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, 2020 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 ocaml)
  52   #:use-module (gnu packages perl)
  53   #:use-module (gnu packages pkg-config)
  54   #:use-module (gnu packages pulseaudio)
  55   #:use-module (gnu packages python)
  56   #:use-module (gnu packages python-xyz)
  57   #:use-module (gnu packages readline)
  58   #:use-module (gnu packages shells)
  59   #:use-module (gnu packages tex)
  60   #:use-module (gnu packages texinfo)
  61   #:use-module (gnu packages xiph)
  62   #:use-module (gnu packages xorg)
  63   #:use-module (guix build-system ant)
  64   #:use-module (guix build-system gnu)
  65   #:use-module (guix build-system cmake)
  66   #:use-module (guix build-system python)
  67   #:use-module (guix download)
  68   #:use-module (guix git-download)
  69   #:use-module (guix hg-download)
  70   #:use-module ((guix licenses) #:prefix license:)
  71   #:use-module (guix packages)
  72   #:use-module (guix utils))
  73
  74
  75 (define-public mpfrcx
  76   (package
  77    (name "mpfrcx")
  78    (version "0.6")
  79    (source (origin
  80             (method url-fetch)
  81             (uri (string-append
  82                   "http://www.multiprecision.org/downloads/mpfrcx-"
  83                   version ".tar.gz"))
  84             (sha256
  85              (base32
  86               "0gz5rma9al2jrifpknqkcnd9dkf8l05jcxy3s4ghwhd4y3h5dwia"))))
  87    (build-system gnu-build-system)
  88    (propagated-inputs
  89      `(("gmp" ,gmp)
  90        ("mpfr" ,mpfr)
  91        ("mpc"  ,mpc))) ; Header files are included by mpfrcx.h.
  92    (synopsis "Arithmetic of polynomials over arbitrary precision numbers")
  93    (description
  94     "Mpfrcx is a library for the arithmetic of univariate polynomials over
  95 arbitrary precision real (mpfr) or complex (mpc) numbers, without control
  96 on the rounding.  For the time being, only the few functions needed to
  97 implement the floating point approach to complex multiplication are
  98 implemented.  On the other hand, these comprise asymptotically fast
  99 multiplication routines such as Toom–Cook and the FFT.")
 100    (license license:lgpl3+)
 101    (home-page "http://www.multiprecision.org/mpfrcx/")))
 102
 103 (define-public gf2x
 104   (package
 105    (name "gf2x")
 106    (version "1.2")
 107    (source (origin
 108             (method url-fetch)
 109             (uri (string-append
 110                   "https://gforge.inria.fr/frs/download.php/file/36934/gf2x-"
 111                   version ".tar.gz"))
 112             (sha256
 113              (base32
 114               "0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1"))))
 115    (build-system gnu-build-system)
 116    (synopsis "Arithmetic of polynomials over binary finite fields")
 117    (description
 118     "The gf2x library provides arithmetic of polynomials over finite fields
 119 of characteristic 2.  It implements the multiplication, squaring and
 120 greatest common divisor operations.")
 121    (license license:gpl3+)
 122    (home-page "https://gforge.inria.fr/projects/gf2x/")))
 123
 124 (define-public cm
 125   (package
 126    (name "cm")
 127    (version "0.3.1")
 128    (source (origin
 129             (method url-fetch)
 130             (uri (string-append
 131                   "http://www.multiprecision.org/downloads/cm-"
 132                   version ".tar.gz"))
 133             (sha256
 134              (base32
 135               "0qq6b1kwb1byj8ws33ya5awq0ilkpm32037pi1l4cf2737fg9m42"))))
 136    (build-system gnu-build-system)
 137    (propagated-inputs
 138      `(("mpfrcx" ,mpfrcx)
 139        ("zlib" ,zlib))) ; Header files included from cm_common.h.
 140    (inputs
 141      `(("pari-gp"  ,pari-gp)))
 142    (synopsis "CM constructions for elliptic curves")
 143    (description
 144     "The CM software implements the construction of ring class fields of
 145 imaginary quadratic number fields and of elliptic curves with complex
 146 multiplication via floating point approximations.  It consists of libraries
 147 that can be called from within a C program and of executable command
 148 line applications.")
 149    (license license:gpl3+)
 150    (home-page "http://www.multiprecision.org/cm/")))
 151
 152 (define-public fplll
 153   (package
 154     (name "fplll")
 155     (version "5.3.3")
 156     (source (origin
 157               (method git-fetch)
 158               (uri (git-reference
 159                     (url "https://github.com/fplll/fplll")
 160                     (commit version)))
 161               (file-name (git-file-name name version))
 162               (sha256
 163                (base32
 164                 "06nyfidagp8pc2kfcw88ldgb2b1xm0a8z31n0sln7j72ihlmd8zj"))
 165               (patches (search-patches "fplll-std-fenv.patch"))))
 166     (build-system gnu-build-system)
 167     (native-inputs
 168      `(("autoconf" ,autoconf)
 169        ("automake" ,automake)
 170        ("libtool" ,libtool)
 171        ("pkg-config" ,pkg-config)))
 172     (propagated-inputs ; header files pulled in by fplll/defs.h
 173      `(("gmp" ,gmp)
 174        ("mpfr" ,mpfr)))
 175     (home-page "https://github.com/fplll/fplll")
 176     (synopsis "Library for LLL-reduction of euclidean lattices")
 177     (description
 178      "fplll contains implementations of several lattice algorithms.
 179 The implementation relies on floating-point orthogonalization, and LLL
 180 is central to the code, hence the name.
 181
 182 It includes implementations of floating-point LLL reduction
 183 algorithms, offering different speed/guarantees ratios.  It contains
 184 a @emph{wrapper} choosing the estimated best sequence of variants in
 185 order to provide a guaranteed output as fast as possible.  In the case
 186 of the wrapper, the succession of variants is oblivious to the user.
 187
 188 It includes an implementation of the BKZ reduction algorithm,
 189 including the BKZ-2.0 improvements (extreme enumeration
 190 pruning, pre-processing of blocks, early termination).  Additionally,
 191 Slide reduction and self dual BKZ are supported.
 192
 193 It also includes a floating-point implementation of the
 194 Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice
 195 vector.  For the same task, the GaussSieve algorithm is also available
 196 in fplll.  Finally, it contains a variant of the enumeration algorithm
 197 that computes a lattice vector closest to a given vector belonging to
 198 the real span of the lattice.")
 199     (license license:lgpl2.1+)))
 200
 201 (define-public python-fpylll
 202   (package
 203     (name "python-fpylll")
 204     (version "0.5.2")
 205     (source
 206      (origin
 207        ;; Pypi contains and older release, so we use a tagged release from
 208        ;; Github instead.
 209        (method git-fetch)
 210        (uri (git-reference
 211              (url "https://github.com/fplll/fpylll")
 212              (commit (string-append version "dev"))))
 213        (file-name (git-file-name name version))
 214        (sha256
 215         (base32
 216          "1a25iibihph626jl4wbs4b77xc4a2c4nfc2ypscf9wpani3dnhjf"))))
 217     (build-system python-build-system)
 218     (inputs
 219      `(("fplll" ,fplll)
 220        ("gmp" ,gmp)
 221        ("mpfr" ,mpfr)
 222        ("pari-gp" ,pari-gp)))
 223     (propagated-inputs
 224      `(("cysignals" ,python-cysignals)
 225        ("cython" ,python-cython)
 226        ("flake8" ,python-flake8)
 227        ("numpy" ,python-numpy)
 228        ("pytest" ,python-pytest)))
 229     (home-page "https://github.com/fplll/fpylll")
 230     (synopsis "Python interface for fplll")
 231     (description "fpylll is a Python wrapper for fplll.")
 232     (license license:gpl2+)))
 233
 234 (define-public pari-gp
 235   (package
 236     (name "pari-gp")
 237     (version "2.13.0")
 238     (source (origin
 239               (method url-fetch)
 240               (uri (string-append
 241                     "https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
 242                     version ".tar.gz"))
 243               (sha256
 244                (base32
 245                 "14xs90wrw8mbdx08hxlbhiahp6kgjq6yh27zjw7fvhfjx5nr84f8"))))
 246     (build-system gnu-build-system)
 247     (native-inputs
 248      `(("texlive" ,(texlive-union
 249                     (list texlive-amsfonts)))))
 250     (inputs `(("gmp" ,gmp)
 251               ("libx11" ,libx11)
 252               ("perl" ,perl)
 253               ("readline" ,readline)))
 254     (arguments
 255      '(#:make-flags '("all")
 256        #:test-target "dobench"
 257        #:phases
 258        (modify-phases %standard-phases
 259          (replace 'configure
 260            (lambda* (#:key outputs #:allow-other-keys)
 261              (invoke "./Configure"
 262                      (string-append "--prefix="
 263                                     (assoc-ref outputs "out"))))))))
 264     (synopsis "PARI/GP, a computer algebra system for number theory")
 265     (description
 266      "PARI/GP is a widely used computer algebra system designed for fast
 267 computations in number theory (factorisations, algebraic number theory,
 268 elliptic curves...), but it also contains a large number of other useful
 269 functions to compute with mathematical entities such as matrices,
 270 polynomials, power series, algebraic numbers, etc., and a lot of
 271 transcendental functions.
 272 PARI is also available as a C library to allow for faster computations.")
 273     (license license:gpl2+)
 274     (home-page "https://pari.math.u-bordeaux.fr/")))
 275
 276 (define-public gp2c
 277   (package
 278    (name "gp2c")
 279    (version "0.0.11pl4")
 280    (source (origin
 281             (method url-fetch)
 282             (uri (string-append
 283                   "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
 284                   version ".tar.gz"))
 285             (sha256
 286               (base32
 287                 "1cnnh7diqc97q76q5pyhpbljbhc0sz8mlrbqgiwi0sjkgh8iqsj0"))))
 288    (build-system gnu-build-system)
 289    (native-inputs `(("perl" ,perl)))
 290    (inputs `(("pari-gp" ,pari-gp)))
 291    (arguments
 292     '(#:configure-flags
 293       (list (string-append "--with-paricfg="
 294                            (assoc-ref %build-inputs "pari-gp")
 295                            "/lib/pari/pari.cfg"))))
 296    (synopsis "PARI/GP, a computer algebra system for number theory")
 297    (description
 298     "PARI/GP is a widely used computer algebra system designed for fast
 299 computations in number theory (factorisations, algebraic number theory,
 300 elliptic curves...), but it also contains a large number of other useful
 301 functions to compute with mathematical entities such as matrices,
 302 polynomials, power series, algebraic numbers, etc., and a lot of
 303 transcendental functions.
 304 PARI is also available as a C library to allow for faster computations.
 305
 306 GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
 307    (license license:gpl2)
 308    (home-page "https://pari.math.u-bordeaux.fr/")))
 309
 310 (define fplll-4-cmh
 311   (package
 312     (inherit fplll)
 313     (name "fplll")
 314     (version "4.0.4")
 315     (source
 316      (origin
 317        (method url-fetch)
 318        (uri (string-append
 319              "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
 320              version ".tar.gz"))
 321        (sha256
 322         (base32 "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))))
 323
 324 (define-public cmh
 325   (package
 326    (name "cmh")
 327    (version "1.0")
 328    (source (origin
 329             (method url-fetch)
 330             (uri (string-append
 331                   "https://gforge.inria.fr/frs/download.php/33497/cmh-"
 332                   version ".tar.gz"))
 333             (sha256
 334              (base32
 335               "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
 336    (build-system gnu-build-system)
 337    (inputs
 338      `(("gmp" ,gmp)
 339        ("mpfr" ,mpfr)
 340        ("mpc" ,mpc)
 341        ("mpfrcx" ,mpfrcx)
 342        ("fplll" ,fplll-4-cmh)
 343        ("pari-gp"  ,pari-gp)))
 344    (synopsis "Igusa class polynomial computations")
 345    (description
 346     "The CMH software computes Igusa (genus 2) class polynomials, which
 347 parameterize the CM points in the moduli space of 2-dimensional abelian
 348 varieties, i.e. Jacobians of hyperelliptic curves.
 349 It can also be used to compute theta constants at arbitrary
 350 precision.")
 351    (license license:gpl3+)
 352    (home-page
 353      "https://gitlab.inria.fr/cmh/cmh#cmh-computation-of-genus-2-class-polynomials")))
 354
 355 (define-public giac
 356   (package
 357     (name "giac")
 358     (version "1.6.0-31")
 359     (source
 360      (origin
 361        (method url-fetch)
 362        ;; "~parisse/giac" is not used because the maintainer regularly
 363        ;; overwrites the release tarball there, introducing a checksum
 364        ;; mismatch every time.  See
 365        ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
 366        (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
 367                            "~parisse/debian/dists/stable/main/source/"
 368                            "giac_" version ".tar.gz"))
 369        (sha256
 370         (base32 "1dr1y88sx2gzldn0zl6p8b1ngjjcmh89iv4kzyhi2cf74j3yw85m"))))
 371     (build-system gnu-build-system)
 372     (arguments
 373      `(#:modules ((ice-9 ftw)
 374                   (guix build utils)
 375                   (guix build gnu-build-system))
 376        #:phases
 377        (modify-phases %standard-phases
 378          (add-after 'unpack 'patch-bin-cp
 379            ;; Some Makefiles contain hard-coded "/bin/cp".
 380            (lambda _
 381              (substitute* (cons "micropython-1.12/xcas/Makefile"
 382                                 (find-files "doc" "^Makefile"))
 383                (("/bin/cp") (which "cp")))
 384              #t))
 385          (add-after 'unpack 'disable-failing-test
 386            ;; FIXME: Test failing.  Not sure why.
 387            (lambda _
 388              (substitute* "check/Makefile.in"
 389                (("chk_fhan11") ""))
 390              #t))
 391          (add-after 'install 'fix-doc
 392            (lambda* (#:key outputs #:allow-other-keys)
 393              (let ((out (assoc-ref outputs "out")))
 394                ;; Most French documentation has a non-commercial
 395                ;; license, so we need to remove it.
 396                (with-directory-excursion (string-append out "/share/giac/doc/fr")
 397                  (for-each delete-file-recursively
 398                            '("cascas" "casexo" "casgeo" "casrouge" "cassim"
 399                              "castor")))
 400                ;; Remove duplicate documentation in
 401                ;; "%out/share/doc/giac/", where Xcas does not expect
 402                ;; to find it.
 403                (delete-file-recursively (string-append out "/share/doc/giac"))
 404                #t)))
 405          (add-after 'install 'remove-unnecessary-executable
 406            (lambda* (#:key outputs #:allow-other-keys)
 407              (let ((out (assoc-ref outputs "out")))
 408                (delete-file (string-append out "/bin/xcasnew"))
 409                #t))))))
 410     (inputs
 411      ;; TODO: Add libnauty, unbundle "libmicropython.a".
 412      `(("fltk" ,fltk)
 413        ("glpk" ,glpk)
 414        ("gmp" ,gmp)
 415        ("gsl" ,gsl)
 416        ("lapack" ,lapack)
 417        ("libao" ,ao)
 418        ("libjpeg" ,libjpeg-turbo)
 419        ("libpng" ,libpng)
 420        ("libsamplerate" ,libsamplerate)
 421        ("libx11" ,libx11)
 422        ("libxinerama" ,libxinerama)
 423        ("libxft" ,libxft)
 424        ("libxt" ,libxt)
 425        ("mesa" ,mesa)
 426        ("mpfi" ,mpfi)
 427        ("mpfr" ,mpfr)
 428        ("ntl" ,ntl)
 429        ("perl" ,perl)
 430        ("pari-gp" ,pari-gp)
 431        ("tcsh" ,tcsh)))
 432     (native-inputs
 433      `(("bison" ,bison)
 434        ("flex" ,flex)
 435        ("hevea" ,hevea)
 436        ("python" ,python-wrapper)
 437        ("readline" ,readline)
 438        ("texlive" ,texlive-tiny)))
 439     (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
 440     (synopsis "Computer algebra system")
 441     (description
 442      "Giac/Xcas is a computer algebra system.  It has a compatibility mode for
 443 maple, mupad and the TI89.  It is available as a standalone program (graphic
 444 or text interfaces) or as a C++ library.")
 445     (license license:gpl3+)))
 446
 447 (define-public flint
 448   (package
 449    (name "flint")
 450    (version "2.6.3")
 451    (source
 452     (origin
 453       (method url-fetch)
 454       (uri (string-append "http://flintlib.org/flint-" version ".tar.gz"))
 455       (sha256
 456        (base32 "1qrf6hzbbmg7mhkhbb0bab8z2xpdnba5cj4kmmf72lzs0457a6nf"))))
 457    (build-system gnu-build-system)
 458    (inputs
 459     `(("ntl" ,ntl)))
 460    (propagated-inputs
 461     `(("gmp" ,gmp)
 462       ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
 463    (arguments
 464     `(#:parallel-tests? #f              ; seems to be necessary on arm
 465       #:phases
 466        (modify-phases %standard-phases
 467          (add-before 'configure 'newer-c++
 468            (lambda _
 469              (substitute* "configure"
 470                (("-ansi") ""))
 471              #t))
 472          (replace 'configure
 473            (lambda* (#:key inputs outputs #:allow-other-keys)
 474              (let ((out (assoc-ref outputs "out"))
 475                    (gmp (assoc-ref inputs "gmp"))
 476                    (mpfr (assoc-ref inputs "mpfr"))
 477                    (ntl (assoc-ref inputs "ntl")))
 478                ;; Do not pass "--enable-fast-install", which makes the
 479                ;; homebrew configure process fail.
 480                (invoke "./configure"
 481                        (string-append "--prefix=" out)
 482                        (string-append "--with-gmp=" gmp)
 483                        (string-append "--with-mpfr=" mpfr)
 484                        (string-append "--with-ntl=" ntl))
 485                #t))))))
 486    (synopsis "Fast library for number theory")
 487    (description
 488     "FLINT is a C library for number theory.  It supports arithmetic
 489 with numbers, polynomials, power series and matrices over many base
 490 rings, including multiprecision integers and rationals, integers
 491 modulo n, p-adic numbers, finite fields (prime and non-prime order)
 492 and real and complex numbers (via the Arb extension library).
 493
 494 Operations that can be performed include conversions, arithmetic,
 495 GCDs, factoring, solving linear systems, and evaluating special
 496 functions.  In addition, FLINT provides various low-level routines for
 497 fast arithmetic.")
 498    (license license:lgpl2.1+)
 499    (home-page "http://flintlib.org/")))
 500
 501 (define-public arb
 502   (package
 503     (name "arb")
 504     (version "2.18.1")
 505     (source (origin
 506               (method git-fetch)
 507               (uri (git-reference
 508                     (url "https://github.com/fredrik-johansson/arb")
 509                     (commit version)))
 510               (file-name (git-file-name name version))
 511               (sha256
 512                (base32
 513                 "15fx3dcbzgwddw9p1nysmx0dbh058afv5m8cj5pdjkcmcl7kw7z9"))))
 514     (build-system gnu-build-system)
 515     (propagated-inputs
 516      `(("flint" ,flint)))               ; flint.h is included by arf.h
 517     (inputs
 518      `(("gmp" ,gmp)
 519        ("mpfr" ,mpfr)))
 520     (arguments
 521      `(#:phases
 522        (modify-phases %standard-phases
 523          (replace 'configure
 524            (lambda* (#:key inputs outputs #:allow-other-keys)
 525              (let ((out (assoc-ref outputs "out"))
 526                    (flint (assoc-ref inputs "flint"))
 527                    (gmp (assoc-ref inputs "gmp"))
 528                    (mpfr (assoc-ref inputs "mpfr")))
 529                ;; Do not pass "--enable-fast-install", which makes the
 530                ;; homebrew configure process fail.
 531                (invoke "./configure"
 532                        (string-append "--prefix=" out)
 533                        (string-append "--with-flint=" flint)
 534                        (string-append "--with-gmp=" gmp)
 535                        (string-append "--with-mpfr=" mpfr))))))))
 536     (synopsis "Arbitrary precision floating-point ball arithmetic")
 537     (description
 538      "Arb is a C library for arbitrary-precision floating-point ball
 539 arithmetic.  It supports efficient high-precision computation with
 540 polynomials, power series, matrices and special functions over the
 541 real and complex numbers, with automatic, rigorous error control.")
 542     (license license:lgpl2.1+)
 543     (home-page "http://arblib.org")))
 544
 545 (define-public python-flint
 546   (package
 547     (name "python-flint")
 548     (version "0.3.0")
 549     (source (origin
 550               (method git-fetch)
 551               (uri (git-reference
 552                     (url "https://github.com/fredrik-johansson/python-flint")
 553                     (commit version)))
 554               (file-name (git-file-name name version))
 555               (sha256
 556                (base32
 557                 "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
 558               (patches (search-patches "python-flint-includes.patch"))))
 559     (build-system python-build-system)
 560     (native-inputs
 561      `(("python-cython" ,python-cython)))
 562     (propagated-inputs
 563      `(("python-numpy" ,python-numpy)))
 564     (inputs
 565      `(("arb" ,arb)
 566        ("flint" ,flint)))
 567     (synopsis "Python module wrapping ARB and FLINT")
 568     (description
 569      "Python-flint is a Python extension module wrapping FLINT
 570 (Fast Library for Number Theory) and Arb (arbitrary-precision ball
 571 arithmetic).  It supports integers, rationals, modular integers,
 572 real and complex ball arithmetic, polynomials and matrices over all
 573 these types and other mathematical functions.")
 574     (license license:expat)
 575     (home-page "http://fredrikj.net/python-flint/")))
 576
 577 (define-public ntl
 578   (package
 579    (name "ntl")
 580    (version "11.4.3")
 581    (source (origin
 582             (method url-fetch)
 583             (uri (string-append "https://shoup.net/ntl/ntl-"
 584                                 version ".tar.gz"))
 585             (sha256
 586              (base32
 587               "1lisp3064rch3jaa2wrhy1s9kll7i3ka3d0y6lj6l3l4ckfcrhdp"))
 588             (modules '((guix build utils)))
 589             (snippet
 590              '(begin
 591                 (delete-file-recursively "src/libtool-origin")
 592                 #t))))
 593    (build-system gnu-build-system)
 594    (native-inputs
 595     `(("libtool" ,libtool)
 596       ("perl" ,perl))) ; for configuration
 597    (inputs
 598     `(("gmp" ,gmp)
 599       ("gf2x" ,gf2x)))
 600    (arguments
 601     `(#:phases
 602       (modify-phases %standard-phases
 603         (replace 'configure
 604          (lambda* (#:key inputs outputs #:allow-other-keys)
 605            (chdir "src")
 606            (invoke "./configure"
 607                     (string-append "PREFIX=" (assoc-ref outputs "out"))
 608                     (string-append "LIBTOOL=" (assoc-ref inputs "libtool") "/bin/libtool")
 609                     ;; set the library prefixes explicitly so that they get
 610                     ;; embedded in the .la file
 611                     (string-append "GMP_PREFIX=" (assoc-ref inputs "gmp"))
 612                     (string-append "GF2X_PREFIX=" (assoc-ref inputs "gf2x"))
 613                     ;; Do not build especially for the build machine.
 614                     "NATIVE=off"
 615                     "NTL_GF2X_LIB=on"
 616                     "SHARED=on"))))))
 617    (synopsis "C++ library for number theory")
 618    (description
 619     "NTL is a C++ library providing data structures and algorithms
 620 for manipulating signed, arbitrary length integers, and for vectors,
 621 matrices, and polynomials over the integers and over finite fields.")
 622    (license license:gpl2+)
 623    (home-page "https://shoup.net/ntl/")))
 624
 625 (define-public singular
 626   (package
 627    (name "singular")
 628    (version "4.1.3p2")
 629    (source
 630     (origin
 631       (method url-fetch)
 632       (uri
 633        (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
 634                       "Singular/SOURCES/"
 635                       (string-join
 636                        (string-split
 637                         (string-trim-right version #\p
 638                                            0 (1- (string-length version)))
 639                         #\.) "-")
 640                       "/singular-" version ".tar.gz"))
 641              (sha256 (base32
 642                       "1524yrni7gh0hir5ckridq671q5s6avfjdsdyahj51kzdl3wcypf"))))
 643    (build-system gnu-build-system)
 644    (native-inputs
 645     `(("doxygen" ,doxygen)
 646       ("graphviz" ,graphviz)
 647       ("perl" ,perl)))
 648    (inputs
 649     `(("cddlib" ,cddlib)
 650       ("gmp" ,gmp)
 651       ("flint" ,flint)
 652       ("mpfr" ,mpfr)
 653       ("ntl" ,ntl)
 654       ("python" ,python-2)
 655       ("readline" ,readline)))
 656    (arguments
 657     `(#:configure-flags
 658       (list (string-append "--with-ntl="
 659                            (assoc-ref %build-inputs "ntl")))))
 660    (synopsis "Computer algebra system for polynomial computations")
 661    (description
 662     "Singular is a computer algebra system for polynomial computations,
 663 with special emphasis on commutative and non-commutative algebra, algebraic
 664 geometry and singularity theory.")
 665    ;; Singular itself is dual licensed gpl2 or gpl3, but some of the
 666    ;; libraries with which it links are licensed under lgpl3+, so the
 667    ;; combined work becomes gpl3. See COPYING in the source code.
 668    (license license:gpl3)
 669    (home-page "http://www.singular.uni-kl.de/index.php")))
 670
 671 (define-public gmp-ecm
 672   (package
 673    (name "gmp-ecm")
 674    (version "7.0.4")
 675    (source (origin
 676              (method url-fetch)
 677              ;; Use the ‘Latest version’ link for a stable URI across releases.
 678              (uri (string-append "https://gforge.inria.fr/frs/download.php/"
 679                                  "latestfile/160/ecm-" version ".tar.gz"))
 680              (sha256 (base32
 681                       "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"))))
 682    (build-system gnu-build-system)
 683    (inputs
 684     `(("gmp" ,gmp)))
 685    (arguments
 686     `(#:configure-flags '("--enable-shared"
 687                           ;; Disable specific assembly routines, which depend
 688                           ;; on the subarchitecture of the build machine,
 689                           ;; and use gmp instead.
 690                           "--disable-asm-redc")))
 691    (synopsis "Integer factorization library using the elliptic curve method")
 692    (description
 693     "GMP-ECM factors integers using the elliptic curve method (ECM) as well
 694 as the P-1 and P+1 algorithms.  It provides a library and a stand-alone
 695 binary.")
 696    ;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+,
 697    ;; so the combined work is under gpl3+.
 698    (license license:gpl3+)
 699    (home-page "http://ecm.gforge.inria.fr/")))
 700
 701 (define-public bc
 702   (package
 703     (name "bc")
 704     (version "1.07.1")
 705     (source (origin
 706              (method url-fetch)
 707              (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
 708              (sha256
 709               (base32
 710                "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))
 711              (patches (search-patches "bc-fix-cross-compilation.patch"))))
 712     (build-system gnu-build-system)
 713     (native-inputs
 714      `(("automake" ,automake)
 715        ("autoconf" ,autoconf)
 716        ("ed" ,ed)
 717        ("flex" ,flex)
 718        ("texinfo" ,texinfo)))
 719     (arguments
 720      '(#:configure-flags
 721        (list "--with-readline")
 722        #:phases
 723        (modify-phases %standard-phases
 724          (add-after 'unpack 'autogen
 725            (lambda _
 726              (invoke "autoreconf" "-vif"))))))
 727     (home-page "https://www.gnu.org/software/bc/")
 728     (synopsis "Arbitrary precision numeric processing language")
 729     (description
 730      "bc is an arbitrary precision numeric processing language.  It includes
 731 an interactive environment for evaluating mathematical statements.  Its
 732 syntax is similar to that of C, so basic usage is familiar.  It also includes
 733 \"dc\", a reverse-polish calculator.")
 734     (license license:gpl2+)))
 735
 736 ;; The original kiss-fft does not have a complete build system and does not
 737 ;; build any shared libraries.  This is a fork used by Extempore.
 738 (define-public kiss-fft-for-extempore
 739   (package
 740     (name "kiss-fft-for-extempore")
 741     (version "1.3.0")
 742     (source (origin
 743               (method git-fetch)
 744               (uri (git-reference
 745                     (url "https://github.com/extemporelang/kiss_fft")
 746                     (commit version)))
 747               (file-name (git-file-name name version))
 748               (sha256
 749                (base32
 750                 "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
 751     (build-system cmake-build-system)
 752     (arguments `(#:tests? #f)) ; no tests included
 753     ;; Extempore refuses to build on architectures other than x86_64
 754     (supported-systems '("x86_64-linux"))
 755     (home-page "https://github.com/extemporelang/kiss_fft")
 756     (synopsis "Mixed-radix Fast Fourier Transform")
 757     (description
 758      "Kiss FFT attempts to be a reasonably efficient, moderately useful FFT
 759 that can use fixed or floating data types and can easily be incorporated into
 760 a C program.")
 761     (license license:bsd-3)))
 762
 763 (define-public fftw
 764   (package
 765     (name "fftw")
 766     (version "3.3.8")
 767     (source (origin
 768              (method url-fetch)
 769              (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
 770                                  version".tar.gz"))
 771              (sha256
 772               (base32
 773                "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
 774     (build-system gnu-build-system)
 775     (arguments
 776      `(#:configure-flags
 777        '("--enable-shared" "--enable-openmp" "--enable-threads"
 778          ,@(let ((system (or (%current-target-system) (%current-system))))
 779              ;; Enable SIMD extensions for codelets.  See details at:
 780              ;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>.
 781              (cond
 782               ((string-prefix? "x86_64" system)
 783                '("--enable-sse2" "--enable-avx" "--enable-avx2"
 784                  "--enable-avx512" "--enable-avx-128-fma"))
 785               ((string-prefix? "i686" system)
 786                '("--enable-sse2"))
 787               ((string-prefix? "aarch64" system)
 788                ;; Note that fftw supports NEON on 32-bit ARM only when
 789                ;; compiled for single-precision.
 790                '("--enable-neon"))
 791               (else
 792                '())))
 793          ;; By default '-mtune=native' is used.  However, that may cause the
 794          ;; use of ISA extensions (e.g. AVX) that are not necessarily
 795          ;; available on the user's machine when that package is built on a
 796          ;; different machine.
 797          "ax_cv_c_flags__mtune_native=no")))
 798     (native-inputs `(("perl" ,perl)))
 799     (home-page "http://fftw.org")
 800     (synopsis "Computing the discrete Fourier transform")
 801     (description
 802      "FFTW is a C subroutine library for computing the discrete Fourier
 803 transform (DFT) in one or more dimensions, of arbitrary input size, and of
 804 both real and complex data (as well as of even/odd data---i.e. the discrete
 805 cosine/ sine transforms or DCT/DST).")
 806     (license license:gpl2+)))
 807
 808 (define-public fftwf
 809   (package (inherit fftw)
 810     (name "fftwf")
 811     (arguments
 812      (substitute-keyword-arguments (package-arguments fftw)
 813        ((#:configure-flags fftw-configure-flags)
 814         `(cons* "--enable-single"
 815                 ,@(if (string-prefix? "arm" (or (%current-target-system)
 816                                                 (%current-system)))
 817                       ;; fftw supports NEON on 32-bit ARM only when compiled
 818                       ;; for single-precision, so add it here.
 819                       '("--enable-neon")
 820                       '())
 821                 ,fftw-configure-flags))))
 822     (description
 823      (string-append (package-description fftw)
 824                     "  Single-precision version."))))
 825
 826 (define-public fftw-openmpi
 827   (package (inherit fftw)
 828     (name "fftw-openmpi")
 829     (inputs
 830      `(("openmpi" ,openmpi)
 831        ,@(package-inputs fftw)))
 832     (arguments
 833      (substitute-keyword-arguments (package-arguments fftw)
 834        ((#:configure-flags cf)
 835         `(cons "--enable-mpi" ,cf))
 836        ((#:phases phases '%standard-phases)
 837         `(modify-phases ,phases
 838            (add-before 'check 'mpi-setup
 839              ,%openmpi-setup)))))
 840     (description
 841      (string-append (package-description fftw)
 842                     "  With OpenMPI parallelism support."))))
 843
 844 (define-public java-la4j
 845   (package
 846     (name "java-la4j")
 847     (version "0.6.0")
 848     (source (origin
 849               (method git-fetch)
 850               (uri (git-reference
 851                     (url "https://github.com/vkostyukov/la4j")
 852                     (commit version)))
 853               (file-name (string-append name "-" version "-checkout"))
 854               (sha256
 855                (base32
 856                 "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
 857     (build-system ant-build-system)
 858     (arguments
 859      `(#:jar-name "la4j.jar"
 860        #:jdk ,icedtea-8
 861        #:test-exclude (list "**/Abstract*.java"
 862                             "**/MatrixTest.java"
 863                             "**/DenseMatrixTest.java"
 864                             "**/SparseMatrixTest.java"
 865                             "**/VectorTest.java"
 866                             "**/SparseVectorTest.java"
 867                             "**/DenseVectorTest.java")))
 868     (native-inputs
 869      `(("java-junit" ,java-junit)
 870        ("java-hamcrest-core" ,java-hamcrest-core)))
 871     (home-page "http://la4j.org/")
 872     (synopsis "Java library that provides Linear Algebra primitives and algorithms")
 873     (description "The la4j library is a Java library that provides Linear
 874 Algebra primitives (matrices and vectors) and algorithms.  The key features of
 875 the la4j library are:
 876
 877 @itemize
 878 @item No dependencies and tiny size
 879 @item Fluent object-oriented/functional API
 880 @item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
 881 @item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
 882 @item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
 883 @item MatrixMarket/CSV IO formats support for matrices and vectors
 884 @end itemize\n")
 885     (license license:asl2.0)))
 886
 887 (define-public java-jlargearrays
 888   (package
 889     (name "java-jlargearrays")
 890     (version "1.6")
 891     (source (origin
 892               (method url-fetch)
 893               (uri (string-append "https://repo1.maven.org/maven2/"
 894                                   "pl/edu/icm/JLargeArrays/"
 895                                   version "/JLargeArrays-" version
 896                                   "-sources.jar"))
 897               (file-name (string-append name "-" version ".jar"))
 898               (sha256
 899                (base32
 900                 "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
 901     (build-system ant-build-system)
 902     (arguments
 903      `(#:jar-name "jlargearrays.jar"
 904        #:tests? #f ; tests are not included in the release archive
 905        #:jdk ,icedtea-8))
 906     (propagated-inputs
 907      `(("java-commons-math3" ,java-commons-math3)))
 908     (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
 909     (synopsis "Library of one-dimensional arrays that can store up to 263 elements")
 910     (description "JLargeArrays is a Java library of one-dimensional arrays
 911 that can store up to 263 elements.")
 912     (license license:bsd-2)))
 913
 914 (define-public java-jtransforms
 915   (package
 916     (name "java-jtransforms")
 917     (version "3.1")
 918     (source (origin
 919               (method url-fetch)
 920               (uri (string-append "https://repo1.maven.org/maven2/"
 921                                   "com/github/wendykierp/JTransforms/"
 922                                   version "/JTransforms-" version "-sources.jar"))
 923               (sha256
 924                (base32
 925                 "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
 926     (build-system ant-build-system)
 927     (arguments
 928      `(#:jar-name "jtransforms.jar"
 929        #:tests? #f ; tests are not included in the release archive
 930        #:jdk ,icedtea-8))
 931     (propagated-inputs
 932      `(("java-commons-math3" ,java-commons-math3)
 933        ("java-jlargearrays" ,java-jlargearrays)))
 934     (home-page "https://github.com/wendykierp/JTransforms")
 935     (synopsis "Multithreaded FFT library written in pure Java")
 936     (description "JTransforms is a multithreaded FFT library written in pure
 937 Java.  Currently, four types of transforms are available: @dfn{Discrete
 938 Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
 939 Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
 940     (license license:bsd-2)))
 941
 942 (define-public lmfit
 943   (package
 944     (name "lmfit")
 945     (version "8.2.2")
 946     (source (origin
 947               (method git-fetch)
 948               (uri (git-reference
 949                     (url "https://jugit.fz-juelich.de/mlz/lmfit.git")
 950                     (commit (string-append "v" version))))
 951               (file-name (git-file-name name version))
 952               (sha256
 953                (base32
 954                 "00bch77a6qgnw6vzsjn2a42n8n683ih3xm0wpr454jxa15hw78vf"))))
 955     (build-system cmake-build-system)
 956     (native-inputs
 957      `(("perl" ,perl)))                   ; for pod2man
 958     (home-page "https://jugit.fz-juelich.de/mlz/lmfit")
 959     (synopsis "Levenberg-Marquardt minimization and least-squares fitting")
 960     (description "lmfit is a C library for Levenberg-Marquardt least-squares
 961 minimization and curve fitting.  It is mature code, based on decades-old
 962 algorithms from the FORTRAN library MINPACK.")
 963     (license license:bsd-2)))
 964
 965 (define-public symengine
 966   (package
 967     (name "symengine")
 968     (version "0.6.0")
 969     (source
 970      (origin
 971        (method git-fetch)
 972        (uri (git-reference
 973              (url "https://github.com/symengine/symengine")
 974              (commit (string-append "v" version))))
 975        (file-name (git-file-name name version))
 976        (sha256
 977         (base32 "129iv9maabmb42ylfdv0l0g94mcbf3y4q3np175008rcqdr8z6h1"))))
 978     (build-system cmake-build-system)
 979     (arguments
 980      '(#:configure-flags
 981        ;; These are the suggested build options in the README.
 982        '("-DCMAKE_BUILD_TYPE=Release"
 983          "-DWITH_GMP=on"
 984          "-DWITH_MPFR=on"
 985          "-DWITH_MPC=on"
 986          "-DINTEGER_CLASS=flint"
 987          "-DWITH_LLVM=on"
 988          "-DWITH_SYMENGINE_THREAD_SAFE=on"
 989          "-DBUILD_SHARED_LIBS=on")))    ;also build libsymengine
 990     (native-inputs
 991      `(("llvm" ,llvm)))
 992     (inputs
 993      `(("flint" ,flint)
 994        ("gmp" ,gmp)
 995        ("mpc" ,mpc)
 996        ("mpfr" ,mpfr)))
 997     (home-page "https://github.com/symengine/symengine")
 998     (synopsis "Fast symbolic manipulation library")
 999     (description
1000      "SymEngine is a standalone fast C++ symbolic manipulation library.
1001 Optional thin wrappers allow usage of the library from other languages.")
1002     (license (list license:expat        ;SymEngine
1003                    license:bsd-3))))    ;3rd party code
1004
1005 (define-public eigen
1006   (package
1007     (name "eigen")
1008     (version "3.3.7")
1009     (source (origin
1010               (method url-fetch)
1011               (uri (list
1012                      (string-append "https://bitbucket.org/eigen/eigen/get/"
1013                                     version ".tar.bz2")
1014                      (string-append "mirror://debian/pool/main/e/eigen3/eigen3_"
1015                                     version ".orig.tar.bz2")))
1016               (sha256
1017                (base32
1018                 "1km3fyfzyqfdvmnl79drps3fjwnz3zbh0c7l34mfbqyvvs8cy4wz"))
1019               (file-name (string-append name "-" version ".tar.bz2"))
1020               (patches (search-patches "eigen-stabilise-sparseqr-test.patch"))
1021               (modules '((guix build utils)))
1022               (snippet
1023                ;; There are 3 test failures in the "unsupported" directory,
1024                ;; but maintainers say it's a known issue and it's unsupported
1025                ;; anyway, so just skip them.
1026                '(begin
1027                   (substitute* "unsupported/CMakeLists.txt"
1028                     (("add_subdirectory\\(test.*")
1029                      "# Do not build the tests for unsupported features.\n"))
1030                   #t))))
1031     (build-system cmake-build-system)
1032     (arguments
1033      '(;; Turn off debugging symbols to save space.
1034        #:build-type "Release"
1035
1036        #:phases (modify-phases %standard-phases
1037                   (replace 'check
1038                     (lambda _
1039                       (let* ((cores  (parallel-job-count))
1040                              (dash-j (format #f "-j~a" cores)))
1041                         (setenv "EIGEN_SEED" "1") ;for reproducibility
1042                         ;; First build the tests, in parallel.  See
1043                         ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
1044                         (invoke "make" "buildtests" dash-j)
1045
1046                         ;; Then run 'CTest' with -V so we get more
1047                         ;; details upon failure.
1048                         (invoke "ctest" "-V" dash-j)))))))
1049     (home-page "https://eigen.tuxfamily.org")
1050     (synopsis "C++ template library for linear algebra")
1051     (description
1052      "Eigen is a C++ template library for linear algebra: matrices, vectors,
1053 numerical solvers, and related algorithms.  It provides an elegant API based
1054 on \"expression templates\".  It is versatile: it supports all matrix sizes,
1055 all standard numeric types, various matrix decompositions and geometry
1056 features, and more.")
1057
1058     ;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3.
1059     ;; See 'COPYING.README' for details.
1060     (license license:mpl2.0)))
1061
1062 (define-public eigen-for-tensorflow
1063   (let ((changeset "fd6845384b86")
1064         (revision "1"))
1065     (package (inherit eigen)
1066       (name "eigen-for-tensorflow")
1067       (version (string-append "3.3.5-" revision "." changeset))
1068       (source (origin
1069                 (method hg-fetch)
1070                 (uri (hg-reference
1071                       (url "https://bitbucket.org/eigen/eigen")
1072                       (changeset changeset)))
1073                 (sha256
1074                  (base32
1075                   "12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5"))
1076                 (file-name (string-append name "-" version "-checkout"))
1077                 (modules '((guix build utils)))
1078                 (snippet
1079                  ;; There are 3 test failures in the "unsupported" directory,
1080                  ;; but maintainers say it's a known issue and it's unsupported
1081                  ;; anyway, so just skip them.
1082                  '(begin
1083                     (substitute* "unsupported/CMakeLists.txt"
1084                       (("add_subdirectory\\(test.*")
1085                        "# Do not build the tests for unsupported features.\n"))
1086                     #t)))))))
1087
1088 (define-public xtensor
1089   (package
1090     (name "xtensor")
1091     (version "0.20.10")
1092     (source (origin
1093               (method git-fetch)
1094               (uri (git-reference
1095                     (url "https://github.com/xtensor-stack/xtensor")
1096                     (commit version)))
1097               (sha256
1098                (base32
1099                 "1fmv2hpx610xwhxrndfsfvlbqfyk4l3gi5q5d7pa9m82kblxjj9l"))
1100               (file-name (git-file-name name version))))
1101     (build-system cmake-build-system)
1102     (native-inputs
1103      `(("googletest" ,googletest)
1104        ("xtl" ,xtl)))
1105     (arguments
1106      `(#:configure-flags
1107        '("-DBUILD_TESTS=ON")
1108        #:test-target "xtest"))
1109     (home-page "https://xtensor.readthedocs.io/en/latest/")
1110     (synopsis "C++ tensors with broadcasting and lazy computing")
1111     (description "xtensor is a C++ library meant for numerical analysis with
1112 multi-dimensional array expressions.
1113
1114 xtensor provides:
1115 @itemize
1116 @item an extensible expression system enabling lazy broadcasting.
1117 @item an API following the idioms of the C++ standard library.
1118 @item tools to manipulate array expressions and build upon xtensor.
1119 @end itemize")
1120     (license license:bsd-3)))
1121
1122 (define-public gap
1123   (package
1124     (name "gap")
1125     (version "4.11.0")
1126     (source
1127      (origin
1128        (method url-fetch)
1129        (uri (string-append "https://files.gap-system.org/gap-"
1130                            (version-major+minor version)
1131                            "/tar.bz2/gap-"
1132                            version
1133                            ".tar.bz2"))
1134        (sha256
1135         (base32 "00l6hvy4iggnlrib4vp805sxdm3j7n3hzpv5zs9hbiiavh80l1xz"))
1136        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
1137        (snippet
1138         '(begin
1139            ;; Delete the external gmp and zlib libraries
1140            ;; and a subdirectory not needed for our build.
1141            (for-each delete-file-recursively
1142                      '("extern" "hpcgap"))
1143            ;; Delete a failing test.
1144            ;; FIXME: This might be fixed in the next release, see
1145            ;; https://github.com/gap-system/gap/issues/3292
1146            (delete-file "tst/testinstall/dir.tst")
1147            ;; Delete all packages except for a fixed list,
1148            ;; given by their names up to version numbers.
1149            (with-directory-excursion "pkg"
1150              (for-each delete-file-recursively
1151                (lset-difference
1152                  (lambda (all keep) (string-prefix? keep all))
1153                  (scandir ".")
1154                  '("." ".."
1155                    ;; Necessary packages.
1156                    "GAPDoc-"
1157                    "primgrp-"
1158                    "SmallGrp-"   ; artistic2.0
1159                    "transgrp"    ; artistic2.0 for data,
1160                                  ; gpl2 or gpl3 for code
1161                    ;; Recommended package.
1162                    "io-"         ; gpl3+
1163                    ;; Optional packages, searched for at start,
1164                    ;; and their depedencies.
1165                    "alnuth-"
1166                    "autpgrp-"
1167                    "crisp-"      ; bsd-2
1168                    "ctbllib"     ; gpl3+, clarified in the next release;
1169                                  ; see
1170                                  ; http://www.math.rwth-aachen.de/~Thomas.Breuer/ctbllib/README.md
1171                    "FactInt-"
1172                    "fga"
1173                    "irredsol-"   ; bsd-2
1174                    "laguna-"
1175                    "polenta-"
1176                    "polycyclic-"
1177                    "radiroot-"
1178                    "resclasses-"
1179                    "sophus-"
1180                    "tomlib-"
1181                    "utils-"))))
1182            #t))))
1183     (build-system gnu-build-system)
1184     (inputs
1185      `(("gmp" ,gmp)
1186        ("readline" ,readline)
1187        ("zlib" ,zlib)))
1188     (arguments
1189      `(#:modules ((ice-9 ftw)
1190                   (srfi srfi-26)
1191                   (guix build gnu-build-system)
1192                   (guix build utils))
1193        #:phases
1194        (modify-phases %standard-phases
1195          (add-after 'build 'build-packages
1196            ;; Compile all packages that have not been deleted by the
1197            ;; code snippet above.
1198            (lambda _
1199              (setenv "CONFIG_SHELL" (which "bash"))
1200              (with-directory-excursion "pkg"
1201                (invoke "../bin/BuildPackages.sh")
1202              #t)))
1203          (add-after 'build-packages 'build-doc
1204            ;; The documentation is bundled, but we create it from source.
1205            (lambda _
1206              (with-directory-excursion "doc"
1207                (invoke "./make_doc"))
1208              #t))
1209          (replace 'install
1210            (lambda* (#:key outputs #:allow-other-keys)
1211              (let* ((out (assoc-ref outputs "out"))
1212                     (bin (string-append out "/bin"))
1213                     (prog (string-append bin "/gap"))
1214                     (prog-real (string-append bin "/.gap-real"))
1215                     (share (string-append out "/share/gap")))
1216                ;; Install only the gap binary; the gac compiler is left
1217                ;; for maybe later. "Wrap" it in a shell script that calls
1218                ;; the binary with the correct parameter.
1219                ;; The make target install-bin is supposed to do that, but
1220                ;; is not currently working.
1221                (mkdir-p bin)
1222                (copy-file "gap" prog-real)
1223                (call-with-output-file prog
1224                  (lambda (port)
1225                    (format port
1226                            "#!~a~%exec ~a -l ~a \"$@\"~%"
1227                            (which "bash")
1228                            prog-real
1229                            share)))
1230                (chmod prog #o755)
1231                ;; Install the headers and library, which are needed by Sage.
1232                (invoke "make" "install-headers")
1233                (invoke "make" "install-libgap")
1234                ;; Remove information on the build directory from sysinfo.gap.
1235                (substitute* "sysinfo.gap"
1236                  (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
1237                  (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
1238                  (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
1239                (invoke "make" "install-gaproot")
1240                ;; Copy the directory of compiled packages; the make target
1241                ;; install-pkg is currently empty.
1242                (copy-recursively "pkg" (string-append share "/pkg")))
1243              #t)))))
1244     (home-page "https://www.gap-system.org/")
1245     (synopsis
1246      "System for computational group theory")
1247     (description
1248      "GAP is a system for computational discrete algebra, with particular
1249 emphasis on computational group theory.  It provides a programming language,
1250 a library of thousands of functions implementing algebraic algorithms
1251 written in the GAP language as well as large data libraries of algebraic
1252 objects.")
1253     ;; Some packages have different licenses (effectively forcing the
1254     ;; combined work to be licensed as gpl3+); if this is the case, this
1255     ;; is mentioned above next to their name.
1256     ;; Some packages have no license mentioned explicitly; supposedly this
1257     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
1258     ;; safe side, we drop them for now.
1259     (license license:gpl2+)))
1260
1261 (define-public givaro
1262   (package
1263     (name "givaro")
1264     (version "4.1.1")
1265     (source (origin
1266               (method git-fetch)
1267               (uri (git-reference
1268                     (url "https://github.com/linbox-team/givaro")
1269                     (commit (string-append "v" version))))
1270               (file-name (git-file-name name version))
1271               (sha256
1272                (base32
1273                 "11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
1274     (build-system gnu-build-system)
1275     (native-inputs
1276      `(("autoconf" ,autoconf)
1277        ("automake" ,automake)
1278        ("libtool" ,libtool)))
1279     (propagated-inputs
1280      `(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
1281     (synopsis "Algebraic computations with exact rings and fields")
1282     (description
1283      "Givaro is a C++ library implementing the basic arithmetic of various
1284 algebraic objects: prime fields, extension fields, finite fields, finite
1285 rings, polynomials, algebraic numbers, arbitrary precision integers and
1286 rationals (C++ wrappers over gmp), fixed precision integers.  It also
1287 provides data-structures and templated classes for the manipulation of
1288 compound objects, such as vectors, matrices and univariate polynomials.")
1289     (license license:cecill-b)
1290     (home-page "https://github.com/linbox-team/givaro")))
1291
1292 (define-public fflas-ffpack
1293   (package
1294     (name "fflas-ffpack")
1295     (version "2.4.3")
1296     (source (origin
1297               (method git-fetch)
1298               (uri (git-reference
1299                     (url "https://github.com/linbox-team/fflas-ffpack")
1300                     (commit version)))
1301               (file-name (git-file-name name version))
1302               (sha256
1303                (base32
1304                 "1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
1305     (build-system gnu-build-system)
1306     (native-inputs
1307      `(("autoconf" ,autoconf)
1308        ("automake" ,automake)
1309        ("libtool" ,libtool)
1310        ("pkg-config" ,pkg-config)))
1311     (inputs
1312      `(("openblas" ,openblas)))
1313     (propagated-inputs
1314      `(("givaro" ,givaro))) ; required according to the .pc file
1315     (arguments
1316      `(#:configure-flags
1317        (list (string-append "--with-blas-libs="
1318                             (assoc-ref %build-inputs "openblas")
1319                             "/lib/libopenblas.so"))))
1320     (synopsis "C++ library for linear algebra over finite fields")
1321     (description
1322      "FFLAS-FFPACK is a C++ template library for basic linear algebra
1323 operations over a finite field.
1324 FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
1325 of a subset of routines of the numerical BLAS; it also supports sparse
1326 matrix-vector products.
1327 FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
1328 library to provide functionalities of higher level, using the kernel
1329 of a BLAS.  Additionally, it provides routines specific to exact linear
1330 algebra, such as the row echelon form.")
1331     (license license:lgpl2.1+)
1332     (home-page "https://linbox-team.github.io/fflas-ffpack/")))
1333
1334 (define-public linbox
1335   (package
1336     (name "linbox")
1337     (version "1.6.3")
1338     (source (origin
1339               (method git-fetch)
1340               (uri (git-reference
1341                     (url "https://github.com/linbox-team/linbox")
1342                     (commit (string-append "v" version))))
1343               (file-name (git-file-name name version))
1344               (sha256
1345                (base32
1346                 "10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))
1347               (patches (search-patches "linbox-fix-pkgconfig.patch"))))
1348     (build-system gnu-build-system)
1349     (native-inputs
1350      `(("autoconf" ,autoconf)
1351        ("automake" ,automake)
1352        ("libtool" ,libtool)
1353        ("pkg-config" ,pkg-config)))
1354     (propagated-inputs
1355      `(("fflas-ffpack" ,fflas-ffpack)))
1356     (synopsis "C++ library for linear algebra over exact rings")
1357     (description
1358      "LinBox is a C++ template library for exact linear algebra computation
1359 with dense, sparse, and structured matrices over the integers and over
1360 finite fields.")
1361     (license license:lgpl2.1+)
1362     (home-page "https://linbox-team.github.io/linbox/")))
1363
1364 (define-public m4ri
1365   (package
1366     (name "m4ri")
1367     (version "20140914")
1368     (source (origin
1369               (method git-fetch)
1370               (uri (git-reference
1371                     (url "https://bitbucket.org/malb/m4ri")
1372                     (commit (string-append "release-" version))))
1373               (file-name (git-file-name name version))
1374               (sha256
1375                (base32
1376                 "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
1377     (build-system gnu-build-system)
1378     (native-inputs
1379      `(("autoconf" ,autoconf)
1380        ("automake" ,automake)
1381        ("libtool" ,libtool)
1382        ("pkg-config" ,pkg-config)))
1383     (inputs
1384      `(("libpng" ,libpng)))
1385     (synopsis "Arithmetic of dense matrices over F_2")
1386     (description "M4RI is a library for fast arithmetic with dense matrices
1387 over F2.  The name M4RI comes from the first implemented algorithm: The
1388 Method of the Four Russians inversion algorithm published by Gregory Bard.
1389 This algorithm in turn is named after the Method of the Four Russians
1390 multiplication algorithm.")
1391     (license license:gpl2+)
1392     (home-page "https://bitbucket.org/malb/m4ri/")))
1393
1394 (define-public symmetrica
1395   (package
1396     (name "symmetrica")
1397     (version "2.0")
1398     (source (origin
1399               (method url-fetch/tarbomb)
1400               (uri (let ((v (string-join (string-split version #\.) "_")))
1401                      (string-append "http://www.algorithm.uni-bayreuth.de/"
1402                                     "en/research/SYMMETRICA/"
1403                                     "SYM" v "_tar.gz")))
1404               (sha256
1405                (base32
1406                 "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
1407               ;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
1408               (patches (search-patches "symmetrica-bruch.patch"
1409                                        "symmetrica-int32.patch"
1410                                        "symmetrica-return_values.patch"
1411                                        "symmetrica-sort_sum_rename.patch"))))
1412     (build-system gnu-build-system)
1413     (arguments
1414      `(#:tests? #f                      ;no test
1415        #:phases
1416        (modify-phases %standard-phases
1417          (add-after 'unpack 'fix-makefile
1418            (lambda _
1419              (substitute* "makefile"
1420                (("cc -c") "gcc -c -fPIC"))
1421              #t))
1422          (add-after 'fix-makefile 'turn-off-banner
1423            (lambda _
1424              (substitute* "de.c"
1425                (("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
1426              #t))
1427          (delete 'configure)            ;no configure script
1428          (replace 'install              ;no install target
1429            (lambda* (#:key outputs #:allow-other-keys)
1430              (let* ((out (assoc-ref outputs "out"))
1431                     (lib (string-append out "/lib"))
1432                     (inc (string-append out "/include/symmetrica"))
1433                     (doc (string-append out "/share/doc/symmetrica-" ,version))
1434                     (static "libsymmetrica.a"))
1435                ;; Build static library.
1436                (apply invoke "ar" "crs" static (find-files "." "\\.o$"))
1437                (invoke "ranlib" static)
1438                ;; Install static library and headers.
1439                (for-each (lambda (f) (install-file f inc))
1440                          (find-files "." "\\.h$"))
1441                (install-file "libsymmetrica.a" lib)
1442                ;; Install documentation.
1443                (for-each (lambda (f) (install-file f doc))
1444                          (find-files "." "\\.doc$"))
1445                #t))))))
1446     (home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
1447     (synopsis "Combinatoric C Library")
1448     (description "Symmetrica is a library for combinatorics.  It has support
1449 for the representation theory of the symmetric group and related groups,
1450 combinatorics of tableaux, symmetric functions and polynomials, Schubert
1451 polynomials, and the representation theory of Hecke algebras of type A_n.")
1452     (license license:public-domain)))
1453
1454 (define-public m4rie
1455   (package
1456     (name "m4rie")
1457     (version "20150908")
1458     (source (origin
1459               (method git-fetch)
1460               (uri (git-reference
1461                     (url "https://bitbucket.org/malb/m4rie")
1462                     (commit (string-append "release-" version))))
1463               (file-name (git-file-name name version))
1464               (sha256
1465                (base32
1466                 "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
1467     (build-system gnu-build-system)
1468     (native-inputs
1469      `(("autoconf" ,autoconf)
1470        ("automake" ,automake)
1471        ("libtool" ,libtool)))
1472     (inputs
1473      `(("m4ri" ,m4ri)))
1474     (synopsis "Arithmetic of dense matrices over F_{2^e}")
1475     (description "M4RI is a library for fast arithmetic with dense matrices
1476 over finite fields of characteristic 2.  So it extends the functionality
1477 of M4RI from F_2 to F_{2^e}.")
1478     (license license:gpl2+)
1479     (home-page "https://bitbucket.org/malb/m4rie/")))
1480
1481 (define-public eclib
1482   (package
1483     (name "eclib")
1484     (version "20190909")
1485     (source (origin
1486               (method git-fetch)
1487               (uri (git-reference
1488                     (url "https://github.com/JohnCremona/eclib/")
1489                     (commit (string-append "v" version))))
1490               (file-name (git-file-name name version))
1491               (sha256
1492                (base32
1493                 "1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n"))))
1494     (build-system gnu-build-system)
1495     (native-inputs
1496      `(("autoconf" ,autoconf)
1497        ("automake" ,automake)
1498        ("libtool" ,libtool)))
1499     (inputs
1500      `(("ntl" ,ntl)
1501        ("pari-gp" ,pari-gp)))
1502     (synopsis "Ranks of elliptic curves and modular symbols")
1503     (description "The eclib package includes mwrank (for 2-descent on
1504 elliptic curves over Q) and modular symbol code; it has been written by
1505 John Cremona to compute his elliptic curve database.")
1506     (license license:gpl2+)
1507     (home-page (string-append "http://homepages.warwick.ac.uk/staff/"
1508                               "J.E.Cremona/mwrank/index.html"))))
1509
1510 (define-public lrcalc
1511   (package
1512     (name "lrcalc")
1513     (version "1.2")
1514     (source (origin
1515               (method git-fetch)
1516               (uri (git-reference
1517                     (url "https://bitbucket.org/asbuch/lrcalc")
1518                     (commit (string-append "lrcalc-" version))))
1519               (file-name (git-file-name name version))
1520               (sha256
1521                (base32
1522                 "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
1523               (patches (search-patches "lrcalc-includes.patch"))))
1524     (build-system gnu-build-system)
1525     (native-inputs
1526      `(("autoconf" ,autoconf)
1527        ("automake" ,automake)
1528        ("libtool" ,libtool)))
1529     (arguments
1530      `(#:phases
1531        (modify-phases %standard-phases
1532          (add-before 'build 'fix-permission
1533            (lambda _
1534              (chmod "lrcalc.maple.src" #o644)
1535              #t)))))
1536     (synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
1537     (description "The Littlewood-Richardson Calculator (lrcalc) is a
1538 program designed to compute Littlewood-Richardson coefficients.  It computes
1539 single Littlewood-Richardson coefficients, products of Schur functions, or
1540 skew Schur functions.  In addition it computes products in the small quantum
1541 cohomology ring of a Grassmann variety.  The software package also includes
1542 a program that performs fast computation of the more general multiplicative
1543 structure constants of Schubert polynomials.")
1544     (license license:gpl2+)
1545     (home-page "https://sites.math.rutgers.edu/~asbuch/lrcalc/")))
1546
1547 (define-public iml
1548   (package
1549     (name "iml")
1550     (version "1.0.5")
1551     (source
1552      (origin
1553        (method url-fetch)
1554        (uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
1555                            version ".tar.bz2"))
1556        (sha256
1557         (base32
1558          "0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
1559     (build-system gnu-build-system)
1560     (inputs
1561      `(("gmp" ,gmp)
1562        ("cblas" ,openblas))) ; or any other BLAS library; the documentation
1563                              ; mentions ATLAS in particular
1564     (arguments
1565      `(#:configure-flags
1566        (list
1567         "--enable-shared"
1568         (string-append "--with-gmp-include="
1569                        (assoc-ref %build-inputs "gmp") "/include")
1570         (string-append "--with-gmp-lib="
1571                        (assoc-ref %build-inputs "gmp") "/lib")
1572         "--with-cblas=-lopenblas"
1573         (string-append "--with-cblas-include="
1574                        (assoc-ref %build-inputs "cblas") "/include")
1575         (string-append "--with-cblas-lib="
1576                        (assoc-ref %build-inputs "cblas") "/lib"))))
1577     (home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
1578     (synopsis
1579      "Solver for systems of linear equations over the integers")
1580     (description
1581      "IML is a C library implementing algorithms for computing exact
1582 solutions to dense systems of linear equations over the integers.
1583 Currently, IML provides the following functionality:
1584
1585 @itemize
1586 @item Nonsingular rational system solving:
1587 compute the unique rational solution X to the system AX=B, where A and B
1588 are integer matrices, A nonsingular.
1589 @item Compute the right nullspace or kernel of an integer matrix.
1590 @item Certified linear system solving:
1591 compute a minimal denominator solution x to a system Ax=b, where b is an
1592 integer vector and A is an integer matrix with arbitrary shape and
1593 rank profile.
1594 @end itemize
1595
1596 In addition, IML provides some low level routines for a variety of mod p
1597 matrix operations: computing the row-echelon form, determinant, rank
1598 profile, and inverse of a mod p matrix. These mod p routines are not
1599 general purpose; they require that p satisfy some preconditions based on
1600 the dimension of the input matrix (usually p should be prime and should be
1601 no more than about 20 bits long).")
1602     (license license:bsd-3)))