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 © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
  12 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
  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 "2.11.3")
 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                 "1jd65h2psrmba2dx7rkf5qidf9ka0cwbsg20pd18k45ggr30l467"))))
 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)
 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 flint
 437   (package
 438    (name "flint")
 439    (version "2.5.2")
 440    (source (origin
 441             (method url-fetch)
 442             (uri (string-append
 443                   "http://flintlib.org/flint-"
 444                   version ".tar.gz"))
 445             (sha256 (base32
 446                      "11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
 447             (patches (search-patches "flint-ldconfig.patch"))))
 448    (build-system gnu-build-system)
 449    (propagated-inputs
 450     `(("gmp" ,gmp)
 451       ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
 452    (arguments
 453     `(#:parallel-tests? #f ; seems to be necessary on arm
 454       #:phases
 455        (modify-phases %standard-phases
 456          (replace 'configure
 457            (lambda* (#:key inputs outputs #:allow-other-keys)
 458              (let ((out (assoc-ref outputs "out"))
 459                    (gmp (assoc-ref inputs "gmp"))
 460                    (mpfr (assoc-ref inputs "mpfr")))
 461                ;; do not pass "--enable-fast-install", which makes the
 462                ;; homebrew configure process fail
 463                (invoke "./configure"
 464                        (string-append "--prefix=" out)
 465                        (string-append "--with-gmp=" gmp)
 466                        (string-append "--with-mpfr=" mpfr))
 467                #t))))))
 468    (synopsis "Fast library for number theory")
 469    (description
 470     "FLINT is a C library for number theory.  It supports arithmetic
 471 with numbers, polynomials, power series and matrices over many base
 472 rings, including multiprecision integers and rationals, integers
 473 modulo n, p-adic numbers, finite fields (prime and non-prime order)
 474 and real and complex numbers (via the Arb extension library).
 475
 476 Operations that can be performed include conversions, arithmetic,
 477 GCDs, factoring, solving linear systems, and evaluating special
 478 functions.  In addition, FLINT provides various low-level routines for
 479 fast arithmetic.")
 480    (license license:gpl2+)
 481    (home-page "http://flintlib.org/")))
 482
 483 (define-public arb
 484   (package
 485     (name "arb")
 486     (version "2.17.0")
 487     (source (origin
 488               (method git-fetch)
 489               (uri (git-reference
 490                     (url "https://github.com/fredrik-johansson/arb.git")
 491                     (commit version)))
 492               (file-name (git-file-name name version))
 493               (sha256
 494                (base32
 495                 "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1"))))
 496     (build-system gnu-build-system)
 497     (propagated-inputs
 498      `(("flint" ,flint)))               ; flint.h is included by arf.h
 499     (inputs
 500      `(("gmp" ,gmp)
 501        ("mpfr" ,mpfr)))
 502     (arguments
 503      `(#:phases
 504        (modify-phases %standard-phases
 505          (replace 'configure
 506            (lambda* (#:key inputs outputs #:allow-other-keys)
 507              (let ((out (assoc-ref outputs "out"))
 508                    (flint (assoc-ref inputs "flint"))
 509                    (gmp (assoc-ref inputs "gmp"))
 510                    (mpfr (assoc-ref inputs "mpfr")))
 511                ;; Do not pass "--enable-fast-install", which makes the
 512                ;; homebrew configure process fail.
 513                (invoke "./configure"
 514                        (string-append "--prefix=" out)
 515                        (string-append "--with-flint=" flint)
 516                        (string-append "--with-gmp=" gmp)
 517                        (string-append "--with-mpfr=" mpfr))))))))
 518     (synopsis "Arbitrary precision floating-point ball arithmetic")
 519     (description
 520      "Arb is a C library for arbitrary-precision floating-point ball
 521 arithmetic.  It supports efficient high-precision computation with
 522 polynomials, power series, matrices and special functions over the
 523 real and complex numbers, with automatic, rigorous error control.")
 524     (license license:lgpl2.1+)
 525     (home-page "http://arblib.org")))
 526
 527 (define-public python-flint
 528   (package
 529     (name "python-flint")
 530     (version "0.3.0")
 531     (source (origin
 532               (method git-fetch)
 533               (uri (git-reference
 534                     (url "https://github.com/fredrik-johansson/python-flint.git")
 535                     (commit version)))
 536               (file-name (git-file-name name version))
 537               (sha256
 538                (base32
 539                 "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
 540               (patches (search-patches "python-flint-includes.patch"))))
 541     (build-system python-build-system)
 542     (native-inputs
 543      `(("python-cython" ,python-cython)))
 544     (propagated-inputs
 545      `(("python-numpy" ,python-numpy)))
 546     (inputs
 547      `(("arb" ,arb)
 548        ("flint" ,flint)))
 549     (synopsis "Python module wrapping ARB and FLINT")
 550     (description
 551      "Python-flint is a Python extension module wrapping FLINT
 552 (Fast Library for Number Theory) and Arb (arbitrary-precision ball
 553 arithmetic).  It supports integers, rationals, modular integers,
 554 real and complex ball arithmetic, polynomials and matrices over all
 555 these types and other mathematical functions.")
 556     (license license:expat)
 557     (home-page "http://fredrikj.net/python-flint/")))
 558
 559 (define-public ntl
 560   (package
 561    (name "ntl")
 562    (version "11.4.3")
 563    (source (origin
 564             (method url-fetch)
 565             (uri (string-append "https://shoup.net/ntl/ntl-"
 566                                 version ".tar.gz"))
 567             (sha256
 568              (base32
 569               "1lisp3064rch3jaa2wrhy1s9kll7i3ka3d0y6lj6l3l4ckfcrhdp"))
 570             (modules '((guix build utils)))
 571             (snippet
 572              '(begin
 573                 (delete-file-recursively "src/libtool-origin")
 574                 #t))))
 575    (build-system gnu-build-system)
 576    (native-inputs
 577     `(("libtool" ,libtool)
 578       ("perl" ,perl))) ; for configuration
 579    (inputs
 580     `(("gmp" ,gmp)
 581       ("gf2x" ,gf2x)))
 582    (arguments
 583     `(#:phases
 584       (modify-phases %standard-phases
 585         (replace 'configure
 586          (lambda* (#:key inputs outputs #:allow-other-keys)
 587            (chdir "src")
 588            (invoke "./configure"
 589                     (string-append "PREFIX=" (assoc-ref outputs "out"))
 590                     (string-append "LIBTOOL=" (assoc-ref inputs "libtool") "/bin/libtool")
 591                     ;; set the library prefixes explicitly so that they get
 592                     ;; embedded in the .la file
 593                     (string-append "GMP_PREFIX=" (assoc-ref inputs "gmp"))
 594                     (string-append "GF2X_PREFIX=" (assoc-ref inputs "gf2x"))
 595                     ;; Do not build especially for the build machine.
 596                     "NATIVE=off"
 597                     "NTL_GF2X_LIB=on"
 598                     "SHARED=on"))))))
 599    (synopsis "C++ library for number theory")
 600    (description
 601     "NTL is a C++ library providing data structures and algorithms
 602 for manipulating signed, arbitrary length integers, and for vectors,
 603 matrices, and polynomials over the integers and over finite fields.")
 604    (license license:gpl2+)
 605    (home-page "https://shoup.net/ntl/")))
 606
 607 (define-public singular
 608   (package
 609    (name "singular")
 610    (version "4.1.2p1")
 611    (source
 612     (origin
 613       (method url-fetch)
 614       (uri
 615        (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
 616                       "Singular/SOURCES/"
 617                       (string-join
 618                        (string-split
 619                         (string-trim-right version #\p
 620                                            0 (1- (string-length version)))
 621                         #\.) "-")
 622                       "/singular-" version ".tar.gz"))
 623              (sha256 (base32
 624                       "0kvd55353fiqyq1msmi0kka66n5h0aqs7m3km60r01b1w2f8085m"))))
 625    (build-system gnu-build-system)
 626    (native-inputs
 627     `(("doxygen" ,doxygen)
 628       ("graphviz" ,graphviz)
 629       ("perl" ,perl)))
 630    (inputs
 631     `(("cddlib" ,cddlib)
 632       ("gmp" ,gmp)
 633       ("flint" ,flint)
 634       ("mpfr" ,mpfr)
 635       ("ntl" ,ntl)
 636       ("python" ,python-2)
 637       ("readline" ,readline)))
 638    (arguments
 639     `(#:configure-flags
 640       (list (string-append "--with-ntl="
 641                            (assoc-ref %build-inputs "ntl")))))
 642    (synopsis "Computer algebra system for polynomial computations")
 643    (description
 644     "Singular is a computer algebra system for polynomial computations,
 645 with special emphasis on commutative and non-commutative algebra, algebraic
 646 geometry and singularity theory.")
 647    ;; Singular itself is dual licensed gpl2 or gpl3, but some of the
 648    ;; libraries with which it links are licensed under lgpl3+, so the
 649    ;; combined work becomes gpl3. See COPYING in the source code.
 650    (license license:gpl3)
 651    (home-page "http://www.singular.uni-kl.de/index.php")))
 652
 653 (define-public gmp-ecm
 654   (package
 655    (name "gmp-ecm")
 656    (version "7.0.4")
 657    (source (origin
 658              (method url-fetch)
 659              ;; Use the ‘Latest version’ link for a stable URI across releases.
 660              (uri (string-append "https://gforge.inria.fr/frs/download.php/"
 661                                  "latestfile/160/ecm-" version ".tar.gz"))
 662              (sha256 (base32
 663                       "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"))))
 664    (build-system gnu-build-system)
 665    (inputs
 666     `(("gmp" ,gmp)))
 667    (arguments
 668     `(#:configure-flags '("--enable-shared"
 669                           ;; Disable specific assembly routines, which depend
 670                           ;; on the subarchitecture of the build machine,
 671                           ;; and use gmp instead.
 672                           "--disable-asm-redc")))
 673    (synopsis "Integer factorization library using the elliptic curve method")
 674    (description
 675     "GMP-ECM factors integers using the elliptic curve method (ECM) as well
 676 as the P-1 and P+1 algorithms.  It provides a library and a stand-alone
 677 binary.")
 678    ;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+,
 679    ;; so the combined work is under gpl3+.
 680    (license license:gpl3+)
 681    (home-page "http://ecm.gforge.inria.fr/")))
 682
 683 (define-public bc
 684   (package
 685     (name "bc")
 686     (version "1.07.1")
 687     (source (origin
 688              (method url-fetch)
 689              (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
 690              (sha256
 691               (base32
 692                "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))))
 693     (build-system gnu-build-system)
 694     (native-inputs
 695      `(("ed" ,ed)
 696        ("flex" ,flex)
 697        ("texinfo" ,texinfo)))
 698     (arguments
 699      '(#:configure-flags
 700        (list "--with-readline")))
 701     (home-page "https://www.gnu.org/software/bc/")
 702     (synopsis "Arbitrary precision numeric processing language")
 703     (description
 704      "bc is an arbitrary precision numeric processing language.  It includes
 705 an interactive environment for evaluating mathematical statements.  Its
 706 syntax is similar to that of C, so basic usage is familiar.  It also includes
 707 \"dc\", a reverse-polish calculator.")
 708     (license license:gpl2+)))
 709
 710 ;; The original kiss-fft does not have a complete build system and does not
 711 ;; build any shared libraries.  This is a fork used by Extempore.
 712 (define-public kiss-fft-for-extempore
 713   (package
 714     (name "kiss-fft-for-extempore")
 715     (version "1.3.0")
 716     (source (origin
 717               (method git-fetch)
 718               (uri (git-reference
 719                     (url "https://github.com/extemporelang/kiss_fft.git")
 720                     (commit version)))
 721               (file-name (git-file-name name version))
 722               (sha256
 723                (base32
 724                 "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
 725     (build-system cmake-build-system)
 726     (arguments `(#:tests? #f)) ; no tests included
 727     ;; Extempore refuses to build on architectures other than x86_64
 728     (supported-systems '("x86_64-linux"))
 729     (home-page "https://github.com/extemporelang/kiss_fft")
 730     (synopsis "Mixed-radix Fast Fourier Transform")
 731     (description
 732      "Kiss FFT attempts to be a reasonably efficient, moderately useful FFT
 733 that can use fixed or floating data types and can easily be incorporated into
 734 a C program.")
 735     (license license:bsd-3)))
 736
 737 (define-public fftw
 738   (package
 739     (name "fftw")
 740     (version "3.3.8")
 741     (source (origin
 742              (method url-fetch)
 743              (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
 744                                  version".tar.gz"))
 745              (sha256
 746               (base32
 747                "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
 748     (build-system gnu-build-system)
 749     (arguments
 750      `(#:configure-flags
 751        '("--enable-shared" "--enable-openmp" "--enable-threads"
 752          ,@(let ((system (or (%current-target-system) (%current-system))))
 753              ;; Enable SIMD extensions for codelets.  See details at:
 754              ;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>.
 755              (cond
 756               ((string-prefix? "x86_64" system)
 757                '("--enable-sse2" "--enable-avx" "--enable-avx2"
 758                  "--enable-avx512" "--enable-avx-128-fma"))
 759               ((string-prefix? "i686" system)
 760                '("--enable-sse2"))
 761               ((string-prefix? "aarch64" system)
 762                ;; Note that fftw supports NEON on 32-bit ARM only when
 763                ;; compiled for single-precision.
 764                '("--enable-neon"))
 765               (else
 766                '())))
 767          ;; By default '-mtune=native' is used.  However, that may cause the
 768          ;; use of ISA extensions (e.g. AVX) that are not necessarily
 769          ;; available on the user's machine when that package is built on a
 770          ;; different machine.
 771          "ax_cv_c_flags__mtune_native=no")))
 772     (native-inputs `(("perl" ,perl)))
 773     (home-page "http://fftw.org")
 774     (synopsis "Computing the discrete Fourier transform")
 775     (description
 776      "FFTW is a C subroutine library for computing the discrete Fourier
 777 transform (DFT) in one or more dimensions, of arbitrary input size, and of
 778 both real and complex data (as well as of even/odd data---i.e. the discrete
 779 cosine/ sine transforms or DCT/DST).")
 780     (license license:gpl2+)))
 781
 782 (define-public fftwf
 783   (package (inherit fftw)
 784     (name "fftwf")
 785     (arguments
 786      (substitute-keyword-arguments (package-arguments fftw)
 787        ((#:configure-flags fftw-configure-flags)
 788         `(cons* "--enable-single"
 789                 ,@(if (string-prefix? "arm" (or (%current-target-system)
 790                                                 (%current-system)))
 791                       ;; fftw supports NEON on 32-bit ARM only when compiled
 792                       ;; for single-precision, so add it here.
 793                       '("--enable-neon")
 794                       '())
 795                 ,fftw-configure-flags))))
 796     (description
 797      (string-append (package-description fftw)
 798                     "  Single-precision version."))))
 799
 800 (define-public fftw-openmpi
 801   (package (inherit fftw)
 802     (name "fftw-openmpi")
 803     (inputs
 804      `(("openmpi" ,openmpi)
 805        ,@(package-inputs fftw)))
 806     (arguments
 807      (substitute-keyword-arguments (package-arguments fftw)
 808        ((#:configure-flags cf)
 809         `(cons "--enable-mpi" ,cf))
 810        ((#:phases phases '%standard-phases)
 811         `(modify-phases ,phases
 812            (add-before 'check 'mpi-setup
 813              ,%openmpi-setup)))))
 814     (description
 815      (string-append (package-description fftw)
 816                     "  With OpenMPI parallelism support."))))
 817
 818 (define-public java-la4j
 819   (package
 820     (name "java-la4j")
 821     (version "0.6.0")
 822     (source (origin
 823               (method git-fetch)
 824               (uri (git-reference
 825                     (url "https://github.com/vkostyukov/la4j.git")
 826                     (commit version)))
 827               (file-name (string-append name "-" version "-checkout"))
 828               (sha256
 829                (base32
 830                 "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
 831     (build-system ant-build-system)
 832     (arguments
 833      `(#:jar-name "la4j.jar"
 834        #:jdk ,icedtea-8
 835        #:test-exclude (list "**/Abstract*.java"
 836                             "**/MatrixTest.java"
 837                             "**/DenseMatrixTest.java"
 838                             "**/SparseMatrixTest.java"
 839                             "**/VectorTest.java"
 840                             "**/SparseVectorTest.java"
 841                             "**/DenseVectorTest.java")))
 842     (native-inputs
 843      `(("java-junit" ,java-junit)
 844        ("java-hamcrest-core" ,java-hamcrest-core)))
 845     (home-page "http://la4j.org/")
 846     (synopsis "Java library that provides Linear Algebra primitives and algorithms")
 847     (description "The la4j library is a Java library that provides Linear
 848 Algebra primitives (matrices and vectors) and algorithms.  The key features of
 849 the la4j library are:
 850
 851 @itemize
 852 @item No dependencies and tiny size
 853 @item Fluent object-oriented/functional API
 854 @item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
 855 @item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
 856 @item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
 857 @item MatrixMarket/CSV IO formats support for matrices and vectors
 858 @end itemize\n")
 859     (license license:asl2.0)))
 860
 861 (define-public java-jlargearrays
 862   (package
 863     (name "java-jlargearrays")
 864     (version "1.6")
 865     (source (origin
 866               (method url-fetch)
 867               (uri (string-append "https://repo1.maven.org/maven2/"
 868                                   "pl/edu/icm/JLargeArrays/"
 869                                   version "/JLargeArrays-" version
 870                                   "-sources.jar"))
 871               (file-name (string-append name "-" version ".jar"))
 872               (sha256
 873                (base32
 874                 "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
 875     (build-system ant-build-system)
 876     (arguments
 877      `(#:jar-name "jlargearrays.jar"
 878        #:tests? #f ; tests are not included in the release archive
 879        #:jdk ,icedtea-8))
 880     (propagated-inputs
 881      `(("java-commons-math3" ,java-commons-math3)))
 882     (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
 883     (synopsis "Library of one-dimensional arrays that can store up to 263 elements")
 884     (description "JLargeArrays is a Java library of one-dimensional arrays
 885 that can store up to 263 elements.")
 886     (license license:bsd-2)))
 887
 888 (define-public java-jtransforms
 889   (package
 890     (name "java-jtransforms")
 891     (version "3.1")
 892     (source (origin
 893               (method url-fetch)
 894               (uri (string-append "https://repo1.maven.org/maven2/"
 895                                   "com/github/wendykierp/JTransforms/"
 896                                   version "/JTransforms-" version "-sources.jar"))
 897               (sha256
 898                (base32
 899                 "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
 900     (build-system ant-build-system)
 901     (arguments
 902      `(#:jar-name "jtransforms.jar"
 903        #:tests? #f ; tests are not included in the release archive
 904        #:jdk ,icedtea-8))
 905     (propagated-inputs
 906      `(("java-commons-math3" ,java-commons-math3)
 907        ("java-jlargearrays" ,java-jlargearrays)))
 908     (home-page "https://github.com/wendykierp/JTransforms")
 909     (synopsis "Multithreaded FFT library written in pure Java")
 910     (description "JTransforms is a multithreaded FFT library written in pure
 911 Java.  Currently, four types of transforms are available: @dfn{Discrete
 912 Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
 913 Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
 914     (license license:bsd-2)))
 915
 916 (define-public eigen
 917   (package
 918     (name "eigen")
 919     (version "3.3.7")
 920     (source (origin
 921               (method url-fetch)
 922               (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
 923                                   version ".tar.bz2"))
 924               (sha256
 925                (base32
 926                 "1km3fyfzyqfdvmnl79drps3fjwnz3zbh0c7l34mfbqyvvs8cy4wz"))
 927               (file-name (string-append name "-" version ".tar.bz2"))
 928               (patches (search-patches "eigen-stabilise-sparseqr-test.patch"))
 929               (modules '((guix build utils)))
 930               (snippet
 931                ;; There are 3 test failures in the "unsupported" directory,
 932                ;; but maintainers say it's a known issue and it's unsupported
 933                ;; anyway, so just skip them.
 934                '(begin
 935                   (substitute* "unsupported/CMakeLists.txt"
 936                     (("add_subdirectory\\(test.*")
 937                      "# Do not build the tests for unsupported features.\n"))
 938                   #t))))
 939     (build-system cmake-build-system)
 940     (arguments
 941      '(;; Turn off debugging symbols to save space.
 942        #:build-type "Release"
 943
 944        #:phases (modify-phases %standard-phases
 945                   (replace 'check
 946                     (lambda _
 947                       (let* ((cores  (parallel-job-count))
 948                              (dash-j (format #f "-j~a" cores)))
 949                         (setenv "EIGEN_SEED" "1") ;for reproducibility
 950                         ;; First build the tests, in parallel.  See
 951                         ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
 952                         (invoke "make" "buildtests" dash-j)
 953
 954                         ;; Then run 'CTest' with -V so we get more
 955                         ;; details upon failure.
 956                         (invoke "ctest" "-V" dash-j)))))))
 957     (home-page "https://eigen.tuxfamily.org")
 958     (synopsis "C++ template library for linear algebra")
 959     (description
 960      "Eigen is a C++ template library for linear algebra: matrices, vectors,
 961 numerical solvers, and related algorithms.  It provides an elegant API based
 962 on \"expression templates\".  It is versatile: it supports all matrix sizes,
 963 all standard numeric types, various matrix decompositions and geometry
 964 features, and more.")
 965
 966     ;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3.
 967     ;; See 'COPYING.README' for details.
 968     (license license:mpl2.0)))
 969
 970 (define-public eigen-for-tensorflow
 971   (let ((changeset "fd6845384b86")
 972         (revision "1"))
 973     (package (inherit eigen)
 974       (name "eigen-for-tensorflow")
 975       (version (string-append "3.3.5-" revision "." changeset))
 976       (source (origin
 977                 (method hg-fetch)
 978                 (uri (hg-reference
 979                       (url "https://bitbucket.org/eigen/eigen")
 980                       (changeset changeset)))
 981                 (sha256
 982                  (base32
 983                   "12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5"))
 984                 (file-name (string-append name "-" version "-checkout"))
 985                 (modules '((guix build utils)))
 986                 (snippet
 987                  ;; There are 3 test failures in the "unsupported" directory,
 988                  ;; but maintainers say it's a known issue and it's unsupported
 989                  ;; anyway, so just skip them.
 990                  '(begin
 991                     (substitute* "unsupported/CMakeLists.txt"
 992                       (("add_subdirectory\\(test.*")
 993                        "# Do not build the tests for unsupported features.\n"))
 994                     #t)))))))
 995
 996 (define-public xtensor
 997   (package
 998     (name "xtensor")
 999     (version "0.20.10")
1000     (source (origin
1001               (method git-fetch)
1002               (uri (git-reference
1003                     (url "https://github.com/QuantStack/xtensor.git")
1004                     (commit version)))
1005               (sha256
1006                (base32
1007                 "1fmv2hpx610xwhxrndfsfvlbqfyk4l3gi5q5d7pa9m82kblxjj9l"))
1008               (file-name (git-file-name name version))))
1009     (build-system cmake-build-system)
1010     (native-inputs
1011      `(("googletest" ,googletest)
1012        ("xtl" ,xtl)))
1013     (arguments
1014      `(#:configure-flags
1015        '("-DBUILD_TESTS=ON")
1016        #:test-target "xtest"))
1017     (home-page "https://quantstack.net/xtensor")
1018     (synopsis "C++ tensors with broadcasting and lazy computing")
1019     (description "xtensor is a C++ library meant for numerical analysis with
1020 multi-dimensional array expressions.
1021
1022 xtensor provides:
1023 @itemize
1024 @item an extensible expression system enabling lazy broadcasting.
1025 @item an API following the idioms of the C++ standard library.
1026 @item tools to manipulate array expressions and build upon xtensor.
1027 @end itemize")
1028     (license license:bsd-3)))
1029
1030 (define-public gap
1031   (package
1032     (name "gap")
1033     (version "4.10.2")
1034     (source
1035      (origin
1036        (method url-fetch)
1037        (uri (string-append "https://www.gap-system.org/pub/gap/gap-"
1038                            (version-major+minor version)
1039                            "/tar.bz2/gap-"
1040                            version
1041                            ".tar.bz2"))
1042        (sha256
1043         (base32 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
1044        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
1045        (snippet
1046         '(begin
1047            ;; Delete the external gmp and zlib libraries
1048            ;; and a subdirectory not needed for our build.
1049            (for-each delete-file-recursively
1050                      '("extern" "hpcgap"))
1051            ;; Delete a failing test.
1052            ;; FIXME: This might be fixed in the next release, see
1053            ;; https://github.com/gap-system/gap/issues/3292
1054            (delete-file "tst/testinstall/dir.tst")
1055            ;; Delete all packages except for a fixed list.
1056            (with-directory-excursion "pkg"
1057              (for-each delete-file-recursively
1058                (lset-difference string=? (scandir ".")
1059                  '("." ".."
1060                    ;; Necessary packages.
1061                    "GAPDoc-1.6.2"
1062                    "primgrp-3.3.2"
1063                    "SmallGrp-1.3"    ; artistic2.0
1064                    "transgrp"        ; artistic2.0 for data,
1065                                      ; gpl2 or gpl3 for code
1066                    ;; Recommanded package.
1067                    "io-4.5.4"        ; gpl3+
1068                    ;; Optional packages, searched for at start,
1069                    ;; and their depedencies.
1070                    "alnuth-3.1.0"
1071                    "autpgrp-1.10"
1072                    "crisp-1.4.4"     ; bsd-2
1073                    "ctbllib"       ; gpl3+ according to doc/chap0.txt
1074                    "FactInt-1.6.2"
1075                    "fga"
1076                    "irredsol-1.4"    ; bsd-2
1077                    "laguna-3.9.2"
1078                    "polenta-1.3.8"
1079                    "polycyclic-2.14"
1080                    "radiroot-2.8"
1081                    "resclasses-4.7.1"
1082                    "sophus-1.24"
1083                    "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
1084                                    ; and the next release
1085                    "utils-0.59"))))
1086            #t))))
1087     (build-system gnu-build-system)
1088     (inputs
1089      `(("gmp" ,gmp)
1090        ("zlib" ,zlib)))
1091     (arguments
1092      `(#:modules ((ice-9 ftw)
1093                   (srfi srfi-26)
1094                   (guix build gnu-build-system)
1095                   (guix build utils))
1096        #:phases
1097        (modify-phases %standard-phases
1098          (add-after 'build 'build-packages
1099            ;; Compile all packages that have not been deleted by the
1100            ;; code snippet above.
1101            (lambda _
1102              (setenv "CONFIG_SHELL" (which "bash"))
1103              (with-directory-excursion "pkg"
1104                (invoke "../bin/BuildPackages.sh")
1105              #t)))
1106          (add-after 'build-packages 'build-doc
1107            ;; The documentation is bundled, but we create it from source.
1108            (lambda _
1109              (with-directory-excursion "doc"
1110                (invoke "./make_doc"))
1111              #t))
1112          (replace 'install
1113            (lambda* (#:key outputs #:allow-other-keys)
1114              (let* ((out (assoc-ref outputs "out"))
1115                     (bin (string-append out "/bin"))
1116                     (lib (string-append out "/lib"))
1117                     (prog (string-append bin "/gap"))
1118                     (prog-real (string-append bin "/.gap-real"))
1119                     (share (string-append out "/share/gap"))
1120                     (include (string-append out "/include/gap"))
1121                     (include-hpc (string-append include "/hpc")))
1122                ;; Install only the gap binary; the gac compiler is left
1123                ;; for maybe later. "Wrap" it in a shell script that calls
1124                ;; the binary with the correct parameter.
1125                (mkdir-p bin)
1126                (copy-file "gap" prog-real)
1127                (call-with-output-file prog
1128                  (lambda (port)
1129                    (format port
1130                            "#!~a~%exec ~a -l ~a \"$@\"~%"
1131                            (which "bash")
1132                            prog-real
1133                            share)))
1134                (chmod prog #o755)
1135                ;; Install the headers, which are needed by Sage. The
1136                ;; Makefile target "install-headers" was available in
1137                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1138                (mkdir-p include-hpc)
1139                (install-file "gen/config.h" include)
1140                (let ((file-name-predicate-without-stat
1141                        (lambda (regex)
1142                          (cut (file-name-predicate regex) <> #f))))
1143                  (with-directory-excursion "src"
1144                    (for-each
1145                      (cut install-file <> include)
1146                      (scandir "."
1147                               (file-name-predicate-without-stat ".*\\.h$"))))
1148                  (with-directory-excursion "src/hpc"
1149                    (for-each
1150                      (cut install-file <> include-hpc)
1151                      (scandir "."
1152                               (file-name-predicate-without-stat ".*\\.h$")))))
1153                ;; Install the library, which is needed by Sage. The
1154                ;; Makefile target "install-libgap" was available in
1155                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1156                ;; Compared to the Makefile, which used libtool, the
1157                ;; following approach of copying files and making symlinks
1158                ;; is rather pedestrian. There is hope that some later
1159                ;; version of gap reinstates and completes the install
1160                ;; targets.
1161                (invoke "make" "libgap.la")
1162                (install-file "libgap.la" lib)
1163                (install-file ".libs/libgap.so.0.0.0" lib)
1164                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so"))
1165                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
1166                ;; Install a certain number of files and directories to
1167                ;; SHARE, where the wrapped shell script expects them.
1168                ;; Remove information on the build directory from sysinfo.gap.
1169                (substitute* "sysinfo.gap"
1170                  (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
1171                  (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
1172                  (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
1173                (install-file "sysinfo.gap" share)
1174                (copy-recursively "grp" (string-append share "/grp"))
1175                (copy-recursively "pkg" (string-append share "/pkg"))
1176                ;; The following is not the C library libgap.so, but a
1177                ;; library of GAP code.
1178                (copy-recursively "lib" (string-append share "/lib"))
1179                ;; The gap binary looks for documentation inside SHARE.
1180                (copy-recursively "doc" (string-append share "/doc")))
1181              #t)))))
1182     (home-page "https://www.gap-system.org/")
1183     (synopsis
1184      "System for computational group theory")
1185     (description
1186      "GAP is a system for computational discrete algebra, with particular
1187 emphasis on computational group theory.  It provides a programming language,
1188 a library of thousands of functions implementing algebraic algorithms
1189 written in the GAP language as well as large data libraries of algebraic
1190 objects.")
1191     ;; Some packages have different licenses (effectively forcing the
1192     ;; combined work to be licensed as gpl3+); if this is the case, this
1193     ;; is mentioned above next to their name.
1194     ;; Some packages have no license mentioned explicitly; supposedly this
1195     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
1196     ;; safe side, we drop them for now.
1197     (license license:gpl2+)))
1198
1199 (define-public givaro
1200   (package
1201     (name "givaro")
1202     (version "4.1.1")
1203     (source (origin
1204               (method git-fetch)
1205               (uri (git-reference
1206                     (url "https://github.com/linbox-team/givaro")
1207                     (commit (string-append "v" version))))
1208               (file-name (git-file-name name version))
1209               (sha256
1210                (base32
1211                 "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
1212     (build-system gnu-build-system)
1213     (native-inputs
1214      `(("autoconf" ,autoconf)
1215        ("automake" ,automake)
1216        ("libtool" ,libtool)))
1217     (propagated-inputs
1218      `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
1219     (arguments
1220      `(#:phases
1221        (modify-phases %standard-phases
1222          (add-before 'bootstrap 'setenv
1223            ;; Prevent the autogen.sh script to carry out the configure
1224            ;; script, which has not yet been patched to replace /bin/sh.
1225            (lambda _
1226              (setenv "NOCONFIGURE" "yes")
1227              #t)))))
1228     (synopsis "Algebraic computations with exact rings and fields")
1229     (description
1230      "Givaro is a C++ library implementing the basic arithmetic of various
1231 algebraic objects: prime fields, extension fields, finite fields, finite
1232 rings, polynomials, algebraic numbers, arbitrary precision integers and
1233 rationals (C++ wrappers over gmp), fixed precision integers.  It also
1234 provides data-structures and templated classes for the manipulation of
1235 compound objects, such as vectors, matrices and univariate polynomials.")
1236     (license license:cecill-b)
1237     (home-page "https://github.com/linbox-team/givaro")))
1238
1239 (define-public fflas-ffpack
1240   (package
1241     (name "fflas-ffpack")
1242     (version "2.4.3")
1243     (source (origin
1244               (method git-fetch)
1245               (uri (git-reference
1246                     (url "https://github.com/linbox-team/fflas-ffpack")
1247                     (commit version)))
1248               (file-name (git-file-name name version))
1249               (sha256
1250                (base32
1251                 "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
1252     (build-system gnu-build-system)
1253     (native-inputs
1254      `(("autoconf" ,autoconf)
1255        ("automake" ,automake)
1256        ("libtool" ,libtool)
1257        ("pkg-config" ,pkg-config)))
1258     (inputs
1259      `(("openblas" ,openblas)))
1260     (propagated-inputs
1261      `(("givaro" ,givaro))) ; required according to the .pc file
1262     (arguments
1263      `(#:configure-flags
1264        (list (string-append "--with-blas-libs="
1265                             (assoc-ref %build-inputs "openblas")
1266                             "/lib/libopenblas.so"))
1267        #:phases
1268        (modify-phases %standard-phases
1269          (add-before 'bootstrap 'setenv
1270            ;; Prevent the autogen.sh script to carry out the configure
1271            ;; script, which has not yet been patched to replace /bin/sh.
1272            (lambda _
1273              (setenv "NOCONFIGURE" "yes")
1274              #t)))))
1275     (synopsis "C++ library for linear algebra over finite fields")
1276     (description
1277      "FFLAS-FFPACK is a C++ template library for basic linear algebra
1278 operations over a finite field.
1279 FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
1280 of a subset of routines of the numerical BLAS; it also supports sparse
1281 matrix-vector products.
1282 FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
1283 library to provide functionalities of higher level, using the kernel
1284 of a BLAS.  Additionally, it provides routines specific to exact linear
1285 algebra, such as the row echelon form.")
1286     (license license:lgpl2.1+)
1287     (home-page "https://linbox-team.github.io/fflas-ffpack/")))
1288
1289 (define-public linbox
1290   (package
1291     (name "linbox")
1292     (version "1.6.3")
1293     (source (origin
1294               (method git-fetch)
1295               (uri (git-reference
1296                     (url "https://github.com/linbox-team/linbox")
1297                     (commit (string-append "v" version))))
1298               (file-name (git-file-name name version))
1299               (sha256
1300                (base32
1301                 "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
1302     (build-system gnu-build-system)
1303     (native-inputs
1304      `(("autoconf" ,autoconf)
1305        ("automake" ,automake)
1306        ("libtool" ,libtool)
1307        ("pkg-config" ,pkg-config)))
1308     (inputs
1309      `(("fflas-ffpack" ,fflas-ffpack)))
1310     (arguments
1311      `(#:phases
1312        (modify-phases %standard-phases
1313          (add-before 'bootstrap 'setenv
1314            ;; Prevent the autogen.sh script to carry out the configure
1315            ;; script, which has not yet been patched to replace /bin/sh.
1316            (lambda _
1317              (setenv "NOCONFIGURE" "yes")
1318              #t)))))
1319     (synopsis "C++ library for linear algebra over exact rings")
1320     (description
1321      "LinBox is a C++ template library for exact linear algebra computation
1322 with dense, sparse, and structured matrices over the integers and over
1323 finite fields.")
1324     (license license:lgpl2.1+)
1325     (home-page "https://linbox-team.github.io/linbox/")))
1326
1327 (define-public m4ri
1328   (package
1329     (name "m4ri")
1330     (version "20140914")
1331     (source (origin
1332               (method git-fetch)
1333               (uri (git-reference
1334                     (url "https://bitbucket.org/malb/m4ri")
1335                     (commit (string-append "release-" version))))
1336               (file-name (git-file-name name version))
1337               (sha256
1338                (base32
1339                 "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
1340     (build-system gnu-build-system)
1341     (native-inputs
1342      `(("autoconf" ,autoconf)
1343        ("automake" ,automake)
1344        ("libtool" ,libtool)
1345        ("pkg-config" ,pkg-config)))
1346     (inputs
1347      `(("libpng" ,libpng)))
1348     (synopsis "Arithmetic of dense matrices over F_2")
1349     (description "M4RI is a library for fast arithmetic with dense matrices
1350 over F2.  The name M4RI comes from the first implemented algorithm: The
1351 Method of the Four Russians inversion algorithm published by Gregory Bard.
1352 This algorithm in turn is named after the Method of the Four Russians
1353 multiplication algorithm.")
1354     (license license:gpl2+)
1355     (home-page "https://bitbucket.org/malb/m4ri/")))
1356
1357 (define-public symmetrica
1358   (package
1359     (name "symmetrica")
1360     (version "2.0")
1361     (source (origin
1362               (method url-fetch/tarbomb)
1363               (uri (let ((v (string-join (string-split version #\.) "_")))
1364                      (string-append "http://www.algorithm.uni-bayreuth.de/"
1365                                     "en/research/SYMMETRICA/"
1366                                     "SYM" v "_tar.gz")))
1367               (sha256
1368                (base32
1369                 "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
1370               ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
1371               (patches (search-patches "symmetrica-bruch.patch"
1372                                        "symmetrica-int32.patch"
1373                                        "symmetrica-return_values.patch"
1374                                        "symmetrica-sort_sum_rename.patch"))))
1375     (build-system gnu-build-system)
1376     (arguments
1377      `(#:tests? #f                      ;no test
1378        #:phases
1379        (modify-phases %standard-phases
1380          (add-after 'unpack 'fix-makefile
1381            (lambda _
1382              (substitute* "makefile"
1383                (("cc -c") "gcc -c -fPIC"))
1384              #t))
1385          (add-after 'fix-makefile 'turn-off-banner
1386            (lambda _
1387              (substitute* "de.c"
1388                (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
1389              #t))
1390          (delete 'configure)            ;no configure script
1391          (replace 'install              ;no install target
1392            (lambda* (#:key outputs #:allow-other-keys)
1393              (let* ((out (assoc-ref outputs "out"))
1394                     (lib (string-append out "/lib"))
1395                     (inc (string-append out "/include/symmetrica"))
1396                     (doc (string-append out "/share/doc/symmetrica-" ,version))
1397                     (static "libsymmetrica.a"))
1398                ;; Build static library.
1399                (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
1400                (invoke "ranlib" static)
1401                ;; Install static library and headers.
1402                (for-each (lambda (f) (install-file f inc))
1403                          (find-files "." "\\.h$"))
1404                (install-file "libsymmetrica.a" lib)
1405                ;; Install documentation.
1406                (for-each (lambda (f) (install-file f doc))
1407                          (find-files "." "\\.doc$"))
1408                #t))))))
1409     (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
1410     (synopsis "Combinatoric C Library")
1411     (description "Symmetrica is a library for combinatorics.  It has support
1412 for the representation theory of the symmetric group and related groups,
1413 combinatorics of tableaux, symmetric functions and polynomials, Schubert
1414 polynomials, and the representation theory of Hecke algebras of type A_n.")
1415     (license license:public-domain)))
1416
1417 (define-public m4rie
1418   (package
1419     (name "m4rie")
1420     (version "20150908")
1421     (source (origin
1422               (method git-fetch)
1423               (uri (git-reference
1424                     (url "https://bitbucket.org/malb/m4rie")
1425                     (commit (string-append "release-" version))))
1426               (file-name (git-file-name name version))
1427               (sha256
1428                (base32
1429                 "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
1430     (build-system gnu-build-system)
1431     (native-inputs
1432      `(("autoconf" ,autoconf)
1433        ("automake" ,automake)
1434        ("libtool" ,libtool)))
1435     (inputs
1436      `(("m4ri" ,m4ri)))
1437     (synopsis "Arithmetic of dense matrices over F_{2^e}")
1438     (description "M4RI is a library for fast arithmetic with dense matrices
1439 over finite fields of characteristic 2.  So it extends the functionality
1440 of M4RI from F_2 to F_{2^e}.")
1441     (license license:gpl2+)
1442     (home-page "https://bitbucket.org/malb/m4rie/")))
1443
1444 (define-public eclib
1445   (package
1446     (name "eclib")
1447     (version "20190909")
1448     (source (origin
1449               (method git-fetch)
1450               (uri (git-reference
1451                     (url "https://github.com/JohnCremona/eclib/")
1452                     (commit (string-append "v" version))))
1453               (file-name (git-file-name name version))
1454               (sha256
1455                (base32
1456                 "1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n"))))
1457     (build-system gnu-build-system)
1458     (native-inputs
1459      `(("autoconf" ,autoconf)
1460        ("automake" ,automake)
1461        ("libtool" ,libtool)))
1462     (inputs
1463      `(("ntl" ,ntl)
1464        ("pari-gp" ,pari-gp)))
1465     (synopsis "Ranks of elliptic curves and modular symbols")
1466     (description "The eclib package includes mwrank (for 2-descent on
1467 elliptic curves over Q) and modular symbol code; it has been written by
1468 John Cremona to compute his elliptic curve database.")
1469     (license license:gpl2+)
1470     (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
1471                               "J.E.Cremona/mwrank/index.html"))))
1472
1473 (define-public lrcalc
1474   (package
1475     (name "lrcalc")
1476     (version "1.2")
1477     (source (origin
1478               (method git-fetch)
1479               (uri (git-reference
1480                     (url "https://bitbucket.org/asbuch/lrcalc")
1481                     (commit (string-append "lrcalc-" version))))
1482               (file-name (git-file-name name version))
1483               (sha256
1484                (base32
1485                 "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
1486               (patches (search-patches "lrcalc-includes.patch"))))
1487     (build-system gnu-build-system)
1488     (native-inputs
1489      `(("autoconf" ,autoconf)
1490        ("automake" ,automake)
1491        ("libtool" ,libtool)))
1492     (arguments
1493      `(#:phases
1494        (modify-phases %standard-phases
1495          (add-before 'build 'fix-permission
1496            (lambda _
1497              (chmod "lrcalc.maple.src" #o644)
1498              #t)))))
1499     (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
1500     (description "The Littlewood-Richardson Calculator (lrcalc) is a
1501 program designed to compute Littlewood-Richardson coefficients.  It computes
1502 single Littlewood-Richardson coefficients, products of Schur functions, or
1503 skew Schur functions.  In addition it computes products in the small quantum
1504 cohomology ring of a Grassmann variety.  The software package also includes
1505 a program that performs fast computation of the more general multiplicative
1506 structure constants of Schubert polynomials.")
1507     (license license:gpl2+)
1508     (home-page "https://sites.math.rutgers.edu/~asbuch/lrcalc/")))
1509
1510 (define-public iml
1511   (package
1512     (name "iml")
1513     (version "1.0.5")
1514     (source
1515      (origin
1516        (method url-fetch)
1517        (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
1518                            version ".tar.bz2"))
1519        (sha256
1520         (base32
1521          "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
1522     (build-system gnu-build-system)
1523     (inputs
1524      `(("gmp", gmp)
1525        ("cblas" ,openblas))) ; or any other BLAS library; the documentation
1526                              ; mentions ATLAS in particular
1527     (arguments
1528      `(#:configure-flags
1529        (list
1530         "--enable-shared"
1531         (string-append "--with-gmp-include="
1532                        (assoc-ref %build-inputs "gmp") "/include")
1533         (string-append "--with-gmp-lib="
1534                        (assoc-ref %build-inputs "gmp") "/lib")
1535         "--with-cblas=-lopenblas"
1536         (string-append "--with-cblas-include="
1537                        (assoc-ref %build-inputs "cblas") "/include")
1538         (string-append "--with-cblas-lib="
1539                        (assoc-ref %build-inputs "cblas") "/lib"))))
1540     (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
1541     (synopsis
1542      "Solver for systems of linear equations over the integers")
1543     (description
1544      "IML is a C library implementing algorithms for computing exact
1545 solutions to dense systems of linear equations over the integers.
1546 Currently, IML provides the following functionality:
1547
1548 @itemize
1549 @item Nonsingular rational system solving:
1550 compute the unique rational solution X to the system AX=B, where A and B
1551 are integer matrices, A nonsingular.
1552 @item Compute the right nullspace or kernel of an integer matrix.
1553 @item Certified linear system solving:
1554 compute a minimal denominator solution x to a system Ax=b, where b is an
1555 integer vector and A is an integer matrix with arbitrary shape and
1556 rank profile.
1557 @end itemize
1558
1559 In addition, IML provides some low level routines for a variety of mod p
1560 matrix operations: computing the row-echelon form, determinant, rank
1561 profile, and inverse of a mod p matrix. These mod p routines are not
1562 general purpose; they require that p satisfy some preconditions based on
1563 the dimension of the input matrix (usually p should be prime and should be
1564 no more than about 20 bits long).")
1565     (license license:bsd-3)))