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        (sha256
 205         (base32
 206          "01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
 207     (build-system python-build-system)
 208     (inputs
 209      `(("fplll" ,fplll)
 210        ("gmp" ,gmp)
 211        ("mpfr" ,mpfr)
 212        ("pari-gp" ,pari-gp)))
 213     (propagated-inputs
 214      `(("cysignals" ,python-cysignals)
 215        ("cython" ,python-cython)
 216        ("flake8" ,python-flake8)
 217        ("numpy" ,python-numpy)
 218        ("pytest" ,python-pytest)))
 219     (home-page "https://github.com/fplll/fpylll")
 220     (synopsis "Python interface for fplll")
 221     (description "fpylll is a Python wrapper for fplll.")
 222     (license license:gpl2+)))
 223
 224 (define-public pari-gp
 225   (package
 226     (name "pari-gp")
 227     (version "2.11.2")
 228     (source (origin
 229               (method url-fetch)
 230               (uri (string-append
 231                     "https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
 232                     version ".tar.gz"))
 233               (sha256
 234                (base32
 235                 "0fck8ssmirl8fy7s4mspgrxjs5sag76xbshqlqzkcl3kqyrk4raa"))))
 236     (build-system gnu-build-system)
 237     (native-inputs
 238      `(("texlive" ,(texlive-union
 239                     (list texlive-amsfonts)))))
 240     (inputs `(("gmp" ,gmp)
 241               ("libx11" ,libx11)
 242               ("perl" ,perl)
 243               ("readline" ,readline)))
 244     (arguments
 245      '(#:make-flags '("all")
 246        #:test-target "dobench"
 247        #:phases
 248        (modify-phases %standard-phases
 249          (replace 'configure
 250            (lambda* (#:key outputs #:allow-other-keys)
 251              (invoke "./Configure"
 252                      (string-append "--prefix="
 253                                     (assoc-ref outputs "out"))))))))
 254     (synopsis "PARI/GP, a computer algebra system for number theory")
 255     (description
 256      "PARI/GP is a widely used computer algebra system designed for fast
 257 computations in number theory (factorisations, algebraic number theory,
 258 elliptic curves...), but it also contains a large number of other useful
 259 functions to compute with mathematical entities such as matrices,
 260 polynomials, power series, algebraic numbers, etc., and a lot of
 261 transcendental functions.
 262 PARI is also available as a C library to allow for faster computations.")
 263     (license license:gpl2+)
 264     (home-page "https://pari.math.u-bordeaux.fr/")))
 265
 266 (define-public gp2c
 267   (package
 268    (name "gp2c")
 269    (version "0.0.11pl2")
 270    (source (origin
 271             (method url-fetch)
 272             (uri (string-append
 273                   "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
 274                   version ".tar.gz"))
 275             (sha256
 276               (base32
 277                 "0wqsf05wgkqvmmsx7jinvzdqav6rl56sr8haibgs31nzz4x9xz9g"))))
 278    (build-system gnu-build-system)
 279    (native-inputs `(("perl" ,perl)))
 280    (inputs `(("pari-gp" ,pari-gp)))
 281    (arguments
 282     '(#:configure-flags
 283       (list (string-append "--with-paricfg="
 284                            (assoc-ref %build-inputs "pari-gp")
 285                            "/lib/pari/pari.cfg"))))
 286    (synopsis "PARI/GP, a computer algebra system for number theory")
 287    (description
 288     "PARI/GP is a widely used computer algebra system designed for fast
 289 computations in number theory (factorisations, algebraic number theory,
 290 elliptic curves...), but it also contains a large number of other useful
 291 functions to compute with mathematical entities such as matrices,
 292 polynomials, power series, algebraic numbers, etc., and a lot of
 293 transcendental functions.
 294 PARI is also available as a C library to allow for faster computations.
 295
 296 GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
 297    (license license:gpl2)
 298    (home-page "https://pari.math.u-bordeaux.fr/")))
 299
 300 (define fplll-4-cmh
 301   (package
 302     (inherit fplll)
 303     (name "fplll")
 304     (version "4.0.4")
 305     (source
 306      (origin
 307        (method url-fetch)
 308        (uri (string-append
 309              "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
 310              version ".tar.gz"))
 311        (sha256
 312         (base32 "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))))
 313
 314 (define-public cmh
 315   (package
 316    (name "cmh")
 317    (version "1.0")
 318    (source (origin
 319             (method url-fetch)
 320             (uri (string-append
 321                   "https://gforge.inria.fr/frs/download.php/33497/cmh-"
 322                   version ".tar.gz"))
 323             (sha256
 324              (base32
 325               "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
 326    (build-system gnu-build-system)
 327    (inputs
 328      `(("gmp" ,gmp)
 329        ("mpfr" ,mpfr)
 330        ("mpc" ,mpc)
 331        ("mpfrcx" ,mpfrcx)
 332        ("fplll" ,fplll-4-cmh)
 333        ("pari-gp"  ,pari-gp)))
 334    (synopsis "Igusa class polynomial computations")
 335    (description
 336     "The CMH software computes Igusa (genus 2) class polynomials, which
 337 parameterize the CM points in the moduli space of 2-dimensional abelian
 338 varieties, i.e. Jacobians of hyperelliptic curves.
 339 It can also be used to compute theta constants at arbitrary
 340 precision.")
 341    (license license:gpl3+)
 342    (home-page "http://cmh.gforge.inria.fr/")))
 343
 344 (define-public giac
 345   (package
 346     (name "giac")
 347     (version "1.5.0-63")
 348     (source (origin
 349               (method url-fetch)
 350               ;; "~parisse/giac" is not used because the maintainer regularly
 351               ;; overwrites the release tarball there, introducing a checksum
 352               ;; mismatch every time.  See
 353               ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
 354               (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
 355                                   "~parisse/debian/dists/stable/main/"
 356                                   "source/giac_" version ".tar.gz"))
 357               (sha256
 358                (base32
 359                 "1jp7awyp8j8w6fhn802z8ddbq1fxhkyk9xdf0mq0mm0chpkylwqk"))))
 360     (build-system gnu-build-system)
 361     (arguments
 362      `(#:modules ((ice-9 ftw)
 363                   (guix build utils)
 364                   (guix build gnu-build-system))
 365        #:phases
 366        (modify-phases %standard-phases
 367          (add-after 'unpack 'patch-bin-cp
 368            ;; Some Makefiles contain hard-coded "/bin/cp".
 369            (lambda _
 370              (substitute* (find-files "doc" "^Makefile")
 371                (("/bin/cp") (which "cp")))
 372              #t))
 373          (add-after 'unpack 'disable-failing-test
 374            ;; FIXME: Test failing.  Not sure why.
 375            (lambda _
 376              (substitute* "check/Makefile.in"
 377                (("chk_fhan11") ""))
 378              #t))
 379          (add-after 'install 'fix-doc
 380            (lambda* (#:key outputs #:allow-other-keys)
 381              (let ((out (assoc-ref outputs "out")))
 382                ;; Most French documentation has a non-commercial
 383                ;; license, so we need to remove it.
 384                (with-directory-excursion (string-append out "/share/giac/doc/fr")
 385                  (for-each delete-file-recursively
 386                            '("cascas" "casexo" "casgeo" "casrouge" "cassim"
 387                              "castor")))
 388                ;; Remove duplicate documentation in
 389                ;; "%out/share/doc/giac/", where Xcas does not expect
 390                ;; to find it.
 391                (delete-file-recursively (string-append out "/share/doc/giac"))
 392                #t)))
 393          (add-after 'install 'remove-unnecessary-executable
 394            (lambda* (#:key outputs #:allow-other-keys)
 395              (let ((out (assoc-ref outputs "out")))
 396                (delete-file (string-append out "/bin/xcasnew"))
 397                #t))))))
 398     (inputs
 399      ;;; TODO: Add libnauty.
 400      `(("fltk" ,fltk)
 401        ("glpk" ,glpk)
 402        ("gmp" ,gmp)
 403        ("gsl" ,gsl)
 404        ("lapack" ,lapack)
 405        ("libao" ,ao)
 406        ("libjpeg" ,libjpeg)
 407        ("libpng" ,libpng)
 408        ("libsamplerate" ,libsamplerate)
 409        ("libx11" ,libx11)
 410        ("libxinerama" ,libxinerama)
 411        ("libxft" ,libxft)
 412        ("libxt" ,libxt)
 413        ("mesa" ,mesa)
 414        ("mpfi" ,mpfi)
 415        ("mpfr" ,mpfr)
 416        ("ntl" ,ntl)
 417        ("perl" ,perl)
 418        ("pari-gp" ,pari-gp)
 419        ("tcsh" ,tcsh)))
 420     (native-inputs
 421      `(("bison" ,bison)
 422        ("flex" ,flex)
 423        ("readline" ,readline)
 424        ("texlive" ,texlive-tiny)))
 425     (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
 426     (synopsis "Computer algebra system")
 427     (description
 428      "Giac/Xcas is a computer algebra system.  It has a compatibility mode for
 429 maple, mupad and the TI89.  It is available as a standalone program (graphic
 430 or text interfaces) or as a C++ library.")
 431     (license license:gpl3+)))
 432
 433 (define-public giac-xcas
 434   (deprecated-package "giac-xcas" giac))
 435
 436 (define-public flint
 437   (package
 438    (name "flint")
 439    (version "2.5.2")
 440    (source (origin
 441             (method url-fetch)
 442             (uri (string-append
 443                   "http://flintlib.org/flint-"
 444                   version ".tar.gz"))
 445             (sha256 (base32
 446                      "11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
 447             (patches (search-patches "flint-ldconfig.patch"))))
 448    (build-system gnu-build-system)
 449    (propagated-inputs
 450     `(("gmp" ,gmp)
 451       ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
 452    (arguments
 453     `(#:parallel-tests? #f ; seems to be necessary on arm
 454       #:phases
 455        (modify-phases %standard-phases
 456          (replace 'configure
 457            (lambda* (#:key inputs outputs #:allow-other-keys)
 458              (let ((out (assoc-ref outputs "out"))
 459                    (gmp (assoc-ref inputs "gmp"))
 460                    (mpfr (assoc-ref inputs "mpfr")))
 461                ;; do not pass "--enable-fast-install", which makes the
 462                ;; homebrew configure process fail
 463                (invoke "./configure"
 464                        (string-append "--prefix=" out)
 465                        (string-append "--with-gmp=" gmp)
 466                        (string-append "--with-mpfr=" mpfr))
 467                #t))))))
 468    (synopsis "Fast library for number theory")
 469    (description
 470     "FLINT is a C library for number theory.  It supports arithmetic
 471 with numbers, polynomials, power series and matrices over many base
 472 rings, including multiprecision integers and rationals, integers
 473 modulo n, p-adic numbers, finite fields (prime and non-prime order)
 474 and real and complex numbers (via the Arb extension library).
 475
 476 Operations that can be performed include conversions, arithmetic,
 477 GCDs, factoring, solving linear systems, and evaluating special
 478 functions.  In addition, FLINT provides various low-level routines for
 479 fast arithmetic.")
 480    (license license:gpl2+)
 481    (home-page "http://flintlib.org/")))
 482
 483 (define-public arb
 484   (package
 485     (name "arb")
 486     (version "2.16.0")
 487     (source (origin
 488               (method git-fetch)
 489               (uri (git-reference
 490                     (url "https://github.com/fredrik-johansson/arb.git")
 491                     (commit version)))
 492               (file-name (git-file-name name version))
 493               (sha256
 494                (base32
 495                 "0478671wfwy3gl26sbxh1jq1ih36z4k72waa8y2y2lvn649gb7cd"))))
 496     (build-system gnu-build-system)
 497     (propagated-inputs
 498      `(("flint" ,flint)))               ; flint.h is included by arf.h
 499     (inputs
 500      `(("gmp" ,gmp)
 501        ("mpfr" ,mpfr)))
 502     (arguments
 503      `(#:phases
 504        (modify-phases %standard-phases
 505          (replace 'configure
 506            (lambda* (#:key inputs outputs #:allow-other-keys)
 507              (let ((out (assoc-ref outputs "out"))
 508                    (flint (assoc-ref inputs "flint"))
 509                    (gmp (assoc-ref inputs "gmp"))
 510                    (mpfr (assoc-ref inputs "mpfr")))
 511                ;; do not pass "--enable-fast-install", which makes the
 512                ;; homebrew configure process fail
 513                (invoke "./configure"
 514                        (string-append "--prefix=" out)
 515                        (string-append "--with-flint=" flint)
 516                        (string-append "--with-gmp=" gmp)
 517                        (string-append "--with-mpfr=" mpfr))))))))
 518     (synopsis "Arbitrary precision floating-point ball arithmetic")
 519     (description
 520      "Arb is a C library for arbitrary-precision floating-point ball
 521 arithmetic.  It supports efficient high-precision computation with
 522 polynomials, power series, matrices and special functions over the
 523 real and complex numbers, with automatic, rigorous error control.")
 524     (license license:lgpl2.1+)
 525     (home-page "http://fredrikj.net/arb/")))
 526
 527 (define-public python-flint
 528   (package
 529     (name "python-flint")
 530     (version "0.3.0")
 531     (source (origin
 532               (method git-fetch)
 533               (uri (git-reference
 534                     (url "https://github.com/fredrik-johansson/python-flint.git")
 535                     (commit version)))
 536               (file-name (git-file-name name version))
 537               (sha256
 538                (base32
 539                 "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
 540               (patches (search-patches "python-flint-includes.patch"))))
 541     (build-system python-build-system)
 542     (native-inputs
 543      `(("python-cython" ,python-cython)))
 544     (propagated-inputs
 545      `(("python-numpy" ,python-numpy)))
 546     (inputs
 547      `(("arb" ,arb)
 548        ("flint" ,flint)))
 549     (synopsis "Python module wrapping ARB and FLINT")
 550     (description
 551      "Python-flint is a Python extension module wrapping FLINT
 552 (Fast Library for Number Theory) and Arb (arbitrary-precision ball
 553 arithmetic).  It supports integers, rationals, modular integers,
 554 real and complex ball arithmetic, polynomials and matrices over all
 555 these types and other mathematical functions.")
 556     (license license:expat)
 557     (home-page "http://fredrikj.net/python-flint/")))
 558
 559 (define-public ntl
 560   (package
 561    (name "ntl")
 562    (version "9.7.0")
 563    (source (origin
 564             (method url-fetch)
 565             (uri (string-append "http://shoup.net/ntl/ntl-"
 566                                 version ".tar.gz"))
 567             (sha256 (base32
 568                      "115frp5flyvw9wghz4zph1b3llmr5nbxk1skgsggckr81fh3gmxq"))))
 569    (build-system gnu-build-system)
 570    (native-inputs
 571     `(("libtool" ,libtool)
 572       ("perl" ,perl))) ; for configuration
 573    ;; FIXME: Add optional input gf2x once available; then also add
 574    ;; configure flag "NTL_GF2X_LIB=on".
 575    (inputs
 576     `(("gmp" ,gmp)))
 577    (arguments
 578     `(#:phases
 579       (modify-phases %standard-phases
 580         (replace 'configure
 581          (lambda* (#:key outputs #:allow-other-keys)
 582            (chdir "src")
 583            (system* "./configure"
 584                     (string-append "PREFIX=" (assoc-ref outputs "out"))
 585                     ;; Do not build especially for the build machine.
 586                     "NATIVE=off"
 587                     ;; Also do not tune to the build machine.
 588                     "WIZARD=off"
 589                     "SHARED=on")
 590            #t)))))
 591    (synopsis "C++ library for number theory")
 592    (description
 593     "NTL is a C++ library providing data structures and algorithms
 594 for manipulating signed, arbitrary length integers, and for vectors,
 595 matrices, and polynomials over the integers and over finite fields.")
 596    (license license:gpl2+)
 597    (home-page "http://shoup.net/ntl/")))
 598
 599 (define-public singular
 600   (package
 601    (name "singular")
 602    (version "4.1.2p1")
 603    (source
 604     (origin
 605       (method url-fetch)
 606       (uri
 607        (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
 608                       "Singular/SOURCES/"
 609                       (string-join
 610                        (string-split
 611                         (string-trim-right version #\p
 612                                            0 (1- (string-length version)))
 613                         #\.) "-")
 614                       "/singular-" version ".tar.gz"))
 615              (sha256 (base32
 616                       "0kvd55353fiqyq1msmi0kka66n5h0aqs7m3km60r01b1w2f8085m"))))
 617    (build-system gnu-build-system)
 618    (native-inputs
 619     `(("doxygen" ,doxygen)
 620       ("graphviz" ,graphviz)
 621       ("perl" ,perl)))
 622    (inputs
 623     `(("cddlib" ,cddlib)
 624       ("gmp" ,gmp)
 625       ("flint" ,flint)
 626       ("mpfr" ,mpfr)
 627       ("ntl" ,ntl)
 628       ("python" ,python-2)
 629       ("readline" ,readline)))
 630    (arguments
 631     `(#:configure-flags
 632       (list (string-append "--with-ntl="
 633                            (assoc-ref %build-inputs "ntl")))))
 634    (synopsis "Computer algebra system for polynomial computations")
 635    (description
 636     "Singular is a computer algebra system for polynomial computations,
 637 with special emphasis on commutative and non-commutative algebra, algebraic
 638 geometry and singularity theory.")
 639    ;; Singular itself is dual licensed gpl2 or gpl3, but some of the
 640    ;; libraries with which it links are licensed under lgpl3+, so the
 641    ;; combined work becomes gpl3. See COPYING in the source code.
 642    (license license:gpl3)
 643    (home-page "http://www.singular.uni-kl.de/index.php")))
 644
 645 (define-public gmp-ecm
 646   (package
 647    (name "gmp-ecm")
 648    (version "7.0.4")
 649    (source (origin
 650              (method url-fetch)
 651              ;; Use the ‘Latest version’ link for a stable URI across releases.
 652              (uri (string-append "https://gforge.inria.fr/frs/download.php/"
 653                                  "latestfile/160/ecm-" version ".tar.gz"))
 654              (sha256 (base32
 655                       "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"))))
 656    (build-system gnu-build-system)
 657    (inputs
 658     `(("gmp" ,gmp)))
 659    (arguments
 660     `(#:configure-flags '("--enable-shared"
 661                           ;; Disable specific assembly routines, which depend
 662                           ;; on the subarchitecture of the build machine,
 663                           ;; and use gmp instead.
 664                           "--disable-asm-redc")))
 665    (synopsis "Integer factorization library using the elliptic curve method")
 666    (description
 667     "GMP-ECM factors integers using the elliptic curve method (ECM) as well
 668 as the P-1 and P+1 algorithms.  It provides a library and a stand-alone
 669 binary.")
 670    ;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+,
 671    ;; so the combined work is under gpl3+.
 672    (license license:gpl3+)
 673    (home-page "http://ecm.gforge.inria.fr/")))
 674
 675 (define-public bc
 676   (package
 677     (name "bc")
 678     (version "1.07.1")
 679     (source (origin
 680              (method url-fetch)
 681              (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
 682              (sha256
 683               (base32
 684                "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))))
 685     (build-system gnu-build-system)
 686     (native-inputs
 687      `(("ed" ,ed)
 688        ("flex" ,flex)
 689        ("texinfo" ,texinfo)))
 690     (arguments
 691      '(#:configure-flags
 692        (list "--with-readline")))
 693     (home-page "https://www.gnu.org/software/bc/")
 694     (synopsis "Arbitrary precision numeric processing language")
 695     (description
 696      "bc is an arbitrary precision numeric processing language.  It includes
 697 an interactive environment for evaluating mathematical statements.  Its
 698 syntax is similar to that of C, so basic usage is familiar.  It also includes
 699 \"dc\", a reverse-polish calculator.")
 700     (license license:gpl2+)))
 701
 702 ;; The original kiss-fft does not have a complete build system and does not
 703 ;; build any shared libraries.  This is a fork used by Extempore.
 704 (define-public kiss-fft-for-extempore
 705   (package
 706     (name "kiss-fft-for-extempore")
 707     (version "1.3.0")
 708     (source (origin
 709               (method git-fetch)
 710               (uri (git-reference
 711                     (url "https://github.com/extemporelang/kiss_fft.git")
 712                     (commit version)))
 713               (file-name (git-file-name name version))
 714               (sha256
 715                (base32
 716                 "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
 717     (build-system cmake-build-system)
 718     (arguments `(#:tests? #f)) ; no tests included
 719     ;; Extempore refuses to build on architectures other than x86_64
 720     (supported-systems '("x86_64-linux"))
 721     (home-page "https://github.com/extemporelang/kiss_fft")
 722     (synopsis "Mixed-radix Fast Fourier Transform")
 723     (description
 724      "Kiss FFT attempts to be a reasonably efficient, moderately useful FFT
 725 that can use fixed or floating data types and can easily be incorporated into
 726 a C program.")
 727     (license license:bsd-3)))
 728
 729 (define-public fftw
 730   (package
 731     (name "fftw")
 732     (version "3.3.8")
 733     (source (origin
 734              (method url-fetch)
 735              (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
 736                                  version".tar.gz"))
 737              (sha256
 738               (base32
 739                "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
 740     (build-system gnu-build-system)
 741     (arguments
 742      `(#:configure-flags
 743        '("--enable-shared" "--enable-openmp" "--enable-threads"
 744          ,@(let ((system (or (%current-target-system) (%current-system))))
 745              ;; Enable SIMD extensions for codelets.  See details at:
 746              ;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>.
 747              (cond
 748               ((string-prefix? "x86_64" system)
 749                '("--enable-sse2" "--enable-avx" "--enable-avx2"
 750                  "--enable-avx512" "--enable-avx-128-fma"))
 751               ((string-prefix? "i686" system)
 752                '("--enable-sse2"))
 753               ((string-prefix? "aarch64" system)
 754                ;; Note that fftw supports NEON on 32-bit ARM only when
 755                ;; compiled for single-precision.
 756                '("--enable-neon"))
 757               (else
 758                '())))
 759          ;; By default '-mtune=native' is used.  However, that may cause the
 760          ;; use of ISA extensions (e.g. AVX) that are not necessarily
 761          ;; available on the user's machine when that package is built on a
 762          ;; different machine.
 763          "ax_cv_c_flags__mtune_native=no")))
 764     (native-inputs `(("perl" ,perl)))
 765     (home-page "http://fftw.org")
 766     (synopsis "Computing the discrete Fourier transform")
 767     (description
 768      "FFTW is a C subroutine library for computing the discrete Fourier
 769 transform (DFT) in one or more dimensions, of arbitrary input size, and of
 770 both real and complex data (as well as of even/odd data---i.e. the discrete
 771 cosine/ sine transforms or DCT/DST).")
 772     (license license:gpl2+)))
 773
 774 (define-public fftwf
 775   (package (inherit fftw)
 776     (name "fftwf")
 777     (arguments
 778      (substitute-keyword-arguments (package-arguments fftw)
 779        ((#:configure-flags fftw-configure-flags)
 780         `(cons* "--enable-single"
 781                 ,@(if (string-prefix? "arm" (or (%current-target-system)
 782                                                 (%current-system)))
 783                       ;; fftw supports NEON on 32-bit ARM only when compiled
 784                       ;; for single-precision, so add it here.
 785                       '("--enable-neon")
 786                       '())
 787                 ,fftw-configure-flags))))
 788     (description
 789      (string-append (package-description fftw)
 790                     "  Single-precision version."))))
 791
 792 (define-public fftw-openmpi
 793   (package (inherit fftw)
 794     (name "fftw-openmpi")
 795     (inputs
 796      `(("openmpi" ,openmpi)
 797        ,@(package-inputs fftw)))
 798     (arguments
 799      (substitute-keyword-arguments (package-arguments fftw)
 800        ((#:configure-flags cf)
 801         `(cons "--enable-mpi" ,cf))
 802        ((#:phases phases '%standard-phases)
 803         `(modify-phases ,phases
 804            (add-before 'check 'mpi-setup
 805              ,%openmpi-setup)))))
 806     (description
 807      (string-append (package-description fftw)
 808                     "  With OpenMPI parallelism support."))))
 809
 810 (define-public java-la4j
 811   (package
 812     (name "java-la4j")
 813     (version "0.6.0")
 814     (source (origin
 815               (method git-fetch)
 816               (uri (git-reference
 817                     (url "https://github.com/vkostyukov/la4j.git")
 818                     (commit version)))
 819               (file-name (string-append name "-" version "-checkout"))
 820               (sha256
 821                (base32
 822                 "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
 823     (build-system ant-build-system)
 824     (arguments
 825      `(#:jar-name "la4j.jar"
 826        #:jdk ,icedtea-8
 827        #:test-exclude (list "**/Abstract*.java"
 828                             "**/MatrixTest.java"
 829                             "**/DenseMatrixTest.java"
 830                             "**/SparseMatrixTest.java"
 831                             "**/VectorTest.java"
 832                             "**/SparseVectorTest.java"
 833                             "**/DenseVectorTest.java")))
 834     (native-inputs
 835      `(("java-junit" ,java-junit)
 836        ("java-hamcrest-core" ,java-hamcrest-core)))
 837     (home-page "http://la4j.org/")
 838     (synopsis "Java library that provides Linear Algebra primitives and algorithms")
 839     (description "The la4j library is a Java library that provides Linear
 840 Algebra primitives (matrices and vectors) and algorithms.  The key features of
 841 the la4j library are:
 842
 843 @itemize
 844 @item No dependencies and tiny size
 845 @item Fluent object-oriented/functional API
 846 @item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
 847 @item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
 848 @item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
 849 @item MatrixMarket/CSV IO formats support for matrices and vectors
 850 @end itemize\n")
 851     (license license:asl2.0)))
 852
 853 (define-public java-jlargearrays
 854   (package
 855     (name "java-jlargearrays")
 856     (version "1.6")
 857     (source (origin
 858               (method url-fetch)
 859               (uri (string-append "http://search.maven.org/remotecontent?"
 860                                   "filepath=pl/edu/icm/JLargeArrays/"
 861                                   version "/JLargeArrays-" version
 862                                   "-sources.jar"))
 863               (file-name (string-append name "-" version ".jar"))
 864               (sha256
 865                (base32
 866                 "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
 867     (build-system ant-build-system)
 868     (arguments
 869      `(#:jar-name "jlargearrays.jar"
 870        #:tests? #f ; tests are not included in the release archive
 871        #:jdk ,icedtea-8))
 872     (propagated-inputs
 873      `(("java-commons-math3" ,java-commons-math3)))
 874     (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
 875     (synopsis "Library of one-dimensional arrays that can store up to 263 elements")
 876     (description "JLargeArrays is a Java library of one-dimensional arrays
 877 that can store up to 263 elements.")
 878     (license license:bsd-2)))
 879
 880 (define-public java-jtransforms
 881   (package
 882     (name "java-jtransforms")
 883     (version "3.1")
 884     (source (origin
 885               (method url-fetch)
 886               (uri (string-append "http://search.maven.org/remotecontent?"
 887                                   "filepath=com/github/wendykierp/JTransforms/"
 888                                   version "/JTransforms-" version "-sources.jar"))
 889               (sha256
 890                (base32
 891                 "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
 892     (build-system ant-build-system)
 893     (arguments
 894      `(#:jar-name "jtransforms.jar"
 895        #:tests? #f ; tests are not included in the release archive
 896        #:jdk ,icedtea-8))
 897     (propagated-inputs
 898      `(("java-commons-math3" ,java-commons-math3)
 899        ("java-jlargearrays" ,java-jlargearrays)))
 900     (home-page "https://github.com/wendykierp/JTransforms")
 901     (synopsis "Multithreaded FFT library written in pure Java")
 902     (description "JTransforms is a multithreaded FFT library written in pure
 903 Java.  Currently, four types of transforms are available: @dfn{Discrete
 904 Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
 905 Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
 906     (license license:bsd-2)))
 907
 908 (define-public eigen
 909   (package
 910     (name "eigen")
 911     (version "3.3.5")
 912     (source (origin
 913               (method url-fetch)
 914               (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
 915                                   version ".tar.bz2"))
 916               (sha256
 917                (base32
 918                 "1qh3yrwn78ms5yhwbpl5wvblk4gbz02cacdygxylr7i9xbrvylkk"))
 919               (file-name (string-append name "-" version ".tar.bz2"))
 920               (modules '((guix build utils)))
 921               (snippet
 922                ;; There are 3 test failures in the "unsupported" directory,
 923                ;; but maintainers say it's a known issue and it's unsupported
 924                ;; anyway, so just skip them.
 925                '(begin
 926                   (substitute* "unsupported/CMakeLists.txt"
 927                     (("add_subdirectory\\(test.*")
 928                      "# Do not build the tests for unsupported features.\n"))
 929                   #t))))
 930     (build-system cmake-build-system)
 931     (arguments
 932      '(;; Turn off debugging symbols to save space.
 933        #:build-type "Release"
 934
 935        #:phases (modify-phases %standard-phases
 936                   (replace 'check
 937                     (lambda _
 938                       (let* ((cores  (parallel-job-count))
 939                              (dash-j (format #f "-j~a" cores)))
 940                         (setenv "EIGEN_SEED" "1") ;for reproducibility
 941                         ;; First build the tests, in parallel.  See
 942                         ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
 943                         (invoke "make" "buildtests" dash-j)
 944
 945                         ;; Then run 'CTest' with -V so we get more
 946                         ;; details upon failure.
 947                         (invoke "ctest" "-V" dash-j)))))))
 948     (home-page "https://eigen.tuxfamily.org")
 949     (synopsis "C++ template library for linear algebra")
 950     (description
 951      "Eigen is a C++ template library for linear algebra: matrices, vectors,
 952 numerical solvers, and related algorithms.  It provides an elegant API based
 953 on \"expression templates\".  It is versatile: it supports all matrix sizes,
 954 all standard numeric types, various matrix decompositions and geometry
 955 features, and more.")
 956
 957     ;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3.
 958     ;; See 'COPYING.README' for details.
 959     (license license:mpl2.0)))
 960
 961 (define-public eigen-for-tensorflow
 962   (let ((changeset "fd6845384b86")
 963         (revision "1"))
 964     (package (inherit eigen)
 965       (name "eigen-for-tensorflow")
 966       (version (string-append "3.3.5-" revision "." changeset))
 967       (source (origin
 968                 (method hg-fetch)
 969                 (uri (hg-reference
 970                       (url "https://bitbucket.org/eigen/eigen")
 971                       (changeset changeset)))
 972                 (sha256
 973                  (base32
 974                   "12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5"))
 975                 (file-name (string-append name "-" version "-checkout"))
 976                 (modules '((guix build utils)))
 977                 (snippet
 978                  ;; There are 3 test failures in the "unsupported" directory,
 979                  ;; but maintainers say it's a known issue and it's unsupported
 980                  ;; anyway, so just skip them.
 981                  '(begin
 982                     (substitute* "unsupported/CMakeLists.txt"
 983                       (("add_subdirectory\\(test.*")
 984                        "# Do not build the tests for unsupported features.\n"))
 985                     #t)))))))
 986
 987 (define-public xtensor
 988   (package
 989     (name "xtensor")
 990     (version "0.20.5")
 991     (source (origin
 992               (method git-fetch)
 993               (uri (git-reference
 994                     (url "https://github.com/QuantStack/xtensor.git")
 995                     (commit version)))
 996               (sha256
 997                (base32
 998                 "0kkc4ar7p2d94jnclmrh46dwv7ldy9lx630vm9gci3pp4hnhbj9f"))
 999               (file-name (git-file-name name version))))
1000     (build-system cmake-build-system)
1001     (native-inputs
1002      `(("googletest" ,googletest)
1003        ("xtl" ,xtl)))
1004     (arguments
1005      `(#:configure-flags
1006        '("-DBUILD_TESTS=ON")
1007        #:test-target "xtest"))
1008     (home-page "http://quantstack.net/xtensor")
1009     (synopsis "C++ tensors with broadcasting and lazy computing")
1010     (description "xtensor is a C++ library meant for numerical analysis with
1011 multi-dimensional array expressions.
1012
1013 xtensor provides:
1014 @itemize
1015 @item an extensible expression system enabling lazy broadcasting.
1016 @item an API following the idioms of the C++ standard library.
1017 @item tools to manipulate array expressions and build upon xtensor.
1018 @end itemize")
1019     (license license:bsd-3)))
1020
1021 (define-public gap
1022   (package
1023     (name "gap")
1024     (version "4.10.2")
1025     (source
1026      (origin
1027        (method url-fetch)
1028        (uri (string-append "https://www.gap-system.org/pub/gap/gap-"
1029                            (version-major+minor version)
1030                            "/tar.bz2/gap-"
1031                            version
1032                            ".tar.bz2"))
1033        (sha256
1034         (base32 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
1035        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
1036        (snippet
1037         '(begin
1038            ;; Delete the external gmp and zlib libraries
1039            ;; and a subdirectory not needed for our build.
1040            (for-each delete-file-recursively
1041                      '("extern" "hpcgap"))
1042            ;; Delete a failing test.
1043            ;; FIXME: This might be fixed in the next release, see
1044            ;; https://github.com/gap-system/gap/issues/3292
1045            (delete-file "tst/testinstall/dir.tst")
1046            ;; Delete all packages except for a fixed list.
1047            (with-directory-excursion "pkg"
1048              (for-each delete-file-recursively
1049                (lset-difference string=? (scandir ".")
1050                  '("." ".."
1051                    ;; Necessary packages.
1052                    "GAPDoc-1.6.2"
1053                    "primgrp-3.3.2"
1054                    "SmallGrp-1.3"    ; artistic2.0
1055                    "transgrp"        ; artistic2.0 for data,
1056                                      ; gpl2 or gpl3 for code
1057                    ;; Recommanded package.
1058                    "io-4.5.4"        ; gpl3+
1059                    ;; Optional packages, searched for at start,
1060                    ;; and their depedencies.
1061                    "alnuth-3.1.0"
1062                    "autpgrp-1.10"
1063                    "crisp-1.4.4"     ; bsd-2
1064                    "ctbllib"       ; gpl3+ according to doc/chap0.txt
1065                    "FactInt-1.6.2"
1066                    "fga"
1067                    "irredsol-1.4"    ; bsd-2
1068                    "laguna-3.9.2"
1069                    "polenta-1.3.8"
1070                    "polycyclic-2.14"
1071                    "radiroot-2.8"
1072                    "resclasses-4.7.1"
1073                    "sophus-1.24"
1074                    "tomlib-1.2.7"  ; gpl2+, clarified in the git repository
1075                                    ; and the next release
1076                    "utils-0.59"))))
1077            #t))))
1078     (build-system gnu-build-system)
1079     (inputs
1080      `(("gmp" ,gmp)
1081        ("zlib" ,zlib)))
1082     (arguments
1083      `(#:modules ((ice-9 ftw)
1084                   (srfi srfi-26)
1085                   (guix build gnu-build-system)
1086                   (guix build utils))
1087        #:phases
1088        (modify-phases %standard-phases
1089          (add-after 'build 'build-packages
1090            ;; Compile all packages that have not been deleted by the
1091            ;; code snippet above.
1092            (lambda _
1093              (setenv "CONFIG_SHELL" (which "bash"))
1094              (with-directory-excursion "pkg"
1095                (invoke "../bin/BuildPackages.sh")
1096              #t)))
1097          (add-after 'build-packages 'build-doc
1098            ;; The documentation is bundled, but we create it from source.
1099            (lambda _
1100              (with-directory-excursion "doc"
1101                (invoke "./make_doc"))
1102              #t))
1103          (replace 'install
1104            (lambda* (#:key outputs #:allow-other-keys)
1105              (let* ((out (assoc-ref outputs "out"))
1106                     (bin (string-append out "/bin"))
1107                     (lib (string-append out "/lib"))
1108                     (prog (string-append bin "/gap"))
1109                     (prog-real (string-append bin "/.gap-real"))
1110                     (share (string-append out "/share/gap"))
1111                     (include (string-append out "/include/gap"))
1112                     (include-hpc (string-append include "/hpc")))
1113                ;; Install only the gap binary; the gac compiler is left
1114                ;; for maybe later. "Wrap" it in a shell script that calls
1115                ;; the binary with the correct parameter.
1116                (mkdir-p bin)
1117                (copy-file "gap" prog-real)
1118                (call-with-output-file prog
1119                  (lambda (port)
1120                    (format port
1121                            "#!~a~%exec ~a -l ~a \"$@\"~%"
1122                            (which "bash")
1123                            prog-real
1124                            share)))
1125                (chmod prog #o755)
1126                ;; Install the headers, which are needed by Sage. The
1127                ;; Makefile target "install-headers" was available in
1128                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1129                (mkdir-p include-hpc)
1130                (install-file "gen/config.h" include)
1131                (let ((file-name-predicate-without-stat
1132                        (lambda (regex)
1133                          (cut (file-name-predicate regex) <> #f))))
1134                  (with-directory-excursion "src"
1135                    (for-each
1136                      (cut install-file <> include)
1137                      (scandir "."
1138                               (file-name-predicate-without-stat ".*\\.h$"))))
1139                  (with-directory-excursion "src/hpc"
1140                    (for-each
1141                      (cut install-file <> include-hpc)
1142                      (scandir "."
1143                               (file-name-predicate-without-stat ".*\\.h$")))))
1144                ;; Install the library, which is needed by Sage. The
1145                ;; Makefile target "install-libgap" was available in
1146                ;; gap-4.10.0, but has been commented out in gap-4.10.1.
1147                ;; Compared to the Makefile, which used libtool, the
1148                ;; following approach of copying files and making symlinks
1149                ;; is rather pedestrian. There is hope that some later
1150                ;; version of gap reinstates and completes the install
1151                ;; targets.
1152                (invoke "make" "libgap.la")
1153                (install-file "libgap.la" lib)
1154                (install-file ".libs/libgap.so.0.0.0" lib)
1155                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so"))
1156                (symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
1157                ;; Install a certain number of files and directories to
1158                ;; SHARE, where the wrapped shell script expects them.
1159                ;; Remove information on the build directory from sysinfo.gap.
1160                (substitute* "sysinfo.gap"
1161                  (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
1162                  (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
1163                  (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
1164                (install-file "sysinfo.gap" share)
1165                (copy-recursively "grp" (string-append share "/grp"))
1166                (copy-recursively "pkg" (string-append share "/pkg"))
1167                ;; The following is not the C library libgap.so, but a
1168                ;; library of GAP code.
1169                (copy-recursively "lib" (string-append share "/lib"))
1170                ;; The gap binary looks for documentation inside SHARE.
1171                (copy-recursively "doc" (string-append share "/doc")))
1172              #t)))))
1173     (home-page "https://www.gap-system.org/")
1174     (synopsis
1175      "System for computational group theory")
1176     (description
1177      "GAP is a system for computational discrete algebra, with particular
1178 emphasis on computational group theory.  It provides a programming language,
1179 a library of thousands of functions implementing algebraic algorithms
1180 written in the GAP language as well as large data libraries of algebraic
1181 objects.")
1182     ;; Some packages have different licenses (effectively forcing the
1183     ;; combined work to be licensed as gpl3+); if this is the case, this
1184     ;; is mentioned above next to their name.
1185     ;; Some packages have no license mentioned explicitly; supposedly this
1186     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
1187     ;; safe side, we drop them for now.
1188     (license license:gpl2+)))
1189
1190 (define-public givaro
1191   (package
1192     (name "givaro")
1193     (version "4.1.1")
1194     (source (origin
1195               (method git-fetch)
1196               (uri (git-reference
1197                     (url "https://github.com/linbox-team/givaro")
1198                     (commit (string-append "v" version))))
1199               (file-name (git-file-name name version))
1200               (sha256
1201                (base32
1202                 "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
1203     (build-system gnu-build-system)
1204     (native-inputs
1205      `(("autoconf" ,autoconf)
1206        ("automake" ,automake)
1207        ("libtool" ,libtool)))
1208     (propagated-inputs
1209      `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
1210     (arguments
1211      `(#:phases
1212        (modify-phases %standard-phases
1213          (add-before 'bootstrap 'setenv
1214            ;; Prevent the autogen.sh script to carry out the configure
1215            ;; script, which has not yet been patched to replace /bin/sh.
1216            (lambda _
1217              (setenv "NOCONFIGURE" "yes")
1218              #t)))))
1219     (synopsis "Algebraic computations with exact rings and fields")
1220     (description
1221      "Givaro is a C++ library implementing the basic arithmetic of various
1222 algebraic objects: prime fields, extension fields, finite fields, finite
1223 rings, polynomials, algebraic numbers, arbitrary precision integers and
1224 rationals (C++ wrappers over gmp), fixed precision integers.  It also
1225 provides data-structures and templated classes for the manipulation of
1226 compound objects, such as vectors, matrices and univariate polynomials.")
1227     (license license:cecill-b)
1228     (home-page "https://github.com/linbox-team/givaro")))
1229
1230 (define-public fflas-ffpack
1231   (package
1232     (name "fflas-ffpack")
1233     (version "2.4.3")
1234     (source (origin
1235               (method git-fetch)
1236               (uri (git-reference
1237                     (url "https://github.com/linbox-team/fflas-ffpack")
1238                     (commit version)))
1239               (file-name (git-file-name name version))
1240               (sha256
1241                (base32
1242                 "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
1243     (build-system gnu-build-system)
1244     (native-inputs
1245      `(("autoconf" ,autoconf)
1246        ("automake" ,automake)
1247        ("libtool" ,libtool)
1248        ("pkg-config" ,pkg-config)))
1249     (inputs
1250      `(("openblas" ,openblas)))
1251     (propagated-inputs
1252      `(("givaro" ,givaro))) ; required according to the .pc file
1253     (arguments
1254      `(#:configure-flags
1255        (list (string-append "--with-blas-libs="
1256                             (assoc-ref %build-inputs "openblas")
1257                             "/lib/libopenblas.so"))
1258        #:phases
1259        (modify-phases %standard-phases
1260          (add-before 'bootstrap 'setenv
1261            ;; Prevent the autogen.sh script to carry out the configure
1262            ;; script, which has not yet been patched to replace /bin/sh.
1263            (lambda _
1264              (setenv "NOCONFIGURE" "yes")
1265              #t)))))
1266     (synopsis "C++ library for linear algebra over finite fields")
1267     (description
1268      "FFLAS-FFPACK is a C++ template library for basic linear algebra
1269 operations over a finite field.
1270 FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
1271 of a subset of routines of the numerical BLAS; it also supports sparse
1272 matrix-vector products.
1273 FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
1274 library to provide functionalities of higher level, using the kernel
1275 of a BLAS.  Additionally, it provides routines specific to exact linear
1276 algebra, such as the row echelon form.")
1277     (license license:lgpl2.1+)
1278     (home-page "https://linbox-team.github.io/fflas-ffpack/")))
1279
1280 (define-public linbox
1281   (package
1282     (name "linbox")
1283     (version "1.6.3")
1284     (source (origin
1285               (method git-fetch)
1286               (uri (git-reference
1287                     (url "https://github.com/linbox-team/linbox")
1288                     (commit (string-append "v" version))))
1289               (file-name (git-file-name name version))
1290               (sha256
1291                (base32
1292                 "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
1293     (build-system gnu-build-system)
1294     (native-inputs
1295      `(("autoconf" ,autoconf)
1296        ("automake" ,automake)
1297        ("libtool" ,libtool)
1298        ("pkg-config" ,pkg-config)))
1299     (inputs
1300      `(("fflas-ffpack" ,fflas-ffpack)))
1301     (arguments
1302      `(#:phases
1303        (modify-phases %standard-phases
1304          (add-before 'bootstrap 'setenv
1305            ;; Prevent the autogen.sh script to carry out the configure
1306            ;; script, which has not yet been patched to replace /bin/sh.
1307            (lambda _
1308              (setenv "NOCONFIGURE" "yes")
1309              #t)))))
1310     (synopsis "C++ library for linear algebra over exact rings")
1311     (description
1312      "LinBox is a C++ template library for exact linear algebra computation
1313 with dense, sparse, and structured matrices over the integers and over
1314 finite fields.")
1315     (license license:lgpl2.1+)
1316     (home-page "https://linbox-team.github.io/linbox/")))
1317
1318 (define-public m4ri
1319   (package
1320     (name "m4ri")
1321     (version "20140914")
1322     (source (origin
1323               (method git-fetch)
1324               (uri (git-reference
1325                     (url "https://bitbucket.org/malb/m4ri")
1326                     (commit (string-append "release-" version))))
1327               (file-name (git-file-name name version))
1328               (sha256
1329                (base32
1330                 "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
1331     (build-system gnu-build-system)
1332     (native-inputs
1333      `(("autoconf" ,autoconf)
1334        ("automake" ,automake)
1335        ("libtool" ,libtool)
1336        ("pkg-config" ,pkg-config)))
1337     (inputs
1338      `(("libpng" ,libpng)))
1339     (synopsis "Arithmetic of dense matrices over F_2")
1340     (description "M4RI is a library for fast arithmetic with dense matrices
1341 over F2.  The name M4RI comes from the first implemented algorithm: The
1342 Method of the Four Russians inversion algorithm published by Gregory Bard.
1343 This algorithm in turn is named after the Method of the Four Russians
1344 multiplication algorithm.")
1345     (license license:gpl2+)
1346     (home-page "https://bitbucket.org/malb/m4ri/")))
1347
1348 (define-public symmetrica
1349   (package
1350     (name "symmetrica")
1351     (version "2.0")
1352     (source (origin
1353               (method url-fetch/tarbomb)
1354               (uri (let ((v (string-join (string-split version #\.) "_")))
1355                      (string-append "http://www.algorithm.uni-bayreuth.de/"
1356                                     "en/research/SYMMETRICA/"
1357                                     "SYM" v "_tar.gz")))
1358               (sha256
1359                (base32
1360                 "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
1361               ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
1362               (patches (search-patches "symmetrica-bruch.patch"
1363                                        "symmetrica-int32.patch"
1364                                        "symmetrica-return_values.patch"
1365                                        "symmetrica-sort_sum_rename.patch"))))
1366     (build-system gnu-build-system)
1367     (arguments
1368      `(#:tests? #f                      ;no test
1369        #:phases
1370        (modify-phases %standard-phases
1371          (add-after 'unpack 'fix-makefile
1372            (lambda _
1373              (substitute* "makefile"
1374                (("cc -c") "gcc -c -fPIC"))
1375              #t))
1376          (add-after 'fix-makefile 'turn-off-banner
1377            (lambda _
1378              (substitute* "de.c"
1379                (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
1380              #t))
1381          (delete 'configure)            ;no configure script
1382          (replace 'install              ;no install target
1383            (lambda* (#:key outputs #:allow-other-keys)
1384              (let* ((out (assoc-ref outputs "out"))
1385                     (lib (string-append out "/lib"))
1386                     (inc (string-append out "/include/symmetrica"))
1387                     (doc (string-append out "/share/doc/symmetrica-" ,version))
1388                     (static "libsymmetrica.a"))
1389                ;; Build static library.
1390                (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
1391                (invoke "ranlib" static)
1392                ;; Install static library and headers.
1393                (for-each (lambda (f) (install-file f inc))
1394                          (find-files "." "\\.h$"))
1395                (install-file "libsymmetrica.a" lib)
1396                ;; Install documentation.
1397                (for-each (lambda (f) (install-file f doc))
1398                          (find-files "." "\\.doc$"))
1399                #t))))))
1400     (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
1401     (synopsis "Combinatoric C Library")
1402     (description "Symmetrica is a library for combinatorics.  It has support
1403 for the representation theory of the symmetric group and related groups,
1404 combinatorics of tableaux, symmetric functions and polynomials, Schubert
1405 polynomials, and the representation theory of Hecke algebras of type A_n.")
1406     (license license:public-domain)))
1407
1408 (define-public m4rie
1409   (package
1410     (name "m4rie")
1411     (version "20150908")
1412     (source (origin
1413               (method git-fetch)
1414               (uri (git-reference
1415                     (url "https://bitbucket.org/malb/m4rie")
1416                     (commit (string-append "release-" version))))
1417               (file-name (git-file-name name version))
1418               (sha256
1419                (base32
1420                 "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
1421     (build-system gnu-build-system)
1422     (native-inputs
1423      `(("autoconf" ,autoconf)
1424        ("automake" ,automake)
1425        ("libtool" ,libtool)))
1426     (inputs
1427      `(("m4ri" ,m4ri)))
1428     (synopsis "Arithmetic of dense matrices over F_{2^e}")
1429     (description "M4RI is a library for fast arithmetic with dense matrices
1430 over finite fields of characteristic 2.  So it extends the functionality
1431 of M4RI from F_2 to F_{2^e}.")
1432     (license license:gpl2+)
1433     (home-page "https://bitbucket.org/malb/m4rie/")))
1434
1435 (define-public eclib
1436   (package
1437     (name "eclib")
1438     (version "20190226")
1439     (source (origin
1440               (method git-fetch)
1441               (uri (git-reference
1442                     (url "https://github.com/JohnCremona/eclib/")
1443                     (commit (string-append "v" version))))
1444               (file-name (git-file-name name version))
1445               (sha256
1446                (base32
1447                 "1910np1xzyjzszay24xn4b81qhpsvhp5aix9vdpknplni2mq8kwb"))))
1448     (build-system gnu-build-system)
1449     (native-inputs
1450      `(("autoconf" ,autoconf)
1451        ("automake" ,automake)
1452        ("libtool" ,libtool)))
1453     (inputs
1454      `(("gmp" ,gmp)
1455        ("ntl" ,ntl)
1456        ("pari-gp" ,pari-gp)))
1457     (synopsis "Ranks of elliptic curves and modular symbols")
1458     (description "The eclib package includes mwrank (for 2-descent on
1459 elliptic curves over Q) and modular symbol code; it has been written by
1460 John Cremona to compute his elliptic curve database.")
1461     (license license:gpl2+)
1462     (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
1463                               "J.E.Cremona/mwrank/index.html"))))
1464
1465 (define-public lrcalc
1466   (package
1467     (name "lrcalc")
1468     (version "1.2")
1469     (source (origin
1470               (method git-fetch)
1471               (uri (git-reference
1472                     (url "https://bitbucket.org/asbuch/lrcalc")
1473                     (commit (string-append "lrcalc-" version))))
1474               (file-name (git-file-name name version))
1475               (sha256
1476                (base32
1477                 "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
1478               (patches (search-patches "lrcalc-includes.patch"))))
1479     (build-system gnu-build-system)
1480     (native-inputs
1481      `(("autoconf" ,autoconf)
1482        ("automake" ,automake)
1483        ("libtool" ,libtool)))
1484     (arguments
1485      `(#:phases
1486        (modify-phases %standard-phases
1487          (add-before 'build 'fix-permission
1488            (lambda _
1489              (chmod "lrcalc.maple.src" #o644)
1490              #t)))))
1491     (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
1492     (description "The Littlewood-Richardson Calculator (lrcalc) is a
1493 program designed to compute Littlewood-Richardson coefficients.  It computes
1494 single Littlewood-Richardson coefficients, products of Schur functions, or
1495 skew Schur functions.  In addition it computes products in the small quantum
1496 cohomology ring of a Grassmann variety.  The software package also includes
1497 a program that performs fast computation of the more general multiplicative
1498 structure constants of Schubert polynomials.")
1499     (license license:gpl2+)
1500     (home-page "http://sites.math.rutgers.edu/~asbuch/lrcalc/")))
1501
1502 (define-public iml
1503   (package
1504     (name "iml")
1505     (version "1.0.5")
1506     (source
1507      (origin
1508        (method url-fetch)
1509        (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
1510                            version ".tar.bz2"))
1511        (sha256
1512         (base32
1513          "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
1514     (build-system gnu-build-system)
1515     (inputs
1516      `(("gmp", gmp)
1517        ("cblas" ,openblas))) ; or any other BLAS library; the documentation
1518                              ; mentions ATLAS in particular
1519     (arguments
1520      `(#:configure-flags
1521        (list
1522         "--enable-shared"
1523         (string-append "--with-gmp-include="
1524                        (assoc-ref %build-inputs "gmp") "/include")
1525         (string-append "--with-gmp-lib="
1526                        (assoc-ref %build-inputs "gmp") "/lib")
1527         "--with-cblas=-lopenblas"
1528         (string-append "--with-cblas-include="
1529                        (assoc-ref %build-inputs "cblas") "/include")
1530         (string-append "--with-cblas-lib="
1531                        (assoc-ref %build-inputs "cblas") "/lib"))))
1532     (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
1533     (synopsis
1534      "Solver for systems of linear equations over the integers")
1535     (description
1536      "IML is a C library implementing algorithms for computing exact
1537 solutions to dense systems of linear equations over the integers.
1538 Currently, IML provides the following functionality:
1539
1540 @itemize
1541 @item Nonsingular rational system solving:
1542 compute the unique rational solution X to the system AX=B, where A and B
1543 are integer matrices, A nonsingular.
1544 @item Compute the right nullspace or kernel of an integer matrix.
1545 @item Certified linear system solving:
1546 compute a minimal denominator solution x to a system Ax=b, where b is an
1547 integer vector and A is an integer matrix with arbitrary shape and
1548 rank profile.
1549 @end itemize
1550
1551 In addition, IML provides some low level routines for a variety of mod p
1552 matrix operations: computing the row-echelon form, determinant, rank
1553 profile, and inverse of a mod p matrix. These mod p routines are not
1554 general purpose; they require that p satisfy some preconditions based on
1555 the dimension of the input matrix (usually p should be prime and should be
1556 no more than about 20 bits long).")
1557     (license license:bsd-3)))