436 lines
16 KiB
Scheme
436 lines
16 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
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;;; Copyright © 2019 Nicolas Goaziou <mail@nicolasgoaziou.fr>
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;;; Copyright © 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
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;;; Copyright © 2021 Efraim Flashner <efraim@flashner.co.il>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages sagemath)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system python)
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (gnu packages)
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#:use-module (gnu packages algebra)
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#:use-module (gnu packages autotools)
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#:use-module (gnu packages bdw-gc)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages image)
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#:use-module (gnu packages lisp)
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#:use-module (gnu packages multiprecision)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-xyz))
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(define-public python-cypari2
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(package
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(name "python-cypari2")
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(version "2.1.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "cypari2" version))
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(sha256
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(base32
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"0ymc4i9y60aazscc1blivirkr1rflzz6akkmvfzyn5l7mgnlbk83"))))
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(build-system python-build-system)
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(native-inputs
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`(("python-cython" ,python-cython)))
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(propagated-inputs
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`(("python-cysignals" ,python-cysignals)))
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(inputs
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`(("gmp" ,gmp)
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("pari-gp" ,pari-gp)))
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(home-page "https://cypari2.readthedocs.io/")
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(synopsis
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"Python interface to the number theory library libpari")
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(description
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"Cypari2 provides a Python interface to the number theory library
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PARI/GP. It has been spun off from the SageMath mathematics software system,
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but it can be used independently.")
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(license license:gpl2+)))
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(define-public python2-cypari2
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(package-with-python2 python-cypari2))
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;; The stable version of the following package is not young enough to be
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;; used with Sage, since it does not support cython; so we use a beta
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;; release.
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(define-public python-gmpy2
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(package
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(name "python-gmpy2")
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(version "2.1.0b1")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/aleaxit/gmpy")
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(commit (string-append "gmpy2-" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0ljvnmhxqdfsp0yy4c2hynhk5sggm63kkqsq4iwq4k9vsnx2xm97"))))
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(build-system python-build-system)
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(native-inputs
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`(("unzip" ,unzip)))
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(inputs
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`(("gmp" ,gmp)
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("mpfr" ,mpfr)
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("mpc" ,mpc)))
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(home-page "https://github.com/aleaxit/gmpy")
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(synopsis
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"GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x")
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(description
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"This package provides a Python interface to the GNU multiprecision
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libraries GMO, MPFR and MPC.")
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(license license:lgpl3+)))
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(define-public python2-gmpy2
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(package-with-python2 python-gmpy2))
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(define-public cliquer
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(package
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(name "cliquer")
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(version "1.21")
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;; The original source package is available from the home page and
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;; has not seen any release since 2010; it comes with only a Makefile
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;; without an "install" target. Instead, there is an autotoolized
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;; tarball available from the Sage project.
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(source
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(origin
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(method url-fetch)
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(uri "http://users.ox.ac.uk/~coml0531/sage/cliquer-1.21.tar.gz")
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(sha256
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(base32
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"1hdzrmrx0nvvj8kbwxrs8swqgkd284khzl623jizixcv28xb77aq"))))
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(build-system gnu-build-system)
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(synopsis "C routines for finding cliques in weighted graphs")
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(description "Cliquer is a set of reentrant C routines for finding
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cliques in a weighted or unweighted graph. It uses an exact
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branch-and-bound algorithm. It can search for maximum or maximum-weight
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cliques or cliques with size or weight within a given range, restrict the
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search to maximal cliques, store cliques in memory and call a user-defined
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function for every found clique.")
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(license license:gpl2+)
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(home-page "https://users.aalto.fi/~pat/cliquer.html")))
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(define-public libbraiding
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(package
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(name "libbraiding")
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(version "1.0")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url (string-append "https://github.com/miguelmarco/"
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name))
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0l68rikfr7k2l547gb3pp3g8cj5zzxwipm79xrb5r8ffj466ydxg"))))
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(build-system gnu-build-system)
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(native-inputs
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`(("autoconf" ,autoconf)
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("automake" ,automake)
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("libtool" ,libtool)))
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(synopsis "Computations with braid groups")
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(description "libbraiding performs computations with braid groups,
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in particular it computes normal forms of group elements.")
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(license license:gpl2+)
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(home-page "https://github.com/miguelmarco/libbraiding")))
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(define-public libhomfly
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(package
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(name "libhomfly")
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(version "1.02r6")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url (string-append "https://github.com/miguelmarco/"
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name))
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0sv3cwrf9v9sb5a8wbhjmarxvya13ma3j8y8592f9ymxlk5y0ldk"))))
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(build-system gnu-build-system)
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(native-inputs
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`(("autoconf" ,autoconf)
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("automake" ,automake)
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("libtool" ,libtool)))
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(inputs
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`(("libgc" ,libgc)))
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(synopsis "Computation of homfly polynomials of links")
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(description "libhomfly computes homfly polynomials of links,
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represented as strings.")
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(license license:public-domain)
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(home-page "https://github.com/miguelmarco/libhomfly")))
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;; Sage 9.1 doesn't build with ECL 20. This won't be necessary once 9.2 is
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;; released. See https://trac.sagemath.org/ticket/22191
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(define-public ecl-16
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(package
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(inherit ecl)
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(version "16.1.3")
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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"https://common-lisp.net/project/ecl/static/files/release/ecl"
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"-" version ".tgz"))
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(sha256
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(base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn"))
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(patches (search-patches
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"ecl-16-libffi.patch"
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"ecl-16-ignore-stderr-write-error.patch"
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"ecl-16-format-directive-limit.patch"))))
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;; Current ECL uses LGPL 2.1+
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(license license:lgpl2.0+)))
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(define-public pynac
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(package
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(name "pynac")
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(version "0.7.26")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/pynac/pynac/")
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(commit (string-append "pynac-" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32 "09d2p74x1arkydlxy6pw4p4byi7r8q7f29w373h4d8a215kadc6d"))))
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(build-system gnu-build-system)
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(native-inputs
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`(("autoconf" ,autoconf)
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("automake" ,automake)
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("libtool" ,libtool)
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("pkg-config" ,pkg-config)))
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(inputs
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`(("flint" ,flint)
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("gmp" ,gmp)
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("python" ,python)
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("singular" ,singular)))
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(synopsis "Sage fork of GiNaC")
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(description "Pynac is a derivative of the C++ library GiNaC, which
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allows manipulation of symbolic expressions. It currently provides the
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backend for symbolic expressions in Sage. The main difference between
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Pynac and GiNaC is that Pynac relies on Sage to provide the operations
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on numerical types, while GiNaC depends on CLN for this purpose.")
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(license license:gpl2+)
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(home-page "http://pynac.org/")))
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;; Sage has become upstream of the following package.
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(define-public zn-poly
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(package
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(name "zn-poly")
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(version "0.9.2")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url (string-append "https://gitlab.com/sagemath/"
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"zn_poly.git/"))
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(commit version)))
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(file-name (git-file-name "zn_poly" version))
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(sha256
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(base32 "1wbc3apxcldxfcw1dnwnn7fvlfb6bwvlr8glvgv6hf79p9r2s4j0"))))
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(build-system gnu-build-system)
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(native-inputs
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`(("python" ,python-2)))
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(inputs
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`(("gmp" ,gmp)))
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(replace 'configure
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;; The configure script chokes on --enable-fast-install.
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(invoke "./configure"
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(string-append "--prefix=" (assoc-ref outputs "out"))
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"--cflags=-O3 -fPIC")))
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(add-before 'build 'prepare-build
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(lambda _
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(setenv "CC" "gcc")
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#t))
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(add-after 'build 'build-so
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(lambda _
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(invoke "make" "libzn_poly.so")))
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(add-after 'install 'install-so
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(lib (string-append out "/lib"))
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(soname (string-append "libzn_poly-" ,version ".so"))
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(target (string-append lib "/" soname)))
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(install-file "libzn_poly.a" lib)
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(install-file soname lib)
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(symlink target
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(string-append lib "/libzn_poly.so"))
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(symlink target
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(string-append lib "/libzn_poly-"
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,(version-major+minor version)
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".so")))
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#t)))))
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(synopsis "Arithmetic for polynomials over Z/NZ")
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(description "zn_poly implements the arithmetic of polynomials the
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coefficients of which are modular integers.")
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(license (list license:gpl2 license:gpl3)) ; dual licensed
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(home-page "https://gitlab.com/sagemath/zn_poly")))
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(define-public brial
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(package
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(name "brial")
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(version "1.2.8")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/BRiAl/BRiAl/")
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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 "0qhgckd4fvbs40jw14mvw89rccv94d3df27kipd27hxd4cx7y80y"))))
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(build-system gnu-build-system)
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(native-inputs
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`(("autoconf" ,autoconf)
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("automake" ,automake)
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("libtool" ,libtool)
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("pkg-config" ,pkg-config)))
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(inputs
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`(("boost" ,boost)
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("libpng" ,libpng)
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("m4ri" ,m4ri)))
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(arguments
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;; We are missing the boost unit test framework.
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`(#:tests? #f
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#:configure-flags (list "--without-boost-unit-test-framework")))
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(synopsis "Arithmetic of polynomials over boolean rings")
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(description "BRiAl is the successor to PolyBoRi maintained by the
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Sage community. Its core is a C++ library, which provides high-level data
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types for Boolean polynomials and monomials, exponent vectors, as well as
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for the underlying polynomial rings and subsets of the powerset of the
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Boolean variables. As a unique approach, binary decision diagrams are
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used as internal storage type for polynomial structures.")
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(license license:gpl2+)
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(home-page "https://github.com/BRiAl/BRiAl/")))
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(define-public lcalc
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(package
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(name "lcalc")
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(version "1.23")
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;; The original home page of the project has disappeared, as well as
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;; code hosted by the original author on Google Code. The latter has
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;; been copied to gitlab.com/sagemath and purportedly contains patches
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;; for a never released version 1.3, that supposedly follows 1.23.
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;; We use the tarball as well as the patches hosted inside the sage
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;; package system distributed with the sage tarball.
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(source
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(origin
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(method url-fetch)
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(uri (string-append "ftp://ftp.fu-berlin.de/unix/misc/sage/spkg/"
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"upstream/lcalc/lcalc-1.23.tar.bz2"))
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(sha256
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(base32
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"1c6dsdshgxhqppjxvxhp8yhpxaqvnz3d1mlh26r571gkq8z2bm43"))
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(patches (search-patches "lcalc-lcommon-h.patch"
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"lcalc-default-parameters-1.patch"
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"lcalc-default-parameters-2.patch"
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"lcalc-using-namespace-std.patch"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ;no tests
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(add-before 'build 'prepare-build
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(lambda* (#:key outputs #:allow-other-keys)
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(chdir "src")
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(let ((out (assoc-ref outputs "out")))
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(substitute* "Makefile"
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(("^INSTALL_DIR= /usr/local")
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(string-append "INSTALL_DIR=" out))))
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#t))
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(add-before 'install 'make-output-dirs
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin"))
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(lib (string-append out "/lib"))
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(include (string-append out "/include")))
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(mkdir-p bin)
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(mkdir-p lib)
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(mkdir-p include))
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#t)))))
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;; FIXME:
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;; We need to add pari-gp and probably pari related patches from the
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;; sage project, as well as uncomment the line setting PARI_DEFINE in
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;; the Makefile to get the full functionality of this package.
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;; For the time being, we hope that sage can be compiled without.
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(synopsis "C++ library for L-functions")
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(description "Lcalc computes L-functions, in particular the Riemann
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zeta function and its twists by quadratic characters.")
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(license license:gpl2+)
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(home-page "https://gitlab.com/sagemath/sage")))
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(define-public ratpoints
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(package
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(name "ratpoints")
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(version "2.1.3")
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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.mathe2.uni-bayreuth.de/stoll/programs/"
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"ratpoints-" version ".tar.gz"))
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(sha256
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(base32
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"0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4"))
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(patches
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;; Taken from
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;; <https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/>
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(search-patches "ratpoints-sturm_and_rp_private.patch"))))
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(build-system gnu-build-system)
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(arguments
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`(#:test-target "test"
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#:make-flags
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(list (string-append "INSTALL_DIR=" (assoc-ref %outputs "out"))
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"CCFLAGS=-fPIC")
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#:phases
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(modify-phases %standard-phases
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(delete 'configure) ;no configure script
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(add-before 'install 'create-install-directories
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out")))
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(mkdir-p out)
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(with-directory-excursion out
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(for-each (lambda (d) (mkdir-p d))
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'("bin" "include" "lib"))))
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#t)))))
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(inputs
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`(("gmp" ,gmp)))
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(home-page "http://www.mathe2.uni-bayreuth.de/stoll/programs/")
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(synopsis "Find rational points on hyperelliptic curves")
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(description "Ratpoints tries to find all rational points within
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a given height bound on a hyperelliptic curve in a very efficient way,
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by using an optimized quadratic sieve algorithm.")
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(license license:gpl2+)))
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