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 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 check)
  31   #:use-module (gnu packages compression)
  32   #:use-module (gnu packages cpp)
  33   #:use-module (gnu packages documentation)
  34   #:use-module (gnu packages ed)
  35   #:use-module (gnu packages flex)
  36   #:use-module (gnu packages fltk)
  37   #:use-module (gnu packages gl)
  38   #:use-module (gnu packages graphviz)
  39   #:use-module (gnu packages image)
  40   #:use-module (gnu packages java)
  41   #:use-module (gnu packages maths)
  42   #:use-module (gnu packages mpi)
  43   #:use-module (gnu packages multiprecision)
  44   #:use-module (gnu packages perl)
  45   #:use-module (gnu packages python)
  46   #:use-module (gnu packages python-xyz)
  47   #:use-module (gnu packages readline)
  48   #:use-module (gnu packages shells)
  49   #:use-module (gnu packages tex)
  50   #:use-module (gnu packages texinfo)
  51   #:use-module (gnu packages xiph)
  52   #:use-module (gnu packages xorg)
  53   #:use-module (guix build-system ant)
  54   #:use-module (guix build-system gnu)
  55   #:use-module (guix build-system cmake)
  56   #:use-module (guix build-system python)
  57   #:use-module (guix download)
  58   #:use-module (guix git-download)
  59   #:use-module (guix hg-download)
  60   #:use-module ((guix licenses) #:prefix license:)
  61   #:use-module (guix packages)
  62   #:use-module (guix utils))
  63
  64
  65 (define-public mpfrcx
  66   (package
  67    (name "mpfrcx")
  68    (version "0.5")
  69    (source (origin
  70             (method url-fetch)
  71             (uri (string-append
  72                   "http://www.multiprecision.org/downloads/mpfrcx-"
  73                   version ".tar.gz"))
  74             (sha256
  75              (base32
  76               "1s968480ymv6w0rnvfp9mxvx98hvi29fkvw8nk4ggzc6azxgwybs"))))
  77    (build-system gnu-build-system)
  78    (propagated-inputs
  79      `(("gmp" ,gmp)
  80        ("mpfr" ,mpfr)
  81        ("mpc"  ,mpc))) ; Header files are included by mpfrcx.h.
  82    (synopsis "Arithmetic of polynomials over arbitrary precision numbers")
  83    (description
  84     "Mpfrcx is a library for the arithmetic of univariate polynomials over
  85 arbitrary precision real (mpfr) or complex (mpc) numbers, without control
  86 on the rounding.  For the time being, only the few functions needed to
  87 implement the floating point approach to complex multiplication are
  88 implemented.  On the other hand, these comprise asymptotically fast
  89 multiplication routines such as Toom–Cook and the FFT.")
  90    (license license:lgpl3+)
  91    (home-page "http://mpfrcx.multiprecision.org/")))
  92
  93 (define-public cm
  94   (package
  95    (name "cm")
  96    (version "0.3")
  97    (source (origin
  98             (method url-fetch)
  99             (uri (string-append
 100                   "http://www.multiprecision.org/cm/download/cm-"
 101                   version ".tar.gz"))
 102             (sha256
 103              (base32
 104               "1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc"))))
 105    (build-system gnu-build-system)
 106    (propagated-inputs
 107      `(("mpfrcx" ,mpfrcx)
 108        ("zlib" ,zlib))) ; Header files included from cm_common.h.
 109    (inputs
 110      `(("pari-gp"  ,pari-gp)))
 111    (synopsis "CM constructions for elliptic curves")
 112    (description
 113     "The CM software implements the construction of ring class fields of
 114 imaginary quadratic number fields and of elliptic curves with complex
 115 multiplication via floating point approximations.  It consists of libraries
 116 that can be called from within a C program and of executable command
 117 line applications.")
 118    (license license:gpl3+)
 119    (home-page "http://cm.multiprecision.org/")))
 120
 121 (define-public fplll
 122   (package
 123    (name "fplll")
 124    (version "4.0.4")
 125    (source (origin
 126             (method url-fetch)
 127             (uri (string-append
 128                   "http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
 129                   version ".tar.gz"))
 130             (sha256 (base32
 131                      "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))
 132    (build-system gnu-build-system)
 133    (inputs `(("gmp" ,gmp)
 134              ("mpfr" ,mpfr)))
 135    (synopsis "Library for LLL-reduction of euclidean lattices")
 136    (description
 137     "fplll LLL-reduces euclidean lattices.  Since version 3, it can also
 138 solve the shortest vector problem.")
 139    (license license:lgpl2.1+)
 140    (home-page "http://perso.ens-lyon.fr/damien.stehle/fplll/")))
 141
 142 (define-public pari-gp
 143   (package
 144     (name "pari-gp")
 145     (version "2.11.1")
 146     (source (origin
 147               (method url-fetch)
 148               (uri (string-append
 149                     "https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
 150                     version ".tar.gz"))
 151               (sha256
 152                (base32
 153                 "1jfax92jpydjd02fwl30r6b8kfzqqd6sm4yx94gidyz9lqjb7a94"))))
 154     (build-system gnu-build-system)
 155     (native-inputs
 156      `(("texlive" ,(texlive-union
 157                     (list texlive-fonts-amsfonts
 158                           texlive-latex-amsfonts)))))
 159     (inputs `(("gmp" ,gmp)
 160               ("libx11" ,libx11)
 161               ("perl" ,perl)
 162               ("readline" ,readline)))
 163     (arguments
 164      '(#:make-flags '("all")
 165        #:test-target "dobench"
 166        #:phases
 167        (modify-phases %standard-phases
 168          (replace 'configure
 169            (lambda* (#:key outputs #:allow-other-keys)
 170              (invoke "./Configure"
 171                      (string-append "--prefix="
 172                                     (assoc-ref outputs "out"))))))))
 173     (synopsis "PARI/GP, a computer algebra system for number theory")
 174     (description
 175      "PARI/GP is a widely used computer algebra system designed for fast
 176 computations in number theory (factorisations, algebraic number theory,
 177 elliptic curves...), but it also contains a large number of other useful
 178 functions to compute with mathematical entities such as matrices,
 179 polynomials, power series, algebraic numbers, etc., and a lot of
 180 transcendental functions.
 181 PARI is also available as a C library to allow for faster computations.")
 182     (license license:gpl2+)
 183     (home-page "https://pari.math.u-bordeaux.fr/")))
 184
 185 (define-public gp2c
 186   (package
 187    (name "gp2c")
 188    (version "0.0.11pl1")
 189    (source (origin
 190             (method url-fetch)
 191             (uri (string-append
 192                   "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
 193                   version ".tar.gz"))
 194             (sha256
 195               (base32
 196                 "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s"))))
 197    (build-system gnu-build-system)
 198    (native-inputs `(("perl" ,perl)))
 199    (inputs `(("pari-gp" ,pari-gp)))
 200    (arguments
 201     '(#:configure-flags
 202       (list (string-append "--with-paricfg="
 203                            (assoc-ref %build-inputs "pari-gp")
 204                            "/lib/pari/pari.cfg"))))
 205    (synopsis "PARI/GP, a computer algebra system for number theory")
 206    (description
 207     "PARI/GP is a widely used computer algebra system designed for fast
 208 computations in number theory (factorisations, algebraic number theory,
 209 elliptic curves...), but it also contains a large number of other useful
 210 functions to compute with mathematical entities such as matrices,
 211 polynomials, power series, algebraic numbers, etc., and a lot of
 212 transcendental functions.
 213 PARI is also available as a C library to allow for faster computations.
 214
 215 GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
 216    (license license:gpl2)
 217    (home-page "https://pari.math.u-bordeaux.fr/")))
 218
 219 (define-public cmh
 220   (package
 221    (name "cmh")
 222    (version "1.0")
 223    (source (origin
 224             (method url-fetch)
 225             (uri (string-append
 226                   "https://gforge.inria.fr/frs/download.php/33497/cmh-"
 227                   version ".tar.gz"))
 228             (sha256
 229              (base32
 230               "1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
 231    (build-system gnu-build-system)
 232    (inputs
 233      `(("gmp" ,gmp)
 234        ("mpfr" ,mpfr)
 235        ("mpc" ,mpc)
 236        ("mpfrcx" ,mpfrcx)
 237        ("fplll" ,fplll)
 238        ("pari-gp"  ,pari-gp)))
 239    (synopsis "Igusa class polynomial computations")
 240    (description
 241     "The CMH software computes Igusa (genus 2) class polynomials, which
 242 parameterize the CM points in the moduli space of 2-dimensional abelian
 243 varieties, i.e. Jacobians of hyperelliptic curves.
 244 It can also be used to compute theta constants at arbitrary
 245 precision.")
 246    (license license:gpl3+)
 247    (home-page "http://cmh.gforge.inria.fr/")))
 248
 249 (define-public giac-xcas
 250   (package
 251     (name "giac-xcas")
 252     (version "1.5.0-49")
 253     (source (origin
 254               (method url-fetch)
 255               ;; "~parisse/giac" is not used because the maintainer regularly
 256               ;; overwrites the release tarball there, introducing a checksum
 257               ;; mismatch every time.  See
 258               ;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
 259               (uri (string-append "https://www-fourier.ujf-grenoble.fr/"
 260                                   "~parisse/debian/dists/stable/main/"
 261                                   "source/giac_" version ".tar.gz"))
 262               (sha256
 263                (base32
 264                 "0f4pkand9vmqfayw18jm5qxbhcwi1405qfd7ibzh9lwzz6amkm3l"))))
 265     (build-system gnu-build-system)
 266     (outputs '("out" "doc"))            ;77MiB of documentation
 267     (arguments
 268      `(#:modules ((ice-9 ftw)
 269                   (guix build utils)
 270                   (guix build gnu-build-system))
 271        #:phases
 272        (modify-phases %standard-phases
 273          (add-after 'unpack 'patch-bin-cp
 274            ;; Some Makefiles contain hard-coded "/bin/cp".
 275            (lambda _
 276              (substitute* (find-files "doc" "^Makefile")
 277                (("/bin/cp") (which "cp")))
 278              #t))
 279          (add-after 'unpack 'disable-failing-test
 280            ;; FIXME: Test failing.  Not sure why.
 281            (lambda _
 282              (substitute* "check/Makefile.in"
 283                (("chk_fhan11") ""))
 284              #t))
 285          (add-after 'install 'install-doc
 286            ;; Setting --docdir to "doc" output isn't sufficient as
 287            ;; documentation and examples are scattered throughout the source.
 288            (lambda* (#:key outputs #:allow-other-keys)
 289              (let* ((out (assoc-ref outputs "out"))
 290                     (doc (assoc-ref outputs "doc"))
 291                     (docdir (string-append doc
 292                                            "/share/doc/"
 293                                            (string-append ,name "-" ,version))))
 294                ;; For some reason, the install process moves
 295                ;; "share/giac/examples" instead of "share/giac/doc" to
 296                ;; "$(docdir)".  Clean up the mess and start over.
 297                (delete-file-recursively (string-append doc "/share"))
 298                (mkdir-p docdir)
 299                (with-directory-excursion out
 300                  (for-each (lambda (f)
 301                              (unless (member f '("." ".."))
 302                                (copy-recursively (string-append "share/giac/" f)
 303                                                  (string-append docdir "/" f))))
 304                            (scandir "share/giac"))
 305                  (delete-file-recursively "share/giac")))
 306              #t)))))
 307     (inputs
 308      `(("fltk" ,fltk)
 309        ("gmp" ,gmp)
 310        ("gsl" ,gsl)
 311        ("lapack" ,lapack)
 312        ("libao" ,ao)
 313        ("libjpeg" ,libjpeg)
 314        ("libpng" ,libpng)
 315        ("libx11" ,libx11)
 316        ("libxinerama" ,libxinerama)
 317        ("libxft" ,libxft)
 318        ("libxt" ,libxt)
 319        ("mesa" ,mesa)
 320        ("mpfi" ,mpfi)
 321        ("mpfr" ,mpfr)
 322        ("ntl" ,ntl)
 323        ("perl" ,perl)
 324        ("pari-gp" ,pari-gp)
 325        ("tcsh" ,tcsh)
 326        ("texlive" ,texlive-tiny)))
 327     (native-inputs `(("readline" ,readline)))
 328     (home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
 329     (synopsis "Computer algebra system")
 330     (description
 331      "Giac/Xcas is a computer algebra system.  It has a compatibility mode for
 332 maple, mupad and the TI89.  It is available as a standalone program (graphic
 333 or text interfaces) or as a C++ library.")
 334     (license license:gpl3+)))
 335
 336 (define-public flint
 337   (package
 338    (name "flint")
 339    (version "2.5.2")
 340    (source (origin
 341             (method url-fetch)
 342             (uri (string-append
 343                   "http://flintlib.org/flint-"
 344                   version ".tar.gz"))
 345             (sha256 (base32
 346                      "11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
 347             (patches (search-patches "flint-ldconfig.patch"))))
 348    (build-system gnu-build-system)
 349    (propagated-inputs
 350     `(("gmp" ,gmp)
 351       ("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
 352    (arguments
 353     `(#:parallel-tests? #f ; seems to be necessary on arm
 354       #:phases
 355        (modify-phases %standard-phases
 356          (replace 'configure
 357            (lambda* (#:key inputs outputs #:allow-other-keys)
 358              (let ((out (assoc-ref outputs "out"))
 359                    (gmp (assoc-ref inputs "gmp"))
 360                    (mpfr (assoc-ref inputs "mpfr")))
 361                ;; do not pass "--enable-fast-install", which makes the
 362                ;; homebrew configure process fail
 363                (invoke "./configure"
 364                        (string-append "--prefix=" out)
 365                        (string-append "--with-gmp=" gmp)
 366                        (string-append "--with-mpfr=" mpfr))
 367                #t))))))
 368    (synopsis "Fast library for number theory")
 369    (description
 370     "FLINT is a C library for number theory.  It supports arithmetic
 371 with numbers, polynomials, power series and matrices over many base
 372 rings, including multiprecision integers and rationals, integers
 373 modulo n, p-adic numbers, finite fields (prime and non-prime order)
 374 and real and complex numbers (via the Arb extension library).
 375
 376 Operations that can be performed include conversions, arithmetic,
 377 GCDs, factoring, solving linear systems, and evaluating special
 378 functions.  In addition, FLINT provides various low-level routines for
 379 fast arithmetic.")
 380    (license license:gpl2+)
 381    (home-page "http://flintlib.org/")))
 382
 383 (define-public arb
 384   (package
 385     (name "arb")
 386     (version "2.16.0")
 387     (source (origin
 388               (method git-fetch)
 389               (uri (git-reference
 390                     (url "https://github.com/fredrik-johansson/arb.git")
 391                     (commit version)))
 392               (file-name (git-file-name name version))
 393               (sha256
 394                (base32
 395                 "0478671wfwy3gl26sbxh1jq1ih36z4k72waa8y2y2lvn649gb7cd"))))
 396     (build-system gnu-build-system)
 397     (propagated-inputs
 398      `(("flint" ,flint)))               ; flint.h is included by arf.h
 399     (inputs
 400      `(("gmp" ,gmp)
 401        ("mpfr" ,mpfr)))
 402     (arguments
 403      `(#:phases
 404        (modify-phases %standard-phases
 405          (replace 'configure
 406            (lambda* (#:key inputs outputs #:allow-other-keys)
 407              (let ((out (assoc-ref outputs "out"))
 408                    (flint (assoc-ref inputs "flint"))
 409                    (gmp (assoc-ref inputs "gmp"))
 410                    (mpfr (assoc-ref inputs "mpfr")))
 411                ;; do not pass "--enable-fast-install", which makes the
 412                ;; homebrew configure process fail
 413                (invoke "./configure"
 414                        (string-append "--prefix=" out)
 415                        (string-append "--with-flint=" flint)
 416                        (string-append "--with-gmp=" gmp)
 417                        (string-append "--with-mpfr=" mpfr))))))))
 418     (synopsis "Arbitrary precision floating-point ball arithmetic")
 419     (description
 420      "Arb is a C library for arbitrary-precision floating-point ball
 421 arithmetic.  It supports efficient high-precision computation with
 422 polynomials, power series, matrices and special functions over the
 423 real and complex numbers, with automatic, rigorous error control.")
 424     (license license:lgpl2.1+)
 425     (home-page "http://fredrikj.net/arb/")))
 426
 427 (define-public python-flint
 428   (package
 429     (name "python-flint")
 430     (version "0.3.0")
 431     (source (origin
 432               (method git-fetch)
 433               (uri (git-reference
 434                     (url "https://github.com/fredrik-johansson/python-flint.git")
 435                     (commit version)))
 436               (file-name (git-file-name name version))
 437               (sha256
 438                (base32
 439                 "1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
 440               (patches (search-patches "python-flint-includes.patch"))))
 441     (build-system python-build-system)
 442     (native-inputs
 443      `(("python-cython" ,python-cython)))
 444     (propagated-inputs
 445      `(("python-numpy" ,python-numpy)))
 446     (inputs
 447      `(("arb" ,arb)
 448        ("flint" ,flint)))
 449     (synopsis "Python module wrapping ARB and FLINT")
 450     (description
 451      "Python-flint is a Python extension module wrapping FLINT
 452 (Fast Library for Number Theory) and Arb (arbitrary-precision ball
 453 arithmetic).  It supports integers, rationals, modular integers,
 454 real and complex ball arithmetic, polynomials and matrices over all
 455 these types and other mathematical functions.")
 456     (license license:expat)
 457     (home-page "http://fredrikj.net/python-flint/")))
 458
 459 (define-public ntl
 460   (package
 461    (name "ntl")
 462    (version "9.7.0")
 463    (source (origin
 464             (method url-fetch)
 465             (uri (string-append "http://shoup.net/ntl/ntl-"
 466                                 version ".tar.gz"))
 467             (sha256 (base32
 468                      "115frp5flyvw9wghz4zph1b3llmr5nbxk1skgsggckr81fh3gmxq"))))
 469    (build-system gnu-build-system)
 470    (native-inputs
 471     `(("libtool" ,libtool)
 472       ("perl" ,perl))) ; for configuration
 473    ;; FIXME: Add optional input gf2x once available; then also add
 474    ;; configure flag "NTL_GF2X_LIB=on".
 475    (inputs
 476     `(("gmp" ,gmp)))
 477    (arguments
 478     `(#:phases
 479       (modify-phases %standard-phases
 480         (replace 'configure
 481          (lambda* (#:key outputs #:allow-other-keys)
 482            (chdir "src")
 483            (system* "./configure"
 484                     (string-append "PREFIX=" (assoc-ref outputs "out"))
 485                     ;; Do not build especially for the build machine.
 486                     "NATIVE=off"
 487                     ;; Also do not tune to the build machine.
 488                     "WIZARD=off"
 489                     "SHARED=on")
 490            #t)))))
 491    (synopsis "C++ library for number theory")
 492    (description
 493     "NTL is a C++ library providing data structures and algorithms
 494 for manipulating signed, arbitrary length integers, and for vectors,
 495 matrices, and polynomials over the integers and over finite fields.")
 496    (license license:gpl2+)
 497    (home-page "http://shoup.net/ntl/")))
 498
 499 (define-public singular
 500   (package
 501    (name "singular")
 502    (version "4.1.1p3")
 503    (source
 504     (origin
 505       (method url-fetch)
 506       (uri
 507        (string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
 508                       "Singular/SOURCES/"
 509                       (string-join
 510                        (string-split
 511                         (string-trim-right version #\p
 512                                            0 (1- (string-length version)))
 513                         #\.) "-")
 514                       "/singular-" version ".tar.gz"))
 515              (sha256 (base32
 516                       "1qqj9bm9pkzm0iyycpvm8x6s79wws3nq60lz25h8x1q61h3426sm"))))
 517    (build-system gnu-build-system)
 518    (native-inputs
 519     `(("doxygen" ,doxygen)
 520       ("graphviz" ,graphviz)
 521       ("perl" ,perl)))
 522    (inputs
 523     `(("cddlib" ,cddlib)
 524       ("gmp" ,gmp)
 525       ("flint" ,flint)
 526       ("mpfr" ,mpfr)
 527       ("ntl" ,ntl)
 528       ("python" ,python-2)
 529       ("readline" ,readline)))
 530    (arguments
 531     `(#:configure-flags
 532       (list (string-append "--with-ntl="
 533                            (assoc-ref %build-inputs "ntl")))))
 534    (synopsis "Computer algebra system for polynomial computations")
 535    (description
 536     "Singular is a computer algebra system for polynomial computations,
 537 with special emphasis on commutative and non-commutative algebra, algebraic
 538 geometry and singularity theory.")
 539    ;; Singular itself is dual licensed gpl2 or gpl3, but some of the
 540    ;; libraries with which it links are licensed under lgpl3+, so the
 541    ;; combined work becomes gpl3. See COPYING in the source code.
 542    (license license:gpl3)
 543    (home-page "http://www.singular.uni-kl.de/index.php")))
 544
 545 (define-public gmp-ecm
 546   (package
 547    (name "gmp-ecm")
 548    (version "7.0.4")
 549    (source (origin
 550              (method url-fetch)
 551              ;; Use the ‘Latest version’ link for a stable URI across releases.
 552              (uri (string-append "https://gforge.inria.fr/frs/download.php/"
 553                                  "latestfile/160/ecm-" version ".tar.gz"))
 554              (sha256 (base32
 555                       "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"))))
 556    (build-system gnu-build-system)
 557    (inputs
 558     `(("gmp" ,gmp)))
 559    (arguments
 560     `(#:configure-flags '("--enable-shared"
 561                           ;; Disable specific assembly routines, which depend
 562                           ;; on the subarchitecture of the build machine,
 563                           ;; and use gmp instead.
 564                           "--disable-asm-redc")))
 565    (synopsis "Integer factorization library using the elliptic curve method")
 566    (description
 567     "GMP-ECM factors integers using the elliptic curve method (ECM) as well
 568 as the P-1 and P+1 algorithms.  It provides a library and a stand-alone
 569 binary.")
 570    ;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+,
 571    ;; so the combined work is under gpl3+.
 572    (license license:gpl3+)
 573    (home-page "http://ecm.gforge.inria.fr/")))
 574
 575 (define-public bc
 576   (package
 577     (name "bc")
 578     (version "1.07.1")
 579     (source (origin
 580              (method url-fetch)
 581              (uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
 582              (sha256
 583               (base32
 584                "0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))))
 585     (build-system gnu-build-system)
 586     (native-inputs
 587      `(("ed" ,ed)
 588        ("flex" ,flex)
 589        ("texinfo" ,texinfo)))
 590     (arguments
 591      '(#:configure-flags
 592        (list "--with-readline")))
 593     (home-page "https://www.gnu.org/software/bc/")
 594     (synopsis "Arbitrary precision numeric processing language")
 595     (description
 596      "bc is an arbitrary precision numeric processing language.  It includes
 597 an interactive environment for evaluating mathematical statements.  Its
 598 syntax is similar to that of C, so basic usage is familiar.  It also includes
 599 \"dc\", a reverse-polish calculator.")
 600     (license license:gpl2+)))
 601
 602 ;; The original kiss-fft does not have a complete build system and does not
 603 ;; build any shared libraries.  This is a fork used by Extempore.
 604 (define-public kiss-fft-for-extempore
 605   (package
 606     (name "kiss-fft-for-extempore")
 607     (version "1.3.0")
 608     (source (origin
 609               (method git-fetch)
 610               (uri (git-reference
 611                     (url "https://github.com/extemporelang/kiss_fft.git")
 612                     (commit version)))
 613               (file-name (git-file-name name version))
 614               (sha256
 615                (base32
 616                 "0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
 617     (build-system cmake-build-system)
 618     (arguments `(#:tests? #f)) ; no tests included
 619     ;; Extempore refuses to build on architectures other than x86_64
 620     (supported-systems '("x86_64-linux"))
 621     (home-page "https://github.com/extemporelang/kiss_fft")
 622     (synopsis "Mixed-radix Fast Fourier Transform")
 623     (description
 624      "Kiss FFT attempts to be a reasonably efficient, moderately useful FFT
 625 that can use fixed or floating data types and can easily be incorporated into
 626 a C program.")
 627     (license license:bsd-3)))
 628
 629 (define-public fftw
 630   (package
 631     (name "fftw")
 632     (version "3.3.8")
 633     (source (origin
 634              (method url-fetch)
 635              (uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
 636                                  version".tar.gz"))
 637              (sha256
 638               (base32
 639                "00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
 640     (build-system gnu-build-system)
 641     (arguments
 642      `(#:configure-flags
 643        '("--enable-shared" "--enable-openmp" "--enable-threads"
 644          ,@(let ((system (or (%current-target-system) (%current-system))))
 645              ;; Enable SIMD extensions for codelets.  See details at:
 646              ;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>.
 647              (cond
 648               ((string-prefix? "x86_64" system)
 649                '("--enable-sse2" "--enable-avx" "--enable-avx2"
 650                  "--enable-avx512" "--enable-avx-128-fma"))
 651               ((string-prefix? "i686" system)
 652                '("--enable-sse2"))
 653               ((string-prefix? "aarch64" system)
 654                ;; Note that fftw supports NEON on 32-bit ARM only when
 655                ;; compiled for single-precision.
 656                '("--enable-neon"))
 657               (else
 658                '())))
 659          ;; By default '-mtune=native' is used.  However, that may cause the
 660          ;; use of ISA extensions (e.g. AVX) that are not necessarily
 661          ;; available on the user's machine when that package is built on a
 662          ;; different machine.
 663          "ax_cv_c_flags__mtune_native=no")))
 664     (native-inputs `(("perl" ,perl)))
 665     (home-page "http://fftw.org")
 666     (synopsis "Computing the discrete Fourier transform")
 667     (description
 668      "FFTW is a C subroutine library for computing the discrete Fourier
 669 transform (DFT) in one or more dimensions, of arbitrary input size, and of
 670 both real and complex data (as well as of even/odd data---i.e. the discrete
 671 cosine/ sine transforms or DCT/DST).")
 672     (license license:gpl2+)))
 673
 674 (define-public fftwf
 675   (package (inherit fftw)
 676     (name "fftwf")
 677     (arguments
 678      (substitute-keyword-arguments (package-arguments fftw)
 679        ((#:configure-flags fftw-configure-flags)
 680         `(cons* "--enable-single"
 681                 ,@(if (string-prefix? "arm" (or (%current-target-system)
 682                                                 (%current-system)))
 683                       ;; fftw supports NEON on 32-bit ARM only when compiled
 684                       ;; for single-precision, so add it here.
 685                       '("--enable-neon")
 686                       '())
 687                 ,fftw-configure-flags))))
 688     (description
 689      (string-append (package-description fftw)
 690                     "  Single-precision version."))))
 691
 692 (define-public fftw-openmpi
 693   (package (inherit fftw)
 694     (name "fftw-openmpi")
 695     (inputs
 696      `(("openmpi" ,openmpi)
 697        ,@(package-inputs fftw)))
 698     (arguments
 699      (substitute-keyword-arguments (package-arguments fftw)
 700        ((#:configure-flags cf)
 701         `(cons "--enable-mpi" ,cf))
 702        ((#:phases phases '%standard-phases)
 703         `(modify-phases ,phases
 704            (add-before 'check 'mpi-setup
 705              ,%openmpi-setup)))))
 706     (description
 707      (string-append (package-description fftw)
 708                     "  With OpenMPI parallelism support."))))
 709
 710 (define-public java-la4j
 711   (package
 712     (name "java-la4j")
 713     (version "0.6.0")
 714     (source (origin
 715               (method git-fetch)
 716               (uri (git-reference
 717                     (url "https://github.com/vkostyukov/la4j.git")
 718                     (commit version)))
 719               (file-name (string-append name "-" version "-checkout"))
 720               (sha256
 721                (base32
 722                 "1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
 723     (build-system ant-build-system)
 724     (arguments
 725      `(#:jar-name "la4j.jar"
 726        #:jdk ,icedtea-8
 727        #:test-exclude (list "**/Abstract*.java"
 728                             "**/MatrixTest.java"
 729                             "**/DenseMatrixTest.java"
 730                             "**/SparseMatrixTest.java"
 731                             "**/VectorTest.java"
 732                             "**/SparseVectorTest.java"
 733                             "**/DenseVectorTest.java")))
 734     (native-inputs
 735      `(("java-junit" ,java-junit)
 736        ("java-hamcrest-core" ,java-hamcrest-core)))
 737     (home-page "http://la4j.org/")
 738     (synopsis "Java library that provides Linear Algebra primitives and algorithms")
 739     (description "The la4j library is a Java library that provides Linear
 740 Algebra primitives (matrices and vectors) and algorithms.  The key features of
 741 the la4j library are:
 742
 743 @itemize
 744 @item No dependencies and tiny size
 745 @item Fluent object-oriented/functional API
 746 @item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
 747 @item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
 748 @item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
 749 @item MatrixMarket/CSV IO formats support for matrices and vectors
 750 @end itemize\n")
 751     (license license:asl2.0)))
 752
 753 (define-public java-jlargearrays
 754   (package
 755     (name "java-jlargearrays")
 756     (version "1.6")
 757     (source (origin
 758               (method url-fetch)
 759               (uri (string-append "http://search.maven.org/remotecontent?"
 760                                   "filepath=pl/edu/icm/JLargeArrays/"
 761                                   version "/JLargeArrays-" version
 762                                   "-sources.jar"))
 763               (file-name (string-append name "-" version ".jar"))
 764               (sha256
 765                (base32
 766                 "0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
 767     (build-system ant-build-system)
 768     (arguments
 769      `(#:jar-name "jlargearrays.jar"
 770        #:tests? #f ; tests are not included in the release archive
 771        #:jdk ,icedtea-8))
 772     (propagated-inputs
 773      `(("java-commons-math3" ,java-commons-math3)))
 774     (home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
 775     (synopsis "Library of one-dimensional arrays that can store up to 263 elements")
 776     (description "JLargeArrays is a Java library of one-dimensional arrays
 777 that can store up to 263 elements.")
 778     (license license:bsd-2)))
 779
 780 (define-public java-jtransforms
 781   (package
 782     (name "java-jtransforms")
 783     (version "3.1")
 784     (source (origin
 785               (method url-fetch)
 786               (uri (string-append "http://search.maven.org/remotecontent?"
 787                                   "filepath=com/github/wendykierp/JTransforms/"
 788                                   version "/JTransforms-" version "-sources.jar"))
 789               (sha256
 790                (base32
 791                 "1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
 792     (build-system ant-build-system)
 793     (arguments
 794      `(#:jar-name "jtransforms.jar"
 795        #:tests? #f ; tests are not included in the release archive
 796        #:jdk ,icedtea-8))
 797     (propagated-inputs
 798      `(("java-commons-math3" ,java-commons-math3)
 799        ("java-jlargearrays" ,java-jlargearrays)))
 800     (home-page "https://github.com/wendykierp/JTransforms")
 801     (synopsis "Multithreaded FFT library written in pure Java")
 802     (description "JTransforms is a multithreaded FFT library written in pure
 803 Java.  Currently, four types of transforms are available: @dfn{Discrete
 804 Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
 805 Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
 806     (license license:bsd-2)))
 807
 808 (define-public eigen
 809   (package
 810     (name "eigen")
 811     (version "3.3.5")
 812     (source (origin
 813               (method url-fetch)
 814               (uri (string-append "https://bitbucket.org/eigen/eigen/get/"
 815                                   version ".tar.bz2"))
 816               (sha256
 817                (base32
 818                 "1qh3yrwn78ms5yhwbpl5wvblk4gbz02cacdygxylr7i9xbrvylkk"))
 819               (file-name (string-append name "-" version ".tar.bz2"))
 820               (modules '((guix build utils)))
 821               (snippet
 822                ;; There are 3 test failures in the "unsupported" directory,
 823                ;; but maintainers say it's a known issue and it's unsupported
 824                ;; anyway, so just skip them.
 825                '(begin
 826                   (substitute* "unsupported/CMakeLists.txt"
 827                     (("add_subdirectory\\(test.*")
 828                      "# Do not build the tests for unsupported features.\n"))
 829                   #t))))
 830     (build-system cmake-build-system)
 831     (arguments
 832      '(;; Turn off debugging symbols to save space.
 833        #:build-type "Release"
 834
 835        #:phases (modify-phases %standard-phases
 836                   (replace 'check
 837                     (lambda _
 838                       (let* ((cores  (parallel-job-count))
 839                              (dash-j (format #f "-j~a" cores)))
 840                         (setenv "EIGEN_SEED" "1") ;for reproducibility
 841                         ;; First build the tests, in parallel.  See
 842                         ;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
 843                         (invoke "make" "buildtests" dash-j)
 844
 845                         ;; Then run 'CTest' with -V so we get more
 846                         ;; details upon failure.
 847                         (invoke "ctest" "-V" dash-j)))))))
 848     (home-page "https://eigen.tuxfamily.org")
 849     (synopsis "C++ template library for linear algebra")
 850     (description
 851      "Eigen is a C++ template library for linear algebra: matrices, vectors,
 852 numerical solvers, and related algorithms.  It provides an elegant API based
 853 on \"expression templates\".  It is versatile: it supports all matrix sizes,
 854 all standard numeric types, various matrix decompositions and geometry
 855 features, and more.")
 856
 857     ;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3.
 858     ;; See 'COPYING.README' for details.
 859     (license license:mpl2.0)))
 860
 861 (define-public eigen-for-tensorflow
 862   (let ((changeset "fd6845384b86")
 863         (revision "1"))
 864     (package (inherit eigen)
 865       (name "eigen-for-tensorflow")
 866       (version (string-append "3.3.5-" revision "." changeset))
 867       (source (origin
 868                 (method hg-fetch)
 869                 (uri (hg-reference
 870                       (url "https://bitbucket.org/eigen/eigen")
 871                       (changeset changeset)))
 872                 (sha256
 873                  (base32
 874                   "12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5"))
 875                 (file-name (string-append name "-" version "-checkout"))
 876                 (modules '((guix build utils)))
 877                 (snippet
 878                  ;; There are 3 test failures in the "unsupported" directory,
 879                  ;; but maintainers say it's a known issue and it's unsupported
 880                  ;; anyway, so just skip them.
 881                  '(begin
 882                     (substitute* "unsupported/CMakeLists.txt"
 883                       (("add_subdirectory\\(test.*")
 884                        "# Do not build the tests for unsupported features.\n"))
 885                     #t)))))))
 886
 887 (define-public xtensor
 888   (package
 889     (name "xtensor")
 890     (version "0.17.1")
 891     (source (origin
 892               (method git-fetch)
 893               (uri (git-reference
 894                     (url "https://github.com/QuantStack/xtensor.git")
 895                     (commit version)))
 896               (sha256
 897                (base32
 898                 "0w40v5lp0hp8ihf8nnvak373sb5xx0768pxgiqh3nzn57wf8px4r"))
 899               (file-name (git-file-name name version))))
 900     (build-system cmake-build-system)
 901     (native-inputs
 902      `(("googletest" ,googletest)
 903        ("xtl" ,xtl)))
 904     (arguments
 905      `(#:configure-flags
 906        '("-DBUILD_TESTS=ON")
 907        #:test-target "xtest"))
 908     (home-page "http://quantstack.net/xtensor")
 909     (synopsis "C++ tensors with broadcasting and lazy computing")
 910     (description "xtensor is a C++ library meant for numerical analysis with
 911 multi-dimensional array expressions.
 912
 913 xtensor provides:
 914 @itemize
 915 @item an extensible expression system enabling lazy broadcasting.
 916 @item an API following the idioms of the C++ standard library.
 917 @item tools to manipulate array expressions and build upon xtensor.
 918 @end itemize")
 919     (license license:bsd-3)))
 920
 921 (define-public gap
 922   (package
 923     (name "gap")
 924     (version "4.10.0")
 925     (source
 926      (origin
 927        (method url-fetch)
 928        (uri (string-append "https://www.gap-system.org/pub/gap/gap-"
 929                            (version-major+minor version)
 930                            "/tar.bz2/gap-"
 931                            version
 932                            ".tar.bz2"))
 933        (sha256
 934         (base32
 935          "1dmb8v4p7j1nnf7sx8sg54b49yln36bi9acwp7w1d3a1nxj17ird"))
 936        (modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
 937        (snippet
 938         '(begin
 939            ;; Delete the external gmp and zlib libraries
 940            ;; and a subdirectory not needed for our build.
 941            (for-each delete-file-recursively
 942                      '("extern" "hpcgap"))
 943            ;; Delete a failing test.
 944            ;; FIXME: This might be fixed in the next release, see
 945            ;; https://github.com/gap-system/gap/issues/3292
 946            (delete-file "tst/testinstall/dir.tst")
 947            ;; Delete all packages except for a fixed list.
 948            (with-directory-excursion "pkg"
 949              (for-each delete-file-recursively
 950                (lset-difference string=? (scandir ".")
 951                  '("." ".."
 952                    ;; Necessary packages.
 953                    "GAPDoc-1.6.2"
 954                    "primgrp-3.3.2"
 955                    "SmallGrp-1.3"    ; artistic2.0
 956                    "transgrp"        ; artistic2.0 for data,
 957                                      ; gpl2 or gpl3 for code
 958                    ;; Recommanded package.
 959                    "io-4.5.4"        ; gpl3+
 960                    ;; Optional packages, searched for at start,
 961                    ;; and their depedencies.
 962                    "alnuth-3.1.0"
 963                    "AutoDoc-2018.09.20"
 964                    "autpgrp-1.10"
 965                    "crisp-1.4.4"     ; bsd-2
 966                    ; "ctbllib"       ; no explicit license, drop
 967                    "FactInt-1.6.2"
 968                    "fga"
 969                    "irredsol-1.4"    ; bsd-2
 970                    "laguna-3.9.0"
 971                    "polenta-1.3.8"
 972                    "polycyclic-2.14"
 973                    "radiroot-2.8"
 974                    "resclasses-4.7.1"
 975                    "sophus-1.24"
 976                    ; "tomlib-1.2.7"  ; no explicit license, drop
 977                    "utils-0.59"))))
 978            #t))))
 979     (build-system gnu-build-system)
 980     (inputs
 981      `(("gmp" ,gmp)
 982        ("zlib" ,zlib)))
 983     (arguments
 984      `(#:phases
 985        (modify-phases %standard-phases
 986          (add-after 'build 'build-packages
 987            ;; Compile all packages that have not been deleted by the
 988            ;; code snippet above.
 989            (lambda _
 990              (setenv "CONFIG_SHELL" (which "bash"))
 991              (with-directory-excursion "pkg"
 992                (invoke "../bin/BuildPackages.sh")
 993              #t)))
 994          (add-after 'build-packages 'build-doc
 995            ;; The documentation is bundled, but we create it from source.
 996            (lambda _
 997              (with-directory-excursion "doc"
 998                (invoke "./make_doc"))
 999              #t))
1000          (replace 'check
1001            (lambda _
1002              ;; "make check" is expected to appear in gap-4.10.1
1003              (invoke "./gap" "tst/testinstall.g")
1004              #t))
1005          (replace 'install
1006            (lambda* (#:key outputs #:allow-other-keys)
1007              (let* ((out (assoc-ref outputs "out"))
1008                     (bin (string-append out "/bin"))
1009                     (prog (string-append bin "/gap"))
1010                     (prog-real (string-append bin "/.gap-real"))
1011                     (share (string-append out "/share/gap"))
1012                     (include (string-append out "/include/gap")))
1013                ;; Install only the gap binary; the gac compiler is left
1014                ;; for maybe later. "Wrap" it in a shell script that calls
1015                ;; the binary with the correct parameter.
1016                (mkdir-p bin)
1017                (copy-file "gap" prog-real)
1018                (call-with-output-file prog
1019                  (lambda (port)
1020                    (format port
1021                            "#!~a~%exec ~a -l ~a \"$@\"~%"
1022                            (which "bash")
1023                            prog-real
1024                            share)))
1025                (chmod prog #o755)
1026                ;; Install the headers and the library, which are needed by
1027                ;; Sage. The Makefile targets are available in gap-4.10.0,
1028                ;; but planned to be removed in gap-4.10.1.
1029                (invoke "make" "install-headers")
1030                (invoke "make" "install-libgap")
1031                (install-file "gen/config.h" include)
1032                ;; Install a certain number of files and directories to
1033                ;; SHARE, where the wrapped shell script expects them.
1034                ;; Remove information on the build directory from sysinfo.gap.
1035                (substitute* "sysinfo.gap"
1036                  (("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
1037                  (("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
1038                  (("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
1039                (install-file "sysinfo.gap" share)
1040                (copy-recursively "grp" (string-append share "/grp"))
1041                (copy-recursively "pkg" (string-append share "/pkg"))
1042                ;; The following is not the C library libgap.so, but a
1043                ;; library of GAP code.
1044                (copy-recursively "lib" (string-append share "/lib"))
1045                ;; The gap binary looks for documentation inside SHARE.
1046                (copy-recursively "doc" (string-append share "/doc")))
1047              #t)))))
1048     (home-page "https://www.gap-system.org/")
1049     (synopsis
1050      "System for computational group theory")
1051     (description
1052      "GAP is a system for computational discrete algebra, with particular
1053 emphasis on computational group theory.  It provides a programming language,
1054 a library of thousands of functions implementing algebraic algorithms
1055 written in the GAP language as well as large data libraries of algebraic
1056 objects.")
1057     ;; Some packages have different licenses (effectively forcing the
1058     ;; combined work to be licensed as gpl3+); if this is the case, this
1059     ;; is mentioned above next to their name.
1060     ;; Some packages have no license mentioned explicitly; supposedly this
1061     ;; means that the gpl2+ licence of GAP itself applies, but to be on the
1062     ;; safe side, we drop them for now.
1063     (license license:gpl2+)))