gnu/packages/algebra.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Andreas Enge <andreas@enge.fr>
   3 ;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
   4 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
   5 ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
   6 ;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
   7 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
   8 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
   9 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
  10 ;;; Copyright © 2017, 2019 Eric Bavier <bavier@member.fsf.org>
  11 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
  12 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
  13 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
  14 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
  15 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
  16 ;;;
  17 ;;; This file is part of GNU Guix.
  18 ;;;
  19 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  20 ;;; under the terms of the GNU General Public License as published by
  21 ;;; the Free Software Foundation; either version 3 of the License, or (at
  22 ;;; your option) any later version.
  23 ;;;
  24 ;;; GNU Guix is distributed in the hope that it will be useful, but
  25 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  26 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  27 ;;; GNU General Public License for more details.
  28 ;;;
  29 ;;; You should have received a copy of the GNU General Public License
  30 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  31
  32 (define-module (gnu packages algebra)
  33   #:use-module (gnu packages)
  34   #:use-module (gnu packages autotools)
  35   #:use-module (gnu packages bison)
  36   #:use-module (gnu packages check)
  37   #:use-module (gnu packages compression)
  38   #:use-module (gnu packages cpp)
  39   #:use-module (gnu packages documentation)
  40   #:use-module (gnu packages ed)
  41   #:use-module (gnu packages flex)
  42   #:use-module (gnu packages fltk)
  43   #:use-module (gnu packages gl)
  44   #:use-module (gnu packages graphviz)
  45   #:use-module (gnu packages image)
  46   #:use-module (gnu packages java)
  47   #:use-module (gnu packages llvm)
  48   #:use-module (gnu packages maths)
  49   #:use-module (gnu packages mpi)
  50   #:use-module (gnu packages multiprecision)
  51   #:use-module (gnu packages perl)
  52   #:use-module (gnu packages pkg-config)
  53   #:use-module (gnu packages pulseaudio)
  54   #:use-module (gnu packages python)
  55   #:use-module (gnu packages python-xyz)
  56   #:use-module (gnu packages readline)
  57   #:use-module (gnu packages shells)
  58   #:use-module (gnu packages tex)
  59   #:use-module (gnu packages texinfo)
  60   #:use-module (gnu packages xiph)
  61   #:use-module (gnu packages xorg)
  62   #:use-module (guix build-system ant)
  63   #:use-module (guix build-system gnu)
  64   #:use-module (guix build-system cmake)
  65   #:use-module (guix build-system python)
  66   #:use-module (guix download)
  67   #:use-module (guix git-download)
  68   #:use-module (guix hg-download)
  69   #:use-module ((guix licenses) #:prefix license:)
  70   #:use-module (guix packages)
  71   #:use-module (guix utils))
  72
  73
  74 (define-public mpfrcx
  75   (package
  76    (name "mpfrcx")
  77    (version "0.5")
  78    (source (origin
  79             (method url-fetch)
  80             (uri (string-append
  81                   "http://www.multiprecision.org/downloads/mpfrcx-"
  82                   version ".tar.gz"))
  83             (sha256
  84              (base32
  85               "1s968480ymv6w0rnvfp9mxvx98hvi29fkvw8nk4ggzc6azxgwybs"))))
  86    (build-system gnu-build-system)
  87    (propagated-inputs
  88      `(("gmp" ,gmp)
  89        ("mpfr" ,mpfr)
  90        ("mpc"  ,mpc))) ; Header files are included by mpfrcx.h.
  91    (synopsis "Arithmetic of polynomials over arbitrary precision numbers")
  92    (description
  93     "Mpfrcx is a library for the arithmetic of univariate polynomials over
  94 arbitrary precision real (mpfr) or complex (mpc) numbers, without control
  95 on the rounding.  For the time being, only the few functions needed to
  96 implement the floating point approach to complex multiplication are
  97 implemented.  On the other hand, these comprise asymptotically fast
  98 multiplication routines such as Toom–Cook and the FFT.")
  99    (license license:lgpl3+)
 100    (home-page "http://www.multiprecision.org/mpfrcx/")))
 101
 102 (define-public gf2x
 103   (package
 104    (name "gf2x")
 105    (version "1.2")
 106    (source (origin
 107             (method url-fetch)
 108             (uri (string-append
 109                   "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-"
 110                   version ".tar.gz"))
 111             (sha256
 112              (base32
 113               "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1"))))
 114    (build-system gnu-build-system)
 115    (synopsis "Arithmetic of polynomials over binary finite fields")
 116    (description
 117     "The gf2x library provides arithmetic of polynomials over finite fields
 118 of characteristic 2.  It implements the multiplication, squaring and
 119 greatest common divisor operations.")
 120    (license license:gpl3+)
 121    (home-page "https://gforge.inria.fr/projects/gf2x/")))
 122
 123 (define-public cm
 124   (package
 125    (name "cm")
 126    (version "0.3")
 127    (source (origin
 128             (method url-fetch)
 129             (uri (string-append
 130                   "http://www.multiprecision.org/cm/download/cm-"
 131                   version ".tar.gz"))
 132             (sha256
 133              (base32
 134               "1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc"))))
 135    (build-system gnu-build-system)
 136    (propagated-inputs
 137      `(("mpfrcx" ,mpfrcx)
 138        ("zlib" ,zlib))) ; Header files included from cm_common.h.
 139    (inputs
 140      `(("pari-gp"  ,pari-gp)))
 141    (synopsis "CM constructions for elliptic curves")
 142    (description
 143     "The CM software implements the construction of ring class fields of
 144 imaginary quadratic number fields and of elliptic curves with complex
 145 multiplication via floating point approximations.  It consists of libraries
 146 that can be called from within a C program and of executable command
 147 line applications.")
 148    (license license:gpl3+)
 149    (home-page "http://www.multiprecision.org/cm/")))
 150
 151 (define-public fplll
 152   (package
 153     (name "fplll")
 154     (version "5.2.1")
 155     (source (origin
 156               (method git-fetch)
 157               (uri (git-reference
 158                     (url "https://github.com/fplll/fplll.git")
 159                     (commit version)))
 160               (file-name (git-file-name name version))
 161               (sha256
 162                (base32
 163                 "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg"))))
 164     (build-system gnu-build-system)
 165     (native-inputs
 166      `(("autoconf" ,autoconf)
 167        ("automake" ,automake)
 168        ("libtool" ,libtool)))
 169     (inputs
 170      `(("gmp" ,gmp)
 171        ("mpfr" ,mpfr)))
 172     (home-page "https://github.com/fplll/fplll")
 173     (synopsis "Library for LLL-reduction of euclidean lattices")
 174     (description
 175      "fplll contains implementations of several lattice algorithms.
 176 The implementation relies on floating-point orthogonalization, and LLL
 177 is central to the code, hence the name.
 178
 179 It includes implementations of floating-point LLL reduction
 180 algorithms, offering different speed/guarantees ratios.  It contains
 181 a @emph{wrapper} choosing the estimated best sequence of variants in
 182 order to provide a guaranteed output as fast as possible.  In the case
 183 of the wrapper, the succession of variants is oblivious to the user.
 184
 185 It includes an implementation of the BKZ reduction algorithm,
 186 including the BKZ-2.0 improvements (extreme enumeration
 187 pruning, pre-processing of blocks, early termination).  Additionally,
 188 Slide reduction and self dual BKZ are supported.
 189
 190 It also includes a floating-point implementation of the
 191 Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice
 192 vector.  For the same task, the GaussSieve algorithm is also available
 193 in fplll.  Finally, it contains a variant of the enumeration algorithm
 194 that computes a lattice vector closest to a given vector belonging to
 195 the real span of the lattice.")
 196     (license license:lgpl2.1+)))
 197
 198 (define-public python-fpylll
 199   (package
 200     (name "python-fpylll")
 201     (version "0.4.1")
 202     (source
 203      (origin
 204        ;; Pypi contains and older release, so we use a tagged release from
 205        ;; Github instead.
 206        (method git-fetch)
 207        (uri (git-reference
 208              (url "https://github.com/fplll/fpylll.git")
 209              (commit (string-append version "dev"))))
 210        (file-name (git-file-name name version))
 211        (sha256
 212         (base32
 213          "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
 214     (build-system python-build-system)
 215     (inputs
 216      `(("fplll" ,fplll)
 217        ("gmp" ,gmp)
 218        ("mpfr" ,mpfr)
 219        ("pari-gp" ,pari-gp)))
 220     (propagated-inputs
 221      `(("cysignals" ,python-cysignals)
 222        ("cython" ,python-cython)
 223        ("flake8" ,python-flake8)
 224        ("numpy" ,python-numpy)
 225        ("pytest" ,python-pytest)))
 226     (home-page "https://github.com/fplll/fpylll")
 227     (synopsis "Python interface for fplll")
 228     (description "fpylll is a Python wrapper for fplll.")
 229     (license license:gpl2+)))
 230
 231 (define-public pari-gp
 232   (package
 233     (name "pari-gp")
 234     (version "2.11.4")
 235     (source (origin
 236               (method url-fetch)
 237               (uri (string-append
 238                     "https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
 239                     version ".tar.gz"))
 240               (sha256
 241                (base32
 242                 "070bjw4kg7r6lqs1hfs08n5fmjv90cpwflp3wr04hbrmyz28zj5z"))))
 243     (build-system gnu-build-system)
 244     (native-inputs
 245      `(("texlive" ,(texlive-union
 246                     (list texlive-amsfonts)))))
 247     (inputs `(("gmp" ,gmp)
 248               ("libx11" ,libx11)
 249               ("perl" ,perl)
 250               ("readline" ,readline)))
 251     (arguments
 252      '(#:make-flags '("all")
 253        #:test-target "dobench"
 254        #:phases
 255        (modify-phases %standard-phases
 256          (replace 'configure
 257            (lambda* (#:key outputs #:allow-other-keys)
 258              (invoke "./Configure"
 259                      (string-append "--prefix="
 260                                     (assoc-ref outputs "out"))))))))
 261     (synopsis "PARI/GP, a computer algebra system for number theory")
 262     (description
 263      "PARI/GP is a widely used computer algebra system designed for fast
 264 computations in number theory (factorisations, algebraic number theory,
 265 elliptic curves...), but it also contains a large number of other useful
 266 functions to compute with mathematical entities such as matrices,
 267 polynomials, power series, algebraic numbers, etc., and a lot of
 268 transcendental functions.
 269 PARI is also available as a C library to allow for faster computations.")
 270     (license license:gpl2+)
 271     (home-page "https://pari.math.u-bordeaux.fr/")))
 272
 273 (define-public gp2c
 274   (package
 275    (name "gp2c")
 276    (version "0.0.11pl3")
 277    (source (origin
 278             (method url-fetch)
 279             (uri (string-append
 280                   "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
 281                   version ".tar.gz"))
 282             (sha256
 283               (base32
 284                 "0yymbrgyjw500hqgmkj5m4nmscd7c9rs9w2c96lxgrcyab8krhrm"))))
 285    (build-system gnu-build-system)
 286    (native-inputs `(("perl" ,perl)))
 287    (inputs `(("pari-gp" ,pari-gp)))
 288    (arguments
 289     '(#:configure-flags
 290       (list (string-append "--with-paricfg="
 291                            (assoc-ref %build-inputs "pari-gp")
 292                            "/lib/pari/pari.cfg"))))
 293    (synopsis "PARI/GP, a computer algebra system for number theory")
 294    (description
 295     "PARI/GP is a widely used computer algebra system designed for fast
 296 computations in number theory (factorisations, algebraic number theory,
 297 elliptic curves...), but it also contains a large number of other useful
 298 functions to compute with mathematical entities such as matrices,
 299 polynomials, power series, algebraic numbers, etc., and a lot of
 300 transcendental functions.
 301 PARI is also available as a C library to allow for faster computations.
 302
 303 GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
 304    (license license:gpl2)
 305    (home-page "https://pari.math.u-bordeaux.fr/")))
 306
 307 (define fplll-4-cmh
 308   (package
 309     (inherit fplll)
 310     (name "fplll")
 311     (version "4.0.4")
 312     (source
 313      (origin
 314        (method url-fetch)
 315        (uri (string-append
 316              "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
 317              version ".tar.gz"))
 318        (sha256
 319         (base32 "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))))
 320
 321 (define-public cmh
 322   (package
 323    (name "cmh")
 324    (version "1.0")
 325    (source (origin
 326             (method url-fetch)
 327             (uri (string-append
 328                   "https://gforge.inria.fr/frs/download.php/33497/cmh-"
 329                   version ".tar.gz"))
 330             (sha256
 331              (base32
 332               "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
 333    (build-system gnu-build-system)
 334    (inputs
 335      `(("gmp" ,gmp)
 336        ("mpfr" ,mpfr)
 337        ("mpc" ,mpc)
 338        ("mpfrcx" ,mpfrcx)
 339        ("fplll" ,fplll-4-cmh)
 340        ("pari-gp"  ,pari-gp)))
 341    (synopsis "Igusa class polynomial computations")
 342    (description
 343     "The CMH software computes Igusa (genus 2) class polynomials, which
 344 parameterize the CM points in the moduli space of 2-dimensional abelian
 345 varieties, i.e. Jacobians of hyperelliptic curves.
 346 It can also be used to compute theta constants at arbitrary
 347 precision.")
 348    (license license:gpl3+)
 349    (home-page "http://cmh.gforge.inria.fr/")))
 350
 351 (define-public giac
 352   (package
 353     (name "giac")
 354     (version "1.6.0-7")
 355     (source
 356      (origin
 357        (method url-fetch)
 358        ;; "~parisse/giac" is not used because the maintainer regularly
 359        ;; overwrites the release tarball there, introducing a checksum
 360        ;; mismatch every time.  See
 361        ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
 362        (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
 363                            "~parisse/debian/dists/stable/main/source/"
 364                            "giac_" version ".tar.gz"))
 365        (sha256
 366         (base32 "1pvgp137zcl0rbhdn1j41xxfml7fp771a7x4ph8qrhhlx0hxzn3p"))))
 367     (build-system gnu-build-system)
 368     (arguments
 369      `(#:modules ((ice-9 ftw)
 370                   (guix build utils)
 371                   (guix build gnu-build-system))
 372        #:phases
 373        (modify-phases %standard-phases
 374          (add-after 'unpack 'patch-bin-cp
 375            ;; Some Makefiles contain hard-coded "/bin/cp".
 376            (lambda _
 377              (substitute* (find-files "doc" "^Makefile")
 378                (("/bin/cp") (which "cp")))
 379              #t))
 380          (add-after 'unpack 'disable-failing-test
 381            ;; FIXME: Test failing.  Not sure why.
 382            (lambda _
 383              (substitute* "check/Makefile.in"
 384                (("chk_fhan11") ""))
 385              #t))
 386          (add-after 'install 'fix-doc
 387            (lambda* (#:key outputs #:allow-other-keys)
 388              (let ((out (assoc-ref outputs "out")))
 389                ;; Most French documentation has a non-commercial
 390                ;; license, so we need to remove it.
 391                (with-directory-excursion (string-append out "/share/giac/doc/fr")
 392                  (for-each delete-file-recursively
 393                            '("cascas" "casexo" "casgeo" "casrouge" "cassim"
 394                              "castor")))
 395                ;; Remove duplicate documentation in
 396                ;; "%out/share/doc/giac/", where Xcas does not expect
 397                ;; to find it.
 398                (delete-file-recursively (string-append out "/share/doc/giac"))
 399                #t)))
 400          (add-after 'install 'remove-unnecessary-executable
 401            (lambda* (#:key outputs #:allow-other-keys)
 402              (let ((out (assoc-ref outputs "out")))
 403                (delete-file (string-append out "/bin/xcasnew"))
 404                #t))))))
 405     (inputs
 406 ;;; TODO: Add libnauty.
 407      `(("fltk" ,fltk)
 408        ("glpk" ,glpk)
 409        ("gmp" ,gmp)
 410        ("gsl" ,gsl)
 411        ("lapack" ,lapack)
 412        ("libao" ,ao)
 413        ("libjpeg" ,libjpeg-turbo)
 414        ("libpng" ,libpng)
 415        ("libsamplerate" ,libsamplerate)
 416        ("libx11" ,libx11)
 417        ("libxinerama" ,libxinerama)
 418        ("libxft" ,libxft)
 419        ("libxt" ,libxt)
 420        ("mesa" ,mesa)
 421        ("mpfi" ,mpfi)
 422        ("mpfr" ,mpfr)
 423        ("ntl" ,ntl)
 424        ("perl" ,perl)
 425        ("pari-gp" ,pari-gp)
 426        ("tcsh" ,tcsh)))
 427     (native-inputs
 428      `(("bison" ,bison)
 429        ("flex" ,flex)
 430        ("readline" ,readline)
 431        ("texlive" ,texlive-tiny)))
 432     (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
 433     (synopsis "Computer algebra system")
 434     (description
 435      "Giac/Xcas is a computer algebra system.  It has a compatibility mode for
 436 maple, mupad and the TI89.  It is available as a standalone program (graphic
 437 or text interfaces) or as a C++ library.")
 438     (license license:gpl3+)))
 439
 440 (define-public flint
 441   (package
 442    (name "flint")
 443    (version "2.5.2")
 444    (source (origin
 445             (method url-fetch)
 446             (uri (string-append
 447                   "http://flintlib.org/flint-"
 448                   version ".tar.gz"))
 449             (sha256 (base32
 450                      "11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
 451             (patches (search-patches "flint-ldconfig.patch"))))
 452    (build-system gnu-build-system)
 453    (propagated-inputs
 454     `(("gmp" ,gmp)
 455       ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
 456    (arguments
 457     `(#:parallel-tests? #f ; seems to be necessary on arm
 458       #:phases
 459        (modify-phases %standard-phases
 460          (replace 'configure
 461            (lambda* (#:key inputs outputs #:allow-other-keys)
 462              (let ((out (assoc-ref outputs "out"))
 463                    (gmp (assoc-ref inputs "gmp"))
 464                    (mpfr (assoc-ref inputs "mpfr")))
 465                ;; do not pass "--enable-fast-install", which makes the
 466                ;; homebrew configure process fail
 467                (invoke "./configure"
 468                        (string-append "--prefix=" out)
 469                        (string-append "--with-gmp=" gmp)
 470                        (string-append "--with-mpfr=" mpfr))
 471                #t))))))
 472    (synopsis "Fast library for number theory")
 473    (description
 474     "FLINT is a C library for number theory.  It supports arithmetic
 475 with numbers, polynomials, power series and matrices over many base
 476 rings, including multiprecision integers and rationals, integers
 477 modulo n, p-adic numbers, finite fields (prime and non-prime order)
 478 and real and complex numbers (via the Arb extension library).
 479
 480 Operations that can be performed include conversions, arithmetic,
 481 GCDs, factoring, solving linear systems, and evaluating special
 482 functions.  In addition, FLINT provides various low-level routines for
 483 fast arithmetic.")
 484    (license license:gpl2+)
 485    (home-page "http://flintlib.org/")))
 486
 487 (define-public arb
 488   (package
 489     (name "arb")
 490     (version "2.17.0")
 491     (source (origin
 492               (method git-fetch)
 493               (uri (git-reference
 494                     (url "https://github.com/fredrik-johansson/arb.git")
 495                     (commit version)))
 496               (file-name (git-file-name name version))
 497               (sha256
 498                (base32
 499                 "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1"))))
 500     (build-system gnu-build-system)
 501     (propagated-inputs
 502      `(("flint" ,flint)))               ; flint.h is included by arf.h
 503     (inputs
 504      `(("gmp" ,gmp)
 505        ("mpfr" ,mpfr)))
 506     (arguments
 507      `(#:phases
 508        (modify-phases %standard-phases
 509          (replace 'configure
 510            (lambda* (#:key inputs outputs #:allow-other-keys)
 511              (let ((out (assoc-ref outputs "out"))
 512                    (flint (assoc-ref inputs "flint"))
 513                    (gmp (assoc-ref inputs "gmp"))
 514                    (mpfr (assoc-ref inputs "mpfr")))
 515                ;; Do not pass "--enable-fast-install", which makes the
 516                ;; homebrew configure process fail.
 517                (invoke "./configure"
 518                        (string-append "--prefix=" out)
 519                        (string-append "--with-flint=" flint)
 520                        (string-append "--with-gmp=" gmp)
 521                        (string-append "--with-mpfr=" mpfr))))))))
 522     (synopsis "Arbitrary precision floating-point ball arithmetic")
 523     (description
 524      "Arb is a C library for arbitrary-precision floating-point ball
 525 arithmetic.  It supports efficient high-precision computation with
 526 polynomials, power series, matrices and special functions over the
 527 real and complex numbers, with automatic, rigorous error control.")
 528     (license license:lgpl2.1+)
 529     (home-page "http://arblib.org")))
 530
 531 (define-public python-flint
 532   (package
 533     (name "python-flint")
 534     (version "0.3.0")
 535     (source (origin
 536               (method git-fetch)
 537               (uri (git-reference
 538                     (url "https://github.com/fredrik-johansson/python-flint.git")
 539                     (commit version)))
 540               (file-name (git-file-name name version))
 541               (sha256
 542                (base32
 543                 "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
 544               (patches (search-patches "python-flint-includes.patch"))))
 545     (build-system python-build-system)
 546     (native-inputs
 547      `(("python-cython" ,python-cython)))
 548     (propagated-inputs
 549      `(("python-numpy" ,python-numpy)))
 550     (inputs
 551      `(("arb" ,arb)
 552        ("flint" ,flint)))
 553     (synopsis "Python module wrapping ARB and FLINT")
 554     (description
 555      "Python-flint is a Python extension module wrapping FLINT
 556 (Fast Library for Number Theory) and Arb (arbitrary-precision ball
 557 arithmetic).  It supports integers, rationals, modular integers,
 558 real and complex ball arithmetic, polynomials and matrices over all
 559 these types and other mathematical functions.")
 560     (license license:expat)
 561     (home-page "http://fredrikj.net/python-flint/")))
 562
 563 (define-public ntl
 564   (package
 565    (name "ntl")
 566    (version "11.4.3")
 567    (source (origin
 568             (method url-fetch)
 569             (uri (string-append "https://shoup.net/ntl/ntl-"
 570                                 version ".tar.gz"))
 571             (sha256
 572              (base32
 573               "1lisp3064rch3jaa2wrhy1s9kll7i3ka3d0y6lj6l3l4ckfcrhdp"))
 574             (modules '((guix build utils)))
 575             (snippet
 576              '(begin
 577                 (delete-file-recursively "src/libtool-origin")
 578                 #t))))
 579    (build-system gnu-build-system)
 580    (native-inputs
 581     `(("libtool" ,libtool)
 582       ("perl" ,perl))) ; for configuration
 583    (inputs
 584     `(("gmp" ,gmp)
 585       ("gf2x" ,gf2x)))
 586    (arguments
 587     `(#:phases
 588       (modify-phases %standard-phases
 589         (replace 'configure
 590          (lambda* (#:key inputs outputs #:allow-other-keys)
 591            (chdir "src")
 592            (invoke "./configure"
 593                     (string-append "PREFIX=" (assoc-ref outputs "out"))
 594                     (string-append "LIBTOOL=" (assoc-ref inputs "libtool") "/bin/libtool")
 595                     ;; set the library prefixes explicitly so that they get
 596                     ;; embedded in the .la file
 597                     (string-append "GMP_PREFIX=" (assoc-ref inputs "gmp"))
 598                     (string-append "GF2X_PREFIX=" (assoc-ref inputs "gf2x"))
 599                     ;; Do not build especially for the build machine.
 600                     "NATIVE=off"
 601                     "NTL_GF2X_LIB=on"
 602                     "SHARED=on"))))))
 603    (synopsis "C++ library for number theory")
 604    (description
 605     "NTL is a C++ library providing data structures and algorithms
 606 for manipulating signed, arbitrary length integers, and for vectors,
 607 matrices, and polynomials over the integers and over finite fields.")
 608    (license license:gpl2+)
 609    (home-page "https://shoup.net/ntl/")))
 610
 611 (define-public singular
 612   (package
 613    (name "singular")
 614    (version "4.1.3p2")
 615    (source
 616     (origin
 617       (method url-fetch)
 618       (uri
 619        (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
 620                       "Singular/SOURCES/"
 621                       (string-join
 622                        (string-split
 623                         (string-trim-right version #\p
 624                                            0 (1- (string-length version)))
 625                         #\.) "-")
 626                       "/singular-" version ".tar.gz"))
 627              (sha256 (base32
 628                       "1524yrni7gh0hir5ckridq671q5s6avfjdsdyahj51kzdl3wcypf"))))
 629    (build-system gnu-build-system)
 630    (native-inputs
 631     `(("doxygen" ,doxygen)
 632       ("graphviz" ,graphviz)
 633       ("perl" ,perl)))
 634    (inputs
 635     `(("cddlib" ,cddlib)
 636       ("gmp" ,gmp)
 637       ("flint" ,flint)
 638       ("mpfr" ,mpfr)
 639       ("ntl" ,ntl)
 640       ("python" ,python-2)
 641       ("readline" ,readline)))
 642    (arguments
 643     `(#:configure-flags
 644       (list (string-append "--with-ntl="
 645                            (assoc-ref %build-inputs "ntl")))))
 646    (synopsis "Computer algebra system for polynomial computations")
 647    (description
 648     "Singular is a computer algebra system for polynomial computations,
 649 with special emphasis on commutative and non-commutative algebra, algebraic
 650 geometry and singularity theory.")
 651    ;; Singular itself is dual licensed gpl2 or gpl3, but some of the
 652    ;; libraries with which it links are licensed under lgpl3+, so the
 653    ;; combined work becomes gpl3. See COPYING in the source code.
 654    (license license:gpl3)
 655    (home-page "http://www.singular.uni-kl.de/index.php")))
 656
 657 (define-public gmp-ecm
 658   (package
 659    (name "gmp-ecm")
 660    (version "7.0.4")
 661    (source (origin
 662              (method url-fetch)
 663              ;; Use the ‘Latest version’ link for a stable URI across releases.
 664              (uri (string-append "https://gforge.inria.fr/frs/download.php/"
 665                                  "latestfile/160/ecm-" version ".tar.gz"))
 666              (sha256 (base32
 667                       "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"))))
 668    (build-system gnu-build-system)
 669    (inputs
 670     `(("gmp" ,gmp)))
 671    (arguments
 672     `(#:configure-flags '("--enable-shared"
 673                           ;; Disable specific assembly routines, which depend
 674                           ;; on the subarchitecture of the build machine,
 675                           ;; and use gmp instead.
 676                           "--disable-asm-redc")))
 677    (synopsis "Integer factorization library using the elliptic curve method")
 678    (description
 679     "GMP-ECM factors integers using the elliptic curve method (ECM) as well
 680 as the P-1 and P+1 algorithms.  It provides a library and a stand-alone
 681 binary.")
 682    ;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+,
 683    ;; so the combined work is under gpl3+.
 684    (license license:gpl3+)
 685    (home-page "http://ecm.gforge.inria.fr/")))
 686
 687 (define-public bc
 688   (package
 689     (name "bc")
 690     (version "1.07.1")
 691     (source (origin
 692              (method url-fetch)
 693              (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
 694              (sha256
 695               (base32
 696                "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))
 697              (patches (search-patches "bc-fix-cross-compilation.patch"))))
 698     (build-system gnu-build-system)
 699     (native-inputs
 700      `(("automake" ,automake)
 701        ("autoconf" ,autoconf)
 702        ("ed" ,ed)
 703        ("flex" ,flex)
 704        ("texinfo" ,texinfo)))
 705     (arguments
 706      '(#:configure-flags
 707        (list "--with-readline")
 708        #:phases
 709        (modify-phases %standard-phases
 710          (add-after 'unpack 'autogen
 711            (lambda _
 712              (invoke "autoreconf" "-vif"))))))
 713     (home-page "https://www.gnu.org/software/bc/")
 714     (synopsis "Arbitrary precision numeric processing language")
 715     (description
 716      "bc is an arbitrary precision numeric processing language.  It includes
 717 an interactive environment for evaluating mathematical statements.  Its
 718 syntax is similar to that of C, so basic usage is familiar.  It also includes
 719 \"dc\", a reverse-polish calculator.")
 720     (license license:gpl2+)))
 721
 722 ;; The original kiss-fft does not have a complete build system and does not
 723 ;; build any shared libraries.  This is a fork used by Extempore.
 724 (define-public kiss-fft-for-extempore
 725   (package
 726     (name "kiss-fft-for-extempore")
 727     (version "1.3.0")
 728     (source (origin
 729               (method git-fetch)
 730               (uri (git-reference
 731                     (url "https://github.com/extemporelang/kiss_fft.git")
 732                     (commit version)))
 733               (file-name (git-file-name name version))
 734               (sha256
 735                (base32
 736                 "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
 737     (build-system cmake-build-system)
 738     (arguments `(#:tests? #f)) ; no tests included
 739     ;; Extempore refuses to build on architectures other than x86_64
 740     (supported-systems '("x86_64-linux"))
 741     (home-page "https://github.com/extemporelang/kiss_fft")
 742     (synopsis "Mixed-radix Fast Fourier Transform")
 743     (description
 744      "Kiss FFT attempts to be a reasonably efficient, moderately useful FFT
 745 that can use fixed or floating data types and can easily be incorporated into
 746 a C program.")
 747     (license license:bsd-3)))
 748
 749 (define-public fftw
 750   (package
 751     (name "fftw")
 752     (version "3.3.8")
 753     (source (origin
 754              (method url-fetch)
 755              (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
 756                                  version".tar.gz"))
 757              (sha256
 758               (base32
 759                "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
 760     (build-system gnu-build-system)
 761     (arguments
 762      `(#:configure-flags
 763        '("--enable-shared" "--enable-openmp" "--enable-threads"
 764          ,@(let ((system (or (%current-target-system) (%current-system))))
 765              ;; Enable SIMD extensions for codelets.  See details at:
 766              ;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>.
 767              (cond
 768               ((string-prefix? "x86_64" system)
 769                '("--enable-sse2" "--enable-avx" "--enable-avx2"
 770                  "--enable-avx512" "--enable-avx-128-fma"))
 771               ((string-prefix? "i686" system)
 772                '("--enable-sse2"))
 773               ((string-prefix? "aarch64" system)
 774                ;; Note that fftw supports NEON on 32-bit ARM only when
 775                ;; compiled for single-precision.
 776                '("--enable-neon"))
 777               (else
 778                '())))
 779          ;; By default '-mtune=native' is used.  However, that may cause the
 780          ;; use of ISA extensions (e.g. AVX) that are not necessarily
 781          ;; available on the user's machine when that package is built on a
 782          ;; different machine.
 783          "ax_cv_c_flags__mtune_native=no")))
 784     (native-inputs `(("perl" ,perl)))
 785     (home-page "http://fftw.org")
 786     (synopsis "Computing the discrete Fourier transform")
 787     (description
 788      "FFTW is a C subroutine library for computing the discrete Fourier
 789 transform (DFT) in one or more dimensions, of arbitrary input size, and of
 790 both real and complex data (as well as of even/odd data---i.e. the discrete
 791 cosine/ sine transforms or DCT/DST).")
 792     (license license:gpl2+)))
 793
 794 (define-public fftwf
 795   (package (inherit fftw)
 796     (name "fftwf")
 797     (arguments
 798      (substitute-keyword-arguments (package-arguments fftw)
 799        ((#:configure-flags fftw-configure-flags)
 800         `(cons* "--enable-single"
 801                 ,@(if (string-prefix? "arm" (or (%current-target-system)
 802                                                 (%current-system)))
 803                       ;; fftw supports NEON on 32-bit ARM only when compiled
 804                       ;; for single-precision, so add it here.
 805                       '("--enable-neon")
 806                       '())
 807                 ,fftw-configure-flags))))
 808     (description
 809      (string-append (package-description fftw)
 810                     "  Single-precision version."))))
 811
 812 (define-public fftw-openmpi
 813   (package (inherit fftw)
 814     (name "fftw-openmpi")
 815     (inputs
 816      `(("openmpi" ,openmpi)
 817        ,@(package-inputs fftw)))
 818     (arguments
 819      (substitute-keyword-arguments (package-arguments fftw)
 820        ((#:configure-flags cf)
 821         `(cons "--enable-mpi" ,cf))
 822        ((#:phases phases '%standard-phases)
 823         `(modify-phases ,phases
 824            (add-before 'check 'mpi-setup
 825              ,%openmpi-setup)))))
 826     (description
 827      (string-append (package-description fftw)
 828                     "  With OpenMPI parallelism support."))))
 829
 830 (define-public java-la4j
 831   (package
 832     (name "java-la4j")
 833     (version "0.6.0")
 834     (source (origin
 835               (method git-fetch)
 836               (uri (git-reference
 837                     (url "https://github.com/vkostyukov/la4j.git")
 838                     (commit version)))
 839               (file-name (string-append name "-" version "-checkout"))
 840               (sha256
 841                (base32
 842                 "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
 843     (build-system ant-build-system)
 844     (arguments
 845      `(#:jar-name "la4j.jar"
 846        #:jdk ,icedtea-8
 847        #:test-exclude (list "**/Abstract*.java"
 848                             "**/MatrixTest.java"
 849                             "**/DenseMatrixTest.java"
 850                             "**/SparseMatrixTest.java"
 851                             "**/VectorTest.java"
 852                             "**/SparseVectorTest.java"
 853                             "**/DenseVectorTest.java")))
 854     (native-inputs
 855      `(("java-junit" ,java-junit)
 856        ("java-hamcrest-core" ,java-hamcrest-core)))
 857     (home-page "http://la4j.org/")
 858     (synopsis "Java library that provides Linear Algebra primitives and algorithms")
 859     (description "The la4j library is a Java library that provides Linear
 860 Algebra primitives (matrices and vectors) and algorithms.  The key features of
 861 the la4j library are:
 862
 863 @itemize
 864 @item No dependencies and tiny size
 865 @item Fluent object-oriented/functional API
 866 @item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
 867 @item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
 868 @item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
 869 @item MatrixMarket/CSV IO formats support for matrices and vectors
 870 @end itemize\n")
 871     (license license:asl2.0)))
 872
 873 (define-public java-jlargearrays
 874   (package
 875     (name "java-jlargearrays")
 876     (version "1.6")
 877     (source (origin
 878               (method url-fetch)
 879               (uri (string-append "https://repo1.maven.org/maven2/"
 880                                   "pl/edu/icm/JLargeArrays/"
 881                                   version "/JLargeArrays-" version
 882                                   "-sources.jar"))
 883               (file-name (string-append name "-" version ".jar"))
 884               (sha256
 885                (base32
 886                 "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
 887     (build-system ant-build-system)
 888     (arguments
 889      `(#:jar-name "jlargearrays.jar"
 890        #:tests? #f ; tests are not included in the release archive
 891        #:jdk ,icedtea-8))
 892     (propagated-inputs
 893      `(("java-commons-math3" ,java-commons-math3)))
 894     (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
 895     (synopsis "Library of one-dimensional arrays that can store up to 263 elements")
 896     (description "JLargeArrays is a Java library of one-dimensional arrays
 897 that can store up to 263 elements.")
 898     (license license:bsd-2)))
 899
 900 (define-public java-jtransforms
 901   (package
 902     (name "java-jtransforms")
 903     (version "3.1")
 904     (source (origin
 905               (method url-fetch)
 906               (uri (string-append "https://repo1.maven.org/maven2/"
 907                                   "com/github/wendykierp/JTransforms/"
 908                                   version "/JTransforms-" version "-sources.jar"))
 909               (sha256
 910                (base32
 911                 "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
 912     (build-system ant-build-system)
 913     (arguments
 914      `(#:jar-name "jtransforms.jar"
 915        #:tests? #f ; tests are not included in the release archive
 916        #:jdk ,icedtea-8))
 917     (propagated-inputs
 918      `(("java-commons-math3" ,java-commons-math3)
 919        ("java-jlargearrays" ,java-jlargearrays)))
 920     (home-page "https://github.com/wendykierp/JTransforms")
 921     (synopsis "Multithreaded FFT library written in pure Java")
 922     (description "JTransforms is a multithreaded FFT library written in pure
 923 Java.  Currently, four types of transforms are available: @dfn{Discrete
 924 Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
 925 Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
 926     (license license:bsd-2)))
 927
 928 (define-public lmfit
 929   (package
 930     (name "lmfit")
 931     (version "8.2.2")
 932     (source (origin
 933               (method git-fetch)
 934               (uri (git-reference
 935                     (url "https://jugit.fz-juelich.de/mlz/lmfit.git")
 936                     (commit (string-append "v" version))))
 937               (file-name (git-file-name name version))
 938               (sha256
 939                (base32
 940                 "00bch77a6qgnw6vzsjn2a42n8n683ih3xm0wpr454jxa15hw78vf"))))
 941     (build-system cmake-build-system)
 942     (native-inputs
 943      `(("perl" ,perl)))                   ; for pod2man
 944     (home-page "https://jugit.fz-juelich.de/mlz/lmfit")
 945     (synopsis "Levenberg-Marquardt minimization and least-squares fitting")
 946     (description "lmfit is a C library for Levenberg-Marquardt least-squares
 947 minimization and curve fitting.  It is mature code, based on decades-old
 948 algorithms from the FORTRAN library MINPACK.")
 949     (license license:bsd-2)))
 950
 951 (define-public symengine
 952   (package
 953     (name "symengine")
 954     (version "0.6.0")
 955     (source
 956      (origin
 957        (method git-fetch)
 958        (uri (git-reference
 959              (url "https://github.com/symengine/symengine.git")
 960              (commit (string-append "v" version))))
 961        (file-name (git-file-name name version))
 962        (sha256
 963         (base32 "129iv9maabmb42ylfdv0l0g94mcbf3y4q3np175008rcqdr8z6h1"))))
 964     (build-system cmake-build-system)
 965     (arguments
 966      '(#:configure-flags
 967        ;; These are the suggested build options in the README.
 968        '("-DCMAKE_BUILD_TYPE=Release"
 969          "-DWITH_GMP=on"
 970          "-DWITH_MPFR=on"
 971          "-DWITH_MPC=on"
 972          "-DINTEGER_CLASS=flint"
 973          "-DWITH_LLVM=on"
 974          "-DWITH_SYMENGINE_THREAD_SAFE=on"
 975          "-DBUILD_SHARED_LIBS=on")))    ;also build libsymengine
 976     (native-inputs
 977      `(("llvm" ,llvm)))
 978     (inputs
 979      `(("flint" ,flint)
 980        ("gmp" ,gmp)
 981        ("mpc" ,mpc)
 982        ("mpfr" ,mpfr)))
 983     (home-page "https://github.com/symengine/symengine")
 984     (synopsis "Fast symbolic manipulation library")
 985     (description
 986      "SymEngine is a standalone fast C++ symbolic manipulation library.
 987 Optional thin wrappers allow usage of the library from other languages.")
 988     (license (list license:expat        ;SymEngine
 989                    license:bsd-3))))    ;3rd party code
 990
 991 (define-public eigen
 992   (package
 993     (name "eigen")
 994     (version "3.3.7")
 995     (source (origin
 996               (method url-fetch)
 997               (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
 998                                   version ".tar.bz2"))
 999               (sha256
1000                (base32
1001                 "1km3fyfzyqfdvmnl79drps3fjwnz3zbh0c7l34mfbqyvvs8cy4wz"))
1002               (file-name (string-append name "-" version ".tar.bz2"))
1003               (patches (search-patches "eigen-stabilise-sparseqr-test.patch"))
1004               (modules '((guix build utils)))
1005               (snippet
1006                ;; There are 3 test failures in the "unsupported" directory,
1007                ;; but maintainers say it's a known issue and it's unsupported
1008                ;; anyway, so just skip them.
1009                '(begin
1010                   (substitute* "unsupported/CMakeLists.txt"
1011                     (("add_subdirectory\\(test.*")
1012                      "# Do not build the tests for unsupported features.\n"))
1013                   #t))))
1014     (build-system cmake-build-system)
1015     (arguments
1016      '(;; Turn off debugging symbols to save space.
1017        #:build-type "Release"
1018
1019        #:phases (modify-phases %standard-phases
1020                   (replace 'check
1021                     (lambda _
1022                       (let* ((cores  (parallel-job-count))
1023                              (dash-j (format #f "-j~a" cores)))
1024                         (setenv "EIGEN_SEED" "1") ;for reproducibility
1025                         ;; First build the tests, in parallel.  See
1026                         ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
1027                         (invoke "make" "buildtests" dash-j)
1028
1029                         ;; Then run 'CTest' with -V so we get more
1030                         ;; details upon failure.
1031                         (invoke "ctest" "-V" dash-j)))))))
1032     (home-page "https://eigen.tuxfamily.org")
1033     (synopsis "C++ template library for linear algebra")
1034     (description
1035      "Eigen is a C++ template library for linear algebra: matrices, vectors,
1036 numerical solvers, and related algorithms.  It provides an elegant API based
1037 on \"expression templates\".  It is versatile: it supports all matrix sizes,
1038 all standard numeric types, various matrix decompositions and geometry
1039 features, and more.")
1040
1041     ;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3.
1042     ;; See 'COPYING.README' for details.
1043     (license license:mpl2.0)))
1044
1045 (define-public eigen-for-tensorflow
1046   (let ((changeset "fd6845384b86")
1047         (revision "1"))
1048     (package (inherit eigen)
1049       (name "eigen-for-tensorflow")
1050       (version (string-append "3.3.5-" revision "." changeset))
1051       (source (origin
1052                 (method hg-fetch)
1053                 (uri (hg-reference
1054                       (url "https://bitbucket.org/eigen/eigen")
1055                       (changeset changeset)))
1056                 (sha256
1057                  (base32
1058                   "12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5"))
1059                 (file-name (string-append name "-" version "-checkout"))
1060                 (modules '((guix build utils)))
1061                 (snippet
1062                  ;; There are 3 test failures in the "unsupported" directory,
1063                  ;; but maintainers say it's a known issue and it's unsupported
1064                  ;; anyway, so just skip them.
1065                  '(begin
1066                     (substitute* "unsupported/CMakeLists.txt"
1067                       (("add_subdirectory\\(test.*")
1068                        "# Do not build the tests for unsupported features.\n"))
1069                     #t)))))))
1070
1071 (define-public xtensor
1072   (package
1073     (name "xtensor")
1074     (version "0.20.10")
1075     (source (origin
1076               (method git-fetch)
1077               (uri (git-reference
1078                     (url "https://github.com/QuantStack/xtensor.git")
1079                     (commit version)))
1080               (sha256
1081                (base32
1082                 "1fmv2hpx610xwhxrndfsfvlbqfyk4l3gi5q5d7pa9m82kblxjj9l"))
1083               (file-name (git-file-name name version))))
1084     (build-system cmake-build-system)
1085     (native-inputs
1086      `(("googletest" ,googletest)
1087        ("xtl" ,xtl)))
1088     (arguments
1089      `(#:configure-flags
1090        '("-DBUILD_TESTS=ON")
1091        #:test-target "xtest"))
1092     (home-page "https://quantstack.net/xtensor")
1093     (synopsis "C++ tensors with broadcasting and lazy computing")
1094     (description "xtensor is a C++ library meant for numerical analysis with
1095 multi-dimensional array expressions.
1096
1097 xtensor provides:
1098 @itemize
1099 @item an extensible expression system enabling lazy broadcasting.
1100 @item an API following the idioms of the C++ standard library.
1101 @item tools to manipulate array expressions and build upon xtensor.
1102 @end itemize")
1103     (license license:bsd-3)))
1104
1105 (define-public gap
1106   (package
1107     (name "gap")
1108     (version "4.10.2")
1109     (source
1110      (origin
1111        (method url-fetch)
1112        (uri (string-append "https://www.gap-system.org/pub/gap/gap-"
1113                            (version-major+minor version)
1114                            "/tar.bz2/gap-"
1115                            version
1116                            ".tar.bz2"))
1117        (sha256
1118         (base32 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
1119        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
1120        (snippet
1121         '(begin
1122            ;; Delete the external gmp and zlib libraries
1123            ;; and a subdirectory not needed for our build.
1124            (for-each delete-file-recursively
1125                      '("extern" "hpcgap"))
1126            ;; Delete a failing test.
1127            ;; FIXME: This might be fixed in the next release, see
1128            ;; https://github.com/gap-system/gap/issues/3292
1129            (delete-file "tst/testinstall/dir.tst")
1130            ;; Delete all packages except for a fixed list.
1131            (with-directory-excursion "pkg"
1132              (for-each delete-file-recursively
1133                (lset-difference string=? (scandir ".")
1134                  '("." ".."
1135                    ;; Necessary packages.
1136                    "GAPDoc-1.6.2"
1137                    "primgrp-3.3.2"
1138                    "SmallGrp-1.3"    ; artistic2.0
1139                    "transgrp"        ; artistic2.0 for data,
1140                                      ; gpl2 or gpl3 for code
1141                    ;; Recommanded package.
1142                    "io-4.5.4"        ; gpl3+
1143                    ;; Optional packages, searched for at start,
1144                    ;; and their depedencies.
1145                    "alnuth-3.1.0"
1146                    "autpgrp-1.10"
1147                    "crisp-1.4.4"     ; bsd-2
1148                    "ctbllib"       ; gpl3+ according to doc/chap0.txt
1149                    "FactInt-1.6.2"
1150                    "fga"
1151                    "irredsol-1.4"    ; bsd-2
1152                    "laguna-3.9.2"
1153                    "polenta-1.3.8"
1154                    "polycyclic-2.14"
1155                    "radiroot-2.8"
1156                    "resclasses-4.7.1"
1157                    "sophus-1.24"
1158                    "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
1159                                    ; and the next release
1160                    "utils-0.59"))))
1161            #t))))
1162     (build-system gnu-build-system)
1163     (inputs
1164      `(("gmp" ,gmp)
1165        ("zlib" ,zlib)))
1166     (arguments
1167      `(#:modules ((ice-9 ftw)
1168                   (srfi srfi-26)
1169                   (guix build gnu-build-system)
1170                   (guix build utils))
1171        #:phases
1172        (modify-phases %standard-phases
1173          (add-after 'build 'build-packages
1174            ;; Compile all packages that have not been deleted by the
1175            ;; code snippet above.
1176            (lambda _
1177              (setenv "CONFIG_SHELL" (which "bash"))
1178              (with-directory-excursion "pkg"
1179                (invoke "../bin/BuildPackages.sh")
1180              #t)))
1181          (add-after 'build-packages 'build-doc
1182            ;; The documentation is bundled, but we create it from source.
1183            (lambda _
1184              (with-directory-excursion "doc"
1185                (invoke "./make_doc"))
1186              #t))
1187          (replace 'install
1188            (lambda* (#:key outputs #:allow-other-keys)
1189              (let* ((out (assoc-ref outputs "out"))
1190                     (bin (string-append out "/bin"))
1191                     (lib (string-append out "/lib"))
1192                     (prog (string-append bin "/gap"))
1193                     (prog-real (string-append bin "/.gap-real"))
1194                     (share (string-append out "/share/gap"))
1195                     (include (string-append out "/include/gap"))
1196                     (include-hpc (string-append include "/hpc")))
1197                ;; Install only the gap binary; the gac compiler is left
1198                ;; for maybe later. "Wrap" it in a shell script that calls
1199                ;; the binary with the correct parameter.
1200                (mkdir-p bin)
1201                (copy-file "gap" prog-real)
1202                (call-with-output-file prog
1203                  (lambda (port)
1204                    (format port
1205                            "#!~a~%exec ~a -l ~a \"$@\"~%"
1206                            (which "bash")
1207                            prog-real
1208                            share)))
1209                (chmod prog #o755)
1210                ;; Install the headers, which are needed by Sage. The
1211                ;; Makefile target "install-headers" was available in
1212                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1213                (mkdir-p include-hpc)
1214                (install-file "gen/config.h" include)
1215                (let ((file-name-predicate-without-stat
1216                        (lambda (regex)
1217                          (cut (file-name-predicate regex) <> #f))))
1218                  (with-directory-excursion "src"
1219                    (for-each
1220                      (cut install-file <> include)
1221                      (scandir "."
1222                               (file-name-predicate-without-stat ".*\\.h$"))))
1223                  (with-directory-excursion "src/hpc"
1224                    (for-each
1225                      (cut install-file <> include-hpc)
1226                      (scandir "."
1227                               (file-name-predicate-without-stat ".*\\.h$")))))
1228                ;; Install the library, which is needed by Sage. The
1229                ;; Makefile target "install-libgap" was available in
1230                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1231                ;; Compared to the Makefile, which used libtool, the
1232                ;; following approach of copying files and making symlinks
1233                ;; is rather pedestrian. There is hope that some later
1234                ;; version of gap reinstates and completes the install
1235                ;; targets.
1236                (invoke "make" "libgap.la")
1237                (install-file "libgap.la" lib)
1238                (install-file ".libs/libgap.so.0.0.0" lib)
1239                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so"))
1240                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
1241                ;; Install a certain number of files and directories to
1242                ;; SHARE, where the wrapped shell script expects them.
1243                ;; Remove information on the build directory from sysinfo.gap.
1244                (substitute* "sysinfo.gap"
1245                  (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
1246                  (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
1247                  (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
1248                (install-file "sysinfo.gap" share)
1249                (copy-recursively "grp" (string-append share "/grp"))
1250                (copy-recursively "pkg" (string-append share "/pkg"))
1251                ;; The following is not the C library libgap.so, but a
1252                ;; library of GAP code.
1253                (copy-recursively "lib" (string-append share "/lib"))
1254                ;; The gap binary looks for documentation inside SHARE.
1255                (copy-recursively "doc" (string-append share "/doc")))
1256              #t)))))
1257     (home-page "https://www.gap-system.org/")
1258     (synopsis
1259      "System for computational group theory")
1260     (description
1261      "GAP is a system for computational discrete algebra, with particular
1262 emphasis on computational group theory.  It provides a programming language,
1263 a library of thousands of functions implementing algebraic algorithms
1264 written in the GAP language as well as large data libraries of algebraic
1265 objects.")
1266     ;; Some packages have different licenses (effectively forcing the
1267     ;; combined work to be licensed as gpl3+); if this is the case, this
1268     ;; is mentioned above next to their name.
1269     ;; Some packages have no license mentioned explicitly; supposedly this
1270     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
1271     ;; safe side, we drop them for now.
1272     (license license:gpl2+)))
1273
1274 (define-public givaro
1275   (package
1276     (name "givaro")
1277     (version "4.1.1")
1278     (source (origin
1279               (method git-fetch)
1280               (uri (git-reference
1281                     (url "https://github.com/linbox-team/givaro")
1282                     (commit (string-append "v" version))))
1283               (file-name (git-file-name name version))
1284               (sha256
1285                (base32
1286                 "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
1287     (build-system gnu-build-system)
1288     (native-inputs
1289      `(("autoconf" ,autoconf)
1290        ("automake" ,automake)
1291        ("libtool" ,libtool)))
1292     (propagated-inputs
1293      `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
1294     (synopsis "Algebraic computations with exact rings and fields")
1295     (description
1296      "Givaro is a C++ library implementing the basic arithmetic of various
1297 algebraic objects: prime fields, extension fields, finite fields, finite
1298 rings, polynomials, algebraic numbers, arbitrary precision integers and
1299 rationals (C++ wrappers over gmp), fixed precision integers.  It also
1300 provides data-structures and templated classes for the manipulation of
1301 compound objects, such as vectors, matrices and univariate polynomials.")
1302     (license license:cecill-b)
1303     (home-page "https://github.com/linbox-team/givaro")))
1304
1305 (define-public fflas-ffpack
1306   (package
1307     (name "fflas-ffpack")
1308     (version "2.4.3")
1309     (source (origin
1310               (method git-fetch)
1311               (uri (git-reference
1312                     (url "https://github.com/linbox-team/fflas-ffpack")
1313                     (commit version)))
1314               (file-name (git-file-name name version))
1315               (sha256
1316                (base32
1317                 "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
1318     (build-system gnu-build-system)
1319     (native-inputs
1320      `(("autoconf" ,autoconf)
1321        ("automake" ,automake)
1322        ("libtool" ,libtool)
1323        ("pkg-config" ,pkg-config)))
1324     (inputs
1325      `(("openblas" ,openblas)))
1326     (propagated-inputs
1327      `(("givaro" ,givaro))) ; required according to the .pc file
1328     (arguments
1329      `(#:configure-flags
1330        (list (string-append "--with-blas-libs="
1331                             (assoc-ref %build-inputs "openblas")
1332                             "/lib/libopenblas.so"))))
1333     (synopsis "C++ library for linear algebra over finite fields")
1334     (description
1335      "FFLAS-FFPACK is a C++ template library for basic linear algebra
1336 operations over a finite field.
1337 FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
1338 of a subset of routines of the numerical BLAS; it also supports sparse
1339 matrix-vector products.
1340 FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
1341 library to provide functionalities of higher level, using the kernel
1342 of a BLAS.  Additionally, it provides routines specific to exact linear
1343 algebra, such as the row echelon form.")
1344     (license license:lgpl2.1+)
1345     (home-page "https://linbox-team.github.io/fflas-ffpack/")))
1346
1347 (define-public linbox
1348   (package
1349     (name "linbox")
1350     (version "1.6.3")
1351     (source (origin
1352               (method git-fetch)
1353               (uri (git-reference
1354                     (url "https://github.com/linbox-team/linbox")
1355                     (commit (string-append "v" version))))
1356               (file-name (git-file-name name version))
1357               (sha256
1358                (base32
1359                 "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
1360     (build-system gnu-build-system)
1361     (native-inputs
1362      `(("autoconf" ,autoconf)
1363        ("automake" ,automake)
1364        ("libtool" ,libtool)
1365        ("pkg-config" ,pkg-config)))
1366     (inputs
1367      `(("fflas-ffpack" ,fflas-ffpack)))
1368     (synopsis "C++ library for linear algebra over exact rings")
1369     (description
1370      "LinBox is a C++ template library for exact linear algebra computation
1371 with dense, sparse, and structured matrices over the integers and over
1372 finite fields.")
1373     (license license:lgpl2.1+)
1374     (home-page "https://linbox-team.github.io/linbox/")))
1375
1376 (define-public m4ri
1377   (package
1378     (name "m4ri")
1379     (version "20140914")
1380     (source (origin
1381               (method git-fetch)
1382               (uri (git-reference
1383                     (url "https://bitbucket.org/malb/m4ri")
1384                     (commit (string-append "release-" version))))
1385               (file-name (git-file-name name version))
1386               (sha256
1387                (base32
1388                 "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
1389     (build-system gnu-build-system)
1390     (native-inputs
1391      `(("autoconf" ,autoconf)
1392        ("automake" ,automake)
1393        ("libtool" ,libtool)
1394        ("pkg-config" ,pkg-config)))
1395     (inputs
1396      `(("libpng" ,libpng)))
1397     (synopsis "Arithmetic of dense matrices over F_2")
1398     (description "M4RI is a library for fast arithmetic with dense matrices
1399 over F2.  The name M4RI comes from the first implemented algorithm: The
1400 Method of the Four Russians inversion algorithm published by Gregory Bard.
1401 This algorithm in turn is named after the Method of the Four Russians
1402 multiplication algorithm.")
1403     (license license:gpl2+)
1404     (home-page "https://bitbucket.org/malb/m4ri/")))
1405
1406 (define-public symmetrica
1407   (package
1408     (name "symmetrica")
1409     (version "2.0")
1410     (source (origin
1411               (method url-fetch/tarbomb)
1412               (uri (let ((v (string-join (string-split version #\.) "_")))
1413                      (string-append "http://www.algorithm.uni-bayreuth.de/"
1414                                     "en/research/SYMMETRICA/"
1415                                     "SYM" v "_tar.gz")))
1416               (sha256
1417                (base32
1418                 "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
1419               ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
1420               (patches (search-patches "symmetrica-bruch.patch"
1421                                        "symmetrica-int32.patch"
1422                                        "symmetrica-return_values.patch"
1423                                        "symmetrica-sort_sum_rename.patch"))))
1424     (build-system gnu-build-system)
1425     (arguments
1426      `(#:tests? #f                      ;no test
1427        #:phases
1428        (modify-phases %standard-phases
1429          (add-after 'unpack 'fix-makefile
1430            (lambda _
1431              (substitute* "makefile"
1432                (("cc -c") "gcc -c -fPIC"))
1433              #t))
1434          (add-after 'fix-makefile 'turn-off-banner
1435            (lambda _
1436              (substitute* "de.c"
1437                (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
1438              #t))
1439          (delete 'configure)            ;no configure script
1440          (replace 'install              ;no install target
1441            (lambda* (#:key outputs #:allow-other-keys)
1442              (let* ((out (assoc-ref outputs "out"))
1443                     (lib (string-append out "/lib"))
1444                     (inc (string-append out "/include/symmetrica"))
1445                     (doc (string-append out "/share/doc/symmetrica-" ,version))
1446                     (static "libsymmetrica.a"))
1447                ;; Build static library.
1448                (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
1449                (invoke "ranlib" static)
1450                ;; Install static library and headers.
1451                (for-each (lambda (f) (install-file f inc))
1452                          (find-files "." "\\.h$"))
1453                (install-file "libsymmetrica.a" lib)
1454                ;; Install documentation.
1455                (for-each (lambda (f) (install-file f doc))
1456                          (find-files "." "\\.doc$"))
1457                #t))))))
1458     (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
1459     (synopsis "Combinatoric C Library")
1460     (description "Symmetrica is a library for combinatorics.  It has support
1461 for the representation theory of the symmetric group and related groups,
1462 combinatorics of tableaux, symmetric functions and polynomials, Schubert
1463 polynomials, and the representation theory of Hecke algebras of type A_n.")
1464     (license license:public-domain)))
1465
1466 (define-public m4rie
1467   (package
1468     (name "m4rie")
1469     (version "20150908")
1470     (source (origin
1471               (method git-fetch)
1472               (uri (git-reference
1473                     (url "https://bitbucket.org/malb/m4rie")
1474                     (commit (string-append "release-" version))))
1475               (file-name (git-file-name name version))
1476               (sha256
1477                (base32
1478                 "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
1479     (build-system gnu-build-system)
1480     (native-inputs
1481      `(("autoconf" ,autoconf)
1482        ("automake" ,automake)
1483        ("libtool" ,libtool)))
1484     (inputs
1485      `(("m4ri" ,m4ri)))
1486     (synopsis "Arithmetic of dense matrices over F_{2^e}")
1487     (description "M4RI is a library for fast arithmetic with dense matrices
1488 over finite fields of characteristic 2.  So it extends the functionality
1489 of M4RI from F_2 to F_{2^e}.")
1490     (license license:gpl2+)
1491     (home-page "https://bitbucket.org/malb/m4rie/")))
1492
1493 (define-public eclib
1494   (package
1495     (name "eclib")
1496     (version "20190909")
1497     (source (origin
1498               (method git-fetch)
1499               (uri (git-reference
1500                     (url "https://github.com/JohnCremona/eclib/")
1501                     (commit (string-append "v" version))))
1502               (file-name (git-file-name name version))
1503               (sha256
1504                (base32
1505                 "1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n"))))
1506     (build-system gnu-build-system)
1507     (native-inputs
1508      `(("autoconf" ,autoconf)
1509        ("automake" ,automake)
1510        ("libtool" ,libtool)))
1511     (inputs
1512      `(("ntl" ,ntl)
1513        ("pari-gp" ,pari-gp)))
1514     (synopsis "Ranks of elliptic curves and modular symbols")
1515     (description "The eclib package includes mwrank (for 2-descent on
1516 elliptic curves over Q) and modular symbol code; it has been written by
1517 John Cremona to compute his elliptic curve database.")
1518     (license license:gpl2+)
1519     (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
1520                               "J.E.Cremona/mwrank/index.html"))))
1521
1522 (define-public lrcalc
1523   (package
1524     (name "lrcalc")
1525     (version "1.2")
1526     (source (origin
1527               (method git-fetch)
1528               (uri (git-reference
1529                     (url "https://bitbucket.org/asbuch/lrcalc")
1530                     (commit (string-append "lrcalc-" version))))
1531               (file-name (git-file-name name version))
1532               (sha256
1533                (base32
1534                 "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
1535               (patches (search-patches "lrcalc-includes.patch"))))
1536     (build-system gnu-build-system)
1537     (native-inputs
1538      `(("autoconf" ,autoconf)
1539        ("automake" ,automake)
1540        ("libtool" ,libtool)))
1541     (arguments
1542      `(#:phases
1543        (modify-phases %standard-phases
1544          (add-before 'build 'fix-permission
1545            (lambda _
1546              (chmod "lrcalc.maple.src" #o644)
1547              #t)))))
1548     (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
1549     (description "The Littlewood-Richardson Calculator (lrcalc) is a
1550 program designed to compute Littlewood-Richardson coefficients.  It computes
1551 single Littlewood-Richardson coefficients, products of Schur functions, or
1552 skew Schur functions.  In addition it computes products in the small quantum
1553 cohomology ring of a Grassmann variety.  The software package also includes
1554 a program that performs fast computation of the more general multiplicative
1555 structure constants of Schubert polynomials.")
1556     (license license:gpl2+)
1557     (home-page "https://sites.math.rutgers.edu/~asbuch/lrcalc/")))
1558
1559 (define-public iml
1560   (package
1561     (name "iml")
1562     (version "1.0.5")
1563     (source
1564      (origin
1565        (method url-fetch)
1566        (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
1567                            version ".tar.bz2"))
1568        (sha256
1569         (base32
1570          "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
1571     (build-system gnu-build-system)
1572     (inputs
1573      `(("gmp", gmp)
1574        ("cblas" ,openblas))) ; or any other BLAS library; the documentation
1575                              ; mentions ATLAS in particular
1576     (arguments
1577      `(#:configure-flags
1578        (list
1579         "--enable-shared"
1580         (string-append "--with-gmp-include="
1581                        (assoc-ref %build-inputs "gmp") "/include")
1582         (string-append "--with-gmp-lib="
1583                        (assoc-ref %build-inputs "gmp") "/lib")
1584         "--with-cblas=-lopenblas"
1585         (string-append "--with-cblas-include="
1586                        (assoc-ref %build-inputs "cblas") "/include")
1587         (string-append "--with-cblas-lib="
1588                        (assoc-ref %build-inputs "cblas") "/lib"))))
1589     (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
1590     (synopsis
1591      "Solver for systems of linear equations over the integers")
1592     (description
1593      "IML is a C library implementing algorithms for computing exact
1594 solutions to dense systems of linear equations over the integers.
1595 Currently, IML provides the following functionality:
1596
1597 @itemize
1598 @item Nonsingular rational system solving:
1599 compute the unique rational solution X to the system AX=B, where A and B
1600 are integer matrices, A nonsingular.
1601 @item Compute the right nullspace or kernel of an integer matrix.
1602 @item Certified linear system solving:
1603 compute a minimal denominator solution x to a system Ax=b, where b is an
1604 integer vector and A is an integer matrix with arbitrary shape and
1605 rank profile.
1606 @end itemize
1607
1608 In addition, IML provides some low level routines for a variety of mod p
1609 matrix operations: computing the row-echelon form, determinant, rank
1610 profile, and inverse of a mod p matrix. These mod p routines are not
1611 general purpose; they require that p satisfy some preconditions based on
1612 the dimension of the input matrix (usually p should be prime and should be
1613 no more than about 20 bits long).")
1614     (license license:bsd-3)))