2019-01-31 13:55:22 +00:00
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;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages sagemath)
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#:use-module ((guix licenses) #:prefix license:)
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2019-06-17 13:11:21 +00:00
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#:use-module (guix build-system gnu)
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2019-01-31 13:55:22 +00:00
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#:use-module (guix build-system python)
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2019-06-17 22:04:55 +00:00
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (guix packages)
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2019-06-18 17:48:41 +00:00
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#:use-module (guix utils)
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2019-01-31 13:55:22 +00:00
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#:use-module (gnu packages algebra)
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2019-06-17 22:04:55 +00:00
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#:use-module (gnu packages autotools)
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2019-06-17 22:12:36 +00:00
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#:use-module (gnu packages bdw-gc)
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2019-02-17 16:55:42 +00:00
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#:use-module (gnu packages compression)
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2019-01-31 13:55:22 +00:00
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#:use-module (gnu packages multiprecision)
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2019-06-19 13:33:01 +00:00
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#:use-module (gnu packages pkg-config)
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2019-01-31 13:55:22 +00:00
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-xyz))
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(define-public python-cypari2
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(package
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(name "python-cypari2")
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2019-06-17 13:59:14 +00:00
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(version "2.1.1")
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2019-02-17 21:15:51 +00:00
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(source
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2019-01-31 13:55:22 +00:00
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(origin
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(method url-fetch)
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(uri (pypi-uri "cypari2" version))
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(sha256
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2019-02-17 21:15:51 +00:00
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(base32
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2019-06-17 13:59:14 +00:00
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"1nwkzgqvbw6361x0rpggy1q5nx663fswhpvg8md6xhqyfwpgc7nz"))))
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2019-02-17 21:15:51 +00:00
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(build-system python-build-system)
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(native-inputs
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2019-01-31 13:55:22 +00:00
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`(("python-cython" ,python-cython)))
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2019-02-17 21:15:51 +00:00
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(propagated-inputs
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`(("python-cysignals" ,python-cysignals)))
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2019-02-17 21:15:51 +00:00
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(inputs
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2019-01-31 13:55:22 +00:00
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`(("gmp" ,gmp)
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("pari-gp", pari-gp)))
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2019-02-17 21:15:51 +00:00
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(home-page "https://cypari2.readthedocs.io/")
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(synopsis
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"Python interface to the number theory library libpari")
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2019-02-17 21:15:51 +00:00
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(description
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"Cypari2 provides a Python interface to the number theory library
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PARI/GP. It has been spun off from the SageMath mathematics software system,
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but it can be used independently.")
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2019-02-17 21:15:51 +00:00
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(license license:gpl2+)))
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2019-01-31 13:55:22 +00:00
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(define-public python2-cypari2
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(package-with-python2 python-cypari2))
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2019-02-17 16:55:42 +00:00
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;; The stable version of the following package is not young enough to be
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;; used with Sage, since it does not support cython; so we use a beta
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;; release.
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2019-02-17 16:55:42 +00:00
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(define-public python-gmpy2
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(package
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(name "python-gmpy2")
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2019-06-19 07:55:42 +00:00
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(version "2.1.0b1")
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2019-02-17 19:39:51 +00:00
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/aleaxit/gmpy")
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(commit (string-append "gmpy2-" version))))
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(file-name (git-file-name name version))
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2019-02-17 19:39:51 +00:00
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(sha256
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(base32
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2019-06-19 07:55:42 +00:00
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"0ljvnmhxqdfsp0yy4c2hynhk5sggm63kkqsq4iwq4k9vsnx2xm97"))))
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2019-02-17 19:39:51 +00:00
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(build-system python-build-system)
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(native-inputs
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`(("unzip" ,unzip)))
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(inputs
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`(("gmp" ,gmp)
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("mpfr" ,mpfr)
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("mpc" ,mpc)))
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(home-page "https://github.com/aleaxit/gmpy")
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(synopsis
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"GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x")
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2019-02-17 19:39:51 +00:00
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(description
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2019-02-17 21:14:08 +00:00
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"This package provides a Python interface to the GNU multiprecision
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libraries GMO, MPFR and MPC.")
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2019-02-17 19:39:51 +00:00
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(license license:lgpl3+)))
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2019-02-17 16:55:42 +00:00
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(define-public python2-gmpy2
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(package-with-python2 python-gmpy2))
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2019-06-17 13:11:21 +00:00
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(define-public cliquer
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(package
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(name "cliquer")
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(version "1.21")
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;; The original source package is available from the home page and
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;; has not seen any release since 2010; it comes with only a Makefile
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;; without an "install" target. Instead, there is an autotoolized
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;; tarball available from the Sage project.
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(source
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(origin
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(method url-fetch)
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(uri "http://users.ox.ac.uk/~coml0531/sage/cliquer-1.21.tar.gz")
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(sha256
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(base32
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"1hdzrmrx0nvvj8kbwxrs8swqgkd284khzl623jizixcv28xb77aq"))))
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(build-system gnu-build-system)
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(synopsis "C routines for finding cliques in weighted graphs")
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(description "Cliquer is a set of reentrant C routines for finding
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cliques in a weighted or unweighted graph. It uses an exact
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branch-and-bound algorithm. It can search for maximum or maximum-weight
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cliques or cliques with size or weight within a given range, restrict the
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search to maximal cliques, store cliques in memory and call a user-defined
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function for every found clique.")
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(license license:gpl2+)
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(home-page "https://users.aalto.fi/~pat/cliquer.html")))
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2019-06-17 22:04:55 +00:00
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(define-public libbraiding
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(package
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(name "libbraiding")
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(version "1.0")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url (string-append "https://github.com/miguelmarco/"
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name))
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0l68rikfr7k2l547gb3pp3g8cj5zzxwipm79xrb5r8ffj466ydxg"))))
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(build-system gnu-build-system)
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(native-inputs
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`(("autoconf" ,autoconf)
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("automake" ,automake)
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("libtool" ,libtool)))
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(synopsis "Computations with braid groups")
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(description "libbraiding performs computations with braid groups,
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in particular it computes normal forms of group elements.")
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(license license:gpl2+)
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(home-page "https://github.com/miguelmarco/libbraiding")))
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2019-06-17 22:12:36 +00:00
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(define-public libhomfly
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(package
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(name "libhomfly")
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(version "1.02r6")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url (string-append "https://github.com/miguelmarco/"
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name))
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0sv3cwrf9v9sb5a8wbhjmarxvya13ma3j8y8592f9ymxlk5y0ldk"))))
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(build-system gnu-build-system)
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(native-inputs
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`(("autoconf" ,autoconf)
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("automake" ,automake)
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("libtool" ,libtool)))
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(inputs
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`(("libgc" ,libgc)))
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(synopsis "Computation of homfly polynomials of links")
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(description "libhomfly computes homfly polynomials of links,
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represented as strings.")
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(license license:public-domain)
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(home-page "https://github.com/miguelmarco/libhomfly")))
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2019-06-18 17:32:18 +00:00
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;; The following three packages from the Linbox group are needed in
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;; an outdated version for Sage.
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(define-public givaro-4.0.4
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(package (inherit givaro)
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(name "givaro")
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(version "4.0.4")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/linbox-team/givaro")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"199p8wyj5i63jbnk7j8qbdbfp5rm2lpmcxyk3mdjy9bz7ygx3hhy"))))))
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2019-06-18 17:48:41 +00:00
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(define-public fflas-ffpack-2.3.2
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(package (inherit fflas-ffpack)
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(name "fflas-ffpack")
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(version "2.3.2")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/linbox-team/fflas-ffpack")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1cqhassj2dny3gx0iywvmnpq8ca0d6m82xl5rz4mb8gaxr2kwddl"))))
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(propagated-inputs
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`(("givaro" ,givaro-4.0.4)))
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;; A test fails, but since all tests pass in the latest version,
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;; there is not much point in investigating.
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(arguments
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(substitute-keyword-arguments (package-arguments fflas-ffpack)
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((#:tests? _ #f) #f)))))
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2019-06-18 17:54:59 +00:00
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(define-public linbox-1.5.2
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(package (inherit linbox)
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(version "1.5.2")
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(name "linbox")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/linbox-team/linbox")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1wfivlwp30mzdy1697w7rzb8caajim50mc8h27k82yipn2qc5n4i"))))
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(inputs
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`(("fflas-ffpack" ,fflas-ffpack-2.3.2)))))
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2019-06-19 13:33:01 +00:00
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(define-public pynac
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(package
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(name "pynac")
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(version "0.7.25")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pynac/pynac/")
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(commit (string-append "pynac-" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0nnifvg6kzx0lq6gz7znind8g30v3d2pjfwgsdiks3vv9kv9nbj3"))))
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(build-system gnu-build-system)
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(native-inputs
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`(("autoconf" ,autoconf)
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("automake" ,automake)
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("libtool" ,libtool)
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("pkg-config" ,pkg-config)))
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(inputs
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`(("flint" ,flint)
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("gmp" ,gmp)
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("python" ,python)
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("singular" ,singular)))
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(synopsis "Sage fork of GiNaC")
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(description "Pynac is a derivative of the C++ library GiNaC, which
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allows manipulation of symbolic expressions. It currently provides the
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backend for symbolic expressions in Sage. The main difference between
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Pynac and GiNaC is that Pynac relies on Sage to provide the operations
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on numerical types, while GiNaC depends on CLN for this purpose.")
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(license license:gpl2+)
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(home-page "http://pynac.org/")))
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2019-06-19 14:54:09 +00:00
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;; Sage has become upstream of the following package.
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(define-public zn_poly
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(package
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(name "zn_poly")
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(version "0.9.1")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url (string-append "https://gitlab.com/sagemath/"
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name ".git/"))
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0ra5vy585bqq7g3317iw6fp44iqgqvds3j0l1va6mswimypq4vxb"))))
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(build-system gnu-build-system)
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(native-inputs
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`(("python" ,python-2)))
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(inputs
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`(("gmp" ,gmp)))
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(replace 'configure
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;; The configure script chokes on --enable-fast-install.
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(invoke "./configure"
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(string-append "--prefix=" (assoc-ref outputs "out"))
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"--cflags=-O3 -fPIC")))
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(add-before 'build 'prepare-build
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(lambda _
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(setenv "CC" "gcc")
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#t))
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(add-after 'build 'build-so
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(lambda _
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(invoke "make" "libzn_poly.so")))
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(add-after 'install 'install-so
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((lib (string-append (assoc-ref outputs "out") "/lib")))
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(install-file "libzn_poly.so" lib)))))))
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(synopsis "Arithmetic for polynomials over Z/NZ")
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(description "zn_poly implements the arithmetic of polynomials the
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coefficients of which are modular integers.")
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(license (list license:gpl2 license:gpl3)) ; dual licensed
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(home-page "https://gitlab.com/sagemath/zn_poly")))
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