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;;; 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. 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")))
;; 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)))))
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