;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Andreas Enge <address@hidden>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages sagemath)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system python)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages bdw-gc)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages graph)
  #:use-module (gnu packages lisp)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-xyz))


(define-public python-cypari2
  (package
    (name "python-cypari2")
    (version "2.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "cypari2" version))
       (sha256
        (base32
         "1nwkzgqvbw6361x0rpggy1q5nx663fswhpvg8md6xhqyfwpgc7nz"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-cython" ,python-cython)))
    (propagated-inputs
     `(("python-cysignals" ,python-cysignals)))
    (inputs
     `(("gmp" ,gmp)
       ("pari-gp", pari-gp)))
    (home-page "https://cypari2.readthedocs.io/")
    (synopsis
     "Python interface to the number theory library libpari")
    (description
     "Cypari2 provides a Python interface to the number theory library
PARI/GP.  It has been spun off from the SageMath mathematics software system,
but it can be used independently.")
    (license license:gpl2+)))

(define-public python2-cypari2
  (package-with-python2 python-cypari2))

;; The stable version of the following package is not young enough to be
;; used with Sage, since it does not support cython. One would need to
;; use an alpha release. On the other hand, Sage can be built without it.
(define-public python-gmpy2
  (package
    (name "python-gmpy2")
    (version "2.0.8")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "gmpy2" version ".zip"))
              (sha256
               (base32
                "0grx6zmi99iaslm07w6c2aqpnmbkgrxcqjrqpfq223xri0r3w8yx"))))
    (build-system python-build-system)
    (native-inputs
     `(("unzip" ,unzip)))
    (inputs
     `(("gmp" ,gmp)
       ("mpfr" ,mpfr)
       ("mpc" ,mpc)))
    (home-page "https://github.com/aleaxit/gmpy")
    (synopsis
     "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x")
    (description
     "This package provides a Python interface to the GNU multiprecision
libraries GMO, MPFR and MPC.")
    (license license:lgpl3+)))

(define-public python2-gmpy2
  (package-with-python2 python-gmpy2))

(define-public cliquer
  (package
    (name "cliquer")
    (version "1.21")
    ;; The original source package is available from the home page and
    ;; has not seen any release since 2010; it comes with only a Makefile
    ;; without an "install" target. Instead, there is an autotoolized
    ;; tarball available from the Sage project.
    (source
     (origin
       (method url-fetch)
       (uri "http://users.ox.ac.uk/~coml0531/sage/cliquer-1.21.tar.gz")
       (sha256
        (base32
         "1hdzrmrx0nvvj8kbwxrs8swqgkd284khzl623jizixcv28xb77aq"))))
    (build-system gnu-build-system)
    (synopsis "C routines for finding cliques in weighted graphs")
    (description "Cliquer is a set of reentrant C routines for finding
cliques in a weighted or unweighted graph.  It uses an exact
branch-and-bound algorithm.  It can search for maximum or maximum-weight
cliques or cliques with size or weight within a given range, restrict the
search to maximal cliques, store cliques in memory and call a user-defined
function for every found clique.")
    (license license:gpl2+)
    (home-page "https://users.aalto.fi/~pat/cliquer.html")))

(define-public libbraiding
  (package
    (name "libbraiding")
    (version "1.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url (string-append "https://github.com/miguelmarco/"
                                  name))
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0l68rikfr7k2l547gb3pp3g8cj5zzxwipm79xrb5r8ffj466ydxg"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (synopsis "Computations with braid groups")
    (description "libbraiding performs computations with braid groups,
in particular it computes normal forms of group elements.")
    (license license:gpl2+)
    (home-page "https://github.com/miguelmarco/libbraiding")))

(define-public libhomfly
  (package
    (name "libhomfly")
    (version "1.02r6")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url (string-append "https://github.com/miguelmarco/"
                                  name))
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
        (base32
         "0sv3cwrf9v9sb5a8wbhjmarxvya13ma3j8y8592f9ymxlk5y0ldk"))))
    (build-system gnu-build-system)
    (native-inputs
     `(("autoconf" ,autoconf)
       ("automake" ,automake)
       ("libtool" ,libtool)))
    (inputs
     `(("libgc" ,libgc)))
    (synopsis "Computation of homfly polynomials of links")
    (description "libhomfly computes homfly polynomials of links,
represented as strings.")
    (license license:public-domain)
    (home-page "https://github.com/miguelmarco/libhomfly")))

(define-public sage
  (package
    (name "sage")
    (version "8.6")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "ftp://ftp.fu-berlin.de/unix/misc/sage/src/sage-"
                    version ".tar.gz"))
              (sha256
               (base32
                "1ylpd0ziln50bfghqkgbn1n4gd7w2hl8g1gvg94igkbrknahjb44"))
              (modules '((guix build utils)))
              (snippet '(begin (delete-file-recursively "upstream")
                               (delete-file-recursively ".git")
                               #t))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2
       #:phases
       (modify-phases %standard-phases
         (add-before 'build 'setup
           (lambda _
             (setenv "SAGE_ROOT" (getcwd))
             (setenv "SAGE_LOCAL" (getcwd))
             (setenv "SAGE_SHARE" (string-append (getcwd) "/share"))
             (setenv "PATH" (string-append (getcwd) "/build/bin:" (getcwd) "/src/bin:" (getenv "PATH")))
             (setenv "SAGE_NUM_THREADS" "4")
             (mkdir-p "var/lib/sage/installed")
             (chdir "src")
             #t)))))
    (inputs
     `(("boost" ,boost)
       ("cliquer" ,cliquer)
       ("ecl" ,ecl)
       ("edge-addition-planarity-suite" ,edge-addition-planarity-suite)
       ("flint" ,flint)
       ("gap" ,gap)
       ; ("givaro" ,givaro)
       ("glpk" ,glpk)
       ("gmp" ,gmp)
       ("gsl" ,gsl)
       ("libbraiding" ,libbraiding)
       ("libgc" ,libgc)
       ("libhomfly" ,libhomfly)
       ("mpc" ,mpc)
       ("ntl" ,ntl)
       ("pari-gp" ,pari-gp)
       ("python-cypari2" ,python2-cypari2)
       ("python-numpy" ,python2-numpy)
       ("python-six" ,python2-six)
       ("rw" ,rw)
       ("singular" ,singular)))
    (native-inputs
     `(("cython" ,python2-cython)
       ("pkg-config" ,pkg-config)
       ("python-cysignals" ,python2-cysignals)
       ("python-pkgconfig" ,python2-pkgconfig)
       ("python-jinja2" ,python2-jinja2)))
    (synopsis "SageMath computer algebra system")
    (description
     "SageMath is a mathematics software built on top of many existing
packages such as NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT,
R and others. Their combined power may be accessed through a common,
Python-based language or directly via interfaces or wrappers.")
    ;; documentation under cc-by-sa3.0, bundled packages under various
    ;; other licenses, see COPYING.txt in the distribution
    (license license:gpl3)
    (home-page "https://www.sagemath.org/")))