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 ;;;
  14 ;;; This file is part of GNU Guix.
  15 ;;;
  16 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  17 ;;; under the terms of the GNU General Public License as published by
  18 ;;; the Free Software Foundation; either version 3 of the License, or (at
  19 ;;; your option) any later version.
  20 ;;;
  21 ;;; GNU Guix is distributed in the hope that it will be useful, but
  22 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  23 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  24 ;;; GNU General Public License for more details.
  25 ;;;
  26 ;;; You should have received a copy of the GNU General Public License
  27 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  28
  29 (define-module (gnu packages algebra)
  30   #:use-module (gnu packages)
  31   #:use-module (gnu packages autotools)
  32   #:use-module (gnu packages bison)
  33   #:use-module (gnu packages check)
  34   #:use-module (gnu packages compression)
  35   #:use-module (gnu packages cpp)
  36   #:use-module (gnu packages documentation)
  37   #:use-module (gnu packages ed)
  38   #:use-module (gnu packages flex)
  39   #:use-module (gnu packages fltk)
  40   #:use-module (gnu packages gl)
  41   #:use-module (gnu packages graphviz)
  42   #:use-module (gnu packages image)
  43   #:use-module (gnu packages java)
  44   #:use-module (gnu packages maths)
  45   #:use-module (gnu packages mpi)
  46   #:use-module (gnu packages multiprecision)
  47   #:use-module (gnu packages perl)
  48   #:use-module (gnu packages pkg-config)
  49   #:use-module (gnu packages pulseaudio)
  50   #:use-module (gnu packages python)
  51   #:use-module (gnu packages python-xyz)
  52   #:use-module (gnu packages readline)
  53   #:use-module (gnu packages shells)
  54   #:use-module (gnu packages tex)
  55   #:use-module (gnu packages texinfo)
  56   #:use-module (gnu packages xiph)
  57   #:use-module (gnu packages xorg)
  58   #:use-module (guix build-system ant)
  59   #:use-module (guix build-system gnu)
  60   #:use-module (guix build-system cmake)
  61   #:use-module (guix build-system python)
  62   #:use-module (guix download)
  63   #:use-module (guix git-download)
  64   #:use-module (guix hg-download)
  65   #:use-module ((guix licenses) #:prefix license:)
  66   #:use-module (guix packages)
  67   #:use-module (guix utils))
  68
  69
  70 (define-public mpfrcx
  71   (package
  72    (name "mpfrcx")
  73    (version "0.5")
  74    (source (origin
  75             (method url-fetch)
  76             (uri (string-append
  77                   "http://www.multiprecision.org/downloads/mpfrcx-"
  78                   version ".tar.gz"))
  79             (sha256
  80              (base32
  81               "1s968480ymv6w0rnvfp9mxvx98hvi29fkvw8nk4ggzc6azxgwybs"))))
  82    (build-system gnu-build-system)
  83    (propagated-inputs
  84      `(("gmp" ,gmp)
  85        ("mpfr" ,mpfr)
  86        ("mpc"  ,mpc))) ; Header files are included by mpfrcx.h.
  87    (synopsis "Arithmetic of polynomials over arbitrary precision numbers")
  88    (description
  89     "Mpfrcx is a library for the arithmetic of univariate polynomials over
  90 arbitrary precision real (mpfr) or complex (mpc) numbers, without control
  91 on the rounding.  For the time being, only the few functions needed to
  92 implement the floating point approach to complex multiplication are
  93 implemented.  On the other hand, these comprise asymptotically fast
  94 multiplication routines such as Toom–Cook and the FFT.")
  95    (license license:lgpl3+)
  96    (home-page "http://www.multiprecision.org/mpfrcx/")))
  97
  98 (define-public gf2x
  99   (package
 100    (name "gf2x")
 101    (version "1.2")
 102    (source (origin
 103             (method url-fetch)
 104             (uri (string-append
 105                   "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-"
 106                   version ".tar.gz"))
 107             (sha256
 108              (base32
 109               "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1"))))
 110    (build-system gnu-build-system)
 111    (synopsis "Arithmetic of polynomials over binary finite fields")
 112    (description
 113     "The gf2x library provides arithmetic of polynomials over finite fields
 114 of characteristic 2.  It implements the multiplication, squaring and
 115 greatest common divisor operations.")
 116    (license license:gpl3+)
 117    (home-page "https://gforge.inria.fr/projects/gf2x/")))
 118
 119 (define-public cm
 120   (package
 121    (name "cm")
 122    (version "0.3")
 123    (source (origin
 124             (method url-fetch)
 125             (uri (string-append
 126                   "http://www.multiprecision.org/cm/download/cm-"
 127                   version ".tar.gz"))
 128             (sha256
 129              (base32
 130               "1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc"))))
 131    (build-system gnu-build-system)
 132    (propagated-inputs
 133      `(("mpfrcx" ,mpfrcx)
 134        ("zlib" ,zlib))) ; Header files included from cm_common.h.
 135    (inputs
 136      `(("pari-gp"  ,pari-gp)))
 137    (synopsis "CM constructions for elliptic curves")
 138    (description
 139     "The CM software implements the construction of ring class fields of
 140 imaginary quadratic number fields and of elliptic curves with complex
 141 multiplication via floating point approximations.  It consists of libraries
 142 that can be called from within a C program and of executable command
 143 line applications.")
 144    (license license:gpl3+)
 145    (home-page "http://www.multiprecision.org/cm/")))
 146
 147 (define-public fplll
 148   (package
 149     (name "fplll")
 150     (version "5.2.1")
 151     (source (origin
 152               (method git-fetch)
 153               (uri (git-reference
 154                     (url "https://github.com/fplll/fplll.git")
 155                     (commit version)))
 156               (file-name (git-file-name name version))
 157               (sha256
 158                (base32
 159                 "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg"))))
 160     (build-system gnu-build-system)
 161     (native-inputs
 162      `(("autoconf" ,autoconf)
 163        ("automake" ,automake)
 164        ("libtool" ,libtool)))
 165     (inputs
 166      `(("gmp" ,gmp)
 167        ("mpfr" ,mpfr)))
 168     (home-page "https://github.com/fplll/fplll")
 169     (synopsis "Library for LLL-reduction of euclidean lattices")
 170     (description
 171      "fplll contains implementations of several lattice algorithms.
 172 The implementation relies on floating-point orthogonalization, and LLL
 173 is central to the code, hence the name.
 174
 175 It includes implementations of floating-point LLL reduction
 176 algorithms, offering different speed/guarantees ratios.  It contains
 177 a @emph{wrapper} choosing the estimated best sequence of variants in
 178 order to provide a guaranteed output as fast as possible.  In the case
 179 of the wrapper, the succession of variants is oblivious to the user.
 180
 181 It includes an implementation of the BKZ reduction algorithm,
 182 including the BKZ-2.0 improvements (extreme enumeration
 183 pruning, pre-processing of blocks, early termination).  Additionally,
 184 Slide reduction and self dual BKZ are supported.
 185
 186 It also includes a floating-point implementation of the
 187 Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice
 188 vector.  For the same task, the GaussSieve algorithm is also available
 189 in fplll.  Finally, it contains a variant of the enumeration algorithm
 190 that computes a lattice vector closest to a given vector belonging to
 191 the real span of the lattice.")
 192     (license license:lgpl2.1+)))
 193
 194 (define-public python-fpylll
 195   (package
 196     (name "python-fpylll")
 197     (version "0.4.1")
 198     (source
 199      (origin
 200        ;; Pypi contains and older release, so we use a tagged release from
 201        ;; Github instead.
 202        (method git-fetch)
 203        (uri (git-reference
 204              (url "https://github.com/fplll/fpylll.git")
 205              (commit (string-append version "dev"))))
 206        (file-name (git-file-name name version))
 207        (sha256
 208         (base32
 209          "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
 210     (build-system python-build-system)
 211     (inputs
 212      `(("fplll" ,fplll)
 213        ("gmp" ,gmp)
 214        ("mpfr" ,mpfr)
 215        ("pari-gp" ,pari-gp)))
 216     (propagated-inputs
 217      `(("cysignals" ,python-cysignals)
 218        ("cython" ,python-cython)
 219        ("flake8" ,python-flake8)
 220        ("numpy" ,python-numpy)
 221        ("pytest" ,python-pytest)))
 222     (home-page "https://github.com/fplll/fpylll")
 223     (synopsis "Python interface for fplll")
 224     (description "fpylll is a Python wrapper for fplll.")
 225     (license license:gpl2+)))
 226
 227 (define-public pari-gp
 228   (package
 229     (name "pari-gp")
 230     (version "2.11.2")
 231     (source (origin
 232               (method url-fetch)
 233               (uri (string-append
 234                     "https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
 235                     version ".tar.gz"))
 236               (sha256
 237                (base32
 238                 "0fck8ssmirl8fy7s4mspgrxjs5sag76xbshqlqzkcl3kqyrk4raa"))))
 239     (build-system gnu-build-system)
 240     (native-inputs
 241      `(("texlive" ,(texlive-union
 242                     (list texlive-amsfonts)))))
 243     (inputs `(("gmp" ,gmp)
 244               ("libx11" ,libx11)
 245               ("perl" ,perl)
 246               ("readline" ,readline)))
 247     (arguments
 248      '(#:make-flags '("all")
 249        #:test-target "dobench"
 250        #:phases
 251        (modify-phases %standard-phases
 252          (replace 'configure
 253            (lambda* (#:key outputs #:allow-other-keys)
 254              (invoke "./Configure"
 255                      (string-append "--prefix="
 256                                     (assoc-ref outputs "out"))))))))
 257     (synopsis "PARI/GP, a computer algebra system for number theory")
 258     (description
 259      "PARI/GP is a widely used computer algebra system designed for fast
 260 computations in number theory (factorisations, algebraic number theory,
 261 elliptic curves...), but it also contains a large number of other useful
 262 functions to compute with mathematical entities such as matrices,
 263 polynomials, power series, algebraic numbers, etc., and a lot of
 264 transcendental functions.
 265 PARI is also available as a C library to allow for faster computations.")
 266     (license license:gpl2+)
 267     (home-page "https://pari.math.u-bordeaux.fr/")))
 268
 269 (define-public gp2c
 270   (package
 271    (name "gp2c")
 272    (version "0.0.11pl2")
 273    (source (origin
 274             (method url-fetch)
 275             (uri (string-append
 276                   "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
 277                   version ".tar.gz"))
 278             (sha256
 279               (base32
 280                 "0wqsf05wgkqvmmsx7jinvzdqav6rl56sr8haibgs31nzz4x9xz9g"))))
 281    (build-system gnu-build-system)
 282    (native-inputs `(("perl" ,perl)))
 283    (inputs `(("pari-gp" ,pari-gp)))
 284    (arguments
 285     '(#:configure-flags
 286       (list (string-append "--with-paricfg="
 287                            (assoc-ref %build-inputs "pari-gp")
 288                            "/lib/pari/pari.cfg"))))
 289    (synopsis "PARI/GP, a computer algebra system for number theory")
 290    (description
 291     "PARI/GP is a widely used computer algebra system designed for fast
 292 computations in number theory (factorisations, algebraic number theory,
 293 elliptic curves...), but it also contains a large number of other useful
 294 functions to compute with mathematical entities such as matrices,
 295 polynomials, power series, algebraic numbers, etc., and a lot of
 296 transcendental functions.
 297 PARI is also available as a C library to allow for faster computations.
 298
 299 GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
 300    (license license:gpl2)
 301    (home-page "https://pari.math.u-bordeaux.fr/")))
 302
 303 (define fplll-4-cmh
 304   (package
 305     (inherit fplll)
 306     (name "fplll")
 307     (version "4.0.4")
 308     (source
 309      (origin
 310        (method url-fetch)
 311        (uri (string-append
 312              "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
 313              version ".tar.gz"))
 314        (sha256
 315         (base32 "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))))
 316
 317 (define-public cmh
 318   (package
 319    (name "cmh")
 320    (version "1.0")
 321    (source (origin
 322             (method url-fetch)
 323             (uri (string-append
 324                   "https://gforge.inria.fr/frs/download.php/33497/cmh-"
 325                   version ".tar.gz"))
 326             (sha256
 327              (base32
 328               "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
 329    (build-system gnu-build-system)
 330    (inputs
 331      `(("gmp" ,gmp)
 332        ("mpfr" ,mpfr)
 333        ("mpc" ,mpc)
 334        ("mpfrcx" ,mpfrcx)
 335        ("fplll" ,fplll-4-cmh)
 336        ("pari-gp"  ,pari-gp)))
 337    (synopsis "Igusa class polynomial computations")
 338    (description
 339     "The CMH software computes Igusa (genus 2) class polynomials, which
 340 parameterize the CM points in the moduli space of 2-dimensional abelian
 341 varieties, i.e. Jacobians of hyperelliptic curves.
 342 It can also be used to compute theta constants at arbitrary
 343 precision.")
 344    (license license:gpl3+)
 345    (home-page "http://cmh.gforge.inria.fr/")))
 346
 347 (define-public giac
 348   (package
 349     (name "giac")
 350     (version "1.5.0-87")
 351     (source
 352      (origin
 353        (method url-fetch)
 354        ;; "~parisse/giac" is not used because the maintainer regularly
 355        ;; overwrites the release tarball there, introducing a checksum
 356        ;; mismatch every time.  See
 357        ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
 358        (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
 359                            "~parisse/debian/dists/stable/main/source/"
 360                            "giac_" version ".tar.gz"))
 361        (sha256
 362         (base32 "1d0h1yb7qvh9x7wwv9yrzmcp712f49w1iljkxp4y6g9pzsmg1mmv"))))
 363     (build-system gnu-build-system)
 364     (arguments
 365      `(#:modules ((ice-9 ftw)
 366                   (guix build utils)
 367                   (guix build gnu-build-system))
 368        #:phases
 369        (modify-phases %standard-phases
 370          (add-after 'unpack 'patch-bin-cp
 371            ;; Some Makefiles contain hard-coded "/bin/cp".
 372            (lambda _
 373              (substitute* (find-files "doc" "^Makefile")
 374                (("/bin/cp") (which "cp")))
 375              #t))
 376          (add-after 'unpack 'disable-failing-test
 377            ;; FIXME: Test failing.  Not sure why.
 378            (lambda _
 379              (substitute* "check/Makefile.in"
 380                (("chk_fhan11") ""))
 381              #t))
 382          (add-after 'install 'fix-doc
 383            (lambda* (#:key outputs #:allow-other-keys)
 384              (let ((out (assoc-ref outputs "out")))
 385                ;; Most French documentation has a non-commercial
 386                ;; license, so we need to remove it.
 387                (with-directory-excursion (string-append out "/share/giac/doc/fr")
 388                  (for-each delete-file-recursively
 389                            '("cascas" "casexo" "casgeo" "casrouge" "cassim"
 390                              "castor")))
 391                ;; Remove duplicate documentation in
 392                ;; "%out/share/doc/giac/", where Xcas does not expect
 393                ;; to find it.
 394                (delete-file-recursively (string-append out "/share/doc/giac"))
 395                #t)))
 396          (add-after 'install 'remove-unnecessary-executable
 397            (lambda* (#:key outputs #:allow-other-keys)
 398              (let ((out (assoc-ref outputs "out")))
 399                (delete-file (string-append out "/bin/xcasnew"))
 400                #t))))))
 401     (inputs
 402      ;;; TODO: Add libnauty.
 403      `(("fltk" ,fltk)
 404        ("glpk" ,glpk)
 405        ("gmp" ,gmp)
 406        ("gsl" ,gsl)
 407        ("lapack" ,lapack)
 408        ("libao" ,ao)
 409        ("libjpeg" ,libjpeg-turbo)
 410        ("libpng" ,libpng)
 411        ("libsamplerate" ,libsamplerate)
 412        ("libx11" ,libx11)
 413        ("libxinerama" ,libxinerama)
 414        ("libxft" ,libxft)
 415        ("libxt" ,libxt)
 416        ("mesa" ,mesa)
 417        ("mpfi" ,mpfi)
 418        ("mpfr" ,mpfr)
 419        ("ntl" ,ntl)
 420        ("perl" ,perl)
 421        ("pari-gp" ,pari-gp)
 422        ("tcsh" ,tcsh)))
 423     (native-inputs
 424      `(("bison" ,bison)
 425        ("flex" ,flex)
 426        ("readline" ,readline)
 427        ("texlive" ,texlive-tiny)))
 428     (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
 429     (synopsis "Computer algebra system")
 430     (description
 431      "Giac/Xcas is a computer algebra system.  It has a compatibility mode for
 432 maple, mupad and the TI89.  It is available as a standalone program (graphic
 433 or text interfaces) or as a C++ library.")
 434     (license license:gpl3+)))
 435
 436 (define-public giac-xcas
 437   (deprecated-package "giac-xcas" giac))
 438
 439 (define-public flint
 440   (package
 441    (name "flint")
 442    (version "2.5.2")
 443    (source (origin
 444             (method url-fetch)
 445             (uri (string-append
 446                   "http://flintlib.org/flint-"
 447                   version ".tar.gz"))
 448             (sha256 (base32
 449                      "11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
 450             (patches (search-patches "flint-ldconfig.patch"))))
 451    (build-system gnu-build-system)
 452    (propagated-inputs
 453     `(("gmp" ,gmp)
 454       ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
 455    (arguments
 456     `(#:parallel-tests? #f ; seems to be necessary on arm
 457       #:phases
 458        (modify-phases %standard-phases
 459          (replace 'configure
 460            (lambda* (#:key inputs outputs #:allow-other-keys)
 461              (let ((out (assoc-ref outputs "out"))
 462                    (gmp (assoc-ref inputs "gmp"))
 463                    (mpfr (assoc-ref inputs "mpfr")))
 464                ;; do not pass "--enable-fast-install", which makes the
 465                ;; homebrew configure process fail
 466                (invoke "./configure"
 467                        (string-append "--prefix=" out)
 468                        (string-append "--with-gmp=" gmp)
 469                        (string-append "--with-mpfr=" mpfr))
 470                #t))))))
 471    (synopsis "Fast library for number theory")
 472    (description
 473     "FLINT is a C library for number theory.  It supports arithmetic
 474 with numbers, polynomials, power series and matrices over many base
 475 rings, including multiprecision integers and rationals, integers
 476 modulo n, p-adic numbers, finite fields (prime and non-prime order)
 477 and real and complex numbers (via the Arb extension library).
 478
 479 Operations that can be performed include conversions, arithmetic,
 480 GCDs, factoring, solving linear systems, and evaluating special
 481 functions.  In addition, FLINT provides various low-level routines for
 482 fast arithmetic.")
 483    (license license:gpl2+)
 484    (home-page "http://flintlib.org/")))
 485
 486 (define-public arb
 487   (package
 488     (name "arb")
 489     (version "2.17.0")
 490     (source (origin
 491               (method git-fetch)
 492               (uri (git-reference
 493                     (url "https://github.com/fredrik-johansson/arb.git")
 494                     (commit version)))
 495               (file-name (git-file-name name version))
 496               (sha256
 497                (base32
 498                 "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1"))))
 499     (build-system gnu-build-system)
 500     (propagated-inputs
 501      `(("flint" ,flint)))               ; flint.h is included by arf.h
 502     (inputs
 503      `(("gmp" ,gmp)
 504        ("mpfr" ,mpfr)))
 505     (arguments
 506      `(#:phases
 507        (modify-phases %standard-phases
 508          (replace 'configure
 509            (lambda* (#:key inputs outputs #:allow-other-keys)
 510              (let ((out (assoc-ref outputs "out"))
 511                    (flint (assoc-ref inputs "flint"))
 512                    (gmp (assoc-ref inputs "gmp"))
 513                    (mpfr (assoc-ref inputs "mpfr")))
 514                ;; Do not pass "--enable-fast-install", which makes the
 515                ;; homebrew configure process fail.
 516                (invoke "./configure"
 517                        (string-append "--prefix=" out)
 518                        (string-append "--with-flint=" flint)
 519                        (string-append "--with-gmp=" gmp)
 520                        (string-append "--with-mpfr=" mpfr))))))))
 521     (synopsis "Arbitrary precision floating-point ball arithmetic")
 522     (description
 523      "Arb is a C library for arbitrary-precision floating-point ball
 524 arithmetic.  It supports efficient high-precision computation with
 525 polynomials, power series, matrices and special functions over the
 526 real and complex numbers, with automatic, rigorous error control.")
 527     (license license:lgpl2.1+)
 528     (home-page "http://arblib.org")))
 529
 530 (define-public python-flint
 531   (package
 532     (name "python-flint")
 533     (version "0.3.0")
 534     (source (origin
 535               (method git-fetch)
 536               (uri (git-reference
 537                     (url "https://github.com/fredrik-johansson/python-flint.git")
 538                     (commit version)))
 539               (file-name (git-file-name name version))
 540               (sha256
 541                (base32
 542                 "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
 543               (patches (search-patches "python-flint-includes.patch"))))
 544     (build-system python-build-system)
 545     (native-inputs
 546      `(("python-cython" ,python-cython)))
 547     (propagated-inputs
 548      `(("python-numpy" ,python-numpy)))
 549     (inputs
 550      `(("arb" ,arb)
 551        ("flint" ,flint)))
 552     (synopsis "Python module wrapping ARB and FLINT")
 553     (description
 554      "Python-flint is a Python extension module wrapping FLINT
 555 (Fast Library for Number Theory) and Arb (arbitrary-precision ball
 556 arithmetic).  It supports integers, rationals, modular integers,
 557 real and complex ball arithmetic, polynomials and matrices over all
 558 these types and other mathematical functions.")
 559     (license license:expat)
 560     (home-page "http://fredrikj.net/python-flint/")))
 561
 562 (define-public ntl
 563   (package
 564    (name "ntl")
 565    (version "9.7.0")
 566    (source (origin
 567             (method url-fetch)
 568             (uri (string-append "http://shoup.net/ntl/ntl-"
 569                                 version ".tar.gz"))
 570             (sha256 (base32
 571                      "115frp5flyvw9wghz4zph1b3llmr5nbxk1skgsggckr81fh3gmxq"))))
 572    (build-system gnu-build-system)
 573    (native-inputs
 574     `(("libtool" ,libtool)
 575       ("perl" ,perl))) ; for configuration
 576    ;; FIXME: Add optional input gf2x once available; then also add
 577    ;; configure flag "NTL_GF2X_LIB=on".
 578    (inputs
 579     `(("gmp" ,gmp)))
 580    (arguments
 581     `(#:phases
 582       (modify-phases %standard-phases
 583         (replace 'configure
 584          (lambda* (#:key outputs #:allow-other-keys)
 585            (chdir "src")
 586            (system* "./configure"
 587                     (string-append "PREFIX=" (assoc-ref outputs "out"))
 588                     ;; Do not build especially for the build machine.
 589                     "NATIVE=off"
 590                     ;; Also do not tune to the build machine.
 591                     "WIZARD=off"
 592                     "SHARED=on")
 593            #t)))))
 594    (synopsis "C++ library for number theory")
 595    (description
 596     "NTL is a C++ library providing data structures and algorithms
 597 for manipulating signed, arbitrary length integers, and for vectors,
 598 matrices, and polynomials over the integers and over finite fields.")
 599    (license license:gpl2+)
 600    (home-page "http://shoup.net/ntl/")))
 601
 602 (define-public singular
 603   (package
 604    (name "singular")
 605    (version "4.1.2p1")
 606    (source
 607     (origin
 608       (method url-fetch)
 609       (uri
 610        (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
 611                       "Singular/SOURCES/"
 612                       (string-join
 613                        (string-split
 614                         (string-trim-right version #\p
 615                                            0 (1- (string-length version)))
 616                         #\.) "-")
 617                       "/singular-" version ".tar.gz"))
 618              (sha256 (base32
 619                       "0kvd55353fiqyq1msmi0kka66n5h0aqs7m3km60r01b1w2f8085m"))))
 620    (build-system gnu-build-system)
 621    (native-inputs
 622     `(("doxygen" ,doxygen)
 623       ("graphviz" ,graphviz)
 624       ("perl" ,perl)))
 625    (inputs
 626     `(("cddlib" ,cddlib)
 627       ("gmp" ,gmp)
 628       ("flint" ,flint)
 629       ("mpfr" ,mpfr)
 630       ("ntl" ,ntl)
 631       ("python" ,python-2)
 632       ("readline" ,readline)))
 633    (arguments
 634     `(#:configure-flags
 635       (list (string-append "--with-ntl="
 636                            (assoc-ref %build-inputs "ntl")))))
 637    (synopsis "Computer algebra system for polynomial computations")
 638    (description
 639     "Singular is a computer algebra system for polynomial computations,
 640 with special emphasis on commutative and non-commutative algebra, algebraic
 641 geometry and singularity theory.")
 642    ;; Singular itself is dual licensed gpl2 or gpl3, but some of the
 643    ;; libraries with which it links are licensed under lgpl3+, so the
 644    ;; combined work becomes gpl3. See COPYING in the source code.
 645    (license license:gpl3)
 646    (home-page "http://www.singular.uni-kl.de/index.php")))
 647
 648 (define-public gmp-ecm
 649   (package
 650    (name "gmp-ecm")
 651    (version "7.0.4")
 652    (source (origin
 653              (method url-fetch)
 654              ;; Use the ‘Latest version’ link for a stable URI across releases.
 655              (uri (string-append "https://gforge.inria.fr/frs/download.php/"
 656                                  "latestfile/160/ecm-" version ".tar.gz"))
 657              (sha256 (base32
 658                       "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"))))
 659    (build-system gnu-build-system)
 660    (inputs
 661     `(("gmp" ,gmp)))
 662    (arguments
 663     `(#:configure-flags '("--enable-shared"
 664                           ;; Disable specific assembly routines, which depend
 665                           ;; on the subarchitecture of the build machine,
 666                           ;; and use gmp instead.
 667                           "--disable-asm-redc")))
 668    (synopsis "Integer factorization library using the elliptic curve method")
 669    (description
 670     "GMP-ECM factors integers using the elliptic curve method (ECM) as well
 671 as the P-1 and P+1 algorithms.  It provides a library and a stand-alone
 672 binary.")
 673    ;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+,
 674    ;; so the combined work is under gpl3+.
 675    (license license:gpl3+)
 676    (home-page "http://ecm.gforge.inria.fr/")))
 677
 678 (define-public bc
 679   (package
 680     (name "bc")
 681     (version "1.07.1")
 682     (source (origin
 683              (method url-fetch)
 684              (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
 685              (sha256
 686               (base32
 687                "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))
 688              (patches (search-patches "bc-fix-cross-compilation.patch"))))
 689     (build-system gnu-build-system)
 690     (native-inputs
 691      `(("automake" ,automake)
 692        ("autoconf" ,autoconf)
 693        ("ed" ,ed)
 694        ("flex" ,flex)
 695        ("texinfo" ,texinfo)))
 696     (arguments
 697      '(#:configure-flags
 698        (list "--with-readline")
 699        #:phases
 700        (modify-phases %standard-phases
 701          (add-after 'unpack 'autogen
 702            (lambda _
 703              (invoke "autoreconf" "-vif"))))))
 704     (home-page "https://www.gnu.org/software/bc/")
 705     (synopsis "Arbitrary precision numeric processing language")
 706     (description
 707      "bc is an arbitrary precision numeric processing language.  It includes
 708 an interactive environment for evaluating mathematical statements.  Its
 709 syntax is similar to that of C, so basic usage is familiar.  It also includes
 710 \"dc\", a reverse-polish calculator.")
 711     (license license:gpl2+)))
 712
 713 ;; The original kiss-fft does not have a complete build system and does not
 714 ;; build any shared libraries.  This is a fork used by Extempore.
 715 (define-public kiss-fft-for-extempore
 716   (package
 717     (name "kiss-fft-for-extempore")
 718     (version "1.3.0")
 719     (source (origin
 720               (method git-fetch)
 721               (uri (git-reference
 722                     (url "https://github.com/extemporelang/kiss_fft.git")
 723                     (commit version)))
 724               (file-name (git-file-name name version))
 725               (sha256
 726                (base32
 727                 "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
 728     (build-system cmake-build-system)
 729     (arguments `(#:tests? #f)) ; no tests included
 730     ;; Extempore refuses to build on architectures other than x86_64
 731     (supported-systems '("x86_64-linux"))
 732     (home-page "https://github.com/extemporelang/kiss_fft")
 733     (synopsis "Mixed-radix Fast Fourier Transform")
 734     (description
 735      "Kiss FFT attempts to be a reasonably efficient, moderately useful FFT
 736 that can use fixed or floating data types and can easily be incorporated into
 737 a C program.")
 738     (license license:bsd-3)))
 739
 740 (define-public fftw
 741   (package
 742     (name "fftw")
 743     (version "3.3.8")
 744     (source (origin
 745              (method url-fetch)
 746              (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
 747                                  version".tar.gz"))
 748              (sha256
 749               (base32
 750                "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
 751     (build-system gnu-build-system)
 752     (arguments
 753      `(#:configure-flags
 754        '("--enable-shared" "--enable-openmp" "--enable-threads"
 755          ,@(let ((system (or (%current-target-system) (%current-system))))
 756              ;; Enable SIMD extensions for codelets.  See details at:
 757              ;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>.
 758              (cond
 759               ((string-prefix? "x86_64" system)
 760                '("--enable-sse2" "--enable-avx" "--enable-avx2"
 761                  "--enable-avx512" "--enable-avx-128-fma"))
 762               ((string-prefix? "i686" system)
 763                '("--enable-sse2"))
 764               ((string-prefix? "aarch64" system)
 765                ;; Note that fftw supports NEON on 32-bit ARM only when
 766                ;; compiled for single-precision.
 767                '("--enable-neon"))
 768               (else
 769                '())))
 770          ;; By default '-mtune=native' is used.  However, that may cause the
 771          ;; use of ISA extensions (e.g. AVX) that are not necessarily
 772          ;; available on the user's machine when that package is built on a
 773          ;; different machine.
 774          "ax_cv_c_flags__mtune_native=no")))
 775     (native-inputs `(("perl" ,perl)))
 776     (home-page "http://fftw.org")
 777     (synopsis "Computing the discrete Fourier transform")
 778     (description
 779      "FFTW is a C subroutine library for computing the discrete Fourier
 780 transform (DFT) in one or more dimensions, of arbitrary input size, and of
 781 both real and complex data (as well as of even/odd data---i.e. the discrete
 782 cosine/ sine transforms or DCT/DST).")
 783     (license license:gpl2+)))
 784
 785 (define-public fftwf
 786   (package (inherit fftw)
 787     (name "fftwf")
 788     (arguments
 789      (substitute-keyword-arguments (package-arguments fftw)
 790        ((#:configure-flags fftw-configure-flags)
 791         `(cons* "--enable-single"
 792                 ,@(if (string-prefix? "arm" (or (%current-target-system)
 793                                                 (%current-system)))
 794                       ;; fftw supports NEON on 32-bit ARM only when compiled
 795                       ;; for single-precision, so add it here.
 796                       '("--enable-neon")
 797                       '())
 798                 ,fftw-configure-flags))))
 799     (description
 800      (string-append (package-description fftw)
 801                     "  Single-precision version."))))
 802
 803 (define-public fftw-openmpi
 804   (package (inherit fftw)
 805     (name "fftw-openmpi")
 806     (inputs
 807      `(("openmpi" ,openmpi)
 808        ,@(package-inputs fftw)))
 809     (arguments
 810      (substitute-keyword-arguments (package-arguments fftw)
 811        ((#:configure-flags cf)
 812         `(cons "--enable-mpi" ,cf))
 813        ((#:phases phases '%standard-phases)
 814         `(modify-phases ,phases
 815            (add-before 'check 'mpi-setup
 816              ,%openmpi-setup)))))
 817     (description
 818      (string-append (package-description fftw)
 819                     "  With OpenMPI parallelism support."))))
 820
 821 (define-public java-la4j
 822   (package
 823     (name "java-la4j")
 824     (version "0.6.0")
 825     (source (origin
 826               (method git-fetch)
 827               (uri (git-reference
 828                     (url "https://github.com/vkostyukov/la4j.git")
 829                     (commit version)))
 830               (file-name (string-append name "-" version "-checkout"))
 831               (sha256
 832                (base32
 833                 "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
 834     (build-system ant-build-system)
 835     (arguments
 836      `(#:jar-name "la4j.jar"
 837        #:jdk ,icedtea-8
 838        #:test-exclude (list "**/Abstract*.java"
 839                             "**/MatrixTest.java"
 840                             "**/DenseMatrixTest.java"
 841                             "**/SparseMatrixTest.java"
 842                             "**/VectorTest.java"
 843                             "**/SparseVectorTest.java"
 844                             "**/DenseVectorTest.java")))
 845     (native-inputs
 846      `(("java-junit" ,java-junit)
 847        ("java-hamcrest-core" ,java-hamcrest-core)))
 848     (home-page "http://la4j.org/")
 849     (synopsis "Java library that provides Linear Algebra primitives and algorithms")
 850     (description "The la4j library is a Java library that provides Linear
 851 Algebra primitives (matrices and vectors) and algorithms.  The key features of
 852 the la4j library are:
 853
 854 @itemize
 855 @item No dependencies and tiny size
 856 @item Fluent object-oriented/functional API
 857 @item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
 858 @item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
 859 @item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
 860 @item MatrixMarket/CSV IO formats support for matrices and vectors
 861 @end itemize\n")
 862     (license license:asl2.0)))
 863
 864 (define-public java-jlargearrays
 865   (package
 866     (name "java-jlargearrays")
 867     (version "1.6")
 868     (source (origin
 869               (method url-fetch)
 870               (uri (string-append "https://repo1.maven.org/maven2/"
 871                                   "pl/edu/icm/JLargeArrays/"
 872                                   version "/JLargeArrays-" version
 873                                   "-sources.jar"))
 874               (file-name (string-append name "-" version ".jar"))
 875               (sha256
 876                (base32
 877                 "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
 878     (build-system ant-build-system)
 879     (arguments
 880      `(#:jar-name "jlargearrays.jar"
 881        #:tests? #f ; tests are not included in the release archive
 882        #:jdk ,icedtea-8))
 883     (propagated-inputs
 884      `(("java-commons-math3" ,java-commons-math3)))
 885     (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
 886     (synopsis "Library of one-dimensional arrays that can store up to 263 elements")
 887     (description "JLargeArrays is a Java library of one-dimensional arrays
 888 that can store up to 263 elements.")
 889     (license license:bsd-2)))
 890
 891 (define-public java-jtransforms
 892   (package
 893     (name "java-jtransforms")
 894     (version "3.1")
 895     (source (origin
 896               (method url-fetch)
 897               (uri (string-append "https://repo1.maven.org/maven2/"
 898                                   "com/github/wendykierp/JTransforms/"
 899                                   version "/JTransforms-" version "-sources.jar"))
 900               (sha256
 901                (base32
 902                 "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
 903     (build-system ant-build-system)
 904     (arguments
 905      `(#:jar-name "jtransforms.jar"
 906        #:tests? #f ; tests are not included in the release archive
 907        #:jdk ,icedtea-8))
 908     (propagated-inputs
 909      `(("java-commons-math3" ,java-commons-math3)
 910        ("java-jlargearrays" ,java-jlargearrays)))
 911     (home-page "https://github.com/wendykierp/JTransforms")
 912     (synopsis "Multithreaded FFT library written in pure Java")
 913     (description "JTransforms is a multithreaded FFT library written in pure
 914 Java.  Currently, four types of transforms are available: @dfn{Discrete
 915 Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
 916 Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
 917     (license license:bsd-2)))
 918
 919 (define-public eigen
 920   (package
 921     (name "eigen")
 922     (version "3.3.7")
 923     (source (origin
 924               (method url-fetch)
 925               (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
 926                                   version ".tar.bz2"))
 927               (sha256
 928                (base32
 929                 "1km3fyfzyqfdvmnl79drps3fjwnz3zbh0c7l34mfbqyvvs8cy4wz"))
 930               (file-name (string-append name "-" version ".tar.bz2"))
 931               (patches (search-patches "eigen-stabilise-sparseqr-test.patch"))
 932               (modules '((guix build utils)))
 933               (snippet
 934                ;; There are 3 test failures in the "unsupported" directory,
 935                ;; but maintainers say it's a known issue and it's unsupported
 936                ;; anyway, so just skip them.
 937                '(begin
 938                   (substitute* "unsupported/CMakeLists.txt"
 939                     (("add_subdirectory\\(test.*")
 940                      "# Do not build the tests for unsupported features.\n"))
 941                   #t))))
 942     (build-system cmake-build-system)
 943     (arguments
 944      '(;; Turn off debugging symbols to save space.
 945        #:build-type "Release"
 946
 947        #:phases (modify-phases %standard-phases
 948                   (replace 'check
 949                     (lambda _
 950                       (let* ((cores  (parallel-job-count))
 951                              (dash-j (format #f "-j~a" cores)))
 952                         (setenv "EIGEN_SEED" "1") ;for reproducibility
 953                         ;; First build the tests, in parallel.  See
 954                         ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
 955                         (invoke "make" "buildtests" dash-j)
 956
 957                         ;; Then run 'CTest' with -V so we get more
 958                         ;; details upon failure.
 959                         (invoke "ctest" "-V" dash-j)))))))
 960     (home-page "https://eigen.tuxfamily.org")
 961     (synopsis "C++ template library for linear algebra")
 962     (description
 963      "Eigen is a C++ template library for linear algebra: matrices, vectors,
 964 numerical solvers, and related algorithms.  It provides an elegant API based
 965 on \"expression templates\".  It is versatile: it supports all matrix sizes,
 966 all standard numeric types, various matrix decompositions and geometry
 967 features, and more.")
 968
 969     ;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3.
 970     ;; See 'COPYING.README' for details.
 971     (license license:mpl2.0)))
 972
 973 (define-public eigen-for-tensorflow
 974   (let ((changeset "fd6845384b86")
 975         (revision "1"))
 976     (package (inherit eigen)
 977       (name "eigen-for-tensorflow")
 978       (version (string-append "3.3.5-" revision "." changeset))
 979       (source (origin
 980                 (method hg-fetch)
 981                 (uri (hg-reference
 982                       (url "https://bitbucket.org/eigen/eigen")
 983                       (changeset changeset)))
 984                 (sha256
 985                  (base32
 986                   "12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5"))
 987                 (file-name (string-append name "-" version "-checkout"))
 988                 (modules '((guix build utils)))
 989                 (snippet
 990                  ;; There are 3 test failures in the "unsupported" directory,
 991                  ;; but maintainers say it's a known issue and it's unsupported
 992                  ;; anyway, so just skip them.
 993                  '(begin
 994                     (substitute* "unsupported/CMakeLists.txt"
 995                       (("add_subdirectory\\(test.*")
 996                        "# Do not build the tests for unsupported features.\n"))
 997                     #t)))))))
 998
 999 (define-public xtensor
1000   (package
1001     (name "xtensor")
1002     (version "0.20.10")
1003     (source (origin
1004               (method git-fetch)
1005               (uri (git-reference
1006                     (url "https://github.com/QuantStack/xtensor.git")
1007                     (commit version)))
1008               (sha256
1009                (base32
1010                 "1fmv2hpx610xwhxrndfsfvlbqfyk4l3gi5q5d7pa9m82kblxjj9l"))
1011               (file-name (git-file-name name version))))
1012     (build-system cmake-build-system)
1013     (native-inputs
1014      `(("googletest" ,googletest)
1015        ("xtl" ,xtl)))
1016     (arguments
1017      `(#:configure-flags
1018        '("-DBUILD_TESTS=ON")
1019        #:test-target "xtest"))
1020     (home-page "https://quantstack.net/xtensor")
1021     (synopsis "C++ tensors with broadcasting and lazy computing")
1022     (description "xtensor is a C++ library meant for numerical analysis with
1023 multi-dimensional array expressions.
1024
1025 xtensor provides:
1026 @itemize
1027 @item an extensible expression system enabling lazy broadcasting.
1028 @item an API following the idioms of the C++ standard library.
1029 @item tools to manipulate array expressions and build upon xtensor.
1030 @end itemize")
1031     (license license:bsd-3)))
1032
1033 (define-public gap
1034   (package
1035     (name "gap")
1036     (version "4.10.2")
1037     (source
1038      (origin
1039        (method url-fetch)
1040        (uri (string-append "https://www.gap-system.org/pub/gap/gap-"
1041                            (version-major+minor version)
1042                            "/tar.bz2/gap-"
1043                            version
1044                            ".tar.bz2"))
1045        (sha256
1046         (base32 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
1047        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
1048        (snippet
1049         '(begin
1050            ;; Delete the external gmp and zlib libraries
1051            ;; and a subdirectory not needed for our build.
1052            (for-each delete-file-recursively
1053                      '("extern" "hpcgap"))
1054            ;; Delete a failing test.
1055            ;; FIXME: This might be fixed in the next release, see
1056            ;; https://github.com/gap-system/gap/issues/3292
1057            (delete-file "tst/testinstall/dir.tst")
1058            ;; Delete all packages except for a fixed list.
1059            (with-directory-excursion "pkg"
1060              (for-each delete-file-recursively
1061                (lset-difference string=? (scandir ".")
1062                  '("." ".."
1063                    ;; Necessary packages.
1064                    "GAPDoc-1.6.2"
1065                    "primgrp-3.3.2"
1066                    "SmallGrp-1.3"    ; artistic2.0
1067                    "transgrp"        ; artistic2.0 for data,
1068                                      ; gpl2 or gpl3 for code
1069                    ;; Recommanded package.
1070                    "io-4.5.4"        ; gpl3+
1071                    ;; Optional packages, searched for at start,
1072                    ;; and their depedencies.
1073                    "alnuth-3.1.0"
1074                    "autpgrp-1.10"
1075                    "crisp-1.4.4"     ; bsd-2
1076                    "ctbllib"       ; gpl3+ according to doc/chap0.txt
1077                    "FactInt-1.6.2"
1078                    "fga"
1079                    "irredsol-1.4"    ; bsd-2
1080                    "laguna-3.9.2"
1081                    "polenta-1.3.8"
1082                    "polycyclic-2.14"
1083                    "radiroot-2.8"
1084                    "resclasses-4.7.1"
1085                    "sophus-1.24"
1086                    "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
1087                                    ; and the next release
1088                    "utils-0.59"))))
1089            #t))))
1090     (build-system gnu-build-system)
1091     (inputs
1092      `(("gmp" ,gmp)
1093        ("zlib" ,zlib)))
1094     (arguments
1095      `(#:modules ((ice-9 ftw)
1096                   (srfi srfi-26)
1097                   (guix build gnu-build-system)
1098                   (guix build utils))
1099        #:phases
1100        (modify-phases %standard-phases
1101          (add-after 'build 'build-packages
1102            ;; Compile all packages that have not been deleted by the
1103            ;; code snippet above.
1104            (lambda _
1105              (setenv "CONFIG_SHELL" (which "bash"))
1106              (with-directory-excursion "pkg"
1107                (invoke "../bin/BuildPackages.sh")
1108              #t)))
1109          (add-after 'build-packages 'build-doc
1110            ;; The documentation is bundled, but we create it from source.
1111            (lambda _
1112              (with-directory-excursion "doc"
1113                (invoke "./make_doc"))
1114              #t))
1115          (replace 'install
1116            (lambda* (#:key outputs #:allow-other-keys)
1117              (let* ((out (assoc-ref outputs "out"))
1118                     (bin (string-append out "/bin"))
1119                     (lib (string-append out "/lib"))
1120                     (prog (string-append bin "/gap"))
1121                     (prog-real (string-append bin "/.gap-real"))
1122                     (share (string-append out "/share/gap"))
1123                     (include (string-append out "/include/gap"))
1124                     (include-hpc (string-append include "/hpc")))
1125                ;; Install only the gap binary; the gac compiler is left
1126                ;; for maybe later. "Wrap" it in a shell script that calls
1127                ;; the binary with the correct parameter.
1128                (mkdir-p bin)
1129                (copy-file "gap" prog-real)
1130                (call-with-output-file prog
1131                  (lambda (port)
1132                    (format port
1133                            "#!~a~%exec ~a -l ~a \"$@\"~%"
1134                            (which "bash")
1135                            prog-real
1136                            share)))
1137                (chmod prog #o755)
1138                ;; Install the headers, which are needed by Sage. The
1139                ;; Makefile target "install-headers" was available in
1140                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1141                (mkdir-p include-hpc)
1142                (install-file "gen/config.h" include)
1143                (let ((file-name-predicate-without-stat
1144                        (lambda (regex)
1145                          (cut (file-name-predicate regex) <> #f))))
1146                  (with-directory-excursion "src"
1147                    (for-each
1148                      (cut install-file <> include)
1149                      (scandir "."
1150                               (file-name-predicate-without-stat ".*\\.h$"))))
1151                  (with-directory-excursion "src/hpc"
1152                    (for-each
1153                      (cut install-file <> include-hpc)
1154                      (scandir "."
1155                               (file-name-predicate-without-stat ".*\\.h$")))))
1156                ;; Install the library, which is needed by Sage. The
1157                ;; Makefile target "install-libgap" was available in
1158                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1159                ;; Compared to the Makefile, which used libtool, the
1160                ;; following approach of copying files and making symlinks
1161                ;; is rather pedestrian. There is hope that some later
1162                ;; version of gap reinstates and completes the install
1163                ;; targets.
1164                (invoke "make" "libgap.la")
1165                (install-file "libgap.la" lib)
1166                (install-file ".libs/libgap.so.0.0.0" lib)
1167                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so"))
1168                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
1169                ;; Install a certain number of files and directories to
1170                ;; SHARE, where the wrapped shell script expects them.
1171                ;; Remove information on the build directory from sysinfo.gap.
1172                (substitute* "sysinfo.gap"
1173                  (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
1174                  (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
1175                  (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
1176                (install-file "sysinfo.gap" share)
1177                (copy-recursively "grp" (string-append share "/grp"))
1178                (copy-recursively "pkg" (string-append share "/pkg"))
1179                ;; The following is not the C library libgap.so, but a
1180                ;; library of GAP code.
1181                (copy-recursively "lib" (string-append share "/lib"))
1182                ;; The gap binary looks for documentation inside SHARE.
1183                (copy-recursively "doc" (string-append share "/doc")))
1184              #t)))))
1185     (home-page "https://www.gap-system.org/")
1186     (synopsis
1187      "System for computational group theory")
1188     (description
1189      "GAP is a system for computational discrete algebra, with particular
1190 emphasis on computational group theory.  It provides a programming language,
1191 a library of thousands of functions implementing algebraic algorithms
1192 written in the GAP language as well as large data libraries of algebraic
1193 objects.")
1194     ;; Some packages have different licenses (effectively forcing the
1195     ;; combined work to be licensed as gpl3+); if this is the case, this
1196     ;; is mentioned above next to their name.
1197     ;; Some packages have no license mentioned explicitly; supposedly this
1198     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
1199     ;; safe side, we drop them for now.
1200     (license license:gpl2+)))
1201
1202 (define-public givaro
1203   (package
1204     (name "givaro")
1205     (version "4.1.1")
1206     (source (origin
1207               (method git-fetch)
1208               (uri (git-reference
1209                     (url "https://github.com/linbox-team/givaro")
1210                     (commit (string-append "v" version))))
1211               (file-name (git-file-name name version))
1212               (sha256
1213                (base32
1214                 "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
1215     (build-system gnu-build-system)
1216     (native-inputs
1217      `(("autoconf" ,autoconf)
1218        ("automake" ,automake)
1219        ("libtool" ,libtool)))
1220     (propagated-inputs
1221      `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
1222     (synopsis "Algebraic computations with exact rings and fields")
1223     (description
1224      "Givaro is a C++ library implementing the basic arithmetic of various
1225 algebraic objects: prime fields, extension fields, finite fields, finite
1226 rings, polynomials, algebraic numbers, arbitrary precision integers and
1227 rationals (C++ wrappers over gmp), fixed precision integers.  It also
1228 provides data-structures and templated classes for the manipulation of
1229 compound objects, such as vectors, matrices and univariate polynomials.")
1230     (license license:cecill-b)
1231     (home-page "https://github.com/linbox-team/givaro")))
1232
1233 (define-public fflas-ffpack
1234   (package
1235     (name "fflas-ffpack")
1236     (version "2.4.3")
1237     (source (origin
1238               (method git-fetch)
1239               (uri (git-reference
1240                     (url "https://github.com/linbox-team/fflas-ffpack")
1241                     (commit version)))
1242               (file-name (git-file-name name version))
1243               (sha256
1244                (base32
1245                 "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
1246     (build-system gnu-build-system)
1247     (native-inputs
1248      `(("autoconf" ,autoconf)
1249        ("automake" ,automake)
1250        ("libtool" ,libtool)
1251        ("pkg-config" ,pkg-config)))
1252     (inputs
1253      `(("openblas" ,openblas)))
1254     (propagated-inputs
1255      `(("givaro" ,givaro))) ; required according to the .pc file
1256     (arguments
1257      `(#:configure-flags
1258        (list (string-append "--with-blas-libs="
1259                             (assoc-ref %build-inputs "openblas")
1260                             "/lib/libopenblas.so"))))
1261     (synopsis "C++ library for linear algebra over finite fields")
1262     (description
1263      "FFLAS-FFPACK is a C++ template library for basic linear algebra
1264 operations over a finite field.
1265 FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
1266 of a subset of routines of the numerical BLAS; it also supports sparse
1267 matrix-vector products.
1268 FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
1269 library to provide functionalities of higher level, using the kernel
1270 of a BLAS.  Additionally, it provides routines specific to exact linear
1271 algebra, such as the row echelon form.")
1272     (license license:lgpl2.1+)
1273     (home-page "https://linbox-team.github.io/fflas-ffpack/")))
1274
1275 (define-public linbox
1276   (package
1277     (name "linbox")
1278     (version "1.6.3")
1279     (source (origin
1280               (method git-fetch)
1281               (uri (git-reference
1282                     (url "https://github.com/linbox-team/linbox")
1283                     (commit (string-append "v" version))))
1284               (file-name (git-file-name name version))
1285               (sha256
1286                (base32
1287                 "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
1288     (build-system gnu-build-system)
1289     (native-inputs
1290      `(("autoconf" ,autoconf)
1291        ("automake" ,automake)
1292        ("libtool" ,libtool)
1293        ("pkg-config" ,pkg-config)))
1294     (inputs
1295      `(("fflas-ffpack" ,fflas-ffpack)))
1296     (synopsis "C++ library for linear algebra over exact rings")
1297     (description
1298      "LinBox is a C++ template library for exact linear algebra computation
1299 with dense, sparse, and structured matrices over the integers and over
1300 finite fields.")
1301     (license license:lgpl2.1+)
1302     (home-page "https://linbox-team.github.io/linbox/")))
1303
1304 (define-public m4ri
1305   (package
1306     (name "m4ri")
1307     (version "20140914")
1308     (source (origin
1309               (method git-fetch)
1310               (uri (git-reference
1311                     (url "https://bitbucket.org/malb/m4ri")
1312                     (commit (string-append "release-" version))))
1313               (file-name (git-file-name name version))
1314               (sha256
1315                (base32
1316                 "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
1317     (build-system gnu-build-system)
1318     (native-inputs
1319      `(("autoconf" ,autoconf)
1320        ("automake" ,automake)
1321        ("libtool" ,libtool)
1322        ("pkg-config" ,pkg-config)))
1323     (inputs
1324      `(("libpng" ,libpng)))
1325     (synopsis "Arithmetic of dense matrices over F_2")
1326     (description "M4RI is a library for fast arithmetic with dense matrices
1327 over F2.  The name M4RI comes from the first implemented algorithm: The
1328 Method of the Four Russians inversion algorithm published by Gregory Bard.
1329 This algorithm in turn is named after the Method of the Four Russians
1330 multiplication algorithm.")
1331     (license license:gpl2+)
1332     (home-page "https://bitbucket.org/malb/m4ri/")))
1333
1334 (define-public symmetrica
1335   (package
1336     (name "symmetrica")
1337     (version "2.0")
1338     (source (origin
1339               (method url-fetch/tarbomb)
1340               (uri (let ((v (string-join (string-split version #\.) "_")))
1341                      (string-append "http://www.algorithm.uni-bayreuth.de/"
1342                                     "en/research/SYMMETRICA/"
1343                                     "SYM" v "_tar.gz")))
1344               (sha256
1345                (base32
1346                 "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
1347               ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
1348               (patches (search-patches "symmetrica-bruch.patch"
1349                                        "symmetrica-int32.patch"
1350                                        "symmetrica-return_values.patch"
1351                                        "symmetrica-sort_sum_rename.patch"))))
1352     (build-system gnu-build-system)
1353     (arguments
1354      `(#:tests? #f                      ;no test
1355        #:phases
1356        (modify-phases %standard-phases
1357          (add-after 'unpack 'fix-makefile
1358            (lambda _
1359              (substitute* "makefile"
1360                (("cc -c") "gcc -c -fPIC"))
1361              #t))
1362          (add-after 'fix-makefile 'turn-off-banner
1363            (lambda _
1364              (substitute* "de.c"
1365                (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
1366              #t))
1367          (delete 'configure)            ;no configure script
1368          (replace 'install              ;no install target
1369            (lambda* (#:key outputs #:allow-other-keys)
1370              (let* ((out (assoc-ref outputs "out"))
1371                     (lib (string-append out "/lib"))
1372                     (inc (string-append out "/include/symmetrica"))
1373                     (doc (string-append out "/share/doc/symmetrica-" ,version))
1374                     (static "libsymmetrica.a"))
1375                ;; Build static library.
1376                (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
1377                (invoke "ranlib" static)
1378                ;; Install static library and headers.
1379                (for-each (lambda (f) (install-file f inc))
1380                          (find-files "." "\\.h$"))
1381                (install-file "libsymmetrica.a" lib)
1382                ;; Install documentation.
1383                (for-each (lambda (f) (install-file f doc))
1384                          (find-files "." "\\.doc$"))
1385                #t))))))
1386     (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
1387     (synopsis "Combinatoric C Library")
1388     (description "Symmetrica is a library for combinatorics.  It has support
1389 for the representation theory of the symmetric group and related groups,
1390 combinatorics of tableaux, symmetric functions and polynomials, Schubert
1391 polynomials, and the representation theory of Hecke algebras of type A_n.")
1392     (license license:public-domain)))
1393
1394 (define-public m4rie
1395   (package
1396     (name "m4rie")
1397     (version "20150908")
1398     (source (origin
1399               (method git-fetch)
1400               (uri (git-reference
1401                     (url "https://bitbucket.org/malb/m4rie")
1402                     (commit (string-append "release-" version))))
1403               (file-name (git-file-name name version))
1404               (sha256
1405                (base32
1406                 "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
1407     (build-system gnu-build-system)
1408     (native-inputs
1409      `(("autoconf" ,autoconf)
1410        ("automake" ,automake)
1411        ("libtool" ,libtool)))
1412     (inputs
1413      `(("m4ri" ,m4ri)))
1414     (synopsis "Arithmetic of dense matrices over F_{2^e}")
1415     (description "M4RI is a library for fast arithmetic with dense matrices
1416 over finite fields of characteristic 2.  So it extends the functionality
1417 of M4RI from F_2 to F_{2^e}.")
1418     (license license:gpl2+)
1419     (home-page "https://bitbucket.org/malb/m4rie/")))
1420
1421 (define-public eclib
1422   (package
1423     (name "eclib")
1424     (version "20190909")
1425     (source (origin
1426               (method git-fetch)
1427               (uri (git-reference
1428                     (url "https://github.com/JohnCremona/eclib/")
1429                     (commit (string-append "v" version))))
1430               (file-name (git-file-name name version))
1431               (sha256
1432                (base32
1433                 "1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n"))))
1434     (build-system gnu-build-system)
1435     (native-inputs
1436      `(("autoconf" ,autoconf)
1437        ("automake" ,automake)
1438        ("libtool" ,libtool)))
1439     (inputs
1440      `(("gmp" ,gmp)
1441        ("ntl" ,ntl)
1442        ("pari-gp" ,pari-gp)))
1443     (synopsis "Ranks of elliptic curves and modular symbols")
1444     (description "The eclib package includes mwrank (for 2-descent on
1445 elliptic curves over Q) and modular symbol code; it has been written by
1446 John Cremona to compute his elliptic curve database.")
1447     (license license:gpl2+)
1448     (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
1449                               "J.E.Cremona/mwrank/index.html"))))
1450
1451 (define-public lrcalc
1452   (package
1453     (name "lrcalc")
1454     (version "1.2")
1455     (source (origin
1456               (method git-fetch)
1457               (uri (git-reference
1458                     (url "https://bitbucket.org/asbuch/lrcalc")
1459                     (commit (string-append "lrcalc-" version))))
1460               (file-name (git-file-name name version))
1461               (sha256
1462                (base32
1463                 "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
1464               (patches (search-patches "lrcalc-includes.patch"))))
1465     (build-system gnu-build-system)
1466     (native-inputs
1467      `(("autoconf" ,autoconf)
1468        ("automake" ,automake)
1469        ("libtool" ,libtool)))
1470     (arguments
1471      `(#:phases
1472        (modify-phases %standard-phases
1473          (add-before 'build 'fix-permission
1474            (lambda _
1475              (chmod "lrcalc.maple.src" #o644)
1476              #t)))))
1477     (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
1478     (description "The Littlewood-Richardson Calculator (lrcalc) is a
1479 program designed to compute Littlewood-Richardson coefficients.  It computes
1480 single Littlewood-Richardson coefficients, products of Schur functions, or
1481 skew Schur functions.  In addition it computes products in the small quantum
1482 cohomology ring of a Grassmann variety.  The software package also includes
1483 a program that performs fast computation of the more general multiplicative
1484 structure constants of Schubert polynomials.")
1485     (license license:gpl2+)
1486     (home-page "https://sites.math.rutgers.edu/~asbuch/lrcalc/")))
1487
1488 (define-public iml
1489   (package
1490     (name "iml")
1491     (version "1.0.5")
1492     (source
1493      (origin
1494        (method url-fetch)
1495        (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
1496                            version ".tar.bz2"))
1497        (sha256
1498         (base32
1499          "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
1500     (build-system gnu-build-system)
1501     (inputs
1502      `(("gmp", gmp)
1503        ("cblas" ,openblas))) ; or any other BLAS library; the documentation
1504                              ; mentions ATLAS in particular
1505     (arguments
1506      `(#:configure-flags
1507        (list
1508         "--enable-shared"
1509         (string-append "--with-gmp-include="
1510                        (assoc-ref %build-inputs "gmp") "/include")
1511         (string-append "--with-gmp-lib="
1512                        (assoc-ref %build-inputs "gmp") "/lib")
1513         "--with-cblas=-lopenblas"
1514         (string-append "--with-cblas-include="
1515                        (assoc-ref %build-inputs "cblas") "/include")
1516         (string-append "--with-cblas-lib="
1517                        (assoc-ref %build-inputs "cblas") "/lib"))))
1518     (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
1519     (synopsis
1520      "Solver for systems of linear equations over the integers")
1521     (description
1522      "IML is a C library implementing algorithms for computing exact
1523 solutions to dense systems of linear equations over the integers.
1524 Currently, IML provides the following functionality:
1525
1526 @itemize
1527 @item Nonsingular rational system solving:
1528 compute the unique rational solution X to the system AX=B, where A and B
1529 are integer matrices, A nonsingular.
1530 @item Compute the right nullspace or kernel of an integer matrix.
1531 @item Certified linear system solving:
1532 compute a minimal denominator solution x to a system Ax=b, where b is an
1533 integer vector and A is an integer matrix with arbitrary shape and
1534 rank profile.
1535 @end itemize
1536
1537 In addition, IML provides some low level routines for a variety of mod p
1538 matrix operations: computing the row-echelon form, determinant, rank
1539 profile, and inverse of a mod p matrix. These mod p routines are not
1540 general purpose; they require that p satisfy some preconditions based on
1541 the dimension of the input matrix (usually p should be prime and should be
1542 no more than about 20 bits long).")
1543     (license license:bsd-3)))