618 lines
24 KiB
Scheme
618 lines
24 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2012, 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
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;;; Copyright © 2013, 2015 Ludovic Courtès <ludo@gnu.org>
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;;; Copyright © 2016 Nicolas Goaziou <mail@nicolasgoaziou.fr>
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;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
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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 algebra)
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#:use-module (gnu packages)
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#:use-module (gnu packages autotools)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages doxygen)
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#:use-module (gnu packages fltk)
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#:use-module (gnu packages gl)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages image)
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#:use-module (gnu packages multiprecision)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages flex)
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#:use-module (gnu packages python)
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#:use-module (gnu packages tcsh)
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#:use-module (gnu packages texlive)
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#:use-module (gnu packages xiph)
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#:use-module (gnu packages xorg)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system cmake)
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#:use-module (guix utils))
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(define-public mpfrcx
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(package
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(name "mpfrcx")
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(version "0.4.2")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"http://www.multiprecision.org/mpfrcx/download/mpfrcx-"
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version ".tar.gz"))
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(sha256
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(base32
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"0grw66b255r574lvll1bqccm5myj2m8ajzsjaygcyq9zjnnbnhhy"))))
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(build-system gnu-build-system)
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(propagated-inputs
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`(("gmp" ,gmp)
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("mpfr" ,mpfr)
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("mpc" ,mpc))) ; Header files are included by mpfrcx.h.
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(synopsis "Arithmetic of polynomials over arbitrary precision numbers")
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(description
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"Mpfrcx is a library for the arithmetic of univariate polynomials over
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arbitrary precision real (mpfr) or complex (mpc) numbers, without control
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on the rounding. For the time being, only the few functions needed to
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implement the floating point approach to complex multiplication are
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implemented. On the other hand, these comprise asymptotically fast
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multiplication routines such as Toom–Cook and the FFT.")
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(license license:lgpl2.1+)
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(home-page "http://mpfrcx.multiprecision.org/")))
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(define-public cm
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(package
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(name "cm")
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(version "0.3")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"http://www.multiprecision.org/cm/download/cm-"
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version ".tar.gz"))
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(sha256
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(base32
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"1nf5kr0nqmhbzrsrinky18z0ighjpsmb5cr8zyg8jf04bfbyrfmc"))))
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(build-system gnu-build-system)
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(propagated-inputs
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`(("mpfrcx" ,mpfrcx)
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("zlib" ,zlib))) ; Header files included from cm_common.h.
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(inputs
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`(("pari-gp" ,pari-gp)))
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(synopsis "CM constructions for elliptic curves")
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(description
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"The CM software implements the construction of ring class fields of
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imaginary quadratic number fields and of elliptic curves with complex
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multiplication via floating point approximations. It consists of libraries
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that can be called from within a C program and of executable command
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line applications.")
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(license license:gpl3+)
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(home-page "http://cm.multiprecision.org/")))
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(define-public fplll
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(package
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(name "fplll")
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(version "4.0.4")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
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version ".tar.gz"))
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(sha256 (base32
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"1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))
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(build-system gnu-build-system)
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(inputs `(("gmp" ,gmp)
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("mpfr" ,mpfr)))
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(synopsis "Library for LLL-reduction of euclidean lattices")
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(description
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"fplll LLL-reduces euclidean lattices. Since version 3, it can also
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solve the shortest vector problem.")
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(license license:lgpl2.1+)
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(home-page "http://perso.ens-lyon.fr/damien.stehle/fplll/")))
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(define-public pari-gp
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(package
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(name "pari-gp")
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(version "2.7.5")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"http://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
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version ".tar.gz"))
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(sha256
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(base32
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"0c8l83a0gjq73r9hndsrzkypwxvnnm4pxkkzbg6jm95m80nzwh11"))))
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(build-system gnu-build-system)
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(native-inputs `(("texlive" ,texlive-minimal)))
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(inputs `(("gmp" ,gmp)
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("libx11" ,libx11)
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("perl" ,perl)
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("readline" ,readline)))
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(arguments
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'(#:make-flags '("all")
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#:test-target "dobench"
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#:phases (modify-phases %standard-phases
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(replace 'configure
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out")))
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(zero?
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(system* "./Configure"
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(string-append "--prefix=" out)))))))))
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(synopsis "PARI/GP, a computer algebra system for number theory")
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(description
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"PARI/GP is a widely used computer algebra system designed for fast
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computations in number theory (factorisations, algebraic number theory,
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elliptic curves...), but it also contains a large number of other useful
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functions to compute with mathematical entities such as matrices,
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polynomials, power series, algebraic numbers, etc., and a lot of
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transcendental functions.
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PARI is also available as a C library to allow for faster computations.")
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(license license:gpl2+)
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(home-page "http://pari.math.u-bordeaux.fr/")))
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(define-public gp2c
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(package
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(name "gp2c")
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(version "0.0.9pl5")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"http://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
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version ".tar.gz"))
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(sha256
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(base32
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"1q003mkagc5ib6lqb2xfay7j4ffkwv7xlnznp6wdrq2sbqq4vyak"))))
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(build-system gnu-build-system)
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(native-inputs `(("perl" ,perl)))
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(inputs `(("pari-gp" ,pari-gp)))
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(arguments
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'(#:configure-flags
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(list (string-append "--with-paricfg="
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(assoc-ref %build-inputs "pari-gp")
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"/lib/pari/pari.cfg"))))
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(synopsis "PARI/GP, a computer algebra system for number theory")
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(description
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"PARI/GP is a widely used computer algebra system designed for fast
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computations in number theory (factorisations, algebraic number theory,
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elliptic curves...), but it also contains a large number of other useful
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functions to compute with mathematical entities such as matrices,
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polynomials, power series, algebraic numbers, etc., and a lot of
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transcendental functions.
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PARI is also available as a C library to allow for faster computations.
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GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
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(license license:gpl2)
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(home-page "http://pari.math.u-bordeaux.fr/")))
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(define-public giac-xcas
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(package
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(name "giac-xcas")
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(version "1.2.2-37")
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(source (origin
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(method url-fetch)
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;; "~parisse/giac" is not used because the maintainer regularly
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;; overwrites the release tarball there, introducing a checksum
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;; mismatch every time. See
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;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
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(uri (string-append "https://www-fourier.ujf-grenoble.fr/"
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"~parisse/debian/dists/stable/main/"
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"source/giac_" version ".tar.gz"))
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(sha256
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(base32
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"0cagh9nnaz7ks299b2bs3lrdclv4xbyis24zc8vf3i25p470bxsf"))))
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(build-system gnu-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'patch-bin-cp
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(lambda _
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;; Some Makefiles contain hard-coded "/bin/cp".
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(substitute* (find-files "doc" "^Makefile")
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(("/bin/cp") (which "cp")))
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#t))
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(add-after 'unpack 'disable-broken-test
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(lambda _
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;; Disable failing test. Actually, the results are correct but
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;; a sorting discrepancy prevents the test from being validated.
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(substitute* "check/Makefile.in"
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(("chk_fhan16") ""))
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#t)))))
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(inputs
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`(("fltk" ,fltk)
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("gmp" ,gmp)
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("gsl" ,gsl)
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("lapack" ,lapack)
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("libao" ,ao)
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("libjpeg" ,libjpeg)
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("libpng" ,libpng)
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("libx11" ,libx11)
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("libxft" ,libxft)
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("libxt" ,libxt)
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("mesa" ,mesa)
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("mpfi" ,mpfi)
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("mpfr" ,mpfr)
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("ntl" ,ntl)
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("perl" ,perl)
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("pari-gp" ,pari-gp)
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("tcsh" ,tcsh)
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("texlive" ,texlive-minimal)))
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(native-inputs `(("readline" ,readline)))
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(home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
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(synopsis "Computer algebra system")
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(description
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"Giac/Xcas is a computer algebra system. It has a compatibility mode for
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maple, mupad and the TI89. It is available as a standalone program (graphic
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or text interfaces) or as a C++ library.")
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(license license:gpl3+)))
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(define-public flint
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(package
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(name "flint")
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(version "2.5.2")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"http://flintlib.org/flint-"
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version ".tar.gz"))
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(sha256 (base32
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"11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
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(patches (search-patches "flint-ldconfig.patch"))))
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(build-system gnu-build-system)
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(propagated-inputs
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`(("gmp" ,gmp)
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("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
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(arguments
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`(#:parallel-tests? #f ; seems to be necessary on arm
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#:phases
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(modify-phases %standard-phases
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(replace 'configure
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out"))
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(gmp (assoc-ref inputs "gmp"))
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(mpfr (assoc-ref inputs "mpfr")))
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;; do not pass "--enable-fast-install", which makes the
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;; homebrew configure process fail
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(zero? (system*
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"./configure"
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(string-append "--prefix=" out)
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(string-append "--with-gmp=" gmp)
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(string-append "--with-mpfr=" mpfr)))))))))
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(synopsis "Fast library for number theory")
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(description
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"FLINT is a C library for number theory. It supports arithmetic
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with numbers, polynomials, power series and matrices over many base
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rings, including multiprecision integers and rationals, integers
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modulo n, p-adic numbers, finite fields (prime and non-prime order)
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and real and complex numbers (via the Arb extension library).
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Operations that can be performed include conversions, arithmetic,
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GCDs, factoring, solving linear systems, and evaluating special
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functions. In addition, FLINT provides various low-level routines for
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fast arithmetic.")
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(license license:gpl2+)
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(home-page "http://flintlib.org/")))
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(define-public arb
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(package
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(name "arb")
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(version "2.8.1")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"https://github.com/fredrik-johansson/arb/archive/"
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version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"04hhcpshfkcq9fr4hixbhpps50yf9drk62xgkvlcaj5kb4nyrx7l"))
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(patches (search-patches "arb-ldconfig.patch"))))
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(build-system gnu-build-system)
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(propagated-inputs
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`(("flint" ,flint))) ; flint.h is included by arf.h
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(inputs
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`(("gmp" ,gmp)
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("mpfr" ,mpfr)))
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(arguments
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`(#:phases
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(alist-replace
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'configure
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out"))
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(flint (assoc-ref inputs "flint"))
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(gmp (assoc-ref inputs "gmp"))
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(mpfr (assoc-ref inputs "mpfr")))
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;; do not pass "--enable-fast-install", which makes the
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;; homebrew configure process fail
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(zero? (system*
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"./configure"
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(string-append "--prefix=" out)
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(string-append "--with-flint=" flint)
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(string-append "--with-gmp=" gmp)
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(string-append "--with-mpfr=" mpfr)))))
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%standard-phases)))
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(synopsis "Arbitrary precision floating-point ball arithmetic")
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(description
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"Arb is a C library for arbitrary-precision floating-point ball
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arithmetic. It supports efficient high-precision computation with
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polynomials, power series, matrices and special functions over the
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real and complex numbers, with automatic, rigorous error control.")
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(license license:gpl2+)
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(home-page "http://fredrikj.net/arb/")))
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(define-public ntl
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(package
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(name "ntl")
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(version "9.7.0")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://shoup.net/ntl/ntl-"
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version ".tar.gz"))
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(sha256 (base32
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"115frp5flyvw9wghz4zph1b3llmr5nbxk1skgsggckr81fh3gmxq"))))
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(build-system gnu-build-system)
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||
(native-inputs
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||
`(("libtool" ,libtool)
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||
("perl" ,perl))) ; for configuration
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||
;; FIXME: Add optional input gf2x once available; then also add
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;; configure flag "NTL_GF2X_LIB=on".
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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
|
||
(replace 'configure
|
||
(lambda* (#:key outputs #:allow-other-keys)
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||
(chdir "src")
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||
(system* "./configure"
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||
(string-append "PREFIX=" (assoc-ref outputs "out"))
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||
;; Do not build especially for the build machine.
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||
"NATIVE=off"
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||
;; Also do not tune to the build machine.
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||
"WIZARD=off"
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||
"SHARED=on")
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||
#t)))))
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||
(synopsis "C++ library for number theory")
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||
(description
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||
"NTL is a C++ library providing data structures and algorithms
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for manipulating signed, arbitrary length integers, and for vectors,
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matrices, and polynomials over the integers and over finite fields.")
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||
(license license:gpl2+)
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||
(home-page "http://shoup.net/ntl/")))
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(define-public singular
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||
(package
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(name "singular")
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(version "4.0.3")
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||
(source (origin
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||
(method url-fetch)
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||
(uri (string-append "http://www.mathematik.uni-kl.de/ftp/pub/"
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||
"Math/Singular/SOURCES/"
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||
(string-join (string-split version #\.) "-")
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||
"/singular-" version ".tar.gz"))
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||
(sha256 (base32
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"0viidy2fz62rln9p0s9qfs7fnm55c6fw1agydd1py26gxylp1ksc"))))
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||
(build-system gnu-build-system)
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||
(native-inputs
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||
`(("doxygen" ,doxygen)
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||
("graphviz" ,graphviz)
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||
("perl" ,perl)))
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||
(inputs
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||
`(("cddlib" ,cddlib)
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||
("gmp" ,gmp)
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||
("flint" ,flint)
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||
("mpfr" ,mpfr)
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||
("ntl" ,ntl)
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||
("python" ,python-2)
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||
("readline" ,readline)))
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||
(arguments
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`(#:configure-flags
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||
(list (string-append "--with-ntl="
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(assoc-ref %build-inputs "ntl")))))
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(synopsis "Computer algebra system for polynomial computations")
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||
(description
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||
"Singular is a computer algebra system for polynomial computations,
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with special emphasis on commutative and non-commutative algebra, algebraic
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geometry and singularity theory.")
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||
;; Singular itself is dual licensed gpl2 or gpl3, but some of the
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;; libraries with which it links are licensed under lgpl3+, so the
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;; combined work becomes gpl3. See COPYING in the source code.
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(license license:gpl3)
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(home-page "http://www.singular.uni-kl.de/index.php")))
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(define-public gmp-ecm
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||
(package
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||
(name "gmp-ecm")
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||
(version "7.0")
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||
(source (origin
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||
(method url-fetch)
|
||
(uri (string-append "https://gforge.inria.fr/frs/download.php/"
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||
"file/35642/ecm-"
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||
version ".tar.gz"))
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||
(sha256 (base32
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||
"00jzzwqp49m01vwsr9z1w7bvm8lb69l3f62x7qr8sfz0xiczxnpm"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
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||
`(("gmp" ,gmp)))
|
||
(arguments
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||
`(#:configure-flags '("--enable-shared"
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||
;; Disable specific assembly routines, which depend
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||
;; on the subarchitecture of the build machine,
|
||
;; and use gmp instead.
|
||
"--disable-asm-redc")))
|
||
(synopsis "Integer factorization library using the elliptic curve method")
|
||
(description
|
||
"GMP-ECM factors integers using the elliptic curve method (ECM) as well
|
||
as the P-1 and P+1 algorithms. It provides a library and a stand-alone
|
||
binary.")
|
||
;; Most files are under lgpl3+, but some are under gpl3+ or gpl2+,
|
||
;; so the combined work is under gpl3+.
|
||
(license license:gpl3+)
|
||
(home-page "http://ecm.gforge.inria.fr/")))
|
||
|
||
(define-public bc
|
||
(package
|
||
(name "bc")
|
||
(version "1.06")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0cqf5jkwx6awgd2xc2a0mkpxilzcfmhncdcfg7c9439wgkqxkxjf"))))
|
||
(build-system gnu-build-system)
|
||
(inputs `(("readline" ,readline)))
|
||
(native-inputs `(("flex" ,flex)))
|
||
(arguments
|
||
'(#:phases
|
||
(alist-replace 'configure
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
;; This old `configure' script doesn't support
|
||
;; variables passed as arguments.
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(setenv "CONFIG_SHELL" (which "bash"))
|
||
(zero?
|
||
(system*
|
||
"./configure"
|
||
(string-append "--prefix=" out)
|
||
;; By default, man and info pages are put in
|
||
;; PREFIX/{man,info}, but we want them in
|
||
;; PREFIX/share/{man,info}.
|
||
(string-append "--mandir=" out "/share/man")
|
||
(string-append "--infodir=" out "/share/info")))))
|
||
%standard-phases)))
|
||
(home-page "http://www.gnu.org/software/bc/")
|
||
(synopsis "Arbitrary precision numeric processing language")
|
||
(description
|
||
"bc is an arbitrary precision numeric processing language. It includes
|
||
an interactive environment for evaluating mathematical statements. Its
|
||
syntax is similar to that of C, so basic usage is familiar. It also includes
|
||
\"dc\", a reverse-polish calculator.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public fftw
|
||
(package
|
||
(name "fftw")
|
||
(version "3.3.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
|
||
version".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"10h9mzjxnwlsjziah4lri85scc05rlajz39nqf3mbh4vja8dw34g"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
'(#:configure-flags '("--enable-shared" "--enable-openmp")
|
||
#:phases (alist-cons-before
|
||
'build 'no-native
|
||
(lambda _
|
||
;; By default '-mtune=native' is used. However, that may
|
||
;; cause the use of ISA extensions (SSE2, etc.) that are
|
||
;; not necessarily available on the user's machine when
|
||
;; that package is built on a different machine.
|
||
(substitute* (find-files "." "Makefile$")
|
||
(("-mtune=native") "")))
|
||
%standard-phases)))
|
||
(native-inputs `(("perl" ,perl)))
|
||
(home-page "http://fftw.org")
|
||
(synopsis "Computing the discrete Fourier transform")
|
||
(description
|
||
"FFTW is a C subroutine library for computing the discrete Fourier
|
||
transform (DFT) in one or more dimensions, of arbitrary input size, and of
|
||
both real and complex data (as well as of even/odd data---i.e. the discrete
|
||
cosine/ sine transforms or DCT/DST).")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public fftwf
|
||
(package (inherit fftw)
|
||
(name "fftwf")
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments fftw)
|
||
((#:configure-flags cf)
|
||
`(cons "--enable-float" ,cf))))
|
||
(description
|
||
(string-append (package-description fftw)
|
||
" Single-precision version."))))
|
||
|
||
(define-public fftw-openmpi
|
||
(package (inherit fftw)
|
||
(name "fftw-openmpi")
|
||
(inputs
|
||
`(("openmpi" ,openmpi)
|
||
,@(package-inputs fftw)))
|
||
(arguments
|
||
(substitute-keyword-arguments (package-arguments fftw)
|
||
((#:configure-flags cf)
|
||
`(cons "--enable-mpi" ,cf))))
|
||
(description
|
||
(string-append (package-description fftw)
|
||
" With OpenMPI parallelism support."))))
|
||
|
||
(define-public eigen
|
||
(package
|
||
(name "eigen")
|
||
(version "3.2.7")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://bitbucket.org/eigen/eigen/get/"
|
||
version ".tar.bz2"))
|
||
(sha256
|
||
(base32
|
||
"0gigbjjdlw2q0gvcnyiwc6in314a647rkidk6977bwiwn88im3p5"))
|
||
(file-name (string-append name "-" version ".tar.bz2"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
;; There are 3 test failures in the "unsupported" directory,
|
||
;; but maintainers say it's a known issue and it's unsupported
|
||
;; anyway, so just skip them.
|
||
'(substitute* "CMakeLists.txt"
|
||
(("add_subdirectory\\(unsupported\\)")
|
||
"# Do not build the tests for unsupported features.\n")
|
||
;; Work around
|
||
;; <http://eigen.tuxfamily.org/bz/show_bug.cgi?id=1114>.
|
||
(("\"include/eigen3\"")
|
||
"\"${CMAKE_INSTALL_PREFIX}/include/eigen3\"")))))
|
||
(build-system cmake-build-system)
|
||
(arguments
|
||
'(;; Turn off debugging symbols to save space.
|
||
#:build-type "Release"
|
||
|
||
#:phases (modify-phases %standard-phases
|
||
(replace 'check
|
||
(lambda _
|
||
(let* ((cores (parallel-job-count))
|
||
(dash-j (format #f "-j~a" cores)))
|
||
;; First build the tests, in parallel. See
|
||
;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
|
||
(and (zero? (system* "make" "buildtests" dash-j))
|
||
|
||
;; Then run 'CTest' with -V so we get more
|
||
;; details upon failure.
|
||
(zero? (system* "ctest" "-V" dash-j)))))))))
|
||
(home-page "http://eigen.tuxfamily.org")
|
||
(synopsis "C++ template library for linear algebra")
|
||
(description
|
||
"Eigen is a C++ template library for linear algebra: matrices, vectors,
|
||
numerical solvers, and related algorithms. It provides an elegant API based
|
||
on \"expression templates\". It is versatile: it supports all matrix sizes,
|
||
all standard numeric types, various matrix decompositions and geometry
|
||
features, and more.")
|
||
|
||
;; Most of the code is MPLv2, with a few files under LGPLv2.1+ or BSD-3.
|
||
;; See 'COPYING.README' for details.
|
||
(license license:mpl2.0)))
|