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