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 ;;; Copyright © 2021 Efraim Flashner <efraim@flashner.co.il>
   7 ;;;
   8 ;;; This file is part of GNU Guix.
   9 ;;;
  10 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  11 ;;; under the terms of the GNU General Public License as published by
  12 ;;; the Free Software Foundation; either version 3 of the License, or (at
  13 ;;; your option) any later version.
  14 ;;;
  15 ;;; GNU Guix is distributed in the hope that it will be useful, but
  16 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  17 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  18 ;;; GNU General Public License for more details.
  19 ;;;
  20 ;;; You should have received a copy of the GNU General Public License
  21 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  22
  23 (define-module (gnu packages sagemath)
  24   #:use-module ((guix licenses) #:prefix license:)
  25   #:use-module (guix build-system gnu)
  26   #:use-module (guix build-system python)
  27   #:use-module (guix download)
  28   #:use-module (guix git-download)
  29   #:use-module (guix packages)
  30   #:use-module (guix utils)
  31   #:use-module (gnu packages)
  32   #:use-module (gnu packages algebra)
  33   #:use-module (gnu packages autotools)
  34   #:use-module (gnu packages bdw-gc)
  35   #:use-module (gnu packages boost)
  36   #:use-module (gnu packages compression)
  37   #:use-module (gnu packages image)
  38   #:use-module (gnu packages lisp)
  39   #:use-module (gnu packages multiprecision)
  40   #:use-module (gnu packages pkg-config)
  41   #:use-module (gnu packages python)
  42   #:use-module (gnu packages python-xyz))
  43
  44
  45 (define-public python-cypari2
  46   (package
  47     (name "python-cypari2")
  48     (version "2.1.2")
  49     (source
  50      (origin
  51        (method url-fetch)
  52        (uri (pypi-uri "cypari2" version))
  53        (sha256
  54         (base32
  55          "0ymc4i9y60aazscc1blivirkr1rflzz6akkmvfzyn5l7mgnlbk83"))))
  56     (build-system python-build-system)
  57     (native-inputs
  58      (list python-cython))
  59     (propagated-inputs
  60      (list python-cysignals))
  61     (inputs
  62      (list gmp 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      (list unzip))
  94     (inputs
  95      (list gmp mpfr 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      (list autoconf automake libtool))
 151     (synopsis "Computations with braid groups")
 152     (description "libbraiding performs computations with braid groups,
 153 in particular it computes normal forms of group elements.")
 154     (license license:gpl2+)
 155     (home-page "https://github.com/miguelmarco/libbraiding")))
 156
 157 (define-public libhomfly
 158   (package
 159     (name "libhomfly")
 160     (version "1.02r6")
 161     (source
 162      (origin
 163        (method git-fetch)
 164        (uri (git-reference
 165               (url (string-append "https://github.com/miguelmarco/"
 166                                   name))
 167               (commit version)))
 168        (file-name (git-file-name name version))
 169        (sha256
 170         (base32
 171          "0sv3cwrf9v9sb5a8wbhjmarxvya13ma3j8y8592f9ymxlk5y0ldk"))))
 172     (build-system gnu-build-system)
 173     (native-inputs
 174      (list autoconf automake libtool))
 175     (inputs
 176      (list libgc))
 177     (synopsis "Computation of homfly polynomials of links")
 178     (description "libhomfly computes homfly polynomials of links,
 179 represented as strings.")
 180     (license license:public-domain)
 181     (home-page "https://github.com/miguelmarco/libhomfly")))
 182
 183 ;; Sage 9.1 doesn't build with ECL 20.  This won't be necessary once 9.2 is
 184 ;; released.  See https://trac.sagemath.org/ticket/22191
 185 (define-public ecl-16
 186   (package
 187     (inherit ecl)
 188     (version "16.1.3")
 189     (source
 190      (origin
 191        (method url-fetch)
 192        (uri (string-append
 193              "https://common-lisp.net/project/ecl/static/files/release/ecl"
 194              "-" version ".tgz"))
 195        (sha256
 196         (base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn"))
 197        (patches (search-patches
 198                   "ecl-16-libffi.patch"
 199                   "ecl-16-ignore-stderr-write-error.patch"
 200                   "ecl-16-format-directive-limit.patch"))))
 201     ;; Current ECL uses LGPL 2.1+
 202     (license license:lgpl2.0+)))
 203
 204 (define-public pynac
 205   (package
 206     (name "pynac")
 207     (version "0.7.26")
 208     (source
 209      (origin
 210        (method git-fetch)
 211        (uri (git-reference
 212               (url "https://github.com/pynac/pynac/")
 213               (commit (string-append "pynac-" version))))
 214        (file-name (git-file-name name version))
 215        (sha256
 216         (base32 "09d2p74x1arkydlxy6pw4p4byi7r8q7f29w373h4d8a215kadc6d"))))
 217     (build-system gnu-build-system)
 218     (native-inputs
 219      (list autoconf automake libtool pkg-config))
 220     (inputs
 221      (list flint gmp python singular))
 222     (synopsis "Sage fork of GiNaC")
 223     (description "Pynac is a derivative of the C++ library GiNaC, which
 224 allows manipulation of symbolic expressions.  It currently provides the
 225 backend for symbolic expressions in Sage.  The main difference between
 226 Pynac and GiNaC is that Pynac relies on Sage to provide the operations
 227 on numerical types, while GiNaC depends on CLN for this purpose.")
 228     (license license:gpl2+)
 229     (home-page "http://pynac.org/")))
 230
 231 ;; Sage has become upstream of the following package.
 232 (define-public zn-poly
 233   (package
 234     (name "zn-poly")
 235     (version "0.9.2")
 236     (source
 237      (origin
 238        (method git-fetch)
 239        (uri (git-reference
 240               (url (string-append "https://gitlab.com/sagemath/"
 241                                   "zn_poly.git/"))
 242               (commit version)))
 243        (file-name (git-file-name "zn_poly" version))
 244        (sha256
 245         (base32 "1wbc3apxcldxfcw1dnwnn7fvlfb6bwvlr8glvgv6hf79p9r2s4j0"))))
 246     (build-system gnu-build-system)
 247     (native-inputs
 248      `(("python" ,python-2)))
 249     (inputs
 250      (list gmp))
 251     (arguments
 252      `(#:phases
 253        (modify-phases %standard-phases
 254          (replace 'configure
 255            ;; The configure script chokes on --enable-fast-install.
 256            (lambda* (#:key inputs outputs #:allow-other-keys)
 257              (invoke "./configure"
 258                      (string-append "--prefix=" (assoc-ref outputs "out"))
 259                      "--cflags=-O3 -fPIC")))
 260          (add-before 'build 'prepare-build
 261            (lambda _
 262              (setenv "CC" "gcc")
 263              #t))
 264          (add-after 'build 'build-so
 265            (lambda _
 266              (invoke "make" "libzn_poly.so")))
 267          (add-after 'install 'install-so
 268            (lambda* (#:key outputs #:allow-other-keys)
 269              (let* ((out (assoc-ref outputs "out"))
 270                     (lib (string-append out "/lib"))
 271                     (soname (string-append "libzn_poly-" ,version ".so"))
 272                     (target (string-append lib "/" soname)))
 273                (install-file "libzn_poly.a" lib)
 274                (install-file soname lib)
 275                (symlink target
 276                         (string-append lib "/libzn_poly.so"))
 277                (symlink target
 278                         (string-append lib "/libzn_poly-"
 279                                        ,(version-major+minor version)
 280                                        ".so")))
 281              #t)))))
 282     (synopsis "Arithmetic for polynomials over Z/NZ")
 283     (description "zn_poly implements the arithmetic of polynomials the
 284 coefficients of which are modular integers.")
 285     (license (list license:gpl2 license:gpl3)) ; dual licensed
 286     (home-page "https://gitlab.com/sagemath/zn_poly")))
 287
 288 (define-public brial
 289   (package
 290     (name "brial")
 291     (version "1.2.8")
 292     (source
 293     (origin
 294       (method git-fetch)
 295       (uri (git-reference
 296              (url "https://github.com/BRiAl/BRiAl/")
 297              (commit version)))
 298       (file-name (git-file-name name version))
 299       (sha256
 300        (base32 "0qhgckd4fvbs40jw14mvw89rccv94d3df27kipd27hxd4cx7y80y"))))
 301     (build-system gnu-build-system)
 302     (native-inputs
 303      (list autoconf automake libtool pkg-config))
 304     (inputs
 305      (list boost libpng m4ri))
 306     (arguments
 307     ;; We are missing the boost unit test framework.
 308      `(#:tests? #f
 309        #:configure-flags (list "--without-boost-unit-test-framework")))
 310     (synopsis "Arithmetic of polynomials over boolean rings")
 311     (description "BRiAl is the successor to  PolyBoRi maintained by the
 312 Sage community.  Its core is a C++ library, which provides high-level data
 313 types for Boolean polynomials and monomials, exponent vectors, as well as
 314 for the underlying polynomial rings and subsets of the powerset of the
 315 Boolean variables.  As a unique approach, binary decision diagrams are
 316 used as internal storage type for polynomial structures.")
 317     (license license:gpl2+)
 318     (home-page "https://github.com/BRiAl/BRiAl/")))
 319
 320 (define-public lcalc
 321   (package
 322     (name "lcalc")
 323     (version "1.23")
 324     ;; The original home page of the project has disappeared, as well as
 325     ;; code hosted by the original author on Google Code. The latter has
 326     ;; been copied to gitlab.com/sagemath and purportedly contains patches
 327     ;; for a never released version 1.3, that supposedly follows 1.23.
 328     ;; We use the tarball as well as the patches hosted inside the sage
 329     ;; package system distributed with the sage tarball.
 330     (source
 331      (origin
 332        (method url-fetch)
 333        (uri (string-append "ftp://ftp.fu-berlin.de/unix/misc/sage/spkg/"
 334                            "upstream/lcalc/lcalc-1.23.tar.bz2"))
 335        (sha256
 336         (base32
 337          "1c6dsdshgxhqppjxvxhp8yhpxaqvnz3d1mlh26r571gkq8z2bm43"))
 338        (patches (search-patches "lcalc-lcommon-h.patch"
 339                                 "lcalc-default-parameters-1.patch"
 340                                 "lcalc-default-parameters-2.patch"
 341                                 "lcalc-using-namespace-std.patch"))))
 342     (build-system gnu-build-system)
 343     (arguments
 344      `(#:tests? #f ;no tests
 345        #:phases
 346        (modify-phases %standard-phases
 347          (delete 'configure)
 348          (add-before 'build 'prepare-build
 349            (lambda* (#:key outputs #:allow-other-keys)
 350              (chdir "src")
 351              (let ((out (assoc-ref outputs "out")))
 352                (substitute* "Makefile"
 353                  (("^INSTALL_DIR= /usr/local")
 354                   (string-append "INSTALL_DIR=" out))))
 355              #t))
 356          (add-before 'install 'make-output-dirs
 357            (lambda* (#:key outputs #:allow-other-keys)
 358              (let* ((out (assoc-ref outputs "out"))
 359                     (bin (string-append out "/bin"))
 360                     (lib (string-append out "/lib"))
 361                     (include (string-append out "/include")))
 362                (mkdir-p bin)
 363                (mkdir-p lib)
 364                (mkdir-p include))
 365              #t)))))
 366     ;; FIXME:
 367     ;; We need to add pari-gp and probably pari related patches from the
 368     ;; sage project, as well as uncomment the line setting PARI_DEFINE in
 369     ;; the Makefile to get the full functionality of this package.
 370     ;; For the time being, we hope that sage can be compiled without.
 371     (synopsis "C++ library for L-functions")
 372     (description "Lcalc computes L-functions, in particular the Riemann
 373 zeta function and its twists by quadratic characters.")
 374     (license license:gpl2+)
 375     (home-page "https://gitlab.com/sagemath/sage")))
 376
 377 (define-public ratpoints
 378   (package
 379     (name "ratpoints")
 380     (version "2.1.3")
 381     (source (origin
 382               (method url-fetch)
 383               (uri (string-append
 384                     "http://www.mathe2.uni-bayreuth.de/stoll/programs/"
 385                     "ratpoints-" version ".tar.gz"))
 386               (sha256
 387                (base32
 388                 "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4"))
 389               (patches
 390                ;; Taken from
 391                ;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/>
 392                (search-patches "ratpoints-sturm_and_rp_private.patch"))))
 393     (build-system gnu-build-system)
 394     (arguments
 395      `(#:test-target "test"
 396        #:make-flags
 397        (list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out"))
 398              "CCFLAGS=-fPIC")
 399        #:phases
 400        (modify-phases %standard-phases
 401          (delete 'configure)            ;no configure script
 402          (add-before 'install 'create-install-directories
 403            (lambda* (#:key outputs #:allow-other-keys)
 404              (let ((out (assoc-ref outputs "out")))
 405                (mkdir-p out)
 406                (with-directory-excursion out
 407                  (for-each (lambda (d) (mkdir-p d))
 408                            '("bin" "include" "lib"))))
 409              #t)))))
 410     (inputs
 411      (list gmp))
 412     (home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/")
 413     (synopsis "Find rational points on hyperelliptic curves")
 414     (description "Ratpoints tries to find all rational points within
 415 a given height bound on a hyperelliptic curve in a very efficient way,
 416 by using an optimized quadratic sieve algorithm.")
 417     (license license:gpl2+)))