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
5208            ,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
5209            ;; Don't compile the examples because the source and CMakeLists.txt
5210            ;; are installed anyway, allowing users to do so for themselves.
5211            "-DDEAL_II_COMPILE_EXAMPLES=OFF"
5212            ,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples")))
5213        #:phases
5214        (modify-phases %standard-phases
5215          (add-after 'install 'remove-build-logs
5216            ;; These build logs leak the name of the build directory by storing
5217            ;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR.
5218            (lambda* (#:key outputs #:allow-other-keys)
5219              (let ((doc (string-append (assoc-ref outputs "doc")
5220                                        "/share/doc/" ,name "-" ,version)))
5221                (for-each delete-file (map (lambda (f) (string-append doc "/" f))
5222                                           '("detailed.log" "summary.log"))))
5223              #t)))))
5224     (home-page "https://www.dealii.org/")
5225     (synopsis "Finite element library")
5226     (description
5227      "Deal.II is a C++ program library targeted at the computational solution
5228 of partial differential equations using adaptive finite elements.  The main
5229 aim of deal.II is to enable rapid development of modern finite element codes,
5230 using among other aspects adaptive meshes and a wide array of tools often used
5231 in finite element programs.")
5232     (license license:lgpl2.1+)))
5233
5234 (define-public dealii-openmpi
5235   (package/inherit dealii
5236     (name "dealii-openmpi")
5237     (inputs
5238      `(("arpack" ,arpack-ng-openmpi)
5239        ("metis" ,metis)
5240        ("scalapack" ,scalapack)
5241        ,@(alist-delete "arpack" (package-inputs dealii))))
5242     (propagated-inputs
5243      `(("hdf5" ,hdf5-parallel-openmpi)
5244        ("mpi" ,openmpi)
5245        ("p4est" ,p4est-openmpi)
5246        ("petsc" ,petsc-openmpi)
5247        ("slepc" ,slepc-openmpi)
5248        ("trilinos" ,trilinos-for-dealii-openmpi)
5249        ,@(alist-delete "hdf5" (package-propagated-inputs dealii))))
5250     (arguments
5251      (substitute-keyword-arguments (package-arguments dealii)
5252        ((#:configure-flags flags)
5253         `(cons "-DDEAL_II_WITH_MPI=ON" ,flags))))
5254     (synopsis "Finite element library (with MPI support)")))
5255
5256 (define-public flann
5257   (package
5258     (name "flann")
5259     (version "1.9.1")
5260     (home-page "https://github.com/mariusmuja/flann/")
5261     (source
5262       (origin
5263         (method git-fetch)
5264         (uri (git-reference (url home-page) (commit version)))
5265         (file-name (git-file-name name version))
5266         (sha256
5267           (base32
5268            "0p56fl2yx1r86ds1mgjq40926jdcgq3hka7p3l1hv2acv9jxp15x"))
5269         (patches (search-patches "flann-cmake-3.11.patch"))))
5270     (build-system cmake-build-system)
5271     (outputs '("out"))
5272     (native-inputs
5273      (list unzip))
5274     (inputs
5275      `(("hdf5" ,hdf5)
5276        ;; FIXME: 'mkoctfile' fails with a linker error:
5277        ;;  ld: cannot find -loctinterp
5278        ;;  ld: cannot find -loctave
5279        ;; Disable it for now.
5280        ;;("octave" ,octave-cli)
5281        ("python" ,python-2) ; print syntax
5282        ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
5283        ("zlib" ,zlib)))
5284     (arguments
5285      `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
5286        ;; taken 46 MiB unstripped, and 6 MiB stripped.
5287        #:strip-directories '("lib" "lib64" "libexec"
5288                              "bin" "sbin" "share/flann/octave")
5289
5290        ;; Save 12 MiB by not installing .a files.  Passing
5291        ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
5292        #:phases (modify-phases %standard-phases
5293                   (add-after 'install 'remove-static-libraries
5294                     (lambda* (#:key outputs #:allow-other-keys)
5295                       (let* ((out (assoc-ref outputs "out"))
5296                              (lib (string-append out "/lib")))
5297                         (for-each delete-file
5298                                   (find-files lib "\\.a$"))
5299                         #t))))
5300
5301        #:tests? #f)) ; The test data are downloaded from the Internet.
5302     (synopsis "Library for approximate nearest neighbors computation")
5303     (description "FLANN is a library for performing fast approximate
5304 nearest neighbor searches in high dimensional spaces.  It implements a
5305 collection of algorithms and a system for automatically choosing the best
5306 algorithm and optimum parameters depending on the dataset.
5307
5308 FLANN is written in C++ and contains bindings for C, Octave and Python.")
5309     (license (license:non-copyleft "file://COPYING"
5310                                 "See COPYING in the distribution."))))
5311
5312 (define-public wcalc
5313   (package
5314     (name "wcalc")
5315     (version "2.5")
5316     (source
5317       (origin
5318         (method url-fetch)
5319         (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
5320                             "wcalc-" version ".tar.bz2"))
5321         (sha256
5322           (base32
5323             "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
5324     (build-system gnu-build-system)
5325     (inputs
5326      (list mpfr readline))
5327     (home-page "http://w-calc.sourceforge.net/index.php")
5328     (synopsis "Flexible command-line scientific calculator")
5329     (description "Wcalc is a very capable calculator.  It has standard functions
5330 (sin, asin, and sinh for example, in either radians or degrees), many
5331 pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
5332 variables, a command history, hex/octal/binary input and output, unit
5333 conversions, embedded comments, and an expandable expression entry field.  It
5334 evaluates expressions using the standard order of operations.")
5335     (license license:gpl2+)))
5336
5337 (define-public xaos
5338   (package
5339     (name "xaos")
5340     (version "4.2.1")
5341     (source (origin
5342               (method git-fetch)
5343               (uri (git-reference
5344                     (url "https://github.com/xaos-project/XaoS")
5345                     (commit (string-append "release-" version))))
5346               (file-name (git-file-name name version))
5347               (sha256
5348                (base32
5349                 "0maw5am6rrkyjrprfg113zjq37mqj0iaznkg4h2927ff7wrprc94"))))
5350     (build-system gnu-build-system)
5351     (native-inputs `(("gettext" ,gettext-minimal)
5352                      ("qtbase" ,qtbase-5)
5353                      ("qttools" ,qttools)))
5354     (inputs (list libx11 zlib libpng gsl))
5355     ;; The upstream project file ("XaoS.pro") and the Makefile it generates are
5356     ;; not enough for this package to install properly.  These phases fix that.
5357     (arguments
5358      `(#:tests? #f ;no "check" target
5359        #:phases
5360        (modify-phases %standard-phases
5361          (add-before 'configure 'make-qt-deterministic
5362            (lambda _
5363              ;; Make Qt deterministic.
5364              (setenv "QT_RCC_SOURCE_DATE_OVERRIDE" "1")
5365              #t))
5366          (replace 'configure
5367            (lambda* (#:key outputs #:allow-other-keys)
5368              (let ((out (assoc-ref outputs "out")))
5369                (substitute* "XaoS.pro"
5370                  ;; The DESTDIR is originally set to install the xaos binary to
5371                  ;; the "bin" folder inside the build directory.  Setting make
5372                  ;; flags doesn't seem to change this.
5373                  (("DESTDIR.*$")
5374                   (string-append "DESTDIR=" out "/bin"))
5375                  ;; Set the correct path to the lrelease binary.
5376                  (("lrelease-qt5") "lrelease"))
5377                (substitute* "src/include/config.h"
5378                  (("/usr/share/XaoS")
5379                   (string-append out "/share/XaoS")))
5380                (invoke "qmake"))))
5381          (add-after 'install 'install-data
5382            (lambda* (#:key outputs #:allow-other-keys)
5383              (let* ((out (assoc-ref outputs "out"))
5384                     (share (string-append out "/share")))
5385                (mkdir-p share)
5386                (for-each
5387                 (lambda (folder)
5388                   (copy-recursively folder
5389                                     (string-append share "/XaoS/" folder)))
5390                 '("catalogs" "examples" "tutorial"))
5391                (install-file "xdg/xaos.png"
5392                              (string-append share "/pixmaps"))
5393                (install-file "xdg/xaos.desktop"
5394                              (string-append share "/applications")))
5395              #t)))))
5396     (synopsis "Real-time fractal zoomer")
5397     (description "GNU XaoS is a graphical program that generates fractal
5398 patterns and allows you to zoom in and out of them infinitely in a fluid,
5399 continuous manner.  It also includes tutorials that help to explain how fractals
5400 are built.  It can generate many different fractal types such as the Mandelbrot
5401 set.")
5402     (home-page "https://xaos-project.github.io/")
5403     (license license:gpl2+)))
5404
5405 (define-public hypre
5406   (package
5407     (name "hypre")
5408     (version "2.20.0")
5409     (source
5410      (origin
5411        (method git-fetch)
5412        (uri (git-reference
5413              (url "https://github.com/hypre-space/hypre")
5414              (commit (string-append "v" version))))
5415        (file-name (git-file-name name version))
5416        (sha256
5417         (base32 "14iqjwg5sv1qjn7c2cfv0xxmn9rwamjrhh9hgs8fjbywcbvrkjdi"))))
5418     (build-system gnu-build-system)
5419     (outputs '("out"                    ;5.3 MiB of headers and libraries
5420                "doc"))                  ;12 MiB of documentation
5421     (native-inputs
5422      `(("doc++" ,doc++)
5423        ("doxygen" ,doxygen)
5424        ("python" ,python)
5425        ("python-breathe" ,python-breathe)
5426        ("python-sphinx" ,python-sphinx)
5427        ("texlive" ,(texlive-updmap.cfg (list texlive-adjustbox
5428                                              texlive-amsfonts
5429                                              texlive-bibtex
5430                                              texlive-caption
5431                                              texlive-cm
5432                                              texlive-etoolbox
5433                                              texlive-jknappen
5434                                              texlive-sectsty
5435                                              texlive-tex-gyre
5436                                              texlive-wasy
5437                                              texlive-xcolor
5438                                              texlive-xypic
5439                                              texlive-generic-listofitems
5440                                              texlive-generic-ulem
5441                                              texlive-latex-capt-of
5442                                              texlive-latex-cmap
5443                                              texlive-latex-colortbl
5444                                              texlive-latex-etoc
5445                                              texlive-latex-fancyhdr
5446                                              texlive-latex-fancyvrb
5447                                              texlive-latex-float
5448                                              texlive-latex-fncychap
5449                                              texlive-latex-framed
5450                                              texlive-latex-geometry
5451                                              texlive-latex-hanging
5452                                              texlive-hyperref
5453                                              texlive-latex-multirow
5454                                              texlive-latex-natbib
5455                                              texlive-latex-needspace
5456                                              texlive-latex-newunicodechar
5457                                              texlive-latex-parskip
5458                                              texlive-latex-stackengine
5459                                              texlive-latex-tabulary
5460                                              texlive-latex-titlesec
5461                                              texlive-latex-tocloft
5462                                              texlive-latex-upquote
5463                                              texlive-latex-varwidth
5464                                              texlive-wasysym
5465                                              texlive-latex-wrapfig)))))
5466     (inputs
5467      `(("blas" ,openblas)
5468        ("lapack" ,lapack)))
5469     (arguments
5470      `(#:modules ((srfi srfi-1)
5471                   ,@%gnu-build-system-modules)
5472        #:configure-flags '("--enable-shared"
5473                            "--disable-fortran"
5474                            "--without-MPI"
5475                            "--with-openmp"
5476                            "--with-fei"
5477                            "--with-lapack"
5478                            "--with-blas")
5479        #:phases
5480        (modify-phases %standard-phases
5481          (add-before 'configure 'chdir-src
5482            (lambda _ (chdir "src")))
5483          (replace 'configure
5484            (lambda* (#:key build target configure-flags
5485                            #:allow-other-keys #:rest args)
5486              (let* ((configure (assoc-ref %standard-phases 'configure)))
5487                (apply configure
5488                       (append args
5489                               (list #:configure-flags
5490                                     (cons (string-append
5491                                            "--host=" (or target build))
5492                                           configure-flags)))))))
5493          (add-after 'build 'build-docs
5494            (lambda _
5495              (invoke "make" "-C" "docs")))
5496          (replace 'check
5497            (lambda _
5498              (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
5499              (setenv "PATH" (string-append "." ":" (getenv "PATH")))
5500              (invoke "make" "check" "CHECKRUN=")
5501              (for-each (lambda (filename)
5502                          (let ((size (stat:size (stat filename))))
5503                            (when (positive? size)
5504                              (error (format #f "~a size ~d; error indication~%"
5505                                             filename size)))))
5506                        (find-files "test" ".*\\.err$"))))
5507          (add-after 'install 'install-docs
5508            (lambda* (#:key outputs #:allow-other-keys)
5509              ;; Custom install because docs/Makefile doesn't honor ${docdir}.
5510              (let* ((doc (assoc-ref outputs "doc"))
5511                     (docdir (string-append doc "/share/doc/hypre-" ,version)))
5512                (with-directory-excursion "docs"
5513                  (for-each (lambda (base)
5514                              (install-file (string-append base ".pdf") docdir)
5515                              (copy-recursively (string-append base "-html")
5516                                                (string-append docdir "/" base)))
5517                            '("usr-manual" "ref-manual")))))))))
5518     (home-page "https://computing.llnl.gov/projects\
5519 /hypre-scalable-linear-solvers-multigrid-methods")
5520     (synopsis "Library of solvers and preconditioners for linear equations")
5521     (description
5522      "HYPRE is a software library of high performance preconditioners and
5523 solvers for the solution of large, sparse linear systems of equations.  It
5524 features multigrid solvers for both structured and unstructured grid
5525 problems.")
5526     (license license:lgpl2.1)))
5527
5528 (define-public hypre-openmpi
5529   (package (inherit hypre)
5530     (name "hypre-openmpi")
5531     (inputs
5532      `(("mpi" ,openmpi)
5533        ,@(package-inputs hypre)))
5534     (arguments
5535      (substitute-keyword-arguments (package-arguments hypre)
5536        ((#:configure-flags flags)
5537         ``("--with-MPI"
5538            ,@(delete "--without-MPI" ,flags)))
5539        ((#:phases phases)
5540         `(modify-phases ,phases
5541            (add-before 'check 'mpi-setup
5542              ,%openmpi-setup)))))
5543     (synopsis "Parallel solvers and preconditioners for linear equations")
5544     (description
5545      "HYPRE is a software library of high performance preconditioners and
5546 solvers for the solution of large, sparse linear systems of equations on
5547 parallel computers.  It features parallel multigrid solvers for both
5548 structured and unstructured grid problems.")))
5549
5550 (define-public matio
5551   (package
5552     (name "matio")
5553     (version "1.5.19")
5554     (source
5555      (origin
5556        (method url-fetch)
5557        (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
5558                            "matio-" version ".tar.gz"))
5559        (sha256
5560         (base32
5561          "0vr8c1mz1k6mz0sgh6n3scl5c3a71iqmy5fnydrgq504icj4vym4"))))
5562     (build-system gnu-build-system)
5563     (inputs
5564      (list zlib hdf5-1.8))
5565     (home-page "http://matio.sourceforge.net/")
5566     (synopsis "Library for reading and writing MAT files")
5567     (description "Matio is a library for reading and writing MAT files.  It
5568 supports compressed MAT files, as well as newer (version 7.3) MAT files.")
5569     (license license:bsd-2)))
5570
5571 (define-public vc
5572   (package
5573     (name "vc")
5574     (version "1.4.2")
5575     (source
5576       (origin (method url-fetch)
5577               (uri (string-append "https://github.com/VcDevel/Vc/releases/"
5578                                   "download/" version "/Vc-" version ".tar.gz"))
5579               (sha256
5580                (base32
5581                 "0lirdqzcxys9walz04bllsphydynk7973aimd5k1h1qbwi8z3lsh"))))
5582     (build-system cmake-build-system)
5583     (arguments
5584      '(#:configure-flags
5585        '("-DBUILD_TESTING=ON"
5586          ;; By default, Vc will optimize for the CPU of the build machine.
5587          ;; Setting this to "none" makes it create portable binaries.  See
5588          ;; "cmake/OptimizeForArchitecture.cmake".
5589          "-DTARGET_ARCHITECTURE=none")
5590        #:phases (modify-phases %standard-phases
5591                   (add-after 'unpack 'copy-testdata
5592                     (lambda* (#:key inputs native-inputs #:allow-other-keys)
5593                       (let ((testdata (assoc-ref (or native-inputs inputs)
5594                                                  "testdata")))
5595                         (copy-recursively testdata "tests/testdata")
5596                         #t))))))
5597     (native-inputs
5598      `(("virtest" ,virtest)
5599
5600        ;; This is a submodule in the git project, but not part of the
5601        ;; released sources.  See the git branch for the commit to take.
5602        ("testdata" ,(let ((commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3"))
5603                       (origin
5604                         (method git-fetch)
5605                         (uri (git-reference
5606                               (url "https://github.com/VcDevel/vc-testdata")
5607                               (commit "9ada1f34d6a41f1b5553d6223f277eae72c039d3")))
5608                         (file-name (git-file-name "vc-testdata"
5609                                                   (string-take commit 7)))
5610                         (sha256
5611                          (base32
5612                           "1hkhqib03qlcq412ym2dciynfxcdr2ygqhnplz4l1vissr1wnqn2")))))))
5613     (synopsis "SIMD vector classes for C++")
5614     (description "Vc provides portable, zero-overhead C++ types for explicitly
5615 data-parallel programming.  It is a library designed to ease explicit
5616 vectorization of C++ code.  Its types enable explicitly stating data-parallel
5617 operations on multiple values.  The parallelism is therefore added via the type
5618 system.  Vc has an intuitive API and provides portability between different
5619 compilers and compiler versions as well as portability between different vector
5620 instruction sets.  Thus, an application written with Vc can be compiled for:
5621 @enumerate
5622 @item AVX and AVX2
5623 @item SSE2 up to SSE4.2 or SSE4a
5624 @item Scalar
5625 @item MIC
5626 @item NEON (in development)
5627 @item NVIDIA GPUs / CUDA (in development)
5628 @end enumerate\n")
5629     (home-page "https://github.com/VcDevel/Vc")
5630     ;; "No support_???.cpp file exists for this architecture."
5631     (supported-systems '("x86_64-linux" "i686-linux"))
5632     (license license:bsd-3)))
5633
5634 (define-public reducelcs
5635   ;; This is the last commit which is available upstream, no
5636   ;; release happened since 2010.
5637   (let ((commit "474f88deb968061abe8cf11c959e02319b8ae5c0")
5638         (revision "1"))
5639     (package
5640       (name "reducelcs")
5641       (version (string-append "1.0-" revision "." (string-take commit 7)))
5642       (source
5643        (origin
5644          (method git-fetch)
5645          (uri (git-reference
5646                (url "https://github.com/gdv/Reduce-Expand-for-LCS")
5647                (commit commit)))
5648          (file-name (string-append name "-" version "-checkout"))
5649          (sha256
5650           (base32
5651            "1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
5652       (build-system gnu-build-system)
5653       (inputs
5654        (list openlibm))
5655       (arguments
5656        `(#:tests? #f ; no tests
5657          #:phases
5658          (modify-phases %standard-phases
5659            (delete 'configure) ; No configure script exists.
5660            (replace 'install ; No install phase exists.
5661              (lambda* (#:key outputs #:allow-other-keys)
5662                (let* ((out (assoc-ref outputs "out"))
5663                       (bin (string-append out "/bin")))
5664                  (install-file "Approximation" bin)
5665                  (install-file "CollectResults" bin)
5666                  (install-file "GenerateInstances" bin)
5667                  #t))))))
5668       (synopsis "Approximate Longest Commons Subsequence computation tool")
5669       (description
5670        "@code{reduceLCS} is an implementation of the Reduce-Expand
5671 algorithm for LCS.  It is a fast program to compute the approximate
5672 Longest Commons Subsequence of a set of strings.")
5673       (home-page "https://github.com/gdv/Reduce-Expand-for-LCS")
5674       (license license:gpl3+))))
5675
5676 (define-public jacal
5677   (package
5678     (name "jacal")
5679     (version "1c4")
5680     (source (origin
5681               (method url-fetch)
5682               (uri (string-append
5683                     "http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
5684                     version ".zip"))
5685               (sha256 (base32
5686                        "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
5687               (patches (search-patches "jacal-fix-texinfo.patch"))))
5688     (build-system gnu-build-system)
5689     (arguments
5690      `(#:phases
5691        (modify-phases %standard-phases
5692          (add-before 'build 'pre-build
5693                      ;; Don't use upstream's script - it really doesn't fit into
5694                      ;; Guix's functional paradigm.
5695                      (lambda* (#:key inputs outputs #:allow-other-keys)
5696                        (substitute* "Makefile"
5697                          (("^install: install-script") "install: "))))
5698          (add-after 'install 'post-install
5699                     ;; Instead, we provide our own simplified script.
5700                     (lambda* (#:key inputs outputs #:allow-other-keys)
5701                       (let ((wrapper (string-append (assoc-ref outputs "out")
5702                                                     "/bin/jacal")))
5703                         (format (open wrapper (logior O_WRONLY O_CREAT))
5704                                 (string-append "#!~a\nexec ~a/bin/scm -ip1 "
5705                                 "-e '(slib:load \"~a/lib/jacal/math\") "
5706                                 "(math)' \"$@\"\n")
5707                                 (which  "bash")
5708                                 (assoc-ref inputs "scm")
5709                                 (assoc-ref outputs "out"))
5710                         (chmod wrapper #o555))))
5711          (replace 'configure
5712            (lambda* (#:key outputs #:allow-other-keys)
5713              (invoke "./configure"
5714                      (string-append "--prefix="
5715                                     (assoc-ref outputs "out"))))))))
5716     (inputs (list scm))
5717     (native-inputs (list unzip texinfo))
5718     (synopsis "Symbolic mathematics system")
5719     (description "GNU JACAL is an interactive symbolic mathematics program based on
5720 Scheme.  It manipulate and simplify a range of mathematical expressions such
5721 as equations, scalars, vectors, and matrices.")
5722     (home-page "https://www.gnu.org/software/jacal/")
5723     (license license:gpl3+)))
5724
5725 (define-public z3
5726   (package
5727     (name "z3")
5728     (version "4.8.9")
5729     (home-page "https://github.com/Z3Prover/z3")
5730     (source (origin
5731               (method git-fetch)
5732               (uri (git-reference (url home-page)
5733                                   (commit (string-append "z3-" version))))
5734               (file-name (git-file-name name version))
5735               (sha256
5736                (base32
5737                 "1hnbzq10d23drd7ksm3c1n2611c3kd0q0yxgz8y78zaafwczvwxx"))))
5738     (build-system gnu-build-system)
5739     (arguments
5740      `(#:imported-modules ((guix build python-build-system)
5741                            ,@%gnu-build-system-modules)
5742        #:modules (((guix build python-build-system) #:select (site-packages))
5743                   (guix build gnu-build-system)
5744                   (guix build utils))
5745        #:phases
5746        (modify-phases %standard-phases
5747          (add-after 'unpack 'enable-bytecode-determinism
5748            (lambda _
5749              (setenv "PYTHONHASHSEED" "0")
5750              #t))
5751          (add-after 'unpack 'fix-compatability
5752            ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
5753            (lambda _
5754              (substitute* "src/util/mpz.cpp"
5755                (("#include <immintrin.h>") ""))
5756              #t))
5757          (add-before 'configure 'bootstrap
5758            (lambda _
5759              (invoke "python" "scripts/mk_make.py")))
5760          ;; work around gnu-build-system's setting --enable-fast-install
5761          ;; (z3's `configure' is a wrapper around the above python file,
5762          ;; which fails when passed --enable-fast-install)
5763          (replace 'configure
5764            (lambda* (#:key inputs outputs #:allow-other-keys)
5765              (invoke "./configure"
5766                      "--python"
5767                      (string-append "--prefix=" (assoc-ref outputs "out"))
5768                      (string-append "--pypkgdir=" (site-packages inputs outputs)))))
5769          (add-after 'configure 'change-directory
5770            (lambda _
5771              (chdir "build")
5772              #t))
5773          (add-before 'check 'make-test-z3
5774            (lambda _
5775              ;; Build the test suite executable.
5776              (invoke "make" "test-z3" "-j"
5777                      (number->string (parallel-job-count)))))
5778          (replace 'check
5779            (lambda _
5780              ;; Run all the tests that don't require arguments.
5781              (invoke "./test-z3" "/a"))))))
5782     (native-inputs
5783      `(("which" ,which)
5784        ("python" ,python-wrapper)))
5785     (synopsis "Theorem prover")
5786     (description "Z3 is a theorem prover and @dfn{satisfiability modulo
5787 theories} (SMT) solver.  It provides a C/C++ API, as well as Python bindings.")
5788     (license license:expat)))
5789
5790 (define-public ocaml-z3
5791   (package
5792     (inherit z3)
5793     (name "ocaml-z3")
5794     (arguments
5795      `(#:imported-modules ((guix build python-build-system)
5796                            ,@%gnu-build-system-modules)
5797        #:modules (((guix build python-build-system) #:select (site-packages))
5798                   (guix build gnu-build-system)
5799                   (guix build utils))
5800        #:tests? #f; no ml tests
5801        #:phases
5802        (modify-phases %standard-phases
5803          (add-before 'configure 'bootstrap
5804            (lambda* (#:key outputs #:allow-other-keys)
5805              (let ((out (assoc-ref outputs "out")))
5806                (setenv "OCAMLFIND_LDCONF" "ignore")
5807                (setenv "OCAMLFIND_DESTDIR" (string-append out "/lib/ocaml/site-lib"))
5808                (mkdir-p (string-append out "/lib/ocaml/site-lib"))
5809                (substitute* "scripts/mk_util.py"
5810                  (("LIBZ3 = LIBZ3")
5811                   (string-append "LIBZ3 = LIBZ3 + ' -dllpath " out "/lib'"))
5812                  ;; Do not build z3 again, use the library passed as input
5813                  ;; instead
5814                  (("z3linkdep,") "\"\",")
5815                  (("z3linkdep)") "\"\")"))
5816                (invoke "python" "scripts/mk_make.py"))))
5817          (replace 'configure
5818            (lambda* (#:key inputs outputs #:allow-other-keys)
5819              (invoke "./configure"
5820                      "--ml"
5821                      (string-append "--prefix=" (assoc-ref outputs "out")))))
5822          (add-after 'configure 'change-directory
5823            (lambda _
5824              (chdir "build")
5825              #t))
5826          (replace 'build
5827            (lambda _
5828              (invoke "make" "ml")))
5829          (replace 'install
5830            (lambda* (#:key outputs #:allow-other-keys)
5831              (invoke "ocamlfind" "install" "-destdir"
5832                      (string-append (assoc-ref outputs "out") "/lib/ocaml/site-lib")
5833                      "z3" "api/ml/META" "api/ml/z3enums.mli" "api/ml/z3enums.cmi"
5834                      "api/ml/z3enums.cmx" "api/ml/z3native.mli"
5835                      "api/ml/z3native.cmi" "api/ml/z3native.cmx"
5836                      "../src/api/ml/z3.mli" "api/ml/z3.cmi" "api/ml/z3.cmx"
5837                      "api/ml/libz3ml.a" "api/ml/z3ml.a" "api/ml/z3ml.cma"
5838                      "api/ml/z3ml.cmxa" "api/ml/z3ml.cmxs" "api/ml/dllz3ml.so"))))))
5839     (native-inputs
5840      `(("which" ,which)
5841        ("python" ,python-wrapper)
5842        ("ocaml" ,ocaml)
5843        ("ocaml-findlib" ,ocaml-findlib)))
5844     (propagated-inputs
5845      (list ocaml-zarith))
5846     (inputs
5847      (list z3))))
5848
5849 (define-public elpa
5850   (package
5851     (name "elpa")
5852     (version "2018.11.001")
5853     (source (origin
5854               (method url-fetch)
5855               (uri (string-append "http://elpa.mpcdf.mpg.de/html/Releases/"
5856                                   version "/elpa-" version ".tar.gz"))
5857               (sha256
5858                (base32
5859                 "05hv3v5i6xmziaizw350ff72y1c3k662r85fm3xfdrkclj5zw9yc"))))
5860     (build-system gnu-build-system)
5861     (native-inputs
5862      `(("fortran" ,gfortran)
5863        ("perl" ,perl)))                 ;for configure and deps
5864     (inputs
5865      `(("blas" ,openblas)))
5866     (arguments
5867      `(#:configure-flags
5868        `("--enable-openmp"
5869          "--with-mpi=no"
5870          ;; ELPA unfortunately does not support runtime dispatch, so we can
5871          ;; only enable the "generic" kernels.  See the "Cross compilation"
5872          ;; section of INSTALL.md.
5873          "--enable-generic"
5874          "--disable-sse" "--disable-sse-assembly" ;Require SSE3
5875          "--disable-avx" "--disable-avx2" "--disable-avx512"
5876          ,(string-append "CFLAGS=-O3 "
5877                          "-funsafe-loop-optimizations -funsafe-math-optimizations "
5878                          "-ftree-vect-loop-version -ftree-vectorize "
5879                          ,(let ((system (or (%current-target-system)
5880                                             (%current-system))))
5881                             (cond
5882                              ((or (string-prefix? "x86_64" system)
5883                                   (string-prefix? "i686" system))
5884                               "-msse2")
5885                              (else "")))))
5886        #:parallel-tests? #f             ;tests are multi-threaded, via BLAS
5887        #:phases
5888        (modify-phases %standard-phases
5889          (add-before 'configure 'patch-header-generation
5890            (lambda _
5891              (substitute* "configure"
5892                (("^  *make.*top_srcdir=\"\\$srcdir\"" &)
5893                 (string-append & " CPP=\"$CPP\"")))
5894              #t))
5895          (add-before 'check 'setup-tests
5896            (lambda _
5897              ;; Decrease test time and RAM use by computing fewer eigenvalues.
5898              ;; The flags are (MATRIX-SIZE, EIGENVALUES, BLOCK-SIZE), where
5899              ;; the default is (500, 250, 16) for C tests and (5000, 150, 16)
5900              ;; for Fortran.  This also causes several tests to pass that
5901              ;; otherwise would otherwise fail with matrix size 5000; possibly
5902              ;; due to floating point tolerances that are too tight.
5903              (setenv "TEST_FLAGS" "1500 50 16") ;from elpa.spec
5904              (setenv "OMP_NUM_THREADS" (number->string (parallel-job-count)))
5905              (substitute* "Makefile"
5906                ;; Test scripts are generated, patch the shebang
5907                (("#!/bin/bash") (string-append "#!" (which "sh"))))
5908              #t)))))
5909     (home-page "https://elpa.mpcdf.mpg.de")
5910     (synopsis "Eigenvalue solvers for symmetric matrices")
5911     (description
5912      "The ELPA library provides efficient and scalable direct eigensolvers for
5913 symmetric matrices.")
5914     (license license:lgpl3)))
5915
5916 (define-public elpa-openmpi
5917   (package (inherit elpa)
5918     (name "elpa-openmpi")
5919     (inputs
5920      `(("mpi" ,openmpi)
5921        ("scalapack" ,scalapack)
5922        ,@(package-inputs elpa)))
5923     (arguments
5924      (substitute-keyword-arguments (package-arguments elpa)
5925        ((#:configure-flags cf '())
5926         `(cons "--with-mpi=yes" (delete "--with-mpi=no" ,cf)))
5927        ((#:phases phases '%standard-phases)
5928         `(modify-phases ,phases
5929            (add-before 'check 'mpi-setup
5930              (lambda _
5931                ;; Tests use 2 mpi tasks by default, use our remaining build
5932                ;; cores as OpenMP threads.
5933                (setenv "OMP_NUM_THREADS" (number->string
5934                                           (max (quotient (parallel-job-count) 2)
5935                                                1)))
5936                (,%openmpi-setup)))))))
5937     (synopsis "Eigenvalue solvers for symmetric matrices (with MPI support)")))
5938
5939 (define-public elemental
5940   (package
5941     (name "elemental")
5942     (version "0.87.7")
5943     (source (origin
5944               (method git-fetch)
5945               (uri (git-reference
5946                      (url "https://github.com/elemental/Elemental")
5947                      (commit (string-append "v" version))))
5948               (file-name (git-file-name name version))
5949               (sha256
5950                (base32
5951                 "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
5952     (build-system cmake-build-system)
5953     (home-page "https://github.com/elemental/Elemental")
5954     (native-inputs
5955      (list gfortran))
5956     (inputs
5957      `(("blas" ,openblas)
5958        ("gfortran:lib" ,gfortran "lib")
5959        ("gmp" ,gmp)
5960        ("lapack" ,lapack)
5961        ("metis" ,metis)
5962        ("mpc" ,mpc)
5963        ("mpfr" ,mpfr)
5964        ("mpi" ,openmpi)
5965        ("qd" ,qd)))
5966     (arguments
5967      `(#:build-type "Release"           ;default RelWithDebInfo not supported
5968        #:configure-flags `("-DEL_DISABLE_PARMETIS:BOOL=YES"
5969                            "-DEL_AVOID_COMPLEX_MPI:BOOL=NO"
5970                            "-DEL_CACHE_WARNINGS:BOOL=YES"
5971                            "-DEL_TESTS:BOOL=YES"
5972                            "-DCMAKE_INSTALL_LIBDIR=lib"
5973                            "-DGFORTRAN_LIB=gfortran")
5974        #:phases (modify-phases %standard-phases
5975                   (add-before 'check 'mpi-setup
5976                     ,%openmpi-setup)
5977                   (add-before 'check 'setup-tests
5978                     (lambda _
5979                       ;; Parallelism is done at the MPI layer.
5980                       (setenv "OMP_NUM_THREADS" "1")
5981                       #t))
5982                   (add-after 'install 'remove-tests
5983                     (lambda* (#:key outputs #:allow-other-keys)
5984                       ;; Tests are installed, with no easy configuration
5985                       ;; switch to prevent this, so delete them.
5986                       (delete-file-recursively
5987                         (string-append (assoc-ref outputs "out") "/bin"))
5988                       #t)))))
5989     (synopsis "Dense and sparse-direct linear algebra and optimization")
5990     (description "Elemental is a modern C++ library for distributed-memory
5991 dense and sparse-direct linear algebra, conic optimization, and lattice
5992 reduction.")
5993     (license license:bsd-2)))
5994
5995 (define-public mcrl2
5996   (package
5997     (name "mcrl2")
5998     (version "202106.0")
5999     (source (origin
6000               (method url-fetch)
6001               (uri (string-append
6002                     "https://www.mcrl2.org/download/release/mcrl2-"
6003                     version ".tar.gz"))
6004               (sha256
6005                (base32
6006                 "1xgx3cd57vc7gbjic24j1q2za6j3ybz6nk4afvvpbwsf33xnlf4v"))))
6007     (inputs
6008      (list boost glu mesa qtbase-5))
6009     (build-system cmake-build-system)
6010     (synopsis "Toolset for the mCRL2 formal specification language")
6011     (description
6012      "@dfn{mCRL2} (micro Common Representation Language 2) is a formal
6013 specification language for describing concurrent discrete event systems.  Its
6014 toolset supports analysis and automatic verification, linearisation, simulation,
6015 state-space exploration and generation, and tools to optimise and analyse
6016 specifications.  Also, state spaces can be manipulated, visualised and
6017 analysed.")
6018     (home-page "https://mcrl2.org")
6019     (license license:boost1.0)))
6020
6021 (define-public mcrl2-minimal
6022   (package
6023     (inherit mcrl2)
6024     (name "mcrl2-minimal")
6025     (inputs
6026      (list boost))
6027     (arguments
6028      '(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
6029
6030 (define-public tcalc
6031   (package
6032   (name "tcalc")
6033   (version "2.0")
6034   (source
6035     (origin
6036       (method url-fetch)
6037       (uri (string-append "https://sites.google.com/site/mohammedisam2000/tcalc/tcalc-"
6038                             version ".tar.gz"))
6039       (sha256
6040         (base32
6041           "0jq806m4dqfia85nppfm75mml9w57g0cgv4cdw9bp3zymda83s0m"))))
6042   (build-system gnu-build-system)
6043   (synopsis "The terminal calculator")
6044   (description
6045     "The terminal calculator is a small program to help users of the GNU/Linux
6046 terminal do calculations simply and quickly.  The formula to be calculated can
6047 be fed to @command{tcalc} through the command line.")
6048   (home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
6049   (license license:gpl3+)))
6050
6051 (define-public tiny-bignum
6052   (let ((commit "1d7a1f9b8e77316187a6b3eae8e68d60a6f9a4d4"))
6053     (package
6054      (name "tiny-bignum")
6055      (version (git-version "0" "0" commit))
6056      (source
6057       (origin
6058         (method git-fetch)
6059         (uri (git-reference
6060               (url "https://github.com/kokke/tiny-bignum-c")
6061               (commit commit)))
6062         (file-name (git-file-name "tiny-bignum" commit))
6063         (sha256
6064          (base32 "0vj71qlhlaa7d92bfar1kwqv6582dqrby8x3kdw0yzh82k2023g6"))))
6065      (build-system gnu-build-system)
6066      (arguments
6067       `(#:phases
6068         (modify-phases %standard-phases
6069           (delete 'configure)
6070           (add-after 'unpack 'patch-tests
6071             (lambda _
6072               (substitute* "scripts/test_rand.py"
6073                 (("\t") "  ")
6074                 (("\" % (\\w+)" _ symbol) (string-append "\" % int(" symbol ")")))
6075               #t))
6076           (replace 'check
6077             (lambda* (#:key tests? #:allow-other-keys)
6078               (when tests?
6079                 (invoke "make" "test"))
6080               #t))
6081           (replace 'install
6082             (lambda* (#:key outputs #:allow-other-keys)
6083               (let ((share (string-append (assoc-ref outputs "out") "/share"))
6084                     (doc (string-append (assoc-ref outputs "out") "/doc")))
6085                 (mkdir-p share)
6086                 (install-file "bn.c" share)
6087                 (install-file "bn.h" share)
6088                 (mkdir-p doc)
6089                 (install-file "LICENSE" doc)
6090                 (install-file "README.md" doc))
6091               #t)))))
6092      (native-inputs
6093       `(("python" ,python-wrapper)))
6094      (home-page "https://github.com/kokke/tiny-bignum-c")
6095      (synopsis "Small portable multiple-precision unsigned integer arithmetic in C")
6096      (description
6097       "This library provides portable Arbitrary-precision unsigned integer
6098 arithmetic in C, for calculating with large numbers.  Basic arithmetic (+, -,
6099 *, /, %) and bitwise operations (&, |, ^. <<, >>) plus increments, decrements
6100 and comparisons are supported.")
6101      (license license:unlicense))))
6102
6103 (define-public sundials
6104   (package
6105     (name "sundials")
6106     (version "3.1.1")
6107     (source
6108      (origin
6109        (method url-fetch)
6110        (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
6111                            "sundials-" version ".tar.gz"))
6112        (sha256
6113         (base32
6114          "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
6115     (build-system cmake-build-system)
6116     (native-inputs
6117      `(("python" ,python-2)))    ;for tests; syntax incompatible with python 3
6118     (inputs
6119      `(("fortran" ,gfortran)            ;for fcmix
6120        ("blas" ,openblas)
6121        ("suitesparse" ,suitesparse)))   ;TODO: Add hypre
6122     (arguments
6123      `(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon"
6124                            "-DEXAMPLES_ENABLE_C:BOOL=ON"
6125                            "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
6126                            "-DEXAMPLES_ENABLE_F77:BOOL=ON"
6127                            "-DEXAMPLES_ENABLE_F90:BOOL=ON"
6128                            "-DEXAMPLES_INSTALL:BOOL=OFF"
6129
6130                            "-DFCMIX_ENABLE:BOOL=ON"
6131
6132                            "-DKLU_ENABLE:BOOL=ON"
6133                            ,(string-append "-DKLU_INCLUDE_DIR="
6134                                            (assoc-ref %build-inputs "suitesparse")
6135                                            "/include")
6136                            ,(string-append "-DKLU_LIBRARY_DIR="
6137                                            (assoc-ref %build-inputs "suitesparse")
6138                                            "/lib"))))
6139     (home-page "https://computation.llnl.gov/projects/sundials")
6140     (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
6141     (description "SUNDIALS is a family of software packages implemented with
6142 the goal of providing robust time integrators and nonlinear solvers that can
6143 easily be incorporated into existing simulation codes.")
6144     (properties
6145      '((release-monitoring-url
6146         . "https://computing.llnl.gov/projects/sundials/sundials-software")))
6147     (license license:bsd-3)))
6148
6149 (define-public sundials-openmpi
6150   (package (inherit sundials)
6151     (name "sundials-openmpi")
6152     (inputs
6153      `(("mpi" ,openmpi)
6154        ("petsc" ,petsc-openmpi)         ;support in SUNDIALS requires MPI
6155        ,@(package-inputs sundials)))
6156     (arguments
6157      (substitute-keyword-arguments (package-arguments sundials)
6158        ((#:configure-flags flags '())
6159         `(cons* "-DMPI_ENABLE:BOOL=ON"
6160                 "-DPETSC_ENABLE:BOOL=ON"
6161                 (string-append "-DPETSC_INCLUDE_DIR="
6162                                (assoc-ref %build-inputs "petsc")
6163                                "/include")
6164                 (string-append "-DPETSC_LIBRARY_DIR="
6165                                (assoc-ref %build-inputs "petsc")
6166                                "/lib")
6167                 ,flags))
6168        ((#:phases phases '%standard-phases)
6169         `(modify-phases ,phases
6170            (add-before 'check 'mpi-setup
6171              ,%openmpi-setup)))))
6172     (synopsis "SUNDIALS with OpenMPI support")))
6173
6174 (define-public sundials-julia
6175   (package
6176     (inherit sundials)
6177     (name "sundials-julia")
6178     (version "5.2.0")
6179     (source
6180      (origin
6181        (method git-fetch)
6182        (uri (git-reference
6183              (url "https://github.com/LLNL/sundials")
6184              (commit (string-append "v" version))))
6185        (file-name (git-file-name name version))
6186        (sha256
6187         (base32
6188          "0nx4sqhmi126m14myzm7syv2053harav9snl0a247wnkcgs5rxrv"))))
6189     (inputs
6190      (modify-inputs (package-inputs sundials)
6191        (prepend lapack)))
6192     (arguments
6193      (substitute-keyword-arguments (package-arguments sundials)
6194        ((#:configure-flags flags '())
6195         `(cons* "-DLAPACK_ENABLE:BOOL=ON"
6196                 ,flags))))
6197     (synopsis "SUNDIALS with lapack support as required by julia-sundials-jll")))
6198
6199 (define-public combinatorial-blas
6200   (package
6201     (name "combinatorial-blas")
6202     (version "1.6.2")
6203     (source
6204      (origin
6205        (method url-fetch)
6206        (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
6207                            "CombBLAS_beta_"
6208                            (match (string-split version #\.)
6209                             ((major minor patch)
6210                              (string-append major minor "_" patch))) ;e.g. "16_2"
6211                            ".tgz"))
6212        (sha256
6213         (base32
6214          "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
6215        (patches (search-patches "combinatorial-blas-awpm.patch"
6216                                 "combinatorial-blas-io-fix.patch"))))
6217     (build-system cmake-build-system)
6218     (inputs
6219      `(("mpi" ,openmpi)
6220        ("test-data" ,(origin
6221                        (method url-fetch)
6222                        (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
6223                                            "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
6224                        (sha256
6225                         (base32
6226                          "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
6227     (arguments
6228      `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
6229                            "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
6230        #:parallel-tests? #f             ;tests use 'mpiexec -n4'
6231        #:phases
6232        (modify-phases %standard-phases
6233          (add-before 'check 'mpi-setup
6234            ,%openmpi-setup)
6235          (add-before 'check 'test-setup
6236            (lambda* (#:key inputs #:allow-other-keys)
6237              (setenv "OMP_NUM_THREADS" "2")
6238              (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
6239     (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
6240     (synopsis "Linear algebra primitives for graph analytics")
6241     (description "The Combinatorial BLAS (CombBLAS) is an extensible
6242 distributed-memory parallel graph library offering a small but powerful set of
6243 linear algebra primitives specifically targeting graph analytics.")
6244     (license (list
6245               license:gpl2+             ;include/psort/(funnel|sort)*.h
6246               license:x11               ;usort and psort
6247               license:bsd-3))))         ;CombBLAS and MersenneTwister.h
6248
6249 (define-public dune-common
6250   (package
6251     (name "dune-common")
6252     (version "2.7.0")
6253     (source
6254      (origin
6255        (method url-fetch)
6256        (uri (string-append "https://dune-project.org/download/"
6257                            version "/dune-common-" version ".tar.gz"))
6258        (sha256
6259         (base32
6260          "140q1zh44cr5yrjwg4b5ga803rkqv55vk30l2cqm29aklj1wb0rw"))))
6261     (build-system cmake-build-system)
6262     (arguments
6263      `(#:phases
6264        (modify-phases %standard-phases
6265          (add-after 'build 'build-tests
6266            (lambda* (#:key make-flags #:allow-other-keys)
6267              (apply invoke "make" "build_tests" make-flags))))))
6268     (inputs
6269      (list gmp metis openblas python superlu))
6270     (native-inputs
6271      (list gfortran pkg-config))
6272     (home-page "https://dune-project.org/")
6273     (synopsis "Distributed and Unified Numerics Environment")
6274     (description "DUNE, the Distributed and Unified Numerics Environment is a
6275 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6276 grid-based methods.  It supports the easy implementation of methods like
6277 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6278 Differences} (FD).")
6279     ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2.
6280     (license license:gpl2)))
6281
6282 (define-public dune-geometry
6283   (package
6284     (name "dune-geometry")
6285     (version "2.7.0")
6286     (source
6287      (origin
6288        (method url-fetch)
6289        (uri (string-append "https://dune-project.org/download/"
6290                            version "/dune-geometry-" version ".tar.gz"))
6291        (sha256
6292         (base32
6293          "1cicvlwbyyw76npicnblxckyvhbfn3ip8isydiv3hlrlz8zcg5nr"))))
6294     (build-system cmake-build-system)
6295     (arguments
6296      `(#:phases
6297        (modify-phases %standard-phases
6298          (add-after 'build 'build-tests
6299            (lambda* (#:key make-flags #:allow-other-keys)
6300              (apply invoke "make" "build_tests" make-flags))))))
6301     (inputs
6302      (list dune-common
6303            ;; Optional
6304            openblas gmp python))
6305     (native-inputs
6306      (list gfortran pkg-config))
6307     (home-page "https://dune-project.org/")
6308     (synopsis "Distributed and Unified Numerics Environment")
6309     (description "DUNE, the Distributed and Unified Numerics Environment is a
6310 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6311 grid-based methods.  It supports the easy implementation of methods like
6312 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6313 Differences} (FD).
6314
6315 This package contains the basic DUNE geometry classes.")
6316     ;; GPL version 2 with "runtime exception"
6317     (license license:gpl2)))
6318
6319 (define-public dune-uggrid
6320   (package
6321     (name "dune-uggrid")
6322     (version "2.7.0")
6323     (source
6324      (origin
6325        (method git-fetch)
6326        (uri (git-reference
6327          (url "https://gitlab.dune-project.org/staging/dune-uggrid.git")
6328          (commit (string-append "v" version))))
6329        (file-name (git-file-name name version))
6330        (sha256
6331         (base32
6332          "192miqgmfj6jwk969gydzpbv9ki7jg5nky3ydnrwa2nq29b5xkh0"))))
6333     (build-system cmake-build-system)
6334     (arguments
6335      `(#:phases
6336        (modify-phases %standard-phases
6337          (add-after 'build 'build-tests
6338            (lambda* (#:key make-flags #:allow-other-keys)
6339              (apply invoke "make" "build_tests" make-flags))))))
6340     (inputs
6341      (list dune-common))
6342     (native-inputs
6343      (list gfortran pkg-config))
6344     (home-page "https://dune-project.org/")
6345     (synopsis "Distributed and Unified Numerics Environment")
6346     (description "DUNE, the Distributed and Unified Numerics Environment is a
6347 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6348 grid-based methods.  It supports the easy implementation of methods like
6349 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6350 Differences} (FD).
6351
6352 This package contains the DUNE UG grid classes.")
6353     (license license:lgpl2.1)))
6354
6355 (define-public dune-grid
6356   (package
6357     (name "dune-grid")
6358     (version "2.7.0")
6359     (source
6360      (origin
6361        (method url-fetch)
6362        (uri (string-append "https://dune-project.org/download/"
6363                            version "/dune-grid-" version ".tar.gz"))
6364        (sha256
6365         (base32
6366          "17fjz30qazjgl11sryyxnw9klai4yz1ji4bs68013xcxc5hdv27s"))))
6367     (build-system cmake-build-system)
6368     (arguments
6369      `(#:phases
6370        (modify-phases %standard-phases
6371          (add-after 'build 'build-tests
6372            (lambda* (#:key make-flags #:allow-other-keys)
6373              (apply invoke "make" "build_tests" make-flags))))))
6374     (inputs
6375      (list dune-common
6376            dune-geometry
6377            gmp
6378            metis
6379            openblas
6380            python))
6381     (propagated-inputs
6382      (list dune-uggrid))
6383     (native-inputs
6384      (list gfortran pkg-config))
6385     (home-page "https://dune-project.org/")
6386     (synopsis "Distributed and Unified Numerics Environment")
6387     (description "DUNE, the Distributed and Unified Numerics Environment is a
6388 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6389 grid-based methods.  It supports the easy implementation of methods like
6390 @dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
6391 Differences} (FD).
6392
6393 This package contains the basic DUNE grid classes.")
6394     ;; GPL version 2 with "runtime exception"
6395     (license license:gpl2)))
6396
6397 (define-public dune-istl
6398   (package
6399     (name "dune-istl")
6400     (version "2.7.0")
6401     (source
6402      (origin
6403        (method url-fetch)
6404        (uri (string-append "https://dune-project.org/download/"
6405                            version "/dune-istl-" version ".tar.gz"))
6406        (sha256
6407         (base32
6408          "0gl3wgz5rs6sb4m83440ny45sbx7z7lnbi3gx6r9nm3rvy5j33f9"))
6409        (patches (search-patches "dune-istl-2.7-fix-non-mpi-tests.patch"))))
6410     (build-system cmake-build-system)
6411     (arguments
6412      `(#:phases
6413        (modify-phases %standard-phases
6414          ;; XXX: istl/test/matrixtest.cc includes <fenv.h> and fails to find
6415          ;; the stdlib types when the gfortran header is used.  Remove gfortran
6416          ;; from CPLUS_INCLUDE_PATH as a workaround.
6417          (add-after 'set-paths 'hide-gfortran
6418            (lambda* (#:key inputs #:allow-other-keys)
6419              (let ((gfortran (assoc-ref inputs "gfortran")))
6420                (setenv "CPLUS_INCLUDE_PATH"
6421                        (string-join
6422                         (delete (string-append gfortran "/include/c++")
6423                                 (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
6424                         ":"))
6425                #t)))
6426          (add-after 'build 'build-tests
6427            (lambda* (#:key make-flags #:allow-other-keys)
6428              (apply invoke "make" "build_tests" make-flags))))))
6429     (inputs
6430      (list dune-common
6431            ;; Optional
6432            metis
6433            suitesparse
6434            superlu
6435            openblas
6436            gmp
6437            python))
6438     (native-inputs
6439      (list gfortran pkg-config))
6440     (home-page "https://dune-project.org/")
6441     (synopsis "Distributed and Unified Numerics Environment")
6442     (description "DUNE, the Distributed and Unified Numerics Environment is a
6443 modular toolbox for solving @dfn{partial differential equations} (PDEs) with
6444 grid-based methods.
6445
6446 This is the iterative solver template library which provides generic sparse
6447 matrix/vector classes and a variety of solvers based on these classes.  A
6448 special feature is the use of templates to exploit the recursive block
6449 structure of finite element matrices at compile time.  Available solvers
6450 include Krylov methods, (block-) incomplete decompositions and
6451 aggregation-based algebraic multigrid.")
6452     ;; GPL version 2 with "runtime exception"
6453     (license license:gpl2)))
6454
6455 (define-public dune-localfunctions
6456   (package
6457     (name "dune-localfunctions")
6458     (version "2.7.0")
6459     (source
6460      (origin
6461        (method url-fetch)
6462        (uri (string-append "https://dune-project.org/download/"
6463                            version "/dune-localfunctions-" version ".tar.gz"))
6464        (sha256
6465         (base32
6466          "1yih59h6vngii696bx1c2vil02lriij4kz0nc583mjn9kiaqxfqd"))))
6467     (build-system cmake-build-system)
6468     (arguments
6469      `(#:phases
6470        (modify-phases %standard-phases
6471          ;; XXX: localfunctions/test/lagrangeshapefunctiontest.cc includes <fenv.h>
6472          ;; and fails to find the stdlib types when the gfortran header is used.
6473          ;; Hide gfortran from CPLUS_INCLUDE_PATH to ensure we get the GCC header.
6474          (add-after 'set-paths 'hide-gfortran
6475            (lambda* (#:key inputs #:allow-other-keys)
6476              (let ((gfortran (assoc-ref inputs "gfortran")))
6477                (setenv "CPLUS_INCLUDE_PATH"
6478                        (string-join
6479                         (delete (string-append gfortran "/include/c++")
6480                                 (string-split (getenv "CPLUS_INCLUDE_PATH") #\:))
6481                         ":"))
6482                #t)))
6483          (add-after 'build 'build-tests
6484            (lambda* (#:key make-flags #:allow-other-keys)
6485              (apply invoke "make" "build_tests" make-flags))))))
6486     (inputs
6487      (list dune-common
6488            dune-geometry
6489            ;; Optional
6490            metis
6491            superlu
6492            gmp))
6493     (native-inputs
6494      (list gfortran pkg-config))
6495     (home-page "https://dune-project.org/")
6496     (synopsis "Distributed and Unified Numerics Environment") ; TODO
6497     (description "This DUNE module provides interface and implementation for
6498 shape functions defined on the DUNE reference elements.  In addition to the
6499 shape function, interpolation operators and special keys are provided which
6500 can be used to assemble global function spaces on finite-element grids.
6501
6502 This package provides an interface and implementation for shape functions
6503 defined on the DUNE reference elements.  In addition to the shape function,
6504 interpolation operators and special keys are provided which can be used to
6505 assemble global function spaces on finite-element grids.")
6506     ;; GPL version 2 with "runtime exception"
6507     (license license:gpl2)))
6508
6509 (define-public dune-alugrid
6510   (package
6511     (name "dune-alugrid")
6512     (version "2.7.0-git-81d35682")
6513     (source
6514      (origin
6515        (method git-fetch)
6516        (uri (git-reference
6517              (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git")
6518              (commit "81d356827c84454b971937db02c02b90bbcd7fe5")))
6519        (file-name (git-file-name name version))
6520        (sha256
6521         (base32
6522          "0z54lwfp53prcrs94k8gwh047l9z642jll3l56xlyfr69z0b2zz1"))))
6523     (build-system cmake-build-system)
6524     (arguments
6525      `(#:phases
6526        (modify-phases %standard-phases
6527          (add-after 'unpack 'patch-include
6528            (lambda _
6529              (substitute* "dune/alugrid/test/test-alugrid.cc"
6530                (("doc/grids/gridfactory/testgrids")
6531                 "doc/dune-grid/grids/gridfactory/testgrids"))
6532              #t))
6533          (add-after 'build 'build-tests
6534            (lambda* (#:key inputs make-flags #:allow-other-keys)
6535              (setenv "CPLUS_INCLUDE_PATH"
6536                      (string-append (assoc-ref inputs "dune-grid") "/share"))
6537              (apply invoke "make" "build_tests" make-flags))))))
6538     (inputs
6539      (list dune-common
6540            dune-geometry
6541            dune-grid
6542            ;; Optional
6543            metis
6544            openblas
6545            python
6546            superlu
6547            gmp
6548            zlib))
6549     (native-inputs
6550      (list gfortran pkg-config))
6551     (home-page "https://dune-project.org/")
6552     (synopsis "Distributed and Unified Numerics Environment")
6553     (description "ALUGrid is an adaptive, loadbalancing, unstructured
6554 implementation of the DUNE grid interface supporting either simplices or
6555 cubes.")
6556     (license license:gpl2+)))
6557
6558 (define-public dune-subgrid
6559   (package
6560     (name "dune-subgrid")
6561     (version "2.7.0-git-2103a363")
6562     (source
6563      (origin
6564        (method git-fetch)
6565        (uri (git-reference
6566          (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
6567          (commit "2103a363f32e8d7b60e66eee7ddecf969f6cf762")))
6568        (file-name (git-file-name name version))
6569        (sha256
6570         (base32
6571           "1wsjlypd3835c3arqjkw836cxx5q67zy447wa65q634lf6f6v9ia"))))
6572     (build-system cmake-build-system)
6573     (arguments
6574      `(#:phases
6575        (modify-phases %standard-phases
6576          (add-after 'build 'build-tests
6577            (lambda* (#:key make-flags #:allow-other-keys)
6578              (apply invoke "make" "build_tests" make-flags))))))
6579     (inputs
6580      (list dune-common
6581            dune-geometry
6582            dune-grid
6583            ;; Optional
6584            metis
6585            openblas
6586            gmp))
6587     (native-inputs
6588      (list gfortran pkg-config))
6589     (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php")
6590     (synopsis "Distributed and Unified Numerics Environment")
6591     (description "The dune-subgrid module marks elements of
6592 another hierarchical dune grid.  The set of marked elements can then be
6593 accessed as a hierarchical dune grid in its own right.  Dune-Subgrid
6594 provides the full grid interface including adaptive mesh refinement.")
6595     (license license:gpl2+)))
6596
6597 (define-public dune-typetree
6598   (package
6599     (name "dune-typetree")
6600     (version "2.7.0")
6601     (source
6602      (origin
6603        (method git-fetch)
6604        (uri (git-reference
6605              (url "https://gitlab.dune-project.org/staging/dune-typetree.git")
6606              (commit (string-append "v" version))))
6607        (file-name (git-file-name name version))
6608        (sha256
6609         (base32
6610          "1rhv25yg0q1hw50c8wlfqhgwrjl4mh62zq9v14ilwgzbfgxmpiy7"))))
6611     (build-system cmake-build-system)
6612     (arguments
6613      `(#:phases
6614        (modify-phases %standard-phases
6615          (add-after 'build 'build-tests
6616            (lambda* (#:key make-flags #:allow-other-keys)
6617              (apply invoke "make" "build_tests" make-flags))))))
6618     (inputs
6619      (list dune-common
6620            ;; Optional
6621            openblas
6622            python
6623            metis
6624            superlu
6625            gmp))
6626     (native-inputs
6627      (list gfortran pkg-config))
6628     (home-page "https://dune-project.org/")
6629     (synopsis "Distributed and Unified Numerics Environment")
6630     (description "TypeTree is a template library for constructing and
6631 operating on statically typed trees of objects.")
6632     ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
6633     (license (list license:lgpl3+ license:gpl2))))
6634
6635 (define-public dune-functions
6636   (package
6637     (name "dune-functions")
6638     (version "2.7.0")
6639     (source
6640      (origin
6641        (method git-fetch)
6642        (uri (git-reference
6643              (url "https://gitlab.dune-project.org/staging/dune-functions.git")
6644              (commit (string-append "v" version))))
6645        (file-name (git-file-name name version))
6646        (sha256
6647         (base32
6648          "1na4gcih0kin37ksj2xj07ds04v7zx53pjdhm1hzy55jjfqdjk8h"))))
6649     (build-system cmake-build-system)
6650     (arguments
6651      `(#:phases
6652        (modify-phases %standard-phases
6653          (add-after 'unpack 'disable-failing-tests
6654            (lambda _
6655              (setenv "ARGS"
6656                      ;; unable to load GMSH file in this test
6657                      "--exclude-regex gridviewfunctionspacebasistest")
6658             #t))
6659          (add-after 'build 'build-tests
6660            (lambda* (#:key make-flags #:allow-other-keys)
6661              (apply invoke "make" "build_tests" make-flags))))))
6662     (inputs
6663      (list dune-common
6664            dune-istl
6665            dune-localfunctions
6666            dune-grid
6667            dune-geometry
6668            dune-typetree
6669            openblas
6670            metis
6671            python
6672            superlu
6673            gmp))
6674     (native-inputs
6675      (list gfortran pkg-config))
6676     (home-page "https://dune-project.org/")
6677     (synopsis "Distributed and Unified Numerics Environment")
6678     (description "The dune-functions module provides an abstraction layer for
6679 global finite element functions.  Its two main concepts are functions
6680 implemented as callable objects, and bases of finite element spaces.")
6681     ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
6682     (license (list license:lgpl3+ license:gpl2))))
6683
6684 (define-public dune-pdelab
6685   (package
6686     (name "dune-pdelab")
6687     (version "2.7.0-git-476fe437")
6688     (source
6689      (origin
6690        (method git-fetch)
6691        (uri (git-reference
6692              (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
6693              (commit "476fe43763fa6f459c5e4658e2a2b4b5582db834")))
6694        (file-name (git-file-name name version))
6695        (sha256
6696         (base32
6697          "0cs36piqzn6rq0j2ih3ab3q3q9yg199wk72k5qi86pkzh7i7fdn1"))))
6698     (build-system cmake-build-system)
6699     (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
6700     (inputs
6701      (list dune-common
6702            dune-istl
6703            dune-localfunctions
6704            dune-geometry
6705            dune-grid
6706            dune-typetree
6707            dune-functions
6708            ;; Optional
6709            openblas
6710            eigen
6711            metis
6712            python
6713            superlu
6714            gmp))
6715     (native-inputs
6716      (list gfortran pkg-config))
6717     (home-page "https://dune-project.org/")
6718     (synopsis "Differential equations solver toolbox")
6719     (description "PDELab is a partial differential equations solver toolbox
6720 built on top of DUNE, the Distributed and Unified Numerics Environment.")
6721     ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
6722     (license (list license:lgpl3+ license:gpl2))))
6723
6724 (define add-openmpi-to-dune-package
6725   (let ((dune-package?
6726           (lambda (p) (string-prefix? "dune-" (package-name p)))))
6727     (package-mapping
6728       (lambda (p)
6729         (if (dune-package? p)
6730             (package (inherit p)
6731               (name (string-append (package-name p) "-openmpi"))
6732               (inputs `(,@(package-inputs p)
6733                         ("openmpi" ,openmpi)))
6734               (arguments
6735                (substitute-keyword-arguments (package-arguments p)
6736                  ((#:phases phases '%standard-phases)
6737                   `(modify-phases ,phases
6738                      (add-before 'check 'mpi-setup
6739                        ,%openmpi-setup)))))
6740               (synopsis (string-append (package-synopsis p) " (with MPI support)")))
6741             p))
6742       (negate dune-package?))))
6743
6744 (define-public dune-common-openmpi
6745   (add-openmpi-to-dune-package dune-common))
6746
6747 (define-public dune-geometry-openmpi
6748   (add-openmpi-to-dune-package dune-geometry))
6749
6750 (define-public dune-istl-openmpi
6751   (add-openmpi-to-dune-package dune-istl))
6752
6753 (define-public dune-typetree-openmpi
6754   (add-openmpi-to-dune-package dune-typetree))
6755
6756 (define-public dune-uggrid-openmpi
6757   (add-openmpi-to-dune-package dune-uggrid))
6758
6759 (define-public dune-grid-openmpi
6760   (add-openmpi-to-dune-package dune-grid))
6761
6762 (define-public dune-alugrid-openmpi
6763   (add-openmpi-to-dune-package dune-alugrid))
6764
6765 (define-public dune-subgrid-openmpi
6766   (add-openmpi-to-dune-package dune-subgrid))
6767
6768 (define-public dune-localfunctions-openmpi
6769   (add-openmpi-to-dune-package dune-localfunctions))
6770
6771 (define-public dune-functions-openmpi
6772   (add-openmpi-to-dune-package dune-functions))
6773
6774 (define-public dune-pdelab-openmpi
6775   (add-openmpi-to-dune-package dune-pdelab))
6776
6777 (define-public mlucas
6778   (package
6779     (name "mlucas")
6780     (version "18")
6781     (source
6782      (origin
6783        (method url-fetch)
6784        (uri (string-append
6785              "https://mersenneforum.org/mayer/src/C/mlucas_v" version ".txz"))
6786        (sha256
6787         (base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
6788     (build-system gnu-build-system)
6789     (inputs
6790      (list python-2))
6791     (arguments
6792      `(#:tests? #f                      ; no tests
6793        #:phases
6794        (modify-phases %standard-phases
6795          (replace 'configure
6796            (lambda _
6797              (chdir "src")
6798              (call-with-output-file "Makefile"
6799                (lambda (port)
6800                  (format port "CC = gcc
6801 CFLAGS = -O3 ~a -DUSE_THREADS
6802 LDLIBS = -lm -lpthread -lrt
6803 Mlucas: $(addsuffix .o,$(basename $(wildcard *.c)))
6804 "
6805                          ,(let ((system (or (%current-target-system)
6806                                             (%current-system))))
6807                             (cond
6808                              ((string-prefix? "x86_64" system) "-DUSE_SSE2")
6809                              (else ""))))))
6810              #t))
6811          (replace 'install
6812            (lambda* (#:key outputs #:allow-other-keys)
6813              (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
6814                (install-file "Mlucas" bin)
6815                (install-file "primenet.py" bin))
6816              #t)))))
6817     (home-page "https://www.mersenne.org")
6818     (synopsis "Great Internet Mersenne Prime Search (GIMPS) distributed computing client")
6819     (description "Mlucas performs Lucas-Lehmer primality testing of Mersenne
6820 numbers in search of a world-record prime.  You may use it to test any
6821 suitable number as you wish, but it is preferable that you do so in a
6822 coordinated fashion, as part of the Great Internet Mersenne Prime
6823 Search (GIMPS).  Mlucas also includes a simple Python script for assignment
6824 management via the GIMPS project's Primenet server.")
6825     (license license:gpl2+)))
6826
6827 (define-public nauty
6828   (package
6829     (name "nauty")
6830     (version "2.7r3")
6831     (source
6832      (origin
6833        (method url-fetch)
6834        (uri (string-append
6835              "https://pallini.di.uniroma1.it/"
6836              "nauty" (string-join (string-split version #\.) "") ".tar.gz"))
6837        (sha256
6838         (base32 "1hl81gpf3xjf809w04jczvilq1ixy9ch1qrax8a7lgx52svna1jg"))))
6839     (build-system gnu-build-system)
6840     (outputs '("out" "lib"))
6841     (arguments
6842      `(#:test-target "checks"
6843        #:configure-flags '("--enable-generic") ;prevent -march-native
6844        #:phases
6845        (modify-phases %standard-phases
6846          ;; Default make target does not build all available
6847          ;; executables.  Create them now.
6848          (add-after 'build 'build-extra-programs
6849            (lambda _
6850              (for-each (lambda (target) (invoke "make" target))
6851                        '("blisstog" "bliss2dre" "checks6" "sumlines"))
6852              #t))
6853          ;; Upstream does not provide any install target.
6854          (replace 'install
6855            (lambda* (#:key outputs #:allow-other-keys)
6856              (let* ((out (assoc-ref outputs "out"))
6857                     (lib-output (assoc-ref outputs "lib"))
6858                     (bin (string-append out "/bin"))
6859                     (doc (string-append out "/share/doc/nauty/"))
6860                     (include (string-append lib-output "/include/nauty"))
6861                     (lib (string-append lib-output "/lib/nauty")))
6862                (for-each (lambda (f) (install-file f bin))
6863                          '("addedgeg"  "amtog" "assembleg" "biplabg" "blisstog"
6864                            "bliss2dre" "catg" "checks6" "complg" "converseg"
6865                            "copyg" "countg" "cubhamg" "deledgeg" "delptg"
6866                            "directg"  "dreadnaut" "dretodot" "dretog" "genbg"
6867                            "genbgL" "geng" "genquarticg" "genrang" "genspecialg"
6868                            "gentourng" "gentreeg" "hamheuristic" "labelg"
6869                            "linegraphg" "listg" "multig" "newedgeg" "pickg"
6870                            "planarg" "ranlabg" "shortg" "showg" "subdivideg"
6871                            "sumlines" "twohamg" "underlyingg" "vcolg"
6872                            "watercluster2" "NRswitchg"))
6873                (for-each (lambda (f) (install-file f include))
6874                          (find-files "." "\\.h$"))
6875                (for-each (lambda (f) (install-file f lib))
6876                          (find-files "." "\\.a$"))
6877                (for-each (lambda (f) (install-file f doc))
6878                          (append '("formats.txt" "README" "schreier.txt")
6879                                  (find-files "." "\\.pdf$")))))))))
6880     (inputs
6881      (list gmp))                   ;for sumlines
6882     (home-page "https://pallini.di.uniroma1.it/")
6883     (synopsis "Library for graph automorphisms")
6884     (description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
6885 procedures for computing automorphism groups of graphs and digraphs.
6886
6887 @code{nauty} computes graph information in the form of a set of
6888 generators, the size of the group, and the orbits of the group; it can
6889 also produce a canonical label.  The @code{nauty} suite is written in
6890 C and comes with a command-line interface, a collection of
6891 command-line tools, and an Application Programming Interface (API).
6892
6893 This package provides the static libraries required to run programs
6894 compiled against the nauty library.")
6895     (license license:asl2.0)))
6896
6897 (define-public ppl
6898   (package
6899     (name "ppl")
6900     (version "1.2")
6901     (source
6902      (origin
6903        (method url-fetch)
6904        (uri (string-append "https://www.bugseng.com/products/ppl/download/"
6905                            "ftp/releases/" version
6906                            "/ppl-" version ".tar.gz"))
6907        (sha256
6908         (base32
6909          "1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
6910     (build-system gnu-build-system)
6911     (native-inputs
6912      (list m4))
6913     (inputs
6914      (list glpk gmp))
6915     (home-page "https://www.bugseng.com/parma-polyhedra-library")
6916     (synopsis
6917      "Parma Polyhedra Library for computations with polyhedra")
6918     (description
6919      "The Parma Polyhedra Library (PPL) provides numerical abstractions
6920 especially targeted at applications in the field of analysis and
6921 verification of complex systems.  These abstractions include convex
6922 polyhedra, defined as the intersection of a finite number of (open or
6923 closed) halfspaces, each described by a linear inequality (strict or
6924 non-strict) with rational coefficients; some special classes of polyhedra
6925 shapes that offer interesting complexity/precision tradeoffs; and grids
6926 which represent regularly spaced points that satisfy a set of linear
6927 congruence relations.  The library also supports finite powersets and
6928 products of (any kind of) polyhedra and grids, a mixed integer linear
6929 programming problem solver using an exact-arithmetic version of the simplex
6930 algorithm, a parametric integer programming solver, and primitives for
6931 termination analysis via the automatic synthesis of linear ranking
6932 functions.")
6933     (license license:gpl3+)))
6934
6935 (define-public speedcrunch
6936   (package
6937     (name "speedcrunch")
6938     (version "0.12.0")
6939     (source
6940      (origin
6941       (method git-fetch)
6942       (uri (git-reference
6943         (url "https://bitbucket.org/heldercorreia/speedcrunch.git")
6944         (commit (string-append "release-" version))))
6945       (file-name (git-file-name name version))
6946       (sha256
6947        (base32
6948         "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
6949     (build-system cmake-build-system)
6950     (inputs (list qtbase-5))
6951     (native-inputs (list qttools))
6952     (arguments
6953      `(#:phases
6954        (modify-phases %standard-phases
6955          (add-after 'unpack 'chdir-to-src
6956            (lambda _ (chdir "src") #t)))))
6957     (synopsis "High-precision scientific calculator")
6958     (description
6959      "SpeedCrunch is a high-precision scientific calculator.  It features a
6960 syntax-highlighted scrollable display and is designed to be fully used via
6961 keyboard.  Some distinctive features are auto-completion of functions and
6962 variables, a formula book, and quick insertion of constants from various
6963 fields of knowledge.")
6964     (home-page "https://speedcrunch.org/")
6965     (license license:gpl2+)))
6966
6967 (define-public minisat
6968   ;; This is the last commit which is available upstream, no
6969   ;; release happened since 2010.
6970   (let ((commit "37dc6c67e2af26379d88ce349eb9c4c6160e8543")
6971         (revision "1"))
6972     (package
6973       (name "minisat")
6974       (version (string-append "2.2.0-" revision "." (string-take commit 7)))
6975       (source
6976        (origin
6977          (method git-fetch)
6978          (uri (git-reference
6979                (url "https://github.com/niklasso/minisat")
6980                (commit commit)))
6981          (file-name (string-append name "-" version "-checkout"))
6982          (sha256
6983           (base32
6984            "091hf3qkm197s5r7xcr3m07xsdwyz2rqk1hc9kj0hn13imz09irq"))
6985          (patches
6986           (search-patches "minisat-friend-declaration.patch"
6987                           "minisat-install.patch"))))
6988       (build-system gnu-build-system)
6989       (arguments
6990        '(#:make-flags (list (string-append "prefix=" %output))
6991          #:tests? #f ;no check target
6992          #:phases
6993          (modify-phases %standard-phases
6994            (delete 'configure))))
6995       (inputs
6996        `(("zlib:static" ,zlib "static")
6997          ("zlib" ,zlib)))
6998       (synopsis
6999        "Small, yet efficient, SAT solver")
7000       (description
7001        "MiniSat is a minimalistic, open-source SAT solver, developed to help
7002 researchers and developers alike to get started on SAT.")
7003       (home-page
7004        "http://minisat.se/MiniSat.html")
7005       (license license:expat))))
7006
7007 (define-public libqalculate
7008   (package
7009     (name "libqalculate")
7010     (version "3.19.0")
7011     (source
7012      (origin
7013        (method git-fetch)
7014        (uri (git-reference
7015              (url "https://github.com/Qalculate/libqalculate/")
7016              (commit (string-append "v" version))))
7017        (file-name (git-file-name name version))
7018        (sha256
7019         (base32 "1w44407wb552q21dz4m2nwwdi8b9hzjb2w1l3ffsikzqckc7wbyj"))
7020        (patches
7021         (search-patches "libqalculate-3.8.0-libcurl-ssl-fix.patch"))))
7022     (build-system gnu-build-system)
7023     (native-inputs
7024      `(("pkg-config" ,pkg-config)
7025        ("gettext" ,gettext-minimal)
7026        ("intltool" ,intltool)
7027        ("automake" ,automake)
7028        ("autoconf" ,autoconf)
7029        ("libtool" ,libtool)
7030        ("doxygen" ,doxygen)
7031        ("file" ,file)))
7032     (inputs
7033      (list gmp
7034            mpfr
7035            libxml2
7036            curl
7037            icu4c
7038            gnuplot
7039            readline
7040            libiconv))
7041     (arguments
7042      `(#:phases
7043        (modify-phases %standard-phases
7044          (add-before 'bootstrap 'setenv
7045            ;; Prevent the autogen.sh script to carry out the configure
7046            ;; script, which has not yet been patched to replace /bin/sh.
7047            (lambda _
7048              (setenv "NOCONFIGURE" "TRUE")
7049              #t)))))
7050     (home-page "https://qalculate.github.io/")
7051     (synopsis "Multi-purpose cli desktop calculator and library")
7052     (description
7053      "Libqalculate is a multi-purpose cli desktop calculator and library.
7054 It provides basic and advanced functionality.  Features include customizable
7055 functions, unit calculations, and conversions, physical constants, symbolic
7056 calculations (including integrals and equations), arbitrary precision,
7057 uncertainty propagation, interval arithmetic, plotting and a user-friendly
7058 cli.")
7059     (license license:gpl2+)))
7060
7061 (define-public qalculate-gtk
7062   (package
7063     (name "qalculate-gtk")
7064     (version "3.19.0")
7065     (source
7066      (origin
7067        (method git-fetch)
7068        (uri (git-reference
7069              (url "https://github.com/Qalculate/qalculate-gtk/")
7070              (commit (string-append "v" version))))
7071        (file-name (git-file-name name version))
7072        (sha256
7073         (base32 "1nrx7gp6f1yalbdda1gb97azhbr4xclq2xf08vvbvsk8jfd6fd2v"))))
7074     (build-system glib-or-gtk-build-system)
7075     (native-inputs
7076      (list pkg-config
7077            intltool
7078            automake
7079            autoconf
7080            libtool
7081            file))
7082     (inputs
7083      (list gmp
7084            mpfr
7085            libqalculate
7086            libxml2
7087            glib
7088            gtk+))
7089     (arguments
7090      `(#:phases
7091        (modify-phases %standard-phases
7092          (add-before 'bootstrap 'setenv
7093            ;; Prevent the autogen.sh script to carry out the configure
7094            ;; script, which has not yet been patched to replace /bin/sh.
7095            (lambda _
7096              (setenv "NOCONFIGURE" "TRUE")
7097              #t)))))
7098     (home-page "https://qalculate.github.io/")
7099     (synopsis "Multi-purpose graphical desktop calculator")
7100     (description
7101      "Qalculate-gtk is the GTK frontend for libqalculate.  It is a
7102 multi-purpose GUI desktop calculator.  It provides basic and advanced
7103 functionality.  Features include customizable functions, unit calculations,
7104 and conversions, physical constants, symbolic calculations (including
7105 integrals and equations), arbitrary precision, uncertainty propagation,
7106 interval arithmetic, plotting.")
7107     (license license:gpl2+)))
7108
7109 (define-public numdiff
7110   (package
7111     (name "numdiff")
7112     (version "5.9.0")
7113     (source
7114      (origin
7115        (method url-fetch)
7116        (uri (string-append "mirror://savannah/numdiff/numdiff-"
7117                            version ".tar.gz"))
7118        (sha256
7119         (base32
7120          "1vzmjh8mhwwysn4x4m2vif7q2k8i19x8azq7pzmkwwj4g48lla47"))))
7121     (build-system gnu-build-system)
7122     (arguments
7123      '(#:tests? #f ; There are no tests.
7124        #:phases
7125        (modify-phases %standard-phases
7126          (add-before 'compress-documentation 'delete-precompressed-info-file
7127            (lambda _
7128              (delete-file (string-append (assoc-ref %outputs "out")
7129                                          "/share/info/numdiff.info.gz"))
7130              #t)))))
7131     (home-page "https://nongnu.org/numdiff/")
7132     (synopsis "Compare files with numeric fields")
7133     (description
7134      "Numdiff compares files line by line and field by field, ignoring small
7135 numeric differences and differences in numeric formats.")
7136     (license license:gpl3+)))
7137
7138 (define-public why3
7139   (package
7140     (name "why3")
7141     (version "1.4.0")
7142     (source (origin
7143               (method git-fetch)
7144               (uri (git-reference
7145                      (url "https://gitlab.inria.fr/why3/why3")
7146                      (commit version)))
7147               (file-name (git-file-name name version))
7148               (sha256
7149                (base32
7150                 "0pfsiddnk26f384wbazfpgzh1n1ibf3xq101q74mxvczi7z0a791"))))
7151     (build-system ocaml-build-system)
7152     (native-inputs
7153      (list autoconf automake coq ocaml which))
7154     (propagated-inputs
7155      (list camlzip ocaml-graph ocaml-menhir ocaml-num ocaml-zarith))
7156     (inputs
7157      (list coq-flocq emacs-minimal zlib))
7158     (arguments
7159      `(#:phases
7160        (modify-phases %standard-phases
7161          (add-before 'configure 'bootstrap
7162            (lambda _
7163              (invoke "./autogen.sh")
7164              (setenv "CONFIG_SHELL" (which "sh"))
7165              (substitute* "configure"
7166                (("#! /bin/sh") (string-append "#!" (which "sh")))
7167                ;; find ocaml-num in the correct directory
7168                (("\\$DIR/nums.cma") "$DIR/num.cma")
7169                (("\\$DIR/num.cmi") "$DIR/core/num.cmi"))
7170              #t))
7171          (add-after 'configure 'fix-makefile
7172            (lambda _
7173              (substitute* "Makefile"
7174                ;; find ocaml-num in the correct directory
7175                (("site-lib/num") "site-lib"))
7176              #t))
7177         (add-after 'install 'install-lib
7178           (lambda _
7179             (invoke "make" "byte")
7180             (invoke "make" "install-lib")
7181             #t)))))
7182     (home-page "http://why3.lri.fr")
7183     (synopsis "Deductive program verification")
7184     (description "Why3 provides a language for specification and programming,
7185 called WhyML, and relies on external theorem provers, both automated and
7186 interactive, to discharge verification conditions.  Why3 comes with a standard
7187 library of logical theories (integer and real arithmetic, Boolean operations,
7188 sets and maps, etc.) and basic programming data structures (arrays, queues,
7189 hash tables, etc.).  A user can write WhyML programs directly and get
7190 correct-by-construction OCaml programs through an automated extraction
7191 mechanism.  WhyML is also used as an intermediate language for the verification
7192 of C, Java, or Ada programs.")
7193     (license license:lgpl2.1)))
7194
7195 (define-public frama-c
7196   (package
7197     (name "frama-c")
7198     (version "23.1")
7199     (source (origin
7200               (method url-fetch)
7201               (uri (string-append "http://frama-c.com/download/frama-c-"
7202                                   version "-Vanadium.tar.gz"))
7203               (sha256
7204                (base32
7205                 "1rgkq9sg436smw005ag0j6y3xryhjn18a07m5wjfrfp0s1438nnj"))))
7206     (build-system ocaml-build-system)
7207     (arguments
7208      `(#:tests? #f; no test target in Makefile
7209        #:phases
7210        (modify-phases %standard-phases
7211          (add-before 'configure 'export-shell
7212            (lambda* (#:key inputs #:allow-other-keys)
7213              (setenv "CONFIG_SHELL"
7214                      (search-input-file inputs "/bin/sh")))))))
7215     (inputs
7216      (list gmp))
7217     (propagated-inputs
7218      (list ocaml-biniou
7219            ocaml-easy-format
7220            ocaml-graph
7221            ocaml-yojson
7222            ocaml-zarith
7223            why3))
7224     (native-search-paths
7225      (list (search-path-specification
7226             (variable "FRAMAC_SHARE")
7227             (files '("share/frama-c"))
7228             (separator #f))
7229            (search-path-specification
7230             (variable "FRAMAC_LIB")
7231             (files '("lib/frama-c"))
7232             (separator #f))))
7233     (home-page "http://frama-c.com")
7234     (synopsis "C source code analysis platform")
7235     (description "Frama-C is an extensible and collaborative platform dedicated
7236 to source-code analysis of C software.  The Frama-C analyzers assist you in
7237 various source-code-related activities, from the navigation through unfamiliar
7238 projects up to the certification of critical software.")
7239     (license license:lgpl2.1+)))
7240
7241 (define-public blitz
7242   (package
7243     (name "blitz")
7244     (version "1.0.2")
7245     (source
7246      (origin
7247        (method git-fetch)
7248        (uri (git-reference
7249              (url "https://github.com/blitzpp/blitz")
7250              (commit version)))
7251        (file-name (git-file-name name version))
7252        (sha256
7253         (base32 "0c88gc72j3zggyk4yrrip6i0v7xkx97l140vpy3xhxs2i7xy1461"))))
7254     (build-system cmake-build-system)
7255     (arguments
7256      `(#:configure-flags '("-DBUILD_DOC=ON"
7257                            "-DBUILD_TESTING=ON")
7258        ;; The default "check" target also includes examples and benchmarks.
7259        #:test-target "check-testsuite"
7260        #:phases
7261        (modify-phases %standard-phases
7262          (add-after 'build 'build-doc
7263            (lambda _
7264              (invoke "make" "-j" (number->string (parallel-job-count))
7265                      "blitz-doc"))))))
7266     (native-inputs
7267      (list python texinfo))
7268     (synopsis "C++ template class library for multidimensional arrays")
7269     (description "Blitz++ is a C++ template class library that provides
7270 high-performance multidimensional array containers for scientific computing.")
7271     (home-page "https://github.com/blitzpp/blitz")
7272     (license (list license:artistic2.0
7273                    license:bsd-3
7274                    license:lgpl3+))))
7275
7276 (define-public fxdiv
7277   ;; There is currently no tag in this repo.
7278   (let ((commit "63058eff77e11aa15bf531df5dd34395ec3017c8")
7279         (version "0.0")
7280         (revision "1"))
7281     (package
7282       (name "fxdiv")
7283       (version (git-version version revision commit))
7284       (home-page "https://github.com/Maratyszcza/FXdiv")
7285       (source (origin
7286                 (method git-fetch)
7287                 (uri (git-reference (url home-page) (commit commit)))
7288                 (file-name (git-file-name name version))
7289                 (sha256
7290                  (base32
7291                   "0zwzh8gmbx4m6b18s5nf13b0dk5yjkd1fs8f421bl7fz5f9gjd9f"))
7292                 (patches (search-patches "fxdiv-system-libraries.patch"))))
7293       (build-system cmake-build-system)
7294       (inputs
7295        (list googletest googlebenchmark))
7296       (synopsis
7297        "C++ library for division via fixed-point multiplication by inverse")
7298       (description
7299        "On modern CPUs and GPUs, integer division is several times slower than
7300 multiplication.  FXdiv implements an algorithm to replace an integer division
7301 with a multiplication and two shifts.  This algorithm improves performance
7302 when an application performs repeated divisions by the same divisor.")
7303       (license license:expat))))
7304
7305 (define-public fp16
7306   ;; There is currently no tag in this repo.
7307   (let ((commit "0a92994d729ff76a58f692d3028ca1b64b145d91")
7308         (version "0.0")
7309         (revision "1"))
7310     (package
7311       (name "fp16")
7312       (version (git-version version revision commit))
7313       (home-page "https://github.com/Maratyszcza/FP16")
7314       (source (origin
7315                 (method git-fetch)
7316                 (uri (git-reference (url home-page) (commit commit)))
7317                 (file-name (git-file-name name version))
7318                 (sha256
7319                  (base32
7320                   "05mm4vrxsac35hjf5djif9r6rdxj9ippg97ia3p6q6b8lrp7srwv"))
7321                 (patches (search-patches "fp16-system-libraries.patch"))))
7322       (build-system cmake-build-system)
7323       (arguments
7324        `(#:imported-modules ((guix build python-build-system)
7325                              ,@%cmake-build-system-modules)
7326          #:modules (((guix build python-build-system)
7327                      #:select (site-packages))
7328                     (guix build cmake-build-system)
7329                     (guix build utils))
7330          #:phases (modify-phases %standard-phases
7331                     (add-after 'install 'move-python-files
7332                       (lambda* (#:key inputs outputs #:allow-other-keys)
7333                         ;; Python files get installed to $includedir (!).
7334                         ;; Move them to the usual Python site directory.
7335                         (let* ((out     (assoc-ref outputs "out"))
7336                                (include (string-append out "/include"))
7337                                (site    (site-packages inputs outputs))
7338                                (target  (string-append site "/fp16")))
7339                           (mkdir-p target)
7340                           (for-each (lambda (file)
7341                                       (rename-file file
7342                                                    (string-append target "/"
7343                                                                   (basename
7344                                                                    file))))
7345                                     (find-files include "\\.py$"))))))))
7346       (native-inputs
7347        (list python-wrapper))
7348       (inputs
7349        (list psimd googletest googlebenchmark))
7350       (synopsis "C++ library for half-precision floating point formats")
7351       (description
7352        "This header-only C++ library implements conversion to and from
7353 half-precision floating point formats.")
7354       (license license:expat))))
7355
7356 (define-public optizelle
7357   (let ((commit "ed4160b5287518448caeb34789d92dc6a0b7e2cc"))
7358    (package
7359     (name "optizelle")
7360     (version (git-version "1.3.0" "0" commit))
7361     (source
7362      (origin
7363        (method git-fetch)
7364        (uri (git-reference
7365              (url "https://github.com/OptimoJoe/Optizelle")
7366              (commit commit)))
7367        (file-name (git-file-name "optizelle" commit))
7368        (sha256
7369         (base32
7370          "0rjrs5sdmd33a9f4xm8an7p0953aa0bxsmr4hs3ss1aad9k181vq"))
7371        (modules '((guix build utils)))
7372        (snippet
7373         '(begin
7374            ;; Reduce the stopping tolerance in one test so that the
7375            ;; convergence check returns the correct stopping
7376            ;; condition.
7377            (substitute*
7378             "src/unit/linear_algebra/tcg_loss_of_orthogonality.cpp"
7379             (("1e-13") "5e-14"))
7380            ;; Skip one set of python tests.  See
7381            ;; https://github.com/OptimoJoe/Optizelle/issues/2.
7382            (substitute*
7383             "src/examples/inequality_scaling/CMakeLists.txt"
7384             (("add_unit(.*)\\$\\{interfaces\\}(.*)$" all middle end)
7385              (string-append "add_unit" middle "\"cpp\"" end)))
7386            ;; Install the licence for Optizelle, without also
7387            ;; including the licences for the dependencies.
7388            (substitute* "licenses/CMakeLists.txt"
7389                         (("file.*package.*$" all)
7390                          (string-append "# " all))
7391                         ((".*[^l].[.]txt\\)\n") "")
7392                         (("add_license.*\"\n") ""))
7393            #t))))
7394     (build-system cmake-build-system)
7395     (arguments
7396      `(#:imported-modules ((guix build python-build-system)
7397                            ,@%cmake-build-system-modules)
7398        #:modules (((guix build python-build-system) #:select
7399                    (python-version))
7400                   (guix build cmake-build-system)
7401                   (guix build utils))
7402        #:configure-flags `("-DCMAKE_CXX_FLAGS:STRING=-pthread"
7403                            "-DENABLE_CPP_UNIT:BOOL=ON"
7404                            "-DENABLE_CPP_EXAMPLES:BOOL=ON"
7405                            "-DENABLE_PYTHON:BOOL=ON"
7406                            "-DENABLE_PYTHON_UNIT:BOOL=ON"
7407                            "-DENABLE_PYTHON_EXAMPLES:BOOL=ON"
7408                            ,(string-append "-DBLAS_LIBRARY:FILEPATH="
7409                                            (assoc-ref %build-inputs
7410                                                       "blas/lapack")
7411                                            "/lib/libopenblas.so")
7412                            ,(string-append "-DLAPACK_LIBRARY:FILEPATH="
7413                                            (assoc-ref %build-inputs
7414                                                       "fortran:lib")
7415                                            "/lib/libgfortran.so;"
7416                                            (assoc-ref %build-inputs
7417                                                       "fortran:lib")
7418                                            "/lib/libquadmath.so"))
7419        #:phases
7420        (modify-phases %standard-phases
7421          (add-after 'unpack 'set-numpy-path ; Needed for the unit tests.
7422            (lambda* (#:key inputs #:allow-other-keys)
7423              (let* ((pyver (python-version (assoc-ref inputs "python")))
7424                     (npdir (string-append (assoc-ref inputs "numpy")
7425                                           "/lib/python" pyver
7426                                           "/site-packages")))
7427                 (substitute* "src/cmake/Modules/Optizelle.cmake"
7428                   (("PYTHONPATH=")
7429                    (string-append "LD_LIBRARY_PATH=$ENV{LIBRARY_PATH};"
7430                                   "PYTHONPATH=" npdir ":"))))))
7431          (delete 'install-license-files)))) ; LICENSE.txt is installed.
7432     (inputs
7433      `(("blas/lapack" ,openblas)
7434        ("fortran:lib" ,gfortran "lib")
7435        ("jsoncpp" ,jsoncpp)
7436        ("numpy" ,python-numpy)
7437        ("python" ,python)))
7438     (native-inputs
7439      `(("fortran" ,gfortran)
7440        ("pkg-config" ,pkg-config)))
7441     (home-page "https://www.optimojoe.com/products/optizelle/")
7442     (synopsis "Mathematical optimization library")
7443     (description "@code{optizelle} is a software library designed to
7444 solve nonlinear optimization problems.  Four types of problem are
7445 considered: unconstrained, equality constrained, inequality
7446 constrained and constrained.  Constraints may be applied as values of
7447 functions or sets of partial differential equations (PDEs).
7448
7449 Solution algorithms such as the preconditioned nonlinear conjugate
7450 gradient method, sequential quadratic programming (SQP) and the
7451 primal-dual interior-point method are made available.  Interfaces are
7452 provided for applications written in C++ and Python.  Parallel
7453 computation is supported via MPI.")
7454     (license license:bsd-2))))