;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
;;;
;;; 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 (guix utils)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages bdw-gc)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages multiprecision)
  #: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; so we use a beta
;; release.
(define-public python-gmpy2
  (package
    (name "python-gmpy2")
    (version "2.1.0b1")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/aleaxit/gmpy")
                    (commit (string-append "gmpy2-" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "0ljvnmhxqdfsp0yy4c2hynhk5sggm63kkqsq4iwq4k9vsnx2xm97"))))
    (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")))

;; The following three packages from the Linbox group are needed in
;; an outdated version for Sage.

(define-public givaro-4.0.4
  (package (inherit givaro)
    (name "givaro")
    (version "4.0.4")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/linbox-team/givaro")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "199p8wyj5i63jbnk7j8qbdbfp5rm2lpmcxyk3mdjy9bz7ygx3hhy"))))))

(define-public fflas-ffpack-2.3.2
  (package (inherit fflas-ffpack)
    (name "fflas-ffpack")
    (version "2.3.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/linbox-team/fflas-ffpack")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1cqhassj2dny3gx0iywvmnpq8ca0d6m82xl5rz4mb8gaxr2kwddl"))))
    (propagated-inputs
     `(("givaro" ,givaro-4.0.4)))
    ;; A test fails, but since all tests pass in the latest version,
    ;; there is not much point in investigating.
    (arguments
     (substitute-keyword-arguments (package-arguments fflas-ffpack)
       ((#:tests? _ #f) #f)))))

(define-public linbox-1.5.2
  (package (inherit linbox)
    (version "1.5.2")
    (name "linbox")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/linbox-team/linbox")
                    (commit (string-append "v" version))))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "1wfivlwp30mzdy1697w7rzb8caajim50mc8h27k82yipn2qc5n4i"))))
    (inputs
     `(("fflas-ffpack" ,fflas-ffpack-2.3.2)))))