gnu/packages/sagemath.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
   3 ;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
   4 ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
   5 ;;;
   6 ;;; This file is part of GNU Guix.
   7 ;;;
   8 ;;; GNU Guix is free software; you can redistribute it and/or modify it
   9 ;;; under the terms of the GNU General Public License as published by
  10 ;;; the Free Software Foundation; either version 3 of the License, or (at
  11 ;;; your option) any later version.
  12 ;;;
  13 ;;; GNU Guix is distributed in the hope that it will be useful, but
  14 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  15 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  16 ;;; GNU General Public License for more details.
  17 ;;;
  18 ;;; You should have received a copy of the GNU General Public License
  19 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  20
  21 (define-module (gnu packages sagemath)
  22   #:use-module ((guix licenses) #:prefix license:)
  23   #:use-module (guix build-system gnu)
  24   #:use-module (guix build-system python)
  25   #:use-module (guix download)
  26   #:use-module (guix git-download)
  27   #:use-module (guix packages)
  28   #:use-module (guix utils)
  29   #:use-module (gnu packages)
  30   #:use-module (gnu packages algebra)
  31   #:use-module (gnu packages autotools)
  32   #:use-module (gnu packages bdw-gc)
  33   #:use-module (gnu packages boost)
  34   #:use-module (gnu packages compression)
  35   #:use-module (gnu packages image)
  36   #:use-module (gnu packages multiprecision)
  37   #:use-module (gnu packages pkg-config)
  38   #:use-module (gnu packages python)
  39   #:use-module (gnu packages python-xyz))
  40
  41
  42 (define-public python-cypari2
  43   (package
  44     (name "python-cypari2")
  45     (version "2.1.1")
  46     (source
  47      (origin
  48        (method url-fetch)
  49        (uri (pypi-uri "cypari2" version))
  50        (sha256
  51         (base32
  52          "1nwkzgqvbw6361x0rpggy1q5nx663fswhpvg8md6xhqyfwpgc7nz"))))
  53     (build-system python-build-system)
  54     (native-inputs
  55      `(("python-cython" ,python-cython)))
  56     (propagated-inputs
  57      `(("python-cysignals" ,python-cysignals)))
  58     (inputs
  59      `(("gmp" ,gmp)
  60        ("pari-gp", pari-gp)))
  61     (home-page "https://cypari2.readthedocs.io/")
  62     (synopsis
  63      "Python interface to the number theory library libpari")
  64     (description
  65      "Cypari2 provides a Python interface to the number theory library
  66 PARI/GP.  It has been spun off from the SageMath mathematics software system,
  67 but it can be used independently.")
  68     (license license:gpl2+)))
  69
  70 (define-public python2-cypari2
  71   (package-with-python2 python-cypari2))
  72
  73 ;; The stable version of the following package is not young enough to be
  74 ;; used with Sage, since it does not support cython; so we use a beta
  75 ;; release.
  76 (define-public python-gmpy2
  77   (package
  78     (name "python-gmpy2")
  79     (version "2.1.0b1")
  80     (source (origin
  81               (method git-fetch)
  82               (uri (git-reference
  83                     (url "https://github.com/aleaxit/gmpy")
  84                     (commit (string-append "gmpy2-" version))))
  85               (file-name (git-file-name name version))
  86               (sha256
  87                (base32
  88                 "0ljvnmhxqdfsp0yy4c2hynhk5sggm63kkqsq4iwq4k9vsnx2xm97"))))
  89     (build-system python-build-system)
  90     (native-inputs
  91      `(("unzip" ,unzip)))
  92     (inputs
  93      `(("gmp" ,gmp)
  94        ("mpfr" ,mpfr)
  95        ("mpc" ,mpc)))
  96     (home-page "https://github.com/aleaxit/gmpy")
  97     (synopsis
  98      "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x")
  99     (description
 100      "This package provides a Python interface to the GNU multiprecision
 101 libraries GMO, MPFR and MPC.")
 102     (license license:lgpl3+)))
 103
 104 (define-public python2-gmpy2
 105   (package-with-python2 python-gmpy2))
 106
 107 (define-public cliquer
 108   (package
 109     (name "cliquer")
 110     (version "1.21")
 111     ;; The original source package is available from the home page and
 112     ;; has not seen any release since 2010; it comes with only a Makefile
 113     ;; without an "install" target. Instead, there is an autotoolized
 114     ;; tarball available from the Sage project.
 115     (source
 116      (origin
 117        (method url-fetch)
 118        (uri "http://users.ox.ac.uk/~coml0531/sage/cliquer-1.21.tar.gz")
 119        (sha256
 120         (base32
 121          "1hdzrmrx0nvvj8kbwxrs8swqgkd284khzl623jizixcv28xb77aq"))))
 122     (build-system gnu-build-system)
 123     (synopsis "C routines for finding cliques in weighted graphs")
 124     (description "Cliquer is a set of reentrant C routines for finding
 125 cliques in a weighted or unweighted graph.  It uses an exact
 126 branch-and-bound algorithm.  It can search for maximum or maximum-weight
 127 cliques or cliques with size or weight within a given range, restrict the
 128 search to maximal cliques, store cliques in memory and call a user-defined
 129 function for every found clique.")
 130     (license license:gpl2+)
 131     (home-page "https://users.aalto.fi/~pat/cliquer.html")))
 132
 133 (define-public libbraiding
 134   (package
 135     (name "libbraiding")
 136     (version "1.0")
 137     (source
 138      (origin
 139        (method git-fetch)
 140        (uri (git-reference
 141               (url (string-append "https://github.com/miguelmarco/"
 142                                   name))
 143               (commit version)))
 144        (file-name (git-file-name name version))
 145        (sha256
 146         (base32
 147          "0l68rikfr7k2l547gb3pp3g8cj5zzxwipm79xrb5r8ffj466ydxg"))))
 148     (build-system gnu-build-system)
 149     (native-inputs
 150      `(("autoconf" ,autoconf)
 151        ("automake" ,automake)
 152        ("libtool" ,libtool)))
 153     (synopsis "Computations with braid groups")
 154     (description "libbraiding performs computations with braid groups,
 155 in particular it computes normal forms of group elements.")
 156     (license license:gpl2+)
 157     (home-page "https://github.com/miguelmarco/libbraiding")))
 158
 159 (define-public libhomfly
 160   (package
 161     (name "libhomfly")
 162     (version "1.02r6")
 163     (source
 164      (origin
 165        (method git-fetch)
 166        (uri (git-reference
 167               (url (string-append "https://github.com/miguelmarco/"
 168                                   name))
 169               (commit version)))
 170        (file-name (git-file-name name version))
 171        (sha256
 172         (base32
 173          "0sv3cwrf9v9sb5a8wbhjmarxvya13ma3j8y8592f9ymxlk5y0ldk"))))
 174     (build-system gnu-build-system)
 175     (native-inputs
 176      `(("autoconf" ,autoconf)
 177        ("automake" ,automake)
 178        ("libtool" ,libtool)))
 179     (inputs
 180      `(("libgc" ,libgc)))
 181     (synopsis "Computation of homfly polynomials of links")
 182     (description "libhomfly computes homfly polynomials of links,
 183 represented as strings.")
 184     (license license:public-domain)
 185     (home-page "https://github.com/miguelmarco/libhomfly")))
 186
 187 ;; The following three packages from the Linbox group are needed in
 188 ;; an outdated version for Sage.
 189
 190 (define-public givaro-4.0.4
 191   (package (inherit givaro)
 192     (name "givaro")
 193     (version "4.0.4")
 194     (source (origin
 195               (method git-fetch)
 196               (uri (git-reference
 197                     (url "https://github.com/linbox-team/givaro")
 198                     (commit (string-append "v" version))))
 199               (file-name (git-file-name name version))
 200               (sha256
 201                (base32
 202                 "199p8wyj5i63jbnk7j8qbdbfp5rm2lpmcxyk3mdjy9bz7ygx3hhy"))))))
 203
 204 (define-public fflas-ffpack-2.3.2
 205   (package (inherit fflas-ffpack)
 206     (name "fflas-ffpack")
 207     (version "2.3.2")
 208     (source (origin
 209               (method git-fetch)
 210               (uri (git-reference
 211                     (url "https://github.com/linbox-team/fflas-ffpack")
 212                     (commit (string-append "v" version))))
 213               (file-name (git-file-name name version))
 214               (sha256
 215                (base32
 216                 "1cqhassj2dny3gx0iywvmnpq8ca0d6m82xl5rz4mb8gaxr2kwddl"))))
 217     (propagated-inputs
 218      `(("givaro" ,givaro-4.0.4)))
 219     ;; A test fails, but since all tests pass in the latest version,
 220     ;; there is not much point in investigating.
 221     (arguments
 222      (substitute-keyword-arguments (package-arguments fflas-ffpack)
 223        ((#:tests? _ #f) #f)))))
 224
 225 (define-public linbox-1.5.2
 226   (package (inherit linbox)
 227     (version "1.5.2")
 228     (name "linbox")
 229     (source (origin
 230               (method git-fetch)
 231               (uri (git-reference
 232                     (url "https://github.com/linbox-team/linbox")
 233                     (commit (string-append "v" version))))
 234               (file-name (git-file-name name version))
 235               (sha256
 236                (base32
 237                 "1wfivlwp30mzdy1697w7rzb8caajim50mc8h27k82yipn2qc5n4i"))))
 238     (inputs
 239      `(("fflas-ffpack" ,fflas-ffpack-2.3.2)))))
 240
 241 (define-public pynac
 242   (package
 243     (name "pynac")
 244     (version "0.7.26")
 245     (source
 246      (origin
 247        (method git-fetch)
 248        (uri (git-reference
 249               (url "https://github.com/pynac/pynac/")
 250               (commit (string-append "pynac-" version))))
 251        (file-name (git-file-name name version))
 252        (sha256
 253         (base32 "09d2p74x1arkydlxy6pw4p4byi7r8q7f29w373h4d8a215kadc6d"))))
 254     (build-system gnu-build-system)
 255     (native-inputs
 256      `(("autoconf" ,autoconf)
 257        ("automake" ,automake)
 258        ("libtool" ,libtool)
 259        ("pkg-config" ,pkg-config)))
 260     (inputs
 261      `(("flint" ,flint)
 262        ("gmp" ,gmp)
 263        ("python" ,python)
 264        ("singular" ,singular)))
 265     (synopsis "Sage fork of GiNaC")
 266     (description "Pynac is a derivative of the C++ library GiNaC, which
 267 allows manipulation of symbolic expressions.  It currently provides the
 268 backend for symbolic expressions in Sage.  The main difference between
 269 Pynac and GiNaC is that Pynac relies on Sage to provide the operations
 270 on numerical types, while GiNaC depends on CLN for this purpose.")
 271     (license license:gpl2+)
 272     (home-page "http://pynac.org/")))
 273
 274 ;; Sage has become upstream of the following package.
 275 (define-public zn-poly
 276   (package
 277     (name "zn-poly")
 278     (version "0.9.1")
 279     (source
 280      (origin
 281        (method git-fetch)
 282        (uri (git-reference
 283               (url (string-append "https://gitlab.com/sagemath/"
 284                                   "zn_poly.git/"))
 285               (commit version)))
 286        (file-name (git-file-name "zn_poly" version))
 287        (sha256
 288         (base32
 289          "0ra5vy585bqq7g3317iw6fp44iqgqvds3j0l1va6mswimypq4vxb"))))
 290     (build-system gnu-build-system)
 291     (native-inputs
 292      `(("python" ,python-2)))
 293     (inputs
 294      `(("gmp" ,gmp)))
 295     (arguments
 296      `(#:phases
 297        (modify-phases %standard-phases
 298          (replace 'configure
 299            ;; The configure script chokes on --enable-fast-install.
 300            (lambda* (#:key inputs outputs #:allow-other-keys)
 301              (invoke "./configure"
 302                      (string-append "--prefix=" (assoc-ref outputs "out"))
 303                      "--cflags=-O3 -fPIC")))
 304          (add-before 'build 'prepare-build
 305            (lambda _
 306              (setenv "CC" "gcc")
 307              #t))
 308          (add-after 'build 'build-so
 309            (lambda _
 310              (invoke "make" "libzn_poly.so")))
 311          (add-after 'install 'install-so
 312            (lambda* (#:key outputs #:allow-other-keys)
 313              (let* ((out (assoc-ref outputs "out"))
 314                     (lib (string-append out "/lib"))
 315                     (soname (string-append "libzn_poly-" ,version ".so"))
 316                     (target (string-append lib "/" soname)))
 317                (install-file "libzn_poly.a" lib)
 318                (install-file soname lib)
 319                (symlink target
 320                         (string-append lib "/libzn_poly.so"))
 321                (symlink target
 322                         (string-append lib "/libzn_poly-"
 323                                        ,(version-major+minor version)
 324                                        ".so")))
 325              #t)))))
 326     (synopsis "Arithmetic for polynomials over Z/NZ")
 327     (description "zn_poly implements the arithmetic of polynomials the
 328 coefficients of which are modular integers.")
 329     (license (list license:gpl2 license:gpl3)) ; dual licensed
 330     (home-page "https://gitlab.com/sagemath/zn_poly")))
 331
 332 (define-public brial
 333   (package
 334     (name "brial")
 335     (version "1.2.5")
 336     (source
 337     (origin
 338       (method git-fetch)
 339       (uri (git-reference
 340              (url "https://github.com/BRiAl/BRiAl/")
 341              (commit version)))
 342       (file-name (git-file-name name version))
 343       (sha256
 344        (base32
 345         "1nv56fp3brpzanxj7vwvxqdafqfsfhdgq5imr3m94psw5gdfqwja"))))
 346     (build-system gnu-build-system)
 347     (native-inputs
 348      `(("autoconf" ,autoconf)
 349        ("automake" ,automake)
 350        ("libtool" ,libtool)
 351        ("pkg-config" ,pkg-config)))
 352     (inputs
 353      `(("boost" ,boost)
 354        ("libpng" ,libpng)
 355        ("m4ri" ,m4ri)))
 356     (arguments
 357     ;; We are missing the boost unit test framework.
 358      `(#:tests? #f
 359        #:configure-flags (list "--without-boost-unit-test-framework")))
 360     (synopsis "Arithmetic of polynomials over boolean rings")
 361     (description "BRiAl is the successor to  PolyBoRi maintained by the
 362 Sage community.  Its core is a C++ library, which provides high-level data
 363 types for Boolean polynomials and monomials, exponent vectors, as well as
 364 for the underlying polynomial rings and subsets of the powerset of the
 365 Boolean variables.  As a unique approach, binary decision diagrams are
 366 used as internal storage type for polynomial structures.")
 367     (license license:gpl2+)
 368     (home-page "https://gitlab.com/sagemath/zn_poly")))
 369
 370 (define-public lcalc
 371   (package
 372     (name "lcalc")
 373     (version "1.23")
 374     ;; The original home page of the project has disappeared, as well as
 375     ;; code hosted by the original author on Google Code. The latter has
 376     ;; been copied to gitlab.com/sagemath and purportedly contains patches
 377     ;; for a never released version 1.3, that supposedly follows 1.23.
 378     ;; We use the tarball as well as the patches hosted inside the sage
 379     ;; package system distributed with the sage tarball.
 380     (source
 381      (origin
 382        (method url-fetch)
 383        (uri (string-append "ftp://ftp.fu-berlin.de/unix/misc/sage/spkg/"
 384                            "upstream/lcalc/lcalc-1.23.tar.bz2"))
 385        (sha256
 386         (base32
 387          "1c6dsdshgxhqppjxvxhp8yhpxaqvnz3d1mlh26r571gkq8z2bm43"))
 388        (patches (search-patches "lcalc-lcommon-h.patch"
 389                                 "lcalc-default-parameters-1.patch"
 390                                 "lcalc-default-parameters-2.patch"
 391                                 "lcalc-using-namespace-std.patch"))))
 392     (build-system gnu-build-system)
 393     (arguments
 394      `(#:tests? #f ;no tests
 395        #:phases
 396        (modify-phases %standard-phases
 397          (delete 'configure)
 398          (add-before 'build 'prepare-build
 399            (lambda* (#:key outputs #:allow-other-keys)
 400              (chdir "src")
 401              (let ((out (assoc-ref outputs "out")))
 402                (substitute* "Makefile"
 403                  (("^INSTALL_DIR= /usr/local")
 404                   (string-append "INSTALL_DIR=" out))
 405                  ;; Sage renames the include directory, so we do it also.
 406                  (("include/Lfunction")
 407                   "include/libLfunction")))
 408              #t))
 409          (add-before 'install 'make-output-dirs
 410            (lambda* (#:key outputs #:allow-other-keys)
 411              (let* ((out (assoc-ref outputs "out"))
 412                     (bin (string-append out "/bin"))
 413                     (lib (string-append out "/lib"))
 414                     (include (string-append out "/include")))
 415                (mkdir-p bin)
 416                (mkdir-p lib)
 417                (mkdir-p include))
 418              #t)))))
 419     ;; FIXME:
 420     ;; We need to add pari-gp and probably pari related patches from the
 421     ;; sage project, as well as uncomment the line setting PARI_DEFINE in
 422     ;; the Makefile to get the full functionality of this package.
 423     ;; For the time being, we hope that sage can be compiled without.
 424     (synopsis "C++ library for L-functions")
 425     (description "Lcalc computes L-functions, in particular the Riemann
 426 zeta function and its twists by quadratic characters.")
 427     (license license:gpl2+)
 428     (home-page "https://gitlab.com/sagemath/sage")))
 429
 430 (define-public ratpoints
 431   (package
 432     (name "ratpoints")
 433     (version "2.1.3")
 434     (source (origin
 435               (method url-fetch)
 436               (uri (string-append
 437                     "http://www.mathe2.uni-bayreuth.de/stoll/programs/"
 438                     "ratpoints-" version ".tar.gz"))
 439               (sha256
 440                (base32
 441                 "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4"))
 442               (patches
 443                ;; Taken from
 444                ;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/>
 445                (search-patches "ratpoints-sturm_and_rp_private.patch"))))
 446     (build-system gnu-build-system)
 447     (arguments
 448      `(#:test-target "test"
 449        #:make-flags
 450        (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out"))
 451              "CCFLAGS=-fPIC")
 452        #:phases
 453        (modify-phases %standard-phases
 454          (delete 'configure)            ;no configure script
 455          (add-before 'install 'create-install-directories
 456            (lambda* (#:key outputs #:allow-other-keys)
 457              (let ((out (assoc-ref outputs "out")))
 458                (mkdir-p out)
 459                (with-directory-excursion out
 460                  (for-each (lambda (d) (mkdir-p d))
 461                            '("bin" "include" "lib"))))
 462              #t)))))
 463     (inputs
 464      `(("gmp" ,gmp)))
 465     (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/")
 466     (synopsis "Find rational points on hyperelliptic curves")
 467     (description "Ratpoints tries to find all rational points within
 468 a given height bound on a hyperelliptic curve in a very efficient way,
 469 by using an optimized quadratic sieve algorithm.")
 470     (license license:gpl2+)))