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 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 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 ;;;
  12 ;;; This file is part of GNU Guix.
  13 ;;;
  14 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  15 ;;; under the terms of the GNU General Public License as published by
  16 ;;; the Free Software Foundation; either version 3 of the License, or (at
  17 ;;; your option) any later version.
  18 ;;;
  19 ;;; GNU Guix is distributed in the hope that it will be useful, but
  20 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  21 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  22 ;;; GNU General Public License for more details.
  23 ;;;
  24 ;;; You should have received a copy of the GNU General Public License
  25 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  26
  27 (define-module (gnu packages algebra)
  28   #:use-module (gnu packages)
  29   #:use-module (gnu packages autotools)
  30   #:use-module (gnu packages bison)
  31   #:use-module (gnu packages check)
  32   #:use-module (gnu packages compression)
  33   #:use-module (gnu packages cpp)
  34   #:use-module (gnu packages documentation)
  35   #:use-module (gnu packages ed)
  36   #:use-module (gnu packages flex)
  37   #:use-module (gnu packages fltk)
  38   #:use-module (gnu packages gl)
  39   #:use-module (gnu packages graphviz)
  40   #:use-module (gnu packages image)
  41   #:use-module (gnu packages java)
  42   #:use-module (gnu packages maths)
  43   #:use-module (gnu packages mpi)
  44   #:use-module (gnu packages multiprecision)
  45   #:use-module (gnu packages perl)
  46   #:use-module (gnu packages pkg-config)
  47   #:use-module (gnu packages pulseaudio)
  48   #:use-module (gnu packages python)
  49   #:use-module (gnu packages python-xyz)
  50   #:use-module (gnu packages readline)
  51   #:use-module (gnu packages shells)
  52   #:use-module (gnu packages tex)
  53   #:use-module (gnu packages texinfo)
  54   #:use-module (gnu packages xiph)
  55   #:use-module (gnu packages xorg)
  56   #:use-module (guix build-system ant)
  57   #:use-module (guix build-system gnu)
  58   #:use-module (guix build-system cmake)
  59   #:use-module (guix build-system python)
  60   #:use-module (guix download)
  61   #:use-module (guix git-download)
  62   #:use-module (guix hg-download)
  63   #:use-module ((guix licenses) #:prefix license:)
  64   #:use-module (guix packages)
  65   #:use-module (guix utils))
  66
  67
  68 (define-public mpfrcx
  69   (package
  70    (name "mpfrcx")
  71    (version "0.5")
  72    (source (origin
  73             (method url-fetch)
  74             (uri (string-append
  75                   "http://www.multiprecision.org/downloads/mpfrcx-"
  76                   version ".tar.gz"))
  77             (sha256
  78              (base32
  79               "1s968480ymv6w0rnvfp9mxvx98hvi29fkvw8nk4ggzc6azxgwybs"))))
  80    (build-system gnu-build-system)
  81    (propagated-inputs
  82      `(("gmp" ,gmp)
  83        ("mpfr" ,mpfr)
  84        ("mpc"  ,mpc))) ; Header files are included by mpfrcx.h.
  85    (synopsis "Arithmetic of polynomials over arbitrary precision numbers")
  86    (description
  87     "Mpfrcx is a library for the arithmetic of univariate polynomials over
  88 arbitrary precision real (mpfr) or complex (mpc) numbers, without control
  89 on the rounding.  For the time being, only the few functions needed to
  90 implement the floating point approach to complex multiplication are
  91 implemented.  On the other hand, these comprise asymptotically fast
  92 multiplication routines such as Toom–Cook and the FFT.")
  93    (license license:lgpl3+)
  94    (home-page "http://mpfrcx.multiprecision.org/")))
  95
  96 (define-public gf2x
  97   (package
  98    (name "gf2x")
  99    (version "1.2")
 100    (source (origin
 101             (method url-fetch)
 102             (uri (string-append
 103                   "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-"
 104                   version ".tar.gz"))
 105             (sha256
 106              (base32
 107               "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1"))))
 108    (build-system gnu-build-system)
 109    (synopsis "Arithmetic of polynomials over binary finite fields")
 110    (description
 111     "The gf2x library provides arithmetic of polynomials over finite fields
 112 of characteristic 2.  It implements the multiplication, squaring and
 113 greatest common divisor operations.")
 114    (license license:gpl3+)
 115    (home-page "https://gforge.inria.fr/projects/gf2x/")))
 116
 117 (define-public cm
 118   (package
 119    (name "cm")
 120    (version "0.3")
 121    (source (origin
 122             (method url-fetch)
 123             (uri (string-append
 124                   "http://www.multiprecision.org/cm/download/cm-"
 125                   version ".tar.gz"))
 126             (sha256
 127              (base32
 128               "1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc"))))
 129    (build-system gnu-build-system)
 130    (propagated-inputs
 131      `(("mpfrcx" ,mpfrcx)
 132        ("zlib" ,zlib))) ; Header files included from cm_common.h.
 133    (inputs
 134      `(("pari-gp"  ,pari-gp)))
 135    (synopsis "CM constructions for elliptic curves")
 136    (description
 137     "The CM software implements the construction of ring class fields of
 138 imaginary quadratic number fields and of elliptic curves with complex
 139 multiplication via floating point approximations.  It consists of libraries
 140 that can be called from within a C program and of executable command
 141 line applications.")
 142    (license license:gpl3+)
 143    (home-page "http://cm.multiprecision.org/")))
 144
 145 (define-public fplll
 146   (package
 147     (name "fplll")
 148     (version "5.2.1")
 149     (source (origin
 150               (method git-fetch)
 151               (uri (git-reference
 152                     (url "https://github.com/fplll/fplll.git")
 153                     (commit version)))
 154               (file-name (git-file-name name version))
 155               (sha256
 156                (base32
 157                 "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg"))))
 158     (build-system gnu-build-system)
 159     (native-inputs
 160      `(("autoconf" ,autoconf)
 161        ("automake" ,automake)
 162        ("libtool" ,libtool)))
 163     (inputs
 164      `(("gmp" ,gmp)
 165        ("mpfr" ,mpfr)))
 166     (home-page "https://github.com/fplll/fplll")
 167     (synopsis "Library for LLL-reduction of euclidean lattices")
 168     (description
 169      "fplll contains implementations of several lattice algorithms.
 170 The implementation relies on floating-point orthogonalization, and LLL
 171 is central to the code, hence the name.
 172
 173 It includes implementations of floating-point LLL reduction
 174 algorithms, offering different speed/guarantees ratios.  It contains
 175 a @emph{wrapper} choosing the estimated best sequence of variants in
 176 order to provide a guaranteed output as fast as possible.  In the case
 177 of the wrapper, the succession of variants is oblivious to the user.
 178
 179 It includes an implementation of the BKZ reduction algorithm,
 180 including the BKZ-2.0 improvements (extreme enumeration
 181 pruning, pre-processing of blocks, early termination).  Additionally,
 182 Slide reduction and self dual BKZ are supported.
 183
 184 It also includes a floating-point implementation of the
 185 Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice
 186 vector.  For the same task, the GaussSieve algorithm is also available
 187 in fplll.  Finally, it contains a variant of the enumeration algorithm
 188 that computes a lattice vector closest to a given vector belonging to
 189 the real span of the lattice.")
 190     (license license:lgpl2.1+)))
 191
 192 (define-public python-fpylll
 193   (package
 194     (name "python-fpylll")
 195     (version "0.4.1")
 196     (source
 197      (origin
 198        ;; Pypi contains and older release, so we use a tagged release from
 199        ;; Github instead.
 200        (method git-fetch)
 201        (uri (git-reference
 202              (url "https://github.com/fplll/fpylll.git")
 203              (commit (string-append version "dev"))))
 204        (file-name (git-file-name name version))
 205        (sha256
 206         (base32
 207          "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
 208     (build-system python-build-system)
 209     (inputs
 210      `(("fplll" ,fplll)
 211        ("gmp" ,gmp)
 212        ("mpfr" ,mpfr)
 213        ("pari-gp" ,pari-gp)))
 214     (propagated-inputs
 215      `(("cysignals" ,python-cysignals)
 216        ("cython" ,python-cython)
 217        ("flake8" ,python-flake8)
 218        ("numpy" ,python-numpy)
 219        ("pytest" ,python-pytest)))
 220     (home-page "https://github.com/fplll/fpylll")
 221     (synopsis "Python interface for fplll")
 222     (description "fpylll is a Python wrapper for fplll.")
 223     (license license:gpl2+)))
 224
 225 (define-public pari-gp
 226   (package
 227     (name "pari-gp")
 228     (version "2.11.2")
 229     (source (origin
 230               (method url-fetch)
 231               (uri (string-append
 232                     "https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
 233                     version ".tar.gz"))
 234               (sha256
 235                (base32
 236                 "0fck8ssmirl8fy7s4mspgrxjs5sag76xbshqlqzkcl3kqyrk4raa"))))
 237     (build-system gnu-build-system)
 238     (native-inputs
 239      `(("texlive" ,(texlive-union
 240                     (list texlive-amsfonts)))))
 241     (inputs `(("gmp" ,gmp)
 242               ("libx11" ,libx11)
 243               ("perl" ,perl)
 244               ("readline" ,readline)))
 245     (arguments
 246      '(#:make-flags '("all")
 247        #:test-target "dobench"
 248        #:phases
 249        (modify-phases %standard-phases
 250          (replace 'configure
 251            (lambda* (#:key outputs #:allow-other-keys)
 252              (invoke "./Configure"
 253                      (string-append "--prefix="
 254                                     (assoc-ref outputs "out"))))))))
 255     (synopsis "PARI/GP, a computer algebra system for number theory")
 256     (description
 257      "PARI/GP is a widely used computer algebra system designed for fast
 258 computations in number theory (factorisations, algebraic number theory,
 259 elliptic curves...), but it also contains a large number of other useful
 260 functions to compute with mathematical entities such as matrices,
 261 polynomials, power series, algebraic numbers, etc., and a lot of
 262 transcendental functions.
 263 PARI is also available as a C library to allow for faster computations.")
 264     (license license:gpl2+)
 265     (home-page "https://pari.math.u-bordeaux.fr/")))
 266
 267 (define-public gp2c
 268   (package
 269    (name "gp2c")
 270    (version "0.0.11pl2")
 271    (source (origin
 272             (method url-fetch)
 273             (uri (string-append
 274                   "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
 275                   version ".tar.gz"))
 276             (sha256
 277               (base32
 278                 "0wqsf05wgkqvmmsx7jinvzdqav6rl56sr8haibgs31nzz4x9xz9g"))))
 279    (build-system gnu-build-system)
 280    (native-inputs `(("perl" ,perl)))
 281    (inputs `(("pari-gp" ,pari-gp)))
 282    (arguments
 283     '(#:configure-flags
 284       (list (string-append "--with-paricfg="
 285                            (assoc-ref %build-inputs "pari-gp")
 286                            "/lib/pari/pari.cfg"))))
 287    (synopsis "PARI/GP, a computer algebra system for number theory")
 288    (description
 289     "PARI/GP is a widely used computer algebra system designed for fast
 290 computations in number theory (factorisations, algebraic number theory,
 291 elliptic curves...), but it also contains a large number of other useful
 292 functions to compute with mathematical entities such as matrices,
 293 polynomials, power series, algebraic numbers, etc., and a lot of
 294 transcendental functions.
 295 PARI is also available as a C library to allow for faster computations.
 296
 297 GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
 298    (license license:gpl2)
 299    (home-page "https://pari.math.u-bordeaux.fr/")))
 300
 301 (define fplll-4-cmh
 302   (package
 303     (inherit fplll)
 304     (name "fplll")
 305     (version "4.0.4")
 306     (source
 307      (origin
 308        (method url-fetch)
 309        (uri (string-append
 310              "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
 311              version ".tar.gz"))
 312        (sha256
 313         (base32 "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))))
 314
 315 (define-public cmh
 316   (package
 317    (name "cmh")
 318    (version "1.0")
 319    (source (origin
 320             (method url-fetch)
 321             (uri (string-append
 322                   "https://gforge.inria.fr/frs/download.php/33497/cmh-"
 323                   version ".tar.gz"))
 324             (sha256
 325              (base32
 326               "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
 327    (build-system gnu-build-system)
 328    (inputs
 329      `(("gmp" ,gmp)
 330        ("mpfr" ,mpfr)
 331        ("mpc" ,mpc)
 332        ("mpfrcx" ,mpfrcx)
 333        ("fplll" ,fplll-4-cmh)
 334        ("pari-gp"  ,pari-gp)))
 335    (synopsis "Igusa class polynomial computations")
 336    (description
 337     "The CMH software computes Igusa (genus 2) class polynomials, which
 338 parameterize the CM points in the moduli space of 2-dimensional abelian
 339 varieties, i.e. Jacobians of hyperelliptic curves.
 340 It can also be used to compute theta constants at arbitrary
 341 precision.")
 342    (license license:gpl3+)
 343    (home-page "http://cmh.gforge.inria.fr/")))
 344
 345 (define-public giac
 346   (package
 347     (name "giac")
 348     (version "1.5.0-85")
 349     (source (origin
 350               (method url-fetch)
 351               ;; "~parisse/giac" is not used because the maintainer regularly
 352               ;; overwrites the release tarball there, introducing a checksum
 353               ;; mismatch every time.  See
 354               ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
 355               (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
 356                                   "~parisse/debian/dists/stable/main/"
 357                                   "source/giac_" version ".tar.gz"))
 358               (sha256
 359                (base32
 360                 "03icgrfhb1xiy95cqmfgmcb1lw3775mr2ybnzandmyn44iycs6rh"))))
 361     (build-system gnu-build-system)
 362     (arguments
 363      `(#:modules ((ice-9 ftw)
 364                   (guix build utils)
 365                   (guix build gnu-build-system))
 366        #:phases
 367        (modify-phases %standard-phases
 368          (add-after 'unpack 'patch-bin-cp
 369            ;; Some Makefiles contain hard-coded "/bin/cp".
 370            (lambda _
 371              (substitute* (find-files "doc" "^Makefile")
 372                (("/bin/cp") (which "cp")))
 373              #t))
 374          (add-after 'unpack 'disable-failing-test
 375            ;; FIXME: Test failing.  Not sure why.
 376            (lambda _
 377              (substitute* "check/Makefile.in"
 378                (("chk_fhan11") ""))
 379              #t))
 380          (add-after 'install 'fix-doc
 381            (lambda* (#:key outputs #:allow-other-keys)
 382              (let ((out (assoc-ref outputs "out")))
 383                ;; Most French documentation has a non-commercial
 384                ;; license, so we need to remove it.
 385                (with-directory-excursion (string-append out "/share/giac/doc/fr")
 386                  (for-each delete-file-recursively
 387                            '("cascas" "casexo" "casgeo" "casrouge" "cassim"
 388                              "castor")))
 389                ;; Remove duplicate documentation in
 390                ;; "%out/share/doc/giac/", where Xcas does not expect
 391                ;; to find it.
 392                (delete-file-recursively (string-append out "/share/doc/giac"))
 393                #t)))
 394          (add-after 'install 'remove-unnecessary-executable
 395            (lambda* (#:key outputs #:allow-other-keys)
 396              (let ((out (assoc-ref outputs "out")))
 397                (delete-file (string-append out "/bin/xcasnew"))
 398                #t))))))
 399     (inputs
 400      ;;; TODO: Add libnauty.
 401      `(("fltk" ,fltk)
 402        ("glpk" ,glpk)
 403        ("gmp" ,gmp)
 404        ("gsl" ,gsl)
 405        ("lapack" ,lapack)
 406        ("libao" ,ao)
 407        ("libjpeg" ,libjpeg)
 408        ("libpng" ,libpng)
 409        ("libsamplerate" ,libsamplerate)
 410        ("libx11" ,libx11)
 411        ("libxinerama" ,libxinerama)
 412        ("libxft" ,libxft)
 413        ("libxt" ,libxt)
 414        ("mesa" ,mesa)
 415        ("mpfi" ,mpfi)
 416        ("mpfr" ,mpfr)
 417        ("ntl" ,ntl)
 418        ("perl" ,perl)
 419        ("pari-gp" ,pari-gp)
 420        ("tcsh" ,tcsh)))
 421     (native-inputs
 422      `(("bison" ,bison)
 423        ("flex" ,flex)
 424        ("readline" ,readline)
 425        ("texlive" ,texlive-tiny)))
 426     (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
 427     (synopsis "Computer algebra system")
 428     (description
 429      "Giac/Xcas is a computer algebra system.  It has a compatibility mode for
 430 maple, mupad and the TI89.  It is available as a standalone program (graphic
 431 or text interfaces) or as a C++ library.")
 432     (license license:gpl3+)))
 433
 434 (define-public giac-xcas
 435   (deprecated-package "giac-xcas" giac))
 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 "9.7.0")
 564    (source (origin
 565             (method url-fetch)
 566             (uri (string-append "http://shoup.net/ntl/ntl-"
 567                                 version ".tar.gz"))
 568             (sha256 (base32
 569                      "115frp5flyvw9wghz4zph1b3llmr5nbxk1skgsggckr81fh3gmxq"))))
 570    (build-system gnu-build-system)
 571    (native-inputs
 572     `(("libtool" ,libtool)
 573       ("perl" ,perl))) ; for configuration
 574    ;; FIXME: Add optional input gf2x once available; then also add
 575    ;; configure flag "NTL_GF2X_LIB=on".
 576    (inputs
 577     `(("gmp" ,gmp)))
 578    (arguments
 579     `(#:phases
 580       (modify-phases %standard-phases
 581         (replace 'configure
 582          (lambda* (#:key outputs #:allow-other-keys)
 583            (chdir "src")
 584            (system* "./configure"
 585                     (string-append "PREFIX=" (assoc-ref outputs "out"))
 586                     ;; Do not build especially for the build machine.
 587                     "NATIVE=off"
 588                     ;; Also do not tune to the build machine.
 589                     "WIZARD=off"
 590                     "SHARED=on")
 591            #t)))))
 592    (synopsis "C++ library for number theory")
 593    (description
 594     "NTL is a C++ library providing data structures and algorithms
 595 for manipulating signed, arbitrary length integers, and for vectors,
 596 matrices, and polynomials over the integers and over finite fields.")
 597    (license license:gpl2+)
 598    (home-page "http://shoup.net/ntl/")))
 599
 600 (define-public singular
 601   (package
 602    (name "singular")
 603    (version "4.1.2p1")
 604    (source
 605     (origin
 606       (method url-fetch)
 607       (uri
 608        (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
 609                       "Singular/SOURCES/"
 610                       (string-join
 611                        (string-split
 612                         (string-trim-right version #\p
 613                                            0 (1- (string-length version)))
 614                         #\.) "-")
 615                       "/singular-" version ".tar.gz"))
 616              (sha256 (base32
 617                       "0kvd55353fiqyq1msmi0kka66n5h0aqs7m3km60r01b1w2f8085m"))))
 618    (build-system gnu-build-system)
 619    (native-inputs
 620     `(("doxygen" ,doxygen)
 621       ("graphviz" ,graphviz)
 622       ("perl" ,perl)))
 623    (inputs
 624     `(("cddlib" ,cddlib)
 625       ("gmp" ,gmp)
 626       ("flint" ,flint)
 627       ("mpfr" ,mpfr)
 628       ("ntl" ,ntl)
 629       ("python" ,python-2)
 630       ("readline" ,readline)))
 631    (arguments
 632     `(#:configure-flags
 633       (list (string-append "--with-ntl="
 634                            (assoc-ref %build-inputs "ntl")))))
 635    (synopsis "Computer algebra system for polynomial computations")
 636    (description
 637     "Singular is a computer algebra system for polynomial computations,
 638 with special emphasis on commutative and non-commutative algebra, algebraic
 639 geometry and singularity theory.")
 640    ;; Singular itself is dual licensed gpl2 or gpl3, but some of the
 641    ;; libraries with which it links are licensed under lgpl3+, so the
 642    ;; combined work becomes gpl3. See COPYING in the source code.
 643    (license license:gpl3)
 644    (home-page "http://www.singular.uni-kl.de/index.php")))
 645
 646 (define-public gmp-ecm
 647   (package
 648    (name "gmp-ecm")
 649    (version "7.0.4")
 650    (source (origin
 651              (method url-fetch)
 652              ;; Use the ‘Latest version’ link for a stable URI across releases.
 653              (uri (string-append "https://gforge.inria.fr/frs/download.php/"
 654                                  "latestfile/160/ecm-" version ".tar.gz"))
 655              (sha256 (base32
 656                       "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"))))
 657    (build-system gnu-build-system)
 658    (inputs
 659     `(("gmp" ,gmp)))
 660    (arguments
 661     `(#:configure-flags '("--enable-shared"
 662                           ;; Disable specific assembly routines, which depend
 663                           ;; on the subarchitecture of the build machine,
 664                           ;; and use gmp instead.
 665                           "--disable-asm-redc")))
 666    (synopsis "Integer factorization library using the elliptic curve method")
 667    (description
 668     "GMP-ECM factors integers using the elliptic curve method (ECM) as well
 669 as the P-1 and P+1 algorithms.  It provides a library and a stand-alone
 670 binary.")
 671    ;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+,
 672    ;; so the combined work is under gpl3+.
 673    (license license:gpl3+)
 674    (home-page "http://ecm.gforge.inria.fr/")))
 675
 676 (define-public bc
 677   (package
 678     (name "bc")
 679     (version "1.07.1")
 680     (source (origin
 681              (method url-fetch)
 682              (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
 683              (sha256
 684               (base32
 685                "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))))
 686     (build-system gnu-build-system)
 687     (native-inputs
 688      `(("ed" ,ed)
 689        ("flex" ,flex)
 690        ("texinfo" ,texinfo)))
 691     (arguments
 692      '(#:configure-flags
 693        (list "--with-readline")))
 694     (home-page "https://www.gnu.org/software/bc/")
 695     (synopsis "Arbitrary precision numeric processing language")
 696     (description
 697      "bc is an arbitrary precision numeric processing language.  It includes
 698 an interactive environment for evaluating mathematical statements.  Its
 699 syntax is similar to that of C, so basic usage is familiar.  It also includes
 700 \"dc\", a reverse-polish calculator.")
 701     (license license:gpl2+)))
 702
 703 ;; The original kiss-fft does not have a complete build system and does not
 704 ;; build any shared libraries.  This is a fork used by Extempore.
 705 (define-public kiss-fft-for-extempore
 706   (package
 707     (name "kiss-fft-for-extempore")
 708     (version "1.3.0")
 709     (source (origin
 710               (method git-fetch)
 711               (uri (git-reference
 712                     (url "https://github.com/extemporelang/kiss_fft.git")
 713                     (commit version)))
 714               (file-name (git-file-name name version))
 715               (sha256
 716                (base32
 717                 "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
 718     (build-system cmake-build-system)
 719     (arguments `(#:tests? #f)) ; no tests included
 720     ;; Extempore refuses to build on architectures other than x86_64
 721     (supported-systems '("x86_64-linux"))
 722     (home-page "https://github.com/extemporelang/kiss_fft")
 723     (synopsis "Mixed-radix Fast Fourier Transform")
 724     (description
 725      "Kiss FFT attempts to be a reasonably efficient, moderately useful FFT
 726 that can use fixed or floating data types and can easily be incorporated into
 727 a C program.")
 728     (license license:bsd-3)))
 729
 730 (define-public fftw
 731   (package
 732     (name "fftw")
 733     (version "3.3.8")
 734     (source (origin
 735              (method url-fetch)
 736              (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
 737                                  version".tar.gz"))
 738              (sha256
 739               (base32
 740                "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
 741     (build-system gnu-build-system)
 742     (arguments
 743      `(#:configure-flags
 744        '("--enable-shared" "--enable-openmp" "--enable-threads"
 745          ,@(let ((system (or (%current-target-system) (%current-system))))
 746              ;; Enable SIMD extensions for codelets.  See details at:
 747              ;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>.
 748              (cond
 749               ((string-prefix? "x86_64" system)
 750                '("--enable-sse2" "--enable-avx" "--enable-avx2"
 751                  "--enable-avx512" "--enable-avx-128-fma"))
 752               ((string-prefix? "i686" system)
 753                '("--enable-sse2"))
 754               ((string-prefix? "aarch64" system)
 755                ;; Note that fftw supports NEON on 32-bit ARM only when
 756                ;; compiled for single-precision.
 757                '("--enable-neon"))
 758               (else
 759                '())))
 760          ;; By default '-mtune=native' is used.  However, that may cause the
 761          ;; use of ISA extensions (e.g. AVX) that are not necessarily
 762          ;; available on the user's machine when that package is built on a
 763          ;; different machine.
 764          "ax_cv_c_flags__mtune_native=no")))
 765     (native-inputs `(("perl" ,perl)))
 766     (home-page "http://fftw.org")
 767     (synopsis "Computing the discrete Fourier transform")
 768     (description
 769      "FFTW is a C subroutine library for computing the discrete Fourier
 770 transform (DFT) in one or more dimensions, of arbitrary input size, and of
 771 both real and complex data (as well as of even/odd data---i.e. the discrete
 772 cosine/ sine transforms or DCT/DST).")
 773     (license license:gpl2+)))
 774
 775 (define-public fftwf
 776   (package (inherit fftw)
 777     (name "fftwf")
 778     (arguments
 779      (substitute-keyword-arguments (package-arguments fftw)
 780        ((#:configure-flags fftw-configure-flags)
 781         `(cons* "--enable-single"
 782                 ,@(if (string-prefix? "arm" (or (%current-target-system)
 783                                                 (%current-system)))
 784                       ;; fftw supports NEON on 32-bit ARM only when compiled
 785                       ;; for single-precision, so add it here.
 786                       '("--enable-neon")
 787                       '())
 788                 ,fftw-configure-flags))))
 789     (description
 790      (string-append (package-description fftw)
 791                     "  Single-precision version."))))
 792
 793 (define-public fftw-openmpi
 794   (package (inherit fftw)
 795     (name "fftw-openmpi")
 796     (inputs
 797      `(("openmpi" ,openmpi)
 798        ,@(package-inputs fftw)))
 799     (arguments
 800      (substitute-keyword-arguments (package-arguments fftw)
 801        ((#:configure-flags cf)
 802         `(cons "--enable-mpi" ,cf))
 803        ((#:phases phases '%standard-phases)
 804         `(modify-phases ,phases
 805            (add-before 'check 'mpi-setup
 806              ,%openmpi-setup)))))
 807     (description
 808      (string-append (package-description fftw)
 809                     "  With OpenMPI parallelism support."))))
 810
 811 (define-public java-la4j
 812   (package
 813     (name "java-la4j")
 814     (version "0.6.0")
 815     (source (origin
 816               (method git-fetch)
 817               (uri (git-reference
 818                     (url "https://github.com/vkostyukov/la4j.git")
 819                     (commit version)))
 820               (file-name (string-append name "-" version "-checkout"))
 821               (sha256
 822                (base32
 823                 "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
 824     (build-system ant-build-system)
 825     (arguments
 826      `(#:jar-name "la4j.jar"
 827        #:jdk ,icedtea-8
 828        #:test-exclude (list "**/Abstract*.java"
 829                             "**/MatrixTest.java"
 830                             "**/DenseMatrixTest.java"
 831                             "**/SparseMatrixTest.java"
 832                             "**/VectorTest.java"
 833                             "**/SparseVectorTest.java"
 834                             "**/DenseVectorTest.java")))
 835     (native-inputs
 836      `(("java-junit" ,java-junit)
 837        ("java-hamcrest-core" ,java-hamcrest-core)))
 838     (home-page "http://la4j.org/")
 839     (synopsis "Java library that provides Linear Algebra primitives and algorithms")
 840     (description "The la4j library is a Java library that provides Linear
 841 Algebra primitives (matrices and vectors) and algorithms.  The key features of
 842 the la4j library are:
 843
 844 @itemize
 845 @item No dependencies and tiny size
 846 @item Fluent object-oriented/functional API
 847 @item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
 848 @item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
 849 @item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
 850 @item MatrixMarket/CSV IO formats support for matrices and vectors
 851 @end itemize\n")
 852     (license license:asl2.0)))
 853
 854 (define-public java-jlargearrays
 855   (package
 856     (name "java-jlargearrays")
 857     (version "1.6")
 858     (source (origin
 859               (method url-fetch)
 860               (uri (string-append "http://search.maven.org/remotecontent?"
 861                                   "filepath=pl/edu/icm/JLargeArrays/"
 862                                   version "/JLargeArrays-" version
 863                                   "-sources.jar"))
 864               (file-name (string-append name "-" version ".jar"))
 865               (sha256
 866                (base32
 867                 "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
 868     (build-system ant-build-system)
 869     (arguments
 870      `(#:jar-name "jlargearrays.jar"
 871        #:tests? #f ; tests are not included in the release archive
 872        #:jdk ,icedtea-8))
 873     (propagated-inputs
 874      `(("java-commons-math3" ,java-commons-math3)))
 875     (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
 876     (synopsis "Library of one-dimensional arrays that can store up to 263 elements")
 877     (description "JLargeArrays is a Java library of one-dimensional arrays
 878 that can store up to 263 elements.")
 879     (license license:bsd-2)))
 880
 881 (define-public java-jtransforms
 882   (package
 883     (name "java-jtransforms")
 884     (version "3.1")
 885     (source (origin
 886               (method url-fetch)
 887               (uri (string-append "http://search.maven.org/remotecontent?"
 888                                   "filepath=com/github/wendykierp/JTransforms/"
 889                                   version "/JTransforms-" version "-sources.jar"))
 890               (sha256
 891                (base32
 892                 "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
 893     (build-system ant-build-system)
 894     (arguments
 895      `(#:jar-name "jtransforms.jar"
 896        #:tests? #f ; tests are not included in the release archive
 897        #:jdk ,icedtea-8))
 898     (propagated-inputs
 899      `(("java-commons-math3" ,java-commons-math3)
 900        ("java-jlargearrays" ,java-jlargearrays)))
 901     (home-page "https://github.com/wendykierp/JTransforms")
 902     (synopsis "Multithreaded FFT library written in pure Java")
 903     (description "JTransforms is a multithreaded FFT library written in pure
 904 Java.  Currently, four types of transforms are available: @dfn{Discrete
 905 Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
 906 Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
 907     (license license:bsd-2)))
 908
 909 (define-public eigen
 910   (package
 911     (name "eigen")
 912     (version "3.3.5")
 913     (source (origin
 914               (method url-fetch)
 915               (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
 916                                   version ".tar.bz2"))
 917               (sha256
 918                (base32
 919                 "1qh3yrwn78ms5yhwbpl5wvblk4gbz02cacdygxylr7i9xbrvylkk"))
 920               (file-name (string-append name "-" version ".tar.bz2"))
 921               (modules '((guix build utils)))
 922               (snippet
 923                ;; There are 3 test failures in the "unsupported" directory,
 924                ;; but maintainers say it's a known issue and it's unsupported
 925                ;; anyway, so just skip them.
 926                '(begin
 927                   (substitute* "unsupported/CMakeLists.txt"
 928                     (("add_subdirectory\\(test.*")
 929                      "# Do not build the tests for unsupported features.\n"))
 930                   #t))))
 931     (build-system cmake-build-system)
 932     (arguments
 933      '(;; Turn off debugging symbols to save space.
 934        #:build-type "Release"
 935
 936        #:phases (modify-phases %standard-phases
 937                   (replace 'check
 938                     (lambda _
 939                       (let* ((cores  (parallel-job-count))
 940                              (dash-j (format #f "-j~a" cores)))
 941                         (setenv "EIGEN_SEED" "1") ;for reproducibility
 942                         ;; First build the tests, in parallel.  See
 943                         ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
 944                         (invoke "make" "buildtests" dash-j)
 945
 946                         ;; Then run 'CTest' with -V so we get more
 947                         ;; details upon failure.
 948                         (invoke "ctest" "-V" dash-j)))))))
 949     (home-page "https://eigen.tuxfamily.org")
 950     (synopsis "C++ template library for linear algebra")
 951     (description
 952      "Eigen is a C++ template library for linear algebra: matrices, vectors,
 953 numerical solvers, and related algorithms.  It provides an elegant API based
 954 on \"expression templates\".  It is versatile: it supports all matrix sizes,
 955 all standard numeric types, various matrix decompositions and geometry
 956 features, and more.")
 957
 958     ;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3.
 959     ;; See 'COPYING.README' for details.
 960     (license license:mpl2.0)))
 961
 962 (define-public eigen-for-tensorflow
 963   (let ((changeset "fd6845384b86")
 964         (revision "1"))
 965     (package (inherit eigen)
 966       (name "eigen-for-tensorflow")
 967       (version (string-append "3.3.5-" revision "." changeset))
 968       (source (origin
 969                 (method hg-fetch)
 970                 (uri (hg-reference
 971                       (url "https://bitbucket.org/eigen/eigen")
 972                       (changeset changeset)))
 973                 (sha256
 974                  (base32
 975                   "12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5"))
 976                 (file-name (string-append name "-" version "-checkout"))
 977                 (modules '((guix build utils)))
 978                 (snippet
 979                  ;; There are 3 test failures in the "unsupported" directory,
 980                  ;; but maintainers say it's a known issue and it's unsupported
 981                  ;; anyway, so just skip them.
 982                  '(begin
 983                     (substitute* "unsupported/CMakeLists.txt"
 984                       (("add_subdirectory\\(test.*")
 985                        "# Do not build the tests for unsupported features.\n"))
 986                     #t)))))))
 987
 988 (define-public xtensor
 989   (package
 990     (name "xtensor")
 991     (version "0.20.10")
 992     (source (origin
 993               (method git-fetch)
 994               (uri (git-reference
 995                     (url "https://github.com/QuantStack/xtensor.git")
 996                     (commit version)))
 997               (sha256
 998                (base32
 999                 "1fmv2hpx610xwhxrndfsfvlbqfyk4l3gi5q5d7pa9m82kblxjj9l"))
1000               (file-name (git-file-name name version))))
1001     (build-system cmake-build-system)
1002     (native-inputs
1003      `(("googletest" ,googletest)
1004        ("xtl" ,xtl)))
1005     (arguments
1006      `(#:configure-flags
1007        '("-DBUILD_TESTS=ON")
1008        #:test-target "xtest"))
1009     (home-page "https://quantstack.net/xtensor")
1010     (synopsis "C++ tensors with broadcasting and lazy computing")
1011     (description "xtensor is a C++ library meant for numerical analysis with
1012 multi-dimensional array expressions.
1013
1014 xtensor provides:
1015 @itemize
1016 @item an extensible expression system enabling lazy broadcasting.
1017 @item an API following the idioms of the C++ standard library.
1018 @item tools to manipulate array expressions and build upon xtensor.
1019 @end itemize")
1020     (license license:bsd-3)))
1021
1022 (define-public gap
1023   (package
1024     (name "gap")
1025     (version "4.10.2")
1026     (source
1027      (origin
1028        (method url-fetch)
1029        (uri (string-append "https://www.gap-system.org/pub/gap/gap-"
1030                            (version-major+minor version)
1031                            "/tar.bz2/gap-"
1032                            version
1033                            ".tar.bz2"))
1034        (sha256
1035         (base32 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
1036        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
1037        (snippet
1038         '(begin
1039            ;; Delete the external gmp and zlib libraries
1040            ;; and a subdirectory not needed for our build.
1041            (for-each delete-file-recursively
1042                      '("extern" "hpcgap"))
1043            ;; Delete a failing test.
1044            ;; FIXME: This might be fixed in the next release, see
1045            ;; https://github.com/gap-system/gap/issues/3292
1046            (delete-file "tst/testinstall/dir.tst")
1047            ;; Delete all packages except for a fixed list.
1048            (with-directory-excursion "pkg"
1049              (for-each delete-file-recursively
1050                (lset-difference string=? (scandir ".")
1051                  '("." ".."
1052                    ;; Necessary packages.
1053                    "GAPDoc-1.6.2"
1054                    "primgrp-3.3.2"
1055                    "SmallGrp-1.3"    ; artistic2.0
1056                    "transgrp"        ; artistic2.0 for data,
1057                                      ; gpl2 or gpl3 for code
1058                    ;; Recommanded package.
1059                    "io-4.5.4"        ; gpl3+
1060                    ;; Optional packages, searched for at start,
1061                    ;; and their depedencies.
1062                    "alnuth-3.1.0"
1063                    "autpgrp-1.10"
1064                    "crisp-1.4.4"     ; bsd-2
1065                    "ctbllib"       ; gpl3+ according to doc/chap0.txt
1066                    "FactInt-1.6.2"
1067                    "fga"
1068                    "irredsol-1.4"    ; bsd-2
1069                    "laguna-3.9.2"
1070                    "polenta-1.3.8"
1071                    "polycyclic-2.14"
1072                    "radiroot-2.8"
1073                    "resclasses-4.7.1"
1074                    "sophus-1.24"
1075                    "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
1076                                    ; and the next release
1077                    "utils-0.59"))))
1078            #t))))
1079     (build-system gnu-build-system)
1080     (inputs
1081      `(("gmp" ,gmp)
1082        ("zlib" ,zlib)))
1083     (arguments
1084      `(#:modules ((ice-9 ftw)
1085                   (srfi srfi-26)
1086                   (guix build gnu-build-system)
1087                   (guix build utils))
1088        #:phases
1089        (modify-phases %standard-phases
1090          (add-after 'build 'build-packages
1091            ;; Compile all packages that have not been deleted by the
1092            ;; code snippet above.
1093            (lambda _
1094              (setenv "CONFIG_SHELL" (which "bash"))
1095              (with-directory-excursion "pkg"
1096                (invoke "../bin/BuildPackages.sh")
1097              #t)))
1098          (add-after 'build-packages 'build-doc
1099            ;; The documentation is bundled, but we create it from source.
1100            (lambda _
1101              (with-directory-excursion "doc"
1102                (invoke "./make_doc"))
1103              #t))
1104          (replace 'install
1105            (lambda* (#:key outputs #:allow-other-keys)
1106              (let* ((out (assoc-ref outputs "out"))
1107                     (bin (string-append out "/bin"))
1108                     (lib (string-append out "/lib"))
1109                     (prog (string-append bin "/gap"))
1110                     (prog-real (string-append bin "/.gap-real"))
1111                     (share (string-append out "/share/gap"))
1112                     (include (string-append out "/include/gap"))
1113                     (include-hpc (string-append include "/hpc")))
1114                ;; Install only the gap binary; the gac compiler is left
1115                ;; for maybe later. "Wrap" it in a shell script that calls
1116                ;; the binary with the correct parameter.
1117                (mkdir-p bin)
1118                (copy-file "gap" prog-real)
1119                (call-with-output-file prog
1120                  (lambda (port)
1121                    (format port
1122                            "#!~a~%exec ~a -l ~a \"$@\"~%"
1123                            (which "bash")
1124                            prog-real
1125                            share)))
1126                (chmod prog #o755)
1127                ;; Install the headers, which are needed by Sage. The
1128                ;; Makefile target "install-headers" was available in
1129                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1130                (mkdir-p include-hpc)
1131                (install-file "gen/config.h" include)
1132                (let ((file-name-predicate-without-stat
1133                        (lambda (regex)
1134                          (cut (file-name-predicate regex) <> #f))))
1135                  (with-directory-excursion "src"
1136                    (for-each
1137                      (cut install-file <> include)
1138                      (scandir "."
1139                               (file-name-predicate-without-stat ".*\\.h$"))))
1140                  (with-directory-excursion "src/hpc"
1141                    (for-each
1142                      (cut install-file <> include-hpc)
1143                      (scandir "."
1144                               (file-name-predicate-without-stat ".*\\.h$")))))
1145                ;; Install the library, which is needed by Sage. The
1146                ;; Makefile target "install-libgap" was available in
1147                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1148                ;; Compared to the Makefile, which used libtool, the
1149                ;; following approach of copying files and making symlinks
1150                ;; is rather pedestrian. There is hope that some later
1151                ;; version of gap reinstates and completes the install
1152                ;; targets.
1153                (invoke "make" "libgap.la")
1154                (install-file "libgap.la" lib)
1155                (install-file ".libs/libgap.so.0.0.0" lib)
1156                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so"))
1157                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
1158                ;; Install a certain number of files and directories to
1159                ;; SHARE, where the wrapped shell script expects them.
1160                ;; Remove information on the build directory from sysinfo.gap.
1161                (substitute* "sysinfo.gap"
1162                  (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
1163                  (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
1164                  (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
1165                (install-file "sysinfo.gap" share)
1166                (copy-recursively "grp" (string-append share "/grp"))
1167                (copy-recursively "pkg" (string-append share "/pkg"))
1168                ;; The following is not the C library libgap.so, but a
1169                ;; library of GAP code.
1170                (copy-recursively "lib" (string-append share "/lib"))
1171                ;; The gap binary looks for documentation inside SHARE.
1172                (copy-recursively "doc" (string-append share "/doc")))
1173              #t)))))
1174     (home-page "https://www.gap-system.org/")
1175     (synopsis
1176      "System for computational group theory")
1177     (description
1178      "GAP is a system for computational discrete algebra, with particular
1179 emphasis on computational group theory.  It provides a programming language,
1180 a library of thousands of functions implementing algebraic algorithms
1181 written in the GAP language as well as large data libraries of algebraic
1182 objects.")
1183     ;; Some packages have different licenses (effectively forcing the
1184     ;; combined work to be licensed as gpl3+); if this is the case, this
1185     ;; is mentioned above next to their name.
1186     ;; Some packages have no license mentioned explicitly; supposedly this
1187     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
1188     ;; safe side, we drop them for now.
1189     (license license:gpl2+)))
1190
1191 (define-public givaro
1192   (package
1193     (name "givaro")
1194     (version "4.1.1")
1195     (source (origin
1196               (method git-fetch)
1197               (uri (git-reference
1198                     (url "https://github.com/linbox-team/givaro")
1199                     (commit (string-append "v" version))))
1200               (file-name (git-file-name name version))
1201               (sha256
1202                (base32
1203                 "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
1204     (build-system gnu-build-system)
1205     (native-inputs
1206      `(("autoconf" ,autoconf)
1207        ("automake" ,automake)
1208        ("libtool" ,libtool)))
1209     (propagated-inputs
1210      `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
1211     (arguments
1212      `(#:phases
1213        (modify-phases %standard-phases
1214          (add-before 'bootstrap 'setenv
1215            ;; Prevent the autogen.sh script to carry out the configure
1216            ;; script, which has not yet been patched to replace /bin/sh.
1217            (lambda _
1218              (setenv "NOCONFIGURE" "yes")
1219              #t)))))
1220     (synopsis "Algebraic computations with exact rings and fields")
1221     (description
1222      "Givaro is a C++ library implementing the basic arithmetic of various
1223 algebraic objects: prime fields, extension fields, finite fields, finite
1224 rings, polynomials, algebraic numbers, arbitrary precision integers and
1225 rationals (C++ wrappers over gmp), fixed precision integers.  It also
1226 provides data-structures and templated classes for the manipulation of
1227 compound objects, such as vectors, matrices and univariate polynomials.")
1228     (license license:cecill-b)
1229     (home-page "https://github.com/linbox-team/givaro")))
1230
1231 (define-public fflas-ffpack
1232   (package
1233     (name "fflas-ffpack")
1234     (version "2.4.3")
1235     (source (origin
1236               (method git-fetch)
1237               (uri (git-reference
1238                     (url "https://github.com/linbox-team/fflas-ffpack")
1239                     (commit version)))
1240               (file-name (git-file-name name version))
1241               (sha256
1242                (base32
1243                 "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
1244     (build-system gnu-build-system)
1245     (native-inputs
1246      `(("autoconf" ,autoconf)
1247        ("automake" ,automake)
1248        ("libtool" ,libtool)
1249        ("pkg-config" ,pkg-config)))
1250     (inputs
1251      `(("openblas" ,openblas)))
1252     (propagated-inputs
1253      `(("givaro" ,givaro))) ; required according to the .pc file
1254     (arguments
1255      `(#:configure-flags
1256        (list (string-append "--with-blas-libs="
1257                             (assoc-ref %build-inputs "openblas")
1258                             "/lib/libopenblas.so"))
1259        #:phases
1260        (modify-phases %standard-phases
1261          (add-before 'bootstrap 'setenv
1262            ;; Prevent the autogen.sh script to carry out the configure
1263            ;; script, which has not yet been patched to replace /bin/sh.
1264            (lambda _
1265              (setenv "NOCONFIGURE" "yes")
1266              #t)))))
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     (arguments
1303      `(#:phases
1304        (modify-phases %standard-phases
1305          (add-before 'bootstrap 'setenv
1306            ;; Prevent the autogen.sh script to carry out the configure
1307            ;; script, which has not yet been patched to replace /bin/sh.
1308            (lambda _
1309              (setenv "NOCONFIGURE" "yes")
1310              #t)))))
1311     (synopsis "C++ library for linear algebra over exact rings")
1312     (description
1313      "LinBox is a C++ template library for exact linear algebra computation
1314 with dense, sparse, and structured matrices over the integers and over
1315 finite fields.")
1316     (license license:lgpl2.1+)
1317     (home-page "https://linbox-team.github.io/linbox/")))
1318
1319 (define-public m4ri
1320   (package
1321     (name "m4ri")
1322     (version "20140914")
1323     (source (origin
1324               (method git-fetch)
1325               (uri (git-reference
1326                     (url "https://bitbucket.org/malb/m4ri")
1327                     (commit (string-append "release-" version))))
1328               (file-name (git-file-name name version))
1329               (sha256
1330                (base32
1331                 "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
1332     (build-system gnu-build-system)
1333     (native-inputs
1334      `(("autoconf" ,autoconf)
1335        ("automake" ,automake)
1336        ("libtool" ,libtool)
1337        ("pkg-config" ,pkg-config)))
1338     (inputs
1339      `(("libpng" ,libpng)))
1340     (synopsis "Arithmetic of dense matrices over F_2")
1341     (description "M4RI is a library for fast arithmetic with dense matrices
1342 over F2.  The name M4RI comes from the first implemented algorithm: The
1343 Method of the Four Russians inversion algorithm published by Gregory Bard.
1344 This algorithm in turn is named after the Method of the Four Russians
1345 multiplication algorithm.")
1346     (license license:gpl2+)
1347     (home-page "https://bitbucket.org/malb/m4ri/")))
1348
1349 (define-public symmetrica
1350   (package
1351     (name "symmetrica")
1352     (version "2.0")
1353     (source (origin
1354               (method url-fetch/tarbomb)
1355               (uri (let ((v (string-join (string-split version #\.) "_")))
1356                      (string-append "http://www.algorithm.uni-bayreuth.de/"
1357                                     "en/research/SYMMETRICA/"
1358                                     "SYM" v "_tar.gz")))
1359               (sha256
1360                (base32
1361                 "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
1362               ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
1363               (patches (search-patches "symmetrica-bruch.patch"
1364                                        "symmetrica-int32.patch"
1365                                        "symmetrica-return_values.patch"
1366                                        "symmetrica-sort_sum_rename.patch"))))
1367     (build-system gnu-build-system)
1368     (arguments
1369      `(#:tests? #f                      ;no test
1370        #:phases
1371        (modify-phases %standard-phases
1372          (add-after 'unpack 'fix-makefile
1373            (lambda _
1374              (substitute* "makefile"
1375                (("cc -c") "gcc -c -fPIC"))
1376              #t))
1377          (add-after 'fix-makefile 'turn-off-banner
1378            (lambda _
1379              (substitute* "de.c"
1380                (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
1381              #t))
1382          (delete 'configure)            ;no configure script
1383          (replace 'install              ;no install target
1384            (lambda* (#:key outputs #:allow-other-keys)
1385              (let* ((out (assoc-ref outputs "out"))
1386                     (lib (string-append out "/lib"))
1387                     (inc (string-append out "/include/symmetrica"))
1388                     (doc (string-append out "/share/doc/symmetrica-" ,version))
1389                     (static "libsymmetrica.a"))
1390                ;; Build static library.
1391                (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
1392                (invoke "ranlib" static)
1393                ;; Install static library and headers.
1394                (for-each (lambda (f) (install-file f inc))
1395                          (find-files "." "\\.h$"))
1396                (install-file "libsymmetrica.a" lib)
1397                ;; Install documentation.
1398                (for-each (lambda (f) (install-file f doc))
1399                          (find-files "." "\\.doc$"))
1400                #t))))))
1401     (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
1402     (synopsis "Combinatoric C Library")
1403     (description "Symmetrica is a library for combinatorics.  It has support
1404 for the representation theory of the symmetric group and related groups,
1405 combinatorics of tableaux, symmetric functions and polynomials, Schubert
1406 polynomials, and the representation theory of Hecke algebras of type A_n.")
1407     (license license:public-domain)))
1408
1409 (define-public m4rie
1410   (package
1411     (name "m4rie")
1412     (version "20150908")
1413     (source (origin
1414               (method git-fetch)
1415               (uri (git-reference
1416                     (url "https://bitbucket.org/malb/m4rie")
1417                     (commit (string-append "release-" version))))
1418               (file-name (git-file-name name version))
1419               (sha256
1420                (base32
1421                 "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
1422     (build-system gnu-build-system)
1423     (native-inputs
1424      `(("autoconf" ,autoconf)
1425        ("automake" ,automake)
1426        ("libtool" ,libtool)))
1427     (inputs
1428      `(("m4ri" ,m4ri)))
1429     (synopsis "Arithmetic of dense matrices over F_{2^e}")
1430     (description "M4RI is a library for fast arithmetic with dense matrices
1431 over finite fields of characteristic 2.  So it extends the functionality
1432 of M4RI from F_2 to F_{2^e}.")
1433     (license license:gpl2+)
1434     (home-page "https://bitbucket.org/malb/m4rie/")))
1435
1436 (define-public eclib
1437   (package
1438     (name "eclib")
1439     (version "20190909")
1440     (source (origin
1441               (method git-fetch)
1442               (uri (git-reference
1443                     (url "https://github.com/JohnCremona/eclib/")
1444                     (commit (string-append "v" version))))
1445               (file-name (git-file-name name version))
1446               (sha256
1447                (base32
1448                 "1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n"))))
1449     (build-system gnu-build-system)
1450     (native-inputs
1451      `(("autoconf" ,autoconf)
1452        ("automake" ,automake)
1453        ("libtool" ,libtool)))
1454     (inputs
1455      `(("gmp" ,gmp)
1456        ("ntl" ,ntl)
1457        ("pari-gp" ,pari-gp)))
1458     (synopsis "Ranks of elliptic curves and modular symbols")
1459     (description "The eclib package includes mwrank (for 2-descent on
1460 elliptic curves over Q) and modular symbol code; it has been written by
1461 John Cremona to compute his elliptic curve database.")
1462     (license license:gpl2+)
1463     (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
1464                               "J.E.Cremona/mwrank/index.html"))))
1465
1466 (define-public lrcalc
1467   (package
1468     (name "lrcalc")
1469     (version "1.2")
1470     (source (origin
1471               (method git-fetch)
1472               (uri (git-reference
1473                     (url "https://bitbucket.org/asbuch/lrcalc")
1474                     (commit (string-append "lrcalc-" version))))
1475               (file-name (git-file-name name version))
1476               (sha256
1477                (base32
1478                 "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
1479               (patches (search-patches "lrcalc-includes.patch"))))
1480     (build-system gnu-build-system)
1481     (native-inputs
1482      `(("autoconf" ,autoconf)
1483        ("automake" ,automake)
1484        ("libtool" ,libtool)))
1485     (arguments
1486      `(#:phases
1487        (modify-phases %standard-phases
1488          (add-before 'build 'fix-permission
1489            (lambda _
1490              (chmod "lrcalc.maple.src" #o644)
1491              #t)))))
1492     (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
1493     (description "The Littlewood-Richardson Calculator (lrcalc) is a
1494 program designed to compute Littlewood-Richardson coefficients.  It computes
1495 single Littlewood-Richardson coefficients, products of Schur functions, or
1496 skew Schur functions.  In addition it computes products in the small quantum
1497 cohomology ring of a Grassmann variety.  The software package also includes
1498 a program that performs fast computation of the more general multiplicative
1499 structure constants of Schubert polynomials.")
1500     (license license:gpl2+)
1501     (home-page "http://sites.math.rutgers.edu/~asbuch/lrcalc/")))
1502
1503 (define-public iml
1504   (package
1505     (name "iml")
1506     (version "1.0.5")
1507     (source
1508      (origin
1509        (method url-fetch)
1510        (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
1511                            version ".tar.bz2"))
1512        (sha256
1513         (base32
1514          "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
1515     (build-system gnu-build-system)
1516     (inputs
1517      `(("gmp", gmp)
1518        ("cblas" ,openblas))) ; or any other BLAS library; the documentation
1519                              ; mentions ATLAS in particular
1520     (arguments
1521      `(#:configure-flags
1522        (list
1523         "--enable-shared"
1524         (string-append "--with-gmp-include="
1525                        (assoc-ref %build-inputs "gmp") "/include")
1526         (string-append "--with-gmp-lib="
1527                        (assoc-ref %build-inputs "gmp") "/lib")
1528         "--with-cblas=-lopenblas"
1529         (string-append "--with-cblas-include="
1530                        (assoc-ref %build-inputs "cblas") "/include")
1531         (string-append "--with-cblas-lib="
1532                        (assoc-ref %build-inputs "cblas") "/lib"))))
1533     (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
1534     (synopsis
1535      "Solver for systems of linear equations over the integers")
1536     (description
1537      "IML is a C library implementing algorithms for computing exact
1538 solutions to dense systems of linear equations over the integers.
1539 Currently, IML provides the following functionality:
1540
1541 @itemize
1542 @item Nonsingular rational system solving:
1543 compute the unique rational solution X to the system AX=B, where A and B
1544 are integer matrices, A nonsingular.
1545 @item Compute the right nullspace or kernel of an integer matrix.
1546 @item Certified linear system solving:
1547 compute a minimal denominator solution x to a system Ax=b, where b is an
1548 integer vector and A is an integer matrix with arbitrary shape and
1549 rank profile.
1550 @end itemize
1551
1552 In addition, IML provides some low level routines for a variety of mod p
1553 matrix operations: computing the row-echelon form, determinant, rank
1554 profile, and inverse of a mod p matrix. These mod p routines are not
1555 general purpose; they require that p satisfy some preconditions based on
1556 the dimension of the input matrix (usually p should be prime and should be
1557 no more than about 20 bits long).")
1558     (license license:bsd-3)))