gnu/packages/algebra.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Andreas Enge <andreas@enge.fr>
   3 ;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
   4 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Nicolas Goaziou <mail@nicolasgoaziou.fr>
   5 ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
   6 ;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
   7 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
   8 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
   9 ;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
  10 ;;; Copyright © 2017, 2019 Eric Bavier <bavier@member.fsf.org>
  11 ;;; Copyright © 2019 Mathieu Othacehe <m.othacehe@gmail.com>
  12 ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
  13 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
  14 ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
  15 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
  16 ;;;
  17 ;;; This file is part of GNU Guix.
  18 ;;;
  19 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  20 ;;; under the terms of the GNU General Public License as published by
  21 ;;; the Free Software Foundation; either version 3 of the License, or (at
  22 ;;; your option) any later version.
  23 ;;;
  24 ;;; GNU Guix is distributed in the hope that it will be useful, but
  25 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  26 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  27 ;;; GNU General Public License for more details.
  28 ;;;
  29 ;;; You should have received a copy of the GNU General Public License
  30 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  31
  32 (define-module (gnu packages algebra)
  33   #:use-module (gnu packages)
  34   #:use-module (gnu packages autotools)
  35   #:use-module (gnu packages bison)
  36   #:use-module (gnu packages check)
  37   #:use-module (gnu packages compression)
  38   #:use-module (gnu packages cpp)
  39   #:use-module (gnu packages documentation)
  40   #:use-module (gnu packages ed)
  41   #:use-module (gnu packages flex)
  42   #:use-module (gnu packages fltk)
  43   #:use-module (gnu packages gl)
  44   #:use-module (gnu packages graphviz)
  45   #:use-module (gnu packages image)
  46   #:use-module (gnu packages java)
  47   #:use-module (gnu packages llvm)
  48   #:use-module (gnu packages maths)
  49   #:use-module (gnu packages mpi)
  50   #:use-module (gnu packages multiprecision)
  51   #:use-module (gnu packages perl)
  52   #:use-module (gnu packages pkg-config)
  53   #:use-module (gnu packages pulseaudio)
  54   #:use-module (gnu packages python)
  55   #:use-module (gnu packages python-xyz)
  56   #:use-module (gnu packages readline)
  57   #:use-module (gnu packages shells)
  58   #:use-module (gnu packages tex)
  59   #:use-module (gnu packages texinfo)
  60   #:use-module (gnu packages xiph)
  61   #:use-module (gnu packages xorg)
  62   #:use-module (guix build-system ant)
  63   #:use-module (guix build-system gnu)
  64   #:use-module (guix build-system cmake)
  65   #:use-module (guix build-system python)
  66   #:use-module (guix download)
  67   #:use-module (guix git-download)
  68   #:use-module (guix hg-download)
  69   #:use-module ((guix licenses) #:prefix license:)
  70   #:use-module (guix packages)
  71   #:use-module (guix utils))
  72
  73
  74 (define-public mpfrcx
  75   (package
  76    (name "mpfrcx")
  77    (version "0.5")
  78    (source (origin
  79             (method url-fetch)
  80             (uri (string-append
  81                   "http://www.multiprecision.org/downloads/mpfrcx-"
  82                   version ".tar.gz"))
  83             (sha256
  84              (base32
  85               "1s968480ymv6w0rnvfp9mxvx98hvi29fkvw8nk4ggzc6azxgwybs"))))
  86    (build-system gnu-build-system)
  87    (propagated-inputs
  88      `(("gmp" ,gmp)
  89        ("mpfr" ,mpfr)
  90        ("mpc"  ,mpc))) ; Header files are included by mpfrcx.h.
  91    (synopsis "Arithmetic of polynomials over arbitrary precision numbers")
  92    (description
  93     "Mpfrcx is a library for the arithmetic of univariate polynomials over
  94 arbitrary precision real (mpfr) or complex (mpc) numbers, without control
  95 on the rounding.  For the time being, only the few functions needed to
  96 implement the floating point approach to complex multiplication are
  97 implemented.  On the other hand, these comprise asymptotically fast
  98 multiplication routines such as Toom–Cook and the FFT.")
  99    (license license:lgpl3+)
 100    (home-page "http://www.multiprecision.org/mpfrcx/")))
 101
 102 (define-public gf2x
 103   (package
 104    (name "gf2x")
 105    (version "1.2")
 106    (source (origin
 107             (method url-fetch)
 108             (uri (string-append
 109                   "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-"
 110                   version ".tar.gz"))
 111             (sha256
 112              (base32
 113               "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1"))))
 114    (build-system gnu-build-system)
 115    (synopsis "Arithmetic of polynomials over binary finite fields")
 116    (description
 117     "The gf2x library provides arithmetic of polynomials over finite fields
 118 of characteristic 2.  It implements the multiplication, squaring and
 119 greatest common divisor operations.")
 120    (license license:gpl3+)
 121    (home-page "https://gforge.inria.fr/projects/gf2x/")))
 122
 123 (define-public cm
 124   (package
 125    (name "cm")
 126    (version "0.3")
 127    (source (origin
 128             (method url-fetch)
 129             (uri (string-append
 130                   "http://www.multiprecision.org/cm/download/cm-"
 131                   version ".tar.gz"))
 132             (sha256
 133              (base32
 134               "1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc"))))
 135    (build-system gnu-build-system)
 136    (propagated-inputs
 137      `(("mpfrcx" ,mpfrcx)
 138        ("zlib" ,zlib))) ; Header files included from cm_common.h.
 139    (inputs
 140      `(("pari-gp"  ,pari-gp)))
 141    (synopsis "CM constructions for elliptic curves")
 142    (description
 143     "The CM software implements the construction of ring class fields of
 144 imaginary quadratic number fields and of elliptic curves with complex
 145 multiplication via floating point approximations.  It consists of libraries
 146 that can be called from within a C program and of executable command
 147 line applications.")
 148    (license license:gpl3+)
 149    (home-page "http://www.multiprecision.org/cm/")))
 150
 151 (define-public fplll
 152   (package
 153     (name "fplll")
 154     (version "5.2.1")
 155     (source (origin
 156               (method git-fetch)
 157               (uri (git-reference
 158                     (url "https://github.com/fplll/fplll")
 159                     (commit version)))
 160               (file-name (git-file-name name version))
 161               (sha256
 162                (base32
 163                 "015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg"))))
 164     (build-system gnu-build-system)
 165     (native-inputs
 166      `(("autoconf" ,autoconf)
 167        ("automake" ,automake)
 168        ("libtool" ,libtool)))
 169     (inputs
 170      `(("gmp" ,gmp)
 171        ("mpfr" ,mpfr)))
 172     (home-page "https://github.com/fplll/fplll")
 173     (synopsis "Library for LLL-reduction of euclidean lattices")
 174     (description
 175      "fplll contains implementations of several lattice algorithms.
 176 The implementation relies on floating-point orthogonalization, and LLL
 177 is central to the code, hence the name.
 178
 179 It includes implementations of floating-point LLL reduction
 180 algorithms, offering different speed/guarantees ratios.  It contains
 181 a @emph{wrapper} choosing the estimated best sequence of variants in
 182 order to provide a guaranteed output as fast as possible.  In the case
 183 of the wrapper, the succession of variants is oblivious to the user.
 184
 185 It includes an implementation of the BKZ reduction algorithm,
 186 including the BKZ-2.0 improvements (extreme enumeration
 187 pruning, pre-processing of blocks, early termination).  Additionally,
 188 Slide reduction and self dual BKZ are supported.
 189
 190 It also includes a floating-point implementation of the
 191 Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice
 192 vector.  For the same task, the GaussSieve algorithm is also available
 193 in fplll.  Finally, it contains a variant of the enumeration algorithm
 194 that computes a lattice vector closest to a given vector belonging to
 195 the real span of the lattice.")
 196     (license license:lgpl2.1+)))
 197
 198 (define-public python-fpylll
 199   (package
 200     (name "python-fpylll")
 201     (version "0.4.1")
 202     (source
 203      (origin
 204        ;; Pypi contains and older release, so we use a tagged release from
 205        ;; Github instead.
 206        (method git-fetch)
 207        (uri (git-reference
 208              (url "https://github.com/fplll/fpylll")
 209              (commit (string-append version "dev"))))
 210        (file-name (git-file-name name version))
 211        (sha256
 212         (base32
 213          "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
 214     (build-system python-build-system)
 215     (inputs
 216      `(("fplll" ,fplll)
 217        ("gmp" ,gmp)
 218        ("mpfr" ,mpfr)
 219        ("pari-gp" ,pari-gp)))
 220     (propagated-inputs
 221      `(("cysignals" ,python-cysignals)
 222        ("cython" ,python-cython)
 223        ("flake8" ,python-flake8)
 224        ("numpy" ,python-numpy)
 225        ("pytest" ,python-pytest)))
 226     (home-page "https://github.com/fplll/fpylll")
 227     (synopsis "Python interface for fplll")
 228     (description "fpylll is a Python wrapper for fplll.")
 229     (license license:gpl2+)))
 230
 231 (define-public pari-gp
 232   (package
 233     (name "pari-gp")
 234     (version "2.11.4")
 235     (source (origin
 236               (method url-fetch)
 237               (uri (string-append
 238                     "https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
 239                     version ".tar.gz"))
 240               (sha256
 241                (base32
 242                 "070bjw4kg7r6lqs1hfs08n5fmjv90cpwflp3wr04hbrmyz28zj5z"))))
 243     (build-system gnu-build-system)
 244     (native-inputs
 245      `(("texlive" ,(texlive-union
 246                     (list texlive-amsfonts)))))
 247     (inputs `(("gmp" ,gmp)
 248               ("libx11" ,libx11)
 249               ("perl" ,perl)
 250               ("readline" ,readline)))
 251     (arguments
 252      '(#:make-flags '("all")
 253        #:test-target "dobench"
 254        #:phases
 255        (modify-phases %standard-phases
 256          (replace 'configure
 257            (lambda* (#:key outputs #:allow-other-keys)
 258              (invoke "./Configure"
 259                      (string-append "--prefix="
 260                                     (assoc-ref outputs "out"))))))))
 261     (synopsis "PARI/GP, a computer algebra system for number theory")
 262     (description
 263      "PARI/GP is a widely used computer algebra system designed for fast
 264 computations in number theory (factorisations, algebraic number theory,
 265 elliptic curves...), but it also contains a large number of other useful
 266 functions to compute with mathematical entities such as matrices,
 267 polynomials, power series, algebraic numbers, etc., and a lot of
 268 transcendental functions.
 269 PARI is also available as a C library to allow for faster computations.")
 270     (license license:gpl2+)
 271     (home-page "https://pari.math.u-bordeaux.fr/")))
 272
 273 (define-public gp2c
 274   (package
 275    (name "gp2c")
 276    (version "0.0.11pl3")
 277    (source (origin
 278             (method url-fetch)
 279             (uri (string-append
 280                   "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
 281                   version ".tar.gz"))
 282             (sha256
 283               (base32
 284                 "0yymbrgyjw500hqgmkj5m4nmscd7c9rs9w2c96lxgrcyab8krhrm"))))
 285    (build-system gnu-build-system)
 286    (native-inputs `(("perl" ,perl)))
 287    (inputs `(("pari-gp" ,pari-gp)))
 288    (arguments
 289     '(#:configure-flags
 290       (list (string-append "--with-paricfg="
 291                            (assoc-ref %build-inputs "pari-gp")
 292                            "/lib/pari/pari.cfg"))))
 293    (synopsis "PARI/GP, a computer algebra system for number theory")
 294    (description
 295     "PARI/GP is a widely used computer algebra system designed for fast
 296 computations in number theory (factorisations, algebraic number theory,
 297 elliptic curves...), but it also contains a large number of other useful
 298 functions to compute with mathematical entities such as matrices,
 299 polynomials, power series, algebraic numbers, etc., and a lot of
 300 transcendental functions.
 301 PARI is also available as a C library to allow for faster computations.
 302
 303 GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
 304    (license license:gpl2)
 305    (home-page "https://pari.math.u-bordeaux.fr/")))
 306
 307 (define fplll-4-cmh
 308   (package
 309     (inherit fplll)
 310     (name "fplll")
 311     (version "4.0.4")
 312     (source
 313      (origin
 314        (method url-fetch)
 315        (uri (string-append
 316              "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
 317              version ".tar.gz"))
 318        (sha256
 319         (base32 "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))))
 320
 321 (define-public cmh
 322   (package
 323    (name "cmh")
 324    (version "1.0")
 325    (source (origin
 326             (method url-fetch)
 327             (uri (string-append
 328                   "https://gforge.inria.fr/frs/download.php/33497/cmh-"
 329                   version ".tar.gz"))
 330             (sha256
 331              (base32
 332               "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
 333    (build-system gnu-build-system)
 334    (inputs
 335      `(("gmp" ,gmp)
 336        ("mpfr" ,mpfr)
 337        ("mpc" ,mpc)
 338        ("mpfrcx" ,mpfrcx)
 339        ("fplll" ,fplll-4-cmh)
 340        ("pari-gp"  ,pari-gp)))
 341    (synopsis "Igusa class polynomial computations")
 342    (description
 343     "The CMH software computes Igusa (genus 2) class polynomials, which
 344 parameterize the CM points in the moduli space of 2-dimensional abelian
 345 varieties, i.e. Jacobians of hyperelliptic curves.
 346 It can also be used to compute theta constants at arbitrary
 347 precision.")
 348    (license license:gpl3+)
 349    (home-page "http://cmh.gforge.inria.fr/")))
 350
 351 (define-public giac
 352   (package
 353     (name "giac")
 354     (version "1.6.0-7")
 355     (source
 356      (origin
 357        (method url-fetch)
 358        ;; "~parisse/giac" is not used because the maintainer regularly
 359        ;; overwrites the release tarball there, introducing a checksum
 360        ;; mismatch every time.  See
 361        ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
 362        (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
 363                            "~parisse/debian/dists/stable/main/source/"
 364                            "giac_" version ".tar.gz"))
 365        (sha256
 366         (base32 "1pvgp137zcl0rbhdn1j41xxfml7fp771a7x4ph8qrhhlx0hxzn3p"))))
 367     (build-system gnu-build-system)
 368     (arguments
 369      `(#:modules ((ice-9 ftw)
 370                   (guix build utils)
 371                   (guix build gnu-build-system))
 372        #:phases
 373        (modify-phases %standard-phases
 374          (add-after 'unpack 'patch-bin-cp
 375            ;; Some Makefiles contain hard-coded "/bin/cp".
 376            (lambda _
 377              (substitute* (find-files "doc" "^Makefile")
 378                (("/bin/cp") (which "cp")))
 379              #t))
 380          (add-after 'unpack 'disable-failing-test
 381            ;; FIXME: Test failing.  Not sure why.
 382            (lambda _
 383              (substitute* "check/Makefile.in"
 384                (("chk_fhan11") ""))
 385              #t))
 386          (add-after 'install 'fix-doc
 387            (lambda* (#:key outputs #:allow-other-keys)
 388              (let ((out (assoc-ref outputs "out")))
 389                ;; Most French documentation has a non-commercial
 390                ;; license, so we need to remove it.
 391                (with-directory-excursion (string-append out "/share/giac/doc/fr")
 392                  (for-each delete-file-recursively
 393                            '("cascas" "casexo" "casgeo" "casrouge" "cassim"
 394                              "castor")))
 395                ;; Remove duplicate documentation in
 396                ;; "%out/share/doc/giac/", where Xcas does not expect
 397                ;; to find it.
 398                (delete-file-recursively (string-append out "/share/doc/giac"))
 399                #t)))
 400          (add-after 'install 'remove-unnecessary-executable
 401            (lambda* (#:key outputs #:allow-other-keys)
 402              (let ((out (assoc-ref outputs "out")))
 403                (delete-file (string-append out "/bin/xcasnew"))
 404                #t))))))
 405     (inputs
 406 ;;; TODO: Add libnauty.
 407      `(("fltk" ,fltk)
 408        ("glpk" ,glpk)
 409        ("gmp" ,gmp)
 410        ("gsl" ,gsl)
 411        ("lapack" ,lapack)
 412        ("libao" ,ao)
 413        ("libjpeg" ,libjpeg-turbo)
 414        ("libpng" ,libpng)
 415        ("libsamplerate" ,libsamplerate)
 416        ("libx11" ,libx11)
 417        ("libxinerama" ,libxinerama)
 418        ("libxft" ,libxft)
 419        ("libxt" ,libxt)
 420        ("mesa" ,mesa)
 421        ("mpfi" ,mpfi)
 422        ("mpfr" ,mpfr)
 423        ("ntl" ,ntl)
 424        ("perl" ,perl)
 425        ("pari-gp" ,pari-gp)
 426        ("tcsh" ,tcsh)))
 427     (native-inputs
 428      `(("bison" ,bison)
 429        ("flex" ,flex)
 430        ("readline" ,readline)
 431        ("texlive" ,texlive-tiny)))
 432     (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
 433     (synopsis "Computer algebra system")
 434     (description
 435      "Giac/Xcas is a computer algebra system.  It has a compatibility mode for
 436 maple, mupad and the TI89.  It is available as a standalone program (graphic
 437 or text interfaces) or as a C++ library.")
 438     (license license:gpl3+)))
 439
 440 (define-public flint
 441   (package
 442    (name "flint")
 443    (version "2.6.0")
 444    (source (origin
 445             (method url-fetch)
 446             (uri (string-append
 447                   "http://flintlib.org/flint-"
 448                   version ".tar.gz"))
 449             (sha256 (base32
 450                      "0h08a71kn8347zsqjamqnmrxjpsnnzpmhvxb6d2xmfrcs6nyv2ch"))))
 451    (build-system gnu-build-system)
 452    (inputs
 453     `(("ntl" ,ntl)))
 454    (propagated-inputs
 455     `(("gmp" ,gmp)
 456       ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
 457    (arguments
 458     `(#:parallel-tests? #f ; seems to be necessary on arm
 459       #:phases
 460        (modify-phases %standard-phases
 461          (add-before 'configure 'newer-c++
 462            (lambda _
 463              (substitute* "configure"
 464                (("-ansi") ""))
 465              #t))
 466          (replace 'configure
 467            (lambda* (#:key inputs outputs #:allow-other-keys)
 468              (let ((out (assoc-ref outputs "out"))
 469                    (gmp (assoc-ref inputs "gmp"))
 470                    (mpfr (assoc-ref inputs "mpfr"))
 471                    (ntl (assoc-ref inputs "ntl")))
 472                ;; do not pass "--enable-fast-install", which makes the
 473                ;; homebrew configure process fail
 474                (invoke "./configure"
 475                        (string-append "--prefix=" out)
 476                        (string-append "--with-gmp=" gmp)
 477                        (string-append "--with-mpfr=" mpfr)
 478                        (string-append "--with-ntl=" ntl))
 479                #t))))))
 480    (synopsis "Fast library for number theory")
 481    (description
 482     "FLINT is a C library for number theory.  It supports arithmetic
 483 with numbers, polynomials, power series and matrices over many base
 484 rings, including multiprecision integers and rationals, integers
 485 modulo n, p-adic numbers, finite fields (prime and non-prime order)
 486 and real and complex numbers (via the Arb extension library).
 487
 488 Operations that can be performed include conversions, arithmetic,
 489 GCDs, factoring, solving linear systems, and evaluating special
 490 functions.  In addition, FLINT provides various low-level routines for
 491 fast arithmetic.")
 492    (license license:gpl2+)
 493    (home-page "http://flintlib.org/")))
 494
 495 (define-public arb
 496   (package
 497     (name "arb")
 498     (version "2.17.0")
 499     (source (origin
 500               (method git-fetch)
 501               (uri (git-reference
 502                     (url "https://github.com/fredrik-johansson/arb")
 503                     (commit version)))
 504               (file-name (git-file-name name version))
 505               (sha256
 506                (base32
 507                 "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1"))
 508               (patches (search-patches "arb-flint-2.6.patch"))))
 509     (build-system gnu-build-system)
 510     (propagated-inputs
 511      `(("flint" ,flint)))               ; flint.h is included by arf.h
 512     (inputs
 513      `(("gmp" ,gmp)
 514        ("mpfr" ,mpfr)))
 515     (arguments
 516      `(#:phases
 517        (modify-phases %standard-phases
 518          (replace 'configure
 519            (lambda* (#:key inputs outputs #:allow-other-keys)
 520              (let ((out (assoc-ref outputs "out"))
 521                    (flint (assoc-ref inputs "flint"))
 522                    (gmp (assoc-ref inputs "gmp"))
 523                    (mpfr (assoc-ref inputs "mpfr")))
 524                ;; Do not pass "--enable-fast-install", which makes the
 525                ;; homebrew configure process fail.
 526                (invoke "./configure"
 527                        (string-append "--prefix=" out)
 528                        (string-append "--with-flint=" flint)
 529                        (string-append "--with-gmp=" gmp)
 530                        (string-append "--with-mpfr=" mpfr))))))))
 531     (synopsis "Arbitrary precision floating-point ball arithmetic")
 532     (description
 533      "Arb is a C library for arbitrary-precision floating-point ball
 534 arithmetic.  It supports efficient high-precision computation with
 535 polynomials, power series, matrices and special functions over the
 536 real and complex numbers, with automatic, rigorous error control.")
 537     (license license:lgpl2.1+)
 538     (home-page "http://arblib.org")))
 539
 540 (define-public python-flint
 541   (package
 542     (name "python-flint")
 543     (version "0.3.0")
 544     (source (origin
 545               (method git-fetch)
 546               (uri (git-reference
 547                     (url "https://github.com/fredrik-johansson/python-flint")
 548                     (commit version)))
 549               (file-name (git-file-name name version))
 550               (sha256
 551                (base32
 552                 "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
 553               (patches (search-patches "python-flint-includes.patch"))))
 554     (build-system python-build-system)
 555     (native-inputs
 556      `(("python-cython" ,python-cython)))
 557     (propagated-inputs
 558      `(("python-numpy" ,python-numpy)))
 559     (inputs
 560      `(("arb" ,arb)
 561        ("flint" ,flint)))
 562     (synopsis "Python module wrapping ARB and FLINT")
 563     (description
 564      "Python-flint is a Python extension module wrapping FLINT
 565 (Fast Library for Number Theory) and Arb (arbitrary-precision ball
 566 arithmetic).  It supports integers, rationals, modular integers,
 567 real and complex ball arithmetic, polynomials and matrices over all
 568 these types and other mathematical functions.")
 569     (license license:expat)
 570     (home-page "http://fredrikj.net/python-flint/")))
 571
 572 (define-public ntl
 573   (package
 574    (name "ntl")
 575    (version "11.4.3")
 576    (source (origin
 577             (method url-fetch)
 578             (uri (string-append "https://shoup.net/ntl/ntl-"
 579                                 version ".tar.gz"))
 580             (sha256
 581              (base32
 582               "1lisp3064rch3jaa2wrhy1s9kll7i3ka3d0y6lj6l3l4ckfcrhdp"))
 583             (modules '((guix build utils)))
 584             (snippet
 585              '(begin
 586                 (delete-file-recursively "src/libtool-origin")
 587                 #t))))
 588    (build-system gnu-build-system)
 589    (native-inputs
 590     `(("libtool" ,libtool)
 591       ("perl" ,perl))) ; for configuration
 592    (inputs
 593     `(("gmp" ,gmp)
 594       ("gf2x" ,gf2x)))
 595    (arguments
 596     `(#:phases
 597       (modify-phases %standard-phases
 598         (replace 'configure
 599          (lambda* (#:key inputs outputs #:allow-other-keys)
 600            (chdir "src")
 601            (invoke "./configure"
 602                     (string-append "PREFIX=" (assoc-ref outputs "out"))
 603                     (string-append "LIBTOOL=" (assoc-ref inputs "libtool") "/bin/libtool")
 604                     ;; set the library prefixes explicitly so that they get
 605                     ;; embedded in the .la file
 606                     (string-append "GMP_PREFIX=" (assoc-ref inputs "gmp"))
 607                     (string-append "GF2X_PREFIX=" (assoc-ref inputs "gf2x"))
 608                     ;; Do not build especially for the build machine.
 609                     "NATIVE=off"
 610                     "NTL_GF2X_LIB=on"
 611                     "SHARED=on"))))))
 612    (synopsis "C++ library for number theory")
 613    (description
 614     "NTL is a C++ library providing data structures and algorithms
 615 for manipulating signed, arbitrary length integers, and for vectors,
 616 matrices, and polynomials over the integers and over finite fields.")
 617    (license license:gpl2+)
 618    (home-page "https://shoup.net/ntl/")))
 619
 620 (define-public singular
 621   (package
 622    (name "singular")
 623    (version "4.1.3p2")
 624    (source
 625     (origin
 626       (method url-fetch)
 627       (uri
 628        (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
 629                       "Singular/SOURCES/"
 630                       (string-join
 631                        (string-split
 632                         (string-trim-right version #\p
 633                                            0 (1- (string-length version)))
 634                         #\.) "-")
 635                       "/singular-" version ".tar.gz"))
 636              (sha256 (base32
 637                       "1524yrni7gh0hir5ckridq671q5s6avfjdsdyahj51kzdl3wcypf"))))
 638    (build-system gnu-build-system)
 639    (native-inputs
 640     `(("doxygen" ,doxygen)
 641       ("graphviz" ,graphviz)
 642       ("perl" ,perl)))
 643    (inputs
 644     `(("cddlib" ,cddlib)
 645       ("gmp" ,gmp)
 646       ("flint" ,flint)
 647       ("mpfr" ,mpfr)
 648       ("ntl" ,ntl)
 649       ("python" ,python-2)
 650       ("readline" ,readline)))
 651    (arguments
 652     `(#:configure-flags
 653       (list (string-append "--with-ntl="
 654                            (assoc-ref %build-inputs "ntl")))))
 655    (synopsis "Computer algebra system for polynomial computations")
 656    (description
 657     "Singular is a computer algebra system for polynomial computations,
 658 with special emphasis on commutative and non-commutative algebra, algebraic
 659 geometry and singularity theory.")
 660    ;; Singular itself is dual licensed gpl2 or gpl3, but some of the
 661    ;; libraries with which it links are licensed under lgpl3+, so the
 662    ;; combined work becomes gpl3. See COPYING in the source code.
 663    (license license:gpl3)
 664    (home-page "http://www.singular.uni-kl.de/index.php")))
 665
 666 (define-public gmp-ecm
 667   (package
 668    (name "gmp-ecm")
 669    (version "7.0.4")
 670    (source (origin
 671              (method url-fetch)
 672              ;; Use the ‘Latest version’ link for a stable URI across releases.
 673              (uri (string-append "https://gforge.inria.fr/frs/download.php/"
 674                                  "latestfile/160/ecm-" version ".tar.gz"))
 675              (sha256 (base32
 676                       "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"))))
 677    (build-system gnu-build-system)
 678    (inputs
 679     `(("gmp" ,gmp)))
 680    (arguments
 681     `(#:configure-flags '("--enable-shared"
 682                           ;; Disable specific assembly routines, which depend
 683                           ;; on the subarchitecture of the build machine,
 684                           ;; and use gmp instead.
 685                           "--disable-asm-redc")))
 686    (synopsis "Integer factorization library using the elliptic curve method")
 687    (description
 688     "GMP-ECM factors integers using the elliptic curve method (ECM) as well
 689 as the P-1 and P+1 algorithms.  It provides a library and a stand-alone
 690 binary.")
 691    ;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+,
 692    ;; so the combined work is under gpl3+.
 693    (license license:gpl3+)
 694    (home-page "http://ecm.gforge.inria.fr/")))
 695
 696 (define-public bc
 697   (package
 698     (name "bc")
 699     (version "1.07.1")
 700     (source (origin
 701              (method url-fetch)
 702              (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
 703              (sha256
 704               (base32
 705                "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))
 706              (patches (search-patches "bc-fix-cross-compilation.patch"))))
 707     (build-system gnu-build-system)
 708     (native-inputs
 709      `(("automake" ,automake)
 710        ("autoconf" ,autoconf)
 711        ("ed" ,ed)
 712        ("flex" ,flex)
 713        ("texinfo" ,texinfo)))
 714     (arguments
 715      '(#:configure-flags
 716        (list "--with-readline")
 717        #:phases
 718        (modify-phases %standard-phases
 719          (add-after 'unpack 'autogen
 720            (lambda _
 721              (invoke "autoreconf" "-vif"))))))
 722     (home-page "https://www.gnu.org/software/bc/")
 723     (synopsis "Arbitrary precision numeric processing language")
 724     (description
 725      "bc is an arbitrary precision numeric processing language.  It includes
 726 an interactive environment for evaluating mathematical statements.  Its
 727 syntax is similar to that of C, so basic usage is familiar.  It also includes
 728 \"dc\", a reverse-polish calculator.")
 729     (license license:gpl2+)))
 730
 731 ;; The original kiss-fft does not have a complete build system and does not
 732 ;; build any shared libraries.  This is a fork used by Extempore.
 733 (define-public kiss-fft-for-extempore
 734   (package
 735     (name "kiss-fft-for-extempore")
 736     (version "1.3.0")
 737     (source (origin
 738               (method git-fetch)
 739               (uri (git-reference
 740                     (url "https://github.com/extemporelang/kiss_fft")
 741                     (commit version)))
 742               (file-name (git-file-name name version))
 743               (sha256
 744                (base32
 745                 "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
 746     (build-system cmake-build-system)
 747     (arguments `(#:tests? #f)) ; no tests included
 748     ;; Extempore refuses to build on architectures other than x86_64
 749     (supported-systems '("x86_64-linux"))
 750     (home-page "https://github.com/extemporelang/kiss_fft")
 751     (synopsis "Mixed-radix Fast Fourier Transform")
 752     (description
 753      "Kiss FFT attempts to be a reasonably efficient, moderately useful FFT
 754 that can use fixed or floating data types and can easily be incorporated into
 755 a C program.")
 756     (license license:bsd-3)))
 757
 758 (define-public fftw
 759   (package
 760     (name "fftw")
 761     (version "3.3.8")
 762     (source (origin
 763              (method url-fetch)
 764              (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
 765                                  version".tar.gz"))
 766              (sha256
 767               (base32
 768                "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
 769     (build-system gnu-build-system)
 770     (arguments
 771      `(#:configure-flags
 772        '("--enable-shared" "--enable-openmp" "--enable-threads"
 773          ,@(let ((system (or (%current-target-system) (%current-system))))
 774              ;; Enable SIMD extensions for codelets.  See details at:
 775              ;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>.
 776              (cond
 777               ((string-prefix? "x86_64" system)
 778                '("--enable-sse2" "--enable-avx" "--enable-avx2"
 779                  "--enable-avx512" "--enable-avx-128-fma"))
 780               ((string-prefix? "i686" system)
 781                '("--enable-sse2"))
 782               ((string-prefix? "aarch64" system)
 783                ;; Note that fftw supports NEON on 32-bit ARM only when
 784                ;; compiled for single-precision.
 785                '("--enable-neon"))
 786               (else
 787                '())))
 788          ;; By default '-mtune=native' is used.  However, that may cause the
 789          ;; use of ISA extensions (e.g. AVX) that are not necessarily
 790          ;; available on the user's machine when that package is built on a
 791          ;; different machine.
 792          "ax_cv_c_flags__mtune_native=no")))
 793     (native-inputs `(("perl" ,perl)))
 794     (home-page "http://fftw.org")
 795     (synopsis "Computing the discrete Fourier transform")
 796     (description
 797      "FFTW is a C subroutine library for computing the discrete Fourier
 798 transform (DFT) in one or more dimensions, of arbitrary input size, and of
 799 both real and complex data (as well as of even/odd data---i.e. the discrete
 800 cosine/ sine transforms or DCT/DST).")
 801     (license license:gpl2+)))
 802
 803 (define-public fftwf
 804   (package (inherit fftw)
 805     (name "fftwf")
 806     (arguments
 807      (substitute-keyword-arguments (package-arguments fftw)
 808        ((#:configure-flags fftw-configure-flags)
 809         `(cons* "--enable-single"
 810                 ,@(if (string-prefix? "arm" (or (%current-target-system)
 811                                                 (%current-system)))
 812                       ;; fftw supports NEON on 32-bit ARM only when compiled
 813                       ;; for single-precision, so add it here.
 814                       '("--enable-neon")
 815                       '())
 816                 ,fftw-configure-flags))))
 817     (description
 818      (string-append (package-description fftw)
 819                     "  Single-precision version."))))
 820
 821 (define-public fftw-openmpi
 822   (package (inherit fftw)
 823     (name "fftw-openmpi")
 824     (inputs
 825      `(("openmpi" ,openmpi)
 826        ,@(package-inputs fftw)))
 827     (arguments
 828      (substitute-keyword-arguments (package-arguments fftw)
 829        ((#:configure-flags cf)
 830         `(cons "--enable-mpi" ,cf))
 831        ((#:phases phases '%standard-phases)
 832         `(modify-phases ,phases
 833            (add-before 'check 'mpi-setup
 834              ,%openmpi-setup)))))
 835     (description
 836      (string-append (package-description fftw)
 837                     "  With OpenMPI parallelism support."))))
 838
 839 (define-public java-la4j
 840   (package
 841     (name "java-la4j")
 842     (version "0.6.0")
 843     (source (origin
 844               (method git-fetch)
 845               (uri (git-reference
 846                     (url "https://github.com/vkostyukov/la4j")
 847                     (commit version)))
 848               (file-name (string-append name "-" version "-checkout"))
 849               (sha256
 850                (base32
 851                 "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
 852     (build-system ant-build-system)
 853     (arguments
 854      `(#:jar-name "la4j.jar"
 855        #:jdk ,icedtea-8
 856        #:test-exclude (list "**/Abstract*.java"
 857                             "**/MatrixTest.java"
 858                             "**/DenseMatrixTest.java"
 859                             "**/SparseMatrixTest.java"
 860                             "**/VectorTest.java"
 861                             "**/SparseVectorTest.java"
 862                             "**/DenseVectorTest.java")))
 863     (native-inputs
 864      `(("java-junit" ,java-junit)
 865        ("java-hamcrest-core" ,java-hamcrest-core)))
 866     (home-page "http://la4j.org/")
 867     (synopsis "Java library that provides Linear Algebra primitives and algorithms")
 868     (description "The la4j library is a Java library that provides Linear
 869 Algebra primitives (matrices and vectors) and algorithms.  The key features of
 870 the la4j library are:
 871
 872 @itemize
 873 @item No dependencies and tiny size
 874 @item Fluent object-oriented/functional API
 875 @item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
 876 @item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
 877 @item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
 878 @item MatrixMarket/CSV IO formats support for matrices and vectors
 879 @end itemize\n")
 880     (license license:asl2.0)))
 881
 882 (define-public java-jlargearrays
 883   (package
 884     (name "java-jlargearrays")
 885     (version "1.6")
 886     (source (origin
 887               (method url-fetch)
 888               (uri (string-append "https://repo1.maven.org/maven2/"
 889                                   "pl/edu/icm/JLargeArrays/"
 890                                   version "/JLargeArrays-" version
 891                                   "-sources.jar"))
 892               (file-name (string-append name "-" version ".jar"))
 893               (sha256
 894                (base32
 895                 "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
 896     (build-system ant-build-system)
 897     (arguments
 898      `(#:jar-name "jlargearrays.jar"
 899        #:tests? #f ; tests are not included in the release archive
 900        #:jdk ,icedtea-8))
 901     (propagated-inputs
 902      `(("java-commons-math3" ,java-commons-math3)))
 903     (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
 904     (synopsis "Library of one-dimensional arrays that can store up to 263 elements")
 905     (description "JLargeArrays is a Java library of one-dimensional arrays
 906 that can store up to 263 elements.")
 907     (license license:bsd-2)))
 908
 909 (define-public java-jtransforms
 910   (package
 911     (name "java-jtransforms")
 912     (version "3.1")
 913     (source (origin
 914               (method url-fetch)
 915               (uri (string-append "https://repo1.maven.org/maven2/"
 916                                   "com/github/wendykierp/JTransforms/"
 917                                   version "/JTransforms-" version "-sources.jar"))
 918               (sha256
 919                (base32
 920                 "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
 921     (build-system ant-build-system)
 922     (arguments
 923      `(#:jar-name "jtransforms.jar"
 924        #:tests? #f ; tests are not included in the release archive
 925        #:jdk ,icedtea-8))
 926     (propagated-inputs
 927      `(("java-commons-math3" ,java-commons-math3)
 928        ("java-jlargearrays" ,java-jlargearrays)))
 929     (home-page "https://github.com/wendykierp/JTransforms")
 930     (synopsis "Multithreaded FFT library written in pure Java")
 931     (description "JTransforms is a multithreaded FFT library written in pure
 932 Java.  Currently, four types of transforms are available: @dfn{Discrete
 933 Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
 934 Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
 935     (license license:bsd-2)))
 936
 937 (define-public lmfit
 938   (package
 939     (name "lmfit")
 940     (version "8.2.2")
 941     (source (origin
 942               (method git-fetch)
 943               (uri (git-reference
 944                     (url "https://jugit.fz-juelich.de/mlz/lmfit.git")
 945                     (commit (string-append "v" version))))
 946               (file-name (git-file-name name version))
 947               (sha256
 948                (base32
 949                 "00bch77a6qgnw6vzsjn2a42n8n683ih3xm0wpr454jxa15hw78vf"))))
 950     (build-system cmake-build-system)
 951     (native-inputs
 952      `(("perl" ,perl)))                   ; for pod2man
 953     (home-page "https://jugit.fz-juelich.de/mlz/lmfit")
 954     (synopsis "Levenberg-Marquardt minimization and least-squares fitting")
 955     (description "lmfit is a C library for Levenberg-Marquardt least-squares
 956 minimization and curve fitting.  It is mature code, based on decades-old
 957 algorithms from the FORTRAN library MINPACK.")
 958     (license license:bsd-2)))
 959
 960 (define-public symengine
 961   (package
 962     (name "symengine")
 963     (version "0.6.0")
 964     (source
 965      (origin
 966        (method git-fetch)
 967        (uri (git-reference
 968              (url "https://github.com/symengine/symengine")
 969              (commit (string-append "v" version))))
 970        (file-name (git-file-name name version))
 971        (sha256
 972         (base32 "129iv9maabmb42ylfdv0l0g94mcbf3y4q3np175008rcqdr8z6h1"))))
 973     (build-system cmake-build-system)
 974     (arguments
 975      '(#:configure-flags
 976        ;; These are the suggested build options in the README.
 977        '("-DCMAKE_BUILD_TYPE=Release"
 978          "-DWITH_GMP=on"
 979          "-DWITH_MPFR=on"
 980          "-DWITH_MPC=on"
 981          "-DINTEGER_CLASS=flint"
 982          "-DWITH_LLVM=on"
 983          "-DWITH_SYMENGINE_THREAD_SAFE=on"
 984          "-DBUILD_SHARED_LIBS=on")))    ;also build libsymengine
 985     (native-inputs
 986      `(("llvm" ,llvm)))
 987     (inputs
 988      `(("flint" ,flint)
 989        ("gmp" ,gmp)
 990        ("mpc" ,mpc)
 991        ("mpfr" ,mpfr)))
 992     (home-page "https://github.com/symengine/symengine")
 993     (synopsis "Fast symbolic manipulation library")
 994     (description
 995      "SymEngine is a standalone fast C++ symbolic manipulation library.
 996 Optional thin wrappers allow usage of the library from other languages.")
 997     (license (list license:expat        ;SymEngine
 998                    license:bsd-3))))    ;3rd party code
 999
1000 (define-public eigen
1001   (package
1002     (name "eigen")
1003     (version "3.3.7")
1004     (source (origin
1005               (method url-fetch)
1006               (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
1007                                   version ".tar.bz2"))
1008               (sha256
1009                (base32
1010                 "1km3fyfzyqfdvmnl79drps3fjwnz3zbh0c7l34mfbqyvvs8cy4wz"))
1011               (file-name (string-append name "-" version ".tar.bz2"))
1012               (patches (search-patches "eigen-stabilise-sparseqr-test.patch"))
1013               (modules '((guix build utils)))
1014               (snippet
1015                ;; There are 3 test failures in the "unsupported" directory,
1016                ;; but maintainers say it's a known issue and it's unsupported
1017                ;; anyway, so just skip them.
1018                '(begin
1019                   (substitute* "unsupported/CMakeLists.txt"
1020                     (("add_subdirectory\\(test.*")
1021                      "# Do not build the tests for unsupported features.\n"))
1022                   #t))))
1023     (build-system cmake-build-system)
1024     (arguments
1025      '(;; Turn off debugging symbols to save space.
1026        #:build-type "Release"
1027
1028        #:phases (modify-phases %standard-phases
1029                   (replace 'check
1030                     (lambda _
1031                       (let* ((cores  (parallel-job-count))
1032                              (dash-j (format #f "-j~a" cores)))
1033                         (setenv "EIGEN_SEED" "1") ;for reproducibility
1034                         ;; First build the tests, in parallel.  See
1035                         ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
1036                         (invoke "make" "buildtests" dash-j)
1037
1038                         ;; Then run 'CTest' with -V so we get more
1039                         ;; details upon failure.
1040                         (invoke "ctest" "-V" dash-j)))))))
1041     (home-page "https://eigen.tuxfamily.org")
1042     (synopsis "C++ template library for linear algebra")
1043     (description
1044      "Eigen is a C++ template library for linear algebra: matrices, vectors,
1045 numerical solvers, and related algorithms.  It provides an elegant API based
1046 on \"expression templates\".  It is versatile: it supports all matrix sizes,
1047 all standard numeric types, various matrix decompositions and geometry
1048 features, and more.")
1049
1050     ;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3.
1051     ;; See 'COPYING.README' for details.
1052     (license license:mpl2.0)))
1053
1054 (define-public eigen-for-tensorflow
1055   (let ((changeset "fd6845384b86")
1056         (revision "1"))
1057     (package (inherit eigen)
1058       (name "eigen-for-tensorflow")
1059       (version (string-append "3.3.5-" revision "." changeset))
1060       (source (origin
1061                 (method hg-fetch)
1062                 (uri (hg-reference
1063                       (url "https://bitbucket.org/eigen/eigen")
1064                       (changeset changeset)))
1065                 (sha256
1066                  (base32
1067                   "12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5"))
1068                 (file-name (string-append name "-" version "-checkout"))
1069                 (modules '((guix build utils)))
1070                 (snippet
1071                  ;; There are 3 test failures in the "unsupported" directory,
1072                  ;; but maintainers say it's a known issue and it's unsupported
1073                  ;; anyway, so just skip them.
1074                  '(begin
1075                     (substitute* "unsupported/CMakeLists.txt"
1076                       (("add_subdirectory\\(test.*")
1077                        "# Do not build the tests for unsupported features.\n"))
1078                     #t)))))))
1079
1080 (define-public xtensor
1081   (package
1082     (name "xtensor")
1083     (version "0.20.10")
1084     (source (origin
1085               (method git-fetch)
1086               (uri (git-reference
1087                     (url "https://github.com/QuantStack/xtensor")
1088                     (commit version)))
1089               (sha256
1090                (base32
1091                 "1fmv2hpx610xwhxrndfsfvlbqfyk4l3gi5q5d7pa9m82kblxjj9l"))
1092               (file-name (git-file-name name version))))
1093     (build-system cmake-build-system)
1094     (native-inputs
1095      `(("googletest" ,googletest)
1096        ("xtl" ,xtl)))
1097     (arguments
1098      `(#:configure-flags
1099        '("-DBUILD_TESTS=ON")
1100        #:test-target "xtest"))
1101     (home-page "https://quantstack.net/xtensor")
1102     (synopsis "C++ tensors with broadcasting and lazy computing")
1103     (description "xtensor is a C++ library meant for numerical analysis with
1104 multi-dimensional array expressions.
1105
1106 xtensor provides:
1107 @itemize
1108 @item an extensible expression system enabling lazy broadcasting.
1109 @item an API following the idioms of the C++ standard library.
1110 @item tools to manipulate array expressions and build upon xtensor.
1111 @end itemize")
1112     (license license:bsd-3)))
1113
1114 (define-public gap
1115   (package
1116     (name "gap")
1117     (version "4.10.2")
1118     (source
1119      (origin
1120        (method url-fetch)
1121        (uri (string-append "https://www.gap-system.org/pub/gap/gap-"
1122                            (version-major+minor version)
1123                            "/tar.bz2/gap-"
1124                            version
1125                            ".tar.bz2"))
1126        (sha256
1127         (base32 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
1128        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
1129        (snippet
1130         '(begin
1131            ;; Delete the external gmp and zlib libraries
1132            ;; and a subdirectory not needed for our build.
1133            (for-each delete-file-recursively
1134                      '("extern" "hpcgap"))
1135            ;; Delete a failing test.
1136            ;; FIXME: This might be fixed in the next release, see
1137            ;; https://github.com/gap-system/gap/issues/3292
1138            (delete-file "tst/testinstall/dir.tst")
1139            ;; Delete all packages except for a fixed list.
1140            (with-directory-excursion "pkg"
1141              (for-each delete-file-recursively
1142                (lset-difference string=? (scandir ".")
1143                  '("." ".."
1144                    ;; Necessary packages.
1145                    "GAPDoc-1.6.2"
1146                    "primgrp-3.3.2"
1147                    "SmallGrp-1.3"    ; artistic2.0
1148                    "transgrp"        ; artistic2.0 for data,
1149                                      ; gpl2 or gpl3 for code
1150                    ;; Recommanded package.
1151                    "io-4.5.4"        ; gpl3+
1152                    ;; Optional packages, searched for at start,
1153                    ;; and their depedencies.
1154                    "alnuth-3.1.0"
1155                    "autpgrp-1.10"
1156                    "crisp-1.4.4"     ; bsd-2
1157                    "ctbllib"       ; gpl3+ according to doc/chap0.txt
1158                    "FactInt-1.6.2"
1159                    "fga"
1160                    "irredsol-1.4"    ; bsd-2
1161                    "laguna-3.9.2"
1162                    "polenta-1.3.8"
1163                    "polycyclic-2.14"
1164                    "radiroot-2.8"
1165                    "resclasses-4.7.1"
1166                    "sophus-1.24"
1167                    "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
1168                                    ; and the next release
1169                    "utils-0.59"))))
1170            #t))))
1171     (build-system gnu-build-system)
1172     (inputs
1173      `(("gmp" ,gmp)
1174        ("zlib" ,zlib)))
1175     (arguments
1176      `(#:modules ((ice-9 ftw)
1177                   (srfi srfi-26)
1178                   (guix build gnu-build-system)
1179                   (guix build utils))
1180        #:phases
1181        (modify-phases %standard-phases
1182          (add-after 'build 'build-packages
1183            ;; Compile all packages that have not been deleted by the
1184            ;; code snippet above.
1185            (lambda _
1186              (setenv "CONFIG_SHELL" (which "bash"))
1187              (with-directory-excursion "pkg"
1188                (invoke "../bin/BuildPackages.sh")
1189              #t)))
1190          (add-after 'build-packages 'build-doc
1191            ;; The documentation is bundled, but we create it from source.
1192            (lambda _
1193              (with-directory-excursion "doc"
1194                (invoke "./make_doc"))
1195              #t))
1196          (replace 'install
1197            (lambda* (#:key outputs #:allow-other-keys)
1198              (let* ((out (assoc-ref outputs "out"))
1199                     (bin (string-append out "/bin"))
1200                     (lib (string-append out "/lib"))
1201                     (prog (string-append bin "/gap"))
1202                     (prog-real (string-append bin "/.gap-real"))
1203                     (share (string-append out "/share/gap"))
1204                     (include (string-append out "/include/gap"))
1205                     (include-hpc (string-append include "/hpc")))
1206                ;; Install only the gap binary; the gac compiler is left
1207                ;; for maybe later. "Wrap" it in a shell script that calls
1208                ;; the binary with the correct parameter.
1209                (mkdir-p bin)
1210                (copy-file "gap" prog-real)
1211                (call-with-output-file prog
1212                  (lambda (port)
1213                    (format port
1214                            "#!~a~%exec ~a -l ~a \"$@\"~%"
1215                            (which "bash")
1216                            prog-real
1217                            share)))
1218                (chmod prog #o755)
1219                ;; Install the headers, which are needed by Sage. The
1220                ;; Makefile target "install-headers" was available in
1221                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1222                (mkdir-p include-hpc)
1223                (install-file "gen/config.h" include)
1224                (let ((file-name-predicate-without-stat
1225                        (lambda (regex)
1226                          (cut (file-name-predicate regex) <> #f))))
1227                  (with-directory-excursion "src"
1228                    (for-each
1229                      (cut install-file <> include)
1230                      (scandir "."
1231                               (file-name-predicate-without-stat ".*\\.h$"))))
1232                  (with-directory-excursion "src/hpc"
1233                    (for-each
1234                      (cut install-file <> include-hpc)
1235                      (scandir "."
1236                               (file-name-predicate-without-stat ".*\\.h$")))))
1237                ;; Install the library, which is needed by Sage. The
1238                ;; Makefile target "install-libgap" was available in
1239                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1240                ;; Compared to the Makefile, which used libtool, the
1241                ;; following approach of copying files and making symlinks
1242                ;; is rather pedestrian. There is hope that some later
1243                ;; version of gap reinstates and completes the install
1244                ;; targets.
1245                (invoke "make" "libgap.la")
1246                (install-file "libgap.la" lib)
1247                (install-file ".libs/libgap.so.0.0.0" lib)
1248                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so"))
1249                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
1250                ;; Install a certain number of files and directories to
1251                ;; SHARE, where the wrapped shell script expects them.
1252                ;; Remove information on the build directory from sysinfo.gap.
1253                (substitute* "sysinfo.gap"
1254                  (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
1255                  (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
1256                  (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
1257                (install-file "sysinfo.gap" share)
1258                (copy-recursively "grp" (string-append share "/grp"))
1259                (copy-recursively "pkg" (string-append share "/pkg"))
1260                ;; The following is not the C library libgap.so, but a
1261                ;; library of GAP code.
1262                (copy-recursively "lib" (string-append share "/lib"))
1263                ;; The gap binary looks for documentation inside SHARE.
1264                (copy-recursively "doc" (string-append share "/doc")))
1265              #t)))))
1266     (home-page "https://www.gap-system.org/")
1267     (synopsis
1268      "System for computational group theory")
1269     (description
1270      "GAP is a system for computational discrete algebra, with particular
1271 emphasis on computational group theory.  It provides a programming language,
1272 a library of thousands of functions implementing algebraic algorithms
1273 written in the GAP language as well as large data libraries of algebraic
1274 objects.")
1275     ;; Some packages have different licenses (effectively forcing the
1276     ;; combined work to be licensed as gpl3+); if this is the case, this
1277     ;; is mentioned above next to their name.
1278     ;; Some packages have no license mentioned explicitly; supposedly this
1279     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
1280     ;; safe side, we drop them for now.
1281     (license license:gpl2+)))
1282
1283 (define-public givaro
1284   (package
1285     (name "givaro")
1286     (version "4.1.1")
1287     (source (origin
1288               (method git-fetch)
1289               (uri (git-reference
1290                     (url "https://github.com/linbox-team/givaro")
1291                     (commit (string-append "v" version))))
1292               (file-name (git-file-name name version))
1293               (sha256
1294                (base32
1295                 "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
1296     (build-system gnu-build-system)
1297     (native-inputs
1298      `(("autoconf" ,autoconf)
1299        ("automake" ,automake)
1300        ("libtool" ,libtool)))
1301     (propagated-inputs
1302      `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
1303     (synopsis "Algebraic computations with exact rings and fields")
1304     (description
1305      "Givaro is a C++ library implementing the basic arithmetic of various
1306 algebraic objects: prime fields, extension fields, finite fields, finite
1307 rings, polynomials, algebraic numbers, arbitrary precision integers and
1308 rationals (C++ wrappers over gmp), fixed precision integers.  It also
1309 provides data-structures and templated classes for the manipulation of
1310 compound objects, such as vectors, matrices and univariate polynomials.")
1311     (license license:cecill-b)
1312     (home-page "https://github.com/linbox-team/givaro")))
1313
1314 (define-public fflas-ffpack
1315   (package
1316     (name "fflas-ffpack")
1317     (version "2.4.3")
1318     (source (origin
1319               (method git-fetch)
1320               (uri (git-reference
1321                     (url "https://github.com/linbox-team/fflas-ffpack")
1322                     (commit version)))
1323               (file-name (git-file-name name version))
1324               (sha256
1325                (base32
1326                 "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
1327     (build-system gnu-build-system)
1328     (native-inputs
1329      `(("autoconf" ,autoconf)
1330        ("automake" ,automake)
1331        ("libtool" ,libtool)
1332        ("pkg-config" ,pkg-config)))
1333     (inputs
1334      `(("openblas" ,openblas)))
1335     (propagated-inputs
1336      `(("givaro" ,givaro))) ; required according to the .pc file
1337     (arguments
1338      `(#:configure-flags
1339        (list (string-append "--with-blas-libs="
1340                             (assoc-ref %build-inputs "openblas")
1341                             "/lib/libopenblas.so"))))
1342     (synopsis "C++ library for linear algebra over finite fields")
1343     (description
1344      "FFLAS-FFPACK is a C++ template library for basic linear algebra
1345 operations over a finite field.
1346 FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
1347 of a subset of routines of the numerical BLAS; it also supports sparse
1348 matrix-vector products.
1349 FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
1350 library to provide functionalities of higher level, using the kernel
1351 of a BLAS.  Additionally, it provides routines specific to exact linear
1352 algebra, such as the row echelon form.")
1353     (license license:lgpl2.1+)
1354     (home-page "https://linbox-team.github.io/fflas-ffpack/")))
1355
1356 (define-public linbox
1357   (package
1358     (name "linbox")
1359     (version "1.6.3")
1360     (source (origin
1361               (method git-fetch)
1362               (uri (git-reference
1363                     (url "https://github.com/linbox-team/linbox")
1364                     (commit (string-append "v" version))))
1365               (file-name (git-file-name name version))
1366               (sha256
1367                (base32
1368                 "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))
1369               (patches (search-patches "linbox-fix-pkgconfig.patch"))))
1370     (build-system gnu-build-system)
1371     (native-inputs
1372      `(("autoconf" ,autoconf)
1373        ("automake" ,automake)
1374        ("libtool" ,libtool)
1375        ("pkg-config" ,pkg-config)))
1376     (propagated-inputs
1377      `(("fflas-ffpack" ,fflas-ffpack)))
1378     (synopsis "C++ library for linear algebra over exact rings")
1379     (description
1380      "LinBox is a C++ template library for exact linear algebra computation
1381 with dense, sparse, and structured matrices over the integers and over
1382 finite fields.")
1383     (license license:lgpl2.1+)
1384     (home-page "https://linbox-team.github.io/linbox/")))
1385
1386 (define-public m4ri
1387   (package
1388     (name "m4ri")
1389     (version "20140914")
1390     (source (origin
1391               (method git-fetch)
1392               (uri (git-reference
1393                     (url "https://bitbucket.org/malb/m4ri")
1394                     (commit (string-append "release-" version))))
1395               (file-name (git-file-name name version))
1396               (sha256
1397                (base32
1398                 "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
1399     (build-system gnu-build-system)
1400     (native-inputs
1401      `(("autoconf" ,autoconf)
1402        ("automake" ,automake)
1403        ("libtool" ,libtool)
1404        ("pkg-config" ,pkg-config)))
1405     (inputs
1406      `(("libpng" ,libpng)))
1407     (synopsis "Arithmetic of dense matrices over F_2")
1408     (description "M4RI is a library for fast arithmetic with dense matrices
1409 over F2.  The name M4RI comes from the first implemented algorithm: The
1410 Method of the Four Russians inversion algorithm published by Gregory Bard.
1411 This algorithm in turn is named after the Method of the Four Russians
1412 multiplication algorithm.")
1413     (license license:gpl2+)
1414     (home-page "https://bitbucket.org/malb/m4ri/")))
1415
1416 (define-public symmetrica
1417   (package
1418     (name "symmetrica")
1419     (version "2.0")
1420     (source (origin
1421               (method url-fetch/tarbomb)
1422               (uri (let ((v (string-join (string-split version #\.) "_")))
1423                      (string-append "http://www.algorithm.uni-bayreuth.de/"
1424                                     "en/research/SYMMETRICA/"
1425                                     "SYM" v "_tar.gz")))
1426               (sha256
1427                (base32
1428                 "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
1429               ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
1430               (patches (search-patches "symmetrica-bruch.patch"
1431                                        "symmetrica-int32.patch"
1432                                        "symmetrica-return_values.patch"
1433                                        "symmetrica-sort_sum_rename.patch"))))
1434     (build-system gnu-build-system)
1435     (arguments
1436      `(#:tests? #f                      ;no test
1437        #:phases
1438        (modify-phases %standard-phases
1439          (add-after 'unpack 'fix-makefile
1440            (lambda _
1441              (substitute* "makefile"
1442                (("cc -c") "gcc -c -fPIC"))
1443              #t))
1444          (add-after 'fix-makefile 'turn-off-banner
1445            (lambda _
1446              (substitute* "de.c"
1447                (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
1448              #t))
1449          (delete 'configure)            ;no configure script
1450          (replace 'install              ;no install target
1451            (lambda* (#:key outputs #:allow-other-keys)
1452              (let* ((out (assoc-ref outputs "out"))
1453                     (lib (string-append out "/lib"))
1454                     (inc (string-append out "/include/symmetrica"))
1455                     (doc (string-append out "/share/doc/symmetrica-" ,version))
1456                     (static "libsymmetrica.a"))
1457                ;; Build static library.
1458                (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
1459                (invoke "ranlib" static)
1460                ;; Install static library and headers.
1461                (for-each (lambda (f) (install-file f inc))
1462                          (find-files "." "\\.h$"))
1463                (install-file "libsymmetrica.a" lib)
1464                ;; Install documentation.
1465                (for-each (lambda (f) (install-file f doc))
1466                          (find-files "." "\\.doc$"))
1467                #t))))))
1468     (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
1469     (synopsis "Combinatoric C Library")
1470     (description "Symmetrica is a library for combinatorics.  It has support
1471 for the representation theory of the symmetric group and related groups,
1472 combinatorics of tableaux, symmetric functions and polynomials, Schubert
1473 polynomials, and the representation theory of Hecke algebras of type A_n.")
1474     (license license:public-domain)))
1475
1476 (define-public m4rie
1477   (package
1478     (name "m4rie")
1479     (version "20150908")
1480     (source (origin
1481               (method git-fetch)
1482               (uri (git-reference
1483                     (url "https://bitbucket.org/malb/m4rie")
1484                     (commit (string-append "release-" version))))
1485               (file-name (git-file-name name version))
1486               (sha256
1487                (base32
1488                 "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
1489     (build-system gnu-build-system)
1490     (native-inputs
1491      `(("autoconf" ,autoconf)
1492        ("automake" ,automake)
1493        ("libtool" ,libtool)))
1494     (inputs
1495      `(("m4ri" ,m4ri)))
1496     (synopsis "Arithmetic of dense matrices over F_{2^e}")
1497     (description "M4RI is a library for fast arithmetic with dense matrices
1498 over finite fields of characteristic 2.  So it extends the functionality
1499 of M4RI from F_2 to F_{2^e}.")
1500     (license license:gpl2+)
1501     (home-page "https://bitbucket.org/malb/m4rie/")))
1502
1503 (define-public eclib
1504   (package
1505     (name "eclib")
1506     (version "20190909")
1507     (source (origin
1508               (method git-fetch)
1509               (uri (git-reference
1510                     (url "https://github.com/JohnCremona/eclib/")
1511                     (commit (string-append "v" version))))
1512               (file-name (git-file-name name version))
1513               (sha256
1514                (base32
1515                 "1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n"))))
1516     (build-system gnu-build-system)
1517     (native-inputs
1518      `(("autoconf" ,autoconf)
1519        ("automake" ,automake)
1520        ("libtool" ,libtool)))
1521     (inputs
1522      `(("ntl" ,ntl)
1523        ("pari-gp" ,pari-gp)))
1524     (synopsis "Ranks of elliptic curves and modular symbols")
1525     (description "The eclib package includes mwrank (for 2-descent on
1526 elliptic curves over Q) and modular symbol code; it has been written by
1527 John Cremona to compute his elliptic curve database.")
1528     (license license:gpl2+)
1529     (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
1530                               "J.E.Cremona/mwrank/index.html"))))
1531
1532 (define-public lrcalc
1533   (package
1534     (name "lrcalc")
1535     (version "1.2")
1536     (source (origin
1537               (method git-fetch)
1538               (uri (git-reference
1539                     (url "https://bitbucket.org/asbuch/lrcalc")
1540                     (commit (string-append "lrcalc-" version))))
1541               (file-name (git-file-name name version))
1542               (sha256
1543                (base32
1544                 "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
1545               (patches (search-patches "lrcalc-includes.patch"))))
1546     (build-system gnu-build-system)
1547     (native-inputs
1548      `(("autoconf" ,autoconf)
1549        ("automake" ,automake)
1550        ("libtool" ,libtool)))
1551     (arguments
1552      `(#:phases
1553        (modify-phases %standard-phases
1554          (add-before 'build 'fix-permission
1555            (lambda _
1556              (chmod "lrcalc.maple.src" #o644)
1557              #t)))))
1558     (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
1559     (description "The Littlewood-Richardson Calculator (lrcalc) is a
1560 program designed to compute Littlewood-Richardson coefficients.  It computes
1561 single Littlewood-Richardson coefficients, products of Schur functions, or
1562 skew Schur functions.  In addition it computes products in the small quantum
1563 cohomology ring of a Grassmann variety.  The software package also includes
1564 a program that performs fast computation of the more general multiplicative
1565 structure constants of Schubert polynomials.")
1566     (license license:gpl2+)
1567     (home-page "https://sites.math.rutgers.edu/~asbuch/lrcalc/")))
1568
1569 (define-public iml
1570   (package
1571     (name "iml")
1572     (version "1.0.5")
1573     (source
1574      (origin
1575        (method url-fetch)
1576        (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
1577                            version ".tar.bz2"))
1578        (sha256
1579         (base32
1580          "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
1581     (build-system gnu-build-system)
1582     (inputs
1583      `(("gmp", gmp)
1584        ("cblas" ,openblas))) ; or any other BLAS library; the documentation
1585                              ; mentions ATLAS in particular
1586     (arguments
1587      `(#:configure-flags
1588        (list
1589         "--enable-shared"
1590         (string-append "--with-gmp-include="
1591                        (assoc-ref %build-inputs "gmp") "/include")
1592         (string-append "--with-gmp-lib="
1593                        (assoc-ref %build-inputs "gmp") "/lib")
1594         "--with-cblas=-lopenblas"
1595         (string-append "--with-cblas-include="
1596                        (assoc-ref %build-inputs "cblas") "/include")
1597         (string-append "--with-cblas-lib="
1598                        (assoc-ref %build-inputs "cblas") "/lib"))))
1599     (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
1600     (synopsis
1601      "Solver for systems of linear equations over the integers")
1602     (description
1603      "IML is a C library implementing algorithms for computing exact
1604 solutions to dense systems of linear equations over the integers.
1605 Currently, IML provides the following functionality:
1606
1607 @itemize
1608 @item Nonsingular rational system solving:
1609 compute the unique rational solution X to the system AX=B, where A and B
1610 are integer matrices, A nonsingular.
1611 @item Compute the right nullspace or kernel of an integer matrix.
1612 @item Certified linear system solving:
1613 compute a minimal denominator solution x to a system Ax=b, where b is an
1614 integer vector and A is an integer matrix with arbitrary shape and
1615 rank profile.
1616 @end itemize
1617
1618 In addition, IML provides some low level routines for a variety of mod p
1619 matrix operations: computing the row-echelon form, determinant, rank
1620 profile, and inverse of a mod p matrix. These mod p routines are not
1621 general purpose; they require that p satisfy some preconditions based on
1622 the dimension of the input matrix (usually p should be prime and should be
1623 no more than about 20 bits long).")
1624     (license license:bsd-3)))