gnu/packages/algebra.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Andreas Enge <andreas@enge.fr>
   3 ;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
   4 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
   5 ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
   6 ;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
   7 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
   8 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
   9 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
  10 ;;; Copyright © 2017, 2019 Eric Bavier <bavier@member.fsf.org>
  11 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
  12 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
  13 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
  14 ;;;
  15 ;;; This file is part of GNU Guix.
  16 ;;;
  17 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  18 ;;; under the terms of the GNU General Public License as published by
  19 ;;; the Free Software Foundation; either version 3 of the License, or (at
  20 ;;; your option) any later version.
  21 ;;;
  22 ;;; GNU Guix is distributed in the hope that it will be useful, but
  23 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  24 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  25 ;;; GNU General Public License for more details.
  26 ;;;
  27 ;;; You should have received a copy of the GNU General Public License
  28 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  29
  30 (define-module (gnu packages algebra)
  31   #:use-module (gnu packages)
  32   #:use-module (gnu packages autotools)
  33   #:use-module (gnu packages bison)
  34   #:use-module (gnu packages check)
  35   #:use-module (gnu packages compression)
  36   #:use-module (gnu packages cpp)
  37   #:use-module (gnu packages documentation)
  38   #:use-module (gnu packages ed)
  39   #:use-module (gnu packages flex)
  40   #:use-module (gnu packages fltk)
  41   #:use-module (gnu packages gl)
  42   #:use-module (gnu packages graphviz)
  43   #:use-module (gnu packages image)
  44   #:use-module (gnu packages java)
  45   #:use-module (gnu packages maths)
  46   #:use-module (gnu packages mpi)
  47   #:use-module (gnu packages multiprecision)
  48   #:use-module (gnu packages perl)
  49   #:use-module (gnu packages pkg-config)
  50   #:use-module (gnu packages pulseaudio)
  51   #:use-module (gnu packages python)
  52   #:use-module (gnu packages python-xyz)
  53   #:use-module (gnu packages readline)
  54   #:use-module (gnu packages shells)
  55   #:use-module (gnu packages tex)
  56   #:use-module (gnu packages texinfo)
  57   #:use-module (gnu packages xiph)
  58   #:use-module (gnu packages xorg)
  59   #:use-module (guix build-system ant)
  60   #:use-module (guix build-system gnu)
  61   #:use-module (guix build-system cmake)
  62   #:use-module (guix build-system python)
  63   #:use-module (guix download)
  64   #:use-module (guix git-download)
  65   #:use-module (guix hg-download)
  66   #:use-module ((guix licenses) #:prefix license:)
  67   #:use-module (guix packages)
  68   #:use-module (guix utils))
  69
  70
  71 (define-public mpfrcx
  72   (package
  73    (name "mpfrcx")
  74    (version "0.5")
  75    (source (origin
  76             (method url-fetch)
  77             (uri (string-append
  78                   "http://www.multiprecision.org/downloads/mpfrcx-"
  79                   version ".tar.gz"))
  80             (sha256
  81              (base32
  82               "1s968480ymv6w0rnvfp9mxvx98hvi29fkvw8nk4ggzc6azxgwybs"))))
  83    (build-system gnu-build-system)
  84    (propagated-inputs
  85      `(("gmp" ,gmp)
  86        ("mpfr" ,mpfr)
  87        ("mpc"  ,mpc))) ; Header files are included by mpfrcx.h.
  88    (synopsis "Arithmetic of polynomials over arbitrary precision numbers")
  89    (description
  90     "Mpfrcx is a library for the arithmetic of univariate polynomials over
  91 arbitrary precision real (mpfr) or complex (mpc) numbers, without control
  92 on the rounding.  For the time being, only the few functions needed to
  93 implement the floating point approach to complex multiplication are
  94 implemented.  On the other hand, these comprise asymptotically fast
  95 multiplication routines such as Toom–Cook and the FFT.")
  96    (license license:lgpl3+)
  97    (home-page "http://www.multiprecision.org/mpfrcx/")))
  98
  99 (define-public gf2x
 100   (package
 101    (name "gf2x")
 102    (version "1.2")
 103    (source (origin
 104             (method url-fetch)
 105             (uri (string-append
 106                   "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-"
 107                   version ".tar.gz"))
 108             (sha256
 109              (base32
 110               "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1"))))
 111    (build-system gnu-build-system)
 112    (synopsis "Arithmetic of polynomials over binary finite fields")
 113    (description
 114     "The gf2x library provides arithmetic of polynomials over finite fields
 115 of characteristic 2.  It implements the multiplication, squaring and
 116 greatest common divisor operations.")
 117    (license license:gpl3+)
 118    (home-page "https://gforge.inria.fr/projects/gf2x/")))
 119
 120 (define-public cm
 121   (package
 122    (name "cm")
 123    (version "0.3")
 124    (source (origin
 125             (method url-fetch)
 126             (uri (string-append
 127                   "http://www.multiprecision.org/cm/download/cm-"
 128                   version ".tar.gz"))
 129             (sha256
 130              (base32
 131               "1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc"))))
 132    (build-system gnu-build-system)
 133    (propagated-inputs
 134      `(("mpfrcx" ,mpfrcx)
 135        ("zlib" ,zlib))) ; Header files included from cm_common.h.
 136    (inputs
 137      `(("pari-gp"  ,pari-gp)))
 138    (synopsis "CM constructions for elliptic curves")
 139    (description
 140     "The CM software implements the construction of ring class fields of
 141 imaginary quadratic number fields and of elliptic curves with complex
 142 multiplication via floating point approximations.  It consists of libraries
 143 that can be called from within a C program and of executable command
 144 line applications.")
 145    (license license:gpl3+)
 146    (home-page "http://www.multiprecision.org/cm/")))
 147
 148 (define-public fplll
 149   (package
 150     (name "fplll")
 151     (version "5.2.1")
 152     (source (origin
 153               (method git-fetch)
 154               (uri (git-reference
 155                     (url "https://github.com/fplll/fplll.git")
 156                     (commit version)))
 157               (file-name (git-file-name name version))
 158               (sha256
 159                (base32
 160                 "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg"))))
 161     (build-system gnu-build-system)
 162     (native-inputs
 163      `(("autoconf" ,autoconf)
 164        ("automake" ,automake)
 165        ("libtool" ,libtool)))
 166     (inputs
 167      `(("gmp" ,gmp)
 168        ("mpfr" ,mpfr)))
 169     (home-page "https://github.com/fplll/fplll")
 170     (synopsis "Library for LLL-reduction of euclidean lattices")
 171     (description
 172      "fplll contains implementations of several lattice algorithms.
 173 The implementation relies on floating-point orthogonalization, and LLL
 174 is central to the code, hence the name.
 175
 176 It includes implementations of floating-point LLL reduction
 177 algorithms, offering different speed/guarantees ratios.  It contains
 178 a @emph{wrapper} choosing the estimated best sequence of variants in
 179 order to provide a guaranteed output as fast as possible.  In the case
 180 of the wrapper, the succession of variants is oblivious to the user.
 181
 182 It includes an implementation of the BKZ reduction algorithm,
 183 including the BKZ-2.0 improvements (extreme enumeration
 184 pruning, pre-processing of blocks, early termination).  Additionally,
 185 Slide reduction and self dual BKZ are supported.
 186
 187 It also includes a floating-point implementation of the
 188 Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice
 189 vector.  For the same task, the GaussSieve algorithm is also available
 190 in fplll.  Finally, it contains a variant of the enumeration algorithm
 191 that computes a lattice vector closest to a given vector belonging to
 192 the real span of the lattice.")
 193     (license license:lgpl2.1+)))
 194
 195 (define-public python-fpylll
 196   (package
 197     (name "python-fpylll")
 198     (version "0.4.1")
 199     (source
 200      (origin
 201        ;; Pypi contains and older release, so we use a tagged release from
 202        ;; Github instead.
 203        (method git-fetch)
 204        (uri (git-reference
 205              (url "https://github.com/fplll/fpylll.git")
 206              (commit (string-append version "dev"))))
 207        (file-name (git-file-name name version))
 208        (sha256
 209         (base32
 210          "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
 211     (build-system python-build-system)
 212     (inputs
 213      `(("fplll" ,fplll)
 214        ("gmp" ,gmp)
 215        ("mpfr" ,mpfr)
 216        ("pari-gp" ,pari-gp)))
 217     (propagated-inputs
 218      `(("cysignals" ,python-cysignals)
 219        ("cython" ,python-cython)
 220        ("flake8" ,python-flake8)
 221        ("numpy" ,python-numpy)
 222        ("pytest" ,python-pytest)))
 223     (home-page "https://github.com/fplll/fpylll")
 224     (synopsis "Python interface for fplll")
 225     (description "fpylll is a Python wrapper for fplll.")
 226     (license license:gpl2+)))
 227
 228 (define-public pari-gp
 229   (package
 230     (name "pari-gp")
 231     (version "2.11.4")
 232     (source (origin
 233               (method url-fetch)
 234               (uri (string-append
 235                     "https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
 236                     version ".tar.gz"))
 237               (sha256
 238                (base32
 239                 "070bjw4kg7r6lqs1hfs08n5fmjv90cpwflp3wr04hbrmyz28zj5z"))))
 240     (build-system gnu-build-system)
 241     (native-inputs
 242      `(("texlive" ,(texlive-union
 243                     (list texlive-amsfonts)))))
 244     (inputs `(("gmp" ,gmp)
 245               ("libx11" ,libx11)
 246               ("perl" ,perl)
 247               ("readline" ,readline)))
 248     (arguments
 249      '(#:make-flags '("all")
 250        #:test-target "dobench"
 251        #:phases
 252        (modify-phases %standard-phases
 253          (replace 'configure
 254            (lambda* (#:key outputs #:allow-other-keys)
 255              (invoke "./Configure"
 256                      (string-append "--prefix="
 257                                     (assoc-ref outputs "out"))))))))
 258     (synopsis "PARI/GP, a computer algebra system for number theory")
 259     (description
 260      "PARI/GP is a widely used computer algebra system designed for fast
 261 computations in number theory (factorisations, algebraic number theory,
 262 elliptic curves...), but it also contains a large number of other useful
 263 functions to compute with mathematical entities such as matrices,
 264 polynomials, power series, algebraic numbers, etc., and a lot of
 265 transcendental functions.
 266 PARI is also available as a C library to allow for faster computations.")
 267     (license license:gpl2+)
 268     (home-page "https://pari.math.u-bordeaux.fr/")))
 269
 270 (define-public gp2c
 271   (package
 272    (name "gp2c")
 273    (version "0.0.11pl3")
 274    (source (origin
 275             (method url-fetch)
 276             (uri (string-append
 277                   "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
 278                   version ".tar.gz"))
 279             (sha256
 280               (base32
 281                 "0yymbrgyjw500hqgmkj5m4nmscd7c9rs9w2c96lxgrcyab8krhrm"))))
 282    (build-system gnu-build-system)
 283    (native-inputs `(("perl" ,perl)))
 284    (inputs `(("pari-gp" ,pari-gp)))
 285    (arguments
 286     '(#:configure-flags
 287       (list (string-append "--with-paricfg="
 288                            (assoc-ref %build-inputs "pari-gp")
 289                            "/lib/pari/pari.cfg"))))
 290    (synopsis "PARI/GP, a computer algebra system for number theory")
 291    (description
 292     "PARI/GP is a widely used computer algebra system designed for fast
 293 computations in number theory (factorisations, algebraic number theory,
 294 elliptic curves...), but it also contains a large number of other useful
 295 functions to compute with mathematical entities such as matrices,
 296 polynomials, power series, algebraic numbers, etc., and a lot of
 297 transcendental functions.
 298 PARI is also available as a C library to allow for faster computations.
 299
 300 GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
 301    (license license:gpl2)
 302    (home-page "https://pari.math.u-bordeaux.fr/")))
 303
 304 (define fplll-4-cmh
 305   (package
 306     (inherit fplll)
 307     (name "fplll")
 308     (version "4.0.4")
 309     (source
 310      (origin
 311        (method url-fetch)
 312        (uri (string-append
 313              "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
 314              version ".tar.gz"))
 315        (sha256
 316         (base32 "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))))
 317
 318 (define-public cmh
 319   (package
 320    (name "cmh")
 321    (version "1.0")
 322    (source (origin
 323             (method url-fetch)
 324             (uri (string-append
 325                   "https://gforge.inria.fr/frs/download.php/33497/cmh-"
 326                   version ".tar.gz"))
 327             (sha256
 328              (base32
 329               "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
 330    (build-system gnu-build-system)
 331    (inputs
 332      `(("gmp" ,gmp)
 333        ("mpfr" ,mpfr)
 334        ("mpc" ,mpc)
 335        ("mpfrcx" ,mpfrcx)
 336        ("fplll" ,fplll-4-cmh)
 337        ("pari-gp"  ,pari-gp)))
 338    (synopsis "Igusa class polynomial computations")
 339    (description
 340     "The CMH software computes Igusa (genus 2) class polynomials, which
 341 parameterize the CM points in the moduli space of 2-dimensional abelian
 342 varieties, i.e. Jacobians of hyperelliptic curves.
 343 It can also be used to compute theta constants at arbitrary
 344 precision.")
 345    (license license:gpl3+)
 346    (home-page "http://cmh.gforge.inria.fr/")))
 347
 348 (define-public giac
 349   (package
 350     (name "giac")
 351     (version "1.5.0-87")
 352     (source
 353      (origin
 354        (method url-fetch)
 355        ;; "~parisse/giac" is not used because the maintainer regularly
 356        ;; overwrites the release tarball there, introducing a checksum
 357        ;; mismatch every time.  See
 358        ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
 359        (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
 360                            "~parisse/debian/dists/stable/main/source/"
 361                            "giac_" version ".tar.gz"))
 362        (sha256
 363         (base32 "1d0h1yb7qvh9x7wwv9yrzmcp712f49w1iljkxp4y6g9pzsmg1mmv"))))
 364     (build-system gnu-build-system)
 365     (arguments
 366      `(#:modules ((ice-9 ftw)
 367                   (guix build utils)
 368                   (guix build gnu-build-system))
 369        #:phases
 370        (modify-phases %standard-phases
 371          (add-after 'unpack 'patch-bin-cp
 372            ;; Some Makefiles contain hard-coded "/bin/cp".
 373            (lambda _
 374              (substitute* (find-files "doc" "^Makefile")
 375                (("/bin/cp") (which "cp")))
 376              #t))
 377          (add-after 'unpack 'disable-failing-test
 378            ;; FIXME: Test failing.  Not sure why.
 379            (lambda _
 380              (substitute* "check/Makefile.in"
 381                (("chk_fhan11") ""))
 382              #t))
 383          (add-after 'install 'fix-doc
 384            (lambda* (#:key outputs #:allow-other-keys)
 385              (let ((out (assoc-ref outputs "out")))
 386                ;; Most French documentation has a non-commercial
 387                ;; license, so we need to remove it.
 388                (with-directory-excursion (string-append out "/share/giac/doc/fr")
 389                  (for-each delete-file-recursively
 390                            '("cascas" "casexo" "casgeo" "casrouge" "cassim"
 391                              "castor")))
 392                ;; Remove duplicate documentation in
 393                ;; "%out/share/doc/giac/", where Xcas does not expect
 394                ;; to find it.
 395                (delete-file-recursively (string-append out "/share/doc/giac"))
 396                #t)))
 397          (add-after 'install 'remove-unnecessary-executable
 398            (lambda* (#:key outputs #:allow-other-keys)
 399              (let ((out (assoc-ref outputs "out")))
 400                (delete-file (string-append out "/bin/xcasnew"))
 401                #t))))))
 402     (inputs
 403      ;;; TODO: Add libnauty.
 404      `(("fltk" ,fltk)
 405        ("glpk" ,glpk)
 406        ("gmp" ,gmp)
 407        ("gsl" ,gsl)
 408        ("lapack" ,lapack)
 409        ("libao" ,ao)
 410        ("libjpeg" ,libjpeg-turbo)
 411        ("libpng" ,libpng)
 412        ("libsamplerate" ,libsamplerate)
 413        ("libx11" ,libx11)
 414        ("libxinerama" ,libxinerama)
 415        ("libxft" ,libxft)
 416        ("libxt" ,libxt)
 417        ("mesa" ,mesa)
 418        ("mpfi" ,mpfi)
 419        ("mpfr" ,mpfr)
 420        ("ntl" ,ntl)
 421        ("perl" ,perl)
 422        ("pari-gp" ,pari-gp)
 423        ("tcsh" ,tcsh)))
 424     (native-inputs
 425      `(("bison" ,bison)
 426        ("flex" ,flex)
 427        ("readline" ,readline)
 428        ("texlive" ,texlive-tiny)))
 429     (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
 430     (synopsis "Computer algebra system")
 431     (description
 432      "Giac/Xcas is a computer algebra system.  It has a compatibility mode for
 433 maple, mupad and the TI89.  It is available as a standalone program (graphic
 434 or text interfaces) or as a C++ library.")
 435     (license license:gpl3+)))
 436
 437 (define-public flint
 438   (package
 439    (name "flint")
 440    (version "2.5.2")
 441    (source (origin
 442             (method url-fetch)
 443             (uri (string-append
 444                   "http://flintlib.org/flint-"
 445                   version ".tar.gz"))
 446             (sha256 (base32
 447                      "11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
 448             (patches (search-patches "flint-ldconfig.patch"))))
 449    (build-system gnu-build-system)
 450    (propagated-inputs
 451     `(("gmp" ,gmp)
 452       ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
 453    (arguments
 454     `(#:parallel-tests? #f ; seems to be necessary on arm
 455       #:phases
 456        (modify-phases %standard-phases
 457          (replace 'configure
 458            (lambda* (#:key inputs outputs #:allow-other-keys)
 459              (let ((out (assoc-ref outputs "out"))
 460                    (gmp (assoc-ref inputs "gmp"))
 461                    (mpfr (assoc-ref inputs "mpfr")))
 462                ;; do not pass "--enable-fast-install", which makes the
 463                ;; homebrew configure process fail
 464                (invoke "./configure"
 465                        (string-append "--prefix=" out)
 466                        (string-append "--with-gmp=" gmp)
 467                        (string-append "--with-mpfr=" mpfr))
 468                #t))))))
 469    (synopsis "Fast library for number theory")
 470    (description
 471     "FLINT is a C library for number theory.  It supports arithmetic
 472 with numbers, polynomials, power series and matrices over many base
 473 rings, including multiprecision integers and rationals, integers
 474 modulo n, p-adic numbers, finite fields (prime and non-prime order)
 475 and real and complex numbers (via the Arb extension library).
 476
 477 Operations that can be performed include conversions, arithmetic,
 478 GCDs, factoring, solving linear systems, and evaluating special
 479 functions.  In addition, FLINT provides various low-level routines for
 480 fast arithmetic.")
 481    (license license:gpl2+)
 482    (home-page "http://flintlib.org/")))
 483
 484 (define-public arb
 485   (package
 486     (name "arb")
 487     (version "2.17.0")
 488     (source (origin
 489               (method git-fetch)
 490               (uri (git-reference
 491                     (url "https://github.com/fredrik-johansson/arb.git")
 492                     (commit version)))
 493               (file-name (git-file-name name version))
 494               (sha256
 495                (base32
 496                 "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1"))))
 497     (build-system gnu-build-system)
 498     (propagated-inputs
 499      `(("flint" ,flint)))               ; flint.h is included by arf.h
 500     (inputs
 501      `(("gmp" ,gmp)
 502        ("mpfr" ,mpfr)))
 503     (arguments
 504      `(#:phases
 505        (modify-phases %standard-phases
 506          (replace 'configure
 507            (lambda* (#:key inputs outputs #:allow-other-keys)
 508              (let ((out (assoc-ref outputs "out"))
 509                    (flint (assoc-ref inputs "flint"))
 510                    (gmp (assoc-ref inputs "gmp"))
 511                    (mpfr (assoc-ref inputs "mpfr")))
 512                ;; Do not pass "--enable-fast-install", which makes the
 513                ;; homebrew configure process fail.
 514                (invoke "./configure"
 515                        (string-append "--prefix=" out)
 516                        (string-append "--with-flint=" flint)
 517                        (string-append "--with-gmp=" gmp)
 518                        (string-append "--with-mpfr=" mpfr))))))))
 519     (synopsis "Arbitrary precision floating-point ball arithmetic")
 520     (description
 521      "Arb is a C library for arbitrary-precision floating-point ball
 522 arithmetic.  It supports efficient high-precision computation with
 523 polynomials, power series, matrices and special functions over the
 524 real and complex numbers, with automatic, rigorous error control.")
 525     (license license:lgpl2.1+)
 526     (home-page "http://arblib.org")))
 527
 528 (define-public python-flint
 529   (package
 530     (name "python-flint")
 531     (version "0.3.0")
 532     (source (origin
 533               (method git-fetch)
 534               (uri (git-reference
 535                     (url "https://github.com/fredrik-johansson/python-flint.git")
 536                     (commit version)))
 537               (file-name (git-file-name name version))
 538               (sha256
 539                (base32
 540                 "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
 541               (patches (search-patches "python-flint-includes.patch"))))
 542     (build-system python-build-system)
 543     (native-inputs
 544      `(("python-cython" ,python-cython)))
 545     (propagated-inputs
 546      `(("python-numpy" ,python-numpy)))
 547     (inputs
 548      `(("arb" ,arb)
 549        ("flint" ,flint)))
 550     (synopsis "Python module wrapping ARB and FLINT")
 551     (description
 552      "Python-flint is a Python extension module wrapping FLINT
 553 (Fast Library for Number Theory) and Arb (arbitrary-precision ball
 554 arithmetic).  It supports integers, rationals, modular integers,
 555 real and complex ball arithmetic, polynomials and matrices over all
 556 these types and other mathematical functions.")
 557     (license license:expat)
 558     (home-page "http://fredrikj.net/python-flint/")))
 559
 560 (define-public ntl
 561   (package
 562    (name "ntl")
 563    (version "11.4.3")
 564    (source (origin
 565             (method url-fetch)
 566             (uri (string-append "https://shoup.net/ntl/ntl-"
 567                                 version ".tar.gz"))
 568             (sha256
 569              (base32
 570               "1lisp3064rch3jaa2wrhy1s9kll7i3ka3d0y6lj6l3l4ckfcrhdp"))
 571             (modules '((guix build utils)))
 572             (snippet
 573              '(begin
 574                 (delete-file-recursively "src/libtool-origin")
 575                 #t))))
 576    (build-system gnu-build-system)
 577    (native-inputs
 578     `(("libtool" ,libtool)
 579       ("perl" ,perl))) ; for configuration
 580    (inputs
 581     `(("gmp" ,gmp)
 582       ("gf2x" ,gf2x)))
 583    (arguments
 584     `(#:phases
 585       (modify-phases %standard-phases
 586         (replace 'configure
 587          (lambda* (#:key inputs outputs #:allow-other-keys)
 588            (chdir "src")
 589            (invoke "./configure"
 590                     (string-append "PREFIX=" (assoc-ref outputs "out"))
 591                     (string-append "LIBTOOL=" (assoc-ref inputs "libtool") "/bin/libtool")
 592                     ;; set the library prefixes explicitly so that they get
 593                     ;; embedded in the .la file
 594                     (string-append "GMP_PREFIX=" (assoc-ref inputs "gmp"))
 595                     (string-append "GF2X_PREFIX=" (assoc-ref inputs "gf2x"))
 596                     ;; Do not build especially for the build machine.
 597                     "NATIVE=off"
 598                     "NTL_GF2X_LIB=on"
 599                     "SHARED=on"))))))
 600    (synopsis "C++ library for number theory")
 601    (description
 602     "NTL is a C++ library providing data structures and algorithms
 603 for manipulating signed, arbitrary length integers, and for vectors,
 604 matrices, and polynomials over the integers and over finite fields.")
 605    (license license:gpl2+)
 606    (home-page "https://shoup.net/ntl/")))
 607
 608 (define-public singular
 609   (package
 610    (name "singular")
 611    (version "4.1.2p1")
 612    (source
 613     (origin
 614       (method url-fetch)
 615       (uri
 616        (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
 617                       "Singular/SOURCES/"
 618                       (string-join
 619                        (string-split
 620                         (string-trim-right version #\p
 621                                            0 (1- (string-length version)))
 622                         #\.) "-")
 623                       "/singular-" version ".tar.gz"))
 624              (sha256 (base32
 625                       "0kvd55353fiqyq1msmi0kka66n5h0aqs7m3km60r01b1w2f8085m"))))
 626    (build-system gnu-build-system)
 627    (native-inputs
 628     `(("doxygen" ,doxygen)
 629       ("graphviz" ,graphviz)
 630       ("perl" ,perl)))
 631    (inputs
 632     `(("cddlib" ,cddlib)
 633       ("gmp" ,gmp)
 634       ("flint" ,flint)
 635       ("mpfr" ,mpfr)
 636       ("ntl" ,ntl)
 637       ("python" ,python-2)
 638       ("readline" ,readline)))
 639    (arguments
 640     `(#:configure-flags
 641       (list (string-append "--with-ntl="
 642                            (assoc-ref %build-inputs "ntl")))))
 643    (synopsis "Computer algebra system for polynomial computations")
 644    (description
 645     "Singular is a computer algebra system for polynomial computations,
 646 with special emphasis on commutative and non-commutative algebra, algebraic
 647 geometry and singularity theory.")
 648    ;; Singular itself is dual licensed gpl2 or gpl3, but some of the
 649    ;; libraries with which it links are licensed under lgpl3+, so the
 650    ;; combined work becomes gpl3. See COPYING in the source code.
 651    (license license:gpl3)
 652    (home-page "http://www.singular.uni-kl.de/index.php")))
 653
 654 (define-public gmp-ecm
 655   (package
 656    (name "gmp-ecm")
 657    (version "7.0.4")
 658    (source (origin
 659              (method url-fetch)
 660              ;; Use the ‘Latest version’ link for a stable URI across releases.
 661              (uri (string-append "https://gforge.inria.fr/frs/download.php/"
 662                                  "latestfile/160/ecm-" version ".tar.gz"))
 663              (sha256 (base32
 664                       "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"))))
 665    (build-system gnu-build-system)
 666    (inputs
 667     `(("gmp" ,gmp)))
 668    (arguments
 669     `(#:configure-flags '("--enable-shared"
 670                           ;; Disable specific assembly routines, which depend
 671                           ;; on the subarchitecture of the build machine,
 672                           ;; and use gmp instead.
 673                           "--disable-asm-redc")))
 674    (synopsis "Integer factorization library using the elliptic curve method")
 675    (description
 676     "GMP-ECM factors integers using the elliptic curve method (ECM) as well
 677 as the P-1 and P+1 algorithms.  It provides a library and a stand-alone
 678 binary.")
 679    ;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+,
 680    ;; so the combined work is under gpl3+.
 681    (license license:gpl3+)
 682    (home-page "http://ecm.gforge.inria.fr/")))
 683
 684 (define-public bc
 685   (package
 686     (name "bc")
 687     (version "1.07.1")
 688     (source (origin
 689              (method url-fetch)
 690              (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
 691              (sha256
 692               (base32
 693                "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))
 694              (patches (search-patches "bc-fix-cross-compilation.patch"))))
 695     (build-system gnu-build-system)
 696     (native-inputs
 697      `(("automake" ,automake)
 698        ("autoconf" ,autoconf)
 699        ("ed" ,ed)
 700        ("flex" ,flex)
 701        ("texinfo" ,texinfo)))
 702     (arguments
 703      '(#:configure-flags
 704        (list "--with-readline")
 705        #:phases
 706        (modify-phases %standard-phases
 707          (add-after 'unpack 'autogen
 708            (lambda _
 709              (invoke "autoreconf" "-vif"))))))
 710     (home-page "https://www.gnu.org/software/bc/")
 711     (synopsis "Arbitrary precision numeric processing language")
 712     (description
 713      "bc is an arbitrary precision numeric processing language.  It includes
 714 an interactive environment for evaluating mathematical statements.  Its
 715 syntax is similar to that of C, so basic usage is familiar.  It also includes
 716 \"dc\", a reverse-polish calculator.")
 717     (license license:gpl2+)))
 718
 719 ;; The original kiss-fft does not have a complete build system and does not
 720 ;; build any shared libraries.  This is a fork used by Extempore.
 721 (define-public kiss-fft-for-extempore
 722   (package
 723     (name "kiss-fft-for-extempore")
 724     (version "1.3.0")
 725     (source (origin
 726               (method git-fetch)
 727               (uri (git-reference
 728                     (url "https://github.com/extemporelang/kiss_fft.git")
 729                     (commit version)))
 730               (file-name (git-file-name name version))
 731               (sha256
 732                (base32
 733                 "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
 734     (build-system cmake-build-system)
 735     (arguments `(#:tests? #f)) ; no tests included
 736     ;; Extempore refuses to build on architectures other than x86_64
 737     (supported-systems '("x86_64-linux"))
 738     (home-page "https://github.com/extemporelang/kiss_fft")
 739     (synopsis "Mixed-radix Fast Fourier Transform")
 740     (description
 741      "Kiss FFT attempts to be a reasonably efficient, moderately useful FFT
 742 that can use fixed or floating data types and can easily be incorporated into
 743 a C program.")
 744     (license license:bsd-3)))
 745
 746 (define-public fftw
 747   (package
 748     (name "fftw")
 749     (version "3.3.8")
 750     (source (origin
 751              (method url-fetch)
 752              (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
 753                                  version".tar.gz"))
 754              (sha256
 755               (base32
 756                "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
 757     (build-system gnu-build-system)
 758     (arguments
 759      `(#:configure-flags
 760        '("--enable-shared" "--enable-openmp" "--enable-threads"
 761          ,@(let ((system (or (%current-target-system) (%current-system))))
 762              ;; Enable SIMD extensions for codelets.  See details at:
 763              ;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>.
 764              (cond
 765               ((string-prefix? "x86_64" system)
 766                '("--enable-sse2" "--enable-avx" "--enable-avx2"
 767                  "--enable-avx512" "--enable-avx-128-fma"))
 768               ((string-prefix? "i686" system)
 769                '("--enable-sse2"))
 770               ((string-prefix? "aarch64" system)
 771                ;; Note that fftw supports NEON on 32-bit ARM only when
 772                ;; compiled for single-precision.
 773                '("--enable-neon"))
 774               (else
 775                '())))
 776          ;; By default '-mtune=native' is used.  However, that may cause the
 777          ;; use of ISA extensions (e.g. AVX) that are not necessarily
 778          ;; available on the user's machine when that package is built on a
 779          ;; different machine.
 780          "ax_cv_c_flags__mtune_native=no")))
 781     (native-inputs `(("perl" ,perl)))
 782     (home-page "http://fftw.org")
 783     (synopsis "Computing the discrete Fourier transform")
 784     (description
 785      "FFTW is a C subroutine library for computing the discrete Fourier
 786 transform (DFT) in one or more dimensions, of arbitrary input size, and of
 787 both real and complex data (as well as of even/odd data---i.e. the discrete
 788 cosine/ sine transforms or DCT/DST).")
 789     (license license:gpl2+)))
 790
 791 (define-public fftwf
 792   (package (inherit fftw)
 793     (name "fftwf")
 794     (arguments
 795      (substitute-keyword-arguments (package-arguments fftw)
 796        ((#:configure-flags fftw-configure-flags)
 797         `(cons* "--enable-single"
 798                 ,@(if (string-prefix? "arm" (or (%current-target-system)
 799                                                 (%current-system)))
 800                       ;; fftw supports NEON on 32-bit ARM only when compiled
 801                       ;; for single-precision, so add it here.
 802                       '("--enable-neon")
 803                       '())
 804                 ,fftw-configure-flags))))
 805     (description
 806      (string-append (package-description fftw)
 807                     "  Single-precision version."))))
 808
 809 (define-public fftw-openmpi
 810   (package (inherit fftw)
 811     (name "fftw-openmpi")
 812     (inputs
 813      `(("openmpi" ,openmpi)
 814        ,@(package-inputs fftw)))
 815     (arguments
 816      (substitute-keyword-arguments (package-arguments fftw)
 817        ((#:configure-flags cf)
 818         `(cons "--enable-mpi" ,cf))
 819        ((#:phases phases '%standard-phases)
 820         `(modify-phases ,phases
 821            (add-before 'check 'mpi-setup
 822              ,%openmpi-setup)))))
 823     (description
 824      (string-append (package-description fftw)
 825                     "  With OpenMPI parallelism support."))))
 826
 827 (define-public java-la4j
 828   (package
 829     (name "java-la4j")
 830     (version "0.6.0")
 831     (source (origin
 832               (method git-fetch)
 833               (uri (git-reference
 834                     (url "https://github.com/vkostyukov/la4j.git")
 835                     (commit version)))
 836               (file-name (string-append name "-" version "-checkout"))
 837               (sha256
 838                (base32
 839                 "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
 840     (build-system ant-build-system)
 841     (arguments
 842      `(#:jar-name "la4j.jar"
 843        #:jdk ,icedtea-8
 844        #:test-exclude (list "**/Abstract*.java"
 845                             "**/MatrixTest.java"
 846                             "**/DenseMatrixTest.java"
 847                             "**/SparseMatrixTest.java"
 848                             "**/VectorTest.java"
 849                             "**/SparseVectorTest.java"
 850                             "**/DenseVectorTest.java")))
 851     (native-inputs
 852      `(("java-junit" ,java-junit)
 853        ("java-hamcrest-core" ,java-hamcrest-core)))
 854     (home-page "http://la4j.org/")
 855     (synopsis "Java library that provides Linear Algebra primitives and algorithms")
 856     (description "The la4j library is a Java library that provides Linear
 857 Algebra primitives (matrices and vectors) and algorithms.  The key features of
 858 the la4j library are:
 859
 860 @itemize
 861 @item No dependencies and tiny size
 862 @item Fluent object-oriented/functional API
 863 @item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
 864 @item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
 865 @item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
 866 @item MatrixMarket/CSV IO formats support for matrices and vectors
 867 @end itemize\n")
 868     (license license:asl2.0)))
 869
 870 (define-public java-jlargearrays
 871   (package
 872     (name "java-jlargearrays")
 873     (version "1.6")
 874     (source (origin
 875               (method url-fetch)
 876               (uri (string-append "https://repo1.maven.org/maven2/"
 877                                   "pl/edu/icm/JLargeArrays/"
 878                                   version "/JLargeArrays-" version
 879                                   "-sources.jar"))
 880               (file-name (string-append name "-" version ".jar"))
 881               (sha256
 882                (base32
 883                 "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
 884     (build-system ant-build-system)
 885     (arguments
 886      `(#:jar-name "jlargearrays.jar"
 887        #:tests? #f ; tests are not included in the release archive
 888        #:jdk ,icedtea-8))
 889     (propagated-inputs
 890      `(("java-commons-math3" ,java-commons-math3)))
 891     (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
 892     (synopsis "Library of one-dimensional arrays that can store up to 263 elements")
 893     (description "JLargeArrays is a Java library of one-dimensional arrays
 894 that can store up to 263 elements.")
 895     (license license:bsd-2)))
 896
 897 (define-public java-jtransforms
 898   (package
 899     (name "java-jtransforms")
 900     (version "3.1")
 901     (source (origin
 902               (method url-fetch)
 903               (uri (string-append "https://repo1.maven.org/maven2/"
 904                                   "com/github/wendykierp/JTransforms/"
 905                                   version "/JTransforms-" version "-sources.jar"))
 906               (sha256
 907                (base32
 908                 "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
 909     (build-system ant-build-system)
 910     (arguments
 911      `(#:jar-name "jtransforms.jar"
 912        #:tests? #f ; tests are not included in the release archive
 913        #:jdk ,icedtea-8))
 914     (propagated-inputs
 915      `(("java-commons-math3" ,java-commons-math3)
 916        ("java-jlargearrays" ,java-jlargearrays)))
 917     (home-page "https://github.com/wendykierp/JTransforms")
 918     (synopsis "Multithreaded FFT library written in pure Java")
 919     (description "JTransforms is a multithreaded FFT library written in pure
 920 Java.  Currently, four types of transforms are available: @dfn{Discrete
 921 Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
 922 Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
 923     (license license:bsd-2)))
 924
 925 (define-public eigen
 926   (package
 927     (name "eigen")
 928     (version "3.3.7")
 929     (source (origin
 930               (method url-fetch)
 931               (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
 932                                   version ".tar.bz2"))
 933               (sha256
 934                (base32
 935                 "1km3fyfzyqfdvmnl79drps3fjwnz3zbh0c7l34mfbqyvvs8cy4wz"))
 936               (file-name (string-append name "-" version ".tar.bz2"))
 937               (patches (search-patches "eigen-stabilise-sparseqr-test.patch"))
 938               (modules '((guix build utils)))
 939               (snippet
 940                ;; There are 3 test failures in the "unsupported" directory,
 941                ;; but maintainers say it's a known issue and it's unsupported
 942                ;; anyway, so just skip them.
 943                '(begin
 944                   (substitute* "unsupported/CMakeLists.txt"
 945                     (("add_subdirectory\\(test.*")
 946                      "# Do not build the tests for unsupported features.\n"))
 947                   #t))))
 948     (build-system cmake-build-system)
 949     (arguments
 950      '(;; Turn off debugging symbols to save space.
 951        #:build-type "Release"
 952
 953        #:phases (modify-phases %standard-phases
 954                   (replace 'check
 955                     (lambda _
 956                       (let* ((cores  (parallel-job-count))
 957                              (dash-j (format #f "-j~a" cores)))
 958                         (setenv "EIGEN_SEED" "1") ;for reproducibility
 959                         ;; First build the tests, in parallel.  See
 960                         ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
 961                         (invoke "make" "buildtests" dash-j)
 962
 963                         ;; Then run 'CTest' with -V so we get more
 964                         ;; details upon failure.
 965                         (invoke "ctest" "-V" dash-j)))))))
 966     (home-page "https://eigen.tuxfamily.org")
 967     (synopsis "C++ template library for linear algebra")
 968     (description
 969      "Eigen is a C++ template library for linear algebra: matrices, vectors,
 970 numerical solvers, and related algorithms.  It provides an elegant API based
 971 on \"expression templates\".  It is versatile: it supports all matrix sizes,
 972 all standard numeric types, various matrix decompositions and geometry
 973 features, and more.")
 974
 975     ;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3.
 976     ;; See 'COPYING.README' for details.
 977     (license license:mpl2.0)))
 978
 979 (define-public eigen-for-tensorflow
 980   (let ((changeset "fd6845384b86")
 981         (revision "1"))
 982     (package (inherit eigen)
 983       (name "eigen-for-tensorflow")
 984       (version (string-append "3.3.5-" revision "." changeset))
 985       (source (origin
 986                 (method hg-fetch)
 987                 (uri (hg-reference
 988                       (url "https://bitbucket.org/eigen/eigen")
 989                       (changeset changeset)))
 990                 (sha256
 991                  (base32
 992                   "12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5"))
 993                 (file-name (string-append name "-" version "-checkout"))
 994                 (modules '((guix build utils)))
 995                 (snippet
 996                  ;; There are 3 test failures in the "unsupported" directory,
 997                  ;; but maintainers say it's a known issue and it's unsupported
 998                  ;; anyway, so just skip them.
 999                  '(begin
1000                     (substitute* "unsupported/CMakeLists.txt"
1001                       (("add_subdirectory\\(test.*")
1002                        "# Do not build the tests for unsupported features.\n"))
1003                     #t)))))))
1004
1005 (define-public xtensor
1006   (package
1007     (name "xtensor")
1008     (version "0.20.10")
1009     (source (origin
1010               (method git-fetch)
1011               (uri (git-reference
1012                     (url "https://github.com/QuantStack/xtensor.git")
1013                     (commit version)))
1014               (sha256
1015                (base32
1016                 "1fmv2hpx610xwhxrndfsfvlbqfyk4l3gi5q5d7pa9m82kblxjj9l"))
1017               (file-name (git-file-name name version))))
1018     (build-system cmake-build-system)
1019     (native-inputs
1020      `(("googletest" ,googletest)
1021        ("xtl" ,xtl)))
1022     (arguments
1023      `(#:configure-flags
1024        '("-DBUILD_TESTS=ON")
1025        #:test-target "xtest"))
1026     (home-page "https://quantstack.net/xtensor")
1027     (synopsis "C++ tensors with broadcasting and lazy computing")
1028     (description "xtensor is a C++ library meant for numerical analysis with
1029 multi-dimensional array expressions.
1030
1031 xtensor provides:
1032 @itemize
1033 @item an extensible expression system enabling lazy broadcasting.
1034 @item an API following the idioms of the C++ standard library.
1035 @item tools to manipulate array expressions and build upon xtensor.
1036 @end itemize")
1037     (license license:bsd-3)))
1038
1039 (define-public gap
1040   (package
1041     (name "gap")
1042     (version "4.10.2")
1043     (source
1044      (origin
1045        (method url-fetch)
1046        (uri (string-append "https://www.gap-system.org/pub/gap/gap-"
1047                            (version-major+minor version)
1048                            "/tar.bz2/gap-"
1049                            version
1050                            ".tar.bz2"))
1051        (sha256
1052         (base32 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
1053        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
1054        (snippet
1055         '(begin
1056            ;; Delete the external gmp and zlib libraries
1057            ;; and a subdirectory not needed for our build.
1058            (for-each delete-file-recursively
1059                      '("extern" "hpcgap"))
1060            ;; Delete a failing test.
1061            ;; FIXME: This might be fixed in the next release, see
1062            ;; https://github.com/gap-system/gap/issues/3292
1063            (delete-file "tst/testinstall/dir.tst")
1064            ;; Delete all packages except for a fixed list.
1065            (with-directory-excursion "pkg"
1066              (for-each delete-file-recursively
1067                (lset-difference string=? (scandir ".")
1068                  '("." ".."
1069                    ;; Necessary packages.
1070                    "GAPDoc-1.6.2"
1071                    "primgrp-3.3.2"
1072                    "SmallGrp-1.3"    ; artistic2.0
1073                    "transgrp"        ; artistic2.0 for data,
1074                                      ; gpl2 or gpl3 for code
1075                    ;; Recommanded package.
1076                    "io-4.5.4"        ; gpl3+
1077                    ;; Optional packages, searched for at start,
1078                    ;; and their depedencies.
1079                    "alnuth-3.1.0"
1080                    "autpgrp-1.10"
1081                    "crisp-1.4.4"     ; bsd-2
1082                    "ctbllib"       ; gpl3+ according to doc/chap0.txt
1083                    "FactInt-1.6.2"
1084                    "fga"
1085                    "irredsol-1.4"    ; bsd-2
1086                    "laguna-3.9.2"
1087                    "polenta-1.3.8"
1088                    "polycyclic-2.14"
1089                    "radiroot-2.8"
1090                    "resclasses-4.7.1"
1091                    "sophus-1.24"
1092                    "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
1093                                    ; and the next release
1094                    "utils-0.59"))))
1095            #t))))
1096     (build-system gnu-build-system)
1097     (inputs
1098      `(("gmp" ,gmp)
1099        ("zlib" ,zlib)))
1100     (arguments
1101      `(#:modules ((ice-9 ftw)
1102                   (srfi srfi-26)
1103                   (guix build gnu-build-system)
1104                   (guix build utils))
1105        #:phases
1106        (modify-phases %standard-phases
1107          (add-after 'build 'build-packages
1108            ;; Compile all packages that have not been deleted by the
1109            ;; code snippet above.
1110            (lambda _
1111              (setenv "CONFIG_SHELL" (which "bash"))
1112              (with-directory-excursion "pkg"
1113                (invoke "../bin/BuildPackages.sh")
1114              #t)))
1115          (add-after 'build-packages 'build-doc
1116            ;; The documentation is bundled, but we create it from source.
1117            (lambda _
1118              (with-directory-excursion "doc"
1119                (invoke "./make_doc"))
1120              #t))
1121          (replace 'install
1122            (lambda* (#:key outputs #:allow-other-keys)
1123              (let* ((out (assoc-ref outputs "out"))
1124                     (bin (string-append out "/bin"))
1125                     (lib (string-append out "/lib"))
1126                     (prog (string-append bin "/gap"))
1127                     (prog-real (string-append bin "/.gap-real"))
1128                     (share (string-append out "/share/gap"))
1129                     (include (string-append out "/include/gap"))
1130                     (include-hpc (string-append include "/hpc")))
1131                ;; Install only the gap binary; the gac compiler is left
1132                ;; for maybe later. "Wrap" it in a shell script that calls
1133                ;; the binary with the correct parameter.
1134                (mkdir-p bin)
1135                (copy-file "gap" prog-real)
1136                (call-with-output-file prog
1137                  (lambda (port)
1138                    (format port
1139                            "#!~a~%exec ~a -l ~a \"$@\"~%"
1140                            (which "bash")
1141                            prog-real
1142                            share)))
1143                (chmod prog #o755)
1144                ;; Install the headers, which are needed by Sage. The
1145                ;; Makefile target "install-headers" was available in
1146                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1147                (mkdir-p include-hpc)
1148                (install-file "gen/config.h" include)
1149                (let ((file-name-predicate-without-stat
1150                        (lambda (regex)
1151                          (cut (file-name-predicate regex) <> #f))))
1152                  (with-directory-excursion "src"
1153                    (for-each
1154                      (cut install-file <> include)
1155                      (scandir "."
1156                               (file-name-predicate-without-stat ".*\\.h$"))))
1157                  (with-directory-excursion "src/hpc"
1158                    (for-each
1159                      (cut install-file <> include-hpc)
1160                      (scandir "."
1161                               (file-name-predicate-without-stat ".*\\.h$")))))
1162                ;; Install the library, which is needed by Sage. The
1163                ;; Makefile target "install-libgap" was available in
1164                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1165                ;; Compared to the Makefile, which used libtool, the
1166                ;; following approach of copying files and making symlinks
1167                ;; is rather pedestrian. There is hope that some later
1168                ;; version of gap reinstates and completes the install
1169                ;; targets.
1170                (invoke "make" "libgap.la")
1171                (install-file "libgap.la" lib)
1172                (install-file ".libs/libgap.so.0.0.0" lib)
1173                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so"))
1174                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
1175                ;; Install a certain number of files and directories to
1176                ;; SHARE, where the wrapped shell script expects them.
1177                ;; Remove information on the build directory from sysinfo.gap.
1178                (substitute* "sysinfo.gap"
1179                  (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
1180                  (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
1181                  (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
1182                (install-file "sysinfo.gap" share)
1183                (copy-recursively "grp" (string-append share "/grp"))
1184                (copy-recursively "pkg" (string-append share "/pkg"))
1185                ;; The following is not the C library libgap.so, but a
1186                ;; library of GAP code.
1187                (copy-recursively "lib" (string-append share "/lib"))
1188                ;; The gap binary looks for documentation inside SHARE.
1189                (copy-recursively "doc" (string-append share "/doc")))
1190              #t)))))
1191     (home-page "https://www.gap-system.org/")
1192     (synopsis
1193      "System for computational group theory")
1194     (description
1195      "GAP is a system for computational discrete algebra, with particular
1196 emphasis on computational group theory.  It provides a programming language,
1197 a library of thousands of functions implementing algebraic algorithms
1198 written in the GAP language as well as large data libraries of algebraic
1199 objects.")
1200     ;; Some packages have different licenses (effectively forcing the
1201     ;; combined work to be licensed as gpl3+); if this is the case, this
1202     ;; is mentioned above next to their name.
1203     ;; Some packages have no license mentioned explicitly; supposedly this
1204     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
1205     ;; safe side, we drop them for now.
1206     (license license:gpl2+)))
1207
1208 (define-public givaro
1209   (package
1210     (name "givaro")
1211     (version "4.1.1")
1212     (source (origin
1213               (method git-fetch)
1214               (uri (git-reference
1215                     (url "https://github.com/linbox-team/givaro")
1216                     (commit (string-append "v" version))))
1217               (file-name (git-file-name name version))
1218               (sha256
1219                (base32
1220                 "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
1221     (build-system gnu-build-system)
1222     (native-inputs
1223      `(("autoconf" ,autoconf)
1224        ("automake" ,automake)
1225        ("libtool" ,libtool)))
1226     (propagated-inputs
1227      `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
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     (synopsis "C++ library for linear algebra over finite fields")
1268     (description
1269      "FFLAS-FFPACK is a C++ template library for basic linear algebra
1270 operations over a finite field.
1271 FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
1272 of a subset of routines of the numerical BLAS; it also supports sparse
1273 matrix-vector products.
1274 FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
1275 library to provide functionalities of higher level, using the kernel
1276 of a BLAS.  Additionally, it provides routines specific to exact linear
1277 algebra, such as the row echelon form.")
1278     (license license:lgpl2.1+)
1279     (home-page "https://linbox-team.github.io/fflas-ffpack/")))
1280
1281 (define-public linbox
1282   (package
1283     (name "linbox")
1284     (version "1.6.3")
1285     (source (origin
1286               (method git-fetch)
1287               (uri (git-reference
1288                     (url "https://github.com/linbox-team/linbox")
1289                     (commit (string-append "v" version))))
1290               (file-name (git-file-name name version))
1291               (sha256
1292                (base32
1293                 "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
1294     (build-system gnu-build-system)
1295     (native-inputs
1296      `(("autoconf" ,autoconf)
1297        ("automake" ,automake)
1298        ("libtool" ,libtool)
1299        ("pkg-config" ,pkg-config)))
1300     (inputs
1301      `(("fflas-ffpack" ,fflas-ffpack)))
1302     (synopsis "C++ library for linear algebra over exact rings")
1303     (description
1304      "LinBox is a C++ template library for exact linear algebra computation
1305 with dense, sparse, and structured matrices over the integers and over
1306 finite fields.")
1307     (license license:lgpl2.1+)
1308     (home-page "https://linbox-team.github.io/linbox/")))
1309
1310 (define-public m4ri
1311   (package
1312     (name "m4ri")
1313     (version "20140914")
1314     (source (origin
1315               (method git-fetch)
1316               (uri (git-reference
1317                     (url "https://bitbucket.org/malb/m4ri")
1318                     (commit (string-append "release-" version))))
1319               (file-name (git-file-name name version))
1320               (sha256
1321                (base32
1322                 "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
1323     (build-system gnu-build-system)
1324     (native-inputs
1325      `(("autoconf" ,autoconf)
1326        ("automake" ,automake)
1327        ("libtool" ,libtool)
1328        ("pkg-config" ,pkg-config)))
1329     (inputs
1330      `(("libpng" ,libpng)))
1331     (synopsis "Arithmetic of dense matrices over F_2")
1332     (description "M4RI is a library for fast arithmetic with dense matrices
1333 over F2.  The name M4RI comes from the first implemented algorithm: The
1334 Method of the Four Russians inversion algorithm published by Gregory Bard.
1335 This algorithm in turn is named after the Method of the Four Russians
1336 multiplication algorithm.")
1337     (license license:gpl2+)
1338     (home-page "https://bitbucket.org/malb/m4ri/")))
1339
1340 (define-public symmetrica
1341   (package
1342     (name "symmetrica")
1343     (version "2.0")
1344     (source (origin
1345               (method url-fetch/tarbomb)
1346               (uri (let ((v (string-join (string-split version #\.) "_")))
1347                      (string-append "http://www.algorithm.uni-bayreuth.de/"
1348                                     "en/research/SYMMETRICA/"
1349                                     "SYM" v "_tar.gz")))
1350               (sha256
1351                (base32
1352                 "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
1353               ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
1354               (patches (search-patches "symmetrica-bruch.patch"
1355                                        "symmetrica-int32.patch"
1356                                        "symmetrica-return_values.patch"
1357                                        "symmetrica-sort_sum_rename.patch"))))
1358     (build-system gnu-build-system)
1359     (arguments
1360      `(#:tests? #f                      ;no test
1361        #:phases
1362        (modify-phases %standard-phases
1363          (add-after 'unpack 'fix-makefile
1364            (lambda _
1365              (substitute* "makefile"
1366                (("cc -c") "gcc -c -fPIC"))
1367              #t))
1368          (add-after 'fix-makefile 'turn-off-banner
1369            (lambda _
1370              (substitute* "de.c"
1371                (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
1372              #t))
1373          (delete 'configure)            ;no configure script
1374          (replace 'install              ;no install target
1375            (lambda* (#:key outputs #:allow-other-keys)
1376              (let* ((out (assoc-ref outputs "out"))
1377                     (lib (string-append out "/lib"))
1378                     (inc (string-append out "/include/symmetrica"))
1379                     (doc (string-append out "/share/doc/symmetrica-" ,version))
1380                     (static "libsymmetrica.a"))
1381                ;; Build static library.
1382                (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
1383                (invoke "ranlib" static)
1384                ;; Install static library and headers.
1385                (for-each (lambda (f) (install-file f inc))
1386                          (find-files "." "\\.h$"))
1387                (install-file "libsymmetrica.a" lib)
1388                ;; Install documentation.
1389                (for-each (lambda (f) (install-file f doc))
1390                          (find-files "." "\\.doc$"))
1391                #t))))))
1392     (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
1393     (synopsis "Combinatoric C Library")
1394     (description "Symmetrica is a library for combinatorics.  It has support
1395 for the representation theory of the symmetric group and related groups,
1396 combinatorics of tableaux, symmetric functions and polynomials, Schubert
1397 polynomials, and the representation theory of Hecke algebras of type A_n.")
1398     (license license:public-domain)))
1399
1400 (define-public m4rie
1401   (package
1402     (name "m4rie")
1403     (version "20150908")
1404     (source (origin
1405               (method git-fetch)
1406               (uri (git-reference
1407                     (url "https://bitbucket.org/malb/m4rie")
1408                     (commit (string-append "release-" version))))
1409               (file-name (git-file-name name version))
1410               (sha256
1411                (base32
1412                 "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
1413     (build-system gnu-build-system)
1414     (native-inputs
1415      `(("autoconf" ,autoconf)
1416        ("automake" ,automake)
1417        ("libtool" ,libtool)))
1418     (inputs
1419      `(("m4ri" ,m4ri)))
1420     (synopsis "Arithmetic of dense matrices over F_{2^e}")
1421     (description "M4RI is a library for fast arithmetic with dense matrices
1422 over finite fields of characteristic 2.  So it extends the functionality
1423 of M4RI from F_2 to F_{2^e}.")
1424     (license license:gpl2+)
1425     (home-page "https://bitbucket.org/malb/m4rie/")))
1426
1427 (define-public eclib
1428   (package
1429     (name "eclib")
1430     (version "20190909")
1431     (source (origin
1432               (method git-fetch)
1433               (uri (git-reference
1434                     (url "https://github.com/JohnCremona/eclib/")
1435                     (commit (string-append "v" version))))
1436               (file-name (git-file-name name version))
1437               (sha256
1438                (base32
1439                 "1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n"))))
1440     (build-system gnu-build-system)
1441     (native-inputs
1442      `(("autoconf" ,autoconf)
1443        ("automake" ,automake)
1444        ("libtool" ,libtool)))
1445     (inputs
1446      `(("ntl" ,ntl)
1447        ("pari-gp" ,pari-gp)))
1448     (synopsis "Ranks of elliptic curves and modular symbols")
1449     (description "The eclib package includes mwrank (for 2-descent on
1450 elliptic curves over Q) and modular symbol code; it has been written by
1451 John Cremona to compute his elliptic curve database.")
1452     (license license:gpl2+)
1453     (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
1454                               "J.E.Cremona/mwrank/index.html"))))
1455
1456 (define-public lrcalc
1457   (package
1458     (name "lrcalc")
1459     (version "1.2")
1460     (source (origin
1461               (method git-fetch)
1462               (uri (git-reference
1463                     (url "https://bitbucket.org/asbuch/lrcalc")
1464                     (commit (string-append "lrcalc-" version))))
1465               (file-name (git-file-name name version))
1466               (sha256
1467                (base32
1468                 "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
1469               (patches (search-patches "lrcalc-includes.patch"))))
1470     (build-system gnu-build-system)
1471     (native-inputs
1472      `(("autoconf" ,autoconf)
1473        ("automake" ,automake)
1474        ("libtool" ,libtool)))
1475     (arguments
1476      `(#:phases
1477        (modify-phases %standard-phases
1478          (add-before 'build 'fix-permission
1479            (lambda _
1480              (chmod "lrcalc.maple.src" #o644)
1481              #t)))))
1482     (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
1483     (description "The Littlewood-Richardson Calculator (lrcalc) is a
1484 program designed to compute Littlewood-Richardson coefficients.  It computes
1485 single Littlewood-Richardson coefficients, products of Schur functions, or
1486 skew Schur functions.  In addition it computes products in the small quantum
1487 cohomology ring of a Grassmann variety.  The software package also includes
1488 a program that performs fast computation of the more general multiplicative
1489 structure constants of Schubert polynomials.")
1490     (license license:gpl2+)
1491     (home-page "https://sites.math.rutgers.edu/~asbuch/lrcalc/")))
1492
1493 (define-public iml
1494   (package
1495     (name "iml")
1496     (version "1.0.5")
1497     (source
1498      (origin
1499        (method url-fetch)
1500        (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
1501                            version ".tar.bz2"))
1502        (sha256
1503         (base32
1504          "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
1505     (build-system gnu-build-system)
1506     (inputs
1507      `(("gmp", gmp)
1508        ("cblas" ,openblas))) ; or any other BLAS library; the documentation
1509                              ; mentions ATLAS in particular
1510     (arguments
1511      `(#:configure-flags
1512        (list
1513         "--enable-shared"
1514         (string-append "--with-gmp-include="
1515                        (assoc-ref %build-inputs "gmp") "/include")
1516         (string-append "--with-gmp-lib="
1517                        (assoc-ref %build-inputs "gmp") "/lib")
1518         "--with-cblas=-lopenblas"
1519         (string-append "--with-cblas-include="
1520                        (assoc-ref %build-inputs "cblas") "/include")
1521         (string-append "--with-cblas-lib="
1522                        (assoc-ref %build-inputs "cblas") "/lib"))))
1523     (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
1524     (synopsis
1525      "Solver for systems of linear equations over the integers")
1526     (description
1527      "IML is a C library implementing algorithms for computing exact
1528 solutions to dense systems of linear equations over the integers.
1529 Currently, IML provides the following functionality:
1530
1531 @itemize
1532 @item Nonsingular rational system solving:
1533 compute the unique rational solution X to the system AX=B, where A and B
1534 are integer matrices, A nonsingular.
1535 @item Compute the right nullspace or kernel of an integer matrix.
1536 @item Certified linear system solving:
1537 compute a minimal denominator solution x to a system Ax=b, where b is an
1538 integer vector and A is an integer matrix with arbitrary shape and
1539 rank profile.
1540 @end itemize
1541
1542 In addition, IML provides some low level routines for a variety of mod p
1543 matrix operations: computing the row-echelon form, determinant, rank
1544 profile, and inverse of a mod p matrix. These mod p routines are not
1545 general purpose; they require that p satisfy some preconditions based on
1546 the dimension of the input matrix (usually p should be prime and should be
1547 no more than about 20 bits long).")
1548     (license license:bsd-3)))