mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-11-08 16:06:16 -05:00
fdb513a704
This fixes a regression introduced in
6d3896b9fc.
* gnu/packages/algebra.scm: Use the (gnu packages bison) module.
1070 lines
42 KiB
Scheme
1070 lines
42 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019 Andreas Enge <andreas@enge.fr>
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;;; Copyright © 2013, 2015, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
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;;; Copyright © 2016, 2017, 2018, 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
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;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
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;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
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;;; Copyright © 2017, 2019 Eric Bavier <bavier@member.fsf.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
|
||
;;; 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/>.
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|
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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 bison)
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#:use-module (gnu packages check)
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||
#:use-module (gnu packages compression)
|
||
#:use-module (gnu packages cpp)
|
||
#:use-module (gnu packages documentation)
|
||
#:use-module (gnu packages ed)
|
||
#:use-module (gnu packages flex)
|
||
#:use-module (gnu packages fltk)
|
||
#:use-module (gnu packages gl)
|
||
#:use-module (gnu packages graphviz)
|
||
#:use-module (gnu packages image)
|
||
#:use-module (gnu packages java)
|
||
#:use-module (gnu packages maths)
|
||
#:use-module (gnu packages mpi)
|
||
#:use-module (gnu packages multiprecision)
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||
#:use-module (gnu packages perl)
|
||
#:use-module (gnu packages pulseaudio)
|
||
#:use-module (gnu packages python)
|
||
#:use-module (gnu packages python-xyz)
|
||
#:use-module (gnu packages readline)
|
||
#:use-module (gnu packages shells)
|
||
#:use-module (gnu packages tex)
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||
#:use-module (gnu packages texinfo)
|
||
#:use-module (gnu packages xiph)
|
||
#:use-module (gnu packages xorg)
|
||
#:use-module (guix build-system ant)
|
||
#:use-module (guix build-system gnu)
|
||
#:use-module (guix build-system cmake)
|
||
#:use-module (guix build-system python)
|
||
#:use-module (guix download)
|
||
#:use-module (guix git-download)
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||
#:use-module (guix hg-download)
|
||
#:use-module ((guix licenses) #:prefix license:)
|
||
#:use-module (guix packages)
|
||
#:use-module (guix utils))
|
||
|
||
|
||
(define-public mpfrcx
|
||
(package
|
||
(name "mpfrcx")
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||
(version "0.5")
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||
(source (origin
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||
(method url-fetch)
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||
(uri (string-append
|
||
"http://www.multiprecision.org/downloads/mpfrcx-"
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||
version ".tar.gz"))
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||
(sha256
|
||
(base32
|
||
"1s968480ymv6w0rnvfp9mxvx98hvi29fkvw8nk4ggzc6azxgwybs"))))
|
||
(build-system gnu-build-system)
|
||
(propagated-inputs
|
||
`(("gmp" ,gmp)
|
||
("mpfr" ,mpfr)
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||
("mpc" ,mpc))) ; Header files are included by mpfrcx.h.
|
||
(synopsis "Arithmetic of polynomials over arbitrary precision numbers")
|
||
(description
|
||
"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
|
||
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:lgpl3+)
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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"))))
|
||
(build-system gnu-build-system)
|
||
(propagated-inputs
|
||
`(("mpfrcx" ,mpfrcx)
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("zlib" ,zlib))) ; Header files included from cm_common.h.
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||
(inputs
|
||
`(("pari-gp" ,pari-gp)))
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||
(synopsis "CM constructions for elliptic curves")
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||
(description
|
||
"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
|
||
"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")
|
||
(description
|
||
"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 "2.11.1")
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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://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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||
"1jfax92jpydjd02fwl30r6b8kfzqqd6sm4yx94gidyz9lqjb7a94"))))
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||
(build-system gnu-build-system)
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||
(native-inputs
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||
`(("texlive" ,(texlive-union
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||
(list texlive-fonts-amsfonts
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||
texlive-latex-amsfonts)))))
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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
|
||
(replace 'configure
|
||
(lambda* (#:key outputs #:allow-other-keys)
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||
(invoke "./Configure"
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||
(string-append "--prefix="
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||
(assoc-ref outputs "out"))))))))
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||
(synopsis "PARI/GP, a computer algebra system for number theory")
|
||
(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
|
||
functions to compute with mathematical entities such as matrices,
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||
polynomials, power series, algebraic numbers, etc., and a lot of
|
||
transcendental functions.
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||
PARI is also available as a C library to allow for faster computations.")
|
||
(license license:gpl2+)
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||
(home-page "https://pari.math.u-bordeaux.fr/")))
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||
|
||
(define-public gp2c
|
||
(package
|
||
(name "gp2c")
|
||
(version "0.0.11pl1")
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||
(source (origin
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||
(method url-fetch)
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||
(uri (string-append
|
||
"https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
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||
version ".tar.gz"))
|
||
(sha256
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||
(base32
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||
"1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s"))))
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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"))))
|
||
(synopsis "PARI/GP, a computer algebra system for number theory")
|
||
(description
|
||
"PARI/GP is a widely used computer algebra system designed for fast
|
||
computations in number theory (factorisations, algebraic number theory,
|
||
elliptic curves...), but it also contains a large number of other useful
|
||
functions to compute with mathematical entities such as matrices,
|
||
polynomials, power series, algebraic numbers, etc., and a lot of
|
||
transcendental functions.
|
||
PARI is also available as a C library to allow for faster computations.
|
||
|
||
GP2C, the GP to C compiler, translates GP scripts to PARI programs.")
|
||
(license license:gpl2)
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||
(home-page "https://pari.math.u-bordeaux.fr/")))
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||
|
||
(define-public cmh
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||
(package
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||
(name "cmh")
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||
(version "1.0")
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||
(source (origin
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||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://gforge.inria.fr/frs/download.php/33497/cmh-"
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||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
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||
"1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("gmp" ,gmp)
|
||
("mpfr" ,mpfr)
|
||
("mpc" ,mpc)
|
||
("mpfrcx" ,mpfrcx)
|
||
("fplll" ,fplll)
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||
("pari-gp" ,pari-gp)))
|
||
(synopsis "Igusa class polynomial computations")
|
||
(description
|
||
"The CMH software computes Igusa (genus 2) class polynomials, which
|
||
parameterize the CM points in the moduli space of 2-dimensional abelian
|
||
varieties, i.e. Jacobians of hyperelliptic curves.
|
||
It can also be used to compute theta constants at arbitrary
|
||
precision.")
|
||
(license license:gpl3+)
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||
(home-page "http://cmh.gforge.inria.fr/")))
|
||
|
||
(define-public giac
|
||
(package
|
||
(name "giac")
|
||
(version "1.5.0-49")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; "~parisse/giac" is not used because the maintainer regularly
|
||
;; overwrites the release tarball there, introducing a checksum
|
||
;; mismatch every time. See
|
||
;; <https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/README>
|
||
(uri (string-append "https://www-fourier.ujf-grenoble.fr/"
|
||
"~parisse/debian/dists/stable/main/"
|
||
"source/giac_" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0f4pkand9vmqfayw18jm5qxbhcwi1405qfd7ibzh9lwzz6amkm3l"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:modules ((ice-9 ftw)
|
||
(guix build utils)
|
||
(guix build gnu-build-system))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'patch-bin-cp
|
||
;; Some Makefiles contain hard-coded "/bin/cp".
|
||
(lambda _
|
||
(substitute* (find-files "doc" "^Makefile")
|
||
(("/bin/cp") (which "cp")))
|
||
#t))
|
||
(add-after 'unpack 'disable-failing-test
|
||
;; FIXME: Test failing. Not sure why.
|
||
(lambda _
|
||
(substitute* "check/Makefile.in"
|
||
(("chk_fhan11") ""))
|
||
#t))
|
||
(add-after 'install 'fix-doc
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out")))
|
||
;; Most French documentation has a non-commercial
|
||
;; license, so we need to remove it.
|
||
(with-directory-excursion (string-append out "/share/giac/doc/fr")
|
||
(for-each delete-file-recursively
|
||
'("cascas" "casexo" "casgeo" "casrouge" "cassim"
|
||
"castor")))
|
||
;; Remove duplicate documentation in
|
||
;; "%out/share/doc/giac/", where Xcas does not expect
|
||
;; to find it.
|
||
(delete-file-recursively (string-append out "/share/doc/giac"))
|
||
#t)))
|
||
(add-after 'install 'remove-unnecessary-executable
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out")))
|
||
(delete-file (string-append out "/bin/xcasnew"))
|
||
#t))))))
|
||
(inputs
|
||
;;; TODO: Add libnauty.
|
||
`(("fltk" ,fltk)
|
||
("glpk" ,glpk)
|
||
("gmp" ,gmp)
|
||
("gsl" ,gsl)
|
||
("lapack" ,lapack)
|
||
("libao" ,ao)
|
||
("libjpeg" ,libjpeg)
|
||
("libpng" ,libpng)
|
||
("libsamplerate" ,libsamplerate)
|
||
("libx11" ,libx11)
|
||
("libxinerama" ,libxinerama)
|
||
("libxft" ,libxft)
|
||
("libxt" ,libxt)
|
||
("mesa" ,mesa)
|
||
("mpfi" ,mpfi)
|
||
("mpfr" ,mpfr)
|
||
("ntl" ,ntl)
|
||
("perl" ,perl)
|
||
("pari-gp" ,pari-gp)
|
||
("tcsh" ,tcsh)))
|
||
(native-inputs
|
||
`(("bison" ,bison)
|
||
("flex" ,flex)
|
||
("readline" ,readline)
|
||
("texlive" ,texlive-tiny)))
|
||
(home-page "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html")
|
||
(synopsis "Computer algebra system")
|
||
(description
|
||
"Giac/Xcas is a computer algebra system. It has a compatibility mode for
|
||
maple, mupad and the TI89. It is available as a standalone program (graphic
|
||
or text interfaces) or as a C++ library.")
|
||
(license license:gpl3+)))
|
||
|
||
(define-public giac-xcas
|
||
(deprecated-package "giac-xcas" giac))
|
||
|
||
(define-public flint
|
||
(package
|
||
(name "flint")
|
||
(version "2.5.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"http://flintlib.org/flint-"
|
||
version ".tar.gz"))
|
||
(sha256 (base32
|
||
"11syazv1a8rrnac3wj3hnyhhflpqcmq02q8pqk2m6g2k6h0gxwfb"))
|
||
(patches (search-patches "flint-ldconfig.patch"))))
|
||
(build-system gnu-build-system)
|
||
(propagated-inputs
|
||
`(("gmp" ,gmp)
|
||
("mpfr" ,mpfr))) ; header files from both are included by flint/arith.h
|
||
(arguments
|
||
`(#:parallel-tests? #f ; seems to be necessary on arm
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'configure
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out"))
|
||
(gmp (assoc-ref inputs "gmp"))
|
||
(mpfr (assoc-ref inputs "mpfr")))
|
||
;; do not pass "--enable-fast-install", which makes the
|
||
;; homebrew configure process fail
|
||
(invoke "./configure"
|
||
(string-append "--prefix=" out)
|
||
(string-append "--with-gmp=" gmp)
|
||
(string-append "--with-mpfr=" mpfr))
|
||
#t))))))
|
||
(synopsis "Fast library for number theory")
|
||
(description
|
||
"FLINT is a C library for number theory. It supports arithmetic
|
||
with numbers, polynomials, power series and matrices over many base
|
||
rings, including multiprecision integers and rationals, integers
|
||
modulo n, p-adic numbers, finite fields (prime and non-prime order)
|
||
and real and complex numbers (via the Arb extension library).
|
||
|
||
Operations that can be performed include conversions, arithmetic,
|
||
GCDs, factoring, solving linear systems, and evaluating special
|
||
functions. In addition, FLINT provides various low-level routines for
|
||
fast arithmetic.")
|
||
(license license:gpl2+)
|
||
(home-page "http://flintlib.org/")))
|
||
|
||
(define-public arb
|
||
(package
|
||
(name "arb")
|
||
(version "2.16.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/fredrik-johansson/arb.git")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0478671wfwy3gl26sbxh1jq1ih36z4k72waa8y2y2lvn649gb7cd"))))
|
||
(build-system gnu-build-system)
|
||
(propagated-inputs
|
||
`(("flint" ,flint))) ; flint.h is included by arf.h
|
||
(inputs
|
||
`(("gmp" ,gmp)
|
||
("mpfr" ,mpfr)))
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'configure
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(let ((out (assoc-ref outputs "out"))
|
||
(flint (assoc-ref inputs "flint"))
|
||
(gmp (assoc-ref inputs "gmp"))
|
||
(mpfr (assoc-ref inputs "mpfr")))
|
||
;; do not pass "--enable-fast-install", which makes the
|
||
;; homebrew configure process fail
|
||
(invoke "./configure"
|
||
(string-append "--prefix=" out)
|
||
(string-append "--with-flint=" flint)
|
||
(string-append "--with-gmp=" gmp)
|
||
(string-append "--with-mpfr=" mpfr))))))))
|
||
(synopsis "Arbitrary precision floating-point ball arithmetic")
|
||
(description
|
||
"Arb is a C library for arbitrary-precision floating-point ball
|
||
arithmetic. It supports efficient high-precision computation with
|
||
polynomials, power series, matrices and special functions over the
|
||
real and complex numbers, with automatic, rigorous error control.")
|
||
(license license:lgpl2.1+)
|
||
(home-page "http://fredrikj.net/arb/")))
|
||
|
||
(define-public python-flint
|
||
(package
|
||
(name "python-flint")
|
||
(version "0.3.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/fredrik-johansson/python-flint.git")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1v0anazbj1cfi68nl2j6dbd31kgkc1563xmr0zk5xk3xj78569pw"))
|
||
(patches (search-patches "python-flint-includes.patch"))))
|
||
(build-system python-build-system)
|
||
(native-inputs
|
||
`(("python-cython" ,python-cython)))
|
||
(propagated-inputs
|
||
`(("python-numpy" ,python-numpy)))
|
||
(inputs
|
||
`(("arb" ,arb)
|
||
("flint" ,flint)))
|
||
(synopsis "Python module wrapping ARB and FLINT")
|
||
(description
|
||
"Python-flint is a Python extension module wrapping FLINT
|
||
(Fast Library for Number Theory) and Arb (arbitrary-precision ball
|
||
arithmetic). It supports integers, rationals, modular integers,
|
||
real and complex ball arithmetic, polynomials and matrices over all
|
||
these types and other mathematical functions.")
|
||
(license license:expat)
|
||
(home-page "http://fredrikj.net/python-flint/")))
|
||
|
||
(define-public ntl
|
||
(package
|
||
(name "ntl")
|
||
(version "9.7.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://shoup.net/ntl/ntl-"
|
||
version ".tar.gz"))
|
||
(sha256 (base32
|
||
"115frp5flyvw9wghz4zph1b3llmr5nbxk1skgsggckr81fh3gmxq"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("libtool" ,libtool)
|
||
("perl" ,perl))) ; for configuration
|
||
;; FIXME: Add optional input gf2x once available; then also add
|
||
;; configure flag "NTL_GF2X_LIB=on".
|
||
(inputs
|
||
`(("gmp" ,gmp)))
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'configure
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(chdir "src")
|
||
(system* "./configure"
|
||
(string-append "PREFIX=" (assoc-ref outputs "out"))
|
||
;; Do not build especially for the build machine.
|
||
"NATIVE=off"
|
||
;; Also do not tune to the build machine.
|
||
"WIZARD=off"
|
||
"SHARED=on")
|
||
#t)))))
|
||
(synopsis "C++ library for number theory")
|
||
(description
|
||
"NTL is a C++ library providing data structures and algorithms
|
||
for manipulating signed, arbitrary length integers, and for vectors,
|
||
matrices, and polynomials over the integers and over finite fields.")
|
||
(license license:gpl2+)
|
||
(home-page "http://shoup.net/ntl/")))
|
||
|
||
(define-public singular
|
||
(package
|
||
(name "singular")
|
||
(version "4.1.2p1")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri
|
||
(string-append "http://www.mathematik.uni-kl.de/ftp/pub/Math/"
|
||
"Singular/SOURCES/"
|
||
(string-join
|
||
(string-split
|
||
(string-trim-right version #\p
|
||
0 (1- (string-length version)))
|
||
#\.) "-")
|
||
"/singular-" version ".tar.gz"))
|
||
(sha256 (base32
|
||
"0kvd55353fiqyq1msmi0kka66n5h0aqs7m3km60r01b1w2f8085m"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("doxygen" ,doxygen)
|
||
("graphviz" ,graphviz)
|
||
("perl" ,perl)))
|
||
(inputs
|
||
`(("cddlib" ,cddlib)
|
||
("gmp" ,gmp)
|
||
("flint" ,flint)
|
||
("mpfr" ,mpfr)
|
||
("ntl" ,ntl)
|
||
("python" ,python-2)
|
||
("readline" ,readline)))
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list (string-append "--with-ntl="
|
||
(assoc-ref %build-inputs "ntl")))))
|
||
(synopsis "Computer algebra system for polynomial computations")
|
||
(description
|
||
"Singular is a computer algebra system for polynomial computations,
|
||
with special emphasis on commutative and non-commutative algebra, algebraic
|
||
geometry and singularity theory.")
|
||
;; Singular itself is dual licensed gpl2 or gpl3, but some of the
|
||
;; libraries with which it links are licensed under lgpl3+, so the
|
||
;; combined work becomes gpl3. See COPYING in the source code.
|
||
(license license:gpl3)
|
||
(home-page "http://www.singular.uni-kl.de/index.php")))
|
||
|
||
(define-public gmp-ecm
|
||
(package
|
||
(name "gmp-ecm")
|
||
(version "7.0.4")
|
||
(source (origin
|
||
(method url-fetch)
|
||
;; Use the ‘Latest version’ link for a stable URI across releases.
|
||
(uri (string-append "https://gforge.inria.fr/frs/download.php/"
|
||
"latestfile/160/ecm-" version ".tar.gz"))
|
||
(sha256 (base32
|
||
"0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("gmp" ,gmp)))
|
||
(arguments
|
||
`(#:configure-flags '("--enable-shared"
|
||
;; Disable specific assembly routines, which depend
|
||
;; 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 "1.07.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "mirror://gnu/bc/bc-" version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0amh9ik44jfg66csyvf4zz1l878c4755kjndq9j0270akflgrbb2"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("ed" ,ed)
|
||
("flex" ,flex)
|
||
("texinfo" ,texinfo)))
|
||
(arguments
|
||
'(#:configure-flags
|
||
(list "--with-readline")))
|
||
(home-page "https://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+)))
|
||
|
||
;; The original kiss-fft does not have a complete build system and does not
|
||
;; build any shared libraries. This is a fork used by Extempore.
|
||
(define-public kiss-fft-for-extempore
|
||
(package
|
||
(name "kiss-fft-for-extempore")
|
||
(version "1.3.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/extemporelang/kiss_fft.git")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0jasbmqy4wkqrqx3w64s1dfmj34875xmsl72mb26aa4hpyn14bi2"))))
|
||
(build-system cmake-build-system)
|
||
(arguments `(#:tests? #f)) ; no tests included
|
||
;; Extempore refuses to build on architectures other than x86_64
|
||
(supported-systems '("x86_64-linux"))
|
||
(home-page "https://github.com/extemporelang/kiss_fft")
|
||
(synopsis "Mixed-radix Fast Fourier Transform")
|
||
(description
|
||
"Kiss FFT attempts to be a reasonably efficient, moderately useful FFT
|
||
that can use fixed or floating data types and can easily be incorporated into
|
||
a C program.")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public fftw
|
||
(package
|
||
(name "fftw")
|
||
(version "3.3.8")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "ftp://ftp.fftw.org/pub/fftw/fftw-"
|
||
version".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"00z3k8fq561wq2khssqg0kallk0504dzlx989x3vvicjdqpjc4v1"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:configure-flags
|
||
'("--enable-shared" "--enable-openmp" "--enable-threads"
|
||
,@(let ((system (or (%current-target-system) (%current-system))))
|
||
;; Enable SIMD extensions for codelets. See details at:
|
||
;; <http://fftw.org/fftw3_doc/Installation-on-Unix.html>.
|
||
(cond
|
||
((string-prefix? "x86_64" system)
|
||
'("--enable-sse2" "--enable-avx" "--enable-avx2"
|
||
"--enable-avx512" "--enable-avx-128-fma"))
|
||
((string-prefix? "i686" system)
|
||
'("--enable-sse2"))
|
||
((string-prefix? "aarch64" system)
|
||
;; Note that fftw supports NEON on 32-bit ARM only when
|
||
;; compiled for single-precision.
|
||
'("--enable-neon"))
|
||
(else
|
||
'())))
|
||
;; By default '-mtune=native' is used. However, that may cause the
|
||
;; use of ISA extensions (e.g. AVX) that are not necessarily
|
||
;; available on the user's machine when that package is built on a
|
||
;; different machine.
|
||
"ax_cv_c_flags__mtune_native=no")))
|
||
(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 fftw-configure-flags)
|
||
`(cons* "--enable-single"
|
||
,@(if (string-prefix? "arm" (or (%current-target-system)
|
||
(%current-system)))
|
||
;; fftw supports NEON on 32-bit ARM only when compiled
|
||
;; for single-precision, so add it here.
|
||
'("--enable-neon")
|
||
'())
|
||
,fftw-configure-flags))))
|
||
(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))
|
||
((#:phases phases '%standard-phases)
|
||
`(modify-phases ,phases
|
||
(add-before 'check 'mpi-setup
|
||
,%openmpi-setup)))))
|
||
(description
|
||
(string-append (package-description fftw)
|
||
" With OpenMPI parallelism support."))))
|
||
|
||
(define-public java-la4j
|
||
(package
|
||
(name "java-la4j")
|
||
(version "0.6.0")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/vkostyukov/la4j.git")
|
||
(commit version)))
|
||
(file-name (string-append name "-" version "-checkout"))
|
||
(sha256
|
||
(base32
|
||
"1qir8dr978cfvz9k12m2kbdwpyf6cqdf1d0ilb7lnkhbgq5i53w3"))))
|
||
(build-system ant-build-system)
|
||
(arguments
|
||
`(#:jar-name "la4j.jar"
|
||
#:jdk ,icedtea-8
|
||
#:test-exclude (list "**/Abstract*.java"
|
||
"**/MatrixTest.java"
|
||
"**/DenseMatrixTest.java"
|
||
"**/SparseMatrixTest.java"
|
||
"**/VectorTest.java"
|
||
"**/SparseVectorTest.java"
|
||
"**/DenseVectorTest.java")))
|
||
(native-inputs
|
||
`(("java-junit" ,java-junit)
|
||
("java-hamcrest-core" ,java-hamcrest-core)))
|
||
(home-page "http://la4j.org/")
|
||
(synopsis "Java library that provides Linear Algebra primitives and algorithms")
|
||
(description "The la4j library is a Java library that provides Linear
|
||
Algebra primitives (matrices and vectors) and algorithms. The key features of
|
||
the la4j library are:
|
||
|
||
@itemize
|
||
@item No dependencies and tiny size
|
||
@item Fluent object-oriented/functional API
|
||
@item Sparse (CRS, CCS) and dense (1D/2D arrays) matrices
|
||
@item Linear systems solving (Gaussian, Jacobi, Zeidel, Square Root, Sweep and other)
|
||
@item Matrices decomposition (Eigenvalues/Eigenvectors, SVD, QR, LU, Cholesky and other)
|
||
@item MatrixMarket/CSV IO formats support for matrices and vectors
|
||
@end itemize\n")
|
||
(license license:asl2.0)))
|
||
|
||
(define-public java-jlargearrays
|
||
(package
|
||
(name "java-jlargearrays")
|
||
(version "1.6")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://search.maven.org/remotecontent?"
|
||
"filepath=pl/edu/icm/JLargeArrays/"
|
||
version "/JLargeArrays-" version
|
||
"-sources.jar"))
|
||
(file-name (string-append name "-" version ".jar"))
|
||
(sha256
|
||
(base32
|
||
"0v05iphpxbjnd7f4jf1rlqq3m8hslhcm0imdbsgxr20pi3xkaf2a"))))
|
||
(build-system ant-build-system)
|
||
(arguments
|
||
`(#:jar-name "jlargearrays.jar"
|
||
#:tests? #f ; tests are not included in the release archive
|
||
#:jdk ,icedtea-8))
|
||
(propagated-inputs
|
||
`(("java-commons-math3" ,java-commons-math3)))
|
||
(home-page "https://gitlab.com/ICM-VisLab/JLargeArrays")
|
||
(synopsis "Library of one-dimensional arrays that can store up to 263 elements")
|
||
(description "JLargeArrays is a Java library of one-dimensional arrays
|
||
that can store up to 263 elements.")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public java-jtransforms
|
||
(package
|
||
(name "java-jtransforms")
|
||
(version "3.1")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://search.maven.org/remotecontent?"
|
||
"filepath=com/github/wendykierp/JTransforms/"
|
||
version "/JTransforms-" version "-sources.jar"))
|
||
(sha256
|
||
(base32
|
||
"1haw5m8shv5srgcpwkl853dz8bv6h90bzlhcps6mdpb4cixjirsg"))))
|
||
(build-system ant-build-system)
|
||
(arguments
|
||
`(#:jar-name "jtransforms.jar"
|
||
#:tests? #f ; tests are not included in the release archive
|
||
#:jdk ,icedtea-8))
|
||
(propagated-inputs
|
||
`(("java-commons-math3" ,java-commons-math3)
|
||
("java-jlargearrays" ,java-jlargearrays)))
|
||
(home-page "https://github.com/wendykierp/JTransforms")
|
||
(synopsis "Multithreaded FFT library written in pure Java")
|
||
(description "JTransforms is a multithreaded FFT library written in pure
|
||
Java. Currently, four types of transforms are available: @dfn{Discrete
|
||
Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete
|
||
Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).")
|
||
(license license:bsd-2)))
|
||
|
||
(define-public eigen
|
||
(package
|
||
(name "eigen")
|
||
(version "3.3.5")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://bitbucket.org/eigen/eigen/get/"
|
||
version ".tar.bz2"))
|
||
(sha256
|
||
(base32
|
||
"1qh3yrwn78ms5yhwbpl5wvblk4gbz02cacdygxylr7i9xbrvylkk"))
|
||
(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.
|
||
'(begin
|
||
(substitute* "unsupported/CMakeLists.txt"
|
||
(("add_subdirectory\\(test.*")
|
||
"# Do not build the tests for unsupported features.\n"))
|
||
#t))))
|
||
(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)))
|
||
(setenv "EIGEN_SEED" "1") ;for reproducibility
|
||
;; First build the tests, in parallel. See
|
||
;; <http://eigen.tuxfamily.org/index.php?title=Tests>.
|
||
(invoke "make" "buildtests" dash-j)
|
||
|
||
;; Then run 'CTest' with -V so we get more
|
||
;; details upon failure.
|
||
(invoke "ctest" "-V" dash-j)))))))
|
||
(home-page "https://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)))
|
||
|
||
(define-public eigen-for-tensorflow
|
||
(let ((changeset "fd6845384b86")
|
||
(revision "1"))
|
||
(package (inherit eigen)
|
||
(name "eigen-for-tensorflow")
|
||
(version (string-append "3.3.5-" revision "." changeset))
|
||
(source (origin
|
||
(method hg-fetch)
|
||
(uri (hg-reference
|
||
(url "https://bitbucket.org/eigen/eigen")
|
||
(changeset changeset)))
|
||
(sha256
|
||
(base32
|
||
"12cwgah63wqwb66xji048hcxc1z5zjg8a7701zlia5zbilnnk1n5"))
|
||
(file-name (string-append name "-" version "-checkout"))
|
||
(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.
|
||
'(begin
|
||
(substitute* "unsupported/CMakeLists.txt"
|
||
(("add_subdirectory\\(test.*")
|
||
"# Do not build the tests for unsupported features.\n"))
|
||
#t)))))))
|
||
|
||
(define-public xtensor
|
||
(package
|
||
(name "xtensor")
|
||
(version "0.17.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/QuantStack/xtensor.git")
|
||
(commit version)))
|
||
(sha256
|
||
(base32
|
||
"0w40v5lp0hp8ihf8nnvak373sb5xx0768pxgiqh3nzn57wf8px4r"))
|
||
(file-name (git-file-name name version))))
|
||
(build-system cmake-build-system)
|
||
(native-inputs
|
||
`(("googletest" ,googletest)
|
||
("xtl" ,xtl)))
|
||
(arguments
|
||
`(#:configure-flags
|
||
'("-DBUILD_TESTS=ON")
|
||
#:test-target "xtest"))
|
||
(home-page "http://quantstack.net/xtensor")
|
||
(synopsis "C++ tensors with broadcasting and lazy computing")
|
||
(description "xtensor is a C++ library meant for numerical analysis with
|
||
multi-dimensional array expressions.
|
||
|
||
xtensor provides:
|
||
@itemize
|
||
@item an extensible expression system enabling lazy broadcasting.
|
||
@item an API following the idioms of the C++ standard library.
|
||
@item tools to manipulate array expressions and build upon xtensor.
|
||
@end itemize")
|
||
(license license:bsd-3)))
|
||
|
||
(define-public gap
|
||
(package
|
||
(name "gap")
|
||
(version "4.10.0")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://www.gap-system.org/pub/gap/gap-"
|
||
(version-major+minor version)
|
||
"/tar.bz2/gap-"
|
||
version
|
||
".tar.bz2"))
|
||
(sha256
|
||
(base32
|
||
"1dmb8v4p7j1nnf7sx8sg54b49yln36bi9acwp7w1d3a1nxj17ird"))
|
||
(modules '((guix build utils) (ice-9 ftw) (srfi srfi-1)))
|
||
(snippet
|
||
'(begin
|
||
;; Delete the external gmp and zlib libraries
|
||
;; and a subdirectory not needed for our build.
|
||
(for-each delete-file-recursively
|
||
'("extern" "hpcgap"))
|
||
;; Delete a failing test.
|
||
;; FIXME: This might be fixed in the next release, see
|
||
;; https://github.com/gap-system/gap/issues/3292
|
||
(delete-file "tst/testinstall/dir.tst")
|
||
;; Delete all packages except for a fixed list.
|
||
(with-directory-excursion "pkg"
|
||
(for-each delete-file-recursively
|
||
(lset-difference string=? (scandir ".")
|
||
'("." ".."
|
||
;; Necessary packages.
|
||
"GAPDoc-1.6.2"
|
||
"primgrp-3.3.2"
|
||
"SmallGrp-1.3" ; artistic2.0
|
||
"transgrp" ; artistic2.0 for data,
|
||
; gpl2 or gpl3 for code
|
||
;; Recommanded package.
|
||
"io-4.5.4" ; gpl3+
|
||
;; Optional packages, searched for at start,
|
||
;; and their depedencies.
|
||
"alnuth-3.1.0"
|
||
"AutoDoc-2018.09.20"
|
||
"autpgrp-1.10"
|
||
"crisp-1.4.4" ; bsd-2
|
||
; "ctbllib" ; no explicit license, drop
|
||
"FactInt-1.6.2"
|
||
"fga"
|
||
"irredsol-1.4" ; bsd-2
|
||
"laguna-3.9.0"
|
||
"polenta-1.3.8"
|
||
"polycyclic-2.14"
|
||
"radiroot-2.8"
|
||
"resclasses-4.7.1"
|
||
"sophus-1.24"
|
||
; "tomlib-1.2.7" ; no explicit license, drop
|
||
"utils-0.59"))))
|
||
#t))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("gmp" ,gmp)
|
||
("zlib" ,zlib)))
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'build 'build-packages
|
||
;; Compile all packages that have not been deleted by the
|
||
;; code snippet above.
|
||
(lambda _
|
||
(setenv "CONFIG_SHELL" (which "bash"))
|
||
(with-directory-excursion "pkg"
|
||
(invoke "../bin/BuildPackages.sh")
|
||
#t)))
|
||
(add-after 'build-packages 'build-doc
|
||
;; The documentation is bundled, but we create it from source.
|
||
(lambda _
|
||
(with-directory-excursion "doc"
|
||
(invoke "./make_doc"))
|
||
#t))
|
||
(replace 'check
|
||
(lambda _
|
||
;; "make check" is expected to appear in gap-4.10.1
|
||
(invoke "./gap" "tst/testinstall.g")
|
||
#t))
|
||
(replace 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin"))
|
||
(prog (string-append bin "/gap"))
|
||
(prog-real (string-append bin "/.gap-real"))
|
||
(share (string-append out "/share/gap"))
|
||
(include (string-append out "/include/gap")))
|
||
;; Install only the gap binary; the gac compiler is left
|
||
;; for maybe later. "Wrap" it in a shell script that calls
|
||
;; the binary with the correct parameter.
|
||
(mkdir-p bin)
|
||
(copy-file "gap" prog-real)
|
||
(call-with-output-file prog
|
||
(lambda (port)
|
||
(format port
|
||
"#!~a~%exec ~a -l ~a \"$@\"~%"
|
||
(which "bash")
|
||
prog-real
|
||
share)))
|
||
(chmod prog #o755)
|
||
;; Install the headers and the library, which are needed by
|
||
;; Sage. The Makefile targets are available in gap-4.10.0,
|
||
;; but planned to be removed in gap-4.10.1.
|
||
(invoke "make" "install-headers")
|
||
(invoke "make" "install-libgap")
|
||
(install-file "gen/config.h" include)
|
||
;; Install a certain number of files and directories to
|
||
;; SHARE, where the wrapped shell script expects them.
|
||
;; Remove information on the build directory from sysinfo.gap.
|
||
(substitute* "sysinfo.gap"
|
||
(("GAP_BIN_DIR=\".*\"") "GAP_BIN_DIR=\"\"")
|
||
(("GAP_LIB_DIR=\".*\"") "GAP_LIB_DIR=\"\"")
|
||
(("GAP_CPPFLAGS=\".*\"") "GAP_CPPFLAGS=\"\""))
|
||
(install-file "sysinfo.gap" share)
|
||
(copy-recursively "grp" (string-append share "/grp"))
|
||
(copy-recursively "pkg" (string-append share "/pkg"))
|
||
;; The following is not the C library libgap.so, but a
|
||
;; library of GAP code.
|
||
(copy-recursively "lib" (string-append share "/lib"))
|
||
;; The gap binary looks for documentation inside SHARE.
|
||
(copy-recursively "doc" (string-append share "/doc")))
|
||
#t)))))
|
||
(home-page "https://www.gap-system.org/")
|
||
(synopsis
|
||
"System for computational group theory")
|
||
(description
|
||
"GAP is a system for computational discrete algebra, with particular
|
||
emphasis on computational group theory. It provides a programming language,
|
||
a library of thousands of functions implementing algebraic algorithms
|
||
written in the GAP language as well as large data libraries of algebraic
|
||
objects.")
|
||
;; Some packages have different licenses (effectively forcing the
|
||
;; combined work to be licensed as gpl3+); if this is the case, this
|
||
;; is mentioned above next to their name.
|
||
;; Some packages have no license mentioned explicitly; supposedly this
|
||
;; means that the gpl2+ licence of GAP itself applies, but to be on the
|
||
;; safe side, we drop them for now.
|
||
(license license:gpl2+)))
|