mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-12-26 06:18:07 -05:00
1565 lines
62 KiB
Scheme
1565 lines
62 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, 2020 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, 2020 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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;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
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;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
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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.
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||
;;;
|
||
;;; 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)
|
||
#:use-module (gnu packages bison)
|
||
#:use-module (gnu packages check)
|
||
#: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 pkg-config)
|
||
#: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)
|
||
#: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)
|
||
#:use-module (guix hg-download)
|
||
#:use-module ((guix licenses) #:prefix license:)
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||
#: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)
|
||
(uri (string-append
|
||
"http://www.multiprecision.org/downloads/mpfrcx-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1s968480ymv6w0rnvfp9mxvx98hvi29fkvw8nk4ggzc6azxgwybs"))))
|
||
(build-system gnu-build-system)
|
||
(propagated-inputs
|
||
`(("gmp" ,gmp)
|
||
("mpfr" ,mpfr)
|
||
("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
|
||
arbitrary precision real (mpfr) or complex (mpc) numbers, without control
|
||
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
|
||
multiplication routines such as Toom–Cook and the FFT.")
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||
(license license:lgpl3+)
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||
(home-page "http://www.multiprecision.org/mpfrcx/")))
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||
|
||
(define-public gf2x
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||
(package
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||
(name "gf2x")
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||
(version "1.2")
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||
(source (origin
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||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://gforge.inria.fr/frs/download.php/file/36934/gf2x-"
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||
version ".tar.gz"))
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||
(sha256
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||
(base32
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||
"0d6vh1mxskvv3bxl6byp7gxxw3zzpkldrxnyajhnl05m0gx7yhk1"))))
|
||
(build-system gnu-build-system)
|
||
(synopsis "Arithmetic of polynomials over binary finite fields")
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||
(description
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||
"The gf2x library provides arithmetic of polynomials over finite fields
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||
of characteristic 2. It implements the multiplication, squaring and
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||
greatest common divisor operations.")
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||
(license license:gpl3+)
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||
(home-page "https://gforge.inria.fr/projects/gf2x/")))
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||
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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
|
||
"http://www.multiprecision.org/cm/download/cm-"
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||
version ".tar.gz"))
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||
(sha256
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||
(base32
|
||
"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://www.multiprecision.org/cm/")))
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||
|
||
(define-public fplll
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||
(package
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||
(name "fplll")
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||
(version "5.2.1")
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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/fplll/fplll.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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||
"015qmrd7nfaysbv1hbwiprz9g6hnww1y1z1xw8f43ysb7k1b5nbg"))))
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||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("autoconf" ,autoconf)
|
||
("automake" ,automake)
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||
("libtool" ,libtool)))
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||
(inputs
|
||
`(("gmp" ,gmp)
|
||
("mpfr" ,mpfr)))
|
||
(home-page "https://github.com/fplll/fplll")
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||
(synopsis "Library for LLL-reduction of euclidean lattices")
|
||
(description
|
||
"fplll contains implementations of several lattice algorithms.
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||
The implementation relies on floating-point orthogonalization, and LLL
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||
is central to the code, hence the name.
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||
|
||
It includes implementations of floating-point LLL reduction
|
||
algorithms, offering different speed/guarantees ratios. It contains
|
||
a @emph{wrapper} choosing the estimated best sequence of variants in
|
||
order to provide a guaranteed output as fast as possible. In the case
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||
of the wrapper, the succession of variants is oblivious to the user.
|
||
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||
It includes an implementation of the BKZ reduction algorithm,
|
||
including the BKZ-2.0 improvements (extreme enumeration
|
||
pruning, pre-processing of blocks, early termination). Additionally,
|
||
Slide reduction and self dual BKZ are supported.
|
||
|
||
It also includes a floating-point implementation of the
|
||
Kannan-Fincke-Pohst algorithm that finds a shortest non-zero lattice
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||
vector. For the same task, the GaussSieve algorithm is also available
|
||
in fplll. Finally, it contains a variant of the enumeration algorithm
|
||
that computes a lattice vector closest to a given vector belonging to
|
||
the real span of the lattice.")
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||
(license license:lgpl2.1+)))
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||
|
||
(define-public python-fpylll
|
||
(package
|
||
(name "python-fpylll")
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||
(version "0.4.1")
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||
(source
|
||
(origin
|
||
;; Pypi contains and older release, so we use a tagged release from
|
||
;; Github instead.
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||
(method git-fetch)
|
||
(uri (git-reference
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||
(url "https://github.com/fplll/fpylll.git")
|
||
(commit (string-append version "dev"))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"01x2sqdv0sbjj4g4waj0hj4rcn4bq7h17442xaqwbznym9azmn9w"))))
|
||
(build-system python-build-system)
|
||
(inputs
|
||
`(("fplll" ,fplll)
|
||
("gmp" ,gmp)
|
||
("mpfr" ,mpfr)
|
||
("pari-gp" ,pari-gp)))
|
||
(propagated-inputs
|
||
`(("cysignals" ,python-cysignals)
|
||
("cython" ,python-cython)
|
||
("flake8" ,python-flake8)
|
||
("numpy" ,python-numpy)
|
||
("pytest" ,python-pytest)))
|
||
(home-page "https://github.com/fplll/fpylll")
|
||
(synopsis "Python interface for fplll")
|
||
(description "fpylll is a Python wrapper for fplll.")
|
||
(license license:gpl2+)))
|
||
|
||
(define-public pari-gp
|
||
(package
|
||
(name "pari-gp")
|
||
(version "2.11.2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://pari.math.u-bordeaux.fr/pub/pari/unix/pari-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0fck8ssmirl8fy7s4mspgrxjs5sag76xbshqlqzkcl3kqyrk4raa"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("texlive" ,(texlive-union
|
||
(list texlive-amsfonts)))))
|
||
(inputs `(("gmp" ,gmp)
|
||
("libx11" ,libx11)
|
||
("perl" ,perl)
|
||
("readline" ,readline)))
|
||
(arguments
|
||
'(#:make-flags '("all")
|
||
#:test-target "dobench"
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'configure
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(invoke "./Configure"
|
||
(string-append "--prefix="
|
||
(assoc-ref outputs "out"))))))))
|
||
(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.")
|
||
(license license:gpl2+)
|
||
(home-page "https://pari.math.u-bordeaux.fr/")))
|
||
|
||
(define-public gp2c
|
||
(package
|
||
(name "gp2c")
|
||
(version "0.0.11pl2")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://pari.math.u-bordeaux.fr/pub/pari/GP2C/gp2c-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"0wqsf05wgkqvmmsx7jinvzdqav6rl56sr8haibgs31nzz4x9xz9g"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs `(("perl" ,perl)))
|
||
(inputs `(("pari-gp" ,pari-gp)))
|
||
(arguments
|
||
'(#:configure-flags
|
||
(list (string-append "--with-paricfg="
|
||
(assoc-ref %build-inputs "pari-gp")
|
||
"/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)
|
||
(home-page "https://pari.math.u-bordeaux.fr/")))
|
||
|
||
(define fplll-4-cmh
|
||
(package
|
||
(inherit fplll)
|
||
(name "fplll")
|
||
(version "4.0.4")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"http://perso.ens-lyon.fr/damien.stehle/fplll/libfplll-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32 "1cbiby7ykis4z84swclpysrljmqhfcllpkcbll1m08rzskgb1a6b"))))))
|
||
|
||
(define-public cmh
|
||
(package
|
||
(name "cmh")
|
||
(version "1.0")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append
|
||
"https://gforge.inria.fr/frs/download.php/33497/cmh-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1a28xr9bs0igms0ik99x0w8lnb0jyfcmvyi26pbyh9ggcdivd33p"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("gmp" ,gmp)
|
||
("mpfr" ,mpfr)
|
||
("mpc" ,mpc)
|
||
("mpfrcx" ,mpfrcx)
|
||
("fplll" ,fplll-4-cmh)
|
||
("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+)
|
||
(home-page "http://cmh.gforge.inria.fr/")))
|
||
|
||
(define-public giac
|
||
(package
|
||
(name "giac")
|
||
(version "1.5.0-87")
|
||
(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 "1d0h1yb7qvh9x7wwv9yrzmcp712f49w1iljkxp4y6g9pzsmg1mmv"))))
|
||
(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 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 "2.17.0")
|
||
(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
|
||
"05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1"))))
|
||
(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://arblib.org")))
|
||
|
||
(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 "11.4.3")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://shoup.net/ntl/ntl-"
|
||
version ".tar.gz"))
|
||
(sha256
|
||
(base32
|
||
"1lisp3064rch3jaa2wrhy1s9kll7i3ka3d0y6lj6l3l4ckfcrhdp"))
|
||
(modules '((guix build utils)))
|
||
(snippet
|
||
'(begin
|
||
(delete-file-recursively "src/libtool-origin")
|
||
#t))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("libtool" ,libtool)
|
||
("perl" ,perl))) ; for configuration
|
||
(inputs
|
||
`(("gmp" ,gmp)
|
||
("gf2x" ,gf2x)))
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(replace 'configure
|
||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||
(chdir "src")
|
||
(invoke "./configure"
|
||
(string-append "PREFIX=" (assoc-ref outputs "out"))
|
||
(string-append "LIBTOOL=" (assoc-ref inputs "libtool") "/bin/libtool")
|
||
;; set the library prefixes explicitly so that they get
|
||
;; embedded in the .la file
|
||
(string-append "GMP_PREFIX=" (assoc-ref inputs "gmp"))
|
||
(string-append "GF2X_PREFIX=" (assoc-ref inputs "gf2x"))
|
||
;; Do not build especially for the build machine.
|
||
"NATIVE=off"
|
||
"NTL_GF2X_LIB=on"
|
||
"SHARED=on"))))))
|
||
(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 "https://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 "https://repo1.maven.org/maven2/"
|
||
"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 "https://repo1.maven.org/maven2/"
|
||
"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 "3.3.7")
|
||
(source (origin
|
||
(method url-fetch)
|
||
(uri (string-append "https://bitbucket.org/eigen/eigen/get/"
|
||
version ".tar.bz2"))
|
||
(sha256
|
||
(base32
|
||
"1km3fyfzyqfdvmnl79drps3fjwnz3zbh0c7l34mfbqyvvs8cy4wz"))
|
||
(file-name (string-append name "-" version ".tar.bz2"))
|
||
(patches (search-patches "eigen-stabilise-sparseqr-test.patch"))
|
||
(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 "0.20.10")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/QuantStack/xtensor.git")
|
||
(commit version)))
|
||
(sha256
|
||
(base32
|
||
"1fmv2hpx610xwhxrndfsfvlbqfyk4l3gi5q5d7pa9m82kblxjj9l"))
|
||
(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 "https://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 "4.10.2")
|
||
(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 "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"))
|
||
(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"
|
||
"autpgrp-1.10"
|
||
"crisp-1.4.4" ; bsd-2
|
||
"ctbllib" ; gpl3+ according to doc/chap0.txt
|
||
"FactInt-1.6.2"
|
||
"fga"
|
||
"irredsol-1.4" ; bsd-2
|
||
"laguna-3.9.2"
|
||
"polenta-1.3.8"
|
||
"polycyclic-2.14"
|
||
"radiroot-2.8"
|
||
"resclasses-4.7.1"
|
||
"sophus-1.24"
|
||
"tomlib-1.2.7" ; gpl2+, clarified in the git repository
|
||
; and the next release
|
||
"utils-0.59"))))
|
||
#t))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("gmp" ,gmp)
|
||
("zlib" ,zlib)))
|
||
(arguments
|
||
`(#:modules ((ice-9 ftw)
|
||
(srfi srfi-26)
|
||
(guix build gnu-build-system)
|
||
(guix build utils))
|
||
#: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 'install
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(bin (string-append out "/bin"))
|
||
(lib (string-append out "/lib"))
|
||
(prog (string-append bin "/gap"))
|
||
(prog-real (string-append bin "/.gap-real"))
|
||
(share (string-append out "/share/gap"))
|
||
(include (string-append out "/include/gap"))
|
||
(include-hpc (string-append include "/hpc")))
|
||
;; 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 \"$@\"~%"
|
||
(which "bash")
|
||
prog-real
|
||
share)))
|
||
(chmod prog #o755)
|
||
;; Install the headers, which are needed by Sage. The
|
||
;; Makefile target "install-headers" was available in
|
||
;; gap-4.10.0, but has been commented out in gap-4.10.1.
|
||
(mkdir-p include-hpc)
|
||
(install-file "gen/config.h" include)
|
||
(let ((file-name-predicate-without-stat
|
||
(lambda (regex)
|
||
(cut (file-name-predicate regex) <> #f))))
|
||
(with-directory-excursion "src"
|
||
(for-each
|
||
(cut install-file <> include)
|
||
(scandir "."
|
||
(file-name-predicate-without-stat ".*\\.h$"))))
|
||
(with-directory-excursion "src/hpc"
|
||
(for-each
|
||
(cut install-file <> include-hpc)
|
||
(scandir "."
|
||
(file-name-predicate-without-stat ".*\\.h$")))))
|
||
;; Install the library, which is needed by Sage. The
|
||
;; Makefile target "install-libgap" was available in
|
||
;; gap-4.10.0, but has been commented out in gap-4.10.1.
|
||
;; Compared to the Makefile, which used libtool, the
|
||
;; following approach of copying files and making symlinks
|
||
;; is rather pedestrian. There is hope that some later
|
||
;; version of gap reinstates and completes the install
|
||
;; targets.
|
||
(invoke "make" "libgap.la")
|
||
(install-file "libgap.la" lib)
|
||
(install-file ".libs/libgap.so.0.0.0" lib)
|
||
(symlink "libgap.so.0.0.0" (string-append lib "/libgap.so"))
|
||
(symlink "libgap.so.0.0.0" (string-append lib "/libgap.so.0"))
|
||
;; 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+)))
|
||
|
||
(define-public givaro
|
||
(package
|
||
(name "givaro")
|
||
(version "4.1.1")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/linbox-team/givaro")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"11wz57q6ijsvfs5r82masxgr319as92syi78lnl9lgdblpc6xigk"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("autoconf" ,autoconf)
|
||
("automake" ,automake)
|
||
("libtool" ,libtool)))
|
||
(propagated-inputs
|
||
`(("gmp" ,gmp))) ; gmp++.h includes gmpxx.h
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'bootstrap 'setenv
|
||
;; Prevent the autogen.sh script to carry out the configure
|
||
;; script, which has not yet been patched to replace /bin/sh.
|
||
(lambda _
|
||
(setenv "NOCONFIGURE" "yes")
|
||
#t)))))
|
||
(synopsis "Algebraic computations with exact rings and fields")
|
||
(description
|
||
"Givaro is a C++ library implementing the basic arithmetic of various
|
||
algebraic objects: prime fields, extension fields, finite fields, finite
|
||
rings, polynomials, algebraic numbers, arbitrary precision integers and
|
||
rationals (C++ wrappers over gmp), fixed precision integers. It also
|
||
provides data-structures and templated classes for the manipulation of
|
||
compound objects, such as vectors, matrices and univariate polynomials.")
|
||
(license license:cecill-b)
|
||
(home-page "https://github.com/linbox-team/givaro")))
|
||
|
||
(define-public fflas-ffpack
|
||
(package
|
||
(name "fflas-ffpack")
|
||
(version "2.4.3")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/linbox-team/fflas-ffpack")
|
||
(commit version)))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1ynbjd72qrwp0b4kpn0p5d7gddpvj8dlb5fwdxajr5pvkvi3if74"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("autoconf" ,autoconf)
|
||
("automake" ,automake)
|
||
("libtool" ,libtool)
|
||
("pkg-config" ,pkg-config)))
|
||
(inputs
|
||
`(("openblas" ,openblas)))
|
||
(propagated-inputs
|
||
`(("givaro" ,givaro))) ; required according to the .pc file
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list (string-append "--with-blas-libs="
|
||
(assoc-ref %build-inputs "openblas")
|
||
"/lib/libopenblas.so"))
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'bootstrap 'setenv
|
||
;; Prevent the autogen.sh script to carry out the configure
|
||
;; script, which has not yet been patched to replace /bin/sh.
|
||
(lambda _
|
||
(setenv "NOCONFIGURE" "yes")
|
||
#t)))))
|
||
(synopsis "C++ library for linear algebra over finite fields")
|
||
(description
|
||
"FFLAS-FFPACK is a C++ template library for basic linear algebra
|
||
operations over a finite field.
|
||
FFLAS (Finite Field Linear Algebra Subprograms) provides the implementation
|
||
of a subset of routines of the numerical BLAS; it also supports sparse
|
||
matrix-vector products.
|
||
FFPACK (Finite Field Linear Algebra Package) is inspired by the LAPACK
|
||
library to provide functionalities of higher level, using the kernel
|
||
of a BLAS. Additionally, it provides routines specific to exact linear
|
||
algebra, such as the row echelon form.")
|
||
(license license:lgpl2.1+)
|
||
(home-page "https://linbox-team.github.io/fflas-ffpack/")))
|
||
|
||
(define-public linbox
|
||
(package
|
||
(name "linbox")
|
||
(version "1.6.3")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/linbox-team/linbox")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"10j6dspbsq7d2l4q3y0c1l1xwmaqqba2fxg59q5bhgk9h5d7q571"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("autoconf" ,autoconf)
|
||
("automake" ,automake)
|
||
("libtool" ,libtool)
|
||
("pkg-config" ,pkg-config)))
|
||
(inputs
|
||
`(("fflas-ffpack" ,fflas-ffpack)))
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'bootstrap 'setenv
|
||
;; Prevent the autogen.sh script to carry out the configure
|
||
;; script, which has not yet been patched to replace /bin/sh.
|
||
(lambda _
|
||
(setenv "NOCONFIGURE" "yes")
|
||
#t)))))
|
||
(synopsis "C++ library for linear algebra over exact rings")
|
||
(description
|
||
"LinBox is a C++ template library for exact linear algebra computation
|
||
with dense, sparse, and structured matrices over the integers and over
|
||
finite fields.")
|
||
(license license:lgpl2.1+)
|
||
(home-page "https://linbox-team.github.io/linbox/")))
|
||
|
||
(define-public m4ri
|
||
(package
|
||
(name "m4ri")
|
||
(version "20140914")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://bitbucket.org/malb/m4ri")
|
||
(commit (string-append "release-" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("autoconf" ,autoconf)
|
||
("automake" ,automake)
|
||
("libtool" ,libtool)
|
||
("pkg-config" ,pkg-config)))
|
||
(inputs
|
||
`(("libpng" ,libpng)))
|
||
(synopsis "Arithmetic of dense matrices over F_2")
|
||
(description "M4RI is a library for fast arithmetic with dense matrices
|
||
over F2. The name M4RI comes from the first implemented algorithm: The
|
||
Method of the Four Russians inversion algorithm published by Gregory Bard.
|
||
This algorithm in turn is named after the Method of the Four Russians
|
||
multiplication algorithm.")
|
||
(license license:gpl2+)
|
||
(home-page "https://bitbucket.org/malb/m4ri/")))
|
||
|
||
(define-public symmetrica
|
||
(package
|
||
(name "symmetrica")
|
||
(version "2.0")
|
||
(source (origin
|
||
(method url-fetch/tarbomb)
|
||
(uri (let ((v (string-join (string-split version #\.) "_")))
|
||
(string-append "http://www.algorithm.uni-bayreuth.de/"
|
||
"en/research/SYMMETRICA/"
|
||
"SYM" v "_tar.gz")))
|
||
(sha256
|
||
(base32
|
||
"1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"))
|
||
;; Taken from <https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/>
|
||
(patches (search-patches "symmetrica-bruch.patch"
|
||
"symmetrica-int32.patch"
|
||
"symmetrica-return_values.patch"
|
||
"symmetrica-sort_sum_rename.patch"))))
|
||
(build-system gnu-build-system)
|
||
(arguments
|
||
`(#:tests? #f ;no test
|
||
#:phases
|
||
(modify-phases %standard-phases
|
||
(add-after 'unpack 'fix-makefile
|
||
(lambda _
|
||
(substitute* "makefile"
|
||
(("cc -c") "gcc -c -fPIC"))
|
||
#t))
|
||
(add-after 'fix-makefile 'turn-off-banner
|
||
(lambda _
|
||
(substitute* "de.c"
|
||
(("(INT no_banner = )FALSE" _ pre) (string-append pre "TRUE")))
|
||
#t))
|
||
(delete 'configure) ;no configure script
|
||
(replace 'install ;no install target
|
||
(lambda* (#:key outputs #:allow-other-keys)
|
||
(let* ((out (assoc-ref outputs "out"))
|
||
(lib (string-append out "/lib"))
|
||
(inc (string-append out "/include/symmetrica"))
|
||
(doc (string-append out "/share/doc/symmetrica-" ,version))
|
||
(static "libsymmetrica.a"))
|
||
;; Build static library.
|
||
(apply invoke "ar" "crs" static (find-files "." "\\.o$"))
|
||
(invoke "ranlib" static)
|
||
;; Install static library and headers.
|
||
(for-each (lambda (f) (install-file f inc))
|
||
(find-files "." "\\.h$"))
|
||
(install-file "libsymmetrica.a" lib)
|
||
;; Install documentation.
|
||
(for-each (lambda (f) (install-file f doc))
|
||
(find-files "." "\\.doc$"))
|
||
#t))))))
|
||
(home-page "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/")
|
||
(synopsis "Combinatoric C Library")
|
||
(description "Symmetrica is a library for combinatorics. It has support
|
||
for the representation theory of the symmetric group and related groups,
|
||
combinatorics of tableaux, symmetric functions and polynomials, Schubert
|
||
polynomials, and the representation theory of Hecke algebras of type A_n.")
|
||
(license license:public-domain)))
|
||
|
||
(define-public m4rie
|
||
(package
|
||
(name "m4rie")
|
||
(version "20150908")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://bitbucket.org/malb/m4rie")
|
||
(commit (string-append "release-" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("autoconf" ,autoconf)
|
||
("automake" ,automake)
|
||
("libtool" ,libtool)))
|
||
(inputs
|
||
`(("m4ri" ,m4ri)))
|
||
(synopsis "Arithmetic of dense matrices over F_{2^e}")
|
||
(description "M4RI is a library for fast arithmetic with dense matrices
|
||
over finite fields of characteristic 2. So it extends the functionality
|
||
of M4RI from F_2 to F_{2^e}.")
|
||
(license license:gpl2+)
|
||
(home-page "https://bitbucket.org/malb/m4rie/")))
|
||
|
||
(define-public eclib
|
||
(package
|
||
(name "eclib")
|
||
(version "20190909")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://github.com/JohnCremona/eclib/")
|
||
(commit (string-append "v" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1gw27lqc3f525n8qdcmr2nyn16y9g10z9f6dnmckyyxcdzvhq35n"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("autoconf" ,autoconf)
|
||
("automake" ,automake)
|
||
("libtool" ,libtool)))
|
||
(inputs
|
||
`(("ntl" ,ntl)
|
||
("pari-gp" ,pari-gp)))
|
||
(synopsis "Ranks of elliptic curves and modular symbols")
|
||
(description "The eclib package includes mwrank (for 2-descent on
|
||
elliptic curves over Q) and modular symbol code; it has been written by
|
||
John Cremona to compute his elliptic curve database.")
|
||
(license license:gpl2+)
|
||
(home-page (string-append "http://homepages.warwick.ac.uk/staff/"
|
||
"J.E.Cremona/mwrank/index.html"))))
|
||
|
||
(define-public lrcalc
|
||
(package
|
||
(name "lrcalc")
|
||
(version "1.2")
|
||
(source (origin
|
||
(method git-fetch)
|
||
(uri (git-reference
|
||
(url "https://bitbucket.org/asbuch/lrcalc")
|
||
(commit (string-append "lrcalc-" version))))
|
||
(file-name (git-file-name name version))
|
||
(sha256
|
||
(base32
|
||
"1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"))
|
||
(patches (search-patches "lrcalc-includes.patch"))))
|
||
(build-system gnu-build-system)
|
||
(native-inputs
|
||
`(("autoconf" ,autoconf)
|
||
("automake" ,automake)
|
||
("libtool" ,libtool)))
|
||
(arguments
|
||
`(#:phases
|
||
(modify-phases %standard-phases
|
||
(add-before 'build 'fix-permission
|
||
(lambda _
|
||
(chmod "lrcalc.maple.src" #o644)
|
||
#t)))))
|
||
(synopsis "Littlewood-Richardson calculator in algebraic combinatorics")
|
||
(description "The Littlewood-Richardson Calculator (lrcalc) is a
|
||
program designed to compute Littlewood-Richardson coefficients. It computes
|
||
single Littlewood-Richardson coefficients, products of Schur functions, or
|
||
skew Schur functions. In addition it computes products in the small quantum
|
||
cohomology ring of a Grassmann variety. The software package also includes
|
||
a program that performs fast computation of the more general multiplicative
|
||
structure constants of Schubert polynomials.")
|
||
(license license:gpl2+)
|
||
(home-page "https://sites.math.rutgers.edu/~asbuch/lrcalc/")))
|
||
|
||
(define-public iml
|
||
(package
|
||
(name "iml")
|
||
(version "1.0.5")
|
||
(source
|
||
(origin
|
||
(method url-fetch)
|
||
(uri (string-append "http://www.cs.uwaterloo.ca/~astorjoh/iml-"
|
||
version ".tar.bz2"))
|
||
(sha256
|
||
(base32
|
||
"0akwhhz9b40bz6lrfxpamp7r7wkk48p455qbn04mfnl9a1l6db8x"))))
|
||
(build-system gnu-build-system)
|
||
(inputs
|
||
`(("gmp", gmp)
|
||
("cblas" ,openblas))) ; or any other BLAS library; the documentation
|
||
; mentions ATLAS in particular
|
||
(arguments
|
||
`(#:configure-flags
|
||
(list
|
||
"--enable-shared"
|
||
(string-append "--with-gmp-include="
|
||
(assoc-ref %build-inputs "gmp") "/include")
|
||
(string-append "--with-gmp-lib="
|
||
(assoc-ref %build-inputs "gmp") "/lib")
|
||
"--with-cblas=-lopenblas"
|
||
(string-append "--with-cblas-include="
|
||
(assoc-ref %build-inputs "cblas") "/include")
|
||
(string-append "--with-cblas-lib="
|
||
(assoc-ref %build-inputs "cblas") "/lib"))))
|
||
(home-page "https://cs.uwaterloo.ca/~astorjoh/iml.html")
|
||
(synopsis
|
||
"Solver for systems of linear equations over the integers")
|
||
(description
|
||
"IML is a C library implementing algorithms for computing exact
|
||
solutions to dense systems of linear equations over the integers.
|
||
Currently, IML provides the following functionality:
|
||
|
||
@itemize
|
||
@item Nonsingular rational system solving:
|
||
compute the unique rational solution X to the system AX=B, where A and B
|
||
are integer matrices, A nonsingular.
|
||
@item Compute the right nullspace or kernel of an integer matrix.
|
||
@item Certified linear system solving:
|
||
compute a minimal denominator solution x to a system Ax=b, where b is an
|
||
integer vector and A is an integer matrix with arbitrary shape and
|
||
rank profile.
|
||
@end itemize
|
||
|
||
In addition, IML provides some low level routines for a variety of mod p
|
||
matrix operations: computing the row-echelon form, determinant, rank
|
||
profile, and inverse of a mod p matrix. These mod p routines are not
|
||
general purpose; they require that p satisfy some preconditions based on
|
||
the dimension of the input matrix (usually p should be prime and should be
|
||
no more than about 20 bits long).")
|
||
(license license:bsd-3)))
|