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, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
   5 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
   6 ;;;
   7 ;;; This file is part of GNU Guix.
   8 ;;;
   9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  10 ;;; under the terms of the GNU General Public License as published by
  11 ;;; the Free Software Foundation; either version 3 of the License, or (at
  12 ;;; your option) any later version.
  13 ;;;
  14 ;;; GNU Guix is distributed in the hope that it will be useful, but
  15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  17 ;;; GNU General Public License for more details.
  18 ;;;
  19 ;;; You should have received a copy of the GNU General Public License
  20 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  21
  22 (define-module (gnu packages sagemath)
  23   #:use-module ((guix licenses) #:prefix license:)
  24   #:use-module (guix build-system gnu)
  25   #:use-module (guix build-system python)
  26   #:use-module (guix download)
  27   #:use-module (guix git-download)
  28   #:use-module (guix packages)
  29   #:use-module (guix utils)
  30   #:use-module (gnu packages)
  31   #:use-module (gnu packages algebra)
  32   #:use-module (gnu packages autotools)
  33   #:use-module (gnu packages bdw-gc)
  34   #:use-module (gnu packages boost)
  35   #:use-module (gnu packages compression)
  36   #:use-module (gnu packages image)
  37   #:use-module (gnu packages lisp)
  38   #:use-module (gnu packages multiprecision)
  39   #:use-module (gnu packages pkg-config)
  40   #:use-module (gnu packages python)
  41   #:use-module (gnu packages python-xyz))
  42
  43
  44 (define-public python-cypari2
  45   (package
  46     (name "python-cypari2")
  47     (version "2.1.1")
  48     (source
  49      (origin
  50        (method url-fetch)
  51        (uri (pypi-uri "cypari2" version))
  52        (sha256
  53         (base32
  54          "1nwkzgqvbw6361x0rpggy1q5nx663fswhpvg8md6xhqyfwpgc7nz"))))
  55     (build-system python-build-system)
  56     (native-inputs
  57      `(("python-cython" ,python-cython)))
  58     (propagated-inputs
  59      `(("python-cysignals" ,python-cysignals)))
  60     (inputs
  61      `(("gmp" ,gmp)
  62        ("pari-gp", pari-gp)))
  63     (home-page "https://cypari2.readthedocs.io/")
  64     (synopsis
  65      "Python interface to the number theory library libpari")
  66     (description
  67      "Cypari2 provides a Python interface to the number theory library
  68 PARI/GP.  It has been spun off from the SageMath mathematics software system,
  69 but it can be used independently.")
  70     (license license:gpl2+)))
  71
  72 (define-public python2-cypari2
  73   (package-with-python2 python-cypari2))
  74
  75 ;; The stable version of the following package is not young enough to be
  76 ;; used with Sage, since it does not support cython; so we use a beta
  77 ;; release.
  78 (define-public python-gmpy2
  79   (package
  80     (name "python-gmpy2")
  81     (version "2.1.0b1")
  82     (source (origin
  83               (method git-fetch)
  84               (uri (git-reference
  85                     (url "https://github.com/aleaxit/gmpy")
  86                     (commit (string-append "gmpy2-" version))))
  87               (file-name (git-file-name name version))
  88               (sha256
  89                (base32
  90                 "0ljvnmhxqdfsp0yy4c2hynhk5sggm63kkqsq4iwq4k9vsnx2xm97"))))
  91     (build-system python-build-system)
  92     (native-inputs
  93      `(("unzip" ,unzip)))
  94     (inputs
  95      `(("gmp" ,gmp)
  96        ("mpfr" ,mpfr)
  97        ("mpc" ,mpc)))
  98     (home-page "https://github.com/aleaxit/gmpy")
  99     (synopsis
 100      "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x")
 101     (description
 102      "This package provides a Python interface to the GNU multiprecision
 103 libraries GMO, MPFR and MPC.")
 104     (license license:lgpl3+)))
 105
 106 (define-public python2-gmpy2
 107   (package-with-python2 python-gmpy2))
 108
 109 (define-public cliquer
 110   (package
 111     (name "cliquer")
 112     (version "1.21")
 113     ;; The original source package is available from the home page and
 114     ;; has not seen any release since 2010; it comes with only a Makefile
 115     ;; without an "install" target. Instead, there is an autotoolized
 116     ;; tarball available from the Sage project.
 117     (source
 118      (origin
 119        (method url-fetch)
 120        (uri "http://users.ox.ac.uk/~coml0531/sage/cliquer-1.21.tar.gz")
 121        (sha256
 122         (base32
 123          "1hdzrmrx0nvvj8kbwxrs8swqgkd284khzl623jizixcv28xb77aq"))))
 124     (build-system gnu-build-system)
 125     (synopsis "C routines for finding cliques in weighted graphs")
 126     (description "Cliquer is a set of reentrant C routines for finding
 127 cliques in a weighted or unweighted graph.  It uses an exact
 128 branch-and-bound algorithm.  It can search for maximum or maximum-weight
 129 cliques or cliques with size or weight within a given range, restrict the
 130 search to maximal cliques, store cliques in memory and call a user-defined
 131 function for every found clique.")
 132     (license license:gpl2+)
 133     (home-page "https://users.aalto.fi/~pat/cliquer.html")))
 134
 135 (define-public libbraiding
 136   (package
 137     (name "libbraiding")
 138     (version "1.0")
 139     (source
 140      (origin
 141        (method git-fetch)
 142        (uri (git-reference
 143               (url (string-append "https://github.com/miguelmarco/"
 144                                   name))
 145               (commit version)))
 146        (file-name (git-file-name name version))
 147        (sha256
 148         (base32
 149          "0l68rikfr7k2l547gb3pp3g8cj5zzxwipm79xrb5r8ffj466ydxg"))))
 150     (build-system gnu-build-system)
 151     (native-inputs
 152      `(("autoconf" ,autoconf)
 153        ("automake" ,automake)
 154        ("libtool" ,libtool)))
 155     (synopsis "Computations with braid groups")
 156     (description "libbraiding performs computations with braid groups,
 157 in particular it computes normal forms of group elements.")
 158     (license license:gpl2+)
 159     (home-page "https://github.com/miguelmarco/libbraiding")))
 160
 161 (define-public libhomfly
 162   (package
 163     (name "libhomfly")
 164     (version "1.02r6")
 165     (source
 166      (origin
 167        (method git-fetch)
 168        (uri (git-reference
 169               (url (string-append "https://github.com/miguelmarco/"
 170                                   name))
 171               (commit version)))
 172        (file-name (git-file-name name version))
 173        (sha256
 174         (base32
 175          "0sv3cwrf9v9sb5a8wbhjmarxvya13ma3j8y8592f9ymxlk5y0ldk"))))
 176     (build-system gnu-build-system)
 177     (native-inputs
 178      `(("autoconf" ,autoconf)
 179        ("automake" ,automake)
 180        ("libtool" ,libtool)))
 181     (inputs
 182      `(("libgc" ,libgc)))
 183     (synopsis "Computation of homfly polynomials of links")
 184     (description "libhomfly computes homfly polynomials of links,
 185 represented as strings.")
 186     (license license:public-domain)
 187     (home-page "https://github.com/miguelmarco/libhomfly")))
 188
 189 ;; Sage 9.1 doesn't build with ECL 20.  This won't be necessary once 9.2 is
 190 ;; released.  See https://trac.sagemath.org/ticket/22191
 191 (define-public ecl-16
 192   (package
 193     (inherit ecl)
 194     (version "16.1.3")
 195     (source
 196      (origin
 197        (method url-fetch)
 198        (uri (string-append
 199              "https://common-lisp.net/project/ecl/static/files/release/ecl"
 200              "-" version ".tgz"))
 201        (sha256
 202         (base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn"))
 203        (patches (search-patches
 204                   "ecl-16-libffi.patch"
 205                   "ecl-16-ignore-stderr-write-error.patch"
 206                   "ecl-16-format-directive-limit.patch"))))
 207     ;; Current ECL uses LGPL 2.1+
 208     (license license:lgpl2.0+)))
 209
 210 (define-public pynac
 211   (package
 212     (name "pynac")
 213     (version "0.7.26")
 214     (source
 215      (origin
 216        (method git-fetch)
 217        (uri (git-reference
 218               (url "https://github.com/pynac/pynac/")
 219               (commit (string-append "pynac-" version))))
 220        (file-name (git-file-name name version))
 221        (sha256
 222         (base32 "09d2p74x1arkydlxy6pw4p4byi7r8q7f29w373h4d8a215kadc6d"))))
 223     (build-system gnu-build-system)
 224     (native-inputs
 225      `(("autoconf" ,autoconf)
 226        ("automake" ,automake)
 227        ("libtool" ,libtool)
 228        ("pkg-config" ,pkg-config)))
 229     (inputs
 230      `(("flint" ,flint)
 231        ("gmp" ,gmp)
 232        ("python" ,python)
 233        ("singular" ,singular)))
 234     (synopsis "Sage fork of GiNaC")
 235     (description "Pynac is a derivative of the C++ library GiNaC, which
 236 allows manipulation of symbolic expressions.  It currently provides the
 237 backend for symbolic expressions in Sage.  The main difference between
 238 Pynac and GiNaC is that Pynac relies on Sage to provide the operations
 239 on numerical types, while GiNaC depends on CLN for this purpose.")
 240     (license license:gpl2+)
 241     (home-page "http://pynac.org/")))
 242
 243 ;; Sage has become upstream of the following package.
 244 (define-public zn-poly
 245   (package
 246     (name "zn-poly")
 247     (version "0.9.2")
 248     (source
 249      (origin
 250        (method git-fetch)
 251        (uri (git-reference
 252               (url (string-append "https://gitlab.com/sagemath/"
 253                                   "zn_poly.git/"))
 254               (commit version)))
 255        (file-name (git-file-name "zn_poly" version))
 256        (sha256
 257         (base32 "1wbc3apxcldxfcw1dnwnn7fvlfb6bwvlr8glvgv6hf79p9r2s4j0"))))
 258     (build-system gnu-build-system)
 259     (native-inputs
 260      `(("python" ,python-2)))
 261     (inputs
 262      `(("gmp" ,gmp)))
 263     (arguments
 264      `(#:phases
 265        (modify-phases %standard-phases
 266          (replace 'configure
 267            ;; The configure script chokes on --enable-fast-install.
 268            (lambda* (#:key inputs outputs #:allow-other-keys)
 269              (invoke "./configure"
 270                      (string-append "--prefix=" (assoc-ref outputs "out"))
 271                      "--cflags=-O3 -fPIC")))
 272          (add-before 'build 'prepare-build
 273            (lambda _
 274              (setenv "CC" "gcc")
 275              #t))
 276          (add-after 'build 'build-so
 277            (lambda _
 278              (invoke "make" "libzn_poly.so")))
 279          (add-after 'install 'install-so
 280            (lambda* (#:key outputs #:allow-other-keys)
 281              (let* ((out (assoc-ref outputs "out"))
 282                     (lib (string-append out "/lib"))
 283                     (soname (string-append "libzn_poly-" ,version ".so"))
 284                     (target (string-append lib "/" soname)))
 285                (install-file "libzn_poly.a" lib)
 286                (install-file soname lib)
 287                (symlink target
 288                         (string-append lib "/libzn_poly.so"))
 289                (symlink target
 290                         (string-append lib "/libzn_poly-"
 291                                        ,(version-major+minor version)
 292                                        ".so")))
 293              #t)))))
 294     (synopsis "Arithmetic for polynomials over Z/NZ")
 295     (description "zn_poly implements the arithmetic of polynomials the
 296 coefficients of which are modular integers.")
 297     (license (list license:gpl2 license:gpl3)) ; dual licensed
 298     (home-page "https://gitlab.com/sagemath/zn_poly")))
 299
 300 (define-public brial
 301   (package
 302     (name "brial")
 303     (version "1.2.8")
 304     (source
 305     (origin
 306       (method git-fetch)
 307       (uri (git-reference
 308              (url "https://github.com/BRiAl/BRiAl/")
 309              (commit version)))
 310       (file-name (git-file-name name version))
 311       (sha256
 312        (base32 "0qhgckd4fvbs40jw14mvw89rccv94d3df27kipd27hxd4cx7y80y"))))
 313     (build-system gnu-build-system)
 314     (native-inputs
 315      `(("autoconf" ,autoconf)
 316        ("automake" ,automake)
 317        ("libtool" ,libtool)
 318        ("pkg-config" ,pkg-config)))
 319     (inputs
 320      `(("boost" ,boost)
 321        ("libpng" ,libpng)
 322        ("m4ri" ,m4ri)))
 323     (arguments
 324     ;; We are missing the boost unit test framework.
 325      `(#:tests? #f
 326        #:configure-flags (list "--without-boost-unit-test-framework")))
 327     (synopsis "Arithmetic of polynomials over boolean rings")
 328     (description "BRiAl is the successor to  PolyBoRi maintained by the
 329 Sage community.  Its core is a C++ library, which provides high-level data
 330 types for Boolean polynomials and monomials, exponent vectors, as well as
 331 for the underlying polynomial rings and subsets of the powerset of the
 332 Boolean variables.  As a unique approach, binary decision diagrams are
 333 used as internal storage type for polynomial structures.")
 334     (license license:gpl2+)
 335     (home-page "https://github.com/BRiAl/BRiAl/")))
 336
 337 (define-public lcalc
 338   (package
 339     (name "lcalc")
 340     (version "1.23")
 341     ;; The original home page of the project has disappeared, as well as
 342     ;; code hosted by the original author on Google Code. The latter has
 343     ;; been copied to gitlab.com/sagemath and purportedly contains patches
 344     ;; for a never released version 1.3, that supposedly follows 1.23.
 345     ;; We use the tarball as well as the patches hosted inside the sage
 346     ;; package system distributed with the sage tarball.
 347     (source
 348      (origin
 349        (method url-fetch)
 350        (uri (string-append "ftp://ftp.fu-berlin.de/unix/misc/sage/spkg/"
 351                            "upstream/lcalc/lcalc-1.23.tar.bz2"))
 352        (sha256
 353         (base32
 354          "1c6dsdshgxhqppjxvxhp8yhpxaqvnz3d1mlh26r571gkq8z2bm43"))
 355        (patches (search-patches "lcalc-lcommon-h.patch"
 356                                 "lcalc-default-parameters-1.patch"
 357                                 "lcalc-default-parameters-2.patch"
 358                                 "lcalc-using-namespace-std.patch"))))
 359     (build-system gnu-build-system)
 360     (arguments
 361      `(#:tests? #f ;no tests
 362        #:phases
 363        (modify-phases %standard-phases
 364          (delete 'configure)
 365          (add-before 'build 'prepare-build
 366            (lambda* (#:key outputs #:allow-other-keys)
 367              (chdir "src")
 368              (let ((out (assoc-ref outputs "out")))
 369                (substitute* "Makefile"
 370                  (("^INSTALL_DIR= /usr/local")
 371                   (string-append "INSTALL_DIR=" out))))
 372              #t))
 373          (add-before 'install 'make-output-dirs
 374            (lambda* (#:key outputs #:allow-other-keys)
 375              (let* ((out (assoc-ref outputs "out"))
 376                     (bin (string-append out "/bin"))
 377                     (lib (string-append out "/lib"))
 378                     (include (string-append out "/include")))
 379                (mkdir-p bin)
 380                (mkdir-p lib)
 381                (mkdir-p include))
 382              #t)))))
 383     ;; FIXME:
 384     ;; We need to add pari-gp and probably pari related patches from the
 385     ;; sage project, as well as uncomment the line setting PARI_DEFINE in
 386     ;; the Makefile to get the full functionality of this package.
 387     ;; For the time being, we hope that sage can be compiled without.
 388     (synopsis "C++ library for L-functions")
 389     (description "Lcalc computes L-functions, in particular the Riemann
 390 zeta function and its twists by quadratic characters.")
 391     (license license:gpl2+)
 392     (home-page "https://gitlab.com/sagemath/sage")))
 393
 394 (define-public ratpoints
 395   (package
 396     (name "ratpoints")
 397     (version "2.1.3")
 398     (source (origin
 399               (method url-fetch)
 400               (uri (string-append
 401                     "http://www.mathe2.uni-bayreuth.de/stoll/programs/"
 402                     "ratpoints-" version ".tar.gz"))
 403               (sha256
 404                (base32
 405                 "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4"))
 406               (patches
 407                ;; Taken from
 408                ;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/>
 409                (search-patches "ratpoints-sturm_and_rp_private.patch"))))
 410     (build-system gnu-build-system)
 411     (arguments
 412      `(#:test-target "test"
 413        #:make-flags
 414        (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out"))
 415              "CCFLAGS=-fPIC")
 416        #:phases
 417        (modify-phases %standard-phases
 418          (delete 'configure)            ;no configure script
 419          (add-before 'install 'create-install-directories
 420            (lambda* (#:key outputs #:allow-other-keys)
 421              (let ((out (assoc-ref outputs "out")))
 422                (mkdir-p out)
 423                (with-directory-excursion out
 424                  (for-each (lambda (d) (mkdir-p d))
 425                            '("bin" "include" "lib"))))
 426              #t)))))
 427     (inputs
 428      `(("gmp" ,gmp)))
 429     (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/")
 430     (synopsis "Find rational points on hyperelliptic curves")
 431     (description "Ratpoints tries to find all rational points within
 432 a given height bound on a hyperelliptic curve in a very efficient way,
 433 by using an optimized quadratic sieve algorithm.")
 434     (license license:gpl2+)))